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github
|
lcnbeapp/beapp-master
|
rsadjust.m
|
.m
|
beapp-master/Packages/eeglab14_1_2b/functions/timefreqfunc/rsadjust.m
| 2,955 |
utf_8
|
45d8f416e2d360293ee83cb15f5e3976
|
% rsadjust() - adjust l-values (Ramberg-Schmeiser distribution)
% with respect to signal mean and variance
%
% Usage: p = rsadjust(l3, l4, m, var, skew)
%
% Input:
% l3 - value lambda3 for Ramberg-Schmeiser distribution
% l4 - value lambda4 for Ramberg-Schmeiser distribution
% m - mean of the signal distribution
% var - variance of the signal distribution
% skew - skewness of the signal distribution (only the sign of
% this parameter is used).
%
% Output:
% l1 - value lambda3 for Ramberg-Schmeiser distribution
% l2 - value lambda4 for Ramberg-Schmeiser distribution
% l3 - value lambda3 for Ramberg-Schmeiser distribution (copy
% from input)
% l4 - value lambda4 for Ramberg-Schmeiser distribution (copy
% from input)
%
% Author: Arnaud Delorme, SCCN, 2003
%
% See also: rsfit(), rsget()
%
% Reference: Ramberg, J.S., Tadikamalla, P.R., Dudewicz E.J., Mykkytka, E.F.
% A probability distribution and its uses in fitting data.
% Technimetrics, 1979, 21: 201-214.
% Copyright (C) 2003 Arnaud Delorme, SCCN, [email protected]
%
% This program is free software; you can redistribute it and/or modify
% it under the terms of the GNU General Public License as published by
% the Free Software Foundation; either version 2 of the License, or
% (at your option) any later version.
%
% This program is distributed in the hope that it will be useful,
% but WITHOUT ANY WARRANTY; without even the implied warranty of
% MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
% GNU General Public License for more details.
%
% You should have received a copy of the GNU General Public License
% along with this program; if not, write to the Free Software
% Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
function [l1,l2,l3,l4] = rsadjust( l3, l4, mu, sigma2, m3);
% swap l3 and l4 for negative skewness
% ------------------------------------
if m3 < 0
ltmp = l4;
l4 = l3;
l3 = ltmp;
end;
A = 1/(1 + l3) - 1/(1 + l4);
B = 1/(1 + 2*l3) + 1/(1 + 2*l4) - 2*beta(1+l3, 1+l4);
C = 1/(1 + 3*l3) - 1/(1 + 3*l4) ...
- 3*beta(1+2*l3, 1+l4) + 3*beta(1+l3, 1+2*l4);
% compute l2 (and its sign)
% ------------------------
l2 = sqrt( (B-A^2)/sigma2 );
if m3 == 0, m3 = -0.000000000000001; end;
if (m3*(C - 2*A*B + 2*A^3)) < 0, l2 = -l2; end;
%l22 = ((C - 2*A*B + 2*A^3)/m3)^(1/3) % also equal to l2
% compute l1
% ----------
l1 = mu - A/l2;
return;
% fitting table 1 of
% ---------------
[l1 l2] = pdffitsolv2(-.0187,-.0388, 0, 1, 1)
[l1 l2] = pdffitsolv2(-.1359,-.1359, 0, 1, 0)
% sign problem
[l1 l2] = pdffitsolv2(1.4501,1.4501, 0, 1)
% numerical problem for l1
[l1 l2] = pdffitsolv2(-.00000407,-.001076, 0, 1, 2)
[l1 l2] = pdffitsolv2(0,-.000580, 0, 1, 2)
|
github
|
lcnbeapp/beapp-master
|
newcrossf.m
|
.m
|
beapp-master/Packages/eeglab14_1_2b/functions/timefreqfunc/newcrossf.m
| 63,870 |
utf_8
|
cb2a530dbabd60d30681d5c293194574
|
% newcrossf() - Returns estimates and plots event-related coherence (ERCOH)
% between two input data time series. A lower panel (optionally) shows
% the coherence phase difference between the processes. In this panel:
% In the plot output by > newcrossf(x,y,...);
% 90 degrees (orange) means x leads y by a quarter cycle.
% -90 degrees (blue) means y leads x by a quarter cycle.
% Click on any subplot to view separately and zoom in/out.
%
% Function description:
% Uses EITHER fixed-window, zero-padded FFTs (fastest) OR constant-Q
% 0-padded wavelet DFTs (more even sensitivity across frequencies),
% both Hanning-tapered. Output frequency spacing is the lowest
% frequency ('srate'/'winsize') divided by the 'padratio'.
%
% If an 'alpha' value is given, then bootstrap statistics are
% computed (from a distribution of 'naccu' (200) surrogate baseline
% data epochs) for the baseline epoch, and non-significant features
% of the output plots are zeroed (and shown in green). The baseline
% epoch is all windows with center latencies < the given 'baseline' value
% or, if 'baseboot' is 1, the whole epoch.
%
% Usage with single dataset:
% >> [coh,mcoh,timesout,freqsout,cohboot,cohangles,...
% allcoher,alltfX,alltfY] = newcrossf(x,y,frames,tlimits,srate, ...
% cycles, 'key1', 'val1', 'key2', val2' ...);
%
% Example to compare two condition (coh. comp 1-2 EEG versus ALLEEG(2)):
% >> [coh,mcoh,timesout,freqsout,cohboot,cohangles,...
% allcoher,alltfX,alltfY] = newcrossf({EEG.icaact(1,:,:) ...
% ALLEEG(2).icaact(1,:,:)},{{EEG.icaact(2,:,:) ...
% ALLEEG(2).icaact(2,:,:)}},frames,tlimits,srate, ...
% cycles, 'key1', 'val1', 'key2', val2' ...);
%
% Required inputs:
% x = First single-channel data set (1,frames*nepochs)
% Else, cell array {x1,x2} of two such data vectors to also
% estimate (significant) coherence differences between two
% conditions.
% y = Second single-channel data set (1,frames*nepochs)
% Else, cell array {y1,y2} of two such data vectors.
% frames = Frames per epoch {750}
% tlimits = [mintime maxtime] (ms) Epoch latency limits {[-1000 2000]}
% srate = Data sampling rate (Hz) {250}
% cycles = 0 -> Use FFTs (with constant window length)
% = >0 -> Number of cycles in each analysis wavelet
% = [cycles expfactor] -> if 0 < expfactor < 1, the number
% of wavelet cycles expands with frequency from cycles
% If expfactor = 1, no expansion; if = 0, constant
% window length (as in FFT) {default cycles: 0}
%
% Optional Coherence Type:
% 'type' = ['coher'|'phasecoher'|'amp'] Compute either linear coherence
% ('coher'), phase coherence ('phasecoher') also known
% as phase coupling factor', or amplitude correlations ('amp')
% {default: 'phasecoher'}. Note that for amplitude correlation,
% the significance threshold is computed using the corrcoef
% function, so can be set arbitrary low without increase in
% computation load. An additional type is 'crossspec' to compute
% cross-spectrum between 2 processes (single-trial). This type
% is automatically selected if user enter continuous data.
% 'amplag' = [integer vector] allow to compute non 0 amplitude correlation
% (using option 'amp' above). The vector given as parameter
% indicates the point lags ([-4 -2 0 2 4] would compute the
% correlation at time t-4, t-2, t, t+2, t+4, and return the
% maximum correlation at these points).
% 'subitc' = ['on'|'off'] Subtract stimulus locked Inter-Trial Coherence
% from x and y. This computes the 'intrinsic' coherence
% x and y not arising from common synchronization to
% experimental events. For cell array input, one may provide
% a cell array ({'on','off'} for example). {default: 'off'}
% 'shuffle' = Integer indicating the number of estimates to compute
% bootstrap coherence based on shuffled trials. This estimates
% the coherence arising only from time locking of x and y
% to experimental events (opposite of 'subitc'). For cell array
% input, one may provide a cell array, for example { 1 0 }.
% { default 0: no shuffling }.
%
% Optional Detrend:
% 'detrend' = ['on'|'off'], Linearly detrend each data epoch {'off'}
% 'rmerp' = ['on'|'off'], Remove epoch mean from data epochs {'off'}
%
% Optional FFT/DFT:
% 'winsize' = If cycles==0: data subwindow length (fastest, 2^n<frames);
% if cycles >0: *longest* window length to use. This
% determines the lowest output frequency {~frames/8}
% 'timesout' = Number of output latencies (int<frames-winframes). {200)
% A negative value (-S) subsamples the original latencies
% by S. An array of latencies computes spectral
% decompositions at specific latency values (Note: the
% algorithm finds the closest latencies in the data,
% possibly resulting in slightly unevenly spaced
% output latencies.
% 'padratio' = FFT-length/winframes (2^k) {2}
% Multiplies the number of output frequencies by dividing
% their spacing (standard FFT padding). When cycles~=0,
% frequency spacing is divided by padratio.
% 'maxfreq' = Maximum frequency (Hz) to plot (& output if cycles>0)
% If cycles==0, all FFT frequencies are output.{def: 50}
% Note: NOW DEPRECATED, use 'freqs' instead,
% 'freqs' = [min max] Frequency limits. {Default: [minfreq 50],
% minfreq being determined by the number of data points,
% cycles and sampling frequency}.
% 'nfreqs' = Number of output frequencies. For FFT, closest computed
% frequency will be returned. Overwrite 'padratio' effects
% for wavelets. {Default: use 'padratio'}.
% 'freqscale' = ['log'|'linear'] Frequency scaling. {Default: 'linear'}.
% Note that for obtaining 'log' spaced freqs using FFT,
% closest correspondant frequencies in the 'linear' space
% are returned.
% 'baseline' = Spectral baseline end-time (in ms). NaN imply that no
% baseline is used. A range [min max] may also be entered
% You may also enter one row per region for baseline
% e.g. [0 100; 300 400] considers the window 0 to 100 ms and
% 300 to 400 ms. This is only valid for the coherence amplitude
% not for the coherence phase. { default NaN }
% 'lowmem' = ['on'|'off'] {'off'} Compute frequency by frequency to
% save memory.
%
% Optional Bootstrap:
% 'alpha' = If non-0, compute two-tailed bootstrap significance prob.
% level. Show non-signif output values in neutral green. {0}
% 'naccu' = Number of bootstrap replications to compute {200}
% 'boottype' = ['shuffle'|'shufftrials'|'rand'|'randall'] Bootstrap type: Either
% shuffle time and trial windows ('shuffle' default) or trials only
% using a separate bootstrap for each time window ('shufftrials').
% Option 'rand' randomize the phase. Option 'randall' randomize the
% phase for each individual time/frequency point.
% 'baseboot' = Bootstrap baseline subtract (1 -> use 'baseline'; Default
% 0 -> use whole trial
% [min max] -> use time range)
% Default is to use the baseline unless no baseline is
% specified (then the function uses all sample up to time 0)
% You may also enter one row per region for baseline
% e.g. [0 100; 300 400] considers the window 0 to 100 ms and
% 300 to 400 ms.
% 'condboot' = ['abs'|'angle'|'complex'] In comparing two conditions,
% either subtract complex spectral values' absolute vales
% ('abs'), angles ('angles') or the complex values themselves
% ('complex'). {default: 'abs'}
% 'rboot' = Input bootstrap coherence limits (e.g., from newcrossf())
% The bootstrap type should be identical to that used
% to obtain the input limits. {default: compute from data}
% Optional scalp map plot:
% 'topovec' = (2,nchans) matrix. Scalp maps to plot {[]}
% ELSE [c1,c2], plot two cartoons showing channel locations.
% 'elocs' = Electrode location file for scalp map {none}
% File should be ascii in format of >> topoplot example
% 'chaninfo' = Electrode location additional information (nose position...)
% {default: none}
%
% Optional plot and compute features:
% 'plottype' = ['image'|'curve'] plot time frequency images or
% curves (one curve per frequency). Default is 'image'.
% 'plotmean' = ['on'|'off'] For 'curve' plots only. Average all
% frequencies given as input. Default: 'on'.
% 'highlightmode' = ['background'|'bottom'] For 'curve' plots only,
% display significant time regions either in the plot background
% or underneatht the curve.
% 'plotamp' = ['on'|'off']. Plot coherence magnitude {'on'}
% 'maxamp' = [real] Set the maximum for the amplitude scale {auto}
% 'plotphase' = ['on'|'off']. Plot coherence phase angle {'on'}
% 'angleunit' = Phase units: 'ms' for msec or 'deg' for degrees or 'rad'
% for radians {'deg'}
% 'title' = Optional figure title. If two conditions are given
% as input, title can be a cell array with two text
% string elements {none}
% 'vert' = Latencies to mark with a dotted vertical line {none}
% 'linewidth' = Line width for marktimes traces (thick=2, thin=1) {2}
% 'newfig' = ['on'|'off'] Create new figure for difference plots {'on'}
% 'axesfont' = Axes font size {10}
% 'titlefont' = Title font size {8}
%
% Outputs:
% coh = Matrix (nfreqs,timesout) of coherence magnitudes. Not
% that for continuous data, the function is returning the
% cross-spectrum.
% mcoh = Vector of mean baseline coherence at each frequency
% see 'baseline' parameter.
% timesout = Vector of output latencies (window centers) (ms).
% freqsout = Vector of frequency bin centers (Hz).
% cohboot = Matrix (nfreqs) of upper coher signif. limits
% if 'boottype' is 'trials', (nfreqs,timesout)
% cohangle = (nfreqs,timesout) matrix of coherence angles in radian
% allcoher = single trial coherence
% alltfX = single trial spectral decomposition of X
% alltfY = single trial spectral decomposition of Y
%
% Plot description:
% Assuming both 'plotamp' and 'plotphase' options are 'on' (=default), the upper panel
% presents the magnitude of either phase coherence or linear coherence, depending on
% the 'type' parameter (above). The lower panel presents the coherence phase difference
% (in degrees). Click on any plot to pop up a new window (using 'axcopy()').
% -- The upper left marginal panel shows mean coherence during the baseline period
% (blue), and when significance is set, the significance threshold (dotted black-green).
% -- The horizontal panel under the coherence magnitude image indicates the maximum
% (green) and minimum (blue) coherence values across all frequencies. When significance
% is set (using option 'trials' for 'boottype'), an additional curve indicates the
% significance threshold (dotted black-green).
%
% Notes: 1) When cycles==0, nfreqs is total number of FFT frequencies.
% 2) 'blue' coherence lag -> x leads y; 'red' -> y leads x
% 3) The 'boottype' should be ideally 'timestrials', but this creates
% large memory demands, so 'times' must be used in many cases.
% 4) If 'boottype' is 'trials', the average of the complex bootstrap
% is subtracted from the coherence to compensate for phase differences
% (the average is also subtracted from the bootstrap distribution).
% For other bootstraps, this is not necessary since there the phase
% distribution should be random.
% 5) If baseline is non-NaN, the baseline is subtracted from
% the complex coherence. On the left hand side of the coherence
% amplitude image, the baseline is displayed as a magenta line.
% (If no baseline is selected, this curve represents the average
% coherence at every given frequency).
%
% Authors: Arnaud Delorme, Sigurd Enghoff & Scott Makeig
% CNL/Salk Institute 1998-2001; SCCN/INC/UCSD, La Jolla, 2002-
%
% See also: timef()
% NOTE: one hidden parameter 'savecoher', 0 or 1
% Copyright (C) 8/1/98 Arnaud Delorme, Sigurd Enghoff & Scott Makeig, SCCN/INC/UCSD
%
% This program is free software; you can redistribute it and/or modify
% it under the terms of the GNU General Public License as published by
% the Free Software Foundation; either version 2 of the License, or
% (at your option) any later version.
%
% This program is distributed in the hope that it will be useful,
% but WITHOUT ANY WARRANTY; without even the implied warranty of
% MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
% GNU General Public License for more details.
%
% You should have received a copy of the GNU General Public License
% along with this program; if not, write to the Free Software
% Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
% 11-20-98 defined g.linewidth constant -sm
% 04-01-99 made number of frequencies consistent -se
% 06-29-99 fixed constant-Q freq indexing -se
% 08-13-99 added cohangle plotting -sm
% 08-20-99 made bootstrap more efficient -sm
% 08-24-99 allow nan values introduced by possible eventlock() preproc. -sm
% 03-16-00 added lead/lag interpretation to help msg - sm & eric visser
% 03-16-00 added axcopy() feature -sm & tpj
% 04-20-00 fixed Rangle sign for wavelets, added verts array -sm
% 01-22-01 corrected help msg when nargin<2 -sm & arno delorme
% 01-25-02 reformated help & license, added links -ad
% 03-09-02 function restructuration -ad
% add 'key', val arguments (+ external baseboot, baseline, color axis, angleunit...)
% add detrending (across time and trials) + 'coher' option for amplitude coherence
% significance only if alpha is given, ploting options in 'plotamp' and 'plotphase'
% 03-16-02 timeout automatically adjusted if too high -ad
% 04-03-02 added new options for bootstrap -ad
% There are 3 "objects" Tf, Coher and Boot which are handled
% - by specific functions under Matlab
% (Tf) function Tf = tfinit(...) - create object Time Frequency (Tf) associated with some data
% (Tf) function [Tf, itcvals] = tfitc(...) - compute itc for the selected data
% (Tf) function [Tf, itcvals] = tfitcpost(Tf, trials) - itc normlisation
% (Tf) function [Tf, tmpX] = tfcomp(Tf, trials, times) - compute time freq. decomposition
% (Coher) function Coher = coherinit(...) - initialize coherence object
% (Coher) function Coher = cohercomp(Coher, tmpX, tmpY, trial, time) - compute coherence
% (Coher) function Coher = cohercomppost(Coher, trials) - coherence normalization
% (Boot) function Boot = bootinit(...) - intialize bootstrap object
% (Boot) function Boot = bootcomp(...) - compute bootstrap
% (Boot) function [Boot, Rbootout] = bootcomppost(...) - bootstrap normalization
% - by real objects under C++ (see C++ code)
function [R,mbase,timesout,freqs,Rbootout,Rangle, coherresout, alltfX, alltfY] = newcrossf(X, Y, frame, tlimits, Fs, varwin, varargin)
%varwin,winsize,nwin,oversmp,maxfreq,alpha,verts,caxmax)
% Commandline arg defaults:
DEFAULT_ANGLEUNITS = 'deg'; % angle plotting units - 'ms' or 'deg'
DEFAULT_EPOCH = 750; % Frames per epoch
DEFAULT_TIMELIM = [-1000 2000]; % Time range of epochs (ms)
DEFAULT_FS = 250; % Sampling frequency (Hz)
DEFAULT_NWIN = 200; % Number of windows = horizontal resolution
DEFAULT_VARWIN = 0; % Fixed window length or base on cycles.
% =0: fix window length to nwin
% >0: set window length equal varwin cycles
% bounded above by winsize, also determines
% the min. freq. to be computed.
DEFAULT_OVERSMP = 2; % Number of times to oversample = vertical resolution
DEFAULT_MAXFREQ = 50; % Maximum frequency to display (Hz)
DEFAULT_TITLE = 'Event-Related Coherence'; % Figure title
DEFAULT_ALPHA = NaN; % Default two-sided significance probability threshold
%disp('WARNING: this function is not part of the EEGLAB toolbox and should not be distributed');
%disp(' you must contact Arnaud Delorme ([email protected]) for terms of use');
if (nargin < 2)
help newcrossf
return
end
coherresout = [];
if ~iscell(X)
if (min(size(X))~=1 | length(X)<2)
fprintf('crossf(): x must be a row or column vector.\n');
return
elseif (min(size(Y))~=1 | length(Y)<2)
fprintf('crossf(): y must be a row or column vector.\n');
return
elseif (length(X) ~= length(Y))
fprintf('crossf(): x and y must have same length.\n');
return
end
end;
if (nargin < 3)
frame = DEFAULT_EPOCH;
elseif (~isnumeric(frame) | length(frame)~=1 | frame~=round(frame))
fprintf('crossf(): Value of frames must be an integer.\n');
return
elseif (frame <= 0)
fprintf('crossf(): Value of frames must be positive.\n');
return
elseif ~iscell(X) & (rem(size(X,2),frame) ~= 0) & (rem(size(X,1),frame) ~= 0)
fprintf('crossf(): Length of data vectors must be divisible by frames.\n');
return
end
if (nargin < 4)
tlimits = DEFAULT_TIMELIM;
elseif (~isnumeric(tlimits) | sum(size(tlimits))~=3)
error('crossf(): Value of tlimits must be a vector containing two numbers.');
elseif (tlimits(1) >= tlimits(2))
error('crossf(): tlimits interval must be [min,max].');
end
if (nargin < 5)
Fs = DEFAULT_FS;
elseif (~isnumeric(Fs) | length(Fs)~=1)
error('crossf(): Value of srate must be a number.');
elseif (Fs <= 0)
error('crossf(): Value of srate must be positive.');
end
if (nargin < 6)
varwin = DEFAULT_VARWIN;
elseif (~isnumeric(varwin) | length(varwin)>2)
error('crossf(): Value of cycles must be a number or a (1,2) vector.');
elseif (varwin < 0)
error('crossf(): Value of cycles must be either zero or positive.');
end
% consider structure for these arguments
% --------------------------------------
vararginori = varargin;
for index=1:length(varargin)
if iscell(varargin{index}), varargin{index} = { varargin{index} }; end;
end;
if ~isempty(varargin)
[tmp indices] = unique_bc(varargin(1:2:end)); % keep the first one
varargin = varargin(sort(union(indices*2-1, indices*2))); % these 2 line remove duplicate arguments
try, g = struct(varargin{:});
catch, error('Argument error in the {''param'', value} sequence'); end;
else
g = [];
end;
try, g.condboot; catch, g.condboot = 'abs'; end;
try, g.shuffle; catch, g.shuffle = 0; end;
try, g.title; catch, g.title = DEFAULT_TITLE; end;
try, g.winsize; catch, g.winsize = max(pow2(nextpow2(frame)-3),4); end;
try, g.pad; catch, g.pad = max(pow2(nextpow2(g.winsize)),4); end;
try, g.timesout; catch, g.timesout = DEFAULT_NWIN; end;
try, g.padratio; catch, g.padratio = DEFAULT_OVERSMP; end;
try, g.topovec; catch, g.topovec = []; end;
try, g.elocs; catch, g.elocs = ''; end;
try, g.alpha; catch, g.alpha = DEFAULT_ALPHA; end;
try, g.marktimes; catch, g.marktimes = []; end; % default no vertical lines
try, g.marktimes = g.vert; catch, g.vert = []; end; % default no vertical lines
try, g.rboot; catch, g.rboot = []; end;
try, g.plotamp; catch, g.plotamp = 'on'; end;
try, g.plotphase; catch, g.plotphase = 'on'; end;
try, g.plotbootsub; catch, g.plotbootsub = 'on'; end;
try, g.detrend; catch, g.detrend = 'off'; end;
try, g.rmerp; catch, g.rmerp = 'off'; end;
try, g.baseline; catch, g.baseline = NaN; end;
try, g.baseboot; catch, g.baseboot = 1; end;
try, g.linewidth; catch, g.linewidth = 2; end;
try, g.maxfreq; catch, g.maxfreq = DEFAULT_MAXFREQ; end;
try, g.freqs; catch, g.freqs = [0 g.maxfreq]; end;
try, g.nfreqs; catch, g.nfreqs = []; end;
try, g.freqscale; catch, g.freqscale = 'linear'; end;
try, g.naccu; catch, g.naccu = 200; end;
try, g.angleunit; catch, g.angleunit = DEFAULT_ANGLEUNITS; end;
try, g.type; catch, g.type = 'phasecoher'; end;
try, g.newfig; catch, g.newfig = 'on'; end;
try, g.boottype; catch, g.boottype = 'shuffle'; end;
try, g.subitc; catch, g.subitc = 'off'; end;
try, g.compute; catch, g.compute = 'matlab'; end;
try, g.maxamp; catch, g.maxamp = []; end;
try, g.savecoher; catch, g.savecoher = 0; end;
try, g.amplag; catch, g.amplag = 0; end;
try, g.noinput; catch, g.noinput = 'no'; end;
try, g.lowmem; catch, g.lowmem = 'off'; end;
try, g.plottype; catch, g.plottype = 'image'; end;
try, g.plotmean; catch, g.plotmean = 'on'; end;
try, g.highlightmode; catch, g.highlightmode = 'background'; end;
try, g.chaninfo; catch, g.chaninfo = []; end;
if isfield(g, 'detret'), g.detrend = g.detret; end;
if isfield(g, 'detrep'), g.rmerp = g.detrep; end;
if ~isnan(g.alpha) && ndims(X) == 2 && (size(X,1) == 1 || size(X,2) == 1)
error('Cannot compute significance for continuous data');
end;
allfields = fieldnames(g);
for index = 1:length(allfields)
switch allfields{index}
case { 'shuffle' 'title' 'winsize' 'pad' 'timesout' 'padratio' 'maxfreq' 'topovec' 'elocs' 'alpha' ...
'marktimes' 'vert' 'rboot' 'plotamp' 'plotphase' 'plotbootsub' 'detrep' 'rmerp' 'detret' 'detrend' ...
'baseline' 'baseboot' 'linewidth' 'naccu' 'angleunit' 'type' 'boottype' 'subitc' 'lowmem' 'plottype' ...
'compute' 'maxamp' 'savecoher' 'noinput' 'condboot' 'newfig' 'freqs' 'nfreqs' 'freqscale' 'amplag' ...
'highlightmode' 'plotmean' 'chaninfo' };
case {'plotersp' 'plotitc' }, disp(['crossf warning: timef option ''' allfields{index} ''' ignored']);
otherwise disp(['crossf error: unrecognized option ''' allfields{index} '''']); beep; return;
end;
end;
g.tlimits = tlimits;
g.frame = frame;
if ~iscell(X) g.trials = prod(size(X))/g.frame;
else g.trials = prod(size(X{1}))/g.frame;
end;
g.srate = Fs;
g.cycles = varwin;
g.type = lower(g.type);
g.boottype = lower(g.boottype);
g.rmerp = lower(g.rmerp);
g.detrend = lower(g.detrend);
g.plotphase = lower(g.plotphase);
g.plotbootsub = lower(g.plotbootsub);
g.subitc = lower(g.subitc);
g.plotamp = lower(g.plotamp);
g.compute = lower(g.compute);
g.AXES_FONT = 10;
g.TITLE_FONT = 14;
% change type if necessary
if g.trials == 1 & ~strcmpi(g.type, 'crossspec')
disp('Continuous data: switching to crossspectrum');
g.type = 'crossspec';
end;
if strcmpi(g.freqscale, 'log') & g.freqs(1) == 0, g.freqs(1) = 3; end;
% reshape 3D inputs
% -----------------
if ndims(X) == 3
X = reshape(X, size(X,1), size(X,2)*size(X,3));
Y = reshape(Y, size(Y,1), size(Y,2)*size(Y,3));
end;
% testing arguments consistency
% -----------------------------
if strcmpi(g.title, DEFAULT_TITLE)
switch g.type
case 'coher', g.title = 'Event-Related Coherence'; % Figure title
case 'phasecoher', g.title = 'Event-Related Phase Coherence';
case 'phasecoher2', g.title = 'Event-Related Phase Coherence 2';
case 'amp' , g.title = 'Event-Related Amplitude Correlation';
case 'crossspec', g.title = 'Event-Related Amplitude Correlation';
end;
end;
if ~ischar(g.title) & ~iscell(g.title)
error('Title must be a string or a cell array.');
end
if isempty(g.topovec)
g.topovec = [];
elseif min(size(g.topovec))==1
g.topovec = g.topovec(:);
if size(g.topovec,1)~=2
error('topovec must be a row or column vector.');
end
end;
if isempty(g.elocs)
g.elocs = '';
elseif (~ischar(g.elocs)) & ~isstruct(g.elocs)
error('Channel location file must be a valid text file.');
end
if (~isnumeric(g.alpha) | length(g.alpha)~=1)
error('timef(): Value of g.alpha must be a number.\n');
elseif (round(g.naccu*g.alpha) < 2)
fprintf('Value of g.alpha is out of the normal range [%g,0.5]\n',2/g.naccu);
g.naccu = round(2/g.alpha);
fprintf(' Increasing the number of bootstrap iterations to %d\n',g.naccu);
end
if g.alpha>0.5 | g.alpha<=0
error('Value of g.alpha is out of the allowed range (0.00,0.5).');
end
switch lower(g.newfig)
case { 'on', 'off' }, ;
otherwise error('newfig must be either on or off');
end;
switch g.angleunit
case { 'ms', 'deg', 'rad' },;
otherwise error('Angleunit must be either ''deg'', ''rad'', or ''ms''');
end;
switch g.type
case { 'coher', 'phasecoher' 'phasecoher2' 'amp' 'crossspec' },;
otherwise error('Type must be either ''coher'', ''phasecoher'', ''crossspec'', or ''amp''');
end;
switch g.boottype
case { 'shuffle' 'shufftrials' 'rand' 'randall'},;
otherwise error('Invalid boot type');
end;
if ~isnumeric(g.shuffle) & ~iscell(g.shuffle)
error('Shuffle argument type must be numeric');
end;
switch g.compute
case { 'matlab', 'c' },;
otherwise error('compute must be either ''matlab'' or ''c''');
end;
if ~strcmpi(g.condboot, 'abs') & ~strcmpi(g.condboot, 'angle') ...
& ~strcmpi(g.condboot, 'complex')
error('Condboot must be either ''abs'', ''angle'' or ''complex''.');
end;
if g.tlimits(2)-g.tlimits(1) < 30
disp('Crossf WARNING: time range is very small (<30 ms). Times limits are in millisenconds not seconds.');
end;
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
% compute frequency by frequency if low memory
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
if strcmpi(g.lowmem, 'on') & ~iscell(X) & length(X) ~= g.frame & (isempty(g.nfreqs) | g.nfreqs ~= 1)
% compute for first 2 trials to get freqsout
XX = reshape(X, 1, frame, length(X)/g.frame);
YY = reshape(Y, 1, frame, length(Y)/g.frame);
[coh,mcoh,timesout,freqs] = newcrossf(XX(1,:,1), YY(1,:,1), frame, tlimits, Fs, varwin, 'plotamp', 'off', 'plotphase', 'off',varargin{:});
% scan all frequencies
for index = 1:length(freqs)
if nargout < 6
[R(index,:),mbase(index),timesout,tmpfreqs(index),Rbootout(index,:),Rangle(index,:)] = ...
newcrossf(X, Y, frame, tlimits, Fs, varwin, 'freqs', [freqs(index) freqs(index)], 'nfreqs', 1, ...
'plotamp', 'off', 'plotphase', 'off',varargin{:}, 'lowmem', 'off', 'timesout', timesout);
elseif nargout == 7 % requires RAM
[R(index,:),mbase(index),timesout,tmpfreqs(index),Rbootout(index,:),Rangle(index,:), ...
coherresout(index,:,:)] = ...
newcrossf(X, Y, frame, tlimits, Fs, varwin, 'freqs', [freqs(index) freqs(index)], 'nfreqs', 1, ...
'plotamp', 'off', 'plotphase', 'off',varargin{:}, 'lowmem', 'off', 'timesout', timesout);
else
[R(index,:),mbase(index),timesout,tmpfreqs(index),Rbootout(index,:),Rangle(index,:), ...
coherresout(index,:,:),alltfX(index,:,:),alltfY(index,:,:)] = ...
newcrossf(X, Y, frame, tlimits, Fs, varwin, 'freqs', [freqs(index) freqs(index)], 'nfreqs', 1, ...
'plotamp', 'off', 'plotphase', 'off',varargin{:}, 'lowmem', 'off', 'timesout', timesout);
end;
end;
% plot and return
plotall(R.*exp(j*Rangle), Rbootout, timesout, freqs, mbase, g);
return;
end;
%%%%%%%%%%%%%%%%%%%%%%%%%%%
% compare 2 conditions part
%%%%%%%%%%%%%%%%%%%%%%%%%%%
if iscell(X)
if length(X) ~= 2 | length(Y) ~= 2
error('crossf: to compare conditions, X and Y input must be 2-elements cell arrays');
end;
% deal with titles
% ----------------
for index = length(vararginori)-1:-2:1
if index<=length(vararginori) % needed: if elemenets are deleted
if strcmp(vararginori{index}, 'title') , vararginori(index:index+1) = []; end;
if strcmp(vararginori{index}, 'subitc'), vararginori(index:index+1) = []; end;
if strcmp(vararginori{index}, 'shuffle'), vararginori(index:index+1) = []; end;
end;
end;
if ~iscell(g.subitc)
g.subitc = { g.subitc g.subitc };
end;
if ~iscell(g.shuffle)
g.shuffle = { g.shuffle g.shuffle };
end;
if iscell(g.title)
if length(g.title) <= 2,
g.title{3} = 'Condition 1 - condition 2';
end;
else
g.title = { 'Condition 1', 'Condition 2', 'Condition 1 - condition 2' };
end;
fprintf('Running newcrossf on condition 1 *********************\n');
fprintf('Note: if an out-of-memory error occurs, try reducing the\n');
fprintf(' number of time points or number of frequencies\n');
fprintf(' (the ''coher'' options takes 3 times more memory than other options)\n');
if strcmpi(g.plotamp, 'on') | strcmpi(g.plotphase, 'on')
if strcmpi(g.newfig, 'on'), figure; end;
subplot(1,3,1);
end;
if ~strcmp(g.type, 'coher') & nargout < 9
[R1,mbase,timesout,freqs,Rbootout1,Rangle1, savecoher1] = newcrossf(X{1}, Y{1}, ...
frame, tlimits, Fs, varwin, 'savecoher', 1, 'title', g.title{1}, ...
'shuffle', g.shuffle{1}, 'subitc', g.subitc{1}, vararginori{:});
else
[R1,mbase,timesout,freqs,Rbootout1,Rangle1, savecoher1, Tfx1, Tfy1] = newcrossf(X{1}, Y{1}, ...
frame, tlimits, Fs, varwin, 'savecoher', 1, 'title', g.title{1}, ...
'shuffle', g.shuffle{1}, 'subitc', g.subitc{1}, vararginori{:});
end;
R1 = R1.*exp(j*Rangle1/180*pi);
fprintf('\nRunning newcrossf on condition 2 *********************\n');
if strcmpi(g.plotamp, 'on') | strcmpi(g.plotphase, 'on')
subplot(1,3,2);
end;
if ~strcmp(g.type, 'coher') & nargout < 9
[R2,mbase,timesout,freqs,Rbootout2,Rangle2, savecoher2] = newcrossf(X{2}, Y{2}, ...
frame, tlimits, Fs, varwin,'savecoher', 1, 'title', g.title{2}, ...
'shuffle', g.shuffle{2}, 'subitc', g.subitc{2}, vararginori{:});
else
[R2,mbase,timesout,freqs,Rbootout2,Rangle2, savecoher2, Tfx2, Tfy2] = newcrossf(X{2}, Y{2}, ...
frame, tlimits, Fs, varwin,'savecoher', 1, 'title', g.title{2}, ...
'shuffle', g.shuffle{2}, 'subitc', g.subitc{2}, vararginori{:} );
end;
%figure; imagesc(abs( sum( savecoher1 ./ abs(savecoher1), 3)) - abs( sum( savecoher2 ./ abs(savecoher2), 3) )); cbar; return;
%figure; imagesc(abs( R2 ) - abs( R1) ); cbar; return;
R2 = R2.*exp(j*Rangle2/180*pi);
if strcmpi(g.plotamp, 'on') | strcmpi(g.plotphase, 'on')
subplot(1,3,3);
end;
if isnan(g.alpha)
switch(g.condboot)
case 'abs', Rdiff = abs(R1)-abs(R2);
case 'angle', Rdiff = angle(R1)-angle(R2);
case 'complex', Rdiff = R1-R2;
end;
g.title = g.title{3};
if strcmpi(g.plotamp, 'on') | strcmpi(g.plotphase, 'on')
plotall(Rdiff, [], timesout, freqs, mbase, g);
end;
Rbootout = [];
else
% preprocess data and run condstat
% --------------------------------
switch g.type
case 'coher', % take the square of alltfx and alltfy first to speed up
Tfx1 = Tfx1.*conj(Tfx1); Tfx2 = Tfx2.*conj(Tfx2);
Tfy1 = Tfy1.*conj(Tfy1); Tfy2 = Tfy2.*conj(Tfy2);
formula = 'sum(arg1(:,:,X),3) ./ sqrt(sum(arg2(:,:,X),3)) ./ sqrt(sum(arg3(:,:,X),3))';
if strcmpi(g.lowmem, 'on')
for ind = 1:2:size(savecoher1,1)
if ind == size(savecoher1,1), indarr = ind; else indarr = [ind:ind+1]; end;
[Rdiff(indarr,:,:) coherimages(indarr,:,:) coher1(indarr,:,:) coher2(indarr,:,:)] = condstat(formula, g.naccu, g.alpha, ...
'both', g.condboot, { savecoher1(indarr,:,:) savecoher2(indarr,:,:) }, ...
{ Tfx1(indarr,:,:) Tfx2(indarr,:,:) }, { Tfy1(indarr,:,:) Tfy2(indarr,:,:) });
end;
else
[Rdiff coherimages coher1 coher2] = condstat(formula, g.naccu, g.alpha, ...
'both', g.condboot, { savecoher1 savecoher2 }, { Tfx1 Tfx2 }, { Tfy1 Tfy2 });
end;
case 'amp' % amplitude correlation
error('Cannot compute difference of amplitude correlation images yet');
case 'crossspec' % amplitude correlation
error('Cannot compute difference of cross-spectral decomposition');
case 'phasecoher', % normalize first to speed up
savecoher1 = savecoher1 ./ sqrt(savecoher1.*conj(savecoher1));
savecoher2 = savecoher2 ./ sqrt(savecoher2.*conj(savecoher2)); % twice faster than abs()
formula = 'sum(arg1(:,:,X),3) ./ length(X)';
if strcmpi(g.lowmem, 'on')
for ind = 1:2:size(savecoher1,1)
if ind == size(savecoher1,1), indarr = ind; else indarr = [ind:ind+1]; end;
[Rdiff(indarr,:,:) coherimages(indarr,:,:) coher1(indarr,:,:) coher2(indarr,:,:)] = condstat(formula, g.naccu, g.alpha, ...
'both', g.condboot, { savecoher1(indarr,:,:) savecoher2(indarr,:,:) } );
end;
else
[Rdiff coherimages coher1 coher2] = condstat(formula, g.naccu, g.alpha, 'both', g.condboot, ...
{ savecoher1 savecoher2 });
end;
case 'phasecoher2',
savecoher1 = savecoher1 ./ sqrt(savecoher1.*conj(savecoher1));
savecoher2 = savecoher2 ./ sqrt(savecoher2.*conj(savecoher2)); % twice faster than abs()
formula = 'sum(arg1(:,:,X),3) ./ sum(sqrt(arg1(:,:,X).*conj(arg1(:,:,X)))),3)';
% sqrt(a.*conj(a)) is about twice faster than abs()
if strcmpi(g.lowmem, 'on')
for ind = 1:2:size(savecoher1,1)
if ind == size(savecoher1,1), indarr = ind; else indarr = [ind:ind+1]; end;
[Rdiff(indarr,:,:) coherimages(indarr,:,:) coher1(indarr,:,:) coher2(indarr,:,:)] = condstat(formula, g.naccu, g.alpha, ...
'both', g.condboot, { savecoher1(indarr,:,:) savecoher2(indarr,:,:) } );
end;
else
[Rdiff coherimages coher1 coher2] = condstat(formula, g.naccu, g.alpha, 'both', g.condboot, ...
{ savecoher1 savecoher2 });
end;
end;
%Boot = bootinit( [], size(savecoher1,1), g.timesout, g.naccu, 0, g.baseboot, 'noboottype', g.alpha, g.rboot);
%Boot.Coherboot.R = coherimages;
%Boot = bootcomppost(Boot, [], [], []);
g.title = g.title{3};
g.boottype = 'shufftrials';
if strcmpi(g.plotamp, 'on') | strcmpi(g.plotphase, 'on')
plotall(Rdiff, coherimages, timesout, freqs, mbase, g);
end;
% outputs
Rbootout = {Rbootout1 Rbootout2 coherimages};
end;
if size(Rdiff,3) > 1, Rdiff = reshape(Rdiff, 1, size(Rdiff,3)); end;
R = { abs(R1) abs(R2) fastif(isreal(Rdiff), Rdiff, abs(Rdiff)) };
Rangle = { angle(R1) angle(R2) angle(Rdiff) };
coherresout = [];
if nargout >=9
alltfX = { Tfx1 Tfx2 };
alltfY = { Tfy1 Tfy2 };
end;
return; % ********************************** END FOR SEVERAL CONDITIONS
end;
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
% shuffle trials if necessary
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
if g.shuffle ~= 0
fprintf('x and y data trials being shuffled %d times\n',g.shuffle);
XX = reshape(X, 1, frame, length(X)/g.frame);
YY = Y;
X = [];
Y = [];
for index = 1:g.shuffle
XX = shuffle(XX,3);
X = [X XX(:,:)];
Y = [Y YY];
end;
end;
% detrend over epochs (trials) if requested
% -----------------------------------------
switch g.rmerp
case 'on'
X = reshape(X, g.frame, length(X)/g.frame);
X = X - mean(X,2)*ones(1, length(X(:))/g.frame);
Y = reshape(Y, g.frame, length(Y)/g.frame);
Y = Y - mean(Y,2)*ones(1, length(Y(:))/g.frame);
end;
%%%%%%%%%%%%%%%%%%%%%%
% display text to user
%%%%%%%%%%%%%%%%%%%%%%
fprintf('\nComputing the Event-Related \n');
switch g.type
case 'phasecoher', fprintf('Phase Coherence (ITC) images based on %d trials\n',g.trials);
case 'phasecoher2', fprintf('Phase Coherence 2 (ITC) images based on %d trials\n',g.trials);
case 'coher', fprintf('Linear Coherence (ITC) images based on %d trials\n',g.trials);
case 'amp', fprintf('Amplitude correlation images based on %d trials\n',g.trials);
case 'crossspec', fprintf('Cross-spectral images based on %d trials\n',g.trials);
end;
if ~isnan(g.alpha)
fprintf('Bootstrap confidence limits will be computed based on alpha = %g\n', g.alpha);
else
fprintf('Bootstrap confidence limits will NOT be computed.\n');
end
switch g.plotphase
case 'on', fprintf(['Coherence angles will be imaged in ',g.angleunit,'\n']);
end;
%%%%%%%%%%%%%%%%%%%%%%%
% main computation loop
%%%%%%%%%%%%%%%%%%%%%%%
% -------------------------------------
% compute time frequency decompositions
% -------------------------------------
if length(g.timesout) > 1, tmioutopt = { 'timesout' , g.timesout };
else tmioutopt = { 'ntimesout', g.timesout };
end;
spectraloptions = { tmioutopt{:}, 'winsize', g.winsize, 'tlimits', g.tlimits, 'detrend', ...
g.detrend, 'subitc', g.subitc, 'wavelet', g.cycles, 'padratio', g.padratio, ...
'freqs' g.freqs 'freqscale' g.freqscale 'nfreqs' g.nfreqs };
if ~strcmpi(g.type, 'amp') & ~strcmpi(g.type, 'crossspec')
spectraloptions = { spectraloptions{:} 'itctype' g.type };
end;
fprintf('\nProcessing first input\n');
X = reshape(X, g.frame, g.trials);
[alltfX freqs timesout] = timefreq(X, g.srate, spectraloptions{:});
fprintf('\nProcessing second input\n');
Y = reshape(Y, g.frame, g.trials);
[alltfY] = timefreq(Y, g.srate, spectraloptions{:});
% ------------------
% compute coherences
% ------------------
tmpprod = alltfX .* conj(alltfY);
if nargout > 6 | strcmpi(g.type, 'phasecoher2') | strcmpi(g.type, 'phasecoher')
coherresout = alltfX .* conj(alltfY);
end;
switch g.type
case 'crossspec',
coherres = alltfX .* conj(alltfY); % no normalization
case 'coher',
coherres = sum(alltfX .* conj(alltfY), 3) ./ sqrt( sum(abs(alltfX).^2,3) .* sum(abs(alltfY).^2,3) );
case 'amp'
alltfX = abs(alltfX);
alltfY = abs(alltfY);
coherres = ampcorr(alltfX, alltfY, freqs, timesout, g);
g.alpha = NaN;
coherresout = [];
case 'phasecoher2',
coherres = sum(coherresout, 3) ./ sum(abs(coherresout),3);
case 'phasecoher',
coherres = sum( coherresout ./ abs(coherresout), 3) / g.trials;
end;
%%%%%%%%%%
% baseline
%%%%%%%%%%
if size(g.baseline,2) == 2
baseln = [];
for index = 1:size(g.baseline,1)
tmptime = find(timesout >= g.baseline(index,1) & timesout <= g.baseline(index,2));
baseln = union_bc(baseln, tmptime);
end;
if length(baseln)==0
error('No point found in baseline');
end;
else
if ~isempty(find(timesout < g.baseline))
baseln = find(timesout < g.baseline); % subtract means of pre-0 (centered) windows
else
baseln = 1:length(timesout); % use all times as baseline
end
end;
if ~isnan(g.alpha) & length(baseln)==0
fprintf('timef(): no window centers in baseline (times<%g) - shorten (max) window length.\n', g.baseline)
return
end
mbase = mean(abs(coherres(:,baseln)')); % mean baseline coherence magnitude
% -----------------
% compute bootstrap
% -----------------
if ~isempty(g.rboot)
Rbootout = g.rboot;
else
if ~isnan(g.alpha)
% getting formula for coherence
% -----------------------------
switch g.type
case 'coher',
inputdata = { alltfX alltfY }; % default
formula = 'sum(arg1 .* conj(arg2), 3) ./ sqrt( sum(abs(arg1).^2,3) .* sum(abs(arg2).^2,3) );';
case 'amp', % not implemented
inputdata = { abs(alltfX) abs(alltfY) }; % default
case 'phasecoher2',
inputdata = { alltfX alltfY }; % default
formula = [ 'tmp = arg1 .* conj(arg2);' ...
'res = sum(tmp, 3) ./ sum(abs(tmp),3);' ];
case 'phasecoher',
inputdata = { alltfX./abs(alltfX) alltfY./abs(alltfY) };
formula = [ 'mean(arg1 .* conj(arg2),3);' ];
case 'crossspec',
inputdata = { alltfX./abs(alltfX) alltfY./abs(alltfY) };
formulainit = [ 'arg1 .* conj(arg2);' ];
end;
% finding baseline for bootstrap
% ------------------------------
if size(g.baseboot,2) == 1
if g.baseboot == 0, baselntmp = [];
elseif ~isnan(g.baseline(1))
baselntmp = baseln;
else baselntmp = find(timesout <= 0); % if it is empty use whole epoch
end;
else
baselntmp = [];
for index = 1:size(g.baseboot,1)
tmptime = find(timesout >= g.baseboot(index,1) & timesout <= g.baseboot(index,2));
baselntmp = union_bc(baselntmp, tmptime);
end;
end;
if prod(size(g.baseboot)) > 2
fprintf('Bootstrap analysis will use data in multiple selected windows.\n');
elseif size(g.baseboot,2) == 2
fprintf('Bootstrap analysis will use data in range %3.2g-%3.2g ms.\n', g.baseboot(1), g.baseboot(2));
elseif g.baseboot
fprintf(' %d bootstrap windows in baseline (times<%g).\n', length(baselntmp), g.baseboot)
end;
if strcmpi(g.boottype, 'shuffle') | strcmpi(g.boottype, 'rand')
Rbootout = bootstat(inputdata, formula, 'boottype', g.boottype, 'label', 'coherence', ...
'bootside', 'upper', 'shuffledim', [2 3], 'dimaccu', 2, ...
'naccu', g.naccu, 'alpha', g.alpha, 'basevect', baselntmp);
elseif strcmpi(g.boottype, 'randall')
% randomize phase but do not accumulate over time
% dimension (NOT TESTED)
% note the absence of dimaccu and the shuffledim 3
Rbootout = bootstat(inputdata, formula, 'boottype', 'rand', ...
'bootside', 'upper', 'shuffledim', 3, ...
'naccu', g.naccu, 'alpha', g.alpha, 'basevect', baselntmp);
else % shuffle only trials (NOT TESTED)
% note the absence of dimaccu and the shuffledim 3
Rbootout = bootstat(inputdata, formula, 'boottype', 'shuffle', ...
'bootside', 'upper', 'shuffledim', 3, ...
'naccu', g.naccu, 'alpha', g.alpha, 'basevect', baselntmp);
end;
else Rbootout = [];
end;
% note that the bootstrap thresholding is actually performed in the display subfunction plotall()
end;
% plot everything
% ---------------
if strcmpi(g.plotamp, 'on') | strcmpi(g.plotphase, 'on')
if strcmpi(g.plottype, 'image')
plotall ( coherres, Rbootout, timesout, freqs, mbase, g);
else
plotallcurves( coherres, Rbootout, timesout, freqs, mbase, g);
end;
end;
% proces outputs
% --------------
Rangle = angle(coherres);
R = abs(coherres);
return;
% ***********************************************************************
% ------------------------------
% amplitude correlation function
% ------------------------------
function [coherres, lagmap] = ampcorr(alltfX, alltfY, freqs, timesout, g)
% initialize variables
% --------------------
coherres = zeros(length(freqs), length(timesout), length(g.amplag));
alpha = zeros(length(freqs), length(timesout), length(g.amplag));
countlag = 1;
for lag = g.amplag
fprintf('Computing %d point lag amplitude correlation, please wait...\n', lag);
for i1 = 1:length(freqs)
for i2 = max(1, 1-lag):min(length(timesout)-lag, length(timesout))
if ~isnan(g.alpha)
[tmp1 tmp2] = corrcoef( squeeze(alltfX(i1,i2,:)), squeeze(alltfY(i1,i2+lag,:)) );
coherres(i1,i2,countlag) = tmp1(1,2);
alpha(i1,i2,countlag) = tmp2(1,2);
else
tmp1 = corrcoef( squeeze(alltfX(i1,i2,:)), squeeze(alltfY(i1,i2+lag,:)) );
coherres(i1,i2,countlag) = tmp1(1,2);
end;
end;
end;
countlag = countlag + 1;
end;
% find max corr if different lags
% -------------------------------
if length(g.amplag) > 1
[coherres lagmap] = max(coherres, [], 3);
dimsize = length(freqs)*length(timesout);
alpha = reshape(alpha((lagmap(:)-1)*dimsize+[1:dimsize]'),length(freqs), length(timesout));
% above is same as (but faster)
% for i1 = 1:length(freqs)
% for i2 = 1:length(timesout)
% alphanew(i1, i2) = alpha(i1, i2, lagmap(i1, i2));
% end;
% end;
lagmap = g.amplag(lagmap); % real lag
coherres = coherres.*exp(j*lagmap/max(abs(g.amplag))); % encode lag in the phase
else
lagmap = [];
end;
% apply significance mask
% -----------------------
if ~isnan(g.alpha)
tmpind = find(alpha(:) > g.alpha);
coherres(tmpind) = 0;
end;
% ------------------
% plotting functions
% ------------------
function plotall(R, Rboot, times, freqs, mbase, g)
switch lower(g.plotphase)
case 'on',
switch lower(g.plotamp),
case 'on', ordinate1 = 0.67; ordinate2 = 0.1; height = 0.33; g.plot = 1;
case 'off', ordinate2 = 0.1; height = 0.9; g.plot = 1;
end;
case 'off', ordinate1 = 0.1; height = 0.9;
switch lower(g.plotamp),
case 'on', ordinate1 = 0.1; height = 0.9; g.plot = 1;
case 'off', g.plot = 0;
end;
end;
% compute angles
% --------------
Rangle = angle(R);
if ~isreal(R)
R = abs(R);
Rraw =R; % raw coherence values
setylim = 1;
if ~isnan(g.baseline)
R = R - repmat(mbase',[1 g.timesout]); % remove baseline mean
end;
else
Rraw = R;
setylim = 0;
end;
if g.plot
fprintf('\nNow plotting...\n');
set(gcf,'DefaultAxesFontSize',g.AXES_FONT)
colormap(jet(256));
pos = get(gca,'position'); % plot relative to current axes
q = [pos(1) pos(2) 0 0];
s = [pos(3) pos(4) pos(3) pos(4)];
axis('off')
end;
switch lower(g.plotamp)
case 'on'
%
% Image the coherence [% perturbations]
%
RR = R;
if ~isnan(g.alpha) % zero out (and 'green out') nonsignif. R values
switch dims(Rboot)
case 3, RR (find(RR > Rboot(:,:,1) & (RR < Rboot(:,:,2)))) = 0;
Rraw(find(RR > Rboot(:,:,1) & (RR < Rboot(:,:,2)))) = 0;
case 2, RR (find(RR < Rboot)) = 0;
Rraw(find(RR < Rboot)) = 0;
case 1, RR (find(RR < repmat(Rboot(:),[1 size(RR,2)]))) = 0;
Rraw(find(RR < repmat(Rboot(:),[1 size(Rraw,2)]))) = 0;
end;
end
h(6) = axes('Units','Normalized', 'Position',[.1 ordinate1 .8 height].*s+q);
map=hsv(300); % install circular color map - green=0, yellow, orng, red, violet = max
% cyan, blue, violet = min
map = flipud([map(251:end,:);map(1:250,:)]);
map(151,:) = map(151,:)*0.9; % tone down the (0=) green!
colormap(map);
if ~strcmpi(g.freqscale, 'log')
try, imagesc(times,freqs,RR,max(max(RR))*[-1 1]); % plot the coherence image
catch, imagesc(times,freqs,RR,[-1 1]); end;
else
try, imagesclogy(times,freqs,RR,max(max(RR))*[-1 1]); % plot the coherence image
catch, imagesclogy(times,freqs,RR,[-1 1]); end;
end;
set(gca,'ydir','norm');
if ~isempty(g.maxamp)
caxis([-g.maxamp g.maxamp]);
end;
tmpscale = caxis;
hold on
plot([0 0],[0 freqs(end)],'--m','LineWidth',g.linewidth)
for i=1:length(g.marktimes)
plot([g.marktimes(i) g.marktimes(i)],[0 freqs(end)],'--m','LineWidth',g.linewidth);
end;
hold off
set(h(6),'YTickLabel',[],'YTick',[])
set(h(6),'XTickLabel',[],'XTick',[])
h(8) = axes('Position',[.95 ordinate1 .05 height].*s+q);
if setylim
cbar(h(8),151:300, [0 tmpscale(2)]); % use only positive colors (gyorv)
else cbar(h(8),1:300 , [-tmpscale(2) tmpscale(2)]); % use only positive colors (gyorv)
end;
%
% Plot delta-mean min and max coherence at each time point on bottom of image
%
h(10) = axes('Units','Normalized','Position',[.1 ordinate1-0.1 .8 .1].*s+q); % plot marginal means below
Emax = max(R); % mean coherence at each time point
Emin = min(R); % mean coherence at each time point
plot(times,Emin, times, Emax, 'LineWidth',g.linewidth); hold on;
plot([times(1) times(length(times))],[0 0],'LineWidth',0.7);
plot([0 0],[-500 500],'--m','LineWidth',g.linewidth);
for i=1:length(g.marktimes)
plot([g.marktimes(i) g.marktimes(i)],[-500 500],'--m','LineWidth',g.linewidth);
end;
if ~isnan(g.alpha) & dims(Rboot) > 1
% plot bootstrap significance limits (base mean +/-)
switch dims(Rboot)
case 2, plot(times,mean(Rboot(:,:),1),'g' ,'LineWidth',g.linewidth);
plot(times,mean(Rboot(:,:),1),'k:','LineWidth',g.linewidth);
case 3, plot(times,mean(Rboot(:,:,1),1),'g' ,'LineWidth',g.linewidth);
plot(times,mean(Rboot(:,:,1),1),'k:','LineWidth',g.linewidth);
plot(times,mean(Rboot(:,:,2),1),'g' ,'LineWidth',g.linewidth);
plot(times,mean(Rboot(:,:,2),1),'k:','LineWidth',g.linewidth);
end;
axis([min(times) max(times) 0 max([Emax(:)' Rboot(:)'])*1.2])
else
axis([min(times) max(times) 0 max(Emax)*1.2])
end;
tick = get(h(10),'YTick');
set(h(10),'YTick',[tick(1) ; tick(length(tick))])
set(h(10),'YAxisLocation','right')
xlabel('Time (ms)')
ylabel('coh.')
%
% Plot mean baseline coherence at each freq on left side of image
%
h(11) = axes('Units','Normalized','Position',[0 ordinate1 .1 height].*s+q); % plot mean spectrum
E = abs(mbase); % baseline mean coherence at each frequency
if ~strcmpi(g.freqscale, 'log')
plot(freqs,E,'b','LineWidth',g.linewidth); % plot mbase
else
semilogx(freqs,E,'b','LineWidth',g.linewidth); % plot mbase
set(h(11),'View',[90 90])
divs = linspace(log(freqs(1)), log(freqs(end)), 10);
set(gca, 'xtickmode', 'manual');
divs = ceil(exp(divs)); divs = unique_bc(divs); % ceil is critical here, round might misalign
% out-of border label with within border ticks
set(gca, 'xtick', divs);
end;
if ~isnan(g.alpha) % plot bootstrap significance limits (base mean +/-)
hold on
if ~strcmpi(g.freqscale, 'log')
switch dims(Rboot)
case 1, plot(freqs,Rboot(:),'g' ,'LineWidth',g.linewidth);
plot(freqs,Rboot(:),'k:','LineWidth',g.linewidth);
case 2, plot(freqs,mean(Rboot(:,:),2),'g' ,'LineWidth',g.linewidth);
plot(freqs,mean(Rboot(:,:),2),'k:','LineWidth',g.linewidth);
case 3, plot(freqs,mean(Rboot(:,:,1),2),'g' ,'LineWidth',g.linewidth);
plot(freqs,mean(Rboot(:,:,1),2),'k:','LineWidth',g.linewidth);
plot(freqs,mean(Rboot(:,:,2),2),'g' ,'LineWidth',g.linewidth);
plot(freqs,mean(Rboot(:,:,2),2),'k:','LineWidth',g.linewidth);
end;
else
switch dims(Rboot)
case 1, semilogy(freqs,Rboot(:),'g' ,'LineWidth',g.linewidth);
semilogy(freqs,Rboot(:),'k:','LineWidth',g.linewidth);
case 2, semilogy(freqs,mean(Rboot(:,:),2),'g' ,'LineWidth',g.linewidth);
semilogy(freqs,mean(Rboot(:,:),2),'k:','LineWidth',g.linewidth);
case 3, semilogy(freqs,mean(Rboot(:,:,1),2),'g' ,'LineWidth',g.linewidth);
semilogy(freqs,mean(Rboot(:,:,1),2),'k:','LineWidth',g.linewidth);
semilogy(freqs,mean(Rboot(:,:,2),2),'g' ,'LineWidth',g.linewidth);
semilogy(freqs,mean(Rboot(:,:,2),2),'k:','LineWidth',g.linewidth);
end;
end;
if ~isnan(max(E))
axis([freqs(1) freqs(end) 0 max([E Rboot(:)'])*1.2]);
end;
else % plot marginal mean coherence only
if ~isnan(max(E))
axis([freqs(1) freqs(end) 0 max(E)*1.2]);
end;
end
set(gca,'xdir','rev'); % nima
tick = get(h(11),'YTick');
set(h(11),'YTick',[tick(1) ; tick(length(tick))]); % crashes for log
set(h(11),'View',[90 90])
xlabel('Freq. (Hz)')
ylabel('coh.')
end;
switch lower(g.plotphase)
case 'on'
%
% Plot coherence phase lags in bottom panel
%
h(13) = axes('Units','Normalized','Position',[.1 ordinate2 .8 height].*s+q);
if setylim
if strcmpi(g.type, 'amp') % currrently -1 to 1
maxangle = max(abs(g.amplag)) * mean(times(2:end) - times(1:end-1));
Rangle = Rangle * maxangle;
maxangle = maxangle+5; % so that the min and the max does not mix
else
if strcmp(g.angleunit,'ms') % convert to ms
Rangle = (Rangle/(2*pi)).*repmat(1000./freqs(:)',1,length(times));
maxangle = max(max(abs(Rangle)));
elseif strcmpi(g.angleunit,'deg') % convert to degrees
Rangle = Rangle*180/pi; % convert to degrees
maxangle = 180; % use full-cycle plotting
else
maxangle = pi;
end
end;
Rangle(find(Rraw==0)) = 0; % set angle at non-signif coher points to 0
if ~strcmpi(g.freqscale, 'log')
imagesc(times,freqs,Rangle,[-maxangle maxangle]); % plot the coherence phase angles
else
imagesclogy(times,freqs,Rangle,[-maxangle maxangle]); % plot the coherence phase angles
end;
hold on
plot([0 0],[0 freqs(end)],'--m','LineWidth',g.linewidth); % zero-time line
for i=1:length(g.marktimes)
plot([g.marktimes(i) g.marktimes(i)],[0 freqs(end)],'--m','LineWidth',g.linewidth);
end;
set(gca,'ydir','norm'); % nima
ylabel('Freq. (Hz)')
xlabel('Time (ms)')
h(14)=axes('Position',[.95 ordinate2 .05 height].*s+q);
cbar(h(14),0,[-maxangle maxangle]); % two-sided colorbar
else
axis off;
text(0, 0.5, 'Real values, no angles');
end;
end
if g.plot
try, icadefs; set(gcf, 'color', BACKCOLOR); catch, end;
if (length(g.title) > 0) % plot title
axes('Position',pos,'Visible','Off');
h(13) = text(-.05,1.01,g.title);
set(h(13),'VerticalAlignment','bottom')
set(h(13),'HorizontalAlignment','left')
set(h(13),'FontSize',g.TITLE_FONT)
end
%
%%%%%%%%%%%%%%% plot topoplot() %%%%%%%%%%%%%%%%%%%%%%%
%
if (~isempty(g.topovec)) & strcmpi(g.plotamp, 'on') & strcmpi(g.plotphase, 'on')
h(15) = subplot('Position',[-.1 .43 .2 .14].*s+q);
if size(g.topovec,2) <= 2
topoplot(g.topovec(1),g.elocs,'electrodes','off', ...
'style', 'blank', 'emarkersize1chan', 10, 'chaninfo', g.chaninfo);
else
topoplot(g.topovec(1,:),g.elocs,'electrodes','off', 'chaninfo', g.chaninfo);
end;
axis('square')
h(16) = subplot('Position',[.9 .43 .2 .14].*s+q);
if size(g.topovec,2) <= 2
topoplot(g.topovec(2),g.elocs,'electrodes','off', ...
'style', 'blank', 'emarkersize1chan', 10, 'chaninfo', g.chaninfo);
else
topoplot(g.topovec(2,:),g.elocs,'electrodes','off', 'chaninfo', g.chaninfo);
end;
axis('square')
end
try, axcopy(gcf); catch, end;
end;
% ---------------
% Plotting curves
% ---------------
function plotallcurves(R, Rboot, times, freqs, mbase, g)
% compute angles
% --------------
Rangle = angle(R);
pos = get(gca,'position'); % plot relative to current axes
q = [pos(1) pos(2) 0 0];
s = [pos(3) pos(4) pos(3) pos(4)];
if ~isreal(R)
R = abs(R);
Rraw =R; % raw coherence values
if ~isnan(g.baseline)
R = R - repmat(mbase',[1 g.timesout]); % remove baseline mean
end;
else
Rraw = R;
setylim = 0;
end;
% time unit
% ---------
if times(end) > 10000
times = times/1000;
timeunit = 's';
else
timeunit = 'ms';
end;
% legend
% ------
alllegend = {};
if strcmpi(g.plotmean, 'on') & freqs(1) ~= freqs(end)
alllegend = { [ num2str(freqs(1)) '-' num2str(freqs(end)) 'Hz' ] };
else
for index = 1:length(freqs)
alllegend{index} = [ num2str(freqs(index)) 'Hz' ];
end;
end;
fprintf('\nNow plotting...\n');
if strcmpi(g.plotamp, 'on')
%
% Plot coherence amplitude in top panel
%
if strcmpi(g.plotphase, 'on'), subplot(2,1,1); end;
if isempty(g.maxamp), g.maxamp = 0; end;
plotcurve(times, R, 'maskarray', Rboot, 'title', 'Coherence amplitude', ...
'xlabel', [ 'Time (' timeunit ')' ], 'ylabel', '0-1', 'ylim', g.maxamp, ...
'vert', g.vert, 'marktimes', g.marktimes, 'legend', alllegend, ...
'linewidth', g.linewidth, 'highlightmode', g.highlightmode, 'plotmean', g.plotmean);
end;
if strcmpi(g.plotphase, 'on')
%
% Plot coherence phase lags in bottom panel
%
if strcmpi(g.plotamp, 'on'), subplot(2,1,2); end;
plotcurve(times, Rangle/pi*180, 'maskarray', Rboot, 'val2mask', R, 'title', 'Coherence phase', ...
'xlabel', [ 'Time (' timeunit ')' ], 'ylabel', 'Angle (deg.)', 'ylim', [-180 180], ...
'vert', g.vert, 'marktimes', g.marktimes, 'legend', alllegend, ...
'linewidth', g.linewidth, 'highlightmode', g.highlightmode, 'plotmean', g.plotmean);
end
if strcmpi(g.plotamp, 'on') | strcmpi(g.plotphase, 'on')
try, icadefs; set(gcf, 'color', BACKCOLOR); catch, end;
if (length(g.title) > 0) % plot title
h(13) = textsc(g.title, 'title');
end
%
%%%%%%%%%%%%%%% plot topoplot() %%%%%%%%%%%%%%%%%%%%%%%
%
if (~isempty(g.topovec))
h(15) = subplot('Position',[-.1 .43 .2 .14].*s+q);
if size(g.topovec,2) <= 2
topoplot(g.topovec(1),g.elocs,'electrodes','off', ...
'style', 'blank', 'emarkersize1chan', 10);
else
topoplot(g.topovec(1,:),g.elocs,'electrodes','off');
end;
axis('square')
h(16) = subplot('Position',[.9 .43 .2 .14].*s+q);
if size(g.topovec,2) <= 2
topoplot(g.topovec(2),g.elocs,'electrodes','off', ...
'style', 'blank', 'emarkersize1chan', 10);
else
topoplot(g.topovec(2,:),g.elocs,'electrodes','off');
end;
axis('square')
end
try, axcopy(gcf); catch, end;
end;
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% COHERENCE OBSOLETE %%%%%%%%%%%%%%%%%%%%%%%%%
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
% function for coherence initialisation
% -------------------------------------
function Coher = coherinit(nb_points, trials, timesout, type);
Coher.R = zeros(nb_points,timesout); % mean coherence
%Coher.RR = repmat(nan,nb_points,timesout); % initialize with nans
Coher.type = type;
Coher.Rn=zeros(trials,timesout);
switch type
case 'coher',
Coher.cumulX = zeros(nb_points,timesout);
Coher.cumulY = zeros(nb_points,timesout);
case 'phasecoher2',
Coher.cumul = zeros(nb_points,timesout);
end;
% function for coherence calculation
% -------------------------------------
%function Coher = cohercomparray(Coher, tmpX, tmpY, trial);
%switch Coher.type
% case 'coher',
% Coher.R = Coher.R + tmpX.*conj(tmpY); % complex coher.
% Coher.cumulXY = Coher.cumulXY + abs(tmpX).*abs(tmpY);
% case 'phasecoher',
% Coher.R = Coher.R + tmpX.*conj(tmpY) ./ (abs(tmpX).*abs(tmpY)); % complex coher.
% Coher.Rn(trial,:) = 1;
%end % ~any(isnan())
function [Coher,tmptrialcoh] = cohercomp(Coher, tmpX, tmpY, trial, time);
tmptrialcoh = tmpX.*conj(tmpY);
switch Coher.type
case 'coher',
Coher.R(:,time) = Coher.R(:,time) + tmptrialcoh; % complex coher.
Coher.cumulX(:,time) = Coher.cumulX(:,time) + abs(tmpX).^2;
Coher.cumulY(:,time) = Coher.cumulY(:,time) + abs(tmpY).^2;
case 'phasecoher2',
Coher.R(:,time) = Coher.R(:,time) + tmptrialcoh; % complex coher.
Coher.cumul(:,time) = Coher.cumul(:,time) + abs(tmptrialcoh);
case 'phasecoher',
Coher.R(:,time) = Coher.R(:,time) + tmptrialcoh ./ abs(tmptrialcoh); % complex coher.
%figure; imagesc(abs(tmpX.*conj(tmpY) ./ (abs(tmpX).*abs(tmpY))));
Coher.Rn(trial,time) = Coher.Rn(trial,time)+1;
end % ~any(isnan())
% function for post coherence calculation
% ---------------------------------------
function Coher = cohercomppost(Coher, trials);
switch Coher.type
case 'coher',
Coher.R = Coher.R ./ sqrt(Coher.cumulX) ./ sqrt(Coher.cumulY);
case 'phasecoher2',
Coher.R = Coher.R ./ Coher.cumul;
case 'phasecoher',
Coher.Rn = sum(Coher.Rn, 1);
Coher.R = Coher.R ./ (ones(size(Coher.R,1),1)*Coher.Rn); % coherence magnitude
end;
% function for 2 conditions coherence calculation
% -----------------------------------------------
function [coherimage, coherimage1, coherimage2] = coher2conddiff( allsavedcoher, alltrials, cond1trials, type, tfx, tfy);
t1s = alltrials(1:cond1trials);
t2s = alltrials(cond1trials+1:end);
switch type
case 'coher',
coherimage1 = sum(allsavedcoher(:,:,t1s),3) ./ sqrt(sum(tfx(:,:,t1s))) ./ sqrt(sum(tfy(:,:,t1s)));
coherimage2 = sum(allsavedcoher(:,:,t2s),3) ./ sqrt(sum(tfx(:,:,t2s))) ./ sqrt(sum(tfy(:,:,t1s)));
case 'phasecoher2',
coherimage1 = sum(allsavedcoher(:,:,t1s),3) ./ sum(abs(allsavedcoher(:,:,t1s)),3);
coherimage2 = sum(allsavedcoher(:,:,t2s),3) ./ sum(abs(allsavedcoher(:,:,t2s)),3);
case 'phasecoher',
coherimage1 = sum(allsavedcoher(:,:,t1s),3) / cond1trials;
coherimage2 = sum(allsavedcoher(:,:,t2s),3) / (size(allsavedcoher,3)-cond1trials);
end;
coherimage = coherimage2 - coherimage1;
function w = hanning(n)
if ~rem(n,2)
w = .5*(1 - cos(2*pi*(1:n/2)'/(n+1)));
w = [w; w(end:-1:1)];
else
w = .5*(1 - cos(2*pi*(1:(n+1)/2)'/(n+1)));
w = [w; w(end-1:-1:1)];
end
function res = dims(array)
res = min(ndims(array), max(size(array,2),size(array,3)));
|
github
|
lcnbeapp/beapp-master
|
crossf.m
|
.m
|
beapp-master/Packages/eeglab14_1_2b/functions/timefreqfunc/crossf.m
| 59,295 |
utf_8
|
395468032fe3d1abba14d59dfe6d1317
|
% crossf() - Returns estimates and plots event-related coherence (ERCOH)
% between two input data time series (X,Y). A lower panel (optionally)
% shows the coherence phase difference between the processes.
% In this panel, output by > crossf(X,Y,...);
% 90 degrees (orange) means X leads Y by a quarter cycle.
% -90 degrees (blue) means Y leads X by a quarter cycle.
% Coherence phase units may be radians, degrees, or msec.
% Click on any subplot to view separately and zoom in/out.
%
% Function description:
% Uses EITHER fixed-window, zero-padded FFTs (fastest) OR constant-Q
% 0-padded wavelet DFTs (more even sensitivity across frequencies),
% both Hanning-tapered. Output frequency spacing is the lowest
% frequency ('srate'/'winsize') divided by the 'padratio'.
%
% If an 'alpha' value is given, then bootstrap statistics are
% computed (from a distribution of 'naccu' {200} surrogate baseline
% data epochs) for the baseline epoch, and non-significant features
% of the output plots are zeroed (and shown in green). The baseline
% epoch is all windows with center latencies < the given 'baseline'
% value, or if 'baseboot' is 1, the whole epoch.
% Usage:
% >> [coh,mcoh,timesout,freqsout,cohboot,cohangles] ...
% = crossf(X,Y,frames,tlimits,srate,cycles, ...
% 'key1', 'val1', 'key2', val2' ...);
% Required inputs:
% X = first single-channel data set (1,frames*nepochs)
% Y = second single-channel data set (1,frames*nepochs)
% frames = frames per epoch {default: 750}
% tlimits = [mintime maxtime] (ms) epoch latency limits {def: [-1000 2000]}
% srate = data sampling rate (Hz) {default: 250}
% cycles = 0 -> Use FFTs (with constant window length)
% = >0 -> Number of cycles in each analysis wavelet
% = [cycles expfactor] -> if 0 < expfactor < 1, the number
% of wavelet cycles expands with frequency from cycles
% If expfactor = 1, no expansion; if = 0, constant
% window length (as in FFT) {default: 0}
% Optional Coherence Type:
% 'type' = ['coher'|'phasecoher'] Compute either linear coherence
% ('coher') or phase coherence ('phasecoher') also known
% as phase coupling factor' {default: 'phasecoher'}.
% 'subitc' = ['on'|'off'] subtract stimulus locked Inter-Trial Coherence
% from X and Y. This computes the 'intrinsic' coherence
% X and Y not arising from common synchronization to
% experimental events. See notes. {default: 'off'}
% 'shuffle' = integer indicating the number of estimates to compute
% bootstrap coherence based on shuffled trials. This estimates
% the coherence arising only from time locking of X and Y
% to experimental events (opposite of 'subitc') {default: 0}
% Optional Detrend:
% 'detret' = ['on'|'off'], Linearly detrend data within epochs {def: 'off'}
% 'detrep' = ['on'|'off'], Linearly detrend data across trials {def: 'off'}
%
% Optional FFT/DFT:
% 'winsize' = If cycles==0: data subwindow length (fastest, 2^n<frames);
% if cycles >0: *longest* window length to use. This
% determines the lowest output frequency {default: ~frames/8}
% 'timesout' = Number of output latencies (int<frames-winsize) {def: 200}
% 'padratio' = FFTlength/winsize (2^k) {default: 2}
% Multiplies the number of output frequencies by
% dividing their spacing. When cycles==0, frequency
% spacing is (low_frequency/padratio).
% 'maxfreq' = Maximum frequency (Hz) to plot (& output if cycles>0)
% If cycles==0, all FFT frequencies are output {default: 50}
% 'baseline' = Coherence baseline end latency (ms). NaN -> No baseline
% {default:NaN}
% 'powbase' = Baseline spectrum to log-subtract {default: from data}
%
% Optional Bootstrap:
% 'alpha' = If non-0, compute two-tailed bootstrap significance prob.
% level. Show non-signif output values as green. {def: 0}
% 'naccu' = Number of bootstrap replications to compute {def: 200}
% 'boottype' = ['times'|'timestrials'] Bootstrap type: Either shuffle
% windows ('times') or windows and trials ('timestrials')
% Option 'timestrials' requires more memory {default: 'times'}
% 'memory' = ['low'|'high'] 'low' -> decrease memory use {default: 'high'}
% 'baseboot' = Extent of bootstrap shuffling (0=to 'baseline'; 1=whole epoch)
% If no baseline is given (NaN), extent of bootstrap shuffling
% is the whole epoch {default: 0}
% 'rboot' = Input bootstrap coherence limits (e.g., from crossf())
% The bootstrap type should be identical to that used
% to obtain the input limits. {default: compute from data}
% Optional Scalp Map:
% 'topovec' = (2,nchans) matrix, plot scalp maps to plot {default: []}
% ELSE (c1,c2), plot two cartoons showing channel locations.
% 'elocs' = Electrode location structure or file for scalp map
% {default: none}
% 'chaninfo' = Electrode location additional information (nose position...)
% {default: none}
%
% Optional Plot and Compute Features:
% 'compute' = ['matlab'|'c'] Use C subroutines to speed up the
% computation (currently unimplemented) {def: 'matlab'}
% 'savecoher' - [0|1] 1 --> Accumulate the individual trial coherence
% vectors; output them as cohangles {default: 0 = off}
% 'plotamp' = ['on'|'off'], Plot coherence magnitude {def: 'on'}
% 'maxamp' = [real] Set the maximum for the amp. scale {def: auto}
% 'plotphase' = ['on'|'off'], Plot coherence phase angle {def: 'on'}
% 'angleunit' = Phase units: 'ms' -> msec, 'deg' -> degrees,
% or 'rad' -> radians {default: 'deg'}
% 'title' = Optional figure title {default: none}
% 'vert' = Latencies to mark with a dotted vertical line
% {default: none}
% 'linewidth' = Line width for marktimes traces (thick=2, thin=1)
% {default: 2}
% 'cmax' = Maximum amplitude for color scale {def: data limits}
% 'axesfont' = Axes font size {default: 10}
% 'titlefont' = Title font size {default: 8}
%
% Outputs:
% coh = Matrix (nfreqs,timesout) of coherence magnitudes
% mcoh = Vector of mean baseline coherence at each frequency
% timesout = Vector of output latencies (window centers) (ms).
% freqsout = Vector of frequency bin centers (Hz).
% cohboot = Matrix (nfreqs,2) of [lower;upper] coher signif. limits
% if 'boottype' is 'trials', (nfreqs,timesout, 2)
% cohangle = (nfreqs,timesout) matrix of coherence angles (in radians)
% cohangles = (nfreqs,timesout,trials) matrix of single-trial coherence
% angles (in radians), saved and output only if 'savecoher',1
%
% Plot description:
% Assuming both 'plotamp' and 'plotphase' options are 'on' (=default), the upper panel
% presents the magnitude of either phase coherence or linear coherence, depending on
% the 'type' parameter (above). The lower panel presents the coherence phase difference
% (in degrees). Click on any plot to pop up a new window (using 'axcopy()').
% -- The upper left marginal panel shows mean coherence during the baseline period
% (blue), and when significance is set, the significance threshold (dotted black-green).
% -- The horizontal panel under the coherence magnitude image indicates the maximum
% (green) and minimum (blue) coherence values across all frequencies. When significance
% is set (using option 'trials' for 'boottype'), an additional curve indicates the
% significance threshold (dotted black-green).
%
% Notes: 1) When cycles==0, nfreqs is total number of FFT frequencies.
% 2) As noted above: 'blue' coherence angle -> X leads Y; 'red' -> Y leads X
% 3) The 'boottype' should be ideally 'timesframes', but this creates high
% memory demands, so the 'times' method must be used in many cases.
% 4) If 'boottype' is 'trials', the average of the complex bootstrap
% is subtracted from the coherence to compensate for phase differences
% (the average is also subtracted from the bootstrap distribution).
% For other bootstraps, this is not necessary since the phase is random.
% 5) If baseline is non-NaN, the baseline is subtracted from
% the complex coherence. On the left hand side of the coherence
% amplitude image, the baseline is displayed as a magenta line
% (if no baseline is selected, this curve represents the average
% coherence at every given frequency).
% 6) If a out-of-memory error occurs, set the 'memory' option to 'low'
% (Makes computation time slower; Only the 'times' bootstrap method
% can be used in this mode).
%
% Authors: Arnaud Delorme, Sigurd Enghoff & Scott Makeig
% CNL/Salk Institute 1998-2001; SCCN/INC/UCSD, La Jolla, 2002-
%
% See also: timef()
% Copyright (C) 8/1/98 Arnaud Delorme, Sigurd Enghoff & Scott Makeig, SCCN/INC/UCSD
%
% This program is free software; you can redistribute it and/or modify
% it under the terms of the GNU General Public License as published by
% the Free Software Foundation; either version 2 of the License, or
% (at your option) any later version.
%
% This program is distributed in the hope that it will be useful,
% but WITHOUT ANY WARRANTY; without even the implied warranty of
% MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
% GNU General Public License for more details.
%
% You should have received a copy of the GNU General Public License
% along with this program; if not, write to the Free Software
% Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
% 11-20-98 defined g.linewidth constant -sm
% 04-01-99 made number of frequencies consistent -se
% 06-29-99 fixed constant-Q freq indexing -se
% 08-13-99 added cohangle plotting -sm
% 08-20-99 made bootstrap more efficient -sm
% 08-24-99 allow nan values introduced by possible eventlock() preproc. -sm
% 03-05-2007 eventlock.m deprecated to eegalign.m. -tf
% 03-16-00 added lead/lag interpretation to help msg - sm & eric visser
% 03-16-00 added axcopy() feature -sm & tpj
% 04-20-00 fixed Rangle sign for wavelets, added verts array -sm
% 01-22-01 corrected help msg when nargin<2 -sm & arno delorme
% 01-25-02 reformated help & license, added links -ad
% 03-09-02 function restructuration -ad
% add 'key', val arguments (+ external baseboot, baseline, color axis, angleunit...)
% add detrending (across time and trials) + 'coher' option for amplitude coherence
% significance only if alpha is given, ploting options in 'plotamp' and 'plotphase'
% 03-16-02 timeout automatically adjusted if too high -ad
% 04-03-02 added new options for bootstrap -ad
% Note: 3 "objects" (Tf, Coher and Boot) are handled by specific functions under Matlab
% (Tf) function Tf = tfinit(...) - create object Time Frequency (Tf) associated with some data
% (Tf) function [Tf, itcvals] = tfitc(...) - compute itc for the selected data
% (Tf) function [Tf, itcvals] = tfitcpost(Tf, trials) - itc normlisation
% (Tf) function [Tf, tmpX] = tfcomp(Tf, trials, times) - compute time freq. decomposition
% (Coher) function Coher = coherinit(...) - initialize coherence object
% (Coher) function Coher = cohercomp(Coher, tmpX, tmpY, trial, time) - compute coherence
% (Coher) function Coher = cohercomppost(Coher, trials) - coherence normalization
% (Boot) function Boot = bootinit(...) - intialize bootstrap object
% (Boot) function Boot = bootcomp(...) - compute bootstrap
% (Boot) function [Boot, Rbootout] = bootcomppost(...) - bootstrap normalization
% and by real objects under C++ (C++ code, incomplete)
function [R,mbase,times,freqs,Rbootout,Rangle, trialcoher, Tfx, Tfy] = crossf(X, Y, frame, tlimits, Fs, varwin, varargin)
%varwin,winsize,nwin,oversmp,maxfreq,alpha,verts,caxmax)
% ------------------------
% Commandline arg defaults:
% ------------------------
DEFAULT_ANGLEUNIT = 'deg'; % angle plotting units - 'rad', 'ms', or 'deg'
DEFAULT_EPOCH = 750; % Frames per epoch
DEFAULT_TIMELIM = [-1000 2000]; % Time range of epochs (ms)
DEFAULT_FS = 250; % Sampling frequency (Hz)
DEFAULT_NWIN = 200; % Number of windows = horizontal resolution
DEFAULT_VARWIN = 0; % Fixed window length or base on cycles.
% =0: fix window length to nwin
% >0: set window length equal varwin cycles
% bounded above by winsize, also determines
% the min. freq. to be computed.
DEFAULT_OVERSMP = 2; % Number of times to oversample = vertical resolution
DEFAULT_MAXFREQ = 50; % Maximum frequency to display (Hz)
DEFAULT_TITLE = 'Event-Related Coherence'; % Figure title
DEFAULT_ALPHA = NaN; % Default two-sided significance probability threshold
if (nargin < 2)
help crossf
return
end
if ~iscell(X)
if (min(size(X))~=1 | length(X)<2)
fprintf('crossf(): X must be a row or column vector.\n');
return
elseif (min(size(Y))~=1 | length(Y)<2)
fprintf('crossf(): Y must be a row or column vector.\n');
return
elseif (length(X) ~= length(Y))
fprintf('crossf(): X and Y must have same length.\n');
return
end
end;
if (nargin < 3)
frame = DEFAULT_EPOCH;
elseif (~isnumeric(frame) | length(frame)~=1 | frame~=round(frame))
fprintf('crossf(): Value of frames must be an integer.\n');
return
elseif (frame <= 0)
fprintf('crossf(): Value of frames must be positive.\n');
return
elseif ~iscell(X) & (rem(length(X),frame) ~= 0)
fprintf('crossf(): Length of data vectors must be divisible by frames.\n');
return
end
if (nargin < 4)
tlimits = DEFAULT_TIMELIM;
elseif (~isnumeric(tlimits) | sum(size(tlimits))~=3)
error('crossf(): Value of tlimits must be a vector containing two numbers.');
elseif (tlimits(1) >= tlimits(2))
error('crossf(): tlimits interval must be [min,max].');
end
if (nargin < 5)
Fs = DEFAULT_FS;
elseif (~isnumeric(Fs) | length(Fs)~=1)
error('crossf(): Value of srate must be a number.');
elseif (Fs <= 0)
error('crossf(): Value of srate must be positive.');
end
if (nargin < 6)
varwin = DEFAULT_VARWIN;
elseif (~isnumeric(varwin) | length(varwin)>2)
error('crossf(): Value of cycles must be a number or a (1,2) vector.');
elseif (varwin < 0)
error('crossf(): Value of cycles must be either zero or positive.');
end
% consider structure for these arguments
% --------------------------------------
vararginori = varargin;
for index=1:length(varargin)
if iscell(varargin{index}), varargin{index} = { varargin{index} }; end;
end;
if ~isempty(varargin)
try, g = struct(varargin{:});
catch, error('Argument error in the {''param'', value} sequence'); end;
else
g = [];
end;
try, g.shuffle; catch, g.shuffle = 0; end;
try, g.title; catch, g.title = DEFAULT_TITLE; end;
try, g.winsize; catch, g.winsize = max(pow2(nextpow2(frame)-3),4); end;
try, g.pad; catch, g.pad = max(pow2(nextpow2(g.winsize)),4); end;
try, g.timesout; catch, g.timesout = DEFAULT_NWIN; end;
try, g.padratio; catch, g.padratio = DEFAULT_OVERSMP; end;
try, g.maxfreq; catch, g.maxfreq = DEFAULT_MAXFREQ; end;
try, g.topovec; catch, g.topovec = []; end;
try, g.elocs; catch, g.elocs = ''; end;
try, g.alpha; catch, g.alpha = DEFAULT_ALPHA; end;
try, g.marktimes; catch, g.marktimes = []; end; % default no vertical lines
try, g.marktimes = g.vert; catch, g.vert = []; end; % default no vertical lines
try, g.powbase; catch, g.powbase = nan; end;
try, g.rboot; catch, g.rboot = nan; end;
try, g.plotamp; catch, g.plotamp = 'on'; end;
try, g.plotphase; catch, g.plotphase = 'on'; end;
try, g.plotbootsub; catch, g.plotbootsub = 'on'; end;
try, g.detrep; catch, g.detrep = 'off'; end;
try, g.detret; catch, g.detret = 'off'; end;
try, g.baseline; catch, g.baseline = NaN; end;
try, g.baseboot; catch, g.baseboot = 0; end;
try, g.linewidth; catch, g.linewidth = 2; end;
try, g.naccu; catch, g.naccu = 200; end;
try, g.angleunit; catch, g.angleunit = DEFAULT_ANGLEUNIT; end;
try, g.cmax; catch, g.cmax = 0; end; % 0=use data limits
try, g.type; catch, g.type = 'phasecoher'; end;
try, g.boottype; catch, g.boottype = 'times'; end;
try, g.subitc; catch, g.subitc = 'off'; end;
try, g.memory; catch, g.memory = 'high'; end;
try, g.compute; catch, g.compute = 'matlab'; end;
try, g.maxamp; catch, g.maxamp = []; end;
try, g.savecoher; catch, g.savecoher = 0; end;
try, g.noinput; catch, g.noinput = 'no'; end;
try, g.chaninfo; catch, g.chaninfo = []; end;
allfields = fieldnames(g);
for index = 1:length(allfields)
switch allfields{index}
case { 'shuffle' 'title' 'winsize' 'pad' 'timesout' 'padratio' 'maxfreq' 'topovec' 'elocs' 'alpha' ...
'marktimes' 'vert' 'powbase' 'rboot' 'plotamp' 'plotphase' 'plotbootsub' 'detrep' 'detret' ...
'baseline' 'baseboot' 'linewidth' 'naccu' 'angleunit' 'cmax' 'type' 'boottype' 'subitc' ...
'memory' 'compute' 'maxamp' 'savecoher' 'noinput' 'chaninfo' };
case {'plotersp' 'plotitc' }, disp(['crossf warning: timef option ''' allfields{index} ''' ignored']);
otherwise disp(['crossf error: unrecognized option ''' allfields{index} '''']); beep; return;
end;
end;
g.tlimits = tlimits;
g.frame = frame;
g.srate = Fs;
g.cycles = varwin(1);
if length(varwin)>1
g.cyclesfact = varwin(2);
else
g.cyclesfact = 1;
end;
g.type = lower(g.type);
g.boottype = lower(g.boottype);
g.detrep = lower(g.detrep);
g.detret = lower(g.detret);
g.plotphase = lower(g.plotphase);
g.plotbootsub = lower(g.plotbootsub);
g.subitc = lower(g.subitc);
g.plotamp = lower(g.plotamp);
g.shuffle = lower(g.shuffle);
g.compute = lower(g.compute);
g.AXES_FONT = 10;
g.TITLE_FONT = 14;
% testing arguments consistency
% -----------------------------
if (~ischar(g.title))
error('Title must be a string.');
end
if (~isnumeric(g.winsize) | length(g.winsize)~=1 | g.winsize~=round(g.winsize))
error('Value of winsize must be an integer number.');
elseif (g.winsize <= 0)
error('Value of winsize must be positive.');
elseif (g.cycles == 0 & pow2(nextpow2(g.winsize)) ~= g.winsize)
error('Value of winsize must be an integer power of two [1,2,4,8,16,...]');
elseif (g.winsize > g.frame)
error('Value of winsize must be less than frame length.');
end
if (~isnumeric(g.timesout) | length(g.timesout)~=1 | g.timesout~=round(g.timesout))
error('Value of timesout must be an integer number.');
elseif (g.timesout <= 0)
error('Value of timesout must be positive.');
end
if (g.timesout > g.frame-g.winsize)
g.timesout = g.frame-g.winsize;
disp(['Value of timesout must be <= frame-winsize, timeout adjusted to ' int2str(g.timesout) ]);
end
if (~isnumeric(g.padratio) | length(g.padratio)~=1 | g.padratio~=round(g.padratio))
error('Value of padratio must be an integer.');
elseif (g.padratio <= 0)
error('Value of padratio must be positive.');
elseif (pow2(nextpow2(g.padratio)) ~= g.padratio)
error('Value of padratio must be an integer power of two [1,2,4,8,16,...]');
end
if (~isnumeric(g.maxfreq) | length(g.maxfreq)~=1)
error('Value of g.maxfreq must be a number.');
elseif (g.maxfreq <= 0)
error('Value of g.maxfreq must be positive.');
elseif (g.maxfreq > Fs/2)
fprintf('Warning: input value of g.maxfreq larger that Nyquist frequency %3.4 Hz\n\n',Fs/2);
end
if isempty(g.topovec)
g.topovec = [];
elseif min(size(g.topovec))==1
g.topovec = g.topovec(:);
if size(g.topovec,1)~=2
error('topovec must be a row or column vector.');
end
end;
if isempty(g.elocs)
g.elocs = '';
elseif (~ischar(g.elocs)) & ~isstruct(g.elocs)
error('Channel location file must be a valid text file.');
end
if (~isnumeric(g.alpha) | length(g.alpha)~=1)
error('timef(): Value of g.alpha must be a number.\n');
elseif (round(g.naccu*g.alpha) < 2)
fprintf('Value of g.alpha is out of the normal range [%g,0.5]\n',2/g.naccu);
g.naccu = round(2/g.alpha);
fprintf(' Increasing the number of bootstrap iterations to %d\n',g.naccu);
end
if g.alpha>0.5 | g.alpha<=0
error('Value of g.alpha is out of the allowed range (0.00,0.5).');
end
if ~isnan(g.alpha)
if g.baseboot > 0
fprintf('Bootstrap analysis will use data in baseline (pre-0) subwindows only.\n')
else
fprintf('Bootstrap analysis will use data in all subwindows.\n')
end
end
switch g.angleunit
case { 'rad', 'ms', 'deg' },;
otherwise error('Angleunit must be either ''rad'', ''deg'', or ''ms''');
end;
switch g.type
case { 'coher', 'phasecoher' 'phasecoher2' },;
otherwise error('Type must be either ''coher'' or ''phasecoher''');
end;
switch g.boottype
case { 'times' 'timestrials' 'trials'},;
otherwise error('Boot type must be either ''times'', ''trials'' or ''timestrials''');
end;
if (~isnumeric(g.shuffle))
error('Shuffle argument type must be numeric');
end;
switch g.memory
case { 'low', 'high' },;
otherwise error('memory must be either ''low'' or ''high''');
end;
if strcmp(g.memory, 'low') & ~strcmp(g.boottype, 'times')
error(['Bootstrap type ''' g.boottype ''' cannot be used in low memory mode']);
end;
switch g.compute
case { 'matlab', 'c' },;
otherwise error('compute must be either ''matlab'' or ''c''');
end;
%%%%%%%%%%%%%%%%%%%%%%%%%%%
% Compare 2 conditions
%%%%%%%%%%%%%%%%%%%%%%%%%%%
if iscell(X)
if length(X) ~= 2 | length(Y) ~= 2
error('crossf: to compare conditions, X and Y input must be 2-elements cell arrays');
end;
if ~strcmp(g.boottype, 'times')
disp('crossf warning: The significance bootstrap type is irrelevant when comparing conditions');
end;
for index = 1:2:length(vararginori)
if index<=length(vararginori) % needed: if elemenets are deleted
%if strcmp(vararginori{index}, 'alpha'), vararginori(index:index+1) = [];
if strcmp(vararginori{index}, 'title'), vararginori(index:index+1) = [];
end;
end;
end;
if iscell(g.title)
if length(g.title) <= 2,
g.title{3} = 'Condition 2 - condition 1';
end;
else
g.title = { 'Condition 1', 'Condition 2', 'Condition 2 - condition 1' };
end;
fprintf('Running crossf on condition 1 *********************\n');
fprintf('Note: If an out-of-memory error occurs, try reducing the\n');
fprintf(' number of time points or number of frequencies\n');
if ~strcmp(g.type, 'coher')
fprintf('Note: Type ''coher'' takes 3 times as much memory as other options!)\n');
end
figure;
subplot(1,3,1); title(g.title{1});
if ~strcmp(g.type, 'coher')
[R1,mbase,times,freqs,Rbootout1,Rangle1, savecoher1] = crossf(X{1}, Y{1}, ...
frame, tlimits, Fs, varwin, 'savecoher', 1, 'title', ' ',vararginori{:});
else
[R1,mbase,times,freqs,Rbootout1,Rangle1, savecoher1, Tfx1, Tfy1] = crossf(X{1}, Y{1}, ...
frame, tlimits, Fs, varwin, 'savecoher', 1,'title', ' ',vararginori{:});
end;
R1 = R1.*exp(j*Rangle1); % output Rangle is in radians
% Asking user for memory limitations
% if ~strcmp(g.noinput, 'yes')
% tmp = whos('Tfx1');
% fprintf('This function will require an additional %d bytes, do you wish\n', ...
% tmp.bytes*6+size(savecoher1,1)*size(savecoher1,2)*g.naccu*8);
% res = input('to continue (y/n) (use the ''noinput'' option to disable this message):', 's');
% if res == 'n', return; end;
% end;
fprintf('\nRunning crossf on condition 2 *********************\n');
subplot(1,3,2); title(g.title{2});
if ~strcmp(g.type, 'coher')
[R2,mbase,times,freqs,Rbootout2,Rangle2, savecoher2] = crossf(X{2}, Y{2}, ...
frame, tlimits, Fs, varwin,'savecoher', 1, 'title', ' ',vararginori{:});
else
[R2,mbase,times,freqs,Rbootout2,Rangle2, savecoher2, Tfx2, Tfy2] = crossf(X{2}, Y{2}, ...
frame, tlimits, Fs, varwin,'savecoher', 1, 'title', ' ',vararginori{:});
end;
R2 = R2.*exp(j*Rangle2); % output Rangle is in radians
subplot(1,3,3); title(g.title{3});
if isnan(g.alpha)
plotall(R2-R1, [], [], times, freqs, mbase, find(freqs <= g.maxfreq), g);
else
% accumulate coherence images (all arrays [nb_points * timesout * trials])
% ---------------------------
allsavedcoher = zeros(size(savecoher1,1), ...
size(savecoher1,2), ...
size(savecoher1,3)+size(savecoher2,3));
allsavedcoher(:,:,1:size(savecoher1,3)) = savecoher1;
allsavedcoher(:,:,size(savecoher1,3)+1:end) = savecoher2;
clear savecoher1 savecoher2;
if strcmp(g.type, 'coher')
alltfx = zeros(size(Tfx1,1), size(Tfx2,2), size(Tfx1,3)+size(Tfx2,3));
alltfx(:,:,1:size(Tfx1,3)) = Tfx1;
alltfx(:,:,size(Tfx1,3)+1:end) = Tfx2;
clear Tfx1 Tfx2;
alltfy = zeros(size(Tfy1,1), size(Tfy2,2), size(Tfy1,3)+size(Tfy2,3));
alltfy(:,:,1:size(Tfy1,3)) = Tfy1;
alltfy(:,:,size(Tfy1,3)+1:end) = Tfy2;
clear Tfy1 Tfy2;
end;
coherimages = zeros(size(allsavedcoher,1), size(allsavedcoher,2), g.naccu);
cond1trials = length(X{1})/g.frame;
cond2trials = length(X{2})/g.frame;
alltrials = [1:cond1trials+cond2trials];
fprintf('Accumulating bootstrap:');
% preprocess data
% ---------------
switch g.type
case 'coher', % take the square of alltfx and alltfy
alltfx = alltfx.^2;
alltfy = alltfy.^2;
case 'phasecoher', % normalize
allsavedcoher = allsavedcoher ./ abs(allsavedcoher);
case 'phasecoher2', % don't do anything
end;
if strcmp(g.type, 'coher')
[coherdiff coher1 coher2] = coher2conddiff( allsavedcoher, alltrials, ...
cond1trials, g.type, alltfx, alltfy);
else
[coherdiff coher1 coher2] = coher2conddiff( allsavedcoher, alltrials, ...
cond1trials, g.type);
end;
%figure; g.alpha = NaN; & to check that the new images are the same as the original
%subplot(1,3,1); plotall(coher1, [], [], times, freqs, mbase, find(freqs <= g.maxfreq), g);
%subplot(1,3,2); plotall(coher2, [], [], times, freqs, mbase, find(freqs <= g.maxfreq), g);
%return;
for index=1:g.naccu
if rem(index,10) == 0, fprintf(' %d',index); end
if rem(index,120) == 0, fprintf('\n'); end
if strcmp(g.type, 'coher')
coherimages(:,:,index) = coher2conddiff( allsavedcoher, shuffle(alltrials), ...
cond1trials, g.type, alltfx, alltfy);
else
coherimages(:,:,index) = coher2conddiff( allsavedcoher, shuffle(alltrials), ...
cond1trials, g.type);
end;
end;
fprintf('\n');
% create articially a Bootstrap object to compute significance
Boot = bootinit( [], size(allsavedcoher,1), g.timesout, g.naccu, 0, g.baseboot, ...
'noboottype', g.alpha, g.rboot);
Boot.Coherboot.R = coherimages;
Boot = bootcomppost(Boot, [], [], []);
g.title = '';
plotall(coherdiff, Boot.Coherboot.R, Boot.Rsignif, times, freqs, mbase, ...
find(freqs <= g.maxfreq), g);
end;
return; % ********************************** END PROCESSING TWO CONDITIONS
end;
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
% shuffle trials if necessary
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
if g.shuffle ~= 0
fprintf('x and y data trials being shuffled %d times\n',g.shuffle);
XX = reshape(X, 1, frame, length(X)/g.frame);
YY = Y;
X = [];
Y = [];
for index = 1:g.shuffle
XX = shuffle(XX,3);
X = [X XX(:,:)];
Y = [Y YY];
end;
end;
% detrend over epochs (trials) if requested
% -----------------------------------------
switch g.detrep
case 'on'
X = reshape(X, g.frame, length(X)/g.frame);
X = X - mean(X,2)*ones(1, length(X(:))/g.frame);
Y = reshape(Y, g.frame, length(Y)/g.frame);
Y = Y - mean(Y,2)*ones(1, length(Y(:))/g.frame);
end;
% time limits
wintime = 500*g.winsize/g.srate;
times = [g.tlimits(1)+wintime:(g.tlimits(2)-g.tlimits(1)-2*wintime)/(g.timesout-1):g.tlimits(2)-wintime];
%%%%%%%%%%
% baseline
%%%%%%%%%%
if ~isnan(g.baseline)
baseln = find(times < g.baseline); % subtract means of pre-0 (centered) windows
if isempty(baseln)
baseln = 1:length(times); % use all times as baseline
disp('Bootstrap baseline empty, using the whole epoch.');
end;
baselength = length(baseln);
else
baseln = 1:length(times); % use all times as baseline
baselength = length(times); % used for bootstrap
end;
%%%%%%%%%%%%%%%%%%%%
% Initialize objects
%%%%%%%%%%%%%%%%%%%%
tmpsaveall = (~isnan(g.alpha) & isnan(g.rboot) & strcmp(g.memory, 'high')) ...
| (strcmp(g.subitc, 'on') & strcmp(g.memory, 'high'));
trials = length(X)/g.frame;
if ~strcmp(g.compute, 'c')
Tfx = tfinit(X, g.timesout, g.winsize, g.cycles, g.frame, g.padratio, g.detret, ...
g.srate, g.maxfreq, g.subitc, g.type, g.cyclesfact, tmpsaveall);
Tfy = tfinit(Y, g.timesout, g.winsize, g.cycles, g.frame, g.padratio, g.detret, ...
g.srate, g.maxfreq, g.subitc, g.type, g.cyclesfact, tmpsaveall);
Coher = coherinit(Tfx.nb_points, trials, g.timesout, g.type);
Coherboot = coherinit(Tfx.nb_points, trials, g.naccu , g.type);
Boot = bootinit( Coherboot, Tfx.nb_points, g.timesout, g.naccu, baselength, ...
g.baseboot, g.boottype, g.alpha, g.rboot);
freqs = Tfx.freqs;
dispf = find(freqs <= g.maxfreq);
freqs = freqs(dispf);
else
freqs = g.srate*g.cycles/g.winsize*[2:2/g.padratio:g.winsize]/2;
end;
dispf = find(Tfx.freqs <= g.maxfreq);
%-------------
% Reserve space
%-------------
% R = zeros(tfx.nb_points,g.timesout); % mean coherence
% RR = repmat(nan,tfx.nb_points,g.timesout); % initialize with nans
% Rboot = zeros(tfx.nb_points,g.naccu); % summed bootstrap coher
% switch g.type
% case 'coher',
% cumulXY = zeros(tfx.nb_points,g.timesout);
% cumulXYboot = zeros(tfx.nb_points,g.naccu);
% end;
% if g.bootsub > 0
% Rboottrial = zeros(tfx.nb_points, g.timesout, g.bootsub); % summed bootstrap coher
% cumulXYboottrial = zeros(tfx.nb_points, g.timesout, g.bootsub);
% end;
% if ~isnan(g.alpha) & isnan(g.rboot)
% tf.tmpalltimes = repmat(nan,tfx.nb_points,g.timesout);
% end
% --------------------
% Display text to user
% --------------------
fprintf('\nComputing Event-Related ');
switch g.type
case 'phasecoher', fprintf('Phase Coherence (ITC) images for %d trials.\n',length(X)/g.frame);
case 'phasecoher2', fprintf('Phase Coherence 2 (ITC) images for %d trials.\n',length(X)/g.frame);
case 'coher', fprintf('Linear Coherence (ITC) images for %d trials.\n',length(X)/g.frame);
end;
fprintf('The trial latency range is from %4.5g ms before to %4.5g ms after\n the time-locking event.\n', g.tlimits(1),g.tlimits(2));
fprintf('The frequency range displayed will be %g-%g Hz.\n',min(freqs),g.maxfreq);
if ~isnan(g.baseline)
if length(baseln) == length(times)
fprintf('Using the full trial latency range as baseline.\n');
else
fprintf('Using trial latencies from %4.5g ms to %4.5g ms as baseline.\n', g.tlimits,g.baseline);
end;
else
fprintf('No baseline time range was specified.\n');
end;
if g.cycles==0
fprintf('The data window size will be %d samples (%g ms).\n',g.winsize,2*wintime);
fprintf('The FFT length will be %d samples\n',g.winsize*g.padratio);
else
fprintf('The window size will be %2.3g cycles.\n',g.cycles);
fprintf('The maximum window size will be %d samples (%g ms).\n',g.winsize,2*wintime);
end
fprintf('The window will be applied %d times\n',g.timesout);
fprintf(' with an average step size of %2.2g samples (%2.4g ms).\n', Tfx.stp,1000*Tfx.stp/g.srate);
fprintf('Results will be oversampled %d times.\n',g.padratio);
if ~isnan(g.alpha)
fprintf('Bootstrap confidence limits will be computed based on alpha = %g\n', g.alpha);
else
fprintf('Bootstrap confidence limits will NOT be computed.\n');
end
switch g.plotphase
case 'on',
if strcmp(g.angleunit,'deg')
fprintf(['Coherence angles will be imaged in degrees.\n']);
elseif strcmp(g.angleunit,'rad')
fprintf(['Coherence angles will be imaged in radians.\n']);
elseif strcmp(g.angleunit,'ms')
fprintf(['Coherence angles will be imaged in ms.\n']);
end
end;
fprintf('\nProcessing trial (of %d): ',trials);
% firstboot = 1;
% Rn=zeros(trials,g.timesout);
% X = X(:)'; % make X and Y column vectors
% Y = Y(:)';
% tfy = tfx;
if strcmp(g.compute, 'c')
% C PART
filename = [ 'tmpcrossf' num2str(round(rand(1)*1000)) ];
f = fopen([ filename '.in'], 'w');
fwrite(f, tmpsaveall, 'int32');
fwrite(f, g.detret, 'int32');
fwrite(f, g.srate, 'int32');
fwrite(f, g.maxfreq, 'int32');
fwrite(f, g.padratio, 'int32');
fwrite(f, g.cycles, 'int32');
fwrite(f, g.winsize, 'int32');
fwrite(f, g.timesout, 'int32');
fwrite(f, g.subitc, 'int32');
fwrite(f, g.type, 'int32');
fwrite(f, trials, 'int32');
fwrite(f, g.naccu, 'int32');
fwrite(f, length(X), 'int32');
fwrite(f, X, 'double');
fwrite(f, Y, 'double');
fclose(f);
command = [ '!cppcrosff ' filename '.in ' filename '.out' ];
eval(command);
f = fopen([ filename '.out'], 'r');
size1 = fread(f, 'int32', 1);
size2 = fread(f, 'int32', 1);
Rreal = fread(f, 'double', [size1 size2]);
Rimg = fread(f, 'double', [size1 size2]);
Coher.R = Rreal + j*Rimg;
Boot.Coherboot.R = [];
Boot.Rsignif = [];
else
% ------------------------
% MATLAB PART
% compute ITC if necessary
% ------------------------
if strcmp(g.subitc, 'on')
for t=1:trials
if rem(t,10) == 0, fprintf(' %d',t); end
if rem(t,120) == 0, fprintf('\n'); end
Tfx = tfitc( Tfx, t, 1:g.timesout);
Tfy = tfitc( Tfy, t, 1:g.timesout);
end;
fprintf('\n');
Tfx = tfitcpost( Tfx, trials);
Tfy = tfitcpost( Tfy, trials);
end;
% ---------
% Main loop
% ---------
if g.savecoher,
trialcoher = zeros(Tfx.nb_points, g.timesout, trials);
else
trialcoher = [];
end;
for t=1:trials
if rem(t,10) == 0, fprintf(' %d',t); end
if rem(t,120) == 0, fprintf('\n'); end
Tfx = tfcomp( Tfx, t, 1:g.timesout);
Tfy = tfcomp( Tfy, t, 1:g.timesout);
if g.savecoher
[Coher trialcoher(:,:,t)] = cohercomp( Coher, Tfx.tmpalltimes, ...
Tfy.tmpalltimes, t, 1:g.timesout);
else
Coher = cohercomp( Coher, Tfx.tmpalltimes, Tfy.tmpalltimes, t, 1:g.timesout);
end;
Boot = bootcomp( Boot, Coher.Rn(t,:), Tfx.tmpalltimes, Tfy.tmpalltimes);
end % t = trial
[Boot Rbootout] = bootcomppost(Boot, Coher.Rn, Tfx.tmpall, Tfy.tmpall);
% Note that the bootstrap thresholding is actually performed
% in the display subfunction plotall()
Coher = cohercomppost(Coher, trials);
end;
% ----------------------------------
% If coherence, perform the division
% ----------------------------------
% switch g.type
% case 'coher',
% R = R ./ cumulXY;
% if ~isnan(g.alpha) & isnan(g.rboot)
% Rboot = Rboot ./ cumulXYboot;
% end;
% if g.bootsub > 0
% Rboottrial = Rboottrial ./ cumulXYboottrial;
% end;
% case 'phasecoher',
% Rn = sum(Rn, 1);
% R = R ./ (ones(size(R,1),1)*Rn); % coherence magnitude
% if ~isnan(g.alpha) & isnan(g.rboot)
% Rboot = Rboot / trials;
% end;
% if g.bootsub > 0
% Rboottrial = Rboottrial / trials;
% end;
% end;
% ----------------
% Compute baseline
% ----------------
mbase = mean(abs(Coher.R(:,baseln)')); % mean baseline coherence magnitude
% ---------------
% Plot everything
% ---------------
plotall(Coher.R, Boot.Coherboot.R, Boot.Rsignif, times, freqs, mbase, dispf, g);
% --------------------------------------
% Convert output Rangle to degrees or ms - Disabled to keep original default: radians output
% --------------------------------------
% Rangle = angle(Coher.R); % returns radians
% if strcmp(g.angleunit,'ms') % convert to ms
% Rangle = (Rangle/(2*pi)).*repmat(1000./freqs(dispf)',1,length(times));
% elseif strcmp(g.angleunit,'deg') % convert to deg
% Rangle = Rangle*180/pi; % convert to degrees
% else % angleunit is 'rad'
% % Rangle = Rangle;
% end
% Rangle(find(Rraw==0)) = 0; % mask for significance - set angle at non-signif coher points to 0
R = abs(Coher.R);
Rsignif = Boot.Rsignif;
Tfx = permute(Tfx.tmpall, [3 2 1]); % from [trials timesout nb_points]
% to [nb_points timesout trials]
Tfy = permute(Tfy.tmpall, [3 2 1]);
return; % end crossf() *************************************************
%
% crossf() plotting functions
% ----------------------------------------------------------------------
function plotall(R, Rboot, Rsignif, times, freqs, mbase, dispf, g)
switch lower(g.plotphase)
case 'on',
switch lower(g.plotamp),
case 'on', ordinate1 = 0.67; ordinate2 = 0.1; height = 0.33; g.plot = 1;
case 'off', ordinate2 = 0.1; height = 0.9; g.plot = 1;
end;
case 'off', ordinate1 = 0.1; height = 0.9;
switch lower(g.plotamp),
case 'on', ordinate1 = 0.1; height = 0.9; g.plot = 1;
case 'off', g.plot = 0;
end;
end;
%
% Compute cross-spectral angles
% -----------------------------
Rangle = angle(R); % returns radians
%
% Optionally convert Rangle to degrees or ms
% ------------------------------------------
if strcmp(g.angleunit,'ms') % convert to ms
Rangle = (Rangle/(2*pi)).*repmat(1000./freqs(dispf)',1,length(times));
maxangle = max(max(abs(Rangle)));
elseif strcmp(g.angleunit,'deg') % convert to degrees
Rangle = Rangle*180/pi; % convert to degrees
maxangle = 180; % use full-cycle plotting
else
maxangle = pi; % radians
end
R = abs(R);
% if ~isnan(g.baseline)
% R = R - repmat(mbase',[1 g.timesout]); % remove baseline mean
% end;
Rraw = R; % raw coherence (e.g., coherency) magnitude values output
if g.plot
fprintf('\nNow plotting...\n');
set(gcf,'DefaultAxesFontSize',g.AXES_FONT)
colormap(jet(256));
pos = get(gca,'position'); % plot relative to current axes
q = [pos(1) pos(2) 0 0];
s = [pos(3) pos(4) pos(3) pos(4)];
axis('off')
end;
switch lower(g.plotamp)
case 'on'
%
% Image the coherence [% perturbations]
%
RR = R;
if ~isnan(g.alpha) % zero out (and 'green out') nonsignif. R values
RR(find(RR < repmat(Rboot(:),[1 g.timesout]))) = 0;
Rraw(find(repmat(Rsignif(:),[1,size(Rraw,2)])>=Rraw))=0;
end
if g.cmax == 0
coh_caxis = max(max(R(dispf,:)))*[-1 1];
else
coh_caxis = g.cmax*[-1 1];
end
h(6) = axes('Units','Normalized', 'Position',[.1 ordinate1 .8 height].*s+q);
map=hsv(300); % install circular color map - green=0, yellow, orng, red, violet = max
% cyan, blue, violet = min
map = flipud([map(251:end,:);map(1:250,:)]);
map(151,:) = map(151,:)*0.9; % tone down the (0=) green!
colormap(map);
imagesc(times,freqs(dispf),RR(dispf,:),coh_caxis); % plot the coherence image
if ~isempty(g.maxamp)
caxis([-g.maxamp g.maxamp]);
end;
tmpscale = caxis;
hold on
plot([0 0],[0 freqs(max(dispf))],'--m','LineWidth',g.linewidth)
for i=1:length(g.marktimes)
plot([g.marktimes(i) g.marktimes(i)],[0 freqs(max(dispf))],'--m','LineWidth',g.linewidth);
end;
hold off
set(h(6),'YTickLabel',[],'YTick',[])
set(h(6),'XTickLabel',[],'XTick',[])
%title('Event-Related Coherence')
h(8) = axes('Position',[.95 ordinate1 .05 height].*s+q);
cbar(h(8),151:300, [0 tmpscale(2)]); % use only positive colors (gyorv)
%
% Plot delta-mean min and max coherence at each time point on bottom of image
%
h(10) = axes('Units','Normalized','Position',[.1 ordinate1-0.1 .8 .1].*s+q);
% plot marginal means below
Emax = max(R(dispf,:)); % mean coherence at each time point
Emin = min(R(dispf,:)); % mean coherence at each time point
plot(times,Emin, times, Emax, 'LineWidth',g.linewidth); hold on;
plot([times(1) times(length(times))],[0 0],'LineWidth',0.7);
plot([0 0],[-500 500],'--m','LineWidth',g.linewidth);
for i=1:length(g.marktimes)
plot([g.marktimes(i) g.marktimes(i)],[-500 500],'--m','LineWidth',g.linewidth);
end;
if ~isnan(g.alpha) & strcmp(g.boottype, 'trials')
% plot bootstrap significance limits (base mean +/-)
plot(times,mean(Rboot(dispf,:)),'g','LineWidth',g.linewidth); hold on;
plot(times,mean(Rsignif(dispf,:)),'k:','LineWidth',g.linewidth);
axis([min(times) max(times) 0 max([Emax(:)' Rsignif(:)'])*1.2])
else
axis([min(times) max(times) 0 max(Emax)*1.2])
end;
tick = get(h(10),'YTick');
set(h(10),'YTick',[tick(1) ; tick(length(tick))])
set(h(10),'YAxisLocation','right')
xlabel('Time (ms)')
ylabel('coh.')
%
% Plot mean baseline coherence at each freq on left side of image
%
h(11) = axes('Units','Normalized','Position',[0 ordinate1 .1 height].*s+q);
% plot mean spectrum
E = abs(mbase(dispf)); % baseline mean coherence at each frequency
plot(freqs(dispf),E,'LineWidth',g.linewidth); % plot mbase
if ~isnan(g.alpha) % plot bootstrap significance limits (base mean +/-)
hold on
% plot(freqs(dispf),Rboot(:,dispf)+[E;E],'g','LineWidth',g.linewidth);
plot(freqs(dispf),mean(Rboot (dispf,:),2),'g','LineWidth',g.linewidth);
plot(freqs(dispf),mean(Rsignif(dispf,:),2),'k:','LineWidth',g.linewidth);
axis([freqs(1) freqs(max(dispf)) 0 max([E Rsignif(:)'])*1.2]);
else % plot marginal mean coherence only
if ~isnan(max(E))
axis([freqs(1) freqs(max(dispf)) 0 max(E)*1.2]);
end;
end
tick = get(h(11),'YTick');
set(h(11),'YTick',[tick(1) ; tick(length(tick))])
set(h(11),'View',[90 90])
xlabel('Freq. (Hz)')
ylabel('coh.')
end;
switch lower(g.plotphase)
case 'on'
%
% Plot coherence phase lags in bottom panel
%
h(13) = axes('Units','Normalized','Position',[.1 ordinate2 .8 height].*s+q);
Rangle(find(Rraw==0)) = 0; % when plotting, mask for significance
% = set angle at non-signif coher points to 0
imagesc(times,freqs(dispf),Rangle(dispf,:),[-maxangle maxangle]); % plot the
hold on % coherence phase angles
plot([0 0],[0 freqs(max(dispf))],'--m','LineWidth',g.linewidth); % zero-time line
for i=1:length(g.marktimes)
plot([g.marktimes(i) g.marktimes(i)],[0 freqs(max(dispf))],'--m','LineWidth',g.linewidth);
end;
ylabel('Freq. (Hz)')
xlabel('Time (ms)')
h(14)=axes('Position',[.95 ordinate2 .05 height].*s+q);
cbar(h(14),0,[-maxangle maxangle]); % two-sided colorbar
end
if g.plot
try, icadefs; set(gcf, 'color', BACKCOLOR); catch, end;
if (length(g.title) > 0) % plot title
if h(6) ~= 0, axes(h(6)); else axes(h(13)); end;
%h = subplot('Position',[0 0 1 1].*s+q, 'Visible','Off');
%h(13) = text(-.05,1.01,g.title);
h(13) = title(g.title);
%set(h(13),'VerticalAlignment','bottom')
%set(h(13),'HorizontalAlignment','left')
set(h(13),'FontSize',g.TITLE_FONT);
end
%
%%%%%%%%%%%%%%% plot topoplot() %%%%%%%%%%%%%%%%%%%%%%%
%
if (~isempty(g.topovec))
h(15) = subplot('Position',[-.1 .43 .2 .14].*s+q);
if size(g.topovec,2) <= 2
topoplot(g.topovec(1),g.elocs,'electrodes','off', ...
'style', 'blank', 'emarkersize1chan', 10, 'chaninfo', g.chaninfo);
else
topoplot(g.topovec(1,:),g.elocs,'electrodes','off', 'chaninfo', g.chaninfo);
end;
axis('square')
h(16) = subplot('Position',[.9 .43 .2 .14].*s+q);
if size(g.topovec,2) <= 2
topoplot(g.topovec(2),g.elocs,'electrodes','off', ...
'style', 'blank', 'emarkersize1chan', 10, 'chaninfo', g.chaninfo);
else
topoplot(g.topovec(2,:),g.elocs,'electrodes','off', 'chaninfo', g.chaninfo);
end;
axis('square')
end
axcopy(gcf);
end;
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% TIME FREQUENCY %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
% function for time freq initialisation
% -------------------------------------
function Tf = tfinit(X, timesout, winsize, ...
cycles, frame, padratio, detret, srate, maxfreq, subitc, type, cyclesfact, saveall);
Tf.X = X(:)'; % make X column vectors
Tf.winsize = winsize;
Tf.cycles = cycles;
Tf.frame = frame;
Tf.padratio = padratio;
Tf.detret = detret;
Tf.stp = (frame-winsize)/(timesout-1);
Tf.subitc = subitc; % for ITC
Tf.type = type; % for ITC
Tf.saveall = saveall;
if (Tf.cycles == 0) %%%%%%%%%%%%%% constant window-length FFTs %%%%%%%%%%%%%%%%
% Tf.freqs = srate/winsize*[1:2/padratio:winsize]/2; % incorect for padratio > 2
Tf.freqs = linspace(0, srate/2, length([1:2/padratio:winsize])+1);
Tf.freqs = Tf.freqs(2:end);
Tf.win = hanning(winsize);
Tf.nb_points = padratio*winsize/2;
else % %%%%%%%%%%%%%%%%%% Constant-Q (wavelet) DFTs %%%%%%%%%%%%%%%%%%%%%%%%%%%%
Tf.freqs = srate*cycles/winsize*[2:2/padratio:winsize]/2;
Tf.win = dftfilt(winsize,maxfreq/srate,cycles,padratio,cyclesfact);
Tf.nb_points = size(Tf.win,2);
end;
Tf.tmpalltimes = zeros(Tf.nb_points, timesout);
trials = length(X)/frame;
if saveall
Tf.tmpall = repmat(nan,[trials timesout Tf.nb_points]);
else
Tf.tmpall = [];
end
Tf.tmpallbool = zeros(trials,timesout);
Tf.ITCdone = 0;
if Tf.subitc
Tf.ITC = zeros(Tf.nb_points, timesout);
switch Tf.type,
case { 'coher' 'phasecoher2' }
Tf.ITCcumul = zeros(Tf.nb_points, timesout);
end;
end;
% function for itc
% ----------------
function [Tf, itcvals] = tfitc(Tf, trials, times);
Tf = tfcomp(Tf, trials, times);
switch Tf.type
case 'coher',
Tf.ITC(:,times) = Tf.ITC(:,times) + Tf.tmpalltimes; % complex coher.
Tf.ITCcumul(:,times) = Tf.ITCcumul(:,times)+abs(Tf.tmpalltimes).^2;
case 'phasecoher2',
Tf.ITC(:,times) = Tf.ITC(:,times) + Tf.tmpalltimes; % complex coher.
Tf.ITCcumul(:,times) = Tf.ITCcumul(:,times)+abs(Tf.tmpalltimes);
case 'phasecoher',
Tf.ITC(:,times) = Tf.ITC(:,times) + Tf.tmpalltimes ./ abs(Tf.tmpalltimes);
% complex coher.
end % ~any(isnan())
return;
function [Tf, itcvals] = tfitcpost(Tf, trials);
switch Tf.type
case 'coher', Tf.ITC = Tf.ITC ./ sqrt(trials * Tf.ITCcumul);
case 'phasecoher2', Tf.ITC = Tf.ITC ./ Tf.ITCcumul;
case 'phasecoher', Tf.ITC = Tf.ITC / trials; % complex coher.
end % ~any(isnan())
if Tf.saveall
Tf.ITC = transpose(Tf.ITC); % do not use ' otherwise conjugate
%imagesc(abs(Tf.ITC)); colorbar; figure;
%squeeze(Tf.tmpall(1,1,1:Tf.nb_points))
%squeeze(Tf.ITC (1,1,1:Tf.nb_points))
%Tf.ITC = shiftdim(Tf.ITC, -1);
Tf.ITC = repmat(shiftdim(Tf.ITC, -1), [trials 1 1]);
Tf.tmpall = (Tf.tmpall - abs(Tf.tmpall) .* Tf.ITC) ./ abs(Tf.tmpall);
% for index = 1:trials
% imagesc(squeeze(abs(Tf.tmpall(index,:,:)))); drawnow; figure;
% Tf.tmpall(index,:,:) = (Tf.tmpall(index,:,:) - Tf.tmpall(index,:,:) .* Tf.ITC)./Tf.tmpall(index,:,:);
% imagesc(squeeze(abs(Tf.tmpall(index,:,:)))); drawnow;
% subplot(10,10, index); imagesc(squeeze(abs(Tf.tmpall(index,:,:)))); caxis([0 1]); drawnow;
% end;
% squeeze(Tf.tmpall(1,1,1:Tf.nb_points))
% figure; axcopy;
end;
Tf.ITCdone = 1;
return;
% function for time freq decomposition
% ------------------------------------
function [Tf, tmpX] = tfcomp(Tf, trials, times);
% tf is an structure containing all the information about the decomposition
for trial = trials
for index = times
if ~Tf.tmpallbool(trial, index) % already computed
tmpX = Tf.X([1:Tf.winsize]+floor((index-1)*Tf.stp)+(trial-1)*Tf.frame);
if ~any(isnan(tmpX)) % perform the decomposition
tmpX = tmpX - mean(tmpX);
switch Tf.detret, case 'on',
tmpX = detrend(tmpX);
end;
if Tf.cycles == 0 % use FFTs
tmpX = Tf.win .* tmpX(:);
tmpX = fft(tmpX,Tf.padratio*Tf.winsize);
tmpX = tmpX(2:Tf.padratio*Tf.winsize/2+1);
else
tmpX = transpose(Tf.win) * tmpX(:);
end
else
tmpX = NaN;
end;
if Tf.ITCdone
tmpX = (tmpX - abs(tmpX) .* Tf.ITC(:,index)) ./ abs(tmpX);
end;
Tf.tmpalltimes(:,index) = tmpX;
if Tf.saveall
Tf.tmpall(trial, index,:) = tmpX;
Tf.tmpallbool(trial, index) = 1;
end
else
Tf.tmpalltimes(:,index) = Tf.tmpall(trial, index,:);
end;
end;
end;
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% COHERENCE %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
% function for coherence initialisation
% -------------------------------------
function Coher = coherinit(nb_points, trials, timesout, type);
Coher.R = zeros(nb_points,timesout); % mean coherence
% Coher.RR = repmat(nan,nb_points,timesout); % initialize with nans
Coher.type = type;
Coher.Rn=zeros(trials,timesout);
switch type
case 'coher',
Coher.cumulX = zeros(nb_points,timesout);
Coher.cumulY = zeros(nb_points,timesout);
case 'phasecoher2',
Coher.cumul = zeros(nb_points,timesout);
end;
% function for coherence calculation
% -------------------------------------
% function Coher = cohercomparray(Coher, tmpX, tmpY, trial);
% switch Coher.type
% case 'coher',
% Coher.R = Coher.R + tmpX.*conj(tmpY); % complex coher.
% Coher.cumulXY = Coher.cumulXY + abs(tmpX).*abs(tmpY);
% case 'phasecoher',
% Coher.R = Coher.R + tmpX.*conj(tmpY) ./ (abs(tmpX).*abs(tmpY)); % complex coher.
% Coher.Rn(trial,:) = 1;
% end % ~any(isnan())
function [Coher,tmptrialcoh] = cohercomp(Coher, tmpX, tmpY, trial, time);
tmptrialcoh = tmpX.*conj(tmpY);
switch Coher.type
case 'coher',
Coher.R(:,time) = Coher.R(:,time) + tmptrialcoh; % complex coher.
Coher.cumulX(:,time) = Coher.cumulX(:,time) + abs(tmpX).^2;
Coher.cumulY(:,time) = Coher.cumulY(:,time) + abs(tmpY).^2;
case 'phasecoher2',
Coher.R(:,time) = Coher.R(:,time) + tmptrialcoh; % complex coher.
Coher.cumul(:,time) = Coher.cumul(:,time) + abs(tmptrialcoh);
case 'phasecoher',
Coher.R(:,time) = Coher.R(:,time) + tmptrialcoh ./ abs(tmptrialcoh); % complex coher.
%figure; imagesc(abs(tmpX.*conj(tmpY) ./ (abs(tmpX).*abs(tmpY))));
Coher.Rn(trial,time) = Coher.Rn(trial,time)+1;
end % ~any(isnan())
% function for post coherence calculation
% ---------------------------------------
function Coher = cohercomppost(Coher, trials);
switch Coher.type
case 'coher',
Coher.R = Coher.R ./ sqrt(Coher.cumulX) ./ sqrt(Coher.cumulY);
case 'phasecoher2',
Coher.R = Coher.R ./ Coher.cumul;
case 'phasecoher',
Coher.Rn = sum(Coher.Rn, 1);
Coher.R = Coher.R ./ (ones(size(Coher.R,1),1)*Coher.Rn); % coherence magnitude
end;
% function for 2 conditions coherence calculation
% -----------------------------------------------
function [coherimage, coherimage1, coherimage2] = coher2conddiff( allsavedcoher, alltrials, cond1trials, type, tfx, tfy);
t1s = alltrials(1:cond1trials);
t2s = alltrials(cond1trials+1:end);
switch type
case 'coher',
coherimage1 = sum(allsavedcoher(:,:,t1s),3) ./ sqrt(sum(tfx(:,:,t1s),3)) ./ sqrt(sum(tfy(:,:,t1s),3));
coherimage2 = sum(allsavedcoher(:,:,t2s),3) ./ sqrt(sum(tfx(:,:,t2s),3)) ./ sqrt(sum(tfy(:,:,t1s),3));
case 'phasecoher2',
coherimage1 = sum(allsavedcoher(:,:,t1s),3) ./ sum(abs(allsavedcoher(:,:,t1s)),3);
coherimage2 = sum(allsavedcoher(:,:,t2s),3) ./ sum(abs(allsavedcoher(:,:,t2s)),3);
case 'phasecoher',
coherimage1 = sum(allsavedcoher(:,:,t1s),3) / cond1trials;
coherimage2 = sum(allsavedcoher(:,:,t2s),3) / (size(allsavedcoher,3)-cond1trials);
end;
coherimage = coherimage2 - coherimage1;
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% BOOTSTRAP %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
% function for bootstrap initialisation
% -------------------------------------
function Boot = bootinit(Coherboot, nb_points, timesout, naccu, baselength, baseboot, boottype, alpha, rboot);
Boot.Rboot = zeros(nb_points,naccu); % summed bootstrap coher
Boot.boottype = boottype;
Boot.baselength = baselength;
Boot.baseboot = baseboot;
Boot.Coherboot = Coherboot;
Boot.naccu = naccu;
Boot.alpha = alpha;
Boot.rboot = rboot;
% function for bootstrap computation
% ----------------------------------
function Boot = bootcomp(Boot, Rn, tmpalltimesx, tmpalltimesy);
if ~isnan(Boot.alpha) & isnan(Boot.rboot)
if strcmp(Boot.boottype, 'times') % get g.naccu bootstrap estimates for each trial
goodbasewins = find(Rn==1);
if Boot.baseboot % use baseline windows only
goodbasewins = find(goodbasewins<=Boot.baselength);
end
ngdbasewins = length(goodbasewins);
j=1;
tmpsX = zeros(size(tmpalltimesx,1), Boot.naccu);
tmpsY = zeros(size(tmpalltimesx,1), Boot.naccu);
if ngdbasewins > 1
while j<=Boot.naccu
s = ceil(rand([1 2])*ngdbasewins); % random ints [1,g.timesout]
s = goodbasewins(s);
if ~any(isnan(tmpalltimesx(:,s(1)))) & ~any(isnan(tmpalltimesy(:,s(2))))
tmpsX(:,j) = tmpalltimesx(:,s(1));
tmpsY(:,j) = tmpalltimesy(:,s(2));
j = j+1;
end
end
Boot.Coherboot = cohercomp(Boot.Coherboot, tmpsX, tmpsY, 1, 1:Boot.naccu);
end;
end
end;
% handle other trial bootstrap types
% ----------------------------------
function [Boot, Rbootout] = bootcomppost(Boot, allRn, alltmpsX, alltmpsY);
trials = size(alltmpsX, 1);
times = size(alltmpsX, 2);
nb_points = size(alltmpsX, 3);
if ~isnan(Boot.alpha) & isnan(Boot.rboot)
if strcmp(Boot.boottype, 'trials') % get g.naccu bootstrap estimates for each trial
fprintf('\nProcessing trial bootstrap (of %d):',times(end));
tmpsX = zeros(size(alltmpsX,3), Boot.naccu);
tmpsY = zeros(size(alltmpsY,3), Boot.naccu );
Boot.fullcoherboot = zeros(nb_points, Boot.naccu, times);
for index=1:times
if rem(index,10) == 0, fprintf(' %d',index); end
if rem(index,120) == 0, fprintf('\n'); end
for allt=1:trials
j=1;
while j<=Boot.naccu
t = ceil(rand([1 2])*trials); % random ints [1,g.timesout]
if (allRn(t(1),index) == 1) & (allRn(t(2),index) == 1)
tmpsX(:,j) = squeeze(alltmpsX(t(1),index,:));
tmpsY(:,j) = squeeze(alltmpsY(t(2),index,:));
j = j+1;
end
end
Boot.Coherboot = cohercomp(Boot.Coherboot, tmpsX, tmpsY, 1, 1:Boot.naccu);
end;
Boot.Coherboot = cohercomppost(Boot.Coherboot); % CHECK IF NECSSARY FOR ALL BOOT TYPE
Boot.fullcoherboot(:,:,index) = Boot.Coherboot.R;
Boot.Coherboot = coherinit(nb_points, trials, Boot.naccu, Boot.Coherboot.type);
end;
Boot.Coherboot.R = Boot.fullcoherboot;
Boot = rmfield(Boot, 'fullcoherboot');
elseif strcmp(Boot.boottype, 'timestrials') % handle timestrials bootstrap
fprintf('\nProcessing time and trial bootstrap (of %d):',trials);
tmpsX = zeros(size(alltmpsX,3), Boot.naccu);
tmpsY = zeros(size(alltmpsY,3), Boot.naccu );
for allt=1:trials
if rem(allt,10) == 0, fprintf(' %d',allt); end
if rem(allt,120) == 0, fprintf('\n'); end
j=1;
while j<=Boot.naccu
t = ceil(rand([1 2])*trials); % random ints [1,g.timesout]
goodbasewins = find((allRn(t(1),:) & allRn(t(2),:)) ==1);
if Boot.baseboot % use baseline windows only
goodbasewins = find(goodbasewins<=baselength);
end
ngdbasewins = length(goodbasewins);
if ngdbasewins>1
s = ceil(rand([1 2])*ngdbasewins); % random ints [1,g.timesout]
s=goodbasewins(s);
if all(allRn(t(1),s(1)) == 1) & all(allRn(t(2),s(2)) == 1)
tmpsX(:,j) = squeeze(alltmpsX(t(1),s(1),:));
tmpsY(:,j) = squeeze(alltmpsY(t(2),s(2),:));
j = j+1;
end
end
end
Boot.Coherboot = cohercomp(Boot.Coherboot, tmpsX, tmpsY, 1, 1:Boot.naccu);
end
Boot.Coherboot = cohercomppost(Boot.Coherboot);
elseif strcmp(Boot.boottype, 'times') % boottype is 'times'
Boot.Coherboot = cohercomppost(Boot.Coherboot);
end;
end;
% test if precomputed
if ~isnan(Boot.alpha) & isnan(Boot.rboot) % if bootstrap analysis included . . .
% 'boottype'='times' or 'timestrials', size(R)=nb_points*naccu
% 'boottype'='trials', size(R)=nb_points*naccu*times
Boot.Coherboot.R = abs (Boot.Coherboot.R);
Boot.Coherboot.R = sort(Boot.Coherboot.R,2);
% compute bootstrap significance level
i = round(Boot.naccu*Boot.alpha);
Boot.Rsignif = mean(Boot.Coherboot.R(:,Boot.naccu-i+1:Boot.naccu),2); % significance levels for Rraw
Boot.Coherboot.R = squeeze(mean(Boot.Coherboot.R(:,Boot.naccu-i+1:Boot.naccu),2));
if size(Boot.Coherboot.R, 2) == 1
Rbootout(:,2) = Boot.Coherboot.R;
else
Rbootout(:,:,2) = Boot.Coherboot.R;
end;
% BEFORE
%Rboot = [mean(Rboot(1:i,:)) ; mean(Rboot(g.naccu-i+1:g.naccu,:))];
elseif ~isnan(Boot.rboot)
Boot.Coherboot.R = Boot.rboot;
Boot.Rsignif = Boot.rboot;
Rbootout = Boot.rboot;
else
Boot.Coherboot.R = [];
Boot.Rsignif = [];
Rbootout = [];
end % NOTE: above, mean ?????
function w = hanning(n)
if ~rem(n,2)
w = .5*(1 - cos(2*pi*(1:n/2)'/(n+1)));
w = [w; w(end:-1:1)];
else
w = .5*(1 - cos(2*pi*(1:(n+1)/2)'/(n+1)));
w = [w; w(end-1:-1:1)];
end
|
github
|
lcnbeapp/beapp-master
|
dftfilt2.m
|
.m
|
beapp-master/Packages/eeglab14_1_2b/functions/timefreqfunc/dftfilt2.m
| 5,665 |
utf_8
|
fa2b4cd1d3a209b72ce506ee4e6fee46
|
% dftfilt2() - discrete complex wavelet filters
%
% Usage:
% >> wavelet = dftfilt2( freqs, cycles, srate, cyclefact)
%
% Inputs:
% freqs - frequency array
% cycles - cycles array. If one value is given, all wavelets have
% the same number of cycles. If two values are given, the
% two values are used for the number of cycles at the lowest
% frequency and at the highest frequency, with linear
% interpolation between these values for intermediate
% frequencies
% srate - sampling rate (in Hz)
%
% cycleinc - ['linear'|'log'] increase mode if [min max] cycles is
% provided in 'cycle' parameter. {default: 'linear'}
% type - ['sinus'|'morlet'] wavelet type is a sinusoid with
% cosine (real) and sine (imaginary) parts tapered by
% a Hanning or Morlet function. 'morlet' is a typical Morlet
% wavelet (with p=2*pi and sigma=0.7) best matching the
% 'sinus' Hanning taper) {default: 'morlet'}
% Output:
% wavelet - cell array of wavelet filters
%
% Note: The length of the window is automatically computed from the
% number of cycles and is always made odd.
%
% Authors: Arnaud Delorme, SCCN/INC/UCSD, La Jolla, 3/28/2003
% Copyright (C) 3/28/2003 Arnaud Delorme 8, SCCN/INC/UCSD, [email protected]
%
% This program is free software; you can redistribute it and/or modify
% it under the terms of the GNU General Public License as published by
% the Free Software Foundation; either version 2 of the License, or
% (at your option) any later version.
%
% This program is distributed in the hope that it will be useful,
% but WITHOUT ANY WARRANTY; without even the implied warranty of
% MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
% GNU General Public License for more details.
%
% You should have received a copy of the GNU General Public License
% along with this program; if not, write to the Free Software
% Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
function wavelet = dftfilt2( freqs, cycles, srate, cycleinc, type);
if nargin < 3
error('3 arguments required');
end;
if nargin < 5
type = 'morlet';
end;
% compute number of cycles at each frequency
% ------------------------------------------
if length(cycles) == 1
cycles = cycles*ones(size(freqs));
elseif length(cycles) == 2
if nargin == 4 & strcmpi(cycleinc, 'log') % cycleinc
cycles = linspace(log(cycles(1)), log(cycles(2)), length(freqs));
cycles = exp(cycles);
else
cycles = linspace(cycles(1), cycles(2), length(freqs));
end;
end;
% compute wavelet
for index = 1:length(freqs)
% number of cycles depend on window size
% number of cycles automatically reduced if smaller window
% note: as the number of cycle changes, the frequency shifts a little
% this has to be fixed
winlen = cycles(index)*srate/freqs(index);
winlenint = floor(winlen);
if mod(winlenint,2) == 1, winlenint = winlenint+1; end;
winval = linspace(winlenint/2, -winlenint/2, winlenint+1);
if strcmpi(type, 'sinus') % Hanning
win = exp(2i*pi*freqs(index)*winval/srate);
wavelet{index} = win .* hanning(length(winval))';
else % Morlet
t = freqs(index)*winval/srate;
p = 2*pi;
s = cycles(index)/5;
wavelet{index} = exp(j*t*p)/sqrt(2*pi) .* ...
(exp(-t.^2/(2*s^2))-sqrt(2)*exp(-t.^2/(s^2)-p^2*s^2/4));
end;
end;
return;
% testing
% -------
wav1 = dftfilt2(5, 5, 256); wav1 = wav1{1};
abs1 = linspace(-floor(length(wav1)),floor(length(wav1)), length(wav1));
figure; plot(abs1, real(wav1), 'b');
wav2 = dftfilt2(5, 3, 256); wav2 = wav2{1};
abs2 = linspace(-floor(length(wav2)),floor(length(wav2)), length(wav2));
hold on; plot(abs2, real(wav2), 'r');
wav3 = dftfilt2(5, 1.4895990, 256); wav3 = wav3{1};
abs3 = linspace(-floor(length(wav3)),floor(length(wav3)), length(wav3));
hold on; plot(abs3, real(wav3), 'g');
wav4 = dftfilt2(5, 8.73, 256); wav4 = wav4{1};
abs4 = linspace(-floor(length(wav4)),floor(length(wav4)), length(wav4));
hold on; plot(abs4, real(wav4), 'm');
% more testing
% ------------
freqs = exp(linspace(0,log(10),10));
win = dftfilt2(freqs, [3 3], 256, 'linear', 'sinus');
win = dftfilt2(freqs, [3 3], 256, 'linear', 'morlet');
freqs = [12.0008 13.2675 14.5341 15.8007 17.0674 18.3340 19.6007 20.8673 22.1339 23.4006 24.6672 25.9339 27.2005 28.4671 29.7338 31.0004 32.2670 33.5337 34.8003 36.0670 37.3336 38.6002 39.8669 41.1335 42.4002 43.6668 44.9334 46.2001 47.4667 ...
48.7334 50.0000];
win = dftfilt2(freqs, [3 12], 256, 'linear'); size(win)
winsize = 0;
for index = 1:length(win)
winsize = max(winsize,length(win{index}));
end;
allwav = zeros(winsize, length(win));
for index = 1:length(win)
wav1 = win{index};
abs1 = linspace(-(length(wav1)-1)/2,(length(wav1)-1)/2, length(wav1));
allwav(abs1+(winsize+1)/2,index) = wav1(:);
end;
figure; imagesc(imag(allwav));
% syemtric hanning function
function w = hanning(n)
if ~rem(n,2)
w = .5*(1 - cos(2*pi*(1:n/2)'/(n+1)));
w = [w; w(end:-1:1)];
else
w = .5*(1 - cos(2*pi*(1:(n+1)/2)'/(n+1)));
w = [w; w(end-1:-1:1)];
end
|
github
|
lcnbeapp/beapp-master
|
newtimef.m
|
.m
|
beapp-master/Packages/eeglab14_1_2b/functions/timefreqfunc/newtimef.m
| 97,481 |
utf_8
|
9b205e33083e0973b5d9e671eac0abb5
|
% newtimef() - Return estimates and plots of mean event-related (log) spectral
% perturbation (ERSP) and inter-trial coherence (ITC) events across
% event-related trials (epochs) of a single input channel time series.
%
% * Also can compute and statistically compare transforms for two time
% series. Use this to compare ERSP and ITC means in two conditions.
%
% * Uses either fixed-window, zero-padded FFTs (fastest), or wavelet
% 0-padded DFTs. FFT uses Hanning tapers; wavelets use (similar) Morlet
% tapers.
%
% * For the wavelet and FFT methods, output frequency spacing
% is the lowest frequency ('srate'/'winsize') divided by 'padratio'.
% NaN input values (such as returned by eventlock()) are ignored.
%
% * If 'alpha' is given (see below), permutation statistics are computed
% (from a distribution of 'naccu' surrogate data trials) and
% non-significant features of the output plots are zeroed out
% and plotted in green.
%
% * Given a 'topovec' topo vector and 'elocs' electrode location file,
% the figure also shows a topoplot() view of the specified scalp map.
%
% * Note: Left-click on subplots to view and zoom in separate windows.
%
% Usage with single dataset:
% >> [ersp,itc,powbase,times,freqs,erspboot,itcboot] = ...
% newtimef(data, frames, epochlim, srate, cycles,...
% 'key1',value1, 'key2',value2, ... );
%
% Example to compare two condition (channel 1 EEG versus ALLEEG(2)):
% >> [ersp,itc,powbase,times,freqs,erspboot,itcboot] = ...
% newtimef({EEG.data(1,:,:) ALLEEG(2).data(1,:,:)},
% EEG.pnts, [EEG.xmin EEG.xmax]*1000, EEG.srate, cycles);
% NOTE:
% >> timef details % presents more detailed argument information
% % Note: version timef() also computes multitaper transforms
%
% Required inputs: Value {default}
% data = Single-channel data vector (1,frames*ntrials), else
% 2-D array (frames,trials) or 3-D array (1,frames,trials).
% To compare two conditions (data1 versus data2), in place of
% a single data matrix enter a cell array {data1 data2}
% frames = Frames per trial. Ignored if data are 2-D or 3-D. {750}
% tlimits = [mintime maxtime] (ms). Note that these are the time limits
% of the data epochs themselves, NOT A SUB-WINDOW TO EXTRACT
% FROM THE EPOCHS as is the case for pop_newtimef(). {[-1000 2000]}
% Fs = data sampling rate (Hz) {default: read from icadefs.m or 250}
% varwin = [real] indicates the number of cycles for the time-frequency
% decomposition {default: 0}
% If 0, use FFTs and Hanning window tapering.
% If [real positive scalar], the number of cycles in each Morlet
% wavelet, held constant across frequencies.
% If [cycles cycles(2)] wavelet cycles increase with
% frequency beginning at cycles(1) and, if cycles(2) > 1,
% increasing to cycles(2) at the upper frequency,
% If cycles(2) = 0, use same window size for all frequencies
% (similar to FFT when cycles(1) = 1)
% If cycles(2) = 1, cycles do not increase (same as giving
% only one value for 'cycles'). This corresponds to a pure
% wavelet decomposition, same number of cycles at each frequency.
% If 0 < cycles(2) < 1, cycles increase linearly with frequency:
% from 0 --> FFT (same window width at all frequencies)
% to 1 --> wavelet (same number of cycles at all frequencies).
% The exact number of cycles in the highest frequency window is
% indicated in the command line output. Typical value: 'cycles', [3 0.5]
%
% Optional inter-trial coherence (ITC) Type:
% 'itctype' = ['coher'|'phasecoher'|'phasecoher2'] Compute either linear
% coherence ('coher') or phase coherence ('phasecoher').
% Originall called 'phase-locking factor' {default: 'phasecoher'}
%
% Optional detrending:
% 'detrend' = ['on'|'off'], Linearly detrend each data epoch {'off'}
% 'rmerp' = ['on'|'off'], Remove epoch mean from data epochs {'off'}
%
% Optional FFT/DFT parameters:
% 'winsize' = If cycles==0: data subwindow length (fastest, 2^n<frames);
% If cycles >0: The *longest* window length to use. This
% determines the lowest output frequency. Note: this parameter
% is overwritten when the minimum frequency requires
% a longer time window {default: ~frames/8}
% 'timesout' = Number of output times (int<frames-winframes). Enter a
% negative value [-S] to subsample original times by S.
% Enter an array to obtain spectral decomposition at
% specific times (Note: The algorithm finds the closest time
% point in data; this could give a slightly unevenly spaced
% time array {default: 200}
% 'padratio' = FFT-length/winframes (2^k) {default: 2}
% Multiplies the number of output frequencies by dividing
% their spacing (standard FFT padding). When cycles~=0,
% frequency spacing is divided by padratio.
% 'maxfreq' = Maximum frequency (Hz) to plot (& to output, if cycles>0)
% If cycles==0, all FFT frequencies are output. {default: 50}
% DEPRECATED, use 'freqs' instead,and never both.
% 'freqs' = [min max] frequency limits. {default [minfreq 50],
% minfreq being determined by the number of data points,
% cycles and sampling frequency.
% 'nfreqs' = number of output frequencies. For FFT, closest computed
% frequency will be returned. Overwrite 'padratio' effects
% for wavelets. {default: use 'padratio'}
% 'freqscale' = ['log'|'linear'] frequency scale. {default: 'linear'}
% Note that for obtaining 'log' spaced freqs using FFT,
% closest correspondant frequencies in the 'linear' space
% are returned.
% 'verbose' = ['on'|'off'] print text {'on'}
% 'subitc' = ['on'|'off'] subtract stimulus locked Inter-Trial Coherence
% (ITC) from x and y. This computes an 'intrinsic' coherence
% of x and y not arising directly from common phase locking
% to experimental events. See notes. {default: 'off'}
% 'wletmethod' = ['dftfilt'|'dftfilt2'|'dftfilt3'] Wavelet type to use.
% 'dftfilt2' -> Morlet-variant wavelets, or Hanning DFT.
% 'dftfilt3' -> Morlet wavelets. See the timefreq() function
% for more detials {default: 'dftfilt3'}
% 'cycleinc' ['linear'|'log'] mode of cycles increase when [min max] cycles
% are provided in 'cycle' parameter. Applies only to
% 'wletmethod','dftfilt' {default: 'linear'}
%
% Optional baseline parameters:
% 'baseline' = Spectral baseline end-time (in ms). NaN --> no baseline is used.
% A [min max] range may also be entered
% You may also enter one row per region for baseline
% e.g. [0 100; 300 400] considers the window 0 to 100 ms and
% 300 to 400 ms This parameter validly defines all baseline types
% below. Again, [NaN] Prevent baseline subtraction.
% {default: 0 -> all negative time values}.
% 'powbase' = Baseline spectrum to log-subtract {default|NaN -> from data}
% 'commonbase' = ['on'|'off'] use common baseline when comparing two
% conditions {default: 'on'}.
% 'basenorm' = ['on'|'off'] 'on' normalize baseline in the power spectral
% average; else 'off', divide by the average power across
% trials at each frequency (gain model). {default: 'off'}
% 'trialbase' = ['on'|'off'|'full'] perform baseline (normalization or division
% above in single trial instead of the trial average. Default
% if 'off'. 'full' is an option that perform single
% trial normalization (or simple division based on the
% 'basenorm' input over the full trial length before
% performing standard baseline removal. It has been
% shown to be less sensitive to noisy trials in Grandchamp R,
% Delorme A. (2011) Single-trial normalization for event-related
% spectral decomposition reduces sensitivity to noisy trials.
% Front Psychol. 2:236.
%
% Optional time warping parameter:
% 'timewarp' = [eventms matrix] Time-warp amplitude and phase time-
% courses(following time/freq transform but before
% smoothing across trials). 'eventms' is a matrix
% of size (all_trials,epoch_events) whose columns
% specify the epoch times (latencies) (in ms) at which
% the same series of successive events occur in each
% trial. If two data conditions, eventms should be
% [eventms1;eventms2] --> all trials stacked vertically.
% 'timewarpms' = [warpms] optional vector of event times (latencies) (in ms)
% to which the series of events should be warped.
% (Note: Epoch start and end should not be declared
% as eventms or warpms}. If 'warpms' is absent or [],
% the median of each 'eventms' column will be used;
% If two datasets, the grand medians of the two are used.
% 'timewarpidx' = [plotidx] is an vector of indices telling which of
% the time-warped 'eventms' columns (above) to show with
% vertical lines. If undefined, all columns are plotted.
% Overwrites the 'vert' argument (below) if any.
%
% Optional permutation parameters:
% 'alpha' = If non-0, compute two-tailed permutation significance
% probability level. Show non-signif. output values
% as green. {default: 0}
% 'mcorrect' = ['none'|'fdr'] correction for multiple comparison
% 'fdr' uses false detection rate (see function fdr()).
% Not available for condition comparisons. {default:'none'}
% 'pcontour' = ['on'|'off'] draw contour around significant regions
% instead of masking them. Not available for condition
% comparisons. {default:'off'}
% 'naccu' = Number of permutation replications to accumulate {200}
% 'baseboot' = permutation baseline subtract (1 -> use 'baseline';
% 0 -> use whole trial
% [min max] -> use time range)
% You may also enter one row per region for baseline,
% e.g. [0 100; 300 400] considers the window 0 to 100 ms
% and 300 to 400 ms. {default: 1}
% 'boottype' = ['shuffle'|'rand'|'randall'] 'shuffle' -> shuffle times
% and trials; 'rand' -> invert polarity of spectral data
% (for ERSP) or randomize phase (for ITC); 'randall' ->
% compute significances by accumulating random-polarity
% inversions for each time/frequency point (slow!). Note
% that in the previous revision of this function, this
% method was called 'bootstrap' though it is actually
% permutation {default: 'shuffle'}
% 'condboot' = ['abs'|'angle'|'complex'] to compare two conditions,
% either subtract ITC absolute values ('abs'), angles
% ('angles'), or complex values ('complex'). {default: 'abs'}
% 'pboot' = permutation power limits (e.g., from newtimef()) {def: from data}
% 'rboot' = permutation ITC limits (e.g., from newtimef()).
% Note: Both 'pboot' and 'rboot' must be provided to avoid
% recomputing the surrogate data! {default: from data}
%
% Optional Scalp Map:
% 'topovec' = Scalp topography (map) to plot {none}
% 'elocs' = Electrode location file for scalp map {none}
% Value should be a string array containing the path
% and name of the file. For file format, see
% >> topoplot example
% 'chaninfo' Passed to topoplot, if called.
% [struct] optional structure containing fields
% 'nosedir', 'plotrad', and/or 'chantype'. See these
% field definitions above, below.
% {default: nosedir +X, plotrad 0.5, all channels}
%
% Optional Plotting Parameters:
% 'scale' = ['log'|'abs'] visualize power in log scale (dB) or absolute
% scale. {default: 'log'}
% 'plottype' = ['image'|'curve'] plot time/frequency images or traces
% (curves, one curve per frequency). {default: 'image'}
% 'plotmean' = ['on'|'off'] For 'curve' plots only. Average all
% frequencies given as input. {default: 'on'}
% 'highlightmode' = ['background'|'bottom'] For 'curve' plots only,
% display significant time regions either in the plot background
% or under the curve.
% 'plotersp' = ['on'|'off'] Plot power spectral perturbations {'on'}
% 'plotitc' = ['on'|'off'] Plot inter-trial coherence {'on'}
% 'plotphasesign' = ['on'|'off'] Plot phase sign in the inter trial coherence {'on'}
% 'plotphaseonly' = ['on'|'off'] Plot ITC phase instead of ITC amplitude {'off'}
% 'erspmax' = [real] set the ERSP max. For the color scale (min= -max) {auto}
% 'itcmax' = [real] set the ITC image maximum for the color scale {auto}
% 'hzdir' = ['up' or 'normal'|'down' or 'reverse'] Direction of
% the frequency axes {default: as in icadefs.m, or 'up'}
% 'ydir' = ['up' or 'normal'|'down' or 'reverse'] Direction of
% the ERP axis plotted below the ITC {as in icadefs.m, or 'up'}
% 'erplim' = [min max] ERP limits for ITC (below ITC image) {auto}
% 'itcavglim' = [min max] average ITC limits for all freq. (left of ITC) {auto}
% 'speclim' = [min max] average spectrum limits (left of ERSP image) {auto}
% 'erspmarglim' = [min max] average marginal ERSP limits (below ERSP image) {auto}
% 'title' = Optional figure or (brief) title {none}. For multiple conditions
% this must contain a cell array of 2 or 3 title strings.
% 'marktimes' = Non-0 times to mark with a dotted vertical line (ms) {none}
% 'linewidth' = Line width for 'marktimes' traces (thick=2, thin=1) {2}
% 'axesfont' = Axes text font size {10}
% 'titlefont' = Title text font size {8}
% 'vert' = [times_vector] -> plot vertical dashed lines at specified times
% in ms. {default: none}
% 'newfig' = ['on'|'off'] Create new figure for difference plots {'on'}
% 'caption' = Caption of the figure {none}
% 'outputformat' = ['old'|'plot'] for compatibility with script that used the
% old output format, set to 'old' (mbase in absolute amplitude (not
% dB) and real itc instead of complex itc). 'plot' returns
% the plotted result {default: 'plot'}
% Outputs:
% ersp = (nfreqs,timesout) matrix of log spectral diffs from baseline
% (in dB log scale or absolute scale). Use the 'plot' output format
% above to output the ERSP as shown on the plot.
% itc = (nfreqs,timesout) matrix of complex inter-trial coherencies.
% itc is complex -- ITC magnitude is abs(itc); ITC phase in radians
% is angle(itc), or in deg phase(itc)*180/pi.
% powbase = baseline power spectrum. Note that even, when selecting the
% the 'trialbase' option, the average power spectrum is
% returned (not trial based). To obtain the baseline of
% each trial, recompute it manually using the tfdata
% output described below.
% times = vector of output times (spectral time window centers) (in ms).
% freqs = vector of frequency bin centers (in Hz).
% erspboot = (nfreqs,2) matrix of [lower upper] ERSP significance.
% itcboot = (nfreqs) matrix of [upper] abs(itc) threshold.
% tfdata = optional (nfreqs,timesout,trials) time/frequency decomposition
% of the single data trials. Values are complex.
%
% Plot description:
% Assuming both 'plotersp' and 'plotitc' options are 'on' (= default).
% The upper panel presents the data ERSP (Event-Related Spectral Perturbation)
% in dB, with mean baseline spectral activity (in dB) subtracted. Use
% "'baseline', NaN" to prevent timef() from removing the baseline.
% The lower panel presents the data ITC (Inter-Trial Coherence).
% Click on any plot axes to pop up a new window (using 'axcopy()')
% -- Upper left marginal panel presents the mean spectrum during the baseline
% period (blue), and when significance is set, the significance threshold
% at each frequency (dotted green-black trace).
% -- The marginal panel under the ERSP image shows the maximum (green) and
% minimum (blue) ERSP values relative to baseline power at each frequency.
% -- The lower left marginal panel shows mean ITC across the imaged time range
% (blue), and when significance is set, the significance threshold (dotted
% green-black).
% -- The marginal panel under the ITC image shows the ERP (which is produced by
% ITC across the data spectral pass band).
%
% Authors: Arnaud Delorme, Jean Hausser from timef() by Sigurd Enghoff, Scott Makeig
% CNL / Salk Institute 1998- | SCCN/INC, UCSD 2002-
%
% See also: timefreq(), condstat(), newcrossf(), tftopo()
% Deprecated Multitaper Parameters: [not included here]
% 'mtaper' = If [N W], performs multitaper decomposition.
% (N is the time resolution and W the frequency resolution;
% maximum taper number is 2NW-1). Overwrites 'winsize' and 'padratio'.
% If [N W K], forces the use of K Slepian tapers (if possible).
% Phase is calculated using standard methods.
% The use of mutitaper with wavelets (cycles>0) is not
% recommended (as multiwavelets are not implemented).
% Uses Matlab functions DPSS, PMTM. {no multitaper}
% Deprecated time warp keywords (working?)
% 'timewarpfr' = {{[events], [warpfr], [plotidx]}} Time warp amplitude and phase
% time-courses (after time/freq transform but before smoothingtimefreqfunc
% across trials). 'events' is a matrix whose columns specify the
% epoch frames [1 ... end] at which a series of successive events
% occur in each trial. 'warpfr' is an optional vector of event
% frames to which the series of events should be time locked.
% (Note: Epoch start and end should not be declared as events or
% warpfr}. If 'warpfr' is absent or [], the median of each 'events'
% column will be used. [plotidx] is an optional vector of indices
% telling which of the warpfr to plot with vertical lines. If
% undefined, all marks are plotted. Overwrites 'vert' argument,
% if any. [Note: In future releases, 'timewarpfr' will be deprecated
% in favor of 'timewarp' using latencies in ms instead of frames].
% Deprecated original time warp keywords (working?)
% 'timeStretchMarks' = [(marks,trials) matrix] Each trial data will be
% linearly warped (after time/freq. transform) so that the
% event marks are time locked to the reference frames
% (see timeStretchRefs). Marks must be specified in frames
% 'timeStretchRefs' = [1 x marks] Common reference frames to all trials.
% If empty or undefined, median latency for each mark will be used.boottype
% 'timeStretchPlot' = [vector] Indicates the indices of the reference frames
% (in StretchRefs) should be overplotted on the ERSP and ITC.
%
%
% Copyright (C) University of California San Diego, La Jolla, CA
%
% First built as timef.m at CNL / Salk Institute 8/1/98-8/28/01 by
% Sigurd Enghoff and Scott Makeig, edited by Arnaud Delorme
% SCCN/INC/UCSD/ reprogrammed as newtimef -Arnaud Delorme 2002-
% SCCN/INC/UCSD/ added time warping capabilities -Jean Hausser 2005
%
% This program is free software; you can redistribute it and/or modify
% it under the terms of the GNU General Public License as published by
% the Free Software Foundation; either version 2 of the License, or
% (at your option) any later version.
%
% This program is distributed in the hope that it will be useful,
% but WITHOUT ANY WARRANTY; without even the implied warranty of
% MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
% GNU General Public License for more details.
%
% You should have received a copy of the GNU General Public License
% along with this program; if not, write to the Free Software
% Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
% 10-19-98 avoided division by zero (using MIN_ABS) -sm
% 10-19-98 improved usage message and commandline info printing -sm
% 10-19-98 made valid [] values for tvec and g.elocs -sm
% 04-01-99 added missing freq in freqs and plots, fixed log scaling bug -se && -tpj
% 06-29-99 fixed frequency indexing for constant-Q -se
% 08-24-99 reworked to handle NaN input values -sm
% 12-07-99 adjusted ERPtimes to plot ERP under ITC -sm
% 12-22-99 debugged ERPtimes, added BASE_BOOT -sm
% 01-10-00 debugged BASE_BOOT=0 -sm
% 02-28-00 added NOTE on formula derivation below -sm
% 03-16-00 added axcopy() feature -sm && tpj
% 04-16-00 added multiple marktimes loop -sm
% 04-20-00 fixed ITC cbar limits when spcified in input -sm
% 07-29-00 changed frequencies displayed msg -sm
% 10-12-00 fixed bug in freqs when cycles>0 -sm
% 02-07-01 fixed inconsistency in BASE_BOOT use -sm
% 08-28-01 matlab 'key' value arguments -ad
% 08-28-01 multitaper decomposition -ad
% 01-25-02 reformated help && license -ad
% 03-08-02 debug && compare to old timef function -ad
% 03-16-02 timeout automatically adjusted if too high -ad
% 04-02-02 added 'coher' option -ad
function [P,R,mbase,timesout,freqs,Pboot,Rboot,alltfX,PA] = newtimef( data, frames, tlimits, Fs, varwin, varargin);
% Note: Above, PA is output of 'phsamp','on'
% For future 'timewarp' keyword help: 'timewarp' 3rd element {colors} contains a
% list of Matlab linestyles to use for vertical lines marking the occurence
% of the time warped events. If '', no line will be drawn for this event
% column. If fewer colors than event columns, cycles through the given color
% labels. Note: Not compatible with 'vert' (below).
%varwin,winsize,g.timesout,g.padratio,g.maxfreq,g.topovec,g.elocs,g.alpha,g.marktimes,g.powbase,g.pboot,g.rboot)
% ITC: Normally, R = |Sum(Pxy)| / (Sum(|Pxx|)*Sum(|Pyy|)) is coherence.
% But here, we consider Phase(Pyy) = 0 and |Pyy| = 1 -> Pxy = Pxx
% Giving, R = |Sum(Pxx)|/Sum(|Pxx|), the inter-trial coherence (ITC)
% Also called 'phase-locking factor' by Tallon-Baudry et al. (1996)
if nargin < 1
help newtimef;
return;
end;
% Read system (or directory) constants and preferences:
% ------------------------------------------------------
icadefs % read local EEGLAB constants: HZDIR, YDIR, DEFAULT_SRATE, DEFAULT_TIMLIM
if ~exist('HZDIR'), HZDIR = 'up'; end; % ascending freqs
if ~exist('YDIR'), YDIR = 'up'; end; % positive up
if YDIR == 1, YDIR = 'up'; end; % convert from [-1|1] as set in icadefs.m
if YDIR == -1, YDIR = 'down'; end; % and read by other plotting functions
if ~exist('DEFAULT_SRATE'), DEFAULT_SRATE = 250; end; % 250 Hz
if ~exist('DEFAULT_TIMLIM'), DEFAULT_TIMLIM = [-1000 2000]; end; % [-1 2] s epochs
% Constants set here:
% ------------------
ERSP_CAXIS_LIMIT = 0; % 0 -> use data limits; else positive value
% giving symmetric +/- caxis limits.
ITC_CAXIS_LIMIT = 0; % 0 -> use data limits; else positive value
% giving symmetric +/- caxis limits.
MIN_ABS = 1e-8; % avoid division by ~zero
% Command line argument defaults:
% ------------------------------
DEFAULT_NWIN = 200; % Number of windows = horizontal resolution
DEFAULT_VARWIN = 0; % Fixed window length or fixed number of cycles.
% =0: fix window length to that determined by nwin
% >0: set window length equal to varwin cycles
% Bounded above by winsize, which determines
% the min. freq. to be computed.
DEFAULT_OVERSMP = 2; % Number of times to oversample frequencies
DEFAULT_MAXFREQ = 50; % Maximum frequency to display (Hz)
DEFAULT_TITLE = ''; % Figure title (no default)
DEFAULT_ELOC = 'chan.locs'; % Channel location file
DEFAULT_ALPHA = NaN; % Percentile of bins to keep
DEFAULT_MARKTIME= NaN;
% Font sizes:
AXES_FONT = 10; % axes text FontSize
TITLE_FONT = 8;
if (nargin < 2)
frames = floor((DEFAULT_TIMLIN(2)-DEFAULT_TIMLIM(1))/DEFAULT_SRATE);
elseif (~isnumeric(frames) | length(frames)~=1 | frames~=round(frames))
error('Value of frames must be an integer.');
elseif (frames <= 0)
error('Value of frames must be positive.');
end;
DEFAULT_WINSIZE = max(pow2(nextpow2(frames)-3),4);
DEFAULT_PAD = max(pow2(nextpow2(DEFAULT_WINSIZE)),4);
if (nargin < 1)
help newtimef
return
end
if isstr(data) && strcmp(data,'details')
more on
help timefdetails
more off
return
end
if ~iscell(data)
data = reshape_data(data, frames);
trials = size(data,ndims(data));
else
if ndims(data) == 3 && size(data,1) == 1
error('Cannot process multiple channel component in compare mode');
end;
[data{1}, frames] = reshape_data(data{1}, frames);
[data{2}, frames] = reshape_data(data{2}, frames);
trials = size(data{1},2);
end;
if (nargin < 3)
tlimits = DEFAULT_TIMLIM;
elseif (~isnumeric(tlimits) | sum(size(tlimits))~=3)
error('Value of tlimits must be a vector containing two numbers.');
elseif (tlimits(1) >= tlimits(2))
error('tlimits interval must be ascending.');
end
if (nargin < 4)
Fs = DEFAULT_SRATE;
elseif (~isnumeric(Fs) | length(Fs)~=1)
error('Value of srate must be a number.');
elseif (Fs <= 0)
error('Value of srate must be positive.');
end
if (nargin < 5)
varwin = DEFAULT_VARWIN;
elseif ~isnumeric(varwin) && strcmpi(varwin, 'cycles')
varwin = varargin{1};
varargin(1) = [];
elseif (varwin < 0)
error('Value of cycles must be zero or positive.');
end
% build a structure for keyword arguments
% --------------------------------------
if ~isempty(varargin)
[tmp indices] = unique_bc(varargin(1:2:end));
varargin = varargin(sort(union(indices*2-1, indices*2))); % these 2 lines remove duplicate arguments
try, g = struct(varargin{:});
catch, error('Argument error in the {''param'', value} sequence'); end;
end
%}
[ g timefreqopts ] = finputcheck(varargin, ...
{'boottype' 'string' {'shuffle','rand','randall'} 'shuffle'; ...
'condboot' 'string' {'abs','angle','complex'} 'abs'; ...
'title' { 'string','cell' } { [] [] } DEFAULT_TITLE; ...
'title2' 'string' [] DEFAULT_TITLE; ...
'winsize' 'integer' [0 Inf] DEFAULT_WINSIZE; ...
'pad' 'real' [] DEFAULT_PAD; ...
'timesout' 'integer' [] DEFAULT_NWIN; ...
'padratio' 'integer' [0 Inf] DEFAULT_OVERSMP; ...
'topovec' 'real' [] []; ...
'elocs' {'string','struct'} [] DEFAULT_ELOC; ...
'alpha' 'real' [0 0.5] DEFAULT_ALPHA; ...
'marktimes' 'real' [] DEFAULT_MARKTIME; ...
'powbase' 'real' [] NaN; ...
'pboot' 'real' [] NaN; ...
'rboot' 'real' [] NaN; ...
'plotersp' 'string' {'on','off'} 'on'; ...
'plotamp' 'string' {'on','off'} 'on'; ...
'plotitc' 'string' {'on','off'} 'on'; ...
'detrend' 'string' {'on','off'} 'off'; ...
'rmerp' 'string' {'on','off'} 'off'; ...
'basenorm' 'string' {'on','off'} 'off'; ...
'commonbase' 'string' {'on','off'} 'on'; ...
'baseline' 'real' [] 0; ...
'baseboot' 'real' [] 1; ...
'linewidth' 'integer' [1 2] 2; ...
'naccu' 'integer' [1 Inf] 200; ...
'mtaper' 'real' [] []; ...
'maxfreq' 'real' [0 Inf] DEFAULT_MAXFREQ; ...
'freqs' 'real' [0 Inf] [0 DEFAULT_MAXFREQ]; ...
'cycles' 'integer' [] []; ...
'nfreqs' 'integer' [] []; ...
'freqscale' 'string' [] 'linear'; ...
'vert' 'real' [] []; ...
'newfig' 'string' {'on','off'} 'on'; ...
'type' 'string' {'coher','phasecoher','phasecoher2'} 'phasecoher'; ...
'itctype' 'string' {'coher','phasecoher','phasecoher2'} 'phasecoher'; ...
'phsamp' 'string' {'on','off'} 'off'; ... % phsamp not completed - Toby 9.28.2006
'plotphaseonly' 'string' {'on','off'} 'off'; ...
'plotphasesign' 'string' {'on','off'} 'on'; ...
'plotphase' 'string' {'on','off'} 'on'; ... % same as above for backward compatibility
'pcontour' 'string' {'on','off'} 'off'; ...
'outputformat' 'string' {'old','new','plot' } 'plot'; ...
'itcmax' 'real' [] []; ...
'erspmax' 'real' [] []; ...
'lowmem' 'string' {'on','off'} 'off'; ...
'verbose' 'string' {'on','off'} 'on'; ...
'plottype' 'string' {'image','curve'} 'image'; ...
'mcorrect' 'string' {'fdr','none'} 'none'; ...
'plotmean' 'string' {'on','off'} 'on'; ...
'plotmode' 'string' {} ''; ... % for metaplottopo
'highlightmode' 'string' {'background','bottom'} 'background'; ...
'chaninfo' 'struct' [] struct([]); ...
'erspmarglim' 'real' [] []; ...
'itcavglim' 'real' [] []; ...
'erplim' 'real' [] []; ...
'speclim' 'real' [] []; ...
'ntimesout' 'real' [] []; ...
'scale' 'string' { 'log','abs'} 'log'; ...
'timewarp' 'real' [] []; ...
'precomputed' 'struct' [] struct([]); ...
'timewarpms' 'real' [] []; ...
'timewarpfr' 'real' [] []; ...
'timewarpidx' 'real' [] []; ...
'timewarpidx' 'real' [] []; ...
'timeStretchMarks' 'real' [] []; ...
'timeStretchRefs' 'real' [] []; ...
'timeStretchPlot' 'real' [] []; ...
'trialbase' 'string' {'on','off','full'} 'off';
'caption' 'string' [] ''; ...
'hzdir' 'string' {'up','down','normal','reverse'} HZDIR; ...
'ydir' 'string' {'up','down','normal','reverse'} YDIR; ...
'cycleinc' 'string' {'linear','log'} 'linear'
}, 'newtimef', 'ignore');
if isstr(g), error(g); end;
if strcmpi(g.plotamp, 'off'), g.plotersp = 'off'; end;
if strcmpi(g.basenorm, 'on'), g.scale = 'abs'; end;
if ~strcmpi(g.itctype , 'phasecoher'), g.type = g.itctype; end;
g.tlimits = tlimits;
g.frames = frames;
g.srate = Fs;
if isempty(g.cycles)
g.cycles = varwin;
end;
g.AXES_FONT = AXES_FONT; % axes text FontSize
g.TITLE_FONT = TITLE_FONT;
g.ERSP_CAXIS_LIMIT = ERSP_CAXIS_LIMIT;
g.ITC_CAXIS_LIMIT = ITC_CAXIS_LIMIT;
if ~strcmpi(g.plotphase, 'on'), g.plotphasesign = g.plotphase; end;
% unpack 'timewarp' (and undocumented 'timewarpfr') arguments
%------------------------------------------------------------
if isfield(g,'timewarpfr')
if iscell(g.timewarpfr) && length(g.timewarpfr) > 3
error('undocumented ''timewarpfr'' cell array may have at most 3 elements');
end
end
if ~isempty(g.nfreqs)
verboseprintf(g.verbose, 'Warning: ''nfreqs'' input overwrite ''padratio''\n');
end;
if strcmpi(g.basenorm, 'on')
verboseprintf(g.verbose, 'Baseline normalization is on (results will be shown as z-scores)\n');
end;
if isfield(g,'timewarp') && ~isempty(g.timewarp)
if ndims(data) == 3
error('Cannot perform time warping on 3-D data input');
end;
if ~isempty(g.timewarp) % convert timewarp ms to timewarpfr frames -sm
fprintf('\n')
if iscell(g.timewarp)
error('timewarp argument must be a (total_trials,epoch_events) matrix');
end
evntms = g.timewarp;
warpfr = round((evntms - g.tlimits(1))/1000*g.srate)+1;
g.timewarpfr{1} = warpfr';
if isfield(g,'timewarpms')
refms = g.timewarpms;
reffr = round((refms - g.tlimits(1))/1000*g.srate)+1;
g.timewarpfr{2} = reffr';
end
if isfield(g,'timewarpidx')
g.timewarpfr{3} = g.timewarpidx;
end
end
% convert again to timeStretch parameters
% ---------------------------------------
if ~isempty(g.timewarpfr)
g.timeStretchMarks = g.timewarpfr{1};
if length(g.timewarpfr) > 1
g.timeStretchRefs = g.timewarpfr{2};
end
if length(g.timewarpfr) > 2
if isempty(g.timewarpfr{3})
stretchevents = size(g.timeStretchMarks,1);
g.timeStretchPlot = [1:stretchevents]; % default to plotting all lines
else
g.timeStretchPlot = g.timewarpfr{3};
end
end
if max(max(g.timeStretchMarks)) > frames-2 | min(min(g.timeStretchMarks)) < 3
error('Time warping events must be inside the epochs.');
end
if ~isempty(g.timeStretchRefs)
if max(g.timeStretchRefs) > frames-2 | min(g.timeStretchRefs) < 3
error('Time warping reference latencies must be within the epochs.');
end
end
end
end
% Determining source of the call
% --------------------------------------% 'guicall'= 1 if newtimef is called
callerstr = dbstack(1); % from EEGLAB GUI, otherwise 'guicall'= 0
if isempty(callerstr) % 7/3/2014, Ramon
guicall = 0;
elseif strcmp(callerstr(end).name,'pop_newtimef')
guicall = 1;
else
guicall = 0;
end
% test argument consistency
% --------------------------
if g.tlimits(2)-g.tlimits(1) < 30
verboseprintf(g.verbose, 'newtimef(): WARNING: Specified time range is very small (< 30 ms)???\n');
verboseprintf(g.verbose, ' Epoch time limits should be in msec, not seconds!\n');
end
if (g.winsize > g.frames)
error('Value of winsize must be smaller than epoch frames.');
end
if length(g.timesout) == 1 && g.timesout > 0
if g.timesout > g.frames-g.winsize
g.timesout = g.frames-g.winsize;
disp(['Value of timesout must be <= frames-winsize, timeout adjusted to ' int2str(g.timesout) ]);
end
end;
if (pow2(nextpow2(g.padratio)) ~= g.padratio)
error('Value of padratio must be an integer power of two [1,2,4,8,16,...]');
end
if (g.maxfreq > Fs/2)
verboseprintf(g.verbose, ['Warning: value of maxfreq reduced to Nyquist rate' ...
' (%3.2f)\n\n'], Fs/2);
g.maxfreq = Fs/2;
end
if g.maxfreq ~= DEFAULT_MAXFREQ, g.freqs(2) = g.maxfreq; end;
if isempty(g.topovec)
g.topovec = [];
if isempty(g.elocs)
error('Channel location file must be specified.');
end;
end
if (round(g.naccu*g.alpha) < 2)
verboseprintf(g.verbose, 'Value of alpha is outside its normal range [%g,0.5]\n',2/g.naccu);
g.naccu = round(2/g.alpha);
verboseprintf(g.verbose, ' Increasing the number of iterations to %d\n',g.naccu);
end
if ~isnan(g.alpha)
if length(g.baseboot) == 2
verboseprintf(g.verbose, 'Permutation analysis will use data from %3.2g to %3.2g ms.\n', ...
g.baseboot(1), g.baseboot(2))
elseif g.baseboot > 0
verboseprintf(g.verbose, 'Permutation analysis will use data in (pre-0) baseline subwindows only.\n')
else
verboseprintf(g.verbose, 'Permutation analysis will use data in all subwindows.\n')
end
end
if ~isempty(g.timeStretchMarks) % timeStretch code by Jean Hauser
if isempty(g.timeStretchRefs)
verboseprintf(g.verbose, ['Using median event latencies as reference event times for time warping.\n']);
g.timeStretchRefs = median(g.timeStretchMarks,2);
% Note: Uses (grand) median latencies for two conditions
else
verboseprintf(g.verbose, ['Using supplied latencies as reference event times for time warping.\n']);
end
if isempty(g.timeStretchPlot)
verboseprintf(g.verbose, 'Will not overplot the reference event times on the ERSP.\n');
elseif length(g.timeStretchPlot) > 0
g.vert = ((g.timeStretchRefs(g.timeStretchPlot)-1) ...
/g.srate+g.tlimits(1)/1000)*1000;
fprintf('Plotting timewarp markers at ')
for li = 1:length(g.vert), fprintf('%d ',g.vert(li)); end
fprintf(' ms.\n')
end
end
if min(g.vert) < g.tlimits(1) | max(g.vert) > g.tlimits(2)
error('vertical line (''vert'') latency outside of epoch boundaries');
end
if strcmp(g.hzdir,'up')| strcmp(g.hzdir,'normal')
g.hzdir = 'normal'; % convert to Matlab graphics constants
elseif strcmp(g.hzdir,'down') | strcmp(g.hzdir,'reverse')| g.hzdir==-1
g.hzdir = 'reverse';
else
error('unknown ''hzdir'' argument');
end
if strcmp(g.ydir,'up')| strcmp(g.ydir,'normal')
g.ydir = 'normal'; % convert to Matlab graphics constants
elseif strcmp(g.ydir,'down') | strcmp(g.ydir,'reverse')
g.ydir = 'reverse';
else
error('unknown ''ydir'' argument');
end
% -----------------
% ERSP scaling unit
% -----------------
if strcmpi(g.scale, 'log')
if strcmpi(g.basenorm, 'on')
g.unitpower = '10*log(std.)'; % impossible
elseif isnan(g.baseline)
g.unitpower = '10*log10(\muV^{2}/Hz)';
else
g.unitpower = 'dB';
end;
else
if strcmpi(g.basenorm, 'on')
g.unitpower = 'std.';
elseif isnan(g.baseline)
g.unitpower = '\muV^{2}/Hz';
else
g.unitpower = '% of baseline';
end;
end;
% Multitaper - used in timef
% --------------------------
if ~isempty(g.mtaper) % multitaper, inspired from a Bijan Pesaran matlab function
if length(g.mtaper) < 3
%error('mtaper arguement must be [N W] or [N W K]');
if g.mtaper(1) * g.mtaper(2) < 1
error('mtaper 2 first arguments'' product must be larger than 1');
end;
if length(g.mtaper) == 2
g.mtaper(3) = floor( 2*g.mtaper(2)*g.mtaper(1) - 1);
end
if length(g.mtaper) == 3
if g.mtaper(3) > 2 * g.mtaper(1) * g.mtaper(2) -1
error('mtaper number too high (maximum (2*N*W-1))');
end;
end
disp(['Using ' num2str(g.mtaper(3)) ' tapers.']);
NW = g.mtaper(1)*g.mtaper(2); % product NW
N = g.mtaper(1)*g.srate;
[e,v] = dpss(N, NW, 'calc');
e=e(:,1:g.mtaper(3));
g.alltapers = e;
else
g.alltapers = g.mtaper;
disp('mtaper argument not [N W] or [N W K]; considering raw taper matrix');
end;
g.winsize = size(g.alltapers, 1);
g.pad = max(pow2(nextpow2(g.winsize)),256); % pad*nextpow
nfk = floor([0 g.maxfreq]./g.srate.*g.pad);
g.padratio = 2*nfk(2)/g.winsize;
%compute number of frequencies
%nf = max(256, g.pad*2^nextpow2(g.winsize+1));
%nfk = floor([0 g.maxfreq]./g.srate.*nf);
%freqs = linspace( 0, g.maxfreq, diff(nfk)); % this also works in the case of a FFT
end
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
% compute frequency by frequency if low memory
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
if strcmpi(g.lowmem, 'on') && numel(data) ~= g.frames && isempty(g.nfreqs) && ~iscell(data)
disp('Lowmem is a deprecated option that is not functional any more');
return;
% NOTE: the code below is functional but the graphical output is
% different when the 'lowmem' option is used compared to when it is not
% used - AD, 29 April 2011
% compute for first 2 trials to get freqsout
XX = reshape(data, 1, frames, prod(size(data))/g.frames);
[P,R,mbase,timesout,freqsout] = newtimef(XX(1,:,1), frames, tlimits, Fs, g.cycles, 'plotitc', 'off', 'plotamp', 'off',varargin{:}, 'lowmem', 'off');
% scan all frequencies
for index = 1:length(freqsout)
if nargout < 8
[P(index,:),R(index,:),mbase(index),timesout,tmpfreqs(index),Pboottmp,Rboottmp] = ...
newtimef(data, frames, tlimits, Fs, g.cycles, ...
'freqs', [freqsout(index) freqsout(index)], 'nfreqs', 1, ...
'plotamp', 'off', 'plotitc', 'off', 'plotphasesign', 'off',varargin{:}, ...
'lowmem', 'off', 'timesout', timesout);
if ~isempty(Pboottmp)
Pboot(index,:) = Pboottmp;
Rboot(index,:) = Rboottmp;
else
Pboot = [];
Rboot = [];
end;
else
[P(index,:),R(index,:),mbase(index),timesout,tmpfreqs(index),Pboot(index,:),Rboot(index,:), ...
alltfX(index,:,:)] = ...
newtimef(data, frames, tlimits, Fs, g.cycles, ...
'freqs', [freqsout(index) freqsout(index)], 'nfreqs', 1, ...
'plotamp', 'off', 'plotphasesign', 'off',varargin{:}, ...
'lowmem', 'off', 'timesout', timesout);
end;
end;
% compute trial-average ERP
% -------------------------
ERP = mean(data,2);
% plot results
%-------------
plottimef(P, R, Pboot, Rboot, ERP, freqsout, timesout, mbase, [], [], g);
return; % finished
end;
%%%%%%%%%%%%%%%%%%%%%%%
% compare 2 conditions
%%%%%%%%%%%%%%%%%%%%%%%
if iscell(data)
if ~guicall && (strcmp(g.basenorm, 'on') || strcmp(g.trialbase, 'on')) % ------------------------------------- Temporary fix for error when using
error('EEGLAB error: basenorm and/or trialbase options cannot be used when processing 2 conditions'); % basenorm or trialbase with two conditions
end;
Pboot = [];
Rboot = [];
if ~strcmpi(g.mcorrect, 'none')
error('Correction for multiple comparison not implemented for comparing conditions');
end;
vararginori = varargin;
if length(data) ~= 2
error('newtimef: to compare two conditions, data must be a length-2 cell array');
end;
% deal with titles
% ----------------
for index = 1:2:length(vararginori)
if index<=length(vararginori) % needed if elements are deleted
% if strcmp(vararginori{index}, 'title') | ... % Added by Jean Hauser
% strcmp(vararginori{index}, 'title2') | ...
if strcmp(vararginori{index}, 'timeStretchMarks') | ...
strcmp(vararginori{index}, 'timeStretchRefs') | ...
strcmp(vararginori{index}, 'timeStretchPlots')
vararginori(index:index+1) = [];
end;
end;
end;
if iscell(g.title) && length(g.title) >= 2 % Changed that part because providing titles
% as cells caused the function to crash (why?)
% at line 704 (g.tlimits = tlimits) -Jean
if length(g.title) == 2,
g.title{3} = [ g.title{1} ' - ' g.title{2} ];
end;
else
disp('Warning: title must be a cell array');
g.title = { 'Condition 1' 'Condition 2' 'Condition 1 minus Condition 2' };
end;
verboseprintf(g.verbose, '\nRunning newtimef() on Condition 1 **********************\n\n');
verboseprintf(g.verbose, 'Note: If an out-of-memory error occurs, try reducing the\n');
verboseprintf(g.verbose, ' the number of time points or number of frequencies\n');
verboseprintf(g.verbose, '(''coher'' options take 3 times the memory of other options)\n\n');
cond_1_epochs = size(data{1},2);
if ~isempty(g.timeStretchMarks)
[P1,R1,mbase1,timesout,freqs,Pboot1,Rboot1,alltfX1] = ...
newtimef( data{1}, frames, tlimits, Fs, g.cycles, 'plotitc', 'off', ...
'plotersp', 'off', vararginori{:}, 'lowmem', 'off', ...
'timeStretchMarks', g.timeStretchMarks(:,1:cond_1_epochs), ...
'timeStretchRefs', g.timeStretchRefs);
else
[P1,R1,mbase1,timesout,freqs,Pboot1,Rboot1,alltfX1] = ...
newtimef( data{1}, frames, tlimits, Fs, g.cycles, 'plotitc', 'off', ...
'plotersp', 'off', vararginori{:}, 'lowmem', 'off');
end
verboseprintf(g.verbose,'\nRunning newtimef() on Condition 2 **********************\n\n');
[P2,R2,mbase2,timesout,freqs,Pboot2,Rboot2,alltfX2] = ...
newtimef( data{2}, frames, tlimits, Fs, g.cycles, 'plotitc', 'off', ...
'plotersp', 'off', vararginori{:}, 'lowmem', 'off', ...
'timeStretchMarks', g.timeStretchMarks(:,cond_1_epochs+1:end), ...
'timeStretchRefs', g.timeStretchRefs);
verboseprintf(g.verbose,'\nComputing difference **********************\n\n');
% recompute power baselines
% -------------------------
if ~isnan( g.baseline(1) ) && ~isnan( mbase1(1) ) && isnan(g.powbase(1)) && strcmpi(g.commonbase, 'on')
disp('Recomputing baseline power: using the grand mean of both conditions ...');
mbase = (mbase1 + mbase2)/2;
P1 = P1 + repmat(mbase1(1:size(P1,1))',[1 size(P1,2)]);
P2 = P2 + repmat(mbase2(1:size(P1,1))',[1 size(P1,2)]);
P1 = P1 - repmat(mbase (1:size(P1,1))',[1 size(P1,2)]);
P2 = P2 - repmat(mbase (1:size(P1,1))',[1 size(P1,2)]);
if ~isnan(g.alpha)
Pboot1 = Pboot1 + repmat(mbase1(1:size(Pboot1,1))',[1 size(Pboot1,2) size(Pboot1,3)]);
Pboot2 = Pboot2 + repmat(mbase2(1:size(Pboot1,1))',[1 size(Pboot1,2) size(Pboot1,3)]);
Pboot1 = Pboot1 - repmat(mbase (1:size(Pboot1,1))',[1 size(Pboot1,2) size(Pboot1,3)]);
Pboot2 = Pboot2 - repmat(mbase (1:size(Pboot1,1))',[1 size(Pboot1,2) size(Pboot1,3)]);
end;
verboseprintf(g.verbose, '\nSubtracting the common power baseline ...\n');
meanmbase = mbase;
mbase = { mbase mbase };
elseif strcmpi(g.commonbase, 'on')
mbase = { NaN NaN };
meanmbase = mbase{1}; %Ramon :for bug 1657
else
meanmbase = (mbase1 + mbase2)/2;
mbase = { mbase1 mbase2 };
end;
% plotting
% --------
if strcmpi(g.plotersp, 'on') | strcmpi(g.plotitc, 'on')
g.titleall = g.title;
if strcmpi(g.newfig, 'on'), figure; end; % declare a new figure
% using same color scale
% ----------------------
if ~isfield(g, 'erspmax')
g.erspmax = max( max(max(abs(Pboot1))), max(max(abs(Pboot2))) );
end;
if ~isfield(g, 'itcmax')
g.itcmax = max( max(max(abs(Rboot1))), max(max(abs(Rboot2))) );
end;
subplot(1,3,1); % plot Condition 1
g.title = g.titleall{1};
g = plottimef(P1, R1, Pboot1, Rboot1, mean(data{1},2), freqs, timesout, mbase{1}, [], [], g);
g.itcavglim = [];
subplot(1,3,2); % plot Condition 2
g.title = g.titleall{2};
plottimef(P2, R2, Pboot2, Rboot2, mean(data{2},2), freqs, timesout, mbase{2}, [], [], g);
subplot(1,3,3); % plot Condition 1 - Condition 2
g.title = g.titleall{3};
end;
if isnan(g.alpha)
switch(g.condboot)
case 'abs', Rdiff = abs(R1)-abs(R2);
case 'angle', Rdiff = angle(R1)-angle(R2);
case 'complex', Rdiff = R1-R2;
end;
if strcmpi(g.plotersp, 'on') | strcmpi(g.plotitc, 'on')
g.erspmax = []; g.itcmax = []; % auto scale inserted for diff
plottimef(P1-P2, Rdiff, [], [], mean(data{1},2)-mean(data{2},2), freqs, timesout, meanmbase, [], [], g);
end;
else
% preprocess data and run compstat() function
% -------------------------------------------
alltfX1power = alltfX1.*conj(alltfX1);
alltfX2power = alltfX2.*conj(alltfX2);
if ~isnan(mbase{1}(1))
mbase1 = 10.^(mbase{1}(1:size(alltfX1,1))'/20);
mbase2 = 10.^(mbase{2}(1:size(alltfX1,1))'/20);
alltfX1 = alltfX1./repmat(mbase1/2,[1 size(alltfX1,2) size(alltfX1,3)]);
alltfX2 = alltfX2./repmat(mbase2/2,[1 size(alltfX2,2) size(alltfX2,3)]);
alltfX1power = alltfX1power./repmat(mbase1,[1 size(alltfX1power,2) size(alltfX1power,3)]);
alltfX2power = alltfX2power./repmat(mbase2,[1 size(alltfX2power,2) size(alltfX2power,3)]);
end;
%formula = {'log10(mean(arg1,3))'}; % toby 10.02.2006
%formula = {'log10(mean(arg1(:,:,data),3))'};
formula = {'log10(mean(arg1(:,:,X),3))'};
switch g.type
case 'coher', % take the square of alltfx and alltfy first to speed up
formula = { formula{1} ['sum(arg2(:,:,data),3)./sqrt(sum(arg1(:,:,data),3)*length(data) )'] };
if strcmpi(g.lowmem, 'on')
for ind = 1:2:size(alltfX1power,1)
if ind == size(alltfX1,1), indarr = ind; else indarr = [ind:ind+1]; end;
[resdifftmp resimagestmp res1tmp res2tmp] = ...
condstat(formula, g.naccu, g.alpha, {'both' 'upper'}, { '' g.condboot}, ...
{ alltfX1power(indarr,:,:) alltfX2power(indarr,:,:) }, {alltfX1(indarr,:,:) alltfX2(indarr,:,:)});
resdiff{1}(indarr,:) = resdifftmp{1}; resdiff{2}(indarr,:) = resdifftmp{2};
resimages{1}(indarr,:,:) = resimagestmp{1}; resimages{2}(indarr,:,:) = resimagestmp{2};
res1{1}(indarr,:) = res1tmp{1}; res1{2}(indarr,:) = res1tmp{2};
res2{1}(indarr,:) = res2tmp{1}; res2{2}(indarr,:) = res2tmp{2};
end;
else
alltfXpower = { alltfX1power alltfX2power };
alltfX = { alltfX1 alltfX2 };
alltfXabs = { alltfX1abs alltfX2abs };
[resdiff resimages res1 res2] = condstat(formula, g.naccu, g.alpha, {'both' 'upper'}, { '' g.condboot}, alltfXpower, alltfX, alltfXabs);
end;
case 'phasecoher2', % normalize first to speed up
%formula = { formula{1} ['sum(arg2(:,:,data),3)./sum(arg3(:,:,data),3)'] };
% toby 10/3/2006
formula = { formula{1} ['sum(arg2(:,:,X),3)./sum(arg3(:,:,X),3)'] };
alltfX1abs = sqrt(alltfX1power); % these 2 lines can be suppressed
alltfX2abs = sqrt(alltfX2power); % by inserting sqrt(arg1(:,:,data)) instead of arg3(:,:,data))
if strcmpi(g.lowmem, 'on')
for ind = 1:2:size(alltfX1abs,1)
if ind == size(alltfX1,1), indarr = ind; else indarr = [ind:ind+1]; end;
[resdifftmp resimagestmp res1tmp res2tmp] = ...
condstat(formula, g.naccu, g.alpha, {'both' 'upper'}, { '' g.condboot}, ...
{ alltfX1power(indarr,:,:) alltfX2power(indarr,:,:) }, {alltfX1(indarr,:,:) ...
alltfX2(indarr,:,:)}, { alltfX1abs(indarr,:,:) alltfX2abs(indarr,:,:) });
resdiff{1}(indarr,:) = resdifftmp{1}; resdiff{2}(indarr,:) = resdifftmp{2};
resimages{1}(indarr,:,:) = resimagestmp{1}; resimages{2}(indarr,:,:) = resimagestmp{2};
res1{1}(indarr,:) = res1tmp{1}; res1{2}(indarr,:) = res1tmp{2};
res2{1}(indarr,:) = res2tmp{1}; res2{2}(indarr,:) = res2tmp{2};
end;
else
alltfXpower = { alltfX1power alltfX2power };
alltfX = { alltfX1 alltfX2 };
alltfXabs = { alltfX1abs alltfX2abs };
[resdiff resimages res1 res2] = condstat(formula, g.naccu, g.alpha, {'both' 'upper'}, { '' g.condboot}, alltfXpower, alltfX, alltfXabs);
end;
case 'phasecoher',
%formula = { formula{1} ['mean(arg2,3)'] }; % toby 10.02.2006
%formula = { formula{1} ['mean(arg2(:,:,data),3)'] };
formula = { formula{1} ['mean(arg2(:,:,X),3)'] };
if strcmpi(g.lowmem, 'on')
for ind = 1:2:size(alltfX1,1)
if ind == size(alltfX1,1), indarr = ind; else indarr = [ind:ind+1]; end;
alltfX1norm = alltfX1(indarr,:,:)./sqrt(alltfX1(indarr,:,:).*conj(alltfX1(indarr,:,:)));
alltfX2norm = alltfX2(indarr,:,:)./sqrt(alltfX2(indarr,:,:).*conj(alltfX2(indarr,:,:)));
alltfXpower = { alltfX1power(indarr,:,:) alltfX2power(indarr,:,:) };
alltfXnorm = { alltfX1norm alltfX2norm };
[resdifftmp resimagestmp res1tmp res2tmp] = ...
condstat(formula, g.naccu, g.alpha, {'both' 'both'}, { '' g.condboot}, ...
alltfXpower, alltfXnorm);
resdiff{1}(indarr,:) = resdifftmp{1}; resdiff{2}(indarr,:) = resdifftmp{2};
resimages{1}(indarr,:,:) = resimagestmp{1}; resimages{2}(indarr,:,:) = resimagestmp{2};
res1{1}(indarr,:) = res1tmp{1}; res1{2}(indarr,:) = res1tmp{2};
res2{1}(indarr,:) = res2tmp{1}; res2{2}(indarr,:) = res2tmp{2};
end;
else
alltfX1norm = alltfX1./sqrt(alltfX1.*conj(alltfX1));
alltfX2norm = alltfX2./sqrt(alltfX2.*conj(alltfX2)); % maybe have to suppress preprocessing -> lot of memory
alltfXpower = { alltfX1power alltfX2power };
alltfXnorm = { alltfX1norm alltfX2norm };
[resdiff resimages res1 res2] = condstat(formula, g.naccu, g.alpha, {'both' 'both'}, { '' g.condboot}, ...
alltfXpower, alltfXnorm);
end;
end;
% same as below: plottimef(P1-P2, R2-R1, 10*resimages{1}, resimages{2}, mean(data{1},2)-mean(data{2},2), freqs, times, mbase, g);
if strcmpi(g.plotersp, 'on') | strcmpi(g.plotitc, 'on')
g.erspmax = []; % auto scale
g.itcmax = []; % auto scale
plottimef(10*resdiff{1}, resdiff{2}, 10*resimages{1}, resimages{2}, ...
mean(data{1},2)-mean(data{2},2), freqs, timesout, meanmbase, [], [], g);
end;
R1 = res1{2};
R2 = res2{2};
Rdiff = resdiff{2};
Pboot = { Pboot1 Pboot2 10*resimages{1} };
Rboot = { Rboot1 Rboot2 resimages{2} };
end;
P = { P1 P2 P1-P2 };
R = { R1 R2 Rdiff };
if nargout >= 8, alltfX = { alltfX1 alltfX2 }; end;
return; % ********************************** END FOR MULTIPLE CONDITIONS
end;
%%%%%%%%%%%%%%%%%%%%%%
% display text to user (computation perfomed only for display)
%%%%%%%%%%%%%%%%%%%%%%
verboseprintf(g.verbose, 'Computing Event-Related Spectral Perturbation (ERSP) and\n');
switch g.type
case 'phasecoher', verboseprintf(g.verbose, ' Inter-Trial Phase Coherence (ITC) images based on %d trials\n',trials);
case 'phasecoher2', verboseprintf(g.verbose, ' Inter-Trial Phase Coherence 2 (ITC) images based on %d trials\n',trials);
case 'coher', verboseprintf(g.verbose, ' Linear Inter-Trial Coherence (ITC) images based on %d trials\n',trials);
end;
verboseprintf(g.verbose, ' of %d frames sampled at %g Hz.\n',g.frames,g.srate);
verboseprintf(g.verbose, 'Each trial contains samples from %1.0f ms before to\n',g.tlimits(1));
verboseprintf(g.verbose, ' %1.0f ms after the timelocking event.\n',g.tlimits(2));
if ~isnan(g.alpha)
verboseprintf(g.verbose, 'Only significant values (permutation statistics p<%g) will be colored;\n',g.alpha)
verboseprintf(g.verbose, ' non-significant values will be plotted in green\n');
end
verboseprintf(g.verbose,' Image frequency direction: %s\n',g.hzdir);
if isempty(g.precomputed)
% -----------------------------------------
% detrend over epochs (trials) if requested
% -----------------------------------------
if strcmpi(g.rmerp, 'on')
if ndims(data) == 2
data = data - mean(data,2)*ones(1, length(data(:))/g.frames);
else data = data - repmat(mean(data,3), [1 1 trials]);
end;
end;
% ----------------------------------------------------
% compute time frequency decompositions, power and ITC
% ----------------------------------------------------
if length(g.timesout) > 1, tmioutopt = { 'timesout' , g.timesout };
elseif ~isempty(g.ntimesout) tmioutopt = { 'ntimesout', g.ntimesout };
else tmioutopt = { 'ntimesout', g.timesout };
end;
[alltfX freqs timesout R] = timefreq(data, g.srate, tmioutopt{:}, ...
'winsize', g.winsize, 'tlimits', g.tlimits, 'detrend', g.detrend, ...
'itctype', g.type, 'wavelet', g.cycles, 'verbose', g.verbose, ...
'padratio', g.padratio, 'freqs', g.freqs, 'freqscale', g.freqscale, ...
'nfreqs', g.nfreqs, 'timestretch', {g.timeStretchMarks', g.timeStretchRefs}, timefreqopts{:});
else
alltfX = g.precomputed.tfdata;
timesout = g.precomputed.times;
freqs = g.precomputed.freqs;
if strcmpi(g.precomputed.recompute, 'ersp')
R = [];
else
switch g.itctype
case 'coher', R = alltfX ./ repmat(sqrt(sum(alltfX .* conj(alltfX),3) * size(alltfX,3)), [1 1 size(alltfX,3)]);
case 'phasecoher2', R = alltfX ./ repmat(sum(sqrt(alltfX .* conj(alltfX)),3), [1 1 size(alltfX,3)]);
case 'phasecoher', R = alltfX ./ sqrt(alltfX .* conj(alltfX));
end;
P = []; mbase = []; return;
end;
end;
if g.cycles(1) == 0
alltfX = 2/0.375*alltfX/g.winsize; % TF and MC (12/11/2006): normalization, divide by g.winsize
P = alltfX.*conj(alltfX); % power
% TF and MC (12/14/2006): multiply by 2 account for negative frequencies,
% and ounteract the reduction by a factor 0.375 that occurs as a result of
% cosine (Hann) tapering. Refer to Bug 446
% Modified again 04/29/2011 due to comment in bug 1032
else
P = alltfX.*conj(alltfX); % power for wavelets
end;
% ---------------
% baseline length
% ---------------
if size(g.baseline,2) == 2
baseln = [];
for index = 1:size(g.baseline,1)
tmptime = find(timesout >= g.baseline(index,1) & timesout <= g.baseline(index,2));
baseln = union_bc(baseln, tmptime);
end;
if length(baseln)==0
error( [ 'There are no sample points found in the default baseline.' 10 ...
'This may happen even though data time limits overlap with' 10 ...
'the baseline period (because of the time-freq. window width).' 10 ...
'Either disable the baseline, change the baseline limits.' ] );
end
else
if ~isempty(find(timesout < g.baseline))
baseln = find(timesout < g.baseline); % subtract means of pre-0 (centered) windows
else baseln = 1:length(timesout); % use all times as baseline
end
end;
if ~isnan(g.alpha) && length(baseln)==0
verboseprintf(g.verbose, 'timef(): no window centers in baseline (times<%g) - shorten (max) window length.\n', g.baseline)
return
end
% -----------------------------------------
% remove baseline on a trial by trial basis
% -----------------------------------------
if strcmpi(g.trialbase, 'on'), tmpbase = baseln;
else tmpbase = 1:size(P,2); % full baseline
end;
if ndims(P) == 4
if ~strcmpi(g.trialbase, 'off') && isnan( g.powbase(1) )
mbase = mean(P(:,:,tmpbase,:),3);
if strcmpi(g.basenorm, 'on')
mstd = std(P(:,:,tmpbase,:),[],3);
P = bsxfun(@rdivide, bsxfun(@minus, P, mbase), mstd);
else P = bsxfun(@rdivide, P, mbase);
end;
end;
else
if ~strcmpi(g.trialbase, 'off') && isnan( g.powbase(1) )
mbase = mean(P(:,tmpbase,:),2);
if strcmpi(g.basenorm, 'on')
mstd = std(P(:,tmpbase,:),[],2);
P = (P-repmat(mbase,[1 size(P,2) 1]))./repmat(mstd,[1 size(P,2) 1]); % convert to log then back to normal
else
P = P./repmat(mbase,[1 size(P,2) 1]);
%P = 10 .^ (log10(P) - repmat(log10(mbase),[1 size(P,2) 1])); % same as above
end;
end;
end;
if ~isempty(g.precomputed)
return; % return single trial power
end;
% -----------------------
% compute baseline values
% -----------------------
if isnan(g.powbase(1))
verboseprintf(g.verbose, 'Computing the mean baseline spectrum\n');
if ndims(P) == 4
if ndims(P) > 3, Pori = mean(P, 4); else Pori = P; end;
mbase = mean(Pori(:,:,baseln),3);
else
if ndims(P) > 2, Pori = mean(P, 3); else Pori = P; end;
mbase = mean(Pori(:,baseln),2);
end;
else
verboseprintf(g.verbose, 'Using the input baseline spectrum\n');
mbase = g.powbase;
if strcmpi(g.scale, 'log'), mbase = 10.^(mbase/10); end;
if size(mbase,1) == 1 % if input was a row vector, flip to be a column
mbase = mbase';
end;
end
baselength = length(baseln);
% -------------------------
% remove baseline (average)
% -------------------------
% original ERSP baseline removal
if ~strcmpi(g.trialbase, 'on')
if ~isnan( g.baseline(1) ) && any(~isnan( mbase(1) )) && strcmpi(g.basenorm, 'off')
P = bsxfun(@rdivide, P, mbase); % use single trials
% ERSP baseline normalized
elseif ~isnan( g.baseline(1) ) && ~isnan( mbase(1) ) && strcmpi(g.basenorm, 'on')
if ndims(Pori) == 3,
mstd = std(Pori(:,:,baseln),[],3);
else mstd = std(Pori(:,baseln),[],2);
end;
P = bsxfun(@rdivide, bsxfun(@minus, P, mbase), mstd);
end;
end;
% ----------------
% phase amp option
% ----------------
if strcmpi(g.phsamp, 'on')
disp( 'phsamp option is deprecated');
% switch g.phsamp
% case 'on'
%PA = zeros(size(P,1),size(P,1),g.timesout); % NB: (freqs,freqs,times)
% $$$ end % phs amp
%PA (freq x freq x time)
%PA(:,:,j) = PA(:,:,j) + (tmpX ./ abs(tmpX)) * ((P(:,j)))';
% x-product: unit phase column
% times amplitude row
%tmpcx(1,:,:) = cumulX; % allow ./ below
%for jj=1:g.timesout
% PA(:,:,jj) = PA(:,:,jj) ./ repmat(P(:,jj)', [size(P,1) 1]);
%end
end
% ---------
% bootstrap
% --------- % this ensures that if bootstrap limits provided that no
% 'alpha' won't prevent application of the provided limits
if ~isnan(g.alpha) | ~isempty(find(~isnan(g.pboot))) | ~isempty(find(~isnan(g.rboot)))% if bootstrap analysis requested . . .
% ERSP bootstrap
% --------------
if ~isempty(find(~isnan(g.pboot))) % if ERSP bootstrap limits provided already
Pboot = g.pboot(:);
else
if size(g.baseboot,2) == 1
if g.baseboot == 0, baselntmp = [];
elseif ~isnan(g.baseline(1))
baselntmp = baseln;
else baselntmp = find(timesout <= 0); % if it is empty use whole epoch
end;
else
baselntmp = [];
for index = 1:size(g.baseboot,1)
tmptime = find(timesout >= g.baseboot(index,1) & timesout <= g.baseboot(index,2));
if isempty(tmptime),
fprintf('Warning: empty baseline interval [%3.2f %3.2f]\n', g.baseboot(index,1), g.baseboot(index,2));
end;
baselntmp = union_bc(baselntmp, tmptime);
end;
end;
if prod(size(g.baseboot)) > 2
fprintf('Permutation statistics will use data in multiple selected windows.\n');
elseif size(g.baseboot,2) == 2
fprintf('Permutation statistics will use data in range %3.2g-%3.2g ms.\n', g.baseboot(1), g.baseboot(2));
elseif g.baseboot
fprintf(' %d permutation statistics windows in baseline (times<%g).\n', length(baselntmp), g.baseboot)
end;
% power significance
% ------------------
if strcmpi(g.boottype, 'shuffle')
formula = 'mean(arg1,3);';
[ Pboot Pboottrialstmp Pboottrials] = bootstat(P, formula, 'boottype', 'shuffle', ...
'label', 'ERSP', 'bootside', 'both', 'naccu', g.naccu, ...
'basevect', baselntmp, 'alpha', g.alpha, 'dimaccu', 2 );
clear Pboottrialstmp;
else
center = 0;
if strcmpi(g.basenorm, 'off'), center = 1; end;
% bootstrap signs
Pboottmp = P;
Pboottrials = zeros([ size(P,1) size(P,2) g.naccu ]);
for index = 1:g.naccu
Pboottmp = (Pboottmp-center).*(ceil(rand(size(Pboottmp))*2-1)*2-1)+center;
Pboottrials(:,:,index) = mean(Pboottmp,3);
end;
Pboot = [];
end;
if size(Pboot,2) == 1, Pboot = Pboot'; end;
end;
% ITC bootstrap
% -------------
if ~isempty(find(~isnan(g.rboot))) % if itc bootstrap provided
Rboot = g.rboot;
else
if ~isempty(find(~isnan(g.pboot))) % if ERSP limits were provided (but ITC not)
if size(g.baseboot,2) == 1
if g.baseboot == 0, baselntmp = [];
elseif ~isnan(g.baseline(1))
baselntmp = baseln;
else baselntmp = find(timesout <= 0); % if it is empty use whole epoch
end;
else
baselntmp = [];
for index = 1:size(g.baseboot,1)
tmptime = find(timesout >= g.baseboot(index,1) && timesout <= g.baseboot(index,2));
if isempty(tmptime),
fprintf('Warning: empty baseline interval [%3.2f %3.2f]\n', g.baseboot(index,1), g.baseboot(index,2));
end;
baselntmp = union_bc(baselntmp, tmptime);
end;
end;
if prod(size(g.baseboot)) > 2
fprintf('Permutation statistics will use data in multiple selected windows.\n');
elseif size(g.baseboot,2) == 2
fprintf('Permutation statistics will use data in range %3.2g-%3.2g ms.\n', g.baseboot(1), g.baseboot(2));
elseif g.baseboot
fprintf(' %d permutation statistics windows in baseline (times<%g).\n', length(baselntmp), g.baseboot)
end;
end;
% ITC significance
% ----------------
inputdata = alltfX;
switch g.type
case 'coher', formula = [ 'sum(arg1,3)./sqrt(sum(arg1.*conj(arg1),3))/ sqrt(' int2str(size(alltfX,3)) ');' ];
case 'phasecoher', formula = [ 'mean(arg1,3);' ]; inputdata = alltfX./sqrt(alltfX.*conj(alltfX));
case 'phasecoher2', formula = [ 'sum(arg1,3)./sum(sqrt(arg1.*conj(arg1)),3);' ];
end;
if strcmpi(g.boottype, 'randall'), dimaccu = []; g.boottype = 'rand';
else dimaccu = 2;
end;
[Rboot Rboottmp Rboottrials] = bootstat(inputdata, formula, 'boottype', g.boottype, ...
'label', 'ITC', 'bootside', 'upper', 'naccu', g.naccu, ...
'basevect', baselntmp, 'alpha', g.alpha, 'dimaccu', 2 );
fprintf('\n');
clear Rboottmp;
end;
else
Pboot = []; Rboot = [];
end
% average the power
% -----------------
PA = P;
if ndims(P) == 4, P = mean(P, 4);
elseif ndims(P) == 3, P = mean(P, 3);
end;
% correction for multiple comparisons
% -----------------------------------
maskersp = [];
maskitc = [];
if ~isnan(g.alpha)
if isempty(find(~isnan(g.pboot))) % if ERSP lims not provided
if ndims(Pboottrials) < 3, Pboottrials = Pboottrials'; end;
exactp_ersp = compute_pvals(P, Pboottrials);
if strcmpi(g.mcorrect, 'fdr')
alphafdr = fdr(exactp_ersp, g.alpha);
if alphafdr ~= 0
fprintf('ERSP correction for multiple comparisons using FDR, alpha_fdr = %3.6f\n', alphafdr);
else fprintf('ERSP correction for multiple comparisons using FDR, nothing significant\n', alphafdr);
end;
maskersp = exactp_ersp <= alphafdr;
else
maskersp = exactp_ersp <= g.alpha;
end;
end;
if isempty(find(~isnan(g.rboot))) % if ITC lims not provided
exactp_itc = compute_pvals(abs(R), abs(Rboottrials'));
if strcmpi(g.mcorrect, 'fdr')
alphafdr = fdr(exactp_itc, g.alpha);
if alphafdr ~= 0
fprintf('ITC correction for multiple comparisons using FDR, alpha_fdr = %3.6f\n', alphafdr);
else fprintf('ITC correction for multiple comparisons using FDR, nothing significant\n', alphafdr);
end;
maskitc = exactp_itc <= alphafdr;
else
maskitc = exactp_itc <= g.alpha;
end
end;
end;
% convert to log if necessary
% ---------------------------
if strcmpi(g.scale, 'log')
if ~isnan( g.baseline(1) ) && ~isnan( mbase(1) ) && strcmpi(g.trialbase, 'off'), mbase = log10(mbase)*10; end;
P = 10 * log10(P);
if ~isempty(Pboot)
Pboot = 10 * log10(Pboot);
end;
end;
if isempty(Pboot) && exist('maskersp')
Pboot = maskersp;
end;
% auto scalling
% -------------
if isempty(g.erspmax)
g.erspmax = [max(max(abs(P)))]/2;
if strcmpi(g.scale, 'abs') && strcmpi(g.basenorm, 'off') % % of baseline
g.erspmax = [max(max(abs(P)))];
if g.erspmax > 1
g.erspmax = [1-(g.erspmax-1) g.erspmax];
else g.erspmax = [g.erspmax 1+(1-g.erspmax)];
end;
end;
%g.erspmax = [-g.erspmax g.erspmax]+1;
end;
% --------
% plotting
% --------
if strcmpi(g.plotersp, 'on') || strcmpi(g.plotitc, 'on')
if ndims(P) == 3
P = squeeze(P(2,:,:,:));
R = squeeze(R(2,:,:,:));
mbase = squeeze(mbase(2,:));
ERP = mean(squeeze(data(1,:,:)),2);
else
ERP = mean(data,2);
end;
if strcmpi(g.plottype, 'image')
plottimef(P, R, Pboot, Rboot, ERP, freqs, timesout, mbase, maskersp, maskitc, g);
else
plotallcurves(P, R, Pboot, Rboot, ERP, freqs, timesout, mbase, g);
end;
end;
% --------------
% format outputs
% --------------
if strcmpi(g.outputformat, 'old')
R = abs(R); % convert coherence vector to magnitude
if strcmpi(g.scale, 'log'), mbase = 10^(mbase/10); end;
end;
if strcmpi(g.verbose, 'on')
disp('Note: Add output variables to command line call in history to');
disp(' retrieve results and use the tftopo function to replot them');
end;
mbase = mbase';
if ~isempty(g.caption)
h = textsc(g.caption, 'title');
set(h, 'FontWeight', 'bold');
end
return;
% -----------------
% plotting function
% -----------------
function g = plottimef(P, R, Pboot, Rboot, ERP, freqs, times, mbase, maskersp, maskitc, g);
persistent showwarning;
if isempty(showwarning)
warning( [ 'Some versions of Matlab crash on this function. If this is' 10 ...
'the case, simply comment the code line 1655-1673 in newtimef.m' 10 ...
'which aims at "ploting marginal ERSP mean below ERSP image"' ]);
showwarning = 1;
end;
%
% compute ERP
%
ERPtimes = [g.tlimits(1):(g.tlimits(2)-g.tlimits(1))/(g.frames-1):g.tlimits(2)+0.000001];
ERPindices = zeros(1, length(times));
for ti=1:length(times)
[tmp ERPindices(ti)] = min(abs(ERPtimes-times(ti)));
end
ERPtimes = ERPtimes(ERPindices); % subset of ERP frames on t/f window centers
ERP = ERP(ERPindices);
if ~isreal(R)
Rangle = angle(R);
Rsign = sign(imag(R));
R = abs(R); % convert coherence vector to magnitude
setylim = 1;
else
Rangle = zeros(size(R)); % Ramon: if isreal(R) then we get an error because Rangle does not exist
Rsign = ones(size(R));
setylim = 0;
end;
switch lower(g.plotitc)
case 'on',
switch lower(g.plotersp),
case 'on', ordinate1 = 0.67; ordinate2 = 0.1; height = 0.33; g.plot = 1;
case 'off', ordinate2 = 0.1; height = 0.9; g.plot = 1;
end;
case 'off', ordinate1 = 0.1; height = 0.9;
switch lower(g.plotersp),
case 'on', ordinate1 = 0.1; height = 0.9; g.plot = 1;
case 'off', g.plot = 0;
end;
end;
if g.plot
% verboseprintf(g.verbose, '\nNow plotting...\n');
set(gcf,'DefaultAxesFontSize',g.AXES_FONT)
colormap(jet(256));
pos = get(gca,'position');
q = [pos(1) pos(2) 0 0];
s = [pos(3) pos(4) pos(3) pos(4)];
axis off;
end;
switch lower(g.plotersp)
case 'on'
%
%%%%%%% image the ERSP %%%%%%%%%%%%%%%%%%%%%%%%%%
%
h(1) = axes('Position',[.1 ordinate1 .9 height].*s+q);
set(h(1), 'tag', 'ersp');
PP = P;
if strcmpi(g.scale, 'abs') && strcmpi(g.basenorm, 'off')
baseval = 1;
else baseval = 0;
end;
if ~isnan(g.alpha)
if strcmpi(g.pcontour, 'off') && ~isempty(maskersp) % zero out nonsignif. power differences
PP(~maskersp) = baseval;
%PP = PP .* maskersp;
elseif isempty(maskersp)
if size(PP,1) == size(Pboot,1) && size(PP,2) == size(Pboot,2)
PP(find(PP > Pboot(:,:,1) & (PP < Pboot(:,:,2)))) = baseval;
Pboot = squeeze(mean(Pboot,2));
if size(Pboot,2) == 1, Pboot = Pboot'; end;
else
PP(find((PP > repmat(Pboot(:,1),[1 length(times)])) ...
& (PP < repmat(Pboot(:,2),[1 length(times)])))) = baseval;
end
end;
end;
% find color limits
% -----------------
if isempty(g.erspmax)
if g.ERSP_CAXIS_LIMIT == 0
g.erspmax = [-1 1]*1.1*max(max(abs(P(:,:))));
else
g.erspmax = g.ERSP_CAXIS_LIMIT*[-1 1];
end
elseif length(g.erspmax) == 1
g.erspmax = [ -g.erspmax g.erspmax];
end
if isnan( g.baseline(1) ) && g.erspmax(1) < 0
g.erspmax = [ min(min(P(:,:))) max(max(P(:,:)))];
end;
% plot image
% ----------
if ~strcmpi(g.freqscale, 'log')
imagesc(times,freqs,PP(:,:), g.erspmax);
else
imagesclogy(times,freqs,PP(:,:),g.erspmax);
end;
set(gca,'ydir',g.hzdir); % make frequency ascend or descend
% put contour for multiple comparison masking
if ~isempty(maskersp) && strcmpi(g.pcontour, 'on')
hold on; [tmpc tmph] = contour(times, freqs, maskersp);
set(tmph, 'linecolor', 'k', 'linewidth', 0.25)
end;
hold on
plot([0 0],[0 freqs(end)],'--m','LineWidth',g.linewidth); % plot time 0
if ~isnan(g.marktimes) % plot marked time
for mt = g.marktimes(:)'
plot([mt mt],[0 freqs(end)],'--k','LineWidth',g.linewidth);
end
end
hold off
set(h(1),'YTickLabel',[],'YTick',[])
set(h(1),'XTickLabel',[],'XTick',[])
if ~isempty(g.vert)
for index = 1:length(g.vert)
line([g.vert(index), g.vert(index)], [min(freqs) max(freqs)], 'linewidth', 1, 'color', 'm');
end;
end;
h(2) = gca;
h(3) = cbar('vert'); % ERSP colorbar axes
set(h(2),'Position',[.1 ordinate1 .8 height].*s+q)
set(h(3),'Position',[.95 ordinate1 .05 height].*s+q)
title([ 'ERSP(' g.unitpower ')' ])
%
%%%%% plot marginal ERSP mean below ERSP image %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%
h(4) = axes('Position',[.1 ordinate1-0.1 .8 .1].*s+q);
E = [min(P(:,:),[],1);max(P(:,:),[],1)];
% plotting limits
if isempty(g.erspmarglim)
g.erspmarglim = [min(E(1,:))-max(max(abs(E)))/3 max(E(2,:))+max(max(abs(E)))/3];
end;
plot(times,E,[0 0],g.erspmarglim, '--m','LineWidth',g.linewidth)
xlim([min(times) max(times)])
ylim(g.erspmarglim)
tick = get(h(4),'YTick');
set(h(4),'YTick',[tick(1) ; tick(end)])
set(h(4),'YAxisLocation','right')
set(h(4),'TickLength',[0.020 0.025]);
xlabel('Time (ms)')
ylabel(g.unitpower)
%
%%%%% plot mean spectrum to left of ERSP image %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%
h(5) = axes('Position',[0 ordinate1 .1 height].*s+q);
if isnan(g.baseline) % Ramon :for bug 1657
E = zeros(size(freqs));
else
E = mbase;
end
if ~isnan(E(1))
% plotting limits
if isempty(g.speclim)
% g.speclim = [min(E)-max(abs(E))/3 max(E)+max(abs(E))/3];
if all(~isnan(mbase))
g.speclim = [min(mbase)-max(abs(mbase))/3 max(mbase)+max(abs(mbase))/3]; % RMC: Just for plotting
else
g.speclim = [min(E)-max(abs(E))/3 max(E)+max(abs(E))/3];
end
end;
% plot curves
if ~strcmpi(g.freqscale, 'log')
plot(freqs,E,'LineWidth',g.linewidth); hold on;
if ~isnan(g.alpha) && size(Pboot,2) == 2
try
plot(freqs,Pboot(:,:)'+[E;E], 'g', 'LineWidth',g.linewidth)
plot(freqs,Pboot(:,:)'+[E;E], 'k:','LineWidth',g.linewidth)
catch
plot(freqs,Pboot(:,:)+[E E], 'g', 'LineWidth',g.linewidth)
plot(freqs,Pboot(:,:)+[E E], 'k:','LineWidth',g.linewidth)
end;
end
if freqs(1) ~= freqs(end), xlim([freqs(1) freqs(end)]); end;
if g.speclim(1) ~= g.speclim(2), ylim(g.speclim); end; % Ramon :for bug 1657
else % 'log'
semilogx(freqs,E,'LineWidth',g.linewidth); hold on;
if ~isnan(g.alpha)
try
semilogx(freqs,Pboot(:,:)'+[E;E],'g', 'LineWidth',g.linewidth)
semilogx(freqs,Pboot(:,:)'+[E;E],'k:','LineWidth',g.linewidth)
catch
semilogx(freqs,Pboot(:,:)+[E E],'g', 'LineWidth',g.linewidth)
semilogx(freqs,Pboot(:,:)+[E E],'k:','LineWidth',g.linewidth)
end;
end
if freqs(1) ~= freqs(end), xlim([freqs(1) freqs(end)]); end;
if g.speclim(1) ~= g.speclim(2), ylim(g.speclim); end; %RMC
set(h(5),'View',[90 90])
divs = linspace(log(freqs(1)), log(freqs(end)), 10);
set(gca, 'xtickmode', 'manual');
divs = ceil(exp(divs)); divs = unique_bc(divs); % ceil is critical here, round might misalign
set(gca, 'xtick', divs);
end;
set(h(5),'TickLength',[0.020 0.025]);
set(h(5),'View',[90 90])
xlabel('Frequency (Hz)')
if strcmp(g.hzdir,'normal')
set(gca,'xdir','reverse');
else
set(gca,'xdir','normal');
end
ylabel(g.unitpower)
tick = get(h(5),'YTick');
if (length(tick)>2)
set(h(5),'YTick',[tick(1) ; tick(end-1)])
end
end;
end;
switch lower(g.plotitc)
case 'on'
%
%%%%%%%%%%%% Image the ITC %%%%%%%%%%%%%%%%%%
%
h(6) = axes('Position',[.1 ordinate2 .9 height].*s+q); % ITC image
if ishandle(h(1));set(h(1), 'tag', 'itc');end;
if abs(R(1,1)-1) < 0.0001, g.plotphaseonly = 'on'; end;
if strcmpi(g.plotphaseonly, 'on')
RR = Rangle/pi*180;
else
RR = R;
end;
if ~isnan(g.alpha)
if ~isempty(maskitc) && strcmpi(g.pcontour, 'off')
RR = RR .* maskitc;
elseif isempty(maskitc)
if size(RR,1) == size(Rboot,1) && size(RR,2) == size(Rboot,2)
tmp = gcf;
if size(Rboot,3) == 2 RR(find(RR > Rboot(:,:,1) & RR < Rboot(:,:,2))) = 0;
else RR(find(RR < Rboot)) = 0;
end;
Rboot = mean(Rboot(:,:,end),2);
else
RR(find(RR < repmat(Rboot(:),[1 length(times)]))) = 0;
end;
end;
end
if g.ITC_CAXIS_LIMIT == 0
coh_caxis = min(max(max(R(:,:))),1)*[-1 1]; % 1 WAS 0.4 !
else
coh_caxis = g.ITC_CAXIS_LIMIT*[-1 1];
end
if strcmpi(g.plotphaseonly, 'on')
if ~strcmpi(g.freqscale, 'log')
imagesc(times,freqs,RR(:,:)); % <---
else
imagesclogy(times,freqs,RR(:,:)); % <---
end;
g.itcmax = [-180 180];
setylim = 0;
else
if max(coh_caxis) == 0, % toby 10.02.2006
coh_caxis = [-1 1];
end
if ~strcmpi(g.freqscale, 'log')
if exist('Rsign') && strcmp(g.plotphasesign, 'on')
imagesc(times,freqs,Rsign(:,:).*RR(:,:),coh_caxis); % <---
else
imagesc(times,freqs,RR(:,:),coh_caxis); % <---
end
else
if exist('Rsign') && strcmp(g.plotphasesign, 'on')
imagesclogy(times,freqs,Rsign(:,:).*RR(:,:),coh_caxis); % <---
else
imagesclogy(times,freqs,RR(:,:),coh_caxis); % <---
end
end;
end;
set(gca,'ydir',g.hzdir); % make frequency ascend or descend
% plot contour if necessary
if ~isempty(maskitc) && strcmpi(g.pcontour, 'on')
hold on; [tmpc tmph] = contour(times, freqs, maskitc);
set(tmph, 'linecolor', 'k', 'linewidth', 0.25)
end;
if isempty(g.itcmax)
g.itcmax = caxis;
elseif length(g.itcmax) == 1
g.itcmax = [ -g.itcmax g.itcmax ];
end;
caxis(g.itcmax);
hold on
plot([0 0],[0 freqs(end)],'--m','LineWidth',g.linewidth);
if ~isnan(g.marktimes)
for mt = g.marktimes(:)'
plot([mt mt],[0 freqs(end)],'--k','LineWidth',g.linewidth);
end
end
hold off
set(h(6),'YTickLabel',[],'YTick',[])
set(h(6),'XTickLabel',[],'XTick',[])
if ~isempty(g.vert)
for index = 1:length(g.vert)
line([g.vert(index), g.vert(index)], [min(freqs) max(freqs)], 'linewidth', 1, 'color', 'm');
end;
end;
h(7) = gca;
h(8) = cbar('vert');
%h(9) = get(h(8),'Children'); % make the function crash
set(h(7),'Position',[.1 ordinate2 .8 height].*s+q)
set(h(8),'Position',[.95 ordinate2 .05 height].*s+q)
if setylim
set(h(8),'YLim',[0 g.itcmax(2)]);
end;
if strcmpi(g.plotphaseonly, 'on')
title('ITC phase')
else
title('ITC')
end;
%
%%%%% plot the ERP below the ITC image %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%
h(10) = axes('Position',[.1 ordinate2-0.1 .8 .1].*s+q); % ERP
if isempty(g.erplim)
ERPmax = max(ERP);
ERPmin = min(ERP);
g.erplim = [ ERPmin - 0.1*(ERPmax-ERPmin) ERPmax + 0.1*(ERPmax-ERPmin) ];
end;
plot(ERPtimes,ERP, [0 0],g.erplim,'--m','LineWidth',g.linewidth);
hold on;
plot([times(1) times(length(times))],[0 0], 'k');
xlim([min(ERPtimes) max(ERPtimes)]);
ylim(g.erplim)
set(gca,'ydir',g.ydir);
tick = get(h(10),'YTick');
set(h(10),'YTick',[tick(1) ; tick(end)])
set(h(10),'TickLength',[0.02 0.025]);
set(h(10),'YAxisLocation','right')
xlabel('Time (ms)')
ylabel('\muV')
if (~isempty(g.topovec))
if length(g.topovec) ~= 1, ylabel(''); end; % ICA component
end;
E = nan_mean(R(:,:)'); % don't let a few NaN's crash this
%
%%%%% plot the marginal mean left of the ITC image %%%%%%%%%%%%%%%%%%%%%
%
h(11) = axes('Position',[0 ordinate2 .1 height].*s+q); % plot the marginal mean
% ITC left of the ITC image
% set plotting limits
if isempty(g.itcavglim)
if ~isnan(g.alpha)
g.itcavglim = [ min(E)-max(E)/3 max(Rboot)+max(Rboot)/3];
else
g.itcavglim = [ min(E)-max(E)/3 max(E)+max(E)/3];
end;
end;
if max(g.itcavglim) == 0 || any(isnan(g.itcavglim))
g.itcavglim = [-1 1];
end
% plot marginal ITC
if ~strcmpi(g.freqscale, 'log')
plot(freqs,E,'LineWidth',g.linewidth); hold on;
if ~isnan(g.alpha)
plot(freqs,Rboot,'g', 'LineWidth',g.linewidth)
plot(freqs,Rboot,'k:','LineWidth',g.linewidth)
end
if freqs(1) ~= freqs(end), xlim([freqs(1) freqs(end)]); end
ylim(g.itcavglim)
else
semilogx(freqs,E,'LineWidth',g.linewidth); hold on;
if ~isnan(g.alpha)
semilogx(freqs,Rboot(:),'g', 'LineWidth',g.linewidth)
semilogx(freqs,Rboot(:),'k:','LineWidth',g.linewidth)
end
if freqs(1) ~= freqs(end), xlim([freqs(1) freqs(end)]); end;
ylim(g.itcavglim)
divs = linspace(log(freqs(1)), log(freqs(end)), 10);
set(gca, 'xtickmode', 'manual');
divs = ceil(exp(divs)); divs = unique_bc(divs); % ceil is critical here, round might misalign
set(gca, 'xtick', divs);
end;
% ITC plot details
tick = get(h(11),'YTick');
if length(tick) > 1
set(h(11),'YTick',[tick(1) ; tick(length(tick))])
end;
set(h(11),'View',[90 90])
%set(h(11),'TickLength',[0.020 0.025]);
xlabel('Frequency (Hz)')
if strcmp(g.hzdir,'normal')
set(gca,'xdir','reverse');
else
set(gca,'xdir','normal');
end
ylabel('ERP')
end; %switch
%
%%%%%%%%%%%%%%% plot a topoplot() %%%%%%%%%%%%%%%%%%%%%%%
%
if (~isempty(g.topovec)) && strcmpi(g.plotitc, 'on') && strcmpi(g.plotersp, 'on')
if strcmp(g.plotersp,'off')
h(12) = axes('Position',[-.207 .95 .2 .14].*s+q); % place the scalp map at top-left
else
h(12) = axes('Position',[-.1 .43 .2 .14].*s+q); % place the scalp map at middle-left
end;
if length(g.topovec) == 1
topoplot(g.topovec,g.elocs,'electrodes','off', ...
'style', 'blank', 'emarkersize1chan', 10, 'chaninfo', g.chaninfo);
else
topoplot(g.topovec,g.elocs,'electrodes','off', 'chaninfo', g.chaninfo);
end;
axis('square')
end
if g.plot
try, icadefs; set(gcf, 'color', BACKCOLOR); catch, end;
if (length(g.title) > 0) && ~iscell(g.title)
axes('Position',pos,'Visible','Off');
h(13) = text(-.05,1.01,g.title);
set(h(13),'VerticalAlignment','bottom')
set(h(13),'HorizontalAlignment','left')
set(h(13),'FontSize',g.TITLE_FONT);
end
try, axcopy(gcf); catch, end;
end;
% ---------------
% Plotting curves
% ---------------
function plotallcurves(P, R, Pboot, Rboot, ERP, freqs, times, mbase, g);
if ~isreal(R)
Rangle = angle(R);
R = abs(R); % convert coherence vector to magnitude
setylim = 1;
else
Rangle = zeros(size(R)); % Ramon: if isreal(R) then we get an error because Rangle does not exist
Rsign = ones(size(R));
setylim = 0;
end;
if strcmpi(g.plotitc, 'on') | strcmpi(g.plotersp, 'on')
verboseprintf(g.verbose, '\nNow plotting...\n');
pos = get(gca,'position');
q = [pos(1) pos(2) 0 0];
s = [pos(3) pos(4) pos(3) pos(4)];
end;
% time unit
% ---------
if times(end) > 10000
times = times/1000;
timeunit = 's';
else
timeunit = 'ms';
end;
if strcmpi(g.plotersp, 'on')
%
%%%%%%% image the ERSP %%%%%%%%%%%%%%%%%%%%%%%%%%
%
if strcmpi(g.plotitc, 'on'), subplot(2,1,1); end;
set(gca, 'tag', 'ersp');
alllegend = {};
for index = 1:length(freqs)
alllegend{index} = [ num2str(freqs(index)) 'Hz baseline ' num2str(mbase(index)) ' dB' ];
end;
if strcmpi(g.plotmean, 'on') && freqs(1) ~= freqs(end)
alllegend = { alllegend{:} [ num2str(freqs(1)) '-' num2str(freqs(end)) ...
'Hz mean baseline ' num2str(mean(mbase)) ' dB' ] };
end;
plotcurve(times, P, 'maskarray', Pboot, 'title', 'ERSP', ...
'xlabel', [ 'Time (' timeunit ')' ], 'ylabel', 'dB', 'ylim', [-g.erspmax g.erspmax], ...
'vert', g.vert, 'marktimes', g.marktimes, 'legend', alllegend, ...
'linewidth', g.linewidth, 'highlightmode', g.highlightmode, 'plotmean', g.plotmean);
end;
if strcmpi(g.plotitc, 'on')
%
%%%%%%%%%%%% Image the ITC %%%%%%%%%%%%%%%%%%
%
if strcmpi(g.plotersp, 'on'), subplot(2,1,2); end;
set(gca, 'tag', 'itc');
if abs(R(1,1)-1) < 0.0001, g.plotphaseonly = 'on'; end;
if strcmpi(g.plotphaseonly, 'on') % plot ITC phase instead of amplitude (e.g. for continuous data)
RR = Rangle/pi*180;
else RR = R;
end;
% find regions of significance
% ----------------------------
alllegend = {};
for index = 1:length(freqs)
alllegend{index} = [ num2str(freqs(index)) 'Hz baseline ' num2str(mbase(index)) ' dB' ];
end;
if strcmpi(g.plotmean, 'on') && freqs(1) ~= freqs(end)
alllegend = { alllegend{:} [ num2str(freqs(1)) '-' num2str(freqs(end)) ...
'Hz mean baseline ' num2str(mean(mbase)) ' dB' ] };
end;
plotcurve(times, RR, 'maskarray', Rboot, 'val2mask', R, 'title', 'ITC', ...
'xlabel', [ 'Time (' timeunit ')' ], 'ylabel', 'dB', 'ylim', g.itcmax, ...
'vert', g.vert, 'marktimes', g.marktimes, 'legend', alllegend, ...
'linewidth', g.linewidth, 'highlightmode', g.highlightmode, 'plotmean', g.plotmean);
end;
if strcmpi(g.plotitc, 'on') | strcmpi(g.plotersp, 'on')
%
%%%%%%%%%%%%%%% plot a topoplot() %%%%%%%%%%%%%%%%%%%%%%%
%
if (~isempty(g.topovec))
h(12) = axes('Position',[-.1 .43 .2 .14].*s+q);
if length(g.topovec) == 1
topoplot(g.topovec,g.elocs,'electrodes','off', ...
'style', 'blank', 'emarkersize1chan', 10);
else
topoplot(g.topovec,g.elocs,'electrodes','off');
end;
axis('square')
end
try, icadefs; set(gcf, 'color', BACKCOLOR); catch, end;
if (length(g.title) > 0) && ~iscell(g.title)
axes('Position',pos,'Visible','Off');
h(13) = text(-.05,1.01,g.title);
set(h(13),'VerticalAlignment','bottom')
set(h(13),'HorizontalAlignment','left')
set(h(13),'FontSize',g.TITLE_FONT);
end
try, axcopy(gcf); catch, end;
end;
%
%%%%%%%%%%%%%%%%%%%%%%% Highlight regions %%%%%%%%%%%%%%%%%%%%%%%%%%
%
function highlight(ax, times, regions, highlightmode);
color1 = [0.75 0.75 0.75];
color2 = [0 0 0];
yl = ylim;
if ~strcmpi(highlightmode, 'background')
yl2 = [ yl(1)-(yl(2)-yl(1))*0.15 yl(1)-(yl(2)-yl(1))*0.1 ];
tmph = patch([times(1) times(end) times(end) times(1)], ...
[yl2(1) yl2(1) yl2(2) yl2(2)], [1 1 1]); hold on;
ylim([ yl2(1) yl(2)]);
set(tmph, 'edgecolor', [1 1 1]);
end;
if ~isempty(regions)
axes(ax);
in_a_region = 0;
for index=1:length(regions)
if regions(index) && ~in_a_region
tmpreg(1) = times(index);
in_a_region = 1;
end;
if ~regions(index) && in_a_region
tmpreg(2) = times(index);
in_a_region = 0;
if strcmpi(highlightmode, 'background')
tmph = patch([tmpreg(1) tmpreg(2) tmpreg(2) tmpreg(1)], ...
[yl(1) yl(1) yl(2) yl(2)], color1); hold on;
set(tmph, 'edgecolor', color1);
else
tmph = patch([tmpreg(1) tmpreg(2) tmpreg(2) tmpreg(1)], ...
[yl2(1) yl2(1) yl2(2) yl2(2)], color2); hold on;
set(tmph, 'edgecolor', color2);
end;
end;
end;
end;
% reshaping data
% -----------
function [data, frames] = reshape_data(data, frames)
data = squeeze(data);
if min(size(data)) == 1
if (rem(length(data),frames) ~= 0)
error('Length of data vector must be divisible by frames.');
end
data = reshape(data, frames, length(data)/frames);
else
frames = size(data,1);
end
function verboseprintf(verbose, varargin)
if strcmpi(verbose, 'on')
fprintf(varargin{:});
end;
% reshaping data
% -----------
function pvals = compute_pvals(oridat, surrog, tail)
if nargin < 3
tail = 'both';
end;
if myndims(oridat) > 1
if size(oridat,2) ~= size(surrog, 2) | myndims(surrog) == 2
if size(oridat,1) == size(surrog, 1)
surrog = repmat( reshape(surrog, [size(surrog,1) 1 size(surrog,2)]), [1 size(oridat,2) 1]);
elseif size(oridat,2) == size(surrog, 1)
surrog = repmat( reshape(surrog, [1 size(surrog,1) size(surrog,2)]), [size(oridat,1) 1 1]);
else
error('Permutation statistics array size error');
end;
end;
end;
surrog = sort(surrog, myndims(surrog)); % sort last dimension
if myndims(surrog) == 1
surrog(end+1) = oridat;
elseif myndims(surrog) == 2
surrog(:,end+1) = oridat;
elseif myndims(surrog) == 3
surrog(:,:,end+1) = oridat;
else
surrog(:,:,:,end+1) = oridat;
end;
[tmp idx] = sort( surrog, myndims(surrog) );
[tmp mx] = max( idx,[], myndims(surrog));
len = size(surrog, myndims(surrog) );
pvals = 1-(mx-0.5)/len;
if strcmpi(tail, 'both')
pvals = min(pvals, 1-pvals);
pvals = 2*pvals;
end;
function val = myndims(a)
if ndims(a) > 2
val = ndims(a);
else
if size(a,1) == 1,
val = 2;
elseif size(a,2) == 1,
val = 1;
else
val = 2;
end;
end;
|
github
|
lcnbeapp/beapp-master
|
rspdfsolv.m
|
.m
|
beapp-master/Packages/eeglab14_1_2b/functions/timefreqfunc/rspdfsolv.m
| 2,680 |
utf_8
|
f54da2906c104216b972ff3b6bbf6f3e
|
% rspdfsolv() - sub-function used by rsfit() to searc for optimal
% parameter for Ramberg-Schmeiser distribution
%
% Usage: res = rspdfsolv(l, l3, l4)
%
% Input:
% l - [lambda3 lamda4] parameters to optimize
% skew - expected skewness
% kurt - expected kurtosis
%
% Output:
% res - residual
%
% Author: Arnaud Delorme, SCCN, 2003
%
% See also: rsget()
%
% Reference: Ramberg, J.S., Tadikamalla, P.R., Dudewicz E.J., Mykkytka, E.F.
% A probability distribution and its uses in fitting data.
% Technimetrics, 1979, 21: 201-214.
% Copyright (C) 2003 Arnaud Delorme, SCCN, [email protected]
%
% This program is free software; you can redistribute it and/or modify
% it under the terms of the GNU General Public License as published by
% the Free Software Foundation; either version 2 of the License, or
% (at your option) any later version.
%
% This program is distributed in the hope that it will be useful,
% but WITHOUT ANY WARRANTY; without even the implied warranty of
% MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
% GNU General Public License for more details.
%
% You should have received a copy of the GNU General Public License
% along with this program; if not, write to the Free Software
% Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
function res = rspdfsolv( l, a3, a4);
A = 1/(1 + l(1)) - 1/(1 + l(2));
B = 1/(1 + 2*l(1)) + 1/(1 + 2*l(2)) - 2*beta(1+l(1), 1+l(2));
C = 1/(1 + 3*l(1)) - 1/(1 + 3*l(2)) ...
- 3*beta(1+2*l(1), 1+l(2)) + 3*beta(1+l(1), 1+2*l(2));
D = 1/(1 + 4*l(1)) + 1/(1 + 4*l(2)) ...
- 4*beta(1+3*l(1), 1+l(2)) - 4*beta(1+l(1), 1+3*l(2)) ...
+ 6*beta(1+2*l(1), 1+2*l(2));
estim_a3 = (C - 3*A*B + 2*A^3)/(B-A^2)^(3/2);
estim_a4 = (D - 4*A*C + 6*A^2*B - 3*A^4)/(B-A^2)^2;
res = (estim_a3 - a3)^2 + (estim_a4 - a4)^2;
% the last term try to ensures that l(1) and l(2) are of the same sign
if sign(l(1)*l(2)) == -1, res = 2*res; end;
return;
% original equations
% $$$ A = 1(1 + l(3)) - 1/(1 + l(4));
% $$$ B = 1(1 + 2*l(3)) + 1/(1 + 2*l(4)) - 2*beta(1+l(3), 1+l(4));
% $$$ C = 1(1 + 3*l(3)) - 1/(1 + 3*l(4)) ...
% $$$ - 3*beta(1+2*l(3), 1+l(4)) + 3*beta(1+l(3), 1+2*l(4));
% $$$ D = 1(1 + 4*l(3)) + 1/(1 + 4*l(4)) ...
% $$$ - 4*beta(1+3*l(3), 1+l(4)) - 4*beta(1+l(3), 1+3*l(4)) ...
% $$$ + 6*beta(1+2*l(3), 1+2*l(4));
% $$$
% $$$ R(1) = l(1) + A/l(2);
% $$$ R(2) = (B-A^2)/l(2)^2;
% $$$ R(3) = (C - 3*A*B + 2*A^3)/l(2)^3;
% $$$ R(4) = (D - 4*A*C + 6*A^2*B - 3*A^4)/l(2)^4;
|
github
|
lcnbeapp/beapp-master
|
dftfilt.m
|
.m
|
beapp-master/Packages/eeglab14_1_2b/functions/timefreqfunc/dftfilt.m
| 2,686 |
utf_8
|
b950c4302f749a1e9cffcd4c7f4ebe6a
|
% dftfilt() - discrete Fourier filter
%
% Usage:
% >> b = dftfilt(n,W,c,k,q)
%
% Inputs:
% n - number of input samples
% W - maximum angular freq. relative to n, 0 < W <= .5
% c - cycles
% k - oversampling
% q - [0;1] 0->fft, 1->c cycles
%
% Authors: Sigurd Enghoff, Arnaud Delorme & Scott Makeig,
% SCCN/INC/UCSD, La Jolla, 8/1/98
% Copyright (C) 8/1/98 Sigurd Enghoff & Scott Makei, SCCN/INC/UCSD, [email protected]
%
% This program is free software; you can redistribute it and/or modify
% it under the terms of the GNU General Public License as published by
% the Free Software Foundation; either version 2 of the License, or
% (at your option) any later version.
%
% This program is distributed in the hope that it will be useful,
% but WITHOUT ANY WARRANTY; without even the implied warranty of
% MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
% GNU General Public License for more details.
%
% You should have received a copy of the GNU General Public License
% along with this program; if not, write to the Free Software
% Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
% 01-25-02 reformated help & license -ad
% future developments
% -------------------
% input into dftfilt:
% - lowfreq and maxfreq (of interest)
% - lowcycle and maxcyle (ex: 3 cycles at low freq and 10 cycles at maxfreq)
% - the delta in frequency: ex 0.5 Hz
% The function should: compute the number of points (len) automatically
% Warning with FFT compatibility
% Still, something has to be done about the masking so that it would be comaptible
function b = dftfilt(len,maxfreq,cycle,oversmp,wavfact)
count = 1;
for index = 1:1/oversmp:maxfreq*len/cycle % scan frequencies
w(:,count) = j * index * cycle * linspace(-pi+2*pi/len, pi-2*pi/len, len)'; % exp(-w) is a sinus curve
count = count+1; % -2*pi/len ensures that we really scan from -pi to pi without redundance (-pi=+pi)
end;
b = exp(-w);
%srate = 2*pi/len; % Angular increment.
%w = j * cycle * [0:srate:2*pi-srate/2]'; % Column.
%x = 1:1/oversmp:maxfreq*len/cycle; % Row.
%b = exp(-w*x); % Exponentiation of outer product.
for i = 1:size(b,2),
m = round(wavfact*len*(i-1)/(i+oversmp-1)); % Number of elements to discard.
mu = round(m/2); % Number of upper elemnts.
ml = m-round(m/2); % Number of lower elemnts.
b(:,i) = b(:,i) .* [zeros(mu,1) ; hanning(len-m) ; zeros(ml,1)];
end
% syemtric hanning function
function w = hanning(n)
if ~rem(n,2)
w = .5*(1 - cos(2*pi*(1:n/2)'/(n+1)));
w = [w; w(end:-1:1)];
else
w = .5*(1 - cos(2*pi*(1:(n+1)/2)'/(n+1)));
w = [w; w(end-1:-1:1)];
end
|
github
|
lcnbeapp/beapp-master
|
rspfunc.m
|
.m
|
beapp-master/Packages/eeglab14_1_2b/functions/timefreqfunc/rspfunc.m
| 1,468 |
utf_8
|
d6a6d26022ec2e38fa4adca9a28a5dde
|
% rspfunc() - sub-function used by rsget()
%
% Usage: res = rspfunc(pval, l, rval)
%
% Input:
% pval - p-value to optimize
% l - [l1 l2 l3 l4] l-values for Ramberg-Schmeiser distribution
% rval - expected r-value
%
% Output:
% res - residual
%
% Author: Arnaud Delorme, SCCN, 2003
%
% See also: rsget()
%
% Reference: Ramberg, J.S., Tadikamalla, P.R., Dudewicz E.J., Mykkytka, E.F.
% A probability distribution and its uses in fitting data.
% Technimetrics, 1979, 21: 201-214.
% Copyright (C) 2003 Arnaud Delorme, SCCN, [email protected]
%
% This program is free software; you can redistribute it and/or modify
% it under the terms of the GNU General Public License as published by
% the Free Software Foundation; either version 2 of the License, or
% (at your option) any later version.
%
% This program is distributed in the hope that it will be useful,
% but WITHOUT ANY WARRANTY; without even the implied warranty of
% MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
% GNU General Public License for more details.
%
% You should have received a copy of the GNU General Public License
% along with this program; if not, write to the Free Software
% Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
function rp = rspfunc( pval, l, rval);
% for fiting rp with fminsearch
% -----------------------------
rp = l(1) + (pval.^l(3) - (1-pval).^l(4))/l(2);
rp = abs(rval-rp);
|
github
|
lcnbeapp/beapp-master
|
correct_mc.m
|
.m
|
beapp-master/Packages/eeglab14_1_2b/functions/timefreqfunc/correct_mc.m
| 5,698 |
utf_8
|
92f18a363d2fec001a50fafbcf9e06b5
|
% correct_mc() - compute an upper limit for the number of independant
% time-frequency estimate in a given time-frequency image.
% This number can be used to correct for multiple comparisons.
%
% Usage:
% [ncorrect array] = correct_mc( EEG, cycles, maxfreq, timesout);
%
% Inputs:
% EEG - EEGLAB structure
% cycles - [float] same as the cycle input to timef(). Default is [3 0.5].
% freqrange - [float] minimum and maximum frequency. Default is [2 50] Hz.
% timesout - [integer] array of number of time points to test.
%
% Output:
% ncorrect - number of independant tf estimate in the time-freq image
% array - array of size (freqs x timesout) containing pvalues.
%
% Method details:
%
% Dividing by the total number of time-frequency estimate in the 2-D
% time-frequency image decomposition would be too conservative since
% spectral estimates of neighboring time-frequency points are highly
% correlated. One must thus estimate the number of independent
% time-frequency points in the TF image. Here, I used geometrical wavelets
% which are optimal in terms of image compression, so neighboring
% frequencies can be assume to carry independent spectral estimates.
% We thus had time-frequency decompositions at only X frequencies (e.g. 120,
% 60, 30, 15, 7.5, 3.25, 1.625 Hz). For each frequency, I then found
% the minimum number of time points for which there was a significant
% correlation of the spectral estimates between neighboring time points
% (for each frequency and number of time point, I computed the correlation
% from 0 to 1 for all data channel to obtain an a probability distribution
% of correlation; we then fitted this distribution using a 4th order curve
% (Ramberg, J. S., E. J. Dudewicz, et al. (1979). "A probability
% distribution and its uses in fitting data." Technometrics 21(2)) and
% assessed the probability of significance for the value 0 (no correlation)
% to be within the distribution of estimated correlation). For instance,
% using 28 time points at 120 Hz, there was no significant (p>0.05 taking
% into account Bonferoni correction for multiple comparisons) correlation
% between neighboring time-frequency power estimate, but there was a
% significant correlation using 32 time points instead of 28 (p<0.05).
% Applying the same approach for the X geometrical frequencies and summing
% the minimum number of time points for observing a significant correlation
% at all frequencies, ones obtain in general a number below 200 (with the
% defaults above and 3-second data epochs) independent estimates. In all
% the time-frequency plots, one has to used a significance mask at p<0.00025
% (0.05/200). An alternative method for correcting for multiple comparisons
% is presented in Nichols & Holmes, Human Brain Mapping, 2001.
%
% Author: Arnaud Delorme, SCCN, Jan 17, 2004
% Copyright (C) 2004 Arnaud Delorme, SCCN, [email protected]
%
% This program is free software; you can redistribute it and/or modify
% it under the terms of the GNU General Public License as published by
% the Free Software Foundation; either version 2 of the License, or
% (at your option) any later version.
%
% This program is distributed in the hope that it will be useful,
% but WITHOUT ANY WARRANTY; without even the implied warranty of
% MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
% GNU General Public License for more details.
%
% You should have received a copy of the GNU General Public License
% along with this program; if not, write to the Free Software
% Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
function [ncorrect, pval] = correct_mc( EEG, cycles, freqrange, timesout);
if nargin < 1
help correct_mc;
return;
end;
if nargin < 2
cycles = [3 0.5];
end;
if nargin < 3
freqrange = [2 50];
end;
if nargin < 4
% possible number of time outputs
% -------------------------------
timesout = [5 6 7 8 9 10 12 14 16 18 20 24 28 32 36 40];
end;
nfreqs = ceil(log2(freqrange(2)));
% scan times
% ----------
for ti = 1:length(timesout)
clear tmpf
% scan data channels
% ------------------
for index = 1:EEG.nbchan
clf; [ersp,itc,powbase,times,freqs,erspboot,itcboot] = newtimef(EEG.data(index,:),EEG.pnts, ...
[EEG.xmin EEG.xmax]*1000,EEG.srate, cycles, 'timesout', timesout(ti), ...
'freqscale', 'log', 'nfreqs', nfreqs, 'freqrange', freqrange, 'plotitc', 'off', 'plotersp', 'off');
% compute correlation
% -------------------
for fi = 1:length(freqs)
tmp = corrcoef(ersp(fi,1:end-1), ersp(fi,2:end));
tmpf(index,fi) = tmp(2,1);
end;
end;
% fit curve and determine if the result is significant
% ----------------------------------------------------
for fi = 1:length(freqs)
pval(fi, ti) = rsfit(tmpf(:,fi)', 0);
if pval(fi,ti) > 0.9999, pval(fi,ti) = NaN; end;
end;
end;
% find minimum number of points for each frequency
% ------------------------------------------------
ncorrect = 0;
threshold = 0.05 / prod(size(pval));
for fi = 1:size(pval,1)
ti = 1;
while ti <= size(pval,2)
if pval(fi,ti) < threshold
ncorrect = ncorrect + timesout(ti);
ti = size(pval,2)+1;
end;
ti = ti+1;
end;
end;
|
github
|
lcnbeapp/beapp-master
|
pac.m
|
.m
|
beapp-master/Packages/eeglab14_1_2b/functions/timefreqfunc/pac.m
| 21,849 |
utf_8
|
a7d13b249d1c873e24a0f43a7cda2c5c
|
% pac() - compute phase-amplitude coupling (power of first input
% correlation with phase of second). There is no graphical output
% to this function.
%
% Usage:
% >> pac(x,y,srate);
% >> [coh,timesout,freqsout1,freqsout2,cohboot] ...
% = pac(x,y,srate,'key1', 'val1', 'key2', val2' ...);
% Inputs:
% x = [float array] 2-D data array of size (times,trials) or
% 3-D (1,times,trials)
% y = [float array] 2-D or 3-d data array
% srate = data sampling rate (Hz)
%
% Most important optional inputs
% 'method' = ['mod'|'corrsin'|'corrcos'|'latphase'] modulation
% method or correlation of amplitude with sine or cosine of
% angle (see ref). 'laphase' compute the phase
% histogram at a specific time and requires the
% 'powerlat' option to be set.
% 'freqs' = [min max] frequency limits. Default [minfreq 50],
% minfreq being determined by the number of data points,
% cycles and sampling frequency. Use 0 for minimum frequency
% to compute default minfreq. You may also enter an
% array of frequencies for the spectral decomposition
% (for FFT, closest computed frequency will be returned; use
% 'padratio' to change FFT freq. resolution).
% 'freqs2' = [float array] array of frequencies for the second
% argument. 'freqs' is used for the first argument.
% By default it is the same as 'freqs'.
% 'wavelet' = 0 -> Use FFTs (with constant window length) { Default }
% = >0 -> Number of cycles in each analysis wavelet
% = [cycles expfactor] -> if 0 < expfactor < 1, the number
% of wavelet cycles expands with frequency from cycles
% If expfactor = 1, no expansion; if = 0, constant
% window length (as in FFT) {default wavelet: 0}
% = [cycles array] -> cycle for each frequency. Size of array
% must be the same as the number of frequencies
% {default cycles: 0}
% 'wavelet2' = same as 'wavelet' for the second argument. Default is
% same as cycles. Note that if the lowest frequency for X
% and Y are different and cycle is [cycles expfactor], it
% may result in discrepencies in the number of cycles at
% the same frequencies for X and Y.
% 'ntimesout' = Number of output times (int<frames-winframes). Enter a
% negative value [-S] to subsample original time by S.
% 'timesout' = Enter an array to obtain spectral decomposition at
% specific time values (note: algorithm find closest time
% point in data and this might result in an unevenly spaced
% time array). Overwrite 'ntimesout'. {def: automatic}
% 'powerlat' = [float] latency in ms at which to compute phase
% histogram
% 'tlimits' = [min max] time limits in ms.
%
% Optional Detrending:
% 'detrend' = ['on'|'off'], Linearly detrend each data epoch {'off'}
% 'rmerp' = ['on'|'off'], Remove epoch mean from data epochs {'off'}
%
% Optional FFT/DFT Parameters:
% 'winsize' = If cycles==0: data subwindow length (fastest, 2^n<frames);
% If cycles >0: *longest* window length to use. This
% determines the lowest output frequency. Note that this
% parameter is overwritten if the minimum frequency has been set
% manually and requires a longer time window {~frames/8}
% 'padratio' = FFT-length/winframes (2^k) {2}
% Multiplies the number of output frequencies by dividing
% their spacing (standard FFT padding). When cycles~=0,
% frequency spacing is divided by padratio.
% 'nfreqs' = number of output frequencies. For FFT, closest computed
% frequency will be returned. Overwrite 'padratio' effects
% for wavelets. Default: use 'padratio'.
% 'freqscale' = ['log'|'linear'] frequency scale. Default is 'linear'.
% Note that for obtaining 'log' spaced freqs using FFT,
% closest correspondant frequencies in the 'linear' space
% are returned.
% 'subitc' = ['on'|'off'] subtract stimulus locked Inter-Trial Coherence
% (ITC) from x and y. This computes the 'intrinsic' coherence
% x and y not arising from common synchronization to
% experimental events. See notes. {default: 'off'}
% 'itctype' = ['coher'|'phasecoher'] For use with 'subitc', see timef()
% for more details {default: 'phasecoher'}.
% 'subwin' = [min max] sub time window in ms (this windowing is
% performed after the spectral decomposition).
%
% Outputs:
% pac = Matrix (nfreqs1,nfreqs2,timesout) of coherence (complex).
% Use 20*log(abs(crossfcoh)) to vizualize log spectral diffs.
% timesout = Vector of output times (window centers) (ms).
% freqsout1 = Vector of frequency bin centers for first argument (Hz).
% freqsout2 = Vector of frequency bin centers for second argument (Hz).
% alltfX = single trial spectral decomposition of X
% alltfY = single trial spectral decomposition of Y
%
% Author: Arnaud Delorme, SCCN/INC, UCSD 2005-
%
% Ref: Testing for Nested Oscilations (2008) J Neuro Methods 174(1):50-61
%
% See also: timefreq(), crossf()
% Copyright (C) 2002 Arnaud Delorme, Salk Institute, [email protected]
%
% This program is free software; you can redistribute it and/or modify
% it under the terms of the GNU General Public License as published by
% the Free Software Foundation; either version 2 of the License, or
% (at your option) any later version.
%
% This program is distributed in the hope that it will be useful,
% but WITHOUT ANY WARRANTY; without even the implied warranty of
% MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
% GNU General Public License for more details.
%
% You should have received a copy of the GNU General Public License
% along with this program; if not, write to the Free Software
% Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
function [crossfcoh, timesout1, freqs1, freqs2, crossfcohall, alltfX, alltfY] = pac(X, Y, srate, varargin);
if nargin < 1
help pac;
return;
end;
% deal with 3-D inputs
% --------------------
if ndims(X) == 3, X = reshape(X, size(X,2), size(X,3)); end;
if ndims(Y) == 3, Y = reshape(Y, size(Y,2), size(Y,3)); end;
frame = size(X,2);
g = finputcheck(varargin, ...
{ 'alpha' 'real' [0 0.2] [];
'baseboot' 'float' [] 0;
'boottype' 'string' {'times','trials','timestrials'} 'timestrials';
'detrend' 'string' {'on','off'} 'off';
'freqs' 'real' [0 Inf] [0 srate/2];
'freqs2' 'real' [0 Inf] [];
'freqscale' 'string' { 'linear','log' } 'linear';
'itctype' 'string' {'phasecoher','phasecoher2','coher'} 'phasecoher';
'nfreqs' 'integer' [0 Inf] [];
'lowmem' 'string' {'on','off'} 'off';
'method' 'string' { 'mod','corrsin','corrcos','latphase' } 'mod';
'naccu' 'integer' [1 Inf] 250;
'newfig' 'string' {'on','off'} 'on';
'padratio' 'integer' [1 Inf] 2;
'rmerp' 'string' {'on','off'} 'off';
'rboot' 'real' [] [];
'subitc' 'string' {'on','off'} 'off';
'subwin' 'real' [] []; ...
'gammapowerlim' 'real' [] []; ...
'powerlim' 'real' [] []; ...
'powerlat' 'real' [] []; ...
'gammabase' 'real' [] []; ...
'timesout' 'real' [] []; ...
'ntimesout' 'integer' [] 200; ...
'tlimits' 'real' [] [0 frame/srate];
'title' 'string' [] '';
'vert' { 'real','cell' } [] [];
'wavelet' 'real' [0 Inf] 0;
'wavelet2' 'real' [0 Inf] [];
'winsize' 'integer' [0 Inf] max(pow2(nextpow2(frame)-3),4) }, 'pac');
if isstr(g), error(g); end;
% more defaults
% -------------
if isempty(g.wavelet2), g.wavelet2 = g.wavelet; end;
if isempty(g.freqs2), g.freqs2 = g.freqs; end;
% remove ERP if necessary
% -----------------------
X = squeeze(X);
Y = squeeze(Y);X = squeeze(X);
trials = size(X,2);
if strcmpi(g.rmerp, 'on')
X = X - repmat(mean(X,2), [1 trials]);
Y = Y - repmat(mean(Y,2), [1 trials]);
end;
% perform timefreq decomposition
% ------------------------------
[alltfX freqs1 timesout1] = timefreq(X, srate, 'ntimesout', g.ntimesout, 'timesout', g.timesout, 'winsize', g.winsize, ...
'tlimits', g.tlimits, 'detrend', g.detrend, 'itctype', g.itctype, ...
'subitc', g.subitc, 'wavelet', g.wavelet, 'padratio', g.padratio, ...
'freqs', g.freqs, 'freqscale', g.freqscale, 'nfreqs', g.nfreqs);
[alltfY freqs2 timesout2] = timefreq(Y, srate, 'ntimesout', g.ntimesout, 'timesout', g.timesout, 'winsize', g.winsize, ...
'tlimits', g.tlimits, 'detrend', g.detrend, 'itctype', g.itctype, ...
'subitc', g.subitc, 'wavelet', g.wavelet2, 'padratio', g.padratio, ...
'freqs', g.freqs2, 'freqscale', g.freqscale, 'nfreqs', g.nfreqs);
% check time limits
% -----------------
if ~isempty(g.subwin)
ind1 = find(timesout1 > g.subwin(1) & timesout1 < g.subwin(2));
ind2 = find(timesout2 > g.subwin(1) & timesout2 < g.subwin(2));
alltfX = alltfX(:, ind1, :);
alltfY = alltfY(:, ind2, :);
timesout1 = timesout1(ind1);
timesout2 = timesout2(ind2);
end;
if length(timesout1) ~= length(timesout2) | any( timesout1 ~= timesout2)
disp('Warning: Time points are different for X and Y. Use ''timesout'' to specify common time points');
[vals ind1 ind2 ] = intersect_bc(timesout1, timesout2);
fprintf('Searching for common time points: %d found\n', length(vals));
if length(vals) < 10, error('Less than 10 common data points'); end;
timesout1 = vals;
timesout2 = vals;
alltfX = alltfX(:, ind1, :);
alltfY = alltfY(:, ind2, :);
end;
% scan accross frequency and time
% -------------------------------
%if isempty(g.alpha)
% disp('Warning: if significance mask is not applied, result might be slightly')
% disp('different (since angle is not made uniform and amplitude interpolated)')
%end;
cohboot =[];
if ~strcmpi(g.method, 'latphase')
for find1 = 1:length(freqs1)
for find2 = 1:length(freqs2)
for ti = 1:length(timesout1)
% get data
% --------
tmpalltfx = squeeze(alltfX(find1,ti,:));
tmpalltfy = squeeze(alltfY(find2,ti,:));
%if ~isempty(g.alpha)
% tmpalltfy = angle(tmpalltfy);
% tmpalltfx = abs( tmpalltfx);
% [ tmp cohboot(find1,find2,ti,:) newamp newangle ] = ...
% bootcircle(tmpalltfx, tmpalltfy, 'naccu', g.naccu);
% crossfcoh(find1,find2,ti) = sum ( newamp .* exp(j*newangle) );
%else
tmpalltfy = angle(tmpalltfy);
tmpalltfx = abs( tmpalltfx);
if strcmpi(g.method, 'mod')
crossfcoh(find1,find2,ti) = sum( tmpalltfx .* exp(j*tmpalltfy) );
elseif strcmpi(g.method, 'corrsin')
tmp = corrcoef( sin(tmpalltfy), tmpalltfx);
crossfcoh(find1,find2,ti) = tmp(2);
else
tmp = corrcoef( cos(tmpalltfy), tmpalltfx);
crossfcoh(find1,find2,ti) = tmp(2);
end;
end;
end;
end;
elseif 1
% this option computes power at a given latency
% then computes the same as above (vectors)
%if isempty(g.powerlat)
% error('You need to specify a latency for the ''powerlat'' option');
%end;
gammapower = mean(10*log10(alltfX(:,:,:).*conj(alltfX)),1); % average all frequencies for power
if isempty(g.gammapowerlim)
g.gammapowerlim = [ min(gammapower(:)) max(gammapower(:)) ];
end;
fprintf('Gamma power limits: %3.2f to %3.2f\n', g.gammapowerlim(1), g.gammapowerlim(2));
power = 10*log10(alltfY(:,:,:).*conj(alltfY));
if isempty(g.powerlim)
for freq = 1:size(power,1)
g.powerlim(freq,:) = [ min(power(freq,:)) max(power(freq,:)) ];
end;
end;
for freq = 1:size(power,1)
fprintf('Freq %d power limits: %3.2f to %3.2f\n', freqs2(freq), g.powerlim(freq,1), g.powerlim(freq,2));
end;
% power plot
%figure; plot(timesout2/1000, (mean(power(9,:,:),3)-mean(power(9,:)))/50);
%hold on; plot(linspace(0, length(Y)/srate, length(Y)), mean(Y'), 'g');
% phase with power
% figure; plot(timesout2/1000, (mean(phaseangle(9,:,:),3)-mean(phaseangle(9,:)))/50);
% hold on; plot(timesout1/1000, (mean(gammapower,3)-mean(gammapower(:)))/100, 'r');
%figure; plot((mean(phaseangle(9,:,:),3)-mean(phaseangle(9,:)))/50+j*(mean(gammapower,3)-mean(gammapower(:)))/100, '.');
matsize = 32;
matcenter = (matsize-1)/2+1;
matrixfinalgammapower = zeros(size(alltfY,1),size(alltfX,3),matsize,matsize);
matrixfinalcount = zeros(size(alltfY,1),size(alltfX,3),matsize,matsize);
% get power indices
if isempty(g.gammabase)
g.gammabase = mean(gammapower(:));
end;
fprintf('Gamma power average: %3.2f\n', g.gammabase);
gammapoweradd = gammapower-g.gammabase;
gammapower = floor((gammapower-g.gammapowerlim(1))/(g.gammapowerlim(2)-g.gammapowerlim(1))*(matsize-2))+1;
phaseangle = angle(alltfY);
posx = zeros(size(power));
posy = zeros(size(power));
for freq = 1:length(freqs2)
fprintf('Processing frequency %3.2f\n', freqs2(freq));
power(freq,:,:) = (power(freq,:,:)-g.powerlim(freq,1))/(g.powerlim(freq,2)-g.powerlim(freq,1))*(matsize-3)/2+1;
complexval = power(freq,:,:).*exp(j*phaseangle(freq,:,:));
posx(freq,:,:) = round(real(complexval)+matcenter);
posy(freq,:,:) = round(imag(complexval)+matcenter);
for trial = 1:size(alltfX,3) % scan trials
for time = 1:size(alltfX,2)
%matrixfinal(freq,posx(freq,time,trial),posy(freq,time,trial),gammapower(1,time,trial)) = ...
% matrixfinal(freq,posx(freq,time,trial),posy(freq,time,trial),gammapower(1,time,trial))+1;
matrixfinalgammapower(freq,trial,posx(freq,time,trial),posy(freq,time,trial)) = ...
matrixfinalgammapower(freq,trial,posx(freq,time,trial),posy(freq,time,trial))+gammapoweradd(1,time,trial);
matrixfinalcount(freq,trial,posx(freq,time,trial),posy(freq,time,trial)) = ...
matrixfinalcount(freq,trial,posx(freq,time,trial),posy(freq,time,trial))+1;
end;
end;
%matrixfinal(freq,:,:,:) = convn(squeeze(matrixfinal(freq,:,:,:)), gs, 'same');
%tmpmat = posx(index,:)+(posy(index,:)-1)*64+(gammapower(:)-1)*64*64;
matrixfinalcount(freq, find(matrixfinalcount(freq,:) == 0)) = 1;
matrixfinalgammapower(freq,:,:,:) = matrixfinalgammapower(freq,:,:,:)./matrixfinalcount(freq,:,:,:);
end;
% average and smooth
matrixfinalgammapowermean = squeeze(mean(matrixfinalgammapower,2));
for freq = 1:length(freqs2)
matrixfinalgammapowermean(freq,:,:) = conv2(squeeze(matrixfinalgammapowermean(freq,:,:)), gauss2d(5,5), 'same');
end;
%matrixfinalgammapower = matrixfinalgammapower/size(alltfX,3)/size(alltfX,2);
%vect = linspace(-pi,pi,50);
%for f = 1:length(freqs2)
% crossfcoh(f,:) = hist(tmpalltfy(f,:), vect);
%end;
% smoothing of output image
% -------------------------
%gs = gauss2d(6, 6, 6);
%crossfcoh = convn(crossfcoh, gs, 'same');
%freqs1 = freqs2;
%timesout1 = linspace(-180, 180, size(crossfcoh,2));
crossfcoh = matrixfinalgammapowermean;
crossfcohall = matrixfinalgammapower;
else
% this option computes power at a given latency
% then computes the same as above (vectors)
%if isempty(g.powerlat)
% error('You need to specify a latency for the ''powerlat'' option');
%end;
gammapower = mean(10*log10(alltfX(:,:,:).*conj(alltfX)),1); % average all frequencies for power
if isempty(g.gammapowerlim)
g.gammapowerlim = [ min(gammapower(:)) max(gammapower(:)) ];
end;
power = 10*log10(alltfY(:,:,:).*conj(alltfY));
if isempty(g.powerlim)
for freq = 1:size(power,1)
g.powerlim(freq,:) = [ min(power(freq,:)) max(power(freq,:)) ];
end;
end;
% power plot
%figure; plot(timesout2/1000, (mean(power(9,:,:),3)-mean(power(9,:)))/50);
%hold on; plot(linspace(0, length(Y)/srate, length(Y)), mean(Y'), 'g');
% phase with power
% figure; plot(timesout2/1000, (mean(phaseangle(9,:,:),3)-mean(phaseangle(9,:)))/50);
% hold on; plot(timesout1/1000, (mean(gammapower,3)-mean(gammapower(:)))/100, 'r');
%figure; plot((mean(phaseangle(9,:,:),3)-mean(phaseangle(9,:)))/50+j*(mean(gammapower,3)-mean(gammapower(:)))/100, '.');
matsize = 64;
matcenter = (matsize-1)/2+1;
matrixfinal = zeros(size(alltfY,1),64,64,64);
matrixfinalgammapower = zeros(size(alltfY,1),matsize,matsize);
matrixfinalcount = zeros(size(alltfY,1),matsize,matsize);
% get power indices
gammapoweradd = gammapower-mean(gammapower(:));
gammapower = floor((gammapower-g.gammapowerlim(1))/(g.gammapowerlim(2)-g.gammapowerlim(1))*(matsize-1))+1;
phaseangle = angle(alltfY);
posx = zeros(size(power));
posy = zeros(size(power));
gs = gauss3d(6, 6, 6);
for freq = 1:size(alltfY)
fprintf('Processing frequency %3.2f\n', freqs2(freq));
power(freq,:,:) = (power(freq,:,:)-g.powerlim(freq,1))/(g.powerlim(freq,2)-g.powerlim(freq,1))*(matsize-2)/2;
complexval = power(freq,:,:).*exp(j*phaseangle(freq,:,:));
posx(freq,:,:) = round(real(complexval)+matcenter);
posy(freq,:,:) = round(imag(complexval)+matcenter);
for trial = 1:size(alltfX,3) % scan trials
for time = 1:size(alltfX,2)
%matrixfinal(freq,posx(freq,time,trial),posy(freq,time,trial),gammapower(1,time,trial)) = ...
% matrixfinal(freq,posx(freq,time,trial),posy(freq,time,trial),gammapower(1,time,trial))+1;
matrixfinalgammapower(freq,posx(freq,time,trial),posy(freq,time,trial)) = ...
matrixfinalgammapower(freq,posx(freq,time,trial),posy(freq,time,trial))+gammapoweradd(1,time,trial);
matrixfinalcount(freq,posx(freq,time,trial),posy(freq,time,trial)) = ...
matrixfinalcount(freq,posx(freq,time,trial),posy(freq,time,trial))+1;
end;
end;
%matrixfinal(freq,:,:,:) = convn(squeeze(matrixfinal(freq,:,:,:)), gs, 'same');
%tmpmat = posx(index,:)+(posy(index,:)-1)*64+(gammapower(:)-1)*64*64;
matrixfinalcount(freq, find(matrixfinalcount(freq,:) == 0)) = 1;
matrixfinalgammapower(freq,:,:) = matrixfinalgammapower(freq,:,:)./matrixfinalcount(freq, :,:);
matrixfinalgammapower(freq,:,:) = conv2(squeeze(matrixfinalgammapower(freq,:,:)), gauss2d(5,5), 'same');
end;
%matrixfinalgammapower = matrixfinalgammapower/size(alltfX,3)/size(alltfX,2);
%vect = linspace(-pi,pi,50);
%for f = 1:length(freqs2)
% crossfcoh(f,:) = hist(tmpalltfy(f,:), vect);
%end;
% smoothing of output image
% -------------------------
%gs = gauss2d(6, 6, 6);
%crossfcoh = convn(crossfcoh, gs, 'same');
%freqs1 = freqs2;
%timesout1 = linspace(-180, 180, size(crossfcoh,2));
crossfcoh = matrixfinalgammapower;
end;
% 7/31/2014 Ramon: crossfcohall sometimes does not exist depending on choice of input options
if ~exist('crossfcohall', 'var')
crossfcohall = [];
end
|
github
|
lcnbeapp/beapp-master
|
bootstat.m
|
.m
|
beapp-master/Packages/eeglab14_1_2b/functions/timefreqfunc/bootstat.m
| 20,825 |
utf_8
|
406a9744b6812cd9f9f1eed16ca63e82
|
% bootstat() - accumulate surrogate data to assess significance by permutation of some
% measure of two input variables.
%
% If 'distfit','on', fits the psd with a 4th-order polynomial using the
% data kurtosis, as in Ramberg, J.S., Tadikamalla, P.R., Dudewicz E.J.,
% Mykkytka, E.F. "A probability distribution and its uses in fitting data."
% Technometrics, 21:201-214, 1979.
% Usage:
% >> [rsignif,rboot] = bootstat( { arg1 arg2 ...}, formula, varargin ...);
% Inputs:
% arg1 - [array] 1-D, 2-D or 3-D array of values
% arg2 - [array] 1-D, 2-D or 3-D array of values
% formula - [string] formula to compute the given measure. Takes arguments
% 'arg1', 'arg2' as inputs and 'res' (result, by default) as output.
% For data arrays of more than 1 dimension, the formula must be iterative
% so that shuffling can occur at each step while scanning the last
% array dimension. Examples:
% 'res = arg1 - arg2' % difference of two 1-D data arrays
% 'res = mean( arg1 .* arg2)' % mean projection of two 1-D data arrays
% 'res = res + arg1 .* conj(arg2)' % iterative, for use with 2|3-D arrays
% Optional inputs:
% 'boottype ' - ['rand'|'shuffle']
% 'rand' = do not shuffle data. Only flip polarity randomly (for real
% number) or phase (for complex numbers).
% 'shuffle' = shuffle values of first argument (see two options below).
% Default.
% 'shuffledim' - [integer] indices of dimensions to shuffle. For instance, [1 2] will
% shuffle the first two dimensions. Default is to shuffle along
% dimension 2.
% 'shufflemode' - ['swap'|'regular'] shuffle mode. Either swap dimensions (for instance
% swap rows then columns if dimension [1 2] are selected) or shuffle
% in each dimension independently (slower). If only one dimension is
% selected for shuffling, this option does not change the result.
% 'randmode' - ['opposite'|'inverse'] randomize sign (or phase for complex number,
% or randomly set half the value to reference.
% 'alpha' - [real] significance level (between 0 and 1) {default 0.05}.
% 'naccu' - [integer] number of exemplars to accumulate {default 200}.
% 'bootside' - ['both'|'upper'] side of the surrogate distribution to
% consider for significance. This parameter affects the size
% of the last dimension of the accumulation array ('accres')
% (size is 2 for 'both' and 1 for 'upper') {default: 'both'}.
% 'basevect' - [integer vector] time vector indices for baseline in second dimension.
% {default: all time points}.
% 'rboot' - accumulation array (from a previous call). Allows faster
% computation of the 'rsignif' output {default: none}.
% 'formulaout' - [string] name of the computed variable {default: 'res'}.
% 'dimaccu' - [integer] use dimension in result to accumulate data.
% For instance if the result array is size [60x50] and this value is 2,
% the function will consider than 50 times 60 value have been accumulated.
%
% Fitting distribution:
% 'distfit' - ['on'|'off'] fit distribution with known function to compute more accurate
% limits or exact p-value (see 'vals' option). The MATLAB statistical toolbox
% is required. This option is currently implemented only for 1-D data.
% 'vals' - [float array] significance values. 'alpha' is ignored and
% rsignif returns the p-values. Requires 'distfit' (see above).
% This option currently implemented only for 1-D data.
% 'correctp' - [phat pci zerofreq] parameters for correcting for a biased probability
% distribution (requires 'distfit' above). See help of correctfit().
% Outputs:
% rsignif - significance arrays. 2 values (low high) for each point (use
% 'alpha' to change these limits).
% rboot - accumulated surrogate data values.
%
% Authors: Arnaud Delorme, Bhaktivedcanta Institute, Mumbai, India, Nov 2004
%
% See also: timef()
% NOTE: There is an undocumented parameter, 'savecoher', [0|1]
% HELP TEXT REMOVED: (Ex: Using option 'both', coherence during baseline would be
% ignored since times are shuffled during each accumulation.
% Copyright (C) 9/2002 Arnaud Delorme & Scott Makeig, SCCN/INC/UCSD
%
% This program is free software; you can redistribute it and/or modify
% it under the terms of the GNU General Public License as published by
% the Free Software Foundation; either version 2 of the License, or
% (at your option) any later version.
%
% This program is distributed in the hope that it will be useful,
% but WITHOUT ANY WARRANTY; without even the implied warranty of
% MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
% GNU General Public License for more details.
%
% You should have received a copy of the GNU General Public License
% along with this program; if not, write to the Free Software
% Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
% *************************************
% To fit the psd with as 4th order polynomial using the distribution kurtosis,
% Reference: Ramberg, J.S., Tadikamalla, P.R., Dudewicz E.J., Mykkytka, E.F.
% "A probability distribution and its uses in fitting data."
% Technimetrics, 1979, 21: 201-214.
% *************************************
function [accarrayout, Rbootout, Rbootout2] = bootstat(oriargs, formula, varargin)
% nb_points, timesout, naccu, baselength, baseboot, boottype, alpha, rboot);
if nargin < 2
help bootstat;
return;
end;
if ~isstr(formula)
error('The second argument must be a string formula');
end;
g = finputcheck(varargin, ...
{ 'dims' 'integer' [] []; ...
'naccu' 'integer' [0 10000] 200; ...
'bootside' 'string' { 'both','upper' } 'both'; ...
'basevect' 'integer' [] []; ...
'boottype' 'string' { 'rand','shuffle' } 'shuffle'; ...
'shufflemode' 'string' { 'swap','regular' } 'swap'; ...
'randmode' 'string' { 'opposite','inverse' } 'opposite'; ...
'shuffledim' 'integer' [0 Inf] []; ...
'label' 'string' [] formula; ...
'alpha' 'real' [0 1] 0.05; ...
'vals' 'real' [] []; ...
'distfit' 'string' {'on','off' } 'off'; ...
'dimaccu' 'integer' [1 Inf] []; ...
'correctp' 'real' [] []; ...
'rboot' 'real' [] NaN });
if isstr(g)
error(g);
end;
if isempty(g.shuffledim) & strcmpi(g.boottype, 'rand')
g.shuffledim = [];
elseif isempty(g.shuffledim)
g.shuffledim = 2;
end;
unitname = '';
if 2/g.alpha > g.naccu
if strcmpi(g.distfit, 'off') | ~((size(oriarg1,1) == 1 | size(oriarg1,2) == 1) & size(oriarg1,3) == 1)
g.naccu = 2/g.alpha;
fprintf('Adjusting naccu to compute alpha value');
end;
end;
if isempty(g.rboot)
g.rboot = NaN;
end;
% function for bootstrap computation
% ----------------------------------
if ~iscell(oriargs) | length(oriargs) == 1,
oriarg1 = oriargs;
oriarg2 = [];
else
oriarg1 = oriargs{1};
oriarg2 = oriargs{2};
end;
[nb_points times trials] = size(oriarg1);
if times == 1, disp('Warning 1 value only for shuffling dimension'); end;
% only consider baseline
% ----------------------
if ~isempty(g.basevect)
fprintf('\nPermutation statistics baseline length is %d (out of %d) points\n', length(g.basevect), times);
arg1 = oriarg1(:,g.basevect,:);
if ~isempty(oriarg2)
arg2 = oriarg2(:,g.basevect,:);
end;
else
arg1 = oriarg1;
arg2 = oriarg2;
end;
% formula for accumulation array
% ------------------------------
% if g.dimaccu is not empty, accumulate over that dimension
% of the resulting array to speed up computation
formula = [ 'res=' formula ];
g.formulapost = [ 'if index == 1, ' ...
' if ~isempty(g.dimaccu), ' ...
' Rbootout= zeros([ ceil(g.naccu/size(res,g.dimaccu)) size( res ) ]);' ...
' else,' ...
' Rbootout= zeros([ g.naccu size( res ) ]);' ...
' end;' ...
'end,' ...
'Rbootout(count,:,:,:) = res;' ...
'count = count+1;' ...
'if ~isempty(g.dimaccu), ' ...
' index = index + size(res,g.dimaccu);' ...
' fprintf(''%d '', index-1);' ...
'else ' ...
' index=index+1;' ...
' if rem(index,10) == 0, fprintf(''%d '', index); end;' ...
' if rem(index,100) == 0, fprintf(''\n''); end;' ...
'end;' ];
% **************************
% case 1: precomputed values
% **************************
if ~isnan(g.rboot)
Rbootout = g.rboot;
% ***********************************
% case 2: randomize polarity or phase
% ***********************************
elseif strcmpi(g.boottype, 'rand') & strcmpi(g.randmode, 'inverse')
fprintf('Bootstat function: randomize inverse values\n');
fprintf('Processing permutation statistics for %s (naccu=%d):', g.label, g.naccu);
% compute random array
% --------------------
multarray = ones(size(arg1));
totlen = prod(size(arg1));
if isreal(arg1),
multarray(1:round(totlen/2)) = 0;
end;
for shuff = 1:ndims(multarray)
multarray = supershuffle(multarray,shuff); % initial shuffling
end;
if isempty(g.shuffledim), g.shuffledim = 1:ndims(multarray); end;
invarg1 = 1./arg1;
% accumulate
% ----------
index = 1;
count = 1;
while index <= g.naccu
for shuff = g.shuffledim
multarray = supershuffle(multarray,shuff);
end;
tmpinds = find(reshape(multarray, 1, prod(size(multarray))));
arg1 = oriarg1;
arg1(tmpinds) = invarg1(tmpinds);
eval([ formula ';' ]);
eval( g.formulapost ); % also contains index = index+1
end
elseif strcmpi(g.boottype, 'rand') % opposite
fprintf('Bootstat function: randomize polarity or phase\n');
fprintf('Processing permutation statistics for %s (naccu=%d):', g.label, g.naccu);
% compute random array
% --------------------
multarray = ones(size(arg1));
totlen = prod(size(arg1));
if isreal(arg1),
multarray(1:round(totlen/2)) = -1;
else
tmparray = exp(j*linspace(0,2*pi,totlen+1));
multarray(1:totlen) = tmparray(1:end-1);
end;
for shuff = 1:ndims(multarray)
multarray = supershuffle(multarray,shuff); % initial shuffling
end;
if isempty(g.shuffledim), g.shuffledim = 1:ndims(multarray); end;
% accumulate
% ----------
index = 1;
count = 1;
while index <= g.naccu
for shuff = g.shuffledim
multarray = supershuffle(multarray,shuff);
end;
arg1 = arg1.*multarray;
eval([ formula ';' ]);
eval( g.formulapost ); % also contains index = index+1
end
% ********************************************
% case 3: shuffle vector of only one dimension
% ********************************************
elseif length(g.shuffledim) == 1
fprintf('Bootstat function: shuffling along dimension %d only\n', g.shuffledim);
fprintf('Processing permutation statistics for %s (naccu=%d):', g.label, g.naccu);
index = 1;
count = 1;
while index <= g.naccu
arg1 = shuffleonedim(arg1,g.shuffledim);
eval([ formula ';' ]);
eval( g.formulapost );
end
% ***********************************************
% case 5: shuffle vector along several dimensions
% ***********************************************
else
if strcmpi(g.shufflemode, 'swap') % swap mode
fprintf('Bootstat function: shuffling along dimension %s (swap mode)\n', int2str(g.shuffledim));
fprintf('Processing permutation statistics for %s (naccu=%d):', g.label, g.naccu);
index = 1;
count = 1;
while index <= g.naccu
for shuff = g.shuffledim
arg1 = supershuffle(arg1,shuff);
end;
eval([ formula ';' ]);
eval( g.formulapost );
end
else % regular shuffling
fprintf('Bootstat function: shuffling along dimension %s (regular mode)\n', int2str(g.shuffledim));
fprintf('Processing permutation statistics for %s (naccu=%d):', g.label, g.naccu);
index = 1;
count = 1;
while index <= g.naccu
for shuff = g.shuffledim
arg1 = shuffleonedim(arg1,shuff);
end;
eval([ formula ';' ]);
eval( g.formulapost );
end
end;
end;
Rbootout(count:end,:,:,:) = [];
% **********************
% assessing significance
% **********************
% get accumulation array
% ----------------------
accarray = Rbootout;
if ~isreal(accarray)
accarray = sqrt(accarray .* conj(accarray)); % faster than abs()
end;
% reshape the output if necessary
% -------------------------------
if ~isempty(g.dimaccu)
if g.dimaccu+1 == 3
accarray = permute( accarray, [1 3 2]);
end;
accarray = reshape( accarray, size(accarray,1)*size(accarray,2), size(accarray,3) );
end;
if size(accarray,1) == 1, accarray = accarray'; end; % first dim contains g.naccu
% ******************************************************
% compute thresholds on array not fitting a distribution
% ******************************************************
if strcmpi(g.distfit, 'off')
% compute bootstrap significance level
% ------------------------------------
accarray = sort(accarray,1); % always sort on naccu
Rbootout2 = accarray;
i = round(size(accarray,1)*g.alpha);
accarray1 = squeeze(mean(accarray(size(accarray,1)-i+1:end,:,:),1));
accarray2 = squeeze(mean(accarray(1:i ,:,:),1));
if abs(accarray(1,1,1) - accarray(end,1,1)) < abs(accarray(1,1,1))*1e-15
accarray1(:) = NaN;
accarray2(:) = NaN;
end;
else
% *******************
% fit to distribution
% *******************
sizerboot = size (accarray);
accarray1 = zeros(sizerboot(2:end));
accarray2 = zeros(sizerboot(2:end));
if ~isempty(g.vals{index})
if ~all(size(g.vals{index}) == sizerboot(2:end) )
error('For fitting, vals must have the same dimension as the output array (try transposing)');
end;
end;
% fitting with Ramberg-Schmeiser distribution
% -------------------------------------------
if ~isempty(g.vals{index}) % compute significance for value
for index1 = 1:size(accarrayout,1)
for index2 = 1:size(accarrayout,2)
accarray1(index1,index2) = 1 - rsfit(squeeze(accarray(:,index1,index2)), g.vals{index}(index1, index2));
if length(g.correctp) == 2
accarray1(index1,index2) = correctfit(accarray1, 'gamparams', [g.correctp 0]); % no correction for p=0
else
accarray1(index1,index2) = correctfit(accarray1, 'gamparams', g.correctp);
end;
end;
end;
else % compute value for significance
for index1 = 1:size(accarrayout,1)
for index2 = 1:size(accarrayout,2)
[p c l chi2] = rsfit(Rbootout(:),0);
pval = g.alpha; accarray1(index1,index2) = l(1) + (pval.^l(3) - (1-pval).^l(4))/l(2);
pval = 1-g.alpha; accarray2(index1,index2) = l(1) + (pval.^l(3) - (1-pval).^l(4))/l(2);
end;
end;
end;
% plot results
% -------------------------------------
% figure;
% hist(abs(Rbootout)); tmpax = axis;
% hold on;
% valcomp = linspace(min(abs(Rbootout(:))), max(abs(Rbootout(:))), 100);
% normy = normpdf(valcomp, mu, sigma);
% plot(valcomp, normy/max(normy)*tmpax(4), 'r');
% return;
end;
% set output array: backward compatible
% -------------------------------------
if strcmpi(g.bootside, 'upper'); % only upper significance
accarrayout = accarray1;
else
if size(accarray1,1) ~= 1 & size(accarray1,2) ~= 1
accarrayout = accarray2;
accarrayout(:,:,2) = accarray1;
else
accarrayout = [ accarray2(:) accarray1(:) ];
end;
end;
accarrayout = squeeze(accarrayout);
if size(accarrayout,1) == 1 & size(accarrayout,3) == 1, accarrayout = accarrayout'; end;
% better but not backward compatible
% ----------------------------------
% accarrayout = { accarray1 accarray2 };
return;
% fitting with normal distribution (deprecated)
% --------------------------------
[mu sigma] = normfit(abs(Rbootout(:)));
accarrayout = 1 - normcdf(g.vals, mu, sigma); % cumulative density distribution
% formula of normal distribution
% y = 1/sqrt(2) * exp( -(x-mu).^2/(sigma*sigma*2) ) / (sqrt(pi)*sigma);
% % Gamma and Beta fits:
% elseif strcmpi(g.distfit, 'gamma')
% [phatgam pcigam] = gamfit(abs(Rbootout(:)));
% gamy = gampdf(valcomp, phatgam(1), pcigam(2))
% p = 1 - gamcdf(g.vals, phatgam(1), pcigam(2)); % cumulative density distribution
% elseif strcmpi(g.distfit, 'beta')
% [phatbeta pcibeta] = betafit(abs(Rbootout(:)));
% betay = betapdf(valcomp, phatbeta(1), pcibeta(1));
% p = 1 - betacdf(g.vals, phatbeta(1), pcibeta(1)); % cumulative density distribution
% end
if strcmpi(g.distfit, 'off')
tmpsort = sort(Rbootout);
i = round(g.alpha*g.naccu);
sigval = [mean(tmpsort(1:i)) mean(tmpsort(g.naccu-i+1:g.naccu))];
if strcmpi(g.bootside, 'upper'), sigval = sigval(2); end;
accarrayout = sigval;
end;
% this shuffling preserve the number of -1 and 1
% for cloumns and rows (assuming matrix size is multiple of 2
% -----------------------------------------------------------
function array = supershuffle(array, dim)
if size(array, 1) == 1 | size(array,2) == 1
array = shuffle(array);
return;
end;
if size(array, dim) == 1, return; end;
if dim == 1
indrows = shuffle(1:size(array,1));
for index = 1:2:length(indrows)-rem(length(indrows),2) % shuffle rows
tmparray = array(indrows(index),:,:);
array(indrows(index),:,:) = array(indrows(index+1),:,:);
array(indrows(index+1),:,:) = tmparray;
end;
elseif dim == 2
indcols = shuffle(1:size(array,2));
for index = 1:2:length(indcols)-rem(length(indcols),2) % shuffle colums
tmparray = array(:,indcols(index),:);
array(:,indcols(index),:) = array(:,indcols(index+1),:);
array(:,indcols(index+1),:) = tmparray;
end;
else
ind3d = shuffle(1:size(array,3));
for index = 1:2:length(ind3d)-rem(length(ind3d),2) % shuffle colums
tmparray = array(:,:,ind3d(index));
array(:,:,ind3d(index)) = array(:,:,ind3d(index+1));
array(:,:,ind3d(index+1)) = tmparray;
end;
end;
% shuffle one dimension, one row/colums at a time
% -----------------------------------------------
function array = shuffleonedim(array, dim)
if size(array, 1) == 1 | size(array,2) == 1
array = shuffle(array, dim);
else
if dim == 1
for index1 = 1:size(array,3)
for index2 = 1:size(array,2)
array(:,index2,index1) = shuffle(array(:,index2,index1));
end;
end;
elseif dim == 2
for index1 = 1:size(array,3)
for index2 = 1:size(array,1)
array(index2,:,index1) = shuffle(array(index2,:,index1));
end;
end;
else
for index1 = 1:size(array,1)
for index2 = 1:size(array,2)
array(index1,index2,:) = shuffle(array(index1,index2,:));
end;
end;
end;
end;
|
github
|
lcnbeapp/beapp-master
|
timefreq.m
|
.m
|
beapp-master/Packages/eeglab14_1_2b/functions/timefreqfunc/timefreq.m
| 33,427 |
utf_8
|
dc70f7b5afd51d05bcf926a934072865
|
% timefreq() - compute time/frequency decomposition of data trials. This
% function is a compute-only function called by
% the more complete time/frequency functions newtimef()
% and newcrossf() which also plot timefreq() results.
%
% Usage:
% >> [tf, freqs, times] = timefreq(data, srate);
% >> [tf, freqs, times, itcvals] = timefreq(data, srate, ...
% 'key1', 'val1', 'key2', 'val2' ...)
% Inputs:
% data = [float array] 2-D data array of size (times,trials)
% srate = sampling rate
%
% Optional inputs:
% 'cycles' = [real] indicates the number of cycles for the
% time-frequency decomposition {default: 0}
% if 0, use FFTs and Hanning window tapering.
% or [real positive scalar] Number of cycles in each Morlet
% wavelet, constant across frequencies.
% or [cycles cycles(2)] wavelet cycles increase with
% frequency starting at cycles(1) and,
% if cycles(2) > 1, increasing to cycles(2) at
% the upper frequency,
% or if cycles(2) = 0, same window size at all
% frequencies (similar to FFT if cycles(1) = 1)
% or if cycles(2) = 1, not increasing (same as giving
% only one value for 'cycles'). This corresponds to pure
% wavelet with the same number of cycles at each frequencies
% if 0 < cycles(2) < 1, linear variation in between pure
% wavelets (1) and FFT (0). The exact number of cycles
% at the highest frequency is indicated on the command line.
% 'wavelet' = DEPRECATED, please use 'cycles'. This function does not
% support multitaper. For multitaper, use timef().
% 'wletmethod' = ['dftfilt2'|'dftfilt3'] Wavelet method/program to use.
% {default: 'dftfilt3'}
% 'dftfilt' DEPRECATED. Method used in regular timef()
% program. Not available any more.
% 'dftfilt2' Morlet-variant or Hanning DFT (calls dftfilt2()
% to generate wavelets).
% 'dftfilt3' Morlet wavelet or Hanning DFT (exact Tallon
% Baudry). Calls dftfilt3().
% 'ffttaper' = ['none'|'hanning'|'hamming'|'blackmanharris'] FFT tapering
% function. Default is 'hanning'. Note that 'hamming' and
% 'blackmanharris' require the signal processing toolbox.
% Optional ITC type:
% 'type' = ['coher'|'phasecoher'] Compute either linear coherence
% ('coher') or phase coherence ('phasecoher') also known
% as phase coupling factor' {default: 'phasecoher'}.
% 'subitc' = ['on'|'off'] subtract stimulus locked Inter-Trial Coherence
% (ITC) from x and y. This computes the 'intrinsic' coherence
% x and y not arising from common synchronization to
% experimental events. See notes. {default: 'off'}
%
% Optional detrending:
% 'detrend' = ['on'|'off'], Linearly detrend each data epoch {'off'}
%
% Optional FFT/DFT parameters:
% 'tlimits' = [min max] time limits in ms.
% 'winsize' = If cycles==0 (FFT, see 'wavelet' input): data subwindow
% length (fastest, 2^n<frames);
% if cycles >0: *longest* window length to use. This
% determines the lowest output frequency {~frames/8}
% 'ntimesout' = Number of output times (int<frames-winsize). Enter a
% negative value [-S] to subsample original time by S.
% 'timesout' = Enter an array to obtain spectral decomposition at
% specific time values (note: algorithm find closest time
% point in data and this might result in an unevenly spaced
% time array). Overwrite 'ntimesout'. {def: automatic}
% 'freqs' = [min max] frequency limits. Default [minfreq srate/2],
% minfreq being determined by the number of data points,
% cycles and sampling frequency. Enter a single value
% to compute spectral decompisition at a single frequency
% (note: for FFT the closest frequency will be estimated).
% For wavelet, reducing the max frequency reduce
% the computation load.
% 'padratio' = FFTlength/winsize (2^k) {def: 2}
% Multiplies the number of output frequencies by
% dividing their spacing. When cycles==0, frequency
% spacing is (low_frequency/padratio).
% 'nfreqs' = number of output frequencies. For FFT, closest computed
% frequency will be returned. Overwrite 'padratio' effects
% for wavelets. Default: use 'padratio'.
% 'freqscale' = ['log'|'linear'] frequency scale. Default is 'linear'.
% Note that for obtaining 'log' spaced freqs using FFT,
% closest correspondant frequencies in the 'linear' space
% are returned.
% 'wletmethod'= ['dftfilt2'|'dftfilt3'] Wavelet method/program to use.
% Default is 'dftfilt3'
% 'dftfilt3' Morlet wavelet or Hanning DFT
% 'dftfilt2' Morlet-variant or Hanning DFT.
% Note that there are differences betweeen the Hanning
% DFTs in the two programs.
% 'causal' = ['on'|'off'] apply FFT or time-frequency in a causal
% way where only data before any given latency can
% influence the spectral decomposition. (default: 'off'}
%
% Optional time warping:
% 'timestretch' = {[Refmarks], [Refframes]}
% Stretch amplitude and phase time-course before smoothing.
% Refmarks is a (trials,eventframes) matrix in which rows are
% event marks to time-lock to for a given trial. Each trial
% will be stretched so that its marked events occur at frames
% Refframes. If Refframes is [], the median frame, across trials,
% of the Refmarks latencies will be used. Both Refmarks and
% Refframes are given in frames in this version - will be
% changed to ms in future.
% Outputs:
% tf = complex time frequency array for all trials (freqs,
% times, trials)
% freqs = vector of computed frequencies (Hz)
% times = vector of computed time points (ms)
% itcvals = time frequency "average" for all trials (freqs, times).
% In the coherence case, it is the real mean of the time
% frequency decomposition, but in the phase coherence case
% (see 'type' input'), this is the mean of the normalized
% spectral estimate.
%
% Authors: Arnaud Delorme, Jean Hausser & Scott Makeig
% CNL/Salk Institute 1998-2001; SCCN/INC/UCSD, La Jolla, 2002-
% Fix FFT frequency innacuracy, bug 874 by WuQiang
%
% See also: timef(), newtimef(), crossf(), newcrossf()
% Note: it is not advised to use a FFT decomposition in a log scale. Output
% value are accurate but plotting might not be because of the non-uniform
% frequency output values in log-space. If you have to do it, use a
% padratio as large as possible, or interpolate time-freq image at
% exact log scale values before plotting.
% Copyright (C) 8/1/98 Arnaud Delorme, Sigurd Enghoff & Scott Makeig, SCCN/INC/UCSD
%
% This program is free software; you can redistribute it and/or modify
% it under the terms of the GNU General Public License as published by
% the Free Software Foundation; either version 2 of the License, or
% (at your option) any later version.
%
% This program is distributed in the hope that it will be useful,
% but WITHOUT ANY WARRANTY; without even the implied warranty of
% MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
% GNU General Public License for more details.
%
% You should have received a copy of the GNU General Public License
% along with this program; if not, write to the Free Software
% Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
function [tmpall, freqs, timesout, itcvals] = timefreq(data, srate, varargin)
if nargin < 2
help timefreq;
return;
end;
[chan frame trials]= size(data);
if trials == 1 && chan ~= 1
trials = frame;
frame = chan;
chan = 1;
end;
g = finputcheck(varargin, ...
{ 'ntimesout' 'integer' [] []; ...
'timesout' 'real' [] []; ...
'winsize' 'integer' [0 Inf] []; ...
'tlimits' 'real' [] []; ...
'detrend' 'string' {'on','off'} 'off'; ...
'causal' 'string' {'on','off'} 'off'; ...
'verbose' 'string' {'on','off'} 'on'; ...
'freqs' 'real' [0 Inf] []; ...
'nfreqs' 'integer' [0 Inf] []; ...
'freqscale' 'string' { 'linear','log','' } 'linear'; ...
'ffttaper' 'string' { 'hanning','hamming','blackmanharris','none' } 'hanning';
'wavelet' 'real' [0 Inf] 0; ...
'cycles' {'real','integer'} [0 Inf] 0; ...
'padratio' 'integer' [1 Inf] 2; ...
'itctype' 'string' {'phasecoher','phasecoher2','coher'} 'phasecoher'; ...
'subitc' 'string' {'on','off'} 'off'; ...
'timestretch' 'cell' [] {}; ...
'wletmethod' 'string' {'dftfilt2','dftfilt3'} 'dftfilt3'; ...
});
if isstr(g), error(g); end;
if isempty(g.freqscale), g.freqscale = 'linear'; end;
if isempty(g.winsize), g.winsize = max(pow2(nextpow2(frame)-3),4); end;
if isempty(g.ntimesout), g.ntimesout = 200; end;
if isempty(g.freqs), g.freqs = [0 srate/2]; end;
if isempty(g.tlimits), g.tlimits = [0 frame/srate*1000]; end;
% checkin parameters
% ------------------
% Use 'wavelet' if 'cycles' undefined for backwards compatibility
if g.cycles == 0
g.cycles = g.wavelet;
end
if (g.winsize > frame)
error('Value of winsize must be less than frame length.');
end
if (pow2(nextpow2(g.padratio)) ~= g.padratio)
error('Value of padratio must be an integer power of two [1,2,4,8,16,...]');
end
% finding frequency limits
% ------------------------
if g.cycles(1) ~= 0 & g.freqs(1) == 0, g.freqs(1) = srate*g.cycles(1)/g.winsize; end;
% finding frequencies
% -------------------
if length(g.freqs) == 2
% min and max
% -----------
if g.freqs(1) == 0 & g.cycles(1) ~= 0
g.freqs(1) = srate*g.cycles(1)/g.winsize;
end;
% default number of freqs using padratio
% --------------------------------------
if isempty(g.nfreqs)
g.nfreqs = g.winsize/2*g.padratio+1;
% adjust nfreqs depending on frequency range
tmpfreqs = linspace(0, srate/2, g.nfreqs);
tmpfreqs = tmpfreqs(2:end); % remove DC (match the output of PSD)
% adjust limits for FFT (only linear scale)
if g.cycles(1) == 0 & ~strcmpi(g.freqscale, 'log')
if ~any(tmpfreqs == g.freqs(1))
[tmp minind] = min(abs(tmpfreqs-g.freqs(1)));
g.freqs(1) = tmpfreqs(minind);
verboseprintf(g.verbose, 'Adjust min freq. to %3.2f Hz to match FFT output frequencies\n', g.freqs(1));
end;
if ~any(tmpfreqs == g.freqs(2))
[tmp minind] = min(abs(tmpfreqs-g.freqs(2)));
g.freqs(2) = tmpfreqs(minind);
verboseprintf(g.verbose, 'Adjust max freq. to %3.2f Hz to match FFT output frequencies\n', g.freqs(2));
end;
end;
% find number of frequencies
% --------------------------
g.nfreqs = length(tmpfreqs( intersect( find(tmpfreqs >= g.freqs(1)), find(tmpfreqs <= g.freqs(2)))));
if g.freqs(1)==g.freqs(2), g.nfreqs = 1; end;
end;
% find closest freqs for FFT
% --------------------------
if strcmpi(g.freqscale, 'log')
g.freqs = linspace(log(g.freqs(1)), log(g.freqs(end)), g.nfreqs);
g.freqs = exp(g.freqs);
else
g.freqs = linspace(g.freqs(1), g.freqs(2), g.nfreqs); % this should be OK for FFT
% because of the limit adjustment
end;
end;
g.nfreqs = length(g.freqs);
% function for time freq initialisation
% -------------------------------------
if (g.cycles(1) == 0) %%%%%%%%%%%%%% constant window-length FFTs %%%%%%%%%%%%%%%%
freqs = linspace(0, srate/2, g.winsize*g.padratio/2+1);
freqs = freqs(2:end); % remove DC (match the output of PSD)
%srate/g.winsize*[1:2/g.padratio:g.winsize]/2
verboseprintf(g.verbose, 'Using %s FFT tapering\n', g.ffttaper);
switch g.ffttaper
case 'hanning', g.win = hanning(g.winsize);
case 'hamming', g.win = hamming(g.winsize);
case 'blackmanharris', g.win = blackmanharris(g.winsize);
case 'none', g.win = ones(g.winsize,1);
end;
else % %%%%%%%%%%%%%%%%%% Constant-Q (wavelet) DFTs %%%%%%%%%%%%%%%%%%%%%%%%%%%%
%freqs = srate*g.cycles/g.winsize*[2:2/g.padratio:g.winsize]/2;
%g.win = dftfilt(g.winsize,g.freqs(2)/srate,g.cycles,g.padratio,g.cyclesfact);
freqs = g.freqs;
if length(g.cycles) == 2
if g.cycles(2) < 1
g.cycles = [ g.cycles(1) g.cycles(1)*g.freqs(end)/g.freqs(1)*(1-g.cycles(2))];
end
verboseprintf(g.verbose, 'Using %g cycles at lowest frequency to %g at highest.\n', g.cycles(1), g.cycles(2));
elseif length(g.cycles) == 1
verboseprintf(g.verbose, 'Using %d cycles at all frequencies.\n',g.cycles);
else
verboseprintf(g.verbose, 'Using user-defined cycle for each frequency\n');
end
if strcmp(g.wletmethod, 'dftfilt2')
g.win = dftfilt2(g.freqs,g.cycles,srate, g.freqscale); % uses Morlet taper by default
elseif strcmp(g.wletmethod, 'dftfilt3') % Default
g.win = dftfilt3(g.freqs,g.cycles,srate, 'cycleinc', g.freqscale); % uses Morlet taper by default
else return
end
g.winsize = 0;
for index = 1:length(g.win)
g.winsize = max(g.winsize,length(g.win{index}));
end;
end;
% compute time vector
% -------------------
[ g.timesout g.indexout ] = gettimes(frame, g.tlimits, g.timesout, g.winsize, g.ntimesout, g.causal, g.verbose);
% -------------------------------
% compute time freq decomposition
% -------------------------------
verboseprintf(g.verbose, 'The window size used is %d samples (%g ms) wide.\n',g.winsize, 1000/srate*g.winsize);
if strcmpi(g.freqscale, 'log') % fastif was having strange "function not available" messages
scaletoprint = 'log';
else scaletoprint = 'linear';
end
verboseprintf(g.verbose, 'Estimating %d %s-spaced frequencies from %2.1f Hz to %3.1f Hz.\n', length(g.freqs), ...
scaletoprint, g.freqs(1), g.freqs(end));
%verboseprintf(g.verbose, 'Estimating %d %s-spaced frequencies from %2.1f Hz to %3.1f Hz.\n', length(g.freqs), ...
% fastif(strcmpi(g.freqscale, 'log'), 'log', 'linear'), g.freqs(1), g.freqs(end));
if g.cycles(1) == 0
if 1
% build large matrix to compute FFT
% ---------------------------------
indices = repmat([-g.winsize/2+1:g.winsize/2]', [1 length(g.indexout) trials]);
indices = indices + repmat(g.indexout, [size(indices,1) 1 trials]);
indices = indices + repmat(reshape(([1:trials]-1)*frame,1,1,trials), [size(indices,1) length(g.indexout) 1]);
if chan > 1
tmpall = repmat(nan,[chan length(freqs) length(g.timesout) trials]);
tmpX = reshape(data(:,indices), [ size(data,1) size(indices)]);
tmpX = bsxfun(@minus, tmpX, mean( tmpX, 2)); % avoids repmat - faster than tmpX = tmpX - repmat(mean(tmpX), [size(tmpX,1) 1 1]);
tmpX = bsxfun(@times, tmpX, g.win');
tmpX = fft(tmpX,g.padratio*g.winsize,2);
tmpall = squeeze(tmpX(:,2:g.padratio*g.winsize/2+1,:,:));
else
tmpall = repmat(nan,[length(freqs) length(g.timesout) trials]);
tmpX = data(indices);
tmpX = bsxfun(@minus, tmpX, mean( tmpX, 1)); % avoids repmat - faster than tmpX = tmpX - repmat(mean(tmpX), [size(tmpX,1) 1 1]);
tmpX = bsxfun(@times, tmpX, g.win);
%tmpX = fft(tmpX,2^ceil(log2(g.padratio*g.winsize)));
%tmpall = tmpX(2:g.padratio*g.winsize/2+1,:,:);
tmpX = fft(tmpX,g.padratio*g.winsize);
tmpall = tmpX(2:g.padratio*g.winsize/2+1,:,:);
end;
else % old iterative computation
tmpall = repmat(nan,[length(freqs) length(g.timesout) trials]);
verboseprintf(g.verbose, 'Processing trial (of %d):',trials);
for trial = 1:trials
if rem(trial,10) == 0, verboseprintf(g.verbose, ' %d',trial); end
if rem(trial,120) == 0, verboseprintf(g.verbose, '\n'); end
for index = 1:length(g.indexout)
if strcmpi(g.causal, 'off')
tmpX = data([-g.winsize/2+1:g.winsize/2]+g.indexout(index)+(trial-1)*frame); % 1 point imprecision
else
tmpX = data([-g.winsize+1:0]+g.indexout(index)+(trial-1)*frame); % 1 point imprecision
end;
tmpX = tmpX - mean(tmpX);
if strcmpi(g.detrend, 'on'),
tmpX = detrend(tmpX);
end;
tmpX = g.win .* tmpX(:);
tmpX = fft(tmpX,g.padratio*g.winsize);
tmpX = tmpX(2:g.padratio*g.winsize/2+1);
tmpall(:,index, trial) = tmpX(:);
end;
end;
end;
else % wavelet
if chan > 1
% wavelets are processed in groups of the same size
% to speed up computation. Wavelet of groups of different size
% can be processed together but at a cost of a lot of RAM and
% a lot of extra computation -> not efficient
tmpall = repmat(nan,[chan length(freqs) length(g.timesout) trials]);
wt = [ 1 find(diff(cellfun(@length,g.win)))+1 length(g.win)+1];
verboseprintf(g.verbose, 'Computing of %d:', length(wt));
for ind = 1:length(wt)-1
verboseprintf(g.verbose, '.');
wavarray = reshape([ g.win{wt(ind):wt(ind+1)-1} ], [ length(g.win{wt(ind)}) wt(ind+1)-wt(ind) ]);
sizewav = size(wavarray,1)-1;
indices = repmat([-sizewav/2:sizewav/2]', [1 size(wavarray,2) length(g.indexout) trials]);
indices = indices + repmat(reshape(g.indexout, 1,1,length(g.indexout)), [size(indices,1) size(indices,2) 1 trials]);
indices = indices + repmat(reshape(([1:trials]-1)*frame,1,1,1,trials), [size(indices,1) size(indices,2) size(indices,3) 1]);
szfreqdata = [ size(data,1) size(indices) ];
tmpX = reshape(data(:,indices), szfreqdata);
tmpX = bsxfun(@minus, tmpX, mean( tmpX, 2)); % avoids repmat - faster than tmpX = tmpX - repmat(mean(tmpX), [size(tmpX,1) 1 1]);
wavarray = reshape(wavarray, [1 size(wavarray,1) size(wavarray,2)]);
tmpall(:,wt(ind):wt(ind+1)-1,:,:,:) = reshape(sum(bsxfun(@times, tmpX, wavarray),2), [szfreqdata(1) szfreqdata(3:end)]);
end;
verboseprintf(g.verbose, '\n');
%tmpall = squeeze(tmpall(1,:,:,:));
elseif 0
tmpall = repmat(nan,[length(freqs) length(g.timesout) trials]);
% wavelets are processed in groups of the same size
% to speed up computation. Wavelet of groups of different size
% can be processed together but at a cost of a lot of RAM and
% a lot of extra computation -> not faster than the regular
% iterative method
wt = [ 1 find(diff(cellfun(@length,g.win)))+1 length(g.win)+1];
for ind = 1:length(wt)-1
wavarray = reshape([ g.win{wt(ind):wt(ind+1)-1} ], [ length(g.win{wt(ind)}) wt(ind+1)-wt(ind) ]);
sizewav = size(wavarray,1)-1;
indices = repmat([-sizewav/2:sizewav/2]', [1 size(wavarray,2) length(g.indexout) trials]);
indices = indices + repmat(reshape(g.indexout, 1,1,length(g.indexout)), [size(indices,1) size(indices,2) 1 trials]);
indices = indices + repmat(reshape(([1:trials]-1)*frame,1,1,1,trials), [size(indices,1) size(indices,2) size(indices,3) 1]);
tmpX = data(indices);
tmpX = bsxfun(@minus, tmpX, mean( tmpX, 1)); % avoids repmat - faster than tmpX = tmpX - repmat(mean(tmpX), [size(tmpX,1) 1 1]);
tmpall(wt(ind):wt(ind+1)-1,:,:) = squeeze(sum(bsxfun(@times, tmpX, wavarray),1));
end;
elseif 0
% wavelets are processed one by one but all windows simultaneously
% -> not faster than the regular iterative method
tmpall = repmat(nan,[length(freqs) length(g.timesout) trials]);
sizewav = length(g.win{1})-1; % max window size
mainc = sizewav/2;
indices = repmat([-sizewav/2:sizewav/2]', [1 length(g.indexout) trials]);
indices = indices + repmat(g.indexout, [size(indices,1) 1 trials]);
indices = indices + repmat(reshape(([1:trials]-1)*frame,1,1,trials), [size(indices,1) length(g.indexout) 1]);
for freqind = 1:length(g.win)
winc = (length(g.win{freqind})-1)/2;
wins = length(g.win{freqind})-1;
wini = [-wins/2:wins/2]+winc+mainc-winc+1;
tmpX = data(indices(wini,:,:));
tmpX = bsxfun(@minus, tmpX, mean( tmpX, 1)); % avoids repmat - faster than tmpX = tmpX - repmat(mean(tmpX), [size(tmpX,1) 1 1]);
tmpX = sum(bsxfun(@times, tmpX, g.win{freqind}'),1);
tmpall(freqind,:,:) = tmpX;
end;
else
% prepare wavelet filters
% -----------------------
for index = 1:length(g.win)
g.win{index} = transpose(repmat(g.win{index}, [trials 1]));
end;
% apply filters
% -------------
verboseprintf(g.verbose, 'Processing time point (of %d):',length(g.timesout));
tmpall = zeros(length(g.win), length(g.indexout), size(data,2));
for index = 1:length(g.indexout)
if rem(index,10) == 0, verboseprintf(g.verbose, ' %d',index); end
if rem(index,120) == 0, verboseprintf(g.verbose, '\n'); end
for freqind = 1:length(g.win)
wav = g.win{freqind};
sizewav = size(wav,1)-1;
%g.indexout(index), size(wav,1), g.freqs(freqind)
if strcmpi(g.causal, 'off')
tmpX = data([-sizewav/2:sizewav/2]+g.indexout(index),:);
else
tmpX = data([-sizewav:0]+g.indexout(index),:);
end;
tmpX = tmpX - ones(size(tmpX,1),1)*mean(tmpX);
if strcmpi(g.detrend, 'on'),
for trial = 1:trials
tmpX(:,trial) = detrend(tmpX(:,trial));
end;
end;
tmpX = sum(wav .* tmpX);
tmpall( freqind, index, :) = tmpX;
end;
end;
end;
end;
verboseprintf(g.verbose, '\n');
% time-warp code begins -Jean
% ---------------------------
if ~isempty(g.timestretch) && length(g.timestretch{1}) > 0
timemarks = g.timestretch{1}';
if isempty(g.timestretch{2}) | length(g.timestretch{2}) == 0
timerefs = median(g.timestretch{1}',2);
else
timerefs = g.timestretch{2};
end
trials = size(tmpall,3);
% convert timerefs to subsampled ERSP space
% -----------------------------------------
[dummy refsPos] = min(transpose(abs( ...
repmat(timerefs, [1 length(g.indexout)]) - repmat(g.indexout, [length(timerefs) 1]))));
refsPos(end+1) = 1;
refsPos(end+1) = length(g.indexout);
refsPos = sort(refsPos);
for t=1:trials
% convert timemarks to subsampled ERSP space
% ------------------------------------------
%[dummy pos]=min(abs(repmat(timemarks(2:7,1), [1 length(g.indexout)])-repmat(g.indexout,[6 1])));
outOfTimeRangeTimeWarpMarkers = find(timemarks(:,t) < min(g.indexout) | timemarks(:,t) > max(g.indexout));
% if ~isempty(outOfTimeRangeTimeWarpMarkers)
% verboseprintf(g.verbose, 'Timefreq warning: time-warp latencies in epoch %d are out of time range defined for calculation of ERSP.\n', t);
% end;
[dummy marksPos] = min(transpose( ...
abs( ...
repmat(timemarks(:,t), [1 length(g.indexout)]) ...
- repmat(g.indexout, [size(timemarks,1) 1]) ...
) ...
));
marksPos(end+1) = 1;
marksPos(end+1) = length(g.indexout);
marksPos = sort(marksPos);
%now warp tmpall
mytmpall = tmpall(:,:,t);
r = sqrt(mytmpall.*conj(mytmpall));
theta = angle(mytmpall);
% So mytmpall is almost equal to r.*exp(i*theta)
% whos marksPos refsPos
M = timewarp(marksPos, refsPos);
TSr = transpose(M*r');
TStheta = zeros(size(theta,1), size(theta,2));
for freqInd=1:size(TStheta,1)
TStheta(freqInd, :) = angtimewarp(marksPos, refsPos, theta(freqInd, :));
end
TStmpall = TSr.*exp(i*TStheta);
% $$$ keyboard;
tmpall(:,:,t) = TStmpall;
end
end
%time-warp ends
zerovals = tmpall == 0;
if any(reshape(zerovals, 1, prod(size(zerovals))))
tmpall(zerovals) = Inf;
minval = min(tmpall(:)); % remove bug
tmpall(zerovals) = minval;
end;
% compute and subtract ITC
% ------------------------
if nargout > 3 || strcmpi(g.subitc, 'on')
itcvals = tfitc(tmpall, g.itctype);
end;
if strcmpi(g.subitc, 'on')
%a = gcf; figure; imagesc(abs(itcvals)); cbar; figure(a);
if ndims(tmpall) <= 3
tmpall = (tmpall - abs(tmpall) .* repmat(itcvals, [1 1 trials])) ./ abs(tmpall);
else tmpall = (tmpall - abs(tmpall) .* repmat(itcvals, [1 1 1 trials])) ./ abs(tmpall);
end;
end;
% find closest output frequencies
% -------------------------------
if length(g.freqs) ~= length(freqs) || any(g.freqs ~= freqs)
allindices = zeros(1,length(g.freqs));
for index = 1:length(g.freqs)
[dum ind] = min(abs(freqs-g.freqs(index)));
allindices(index) = ind;
end;
verboseprintf(g.verbose, 'finding closest frequencies: %d freqs removed\n', length(freqs)-length(allindices));
freqs = freqs(allindices);
if ndims(tmpall) <= 3
tmpall = tmpall(allindices,:,:);
else tmpall = tmpall(:,allindices,:,:);
end;
if nargout > 3 | strcmpi(g.subitc, 'on')
if ndims(tmpall) <= 3
itcvals = itcvals(allindices,:,:);
else itcvals = itcvals(:,allindices,:,:);
end;
end;
end;
timesout = g.timesout;
%figure; imagesc(abs(sum(itcvals,3))); cbar;
return;
% function for itc
% ----------------
function [itcvals] = tfitc(tfdecomp, itctype);
% first dimension are trials
nd = max(3,ndims(tfdecomp));
switch itctype
case 'coher',
try,
itcvals = sum(tfdecomp,nd) ./ sqrt(sum(tfdecomp .* conj(tfdecomp),nd) * size(tfdecomp,nd));
catch, % scan rows if out of memory
for index =1:size(tfdecomp,1)
itcvals(index,:,:) = sum(tfdecomp(index,:,:,:),nd) ./ sqrt(sum(tfdecomp(index,:,:,:) .* conj(tfdecomp(index,:,:,:)),nd) * size(tfdecomp,nd));
end;
end;
case 'phasecoher2',
try,
itcvals = sum(tfdecomp,nd) ./ sum(sqrt(tfdecomp .* conj(tfdecomp)),nd);
catch, % scan rows if out of memory
for index =1:size(tfdecomp,1)
itcvals(index,:,:) = sum(tfdecomp(index,:,:,:),nd) ./ sum(sqrt(tfdecomp(index,:,:,:) .* conj(tfdecomp(index,:,:,:))),nd);
end;
end;
case 'phasecoher',
try,
itcvals = sum(tfdecomp ./ sqrt(tfdecomp .* conj(tfdecomp)) ,nd) / size(tfdecomp,nd);
catch, % scan rows if out of memory
for index =1:size(tfdecomp,1)
itcvals(index,:,:) = sum(tfdecomp(index,:,:,:) ./ sqrt(tfdecomp(index,:,:,:) .* conj(tfdecomp(index,:,:,:))) ,nd) / size(tfdecomp,nd);
end;
end;
end % ~any(isnan())
return;
function w = hanning(n)
if ~rem(n,2)
w = .5*(1 - cos(2*pi*(1:n/2)'/(n+1)));
w = [w; w(end:-1:1)];
else
w = .5*(1 - cos(2*pi*(1:(n+1)/2)'/(n+1)));
w = [w; w(end-1:-1:1)];
end
% get time points
% ---------------
function [ timevals, timeindices ] = gettimes(frames, tlimits, timevar, winsize, ntimevar, causal, verbose);
timevect = linspace(tlimits(1), tlimits(2), frames);
srate = 1000*(frames-1)/(tlimits(2)-tlimits(1));
if isempty(timevar) % no pre-defined time points
if ntimevar(1) > 0
% generate linearly space vector
% ------------------------------
if (ntimevar > frames-winsize)
ntimevar = frames-winsize;
if ntimevar < 0
error('Not enough data points, reduce the window size or lowest frequency');
end;
verboseprintf(verbose, ['Value of ''timesout'' must be <= frame-winsize, ''timesout'' adjusted to ' int2str(ntimevar) '\n']);
end
npoints = ntimevar(1);
wintime = 500*winsize/srate;
if strcmpi(causal, 'on')
timevals = linspace(tlimits(1)+2*wintime, tlimits(2), npoints);
else timevals = linspace(tlimits(1)+wintime, tlimits(2)-wintime, npoints);
end;
verboseprintf(verbose, 'Generating %d time points (%1.1f to %1.1f ms)\n', npoints, min(timevals), max(timevals));
else
% subsample data
% --------------
nsub = -ntimevar(1);
if strcmpi(causal, 'on')
timeindices = [ceil(winsize+nsub):nsub:length(timevect)];
else timeindices = [ceil(winsize/2+nsub/2):nsub:length(timevect)-ceil(winsize/2)-1];
end;
timevals = timevect( timeindices ); % the conversion at line 741 leaves timeindices unchanged
verboseprintf(verbose, 'Subsampling by %d (%1.1f to %1.1f ms)\n', nsub, min(timevals), max(timevals));
end;
else
timevals = timevar;
% check boundaries
% ----------------
wintime = 500*winsize/srate;
if strcmpi(causal, 'on')
tmpind = find( (timevals >= tlimits(1)+2*wintime-0.0001) & (timevals <= tlimits(2)) );
else tmpind = find( (timevals >= tlimits(1)+wintime-0.0001) & (timevals <= tlimits(2)-wintime+0.0001) );
end;
% 0.0001 account for numerical innacuracies on opteron computers
if isempty(tmpind)
error('No time points. Reduce time window or minimum frequency.');
end;
if length(timevals) ~= length(tmpind)
verboseprintf(verbose, 'Warning: %d out of %d time values were removed (now %3.2f to %3.2f ms) so the lowest\n', ...
length(timevals)-length(tmpind), length(timevals), timevals(tmpind(1)), timevals(tmpind(end)));
verboseprintf(verbose, ' frequency could be computed with the requested accuracy\n');
end;
timevals = timevals(tmpind);
end;
% find closet points in data
% --------------------------
timeindices = round(eeg_lat2point(timevals, 1, srate, tlimits, 1E-3));
if length(timeindices) < length(unique(timeindices))
timeindices = unique_bc(timeindices)
verboseprintf(verbose, 'Warning: duplicate times, reduce the number of output times\n');
end;
if length(unique(timeindices(2:end)-timeindices(1:end-1))) > 1
verboseprintf(verbose, 'Finding closest points for time variable\n');
verboseprintf(verbose, 'Time values for time/freq decomposition is not perfectly uniformly distributed\n');
else
verboseprintf(verbose, 'Distribution of data point for time/freq decomposition is perfectly uniform\n');
end;
timevals = timevect(timeindices);
% DEPRECATED, FOR C INTERFACE
function nofunction()
% C PART %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
filename = [ 'tmpcrossf' num2str(round(rand(1)*1000)) ];
f = fopen([ filename '.in'], 'w');
fwrite(f, tmpsaveall, 'int32');
fwrite(f, g.detret, 'int32');
fwrite(f, g.srate, 'int32');
fwrite(f, g.maxfreq, 'int32');
fwrite(f, g.padratio, 'int32');
fwrite(f, g.cycles, 'int32');
fwrite(f, g.winsize, 'int32');
fwrite(f, g.timesout, 'int32');
fwrite(f, g.subitc, 'int32');
fwrite(f, g.type, 'int32');
fwrite(f, trials, 'int32');
fwrite(f, g.naccu, 'int32');
fwrite(f, length(X), 'int32');
fwrite(f, X, 'double');
fwrite(f, Y, 'double');
fclose(f);
command = [ '!cppcrosff ' filename '.in ' filename '.out' ];
eval(command);
f = fopen([ filename '.out'], 'r');
size1 = fread(f, 'int32', 1);
size2 = fread(f, 'int32', 1);
Rreal = fread(f, 'double', [size1 size2]);
Rimg = fread(f, 'double', [size1 size2]);
Coher.R = Rreal + j*Rimg;
Boot.Coherboot.R = [];
Boot.Rsignif = [];
function verboseprintf(verbose, varargin)
if strcmpi(verbose, 'on')
fprintf(varargin{:});
end;
|
github
|
lcnbeapp/beapp-master
|
pac_cont.m
|
.m
|
beapp-master/Packages/eeglab14_1_2b/functions/timefreqfunc/pac_cont.m
| 17,447 |
utf_8
|
9b94d431be58419e3715e54645687469
|
% pac_cont() - compute phase-amplitude coupling (power of first input
% correlation with phase of second). There is no graphical output
% to this function.
%
% Usage:
% >> pac_cont(x,y,srate);
% >> [pac timesout pvals] = pac_cont(x,y,srate,'key1', 'val1', 'key2', val2' ...);
%
% Inputs:
% x = [float array] 1-D data vector of size (1xtimes)
% y = [float array] 1-D data vector of size (1xtimes)
% srate = data sampling rate (Hz)
%
% Optional time information intputs:
% 'winsize' = If cycles==0: data subwindow length (fastest, 2^n<frames);
% If cycles >0: *longest* window length to use. This
% determines the lowest output frequency. Note that this
% parameter is overwritten if the minimum frequency has been set
% manually and requires a longer time window {~frames/8}
% 'ntimesout' = Number of output times (int<frames-winframes). Enter a
% negative value [-S] to subsample original time by S.
% 'timesout' = Enter an array to obtain spectral decomposition at
% specific time values (note: algorithm find closest time
% point in data and this might result in an unevenly spaced
% time array). Overwrite 'ntimesout'. {def: automatic}
% 'tlimits' = [min max] time limits in ms.
%
% Optional PAC inputs:
% 'method' = ['modulation'|'plv'|'corr'|'glm'] (see reference).
% 'freqphase' = [min max] frequency limits. Default [minfreq 50],
% minfreq being determined by the number of data points,
% cycles and sampling frequency. Use 0 for minimum frequency
% to compute default minfreq. You may also enter an
% array of frequencies for the spectral decomposition
% (for FFT, closest computed frequency will be returned; use
% 'padratio' to change FFT freq. resolution).
% 'freqamp' = [float array] array of frequencies for the second
% argument. 'freqs' is used for the first argument.
% By default it is the same as 'freqs'.
% 'filterfunc' = ['eegfilt'|'iirfilt'|'eegfftfilt'] filtering function.
% Default is iirfilt. Warning, filtering may dramatically
% affect the result. With the 'corr' method, make sure you
% have a large window size because each window is filtered
% independently.
% 'filterphase' = @f_handle. Function handle to filter the data for the
% phase information. For example, @(x)iirfilt(x, 1000, 2,
% 20). Note that 'freqphase' is ignore in this case.
% 'filteramp' = @f_handle. Function handle to filter the data for the
% amplitude information. Note that 'freqamp' is ignore in
% this case.
%
% Inputs for statistics:
% 'alpha' = [float] p-value threshold. Default is none (no statistics).
% 'mcorrect' = ['none'|'fdr'] method to correct for multiple comparison.
% Default is 'none'.
% 'baseline' = [min max] baseline period for the Null distribution. Default
% is the whole data range. Note that this option is ignored
% for instanstaneous statistics.
% 'instantstat' = ['on'|'off'] performs statistics for each time window
% independently. Default is 'off'.
% 'naccu' = [integer] number of accumulations for surrogate
% statistics.
% 'statlim' = ['parametric'|'surrogate'] use a parametric methods to
% asseess the limit of the surrogate distribution or use
% the tail of the distribution ('surrogate' method)
%
% Other inputs:
% 'title' = [string] figure title. Default is none.
% 'vert' = [float array] array of time value for which to plot
% vertical lines. Default is none.
%
% Outputs:
% pac = Phase-amplitude coupling values.
% timesout = vector of time indices
% pvals = Associated p-values
%
% Author: Arnaud Delorme and Makoto Miyakoshi, SCCN/INC, UCSD 2012-
%
% References:
% Methods used here are introduced and compared in:
% Penny, Duzel, Miller, Ojemann. (20089). Testing for Nested Oscilations.
% J Neuro Methods. 174:50-61
%
% Modulation Index is defined in:
% Canolty, Edwards, Dalal, Soltani, Nagarajan, Kirsch, et al. (2006). Modulation index is defined in High Gamma Power Is Phase-Locked to Theta
% Oscillations in Human Neocortex. Science. 313:1626-8.
%
% PLV (Phase locking value) is defined in:
% Lachaux, Rodriguez, Martiniere, Varela. (1999). Measuring phase synchrony
% in brain signal. Hum Brain Mapp. 8:194-208.
%
% corr (correlation) method is defined in:
% Brunce, Eckhorn. (2004). Task-related coupling from high- to
% low-frequency signals among visual cortical areas in human subdural
% recordings. Int J Psychophysiol. 51:97-116.
%
% glm (general linear model) is defined in
% Penny, Duzel, Miller, Ojemann. (20089). Testing for Nested Oscilations.
% J Neuro Methods. 174:50-61
% Copyright (C) 2012 Arnaud Delorme, UCSD
%
% This program is free software; you can redistribute it and/or modify
% it under the terms of the GNU General Public License as published by
% the Free Software Foundation; either version 2 of the License, or
% (at your option) any later version.
%
% This program is distributed in the hope that it will be useful,
% but WITHOUT ANY WARRANTY; without even the implied warranty of
% MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
% GNU General Public License for more details.
%
% You should have received a copy of the GNU General Public License
% along with this program; if not, write to the Free Software
% Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
function [m_raw pvals indexout] = pac_cont(X, Y, srate, varargin);
if nargin < 1
help pac_cont;
return;
end;
% deal with 3-D inputs
% --------------------
if ndims(X) == 3 || ndims(Y) == 3, error('Cannot process 3-D input'); end;
if size(X,1) > 1, X = X'; end;
if size(Y,1) > 1, Y = Y'; end;
if size(X,1) ~= 1 || size(Y,1) ~= 1, error('Cannot only process vector input'); end;
frame = size(X,2);
pvals = [];
g = finputcheck(varargin, ...
{ ...
'alpha' 'real' [0 0.2] [];
'baseline' 'float' [] [];
'freqphase' 'real' [0 Inf] [0 srate/2];
'freqamp' 'real' [0 Inf] [];
'mcorrect' 'string' { 'none' 'fdr' } 'none';
'method' 'string' { 'plv' 'modulation' 'glm' 'corr' } 'modulation';
'naccu' 'integer' [1 Inf] 250;
'instantstat' 'string' {'on','off'} 'off';
'newfig' 'string' {'on','off'} 'on';
'nofig' 'string' {'on','off'} 'off';
'statlim' 'string' {'surrogate','parametric'} 'parametric';
'timesout' 'real' [] []; ...
'filterfunc' 'string' { 'eegfilt' 'iirfilt' 'eegfiltfft' } 'eegfiltfft'; ...
'filterphase' '' {} [];
'filteramp' '' {} [];
'ntimesout' 'integer' [] 200; ...
'tlimits' 'real' [] [0 frame/srate];
'title' 'string' [] '';
'vert' 'real' [] [];
'winsize' 'integer' [0 Inf] max(pow2(nextpow2(frame)-3),4) }, 'pac');
if isstr(g), error(g); end;
if ~isempty(g.filterphase)
x_freqphase = feval(g.filterphase, X(:)');
else x_freqphase = feval(g.filterfunc, X(:)', srate, g.freqphase(1), g.freqphase(end));
end;
if ~isempty(g.filteramp)
x_freqamp = feval(g.filteramp, Y(:)');
else x_freqamp = feval(g.filterfunc, Y(:)', srate, g.freqamp( 1), g.freqamp( end));
end;
z_phasedata = hilbert(x_freqphase);
z_ampdata = hilbert(x_freqamp);
phase = angle(z_phasedata);
amplitude = abs( z_ampdata);
z = amplitude.*exp(i*phase); % this is the pac measure
% get time windows
% ----------------
g.verbose = 'on';
g.causal = 'off';
[ timesout1 indexout ] = gettimes(frame, g.tlimits, g.timesout, g.winsize, g.ntimesout, g.causal, g.verbose);
% scan time windows
% -----------------
if ~isempty(g.alpha)
m_raw = zeros(1,length(indexout));
pvals = zeros(1,length(indexout));
end;
fprintf('Computing PAC:\n');
for iWin = 1:length(indexout)
x_phaseEpoch = x_freqphase(indexout(iWin)+[-g.winsize/2+1:g.winsize/2]);
x_ampEpoch = x_freqamp( indexout(iWin)+[-g.winsize/2+1:g.winsize/2]);
z_phaseEpoch = z_phasedata(indexout(iWin)+[-g.winsize/2+1:g.winsize/2]);
z_ampEpoch = z_ampdata( indexout(iWin)+[-g.winsize/2+1:g.winsize/2]);
z_epoch = z( indexout(iWin)+[-g.winsize/2+1:g.winsize/2]);
numpoints=length(x_phaseEpoch);
if rem(iWin,10) == 0, verboseprintf(g.verbose, ' %d',iWin); end
if rem(iWin,120) == 0, verboseprintf(g.verbose, '\n'); end
% Choose method
% -------------
if strcmpi(g.method, 'modulation')
% Modulation index
m_raw(iWin) = abs(sum(z_epoch))/numpoints;
elseif strcmpi(g.method, 'plv')
if iWin == 145
%dsfsd;
end;
%amplitude_filt = sgolayfilt(amplitude, 3, 101);
if ~isempty(g.filterphase)
amplitude_filt = feval(g.filterphase, z_ampEpoch);
else amplitude_filt = feval(g.filterfunc , z_ampEpoch, srate, g.freqphase(1), g.freqphase(end));
end;
z_amplitude_filt = hilbert(amplitude_filt);
phase_amp_modulation = angle(z_amplitude_filt);
m_raw(iWin) = abs(sum(exp(i*(x_phaseEpoch - phase_amp_modulation)))/numpoints);
elseif strcmpi(g.method, 'corr')
if iWin == inf %145
figure; plot(abs(z_ampdata))
hold on; plot(x_phasedata/10000000000, 'r')
x = X(indexout(iWin)+[-g.winsize/2+1:g.winsize/2]);
hold on; plot(x, 'g');
dsfsd;
end;
[r_ESC pval_corr] = corrcoef(x_phaseEpoch, abs(z_ampEpoch));
m_raw(iWin) = r_ESC(1,2);
pvals(iWin) = pval_corr(1,2);
elseif strcmpi(g.method, 'glm')
[b dev stats] = glmfit(x_phaseEpoch', abs(z_ampEpoch)', 'normal');
GLM_beta = stats.beta(2,1);
pvals(iWin) = stats.p(2,1);
m_raw(iWin) = b(1);
end;
%% compute statistics (instantaneous)
% -----------------------------------
if ~isempty(g.alpha) && strcmpi(g.instantstat, 'on') && ~strcmpi(g.method, 'corr') && ~strcmpi(g.method, 'glm')
% compute surrogate values
numsurrogate=g.naccu;
minskip=srate;
maxskip=numpoints-srate; % max variation half a second
if maxskip < 1
error('Window size shorter than 1 second; too short for computing surrogate data');
end;
skip=ceil(numpoints.*rand(numsurrogate*4,1));
skip(skip>maxskip)=[];
skip(skip<minskip)=[];
skip=skip(1:numsurrogate,1);
surrogate_m=zeros(numsurrogate,1);
for s=1:numsurrogate
surrogate_amplitude=[amplitude(skip(s):end) amplitude(1:skip(s)-1)]; % consider circular shifts
surrogate_m(s)=abs(mean(surrogate_amplitude.*exp(i*phase)));
%disp(numsurrogate-s)
end
if strcmpi(g.statlim, 'surrogate')
pvals(iWin) = stat_surrogate_pvals(surrogate_m, m_raw(iWin), 'upper');
%fprintf('Raw PAC is %3.2f (p-value=%1.3f)\n', m_raw(iWin), pvals(iWin));
else
% Canolty method below
%% fit gaussian to surrogate data, uses normfit.m from MATLAB Statistics toolbox
[surrogate_mean,surrogate_std]=normfit(surrogate_m);
%% normalize length using surrogate data (z-score)
m_norm_length=(abs(m_raw(iWin))-surrogate_mean)/surrogate_std;
pvals(iWin) = normcdf(0, m_norm_length, 1);
m_norm_phase=angle(m_raw(iWin));
m_norm=m_norm_length*exp(i*m_norm_phase);
% compare parametric and non-parametric methods (return similar
% results)
if iWin == length(indexout)
figure;
plot(-log10(pvals));
hold on; plot(-log10(pvals2), 'r');
end;
end;
end;
end;
fprintf('\n');
% Computes alpha
% --------------
if ~isempty(g.alpha) && strcmpi(g.instantstat, 'off')
if isempty(g.baseline)
g.baseline = [ timesout1(1) timesout1(end) ];
end;
baselineInd = find(timesout1 >= g.baseline(1) & timesout1 <= g.baseline(end));
m_raw_base = abs(m_raw(baselineInd));
if strcmpi(g.statlim, 'surrogate')
for index = 1:length(m_raw)
pvals(index) = stat_surrogate_pvals(m_raw_base, m_raw(index), 'upper');
end;
else
[surrogate_mean,surrogate_std]=normfit(m_raw_base);
m_norm_length=(abs(m_raw)-surrogate_mean)/surrogate_std;
pvals = normcdf(0, m_norm_length, 1);
end;
if strcmpi(g.mcorrect, 'fdr')
pvals = fdr(pvals);
end;
end;
%% plot results
% -------------
if strcmpi(g.nofig, 'on')
return
end;
if strcmpi(g.newfig, 'on')
figure;
end;
if ~isempty(g.alpha)
plotcurve(timesout1, m_raw, 'maskarray', pvals < g.alpha);
else plotcurve(timesout1, m_raw);
end;
xlabel('Time (ms)');
ylabel('PAC (0 to 1)');
title(g.title);
% plot vertical lines
% -------------------
if ~isempty(g.vert)
hold on;
yl = ylim;
for index = 1:length(g.vert)
plot([g.vert(index) g.vert(index)], yl, 'g');
end;
end;
% -------------
% gettime function identical to timefreq function
% DO NOT MODIFY
% -------------
function [ timevals, timeindices ] = gettimes(frames, tlimits, timevar, winsize, ntimevar, causal, verbose);
timevect = linspace(tlimits(1), tlimits(2), frames);
srate = 1000*(frames-1)/(tlimits(2)-tlimits(1));
if isempty(timevar) % no pre-defined time points
if ntimevar(1) > 0
% generate linearly space vector
% ------------------------------
if (ntimevar > frames-winsize)
ntimevar = frames-winsize;
if ntimevar < 0
error('Not enough data points, reduce the window size or lowest frequency');
end;
verboseprintf(verbose, ['Value of ''timesout'' must be <= frame-winsize, ''timesout'' adjusted to ' int2str(ntimevar) '\n']);
end
npoints = ntimevar(1);
wintime = 500*winsize/srate;
if strcmpi(causal, 'on')
timevals = linspace(tlimits(1)+2*wintime, tlimits(2), npoints);
else timevals = linspace(tlimits(1)+wintime, tlimits(2)-wintime, npoints);
end;
verboseprintf(verbose, 'Generating %d time points (%1.1f to %1.1f ms)\n', npoints, min(timevals), max(timevals));
else
% subsample data
% --------------
nsub = -ntimevar(1);
if strcmpi(causal, 'on')
timeindices = [ceil(winsize+nsub):nsub:length(timevect)];
else timeindices = [ceil(winsize/2+nsub/2):nsub:length(timevect)-ceil(winsize/2)-1];
end;
timevals = timevect( timeindices ); % the conversion at line 741 leaves timeindices unchanged
verboseprintf(verbose, 'Subsampling by %d (%1.1f to %1.1f ms)\n', nsub, min(timevals), max(timevals));
end;
else
timevals = timevar;
% check boundaries
% ----------------
wintime = 500*winsize/srate;
if strcmpi(causal, 'on')
tmpind = find( (timevals >= tlimits(1)+2*wintime-0.0001) & (timevals <= tlimits(2)) );
else tmpind = find( (timevals >= tlimits(1)+wintime-0.0001) & (timevals <= tlimits(2)-wintime+0.0001) );
end;
% 0.0001 account for numerical innacuracies on opteron computers
if isempty(tmpind)
error('No time points. Reduce time window or minimum frequency.');
end;
if length(timevals) ~= length(tmpind)
verboseprintf(verbose, 'Warning: %d out of %d time values were removed (now %3.2f to %3.2f ms) so the lowest\n', ...
length(timevals)-length(tmpind), length(timevals), timevals(tmpind(1)), timevals(tmpind(end)));
verboseprintf(verbose, ' frequency could be computed with the requested accuracy\n');
end;
timevals = timevals(tmpind);
end;
% find closet points in data
% --------------------------
timeindices = round(eeg_lat2point(timevals, 1, srate, tlimits, 1E-3));
if length(timeindices) < length(unique(timeindices))
timeindices = unique_bc(timeindices)
verboseprintf(verbose, 'Warning: duplicate times, reduce the number of output times\n');
end;
if length(unique(timeindices(2:end)-timeindices(1:end-1))) > 1
verboseprintf(verbose, 'Finding closest points for time variable\n');
verboseprintf(verbose, 'Time values for time/freq decomposition is not perfectly uniformly distributed\n');
else
verboseprintf(verbose, 'Distribution of data point for time/freq decomposition is perfectly uniform\n');
end;
timevals = timevect(timeindices);
function verboseprintf(verbose, varargin)
if strcmpi(verbose, 'on')
fprintf(varargin{:});
end;
|
github
|
lcnbeapp/beapp-master
|
dftfilt3.m
|
.m
|
beapp-master/Packages/eeglab14_1_2b/functions/timefreqfunc/dftfilt3.m
| 7,390 |
utf_8
|
7ef2a5114ee38513d5a55a8f38553cb1
|
% dftfilt3() - discrete complex wavelet filters
%
% Usage:
% >> [wavelet,cycles,freqresol,timeresol] = dftfilt3( freqs, cycles, srate, varargin)
%
% Inputs:
% freqs - vector of frequencies of interest.
% cycles - cycles array. If cycles=0, then the Hanning tapered Short-term FFT is used.
% If one value is given and cycles>0, all wavelets have
% the same number of cycles. If two values are given, the
% two values are used for the number of cycles at the lowest
% frequency and at the highest frequency, with linear or
% log-linear interpolation between these values for intermediate
% frequencies
% srate - sampling rate (in Hz)
%
% Optional Inputs: Input these as 'key/value pairs.
% 'cycleinc' - ['linear'|'log'] increase mode if [min max] cycles is
% provided in 'cycle' parameter. {default: 'linear'}
% 'winsize' Use this option for Hanning tapered FFT or if you prefer to set the length of the
% wavelets to be equal for all of them (e.g., to set the
% length to 256 samples input: 'winsize',256). {default: [])
% Note: the output 'wavelet' will be a matrix and it may be
% incompatible with current versions of timefreq and newtimef.
% 'timesupport' The number of temporal standard deviation used for wavelet lengths {default: 7)
%
% Output:
% wavelet - cell array or matrix of wavelet filters
% timeresol - temporal resolution of Morlet wavelets.
% freqresol - frequency resolution of Morlet wavelets.
%
% Note: The length of the window is always made odd.
%
% Authors: Arnaud Delorme, SCCN/INC/UCSD, La Jolla, 3/28/2003
% Rey Ramirez, SCCN/INC/UCSD, La Jolla, 9/26/2006
% Copyright (C) 3/28/2003 Arnaud Delorme 8, SCCN/INC/UCSD, [email protected]
%
% This program is free software; you can redistribute it and/or modify
% it under the terms of the GNU General Public License as published by
% the Free Software Foundation; either version 2 of the License, or
% (at your option) any later version.
%
% This program is distributed in the hope that it will be useful,
% but WITHOUT ANY WARRANTY; without even the implied warranty of
% MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
% GNU General Public License for more details.
%
% You should have received a copy of the GNU General Public License
% along with this program; if not, write to the Free Software
% Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
%
% Revision 1.12 2006/09/25 rey r
% Almost complete rewriting of dftfilt2.m, changing both Morlet and Hanning
% DFT to be more in line with conventional implementations.
%
% Revision 1.11 2006/09/07 19:05:34 scott
% further clarified the Morlet/Hanning distinction -sm
%
% Revision 1.10 2006/09/07 18:55:15 scott
% clarified window types in help msg -sm
%
% Revision 1.9 2006/05/05 16:17:36 arno
% implementing cycle array
%
% Revision 1.8 2004/03/04 19:31:03 arno
% email
%
% Revision 1.7 2004/02/25 01:45:55 arno
% sinus test
%
% Revision 1.6 2004/02/15 22:23:08 arno
% implementing morlet wavelet
%
% Revision 1.5 2003/05/09 20:55:10 arno
% adding hanning function
%
% Revision 1.4 2003/04/29 16:02:54 arno
% header typos
%
% Revision 1.3 2003/04/29 01:09:16 arno
% debug imaginary part
%
% Revision 1.2 2003/04/28 23:01:13 arno
% *** empty log message ***
%
% Revision 1.1 2003/04/28 22:46:49 arno
% Initial revision
%
function [wavelet,cycles,freqresol,timeresol] = dftfilt3( freqs, cycles, srate, varargin);
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
% Rey fixed all input parameter sorting.
if nargin < 3
error(' A minimum of 3 arguments is required');
end;
numargin=length(varargin);
if rem(numargin,2)
error('There is an uneven number key/value inputs. You are probably missing a keyword or its value.')
end
varargin(1:2:end)=lower(varargin(1:2:end));
% Setting default parameter values.
cycleinc='linear';
winsize=[];
timesupport=7; % Setting default of 7 temporal standard deviations for wavelet's length.
for n=1:2:numargin
keyword=varargin{n};
if strcmpi('cycleinc',keyword)
cycleinc=varargin{n+1};
elseif strcmpi('winsize',keyword)
winsize=varargin{n+1};
if ~mod(winsize,2)
winsize=winsize+1; % Always set to odd length wavelets and hanning windows;
end
elseif strcmpi('timesupport',keyword)
timesupport=varargin{n+1};
else
error(['What is ' keyword '? The only legal keywords are: type, cycleinc, winsize, or timesupport.'])
end
end
if isempty(winsize) & cycles==0
error('If you are using a Hanning tapered FFT, please supply the winsize input-pair.')
end
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
% compute number of cycles at each frequency
% ------------------------------------------
type='morlet';
if length(cycles) == 1 & cycles(1)~=0
cycles = cycles*ones(size(freqs));
elseif length(cycles) == 2
if strcmpi(cycleinc, 'log') % cycleinc
cycles = linspace(log(cycles(1)), log(cycles(2)), length(freqs));
cycles = exp(cycles);
%cycles=logspace(log10(cycles(1)),log10(cycles(2)),length(freqs)); %rey
else
cycles = linspace(cycles(1), cycles(2), length(freqs));
end;
end;
if cycles==0
type='sinus';
end
sp=1/srate; % Rey added this line (i.e., sampling period).
% compute wavelet
for index = 1:length(freqs)
fk=freqs(index);
if strcmpi(type, 'morlet') % Morlet.
sigf=fk/cycles(index); % Computing time and frequency standard deviations, resolutions, and normalization constant.
sigt=1./(2*pi*sigf);
A=1./sqrt(sigt*sqrt(pi));
timeresol(index)=2*sigt;
freqresol(index)=2*sigf;
if isempty(winsize) % bases will be a cell array.
tneg=[-sp:-sp:-sigt*timesupport/2];
tpos=[0:sp:sigt*timesupport/2];
t=[fliplr(tneg) tpos];
psi=A.*(exp(-(t.^2)./(2*(sigt^2))).*exp(2*i*pi*fk*t));
wavelet{index}=psi; % These are the wavelets with variable number of samples based on temporal standard deviations (sigt).
else % bases will be a matrix.
tneg=[-sp:-sp:-sp*winsize/2];
tpos=[0:sp:sp*winsize/2];
t=[fliplr(tneg) tpos];
psi=A.*(exp(-(t.^2)./(2*(sigt^2))).*exp(2*i*pi*fk*t));
wavelet(index,:)=psi; % These are the wavelets with the same length.
% This is useful for doing time-frequency analysis as a matrix vector or matrix matrix multiplication.
end
elseif strcmpi(type, 'sinus') % Hanning
tneg=[-sp:-sp:-sp*winsize/2];
tpos=[0:sp:sp*winsize/2];
t=[fliplr(tneg) tpos];
win = exp(2*i*pi*fk*t);
wavelet(index,:) = win .* hanning(winsize)';
%wavelet{index} = win .* hanning(winsize)';
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
end;
end;
% symmetric hanning function
function w = hanning(n)
if ~rem(n,2)
w = .5*(1 - cos(2*pi*(1:n/2)'/(n+1)));
w = [w; w(end:-1:1)];
else
w = .5*(1 - cos(2*pi*(1:(n+1)/2)'/(n+1)));
w = [w; w(end-1:-1:1)];
end
|
github
|
lcnbeapp/beapp-master
|
rsget.m
|
.m
|
beapp-master/Packages/eeglab14_1_2b/functions/timefreqfunc/rsget.m
| 1,800 |
utf_8
|
47daf6498859ced84787d07802f22789
|
% rsget() - get the p-value for a given collection of l-values
% (Ramberg-Schmeiser distribution)
%
% Usage: p = getfit(l, val)
%
% Input:
% l - [l1 l2 l3 l4] l-values for Ramberg-Schmeiser distribution
% val - value in the distribution to get a p-value estimate at
%
% Output:
% p - p-value
%
% Author: Arnaud Delorme, SCCN, 2003
%
% see also: rspfunc()
%
% Reference: Ramberg, J.S., Tadikamalla, P.R., Dudewicz E.J., Mykkytka, E.F.
% A probability distribution and its uses in fitting data.
% Technimetrics, 1979, 21: 201-214.
% Copyright (C) 2003 Arnaud Delorme, SCCN, [email protected]
%
% This program is free software; you can redistribute it and/or modify
% it under the terms of the GNU General Public License as published by
% the Free Software Foundation; either version 2 of the License, or
% (at your option) any later version.
%
% This program is distributed in the hope that it will be useful,
% but WITHOUT ANY WARRANTY; without even the implied warranty of
% MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
% GNU General Public License for more details.
%
% You should have received a copy of the GNU General Public License
% along with this program; if not, write to the Free Software
% Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
function p = rsget( l, val);
% plot the curve
% --------------
%pval = linspace(0,1, 102); pval(1) = []; pval(end) = [];
%rp = l(1) + (pval.^l(3) - (1-pval).^l(4))/l(2);
%fp = l(2)*1./(l(3).*(pval.^(l(3)-1)) + l(4).*((1-pval).^(l(4)-1)));
%figure; plot(pval, rp);
%figure; plot(rp, fp);
% find p value for a given val
% ----------------------------
p = fminbnd('rspfunc', 0, 1, optimset('TolX',1e-300), l, val);
|
github
|
lcnbeapp/beapp-master
|
rsfit.m
|
.m
|
beapp-master/Packages/eeglab14_1_2b/functions/timefreqfunc/rsfit.m
| 6,481 |
utf_8
|
ea9ce35750ccb745a5f9471fc6554a91
|
% rsfit() - find p value for a given value in a given distribution
% using Ramberg-Schmeiser distribution
%
% Usage: >> p = rsfit(x, val)
% >> [p c l chi2] = rsfit(x, val, plot)
%
% Input:
% x - [float array] accumulation values
% val - [float] value to test
% plot - [0|1|2] plot fit. Using 2, the function avoids creating
% a new figure. Default: 0.
%
% Output:
% p - p value
% c - [mean var skewness kurtosis] distribution cumulants
% l - [4x float vector] Ramberg-Schmeiser distribution best fit
% parameters.
% chi2 - [float] chi2 for goodness of fit (based on 12 bins).
% Fit is significantly different from data histogram if
% chi2 > 19 (5%)
%
% Author: Arnaud Delorme, SCCN, 2003
%
% See also: rsadjust(), rsget(), rspdfsolv(), rspfunc()
%
% Reference: Ramberg, J.S., Tadikamalla, P.R., Dudewicz E.J., Mykkytka, E.F.
% A probability distribution and its uses in fitting data.
% Technimetrics, 1979, 21: 201-214.
% Copyright (C) 2003 Arnaud Delorme, SCCN, [email protected]
%
% This program is free software; you can redistribute it and/or modify
% it under the terms of the GNU General Public License as published by
% the Free Software Foundation; either version 2 of the License, or
% (at your option) any later version.
%
% This program is distributed in the hope that it will be useful,
% but WITHOUT ANY WARRANTY; without even the implied warranty of
% MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
% GNU General Public License for more details.
%
% You should have received a copy of the GNU General Public License
% along with this program; if not, write to the Free Software
% Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
function [p, c, l, res] = rsfit(x, val, plotflag)
if nargin < 2
help rsfit;
return;
end;
if nargin < 3
plotflag = 0;
end;
% moments
% -------
m1 = mean(x);
m2 = sum((x-m1).^2)/length(x);
m3 = sum((x-m1).^3)/length(x);
m4 = sum((x-m1).^4)/length(x);
xmean = m1;
xvar = m2;
xskew = m3/(m2^1.5);
xkurt = m4/(m2^2);
c = [ xmean xvar xskew xkurt ];
if xkurt < 0
disp('rsfit error: Can not fit negative kurtosis');
save('/home/arno/temp/dattmp.mat', '-mat', 'x');
disp('data saved to disk in /home/arno/temp/dattmp.mat');
end;
% find fit
% --------
try,
[sol tmp exitcode] = fminsearch('rspdfsolv', [0.1 0.1], optimset('TolX',1e-12, 'MaxFunEvals', 100000000), abs(xskew), xkurt);
catch, exitcode = 0; % did not converge
end;
if ~exitcode
try, [sol tmp exitcode] = fminsearch('rspdfsolv', -[0.1 0.1], optimset('TolX',1e-12, 'MaxFunEvals', 100000000), abs(xskew), xkurt);
catch, exitcode = 0; end;
end;
if ~exitcode, error('No convergence'); end;
if sol(2)*sol(1) == -1, error('Wrong sign for convergence'); end;
%fprintf(' l-val:%f\n', sol);
res = rspdfsolv(sol, abs(xskew), xkurt);
l3 = sol(1);
l4 = sol(2);
%load res;
%[tmp indalpha3] = min( abs(rangealpha3 - xskew) );
%[tmp indalpha4] = min( abs(rangealpha4 - xkurt) );
%l3 = res(indalpha3,indalpha4,1);
%l4 = res(indalpha3,indalpha4,2);
%res = res(indalpha3,indalpha4,3);
% adjust fit
% ----------
[l1 l2 l3 l4] = rsadjust(l3, l4, xmean, xvar, xskew);
l = [l1 l2 l3 l4];
p = rsget(l, val);
% compute goodness of fit
% -----------------------
if nargout > 3 | plotflag
% histogram of value 12 bins
% --------------------------
[N X] = hist(x, 25);
interval = X(2)-X(1);
X = [X-interval/2 X(end)+interval/2]; % borders
% regroup bin with less than 5 values
% -----------------------------------
indices2rm = [];
for index = 1:length(N)-1
if N(index) < 5
N(index+1) = N(index+1) + N(index);
indices2rm = [ indices2rm index];
end;
end;
N(indices2rm) = [];
X(indices2rm+1) = [];
indices2rm = [];
for index = length(N):-1:2
if N(index) < 5
N(index-1) = N(index-1) + N(index);
indices2rm = [ indices2rm index];
end;
end;
N(indices2rm) = [];
X(indices2rm) = [];
% compute expected values
% -----------------------
for index = 1:length(X)-1
p1 = rsget( l, X(index+1));
p2 = rsget( l, X(index ));
expect(index) = length(x)*(p1-p2);
end;
% value of X2
% -----------
res = sum(((expect - N).^2)./expect);
% plot fit
% --------
if plotflag
if plotflag ~= 2, figure('paperpositionmode', 'auto'); end;
hist(x, 10);
% plot fit
% --------
xdiff = X(end)-X(1);
abscisia = linspace(X(1)-0.2*xdiff, X(end)+0.2*xdiff, 100);
%abscisia = (X(1:end-1)+X(2:end))/2;
expectplot = zeros(1,length(abscisia)-1);
for index = 2:length(abscisia);
p1 = rsget( l, abscisia(index-1));
p2 = rsget( l, abscisia(index ));
expectplot(index-1) = length(x)*(p2-p1);
% have to do this subtraction since this a cumulate density distribution
end;
abscisia = (abscisia(2:end)+abscisia(1:end-1))/2;
hold on; plot(abscisia, expectplot, 'r');
% plot PDF
% ----------
pval = linspace(0,1, 102); pval(1) = []; pval(end) = [];
rp = l(1) + (pval.^l(3) - (1-pval).^l(4))/l(2);
fp = l(2)*1./(l(3).*(pval.^(l(3)-1)) + l(4).*((1-pval).^(l(4)-1)));
[maxval index] = max(expect);
[tmp closestind] = min(abs(rp - abscisia(index)));
fp = fp./fp(closestind)*maxval;
plot(rp, fp, 'g');
legend('Chi2 fit (some bins have been grouped)', 'Pdf', 'Data histogram' );
xlabel('Bins');
ylabel('# of data point per bin');
title (sprintf('Fit of distribution using Ramberg-Schmeiser distribution (Chi2 = %2.4g)', res));
end;
end;
return
|
github
|
lcnbeapp/beapp-master
|
timewarp.m
|
.m
|
beapp-master/Packages/eeglab14_1_2b/functions/timefreqfunc/timewarp.m
| 3,452 |
utf_8
|
910bc9b6a9fca6b6a50908d815239dc6
|
% timewarp() - Given two event marker vectors, computes a matrix
% that can be used to warp a time series so that its
% evlatencies match newlatencies. Values of the warped
% timeserie that falls between two frames in the original
% timeserie will be linear interpolated.
% Usage:
% >> warpmat = timewarp(evlatency, newlatency)
%
% Necessary inputs:
% evlatency - [vector] event markers in the original time series, in frames
% Markers must be ordered by increasing frame latency.
% If you want to warp the entire time-series, make sure
% the first (1) and last frames are in the vector.
% newlatency - [vector] desired warped event time latencies. The original
% time series will be warped so that the frame numbers of its
% events (see evlatency above) match the frame numbers in
% newlatency. newlatency frames must be sorted by ascending
% latency. Both vectors must be the same length.
%
% Optional outputs:
% warpmat - [matrix] Multiplying this matrix with the original
% time series (column) vectors performs the warping.
%
% Example:
% % In 10-frame vectors, warp frames 3 and 5 to frames 4 and 8,
% % respectively. Generate a matrix to warp data epochs in
% % variable 'data' of size (10,k)
% >> warpmat = timewarp([1 3 5 10], [1 4 8 10])
% >> warped_data = warpmat*data;
%
% Authors: Jean Hausser, SCCN/INC/UCSD, 2006
%
% See also: angtimewarp(), phasecoher(), erpimage()
%
function M=timewarp(evLatency, newLatency)
M = [0];
if min(sort(evLatency) == evLatency) == 0
error('evLatency should be in ascending order');
return;
end
if min(sort(newLatency) == newLatency) == 0
error('newLatency should be in ascending order');
return;
end
if length(evLatency) ~= length(newLatency)
error('evLatency and newLatency must have the same length.');
return;
end
if length(evLatency) < 2 | length(newLatency) < 2
error(['There should be at least two events in evlatency and ' ...
'newlatency (e.g., "begin" and "end")'] );
return;
end
if evLatency(1) ~= 1
disp(['Assuming old and new time series beginnings are synchronized.']);
disp(['Make sure you have defined an ending event in both the old and new time series!']);
evLatency(end+1)=1;
newLatency(end+1)=1;
evLatency = sort(evLatency);
newLatency = sort(newLatency);
end
t = 1:max(evLatency);
for k=1:length(evLatency)-1
for i=evLatency(k):evLatency(k+1)-1
tp(i) = (t(i)-evLatency(k)) * ...
(newLatency(k+1) - newLatency(k))/...
(evLatency(k+1) - evLatency(k)) + ...
newLatency(k);
end
end
% Check what's going on at tp(max(newLatency)), should equal t(max(evLatency))
tp(max(evLatency)) = max(newLatency);
ts = tp-min(newLatency)+1;
% $$$ M = sparse(max(newLatency)-min(newLatency)+1, max(evLatency));
M = zeros(max(newLatency)-min(newLatency)+1, max(evLatency));
k = 0;
for i=1:size(M,1)
while i > ts(k+1)
k = k+1;
end
% $$$ k = k-1;
if k == 0
% Check wether i == ts(1) and i == 1
% In that case, M(1,1) = 1
M(1,1) = 1;
else
M(i,k) = 1 - (i-ts(k))/(ts(k+1)-ts(k));
M(i,k+1) = 1 - (ts(k+1)-i)/(ts(k+1)-ts(k));
end
end
|
github
|
lcnbeapp/beapp-master
|
angtimewarp.m
|
.m
|
beapp-master/Packages/eeglab14_1_2b/functions/timefreqfunc/angtimewarp.m
| 4,683 |
utf_8
|
f46e870ae5d7873544a08ffa9a4ff38b
|
% angtimewarp() - Given two event marker vectors, computes a
% warping of the input angular time series so that its
% evlatencies match newlatencies. Values of the warped
% timeserie that falls between two frames in the original
% timeserie will be linearly interpolated under the
% assumption that phase change is minimal between two
% successive time points.
% Usage:
% >> warpAngs = angtimewarp(evlatency, newlatency, angData)
%
% Necessary inputs:
% evlatency - [vector] time markers on the original time-series, in
% frames. Markers must be ordered by increasing
% latency. If you want to warp the entire time series,
% make sure frame 1 and the last frame are in the vector.
% newlatency - [vector] desired time marker latencies. The original
% time series will be warped so that its time markers (see
% evlatency) match the ones in newlatency. newlatency
% frames must be sorted by ascending latencies in frames.
% Both vectors have to be the same length.
% angData - [vector] original angular time series (in radians).
% Angles should be between -pi and pi.
%
% Optional outputs:
% warpAngs - [vector] warped angular time-course, with values between
% -pi and pi
%
% Example:
% >> angs = 2*pi*rand(1,10)-pi;
% >> warpangs = angtimewarp([1 5 10], [1 6 10], angs)
%
% Authors: Jean Hausser, SCCN/INC/UCSD, 2006
%
% See also: timeWarp(), phasecoher(), erpimage(), newtimef()
%
function angdataw=angtimewarp(evLatency, newLatency, angdata)
if min(sort(evLatency) == evLatency) == 0
error('evlatency should be sorted');
return;
end
if min(sort(newLatency) == newLatency) == 0
error('newlatency should be sorted');
return;
end
if length(evLatency) ~= length(newLatency)
error('evlatency and newlatency must have the same length.');
return;
end
if length(evLatency) < 2 | length(newLatency) < 2
error(['There should be at least two events in evlatency and ' ...
'newlatency, that is "begin" and "end"' ]);
return;
end
if evLatency(1) ~= 1
disp(['Assuming old and new time series beginnings are ' ...
'synchronized']);
disp(['Make sure you defined an end event for both old and new time ' ...
'series !']);
evLatency(end+1)=1;
newLatency(end+1)=1;
evLatency = sort(evLatency);
newLatency = sort(newLatency);
end
t = 1:max(evLatency);
for k=1:length(evLatency)-1
for i=evLatency(k):evLatency(k+1)-1
tp(i) = (t(i)-evLatency(k)) * ...
(newLatency(k+1) - newLatency(k))/...
(evLatency(k+1) - evLatency(k)) + ...
newLatency(k);
end
end
%Check what's going on at tp(max(newLatency)), should equal t(max(evLatency))
tp(max(evLatency)) = max(newLatency);
ts = tp-min(newLatency)+1;
angdataw = zeros(1, max(newLatency)-min(newLatency)+1);
k = 0;
for i=1:length(angdataw)
while i > ts(k+1)
k = k+1;
end
if k == 0
angdataw(1) = angdata(1);
else
%Linear interp
angdataw(i) = angdata(k)*(1 - (i-ts(k))/(ts(k+1)-ts(k))) + ...
angdata(k+1)*(1 - (ts(k+1)-i)/(ts(k+1)-ts(k)));
% %Correction because angles have a ring structure
% theta1 = [angdata(k) angdata(k+1) angdataw(i)];
% theta2 = theta1 - min(angdata(k), angdata(k+1));
% theta2max = max(theta2(1), theta2(2));
% if ~ ( (theta2max <= pi & theta2(3) <= theta2max) | ...
% (theta2max >= pi & theta2(3) >= theta2max) | ...
% theta2(3) == theta2(1) | theta2(3) == theta2(2) )
% angdataw(i) = angdataw(i) + pi;
% end
% if angdataw(i) > pi %Make sure we're still on [-pi, pi]
% angdataw(i) = angdataw(i) - 2*pi;
% end
end
end
angdataw = wrap2pi(angdataw);
function a = wrap2pi(a, a_center )
% function a = wrap(a,a_center)
%
% Wraps angles to a range of 2*pi.
% Inverse of Matlab's "unwrap", and better than wrapToPi ( which has
% redundant [-pi,pi])
% Optional input "a_center" defines the center angle. Default is 0, giving
% angles from (-pi,pi], chosen to match angle(complex(-1,0)). Maximum
% possible value is pi.
% T.Hilmer, UH
% 2010.10.18 version 2
% removed code from version 1. Have not bug-checked second input
% "a_center"
if nargin < 2, a_center = 0; end
% new way
a = mod(a,2*pi); % [0 2pi)
% shift
j = a > pi - a_center;
a(j) = a(j) - 2*pi;
j = a < a_center - pi;
a(j) = a(j) + 2*pi;
|
github
|
lcnbeapp/beapp-master
|
shortread.m
|
.m
|
beapp-master/Packages/eeglab14_1_2b/functions/miscfunc/shortread.m
| 2,642 |
utf_8
|
7efadd1fb9c9395f1cd3c917e6a93675
|
% shortread() - Read matrix from short file.
%
% Usage:
% >> A = shortread(filename,size,'format',offset)
%
% Inputs:
% filename - Read matrix a from specified file while assuming four byte
% short integers.
% size - The vector SIZE determine the number of short elements to be
% read and the dimensions of the resulting matrix. If the last
% element of SIZE is INF the size of the last dimension is determined
% by the file length.
%
% Optional inputs:
% 'format' - The option FORMAT argument specifies the storage format as
% defined by fopen(). Default format ([]) is 'native'.
% offset - The option OFFSET is offset in shorts from the beginning of file (=0)
% to start reading (2-byte shorts assumed).
% It uses fseek to read a portion of a large data file.
%
% Author: Sigurd Enghoff, CNL / Salk Institute, La Jolla, 7/1998
%
% See also: floatread(), floatwrite(), fopen()
% Copyright (C) Sigurd Enghoff, CNL / Salk Institute, La Jolla, 7/1998
%
% This program is free software; you can redistribute it and/or modify
% it under the terms of the GNU General Public License as published by
% the Free Software Foundation; either version 2 of the License, or
% (at your option) any later version.
%
% This program is distributed in the hope that it will be useful,
% but WITHOUT ANY WARRANTY; without even the implied warranty of
% MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
% GNU General Public License for more details.
%
% You should have received a copy of the GNU General Public License
% along with this program; if not, write to the Free Software
% Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
% xx-07-98 written by Sigurd Enghoff, Salk Institute
% 04-26-99 modified by Sigurd Enghoff to handle variable-sized and
% multi-dimensional data.
% 07-08-99 modified by Sigurd Enghoff, FORMAT argument added.
% 02-08-00 help updated for toolbox inclusion -sm
% 02-14-00 added segment arg -sm
function A = shortread(fname,Asize,fform,offset)
if ~exist('fform') | isempty(fform)|fform==0
fform = 'native';
end
fid = fopen(fname,'rb',fform);
if fid>0
if exist('offset')
stts = fseek(fid,2*offset,'bof');
if stts ~= 0
error('shortread(): fseek() error.');
return
end
end
A = fread(fid,prod(Asize),'short');
else
error('shortread(): fopen() error.');
return
end
fprintf(' %d shorts read\n',prod(size(A)));
if Asize(end) == Inf
Asize = Asize(1:end-1);
A = reshape(A,[Asize length(A)/prod(Asize)]);
else
A = reshape(A,Asize);
end
fclose(fid);
|
github
|
lcnbeapp/beapp-master
|
scanfold.m
|
.m
|
beapp-master/Packages/eeglab14_1_2b/functions/miscfunc/scanfold.m
| 2,396 |
utf_8
|
fc03538051488f1358961f46484d958d
|
% scanfold() - scan folder content
%
% Usage:
% >> [cellres textres] = scanfold(foldname);
% >> [cellres textres] = scanfold(foldname, ignorelist, maxdepth);
%
% Inputs:
% foldname - [string] name of the folder
% ignorelist - [cell] list of folders to ignore
% maxdepth - [integer] maximum folder depth
%
% Outputs:
% cellres - cell array containing all the files
% textres - string array containing all the names preceeded by "-a"
%
% Authors: Arnaud Delorme, SCCN, INC, UCSD, 2009
% Copyright (C) Arnaud Delorme, SCCN, INC, UCSD, October 11, 2004, [email protected]
%
% This program is free software; you can redistribute it and/or modify
% it under the terms of the GNU General Public License as published by
% the Free Software Foundation; either version 2 of the License, or
% (at your option) any later version.
%
% This program is distributed in the hope that it will be useful,
% but WITHOUT ANY WARRANTY; without even the implied warranty of
% MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
% GNU General Public License for more details.
%
% You should have received a copy of the GNU General Public License
% along with this program; if not, write to the Free Software
% Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
function [ cellres, textres ] = scanfold(foldname, ignorelist, maxdepth)
if nargin < 2, ignorelist = {}; end;
if nargin < 3, maxdepth = 100; end;
foldcontent = dir(foldname);
textres = '';
cellres = {};
if maxdepth == 0, return; end;
for i = 1:length(foldcontent)
if (exist(foldcontent(i).name) == 7 || strcmpi(foldcontent(i).name, 'functions')) && ~ismember(foldcontent(i).name, ignorelist)
if ~strcmpi(foldcontent(i).name, '..') && ~strcmpi(foldcontent(i).name, '.')
disp(fullfile(foldname, foldcontent(i).name));
[tmpcellres tmpres] = scanfold(fullfile(foldname, foldcontent(i).name), ignorelist, maxdepth-1);
textres = [ textres tmpres ];
cellres = { cellres{:} tmpcellres{:} };
end;
elseif length(foldcontent(i).name) > 2
if strcmpi(foldcontent(i).name(end-1:end), '.m')
textres = [ textres ' -a ' foldcontent(i).name ];
cellres = { cellres{:} foldcontent(i).name };
end;
else
disp( [ 'Skipping ' fullfile(foldname, foldcontent(i).name) ]);
end;
end;
return;
|
github
|
lcnbeapp/beapp-master
|
datlim.m
|
.m
|
beapp-master/Packages/eeglab14_1_2b/functions/miscfunc/datlim.m
| 641 |
utf_8
|
f4c0160c492f5049e9dbcc932cafe0e7
|
% datlim() - return min and max of a matrix
%
% Usage:
% >> limits_vector = datlim(data);
%
% Input:
% data - numeric array
% Outputs:
% limits_vector = [minval maxval]
%
% Author: Scott Makeig, SCCN/INC/UCSD, May 28, 2005
function [limits_vector] = datlim(data)
if ~isnumeric(data)
error('data must be a numeric array')
return
end
limits_vector = [ min(data(:)) max(data(:)) ]; % thanks to Arno Delorme
% minval = squeeze(min(data)); maxval = squeeze(max(data));
% while numel(minval) > 1
% minval = squeeze(min(minval)); maxval = squeeze(max(maxval));
% end
% limits_vector = [minval maxval];
|
github
|
lcnbeapp/beapp-master
|
lapplot.m
|
.m
|
beapp-master/Packages/eeglab14_1_2b/functions/miscfunc/lapplot.m
| 4,148 |
utf_8
|
bbfb726aee519b4b7b446c516439e24f
|
% lapplot() - Compute the discrete laplacian of EEG scalp distribution(s)
%
% Usage:
% >> laplace = lapplot(map,eloc_file,draw)
%
% Inputs:
% map - Activity levels, size (nelectrodes,nmaps)
% eloc_file - Electrode location filename (.loc file)
% For format, see >> topoplot example
% draw - If defined, draw the map(s) {default: no}
%
% Output:
% laplace - Laplacian map, size (nelectrodes,nmaps)
%
% Note: uses del2()
%
% Author: Scott Makeig, SCCN/INC/UCSD, La Jolla, 1998
%
% See also: topoplot(), gradplot()
% Copyright (C) Scott Makeig, SCCN/INC/UCSD, La Jolla, 1998
%
% This program is free software; you can redistribute it and/or modify
% it under the terms of the GNU General Public License as published by
% the Free Software Foundation; either version 2 of the License, or
% (at your option) any later version.
%
% This program is distributed in the hope that it will be useful,
% but WITHOUT ANY WARRANTY; without even the implied warranty of
% MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
% GNU General Public License for more details.
%
% You should have received a copy of the GNU General Public License
% along with this program; if not, write to the Free Software
% Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
% 01-25-02 reformated help & license, added links -ad
function [laplac] = lapplot(map,filename,draw)
if nargin < 2
help lapplot;
return;
end;
MAXCHANS = size(map,1);
GRID_SCALE = 2*MAXCHANS+5;
MAX_RADIUS = 0.5;
% ---------------------
% Read the channel file
% ---------------------
if isstr( filename )
fid = fopen(filename);
locations = fscanf(fid,'%d %f %f %s',[7 MAXCHANS]);
fclose(fid);
locations = locations';
Th = pi/180*locations(:,2); % convert degrees to rads
Rd = locations(:,3);
ii = find(Rd <= MAX_RADIUS); % interpolate on-scalp channels only
Th = Th(ii);
Rd = Rd(ii);
[x,y] = pol2cart(Th,Rd);
else
x = real(filename);
y = imag(filename);
end;
% ---------------------------------------------------
% Locate nearest position of an electrode in the grid
% ---------------------------------------------------
xi = linspace(-0.5,0.5,GRID_SCALE); % x-axis description (row vector)
yi = linspace(-0.5,0.5,GRID_SCALE); % y-axis description (row vector)
for i=1:MAXCHANS
[useless_var horizidx(i)] = min(abs(y(i) - xi)); % find pointers to electrode
[useless_var vertidx(i)] = min(abs(x(i) - yi)); % positions in Zi
end;
% -----------------
% Compute laplacian
% -----------------
for i=1:size(map,2)
[Xi,Yi,Zi] = griddata(y,x,map(:,i),yi',xi, 'v4'); % interpolate data
laplac2D = del2(Zi);
positions = horizidx + (vertidx-1)*GRID_SCALE;
laplac(:,i) = laplac2D(positions(:));
% ------------------
% Draw laplacian map
% ------------------
if exist('draw');
mask = (sqrt(Xi.^2+Yi.^2) <= MAX_RADIUS);
laplac2D(find(mask==0)) = NaN;
subplot(ceil(sqrt(size(map,2))), ceil(sqrt(size(map,2))), i);
contour(laplac2D);
title( int2str(i) );
% %%% Draw Head %%%%
ax = axis;
width = ax(2)-ax(1);
axis([ax(1)-width/3 ax(2)+width/3 ax(3)-width/3 ax(4)+width/3])
steps = 0:2*pi/100:2*pi;
basex = .18*MAX_RADIUS;
tip = MAX_RADIUS*1.15;
base = MAX_RADIUS-.004;
EarX = [.497 .510 .518 .5299 .5419 .54 .547 .532 .510 .489];
EarY = [.0555 .0775 .0783 .0746 .0555 -.0055 -.0932 -.1313 -.1384 -.1199];
HCOLOR = 'k';
HLINEWIDTH = 1.8;
% Plot Head, Ears, Nose
hold on
plot(1+width/2+cos(steps).*MAX_RADIUS*width,...
1+width/2+sin(steps).*MAX_RADIUS*width,...
'color',HCOLOR,'Linestyle','-','LineWidth',HLINEWIDTH); % head
plot(1+width/2+[.18*MAX_RADIUS*width;0;-.18*MAX_RADIUS*width],...
1+width/2+[base;tip;base]*width,...
'Color',HCOLOR,'LineWidth',HLINEWIDTH); % nose
plot(1+width/2+EarX*width,...
1+width/2+EarY*width,...
'color',HCOLOR,'LineWidth',HLINEWIDTH) % l ear
plot(1+width/2-EarX*width,...
1+width/2+EarY*width,...
'color',HCOLOR,'LineWidth',HLINEWIDTH) % r ear
hold off
axis off
end;
end;
return;
|
github
|
lcnbeapp/beapp-master
|
compmap.m
|
.m
|
beapp-master/Packages/eeglab14_1_2b/functions/miscfunc/compmap.m
| 9,132 |
utf_8
|
91717f8d02db6c0193adc7ece08828ca
|
% compmap() - Plot multiple topoplot() maps of ICA component topographies
% Click on an individual map to view separately.
% Usage:
% >> compmap (winv,'eloc_file',compnos,'title',rowscols,labels,printflag)
%
% Inputs:
% winv - Inverse weight matrix = EEG scalp maps. Each column is a
% map; the rows correspond to the electrode positions
% defined in the eloc_file. Normally, winv = inv(weights*sphere).
% 'eloc_file' - Name of the eloctrode position file in the style defined
% by >> topoplot example {default|0 ->'chan_file'}
% compnos - Vector telling which (order of) component maps to show
% Indices <0 tell compmap to invert a map; = 0 leave blank sbplot
% Example [1 0 -2 3 0 -6] {default|0 -> 1:columns_in_winv}
% 'title' - Title string for each page {default|0 -> 'ICA Component Maps'}
% rowscols - Vector of the form [m,n] where m is total vertical tiles and n
% is horizontal tiles per page. If the number of maps exceeds m*n,
% multiple figures will be produced {def|0 -> one near-square page}.
% labels - Vector of numbers or a matrix of strings to use as labels for
% each map, else ' ' -> no labels {default|0 -> 1:ncolumns_in_winv}
% printflag - 0= screen-plot colors {default}
% 1= printer-plot colors
%
% Note: Map scaling is to +/-max(abs(data); green = 0
%
% Author: Colin Humphries, CNL / Salk Institute, Aug, 1996
%
% See also: topoplot()
% This function calls topoplot(). and cbar().
% Copyright (C) Colin Humphries & Scott Makeig, CNL / Salk Institute, Aug, 1996
%
% This program is free software; you can redistribute it and/or modify
% it under the terms of the GNU General Public License as published by
% the Free Software Foundation; either version 2 of the License, or
% (at your option) any later version.
%
% This program is distributed in the hope that it will be useful,
% but WITHOUT ANY WARRANTY; without even the implied warranty of
% MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
% GNU General Public License for more details.
%
% You should have received a copy of the GNU General Public License
% along with this program; if not, write to the Free Software
% Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
% Colin Humphries, CNL / Salk Institute, Aug, 1996
% 03-97 revised -CH
% 11-05-97 revised for Matlab 5.0.0.4064; added negative compnnos option
% improved help msg; added figure offsets -Scott Makeig & CH
% 11-13-97 fixed compnos<0 bug -sm
% 11-18-97 added test for labels=comps -sm
% 12-08-97 added test for colorbar_tp() -sm
% 12-15-97 added axis('square'), see SQUARE below -sm
% 03-09-98 added test for eloc_file, fixed size checking for labels -sm
% 02-09-00 added test for ' ' for srclabels(1,1) -sm
% 02-23-00 added srclabels==' ' -> no labels -sm
% 03-16-00 added axcopy() -sm & tpj
% 02-25-01 added test for max(compnos) -sm
% 05-24-01 added HEADPLOT logical flag below -sm
% 01-25-02 reformated help & license -ad
% NOTE:
% There is a minor problem with the Matlab function colorbar().
% Use the toolbox cbar() instead.
function compmap(Winv,eloc_file,compnos,titleval,pagesize,srclabels,printlabel,caxis)
DEFAULT_TITLE = 'ICA Component Maps';
DEFAULT_EFILE = 'chan_file';
NUMCONTOUR = 5; % topoplot() style settings
OUTPUT = 'screen'; % default: 'screen' for screen colors,
% 'printer' for printer colors
STYLE = 'both';
INTERPLIMITS = 'head';
MAPLIMITS = 'absmax';
SQUARE = 1; % 1/0 flag making topoplot() asex square -> round heads
ELECTRODES = 'on'; % default: 'on' or 'off'
ELECTRODESIZE = []; % defaults 1-10 set in topoplot text.
HEADPLOT = 0; % 1/0 plot 3-D headplots instead of 2-d topoplots.
if nargin<1
help compmap
return
end
curaxes = gca;
curpos = get(curaxes,'Position');
mapaxes = axes('Position',[curpos(1) curpos(2)+0.09 curpos(3) curpos(4)-0.09],...
'Visible','off');
% leave room for cbar
set(mapaxes,'visible','off');
pos = get(mapaxes,'Position');
% delete(gca);
% ax = axes('Position',pos);
[chans, frames] = size (Winv);
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
% check inputs and set defaults
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
if nargin==8
if strcmp(caxis(1,1:2), 'mi') % min/max of data
MAPLIMITS = [min(min(Winv(:,compnos))) max(max(Winv(:,compnos)))];
elseif caxis(1,1:2) == 'ab' % +/-max abs data
absmax = max([abs(min(min(Winv(:,compnos)))) abs(max(max(Winv(:,compnos))))]);
MAPLIMITS = [-absmax absmax];
elseif size(caxis) == [1,2] % given color axis limits
MAPLIMITS = caxis;
end % else default
end
if nargin < 7
printlabel = 0;
end
if printlabel == 0
printlabel = OUTPUT; % default set above
else
printlabel = 'printer';
end
if nargin < 6
srclabels = 0;
end
if nargin < 5
pagesize = 0;
end
if nargin < 4
titleval = 0;
end
if nargin < 3
compnos = 0;
end
if nargin < 2
eloc_file = 0;
end
if srclabels == 0
srclabels = [];
end
if titleval == 0;
titleval = DEFAULT_TITLE;
end
if compnos == 0
compnos = (1:frames);
end
if max(compnos)>frames
fprintf('compmap(): Cannot show comp %d. Only %d components in inverse weights\n',...
max(compnos),frames);
return
end
if pagesize == 0
numsources = length(compnos);
DEFAULT_PAGE_SIZE = ...
[floor(sqrt(numsources)) ceil(numsources/floor(sqrt(numsources)))];
m = DEFAULT_PAGE_SIZE(1);
n = DEFAULT_PAGE_SIZE(2);
elseif length(pagesize) ==1
help compmap
return
else
m = pagesize(1);
n = pagesize(2);
end
if eloc_file == 0
eloc_file = DEFAULT_EFILE;
end
totalsources = length(compnos);
if ~isempty(srclabels)
if ~ischar(srclabels(1,1)) | srclabels(1,1)==' ' % if numbers
if size(srclabels,1) == 1
srclabels = srclabels';
end
end
if size(srclabels,1)==1 & size(srclabels,2)==1 & srclabels==' '
srclabels = repmat(srclabels,totalsources,1);
end
if size(srclabels,1) ~= totalsources,
fprintf('compmap(): numbers of components and component labels do not agree.\n');
return
end
end
pages = ceil(totalsources/(m*n));
if pages > 1
fprintf('compmap(): will create %d figures of %d by %d maps: ',...
pages,m,n);
end
off = [ 25 -25 0 0]; % position offsets for multiple figures
fid = fopen(eloc_file);
if fid<1,
fprintf('compmap()^G: cannot open eloc_file (%s).\n',eloc_file);
return
end
fclose(fid);
%%%%%%%%%%%%%%%%%%%%%%%%%%%%% plot the maps %%%%%%%%%%%%%%%%%%%%%%%
for i = (1:pages)
if i > 1
figure('Position',pos+(i-1)*off); % place figures in right-downward stack
set(gca,'Color','w') %CJH - set background color to white
curaxes = gca;
curpos = get(curaxes,'Position'); % new whole-figure axes
end
if (totalsources > i*m*n)
sbreak = n*m;
else
sbreak = totalsources - (i-1)*m*n; % change page/figure after this many
end
for j = (1:sbreak) % maps on this page/figure
comp = j+(i-1)*m*n; % compno index
if compnos(comp)~=0
if compnos(comp)>0
source_var = Winv(:,compnos(comp))'; % plot map
elseif compnos(comp)<0
source_var = -1*Winv(:,-1*compnos(comp))'; % invert map
end
sbplot(m,n,j,'ax',mapaxes);
if HEADPLOT
headplot(source_var,eloc_file,'electrodes','off'); % 3-d image
else
topoplot(source_var,eloc_file,...
'style',STYLE,...
'electrodes',ELECTRODES,...
'emarkersize',ELECTRODESIZE,...
'numcontour',NUMCONTOUR,...
'interplimits',INTERPLIMITS,...
'maplimits',MAPLIMITS); % draw 2-d scalp map
end
if SQUARE,
axis('square');
end
if isempty(srclabels)
title(int2str(compnos(comp))) ;
else
if ischar(srclabels)
title(srclabels(comp,:));
else
title(num2str(srclabels(comp)));
end
end
drawnow % draw one map at a time
end
end
% ax = axes('Units','Normal','Position',[.5 .06 .32 .05],'Visible','Off');
axes(curaxes);
set(gca,'Visible','off','Units','normalized');
curpos = get(gca,'position');
ax = axes('Units','Normalized','Position',...
[curpos(1)+0.5*curpos(3) curpos(2)+0.01*curpos(4) ...
0.32*curpos(3) 0.05*curpos(4)],'Visible','Off');
if exist('cbar') == 2
cbar(ax); % Slightly altered Matlab colorbar()
% Write authors for further information.
else
colorbar(ax); % Note: there is a minor problem with this call.
end
axval = axis;
Xlim = get(ax,'Xlim');
set(ax,'XTick',(Xlim(2)+Xlim(1))/2);
set(ax,'XTickMode','manual');
set(ax,'XTickLabelMode','manual');
set(ax,'XTickLabel','0');
axes(curaxes);
axis off;
% axbig = axes('Units','Normalized','Position',[0 0 1 1],'Visible','off');
t1 = text(.25,.07,titleval,'HorizontalAlignment','center');
if pages > 1
fprintf('%d ',i);
end
axcopy(gcf); % allow popup window of single map with mouse click
end
if pages > 1
fprintf('\n');
end
|
github
|
lcnbeapp/beapp-master
|
topoimage.m
|
.m
|
beapp-master/Packages/eeglab14_1_2b/functions/miscfunc/topoimage.m
| 21,312 |
utf_8
|
952b9066313797fa812f1352f2586565
|
% topoimage() - plot concatenated multichannel time/frequency images
% in a topographic format
% Uses a channel location file with the same format as topoplot()
% or else plots data on a rectangular grid of axes.
% Click on individual images to examine separately.
%
% Usage:
% >> topoimage(data,'chan_locs',ntimes,limits);
% >> topoimage(data,[rows cols],ntimes,limits);
% >> topoimage(data,'chan_locs',ntimes,limits,title,...
% channels,axsize,colors,ydir,rmbase)
%
% Inputs:
% data = data consisting of nchans images, each size (rows,ntimes*chans)
% 'chan_locs' = file of channel locations as in >> topoplot example
% Else [rows cols] matrix of locations. Example: [6 4]
% ntimes = columns per image
% [limits] = [mintime maxtime minfreq maxfreq mincaxis maxcaxis]
% Give times in msec {default|0 (|both caxis 0) -> use data limits)
% 'title' = plot title {0 -> none}
% channels = vector of channel numbers to plot & label {0 -> all}
% axsize = [x y] axis size {default [.08 .07]}
% 'colors' = file of color codes, 3 chars per line
% ( '.' = space) {0 -> default color order}
% ydir = y-axis polarity (pos-up = 1; neg-up = -1) {def -> pos-up}
% rmbase = if ~=0, remove the mean value for times<=0 for each freq {def -> no}
%
% Author: Scott Makeig, SCCN/INC/UCSD, La Jolla, 12-10-1999
%
% See also: topoplot(), timef()
% Copyright (C) 12-10-99 Scott Makeig, SCCN/INC/UCSD, [email protected]
%
% This program is free software; you can redistribute it and/or modify
% it under the terms of the GNU General Public License as published by
% the Free Software Foundation; either version 2 of the License, or
% (at your option) any later version.
%
% This program is distributed in the hope that it will be useful,
% but WITHOUT ANY WARRANTY; without even the implied warranty of
% MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
% GNU General Public License for more details.
%
% You should have received a copy of the GNU General Public License
% along with this program; if not, write to the Free Software
% Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
% 1-16-00 debugged help msg and improved presentation -sm
% 3-16-00 added axcopy() -sm
% 8-07-00 added logimagesc() via 'LOGIT' -sm
% 9-02-00 added RMBASE option below, plus colorbar to key image -sm ???
% 1-25-02 reformated help & license, added link -ad
function topoimage(data,loc_file,times,limits,plottitle,channels,axsize,colors,ydr,rmbas)
% Options:
% LOGIT = 1; % comment out for non-log imaging
% YVAL = 10; % plot horizontal lines at 10 Hz (comment to omit)
% RMBASE = 0; % remove <0 mean for each image row
MAXCHANS = 256;
DEFAULT_AXWIDTH = 0.08;
DEFAULT_AXHEIGHT = 0.07;
DEFAULT_SIGN = 1; % Default - plot positive-up
LINEWIDTH = 2.0;
FONTSIZE = 14; % font size to use for labels
CHANFONTSIZE = 10; % font size to use for channel names
TICKFONTSIZE=10; % font size to use for axis labels
TITLEFONTSIZE = 16;
PLOT_WIDTH = 0.75; % width and height of plot array on figure!
PLOT_HEIGHT = 0.81;
ISRECT = 0; % default
if nargin < 1,
help topoimage
return
end
if nargin < 4,
help topoimage
error('topoimage(): needs four arguments');
end
if times <0,
help topoimage
return
elseif times==1,
fprintf('topoimage: cannot plot less than 2 times per image.\n');
return
else
freqs = 0;
end;
axcolor= get(0,'DefaultAxesXcolor'); % find what the default x-axis color is
plotfile = 'topoimage.ps';
ls_plotfile = 'ls -l topoimage.ps';
%
%%%%%%%%%%%%%%%%%%%%%%%%%% Substitute defaults for missing parameters %%%%%
%
SIGN = DEFAULT_SIGN;
if nargin < 10
rmbas = 0;
end
if nargin < 9
ydr = 0;
end
if ydr == -1
SIGN = -1;
end
if nargin < 8
colors = 0;
end
if nargin < 7,
axwidth = DEFAULT_AXWIDTH;
axheight = DEFAULT_AXHEIGHT;
elseif size(axsize) == [1 1] & axsize(1) == 0
axwidth = DEFAULT_AXWIDTH;
axheight = DEFAULT_AXHEIGHT;
elseif size(axsize) == [1 2]
axwidth = axsize(1);
axheight = axsize(2);
if axwidth > 1 | axwidth < 0 | axheight > 1 | axwidth < 0
help topoimage
return
end
else
help topoimage
return
end
[freqs,framestotal]=size(data); % data size
chans = framestotal/times;
fprintf('\nPlotting data using axis size [%g,%g]\n',axwidth,axheight);
if nargin < 6
channels = 0;
end
if channels == 0
channels = 1:chans;
end
if nargin < 5
plottitle = 0; %CJH
end
limitset = 0;
if nargin < 4,
limits = 0;
elseif length(limits)>1
limitset = 1;
end
%%%%%%%%%%%%%%%%%%%%%%%%%%% Test parameters %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%
icadefs; % read MAXPLOTDATACHANS constant from icadefs.m
if max(channels) > chans
fprintf('topoimage(): max channel index > %d channels in data.\n',...
chans);
return
end
if min(channels) < 1
fprintf('topoimage(): min channel index (%g) < 1.\n',...
min(channels));
return
end;
if length(channels)>MAXPLOTDATACHANS,
fprintf('topoimage(): not set up to plot more than %d channels.\n',...
MAXPLOTDATACHANS);
return
end;
%
%%%%%%%%%%%%% Extend the size of the plotting area in the window %%%%%%%%%%%%
%
curfig = gcf;
h=figure(curfig);
set(h,'Color',BACKCOLOR); % set the background color
set(h,'PaperUnits','normalized'); % use percentages to avoid US/A4 difference
set(h,'PaperPosition',[0.0235308 0.0272775 0.894169 0.909249]); % equivalent
% orient portrait
axis('normal');
%
%%%%%%%%%%%%%%%%%%%% Read the channel names %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%
if isstr(channels) == 0,
% channames = zeros(MAXPLOTDATACHANS,4);
% for c=1:length(channels),
% channames(c,:)= sprintf('%4d',channels(c));
% end;
channames = num2str(channels(:)); %%CJH
else,
if ~isstr(channels)
fprintf('topoimage(): channel file name must be a string.\n');
return
end
chid = fopen(channels,'r');
if chid <3,
fprintf('topoimage(): cannot open file %s.\n',channels);
return
end;
channames = fscanf(chid,'%s',[4 MAXPLOTDATACHANS]);
channames = channames';
[r c] = size(channames);
for i=1:r
for j=1:c
if channames(i,j)=='.',
channames(i,j)=' ';
end;
end;
end;
end; % setting channames
%
%%%%%%%%%%%%%%%%%%%%%%%%% Plot and label specified channels %%%%%%%%%%%%%%%%%%
%
data = matsel(data,times,0,0,channels);
chans = length(channels);
%
%%%%%%%%%%%%%%%%%%%%%%%%% Read the color names %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%
if colors ~=0,
if ~isstr(colors)
fprintf('topoimage(): color file name must be a string.\n');
return
end
cid = fopen(colors,'r');
% fprintf('cid = %d\n',cid);
if cid <3,
fprintf('topoimage: cannot open file %s.\n',colors);
return
end;
colors = fscanf(cid,'%s',[3 MAXPLOTDATAEPOCHS]);
colors = colors';
[r c] = size(colors);
for i=1:r
for j=1:c
if colors(i,j)=='.',
colors(i,j)=' ';
end;
end;
end;
else % use default color order (no yellow!)
colors =['r ';'b ';'g ';'c ';'m ';'r ';'b ';'g ';'c ';'m ';'r ';'b ';'g ';'c ';'m ';'r ';'b ';'g ';'c ';'m ';'r ';'b ';'g ';'c ';'m ';'r ';'b ';'g ';'c ';'m ';'r ';'b ';'g ';'c ';'m '];
colors = [colors; colors]; % make > 64 available
end;
for c=1:length(colors) % make white traces black unless axis color is white
if colors(c,1)=='w' & axcolor~=[1 1 1]
colors(c,1)='k';
end
end
%
%%%%%%%%%%%%%%%%%%%%%%% Read and adjust limits %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%
if limits==0, % == 0 or [0 0 0 0]
xmin=min(times);
xmax=max(times);
ymin=min(freqs);
ymax=max(freqs);
else
if length(limits)~=6,
fprintf( ...
'topoimage: limits should be 0 or an array [xmin xmax ymin ymax zmin zmax].\n');
return
end;
xmin = limits(1);
xmax = limits(2);
ymin = limits(3);
ymax = limits(4);
zmin = limits(5);
zmax = limits(6);
end;
if xmax == 0 & xmin == 0,
x = [0:1:times-1];
xmin = min(x);
xmax = max(x);
else
dx = (xmax-xmin)/(times-1);
x=xmin*ones(1,times)+dx*(0:times-1); % compute x-values
xmax = xmax*times/times;
end;
if xmax<=xmin,
fprintf('topoimage() - xmax must be > xmin.\n')
return
end
if ymax == 0 & ymin == 0,
y=[1:1:freqs];
ymax=freqs;
ymin=1;
else
dy = (ymax-ymin)/(freqs-1);
y=ymin*ones(1,freqs)+dy*(0:freqs-1); % compute y-values
ymax = max(y);
end
if ymax<=ymin,
fprintf('topoimage() - ymax must be > ymin.\n')
return
end
if zmax == 0 & zmin == 0,
zmax=max(max(data));
zmin=min(min(data));
fprintf('Color axis limits [%g,%g]\n',zmin,zmax);
end
if zmax<=zmin,
fprintf('topoimage() - zmax must be > zmin.\n')
return
end
xlabel = 'Time (ms)';
ylabel = 'Hz';
%
%%%%%%%%%%%%%%%%%%%%%%%% Set up plotting environment %%%%%%%%%%%%%%%%%%%%%%%%%
%
h = gcf;
% set(h,'YLim',[ymin ymax]); % set default plotting parameters
% set(h,'XLim',[xmin xmax]);
% set(h,'FontSize',18);
% set(h,'DefaultLineLineWidth',1); % for thinner postscript lines
%
%%%%%%%%%%%%%%%%%%%%%%%%%% Print plot info %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%
% clf; % clear the current figure
% print plottitle over (left) subplot 1
if plottitle==0,
plottitle = '';
end
h=gca;title(plottitle,'FontSize',TITLEFONTSIZE); % title plot and
hold on
msg = ['\nPlotting %d traces of %d frames with colors: '];
msg = [msg ' -> \n']; % print starting info on screen . . .
fprintf(...
'\nlimits: [xmin,xmax,ymin,ymax] = [%4.1f %4.1f %4.2f %4.2f]\n',...
xmin,xmax,ymin,ymax);
set(h,'YLim',[ymin ymax]); % set default plotting parameters
set(h,'XLim',[xmin xmax]);
set(h,'FontSize',FONTSIZE); % choose font size
set(h,'FontSize',FONTSIZE); % choose font size
set(h,'YLim',[ymin ymax]); % set default plotting parameters
set(h,'XLim',[xmin xmax]);
axis('off')
%
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% Read chan_locs %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%
if size(loc_file,2) == 2 % plot in a rectangular grid
ISRECT = 1;
ht = loc_file(1);
wd = loc_file(2);
if chans > ht*wd
fprintf(...
'\ntopoimage(): (d%) channels to be plotted > grid size [%d %d]\n\n',...
chans,ht,wd);
return
end
hht = (ht-1)/2;
hwd = (wd-1)/2;
xvals = zeros(ht*wd,1);
yvals = zeros(ht*wd,1);
dist = zeros(ht*wd,1);
for i=1:wd
for j=1:ht
xvals(i+(j-1)*wd) = -hwd+(i-1);
yvals(i+(j-1)*wd) = hht-(j-1);
dist(i+(j-1)*wd) = sqrt(xvals(j+(i-1)*ht).^2+yvals(j+(i-1)*ht).^2);
end
end
maxdist = max(dist);
for i=1:wd
for j=1:ht
xvals(i+(j-1)*wd) = 0.499*xvals(i+(j-1)*wd)/maxdist;
yvals(i+(j-1)*wd) = 0.499*yvals(i+(j-1)*wd)/maxdist;
end
end
channames = repmat(' ',ht*wd,4);
for i=1:ht*wd
channum = num2str(i);
channames(i,1:length(channum)) = channum;
end
else % read chan_locs file
fid = fopen(loc_file);
if fid<1,
fprintf('topoimage(): cannot open eloc_file "%s"\n',loc_file)
return
end
A = fscanf(fid,'%d %f %f %s',[7 MAXCHANS]);
fclose(fid);
A = A';
if length(channels) > size(A,1),
error('topoimage(): data channels must be <= chan_locs channels')
end
channames = setstr(A(channels,4:7));
idx = find(channames == '.'); % some labels have dots
channames(idx) = setstr(abs(' ')*ones(size(idx))); % replace them with spaces
Th = pi/180*A(channels,2); % convert degrees to rads
Rd = A(channels,3);
% ii = find(Rd <= 0.5); % interpolate on-head channels only
% Th = Th(ii);
% Rd = Rd(ii);
[yvals,xvals] = pol2cart(Th,Rd);
end
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
xvals = 0.5+PLOT_WIDTH*xvals; % controls width of plot array on page!
yvals = 0.5+PLOT_HEIGHT*yvals; % controls height of plot array on page!
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%
%%%%%%%%%%%%%%%%%%%%%%%%%%%%% Plot traces %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%
xdiff=xmax-xmin;
rightmost = max(xvals);
basetimes = find(x<=0);
P=0;
Axes = [];
fprintf('\ntrace %d: ',P+1);
for I=1:chans,%%%%%%%%%% for each data channel %%%%%%%%%%%%%%%%%%%%%%%%%%
if P>0
axes(Axes(I))
hold on; % plot down left side of page first
axis('off')
else % P <= 0
%
%%%%%%%%%%%%%%%%%%%%%%% Plot data images %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%
xcenter = xvals(I);
ycenter = yvals(I);
Axes = [Axes axes('Units','Normal','Position', ...
[xcenter-axwidth/2 ycenter-axheight/2 axwidth axheight])];
axes(Axes(I))
imageaxes = gca;
axislcolor = get(gca,'Xcolor'); %%CJH
dataimage = matsel(data,times,0,0,I);
if rmbas~=0 % rm baseline
dataimage = dataimage ...
- repmat(mean(matsel(data,times,basetimes,0,I)')',1,times);
end
if exist('LOGIT')
logimagesc(x,y,dataimage); % <---- plot logfreq image
if exist('YVAL')
YVAL = log(YVAL);
end
else
imagesc(x,y,dataimage); % <---- plot image
end
hold on
curax = axis;
xtk = get(gca,'xtick'); % use these for cal axes below
xtkl = get(gca,'xticklabel');
ytk = get(gca,'ytick');
ytkl = get(gca,'yticklabel');
set(gca,'tickdir','out');
set(gca,'ticklength',[0.02 0.05]);
set(gca,'xticklabel',[]);
set(gca,'yticklabel',[]);
set(gca,'ydir','normal');
caxis([zmin zmax]);
if exist('YVAL') & YVAL>=curax(3) & YVAL<=curax(4)
hold on
hp=plot([xmin xmax],[YVAL YVAL],'r-');%,'color',axislcolor);
% draw horizontal axis
set(hp,'Linewidth',1.0)
end
if xmin<0 & xmax>0
hold on
vl= plot([0 0],[curax(3) curax(4)],'color',axislcolor); % draw vert axis
set(vl,'linewidth',2);
end
% if xcenter == rightmost
% colorbar
% rightmost = Inf;
% end
% secondx = 200; % draw second vert axis
% axis('off');plot([secondx secondx],[ymin ymax],'color',axislcolor);
%
%%%%%%%%%%%%%%%%%%%%%%% Print channel names %%%%%%%%%%%%%%%%%%%%%%%%%%
%
NAME_OFFSET = 0.01;
if channels~=0, % print channames
if ~ISRECT % print before topographically arrayed image
% axis('off');
hold on
h=text(xmin-NAME_OFFSET*xdiff,(curax(4)+curax(3))*0.5,[channames(I,:)]);
set(h,'HorizontalAlignment','right');
set(h,'FontSize',CHANFONTSIZE); % choose font size
else % print before rectangularly arrayed image
if xmin<0
xmn = 0;
else
xmn = xmin;
end
% axis('off');
h=text(xmin-NAME_OFFSET*xdiff,ymax,[channames(I,:)]);
set(h,'HorizontalAlignment','right');
set(h,'FontSize',TICKFONTSIZE); % choose font size
end
end; % channels
end; % P=0
% if xcenter == rightmost
% colorbar
% rightmost = Inf;
% end
% if xmin<0 & xmax>0
% axes(imageaxes);
% hold on; plot([0 0],[curax(3) curax(4)],'k','linewidth',2);
% end
drawnow
fprintf(' %d',I);
end; % %%%%%%%%%%%%%%% chan I %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
fprintf('\n');
%
%%%%%%%%%%%%%%%%%%%%% Make time and freq cal axis %%%%%%%%%%%%%%%%%%%%%%%%%
%
ax = axes('Units','Normal','Position', ...
[0.80 0.1 axwidth axheight]);
axes(ax)
axis('off');
imagesc(x,y,zeros(size(dataimage))); hold on % <---- plot green
caxis([zmin zmax]);
set(gca,'ydir','normal');
if xmin <=0
py=plot([0 0],[curax(3) curax(4)],'color','k'); % draw vert axis at time zero
else
py=plot([xmin xmin],[curax(3) curax(4)],'color','k'); % vert axis at xmin
end
hold on
if exist('YVAL') & YVAL>=curax(3)
px=plot([xmin xmax],[YVAL YVAL],'color',axislcolor);
% draw horiz axis at YVAL
else
px=plot([xmin xmax],[curax(3) curax(4)],'color',axislcolor);
% draw horiz axis at ymin
end
axis(curax);
set(gca,'xtick',xtk); % use these for cal axes
set(gca,'xticklabel',xtkl);
set(gca,'ytick',ytk);
set(gca,'yticklabel',ytkl);
set(gca,'ticklength',[0.02 0.05]);
set(gca,'tickdir','out');
h = colorbar;
cbp = get(h,'position');
set(h,'position',[cbp(1) cbp(2) 2*cbp(3) cbp(4)]);
caxis([zmin zmax]);
% secondx = 200; % draw second vert axis
% axis('off');plot([secondx secondx],[curax(3) curax(4)],'color',axislcolor);
%
%%%%%%%%%%%%%%%%%%%%% Plot axis values %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%
if 0 % DETOUR
signx = xmin-0.15*xdiff;
axis('off');h=text(signx,SIGN*curax(3),num2str(curax(3),3));
set(h,'FontSize',TICKFONTSIZE); % choose font size
set(h,'HorizontalAlignment','right','Clipping','off');
textx = xmin-0.6*xdiff;
axis('off');h=text(textx,(curax(3)+curax(4))/2,ylabel); % text Hz
set(h,'Rotation',90);
set(h,'FontSize',TICKFONTSIZE); % choose font size
set(h,'HorizontalAlignment','center','Clipping','off');
% axis('off');h=text(signx,SIGN*ymax,['+' num2str(ymax,3)]); % text +ymax
axis('off');h=text(signx,SIGN*ymax,[ num2str(ymax,3)]); % text ymax
set(h,'FontSize',TICKFONTSIZE); % choose font size
set(h,'HorizontalAlignment','right','Clipping','off');
ytick = curax(3)-0.3*(curax(4)-curax(3));
tick = [int2str(xmin)]; h=text(xmin,ytick,tick); % text xmin
set(h,'FontSize',TICKFONTSIZE); % choose font size
set(h,'HorizontalAlignment','center',...
'Clipping','off'); % center text
h=text(xmin+xdiff/2,ytick-0.5*(curax(4)-curax(3)),xlabel);% text Times
set(h,'FontSize',TICKFONTSIZE); % choose font size
set(h,'HorizontalAlignment','center',...
'Clipping','off'); % center text
tick = [int2str(xmax)]; h=text(xmax,ytick,tick); % text xmax
set(h,'FontSize',TICKFONTSIZE); % choose font size
set(h,'HorizontalAlignment','center',...
'Clipping','off'); % center text
axis on
set(ax,'xticklabel','');
set(ax,'yticklabel','');
set(ax,'ticklength',[0.02 0.05]);
set(ax,'tickdir','out');
caxis([zmin zmax]);
hc=colorbar;
cmapsize = size(colormap,1);
set(hc,'ytick',[1 cmapsize]); %
minlabel = num2str(zmin,3);
while (length(minlabel)<4)
if ~contains(minlabel,'.')
minlabel = [minlabel '.'];
else
minlabel = [minlabel '0'];
end
end
maxlabel = num2str(zmax,3);
if zmin<0 & zmax>0
maxlabel = ['+' maxlabel];
end
while (length(maxlabel)<length(minlabel))
if ~contains(maxlabel,'.')
maxlabel = [maxlabel '.'];
else
maxlabel = [maxlabel '0'];
end
end
while (length(maxlabel)>length(minlabel))
if ~contains(minlabel,'.')
minlabel = [minlabel '.'];
else
minlabel = [minlabel '0'];
end
end
set(hc,'yticklabel',[minlabel;maxlabel]);
set(hc,'Color',BACKCOLOR);
set(hc,'Zcolor',BACKCOLOR);
end % DETOUR
axcopy(gcf); % turn on pop-up axes
%
%%%%%%%%%%%%%%%%%% Make printed figure fill page %%%%%%%%%%%%%%%%%%%%%%%%%%%
%
% orient tall
% curfig = gcf;
% h=figure(curfig);
% set(h,'PaperPosition',[0.2 0.3 7.6 10]); % stretch out the plot on the page
function [returnval] = contains(strng,chr)
returnval=0;
for i=1:length(strng)
if strng(i)==chr
returnval=1;
break
end
end
|
github
|
lcnbeapp/beapp-master
|
getallmenuseeglab.m
|
.m
|
beapp-master/Packages/eeglab14_1_2b/functions/miscfunc/getallmenuseeglab.m
| 3,609 |
utf_8
|
3f20087025ca923857b9ce9ec4553255
|
% getallmenuseeglab() - get all submenus of a window or a menu and return
% a tree. The function will also look for callback.
%
% Usage:
% >> [tree nb] = getallmenuseeglab( handler );
%
% Inputs:
% handler - handler of the window or of a menu
%
% Outputs:
% tree - text output
% nb - number of elements in the tree
%
% Author: Arnaud Delorme, CNL / Salk Institute, 2001
% Copyright (C) 2001 Arnaud Delorme, Salk Institute, [email protected]
%
% This program is free software; you can redistribute it and/or modify
% it under the terms of the GNU General Public License as published by
% the Free Software Foundation; either version 2 of the License, or
% (at your option) any later version.
%
% This program is distributed in the hope that it will be useful,
% but WITHOUT ANY WARRANTY; without even the implied warranty of
% MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
% GNU General Public License for more details.
%
% You should have received a copy of the GNU General Public License
% along with this program; if not, write to the Free Software
% Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
function [txt, nb, labels] = getallmenuseeglab( handler, level )
NBBLANK = 6; % number of blank for each submenu input
if nargin < 1
help getallmenuseeglab;
return;
end;
if nargin < 2
level = 0;
end;
txt = '';
nb = 0;
labels = {};
allmenu = findobj('parent', handler, 'type', 'uimenu');
allmenu = allmenu(end:-1:1);
if ~isempty(allmenu)
for i=length(allmenu):-1:1
[txtmp nbtmp tmplab] = getallmenuseeglab(allmenu(i), level+1);
txtmp = [ '% ' blanks(level*NBBLANK) txtmp ];
txt = [ txtmp txt ];
labels = { tmplab labels{:} };
nb = nb+nbtmp;
end;
end;
try
lab = get(handler, 'Label');
cb = get(handler, 'Callback');
cb = extract_callback(cb);
if ~isempty(cb)
newtxt = [ lab ' - <a href="matlab:helpwin ' cb '">' cb '</a>'];
else newtxt = [ lab ];
end;
txt = [ newtxt 10 txt ];
%txt = [ get(handler, 'Label') 10 txt ];
nb = nb+1;
catch, end;
if isempty(labels)
labels = { nb };
end;
if level == 0
fid = fopen('tmpfile.m', 'w');
fprintf(fid, '%s', txt);
fclose(fid);
disp(' ');
disp('Results saved in tmpfile.m');
end;
% transform into array of text
% ----------------------------
if nargin < 2
txt = [10 txt];
newtext = zeros(1000, 1000);
maxlength = 0;
lines = find( txt == 10 );
for index = 1:length(lines)-1
tmptext = txt(lines(index)+1:lines(index+1)-1);
if maxlength < length( tmptext ), maxlength = length( tmptext ); end;
newtext(index, 1:length(tmptext)) = tmptext;
end;
txt = char( newtext(1:index+1, 1:maxlength) );
end;
% extract plugin name
% -------------------
function cbout = extract_callback(cbin);
funcList = { 'pop_' 'topoplot' 'eeg_' };
for iList = 1:3
indList = findstr(funcList{iList}, cbin);
if ~isempty(indList),
if strcmpi(cbin(indList(1):indList(1)+length('pop_stdwarn')-1), 'pop_stdwarn')
indList = findstr(funcList{iList}, cbin(indList(1)+1:end))+indList(1);
end;
break;
end;
end;
if ~isempty(indList)
indEndList = find( cbin(indList(1):end) == '(' );
if isempty(indEndList) || indEndList(1) > 25
indEndList = find( cbin(indList(1):end) == ';' );
if cbin(indList(1)+indEndList(1)-2) == ')'
indEndList = indEndList-2;
end;
end;
cbout = cbin(indList(1):indList(1)+indEndList(1)-2);
else
cbout = '';
end;
|
github
|
lcnbeapp/beapp-master
|
loglike.m
|
.m
|
beapp-master/Packages/eeglab14_1_2b/functions/miscfunc/loglike.m
| 1,238 |
utf_8
|
b9a8aa64d20e0fc72257880d837f9f19
|
% loglike() - log likehood function to estimate dependence between components
%
% Usage: f = loglike(W, S);
%
% Computation of the log-likelihood function under the model
% that the ICs are 1/cosh(s) distributed (according to the tanh
% nonlinearity in ICA). It does not exactly match for the logistic
% nonlinearity, but should be a decent approximation
%
% negative log likelihood function
% f = -( log(abs(det(W))) - sum(sum(log( cosh(S) )))/N - M*log(pi) );
%
% With these meanings:
% W: total unmixing matrix, ie, icaweights*icasphere
% S: 2-dim Matrix of source estimates
% N: number of time points
% M: number of components
%
% Author: Arnaud Delorme and Jorn Anemuller
function f=loglike(W, S);
W = double(W);
S = double(S);
% normalize activities
stds = std(S, [], 2);
S = S./repmat(stds, [1 size(S,2)]);
W = W./repmat(stds, [1 size(W,2)]);
M = size(W,1);
if ndims(S) == 3
S = reshape(S, size(S,1), size(S,3)*size(S,2));
end;
N = size(S,2);
% detect infinite and remove them
tmpcoh = log( cosh(S) );
tmpinf = find(isinf(tmpcoh));
tmpcoh(tmpinf) = [];
N = (N*M-length(tmpinf))/M;
f=-( log(abs(det(W))) - sum(sum(tmpcoh))/N - M*log(pi) );
|
github
|
lcnbeapp/beapp-master
|
corrimage.m
|
.m
|
beapp-master/Packages/eeglab14_1_2b/functions/miscfunc/corrimage.m
| 25,394 |
utf_8
|
aaddb89d7d26c507e8075ec38d644f0a
|
% corrimage() - compute correlation image between an event and amplitude
% and phase in the time-frequency domain.
%
% Usage:
% corrimage(data, sortvar, times);
% [times, freqs, alpha, sigout, limits ] = corrimage(data, sortvar, ...
% times, 'key1', val1, 'key2', val2, ...)
%
% Inputs:
% data - [float array] data of size (times,trials)
% sortvar - [float array] sorting variable of size (trials)
% times - [float array] time indices for every data point. Size of
% (times). Note: same input as the times vector for erpimage.
%
% Optional input:
% 'mode' - ['phase'|'amp'] compute correlation of event values with
% phase ('phase') or amplitude ('amp') of signal at the
% given time-frequency points. Default is 'amp'.
% 'freqs' - [min nfreqs max] build a frequency vector of size nfreqs
% with frequency spaced in a log scale. Then compute
% correlation at these frequency value.
% Default is 50 points in a log scale between 2.5Hz to 50Hz.
% 'times' - [float vector] compute correlation at these time value (ms).
% (uses closest times points in 'times' input and return
% them in the times output).
% Default is 100 steps between min time+5% of time range and
% max time-5%. Enter only 2 values [N X] to generate N
% time points and trim by X %. If N is negative, uses it as
% a subsampling factor [-3 5] trims times by 5% and subsample
% by 3 (by subsampling one obtains a regularly spaced times).
% 'trim' - [low high] low and high percentile of sorted sortvar values
% to retain. i.e. [5 95] remove the 5 lowest and highest
% percentile of sortvar values (and associated data) before
% computing statistics. Default is [0 100].
% 'align' - [float] same as 'align' parameter of erpimage(). This
% parameter is used to contrain the 'times' parameter so
% correlation with data trials containing 0-values (as a
% result of data alignment) are avoided: computing these
% correlations would produce spurious significant results.
% Default is no alignment.
% 'method' - ['erpimage'|timefreq'] use either the erpimage() function
% of the timefreq() function to compute spectral decomposition.
% Default is 'timefreq' for speed reasons (note that both
% methods should return the same results).
% 'erpout' - [min max] regress out ERP using the selected time-window [min
% max] in ms (the ERP is subtracted from the whole time period
% but only regressed out in the selected time window).
% 'triallimit' - [integer array] specify trial boundaries for subjects. For
% instance [1 200 400] indicates 2 subjects, trials 1 to 199
% for subject 1 and trials 200 to 399 for subject 2. This is
% currently only used for regressing erp out.
%
% Processing options:
% 'erpimopt' - [cell array] erpimage additional options (number of cycle ...).
% 'tfopt' - [cell array] timefreq additional options (number of cycle ...).
%
% Plotting options:
% 'plotvals' - [cell array of output values] enter output values here
% { times freqs alpha sigout} to replot them.
% 'nofig' - ['on'|'off'] do not create figure.
% 'cbar' - ['on'|'off'] plot color bar. Default: 'on'.
% 'smooth' - ['on'|'off'] smooth significance array. Default: 'on'.
% 'plot' - ['no'|'alpha'|'sigout'|'sigoutm'|'sigoutm2'] plot -10*log(alpha)
% values ('alpha'); output signal (slope or ITC) ('sigout'),
% output signal masked by significance ('sigoutm') or the last
% 2 option combined ('sigoutm2'). 'no' prevent the function
% from plotting. In addition, see pmask. Default is 'sigoutmasked'.
% 'pmask' - [real] maximum p value to show in plot. Default is 0.00001
% (0.001 taking into account multiple comparisons (100)). Enter
% 0.9XXX to get the higher tail or a negative value (e.e., -0.001
% to get both tails).
% 'vert' - [real array] time vector for vertivcal lines.
% 'limits' - [min max] plotting limits.
%
% Outputs:
% times - [float vector] vector of times (ms)
% freqs - [float vector] vector of frequencies (Hz)
% alpha - [float array] array (freqs,times) of p-values.
% sigout - [float array] array (freqs,times) of signal out (coherence
% for phase and slope for amplitude).
%
% Important note: the 'timefreq' method may truncate the time window to
% compute the spectral decomposition at the lowest freq.
%
% Author: Arnaud Delorme & Scott Makeig, SCCN UCSD,
% and CNL Salk Institute, 18 April 2003
%
% See also: erpimage()
%123456789012345678901234567890123456789012345678901234567890123456789012
% Copyright (C) 2002 Arnaud Delorme
%
% This program is free software; you can redistribute it and/or modify
% it under the terms of the GNU General Public License as published by
% the Free Software Foundation; either version 2 of the License, or
% (at your option) any later version.
%
% This program is distributed in the hope that it will be useful,
% but WITHOUT ANY WARRANTY; without even the implied warranty of
% MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
% GNU General Public License for more details.
%
% You should have received a copy of the GNU General Public License
% along with this program; if not, write to the Free Software
% Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
function [time, freq, alpha, sigout, limits, tf, sortvar] = corrimage(data, sortvar, timevect, varargin)
if nargin < 3
help corrimage;
return;
end;
if isempty(timevect), timevect = [1 2]; end;
% check inputs
% ------------
g = finputcheck(varargin, { 'freqs' 'real' [0 Inf] [2.5 50 50];
'times' 'real' [] [100 5]; % see function at the end
'mode' 'string' { 'phase','amp' } 'amp';
'vert' 'real' [] [];
'align' { 'real','cell' } [] [];
'plotvals' 'cell' [] {};
'pmask' 'real' [] 0.00001;
'triallimit' 'integer' [] [];
'trim' 'real' [0 100] [0 100];
'limits' 'real' [] [];
'method' 'string' { 'erpimage','timefreq' } 'timefreq';
'plot' 'string' { 'no','alpha','sigout','sigoutm','sigoutp','sigoutm2' } 'sigoutm';
'nofig' 'string' { 'on','off' } 'off';
'cbar' 'string' { 'on','off' } 'on';
'smooth' 'string' { 'on','off' } 'off';
'erpout' 'real' [] [];
'tfopt' 'cell' [] {};
'erpimopt' 'cell' [] {} });
if isstr(g), error(g); end;
fprintf('Generating %d frequencies in log scale (ignore message on linear scale)\n', g.freqs(2));
g.freqs = logscale(g.freqs(1), g.freqs(3), g.freqs(2));
frames = length(timevect);
if size(data,1) == 1
data = reshape(data, frames, size(data,2)*size(data,3)/frames);
end;
% trim sortvar values
% -------------------
[sortvar sortorder] = sort(sortvar);
data = data(:, sortorder);
len = length(sortvar);
lowindex = round(len*g.trim(1)/100)+1;
highindex = round(len*g.trim(2)/100);
sortvar = sortvar(lowindex:highindex);
data = data(:, lowindex:highindex);
if lowindex ~=1 | highindex ~= length(sortorder)
fprintf('Actual percentiles %1.2f-%1.2f (indices 1-%d -> %d-%d): event vals min %3.2f; max %3.2f\n', ...
100*(lowindex-1)/len, 100*highindex/len, len, lowindex, highindex, min(sortvar), max(sortvar));
end;
% assign subject number for each trial
% ------------------------------------
if ~isempty(g.triallimit)
alltrials = zeros(1,len);
for index = 1:length(g.triallimit)-1
alltrials([g.triallimit(index):g.triallimit(index+1)-1]) = index;
end;
alltrials = alltrials(sortorder);
alltrials = alltrials(lowindex:highindex);
end;
%figure; hist(sortvar)
% constraining time values depending on data alignment
% ----------------------------------------------------
srate = 1000*(length(timevect)-1)/(timevect(end)-timevect(1));
if ~isempty(g.align)
if iscell(g.align)
fprintf('Realigned sortvar plotted at %g ms.\n',g.align{1});
shifts = round((g.align{1}-g.align{2})*srate/1000); % shifts can be positive or negative
g.align = g.align{1};
else
if isinf(g.align)
g.align = median(sortvar);
end
fprintf('Realigned sortvar plotted at %g ms.\n',g.align);
% compute shifts
% --------------
shifts = round((g.align-sortvar)*srate/1000); % shifts can be positive or negative
end;
%figure; hist(shifts)
minshift = min(shifts); % negative
maxshift = max(shifts); % positive
if minshift > 0, error('minshift has to be negative'); end;
if maxshift < 0, error('maxshift has to be positive'); end;
% realign data for all trials
% ---------------------------
aligndata=zeros(size(data))+NaN; % begin with matrix of zeros()
for t=1:size(data,2), %%%%%%%%% foreach trial %%%%%%%%%
shft = shifts(t);
if shft>0, % shift right
aligndata(shft+1:frames,t)=data(1:frames-shft,t);
elseif shft < 0 % shift left
aligndata(1:frames+shft,t)=data(1-shft:frames,t);
else % shft == 0
aligndata(:,t) = data(:,t);
end
end % end trial
data = aligndata(maxshift+1:frames+minshift,:);
if any(any(isnan(data))), error('NaNs remaining after data alignment'); end;
timevect = timevect(maxshift+1:frames+minshift);
% take the time vector subset
% ---------------------------
if isempty(timevect), error('Shift too big, empty time vector');
else fprintf('Time vector truncated for data alignment between %1.0f and %1.0f\n', ...
min(timevect), max(timevect));
end;
end;
% regress out the ERP from the data (4 times to have residual ERP close to 0)
% ---------------------------------------------------------------------------
if ~isempty(g.erpout)
%data = erpregout(data);
%data = erpregout(data);
%data = erpregout(data);
disp('Regressing out ERP');
erpbeg = mean(data,2);
if ~isempty(g.triallimit)
for index = 1:length(g.triallimit)-1
trials = find(alltrials == index);
%[data(:,trials) erp factors]= erpregout(data(:,trials), [timevect(1) timevect(end)], [300 400]);
erpstart = mean(data(:,trials),2);
data(:,trials) = erpregout(data(:,trials));
data(:,trials) = erpregout(data(:,trials));
data(:,trials) = erpregout(data(:,trials));
data(:,trials) = erpregout(data(:,trials));
erpend = mean(data(:,trials),2);
fprintf([ '***********************************************\n' ...
'Ratio in ERP after regression (compare to before) is %3.2f\n' ...
'***********************************************\n' ], mean(erpend./erpstart));
end;
end;
erpend = mean(data,2);
fprintf([ '***********************************************\n' ...
'Ratio in grand ERP after regression (compare to before) is %3.2f\n' ...
'***********************************************\n' ], mean(erpend./erpbeg));
if 0
%trials = find(alltrials == 1);
data2 = data;
dasf
[data(:,trials) erp factors]= erpregout(data(:,trials), [timevect(1) timevect(end)], [300 400]);
figure; subplot(1,2,1); erpimage(data, sortvar, timevect, '', 300, 500, 'erp');
figure;
subplot(1,2,1); erpimage(data2, sortvar, timevect, '', 300, 500, 'erp');
subplot(1,2,2); erpimage(data , sortvar, timevect, '', 300, 500, 'erp');
figure;
subplot(1,2,1); erpimage(data2(:,trials), sortvar(trials), timevect, '', 0, 0, 'erp');
subplot(1,2,2); erpimage(data (:,trials), sortvar(trials), timevect, '', 0, 0, 'erp');
figure;
for index = 1:length(g.triallimit)-1
subplot(3,5,index);
trials = find(alltrials == index);
erpimage(data(:,trials), sortvar(trials), timevect, '', 50, 100, 'erp');
end;
disp('Regressing out ERP');
if ~isempty(g.triallimit)
for index = 1:length(g.triallimit)-1
trials = find(alltrials == index);
[data(:,trials) erp factors]= erpregout(data(:,trials), [timevect(1) timevect(end)], [300 400]);
data(:,trials) = erpregout(data(:,trials));
data(:,trials) = erpregout(data(:,trials));
data(:,trials) = erpregout(data(:,trials));
data(:,trials) = erpregout(data(:,trials));
data(:,trials) = erpregout(data(:,trials));
data(:,trials) = erpregout(data(:,trials));
data(:,trials) = erpregout(data(:,trials));
%data(:,trials) = erpregout(data(:,trials), [timevect(1) timevect(end)], g.erpout);
%data(:,trials) = erpregout(data(:,trials), [timevect(1) timevect(end)], g.erpout);
%data(:,trials) = erpregout(data(:,trials), [timevect(1) timevect(end)], g.erpout);
%data(:,trials) = erpregout(data(:,trials), [timevect(1) timevect(end)], g.erpout);
%data(:,trials) = erpregout(data(:,trials), [timevect(1) timevect(end)], g.erpout);
%data(:,trials) = erpregout(data(:,trials), [timevect(1) timevect(end)], g.erpout);
%data(:,trials) = erpregout(data(:,trials), [timevect(1) timevect(end)], g.erpout);
%data(:,trials) = erpregout(data(:,trials), [timevect(1) timevect(end)], g.erpout);
end;
else
%data = erpregout(data, [timevect(1) timevect(end)], g.erpout);
end;
end;
end;
% generate time points
% --------------------
g.times = gettimes(timevect, g.times);
data = reshape(data, 1, size(data,2)*size(data,1));
% time frequency decomposition
% ----------------------------
if strcmpi(g.method, 'timefreq') & isempty(g.plotvals)
data = reshape(data, length(data)/length(sortvar), length(sortvar));
[tf, g.freqs, g.times] = timefreq(data, srate, 'freqs', g.freqs, 'timesout', g.times, ...
'tlimits', [min(timevect) max(timevect)], 'wavelet', 3);
outvar = sortvar;
end;
% compute correlation
% -------------------
if strcmpi(g.mode, 'phase') & isempty(g.plotvals)
for freq = 1:length(g.freqs)
fprintf('Computing correlation with phase %3.2f Hz ----------------------\n', g.freqs(freq));
for time = 1:length(g.times)
if strcmpi(g.method, 'erpimage')
[outdata,outvar,outtrials,limits,axhndls,erp, ...
amps,cohers,cohsig,ampsig,outamps,phsangls,phsamp,sortidx] =erpimage(data,sortvar,timevect, ...
'', 0,0,g.erpimopt{:}, 'phasesort', [g.times(time) 0 g.freqs(freq)], 'noshow', 'yes');
else
phsangls = angle( squeeze(tf(freq, time, :))' );
end;
% computing ITCs
[ ITC(freq, time) alpha(freq, time) ] = ...
bootcircle(outvar/mean(outvar), exp(j*phsangls), 'naccu', 250);
% accumulate 200 values, fitted with a normal distribution
% --------------------------------------------------------
%cmplx = outvar .* exp(j*phsangls)/mean(outvar);
%ITC(freq, time) = mean(cmplx);
%alpha(freq,time) = bootstat(outvar/mean(outvar), exp(j*phsangls), 'res = mean(arg1 .* arg2)', ...
% 'naccu', 100, 'vals', abs(ITC(freq, time)), 'distfit', 'norm');
end;
end;
sigout = ITC;
elseif isempty(g.plotvals)
for freq = 1:length(g.freqs)
fprintf('Computing correlation with amplitude %3.2f Hz ----------------------\n', g.freqs(freq));
for time = 1:length(g.times)
if strcmpi(g.method, 'erpimage')
[outdata,outvar,outtrials,limits,axhndls,erp, ...
amps,cohers,cohsig,ampsig,outamps,phsangls,phsamp,sortidx] =erpimage(data,sortvar,timevect, ...
'', 0,0,g.erpimopt{:}, 'ampsort', [g.times(time) 0 g.freqs(freq)], 'noshow', 'yes');
else
phsamp = abs(squeeze(tf(freq, time, :)))';
end;
% computing ITCs
[ypred alpha(freq, time) Rsq slope(freq, time)] = myregress(outvar, 20*log10(phsamp));
end;
end;
sigout = slope;
else
g.times = g.plotvals{1};
g.freqs = g.plotvals{2};
alpha = g.plotvals{3};
sigout = g.plotvals{4};
end;
% plot correlation
% ----------------
if ~strcmp('plot', 'no')
if ~isreal(sigout),
if strcmpi(g.plot, 'sigoutp')
sigoutplot = angle(sigout);
else
sigoutplot = abs(sigout);
end;
else sigoutplot = sigout;
end;
sigouttmp = sigoutplot;
if strcmpi(g.smooth, 'on')
tmpfilt = gauss2d(3,3,.3,.3);
tmpfilt = tmpfilt/sum(sum(tmpfilt));
alpha = conv2(alpha, tmpfilt, 'same');
end;
% mask signal out
if g.pmask > 0.5
indices = find( alpha(:) < g.pmask);
sigouttmp = sigoutplot;
sigouttmp(indices) = 0;
elseif g.pmask < 0 % both sides, i.e. 0.01
sigouttmp = sigoutplot;
indices = intersect_bc(find( alpha(:) > -g.pmask), find( alpha(:) < 1+g.pmask));
sigouttmp(indices) = 0;
else
sigouttmp = sigoutplot;
indices = find( alpha(:) > g.pmask);
sigouttmp(indices) = 0;
end;
if strcmpi(g.nofig, 'off'), figure; end;
switch g.plot
case 'alpha', limits = plotfig(g.times, g.freqs, -log10(alpha), g);
case 'sigout', limits = plotfigsim(g.times, g.freqs, sigoutplot, g);
case { 'sigoutm' 'sigoutp' }, limits = plotfigsim(g.times, g.freqs, sigouttmp, g);
case 'sigoutm2', limits = subplot(1,2,1); plotfigsim(g.times, g.freqs, sigoutplot, g);
limits = subplot(1,2,2); plotfigsim(g.times, g.freqs, sigouttmp, g);
end;
end;
time = g.times;
freq = g.freqs;
return;
% formula for the normal distribution
% -----------------------------------
function y = norm(mu, sigma, x);
y = 1/sqrt(2) * exp( -(x-mu).^2/(sigma*sigma*2) ) / (sqrt(pi)*sigma);
% get time points
% ---------------
function val = gettimes(timevect, timevar);
if length(timevar) == 2
if timevar(1) > 0
% generate linearly space vector
% ------------------------------
npoints = timevar(1);
trim = timevar(2);
if length(timevect)-2*round(trim/100*length(timevect)) < npoints
npoints = length(timevect)-round(trim/100*length(timevect));
end;
fprintf('Generating %d times points trimmed by %1.1f percent\n', npoints, trim);
timer = max(timevect) - min(timevect);
maxt = max(timevect)-timer*trim/100;
mint = min(timevect)+timer*trim/100;
val = linspace(mint,maxt, npoints);
else
% subsample data
% --------------
nsub = -timevar(1);
trim = timevar(2);
len = length(timevect);
trimtimevect = timevect(round(trim/100*len)+1:len-round(trim/100*len));
fprintf('Subsampling by %d and triming data by %1.1f percent (%d points)\n', nsub, trim, round(trim/100*len));
val = trimtimevect(1:nsub:end);
end;
else
val = timevar;
end;
% find closet points in data
oldval = val;
for index = 1:length(val)
[dum ind] = min(abs(timevect-val(index)));
val(index) = timevect(ind);
end;
if length(val) < length(unique(val))
disp('Warning: duplicate times, reduce the number of output times');
end;
if all(oldval == val)
disp('Debug msg: Time value unchanged by finding closest in data');
end;
% get log scale (for frequency)
% -------------
function val = logscale(a,b,n);
%val = [5 7 9]; return;
val = linspace(log(a), log(b), n);
val = exp(val);
% plot figure
% -----------
function limits = plotfig(times, freqs, vals, g)
icadefs;
imagesc(times, [1:size(vals,1)], vals);
colormap(DEFAULT_COLORMAP);
ticks = linspace(1, size(vals,1), length(freqs));
ticks = ticks(1:4:end);
set(gca, 'ytick', ticks);
set(gca, 'yticklabel', num2str(freqs(1:4:end)', 3))
xlabel('Time (ms)'); ylabel('Freq (Hz)');
if ~isempty(g.limits), caxis(g.limits); end;
limits = caxis;
if ~isempty(g.vert)
for vert = g.vert(:)'
hold on; plot([vert vert], [0.001 500], 'k', 'linewidth', 2);
end;
end;
if strcmpi(g.cbar,'on')
cbar;
end;
% plot figure with symetrical phase
% ---------------------------------
function limits = plotfigsim(times, freqs, vals, g)
icadefs;
imagesc(times, [1:size(vals,1)], vals);
colormap(DEFAULT_COLORMAP);
ticks = linspace(1, size(vals,1), length(freqs));
ticks = ticks(1:4:end);
set(gca, 'ytick', ticks);
set(gca, 'yticklabel', num2str(freqs(1:4:end)', 3))
if ~isempty(g.limits)
caxis(g.limits);
limits = g.limits;
else
clim = max(abs(caxis));
limits = [-clim clim];
caxis(limits);
end;
xlabel('Time (ms)'); ylabel('Freq (Hz)');
if ~isempty(g.vert)
for vert = g.vert(:)'
hold on; plot([vert vert], [0.01 500], 'k', 'linewidth', 2);
end;
end;
if strcmpi(g.cbar,'on')
cbar;
end;
return;
% -----------------------------------------
% plot time-freq point (when clicking on it
% -----------------------------------------
function plotpoint(data, sortvar, timevect, freq, timepnts);
figure;
subplot(2,2,1);
erpimage(act_all(:,:),sortvar_all,timepnts, ...
'', 300,10,'erp', 'erpstd', 'caxis',[-1.0 1.0], 'srate',256,'align',352, 'yerplabel', '', erpimopt{:}, ...
'phasesort', [500 0 5]); % aligned to median rt
% plot in polar coordinates phase versus RT
% -----------------------------------------
phaseang2 = [phsangls phsangls-2*pi]; phaseang2 = movav(phaseang2,[], 100);
outvar2 = [outvar outvar]; outvar2 = movav(outvar2,[], 100);
phaseang2 = phaseang2(length(phsangls)/2-50:length(phsangls)+length(phsangls)/2-50);
outvar2 = outvar2 (length(phsangls)/2-50:length(phsangls)+length(phsangls)/2-50);
subplot(2,2,3);
polar(phsangls, outvar, '.');
hold on; polar(phaseang2, outvar2, 'r');
% computing ITC
% -------------
cmplx = outvar .* exp(j*phsangls);
ITCval = mean(cmplx);
angle(ITCval)/pi*180;
abs(ITCval)/mean(outvar);
text(-1300,-1400,sprintf('ITC value: amplitude %3.4f, angle %3.1f\n', abs(ITCval)/mean(outvar), angle(ITCval)/pi*180));
% accumulate 200 values
% ---------------------
alpha = 0.05;
if exist('accarray') ~= 1, accarray = NaN; end;
[sigval accarray] = bootstat(outvar/mean(outvar), phsangls, 'res = mean(arg1 .* exp(arg2*complex(0,1)))', ...
'accarray', accarray, 'bootside', 'upper', 'alpha', alpha);
text(-1300,-1600,sprintf('Threshold for significance at %d percent(naccu=200): %3.4f\n', alpha*100, sigval));
title(sprintf('Clust %d corr. theta phase at 500 ms and RT', clust));
% amplitude sorting
% -----------------
figure;
[outdata,outvar,outtrials,limits,axhndls,erp, ...
amps,cohers,cohsig,ampsig,outamps,phsangls,phsamp,sortidx]=erpimage(act_all(:,:),sortvar_all,timepnts, ...
'', 0,0,'erp', 'erpstd', 'caxis', 0.5, 'cbar', ...
'srate',256,'align',352, 'yerplabel', '', erpimopt{:}, 'ampsort', [500 0 5]); % aligned to median rt
close;
subplot(2,2,2);
erpimage(act_all(:,:),sortvar_all,timevect, ...
'', 300,10,'erp', 'erpstd', 'caxis', 0.5, 'cbar', ...
'srate',256,'align',352, 'yerplabel', '', erpimopt{:}, 'ampsort', [500 0 5]); % aligned to median rt
% compute correlation
% -------------------
[ypred alpha Rsq] = myregress(outvar, phsamp);
subplot(2,2,4);
plot(outvar, phsamp, '.');
hold on;
plot(outvar, ypred, 'r');
xlabel('Reaction time');
ylabel('Amplitude');
title(sprintf('Theta amp. at 500 ms vs RT (p=%1.8f, R^2=%3.4f)', alpha, Rsq));
set(gcf, 'position', [336 485 730 540], 'paperpositionmode', 'auto');
setfont(gcf, 'fontsize', 10);
eval(['print -djpeg clust' int2str(clust) 'corrthetart.jpg']);
% set up for command line call
% copy text from plotcorrthetaart
%timevect = times;
sortvar = sortvar_all;
data = act_all;
time = 1
freq = 1
g.times = 0;
g.freqs = 5;
g.erpimopt = {};
|
github
|
lcnbeapp/beapp-master
|
dendhier.m
|
.m
|
beapp-master/Packages/eeglab14_1_2b/functions/miscfunc/dendhier.m
| 1,290 |
utf_8
|
4ad99782a7d86d471c4ce68b9a0dbf1e
|
% DENDHIER: Recursive algorithm to find links and distance coordinates on a
% dendrogram, given the topology matrix.
%
% Usage: [links,topology,node] = dendhier(links,topology,node)
%
% links = 4-col matrix of descendants, ancestors, descendant
% distances, and ancestor distances; pass to
% function as null vector []
% topology = dendrogram topology matrix
% node = current node; pass as N-1
%
% RE Strauss, 7/13/95
function [links,topology,node] = dendhier(links,topology,node)
n = size(topology,1)+1; % Number of OTUs
c1 = topology(node,1);
c2 = topology(node,2);
clst = topology(node,3);
dist = topology(node,4);
if (c1 <= n)
links = [links; c1 clst 0 dist];
else
prevnode = find(topology(:,3)==c1);
prevdist = topology(prevnode,4);
links = [links; c1 clst prevdist dist];
[links,topology,node] = dendhier(links,topology,prevnode);
end;
if (c2 <= n)
links = [links; c2 clst 0 dist];
else
prevnode = find(topology(:,3)==c2);
prevdist = topology(prevnode,4);
links = [links; c2 clst prevdist dist];
[links,topology,node] = dendhier(links,topology,prevnode);
end;
return;
|
github
|
lcnbeapp/beapp-master
|
runicalowmem.m
|
.m
|
beapp-master/Packages/eeglab14_1_2b/functions/miscfunc/runicalowmem.m
| 62,951 |
utf_8
|
ae726ddb4771edbac5539b0c00cf3fb9
|
% runica() - Perform Independent Component Analysis (ICA) decomposition
% of input data using the logistic infomax ICA algorithm of
% Bell & Sejnowski (1995) with the natural gradient feature
% of Amari, Cichocki & Yang, or optionally the extended-ICA
% algorithm of Lee, Girolami & Sejnowski, with optional PCA
% dimension reduction. Annealing based on weight changes is
% used to automate the separation process.
% Usage:
% >> [weights,sphere] = runica(data); % train using defaults
% else
% >> [weights,sphere,compvars,bias,signs,lrates,activations] ...
% = runica(data,'Key1',Value1',...);
% Input:
% data = input data (chans,frames*epochs).
% Note that if data consists of multiple discontinuous epochs,
% each epoch should be separately baseline-zero'd using
% >> data = rmbase(data,frames,basevector);
%
% Optional keywords [argument]:
% 'extended' = [N] perform tanh() "extended-ICA" with sign estimation
% N training blocks. If N > 0, automatically estimate the
% number of sub-Gaussian sources. If N < 0, fix number of
% sub-Gaussian comps to -N [faster than N>0] (default|0 -> off)
% 'pca' = [N] decompose a principal component (default -> 0=off)
% subspace of the data. Value is the number of PCs to retain.
% 'sphering' = ['on'/'off'] flag sphering of data (default -> 'on')
% 'weights' = [W] initial weight matrix (default -> eye())
% (Note: if 'sphering' 'off', default -> spher())
% 'lrate' = [rate] initial ICA learning rate (<< 1) (default -> heuristic)
% 'block' = [N] ICA block size (<< datalength) (default -> heuristic)
% 'anneal' = annealing constant (0,1] (defaults -> 0.90, or 0.98, extended)
% controls speed of convergence
% 'annealdeg' = [N] degrees weight change for annealing (default -> 70)
% 'stop' = [f] stop training when weight-change < this (default -> 1e-6
% if less than 33 channel and 1E-7 otherwise)
% 'maxsteps' = [N] max number of ICA training steps (default -> 512)
% 'bias' = ['on'/'off'] perform bias adjustment (default -> 'on')
% 'momentum' = [0<f<1] training momentum (default -> 0)
% 'specgram' = [srate loHz hiHz frames winframes] decompose a complex time/frequency
% transform of the data - though not optimally. (Note: winframes must
% divide frames) (defaults [srate 0 srate/2 size(data,2) size(data,2)])
% 'posact' = make all component activations net-positive(default 'off'}
% Requires time and memory; posact() may be applied separately.
% 'ncomps' = [N] number of ICA components to compute (default -> chans or 'pca' arg)
% using rectangular ICA decomposition. This parameter may return
% strange results. This is because the weight matrix is rectangular
% instead of being square. Do not use except to try to fix the problem.
% 'verbose' = give ascii messages ('on'/'off') (default -> 'on')
% 'submean' = ['on'|'off'] subtract mean from each channel (default -> 'on')
% 'logfile' = [filename] save all message in a log file in addition to showing them
% on screen (default -> none)
%
% Outputs: [Note: RO means output in reverse order of projected mean variance
% unless starting weight matrix passed ('weights' above)]
% weights = ICA weight matrix (comps,chans) [RO]
% sphere = data sphering matrix (chans,chans) = spher(data)
% Note that unmixing_matrix = weights*sphere {if sphering off -> eye(chans)}
% compvars = back-projected component variances [RO]
% bias = vector of final (ncomps) online bias [RO] (default = zeros())
% signs = extended-ICA signs for components [RO] (default = ones())
% [ -1 = sub-Gaussian; 1 = super-Gaussian]
% lrates = vector of learning rates used at each training step [RO]
% activations = activation time courses of the output components (ncomps,frames*epochs)
%
% Authors: Scott Makeig with contributions from Tony Bell, Te-Won Lee,
% Tzyy-Ping Jung, Sigurd Enghoff, Michael Zibulevsky, Delorme Arnaud,
% CNL/The Salk Institute, La Jolla, 1996-
% Reference (please cite):
%
% Makeig, S., Bell, A.J., Jung, T-P and Sejnowski, T.J.,
% "Independent component analysis of electroencephalographic data,"
% In: D. Touretzky, M. Mozer and M. Hasselmo (Eds). Advances in Neural
% Information Processing Systems 8:145-151, MIT Press, Cambridge, MA (1996).
%
% Toolbox Citation:
%
% Makeig, Scott et al. "EEGLAB: ICA Toolbox for Psychophysiological Research".
% WWW Site, Swartz Center for Computational Neuroscience, Institute of Neural
% Computation, University of San Diego California
% <www.sccn.ucsd.edu/eeglab/>, 2000. [World Wide Web Publication].
%
% For more information:
% http://www.sccn.ucsd.edu/eeglab/icafaq.html - FAQ on ICA/EEG
% http://www.sccn.ucsd.edu/eeglab/icabib.html - mss. on ICA & biosignals
% http://www.cnl.salk.edu/~tony/ica.html - math. mss. on ICA
% Copyright (C) 1996 Scott Makeig et al, SCCN/INC/UCSD, [email protected]
%
% This program is free software; you can redistribute it and/or modify
% it under the terms of the GNU General Public License as published by
% the Free Software Foundation; either version 2 of the License, or
% (at your option) any later version.
%
% This program is distributed in the hope that it will be useful,
% but WITHOUT ANY WARRANTY; without even the implied warranty of
% MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
% GNU General Public License for more details.
%
% You should have received a copy of the GNU General Public License
% along with this program; if not, write to the Free Software
% Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
%%%%%%%%%%%%%%%%%%%%%%%%%%% Edit history %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%
% runica() - by Scott Makeig with contributions from Tony Bell, Te-Won Lee
% Tzyy-Ping Jung, Sigurd Enghoff, Michael Zibulevsky et al.
% CNL / Salk Institute 1996-00
% 04-30-96 built from icatest.m and ~jung/.../wtwpwica.m -sm
% 07-28-97 new runica(), adds bias (default on), momentum (default off),
% extended-ICA (Lee & Sejnowski, 1997), cumulative angledelta
% (until lrate drops), keywords, signcount for speeding extended-ICA
% 10-07-97 put acos() outside verbose loop; verbose 'off' wasn't stopping -sm
% 11-11-97 adjusted help msg -sm
% 11-30-97 return eye(chans) if sphering 'off' or 'none' (undocumented option) -sm
% 02-27-98 use pinv() instead of inv() to rank order comps if ncomps < chans -sm
% 04-28-98 added 'posact' and 'pca' flags -sm
% 07-16-98 reduced length of randperm() for kurtosis subset calc. -se & sm
% 07-19-98 fixed typo in weights def. above -tl & sm
% 12-21-99 added 'specgram' option suggested by Michael Zibulevsky, UNM -sm
% 12-22-99 fixed rand() sizing inefficiency on suggestion of Mike Spratling, UK -sm
% 01-11-00 fixed rand() sizing bug on suggestion of Jack Foucher, Strasbourg -sm
% 12-18-00 test for existence of Sig Proc Tlbx function 'specgram'; improve
% 'specgram' option arguments -sm
% 01-25-02 reformated help & license -ad
% 01-25-02 lowered default lrate and block -ad
%
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
function [weights,sphere,meanvar,bias,signs,lrates,data,y] = runica(data,varargin) % NB: Now optionally returns activations as variable 'data' -sm 7/05
if nargin < 1
help runica
return
end
[chans frames] = size(data); % determine the data size
urchans = chans; % remember original data channels
datalength = frames;
if chans<2
fprintf('\nrunica() - data size (%d,%d) too small.\n\n', chans,frames);
return
end
%
%%%%%%%%%%%%%%%%%%%%%% Declare defaults used below %%%%%%%%%%%%%%%%%%%%%%%%
%
MAX_WEIGHT = 1e8; % guess that weights larger than this have blown up
DEFAULT_STOP = 0.000001; % stop training if weight changes below this
DEFAULT_ANNEALDEG = 60; % when angle change reaches this value,
DEFAULT_ANNEALSTEP = 0.90; % anneal by multiplying lrate by this
DEFAULT_EXTANNEAL = 0.98; % or this if extended-ICA
DEFAULT_MAXSTEPS = 512; % ]top training after this many steps
DEFAULT_MOMENTUM = 0.0; % default momentum weight
DEFAULT_BLOWUP = 1000000000.0; % = learning rate has 'blown up'
DEFAULT_BLOWUP_FAC = 0.8; % when lrate 'blows up,' anneal by this fac
DEFAULT_RESTART_FAC = 0.9; % if weights blowup, restart with lrate
% lower by this factor
MIN_LRATE = 0.000001; % if weight blowups make lrate < this, quit
MAX_LRATE = 0.1; % guard against uselessly high learning rate
DEFAULT_LRATE = 0.00065/log(chans);
% heuristic default - may need adjustment
% for large or tiny data sets!
% DEFAULT_BLOCK = floor(sqrt(frames/4)); % heuristic default
DEFAULT_BLOCK = ceil(min(5*log(frames),0.3*frames)); % heuristic
% - may need adjustment!
% Extended-ICA option:
DEFAULT_EXTENDED = 0; % default off
DEFAULT_EXTBLOCKS = 1; % number of blocks per kurtosis calculation
DEFAULT_NSUB = 1; % initial default number of assumed sub-Gaussians
% for extended-ICA
DEFAULT_EXTMOMENTUM = 0.5; % momentum term for computing extended-ICA kurtosis
MAX_KURTSIZE = 6000; % max points to use in kurtosis calculation
MIN_KURTSIZE = 2000; % minimum good kurtosis size (flag warning)
SIGNCOUNT_THRESHOLD = 25; % raise extblocks when sign vector unchanged
% after this many steps
SIGNCOUNT_STEP = 2; % extblocks increment factor
DEFAULT_SPHEREFLAG = 'on'; % use the sphere matrix as the default
% starting weight matrix
DEFAULT_PCAFLAG = 'off'; % don't use PCA reduction
DEFAULT_POSACTFLAG = 'off'; % don't use posact(), to save space -sm 7/05
DEFAULT_SUBMEAN = 'on';
DEFAULT_VERBOSE = 1; % write ascii info to calling screen
DEFAULT_BIASFLAG = 1; % default to using bias in the ICA update rule
%
%%%%%%%%%%%%%%%%%%%%%%% Set up keyword default values %%%%%%%%%%%%%%%%%%%%%%%%%
%
if nargout < 2,
fprintf('runica() - needs at least two output arguments.\n');
return
end
epochs = 1; % do not care how many epochs in data
pcaflag = DEFAULT_PCAFLAG;
sphering = DEFAULT_SPHEREFLAG; % default flags
posactflag = DEFAULT_POSACTFLAG;
verbose = DEFAULT_VERBOSE;
logfile = [];
block = DEFAULT_BLOCK; % heuristic default - may need adjustment!
lrate = DEFAULT_LRATE;
annealdeg = DEFAULT_ANNEALDEG;
annealstep = 0; % defaults declared below
nochange = NaN;
momentum = DEFAULT_MOMENTUM;
maxsteps = DEFAULT_MAXSTEPS;
weights = 0; % defaults defined below
ncomps = chans;
biasflag = DEFAULT_BIASFLAG;
extended = DEFAULT_EXTENDED;
extblocks = DEFAULT_EXTBLOCKS;
kurtsize = MAX_KURTSIZE;
signsbias = 0.02; % bias towards super-Gaussian components
extmomentum= DEFAULT_EXTMOMENTUM; % exp. average the kurtosis estimates
nsub = DEFAULT_NSUB;
wts_blowup = 0; % flag =1 when weights too large
wts_passed = 0; % flag weights passed as argument
submean = DEFAULT_SUBMEAN;
%
%%%%%%%%%% Collect keywords and values from argument list %%%%%%%%%%%%%%%
%
if (nargin> 1 & rem(nargin,2) == 0)
fprintf('runica(): Even number of input arguments???')
return
end
for i = 1:2:length(varargin) % for each Keyword
Keyword = varargin{i};
Value = varargin{i+1};
if ~isstr(Keyword)
fprintf('runica(): keywords must be strings')
return
end
Keyword = lower(Keyword); % convert upper or mixed case to lower
if strcmp(Keyword,'weights') | strcmp(Keyword,'weight')
if isstr(Value)
fprintf(...
'runica(): weights value must be a weight matrix or sphere')
return
else
weights = Value;
wts_passed =1;
end
elseif strcmp(Keyword,'ncomps')
if isstr(Value)
fprintf('runica(): ncomps value must be an integer')
return
end
if ncomps < urchans & ncomps ~= Value
fprintf('runica(): Use either PCA or ICA dimension reduction');
return
end
fprintf('*****************************************************************************************');
fprintf('************** WARNING: NCOMPS OPTION OFTEN DOES NOT RETURN ACCURATE RESULTS ************');
fprintf('************** WARNING: IF YOU FIND THE PROBLEM, PLEASE LET US KNOW ************');
fprintf('*****************************************************************************************');
ncomps = Value;
if ~ncomps,
ncomps = chans;
end
elseif strcmp(Keyword,'pca')
if ncomps < urchans & ncomps ~= Value
fprintf('runica(): Use either PCA or ICA dimension reduction');
return
end
if isstr(Value)
fprintf(...
'runica(): pca value should be the number of principal components to retain')
return
end
pcaflag = 'on';
ncomps = Value;
if ncomps > chans | ncomps < 1,
fprintf('runica(): pca value must be in range [1,%d]\n',chans)
return
end
chans = ncomps;
elseif strcmp(Keyword,'posact')
if ~isstr(Value)
fprintf('runica(): posact value must be on or off')
return
else
Value = lower(Value);
if ~strcmp(Value,'on') & ~strcmp(Value,'off'),
fprintf('runica(): posact value must be on or off')
return
end
posactflag = Value;
end
elseif strcmp(Keyword,'submean')
if ~isstr(Value)
fprintf('runica(): submean value must be on or off')
return
else
Value = lower(Value);
if ~strcmp(Value,'on') & ~strcmp(Value,'off'),
fprintf('runica(): submean value must be on or off')
return
end
submean = Value;
end
elseif strcmp(Keyword,'lrate')
if isstr(Value)
fprintf('runica(): lrate value must be a number')
return
end
lrate = Value;
if lrate>MAX_LRATE | lrate <0,
fprintf('runica(): lrate value is out of bounds');
return
end
if ~lrate,
lrate = DEFAULT_LRATE;
end
elseif strcmp(Keyword,'block') | strcmp(Keyword,'blocksize')
if isstr(Value)
fprintf('runica(): block size value must be a number')
return
end
block = floor(Value);
if ~block,
block = DEFAULT_BLOCK;
end
elseif strcmp(Keyword,'stop') | strcmp(Keyword,'nochange') ...
| strcmp(Keyword,'stopping')
if isstr(Value)
fprintf('runica(): stop wchange value must be a number')
return
end
nochange = Value;
elseif strcmp(Keyword,'logfile')
if ~isstr(Value)
fprintf('runica(): logfile value must be a string')
return
end
logfile = Value;
elseif strcmp(Keyword,'maxsteps') | strcmp(Keyword,'steps')
if isstr(Value)
fprintf('runica(): maxsteps value must be an integer')
return
end
maxsteps = Value;
if ~maxsteps,
maxsteps = DEFAULT_MAXSTEPS;
end
if maxsteps < 0
fprintf('runica(): maxsteps value (%d) must be a positive integer',maxsteps)
return
end
elseif strcmp(Keyword,'anneal') | strcmp(Keyword,'annealstep')
if isstr(Value)
fprintf('runica(): anneal step value (%2.4f) must be a number (0,1)',Value)
return
end
annealstep = Value;
if annealstep <=0 | annealstep > 1,
fprintf('runica(): anneal step value (%2.4f) must be (0,1]',annealstep)
return
end
elseif strcmp(Keyword,'annealdeg') | strcmp(Keyword,'degrees')
if isstr(Value)
fprintf('runica(): annealdeg value must be a number')
return
end
annealdeg = Value;
if ~annealdeg,
annealdeg = DEFAULT_ANNEALDEG;
elseif annealdeg > 180 | annealdeg < 0
fprintf('runica(): annealdeg (%3.1f) is out of bounds [0,180]',...
annealdeg);
return
end
elseif strcmp(Keyword,'momentum')
if isstr(Value)
fprintf('runica(): momentum value must be a number')
return
end
momentum = Value;
if momentum > 1.0 | momentum < 0
fprintf('runica(): momentum value is out of bounds [0,1]')
return
end
elseif strcmp(Keyword,'sphering') | strcmp(Keyword,'sphereing') ...
| strcmp(Keyword,'sphere')
if ~isstr(Value)
fprintf('runica(): sphering value must be on, off, or none')
return
else
Value = lower(Value);
if ~strcmp(Value,'on') & ~strcmp(Value,'off') & ~strcmp(Value,'none'),
fprintf('runica(): sphering value must be on or off')
return
end
sphering = Value;
end
elseif strcmp(Keyword,'bias')
if ~isstr(Value)
fprintf('runica(): bias value must be on or off')
return
else
Value = lower(Value);
if strcmp(Value,'on')
biasflag = 1;
elseif strcmp(Value,'off'),
biasflag = 0;
else
fprintf('runica(): bias value must be on or off')
return
end
end
elseif strcmp(Keyword,'specgram') | strcmp(Keyword,'spec')
if ~exist('specgram') < 2 % if ~exist or defined workspace variable
fprintf(...
'runica(): MATLAB Sig. Proc. Toolbox function "specgram" not found.\n')
return
end
if isstr(Value)
fprintf('runica(): specgram argument must be a vector')
return
end
srate = Value(1);
if (srate < 0)
fprintf('runica(): specgram srate (%4.1f) must be >=0',srate)
return
end
if length(Value)>1
loHz = Value(2);
if (loHz < 0 | loHz > srate/2)
fprintf('runica(): specgram loHz must be >=0 and <= srate/2 (%4.1f)',srate/2)
return
end
else
loHz = 0; % default
end
if length(Value)>2
hiHz = Value(3);
if (hiHz < loHz | hiHz > srate/2)
fprintf('runica(): specgram hiHz must be >=loHz (%4.1f) and <= srate/2 (%4.1f)',loHz,srate/2)
return
end
else
hiHz = srate/2; % default
end
if length(Value)>3
Hzframes = Value(5);
if (Hzframes<0 | Hzframes > size(data,2))
fprintf('runica(): specgram frames must be >=0 and <= data length (%d)',size(data,2))
return
end
else
Hzframes = size(data,2); % default
end
if length(Value)>4
Hzwinlen = Value(4);
if rem(Hzframes,Hzwinlen) % if winlen doesn't divide frames
fprintf('runica(): specgram Hzinc must divide frames (%d)',Hzframes)
return
end
else
Hzwinlen = Hzframes; % default
end
Specgramflag = 1; % set flag to perform specgram()
elseif strcmp(Keyword,'extended') | strcmp(Keyword,'extend')
if isstr(Value)
fprintf('runica(): extended value must be an integer (+/-)')
return
else
extended = 1; % turn on extended-ICA
extblocks = fix(Value); % number of blocks per kurt() compute
if extblocks < 0
nsub = -1*fix(extblocks); % fix this many sub-Gauss comps
elseif ~extblocks,
extended = 0; % turn extended-ICA off
elseif kurtsize>frames, % length of kurtosis calculation
kurtsize = frames;
if kurtsize < MIN_KURTSIZE
fprintf(...
'runica() warning: kurtosis values inexact for << %d points.\n',...
MIN_KURTSIZE);
end
end
end
elseif strcmp(Keyword,'verbose')
if ~isstr(Value)
fprintf('runica(): verbose flag value must be on or off')
return
elseif strcmp(Value,'on'),
verbose = 1;
elseif strcmp(Value,'off'),
verbose = 0;
else
fprintf('runica(): verbose flag value must be on or off')
return
end
else
fprintf('runica(): unknown flag')
return
end
end
%
%%%%%%%%%%%%%%%%%%%%%%%% Initialize weights, etc. %%%%%%%%%%%%%%%%%%%%%%%%
%
if ~annealstep,
if ~extended,
annealstep = DEFAULT_ANNEALSTEP; % defaults defined above
else
annealstep = DEFAULT_EXTANNEAL; % defaults defined above
end
end % else use annealstep from commandline
if ~annealdeg,
annealdeg = DEFAULT_ANNEALDEG - momentum*90; % heuristic
if annealdeg < 0,
annealdeg = 0;
end
end
if ncomps > chans | ncomps < 1
fprintf('runica(): number of components must be 1 to %d.\n',chans);
return
end
%
%%%%%%%%%%%%%%%%%%%%% Check keyword values %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%
if frames<chans,
fprintf('runica(): data length (%d) < data channels (%d)!\n',frames,chans)
return
elseif block < 2,
fprintf('runica(): block size %d too small!\n',block)
return
elseif block > frames,
fprintf('runica(): block size exceeds data length!\n');
return
elseif floor(epochs) ~= epochs,
fprintf('runica(): data length is not a multiple of the epoch length!\n');
return
elseif nsub > ncomps
fprintf('runica(): there can be at most %d sub-Gaussian components!\n',ncomps);
return
end;
if ~isempty(logfile)
fid = fopen(logfile, 'w');
if fid == -1, error('Cannot open logfile for writing'); end;
else
fid = [];
end;
verb = verbose;
if weights ~= 0, % initialize weights
% starting weights are being passed to runica() from the commandline
if chans>ncomps & weights ~=0,
[r,c]=size(weights);
if r~=ncomps | c~=chans,
fprintf('runica(): weight matrix must have %d rows, %d columns.\n', ...
chans,ncomps);
return;
end
end
icaprintf(verb,fid,'Using starting weight matrix named in argument list ...\n');
end;
%
% adjust nochange if necessary
%
if isnan(nochange)
if ncomps > 32
nochange = 1E-7;
nochangeupdated = 1; % for fprinting purposes
else
nochangeupdated = 1; % for fprinting purposes
nochange = DEFAULT_STOP;
end;
else
nochangeupdated = 0;
end;
%
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% Process the data %%%%%%%%%%%%%%%%%%%%%%%%%%
%
icaprintf(verb,fid,'\nInput data size [%d,%d] = %d channels, %d frames\n', ...
chans,frames,chans,frames);
if strcmp(pcaflag,'on')
icaprintf(verb,fid,'After PCA dimension reduction,\n finding ');
else
icaprintf(verb,fid,'Finding ');
end
if ~extended
icaprintf(verb,fid,'%d ICA components using logistic ICA.\n',ncomps);
else % if extended
icaprintf(verb,fid,'%d ICA components using extended ICA.\n',ncomps);
if extblocks > 0
icaprintf(verb,fid,'Kurtosis will be calculated initially every %d blocks using %d data points.\n',...
extblocks, kurtsize);
else
icaprintf(verb,fid,'Kurtosis will not be calculated. Exactly %d sub-Gaussian components assumed.\n',nsub);
end
end
icaprintf(verb,fid,'Decomposing %d frames per ICA weight ((%d)^2 = %d weights, %d frames)\n',...
floor(frames/ncomps.^2),ncomps.^2,frames);
icaprintf(verb,fid,'Initial learning rate will be %g, block size %d.\n',...
lrate,block);
if momentum>0,
icaprintf(verb,fid,'Momentum will be %g.\n',momentum);
end
icaprintf(verb,fid,'Learning rate will be multiplied by %g whenever angledelta >= %g deg.\n', ...
annealstep,annealdeg);
if nochangeupdated
icaprintf(verb,fid,'More than 32 channels: default stopping weight change 1E-7\n');
end;
icaprintf(verb,fid,'Training will end when wchange < %g or after %d steps.\n', nochange,maxsteps);
if biasflag,
icaprintf(verb,fid,'Online bias adjustment will be used.\n');
else
icaprintf(verb,fid,'Online bias adjustment will not be used.\n');
end
%
%%%%%%%%%%%%%%%%% Remove overall row means of data %%%%%%%%%%%%%%%%%%%%%%%
%
if strcmpi(submean, 'on')
icaprintf(verb,fid,'Removing mean of each channel ...\n');
rowmeans = mean(data,2);
for index = 1:size(data,1)
data(index,:) = data(index,:) - rowmeans(index); % subtract row means
end;
end;
icaprintf(verb,fid,'Final training data range: %g to %g\n', min(min(data,[],2)),max(max(data,[],2)));
%
%%%%%%%%%%%%%%%%%%% Perform PCA reduction %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%
if strcmp(pcaflag,'on')
icaprintf(verb,fid,'Reducing the data to %d principal dimensions...\n',ncomps);
[eigenvectors,eigenvalues,data] = pcsquash(data,ncomps);
% make data its projection onto the ncomps-dim principal subspace
end
%
%%%%%%%%%%%%%%%%%%% Perform specgram transformation %%%%%%%%%%%%%%%%%%%%%%%
%
if exist('Specgramflag') == 1
% [P F T] = SPECGRAM(A,NFFT,Fs,WINDOW,NOVERLAP) % MATLAB Sig Proc Toolbox
% Hzwinlen = fix(srate/Hzinc); % CHANGED FROM THIS 12/18/00 -sm
Hzfftlen = 2^(ceil(log(Hzwinlen)/log(2))); % make FFT length next higher 2^k
Hzoverlap = 0; % use sequential windows
%
% Get freqs and times from 1st channel analysis
%
[tmp,freqs,tms] = specgram(data(1,:),Hzfftlen,srate,Hzwinlen,Hzoverlap);
fs = find(freqs>=loHz & freqs <= hiHz);
icaprintf(verb,fid,'runica(): specified frequency range too narrow, exiting!\n');
specdata = reshape(tmp(fs,:),1,length(fs)*size(tmp,2));
specdata = [real(specdata) imag(specdata)];
% fprintf(' size(fs) = %d,%d\n',size(fs,1),size(fs,2));
% fprintf(' size(tmp) = %d,%d\n',size(tmp,1),size(tmp,2));
%
% Loop through remaining channels
%
for ch=2:chans
[tmp] = specgram(data(ch,:),Hzwinlen,srate,Hzwinlen,Hzoverlap);
tmp = reshape((tmp(fs,:)),1,length(fs)*size(tmp,2));
specdata = [specdata;[real(tmp) imag(tmp)]]; % channels are rows
end
%
% Print specgram confirmation and details
%
icaprintf(verb,fid,'Converted data to %d channels by %d=2*%dx%d points spectrogram data.\n',...
chans,2*length(fs)*length(tms),length(fs),length(tms));
if length(fs) > 1
icaprintf(verb,fid,' Low Hz %g, high Hz %g, Hz incr %g, window length %d\n',freqs(fs(1)),freqs(fs(end)),freqs(fs(2))-freqs(fs(1)),Hzwinlen);
else
icaprintf(verb,fid,' Low Hz %g, high Hz %g, window length %d\n',freqs(fs(1)),freqs(fs(end)),Hzwinlen);
end
%
% Replace data with specdata
%
data = specdata;
datalength=size(data,2);
end
%
%%%%%%%%%%%%%%%%%%% Perform sphering %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%
if strcmp(sphering,'on'), %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
icaprintf(verb,fid,'Computing the sphering matrix...\n');
sphere = 2.0*inv(sqrtm(double(mycov(data)))); % find the "sphering" matrix = spher()
if ~weights,
icaprintf(verb,fid,'Starting weights are the identity matrix ...\n');
weights = eye(ncomps,chans); % begin with the identity matrix
else % weights given on commandline
icaprintf(verb,fid,'Using starting weights named on commandline ...\n');
end
icaprintf(verb,fid,'Sphering the data ...\n');
elseif strcmp(sphering,'off') %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
if ~weights % is starting weights not given
icaprintf(verb,fid,'Using the sphering matrix as the starting weight matrix ...\n');
icaprintf(verb,fid,'Returning the identity matrix in variable "sphere" ...\n');
sphere = 2.0*inv(sqrtm(mycov(data))); % find the "sphering" matrix = spher()
weights = eye(ncomps,chans)*sphere; % begin with the identity matrix
sphere = eye(chans); % return the identity matrix
else % weights ~= 0
icaprintf(verb,fid,'Using starting weights from commandline ...\n');
icaprintf(verb,fid,'Returning the identity matrix in variable "sphere" ...\n');
sphere = eye(chans); % return the identity matrix
end
elseif strcmp(sphering,'none')
sphere = eye(chans,chans);% return the identity matrix
if ~weights
icaprintf(verb,fid,'Starting weights are the identity matrix ...\n');
icaprintf(verb,fid,'Returning the identity matrix in variable "sphere" ...\n');
weights = eye(ncomps,chans); % begin with the identity matrix
else % weights ~= 0
icaprintf(verb,fid,'Using starting weights named on commandline ...\n');
icaprintf(verb,fid,'Returning the identity matrix in variable "sphere" ...\n');
end
icaprintf(verb,fid,'Returned variable "sphere" will be the identity matrix.\n');
end
%
%%%%%%%%%%%%%%%%%%%%%%%% Initialize ICA training %%%%%%%%%%%%%%%%%%%%%%%%%
%
lastt=fix((datalength/block-1)*block+1);
BI=block*eye(ncomps,ncomps);
delta=zeros(1,chans*ncomps);
changes = [];
degconst = 180./pi;
startweights = weights;
prevweights = startweights;
oldweights = startweights;
prevwtchange = zeros(chans,ncomps);
oldwtchange = zeros(chans,ncomps);
lrates = zeros(1,maxsteps);
onesrow = ones(1,block);
bias = zeros(ncomps,1);
signs = ones(1,ncomps); % initialize signs to nsub -1, rest +1
for k=1:nsub
signs(k) = -1;
end
if extended & extblocks < 0,
icaprintf(verb,fid,'Fixed extended-ICA sign assignments: ');
for k=1:ncomps
icaprintf(verb,fid,'%d ',signs(k));
end; icaprintf(verb,fid,'\n');
end
signs = diag(signs); % make a diagonal matrix
oldsigns = zeros(size(signs));;
signcount = 0; % counter for same-signs
signcounts = [];
urextblocks = extblocks; % original value, for resets
old_kk = zeros(1,ncomps); % for kurtosis momemtum
%
%%%%%%%% ICA training loop using the logistic sigmoid %%%%%%%%%%%%%%%%%%%
%
icaprintf(verb,fid,'Beginning ICA training ...');
if extended,
icaprintf(verb,fid,' first training step may be slow ...\n');
else
icaprintf(verb,fid,'\n');
end
step=0;
laststep=0;
blockno = 1; % running block counter for kurtosis interrupts
rand('state',sum(100*clock)); % set the random number generator state to
% a position dependent on the system clock
%% Compute ICA Weights
if biasflag & extended
while step < maxsteps, %%% ICA step = pass through all the data %%%%%%%%%
timeperm=randperm(datalength); % shuffle data order at each step
for t=1:block:lastt, %%%%%%%%% ICA Training Block %%%%%%%%%%%%%%%%%%%
pause(0);
if ~isempty(get(0, 'currentfigure')) % look for user abort
if strcmp(get(gcf, 'tag'), 'stop')
if ~isempty(fid), fclose(fid); end;
close; error('USER ABORT');
end;
end
%% promote data block (only) to double to keep u and weights double
u=(weights*sphere)*double(data(:,timeperm(t:t+block-1))) + bias*onesrow;
y=tanh(u);
weights = weights + lrate*(BI-signs*y*u'-u*u')*weights;
bias = bias + lrate*sum((-2*y)')'; % for tanh() nonlin.
if momentum > 0 %%%%%%%%% Add momentum %%%%%%%%%%%%%%%%%%%%%%%%%%%%
weights = weights + momentum*prevwtchange;
prevwtchange = weights-prevweights;
prevweights = weights;
end %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
if max(max(abs(weights))) > MAX_WEIGHT
wts_blowup = 1;
change = nochange;
end
if ~wts_blowup
%
%%%%%%%%%%% Extended-ICA kurtosis estimation %%%%%%%%%%%%%%%%%%%%%
%while step < maxsteps
if extblocks > 0 & rem(blockno,extblocks) == 0,
% recompute signs vector using kurtosis
if kurtsize < frames % 12-22-99 rand() size suggestion by M. Spratling
rp = fix(rand(1,kurtsize)*datalength); % pick random subset
% Accout for the possibility of a 0 generation by rand
ou = find(rp == 0);
while ~isempty(ou) % 1-11-00 suggestion by J. Foucher
rp(ou) = fix(rand(1,length(ou))*datalength);
ou = find(rp == 0);
end
partact=(weights*sphere)*double(data(:,rp(1:kurtsize)));
else % for small data sets,
partact=(weights*sphere)*double(data); % use whole data
end
m2=mean(partact'.^2).^2;
m4= mean(partact'.^4);
kk= (m4./m2)-3.0; % kurtosis estimates
if extmomentum
kk = extmomentum*old_kk + (1.0-extmomentum)*kk; % use momentum
old_kk = kk;
end
signs=diag(sign(kk+signsbias)); % pick component signs
if signs == oldsigns,
signcount = signcount+1;
else
signcount = 0;
end
oldsigns = signs;
signcounts = [signcounts signcount];
if signcount >= SIGNCOUNT_THRESHOLD,
extblocks = fix(extblocks * SIGNCOUNT_STEP);% make kurt() estimation
signcount = 0; % less frequent if sign
end % is not changing
end % extblocks > 0 & . . .
end % if extended & ~wts_blowup %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
blockno = blockno + 1;
if wts_blowup
break
end
end % for t=1:block:lastt %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
if ~wts_blowup
oldwtchange = weights-oldweights;
step=step+1;
%
%%%%%%% Compute and print weight and update angle changes %%%%%%%%%
%
lrates(1,step) = lrate;
angledelta=0.;
delta=reshape(oldwtchange,1,chans*ncomps);
change=delta*delta';
end
%
%%%%%%%%%%%%%%%%%%%%%% Restart if weights blow up %%%%%%%%%%%%%%%%%%%%
%
if wts_blowup | isnan(change)|isinf(change), % if weights blow up,
icaprintf(verb,fid,'');
step = 0; % start again
change = nochange;
wts_blowup = 0; % re-initialize variables
blockno = 1;
lrate = lrate*DEFAULT_RESTART_FAC; % with lower learning rate
weights = startweights; % and original weight matrix
oldweights = startweights;
change = nochange;
oldwtchange = zeros(chans,ncomps);
delta=zeros(1,chans*ncomps);
olddelta = delta;
extblocks = urextblocks;
prevweights = startweights;
prevwtchange = zeros(chans,ncomps);
lrates = zeros(1,maxsteps);
bias = zeros(ncomps,1);
signs = ones(1,ncomps); % initialize signs to nsub -1, rest +1
for k=1:nsub
signs(k) = -1;
end
signs = diag(signs); % make a diagonal matrix
oldsigns = zeros(size(signs));;
if lrate> MIN_LRATE
r = rank(double(data(:,1:min(10000,size(data,2))))); % determine if data rank is too low
if r<ncomps
icaprintf(verb,fid,'Data has rank %d. Cannot compute %d components.\n',...
r,ncomps);
return
else
icaprintf(verb,fid,...
'Lowering learning rate to %g and starting again.\n',lrate);
end
else
icaprintf(verb,fid, ...
'runica(): QUITTING - weight matrix may not be invertible!\n');
return;
end
else % if weights in bounds
%
%%%%%%%%%%%%% Print weight update information %%%%%%%%%%%%%%%%%%%%%%
%
if step> 2
angledelta=acos((delta*olddelta')/sqrt(change*oldchange));
end
places = -floor(log10(nochange));
icaprintf(verb,fid,'step %d - lrate %5f, wchange %8.8f, angledelta %4.1f deg\n', ...
step, lrate, change, degconst*angledelta);
%
%%%%%%%%%%%%%%%%%%%% Save current values %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%
changes = [changes change];
oldweights = weights;
%
%%%%%%%%%%%%%%%%%%%% Anneal learning rate %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%
if degconst*angledelta > annealdeg,
lrate = lrate*annealstep; % anneal learning rate
olddelta = delta; % accumulate angledelta until
oldchange = change; % annealdeg is reached
elseif step == 1 % on first step only
olddelta = delta; % initialize
oldchange = change;
end
%
%%%%%%%%%%%%%%%%%%%% Apply stopping rule %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%
if step >2 & change < nochange, % apply stopping rule
laststep=step;
step=maxsteps; % stop when weights stabilize
elseif change > DEFAULT_BLOWUP, % if weights blow up,
lrate=lrate*DEFAULT_BLOWUP_FAC; % keep trying
end; % with a smaller learning rate
end; % end if weights in bounds
end; % end while step < maxsteps (ICA Training) %%%%%%%%%%%%%%%%%%%%%%%%%
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
end
%% Compute ICA Weights
if biasflag & ~extended
while step < maxsteps, %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
timeperm=randperm(datalength); % shuffle data order at each step
for t=1:block:lastt, %%%%%%%%% ICA Training Block %%%%%%%%%%%%%%%%%%%
pause(0);
if ~isempty(get(0, 'currentfigure')) & strcmp(get(gcf, 'tag'), 'stop')
close; error('USER ABORT');
end;
u=(weights*sphere)*double(data(:,timeperm(t:t+block-1))) + bias*onesrow;
y=1./(1+exp(-u));
weights = weights + lrate*(BI+(1-2*y)*u')*weights;
bias = bias + lrate*sum((1-2*y)')'; % for logistic nonlin. %
if momentum > 0 %%%%%%%%% Add momentum %%%%%%%%%%%%%%%%%%%%%%%%%%%%
weights = weights + momentum*prevwtchange;
prevwtchange = weights-prevweights;
prevweights = weights;
end %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
if max(max(abs(weights))) > MAX_WEIGHT
wts_blowup = 1;
change = nochange;
end
blockno = blockno + 1;
if wts_blowup
break
end
end % for t=1:block:lastt %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
if ~wts_blowup
oldwtchange = weights-oldweights;
step=step+1;
%
%%%%%%% Compute and print weight and update angle changes %%%%%%%%%
%
lrates(1,step) = lrate;
angledelta=0.;
delta=reshape(oldwtchange,1,chans*ncomps);
change=delta*delta';
end
%
%%%%%%%%%%%%%%%%%%%%%% Restart if weights blow up %%%%%%%%%%%%%%%%%%%%
%
if wts_blowup | isnan(change)|isinf(change), % if weights blow up,
icaprintf(verb,fid,'');
step = 0; % start again
change = nochange;
wts_blowup = 0; % re-initialize variables
blockno = 1;
lrate = lrate*DEFAULT_RESTART_FAC; % with lower learning rate
weights = startweights; % and original weight matrix
oldweights = startweights;
change = nochange;
oldwtchange = zeros(chans,ncomps);
delta=zeros(1,chans*ncomps);
olddelta = delta;
extblocks = urextblocks;
prevweights = startweights;
prevwtchange = zeros(chans,ncomps);
lrates = zeros(1,maxsteps);
bias = zeros(ncomps,1);
if lrate> MIN_LRATE
r = rank(double(data(:,1:min(10000,size(data,2))))); % determine if data rank is too low
if r<ncomps
icaprintf(verb,fid,'Data has rank %d. Cannot compute %d components.\n',r,ncomps);
return
else
icaprintf(verb,fid,'Lowering learning rate to %g and starting again.\n',lrate);
end
else
icaprintf(verb,fid,'runica(): QUITTING - weight matrix may not be invertible!\n');
return;
end
else % if weights in bounds
%
%%%%%%%%%%%%% Print weight update information %%%%%%%%%%%%%%%%%%%%%%
%
if step> 2
angledelta=acos((delta*olddelta')/sqrt(change*oldchange));
end
places = -floor(log10(nochange));
icaprintf(verb,fid,'step %d - lrate %5f, wchange %8.8f, angledelta %4.1f deg\n', ...
step, lrate, change, degconst*angledelta);
%
%%%%%%%%%%%%%%%%%%%% Save current values %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%
changes = [changes change];
oldweights = weights;
%
%%%%%%%%%%%%%%%%%%%% Anneal learning rate %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%
if degconst*angledelta > annealdeg,
lrate = lrate*annealstep; % anneal learning rate
olddelta = delta; % accumulate angledelta until
oldchange = change; % annealdeg is reached
elseif step == 1 % on first step only
olddelta = delta; % initialize
oldchange = change;
end
%
%%%%%%%%%%%%%%%%%%%% Apply stopping rule %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%
if step >2 & change < nochange, % apply stopping rule
laststep=step;
step=maxsteps; % stop when weights stabilize
elseif change > DEFAULT_BLOWUP, % if weights blow up,
lrate=lrate*DEFAULT_BLOWUP_FAC; % keep trying
end; % with a smaller learning rate
end; % end if weights in bounds
end; % end while step < maxsteps (ICA Training) %%%%%%%%%%%%%%%%%%%%%%%%%
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
end
%% Compute ICA Weights
if ~biasflag & extended
while step < maxsteps, %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
timeperm=randperm(datalength); % shuffle data order at each step through data
for t=1:block:lastt, %%%%%%%%% ICA Training Block %%%%%%%%%%%%%%%%%%%
pause(0);
if ~isempty(get(0, 'currentfigure')) & strcmp(get(gcf, 'tag'), 'stop')
close; error('USER ABORT'); % detect user abort
end
u=(weights*sphere)*double(data(:,timeperm(t:t+block-1))); % promote block to dbl
y=tanh(u); %
weights = weights + lrate*(BI-signs*y*u'-u*u')*weights;
if momentum > 0 %%%%%%%%% Add momentum %%%%%%%%%%%%%%%%%%%%%%%%%%%%
weights = weights + momentum*prevwtchange;
prevwtchange = weights-prevweights;
prevweights = weights;
end %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
if max(max(abs(weights))) > MAX_WEIGHT
wts_blowup = 1;
change = nochange;
end
if ~wts_blowup
%
%%%%%%%%%%% Extended-ICA kurtosis estimation %%%%%%%%%%%%%%%%%%%%%
%while step < maxsteps
if extblocks > 0 & rem(blockno,extblocks) == 0,
% recompute signs vector using kurtosis
if kurtsize < frames % 12-22-99 rand() size suggestion by M. Spratling
rp = fix(rand(1,kurtsize)*datalength); % pick random subset
% Accout for the possibility of a 0 generation by rand
ou = find(rp == 0);
while ~isempty(ou) % 1-11-00 suggestion by J. Foucher
rp(ou) = fix(rand(1,length(ou))*datalength);
ou = find(rp == 0);
end
partact=(weights*sphere)*double(data(:,rp(1:kurtsize)));
else % for small data sets,
partact=(weights*sphere)*double(data); % use whole data
end
m2=mean(partact'.^2).^2;
m4= mean(partact'.^4);
kk= (m4./m2)-3.0; % kurtosis estimates
if extmomentum
kk = extmomentum*old_kk + (1.0-extmomentum)*kk; % use momentum
old_kk = kk;
end
signs=diag(sign(kk+signsbias)); % pick component signs
if signs == oldsigns,
signcount = signcount+1;
else
signcount = 0;
end
oldsigns = signs;
signcounts = [signcounts signcount];
if signcount >= SIGNCOUNT_THRESHOLD,
extblocks = fix(extblocks * SIGNCOUNT_STEP);% make kurt() estimation
signcount = 0; % less frequent if sign
end % is not changing
end % extblocks > 0 & . . .
end % if ~wts_blowup %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
blockno = blockno + 1;
if wts_blowup
break
end
end % for t=1:block:lastt %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
if ~wts_blowup
oldwtchange = weights-oldweights;
step=step+1;
%
%%%%%%% Compute and print weight and update angle changes %%%%%%%%%
%
lrates(1,step) = lrate;
angledelta=0.;
delta=reshape(oldwtchange,1,chans*ncomps);
change=delta*delta';
end
%
%%%%%%%%%%%%%%%%%%%%%% Restart if weights blow up %%%%%%%%%%%%%%%%%%%%
%
if wts_blowup | isnan(change)|isinf(change), % if weights blow up,
icaprintf(verb,fid,'');
step = 0; % start again
change = nochange;
wts_blowup = 0; % re-initialize variables
blockno = 1;
lrate = lrate*DEFAULT_RESTART_FAC; % with lower learning rate
weights = startweights; % and original weight matrix
oldweights = startweights;
change = nochange;
oldwtchange = zeros(chans,ncomps);
delta=zeros(1,chans*ncomps);
olddelta = delta;
extblocks = urextblocks;
prevweights = startweights;
prevwtchange = zeros(chans,ncomps);
lrates = zeros(1,maxsteps);
bias = zeros(ncomps,1);
signs = ones(1,ncomps); % initialize signs to nsub -1, rest +1
for k=1:nsub
signs(k) = -1;
end
signs = diag(signs); % make a diagonal matrix
oldsigns = zeros(size(signs));
if lrate> MIN_LRATE
r = rank(data); % find whether data rank is too low
if r<ncomps
icaprintf(verb,fid,'Data has rank %d. Cannot compute %d components.\n',...
r,ncomps);
return
else
icaprintf(verb,fid,...
'Lowering learning rate to %g and starting again.\n',lrate);
end
else
icaprintf(verb,fid, ...
'runica(): QUITTING - weight matrix may not be invertible!\n');
return;
end
else % if weights in bounds
%
%%%%%%%%%%%%% Print weight update information %%%%%%%%%%%%%%%%%%%%%%
%
if step> 2
angledelta=acos((delta*olddelta')/sqrt(change*oldchange));
end
places = -floor(log10(nochange));
icaprintf(verb,fid,'step %d - lrate %5f, wchange %8.8f, angledelta %4.1f deg\n', ...
step, lrate, change, degconst*angledelta);
%
%%%%%%%%%%%%%%%%%%%% Save current values %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%
changes = [changes change];
oldweights = weights;
%
%%%%%%%%%%%%%%%%%%%% Anneal learning rate %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%
if degconst*angledelta > annealdeg,
lrate = lrate*annealstep; % anneal learning rate
olddelta = delta; % accumulate angledelta until
oldchange = change; % annealdeg is reached
elseif step == 1 % on first step only
olddelta = delta; % initialize
oldchange = change;
end
%
%%%%%%%%%%%%%%%%%%%% Apply stopping rule %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%
if step >2 & change < nochange, % apply stopping rule
laststep=step;
step=maxsteps; % stop when weights stabilize
elseif change > DEFAULT_BLOWUP, % if weights blow up,
lrate=lrate*DEFAULT_BLOWUP_FAC; % keep trying
end; % with a smaller learning rate
end; % end if weights in bounds
end; % end while step < maxsteps (ICA Training) %%%%%%%%%%%%%%%%%%%%%%%%%
end
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%% Compute ICA Weights
if ~biasflag & ~extended
while step < maxsteps, %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
timeperm=randperm(datalength); % shuffle data order at each step
for t=1:block:lastt, %%%%%%%%% ICA Training Block %%%%%%%%%%%%%%%%%%%
pause(0);
if ~isempty(get(0, 'currentfigure')) & strcmp(get(gcf, 'tag'), 'stop')
close; error('USER ABORT');
end;
u=(weights*sphere)*double(data(:,timeperm(t:t+block-1)));
y=1./(1+exp(-u)); %
weights = weights + lrate*(BI+(1-2*y)*u')*weights;
if momentum > 0 %%%%%%%%% Add momentum %%%%%%%%%%%%%%%%%%%%%%%%%%%%
weights = weights + momentum*prevwtchange;
prevwtchange = weights-prevweights;
prevweights = weights;
end %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
if max(max(abs(weights))) > MAX_WEIGHT
wts_blowup = 1;
change = nochange;
end
blockno = blockno + 1;
if wts_blowup
break
end
end % for t=1:block:lastt %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
if ~wts_blowup
oldwtchange = weights-oldweights;
step=step+1;
%
%%%%%%% Compute and print weight and update angle changes %%%%%%%%%
%
lrates(1,step) = lrate;
angledelta=0.;
delta=reshape(oldwtchange,1,chans*ncomps);
change=delta*delta';
end
%
%%%%%%%%%%%%%%%%%%%%%% Restart if weights blow up %%%%%%%%%%%%%%%%%%%%
%
if wts_blowup | isnan(change)|isinf(change), % if weights blow up,
icaprintf(verb,fid,'');
step = 0; % start again
change = nochange;
wts_blowup = 0; % re-initialize variables
blockno = 1;
lrate = lrate*DEFAULT_RESTART_FAC; % with lower learning rate
weights = startweights; % and original weight matrix
oldweights = startweights;
change = nochange;
oldwtchange = zeros(chans,ncomps);
delta=zeros(1,chans*ncomps);
olddelta = delta;
extblocks = urextblocks;
prevweights = startweights;
prevwtchange = zeros(chans,ncomps);
lrates = zeros(1,maxsteps);
bias = zeros(ncomps,1);
if lrate> MIN_LRATE
r = rank(data); % find whether data rank is too low
if r<ncomps
icaprintf(verb,fid,'Data has rank %d. Cannot compute %d components.\n',...
r,ncomps);
return
else
icaprintf(verb,fid,...
'Lowering learning rate to %g and starting again.\n',lrate);
end
else
icaprintf(verb,fid, ...
'runica(): QUITTING - weight matrix may not be invertible!\n');
return;
end
else % if weights in bounds
%
%%%%%%%%%%%%% Print weight update information %%%%%%%%%%%%%%%%%%%%%%
%
if step> 2
angledelta=acos((delta*olddelta')/sqrt(change*oldchange));
end
places = -floor(log10(nochange));
icaprintf(verb,fid,'step %d - lrate %5f, wchange %8.8f, angledelta %4.1f deg\n', ...
step, lrate, change, degconst*angledelta);
%
%%%%%%%%%%%%%%%%%%%% Save current values %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%
changes = [changes change];
oldweights = weights;
%
%%%%%%%%%%%%%%%%%%%% Anneal learning rate %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%
if degconst*angledelta > annealdeg,
lrate = lrate*annealstep; % anneal learning rate
olddelta = delta; % accumulate angledelta until
oldchange = change; % annealdeg is reached
elseif step == 1 % on first step only
olddelta = delta; % initialize
oldchange = change;
end
%
%%%%%%%%%%%%%%%%%%%% Apply stopping rule %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%
if step >2 & change < nochange, % apply stopping rule
laststep=step;
step=maxsteps; % stop when weights stabilize
elseif change > DEFAULT_BLOWUP, % if weights blow up,
lrate=lrate*DEFAULT_BLOWUP_FAC; % keep trying
end; % with a smaller learning rate
end; % end if weights in bounds
end; % end while step < maxsteps (ICA Training) %%%%%%%%%%%%%%%%%%%%%%%%%
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
end
%% Finalize Computed Data for Output
if ~laststep
laststep = step;
end;
lrates = lrates(1,1:laststep); % truncate lrate history vector
%
%%%%%%%%%%%%%% Orient components towards max positive activation %%%%%%
%
if nargout > 6 | strcmp(posactflag,'on')
% make activations from sphered and pca'd data; -sm 7/05
% add back the row means removed from data before sphering
if strcmp(pcaflag,'off')
sr = sphere * rowmeans';
for r = 1:ncomps
data(r,:) = data(r,:)+sr(r); % add back row means
end
data = (weights*sphere)*data; % OK in single
else
ser = sphere*eigenvectors(:,1:ncomps)'*rowmeans';
for r = 1:ncomps
data(r,:) = data(r,:)+ser(r); % add back row means
end
data = (weights*sphere)*data; % OK in single
end;
end
%
% NOTE: Now 'data' are the component activations = weights*sphere*raw_data
%
%
%%%%%%%%%%%%%% If pcaflag, compose PCA and ICA matrices %%%%%%%%%%%%%%%
%
if strcmp(pcaflag,'on')
icaprintf(verb,fid,'Composing the eigenvector, weights, and sphere matrices\n');
icaprintf(verb,fid,' into a single rectangular weights matrix; sphere=eye(%d)\n'...
,chans);
weights= weights*sphere*eigenvectors(:,1:ncomps)';
sphere = eye(urchans);
end
%
%%%%%% Sort components in descending order of max projected variance %%%%
%
icaprintf(verb,fid,'Sorting components in descending order of mean projected variance ...\n');
%
%%%%%%%%%%%%%%%%%%%% Find mean variances %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%
% meanvar = zeros(ncomps,1); % size of the projections
if ncomps == urchans % if weights are square . . .
winv = inv(weights*sphere);
else
icaprintf(verb,fid,'Using pseudo-inverse of weight matrix to rank order component projections.\n');
winv = pinv(weights*sphere);
end
%
% compute variances without backprojecting to save time and memory -sm 7/05
%
for index = 1:size(data,1)
meanvar(index) = sum(winv(:,index).^2).*sum(double(data(index,:)).^2)/((chans*frames)-1); % from Rey Ramirez 8/07
end;
%
%%%%%%%%%%%%%% Sort components by mean variance %%%%%%%%%%%%%%%%%%%%%%%%
%
[sortvar, windex] = sort(meanvar);
windex = windex(ncomps:-1:1); % order large to small
meanvar = meanvar(windex);
%
%%%%%%%%%%%% re-orient max(abs(activations)) to >=0 ('posact') %%%%%%%%
%
if strcmp(posactflag,'on') % default is now off to save processing and memory
icaprintf(verb,fid,'Making the max(abs(activations)) positive ...\n');
for index = 1:ize(data,2)
[tmp ix(index)] = max(abs(data(index,:))); % = max abs activations
end;
signsflipped = 0;
for r=1:ncomps
if sign(data(r,ix(r))) < 0
if nargout>6 % if activations are to be returned (only)
data(r,:) = -1*data(r,:); % flip activations so max(abs()) is >= 0
end
winv(:,r) = -1*winv(:,r); % flip component maps
signsflipped = 1;
end
end
if signsflipped == 1
weights = pinv(winv)*inv(sphere); % re-invert the component maps
end
% [data,winvout,weights] = posact(data,weights); % overwrite data with activations
% changes signs of activations (now = data) and weights
% to make activations (data) net rms-positive
% can call this outside of runica() - though it is inefficient!
end
%
%%%%%%%%%%%%%%%%%%%%% Filter data using final weights %%%%%%%%%%%%%%%%%%
%
if nargout>6, % if activations are to be returned
icaprintf(verb,fid,'Permuting the activation wave forms ...\n');
data = data(windex,:); % data is now activations -sm 7/05
else
clear data
end
weights = weights(windex,:);% reorder the weight matrix
bias = bias(windex); % reorder them
signs = diag(signs); % vectorize the signs matrix
signs = signs(windex); % reorder them
if ~isempty(fid), fclose(fid); end; % close logfile
%
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% end %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%
return
% printing functions
% ------------------
function icaprintf(verb,fid, varargin);
if verb
if ~isempty(fid)
fprintf(fid, varargin{:});
end;
fprintf(varargin{:});
end;
% this function compute covariance
% without using much memory (no need to transpose a)
% --------------------------------
function c = mycov(a) % same as cov(a')
try
c = cov(a');
catch,
c = zeros(size(a,1), size(a,1));
for i1=1:size(a,1)
for i2=1:size(a,1)
%c(i1,i2) = sum(double((a(i1,:)-mean(a(i1,:)))).*(double(a(i2,:)-mean(a(i2,:)))))/(size(a,2)-1);
c(i1,i2) = sum(double(a(i1,:).*a(i2,:)))/(size(a,2)-1); % mean has already been subtracted
end;
end;
end;
|
github
|
lcnbeapp/beapp-master
|
eeg_time2prev.m
|
.m
|
beapp-master/Packages/eeglab14_1_2b/functions/miscfunc/eeg_time2prev.m
| 6,514 |
utf_8
|
b09492c5bf451c4d42c06b87dc8921af
|
% eeg_time2prev() - returns a vector giving, for each event of specified ("target") type(s),
% the delay (in ms) since the preceding event (if any) of specified
% ("previous") type(s). Requires the EEG.urevent structure, plus
% EEG.event().urevent pointers to it.
%
% NOW SUPERCEDED BY eeg_context()
% Usage:
% >> [delays,targets,urtargs,urprevs] = eeg_time2prev(EEG,{target},{previous});
% Inputs:
% EEG - structure containing an EEGLAB dataset
% {target} - cell array of strings naming event type(s) of the specified target events
%{previous} - cell array of strings naming event type(s) of the specified previous events
%
% Outputs:
% delays - vector giving, for each event of a type listed in "target", the delay (in ms)
% since the last preceding event of a type listed in "previous" (0 if none such).
% targets - vector of indices of the "target" events in the event structure
% urtargs - vector of indices of the "target" events in the urevent structure
% urprevs - vector of indices of the "previous" events in the urevent structure (0 if none).
%
% Example:
% >> target = {'novel'}; % target event type 'novel'
% >> previous = {'novel', 'rare'}; % either 'novel' or 'rare'
% >> [delays,targets] = eeg_time2prev(EEG,target,previous);
%% Vector 'delays' now contains delays (in ms) from each 'novel' event to the previous
%% 'rare' OR 'novel' event, else 0 if none such. Vector 'targets' now contains the
%% 'novel' event indices.
%%
% Scott Makeig & Arnaud Delorme, SCCN/INC/UCSD, August 28, 2003
function [delays,targets,urtargets,urprevs] = eeg_time2prev(EEG,target,previous);
verbose = 1; % FLAG (1=on|0=off)
nevents = length(EEG.event);
%
%%%%%%%%%%%%%%%%%%%% Test input arguments %%%%%%%%%%%%%%%%%%%%%%%%%
%
if ~iscell(target)
error('2nd argument "target" must be a {cell array} of event type strings.');
return
end
for k=1:length(target)
if ~ischar([ target{k}{:} ])
error('2nd argument "target" must be a {cell array} of event type strings.');
end
end
if ~iscell(previous)
error('3rd argument "previous" must be a {cell array} of event types.');
return
end
for k=1:length(target) % make all target types strings
if ~ischar(target{k})
target{k} = num2str(target{k});
end
end
for k=1:length(previous) % make all previous types strings
if ~ischar(previous{k})
previous{k} = num2str(previous{k});
end
end
if ~isfield(EEG,'urevent')
error('requires the urevent structure be present.');
return
end
if length(EEG.urevent) < nevents
error('WARNING: In dataset, number of urevents < number of events!?');
return
end
%
%%%%%%%%%%%%%%%%%%%% Initialize output arrays %%%%%%%%%%%%%%%%%%%%%%
%
delays = zeros(1,nevents); % holds output times in ms
targets = zeros(1,nevents); % holds indxes of targets
urtargets = zeros(1,nevents); % holds indxes of targets
urprevs = zeros(1,nevents); % holds indxes of prevs
targetcount = 0; % index of current target
% Below:
% idx = current event index
% uridx = current urevent index
% tidx = target type index
% uidx = previous urevent index
% pidx = previous type index
%
%%%%%%%%%%%for each event in the dataset %%%%%%%%%%%%%%%%%%%%
%
for idx = 1:nevents % for each event in the dataset
%
%%%%%%%%%%%%%%%%%%%%%%%% find target events %%%%%%%%%%%%%%%%%
%
uridx = EEG.event(idx).urevent; % find its urevent index
istarget = 0; % initialize target flag
tidx = 1; % initialize target type index
while ~istarget & tidx<=length(target) % for each potential target type
if strcmpi(num2str(EEG.urevent(uridx).type),target(tidx))
istarget=1; % flag event as target
targetcount = targetcount+1; % increment target count
targets(targetcount) = idx; % save event index
urtargets(targetcount) = uridx; % save urevent index
break % stop target type checking
else
tidx = tidx+1; % else try next target type
end
end
if istarget % if current event is a target type
%
%%%%%%%%%%%%%%%%%%% Find a 'previous' event %%%%%%%%%%%%%%%%%%
%
isprevious = 0; % initialize previous flag
uidx = uridx-1; % begin with the previous urevent
while uridx > 0
pidx = 1; % initialize previous type index
while ~isprevious & pidx<=length(previous) % for each previous event type
if strcmpi(num2str(EEG.urevent(uidx).type),previous(pidx))
isprevious=1; % flag 'previous' event
urprevs(targetcount) = uidx; % mark event as previous
break % stop previous type checking
else
pidx = pidx+1; % try next 'previous' event type
end
end % pidx
if isprevious
break % stop previous event checking
else
uidx = uidx-1; % keep checking for a 'previous' type event
end % isprevious
end % uidx
%
%%% Compute delay from current target to previous event %%%%%
%
if isprevious % if type 'previous' event found
delays(targetcount) = 1000/EEG.srate * ...
(-1)*(EEG.urevent(uridx).latency - EEG.urevent(urprevs(targetcount)).latency);
else
delays(targetcount) = 0; % mark no previous event with 0
end
if verbose
fprintf('%4d. (targ %s) %4d - (prev %s) %4d = %4.1f ms\n',...
targetcount, targets(tidx),idx, ...
previous(pidx),urprevs(targetcount),...
delays(targetcount));
end % verbose
end % istarget
end % event loop
%
%%%%%%%%%%%%%% Truncate the output arrays %%%%%%%%%%%%%%%%%%%%%%
%
if targetcount > 0
targets = targets(1:targetcount);
urtargets = urtargets(1:targetcount);
urprevs = urprevs(1:targetcount);
delays = delays(1:targetcount);
else
if verbose
fprintf('eeg_time2prev(): No target type events found.\n')
end
targets = [];
urtargets = [];
urprevs = [];
delays = [];
end
|
github
|
lcnbeapp/beapp-master
|
helpforexe.m
|
.m
|
beapp-master/Packages/eeglab14_1_2b/functions/miscfunc/helpforexe.m
| 2,556 |
utf_8
|
dc086adf5a27490f1a3e39f6d218bbd1
|
% helpforexe() - Write help files for exe version
%
% Usage:
% histtoexe( mfile, folder)
%
% Inputs:
% mfile - [cell of string] Matlab files with help message
% folder - [string] Output folder
%
% Output:
% text files name help_"mfile".m
%
% Author: Arnaud Delorme, 2006
%
% See also: eeglab()
% Copyright (C) 2006 Arnaud Delorme
%
% This program is free software; you can redistribute it and/or modify
% it under the terms of the GNU General Public License as published by
% the Free Software Foundation; either version 2 of the License, or
% (at your option) any later version.
%
% This program is distributed in the hope that it will be useful,
% but WITHOUT ANY WARRANTY; without even the implied warranty of
% MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
% GNU General Public License for more details.
%
% You should have received a copy of the GNU General Public License
% along with this program; if not, write to the Free Software
% Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
function helpforexe( funct, fold );
if nargin <1
help histforexe;
return;
end;
nonmatlab = 0;
% write all files
% ---------------
for index = 1:length(funct)
doc1 = readfunc(funct{index}, nonmatlab);
fid = fopen( fullfile(fold, [ 'help_' funct{index} ]), 'w');
for ind2 = 1:length(doc1)
if isempty(doc1{ind2}) fprintf(fid, [ 'disp('' '');\n' ]);
else fprintf(fid, [ 'disp(' vararg2str({ doc1{ind2} }) ');\n' ]);
end;
end;
fclose(fid);
%fprintf(fid, 'for tmpind = 1:length(tmptxt), if isempty(tmptxt{tmpind}), disp('' ''); else disp(tmptxt{tmpind}); end; end; clear tmpind tmptxt;\n' );
end;
% try all functions
% -----------------
tmppath = pwd;
cd(fold);
for index = 1:length(funct)
evalc([ 'help_' funct{index}(1:end-2) ]);
end;
cd(tmppath);
return;
%-------------------------------------
function [doc] = readfunc(funct, nonmatlab)
doc = {};
if nonmatlab
fid = fopen( funct, 'r');
else
if findstr( funct, '.m')
fid = fopen( funct, 'r');
else
fid = fopen( [funct '.m'], 'r');
end;
end;
if fid == -1
error('File not found');
end;
sub = 1;
try,
if ~isunix, sub = 0; end;
catch, end;
if nonmatlab
str = fgets( fid );
while ~feof(fid)
str = deblank(str(1:end-sub));
doc = { doc{:} str(1:end) };
str = fgets( fid );
end;
else
str = fgets( fid );
while (str(1) == '%')
str = deblank(str(1:end-sub));
doc = { doc{:} str(2:end) };
str = fgets( fid );
end;
end;
fclose(fid);
|
github
|
lcnbeapp/beapp-master
|
imagesclogy.m
|
.m
|
beapp-master/Packages/eeglab14_1_2b/functions/miscfunc/imagesclogy.m
| 3,685 |
utf_8
|
73cfa531e2316e4148fec6793f6f8646
|
% imagesclogy() - make an imagesc(0) plot with log y-axis values (ala semilogy())
%
% Usage: >> imagesclogy(times,freqs,data);
% Usage: >> imagesclogy(times,freqs,data,clim,xticks,yticks,'key','val',...);
%
% Inputs:
% times = vector of x-axis values
% freqs = vector of y-axis values (LOG spaced)
% data = matrix of size (freqs,times)
%
% Optional inputs:
% clim = optional color limit
% xticks = graduation for x axis
% yticks = graduation for y axis
% ... = 'key', 'val' properties for figure
%
% Author: Arnaud Delorme, SCCN/INC/UCSD, La Jolla, 4/2003
% Copyright (C) 4/2003 Arnaud Delorme, SCCN/INC/UCSD, [email protected]
%
% This program is free software; you can redistribute it and/or modify
% it under the terms of the GNU General Public License as published by
% the Free Software Foundation; either version 2 of the License, or
% (at your option) any later version.
%
% This program is distributed in the hope that it will be useful,
% but WITHOUT ANY WARRANTY; without even the implied warranty of
% MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
% GNU General Public License for more details.
%
% You should have received a copy of the GNU General Public License
% along with this program; if not, write to the Free Software
% Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
function imagesclogy(times,freqs,data,clim, xticks, yticks, varargin)
if size(data,1) ~= length(freqs)
fprintf('imagesclogy(): data matrix must have %d rows!\n',length(freqs));
return
end
if size(data,2) ~= length(times)
fprintf('imagesclogy(): data matrix must have %d columns!\n',length(times));
return
end
if min(freqs)<= 0
fprintf('imagesclogy(): frequencies must be > 0!\n');
return
end
% problem with log images in Matlab: border are automatically added
% to account for half of the width of a line: but they are added as
% if the data was linear. The commands below compensate for this effect
steplog = log(freqs(2))-log(freqs(1)); % same for all points
realborders = [exp(log(freqs(1))-steplog/2) exp(log(freqs(end))+steplog/2)];
newfreqs = linspace(realborders(1), realborders(2), length(freqs));
% regressing 3 times
border = mean(newfreqs(2:end)-newfreqs(1:end-1))/2; % automatically added to the borders in imagesc
newfreqs = linspace(realborders(1)+border, realborders(2)-border, length(freqs));
border = mean(newfreqs(2:end)-newfreqs(1:end-1))/2; % automatically added to the borders in imagesc
newfreqs = linspace(realborders(1)+border, realborders(2)-border, length(freqs));
border = mean(newfreqs(2:end)-newfreqs(1:end-1))/2; % automatically added to the borders in imagesc
newfreqs = linspace(realborders(1)+border, realborders(2)-border, length(freqs));
if nargin == 4 & ~isempty(clim)
imagesc(times,newfreqs,data,clim);
else
imagesc(times,newfreqs,data);
end;
set(gca, 'yscale', 'log');
% puting ticks
% ------------
if nargin >= 5, set(gca, 'xtick', xticks); end;
if nargin >= 6
divs = yticks;
else
divs = linspace(log(freqs(1)), log(freqs(end)), 10);
divs = ceil(exp(divs)); divs = unique_bc(divs); % ceil is critical here, round might misalign
% out-of border label with within border ticks
end;
set(gca, 'ytickmode', 'manual');
set(gca, 'ytick', divs);
% additional properties
% ---------------------
set(gca, 'yminortick', 'off', 'xaxislocation', 'bottom', 'box', 'off', 'ticklength', [0.03 0], 'tickdir','out', 'color', 'none');
if ~isempty(varargin)
set(gca, varargin{:});
end;
|
github
|
lcnbeapp/beapp-master
|
gauss.m
|
.m
|
beapp-master/Packages/eeglab14_1_2b/functions/miscfunc/gauss.m
| 431 |
utf_8
|
ac68a4b38603e75bbb97ab7770117c1c
|
% gauss() - return a smooth Gaussian window
%
% Usage:
% >> outvector = gauss(frames,sds);
%
% Inputs:
% frames = window length
% sds = number of +/-std. deviations = steepness
% (~0+ -> flat; >>10 -> spike)
function outvec = gauss(frames,sds)
outvec = [];
if nargin < 2
help gauss
return
end
if sds <=0 | frames < 1
help gauss
return
end
incr = 2*sds/(frames-1);
outvec = exp(-(-sds:incr:sds).^2);
|
github
|
lcnbeapp/beapp-master
|
runpca2.m
|
.m
|
beapp-master/Packages/eeglab14_1_2b/functions/miscfunc/runpca2.m
| 2,347 |
utf_8
|
bec4863264e507c374a64d5ecbfe4132
|
% runpca() - perform principal component analysis (PCA) using singular value
% decomposition (SVD) using Matlab svd() or svds()
% >> inv(eigvec)*data = pc;
% Usage:
% >> [pc,eigvec,sv] = runpca(data);
% >> [pc,eigvec,sv] = runpca(data,num,norm)
%
% Inputs:
% data - input data matrix (rows are variables, columns observations)
% num - number of principal comps to return {def|0|[] -> rows in data}
% norm - 1/0 = do/don't normalize the eigvec's to be equivariant
% {def|0 -> no normalization}
% Outputs:
% pc - the principal components, i.e. >> inv(eigvec)*data = pc;
% eigvec - the inverse weight matrix (=eigenvectors). >> data = eigvec*pc;
% sv - the singular values (=eigenvalues)
%
% Author: Colin Humphries, CNL / Salk Institute, 1997
%
% See also: runica()
% Copyright (C) Colin Humphries, CNL / Salk Institute, Aug, 1997
%
% This program is free software; you can redistribute it and/or modify
% it under the terms of the GNU General Public License as published by
% the Free Software Foundation; either version 2 of the License, or
% (at your option) any later version.
%
% This program is distributed in the hope that it will be useful,
% but WITHOUT ANY WARRANTY; without even the implied warranty of
% MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
% GNU General Public License for more details.
%
% You should have received a copy of the GNU General Public License
% along with this program; if not, write to the Free Software
% Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
% 01/31/00 renamed runpca() and improved usage message -sm
% 01-25-02 reformated help & license, added links -ad
function [pc,A,sv]= runpca2(data,K,dosym)
[chans,frames] = size(data);
if nargin < 3 || K < chans
dosym = 1;
end
if nargin < 2
K = chans;
end
if nargin < 1
help runpca
return
end
% remove the mean
for i = 1:chans
data(i,:) = data(i,:) - mean(data(i,:));
end
% do svd
[U,S,V] = svd(data*data'/frames); % U and V should be the same since data*data' is symmetric
sv = sqrt(diag(S));
if dosym == 1
pc = pinv(diag(sv(1:K))) * V(:,1:K)' * data;
A = U(:,1:K) * diag(sv(1:K));
else
pc = U * pinv(diag(sv)) * V' * data;
A = U * diag(sv) * V';
end
|
github
|
lcnbeapp/beapp-master
|
loc_subsets.m
|
.m
|
beapp-master/Packages/eeglab14_1_2b/functions/miscfunc/loc_subsets.m
| 8,435 |
utf_8
|
0d9bef14db75412fc13a4088966c510a
|
% loc_subsets() - Separate channels into maximally evenly-spaced subsets.
% This is achieved by exchanging channels between subsets so as to
% increase the sum of average of distances within each channel subset.
% Usage:
% >> subset = loc_subsets(chanlocs, nchans); % select an evenly spaced nchans
% >> [subsets subidx pos] = loc_subsets(chanlocs, nchans, plotobj, plotchans, keepchans);
%
% Inputs:
%
% chanlocs - EEGLAB dataset channel locations structure (e.g., EEG.chanlocs)
%
% nchans - (1,N) matrix containing number of channels that should be in each
% of N channel subsets respectively. if total number of channels in
% all subsets is less than the number of EEG channels in the chanlocs
% structure, N+1 subsets are created. The last subset includes the
% remaining channels.
%
% Optional inputs:
%
% plotobj - (true|false|1|0) plot the time course of the objective function
% {default: false|0)
% plotchans - (true|false|1|0) make 3-D plots showing the channel locations of
% the subsets {default: false|0)
% keepchans - (cell array) channels that has to be kept in each set and
% not undergo optimization. You can use this option to make
% sure certain channels will be assigned to each set. For
% example, to keep channels 1:10 to the first subset and
% channels 20:30 to the second, use keepchans = {[1:10], [20:30]}.
% To only keeps channels 1:5 in the first set, use
% keepchans = {1:5}. {default: {}}
%
% Outputs:
%
% subsets - {1,N} or {1,N+1} cell array containing channel indices for each
% requested channel subset.
% subidx - (1, EEG.nbchans) vector giving the index of the subset associated
% with each channel.
% pos - (3,N) matrix, columns containing the cartesian (x,y,z) channel
% positions plotted.
% Example:
%
% % Create three sub-montages of a 256-channel montage containing 32, 60, and 100
% % channels respectively.The 64 remaining channels will be put into a fourth subset.
% % Also visualize time course of optimization and the channel subset head locations.
%
% >> subset = loc_subsets(EEG.chanlocs, [32 60 100], true, true);
%
% Author: Nima Bigdely Shamlo, SCCN/INC/UCSD, 2007
% Copyright (C) 2007 Nima Bigdely Shamlo, SCCN/INC/UCSD, [email protected]
%
% This program is free software; you can redistribute it and/or modify
% it under the terms of the GNU General Public License as published by
% the Free Software Foundation; either version 2 of the License, or
% (at your option) any later version.
%
% This program is distributed in the hope that it will be useful,
% but WITHOUT ANY WARRANTY; without even the implied warranty of
% MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
% GNU General Public License for more details.
%
% You should have received a copy of the GNU General Public License
% along with this program; if not, write to the Free Software
% Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
% if plotOptimization|plotSubsets in line 130 removed by nima 3/6/2007
% line 133, removed num2str removed by nima 3/6/2007
function [subset idx pos] = loc_subsets(chanlocs, numberOfChannelsInSubset, plotOptimization, plotSubsets, mandatoryChannelsForSet);
if sum(numberOfChannelsInSubset)> length(chanlocs)
error('Total channels in requested subsets larger than number of EEG channels.');
end;
if min(numberOfChannelsInSubset) < 2
error('Number of channels in the requested subsets must be >= 2.');
end;
rand('state',0);
if nargin < 5
mandatoryChannelsForSet = {};
end;
if nargin < 4
plotSubsets = false;
end;
if nargin < 3
plotOptimization = false;
end;
pos=[cell2mat({chanlocs.X}); cell2mat({chanlocs.Y}); cell2mat({chanlocs.Z});];
dist = squareform(pdist(pos'));
nChans = length(chanlocs);
idx = ones(nChans,1);
setId = cell(1, length(numberOfChannelsInSubset)); % cell array containing channels in each set
remainingChannels = 1:nChans; % channles that are to be assigned to subsets
% channels that have to stay in their original subset (as in
% mandatoryChannelsForSet) and should not be re-assigned
allMandatoryChannels = cell2mat(mandatoryChannelsForSet);
% assign requested mandatory channels to subset
for i=1:length(mandatoryChannelsForSet)
setId{i} = mandatoryChannelsForSet{i};
remainingChannels(mandatoryChannelsForSet{i}) = NaN; % flag with Nan so they can be deleted later, this is to keep indexing simple
end;
remainingChannels(isnan(remainingChannels)) = [];
r = remainingChannels(randperm(length(remainingChannels)));
% randomly assign remaining channels to subsets
for i=1:length(numberOfChannelsInSubset)
numberOfChannelsTobeAddedToSubset = numberOfChannelsInSubset(i) - length(setId{i})
setId{i} = [setId{i} r(1:numberOfChannelsTobeAddedToSubset)];
r(1:numberOfChannelsTobeAddedToSubset) = [];
end;
if length(r) > 0
setId{length(numberOfChannelsInSubset) + 1} = r; % last set gets remaining channels
end;
if plotOptimization|plotSubsets
fprintf(['Creating total of ' num2str(length(setId)) ' channel subsets:\n']);
end
if plotOptimization
figure;
xp = floor(sqrt(length(setId)));
yp = ceil(length(setId)/xp);
end;
counter = 1;
exchangeHappened = true;
while exchangeHappened
exchangeHappened = false;
for set1 = 1:length(setId)
for set2 = (set1 + 1):length(setId)
for i = 1:length(setId{set1})
for j = 1:length(setId{set2})
chan(1) = setId{set1}(i);
chan(2) = setId{set2}(j);
if cost_of_exchanging_channels(chan,[set1 set2], setId, dist) < 0 & ~ismember(chan, allMandatoryChannels)
setId{set1}(find(setId{set1} == chan(1))) = chan(2);
setId{set2}(find(setId{set2} == chan(2))) = chan(1);
sumDistances(counter) = 0;
for s = 1:length(setId)
sumDistances(counter) = sumDistances(counter) ...
+ (sum(sum(dist(setId{s},setId{s}))) / length(setId{s}));
end;
if plotOptimization
plot(1:counter,sumDistances,'-b');
xlabel('number of exchanges');
ylabel('sum mean distances within each channel subset');
drawnow;
else
if mod(counter, 20) ==0
fprintf('number of exchanges = %d\nsum of mean distances = %g\n',...
counter, sumDistances(counter));
end;
end
counter = counter + 1;
exchangeHappened = true;
end;
end;
end;
end;
end;
end;
for set = 1:length(setId)
idx(setId{set}) = set;
% legendTitle{set} = ['subset ' num2str(set)];
end;
subset = setId;
if plotSubsets
FIG_OFFSET = 40;
fpos = get(gcf,'position');
figure('position',[fpos(1)+FIG_OFFSET,fpos(2)-FIG_OFFSET,fpos(3),fpos(4)]);
scatter3(pos(1,:), pos(2,:), pos(3,:),100,idx,'fill');
axis equal;
%legend(legendTitle); it does not work propr
th=title('Channel Subsets');
%set(th,'fontsize',14)
end;
if length(r)>0 & (plotOptimization|plotSubsets)
fprintf('The last subset returned contains the %d unused channels.\n',...
length(r));
end
function cost = cost_of_exchanging_channels(chan, betweenSets, setId, dist);
mirrorChan(1) = 2;
mirrorChan(2) = 1;
for i=1:2
newSetId{betweenSets(i)} = setId{betweenSets(i)};
newSetId{betweenSets(i)}(find(newSetId{betweenSets(i)} == chan(i))) = chan(mirrorChan(i));
end;
cost = 0;
for i=betweenSets
distSumBefore{i} = sum(sum(dist(setId{i},setId{i})));
distSumAfter{i} = sum(sum(dist(newSetId{i},newSetId{i})));
cost = cost + (distSumBefore{i} - distSumAfter{i}) / length(setId{i});
end;
%cost = (distSumAfter{1} > distSumBefore{1}) && (distSumAfter{2} > distSumBefore{2});
|
github
|
lcnbeapp/beapp-master
|
pcexpand.m
|
.m
|
beapp-master/Packages/eeglab14_1_2b/functions/miscfunc/pcexpand.m
| 2,209 |
utf_8
|
2e520d826d0abe34ee1356fd8766e594
|
% pcexpand() - expand data using Principal Component Analysis (PCA)
% returns data expanded from a principal component subspace
% [compare pcsquash()]
% Usage:
% After >> [eigenvectors,eigenvalues,projections] = pcsquash(data,ncomps);
% then >> [expanded_data] = pcexpand(projections,eigenvectors,mean(data'));
%
% Inputs:
% projections = (comps,frames) each row is a component, each column a time point
% eigenvectors = square matrix of (column) eigenvectors
% datameans = vector of original data channel means
%
% Outputs:
% projections = data projected back into the original data space
% size (chans=eigenvector_rows,frames)
%
% Author: Scott Makeig, SCCN/INC/UCSD, La Jolla, 2000
%
% See also: pcsquash(), svd()
% Copyright (C) 6-97 Scott Makeig, SCCN/INC/UCSD, [email protected]
%
% This program is free software; you can redistribute it and/or modify
% it under the terms of the GNU General Public License as published by
% the Free Software Foundation; either version 2 of the License, or
% (at your option) any later version.
%
% This program is distributed in the hope that it will be useful,
% but WITHOUT ANY WARRANTY; without even the implied warranty of
% MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
% GNU General Public License for more details.
%
% You should have received a copy of the GNU General Public License
% along with this program; if not, write to the Free Software
% Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
% 4-15-98 debugged -sm & t-pj
% 01-25-02 reformated help & license, added links -ad
function [expanded_data]=pcexpand(PCAproj,EigenVectors,Datameans)
if nargin < 2
help pcexpand
return;
end
[ncomps,frames]=size(PCAproj);
[j,k]=size(EigenVectors);
if j ~= k
error('Wrong array input size (eigenvectors matrix not square');
end
if j < ncomps
error('Wrong array input size (eigenvectors rows must be equal to projection matrix rows');
end
if size(Datameans,1) == 1,
Datameans = Datameans'; % make a column vector
end
expanded_data = EigenVectors(:,1:ncomps)*PCAproj + Datameans*ones(1,frames);
|
github
|
lcnbeapp/beapp-master
|
detectmalware.m
|
.m
|
beapp-master/Packages/eeglab14_1_2b/functions/miscfunc/detectmalware.m
| 1,726 |
utf_8
|
805aa37c62f2d84ecb6d36df2499d684
|
% this function detects potential malware in the current folder and subfolders
%
% Author: A. Delorme, Cotober 2013
function detectmalware(currentFolder);
if nargin < 1
currentFolder = pwd;
end;
folderContent = dir(currentFolder);
folderContent = { folderContent.name };
malwareStrings = { 'eval(' 'evalin(' 'evalc(' 'delete(' 'movefile(' 'rmdir' 'mkdir' 'copyfile' 'system(' '!' };
for iFile = 1:length(folderContent)
currentFile = folderContent{iFile};
if length(currentFile) > 2 && strcmpi(currentFile(end-1:end), '.m')
fid = fopen(fullfile(currentFolder, currentFile), 'r');
countLine = 0;
prevstr = '';
while ~feof(fid)
str = fgetl(fid);
countLine = countLine+1;
if length(str) > 1 && str(1) ~= '%'
res = cellfun(@(x)~isempty(findstr(x, str)), malwareStrings(1:end-1));
if str(1) == '!', res(end+1) = 1; end;
if any(res)
pos = find(res); pos = pos(1);
disp('************************************')
fprintf('Potential malware command detected containing "%s" in\n %s line %d\n', malwareStrings{pos}, fullfile(currentFolder, currentFile), countLine);
fprintf('%d: %s\n%d: %s\n%d: %s\n', countLine-1, prevstr, countLine, str, countLine+1, fgetl(fid));
countLine = countLine+1;
end;
end;
prevstr = str;
end;
fclose(fid);
elseif exist(currentFile) == 7 && ~strcmpi(currentFile, '..') && ~strcmpi(currentFile, '.')
detectmalware(fullfile(currentFolder, currentFile));
end;
end;
|
github
|
lcnbeapp/beapp-master
|
loadelec.m
|
.m
|
beapp-master/Packages/eeglab14_1_2b/functions/miscfunc/loadelec.m
| 2,360 |
utf_8
|
655d4fbe32be8c99d9d4a2f4deb754a6
|
% loadelec() - Load electrode names file for eegplot()
%
% Usage: >> labelmatrix = loadelec('elec_file');
%
% Author: Colin Humprhies, CNL / Salk Institute, 1996
%
% See also: eegplot()
% Copyright (C) Colin Humphries, CNL / Salk Institute, Aug, 1996
%
% This program is free software; you can redistribute it and/or modify
% it under the terms of the GNU General Public License as published by
% the Free Software Foundation; either version 2 of the License, or
% (at your option) any later version.
%
% This program is distributed in the hope that it will be useful,
% but WITHOUT ANY WARRANTY; without even the implied warranty of
% MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
% GNU General Public License for more details.
%
% You should have received a copy of the GNU General Public License
% along with this program; if not, write to the Free Software
% Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
% 01-25-02 reformated help & license, added links -ad
function channames = loadelec(channamefile)
MAXCHANS = 256;
chans = MAXCHANS;
errorcode = 0;
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
% Read the channel names
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
if channamefile ~= 0 & channamefile ~= '0' % read file of channel names
chid = fopen(channamefile,'r');
if chid <3,
fprintf('cannot open file %s.\n',channamefile);
errorcode=2;
channamefile = 0;
else
fprintf('Channamefile %s opened\n',channamefile);
end;
if errorcode==0,
channames = fscanf(chid,'%s',[6 MAXCHANS]);
channames = channames';
[r c] = size(channames);
for i=1:r
for j=1:c
if channames(i,j)=='.',
channames(i,j)=' ';
end;
end;
end;
% fprintf('%d channel names read from file.\n',r);
if (r>chans)
fprintf('Using first %d names.\n',chans);
channames = channames(1:chans,:);
end;
if (r<chans)
fprintf('Only %d channel names read.\n',r);
end;
end;
end
if channamefile == 0 | channamefile == '0', % plot channel numbers
channames = [];
for c=1:chans
if c<10,
numeric = [' ' int2str(c)]; % four-character fields
else
numeric = [' ' int2str(c)];
end
channames = [channames;numeric];
end;
end; % setting channames
channames = str2mat(channames, ' '); % add padding element to Y labels
|
github
|
lcnbeapp/beapp-master
|
erpregout.m
|
.m
|
beapp-master/Packages/eeglab14_1_2b/functions/miscfunc/erpregout.m
| 3,083 |
utf_8
|
a7430431f9ce614aaa04b826032bfcd5
|
% erpregout() - regress out the ERP from the data
%
% Usage:
% newdata = erpregout(data);
% [newdata erp factors] = erpregout(data, tlim, reglim);
%
% Inputs:
% data - [float] 2-D data (times x trials) or 3-D data
% (channels x times x trials).
%
% Optional inputs:
% tlim - [min max] time limits in ms.
% reglim - [min max] regression time window in ms (by default
% the whole time period is used
% Outputs:
% newdata - data with ERP regressed out
% erp - data ERP
% factors - factors used for regressing out the ERP (size is the same
% as the number of trials or (channels x trials)
%
% Note: it is better to regress out the ERP about 4 times (launch the
% function 4 times in a row) to really be able to regress out the
% ERP and have a residual ERP close to 0.
%
% Author: Arnaud Delorme, Salk, SCCN, UCSD, CA, April 29, 2004
%123456789012345678901234567890123456789012345678901234567890123456789012
% Copyright (C) 2004 Arnaud Delorme
%
% This program is free software; you can redistribute it and/or modify
% it under the terms of the GNU General Public License as published by
% the Free Software Foundation; either version 2 of the License, or
% (at your option) any later version.
%
% This program is distributed in the hope that it will be useful,
% but WITHOUT ANY WARRANTY; without even the implied warranty of
% MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
% GNU General Public License for more details.
%
% You should have received a copy of the GNU General Public License
% along with this program; if not, write to the Free Software
% Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
function [data, erp, factors] = erpregout(data, tlim, reglim);
if nargin < 1
help erpregout;
return;
end;
if nargin < 2
tlim = [0 1];
end;
if nargin < 3
reglim = tlim;
end;
if ndims(data) == 2
data = reshape(data, 1, size(data,1), size(data,2));
redim = 1;
else
redim = 0;
end;
% find closest points
% -------------------
timevect = linspace(tlim(1), tlim(2), size(data,2));
[tmp begpoint] = min( abs(timevect-reglim(1)) );
[tmp endpoint] = min( abs(timevect-reglim(2)) );
erp = mean(data, 3);
% regressing out erp in channels and trials
% -----------------------------------------
for chan = 1:size(data,1)
fprintf('Channel %d (trials out of %d):', chan, size(data,3));
for trial = 1:size(data,3)
if ~mod(trial, 10) , fprintf('%d ', trial); end;
if ~mod(trial, 200), fprintf('\n', trial); end;
[factors(chan, trial) tmpf exitflag] = fminbnd('erpregoutfunc', 0, 10, [], ...
data(chan, begpoint:endpoint, trial), erp(chan, begpoint:endpoint));
data(chan,:,trial) = data(chan,:,trial) - factors(chan, trial)*erp(chan, :);
end;
fprintf('\n');
end;
if redim
data = squeeze(data);
end;
|
github
|
lcnbeapp/beapp-master
|
compdsp.m
|
.m
|
beapp-master/Packages/eeglab14_1_2b/functions/miscfunc/compdsp.m
| 7,154 |
utf_8
|
d81cd429eda825751f36ef7706ea02bc
|
% compdsp() - Display standard info figures for a data decomposition
% Creates four figure windows showing: Component amplitudes,
% scalp maps, activations and activation spectra.
% Usage:
% >> compdsp(data,weights,locfile,[srate],[title],[compnums],[amps],[act]);
%
% Inputs:
% data = data matrix used to train the decomposition
% weights = the unmixing matrix (e.g., weights*sphere from runica())
%
% Optional:
% locfile = 2-d electrode locations file (as in >> topoplot example)
% {default|[]: default locations file given in icadefs.m
% srate = sampling rate in Hz {default|[]: as in icadefs.m}
% title = optional figure title text
% {default|'': none}
% compnums = optional vector of component numbers to display
% {default|[] -> all}
% amps = all component amplitudes (from runica())
% {default|[]->recompute}
% act = activations matrix (from runica())
% {default|[]->recompute}
%
% Author: Scott Makeig, SCCN/INC/UCSD, La Jolla, 2000
% Copyright (C) 12/16/00 Scott Makeig, SCCN/INC/UCSD, [email protected]
%
% This program is free software; you can redistribute it and/or modify
% it under the terms of the GNU General Public License as published by
% the Free Software Foundation; either version 2 of the License, or
% (at your option) any later version.
%
% This program is distributed in the hope that it will be useful,
% but WITHOUT ANY WARRANTY; without even the implied warranty of
% MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
% GNU General Public License for more details.
%
% You should have received a copy of the GNU General Public License
% along with this program; if not, write to the Free Software
% Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
% 02-01-01 replaced std() with rms() -sm
% 02-10-01 made srate optional -sm
% 01-25-02 reformated help & license -ad
function compdsp(data,unmix,locfile,srate,titl,compnums,amps,act)
minHz = 2; % frequency display limits
maxHz = 40;
ACTS_PER_EEGPLOT = 32;
%
%%%%%%%%%%%%%%%%%%%%%% Read and test arguments %%%%%%%%%%%%%%%%%%%%%%%%
%
icadefs % read BACKCOLOR, DEFAULT_SRATE
if nargin<2
help compdsp
return
end
chans = size(data,1);
frames = size(data,2);
ncomps = size(unmix,1);
if ncomps < 1
error('Unmixing matrix must have at least one component');
end
if chans < 2
error('Data must have at least two channels');
end
if frames < 2
error('Data must have at least two frames');
end
if size(unmix,2) ~= chans
error('Sizes of unmix and data do not match');
end
if nargin<3
locfile=[];
end
if isempty(locfile)
locfile = DEFAULT_ELOC; % from icsdefs.m
end
if ~exist(locfile)
error('Cannot find electrode locations file');
end
if nargin<4
srate = 0; % from icadefs
end
if isempty(srate) | srate==0
srate = DEFAULT_SRATE; % from icadefs
end
if nargin<5
titl = ''; % default - no title text
end
if isempty(titl)
titl = '';
end
if nargin<6
compnums = 0; % default - all components
end
if isempty(compnums)
compnums = 0;
end
if nargin<7
amps = NaN; % default - recompute amps
end
if isempty(amps)
amps = NaN;
end
if ~isnan(amps) & length(amps) ~= ncomps
error('Supplied amps does not match the number of unmixed components');
end
if compnums(1) == 0
compnums = 1:ncomps;
end
if min(compnums) < 1
error('Compnums must be positive');
end
if min(compnums) > ncomps
error('Some compnum > number of components in unmix');
end
if nargin<8
act = NaN; % default - recompute act
end
%
%%%%%%%%%%%%%%%%%%%%%%%%%%% Create plots %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%
if chans == ncomps
winv = inv(unmix);
elseif chans < ncomps
error('More components than channels?');
else
winv = pinv(unmix);
end
if isnan(act)
fprintf('Computing activations ...')
act = unmix(compnums,:)*data;
fprintf('\n');
elseif size(act,2) ~= frames
error('Supplied activations do not match data length');
elseif size(act,1) ~= ncomps & size(act,1) ~= length(compnums)
error('Number of supplied activations matrix does not match data or weights');
elseif size(act,1) == ncomps
act = act(compnums,:); % cut down matrix to desired components
end
%
%%%%%%%%%%%%%%%%%%%%% I. Plot component amps %%%%%%%%%%%%%%%%%%%%%%%%%%%
%
pos = [40,520,550,400]; figure('Position',pos);
if isnan(amps)
fprintf('Computing component rms amplitudes ');
amps = zeros(1,length(compnums));
for j=1:length(compnums)
amps(j) = rms(winv(:,compnums(j)))*rms(act(j,:)');
fprintf('.')
end
fprintf('\n');
else
amps = amps(compnums); % truncate passed amps to desired compnums
end
plot(compnums,amps,'k');
hold on
plot(compnums,amps,'r^');
xl=xlabel('Component numbers');
yl=ylabel('RMS Amplitudes');
tl=title([titl ' Amplitudes']);
ax = axis;
axis([min(compnums)-1 max(compnums)+1 0 ax(4)]);
%
%%%%%%%%%%%%%%%%%%%%%%%%% II. Plot component maps %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%
pos = [40,40,550,400]; figure('Position',pos);
fprintf('Plotting component scalp maps ...') % compmaps() may make multiple figures
compmap(winv,locfile,compnums,[titl ' Scalp Maps'],0,compnums);
fprintf('\n');
%
%%%%%%%%%%%%%%%%%%%%%% III. eegplot() activations %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%
if frames/srate < 10
dispsecs = ceil(frames/srate);
else
dispsecs = 10; % defaults - display 10s data per screen
end
range = 0.8*max(max(act')-min(act'));
stact=1;
lact=ACTS_PER_EEGPLOT;
if lact>size(act,1)
lact = size(act,1);
end
pos = [620,520,550,400]; figure('Position',pos);
while stact <= size(act,1)
% eegplot(data,srate,spacing,eloc_file,windowlength,title,posn)
eegplot(act(stact:lact,:),srate,range,compnums(stact:lact),...
dispsecs,[titl ' Activations'],pos);
pos = pos + [.02 .02 0 0];
stact = stact+ACTS_PER_EEGPLOT;
lact = lact +ACTS_PER_EEGPLOT;
if lact>size(act,1)
lact = size(act,1);
end
end
%
%%%%%%%%%%%%%%%%%%%%%%% IV. plotdata() spectra %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%
pos = [620,40,550,400]; figure('Position',pos);
if frames > 2048
windw = 512;
elseif frames > 1024
windw = 256;
else
windw = 128;
end
fprintf('Computing component spectra ')
for j = 1:length(compnums)
% [Pxx,F] = PSD(X,NFFT,Fs,WINDOW,NOVERLAP)
[spec,freqs] = psd(act(j,:),1024,srate,windw,ceil(windw*0.5));
if ~exist('specs')
specs = zeros(length(compnums),length(freqs));
end
specs(j,:) = spec';
fprintf('.')
end
fprintf('\n');
specs = 10*log10(specs);
tmp = ceil(sqrt(length(compnums)));
tmp2 = ceil(length(compnums)/tmp);
for j=1:length(compnums)
sbplot(tmp2,tmp,j)
plot(freqs,specs(j,:))
set(gca,'box','off')
set(gca,'color',BACKCOLOR);
ax=axis;
axis([minHz,maxHz,ax(3),ax(4)]);
tl = title(int2str(compnums(j)));
end
xl=xlabel('Frequency (Hz)');
yl=ylabel('Power (dB)');
set(gca,'YAxisLocation','right');
txl=textsc([titl ' Activation Spectra'],'title');
axcopy % pop-up axes on mouse click
% plottopo(specs,[tmp2 tmp],0,[2,70 min(min(specs)) max(max(specs))],...
% [titl ' Activation Power Spectra']);
function rmsval = rms(column)
rmsval = sqrt(mean(column.*column)); % don't remove mean
|
github
|
lcnbeapp/beapp-master
|
perminv.m
|
.m
|
beapp-master/Packages/eeglab14_1_2b/functions/miscfunc/perminv.m
| 1,386 |
utf_8
|
d5fe91da3ab79a692c0adbd6b4a9498a
|
% perminv() - returns the inverse permutation vector
%
% Usage: >> [invvec] = perminverse(vector);
%
% Author: Scott Makeig, SCCN/INC/UCSD, La Jolla, 11-30-96
% Copyright (C) 11-30-96 Scott Makeig, SCCN/INC/UCSD, [email protected]
%
% This program is free software; you can redistribute it and/or modify
% it under the terms of the GNU General Public License as published by
% the Free Software Foundation; either version 2 of the License, or
% (at your option) any later version.
%
% This program is distributed in the hope that it will be useful,
% but WITHOUT ANY WARRANTY; without even the implied warranty of
% MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
% GNU General Public License for more details.
%
% You should have received a copy of the GNU General Public License
% along with this program; if not, write to the Free Software
% Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
% 4-4-97 shortened name to perminv() -sm
% 4-7-97 allowed row vector, added tests -sm
% 01-25-02 reformated help & license -ad
function [invvec]=perminv(vector)
[n,c] = size(vector);
if n>1 & c>1,
fprintf('perminv(): input must be a vector.\n');
return
end
transpose=0;
if c>1
vector = vector';
transpose =1;
end
invvec = zeros(size(vector));
for i=1:length(vector)
invvec(vector(i)) = i;
end;
if transpose==1,
invvec = invvec';
end
|
github
|
lcnbeapp/beapp-master
|
runicatest.m
|
.m
|
beapp-master/Packages/eeglab14_1_2b/functions/miscfunc/runicatest.m
| 40,794 |
utf_8
|
39e884850dab339c9c4e2a052d4cf934
|
% runicatest() - Perform Independent Component Analysis (ICA) decomposition
% using natural-gradient infomax - the infomax ICA algorithm of
% Bell & Sejnowski (1995) with the natural gradient method
% of Amari, Cichocki & Yang, the extended-ICA algorithm
% of Lee, Girolami & Sejnowski, PCA dimension reduction,
% and/or specgram() preprocessing (suggested by M. Zibulevsky).
% Usage:
% >> [weights,sphere] = runica(data);
% >> [weights,sphere,activations,bias,signs,lrates] ...
% = runica(data,'Key1',Value1',...);
% Input:
% data = input data (chans,frames*epochs).
% Note that if data consists of multiple discontinuous epochs,
% each epoch should be separately baseline-zero'd using
% >> data = rmbase(data,frames,basevector);
%
% Optional keywords:
% 'ncomps' = [N] number of ICA components to compute (default -> chans)
% using rectangular ICA decomposition
% 'pca' = [N] decompose a principal component (default -> 0=off)
% subspace of the data. Value is the number of PCs to retain.
% 'sphering' = ['on'/'off'] flag sphering of data (default -> 'on')
% 'weights' = [W] initial weight matrix (default -> eye())
% (Note: if 'sphering' 'off', default -> spher())
% 'lrate' = [rate] initial ICA learning rate (<< 1) (default -> heuristic)
% 'block' = [N] ICA block size (<< datalength) (default -> heuristic)
% 'anneal' = annealing constant (0,1] (defaults -> 0.90, or 0.98, extended)
% controls speed of convergence
% 'annealdeg' = [N] degrees weight change for annealing (default -> 70)
% 'stop' = [f] stop training when weight-change < this (default -> 1e-6)
% 'maxsteps' = [N] max number of ICA training steps (default -> 512)
% 'bias' = ['on'/'off'] perform bias adjustment (default -> 'on')
% 'momentum' = [0<f<1] training momentum (default -> 0)
% 'extended' = [N] perform tanh() "extended-ICA" with sign estimation
% every N training blocks. If N > 0, automatically estimate the
% number of sub-Gaussian sources. If N < 0, fix number of sub-Gaussian
% components to -N [faster than N>0] (default|0 -> off)
% 'specgram' = [srate loHz hiHz frames winframes] decompose a complex time/frequency
% transform of the data (Note: winframes must divide frames)
% (defaults [srate 0 srate/2 size(data,2) size(data,2)])
% 'posact' = make all component activations net-positive(default 'on'}
% 'verbose' = give ascii messages ('on'/'off') (default -> 'on')
%
% Outputs: [RO: output in reverse order of projected mean variance
% unless starting weight matrix passed ('weights' above)]
% weights = ICA weight matrix (comps,chans) [RO]
% sphere = data sphering matrix (chans,chans) = spher(data)
% Note that unmixing_matrix = weights*sphere {sphering off -> eye(chans)}
% activations = activation time courses of the output components (ncomps,frames*epochs)
% bias = vector of final (ncomps) online bias [RO] (default = zeros())
% signs = extended-ICA signs for components [RO] (default = ones())
% [ -1 = sub-Gaussian; 1 = super-Gaussian]
% lrates = vector of learning rates used at each training step
%
% Authors: Scott Makeig with contributions from Tony Bell, Te-Won Lee,
% Tzyy-Ping Jung, Sigurd Enghoff, Michael Zibulevsky, CNL/The Salk Institute,
% La Jolla, 1996-
% Uses: posact()
% Reference (please cite):
%
% Makeig, S., Bell, A.J., Jung, T-P and Sejnowski, T.J.,
% "Independent component analysis of electroencephalographic data,"
% In: D. Touretzky, M. Mozer and M. Hasselmo (Eds). Advances in Neural
% Information Processing Systems 8:145-151, MIT Press, Cambridge, MA (1996).
%
% Toolbox Citation:
%
% Makeig, Scott et al. "EEGLAB: Matlab ICA Toolbox for Psychophysiological Research".
% WWW Site, Swartz Center for Computational Neuroscience, Institute of Neural
% Computation, University of San Diego California
% <www.sccn.ucsd.edu/eeglab/>, 2000. [World Wide Web Publication].
%
% For more information:
% http://www.sccn.ucsd.edu/eeglab/icafaq.html - FAQ on ICA/EEG
% http://www.sccn.ucsd.edu/eeglab/icabib.html - mss. on ICA & biosignals
% http://www.cnl.salk.edu/~tony/ica.html - math. mss. on ICA
% Copyright (C) 1996 Scott Makeig et al, SCCN/INC/UCSD, [email protected]
%
% This program is free software; you can redistribute it and/or modify
% it under the terms of the GNU General Public License as published by
% the Free Software Foundation; either version 2 of the License, or
% (at your option) any later version.
%
% This program is distributed in the hope that it will be useful,
% but WITHOUT ANY WARRANTY; without even the implied warranty of
% MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
% GNU General Public License for more details.
%
% You should have received a copy of the GNU General Public License
% along with this program; if not, write to the Free Software
% Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
%%%%%%%%%%%%%%%%%%%%%%%%%%% Edit history %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%
% runica() - by Scott Makeig with contributions from Tony Bell, Te-Won Lee
% Tzyy-Ping Jung, Sigurd Enghoff, Michael Zibulevsky et al.
% CNL / Salk Institute 1996-00
% 04-30-96 built from icatest.m and ~jung/.../wtwpwica.m -sm
% 07-28-97 new runica(), adds bias (default on), momentum (default off),
% extended-ICA (Lee & Sejnowski, 1997), cumulative angledelta
% (until lrate drops), keywords, signcount for speeding extended-ICA
% 10-07-97 put acos() outside verbose loop; verbose 'off' wasn't stopping -sm
% 11-11-97 adjusted help msg -sm
% 11-30-97 return eye(chans) if sphering 'off' or 'none' (undocumented option) -sm
% 02-27-98 use pinv() instead of inv() to rank order comps if ncomps < chans -sm
% 04-28-98 added 'posact' and 'pca' flags -sm
% 07-16-98 reduced length of randperm() for kurtosis subset calc. -se & sm
% 07-19-98 fixed typo in weights def. above -tl & sm
% 12-21-99 added 'specgram' option suggested by Michael Zibulevsky, UNM -sm
% 12-22-99 fixed rand() sizing inefficiency on suggestion of Mike Spratling, UK -sm
% 01-11-00 fixed rand() sizing bug on suggestion of Jack Foucher, Strasbourg -sm
% 12-18-00 test for existence of Sig Proc Tlbx function 'specgram'; improve
% 'specgram' option arguments -sm
% 01-25-02 reformated help & license -ad
% 01-25-02 lowered default lrate and block -ad
%
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
function [weights,sphere,activations,bias,signs,lrates,y] = runica(data,p1,v1,p2,v2,p3,v3,p4,v4,p5,v5,p6,v6,p7,v7,p8,v8,p9,v9,p10,v10,p11,v11,p12,v12,p13,v13,p14,v14)
if nargin < 1
help runica
return
end
if ndims(data) > 2
data = data(:,:); % make data two-dimensional
elseif ndims(data) < 2
help runica
return
end
[chans frames] = size(data); % determine the data size
urchans = chans; % remember original data channels
datalength = frames;
if chans<2
fprintf('\nrunica() - data size (%d,%d) too small.\n\n', chans,frames);
return
end
%
%%%%%%%%%%%%%%%%%%%%%% Declare defaults used below %%%%%%%%%%%%%%%%%%%%%%%%
%
MAX_WEIGHT = 1e8; % guess that weights larger than this have blown up
DEFAULT_STOP = 0.000001; % stop training if weight changes below this
DEFAULT_ANNEALDEG = 60; % when angle change reaches this value,
DEFAULT_ANNEALSTEP = 0.90; % anneal by multiplying lrate by this
DEFAULT_EXTANNEAL = 0.98; % or this if extended-ICA
DEFAULT_MAXSTEPS = 512; % ]top training after this many steps
DEFAULT_MOMENTUM = 0.0; % default momentum weight
DEFAULT_BLOWUP = 1000000000.0; % = learning rate has 'blown up'
DEFAULT_BLOWUP_FAC = 0.8; % when lrate 'blows up,' anneal by this fac
DEFAULT_RESTART_FAC = 0.9; % if weights blowup, restart with lrate
% lower by this factor
MIN_LRATE = 0.000001; % if weight blowups make lrate < this, quit
MAX_LRATE = 0.1; % guard against uselessly high learning rate
DEFAULT_LRATE = 0.00065/log(chans);
% heuristic default - may need adjustment
% for large or tiny data sets!
% DEFAULT_BLOCK = floor(sqrt(frames/4)); % heuristic default
DEFAULT_BLOCK = min(floor(5*log(frames)),0.3*frames); % heuristic
% - may need adjustment!
% Extended-ICA option:
DEFAULT_EXTENDED = 0; % default off
DEFAULT_EXTBLOCKS = 1; % number of blocks per kurtosis calculation
DEFAULT_NSUB = 1; % initial default number of assumed sub-Gaussians
% for extended-ICA
DEFAULT_EXTMOMENTUM = 0.5; % momentum term for computing extended-ICA kurtosis
MAX_KURTSIZE = 6000; % max points to use in kurtosis calculation
MIN_KURTSIZE = 2000; % minimum good kurtosis size (flag warning)
SIGNCOUNT_THRESHOLD = 25; % raise extblocks when sign vector unchanged
% after this many steps
SIGNCOUNT_STEP = 2; % extblocks increment factor
DEFAULT_SPHEREFLAG = 'on'; % use the sphere matrix as the default
% starting weight matrix
DEFAULT_PCAFLAG = 'off'; % don't use PCA reduction
DEFAULT_POSACTFLAG = 'on'; % use posact()
DEFAULT_VERBOSE = 1; % write ascii info to calling screen
DEFAULT_BIASFLAG = 1; % default to using bias in the ICA update rule
%
%%%%%%%%%%%%%%%%%%%%%%% Set up keyword default values %%%%%%%%%%%%%%%%%%%%%%%%%
%
if nargout < 2,
fprintf('runica() - needs at least two output arguments.\n');
return
end
epochs = 1; % do not care how many epochs in data
pcaflag = DEFAULT_PCAFLAG;
sphering = DEFAULT_SPHEREFLAG; % default flags
posactflag = DEFAULT_POSACTFLAG;
verbose = DEFAULT_VERBOSE;
block = DEFAULT_BLOCK; % heuristic default - may need adjustment!
lrate = DEFAULT_LRATE;
annealdeg = DEFAULT_ANNEALDEG;
annealstep = 0; % defaults declared below
nochange = DEFAULT_STOP;
momentum = DEFAULT_MOMENTUM;
maxsteps = DEFAULT_MAXSTEPS;
weights = 0; % defaults defined below
ncomps = chans;
biasflag = DEFAULT_BIASFLAG;
extended = DEFAULT_EXTENDED;
extblocks = DEFAULT_EXTBLOCKS;
kurtsize = MAX_KURTSIZE;
signsbias = 0.02; % bias towards super-Gaussian components
extmomentum= DEFAULT_EXTMOMENTUM; % exp. average the kurtosis estimates
nsub = DEFAULT_NSUB;
wts_blowup = 0; % flag =1 when weights too large
wts_passed = 0; % flag weights passed as argument
%
%%%%%%%%%% Collect keywords and values from argument list %%%%%%%%%%%%%%%
%
if (nargin> 1 & rem(nargin,2) == 0)
fprintf('runica(): Even number of input arguments???')
return
end
for i = 3:2:nargin % for each Keyword
Keyword = eval(['p',int2str((i-3)/2 +1)]);
Value = eval(['v',int2str((i-3)/2 +1)]);
if ~isstr(Keyword)
fprintf('runica(): keywords must be strings')
return
end
Keyword = lower(Keyword); % convert upper or mixed case to lower
if strcmp(Keyword,'weights') | strcmp(Keyword,'weight')
if isstr(Value)
fprintf(...
'runica(): weights value must be a weight matrix or sphere')
return
else
weights = Value;
wts_passed =1;
end
elseif strcmp(Keyword,'ncomps')
if isstr(Value)
fprintf('runica(): ncomps value must be an integer')
return
end
if ncomps < urchans & ncomps ~= Value
fprintf('runica(): Use either PCA or ICA dimension reduction');
return
end
ncomps = Value;
if ~ncomps,
ncomps = chans;
end
elseif strcmp(Keyword,'pca')
if ncomps < urchans & ncomps ~= Value
fprintf('runica(): Use either PCA or ICA dimension reduction');
return
end
if isstr(Value)
fprintf(...
'runica(): pca value should be the number of principal components to retain')
return
end
pcaflag = 'on';
ncomps = Value;
if ncomps >= chans | ncomps < 1,
fprintf('runica(): pca value must be in range [1,%d]\n',chans-1)
return
end
chans = ncomps;
elseif strcmp(Keyword,'posact')
if ~isstr(Value)
fprintf('runica(): posact value must be on or off')
return
else
Value = lower(Value);
if ~strcmp(Value,'on') & ~strcmp(Value,'off'),
fprintf('runica(): posact value must be on or off')
return
end
posactflag = Value;
end
elseif strcmp(Keyword,'lrate')
if isstr(Value)
fprintf('runica(): lrate value must be a number')
return
end
lrate = Value;
if lrate>MAX_LRATE | lrate <0,
fprintf('runica(): lrate value is out of bounds');
return
end
if ~lrate,
lrate = DEFAULT_LRATE;
end
elseif strcmp(Keyword,'block') | strcmp(Keyword,'blocksize')
if isstr(Value)
fprintf('runica(): block size value must be a number')
return
end
block = Value;
if ~block,
block = DEFAULT_BLOCK;
end
elseif strcmp(Keyword,'stop') | strcmp(Keyword,'nochange') ...
| strcmp(Keyword,'stopping')
if isstr(Value)
fprintf('runica(): stop wchange value must be a number')
return
end
nochange = Value;
elseif strcmp(Keyword,'maxsteps') | strcmp(Keyword,'steps')
if isstr(Value)
fprintf('runica(): maxsteps value must be an integer')
return
end
maxsteps = Value;
if ~maxsteps,
maxsteps = DEFAULT_MAXSTEPS;
end
if maxsteps < 0
fprintf('runica(): maxsteps value (%d) must be a positive integer',maxsteps)
return
end
elseif strcmp(Keyword,'anneal') | strcmp(Keyword,'annealstep')
if isstr(Value)
fprintf('runica(): anneal step value (%2.4f) must be a number (0,1)',Value)
return
end
annealstep = Value;
if annealstep <=0 | annealstep > 1,
fprintf('runica(): anneal step value (%2.4f) must be (0,1]',annealstep)
return
end
elseif strcmp(Keyword,'annealdeg') | strcmp(Keyword,'degrees')
if isstr(Value)
fprintf('runica(): annealdeg value must be a number')
return
end
annealdeg = Value;
if ~annealdeg,
annealdeg = DEFAULT_ANNEALDEG;
elseif annealdeg > 180 | annealdeg < 0
fprintf('runica(): annealdeg (%3.1f) is out of bounds [0,180]',...
annealdeg);
return
end
elseif strcmp(Keyword,'momentum')
if isstr(Value)
fprintf('runica(): momentum value must be a number')
return
end
momentum = Value;
if momentum > 1.0 | momentum < 0
fprintf('runica(): momentum value is out of bounds [0,1]')
return
end
elseif strcmp(Keyword,'sphering') | strcmp(Keyword,'sphereing') ...
| strcmp(Keyword,'sphere')
if ~isstr(Value)
fprintf('runica(): sphering value must be on, off, or none')
return
else
Value = lower(Value);
if ~strcmp(Value,'on') & ~strcmp(Value,'off') & ~strcmp(Value,'none'),
fprintf('runica(): sphering value must be on or off')
return
end
sphering = Value;
end
elseif strcmp(Keyword,'bias')
if ~isstr(Value)
fprintf('runica(): bias value must be on or off')
return
else
Value = lower(Value);
if strcmp(Value,'on')
biasflag = 1;
elseif strcmp(Value,'off'),
biasflag = 0;
else
fprintf('runica(): bias value must be on or off')
return
end
end
elseif strcmp(Keyword,'specgram') | strcmp(Keyword,'spec')
if ~exist('specgram') < 2 % if ~exist or defined workspace variable
fprintf(...
'runica(): MATLAB Sig. Proc. Toolbox function "specgram" not found.\n')
return
end
if isstr(Value)
fprintf('runica(): specgram argument must be a vector')
return
end
srate = Value(1);
if (srate < 0)
fprintf('runica(): specgram srate (%4.1f) must be >=0',srate)
return
end
if length(Value)>1
loHz = Value(2);
if (loHz < 0 | loHz > srate/2)
fprintf('runica(): specgram loHz must be >=0 and <= srate/2 (%4.1f)',srate/2)
return
end
else
loHz = 0; % default
end
if length(Value)>2
hiHz = Value(3);
if (hiHz < loHz | hiHz > srate/2)
fprintf('runica(): specgram hiHz must be >=loHz (%4.1f) and <= srate/2 (%4.1f)',loHz,srate/2)
return
end
else
hiHz = srate/2; % default
end
if length(Value)>3
Hzframes = Value(5);
if (Hzframes<0 | Hzframes > size(data,2))
fprintf('runica(): specgram frames must be >=0 and <= data length (%d)',size(data,2))
return
end
else
Hzframes = size(data,2); % default
end
if length(Value)>4
Hzwinlen = Value(4);
if rem(Hzframes,Hzwinlen) % if winlen doesn't divide frames
fprintf('runica(): specgram Hzinc must divide frames (%d)',Hzframes)
return
end
else
Hzwinlen = Hzframes; % default
end
Specgramflag = 1; % set flag to perform specgram()
elseif strcmp(Keyword,'extended') | strcmp(Keyword,'extend')
if isstr(Value)
fprintf('runica(): extended value must be an integer (+/-)')
return
else
extended = 1; % turn on extended-ICA
extblocks = fix(Value); % number of blocks per kurt() compute
if extblocks < 0
nsub = -1*fix(extblocks); % fix this many sub-Gauss comps
elseif ~extblocks,
extended = 0; % turn extended-ICA off
elseif kurtsize>frames, % length of kurtosis calculation
kurtsize = frames;
if kurtsize < MIN_KURTSIZE
fprintf(...
'runica() warning: kurtosis values inexact for << %d points.\n',...
MIN_KURTSIZE);
end
end
end
elseif strcmp(Keyword,'verbose')
if ~isstr(Value)
fprintf('runica(): verbose flag value must be on or off')
return
elseif strcmp(Value,'on'),
verbose = 1;
elseif strcmp(Value,'off'),
verbose = 0;
else
fprintf('runica(): verbose flag value must be on or off')
return
end
else
fprintf('runica(): unknown flag')
return
end
end
%
%%%%%%%%%%%%%%%%%%%%%%%% Initialize weights, etc. %%%%%%%%%%%%%%%%%%%%%%%%
%
if ~annealstep,
if ~extended,
annealstep = DEFAULT_ANNEALSTEP; % defaults defined above
else
annealstep = DEFAULT_EXTANNEAL; % defaults defined above
end
end % else use annealstep from commandline
if ~annealdeg,
annealdeg = DEFAULT_ANNEALDEG - momentum*90; % heuristic
if annealdeg < 0,
annealdeg = 0;
end
end
if ncomps > chans | ncomps < 1
fprintf('runica(): number of components must be 1 to %d.\n',chans);
return
end
if weights ~= 0, % initialize weights
% starting weights are being passed to runica() from the commandline
if verbose,
fprintf('Using starting weight matrix named in argument list ...\n')
end
if chans>ncomps & weights ~=0,
[r,c]=size(weights);
if r~=ncomps | c~=chans,
fprintf(...
'runica(): weight matrix must have %d rows, %d columns.\n', ...
chans,ncomps);
return;
end
end
end;
%
%%%%%%%%%%%%%%%%%%%%% Check keyword values %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%
if frames<chans,
fprintf('runica(): data length (%d) < data channels (%d)!\n',frames,chans)
return
elseif block < 2,
fprintf('runica(): block size %d too small!\n',block)
return
elseif block > frames,
fprintf('runica(): block size exceeds data length!\n');
return
elseif floor(epochs) ~= epochs,
fprintf('runica(): data length is not a multiple of the epoch length!\n');
return
elseif nsub > ncomps
fprintf('runica(): there can be at most %d sub-Gaussian components!\n',ncomps);
return
end;
%
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% Process the data %%%%%%%%%%%%%%%%%%%%%%%%%%
%
if verbose,
fprintf( ...
'\nInput data size [%d,%d] = %d channels, %d frames.\n', ...
chans,frames,chans,frames);
if strcmp(pcaflag,'on')
fprintf('After PCA dimension reduction,\n finding ');
else
fprintf('Finding ');
end
if ~extended
fprintf('%d ICA components using logistic ICA.\n',ncomps);
else % if extended
fprintf('%d ICA components using extended ICA.\n',ncomps);
if extblocks > 0
fprintf(...
'Kurtosis will be calculated initially every %d blocks using %d data points.\n',...
extblocks, kurtsize);
else
fprintf(...
'Kurtosis will not be calculated. Exactly %d sub-Gaussian components assumed.\n',...
nsub);
end
end
fprintf('Initial learning rate will be %g, block size %d.\n',lrate,block);
if momentum>0,
fprintf('Momentum will be %g.\n',momentum);
end
fprintf( ...
'Learning rate will be multiplied by %g whenever angledelta >= %g deg.\n', ...
annealstep,annealdeg);
fprintf('Training will end when wchange < %g or after %d steps.\n', ...
nochange,maxsteps);
if biasflag,
fprintf('Online bias adjustment will be used.\n');
else
fprintf('Online bias adjustment will not be used.\n');
end
end
%
%%%%%%%%%%%%%%%%%%%%%%%%% Remove overall row means %%%%%%%%%%%%%%%%%%%%%%%%
%
if verbose,
fprintf('Removing mean of each channel ...\n');
end
data = data - mean(data')'*ones(1,frames); % subtract row means
if verbose,
fprintf('Final training data range: %g to %g\n', ...
min(min(data)),max(max(data)));
end
%
%%%%%%%%%%%%%%%%%%% Perform PCA reduction %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%
if strcmp(pcaflag,'on')
fprintf('Reducing the data to %d principal dimensions...\n',ncomps);
[eigenvectors,eigenvalues,data] = pcsquash(data,ncomps);
% make data its projection onto the ncomps-dim principal subspace
end
%
%%%%%%%%%%%%%%%%%%% Perform specgram transformation %%%%%%%%%%%%%%%%%%%%%%%
%
if exist('Specgramflag') == 1
% [P F T] = SPECGRAM(A,NFFT,Fs,WINDOW,NOVERLAP) % MATLAB Sig Proc Toolbox
% Hzwinlen = fix(srate/Hzinc); % CHANGED FROM THIS 12/18/00 -sm
Hzfftlen = 2^(ceil(log(Hzwinlen)/log(2))); % make FFT length next higher 2^k
Hzoverlap = 0; % use sequential windows
%
% Get freqs and times from 1st channel analysis
%
[tmp,freqs,tms] = specgram(data(1,:),Hzfftlen,srate,Hzwinlen,Hzoverlap);
fs = find(freqs>=loHz & freqs <= hiHz);
if isempty(fs)
fprintf('runica(): specified frequency range too narrow!\n');
return
end;
specdata = reshape(tmp(fs,:),1,length(fs)*size(tmp,2));
specdata = [real(specdata) imag(specdata)];
% fprintf(' size(fs) = %d,%d\n',size(fs,1),size(fs,2));
% fprintf(' size(tmp) = %d,%d\n',size(tmp,1),size(tmp,2));
%
% Loop through remaining channels
%
for ch=2:chans
[tmp] = specgram(data(ch,:),Hzwinlen,srate,Hzwinlen,Hzoverlap);
tmp = reshape((tmp(fs,:)),1,length(fs)*size(tmp,2));
specdata = [specdata;[real(tmp) imag(tmp)]]; % channels are rows
end
%
% Print specgram confirmation and details
%
fprintf(...
'Converted data to %d channels by %d=2*%dx%d points spectrogram data.\n',...
chans,2*length(fs)*length(tms),length(fs),length(tms));
if length(fs) > 1
fprintf(...
' Low Hz %g, high Hz %g, Hz incr %g, window length %d\n',freqs(fs(1)),freqs(fs(end)),freqs(fs(2))-freqs(fs(1)),Hzwinlen);
else
fprintf(...
' Low Hz %g, high Hz %g, window length %d\n',freqs(fs(1)),freqs(fs(end)),Hzwinlen);
end
%
% Replace data with specdata
%
data = specdata;
datalength=size(data,2);
end
%
%%%%%%%%%%%%%%%%%%% Perform sphering %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%
if strcmp(sphering,'on'), %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
if verbose,
fprintf('Computing the sphering matrix...\n');
end
sphere = 2.0*inv(sqrtm(cov(data'))); % find the "sphering" matrix = spher()
if ~weights,
if verbose,
fprintf('Starting weights are the identity matrix ...\n');
end
weights = eye(ncomps,chans); % begin with the identity matrix
else % weights given on commandline
if verbose,
fprintf('Using starting weights named on commandline ...\n');
end
end
if verbose,
fprintf('Sphering the data ...\n');
end
data = sphere*data; % actually decorrelate the electrode signals
elseif strcmp(sphering,'off') %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
if ~weights
if verbose,
fprintf('Using the sphering matrix as the starting weight matrix ...\n');
fprintf('Returning the identity matrix in variable "sphere" ...\n');
end
sphere = 2.0*inv(sqrtm(cov(data'))); % find the "sphering" matrix = spher()
weights = eye(ncomps,chans)*sphere; % begin with the identity matrix
sphere = eye(chans); % return the identity matrix
else % weights ~= 0
if verbose,
fprintf('Using starting weights named on commandline ...\n');
fprintf('Returning the identity matrix in variable "sphere" ...\n');
end
sphere = eye(chans); % return the identity matrix
end
elseif strcmp(sphering,'none')
sphere = eye(chans); % return the identity matrix
if ~weights
if verbose,
fprintf('Starting weights are the identity matrix ...\n');
fprintf('Returning the identity matrix in variable "sphere" ...\n');
end
weights = eye(ncomps,chans); % begin with the identity matrix
else % weights ~= 0
if verbose,
fprintf('Using starting weights named on commandline ...\n');
fprintf('Returning the identity matrix in variable "sphere" ...\n');
end
end
sphere = eye(chans,chans);
if verbose,
fprintf('Returned variable "sphere" will be the identity matrix.\n');
end
end
%
%%%%%%%%%%%%%%%%%%%%%%%% Initialize ICA training %%%%%%%%%%%%%%%%%%%%%%%%%
%
lastt=fix((datalength/block-1)*block+1);
BI=block*eye(ncomps,ncomps);
delta=zeros(1,chans*ncomps);
changes = [];
degconst = 180./pi;
startweights = weights;
prevweights = startweights;
oldweights = startweights;
prevwtchange = zeros(chans,ncomps);
oldwtchange = zeros(chans,ncomps);
lrates = zeros(1,maxsteps);
onesrow = ones(1,block);
bias = zeros(ncomps,1);
signs = ones(1,ncomps); % initialize signs to nsub -1, rest +1
for k=1:nsub
signs(k) = -1;
end
if extended & extblocks < 0 & verbose,
fprintf('Fixed extended-ICA sign assignments: ');
for k=1:ncomps
fprintf('%d ',signs(k));
end; fprintf('\n');
end
signs = diag(signs); % make a diagonal matrix
oldsigns = zeros(size(signs));;
signcount = 0; % counter for same-signs
signcounts = [];
urextblocks = extblocks; % original value, for resets
old_kk = zeros(1,ncomps); % for kurtosis momemtum
%
%%%%%%%% ICA training loop using the logistic sigmoid %%%%%%%%%%%%%%%%%%%
%
if verbose,
fprintf('Beginning ICA training ...');
if extended,
fprintf(' first training step may be slow ...\n');
else
fprintf('\n');
end
end
step=0;
laststep=0;
blockno = 1; % running block counter for kurtosis interrupts
while step < maxsteps, %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
% permute=randperm(datalength); % shuffle data order at each step
bootstrap = round(datalength*rand(1,datalength)+0.5); % draw a new bootstrap dataset at each step
for t=1:block:lastt, %%%%%%%%% ICA Training Block %%%%%%%%%%%%%%%%%%%
pause(0);
if ~isempty(get(0, 'currentfigure')) & strcmp(get(gcf, 'tag'), 'stop')
close; error('USER ABORT');
end;
if biasflag
u=weights*data(:,bootstrap(t:t+block-1)) + bias*onesrow;
else
u=weights*data(:,bootstrap(t:t+block-1));
end
if ~extended
%%%%%%%%%%%%%%%%%%% Logistic ICA weight update %%%%%%%%%%%%%%%%%%%
y=1./(1+exp(-u)); %
weights=weights+lrate*(BI+(1-2*y)*u')*weights; %
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
else % extended-ICA
%%%%%%%%%%%%%%%%%%% Extended-ICA weight update %%%%%%%%%%%%%%%%%%%
y=tanh(u); %
weights = weights + lrate*(BI-signs*y*u'-u*u')*weights; %
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
end
if biasflag
if ~extended
%%%%%%%%%%%%%%%%%%%%%%%% Logistic ICA bias %%%%%%%%%%%%%%%%%%%%%%%
bias = bias + lrate*sum((1-2*y)')'; % for logistic nonlin. %
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
else % extended
%%%%%%%%%%%%%%%%%%% Extended-ICA bias %%%%%%%%%%%%%%%%%%%%%%%%%%%%
bias = bias + lrate*sum((-2*y)')'; % for tanh() nonlin. %
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
end
end
if momentum > 0 %%%%%%%%% Add momentum %%%%%%%%%%%%%%%%%%%%%%%%%%%%
weights = weights + momentum*prevwtchange;
prevwtchange = weights-prevweights;
prevweights = weights;
end %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
if max(max(abs(weights))) > MAX_WEIGHT
wts_blowup = 1;
change = nochange;
end
if extended & ~wts_blowup
%
%%%%%%%%%%% Extended-ICA kurtosis estimation %%%%%%%%%%%%%%%%%%%%%
%
if extblocks > 0 & rem(blockno,extblocks) == 0,
% recompute signs vector using kurtosis
if kurtsize < frames % 12-22-99 rand() size suggestion by M. Spratling
rp = fix(rand(1,kurtsize)*datalength); % pick random subset
% Accout for the possibility of a 0 generation by rand
ou = find(rp == 0);
while ~isempty(ou) % 1-11-00 suggestion by J. Foucher
rp(ou) = fix(rand(1,length(ou))*datalength);
ou = find(rp == 0);
end
partact=weights*data(:,rp(1:kurtsize));
else % for small data sets,
partact=weights*data; % use whole data
end
m2=mean(partact'.^2).^2;
m4= mean(partact'.^4);
kk= (m4./m2)-3.0; % kurtosis estimates
if extmomentum
kk = extmomentum*old_kk + (1.0-extmomentum)*kk; % use momentum
old_kk = kk;
end
signs=diag(sign(kk+signsbias)); % pick component signs
if signs == oldsigns,
signcount = signcount+1;
else
signcount = 0;
end
oldsigns = signs;
signcounts = [signcounts signcount];
if signcount >= SIGNCOUNT_THRESHOLD,
extblocks = fix(extblocks * SIGNCOUNT_STEP);% make kurt() estimation
signcount = 0; % less frequent if sign
end % is not changing
end % extblocks > 0 & . . .
end % if extended %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
blockno = blockno + 1;
if wts_blowup
break
end
end % training block %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
if ~wts_blowup
oldwtchange = weights-oldweights;
step=step+1;
%
%%%%%%% Compute and print weight and update angle changes %%%%%%%%%
%
lrates(1,step) = lrate;
angledelta=0.;
delta=reshape(oldwtchange,1,chans*ncomps);
change=delta*delta';
end
%
%%%%%%%%%%%%%%%%%%%%%% Restart if weights blow up %%%%%%%%%%%%%%%%%%%%
%
if wts_blowup | isnan(change)|isinf(change), % if weights blow up,
fprintf('');
step = 0; % start again
change = nochange;
wts_blowup = 0; % re-initialize variables
blockno = 1;
lrate = lrate*DEFAULT_RESTART_FAC; % with lower learning rate
weights = startweights; % and original weight matrix
oldweights = startweights;
change = nochange;
oldwtchange = zeros(chans,ncomps);
delta=zeros(1,chans*ncomps);
olddelta = delta;
extblocks = urextblocks;
prevweights = startweights;
prevwtchange = zeros(chans,ncomps);
lrates = zeros(1,maxsteps);
bias = zeros(ncomps,1);
if extended
signs = ones(1,ncomps); % initialize signs to nsub -1, rest +1
for k=1:nsub
signs(k) = -1;
end
signs = diag(signs); % make a diagonal matrix
oldsigns = zeros(size(signs));;
end
if lrate> MIN_LRATE
r = rank(data);
if r<ncomps
fprintf('Data has rank %d. Cannot compute %d components.\n',...
r,ncomps);
return
else
fprintf(...
'Lowering learning rate to %g and starting again.\n',lrate);
end
else
fprintf( ...
'runica(): QUITTING - weight matrix may not be invertible!\n');
return;
end
else % if weights in bounds
%
%%%%%%%%%%%%% Print weight update information %%%%%%%%%%%%%%%%%%%%%%
%
if step> 2
angledelta=acos((delta*olddelta')/sqrt(change*oldchange));
end
if verbose,
if step > 2,
if ~extended,
fprintf(...
'step %d - lrate %5f, wchange %7.6f, angledelta %4.1f deg\n', ...
step,lrate,change,degconst*angledelta);
else
fprintf(...
'step %d - lrate %5f, wchange %7.6f, angledelta %4.1f deg, %d subgauss\n',...
step,lrate,change,degconst*angledelta,(ncomps-sum(diag(signs)))/2);
end
elseif ~extended
fprintf(...
'step %d - lrate %5f, wchange %7.6f\n',step,lrate,change);
else
fprintf(...
'step %d - lrate %5f, wchange %7.6f, %d subgauss\n',...
step,lrate,change,(ncomps-sum(diag(signs)))/2);
end % step > 2
end; % if verbose
%
%%%%%%%%%%%%%%%%%%%% Save current values %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%
changes = [changes change];
oldweights = weights;
%
%%%%%%%%%%%%%%%%%%%% Anneal learning rate %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%
if degconst*angledelta > annealdeg,
lrate = lrate*annealstep; % anneal learning rate
olddelta = delta; % accumulate angledelta until
oldchange = change; % annealdeg is reached
elseif step == 1 % on first step only
olddelta = delta; % initialize
oldchange = change;
end
%
%%%%%%%%%%%%%%%%%%%% Apply stopping rule %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%
if step >2 & change < nochange, % apply stopping rule
laststep=step;
step=maxsteps; % stop when weights stabilize
elseif change > DEFAULT_BLOWUP, % if weights blow up,
lrate=lrate*DEFAULT_BLOWUP_FAC; % keep trying
end; % with a smaller learning rate
end; % end if weights in bounds
end; % end training %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
if ~laststep
laststep = step;
end;
lrates = lrates(1,1:laststep); % truncate lrate history vector
%
%%%%%%%%%%%%%% Orient components towards max positive activation %%%%%%
%
if strcmp(posactflag,'on')
[activations,winvout,weights] = posact(data,weights);
% changes signs of activations and weights to make activations
% net rms-positive
else
activations = weights*data;
end
%
%%%%%%%%%%%%%% If pcaflag, compose PCA and ICA matrices %%%%%%%%%%%%%%%
%
if strcmp(pcaflag,'on')
fprintf('Composing the eigenvector, weights, and sphere matrices\n');
fprintf(' into a single rectangular weights matrix; sphere=eye(%d)\n'...
,chans);
weights= weights*sphere*eigenvectors(:,1:ncomps)';
sphere = eye(urchans);
end
%
%%%%%% Sort components in descending order of max projected variance %%%%
%
if verbose,
fprintf(...
'Sorting components in descending order of mean projected variance ...\n');
end
if wts_passed == 0
%
%%%%%%%%%%%%%%%%%%%% Find mean variances %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%
meanvar = zeros(ncomps,1); % size of the projections
if ncomps == urchans % if weights are square . . .
winv = inv(weights*sphere);
else
fprintf('Using pseudo-inverse of weight matrix to rank order component projections.\n');
winv = pinv(weights*sphere);
end
for s=1:ncomps
if verbose,
fprintf('%d ',s); % construct single-component data matrix
end
% project to scalp, then add row means
compproj = winv(:,s)*activations(s,:);
meanvar(s) = mean(sum(compproj.*compproj)/(size(compproj,1)-1));
% compute mean variance
end % at all scalp channels
if verbose,
fprintf('\n');
end
%
%%%%%%%%%%%%%% Sort components by mean variance %%%%%%%%%%%%%%%%%%%%%%%%
%
[sortvar, windex] = sort(meanvar);
windex = windex(ncomps:-1:1); % order large to small
meanvar = meanvar(windex);
%
%%%%%%%%%%%%%%%%%%%%% Filter data using final weights %%%%%%%%%%%%%%%%%%
%
if nargout>2, % if activations are to be returned
if verbose,
fprintf('Permuting the activation wave forms ...\n');
end
activations = activations(windex,:);
else
clear activations
end
weights = weights(windex,:);% reorder the weight matrix
bias = bias(windex); % reorder them
signs = diag(signs); % vectorize the signs matrix
signs = signs(windex); % reorder them
else
fprintf('Components not ordered by variance.\n');
end
%
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% end %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%
return
if nargout > 6
u=weights*data + bias*ones(1,frames);
y = zeros(size(u));
for c=1:chans
for f=1:frames
y(c,f) = 1/(1+exp(-u(c,f)));
end
end
end
|
github
|
lcnbeapp/beapp-master
|
headmovie.m
|
.m
|
beapp-master/Packages/eeglab14_1_2b/functions/miscfunc/headmovie.m
| 8,690 |
utf_8
|
38629f7b7a3e0c3097687e8c0aaf3250
|
% ########## This function is deprecated. Use eegmovie instead. ##########
%
% headmovie() - Record a Matlab movie of scalp data.
% Use seemovie() to display the movie.
%
% Usage: >> [Movie,Colormap] = headmovie(data,elec_loc,spline_file);
% >> [Movie,Colormap,minc,maxc] = headmovie(data,elec_loc,spline_file,...
% srate,title,camerapath,movieframes,minmax,startsec);
% Inputs:
% data = (chans,frames) EEG data set to plot
% elec_loc = electrode locations file for eegplot {default 'chan.loc'}
% spline_file = headplot() produced spline 'filename' {default 'chan.spline'}
% srate = sampling rate in Hz {default|0 -> 256 Hz}
% title = 'plot title' {default|0 -> none}
% camerapath = [az_start az_step el_start el_step] {default [-127 0 30 0]}
% Setting all four non-0 creates a spiral camera path
% Partial entries allowed, e.g. [az_start]
% Subsequent rows [movieframe az_step 0 el_step] adapt step
% sizes allowing starts/stops, panning back and forth, etc.
% movieframes = vector of data frames to animate {default|0 -> all}
% minmax = Data [lower_bound, upper_bound] Lower->blue, upper->red
% {default|0 -> +/-abs max of data}
% startsec = starting time in seconds {default|0 -> 0.0}
%
% Note: BUG IN MATLAB 5.0-5.1 -- CANT SHOW MOVIES IN CORRECT COLORS
%
% Authors: Scott Makeig & Colin Humphries, SCCN/INC/UCSD, La Jolla, 2/1998
%
% See also: seemovie(), eegmovie(), headplot()
% Copyright (C) 2.6.98 Scott Makeig & Colin Humphries, SCCN/INC/UCSD, [email protected]
%
% This program is free software; you can redistribute it and/or modify
% it under the terms of the GNU General Public License as published by
% the Free Software Foundation; either version 2 of the License, or
% (at your option) any later version.
%
% This program is distributed in the hope that it will be useful,
% but WITHOUT ANY WARRANTY; without even the implied warranty of
% MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
% GNU General Public License for more details.
%
% You should have received a copy of the GNU General Public License
% along with this program; if not, write to the Free Software
% Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
% 01-25-02 reformated help & license, added links -ad
function [Movie, Colormap, minc, maxc] = headmovie(data,eloc_file,spline_file,srate,titl,camerapath,movieframes,minmax,startsec,varargin)
if nargin<1
help headmovie
return
end
clf
[chans,frames] = size(data);
icadefs; % read DEFAULT_SRATE;
if nargin<9
startsec = 0;
end
if nargin<8
minmax = 0;
end
if size(minmax)==[1 1] & minmax ~= 0
minmax = [-minmax minmax];
end
if minmax ==0,
minc = min(min(data));
maxc = max(max(data));
absmax = max([abs(minc), abs(maxc)]);
fudge = 0.05*(maxc-minc); % allow for slight extrapolation
minc = -absmax-fudge;
maxc = absmax+fudge;
minmax = [minc maxc];
end
if nargin <7
movieframes = 0;
end
if nargin<6
camerapath = 0;
end
if movieframes == 0
movieframes = 1:frames; % default
end
if nargin <5
titl = '';
end
if titl == 0
titl = '';
end
if nargin <4
srate = 0;
end
if nargin <3
spline_file = 0;
end
if nargin <2
eloc_file = 0;
end
if movieframes(1) < 1 | movieframes(length(movieframes))>frames
fprintf('headmovie(): specified movieframes not in data!\n');
return
end
if srate ==0,
srate = DEFAULT_SRATE;
end
mframes = length(movieframes);
fprintf('Making a movie of %d frames\n',mframes)
Movie = moviein(mframes,gcf);
if size(camerapath) == [1,1]
if camerapath==0
camerapath = [-127 0 30 0];
fprintf('Using default view [-127 0 30 0].');
else
camerapath = [camerapath 0 30 0];
end
elseif size(camerapath,2) == 2
camerapath(1,:) = [camerapath(1,1) camerapath(1,2) 30 0]
elseif size(camerapath,2) == 3
camerapath(1,:) = [camerapath(1,1) camerapath(1,2) camerapath(1,3) 0]
elseif size(camerapath,2) > 4
help headmovie
return
end
if size(camerapath,1) > 1 & size(camerapath,2)~=4
help headmovie
return
end
azimuth = camerapath(1,1); % initial camerapath variables
az_step = camerapath(1,2);
elevation = camerapath(1,3);
el_step = camerapath(1,4);
if ~isstruct(eloc_file) && eloc_file(1) == 0
eloc_file = 'chan.angles';
end
if spline_file(1) == 0
spline_file = 'chan.spline';
end
figure(gcf); % bring figure to front
clf % clear figure
%%%%%%%%%%%%%%%%%%%%% eegplot() of data %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
axeegplot = axes('Units','Normalized','Position',[.75 .05 .2 .9]);
if isstruct(eloc_file)
eegplotold('noui',-data,srate,0,[],startsec,'r');
%eegplotsold(-data,srate,[],' ',0,frames/srate,'r',startsec); %CJH
else
eegplotold('noui',-data,srate,0,eloc_file,startsec,'r');
%eegplotsold(-data,srate,eloc_file,' ',0,frames/srate,'r',startsec); %CJH
end;
set(axeegplot,'XTick',[]) %%CJH
% plot negative up
limits = get(axeegplot,'Ylim'); % list channel numbers only
set(axeegplot,'GridLineStyle',':')
set(axeegplot,'Xgrid','off')
set(axeegplot,'Ygrid','on')
axcolor = get(gcf,'Color');
%%%%%%%%%%%%%%%%%%%%%%% print title text %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
axtitle = axes('Units','Normalized','Position',[0 .9 .72 .1],'Color',axcolor);
axes(axtitle)
text(0.5,0.5,titl,'FontSize',16,'horizontalalignment','center')
axis('off')
%%%%%%%%%%%%%%%%%%%%%%% display colorbar %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
axcolorbar = axes('Units','Normalized','Position',[.05 .05 .055 .18]);
axes(axcolorbar)
if exist('colorbar_tp')==2
h=colorbar_tp(axcolorbar); % Slightly altered Matlab colorbar() routine
else
h=colorbar(axcolorbar); % Note: there is a minor problem with this call.
end % Write authors for further information.
hkids=get(h,'children');
for k=1:1
delete(hkids(k));
end
set(axcolorbar,'Ytick',[0 0.5 1.0],'Yticklabel',[' - ';' 0 ';' + '],'FontSize',16);
axis('off')
%%%%%%%%%%%%%%%%%%%%%%%%%%%% "Roll'em!" %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
axheadplot = axes('Units','Normalized','Position',[0 .1 .72 .8],'Color',axcolor);
TPAXCOLOR = get(axheadplot,'Color');
Colormap = [jet(64);TPAXCOLOR];
fprintf('Warning: do not resize plot window during movie creation ...\n ');
newpan = length(movieframes)+1;
posrow = 2;
if size(camerapath,1) > 1
newpan = camerapath(posrow,1); % pick up next frame to change camerapos step values
end
for i = movieframes % make the movie, frame by frame
fprintf('%d ',i-movieframes(1)+1);
axes(axeegplot)
x1 = startsec+(i-1)/srate;
l1 = line([x1 x1],limits,'color','b'); % draw vertical line at data frame
timetext = num2str(x1,3); % Note: Matlab4 doesn't take '%4.3f'
set(axeegplot,'Xtick',x1,'XtickLabel',num2str(x1,'%4.3f'));
axes(axheadplot)
cla
set(axheadplot,'Color',axcolor);
headplot(data(:,i),spline_file,'maplimits',minmax,...
'view',[azimuth elevation],'verbose','off', varargin{:});
if i== newpan % adapt camerapath step sizes
az_step = camerapath(posrow,2);
el_step = camerapath(posrow,4);
posrow = posrow+1;
if size(camerapath,1)>=posrow
newpan = camerapath(posrow,1);
else
newpan = length(movieframes)+1;
end
end
azimuth = azimuth+az_step; % update camera position
elevation = elevation+el_step;
if elevation>=90
fprintf('headplot(): warning -- elevation out of range!\n');
elevation = 89.99;
end
if elevation<=-90
fprintf('headplot(): warning -- elevation out of range!\n');
elevation = -89.99;
end
set(axheadplot,'Units','pixels',...
'CameraViewAngleMode','manual',...
'YTickMode','manual','ZTickMode','manual',...
'PlotBoxAspectRatioMode','manual',...
'DataAspectRatioMode','manual'); % keep camera distance constant
txt = [int2str(i-movieframes(1)+1)];
text(0.45,-0.45,txt,'Color','k','FontSize',14); % show frame number
[Movie(:,i+1-movieframes(1))] = getframe(gcf); % can't show this - colors wrong!
% known Matlab 5.0-5.1 bug!
% [M,Cmap] = getframe(gcf);
% if i==1
% [m,n] = size(M);
% Movie = zeros(m,n*length(movieframes));
% whos Movie
% end
% Movie((i-1)*m+1:i*m,(i-1)*n+1:i*n) = M;
drawnow
delete(l1)
end
% colormap(Cmap);
% montage(Movie)
% Movie = immovie(Movie,[m n length(movieframes)]);
% whos Movie
fprintf('\nDone!\n');
|
github
|
lcnbeapp/beapp-master
|
arrow.m
|
.m
|
beapp-master/Packages/eeglab14_1_2b/functions/miscfunc/arrow.m
| 51,888 |
utf_8
|
6310afbf5a0ed2b3cfdc0469d9b0c9cd
|
% arrow() - Draw a line with an arrowhead.
%
% Usage:
% >> arrow('Property1',PropVal1,'Property2',PropVal2,...)
% >> arrow(H,'Prop1',PropVal1,...)
% >> arrow(Start,Stop)
% >> arrow(Start,Stop,Length,BaseAngle,TipAngle,Width,Page,CrossDir)
% >> arrow demo %2-D demos of the capabilities of arrow()
% >> arrow demo2 %3-D demos of the capabilities of arrow()
%
% Inputs:
% H - vector of handles to previously created arrows and/or
% line objects, will update the previously-created
% arrows according to the current view and any specified
% properties, and will convert two-point line objects to
% corresponding arrows. Note that arrow(H) will update the
% arrows if the current view has changed.
% Start - vectors of length 2 or 3, or matrices with 2 or 3 columns
% Stop - same as Start
% 'Start' - The starting points. B
% 'Stop' - The end points. /|\ ^
% 'Length' - Length of the arrowhead in pixels. /|||\ |
% 'BaseAngle' - Base angle in degrees (ADE). //|||\\ L|
% 'TipAngle' - Tip angle in degrees (ABC). ///|||\\\ e|
% 'Width' - Width of the base in pixels. ////|||\\\\ n|
% 'Page' - Use hardcopy proportions. /////|D|\\\\\ g|
% 'CrossDir' - Vector || to arrowhead plane. //// ||| \\\\ t|
% 'NormalDir' - Vector out of arrowhead plane. /// ||| \\\ h|
% 'Ends' - Which end has an arrowhead. //<----->|| \\ |
% 'ObjectHandles' - Vector of handles to update. / base ||| \ V
% 'LineStyle' - The linestyle of the arrow. E angle||<-------->C
% 'LineWidth' - Line thicknesses. |||tipangle
% 'FaceColor' - FaceColor of patch arrows. |||
% 'EdgeColor' - EdgeColor/Color of patch/line arrows. |||
% 'Color' - Set FaceColor & EdgeColor properties. -->|A|<-- width
%
% Notes:
% A property list can follow any specified normal argument list, e.g.,
% ARROW([1 2 3],[0 0 0],36,'BaseAngle',60) creates an arrow from (1,2,3) to
% the origin, with an arrowhead of length 36 pixels and 60-degree base angle.
%
% The basic arguments or properties can generally be vectorized to create
% multiple arrows with the same call. This is done by passing a property
% with one row per arrow, or, if all arrows are to have the same property
% value, just one row may be specified.
%
% You may want to execute AXIS(AXIS) before calling ARROW so it doesn't change
% the axes on you; ARROW determines the sizes of arrow components BEFORE the
% arrow is plotted, so if ARROW changes axis limits, arrows may be malformed.
%
% ARROW uses features of Matlab 4.2c and later, so earlier versions may be
% incompatible; call ARROW VERSION for more details.
%
% Author: Erik A. Johnson <[email protected]>, 1995
% Copyright (c)1995, Erik A. Johnson <[email protected]>, 10/6/95
% Many thanks to Keith Rogers <[email protected]> for his many excellent
% suggestions and beta testing. Check out his shareware package MATDRAW.
% He has permission to distribute ARROW with MATDRAW.
% $Log: arrow.m,v $
% Revision 1.5 2009/10/20 22:19:56 dev
%
% added log to file
%
function [h,yy,zz] = arrow(arg1,arg2,arg3,arg4,arg5,arg6,arg7,arg8, ...
arg9,arg10,arg11,arg12,arg13,arg14,arg15,arg16, ...
arg17,arg18,arg19,arg20,arg21,arg22,arg23,arg24)
% Are we doing the demo?
c = sprintf('\n');
if (nargin==1),
if (ischar(arg1)),
arg1 = lower([arg1 ' ']);
if (strcmp(arg1(1:4),'prop')),
disp([c ...
'ARROW Properties: Default values are given in [square brackets], and other' c ...
' acceptable equivalent property names are in (parenthesis).' c c ...
' Start The starting points. For N arrows, B' c ...
' this should be a Nx2 or Nx3 matrix. /|\ ^' c ...
' Stop The end points. For N arrows, this /|||\ |' c ...
' should be a Nx2 or Nx3 matrix. //|||\\ L|' c ...
' Length Length of the arrowhead (in pixels on ///|||\\\ e|' c ...
' screen, points on a page). [16] (Len) ////|||\\\\ n|' c ...
' BaseAngle Angle (degrees) of the base angle /////|D|\\\\\ g|' c ...
' ADE. For a simple stick arrow, use //// ||| \\\\ t|' c ...
' BaseAngle=TipAngle. [90] (Base) /// ||| \\\ h|' c ...
' TipAngle Angle (degrees) of tip angle ABC. //<----->|| \\ |' c ...
' [16] (Tip) / base ||| \ V' c ...
' Width Width of the base in pixels. Not E angle ||<-------->C' c ...
' the ''LineWidth'' prop. [0] (Wid) |||tipangle' c ...
' Page If provided, non-empty, and not NaN, |||' c ...
' this causes ARROW to use hardcopy |||' c ...
' rather than onscreen proportions. A' c ...
' This is important if screen aspect --> <-- width' c ...
' ratio and hardcopy aspect ratio are ----CrossDir---->' c ...
' vastly different. []' c...
' CrossDir A vector giving the direction towards which the fletches' c ...
' on the arrow should go. [computed such that it is perpen-' c ...
' dicular to both the arrow direction and the view direction' c ...
' (i.e., as if it was pasted on a normal 2-D graph)] (Note' c ...
' that CrossDir is a vector; if an axis is plotted on a log' c ...
' scale, then the corresponding component of CrossDir must' c ...
' also be set appropriately, i.e., to 1 for no change in' c ...
' that direction, >1 for a positive change, >0 and <1 for' c ...
' negative change.)' c ...
' NormalDir A vector normal to the fletch direction (CrossDir is then' c ...
' computed by the vector cross product {Line}x{NormalDir}). []' c ...
' Ends Set which end has an arrowhead. Valid values are ''none'',' c ...
' ''stop'', ''start'', and ''both''. [''stop''] (End)' c...
' ObjectHandles Vector of handles to previously-created arrows to be' c ...
' updated or line objects to be converted to arrows.' c ...
' [] (Object,Handle)' c ...
' LineStyle The linestyle of the arrow. If anything other than ''-'',' c ...
' the arrow will be drawn with a line object, otherwise it' c ...
' will be drawn with a patch. [''-''] (LineS)' c ...
' LineWidth Same as used in SET commands, but may be passed a vector' c ...
' for multiple arrows. [default of the line or patch]' c ...
' FaceColor Set the FaceColor of patch arrows. May be one of' c ...
' ''ymcrgbwkfn'' (f=flat,n=none) or a column-vector colorspec' c ...
' (or Nx3 matrix for N arrows). [1 1 1] (FaceC)' c ...
' EdgeColor Set the EdgeColor of patch arrows and Color of line' c ...
' arrows. [1 1 1] (EdgeC)' c ...
' Color Sets both FaceColor and EdgeColor properties.' c ...
' Included for compatibility with line objects.' c c ...
' ARROW(''Start'',P,''Stop'',[]) or ARROW(''Start'',[],''Stop'',P), with size(P)=[N 3]' c ...
' will create N-1 arrows, just like ARROW(''Start'',P1,''Stop'',P2), where' c c ...
' / x1 y1 z1 \ / x1 y1 z1 \ / x2 y2 z2 \' c ...
' | . . . | | . . . | | . . . |' c ...
' P = | . . . | P1 = | . . . | P2 = | . . . |' c ...
' | . . . | | . . . | | . . . |' c ...
' \ xN yN zN / \ xN-1 yN-1 zN-1 / \ xN yN zN /' c]);
elseif (strcmp(arg1(1:4),'vers')),
disp([c ...
'ARROW Version: There are two compatibility problems for ARROW in Matlab' c ...
' versions earlier than 4.2c:' c c c ...
' 1) In Matlab <4.2, the ''Tag'' property does not exist. ARROW uses this' c ...
' ''Tag'' to identify arrow objects for subsequent calls to ARROW.' c c ...
' Solution: (a) delete all instances of the string' c c ...
' ,''Tag'',ArrowTag' c c ...
' (b) and replace all instances of the string' c c ...
' strcmp(get(oh,''Tag''),ArrowTag)' c c ...
' with the string' c c ...
' all(size(ud)==[1 15])' c c c ...
' 2) In Matlab <4.2c, FINDOBJ is buggy (it can cause Matlab to crash if' c ...
' more than 100 objects are returned). ARROW uses FINDOBJ to make sure' c ...
' that any handles it receives are truly handles to existing objects.' c c ...
' Solution: replace the line' c c ...
' objs = findobj;' c c ...
' with the lines' c c ...
' objs=0; k=1;' c ...
' while (k<=length(objs)),' c ...
' objs = [objs; get(objs(k),''Children'')];' c ...
' if (strcmp(get(objs(k),''Type''),''axes'')),' c ...
' objs=[objs;get(objs(k),''XLabel''); ...' c ...
' get(objs(k),''YLabel''); ...' c ...
' get(objs(k),''ZLabel''); ...' c ...
' get(objs(k),''Title'')];' c ...
' end;' c ...
' k=k+1;' c ...
' end;' c c]);
elseif (strcmp(arg1(1:4),'demo')),
% demo
% create the data
[x,y,z] = peaks;
[ddd,iii]=max(z(:));
axlim = [min(x(:)) max(x(:)) min(y(:)) max(y(:)) min(z(:)) max(z(:))];
% modify it by inserting some NaN's
[m,n] = size(z);
m = floor(m/2);
n = floor(n/2);
z(1:m,1:n) = NaN*ones(m,n);
% graph it
clf('reset');
hs=surf(x,y,z);
xlabel('x'); ylabel('y');
if (~strcmp(arg1(1:5),'demo2')),
% set the view
axis(axlim);
zlabel('z');
%shading('interp'); set(hs,'EdgeColor','k');
view(viewmtx(-37.5,30,20));
title('Demo of the capabilities of the ARROW function in 3-D');
% Normal yellow arrow
h1 = arrow([axlim(1) axlim(4) 4],[-.8 1.2 4], ...
'EdgeColor','y','FaceColor','y');
% Normal white arrow, clipped by the surface
h2 = arrow(axlim([1 4 6]),[0 2 4]);
t=text(-2.4,2.7,7.7,'arrow clipped by surf');
% Baseangle<90
h3 = arrow([3 .125 3.5],[1.375 0.125 3.5],30,50);
t2=text(3.1,.125,3.5,'local maximum');
% Baseangle<90, fill and edge colors different
h4 = arrow(axlim(1:2:5)*.5,[0 0 0],36,60,25, ...
'EdgeColor','b','FaceColor','c');
t3=text(axlim(1)*.5,axlim(3)*.5,axlim(5)*.5-.75,'origin');
set(t3,'HorizontalAlignment','center');
% Baseangle>90, black fill
h5 = arrow([-2.9 2.9 3],[-1.3 .4 3.2],30,120,[],6, ...
'EdgeColor','r','FaceColor','k','LineWidth',2);
% Baseangle>90, no fill
h6 = arrow([-2.9 2.9 1.3],[-1.3 .4 1.5],30,120,[],6, ...
'EdgeColor','r','FaceColor','none','LineWidth',2);
% Stick arrow
h7 = arrow([-1.6 -1.65 -6.5],[0 -1.65 -6.5],[],16,16);
t4=text(-1.5,-1.65,-7.25,'global mininum');
set(t4,'HorizontalAlignment','center');
% Normal, black fill
h8 = arrow([-1.4 0 -7.2],[-1.4 0 -3],'FaceColor','k');
t5=text(-1.5,0,-7.75,'local minimum');
set(t5,'HorizontalAlignment','center');
% Gray fill, crossdir specified
h9 = arrow([-3 2.2 -6],[-3 2.2 -.05],36,[],27,6,[],[0 -1 0], ...
'EdgeColor','w','FaceColor',.2*[1 1 1]);
% a series of normal arrows, linearly spaced, crossdir specified
h10y=(0:4)'/3;
h10 = arrow([-3*ones(size(h10y)) h10y -6.5*ones(size(h10y))], ...
[-3*ones(size(h10y)) h10y -.05*ones(size(h10y))], ...
12,[],[],[],[],[0 -1 0]);
% a series of normal arrows, linearly spaced
h11x=(1:.33:2.8)';
h11 = arrow([h11x -3*ones(size(h11x)) 6.5*ones(size(h11x))], ...
[h11x -3*ones(size(h11x)) -.05*ones(size(h11x))]);
% series of black-filled arrows, radially oriented, crossdir specified
h12x=2; h12y=-3; h12z=axlim(5)/2; h12xr=1; h12zr=h12z; ir=.15;or=.81;
h12t=(0:11)'/6*pi;
h12 = arrow([h12x+h12xr*cos(h12t)*ir h12y*ones(size(h12t)) ...
h12z+h12zr*sin(h12t)*ir],[h12x+h12xr*cos(h12t)*or ...
h12y*ones(size(h12t)) h12z+h12zr*sin(h12t)*or], ...
10,[],[],[],[], ...
[-h12xr*sin(h12t) zeros(size(h12t)) h12zr*cos(h12t)],...
'FaceColor','none','EdgeColor','m');
% series of normal arrows, tangentially oriented, crossdir specified
or13=.91; h13t=(0:.5:12)'/6*pi;
h13 = arrow([h12x+h12xr*cos(h13t)*or13 ...
h12y*ones(size(h13t)) ...
h12z+h12zr*sin(h13t)*or13],[],6);
% arrow with no line ==> oriented upwards
h14 = arrow([3 3 3],[3 3 3],30);
t6=text(3,3,3.6,'no line'); set(t6,'HorizontalAlignment','center');
% arrow with -- linestyle
h15 = arrow([-.5 -3 -3],[1 -3 -3],'LineStyle','--','EdgeColor','g');
if (nargout>=1), h=[h1;h2;h3;h4;h5;h6;h7;h8;h9;h10;h11;h12;h13;h14;h15]; end;
else,
set(hs,'YData',10.^get(hs,'YData'));
shading('interp');
view(2);
title('Demo of the capabilities of the ARROW function in 2-D');
hold on; [C,H]=contour(x,y,z,20); hold off;
for k=H', set(k,'ZData',(axlim(6)+1)*ones(size(get(k,'XData'))),...
'YData',10.^get(k,'YData'),'Color','k'); end;
set(gca,'YScale','log');
axis([axlim(1:2) 10.^axlim(3:4)]);
% Normal yellow arrow
h1 = arrow([axlim(1) 10^axlim(4) axlim(6)+2],[x(iii) 10^y(iii) axlim(6)+2], ...
'EdgeColor','y','FaceColor','y');
% three arrows with varying fill, width, and baseangle
h2 = arrow([-3 10^(-3) 10; -3 10^(-1.5) 10; -1.5 10^(-3) 10], ...
[-.03 10^(-.03) 10; -.03 10^(-1.5) 10; -1.5 10^(-.03) 10], ...
24,[90;60;120],[],[0;0;4]);
set(h2(2),'EdgeColor','g','FaceColor','c');
set(h2(3),'EdgeColor','m','FaceColor','r');
if (nargout>=1), h=[h1;h2]; end;
end;
else,
error(['ARROW got an unknown single-argument string ''' deblank(arg1) '''.']);
end;
return;
end;
end;
% Check # of arguments
if (nargin==0), help arrow ; return;
elseif (nargout>3), error('ARROW produces at most 3 output arguments.');
end;
% find first property number
firstprop = nargin+1;
if (nargin<=3), % to speed things up a bit
if (nargin==1),
elseif (ischar(arg1)), firstprop=1;
elseif (ischar(arg2)), firstprop=2;
elseif (nargin==3),
if (ischar(arg3)), firstprop=3; end;
end;
else,
for k=1:nargin,
curarg = eval(['arg' num2str(k)]);
if (ischar(curarg)),
firstprop = k;
break;
end;
end;
end;
% check property list
if (firstprop<=nargin),
for k=firstprop:2:nargin,
curarg = eval(['arg' num2str(k)]);
if ((~ischar(curarg))|(min(size(curarg))~=1)),
error('ARROW requires that a property name be a single string.');
end;
end;
if (rem(nargin-firstprop,2)~=1),
error(['ARROW requires that the property ''' eval(['arg' num2str(nargin)]) ...
''' be paired with a property value.']);
end;
end;
% default output
if (nargout>0), h=[]; end;
if (nargout>1), yy=[]; end;
if (nargout>2), zz=[]; end;
% set values to empty matrices
start = [];
stop = [];
len = [];
baseangle = [];
tipangle = [];
wid = [];
page = [];
crossdir = [];
ends = [];
linewidth = [];
linestyle = [];
edgecolor = [];
facecolor = [];
ax = [];
oldh = [];
defstart = [NaN NaN NaN];
defstop = [NaN NaN NaN];
deflen = 16;
defbaseangle = 90;
deftipangle = 16;
defwid = 0;
defpage = 0;
defcrossdir = [NaN NaN NaN];
defends = 1;
deflinewidth = NaN;
deflinestyle = '- ';
defedgecolor = [1 1 1];
deffacecolor = [1 1 1];
defoldh = [];
% The 'Tag' we'll put on our arrows
ArrowTag = 'Arrow';
% check for oldstyle arguments
if (firstprop>2),
% if old style arguments, get them
if (firstprop==3), start=arg1; stop=arg2;
elseif (firstprop==4), start=arg1; stop=arg2; len=arg3(:);
elseif (firstprop==5), start=arg1; stop=arg2; len=arg3(:); baseangle=arg4(:);
elseif (firstprop==6), start=arg1; stop=arg2; len=arg3(:); baseangle=arg4(:); tipangle=arg5(:);
elseif (firstprop==7), start=arg1; stop=arg2; len=arg3(:); baseangle=arg4(:); tipangle=arg5(:); wid=arg6(:);
elseif (firstprop==8), start=arg1; stop=arg2; len=arg3(:); baseangle=arg4(:); tipangle=arg5(:); wid=arg6(:); page=arg7(:);
elseif (firstprop==9), start=arg1; stop=arg2; len=arg3(:); baseangle=arg4(:); tipangle=arg5(:); wid=arg6(:); page=arg7(:); crossdir=arg8;
else, error('ARROW takes at most 8 non-property arguments.');
end;
elseif (firstprop==2),
% assume arg1 is a set of handles
oldh = arg1(:);
end;
% parse property pairs
extraprops=char([]);
for k=firstprop:2:nargin,
prop = eval(['arg' num2str(k)]);
val = eval(['arg' num2str(k+1)]);
prop = [lower(prop(:)') ' '];
if (all(prop(1:5)=='start')), start = val;
elseif (all(prop(1:4)=='stop')), stop = val;
elseif (all(prop(1:3)=='len')), len = val(:);
elseif (all(prop(1:4)=='base')), baseangle = val(:);
elseif (all(prop(1:3)=='tip')), tipangle = val(:);
elseif (all(prop(1:3)=='wid')), wid = val(:);
elseif (all(prop(1:4)=='page')), page = val;
elseif (all(prop(1:5)=='cross')), crossdir = val;
elseif (all(prop(1:4)=='norm')), if (ischar(val)), crossdir=val; else, crossdir=val*sqrt(-1); end;
elseif (all(prop(1:3)=='end')), ends = val;
elseif (all(prop(1:5)=='linew')), linewidth = val(:);
elseif (all(prop(1:5)=='lines')), linestyle = val;
elseif (all(prop(1:5)=='color')), edgecolor = val; facecolor=val;
elseif (all(prop(1:5)=='edgec')), edgecolor = val;
elseif (all(prop(1:5)=='facec')), facecolor = val;
elseif (all(prop(1:6)=='object')), oldh = val(:);
elseif (all(prop(1:6)=='handle')), oldh = val(:);
elseif (all(prop(1:5)=='userd')), %ignore it
else, extraprops=[extraprops ',arg' num2str(k) ',arg' num2str(k+1)];
end;
end;
% Check if we got 'default' values
if (ischar(start )), s=lower([start(:)' ' ']); if (all(s(1:3)=='def')), start = defstart; else, error(['ARROW does not recognize ''' start(:)' ''' as a valid ''Start'' string.']); end; end;
if (ischar(stop )), s=lower([stop(:)' ' ']); if (all(s(1:3)=='def')), stop = defstop; else, error(['ARROW does not recognize ''' stop(:)' ''' as a valid ''Stop'' string.']); end; end;
if (ischar(len )), s=lower([len(:)' ' ']); if (all(s(1:3)=='def')), len = deflen; else, error(['ARROW does not recognize ''' len(:)' ''' as a valid ''Length'' string.']); end; end;
if (ischar(baseangle )), s=lower([baseangle(:)' ' ']); if (all(s(1:3)=='def')), baseangle = defbaseangle; else, error(['ARROW does not recognize ''' baseangle(:)' ''' as a valid ''BaseAngle'' string.']); end; end;
if (ischar(tipangle )), s=lower([tipangle(:)' ' ']); if (all(s(1:3)=='def')), tipangle = deftipangle; else, error(['ARROW does not recognize ''' tipangle(:)' ''' as a valid ''TipAngle'' string.']); end; end;
if (ischar(wid )), s=lower([wid(:)' ' ']); if (all(s(1:3)=='def')), wid = defwid; else, error(['ARROW does not recognize ''' wid(:)' ''' as a valid ''Width'' string.']); end; end;
if (ischar(crossdir )), s=lower([crossdir(:)' ' ']); if (all(s(1:3)=='def')), crossdir = defcrossdir; else, error(['ARROW does not recognize ''' crossdir(:)' ''' as a valid ''CrossDir'' or ''NormalDir'' string.']); end; end;
if (ischar(page )), s=lower([page(:)' ' ']); if (all(s(1:3)=='def')), page = defpage; else, error(['ARROW does not recognize ''' page(:)' ''' as a valid ''Page'' string.']); end; end;
if (ischar(ends )), s=lower([ends(:)' ' ']); if (all(s(1:3)=='def')), ends = defends; end; end;
if (ischar(linewidth )), s=lower([linewidth(:)' ' ']); if (all(s(1:3)=='def')), linewidth = deflinewidth; else, error(['ARROW does not recognize ''' linewidth(:)' ''' as a valid ''LineWidth'' string.']); end; end;
if (ischar(linestyle )), s=lower([linestyle(:)' ' ']); if (all(s(1:3)=='def')), linestyle = deflinestyle; end; end;
if (ischar(edgecolor )), s=lower([edgecolor(:)' ' ']); if (all(s(1:3)=='def')), edgecolor = defedgecolor; end; end;
if (ischar(facecolor )), s=lower([facecolor(:)' ' ']); if (all(s(1:3)=='def')), facecolor = deffacecolor; end; end;
if (ischar(oldh )), s=lower([oldh(:)' ' ']); if (all(s(1:3)=='def')), oldh = []; else, error(['ARROW does not recognize ''' oldh(:)' ''' as a valid ''ObjectHandles'' string.']); end; end;
% check transpose on arguments; convert strings to numbers
if (((size(start ,1)==2)|(size(start ,1)==3))&((size(start ,2)==1)|(size(start ,2)>3))), start = start'; end;
if (((size(stop ,1)==2)|(size(stop ,1)==3))&((size(stop ,2)==1)|(size(stop ,2)>3))), stop = stop'; end;
if (((size(crossdir,1)==2)|(size(crossdir,1)==3))&((size(crossdir,2)==1)|(size(crossdir,2)>3))), crossdir = crossdir'; end;
if ((size(linestyle,2)>2)&(size(linestyle,1)<=2)), linestyle=linestyle'; end;
if (all(size(edgecolor))),
if (ischar(edgecolor)),
col = lower(edgecolor(:,1));
edgecolor = zeros(length(col),3);
ii=find(col=='y'); if (all(size(ii))), edgecolor(ii,:)=ones(length(ii),1)*[1 1 0]; end;
ii=find(col=='m'); if (all(size(ii))), edgecolor(ii,:)=ones(length(ii),1)*[1 0 1]; end;
ii=find(col=='c'); if (all(size(ii))), edgecolor(ii,:)=ones(length(ii),1)*[0 1 1]; end;
ii=find(col=='r'); if (all(size(ii))), edgecolor(ii,:)=ones(length(ii),1)*[1 0 0]; end;
ii=find(col=='g'); if (all(size(ii))), edgecolor(ii,:)=ones(length(ii),1)*[0 1 0]; end;
ii=find(col=='b'); if (all(size(ii))), edgecolor(ii,:)=ones(length(ii),1)*[0 0 1]; end;
ii=find(col=='w'); if (all(size(ii))), edgecolor(ii,:)=ones(length(ii),1)*[1 1 1]; end;
ii=find(col=='k'); if (all(size(ii))), edgecolor(ii,:)=ones(length(ii),1)*[0 0 0]; end;
ii=find(col=='f'); if (all(size(ii))), edgecolor(ii,:)=ones(length(ii),1)*[1 1 1]*inf; end;
ii=find(col=='n'); if (all(size(ii))), edgecolor(ii,:)=ones(length(ii),1)*[1 1 1]*(-inf); end;
elseif ((size(edgecolor,2)~=3)&(size(edgecolor,1)==3)),
edgecolor=edgecolor';
elseif (size(edgecolor,2)~=3),
error('ARROW requires that color specifications must be a ?x3 RGB matrix.');
end;
end;
if (all(size(facecolor))),
if (ischar(facecolor)),
col = lower(facecolor(:,1));
facecolor = zeros(length(col),3);
ii=find(col=='y'); if (all(size(ii))), facecolor(ii,:)=ones(length(ii),1)*[1 1 0]; end;
ii=find(col=='m'); if (all(size(ii))), facecolor(ii,:)=ones(length(ii),1)*[1 0 1]; end;
ii=find(col=='c'); if (all(size(ii))), facecolor(ii,:)=ones(length(ii),1)*[0 1 1]; end;
ii=find(col=='r'); if (all(size(ii))), facecolor(ii,:)=ones(length(ii),1)*[1 0 0]; end;
ii=find(col=='g'); if (all(size(ii))), facecolor(ii,:)=ones(length(ii),1)*[0 1 0]; end;
ii=find(col=='b'); if (all(size(ii))), facecolor(ii,:)=ones(length(ii),1)*[0 0 1]; end;
ii=find(col=='w'); if (all(size(ii))), facecolor(ii,:)=ones(length(ii),1)*[1 1 1]; end;
ii=find(col=='k'); if (all(size(ii))), facecolor(ii,:)=ones(length(ii),1)*[0 0 0]; end;
ii=find(col=='f'); if (all(size(ii))), facecolor(ii,:)=ones(length(ii),1)*[1 1 1]*inf; end;
ii=find(col=='n'); if (all(size(ii))), facecolor(ii,:)=ones(length(ii),1)*[1 1 1]*(-inf); end;
elseif ((size(facecolor,2)~=3)&(size(facecolor,1)==3)),
facecolor=facecolor';
elseif (size(facecolor,2)~=3),
error('ARROW requires that color specifications must be a ?x3 RGB matrix.');
end;
end;
if (all(size(ends))),
if (ischar(ends)),
endsorig = ends;
col = lower([ends(:,1:min(3,size(ends,2))) ones(size(ends,1),max(0,3-size(ends,2)))*' ']);
ends = NaN*ones(size(ends,1),1);
oo = ones(1,size(ends,1));
ii=find(all(col'==['non']'*oo)'); if (all(size(ii))), ends(ii)=ones(length(ii),1)*0; end;
ii=find(all(col'==['sto']'*oo)'); if (all(size(ii))), ends(ii)=ones(length(ii),1)*1; end;
ii=find(all(col'==['sta']'*oo)'); if (all(size(ii))), ends(ii)=ones(length(ii),1)*2; end;
ii=find(all(col'==['bot']'*oo)'); if (all(size(ii))), ends(ii)=ones(length(ii),1)*3; end;
if (any(isnan(ends))),
ii = min(find(isnan(ends)));
error(['ARROW does not recognize ''' deblank(endsorig(ii,:)) ''' as a valid ''Ends'' value.']);
end;
else,
ends = ends(:);
end;
end;
oldh = oldh(:);
% check object handles
if (all(size(oldh))),
oldh = oldh.';
objs = findobj;
if (length(objs)==0), error('ARROW found no graphics handles.');
elseif (length(objs)==1), objs=[objs;objs]; end;
if (~all(any(objs(:,ones(1,length(oldh)))==oldh(ones(length(objs),1),:)))),
error('ARROW got invalid object handles.');
end;
oldh = oldh.';
end;
% Check for an empty Start or Stop (but not both) with no object handles
if ((~all(size(oldh)))&(all(size(start))~=all(size(stop)))),
if (~all(size(start))), start=stop; end;
ii = find(all(diff(start)'==0)');
if (size(start,1)==1),
stop = start;
elseif (length(ii)==size(start,1)-1)
stop = start(1,:);
start = stop;
else,
if (all(size(ii))),
jj = (1:size(start,1))';
jj(ii) = zeros(length(ii),1);
jj = jj(find(jj>0));
start = start(jj,:);
end;
stop = start(2:size(start,1),:);
start = start(1:size(start,1)-1,:);
end;
end;
% largest argument length
argsizes = [length(oldh) size(start,1) size(stop,1) ...
length(len) length(baseangle) length(tipangle) ...
length(wid) length(page) size(crossdir,1) length(ends) ...
length(linewidth) size(edgecolor,1) size(facecolor,1)];
args=['length(ObjectHandle) '; ...
'#rows(Start) '; ...
'#rows(Stop) '; ...
'length(Length) '; ...
'length(BaseAngle) '; ...
'length(TipAngle) '; ...
'length(Width) '; ...
'length(Page) '; ...
'#rows(CrossDir) '; ...
'#rows(Ends) '; ...
'length(LineWidth) '; ...
'#colors in EdgeColor '; ...
'#colors in FaceColor '];
if (any(imag(crossdir(:))~=0)),
args(9,:) = '#rows(NormalDir) ';
end;
if (~all(size(oldh))),
narrows = max(argsizes);
else,
narrows = length(oldh);
end;
% Check size of arguments
ii = find((argsizes~=0)&(argsizes~=1)&(argsizes~=narrows));
if (all(size(ii))),
s = args(ii',:);
while ((size(s,2)>1)&((abs(s(:,size(s,2)))==0)|(abs(s(:,size(s,2)))==abs(' ')))),
s = s(:,1:size(s,2)-1);
end;
s = [ones(length(ii),1)*'ARROW requires that ' s ...
ones(length(ii),1)*[' equal the # of arrows (' num2str(narrows) ').' c]];
s = s';
s = s(:)';
s = s(1:length(s)-1);
error(char(s));
end;
% check element length in Start, Stop, and CrossDir
if (all(size(start))),
if (size(start,2)==2),
start = [start NaN*ones(size(start,1),1)];
elseif (size(start,2)~=3),
error('ARROW requires 2- or 3-element Start points.');
end;
end;
if (all(size(stop))),
if (size(stop,2)==2),
stop = [stop NaN*ones(size(stop,1),1)];
elseif (size(stop,2)~=3),
error('ARROW requires 2- or 3-element Stop points.');
end;
end;
if (all(size(crossdir))),
if (size(crossdir,2)<3),
crossdir = [crossdir NaN*ones(size(crossdir,1),3-size(crossdir,2))];
elseif (size(crossdir,2)~=3),
if (all(imag(crossdir(:))==0)),
error('ARROW requires 2- or 3-element CrossDir vectors.');
else,
error('ARROW requires 2- or 3-element NormalDir vectors.');
end;
end;
end;
% fill empty arguments
if (~all(size(start ))), start = [NaN NaN NaN]; end;
if (~all(size(stop ))), stop = [NaN NaN NaN]; end;
if (~all(size(len ))), len = NaN; end;
if (~all(size(baseangle ))), baseangle = NaN; end;
if (~all(size(tipangle ))), tipangle = NaN; end;
if (~all(size(wid ))), wid = NaN; end;
if (~all(size(page ))), page = NaN; end;
if (~all(size(crossdir ))), crossdir = [NaN NaN NaN]; end;
if (~all(size(ends ))), ends = NaN; end;
if (~all(size(linewidth ))), linewidth = NaN; end;
if (~all(size(linestyle ))), linestyle = char(['-']); end; % was NaN
if (~all(size(edgecolor ))), edgecolor = [NaN NaN NaN]; end;
if (~all(size(facecolor ))), facecolor = [NaN NaN NaN]; end;
% expand single-column arguments
o = ones(narrows,1);
if (size(start ,1)==1), start = o * start ; end;
if (size(stop ,1)==1), stop = o * stop ; end;
if (length(len )==1), len = o * len ; end;
if (length(baseangle )==1), baseangle = o * baseangle ; end;
if (length(tipangle )==1), tipangle = o * tipangle ; end;
if (length(wid )==1), wid = o * wid ; end;
if (length(page )==1), page = o * page ; end;
if (size(crossdir ,1)==1), crossdir = o * crossdir ; end;
if (length(ends )==1), ends = o * ends ; end;
if (length(linewidth )==1), linewidth = o * linewidth ; end;
if (size(linestyle ,1)==1), linestyle = o * linestyle ; end;
if (size(edgecolor ,1)==1), edgecolor = o * edgecolor ; end;
if (size(facecolor ,1)==1), facecolor = o * facecolor ; end;
ax = o * gca;
if (size(linestyle ,2)==1), linestyle = char([linestyle o*' ']); end;
linestyle = char(linestyle);
% if we've got handles, get the defaults from the handles
oldlinewidth = NaN*ones(narrows,1);
oldlinestyle = char(zeros(narrows,2));
oldedgecolor = NaN*ones(narrows,3);
oldfacecolor = NaN*ones(narrows,3);
if (all(size(oldh))),
fromline = zeros(narrows,1);
for k=1:narrows,
oh = oldh(k);
ud = get(oh,'UserData');
isarrow = strcmp(get(oh,'Tag'),ArrowTag);
ohtype = get(oh,'Type');
ispatch = strcmp(ohtype,'patch');
isline = strcmp(ohtype,'line');
if (isarrow|isline),
% arrow UserData format: [start' stop' len base tip wid page crossdir' ends]
if (isarrow),
start0 = ud(1:3);
stop0 = ud(4:6);
if (isnan(len(k))), len(k) = ud( 7); end;
if (isnan(baseangle(k))), baseangle(k) = ud( 8); end;
if (isnan(tipangle(k))), tipangle(k) = ud( 9); end;
if (isnan(wid(k))), wid(k) = ud(10); end;
if (isnan(page(k))), page(k) = ud(11); end;
if (isnan(crossdir(k,1))), crossdir(k,1) = ud(12); end;
if (isnan(crossdir(k,2))), crossdir(k,2) = ud(13); end;
if (isnan(crossdir(k,3))), crossdir(k,3) = ud(14); end;
if (isnan(ends(k))), ends(k) = ud(15); end;
end;
if (isline),
fromline(k) = 1;
if (isarrow),
fc = -inf*[1 1 1];
else,
fc = get(oh,'Color');
x = get(oh,'XData');
y = get(oh,'YData');
z = get(oh,'ZData');
if (any(size(x)~=[1 2])|any(size(y)~=[1 2])),
error('ARROW only converts two-point lines.');
end;
if (~all(size(z))), z=NaN*ones(size(x)); end;
start0 = [x(1) y(1) z(1)];
stop0 = [x(2) y(2) z(2)];
end;
ec = get(oh,'Color');
ls = [get(oh,'LineStyle') ' ']; ls=char(ls(1:2));
lw = get(oh,'LineWidth');
else, % an arrow patch
fc = get(oh,'FaceColor');if (ischar(fc)),
if (strcmp(fc,'none')), fc=-inf*[1 1 1];
elseif (strcmp(fc,'flat')), fc=inf*[1 1 1];
else, fc=[1 1 1]; end;
end;
ec = get(oh,'EdgeColor');if (ischar(ec)),
if (strcmp(ec,'none')), ec=-inf*[1 1 1];
elseif (strcmp(ec,'flat')), ec=inf*[1 1 1];
else, ec=[1 1 1]; end;
end;
ls = char('- ');
lw = get(oh,'LineWidth');
end;
ax(k) = get(oh,'Parent');
else,
error(['ARROW cannot convert ' ohtype ' objects.']);
end;
oldlinewidth(k) = lw;
oldlinestyle(k,:) = ls;
oldedgecolor(k,:) = ec;
oldfacecolor(k,:) = fc;
ii=find(isnan(start(k,:))); if (all(size(ii))), start(k,ii)=start0(ii); end;
ii=find(isnan(stop( k,:))); if (all(size(ii))), stop( k,ii)=stop0( ii); end;
if (isnan(linewidth(k))), linewidth(k) = lw; end;
if (isnan(linestyle(k,1))), linestyle(k,1:2) = ls; end;
if (any(isnan(facecolor(k,:)))), facecolor(k,:) = fc; end;
if (any(isnan(edgecolor(k,:)))), edgecolor(k,:) = ec; end;
end;
else
fromline = [];
end;
% set up the UserData data
% (do it here so it is not corrupted by log10's and such)
ud = [start stop len baseangle tipangle wid page crossdir ends];
% Set Page defaults
if isnan(page)
page = ~isnan(page);
end;
% Get axes limits, range, min; correct for aspect ratio and log scale
axm = zeros(3,narrows);
axr = zeros(3,narrows);
ap = zeros(2,narrows);
xyzlog = zeros(3,narrows);
limmin = zeros(2,narrows);
limrange = zeros(2,narrows);
oneax = all(ax==ax(1));
if (oneax),
T = zeros(4,4);
invT = zeros(4,4);
else,
T = zeros(16,narrows);
invT = zeros(16,narrows);
end;
axnotdone = ones(size(ax));
while (any(axnotdone)),
ii = min(find(axnotdone));
curax = ax(ii);
curpage = page(ii);
% get axes limits and aspect ratio
axl = [get(curax,'XLim'); get(curax,'YLim'); get(curax,'ZLim')];
ar = get(curax,'DataAspectRatio');
% get axes size in pixels (points)
u = get(curax,'Units');
axposoldunits = get(curax,'Position');
if (curpage),
curfig = get(curax,'Parent');
pu = get(curfig,'PaperUnits');
set(curfig,'PaperUnits','points');
pp = get(curfig,'PaperPosition');
set(curfig,'PaperUnits',pu);
set(curax,'Units','normalized');
curap = get(curax,'Position');
curap = pp.*curap;
else,
set(curax,'Units','pixels');
curap = get(curax,'Position');
end;
set(curax,'Units',u);
set(curax,'Position',axposoldunits);
% adjust limits for log scale on axes
curxyzlog = [strcmp(get(curax,'XScale'),'log'); ...
strcmp(get(curax,'YScale'),'log'); ...
strcmp(get(curax,'ZScale'),'log')];
if (any(curxyzlog)),
ii = find([curxyzlog;curxyzlog]);
if (any(axl(ii)<=0)),
error('ARROW does not support non-positive limits on log-scaled axes.');
else,
axl(ii) = log10(axl(ii));
end;
end;
% correct for aspect ratio
if (~isnan(ar(1))),
if (curap(3) < ar(1)*curap(4)),
curap(2) = curap(2) + (curap(4)-curap(3)/ar(1))/2;
curap(4) = curap(3)/ar(1);
else,
curap(1) = curap(1) + (curap(3)-curap(4)*ar(1))/2;
curap(3) = curap(4)*ar(1);
end;
end;
% correct for 'equal'
% may only want to do this for 2-D views, but seems right for 3-D also
if (~isnan(ar(2))),
if ((curap(3)/(axl(1,2)-axl(1,1)))/(curap(4)/(axl(2,2)-axl(2,1)))>ar(2)),
incr = curap(3)*(axl(2,2)-axl(2,1))/(curap(4)*ar(2)) - (axl(1,2)-axl(1,1));
axl(1,:) = axl(1,:) + incr/2*[-1 1];
else,
incr = ar(2)*(axl(1,2)-axl(1,1))*curap(4)/curap(3) - (axl(2,2)-axl(2,1));
axl(2,:) = axl(2,:) + incr/2*[-1 1];
end;
end;
% compute the range of 2-D values
curT = get(curax,'Xform');
lim = curT*[0 1 0 1 0 1 0 1;0 0 1 1 0 0 1 1;0 0 0 0 1 1 1 1;1 1 1 1 1 1 1 1];
lim = lim(1:2,:)./([1;1]*lim(4,:));
curlimmin = min(lim')';
curlimrange = max(lim')' - curlimmin;
curinvT = inv(curT);
if (~oneax),
curT = curT.';
curinvT = curinvT.';
curT = curT(:);
curinvT = curinvT(:);
end;
% check which arrows to which cur corresponds
ii = find((ax==curax)&(page==curpage));
oo = ones(1,length(ii));
axr(:,ii) = diff(axl')' * oo;
axm(:,ii) = axl(:,1) * oo;
ap(:,ii) = curap(3:4)' * oo;
xyzlog(:,ii) = curxyzlog * oo;
limmin(:,ii) = curlimmin * oo;
limrange(:,ii) = curlimrange * oo;
if (oneax),
T = curT;
invT = curinvT;
else,
T(:,ii) = curT * oo;
invT(:,ii) = curinvT * oo;
end;
axnotdone(ii) = zeros(1,length(ii));
end;
% correct for log scales
curxyzlog = xyzlog.';
ii = find(curxyzlog(:));
if (all(size(ii))),
start( ii) = real(log10(start( ii)));
stop( ii) = real(log10(stop( ii)));
if (all(imag(crossdir(ii))==0)),
crossdir(ii) = real(log10(crossdir(ii)));
else,
jj = find(imag(crossdir(ii))==0);
if (all(size(jj))), crossdir(jj) = real(log10(crossdir(jj))); end;
jj = find(imag(crossdir(ii))~=0);
if (all(size(jj))), crossdir(jj) = real(log10(imag(crossdir(jj))))*sqrt(-1); end;
end;
end;
% take care of defaults, page was done above
ii=find(isnan(start(:) )); if (all(size(ii))), start(ii) = axm(ii)+axr(ii)/2; end;
ii=find(isnan(stop(:) )); if (all(size(ii))), stop(ii) = axm(ii)+axr(ii)/2; end;
ii=find(isnan(crossdir(:) )); if (all(size(ii))), crossdir(ii) = zeros(length(ii),1); end;
ii=find(isnan(len )); if (all(size(ii))), len(ii) = ones(length(ii),1)*deflen; end;
ii=find(isnan(baseangle )); if (all(size(ii))), baseangle(ii) = ones(length(ii),1)*defbaseangle; end;
ii=find(isnan(tipangle )); if (all(size(ii))), tipangle(ii) = ones(length(ii),1)*deftipangle; end;
ii=find(isnan(wid )); if (all(size(ii))), wid(ii) = ones(length(ii),1)*defwid; end;
ii=find(isnan(ends )); if (all(size(ii))), ends(ii) = ones(length(ii),1)*defends; end;
ii=find(isnan(linewidth )); if (all(size(ii))), linewidth(ii) = ones(length(ii),1)*deflinewidth; end;
ii=find(any(isnan(edgecolor'))); if (all(size(ii))), edgecolor(ii,:) = ones(length(ii),1)*defedgecolor; end;
ii=find(any(isnan(facecolor'))); if (all(size(ii))), facecolor(ii,:) = ones(length(ii),1)*deffacecolor; end;
ii=find(isnan(linestyle(:,1) )); if (all(size(ii))), linestyle(ii,:) = ones(length(ii),1)*deflinestyle; end;
ii=find(isnan(linestyle(:,2) )); if (all(size(ii))), linestyle(ii,2) = ones(length(ii),1)*' '; end; %just in case
% transpose all values
start = start.';
stop = stop.';
len = len.';
baseangle = baseangle.';
tipangle = tipangle.';
wid = wid.';
page = page.';
crossdir = crossdir.';
ends = ends.';
linewidth = linewidth.';
linestyle = linestyle.';
facecolor = facecolor.';
edgecolor = edgecolor.';
fromline = fromline.';
ax = ax.';
oldlinewidth = oldlinewidth.';
oldlinestyle = oldlinestyle.';
oldedgecolor = oldedgecolor.';
oldfacecolor = oldfacecolor.';
% given x, a 3xN matrix of points in 3-space;
% want to convert to X, the corresponding 4xN 2-space matrix
%
% tmp1=[(x-axm)./axr; ones(1,size(x,1))];
% if (oneax), X=T*tmp1;
% else, tmp1=[tmp1;tmp1;tmp1;tmp1]; tmp1=T.*tmp1;
% tmp2=zeros(4,4*N); tmp2(:)=tmp1(:);
% X=zeros(4,N); X(:)=sum(tmp2)'; end;
% X = X ./ (X(:,4)*ones(1,4));
% for all points with start==stop, start=stop-(verysmallvalue)*(up-direction);
ii = find(all(start==stop));
if (all(size(ii))),
% find an arrowdir vertical on screen and perpendicular to viewer
% transform to 2-D
tmp1 = [(stop(:,ii)-axm(:,ii))./axr(:,ii);ones(1,length(ii))];
if (oneax), twoD=T*tmp1;
else, tmp1=[tmp1;tmp1;tmp1;tmp1]; tmp1=T(:,ii).*tmp1;
tmp2=zeros(4,4*length(ii)); tmp2(:)=tmp1(:);
twoD=zeros(4,length(ii)); twoD(:)=sum(tmp2)'; end;
twoD=twoD./(ones(4,1)*twoD(4,:));
% move the start point down just slightly
tmp1 = twoD + [0;-1/1000;0;0]*(limrange(2,ii)./ap(2,ii));
% transform back to 3-D
if (oneax), threeD=invT*tmp1;
else, tmp1=[tmp1;tmp1;tmp1;tmp1]; tmp1=invT(:,ii).*tmp1;
tmp2=zeros(4,4*length(ii)); tmp2(:)=tmp1(:);
threeD=zeros(4,length(ii)); threeD(:)=sum(tmp2)'; end;
start(:,ii) = (threeD(1:3,:)./(ones(3,1)*threeD(4,:))).*axr(:,ii)+axm(:,ii);
end;
% compute along-arrow points
% transform Start points
tmp1=[(start-axm)./axr;ones(1,narrows)];
if (oneax), X0=T*tmp1;
else, tmp1=[tmp1;tmp1;tmp1;tmp1]; tmp1=T.*tmp1;
tmp2=zeros(4,4*narrows); tmp2(:)=tmp1(:);
X0=zeros(4,narrows); X0(:)=sum(tmp2)'; end;
X0=X0./(ones(4,1)*X0(4,:));
% transform Stop points
tmp1=[(stop-axm)./axr;ones(1,narrows)];
if (oneax), Xf=T*tmp1;
else, tmp1=[tmp1;tmp1;tmp1;tmp1]; tmp1=T.*tmp1;
tmp2=zeros(4,4*narrows); tmp2(:)=tmp1(:);
Xf=zeros(4,narrows); Xf(:)=sum(tmp2)'; end;
Xf=Xf./(ones(4,1)*Xf(4,:));
% compute pixel distance between points
D = sqrt(sum(((Xf(1:2,:)-X0(1:2,:)).*(ap./limrange)).^2));
% compute and modify along-arrow distances
len1 = len;
len2 = len - (len.*tan(tipangle/180*pi)-wid/2).*tan((90-baseangle)/180*pi);
slen0 = zeros(1,narrows);
slen1 = len1 .* ((ends==2)|(ends==3));
slen2 = len2 .* ((ends==2)|(ends==3));
len0 = zeros(1,narrows);
len1 = len1 .* ((ends==1)|(ends==3));
len2 = len2 .* ((ends==1)|(ends==3));
% for no start arrowhead
ii=find((ends==1)&(D<len2));
if (all(size(ii))),
slen0(ii) = D(ii)-len2(ii);
end;
% for no end arrowhead
ii=find((ends==2)&(D<slen2));
if (all(size(ii))),
len0(ii) = D(ii)-slen2(ii);
end;
len1 = len1 + len0;
len2 = len2 + len0;
slen1 = slen1 + slen0;
slen2 = slen2 + slen0;
% compute stoppoints
tmp1=X0.*(ones(4,1)*(len0./D))+Xf.*(ones(4,1)*(1-len0./D));
if (oneax), tmp3=invT*tmp1;
else, tmp1=[tmp1;tmp1;tmp1;tmp1]; tmp1=invT.*tmp1;
tmp2=zeros(4,4*narrows); tmp2(:)=tmp1(:);
tmp3=zeros(4,narrows); tmp3(:)=sum(tmp2)'; end;
stoppoint = tmp3(1:3,:)./(ones(3,1)*tmp3(4,:)).*axr+axm;
% compute tippoints
tmp1=X0.*(ones(4,1)*(len1./D))+Xf.*(ones(4,1)*(1-len1./D));
if (oneax), tmp3=invT*tmp1;
else, tmp1=[tmp1;tmp1;tmp1;tmp1]; tmp1=invT.*tmp1;
tmp2=zeros(4,4*narrows); tmp2(:)=tmp1(:);
tmp3=zeros(4,narrows); tmp3(:)=sum(tmp2)'; end;
tippoint = tmp3(1:3,:)./(ones(3,1)*tmp3(4,:)).*axr+axm;
% compute basepoints
tmp1=X0.*(ones(4,1)*(len2./D))+Xf.*(ones(4,1)*(1-len2./D));
if (oneax), tmp3=invT*tmp1;
else, tmp1=[tmp1;tmp1;tmp1;tmp1]; tmp1=invT.*tmp1;
tmp2=zeros(4,4*narrows); tmp2(:)=tmp1(:);
tmp3=zeros(4,narrows); tmp3(:)=sum(tmp2)'; end;
basepoint = tmp3(1:3,:)./(ones(3,1)*tmp3(4,:)).*axr+axm;
% compute startpoints
tmp1=X0.*(ones(4,1)*(1-slen0./D))+Xf.*(ones(4,1)*(slen0./D));
if (oneax), tmp3=invT*tmp1;
else, tmp1=[tmp1;tmp1;tmp1;tmp1]; tmp1=invT.*tmp1;
tmp2=zeros(4,4*narrows); tmp2(:)=tmp1(:);
tmp3=zeros(4,narrows); tmp3(:)=sum(tmp2)'; end;
startpoint = tmp3(1:3,:)./(ones(3,1)*tmp3(4,:)).*axr+axm;
% compute stippoints
tmp1=X0.*(ones(4,1)*(1-slen1./D))+Xf.*(ones(4,1)*(slen1./D));
if (oneax), tmp3=invT*tmp1;
else, tmp1=[tmp1;tmp1;tmp1;tmp1]; tmp1=invT.*tmp1;
tmp2=zeros(4,4*narrows); tmp2(:)=tmp1(:);
tmp3=zeros(4,narrows); tmp3(:)=sum(tmp2)'; end;
stippoint = tmp3(1:3,:)./(ones(3,1)*tmp3(4,:)).*axr+axm;
% compute sbasepoints
tmp1=X0.*(ones(4,1)*(1-slen2./D))+Xf.*(ones(4,1)*(slen2./D));
if (oneax), tmp3=invT*tmp1;
else, tmp1=[tmp1;tmp1;tmp1;tmp1]; tmp1=invT.*tmp1;
tmp2=zeros(4,4*narrows); tmp2(:)=tmp1(:);
tmp3=zeros(4,narrows); tmp3(:)=sum(tmp2)'; end;
sbasepoint = tmp3(1:3,:)./(ones(3,1)*tmp3(4,:)).*axr+axm;
% compute cross-arrow directions for arrows with NormalDir specified
if (any(imag(crossdir(:))~=0)),
ii = find(any(imag(crossdir)~=0));
crossdir(:,ii) = cross((stop(:,ii)-start(:,ii))./axr(:,ii), ...
imag(crossdir(:,ii))).*axr(:,ii);
end;
% compute cross-arrow directions
basecross = crossdir + basepoint;
tipcross = crossdir + tippoint;
sbasecross = crossdir + sbasepoint;
stipcross = crossdir + stippoint;
ii = find(all(crossdir==0)|any(isnan(crossdir)));
if (all(size(ii))),
numii = length(ii);
% transform start points
tmp1 = [basepoint(:,ii) tippoint(:,ii) sbasepoint(:,ii) stippoint(:,ii)];
tmp1 = (tmp1-axm(:,[ii ii ii ii])) ./ axr(:,[ii ii ii ii]);
tmp1 = [tmp1; ones(1,4*numii)];
if (oneax), X0=T*tmp1;
else, tmp1=[tmp1;tmp1;tmp1;tmp1]; tmp1=T(:,[ii ii ii ii]).*tmp1;
tmp2=zeros(4,16*numii); tmp2(:)=tmp1(:);
X0=zeros(4,4*numii); X0(:)=sum(tmp2)'; end;
X0=X0./(ones(4,1)*X0(4,:));
% transform stop points
tmp1 = [(2*stop(:,ii)-start(:,ii)-axm(:,ii))./axr(:,ii);ones(1,numii)];
tmp1 = [tmp1 tmp1 tmp1 tmp1];
if (oneax), Xf=T*tmp1;
else, tmp1=[tmp1;tmp1;tmp1;tmp1]; tmp1=T(:,[ii ii ii ii]).*tmp1;
tmp2=zeros(4,16*numii); tmp2(:)=tmp1(:);
Xf=zeros(4,4*numii); Xf(:)=sum(tmp2)'; end;
Xf=Xf./(ones(4,1)*Xf(4,:));
% compute perpendicular directions
pixfact = ((limrange(1,ii)./limrange(2,ii)).*(ap(2,ii)./ap(1,ii))).^2;
pixfact = [pixfact pixfact pixfact pixfact];
pixfact = [pixfact;1./pixfact];
[dummyval,jj] = max(abs(Xf(1:2,:)-X0(1:2,:)));
jj1 = ((1:4)'*ones(1,length(jj))==ones(4,1)*jj);
jj2 = ((1:4)'*ones(1,length(jj))==ones(4,1)*(3-jj));
jj3 = jj1(1:2,:);
Xp = X0;
Xp(jj2) = X0(jj2) + ones(sum(jj2(:)),1);
Xp(jj1) = X0(jj1) - (Xf(jj2)-X0(jj2))./(Xf(jj1)-X0(jj1)) .* pixfact(jj3);
% inverse transform the cross points
if (oneax), Xp=invT*Xp;
else, tmp1=[Xp;Xp;Xp;Xp]; tmp1=invT(:,[ii ii ii ii]).*tmp1;
tmp2=zeros(4,16*numii); tmp2(:)=tmp1(:);
Xp=zeros(4,4*numii); Xp(:)=sum(tmp2)'; end;
Xp=(Xp(1:3,:)./(ones(3,1)*Xp(4,:))).*axr(:,[ii ii ii ii])+axm(:,[ii ii ii ii]);
basecross(:,ii) = Xp(:,0*numii+(1:numii));
tipcross(:,ii) = Xp(:,1*numii+(1:numii));
sbasecross(:,ii) = Xp(:,2*numii+(1:numii));
stipcross(:,ii) = Xp(:,3*numii+(1:numii));
end;
% compute all points
% compute start points
axm11 = [axm axm axm axm axm axm axm axm axm axm axm];
axr11 = [axr axr axr axr axr axr axr axr axr axr axr];
st = [stoppoint tippoint basepoint sbasepoint stippoint startpoint stippoint sbasepoint basepoint tippoint stoppoint];
tmp1 = (st - axm11) ./ axr11;
tmp1 = [tmp1; ones(1,size(tmp1,2))];
if (oneax), X0=T*tmp1;
else, tmp1=[tmp1;tmp1;tmp1;tmp1]; tmp1=[T T T T T T T T T T T].*tmp1;
tmp2=zeros(4,44*narrows); tmp2(:)=tmp1(:);
X0=zeros(4,11*narrows); X0(:)=sum(tmp2)'; end;
X0=X0./(ones(4,1)*X0(4,:));
% compute stop points
tmp1 = ([start tipcross basecross sbasecross stipcross stop stipcross sbasecross basecross tipcross start] ...
- axm11) ./ axr11;
tmp1 = [tmp1; ones(1,size(tmp1,2))];
if (oneax), Xf=T*tmp1;
else, tmp1=[tmp1;tmp1;tmp1;tmp1]; tmp1=[T T T T T T T T T T T].*tmp1;
tmp2=zeros(4,44*narrows); tmp2(:)=tmp1(:);
Xf=zeros(4,11*narrows); Xf(:)=sum(tmp2)'; end;
Xf=Xf./(ones(4,1)*Xf(4,:));
% compute lengths
len0 = len.*((ends==1)|(ends==3)).*tan(tipangle/180*pi);
slen0 = len.*((ends==2)|(ends==3)).*tan(tipangle/180*pi);
le = [zeros(1,narrows) len0 wid/2 wid/2 slen0 zeros(1,narrows) -slen0 -wid/2 -wid/2 -len0 zeros(1,narrows)];
aprange = ap./limrange;
aprange = [aprange aprange aprange aprange aprange aprange aprange aprange aprange aprange aprange];
D = sqrt(sum(((Xf(1:2,:)-X0(1:2,:)).*aprange).^2));
Dii=find(D==0); if (all(size(Dii))), D=D+(D==0); le(Dii)=zeros(1,length(Dii)); end; %should fix DivideByZero warnings
tmp1 = X0.*(ones(4,1)*(1-le./D)) + Xf.*(ones(4,1)*(le./D));
% inverse transform
if (oneax), tmp3=invT*tmp1;
else, tmp1=[tmp1;tmp1;tmp1;tmp1]; tmp1=[invT invT invT invT invT invT invT invT invT invT invT].*tmp1;
tmp2=zeros(4,44*narrows); tmp2(:)=tmp1(:);
tmp3=zeros(4,11*narrows); tmp3(:)=sum(tmp2)'; end;
pts = tmp3(1:3,:)./(ones(3,1)*tmp3(4,:)) .* axr11 + axm11;
% correct for ones where the crossdir was specified
ii = find(~(all(crossdir==0)|any(isnan(crossdir))));
if (all(size(ii))),
D1 = [pts(:,1*narrows+ii)-pts(:,9*narrows+ii) ...
pts(:,2*narrows+ii)-pts(:,8*narrows+ii) ...
pts(:,3*narrows+ii)-pts(:,7*narrows+ii) ...
pts(:,4*narrows+ii)-pts(:,6*narrows+ii) ...
pts(:,6*narrows+ii)-pts(:,4*narrows+ii) ...
pts(:,7*narrows+ii)-pts(:,3*narrows+ii) ...
pts(:,8*narrows+ii)-pts(:,2*narrows+ii) ...
pts(:,9*narrows+ii)-pts(:,1*narrows+ii)]/2;
ii = ii'*ones(1,8) + ones(length(ii),1)*[1:4 6:9]*narrows;
ii = ii(:)';
pts(:,ii) = st(:,ii) + D1;
end;
% readjust for log scale on axes
tmp1=[xyzlog xyzlog xyzlog xyzlog xyzlog xyzlog xyzlog xyzlog xyzlog xyzlog xyzlog];
ii = find(tmp1(:)); if (all(size(ii))), pts(ii)=10.^pts(ii); end;
% compute the x,y,z coordinates of the patches;
ii = narrows*(0:10)'*ones(1,narrows) + ones(11,1)*(1:narrows);
ii = ii(:)';
x = zeros(11,narrows);
y = zeros(11,narrows);
z = zeros(11,narrows);
x(:) = pts(1,ii)';
y(:) = pts(2,ii)';
z(:) = pts(3,ii)';
% do the output
if (nargout<=1),
% % create or modify the patches
p = (linestyle(1,:)=='-')&(linestyle(2,:)==' ');
if (all(size(oldh))),
H = oldh;
else,
fromline = p;
H = zeros(narrows,1);
end;
% % new patches
ii = find(p&fromline);
if (all(size(ii))),
if (all(size(oldh))), delete(oldh(ii)); end;
H(ii) = patch(x(:,ii),y(:,ii),z(:,ii),zeros(11,length(ii)),'Tag',ArrowTag);
end;
% % new lines
ii = find((~p)&(~fromline));
if (all(size(ii))),
if (all(size(oldh))), delete(oldh(ii)); end;
H(ii) = line(x(:,ii),y(:,ii),z(:,ii),'Tag',ArrowTag);
end;
% % additional properties
for k=1:narrows,
s = 'set(H(k),''UserData'',ud(k,:)';
if (p(k)~=fromline(k)), % modifying the data
s = [s ',''XData'',x(:,k)'',''YData'',y(:,k)'',''ZData'',z(:,k)'''];
end;
if ((~isnan(linewidth(k)))&(linewidth(k)~=oldlinewidth(k))),
s=[s ',''LineWidth'',linewidth(k)'];
end;
if (p(k)), % a patch
if (any(edgecolor(:,k)~=oldedgecolor(:,k))|(fromline(k))),
if (edgecolor(1,k)==inf),
s=[s ',''EdgeColor'',''flat'''];
elseif (edgecolor(1,k)==-inf),
s=[s ',''EdgeColor'',''none'''];
else,
s=[s ',''EdgeColor'',edgecolor(:,k)'''];
end;
end;
if (any(facecolor(:,k)~=oldfacecolor(:,k))|(fromline(k))),
if (facecolor(1,k)==inf),
s=[s ',''FaceColor'',''flat'''];
elseif (facecolor(1,k)==-inf),
s=[s ',''FaceColor'',''none'''];
else,
s=[s ',''FaceColor'',facecolor(:,k)'''];
end;
end;
else, % a line
s = [s ',''LineStyle'',''' deblank(char(linestyle(:,k)')) ''''];
if (any(facecolor(:,k)~=oldfacecolor(:,k))|any(edgecolor(:,k)~=oldedgecolor(:,k))), % a line
if (isinf(edgecolor(1,k))&(facecolor(1,k)~=-inf)),
s = [s ',''Color'',facecolor(:,k)'''];
else,
s = [s ',''Color'',edgecolor(:,k)'''];
end;
end;
end;
eval([s extraprops ');']);
end;
% set the output
if (nargout>0), h=H; end;
else,
% don't create the patch, just return the data
h=x;
yy=y;
zz=z;
end;
|
github
|
lcnbeapp/beapp-master
|
runpca.m
|
.m
|
beapp-master/Packages/eeglab14_1_2b/functions/miscfunc/runpca.m
| 2,702 |
utf_8
|
6fff3a9e04e75993c00583d5969ea9ec
|
% runpca() - perform principal component analysis (PCA) using singular value
% decomposition (SVD) using Matlab svd() or svds()
% >> inv(eigvec)*data = pc;
% Usage:
% >> [pc,eigvec,sv] = runpca(data);
% >> [pc,eigvec,sv] = runpca(data,num,norm)
%
% Inputs:
% data - input data matrix (rows are variables, columns observations)
% num - number of principal comps to return {def|0|[] -> rows in data}
% norm - 1/0 = do/don't normalize the eigvec's to be equivariant
% {def|0 -> no normalization}
% Outputs:
% pc - the principal components, i.e. >> inv(eigvec)*data = pc;
% eigvec - the inverse weight matrix (=eigenvectors). >> data = eigvec*pc;
% sv - the singular values (=eigenvalues)
%
% Author: Colin Humphries, CNL / Salk Institute, 1997
%
% See also: runica()
% Copyright (C) Colin Humphries, CNL / Salk Institute, Aug, 1997
%
% This program is free software; you can redistribute it and/or modify
% it under the terms of the GNU General Public License as published by
% the Free Software Foundation; either version 2 of the License, or
% (at your option) any later version.
%
% This program is distributed in the hope that it will be useful,
% but WITHOUT ANY WARRANTY; without even the implied warranty of
% MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
% GNU General Public License for more details.
%
% You should have received a copy of the GNU General Public License
% along with this program; if not, write to the Free Software
% Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
% 01/31/00 renamed runpca() and improved usage message -sm
% 01-25-02 reformated help & license, added links -ad
function [pc,M,S] = runpca(data,N,norm)
BIG_N = 50; % for efficiency, switch to sdvs() when BIG_N<=N or N==rows
if nargin < 1
help runpca
return
end
rows = size(data,1);
% remove the mean
for i = 1:rows
data(i,:) = data(i,:) - mean(data(i,:));
end
if nargin < 3
norm = 0;
elseif isempty(norm)
norm = 0;
end
if nargin < 2
N = 0;
end
if isempty(N)
N = 0;
end
if N == 0 | N == rows
N = rows;
[U,S,V] = svd(data',0); % performa SVD
if norm == 0
pc = U';
M = (S*V')';
else % norm
pc = (U*S)';
M = V;
end
else
if N > size(data,1)
error('N must be <= the number of rows in data.')
end
%if N <= BIG_N | N == rows
%[U,S,V] = svd(data',0);
%else
[U,S,V] = svds(data',N);
%end
if norm == 0
pc = U';
M = (S*V')';
else % norm
pc = (U*S)';
M = V;
end
%if N > BIG_N & N < rows
%pc = pc(1:N,:);
%M = M(:,1:N);
%end
end
%S = diag(S(1:N,1:N));
|
github
|
lcnbeapp/beapp-master
|
dendplot.m
|
.m
|
beapp-master/Packages/eeglab14_1_2b/functions/miscfunc/dendplot.m
| 2,407 |
utf_8
|
b7fd4f2ab62ff9c468fbca95378a2da7
|
% DENDPLOT: Plots a dendrogram given a topology matrix.
%
% Usage: dendplot(topology,{labels},{fontsize})
%
% topology = [(n-1) x 4] matrix summarizing dendrogram topology:
% col 1 = 1st OTU/cluster being grouped at current step
% col 2 = 2nd OTU/cluster
% col 3 = ID of cluster being produced
% col 4 = distance at node
% labels = optional [n x q] matrix of group labels for dendrogram.
% fontsize = optional font size for labels [default = 10].
%
% RE Strauss, 5/27/98
% 8/20/99 - miscellaneous changes for Matlab v5
function dendplot(topology,labels,fontsize)
if (nargin<2)
labels = [];
end;
if (nargin < 3)
fontsize = [];
end;
if (isempty(fontsize)) % Default font size for labels
fontsize = 10;
end;
r = size(topology,1);
n = r+1; % Number of taxa
links = dendhier([],topology,n-1); % Find dendrogram links (branches)
otu_indx = find(links(:,1)<=n); % Get sequence of OTUs
otus = links(otu_indx,1);
y = zeros(2*n-1,1); % Y-coords for plot
y(otus) = 0.5:(n-0.5);
for i = 1:(n-1)
y(topology(i,3)) = mean([y(topology(i,1)),y(topology(i,2))]);
end;
clf; % Begin plot
hold on;
for i = 1:(2*n-2) % Horizontal lines
desc = links(i,1);
anc = links(i,2);
X = [links(i,3) links(i,4)];
Y = [y(desc) y(desc)];
plot(X,Y,'k');
end;
for i = (n+1):(2*n-1) % Vertical lines
indx = find(links(:,2)==i);
X = [links(indx,4)];
Y = [y(links(indx(1),1)) y(links(indx(2),1))];
plot(X,Y,'k');
end;
maxdist = max(links(:,4));
for i = 1:n % OTU labels
if (~isempty(labels))
h = text(-.02*maxdist,y(i),labels(i,:)); % For OTUs on right
set(h,'fontsize',fontsize);
else
h = text(-.02*maxdist,y(i),num2str(i)); % For OTUs on right
set(h,'fontsize',fontsize);
% text(-.06*maxdist,y(i),num2str(i)); % For UTOs on left
end;
end;
axis([0 maxdist+0.03*maxdist 0 n]); % Axes
axis('square');
set(gca,'Ytick',[]); % Suppress y-axis labels and tick marks
set(gca,'Ycolor','w'); % Make y-axes invisible
set(gca,'Xdir','reverse'); % For OTUs on right
hold off;
return;
|
github
|
lcnbeapp/beapp-master
|
qrtimax.m
|
.m
|
beapp-master/Packages/eeglab14_1_2b/functions/miscfunc/qrtimax.m
| 4,605 |
utf_8
|
64e79c295baa267e2aacf1bcca2c6769
|
% qrtimax() - perform Quartimax rotation of rows of a data matrix.
%
% Usage: >> [Q,B] = qrtimax(data);
% >> [Q,B] = qrtimax(data,tol,'[no]reorder');
%
% Inputs:
% data - input matrix
% tol - the termination tolerance {default: 1e-4}
% noreorder - rotate without negation/reordering
%
% Outputs:
% B - B=Q*A the Quartimax rotation of A
% Q - the orthogonal rotation matrix
%
% Author: Sigurd Enghoff, CNL / Salk Institute, 6/18/98
% Copyright (C) Sigurd Enghoff - CNL / Salk Institute, La Jolla 6/18/98
%
% This program is free software; you can redistribute it and/or modify
% it under the terms of the GNU General Public License as published by
% the Free Software Foundation; either version 2 of the License, or
% (at your option) any later version.
%
% This program is distributed in the hope that it will be useful,
% but WITHOUT ANY WARRANTY; without even the implied warranty of
% MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
% GNU General Public License for more details.
%
% You should have received a copy of the GNU General Public License
% along with this program; if not, write to the Free Software
% Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
% Reference: Jack O. Nehaus and Charles Wrigley (1954)
% The Quartimax Method: an analytic approach to orthogonal
% simple structure, Br J Stat Psychol, 7:81-91.
% 01-25-02 reformated help & license -ad
function [Q,B] = qrtimax(A,tol,reorder)
if nargin < 1
help qrtimax
return
end
DEFAULT_TOL = 1e-4;
MAX_ITERATIONS = 50;
if nargin < 3
reorder = 1;
elseif isempty(reorder) | reorder == 0
reorder = 1; % set default
else
reorder = strcmp('reorder',reorder);
end
if nargin < 2
eps1 = DEFAULT_TOL;
eps2 = DEFAULT_TOL;
else
eps1 = tol;
eps2 = tol;
end
% Do unto 'Q' what is done to A
Q = eye(size(A,1));
% Compute the cross-products of the rows of the squared loadings,
% i.e. the cost function.
%
% --- ---
% \ \ 2 2
% / / f f
% --- --- ij ik
% i j<k
%
% See reference, p. 85, line 3
B = tril((A.^2)*(A.^2)');
crit = [sum(sum(B)) - trace(B) , 0];
% Initialize variables
inoim = 0;
iflip = 1;
ict = 0;
% Main iterative loop: keep looping while no two consecutive trials
% satisfy tolerance constraint AND less than MAX_ITERATIONS trials
% AND one or more rotations were performed during last trial.
while inoim < 2 & ict < MAX_ITERATIONS & iflip,
iflip = 0;
% Run through all combinations of j and k
for j = 1:size(A,1)-1,
for k = j+1:size(A,1),
%
% --- ---
% \ 2 2 \ 2 2 2 2 2
% fnum = 4 / [f f (f - f )] , fden = / [(f - f ) - 4 f f ]
% --- ki kj ki kj --- ki kj ki kj
% k k
%
% See equation (5)
u = A(j,:) .^ 2 - A(k,:) .^2;
v = 2 * A(j,:) .* A(k,:);
c = sum(u .^ 2 - v .^ 2);
d = sum(u .* v);
fden = c;
fnum = 2 * d;
% Skip rotation if angle is too small
if abs(fnum) > eps1 * abs(fden)
iflip = 1;
angl = atan2(fnum, fden);
% Set angle of rotation according to Table I
if fnum > 0
if fden > 0
angl = .25 * angl;
else
angl = .25 * (pi - angl);
end
else
if fden > 0
angl = .25 * (2 * pi - angl);
else
angl = .25 * (pi + angl);
end
end
% Perform rotation
tmp = cos(angl) * Q(j,:) + sin(angl) * Q(k,:);
Q(k,:) = -sin(angl) * Q(j,:) + cos(angl) * Q(k,:);
Q(j,:) = tmp;
tmp = cos(angl) * A(j,:) + sin(angl) * A(k,:);
A(k,:) = -sin(angl) * A(j,:) + cos(angl) * A(k,:);
A(j,:) = tmp;
end
end
end
% Compute cost function.
B = tril((A.^2)*(A.^2)');
crit = [sum(sum(B)) - trace(B) , crit(1)];
inoim = inoim + 1;
ict = ict + 1;
fprintf('#%d - crit = %g\n',ict,(crit(1)-crit(2))/crit(1));
% Check relative change of cost function (termination criterion).
if (crit(1) - crit(2)) / crit(1) > eps2
inoim = 0;
end
end
% Reorder and negate if required. Determine new row order based on
% row norms and reorder accordingly. Negate those rows in which the
% accumulated sum is negative.
if reorder
fprintf('Reordering rows...');
[fnorm index] = sort(sum(A'.^2));
Q = Q .* ((2 * (sum(A') > 0) - 1)' * ones(1, size(Q,2)));
A = A .* ((2 * (sum(A') > 0) - 1)' * ones(1, size(A,2)));
Q = Q(fliplr(index),:);
A = A(fliplr(index),:);
fprintf('\n');
else
fprintf('Not reordering rows.\n');
end
B=A;
|
github
|
lcnbeapp/beapp-master
|
matcorr.m
|
.m
|
beapp-master/Packages/eeglab14_1_2b/functions/miscfunc/matcorr.m
| 5,853 |
utf_8
|
d0e3089eda2df7656eb20c1f476894f8
|
% matcorr() - Find matching rows in two matrices and their corrs.
% Uses the Hungarian (default), VAM, or maxcorr assignment methods.
% (Follow with matperm() to permute and sign x -> y).
%
% Usage: >> [corr,indx,indy,corrs] = matcorr(x,y,rmmean,method,weighting);
%
% Inputs:
% x = first input matrix
% y = matrix with same number of columns as x
%
% Optional inputs:
% rmmean = When present and non-zero, remove row means prior to correlation
% {default: 0}
% method = Method used to find assignments.
% 0= Hungarian Method - maximize sum of abs corrs {default: 2}
% 1= Vogel's Assignment Method -find pairs in order of max contrast
% 2= Max Abs Corr Method - find pairs in order of max abs corr
% Note that the methods 0 and 1 require matrices to be square.
% weighting = An optional weighting matrix size(weighting) = size(corrs) that
% weights the corrs matrix before pair assignment {def: 0/[]->ones()}
% Outputs:
% corr = a column vector of correlation coefficients between
% best-correlating rows of matrice x and y
% indx = a column vector containing the index of the maximum
% abs-correlated x row in descending order of abs corr
% (no duplications)
% indy = a column vector containing the index of the maximum
% abs-correlated row of y in descending order of abs corr
% (no duplications)
% corrs = an optional square matrix of row-correlation coefficients
% between matrices x and y
%
% Note: outputs are sorted by abs(corr)
%
% Authors: Scott Makeig & Sigurd Enghoff, SCCN/INC/UCSD, La Jolla, 11-30-96
% Copyright (C) 11-30-96 Scott Makeig, SCCN/INC/UCSD, [email protected]
%
% This program is free software; you can redistribute it and/or modify
% it under the terms of the GNU General Public License as published by
% the Free Software Foundation; either version 2 of the License, or
% (at your option) any later version.
%
% This program is distributed in the hope that it will be useful,
% but WITHOUT ANY WARRANTY; without even the implied warranty of
% MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
% GNU General Public License for more details.
%
% You should have received a copy of the GNU General Public License
% along with this program; if not, write to the Free Software
% Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
% 04-22-99 Re-written using VAM by Sigurd Enghoff, CNL/Salk
% 04-30-99 Added revision of algorthm loop by SE -sm
% 05-25-99 Added Hungarian method assignment by SE
% 06-15-99 Maximum correlation method reinstated by SE
% 08-02-99 Made order of outpus match help msg -sm
% 02-16-00 Fixed order of corr output under VAM added method explanations,
% and returned corr signs in abs max method -sm
% 01-25-02 reformated help & license, added links -ad
% Uses function hungarian.m
function [corr,indx,indy,corrs] = matcorr(x,y,rmmean,method,weighting)
%
if nargin < 2 | nargin > 5
help matcorr
return
end
if nargin < 4
method = 2; % default: Max Abs Corr - select successive best abs(corr) pairs
end
[m,n] = size(x);
[p,q] = size(y);
m = min(m,p);
if m~=n | p~=q
if nargin>3 & method~=2
fprintf('matcorr(): Matrices are not square: using max abs corr method (2).\n');
end
method = 2; % Can accept non-square matrices
end
if n~=q
error('Rows in the two input matrices must be the same length.');
end
if nargin < 3 | isempty(rmmean)
rmmean = 0;
end
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
if rmmean
x = x - mean(x')'*ones(1,n); % optionally remove means
y = y - mean(y')'*ones(1,n);
end
dx = sum(x'.^2);
dy = sum(y'.^2);
dx(find(dx==0)) = 1;
dy(find(dy==0)) = 1;
corrs = x*y'./sqrt(dx'*dy);
if nargin > 4 && ~isempty(weighting) && norm(weighting) > 0,
if any(size(corrs) ~= size(weighting))
fprintf('matcorr(): weighting matrix size must match that of corrs\n.')
return
else
corrs = corrs.*weighting;
end
end
cc = abs(corrs);
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
switch method
case 0
ass = hungarian(-cc); % Performs Hungarian algorithm matching
idx1 = sub2ind(size(cc),ass,1:m);
[dummy idx2] = sort(-cc(idx1));
corr = corrs(idx1);
corr = corr(idx2)';
indy = [1:m]';
indx = ass(idx2)';
indy = indy(idx2);
case 1 % Implements the VAM assignment method
indx = zeros(m,1);
indy = zeros(m,1);
corr = zeros(m,1);
for i=1:m,
[sx ix] = sort(cc); % Looks for maximum salience along a row/column
[sy iy] = sort(cc'); % rather than maximum correlation.
[sxx ixx] = max(sx(end,:)-sx(end-1,:));
[syy iyy] = max(sy(end,:)-sy(end-1,:));
if sxx == syy
if sxx == 0 & syy == 0
[sxx ixx] = max((sx(end,:)-sx(end-1,:)) .* sx(end,:));
[syy iyy] = max((sy(end,:)-sy(end-1,:)) .* sy(end,:));
else
sxx = sx(end,ixx); % takes care of identical vectors
syy = sy(end,iyy); % and zero vectors
end
end
if sxx > syy
indx(i) = ix(end,ixx);
indy(i) = ixx;
else
indx(i) = iyy;
indy(i) = iy(end,iyy);
end
cc(indx(i),:) = -1;
cc(:,indy(i)) = -1;
end
i = sub2ind(size(corrs),indx,indy);
corr = corrs(i);
[tmp j] = sort(-abs(corr)); % re-sort by abs(correlation)
corr = corr(j);
indx = indx(j);
indy = indy(j);
case 2 % match successive max(abs(corr)) pairs
indx = zeros(size(cc,1),1);
indy = zeros(size(cc,1),1);
corr = zeros(size(cc,1),1);
for i = 1:size(cc,1)
[tmp j] = max(cc(:));
% [corr(i) j] = max(cc(:));
[indx(i) indy(i)] = ind2sub(size(cc),j);
corr(i) = corrs(indx(i),indy(i));
cc(indx(i),:) = -1; % remove from contention
cc(:,indy(i)) = -1;
end
otherwise
error('Unknown method');
end
|
github
|
lcnbeapp/beapp-master
|
seemovie.m
|
.m
|
beapp-master/Packages/eeglab14_1_2b/functions/miscfunc/seemovie.m
| 2,366 |
utf_8
|
e435662809faced2ec20372ec434b114
|
% seemovie() - see an EEG movie produced by eegmovie()
%
% Usage: >> seemovie(Movie,ntimes,Colormap)
%
% Inputs:
% Movie = Movie matrix returned by eegmovie()
% ntimes = Number of times to display {0 -> -10}
% If ntimes < 0, movie will play forward|backward
% Colormap = Color map returned by eegmovie() {0 -> default}
%
% Author: Scott Makeig & Colin Humphries, CNL / Salk Institute, 6/3/97
%
% See also: eegmovie()
% Copyright (C) 6/3/97 Scott Makeig & Colin Humphries, CNL / Salk Institute, La Jolla CA
%
% This program is free software; you can redistribute it and/or modify
% it under the terms of the GNU General Public License as published by
% the Free Software Foundation; either version 2 of the License, or
% (at your option) any later version.
%
% This program is distributed in the hope that it will be useful,
% but WITHOUT ANY WARRANTY; without even the implied warranty of
% MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
% GNU General Public License for more details.
%
% You should have received a copy of the GNU General Public License
% along with this program; if not, write to the Free Software
% Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
% 10-31-97 changed test for user-defined colormap -ch & sm
% 1-8-98 added '\n' at end, improved help msg -sm
% 01-25-02 reformated help, added link -ad
function seemovie(Movie,ntimes,Colormap)
fps = 10; % projetion speed (requested frames per second)
if nargin<1
help seemovie
return
end
if nargin<3
Colormap = 0;
end
if nargin<2
ntimes = -10; % default to playing foward|backward endlessly
end
if ntimes == 0
ntimes = -10;
end
clf
axes('Position',[0 0 1 1]);
if size(Colormap,2) == 3 % if colormap user-defined
colormap(Colormap)
else
colormap([jet(64);0 0 0]); % set up the default topoplot color map
end
if ntimes > 0,
fprintf('Movie will play slowly once, then %d times faster.\n',ntimes);
else
fprintf('Movie will play slowly once, then %d times faster forwards and backwards.\n',-ntimes);
end
if abs(ntimes) > 7
fprintf(' Close figure to abort: ');
end
%%%%%%%%%%%%%%%%%%%%%%%% Show the movie %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
movie(Movie,ntimes,fps);
%%%%%%%%%%%%%%%%%%%%%%%% The End %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
if abs(ntimes) > 7
fprintf('\n');
end
|
github
|
lcnbeapp/beapp-master
|
abspeak.m
|
.m
|
beapp-master/Packages/eeglab14_1_2b/functions/miscfunc/abspeak.m
| 2,026 |
utf_8
|
2258e70a7386f00bc23dd3f8620aa48b
|
% abspeak() - find peak amps/latencies in each row of a single-epoch data matrix
%
% Usage:
% >> [amps,frames,signs] = abspeak(data);
% >> [amps,frames,signs] = abspeak(data,frames);
%
% Inputs:
% data - single-epoch data matrix
% frames - frames per epoch in data {default|0 -> whole data}
%
% Outputs:
% amps - amplitude array
% frames - array of indexes
% sign - sign array
%
% Author: Scott Makeig, SCCN/INC/UCSD, La Jolla, 1998
% Copyright (C) 1998 Scott Makeig, SCCN/INC/UCSD, [email protected]
%
% This program is free software; you can redistribute it and/or modify
% it under the terms of the GNU General Public License as published by
% the Free Software Foundation; either version 2 of the License, or
% (at your option) any later version.
%
% This program is distributed in the hope that it will be useful,
% but WITHOUT ANY WARRANTY; without even the implied warranty of
% MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
% GNU General Public License for more details.
%
% You should have received a copy of the GNU General Public License
% along with this program; if not, write to the Free Software
% Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
% 3-9-98 added frames arg -sm
% 01-25-02 reformated help & license -ad
function [amps,frames,signs]= abspeak(data,fepoch);
if nargin < 1
help abspeak
return
end
[chans,ftot] = size(data);
if nargin < 2
fepoch = 0;
end
if fepoch == 0
fepoch = ftot;
end
epochs = floor(ftot/fepoch);
if fepoch*epochs ~= ftot
fprintf('abspeak(): frames arg does not divide data length.\n')
return
end
amps = zeros(chans,epochs);
frames = zeros(chans,epochs);
signs = zeros(chans,epochs);
for e=1:epochs
for c=1:chans
dat = abs(matsel(data,fepoch,0,c,e))';
[sdat,si] = sort(dat);
amps(c,e) = dat(si(fepoch)); % abs value at peak
frames(c,e) = si(fepoch); % peak frame
signs(c,e) = sign(data(c,frames(c,e))); % sign at peak
end
end
|
github
|
lcnbeapp/beapp-master
|
eegplotgold.m
|
.m
|
beapp-master/Packages/eeglab14_1_2b/functions/miscfunc/eegplotgold.m
| 12,958 |
utf_8
|
d4c4acff7303a59ede1e32c3911c3af7
|
% eegplotgold() - display EEG data in a clinical format
%
% Usage:
% >> eegplotgold('dataname', samplerate, 'chanfile', 'title', yscaling, range)
%
% Inputs:
% 'dataname' - quoted name of a desktop global variable (see Ex. below)
% samplerate - EEG sampling rate in Hz (0 -> default 256 Hz)
% 'chanfile' - file of channel info in topoplot() style
% (0 -> channel numbers)
% 'title' - plot title string (0 -> 'eegplotgold()')
% yscaling - initial y scaling factor (0 - default is 300)
% range - how many seconds to display in window (0 -> 10)
%
% Note: this version of eegplotgold() reguires that your data matrix
% be defined as a global variable before running this routine.
%
% Example: >> global dataname
% >> eegplotgold('dataname')
%
% Author: Colin Humphries, CNL, Salk Institute, La Jolla, 3/97
%
% See also: eegplot(), eegplotold(), eegplotsold()
% Copyright (C) Colin Humphries, CNL, Salk Institute 3/97 from eegplotold()
%
% This program is free software; you can redistribute it and/or modify
% it under the terms of the GNU General Public License as published by
% the Free Software Foundation; either version 2 of the License, or
% (at your option) any later version.
%
% This program is distributed in the hope that it will be useful,
% but WITHOUT ANY WARRANTY; without even the implied warranty of
% MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
% GNU General Public License for more details.
%
% You should have received a copy of the GNU General Public License
% along with this program; if not, write to the Free Software
% Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
% 4-4-97 shortened name to eegplotgold() -sm
% 5-20-97 added read of icadefs.m for MAXEEGPLOTCHANS -sm
% 8-10-97 Clarified chanfile type -sm
% 01-25-02 reformated help & license, added links -ad
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
function y = eegplotold(dataname, samplerate, channamefile, titleval, yscaling, range)
eval (['global ',dataname])
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
% Define defaults
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
icadefs;
% set initial spacing
eval(['DEFAULT_SPACING = max(max(',dataname,''')-min(',dataname,'''));'])
% spacing_var/20 = microvolts/millimeter with 21 channels
% for n channels: 21/n * spacing_var/20 = microvolts/mm
% for clinical data.
DEFAULT_SAMPLERATE = 256; % default rate in Hz.
DEFAULT_PLOTTIME = 10; % default 10 second window
DEFAULT_TITLE = 'eegplotgold()';
errorcode=0; % initialize error indicator
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
% Allow for different numbers of arguments
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
if nargin < 6
PLOT_TIME = DEFAULT_PLOTTIME;
else
PLOT_TIME = range;
end
if nargin < 5
spacing_var = DEFAULT_SPACING;
else
spacing_var = yscaling;
end
if spacing_var == 0
spacing_var = DEFAULT_SPACING;
end
if nargin < 4
titleval = DEFAULT_TITLE;
end
if titleval == 0
titleval = DEFAULT_TITLE;
end
if nargin < 3
channamefile = 0;
end
if nargin < 2
samplerate = DEFAULT_SAMPLERATE;
end
if samplerate == 0,
samplerate = DEFAULT_SAMPLERATE;
end;
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
% Define internal variables
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
SAMPLE_RATE = samplerate;
time = 0;
eval(['[chans,frames] = size(',dataname,');']) %size of data matrix
maxtime = frames / samplerate; %size of matrix in seconds
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
% Read the channel names
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
if channamefile ~=0, % read file of channel names
chid = fopen(channamefile,'r');
if chid <3,
fprintf('plotdata: cannot open file %s.\n',channamefile);
errorcode=2;
channamefile = 0;
else
fprintf('Chan info file %s opened\n',channamefile);
end;
icadefs; % read MAXEEGPLOTCHANS from icadefs.m
if errorcode==0,
channames = fscanf(chid,'%s',[6 MAXEEGPLOTCHANS]);
channames = channames';
[r c] = size(channames);
for i=1:r
for j=1:c
if channames(i,j)=='.',
channames(i,j)=' ';
end;
end;
end;
% fprintf('%d channel names read from file.\n',r);
if (r>chans)
fprintf('Using first %d names.\n',chans);
channames = channames(1:chans,:);
end;
if (r<chans)
fprintf('Only %d channel names read.\n',r);
end;
end;
end
if channamefile ==0, % plot channel numbers
channames = [];
for c=1:chans
if c<10,
numeric = [' ' int2str(c)]; % four-character fields
else
numeric = [' ' int2str(c)];
end
channames = [channames;numeric];
end;
end; % setting channames
channames = str2mat(channames, ' '); % add padding element to Y labels
Xlab = num2str(time);
for j = 1:1:PLOT_TIME
Q = num2str(time+j);
Xlab = str2mat(Xlab, Q);
end
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
% Set Graph Characteristics
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
figure; % plot a new figure
fighandle = gcf;
orient landscape % choose landscape printer mode
hold on;
set(gcf,'NumberTitle','off')
if VERS >= 8.04
set(gcf,'Name',['EEGPLOTOLD #',num2str(fighandle.Number)]);
else
set(gcf,'Name',['EEGPLOTOLD #',num2str(gcf)]);
end
set (gca, 'xgrid', 'on') %Xaxis gridlines only
set (gca, 'GridLineStyle','-') %Solid grid lines
set (gca, 'XTickLabels', Xlab) %Use Xlab for tick labels
set (gca, 'Box', 'on')
set (gca, 'XTick', time*samplerate:1.0*samplerate:PLOT_TIME*samplerate)
set (gca, 'Ytick', 0:spacing_var:chans*spacing_var) % ytickspacing on channels
set (gca, 'TickLength', [0.001 0.001])
title(titleval) % title is titleval
axis([0 PLOT_TIME*samplerate 0 (chans+1)*spacing_var]); % set axis values
set (gca, 'YTickLabels', flipud(channames)) % write channel names
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
% Plot the selected EEG data epoch
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
for i = 1:chans
if (maxtime-time>PLOT_TIME)
eval(['F = ',dataname,'(chans-i+1,(time*samplerate)+1:(time+PLOT_TIME*samplerate));'])
else
eval(['F = ',dataname,'(chans-i+1,(time*samplerate)+1:(maxtime*samplerate));'])
end
F = F - mean(F) + i*spacing_var;
plot (F,'clipping','off')
end
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
% Plot Scaling I
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
line([(PLOT_TIME+.3)*samplerate,(PLOT_TIME+.3)*samplerate],[1.5*spacing_var 2.5*spacing_var],'clipping','off','color','w')
line([(PLOT_TIME+.3)*samplerate-10,(PLOT_TIME+.3)*samplerate+10],[2.5*spacing_var,2.5*spacing_var],'clipping','off','color','w')
line([(PLOT_TIME+.3)*samplerate-10,(PLOT_TIME+.3)*samplerate+10],[1.5*spacing_var,1.5*spacing_var],'clipping','off','color','w')
text((PLOT_TIME+.5)*samplerate,2*spacing_var,num2str(round(spacing_var)),'clipping','off')
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
% User Control Routines
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
slider_position = [.125 .030 .3 .024]; % position of user-controlled slider
edit_position = [.65 .025 .1 .05]; % position of edit box
slider_position2 = [.8 .03 .1 .024];
b1_position = [.175 .022 .09 .047];
b2_position = [.29 .022 .09 .047];
b3_position = [.125 .022 .045 .047];
b4_position = [.385 .022 .045 .047];
Max_Space = 1;
Min_Space = DEFAULT_SPACING*2;
% User_Data_Mat = [data;zeros(1,length(data))];
axhandle = gca;
User_Data_Mat(1) = samplerate;
User_Data_Mat(2) = PLOT_TIME;
User_Data_Mat(3) = spacing_var;
User_Data_Mat(4) = time;
User_Data_Mat(5) = maxtime;
User_Data_Mat(6) = axhandle;
User_Data_Mat(7) = 1; % color
User_Data_Mat(8) = frames;
User_Data_Mat(9) = chans;
User_Data_Mat(12) = 1;
tstring1 = 'data1973 = get(gcf,''UserData'');';
tstring2 = 'set(gcf,''UserData'',data1973);';
tstring3 = 'eegdrawgv(gcf);';
TIMESTRING = [tstring1,'if (data1973(4)-data1973(2))<0;','data1973(4) = 0;','else;','data1973(4) = data1973(4) - data1973(2);','end;',tstring2,tstring3,'clear data1973'];
hb = uicontrol('Style','PushButton','Units','Normalized','position',b1_position,'String','PREV','Callback',TIMESTRING);
TIMESTRING = [tstring1,'if (data1973(4)+data1973(2))>=data1973(5);','data1973(4)=data1973(4);','else;','data1973(4) = data1973(4) + data1973(2);','end;',tstring2,tstring3,'clear data1973'];
hf = uicontrol('Style','PushButton','Units','Normalized','position',b2_position,'String','NEXT','Callback',TIMESTRING);
TIMESTRING = [tstring1,'if (data1973(4)-1)<0;','data1973(4) = 0;','else;','data1973(4) = data1973(4) - 1;','end;',tstring2,tstring3,'clear data1973'];
hbos = uicontrol('Style','PushButton','Units','Normalized','position',b3_position,'String','<<','Callback',TIMESTRING);
TIMESTRING = [tstring1,'if (data1973(4)+1)>=data1973(5);','data1973(4)=data1973(4);','else;','data1973(4) = data1973(4) + 1;','end;',tstring2,tstring3,'clear data1973'];
hfos = uicontrol('Style','PushButton','Units','Normalized','position',b4_position,'String','>>','Callback',TIMESTRING);
TIMESTRING = [tstring1,'time1973 = get(gco,''string'');','time1973 = str2num(time1973);','data1973(4) = time1973;',tstring2,tstring3,'clear time1973 data1973'];
w=uicontrol('style','edit','units','normalized','HorizontalAlignment','left','position',edit_position,'UserData',axhandle,'callback',TIMESTRING);
TIMESTRING = [tstring1,'data1973(3) = get(gco,''value'');',tstring2,tstring3,'clear time1973 data1973'];
u=uicontrol('style','slider','units','normalized','position',slider_position2,'Max',Max_Space,'Min',Min_Space,'value',spacing_var,'UserData',axhandle,'callback',TIMESTRING);
%%%%%%%%%%%%%%%%%%%%%%%%%
%Set up ui menus
%%%%%%%%%%%%%%%%%%%%%%%%%
%Window menu:
TIMESTRING = ['fighand1973 = gcf;','delete(fighand1973);','clear fighand1973;'];
fm1 = uimenu('Label','Window');
fm2 = uimenu(fm1,'Label','Close ','UserData',fighandle,'Callback',TIMESTRING);
%Display menu:
TIMESTRING = [tstring1,'out1973 = gettext(''Input new windowlength(sec).'');','if isempty(out1973);','out1973 = 0;','else;','data1973(2) = str2num(out1973);',tstring2,tstring3,'end;','clear data1973 out1973'];
dm1 = uimenu('Label','Display');
dm2 = uimenu(dm1,'Label',' Window Length','Interruptible','on','Callback',TIMESTRING);
dm3 = uimenu(dm1,'Label',' Color');
TIMESTRING = [tstring1,'data1973(7) = 1;',tstring2,tstring3,'clear data1973;'];
dm4 = uimenu(dm3,'Label','Yellow ','UserData',axhandle,'Interruptible','on','Callback',TIMESTRING);
TIMESTRING = [tstring1,'data1973(7) = 2;',tstring2,tstring3,'clear data1973;'];
dm5 = uimenu(dm3,'Label','White ','UserData',axhandle,'Interruptible','on','Callback',TIMESTRING);
TIMESTRING = ['label1973 = gettext(''Enter new title.'');','if isempty(label1973);','label1973 = 0;','else;','title(label1973);','end;','clear label1973;'];
dm6 = uimenu(dm1,'Label','Title ','Interruptible','on','Callback',TIMESTRING);
TIMESTRING = [tstring1,'Check1973 = get(data1973(10),''checked'');','if (Check1973(1:2) == ''on'');','set(data1973(10),''Checked'',''off'');','set(data1973(6),''XGrid'',''off'');','else;','set(data1973(10),''Checked'',''on'');','set(data1973(6),''XGrid'',''on'');','end;','clear data1973 Check1973;'];
dm7 = uimenu(dm1,'Label','Grid','Checked','on','Callback',TIMESTRING);
User_Data_Mat(10) = dm7;
TIMESTRING = [tstring1,'Check1973 = get(data1973(11),''checked'');','if (Check1973(1:2) == ''on'');','set(data1973(11),''Checked'',''off'');','data1973(12)= 0;','else;','set(data1973(11),''Checked'',''on'');','data1973(12) = 1;','end;',tstring2,tstring3,'clear data1973 Check1973;'];
dm8 = uimenu(dm1,'Label','Scaling I','Checked','on','Callback',TIMESTRING);
User_Data_Mat(11) = dm8;
%Settings menu:
sm1 = uimenu('Label','Settings');
TIMESTRING = [tstring1,'Srate1973 = gettext(''Enter new samplerate'');','if isempty(Srate1973);','Srate1973 = 0;','else;','data1973(1) = str2num(Srate1973);','data1973(5) = data1973(8)/data1973(1);','data1973(4) = 0;',tstring2,tstring3,'end;','clear Srate1973 data1973'];
sm2 = uimenu(sm1,'Label','Samplerate','Interruptible','on','Callback',TIMESTRING);
%Electrodes menu:
em1 = uimenu('Label','Electrodes');
TIMESTRING = [tstring1,'ChanNamefile1973 = gettext(''Enter Electrode file to load.'');','if isempty(ChanNamefile1973);','ChanNamefile1973=0;','else;','ChanNames1973 = loadelec(ChanNamefile1973);','set(data1973(6),''YTickLabels'',flipud(ChanNames1973));','end;','clear data1973 ChanNamefile1973 ChanNames1973'];
em2 = uimenu(em1,'Label','Load Electrode File ','Interruptible','on','Callback',TIMESTRING);
TIMESTRING = [tstring1,'ChanNames1973 = makeelec(data1973(9));','if isempty(ChanNames1973);','ChanNames1973=0;','else;','set(data1973(6),''YTickLabels'',flipud(ChanNames1973));','end;','clear data1973 ChanNames1973'];
em3 = uimenu(em1,'Label','Make Electrode File ','Interruptible','on','Callback',TIMESTRING);
set(axhandle,'UserData',dataname)
set(fighandle,'UserData',User_Data_Mat)
|
github
|
lcnbeapp/beapp-master
|
makehelpfiles.m
|
.m
|
beapp-master/Packages/eeglab14_1_2b/functions/miscfunc/makehelpfiles.m
| 4,318 |
utf_8
|
8a0860d1b106b9754aedcaed8ace4442
|
% makehelpfiles() - generate function help pages
%
% Usage:
% >> makehelpfiles(list);
%
% Input:
% 'folder' - [string] folder name to process
% 'outputfile' - [string] file in which to write the help
% 'title' - [string] title for the help
%
% Author: Arnaud Delorme, UCSD, 2013
%
% Example: Generate EEGLAB help menus for adminfunc folder
% makehelpfiles('folder', 'adminfunc' ,'title', 'Admin functions', 'outputfile','adminfunc/eeg_helpadmin.m' );
% makehelpfiles('folder', 'guifunc' ,'title', 'Graphic interface builder functions', 'outputfile','adminfunc/eeg_helpgui.m' );
% makehelpfiles('folder', 'miscfunc' ,'title', 'Miscelaneous functions not used by EEGLAB graphic interface', 'outputfile','adminfunc/eeg_helpmisc.m' );
% makehelpfiles('folder', 'popfunc' ,'title', 'EEGLAB graphic interface functions', 'outputfile','adminfunc/eeg_helppop.m' );
% makehelpfiles('folder', 'sigprocfunc' ,'title', 'EEGLAB signal processing functions', 'outputfile','adminfunc/eeg_helpsigproc.m' );
% makehelpfiles('folder', 'statistics' ,'title', 'EEGLAB statistics functions', 'outputfile','adminfunc/eeg_helpstatistics.m' );
% makehelpfiles('folder', 'studyfunc' ,'title', 'EEGLAB group processing (STUDY) functions', 'outputfile','adminfunc/eeg_helpstudy.m' );
% makehelpfiles('folder', 'timefreqfunc','title', 'EEGLAB time-frequency functions', 'outputfile','adminfunc/eeg_helptimefreq.m' );
% Copyright (C) Arnaud Delorme, CNL / Salk Institute, 2002
%
% This program is free software; you can redistribute it and/or modify
% it under the terms of the GNU General Public License as published by
% the Free Software Foundation; either version 2 of the License, or
% (at your option) any later version.
%
% This program is distributed in the hope that it will be useful,
% but WITHOUT ANY WARRANTY; without even the implied warranty of
% MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
% GNU General Public License for more details.
%
% You should have received a copy of the GNU General Public License
% along with this program; if not, write to the Free Software
% Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
function makehelpfiles( varargin );
if nargin < 1
help makehelpfiles;
return;
end;
opt = finputcheck( varargin, { 'folder' 'string' { } '';
'outputfile' 'string' { } '';
'title' 'string' { } '' }, 'makehelpfiles');
if isstr(opt), error(opt); end;
if isempty(opt.folder), error('You need to specify a folder'); end;
if isempty(opt.outputfile), error('You need to specify an output file'); end;
fo = fopen( opt.outputfile, 'w');
if ~isempty(opt.title)
fprintf(fo, '%%%s (%s folder):\n', opt.title, opt.folder);
else fprintf(fo, '%% *Content of %s folder:*\n', opt.folder);
end;
dirContent = dir(fullfile(opt.folder, '*.m'));
dirContent = { dirContent.name };
for iFile = 1:length(dirContent)
fileName = dirContent{iFile};
fidTmp = fopen(fullfile(opt.folder, fileName), 'r');
firstLine = fgetl(fidTmp);
% get help from the first line
if isempty(firstLine) || firstLine(1) ~= '%'
firstLine = fgetl(fidTmp);
end;
fclose(fidTmp);
if isempty(firstLine) || firstLine(1) ~= '%'
firstLineText = 'No help information';
else
indexMinus = find(firstLine == '-');
if ~isempty(indexMinus)
firstLineText = deblank(firstLine(indexMinus(1)+1:end));
else firstLineText = deblank(firstLine(2:end));
end;
if isempty(firstLineText), firstLineText = 'No help information'; end;
if firstLineText(1) == ' ', firstLineText(1) = []; end;
if firstLineText(1) == ' ', firstLineText(1) = []; end;
if firstLineText(1) == ' ', firstLineText(1) = []; end;
firstLineText(1) = upper(firstLineText(1));
if firstLineText(end) ~= '.', firstLineText = [ firstLineText '...' ]; end;
end;
refFunction = sprintf('<a href="matlab:helpwin %s">%s</a>', fileName(1:end-2), fileName(1:end-2));
fprintf(fo, '%% %-*s - %s\n', 50+length(fileName(1:end-2)), refFunction, firstLineText);
end;
fclose( fo );
|
github
|
lcnbeapp/beapp-master
|
gauss2d.m
|
.m
|
beapp-master/Packages/eeglab14_1_2b/functions/miscfunc/gauss2d.m
| 2,336 |
utf_8
|
eb62296c929c63d59753f67dac83f70d
|
% gauss2d() - generate a 2-dimensional gaussian matrix
%
% Usage:
% >> [ gaussmatrix ] = gauss2d( rows, columns, ...
% sigmaR, sigmaC, peakR, peakC, mask)
%
% Example:
% >> imagesc(gauss2d(50, 50)); % image a size (50,50) 2-D gaussian matrix
%
% Inputs:
% rows - number of rows in matrix
% columns - number of columns in matrix
% sigmaR - width of standard deviation in rows (default: rows/5)
% sigmaC - width of standard deviation in columns (default: columns/5)
% peakR - location of the peak in each row (default: rows/2)
% peakC - location of the peak in each column (default: columns/2)
% mask - (0->1) portion of the matrix to mask with zeros (default: 0)
%
% Ouput:
% gaussmatrix - 2-D gaussian matrix
%
% Author: Arnaud Delorme, CNL/Salk Institute, 2001
% Copyright (C) 2001 Arnaud Delorme, Salk Institute, [email protected]
%
% This program is free software; you can redistribute it and/or modify
% it under the terms of the GNU General Public License as published by
% the Free Software Foundation; either version 2 of the License, or
% (at your option) any later version.
%
% This program is distributed in the hope that it will be useful,
% but WITHOUT ANY WARRANTY; without even the implied warranty of
% MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
% GNU General Public License for more details.
%
% You should have received a copy of the GNU General Public License
% along with this program; if not, write to the Free Software
% Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
function mat = gauss2d( sizeX, sizeY, sigmaX, sigmaY, meanX, meanY, cut);
if nargin < 2
help gauss2d
return;
end;
if nargin < 3
sigmaX = sizeX/5;
end;
if nargin < 4
sigmaY = sizeY/5;
end;
if nargin < 5
meanX = (sizeX+1)/2;
end;
if nargin < 6
meanY = (sizeY+1)/2;
end;
if nargin < 7
cut = 0;
end;
X = linspace(1, sizeX, sizeX)'* ones(1,sizeY);
Y = ones(1,sizeX)' * linspace(1, sizeY, sizeY);
%[-sizeX/2:sizeX/2]'*ones(1,sizeX+1);
%Y = ones(1,sizeY+1)' *[-sizeY/2:sizeY/2];
mat = exp(-0.5*( ((X-meanX)/sigmaX).*((X-meanX)/sigmaX)...
+((Y-meanY)/sigmaY).*((Y-meanY)/sigmaY)))...
/((sigmaX*sigmaY)^(0.5)*pi);
if cut > 0
maximun = max(max(mat))*cut;
I = find(mat < maximun);
mat(I) = 0;
end;
return;
|
github
|
lcnbeapp/beapp-master
|
logimagesc.m
|
.m
|
beapp-master/Packages/eeglab14_1_2b/functions/miscfunc/logimagesc.m
| 3,574 |
utf_8
|
343cd485721e4ef9c77204704ae0180c
|
% logimagesc() - make an imagesc(0) plot with log y-axis values (ala semilogy())
%
% Usage: >> [logfreqs,dataout] = logimagesc(times,freqs,data);
%
% Input:
% times = vector of x-axis values
% freqs = vector of y-axis values
% data = matrix of size (freqs,times)
%
% Optional Input:
% plot = ['on'|'off'] plot image or return output (default 'on').
%
% Note: Entering text() onto the image requires specifying (x,log(y)).
% Author: Scott Makeig, SCCN/INC/UCSD, La Jolla, 4/2000
% Copyright (C) 4/2000 Scott Makeig, SCCN/INC/UCSD, [email protected]
%
% This program is free software; you can redistribute it and/or modify
% it under the terms of the GNU General Public License as published by
% the Free Software Foundation; either version 2 of the License, or
% (at your option) any later version.
%
% This program is distributed in the hope that it will be useful,
% but WITHOUT ANY WARRANTY; without even the implied warranty of
% MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
% GNU General Public License for more details.
%
% You should have received a copy of the GNU General Public License
% along with this program; if not, write to the Free Software
% Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
% 08-07-00 made ydir normal -sm
% 01-25-02 reformated help & license -ad
function [lgfreqs,datout, h, yt, yl] = logimagesc(times,freqs,data,varargin)
if nargin < 1
help logimagesc;
return
end;
if size(data,1) ~= length(freqs)
fprintf('logfreq(): data matrix must have %d rows!\n',length(freqs));
datout = data;
return
end
if size(data,2) ~= length(times)
fprintf('logfreq(): data matrix must have %d columns!\n',length(times));
datout = data;
return
end
if min(freqs)<= 0
fprintf('logfreq(): frequencies must be > 0!\n');
datout = data;
return
end
try, icadefs; catch, warning('Using MATLAB default colormap'); end
lfreqs = log(freqs);
lgfreqs = linspace(lfreqs(1),lfreqs(end),length(lfreqs));
lgfreqs = lgfreqs(:);
lfreqs = lfreqs(:);
[mesht meshf] = meshgrid(times,lfreqs);
try
datout = griddata(mesht,meshf,double(data),times,lgfreqs);
catch
fprintf('error in logimagesc.m calling griddata.m, trying v4 method.');
datout = griddata(mesht,meshf,data,times,lgfreqs,'v4');
end
datout(find(isnan(datout(:)))) = 0;
if ~isempty(varargin)
plot = varargin{2};
else
plot = 'on';
end
if strcmp(plot, 'on')
imagesc(times,freqs,data);
try colormap(DEFAULT_COLORMAP); catch, end;
nt = ceil(min(freqs)); % new tick - round up min y to int
ht = floor(max(freqs)); % high freq - round down
yt=get(gca,'ytick');
yl=get(gca,'yticklabel');
h=imagesc(times,lgfreqs,datout); % plot the image
set(gca,'ydir','normal')
i = 0; yt = [];
yl = cell(1,100);
tickscale = 1.618; % log scaling power for frequency ticks
while (nt*tickscale^i < ht )
yt = [yt log(round(nt*tickscale^i))];
yl{i+1}=int2str(round(nt*tickscale^i));
i=i+1;
end
if ht/(nt*tickscale^(i-1)) > 1.35
yt = [yt log(ht)];
yl{i+1} = ht;
else
i=i-1;
end
yl = {yl{1:i+1}};
set(gca,'ytick',yt);
set(gca,'yticklabel',yl);
% if nt > min(yt),
% set(gca,'ytick',log([nt yt]));
% set(gca,'yticklabel',{int2str(nt) yl});
% else
% set(gca,'ytick',log([yt]));
% set(gca,'yticklabel',{yl});
% end
end
|
github
|
lcnbeapp/beapp-master
|
eucl.m
|
.m
|
beapp-master/Packages/eeglab14_1_2b/functions/miscfunc/eucl.m
| 4,052 |
utf_8
|
d05e24c412ee9044fefe12a801a4f9aa
|
% EUCL: Calculates the euclidean distances among a set of points, or between a
% reference point and a set of points, or among all possible pairs of two
% sets of points, in P dimensions. Returns a single distance for two points.
%
% Syntax: dists = eucl(crds1,crds2)
%
% crds1 = [N1 x P] matrix of point coordinates. If N=1, it is taken to
% be the reference point.
% crds2 = [N2 x P] matrix of point coordinates. If N=1, it is taken to
% be the reference point.
% -----------------------------------------------------------------------
% dists = [N1 x N1] symmetric matrix of pairwise distances (if only crds1
% is specified);
% [N1 x 1] col vector of euclidean distances (if crds1 & ref
% are specified);
% [1 x N2] row vector of euclidean distances (if ref & crds2
% are specified);
% [N1 x N2] rectangular matrix of pairwise distances (if crds1
% & crds2 are specified);
% [1 x 1] scalar (if crds1 is a [2 x P] matrix or ref1 & ref2
% are specified);
%
% RE Strauss, 5/4/94
% 10/28/95 - output row (rather than column) vector for the (reference
% point)-(set of points) case; still outputs column vector for the
% (set of points)-(reference point) case.
% 10/30/95 - for double for-loops, put one matrix-col access in outer loop
% to increase speed.
% 10/12/96 - vectorize inner loop to increase speed.
% 6/12/98 - allow for P=1.
% 11/11/03 - initialize dists to NaN for error return.
function dists = eucl(crds1,crds2)
if nargin == 0, help eucl; return; end;
dists = NaN;
if (nargin < 2) % If only crds1 provided,
[N,P] = size(crds1);
if (N<2)
error(' EUCL: need at least two points');
end;
crds1 = crds1'; % Transpose crds
dists = zeros(N,N); % Calculate pairwise distances
for i = 1:N-1
c1 = crds1(:,i) * ones(1,N-i);
if (P>1)
d = sqrt(sum((c1-crds1(:,(i+1:N))).^2));
else
d = abs(c1-crds1(:,(i+1:N)));
end;
dists(i,(i+1:N)) = d;
dists((i+1:N),i) = d';
end;
if (N==2) % Single distance for two points
dists = dists(1,2);
end;
else % If crds1 & crds2 provided,
[N1,P1] = size(crds1);
[N2,P2] = size(crds2);
if (P1~=P2)
error(' EUCL: sets of coordinates must be of same dimension');
else
P = P1;
end;
crds1 = crds1'; % Transpose crds
crds2 = crds2';
if (N1>1 & N2>1) % If two matrices provided,
dists = zeros(N1,N2); % Calc all pairwise distances between them
for i = 1:N1
c1 = crds1(:,i) * ones(1,N2);
if (P>1)
d = sqrt(sum((c1-crds2).^2));
else
d = abs(c1-crds2);
end;
dists(i,:) = d;
end;
end;
if (N1==1 & N2==1) % If two vectors provided,
dists = sqrt(sum((crds1-crds2).^2)); % Calc scalar
end;
if (N1>1 & N2==1) % If matrix & reference point provided,
crds1 = crds1 - (ones(N1,1)*crds2')'; % Center points on reference point
if (P>1) % Calc euclidean distances in P-space
dists = sqrt(sum(crds1.^2))';
else
dists = abs(crds1)';
end;
end; % Return column vector
if (N1==1 & N2>1) % If reference point & matrix provided,
crds2 = crds2 - (ones(N2,1)*crds1')'; % Center points on reference point
if (P>1) % Calc euclidean distances in P-space
dists = sqrt(sum(crds2.^2));
else
dists = abs(crds2);
end;
end; % Return row vector
end;
return;
|
github
|
lcnbeapp/beapp-master
|
uniquef.m
|
.m
|
beapp-master/Packages/eeglab14_1_2b/functions/miscfunc/uniquef.m
| 2,819 |
utf_8
|
81584771d690f2251ea088c5ccfebb54
|
% UNIQUEF: Given a matrix containing group labels, returns a vector containing
% a list of unique group labels, in the sequence found, and a
% vector of corresponding frequencies of each group.
% Optionally sorts the indices into ascending sequence.
%
% Note: it might be necessary to truncate ('de-fuzz') real numbers to
% some arbitrary number of decimal positions (see TRUNCATE) before
% finding unique values.
%
% Syntax: [value,freq,index] = uniquef(grp,sortflag)
%
% grp - matrix of a set of labels.
% sortflag - boolean flag indicating that list of labels, and
% corresponding frequencies, are to be so sorted
% [default=0, =FALSE].
% ------------------------------------------------------------
% value - column vector of unique labels.
% freq - corresponding absolute frequencies.
% index - indices of the first observation having each value.
%
% RE Strauss, 6/5/95
% 6/29/98 - modified to return indices.
% 1/25/00 - changed name from unique to uniquef to avoid conflict with
% Matlab v5 function.
function [value,freq,index] = uniquef(grp,sortflag)
if (nargin < 2) sortflag = []; end;
get_index = 0;
if (nargout > 2)
get_index = 1;
end;
if (isempty(sortflag))
sortflag = 0;
end;
tol = eps * 10.^4;
grp = grp(:); % Convert input matrix to vector
if (get_index) % Create vector of indices
ind = [1:length(grp)]';
end;
if (any([~isfinite(grp)])) % Remove NaN's and infinite values
i = find(~isfinite(grp)); % from input vector and index vector
grp(i) = [];
if (get_index)
ind(i) = [];
end;
end;
value = [];
freq = [];
for i = 1:length(grp) % For each element of grp,
b = (abs(value-grp(i)) < tol); % check if already in value list
if (sum(b) > 0) % If so,
freq(b) = freq(b) + 1; % increment frequency counter
else % If not,
value = [value; grp(i)]; % add to value list
freq = [freq; 1]; % and initialize frequency counter
end;
end;
if (sortflag)
[value,i] = sort(value);
freq = freq(i);
end;
if (get_index)
nval = length(value); % Number of unique values
index = zeros(nval,1); % Allocate vector of indices
for v = 1:nval % For each unique value,
i = find(grp == value(v)); % Find observations having value
index(v) = ind(i(1)); % Save first
end;
end;
return;
|
github
|
lcnbeapp/beapp-master
|
getipsph.m
|
.m
|
beapp-master/Packages/eeglab14_1_2b/functions/miscfunc/getipsph.m
| 2,850 |
utf_8
|
d0e227ab4596c6de73b76d9f3bd83f99
|
% getipsph() - Compute "in place" (m by n) sphering or quasi-sphering matrix for an (n by t)
% input data matrix. Quasi-sphering reduces dimensionality of the data, while
% maintaining approximately the "original" positions of the axes. That is,
% quasi-sphering "rotates back" as much as possible into the original channel
% axes, versus simple PCA reduction to the principal subspace (i.e., projecting
% the data onto a largest eigenvector basis).
% Usage:
% >> S = getipsph(x,m)
%
% Input:
% x size [n,t] input n-channel data matrix
%
% Optional input:
% m (int <= n) Reduce output dimensions to [n,m]. If m is not present, or m==n,
% then the usual sphering matrix (the symmetric square root of the data
% covariance matrix) is returned. {default: [], return usual sphering matrix).
% Output:
%
% S size [m,n] (if m==n) sphering matrix, or (if m < n) quasi-sphering matrix
% Example:
% >> x = nrand(10,1000); % random (10,1000) matrix
% >> S = getipsph(x,8); % return quasi-sphering matrix reducing dimension to 8
% >> d = S*x; % d is the quasi-sphered 8-dimensional data
% %
% % If ICA decomposition is performed on d, as >> [w] = runica(d,'sphering','off');
% % then the mixing matrix containing the 8 component maps in original channel
% % coordinates is >> A = pinv(W*S); % where A is size [n,m]
%
% Author: Jason Palmer, SCCN / INC / UCSD, 2008
% Copyright (C) Jason Palmer, SCCN / INC / UCSD , La Jolla 2008
%
% This program is free software; you can redistribute it and/or modify
% it under the terms of the GNU General Public License as published by
% the Free Software Foundation; either version 2 of the License, or
% (at your option) any later version.
%
% This program is distributed in the hope that it will be useful,
% but WITHOUT ANY WARRANTY; without even the implied warranty of
% MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
% GNU General Public License for more details.
%
% You should have received a copy of the GNU General Public License
% along with this program; if not, write to the Free Software
% Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
function S = getipsph(x,m)
[n,N] = size(x);
if nargin < 2
m = n;
end
if m>n
help getipsph
return
end
mn = mean(x,2);
for i = 1:n
x(i,:) = x(i,:) - mn(i);
end
Sxx = x*x'/N; Sxx = (Sxx+Sxx')/2;
[U,D,V] = svd(Sxx);
ds = diag(D);
if m == n
S = U * pinv(diag(sqrt(ds))) * U';
elseif m < n
[sd,so] = sort(diag(Sxx),1,'descend');
[uv,sv,vv] = svd(U(so(1:m),1:m));
S = uv * vv' * pinv(diag(sqrt(ds(1:m)))) * U(:,1:m)';
else
error('m must be less than or equal to n');
end
|
github
|
lcnbeapp/beapp-master
|
gauss3d.m
|
.m
|
beapp-master/Packages/eeglab14_1_2b/functions/miscfunc/gauss3d.m
| 2,601 |
utf_8
|
8b9e654379dccd6f84b0036766f86da3
|
% gauss3d() - generate a 3-dimensional gaussian matrix
%
% Usage:
% >> [ gaussmatrix ] = gauss2d( nX, nY, nZ);
% >> [ gaussmatrix ] = gauss2d( nX, nY, nZ, ...
% sigmaX, sigmaY, sigmaZ, ...
% centerX, centerY, centerZ, mask)
%
% Example:
% >> gauss3d(3,3,3); % generate a 3x3x3 gaussian matrix
%
% Inputs:
% nX - number of values in first dimension
% nY - number of values in second dimension
% nZ - number of values in third dimension
% sigmaX - width of standard deviation in first dim (default: nX/5)
% sigmaY - width of standard deviation in second dim (default: nY/5)
% sigmaZ - width of standard deviation in third dim (default: nZ/5)
% centerX - location of center (default: nX/2)
% centerY - location of center (default: nY/2)
% centerZ - location of center (default: nZ/2)
% mask - (0->1) percentage of low values in the matrix to mask
% with zeros (default: 0 or none)
%
% Ouput:
% gaussmatrix - 3-D gaussian matrix
%
% Author: Arnaud Delorme, 2009
% Copyright (C) 2009 Arnaud Delorme, Salk Institute, [email protected]
%
% This program is free software; you can redistribute it and/or modify
% it under the terms of the GNU General Public License as published by
% the Free Software Foundation; either version 2 of the License, or
% (at your option) any later version.
%
% This program is distributed in the hope that it will be useful,
% but WITHOUT ANY WARRANTY; without even the implied warranty of
% MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
% GNU General Public License for more details.
%
% You should have received a copy of the GNU General Public License
% along with this program; if not, write to the Free Software
% Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
function mat = gauss3d( sizeX, sizeY, sizeZ, sigmaX, sigmaY, sigmaZ, meanX, meanY, meanZ, cut);
if nargin < 2
help gauss2d
return;
end;
if nargin < 4
sigmaX = sizeX/5;
end;
if nargin < 5
sigmaY = sizeY/5;
end;
if nargin < 6
sigmaZ = sizeZ/5;
end;
if nargin < 7
meanX = (sizeX+1)/2;
end;
if nargin < 8
meanY = (sizeY+1)/2;
end;
if nargin < 9
meanZ = (sizeZ+1)/2;
end;
if nargin < 10
cut = 0;
end;
[X,Y,Z] = ndgrid(1:sizeX,1:sizeY,1:sizeZ);
mat = exp(-0.5*( ((X-meanX)/sigmaX).*((X-meanX)/sigmaX)...
+((Y-meanY)/sigmaY).*((Y-meanY)/sigmaY)...
+((Z-meanZ)/sigmaZ).*((Z-meanZ)/sigmaZ)))...
/((sigmaX*sigmaY*sigmaZ)^(0.5)*pi);
if cut > 0
maximun = max(mat(:))*cut;
I = find(mat < maximun);
mat(I) = 0;
end;
return;
|
github
|
lcnbeapp/beapp-master
|
means.m
|
.m
|
beapp-master/Packages/eeglab14_1_2b/functions/miscfunc/means.m
| 2,133 |
utf_8
|
9692b1df9d31cb08b359424b637cfeff
|
% MEANS: Means, standard errors and variances. For column vectors, means(x)
% returns the mean value. For matrices or row vectors, means(x) is a
% row vector containing the mean value of each column. The basic
% difference from the Matlab functions mean() and var() is for a row vector,
% where means() returns the row vector instead of the mean value of the
% elements of the row. Also allows for missing data, passed as NaNs.
%
% If an optional grouping vector is supplied, returns a vector of means
% for each group in collating sequence.
%
% Usage: [M,stderr,V,grpids] = means(X,{grps})
%
% X = [n x p] data matrix.
% grps = optional [n x 1] grouping vector for k groups.
% -----------------------------------------------------------------------
% M = [k x p] matrix of group means.
% stderr = corresponding [k x 1] vector of standard errors of the means.
% V = corresponding vector of variances.
% grpids = corresponding vector of group identifiers, for multiple
% groups.
%
% RE Strauss, 2/2/99
% 12/26/99 - added standard errors.
% 10/19/00 - sort group-identifiers into collating sequence.
% 12/21/00 - corrected problem with uninitialized 'fg' for single group.
% 2/24/02 - added estimation of variances.
% 10/15/02 - corrected documentation.
function [M,stderr,V,grpids] = means(X,grps)
if nargin == 0, help means; return; end;
if (nargin < 2) grps = []; end;
[n,p] = size(X);
if (isempty(grps))
grps = ones(n,1);
ug = 1;
fg = n;
k = 1;
else
[ug,fg] = uniquef(grps,1);
k = length(ug);
end;
grpids = ug;
M = zeros(k,p);
stderr = zeros(k,p);
for ik = 1:k
ir = find(grps==ug(ik));
for c = 1:p
x = X(ir,c);
ic = find(isfinite(x));
if (isempty(ic))
M(ik,c) = NaN;
stderr(ik,c) = NaN;
else
M(ik,c) = mean(x(ic));
s = std(x(ic));
stderr(ik,c) = s./sqrt(fg(ik));
V(ik,c) = s.^2;
end;
end;
end;
return;
|
github
|
lcnbeapp/beapp-master
|
eegdrawg.m
|
.m
|
beapp-master/Packages/eeglab14_1_2b/functions/miscfunc/eegdrawg.m
| 3,602 |
utf_8
|
5bf94e46002cff31e2f4befee9f9d78f
|
% eegdrawg() - subroutine used by eegplotgold() to plot data.
%
% Author: Colin Humphries, CNL, Salk Institute, La Jolla, 7/96
% Copyright (C) Colin Humphries, CNL, Salk Institute 7/96 from eegplot()
%
% This program is free software; you can redistribute it and/or modify
% it under the terms of the GNU General Public License as published by
% the Free Software Foundation; either version 2 of the License, or
% (at your option) any later version.
%
% This program is distributed in the hope that it will be useful,
% but WITHOUT ANY WARRANTY; without even the implied warranty of
% MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
% GNU General Public License for more details.
%
% You should have received a copy of the GNU General Public License
% along with this program; if not, write to the Free Software
% Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
% 4-4-97 shortened name to eegdrawq() -sm
% 4-7-97 allowed data names other than 'data' -ch
% 01-25-02 reformated help & license -ad
function y = eegdrawg(fighandle)
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
% Extract variables from figure and axes
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
userdata = get(fighandle,'UserData');
samplerate = userdata(1);
PLOT_TIME = userdata(2);
spacing_var = userdata(3);
time = userdata(4);
maxtime = userdata(5);
axhandle = userdata(6);
plotcolor = userdata(7);
disp_scale = userdata(12);
colors = ['y','w'];
dataname = get(axhandle,'UserData');
eval(['global ',dataname])
cla % Clear figure
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
% Define internal variables
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
eval(['[chans,frames] = size(',dataname,');']);
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
% Label x-axis
% This routine relabels the x-axis based on the new value of time.
% Labels are placed on one second intervals
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
Xlab = num2str(time);
for j = 1:1:PLOT_TIME
Q = num2str(time+j);
Xlab = str2mat(Xlab, Q);
end
set (gca, 'Ytick', 0:spacing_var:chans*spacing_var)
set (gca, 'XTickLabels', Xlab)
set (gca, 'XTick',(0:samplerate:PLOT_TIME*samplerate))
axis([0 PLOT_TIME*samplerate 0 (chans+1)*spacing_var]);
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
% plotting routine
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
for i = 1:chans %repeat for each channel
if (maxtime-time>PLOT_TIME)
eval(['F = ',dataname,'(chans-i+1,(time*samplerate)+1:((time+PLOT_TIME)*samplerate));'])
else
eval(['F = ',dataname,'(chans-i+1,(time*samplerate)+1:(maxtime*samplerate));'])
end
F = F - mean(F) + i*spacing_var;
plot (F,'clipping','off','color',colors(plotcolor))
end
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
% Plot Scaling I
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
if disp_scale == 1
line([(PLOT_TIME+.3)*samplerate,(PLOT_TIME+.3)*samplerate],[1.5*spacing_var 2.5*spacing_var],'clipping','off','color','w')
line([(PLOT_TIME+.3)*samplerate-10,(PLOT_TIME+.3)*samplerate+10],[2.5*spacing_var,2.5*spacing_var],'clipping','off','color','w')
line([(PLOT_TIME+.3)*samplerate-10,(PLOT_TIME+.3)*samplerate+10],[1.5*spacing_var,1.5*spacing_var],'clipping','off','color','w')
text((PLOT_TIME+.5)*samplerate,2*spacing_var,num2str(round(spacing_var)),'clipping','off')
end
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
% Set slider=edit
% This routine resets the value of the user controls so that
% they agree.
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
H = findobj(fighandle,'style','slider');
D = findobj(fighandle,'style','edit');
set (D, 'string', num2str(time));
|
github
|
lcnbeapp/beapp-master
|
averef.m
|
.m
|
beapp-master/Packages/eeglab14_1_2b/functions/miscfunc/averef.m
| 2,628 |
utf_8
|
a00dedfa26c8a0304625f45a9689b499
|
% averef() - convert common-reference EEG data to average reference
% Note that this old function is not being used in EEGLAB. The
% function used by EEGLAB is reref().
%
% Usage:
% >> data = averef(data);
% >> [data_out W_out S_out meandata] = averef(data,W);
%
% Inputs:
% data - 2D data matrix (chans,frames*epochs)
% W - ICA weight matrix
%
% Outputs:
% data_out - Input data converted to average reference.
% W_out - ICA weight matrix converted to average reference
% S_out - ICA sphere matrix converted to eye()
% meandata - (1,dataframes) mean removed from each data frame (point)
%
% Note: If 2 args, also converts the weight matrix W to average reference:
% If ica_act = W*data, then data = inv(W)*ica_act;
% If R*data is the average-referenced data,
% R*data=(R*inv(W))*ica_act and W_out = inv(R*inv(W));
% The average-reference ICA maps are the columns of inv(W_out).
%
% Authors: Scott Makeig and Arnaud Delorme, SCCN/INC/UCSD, La Jolla, 1999
%
% See also: reref()
% Copyright (C) 1999 Scott Makeig, SCCN/INC/UCSD, [email protected]
%
% This program is free software; you can redistribute it and/or modify
% it under the terms of the GNU General Public License as published by
% the Free Software Foundation; either version 2 of the License, or
% (at your option) any later version.
%
% This program is distributed in the hope that it will be useful,
% but WITHOUT ANY WARRANTY; without even the implied warranty of
% MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
% GNU General Public License for more details.
%
% You should have received a copy of the GNU General Public License
% along with this program; if not, write to the Free Software
% Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
% 12/16/99 Corrected denomiator on the suggestion of Ian Nimmo-Smith, Cambridge UK
% 01-25-02 reformated help & license -ad
function [data, W, S, meandata] = averef(data, W, S)
if nargin<1
help averef
return
end
chans = size(data,1);
if chans < 2
help averef
return
end
% avematrix = eye(chans)-ones(chans)*1/chans;
% data = avematrix*data; % implement as a matrix multiply
% else (faster?)
meandata = sum(data)/chans;
data = data - ones(chans,1)*meandata;
% treat optional ica parameters
if nargin == 2
winv = pinv(W);
size1 = size(winv,1);
avematrix = eye(size1)-ones(size1)*1/size1;
W = pinv(avematrix*winv);
end;
if nargin >= 3
winv = pinv(W*S);
size1 = size(winv,1);
avematrix = eye(size1)-ones(size1)*1/size1;
W = pinv(avematrix*winv);
S = eye(chans);
end;
|
github
|
lcnbeapp/beapp-master
|
laplac2d.m
|
.m
|
beapp-master/Packages/eeglab14_1_2b/functions/miscfunc/laplac2d.m
| 2,365 |
utf_8
|
1b371aaa27a868a1cba1dfb75b3ed92d
|
% laplac2d() - generate a 2 dimensional gaussian matrice
%
% Usage :
% >> [ gaussmatrix ] = laplac2d( rows, columns, sigma, ...
% meanR, meanC, cut)
%
% Example :
% >> laplac2d( 5, 5)
%
% Inputs:
% rows - number of rows
% columns - number of columns
% sigma - standart deviation (default: rows/5)
% meanR - mean for rows (default: center of the row)
% meanC - mean for columns (default: center of the column)
% cut - percentage (0->1) of the maximum value for removing
% values in the matrix (default: 0)
%
% Note: this function implements a simple laplacian for exploratory
% research. For a more rigorous validated approach use the freely
% available Current Source Density Matlab toolbox.
%
% See also: eeg_laplac()
%
% Author: Arnaud Delorme, CNL, Salk Institute, 2001
% Copyright (C) 2001 Arnaud Delorme, Salk Institute, [email protected]
%
% This program is free software; you can redistribute it and/or modify
% it under the terms of the GNU General Public License as published by
% the Free Software Foundation; either version 2 of the License, or
% (at your option) any later version.
%
% This program is distributed in the hope that it will be useful,
% but WITHOUT ANY WARRANTY; without even the implied warranty of
% MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
% GNU General Public License for more details.
%
% You should have received a copy of the GNU General Public License
% along with this program; if not, write to the Free Software
% Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
function mat = laplac2d( sizeX, sizeY, sigma, meanX, meanY, cut);
if nargin < 2
help laplac2d
return;
end;
if nargin < 3
sigma = sizeX/5;
end;
if nargin < 4
meanX = (sizeX+1)/2;
end;
if nargin < 5
meanY = (sizeY+1)/2;
end;
if nargin < 6
cut = 0;
end;
X = linspace(1, sizeX, sizeX)'* ones(1,sizeY);
Y = ones(1,sizeX)' * linspace(1, sizeY, sizeY);
%[-sizeX/2:sizeX/2]'*ones(1,sizeX+1);
%Y = ones(1,sizeY+1)' *[-sizeY/2:sizeY/2];
r2 = (X-meanX).*(X-meanX) + (Y-meanY).*(Y-meanY);
sigma2 = sigma*sigma;
mat = - exp(-0.5*r2/sigma2) .* ((r2 - sigma2)/(sigma2*sigma2));
% zeros crossing at r = -/+ sigma;
% mat = r2;
if cut > 0
maximun = max(max(mat))*cut;
I = find(mat < maximun);
mat(I) = 0;
end;
return;
|
github
|
lcnbeapp/beapp-master
|
varsort.m
|
.m
|
beapp-master/Packages/eeglab14_1_2b/functions/miscfunc/varsort.m
| 3,451 |
utf_8
|
f28836747df60204b4cb5eba5a4f1810
|
% varsort() - reorder ICA components, largest to smallest, by
% the size of their MEAN projected variance
% across all time points
% Usage:
% >> [windex,meanvar] = varsort(activations,weights,sphere);
%
% Inputs:
% activations = (chans,framestot) the runica() activations
% weights = ica weight matrix from runica()
% sphere = sphering matrix from runica()
%
% Outputs:
% windex = order of projected component mean variances (large to small)
% meanvar = projected component mean variance (in windex order)
%
% Author: Scott Makeig & Martin McKeown, SCCN/INC/UCSD, La Jolla, 09-01-1997
%
% See also: runica()
% Copyright (C) 9-01-1997 Scott Makeig & Martin McKeown, SCCN/INC/UCSD,
% [email protected]
%
% This program is free software; you can redistribute it and/or modify
% it under the terms of the GNU General Public License as published by
% the Free Software Foundation; either version 2 of the License, or
% (at your option) any later version.
%
% This program is distributed in the hope that it will be useful,
% but WITHOUT ANY WARRANTY; without even the implied warranty of
% MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
% GNU General Public License for more details.
%
% You should have received a copy of the GNU General Public License
% along with this program; if not, write to the Free Software
% Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
% 03-19-97 simplified, replaced grandmean with datamean info in calculation,
% made function return mean projected variance across the data,
% changed var() to diag(cov()) -sm
% 05-20-97 use sum-of-squares instead of diag() to allow long data sets -sm
% 06-07-97 changed order of args to conform to runica, fixed meanvar computation -sm
% 07-25-97 removed datamean -sm
% 01-25-02 reformated help & license, added link -ad
function [windex,meanvar] = varsort(activations,weights,sphere)
%
if nargin ~= 3 % needs all 3 args
help varsort
return
end
[chans,framestot] = size(activations);
if framestot==0,
fprintf('Gvarsort(): cannot process an empty activations array.\n\n');
return
end;
[srows,scols] = size(sphere);
[wrows,wcols] = size(weights);
if nargin<3,
fprintf('Gvarsort(): needs at least 3 arguments.\n\n');
return
end;
% activations = (wrows,wcols)X(srows,scols)X(chans,framestot)
if chans ~= scols | srows ~= wcols,
fprintf('varsort(): input data dimensions do not match.\n');
fprintf(' i.e., Either %d ~= %d or %d ~= %d\n',...
chans,scols,srows,wcols);
return
end
%%%%%%%%%%%%%%%%%%%% Find mean variances %%%%%%%%%%%%%%%%%%%%%%%%%%%%%
fprintf('Computing mean projected variance for all %d components:\n',wrows);
meanvar = zeros(wrows,1); % size of the projections
winv = inv(weights*sphere);
for s=1:wrows
fprintf('%d ',s); % construct single-component data matrix
% project to scalp, then add row means
compproj = winv(:,s)*activations(s,:);
meanvar(s) = mean(sum(compproj.*compproj)/(size(compproj,1)-1));
% compute mean variance
end % at all scalp channels
%%%%%%%%%%%%%%%%%%% sort by mean variance %%%%%%%%%%%%%%%%%%%%%%%%%%%%%
[sortvar, windex] = sort(meanvar);
windex = windex(wrows:-1:1);% order large to small
meanvar = meanvar(windex);
fprintf('\n');
|
github
|
lcnbeapp/beapp-master
|
eegdraw.m
|
.m
|
beapp-master/Packages/eeglab14_1_2b/functions/miscfunc/eegdraw.m
| 3,816 |
utf_8
|
8cf02a8c097d9de09a6aa145d4bfba65
|
% eegdraw() - subroutine used by eegplotold() to plot data.
%
% Author: Colin Humphries, CNL, Salk Institute, La Jolla, 7/96
% Copyright (C) Colin Humphries, CNL, Salk Institute 7/96 from eegplot()
%
% This program is free software; you can redistribute it and/or modify
% it under the terms of the GNU General Public License as published by
% the Free Software Foundation; either version 2 of the License, or
% (at your option) any later version.
%
% This program is distributed in the hope that it will be useful,
% but WITHOUT ANY WARRANTY; without even the implied warranty of
% MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
% GNU General Public License for more details.
%
% You should have received a copy of the GNU General Public License
% along with this program; if not, write to the Free Software
% Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
% 11-07-97 fix incorrect start times -Scott Makeig
% 01-25-02 reformated help & license -ad
function y = eegdraw(fighandle)
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
% Extract variables from figure and axes
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
userdata = get(fighandle,'UserData');
samplerate = userdata(1);
PLOT_TIME = userdata(2);
spacing_var = userdata(3);
time = userdata(4);
maxtime = userdata(5);
axhandle = userdata(6);
plotcolor = userdata(7);
disp_scale = userdata(12);
colors = ['y','w'];
data = get(axhandle,'UserData');
if samplerate <=0
fprintf('Samplerate too small! Resetting it to 1.0.\n')
samplerate = 1.0;
end
if PLOT_TIME < 2/samplerate
PLOT_TIME = 2/samplerate;
fprintf('Window width too small! Resetting it to 2 samples.\n');
end
if time >= maxtime % fix incorrect start time
time = max(maxtime-PLOT_TIME,0);
fprintf('Start time too large! Resetting it to %f.\n',time)
elseif time < 0
time = 0;
fprintf('Start time cannot be negative! Resetting it to 0.\n')
end
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
% Define internal variables
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
[chans,frames] = size(data);
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
% Label x-axis - relabel the x-axis based on
% the new value of time.
% Labels are placed at one-second intervals
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
cla % Clear figure
Xlab = num2str(time);
for j = 1:1:PLOT_TIME
Q = num2str(time+j);
Xlab = str2mat(Xlab, Q);
end
set (gca, 'Ytick', 0:spacing_var:chans*spacing_var)
set (gca, 'XTickLabels', Xlab) % needs TickLabels with s in Matlab 4.2
set (gca, 'XTick',(0:samplerate:PLOT_TIME*samplerate))
axis([0 PLOT_TIME*samplerate 0 (chans+1)*spacing_var]);
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
% Plot data
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
for i = 1:chans %repeat for each channel
if (maxtime-time>PLOT_TIME)
F = data(chans-i+1,(time*samplerate)+1:((time+PLOT_TIME)*samplerate));
else
F = data(chans-i+1,(time*samplerate)+1:(maxtime*samplerate));
end
F = F - mean(F) + i*spacing_var;
plot (F,'clipping','off','color',colors(plotcolor))
end
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
% Plot scaling I
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
if disp_scale == 1
ps = PLOT_TIME*samplerate;
sv = spacing_var;
line([1.03*ps,1.03*ps],[1.5*sv 2.5*sv],'clipping','off','color','w')
line([1.01*ps,1.05*ps],[2.5*sv,2.5*sv],'clipping','off','color','w')
line([1.01*ps,1.05*ps],[1.5*sv,1.5*sv],'clipping','off','color','w')
text(1.05*ps,2*sv,num2str(round(sv)),'clipping','off')
end
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
% Set slider=edit - reset the value of
% the user controls so they agree.
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
H = findobj(fighandle,'style','slider');
D = findobj(fighandle,'style','edit');
set (D, 'string', num2str(time));
|
github
|
lcnbeapp/beapp-master
|
eegmovie.m
|
.m
|
beapp-master/Packages/eeglab14_1_2b/functions/miscfunc/eegmovie.m
| 10,994 |
utf_8
|
e8d4266027ffe169448945aed8f2b937
|
% eegmovie() - Compile and view a Matlab movie.
% Uses scripts eegplotold() and topoplot().
% Use seemovie() to display the movie.
% Usage:
% >> [Movie,Colormap] = eegmovie(data,srate,elec_locs, 'key', val, ...);
%
% Or legacy call
% >> [Movie,Colormap] = eegmovie(data,srate,elec_locs,title,movieframes,minmax,startsec,...);
%
% Inputs:
% data = (chans,frames) EEG data set to plot
% srate = sampling rate in Hz
% elec_locs = electrode locations structure or file
%
% Optional inputs:
% 'mode' = ['2D'|'3D'] plot in 2D using topoplot or in 3D using
% headplot. Default is 2D.
% 'headplotopt' = [cell] optional inputs for headplot. Default is none.
% 'topoplotopt' = [cell] optional inputs for topoplot. Default is none.
% 'title' = plot title. Default is none.
% 'movieframes' = vector of frames indices to animate. Default is all.
% 'minmax' = [blue_lower_bound, red_upper_bound]. Default is
% +/-abs max of data.
% 'startsec' = starting time in seconds. Default is 0.
% 'timecourse' = ['on'|'off'] show time course for all electrodes. Default is 'on'.
% 'framenum' = ['on'|'off'] show frame number. Default is 'on'.
% 'time' = ['on'|'off'] show time in ms. Default is 'off'.
% 'vert' = [float] plot vertical lines at given latencies. Default is none.
% 'camerapath' = [az_start az_step el_start el_step] {default [-127 0 30 0]}
% Setting all four non-0 creates a spiral camera path
% Subsequent rows [movieframe az_step 0 el_step] adapt step
% sizes allowing starts/stops, panning back and forth, etc.
%
% Legacy inputs:
% data = (chans,frames) EEG data set to plot
% srate = sampling rate in Hz {0 -> 256 Hz}
% elec_locs = ascii file of electrode locations {0 -> 'chan_file'}
% title = 'plot title' {0 -> none}
% movieframes = vector of frames to animate {0 -> all}
% minmax = [blue_lower_bound, red_upper_bound]
% {0 -> +/-abs max of data}
% startsec = starting time in seconds {0 -> 0.0}
% additional options from topoplot are allowed
%
% Author: Arnaud Delorme, Colin Humphries & Scott Makeig, CNL, Salk Institute, La Jolla, 3/97
%
% See also: seemovie(), eegplotold(), topoplot()
% Copyright (C) 6/4/97 Colin Humphries & Scott Makeig, CNL / Salk Institute / La Jolla CA
%
% This program is free software; you can redistribute it and/or modify
% it under the terms of the GNU General Public License as published by
% the Free Software Foundation; either version 2 of the License, or
% (at your option) any later version.
%
% This program is distributed in the hope that it will be useful,
% but WITHOUT ANY WARRANTY; without even the implied warranty of
% MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
% GNU General Public License for more details.
%
% You should have received a copy of the GNU General Public License
% along with this program; if not, write to the Free Software
% Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
% 6/6/97 added movieframes arg -sm
% 6/12/97 removed old 'startframes' var., fixed vertical line frame selection -sm
% 6/27/97 debugged vertical line position -sm
% 10/4/97 clarified order of srate and eloc_locs -sm
% 3/18/97 changed eegplots -> eegplot('noui') -sm
% 10/10/99 added newlines to frame print at suggestion of Ian Lee, Singapore -sm
% 01/05/01 debugged plot details -sm
% 01/24/02 updated eegplot to eegplotold -ad
% 01-25-02 reformated help & license, added links -ad
function [Movie, Colormap] = eegmovie(data,srate,eloc_locs,varargin);
%titl,movieframes,minmax,startsec,varargin)
if nargin<1
help eegmovie
return
end
clf
[chans,frames] = size(data);
icadefs; % read DEFAULT_SRATE;
if nargin <2
srate = 0;
end
if nargin <3
eloc_locs = 0;
end
if nargin > 5 && ~ischar(varargin{3}) || nargin == 4 && ~ischar(varargin{2})
% legacy mode
options = {};
if nargin>=8, options = { options{:} 'topoplotopt' varargin(5:end) }; end
if nargin>=7, options = { options{:} 'startsec' varargin{4} }; end
if nargin>=6, options = { options{:} 'minmax' varargin{3} }; end
if nargin>=5, options = { options{:} 'movieframes' varargin{2} }; end
if nargin>=4, options = { options{:} 'title' varargin{1} }; end
else
options = varargin;
end;
opt = finputcheck(options, { 'startsec' 'real' {} 0;
'minmax' 'real' {} 0;
'movieframes' 'integer' {} 0;
'title' 'string' {} '';
'vert' 'real' {} [];
'mode' 'string' { '2D' '3D' } '2D';
'timecourse' 'string' { 'on' 'off' } 'on';
'framenum' 'string' { 'on' 'off' } 'on';
'camerapath' 'real' [] 0;
'time' 'string' { 'on' 'off' } 'off';
'topoplotopt' 'cell' {} {};
'headplotopt' 'cell' {} {} }, 'eegmovie');
if isstr(opt), error(opt); end;
if opt.minmax ==0,
datamin = min(min(data));
datamax = max(max(data));
absmax = max([abs(datamin), abs(datamax)]);
fudge = 0.05*(datamax-datamin); % allow for slight extrapolation
datamin = -absmax-fudge;
datamax = absmax+fudge;
opt.minmax = [datamin datamax];
end
if opt.movieframes == 0
opt.movieframes = 1:frames;
end
if opt.movieframes(1) < 1 || opt.movieframes(length(opt.movieframes))>frames
fprintf('eegmovie(): specified movieframes not in data!\n');
return
end
if srate ==0,
srate = DEFAULT_SRATE;
end
if strcmpi(opt.time, 'on'), opt.framenum = 'off'; end;
mframes = length(opt.movieframes);
fprintf('Making a movie of %d frames\n',mframes)
Movie = moviein(mframes,gcf);
%%%%%%%%%%%%%%%%%%%%% eegplot() of data %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
if strcmpi(opt.timecourse, 'on')
axeegplot = axes('Units','Normalized','Position',[.75 .05 .2 .9]);
% >> eegplotold('noui',data,srate,spacing,eloc_file,startsec,color)
if isstruct(eloc_locs)
fid = fopen('tmp_file.loc', 'w');
adddots = '...';
for iChan = 1:length(eloc_locs)
fprintf(fid, '0 0 0 %s\n', [ eloc_locs(iChan).labels adddots(length(eloc_locs(iChan).labels):end) ]);
end;
fclose(fid);
eegplotold('noui',-data,srate,0,'tmp_file.loc',opt.startsec,'r');
else
eegplotold('noui',-data,srate,0,eloc_locs,opt.startsec,'r');
end;
% set(axeegplot,'XTick',[]) %%CJH
% plot negative up
limits = get(axeegplot,'Ylim'); % list channel numbers only
set(axeegplot,'GridLineStyle','none')
set(axeegplot,'Xgrid','off')
set(axeegplot,'Ygrid','on')
for ind = 1:length(opt.vert)
frameind = (opt.vert(ind)-opt.startsec)*srate+1;
line([frameind frameind],limits,'color','k'); % draw vertical line at map timepoint
set(axeegplot,'Xtick',frameind,'XtickLabel',num2str(opt.vert(ind),'%4.3f'));
end;
end;
%%%%%%%%%%%%%%%%%%%%% topoplot/headplot axis %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
axcolor = get(gcf,'Color');
axtopoplot = axes('Units','Normalized','Position',[0 .1 .72 .8],'Color',axcolor);
TPAXCOLOR = get(axtopoplot,'Color'); %%CJH
Colormap = [jet(64);TPAXCOLOR]; %%CJH
fprintf('Warning: do not resize plot window during movie creation ...\n ');
h = textsc(opt.title, 'title'); set(h,'FontSize',16)
%%%%%%%%%%%%%%%%%%%%% headplot setup %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
if strcmpi(opt.mode, '3d')
headplot('setup',eloc_locs, 'tmp.spl', opt.headplotopt{:});
if isequal(opt.camerapath, 0)
opt.camerapath = [-127 0 30 0];
fprintf('Using default view [-127 0 30 0].');
end;
if size(opt.camerapath,2)~=4
error('Camerapath parameter must have exact 4 columns');
end
newpan = length(opt.movieframes)+1;
posrow = 2;
if size(opt.camerapath,1) > 1
newpan = opt.camerapath(posrow,1); % pick up next frame to change camerapos step values
end
azimuth = opt.camerapath(1,1); % initial camerapath variables
az_step = opt.camerapath(1,2);
elevation = opt.camerapath(1,3);
el_step = opt.camerapath(1,4);
end;
%%%%%%%%%%%%%%%%%%%%%%%%% "Roll'em!" %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
for f = 1:length(opt.movieframes) % make the movie, frame by frame
indFrame = opt.movieframes(f);
% show time course
if strcmpi(opt.timecourse, 'on')
axes(axeegplot)
x1 = opt.startsec+(indFrame-1)/srate;
l1 = line([indFrame indFrame],limits,'color','b'); % draw vertical line at map timepoint
set(axeegplot,'Xtick',indFrame,'XtickLabel',num2str(x1,'%4.3f'));
end;
% plot headplot or topoplot
axes(axtopoplot)
cla
set(axtopoplot,'Color',axcolor);
if strcmpi(opt.mode, '2d')
topoplot(data(:,indFrame),eloc_locs,'maplimits',opt.minmax, opt.topoplotopt{:});
else
headplot(data(:,indFrame),'tmp.spl','view',[azimuth elevation], opt.headplotopt{:});
% adapt camerapath step sizes
if indFrame == newpan
az_step = opt.camerapath(posrow,2);
el_step = opt.camerapath(posrow,4);
posrow = posrow+1;
if size(opt.camerapath,1)>=posrow
newpan = opt.camerapath(posrow,1);
else
newpan = length(opt.movieframes)+1;
end
end
% update camera position
azimuth = azimuth+az_step;
elevation = elevation+el_step;
if elevation>=90
fprintf('headplot(): warning -- elevation out of range!\n');
elevation = 89.99;
end
if elevation<=-90
fprintf('headplot(): warning -- elevation out of range!\n');
elevation = -89.99;
end
set(axtopoplot,'Units','pixels',...
'CameraViewAngleMode','manual',...
'YTickMode','manual','ZTickMode','manual',...
'PlotBoxAspectRatioMode','manual',...
'DataAspectRatioMode','manual'); % keep camera distance constant
end;
% show frame number
if strcmpi(opt.framenum, 'on')
txt = [ int2str(f)];
text(-0.5,-0.5,txt,'FontSize',14);
elseif strcmpi(opt.time, 'on')
txt = sprintf('%3.3f s', opt.startsec+(indFrame-1)/srate);
text(-0.5,-0.5,txt,'FontSize',14);
end;
Movie(:,f) = getframe(gcf);
drawnow
if strcmpi(opt.timecourse, 'on')
delete(l1)
end;
% print advancement
fprintf('.',f);
if rem(indFrame,10) == 0, fprintf('%d',f); end;
if rem(indFrame,50) == 0, fprintf('\n'); end
end
fprintf('\nDone\n');
|
github
|
lcnbeapp/beapp-master
|
gabor2d.m
|
.m
|
beapp-master/Packages/eeglab14_1_2b/functions/miscfunc/gabor2d.m
| 3,449 |
utf_8
|
669aa44c02685a4e73e5568196a23efb
|
% gabor2d() - generate a two-dimensional gabor matrice.
%
% Usage:
% >> [ matrix ] = gabor2d(rows, columns);
% >> [ matrix ] = gabor2d( rows, columns, freq, ...
% angle, sigmaR, sigmaC, meanR, meanC, dephase, cut)
% Example :
% >> imagesc(gabor2d( 50, 50))
%
% Inputs:
% rows - number of rows
% columns - number of columns
% freq - frequency of the sinusoidal function in degrees (default: 360/rows)
% angle - angle of rotation of the resulting 2-D array in
% degrees of angle {default: 0}.
% sigmaR - standard deviation for rows {default: rows/5}
% sigmaC - standard deviation for columns {default: columns/5}
% meanR - mean for rows {default: center of the row}
% meanC - mean for columns {default: center of the column}
% dephase - phase offset in degrees {default: 0}. A complex Gabor wavelet
% can be build using gabor2dd(...., 0) + i*gabor2d(...., 90),
% 0 and 90 being the phase offset of the real and imaginary parts
% cut - percentage (0->1) of maximum value below which to remove values
% from the matrix {default: 0}
% Ouput:
% matrix - output gabor matrix
%
% Author: Arnaud Delorme, CNL / Salk Institute, 2001
% Copyright (C) 2001 Arnaud Delorme, Salk Institute, [email protected]
%
% This program is free software; you can redistribute it and/or modify
% it under the terms of the GNU General Public License as published by
% the Free Software Foundation; either version 2 of the License, or
% (at your option) any later version.
%
% This program is distributed in the hope that it will be useful,
% but WITHOUT ANY WARRANTY; without even the implied warranty of
% MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
% GNU General Public License for more details.
%
% You should have received a copy of the GNU General Public License
% along with this program; if not, write to the Free Software
% Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
function mat = gabor2d( sizeX, sizeY, freq, angle, sigmaX, sigmaY, meanX, ...
meanY, dephase, cut);
if nargin < 2
help gabor2d
return;
end;
if nargin < 3
freq = 360/sizeX;
end;
if nargin < 4
angle = 0;
end;
if nargin < 5
sigmaX = sizeX/5;
end;
if nargin < 6
sigmaY = sizeY/5;
end;
if nargin < 7
meanX = (sizeX+1)/2;
end;
if nargin < 8
meanY = (sizeY+1)/2;
end;
if nargin < 9
dephase = 0;
end;
if nargin < 10
cut = 0;
end;
freq = freq/180*pi;
X = linspace(1, sizeX, sizeX)'* ones(1,sizeY);
Y = ones(1,sizeX)' * linspace(1, sizeY, sizeY);
%[-sizeX/2:sizeX/2]'*ones(1,sizeX+1);
%Y = ones(1,sizeY+1)' *[-sizeY/2:sizeY/2];
rotatedmat = ((X-meanX)+i*(Y-meanY)) * exp(i*angle/180*pi);
mat = sin(real(rotatedmat)*freq + dephase/180*pi).*exp(-0.5*( ((X-meanX)/sigmaX).*((X-meanX)/sigmaX)...
+((Y-meanY)/sigmaY).*((Y-meanY)/sigmaY)))...
/((sigmaX*sigmaY)^(0.5)*pi);
if cut > 0
maximun = max(max(mat))*cut;
I = find(mat < maximun);
mat(I) = 0;
end;
return;
% other solution
% --------------
for X = 1:sizeX
for Y = 1:sizeY
mat(X,Y) = sin(real((X-meanX+j*(Y-meanY))*exp(i*angle/180*pi))*freq + dephase/180*pi) ...
.*exp(-0.5*( ((X-meanX)/sigmaX).*((X-meanX)/sigmaX)...
+((Y-meanY)/sigmaY).*((Y-meanY)/sigmaY)))...
/((sigmaX*sigmaY)^(0.5)*pi);
end;
end;
return;
|
github
|
lcnbeapp/beapp-master
|
makehtml.m
|
.m
|
beapp-master/Packages/eeglab14_1_2b/functions/miscfunc/makehtml.m
| 13,268 |
utf_8
|
ab43eb5b6d347b47f14edde57f938911
|
% makehtml() - generate .html function-index page and function help pages
% composed automatically from formatted Matlab function help messages
%
% Usage:
% >> makehtml(list, outputdir);
% >> makehtml(list, outputdir, 'key1', val1, 'key2', val2, ...);
%
% Input:
% list - (1) List (cell array) of filenames to convert.
% Ex: {'filename1' 'filename2' 'filename3'}
% By default, the filename extension .m is understood.
% (2) Cell array of filenames to convert and the text link
% on the summary page for them.
% {{'filename1' 'link1'} {'filename2' 'link2'}} ...
% Ex: 'link1' = 'Reject by kurtosis'.
% (3) Cell array of 2 or 3 cell array elements containing
% info to generate .html function-index and help pages.
% Ex: { {'directory1' 'heading1' 'dirindexfunc1'} ...
% {'directory2' 'heading2' 'dirindexfunc2'} }
% - 'directory': Function file directory name
% - 'heading': Index-file heading for the directory functions
% - 'dirindexfunc': A optional Matlab pop-up help function for
% referencing the directory functions {default: none}
% (4) To scan several directories under the same heading, use
% {{{'directory1' 'directory2'} 'heading1' 'dirindexfunc1' ... }
% outputdir - Directory for output .html help files
%
% Optional inputs:
% 'outputfile' - Output file name. {default: 'index.html'}
% 'header' - Command to insert in the header of all .html files (e.g., javascript
% declaration or meta-tag). {default: javascript 'openhelp()'
% function. See help2htm() code for details.}
% 'footer' - Command to insert at the end of all .html files (e.g., back
% button. {default: reference back to the function-index file}
% 'refcall' - Syntax format to call references. {default is
% 'javascript:openhelp(''%s.js'')'} Use '%s.html' for an .html link.
% 'font' - Font name (default: 'Helvetica')
% 'background' - Background HTML body section. Include "<" and ">".
% 'outputlink' - Help page calling command for the function index page. {default is
% 'javascript:openhelp(''%s.js'')'. Use '%s.html' to use a
% standard .html page link instead.}
% 'fontindex' - Font for the .html index file (default: 'Helvetica')
% 'backindex' - Background tag for the index file (c.f. 'background')
% 'mainheader' - Text file to insert at the beggining of the index page. Default is
% none.
% 'mainonly' - ['on'|'off'] 'on' -> Generate the index page only.
% {default: 'off' -> generate both the index and help pages}
%
% Author: Arnaud Delorme, CNL / Salk Institute, 2002
%
% Example: Generate EEGLAB help menus at SCCN:
% makehtml({ { 'adminfunc' 'Admin functions' 'adminfunc/eeg_helpadmin.m' } ...
% { 'popfunc', 'Interactive pop_functions' 'adminfunc/eeg_helppop.m' } ...
% { { 'toolbox', 'toolbox2' } 'Signal processing functions' 'adminfunc/eeg_helpsigproc.m' }}, ...
% '/home/www/eeglab/allfunctions', 'mainheader', '/data/common/matlab/indexfunchdr.txt');
%
% See also: help2html2()
% Copyright (C) Arnaud Delorme, CNL / Salk Institute, 2002
%
% This program is free software; you can redistribute it and/or modify
% it under the terms of the GNU General Public License as published by
% the Free Software Foundation; either version 2 of the License, or
% (at your option) any later version.
%
% This program is distributed in the hope that it will be useful,
% but WITHOUT ANY WARRANTY; without even the implied warranty of
% MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
% GNU General Public License for more details.
%
% You should have received a copy of the GNU General Public License
% along with this program; if not, write to the Free Software
% Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
function makehtml( directorylist, outputdir, varargin );
if nargin < 2
help makehtml;
return;
end;
if outputdir(end) ~= '/', outputdir(end+1) = '/'; end;
if ~isempty( varargin )
g = struct( varargin{:} );
else
g = [];
end;
try, g.mainonly; catch, g.mainonly = 'off'; end;
try, g.mainheader; catch, g.mainheader = ''; end;
try, g.outputfile; catch, g.outputfile = 'index.html'; end;
try, g.fontindex; catch, g.fontindex = 'Helvetica'; end;
try, g.backindex; catch, g.backindex = '<body bgcolor="#fcffff">'; end;
try, g.header; catch, g.header = [ '<script language="JavaScript"><!--' 10 'function openhelp(fnc){' 10 'self.window.location = fnc;' 10 '}' 10 '//--></script>' ]; end;
try, g.background; catch, g.background = '<body bgcolor="#fcffff">'; end;
%try, g.background; catch, g.background = '<body BACKGROUND="cream_stucco.jpg" bgproperties="fixed" bgcolor="#ffffe5">'; end;
try, g.refcall; catch, g.refcall = 'javascript:openhelp(''%s.html'')'; end;
try, g.font; catch, g.font = 'Helvetica'; end;
try, g.footer; catch, g.footer = '<A HREF ="index.html">Back to functions</A>'; end;
try, g.outputlink; catch, g.outputlink = [ '<tr><td VALIGN=TOP ALIGN=RIGHT NOSAVE><A HREF="javascript:openhelp(''%s.html'')">%s</A></td><td>%s</td></tr>' ]; end;
% read header text file
% ---------------------
if ~isempty(g.mainheader)
doc = [];
fid = fopen(g.mainheader , 'r');
if (fid == -1), error(['Can not open file ''' g.mainheader '''' ]); end;
str = fgets( fid );
while ~feof(fid)
str = deblank(str(1:end-1));
doc = [ doc str(1:end) ];
str = fgets( fid );
end;
g.backindex = [ g.backindex doc ];
end;
options = { 'footer', g.footer, 'background', g.background, ...
'refcall', g.refcall, 'font', g.font, 'header', g.header, 'outputlink', g.outputlink};
if strcmpi( g.mainonly, 'on')
options = { options{:}, 'outputonly', g.mainonly };
end;
% -------------------------------------------
% scrips which generate a web page for eeglab
% -------------------------------------------
STYLEHEADER = '<BR><a name="%s"></a><H2>%s</H2>\n';
OPENWIN = [ '<script language="JavaScript"><!--' 10 'function openhelp(fnc){' 10 ...
'self.window.location = fnc;' 10 '}' 10 '//--></script>'];
ORIGIN = pwd;
% determine mode
% --------------
if iscell(directorylist{1}) & exist(directorylist{1}{1}) == 7
fprintf('First cell array element is not a file\n');
fprintf('Scanning directories...\n');
mode = 'dir';
% scan directories
% ----------------
for index = 1:length( directorylist )
direct{ index } = scandir( directorylist{index}{1} );
end;
else
fprintf('First cell array element has been identified as a file\n');
fprintf('Scanning all files...\n');
mode = 'files';
end;
% remove . directory
% ------------------
rmpath('.');
% write .html file
% ----------------
fo = fopen([ outputdir g.outputfile], 'w');
if fo == -1, error(['cannot open file ''' [ outputdir g.outputfile] '''']); end;
fprintf(fo, '<HTML><HEAD>%s</HEAD>%s<FONT FACE="%s">\n', OPENWIN, g.backindex, g.fontindex);
if strcmp(mode, 'files')
makehelphtml( directorylist, fo, 'MAIN TITLE', STYLEHEADER, outputdir, mode, options, g.mainonly );
else % direcotry
for index = 1:length( directorylist )
makehelphtml( direct{ index }, fo, directorylist{index}{2}, STYLEHEADER, outputdir, mode, options, g.mainonly );
end;
end;
fprintf( fo, '</FONT></BODY></HTML>');
fclose( fo );
if isunix
chmodcom = sprintf('!chmod 777 %s*', outputdir);
eval(chmodcom);
end;
% ------------------------------
% Generate help files for EEGLAB
% ------------------------------
if strcmp(mode, 'dir')
for index = 1:length( directorylist )
if length(directorylist{index}) > 2
makehelpmatlab( directorylist{index}{3}, direct{ index },directorylist{index}{2});
end;
end;
end;
addpath('.');
return;
% scan directory list or directory
% --------------------------------
function filelist = scandir( dirlist )
filelist = {};
if iscell( dirlist )
for index = 1:length( dirlist )
tmplist = scandir( dirlist{index} );
filelist = { filelist{:} tmplist{:} };
end;
else
if dirlist(end) ~= '/', dirlist(end+1) = '/'; end;
if exist(dirlist) ~= 7
error([ dirlist ' is not a directory']);
end;
tmpdir = dir([dirlist '*.m']);
filelist = { tmpdir(:).name };
end;
filelist = sort( filelist );
return;
% ------------------------------ Function to generate help for a bunch of files -
function makehelphtml( files, fo, title, STYLEHEADER, DEST, mode, options, mainonly);
% files = cell array of string containing file names or
% cell array of 2-strings cell array containing titles and filenames
% fo = output file
% title = title of the page or section
tmpdir = pwd;
if strcmp(mode, 'files') % processing subtitle and File
fprintf(fo, '<UL>' );
for index = 1:length(files)
if iscell(files{index})
filename = files{index}{1};
filelink = files{index}{2};
else
filename = files{index};
filelink = '';
end;
fprintf('Processing (mode file) %s:%s\n', filename, filelink );
if ~isempty(filename)
if ~exist(fullfile(DEST, [ filename(1:end-1) 'html' ]))
cd(DEST);
try, delete([ DEST filename ]);
catch, end;
help2html2( filename, [], 'outputtext', filelink, options{:}); cd(tmpdir);
if strcmp(mainonly,'off')
inputfile = which( filename);
try, copyfile( inputfile, [ DEST filename ]); % asuming the file is in the path
catch, fprintf('Cannot copy file %s\n', inputfile); end;
end;
indexdot = find(filename == '.');
end;
if ~isempty(filelink)
com = [ space2html(filelink) ' -- ' space2html([ filename(1:indexdot(end)-1) '()'], ...
[ '<A HREF="' filename(1:indexdot(end)-1) '.html">' ], '</A><BR>')];
else
com = [ space2html([ filename(1:indexdot(end)-1) '()'], ...
[ '<A HREF="' filename(1:indexdot(end)-1) '.html">' ], '</A><BR>')];
end;
else
com = space2html(filelink, '<B>', '</B><BR>');
end;
fprintf( fo, '%s', com);
end;
fprintf(fo, '</UL>' );
else
fprintf(fo, STYLEHEADER, title, title );
fprintf(fo, '<table WIDTH="100%%" NOSAVE>' );
for index = 1:length(files)
% Processing file only
if ~exist(fullfile(DEST, [ files{index}(1:end-1) 'html' ]))
fprintf('Processing %s\n', files{index});
cd(DEST); com = help2html2( files{index}, [], options{:}); cd(tmpdir);
fprintf( fo, '%s', com);
if strcmp(mainonly,'off')
inputfile = which( files{index});
try, copyfile( inputfile, [ DEST files{index} ]); % asuming the file is in the path
catch, fprintf('Cannot copy file %s\n', inputfile); end;
end;
else
fprintf('Skipping %s\n', files{index});
cd(DEST);
com = help2html2( files{index}, [], options{:}, ...
'outputonly','on');
fprintf( fo, '%s', com);
cd(tmpdir);
end
end;
fprintf(fo, '</table>' );
end;
return;
% ------------------------------ Function to pop-out a Matlab help window --------
function makehelpmatlab( filename, directory, titlewindow);
fo = fopen( filename, 'w');
fprintf(fo, '%%%s() - Help file for EEGLAB\n\n', filename);
fprintf(fo, 'function noname();\n\n');
fprintf(fo, 'command = { ...\n');
for index = 1:length(directory)
fprintf(fo, '''pophelp(''''%s'''');'' ...\n', directory{index});
end;
fprintf(fo, '};\n');
fprintf(fo, 'text = { ...\n');
for index = 1:length(directory)
fprintf(fo, '''%s'' ...\n', directory{index});
end;
fprintf(fo, '};\n');
fprintf(fo, ['textgui( text, command,' ...
'''fontsize'', 15, ''fontname'', ''times'', ''linesperpage'', 18, ', ...
'''title'',strvcat( ''%s'', ''(Click on blue text for help)''));\n'], titlewindow);
fprintf(fo, 'icadefs; set(gcf, ''COLOR'', BACKCOLOR);');
fprintf(fo, 'h = findobj(''parent'', gcf, ''style'', ''slider'');');
fprintf(fo, 'set(h, ''backgroundcolor'', GUIBACKCOLOR);');
fprintf(fo, 'return;\n');
fclose( fo );
return
% convert spaces for .html
function strout = space2html(strin, linkb, linke)
strout = [];
index = 1;
while strin(index) == ' '
strout = [ strout ' '];
index = index+1;
end;
if nargin == 3
strout = [strout linkb strin(index:end) linke];
else
strout = [strout strin(index:end)];
end;
|
github
|
lcnbeapp/beapp-master
|
covary.m
|
.m
|
beapp-master/Packages/eeglab14_1_2b/functions/miscfunc/covary.m
| 1,482 |
utf_8
|
be5b9b3870c8f6344a4441160ea51bf0
|
% covary() - For vectors, covary(X) returns the variance of X.
% For matrices, covary(X)is a row vector containing the
% variance of each column of X.
%
% Notes:
% covary(X) normalizes by N-1 where N is the sequence length.
% This makes covary(X) the best unbiased estimate of the
% covariance if X are from a normal distribution.
% Does not require the Matlab Signal Processing Toolbox
%
% Author: Scott Makeig, SCCN/INC/UCSD, La Jolla, 2000
% Copyright (C) 2000 Scott Makeig, SCCN/INC/UCSD, [email protected]
%
% This program is free software; you can redistribute it and/or modify
% it under the terms of the GNU General Public License as published by
% the Free Software Foundation; either version 2 of the License, or
% (at your option) any later version.
%
% This program is distributed in the hope that it will be useful,
% but WITHOUT ANY WARRANTY; without even the implied warranty of
% MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
% GNU General Public License for more details.
%
% You should have received a copy of the GNU General Public License
% along with this program; if not, write to the Free Software
% Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
% 01-25-02 reformated help & license -ad
function covout = covary(data)
data = data - mean(mean(data));
if size(data,1) == 1
data = data'; % make column vector
end
covout = sum(data.*data)/(size(data,1)-1);
|
github
|
lcnbeapp/beapp-master
|
convolve.m
|
.m
|
beapp-master/Packages/eeglab14_1_2b/functions/miscfunc/convolve.m
| 1,721 |
utf_8
|
9bced09132932ed26fd7caf0d6d760f7
|
% convolve() - convolve two matrices (normalize by the sum of convolved
% elements to compensate for border effects).
%
% Usage:
% >> r = convolve( a, b );
%
% Inputs:
% a - first input vector
% b - second input vector
%
% Outputs:
% r - result of the convolution
%
% Author: Arnaud Delorme, CNL / Salk Institute, 2001
%
% See also: conv2(), conv()
% Copyright (C) 2001 Arnaud Delorme, Salk Institute, [email protected]
%
% This program is free software; you can redistribute it and/or modify
% it under the terms of the GNU General Public License as published by
% the Free Software Foundation; either version 2 of the License, or
% (at your option) any later version.
%
% This program is distributed in the hope that it will be useful,
% but WITHOUT ANY WARRANTY; without even the implied warranty of
% MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
% GNU General Public License for more details.
%
% You should have received a copy of the GNU General Public License
% along with this program; if not, write to the Free Software
% Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
function R = convolve( A, B )
% size of B must be odd
% convolve A and B (normalize by the sum of convolved elements)
% -------------------------------------------------------------
R = zeros( size(A) );
for index = 1:length(A)
sumconvo = 0;
for indexB = 1:length(B)
indexconvo = indexB-1-round(length(B)/2);
indexA = index + indexconvo+1;
if indexA > 0 & indexA <= length(A)
R(index) = R(index) + B(indexB)*A(indexA);
sumconvo = sumconvo + B(indexB);
end;
end;
R(index) = R(index) / sumconvo;
end;
return;
|
github
|
lcnbeapp/beapp-master
|
textgui.m
|
.m
|
beapp-master/Packages/eeglab14_1_2b/functions/miscfunc/textgui.m
| 6,446 |
utf_8
|
d4e6f305686806a2d18faf7a89d49999
|
% textgui() - make sliding vertical window. This window contain text
% with optional function calls at each line.
%
% Usage:
% >> textgui( commandnames, helparray, 'key', 'val' ...);
%
% Inputs:
% commandnames - name of the commands. Either char array or cell
% array of char. All style are 'pushbuttons' exept
% for empty commands.
% helparray - cell array of commands to execute for each menu
% (default is empty)
%
% Optional inputs:
% 'title' - window title
% 'fontweight' - font weight. Single value or cell array of value for each line.
% 'fontsize' - font size. Single value or cell array of value for each line.
% 'fontname' - font name. Single value or cell array of value for each line.
% 'linesperpage' - number of line per page. Default is 20.
%
% Author: Arnaud Delorme, CNL / Salk Institute, 2001
%
% Example:
% textgui({ 'function1' 'function2' }, {'hthelp(''function1'')' []});
% % this function will call a pop_up window with one button on
% % 'function1' which will call the help of this function.
%
% Copyright (C) 2001 Arnaud Delorme, Salk Institute, [email protected]
%
% This program is free software; you can redistribute it and/or modify
% it under the terms of the GNU General Public License as published by
% the Free Software Foundation; either version 2 of the License, or
% (at your option) any later version.
%
% This program is distributed in the hope that it will be useful,
% but WITHOUT ANY WARRANTY; without even the implied warranty of
% MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
% GNU General Public License for more details.
%
% You should have received a copy of the GNU General Public License
% along with this program; if not, write to the Free Software
% Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
function tmp = textgui( textmenu, helparray, varargin);
XBORDERS = 0; % pixels
TOPORDINATE = 1.09;
TOPLINES = 2;
if nargin < 1
help textgui;
return;
end;
if nargin <2
helparray = cell(1, length( textmenu ));
end;
% optional parameters
% -------------------
if nargin >2
for i = 1:length(varargin)
if iscell(varargin{i}), varargin(i) = { varargin(i) }; end;
end;
g=struct(varargin{:});
else
g = [];
end;
try, g.title; catch, g.title = ''; end;
try, g.fontname; catch, g.fontname = 'courier'; end;
try, g.fontsize; catch, g.fontsize = 12; end;
try, g.fontweight; catch, g.fontweight = 'normal'; end;
try, g.linesperpage; catch, g.linesperpage = 20; end;
if isempty( helparray )
helparray = cell(1,200);
else
tmpcell = cell(1,200);
helparray = { helparray{:} tmpcell{:} };
end;
% number of elements
% ------------------
if iscell(textmenu) nblines = length(textmenu);
else nblines = size(textmenu,1);
end;
% generating the main figure
% --------------------------
fig = figure('position', [100 100 800 25*15], 'menubar', 'none', 'numbertitle', 'off', 'name', 'Help', 'color', 'w');
pos = get(gca,'position'); % plot relative to current axes
q = [pos(1) pos(2) 0 0];
s = [pos(3) pos(4) pos(3) pos(4)]./100;
% generating cell arrays
% ----------------------
if isstr(g.fontname), tmp1(1:nblines) = {g.fontname}; g.fontname = tmp1; end;
if isnumeric(g.fontsize), tmp2(1:nblines) = {g.fontsize}; g.fontsize = tmp2; end;
if isstr(g.fontweight), tmp3(1:nblines) = {g.fontweight}; g.fontweight = tmp3; end;
switch g.fontname{1}
case 'courrier', CHAR_WIDTH = 11; % pixels
case 'times', CHAR_WIDTH = 11; % pixels
otherwise, CHAR_WIDTH = 11;
end;
topordi = TOPORDINATE;
if ~isempty(g.title)
addlines = size(g.title,1)+1+TOPLINES;
if nblines+addlines < g.linesperpage
divider = g.linesperpage;
else
divider = nblines+addlines;
end;
ordinate = topordi-topordi*TOPLINES/divider;
currentheight = topordi/divider;
for index=1:size(g.title,1)
ordinate = topordi-topordi*(TOPLINES+index-1)/divider;
h = text( -0.1, ordinate, g.title(index,:), 'unit', 'normalized', 'horizontalalignment', 'left', ...
'fontname', g.fontname{1}, 'fontsize', g.fontsize{1},'fontweight', fastif(index ==1, 'bold', ...
'normal'), 'interpreter', 'none' );
end;
%h = uicontrol( gcf, 'unit', 'normalized', 'style', 'text', 'backgroundcolor', get(gcf, 'color'), 'horizontalalignment', 'left', ...
% 'position', [-0.1 ordinate 1.1 currentheight].*s*100+q, 'string', g.title, ...
% 'fontsize', g.fontsize{1}+1, 'fontweight', 'bold', 'fontname', g.fontname{1});
else
addlines = TOPLINES;
if nblines+addlines < g.linesperpage
divider = g.linesperpage;
else
divider = nblines+addlines;
end;
end;
maxlen = size(g.title,2);
for i=1:nblines
if iscell(textmenu) tmptext = textmenu{i};
else tmptext = textmenu(i,:);
end;
ordinate = topordi-topordi*(i-1+addlines)/divider;
currentheight = topordi/divider;
if isempty(helparray{i})
h = text( -0.1, ordinate, tmptext, 'unit', 'normalized', 'horizontalalignment', 'left', ...
'fontname', g.fontname{i}, 'fontsize', g.fontsize{i},'fontweight', g.fontweight{i}, 'interpreter', 'none' );
% h = uicontrol( gcf, 'unit', 'normalized', 'style', 'text', 'backgroundcolor', get(gcf, 'color'), 'horizontalalignment', 'left', ...
% 'position', [-0.1 ordinate 1.1 currentheight].*s*100+q, 'string', tmptext, 'fontname', g.fontname{i}, 'fontsize', g.fontsize{i},'fontweight', g.fontweight{i} );
else
h = text( -0.1, ordinate, tmptext, 'unit', 'normalized', 'color', 'b', 'horizontalalignment', 'left', ...
'fontname', g.fontname{i}, 'buttondownfcn', helparray{i}, 'fontsize', g.fontsize{i},'fontweight', g.fontweight{i}, 'interpreter', 'none' );
% h = uicontrol( gcf, 'callback', helparray{i}, 'unit','normalized', 'style', 'pushbutton', 'horizontalalignment', 'left', ...
% 'position', [-0.1 ordinate 1.1 currentheight].*s*100+q, 'string', tmptext, 'fontname', g.fontname{i}, 'fontsize', g.fontsize{i},'fontweight', g.fontweight{i});
end;
maxlen = max(maxlen, length(tmptext));
end;
pos = get(gcf, 'position');
set(gcf, 'position', [pos(1:2) maxlen*CHAR_WIDTH+2*XBORDERS 400]);
% = findobj('parent', gcf);
%set(h, 'fontname', 'courier');
if nblines+addlines < g.linesperpage
zooming = 1;
else
zooming = (nblines+addlines)/g.linesperpage;
end;
slider(gcf, 0, 1, 1, zooming, 0);
axis off;
|
github
|
lcnbeapp/beapp-master
|
kmeans_st.m
|
.m
|
beapp-master/Packages/eeglab14_1_2b/functions/miscfunc/kmeans_st.m
| 8,156 |
utf_8
|
8dec33b3e9581d7f84c4deb47caa720d
|
% KMEANS: K-means clustering of n points into k clusters so that the
% within-cluster sum of squares is minimized. Based on Algorithm
% AS136, which seeks a local optimum such that no movement of a
% point from one cluster to another will reduced the within-cluster
% sum of squares. Tends to find spherical clusters.
% Not globally optimal against all partitions, which is an NP-complete
% problem; thus allows for multiple restarts.
%
% Usage: [centr,clst,sse] = kmeans(X,k,restarts)
%
% X = [n x p] data matrix.
% k = number of desired clusters.
% restarts = optional number of restarts, after finding a new minimum
% sse, needed to end search [default=0].
% --------------------------------------------------------------------
% centr = [k x p] matrix of cluster centroids.
% clst = [n x 1] vector of cluster memberships.
% sse = total within-cluster sum of squared deviations.
%
% Hartigan,JA & MA Wong. 1979. Algorithm AS 136: A k-means clustering
% algorithm. Appl. Stat. 200:100-108.
% Milligan,G.W. & L. Sokol. 1980. A two-stage clustering algorithm with
% robustness recovery characteristics. Educational and Psychological
% Measurement 40:755-759.
% RE Strauss, 8/26/98
% 8/21/99 - changed misc statements for Matlab v5.
% 10/14/00 - use means() rather than mean() to update cluster centers;
% remove references to TRUE and FALSE.
function [centr,clst,sse] = kmeans_st(X,k,restarts)
if (nargin<3) restarts = []; end;
if (isempty(restarts))
restarts = 0;
end;
[n,p] = size(X);
if (k<1 | k>n)
error('KMEANS: k out of range 1-N');
end;
max_iter = 50;
highval = 10e8;
upgma_flag = 1; % Do UPGMA first time thru
% Repeat optimization until have 'restart' attempts with no better solution
restart_iter = restarts + 1;
best_sse = highval;
while (restart_iter > 0)
restart_iter = restart_iter - 1;
c1 = zeros(n,1);
c2 = c1;
clst = c1;
nclst = zeros(k,1);
% Estimate initial cluster centers via UPGMA the first time, and randomly
% thereafter.
if (upgma_flag) % If UPGMA,
upgma_flag = 0;
dist = eucl(X); % All interpoint distances
topo = upgma(dist,[],0); % UPGMA dendrogram topology
grp = [1:n]'; % Identify obs in each of k grps
for step = 1:(n-k)
t1 = topo(step,1);
t2 = topo(step,2);
t3 = topo(step,3);
indx = find(grp==t1);
grp(indx) = t3 * ones(length(indx),1);
indx = find(grp==t2);
grp(indx) = t3 * ones(length(indx),1);
end;
grpid = uniquef(grp); % Unique group identifiers
centr = zeros(k,p);
for kk = 1:length(grpid); % Calculate group centroids
g = grpid(kk);
indx = find(grp == g);
Xk = X(indx,:);
if (size(Xk,1)>1)
centr(kk,:) = mean(Xk);
else
centr(kk,:) = Xk;
end;
end;
else % Else if randomized,
rndprm = randperm(n); % Pull out random set of points
centr = X(rndprm(1:k),:);
end;
% For each point i, find its two closest centers, c1(i) and c2(i), and
% assign it to c1(i)
dist = zeros(n,k);
for kk = 1:k % Dists to centers of all clusters
dist(:,kk) = eucl(X,centr(kk,:));
end;
[d,indx] = sort(dist'); % Sort points separately
c1 = indx(1,:)';
c2 = indx(2,:)';
% Update cluster centers to be the centroids of points contained within them
for kk = 1:k
indx = find(c1==kk);
len_indx = length(indx);
% if (len_indx>1)
% centr(kk,:) = mean(X(indx,:));
% else
% centr(kk,:) = X(indx,:);
% end;
centr(kk,:) = means(X(indx,:));
nclst(kk) = len_indx;
end;
% Initialize working matrices
live = ones(k,1);
R1 = zeros(n,1);
R2 = zeros(k,1);
adj1 = nclst ./ (nclst+1);
adj2 = nclst ./ (nclst-1+eps);
update = n * ones(k,1);
for i = 1:n % Adjusted dist from each pt to own cluster center
R1(i) = adj2(c1(i)) * eucl(X(i,:),centr(c1(i),:))^2;
end;
% Iterate
iter = 0;
while ((iter < max_iter) & (any(live)))
iter = iter+1;
% Optimal-transfer stage
i = 0;
while ((i<n) & any(live)) % Cycle thru points
i = i+1;
update = update-1; % Decrement cluster update counters
L1 = c1(i); % Pt i is in cluster L1
if (nclst(L1)>1) % If point i is not sole member of L1,
R2 = adj1(L1) .* eucl(centr,X(i,:)).^2; % Dists from pt to cluster centers
if (live(L1)) % If L1 is in live set,
R2(L1) = highval; % find min R2 over all clusters
[r2min,L2] = min(R2);
else % If L1 is not in live set,
indx = find(~live); % find min R2 over live clusters only
R2([L1;indx]) = highval * ones(length(indx)+1,1);
[r2min,L2] = min(R2);
end;
if (r2min >= R1(i)) % No reallocation necessary
c2(i) = L2;
else % Else reallocate pt to new cluster
c1(i) = L2;
c2(i) = L1;
for kk = [L1,L2] % Recalc cluster centers and sizes
indx = find(c1==kk);
len_indx = length(indx);
if (len_indx>1)
centr(kk,:) = mean(X(indx,:));
else
centr(kk,:) = X(indx,:);
end;
nclst(kk) = len_indx;
end;
adj1([L1,L2]) = nclst([L1,L2]) ./ (nclst([L1,L2])+1);
adj2([L1,L2]) = nclst([L1,L2]) ./ (nclst([L1,L2])-1+eps);
R1(i) = adj2(c1(i)) * eucl(X(i,:),centr(c1(i),:))^2;
live([L1,L2]) = [1,1]; % Put into live set
update([L1,L2]) = [n,n]; % Reinitialize update counters
end;
end; % if nclst(L1)>1
indx = find(update<1); % Remove clusters from live set
if (~isempty(indx)) % that haven't been recently updated
live(indx) = zeros(length(indx),1);
end;
end; % while (i<n & any(live))
if (any(live))
% Quick transfer stage
for i = 1:n % Cycle thru points
L1 = c1(i);
L2 = c2(i);
if (any(live([L1,L2])) & nclst(L1)>1)
R2 = adj1(L2) .* eucl(centr(L2,:),X(i,:)).^2; % Dists from pt to L2 center
if (R1>=R2)
temp = c1(i); % Switch L1 & L2
c1(i) = c2(i);
c2(i) = temp;
for kk = [L1,L2] % Recalc cluster centers and sizes
indx = find(c1==kk);
centr(kk,:) = mean(X(indx,:));
nclst(kk) = length(indx);
end;
adj1([L1,L2]) = nclst([L1,L2]) ./ (nclst([L1,L2])+1);
adj2([L1,L2]) = nclst([L1,L2]) ./ (nclst([L1,L2])-1+eps);
R1(i) = adj2(c1(i)) * eucl(X(i,:),centr(c1(i),:))^2;
live([L1,L2]) = [1,1]; % Put into live set
update([L1,L2]) = [n,n]; % Reinitialize update counters
end;
end;
end;
end; % if any(live)
end; % while iter<max_iter & any(live)
sse = 0; % Calc final total sum-of-squares
for i=1:n
sse = sse + eucl(X(i,:),centr(c1(i),:))^2;
end;
if (sse < best_sse) % Update best solution so far
best_sse = sse;
best_c1 = c1;
best_centr = centr;
restart_iter = restarts;
end;
end; % while (restart_iter > 0)
clst = best_c1;
centr = best_centr;
sse = best_sse;
return;
|
github
|
lcnbeapp/beapp-master
|
caliper.m
|
.m
|
beapp-master/Packages/eeglab14_1_2b/functions/miscfunc/caliper.m
| 6,421 |
utf_8
|
a3602aa087935fa1182c2455a6e8d7ef
|
% caliper() - Measure a set of spatial components of a given data epoch relative to
% a reference epoch and decomposition.
% Usage:
% >> [amp,window]=caliper(newepoch,refepoch,weights,compnums,filtnums,times,'noplot');
%
% Inputs:
% newepoch = (nchannels,ntimes) new data epoch
% refepoch = a (nchannels,ntimes) reference data epoch
% weights = (nchannels,ncomponents) unmixing matrix (e.g., ICA weights*sphere)
% compnums = vector of component numbers to return amplitudes for {def|0: all}
% filtnums = [srate highpass lowpass] filter limits for refepoch {def|0: allpass}
% times = [start_ms end_ms] epoch latency limits, else latencies vector {def|0: 0:EEG.pnts-1}
% 'noplot' = produce no plots {default: plots windows for the first <=3 components}
%
% Outputs:
% amps = (1,length(compnums)) vector of mean signed component rms amplitudes
% windows = (length(compnums)),length(times)) matrix of tapering windows used
%
% Notes:
% Function caliper() works as follows: First the reference epoch is decomposed using
% the given weight matrix (may be ICA, PCA, or etc). Next, the time course of the
% main lobe of the activation in the reference epoch (from max to 1st min, forward
% and backward in time from abs max, optionally after bandpass filtering) is used
% to window the new epoch. Then, the windowed new epoch is decomposed by the same
% weight matrix, and signed rms amplitude (across the channels) is returned of the
% projection of each of the specified component numbers integrated across the windowed
% epoch. If not otherwise specified, plots the windows for the first <= 3 components listed.
%
% Example: Given a grand mean response epoch and weight matrix, it can be used
% to measure amps of grand mean components in single-subject averages.
%
% Authors: Scott Makeig & Marissa Westerfield, SCCN/INC/UCSD, La Jolla, 11/2000
% Copyright (C) 11/2000 Scott Makeig & Marissa Westerfield,, SCCN/INC/UCSD
%
% This program is free software; you can redistribute it and/or modify
% it under the terms of the GNU General Public License as published by
% the Free Software Foundation; either version 2 of the License, or
% (at your option) any later version.
%
% This program is distributed in the hope that it will be useful,
% but WITHOUT ANY WARRANTY; without even the implied warranty of
% MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
% GNU General Public License for more details.
%
% You should have received a copy of the GNU General Public License
% along with this program; if not, write to the Free Software
% Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
% Edit History:
% 12/05/00 -- added fig showing data, ref activation, and window vector -mw
% 12/19/00 -- adjusted new icaproj() args -sm
% 01-25-02 reformated help & license -ad
function [amps,windows] = caliper(newepoch,refepoch,weights,compnums,filtnums,times,noplot)
if nargin < 3
help caliper
return
end
if nargin<4
compnums = 0;
end
nchans = size(newepoch,1);
ntimes = size(newepoch,2);
if compnums(1) == 0 | isempty(compnums(1))
compnums = 1:nchans;
end
if min(compnums) < 1 | max(compnums) > size(weights,2)
help caliper
return
end
if nargin<5
filtnums = [];
else
if isempty(filtnums)
filtnums = [];
elseif length(filtnums)==1 & filtnums(1)==0
filtnums = [];
elseif length(filtnums) ~= 3
fprintf('\ncaliper(): filter parameters (filtnums) must have length 3.\n')
return
end
end
if nargin< 6 | isempty(times) | (length(times)==1 & times(1)==0)
times = 0:ntimes-1;
else
if length(times) ~= ntimes
if length(times) ~= 2
fprintf('caliper(): times argument should be [startms endms] or vector.\n')
return
else
times = times(1):(times(2)-times(1))/(ntimes-1):times(2);
times = times(1:ntimes);
end
end
end
if nargin < 7
noplot = 0;
else
noplot = 1;
end
refact = weights(compnums,:)*refepoch; % size (length(compnums),ntimes)
newact = weights(compnums,:)*newepoch;
if length(filtnums) == 3
if ~exist('eegfilt')
fprintf('caliper(): function eegfilt() not found - not filtering refepoch.\n');
else
try
refact = eegfilt(refact,filtnums(1),filtnums(2),filtnums(3));
catch
fprintf('\n%s',lasterr)
return
end
end
end
if size(weights,1) == size(weights,2)
winv = inv(weights);
else
winv = pinv(weights);
end
winvrms = sqrt(mean(winv.*winv)); % map rms amplitudes
amps = [];
windows = [];
n = 1; % component index
for c=compnums
if floor(c) ~= c
help caliper
fprintf('\ncaliper(): component numbers must be integers.\n')
return
end
[lobemax i] = max(abs(refact(n,:)));
f = i+1;
oldact = lobemax;
while f>0 & f<=ntimes & abs(refact(n,f)) < oldact
oldact = abs(refact(n,f));
f = f+1;
end % f is now one past end of "main lobe"
lobeend = f-1;
f = i-1;
oldact = lobemax;
while f>0 & f<=ntimes & abs(refact(n,f)) < oldact
oldact = abs(refact(n,f));
f = f-1;
end % f is now one past start of "main lobe"
lobestart = f+1;
refact(n,1:lobestart) = zeros(1,length(1:lobestart));
refact(n,lobeend:end) = zeros(1,length(lobeend:ntimes));
windows = [windows; refact(n,:)];
refnorm = sum(refact(n,:));
if abs(refnorm)<1e-25
fprintf('caliper(): near-zero activation for component %d - returning NaN amp.\n',c)
amps = [amps NaN];
else
refact(n,:) = refact(n,:)/refnorm; % make reference epoch window sum to 1
amps = [amps winvrms(c)*sum(refact(n,:).*newact(n,:))];
end
n = n+1;
if ~noplot & n <= 4 %%% only plot out at most the first 3 components
refproj = icaproj(refepoch,weights,c);
refproj = env(refproj);
windproj = winv(:,c)*(refact(n-1,:)*refnorm);
windproj = env(windproj);
figure; plot(times,newepoch(2:nchans,:),'g');
hold on;h=plot(times,newepoch(1,:),'g');
hold on;h=plot(times,newepoch(1,:),'g',...
times,refproj(1,:),'b',...
times,windproj(1,:),'r','LineWidth',2);
hold on;plot(times,refproj(2,:),'b',times,windproj(2,:),'r','LineWidth',2);
set(h(1),'linewidth',1);
legend(h,'new data','comp. act.','window');
title(['Component ',int2str(c),'; rms amplitude = ',num2str(amps(n-1))],...
'FontSize',14);
ylabel('Potential (uV)');
end; %% endif
end % c
|
github
|
lcnbeapp/beapp-master
|
help2html2.m
|
.m
|
beapp-master/Packages/eeglab14_1_2b/functions/miscfunc/help2html2.m
| 16,616 |
utf_8
|
0b84a93365f77c167a0f2096b04d0f30
|
% help2html() - Convert a Matlab m-file help-message header into an .html help file
%
% Usage:
% >> linktext = help2html( filein, fileout, 'key1', val1, 'key2', val2 ...);
%
% Inputs:
% filein - input filename (with .m extension)
% fileout - output filename (if empty, generated automatically)
%
% Optional inputs:
% 'header' - command to insert in the header (i.e. javascript
% declaration or meta-tags). {default: none}.
% 'footer' - command to insert at the end of the .html file (e.g.,
% back button). {default: none}.
% 'refcall' - syntax to call references. {default: '%s.html'} For
% javascript function uses 'javascript:funcname(''%s.js'')'
% 'font' - font name
% 'background' - background tag (i.e. '<body BACKGROUND="img.jpg">').
% {default: none}.
% 'outputlink' - html command text to link to the generated .html page.
% Must contain two '%s' symbols to the function title
% and to the function link.
% Ex: ... href="%s.html" ... {default: standard .html href}.
% 'outputtext' - Text used in the outputlink. {default: the function
% name}
% 'outputonly' - ['on'|'off'] Only generate the linktext {default: 'off'}
%
% Output:
% fileout - .html file written to disk
% linktext - html-text link to the output file
%
% M-file format:
% The following lines describe the header format of an m-file function
% to allow .html help file generation. Characters '-' and ':' are used
% explicitly by the function for parsing.
%
%% function_name() - description line 1
%% description line 2
%% etc.
%%
%% Title1:
%% descriptor1 - text line 1
%% text line 2
%% descriptor2 - [type] text line 1
%% "descriptor 3" - text line 1 (see notes)
%% etc.
%%
%% Title2:
%% text line 1 [...](see notes)
%% text line 2
%%
%% See also:
%% function1(), function2()
%
% Author: Arnaud Delorme, Salk Institute 2001
%
% Notes: 1) The text lines below Title2 are considered as is (i.e.,
% preserving Matlab carriage returns) unless there is a
% Matlab continuation cue ('...'). In this case, lines are
% contcatenated. As below 'Title1', all text lines following
% each descriptor (i.e., single_word followed by '-' or '='
% or multiple quoted words followed by a '-' or '=')
% are concatenated.
% 2) The pattern 'function()' is detected and is printed in bold
% if it is the first function descriptor. Otherwise,
% it is used as a web link to the .html function file
% 'function.html' if this exists.
% 3) If a 'function.jpg' image file (with same 'function' name) exists,
% the image is inserted into the function .html file following
% the function description. If the .jpg file is absent, the function
% checks for the presence of a .gif file.
% 4) Lines beginning by '%%' are not interpreted and will be printed as is.
% 5) if [type] is present in a "descriptor2 - [type] text line 1"
% type is bolded.
% Copyright (C) 2001 Arnaud Delorme, Salk Institute, [email protected]
%
% This program is free software; you can redistribute it and/or modify
% it under the terms of the GNU General Public License as published by
% the Free Software Foundation; either version 2 of the License, or
% (at your option) any later version.
%
% This program is distributed in the hope that it will be useful,
% but WITHOUT ANY WARRANTY; without even the implied warranty of
% MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
% GNU General Public License for more details.
%
% You should have received a copy of the GNU General Public License
% along with this program; if not, write to the Free Software
% Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
function [linktext,allvars,alltext] = help2html( filename, htmlfile, varargin)
if nargin < 1
help help2html;
return;
end;
if nargin <3
g = [];
else
g = struct( varargin{:});;
end;
try, g.font; catch, g.font = 'Helvetica'; end;
g.functionname = [ '<FONT FACE="' g.font '"><FONT SIZE =+2><B>%s</B></FONT></FONT>' ];
g.description = [ '<FONT FACE="' g.font '">%s</FONT>' ];
g.title = [ '<FONT FACE="' g.font '"><FONT SIZE =+1><B>%s</B></FONT></FONT>' ];
g.var = [ '<DIV ALIGN=RIGHT><FONT FACE="' g.font '"><I>%s </I></FONT></DIV>' ];
g.vartext = [ '<FONT FACE="' g.font '">%s</FONT>' ];
g.text = [ '<FONT FACE="' g.font '">%s</FONT>' ];
g.normrow = '<tr VALIGN=TOP NOSAVE>';
g.normcol1 = '<td VALIGN=TOP NOSAVE>';
g.normcol2 = '<td VALIGN=BOTTOM NOSAVE>';
g.doublecol = '<td ALIGN=CENTER COLSPAN="2" NOSAVE>';
g.seefile = [ '<FONT FACE="' g.font '">See the matlab file <A HREF="%s" target="_blank">%s</A> (may require other functions)</FONT><BR><BR>' ];
try, g.outputonly; catch, g.outputonly = 'off'; end;
try, g.background; catch, g.background = ''; end;
try, g.header; catch, g.header = ''; end;
try, g.footer; catch, g.footer = ''; end;
try, g.refcall; catch, g.refcall = '%s.html'; end;
try, g.outputlink; catch, g.outputlink = [ g.normrow g.normcol1 '<FONT FACE="' g.font '"><A HREF="%s.html">%s.html</A></td>' g.normcol2 '%s</FONT></td></tr>' ]; end;
g.footer = [ '<FONT FACE="' g.font '">' g.footer '</FONT>' ];
if nargin < 1
help help2html;
return;
end;
% output file
% -----------
if nargin < 2 | isempty(htmlfile);
indexdot = findstr( filename, '.');
if isempty(indexdot), indexdot = length(filename)+1; end;
htmlfile = [ filename(1:indexdot(end)-1) '.html' ];
else
indexdot = findstr( filename, '.');
end;
% open files
% ----------
fid = fopen( filename, 'r');
if fid == -1
error('Input file not found');
end;
if ~strcmp(g.outputonly, 'on')
fo = fopen(htmlfile, 'w');
if fo == -1
error('Cannot open output file');
end;
% write header
% ------------
fprintf(fo, '<HTML><HEAD>%s</HEAD><BODY>\n%s\n<table WIDTH="100%%" NOSAVE>\n', g.header, g.background);
end;
cont = 1;
% scan file
% -----------
str = fgets( fid );
% if first line is the name of the function, reload
if str(1) ~= '%', str = fgets( fid ); end;
% state variables
% -----------
maindescription = 1;
varname = [];
oldvarname = [];
vartext = [];
newvar = 0;
allvars = {};
alltext = {};
indexout = 1;
while (str(1) == '%')
str = deblank(str(2:end-1));
% --- DECODING INPUT
newvar = 0;
str = deblank2(str);
if ~isempty(str)
% find a title
% ------------
i2d = findstr(str, ':');
newtitle = 0;
if ~isempty(i2d)
i2d = i2d(1);
switch lower(str(1:i2d))
case { 'usage:' 'authors:' 'author:' 'notes:' 'note:' 'input:' ...
'inputs:' 'outputs:' 'output:' 'example:' 'examples:' 'see also:' }, newtitle = 1;
end;
if (i2d == length(str)) & (str(1) ~= '%'), newtitle = 1; end;
end;
if newtitle
tilehtml = str(1:i2d);
newtitle = 1;
oldvarname = varname;
oldvartext = vartext;
if i2d < length(str)
vartext = formatstr(str(i2d+1:end), g.refcall);
else vartext = [];
end;
varname = [];
else
% not a title
% ------------
% scan lines
[tok1 strrm] = mystrtok( str );
[tok2 strrm] = strtok( strrm );
if ~isempty(tok2) & ( tok2 == '-' | tok2 == '=') % new variable
newvar = 1;
oldvarname = varname;
oldvartext = vartext;
if ~maindescription
varname = formatstr( tok1, g.refcall);
else
varname = tok1;
end;
strrm = deblank(strrm); % remove tail blanks
strrm = deblank(strrm(end:-1:1)); % remove initial blanks
strrm = formatstr( strrm(end:-1:1), g.refcall);
vartext = strrm;
else
% continue current text
str = deblank(str); % remove tail blanks
str = deblank(str(end:-1:1)); % remove initial blanks
str = formatstr( str(end:-1:1), g.refcall );
if isempty(vartext)
vartext = str;
else
if ~isempty(varname)
vartext = [ vartext ' ' str]; % espace if in array
else
if all(vartext( end-2:end) == '.')
vartext = [ deblank2(vartext(1:end-3)) ' ' str]; % espace if '...'
else
vartext = [ vartext '<BR>' str]; % CR otherwise
end;
end;
end;
end;
newtitle = 0;
end;
% --- END OF DECODING
str = fgets( fid );
% test if last entry
% ------------------
if str(1) ~= '%'
if ~newtitle
if ~isempty(oldvarname)
allvars{indexout} = oldvarname;
alltext{indexout} = oldvartext;
indexout = indexout + 1;
fprintf( fo, [ '</tr>' g.normrow g.normcol1 g.var '</td>\n' ], oldvarname);
fprintf( fo, [ g.normcol2 g.vartext '</td></tr>\n' ], finalformat(oldvartext));
else
if ~isempty(oldvartext)
fprintf( fo, [ g.normcol2 g.text '</td></tr>\n' ], finalformat(oldvartext));
end;
end;
newvar = 1;
oldvarname = varname;
oldvartext = vartext;
end;
end;
% test if new input for an array
% ------------------------------
if newvar | newtitle
if maindescription
if ~isempty(oldvartext) % FUNCTION TITLE
maintext = oldvartext;
% generate the output command
% ---------------------------
try, g.outputtext; catch, g.outputtext = ''; end;
if isempty(g.outputtext), g.outputtext = filename(1:indexdot(end)-1); end;
linktext = sprintf( g.outputlink, g.outputtext, filename(1:indexdot(end)-1), maintext );
if strcmp(g.outputonly, 'on')
fclose(fid);
return;
end;
maindescription = 0;
functioname = oldvarname( 1:findstr( oldvarname, '()' )-1);
fprintf( fo, [g.normrow g.normcol1 g.functionname '</td>\n'],upper(functioname));
fprintf( fo, [g.normcol2 g.description '</td></tr>\n'], [ upper(oldvartext(1)) oldvartext(2:end) ]);
% INSERT IMAGE IF PRESENT
imagename = [];
imagename1 = [ htmlfile( 1:findstr( htmlfile, functioname )-1) functioname '.jpg' ];
imagename2 = [ htmlfile( 1:findstr( htmlfile, functioname )-1) functioname '.gif' ];
if exist( imagename2 ), imagename = imagename2; end;
if exist( imagename1 ), imagename = imagename1; end;
if ~isempty(imagename) % do not make link if the file does not exist
imageinfo = imfinfo(imagename);
if imageinfo.Width < 600
fprintf(fo, [ g.normrow g.doublecol ...
'<CENTER><BR><A HREF="' imagename '" target="_blank"><img SRC=' imagename ...
'></A></CENTER></td></tr>' ]);
else
fprintf(fo, [ g.normrow g.doublecol ...
'<CENTER><BR><A HREF="' imagename '" target="_blank"><img SRC=' imagename ...
' width=600></A></CENTER></td></tr>' ]);
end;
end;
end;
elseif ~isempty(oldvarname)
allvars{indexout} = oldvarname;
alltext{indexout} = oldvartext;
indexout = indexout + 1;
fprintf( fo, [ '</tr>' g.normrow g.normcol1 g.var '</td>\n' ], oldvarname);
fprintf( fo, [ g.normcol2 g.vartext '</td></tr>\n' ], finalformat(oldvartext));
else
if ~isempty(oldvartext)
fprintf( fo, [ g.normcol2 g.text '</td></tr>\n' ], finalformat(oldvartext));
end;
end;
end;
% print title
% -----------
if newtitle
fprintf( fo, [ g.normrow g.doublecol '<BR></td></tr>' g.normrow g.normcol1 g.title '</td>\n' ], tilehtml);
if str(1) ~= '%' % last input
fprintf( fo, [ g.normcol2 g.text '</td></tr>\n' ], vartext);
end;
oldvarname = [];
oldvartext = [];
end;
else
str = fgets( fid );
end;
end;
fprintf( fo, [ '</table>\n<BR>' g.seefile '%s</BODY></HTML>'], lower(filename), filename, g.footer);
fclose( fid );
fclose( fo );
return;
% -----------------
% sub-functions
% -----------------
function str = deblank2( str ); % deblank two ways
str = deblank(str(end:-1:1)); % remove initial blanks
str = deblank(str(end:-1:1)); % remove tail blanks
return;
function strout = formatstr( str, refcall );
[tok1 strrm] = strtok( str );
strout = [];
while ~isempty(tok1)
tokout = functionformat( tok1, refcall );
if isempty( strout)
strout = tokout;
else
strout = [strout ' ' tokout ];
end;
[tok1 strrm] = strtok( strrm );
end;
return;
% final formating
function str = finalformat(str); % bold text in bracket if just in the beginning
tmploc = sort(union(find(str == '['), find(str == ']')));
if ~isempty(tmploc) & str(1) == '['
if mod(length(tmploc),2) ~= 0, str, error('Opening but no closing bracket'); end;
tmploc = tmploc(1:2);
str = [ str(1:tmploc(1)) '<b>' str(tmploc(1)+1:tmploc(2)-1) '</b>' str(tmploc(2):end) ];
end;
%tmploc = find(str == '"');
%if ~isempty(tmploc)
% if mod(length(tmploc),2) ~= 0, str, error('Opening but no closing parenthesis'); end;
% for index = length(tmploc):-2:1
% str = [ str(1:tmploc(index-1)-1) '<b>' str(tmploc(index-1)+1:tmploc(index)-1) '</b>' str(tmploc(index)+1:end) ];
% end;
%end;
function tokout = functionformat( tokin, refcall );
tokout = tokin; % default
[test, realtokin, tail, beg] = testfunc1( tokin );
if ~test, [test, realtokin, tail] = testfunc2( tokin ); end;
if test
i1 = findstr( refcall, '%s');
i2 = findstr( refcall(i1(1):end), '''');
if isempty(i2) i2 = length( refcall(i1(1):end) )+1; end;
filename = [ realtokin refcall(i1+2:i1+i2-2)]; % concatenate filename and extension
%disp(filename)
if exist( filename ) % do not make link if the file does not exist
tokout = sprintf( [ beg '<A HREF="' refcall '">%s</A>' tail ' ' ], realtokin, realtokin );
end;
end;
return;
function [test, realtokin, tail, beg] = testfunc1( tokin ) % test if is string is 'function()[,]'
test = 0; realtokin = ''; tail = ''; beg = '';
if ~isempty( findstr( tokin, '()' ) )
if length(tokin)<3, return; end;
realtokin = tokin( 1:findstr( tokin, '()' )-1);
if length(realtokin) < (length(tokin)-2) tail = tokin(end); else tail = []; end;
test = 1;
if realtokin(1) == '(', realtokin = realtokin(2:end); beg = '('; end;
if realtokin(1) == ',', realtokin = realtokin(2:end); beg = ','; end;
end;
return;
function [test, realtokin, tail] = testfunc2( tokin ) % test if is string is 'FUNCTION[,]'
test = 0; realtokin = ''; tail = '';
if all( upper(tokin) == tokin)
if tokin(end) == ','
realtokin = tokin(1:end-1);
tail = ',';
else
realtokin = tokin;
end;
testokin = realtokin;
testokin(findstr(testokin, '_')) = 'A';
testokin(findstr(testokin, '2')) = 'A';
if all(double(testokin) > 64) & all(double(testokin) < 91)
test = 1;
end;
realtokin = lower(realtokin);
end;
return;
function [tok, str] = mystrtok(str)
[tok str] = strtok(str);
if tok(1) == '"'
while tok(end) ~= '"'
[tok2 str] = strtok(str);
if isempty(tok2), tok, error('can not find closing quote ''"'' in previous text'); end;
tok = [tok ' ' tok2];
end;
end;
|
github
|
lcnbeapp/beapp-master
|
getallmenus.m
|
.m
|
beapp-master/Packages/eeglab14_1_2b/functions/miscfunc/getallmenus.m
| 2,254 |
utf_8
|
757fe9c0de1f75dd78ee6012bb2c3ddf
|
% getallmenus() - get all submenus of a window or a menu and return
% a tree.
%
% Usage:
% >> [tree nb] = getallmenus( handler );
%
% Inputs:
% handler - handler of the window or of a menu
%
% Outputs:
% tree - text output
% nb - number of elements in the tree
%
% Author: Arnaud Delorme, CNL / Salk Institute, 2001
% Copyright (C) 2001 Arnaud Delorme, Salk Institute, [email protected]
%
% This program is free software; you can redistribute it and/or modify
% it under the terms of the GNU General Public License as published by
% the Free Software Foundation; either version 2 of the License, or
% (at your option) any later version.
%
% This program is distributed in the hope that it will be useful,
% but WITHOUT ANY WARRANTY; without even the implied warranty of
% MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
% GNU General Public License for more details.
%
% You should have received a copy of the GNU General Public License
% along with this program; if not, write to the Free Software
% Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
function [txt, nb, labels] = getallmenus( handler, level )
NBBLANK = 6; % number of blank for each submenu input
if nargin < 1
help getallmenus;
return;
end;
if nargin < 2
level = 0;
end;
txt = '';
nb = 0;
labels = {};
allmenu = findobj('parent', handler, 'type', 'uimenu');
allmenu = allmenu(end:-1:1);
if ~isempty(allmenu)
for i=1:length( allmenu );
[txtmp nbtmp tmplab] = getallmenus(allmenu(i), level+1);
txtmp = [ blanks(level*NBBLANK) txtmp ];
txt = [ txtmp txt ];
labels = { tmplab labels{:} };
nb = nb+nbtmp;
end;
end;
try
txt = [ get(handler, 'Label') 10 txt ];
nb = nb+1;
catch, end;
if isempty(labels)
labels = { nb };
end;
% transform into array of text
% ----------------------------
if nargin < 2
txt = [10 txt];
newtext = zeros(1000, 1000);
maxlength = 0;
lines = find( txt == 10 );
for index = 1:length(lines)-1
tmptext = txt(lines(index)+1:lines(index+1)-1);
if maxlength < length( tmptext ), maxlength = length( tmptext ); end;
newtext(index, 1:length(tmptext)) = tmptext;
end;
txt = char( newtext(1:index+1, 1:maxlength) );
end;
return;
|
github
|
lcnbeapp/beapp-master
|
eeg_regepochs.m
|
.m
|
beapp-master/Packages/eeglab14_1_2b/functions/miscfunc/eeg_regepochs.m
| 6,723 |
utf_8
|
68a8bef2b1f7b22c806d132a4c322cc6
|
% eeg_regepochs() - Convert a continuous dataset into consecutive epochs of
% a specified regular length by adding dummy events of type
% and epoch the data around these events. Alternatively
% only insert events for extracting these epochs.
% May be used to split up continuous data for
% artifact rejection followed by ICA decomposition.
% The computed EEG.icaweights and EEG.icasphere matrices
% may then be exported to the continuous dataset and/or
% to its epoched descendents.
% Usage:
% >> EEGout = eeg_regepochs(EEG); % use defaults
% >> EEGout = eeg_regepochs(EEG, 'key', val, ...);
%
% Required input:
% EEG - EEG continuous data structure (EEG.trials = 1)
%
% Optional inputs:
% 'recurrence' - [in s] the regular recurrence interval of the dummy
% events used as time-locking events for the
% consecutive epochs {default: 1 s}
% 'limits' - [minsec maxsec] latencies relative to the time-locking
% events to use as epoch boundaries. Stated epoch length
% will be reduced by one data point to avoid overlaps
% {default: [0 recurrence_interval]}
% 'rmbase' - [NaN|latency] remove baseline (s). NaN does not remove
% baseline. 0 remove the pre-0 baseline. To
% remove the full epoch baseline, enter a value
% larger than the upper epoch limit. Default is 0.
% 'eventtype' - [string] name for the event type. Default is 'X'
% 'extractepochs' - ['on'|'off'] extract data epochs ('on') or simply
% insert events ('off'). Default is 'on'.
%
% Outputs:
% EEGout - the input EEG structure separated into consecutive
% epochs.
%
% See also: pop_editeventvals(), pop_epoch(), rmbase();
%
% Authors: Hilit Serby, Arnaud Delorme & Scott Makeig, SCCN/INC/UCSD, Sep 02, 2005
% Copyright (C) Hilit Serby, SCCN, INC, UCSD, Sep 02, 2005, [email protected]
%
% This program is free software; you can redistribute it and/or modify
% it under the terms of the GNU General Public License as published by
% the Free Software Foundation; either version 2 of the License, or
% (at your option) any later version.
%
% This program is distributed in the hope that it will be useful,
% but WITHOUT ANY WARRANTY; without even the implied warranty of
% MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
% GNU General Public License for more details.
%
% You should have received a copy of the GNU General Public License
% along with this program; if not, write to the Free Software
% Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
function EEG = eeg_regepochs(EEG, varargin)
if nargin < 1
help eeg_regepochs;
return;
end;
if length(EEG) > 1
EEG = pop_mergeset(EEG, [1:length(EEG)]);
end;
% test input variables
% --------------------
if ~isstruct(EEG) | ~isfield(EEG,'event')
error('first argument must be an EEG structure')
elseif EEG.trials > 1
error('input dataset must be continuous data (1 epoch)');
end
if nargin > 1 && ~isstr(varargin{1})
options = {};
if nargin >= 2, options = { options{:} 'recurrence' varargin{1} }; end;
if nargin >= 3, options = { options{:} 'limits' varargin{2} }; end;
if nargin >= 4, options = { options{:} 'rmbase' varargin{3} }; end;
else
options = varargin;
end;
g = finputcheck(options, { 'recurrence' 'real' [] 1;
'limits' 'real' [] [0 1];
'rmbase' 'real' [] 0;
'eventtype' 'string' {} 'X';
'extractepochs' 'string' { 'on','off' } 'on' }, 'eeg_regepochs');
if isstr(g), error(g); end;
if g.recurrence < 0 | g.recurrence > EEG.xmax
error('recurrence_interval out of bounds');
end
if nargin < 3
g.limits = [0 g.recurrence];
end
if length(g.limits) ~= 2 | g.limits(2) <= g.limits(1)
error('epoch limits must be a 2-vector [minsec maxsec]')
end
% calculate number of events to add
% ---------------------------------
bg = 0; % beginning of data
en = EEG.xmax; % end of data in sec
nu = floor(EEG.xmax/g.recurrence); % number of type 'X' events to add and epoch on
% bg = EEG.event(1).latency/EEG.srate; % time in sec of first event
% en = EEG.event(end).latency/EEG.srate; % time in sec of last event
% nu = length((bg+g.recurrence):g.recurrence:(en-g.recurrence)); % number of 'X' events, one every 'g.recurrence' sec
if nu < 1
error('specified recurrence_interval too long')
end
% print info on commandline
% -------------------------
eplength = g.limits(2)-g.limits(1);
fprintf('The input dataset will be split into %d epochs of %g s\n',nu,eplength);
fprintf('Epochs will overlap by %2.0f%%.\n',(eplength-g.recurrence)/eplength*100);
% insert events and urevents at the end of the current (ur)event tables
% ---------------------------------------------------------------------
fprintf('Inserting %d type ''%s'' events: ', nu, g.eventtype);
nevents = length(EEG.event);
% convert all event types to strings
for k = 1:nevents
EEG.event(k).type = num2str(EEG.event(k).type);
end
nurevents = length(EEG.urevent);
for k = 1:nu
if rem(k,40)
fprintf('.')
else
fprintf('%d',k)
end
if k==40 | ( k>40 & ~rem(k-40,70))
fprintf('\n');
end
EEG.event(nevents+k).type = g.eventtype;
EEG.event(nevents+k).latency = g.recurrence*(k-1)*EEG.srate+1;
EEG.urevent(nurevents+k).type = g.eventtype;
EEG.urevent(nurevents+k).latency = g.recurrence*(k-1)*EEG.srate+1;
EEG.event(nevents+k).urevent = nurevents+k;
end
fprintf('\n');
% sort the events based on their latency
% --------------------------------------
fprintf('Sorting the event table.\n');
EEG = pop_editeventvals( EEG, 'sort', {'latency' 0});
% split the dataset into epochs
% ------------------------------
if strcmpi(g.extractepochs, 'on')
fprintf('Splitting the data into %d %2.2f-s epochs\n',nu,eplength);
setname = sprintf('%s - %g-s epochs', EEG.setname, g.recurrence);
EEG = pop_epoch( EEG, { g.eventtype }, g.limits, 'newname', ...
setname, 'epochinfo', 'yes');
% baseline zero the epochs
% ------------------------
if ~isnan(g.rmbase) && g.limits(1) < g.rmbase
fprintf('Removing the pre %3.2f second baseline mean of each epoch.\n', g.rmbase);
EEG = pop_rmbase( EEG, [g.limits(1) g.rmbase]*1000);
end
end;
|
github
|
lcnbeapp/beapp-master
|
eegplotold.m
|
.m
|
beapp-master/Packages/eeglab14_1_2b/functions/miscfunc/eegplotold.m
| 33,034 |
utf_8
|
f08480f9c8c3fcde09afda52f574a1f3
|
% eegplotold() - display data in a horizontal scrolling fashion
% with (optional) gui controls (version 2.3)
% Usage:
% >> eegplotold(data,srate,spacing,eloc_file,windowlength,title)
% >> eegplotold('noui',data,srate,spacing,eloc_file,startpoint,color)
%
% Inputs:
% data - Input data matrix (chans,timepoints)
% srate - Sampling rate in Hz {default|0: 256 Hz}
% spacing - Space between channels (default|0: max(data)-min(data))
% eloc_file - Electrode filename as in >> topoplot example
% [] -> no labels; default|0 -> integers 1:nchans
% vector of integers -> channel numbers
% windowlength - Number of seconds of EEG displayed {default 10 s}
% color - EEG plot color {default black/white}
% 'noui' - Display eeg in current axes without user controls
%
% Author: Colin Humphries, CNL, Salk Institute, La Jolla, 5/98
%
% See also: eegplot(), eegplotgold(), eegplotsold()
% Copyright (C) Colin Humphries, CNL, Salk Institute 3/97 from eegplotold()
%
% This program is free software; you can redistribute it and/or modify
% it under the terms of the GNU General Public License as published by
% the Free Software Foundation; either version 2 of the License, or
% (at your option) any later version.
%
% This program is distributed in the hope that it will be useful,
% but WITHOUT ANY WARRANTY; without even the implied warranty of
% MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
% GNU General Public License for more details.
%
% You should have received a copy of the GNU General Public License
% along with this program; if not, write to the Free Software
% Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
% Runs under Matlab 5.0+ (not supported for Matlab 4)
%
% RCS-recorded version number, date, editor and comments
% $Log: eegplotold.m,v $
% Revision 1.3 2007/02/24 02:42:37 toby
% added auto-log line
%
%
% Edit History:
% 5-14-98 v2.1 fixed bug for small-variance data -ch
% 1-31-00 v2.2 exchanged meaning of > and >>, < and << -sm
% 8-15-00 v2.3 turned on SPACING_EYE and added int vector input for eloc_file -sm
% 12-16-00 added undocumented figure position arg (if not 'noui') -sm
% 01-25-02 reformated help & license, added links -ad
function [outvar1] = eegplotold(data,p1,p2,p3,p4,p5,p6)
% Defaults (can be re-defined):
DEFAULT_ELOC_FILE = 0; % Default electrode name file
% [] - none, 0 - numbered, or filename
DEFAULT_SAMPLE_RATE = 256; % Samplerate
DEFAULT_PLOT_COLOR = 'k'; % EEG line color
DEFAULT_AXIS_BGCOLOR = [.8 .8 .8];% EEG Axes Background Color
DEFAULT_FIG_COLOR = [.8 .8 .8]; % Figure Background Color
DEFAULT_AXIS_COLOR = 'k'; % X-axis, Y-axis Color, text Color
DEFAULT_WINLENGTH = 10; % Number of seconds of EEG displayed
DEFAULT_GRID_SPACING = 1; % Grid lines every n seconds
DEFAULT_GRID_STYLE = '-'; % Grid line style
YAXIS_NEG = 'off'; % 'off' = positive up
DEFAULT_NOUI_PLOT_COLOR = 'k'; % EEG line color for noui option
% 0 - 1st color in AxesColorOrder
DEFAULT_TITLEVAL = 2; % Default title
% string, 2 - variable name, 0 - none
SPACING_EYE = 'on'; % spacing I on/off
SPACING_UNITS_STRING = '\muV'; % optional units for spacing I Ex. uV
DEFAULT_AXES_POSITION = [0.0964286 0.15 0.842 0.788095];
% dimensions of main EEG axes
if nargin<1
help eegplotold
return
end
% %%%%%%%%%%%%%%%%%%%%%%%%
% Setup inputs
% %%%%%%%%%%%%%%%%%%%%%%%%
if ~isstr(data) % If NOT a 'noui' call or a callback from uicontrols
if nargin == 7 % undocumented feature - allows position to be specd.
posn = p6;
else
posn = NaN;
end
% if strcmp(YAXIS_NEG,'on')
% data = -data;
% end
if nargin < 6
titleval = 0;
else
titleval = p5;
end
if nargin < 5
winlength = 0;
else
winlength = p4;
end
if nargin < 4
eloc_file = DEFAULT_ELOC_FILE;
else
eloc_file = p3;
end
if nargin < 3
spacing = 0;
else
spacing = p2;
end
if nargin < 2
Fs = 0;
else
Fs = p1;
end
if isempty(titleval)
titleval = 0;
end
if isempty(winlength)
winlength = 0;
end
if isempty(spacing)
spacing = 0;
end
if isempty(Fs)
Fs = 0;
end
[chans,frames] = size(data);
if winlength == 0
winlength = DEFAULT_WINLENGTH; % Set window length
end
if ischar(eloc_file) % Read in electrode names
fid = fopen(eloc_file); % Read file
if fid < 1
error('error opening electrode file')
end
YLabels = fscanf(fid,'%d %f %f%s',[7 128]);
fclose(fid);
YLabels = char(YLabels(4:7,:)');
ii = find(YLabels == '.');
YLabels(ii) = ' ';
YLabels = flipud(str2mat(YLabels,' '));
elseif length(eloc_file) == chans
YLabels = num2str(eloc_file');
elseif length(eloc_file) == 1 & eloc_file(1) == 0
YLabels = num2str((1:chans)'); % Use numbers
else
YLabels = []; % no labels used
end
YLabels = flipud(str2mat(YLabels,' '));
if spacing == 0
spacing = (max(max(data')-min(data'))); % Set spacing to max/min data
if spacing > 10
spacing = round(spacing);
end
end
if titleval == 0
titleval = DEFAULT_TITLEVAL; % Set title value
end
if Fs == 0
Fs = DEFAULT_SAMPLE_RATE; % Set samplerate
end
% %%%%%%%%%%%%%%%%%%%%%%%%
% Prepare figure and axes
% %%%%%%%%%%%%%%%%%%%%%%%%
if isnan(posn) % no user-supplied position vector
figh = figure('UserData',[winlength Fs],...
'Color',DEFAULT_FIG_COLOR,...
'MenuBar','none','tag','eegplotold');
else
figh = figure('UserData',[winlength Fs],...
'Color',DEFAULT_FIG_COLOR,...
'MenuBar','none','tag','eegplotold','Position',posn);
end
%entry
ax1 = axes('tag','eegaxis','parent',figh,...
'userdata',data,...
'Position',DEFAULT_AXES_POSITION,...
'Box','on','xgrid','on',...
'gridlinestyle',DEFAULT_GRID_STYLE,...
'Xlim',[0 winlength*Fs],...
'xtick',[0:Fs*DEFAULT_GRID_SPACING:winlength*Fs],...
'Ylim',[0 (chans+1)*spacing],...
'YTick',[0:spacing:chans*spacing],...
'YTickLabel',YLabels,...
'XTickLabel',num2str((0:DEFAULT_GRID_SPACING:winlength)'),...
'TickLength',[.005 .005],...
'Color',DEFAULT_AXIS_BGCOLOR,...
'XColor',DEFAULT_AXIS_COLOR,...
'YColor',DEFAULT_AXIS_COLOR);
if isstr(titleval) % plot title
title(titleval)
elseif titleval == 2
title(inputname(1))
end
% %%%%%%%%%%%%%%%%%%%%%%%%%
% Set up uicontrols
% %%%%%%%%%%%%%%%%%%%%%%%%%
% Four move buttons: << < > >>
u(1) = uicontrol('Parent',figh, ...
'Units','points', ...
'Position',[49.1294 12.7059 50.8235 16.9412], ...
'Tag','Pushbutton1',...
'string','<<',...
'Callback','eegplotold(''drawp'',1)');
u(2) = uicontrol('Parent',figh, ...
'Units','points', ...
'Position',[105.953 12.7059 33.0353 16.9412], ...
'Tag','Pushbutton2',...
'string','<',...
'Callback','eegplotold(''drawp'',2)');
u(3) = uicontrol('Parent',figh, ...
'Units','points', ...
'Position',[195.882 12.7059 33.8824 16.9412], ...
'Tag','Pushbutton3',...
'string','>',...
'Callback','eegplotold(''drawp'',3)');
u(4) = uicontrol('Parent',figh, ...
'Units','points', ...
'Position',[235.765 12.7059 50.8235 16.9412], ...
'Tag','Pushbutton4',...
'string','>>',...
'Callback','eegplotold(''drawp'',4)');
% Text edit fields: EPosition ESpacing
u(5) = uicontrol('Parent',figh, ...
'Units','points', ...
'BackgroundColor',[1 1 1], ...
'Position',[144.988 10.1647 44.8941 19.4824], ...
'Style','edit', ...
'Tag','EPosition',...
'string','0',...
'Callback','eegplotold(''drawp'',0)');
u(6) = uicontrol('Parent',figh, ...
'Units','points', ...
'BackgroundColor',[1 1 1], ...
'Position',[379.482-30 11.8 46.5882 19.5], ...
'Style','edit', ...
'Tag','ESpacing',...
'string',num2str(spacing),...
'Callback','eegplotold(''draws'',0)');
% ESpacing buttons: + -
u(7) = uicontrol('Parent',figh, ...
'Units','points', ...
'Position',[435-30 22.9 22 13.5], ...
'Tag','Pushbutton5',...
'string','+',...
'FontSize',8,...
'Callback','eegplotold(''draws'',1)');
u(8) = uicontrol('Parent',figh, ...
'Units','points', ...
'Position',[435-30 6.7 22 13.5], ...
'Tag','Pushbutton6',...
'string','-',...
'FontSize',8,...
'Callback','eegplotold(''draws'',2)');
set(u,'Units','Normalized')
% %%%%%%%%%%%%%%%%%%%%%%%%%%%
% Set up uimenus
% %%%%%%%%%%%%%%%%%%%%%%%%%%%
% Figure Menu %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
m(7) = uimenu('Parent',figh,'Label','Figure');
m(8) = uimenu('Parent',m(7),'Label','Orientation');
uimenu('Parent',m(7),'Label','Close',...
'Callback','delete(gcbf)')
% Portrait %%%%%%%%
timestring = ['[OBJ1,FIG1] = gcbo;',...
'PANT1 = get(OBJ1,''parent'');',...
'OBJ2 = findobj(''tag'',''orient'',''parent'',PANT1);',...
'set(OBJ2,''checked'',''off'');',...
'set(OBJ1,''checked'',''on'');',...
'set(FIG1,''PaperOrientation'',''portrait'');',...
'clear OBJ1 FIG1 OBJ2 PANT1;'];
uimenu('Parent',m(8),'Label','Portrait','checked',...
'on','tag','orient','callback',timestring)
% Landscape %%%%%%%
timestring = ['[OBJ1,FIG1] = gcbo;',...
'PANT1 = get(OBJ1,''parent'');',...
'OBJ2 = findobj(''tag'',''orient'',''parent'',PANT1);',...
'set(OBJ2,''checked'',''off'');',...
'set(OBJ1,''checked'',''on'');',...
'set(FIG1,''PaperOrientation'',''landscape'');',...
'clear OBJ1 FIG1 OBJ2 PANT1;'];
uimenu('Parent',m(8),'Label','Landscape','checked',...
'off','tag','orient','callback',timestring)
% Display Menu %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
m(1) = uimenu('Parent',figh,...
'Label','Display');
% X grid %%%%%%%%%%%%
m(3) = uimenu('Parent',m(1),'Label','X Grid');
timestring = ['FIGH = gcbf;',...
'AXESH = findobj(''tag'',''eegaxis'',''parent'',FIGH);',...
'set(AXESH,''xgrid'',''on'');',...
'clear FIGH AXESH;'];
uimenu('Parent',m(3),'Label','on','Callback',timestring)
timestring = ['FIGH = gcbf;',...
'AXESH = findobj(''tag'',''eegaxis'',''parent'',FIGH);',...
'set(AXESH,''xgrid'',''off'');',...
'clear FIGH AXESH;'];
uimenu('Parent',m(3),'Label','off','Callback',timestring)
% Y grid %%%%%%%%%%%%%
m(4) = uimenu('Parent',m(1),'Label','Y Grid');
timestring = ['FIGH = gcbf;',...
'AXESH = findobj(''tag'',''eegaxis'',''parent'',FIGH);',...
'set(AXESH,''ygrid'',''on'');',...
'clear FIGH AXESH;'];
uimenu('Parent',m(4),'Label','on','Callback',timestring)
timestring = ['FIGH = gcbf;',...
'AXESH = findobj(''tag'',''eegaxis'',''parent'',FIGH);',...
'set(AXESH,''ygrid'',''off'');',...
'clear FIGH AXESH;'];
uimenu('Parent',m(4),'Label','off','Callback',timestring)
% Grid Style %%%%%%%%%
m(5) = uimenu('Parent',m(1),'Label','Grid Style');
timestring = ['FIGH = gcbf;',...
'AXESH = findobj(''tag'',''eegaxis'',''parent'',FIGH);',...
'set(AXESH,''gridlinestyle'',''--'');',...
'clear FIGH AXESH;'];
uimenu('Parent',m(5),'Label','- -','Callback',timestring)
timestring = ['FIGH = gcbf;',...
'AXESH = findobj(''tag'',''eegaxis'',''parent'',FIGH);',...
'set(AXESH,''gridlinestyle'',''-.'');',...
'clear FIGH AXESH;'];
uimenu('Parent',m(5),'Label','_ .','Callback',timestring)
timestring = ['FIGH = gcbf;',...
'AXESH = findobj(''tag'',''eegaxis'',''parent'',FIGH);',...
'set(AXESH,''gridlinestyle'','':'');',...
'clear FIGH AXESH;'];
uimenu('Parent',m(5),'Label','. .','Callback',timestring)
timestring = ['FIGH = gcbf;',...
'AXESH = findobj(''tag'',''eegaxis'',''parent'',FIGH);',...
'set(AXESH,''gridlinestyle'',''-'');',...
'clear FIGH AXESH;'];
uimenu('Parent',m(5),'Label','__','Callback',timestring)
% Scale Eye %%%%%%%%%
timestring = ['[OBJ1,FIG1] = gcbo;',...
'eegplotold(''scaleeye'',OBJ1,FIG1);',...
'clear OBJ1 FIG1;'];
m(7) = uimenu('Parent',m(1),'Label','Scale I','Callback',timestring);
% Title %%%%%%%%%%%%
uimenu('Parent',m(1),'Label','Title','Callback','eegplotold(''title'')')
% Settings Menu %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
m(2) = uimenu('Parent',figh,...
'Label','Settings');
% Window %%%%%%%%%%%%
uimenu('Parent',m(2),'Label','Window',...
'Callback','eegplotold(''window'')')
% Samplerate %%%%%%%%
uimenu('Parent',m(2),'Label','Samplerate',...
'Callback','eegplotold(''samplerate'')')
% Electrodes %%%%%%%%
m(6) = uimenu('Parent',m(2),'Label','Electrodes');
timestring = ['FIGH = gcbf;',...
'AXESH = findobj(''tag'',''eegaxis'',''parent'',FIGH);',...
'set(AXESH,''YTickLabel'',[]);',...
'clear FIGH AXESH;'];
uimenu('Parent',m(6),'Label','none','Callback',timestring)
timestring = ['FIGH = gcbf;',...
'AXESH = findobj(''tag'',''eegaxis'',''parent'',FIGH);',...
'YTICK = get(AXESH,''YTick'');',...
'YTICK = length(YTICK);',...
'set(AXESH,''YTickLabel'',flipud(str2mat(num2str((1:YTICK-1)''),'' '')));',...
'clear FIGH AXESH YTICK;'];
uimenu('Parent',m(6),'Label','numbered','Callback',timestring)
uimenu('Parent',m(6),'Label','load file',...
'Callback','eegplotold(''loadelect'');')
% %%%%%%%%%%%%%%%%%%%%%%%%%%
% Plot EEG Data
% %%%%%%%%%%%%%%%%%%%%%%%%%%
meandata = mean(data(:,1:round(min(frames,winlength*Fs)))');
axes(ax1)
hold on
for i = 1:chans
plot(data(chans-i+1,...
1:round(min(frames,winlength*Fs)))-meandata(chans-i+1)+i*spacing,...
'color',DEFAULT_PLOT_COLOR)
end
% %%%%%%%%%%%%%%%%%%%%%%%%%%
% Plot Spacing I
% %%%%%%%%%%%%%%%%%%%%%%%%%%
if strcmp(SPACING_EYE,'on')
YLim = get(ax1,'Ylim');
A = DEFAULT_AXES_POSITION;
axes('Position',[A(1)+A(3) A(2) 1-A(1)-A(3) A(4)],...
'Visible','off','Ylim',YLim,'tag','eyeaxes')
axis manual
Xl = [.3 .6 .45 .45 .3 .6];
Yl = [spacing*2 spacing*2 spacing*2 spacing*1 spacing*1 spacing*1];
line(Xl,Yl,'color',DEFAULT_AXIS_COLOR,'clipping','off',...
'tag','eyeline')
text(.5,YLim(2)/23+Yl(1),num2str(spacing,4),...
'HorizontalAlignment','center','FontSize',10,...
'tag','thescale')
if strcmp(YAXIS_NEG,'off')
text(Xl(2)+.1,Yl(1),'+','HorizontalAlignment','left',...
'verticalalignment','middle')
text(Xl(2)+.1,Yl(4),'-','HorizontalAlignment','left',...
'verticalalignment','middle')
else
text(Xl(2)+.1,Yl(4),'+','HorizontalAlignment','left',...
'verticalalignment','middle')
text(Xl(2)+.1,Yl(1),'-','HorizontalAlignment','left',...
'verticalalignment','middle')
end
if ~isempty(SPACING_UNITS_STRING)
text(.5,-YLim(2)/23+Yl(4),SPACING_UNITS_STRING,...
'HorizontalAlignment','center','FontSize',10)
end
set(m(7),'checked','on')
elseif strcmp(SPACING_EYE,'off')
YLim = get(ax1,'Ylim');
A = DEFAULT_AXES_POSITION;
axes('Position',[A(1)+A(3) A(2) 1-A(1)-A(3) A(4)],...
'Visible','off','Ylim',YLim,'tag','eyeaxes')
axis manual
set(m(7),'checked','off')
end
% %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
% End Main Function
% %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
else
switch data
case 'drawp'
% Redraw EEG and change position
figh = gcbf; % figure handle
if strcmp(get(figh,'tag'),'dialog')
figh = get(figh,'UserData');
end
ax1 = findobj('tag','eegaxis','parent',figh); % axes handle
EPosition = findobj('tag','EPosition','parent',figh); % ui handle
ESpacing = findobj('tag','ESpacing','parent',figh); % ui handle
data = get(ax1,'UserData'); % Data (Note: this could also be global)
timestr = get(EPosition,'string'); % current position
% if timestr == 'end'
% time = ceil(frames/Fs)-winlength;
% fprintf('timestr = %s\n',timestr);
% else
time = str2num(timestr); % current position
% end
spacing = str2num(get(ESpacing,'string')); % current spacing
winlength = get(figh,'UserData');
Fs = winlength(2); % samplerate
winlength = winlength(1); % window length
[chans,frames] = size(data);
if p1 == 1
time = time-winlength; % << subtract one window length
elseif p1 == 2
time = time-1; % < subtract one second
elseif p1 == 3
time = time+1; % > add one second
elseif p1 == 4
time = time+winlength; % >> add one window length
end
time = max(0,min(time,ceil(frames/Fs)-winlength));
set(EPosition,'string',num2str(time)) % Update edit box
% keyboard
% Plot data and update axes
meandata = mean(data(:,round(time*Fs+1):round(min((time+winlength)*Fs,...
frames)))');
axes(ax1)
cla
for i = 1:chans
plot(data(chans-i+1,round(time*Fs+1):round(min((time+winlength)*Fs,...
frames)))-meandata(chans-i+1)+i*spacing,...
'color',DEFAULT_PLOT_COLOR,'clipping','off')
end
set(ax1,'XTickLabel',...
num2str((time:DEFAULT_GRID_SPACING:time+winlength)'),...
'Xlim',[0 winlength*Fs],...
'XTick',[0:Fs*DEFAULT_GRID_SPACING:winlength*Fs])
case 'draws'
% Redraw EEG and change scale
figh = gcbf; % figure handle
ax1 = findobj('tag','eegaxis','parent',figh); % axes handle
EPosition = findobj('tag','EPosition','parent',figh); % ui handle
ESpacing = findobj('tag','ESpacing','parent',figh); % ui handle
data = get(ax1,'UserData'); % data
time = str2num(get(EPosition,'string')); % current position
spacing = str2num(get(ESpacing,'string')); % current spacing
winlength = get(figh,'UserData');
if isempty(spacing) | isempty(time)
return % return if valid numbers are not in the edit boxes
end
Fs = winlength(2); % samplerate
winlength = winlength(1); % window length
orgspacing = round(max(max(data')-min(data'))); % original spacing
[chans,frames] = size(data);
if p1 == 1
spacing = spacing + .05*orgspacing; % increase spacing (5%)
elseif p1 == 2
spacing = max(0,spacing-.05*orgspacing); % decrease spacing (5%)
if spacing == 0
spacing = spacing + .05*orgspacing;
end
end
set(ESpacing,'string',num2str(spacing,4)) % update edit box
% plot data and update axes
meandata = mean(data(:,round(time*Fs+1):round(min((time+winlength)*Fs,...
frames)))');
axes(ax1)
cla
for i = 1:chans
plot(data(chans-i+1,...
round(time*Fs+1):round(min((time+winlength)*Fs,...
frames)))-meandata(chans-i+1)+i*spacing,...
'color',DEFAULT_PLOT_COLOR,'clipping','off')
end
set(ax1,'YLim',[0 (chans+1)*spacing],...
'YTick',[0:spacing:chans*spacing])
% update scaling eye if it exists
eyeaxes = findobj('tag','eyeaxes','parent',figh);
if ~isempty(eyeaxes)
eyetext = findobj('type','text','parent',eyeaxes,'tag','thescale');
set(eyetext,'string',num2str(spacing,4))
end
case 'window'
% get new window length with dialog box
fig = gcbf;
oldwinlen = get(fig,'UserData');
pos = get(fig,'Position');
figx = 400;
figy = 200;
fhand = figure('Units','pixels',...
'Position',...
[pos(1)+pos(3)/2-figx/2 pos(2)+pos(4)/2-figy/2 figx figy],...
'Resize','off','CloseRequestFcn','','menubar','none',...
'numbertitle','off','tag','dialog','userdata',fig);
uicolor = get(fhand,'Color');
uicontrol('Style','Text','Units','Pixels',...
'String','Enter new window length(secs):',...
'Position',[20 figy-40 300 25],'HorizontalAlignment','left',...
'BackgroundColor',uicolor,'FontSize',14)
timestring = ['[OBJ1,FIGH1] = gcbo;',...
'FIH0 = get(OBJ1,''UserData'');',...
'AXH0 = findobj(''tag'',''eegaxis'',''parent'',FIH0);',...
'WLEN = str2num(get(OBJ1,''String''));',...
'if ~isempty(WLEN);',...
'UDATA = get(FIH0,''UserData'');',...
'UDATA(1) = WLEN;',...
'set(FIH0,''UserData'',UDATA);',...
'eegplotold(''drawp'',0);',...
'delete(FIGH1);',...
'end;',...
'clear OBJ1 FIGH1 FIH0 AXH0 WLEN UDATA;'];
ui1 = uicontrol('Style','Edit','Units','Pixels',...
'FontSize',12,...
'Position',[120 figy-100 70 30],...
'Callback',timestring,'UserData',fig,...
'String',num2str(oldwinlen(1)));
timestring = ['[OBJ1,FIGH1] = gcbo;',...
'FIH0 = get(OBJ1,''UserData'');',...
'AXH0 = findobj(''tag'',''eegaxis'',''parent'',FIH0(1));',...
'SRAT = str2num(get(FIH0(2),''String''));',...
'if ~isempty(SRAT);',...
'UDATA = get(FIH0(1),''UserData'');',...
'UDATA(2) = SRAT;',...
'set(FIH0(1),''UserData'',UDATA);',...
'eegplotold(''drawp'',0);',...
'delete(FIGH1);',...
'end;',...
'clear OBJ1 FIGH1 FIH0 AXH0 SRAT UDATA;'];
uicontrol('Style','PushButton','Units','Pixels',...
'String','OK','FontSize',14,...
'Position',[figx/4-20 10 65 30],...
'Callback',timestring,'UserData',[fig,ui1])
TIMESTRING = ['[OBJ1,FIGH1] = gcbo;',...
'delete(FIGH1);',...
'clear OBJ1 FIGH1;'];
uicontrol('Style','PushButton','Units','Pixels',...
'String','Cancel','FontSize',14,...
'Position',[3*figx/4-20 10 65 30],...
'Callback',TIMESTRING)
case 'samplerate'
% Get new samplerate
fig = gcbf;
oldsrate = get(fig,'UserData');
pos = get(fig,'Position');
figx = 400;
figy = 200;
fhand = figure('Units','pixels',...
'Position',...
[pos(1)+pos(3)/2-figx/2 pos(2)+pos(4)/2-figy/2 figx figy],...
'Resize','off','CloseRequestFcn','','menubar','none',...
'numbertitle','off','tag','dialog','userdata',fig);
uicolor = get(fhand,'Color');
uicontrol('Style','Text','Units','Pixels',...
'String','Enter new samplerate:',...
'Position',[20 figy-40 300 25],'HorizontalAlignment','left',...
'BackgroundColor',uicolor,'FontSize',14)
timestring = ['[OBJ1,FIGH1] = gcbo;',...
'FIH0 = get(OBJ1,''UserData'');',...
'AXH0 = findobj(''tag'',''eegaxis'',''parent'',FIH0);',...
'SRAT = str2num(get(OBJ1,''String''));',...
'if ~isempty(SRAT);',...
'UDATA = get(FIH0,''UserData'');',...
'UDATA(2) = SRAT;',...
'set(FIH0,''UserData'',UDATA);',...
'eegplotold(''drawp'',0);',...
'delete(FIGH1);',...
'end;',...
'clear OBJ1 FIGH1 FIH0 AXH0 SRAT UDATA;'];
ui1 = uicontrol('Style','Edit','Units','Pixels',...
'FontSize',12,...
'Position',[120 figy-100 70 30],...
'Callback',timestring,'UserData',fig,...
'String',num2str(oldsrate(2)));
timestring = ['[OBJ1,FIGH1] = gcbo;',...
'FIH0 = get(OBJ1,''UserData'');',...
'AXH0 = findobj(''tag'',''eegaxis'',''parent'',FIH0(1));',...
'SRAT = str2num(get(FIH0(2),''String''));',...
'if ~isempty(SRAT);',...
'UDATA = get(FIH0(1),''UserData'');',...
'UDATA(2) = SRAT;',...
'set(FIH0(1),''UserData'',UDATA);',...
'eegplotold(''drawp'',0);',...
'delete(FIGH1);',...
'end;',...
'clear OBJ1 FIGH1 FIH0 AXH0 SRAT UDATA;'];
uicontrol('Style','PushButton','Units','Pixels',...
'String','OK','FontSize',14,...
'Position',[figx/4-20 10 65 30],...
'Callback',timestring,'UserData',[fig,ui1])
TIMESTRING = ['[OBJ1,FIGH1] = gcbo;',...
'delete(FIGH1);',...
'clear OBJ1 FIGH1;'];
uicontrol('Style','PushButton','Units','Pixels',...
'String','Cancel','FontSize',14,...
'Position',[3*figx/4-20 10 65 30],...
'Callback',TIMESTRING)
case 'loadelect'
% load electrode file
fig = gcbf;
pos = get(fig,'Position');
figx = 400;
figy = 200;
fhand = figure('Units','pixels',...
'Position',...
[pos(1)+pos(3)/2-figx/2 pos(2)+pos(4)/2-figy/2 figx figy],...
'Resize','off','CloseRequestFcn','','menubar','none',...
'numbertitle','off','tag','dialog','userdata',fig);
uicolor = get(fhand,'Color');
uicontrol('Style','Text','Units','Pixels',...
'String','Enter electrode file name:',...
'Position',[20 figy-40 300 25],'HorizontalAlignment','left',...
'BackgroundColor',uicolor,'FontSize',14)
ui1 = uicontrol('Style','Edit','Units','Pixels',...
'FontSize',12,...
'HorizontalAlignment','left',...
'Position',[120 figy-100 210 30],...
'UserData',fig,'tag','electedit');
TIMESTRING = ['[OBJ1,FIGH1] = gcbo;',...
'delete(FIGH1);',...
'clear OBJ1 FIGH1;'];
uicontrol('Style','PushButton','Units','Pixels',...
'String','Cancel','FontSize',14,...
'Position',[3*figx/4-20 10 65 30],...
'Callback',TIMESTRING)
timestring = ['[OBJ1,FIGH1] = gcbo;',...
'OBJ2 = findobj(''tag'',''electedit'');',...
'LAB1 = get(OBJ2,''string'');',...
'FIH0 = get(OBJ1,''UserData'');',...
'AXH0 = findobj(''tag'',''eegaxis'',''parent'',FIH0);',...
'OUT1 = eegplotold(''setelect'',LAB1,AXH0);',...
'if (OUT1);',...
'delete(FIGH1);',...
'end;',...
'clear OBJ1 FIGH1 LAB1 OBJ2 FIH0 AXH0 OUT1;'];
uicontrol('Style','PushButton','Units','Pixels',...
'String','OK','FontSize',14,...
'Position',[figx/4-20 10 65 30],...
'Callback',timestring,'UserData',fig)
timestring = ['OBJ2 = findobj(''tag'',''electedit'');',...
'[LAB1,LAB2] = uigetfile(''*'',''Electrode File'');',...
'if (isstr(LAB1) & isstr(LAB2));',...
'set(OBJ2,''string'',[LAB2,LAB1]);',...
'end;',...
'clear OBJ2 LAB1 LAB2;'];
uicontrol('Style','PushButton','Units','Pixels',...
'String','Browse','FontSize',14,...
'Position',[figx/2-20 10 65 30],'UserData',fig,...
'Callback',timestring)
case 'setelect'
% Set electrodes
eloc_file = p1;
axeshand = p2;
outvar1 = 1;
if isempty(eloc_file)
outvar1 = 0;
return
end
fid = fopen(eloc_file);
if fid < 1
fprintf('Cannot open electrode file.\n\n')
outvar1 = 0;
return
end
YLabels = fscanf(fid,'%d %f %f %s',[7 128]);
if isempty(YLabels)
fprintf('Error reading electrode file.\n\n')
outvar1 = 0;
return
end
fclose(fid);
YLabels = char(YLabels(4:7,:)');
ii = find(YLabels == '.');
YLabels(ii) = ' ';
YLabels = flipud(str2mat(YLabels,' '));
set(axeshand,'YTickLabel',YLabels)
case 'title'
% Get new title
fig = gcbf;
% oldsrate = get(fig,'UserData');
eegaxis = findobj('tag','eegaxis','parent',fig);
oldtitle = get(eegaxis,'title');
oldtitle = get(oldtitle,'string');
pos = get(fig,'Position');
figx = 400;
figy = 200;
fhand = figure('Units','pixels',...
'Position',...
[pos(1)+pos(3)/2-figx/2 pos(2)+pos(4)/2-figy/2 figx figy],...
'Resize','off','CloseRequestFcn','','menubar','none',...
'numbertitle','off','tag','dialog','userdata',fig);
uicolor = get(fhand,'Color');
uicontrol('Style','Text','Units','Pixels',...
'String','Enter new title:',...
'Position',[20 figy-40 300 25],'HorizontalAlignment','left',...
'BackgroundColor',uicolor,'FontSize',14)
timestring = ['[OBJ1,FIGH1] = gcbo;',...
'FIH0 = get(OBJ1,''UserData'');',...
'AXH0 = findobj(''tag'',''eegaxis'',''parent'',FIH0);',...
'SRAT = get(OBJ1,''String'');',...
'AXTH0 = get(AXH0,''title'');',...
'if ~isempty(SRAT);',...
'set(AXTH0,''string'',SRAT);',...
'end;',...
'delete(FIGH1);',...
'clear OBJ1 AXTH0 FIGH1 FIH0 AXH0 SRAT UDATA;'];
ui1 = uicontrol('Style','Edit','Units','Pixels',...
'FontSize',12,...
'Position',[120 figy-100 3*70 30],...
'Callback',timestring,'UserData',fig,...
'String',oldtitle);
timestring = ['[OBJ1,FIGH1] = gcbo;',...
'FIH0 = get(OBJ1,''UserData'');',...
'AXH0 = findobj(''tag'',''eegaxis'',''parent'',FIH0(1));',...
'SRAT = get(FIH0(2),''String'');',...
'AXTH0 = get(AXH0,''title'');',...
'set(AXTH0,''string'',SRAT);',...
'delete(FIGH1);',...
'clear OBJ1 AXTH0 FIGH1 FIH0 AXH0 SRAT UDATA;'];
uicontrol('Style','PushButton','Units','Pixels',...
'String','OK','FontSize',14,...
'Position',[figx/4-20 10 65 30],...
'Callback',timestring,'UserData',[fig,ui1])
TIMESTRING = ['[OBJ1,FIGH1] = gcbo;',...
'delete(FIGH1);',...
'clear OBJ1 FIGH1;'];
uicontrol('Style','PushButton','Units','Pixels',...
'String','Cancel','FontSize',14,...
'Position',[3*figx/4-20 10 65 30],...
'Callback',TIMESTRING)
case 'scaleeye'
% Turn scale I on/off
obj = p1;
figh = p2;
% figh = get(obj,'Parent');
toggle = get(obj,'checked');
if strcmp(toggle,'on')
eyeaxes = findobj('tag','eyeaxes','parent',figh);
children = get(eyeaxes,'children');
delete(children)
set(obj,'checked','off')
elseif strcmp(toggle,'off')
eyeaxes = findobj('tag','eyeaxes','parent',figh);
ESpacing = findobj('tag','ESpacing','parent',figh);
spacing = str2num(get(ESpacing,'string'));
axes(eyeaxes)
YLim = get(eyeaxes,'Ylim');
Xl = [.35 .65 .5 .5 .35 .65];
Yl = [spacing*2 spacing*2 spacing*2 spacing*1 spacing*1 spacing*1];
line(Xl,Yl,'color',DEFAULT_AXIS_COLOR,'clipping','off',...
'tag','eyeline')
text(.5,YLim(2)/23+Yl(1),num2str(spacing,4),...
'HorizontalAlignment','center','FontSize',10,...
'tag','thescale')
if strcmp(YAXIS_NEG,'off')
text(Xl(2)+.1,Yl(1),'+','HorizontalAlignment','left',...
'verticalalignment','middle')
text(Xl(2)+.1,Yl(4),'-','HorizontalAlignment','left',...
'verticalalignment','middle')
else
text(Xl(2)+.1,Yl(4),'+','HorizontalAlignment','left',...
'verticalalignment','middle')
text(Xl(2)+.1,Yl(1),'-','HorizontalAlignment','left',...
'verticalalignment','middle')
end
if ~isempty(SPACING_UNITS_STRING)
text(.5,-YLim(2)/23+Yl(4),SPACING_UNITS_STRING,...
'HorizontalAlignment','center','FontSize',10)
end
set(obj,'checked','on')
end
case 'noui'
% Plott EEG without ui controls
data = p1;
% usage: eegplotold(data,Fs,spacing,eloc_file,startpoint,color)
[chans,frames] = size(data);
nargs = nargin;
if nargs < 7
plotcolor = 0;
else
plotcolor = p6;
end
if nargs < 6
starts = 0;
else
starts = p5;
end
if nargs < 5
eloc_file = DEFAULT_ELOC_FILE;
else
eloc_file = p4;
end
if nargs < 4
spacing = 0;
else
spacing = p3;
end
if nargs < 3
Fs = 0;
else
Fs = p2;
end
if isempty(plotcolor)
plotcolor = 0;
end
if isempty(spacing)
spacing = 0;
end
if isempty(Fs)
Fs = 0;
end
if isempty(starts)
starts = 0;
end
if spacing == 0
spacing = max(max(data')-min(data'));
end
if spacing == 0
spacing = 1;
end;
if Fs == 0
Fs = DEFAULT_SAMPLE_RATE;
end
range = floor(frames/Fs);
axhandle = gca;
if plotcolor == 0
if DEFAULT_NOUI_PLOT_COLOR == 0
colorord = get(axhandle,'ColorOrder');
plotcolor = colorord(1,:);
else
plotcolor = DEFAULT_NOUI_PLOT_COLOR;
end
end
if ~isempty(eloc_file)
if eloc_file == 0
YLabels = num2str((1:chans)');
elseif ischar('eloc_file')
fid = fopen(eloc_file);
if fid < 1
error('error opening electrode file')
end
YLabels = fscanf(fid,'%d %f %f %s',[7 128]);
fclose(fid);
YLabels = char(YLabels(4:7,:)');
ii = find(YLabels == '.');
YLabels(ii) = ' ';
else
YLabels = num2str(eloc_file)';
end
YLabels = flipud(str2mat(YLabels,' '));
else
YLabels = [];
end
set(axhandle,'xgrid','on','GridLineStyle','-',...
'Box','on','YTickLabel',YLabels,...
'ytick',[0:spacing:chans*spacing],...
'Ylim',[0 (chans+1)*spacing],...
'xtick',[0:Fs:range*Fs],...
'Xlim',[0 frames],...
'XTickLabel',num2str((0:1:range)'+starts))
meandata = mean(data');
axes(axhandle)
hold on
for i = 1:chans
plot(data(chans-i+1,:)-meandata(chans-i+1)+i*spacing,'color',plotcolor)
end
otherwise
error(['Error - invalid eegplotold() parameter: ',data])
end
end
|
github
|
lcnbeapp/beapp-master
|
chanproj.m
|
.m
|
beapp-master/Packages/eeglab14_1_2b/functions/miscfunc/chanproj.m
| 7,033 |
utf_8
|
3944e3a2db15df4da52766d602a832d0
|
% chanproj() - make a detailed plot of data returned from plotproj()
% for given channel. Returns the data plotted.
% Usage:
% >> [chandata] = chanproj(projdata,chan);
% >> [chandata] = chanproj(projdata,chan,ncomps,framelist,limits,title,colors);
%
% Inputs:
% projdata = data returned from plotproj()
% chan = single channel to plot
% ncomps = number of component projections in projdata
%
% Optional:
% framelist = data frames to plot per epoch Ex: [1:128] (0|def -> all)
% limits = [xmin xmax ymin ymax] (x's in msec)
% (0, or y's 0 -> data limits)
% title = fairly short single-quoted 'plot title' (0|def -> chan)
% colors = file of color codes, 3 chars per line (NB: '.' = space)
% (0|def -> white is original data)
%
% Author: Scott Makeig, SCCN/INC/UCSD, La Jolla, 1996
% Copyright (C) 1996 Scott Makeig, SCCN/INC/UCSD, [email protected]
%
% This program is free software; you can redistribute it and/or modify
% it under the terms of the GNU General Public License as published by
% the Free Software Foundation; either version 2 of the License, or
% (at your option) any later version.
%
% This program is distributed in the hope that it will be useful,
% but WITHOUT ANY WARRANTY; without even the implied warranty of
% MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
% GNU General Public License for more details.
%
% You should have received a copy of the GNU General Public License
% along with this program; if not, write to the Free Software
% Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
% 11-30-96 Scott Makeig CNL / Salk Institute, La Jolla as plotprojchan.m
% 03-19-97 changed var() to diag(cov()) -sm
% 03-26-97 fix (== -> =) -sm
% 04-03-97 allow framelist to be a col vector, allow 32 traces, fix pvaf, made
% ncomps mandatory -sm
% 04-04-97 shortened name to chanproj() -sm
% 05-20-97 added read of icadefs.m -sm
% 11-05-97 disallowed white traces unless default axis color is white -sm & ch
% 11-13-97 rm'ed errcode variable -sm
% 12-08-97 added LineWidth 2 to data trace, changed whole plot color to BACKCOLOR -sm
% 01-25-02 reformated help & license -ad
function [chandata] = chanproj(projdata,chan,ncomps,framelist,limits,titl,colorfile)
icadefs; % read default MAXPLOTDATACHANS
if nargin < 7,
colorfile =0;
end
if nargin < 6,
titl = 0;
end
if nargin < 5,
limits = 0;
end
if nargin < 4,
framelist = 0;
end
if nargin < 3,
fprintf('chanproj(): requires at least three arguments.\n\n');
help chanproj
return
end
[chans,framestot] = size(projdata);
frames = fix(framestot/(ncomps+1));
if ncomps < 1 | frames*(ncomps+1) ~= framestot,
fprintf(...
'chanproj(): data length (%d) not a multiple of ncomps (%d).\n',...
framestot,ncomps);
return
end;
if chan> chans,
fprintf(...
'chanproj(): specified channel (%d) cannot be > than nchans (%d).\n',...
chan,chans);
return
else
chandata = projdata(chan,:);
epochs = fix(length(chandata)/frames);
end;
if epochs > MAXPLOTDATACHANS
fprintf(...
'chanproj(): maximum number of traces to plot is %d\n',...
MAXPLOTDATACHANS);
return
end
if framestot~=epochs*frames,
fprintf('chanproj(): projdata is wrong length.\n'); % exit
return
end
%
%%%%%%%%%%%%%%%% Find or read plot limits %%%%%%%%%%%%%%%%%%%%%%%%%%%
%
if limits==0,
xmin=0;xmax=0;ymin=0;ymax=0;
else
if length(limits)~=4,
fprintf( ...
'chanproj():^G limits should be 0 or an array [xmin xmax ymin ymax].\n');
return
end;
xmin = limits(1);
xmax = limits(2);
ymin = limits(3);
ymax = limits(4);
end;
if xmin == 0 & xmax == 0,
x = [0:frames-1];
xmin = 0;
xmax = frames-1;
else
dx = (xmax-xmin)/(frames-1);
x=xmin*ones(1,frames)+dx*(0:frames-1); % construct x-values
end;
if ymax == 0 & ymin == 0,
ymax=max(max(projdata(chan,:)));
ymin=min(min(projdata(chan,:)));
end
%
%%%%% Reshape the projdata for plotting and returning to user %%%%%%%%%
%
chandata=reshape(chandata,frames,epochs);
chandata=chandata';
if framelist ==0,
framelist = [1:frames]; % default
end
if size(framelist,2)==1,
if size(framelist,1)>1,
framelist = framelist';
else
fprintf(...
'chanproj(): framelist should be a vector of frames to plot per epoch.\n');
return
end
end
if framelist(1)<1 | framelist(length(framelist))>frames,
fprintf('chanproj(): framelist values must be between 1-%d.\n',frames);
return
else
chandata=chandata(:,framelist);
end
%
%%%%%%%%%%%%%%%%%%% Read the color names %%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%
if colorfile ~=0,
if ~ischar(colorfile)
fprintf('chanproj(); color file name must be a string.\n');
return
end
cid = fopen(colorfile,'r');
if cid <3,
fprintf('chanproj(): cannot open file %s.\n',colorfile);
return
end;
colors = fscanf(cid,'%s',[3 MAXPLOTDATACHANS]);
colors = colors';
[r c] = size(colors);
for i=1:r
for j=1:c
if colors(i,j)=='.',
colors(i,j)=' ';
end;
end;
end;
else % default color order - no yellow
colors =['w ';'r ';'b ';'g ';'c ';'m ';'r ';'b ';'g ';'c ';'m ';'r ';'b ';'g ';'c ';'m ';'r ';'b ';'g ';'c ';'m ';'r ';'b ';'g ';'c ';'m ';'r ';'b ';'g ';'c ';'m ';'r '];
end;
%
% Make vector of x-values
%
x=[xmin:(xmax-xmin)/(frames-1):xmax+0.00001];
xmin=x(framelist(1));
xmax=x(framelist(length(framelist)));
x = x(framelist(1):framelist(length(framelist)));
%
%%%%%%%%% Compute percentage of variance accounted for %%%%%%%%%%%%%%
%
if epochs>1,
sumdata = zeros(1,length(framelist));
for e=2:epochs
sumdata= sumdata + chandata(e,:); % sum the component projections
end
sigvar = diag(cov(chandata(1,:)'));
difvar = diag(cov(((chandata(1,:)-sumdata)')));
% percent variance accounted for
pvaf = round(100.0*(1.0-difvar/sigvar));
end
%
%%%%%%%%%%%%%%%%%%%%%% Plot traces %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%
fprintf('chanproj(): Drawing trace ');
for e=1:epochs,
fprintf ('%d ',e);
set(gcf,'Color',BACKCOLOR); % set the background color to grey
set(gca,'Color','none'); % set the axis color = figure color
if e==1
plot(x,chandata(e,:),colors(e),'LineWidth',2); % plot it!
else
plot(x,chandata(e,:),colors(e),'LineWidth',1); % plot it!
end
hold on;
end;
fprintf('\n');
%
%%%%%%%%%%%%%%%%%%%% Fix axis limits %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%
axis([xmin xmax ymin-0.1*(ymax-ymin) ymax+0.1*(ymax-ymin)]);
%
%%%%%%%%%%%%%%%%%%% Add title and labels %%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%
if titl==0,
titl = ['channel ' int2str(chan)];
end
titl = [ titl ' (p.v.a.f. ' int2str(pvaf) '%)' ];
title(titl);
xlabel('Time (msec)');
ylabel('Potential (uV)');
|
github
|
lcnbeapp/beapp-master
|
zica.m
|
.m
|
beapp-master/Packages/eeglab14_1_2b/functions/miscfunc/zica.m
| 3,366 |
utf_8
|
0daa4d2de301c49787f0d7e9e070ffb9
|
% zica() - Z-transform of ICA activations; useful for studying component SNR
%
% Usage: >> [zact,basesd,maz,mazc,mazf] = zica(activations,frames,baseframes)
%
% Inputs:
% activations - activations matrix produced by runica()
% frames - frames per epoch {0|default -> length(activations)}
% baseframes - vector of frames in z-defining baseline period {default frames}
%
% Outputs:
% zact - activations z-scaled and reorded in reverse order of max abs
% basesd - standard deviations in each activation row (reverse ordered)
% maz - maximum absolute z-value for each activation row (rev ordered)
% mazc - component indices of the reverse-sorted max abs z-values
% (this is the act -> zact reordering)
% mazf - frame indices of the max abs z-values (reverse ordered)
%
% Author: Scott Makeig, SCCN/INC/UCSD, La Jolla, 2-25-98
%
% See also: runica()
function [zact,basesd,maxabsz,maxc,maxabszf] = zica(activations,frames,baseframes)
% Copyright (C) 2-25-98 Scott Makeig, SCCN/INC/UCSD, [email protected]
%
% This program is free software; you can redistribute it and/or modify
% it under the terms of the GNU General Public License as published by
% the Free Software Foundation; either version 2 of the License, or
% (at your option) any later version.
%
% This program is distributed in the hope that it will be useful,
% but WITHOUT ANY WARRANTY; without even the implied warranty of
% MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
% GNU General Public License for more details.
%
% You should have received a copy of the GNU General Public License
% along with this program; if not, write to the Free Software
% Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
% 3-2-98 added frames variable -sm
% 1-25-01 put revsort subfunction in the core of the zica program -ad
% 01-25-02 reformated help & license, added link -ad
if nargin<1
help zica
return
end
[chans,framestot] = size(activations);
if nargin < 3
baseframes = 0;
end
if nargin < 2
frames = 0;
end
if frames == 0
frames = framestot;
end
if baseframes == 0
baseframes = 1:frames
end
epochs = floor(framestot/frames);
if frames*epochs ~= framestot
fprintf('zica(): indicated frames does not divide data length.\n');
return
end
if length(baseframes) < 3
fprintf('\n zica() - too few baseframes (%d).\n',length(baseframes));
help zica
return
end
if min(baseframes) < 1 | max(baseframes) > frames
fprintf('\n zica() - baseframes out of range.\n');
help zica
return
end
baselength = length(baseframes);
baseact = zeros(epochs*baselength,chans);
for e=1:epochs
baseact((e-1)*baselength+1:e*baselength,:) = ...
matsel(activations,frames,baseframes,0,e)';
end
basesd = sqrt(covary(baseact));
zact = activations./(basesd'*ones(1,framestot));
[maxabsz,maxabszf] = sort(abs(zact'));
maxabsz = maxabsz(frames,:);
maxabszf = maxabszf(frames,:);
%
% reorder outputs in reverse order of max abs z
[maxabsz,maxc] = revsort(maxabsz);
zact = zact(maxc,:);
basesd = basesd(maxc);
maxabszf = maxabszf(maxc);
% revsort - reverse sort columns (biggest 1st, ...)
function [out,i] = revsort(in)
if size(in,1) == 1
in = in'; % make column vector
end
[out,i] = sort(in);
out = out(size(in,1):-1:1,:);
i = i(size(in,1):-1:1,:);
return;
|
github
|
lcnbeapp/beapp-master
|
rotatematlab.m
|
.m
|
beapp-master/Packages/eeglab14_1_2b/functions/miscfunc/rotatematlab.m
| 180 |
utf_8
|
1d0c90aba89a0dd6de52d0081b4ad3dd
|
% This function calls the Matlab rotate function
% This prevents the issue with the function in the private folder of Dipfit
function rotatematlab(varargin)
rotate(varargin{:});
|
github
|
lcnbeapp/beapp-master
|
del2map.m
|
.m
|
beapp-master/Packages/eeglab14_1_2b/functions/miscfunc/del2map.m
| 3,940 |
utf_8
|
0e518801cfa22cd909a1faa406f9cf7d
|
% del2map() - compute the discrete laplacian of an EEG distribution.
%
% Usage:
% >> [ laplac ] = del2map( map, filename, draw );
%
% Inputs:
% map - level of activity (size: nbChannel)
% filename - filename (.loc file) countaining the coordinates
% of the electrodes, or array countaining complex positions
% draw - integer, if not nul draw the gradient (default:0)
%
% Output:
% laplac - laplacian map. If the input values are in microV and the
% the sensors placement are in mm, the output values are
% returned in microV/mm^2. In order to use current density
% units like milliamps/mm2, you would need to know skin
% conductance information, which as far as we know is not
% really known with enough accuracy to be worthwhile.
%
% Author: Arnaud Delorme, CNL / Salk Institute, 2001
% Thanks Ramesh Srinivasan and Tom Campbell for the discussion
% on laplacian output units.
% Copyright (C) 2001 Arnaud Delorme, Salk Institute, [email protected]
%
% This program is free software; you can redistribute it and/or modify
% it under the terms of the GNU General Public License as published by
% the Free Software Foundation; either version 2 of the License, or
% (at your option) any later version.
%
% This program is distributed in the hope that it will be useful,
% but WITHOUT ANY WARRANTY; without even the implied warranty of
% MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
% GNU General Public License for more details.
%
% You should have received a copy of the GNU General Public License
% along with this program; if not, write to the Free Software
% Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
function [ laplac, sumLaplac2D ] = del2map( map, filename, draw )
if nargin < 2
help del2map;
return;
end;
% process several maps
if size(map,2) > 1
if size(map,1) > 1
for index = 1:size(map,2)
laplac(:,index) = del2map( map(:,index), filename);
end;
return;
else
map = map';
end;
end;
MAXCHANS = size(map,1);
GRID_SCALE = 2*MAXCHANS+5;
% Read the channel file
% ---------------------
if ischar( filename ) | isstruct( filename )
[tmp lb Th Rd] = readlocs(filename);
Th = pi/180*Th; % convert degrees to rads
[x,y] = pol2cart(Th,Rd);
else
x = real(filename);
y = imag(filename);
if exist('draw') == 1 & draw ~= 0
line( [(x-0.01)' (x+0.01)']', [(y-0.01)' (y+0.01)']');
line( [(x+0.01)' (x-0.01)']', [(y-0.01)' (y+0.01)']');
end;
end;
% locates nearest position of electrod in the grid
% ------------------------------------------------
xi = linspace(-0.5,0.5,GRID_SCALE); % x-axis description (row vector)
yi = linspace(-0.5,0.5,GRID_SCALE); % y-axis description (row vector)
for i=1:MAXCHANS
[useless_var horizidx(i)] = min(abs(x(i) - xi)); % find pointers to electrode
[useless_var vertidx(i)] = min(abs(y(i) - yi)); % positions in Zi
end;
% Compute gradient
% ----------------
sumLaplac2D = zeros(GRID_SCALE, GRID_SCALE);
for i=1:size(map,2)
[Xi,Yi,Zi] = griddata(y,x,map(:,i),yi',xi, 'v4'); % interpolate data
laplac2D = del2(Zi);
positions = horizidx + (vertidx-1)*GRID_SCALE;
laplac(:,i) = laplac2D(positions(:));
sumLaplac2D = sumLaplac2D + laplac2D;
% Draw gradient
% -------------
if exist('draw') == 1 & draw ~= 0
if size(map,2) > 1
subplot(ceil(sqrt(size(map,2))), ceil(sqrt(size(map,2))), i);
end;
plot(y, x, 'x', 'Color', 'black', 'markersize', 5); hold on
contour(Xi, Yi, laplac2D); hold off;
%line( [(x-0.01)' (x+0.01)']', [(y-0.01)' (y+0.01)']', 'Color','black');
%line( [(x+0.01)' (x-0.01)']', [(y-0.01)' (y+0.01)']', 'Color','black');
title( int2str(i) );
end;
end; %
return;
|
github
|
lcnbeapp/beapp-master
|
readlocsold.m
|
.m
|
beapp-master/Packages/eeglab14_1_2b/functions/miscfunc/readlocsold.m
| 3,560 |
utf_8
|
55da540b1b04dfe07379075941625ac1
|
% readlocsold() - Read electrode locations file in style of topoplot() or headplot().
% Output channel information is ordered by channel numbers.
%
% Usage: >> [nums labels th r x y] = readlocsold(locfile);% {default, polar 2-D}
% >> [nums labels th r x y] = readlocsold(locfile,'polar'); % 2-D
% >> [nums labels x y z] = readlocsold(locfile,'spherical'); % 3-D
% >> [nums labels x y z] = readlocsold(locfile,'cartesian'); % 3-D
% Input:
% locfile = 'filename' of electrode location file.
% loctype = File type:'polar' 2-D {default}. See >> topoplot example
% 'spherical' 3-D. See >> headplot example
% 'cartesian' 3-D. See >> headplot cartesian
% Outputs:
% nums = ordered channel numbers (from locfile)
% labels = Matrix of 4-char channel labels (nchannels,4)
% 2-D: r,th = polar coordinates of each electrode (th in radians)
% x,y = 2-D Cartesian coordinates (from pol2cart())
% 3-D: x,y,z = 3-D Cartesian coordinates (normalized, |x,y,z| = 1)
% Scott Makeig, CNL / Salk Institute, La Jolla CA 3/01
% code from topoplot()
function [channums,labels,o1,o2,o3,o4] = readlocsold(loc_file,loctype)
verbose = 0;
if nargin<2
loctype = 'polar'; % default file type
end
icadefs
if nargin<1
loc_file = DEFAULT_ELOC;
end
fid = fopen(loc_file);
if fid<1,
fprintf('readlocsold(): cannot open electrode location file (%s).\n',loc_file);
return
end
if strcmp(loctype,'spherical')| strcmp(loctype,'polar')
A = fscanf(fid,'%d %f %f %s',[7 Inf]);
elseif strcmp(loctype,'cartesian')
A = fscanf(fid,'%d %f %f %f %s',[8 Inf]);
else
fprintf('readlocsold(): unknown electrode location file type %s.\n',loctype);
return
end
fclose(fid);
A = A';
channums = A(:,1);
[channums csi] = sort(channums);
if strcmp(loctype,'cartesian')
labels = setstr(A(csi,5:8));
else
labels = setstr(A(csi,4:7));
end
idx = find(labels == '.'); % some labels have dots
labels(idx) = setstr(abs(' ')*ones(size(idx))); % replace them with spaces
badchars = find(double(labels)<32|double(labels)>127);
if ~isempty(badchars)
fprintf(...
'readlocsold(): Bad label(s) read - Each label must have 4 chars (. => space)\n');
return
end
for c=1:length(channums)
if labels(c,3)== ' ' & labels(c,4)== ' '
labels(c,[2 3]) = labels(c,[1 2]);
labels(c,1) = ' '; % move 1|2-letter labels to middle of string
end
end
if strcmp(loctype,'polar')
th = pi/180*A(csi,2); % convert degrees to radians
rad = A(csi,3);
o2 = rad; o1 = th;
[x,y] = pol2cart(th,rad); % transform from polar to cartesian coordinates
o3 = x; o4 = y;
elseif strcmp(loctype,'spherical')
th = pi/180*A(csi,2);
phi = pi/180*A(csi,3);
x = sin(th).*cos(phi);
y = sin(th).*sin(phi);
z = cos(th);
o1 = x; o2 =y; o3 = z;
elseif strcmp(loctype,'cartesian')
x = A(csi,2);
y = A(csi,3);
z = A(csi,4);
dists = sqrt(x.^2+y.^2+z.^2);
x = y./dists; % normalize [x y z] vector lengths to 1
y = y./dists;
z = z./dists;
o1 = x; o2 =y; o3 = z;
end
if verbose
fprintf('Location data for %d electrodes read from file %s.\n',...
size(A,1),loc_file);
end
if nargout<1
fprintf('\n');
for c=1:length(channums)
if strcmp(loctype,'polar')
fprintf(' %d %s %4.3f %4.3f %4.3f %4.3f\n',...
channums(c),labels(c,:),rad(c),th(c),x(c),y(c));
end
end
fprintf('\n');
o1 = []; o2=[]; o3=[]; o4=[];
labels = [];
end
|
github
|
lcnbeapp/beapp-master
|
crossfreq.m
|
.m
|
beapp-master/Packages/eeglab14_1_2b/functions/miscfunc/crossfreq.m
| 15,218 |
utf_8
|
a9ff87c9098280c7729af6c878a8fd45
|
% crossfreq() - compute cross-frequency coherences. Power of first input
% correlation with phase of second.
%
% Usage:
% >> crossfreq(x,y,srate);
% >> [coh,timesout,freqsout1,freqsout2,cohboot] ...
% = crossfreq(x,y,srate,'key1', 'val1', 'key2', val2' ...);
% Inputs:
% x = [float array] 2-D data array of size (times,trials) or
% 3-D (1,times,trials)
% y = [float array] 2-D or 3-d data array
% srate = data sampling rate (Hz)
%
% Most important optional inputs
% 'mode' = ['amp_amp'|'amp_phase'|'phase_phase'] correlation mode
% is either amplitude-amplitude ('amp_amp'), amplitude
% and phase ('amp_phase') and phase-phase ('phase_phase').
% Default is 'amp_phase'.
% 'method' = ['mod'|'corrsin'|'corrcos'] modulation method ('mod')
% or correlation of amplitude with sine or cosine of
% angle (see ref).
% 'freqs' = [min max] frequency limits. Default [minfreq 50],
% minfreq being determined by the number of data points,
% cycles and sampling frequency. Use 0 for minimum frequency
% to compute default minfreq. You may also enter an
% array of frequencies for the spectral decomposition
% (for FFT, closest computed frequency will be returned; use
% 'padratio' to change FFT freq. resolution).
% 'freqs2' = [float array] array of frequencies for the second
% argument. 'freqs' is used for the first argument.
% By default it is the same as 'freqs'.
% 'wavelet' = 0 -> Use FFTs (with constant window length) { Default }
% = >0 -> Number of cycles in each analysis wavelet
% = [cycles expfactor] -> if 0 < expfactor < 1, the number
% of wavelet cycles expands with frequency from cycles
% If expfactor = 1, no expansion; if = 0, constant
% window length (as in FFT) {default wavelet: 0}
% = [cycles array] -> cycle for each frequency. Size of array
% must be the same as the number of frequencies
% {default cycles: 0}
% 'wavelet2' = same as 'wavelet' for the second argument. Default is
% same as cycles. Note that if the lowest frequency for X
% and Y are different and cycle is [cycles expfactor], it
% may result in discrepencies in the number of cycles at
% the same frequencies for X and Y.
% 'ntimesout' = Number of output times (int<frames-winframes). Enter a
% negative value [-S] to subsample original time by S.
% 'timesout' = Enter an array to obtain spectral decomposition at
% specific time values (note: algorithm find closest time
% point in data and this might result in an unevenly spaced
% time array). Overwrite 'ntimesout'. {def: automatic}
% 'tlimits' = [min max] time limits in ms.
%
% Optional Detrending:
% 'detrend' = ['on'|'off'], Linearly detrend each data epoch {'off'}
% 'rmerp' = ['on'|'off'], Remove epoch mean from data epochs {'off'}
%
% Optional FFT/DFT Parameters:
% 'winsize' = If cycles==0: data subwindow length (fastest, 2^n<frames);
% If cycles >0: *longest* window length to use. This
% determines the lowest output frequency. Note that this
% parameter is overwritten if the minimum frequency has been set
% manually and requires a longer time window {~frames/8}
% 'padratio' = FFT-length/winframes (2^k) {2}
% Multiplies the number of output frequencies by dividing
% their spacing (standard FFT padding). When cycles~=0,
% frequency spacing is divided by padratio.
% 'nfreqs' = number of output frequencies. For FFT, closest computed
% frequency will be returned. Overwrite 'padratio' effects
% for wavelets. Default: use 'padratio'.
% 'freqscale' = ['log'|'linear'] frequency scale. Default is 'linear'.
% Note that for obtaining 'log' spaced freqs using FFT,
% closest correspondant frequencies in the 'linear' space
% are returned.
% 'subitc' = ['on'|'off'] subtract stimulus locked Inter-Trial Coherence
% (ITC) from x and y. This computes the 'intrinsic' coherence
% x and y not arising from common synchronization to
% experimental events. See notes. {default: 'off'}
% 'itctype' = ['coher'|'phasecoher'] For use with 'subitc', see timef()
% for more details {default: 'phasecoher'}.
% 'subwin' = [min max] sub time window in ms (this windowing is
% performed after the spectral decomposition).
% 'lowmem' = ['on'|'off'] compute frequency, by frequency to save
% memory. Default 'off'.
%
% Optional Bootstrap Parameters:
% 'alpha' = If non-0, compute two-tailed bootstrap significance prob.
% level. Show non-signif. output values as green. {0}
% 'naccu' = Number of bootstrap replications to accumulate. Note that
% naccu might be automatically increate depending on the
% value for 'alpha' {250}
% 'baseboot' = Bootstrap baseline subtract time window in ms. If only one
% is entered, baseline is from beginning of data to this
% value. Note: you must specify 'tlimits' for bootstrap {0}
% 'boottype' = ['times'|'timestrials'|'trials'] Bootstrap type: Either
% shuffle windows ('times') or windows and trials ('timestrials')
% or trials only using a separate bootstrap for each time window
% ('trials'). Option 'times' is not recommended but requires less
% memory {default 'timestrials'}
% 'rboot' = Input bootstrap coherence limits (e.g., from crossfreq())
% The bootstrap type should be identical to that used
% to obtain the input limits. {default: compute from data}
%
% Optional Plotting Parameters:
% 'title' = Optional figure title {none}
% 'vert' = [times_vector] plot vertical dashed lines at specified
% times in ms. Can also be a cell array specifying line aspect.
% I.e. { { 0 'color' 'b' 'linewidth' 2 } {1000 'color' 'r' }}
% would draw two lines, one blue thick line at latency 0 and one
% thin red line at latency 1000.
% 'newfig' = ['on'|'off'] Create new figure for difference plots {'on'}
%
% Outputs:
% crossfcoh = Matrix (nfreqs1,nfreqs2,timesout) of coherence (complex).
% Use 20*log(abs(crossfcoh)) to vizualize log spectral diffs.
% timesout = Vector of output times (window centers) (ms).
% freqsout1 = Vector of frequency bin centers for first argument (Hz).
% freqsout2 = Vector of frequency bin centers for second argument (Hz).
% cohboot = Matrix (nfreqs1,nfreqs2,2) of p-value coher signif.
% values. if 'boottype' is 'trials',
% (nfreqs1,nfreqs2,timesout,2)
% alltfX = single trial spectral decomposition of X
% alltfY = single trial spectral decomposition of Y
%
% Author: Arnaud Delorme & Scott Makeig, SCCN/INC, UCSD 2003-
%
% Ref: Testing for Nested Oscilations (2008) J Neuro Methods 174(1):50-61
%
% See also: timefreq(), crossf()
% Copyright (C) 2002 Arnaud Delorme, Salk Institute, [email protected]
%
% This program is free software; you can redistribute it and/or modify
% it under the terms of the GNU General Public License as published by
% the Free Software Foundation; either version 2 of the License, or
% (at your option) any later version.
%
% This program is distributed in the hope that it will be useful,
% but WITHOUT ANY WARRANTY; without even the implied warranty of
% MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
% GNU General Public License for more details.
%
% You should have received a copy of the GNU General Public License
% along with this program; if not, write to the Free Software
% Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
function [crossfcoh, timesout1, freqs1, freqs2, cohboot, alltfX, alltfY] = ...
crossfreq(X, Y, srate, varargin);
if nargin < 1
help crossfreq;
return;
end;
% deal with 3-D inputs
% --------------------
if ndims(X) == 3, X = reshape(X, size(X,2), size(X,3)); end;
if ndims(Y) == 3, Y = reshape(Y, size(Y,2), size(Y,3)); end;
frame = size(X,2);
g = finputcheck(varargin, ...
{ 'alpha' 'real' [0 0.2] [];
'baseboot' 'float' [] 0;
'boottype' 'string' {'times','trials','timestrials'} 'timestrials';
'detrend' 'string' {'on','off'} 'off';
'freqs' 'real' [0 Inf] [0 srate/2];
'freqs2' 'real' [0 Inf] [];
'freqscale' 'string' { 'linear','log' } 'linear';
'itctype' 'string' {'phasecoher','phasecoher2','coher'} 'phasecoher';
'nfreqs' 'integer' [0 Inf] [];
'lowmem' 'string' {'on','off'} 'off';
'mode' 'string' { 'amp_amp','amp_phase','phase_phase' } 'amp_phase';
'method' 'string' { 'mod','corrsin','corrcos' } 'mod';
'naccu' 'integer' [1 Inf] 250;
'newfig' 'string' {'on','off'} 'on';
'padratio' 'integer' [1 Inf] 2;
'rmerp' 'string' {'on','off'} 'off';
'rboot' 'real' [] [];
'subitc' 'string' {'on','off'} 'off';
'subwin' 'real' [] []; ...
'timesout' 'real' [] []; ...
'ntimesout' 'integer' [] 200; ...
'tlimits' 'real' [] [0 frame/srate];
'title' 'string' [] '';
'vert' { 'real','cell' } [] [];
'wavelet' 'real' [0 Inf] 0;
'wavelet2' 'real' [0 Inf] [];
'winsize' 'integer' [0 Inf] max(pow2(nextpow2(frame)-3),4) }, 'crossfreq');
if isstr(g), error(g); end;
% more defaults
% -------------
if isempty(g.wavelet2), g.wavelet2 = g.wavelet; end;
if isempty(g.freqs2), g.freqs2 = g.freqs; end;
% remove ERP if necessary
% -----------------------
X = squeeze(X);
Y = squeeze(Y);X = squeeze(X);
trials = size(X,2);
if strcmpi(g.rmerp, 'on')
X = X - repmat(mean(X,2), [1 trials]);
Y = Y - repmat(mean(Y,2), [1 trials]);
end;
% perform timefreq decomposition
% ------------------------------
[alltfX freqs1 timesout1] = timefreq(X, srate, 'ntimesout', g.ntimesout, 'timesout', g.timesout, 'winsize', g.winsize, ...
'tlimits', g.tlimits, 'detrend', g.detrend, 'itctype', g.itctype, ...
'subitc', g.subitc, 'wavelet', g.wavelet, 'padratio', g.padratio, ...
'freqs', g.freqs, 'freqscale', g.freqscale, 'nfreqs', g.nfreqs);
[alltfY freqs2 timesout2] = timefreq(Y, srate, 'ntimesout', g.ntimesout, 'timesout', g.timesout, 'winsize', g.winsize, ...
'tlimits', g.tlimits, 'detrend', g.detrend, 'itctype', g.itctype, ...
'subitc', g.subitc, 'wavelet', g.wavelet2, 'padratio', g.padratio, ...
'freqs', g.freqs2, 'freqscale', g.freqscale, 'nfreqs', g.nfreqs);
% check time limits
% -----------------
if ~isempty(g.subwin)
ind1 = find(timesout1 > g.subwin(1) & timesout1 < g.subwin(2));
ind2 = find(timesout2 > g.subwin(1) & timesout2 < g.subwin(2));
alltfX = alltfX(:, ind1, :);
alltfY = alltfY(:, ind2, :);
timesout1 = timesout1(ind1);
timesout2 = timesout2(ind2);
end;
if length(timesout1) ~= length(timesout2) | any( timesout1 ~= timesout2)
disp('Warning: Time points are different for X and Y. Use ''timesout'' to specify common time points');
disp('Searching for common points');
[vals ind1 ind2 ] = intersect_bc(timesout1, timesout2);
if length(vals) < 10, error('Less than 10 common data points'); end;
timesout1 = vals;
timesout2 = vals;
alltfX = alltfX(:, ind1, :);
alltfY = alltfY(:, ind2, :);
end;
% scan accross frequency and time
% -------------------------------
if isempty(g.alpha)
disp('Warning: if significance mask is not applied, result might be slightly')
disp('different (since angle is not made uniform and amplitude interpolated)')
end;
cohboot =[];
for find1 = 1:length(freqs1)
for find2 = 1:length(freqs2)
for ti = 1:length(timesout1)
% get data
% --------
tmpalltfx = squeeze(alltfX(find1,ti,:));
tmpalltfy = squeeze(alltfY(find2,ti,:));
if ~isempty(g.alpha)
tmpalltfy = angle(tmpalltfy);
tmpalltfx = abs( tmpalltfx);
[ tmp cohboot(find1,find2,ti,:) newamp newangle ] = ...
bootcircle(tmpalltfx, tmpalltfy, 'naccu', g.naccu);
crossfcoh(find1,find2,ti) = sum ( newamp .* exp(j*newangle) );
else
tmpalltfy = angle(tmpalltfy);
tmpalltfx = abs( tmpalltfx);
if strcmpi(g.method, 'mod')
crossfcoh(find1,find2,ti) = sum( tmpalltfx .* exp(j*tmpalltfy) );
elseif strcmpi(g.method, 'corrsin')
tmp = corrcoef( sin(tmpalltfy), tmpalltfx);
crossfcoh(find1,find2,ti) = tmp(2);
else
tmp = corrcoef( cos(tmpalltfy), tmpalltfx);
crossfcoh(find1,find2,ti) = tmp(2);
end;
end;
end;
end;
end;
|
github
|
lcnbeapp/beapp-master
|
upgma.m
|
.m
|
beapp-master/Packages/eeglab14_1_2b/functions/miscfunc/upgma.m
| 3,664 |
utf_8
|
2bbad43f658a73df320ccccb6256d938
|
% UPGMA: Unweighted pair-group hierarchical cluster analysis of a distance
% matrix. Produces plot of dendrogram. To bootstrap cluster support,
% see cluster().
%
% Usage: [topology,support] = upgma(dist,{labels},{doplot},{fontsize})
%
% dist = [n x n] symmetric distance matrix.
% labels = optional [n x q] matrix of group labels for dendrogram.
% doplot = optional boolean flag indicating, if present and true, that
% graphical dendrogram output is to be produced
% [default = true].
% fontsize = optional font size for labels [default = 10].
% -----------------------------------------------------------------------
% topology = [(n-1) x 4] matrix summarizing dendrogram topology:
% col 1 = 1st OTU/cluster being grouped at current step
% col 2 = 2nd OTU/cluster
% col 3 = ID of cluster being produced
% col 4 = distance at node
% support = [(n-2) x (n-1)] matrix, with one row for all but the base
% node, specifying group membership (support) at each node.
%
% To boostrap cluster support, see cluster().
% RE Strauss, 5/27/96
% 9/7/99 - miscellaneous changes for Matlab v5.
% 9/24/01 - check diagonal elements against eps rather than zero.
% 3/14/04 - changed 'suppress' flag to 'doplot'.
function [topology,support] = upgma(dist,labels,doplot,fontsize)
if (nargin < 2) labels = []; end;
if (nargin < 3) doplot = []; end;
if (nargin < 4) fontsize = []; end;
suprt = 0;
if (nargout > 1) suprt = 1; end;
if (isempty(doplot)) doplot = 1; end;
[n,p] = size(dist);
if (n~=p | any(diag(dist)>eps))
dist
error(' UPGMA: input matrix is not a distance matrix.');
end;
if (~isempty(labels))
if (size(labels,1)~=n)
error(' UPGMA: numbers of taxa and taxon labels do not match.');
end;
end;
clstsize = ones(1,n); % Number of elements in clusters/otus
id = 1:n; % Cluster IDs
topology = zeros(n-1,4); % Output dendrogram-topology matrix
plug = 10e6;
dist = dist + eye(n)*plug; % Replace diagonal with plugs
for step = 1:(n-1) % Clustering steps
min_dist = min(dist(:)); % Find minimum pairwise distance
[ii,jj] = find(dist==min_dist); % Find location of minimum
k = 1; % Use first identified minimum
while (ii(k)>jj(k)) % for which i<j
k = k+1;
if k > length(ii) ,keyboard;end;
end;
i = ii(k);
j = jj(k);
if (id(i)<id(j))
topology(step,:) = [id(i) id(j) n+step min_dist];
else
topology(step,:) = [id(j) id(i) n+step min_dist];
end;
id(i) = n+step;
dist(i,j) = plug;
dist(j,i) = plug;
new_clstsize = clstsize(i) + clstsize(j);
alpha_i = clstsize(i) / new_clstsize;
alpha_j = clstsize(j) / new_clstsize;
clstsize(i) = new_clstsize;
for k = 1:n % For all other clusters/OTUs,
if (k~=i & k~=j) % adjust distances to new cluster
dist(k,i) = alpha_i * dist(k,i) + alpha_j * dist(k,j);
dist(i,k) = alpha_i * dist(i,k) + alpha_j * dist(j,k);
dist(k,j) = plug;
dist(j,k) = plug;
end;
end;
end; % for step
if (doplot) % Plot dendrogram
dendplot(topology,labels,fontsize);
end;
if (suprt) % Specify group membership at nodes
support = clstsupt(topology);
end;
return;
|
github
|
lcnbeapp/beapp-master
|
mapcorr.m
|
.m
|
beapp-master/Packages/eeglab14_1_2b/functions/miscfunc/mapcorr.m
| 6,842 |
utf_8
|
4dc2783fce24c7d3b647bb2d2cac4436
|
% mapcorr() - Find matching rows in two matrices and their corrs.
% Uses the Hungarian (default), VAM, or maxcorr assignment methods.
% (Follow with matperm() to permute and sign x -> y).
%
% Finds correlation of maximum common subset of channels (using
% channel location files to match channel labels.) Thus, number
% of channels can differ in x and y.
%
% Usage:
% >> [corr,indx,indy,corrs] = matcorr(x,y,ch1,ch2);
% >> [corr,indx,indy,corrs] = matcorr(x,y,ch1,ch2,rmmean,method,weighting);
%
% Inputs:
% x = first input matrix. Row are difference components and columns
% the channels for these components.
% y = matrix with same number of columns (channels) as x
% ch1 = channel locations file for x
% ch2 = channel locations file for y
%
% Optional inputs:
% rmmean = When present and non-zero, remove row means prior to correlation
% {default: 0}
% method = Method used to find assignments.
% 0= Hungarian Method - maximize sum of abs corrs {default: 2}
% 1= Vogel's Assignment Method -find pairs in order of max contrast
% 2= Max Abs Corr Method - find pairs in order of max abs corr
% Note that the methods 0 and 1 require matrices to be square.
% weighting = An optional weighting matrix size(weighting) = size(corrs) that
% weights the corrs matrix before pair assignment {def: 0/[]->ones()}
% Outputs:
% corr = a column vector of correlation coefficients between
% best-correlating rows of matrice x and y
% indx = a column vector containing the index of the maximum
% abs-correlated x row in descending order of abs corr
% (no duplications)
% indy = a column vector containing the index of the maximum
% abs-correlated row of y in descending order of abs corr
% (no duplications)
% corrs = an optional square matrix of row-correlation coefficients
% between matrices x and y
%
% Note: outputs are sorted by abs(corr)
%
% Authors: Scott Makeig & Sigurd Enghoff, SCCN/INC/UCSD, La Jolla, 11-30-96
% Copyright (C) 11-30-96 Scott Makeig, SCCN/INC/UCSD, [email protected]
%
% This program is free software; you can redistribute it and/or modify
% it under the terms of the GNU General Public License as published by
% the Free Software Foundation; either version 2 of the License, or
% (at your option) any later version.
%
% This program is distributed in the hope that it will be useful,
% but WITHOUT ANY WARRANTY; without even the implied warranty of
% MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
% GNU General Public License for more details.
%
% You should have received a copy of the GNU General Public License
% along with this program; if not, write to the Free Software
% Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
% 2007/03/20 02:33:48 arno, Andreas fix
% 2003/09/04 23:21:06 scott, changed default matching method to Max Abs Corr
% 04-22-99 Re-written using VAM by Sigurd Enghoff, CNL/Salk
% 04-30-99 Added revision of algorthm loop by SE -sm
% 05-25-99 Added Hungarian method assignment by SE
% 06-15-99 Maximum correlation method reinstated by SE
% 08-02-99 Made order of outpus match help msg -sm
% 02-16-00 Fixed order of corr output under VAM added method explanations,
% and returned corr signs in abs max method -sm
% 01-25-02 reformated help & license, added links -ad
% Uses function hungarian.m
function [corr,indx,indy,corrs] = mapcorr(x,y,ch1,ch2,rmmean,method,weighting)
%
if nargin < 4
help matcorr
return
end
if nargin < 6
method = 2; % default: Max Abs Corr - select successive best abs(corr) pairs
end
[m,n] = size(x);
[p,q] = size(y);
m = min(m,p);
if m~=n | p~=q
if nargin>5 & method~=2
fprintf('matcorr(): Matrices are not square: using max abs corr method (2).\n');
end
method = 2; % Can accept non-square matrices
end
if nargin < 5 | isempty(rmmean)
rmmean = 0;
end
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
if rmmean
x = x - mean(x')'*ones(1,n); % optionally remove means
y = y - mean(y')'*ones(1,n);
end
for i = 1:m
for j = 1:p
corrs(i,j) = compcorr(x(i,:)',ch1,y(j,:)',ch2);
end
end
%dx = sum(x'.^2);
%dy = sum(y'.^2);
%dx(find(dx==0)) = 1;
%dy(find(dy==0)) = 1;
%corrs = x*y'./sqrt(dx'*dy);
if nargin > 6 & ~isempty(weighting) & norm(weighting) > 0,
if any(size(corrs) ~= size(weighting))
fprintf('matcorr(): weighting matrix size must match that of corrs\n.')
return
else
corrs = corrs.*weighting;
end
end
cc = abs(corrs);
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
switch method
case 0
ass = hungarian(-cc); % Performs Hungarian algorithm matching
idx1 = sub2ind(size(cc),ass,1:m);
[dummy idx2] = sort(-cc(idx1));
corr = corrs(idx1);
corr = corr(idx2)';
indy = [1:m]';
indx = ass(idx2)';
indy = indy(idx2);
case 1 % Implements the VAM assignment method
indx = zeros(m,1);
indy = zeros(m,1);
corr = zeros(m,1);
for i=1:m,
[sx ix] = sort(cc); % Looks for maximum salience along a row/column
[sy iy] = sort(cc'); % rather than maximum correlation.
[sxx ixx] = max(sx(end,:)-sx(end-1,:));
[syy iyy] = max(sy(end,:)-sy(end-1,:));
if sxx == syy
if sxx == 0 & syy == 0
[sxx ixx] = max((sx(end,:)-sx(end-1,:)) .* sx(end,:));
[syy iyy] = max((sy(end,:)-sy(end-1,:)) .* sy(end,:));
else
sxx = sx(end,ixx); % takes care of identical vectors
syy = sy(end,iyy); % and zero vectors
end
end
if sxx > syy
indx(i) = ix(end,ixx);
indy(i) = ixx;
else
indx(i) = iyy;
indy(i) = iy(end,iyy);
end
cc(indx(i),:) = -1;
cc(:,indy(i)) = -1;
end
i = sub2ind(size(corrs),indx,indy);
corr = corrs(i);
[tmp j] = sort(-abs(corr)); % re-sort by abs(correlation)
corr = corr(j);
indx = indx(j);
indy = indy(j);
case 2 % match successive max(abs(corr)) pairs
indx = zeros(size(cc,1),1);
indy = zeros(size(cc,1),1);
corr = zeros(size(cc,1),1);
for i = 1:size(cc,1)
[tmp j] = max(cc(:));
% [corr(i) j] = max(cc(:));
[indx(i) indy(i)] = ind2sub(size(cc),j);
corr(i) = corrs(indx(i),indy(i));
cc(indx(i),:) = -1; % remove from contention
cc(:,indy(i)) = -1;
end
otherwise
error('Unknown method');
end
function corr = compcorr(a1,ch1,a2,ch2)
n1 = length(a1);
n2 = length(a2);
%if n1 < n2
cnt = 0;
corr = 0;
for i = 1:n1
for j = 1:n2
if strcmp(ch1(i).labels,ch2(j).labels)
cnt = cnt+1;
b1(cnt,1) = a1(i);
b2(cnt,1) = a2(j);
end
end
end
b1 = b1 / norm(b1);
b2 = b2 / norm(b2);
corr = b1'*b2;
|
github
|
lcnbeapp/beapp-master
|
uniqe_cell_string.m
|
.m
|
beapp-master/Packages/eeglab14_1_2b/functions/miscfunc/uniqe_cell_string.m
| 637 |
utf_8
|
4db73f96310fef763282d550920e9d65
|
function uniqueStrings = uniqe_cell_string(c)
% uniqe string from a cell-array containing only strings, ignores all
% non-strings.
nonStringCells = [];
for i=1:length(c) % remove non-string cells
if ~strcmp(class(c{i}),'char')
nonStringCells = [nonStringCells i];
end;
end;
c(nonStringCells) = [];
uniqueStrings = {};
for i=1:length(c) % remove non-string cells
if ~isAlreadyEncountered(c{i}, uniqueStrings);
uniqueStrings{end+1} = c{i};
end;
end;
function result = isAlreadyEncountered(s, u)
result = false;
for i=1:length(u)
if strcmp(u{i}, s)
result = true;
end;
end;
|
github
|
lcnbeapp/beapp-master
|
make_timewarp.m
|
.m
|
beapp-master/Packages/eeglab14_1_2b/functions/miscfunc/make_timewarp.m
| 9,686 |
utf_8
|
248333ed7e02db8061c3f52067e368ff
|
% make_timewarp() - Select a subset of epochs containing a given event sequence, and return
% a matrix of latencies for time warping the selected epochs to a common
% timebase in newtimef(). Events in the given sequence may be further
% restricted to those with specified event field values.
% Usage:
% >> timeWarp = make_timewarp(EEG, eventSequence, 'key1',value1,
% 'key2',value2,...);
%
% Inputs:
% EEG - dataset structure
% eventSequence - cell array containing a sequence of event type strings.
% For example, to select epochs containing a 'movement Onset'
% event followed by a 'movement peak', use
% {'movement Onset' 'movement peak'}
% The output timeWarp matrix will contain the epoch latencies
% of the two events for each selected epoch.
%
% Optional inputs (in 'key', value format):
% 'baselineLatency' - (ms) the minimum acceptable epoch latency for the first
% event in the sequence {default: 0}
% 'eventConditions' - cell array specifying conditions on event fields.
% For example, for a sequence consisting of two
% events with (velocity) fields vx and vy, use
% {vx>0' 'vx>0 && vy<1'}
% To accept events unconditionally, use empty strings,
% for example {'vx>0','',''} {default: no conditions}
% 'maxSTDForAbsolute' - (positive number of std. devs.) Remove epochs containing events
% whose latencies are more than this number of standard deviations
% from the mean in the selected epochs. {default: Inf -> no removal}
% 'maxSTDForRelative' - (positive number of std. devs.) Remove epochs containing inter-event
% latency differences larger or smaller than this number of standard deviations
% from the mean in the selected epochs. {default: Inf -> no removal}
% Outputs:
% timeWarp - a structure with latencies (time-warp matrix with fields
% timeWarp.latencies - an (N, M) timewarp matrix for use in newtimef()
% where N = number of selected epochs containing the specified sequence,
% M = number of events in specified event sequence.
% timeWarp.epochs - a (1, M) vector giving the index of epochs with the
% specified sequence. Only these epochs should be passed to newtimef().
% timeWarp.eventSequence - same as the 'eventSequence' input variable.
% Example:
% % Create a timewarp matrix for a sequence of events, first an event of type 'movement Onset' followed by
% % a 'movement peak' event, with event fields vx and vy:
%
% >> timeWarp = make_timewarp(EEG, {'movement Onset' 'movement% peak'},'baselineLatency', 0 ...
% ,'eventConditions', {'vx>0' 'vx>0 && vy<1'});
%
% % To remove events with latencies more than 3 standard deviations from the mean OR 2 std. devs.
% % from the mean inter-event difference:
%
% >> timeWarp = make_timewarp(EEG, {'movement Onset' 'movement peak'},'baselineLatency', 0, ...
% 'eventConditions', {'vx>0' 'vx>0 && vy<1'},'maxSTDForAbsolute', 3,'maxSTDForRelative', 2);
%
% Author: Nima Bigdely Shamlo, SCCN/INC/UCSD, 2008
% See also: show_events(), newtimef()
function timeWarpStructure = make_timewarp(EEG, eventSequence, varargin)
inputKeyValues = finputcheck(varargin, ...
{'baselineLatency' 'real' [] 0; ...
'eventConditions' 'cell' {} {} ; ...
'maxSTDForAbsolute' 'real' [0 Inf] Inf; ...
'maxSTDForRelative' 'real' [0 Inf] Inf...
});
baselineLatency = [];
maxSTDForAbsolute = 0;
maxSTDForRelative = 0;
eventConditions = [];
% place key values into function workspace variables
inputKeyValuesFields = fieldnames(inputKeyValues);
for i=1:length(inputKeyValuesFields)
eval([inputKeyValuesFields{i} '= inputKeyValues.' inputKeyValuesFields{i} ';']);
end;
if length(eventConditions) < length(eventSequence)
for i = (length(eventConditions)+1):length(eventSequence)
eventConditions{i} = '';
end;
end;
epochsIsAcceptable = ones(1, length(EEG.epoch));
for epochNumber = 1:length(EEG.epoch)
eventNameID = 1;
minimumLatency = baselineLatency;
timeWarp{epochNumber} = [];
while eventNameID <= length(eventSequence) % go tthrought event names and find the event that comes after a certain event with correct type and higher latency
firstLatency = eventsOfCertainTypeAfterCertainLatencyInEpoch(EEG.epoch(epochNumber), eventSequence{eventNameID}, minimumLatency, eventConditions{eventNameID});
if isempty(firstLatency) % means there were no events, so the epoch is not acceptable
break;
else
timeWarp{epochNumber} = [timeWarp{epochNumber}; firstLatency];
minimumLatency = firstLatency;
eventNameID = eventNameID + 1;
end;
end;
if length(timeWarp{epochNumber}) < length(eventSequence)
epochsIsAcceptable(epochNumber) = false;
end;
end;
acceptableEpochs = find(epochsIsAcceptable);
if isempty(acceptableEpochs)
timeWarp = {}; % no epoch meet the criteria
else
timeWarp = cell2mat(timeWarp(acceptableEpochs));
rejectedEpochesBasedOnLateny = union_bc(rejectEventsBasedOnAbsoluteLatency(timeWarp), rejectEventsBasedOnRelativeLatency(timeWarp));
timeWarp(:,rejectedEpochesBasedOnLateny) = [];
acceptableEpochs(rejectedEpochesBasedOnLateny) = [];
end;
% since latencies and accepted epochs always have to be together, we put them in one structure
timeWarpStructure.latencies = timeWarp'; % make it suitable for newtimef()
if isempty(timeWarpStructure.latencies) % when empty, it becomes a {} instead of [], so we change it to []
timeWarpStructure.latencies = [];
end;
timeWarpStructure.epochs = acceptableEpochs;
timeWarpStructure.eventSequence = eventSequence;
function rejectedBasedOnLateny = rejectEventsBasedOnRelativeLatency(timeWarp)
% remeve epochs in which the time warped event is further than n
% standard deviations to mean of latency distance between events
timeWarpDiff = diff(timeWarp);
rejectedBasedOnLateny = [];
for eventNumber = 1:size(timeWarpDiff, 1)
rejectedBasedOnLateny = [rejectedBasedOnLateny find(abs(timeWarpDiff(eventNumber, :)- mean(timeWarpDiff(eventNumber, :))) > maxSTDForRelative * std(timeWarpDiff(eventNumber, :)))];
end;
rejectedEpochesBasedOnLateny = unique_bc(rejectedBasedOnLateny);
end
function rejectedBasedOnLateny = rejectEventsBasedOnAbsoluteLatency(timeWarp)
% remeve instances in which the time warped event is further than n
% standard deviations to mean
rejectedBasedOnLateny = [];
for eventNumber = 1:size(timeWarp, 1)
rejectedBasedOnLateny = [rejectedBasedOnLateny find(abs(timeWarp(eventNumber, :)- mean(timeWarp(eventNumber, :))) > maxSTDForAbsolute* std(timeWarp(eventNumber, :)))];
end;
rejectedEpochesBasedOnLateny = unique_bc(rejectedBasedOnLateny);
end
function [firstLatency resultEventNumbers] = eventsOfCertainTypeAfterCertainLatencyInEpoch(epoch, certainEventType, certainLatency, certainCondition)
resultEventNumbers = [];
firstLatency = []; % first event latency that meets the critria
for eventNumber = 1:length(epoch.eventtype)
% if strcmp(certainEventType, epoch.eventtype(eventNumber)) && epoch.eventlatency{eventNumber} >= certainLatency && eventMeetsCondition(epoch, eventNumber, certainCondition)
if eventIsOfType(epoch.eventtype(eventNumber), certainEventType) && epoch.eventlatency{eventNumber} >= certainLatency && eventMeetsCondition(epoch, eventNumber, certainCondition)
resultEventNumbers = [resultEventNumbers eventNumber];
if isempty(firstLatency)
firstLatency = epoch.eventlatency{eventNumber};
end;
end;
end;
end
function result = eventMeetsCondition(epoch, eventNumber, condition)
if strcmp(condition,'') || strcmp(condition,'true')
result = true;
else
% get the name thatis before themfor field in the epoch, then remove 'event' name
epochField = fieldnames(epoch);
for i=1:length(epochField)
epochField{i} = strrep(epochField{i},'event',''); % remove event from the beginning of field names
condition = strrep(condition, epochField{i}, ['cell2mat(epoch.event' epochField{i} '(' num2str(eventNumber) '))' ]);
end;
result = eval(condition);
end;
end
function result = eventIsOfType(eventStr, types)
% if events are numbers, turn them into strings before comparison
if ischar(types)
if iscell(eventStr) && isnumeric(cell2mat(eventStr))
eventStr = num2str(cell2mat(eventStr));
end;
result = strcmp(eventStr, types);
else % it must be a cell of strs
result = false;
for i=1:length(types)
result = result || strcmp(eventStr, types{i});
end;
end;
end
end
|
github
|
lcnbeapp/beapp-master
|
fieldtrip2eeglab.m
|
.m
|
beapp-master/Packages/eeglab14_1_2b/functions/miscfunc/fieldtrip2eeglab.m
| 1,269 |
utf_8
|
442a73a6c0d6090b20bc0444bad3aba7
|
% load data file ('dataf') preprocessed with fieldtrip
% and show in eeglab viewer
%
% This function is provided as is. It only works for some specific type of
% data. This is a simple function to help the developer and by no mean
% an all purpose function.
function [EEG] = fieldtrip2eeglab(dataf)
[ALLEEG EEG CURRENTSET ALLCOM] = eeglab;
if exist(dataf,'file')
load(dataf)
end
% load chanlocs.mat
% EEG.chanlocs = chanlocs;
EEG.chanlocs = [];
for i=1:size(data.trial,2)
EEG.data(:,:,i) = single(data.trial{i});
end
EEG.setname = dataf; %data.cfg.dataset;
EEG.filename = '';
EEG.filepath = '';
EEG.subject = '';
EEG.group = '';
EEG.condition = '';
EEG.session = [];
EEG.comments = 'preprocessed with fieldtrip';
EEG.nbchan = size(data.trial{1},1);
EEG.trials = size(data.trial,2);
EEG.pnts = size(data.trial{1},2);
EEG.srate = data.fsample;
EEG.xmin = data.time{1}(1);
EEG.xmax = data.time{1}(end);
EEG.times = data.time{1};
EEG.ref = []; %'common';
EEG.event = [];
EEG.epoch = [];
EEG.icawinv = [];
EEG.icasphere = [];
EEG.icaweights = [];
EEG.icaact = [];
EEG.saved = 'no';
[ALLEEG EEG CURRENTSET] = eeg_store(ALLEEG, EEG);
eeglab redraw
pop_eegplot( EEG, 1, 1, 1);
|
github
|
lcnbeapp/beapp-master
|
rmart.m
|
.m
|
beapp-master/Packages/eeglab14_1_2b/functions/miscfunc/rmart.m
| 6,530 |
utf_8
|
f8a4b6645ed700ac44e8b0933750ef36
|
% rmart() - Remove eye artifacts from EEG data using regression with
% multiple time lags. Each channel is first made mean-zero.
% After JL Kenemans et al., Psychophysiology 28:114-21, 1991.
%
% Usage: >> rmart('datafile','outfile',nchans,chanlist,eogchan,[threshold])
% Example: >> rmart('noisy.floats','clean.floats',31,[2:31],7)
%
% Input: datafile - input float data file, multiplexed by channel
% outfile - name of output float data file
% nchans - number of channels in datafile
% chanlist - indices of EEG channel(s) to process (1,...,nchans)
% eogchan - regressing channel indices(s) (1,...,nchans)
% threshold- abs threshold value to trigger regression {def|0 -> 80}
%
% Output: Writes [length(chanlist),size(data,2)] floats to 'outfile'
%
% Note: Regression epoch length and number of lags are set in the script.
% Some machines may require a new byte_order value in the script.
% note that runica() -> icaproj() should give better results! See
% Jung et al., Psychophysiology 111:1745-58, 2000.
%
% Author: Tzyy-Ping Jung, SCCN/INC/UCSD, La Jolla, 1997
% Copyright (C) 1997 Tzyy-Ping Jung, SCCN/INC/UCSD, [email protected]
%
% This program is free software; you can redistribute it and/or modify
% it under the terms of the GNU General Public License as published by
% the Free Software Foundation; either version 2 of the License, or
% (at your option) any later version.
%
% This program is distributed in the hope that it will be useful,
% but WITHOUT ANY WARRANTY; without even the implied warranty of
% MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
% GNU General Public License for more details.
%
% You should have received a copy of the GNU General Public License
% along with this program; if not, write to the Free Software
% Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
% 2-22-97 Tzyy-Ping Jung CNL/Salk Institute, La Jolla, CA
% 2-24-97 Formatted for ICA package release -Scott Makeig
% 12-10-97 Changed name from rmartifact to rmart for toolbox inclusion -sm
% 12-11-97 Adapted to read/write a float matrix -sm & sw
% 09-14-00 Added comments and help -sm
% 01-25-02 reformated help & license -ad
function rmart(datafile,outfile,nchans,chanlist,eogchan,threshold)
if nargin < 5
help rmart
return
end
%
% The following parameters may be fine-tuned for a data set
%
DEF_THRESHOLD = 80; % trigger regression on blocks exceeding this (default)
epoch = 80; % remove artifacts in successive blocks of this length
nlags = 40; % perform multiple regression filtering of this length
byte_order = 'b';% (machine-dependent) byte order code for fopen();
MAKE_MEAN_ZERO = 1 % 1/0 flag removing mean offset from each channel
fprintf('Performing artifact regression on data in %s.\n',datafile);
if nargin<6
threshold = 0;
end
if threshold == 0,
threshold = DEF_THRESHOLD;
end
fprintf('Regression threshold %g.\n',threshold);
%
% Read the input data
%
[fid,msg]=fopen(datafile,'r',byte_order); % open datafile
if fid < 3,
fprintf('rmart() - could not open data file: %s\n',msg);
exit 1
end
data=(fread(fid,'float'))';
status=fclose('all');
if rem(length(data),nchans) == 0 % check length
fprintf('rmart() - data length not divisible by %d chans.\n',nchans);
return
end
data = reshape(data,nchans,length(data)/nchans);
[chans,frames] = size(data);
fprintf('Data of size [%d,%d] read.\n',chans,frames);
eog = data(eogchan,:);
data = data(chanlist,:);
procchans = length(chanlist);
fprintf('Regression epoch length %d frames.\n',epoch);
fprintf('Using %d regression lags.\n',nlags);
if length(eogchan)> 1
fprintf('Processing %d of %d channels using %d EOG channels.\n',...
procchans,chans,length(eogchan));
else
fprintf('Processing %d of %d channels using EOG channel %d.\n',...
procchans,chans,eogchan);
end
%
% Process the data
%
for i=1:procchans
chan = chanlist(i);
idx=[];
frame=1+epoch/2+nlags/2;
if MAKE_MEAN_ZERO
data(chan,:) = data(chan,:) - mean(data(chan,:)); % make mean-zero
end
% Search the EOG & EEG records for values above threshold,
% Selected frame numbers are registered in the variable "idx".
% The entries in "idx" are at least epoch apart to avoid double
% compensation (regression) on the same portion of the EEG data.
while frame <= length(eog)-epoch/2-nlags/2, % foreach epoch in channel
stop = min(frame+epoch-1,eogframes);
tmp= ...
find( abs(eog(frame:stop)) >= threshold ...
| abs(data(chan,frame:stop)) >= threshold);
% find beyond-threshold values
if length(tmp) ~= 0
mark = tmp(1)+frame-1;
if length(idx) ~= 0
if mark-idx(length(idx)) < epoch,
idx=[idx idx(length(idx))+epoch]; % To guarantee idx(i) & idx(i-1)
% are at least EPOCH points apart
frame = idx(length(idx))+epoch/2;
else
idx=[idx mark];
frame = mark + epoch/2;
end
else
idx=[idx mark];
frame = mark + epoch/2;
end
else
frame=frame+epoch;
end
end % while
% For each registered frame, take "epoch" points
% surrounding it from the EEG, and "epoch + lag" points
% from the EOG channel. Then perform multivariate
% linear regression on EEG channel.
for j=1:length(idx);
art=ones(1,epoch);
eogtmp=eog(idx(j)-epoch/2-nlags/2:idx(j)+epoch/2-1+nlags/2);
% Collect EOG data from lag/2 points before to lag/2 points
% after the regression window.
for J=nlags:-1:1,
art=[art ; eogtmp(J:J+epoch-1)];
end
eegtmp=data(chan,idx(j)-epoch/2:idx(j)+epoch/2-1);
eegeog=eegtmp*art'; % perform the regression here
eogeog=art*art';
b=eegeog/eogeog;
eegtmp=eegtmp-b*art;
data(chan,idx(j)-epoch/2:idx(j)+epoch/2-1)=eegtmp;
end % j
end % i
%
% Write output file
%
[fid,msg]=fopen(outfile,'w',byte_order);
if fid < 3
fprintf('rmart() - could not open output file: %s\n',msg);
return
end
count = fwrite(fid,data,'float');
if count == procchans*frames,
fprintf('Output file "%s" written, size = [%d,%d] \n\n',...
outfile,procchans,frames);
else
fprintf('rmart(): Output file "%s" written, SIZE ONLY [%d,%g]\n',...
outfile,procchans,count/procchans);
end
fclose('all');
|
github
|
lcnbeapp/beapp-master
|
vectdata.m
|
.m
|
beapp-master/Packages/eeglab14_1_2b/functions/miscfunc/vectdata.m
| 4,693 |
utf_8
|
e2d5960f3405659d0cdcb6645ef43835
|
% vectdata() - vector data interpolation with optional moving
% average.
%
% Usage:
% >> [interparray timesout] = vectdata( array, timesin, 'key', 'val', ... );
%
% Inputs:
% array - 1-D or 2-D float array. If 2-D, the second dimension
% only is interpolated.
% timesin - [float vector] time point indices. Same dimension as
% the interpolated dimension in array.
%
% Optional inputs
% 'timesout' - [float vector] time point indices for interpolating
% data.
% 'method' - method for interpolation
% 'linear' -> Triangle-based linear interpolation (default).
% 'cubic' -> Triangle-based cubic interpolation.
% 'nearest' -> Nearest neighbor interpolation.
% 'v4' -> MATLAB 4 griddata method.
% 'average' - [real] moving average in the dimension of timesin
% note that extreme values might be inacurate (see 'borders').
% Default none or [].
% 'avgtype' - ['const'|'gauss'] use a const value when averaging (array of
% ones) or a gaussian window. Default is 'const'.
% 'border' - ['on'|'off'] correct border effect when smoothing.
% default is 'off'.
%
% Outputs:
% interparray - interpolated array
% timesout - output time points
%
% Author: Arnaud Delorme, CNL / Salk Institute, 20 Oct 2002
%
% See also: griddata()
% Copyright (C) 2002 Arnaud Delorme, Salk Institute, [email protected]
%
% This program is free software; you can redistribute it and/or modify
% it under the terms of the GNU General Public License as published by
% the Free Software Foundation; either version 2 of the License, or
% (at your option) any later version.
%
% This program is distributed in the hope that it will be useful,
% but WITHOUT ANY WARRANTY; without even the implied warranty of
% MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
% GNU General Public License for more details.
%
% You should have received a copy of the GNU General Public License
% along with this program; if not, write to the Free Software
% Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
function [interparray, timesout] = vectdata( array, timevect, varargin );
if nargin < 3
help vectdata;
return;
end;
g = finputcheck( varargin, { 'timesout' 'real' [] [];
'average' 'real' [] [];
'gauss' 'real' [] [];
'border' 'string' { 'on','off' } 'off';
'avgtype' 'string' { 'const','gauss' } 'const';
'method' 'string' { 'linear','cubic','nearest','v4' } 'linear'});
if isstr(g), error(g); end;
if size(array,2) == 1
array = transpose(array);
end;
if ~isempty(g.average)
timediff = timevect(2:end) -timevect(1:end-1);
if any( (timediff - mean(timediff)) > 1e-8 ) % not uniform values
fprintf('Data has to be interpolated uniformly for moving average\n');
minspace = mean(timediff);
newtimevect = linspace(timevect(1), timevect(end), ceil((timevect(end)-timevect(1))/minspace));
array = interpolate( array, timevect, newtimevect, g.method);
timevect = newtimevect;
end;
oldavg = g.average;
g.average = round(g.average/(timevect(2)-timevect(1)));
if oldavg ~= g.average
fprintf('Moving average updated from %3.2f to %3.2f (=%d points)\n', ...
oldavg, g.average*(timevect(2)-timevect(1)), g.average);
end;
if strcmpi(g.border, 'on')
if strcmpi(g.avgtype, 'const')
array = convolve(array, ones(1, g.average));
else
convolution = gauss2d(1,g.average,1,round(0.15*g.average));
array = convolve(array, convolution);
end;
else
if strcmpi(g.avgtype, 'const')
array = conv2(array, ones(1, g.average)/g.average, 'same');
else
convolution = gauss2d(1,g.average,1,round(0.15*g.average));
array = conv2(array, convolution/sum(convolution), 'same');
end;
end;
end;
interparray = interpolate( array, timevect, g.timesout, g.method);
timesout = g.timesout;
% interpolation function
% ----------------------
function [interparray] = interpolate( array, timesin, timesout, method);
interparray = zeros(size(array,1), length(timesout));
for index = 1:size(array,1)
tmpa = [array(index,:) ; array(index,:)];
[Xi,Yi,Zi] = griddata(timesin, [1 2]', tmpa, timesout, [1 2]', method); % Interpolate data
interparray(index,:) = Zi(1,:);
end;
|
github
|
lcnbeapp/beapp-master
|
matperm.m
|
.m
|
beapp-master/Packages/eeglab14_1_2b/functions/miscfunc/matperm.m
| 2,919 |
utf_8
|
697c96bef1109a7011a0d4781bfbedc3
|
% matperm() - transpose and sign rows of x to match y (run after matcorr() )
%
% Usage: >> [permx indperm] = matperm(x,y,indx,indy,corr);
%
% Inputs:
% x = first input matrix
% y = matrix with same number of columns as x
% indx = column containing row indices for x (from matcorr())
% indy = column containing row indices for y (from matcorr())
% corr = column of correlations between indexed rows of x,y (from matcorr())
% (used only for its signs, +/-)
% Outputs:
% permx = the matrix x permuted and signed according to (indx, indy,corr)
% to best match y. Rows of 0s added to x to match size of y if nec.
% indperm = permutation index turning x into y;
%
% Authors: Scott Makeig, Sigurd Enghoff & Tzyy-Ping Jung
% SCCN/INC/UCSD, La Jolla, 2000
% Copyright (C) 1996 Scott Makeig, SCCN/INC/UCSD, [email protected]
%
% This program is free software; you can redistribute it and/or modify
% it under the terms of the GNU General Public License as published by
% the Free Software Foundation; either version 2 of the License, or
% (at your option) any later version.
%
% This program is distributed in the hope that it will be useful,
% but WITHOUT ANY WARRANTY; without even the implied warranty of
% MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
% GNU General Public License for more details.
%
% You should have received a copy of the GNU General Public License
% along with this program; if not, write to the Free Software
% Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
% 04-22-99 Adjusted for fixes and speed by Sigurd Enghoff & Tzyy-Ping Jung
% 01-25-02 Reformated help & license, added links -ad
function [permx,indperm]= matperm(x,y,indx,indy,corr)
[m,n] = size(x);
[p,q] = size(y);
[ix,z] = size(indx);
[iy,z] = size(indy);
oldm = m;
errcode=0;
if ix ~= iy | p ~= iy,
fprintf('matperm: indx and indy must be column vectors, same height as y.\n');
errcode=1
end;
if n~=q,
fprintf('matperm(): two matrices must be same number of columns.\n');
errcode=2;
else
if m<p,
x = [x;zeros(p-m,n)]; % add rows to x to match height of y
p=m;
elseif p<m,
y = [y;zeros(m-p,n)]; % add rows to y to match height of x
m=p;
end;
end;
if errcode==0,
%
% Return the row permutation of matrix x most correlated with matrix y:
% plus the resulting permutation index
%
indperm = [1:length(indx)]'; % column vector [1 2 ...nrows]
permx = x(indx,:);
indperm = indperm(indx,:);
ydni(indy) = 1:length(indy);
permx = permx(ydni,:);% put x in y row-order
indperm = indperm(ydni,:);
permx = permx.*(sgn(corr(ydni))*ones(1,size(permx,2)));
% make x signs agree with y
permx = permx(1:oldm,:); % throw out bottom rows if
% they were added to match y
indperm = indperm(1:oldm,:);
end;
return
function vals=sgn(data)
vals = 2*(data>=0)-1;
return
|
github
|
lcnbeapp/beapp-master
|
varimax.m
|
.m
|
beapp-master/Packages/eeglab14_1_2b/functions/miscfunc/varimax.m
| 4,437 |
utf_8
|
d87cb189d37524e4920c2f9ad9c41aa4
|
% varimax() - Perform orthogonal Varimax rotation on rows of a data
% matrix.
%
% Usage: >> V = varimax(data);
% >> [V,rotdata] = varimax(data,tol);
% >> [V,rotdata] = varimax(data,tol,'noreorder')
%
% Inputs:
% data - data matrix
% tol - set the termination tolerance to tol {default: 1e-4}
% 'noreorder' - Perform the rotation without component reorientation
% or reordering by size. This suppression is desirable
% when doing a q-mode analysis. {default|0|[] -> reorder}
% Outputs:
% V - orthogonal rotation matrix, hence
% rotdata - rotated matrix, rotdata = V*data;
%
% Author: Sigurd Enghoff - CNL / Salk Institute, La Jolla 6/18/98
%
% See also: runica(), pcasvd(), promax()
% Copyright (C) Sigurd Enghoff - CNL / Salk Institute, La Jolla 6/18/98
%
% This program is free software; you can redistribute it and/or modify
% it under the terms of the GNU General Public License as published by
% the Free Software Foundation; either version 2 of the License, or
% (at your option) any later version.
%
% This program is distributed in the hope that it will be useful,
% but WITHOUT ANY WARRANTY; without even the implied warranty of
% MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
% GNU General Public License for more details.
%
% You should have received a copy of the GNU General Public License
% along with this program; if not, write to the Free Software
% Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
% Reference: % Henry F. Kaiser (1958) The Varimx criterion for
% analytic rotation in factor analysis. Pychometrika 23:187-200.
%
% modified to return V alone by Scott Makeig, 6/23/98
% 01-25-02 reformated help & license, added link -ad
function [V,data] = varimax(data,tol,reorder)
if nargin < 1
help varimax
return
end
DEFAULT_TOL = 1e-4; % default tolerance, for use in stopping the iteration
DEFAULT_REORDER = 1; % default to reordering the output rows by size
% and adjusting their sign to be rms positive.
MAX_ITERATIONS = 50; % Default
qrtr = .25; % fixed value
if nargin < 3
reorder = DEFAULT_REORDER;
elseif isempty(reorder) | reorder == 0
reorder = 1; % set default
else
reorder = strcmp('reorder',reorder);
end
if nargin < 2
tol = 0;
end
if tol == 0
tol = DEFAULT_TOL;
end
if ischar(tol)
fprintf('varimax(): tol must be a number > 0\n');
help varimax
return
end
eps1 = tol; % varimax toler
eps2 = tol;
V = eye(size(data,1)); % do unto 'V' what is done to data
crit = [sum(sum(data'.^4)-sum(data'.^2).^2/size(data,2)) 0];
inoim = 0;
iflip = 1;
ict = 0;
fprintf(...
'Finding the orthogonal Varimax rotation using delta tolerance %d...\n',...
eps1);
while inoim < 2 & ict < MAX_ITERATIONS & iflip,
iflip = 0;
for j = 1:size(data,1)-1,
for k = j+1:size(data,1),
u = data(j,:).^2-data(k,:).^2;
v = 2*data(j,:).*data(k,:);
a = sum(u);
b = sum(v);
c = sum(u.^2-v.^2);
d = sum(u.*v);
fden = size(data,2)*c + b^2 - a^2;
fnum = 2 * (size(data,2)*d - a*b);
if abs(fnum) > eps1*abs(fden)
iflip = 1;
angl = qrtr*atan2(fnum,fden);
tmp = cos(angl)*V(j,:)+sin(angl)*V(k,:);
V(k,:) = -sin(angl)*V(j,:)+cos(angl)*V(k,:);
V(j,:) = tmp;
tmp = cos(angl)*data(j,:)+sin(angl)*data(k,:);
data(k,:) = -sin(angl)*data(j,:)+cos(angl)*data(k,:);
data(j,:) = tmp;
end
end
end
crit = [sum(sum(data'.^4)-sum(data'.^2).^2/size(data,2)) crit(1)];
inoim = inoim + 1;
ict = ict + 1;
fprintf('#%d - delta = %g\n',ict,(crit(1)-crit(2))/crit(1));
if (crit(1) - crit(2)) / crit(1) > eps2
inoim = 0;
end
end
%
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%
if reorder
fprintf('Reordering rows...');
[fnorm index] = sort(sum(data'.^2));
V = V .* ((2 * (sum(data') > 0) - 1)' * ones(1, size(V,2)));
data = data .* ((2 * (sum(data') > 0) - 1)' * ones(1, size(data,2)));
V = V(fliplr(index),:);
data = data(fliplr(index),:);
fprintf('\n');
else
fprintf('Not reordering rows.\n');
end
|
github
|
lcnbeapp/beapp-master
|
pcsquash.m
|
.m
|
beapp-master/Packages/eeglab14_1_2b/functions/miscfunc/pcsquash.m
| 2,802 |
utf_8
|
9e0a0372b72b09c731ef70785b8ce862
|
% pcsquash() - compress data using Principal Component Analysis (PCA)
% into a principal component subspace. To project back
% into the original channel space, use pcexpand()
%
% Usage:
% >> [eigenvectors,eigenvalues] = pcsquash(data,ncomps);
% >> [eigenvectors,eigenvalues,compressed,datamean] ...
% = pcsquash(data,ncomps);
%
% Inputs:
% data = (chans,frames) each row is a channel, each column a time point
% ncomps = numbers of components to retain
%
% Outputs:
% eigenvectors = square matrix of (column) eigenvectors
% eigenvalues = vector of associated eigenvalues
% compressed = data compressed into space of the ncomps eigenvectors
% with largest eigenvalues (ncomps,frames)
% Note that >> compressed = eigenvectors(:,1:ncomps)'*data;
% datamean = input data channel (row) means (used internally)
%
% Author: Tzyy-Ping Jung & Scott Makeig, SCCN/INC/UCSD, La Jolla, 6-97
%
% See also: pcexpand(), svd()
% Copyright (C) 2000 Tzyy-Ping Jung & Scott Makeig, SCCN/INC/UCSD,
% [email protected]
%
% This program is free software; you can redistribute it and/or modify
% it under the terms of the GNU General Public License as published by
% the Free Software Foundation; either version 2 of the License, or
% (at your option) any later version.
%
% This program is distributed in the hope that it will be useful,
% but WITHOUT ANY WARRANTY; without even the implied warranty of
% MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
% GNU General Public License for more details.
%
% You should have received a copy of the GNU General Public License
% along with this program; if not, write to the Free Software
% Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
% 01-25-02 reformated help & license, added links -ad
function [EigenVectors,EigenValues,Compressed,Datamean]=pcsquash(matrix,ncomps)
if nargin < 1
help pcsquash
return
end
if nargin < 2
ncomps = 0;
end
if ncomps == 0
ncomps = size(matrix,1);
end
if ncomps < 1
help pcsquash
return
end
data = matrix'; % transpose data
[n,p]=size(data); % now p chans,n time points
if ncomps > p
fprintf('pcsquash(): components must be <= number of data rows (%d).\n',p);
return;
end
Datamean = mean(data,1); % remove column (channel) means
data = data-ones(n,1)*Datamean; % remove column (channel) means
out=data'*data/n;
[V,D] = eig(out); % get eigenvectors/eigenvalues
diag(D);
[eigenval,index] = sort(diag(D));
index=rot90(rot90(index));
EigenValues=rot90(rot90(eigenval))';
EigenVectors=V(:,index);
if nargout >= 3
Compressed = EigenVectors(:,1:ncomps)'*data';
end
|
github
|
lcnbeapp/beapp-master
|
nan_std.m
|
.m
|
beapp-master/Packages/eeglab14_1_2b/functions/miscfunc/nan_std.m
| 1,304 |
utf_8
|
d53859297282cc1d957ec0f2cc0b3617
|
% nan_std() - std, not considering NaN values
%
% Usage: std across the first dimension
% Author: Arnaud Delorme, CNL / Salk Institute, Sept 2003
% Copyright (C) 2003 Arnaud Delorme, Salk Institute, [email protected]
%
% This program is free software; you can redistribute it and/or modify
% it under the terms of the GNU General Public License as published by
% the Free Software Foundation; either version 2 of the License, or
% (at your option) any later version.
%
% This program is distributed in the hope that it will be useful,
% but WITHOUT ANY WARRANTY; without even the implied warranty of
% MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
% GNU General Public License for more details.
%
% You should have received a copy of the GNU General Public License
% along with this program; if not, write to the Free Software
% Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
function out = nan_std(in)
if nargin < 1
help nan_std;
return;
end;
nans = find(isnan(in));
in(nans) = 0;
nonnans = ones(size(in));
nonnans(nans) = 0;
nonnans = sum(nonnans);
nononnans = find(nonnans==0);
nonnans(nononnans) = NaN;
out = sqrt((sum(in.^2)-sum(in).^2./nonnans)./(nonnans-1));
out(nononnans) = NaN;
|
github
|
lcnbeapp/beapp-master
|
plotproj.m
|
.m
|
beapp-master/Packages/eeglab14_1_2b/functions/miscfunc/plotproj.m
| 5,772 |
utf_8
|
a22a956e9c31d1ee84c4bbb5a663cd53
|
% plotproj() - plot projections of one or more ICA components along with
% the original data (returns the data plotted)
%
% Usage:
% >> [projdata] = plotproj(data,weights,compnums);
% >> [projdata] = plotproj(data,weights,compnums, ...
% title,limits,chanlist,channames,colors);
%
% Inputs:
% data = single epoch of runica() input data (chans,frames)
% weights = unmixing matrix (=weights*sphere)
% compnums = vector of component numbers to project and plot
%
% Optional inputs:
% title = 'fairly short plot title' {0 -> 'plotproj()'}
% limits = [xmin xmax ymin ymax] (x's in msec)
% {0, or both y's 0 -> data limits}
% chanlist = list of data channels to plot {0 -> all}
% channames = channel location file or structure (see readlocs())
% colors = file of color codes, 3 chars per line ('.' = space)
% {0 -> default color order (black/white first)}
%
% Author: Scott Makeig, SCCN/INC/UCSD, La Jolla, 05-01-96
%
% See also: plotdata()
% Without color arg, reads filename for PROJCOLORS from icadefs.m
% Copyright (C) 05-01-96 from plotdata() Scott Makeig, SCCN/INC/UCSD,
% [email protected]
%
% This program is free software; you can redistribute it and/or modify
% it under the terms of the GNU General Public License as published by
% the Free Software Foundation; either version 2 of the License, or
% (at your option) any later version.
%
% This program is distributed in the hope that it will be useful,
% but WITHOUT ANY WARRANTY; without even the implied warranty of
% MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
% GNU General Public License for more details.
%
% You should have received a copy of the GNU General Public License
% along with this program; if not, write to the Free Software
% Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
% 05-25-96 added chanlist, nargin tests, rearranged variable order -sm
% 07-29-96 debugged, added chanlist channames option -sm
% 10-26-96 added test for column of compnums -sm
% 02-18-97 improved usage message -sm
% 02-19-97 merged versions -sm
% 03-19-97 changed var() to diag(cov()), use datamean arg instead of frames/baseframes -sm
% 04-24-97 tested datamean for 1-epoch; replaced cov() with mean-squares -sm
% 05-20-97 read icadefs for PROJCOLORS & MAXPLOTDATACHANS -sm
% 06-05-97 use arbitrary chanlist as default channames -sm
% 06-07-97 changed order of args to conform to runica -sm
% 06-12-97 made sumdata(chanlist in line 159 below -sm
% 07-23-97 removed datamean from args; let mean distribut4e over components -sm
% 09-09-97 corrected write out line " summing " -sm
% 10-31-97 removed errcode var -sm
% 11-05-97 added test for channames when chanlist ~= 1:length(chanlist) -sm & ch
% 12-19-00 adjusted new icaproj() args -sm
% 01-12-01 removed sphere arg -sm
% 01-25-02 reformated help & license, added links -ad
function [projdata] = plotproj(data,weights,compnums,titl,limits,chanlist,channels,colors);
icadefs % read default PROJCOLORS & MAXPLOTDATACHANS variables from icadefs.m
DEFAULT_TITLE = 'plotproj()';
%
% Substitute for missing arguments
%
if nargin < 8,
colors = 'white1st.col';
elseif colors==0,
colors = 'white1st.col';
end
if nargin < 7,
channels = 0;
end
if nargin < 6
chanlist = 0;
end
if nargin < 5,
limits = 0;
end
if nargin < 4,
titl = 0;
end
if titl==0,
titl = DEFAULT_TITLE;
end
if nargin < 3,
fprintf('plotproj(): must have at least four arguments.\n\n');
help plotproj
return
end
%
% Test data size
%
[chans,framestot] = size(data);
frames = framestot; % assume one epoch
[wr,wc] = size(weights);
if wc ~= chans
fprintf('plotproj(): sizes of weights and data incompatible.\n\n');
return
end
%
% Substitute for 0 arguments
%
if chanlist == 0,
chanlist = [1:chans];
end;
if compnums == 0,
compnums = [1:wr];
end;
if size(compnums,1)>1, % handle column of compnums !
compnums = compnums';
end;
if length(compnums) > 256,
fprintf('plotproj(): cannot plot more than %d channels of data at once.\n',256);
return
end;
if channels ~= 0 % if chan name file given
if ~all(chanlist == [1:length(chanlist)])
fprintf('plotproj(): Cannot read an arbitrary chanlist of channel names.\n');
return
end
end
if channels==0,
channels = chanlist;
end
if max(compnums)>wr,
fprintf(...
'\n plotproj(): Component index (%d) > number of components (%d).\n', ...
max(compnums),wr);
return
end
fprintf('Reconstructing (%d chan, %d frame) data summing %d components.\n', ...
chans,frames,length(compnums));
%
% Compute projected data for single components
%
projdata = data(chanlist,:);
fprintf('plotproj(): Projecting component(s) ');
for s=compnums, % for each component
fprintf('%d ',s);
proj = icaproj(data,weights,s); % let offsets distribute
projdata = [projdata proj(chanlist,:)]; % append projected data onto projdata
% size(projdata) = [length(chanlist) framestot*(length(compnums)+1)]
end;
fprintf('\n');
%
% Compute percentage of variance accounted for
%
sumdata = icaproj(data,weights,compnums);% let offsets distribute
sigmssq = mean(sum(data(chanlist,:).*data(chanlist,:)));
data(chanlist,:) = data(chanlist,:) - sumdata(chanlist,:);
difmssq = mean(sum(data(chanlist,:).*data(chanlist,:)));
pvaf = round(100.0*(1.0-difmssq/sigmssq)); % percent variance accounted for
rtitl = ['(p.v.a.f. ' int2str(pvaf) '%)'];
%
% Make the plot
%
plotdata(projdata,length(data),limits,titl,channels,colors,rtitl);
% make the plot
|
github
|
lcnbeapp/beapp-master
|
numdim.m
|
.m
|
beapp-master/Packages/eeglab14_1_2b/functions/miscfunc/numdim.m
| 2,007 |
utf_8
|
220904d43bdb749aef158ee0bdef4040
|
% numdim() - estimate a lower bound on the (minimum) number of discrete sources
% in the data via their second-order statistics.
% Usage:
% >> num = numdim( data );
%
% Inputs:
% data - 2-D data (nchannel x npoints)
%
% Outputs:
% num - number of sources (estimated from second order measures)
%
% References:
% WACKERMANN, J. 1996. Beyond mapping: estimating complexity
% of multichannel EEG recordings. Acta Neurobiologiae
% Experimentalis, 56, 197-208.
% WACKERMANN, J. 1999. Towards a quantitative characterization
% of functional states of the brain: from non-linear methodology
% to the global linear description. International Journal of
% Psychophysiology, 34, 65-80.
%
% Author: Arnaud Delorme, CNL / Salk Institute, 23 January 2003
% Copyright (C) 2002 Arnaud Delorme, Salk Institute, [email protected]
%
% This program is free software; you can redistribute it and/or modify
% it under the terms of the GNU General Public License as published by
% the Free Software Foundation; either version 2 of the License, or
% (at your option) any later version.
%
% This program is distributed in the hope that it will be useful,
% but WITHOUT ANY WARRANTY; without even the implied warranty of
% MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
% GNU General Public License for more details.
%
% You should have received a copy of the GNU General Public License
% along with this program; if not, write to the Free Software
% Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
function lambda = numdim( a )
if nargin < 1
help numdim;
return;
end;
% Akaike, Identification toolbox (linear identification)
a = a';
b = a'*a/100; % correlation
[v d] = eig(b);
%det(d-b); % checking
l = diag(d);
l = l/sum(l);
lambda = real(exp(-sum(l.*log(l))));
return;
% testing by duplicating columns
a = rand(100,5)*2-1;
a = [a a];
numdim( a )
|
github
|
lcnbeapp/beapp-master
|
eeg_ms2f.m
|
.m
|
beapp-master/Packages/eeglab14_1_2b/functions/miscfunc/eeg_ms2f.m
| 623 |
utf_8
|
bf8ab362a73704ef273b03319ce179c0
|
% eeg_ms2f() - convert epoch latency in ms to nearest epoch frame number
%
% Usage:
% >> outf = eeg_ms2f(EEG,ms);
% Inputs:
% EEG - EEGLAB data set structure
% ms - epoch latency in milliseconds
% Output:
% outf - nearest epoch frame to the specified epoch latency
%
% Author: Scott Makeig, SCCN/INC, 12/05
function outf = eeg_ms2f(EEG,ms)
ms = ms/1000;
if ms < EEG.xmin | ms > EEG.xmax
error('time out of range');
end
outf = 1+round((EEG.pnts-1)*(ms-EEG.xmin)/(EEG.xmax-EEG.xmin));
% else
% [tmp outf] = min(abs(EEG.times-ms));
|
github
|
lcnbeapp/beapp-master
|
compsort.m
|
.m
|
beapp-master/Packages/eeglab14_1_2b/functions/miscfunc/compsort.m
| 8,288 |
utf_8
|
43da793b46f111b7671ea6db2e79e699
|
% compsort() - reorder ICA components, first largest to smallest by the size
% of their maximum variance in the single-component projections,
% then (if specified) the nlargest component projections are
% reordered by the (within-epoch) time point at which they reach
% their max variance.
%
% Usage:
% >> [windex,maxvar,maxframe,maxepoch,maxmap] ...
% = compsort(data,weights,sphere,datamean, ...
% frames,nlargest,chanlist);
% Inputs:
% data = (chans,frames*epochs) the input data set decomposed by runica()
% weights = ica weight matrix returned by runica()
% sphere = sphering matrix returned by runica()
%
% Optional:
% datamean = means removed from each row*epoch in runica()
% (Note: 0 -> input data means are distributed among components
% : 1 -> input data means are removed from the components (default))
% frames = frames per epoch in data (0 -> all)
% nlargest = number of largest ICA components to order by latency to max var
% (other returned in reverse order of variance) (0 -> none)
% chanlist = list of channel numbers to sort on (0 -> all)
%
% Outputs:
% windex = permuted order of rows in output weights (1-chans)
% maxvar = maximum variance of projected components (in perm. order)
% maxframe = frame of maximum variance (1-frames) (in perm. order)
% maxepoch = epoch number of frame of maxvar (1-nepochs) (in perm. order)
% maxmap = projected scalp map at max (in perm. order)
%
% Authors: Scott Makeig, SCCN/INC/UCSD, La Jolla, 1996
%
% See also: runica()
% Copyright (C) 1996 Scott Makeig, SCCN/INC/UCSD, [email protected]
%
% This program is free software; you can redistribute it and/or modify
% it under the terms of the GNU General Public License as published by
% the Free Software Foundation; either version 2 of the License, or
% (at your option) any later version.
%
% This program is distributed in the hope that it will be useful,
% but WITHOUT ANY WARRANTY; without even the implied warranty of
% MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
% GNU General Public License for more details.
%
% You should have received a copy of the GNU General Public License
% along with this program; if not, write to the Free Software
% Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
% 11-30-96 as compsort.m
% 12-19-96 moved def of epochs below default frames def -sm
% 02-18-97 added chanlist -sm
% 03-11-97 added default chanlist=0 -> all chans, fixed datamean and var() -sm
% 03-17-97 made nlargest default -> nlargest=0 -sm
% 04-03-97 fixed problems and removed permweights, permcomps outputs -sm
% 04-04-97 shortened name to compsort() -sm
% 06-05-97 corrected variance computation -sm
% 06-07-97 changed order of args to conform to runica -sm
% 06-10-97 fixed recent bug in maxvar order -sm
% 07-23-97 made datamean==0 distribute means among components -sm
% 08-04-97 added datamean=1 option -sm
% 01-25-02 reformated help & license, added links -ad
function [windex,maxvar,maxframe,maxepoch,maxmap] = compsort(data,weights,sphere,datamean,frames,nlargest,chanlist)
if nargin<3,
fprintf('compsort(): needs at least three arguments.\n\n');
help compsort
return
end
[chans,framestot] = size(data);
if framestot==0,
fprintf('Gcompsort(): cannot process an empty data array.\n');
return
end;
[srows,scols] = size(sphere);
[wrows,wcols] = size(weights);
if nargin<7,
chanlist = [1:chans];
end
if chanlist==0,
chanlist = [1:chans];
end
if length(chanlist)~=chans & wrows<chans, % if non-square weight matrix
fprintf('compsort(): chanlist not allowed with non-square weights.\n');
return
end
if size(chanlist,1)>1
chanlist = chanlist'; % make a row vector
end
if size(chanlist,1)>1
fprintf('compsort(): chanlist must be a vector.\n');
return
end
if nargin<6,
nlargest=0;
end;
if nargin<5,
frames = 0;
end;
if nargin<4,
datamean = 1;
end;
if frames ==0,
frames = framestot;
end
epochs = framestot/frames;
% activations = (wrows,wcols)x(srows,scols)x(chans,framestot)
if chans ~= scols | srows ~= wcols,
fprintf('compsort(): input data dimensions do not match.\n');
fprintf(...
' i.e., Either chans %d ~= sphere cols %d or sphere rows %d ~= weights cols %d\n',...
chans,scols,srows,wcols);
return
end
if wrows ~= chans & nlargest ~= 0 & nlargest ~= wrows,
fprintf(...
'compsort(): cannot project components back to order by size - nchans ~= ncomponents.\n');
return
end
if floor(framestot/frames)*frames ~= framestot
fprintf(...
'compsort(): input data frames does not divide data length.\n');
return
end
if nlargest > wrows,
fprintf(...
'compsort(): there are only %d rows in the weight matrix.\n',wrows);
return
end
if epochs ~= floor(epochs),
fprintf(...
'compsort(): input frames does not subdivide data length.\n');
return
end
%
%%%%%%%%%%%%%%%%%%%% Reorder weight matrix %%%%%%%%%%%%%%%%%%%%%
%
if datamean == 1,
data = data - mean(data')'*ones(1,framestot); % remove channel means
elseif datamean~=0, % remove given means
if size(datamean,2) ~= epochs | size(datamean,1) ~= chans,
fprintf('compsort(): datamean must be 0, 1, or (chans,epochs)\n');
return
end
for e=1:epochs
data(:,(e-1)*frames+1:e*frames) = data(:,(e-1)*frames+1:e*frames)...
- datamean(:,e)*ones(1,frames);
end
end % compute mean data matrix inherited from runica()
comps = weights*sphere*data; % Note: distributes means if datamean==0
maxvar = zeros(wrows,1); % size of the projections
maxframe = zeros(wrows,1); % frame of the abs(max) projection
maxepoch = zeros(wrows,1); % epoch of the abs(max) projection
maxmap = zeros(wrows,chans); % leave 0s unless weights is square
if chans==wrows,
icainv = inv(weights*sphere);
fprintf('Computing projected variance for all %d components:\n',wrows);
for s=1:wrows
fprintf('%d ',s); % construct single-component data matrix
% project to scalp
compproj = icainv(:,s)*comps(s,:);
compv = zeros(frames*epochs,1);
compv = (sum(compproj(chanlist,:).*compproj(chanlist,:)))' ...
/(length(chanlist)-1);
[m,mi] = max(compv); % find max variance
maxvar(s) = m;
maxframe(s)=rem(mi,frames); % count from beginning of each epoch!
maxepoch(s)=floor(mi/frames)+1;% record epoch number of max
if maxframe(s)==0, % if max var is in last frame . . .
maxframe(s) = frames;
maxepoch(s) = maxepoch(s)-1;
end
maxmap(:,s) = compproj(:,mi); % record scalp projection at max(var(proj))
end
else % weight matrix is non-square, sort components by latency only
fprintf('compsort() - non-square weights - finding max latencies.\n');
for s=1:wrows
compv = comps(s).*comps(s,:)'; % get variance analogues at each time point
[m,mi] = max(abs(compv)'); % find abs(max)'s
maxvar(s) = m;
maxframe(s)=rem(mi,frames); % count from beginning of each epoch!
maxepoch(s)=floor(mi/frames)+1;% record epoch number of max
if maxframe(s)==0, % if max var is in last frame . . .
maxframe(s) = frames;
maxepoch(s) = maxepoch(s)-1;
end
end
end
fprintf('\n');
[maxvar windex] = sort(maxvar');% sort components by relative size
windex = windex(wrows:-1:1)'; % reverse order
maxvar = maxvar(wrows:-1:1)'; % make each returned vector a column vector
% Note: maxvar reordered by sort() above
maxframe = maxframe(windex); % reorder maxframes
maxepoch = maxepoch(windex); % reorder maxepoch
maxmap = maxmap(:,windex); % reorder maxmap columns
if nlargest>0,
fprintf('Ordering largest %d components by frame of abs(max): ',nlargest);
[m mfi] = sort(maxframe(1:nlargest)); % sort by frame order
windex(1:nlargest) = windex(mfi);
maxframe(1:nlargest) = m;
maxvar(1:nlargest) = maxvar(mfi);
maxepoch(1:nlargest) = maxepoch(mfi);
maxmap(:,1:nlargest) = maxmap(:,mfi); % reorder largest maxmap columns
fprintf('\n');
end
|
github
|
lcnbeapp/beapp-master
|
compheads.m
|
.m
|
beapp-master/Packages/eeglab14_1_2b/functions/miscfunc/compheads.m
| 6,160 |
utf_8
|
96edaf4aa50c50ccb4f752823d03b1d4
|
% compheads() - plot multiple topoplot() maps of ICA component topographies
%
% Usage:
% >> compheads(winv,'spline_file',compnos,'title',rowscols,labels,view)
%
% Inputs:
% winv - Inverse weight matrix = EEG scalp maps. Each column is a
% map; the rows correspond to the electrode positions
% defined in the eloc_file. Normally, winv = inv(weights*sphere).
% spline_file - Name of the eloctrode position file in BESA spherical coords.
% compnos - Vector telling which (order of) component maps to show
% Indices <0 tell compheads() to invert a map; = 0 leave blank subplot
% Example [1 0 -2 3 0 -6] {default|0 -> 1:columns_in_winv}
% 'title' - Title string for each page {default|0 -> 'ICA Component Maps'}
% rowscols - Vector of the form [m,n] where m is total vertical tiles and n
% is horizontal tiles per page. If the number of maps exceeds m*n,
% multiple figures will be produced {def|0 -> one near-square page}.
% labels - Vector of numbers or a matrix of strings to use as labels for
% each map {default|0 -> 1:ncolumns_in_winv}
% view - topoplot() view, either [az el] or keyword ('top',...)
% See >> help topoplot() for options.
%
% Note: Map scaling is to +/-max(abs(data); green = 0
%
% Author: Scott Makeig, SCCN/INC/UCSD, La Jolla, 4-28-1998
%
% See also: topoplot()
% Copyright (C) 4-28-98 from compmap.m Scott Makeig, SCCN/INC/UCSD, [email protected]
%
% This program is free software; you can redistribute it and/or modify
% it under the terms of the GNU General Public License as published by
% the Free Software Foundation; either version 2 of the License, or
% (at your option) any later version.
%
% This program is distributed in the hope that it will be useful,
% but WITHOUT ANY WARRANTY; without even the implied warranty of
% MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
% GNU General Public License for more details.
%
% You should have received a copy of the GNU General Public License
% along with this program; if not, write to the Free Software
% Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
% 01-25-02 reformated help & license, added links -ad
function compheads(Winv,eloc_file,compnos,titleval,pagesize,srclabels,view)
if nargin<1
help compheads
return
end
[chans, frames] = size (Winv);
DEFAULT_TITLE = 'ICA Component Maps';
DEFAULT_EFILE = 'chan_file';
NUMCONTOUR = 5; % topoplot() style settings
OUTPUT = 'screen'; % default: 'screen' for screen colors,
% 'printer' for printer colors
STYLE = 'both';
INTERPLIMITS = 'head';
MAPLIMITS = 'absmax';
SQUARE = 1; % 1/0 flag making topoplot() asex square -> round heads
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
% check inputs and set defaults
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
printlabel = OUTPUT; % default set above
if nargin < 7
view = [-127 30];
end
if nargin < 6
srclabels = 0;
end
if nargin < 5
pagesize = 0;
end
if nargin < 4
titleval = 0;
end
if nargin < 3
compnos = 0;
end
if nargin < 2
eloc_file = 0;
end
if srclabels == 0
srclabels = [];
end
if titleval == 0;
titleval = DEFAULT_TITLE;
end
if compnos == 0
compnos = (1:frames);
end
if pagesize == 0
numsources = length(compnos);
DEFAULT_PAGE_SIZE = ...
[floor(sqrt(numsources)) ceil(numsources/floor(sqrt(numsources)))];
m = DEFAULT_PAGE_SIZE(1);
n = DEFAULT_PAGE_SIZE(2);
elseif length(pagesize) ==1
help compheads
return
else
m = pagesize(1);
n = pagesize(2);
end
if eloc_file == 0
eloc_file = DEFAULT_EFILE;
end
totalsources = length(compnos);
if ~isempty(srclabels)
if ~ischar(srclabels(1,1)) % if numbers
if size(srclabels,1) == 1
srclabels = srclabels';
end
end
if size(srclabels,1) ~= totalsources,
fprintf('compheads(): numbers of components and component labels do not agree.\n');
return
end
end
pages = ceil(totalsources/(m*n));
if pages > 1
fprintf('compheads(): will create %d figures of %d by %d maps: ',...
pages,m,n);
end
pos = get(gcf,'Position');
off = [ 25 -25 0 0]; % position offsets for multiple figures
fid = fopen(eloc_file);
if fid<1,
fprintf('compheads()^G: cannot open eloc_file (%s).\n',eloc_file);
return
end
fclose(fid);
%%%%%%%%%%%%%%%%%%%%%%%%%%%%% plot the maps %%%%%%%%%%%%%%%%%%%%%%%
for i = (1:pages)
if i > 1
figure('Position',pos+(i-1)*off); % place figures in right-downward stack
end
set(gcf,'Color','w') %CJH - set background color to white
if (totalsources > i*m*n)
sbreak = n*m;
else
sbreak = totalsources - (i-1)*m*n;
end
for j = (1:sbreak) % maps on this page
comp = j+(i-1)*m*n; % compno index
if compnos(comp)~=0
if compnos(comp)>0
source_var = Winv(:,compnos(comp))'; % plot map
elseif compnos(comp)<0
source_var = -1*Winv(:,-1*compnos(comp))'; % invert map
end
subplot(m,n,j)
headplot(source_var,eloc_file,'electrodes','off','view',view);
%topoplot(source_var,eloc_file,'style',STYLE,...
% 'numcontour',NUMCONTOUR,'interplimits',INTERPLIMITS,...
% 'maplimits',MAPLIMITS); % draw map
if SQUARE,
axis('square');
end
if isempty(srclabels)
t=title(int2str(compnos(comp)));
set(t,'FontSize',16);
else
if ischar(srclabels)
t=title(srclabels(comp,:));
set(t,'FontSize',16);
else
t=title(num2str(srclabels(comp)));
set(t,'FontSize',16);
end
end
drawnow % draw one map at a time
end
end
ax = axes('Units','Normal','Position',[.5 .04 .32 .05],'Visible','Off');
colorbar(ax)
axval = axis;
Xlim = get(ax,'Xlim');
set(ax,'XTick',(Xlim(2)+Xlim(1))/2)
set(gca,'XTickLabel','0')
set(gca,'XTickMode','manual')
axbig = axes('Units','Normalized','Position',[0 0 1 1],'Visible','off');
t1 = text(.25,.070,titleval,'HorizontalAlignment','center','FontSize',14);
if pages > 1
fprintf('%d ',i);
end
end
if pages > 1
fprintf('\n');
end
|
github
|
lcnbeapp/beapp-master
|
logspec.m
|
.m
|
beapp-master/Packages/eeglab14_1_2b/functions/miscfunc/logspec.m
| 4,318 |
utf_8
|
233385ae8dbccb9910ad8e624d8d7244
|
% logspec() - plot mean log power spectra of submitted data on loglog scale
% using plotdata() or plottopo() formats
%
% Usage:
% >> [spectra,freqs] = logspec(data,frames,srate);
% >> [spectra,freqs] = logspec(data,frames,srate,'title',...
% [loHz-hiHz],'chan_locs',rm_mean);
% Inputs:
% data = input data (chans,frames*epochs)
% frames = data samples per epoch {default length(data)}
% srate = data sampling rate in Hz {default 256 Hz};
% 'title' = plot title {default: none}
% [loHz-hiHz] = [loHz hiHz] plotting limits
% {default: [srate/fftlength srate/2]}
% 'chan_locs' = channel location file (ala topoplot())
% Else [rows cols] to plot data in a grid array
% rm_mean = [0/1] 1 -> remove log mean spectrum from all
%
% Author: Scott Makeig, SCCN/INC/UCSD, La Jolla, 11-07-97
%
% See also: plotdata(), plottopo()
% Copyright (C) 11-07-97 Scott Makeig, SCCN/INC/UCSD, [email protected]
%
% This program is free software; you can redistribute it and/or modify
% it under the terms of the GNU General Public License as published by
% the Free Software Foundation; either version 2 of the License, or
% (at your option) any later version.
%
% This program is distributed in the hope that it will be useful,
% but WITHOUT ANY WARRANTY; without even the implied warranty of
% MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
% GNU General Public License for more details.
%
% You should have received a copy of the GNU General Public License
% along with this program; if not, write to the Free Software
% Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
% Changed plotdata() below to plottopo() 11/12/99 -sm
% Mentioned new grid array option 12/22/99 -sm
% 01-25-02 reformated help & license, added links -ad
function [spectra,freqs] = logspec(data,frames,srate,titl,Hzlimits,chanlocs,rmmean)
if nargin < 1
help logspec
return
end
[rows,cols] = size(data);
icadefs % read plotdata chan limit
if rows > MAXPLOTDATACHANS
fprintf('logspec(): max plotdata() channels is %d.\n',MAXPLOTDATACHANS);
return
end
if rows < 2
fprintf('logspec(): min plotdata() channels is %d.\n',2);
return
end
if nargin<7
rmmean = 0; % default
end
if nargin < 5
Hzlimits = 0;
end
if nargin < 4
titl = ' ';
end
if nargin < 3
srate = 256;
end
if nargin < 2,
frames = cols;
end
epochs = fix(cols/frames);
if epochs*frames ~= cols
fprintf('logspec() - frames does not divide data length.\n');
return
end
fftlength = 2^floor(log(frames)/log(2));
spectra = zeros(rows,epochs*fftlength/2);
f2 = fftlength/2;
dB = 10/log(10);
if length(Hzlimits) < 2
Hzlimits = [srate/fftlength srate/2];
end
if Hzlimits(2) <= Hzlimits(1)
help logspec
return
end
for e=1:epochs
for r=1:rows,
[Pxx,freqs] = psd(data(r,(e-1)*frames+1:e*frames),fftlength,srate,...
fftlength,fftlength/4);
spectra(r,(e-1)*f2+1:e*f2) = Pxx(2:f2+1)'; % omit DC bin
end
end
clf
freqs = freqs(2:f2+1);
fsi = find(freqs >= Hzlimits(1) & freqs <= Hzlimits(2));
minf = freqs(fsi(1));
maxf = freqs(fsi(length(fsi)));
nfs = length(fsi);
showspec = zeros(rows,length(fsi)*epochs);
for e = 1:epochs
showspec(:,(e-1)*nfs+1:e*nfs) = dB*log(spectra(:,(e-1)*f2+fsi));
end
% minspec = min(min(showspec));
% showspec = showspec-minspec; % make minimum 0 dB
showspec = blockave(showspec,nfs);
% meanspec = mean(showspec);
% showspec = showspec - ones(rows,1)*meanspec;
% >> plotdata(data,frames,limits,title,channames,colors,rtitle)
% diff = 0;
% MINUEND = 6;
% for r=1:rows
% diff = diff - MINUEND;
% showspec(r,:) = showspec(r<:)-diff;
% end
% semilogx(freqs(fsi),showspec');
% ax = axis;
% axis([minf maxf ax(3) ax(4)]);
% title(titl);
if nargin<6
% >> plotdata(data,frames,limits,title,channames,colors,rtitle,ydir)
if rmmean
showspec = showspec - ones(rows,1)*mean(showspec);
end
plotdata(showspec,nfs,[minf maxf 0 0],titl);
else
% >> plottopo(data,'chan_locs',frames,limits,title,channels,axsize,colors,ydir)
if rmmean
showspec = showspec - ones(rows,1)*mean(showspec);
end
plottopo(showspec,chanlocs,nfs,[minf maxf 0 0],titl);
end
ax = get(gcf,'children');
for a = ax
set(a,'XScale','log')
end
|
github
|
lcnbeapp/beapp-master
|
tftopo.m
|
.m
|
beapp-master/Packages/eeglab14_1_2b/functions/miscfunc/tftopo.m
| 25,662 |
utf_8
|
927788fa42a8c1c1676c74297725af98
|
% tftopo() - Generate a figure showing a selected or representative image (e.g.,
% an ERSP, ITC or ERP-image) from a supplied set of images, one for each
% scalp channel. Then, plot topoplot() scalp maps of value distributions
% at specified (time, frequency) image points. Else, image the signed
% (selected) between-channel std(). Inputs may be outputs of
% timef(), crossf(), or erpimage().
% Usage:
% >> tftopo(tfdata,times,freqs, 'key1', 'val1', 'key2', val2' ...)
% Inputs:
% tfdata = Set of time/freq images, one for each channel. Matrix dims:
% (time,freq),(time,freq,chans). Else, (time,freq,chans,subjects) for grand mean
% RMS plotting.
% times = Vector of image (x-value) times in msec, from timef()).
% freqs = Vector of image (y-value) frequencies in Hz, from timef()).
%
% Optional inputs:
% 'timefreqs' = Array of time/frequency points at which to plot topoplot() maps.
% Size: (nrows,2), each row given the [ms Hz] location
% of one point. Or size (nrows,4), each row given [min_ms
% max_ms min_hz max_hz].
% 'showchan' = [integer] Channel number of the tfdata to image. Else 0 to image
% the (median-signed) RMS values across channels. {default: 0}
% 'chanlocs' = ['string'|structure] Electrode locations file (for format, see
% >> topoplot example) or EEG.chanlocs structure {default: none}
% 'limits' = Vector of plotting limits [minms maxms minhz maxhz mincaxis maxcaxis]
% May omit final vales, or use NaN's to use the input data limits.
% Ex: [nan nan -100 400];
% 'signifs' = (times,freqs) Matrix of significance level(s) (e.g., from timef())
% to zero out non-signif. tfdata points. Matrix size must be
% ([1|2], freqs, chans, subjects)
% if using the same threshold for all time points at each frequency, or
% ([1|2], freqs, times, chans, subjects).
% If first dimension is of size 1, data are assumed to contain
% positive values only {default: none}
% 'sigthresh' = [K L] After masking time-frequency decomposition using the 'signifs'
% array (above), concatenate (time,freq) values for which no more than
% K electrodes have non-0 (significant) values. If several subjects,
% the second value L is used to concatenate subjects in the same way.
% {default: [1 1]}
% 'selchans' = Channels to include in the topoplot() scalp maps (and image values)
% {default: all}
% 'smooth' = [pow2] magnification and smoothing factor. power of 2 (default: 1}.
% 'mode' = ['rms'|'ave'] ('rms') return root-mean-square, else ('ave') average
% power {default: 'rms' }
% 'logfreq' = ['on'|'off'|'native'] plot log frequencies {default: 'off'}
% 'native' means that the input is already in log frequencies
% 'vert' = [times vector] (in msec) plot vertical dashed lines at specified times
% {default: 0}
% 'ylabel' = [string] label for the ordinate axis. Default is
% "Frequency (Hz)"
% 'shiftimgs' = [response_times_vector] shift time/frequency images from several
% subjects by each subject's response time {default: no shift}
% 'title' = [quoted_string] plot title (default: provided_string).
% 'cbar' = ['on'|'off'] plot color bar {default: 'on'}
% 'cmode' = ['common'|'separate'] 'common' or 'separate' color axis for each
% topoplot {default: 'common'}
% 'plotscalponly' = [x,y] location (e.g. msec,hz). Plot one scalp map only; no
% time-frequency image.
% 'events' = [real array] plot event latencies. The number of event
% must be the same as the number of "frequecies".
% 'verbose' = ['on'|'off'] comment on operations on command line {default: 'on'}.
% 'axcopy' = ['on'|'off'] creates a copy of the figure axis and its graphic objects in a new pop-up window
% using the left mouse button {default: 'on'}..
% 'denseLogTicks' = ['on'|'off'] creates denser labels on log freuqncy axis {default: 'off'}
%
% Notes:
% 1) Additional topoplot() optional arguments can be used.
% 2) In the topoplot maps, average power (not masked by significance) is used
% instead of the (signed and masked) root-mean-square (RMS) values used in the image.
% 3) If tfdata from several subjects is used (via a 4-D tfdata input), RMS power is first
% computed across electrodes, then across the subjects.
%
% Authors: Scott Makeig, Arnaud Delorme & Marissa Westerfield, SCCN/INC/UCSD, La Jolla, 3/01
%
% See also: timef(), topoplot(), spectopo(), timtopo(), envtopo(), changeunits()
% hidden parameter: 'shiftimgs' = array with one value per subject for shifting in time the
% time/freq images. Had to be inserted in tftopo because
% the shift happen after the smoothing
% Copyright (C) Scott Makeig, Arnaud Delorme & Marissa Westerfield, SCCN/INC/UCSD,
% La Jolla, 3/01
%
% This program is free software; you can redistribute it and/or modify
% it under the terms of the GNU General Public License as published by
% the Free Software Foundation; either version 2 of the License, or
% (at your option) any later version.
%
% This program is distributed in the hope that it will be useful,
% but WITHOUT ANY WARRANTY; without even the implied warranty of
% MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
% GNU General Public License for more details.
%
% You should have received a copy of the GNU General Public License
% along with this program; if not, write to the Free Software
% Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
% 01-25-02 reformated help & license -ad
function tfave = tftopo(tfdata,times,freqs,varargin);
%timefreqs,showchan,chanlocs,limits,signifs,selchans)
LINECOLOR= 'k';
LINEWIDTH = 2;
ZEROLINEWIDTH = 2.8;
if nargin<3
help tftopo
return
end
icadefs_flag = 1;
try
icadefs;
catch
warning('icadefs.m can not be located in the path');
icadefs_flag = 0 ;
end
if ~icadefs_flag
AXES_FONTSIZE = 10;
PLOT_LINEWIDTH = 2;
end
% reshape tfdata
% --------------
if length(size(tfdata))==2
if size(tfdata,1) ~= length(freqs), tfdata = tfdata'; end;
nchans = round(size(tfdata,2)/length(times));
tfdata = reshape(tfdata, size(tfdata,1), length(times), nchans);
elseif length(size(tfdata))>=3
nchans = size(tfdata,3);
else
help tftopo
return
end
% for topoplot
if length(size(tfdata)) >= 4
tfdataori = mean(tfdata,4);
else
tfdataori = tfdata;
end
% test inputs
% -----------
% 'key' 'val' sequence
fieldlist = { 'chanlocs' { 'string','struct' } [] '' ;
'limits' 'real' [] [nan nan nan nan nan nan];
'logfreq' 'string' {'on','off','native'} 'off';
'cbar' 'string' {'on','off' } 'on';
'mode' 'string' { 'ave','rms' } 'rms';
'title' 'string' [] '';
'verbose' 'string' {'on','off' } 'on';
'axcopy' 'string' {'on','off' } 'on';
'cmode' 'string' {'common','separate' } 'common';
'selchans' 'integer' [1 nchans] [1:nchans];
'shiftimgs' 'real' [] [];
'plotscalponly' 'real' [] [];
'events' 'real' [] [];
'showchan' 'integer' [0 nchans] 0 ;
'signifs' 'real' [] [];
'sigthresh' 'integer' [1 Inf] [1 1];
'smooth' 'real' [0 Inf] 1;
'timefreqs' 'real' [] [];
'ylabel' 'string' {} 'Frequency (Hz)';
'vert' 'real' [times(1) times(end)] [min(max(0, times(1)), times(end))];
'denseLogTicks' 'string' {'on','off'} 'off'
};
[g varargin] = finputcheck( varargin, fieldlist, 'tftopo', 'ignore');
if isstr(g), error(g); end;
% setting more defaults
% ---------------------
if length(times) ~= size(tfdata,2)
fprintf('tftopo(): tfdata columns must be a multiple of the length of times (%d)\n',...
length(times));
return
end
if length(g.showchan) > 1
error('tftopo(): showchan must be a single number');
end;
if length(g.limits)<1 | isnan(g.limits(1))
g.limits(1) = times(1);
end
if length(g.limits)<2 | isnan(g.limits(2))
g.limits(2) = times(end);
end
if length(g.limits)<3 | isnan(g.limits(3))
g.limits(3) = freqs(1);
end
if length(g.limits)<4 | isnan(g.limits(4))
g.limits(4) = freqs(end);
end
if length(g.limits)<5 | isnan(g.limits(5)) % default caxis plotting limits
g.limits(5) = -max(abs(tfdata(:)));
mincax = g.limits(5);
end
if length(g.limits)<6 | isnan(g.limits(6))
defaultlim = 1;
if exist('mincax')
g.limits(6) = -mincax; % avoid recalculation
else
g.limits(6) = max(abs(tfdata(:)));
end
else
defaultlim = 0;
end
if length(g.sigthresh) == 1
g.sigthresh(2) = 1;
end;
if g.sigthresh(1) > nchans
error('tftopo(): ''sigthresh'' first number must be less than or equal to the number of channels');
end;
if g.sigthresh(2) > size(tfdata,4)
error('tftopo(): ''sigthresh'' second number must be less than or equal to the number of subjects');
end;
if ~isempty(g.signifs)
if size(g.signifs,1) > 2 | size(g.signifs,2) ~= size(tfdata,1)| ...
(size(g.signifs,3) ~= size(tfdata,3) & size(g.signifs,4) ~= size(tfdata,3))
fprintf('tftopo(): error in ''signifs'' array size not compatible with data size, trying to transpose.\n');
g.signifs = permute(g.signifs, [2 1 3 4]);
if size(g.signifs,1) > 2 | size(g.signifs,2) ~= size(tfdata,1)| ...
(size(g.signifs,3) ~= size(tfdata,3) & size(g.signifs,4) ~= size(tfdata,3))
fprintf('tftopo(): ''signifs'' still the wrong size.\n');
return
end;
end
end;
if length(g.selchans) ~= nchans,
selchans_opt = { 'plotchans' g.selchans };
else selchans_opt = { };
end;
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
% process time/freq data points
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
if ~isempty(g.timefreqs)
if size(g.timefreqs,2) == 2
g.timefreqs(:,3) = g.timefreqs(:,2);
g.timefreqs(:,4) = g.timefreqs(:,2);
g.timefreqs(:,2) = g.timefreqs(:,1);
end;
if isempty(g.chanlocs)
error('tftopo(): ''chanlocs'' must be defined to plot time/freq points');
end;
if min(min(g.timefreqs(:,[3 4])))<min(freqs)
fprintf('tftopo(): selected plotting frequency %g out of range.\n',min(min(g.timefreqs(:,[3 4]))));
return
end
if max(max(g.timefreqs(:,[3 4])))>max(freqs)
fprintf('tftopo(): selected plotting frequency %g out of range.\n',max(max(g.timefreqs(:,[3 4]))));
return
end
if min(min(g.timefreqs(:,[1 2])))<min(times)
fprintf('tftopo(): selected plotting time %g out of range.\n',min(min(g.timefreqs(:,[1 2]))));
return
end
if max(max(g.timefreqs(:,[1 2])))>max(times)
fprintf('tftopo(): selected plotting time %g out of range.\n',max(max(g.timefreqs(:,[1 2]))));
return
end
if 0 % USE USER-SUPPLIED SCALP MAP ORDER. A GOOD ALGORITHM FOR SELECTING
% g.timefreqs POINT ORDER GIVING MAX UNCROSSED LINES IS DIFFICULT!
[tmp tfi] = sort(g.timefreqs(:,1)); % sort on times
tmp = g.timefreqs;
for t=1:size(g.timefreqs,1)
g.timefreqs(t,:) = tmp(tfi(t),:);
end
end
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
% Compute timefreqs point indices
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
tfpoints = size(g.timefreqs,1);
for f=1:tfpoints
[tmp fi1] = min(abs(freqs-g.timefreqs(f,3)));
[tmp fi2] = min(abs(freqs-g.timefreqs(f,4)));
freqidx{f}=[fi1:fi2];
end
for f=1:tfpoints
[tmp fi1] = min(abs(times-g.timefreqs(f,1)));
[tmp fi2] = min(abs(times-g.timefreqs(f,2)));
timeidx{f}=[fi1:fi2];
end
else
tfpoints = 0;
end;
% only plot one scalp map
% -----------------------
if ~isempty(g.plotscalponly)
[tmp fi] = min(abs(freqs-g.plotscalponly(2)));
[tmp ti] = min(abs(times-g.plotscalponly(1)));
scalpmap = squeeze(tfdataori(fi, ti, :));
if ~isempty(varargin)
topoplot(scalpmap,g.chanlocs,'electrodes','on', selchans_opt{:}, varargin{:});
else
topoplot(scalpmap,g.chanlocs,'electrodes','on', selchans_opt{:});
end;
% 'interlimits','electrodes')
axis square;
hold on
tl=title([int2str(g.plotscalponly(2)),' ms, ',int2str(g.plotscalponly(1)),' Hz']);
set(tl,'fontsize',AXES_FONTSIZE+3); % 13
return;
end;
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
% Zero out non-significant image features
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
range = g.limits(6)-g.limits(5);
cc = jet(256);
if ~isempty(g.signifs)
if strcmpi(g.verbose, 'on')
fprintf('Applying ''signifs'' mask by zeroing non-significant values\n');
end
for subject = 1:size(tfdata,4)
for elec = 1:size(tfdata,3)
if size(g.signifs,1) == 2
if ndims(g.signifs) > ndims(tfdata)
tmpfilt = (tfdata(:,:,elec,subject) >= squeeze(g.signifs(2,:,:,elec, subject))') | ...
(tfdata(:,:,elec,subject) <= squeeze(g.signifs(1,:,:,elec, subject))');
else
tmpfilt = (tfdata(:,:,elec,subject) >= repmat(g.signifs(2,:,elec, subject)', [1 size(tfdata,2)])) | ...
(tfdata(:,:,elec,subject) <= repmat(g.signifs(1,:,elec, subject)', [1 size(tfdata,2)]));
end;
else
if ndims(g.signifs) > ndims(tfdata)
tmpfilt = (tfdata(:,:,elec,subject) >= squeeze(g.signifs(1,:,:,elec, subject))');
else
tmpfilt = (tfdata(:,:,elec,subject) >= repmat(g.signifs(1,:,elec, subject)', [1 size(tfdata,2)]));
end;
end;
tfdata(:,:,elec,subject) = tfdata(:,:,elec,subject) .* tmpfilt;
end;
end;
end;
%%%%%%%%%%%%%%%%
% magnify inputs
%%%%%%%%%%%%%%%%
if g.smooth ~= 1
if strcmpi(g.verbose, 'on'),
fprintf('Smoothing...\n');
end
for index = 1:round(log2(g.smooth))
[tfdata times freqs] = magnifytwice(tfdata, times, freqs);
end;
end;
%%%%%%%%%%%%%%%%%%%%%%%%
% Shift time/freq images
%%%%%%%%%%%%%%%%%%%%%%%%
if ~isempty(g.shiftimgs)
timestep = times(2) - times(1);
for S = 1:size(tfdata,4)
nbsteps = round(g.shiftimgs(S)/timestep);
if strcmpi(g.verbose, 'on'),
fprintf('Shifing images of subect %d by %3.3f ms or %d time steps\n', S, g.shiftimgs(S), nbsteps);
end
if nbsteps < 0, tfdata(:,-nbsteps+1:end,:,S) = tfdata(:,1:end+nbsteps,:,S);
else tfdata(:,1:end-nbsteps,:,S) = tfdata(:,nbsteps+1:end,:,S);
end;
end;
end;
%%%%%%%%%%%%%%%%%%%%%%%%%
% Adjust plotting limits
%%%%%%%%%%%%%%%%%%%%%%%%%
[tmp minfreqidx] = min(abs(g.limits(3)-freqs)); % adjust min frequency
g.limits(3) = freqs(minfreqidx);
[tmp maxfreqidx] = min(abs(g.limits(4)-freqs)); % adjust max frequency
g.limits(4) = freqs(maxfreqidx);
[tmp mintimeidx] = min(abs(g.limits(1)-times)); % adjust min time
g.limits(1) = times(mintimeidx);
[tmp maxtimeidx] = min(abs(g.limits(2)-times)); % adjust max time
g.limits(2) = times(maxtimeidx);
mmidx = [mintimeidx maxtimeidx minfreqidx maxfreqidx];
%colormap('jet');
%c = colormap;
%cc = zeros(256,3);
%if size(c,1)==64
% for i=1:3
% cc(:,i) = interp(c(:,i),4);
% end
%else
% cc=c;
%nd
%cc(find(cc<0))=0;
%cc(find(cc>1))=1;
%if exist('g.signif')
% minnull = round(256*(g.signif(1)-g.limits(5))/range);
% if minnull<1
% minnull = 1;
% end
% maxnull = round(256*(g.signif(2)-g.limits(5))/range);
% if maxnull>256
% maxnull = 256;
% end
% nullrange = minnull:maxnull;
% cc(nullrange,:) = repmat(cc(128,:),length(nullrange),1);
%end
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
% Plot tfdata image for specified channel or selchans std()
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
axis off;
colormap(cc);
curax = gca; % current plot axes to plot into
if tfpoints ~= 0
plotdim = max(1+floor(tfpoints/2),4); % number of topoplots on top of image
imgax = sbplot(plotdim,plotdim,[plotdim*(plotdim-1)+1,2*plotdim-1],'ax',curax);
else
imgax = curax;
end;
tftimes = mmidx(1):mmidx(2);
tffreqs = mmidx(3):mmidx(4);
if g.showchan>0 % -> image showchan data
tfave = tfdata(tffreqs, tftimes,g.showchan);
else % g.showchan==0 -> image std() of selchans
tfdat = tfdata(tffreqs,tftimes,g.selchans,:);
% average across electrodes
if strcmpi(g.verbose, 'on'),
fprintf('Applying RMS across channels (mask for at least %d non-zeros values at each time/freq)\n', g.sigthresh(1));
end
tfdat = avedata(tfdat, 3, g.sigthresh(1), g.mode);
% if several subject, first (RMS) averaging across subjects
if size(tfdata,4) > 1
if strcmpi(g.verbose, 'on'),
fprintf('Applying RMS across subjects (mask for at least %d non-zeros values at each time/freq)\n', g.sigthresh(2));
end
tfdat = avedata(tfdat, 4, g.sigthresh(2), g.mode);
end;
tfave = tfdat;
if defaultlim
g.limits(6) = max(max(abs(tfave)));
g.limits(5) = -g.limits(6); % make symmetrical
end;
end
if ~isreal(tfave(1)), tfave = abs(tfave); end;
if strcmpi(g.logfreq, 'on'),
logimagesc(times(tftimes),freqs(tffreqs),tfave);
axis([g.limits(1) g.limits(2) log(g.limits(3)), log(g.limits(4))]);
elseif strcmpi(g.logfreq, 'native'),
imagesc(times(tftimes),log(freqs(tffreqs)),tfave);
axis([g.limits(1:2) log(g.limits(3:4))]);
if g.denseLogTicks
minTick = min(ylim);
maxTick = max(ylim);
set(gca,'ytick',linspace(minTick, maxTick,50));
end;
tmpval = get(gca,'yticklabel');
if iscell(tmpval)
% MATLAB version >= 8.04
try
ft = str2num(cell2mat(tmpval));
catch
% To avoid bug in matlab cell2mat. i.e. when tmpval = {'0';'0.5'}
for i = 1:length(tmpval)
ft(i,1) = str2num(cell2mat(tmpval(i)));
end
end
else
% MATLAB version < 8.04
ft = str2num(tmpval);
end
ft = exp(1).^ft;
ft = unique_bc(round(ft));
ftick = get(gca,'ytick');
ftick = exp(1).^ftick;
ftick = unique_bc(round(ftick));
ftick = log(ftick);
inds = unique_bc(round(exp(linspace(log(1), log(length(ft))))));
set(gca,'ytick',ftick(inds(1:2:end)));
set(gca,'yticklabel', num2str(ft(inds(1:2:end))));
else
imagesc(times(tftimes),freqs(tffreqs),tfave);
axis([g.limits(1:4)]);
end;
caxis([g.limits(5:6)]);
hold on;
%%%%%%%%%%%%%%%%%%%%%%%%%%
% Title and vertical lines
%%%%%%%%%%%%%%%%%%%%%%%%%%
axes(imgax)
xl=xlabel('Time (ms)');
set(xl,'fontsize',AXES_FONTSIZE+2);%12
set(gca,'yaxislocation','left')
if g.showchan>0
% tl=title(['Channel ',int2str(g.showchan)]);
% set(tl,'fontsize',14);
else
if isempty(g.title)
if strcmpi(g.mode, 'rms')
tl=title(['Signed channel rms']);
else
tl=title(['Signed channel average']);
end;
else
tl = title(g.title);
end
set(tl,'fontsize',AXES_FONTSIZE + 2); %12
set(tl,'fontweigh','normal');
end
yl=ylabel(g.ylabel);
set(yl,'fontsize',AXES_FONTSIZE + 2); %12
set(gca,'fontsize',AXES_FONTSIZE + 2); %12
set(gca,'ydir','normal');
for indtime = g.vert
tmpy = ylim;
htmp = plot([indtime indtime],tmpy,[LINECOLOR ':']);
set(htmp,'linewidth',PLOT_LINEWIDTH)
end
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
% Plot topoplot maps at specified timefreqs points
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
if ~isempty(g.events)
tmpy = ylim;
yvals = linspace(tmpy(1), tmpy(2), length(g.events));
plot(g.events, yvals, 'k', 'linewidth', 2);
end;
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
% Plot topoplot maps at specified timefreqs points
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
if ~isempty(g.timefreqs)
wholeax = sbplot(1,1,1,'ax',curax);
topoaxes = zeros(1,tfpoints);
for n=1:tfpoints
if n<=plotdim
topoaxes(n)=sbplot(plotdim,plotdim,n,'ax',curax);
else
topoaxes(n)=sbplot(plotdim,plotdim,plotdim*(n+1-plotdim),'ax',curax);
end
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
% Plot connecting lines using changeunits()
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
tmptimefreq = [ mean(g.timefreqs(n,[1 2])) mean(g.timefreqs(n,[3 4])) ];
if strcmpi(g.logfreq, 'off')
from = changeunits(tmptimefreq,imgax,wholeax);
else
from = changeunits([tmptimefreq(1) log(tmptimefreq(2))],imgax,wholeax);
end;
to = changeunits([0.5,0.5],topoaxes(n),wholeax);
axes(wholeax);
plot([from(1) to(1)],[from(2) to(2)],LINECOLOR,'linewidth',LINEWIDTH);
hold on
mk=plot(from(1),from(2),[LINECOLOR 'o'],'markersize',9);
set(mk,'markerfacecolor',LINECOLOR);
axis([0 1 0 1]);
axis off;
end
endcaxis = 0;
for n=1:tfpoints
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
% Plot scalp map using topoplot()
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
axes(topoaxes(n));
scalpmap = squeeze(mean(mean(tfdataori(freqidx{n},timeidx{n},:),1),2));
%topoplot(scalpmap,g.chanlocs,'maplimits',[g.limits(5) g.limits(6)],...
% 'electrodes','on');
if ~isempty(varargin)
topoplot(scalpmap,g.chanlocs,'electrodes','on', selchans_opt{:}, varargin{:});
else
topoplot(scalpmap,g.chanlocs,'electrodes','on', selchans_opt{:});
end;
% 'interlimits','electrodes')
axis square;
hold on
if g.timefreqs(n,1) == g.timefreqs(n,2)
tl=title([int2str(g.timefreqs(n,1)),' ms, ',int2str(g.timefreqs(n,3)),' Hz']);
else
tl=title([int2str(g.timefreqs(n,1)) '-' int2str(g.timefreqs(n,2)) 'ms, ' ...
int2str(g.timefreqs(n,3)) '-' int2str(g.timefreqs(n,4)) ' Hz']);
end;
set(tl,'fontsize',AXES_FONTSIZE + 3); %13
endcaxis = max(endcaxis,max(abs(caxis)));
%caxis([g.limits(5:6)]);
end;
if strcmpi(g.cmode, 'common')
for n=1:tfpoints
axes(topoaxes(n));
caxis([-endcaxis endcaxis]);
if n==tfpoints & strcmpi(g.cbar, 'on') % & (mod(tfpoints,2)~=0) % image color bar by last map
cb=cbar;
pos = get(cb,'position');
set(cb,'position',[pos(1:2) 0.023 pos(4)]);
end
drawnow
end
end;
end;
if g.showchan>0 & ~isempty(g.chanlocs)
sbplot(4,4,1,'ax',imgax);
topoplot(g.showchan,g.chanlocs,'electrodes','off', ...
'style', 'blank', 'emarkersize1chan', 10 );
axis('square');
end
if strcmpi(g.axcopy, 'on')
if strcmpi(g.logfreq, 'native'),
com = [ 'ft = str2num(get(gca,''''yticklabel''''));' ...
'ft = exp(1).^ft;' ...
'ft = unique_bc(round(ft));' ...
'ftick = get(gca,''''ytick'''');' ...
'ftick = exp(1).^ftick;' ...
'ftick = unique_bc(round(ftick));' ...
'ftick = log(ftick);' ...
'set(gca,''''ytick'''',ftick);' ...
'set(gca,''''yticklabel'''', num2str(ft));' ];
axcopy(gcf, com); % turn on axis copying on mouse click
else
axcopy; % turn on axis copying on mouse click
end;
end
%%%%%%%%%%%%%%%%%%%%%%%% embedded functions %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
function tfdat = avedata(tfdat, dim, thresh, mode)
tfsign = sign(mean(tfdat,dim));
tfmask = sum(tfdat ~= 0,dim) >= thresh;
if strcmpi(mode, 'rms')
tfdat = tfmask.*tfsign.*sqrt(mean(tfdat.*tfdat,dim)); % std of all channels
else
tfdat = tfmask.*mean(tfdat,dim); % std of all channels
end;
function [tfdatnew, times, freqs] = magnifytwice(tfdat, times, freqs);
indicetimes = [floor(1:0.5:size(tfdat,1)) size(tfdat,1)];
indicefreqs = [floor(1:0.5:size(tfdat,2)) size(tfdat,2)];
tfdatnew = tfdat(indicetimes, indicefreqs, :, :);
times = linspace(times(1), times(end), size(tfdat,2)*2);
freqs = linspace(freqs(1), freqs(end), size(tfdat,1)*2);
% smoothing
gauss2 = gauss2d(3,3);
for S = 1:size(tfdat,4)
for elec = 1:size(tfdat,3)
tfdatnew(:,:,elec,S) = conv2(tfdatnew(:,:,elec,S), gauss2, 'same');
end;
end;
%tfdatnew = convn(tfdatnew, gauss2, 'same'); % is equivalent to the loop for slowlier
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