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github
|
HelmchenLabSoftware/OCIA-master
|
wt_rotate_coords.m
|
.m
|
OCIA-master/other/functions_widefield/whisker_tracking/wt_knutsen/wt_rotate_coords.m
| 5,599 |
utf_8
|
9e4a334eb51adfbc44014d732fd60204
|
% WT_ROTATE_COORDS
%
% Transform coordinates of objects or whiskers between absolute and
% relative framework. A note on transformations:
% Absolute coordinates are in the framework of the actual image
% Relative coordinates are with respect to head position in the image
%
% Syntax: wt_rotate_coords(COORDS, DIR, RE, LE, NO, S, F, DEB, RAD, HOR), where
% COORDS are pair-wise [X Y] coordinates to be transformed. Any
% number of such pairs may be passed arranged along rows.
% DIR is the transform to be performed:
% 'rel2abs' for a relative to absolute transformation
% 'abs2rel' for an absolute to relative transformation
% RY are right-eye coordinates across frames arranged across rows
% LY are right-eye coordinates across frames arranged across rows
% N are nose coordinates across frames arranged across rows
% S is the side on the face of the whisker:
% 1 = right
% 2 = left
%
% Whisker Tracker (WT)
%
% Authors: Per Magne Knutsen, Dori Derdikman
%
% (c) Copyright 2004 Yeda Research and Development Company Ltd.,
% Rehovot, Israel
%
% This software is protected by copyright and patent law. Any unauthorized
% use, reproduction or distribution of this software or any part thereof
% is strictly forbidden.
%
% Citation:
% Knutsen, Derdikman, Ahissar (2004), Tracking whisker and head movements
% of unrestrained, behaving rodents, J. Neurophys, 2004, IN PRESS
%
function vNewCoords = wt_rotate_coords(vCoords, sDirection, vRightEye, vLeftEye, vNose, nSide, ...
vImCropSize, nRadExt, nHorExt)
% Return immediately if object position is not given for current whiskers
if sum(vCoords) == 0, return; end
% Current frame head coordinates
mHead = [vLeftEye; vRightEye; vNose];
% Initialize output matrix
vNewCoords = repmat(NaN, size(vCoords));
% Iterate over pairs of [X Y] coordinates
for i = 1:size(vCoords,1)
switch sDirection
case 'rel2abs'
vNewCoords(i,:) = TransformRelToAbs(vCoords(i,:), nSide, mHead, vImCropSize, nRadExt, nHorExt);
case 'abs2rel'
vNewCoords(i,:) = TransformAbsToRel(vCoords(i,:), nSide, mHead, vImCropSize, nRadExt, nHorExt);
end
end
return;
%%%% TransformRelToAbs %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
% Transform relative to absolute coordinates
function mCoordsNew = TransformRelToAbs(mCoords, nSide, mHead, vImCropSize, nRadExt, nHorExt)
% Relative to absolute transformation:
% nA = angle between nose-eye and nose-object axis (in relative framework)
% nB = angle of eye relative to nose (in absolute framework)
% nC = unknown angle of object relative to nose (in absolute framework)
% Solution: nC = nA - nB
% From nC we derive the position of the object in the absolute framework.
vNoseAbs = mHead(3,:);
vNoseRel = [1 vImCropSize(2)-nHorExt+6];
if nSide == 1, vEyeAbs = [mHead(2,1) mHead(2,2)]; else vEyeAbs = [mHead(1,1) mHead(1,2)]; end
vObjRel = mCoords - repmat(vNoseRel,size(mCoords,1),1); % note: object relative to nose!
nA = abs(-deg2rad(90)-(atan(vObjRel(:,2)./vObjRel(:,1))));
vEyeRel = vEyeAbs - vNoseAbs; % note: eye relative to nose!
nB = abs(atan(vEyeRel(2)/vEyeRel(1)));
nC = nA - nB;
% Now get position of object in absolute framework and we're done...
nR = sqrt(sum(vObjRel'.^2))';% distance of object from nose
nXRel = nR .* cos(nC); % object x position relative to nose
nYRel = nR .* sin(nC); % object y position relative to nose
if nSide == 1
mCoordsNew = [ ...
repmat(vNoseAbs(1),size(mCoords,1),1) - nXRel ...
repmat(vNoseAbs(2),size(mCoords,1),1) + nYRel
];
elseif nSide == 2
mCoordsNew = repmat(vNoseAbs,size(mCoords,1),1) + [nXRel nYRel];
end
return;
%%%% TransformRelToAbs %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
% Transform absolute to relative coordinates
function vNewCoords = TransformAbsToRel(vCoords, nSide, mHead, vImCropSize, nRadExt, nHorExt)
% 1. Find angle between nose-eye and nose-object axis
% 2. Find distance from nose to object
% Object position relative to nose, and angle
vObjRelNose = [vCoords(1)-mHead(3,1) vCoords(2)-mHead(3,2)];
nLenNose2Obj = sqrt(sum([vObjRelNose.^2]));
nNoseObjAng = rad2deg(atan2(vObjRelNose(2),vObjRelNose(1)));
% Eye position relative to nose, and angle
if nSide == 1, vEyeRelNose = [mHead(2,1)-mHead(3,1) mHead(2,2)-mHead(3,2)];
else, vEyeRelNose = [mHead(1,1)-mHead(3,1) mHead(1,2)-mHead(3,2)]; end
nNoseEyeAng = rad2deg(atan2(vEyeRelNose(2),vEyeRelNose(1)));
% Get new angle of object relative to nose
if nSide == 2
nNewNoseObjAng = nNoseObjAng - (90 - abs(nNoseEyeAng));
else
nNewNoseObjAng = -180 - (nNoseObjAng - (90 - abs(nNoseEyeAng)));
end
% Calculate object position relative to nose
nX = nLenNose2Obj * cos(deg2rad(nNewNoseObjAng));
nY = nLenNose2Obj * sin(deg2rad(nNewNoseObjAng));
vRelObjPos = [nX nY];
% Calculate real position in frame
% IMPORTANT: The code below compensates for the fact that both left and
% right frame are shown in the WT GUI in the same axis. Therefore, to
% obtain true relative position for left-side the cut-out section's width
% (effectively g_tWT.MovieInfo.RadExt) must be subtracted from the object's X
% coordinate.
if nSide == 2
vNose = [nRadExt+2 vImCropSize(2) - nHorExt+6];
vNewCoords = [vNose(1)+vRelObjPos(1) vNose(2)+vRelObjPos(2)];
else
vNose = [1 vImCropSize(2)-nHorExt+6];
vNewCoords = [vNose(1)+vRelObjPos(1) vNose(2)+vRelObjPos(2)];
end
%figure(444); clf; hold on; grid on
%plot(vCoords(1),vCoords(2),'r*')
%plot(mHead(:,1),mHead(:,2),'g*')
return;
|
github
|
HelmchenLabSoftware/OCIA-master
|
wt_extrapolate_position.m
|
.m
|
OCIA-master/other/functions_widefield/whisker_tracking/wt_knutsen/wt_extrapolate_position.m
| 4,880 |
utf_8
|
86fd722243d9611965ccc5bd115194d2
|
function mImgFilter = wt_extrapolate_position(mW0, mImg, mWA)
% WT_EXTRAPOLATE_POSITION
% Create an image-mask that will 'highlight' the likely position of the
% whisker in current frame, based on velocity information in previos
% frames.
%
% 1 - Linear interpolation of whisker shape in the X preceeding frames
% 2 - Select end-points and mid-point (half-way along the interpolated whisker)
% 3 - Filter trajectory of all three points
% 4 - Cubic extrapolation of new position
% 5 - Generate scaled gaussian filter
% 6 - Show debug window that contains: filtered velocity and extrapolated
% position
% Whisker Tracker (WT)
%
% Authors: Per Magne Knutsen, Dori Derdikman
%
% (c) Copyright 2004 Yeda Research and Development Company Ltd.,
% Rehovot, Israel
%
% This software is protected by copyright and patent law. Any unauthorized
% use, reproduction or distribution of this software or any part thereof
% is strictly forbidden.
%
% Citation:
% Knutsen, Derdikman, Ahissar (2004), Tracking whisker and head movements
% of unrestrained, behaving rodents, J. Neurophys, 2004, 2005
global g_tWT
nX = 20; % use 10 frames back
bDebug = g_tWT.VerboseMode;
% Return immediately if fewer than X frames have already been processed
if length(find(mWA(2,1,:))) < nX + 1 % check tracked frames in 2nd X value
mImgFilter = ones(size(mImg));
return;
end
% Resize whisker-coordinates to fit image
mW0 = mW0;% * g_tWT.MovieInfo.ResizeFactor;
mWA = mWA;% * g_tWT.MovieInfo.ResizeFactor;
% Linear extrapolation of whisker shape in X preceeding frames
mXX = []; mYY = [];
for f = size(mWA, 3)-nX:size(mWA, 3)
if isempty(find(mWA(:,1,f))), continue, end
vX = mWA(find(mWA(:,1,f)),1,f);
vY = mWA(find(mWA(:,1,f)),2,f);
vXX = [vX(1) vX(1)+(vX(end)-vX(1))/2 vX(end)];
mYY = [mYY; spline(vX(find(vX)), vY(find(vX)), vXX)];
mXX = [mXX; vXX];
end
% Filter whisker trajectory
persistent A B;
nFilterOrder = 4;
if isempty(A)
nFreq = 1/4;
[B,A] = butter(nFilterOrder, nFreq);
end
if size(mYY, 1) > 3*nFilterOrder
mYY = filtfilt(B, A, mYY);
end
% Cubic extrapolation of new position
vNewY = interp1(1:size(mYY,1), mYY, size(mYY,1)+1, 'cubic', 'extrap');
vNewXX = mXX(end,1):mXX(end,end);
[vXX, vNewYY] = wt_spline(mXX(end,:), vNewY, mXX(end,1):mXX(end,end));
[C,IA,IB] = intersect(round(mXX(end,:)), vNewXX);
vNewX = C;
vNewY = vNewYY(IB);
% Generate scales gaussian filter centered on whisker location, with spread
% scaled according to new whisker position limits.
vJit = g_tWT.MovieInfo.HorJitter;
vJit = [vJit(1) vJit(1)+vJit(2) vJit(1)+vJit(2)+vJit(3)];
[vXX, vNewYYUpLim] = wt_spline(vNewX, vNewY+vJit, vNewXX);
[vXX, vNewYYDownLim] = wt_spline(vNewX, vNewY-vJit, vNewXX);
mImgFilter = zeros(size(mImg));
nMaxHw = round(max(abs((vNewYY - vNewYYUpLim))) * g_tWT.MovieInfo.ExtrapFiltHw) + 10;
mImgFilter = wt_zeropad(mImgFilter, nMaxHw, 0); % zeropad image
nAlpha = 2; % used to characterize the gaussion ('sharpness')
for x = 1:length(vNewXX)
nHw = abs((vNewYY(x) - vNewYYUpLim(x))) * g_tWT.MovieInfo.ExtrapFiltHw;
vFG = gausswin(nHw*2+1, nAlpha)';
vYIndx = (round(vNewYY(x)-nHw):round(vNewYY(x)+nHw)) + nMaxHw;
vYIndx = vYIndx(find(vYIndx > 0));
if length(vYIndx) == 1, break, end
vFG = interp1(linspace(vYIndx(1),vYIndx(end),length(vFG)), vFG, vYIndx, 'nearest');
if vNewXX(x) == size(mImg, 2), break;
else, mImgFilter(vYIndx, vNewXX(x)) = vFG'; end
end
mImgFilter = mImgFilter(nMaxHw+1:(size(mImg,1)+nMaxHw), :); % remove zeropad
mImgFilter = mImgFilter / max(mImgFilter(:)); % normalize to max
% Debug
if bDebug
hFig = findobj('Tag', 'EXTRAPOLATE_POSITION_WINDOW');
if isempty(hFig)
hFig = figure;
set(hFig, 'Tag', 'EXTRAPOLATE_POSITION_WINDOW', 'DoubleBuffer', 'on', 'Name', 'WT - EXTRAPOLATE_POSITION_WINDOW', 'numbertitle', 'off')
else, figure(hFig), end
subplot(2,1,1);
plot(mYY); hold on
plot(repmat([size(mYY,1) size(mYY,1)+1],3,1)', [mYY(end,:); vNewY])
plot(repmat(size(mYY,1),3,1), mYY(end,:)); grid on
title('Extrapolation of new whisker location (Y axis)')
subplot(2,2,3); title('Whisker and generated filter')
plot(mXX(end,:), mYY(end,:), 'g'); hold on
plot(vNewXX, vNewYY, 'b');
plot(vNewX, vNewY, 'bo')
plot(vNewXX, vNewYYUpLim, 'r')
plot(vNewXX, vNewYYDownLim, 'r')
grid on
title('Whisker and limits')
subplot(2,2,4)
imagesc(mImgFilter.*mImg); hold on
plot(mXX(end,:), mYY(end,:), 'g'); hold on
plot(vNewXX, vNewYY, 'b');
plot(vNewXX, vNewYYUpLim, 'r')
plot(vNewXX, vNewYYDownLim, 'r')
title('Filter * Image')
truesize; colormap gray
end
return;
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
function w = gausswin(N, a)
% Index vector
k = -(N-1)/2:(N-1)/2;
% Equation 44a from [1]
w = exp((-1/2)*(a * k/(N/2)).^2)';
return;
|
github
|
HelmchenLabSoftware/OCIA-master
|
wt_calibration.m
|
.m
|
OCIA-master/other/functions_widefield/whisker_tracking/wt_knutsen/wt_calibration.m
| 4,876 |
utf_8
|
a143e384f49f955761952d3ab551c926
|
function wt_calibration(sOption)
% WT_CALIBRATION Calibrate and measure image regions
%
% wt_calibration('calibrate')
% wt_calibration('measure')
% wt_calibration('recalculate')
global g_tWT
switch lower(sOption)
case 'calibrate'
Calibrate
wt_display_frame
case 'calibrate-import-image'
CalibrateWithImportedImage
wt_display_frame
case 'measure'
Measure
case 'recalculate'
RecalculatePixelsPerMM
otherwise
Calibrate
wt_display_frame
end
return
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
function Calibrate
global g_tWT
% Get distance between locations
if ~isempty(g_tWT.MovieInfo.EyeNoseAxLen)
g_tWT.DisplayMode = 0; % go to absolute view
end
wt_display_frame
hLine = [];
try
for i = 1:2
[vX(i) vY(i)] = ginput(1); % press of return will provide no input
hLine(end+1) = plot(vX(i), vY(i), 'r.');
end
catch, return, end
hLine(end+1) = plot(vX, vY, 'r:', 'LineWidth', 1);
nL = round(sqrt(sum([diff(vX).^2 diff(vY).^2])));
% Ask how much the distance corresponds to in millimeters
% Control that input is a number
cAns = [];
sMsg = 'Enter distance in millimeters corresponding to %d pixels.';
while length(str2num(char(cAns))) ~= 1
cAns = inputdlg(sprintf(sMsg, nL), 'WT Calibrate', 1);
sMsg = 'Invalid entry (must be a number; do not use comma).\nEnter distance in millimeters corresponding to %d pixels.';
end
delete(hLine)
g_tWT.MovieInfo.CalibCoords = round([vX' vY']);
g_tWT.MovieInfo.CalBarLength = str2num(cAns{1});
RecalculatePixelsPerMM;
return
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
function CalibrateWithImportedImage
global g_tWT
[sFilename, sFilepath] = uigetfile({'*.bmp';'*.tiff';'*.gif';'*.jpg';'*.png';'*.*'}, 'Select image file'); % select image file
if ~sFilename return; end % return if user cancelled dialog
mImg = imread([sFilepath sFilename]); % Load image
wt_display_frame; cla % refresh and clear display
imagesc(wt_image_preprocess(mImg)) % Display image
hLine = [];
try
for i = 1:2
[vX(i) vY(i)] = ginput(1); % press of return will provide no input
hLine(end+1) = plot(vX(i), vY(i), 'r.');
end
catch, return, end
hLine(end+1) = plot(vX, vY, 'r:', 'LineWidth', 1);
nL = round(sqrt(sum([diff(vX).^2 diff(vY).^2])));
% Ask how much the distance corresponds to in millimeters
% Control that input is a number
cAns = [];
sMsg = 'Enter distance in millimeters corresponding to %d pixels.';
while length(str2num(char(cAns))) ~= 1
cAns = inputdlg(sprintf(sMsg, nL), 'WT Calibrate', 1);
sMsg = 'Invalid entry (must be a number; do not use comma).\nEnter distance in millimeters corresponding to %d pixels.';
end
delete(hLine)
g_tWT.MovieInfo.CalibCoords = round([vX' vY']);
g_tWT.MovieInfo.CalBarLength = str2num(cAns{1});
RecalculatePixelsPerMM;
return
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
function Measure
global g_tWT
if ~isfield(g_tWT.MovieInfo, 'PixelsPerMM') % create field if it does not exist
g_tWT.MovieInfo.PixelsPerMM = [];
end
if isempty(g_tWT.MovieInfo.PixelsPerMM) % check image has been calibrated
sUnit = 'pix';
nPixPerMM = 1;
else
sUnit = 'mm';
nPixPerMM = g_tWT.MovieInfo.PixelsPerMM;
end
hLin = [];
try
for i = 1:2
[vX(i) vY(i)] = ginput(1); % press of return will provide no input
if isempty(hLin)
hLin = plot(vX(i), vY(i), 'rx-');
else
set(hLin, 'XData', vX, 'YData', vY)
end
end
catch % in case user pressed Return
delete(hLin)
end
nDistMM = sqrt(diff(vX)^2 + diff(vY)^2) / nPixPerMM;
hTxt = text(mean(vX), mean(vY), sprintf('%.1f%s', nDistMM, sUnit), ...
'Color', 'w', 'BackgroundColor', 'k', 'FontSize', 8, ...
'HorizontalAlignment', 'center');
set([hLin hTxt], 'UserData', {hLin, hTxt}) % store handles
hCntxtMenu = uicontextmenu;
set([hLin hTxt], 'uicontextmenu', hCntxtMenu)
uimenu(hCntxtMenu, 'Label', 'Remove', 'Callback', 'vU=get(gco, ''UserData'');delete(vU{1}),delete(vU{2})')
return
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
function RecalculatePixelsPerMM
global g_tWT
if sum(sum(g_tWT.MovieInfo.CalibCoords)) == 0, return; end
vX = g_tWT.MovieInfo.CalibCoords(:,1);
vY = g_tWT.MovieInfo.CalibCoords(:,2);
% Store pixels per millimeter
nL = round(sqrt(sum([diff(vX).^2 diff(vY).^2])));
g_tWT.MovieInfo.PixelsPerMM = nL / g_tWT.MovieInfo.CalBarLength;
return
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
|
github
|
HelmchenLabSoftware/OCIA-master
|
wt_get_build_number.m
|
.m
|
OCIA-master/other/functions_widefield/whisker_tracking/wt_knutsen/wt_get_build_number.m
| 511 |
utf_8
|
4cd3f5ac2ca28358b6203bad67c583ad
|
% wt_get_build_number
function sBuild = wt_get_build_number
% Set paths
sWT_dir = which('wt');
sWT_dir = sWT_dir(1:findstr(sWT_dir, 'wt.m')-1);
% Get build number from SVN entries files
sBuild = 'Unknown';
if ispc, sSVNPath = [sWT_dir '.svn\' 'entries'];
else, sSVNPath = [sWT_dir '.svn/' 'entries']; end
if exist(sSVNPath)
fid = fopen(sSVNPath);
for i = 1:5
sLine = fgetl(fid);
if strcmp(sLine, 'dir')
sBuild = fgetl(fid);
end
end
fclose(fid);
end
return
|
github
|
HelmchenLabSoftware/OCIA-master
|
wt_dump_screen.m
|
.m
|
OCIA-master/other/functions_widefield/whisker_tracking/wt_knutsen/wt_dump_screen.m
| 1,849 |
utf_8
|
375701158967ce6a3ae8cf1288e6e117
|
%%%% WT_DUMP_SCREEN *****************************************
%
% Whisker Tracker (WT)
%
% Authors: Per Magne Knutsen, Dori Derdikman
%
% (c) Copyright 2004 Yeda Research and Development Company Ltd.,
% Rehovot, Israel
%
% This software is protected by copyright and patent law. Any unauthorized
% use, reproduction or distribution of this software or any part thereof
% is strictly forbidden.
%
% Citation:
% Knutsen, Derdikman, Ahissar (2004), Tracking whisker and head movements
% of unrestrained, behaving rodents, J. Neurophys, 2004, IN PRESS
%
function wt_dump_screen
global g_tWT
hFrameWin = findobj('Tag', 'WTMainWindow');
sAnswer = questdlg('Select where to dump the screen', ...
'Dump screen', ...
'Copy to clipboard', 'Save to disk', 'Send to printer', ...
'Copy to clipboard');
% Hide slider and text elements
set(g_tWT.Handles.hSlider, 'visible', 'off')
hText = findobj('tag','antpost');
set(hText, 'visible', 'off')
set(findobj('tag','gotoframe'), 'visible', 'off')
set(findobj('tag','movieandframe'), 'visible', 'off')
switch sAnswer
case 'Copy to clipboard' % copy to clipboard
print(hFrameWin, '-dbitmap')
case 'Save to disk' % save to disk
[sFilename sFilepath, nFilterIndx] = uiputfile({'*.tif';'*.eps'}, 'Select output file');
if nFilterIndx == 1 % save as TIDD
print(hFrameWin, '-dtiff', sprintf('%s%s', sFilepath, sFilename));
elseif nFilterIndx == 2 % save as color EPS
print(hFrameWin, '-depsc', sprintf('%s%s', sFilepath, sFilename));
end
case 'Send to printer' % send to printer
print(hFrameWin, '-v')
end
% Turn back on slider
set(g_tWT.Handles.hSlider, 'visible', 'on')
set(hText, 'visible', 'on')
set(findobj('tag','gotoframe'), 'visible', 'on')
set(findobj('tag','movieandframe'), 'visible', 'on')
return;
|
github
|
HelmchenLabSoftware/OCIA-master
|
wt_prep_gui.m
|
.m
|
OCIA-master/other/functions_widefield/whisker_tracking/wt_knutsen/wt_prep_gui.m
| 20,021 |
utf_8
|
00b3b9f97fec08f4c6ae1e7479c20136
|
function wt_prep_gui
% WT_PREP_GUI
global g_tWT
hFrameWin = findobj('Tag', 'WTMainWindow');
set(hFrameWin, 'color', [.8 .8 .8])
figure(hFrameWin); clf; g_tWT.Handles.hSlider = [];
set(hFrameWin, 'NumberTitle', 'off', 'Name', ['WhiskerTracker (Revision ' wt_get_build_number ')'], ...
'resizeFcn', ['wt_resize_slider'])
g_tWT.FrameAx = axes;
set(g_tWT.FrameAx, 'Visible', 'off', ...
'buttondownfcn', ['global g_tWT; g_sLastBtnPress = get(gcf,''selectiontype'')'], ...
'DrawMode', 'fast', ...
'Position', [.03 .06 .94 .9] );
% Create toolbar
sPath = which('wt');
sPath = [sPath(1:end-4) 'icons/'];
hToolbar = uitoolbar('Parent', g_tWT.WTWindow, 'Tag', 'WT_Toolbar');
mCData = im2double(imread([sPath 'tool_open.png'])); mCData(mCData == 0) = NaN; % open
uipushtool('Parent', hToolbar, 'cdata', mCData, 'Tag', 'WT_Toolbar_Open', 'TooltipString', 'Open file', 'ClickedCallback', ['wt_select_file']);
mCData = im2double(imread([sPath 'tool_save.png'])); mCData(mCData == 0) = NaN; % save
uipushtool('Parent', hToolbar, 'cdata', mCData, 'Tag', 'WT_Toolbar_Save', 'TooltipString', 'Save', 'ClickedCallback', ['wt_save_data']);
mCData = im2double(imread([sPath 'tool_zoom_in.png'])); mCData(mCData == 0) = NaN; % zoom in
uipushtool('Parent', hToolbar, 'cdata', mCData, 'Tag', 'Spiky_WaitbarAction_ZoomOut', 'TooltipString', 'Zoom in', 'ClickedCallback', ['zoom on'], 'separator', 'on');
[mCData, mCM] = imread([sPath 'tools_table.gif']); mCData = ind2rgb(mCData, mCM); mCData(mCData == 1) = NaN; % parameters
uipushtool('Parent', hToolbar, 'cdata', mCData, 'Tag', 'Spiky_WaitbarAction_EditParameters', 'TooltipString', 'Edit Parameters', 'ClickedCallback', ['wt_set_parameters']);
mCData = im2double(imread([sPath 'tool_rotate_3d.png'])); mCData(mCData == 0) = NaN; % zoom in
mCData_orig = mCData;
for i = 1:3, mCData(:,:,i) = fliplr(mCData(:,:,i)); end
uipushtool('Parent', hToolbar, 'cdata', mCData, 'Tag', 'Spiky_WaitbarAction_RotateClockwise', 'TooltipString', 'Rotate Clockwise', 'ClickedCallback', ['wt_rotate_frame(1); wt_batch_redo(''wt_rotate_frame(1)'')'], 'separator', 'on');
uipushtool('Parent', hToolbar, 'cdata', mCData_orig, 'Tag', 'Spiky_WaitbarAction_RotateAntiClockwise', 'TooltipString', 'Rotate Anti-Clockwise', 'ClickedCallback', ['wt_rotate_frame(-1); wt_batch_redo(''wt_rotate_frame(-1)'')']);
mCData = im2double(imread([sPath 'tool_plottools_show.png'])); mCData(mCData == 0) = NaN; % zoom in
uipushtool('Parent', hToolbar, 'cdata', mCData, 'Tag', 'Spiky_WaitbarAction_PanRight', 'TooltipString', 'Auto-resize window', 'ClickedCallback', ['wt_autosize_window']);
[mCData, mCM] = imread([sPath 'right.gif']); mCData = ind2rgb(mCData, mCM); mCData(mCData == 1) = NaN; % Start tracking
uipushtool('Parent', hToolbar, 'cdata', mCData, 'Tag', 'Spiky_WaitbarAction_PanRight', 'TooltipString', 'Track SLOW', 'ClickedCallback', ['global g_tWT;g_tWT.StopProc=0;wt_track_auto(''slow'')'], 'separator', 'on');
[mCData, mCM] = imread([sPath 'right_double.gif']); mCData = ind2rgb(mCData, mCM); mCData(mCData == 1) = NaN; % Start tracking
uipushtool('Parent', hToolbar, 'cdata', mCData, 'Tag', 'Spiky_WaitbarAction_PanRight', 'TooltipString', 'Track FAST', 'ClickedCallback', ['global g_tWT;g_tWT.StopProc=0;wt_track_auto(''fast'')']);
mCData = im2double(imread([sPath 'cancel.png'])); mCData(mCData == 0) = NaN; % zoom in
uipushtool('Parent', hToolbar, 'cdata', mCData, 'Tag', 'Spiky_WaitbarAction_CancelTracking', 'TooltipString', 'Cancel Tracking', 'ClickedCallback', ['global g_tWT; g_tWT.StopProc = 1;']);
% Menu
hFile = uimenu(hFrameWin, 'Label', 'File');
uimenu(hFrameWin, 'Label','Open...', 'Parent', hFile, 'Callback', ['wt_select_file'], 'accelerator', 'O');
uimenu(hFrameWin, 'Label','Open Directory...', 'Parent', hFile, 'Callback', ['wt_select_directory'], 'accelerator', 'D');
uimenu(hFrameWin, 'Label','Open Directory Tree...', 'Parent', hFile, 'Callback', ['wt_select_directory_tree'], 'accelerator', 'T');
uimenu(hFrameWin, 'Label','Open Selection...', 'Parent', hFile, 'Callback', ['wt_select_batchfile']);
% Produce list of loaded movies
if ~isempty(g_tWT.Movies)
uimenu(hFrameWin, 'Label','Load Data...', 'Parent', hFile, 'Callback', ['wt_load_data(''deffile'')'], 'Separator', 'on');
uimenu(hFrameWin, 'Label','Save', 'Parent', hFile, 'Callback', ['wt_save_data'], 'accelerator', 'S');
uimenu(hFrameWin, 'Label','Save As...', 'Parent', hFile, 'Callback', ['wt_save_data(''defpath'')']);
hMovies = uimenu(hFrameWin, 'Label', 'Movies', 'Parent', hFile, 'Separator', 'on');
uimenu(hFrameWin, 'Label','Next Movie', 'Parent', hMovies, 'Callback', ['wt_load_movie'], 'accelerator', 'N');
for m = 1:size(g_tWT.Movies,2)
% Menu item label; limit to 50 chars long
sLabel = sprintf('%s', g_tWT.Movies(m).filename);
if length(sLabel) > 50
sLabel = ['..' sLabel(end-47:end)];
end
if m == 1
hCurrFile = uimenu(hFrameWin, 'Label', sLabel, 'Parent', hMovies, 'Callback', [sprintf('wt_load_movie(%d)', m)], 'Separator', 'on');
else
hCurrFile = uimenu(hFrameWin, 'Label', sLabel, 'Parent', hMovies, 'Callback', [sprintf('wt_load_movie(%d)', m)]);
end
% Tick off to indicate if movie already has an associated .mat file
if exist(sprintf('%smat', g_tWT.Movies(m).filename(1:findstr('.avi', g_tWT.Movies(m).filename))), 'file') ...
| exist(sprintf('%smat.gz', g_tWT.Movies(m).filename(1:findstr('.avi', g_tWT.Movies(m).filename))), 'file')
set(hCurrFile, 'checked', 'on')
end
end
% Whisker markers etc
hMarkers = uimenu(hFrameWin, 'Label', 'Whiskers');
uimenu(hFrameWin, 'Label','New...', 'Parent', hMarkers, 'Callback', ['wt_mark_whisker'], 'accelerator', 'W');
uimenu(hFrameWin, 'Label','Paste (B)', 'Parent', hMarkers, 'Callback', ['wt_copy_paste_whisker(''paste'', NaN); wt_batch_redo(''wt_copy_paste_whisker(''''paste'''', NaN)'');'], 'accelerator', 'W');
uimenu(hFrameWin, 'Label','Delete...', 'Parent', hMarkers, 'Callback', ['wt_clear_selected_whisker']);
uimenu(hFrameWin, 'Label','Delete All (B)', 'Parent', hMarkers, 'Callback', ['wt_clear_whisker(''all''); wt_batch_redo(''wt_clear_whisker(''''all'''')'')']);
uimenu(hFrameWin, 'Label','Set Last Frame...', 'Parent', hMarkers, 'Callback', ['wt_set_last_frame'], 'Separator', 'on');
uimenu(hFrameWin, 'Label', 'Whisker Display Width...', 'Parent', hMarkers, 'Callback', 'wt_change_whisker_width')
uimenu(hFrameWin, 'Label', 'Show Whisker Identities', 'Parent', hMarkers, 'Callback', 'wt_toggle_show_identity')
uimenu(hFrameWin, 'Label','Track Labels (B)', 'Parent', hMarkers, 'Callback', ['wt_track_whisker_label(0,''continue-all'',0); wt_batch_redo(''wt_track_whisker_label(0,''''continue-all'''',0)'')'], 'Separator', 'on');
uimenu(hFrameWin, 'Label','Labelling Filter...', 'Parent', hMarkers, 'Callback', ['global g_tWT; g_tWT.LabelFilter=wt_create_filter(g_tWT.LabelFilter);']);
uimenu(hFrameWin, 'Label','Mark Whisker and Label...', 'Parent', hMarkers, 'Callback', ['wt_mark_whisker_and_label;']);
uimenu(hFrameWin, 'Label','Clear Labels (B)', 'Parent', hMarkers, 'Callback', ['wt_track_whisker_label(0, ''delete-all''); wt_batch_redo(''wt_track_whisker_label(0,''''delete-all'''');'')']);
uimenu(hFrameWin, 'Label','Track Whiskers With Labels (B)', 'Parent', hMarkers, 'Callback', ['wt_track_whiskers_with_labels('''')']);
uimenu(hFrameWin, 'Label','Show Label Names', 'Parent', hMarkers, 'Callback', 'wt_toggle_show_label_identity')
% Head related menu items
hHead = uimenu(hFrameWin, 'Label', 'Head');
uimenu(hFrameWin, 'Label','Track Head', 'Parent', hHead, 'Callback', ['wt_init_head_tracker']);
uimenu(hFrameWin, 'Label','Set Head Position...', 'Parent', hHead, 'Callback', ['wt_init_head_tracker(''static_head'')']);
uimenu(hFrameWin, 'Label','Configure Eye Filter...', 'Parent', hHead, 'Callback', ['global g_tWT; g_tWT.EyeFilter=wt_create_filter(g_tWT.EyeFilter);'], 'separator', 'on');
uimenu(hFrameWin, 'Label','Clean Head Movements', 'Parent', hHead, 'Callback', ['wt_clean_splines(0)']);
% Image options
hImage = uimenu(hFrameWin, 'Label', 'View');
uimenu(hFrameWin, 'Label','Select ROI', 'Parent', hImage, 'Callback', ['wt_select_roi']);
uimenu(hFrameWin, 'Label','Toggle View Mode', 'Parent', hImage, 'Callback', 'wt_toggle_display_mode');
uimenu(hFrameWin, 'Label','Rotate Clockwise (B)', 'Parent', hImage, 'Callback', ['wt_rotate_frame(1); wt_batch_redo(''wt_rotate_frame(1)'')'], 'Separator', 'on', 'accelerator', 'c');
uimenu(hFrameWin, 'Label','Rotate Anti-Clockwise (B)', 'Parent', hImage, 'Callback', ['wt_rotate_frame(-1); wt_batch_redo(''wt_rotate_frame(-1)'')'], 'accelerator', 'a');
uimenu(hFrameWin, 'Label','Flip Vertical (B)', 'Parent', hImage, 'Callback', ['wt_flip_frame(''updown''); wt_batch_redo(''wt_flip_frame(''''updown'''')'')'], 'separator', 'on');
uimenu(hFrameWin, 'Label','Flip Horizontal (B)', 'Parent', hImage, 'Callback', ['wt_flip_frame(''leftright''); wt_batch_redo(''wt_flip_frame(''''leftright'''')'')']);
uimenu(hFrameWin, 'Label','Refresh', 'Parent', hImage, 'Callback', ['wt_prep_gui; wt_display_frame'], 'Separator', 'on', 'accelerator', 'R');
uimenu(hFrameWin, 'Label','Zoom', 'Parent', hImage, 'Callback', ['zoom on'], 'accelerator', 'z');
uimenu(hFrameWin, 'Label','Hide', 'Parent', hImage, 'Callback', ['wt_toggle_imageshow'], 'accelerator', 'H');
uimenu(hFrameWin, 'Label','Go To Frame...', 'Parent', hImage, 'Callback', @GoToFrame, 'accelerator', 'G');
uimenu(hFrameWin, 'Label','Reset (B)', 'Parent', hImage, 'Callback', ['wt_reset_all; wt_batch_redo(''wt_reset_all'')'], 'separator', 'on');
% Measure menu
hImage = uimenu(hFrameWin, 'Label', 'Measure');
uimenu(hFrameWin, 'Label','Plot...', 'Parent', hImage, 'Callback', ['wt_graphs']);
hCompute = uimenu(hFrameWin, 'Label', 'Compute', 'Parent', hImage);
uimenu(hFrameWin, 'Label', 'Angle (B)', 'Parent', hCompute, 'Callback', ['wt_compute_kinematics(''angle'', 0); wt_batch_redo(''wt_compute_kinematics(''''angle'''',0)'');']);
uimenu(hFrameWin, 'Label', 'Curvature (B)', 'Parent', hCompute, 'Callback', ['wt_compute_kinematics(''curvature'', 0); wt_batch_redo(''wt_compute_kinematics(''''curvature'''',0)'');']);
uimenu(hFrameWin, 'Label', 'All Parameters (B)', 'Parent', hCompute, 'Callback', ['wt_compute_kinematics(''all'', 0); wt_batch_redo(''wt_compute_kinematics(''''all'''',0)'');']);
uimenu(hFrameWin, 'Label','Set Reference Angle...', 'Parent', hImage, 'Callback', 'wt_set_reference_line');
uimenu(hFrameWin, 'Label','Use Default Reference Angle (B)', 'Parent', hImage, 'Callback', 'wt_set_default_reference_line; wt_batch_redo(''wt_set_default_reference_line'')');
uimenu(hFrameWin, 'Label','Calibrate...', 'Parent', hImage, 'Callback', ['wt_calibration(''calibrate'')'], 'Separator', 'on');
uimenu(hFrameWin, 'Label','Calibrate With Image...', 'Parent', hImage, 'Callback', ['wt_calibration(''calibrate-import-image'')']);
uimenu(hFrameWin, 'Label','Measure...', 'Parent', hImage, 'Callback', ['wt_calibration(''measure'')']);
uimenu(hFrameWin, 'Label','Create Outline', 'Parent', hImage, 'Callback', ['wt_create_outline(''add'')'], 'Separator', 'on');
uimenu(hFrameWin, 'Label','Paste Outline (B)', 'Parent', hImage, 'Callback', ['wt_create_outline(''paste'', NaN); wt_batch_redo(''wt_create_outline(''''paste'''', NaN)'')']);
uimenu(hFrameWin, 'Label','Delete All Outlines (B)', 'Parent', hImage, 'Callback', ['wt_create_outline(''deleteall'', NaN); wt_batch_redo(''wt_create_outline(''''deleteall'''', NaN)'')']);
uimenu(hFrameWin, 'Label','Hide Outlines', 'Parent', hImage, 'Callback', ['wt_create_outline(''hide'')']);
end
% Options menu
hOptions = uimenu(hFrameWin, 'Label', 'Options');
hScripts = uimenu(hFrameWin, 'Label', 'Scripts', 'Parent', hOptions);
uimenu(hFrameWin, 'Label', 'Run Script... (B)', 'Parent', hScripts, 'Callback', ['wt_run_script']);
uimenu(hFrameWin, 'Label', 'Run Batch Script...', 'Parent', hScripts, 'Callback', ['wt_run_script(''batch'')']);
uimenu(hFrameWin, 'Label', 'Get Script Help...', 'Parent', hScripts, 'Callback', ['wt_run_script_help']);
% Get list of existing scripts in ./scripts directory
sPath = which('wt');
sPath = checkfilename([sPath(1:end-4) 'scripts\']);
tFiles = dir(sPath);
bFirst = 1;
for f = 1:length(tFiles)
if ~isempty(strfind(tFiles(f).name, '.m')) & isempty(strfind(tFiles(f).name, '.m~'))
sName = strrep(tFiles(f).name(1:end-2), '_', ' ');
vIndx = strfind(sName, ' ');
sName([1 vIndx+1]) = upper(sName([1 vIndx+1]));
if bFirst
uimenu(hFrameWin, 'Label', sName, 'Parent', hScripts, 'Callback', [sprintf('wt_run_script(''%s'')', tFiles(f).name)], 'Separator', 'on');
bFirst = 0;
else
uimenu(hFrameWin, 'Label', sName, 'Parent', hScripts, 'Callback', [sprintf('wt_run_script(''%s'')', tFiles(f).name)]);
end
end
end
if ~isempty(g_tWT.Movies)
uimenu(hFrameWin, 'Label', 'Batch Redo', 'Parent', hOptions, 'Callback', ['wt_batch_redo(''redo'')'], 'accelerator', 'B');
uimenu(hFrameWin, 'Label', 'Parameters...', 'Parent', hOptions, 'Callback', ['wt_set_parameters'], 'accelerator', 'P');
uimenu(hFrameWin, 'Label', 'User Variables (B)...', 'Parent', hOptions, 'Callback', ['wt_user_variables;wt_batch_redo(''wt_user_variables(''''copyfrommem'''')'')'], 'accelerator', 'U');
%uimenu(hFrameWin, 'Label','Track Stimulus Triggers', 'Parent', hOptions, 'Callback', ['wt_track_stimulus']);
uimenu(hFrameWin, 'Label','Signal-to-Noise', 'Parent', hOptions, 'Callback', ['wt_toggle_signal_noise'], 'Separator', 'on');
uimenu(hFrameWin, 'Label','Notes...', 'Parent', hOptions, 'Callback', ['wt_edit_notes'], 'accelerator', 'e');
uimenu(hFrameWin, 'Label','Debug Window', 'Parent', hOptions, 'Callback', ['wt_toggle_verbose']);
uimenu(hFrameWin, 'Label','Compress Datafiles', 'Parent', hOptions, 'Callback', ['wt_toggle_datacompress'], 'Separator', 'on');
uimenu(hFrameWin, 'Label','Uncompress Movie', 'Parent', hOptions, 'Callback', ['wt_uncompress_movie']);
uimenu(hFrameWin, 'Label','Play Movie', 'Parent', hOptions, 'Callback', ['wt_play_movie'], 'Separator', 'on', 'accelerator', 'M');
uimenu(hFrameWin, 'Label','Save Movie', 'Parent', hOptions, 'Callback', ['wt_play_movie(''save'')']);
uimenu(hFrameWin, 'Label','Dump Screen...', 'Parent', hOptions, 'Callback', ['wt_dump_screen'], 'Separator', 'on');
end
% Help menu
hHelp = uimenu(hFrameWin, 'Label', 'Help');
uimenu(hFrameWin, 'Label','WT Help', 'Parent', hHelp, ...
'Callback', ...
['hWordHandle=actxserver(''Word.Application'');set(hWordHandle,''Visible'',1);invoke(get(hWordHandle,''Documents''),''Open'',which(''WT_Help.doc''))']);
uimenu(hFrameWin, 'Label', 'Keyboard shortcuts', 'Parent', hHelp, 'Callback', ['wt_keyboard_shortcuts']);
uimenu(hFrameWin, 'Label','About WT', 'Parent', hHelp, 'Callback', ['wt_about_wt'], 'Separator', 'on');
if ~isempty(g_tWT.Movies)
% 'Go to frame' push-button
g_tWT.Handles.hGoToButton = uicontrol(g_tWT.WTWindow, 'units', 'normalized' ...
, 'Position', [.88 .025 .07 .03] ... % fig opos = .05 .05 .9 .9
, 'Style', 'edit' ...
, 'String', '' ...
, 'Tag', 'gotoframe' ...
, 'tooltipString', 'Enter value of frame to go to and press Enter' ...
, 'Callback', ['wt_display_frame(str2num(get(gco,''string'')))'] );
% Fix height in pixels
set(g_tWT.Handles.hGoToButton, 'units', 'pixels');
vPos = get(g_tWT.Handles.hGoToButton, 'position');
set(g_tWT.Handles.hGoToButton, 'Position', [vPos(1) 20 vPos(3) 17]);
% 'Go to last tracked frame' push button
g_tWT.Handles.hGoToEndButton = uicontrol(g_tWT.WTWindow, 'units', 'normalized' ...
, 'Position', [.95 .025 .03 .03] ... % fig opos = .05 .05 .9 .9
, 'Style', 'pushbutton' ...
, 'String', 'E' ...
, 'Tag', 'gotoframe' ...
, 'tooltipString', 'Go to last whisker-tracked frame' ...
, 'CallBack', @GotoLastFrame );
% Fix button height in pixels
set(g_tWT.Handles.hGoToEndButton, 'units', 'pixels');
vPos = get(g_tWT.Handles.hGoToEndButton, 'position');
set(g_tWT.Handles.hGoToEndButton, 'Position', [vPos(1) 20 vPos(3) 17]);
% 'Go to first tracked frame' push button
g_tWT.Handles.hGoToFirstButton = uicontrol(g_tWT.WTWindow, 'units', 'normalized' ...
, 'Position', [.02 .025 .03 .03] ... % fig opos = .05 .05 .9 .9
, 'Style', 'pushbutton' ...
, 'String', '1' ...
, 'Tag', 'gotoframe' ...
, 'tooltipString', 'Go to first frame in movie' ...
, 'CallBack', @GotoFirstFrame );
% Fix button height in pixels
set(g_tWT.Handles.hGoToFirstButton, 'units', 'pixels');
vPos = get(g_tWT.Handles.hGoToFirstButton, 'position');
set(g_tWT.Handles.hGoToFirstButton, 'Position', [vPos(1) 20 vPos(3) 17]);
% Status text field below slider
g_tWT.Handles.hStatusText = uicontrol(g_tWT.WTWindow, 'units', 'normalized' ...
, 'Position', [.02 .005 .96 .02] ...
, 'Style', 'text' ...
, 'fontsize', 8 ...
, 'horizontalalignment', 'left' ...
, 'String', '' ...
, 'Tag', 'statustext' ...
, 'FontWeight', 'normal' ...
, 'backgroundcolor', get(g_tWT.WTWindow, 'color'));
% Fix height in pixels
set(g_tWT.Handles.hStatusText, 'units', 'pixels');
vPos = get(g_tWT.Handles.hStatusText, 'position');
set(g_tWT.Handles.hStatusText, 'Position', [vPos(1) 2 vPos(3) 15]);
end
% List of previously accessed paths
if ~isempty(g_tWT.AccessedPaths)
for p = 1:length(g_tWT.AccessedPaths)
sLabel = sprintf('%d %s', p, g_tWT.AccessedPaths{p});
if length(sLabel) > 40
sLabel = ['..' sLabel(end-37:end)];
end
if p == 1
uimenu(hFrameWin, 'Label', sLabel, ...
'Parent', hFile, ...
'Callback', [sprintf('wt_select_directory(''%s'')', g_tWT.AccessedPaths{p})], ...
'Separator', 'on');
else
uimenu(hFrameWin, 'Label', sLabel, ...
'Parent', hFile, ...
'Callback', [sprintf('wt_select_directory(''%s'')', g_tWT.AccessedPaths{p})]);
end
end
end
uimenu(hFrameWin, 'Label','E&xit WT', 'Parent', hFile, 'Callback', ['wt_exit'], 'separator', 'on', 'accelerator', 'q');
set(hFrameWin, 'keypressfcn', @FigKeyPressExec)
set(g_tWT.WTWindow, 'visible', 'on')
return % end of main function
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
function FigKeyPressExec( varargin )
global g_tWT
sKey = lower(get(gcf, 'currentcharacter'));
% If pressed key is a number, then go that number of frames back from
% current
if ~isempty(str2num(sKey))
if str2num(sKey) == 0
nNewFrame = round(get(g_tWT.Handles.hSlider, 'Value')) + 1;
else
nNewFrame = round(get(g_tWT.Handles.hSlider, 'Value')) - str2num(sKey);
end
if nNewFrame < 1 | nNewFrame > g_tWT.MovieInfo.NumFrames
beep; return;
end
wt_display_frame(nNewFrame);
end
if strcmp(' ', sKey)
if isfield(g_tWT, 'StopProc')
if g_tWT.StopProc, g_tWT.StopProc = 0; wt_track_auto('bicubic');
else, g_tWT.StopProc = 1; end
end
end
function GoToFrame(varargin)
global g_tWT
sF = inputdlg('Go to frame', 'Go to frame', 1);
if isempty(sF), return
else, wt_display_frame(str2num(char(sF))); end
return;
function GotoFirstFrame(varargin)
global g_tWT
if ~isempty(g_tWT.MovieInfo.Nose)
f = find(~isnan(g_tWT.MovieInfo.Nose(:,1)));
else, f = 1; end
wt_display_frame(f(1));
return;
function GotoLastFrame(varargin)
global g_tWT
if ~isempty(g_tWT.MovieInfo.SplinePoints)
f = size(g_tWT.MovieInfo.SplinePoints, 3);
else
f = g_tWT.MovieInfo.NumFrames;
end
wt_display_frame(f);
return;
|
github
|
HelmchenLabSoftware/OCIA-master
|
wt_mark_object.m
|
.m
|
OCIA-master/other/functions_widefield/whisker_tracking/wt_knutsen/wt_mark_object.m
| 5,048 |
utf_8
|
c852ba81c9b336c1264876140284470d
|
function wt_mark_object(nWhisker, sOption, nLocation)
% WT_MARK_OBJECT
% Mark object. Accepts whisker ID as its single input parameter.
% Brings up a cross-hair to mark location in frame where whisker touches
% object. Only works in conjunction with the WT GUI.
% Syntax: wt_mark_object(ID)
global g_tWT
nCurrentFrame = round(get(g_tWT.Handles.hSlider, 'Value'));
switch sOption
case 'delete'
g_tWT.MovieInfo.ObjectRadPos(nWhisker, :, nLocation) = NaN;
delete(findobj('Tag', sprintf('object%d%d', nWhisker, nLocation)))
case 'move'
g_tWT.MovieInfo.ObjectRadPos(nWhisker, 1:2, nLocation) = GetCoords(nWhisker);
% - replace zeros with NaNs
g_tWT.MovieInfo.ObjectRadPos(find(g_tWT.MovieInfo.ObjectRadPos==0)) = NaN;
case 'editframe'
% Display current frame value and allow changing it
cNewFrame = inputdlg('New frame number', 'Edit frame', 1, ...
{num2str(g_tWT.MovieInfo.ObjectRadPos(nWhisker, 3, nLocation))});
if ~isempty(cNewFrame)
g_tWT.MovieInfo.ObjectRadPos(nWhisker, 3, nLocation) = str2num(char(cNewFrame));
end
% - replace zeros with NaNs
g_tWT.MovieInfo.ObjectRadPos(find(g_tWT.MovieInfo.ObjectRadPos==0)) = NaN;
case 'add'
% If this is the 1st marked touch location for this whisker, change
% the 1st frame for this location to be the 1st tracked frame
nF = find(squeeze(g_tWT.MovieInfo.SplinePoints(1,1,:,nWhisker)));
if nWhisker > size(g_tWT.MovieInfo.ObjectRadPos,1)
nCurrentFrame = nF(1);
else
% Following lines takes into account that old movies did not
% allow marking of more than one object
if size(g_tWT.MovieInfo.ObjectRadPos,2) == 3
if ~any(g_tWT.MovieInfo.ObjectRadPos(nWhisker,3,:))
nCurrentFrame = nF(1);
end
elseif size(g_tWT.MovieInfo.ObjectRadPos,2) == 2
g_tWT.MovieInfo.ObjectRadPos(nWhisker,3,:) = nF(1); % set frame of previous location to 1st tracked frame
end
end
% Check if there already is a location that starts from current frame
if size(g_tWT.MovieInfo.ObjectRadPos,2) == 3 & size(g_tWT.MovieInfo.ObjectRadPos,1) >= nWhisker
if find(g_tWT.MovieInfo.ObjectRadPos(nWhisker,3,:)==nCurrentFrame)
wt_error('There already is a defined location starting in current frame. Move location instead.')
end
end
vAbsCoords = GetCoords(nWhisker);
% Save in absolute coordinates
% - determine number of locations marked for this whisker
if isempty(g_tWT.MovieInfo.ObjectRadPos)
nObjectNum = 0;
else
try
nObjectNum = length(find(~isnan(g_tWT.MovieInfo.ObjectRadPos(nWhisker, 1:2, :))))/2;
catch, nObjectNum = 0; end
end
% - replace zeros with NaNs
g_tWT.MovieInfo.ObjectRadPos(find(g_tWT.MovieInfo.ObjectRadPos==0)) = NaN;
% - tidy up order of locations
for w = 1:size(g_tWT.MovieInfo.ObjectRadPos,1)
vRows = find(~isnan(g_tWT.MovieInfo.ObjectRadPos(w,1,:)));
tmp = g_tWT.MovieInfo.ObjectRadPos;
tmp(w,:,:) = NaN;
tmp(w,:,1:length(vRows)) = g_tWT.MovieInfo.ObjectRadPos(w,:,vRows);
g_tWT.MovieInfo.ObjectRadPos = tmp;
end
% - allocate new location
g_tWT.MovieInfo.ObjectRadPos(nWhisker, 1:3, nObjectNum+1) = [vAbsCoords nCurrentFrame];
% - replace zeros with NaNs
g_tWT.MovieInfo.ObjectRadPos(find(g_tWT.MovieInfo.ObjectRadPos==0)) = NaN;
% Delete whisker-distance-from-object vector
g_tWT.MovieInfo.PositionOffset(:,nWhisker) = NaN;
end
% Refresh frame
wt_display_frame
return;
%%%% SUB ROUTINES %%%%
function vAbsCoords = GetCoords(nWhisker)
global g_tWT
nCurrentFrame = round(get(g_tWT.Handles.hSlider, 'Value'));
% Get user input in absolute coordinates
[nX nY] = ginput(1);
vAbsCoords = [nX nY];% ./ g_tWT.MovieInfo.ResizeFactor;
% If head-position is known for the *current frame* then transform from
% relative to absolute coordinates.
if ~isempty(g_tWT.MovieInfo.EyeNoseAxLen) & g_tWT.MovieInfo.Nose(nCurrentFrame, 1) & g_tWT.DisplayMode
if ~isempty(g_tWT.MovieInfo.Nose(nCurrentFrame,:)) & ~isnan(prod(g_tWT.MovieInfo.Nose(nCurrentFrame,:)))
nWhiskerSide = g_tWT.MovieInfo.WhiskerSide(nWhisker);
if nWhiskerSide == 2, vAbsCoords(1) = vAbsCoords(1) - (g_tWT.MovieInfo.ImCropSize(1) + 1); end
vAbsCoords = wt_rotate_coords(vAbsCoords, ...
'rel2abs', ...
g_tWT.MovieInfo.RightEye(nCurrentFrame, :), ...
g_tWT.MovieInfo.LeftEye(nCurrentFrame, :), ...
g_tWT.MovieInfo.Nose(nCurrentFrame, :), ...
nWhiskerSide, ...
g_tWT.MovieInfo.ImCropSize, ...
g_tWT.MovieInfo.RadExt, ...
g_tWT.MovieInfo.HorExt );
end
end
return
|
github
|
HelmchenLabSoftware/OCIA-master
|
wt_head_tracker.m
|
.m
|
OCIA-master/other/functions_widefield/whisker_tracking/wt_knutsen/wt_head_tracker.m
| 7,494 |
utf_8
|
8bb26b2011d840cf56a96a3ba9c0b063
|
function bResult = wt_head_tracker(sFileName)
% WT_HEAD_TRACKER
% Track rat head movements
%
warning off MATLAB:divideByZero
warning off MATLAB:mir_warning_variable_used_as_function
global g_tWT
bResult = 1;
wt_toggle_display_mode(0)
g_tWT.MovieInfo.ImCropSize = round([g_tWT.MovieInfo.RadExt g_tWT.MovieInfo.EyeNoseAxLen+g_tWT.MovieInfo.HorExt*2]);
% Open waitbar dialog
hWaitbar = waitbar(0, sprintf('Loading buffer (%d frames)...', g_tWT.MovieInfo.NoFramesToLoad), 'CreateCancelBtn', 'delete(gcbf)');
set(hWaitbar, 'units', get(findobj('tag', 'WTMainWindow'), 'units'))
vFrPos = get(findobj('tag', 'WTMainWindow'), 'position');
vWtPos = get(hWaitbar, 'position');
set(hWaitbar, 'tag', 'auto');
% Add buttons for manual control
uicontrol(hWaitbar, 'Style', 'pushbutton', 'Position', [25 12 50 23], ...
'Callback', 'set(gcf, ''tag'', ''manual_right'')', 'String', 'Right' );
uicontrol(hWaitbar, 'Style', 'pushbutton', 'Position', [85 12 50 23], ...
'Callback', 'set(gcf, ''tag'', ''manual_left'')', 'String', 'Left' );
uicontrol(hWaitbar, 'Style', 'pushbutton', 'Position', [145 12 50 23], ...
'Callback', 'set(gcf, ''tag'', ''manual_both'')', 'String', 'Both' );
uicontrol(hWaitbar, 'Style', 'pushbutton', 'Position', [205 12 50 23], ...
'Callback', 'set(gcf, ''tag'', ''stop'')', 'String', 'Stop' );
drawnow
nYlim = g_tWT.MovieInfo.Height;
nXlim = g_tWT.MovieInfo.Width;
set(g_tWT.Handles.hSlider, 'enable', 'off') % disable slider
% Process frames
nFirstFrame = find(~isnan(g_tWT.MovieInfo.LeftEye(:,1)))+1;
nRealFrame = nFirstFrame(1);
bBreakOuter = 0;
% Outer loop: iterate over frame segments
while nRealFrame <= g_tWT.MovieInfo.NumFrames
nRangeStart = nRealFrame;
nRangeEnd = nRangeStart + g_tWT.MovieInfo.NoFramesToLoad - 1;
nRangeEnd = min([nRangeEnd g_tWT.MovieInfo.NumFrames]);
vFrameRange = nRangeStart:nRangeEnd; % range of frames in buffer
waitbar(nRealFrame/g_tWT.MovieInfo.NumFrames, hWaitbar, sprintf('Loading buffer (%d frames)...', g_tWT.MovieInfo.NoFramesToLoad))
mFrames = wt_load_avi(sFileName, vFrameRange); % load frame buffer
% Inner loop: iterate over individual frames in buffer
nFrame = 1;
bBreakInner = 0;
while nFrame <= length(vFrameRange) & nFrame > 0
nRealFrame = vFrameRange(nFrame);
try
waitbar(nRealFrame/g_tWT.MovieInfo.NumFrames, hWaitbar, sprintf('Processing frame %d', nRealFrame))
catch, bResult = 0; nBreakOuter = 1; break; end
if g_tWT.MovieInfo.Invert == 0, nInvert = -1; else, nInvert = 1; end
% Rotate
if g_tWT.MovieInfo.Rot ~= 0, mFrames(:,:,nFrame) = imrotate(mFrames(:,:,nFrame), g_tWT.MovieInfo.Rot); end
if g_tWT.MovieInfo.Flip(1) mFrames(:,:,nFrame) = flipud(mFrames(:,:,nFrame)); end % flip up-down
if g_tWT.MovieInfo.Flip(2) mFrames(:,:,nFrame) = fliplr(mFrames(:,:,nFrame)); end % flip left-right
if strcmp(get(hWaitbar, 'tag'), 'auto')
% Automatic
try
g_tWT.MovieInfo.RightEye(nRealFrame, :) = wt_track_spot(double(mFrames(:,:,nFrame)).*nInvert, g_tWT.MovieInfo.RightEye(nRealFrame-1, :), [], g_tWT.EyeFilter.Filter, g_tWT.VerboseMode);
g_tWT.MovieInfo.LeftEye(nRealFrame, :) = wt_track_spot(double(mFrames(:,:,nFrame)).*nInvert, g_tWT.MovieInfo.LeftEye(nRealFrame-1, :), [], g_tWT.EyeFilter.Filter, g_tWT.VerboseMode);
catch, bBreakOuter = 1; break, end
nFrame = nFrame + 1;
elseif strcmp(get(hWaitbar, 'tag'), 'stop') % stop tracking at current frame
bBreakOuter = 1; break
else
% Manual (ignore buffer and load frame-by-frame)
nFrame = 0;
while ~strcmp(get(hWaitbar, 'tag'), 'auto')
if nRealFrame < nFirstFrame, nRealFrame = nFirstFrame; end
% Get automatic suggestions
mFrame = wt_load_avi(sFileName, nRealFrame); % load frame buffer
g_tWT.MovieInfo.RightEye(nRealFrame, :) = wt_track_spot(double(mFrame).*nInvert, g_tWT.MovieInfo.RightEye(nRealFrame-1, :), [], g_tWT.EyeFilter.Filter, g_tWT.VerboseMode);
g_tWT.MovieInfo.LeftEye(nRealFrame, :) = wt_track_spot(double(mFrame).*nInvert, g_tWT.MovieInfo.LeftEye(nRealFrame-1, :), [], g_tWT.EyeFilter.Filter, g_tWT.VerboseMode);
g_tWT.MovieInfo.Nose(nRealFrame, :) = wt_find_nose(g_tWT.MovieInfo.RightEye(nRealFrame, :), g_tWT.MovieInfo.LeftEye(nRealFrame, :), g_tWT.MovieInfo.EyeNoseAxLen);
wt_display_frame(nRealFrame); % refresh frame
hLine = line(-10,-10); % indicator line
set(hLine, 'linewidth', 5, 'color', [1 0 0])
% Decide which side(s) to track
switch get(hWaitbar, 'tag')
case 'manual_both', cSides = {'Right' 'Left'};
case 'manual_right', cSides = {'Right'};
case 'manual_left', cSides = {'Left'};
end
for sS = cSides
% Update indicator line
if strcmp(sS,'Right'), set(hLine, 'xdata', [1 1], 'ydata', [0 nYlim]);
else, set(hLine, 'xdata', [nXlim nXlim], 'ydata', [0 nYlim]), end
nX = -1; nY = -1;
% Get input
while ~ValidCoord(nX,nY), [nX, nY, nButton] = ginput(1); end
if nButton == 2 | nButton == 3
% Break if middle or right button was pressed
set(hWaitbar, 'tag', 'auto')
figure(hWaitbar)
bBreakInner = 1;
break
elseif nButton > 3
% Change framenumber if a number key was pressed
nRealFrame = nRealFrame - str2num(char(nButton));
else
% Assign coordinate
eval(sprintf('g_tWT.MovieInfo.%sEye(nRealFrame, :) = round([nX nY]);', char(sS)));
if strcmp(sS,cSides{end}), nRealFrame = nRealFrame + 1; end
end
end
delete(hLine)
if bBreakInner
break
end
end
end
end % inner loop
if bBreakOuter, break
else % refresh frame
g_tWT.MovieInfo.RightEye = g_tWT.MovieInfo.RightEye;
g_tWT.MovieInfo.LeftEye = g_tWT.MovieInfo.LeftEye;
g_tWT.MovieInfo.Nose = wt_find_nose(g_tWT.MovieInfo.RightEye, g_tWT.MovieInfo.LeftEye, g_tWT.MovieInfo.EyeNoseAxLen);
if nFrame
wt_display_frame(nRealFrame, mFrames(:,:,nFrame-1));
else, wt_display_frame(nRealFrame); end
figure(hWaitbar); drawnow
end
end % outer loop
delete(hWaitbar)
g_tWT.MovieInfo.RightEye = g_tWT.MovieInfo.RightEye;
g_tWT.MovieInfo.LeftEye = g_tWT.MovieInfo.LeftEye;
g_tWT.MovieInfo.Nose = wt_find_nose(g_tWT.MovieInfo.RightEye, g_tWT.MovieInfo.LeftEye, g_tWT.MovieInfo.EyeNoseAxLen);
set(g_tWT.Handles.hSlider, 'enable', 'on', 'value', nFirstFrame-1) % enable slider
wt_toggle_display_mode(1) % refresh frame
wt_display_frame(nFirstFrame-1)
return
%%%% VALIDCOORD
%%%% Check if ginput() coordinates is inside the frame
function nB = ValidCoord(nX,nY)
global g_tWT
nB = 1;
vYlim = get(g_tWT.FrameAx, 'ylim');
vXlim = get(g_tWT.FrameAx, 'xlim');
if nX < 1 | nX > vXlim(2), nB = 0; end
if nY < 1 | nY > vYlim(2), nB = 0; end
return
|
github
|
HelmchenLabSoftware/OCIA-master
|
wt_plot_signal_noise.m
|
.m
|
OCIA-master/other/functions_widefield/whisker_tracking/wt_knutsen/wt_plot_signal_noise.m
| 3,785 |
utf_8
|
16ae4d2f5488b3e23f73a272f627ff86
|
function bStop = wt_plot_signal_noise(vSR)
% WT_PLOT_SIGNAL_NOISE
% Plots the signal-to-noise ratio of the whisker against the background.
% The ratio itself is computed in the find_next_whisker.dll. This function
% just accepts the number(s) to plot. Adds a red, horizontal bar for
% setting the threshold at which tracking should be automatically stopped.
%
% Syntax:
% wt_plot_signal_noise(N) : add N to XDATA in SR window
% wt_plot_signal_noise([]) : reset SR plot
global g_tWT
persistent p_hSRWin
persistent p_nAutoclear
persistent p_nClock
persistent p_vFPS
% Clear tracking speed variable
if isempty(vSR), p_vFPS = []; end
% Update tracking speed counter (current and average FPS)
if ~isempty(p_nClock)
nElapsedTime = etime(clock, p_nClock);
p_nClock = clock;
p_vFPS = [p_vFPS length(vSR)/nElapsedTime]; % tracking speed, fps
set(findobj('tag','fps'), 'label', sprintf('Tracking speed: %.1f fps', mean(p_vFPS)))
else, p_nClock = clock; end
if isempty(p_nAutoclear), p_nAutoclear = 500;
else
if ~isempty(findobj('tag', 'AutoClearButton'))
p_nAutoclear = get(findobj('tag', 'AutoClearButton'), 'UserData');
end
end
% Figure
if isempty(p_hSRWin) | ~ishandle(p_hSRWin)
p_hSRWin = figure;
set(p_hSRWin, 'Name', 'S/N Use mouse to set threshold', ...
'MenuBar', 'none', ...
'NumberTitle', 'off', ...
'Position', [450 370 480 200], ...
'CloseRequestFcn', 'wt_toggle_signal_noise;delete(gcbo)', ...
'Color', 'k', ...
'Tag', 'SignalNoiseFig' )
uimenu(gcf, 'Label', 'Clear', 'callback', 'wt_plot_signal_noise([])')
uimenu(gcf, 'Label', sprintf('Set autoclear (%d frames)', p_nAutoclear), 'callback', @SetAutoClear, 'Tag', 'AutoClearButton')
uimenu(gcf, 'Label', 'Tracking speed: 0 fps', 'Tag', 'fps')
end
% Axes
hAxes = findobj('tag', 'sn_plot');
if isempty(hAxes)
hAxes = subplot('Position', [.1 .15 .8 .7]);
set(gca, 'FontSize', 7, 'color', 'k', ...
'xcolor', 'w', 'ycolor', 'w', ...
'ButtonDownFcn', @SetThreshold, ...
'tag', 'sn_plot' )
ylabel('S/N'); xlabel('Time (frames)')
end
% Plot
hLines = get(hAxes(end), 'children'); % there are two line objects: S/N and THRESHOLD
if isempty(hLines)
hLines(1) = line(1,1);
hThreshLine = line(0,2);
set(hLines(1), 'Tag', 'SR', 'Marker', '.', 'color', [0 .8 0]);
set(hThreshLine, 'Tag', 'THRESH', 'color', 'r', 'LineStyle', ':');
end
% Return if the input is empty
if isempty(vSR), vSR = 0;
else, vSR = [get(findobj('tag','SR'),'ydata') vSR]; end
set(hAxes, 'ylim', [min(vSR)-2 max(vSR)+2])
set(findobj('tag','SR'), 'ydata', vSR, 'xdata', 0:length(vSR)-1)
vYdata = get(findobj('tag','THRESH'), 'ydata');
set(findobj('tag','THRESH'), 'ydata', repmat(vYdata(1), 1, length(vSR)), 'xdata', 0:length(vSR)-1)
hLines = get(hAxes(end), 'children'); % there are two line objects: S/N and THRESHOLD
% Evaluate SR
vThresh = get(findobj('tag','THRESH'), 'ydata');
if (vSR(end) <= vThresh(end)) & vSR(end)~=0
beep
g_tWT.StopProc = 1;
end
% If length of vSR > p_nAutoclear, clear the display
if length(vSR) > p_nAutoclear, wt_plot_signal_noise([]), end
return
%%% Change SR threshold %%%
function SetThreshold(varargin)
mPnts = get(gca,'CurrentPoint');
nY = mPnts(1,2);
nXlim = get(gca, 'xlim');
set(findobj('tag','THRESH'), 'xdata', 0:nXlim(2), ...
'ydata', repmat(nY,1,length(0:nXlim(2))) )
return
%%% Change Autoclear %%%
function SetAutoClear( varargin )
sAutoClFrames = inputdlg('Number of frames between autoclear', 'Set autoclear', 1);
if isempty(char(sAutoClFrames)), return, end
nAutoClFrames = str2num(char(sAutoClFrames));
set(findobj('tag', 'AutoClearButton'), 'Label', sprintf('Set autoclear (%d frames)', nAutoClFrames), 'UserData', nAutoClFrames);
return
|
github
|
HelmchenLabSoftware/OCIA-master
|
wt_clear_selected_whisker.m
|
.m
|
OCIA-master/other/functions_widefield/whisker_tracking/wt_knutsen/wt_clear_selected_whisker.m
| 2,251 |
utf_8
|
aba3a703c9cf0c5ea4afc2e0ca864686
|
function wt_clear_selected_whisker()
% WT_CLEAR_SELECTED_WHISKER
% Delete all or parts of tracked data of selected whiskers, or delete all
% tracked whiskers.
global g_tWT
cIdents = {g_tWT.MovieInfo.WhiskerIdentity{:}};
nFontSize = 8;
nLinSep = 10;
vScrnSize = get(0, 'ScreenSize');
nFigHeight = (length(cIdents)-1) * (nFontSize*2 + nLinSep) + 60;
nFigWidth = 150;
vFigPos = [5 vScrnSize(4)-(nFigHeight+21) nFigWidth nFigHeight];
hCurrWin = figure;
set(hCurrWin, 'NumberTitle', 'off', ...
'Name', 'Select whisker', ...
'Position', vFigPos, ...
'Tag', 'ClearSelectedWhiskers', ...
'MenuBar', 'none' )
nCurrLine = nFigHeight;
nCurrLine = nCurrLine - (nFontSize*2 + nLinSep);
for w = 1:length(cIdents)
w_this = w;
if w > 10, w_this = w-10; end
if w > 20, w_this = w-20; end
if w > 30, w_this = w-30; end
if w > 40, w_this = w-40; end
if isempty(cIdents{w}), cIdents{w}{1} = ''; end
hBox = uicontrol(hCurrWin, 'Style', 'checkbox', 'Position', [10 nCurrLine 125 20], ...
'Callback', '', ...
'HorizontalAlignment', 'right', ...
'String', cIdents{w}, ...
'FontWeight', 'bold', ...
'Tag', sprintf('whisker_%d_%s', w, cIdents{w}{:}), ...
'BackgroundColor', g_tWT.Colors(w_this,:) );
nCurrLine = nCurrLine - (nFontSize*2 + nLinSep);
end
% Refresh pushbutton
uicontrol(hCurrWin, 'Style', 'pushbutton', 'Position', [10 nCurrLine 125 20], ...
'Callback', @ClearWhiskers, ...
'String', 'Clear whiskers', ...
'FontWeight', 'bold' );
uiwait(hCurrWin)
return
%%%%%%%%%%%%%% CLEAR WHISKERS %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
function ClearWhiskers(varargin)
global g_tWT
hCurrWin = findobj('Tag', 'ClearSelectedWhiskers');
% Iterate over checkboxes and decide which to delete
vDelWhiskers = [];
cIdents = {g_tWT.MovieInfo.WhiskerIdentity{:}};
for w = 1:length(cIdents)
if isempty(cIdents{w}), cIdents{w}{1} = ''; end
hCheckBox = findobj(hCurrWin, 'Tag', sprintf('whisker_%d_%s', w, cIdents{w}{:}));
if get(hCheckBox, 'Value')
vDelWhiskers(end+1) = w;
end
end
% Clear whiskers
if ~isempty(vDelWhiskers)
wt_clear_whisker(vDelWhiskers)
end
% Close window
close(hCurrWin)
% Re-open window
wt_clear_selected_whisker
return
|
github
|
HelmchenLabSoftware/OCIA-master
|
wt_rotate_frame.m
|
.m
|
OCIA-master/other/functions_widefield/whisker_tracking/wt_knutsen/wt_rotate_frame.m
| 993 |
utf_8
|
a92c107a47390dbb6d73e084fa620630
|
% WT_ROTATE_FRAME
%
function wt_rotate_frame( nDir )
global g_tWT
% Display warning message
if ~isfield(g_tWT.MovieInfo, 'SplinePoints'), return, end
if ~isempty(g_tWT.MovieInfo.SplinePoints)
sQuestResp = questdlg('Changing the ROI will delete already marked whiskers. Continue?', 'Warning', 'Yes', 'No', 'Yes');
if strcmp(sQuestResp, 'No') return; end
end
nAngles = [0 90 180 270];
nCurrPos = find(nAngles == g_tWT.MovieInfo.Rot);
% Determine new 'clock' position
if nDir == 0 % return to default
g_tWT.MovieInfo.Rot = 0;
g_tWT.MovieInfo.Roi = [1 1 g_tWT.MovieInfo.Width-1 g_tWT.MovieInfo.Height-1];% * g_tWT.MovieInfo.ResizeFactor;
else
nNewPos = nCurrPos - nDir;
switch nNewPos
case 0
g_tWT.MovieInfo.Rot = nAngles(4);
case 5
g_tWT.MovieInfo.Rot = nAngles(1);
otherwise
g_tWT.MovieInfo.Rot = nAngles(nNewPos);
end
end
g_tWT.MovieInfo.SplinePoints = [];
% Refresh frame
wt_display_frame
return
|
github
|
HelmchenLabSoftware/OCIA-master
|
wt_flip_frame.m
|
.m
|
OCIA-master/other/functions_widefield/whisker_tracking/wt_knutsen/wt_flip_frame.m
| 866 |
utf_8
|
9b7c021b84096aead6b9a000be27738e
|
%%%% WT_FLIP_FRAME %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%
% Whisker Tracker (WT)
%
% Authors: Per Magne Knutsen, Dori Derdikman
%
% (c) Copyright 2004 Yeda Research and Development Company Ltd.,
% Rehovot, Israel
%
% This software is protected by copyright and patent law. Any unauthorized
% use, reproduction or distribution of this software or any part thereof
% is strictly forbidden.
%
% Citation:
% Knutsen, Derdikman, Ahissar (2004), Tracking whisker and head movements
% of unrestrained, behaving rodents, J. Neurophys, 2004, IN PRESS
%
function wt_flip_frame( sDirection )
global g_tWT
switch sDirection
case 'updown' % Flip Up-Down
g_tWT.MovieInfo.Flip(1) = ~g_tWT.MovieInfo.Flip(1);
case 'leftright' % Flip Left-Right
g_tWT.MovieInfo.Flip(2) = ~g_tWT.MovieInfo.Flip(2);
end
% Refresh display
wt_display_frame
|
github
|
HelmchenLabSoftware/OCIA-master
|
wt_create_filter.m
|
.m
|
OCIA-master/other/functions_widefield/whisker_tracking/wt_knutsen/wt_create_filter.m
| 6,277 |
utf_8
|
38d33983265ffab70c0fc85628361dbe
|
function tFilter = wt_create_filter(tDefaultFilter, sOption)
% Whisker Tracker (WT)
%
% Authors: Per Magne Knutsen, Dori Derdikman
%
% (c) Copyright 2004 Yeda Research and Development Company Ltd.,
% Rehovot, Israel
%
% This software is protected by copyright and patent law. Any unauthorized
% use, reproduction or distribution of this software or any part thereof
% is strictly forbidden.
%
% Citation:
% Knutsen, Derdikman, Ahissar (2004), Tracking whisker and head movements
% of unrestrained, behaving rodents, J. Neurophys, 2004, IN PRESS
% Create a mexican hat (DoG) filter interactively
%
% Usage:
% Set filter interactively
% tFilter = wt_create_filter(tDefaultFilter)
%
% Create filter only (don't open GUI)
% tFilter = wt_create_filter(tDefaultFilter, 'create-only')
%
if exist('sOption')
switch lower(sOption)
case 'create-only'
tFilter = CreateFilter(tDefaultFilter);
return
end
end
hWT_win = findobj('Tag', 'WTMainWindow');
if ~isempty(hWT_win)
wt_display_frame; % refresh frame
end
if ~exist('tDefaultFilter')
tDefaultFilter.Size = 10;
tDefaultFilter.Sigma_A = 3;
tDefaultFilter.Sigma_B = 1;
end
% Open window
hFig = figure;
set(hFig, 'Position', [350 520 520 180], 'MenuBar', 'none', 'NumberTitle', 'off', 'Name' ,'WT - GENERATE FILTER', 'Tag', 'WT_GENERATE_FILTER', 'Resize', 'off')
hSub = subplot('Position', [.65 .1 .35 .8]);
set(hSub, 'xtick', [], 'ytick', [], 'Color', 'k', 'Tag', 'WT_GENERATE_FILTER_SUBPLOT')
axis square
% Slide bars
hSliderAB_size = uicontrol(hFig, 'style', 'slider');
SetSliderProps(hSliderAB_size, [.15 .85 .4 .1], 1, 101, [.01 .1], tDefaultFilter.Size, 'AB_SIZE', 'Size', @UpdateFilter)
hSliderA_sigma = uicontrol(hFig, 'style', 'slider');
SetSliderProps(hSliderA_sigma, [.15 .54 .4 .1], 0.001, 10, [.01 .1], tDefaultFilter.Sigma_A, 'A_SIGMA', 'A sigma', @UpdateFilter)
hSliderB_sigma = uicontrol(hFig, 'style', 'slider');
SetSliderProps(hSliderB_sigma, [.15 .41 .4 .1], 0.001, 10, [.01 .1], tDefaultFilter.Sigma_B, 'B_SIGMA', 'B sigma', @UpdateFilter)
hTxt = uicontrol(gcf, 'style', 'text'); % Text string indicating slider value
set(hTxt, 'units', 'normalized', 'string', 'Size should greater than the maximal expected frame to frame displacement', 'Position', [.05 .675 .575 .15], 'HorizontalAlignment', 'left')
hTxt = uicontrol(gcf, 'style', 'text'); % Text string indicating slider value
set(hTxt, 'units', 'normalized', 'string', 'Sigmas should be adjusted so that the object of interest appears dark in the image', 'Position', [.05 .23 .575 .15], 'HorizontalAlignment', 'left')
hSaveButton = uicontrol(hFig, 'style', 'pushbutton'); % SAVE button
set(hSaveButton, 'units', 'normalized', 'Position', [.15 .05 .15 .15], 'string', 'Save', 'Callback', ['uiresume(gcf);'])
hCancelButton = uicontrol(hFig, 'style', 'pushbutton'); % CANCEL button
set(hCancelButton, 'units', 'normalized', 'Position', [.4 .05 .15 .15], 'string', 'Cancel', 'Callback', ['close(gcf);'])
TestFilter;
uiwait(hFig)
if ~isempty(findobj('Tag', 'WT_GENERATE_FILTER'))
tFilter.Size = round(get(findobj('Tag', 'AB_SIZE'), 'Value'));
tFilter.Sigma_A = get(findobj('Tag', 'A_SIGMA'), 'Value');
tFilter.Sigma_B = get(findobj('Tag', 'B_SIGMA'), 'Value');
tFilter = CreateFilter(tFilter);
close(hFig)
else
tFilter = tDefaultFilter;
end
wt_display_frame
TestFilter('clear')
return
% Create filter
function TestFilter(sOption)
global g_tWT
persistent mImg
if exist('sOption')
switch lower(sOption)
case 'clear'
clear mImg;
return
end
end
nSize = round(get(findobj('Tag', 'AB_SIZE'), 'Value'));
mGaussA = fspecial('gaussian', nSize, get(findobj('Tag', 'A_SIGMA'), 'Value')); % Gaussian A
mGaussB = fspecial('gaussian', nSize, get(findobj('Tag', 'B_SIGMA'), 'Value')); % Gaussian B
mFilter = mGaussA - mGaussB; % DoG (Difference of Gaussians)
hSub = findobj('Tag', 'WT_GENERATE_FILTER_SUBPLOT');
axis(hSub);
imagesc(mFilter);
colormap pink
set(hSub, 'xtick', [], 'ytick', [], 'Color', 'k', 'Tag', 'WT_GENERATE_FILTER_SUBPLOT')
axis square
drawnow
% Convolve WT window
hWT_win = findobj('Tag', 'WTMainWindow');
if ~isempty(hWT_win) % don't convolve if WT window is closed
if isempty(mImg)
hAx = findobj(hWT_win, 'type', 'axes');
mImg = get(findall(hAx, 'type', 'image'), 'cdata');
end
mImg_conv = conv2(double(mImg), mFilter, 'same'); % convolve
wt_display_frame(get(g_tWT.Handles.hSlider, 'value'), mImg_conv); % FIX FRAMENUMBER!!!!!!
end
figure(findobj('Tag', 'WT_GENERATE_FILTER'))
return
% end test filter
% Update filter parameters
function UpdateFilter(varargin)
hAB_SIZE = findobj('Tag', 'AB_SIZE');
hAB_SIZE_txt = findobj('Tag', 'AB_SIZE-txt');
set(hAB_SIZE_txt, 'String', round(get(hAB_SIZE, 'Value')));
hA_SIGMA = findobj('Tag', 'A_SIGMA');
hA_SIGMA_txt = findobj('Tag', 'A_SIGMA-txt');
set(hA_SIGMA_txt, 'String', get(hA_SIGMA, 'Value'));
hB_SIGMA = findobj('Tag', 'B_SIGMA');
hB_SIGMA_txt = findobj('Tag', 'B_SIGMA-txt');
set(hB_SIGMA_txt, 'String', get(hB_SIGMA, 'Value'));
TestFilter;
return
% end update filter
% Set slider properties
function SetSliderProps(hSlider, vPos, nMin, nMax, vStep, nDefault, sTag, sString, sCallback)
set(hSlider, 'units', 'normalized' ...
, 'Position', vPos ...
, 'Style', 'slider' ...
, 'Tag', sTag ...
, 'Min', nMin ...
, 'Max', nMax ...
, 'SliderStep', vStep ...
, 'Value', nDefault ...
, 'CallBack', sCallback );
hTxt = uicontrol(gcf, 'style', 'text'); % Text string indicating slider value
set(hTxt, 'units', 'normalized', 'string', get(hSlider, 'Value'), 'Position', [vPos(1)+vPos(3) vPos(2) .075 vPos(4)], 'Tag', sprintf('%s-txt', sTag))
hTxt = uicontrol(gcf, 'style', 'text'); % Descriptive text string
set(hTxt, 'units', 'normalized', 'string', sString, 'Position', [.05 vPos(2), vPos(1)-.05 vPos(4)], 'HorizontalAlignment', 'left', 'FontWeight','bold')
return
% end slider properties
% Create filter
function tFilter = CreateFilter(tFilter)
mGaussA = fspecial('gaussian', tFilter.Size, tFilter.Sigma_A); % Gaussian A
mGaussB = fspecial('gaussian', tFilter.Size, tFilter.Sigma_B); % Gaussian B
tFilter.Filter = mGaussA - mGaussB; % DoG (Difference of Gaussians)
return
% end create filter
|
github
|
HelmchenLabSoftware/OCIA-master
|
wt_crop_behaving_video.m
|
.m
|
OCIA-master/other/functions_widefield/whisker_tracking/wt_knutsen/wt_crop_behaving_video.m
| 7,146 |
utf_8
|
5176de9198f557e2304c65564f2de0a9
|
% WT_CROP_BEHAVING_VIDEO
% Extract region of interest parallel to whisker-pad.
% wt_crop_behaving_video(M, C, HOR, RAD, METHOD), where
% M is the loaded frame
% C is a 3-by-2 vector containing X Y coordinates of right-eye, left-eye
% and nose.
% HOR is the length of the extracted region (anterior-posterior axis)
% RAD is the width of the extracted region (distance from face)
% METHOD is the interpolation method used when rotating the extracted
% region, either 'linear' (fast) or 'bicubic' (slow, but better).
%
function mCropImg = wt_crop_behaving_video(mImg, mCoords, hor_ext, rad_ext, method);
global g_tWT
% Resize cropping parameters according to the ersize factor
%hor_ext = hor_ext * g_tWT.MovieInfo.ResizeFactor;
%rad_ext = rad_ext * g_tWT.MovieInfo.ResizeFactor;
%mCoords = mCoords * g_tWT.MovieInfo.ResizeFactor;
bDebug = g_tWT.VerboseMode;
switch lower(method)
case 'bicubic'
bBicubic = 1;
case 'nearest'
bBicubic = 0;
otherwise
error('Unknown method in wt_crop_behaving_vide')
end
% Rotate and extract the relevant parts of the image
% A small note: the routine first defines the vertices of the relevant
% section in the coordinates of the original frame. It then extracts this
% part, rotates it and re-crops it so only the defined rectangle is kept.
% An alternative would be to rotate the entire frame, and then crop. This is
% intuitively simpler, but because the imrotate(...) function is slow on
% large matrices (e.g. such as the entire frame), this method takes more
% than 3 times longer to execute than the first method.
% TODO:
% - account for possible errors coordinates are outside the frame
% - return both right and left side and the ROI in absolute coordinates
% - check consistency of mCoords input matrix
if bDebug
hFig = findobj('Tag', 'CROP_FRAME_WINDOW');
if isempty(hFig)
hFig = figure;
set(hFig, 'Tag', 'CROP_FRAME_WINDOW', 'DoubleBuffer', 'on', 'Name', 'WT - CROP_FRAME_WINDOW', 'numbertitle', 'off')
else, figure(hFig), end
clf;
end
nPadFact = 4;
% zero-pad image to avoid boundary errors
mImg = padarray(mImg, [hor_ext*nPadFact rad_ext*nPadFact], mean(mean(mImg(:,:,1))),'both');
% repeat once for right eye and once for left eye
new_coords = zeros(4,2);
for e = 1:2 % 1=right 2=left
% angle between eye and nose
y = abs(mCoords(e,2) - mCoords(3,2));
x = mCoords(e,1) - mCoords(3,1);
if x < 0
theta = -1*(90 + rad2deg(atan(y/x)));
else
theta = 90 - rad2deg(atan(y/abs(x)));
end
if (mCoords(3,1)-mCoords(e,1)) < 0
ang = pi + atan( (mCoords(3,2)-mCoords(e,2))/(mCoords(3,1)-mCoords(e,1)) ); % ang between points
else
ang = atan( (mCoords(3,2)-mCoords(e,2))/(mCoords(3,1)-mCoords(e,1)) ); % ang between points
end
eye_nose_zero_intersect = interp1([mCoords(3,2) mCoords(e,2)], [mCoords(3,1) mCoords(e,1)], 0, 'linear', 'extrap');
r_nose = sqrt(sum([(mCoords(3,1)-eye_nose_zero_intersect) mCoords(3,2)].^2)) + hor_ext;
new_coords(1,:) = [ r_nose*cos(ang)+eye_nose_zero_intersect r_nose*sin(ang) ]; % ant A
r_eye = sqrt(sum([(mCoords(e,1)-eye_nose_zero_intersect) mCoords(e,2)].^2)) - hor_ext;
new_coords(2,:) = [ r_eye*cos(ang)+eye_nose_zero_intersect r_eye*sin(ang) ]; % post A
adj = [rad_ext*cos(ang-deg2rad(90)) rad_ext*sin(ang-deg2rad(90))];
if e == 1 % right eye
new_coords(4,:) = new_coords(1,:) - adj; % ant B
new_coords(3,:) = new_coords(2,:) - adj; % post B
else % left eye
new_coords(4,:) = new_coords(1,:) + adj; % ant B
new_coords(3,:) = new_coords(2,:) + adj; % post B
end
% transform coordinates to take into account zero-padding
new_coords = [new_coords(:,1)+rad_ext*nPadFact new_coords(:,2)+hor_ext*nPadFact];
% extract the rectangle
x = min(new_coords(:,1));
y = min(new_coords(:,2));
w = max(new_coords(:,1)) - x; %end % use width of 1st frame
h = max(new_coords(:,2)) - y; %end % use height of 1st frame
try
mTemp = mImg(round(y:y+h), round(x:x+w));
catch
wt_error('Possible error with head-coordinates. Check by changing display mode.')
end
% calculate what the size of the rotate image will be (uncropped)
theta_rad = deg2rad(theta);
R = [cos(theta_rad) sin(theta_rad); -sin(theta_rad) cos(theta_rad)];
half_w = size(mTemp, 1)/2;
half_h = size(mTemp, 2)/2;
% corners = [up_left; up_right; low_left; low_right]
corners(1,:) = [-half_w half_h];
corners(2,:) = [half_w half_h];
corners(3,:) = [-half_w -half_h];
corners(4,:) = [half_w -half_h];
new_corners = corners * R;
if theta < 0
new_size = abs([new_corners(3,1)*2 new_corners(1,2)*2]);
else
new_size = abs([new_corners(1,1)*2 new_corners(2,2)*2]);
end
% zeropad image before rotating to take into account loss of pixels
% during cropping
vPad = ceil((new_size-size(mTemp))/2);
% remove negative values
vPad(vPad<0) = 0;
mTemp = padarray(mTemp, vPad, 'both');
% rotate rectangle
if bBicubic
% - use Matlab method if choosing bicubic interpolation
mTemp = imrotate(mTemp, theta, 'bicubic', 'crop');
else
% - use C script of choosing nearest interpolation
mTemp = rotate_matrix(double(mTemp), theta);
end
% crop again so only the relevant section is included in final image
% We have replaced the two lines below with parameters defined earlier
% in the global namespace, as we want all frames to have the same size.
%new_w = round(rad_ext);
%new_h = round(hor_ext*2 + sqrt(sum([mCoords(3,1)-mCoords(e,1) mCoords(3,2)-mCoords(e,2)].^2))); %end
new_w = g_tWT.MovieInfo.ImCropSize(1);% * g_tWT.MovieInfo.ResizeFactor;
new_h = g_tWT.MovieInfo.ImCropSize(2);% * g_tWT.MovieInfo.ResizeFactor;
x = round((size(mTemp, 2) - new_w) / 2);
y = round((size(mTemp, 1) - new_h) / 2);
mCropImg{e} = mTemp(round(y:y+new_h), round(x:x+new_w));
if bDebug
subplot(1,4,e+2)
imagesc(mCropImg{e}); SetPlotProps;
end
end
% Plot
if bDebug
subplot(1,4,1:2)
imagesc(mImg(hor_ext:size(mImg,1)-hor_ext,rad_ext:size(mImg,2)-rad_ext))
title('Original')
colormap gray; hold on
scatter(mCoords(:,1),mCoords(:,2),'g.') % eyes/nose
scatter(new_coords(:,1)-rad_ext, new_coords(:,2)-hor_ext, 'r.') % rect coords
plot(new_coords([1 2 3 4 1], 1)-rad_ext, new_coords([1 2 3 4 1], 2)-hor_ext, 'r')
SetPlotProps;
drawnow
end
% make sure that both rectangles have the same dimensions before returning
% them
min_height = min([size(mCropImg{1},1) size(mCropImg{2},1)]);
min_width = min([size(mCropImg{1},2) size(mCropImg{2},2)]);
% crop outwards (from whisker roots) and downwards (from neck)
mCropImg{1} = mCropImg{1}(1:min_height, (size(mCropImg{1},2)+1-min_width):end);
mCropImg{2} = mCropImg{2}(1:min_height, 1:min_width);
% flip right rectangle horizontally
mCropImg{1} = fliplr(mCropImg{1});
return;
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
function SetPlotProps
set(gca, 'xtick', [], 'ytick', [])
|
github
|
HelmchenLabSoftware/OCIA-master
|
wt_subtract_bg_frame.m
|
.m
|
OCIA-master/other/functions_widefield/whisker_tracking/wt_knutsen/wt_subtract_bg_frame.m
| 8,477 |
utf_8
|
aa677748a07abb05bd8819239e12c399
|
% WT_SUBTRACT_BG_FRAME
% IMG_OUT = wt_subtract_bg_frame(IMG, F), where
% IMG is the frame from which to subtract the background frame
% F is the current frame number
% IMG_OUT is IMG minus the background
%
% Subtract background frame from passed image. The passed coordinates are
% used to select what portion of the frames to subtract, in case the passed
% image has alredy been cropped. vCoords are in absolute coordinates. The
% current-frame parameter is used to determine whcih series of frames to
% subtract from the passed image, in case different background-frames have
% been calculated (e.g. before object entry and after object entry)
%
% The background frame is low-pass filtered if a number has been entered in
% the 'Low-pass background image (pixels)' field in the parameters GUI. The
% value entered is used to determine the diameter (in pixels) of a low-pass
% median filter.
%
% IMPORTANT NOTE:
% If in the matrix where background frame series are specified any row
% contains two zeros [0 0] then ALL background frames will be subtracted
% from ALL frames!
%
function mImgOut = wt_subtract_bg_frame(varargin)
global g_tWT
persistent p_tBgFrames
persistent p_nBGLowPass
if nargin == 1
switch varargin{1}
case 'reset'
p_tBgFrames = struct([]);
return;
end
else
mImgIn = varargin{1};
vCoords = [1 1 g_tWT.MovieInfo.Width-1 g_tWT.MovieInfo.Height-1];% * g_tWT.MovieInfo.ResizeFactor;
nCurrentFrame = varargin{2};
end
bDebug = g_tWT.VerboseMode;
% Iterate over p_cBgFrames and decide which background-frames to scrap and
% which to keep. If all are scrapped, calculate all background frames. If
% all are kept, then don't recalculate any of them. Here we also shuffle
% the order of the background frames and case some are kept and new ones
% are inserted. For instance, new background frames will be calculated if
% the user changes the start- and stop-frame values of the background
% frames in the GUI.
% Select frame-series to average
mAvgFrames = g_tWT.MovieInfo.AverageFrames;
% Determine whether to subtract ALL background frames from current frame
nZeroRow = find(any(~all(mAvgFrames,2)));
if ~isempty(nZeroRow)
bSubtractAll = 1;
mAvgFrames(nZeroRow, :) = [];
else, bSubtractAll = 0; end
% Exit immediately if background frames should not be used
if isempty(mAvgFrames)
p_tBgFrames = struct([]);
mImgOut = double(mImgIn);
return;
end
% If the size of the background-frame smoothing window has changed, scrap
% all existing background frames and calculate these again (and then smooth
% with the new window)
if p_nBGLowPass ~= g_tWT.MovieInfo.BGFrameLowPass
p_tBgFrames = struct([]); % clear persistent variable (we concatenate the existing frames below)
end
p_nBGLowPass = g_tWT.MovieInfo.BGFrameLowPass;
% Select which of the existing background frames to keep
tTempFrames = struct([]);
for bgA = 1:size(p_tBgFrames, 2)
for bgB = 1:size(mAvgFrames, 1)
if (p_tBgFrames(bgA).from == mAvgFrames(bgB,1)) ...
& (p_tBgFrames(bgA).to == mAvgFrames(bgB,2))
% Background-frame already exists...
mAvgFrames(bgB,:) = [NaN NaN];
nNewIndx = size(tTempFrames,2)+1;
tTempFrames(nNewIndx).img = p_tBgFrames(bgA).img;
tTempFrames(nNewIndx).from = p_tBgFrames(bgA).from;
tTempFrames(nNewIndx).to = p_tBgFrames(bgA).to;
end
end
end
mAvgFrames(find(isnan(mAvgFrames))) = [];
p_tBgFrames = struct([]); % clear persistent variable (we concatenate the existing frames below)
% Determine how many background frames to calculate.
if isempty(mAvgFrames), nNoBgFrames = 0;
else, nNoBgFrames = size(mAvgFrames, 1); end
% Initialize waitbar
for bg = 1:nNoBgFrames
if ~exist('hWaitBar'), hWaitBar = waitbar(0, ''); end
% Update waitbar
waitbar(bg/(nNoBgFrames+1), hWaitBar, sprintf('Calculating background-frame %d of %d', bg, nNoBgFrames))
nFrom = mAvgFrames(bg,1); % start range
nTo = mAvgFrames(bg,2); % end range
if nFrom == 0, nFrom = 1, end
if nTo == 0, nTo = nFrom + 1; end
if nFrom > nTo % check consistency in input
wt_error('The first background frame has a higher frame-number than the last. Check values in Image->Parameters.')
end
nAviTo = nTo; % limit nTo to max frames
if nTo > g_tWT.MovieInfo.NumFrames
nAviTo = g_tWT.MovieInfo.NumFrames;
end
% Load background frames in chunks to avoid memory problems
if g_tWT.MovieInfo.NoFramesToLoad >= (nTo - nFrom), vRanges = [nFrom nTo];
else, vRanges = nFrom:g_tWT.MovieInfo.NoFramesToLoad:nTo; end
mAveragedFrames = [];
for r = 2:length(vRanges)
vRange = [vRanges(r-1) (vRanges(r)-1)]; % [min max]
vFrames = max([1 vRange(1)]):min([vRange(2) g_tWT.MovieInfo.NumFrames]); % all frames to be loaded
if isempty(g_tWT.MovieInfo.FilenameUncompressed)
mFrames = wt_load_avi(g_tWT.MovieInfo.Filename, vFrames, 'noresize');
else
mFrames = wt_load_avi(g_tWT.MovieInfo.FilenameUncompressed, vFrames, 'noresize');
end
try, mFrames = double(mFrames);
catch, wt_error('Out of memory. Try to reduce the number of background frames.'), end
mAveragedFrame = mean(mFrames, 3);
mAveragedFrames(:,:,r-1) = mAveragedFrame;
end
mAveragedFrame = mean(mAveragedFrames,3);
% Crop image
mAveragedFrame = imcrop(mAveragedFrame, vCoords);%./g_tWT.MovieInfo.ResizeFactor);
% Smooth background image
if isfield(g_tWT.MovieInfo, 'BGFrameLowPass')
nLowPass = g_tWT.MovieInfo.BGFrameLowPass;
if ~isempty(nLowPass) & (nLowPass > 1)
mWin = ones(nLowPass);
mAveragedFrame = conv2(mAveragedFrame, mWin, 'same') ./ prod(size(mWin));
end
end
% Store averaged frame in the persistent holder variable
p_tBgFrames(bg).img = mAveragedFrame;
p_tBgFrames(bg).from = mAvgFrames(bg,1);
p_tBgFrames(bg).to = mAvgFrames(bg,2);
end
if exist('hWaitBar'), close(hWaitBar); end
% Concatenate new background frames with the exisiting ones we stored in the beginning of this function
p_tBgFrames = cat(2, p_tBgFrames, tTempFrames);
% Sort background frames in ascending order by 'from' field
[vNewOrder vNewIndxOrd] = sortrows(char(p_tBgFrames.from));
p_tBgFrames = p_tBgFrames(vNewIndxOrd);
% Show all background frames in debug mode
if bDebug
hFig = findobj('Tag', 'SUBTRACT_BACKGROUND_WINDOW');
if isempty(hFig)
hFig = figure;
set(hFig, 'Tag', 'SUBTRACT_BACKGROUND_WINDOW', 'DoubleBuffer', 'on', 'Name', 'WT - SUBTRACT_BACKGROUND_WINDOW', 'numbertitle', 'off')
else, figure(hFig), end
clf
for bg = 1:size(p_tBgFrames,2)
subplot(2,max([3 size(p_tBgFrames,2)]),bg)
imagesc(p_tBgFrames(bg).img); colormap gray;
title(sprintf('BG frame %d-%d', p_tBgFrames(bg).from, p_tBgFrames(bg).to))
end
end
% Finally, subtract the appropriate background frame from the passed frame
% (use input parameter nCurrentFrame to determine which background frame to
% subtract)
mBgFrame = zeros(size(mImgIn));
mImgOut = mImgIn;
if bSubtractAll
cAll = {p_tBgFrames(:).img};
mAll = cat(3, cAll{:,:,:});
mBgFrame = mean(mAll,3);
mBgFrameRe = mBgFrame;
mImgOut = double(mImgIn) - double(mBgFrameRe);
else
for bg = 1:size(p_tBgFrames,2)
% Subtract background frame is there is a such one for the current frame
if (nCurrentFrame >= p_tBgFrames(bg).from) & (nCurrentFrame <= p_tBgFrames(bg).to)
% Check images have same dimensions
if (size(mImgIn,1) == size(p_tBgFrames(bg).img,1)) & (size(mImgIn,2) == size(p_tBgFrames(bg).img,2))
mBgFrame = double(p_tBgFrames(bg).img);
mBgFrameRe = mBgFrame;
mBgFrameN = mBgFrameRe./max(max(mBgFrameRe));
mImgInN = double(mImgIn)./max(max(double(mImgIn)));
mImgOut = mImgInN - mBgFrameN;
else
wt_error('Current frame and its background frame do not have the same dimensions.')
end
end
end
end
% Plot original, background frame and adjusted image
if bDebug
subplot(2,3,4)
imagesc(mImgIn); title('Original')
subplot(2,3,5)
imagesc(mBgFrame); title('Background')
subplot(2,3,6)
imagesc(mImgOut); title('Adjusted')
colormap gray
drawnow
end
return;
|
github
|
HelmchenLabSoftware/OCIA-master
|
wt_adjust_whisker_length.m
|
.m
|
OCIA-master/other/functions_widefield/whisker_tracking/wt_knutsen/wt_adjust_whisker_length.m
| 2,894 |
utf_8
|
390bc5df4dbfa6f89ebf615bca7636e6
|
% WT_ADJUST_WHISKER_LENGTH
% Adjust whisker length to that of first known frame.
%
% Syntax: [vX, vY] = wt_adjust_whisker_length(I,X,Y), where
% I = I'th whisker
% X = vector of X splinepoints
% Y = vector of Y splinepoints
% Output variables:
% X = adjusted X splinepoints
% Y = adjusted Y splinepoints
%
% This function works in conjunction with the WT GUI.
function [vX, vY] = wt_adjust_whisker_length(nChWhisker, vX, vY)
global g_tWT
vXorig = vX;
vYorig = vY;
% Make sure no values are equal on the x axis
while 1
vIndx = find(~diff(vX));
if length(vIndx) == 0, break, end
vX(vIndx+1) = vX(vIndx) + 3;
end
% Length of initially marked whisker
nKnownFrames = find(g_tWT.MovieInfo.SplinePoints(1, 1, :, nChWhisker));
vXinit = g_tWT.MovieInfo.SplinePoints(:, 1, nKnownFrames(1), nChWhisker);
vYinit = g_tWT.MovieInfo.SplinePoints(:, 2, nKnownFrames(1), nChWhisker);
nWhiskerLength = GetWhiskerLength(vXinit, vYinit);
% Length of new whisker
try, nLen = GetWhiskerLength(vX, vY);
catch, wt_error('Error when recalculating whisker length'); end
if (length(vX) == 4) & (vX(end)>0 & vY(end)>0), nLastIndx = 4;
else, nLastIndx = 3; end
if nLen > nWhiskerLength % new whisker is LONGER than original
vXX = min(vX((1:nLastIndx))):max(vX((1:nLastIndx))); % whisker spline in 1st known frame
[vXX, vYY] = wt_spline(vX(1:nLastIndx), vY(1:nLastIndx), vXX);
vCumLen = cumsum(sqrt(diff(vXX).^2 + diff(vYY).^2));
[nDiff, nDiffIndx] = min(abs(vCumLen - nWhiskerLength));
vX(nLastIndx) = vXX(nDiffIndx+1);
vY(nLastIndx) = vYY(nDiffIndx+1);
elseif nLen < nWhiskerLength % new whisker is SHORTER than original
% Increase length of new whisker by 1 pix until its same length as original
while nLen < nWhiskerLength
% Extrapolate Y value at new X position
vY(nLastIndx) = interp1(vX(1:nLastIndx), vY(1:nLastIndx), vX(nLastIndx)+1, 'spline', 'extrap');
vX(nLastIndx) = vX(nLastIndx)+1;
try, nLen = GetWhiskerLength(vX, vY);
catch, wt_error('Error when computing whisker length'), end
end
end
% Sort splinepoint in case 2nd and 3rd swapped places (should be in
% increasing order along X dimension)
vIndx = find(vX & vY);
mC = [vX vY];
mC(vIndx,:) = sortrows(mC(vIndx,:));
vX = mC(:,1);
vY = mC(:,2);
% Make sure no values are equal on the x axis
while 1
vIndx = find(~diff(vX));
if length(vIndx) == 0, break, end
vX(vIndx+1) = vX(vIndx) + 3;
end
return
%%%% GET_WHISKER_LENGTH %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
function nLen = GetWhiskerLength(vX, vY)
% Remove 4th element if present AND zero
vKeepXIndx = find(vX);
vX = vX(vKeepXIndx);
vY = vY(vKeepXIndx);
vXX = min(vX):max(vX); % whisker spline in 1st known frame
[vXX, vYY] = wt_spline(vX, vY, vXX);
nLen = sum(sqrt(diff(vXX).^2 + diff(vYY).^2));
return;
|
github
|
HelmchenLabSoftware/OCIA-master
|
wt_mark_whisker.m
|
.m
|
OCIA-master/other/functions_widefield/whisker_tracking/wt_knutsen/wt_mark_whisker.m
| 9,460 |
utf_8
|
4d40afc1c5ad815e172aff1e9cf8b192
|
function wt_mark_whisker(varargin)
% WT_MARK_WHISKER
% Mark new whisker, or add/remove spline-points that define whiskerpoints.
% Syntax: wt_mark_whisker(OPT), where
% OPT is an optional string that runs one of the following
% subroutines:
% 'new' - mark a new whisker
% 'addpoint' - add splinepoint to existing whisker
% 'removepoint' - remove splinepoint from existing whisker
% 'movebasepoint' - move the whisker base point
% 'setfulllength' - mark the full length of the whisker
% 'setlastframe' - mark the last frame on which to track the
% whisker
%
% The default subroutine is 'new'. For all other subroutines,
% you must provide a second parameter which is the whisker ID/index
% to modify.
if nargin >= 1
sSub = varargin{1};
nW = varargin{2};
else, sSub = 'new'; end
switch sSub
case 'new'
MarkNewWhisker;
case 'addpoint'
AddPoint(nW);
case 'removepoint'
RemovePoint(nW);
case 'setlastframe'
SetLastFrame(nW);
case 'setfulllength'
SetFullLength(nW);
return
case 'movebasepoint'
MoveBasePoint(nW);
end
wt_display_frame % refresh current frame
return;
%%%% MARKNEWWHISKER %%%%%%%%%%%%%%%%%%%%%%%
function MarkNewWhisker
global g_tWT
nFirstFrame = round(get(g_tWT.Handles.hSlider, 'Value'));
% If current frame is before head was tracked, move it to 1st frame with
% head
if ~isempty(g_tWT.MovieInfo.Nose)
vIndx = find(~isnan(g_tWT.MovieInfo.Nose(:,1)));
if nFirstFrame < vIndx(1), nFirstFrame = vIndx(1); end
wt_display_frame(nFirstFrame);
end
axes(g_tWT.FrameAx); hold on
vX = []; vY = [];
hDots = [];
try
for i = 1:3
[vX(i), vY(i)] = ginput(1); % user can hit RETURN
hDots(end+1) = line(vX(i), vY(i));
set(hDots(end), 'color', 'g', 'marker', '.')
end
catch
return % in case the user did not input data but instead hit RETURN
end
delete(hDots)
% Sort points
mCoords = round(sortrows([vX' vY']));
% If this is a two-sided frame, detect which side this whisker belongs to
nCurrentFrame = get(g_tWT.Handles.hSlider, 'Value');
if ~isempty(g_tWT.MovieInfo.EyeNoseAxLen)
if ~isnan(prod(g_tWT.MovieInfo.Nose(nCurrentFrame, :))) % head is known only if nose is known
vAxSize = get(g_tWT.FrameAx, 'XLim');
% Locate side based on x val of first point
if mCoords(1,1) < vAxSize(2)/2
% Left part of frame (right side of rat). Don't change mCoords
nSide = 1;
else
% Right part of frame (left side of rat)
% Change mCoords to absolute coordinates in right frame part
mCoords(:,1) = mCoords(:,1) - vAxSize(2)/2; % only change X
nSide = 2;
end
else, nSide = 1; end
else nSide = 1; end
% Save whisker splinepoints
if isempty(g_tWT.MovieInfo.SplinePoints), nIndx = 1;
else, nIndx = size(g_tWT.MovieInfo.SplinePoints, 4) + 1; end
g_tWT.MovieInfo.SplinePoints(1:3, 1:2, nFirstFrame, nIndx) = mCoords;% ./ g_tWT.MovieInfo.ResizeFactor;
g_tWT.MovieInfo.Angle(nFirstFrame, nIndx) = 0;
g_tWT.MovieInfo.Intersect(nFirstFrame, 1:2, nIndx) = [0 0];
g_tWT.MovieInfo.MidPointConstr(1:2, nIndx) = [0 0]';
g_tWT.MovieInfo.WhiskerSide(nIndx) = nSide; % 0=left, 1=right
g_tWT.MovieInfo.LastFrame(nIndx) = g_tWT.MovieInfo.NumFrames;
% Set whisker identity
wt_set_identity(nIndx);
return;
%%%% ADDPOINT %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
function AddPoint(nW)
global g_tWT
nPtLim = 4; % max num of allowed splinepoints
nCurrFrame = round(get(g_tWT.Handles.hSlider, 'Value'));
mWhisker = g_tWT.MovieInfo.SplinePoints(:,:,nCurrFrame,nW);
if size(mWhisker,1) >= 4
if mWhisker(4,1) ~= 0
hWarnDlg = warndlg(sprintf('The maximum number of allowed points (%d) has already been reached.', nPtLim), 'WT Error');
waitfor(hWarnDlg); return;
else
mWhisker = mWhisker(1:3,:);
end
end
% Get new point and check that its within X bounds of existing whisker
vAxSize = get(g_tWT.FrameAx, 'XLim');
while 1
[nX, nY] = ginput(1); % get position of new object
if g_tWT.MovieInfo.WhiskerSide(nW) == 2
nX = nX - vAxSize(2)/2;
end
if nX <= max(mWhisker(:,1)) & nX >= min(mWhisker(:,1)), break
else
sAns = questdlg('The marked point is outside boundaries of current whisker.', ...
'Error in input', ...
'Try again', 'Cancel', 'Try again' );
if strcmp(sAns, 'Cancel'), return; end
end
end
plot(nX + vAxSize(2)/2, nY, 'r.'); % plot new point
mWhisker = round(sortrows([mWhisker; nX nY]));
if size(g_tWT.MovieInfo.SplinePoints,1) ~= 4
g_tWT.MovieInfo.SplinePoints(4,1:2,:,nW) = 0; % expand all frames with an extra row of values (NaN)
end
g_tWT.MovieInfo.SplinePoints(:,:,nCurrFrame,nW) = mWhisker; % save new point
return;
%%%% REMOVEPOINT %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
function RemovePoint(nW)
global g_tWT
nCurrFrame = get(g_tWT.Handles.hSlider, 'Value');
mWhisker = g_tWT.MovieInfo.SplinePoints(:,:,nCurrFrame,nW);
if size(mWhisker,1) >= 4
if mWhisker(4,1) == 0
hWarnDlg = warndlg('There are no points to delete.', 'WT Error');
waitfor(hWarnDlg);
return;
end
end
[nX, nY] = ginput(1); % get position of new object
vAxSize = get(g_tWT.FrameAx, 'XLim');
if g_tWT.MovieInfo.WhiskerSide(nW) == 2
nX = nX - vAxSize(2)/2;
end
% Find closest point (only 2nd or 3rd)
[y, nIndx] = min(sqrt(abs(mWhisker(2:3,1)-nX).^2 + abs(mWhisker(2:3,2)-nY).^2));
nIndx = nIndx + 1;
% Verify removal of point
sAns = questdlg(sprintf('You have chosen to delete point number %d from the left. Please confirm.', nIndx), ...
'WT Confirm', ...
'OK', 'Cancel', 'Cancel');
if strcmp(sAns, 'Cancel'), return; end
% Remove point
switch nIndx
case 2 % remove 1st midpoint
g_tWT.MovieInfo.SplinePoints(2:3,:,nCurrFrame,nW) = g_tWT.MovieInfo.SplinePoints(3:4,:,nCurrFrame,nW);
g_tWT.MovieInfo.SplinePoints(4,:,nCurrFrame,nW) = 0;
case 3 % remove 2nd midpoint
g_tWT.MovieInfo.SplinePoints(3,:,nCurrFrame,nW) = g_tWT.MovieInfo.SplinePoints(4,:,nCurrFrame,nW);
g_tWT.MovieInfo.SplinePoints(4,:,nCurrFrame,nW) = 0;
end
return;
%%%% SETLASTFRAME %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
function SetLastFrame(nW);
global g_tWT
% default is current frame
sLastFrame = inputdlg('Set last frame to track', 'Set last frame', 1, {num2str(get(g_tWT.Handles.hSlider, 'value'))});
% Change last frame value unless user hit Cancel or eXit
if ~isempty(sLastFrame)
g_tWT.MovieInfo.LastFrame(nW) = str2num(char(sLastFrame));
end
return;
%%%% SETFULLLENGTH %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
function SetFullLength(nW);
global g_tWT
if ~isfield(g_tWT.MovieInfo, 'WhiskerLength')
g_tWT.MovieInfo.WhiskerLength = zeros(1,size(g_tWT.MovieInfo.SplinePoints,4)).*NaN;
elseif length(g_tWT.MovieInfo.WhiskerLength) < size(g_tWT.MovieInfo.SplinePoints,4)
g_tWT.MovieInfo.WhiskerLength(nW) = NaN;
end
sCurrLen = num2str(g_tWT.MovieInfo.WhiskerLength(nW));
sAns = questdlg('How do you want to set the full whisker length?', 'WT', 'Measure','Enter value','Cancel','Measure');
switch sAns
case 'Enter value'
sLen = inputdlg('Enter whisker length in millimeters', 'WT', 1, {sCurrLen});
if isempty(sLen), return, end
nLen = str2num(cell2mat(sLen));
case 'Measure'
% Check that movie is calibrated
if isempty(g_tWT.MovieInfo.CalBarLength) | all(g_tWT.MovieInfo.CalibCoords(:) == 0)
wt_error('You must calibrate before marking the full whisker length. Select Image -> Calibrate... from the menu.')
end
if g_tWT.DisplayMode == 1, wt_toggle_display_mode, end, wt_display_frame % absolute view mode
axes(g_tWT.FrameAx); hold on % get points
vX = []; vY = [];
try
for i = 1:3
[vX(i), vY(i)] = ginput(1);
plot(vX(i), vY(i), 'g.')
end
catch, return, end
mCoords = round(sortrows([vX' vY'])); % sort
vXX = mCoords(1,1):mCoords(end,1);
[vXX, vYY] = wt_spline(mCoords(:,1), mCoords(:,2), vXX); % spline
plot(vXX, vYY, 'w:', 'linewidth', 2) % plot whisker
nLen = sum(sqrt(diff(vXX).^2 + diff(vYY).^2)); % whisker length (pixels)
nLen = nLen / g_tWT.MovieInfo.PixelsPerMM; % length (mm)
msgbox(sprintf('Whisker length is %.1f mm', nLen), 'WT')
case 'Cancel', return
end
g_tWT.MovieInfo.WhiskerLength(nW) = nLen; % length (mm)
g_tWT.MovieInfo.WhiskerLength(find(g_tWT.MovieInfo.WhiskerLength == 0)) = NaN;
return
%%%% MOVEBASEPOINT %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
function MoveBasePoint(nW)
global g_tWT
nCurrentFrame = get(g_tWT.Handles.hSlider, 'Value');
[nX, nY] = ginput(1);
% If this is a two-sided frame, detect which side this whisker belongs to
nCurrentFrame = get(g_tWT.Handles.hSlider, 'Value');
if ~isempty(g_tWT.MovieInfo.EyeNoseAxLen) % if head has been tracked...
if ~isnan(prod(g_tWT.MovieInfo.Nose(nCurrentFrame, :))) % head is known only if nose is known
vAxSize = get(g_tWT.FrameAx, 'XLim');
if nX > vAxSize(2)/2 % Right part of frame (left side of rat)
nX = nX - vAxSize(2)/2; % change X
end
end
end
g_tWT.MovieInfo.SplinePoints(1,1:2,nCurrentFrame,nW) = [round(nX) nY];
wt_display_frame;
return
|
github
|
HelmchenLabSoftware/OCIA-master
|
wt_user_variables.m
|
.m
|
OCIA-master/other/functions_widefield/whisker_tracking/wt_knutsen/wt_user_variables.m
| 2,835 |
utf_8
|
74f02db2f7a53d0fb75ebcb184aaae2d
|
function wt_user_variables(varargin)
% Create and modify user-defined variables
% The purpose of this function is to provide the user with an easy way to
% store experiment variables inside the WT .mat file. These user variables
% can also be variables that are accessed from within scripts.
%
% Note that adding or modifying experiment variables can be performed as a
% batch job.
% Copy user variables from persistent variable instead of GUI/
% This option is used for batch jobs, i.e. copying the variables of one
% movies to all other movies in directory/tree
if ~isempty(varargin)
if strcmp(varargin{1}, 'copyfrommem')
RetrieveUserVariables();
return;
end
end
global g_tWT;
% Check if variables window is already open. If YES, then retrieve and save
% variables, and close window
hFig = findobj('Tag', 'WTUserVariables', 'type', 'figure');
if ~isempty(hFig)
RetrieveUserVariables();
return
end
hFig = figure('closeRequestFcn', 'set(gcbf,''userdata'',''closed'')');
cColumnNames = {'Variable', 'Value', 'Type'};
cColumnFormat = {'char', 'char', {'String','Number'}};
cColumnEditable = [true true true];
cData = repmat({''},200,3);
if isfield(g_tWT.MovieInfo, 'tUserVariables')
for i = 1:length(g_tWT.MovieInfo.tUserVariables)
cData{i, 1} = g_tWT.MovieInfo.tUserVariables(i).sVariable;
cData{i, 2} = g_tWT.MovieInfo.tUserVariables(i).sValue;
cData{i, 3} = g_tWT.MovieInfo.tUserVariables(i).sType;
end
end
set(hFig, 'color', [.2 .2 .2], 'Name', 'WT User Variables', 'NumberTitle', 'off', 'ToolBar', 'none', ...
'menuBar','none', 'Tag', 'WTUserVariables')
hTable = uitable('Units', 'normalized','Position', [0 0 1 1], 'Data', cData, 'ColumnName', ...
cColumnNames, 'ColumnEditable', cColumnEditable, 'ColumnFormat', cColumnFormat, ...
'ColumnWidth', {120, 282, 100}, 'Tag', 'WTUserVariablesTable');
% Create callback to this function when window is closed
set(hFig, 'CloseRequestFcn', 'wt_user_variables')
return
%%%% Retrieve and save user variables
function RetrieveUserVariables
global g_tWT
persistent cData
% Get figure handle
hFig = findobj('Tag', 'WTUserVariables', 'type', 'figure');
% If no window is open, then used persistent variable to fill g_tWT
if ~isempty(hFig)
% Get table handle
hTable = findobj('Tag', 'WTUserVariablesTable', 'type', 'uitable');
cData = get(hTable, 'data'); % modified data from table
end
g_tWT.MovieInfo.tUserVariables = struct([]); % clear variables
for c = 1:size(cData, 1)
if isempty(cData{c,1}) | isempty(cData{c,2}), continue, end
g_tWT.MovieInfo.tUserVariables(end+1).sVariable = cData{c, 1};
g_tWT.MovieInfo.tUserVariables(end).sValue = cData{c, 2};
g_tWT.MovieInfo.tUserVariables(end).sType = cData{c, 3};
end
% Delete user variables window
delete(hFig)
return
|
github
|
HelmchenLabSoftware/OCIA-master
|
wt_select_directory_tree.m
|
.m
|
OCIA-master/other/functions_widefield/whisker_tracking/wt_knutsen/wt_select_directory_tree.m
| 2,153 |
utf_8
|
417e8fdbcd1f4fd60f3f876e7994ed58
|
function wt_select_directory_tree
% WT_SELECT_DIRECTORY_TREE
% Select all movies recursively from all sub-directories below a selected
% top-level directory.
%
% This function prompts the user to select a top-level directory and
% generates a list of all AVI movies, with complete paths, contained in the
% entire directory tree under the selected top-level directory.
%
% The list of retrieved movies can be accessed through the menu item Files
% -> Movies.
%
global g_tWT
% Select top-level directory
if ~isempty(g_tWT.AccessedPaths), sCurrPath = g_tWT.AccessedPaths{1};
else, sCurrPath = '0'; end
sPath = uigetdir(sCurrPath, 'Select top-level directory of selection');
if ~all(sPath), return; end % cancel if no path was selected
% Iterate recursively over all sub-directories and extract paths of AVI
% movies
cSelection = GetFilePaths(sPath, '.avi');
% Display error and abort if no AVIs were found
if isempty(cSelection)
warndlg('No AVI movies were found below the chosen directory', 'No movies found')
return
end
% Reset current selection list
g_tWT.Movies = struct([]);
% Assign new selection to g_tWT
for f = 1:length(cSelection)
g_tWT.Movies(f).filename = wt_check_path(cSelection{f});
end
% Re-initialize GUI
wt_prep_gui;
% Load and display first movie
wt_load_movie(1);
return
% --- Get paths of videos in a directory and its sub-directories
% Recursive search for .bin files from a selected directory
% inputs: sSuffix Find files this file extension (e.g. '.avi')
% sBaseDir Base directory
function cPaths = GetFilePaths(sBaseDir, sSuffix)
cPaths = {};
tDirList = dir(sBaseDir);
for t1 = 3:length(tDirList)
if tDirList(t1).isdir % depth = 1
% recursively call this function
sBaseDirRecurs = wt_check_path([sBaseDir '/' tDirList(t1).name]);
cPaths2 = GetFilePaths(sBaseDirRecurs, sSuffix);
cPaths = {cPaths{:}, cPaths2{:}};
else
% Add .bin files to paths cell
if strcmp(tDirList(t1).name(end-3:end), sSuffix)
sFilename = wt_check_path([sBaseDir '/' tDirList(t1).name]);
cPaths{end+1} = sFilename;
end
end
end
|
github
|
HelmchenLabSoftware/OCIA-master
|
wt_set_last_frame.m
|
.m
|
OCIA-master/other/functions_widefield/whisker_tracking/wt_knutsen/wt_set_last_frame.m
| 1,021 |
utf_8
|
6199a5377c8aeda55264f84ac6b28483
|
%%%% WT_SET_LAST_FRAME %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
function wt_set_last_frame
% Set Last Frame for all Whiskers defined so far
% Must check for Cancel or eXit
%
% Whisker Tracker (WT)
%
% Authors: Per Magne Knutsen, Dori Derdikman
%
% (c) Copyright 2004 Yeda Research and Development Company Ltd.,
% Rehovot, Israel
%
% This software is protected by copyright and patent law. Any unauthorized
% use, reproduction or distribution of this software or any part thereof
% is strictly forbidden.
%
% Citation:
% Knutsen, Derdikman, Ahissar (2004), Tracking whisker and head movements
% of unrestrained, behaving rodents, J. Neurophys, 2004, IN PRESS
%
global g_tWT
% default is current frame
L = inputdlg('Set last frame to track', 'Set last frame', 1, {num2str(get(g_tWT.Handles.hSlider, 'value'))} );
% Change last frame value unless user hit Cancel or eXit
if ~isempty(L)
for nW = 1:size(g_tWT.MovieInfo.SplinePoints, 4)
g_tWT.MovieInfo.LastFrame(nW) = str2num(char(L));
end
end
|
github
|
HelmchenLabSoftware/OCIA-master
|
wt_create_outline.m
|
.m
|
OCIA-master/other/functions_widefield/whisker_tracking/wt_knutsen/wt_create_outline.m
| 5,411 |
utf_8
|
5fca5ab8f2f3db6a7d388de56b54c24c
|
function wt_create_outline(sOption, nOL)
% WT_CREATE_OUTLINE Mark lines that denote various axis in image
% This function allows points, lines, polygons etc. to be labelled for
% later data analysis. WT itself does not use either of these
%
% wt_create_outline('add', OL)
% wt_create_outline('draw', OL)
% wt_create_outline('copy', OL)
% wt_create_outline('paste', OL)
% If OL is NaN, a new object will be created
% wt_create_outline('delete', OL)
% wt_create_outline('name', OL)
% wt_create_outline('hide', OL)
global g_tWT
switch lower(sOption)
case 'add'
set(g_tWT.Handles.hStatusText, 'string', 'LEFT = Add point, MIDDLE = Exit, RIGHT = Undo last');
tOutline = AddOutline;
set(g_tWT.Handles.hStatusText, 'string', '');
if isempty(tOutline.Coords), return, end % return if no coordinates entered
tOutline.Name = {''};
if ~isfield(g_tWT.MovieInfo, 'Outlines')
g_tWT.MovieInfo.Outlines = tOutline;
else
g_tWT.MovieInfo.Outlines(end+1) = tOutline;
end
wt_set_identity(length(g_tWT.MovieInfo.Outlines), 'outline')
wt_display_frame
case 'draw'
DrawOutline(nOL)
case 'copy'
CopyPasteOutline(nOL, 'copy')
case 'paste'
CopyPasteOutline(nOL, 'paste')
wt_display_frame
case 'delete' % delete outline
g_tWT.MovieInfo.Outlines(nOL) = [];
delete(findobj('tag',sprintf('outline-%d', nOL)))
wt_display_frame
case 'deleteall' % delete ALL outline
if isfield(g_tWT.MovieInfo, 'Outlines')
g_tWT.MovieInfo = rmfield(g_tWT.MovieInfo, 'Outlines');
wt_prep_gui
wt_display_frame
end
case 'name' % rename
wt_set_identity(nOL, 'outline')
case 'hide' % hide all outlines
if ~isfield(g_tWT, 'HideOutlines'), g_tWT.HideOutlines = 0; end
g_tWT.HideOutlines = ~g_tWT.HideOutlines;
switch g_tWT.HideOutlines % update user-menu
case 0, sStatus = 'off';
case 1, sStatus = 'on';
end
set(findobj('Label', 'Hide outlines'), 'checked', sStatus);
wt_display_frame
otherwise
return
end
return
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
function DrawOutline(nOL)
global g_tWT
hOL = findobj('Tag', sprintf('outline-%d', nOL));
vX = g_tWT.MovieInfo.Outlines(nOL).Coords(:,1);
vY = g_tWT.MovieInfo.Outlines(nOL).Coords(:,2);
if ~isempty(hOL) % refresh
if g_tWT.HideOutlines % hide outlines
set(hOL, 'XData', vX, 'YData', vY, 'Visible', 'off')
else
set(hOL, 'XData', vX, 'YData', vY, 'Visible', 'on')
end
else % redraw
if ~isfield(g_tWT, 'HideOutlines'), g_tWT.HideOutlines = 0; end
if g_tWT.HideOutlines % hide outlines
hOL = plot(vX, vY, 'wx-', 'Tag', sprintf('outline-%d', nOL), 'Visible', 'off');
else
hOL = plot(vX, vY, 'wx-', 'Tag', sprintf('outline-%d', nOL), 'Visible', 'on');
end
end
hMenu = uicontextmenu;
set(hOL, 'uicontextmenu', hMenu)
uimenu(hMenu, 'Label', 'Set name', 'Callback', [sprintf('wt_create_outline(''name'',%d)', nOL)])
uimenu(hMenu, 'Label', 'Delete', 'Callback', [sprintf('wt_create_outline(''delete'',%d)', nOL)])
uimenu(hMenu, 'Label', 'Copy', 'Callback', [sprintf('wt_create_outline(''copy'',%d)', nOL)])
uimenu(hMenu, 'Label', 'Paste', 'Callback', [sprintf('wt_create_outline(''paste'',%d)', nOL)])
return
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
function CopyPasteOutline(nOL, sAction)
global g_tWT
persistent vCopiedX
persistent vCopiedY
persistent sCopiedName
hOL = findobj('Tag', sprintf('outline-%d', nOL));
switch sAction
case 'copy'
vCopiedX = g_tWT.MovieInfo.Outlines(nOL).Coords(:,1);
vCopiedY = g_tWT.MovieInfo.Outlines(nOL).Coords(:,2);
sCopiedName = g_tWT.MovieInfo.Outlines(nOL).Name;
case 'paste'
if isempty(vCopiedX) | isempty(vCopiedY)
uiwait(warndlg('Nothing to paste'))
return
end
if ~isfield(g_tWT.MovieInfo, 'Outlines')
g_tWT.MovieInfo.Outlines = struct([]);
end
if isnan(nOL) % create new outline
g_tWT.MovieInfo.Outlines(end+1).Coords = [vCopiedX vCopiedY];
g_tWT.MovieInfo.Outlines(end).Name = sCopiedName;
else % copy coordinates into currently selected outline
g_tWT.MovieInfo.Outlines(nOL).Coords = [vCopiedX vCopiedY];
end
end
return
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
function tOutline = AddOutline()
vX = [];
vY = [];
hOutline = plot(0,0,'wx-'); % outline handle
while 1
[nX, nY, nButton] = ginput(1);
switch nButton
case 1 % left ADD POINT
vX(end+1) = nX;
vY(end+1) = nY;
case 3 % middle UNDO LAST POINT
if ~isempty(vX)
vX(end) = [];
vY(end) = [];
end
case 2 % right FINISHED
break;
end
set(hOutline, 'xdata', vX, 'ydata', vY)
end
delete(hOutline)
tOutline.Coords = [vX' vY'];
return
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
|
github
|
HelmchenLabSoftware/OCIA-master
|
wt_copy_paste_whisker.m
|
.m
|
OCIA-master/other/functions_widefield/whisker_tracking/wt_knutsen/wt_copy_paste_whisker.m
| 2,350 |
utf_8
|
1aa4c51e190eed32144a0a9ad9a72997
|
function wt_copy_paste_whisker(sOption, nW)
% Copy/paste a selected whisker to/from clipoard
switch sOption
case 'copy'
CopyPasteWhisker(nW, 'copy');
case 'paste'
CopyPasteWhisker(nW, 'paste');
wt_display_frame;
end
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
function CopyPasteWhisker(nW, sAction)
global g_tWT
persistent sCopiedName
persistent mCopiedCoords
nCurrFrame = g_tWT.CurrentFrameBuffer.Frame;
switch sAction
case 'copy'
% Get current frame
mCopiedCoords = g_tWT.MovieInfo.SplinePoints(:,:,nCurrFrame,nW); % copy current frame only
sCopiedName = cell2mat(g_tWT.MovieInfo.WhiskerIdentity{nW});
if ~isempty(sCopiedName)
wt_set_status(['Whisker ' sCopiedName ' has been copied to the clipboard'])
else
wt_set_status(['Whisker ' sCopiedName 'has been copied to the clipboard'])
end
case 'paste'
if isempty(mCopiedCoords)
wt_set_status('No available whisker in clipboard to paste')
return
end
% New whisker index
if isempty(g_tWT.MovieInfo.SplinePoints)
nNewW = 1;
else
nNewW = size(g_tWT.MovieInfo.SplinePoints, 4) + 1;
end
% Save whisker data
% Note: Copied whisker is copied into current frame
g_tWT.MovieInfo.SplinePoints(:,:,nCurrFrame,nNewW) = mCopiedCoords;
g_tWT.MovieInfo.Angle(1:nCurrFrame, nNewW) = NaN;
g_tWT.MovieInfo.Angle(nCurrFrame, nNewW) = 0;
g_tWT.MovieInfo.Intersect(1:nCurrFrame, 1:2, nNewW) = [NaN NaN];
g_tWT.MovieInfo.Intersect(nCurrFrame, 1:2, nNewW) = [0 0];
g_tWT.MovieInfo.MidPointConstr(1:2, nNewW) = [0 0]';
g_tWT.MovieInfo.WhiskerSide(nNewW) = 1; % 0=left, 1=right
g_tWT.MovieInfo.LastFrame(nNewW) = g_tWT.MovieInfo.NumFrames;
% TODO: Change all zeros to NaNs in SplinePoints!
%vIndx = find(g_tWT.MovieInfo.SplinePoints(:,:,:,nNewW) == 0);
if isempty(sCopiedName)
g_tWT.MovieInfo.WhiskerIdentity{nNewW} = '';
else
g_tWT.MovieInfo.WhiskerIdentity{nNewW} = mat2cell(sCopiedName);
end
wt_set_status('')
end
return
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
|
github
|
HelmchenLabSoftware/OCIA-master
|
checkfilename.m
|
.m
|
OCIA-master/other/functions_widefield/whisker_tracking/wt_knutsen/bin/checkfilename.m
| 510 |
utf_8
|
6739291d3d5ed243836882af670df101
|
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
% Converts between forward and backward slash on Windows and Linux filesystems
function sFilename = CheckFilename(sFilename)
if ispc
sFilename = strrep(sFilename, '/', '\');
sFilename = strrep(sFilename, '\\', '\');
elseif isunix
sFilename = strrep(sFilename, '\', '/');
sFilename = strrep(sFilename, '//', '/');
end
return
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
|
github
|
HelmchenLabSoftware/OCIA-master
|
wt_create_filters.m
|
.m
|
OCIA-master/other/functions_widefield/whisker_tracking/wt_knutsen/bin/wt_create_filters.m
| 690 |
utf_8
|
77a8b948154ca3fc7b9fcc69b7081298
|
%%%% WT_CREATE_FILTERS %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
% create a filter for each angle for checking "whiskeriness"
function filters_vec = wt_create_filters(whisker_width,whisker_length)
flt = zeros(whisker_length);
start_ind = ceil(whisker_length/2)-floor(3*whisker_width/2);
flt(start_ind:start_ind+3*whisker_width-1,:) = ...
[0.5 * ones(whisker_width,whisker_length); ...
-ones(whisker_width,whisker_length); ...
0.5 * ones(whisker_width,whisker_length)] ...
/whisker_width/ whisker_length;
min_ang = -90;
max_ang = 90;
for ang=min_ang:max_ang
filters_vec(:,:,ang-min_ang+1) = imrotate(flt,-ang,'bicubic','crop');
end
|
github
|
HelmchenLabSoftware/OCIA-master
|
ExportToExcel.m
|
.m
|
OCIA-master/other/functions_widefield/whisker_tracking/wt_knutsen/bin/windows/ExportToExcel.m
| 1,230 |
utf_8
|
9a793be148c08ea1554add206bccaf28
|
% ExportToExcel(cHeaders, cData)
% by Naama Rubin
function ExportToExcel(cHeaders, cData)
% Open new instance of Excel
Excel = actxserver('Excel.Application');
set(Excel, 'Visible', 1);
% Create new workbook
Workbooks = Excel.Workbooks;
Workbook = invoke(Workbooks, 'Add');
Sheets = Excel.ActiveWorkBook.Sheets;
% Sheet columns
cCols = {'A','B','C','D','E','F','G','H','I','J','K','L','M','N','O','P','Q','R','S','T','U','V','W','X','Y','Z'};
% Make the 1st sheet active
invoke(get(Sheets, 'Item', 1), 'Activate');
Activesheet = Excel.Activesheet;
% Iterate over cells that contain data
for c = 1:length(cHeaders)
% Insert header
Range = get(Activesheet, 'Range', sprintf('%s1', cCols{c}), sprintf('%s1', cCols{c}));
set(Range, 'Value', cHeaders{c})
% Insert data
nLastRow = length(cData{c});
Range = get(Activesheet, 'Range', sprintf('%s2', cCols{c}), sprintf('%s%d', cCols{c}, nLastRow));
set(Range, 'Value', cData{c})
% Remove NaN's in data
vNaNIndx = find(isnan(cData{c}));
for i = 1:length(vNaNIndx)
Range = get(Activesheet, 'Range', sprintf('%s%d', cCols{c}, vNaNIndx(i)+1), sprintf('%s%d', cCols{c}, vNaNIndx(i)+1));
set(Range, 'Value', '')
end
end
return;
|
github
|
HelmchenLabSoftware/OCIA-master
|
concatanateSegmentsOriginalMovie.m
|
.m
|
OCIA-master/other/functions_widefield/whisker_tracking/concatanate/concatanateSegmentsOriginalMovie.m
| 1,415 |
utf_8
|
9c753d4f1fb2ae25de3fc6958222f7a6
|
function f= concatanateSegments(dirname)
list = dir(dirname);
i=3;
oldExpName='Experiment';
whiskingAll = [];
mkdir(fullfile(dirname,'whiskByTrial'));
count = 0;
for i=3:length(list)
fname = list(i).name;
ind=strfind(fname,'_Whisker_Tracking');
if(~isempty(ind))
expname = fname(1:ind-1);
load(fullfile(dirname,fname));
if (strcmp(oldExpName,expname))
whiskingAll = [whiskingAll; MovieInfo.AvgWhiskerAngle'];
else
if ~isempty(whiskingAll)
count = count+1;
save(fullfile(dirname,'whiskByTrial',[oldExpName 't' num2str(count) '.mat']),'whiskingAll');
whiskingAll = [];
end
whiskingAll = [whiskingAll; MovieInfo.AvgWhiskerAngle'];
end
oldExpName = expname;
end
end
count=count+1;
save(fullfile(dirname,'whiskByTrial',[oldExpName 't' num2str(count) '.mat']),'whiskingAll');
%%
subdirname=fullfile(dirname,'whiskByTrial');
sublist = dir(subdirname);
load(fullfile(subdirname,sublist(3).name));
[nr nc] = size(whiskingAll);
whiskAngle = nan(nr+5,numel(sublist)-2);
for i=3:numel(sublist)
load(fullfile(subdirname,sublist(i).name));
whiskAngle(1:length(whiskingAll),i-2)=whiskingAll;
end
save(fullfile(dirname, 'whiskAngle.mat'),'whiskAngle');
xlswrite('whiskAngle',whiskAngle);
end
|
github
|
HelmchenLabSoftware/OCIA-master
|
concatanateSegments.m
|
.m
|
OCIA-master/other/functions_widefield/whisker_tracking/concatanate/concatanateSegments.m
| 1,415 |
utf_8
|
f8c5c57461919a03ee74e82fcc5004ed
|
function f= concatanateSegments(dirname)
list = dir(dirname);
i=3;
oldExpName='Experiment';
whiskingAll = [];
mkdir(fullfile(dirname,'whiskByTrial'));
count = 0;
for i=3:length(list)
fname = list(i).name;
ind=strfind(fname,'_Whisker_Tracking');
if(~isempty(ind))
expname = fname(1:ind-3);
load(fullfile(dirname,fname));
if (strcmp(oldExpName,expname))
whiskingAll = [whiskingAll; MovieInfo.AvgWhiskerAngle'];
else
if ~isempty(whiskingAll)
count = count+1;
save(fullfile(dirname,'whiskByTrial',[oldExpName 't' num2str(count) '.mat']),'whiskingAll');
whiskingAll = [];
end
whiskingAll = [whiskingAll; MovieInfo.AvgWhiskerAngle'];
end
oldExpName = expname;
end
end
count=count+1;
save(fullfile(dirname,'whiskByTrial',[oldExpName 't' num2str(count) '.mat']),'whiskingAll');
%%
subdirname=fullfile(dirname,'whiskByTrial');
sublist = dir(subdirname);
load(fullfile(subdirname,sublist(3).name));
[nr nc] = size(whiskingAll);
whiskAngle = nan(nr+5,numel(sublist)-2);
for i=3:numel(sublist)
load(fullfile(subdirname,sublist(i).name));
whiskAngle(1:length(whiskingAll),i-2)=whiskingAll;
end
save(fullfile(dirname, 'whiskAngle.mat'),'whiskAngle');
xlswrite('whiskAngle',whiskAngle);
end
|
github
|
HelmchenLabSoftware/OCIA-master
|
makePureTone_new.m
|
.m
|
OCIA-master/other/functions_widefield/Iwen_auditory_functions/makePureTone_new.m
| 1,496 |
utf_8
|
680b0d87131bb0a6a09654fa8797c3c8
|
function s = makePureTone_new(freqs,duration,varargin)
% generate a pure tone
% in1 ... carrier frequency in Hz
% in2 ... duration in s
% in3 ... sampling frequency in Hz {44100}
% in4 ... play tone {0}; 0 or 1
% in5 ... save wav file {[]}; filename of wav file
% out1 ... the sound vector s
% this file written by Henry Luetcke ([email protected])
if nargin > 2
sf = varargin{1};
if isempty(sf)
sf = 44100;
end
else
sf = 44100;
end
if nargin > 3
doPlay = varargin{2};
else
doPlay = 0;
end
if nargin > 4
saveWav = varargin{3};
else
saveWav = [];
end
modFreq = 0; % modulation frequency
modIndex = 1; % modulation index
rampDur = 0.1; % ramp duration (fraction of total duration, max. 0.5)
for i = 1:length(freqs)
% make the sound
s = MakeSound(sf,duration,freqs(i),modFreq,modIndex,rampDur);
if doPlay
sound(s,sf);
end
if ~isempty(saveWav)
wavwrite(s,sf,16,saveWav);
end
end
function s = MakeSound(sf,d,f,mf,mi,rd)
% frequency modulated sound
n = sf * d; % number of samples
c = (1:n) / sf; % carrier data preparation
c = 2 * pi * f * c;
% m = (1:n) / sf; % modulator data preparation
% m = mi * cos(2 * pi * mf * m); % sinusoidal modulation
m = 0;
s = sin(c + m); % frequency modulation
% ramp
rd = d .* rd;
nr = floor(sf * rd);
r = sin(linspace(0, pi/2, nr));
r = [r, ones(1, n - nr * 2), fliplr(r)];
% make ramped sound
s = s .* r;
|
github
|
HelmchenLabSoftware/OCIA-master
|
TDMS_dataToGroupChanStruct_v4.m
|
.m
|
OCIA-master/other/functions_widefield/behavior_functions/import_lick_data/TDMS_dataToGroupChanStruct_v4.m
| 2,718 |
utf_8
|
0a6dab50f4d81124788a530edfe98382
|
function output = TDMS_dataToGroupChanStruct_v4(inputStruct,varargin)
%TDMS_dataToGroupChanStruct_v4
%
% NOTE: This reproduces the data structure for the old lab functionality
% of the function getStructTDM
%
% See Also: TDMS_genvarname2, TDMS_readTDMSFile
REPLACE_STR = '_';
PREPEND_STR = 'p_';
PREPEND_GRP_STRING = 'g_';
PREPEND_CHAN_STRING = 'c_';
ALWAYS_PREPEND = false;
PROP_NAME = 'Props';
propNames = inputStruct.propNames;
propValues = inputStruct.propValues;
groupIndices = inputStruct.groupIndices;
groupNames = inputStruct.groupNames;
chanIndices = inputStruct.chanIndices;
chanNames = inputStruct.chanNames;
rootIndex = inputStruct.rootIndex;
data = inputStruct.data;
groupNames = cellfun(@(x) TDMS_genvarname2(x,REPLACE_STR,PREPEND_GRP_STRING,ALWAYS_PREPEND),groupNames,'UniformOutput',false);
rootPropStruct = propsToStruct(propNames{rootIndex},propValues{rootIndex},REPLACE_STR,PREPEND_STR,ALWAYS_PREPEND);
output = struct(PROP_NAME,rootPropStruct);
for iGroup = 1:length(groupIndices)
curGroupIndex = groupIndices(iGroup);
curChanIndices = chanIndices{iGroup};
curChanNames = chanNames{iGroup};
curChanNames = cellfun(@(x) TDMS_genvarname2(x,REPLACE_STR,PREPEND_CHAN_STRING,ALWAYS_PREPEND),curChanNames,'UniformOutput',false);
groupPropStruct = propsToStruct(propNames{curGroupIndex},propValues{curGroupIndex},REPLACE_STR,PREPEND_STR,ALWAYS_PREPEND);
groupStruct = struct('name',groupNames(iGroup),PROP_NAME,groupPropStruct);
for iChan = 1:length(curChanIndices)
curChanIndex = curChanIndices(iChan);
chanPropStruct = propsToStruct(propNames{curChanIndex},propValues{curChanIndex},REPLACE_STR,PREPEND_STR,ALWAYS_PREPEND);
chanStruct = struct('name',curChanNames{iChan},PROP_NAME,chanPropStruct,...
'data',[]);
chanStruct.data = data{curChanIndex};
%NOTE: I had a case statement in case the data type was a string,
%which would change the interpretation of the struct input
if strcmp(chanStruct.name,'name')
error('The variable "name" for a channel is off limits, need a different conversion wrapper (probably 2)')
end
groupStruct.(TDMS_genvarname2(chanStruct.name,...
REPLACE_STR,PREPEND_STR,ALWAYS_PREPEND)) = chanStruct;
end
output.(TDMS_genvarname2(groupStruct.name,...
REPLACE_STR,PREPEND_STR,ALWAYS_PREPEND)) = groupStruct;
end
end
function propStruct = propsToStruct(names,values,REPLACE_STR,PREPEND_STR,ALWAYS_PREPEND)
propStruct = struct([]);
for iProp = 1:length(names)
propStruct(1).(TDMS_genvarname2(names{iProp},REPLACE_STR,PREPEND_STR,ALWAYS_PREPEND)) = values{iProp};
end
end
|
github
|
HelmchenLabSoftware/OCIA-master
|
TDMS_dataToGroupChanStruct_v3.m
|
.m
|
OCIA-master/other/functions_widefield/behavior_functions/import_lick_data/TDMS_dataToGroupChanStruct_v3.m
| 2,710 |
utf_8
|
1ca966df0513a1925134cd2633570a53
|
function output = TDMS_dataToGroupChanStruct_v3(inputStruct,varargin)
%TDMS_dataToGroupChanStruct_v3
%
% translates objects AND properties to valid field names
%
% Similar to TDMS_dataToGroupChanStruct_v1, but also translates
% properties
%
% output = TDMS_dataToGroupChanStruct_v3(inputStruct)
%
% OPTIONAL INPUTS (property/value pairs)
% ============================================
% REPLACE_STR = default '_', what to replace invalid characters with
% PREPEND_STR = default 'v' (for variable), gets prepended if first
% character is invalid (must be alpha, not numeric or _)
% ALWAYS_PREPEND = default false, if true always prepends the prepend string,
% regardless of whether or not it is needed
%
%
%
% See Also: TDMS_genvarname2
REPLACE_STR = '_';
PREPEND_STR = 'v';
ALWAYS_PREPEND = false;
propNames = inputStruct.propNames;
propValues = inputStruct.propValues;
groupIndices = inputStruct.groupIndices;
groupNames = inputStruct.groupNames;
chanIndices = inputStruct.chanIndices;
chanNames = inputStruct.chanNames;
rootIndex = inputStruct.rootIndex;
data = inputStruct.data;
rootPropStruct = propsToStruct(propNames{rootIndex},propValues{rootIndex},REPLACE_STR,PREPEND_STR,ALWAYS_PREPEND);
output = struct('props',rootPropStruct);
for iGroup = 1:length(groupIndices)
curGroupIndex = groupIndices(iGroup);
curChanIndices = chanIndices{iGroup};
curChanNames = chanNames{iGroup};
groupPropStruct = propsToStruct(propNames{curGroupIndex},propValues{curGroupIndex},REPLACE_STR,PREPEND_STR,ALWAYS_PREPEND);
groupStruct = struct('name',groupNames(iGroup),'props',groupPropStruct);
for iChan = 1:length(curChanIndices)
curChanIndex = curChanIndices(iChan);
chanPropStruct = propsToStruct(propNames{curChanIndex},propValues{curChanIndex},REPLACE_STR,PREPEND_STR,ALWAYS_PREPEND);
chanStruct = struct('name',curChanNames{iChan},'props',chanPropStruct,...
'data',[]);
chanStruct.data = data{curChanIndex};
%NOTE: I had a case statement in case the data type was a string,
%which would change the interpretation of the struct input
groupStruct.(TDMS_genvarname2(chanStruct.name,...
REPLACE_STR,PREPEND_STR,ALWAYS_PREPEND)) = chanStruct;
end
output.(TDMS_genvarname2(groupStruct.name,...
REPLACE_STR,PREPEND_STR,ALWAYS_PREPEND)) = groupStruct;
end
end
function propStruct = propsToStruct(names,values,REPLACE_STR,PREPEND_STR,ALWAYS_PREPEND)
propStruct = struct([]);
for iProp = 1:length(names)
propStruct(1).(TDMS_genvarname2(names{iProp},REPLACE_STR,PREPEND_STR,ALWAYS_PREPEND)) = values{iProp};
end
end
|
github
|
HelmchenLabSoftware/OCIA-master
|
TDMS_preprocessFile.m
|
.m
|
OCIA-master/other/functions_widefield/behavior_functions/import_lick_data/tdmsSubfunctions/TDMS_preprocessFile.m
| 24,202 |
utf_8
|
9027de756f8016d279addde445319f56
|
function metaStruct = TDMS_preprocessFile(fid,tdmsFileName,params)
%TDMS_preprocessFile Populates props and gets segment information
%
% NOTE: This file shouldn't be called directly by the user
%
% metaStruct = TDMS_preprocessFile(fid,tdmsFileName,params)
%
% INPUTS
% =======================================================================
% fid : file id of opened tdms file, may be null if INDEX_DEBUG is true
% tdmsFileName : full path to tdms file OR tdms index file for INDEX_DEBUG
% params : all optional inputs from TDMS_readTDMSFile
%
% OUTPUTS
% =======================================================================
% metaStruct :
% structure with fields:
%
% The following 3 variables are all the same length, and have one index
% for each unique object. Each object may be one of the following types,
% file root, group object, or channel object. Only channel objects may
% have data.
%
% rawDataInfo : (structure array)
% NOTE: This holds the most recent info for an object, and can be
% changed on a per segment basis, segInfo is used to hold
% information that is needed per segement
%
% .lengthOfIndex - length of raw data index (not used)
% .dataType - enumerated dataType (Labview)
% .dimensionData - currently ignored (should be 1d)
% .numberOfValues - # of values to read each time
% .totalSizeBytes - # of bytes per values
% .numberProperties - # of properties defined for the object
% .infoSet - a logical on whether or not this data has
% been set (for error checking)
% .propNames - a cell array for definining property names
% .propValues - cell array for holding property values
%
% numberDataPoints : an array which specifies the # of data points for
% each object (used for preallocation)
% objectNameList : (cell array of strings) names of all objects in the
% TDMS file
%
% Info for each segment ...
%
% segInfo : (struct array)
% .rawPos - position of raw data for that segment
% .kTocNewObjList - flag on whether a new channel list was
% created or not
% .objOrder - array specifying indices of the objects to assign
% data to, order specifies read order, and values
% are indexed
% into the objectNameList & rawDataInfo struct
% .nRawObjects - length of objOrder
% .nSamplesRead - array, # of samples to read for each object
% .isInterleaved - logical, whether that segment uses interleaved
% data or not
% .isBigEndian - logical
% .nChunks - # of times to read data using the parameters
% above before moving onto the next segment
%
% See also: TDMS_processLeadIn, TDMS_getDataSize, TDMS_getPropValue
%PARAMETERS - passed in from TDMS_readTDMSFile
%==========================================================================
UTC_DIFF = params.UTC_DIFF;
MAX_NUM_OBJECTS = params.MAX_NUM_OBJECTS;
MAX_NUM_PROPS = params.MAX_NUM_PROPS;
N_SEGS_GUESS = params.N_SEGS_GUESS;
N_SEGS_INC = params.N_SEGS_INC;
DEBUG = params.DEBUG;
DATE_STR_FORMAT = params.DATE_STR_FORMAT;
UNICODE_FORMAT = params.STRING_ENCODING;
USE_INDEX = params.USE_INDEX;
INIT_CHUNK_SIZE = params.INIT_CHUNK_SIZE;
TDMS_INDEX_EXT = params.TDMS_INDEX_EXT;
MACHINE_FORMAT = params.MACHINE_FORMAT;
STRING_ENCODING = params.STRING_ENCODING;
CURRENT_VERSION = params.CURRENT_VERSION;
INDEX_DEBUG = params.INDEX_DEBUG;
%DONT CHANGE THESE
%==========================================================================
LEAD_IN_LENGTH = 28; %# of bytes of lead in
%FIGURING OUT WHICH FILE TO READ
%==========================================================================
[tdmsPathToFile,tdmsNameOnly] = fileparts(tdmsFileName);
if isempty(params.META_STRUCT)
isIndexFID = false;
if USE_INDEX || INDEX_DEBUG
if INDEX_DEBUG
indexFile = tdmsFileName;
else
indexFile = fullfile(tdmsPathToFile,[tdmsNameOnly TDMS_INDEX_EXT]);
end
if exist(indexFile,'file')
fid = fopen(indexFile,'r',MACHINE_FORMAT,STRING_ENCODING);
isIndexFID = true;
else
%Just use the tdms file, which we have already tested to exist
if INDEX_DEBUG
%NOTE: With INDEX_DEBUG we explicitly passed in the index
%file to read and parse (generally for debugging purposes
%so if it doesn't exist, then we have a problem
error('Specified tdms_index file doesn not exist')
end
end
end
else
%Quits early if meta struct input is valid
%======================================================================
metaStruct = params.META_STRUCT;
if ~isstruct(metaStruct) || ~isfield(metaStruct,'version') || ~isfield(metaStruct,'fileName')
error('The META_STRUCT parameter passed should be a structure with fields "version" and "fileName"')
end
if metaStruct.version ~= CURRENT_VERSION
error('Mismatch in version creation, version of struct %d, please run with latest version: %d')
end
if ~strcmpi(metaStruct.fileName,tdmsNameOnly)
fprintf('Filename from metaStruct: %s\n',metaStruct.fileName);
fprintf('Filename from input: %s\n',tdmsNameOnly);
error('Mismatch in filenames, see printout above')
end
return
end
if isIndexFID
lastLetter = double('h'); %used for .tdms_index files
else
lastLetter = double('m'); %used for .tdms files
end
%INITIALIZE OUTPUTS
%==========================================================================
curNumTotalObjects = 0; %Current # of objects
numberDataPoints = zeros(1,MAX_NUM_OBJECTS);
objectNameList = cell(1,MAX_NUM_OBJECTS); %names of all objects
rawDataInfo = initRawInfoStruct(MAX_NUM_PROPS,MAX_NUM_OBJECTS);
segInfo = initSegStruct(N_SEGS_GUESS);
%==========================================================================
%TEMP VARIABLES
%==========================================================================
objectHasRawData = false(1,MAX_NUM_OBJECTS); %This is needed for adding
%# of data points together
ranOnce = false;
nSegs = 0;
%Get eof & return to start
fseek(fid,0,1);
eofPosition = ftell(fid);
fseek(fid,0,-1);
%START OF READING
%==========================================================================
curPosCounter = 0; %Used to keep track of where in the actual tdms file we
%would be at various points, this is used for parsing verification as well
%as assisting with more complicated reads
while ftell(fid) ~= eofPosition
nSegs = nSegs + 1;
if nSegs > length(segInfo)
segInfo = [segInfo initSegStruct(N_SEGS_INC)]; %#ok<AGROW>
end
if DEBUG
disp('------ START OF DEBUG -------')
fprintf(2,'CURRENT SEGMENT: %d\n',nSegs);
fprintf(2,'Current file position: %d\n',curPosCounter);
end
%LEAD IN HANDLING
%======================================================================
[flags,info] = TDMS_processLeadIn(fid,lastLetter);
curPosCounter = curPosCounter + LEAD_IN_LENGTH + info.segLength;
segInfo(nSegs).rawPos = curPosCounter - info.segLength + info.metaLength;
if ~ranOnce
%NOTE: This might be false if no channels are defined ...
if flags.kTocNewObjList == false
error('the kTocNewObjList was false when first run, this is not expected')
end
ranOnce = true;
end
%======================================================================
%======================================================================
% META INFORMATION PROCESSING
%======================================================================
if flags.hasMetaData
%Get # of changed objects
numNewObjInSeg = fread(fid,1,'uint32');
%Reinitialize order list if new
if flags.kTocNewObjList
curObjListCount = 0;
objOrder = zeros(1,2*numNewObjInSeg);
nValuesRead = zeros(1,2*numNewObjInSeg);
%NOTE: I padded this by doubling the #, we might append extra
%channels in subsequent reads, I currently don't resize this
%...
end
for iNewObject = 1:numNewObjInSeg
%1) GET OBJECT PATH
%-------------------------------
objPathLength = fread(fid,1,'uint32');
temp = fread(fid,objPathLength,'*uint8');
objName = native2unicode(temp,UNICODE_FORMAT)'; %#ok<*N2UNI>
%POPULATE ALL OBJECT LIST
%----------------------------------------
objIndex = find(strcmp(objectNameList(1:curNumTotalObjects),objName),1);
if isempty(objIndex)
curNumTotalObjects = curNumTotalObjects + 1;
if curNumTotalObjects > length(rawDataInfo)
rawDataInfo = [rawDataInfo ...
initRawInfoStruct(MAX_NUM_PROPS,MAX_NUM_OBJECTS)]; %#ok<AGROW>
numberDataPoints = [numberDataPoints zeros(1,MAX_NUM_OBJECTS)]; %#ok<AGROW>
objectNameList = [objectNameList cell(1,MAX_NUM_OBJECTS)]; %#ok<AGROW>
objectHasRawData = [objectHasRawData false(1,MAX_NUM_OBJECTS)]; %#ok<AGROW>
end
objIndex = curNumTotalObjects;
objectNameList{curNumTotalObjects} = objName;
end
%RAW DATA INDEX PROCESSING
%---------------------------------------------
curPos = ftell(fid);
rawDataIndexLength = fread(fid,1,'uint32');
rawDataInfo(objIndex).lengthOfIndex = rawDataIndexLength;
if DEBUG
fprintf(2,'RawDataLength: %d\n',rawDataIndexLength);
fprintf(2,'CurrentPos: %d\n',curPos);
end
switch rawDataIndexLength
case 0 %Same as previous
if rawDataInfo(objIndex).infoSet == false
error('Channel %s set to use previous rawDataIndex but this channel is new',objName)
end
case 2^32-1 %no raw data
rawDataInfo(objIndex).infoSet = true;
objectHasRawData(objIndex) = false;
otherwise
objectHasRawData(objIndex) = true;
rawDataInfo(objIndex).infoSet = true;
%DATA TYPE HANDLING
%------------------------------------------------------
dataType = fread(fid,1,'uint32');
if rawDataInfo(objIndex).infoSet && dataType ~= rawDataInfo(objIndex).dataType && numberDataPoints(objIndex) > 0
error('Raw data type for channel %s has changed from %d to %d',...
objName,rawDataInfo(objIndex).dataType,dataType)
else
rawDataInfo(objIndex).dataType = dataType;
end
%DATA SIZE HANDLING
%-----------------------------------------------------
rawDataInfo(objIndex).dimensionData = fread(fid,1,'uint32');
if rawDataInfo(objIndex).dimensionData ~= 1
error('Code doesn''t yet handle non 1D data')
end
rawDataInfo(objIndex).numberOfValues = fread(fid,1,'uint64');
%RawDaqMX
%------------------------------------------------------
%NOTES:
if dataType == 2^32-1
%JIM CODE IN PROGRESS
rawDataInfo(objIndex).isRawDAQmx = true; %We can
% % % %post process this to convert from bits to an
% % % %actual value
% % %
% % % %FORMAT:
% % % %1) -
% % % daqMXVersion = rawDataIndexLength;
% % % if ~ismember(daqMXVersion,[4713 4714])
% % % error('Unexpected version: %d',daqMXVersion)
% % % end
% % %
% % %
% % % %2) Let's get the remaining # of bytes
% % % %This seems to be 32 ...
% % %
% % % % % wtf = fread(fid,8,'uint32');
% % % % % disp(wtf)
% % % %4713
% % % %13000012
% % % %15000018
% % % %? -> 8th indicates data type? OR -> bytes per sample
% % %
% % % %4714
% % % %1 0 0 0 256 256 512
% % %
% % % %3) Update datetype - where the heck is it?
% % % %rawDataInfo(objIndex).dataType = dataType;
else %Non RawDAQmx type
if rawDataInfo(objIndex).dataType == 32
%If string, size is specified by an additional field
rawDataInfo(objIndex).totalSizeBytes = fread(fid,1,'uint64');
else
rawDataInfo(objIndex).totalSizeBytes = ...
rawDataInfo(objIndex).numberOfValues*TDMS_getDataSize(dataType);
end
%Another chance to check correct reading
if curPos + rawDataIndexLength ~= ftell(fid)
error(['Raw Data Index length was incorrect: %d stated vs %d observed,' ...
'likely indicates bad code or a bad tdms file'],rawDataIndexLength,ftell(fid) - curPos)
end
end
if DEBUG
fprintf(2,'nSegs: %d\n',nSegs);
fprintf(2,'objName: %s\n',objName);
end
end
%--------------------------------------------------------------
%POPULATE ORDER TO RETRIEVE RAW DATA
%--------------------------------------------------------------
if objectHasRawData(objIndex)
appendToList = false;
if flags.kTocNewObjList
appendToList = true;
else %Only append if not currently specified
I_objOrder = find(objOrder(1:curObjListCount) == objIndex,1);
if isempty(I_objOrder)
appendToList = true;
else
nValuesRead(I_objOrder) = rawDataInfo(objIndex).numberOfValues;
end
end
%NOTE: No overflow code in place yet, however we do
%initialize with twice the # of objects specified to be
%in a segement when a new list is created, new segments
%might add more objects to the list
if appendToList
curObjListCount = curObjListCount + 1;
objOrder(curObjListCount) = objIndex;
nValuesRead(curObjListCount) = rawDataInfo(objIndex).numberOfValues;
end
end
%PROPERTY HANDLING
%--------------------------------------------------------------
numberProperties = fread(fid,1,'uint32');
%Below is the # of props already assigned to that channel
nPropsChan = rawDataInfo(objIndex).numberProperties;
curProps = rawDataInfo(objIndex).propNames;
for iProp = 1:numberProperties
propNameLength = fread(fid,1,'uint32');
temp = fread(fid,propNameLength,'*uint8');
propName = native2unicode(temp,UNICODE_FORMAT)';
propDataType = fread(fid,1,'uint32');
propIndex = find(strcmp(curProps(1:nPropsChan),propName),1);
if isempty(propIndex)
%Updates needed for new properties
nPropsChan = nPropsChan + 1;
propIndex = nPropsChan;
curProps{propIndex} = propName;
rawDataInfo(objIndex).propNames{propIndex} = propName;
end
%Update value
propValue = TDMS_getPropValue(fid,propDataType,UTC_DIFF,DATE_STR_FORMAT);
rawDataInfo(objIndex).propValues{propIndex} = propValue;
end
rawDataInfo(objIndex).numberProperties = nPropsChan;
if DEBUG
fprintf(2,'end of index position: %d\n',ftell(fid));
end
end
end
%======================================================================
% END OF META DATA PROCESSING
%RAW DATA SAMPLE COUNTING
%======================================================================
segInfo(nSegs).kTocNewObjList = flags.kTocNewObjList;
byteSizeRaw = info.segLength - info.metaLength;
if ~flags.hasRawData || byteSizeRaw == 0
segInfo(nSegs).nChunks = 0;
else
segInfo(nSegs).objOrder = objOrder(1:curObjListCount);
segInfo(nSegs).nRawObjects = curObjListCount;
segInfo(nSegs).nSamplesRead = nValuesRead(1:curObjListCount);
segInfo(nSegs).isInterleaved = flags.isInterleaved;
segInfo(nSegs).isBigEndian = flags.isBigEndian;
%# OF CHUNK PROCESSING
%------------------------------------------------------------------
totalBytesPerChunk = sum([rawDataInfo(objOrder(1:curObjListCount)).totalSizeBytes]);
nChunks = byteSizeRaw/totalBytesPerChunk;
%Some error checking
%------------------------------------------
if DEBUG
fprintf(2,'nChunks: %d\n',nChunks);
fprintf(2,'nSamplesRead: %s\n',mat2str(nValuesRead(1:curObjListCount)));
fprintf(2,'totalBytesPerChunk: %d\n',totalBytesPerChunk);
fprintf(2,'byteSizeRaw: %d\n',byteSizeRaw);
end
if nChunks ~= floor(nChunks)
error(['The remaining data doesn''t split evently into' ...
' chunks, estimated # of chunks: %d'],nChunks)
end
chunkByteOffset = 0;
%Increment the number of data points
for iObject = 1:curObjListCount
curIndex = objOrder(iObject);
%This allows us to grow these values if we haven't sufficiently preallocated
if rawDataInfo(curIndex).chunkIndex + nChunks > rawDataInfo(curIndex).chunkLength
rawDataInfo(curIndex).dataMatrix = [rawDataInfo(curIndex).dataMatrix; zeros(INIT_CHUNK_SIZE,3)];
rawDataInfo(curIndex).chunkLength = rawDataInfo(curIndex).chunkLength + INIT_CHUNK_SIZE;
end
%DataMatrix:
%==============================================================
%This information is used for reading parts of an object during
%a single read instead of the entire object
%Column 1, file position
indices = (rawDataInfo(curIndex).chunkIndex+1):(rawDataInfo(curIndex).chunkIndex+nChunks);
rawDataInfo(curIndex).dataMatrix(indices,1) = ...
segInfo(nSegs).rawPos + chunkByteOffset + (0:totalBytesPerChunk:(nChunks-1)*totalBytesPerChunk);
%Column 2, first sample at that position
rawDataInfo(curIndex).dataMatrix(indices,2) = ...
numberDataPoints(curIndex) + (0:rawDataInfo(curIndex).numberOfValues:(nChunks-1)*rawDataInfo(curIndex).numberOfValues) + 1;
%Column 3, segment number
rawDataInfo(curIndex).dataMatrix(indices,3) = nSegs;
chunkByteOffset = chunkByteOffset + rawDataInfo(curIndex).totalSizeBytes;
numberDataPoints(curIndex) = numberDataPoints(curIndex) + rawDataInfo(curIndex).numberOfValues*nChunks;
rawDataInfo(curIndex).chunkIndex = rawDataInfo(curIndex).chunkIndex+nChunks;
end
%nChunksAll = nChunksAll + nChunks;
segInfo(nSegs).nChunks = nChunks;
%This needs to be handled in some manner for RawDaqMx
if ~isIndexFID
fseek(fid,byteSizeRaw,'cof');
end
end
%Addition for raw data (needs to be fixed)
%In general, the tdms_index requires skipping some meta data
%I think this is only needed for raw data (I need to flush this out
%better as it will cause an error when reading index files for regular
%tdms files)
% if isIndexFID
% fseek(fid,segInfo(nSegs).rawPos,'bof');
% end
end
%Trim output:
%==========================================================================
rawDataInfo = rawDataInfo(1:curNumTotalObjects);
for iObject = 1:length(rawDataInfo)
nProps = rawDataInfo(iObject).numberProperties;
rawDataInfo(iObject).propNames = rawDataInfo(iObject).propNames(1:nProps);
rawDataInfo(iObject).propValues = rawDataInfo(iObject).propValues(1:nProps);
%Add extra value for later processing
if rawDataInfo(iObject).chunkIndex ~= 0
rawDataInfo(iObject).chunkIndex = rawDataInfo(iObject).chunkIndex + 1;
rawDataInfo(iObject).dataMatrix(rawDataInfo(iObject).chunkIndex,2) = numberDataPoints(iObject) + 1;
end
end
numberDataPoints = numberDataPoints(1:curNumTotalObjects);
objectNameList = objectNameList(1:curNumTotalObjects);
segInfo = segInfo(1:nSegs);
metaStruct = struct(...
'numberDataPoints', numberDataPoints,...
'objectNameList', {objectNameList},...
'segInfo', segInfo,...
'rawDataInfo', rawDataInfo,...
'fileName', tdmsNameOnly,...
'version', CURRENT_VERSION);
if isIndexFID
%If using the index file to parse meta, close it
fclose(fid);
end
end
function segStruct = initSegStruct(nSegs)
%initSegStruct
%
% segStruct = initSegStruct(nSegs)
%
segStruct = struct(...
'rawPos',repmat({0},[1 nSegs]),...
'kTocNewObjList',0,...
'objOrder',[],...
'nRawObjects',0,...
'nSamplesRead',[],...
'isInterleaved',false,...
'isBigEndian',false,...
'nChunks',false);
end
function rawInfoStruct = initRawInfoStruct(MAX_NUM_PROPS,MAX_NUM_OBJECTS)
rawInfoStruct = struct( ...
'isRawDAQmx', false, ...
'lengthOfIndex', 0,...
'dataType', 0,...
'dimensionData', 0,...
'numberOfValues', 0,...
'totalSizeBytes', 0,... %Only valid for strings
'numberProperties', 0,...
'chunkIndex', 0,...
... %Could initialize to zero, this would save space
... %with non-raw data objects
'chunkLength', 0,...
... %SEE ALSO: chunk loop above for resizing
'dataMatrix', zeros(0,3),...
...%Position #
...%1st Sample #
...%Seg #
'infoSet', false, ...
'propNames', repmat({cell(1,MAX_NUM_PROPS)},1,MAX_NUM_OBJECTS),...
'propValues', repmat({cell(1,MAX_NUM_PROPS)},1,MAX_NUM_OBJECTS));
end
|
github
|
HelmchenLabSoftware/OCIA-master
|
hanning.m
|
.m
|
OCIA-master/other/functions_slovin/spectogram_functions/hanning.m
| 292 |
utf_8
|
56fe015f155b73f7eb537f7a3093ead2
|
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 myprintf(verbose, varargin)
if strcmpi(verbose, 'on')
fprintf(varargin{:});
end;
|
github
|
HelmchenLabSoftware/OCIA-master
|
mtrainer_GUI_export.m
|
.m
|
OCIA-master/behavior/mtrainer_GUI_export.m
| 57,797 |
utf_8
|
bb7ef417782c2fbef69065eee4adb42f
|
function varargout = mtrainer_GUI_export(varargin)
% TODO:
% - stopping the experiment: trial no 100 ? plot ? set buttons to stop ?
% - reward anyway system
% - forbid disconnecting HW or changing mouseID while experiment is running
% - lickThresh calibrator with setter
% - online lick ploting
% - online performance
% - logging into GUI window
% - config setter
% Begin initialization code - DO NOT EDIT
gui_Singleton = 1;
gui_State = struct('gui_Name', mfilename, ...
'gui_Singleton', gui_Singleton, ...
'gui_OpeningFcn', @mtrainer_GUI_export_OpeningFcn, ...
'gui_OutputFcn', @mtrainer_GUI_export_OutputFcn, ...
'gui_LayoutFcn', @mtrainer_GUI_export_LayoutFcn, ...
'gui_Callback', []);
if nargin && ischar(varargin{1});
gui_State.gui_Callback = str2func(varargin{1});
end
if nargout;
[varargout{1:nargout}] = gui_mainfcn(gui_State, varargin{:});
else
gui_mainfcn(gui_State, varargin{:});
end
% End initialization code - DO NOT EDIT
% --- Executes just before mtrainer_GUI_export is made visible.
function mtrainer_GUI_export_OpeningFcn(hObject, eventdata, handles, varargin)
% This function has no output args, see OutputFcn.
% hObject handle to figure
% eventdata reserved - to be defined in a future version of MATLAB
% handles structure with handles and user data (see GUIDATA)
% varargin command line arguments to mtrainer_GUI_export (see VARARGIN)
% Choose default command line output for mtrainer_GUI_export
handles.output = hObject;
% Update handles structure
guidata(hObject, handles);
initialize_gui(hObject, handles, false);
set(hObject, 'DeleteFcn', @onWindowClose);
set(hObject, 'Position', [100 100 800 620]);
% --- Outputs from this function are returned to the command line.
function varargout = mtrainer_GUI_export_OutputFcn(hObject, eventdata, handles) %#ok<*INUSL>
% varargout cell array for returning output args (see VARARGOUT);
% hObject handle to figure
% eventdata reserved - to be defined in a future version of MATLAB
% handles structure with handles and user data (see GUIDATA)
% Get default command line output from handles structure
varargout{1} = handles.output;
% --------------------------------------------------------------------
function initialize_gui(fig_handle, handles, isreset) %#ok<*INUSD>
% If the metricdata field is present and the start flag is false, it means
% we are we are just re-initializing a GUI by calling it from the cmd line
% while it is up. So, bail out as we dont want to start the data.
initMain(handles);
updateGUI();
% --- Executes on button press in connectHW.
function connectHW_Callback(hObject, eventdata, handles)
% hObject handle to connectHWButton_Callback (see GCBO)
% eventdata reserved - to be defined in a future version of MATLAB
% handles structure with handles and user data (see GUIDATA)
global main;
if isfield(main.hw, 'connected') && main.hw.connected;
disconnectHW();
else
connectHW();
end
updateGUI();
% --- Executes on button press in start.
function start_Callback(hObject, eventdata, handles)
% hObject handle to start (see GCBO)
% eventdata reserved - to be defined in a future version of MATLAB
% handles structure with handles and user data (see GUIDATA)
global main;
if main.isRunning;
warning('mtrainerGUI:CannotStartAlreadyRunning', ...
'Cannot start because experiment is already running and not paused.');
updateGUI();
return;
else
startExperiment();
end
updateGUI();
try
mainLoop();
catch e;
closeDiaryAndSaveOutput();
throw(e);
end;
% --- Executes on button press in pause.
function pause_Callback(hObject, eventdata, handles)
% hObject handle to pause (see GCBO)
% eventdata reserved - to be defined in a future version of MATLAB
% handles structure with handles and user data (see GUIDATA)
global main;
if main.isRunning;
if main.isPaused;
main.isPaused = false;
else
main.isPaused = true;
end
else
warning('mtrainerGUI:CannotPauseNotRunning', ...
'Cannot pause because experiment is not running.');
end
updateGUI();
% --- Executes on button press in stop.
function stop_Callback(hObject, eventdata, handles) %#ok<*DEFNU>
% hObject handle to stop (see GCBO)
% eventdata reserved - to be defined in a future version of MATLAB
% handles structure with handles and user data (see GUIDATA)
global main;
if main.isRunning;
main.isRunning = false;
closeDiaryAndSaveOutput();
else
warning('mtrainerGUI:CannotStopNotRunning', 'Cannot stop because experiment is not running.');
end
updateGUI();
% --- Executes on button press in reward.
function reward_Callback(hObject, eventdata, handles)
% hObject handle to reward (see GCBO)
% eventdata reserved - to be defined in a future version of MATLAB
% handles structure with handles and user data (see GUIDATA)
global main;
giveReward(main.rewardDur, 0);
% --- Executes on slider movement.
function rewardDurSetter_Callback(hObject, eventdata, handles)
% hObject handle to rewardDurSetter (see GCBO)
% eventdata reserved - to be defined in a future version of MATLAB
% handles structure with handles and user data (see GUIDATA)
% Hints: get(hObject,'Value') returns position of slider
% get(hObject,'Min') and get(hObject,'Max') to determine range of slider
global main;
main.rewardDur = get(hObject,'Value');
set(handles.rewardDur, 'String', sprintf('%04.2f', main.rewardDur));
% --- Executes on slider movement.
function lickThreshSetter_Callback(hObject, eventdata, handles)
% hObject handle to lickThreshSetter (see GCBO)
% eventdata reserved - to be defined in a future version of MATLAB
% handles structure with handles and user data (see GUIDATA)
% Hints: get(hObject,'Value') returns position of slider
% get(hObject,'Min') and get(hObject,'Max') to determine range of slider
global main;
main.lickThresh = get(hObject,'Value');
set(handles.lickThresh, 'String', sprintf('%04.2f', main.lickThresh));
% --- Executes when selected cell(s) is changed in config.
function config_CellSelectionCallback(hObject, eventdata, handles)
% hObject handle to config (see GCBO)
% eventdata structure with the following fields (see UITABLE)
% Indices: row and column indices of the cell(s) currently selecteds
% handles structure with handles and user data (see GUIDATA)
global main;
o('#config_CellSelectionCallback: selection changed: row %d, col %d.', eventdata.Indices, 3, main.dbgLvl);
row = eventdata.Indices(1);
configCell = get(main.handles.config, 'Data');
main.mouseId = configCell{row, 1};
main.taskType = configCell{row, 2};
main.phase = configCell{row, 3};
main.configLoaded = false;
o('#config_CellSelectionCallback: mouseId: %s, taskType: %s, phase: %s.', ...
main.mouseId, main.taskType, main.phase, 3, main.dbgLvl);
updateGUI();
% --- Executes on button press in loadConfig.
function loadConfig_Callback(hObject, eventdata, handles)
% hObject handle to loadConfig (see GCBO)
% eventdata reserved - to be defined in a future version of MATLAB
% handles structure with handles and user data (see GUIDATA)
loadConfig();
%% #initMain
function initMain(handles)
global main;
main = struct();
main.dbgLvl = 3;
main.debugMode = 0;
main.basePath = 'P:/programming/Work/PhD/matlab/behavior/mtrainer/';
% main.basePath = 'D:/Users/BaL/programming/Work/PhD/matlab/behavior/mtrainer/';
configsPath = sprintf('%sconfigs.mat', main.basePath);
if ~exist(configsPath, 'file');
error('mtrainerGUI:initMain:ConfigsFileNotFound', ...
'Cannot find the configs at "%s" (file not found).', configsPath);
end;
configsMat = load(configsPath);
main.configs = configsMat.configs;
[~, computerName] = system('hostname');
roomMatch = regexp(computerName, '^HIFOWS(?<room>H\d+)\-\d+\s+$', 'names');
if main.debugMode;
warning('mtrainer_GUI:initMain:DebugMode', 'Debug mode is ON.');
roomMatch = struct('room', 'H30');
o('#initMain: debug mode => room tag enforced to: "%s".', roomMatch.room, 1, main.dbgLvl);
end;
if isempty(roomMatch);
error('mtrainerGUI:initMain:HardwareLoad:NoRoomTagFound', ...
'Cannot load hardware because there''s no room tag in the computer''s name.');
elseif ~isfield(main.configs.hardware, roomMatch.room);
error('mtrainerGUI:initMain:HardwareLoad:UnknownRoom', ...
'Cannot load hardware because room "%s" is unknown.', roomMatch.room);
end;
main.hw = main.configs.hardware.(roomMatch.room);
main.hw.connected = false;
main.updateRate = 0.1; % 100ms update rate
main.isRunning = false;
main.isPaused = false;
main.isClosed = false;
main.configLoaded = false;
main.iTrial = 0;
main.rewardDur = str2double(get(handles.rewardDur,'String'));
main.handles = handles;
stateData = get(main.handles.state, 'Data');
stateData(:, 1) = getTrialInfo(0);
stateData(:, 2) = getTrialInfo(0);
stateData(:, 3) = getTrialInfo(0);
set(main.handles.state, 'Data', stateData);
set(main.handles.config, 'Data', main.configs.animals);
main.mouseId = '';
o('Mouse trainer v1.0 initiated.', 1, main.dbgLvl);
function onWindowClose(src, eventData)
global main;
main.isClosed = true;
%% #connectHW
function connectHW()
global main;
o('Connecting hardware ...', 1, main.dbgLvl);
set(main.handles.connectHW, 'BackgroundColor', 'yellow');
if ~main.debugMode;
main.hw.lickSensor = daq.createSession(main.hw.adaptorID);
main.hw.lickSensor.Rate = main.hw.analogIn_SampleRate;
main.hw.lickSensor.addAnalogInputChannel(main.hw.analogIn_Device, main.hw.analogIn_Channel, 'Voltage');
main.hw.lickSensor.Channels(1).InputType = main.hw.analogIn_InputType;
main.hw.lickSensor.Channels(1).Range = main.hw.analogIn_Range;
main.hw.lickSensor.IsNotifyWhenDataAvailableExceedsAuto = true;
main.hw.lickSensorListener = main.hw.lickSensor.addlistener('DataAvailable', ...
@(src, event) recordAndStop(src, event));
main.hw.lickSensor.IsContinuous = true;
main.hw.lickSensor.prepare();
else
o(' "Connecting" fake analog input.', 1, main.dbgLvl);
main.hw.lickSensor = struct();
main.hw.lickSensorListener = struct();
main.hw.lickSensor.stop = 1;
main.hw.lickSensor.startBackground = 1;
% main.hw.lickSensor.IsRunning = @()(round(rand + 0.4));
% main.hw.lickSensor.IsRunning = @()(round(rand - 0.4));
main.hw.lickSensor.IsRunning = 1;
pause(1);
end;
o(' Analog input (lick sensor and listener): OK.', 1, main.dbgLvl);
if ~main.debugMode;
main.hw.valveControl = daq.createSession(main.hw.adaptorID);
main.hw.valveControl.addDigitalChannel(main.hw.digitalOut_Device, main.hw.digitalOut_PortLine, 'OutputOnly');
main.hw.valveControl.outputSingleScan(0); % make sure valve is closed
else
o(' "Connecting" fake digital output.', 1, main.dbgLvl);
main.hw.valveControl = struct();
pause(1);
end;
o(' Digital output (valve control): OK.', 1, main.dbgLvl);
main.hw.connected = true;
o('Hardware connected.', 1, main.dbgLvl);
%% #disconnectHW
function disconnectHW()
global main;
o('Disconnecting hardware ...', 1, main.dbgLvl);
% analog input
if ~main.debugMode;
if isfield(main.hw, 'lickSensorListener');
main.hw = rmfield(main.hw, 'lickSensorListener');
end;
if isfield(main.hw, 'lickSensor');
main.hw.lickSensor.stop();
main.hw = rmfield(main.hw, 'lickSensor');
end;
if isfield(main.hw, 'valveControl');
% main.hw.valveControl.stop();
main.hw = rmfield(main.hw, 'valveControl');
end;
daqreset;
end;
main.hw.connected = false;
o('Hardware disconnected.', 1, main.dbgLvl);
%% #giveReward
function giveReward(rewDur, rewDelay)
global main;
if main.hw.connected && isfield(main.hw, 'valveControl');
if ~main.debugMode;
t_rewardStart = tic;
% wait until for start delay
while toc(t_rewardStart) < rewDelay; end;
t_rewardStart = tic;
% open digital out
% main.hw.valveControl.outputSingleScan(0);
main.hw.valveControl.outputSingleScan(1);
% wait until for open duration
while toc(t_rewardStart) < rewDur; end;
% close digital out
% main.hw.valveControl.outputSingleScan(1);
main.hw.valveControl.outputSingleScan(0);
end;
o('Rewarding for %.2f sec with a delay of %.2f.', rewDur, rewDelay, 3, main.dbgLvl);
else
warning('mtrainerGUI:NoRewardHardwareDisconnected', 'Cannot give reward because hardware is disconnected.');
end
%% #updateGUI
function updateGUI()
global main;
if main.isClosed; return; end;
stateData = get(main.handles.state, 'Data');
handles = main.handles;
if main.hw.connected;
set(handles.connectHW, 'BackgroundColor', 'green');
set(handles.connectHW, 'Value', 1);
else
set(handles.connectHW, 'BackgroundColor', 'red');
set(handles.connectHW, 'Value', 0);
end;
if main.isRunning;
set(handles.start, 'Value', 1);
set(handles.start, 'BackgroundColor', 'green');
if main.isPaused;
set(handles.pause, 'Value', 1);
set(handles.pause, 'BackgroundColor', [1 1 0]);
else
set(handles.pause, 'Value', 0);
set(handles.pause, 'BackgroundColor', 'green');
end;
if isfield(main, 'lickData');
axes(handles.lickSensorAxes);
data = abs(main.lickData);
nSamples = numel(data);
t = (1 : nSamples) / main.hw.analogIn_SampleRate;
plot(t, data);
line([0, t(end)], [main.lickThresh, main.lickThresh], 'Color', 'r');
ylim([0, 1]);
end;
% stateData(:, 1) = stateData(:, 2);
stateData(:, 1) = getTrialInfo(main.iTrial - 1);
stateData(:, 2) = getTrialInfo(main.iTrial);
if main.iTrial < main.config.training.nTrials;
stateData(:, 3) = getTrialInfo(main.iTrial + 1);
else
stateData(:, 3) = getTrialInfo(0);
end;
else
axes(handles.lickSensorAxes);
plot(0, 0);
set(handles.start, 'Value', 0);
set(handles.start, 'BackgroundColor', 'red');
set(handles.pause, 'Value', 0);
set(handles.pause, 'BackgroundColor', 'red');
if main.configLoaded && main.iTrial == 0;
stateData(:, 3) = getTrialInfo(1);
else
stateData(:, 3) = getTrialInfo(0);
end;
end;
set(main.handles.state, 'Data', stateData);
set(main.handles.configLoaded, 'Value', logical(main.configLoaded));
%% #getTrialInfo
function trialInfo = getTrialInfo(iTrial)
global main;
if iTrial;
freq = sprintf('%4.2f', main.config.tone.freqs(main.stims(iTrial)) / 1000);
if isfield(main.config.tone, 'oddProba') && main.config.tone.oddProba > 0; % oddball discrimination
isTarget = double(main.stims(iTrial) ~= main.odds(iTrial) && main.config.tone.goStim);
else % frequency discrimination
isTarget = double(main.stims(iTrial) == main.config.tone.goStim);
end;
if isfield(main, 'resps') && ~isnan(main.resps(iTrial));
resp = main.resps(iTrial);
respTime = main.respTimes(iTrial);
if isnan(respTime); respTime = '-'; end;
corr = double((isTarget && resp) || (~isTarget && ~resp));
ITL = main.nInTriLick(iTrial);
else
resp = '-';
respTime = '-';
corr = '-';
ITL = '-';
end;
trialInfo = {iTrial, freq, isTarget, resp, respTime, corr, ITL};
else
trialInfo = {'-', '-', '-', '-', '-', '-', '-'};
end;
%% #loadConfig
function loadConfig()
global main;
o('Loading configuration ...', 2, main.dbgLvl);
if isempty(main.mouseId);
warning('loadConfig:NoMouseIdSelected', 'Cannot load config because no mouseId is selected.');
return;
end;
% main.doEmptyWater = 0;
% main.doEmptyWater = 1;
% if > 0, sets the number of seconds to wait before a new run of mtrainer
% main.automode = 5;
main.iTrial = 0;
main.lickThresh = 0.14;
% main.lickThresh = NaN;
main.config = main.configs.behavior.(main.taskType).(main.phase);
%% Setup - stimuli and trials
o(' loadConfig#: setup stimuli and trials... ', 3, main.dbgLvl);
% set up stimulus vector
stims = [];
for iFreq = 1 : numel(main.config.tone.freqs);
stimForFreq = repmat(iFreq, 1, ...
round(main.config.tone.stimProba(iFreq) * main.config.training.nTrials));
stims = [stims, stimForFreq]; %#ok<AGROW>
end
% stim vector should not be randomly permuted
stims = stims(randperm(numel(stims)));
stims = stims(1 : main.config.training.nTrials);
clear stim;
switch(main.taskType);
case {'freqDiscr', 'oddDiscr'};
% set up oddball vector by altering stims with a certain probability
odds = stims;
oddPos = zeros(size(odds));
uniqueStims = unique(stims);
isOdd = rand(1, numel(stims)) < main.config.tone.oddProba;
uniqueOddPos = main.config.tone.nTones - 1 : main.config.tone.nTones; % last 2 tones can be odd
for iStim = 1 : numel(isOdd);
if isOdd(iStim);
otherStims = uniqueStims(uniqueStims ~= stims(iStim));
otherStims = otherStims(randperm(numel(otherStims)));
mixedOddPos = uniqueOddPos(randperm(numel(uniqueOddPos)));
odds(iStim) = otherStims(1);
oddPos(iStim) = mixedOddPos(1);
end;
end;
% set up tone array
main.toneArray = MakePureMultiToneOddballArray(main.config.tone.freqs, stims, odds, oddPos, ...
main.config.tone.nTones, main.config.tone.stimDur, main.config.tone.ISI, ...
main.config.tone.samplingFreq);
case 'cotDiscr';
odds = zeros(size(stims));
oddPos = zeros(size(stims));
isOdd = zeros(size(stims));
atten = 0.5;
main.toneArray = MakeCloudOfTonesSound(main.config.tone.uniqueFreqs, main.config.tone.freqIndexes, ...
main.config.tone.cloudDispersion, stims, main.config.tone.toneDur, main.config.tone.toneISI, ...
main.config.tone.stimDur, atten, main.config.tone.samplingFreq, 0, 0);
end;
main.stims = stims;
main.odds = odds;
main.oddPos = oddPos;
main.isOdd = isOdd;
main.configLoaded = true;
updateGUI();
o(' loadConfig#: setup stimuli and trials done. ', 2, main.dbgLvl);
o('Loading configuration done.', 2, main.dbgLvl);
%% #startExperiment
function startExperiment()
global main;
if ~main.configLoaded;
warning('startExperiment:configNotLoaded', 'Cannot start experiment because config is not loaded.');
return;
end;
if isempty(main.mouseId);
warning('startExperiment:NoMouseId', 'Cannot start experiment because there is no mouseId.');
return;
end;
if ~main.hw.connected;
warning('startExperiment:HardwareDisconnected', ...
'Cannot start experiment because hardware is disconnected.');
return;
end;
o('startExperiment#: initializing experiment ... ', 2, main.dbgLvl);
main.isPaused = false;
main.isRunning = true;
main.iTrial = 1;
main.saveTime = datestr(now(), 'yyyy_mm_dd__HH_MM_SS');
% saveFolder = sprintf('D:/Balazs/2013/mtrainerTests/%s/', ...
% saveFolder = sprintf('C:/Users/laurenczy.HIFO/Documents/LocalData/2013/mtrainerTests/%s/', ...
saveFolder = sprintf('C:/Users/laurenczy/mtrainerTests/%s/', main.mouseId);
% saveFolder = sprintf('D:/Users/BaL/PhD/mtrainerTests/%s/', main.mouseId);
main.savePath = sprintf('%s%s__%s', saveFolder, main.mouseId, main.saveTime);
mkdir(saveFolder);
logfile = sprintf('%s_log.txt', main.savePath);
main.logDateFormat = 'yyyy-mm-dd HH:MM:SS.FFF';
% % create an 'onCleanup' function to handle interruptions by CTRL+C
% c = onCleanup(@()closeDiaryAndSaveOutput(main.savePath, main.hw.lickSensorListener, ...
% main.hw.lickSensor, main.hw.valveControl));
o(' startExperiment#: logFile initialized. Starting diary...', 2, main.dbgLvl);
diary(logfile);
%% Start experiment
o('Experiment start: %s\n\n', datestr(now(), main.logDateFormat), 1, main.dbgLvl);
%% Setup - saving settings
global recordedValues;
recordedValues = 0;
o('config: %s phase %s (%dF%dT)', main.taskType, main.phase, numel(main.config.tone.freqs), ...
main.config.tone.nTones, 0, main.dbgLvl);
o('animal: %s', main.mouseId, 0, main.dbgLvl);
o('savePath: %s', main.savePath, 0, main.dbgLvl);
o('lickThresh: %1.2f, ISI: %1.2f', main.lickThresh, main.config.tone.ISI, 1, main.dbgLvl);
o('rewardCollectionTime: %1.2f, InTriLickTimerDur: %1.2f', main.config.training.rewCollTime, ...
main.config.training.InTriLickTimerDur, 1, main.dbgLvl);
nTrials = main.config.training.nTrials;
main.trialStartDelays = zeros(1, nTrials);
main.trialStartTimes = zeros(1, nTrials);
main.trialEndTimes = zeros(1, nTrials);
main.respTimes = nan(1, nTrials);
main.nInTriLick = nan(1, nTrials);
main.resps = nan(1, nTrials);
main.respDelays = nan(1, nTrials);
% for each trial: 1 = correct detect, 2 = correct reject, 3 = false alarm, 4 = miss, 5 = early
main.respTypes = nan(1, nTrials);
main.expStartTime = tic;
main.isPunish = 0;
%% #mainLoop
function mainLoop()
global main;
displayedPause = 0;
while main.isRunning;
o('mainLoop#: iTrial = %d.', main.iTrial, 4, main.dbgLvl);
if ~main.isPaused;
if displayedPause; o(' --- RESUMED --- ', 1, main.dbgLvl); displayedPause = 0; end;
o('mainLoop#: running trial %d.', main.iTrial, 3, main.dbgLvl);
runTrial();
if main.isRunning;
o('Trial %d: pause ended, updating trial number.', main.iTrial, 2, main.dbgLvl);
if main.iTrial == main.config.training.nTrials;
main.isRunning = false;
%% End experiment
o('\nExperiment end: %s', datestr(now(), main.logDateFormat), 1, main.dbgLvl);
main.expTotDurTime = toc(main.expStartTime);
o('Total time: %02.0f:%02.0f', ...
main.expTotDurTime / 60, mod(main.expTotDurTime, 60), main.dbgLvl);
mtrainerAnalyser_performance(main.respTypes, 2, main.savePath, main.nInTriLick);
closeDiaryAndSaveOutput();
else
main.iTrial = main.iTrial + 1;
o('Trial %d: updated trial number: %d.', main.iTrial - 1, main.iTrial, 2, main.dbgLvl);
end;
else
o('Trial %d: not running anymore, no update of trial number.', main.iTrial, 2, main.dbgLvl);
end;
o('mainLoop#: running trial %d done.', main.iTrial, 3, main.dbgLvl);
updateGUI();
else
if ~displayedPause; o(' --- PAUSED --- ', 1, main.dbgLvl); displayedPause = 1; end;
o('mainLoop#: waiting for %f sec (trial %d).', main.updateRate, main.iTrial, 3, main.dbgLvl);
pause(main.updateRate);
end;
end;
%% #runTrial
function runTrial()
global main recordedValues;
nTrials = main.config.training.nTrials;
iTrial = main.iTrial;
% listen for response
main.hw.lickSensor.startBackground();
pause(0.01)
interTrialLickCount = 0;
main.trialStartTimes(iTrial) = tic;
% introduce a random delay for starting the tone
main.trialStartDelays(iTrial) = main.config.training.startDelay + ...
(rand(1) - 0.5) * 2 * main.config.training.startDelayRand;
% add punishement time-out if needed
if main.isPunish;
main.trialStartDelays(iTrial) = main.trialStartDelays(iTrial) + main.config.training.timeoutPunish;
end;
%% Experiment - initial wait
while toc(uint64(main.trialStartTimes(iTrial))) < main.trialStartDelays(iTrial);
% fprintf('CheckingA: main.hw.lickSensor.IsRunning()? %d\n', main.hw.lickSensor.IsRunning());
% check if experiment is paused/stopped
if ~main.isRunning; return; end;
% while main.isPaused; pause(main.updateRate); end;
% if ~main.isRunning; return; end;
% check if no lick has been done
if ~main.hw.lickSensor.IsRunning(); % if not running anymore, it means a licking has been done
remainingTime = main.trialStartDelays(iTrial) - toc(uint64(main.trialStartTimes(iTrial)));
if interTrialLickCount > 0;
fprintf('|%.1f', remainingTime);
else
fprintf(' inter-trial licking: |%.1f', remainingTime);
end;
% reset the starting delay to main.config.training.InTriLickTimerDur
main.trialStartTimes(iTrial) = tic;
if main.isPunish;
main.trialStartDelays(iTrial) = max(main.config.training.InTriLickTimerDur, remainingTime);
else
main.trialStartDelays(iTrial) = main.config.training.InTriLickTimerDur;
end;
interTrialLickCount = interTrialLickCount + 1;
pause(1);
% restart the listening
main.hw.lickSensor.startBackground();
pause(0.1);
% fprintf('CheckingB: main.hw.lickSensor.IsRunning()? %d\n', main.hw.lickSensor.IsRunning());
end
% avoid full-speed looping
pause(0.01);
end;
if interTrialLickCount;
fprintf('|: %d inter-trial lick(s).\n', interTrialLickCount);
end
main.nInTriLick(iTrial) = interTrialLickCount;
resp = 0;
main.isPunish = 0;
% check if experiment is paused/stopped
if ~main.isRunning; return; end;
% while main.isPaused; pause(main.updateRate); end;
% if ~main.isRunning; return; end;
t_trialStart = tic;
fprintf('Trial %03d/%03d - %s ... ', iTrial, nTrials, datestr(now(), main.logDateFormat));
%% Experiment - play sound
if main.hw.lickSensor.IsRunning();
soundToPlay = main.toneArray{iTrial};
player = audioplayer(soundToPlay, main.config.tone.samplingFreq);
player.play;
else
fprintf('early (already licking, lick sensor: min/mean/max: %.2f/%.2f/%.2f).\n', recordedValues);
main.isPunish = 1;
main.respTypes(iTrial) = 5;
% analyse every 10 trials
if ~rem(iTrial, 10) && iTrial ~= nTrials;
mtrainerAnalyser_performance(main.respTypes, 0);
end;
return;
end
breakOut = 0;
%% Experiment - wait for response
while toc(t_trialStart) < main.config.training.trialDur;
% check if experiment is paused/stopped
if ~main.isRunning; return; end;
% while main.isPaused; pause(main.updateRate); end;
% if ~main.isRunning; return; end;
if main.hw.lickSensor.IsRunning()
% no response detected
else
% seconds since trial start
respTime = toc(t_trialStart);
main.respTimes(iTrial) = respTime;
% response should be 'minRespTime' after the end of the tone!
totStimDur = (main.config.tone.stimDur + main.config.tone.ISI) * main.config.tone.nTones - main.config.tone.ISI;
limitRespTime = totStimDur + main.config.training.minRespTime;
% limitRespTime = main.config.training.minRespTime;
main.respDelays(iTrial) = limitRespTime - respTime;
% early response, count as kind of false alarm
if respTime < limitRespTime;
% fprintf('early (lick sensor: min/mean/max: %.2f/%.2f/%.2f).\n', recordedValues);
fprintf('early (response time: %.4f, limit response time: %.4f, diff: %.5f).\n', ...
respTime, limitRespTime, limitRespTime - respTime);
main.isPunish = 1;
main.respTypes(iTrial) = 5;
breakOut = 1;
break;
else
% fprintf('Lick at %s\n', datestr(clock, main.logDateFormat))
resp = 1;
end;
break; % break out of while loop
end;
pause(0.02); % necessary to allow time for data collection
end;
if breakOut;
main.trialEndTimes(iTrial) = toc(uint64(main.trialStartTimes(iTrial)));
% analyse every 10 trials
if ~rem(iTrial, 10) && iTrial ~= nTrials;
mtrainerAnalyser_performance(main.respTypes, 0);
end;
return; % continue for loop
end;
if main.hw.lickSensor.IsRunning();
main.hw.lickSensor.stop();
end;
% check if experiment is paused/stopped
if ~main.isRunning; return; end;
% while main.isPaused; pause(main.updateRate); end;
% if ~main.isRunning; return; end;
%% Experiment - analyse response
main.resps(iTrial) = resp;
isOddTrial = main.stims(iTrial) ~= main.odds(iTrial);
if isfield(main.config.tone, 'oddProba') && main.config.tone.oddProba > 0; % oddball discrimination
isTargetStim = isOddTrial && main.config.tone.goStim;
else % frequency discrimination
isTargetStim = main.stims(iTrial) == main.config.tone.goStim;
end;
if resp == 1 && isTargetStim;
% correct response
% fprintf('correct detection (lick sensor: min/mean/max: %.2f/%.2f/%.2f).\n', recordedValues);
fprintf('correct detection (response time: %.4f, limit response time: %.4f, diff: %.5f).\n', ...
respTime, limitRespTime, limitRespTime - respTime);
main.respTypes(iTrial) = 1;
% give reward
giveReward(main.config.training.rewDur, main.config.training.rewDelay);
% wait to collect the reward
pause(main.config.training.rewCollTime);
elseif resp == 1 && ~isTargetStim;
% false alarm
% fprintf('false alarm (lick sensor: min/mean/max: %.2f/%.2f/%.2f).\n', recordedValues);
fprintf('false alarm (response time: %.4f, limit response time: %.4f, diff: %.5f).\n', ...
respTime, limitRespTime, limitRespTime - respTime);
main.respTypes(iTrial) = 3;
% punish time-out
main.isPunish = 1;
elseif resp == 0 && isTargetStim;
fprintf('miss.\n');
main.respTypes(iTrial) = 4;
% punish time-out
main.isPunish = 1;
elseif resp == 0 && ~isTargetStim;
fprintf('correct rejection.\n');
main.respTypes(iTrial) = 2;
% go to next trial
end
main.trialEndTimes(iTrial) = toc(uint64(main.trialStartTimes(iTrial)));
% analyse every 10 trials
if ~rem(iTrial, 10) && iTrial ~= nTrials;
mtrainerAnalyser_performance(main.respTypes, 0);
end;
%% #recordAndStop
function recordAndStop(src, event)
global main recordedValues;
[recordedValues, main.lickData] = stopWhenExceedThreshold(src, event, main.lickThresh);
updateGUI();
%% #closeDiaryAndSaveOutput
function closeDiaryAndSaveOutput()
global main;
o('\nClosing diary... ', 2, main.dbgLvl);
diary off;
o('Closing diary done.', 1, main.dbgLvl);
out = main;
try out.hw = rmfield(out.hw, 'toneArray'); catch e; end; %#ok<NASGU>
try out.hw = rmfield(out.hw, 'lickSensorListener'); catch e; end; %#ok<NASGU>
try out.hw = rmfield(out.hw, 'lickSensor'); catch e; end; %#ok<NASGU>
try out.hw = rmfield(out.hw, 'valveControl'); catch e; end; %#ok<NASGU>
try out.hw = rmfield(out.hw, 'lickData'); catch e; end; %#ok<NASGU>
if exist('out', 'var');
matFileName = sprintf('%s_out.mat', main.savePath);
o('Saving output as %s... ', matFileName, 2, main.dbgLvl);
save(matFileName, 'out');
o('Saving output done.', matFileName, 1, main.dbgLvl);
else
o('/!\\ Output not saved !', 1, main.dbgLvl);
end;
% disconnectHW();
% --- Creates and returns a handle to the GUI figure.
function h1 = mtrainer_GUI_export_LayoutFcn(policy)
% policy - create a new figure or use a singleton. 'new' or 'reuse'.
persistent hsingleton;
if strcmpi(policy, 'reuse') & ishandle(hsingleton)
h1 = hsingleton;
return;
end
load mtrainer_GUI_export.mat
appdata = [];
appdata.GUIDEOptions = struct(...
'active_h', [], ...
'taginfo', struct(...
'figure', 2, ...
'pushbutton', 15, ...
'text', 24, ...
'edit', 8, ...
'frame', 4, ...
'radiobutton', 22, ...
'uipanel', 15, ...
'slider', 5, ...
'popupmenu', 4, ...
'listbox', 3, ...
'togglebutton', 3, ...
'checkbox', 4, ...
'uitable', 4, ...
'axes', 2), ...
'override', 1, ...
'release', 13, ...
'resize', 'none', ...
'accessibility', 'callback', ...
'mfile', 1, ...
'callbacks', 1, ...
'singleton', 1, ...
'syscolorfig', 1, ...
'blocking', 0, ...
'lastSavedFile', 'P:\programming\Work\PhD\matlab\behavior\mtrainer_GUI_export.m', ...
'lastFilename', 'P:\programming\Work\PhD\matlab\behavior\mtrainer\mtrainer_GUI.fig');
appdata.lastValidTag = 'figure1';
appdata.GUIDELayoutEditor = [];
appdata.initTags = struct(...
'handle', [], ...
'tag', 'figure1');
h1 = figure(...
'PaperUnits',get(0,'defaultfigurePaperUnits'),...
'Color',[0.941176470588235 0.941176470588235 0.941176470588235],...
'Colormap',[0 0 0.5625;0 0 0.625;0 0 0.6875;0 0 0.75;0 0 0.8125;0 0 0.875;0 0 0.9375;0 0 1;0 0.0625 1;0 0.125 1;0 0.1875 1;0 0.25 1;0 0.3125 1;0 0.375 1;0 0.4375 1;0 0.5 1;0 0.5625 1;0 0.625 1;0 0.6875 1;0 0.75 1;0 0.8125 1;0 0.875 1;0 0.9375 1;0 1 1;0.0625 1 1;0.125 1 0.9375;0.1875 1 0.875;0.25 1 0.8125;0.3125 1 0.75;0.375 1 0.6875;0.4375 1 0.625;0.5 1 0.5625;0.5625 1 0.5;0.625 1 0.4375;0.6875 1 0.375;0.75 1 0.3125;0.8125 1 0.25;0.875 1 0.1875;0.9375 1 0.125;1 1 0.0625;1 1 0;1 0.9375 0;1 0.875 0;1 0.8125 0;1 0.75 0;1 0.6875 0;1 0.625 0;1 0.5625 0;1 0.5 0;1 0.4375 0;1 0.375 0;1 0.3125 0;1 0.25 0;1 0.1875 0;1 0.125 0;1 0.0625 0;1 0 0;0.9375 0 0;0.875 0 0;0.8125 0 0;0.75 0 0;0.6875 0 0;0.625 0 0;0.5625 0 0],...
'DockControls','off',...
'IntegerHandle','off',...
'InvertHardcopy',get(0,'defaultfigureInvertHardcopy'),...
'MenuBar','none',...
'Name','mtrainer_GUI',...
'NumberTitle','off',...
'PaperPosition',get(0,'defaultfigurePaperPosition'),...
'PaperSize',get(0,'defaultfigurePaperSize'),...
'PaperType',get(0,'defaultfigurePaperType'),...
'Position',[544 0 801 625],...
'Resize','off',...
'HandleVisibility','callback',...
'UserData',[],...
'Tag','figure1',...
'Visible','on',...
'CreateFcn', {@local_CreateFcn, blanks(0), appdata} );
appdata = [];
appdata.lastValidTag = 'hwPanel';
h2 = uipanel(...
'Parent',h1,...
'Units','characters',...
'Title','Hardware',...
'Tag','hwPanel',...
'Clipping','on',...
'Position',[1.8 28.6923076923077 24.2 18.5384615384615],...
'CreateFcn', {@local_CreateFcn, blanks(0), appdata} );
appdata = [];
appdata.lastValidTag = 'connectHW';
h3 = uicontrol(...
'Parent',h2,...
'Units','characters',...
'BackgroundColor',[1 0 0],...
'Callback',@(hObject,eventdata)mtrainer_GUI_export('connectHW_Callback',hObject,eventdata,guidata(hObject)),...
'Position',[1.8 15.3846153846154 20 1.76923076923077],...
'String','CONNECT HW',...
'Style','togglebutton',...
'Tag','connectHW',...
'CreateFcn', {@local_CreateFcn, blanks(0), appdata} );
appdata = [];
appdata.lastValidTag = 'reward';
h4 = uicontrol(...
'Parent',h2,...
'Units','characters',...
'Callback',@(hObject,eventdata)mtrainer_GUI_export('reward_Callback',hObject,eventdata,guidata(hObject)),...
'CData',[],...
'ListboxTop',0,...
'Position',[1.8 13.0769230769231 20.2 1.76923076923077],...
'String','REWARD',...
'UserData',[],...
'Tag','reward',...
'CreateFcn', {@local_CreateFcn, blanks(0), appdata} );
appdata = [];
appdata.lastValidTag = 'rewardDurLabel';
h5 = uicontrol(...
'Parent',h2,...
'Units','characters',...
'HorizontalAlignment','left',...
'Position',[1.8 10 17.2 2.46153846153846],...
'String',{ 'reward dur.'; '[sec]' },...
'Style','text',...
'Tag','rewardDurLabel',...
'CreateFcn', {@local_CreateFcn, blanks(0), appdata} );
appdata = [];
appdata.lastValidTag = 'rewardDur';
h6 = uicontrol(...
'Parent',h2,...
'Units','characters',...
'FontSize',10,...
'Position',[13.8 10.3076923076923 8.2 1.61538461538462],...
'String','0.3',...
'Style','text',...
'Tag','rewardDur',...
'CreateFcn', {@local_CreateFcn, blanks(0), appdata} );
appdata = [];
appdata.lastValidTag = 'rewardDurSetter';
h7 = uicontrol(...
'Parent',h2,...
'Units','characters',...
'BackgroundColor',[0.9 0.9 0.9],...
'Callback',@(hObject,eventdata)mtrainer_GUI_export('rewardDurSetter_Callback',hObject,eventdata,guidata(hObject)),...
'Max',20,...
'Min',0.01,...
'Position',[1.6 8.38461538461538 20.2 1.61538461538462],...
'String',{ 'Slider' },...
'Style','slider',...
'SliderStep',[0.01 0],...
'Value',0.3,...
'Tag','rewardDurSetter',...
'CreateFcn', {@local_CreateFcn, blanks(0), appdata} );
appdata = [];
appdata.lastValidTag = 'lickThreshLabel';
h8 = uicontrol(...
'Parent',h2,...
'Units','characters',...
'HorizontalAlignment','left',...
'Position',[2 5.46153846153846 17.2 2.46153846153846],...
'String',{ 'lick threshold'; '[sec]' },...
'Style','text',...
'Tag','lickThreshLabel',...
'CreateFcn', {@local_CreateFcn, blanks(0), appdata} );
appdata = [];
appdata.lastValidTag = 'lickThresh';
h9 = uicontrol(...
'Parent',h2,...
'Units','characters',...
'FontSize',10,...
'Position',[14 5.76923076923077 8.2 1.61538461538462],...
'String','0.14',...
'Style','text',...
'Tag','lickThresh',...
'CreateFcn', {@local_CreateFcn, blanks(0), appdata} );
appdata = [];
appdata.lastValidTag = 'lickThreshSetter';
h10 = uicontrol(...
'Parent',h2,...
'Units','characters',...
'BackgroundColor',[0.9 0.9 0.9],...
'Callback',@(hObject,eventdata)mtrainer_GUI_export('lickThreshSetter_Callback',hObject,eventdata,guidata(hObject)),...
'Max',0.5,...
'Min',0.01,...
'Position',[1.8 3.84615384615385 20.2 1.61538461538462],...
'String',{ 'Slider' },...
'Style','slider',...
'SliderStep',[0.01 0],...
'Value',0.3,...
'Tag','lickThreshSetter',...
'CreateFcn', {@local_CreateFcn, blanks(0), appdata} );
appdata = [];
appdata.lastValidTag = 'expControlPanel';
h11 = uipanel(...
'Parent',h1,...
'Units','characters',...
'Title','Experiment control',...
'Tag','expControlPanel',...
'Clipping','on',...
'Position',[26.6 43.3076923076923 56.4 3.92307692307692],...
'CreateFcn', {@local_CreateFcn, blanks(0), appdata} );
appdata = [];
appdata.lastValidTag = 'stop';
h12 = uicontrol(...
'Parent',h11,...
'Units','characters',...
'Callback',@(hObject,eventdata)mtrainer_GUI_export('stop_Callback',hObject,eventdata,guidata(hObject)),...
'CData',[],...
'ListboxTop',0,...
'Position',[38 0.538461538461539 16.4 1.76923076923077],...
'String','STOP',...
'UserData',[],...
'Tag','stop',...
'CreateFcn', {@local_CreateFcn, blanks(0), appdata} );
appdata = [];
appdata.lastValidTag = 'start';
h13 = uicontrol(...
'Parent',h11,...
'Units','characters',...
'Callback',@(hObject,eventdata)mtrainer_GUI_export('start_Callback',hObject,eventdata,guidata(hObject)),...
'CData',[],...
'ListboxTop',0,...
'Position',[1.8 0.538461538461539 16.2 1.76923076923077],...
'String','START',...
'Style','togglebutton',...
'HitTest','off',...
'UserData',[],...
'Tag','start',...
'CreateFcn', {@local_CreateFcn, blanks(0), appdata} );
appdata = [];
appdata.lastValidTag = 'pause';
h14 = uicontrol(...
'Parent',h11,...
'Units','characters',...
'Callback',@(hObject,eventdata)mtrainer_GUI_export('pause_Callback',hObject,eventdata,guidata(hObject)),...
'CData',[],...
'ListboxTop',0,...
'Position',[19.8 0.538461538461539 16.2 1.76923076923077],...
'String','PAUSE',...
'Style','togglebutton',...
'UserData',[],...
'Tag','pause',...
'CreateFcn', {@local_CreateFcn, blanks(0), appdata} );
appdata = [];
appdata.lastValidTag = 'currStatePanel';
h15 = uipanel(...
'Parent',h1,...
'Units','characters',...
'Title','Current state',...
'Tag','currStatePanel',...
'Clipping','on',...
'Position',[27 27.9230769230769 55 14.6923076923077],...
'CreateFcn', {@local_CreateFcn, blanks(0), appdata} );
appdata = [];
appdata.lastValidTag = 'state';
appdata.PropertyMetaData = { { 'DataPropertyDimension' 'DataPropertyConditionedDimension' 'DataPropertySource' 'BackgroundColorPropertyDimension' 'ColumnNameTyped' 'RowNameTyped' } { [4 2] [7 3] 'DataDefault' [2 3] { 'prev' 'curr' 'next' } { 'iTrial' 'freq' 'targ?' 'resp?' 'respTime' 'corr?' 'ITL' } } };
h16 = uitable(...
'Parent',h15,...
'Units','characters',...
'BackgroundColor',[1 1 1;0.96078431372549 0.96078431372549 0.96078431372549],...
'ColumnFormat',{ 'numeric' 'numeric' 'numeric' },...
'ColumnEditable',mat{1},...
'ColumnName',{ 'prev'; 'curr'; 'next' },...
'ColumnWidth',{ 53 53 53 },...
'Data',{ [] [] []; [] [] []; [] [] []; [] [] []; [] [] []; [] [] []; [] [] [] },...
'FontSize',7,...
'Position',[1.8 0.692307692307692 50.4 12.4615384615385],...
'RowName',{ 'iTrial'; 'freq'; 'targ?'; 'resp?'; 'respTime'; 'corr?'; 'ITL' },...
'UserData',[],...
'Tag','state',...
'CreateFcn', {@local_CreateFcn, blanks(0), appdata} );
appdata = [];
appdata.lastValidTag = 'configPanel';
h17 = uipanel(...
'Parent',h1,...
'Units','characters',...
'Title','Config',...
'Tag','configPanel',...
'Clipping','on',...
'Position',[83.8 14.0769230769231 74.2 33.1538461538462],...
'CreateFcn', {@local_CreateFcn, blanks(0), appdata} );
appdata = [];
appdata.lastValidTag = 'config';
appdata.PropertyMetaData = { { 'DataPropertyDimension' 'DataPropertyConditionedDimension' 'DataPropertySource' 'BackgroundColorPropertyDimension' 'ColumnNameTyped' 'RowNameTyped' } { [4 2] [4 3] 'DataDefault' [2 3] { 'mouseId' 'taskType' 'phase' } { blanks(0) blanks(0) blanks(0) blanks(0) } } };
h18 = uitable(...
'Parent',h17,...
'Units','characters',...
'ColumnFormat',{ [] [] [] },...
'ColumnEditable',mat{2},...
'ColumnName',{ 'mouseId'; 'taskType'; 'phase' },...
'ColumnWidth',{ 85 100 50 },...
'Data',{ blanks(0) blanks(0) blanks(0); blanks(0) blanks(0) blanks(0); blanks(0) blanks(0) blanks(0); blanks(0) blanks(0) blanks(0) },...
'Position',[1.4 17.6153846153846 48.6 13.9230769230769],...
'RowName',blanks(0),...
'CellSelectionCallback',@(hObject,eventdata)mtrainer_GUI_export('config_CellSelectionCallback',hObject,eventdata,guidata(hObject)),...
'UserData',[],...
'Tag','config',...
'CreateFcn', {@local_CreateFcn, blanks(0), appdata} );
appdata = [];
appdata.lastValidTag = 'loadConfig';
h19 = uicontrol(...
'Parent',h17,...
'Units','characters',...
'Callback',@(hObject,eventdata)mtrainer_GUI_export('loadConfig_Callback',hObject,eventdata,guidata(hObject)),...
'CData',[],...
'ListboxTop',0,...
'Position',[51.8 29.7692307692308 16.4 1.76923076923077],...
'String','LOAD',...
'UserData',[],...
'Tag','loadConfig',...
'CreateFcn', {@local_CreateFcn, blanks(0), appdata} );
appdata = [];
appdata.lastValidTag = 'configLoaded';
h20 = uicontrol(...
'Parent',h17,...
'Units','characters',...
'Enable','inactive',...
'Position',[51.8 27.4615384615385 21.2 1.76923076923077],...
'String','Config loaded ?',...
'Style','checkbox',...
'SelectionHighlight','off',...
'Tag','configLoaded',...
'CreateFcn', {@local_CreateFcn, blanks(0), appdata} );
appdata = [];
appdata.lastValidTag = 'lickSensorAxes';
h21 = axes(...
'Parent',h1,...
'Units','characters',...
'Position',[5.8 14.8461538461538 74.2 12.4615384615385],...
'CameraPosition',[0.5 0.5 9.16025403784439],...
'CameraPositionMode',get(0,'defaultaxesCameraPositionMode'),...
'Color',get(0,'defaultaxesColor'),...
'ColorOrder',get(0,'defaultaxesColorOrder'),...
'LooseInset',[23.218 6.19384615384616 16.967 4.22307692307692],...
'XColor',get(0,'defaultaxesXColor'),...
'YColor',get(0,'defaultaxesYColor'),...
'ZColor',get(0,'defaultaxesZColor'),...
'Tag','lickSensorAxes',...
'CreateFcn', {@local_CreateFcn, blanks(0), appdata} );
h22 = get(h21,'title');
set(h22,...
'Parent',h21,...
'Units','data',...
'FontUnits','points',...
'BackgroundColor','none',...
'Color',[0 0 0],...
'DisplayName',blanks(0),...
'EdgeColor','none',...
'EraseMode','normal',...
'DVIMode','auto',...
'FontAngle','normal',...
'FontName','Helvetica',...
'FontSize',10,...
'FontWeight','normal',...
'HorizontalAlignment','center',...
'LineStyle','-',...
'LineWidth',0.5,...
'Margin',2,...
'Position',[0.5 1.04012345679012 1.00005459937205],...
'Rotation',0,...
'String',blanks(0),...
'Interpreter','tex',...
'VerticalAlignment','bottom',...
'ButtonDownFcn',[],...
'CreateFcn', {@local_CreateFcn, [], ''} ,...
'DeleteFcn',[],...
'BusyAction','queue',...
'HandleVisibility','off',...
'HelpTopicKey',blanks(0),...
'HitTest','on',...
'Interruptible','on',...
'SelectionHighlight','on',...
'Serializable','on',...
'Tag',blanks(0),...
'UserData',[],...
'Visible','on',...
'XLimInclude','on',...
'YLimInclude','on',...
'ZLimInclude','on',...
'CLimInclude','on',...
'ALimInclude','on',...
'IncludeRenderer','on',...
'Clipping','off');
h23 = get(h21,'xlabel');
set(h23,...
'Parent',h21,...
'Units','data',...
'FontUnits','points',...
'BackgroundColor','none',...
'Color',[0 0 0],...
'DisplayName',blanks(0),...
'EdgeColor','none',...
'EraseMode','normal',...
'DVIMode','auto',...
'FontAngle','normal',...
'FontName','Helvetica',...
'FontSize',10,...
'FontWeight','normal',...
'HorizontalAlignment','center',...
'LineStyle','-',...
'LineWidth',0.5,...
'Margin',2,...
'Position',[0.497304582210243 -0.145061728395062 1.00005459937205],...
'Rotation',0,...
'String',blanks(0),...
'Interpreter','tex',...
'VerticalAlignment','cap',...
'ButtonDownFcn',[],...
'CreateFcn', {@local_CreateFcn, [], ''} ,...
'DeleteFcn',[],...
'BusyAction','queue',...
'HandleVisibility','off',...
'HelpTopicKey',blanks(0),...
'HitTest','on',...
'Interruptible','on',...
'SelectionHighlight','on',...
'Serializable','on',...
'Tag',blanks(0),...
'UserData',[],...
'Visible','on',...
'XLimInclude','on',...
'YLimInclude','on',...
'ZLimInclude','on',...
'CLimInclude','on',...
'ALimInclude','on',...
'IncludeRenderer','on',...
'Clipping','off');
h24 = get(h21,'ylabel');
set(h24,...
'Parent',h21,...
'Units','data',...
'FontUnits','points',...
'BackgroundColor','none',...
'Color',[0 0 0],...
'DisplayName',blanks(0),...
'EdgeColor','none',...
'EraseMode','normal',...
'DVIMode','auto',...
'FontAngle','normal',...
'FontName','Helvetica',...
'FontSize',10,...
'FontWeight','normal',...
'HorizontalAlignment','center',...
'LineStyle','-',...
'LineWidth',0.5,...
'Margin',2,...
'Position',[-0.0768194070080863 0.490740740740741 1.00005459937205],...
'Rotation',90,...
'String',blanks(0),...
'Interpreter','tex',...
'VerticalAlignment','bottom',...
'ButtonDownFcn',[],...
'CreateFcn', {@local_CreateFcn, [], ''} ,...
'DeleteFcn',[],...
'BusyAction','queue',...
'HandleVisibility','off',...
'HelpTopicKey',blanks(0),...
'HitTest','on',...
'Interruptible','on',...
'SelectionHighlight','on',...
'Serializable','on',...
'Tag',blanks(0),...
'UserData',[],...
'Visible','on',...
'XLimInclude','on',...
'YLimInclude','on',...
'ZLimInclude','on',...
'CLimInclude','on',...
'ALimInclude','on',...
'IncludeRenderer','on',...
'Clipping','off');
h25 = get(h21,'zlabel');
set(h25,...
'Parent',h21,...
'Units','data',...
'FontUnits','points',...
'BackgroundColor','none',...
'Color',[0 0 0],...
'DisplayName',blanks(0),...
'EdgeColor','none',...
'EraseMode','normal',...
'DVIMode','auto',...
'FontAngle','normal',...
'FontName','Helvetica',...
'FontSize',10,...
'FontWeight','normal',...
'HorizontalAlignment','right',...
'LineStyle','-',...
'LineWidth',0.5,...
'Margin',2,...
'Position',[-0.0795148247978437 2.65740740740741 1.00005459937205],...
'Rotation',0,...
'String',blanks(0),...
'Interpreter','tex',...
'VerticalAlignment','middle',...
'ButtonDownFcn',[],...
'CreateFcn', {@local_CreateFcn, [], ''} ,...
'DeleteFcn',[],...
'BusyAction','queue',...
'HandleVisibility','off',...
'HelpTopicKey',blanks(0),...
'HitTest','on',...
'Interruptible','on',...
'SelectionHighlight','on',...
'Serializable','on',...
'Tag',blanks(0),...
'UserData',[],...
'Visible','off',...
'XLimInclude','on',...
'YLimInclude','on',...
'ZLimInclude','on',...
'CLimInclude','on',...
'ALimInclude','on',...
'IncludeRenderer','on',...
'Clipping','off');
hsingleton = h1;
% --- Set application data first then calling the CreateFcn.
function local_CreateFcn(hObject, eventdata, createfcn, appdata)
if ~isempty(appdata)
names = fieldnames(appdata);
for i=1:length(names)
name = char(names(i));
setappdata(hObject, name, getfield(appdata,name));
end
end
if ~isempty(createfcn)
if isa(createfcn,'function_handle')
createfcn(hObject, eventdata);
else
eval(createfcn);
end
end
% --- Handles default GUIDE GUI creation and callback dispatch
function varargout = gui_mainfcn(gui_State, varargin)
gui_StateFields = {'gui_Name'
'gui_Singleton'
'gui_OpeningFcn'
'gui_OutputFcn'
'gui_LayoutFcn'
'gui_Callback'};
gui_Mfile = '';
for i=1:length(gui_StateFields)
if ~isfield(gui_State, gui_StateFields{i})
error(message('MATLAB:guide:StateFieldNotFound', gui_StateFields{ i }, gui_Mfile));
elseif isequal(gui_StateFields{i}, 'gui_Name')
gui_Mfile = [gui_State.(gui_StateFields{i}), '.m'];
end
end
numargin = length(varargin);
if numargin == 0
% MTRAINER_GUI_EXPORT
% create the GUI only if we are not in the process of loading it
% already
gui_Create = true;
elseif local_isInvokeActiveXCallback(gui_State, varargin{:})
% MTRAINER_GUI_EXPORT(ACTIVEX,...)
vin{1} = gui_State.gui_Name;
vin{2} = [get(varargin{1}.Peer, 'Tag'), '_', varargin{end}];
vin{3} = varargin{1};
vin{4} = varargin{end-1};
vin{5} = guidata(varargin{1}.Peer);
feval(vin{:});
return;
elseif local_isInvokeHGCallback(gui_State, varargin{:})
% MTRAINER_GUI_EXPORT('CALLBACK',hObject,eventData,handles,...)
gui_Create = false;
else
% MTRAINER_GUI_EXPORT(...)
% create the GUI and hand varargin to the openingfcn
gui_Create = true;
end
if ~gui_Create
% In design time, we need to mark all components possibly created in
% the coming callback evaluation as non-serializable. This way, they
% will not be brought into GUIDE and not be saved in the figure file
% when running/saving the GUI from GUIDE.
designEval = false;
if (numargin>1 && ishghandle(varargin{2}))
fig = varargin{2};
while ~isempty(fig) && ~ishghandle(fig,'figure')
fig = get(fig,'parent');
end
designEval = isappdata(0,'CreatingGUIDEFigure') || isprop(fig,'__GUIDEFigure');
end
if designEval
beforeChildren = findall(fig);
end
% evaluate the callback now
varargin{1} = gui_State.gui_Callback;
if nargout
[varargout{1:nargout}] = feval(varargin{:});
else
feval(varargin{:});
end
% Set serializable of objects created in the above callback to off in
% design time. Need to check whether figure handle is still valid in
% case the figure is deleted during the callback dispatching.
if designEval && ishghandle(fig)
set(setdiff(findall(fig),beforeChildren), 'Serializable','off');
end
else
if gui_State.gui_Singleton
gui_SingletonOpt = 'reuse';
else
gui_SingletonOpt = 'new';
end
% Check user passing 'visible' P/V pair first so that its value can be
% used by oepnfig to prevent flickering
gui_Visible = 'auto';
gui_VisibleInput = '';
for index=1:2:length(varargin)
if length(varargin) == index || ~ischar(varargin{index})
break;
end
% Recognize 'visible' P/V pair
len1 = min(length('visible'),length(varargin{index}));
len2 = min(length('off'),length(varargin{index+1}));
if ischar(varargin{index+1}) && strncmpi(varargin{index},'visible',len1) && len2 > 1
if strncmpi(varargin{index+1},'off',len2)
gui_Visible = 'invisible';
gui_VisibleInput = 'off';
elseif strncmpi(varargin{index+1},'on',len2)
gui_Visible = 'visible';
gui_VisibleInput = 'on';
end
end
end
% Open fig file with stored settings. Note: This executes all component
% specific CreateFunctions with an empty HANDLES structure.
% Do feval on layout code in m-file if it exists
gui_Exported = ~isempty(gui_State.gui_LayoutFcn);
% this application data is used to indicate the running mode of a GUIDE
% GUI to distinguish it from the design mode of the GUI in GUIDE. it is
% only used by actxproxy at this time.
setappdata(0,genvarname(['OpenGuiWhenRunning_', gui_State.gui_Name]),1);
if gui_Exported
gui_hFigure = feval(gui_State.gui_LayoutFcn, gui_SingletonOpt);
% make figure invisible here so that the visibility of figure is
% consistent in OpeningFcn in the exported GUI case
if isempty(gui_VisibleInput)
gui_VisibleInput = get(gui_hFigure,'Visible');
end
set(gui_hFigure,'Visible','off')
% openfig (called by local_openfig below) does this for guis without
% the LayoutFcn. Be sure to do it here so guis show up on screen.
movegui(gui_hFigure,'onscreen');
else
gui_hFigure = local_openfig(gui_State.gui_Name, gui_SingletonOpt, gui_Visible);
% If the figure has InGUIInitialization it was not completely created
% on the last pass. Delete this handle and try again.
if isappdata(gui_hFigure, 'InGUIInitialization')
delete(gui_hFigure);
gui_hFigure = local_openfig(gui_State.gui_Name, gui_SingletonOpt, gui_Visible);
end
end
if isappdata(0, genvarname(['OpenGuiWhenRunning_', gui_State.gui_Name]))
rmappdata(0,genvarname(['OpenGuiWhenRunning_', gui_State.gui_Name]));
end
% Set flag to indicate starting GUI initialization
setappdata(gui_hFigure,'InGUIInitialization',1);
% Fetch GUIDE Application options
gui_Options = getappdata(gui_hFigure,'GUIDEOptions');
% Singleton setting in the GUI M-file takes priority if different
gui_Options.singleton = gui_State.gui_Singleton;
if ~isappdata(gui_hFigure,'GUIOnScreen')
% Adjust background color
if gui_Options.syscolorfig
set(gui_hFigure,'Color', get(0,'DefaultUicontrolBackgroundColor'));
end
% Generate HANDLES structure and store with GUIDATA. If there is
% user set GUI data already, keep that also.
data = guidata(gui_hFigure);
handles = guihandles(gui_hFigure);
if ~isempty(handles)
if isempty(data)
data = handles;
else
names = fieldnames(handles);
for k=1:length(names)
data.(char(names(k)))=handles.(char(names(k)));
end
end
end
guidata(gui_hFigure, data);
end
% Apply input P/V pairs other than 'visible'
for index=1:2:length(varargin)
if length(varargin) == index || ~ischar(varargin{index})
break;
end
len1 = min(length('visible'),length(varargin{index}));
if ~strncmpi(varargin{index},'visible',len1)
try set(gui_hFigure, varargin{index}, varargin{index+1}), catch break, end
end
end
% If handle visibility is set to 'callback', turn it on until finished
% with OpeningFcn
gui_HandleVisibility = get(gui_hFigure,'HandleVisibility');
if strcmp(gui_HandleVisibility, 'callback')
set(gui_hFigure,'HandleVisibility', 'on');
end
feval(gui_State.gui_OpeningFcn, gui_hFigure, [], guidata(gui_hFigure), varargin{:});
if isscalar(gui_hFigure) && ishghandle(gui_hFigure)
% Handle the default callbacks of predefined toolbar tools in this
% GUI, if any
guidemfile('restoreToolbarToolPredefinedCallback',gui_hFigure);
% Update handle visibility
set(gui_hFigure,'HandleVisibility', gui_HandleVisibility);
% Call openfig again to pick up the saved visibility or apply the
% one passed in from the P/V pairs
if ~gui_Exported
gui_hFigure = local_openfig(gui_State.gui_Name, 'reuse',gui_Visible);
elseif ~isempty(gui_VisibleInput)
set(gui_hFigure,'Visible',gui_VisibleInput);
end
if strcmpi(get(gui_hFigure, 'Visible'), 'on')
figure(gui_hFigure);
if gui_Options.singleton
setappdata(gui_hFigure,'GUIOnScreen', 1);
end
end
% Done with GUI initialization
if isappdata(gui_hFigure,'InGUIInitialization')
rmappdata(gui_hFigure,'InGUIInitialization');
end
% If handle visibility is set to 'callback', turn it on until
% finished with OutputFcn
gui_HandleVisibility = get(gui_hFigure,'HandleVisibility');
if strcmp(gui_HandleVisibility, 'callback')
set(gui_hFigure,'HandleVisibility', 'on');
end
gui_Handles = guidata(gui_hFigure);
else
gui_Handles = [];
end
if nargout
[varargout{1:nargout}] = feval(gui_State.gui_OutputFcn, gui_hFigure, [], gui_Handles);
else
feval(gui_State.gui_OutputFcn, gui_hFigure, [], gui_Handles);
end
if isscalar(gui_hFigure) && ishghandle(gui_hFigure)
set(gui_hFigure,'HandleVisibility', gui_HandleVisibility);
end
end
function gui_hFigure = local_openfig(name, singleton, visible)
% openfig with three arguments was new from R13. Try to call that first, if
% failed, try the old openfig.
if nargin('openfig') == 2
% OPENFIG did not accept 3rd input argument until R13,
% toggle default figure visible to prevent the figure
% from showing up too soon.
gui_OldDefaultVisible = get(0,'defaultFigureVisible');
set(0,'defaultFigureVisible','off');
gui_hFigure = openfig(name, singleton);
set(0,'defaultFigureVisible',gui_OldDefaultVisible);
else
gui_hFigure = openfig(name, singleton, visible);
%workaround for CreateFcn not called to create ActiveX
if feature('HGUsingMATLABClasses')
peers=findobj(findall(allchild(gui_hFigure)),'type','uicontrol','style','text');
for i=1:length(peers)
if isappdata(peers(i),'Control')
actxproxy(peers(i));
end
end
end
end
function result = local_isInvokeActiveXCallback(gui_State, varargin)
try
result = ispc && iscom(varargin{1}) ...
&& isequal(varargin{1},gcbo);
catch
result = false;
end
function result = local_isInvokeHGCallback(gui_State, varargin)
try
fhandle = functions(gui_State.gui_Callback);
result = ~isempty(findstr(gui_State.gui_Name,fhandle.file)) || ...
(ischar(varargin{1}) ...
&& isequal(ishghandle(varargin{2}), 1) ...
&& (~isempty(strfind(varargin{1},[get(varargin{2}, 'Tag'), '_'])) || ...
~isempty(strfind(varargin{1}, '_CreateFcn'))) );
catch
result = false;
end
|
github
|
HelmchenLabSoftware/OCIA-master
|
daq_sessionInterfaceH45.m
|
.m
|
OCIA-master/behavior/daq/daq_sessionInterfaceH45.m
| 4,666 |
utf_8
|
4bfeda072efe6d1b8ef7c49d06067dcc
|
function [data, S, F, T, P] = daq_sessionInterfaceH45(dur, recordRate, condition, doPlot)
% s = daq.createSession('ni');
% s.Rate = 50;
% s.DurationInSeconds = 40;
% s.addAnalogInputChannel('Dev1','ai0', 'Voltage');
% s.Channels.InputType = 'SingleEnded';
% s.Channels.Range = [-10 10];
realTimePlot = 0;
recordChanNames = {'shutter'};
recordChanRanges = {1, 1, 1, 5, 5};
nChans = numel(recordChanNames);
recordChans = cell(nChans, 1);
daqreset;
fprintf('Connecting hardware...\n');
s = daq.createSession('nidaq');
s.Rate = recordRate;
for iChan = 1 : nChans;
recordChans{iChan} = s.addAnalogInputChannel('ExtraChannels', iChan, 'Voltage');
recordChans{iChan}.Name = recordChanNames{iChan};
recordChans{iChan}.Range = repmat(recordChanRanges{iChan}, 1, 2) .* [-1 1];
recordChans{iChan}.InputType = 'SingleEnded';
end;
% s.addAnalogInputChannel('ExtraChannels', 'ai0', 'Voltage'); % shutter
% s.addAnalogInputChannel('ExtraChannels', 'ai1', 'Voltage'); % laser power
% s.addAnalogInputChannel('ExtraChannels', 2, 'Voltage'); % motion
% s.addAnalogInputChannel('ExtraChannels', 'ai3', 'Voltage'); % microphone
% s.addAnalogInputChannel('ExtraChannels', 'ai4', 'Voltage'); % resonnance X position
% s.addAnalogInputChannel('ExtraChannels', 'ai5', 'Voltage');
% s.addAnalogInputChannel('ExtraChannels', 'ai6', 'Voltage');
% s.addAnalogInputChannel('ExtraChannels', 'ai7', 'Voltage');
% s.Channels.InputType = 'SingleEnded';
chanRange = [-5, 5];
% s.Channels.Range = chanRange;
fprintf('s1 ok.\n');
% s2 = daq.createSession(config.hardware.adaptorID);
% s2.addDigitalChannel(config.hardware.digitalOut_Device, config.hardware.digitalOut_PortLine, 'OutputOnly');
% fprintf('And s2 ok. Ready to go.\n');
s.DurationInSeconds = dur;
data = [];
if realTimePlot;
% 'Position', [150, 300, 950, 350],
h = figure('Name', 'Recording', 'NumberTitle', 'off', 'WindowStyle', 'docked');
plot(0, 0);
hold on;
ylim(chanRange);
xlim([0, s.DurationInSeconds]);
end;
s.addlistener('DataAvailable', @collectAndPlotData);
s.startForeground();
function collectAndPlotData(~, event)
data = [data (event.Data - bsxfun(@rdivide, event.Data, mean(event.Data)))'];
if realTimePlot;
figure(h);
t = 1 : size(data, 2);
plot(repmat(t ./ recordRate, 1, nChans), data(:, t)');
end;
end
if realTimePlot;
figure(h);
else
h = figure('Name', 'Recording', 'NumberTitle', 'off', 'WindowStyle', 'docked');
end;
colors = jet(nChans);
t = 1 : size(data, 2);
for iChan = 1 : nChans;
subplot(nChans, 1, iChan);
plot(t' ./ recordRate, data(iChan, t)', 'Color', colors(iChan, :));
ylim([min(data(iChan, :)) max(data(iChan, :))]);
ylabel(recordChanNames{iChan});
end;
N = 8;
% figure('Name', 'Spectrogram', 'NumberTitle', 'off', 'WindowStyle', 'docked');
% % spectrogram(data, 512, 480, 512, recordRate);
% spectrogram(data, 128 * N, 120 * N, 128 * N, recordRate);
% colorbar;
S = cell(nChans, 1);
F = cell(nChans, 1);
T = cell(nChans, 1);
P = cell(nChans, 1);
for iChan = 1 : nChans;
[S{iChan}, F{iChan}, T{iChan}, P{iChan}] = spectrogram(data(iChan, :), 128 * N, 120 * N, 128 * N, recordRate);
if ~doPlot; continue; end;
%% plotting
figure('Name', sprintf('Spectrogram_%s_%s', condition, recordChanNames{iChan}), ...
'NumberTitle', 'off', 'WindowStyle', 'docked');
realLogS = real(log(S{iChan}));
subplot(2, 1, 1);
imagesc(realLogS');
nFreqs = size(realLogS, 1);
nSamples = size(realLogS, 2);
maxFreq = recordRate * 0.5;
maxT = s.DurationInSeconds;
freqIDs = (0 : 1000 : round(maxFreq / 1000) * 1000) / 1000;
toShowFreqs = round(0 : nFreqs / (maxFreq / 1000) : nFreqs);
t = 0 : 1 : s.DurationInSeconds;
timeIndex = round(0 : nSamples / (maxT / 1) : nSamples);
set(gca, 'XTick', toShowFreqs, 'XTickLabel', freqIDs, 'YTick', timeIndex, 'YTickLabel', t);
xlabel('Frequencies [kHz]');
ylabel('Time [s]');
subplot(2, 1, 2);
freqDist = sum(realLogS, 2);
secDeriv = diff(freqDist, 2);
secDerivMinThresh = prctile(secDeriv, 2);
peakInd = find(secDeriv < secDerivMinThresh);
peakIndSingle = peakInd;
peakIndSingle(diff(peakIndSingle) < 15) = [];
plot(F{iChan}, freqDist);
hold on;
% scatter(F(peakIndSingle), freqDist(peakIndSingle) + 300, 'bx');
for iPeak = 1 : numel(peakIndSingle);
text(F{iChan}(peakIndSingle(iPeak)) + 100, freqDist(peakIndSingle(iPeak)) + 400, ...
sprintf('%d Hz', round(F{iChan}(peakIndSingle(iPeak)))), 'FontSize', 8);
end;
suptitle(strrep(sprintf('%s_%s', condition, recordChanNames{iChan}), '_', '\_'));
end;
end
|
github
|
HelmchenLabSoftware/OCIA-master
|
daq_sessionInterfaceH30.m
|
.m
|
OCIA-master/behavior/daq/daq_sessionInterfaceH30.m
| 6,252 |
utf_8
|
0ea24a3bcc0b8963af28024c82ae66b6
|
function [data, S, F, T, P] = daq_sessionInterfaceH30(dur, recordRate, condition, doPlot)
% s = daq.createSession('ni');
% s.Rate = 50;
% s.DurationInSeconds = 40;
% s.addAnalogInputChannel('Dev1','ai0', 'Voltage');
% s.Channels.InputType = 'SingleEnded';
% s.Channels.Range = [-10 10];
realTimePlot = 0;
% recordChanNames = {'shutter', 'breathing', 'microphone', 'laserPower', 'resXPos'};
% recordChanNames = {'lickSensor'};
% recordChanNames = {'lickSensor', 'microphone'};
recordChanNames = {'piezo', 'micr', 'yscan'};
% recordChanRanges = {1, 1, 1, 5, 5};
nChans = numel(recordChanNames);
recordChans = cell(nChans, 1);
daqreset;
fprintf('Connecting hardware...\n');
s = daq.createSession('ni');
s.Rate = recordRate;
% for iChan = 1 : nChans;
% recordChans{iChan} = s.addAnalogInputChannel('ExtraChannels', iChan, 'Voltage');
% % recordChans{iChan} = s.addAnalogInputChannel('BehaviorBox', iChan, 'Voltage');
% recordChans{iChan}.Name = recordChanNames{iChan};
% recordChans{iChan}.Range = repmat(recordChanRanges{iChan}, 1, 2) .* [-1 1];
% recordChans{iChan}.InputType = 'SingleEnded';
% end;
% s.addAnalogInputChannel('BehaviorBox', 'ai0', 'Voltage'); % piezo
% s.addAnalogInputChannel('BehaviorBox', 'ai1', 'Voltage'); % micr
% s.addAnalogInputChannel('BehaviorBox', 'ai2', 'Voltage'); % yscan
% s.addAnalogInputChannel('ExtraChannels', 'ai0', 'Voltage'); % shutter
% s.addAnalogInputChannel('ExtraChannels', 'ai1', 'Voltage'); % laser power
% s.addAnalogInputChannel('ExtraChannels', 2, 'Voltage'); % motion
% s.addAnalogInputChannel('ExtraChannels', 'ai3', 'Voltage'); % microphone
% s.addAnalogInputChannel('ExtraChannels', 'ai4', 'Voltage'); % resonnance X position
% s.addAnalogInputChannel('ExtraChannels', 'ai5', 'Voltage');
% s.addAnalogInputChannel('ExtraChannels', 'ai6', 'Voltage');
% s.addAnalogInputChannel('ExtraChannels', 'ai7', 'Voltage');
s.addAnalogOutputChannel('ExtraChannels', 'ao0', 'Voltage'); % imaging TTL gate
% s.Channels.InputType = 'SingleEnded';
chanRange = [-10, 10];
% s.Channels.Range = chanRange;
fprintf('Hardware connected.\n');
% s2 = daq.createSession(config.hardware.adaptorID);
% s2.addDigitalChannel(config.hardware.digitalOut_Device, config.hardware.digitalOut_PortLine, 'OutputOnly');
% fprintf('And s2 ok. Ready to go.\n');
s.DurationInSeconds = dur;
data = [];
if realTimePlot;
% 'Position', [150, 300, 950, 350],
h = figure('Name', 'Recording', 'NumberTitle', 'off', 'WindowStyle', 'docked');
plot(0, 0);
hold on;
ylim(chanRange);
xlim([0, s.DurationInSeconds]);
end;
s.addlistener('DataAvailable', @collectAndPlotData);
% gongMat = load('gong.mat');
% m = load('C:\Users\laurenczy\Desktop\cloudOfTonesParameters.mat');
% cloudOfTones = MakeCloudOfTonesSound(m.freqs * 0.5, m.uniqueCloudCenterIndexes, m.cloudDispersion, m.stims, m.toneDur, ...
% m.toneISI, m.stimDur, 1, m.sampFreq, 0, 0);
% s.startForeground();
s.startBackground();
% pause(1);
% sound(gongMat.y * 0.3);
% sound(repmat(cloudOfTones{2}, 1, 10), m.sampFreq);
% pause(0.5);
% sound(cloudOfTones{2}, m.sampFreq);
% pause(0.5);
% sound(cloudOfTones{3}, m.sampFreq);
% pause(0.5);
% sound(cloudOfTones{4}, m.sampFreq);
% pause(0.5);
% sound(cloudOfTones{5}, m.sampFreq);
s.wait();
function collectAndPlotData(~, event)
currentData = event.Data;
if isempty(data);
currentData(fix(0.001 * recordRate) : end, :) = NaN;
end;
data = [data (currentData - bsxfun(@rdivide, currentData, mean(currentData)))'];
if realTimePlot;
figure(h);
t = 1 : size(data, 2);
plot(repmat(t ./ recordRate, 1, nChans), data(:, t)');
end;
end
if realTimePlot;
figure(h);
else
h = figure('Name', 'Recording', 'NumberTitle', 'off', 'WindowStyle', 'docked');
end;
colors = lines(nChans);
% colors = jet(nChans);
t = 1 : size(data, 2);
for iChan = 1 : nChans;
subplot(nChans, 1, iChan);
dataForChan = data(iChan, :);
% normData = linScale(dataForChan - nanmean(dataForChan), -1, 1);
normData = dataForChan - nanmean(dataForChan);
% normData = dataForChan;
plot(t' ./ recordRate, normData', 'Color', colors(iChan, :));
% minData = nanmin(normData);
% maxData = nanmax(normData);
% ylim([min(minData, -1) max(maxData, 1)]);
ylabel(recordChanNames{iChan});
end;
N = 8;
% figure('Name', 'Spectrogram', 'NumberTitle', 'off', 'WindowStyle', 'docked');
% % spectrogram(data, 512, 480, 512, recordRate);
% spectrogram(data, 128 * N, 120 * N, 128 * N, recordRate);
% colorbar;
S = cell(nChans, 1);
F = cell(nChans, 1);
T = cell(nChans, 1);
P = cell(nChans, 1);
for iChan = 1 : nChans;
[S{iChan}, F{iChan}, T{iChan}, P{iChan}] = spectrogram(data(iChan, :), 128 * N, 120 * N, 128 * N, recordRate);
if ~doPlot; continue; end;
%% plotting
figure('Name', sprintf('Spectrogram_%s_%s', condition, recordChanNames{iChan}), ...
'NumberTitle', 'off', 'WindowStyle', 'docked');
realLogS = real(log(S{iChan}));
subplot(2, 1, 1);
imagesc(realLogS');
nFreqs = size(realLogS, 1);
nSamples = size(realLogS, 2);
maxFreq = recordRate * 0.5;
maxT = s.DurationInSeconds;
freqIDs = (0 : 1000 : round(maxFreq / 1000) * 1000) / 1000;
toShowFreqs = round(0 : nFreqs / (maxFreq / 1000) : nFreqs);
t = 0 : 1 : s.DurationInSeconds;
timeIndex = round(0 : nSamples / (maxT / 1) : nSamples);
set(gca, 'XTick', toShowFreqs, 'XTickLabel', freqIDs, 'YTick', timeIndex, 'YTickLabel', t);
xlabel('Frequencies [kHz]');
ylabel('Time [s]');
subplot(2, 1, 2);
freqDist = nansum(realLogS, 2);
secDeriv = diff(freqDist, 2);
secDerivMinThresh = prctile(secDeriv, 2);
peakInd = find(secDeriv < secDerivMinThresh);
peakIndSingle = peakInd;
peakIndSingle(diff(peakIndSingle) < 15) = [];
plot(F{iChan}, freqDist);
hold on;
% scatter(F(peakIndSingle), freqDist(peakIndSingle) + 300, 'bx');
for iPeak = 1 : numel(peakIndSingle);
text(F{iChan}(peakIndSingle(iPeak)) + 100, freqDist(peakIndSingle(iPeak)) + 400, ...
sprintf('%d Hz', round(F{iChan}(peakIndSingle(iPeak)))), 'FontSize', 8);
end;
suptitle(strrep(sprintf('%s_%s', condition, recordChanNames{iChan}), '_', '\_'));
end;
end
|
github
|
HelmchenLabSoftware/OCIA-master
|
daq_sessionInterface.m
|
.m
|
OCIA-master/behavior/daq/daq_sessionInterface.m
| 1,475 |
utf_8
|
7db7e719bbb05c2ed3fc8276d2d00939
|
function daq_sessionInterface(config)
% s = daq.createSession('ni');
% s.Rate = 50;
% s.DurationInSeconds = 40;
% s.addAnalogInputChannel('Dev1','ai0', 'Voltage');
% s.Channels.InputType = 'SingleEnded';
% s.Channels.Range = [-10 10];
% daqreset;
fprintf('Connecting hardware...\n');
s = daq.createSession(config.hardware.adaptorID);
recordRate = config.hardware.analogIn_SampleRate;
recordRate = 1000;
s.Rate = recordRate;
s.addAnalogInputChannel(config.hardware.analogIn_Device, ...
config.hardware.analogIn_Channel, 'Voltage');
s.Channels.InputType = config.hardware.analogIn_InputType;
s.Channels.Range = config.hardware.analogIn_Range;
fprintf('s1 ok.\n');
% s2 = daq.createSession(config.hardware.adaptorID);
% s2.addDigitalChannel(config.hardware.digitalOut_Device, config.hardware.digitalOut_PortLine, 'OutputOnly');
% fprintf('And s2 ok. Ready to go.\n');
s.DurationInSeconds = 10;
global data;
data = [];
global h;
% 'Position', [150, 300, 950, 350],
h = figure('Name', 'ContinuousRecording', 'NumberTitle', 'off', ...
'MenuBar', 'none', 'ToolBar', 'none', 'WindowStyle', 'docked');
plot(0, 0);
hold on;
xlim([-0.3, s.DurationInSeconds * s.Rate * 1.1]);
% ylim([-0.3 0.3]);
lh = s.addlistener('DataAvailable', @collectAndPlotData);
s.startForeground();
function collectAndPlotData(~, event)
% fprintf('#collectData\n');
data = [data (event.Data - mean(event.Data))'];
t = 1 : numel(data(data ~= 0));
plot(t, data(t));
end
end
|
github
|
HelmchenLabSoftware/OCIA-master
|
daq_ni_usb6008.m
|
.m
|
OCIA-master/behavior/daq/daq_ni_usb6008.m
| 2,637 |
utf_8
|
8f4ab52789a17dc8daf2ef4e7fcd36ee
|
function daq_ni_usb6008
ai=analoginput('nidaq','Dev1');
ao=analogoutput('nidaq','Dev1');
dio=digitalio('nidaq','Dev1');
disp('done create device')
testMode = 'analogIn'; % analogOut or analogIn or digital
switch lower(testMode)
case 'analogin'
%% Collect analog input
% analog input channel
addchannel(ai, 0);
disp('done add channel')
% get available properties
% get(ai);
% set some properties
set(ai,'InputType','SingleEnded')
% sample rate and recording duration
ai.SampleRate = 10000;
ai.SamplesPerTrigger = 50000; % can be Inf for continuous acquisition
disp('Press any key to start')
pause
% start acquisition
start(ai);
% get data
data = getdata(ai);
plot(data)
stop(ai), delete(ai)
case 'analogout'
%% Write analog output
% analog output channel
addchannel(ao, 1)
% get available properties
get(ao);
% sample rate and recording duration
samplingInterval = 0.005; % in s
tMax = 100; n = tMax ./samplingInterval;
a = [0 1]; a = repmat(a,1,n./2);
startDelay = 0.5; % in s
% have to send each sample separately (USB-6008 does not support
% putdata / start combination)
% use a timer object
% create the timer
t = timer('period',samplingInterval,'startDelay',startDelay,...
'TasksToExecute',numel(a),'ExecutionMode','fixedRate');
% callback functions
t.StartFcn = @timerStartFcn;
t.StopFcn = @timerStopFcn;
t.TimerFcn = {@timerFcn,a,ao};
% start timer
start(t)
case 'digital'
%% Digital IO
% digital io
digital_out = addline(dio,0:7,'out');
digital_in = addline(dio,8:11,'in');
% output loop
value = [0 0 0 0 0 0 0 0];
for n = 1:50
if value(1) == 0 % only change line 1
value(1) = 1;
else
value(1) = 0;
end
% change digital out
putvalue(digital_out,value)
% get digital in
io1 = getvalue(dio.Line(9));
fprintf('\nDigital in is %1.0f\n',io1)
pause(0.5)
end
% switch off
value = [1 0 0 0 0 0 0 0];
putvalue(digital_out,value)
end
function timerFcn(t,event,data,ao)
putsample(ao,data(t.TasksExecuted))
function timerStartFcn(t,event)
disp('Timer started')
function timerStopFcn(t,event)
disp('Timer stopped')
delete(t)
|
github
|
HelmchenLabSoftware/OCIA-master
|
waitForExternalTrigger_H30.m
|
.m
|
OCIA-master/behavior/daq/waitForExternalTrigger_H30.m
| 1,558 |
utf_8
|
080163444a2aff0f5793c00952a3c729
|
function status = waitForExternalTrigger_H30(timeout)
% input argument: timeout in seconds
% RETURNS:
% - status = 0 if waiting timed out
% - status = 1 if trigger was successfully received
% - status = 2 if could not connect to the nidaq analog input (or other error)
% created on 2014-02-01 by Balazs Laurenczy ([email protected])
status = 0;
try
s = daq.createSession('ni');
s.Rate = 1000;
s.addAnalogInputChannel('ScanOutputCard', 'ai0', 'Voltage');
s.Channels.Range = [-1 1];
s.Channels.InputType = 'SingleEnded';
s.DurationInSeconds = timeout;
s.NotifyWhenDataAvailableExceeds = 50;
s.addlistener('DataAvailable', @checkTriggerInData);
catch err; %#ok<NASGU>
warning('externalTrigger_nidaq:ConnectError', 'Could not connect to nidaq analog input!');
status = 2;
return;
end;
thresh = NaN;
status = 0;
function checkTriggerInData(~, event)
if isnan(thresh);
thresh = max(max(event.Data) * 5, 0.15);
% o('Defined thresh: %6.4f, max(data): %6.4f.', thresh, max(event.Data), 0, 0);
end;
% o('Collected data, thresh: %6.4f, max(data): %6.4f.', thresh, max(event.Data), 0, 0);
timePointAboveThresh = find(event.Data > thresh, 1);
if ~isempty(timePointAboveThresh);
% firstTimePointAboveThresh = timePointAboveThresh(1);
% o('Found trigger, firstTimePointAboveThresh: %d/%d.', firstTimePointAboveThresh, numel(event.Data), 0, 0);
status = 1;
s.stop();
end;
end
try
s.startForeground();
catch err; %#ok<NASGU>
end;
end
|
github
|
HelmchenLabSoftware/OCIA-master
|
externalTrigger_nidaq.m
|
.m
|
OCIA-master/behavior/daq/externalTrigger_nidaq.m
| 1,910 |
utf_8
|
52a0ca32193ecd4ba0079915dae9e268
|
function status = waitForExternalTrigger_H30(timeout)
% input argument: timeout in seconds
% RETURNS:
% - status = 0 if waiting timed out
% - status = 1 if trigger was successfully received
% - status = 2 if could not connect to the nidaq analog input
% this file written by Henry Luetcke ([email protected])
% modified on 2013-03-20 by Balazs Laurenczy ([email protected])
% modified more on 2013-12-19 by Balazs Laurenczy ([email protected])
status = 0;
% Create an analog input object using Board ID "Dev1".
try
s = daq.createSession('ni');
s.Rate = 2000000;
s.addAnalogInputChannel('ExtraChannels', 'ai0', 'Voltage');
s.Channels.Range = [-1 1];
s.Channels.InputType = 'SingleEnded';
s.DurationInSeconds = 3;
lh = s.addlistener('DataAvailable', @checkTriggerInData);
catch err; %#ok<NASGU>
warning('externalTrigger_nidaq:ConnectError', 'Could not connect to nidaq analog input!');
status = 2;
return;
end;
thresh = NaN;
function checkTriggerInData(~, event)
if isnan(thresh);
thresh = max(event.Data) * 5;
end;
o('Collected data, thresh: %6.4f, max(data): %6.4f.', thresh, max(event.Data), 0, 0);
timePointAboveThresh = find(event.Data > thresh);
if ~isempty(timePointAboveThresh);
firstTimePointAboveThresh = timePointAboveThresh(1);
o('Found trigger, firstTimePointAboveThresh: %d/%d.', firstTimePointAboveThresh, numel(event.Data), 0, 0);
end;
end
% set(ai,'TriggerType','HwAnalog');
% set(s.Channels, 'TriggerType', 'HwDigital');
% set(s.Channels, 'TriggerCondition', 'PositiveEdge'); % for HelioScan
% set(s.Channels, 'HwDigitalTriggerSource', 'PFI0');
s.startForeground();
% % Wait up to timeout seconds for the acquisition to complete
% try
% wait(ai, timeout);
% data = getdata(ai);
% status = 1;
% catch
% status = 0;
% end
%
% % Clean up
% stop(ai);
% delete(ai);
end
|
github
|
HelmchenLabSoftware/OCIA-master
|
analyseBehavPerf.m
|
.m
|
OCIA-master/behavior/perfAnalysis/analyseBehavPerf.m
| 5,182 |
utf_8
|
6051e144aa04de4837f45fd6cc287d3c
|
%% Function - analyseBehavPerf
function counts = analyseBehavPerf(respTypes, binWidthProp, binWidthCum, doBinCout)
dbgLvl = 0;
o(' #analyzeBehavPerf(): nTrials: %d.', size(respTypes, 2), 1, dbgLvl);
% transform the response types into sums
respTypeToRespCountTic = tic; % for performance timing purposes
respCount = zeros(5, 1);
respTypes(isnan(respTypes)) = 6;
for i = 1:5; respCount(i) = sum(respTypes == i); end;
o(' #analyzeBehavPerf(): respTypeToRespCountTic: %.2f ms...', toc(respTypeToRespCountTic) * 1000, 2, dbgLvl);
singleCountsTic = tic; % for performance timing purposes
counts = struct();
% responseCount columns: correct detect, correct reject, false alarm, miss
counts.TOT = sum(respCount);
counts.INVALID = respCount(5);
counts.INVALIDP = counts.INVALID / counts.TOT * 100; % INVALID response (kind of false alarm)
counts.VTOT = counts.TOT - counts.INVALID;
counts.VTOTP = counts.VTOT / counts.TOT * 100; % "valid" responses (non-INVALID)
% all response types with their percent
counts.TGO = respCount(1);
counts.NTNGO = respCount(2);
counts.NTGO = respCount(3);
counts.TNGO = respCount(4);
% targets and targets in percent
counts.T = counts.TGO + counts.TNGO;
counts.TP = counts.T / counts.VTOT * 100;
% non-targets and non-targets in percent
counts.NT = counts.NTNGO + counts.NTGO;
counts.NTP = counts.NT / counts.VTOT * 100;
% GOs and GOs in percent
counts.GO = counts.TGO + counts.NTGO;
counts.GOP = counts.GO / counts.VTOT * 100;
% NO-GOs and NO-GO in percent
counts.NGO = counts.TNGO + counts.NTNGO;
counts.NGOP = counts.NGO / counts.VTOT * 100;
% corrects and corrects in percent
counts.C = counts.TGO + counts.NTNGO;
counts.CP = counts.C / counts.VTOT * 100;
% falses and falses in percent
counts.F = counts.TNGO + counts.NTGO;
counts.FP = counts.F / counts.VTOT * 100;
% correctness index taking into acount falses
counts.CiP = (counts.CP - counts.FP + 100) / 2 ;
counts.DPRIME = dprime(counts.TGO ./ counts.T, ...
counts.NTGO ./ counts.NT, counts.T, counts.NT);
% reponse type percents
counts.TGOP = counts.TGO / counts.T * 100;
counts.NTNGOP = counts.NTNGO / counts.NT * 100;
counts.NTGOP = counts.NTGO / counts.NT * 100;
counts.TNGOP = counts.TNGO / counts.T * 100;
o(' #analyzeBehavPerf(): singleCountsTic: %.2f ms...', toc(singleCountsTic) * 1000, 2, dbgLvl);
if ~doBinCout; return; end;
binCountsTic = tic; % for performance timing purposes
% evolution of indexes over time
counts.TGOs = zeros(1, counts.TOT);
counts.NTNGOs = zeros(1, counts.TOT);
counts.NTGOs = zeros(1, counts.TOT);
counts.TNGOs = zeros(1, counts.TOT);
counts.INVALIDs = zeros(1, counts.TOT);
counts.DPRIMEs = zeros(1, counts.TOT);
if isempty(binWidthCum);
useProp = 1;
binWidth = max(fix(counts.TOT * binWidthProp), 1);
else
useProp = 0;
binWidth = binWidthCum;
end;
if isempty(binWidth);
error('mtrainerAnalyzer_getCounts:NoBinWidth', 'No bin width specified');
end;
for i = 1 : counts.TOT;
if binWidth ~= -1;
if useProp;
iStart = max(i - binWidth, 1);
iEnd = min(i + binWidth, counts.TOT);
else
iStart = ceil(max(i - 0.5 * (binWidth - 1), 1));
iEnd = floor(min(i + 0.5 * (binWidth - 1), counts.TOT));
end;
T = sum(ismember(respTypes(iStart : iEnd), [1 4]));
NT = sum(ismember(respTypes(iStart : iEnd), [2 3]));
counts.TGOs(i) = (sum(respTypes(iStart : iEnd) == 1) / T) * 100;
counts.NTNGOs(i) = (sum(respTypes(iStart : iEnd) == 2) / NT) * 100;
counts.NTGOs(i) = (sum(respTypes(iStart : iEnd) == 3) / NT) * 100;
counts.TNGOs(i) = (sum(respTypes(iStart : iEnd) == 4) / T) * 100;
counts.INVALIDs(i) = (sum(respTypes(iStart : iEnd) == 5) / (iEnd - iStart)) * 100;
countsForBin = analyseBehavPerf(respTypes(iStart : iEnd), binWidthProp, binWidthCum, 0);
counts.DPRIMEs(i) = dprime(countsForBin.TGO ./ countsForBin.T, ...
countsForBin.NTGO ./ countsForBin.NT, countsForBin.T, countsForBin.NT);
else
counts.TGOs(i) = sum(respTypes(1 : i) == 1) / i * 100;
counts.NTNGOs(i) = sum(respTypes(1 : i) == 2) / i * 100;
counts.NTGOs(i) = sum(respTypes(1 : i) == 3) / i * 100;
counts.TNGOs(i) = sum(respTypes(1 : i) == 4) / i * 100;
counts.INVALIDs(i) = sum(respTypes(1 : i) == 5) / i * 100;
countsForBin = analyseBehavPerf(respTypes(1 : i), binWidthProp, binWidthCum, 0);
counts.DPRIMEs(i) = dprime(countsForBin.TGO ./ countsForBin.T, ...
countsForBin.NTGO ./ countsForBin.NT, countsForBin.T, countsForBin.NT);
end;
end;
counts.RESPs = (counts.TGOs + counts.NTGOs) / 2;
o(' #analyzeBehavPerf(): binCountsTic: %.2f ms...', toc(binCountsTic) * 1000, 2, dbgLvl);
end
|
github
|
HelmchenLabSoftware/OCIA-master
|
mtrainerAnalyser_pooledPerformance_bins.m
|
.m
|
OCIA-master/behavior/mtrainer/mtrainerAnalyser_pooledPerformance_bins.m
| 6,607 |
utf_8
|
542605197d955dd0ad8e813ec2c311a0
|
%% Function - mtrainerAnalyser_pooledPerformance
function figHand = mtrainerAnalyser_pooledPerformance_bins(outAll, titleStr, binWidth)
% dbgLevel = 2;
nTrials = length(outAll.respTypes);
% calculate number of bins, make sure that there is at least one
nBins = max(round(nTrials / binWidth), 1);
figName = titleStr;
figName = strrep(figName, '\_', '_');
figName = strrep(figName, '''', '');
figName = strrep(figName, ' ', '');
figHand = figure('NumberTitle', 'off', 'WindowStyle', 'docked', 'Name', figName);
hitRate = zeros(1, nBins); % correct detection, CR+, hitRate
% hitRateError = zeros(1, nBins); % correct detection, CR+, hitRate errors
falsePosRate = zeros(1, nBins); % false alarm, CR-, false positive
% falsePosRateError = zeros(1, nBins); % false alarm, CR-, false positive errors
dprimes = zeros(1, nBins); % d prime
% dprimesError = zeros(1, nBins); % d prime errors
useSEM = 1;
prevNFreqs = 0;
prevNTones = 0;
dprimeMaxVal = 3.5;
dprimeMinVal = -2;
changeOfFreqOrToneNum = zeros(1, nBins);
for iBin = 1 : nBins;
iStart = (iBin - 1) * binWidth + 1; % for binWidth = 10: 1, 11, 21, etc.
iEnd = min(iBin * binWidth, nTrials); % for binWidth = 10: 10, 20, 30, etc.
countsForBin = mtrainerAnalyzer_getCounts(outAll.respTypes(iStart : iEnd));
% extract the current session's number of frequency and number of tones
nFreqs = outAll.nFreqs(iStart : iEnd);
nTones = outAll.nTones(iStart : iEnd);
if ~numel(nFreqs); continue; end;
nFreqs = nFreqs(1);
nTones = nTones(1);
% skip basic sessions
% if nFreqs == 1 && nTones == 1;
% hitRate(iBin) = NaN;
% falsePosRate(iBin) = NaN;
% dprimes(iBin) = NaN;
% continue;
% end;
% if there is a change in the number of frequencies or tones, mark it
if prevNFreqs ~= 0 && (nFreqs ~= prevNFreqs || nTones ~= prevNTones);
changeOfFreqOrToneNum(iBin) = iBin - 1;
end;
% store for next iteration
prevNFreqs = nFreqs;
prevNTones = nTones;
hitRate(iBin) = 100 * countsForBin.TGO / countsForBin.T;
falsePosRate(iBin) = 100 * countsForBin.NTGO / countsForBin.NT;
if isnan(countsForBin.DPRIME) || isinf(countsForBin.DPRIME);
countsForBin.DPRIME = 0;
end;
% restrict the dprime value between +dprimeMaxVal and -dprimeMaxVal
countsForBin.DPRIME = min(dprimeMaxVal, countsForBin.DPRIME);
countsForBin.DPRIME = max(-dprimeMaxVal, countsForBin.DPRIME);
dprimes(iBin) = countsForBin.DPRIME;
end;
TGOsHand = plot(1 : nBins, hitRate, '-sg', 'MarkerFaceColor', 'green');
% TGOsErrHand = errorbar(1 : nBins, hitRate, hitRateError, '-sg', 'MarkerFaceColor', 'green');
% removeErrorBarEnds(TGOsErrHand);
hold all;
hitRateAxes = gca;
NTNGOsHand = plot((1 : nBins) + 0.15, falsePosRate, '-sr', 'MarkerFaceColor', 'red');
% NTNGOsErrHand = errorbar((1 : nBins) + 0.15, falsePosRate, falsePosRateError, '-sr', 'MarkerFaceColor', 'red');
% removeErrorBarEnds(NTNGOsErrHand);
set(hitRateAxes, 'ylim', [0 110], 'YTick', 0 : 10 : 110, 'YTickLabel', 0 : 10 : 110);
if useSEM;
% ylabel('% of Trials \pm SEM'); %%#ok<UNRCH>
ylabel('% of trials'); %%#ok<UNRCH>
else
% ylabel('% of Trials \pm SD'); %#ok<UNRCH>
ylabel('% of trials'); %#ok<UNRCH>
end;
vertLineHandles = zeros(1, sum(changeOfFreqOrToneNum > 0));
vertLineTextHandles = zeros(2, sum(changeOfFreqOrToneNum > 0));
iLineHandle = 1;
for iChange = 1 : numel(changeOfFreqOrToneNum);
if ~changeOfFreqOrToneNum(iChange); continue; end;
changeX = changeOfFreqOrToneNum(iChange) - 0.5;
iBin = changeOfFreqOrToneNum(iChange);
iStart = (iBin - 1) * binWidth + 1; % for binWidth = 10: 1, 11, 21, etc.
iEnd = min(iBin * binWidth, nTrials); % for binWidth = 10: 10, 20, 30, etc.
nFreqs1 = outAll.nFreqs(iStart : iEnd);
nFreqs1 = nFreqs1(1);
iBin = changeOfFreqOrToneNum(iChange) + 1;
iStart = (iBin - 1) * binWidth + 1; % for binWidth = 10: 1, 11, 21, etc.
iEnd = min(iBin * binWidth, nTrials); % for binWidth = 10: 10, 20, 30, etc.
nFreqs2 = outAll.nFreqs(iStart : iEnd);
nFreqs2 = nFreqs2(1);
if mod(iChange, 2) == 0;
changeY = 9;
else
changeY = 12;
end;
vertLineTextHandles(1, iLineHandle) = text(changeX, changeY, ...
sprintf('%d freq \\leftarrow ', nFreqs1), 'HorizontalAlignment', 'right');
vertLineTextHandles(2, iLineHandle) = text(changeX, changeY, sprintf(' \\rightarrow %d freq', nFreqs2));
vertLineHandles(iLineHandle) = line([changeX changeX], [0 100], ...
'LineStyle', ':', 'Color', 'black');
iLineHandle = iLineHandle + 1;
end;
xlimits = [0 nBins * 1.05];
xlim(xlimits);
set(hitRateAxes, 'XTick', [], 'XTickLabel', []);
xTickAxes = axes('Position', get(gca, 'Position'), ...
'YAxisLocation', 'right', 'XAxisLocation', 'bottom', 'Color', 'none');
step = nBins / (nTrials / 500);
set(xTickAxes, 'xlim', xlimits, ...
'XTick', 1 : step : (nBins + 1), 'XTickLabel', 0 : 500 : ((nBins + 1) * binWidth));
set(xTickAxes, 'YTick', [], 'YTickLabel', []);
xlabel('Trials');
dprimeAxes = axes('Position', get(gca, 'Position'), ...
'YAxisLocation', 'right', 'XAxisLocation', 'top', 'Color', 'none');
hold all;
dprimesHand = plot((1 : nBins) + 0.3, dprimes, '-sb', 'MarkerFaceColor', 'blue');
% dprimesErrHand = errorbar((1 : nBins) + 0.3, dprimes, dprimesError, '-sb', 'MarkerFaceColor', 'blue');
% removeErrorBarEnds(dprimesErrHand);
set(dprimeAxes, 'ylim', [dprimeMinVal dprimeMaxVal], 'YTick', dprimeMinVal : 0.5 : dprimeMaxVal, ...
'YTickLabel', dprimeMinVal : 0.5 : dprimeMaxVal);
set(dprimeAxes, 'XTick', [], 'XTickLabel', []);
xlim(xlimits);
if useSEM;
% ylabel('d'' value \pm SEM'); %%#ok<UNRCH>
ylabel('d'' value'); %%#ok<UNRCH>
else
% ylabel('d'' value \pm SD'); %#ok<UNRCH>
ylabel('d'' value'); %#ok<UNRCH>
end;
% legend([TGOsErrHand, NTNGOsErrHand, dprimesErrHand], {'HitRate', 'FalsePos', 'd'''}, ...
% 'Location', 'NorthWest');
legend([TGOsHand, NTNGOsHand, dprimesHand], {'HitRate', 'FalsePos', 'd'''}, ...
'Location', 'NorthWest');
% title(sprintf('%s \\fontsize{10} [Total number of trials = %.0f, binWidth = %.0f]', ...
% titleStr, nTrials, binWidth));
title(titleStr);
hold off;
makePrettyFigure(figHand);
set(xTickAxes, 'FontSize', 9);
for iLineHandle = 1 : numel(vertLineHandles);
set(vertLineHandles(iLineHandle), 'LineWidth', 0.5);
set(vertLineTextHandles(1, iLineHandle), 'FontSize', 10);
set(vertLineTextHandles(2, iLineHandle), 'FontSize', 10);
end;
end
|
github
|
HelmchenLabSoftware/OCIA-master
|
mtrainer.m
|
.m
|
OCIA-master/behavior/mtrainer/mtrainer.m
| 16,753 |
utf_8
|
f5cf1c7c0cf86007548ef75917035e5c
|
function mtrainer()
% main function for mtrainer experiment suite
% all times are in s!
% written by Henry Luetcke ([email protected])
% 2013-05-07
% modified by Balazs Laurenczy ([email protected])
% 2013-05-15
% modified by Balazs Laurenczy ([email protected])
% 2013-08-08
doEmptyWater = 0;
% doEmptyWater = 1;
automode = 5; % if > 0, sets the number of seconds to wait before a new run of mtrainer
lickThresh = 0.13;
% lickThresh = NaN;
unsavedOut = struct();
% mouseId = 'testing'; taskType = 'freqDiscrimination'; phase = 'C';
% mouseId = '130801_01'; taskType = 'freqDiscrimination'; phase = 'F';
mouseId = '130801_03'; taskType = 'freqDiscrimination'; phase = 'F';
% mouseId = '130408_02'; taskType = 'freqDiscrimination'; phase = 'D';
% mouseId = '130416_01'; taskType = 'oddballDiscrimination'; phase = 'E';
% mouseId = '130425_01'; taskType = 'freqDiscrimination'; phase = 'B';
% mouseId = '130425_02'; taskType = 'oddballDiscrimination'; phase = 'C';
% mouseId = '130528_01'; taskType = 'oddballDiscrimination'; phase = 'B';
% mouseId = '130528_02'; taskType = 'oddballDiscrimination'; phase = 'B';
basePath = 'P:\matlab\daq\mtrainer\configs\';
configMat = load([basePath taskType filesep taskType '_phase' phase '.mat']);
config = configMat.config;
unsavedOut.mouseId = mouseId;
unsavedOut.taskType = taskType;
unsavedOut.phase = phase;
unsavedOut.basePath = basePath;
unsavedOut.config = config;
%% Setup - stimuli and trials
fprintf('Setup stimuli and trials... ');
% set up stimulus vector
stims = [];
for iFreq = 1 : numel(config.tone.freqs)
stimForFreq = repmat(iFreq, 1, round(config.tone.stimProba(iFreq) * config.training.nTrials));
stims = [stims, stimForFreq]; %#ok<AGROW>
end
stims = stims(randperm(numel(stims)));
clear stim;
% set up oddball vector by altering stims with a certain probability
odds = stims;
oddPos = zeros(size(odds));
uniqueStims = unique(stims);
isOdd = rand(1, numel(stims)) < config.tone.oddProba;
uniqueOddPos = config.tone.nTones - 1 : config.tone.nTones; % last 2 tones can be odd
for iStim = 1 : numel(isOdd);
if isOdd(iStim);
otherStims = uniqueStims(uniqueStims ~= stims(iStim));
otherStims = otherStims(randperm(numel(otherStims)));
mixedOddPos = uniqueOddPos(randperm(numel(uniqueOddPos)));
odds(iStim) = otherStims(1);
oddPos(iStim) = mixedOddPos(1);
end;
end;
% set up tone array
toneArray = MakePureMultiToneOddballArray(config.tone.freqs, stims, odds, oddPos, ...
config.tone.nTones, config.tone.toneDur, config.tone.ISI, config.tone.samplingFreq);
unsavedOut.stims = stims;
unsavedOut.odds = odds;
unsavedOut.oddPos = oddPos;
unsavedOut.isOdd = isOdd;
fprintf('done.\n');
%% Setup - hardware
% define globals
global recordedValues;
% analog input
daqreset;
fprintf('Connecting hardware...\n');
s1 = daq.createSession(config.hardware.adaptorID);
recordRate = config.hardware.analogIn_SampleRate;
% recordRate = 700;
s1.Rate = recordRate;
s1.addAnalogInputChannel(config.hardware.analogIn_Device, ...
config.hardware.analogIn_Channel, 'Voltage');
s1.Channels(1).InputType = config.hardware.analogIn_InputType;
s1.Channels(1).Range = config.hardware.analogIn_Range;
fprintf('s1 ok.\n');
s2 = daq.createSession(config.hardware.adaptorID);
s2.addDigitalChannel(config.hardware.digitalOut_Device, config.hardware.digitalOut_PortLine, 'OutputOnly');
fprintf('And s2 ok. Ready to go.\n');
if isnan(lickThresh);
% baseline measurement
fprintf('Testing analog input for licking threshold (baseline)... ');
recordDuration = 2;
s1.DurationInSeconds = recordDuration;
baseline = s1.startForeground; % this will block the command line
meanData = mean(baseline);
stdData = std(baseline);
lickThresh = 2.8 * stdData;
fprintf('done.\n')
pause(1);
% lick measurement
fprintf('Testing analog input for licking threshold (licking)... ');
s1.DurationInSeconds = recordDuration;
lick = s1.startForeground; % this will block the command line
fprintf('done.\n2SD: %1.2f, lick threshold: %1.2f\n', 2 * stdData, lickThresh);
% plotting
figure('Name', 'LickingThreshold', 'Position', [150, 300, 950, 350], 'NumberTitle', 'off' ...
... % , 'MenuBar', 'none', 'ToolBar', 'none');
);
plot((1:numel(baseline)) / recordRate, baseline - meanData, 'b');
hold on;
plot((1:numel(lick)) / recordRate, lick - meanData, 'r');
line([0, recordDuration], [lickThresh, lickThresh], 'Color', 'green');
line([0, recordDuration], [2 * stdData, 2 * stdData], 'Color', 'cyan');
line([0, recordDuration], [- 2 * stdData, - 2 * stdData], 'Color', 'cyan');
legend({'baseline', 'licking', 'lickTreshold', '\pm 2SD'});
title(sprintf('2SD: %1.2f, lick thresh %1.2f', 2 * stdData, lickThresh));
else
fprintf('Testing analog input for licking threshold... skipped.\nLick threshold: %1.2f\n', ...
lickThresh);
end;
unsavedOut.lickThresh = lickThresh;
% digital out
fprintf('Testing reward system by opening for %.2fs after a delay of %.2fs... ', ...
config.training.rewDur, config.training.rewDelay);
giveReward(s2, config.training.rewDur * 3, config.training.rewDelay);
fprintf('done!\n')
if doEmptyWater > 0;
doEmptyWater = str2double(input('Empty water ? >0 = yes, <0 = no\n', 's')); %#ok<UNRCH>
while doEmptyWater > 0;
fprintf('Emptying water... ');
giveReward(s2, doEmptyWater, 0);
fprintf(' done.');
doEmptyWater = str2double(input('Empty more ? >0 = yes, <0 = no\n', 's'));
if isnan(doEmptyWater); doEmptyWater = 0; end;
if ~doEmptyWater; break; end;
end;
end;
s1.IsNotifyWhenDataAvailableExceedsAuto = true;
lh = s1.addlistener('DataAvailable', @(src, event) recordAndStop(src, event, lickThresh));
s1.IsContinuous = true;
s1.prepare;
%% Setup - saving settings
recordedValues = 0;
saveTime = datestr(now, 'yyyy_mm_dd__HH_MM_SS');
saveFolder = sprintf('C:\\Users\\laurenczy\\mtrainerData\\%s\\', mouseId);
savePath = sprintf('%s%s__%s', saveFolder, mouseId, saveTime);
mkdir(saveFolder);
logfile = sprintf('%s_log.txt', savePath);
logDateFormat = 'yyyy-mm-dd HH:MM:SS.FFF';
% create an 'onCleanup' function to handle interruptions by CTRL+C
c = onCleanup(@()closeDiaryAndSaveOutput(savePath, lh, s1, s2));
fprintf('Finished setting up and hardware tests.\n');
fprintf('CHECK MOUSE ID!! currently: %s.\n', mouseId);
if automode;
pause(automode);
else
fprintf('Then press any key to start!'); %#ok<UNRCH>
pause;
end;
unsavedOut.savePath = savePath;
unsavedOut.saveTime = saveTime;
diary(logfile);
%% Start experiment
fprintf('Experiment start: %s\n\n', datestr(now, logDateFormat));
try
%% Experiment - initialize variables
dbgLevel = 0;
out = unsavedOut;
o('config: %s phase %s (%dF%dT)', out.taskType, out.phase, numel(config.tone.freqs), ...
config.tone.nTones, 0, dbgLevel);
o('animal: %s', mouseId, 0, dbgLevel);
o('savePath: %s', savePath, 0, dbgLevel);
o('lickThresh: %1.2f, ISI: %1.2f', lickThresh, config.tone.ISI, 0, 0);
o('rewardCollectionTime: %1.2f, InTriLickTimerDur: %1.2f', ...
config.training.rewCollTime, ...
config.training.InTriLickTimerDur, 0, dbgLevel);
nTrials = config.training.nTrials;
% totalTrialDur = config.training.trialDur + config.training.startDelay + ...
% config.training.rewCollTime;
% compute relative start times for each trial
% out.trialStarts_sched = 0 : totalTrialDur : (nTrials - 1) * totalTrialDur;
% out.trialStarts_obs = zeros(1, nTrials);
% out.trialEnds_obs = zeros(1, nTrials);
out.trialStartDelays = zeros(1, nTrials);
out.trialStartTimes = zeros(1, nTrials);
out.trialEndTimes = zeros(1, nTrials);
out.respTimes = nan(1, nTrials);
out.nInTriLick = nan(1, nTrials);
out.resps = nan(1, nTrials);
out.respDelays = nan(1, nTrials);
% for each trial: 1 = correct detect, 2 = correct reject, 3 = false alarm, 4 = miss, 5 = early
out.respTypes = nan(1, nTrials);
out.expStartTime = tic;
isPunish = 0;
for iTrial = 1 : nTrials;
out.iTrial = iTrial;
% listen for response
s1.startBackground;
pause(0.01)
interTrialLickCount = 0;
out.trialStartTimes(iTrial) = tic;
% introduce a random delay for starting the tone
out.trialStartDelays(iTrial) = config.training.startDelay + ...
(rand(1) - 0.5) * 2 * config.training.startDelayRand;
% add punishement time-out if needed
if isPunish;
out.trialStartDelays(iTrial) = out.trialStartDelays(iTrial) + config.training.timeoutPunish;
end;
%% Experiment - initial wait
while toc(uint64(out.trialStartTimes(iTrial))) < out.trialStartDelays(iTrial);
% fprintf('CheckingA: s1.IsRunning? %d\n', s1.IsRunning);
% check if no lick has been done
if ~s1.IsRunning; % if not running anymore, it means a licking has been done
remainingTime = out.trialStartDelays(iTrial) - toc(uint64(out.trialStartTimes(iTrial)));
if interTrialLickCount > 0;
fprintf('|%.1f', remainingTime);
else
fprintf(' inter-trial licking: |%.1f', remainingTime);
end;
% reset the starting delay to config.training.InTriLickTimerDur
out.trialStartTimes(iTrial) = tic;
if isPunish;
out.trialStartDelays(iTrial) = max(config.training.InTriLickTimerDur, remainingTime);
else
out.trialStartDelays(iTrial) = config.training.InTriLickTimerDur;
end;
interTrialLickCount = interTrialLickCount + 1;
pause(1);
% restart the listening
s1.startBackground;
pause(0.1);
% fprintf('CheckingB: s1.IsRunning? %d\n', s1.IsRunning);
end
% avoid full-speed looping
pause(0.01);
end;
if interTrialLickCount;
fprintf('|: %d inter-trial lick(s).\n', interTrialLickCount);
end
out.nInTriLick(iTrial) = interTrialLickCount;
resp = 0;
isPunish = 0;
t_trialStart = tic;
fprintf('Trial %03d/%03d - %s ... ', iTrial, nTrials, datestr(now, logDateFormat));
%% Experiment - play sound
if s1.IsRunning
soundToPlay = toneArray{iTrial};
player = audioplayer(soundToPlay, config.tone.samplingFreq); %#ok<TNMLP>
player.play;
else
fprintf('early (already licking, lick sensor: min/mean/max: %.2f/%.2f/%.2f).\n', ...
recordedValues);
isPunish = 1;
out.respTypes(iTrial) = 5;
% analyse every 10 trials
if ~rem(iTrial, 10) && iTrial ~= nTrials;
mtrainerAnalyser_performance(out.respTypes, 0);
end;
continue;
end
breakOut = 0;
%% Experiment - wait for response
while toc(t_trialStart) < config.training.trialDur;
if s1.IsRunning
% no response detected
else
% seconds since trial start
respTime = toc(t_trialStart);
out.respTimes(iTrial) = respTime;
% response should be 'minRespTime' after the end of the tone!
totToneDur = (config.tone.toneDur + config.tone.ISI) * config.tone.nTones - config.tone.ISI;
limitRespTime = totToneDur + config.training.minRespTime;
% limitRespTime = config.training.minRespTime;
out.respDelays(iTrial) = limitRespTime - respTime;
% early response, count as kind of false alarm
if respTime < limitRespTime;
% fprintf('early (lick sensor: min/mean/max: %.2f/%.2f/%.2f).\n', ...
% recordedValues);
fprintf('early (response time: %.4f, limit response time: %.4f, diff: %.5f).\n', ...
respTime, limitRespTime, limitRespTime - respTime);
isPunish = 1;
out.respTypes(iTrial) = 5;
breakOut = 1;
break;
else
% fprintf('Lick at %s\n', datestr(clock, logDateFormat))
resp = 1;
end;
break; % break out of while loop
end;
pause(0.02); % necessary to allow time for data collection
end;
if breakOut;
out.trialEndTimes(iTrial) = toc(uint64(out.trialStartTimes(iTrial)));
% analyse every 10 trials
if ~rem(iTrial, 10) && iTrial ~= nTrials;
mtrainerAnalyser_performance(out.respTypes, 0);
end;
continue; % continue for loop
end;
if s1.IsRunning;
s1.stop;
end;
%% Experiment - analyse response
out.resps(iTrial) = resp;
isOddTrial = stims(iTrial) ~= odds(iTrial);
if config.tone.oddProba > 0; % oddball discrimination
isTargetStim = isOddTrial && config.tone.goStim;
else % frequency discrimination
isTargetStim = stims(iTrial) == config.tone.goStim;
end;
if resp == 1 && isTargetStim;
% correct response
% fprintf('correct detection (lick sensor: min/mean/max: %.2f/%.2f/%.2f).\n', ...
% recordedValues);
fprintf('correct detection (response time: %.4f, limit response time: %.4f, diff: %.5f).\n', ...
respTime, limitRespTime, limitRespTime - respTime);
out.respTypes(iTrial) = 1;
% give reward
giveReward(s2,config.training.rewDur,config.training.rewDelay);
% wait to collect the reward
pause(config.training.rewCollTime);
elseif resp == 1 && ~isTargetStim;
% false alarm
% fprintf('false alarm (lick sensor: min/mean/max: %.2f/%.2f/%.2f).\n', ...
% recordedValues);
fprintf('false alarm (response time: %.4f, limit response time: %.4f, diff: %.5f).\n', ...
respTime, limitRespTime, limitRespTime - respTime);
out.respTypes(iTrial) = 3;
% punish time-out
isPunish = 1;
elseif resp == 0 && isTargetStim;
fprintf('miss.\n');
out.respTypes(iTrial) = 4;
% punish time-out
isPunish = 1;
elseif resp == 0 && ~isTargetStim;
fprintf('correct rejection.\n');
out.respTypes(iTrial) = 2;
% go to next trial
end
out.trialEndTimes(iTrial) = toc(uint64(out.trialStartTimes(iTrial)));
% analyse every 10 trials
if ~rem(iTrial, 10) && iTrial ~= nTrials;
mtrainerAnalyser_performance(out.respTypes, 0);
end
end
%% End experiment
fprintf('\nExperiment end: %s\n', datestr(now, logDateFormat));
out.expTotDurTime = toc(out.expStartTime);
fprintf('Total time: %02.0f:%02.0f\n', out.expTotDurTime / 60, mod(out.expTotDurTime, 60));
mtrainerAnalyser_performance(out.respTypes, 2, out.savePath, out.nInTriLick);
catch err
fprintf('\n\nAn error occured. Last trial: %1.0f. Cleaning up ...\n\n', iTrial)
rethrow(err);
end
%% Function - giveReward
function giveReward(s2, rewDur, rewDelay)
t_rewardStart = tic;
% wait until for start delay
while toc(t_rewardStart) < rewDelay; end;
t_rewardStart = tic;
% open digital out
s2.outputSingleScan(0);
% wait until for open duration
while toc(t_rewardStart) < rewDur; end;
% close digital out
s2.outputSingleScan(1);
end
function recordAndStop(src, event, lickThresh)
recordedValues = stopWhenExceedThreshold(src, event, lickThresh);
end
function closeDiaryAndSaveOutput(savePath, lh, s1, s2)
fprintf('\nClosing diary... ');
diary off;
fprintf('done.\n');
if (exist('out', 'var'));
matFileName = sprintf('%s_out.mat', savePath);
fprintf('Saving output as %s... ', matFileName);
save(matFileName, 'out');
fprintf('done.\n');
else
fprintf('/!\\ Output not saved\n');
end;
fprintf('Closing channels... ');
if exist('lh', 'var'); delete(lh); end;
if exist('s1', 'var'); delete(s1); end;
if exist('s2', 'var'); delete(s2); end;
fprintf('done.\n');
end
end
|
github
|
HelmchenLabSoftware/OCIA-master
|
mtrainerAnalyser_performance.m
|
.m
|
OCIA-master/behavior/mtrainer/mtrainerAnalyser_performance.m
| 8,824 |
utf_8
|
7c3efc292a98890cdd2df684966b8536
|
%% Function - mtrainerAnalyser_performance
function mtrainerAnalyser_performance(varargin)
if nargin >= 1;
% for each trial: 1 = correct detect, 2 = correct reject, 3 = false alarm, 4 = miss, 5 = early
respTypes = varargin{1};
doSavePlots = 0;
savePath = '';
end;
if nargin >= 2;
doSavePlots = varargin{2};
savePath = 'perf.png';
end;
if nargin >= 3;
savePath = varargin{3};
end;
if nargin == 4;
nIntrLick = varargin{4};
end;
if nargin < 1 || nargin > 4;
error('mtrainerAnalyser_performance:WrongArgumentNumberException', ...
['Number of arguments should be 1 ', ...
'(responseTypeVector), 2 (responseTypeVector, doSavePlots) ', ...
'or 3 (responseTypeVector, doSavePlots, savePath) (or 4 with nIntrLick)', ...
'Please see the help for this function.']);
end;
counts_all = mtrainerAnalyzer_getCounts(respTypes);
% print out a 'nicely' formatted table
% 'fprintf' patterns for the content of the headers and the cells
n = '3'; % number of digits to display for number
np = '3'; % number of digits to display for percents
headerPattern = [' (%0' n 'd|%0' np '.f%%) '];
cellPattern = ['%0' n 'd (%0' np '.0f%%) '];
fprintf(['Performance: d'' = %.3f, early: %0' n 'd/%0' n 'd (%0' np '.f%%), ' ...
'correctness: %0' np '.f%%\n'], counts_all.DPRIME, counts_all.EARLY, counts_all.TOT, ...
counts_all.EARLYP, counts_all.CiP);
if ~counts_all.NT; tableContent = cell(3, 2);
else tableContent = cell(3, 3); end;
% header line
tableContent{1, 1} = sprintf([' VALID: %0' n 'd/%0' n 'd (%0' np '.f%%)'], ...
counts_all.VTOT, counts_all.TOT, counts_all.VTOTP);
tableContent{1, 2} = sprintf(['TARG.', headerPattern], counts_all.T, counts_all.TP);
if counts_all.NT; tableContent{1, 3} = sprintf(['NON-TARG.', headerPattern], ...
counts_all.NT, counts_all.NTP); end;
% GO line
tableContent{2, 1} = sprintf([' GO ', headerPattern], counts_all.GO, counts_all.GOP);
tableContent{2, 2} = sprintf(cellPattern, counts_all.TGO, counts_all.TGOP);
if counts_all.NT; tableContent{2, 3} = sprintf(cellPattern, counts_all.NTGO, counts_all.NTGOP); end;
% NO-GO line
tableContent{3, 1} = sprintf([' NO-GO ', headerPattern], counts_all.NGO, counts_all.NGOP);
tableContent{3, 2} = sprintf(cellPattern, counts_all.TNGO, counts_all.TNGOP);
if counts_all.NT; tableContent{3, 3} = sprintf(cellPattern, counts_all.NTNGO, counts_all.NTNGOP); end;
tprintf(23, tableContent);
fprintf('(Percentages of the table are relative to valid trials (non-early))\n');
if doSavePlots < 1;
return;
end;
saveName = strrep(regexp(savePath, '\\[\d_]+$', 'match'), '\', '');
if numel(saveName);
saveName = ['Perf - ' saveName{1}];
else
saveName = 'Perf';
end;
fprintf('Plotting... (doSavePlots: %d)\n', doSavePlots);
figure('Name', saveName, 'NumberTitle', 'off', 'MenuBar', 'none', 'WindowStyle', 'docked');
title(strrep(saveName, '_', '\_'));
% Valid trials
subplot(3, 2, 1);
bar(1, counts_all.EARLY, 1, 'FaceColor', [0.3 0.3 0.3]);
hold on;
bar(2, counts_all.VTOT, 1, 'FaceColor', [0 1 0]);
text(1.3, - max(ylim) / 10, sprintf('Early (%3.f%%)', counts_all.EARLYP), ...
'horizontalalignment', 'right', 'FontSize', 10);
text(2.3, - max(ylim) / 10, sprintf('Valid (%3.f%%)', counts_all.VTOTP), ...
'horizontalalignment', 'right', 'FontSize', 10);
set(gca, 'XTickLabel', '');
title(sprintf('Early versus valid trials (%d trials)', counts_all.TOT));
% ylim([0 counts_all.TOT * 1.01]);
ylim([0 max(counts_all.EARLY, counts_all.VTOT) * 1.2]);
ylabel('Number of Trials');
% Correct vs false
subplot(3, 2, 2);
bar(1, counts_all.C, 1, 'FaceColor', [0 1 0]);
hold on;
bar(2, counts_all.F, 1, 'FaceColor', [1 0 0]);
text(1.4, - max(ylim) / 10, sprintf('Correct (%3.f%%)', counts_all.CP), ...
'horizontalalignment', 'right', 'FontSize', 10);
text(2.4, - max(ylim) / 10, sprintf('Wrong (%3.f%%)', counts_all.FP), ...
'horizontalalignment', 'right', 'FontSize', 10);
set(gca, 'XTickLabel', '');
title(sprintf('Correct versus wrong trials (%d valid trials)', counts_all.VTOT));
ylim([0 max(counts_all.C, counts_all.F) * 1.2]);
% ylim([0 counts_all.TOT * 1.01]);
ylabel('Number of Trials');
TGOovTimeP = zeros(1, counts_all.TOT);
NTNGOovTimeP = zeros(1, counts_all.TOT);
NTGOovTimeP = zeros(1, counts_all.TOT);
TNGOovTimeP = zeros(1, counts_all.TOT);
EARLYovTimeP = zeros(1, counts_all.TOT);
% binWidth = -1; % cumulative
binWidth = fix(counts_all.TOT * 0.1); % binning
% binWidth = 3; % binning
for i = 1 : counts_all.TOT;
% for i = 1 : binWidth : counts_all.TOT;
if binWidth ~= -1;
% iStart = max(i - 0.5 * (binWidth - 1), 1);
% iEnd = min(i + 0.5 * (binWidth - 1), counts_all.TOT);
iStart = max(i - binWidth, 1);
iEnd = min(i + binWidth, counts_all.TOT);
TGOovTimeP(i) = (sum(respTypes(iStart : iEnd) == 1) / (iEnd - iStart)) * 100;
NTNGOovTimeP(i) = (sum(respTypes(iStart : iEnd) == 2) / (iEnd - iStart)) * 100;
NTGOovTimeP(i) = (sum(respTypes(iStart : iEnd) == 3) / (iEnd - iStart)) * 100;
TNGOovTimeP(i) = (sum(respTypes(iStart : iEnd) == 4) / (iEnd - iStart)) * 100;
EARLYovTimeP(i) = (sum(respTypes(iStart : iEnd) == 5) / (iEnd - iStart)) * 100;
else
TGOovTimeP(i) = sum(respTypes(1 : i) == 1) / i * 100;
NTNGOovTimeP(i) = sum(respTypes(1 : i) == 2) / i * 100;
NTGOovTimeP(i) = sum(respTypes(1 : i) == 3) / i * 100;
TNGOovTimeP(i) = sum(respTypes(1 : i) == 4) / i * 100;
EARLYovTimeP(i) = sum(respTypes(1 : i) == 5) / i * 100;
end;
end;
pause(0.05);
subplot(3, 2, 3);
percents = [TGOovTimeP; NTNGOovTimeP; NTGOovTimeP; ...
TNGOovTimeP; EARLYovTimeP];
bar(percents', 1, 'stacked', 'EdgeColor', 'none');
% bar(percents', binWidth, 'stacked', 'EdgeColor', 'none');
hold off;
title('Percent of trials types over time');
ylim([0 100]);
xlim([1 counts_all.TOT]);
ylabel('% Trials');
xlabel('Trials');
% legHand = legend({'Corr. det.', 'Corr. rej.', 'False alarm', 'Miss', 'Early'}, 'Location', 'EastOutside', ...
% 'FontSize', 12, 'Orientation', 'vertical');
DPRIMEovTimeP = zeros(1, counts_all.TOT);
% binWidth = -1; % cumulative
binWidth = fix(counts_all.TOT * 0.1); % binning
% binWidth = 5; % binning
for i = 1 : counts_all.TOT;
% for i = 1 : binWidth : counts_all.TOT;
if binWidth ~= -1;
% iStart = max(i - 0.5 * (binWidth - 1), 1);
% iEnd = min(i + 0.5 * (binWidth - 1), counts_all.TOT);
iStart = max(i - binWidth, 1);
iEnd = min(i + binWidth, counts_all.TOT);
counts_till_i = mtrainerAnalyzer_getCounts(respTypes(iStart : iEnd));
DPRIMEovTimeP(i) = dprime(counts_till_i.TGO ./ counts_till_i.T, ...
counts_till_i.NTGO ./ counts_till_i.NT, counts_till_i.T, counts_till_i.NT);
else
counts_till_i = mtrainerAnalyzer_getCounts(respTypes(1 : i));
DPRIMEovTimeP(i) = dprime(counts_till_i.TGO ./ counts_till_i.T, ...
counts_till_i.NTGO ./ counts_till_i.NT, counts_till_i.T, counts_till_i.NT);
end;
end;
subplot(3, 2, 4);
plot(1 : counts_all.TOT, DPRIMEovTimeP);
title('d'' over time');
% ylim([0 100]);
xlim([1 counts_all.TOT]);
ylabel('d''');
xlabel('Trials');
% legHand = legend({'Corr. det.', 'Corr. rej.', 'False alarm', 'Miss', 'Early'}, 'Location', 'EastOutside', ...
% 'FontSize', 12, 'Orientation', 'vertical');
subplot(3, 2, 5);
plot(1 : counts_all.TOT, TGOovTimeP + NTGOovTimeP + EARLYovTimeP);
title('Responsiveness');
ylim([0 100]);
xlim([1 counts_all.TOT]);
ylabel('% of GO');
xlabel('Trials');
if exist('nIntrLick', 'var');
subplot(3, 2, 6);
plot(1 : numel(nIntrLick), nIntrLick);
title('Number of inter-trial licking');
% ylim([0 100]);
xlim([1 numel(nIntrLick)]);
ylabel('Number of lick');
xlabel('Trials');
end;
pause(0.05);
% makePrettyFigure(gcf);
% set(legHand, 'FontSize', 12);
if doSavePlots < 2;
return;
end;
fprintf('Saving... (doSavePlots: %d)\n', doSavePlots);
saveas(gcf, [savePath '_perf.png']);
saveas(gcf, [savePath '_perf.fig']);
end
|
github
|
HelmchenLabSoftware/OCIA-master
|
mtrainerAnalyser_loadAllFromFolder.m
|
.m
|
OCIA-master/behavior/mtrainer/mtrainerAnalyser_loadAllFromFolder.m
| 11,698 |
utf_8
|
f65b08bd16909d18e68a76b009bf88ee
|
%% Function - mtrainerAnalyser_loadAllFromFolder
function outAll = mtrainerAnalyser_loadAllFromFolder(folderPath, skipIncomplete, doMakeConsistent, ...
doRemoveUnresponsive, doSavePlots)
%% Initialize variables
dbgLevel = 4;
% output structure for all data in the requested folder
outAll = struct();
% fields that need to be gathered
toGatherFields = {
'respTypes', 'nInTriLick', 'datesAsNum', 'taskTypes', ...
'nFreqs', 'nTones', 'freqs', 'goFreq' ...
};
% initialize the structure with these fields
for iField = 1 : numel(toGatherFields);
outAll.(toGatherFields{iField}) = [];
end;
% remodelling of the saved out structrures
toRemoveField = { ...
'trialEnds_obs'
'trialStarts_obs'
'trialStarts_sched'
}; %#ok<NASGU>
toRenameField = { ... %#ok<NASGU>
% 'responseTypeVector', 'respTypes';
% 'responseTimeVector', 'respTimes';
% 'trial', 'iTrial';
% 'trialEndVector_observed', 'trialEnds_obs';
% 'trialStartVector_observed', 'trialStarts_obs';
% 'trialStartVector_scheduled', 'trialStarts_sched';
'trialEndsTimes', 'trialEndTimes';
'respDelay', 'respDelays';
}; %#ok<NASGU>
requiredFields = { ... %#ok<NASGU>
'mouseId', 'MOUSE_ID';
'taskType', 'TASK_TYPE';
'phase', '?';
'basePath', '?';
'config', struct();
'stims', [];
'odds', [];
'oddPos', [];
'isOdd', [];
'savePath', '?';
'saveTime', 'SAVE_TIME';
% 'trialStarts_sched', [];
% 'trialStarts_obs', [];
% 'trialEnds_obs', [];
'respTimes', [];
'nInTriLick', [];
'resps', [];
'respDelays', [];
'respTypes', [];
'expStartTime', -1;
'expTotDurTime', -1;
}; %#ok<NASGU>
%% Gather mat-files and loop through them
matFiles = dir([folderPath '/*.mat']);
o('#mtrainerAnalyser_loadAllFromFolder: processing %d mat-file(s) in folder "%s" ...', ...
numel(matFiles), folderPath, 1, dbgLevel);
nValidMatFiles = 0;
for iExp = 1 : numel(matFiles);
% get the full path and load the mat-file
fullPath = sprintf('%s/%s', folderPath, matFiles(iExp).name);
mat = load(fullPath);
mouseId = matFiles(iExp).name(1:9); %#ok<NASGU>
saveTime = matFiles(iExp).name(12:31); %#ok<NASGU>
% check for the presence of the 'out' struct inside, otherwise create it
if ~isfield(mat, 'out');
out = mat;
save(fullPath, 'out');
else
out = mat.out;
end;
% extract the task type, the number of tones/frequencies used from the logFile
out = parseLogFile(out, fullPath, iExp, dbgLevel);
% remodelling of the out.mat file: change names, delete useless fields, etc.
if doMakeConsistent;
out = makeConsistent(out, fullPath, iExp, toRemoveField, toRenameField, requiredFields, dbgLevel); %#ok<UNRCH>
end;
% skip problematic vectors
if ~isfield(out, 'respTypes');
o(' #mtrain...FromFolder: %d: %s has no ''respTypes'' field.', ...
iExp, matFiles(iExp).name, 2, dbgLevel);
continue;
elseif skipIncomplete && any(out.respTypes == 0);
o(' #mtrain...FromFolder: %d: %s has an incomplete ''respTypes''.', ...
iExp, matFiles(iExp).name, 2, dbgLevel);
continue;
else
o(' #mtrain...FromFolder: %d: %s is valid.', iExp, matFiles(iExp).name, 2, dbgLevel);
nValidMatFiles = nValidMatFiles + 1;
end;
% remodelling of the out.mat file: removing long non responsive parts
if doRemoveUnresponsive;
outOri = out;
[out, unResps] = removeUnresponsive(out, iExp, dbgLevel); %#ok<UNRCH>
end;
dateAsStr = matFiles(iExp).name(12:31);
if doSavePlots;
mtrainerAnalyser_performance(outOri.respTypes, 1, ['\01_' dateAsStr], outOri.nInTriLick);
mtrainerAnalyser_performance(out.respTypes, 1, ['\02_' dateAsStr], out.nInTriLick);
end;
dateAsNum = datenum(dateAsStr, 'yyyy_mm_dd__HH_MM_SS');
nTrials = numel(out.respTypes);
outAll.respTypes = [outAll.respTypes out.respTypes];
outAll.nInTriLick = [outAll.nInTriLick out.nInTriLick];
outAll.freqs = [outAll.freqs out.config.tone.freqs(out.stims)];
outAll.datesAsNum = [outAll.datesAsNum repmat(dateAsNum, 1, nTrials)];
outAll.taskTypes = [outAll.taskTypes repmat(sum(out.taskType), 1, nTrials)];
outAll.nFreqs = [outAll.nFreqs repmat(numel(out.config.tone.freqs), 1, nTrials)];
outAll.nTones = [outAll.nTones repmat(out.config.tone.nTones, 1, nTrials)];
outAll.goFreq = [outAll.goFreq repmat(out.config.tone.freqs(out.config.tone.goStim), ...
1, nTrials)];
if numel(outAll.respTypes) ~= numel(outAll.nInTriLick);
o(' #mtrain...FromFolder: %d: %s problem!', iExp, matFiles(iExp).name, 0, dbgLevel);
end;
end;
nDays = numel(unique(cellstr(datestr(outAll.datesAsNum, 'yyyymmdd'))));
o('#mtrain...FromFolder: found %d/%d valid file(s), %d trial(s) in %d unique day(s).', ...
nValidMatFiles, numel(matFiles), numel(outAll.respTypes), nDays, 1, dbgLevel);
end
function out = parseLogFile(out, fullPath, iExp, dbgLevel)
% try the taskType first in the out file
if isfield(out, 'taskType') && ~strcmp(out.taskType, '?') && ~strcmp(out.taskType, 'UNKNOWN') ...
&& isfield(out.config, 'tone') && isfield(out.config.tone, 'nTones');
taskType = out.taskType;
o(' #mtrain...FromFolder: %d: checking for taskType, taskType present: "%s"...', ...
iExp, taskType, 3, dbgLevel);
else
taskType = '?';
% extract taskType
o(' #mtrain...FromFolder: %d: checking for taskType, so far unset ("%s")...', ...
iExp, taskType, 3, dbgLevel);
fid = fopen(strrep(fullPath, '_out.mat', '_log.txt'));
line = fgetl(fid);
while ischar(line);
m = regexp(line, '(?<nFreqs>\d+)F(?<nTones>\d+)T', 'names');
if ~isempty(m);
nFreqs = str2double(m.nFreqs);
nTones = str2double(m.nTones);
if nFreqs == 1 && nTones > 1;
taskType = 'oddballDiscrimination';
elseif nFreqs == 2 && nTones > 1;
taskType = 'oddballDiscrimination';
elseif nFreqs > 1 && nTones == 1;
taskType = 'freqDiscrimination';
elseif nFreqs == 1 && nTones == 1;
taskType = 'basic';
else
taskType = 'UNKNOWN';
end;
o(' #mtrain...FromFolder: %d: MATCH: nFreqs = %d, nTones = %d, taskType = "%s".', ...
iExp, nFreqs, nTones, taskType, 3, dbgLevel);
out.taskType = taskType;
if ~isfield(out.config, 'tone');
out.config.tone = struct();
end;
out.config.tone.nTones = nTones;
if ~isfield(out.config.tone, 'freqs');
if nFreqs == 1; out.config.tone.freqs = 12000;
elseif nFreqs == 2; out.config.tone.freqs = [7000, 12000];
elseif nFreqs == 4; out.config.tone.freqs = [5000, 7000, 12000, 15000];
else out.config.freqs = repmat(-1, 1, nFreqs);
end;
end;
save(fullPath, 'out');
break;
end;
line = fgetl(fid);
end
fclose(fid);
end;
if strcmp(out.taskType, '?');
o(' #mtrain...FromFolder: %d: task type not found ("%s")...', ...
iExp', out.taskType, 1, dbgLevel);
end;
end
function out = makeConsistent(out, fullPath, iExp, toRemoveField, toRenameField, requiredFields, dbgLevel)
if exist('toRemoveField', 'var');
nFields = 0;
for iField = 1 : size(toRemoveField, 1);
if isfield(out, toRemoveField{iField});
out = rmfield(out, toRemoveField{iField});
nFields = nFields + 1;
end;
end;
if nFields;
save(fullPath, 'out');
o(' #mtrain...FromFolder: %d: removed %d field(s).', iExp, nFields, 3, dbgLevel);
end;
end;
if exist('toRenameField', 'var');
nFields = 0;
for iField = 1 : size(toRenameField, 1);
if isfield(out, toRenameField{iField, 1});
out.(toRenameField{iField, 2}) = out.(toRenameField{iField, 1});
out = rmfield(out, toRenameField{iField, 1});
nFields = nFields + 1;
end;
end;
if nFields;
o(' #mtrain...FromFolder: %d: renamed %d field(s).', iExp, nFields, 3, dbgLevel);
save(fullPath, 'out');
end;
end;
if exist('requiredFields', 'var');
nFields = 0;
for iField = 1 : size(requiredFields, 1);
if ~isfield(out, requiredFields{iField, 1});
if exist(requiredFields{iField, 1}, 'var');
eval(['out.(requiredFields{iField, 1}) = ' requiredFields{iField, 1} ';']);
else
out.(requiredFields{iField, 1}) = requiredFields{iField, 2};
end;
nFields = nFields + 1;
end;
end;
if nFields;
o(' #mtrain...FromFolder: %d: created %d required fields.', iExp, nFields, 3, dbgLevel);
save(fullPath, 'out');
end;
end;
end
function [out, unResps] = removeUnresponsive(out, iExp, dbgLevel)
o(' #mtrain...FromFolder: %d: removing unresponsive trials ...', iExp, 3, dbgLevel);
unrespSeriesIndexes = [];
unResps = cell(1);
minUnrespLength = 15; % minimum number of consecutive unresponsive trials
toKeepIndexes = true(size(out.resps));
toKeepIndexes(isnan(out.resps)) = false;
fieldNames = {
'stims', 'odds', 'oddPos', 'isOdd', 'trialStartDelays', 'trialStartTimes', 'trialEndTimes', ...
'respTimes', 'nInTriLick', 'resps', 'respDelays', 'respTypes'
};
% remove NaNs
for iField = 1 : numel(fieldNames);
if numel(out.(fieldNames{iField})) < max(toKeepIndexes);
o(' #mtrain...FromFolder: %d: problem with field "%s"...', iExp, fieldNames{iField}, ...
3, dbgLevel);
continue;
end;
out.(fieldNames{iField}) = out.(fieldNames{iField})(toKeepIndexes);
end;
% separate the trials by unresponsive 'bins'/'blobs'
CC = bwconncomp(~out.resps);
% go through each bin of unresponsive consecutive trials
for iBin = 1 : numel(CC.PixelIdxList);
indexList = CC.PixelIdxList{iBin}'; % extract the list of indexes
% if the bin is long enough and contains at least one 'correct rejection' and one 'miss' ...
if numel(indexList) >= minUnrespLength && any(out.respTypes(indexList) == 2) && any(out.respTypes(indexList) == 4);
% then we can consider it as unresponsive and gather the indexes
unrespSeriesIndexes = [unrespSeriesIndexes indexList]; %#ok<AGROW>
unResps{end + 1} = indexList; %#ok<AGROW>
end;
end;
toKeepIndexes = true(size(out.resps));
toKeepIndexes(unrespSeriesIndexes) = false;
for iField = 1 : numel(fieldNames);
if numel(out.(fieldNames{iField})) < max(toKeepIndexes);
o(' #mtrain...FromFolder: %d: problem with field "%s"...', iExp, fieldNames{iField}, ...
3, dbgLevel);
continue;
end;
out.(fieldNames{iField}) = out.(fieldNames{iField})(toKeepIndexes);
end;
end
|
github
|
HelmchenLabSoftware/OCIA-master
|
mtrainerAnalyser_pooledPerformance.m
|
.m
|
OCIA-master/behavior/mtrainer/mtrainerAnalyser_pooledPerformance.m
| 13,056 |
utf_8
|
b60d5cf1801f259ba926464fd19f619c
|
%% Function - mtrainerAnalyser_pooledPerformance
function mtrainerAnalyser_pooledPerformance(outAll, titleStr)
dbgLevel = 2;
uniqueDays = unique(cellstr(datestr(outAll.datesAsNum, 'yyyymmdd')));
nDays = numel(uniqueDays);
o('#mtrain...pooledPerf: %d trial(s) in %d day(s).', numel(outAll.respTypes), nDays, 1, dbgLevel);
runs = unique(cellstr(datestr(outAll.datesAsNum, 'yyyymmdd_HHMMSS')));
nextSessThreshIndiv = 0.08; % pool data with morning and afternoon sessions separately
% nextSessThreshIndiv = 0.0005; % pool data with each run (100 trials) separately
nextSessThreshDaily = 0.35; % pool data daily
[~, sessionIndexesIndiv, nTrialsPerSessIndiv] = separateIntoSessions(outAll, runs, ...
nextSessThreshIndiv, dbgLevel);
[runs, sessionIndexesDaily, nTrialsPerSessDaily] = separateIntoSessions(outAll, runs, ...
nextSessThreshDaily, dbgLevel); %#ok<ASGLU>
sessionIndexes = sessionIndexesDaily;
nTrialsPerSess = nTrialsPerSessDaily;
nSessionIndiv = max(sessionIndexesIndiv);
nSessionDaily = max(sessionIndexesDaily);
nSession = nSessionDaily;
o('#mtrain...pooledPerf: found %d daily session(s) and %d individual session(s).', ...
nSessionDaily, nSessionIndiv, 2, dbgLevel);
o('#mtrain...pooledPerf: mean nTrials per day: %03.0f, per indiv session: %03.0f.', ...
mean(nTrialsPerSessDaily), mean(nTrialsPerSessIndiv), 2, dbgLevel);
figName = titleStr;
figName = strrep(figName, '\_', '_');
figName = strrep(figName, '''', '');
figName = strrep(figName, ' ', '');
figHand = figure('NumberTitle', 'off', 'WindowStyle', 'docked', 'Name', figName);
hitRate = zeros(1, nSession); % correct detection, CR+, hitRate
hitRateError = zeros(1, nSession); % correct detection, CR+, hitRate errors
falsePosRate = zeros(1, nSession); % false alarm, CR-, false positive
falsePosRateError = zeros(1, nSession);% false alarm, CR-, false positive errors
dprimes = zeros(1, nSession); % d prime
dprimesError = zeros(1, nSession); % d prime errors
useSEM = 1;
iBinAll = 1;
prevNFreqs = 0;
prevNTones = 0;
dprimeMaxVal = 3.5;
dprimeMinVal = -2;
changeOfFreqOrToneNum = zeros(1, nSession);
for iSess = 1 : nSession;
% extract the current session's number of frequency and number of tones
nFreqs = outAll.nFreqs(sessionIndexes == iSess);
nTones = outAll.nTones(sessionIndexes == iSess);
if ~numel(nFreqs); continue; end;
nFreqs = nFreqs(1);
nTones = nTones(1);
% skip basic sessions
% if nFreqs == 1 && nTones == 1;
% hitRate(iBinAll) = NaN;
% falsePosRate(iBinAll) = NaN;
% dprimes(iBinAll) = NaN;
% iBinAll = iBinAll + 1;
% continue;
% end;
% if there is a change in the number of frequencies or tones, mark it
if prevNFreqs ~= 0 && (nFreqs ~= prevNFreqs || nTones ~= prevNTones);
changeOfFreqOrToneNum(iSess) = iSess - 1;
end;
% store for next iteration
prevNFreqs = nFreqs;
prevNTones = nTones;
% extract the respTypes for this session
% for each trial, 1 = correct detect, 2 = correct reject, 3 = false alarm, 4 = miss, 5 = early
sessionRespTypes = outAll.respTypes(sessionIndexes == iSess);
sessInDay = sessionIndexesIndiv(sessionIndexes == iSess);
sessStart = min(sessInDay);
sessEnd = max(sessInDay);
dPrimesIndivSess = zeros(1, sessEnd - sessStart + 1);
hitRatesIndivSess = zeros(1, sessEnd - sessStart + 1);
falsePosIndivSess = zeros(1, sessEnd - sessStart + 1);
for iSessIndiv = sessStart : sessEnd;
indivSessionRespTypes = outAll.respTypes(sessionIndexesIndiv == iSessIndiv);
countsForIndivSession = mtrainerAnalyzer_getCounts(indivSessionRespTypes);
if isnan(countsForIndivSession.DPRIME);
countsForIndivSession.DPRIME = 0;
end;
dPrimesIndivSess(iSessIndiv - sessStart + 1) = countsForIndivSession.DPRIME;
hitRatesIndivSess(iSessIndiv - sessStart + 1) = ...
100 * countsForIndivSession.TGO / countsForIndivSession.T;
falsePosIndivSess(iSessIndiv - sessStart + 1) = ...
100 * countsForIndivSession.NTGO / countsForIndivSession.NT;
end;
if useSEM;
dprimesError(iBinAll) = sem(dPrimesIndivSess); %%#ok<UNRCH>
hitRateError(iBinAll) = sem(hitRatesIndivSess);
falsePosRateError(iBinAll) = sem(falsePosIndivSess);
else
dprimesError(iBinAll) = std(dPrimesIndivSess); %#ok<UNRCH>
hitRateError(iBinAll) = std(hitRatesIndivSess);
falsePosRateError(iBinAll) = std(falsePosIndivSess);
end;
% make an overall counting for the session
countsForSession = mtrainerAnalyzer_getCounts(sessionRespTypes);
o(' #mtrain...pooledPerf: session %d, taskType: "%s".', iSess, ...
sprintf('%F%T', nFreqs, nTones), 3, dbgLevel);
hitRate(iBinAll) = 100 * countsForSession.TGO / countsForSession.T;
falsePosRate(iBinAll) = 100 * countsForSession.NTGO / countsForSession.NT;
if isnan(countsForSession.DPRIME);
countsForSession.DPRIME = 0;
end;
% restrict the dprime value between dprimeMaxVal and dprimeMinVal
countsForSession.DPRIME = min(dprimeMaxVal, countsForSession.DPRIME);
countsForSession.DPRIME = max(dprimeMinVal, countsForSession.DPRIME);
dprimes(iBinAll) = countsForSession.DPRIME;
o(' #mtrain...pooledPerf: session %d, HitRate: %04.1f, FalsePosRate = %04.1f, d'' = %.2f.', ...
iSess, hitRate(iBinAll), falsePosRate(iBinAll), dprimes(iBinAll), 3, dbgLevel);
iBinAll = iBinAll + 1;
%
% binWidth = 100;
%
% % calculate number of bins, make sure that there is at least one
% nBins = max(round(countsForSession.TOT / binWidth), 1);
% for iBin = 1 : nBins;
% iStart = (iBin - 1) * binWidth + 1; % for binWidth = 10: 1, 11, 21, etc.
% iEnd = min(iBin * binWidth, countsForSession.TOT); % for binWidth = 10: 10, 20, 30, etc.
% countsForBin = mtrainerAnalyzer_getCounts(sessionRespTypes(iStart : iEnd));
%
% if countsForBin.GOP < 50;
% trialIndex = find(sessionIndexes == iSess);
% trialIndex = trialIndex(1) + iBin * binWidth;
% runsForSession = runs(cell2mat(runs(:, 2)) == iSess);
% iRun = 1;
% while iRun < numel(runsForSession);
% if sum(nTrialsPerSess
% end;
% o(' #mtrain...pooledPerf: session %d, %s, bin %d (trial %.0f) has a GOP of %.2f.', ...
% iSess, runsForSession{1}, iBin, trialIndex, countsForBin.GOP, 3, dbgLevel);
% hitRate(iBinAll) = NaN;
% falsePosRate(iBinAll) = NaN;
% dprimes(iBinAll) = NaN;
% iBinAll = iBinAll + 1;
% continue;
% end;
%
% hitRate(iBinAll) = 100 * countsForBin.TGO / countsForBin.T;
% falsePosRate(iBinAll) = 100 * countsForBin.NTGO / countsForBin.NT;
% if isnan(countsForBin.DPRIME) || isinf(countsForBin.DPRIME);
% countsForBin.DPRIME = 0;
% end;
%
% % restrict the dprime value between +dprimeMaxVal and -dprimeMaxVal
% countsForBin.DPRIME = min(dprimeMaxVal, countsForBin.DPRIME);
% countsForBin.DPRIME = max(-dprimeMaxVal, countsForBin.DPRIME);
%
% dprimes(iBinAll) = countsForBin.DPRIME;
% iBinAll = iBinAll + 1;
% end;
end;
nTotBins = iBinAll - 1;
% TGOsHand = plot(hitRate, '-sg', 'MarkerFaceColor', 'green');
TGOsErrHand = errorbar(1 : nSession, hitRate, hitRateError, '-sg', 'MarkerFaceColor', 'green');
removeErrorBarEnds(TGOsErrHand);
hold all;
hitRateAxes = gca;
% NTNGOsHand = plot(falsePosRate, '-sr', 'MarkerFaceColor', 'red');
NTNGOsErrHand = errorbar((1 : nSession) + 0.15, falsePosRate, falsePosRateError, '-sr', 'MarkerFaceColor', 'red');
removeErrorBarEnds(NTNGOsErrHand);
set(hitRateAxes, 'ylim', [0 110], 'YTick', 0 : 10 : 110, 'YTickLabel', 0 : 10 : 110);
if useSEM;
ylabel('% of Trials \pm SEM'); %%#ok<UNRCH>
else
ylabel('% of Trials \pm SD'); %#ok<UNRCH>
end;
vertLineHandles = zeros(1, sum(changeOfFreqOrToneNum > 0));
vertLineTextHandles = zeros(2, sum(changeOfFreqOrToneNum > 0));
iLineHandle = 1;
for iChange = 1 : numel(changeOfFreqOrToneNum);
if ~changeOfFreqOrToneNum(iChange); continue; end;
changeX = changeOfFreqOrToneNum(iChange) + 0.5;
nFreqs1 = outAll.nFreqs(sessionIndexes == changeOfFreqOrToneNum(iChange));
nFreqs1 = nFreqs1(1);
nFreqs2 = outAll.nFreqs(sessionIndexes ==changeOfFreqOrToneNum(iChange) + 1);
nFreqs2 = nFreqs2(1);
if mod(iChange, 2) == 0;
changeY = 9;
else
changeY = 12;
end;
vertLineTextHandles(1, iLineHandle) = text(changeX, changeY, ...
sprintf('%d freq \\leftarrow ', nFreqs1), 'HorizontalAlignment', 'right');
vertLineTextHandles(2, iLineHandle) = text(changeX, changeY, sprintf(' \\rightarrow %d freq', nFreqs2));
vertLineHandles(iLineHandle) = line([changeX changeX], [0 100], ...
'LineStyle', ':', 'Color', 'black');
iLineHandle = iLineHandle + 1;
end;
xlimits = [0 nTotBins * 1.05];
xlim(xlimits);
set(hitRateAxes, 'XTick', [], 'XTickLabel', []);
xTickAxes = axes('Position', get(gca, 'Position'), ...
'YAxisLocation', 'right', 'XAxisLocation', 'bottom', 'Color', 'none');
sessionLabels = cellstr(datestr(outAll.datesAsNum([diff(sessionIndexes) > 0, true]), 'dd/mm'));
set(xTickAxes, 'xlim', xlimits, ...
'XTick', 1 : nSession, 'XTickLabel', sessionLabels(1 : nSession));
% set(xTickAxes, 'xlim', xlimits, ...
% 'XTick', 0 : 10 : nTotBins, 'XTickLabel', (0 : 10 : nTotBins) * binWidth);
set(xTickAxes, 'YTick', [], 'YTickLabel', []);
xlabel('Sessions');
dprimeAxes = axes('Position', get(gca, 'Position'), ...
'YAxisLocation', 'right', 'XAxisLocation', 'top', 'Color', 'none');
hold all;
% dprimesHand = plot(dprimes, '-sb', 'MarkerFaceColor', 'blue');
dprimesErrHand = errorbar((1 : nSession) + 0.3, dprimes, dprimesError, '-sb', 'MarkerFaceColor', 'blue');
removeErrorBarEnds(dprimesErrHand);
set(dprimeAxes, 'ylim', [dprimeMinVal dprimeMaxVal], 'YTick', dprimeMinVal : 0.5 : dprimeMaxVal, ...
'YTickLabel', dprimeMinVal : 0.5 : dprimeMaxVal);
set(dprimeAxes, 'XTick', [], 'XTickLabel', []);
xlim(xlimits);
if useSEM;
ylabel('d'' value \pm SEM'); %%#ok<UNRCH>
else
ylabel('d'' value \pm SD'); %#ok<UNRCH>
end;
legend([TGOsErrHand, NTNGOsErrHand, dprimesErrHand], {'HitRate', 'FalsePos', 'd'''}, ...
'Location', 'NorthWest');
% legend([TGOsHand, NTNGOsHand, dprimesHand], {'HitRate', 'FalsePos', 'd'''}, ...
% 'Location', 'NorthWest');
title(sprintf('%s \\fontsize{10} [Total number of trials = %.0f, mean trials per session = %.0f]', ...
titleStr, sum(nTrialsPerSess), mean(nTrialsPerSess)));
hold off;
makePrettyFigure(figHand);
set(xTickAxes, 'FontSize', 9);
for iLineHandle = 1 : numel(vertLineHandles);
set(vertLineHandles(iLineHandle), 'LineWidth', 0.5);
set(vertLineTextHandles(1, iLineHandle), 'FontSize', 10);
set(vertLineTextHandles(2, iLineHandle), 'FontSize', 10);
end;
end
function [runs, sessionIndexes, nTrialsPerSess] = separateIntoSessions(outAll, runs, nextSessThresh, dbgLevel)
sessionIndexes = zeros(1, numel(outAll.respTypes));
nTrialsPerSess = zeros(1, 1);
iRun = 1;
iSess = 1;
% loop trough all runs
while iRun <= size(runs, 1);
% current run's date as number
dateAsNum = datenum(runs{iRun, 1}, 'yyyymmdd_HHMMSS');
o(' #mtrain...pooledPerf: run %d, date: %s (%8.3f).', iRun, runs{iRun, 1}, dateAsNum, 3, dbgLevel);
% for all runs before the last, check with next run
if iRun < size(runs, 1);
dateAsNumNext = datenum(runs{iRun + 1, 1}, 'yyyymmdd_HHMMSS');
else % for last run, make the difference big enough
dateAsNumNext = dateAsNum + 100 * nextSessThresh;
end;
runs{iRun, 2} = iSess;
o(' #mtrain...pooledPerf: run %d''s session: %d, dateAsNumNext: %8.3f, diff: %.2f, thresh: %.2f.', ...
iRun, iSess, dateAsNumNext, abs(dateAsNum - dateAsNumNext), nextSessThresh, 3, dbgLevel);
% if they are too different, next run is in a new session
if abs(dateAsNum - dateAsNumNext) > nextSessThresh;
% get all the respTypes for that session (earlier dates that are not yet assigned to a sessions)
respTypesForSession = outAll.respTypes(outAll.datesAsNum <= dateAsNum & ~sessionIndexes);
nTrials = numel(respTypesForSession);
zeroIndex = find(~sessionIndexes); % get indexes where sessionIndex is still 0
sessionIndexes(zeroIndex(1) : zeroIndex(1) + nTrials - 1) = ones(1, nTrials) * iSess;
nTrialsPerSess(iSess) = nTrials;
o(' #mtrain...pooledPerf: run %d is the last of session %d, nTrials: %d, tagging from %d to %d.', ...
iRun, iSess, nTrials, zeroIndex(1), zeroIndex(1) + nTrials - 1, 3, dbgLevel);
iSess = iSess + 1;
iRun = iRun + 1;
else % otherwise if they are not too different, go on
iRun = iRun + 1;
end;
end;
end
|
github
|
HelmchenLabSoftware/OCIA-master
|
mtrainerAnalyser_freqAnalysis_bins.m
|
.m
|
OCIA-master/behavior/mtrainer/mtrainerAnalyser_freqAnalysis_bins.m
| 2,389 |
utf_8
|
e6cff6d257bc5bfe9d98519822f2e677
|
%% Function - mtrainerAnalyser_pooledPerformance
function figHand = mtrainerAnalyser_freqAnalysis_bins(outAll, titleStr, binWidth)
dbgLevel = 2;
nFreqs = 5;
% for each trial: 1 = correct detect, 2 = correct reject, 3 = false alarm, 4 = miss, 5 = early
respTypes = outAll.respTypes(outAll.nFreqs == nFreqs);
freqs = outAll.freqs(outAll.nFreqs == nFreqs);
uniqueFreqs = unique(freqs);
goFreq = unique(outAll.goFreq(outAll.nFreqs == nFreqs));
figHand = 0;
if numel(goFreq) > 1; o('Oh-oh. Problem ! Multiple go freqs', 1, dbgLevel); return; end;
nTrials = length(respTypes);
% calculate number of bins, make sure that there is at least one
nBins = max(round(nTrials / binWidth), 1);
figName = titleStr;
figName = strrep(figName, '\_', '_');
figName = strrep(figName, '''', '');
figName = strrep(figName, ' ', '');
figHand = figure('NumberTitle', 'off', 'WindowStyle', 'docked', 'Name', figName);
% errors = nan(nFreqs, nBins);
errors = nan(nFreqs - 1, nBins);
for iBin = 1 : nBins;
iStart = (iBin - 1) * binWidth + 1; % for binWidth = 10: 1, 11, 21, etc.
iEnd = min(iBin * binWidth, nTrials); % for binWidth = 10: 10, 20, 30, etc.
for iFreq = 1 : nFreqs;
respTypesForFreq = respTypes(freqs(iStart : iEnd) == uniqueFreqs(iFreq));
o('Bin %d - freq %d, respTypes: %d', iBin, iFreq, numel(respTypesForFreq), 3, dbgLevel);
if uniqueFreqs(iFreq) == goFreq;
continue;
% errors(iFreq, iBin) = 100 * sum(respTypesForFreq == 4) / numel(respTypesForFreq);
else
errors(iFreq, iBin) = 100 * sum(respTypesForFreq == 3) / numel(respTypesForFreq);
end;
end;
end;
errors = errors(setdiff(1 : nFreqs, find(uniqueFreqs == goFreq)), :);
colors = lines(nFreqs - 1);
% colors = lines(nFreqs);
plotHandles = plot(errors', '-s');
for iHandle = 1 : numel(plotHandles);
set(plotHandles(iHandle), 'Color', colors(iHandle, :), 'MarkerFaceColor', colors(iHandle, :));
end;
% legend({'4kHz', '8kHz', '12kHz', '16kHz', '20kHz'});
legend({'4kHz', '8kHz', '16kHz', '20kHz'});
ylabel('Errors in %');
step = nBins / (nTrials / 500);
set(gca, 'xlim', [0.8 nBins + 0.2], 'XTick', 1 : step : (nBins + 1), ...
'XTickLabel', 0 : 500 : ((nBins + 1) * binWidth));
% set(gca, 'YTick', [], 'YTickLabel', []);
xlabel('Trials');
title(titleStr);
makePrettyFigure(figHand);
end
|
github
|
HelmchenLabSoftware/OCIA-master
|
mtrainer_oldversion_scheduledStarts.m
|
.m
|
OCIA-master/behavior/mtrainer/mtrainer_oldversion_scheduledStarts.m
| 16,949 |
utf_8
|
cb689fcefe86d96085f1a191049aa7cd
|
function mtrainer()
% main function for mtrainer experiment suite
% all times are in s!
% written by Henry Luetcke ([email protected])
% 2013-05-07
% modified by Balazs Laurenczy ([email protected])
% 2013-05-15
doEmptyWater = 1;
automode = 1;
unsavedOut = struct();
mouseId = 'testing'; taskType = 'freqDiscrimination'; phase = 'D';
% mouseId = '130408_02'; taskType = 'freqDiscrimination'; phase = 'D';
% mouseId = '130416_01'; taskType = 'oddballDiscrimination'; phase = 'E';
% mouseId = '130425_01'; taskType = 'freqDiscrimination'; phase = 'B';
% mouseId = '130425_02'; taskType = 'oddballDiscrimination'; phase = 'C';
% mouseId = '130528_01'; taskType = 'oddballDiscrimination'; phase = 'B';
% mouseId = '130528_02'; taskType = 'oddballDiscrimination'; phase = 'B';
basePath = 'P:\matlab\daq\mtrainer\configs\';
configMat = load([basePath taskType filesep taskType '_phase' phase '.mat']);
config = configMat.config;
unsavedOut.mouseId = mouseId;
unsavedOut.taskType = taskType;
unsavedOut.phase = phase;
unsavedOut.basePath = basePath;
unsavedOut.config = config;
%% Setup - stimuli and trials
fprintf('Setup stimuli and trials... ');
% set up stimulus vector
stims = [];
for iFreq = 1 : numel(config.tone.freqs)
stimForFreq = repmat(iFreq, 1, round(config.tone.stimProba(iFreq) * config.tone.nTrials));
stims = [stims, stimForFreq]; %#ok<AGROW>
end
stims = stims(randperm(numel(stims)));
clear stim;
% set up oddball vector by altering stims with a certain probability
odds = stims;
oddPos = zeros(size(odds));
uniqueStims = unique(stims);
isOdd = rand(1, numel(stims)) < config.tone.oddProba;
uniqueOddPos = config.tone.nTones - 1 : config.tone.nTones; % last 2 tones can be odd
for iStim = 1 : numel(isOdd);
if isOdd(iStim);
otherStims = uniqueStims(uniqueStims ~= stims(iStim));
otherStims = otherStims(randperm(numel(otherStims)));
mixedOddPos = uniqueOddPos(randperm(numel(uniqueOddPos)));
odds(iStim) = otherStims(1);
oddPos(iStim) = mixedOddPos(1);
end;
end;
% set up tone array
toneArray = MakePureMultiToneOddballArray(config.tone.freqs, stims, odds, oddPos, ...
config.tone.nTones, config.tone.toneDur, config.tone.ISI, config.tone.samplingFreq);
unsavedOut.stims = stims;
unsavedOut.odds = odds;
unsavedOut.oddPos = oddPos;
unsavedOut.isOdd = isOdd;
fprintf('done.\n');
%% Setup - hardware
% define globals
global recordedValues;
% analog input
daqreset;
fprintf('Connecting hardware...\n');
s1 = daq.createSession(config.hardware.adaptorID);
s1.Rate = config.hardware.analogIn_SampleRate;
s1.addAnalogInputChannel(config.hardware.analogIn_Device, config.hardware.analogIn_Channel, 'Voltage');
s1.Channels(1).InputType = config.hardware.analogIn_InputType;
s1.Channels(1).Range = config.hardware.analogIn_Range;
fprintf('s1 ok.\n');
s2 = daq.createSession(config.hardware.adaptorID);
s2.addDigitalChannel(config.hardware.digitalOut_Device, config.hardware.digitalOut_PortLine, 'OutputOnly');
fprintf('And s2 ok. Ready to go.\n');
lickThresh = 0.18;
% lickThresh = NaN;
if isnan(lickThresh);
% baseline measurement
fprintf('Testing analog input for licking threshold (baseline)... ');
recordDuration = 2;
s1.DurationInSeconds = recordDuration;
baseline = s1.startForeground; % this will block the command line
meanData = mean(baseline);
stdData = std(baseline);
lickThresh = 2.5 * stdData;
fprintf('done.\n')
pause(1);
% lick measurement
fprintf('Testing analog input for licking threshold (licking)... ');
s1.DurationInSeconds = recordDuration;
lick = s1.startForeground; % this will block the command line
fprintf('done.\n2SD: %1.2f, lick threshold: %1.2f\n', 2 * stdData, lickThresh);
% plotting
figure('Name', 'LickingThreshold', 'Position', [150, 300, 950, 350], 'NumberTitle', 'off', ...
'MenuBar', 'none', 'ToolBar', 'none');
plot((1:numel(baseline)) / 1000, baseline - meanData, 'b');
hold on;
plot((1:numel(lick)) / 1000, lick - meanData, 'r');
line([0, recordDuration], [lickThresh, lickThresh], 'Color', 'green');
line([0, recordDuration], [2 * stdData, 2 * stdData], 'Color', 'cyan');
line([0, recordDuration], [- 2 * stdData, - 2 * stdData], 'Color', 'cyan');
legend({'baseline', 'licking', 'lickTreshold', '\pm 2SD'});
else
fprintf('Testing analog input for licking threshold... skipped.\nLick threshold: %1.2f\n', ...
lickThresh);
end;
unsavedOut.lickThresh = lickThresh;
% digital out
fprintf('Testing reward system by opening for %.2fs after a delay of %.2fs... ', ...
config.training.rewDur, config.training.rewDelay);
giveReward(s2, config.training.rewDur, config.training.rewDelay);
fprintf('done!\n')
if doEmptyWater;
doEmptyWater = str2double(input('Empty water ? 1 = yes, 0 = no\n', 's')); %#ok<UNRCH>
while doEmptyWater;
fprintf('Emptying water... ');
giveReward(s2, 0.03, 0);
% giveReward(s2, 3, 0);
fprintf(' done.');
doEmptyWater = str2double(input('Empty more ? 1 = yes, 0 = no\n', 's'));
if ~doEmptyWater; break; end;
end;
end;
s1.IsNotifyWhenDataAvailableExceedsAuto = true;
lh = s1.addlistener('DataAvailable', @(src, event) recordAndStop(src, event, lickThresh));
s1.IsContinuous = true;
s1.prepare;
%% Setup - saving settings
recordedValues = 0;
saveTime = datestr(now, 'yyyy_mm_dd__HH_MM_SS');
saveFolder = sprintf('C:\\Users\\laurenczy\\mtrainerData\\%s\\', mouseId);
savePath = sprintf('%s%s__%s', saveFolder, mouseId, saveTime);
mkdir(saveFolder);
logfile = sprintf('%s_log.txt', savePath);
logDateFormat = 'yyyy-mm-dd HH:MM:SS.FFF';
% create an 'onCleanup' function to handle interruptions by CTRL+C
c = onCleanup(@()closeDiaryAndSaveOutput(savePath, lh, s1, s2));
fprintf('Finished setting up and hardware tests.\n');
fprintf('CHECK MOUSE ID!! currently: %s.\n', mouseId);
if automode;
pause(5);
else
fprintf('Then press any key to start!'); %#ok<UNRCH>
pause;
end;
unsavedOut.savePath = savePath;
unsavedOut.saveTime = saveTime;
diary(logfile);
%% Start experiment
fprintf('Experiment start: %s\n\n', datestr(now, logDateFormat));
try
%% Experiment - initialize variables
dbgLevel = 0;
out = unsavedOut;
o('config: %s phase %s (%dF%dT)', out.taskType, out.phase, numel(config.tone.freqs), ...
config.tone.nTones, 0, dbgLevel);
o('animal: %s', mouseId, 0, dbgLevel);
o('savePath: %s', savePath, 0, dbgLevel);
o('lickThresh: %1.2f, ISI: %1.2f', lickThresh, config.tone.ISI, 0, 0);
o('rewardCollectionTime: %1.2f, InTriLickTimerDur: %1.2f', ...
config.training.rewCollTime, ...
config.training.InTriLickTimerDur, 0, dbgLevel);
totalTrialDur = config.training.trialDur + config.training.startDelay + ...
config.training.rewCollTime;
nTrials = numel(stims);
% compute relative start times for each trial
out.trialStarts_sched = 0 : totalTrialDur : (nTrials - 1) * totalTrialDur;
out.trialStarts_obs = zeros(1, nTrials);
out.trialEnds_obs = zeros(1, nTrials);
out.respTimes = nan(1, nTrials);
out.nInTriLick = zeros(1, nTrials);
out.resps = nan(1, nTrials);
out.respDelay = nan(1, nTrials);
% for each trial: 1 = correct detect, 2 = correct reject, 3 = false alarm, 4 = miss, 5 = early
out.respTypes = zeros(1, nTrials);
out.expStartTime = tic;
for iTrial = 1 : nTrials;
out.iTrial = iTrial;
% listen for response
s1.startBackground;
pause(0.01)
interTrialLickCount = 0;
%% Experiment - initial wait
while toc(out.expStartTime) < out.trialStarts_sched(iTrial);
% fprintf('CheckingA: s1.IsRunning? %d\n', s1.IsRunning);
% check if no lick has been done
if ~s1.IsRunning;
remainingTime = out.trialStarts_sched(iTrial) - toc(out.expStartTime);
addedDelay = 0;
% delay the schedule if needed
if (remainingTime < config.training.InTriLickTimerDur);
addedDelay = config.training.InTriLickTimerDur - remainingTime;
out.trialStarts_sched(iTrial:end) = out.trialStarts_sched(iTrial:end) + addedDelay;
% refresh the remaining time
remainingTime = out.trialStarts_sched(iTrial) - toc(out.expStartTime);
end;
if interTrialLickCount > 0;
fprintf('|%.1f', remainingTime);
else
fprintf(' inter-trial licking, delaying for %.1fs: |%.1f', ...
addedDelay, remainingTime);
end;
interTrialLickCount = interTrialLickCount + 1;
pause(1);
% restart the listening
s1.startBackground;
pause(0.1);
% fprintf('CheckingB: s1.IsRunning? %d\n', s1.IsRunning);
end
% avoid full-speed looping
pause(0.01);
end
if interTrialLickCount;
fprintf('|: %d inter-trial lick(s).\n', interTrialLickCount);
end
out.nInTriLick(iTrial) = interTrialLickCount;
out.trialStarts_obs(iTrial) = toc(out.expStartTime);
resp = 0;
t_trialStart = tic;
fprintf('Trial %03d/%03d - %s ... ', iTrial, nTrials, datestr(now, logDateFormat));
%% Experiment - play sound
if s1.IsRunning
soundToPlay = toneArray{iTrial};
player = audioplayer(soundToPlay, config.tone.samplingFreq); %#ok<TNMLP>
player.play;
else
fprintf('early (already licking, lick sensor: min/mean/max: %.2f/%.2f/%.2f).\n', ...
recordedValues);
if iTrial < nTrials
out.trialStarts_sched(iTrial+1:end) = ...
out.trialStarts_sched(iTrial+1:end) + config.training.timeoutPunish;
end
out.respTypes(iTrial) = 5;
% analyse every 10 trials
if ~rem(iTrial, 10) && iTrial ~= nTrials;
mtrainerAnalyser_performance(out.respTypes, 0);
end
continue
end
breakOut = 0;
%% Experiment - wait for response
while toc(t_trialStart) < config.training.trialDur
if s1.IsRunning
% no response detected
else
% seconds since trial start
respTime = toc(t_trialStart);
out.respTimes(iTrial) = respTime;
% response should be 'minRespTime' after the end of the tone!
totToneDur = (config.tone.toneDur + config.tone.ISI) * config.tone.nTones - config.tone.ISI;
limitRespTime = totToneDur + config.training.minRespTime;
out.respDelay(iTrial) = limitRespTime - respTime;
% early response, count as kind of false alarm
if respTime < limitRespTime;
% fprintf('early (lick sensor: min/mean/max: %.2f/%.2f/%.2f).\n', ...
% recordedValues);
fprintf('early (response time: %.4f, limit response time: %.4f, diff: %.5f).\n', ...
respTime, limitRespTime, limitRespTime - respTime);
if iTrial < nTrials
out.trialStarts_sched(iTrial+1:end) = out.trialStarts_sched(iTrial+1:end) ...
+ config.training.timeoutPunish;
end;
pause(config.training.timeoutPunish * 0.2);
out.respTypes(iTrial) = 5;
breakOut = 1;
break;
else
% fprintf('Lick at %s\n', datestr(clock, logDateFormat))
resp = 1;
end;
break; % break out of while loop
end;
pause(0.02); % necessary to allow time for data collection
end;
if breakOut;
out.trialEnds_obs(iTrial) = toc(out.expStartTime);
% analyse every 10 trials
if ~rem(iTrial, 10) && iTrial ~= nTrials;
mtrainerAnalyser_performance(out.respTypes, 0);
end;
continue; % continue for loop
end;
if s1.IsRunning;
s1.stop;
end;
%% Experiment - analyse response
out.resps(iTrial) = resp;
isOddTrial = stims(iTrial) ~= odds(iTrial);
if config.tone.oddProba > 0; % oddball discrimination
isTargetStim = isOddTrial && config.tone.goStim;
else % frequency discrimination
isTargetStim = stims(iTrial) == config.tone.goStim;
end;
if resp == 1 && isTargetStim;
% correct response
% fprintf('correct detection (lick sensor: min/mean/max: %.2f/%.2f/%.2f).\n', ...
% recordedValues);
fprintf('correct detection (response time: %.4f, limit response time: %.4f, diff: %.5f).\n', ...
respTime, limitRespTime, limitRespTime - respTime);
out.respTypes(iTrial) = 1;
% give reward
giveReward(s2,config.training.rewDur,config.training.rewDelay);
% wait so they can collect the reward
pause(config.training.rewCollTime);
if iTrial < nTrials;
out.trialStarts_sched(iTrial+1:end) = ...
out.trialStarts_sched(iTrial+1:end) ...
+ (config.training.rewDur + config.training.rewDelay);
end;
elseif resp == 1 && ~isTargetStim;
% false alarm
% fprintf('false alarm (lick sensor: min/mean/max: %.2f/%.2f/%.2f).\n', ...
% recordedValues);
fprintf('false alarm (response time: %.4f, limit response time: %.4f, diff: %.5f).\n', ...
respTime, limitRespTime, limitRespTime - respTime);
out.respTypes(iTrial) = 3;
if iTrial < nTrials;
out.trialStarts_sched(iTrial+1:end) = ...
out.trialStarts_sched(iTrial+1:end) + config.training.timeoutPunish;
end
elseif resp == 0 && isTargetStim;
fprintf('miss.\n');
out.respTypes(iTrial) = 4;
if iTrial < nTrials
out.trialStarts_sched(iTrial+1:end) = ...
out.trialStarts_sched(iTrial+1:end) + config.training.timeoutPunish;
end
elseif resp == 0 && ~isTargetStim;
fprintf('correct rejection.\n');
out.respTypes(iTrial) = 2;
% go to next trial
% give reward and wait so they can collect it
% giveReward(s2,config.training.rewDur,config.training.rewDelay);
% pause(config.training.rewCollTime);
% if iTrial < nTrials
% out.trialStarts_sched(iTrial+1:end) = out.trialStarts_sched(iTrial+1:end) + ...
% config.training.rewDur + config.training.rewDelay;
% end
end
out.trialEnds_obs(iTrial) = toc(out.expStartTime);
% analyse every 10 trials
if ~rem(iTrial, 10) && iTrial ~= nTrials;
mtrainerAnalyser_performance(out.respTypes, 0);
end
end
%% End experiment
fprintf('\nExperiment end: %s\n', datestr(now, logDateFormat));
out.expTotDurTime = toc(out.expStartTime);
fprintf('Total time: %02.0f:%02.0f\n', out.expTotDurTime / 60, mod(out.expTotDurTime, 60));
mtrainerAnalyser_performance(out.respTypes, 2, out.savePath, out.nInTriLick);
catch err
fprintf('\n\nAn error occured. Last trial: %1.0f. Cleaning up ...\n\n', iTrial)
rethrow(err);
end
%% Function - giveReward
function giveReward(s2, rewDur, rewDelay)
t_rewardStart = tic;
% wait until for start delay
while toc(t_rewardStart) < rewDelay; end;
t_rewardStart = tic;
% open digital out
s2.outputSingleScan(0);
% wait until for open duration
while toc(t_rewardStart) < rewDur; end;
% close digital out
s2.outputSingleScan(1);
end
function recordAndStop(src, event, lickThresh)
recordedValues = stopWhenExceedThreshold(src, event, lickThresh);
end
function closeDiaryAndSaveOutput(savePath, lh, s1, s2)
fprintf('\nClosing diary... ');
diary off;
fprintf('done.\n');
if (exist('out', 'var'));
matFileName = sprintf('%s_out.mat', savePath);
fprintf('Saving output as %s... ', matFileName);
save(matFileName, 'out');
fprintf('done.\n');
else
fprintf('/!\\ Output not saved\n');
end;
fprintf('Closing channels... ');
if exist('lh', 'var'); delete(lh); end;
if exist('s1', 'var'); delete(s1); end;
if exist('s2', 'var'); delete(s2); end;
fprintf('done.\n');
end
end
|
github
|
HelmchenLabSoftware/OCIA-master
|
mtrainer_oldversion_legacyInterface.m
|
.m
|
OCIA-master/behavior/mtrainer/mtrainer_oldversion_legacyInterface.m
| 8,514 |
utf_8
|
745363c7c815304e2e4265dd8ef8ab38
|
function mtrainer(varargin)
% main function for mtrainer experiment suite
% all times are in s!
% written by Henry Luetcke ([email protected])
% 2012-11-08
if ~nargin
% gui select mat-file with config structure
[FileName,PathName] = uigetfile('*.mat','Select configuration file');
S = load(fullfile(PathName,FileName));
fields = fieldnames(S);
config = S.(fields{1});
else
config = varargin{1};
end
try
parseConfig(config);
catch
rethrow(lasterror)
error('Failed to parse config struture')
end
%% Setup stimuli and trials
% set up stimVector
stimVector = [];
for n = 1:length(config.tone.fVector)
stim = repmat(n,1,round(config.tone.stimProbabilities(n)*config.tone.trials));
stimVector = [stimVector, stim];
end
stimVector = stimVector(randperm(numel(stimVector)));
% set up tone array
toneArray = MakePureToneArray(config.tone.fVector,stimVector,...
config.tone.toneDuration,config.tone.sf);
%% Start hardware
% analog input
daqreset
ai=analoginput(config.hardware.adaptorID,config.hardware.analogIn_Device);
addchannel(ai, config.hardware.analogIn_Channel);
set(ai,'InputType','SingleEnded')
% sample rate and recording duration
ai.SampleRate = config.hardware.aiSampleRate;
% digital IO
dio=digitalio(config.hardware.adaptorID,config.hardware.digitalIO_Device);
digitalOut = addline(dio,config.hardware.digitalOut_Channel,'out');
% hardware 'warm-up'
% analog in
ai.SamplesPerTrigger = 100;
start(ai);
% get data
data = getdata(ai);
figure, plot(data)
lickThresh = 10.*std(data) + max(data);
fprintf('Lick threshold: %1.2f\n',lickThresh)
stop(ai), clear data
% digital out
putvalue(digitalOut,1) % 1 is light off, 0 is light on (strangely enough)
for n = 1:10; putvalue(digitalOut,0), putvalue(digitalOut,1), pause(0.1); end
% some changes to ai
ai.SamplesPerTrigger = Inf;
% % timer function
% trial = 1; t_trialStart = clock;
% ai.TimerFcn = {@daqTimerFunction};
% ai.TimerPeriod = 0.01;
% set(ai, 'TriggerRepeat', Inf);
logfile = sprintf('mtrainerLogfile_%s.txt',datestr(clock,30));
diary(logfile)
disp('Finished set up and hardware tests. Press any key to start!')
pause
%% Start experiment
fprintf('Experiment start: %s\n\n',datestr(now,'dd-mm-yyyy HH:MM:SS.FFF'))
try
totalTrialDur = config.training.trialDuration(1) + config.training.startDelay;
samplesPerTrial = round((totalTrialDur-0.1).*ai.SampleRate); % a bit less to allow for processing time
maxTrials = numel(stimVector);
maxTrials = 50; % for testing
responseCount = zeros(1,4); % correct detect, correct reject, false alarm, miss
% compute relative start times for each trial
trialStartVector_scheduled = [0:totalTrialDur:(maxTrials-1)*totalTrialDur];
trialStartVector_observed = zeros(1,maxTrials);
trialEndVector_observed = zeros(1,maxTrials);
daqStartTime = cell(1,maxTrials);
start(ai);
t_expStart = tic;
for trial = 1:maxTrials
while toc(t_expStart) < trialStartVector_scheduled(trial)
% do nothing
end
trialStartVector_observed(trial) = toc(t_expStart);
t_trialStart = tic;
fprintf('Trial %1.0f - %s\n',trial, datestr(now, 'HH:MM:SS.FFF'))
% play tone
sound(toneArray{trial},config.tone.sf)
response = 0;
% listen for response
while toc(t_trialStart) < config.training.trialDuration(1)
size = min([ai.SamplesAvailable 10]);
data = peekdata(ai, size);
if max(data) > 0.1 % lick detected
fprintf('Lick at %s (max = %1.2f)\n',datestr(clock,'HH:MM:SS.FFF'),max(data))
response = 1;
if stimVector(trial) == config.tone.goStim
% correct response
fprintf('Correct detection\n')
responseCount(1) = responseCount(1) + 1;
% give reward
giveReward(digitalOut,config.training.rewardDuration,config.training.rewardDelay);
if trial < maxTrials
trialStartVector_scheduled(trial+1:end) = ...
trialStartVector_scheduled(trial+1:end) + (config.training.rewardDuration+config.training.rewardDelay);
end
else
% false alarm
fprintf('False alarm\n')
responseCount(3) = responseCount(3) + 1;
if trial < maxTrials
trialStartVector_scheduled(trial+1:end) = ...
trialStartVector_scheduled(trial+1:end) + config.training.timeoutPunish;
end
end
break
end
end
if ~response && stimVector(trial) == config.tone.goStim
fprintf('Miss\n')
responseCount(4) = responseCount(4) + 1;
if trial < maxTrials
trialStartVector_scheduled(trial+1:end) = ...
trialStartVector_scheduled(trial+1:end) + config.training.timeoutPunish;
end
elseif ~response && stimVector(trial) ~= config.tone.goStim
fprintf('Correct rejection\n')
responseCount(2) = responseCount(2) + 1;
giveReward(digitalOut,config.training.rewardDuration,config.training.rewardDelay);
if trial < maxTrials
trialStartVector_scheduled(trial+1:end) = ...
trialStartVector_scheduled(trial+1:end) + (config.training.rewardDuration+config.training.rewardDelay);
end
end
trialEndVector_observed(trial) = toc(t_expStart);
end
fprintf('\nExperiment end: %s\n\n',datestr(now,'dd-mm-yyyy HH:MM:SS.FFF'))
[lickData,lickDataT,daqStartTime] = ...
getdata(ai,ai.SamplesAcquired);
stop(ai); delete(ai); delete(dio)
save('out.mat','lickData','lickDataT','daqStartTime',...
'trialStartVector_scheduled','trialStartVector_observed',...
'trialEndVector_observed')
figure('Name','Trial start difference')
plot((trialStartVector_observed-trialStartVector_scheduled).*1000,'k')
xlabel('Trial'), ylabel('actual - scheduled / ms')
doPerformanceAnalysis(responseCount);
diary off
catch
disp('An error occured. Cleaning up ...')
stop(ai), delete(ai), delete(dio), diary off
rethrow(lasterror)
end
%% Function - giveReward
function giveReward(digitalOut,rewardDuration,rewardDelay)
t_rewardStart = tic;
while toc(t_rewardStart) < rewardDelay
% do nothing
end
t_rewardStart = tic;
% open digital out
putvalue(digitalOut,0)
while toc(t_rewardStart) < rewardDuration
% do nothing
end
putvalue(digitalOut,1)
%% Function - doPerformanceAnalysis
function doPerformanceAnalysis(responseCount)
% responseCount columns: correct detect, correct reject, false alarm, miss
trials = sum(responseCount);
T = responseCount(1)+responseCount(4); % targets
N = responseCount(2)+responseCount(3); % non-targets
fprintf('\n\nPerformance:\n')
fprintf('Trials: %1.0f\n',trials)
fprintf('Correct detections: %1.0f (%1.2f%%)\n',responseCount(1),responseCount(1)./T.*100)
fprintf('Correct rejections: %1.0f (%1.2f%%)\n',responseCount(2),responseCount(2)./N.*100)
fprintf('False alarms: %1.0f (%1.2f%%)\n',responseCount(3),responseCount(3)./N.*100)
fprintf('Miss: %1.0f (%1.2f%%)\n',responseCount(4),responseCount(4)./T.*100)
fprintf('Total correct: %1.0f (%1.2f%%)\n',sum(responseCount(1:2)),sum(responseCount(1:2))./trials.*100)
fprintf('Total errors: %1.0f (%1.2f%%)\n',sum(responseCount(3:4)),sum(responseCount(3:4))./trials.*100)
dPrim = dprime(responseCount(1)./trials,responseCount(3)./trials,T,N);
fprintf('d'':%1.3f\n',dPrim)
%% Function - parseConfig
function parseConfig(config)
% list of required hardware fields:
requiredFields = {...
'adaptorID'
'analogIn_Device'
'analogIn_Channel'
'aiSampleRate'
'digitalIO_Device'
'digitalOut_Channel'
};
accessFields(config.hardware,requiredFields);
% list of required tone fields:
requiredFields = {...
'sf'
'fVector'
'stimProbabilities'
'trials'
'goStim'
'toneDuration'
};
accessFields(config.tone,requiredFields);
% list of required training fields:
requiredFields = {...
'responseTime'
'trialDuration'
'startDelay'
'rewardDuration'
'rewardDelay'
'timeoutPunish'
};
accessFields(config.training,requiredFields);
function accessFields(S,fields)
for n = 1:numel(fields)
S.(fields{n});
end
|
github
|
HelmchenLabSoftware/OCIA-master
|
mtrainer_GUI.m
|
.m
|
OCIA-master/behavior/mtrainer/mtrainer_GUI.m
| 34,409 |
utf_8
|
3d5a15b6438819e18ebd58da906241e8
|
function varargout = mtrainer_GUI(varargin)
% TODO:
% - stopping the experiment: trial no 100 ? plot ? set buttons to stop ?
% - reward anyway system
% - forbid disconnecting HW or changing mouseID while experiment is running
% - piezoThresh calibrator with setter
% - online lick ploting
% - online performance
% - logging into GUI window
% - config setter
% Begin initialization code - DO NOT EDIT
gui_Singleton = 1;
gui_State = struct('gui_Name', mfilename, ...
'gui_Singleton', gui_Singleton, ...
'gui_OpeningFcn', @mtrainer_GUI_OpeningFcn, ...
'gui_OutputFcn', @mtrainer_GUI_OutputFcn, ...
'gui_LayoutFcn', [] , ...
'gui_Callback', []);
if nargin && ischar(varargin{1});
gui_State.gui_Callback = str2func(varargin{1});
end
if nargout;
[varargout{1:nargout}] = gui_mainfcn(gui_State, varargin{:});
else
gui_mainfcn(gui_State, varargin{:});
end
% End initialization code - DO NOT EDIT
% --- Executes just before mtrainer_GUI is made visible.
function mtrainer_GUI_OpeningFcn(hObject, eventdata, handles, varargin)
% This function has no output args, see OutputFcn.
% hObject handle to figure
% eventdata reserved - to be defined in a future version of MATLAB
% handles structure with handles and user data (see GUIDATA)
% varargin command line arguments to mtrainer_GUI (see VARARGIN)
% Choose default command line output for mtrainer_GUI
handles.output = hObject;
% Update handles structure
guidata(hObject, handles);
initialize_gui(hObject, handles, false);
set(hObject, 'DeleteFcn', @onWindowClose);
set(hObject, 'Position', [200 800 800 620]);
% --- Outputs from this function are returned to the command line.
function varargout = mtrainer_GUI_OutputFcn(hObject, eventdata, handles) %#ok<*INUSL>
% varargout cell array for returning output args (see VARARGOUT);
% hObject handle to figure
% eventdata reserved - to be defined in a future version of MATLAB
% handles structure with handles and user data (see GUIDATA)
% Get default command line output from handles structure
varargout{1} = handles.output;
% --------------------------------------------------------------------
function initialize_gui(fig_handle, handles, isreset) %#ok<*INUSD>
% If the metricdata field is present and the start flag is false, it means
% we are we are just re-initializing a GUI by calling it from the cmd line
% while it is up. So, bail out as we dont want to start the data.
initMain(handles);
% updateGUI();
% --- Executes on button press in connectHW.
function connectHW_Callback(hObject, eventdata, handles)
% hObject handle to connectHWButton_Callback (see GCBO)
% eventdata reserved - to be defined in a future version of MATLAB
% handles structure with handles and user data (see GUIDATA)
global main;
if isfield(main.hw, 'connected') && main.hw.connected;
disconnectHW();
else
connectHW();
end
% updateGUI();
% --- Executes on button press in start.
function start_Callback(hObject, eventdata, handles)
% hObject handle to start (see GCBO)
% eventdata reserved - to be defined in a future version of MATLAB
% handles structure with handles and user data (see GUIDATA)
global main;
if main.isRunning;
warning('mtrainerGUI:CannotStartAlreadyRunning', ...
'Cannot start because experiment is already running and not paused.');
updateGUI();
return;
else
startExperiment();
end
% updateGUI();
try
mainLoop();
catch e;
closeDiaryAndSaveOutput();
throw(e);
end;
% --- Executes on button press in pause.
function pause_Callback(hObject, eventdata, handles)
% hObject handle to pause (see GCBO)
% eventdata reserved - to be defined in a future version of MATLAB
% handles structure with handles and user data (see GUIDATA)
global main;
if main.isRunning;
if main.isPaused;
main.isPaused = false;
else
main.isPaused = true;
end
else
warning('mtrainerGUI:CannotPauseNotRunning', ...
'Cannot pause because experiment is not running.');
end
% updateGUI();
% --- Executes on button press in stop.
function stop_Callback(hObject, eventdata, handles) %#ok<*DEFNU>
% hObject handle to stop (see GCBO)
% eventdata reserved - to be defined in a future version of MATLAB
% handles structure with handles and user data (see GUIDATA)
global main;
if main.isRunning;
main.isRunning = false;
closeDiaryAndSaveOutput();
else
warning('mtrainerGUI:CannotStopNotRunning', 'Cannot stop because experiment is not running.');
end
% updateGUI();
% --- Executes on button press in reward.
function reward_Callback(hObject, eventdata, handles)
% hObject handle to reward (see GCBO)
% eventdata reserved - to be defined in a future version of MATLAB
% handles structure with handles and user data (see GUIDATA)
global main;
giveReward(main.rewardDur, 0);
% --- Executes on slider movement.
function rewardDurSetter_Callback(hObject, eventdata, handles)
% hObject handle to rewardDurSetter (see GCBO)
% eventdata reserved - to be defined in a future version of MATLAB
% handles structure with handles and user data (see GUIDATA)
% Hints: get(hObject,'Value') returns position of slider
% get(hObject,'Min') and get(hObject,'Max') to determine range of slider
global main;
main.rewardDur = get(hObject,'Value');
set(handles.rewardDur, 'String', sprintf('%04.2f', main.rewardDur));
% --- Executes on slider movement.
function piezoThreshSetter_Callback(hObject, eventdata, handles)
% hObject handle to piezoThreshSetter (see GCBO)
% eventdata reserved - to be defined in a future version of MATLAB
% handles structure with handles and user data (see GUIDATA)
% Hints: get(hObject,'Value') returns position of slider
% get(hObject,'Min') and get(hObject,'Max') to determine range of slider
global main;
main.piezoThresh = get(hObject, 'Value');
set(handles.piezoThresh, 'String', sprintf('%04.2f', main.piezoThresh));
% --- Executes when selected cell(s) is changed in config.
function config_CellSelectionCallback(hObject, eventdata, handles)
% hObject handle to config (see GCBO)
% eventdata structure with the following fields (see UITABLE)
% Indices: row and column indices of the cell(s) currently selecteds
% handles structure with handles and user data (see GUIDATA)
global main;
o('#config_CellSelectionCallback: selection changed: row %d, col %d.', eventdata.Indices, 3, main.dbgLvl);
row = eventdata.Indices(1);
configCell = get(main.handles.config, 'Data');
main.mouseId = configCell{row, 1};
main.taskType = configCell{row, 2};
main.phase = configCell{row, 3};
main.configLoaded = false;
o('#config_CellSelectionCallback: mouseId: %s, taskType: %s, phase: %s.', ...
main.mouseId, main.taskType, main.phase, 3, main.dbgLvl);
% updateGUI();
% --- Executes on button press in loadConfig.
function loadConfig_Callback(hObject, eventdata, handles)
% hObject handle to loadConfig (see GCBO)
% eventdata reserved - to be defined in a future version of MATLAB
% handles structure with handles and user data (see GUIDATA)
loadConfig();
%% #initMain
function initMain(handles)
global main;
main = struct();
main.dbgLvl = 3;
main.debugMode = 0;
main.basePath = 'C:/Users/laurenczy/Documents/programming/Work/PhD/matlab/behavior/mtrainer/';
% main.basePath = 'D:/Users/BaL/programming/Work/PhD/matlab/behavior/mtrainer/';
configsPath = sprintf('%sconfigs.mat', main.basePath);
if ~exist(configsPath, 'file');
error('mtrainerGUI:initMain:ConfigsFileNotFound', ...
'Cannot find the configs at "%s" (file not found).', configsPath);
end;
configsMat = load(configsPath);
main.configs = configsMat.configs;
[~, computerName] = system('hostname');
roomMatch = regexp(computerName, '^HIFOWS(?<room>H\d+)\-\d+\s+$', 'names');
if main.debugMode;
warning('mtrainer_GUI:initMain:DebugMode', 'Debug mode is ON.');
roomMatch = struct('room', 'H30');
o('#initMain: debug mode => room tag enforced to: "%s".', roomMatch.room, 1, main.dbgLvl);
end;
if isempty(roomMatch);
error('mtrainerGUI:initMain:HardwareLoad:NoRoomTagFound', ...
'Cannot load hardware because there''s no room tag in the computer''s name.');
elseif ~isfield(main.configs.hardware, roomMatch.room);
error('mtrainerGUI:initMain:HardwareLoad:UnknownRoom', ...
'Cannot load hardware because room "%s" is unknown.', roomMatch.room);
end;
main.hw = struct();
main.hw.conf = main.configs.hardware.(roomMatch.room);
main.hw.connected = false;
main.hw.analogIns = {'piezo', 'micr', 'yscan'};
main.hw.digitalOuts = {'valve'};
main.hw.recordDur = 8.1;
main.updateRate = 0.1; % 100ms update rate
main.piezoThresh = 0.1;
main.isRunning = false;
main.isPaused = false;
main.isClosed = false;
main.configLoaded = false;
main.iTrial = 0;
main.rewardDur = str2double(get(handles.rewardDur,'String'));
main.handles = handles;
stateData = get(main.handles.state, 'Data');
stateData(:, 1) = getTrialInfo(0);
stateData(:, 2) = getTrialInfo(0);
stateData(:, 3) = getTrialInfo(0);
set(main.handles.state, 'Data', stateData);
set(main.handles.config, 'Data', main.configs.animals);
main.GUIUpdateTimer = timer('TimerFcn', @(~, ~)updateGUI(), 'ExecutionMode', 'fixedRate', ...
'Period', main.updateRate * 1, 'StopFcn', @(~, ~)o('GUIUpdateTimer stopped.', 1, main.dbgLvl), ...
'ErrorFcn', @(~, ~)o('GUIUpdateTimer stopped with error.', 1, main.dbgLvl));
start(main.GUIUpdateTimer);
main.mouseId = '';
o('Mouse trainer v1.0 initiated.', 1, main.dbgLvl);
function onWindowClose(src, eventData)
global main;
stop(main.GUIUpdateTimer);
delete(main.GUIUpdateTimer);
main.isClosed = true;
%% #connectHW
function connectHW()
global main;
o('Connecting hardware ...', 1, main.dbgLvl);
set(main.handles.connectHW, 'BackgroundColor', 'yellow');
main.hw.sampleRate = 0;
nAnIn = numel(main.hw.analogIns);
if nAnIn;
main.analogInData = struct();
main.hw.anIn = daq.createSession(main.hw.conf.adaptorID);
end;
for iAnIn = 1 : nAnIn;
anInName = main.hw.analogIns{iAnIn};
if ~main.debugMode;
main.hw.sampleRate = main.hw.sampleRate + main.hw.conf.(anInName).sampleRate;
main.hw.anIn.addAnalogInputChannel(main.hw.conf.(anInName).deviceName, ...
main.hw.conf.(anInName).channel, 'Voltage');
main.hw.anIn.Channels(iAnIn).Name = anInName;
main.hw.anIn.Channels(iAnIn).InputType = main.hw.conf.(anInName).inputType;
main.hw.anIn.Channels(iAnIn).Range = main.hw.conf.(anInName).range;
main.analogInData.(anInName) = [];
else
o(' "Connecting" fake analog input %d/%d (%s).', iAnIn, nAnIn, anInName, 1, main.dbgLvl);
main.hw.(anInName) = struct();
% main.hw.([anInName 'Listener']) = struct();
main.hw.(anInName).stop = 1;
main.hw.(anInName).startBackground = 1;
% main.hw.(analogInName).IsRunning = @()(round(rand + 0.4));
% main.hw.(analogInName).IsRunning = @()(round(rand - 0.4));
main.hw.(anInName).IsRunning = 1;
pause(1);
end;
o(' Analog input %d/%d (%s): OK.', iAnIn, nAnIn, anInName, 1, main.dbgLvl);
end;
if nAnIn;
main.hw.([anInName 'Listener']) = main.hw.anIn.addlistener('DataAvailable', @(src, event) storeData(src, event));
main.hw.anIn.IsNotifyWhenDataAvailableExceedsAuto = true;
main.hw.anIn.IsContinuous = true;
main.hw.sampleRate = main.hw.sampleRate / nAnIn;
main.hw.anIn.Rate = main.hw.sampleRate;
main.hw.anIn.NotifyWhenDataAvailableExceeds = 200;
% main.hw.anIn.Rate = 3000;
main.hw.anIn.prepare();
end;
for iDigOut = 1 : numel(main.hw.digitalOuts);
digOutName = main.hw.digitalOuts{iDigOut};
if ~main.debugMode;
main.hw.(digOutName) = daq.createSession(main.hw.conf.adaptorID);
main.hw.(digOutName).addDigitalChannel(main.hw.conf.(digOutName).deviceName, ...
main.hw.conf.(digOutName).portLine, 'OutputOnly');
main.hw.(digOutName).outputSingleScan(0); % make sure valve is closed
else
o(' "Connecting" fake digital output %d (%s).', iDigOut, digOutName, 1, main.dbgLvl);
main.hw.valve = struct();
pause(1);
end;
o(' Digital output %d (%s): OK.', iDigOut, digOutName, 1, main.dbgLvl);
end;
main.hw.connected = true;
o('Hardware connected.', 1, main.dbgLvl);
if ~strcmp(main.GUIUpdateTimer.Running, 'on');
start(main.GUIUpdateTimer);
end;
main.hw.anIn.startBackground();
%% #disconnectHW
function disconnectHW()
global main;
o('Disconnecting hardware ...', 1, main.dbgLvl);
if ~main.debugMode;
main.hw.anIn.stop();
% % analog inputs
% for iAnIn = 1 : numel(main.hw.analogIns);
% anInName = main.hw.analogIns{iAnIn};
% if isfield(main.hw, ([anInName 'Listener']));
% main.hw = rmfield(main.hw, [anInName 'Listener']);
% end;
% if isfield(main.hw, anInName);
% main.hw.(anInName).stop();
% main.hw = rmfield(main.hw, anInName);
% end;
% end;
% % digital outputs
% for iDigOut = 1 : numel(main.hw.digitalOuts);
% digOutName = main.hw.digitalOuts{iDigOut};
% if isfield(main.hw, digOutName);
% % main.hw.(digOutName).stop();
% main.hw = rmfield(main.hw, digOutName);
% end;
% end;
daqreset();
end;
main.hw.connected = false;
o('Hardware disconnected.', 1, main.dbgLvl);
%% #giveReward
function giveReward(rewDur, rewDelay)
global main;
if main.hw.connected && isfield(main.hw, 'valve');
if ~main.debugMode;
t_rewardStart = tic;
% wait until for start delay
while toc(t_rewardStart) < rewDelay; end;
t_rewardStart = tic;
% open digital out
% main.hw.valve.outputSingleScan(0);
main.hw.valve.outputSingleScan(1);
% wait until for open duration
while toc(t_rewardStart) < rewDur; end;
% close digital out
% main.hw.valve.outputSingleScan(1);
main.hw.valve.outputSingleScan(0);
end;
o('Rewarding for %.2f sec with a delay of %.2f.', rewDur, rewDelay, 3, main.dbgLvl);
else
warning('mtrainerGUI:NoRewardHardwareDisconnected', 'Cannot give reward because hardware is disconnected.');
end
%% #updateGUI
function updateGUI()
global main;
% o('#updateGUI()', 1, main.dbgLvl);
if main.isClosed; return; end;
stateData = get(main.handles.state, 'Data');
handles = main.handles;
if main.hw.connected;
set(handles.connectHW, 'BackgroundColor', 'green');
set(handles.connectHW, 'Value', 1);
else
set(handles.connectHW, 'BackgroundColor', 'red');
set(handles.connectHW, 'Value', 0);
end;
if main.isRunning;
set(handles.start, 'Value', 1);
set(handles.start, 'BackgroundColor', 'green');
if main.isPaused;
set(handles.pause, 'Value', 1);
set(handles.pause, 'BackgroundColor', [1 1 0]);
else
set(handles.pause, 'Value', 0);
set(handles.pause, 'BackgroundColor', 'green');
end;
% stateData(:, 1) = stateData(:, 2);
stateData(:, 1) = getTrialInfo(main.iTrial - 1);
stateData(:, 2) = getTrialInfo(main.iTrial);
if main.iTrial < main.config.training.nTrials;
stateData(:, 3) = getTrialInfo(main.iTrial + 1);
else
stateData(:, 3) = getTrialInfo(0);
end;
else
set(handles.start, 'Value', 0);
set(handles.start, 'BackgroundColor', 'red');
set(handles.pause, 'Value', 0);
set(handles.pause, 'BackgroundColor', 'red');
if main.configLoaded && main.iTrial == 0;
stateData(:, 3) = getTrialInfo(1);
else
stateData(:, 3) = getTrialInfo(0);
end;
end;
delete(get(handles.piezoAxes, 'Children')); % delete previous plot
if isfield(main, 'analogInData');
hold(handles.piezoAxes, 'on');
if isfield(main.analogInData, 'yscan');
nSamples = size(main.analogInData.yscan, 1);
if nSamples;
t = (1 : nSamples) / main.hw.sampleRate;
plot(handles.piezoAxes, t, main.analogInData.yscan * 3, 'b');
end;
end;
if isfield(main.analogInData, 'micr');
nSamples = size(main.analogInData.micr, 1);
if nSamples;
t = (1 : nSamples) / main.hw.sampleRate;
plot(handles.piezoAxes, t, main.analogInData.micr * 2, 'g');
end;
end;
if isfield(main.analogInData, 'piezo');
nSamples = size(main.analogInData.piezo, 1);
if nSamples;
t = (1 : nSamples) / main.hw.sampleRate;
plot(handles.piezoAxes, t, main.analogInData.piezo * 10, 'r');
if isfield(main, 'piezoThresh');
plot(handles.piezoAxes, [0, t(end)], [main.piezoThresh, main.piezoThresh] * 10, 'r:');
end;
end;
end;
end;
xlim(handles.piezoAxes, [0 main.hw.recordDur]);
ylim(handles.piezoAxes, [-3, 3]);
set(main.handles.state, 'Data', stateData);
set(main.handles.configLoaded, 'Value', logical(main.configLoaded));
%% #getTrialInfo
function trialInfo = getTrialInfo(iTrial)
global main;
if iTrial;
freq = sprintf('%4.2f', main.config.tone.freqs(main.stims(iTrial)) / 1000);
if isfield(main.config.tone, 'oddProba') && main.config.tone.oddProba > 0; % oddball discrimination
isTarget = double(main.stims(iTrial) ~= main.odds(iTrial) && main.config.tone.goStim);
else % frequency discrimination
isTarget = double(main.stims(iTrial) == main.config.tone.goStim);
end;
if isfield(main, 'resps') && ~isnan(main.resps(iTrial));
resp = main.resps(iTrial);
respTime = main.respTimes(iTrial);
if isnan(respTime); respTime = '-'; end;
corr = double((isTarget && resp) || (~isTarget && ~resp));
ITL = main.nInTriLick(iTrial);
else
resp = '-';
respTime = '-';
corr = '-';
ITL = '-';
end;
trialInfo = {iTrial, freq, isTarget, resp, respTime, corr, ITL};
else
trialInfo = {'-', '-', '-', '-', '-', '-', '-'};
end;
%% #loadConfig
function loadConfig()
global main;
o('Loading configuration ...', 2, main.dbgLvl);
if isempty(main.mouseId);
warning('loadConfig:NoMouseIdSelected', 'Cannot load config because no mouseId is selected.');
return;
end;
% main.doEmptyWater = 0;
% main.doEmptyWater = 1;
% if > 0, sets the number of seconds to wait before a new run of mtrainer
% main.automode = 5;
main.iTrial = 0;
% main.piezoThresh = NaN;
main.config = main.configs.behavior.(main.taskType).(main.phase);
%% Setup - stimuli and trials
o(' loadConfig#: setup stimuli and trials... ', 3, main.dbgLvl);
% set up stimulus vector
stims = [];
for iFreq = 1 : numel(main.config.tone.freqs);
stimForFreq = repmat(iFreq, 1, ...
round(main.config.tone.stimProba(iFreq) * main.config.training.nTrials));
stims = [stims, stimForFreq]; %#ok<AGROW>
end
% stim vector should not be randomly permuted
stims = stims(randperm(numel(stims)));
stims = stims(1 : main.config.training.nTrials);
clear stim;
switch(main.taskType);
case {'freqDiscr', 'oddDiscr'};
% set up oddball vector by altering stims with a certain probability
odds = stims;
oddPos = zeros(size(odds));
uniqueStims = unique(stims);
isOdd = rand(1, numel(stims)) < main.config.tone.oddProba;
uniqueOddPos = main.config.tone.nTones - 1 : main.config.tone.nTones; % last 2 tones can be odd
for iStim = 1 : numel(isOdd);
if isOdd(iStim);
otherStims = uniqueStims(uniqueStims ~= stims(iStim));
otherStims = otherStims(randperm(numel(otherStims)));
mixedOddPos = uniqueOddPos(randperm(numel(uniqueOddPos)));
odds(iStim) = otherStims(1);
oddPos(iStim) = mixedOddPos(1);
end;
end;
% set up tone array
main.toneArray = MakePureMultiToneOddballArray(main.config.tone.freqs, stims, odds, oddPos, ...
main.config.tone.nTones, main.config.tone.stimDur, main.config.tone.ISI, ...
main.config.tone.samplingFreq);
case 'cotDiscr';
odds = zeros(size(stims));
oddPos = zeros(size(stims));
isOdd = zeros(size(stims));
atten = 0.5;
main.toneArray = MakeCloudOfTonesSound(main.config.tone.uniqueFreqs, main.config.tone.freqIndexes, ...
main.config.tone.cloudDispersion, stims, main.config.tone.toneDur, main.config.tone.toneISI, ...
main.config.tone.stimDur, atten, main.config.tone.samplingFreq, 0, 0);
end;
main.stims = stims;
main.odds = odds;
main.oddPos = oddPos;
main.isOdd = isOdd;
main.configLoaded = true;
updateGUI();
o(' loadConfig#: setup stimuli and trials done. ', 2, main.dbgLvl);
o('Loading configuration done.', 2, main.dbgLvl);
%% #startExperiment
function startExperiment()
global main;
if ~main.configLoaded;
warning('startExperiment:configNotLoaded', 'Cannot start experiment because config is not loaded.');
return;
end;
if isempty(main.mouseId);
warning('startExperiment:NoMouseId', 'Cannot start experiment because there is no mouseId.');
return;
end;
if ~main.hw.connected;
warning('startExperiment:HardwareDisconnected', ...
'Cannot start experiment because hardware is disconnected.');
return;
end;
o('startExperiment#: initializing experiment ... ', 2, main.dbgLvl);
main.isPaused = false;
main.isRunning = true;
main.iTrial = 1;
main.saveTime = datestr(now(), 'yyyy_mm_dd__HH_MM_SS');
% saveFolder = sprintf('D:/Balazs/2013/mtrainerTests/%s/', ...
% saveFolder = sprintf('C:/Users/laurenczy.HIFO/Documents/LocalData/2013/mtrainerTests/%s/', ...
saveFolder = sprintf('C:/Users/laurenczy/mtrainerTests/%s/', main.mouseId);
% saveFolder = sprintf('D:/Users/BaL/PhD/mtrainerTests/%s/', main.mouseId);
main.savePath = sprintf('%s%s__%s', saveFolder, main.mouseId, main.saveTime);
mkdir(saveFolder);
logfile = sprintf('%s_log.txt', main.savePath);
main.logDateFormat = 'yyyy-mm-dd HH:MM:SS.FFF';
% % create an 'onCleanup' function to handle interruptions by CTRL+C
% c = onCleanup(@()closeDiaryAndSaveOutput(main.savePath, main.hw.piezoListener, ...
% main.hw.piezo, main.hw.valve));
o(' startExperiment#: logFile initialized. Starting diary...', 2, main.dbgLvl);
diary(logfile);
%% Start experiment
o('Experiment start: %s\n\n', datestr(now(), main.logDateFormat), 1, main.dbgLvl);
%% Setup - saving settings
global recordedValues;
recordedValues = 0;
o('config: %s phase %s (%dF%dT)', main.taskType, main.phase, numel(main.config.tone.freqs), ...
main.config.tone.nTones, 0, main.dbgLvl);
o('animal: %s', main.mouseId, 0, main.dbgLvl);
o('savePath: %s', main.savePath, 0, main.dbgLvl);
o('piezoThresh: %1.2f, ISI: %1.2f', main.piezoThresh, main.config.tone.ISI, 1, main.dbgLvl);
o('rewardCollectionTime: %1.2f, InTriLickTimerDur: %1.2f', main.config.training.rewCollTime, ...
main.config.training.InTriLickTimerDur, 1, main.dbgLvl);
nTrials = main.config.training.nTrials;
main.trialStartDelays = zeros(1, nTrials);
main.trialStartTimes = zeros(1, nTrials);
main.trialEndTimes = zeros(1, nTrials);
main.respTimes = nan(1, nTrials);
main.nInTriLick = nan(1, nTrials);
main.resps = nan(1, nTrials);
main.respDelays = nan(1, nTrials);
% for each trial: 1 = correct detect, 2 = correct reject, 3 = false alarm, 4 = miss, 5 = early
main.respTypes = nan(1, nTrials);
main.expStartTime = tic;
main.isPunish = 0;
%% #mainLoop
function mainLoop()
global main;
displayedPause = 0;
while main.isRunning;
o('mainLoop#: iTrial = %d.', main.iTrial, 4, main.dbgLvl);
if ~main.isPaused;
if displayedPause; o(' --- RESUMED --- ', 1, main.dbgLvl); displayedPause = 0; end;
o('mainLoop#: running trial %d.', main.iTrial, 3, main.dbgLvl);
runTrial();
if main.isRunning;
% o('Trial %d: pause ended, updating trial number.', main.iTrial, 2, main.dbgLvl);
if main.iTrial == main.config.training.nTrials;
main.isRunning = false;
%% End experiment
o('\nExperiment end: %s', datestr(now(), main.logDateFormat), 1, main.dbgLvl);
main.expTotDurTime = toc(main.expStartTime);
o('Total time: %02.0f:%02.0f', ...
main.expTotDurTime / 60, mod(main.expTotDurTime, 60), main.dbgLvl);
mtrainerAnalyser_performance(main.respTypes, 2, main.savePath, main.nInTriLick);
closeDiaryAndSaveOutput();
else
main.iTrial = main.iTrial + 1;
o('Trial %d: updated trial number: %d.', main.iTrial - 1, main.iTrial, 2, main.dbgLvl);
end;
else
o('Trial %d: not running anymore, no update of trial number.', main.iTrial, 2, main.dbgLvl);
end;
o('mainLoop#: running trial %d done.', main.iTrial, 3, main.dbgLvl);
% updateGUI();
else
if ~displayedPause; o(' --- PAUSED --- ', 1, main.dbgLvl); displayedPause = 1; end;
o('mainLoop#: waiting for %f sec (trial %d).', main.updateRate, main.iTrial, 3, main.dbgLvl);
pause(main.updateRate);
end;
end;
%% #runTrial
function runTrial()
global main;
nTrials = main.config.training.nTrials;
iTrial = main.iTrial;
% listen for response
% main.hw.anIn.startBackground();
pause(0.01)
interTrialLickCount = 0;
main.trialStartTimes(iTrial) = tic;
% introduce a random delay for starting the tone
main.trialStartDelays(iTrial) = main.config.training.startDelay + ...
(rand(1) - 0.5) * 2 * main.config.training.startDelayRand;
% add punishement time-out if needed
if main.isPunish;
main.trialStartDelays(iTrial) = main.trialStartDelays(iTrial) + main.config.training.timeoutPunish;
end;
%% Experiment - initial wait
while toc(uint64(main.trialStartTimes(iTrial))) < main.trialStartDelays(iTrial);
% fprintf('CheckingA: main.hw.piezo.IsRunning()? %d\n', main.hw.piezo.IsRunning());
% check if experiment is paused/stopped
if ~main.isRunning; return; end;
while main.isPaused; pause(main.updateRate); end;
if ~main.isRunning; return; end;
% % check if no lick has been done
% if ~main.hw.piezo.IsRunning(); % if not running anymore, it means a licking has been done
% remainingTime = main.trialStartDelays(iTrial) - toc(uint64(main.trialStartTimes(iTrial)));
% if interTrialLickCount > 0;
% fprintf('|%.1f', remainingTime);
% else
% fprintf(' inter-trial licking: |%.1f', remainingTime);
% end;
%
% % reset the starting delay to main.config.training.InTriLickTimerDur
% main.trialStartTimes(iTrial) = tic;
% if main.isPunish;
% main.trialStartDelays(iTrial) = max(main.config.training.InTriLickTimerDur, remainingTime);
% else
% main.trialStartDelays(iTrial) = main.config.training.InTriLickTimerDur;
% end;
% interTrialLickCount = interTrialLickCount + 1;
% pause(1);
% % restart the listening
% % main.hw.piezo.startBackground();
% % pause(0.1);
% % fprintf('CheckingB: main.hw.piezo.IsRunning()? %d\n', main.hw.piezo.IsRunning());
% end
% avoid full-speed looping
pause(0.1);
% updateGUI();
end;
% if interTrialLickCount;
% fprintf('|: %d inter-trial lick(s).\n', interTrialLickCount);
% end
main.nInTriLick(iTrial) = interTrialLickCount;
resp = 0;
main.isPunish = 0;
% check if experiment is paused/stopped
if ~main.isRunning; return; end;
% while main.isPaused; pause(main.updateRate); end;
% if ~main.isRunning; return; end;
t_trialStart = tic;
fprintf('Trial %03d/%03d - %s ... ', iTrial, nTrials, datestr(now(), main.logDateFormat));
%% Experiment - play sound
% if main.hw.piezo.IsRunning();
soundToPlay = main.toneArray{iTrial};
player = audioplayer(soundToPlay, main.config.tone.samplingFreq);
player.play;
% else
% fprintf('early (already licking, lick sensor: min/mean/max: %.2f/%.2f/%.2f).\n', recordedValues);
% main.isPunish = 1;
% main.respTypes(iTrial) = 5;
% % analyse every 10 trials
% if ~rem(iTrial, 10) && iTrial ~= nTrials;
% mtrainerAnalyser_performance(main.respTypes, 0);
% end;
% return;
% end
breakOut = 0;
%% Experiment - wait for response
while toc(t_trialStart) < main.config.training.trialDur;
% check if experiment is paused/stopped
if ~main.isRunning; return; end;
% while main.isPaused; pause(main.updateRate); end;
% if ~main.isRunning; return; end;
% if main.hw.piezo.IsRunning();
if 1;
% no response detected
else
% seconds since trial start
respTime = toc(t_trialStart);
main.respTimes(iTrial) = respTime;
% response should be 'minRespTime' after the end of the tone!
totStimDur = (main.config.tone.stimDur + main.config.tone.ISI) * main.config.tone.nTones - main.config.tone.ISI;
limitRespTime = totStimDur + main.config.training.minRespTime;
% limitRespTime = main.config.training.minRespTime;
main.respDelays(iTrial) = limitRespTime - respTime;
% early response, count as kind of false alarm
if respTime < limitRespTime;
% fprintf('early (lick sensor: min/mean/max: %.2f/%.2f/%.2f).\n', recordedValues);
fprintf('early (response time: %.4f, limit response time: %.4f, diff: %.5f).\n', ...
respTime, limitRespTime, limitRespTime - respTime);
main.isPunish = 1;
main.respTypes(iTrial) = 5;
breakOut = 1;
break;
else
% fprintf('Lick at %s\n', datestr(clock, main.logDateFormat))
resp = 1;
end;
break; % break out of while loop
end;
pause(0.02); % necessary to allow time for data collection
% updateGUI();
end;
if breakOut;
main.trialEndTimes(iTrial) = toc(uint64(main.trialStartTimes(iTrial)));
% analyse every 10 trials
if ~rem(iTrial, 10) && iTrial ~= nTrials;
mtrainerAnalyser_performance(main.respTypes, 0);
end;
return; % continue for loop
end;
% if main.hw.piezo.IsRunning();
% main.hw.piezo.stop();
% end;
% check if experiment is paused/stopped
if ~main.isRunning; return; end;
% while main.isPaused; pause(main.updateRate); end;
% if ~main.isRunning; return; end;
%% Experiment - analyse response
main.resps(iTrial) = resp;
isOddTrial = main.stims(iTrial) ~= main.odds(iTrial);
if isfield(main.config.tone, 'oddProba') && main.config.tone.oddProba > 0; % oddball discrimination
isTargetStim = isOddTrial && main.config.tone.goStim;
else % frequency discrimination
isTargetStim = main.stims(iTrial) == main.config.tone.goStim;
end;
if resp == 1 && isTargetStim;
% correct response
% fprintf('correct detection (lick sensor: min/mean/max: %.2f/%.2f/%.2f).\n', recordedValues);
fprintf('correct detection (response time: %.4f, limit response time: %.4f, diff: %.5f).\n', ...
respTime, limitRespTime, limitRespTime - respTime);
main.respTypes(iTrial) = 1;
% give reward
giveReward(main.config.training.rewDur, main.config.training.rewDelay);
% wait to collect the reward
pause(main.config.training.rewCollTime);
elseif resp == 1 && ~isTargetStim;
% false alarm
% fprintf('false alarm (lick sensor: min/mean/max: %.2f/%.2f/%.2f).\n', recordedValues);
fprintf('false alarm (response time: %.4f, limit response time: %.4f, diff: %.5f).\n', ...
respTime, limitRespTime, limitRespTime - respTime);
main.respTypes(iTrial) = 3;
% punish time-out
main.isPunish = 1;
elseif resp == 0 && isTargetStim;
fprintf('miss.\n');
main.respTypes(iTrial) = 4;
% punish time-out
main.isPunish = 1;
elseif resp == 0 && ~isTargetStim;
fprintf('correct rejection.\n');
main.respTypes(iTrial) = 2;
% go to next trial
end
main.trialEndTimes(iTrial) = toc(uint64(main.trialStartTimes(iTrial)));
% analyse every 10 trials
if ~rem(iTrial, 10) && iTrial ~= nTrials;
mtrainerAnalyser_performance(main.respTypes, 0);
end;
%% #recordAndStop
function recordAndStop(src, event)
% global main recordedValues;
% [recordedValues, main.recordedData] = stopWhenExceedThreshold(src, event, main.piezoThresh);
% updateGUI();
%% #storeData
function storeData(src, event)
global main;
nChans = size(event.Data, 2);
for iChan = 1 : nChans;
anInName = main.hw.analogIns{iChan};
prevData = main.analogInData.(anInName);
% currChanData = linScale(event.Data(:, iChan) - mean(event.Data(:, iChan)));
currChanData = event.Data(:, iChan) - mean(event.Data(:, iChan));
% currChanData = event.Data(:, iChan);
allChanData = [prevData; currChanData];
if size(allChanData, 1) / main.hw.sampleRate > main.hw.recordDur;
main.analogInData.(anInName) = currChanData;
else
main.analogInData.(anInName) = allChanData;
end;
% if (size(allChanData, 1) + nSamples) / main.hw.sampleRate > main.hw.recordDur;
% updateGUI();
% end;
end;
% normAbsData = abs(normData);
% allData = event.Data;
% supThreshData = normAbsData(normAbsData > main.piezoThresh);
% recordedValues = [min(supThreshData), mean(supThreshData), max(supThreshData)];
% main.recordedData = allData;
% recordDur
% if any(normAbsData > threshold);
% end;
%
% [recordedValues, main.recordedData] = stopWhenExceedThreshold(src, event, main.piezoThresh);
% updateGUI();
%% #closeDiaryAndSaveOutput
function closeDiaryAndSaveOutput()
global main;
o('\nClosing diary... ', 2, main.dbgLvl);
diary off;
o('Closing diary done.', 1, main.dbgLvl);
out = main;
try out.hw = rmfield(out.hw, 'toneArray'); catch e; end; %#ok<NASGU>
try out.hw = rmfield(out.hw, 'piezoListener'); catch e; end; %#ok<NASGU>
try out.hw = rmfield(out.hw, 'piezo'); catch e; end; %#ok<NASGU>
try out.hw = rmfield(out.hw, 'valve'); catch e; end; %#ok<NASGU>
try out.hw = rmfield(out.hw, 'recordedData'); catch e; end; %#ok<NASGU>
if exist('out', 'var');
matFileName = sprintf('%s_out.mat', main.savePath);
o('Saving output as %s... ', matFileName, 2, main.dbgLvl);
save(matFileName, 'out');
o('Saving output done.', matFileName, 1, main.dbgLvl);
else
o('/!\\ Output not saved !', 1, main.dbgLvl);
end;
% disconnectHW();
|
github
|
PacktPublishing/ROS-Programming-Building-Powerful-Robots-master
|
teleop.m
|
.m
|
ROS-Programming-Building-Powerful-Robots-master/Module03/Chapter08/Matlab/teleop.m
| 10,043 |
utf_8
|
7f1f1a8bd40b2cbd4fb318fe3d696aa9
|
function varargout = teleop(varargin)
%Before starting this code, you have to launch any robotic simulation on
%ROS PC or start a ROS robot
% For example, you can test it using turtlebot simulation
% You can launch turtlebot simulation using following command
% $ roslaunch turtlebot_gazebo turtlebot_world.launch
% Retreive IP of the PC and put it on the MATLAB app, also note the command
% velocity
% TELEOP MATLAB code for teleop.fig
% TELEOP, by itself, creates a new TELEOP or raises the existing
% singleton*.
%
% H = TELEOP returns the handle to a new TELEOP or the handle to
% the existing singleton*.
%
% TELEOP('CALLBACK',hObject,eventData,handles,...) calls the local
% function named CALLBACK in TELEOP.M with the given input arguments.
%
% TELEOP('Property','Value',...) creates a new TELEOP or raises the
% existing singleton*. Starting from the left, property value pairs are
% applied to the GUI before teleop_OpeningFcn gets called. An
% unrecognized property name or invalid value makes property application
% stop. All inputs are passed to teleop_OpeningFcn via varargin.
%
% *See GUI Options on GUIDE's Tools menu. Choose "GUI allows only one
% instance to run (singleton)".
%
% See also: GUIDE, GUIDATA, GUIHANDLES
% Edit the above text to modify the response to help teleop
% Last Modified by GUIDE v2.5 07-Dec-2016 22:22:30
% Begin initialization code - DO NOT EDIT
gui_Singleton = 1;
gui_State = struct('gui_Name', mfilename, ...
'gui_Singleton', gui_Singleton, ...
'gui_OpeningFcn', @teleop_OpeningFcn, ...
'gui_OutputFcn', @teleop_OutputFcn, ...
'gui_LayoutFcn', [] , ...
'gui_Callback', []);
if nargin && ischar(varargin{1})
gui_State.gui_Callback = str2func(varargin{1});
end
if nargout
[varargout{1:nargout}] = gui_mainfcn(gui_State, varargin{:});
else
gui_mainfcn(gui_State, varargin{:});
end
% End initialization code - DO NOT EDIT
% --- Executes just before teleop is made visible.
function teleop_OpeningFcn(hObject, eventdata, handles, varargin)
% This function has no output args, see OutputFcn.
% hObject handle to figure
% eventdata reserved - to be defined in a future version of MATLAB
% handles structure with handles and user data (see GUIDATA)
% varargin command line arguments to teleop (see VARARGIN)
% Choose default command line output for teleop
handles.output = hObject;
% Update handles structure
guidata(hObject, handles);
% UIWAIT makes teleop wait for user response (see UIRESUME)
% uiwait(handles.figure1);
%Declaring some initial variables globally
global ros_master_ip
global ros_master_port
global teleop_topic_name
%DEFAULT ROS MASTER IP, PORT AND TELEOP TOPIC
ros_master_ip = '192.168.1.102';
ros_master_port = '11311';
teleop_topic_name = '/cmd_vel_mux/input/teleop';
%Initializing robot speed
global left_spinVelocity
global right_spinVelocity
global forwardVelocity
global backwardVelocity
left_spinVelocity = 2; % Angular velocity (rad/s)
right_spinVelocity = -2; % Angular velocity (rad/s)
forwardVelocity = 3; % Linear velocity (m/s)
backwardVelocity = -3; % Linear velocity (reverse) (m/s)
% --- Outputs from this function are returned to the command line.
function varargout = teleop_OutputFcn(hObject, eventdata, handles)
% varargout cell array for returning output args (see VARARGOUT);
% hObject handle to figure
% eventdata reserved - to be defined in a future version of MATLAB
% handles structure with handles and user data (see GUIDATA)
% Get default command line output from handles structure
varargout{1} = handles.output;
% --- Executes on button press in pushbutton2.
%Right movement
function pushbutton2_Callback(hObject, eventdata, handles)
% hObject handle to pushbutton2 (see GCBO)
% eventdata reserved - to be defined in a future version of MATLAB
% handles structure with handles and user data (see GUIDATA)
global velmsg
global robot
global right_spinVelocity
global teleop_topic_name
%Assigning data to Twist message
velmsg.Angular.Z = right_spinVelocity;
velmsg.Linear.X = 0;
%Publishing message
send(robot,velmsg);
latchpub = rospublisher(teleop_topic_name, 'IsLatching', true);
% --- Executes on button press in pushbutton3.
%Left movement
function pushbutton3_Callback(hObject, eventdata, handles)
% hObject handle to pushbutton3 (see GCBO)
% eventdata reserved - to be defined in a future version of MATLAB
% handles structure with handles and user data (see GUIDATA)
global velmsg
global robot
global left_spinVelocity
global teleop_topic_name
velmsg.Angular.Z = left_spinVelocity;
velmsg.Linear.X = 0;
send(robot,velmsg);
latchpub = rospublisher(teleop_topic_name, 'IsLatching', true);
% --- Executes on button press in pushbutton4.
%Forward movement
function pushbutton4_Callback(hObject, eventdata, handles)
% hObject handle to pushbutton4 (see GCBO)
% eventdata reserved - to be defined in a future version of MATLAB
% handles structure with handles and user data (see GUIDATA)
global velmsg
global robot
global teleop_topic_name
global forwardVelocity
velmsg.Angular.Z = 0;
velmsg.Linear.X = forwardVelocity;
send(robot,velmsg);
latchpub = rospublisher(teleop_topic_name, 'IsLatching', true);
% --- Executes on button press in pushbutton5.
%Backward motion
function pushbutton5_Callback(hObject, eventdata, handles)
% hObject handle to pushbutton5 (see GCBO)
% eventdata reserved - to be defined in a future version of MATLAB
% handles structure with handles and user data (see GUIDATA)
global velmsg
global robot
global backwardVelocity
global teleop_topic_name
velmsg.Angular.Z = 0;
velmsg.Linear.X = backwardVelocity;
send(robot,velmsg);
latchpub = rospublisher(teleop_topic_name, 'IsLatching', true);
% --- Executes on button press in pushbutton6.
%This button will connect to a ROS network
function pushbutton6_Callback(hObject, eventdata, handles)
% hObject handle to pushbutton6 (see GCBO)
% eventdata reserved - to be defined in a future version of MATLAB
% handles structure with handles and user data (see GUIDATA)
global ros_master_ip
global ros_master_port
global teleop_topic_name
global robot
global velmsg
ros_master_uri = strcat('http://',ros_master_ip,':',ros_master_port)
setenv('ROS_MASTER_URI',ros_master_uri)
rosinit
%Initializing ROS publishers
robot = rospublisher(teleop_topic_name,'geometry_msgs/Twist');
velmsg = rosmessage(robot);
% --- Executes on button press in pushbutton7.
%This button disconnect from ROS network
function pushbutton7_Callback(hObject, eventdata, handles)
% hObject handle to pushbutton7 (see GCBO)
% eventdata reserved - to be defined in a future version of MATLAB
% handles structure with handles and user data (see GUIDATA)
rosshutdown
% setting ROS master ip from edit box
%This function will retreive ROS MASTER IP from editbox
function edit1_Callback(hObject, eventdata, handles)
% hObject handle to edit1 (see GCBO)
% eventdata reserved - to be defined in a future version of MATLAB
% handles structure with handles and user data (see GUIDATA)
% Hints: get(hObject,'String') returns contents of edit1 as text
% str2double(get(hObject,'String')) returns contents of edit1 as a double
global ros_master_ip
ros_master_ip = get(hObject,'String')
% --- Executes during object creation, after setting all properties.
function edit1_CreateFcn(hObject, eventdata, handles)
% hObject handle to edit1 (see GCBO)
% eventdata reserved - to be defined in a future version of MATLAB
% handles empty - handles not created until after all CreateFcns called
% Hint: edit controls usually have a white background on Windows.
% See ISPC and COMPUTER.
if ispc && isequal(get(hObject,'BackgroundColor'), get(0,'defaultUicontrolBackgroundColor'))
set(hObject,'BackgroundColor','white');
end
%Retreiving ROS MASTER PORT from edit box
function edit2_Callback(hObject, eventdata, handles)
% hObject handle to edit2 (see GCBO)
% eventdata reserved - to be defined in a future version of MATLAB
% handles structure with handles and user data (see GUIDATA)
% Hints: get(hObject,'String') returns contents of edit2 as text
% str2double(get(hObject,'String')) returns contents of edit2 as a double
global ros_master_port
ros_master_port = get(hObject,'String')
% --- Executes during object creation, after setting all properties.
function edit2_CreateFcn(hObject, eventdata, handles)
% hObject handle to edit2 (see GCBO)
% eventdata reserved - to be defined in a future version of MATLAB
% handles empty - handles not created until after all CreateFcns called
% Hint: edit controls usually have a white background on Windows.
% See ISPC and COMPUTER.
if ispc && isequal(get(hObject,'BackgroundColor'), get(0,'defaultUicontrolBackgroundColor'))
set(hObject,'BackgroundColor','white');
end
%We can retreive teleop topic from this box
function edit3_Callback(hObject, eventdata, handles)
% hObject handle to edit3 (see GCBO)
% eventdata reserved - to be defined in a future version of MATLAB
% handles structure with handles and user data (see GUIDATA)
% Hints: get(hObject,'String') returns contents of edit3 as text
% str2double(get(hObject,'String')) returns contents of edit3 as a double
global teleop_topic_name
teleop_topic_name = get(hObject,'String')
% --- Executes during object creation, after setting all properties.
function edit3_CreateFcn(hObject, eventdata, handles)
% hObject handle to edit3 (see GCBO)
% eventdata reserved - to be defined in a future version of MATLAB
% handles empty - handles not created until after all CreateFcns called
% Hint: edit controls usually have a white background on Windows.
% See ISPC and COMPUTER.
if ispc && isequal(get(hObject,'BackgroundColor'), get(0,'defaultUicontrolBackgroundColor'))
set(hObject,'BackgroundColor','white');
end
|
github
|
thigiacmaytinh/FaceDetection-master
|
modelConvert.m
|
.m
|
FaceDetection-master/lib/opencv320/contrib/ximgproc/tutorials/scripts/modelConvert.m
| 2,117 |
utf_8
|
dd8b0dc376b1da49ced7529a9e3a7723
|
function modelConvert(model, outname)
%% script for converting Piotr's matlab model into YAML format
outfile = fopen(outname, 'w');
fprintf(outfile, '%%YAML:1.0\n\n');
fprintf(outfile, ['options:\n'...
' numberOfTrees: 8\n'...
' numberOfTreesToEvaluate: 4\n'...
' selfsimilarityGridSize: 5\n'...
' stride: 2\n'...
' shrinkNumber: 2\n'...
' patchSize: 32\n'...
' patchInnerSize: 16\n'...
' numberOfGradientOrientations: 4\n'...
' gradientSmoothingRadius: 0\n'...
' regFeatureSmoothingRadius: 2\n'...
' ssFeatureSmoothingRadius: 8\n'...
' gradientNormalizationRadius: 4\n\n']);
fprintf(outfile, 'childs:\n');
printToYML(outfile, model.child', 0);
fprintf(outfile, 'featureIds:\n');
printToYML(outfile, model.fids', 0);
fprintf(outfile, 'thresholds:\n');
printToYML(outfile, model.thrs', 0);
N = 1000;
fprintf(outfile, 'edgeBoundaries:\n');
printToYML(outfile, model.eBnds, N);
fprintf(outfile, 'edgeBins:\n');
printToYML(outfile, model.eBins, N);
fclose(outfile);
gzip(outname);
end
function printToYML(outfile, A, N)
%% append matrix A to outfile as
%% - [a11, a12, a13, a14, ..., a1n]
%% - [a21, a22, a23, a24, ..., a2n]
%% ...
%%
%% if size(A, 2) == 1, A is printed by N elemnent per row
if (length(size(A)) ~= 2)
error('printToYML: second-argument matrix should have two dimensions');
end
if (size(A,2) ~= 1)
for i=1:size(A,1)
fprintf(outfile, ' - [');
fprintf(outfile, '%d,', A(i, 1:end-1));
fprintf(outfile, '%d]\n', A(i, end));
end
else
len = length(A);
for i=1:ceil(len/N)
first = (i-1)*N + 1;
last = min(i*N, len) - 1;
fprintf(outfile, ' - [');
fprintf(outfile, '%d,', A(first:last));
fprintf(outfile, '%d]\n', A(last + 1));
end
end
fprintf(outfile, '\n');
end
|
github
|
imistyrain/ssd-master
|
classification_demo.m
|
.m
|
ssd-master/matlab/demo/classification_demo.m
| 5,412 |
utf_8
|
8f46deabe6cde287c4759f3bc8b7f819
|
function [scores, maxlabel] = classification_demo(im, use_gpu)
% [scores, maxlabel] = classification_demo(im, use_gpu)
%
% Image classification demo using BVLC CaffeNet.
%
% IMPORTANT: before you run this demo, you should download BVLC CaffeNet
% from Model Zoo (http://caffe.berkeleyvision.org/model_zoo.html)
%
% ****************************************************************************
% For detailed documentation and usage on Caffe's Matlab interface, please
% refer to Caffe Interface Tutorial at
% http://caffe.berkeleyvision.org/tutorial/interfaces.html#matlab
% ****************************************************************************
%
% input
% im color image as uint8 HxWx3
% use_gpu 1 to use the GPU, 0 to use the CPU
%
% output
% scores 1000-dimensional ILSVRC score vector
% maxlabel the label of the highest score
%
% You may need to do the following before you start matlab:
% $ export LD_LIBRARY_PATH=/opt/intel/mkl/lib/intel64:/usr/local/cuda-5.5/lib64
% $ export LD_PRELOAD=/usr/lib/x86_64-linux-gnu/libstdc++.so.6
% Or the equivalent based on where things are installed on your system
%
% Usage:
% im = imread('../../examples/images/cat.jpg');
% scores = classification_demo(im, 1);
% [score, class] = max(scores);
% Five things to be aware of:
% caffe uses row-major order
% matlab uses column-major order
% caffe uses BGR color channel order
% matlab uses RGB color channel order
% images need to have the data mean subtracted
% Data coming in from matlab needs to be in the order
% [width, height, channels, images]
% where width is the fastest dimension.
% Here is the rough matlab for putting image data into the correct
% format in W x H x C with BGR channels:
% % permute channels from RGB to BGR
% im_data = im(:, :, [3, 2, 1]);
% % flip width and height to make width the fastest dimension
% im_data = permute(im_data, [2, 1, 3]);
% % convert from uint8 to single
% im_data = single(im_data);
% % reshape to a fixed size (e.g., 227x227).
% im_data = imresize(im_data, [IMAGE_DIM IMAGE_DIM], 'bilinear');
% % subtract mean_data (already in W x H x C with BGR channels)
% im_data = im_data - mean_data;
% If you have multiple images, cat them with cat(4, ...)
% Add caffe/matlab to you Matlab search PATH to use matcaffe
if exist('../+caffe', 'dir')
addpath('..');
else
error('Please run this demo from caffe/matlab/demo');
end
% Set caffe mode
if exist('use_gpu', 'var') && use_gpu
caffe.set_mode_gpu();
gpu_id = 0; % we will use the first gpu in this demo
caffe.set_device(gpu_id);
else
caffe.set_mode_cpu();
end
% Initialize the network using BVLC CaffeNet for image classification
% Weights (parameter) file needs to be downloaded from Model Zoo.
model_dir = '../../models/bvlc_reference_caffenet/';
net_model = [model_dir 'deploy.prototxt'];
net_weights = [model_dir 'bvlc_reference_caffenet.caffemodel'];
phase = 'test'; % run with phase test (so that dropout isn't applied)
if ~exist(net_weights, 'file')
error('Please download CaffeNet from Model Zoo before you run this demo');
end
% Initialize a network
net = caffe.Net(net_model, net_weights, phase);
if nargin < 1
% For demo purposes we will use the cat image
fprintf('using caffe/examples/images/cat.jpg as input image\n');
im = imread('../../examples/images/cat.jpg');
end
% prepare oversampled input
% input_data is Height x Width x Channel x Num
tic;
input_data = {prepare_image(im)};
toc;
% do forward pass to get scores
% scores are now Channels x Num, where Channels == 1000
tic;
% The net forward function. It takes in a cell array of N-D arrays
% (where N == 4 here) containing data of input blob(s) and outputs a cell
% array containing data from output blob(s)
scores = net.forward(input_data);
toc;
scores = scores{1};
scores = mean(scores, 2); % take average scores over 10 crops
[~, maxlabel] = max(scores);
% call caffe.reset_all() to reset caffe
caffe.reset_all();
% ------------------------------------------------------------------------
function crops_data = prepare_image(im)
% ------------------------------------------------------------------------
% caffe/matlab/+caffe/imagenet/ilsvrc_2012_mean.mat contains mean_data that
% is already in W x H x C with BGR channels
d = load('../+caffe/imagenet/ilsvrc_2012_mean.mat');
mean_data = d.mean_data;
IMAGE_DIM = 256;
CROPPED_DIM = 227;
% Convert an image returned by Matlab's imread to im_data in caffe's data
% format: W x H x C with BGR channels
im_data = im(:, :, [3, 2, 1]); % permute channels from RGB to BGR
im_data = permute(im_data, [2, 1, 3]); % flip width and height
im_data = single(im_data); % convert from uint8 to single
im_data = imresize(im_data, [IMAGE_DIM IMAGE_DIM], 'bilinear'); % resize im_data
im_data = im_data - mean_data; % subtract mean_data (already in W x H x C, BGR)
% oversample (4 corners, center, and their x-axis flips)
crops_data = zeros(CROPPED_DIM, CROPPED_DIM, 3, 10, 'single');
indices = [0 IMAGE_DIM-CROPPED_DIM] + 1;
n = 1;
for i = indices
for j = indices
crops_data(:, :, :, n) = im_data(i:i+CROPPED_DIM-1, j:j+CROPPED_DIM-1, :);
crops_data(:, :, :, n+5) = crops_data(end:-1:1, :, :, n);
n = n + 1;
end
end
center = floor(indices(2) / 2) + 1;
crops_data(:,:,:,5) = ...
im_data(center:center+CROPPED_DIM-1,center:center+CROPPED_DIM-1,:);
crops_data(:,:,:,10) = crops_data(end:-1:1, :, :, 5);
|
github
|
LidkeLab/matlab-instrument-control-master
|
readH5File.m
|
.m
|
matlab-instrument-control-master/@MIC_H5/readH5File.m
| 12,944 |
utf_8
|
672b14572a6fdb018bd3c7db059ca5ae
|
function [H5Structure] = readH5File(FilePath, GroupName)
%Extracts contents of an h5 file into H5Structure.
% This method will extract the Data and Attributes from a group
% named GroupName in the .h5 file specified by FilePath.
% Examples:
% H5Structure = readH5File('C:\file.h5') will extract all
% contents of file.h5 and store them in H5Structure.
% H5Structure = readH5File('C:\file.h5', 'Laser647') will extract
% contents of the group 'Laser647' from file.h5 given only
% the group name.
% H5Structure = readH5File('C:\file.h5', ...
% '/Channel01/Zposition001/Laser647') will extract contents
% of the group 'Laser647' from file.h5 given a full group
% path.
%
% INPUTS:
% FilePath: String containing the path to the .h5 file of interest.
% GroupName: (optional) Name of a specific group in the .h5 file to be
% extracted.
%
% OUTPUTS:
% H5Structure: Structured array containing the information extracted from
% the .h5 file at FilePath.
%
% REQUIRES:
% MATLAB 2016b or later
%
% CITATION:
% Created by:
% David James Schodt (LidkeLab, 2018)
% Ensure that FilePath points to a valid file.
% NOTE: == 2 means a file indeed exists at FilePath
if exist(FilePath, 'file') ~= 2
error(['File specified by FilePath = ', ...
'''%s'' does not exist.'], FilePath)
end
% If GroupName was not specified, set a flag to indicate we
% want to extract all contents from the .h5 file.
if exist('GroupName', 'var')
% Groupname was given, don't set the SaveAll flag.
SaveAll = 0;
else
% GroupName was not given, set the SaveAll flag.
SaveAll = 1;
end
% Read in all of the information available about the structure of the h5
% file using MATLAB's built-in h5info() method.
CurrentGroups = h5info(FilePath); % named for later convenience
% Determine the .h5 file structure being used (i.e. is each
% dataset in its own group or does one group contain all of
% the datasets).
% NOTE: DataFormat==1 means each dataset is in its own group,
% DataFormat==0 means each dataset is contained in one
% "supergroup" of all datasets.
DataFormat = contains(CurrentGroups.Groups.Groups.Groups(1).Name, 'Data');
% Search the .h5 file for the desired groups and store their location
% within the file for later extraction.
DesiredGroups = []; % groups that we wish to save
if DataFormat
% For .h5 files in the DataFormat, we need to continue searching
% through the data groups so that we find all instances of the
% requested group.
DataGroupsSearched = 0; % boolean
else
% For .h5 files that do not have the DataFormat, there is only one data
% group to search.
DataGroupsSearched = 1;
end
while isempty(DesiredGroups) || ~DataGroupsSearched
% If we are extracting all contents in the .h5 file at FilePath, we
% don't want to perform the search procedure in this while loop. Set
% DesiredGroups to CurrentGroups (all of the groups found in the .h5
% file) and break out of the loop.
if SaveAll
DesiredGroups = CurrentGroups;
break
end
% Search the current groups for the group of interest.
DesiredGroups = [DesiredGroups, ...
findGroupPaths(CurrentGroups, GroupName)];
% If using the data group format and we are at the .h5 structure data
% group level, we need to search for the group of interest within the
% sub-groups of each data group. Otherwise, we need to move one level
% deeper into the structure to continue the search.
CurrentGroupNameFormat = extractGroupName(CurrentGroups(1).Name);
if contains(CurrentGroupNameFormat, 'Data')
% We are at the data group level and must search each data
% group individually.
for ii = 1:numel(CurrentGroups)
DesiredGroups = [DesiredGroups, ...
findGroupPaths(CurrentGroups(ii).Groups, GroupName)];
end
% Set the DataGroupsSearched flag to indicate we've searched all of
% the data groups.
DataGroupsSearched = 1;
else
% Move one level deeper into the structure and continue searching
% for the group of interest.
try
% Attempt to move one level deeper into the structure.
CurrentGroups = CurrentGroups.Groups;
catch
% We've reached the end of the structure, there are no more
% groups to explore.
error(['No group named ''%s'' was found in ', ...
'the file specified by FilePath = ''%s'''], ...
GroupName, FilePath)
end
end
end
% Now that we've found the desired group(s), store the
% Attributes, Data, and Children in a more useable format.
for ii = 1:numel(DesiredGroups)
% Set DesiredGroup = DesiredGroups(ii) to reduce indexing
% clutter/improve code readability.
DesiredGroup = DesiredGroups(ii);
% Determine if the current group is the child of a data group (this
% will be needed later).
DesiredGroupParentName = extractGroupName(DesiredGroup.Name, 2);
IsDataGroupChild = DataFormat ...
&& contains(DesiredGroupParentName, 'Data');
% If the desired group has attributes, store them in the
% output structure.
if ~isempty(DesiredGroup.Attributes)
for jj = 1:numel(DesiredGroup.Attributes)
% Store each attribute as a field in the output structure
% accesible directly by that attributes name. If the
% DesiredGroup is a data group, we'll place the attribute
% information one level deeper into the output structure.
AttributeName = DesiredGroup.Attributes(jj).Name;
if IsDataGroupChild
% For children of a datagroup, we need a different path
% format within the structure (for consistency with the
% structure produced for non-datagroup files).
H5Structure(ii).Attributes.(AttributeName) = ...
DesiredGroup.Attributes(jj).Value;
else
H5Structure.Attributes.(AttributeName) = ...
DesiredGroup.Attributes(jj).Value;
end
end
else
% Create an empty field for the Attributes to prevent
% issues with functions that may be using this method, proceeding
% depending on whether or not we are currently storing a data group
% (for files that contain separate groups for each dataset).
if IsDataGroupChild
% For children of a datagroup, we need a different path
% format within the structure (for consistency with the
% structure produced for non-datagroup files).
H5Structure(ii).Attributes = [];
else
H5Structure.Attributes = [];
end
end
% If the desired group has data, store the data in the output OldStruct
% structure.
if ~isempty(DesiredGroup.Datasets)
for jj = 1:numel(DesiredGroup.Datasets)
% Read the ii-th dataset from the h5 file and store the data
% in a field of the output structure, matching the datasets
% name in the h5 file to the name of the field in the output
% structure. If the DesiredGroup is a data group, we'll place
% the dataset information one level deeper into the output
% structure.
DatasetName = DesiredGroup.Datasets(jj).Name;
if IsDataGroupChild
% For children of a datagroup, we need a different path
% format within the structure (for consistency with the
% structure produced for non-datagroup files).
H5Structure(ii).Data.(DatasetName) = h5read(...
FilePath, [DesiredGroup.Name, '/', ...
DesiredGroup.Datasets(jj).Name]);
else
H5Structure.Data.(DatasetName) = ...
h5read(FilePath, [DesiredGroup.Name, '/', ...
DesiredGroup.Datasets(jj).Name]);
end
end
else
% Create an empty field for the Data to prevent issues
% with functions that may be using this method, proceeding
% depending on whether or not we are currently storing a data group
% (for files that contain separate groups for each dataset).
if IsDataGroupChild
% For children of a datagroup, we need a different path
% format within the structure (for consistency with the
% structure produced for non-datagroup files).
H5Structure(ii).Data = [];
else
H5Structure.Data = [];
end
end
% If the desired group has Children (subgroups), recurse
% through those to store their Attributes, Data, and
% Children.
if ~isempty(DesiredGroup.Groups)
% Create a cell array of subgroup names (if subgroups
% exist).
% NOTE: If you are comparing the output structure to
% the Data, Attributes, and Children format used in the
% exportState() method, the subgroups are assumed to be
% the Children.
SubgroupNames = {DesiredGroup.Groups.Name};
for jj = 1:numel(SubgroupNames)
% Iteratively explore subgroups of the desired
% group to store their attributes and data.
SubgroupStructure = MIC_H5.readH5File(FilePath, ...
SubgroupNames{jj});
% Remove the path information from the subgroup name, e.g.
% /Channel01/Zposition001 will become Zposition001.
SubgroupName = extractGroupName(SubgroupNames{jj});
% Store the subgroup structure into the output H5Structure.
H5Structure.Children.(SubgroupName) = SubgroupStructure;
end
else
% Create an empty field for the Children to prevent
% issues with functions that may be using this method, proceeding
% depending on whether or not we are currently storing a data group
% (for files that contain separate groups for each dataset).
if IsDataGroupChild
% For children of a datagroup, we need yet another path
% format within the structure (for consistency with the
% structure produced for non-datagroup files).
H5Structure(ii).Children = [];
else
H5Structure.Children = [];
end
end
end
end
function [DesiredGroups] = findGroupPaths(CurrentGroups, GroupName)
% This function will create a list of paths to a group with name GroupName
% within the set of groups CurrentGroups.
% Iterate through each of the CurrentGroups to search for GroupName.
DesiredGroups = [];
CurrentGroupNames = {CurrentGroups.Name};
for ii = 1:numel(CurrentGroupNames)
% If the GroupName isn't provided as a full path, simplify the current
% group name to remove group structure e.g. if
% CurrentGroupNames{ii} = '/Channel01/Zposition001', simplify it to
% 'ZPosition001' for comparison to GroupName.
if GroupName(1) == '/'
% If the first character of the input GroupName is '/', assume
% that a full path was provided to the desired group.
CurrentGroupName = CurrentGroupNames{ii};
else
% The full path was not given, just a raw group name was given.
CurrentGroupName = extractGroupName(CurrentGroupNames{ii});
end
% Check if the CurrentGroupName matches the desired GroupName, storing
% the path to the current group if we have a match.
if strcmp(CurrentGroupName, GroupName)
DesiredGroups = [DesiredGroups, CurrentGroups(ii)];
end
end
end
function [GroupName] = extractGroupName(FullGroupName, PathLength)
% This function will extract the group name from a full group
% path within an .h5 file, e.g. input
% FullGroupName = '/Channel01/Zposition001/Data001'
% will yield GroupName = 'Data001'. The optional input PathLength
% specifies how many levels from the bottom to extract, e.g. in the
% previous example PathLength would be 1, but if PathLength was 2 we would
% have GroupName = 'Zposition001'.
% Set default parameters if needed.
if ~exist('PathLength', 'var')
PathLength = 1;
end
% If the last character of FullGroupName is a '/', we should remove it.
if (FullGroupName(end) == '/') && (numel(FullGroupName) > 1)
FullGroupName = FullGroupName(end-1);
end
% Find the last PathLength indices within FullGroupName corresponding to
% the appearance of a '/' character.
LastSlashIndex = find(FullGroupName=='/', PathLength, 'last');
% Return either the GroupName of interest or the name of the lowest level
% group in FullGroupName as appropriate.
if numel(LastSlashIndex) > 1
GroupName = FullGroupName(LastSlashIndex(1)+1:LastSlashIndex(2)-1);
else
GroupName = FullGroupName(LastSlashIndex+1:end);
end
end
|
github
|
LidkeLab/matlab-instrument-control-master
|
gui.m
|
.m
|
matlab-instrument-control-master/@MIC_GalvoDigital/gui.m
| 7,602 |
utf_8
|
8de2934750c217a43375207089f3210f
|
% gui: Graphical User Interface to MIC_GalvoDigital
%
% Functions: gui2properties, properties2gui, closeFigure, CalAngle,
% setAngle_Button, setParameters_Button, ToggleGalvo
%
% REQUIREMENTS:
% MIC_Abstract.m
% MATLAB NI-DAQmx driver installed via the Support Package Installer
%
% CITATION: Hanieh Mazloom-Farsibaf, Lidlelab, 2017.
function guiFig = gui(obj)
%gui Graphical User Interface to MIC_LightSource_Abstract
%Prevent opening more than one figure for same instrument
if ishandle(obj.GuiFigure)
guiFig = obj.GuiFigure;
figure(obj.GuiFigure);
return
end
%Open figure
guiFig = figure('NumberTitle','off','Resize','off','Units','pixels','MenuBar','none',...
'ToolBar','none','Visible','on', 'Position',[100 300 500 310]);
%Construct the components
handles.output = guiFig;
guidata(guiFig,handles);
% Scanning Parametes
rangeAngle = sprintf('Angle [%g, %g] ',-obj.Range,obj.Range);
textangle = uicontrol('Style','text','String',rangeAngle,...
'Position',[10 250,180,25],'FontSize',10);
textScanningParameters = uicontrol('Style','text','String','Scanning Parameters',...
'Position',[10 200,180,25],'FontSize',11,'FontWeight','bold');
textNoStepsPerScan = uicontrol('Style','text','String','Number of Steps Per Scan',...
'Position',[10 160,180,20],'FontSize',10);
textNoScan = uicontrol('Style','text','String','Number of Scans',...
'Position',[10 120,180,20],'FontSize',10);
textStepSize = uicontrol('Style','text','String','Step Size',...
'Position',[10 80,180,20],'FontSize',10);
textOffset = uicontrol('Style','text','String','Starting Position (offset)',...
'Position',[10 40,180,20],'FontSize',10);
handles.edit_angle = uicontrol('Parent',guiFig, 'Style', 'edit', 'String', ...
'','Position', [210 250 80 25],'Tag','EditAngle','Callback',@CalAngle);
handles.edit_NoStepsPerScan = uicontrol('Parent',guiFig, 'Style', 'edit', 'String', ...
'','Tag','EditNSteps','Position', [210 160 80 25]);
handles.edit_NoScan = uicontrol('Parent',guiFig, 'Style', 'edit', 'String', ...
'','Tag','EditNScans','Position', [210 120 80 25]);
handles.edit_StepSize = uicontrol('Parent',guiFig,'Style', 'edit', 'String', ...
'','Tag','EditStepsize','Position', [210 80 80 25]);
handles.edit_Offset = uicontrol('Parent',guiFig, 'Style', 'edit', 'String', ...
'','Tag','EditOffset','Position', [210 40 80 25]);
handles.setAngle=uicontrol('Style', 'pushbutton', 'String', 'Set Angle',...
'Position', [350 250 80 30], 'Callback', @setAngle_Button);
handles.setParameters=uicontrol('Style', 'pushbutton', 'String', 'Set Parameters',...
'Position', [350 130 110 30], 'Callback', @setParameters_Button);
handles.Toggle_EnableGalvo=uicontrol('Style','togglebutton',...
'String','Disable','Position',[350 50 65,50],...
'BackgroundColor',[0.8 0.8 0.8],'Tag','positionToggle','Callback',@ToggleGalvo);
%
align([textNoStepsPerScan,textNoScan,textStepSize,textOffset,textScanningParameters],'Center','None');
align([handles.edit_NoStepsPerScan,handles.edit_NoScan,handles.edit_StepSize...
,handles.edit_Offset],'Center','None');
align([handles.Toggle_EnableGalvo,handles.setParameters,handles.setAngle],'Center','None');
% Create a property based on GuiFigure
obj.GuiFigure = guiFig;
obj.GuiFigure.Name = obj.InstrumentName;
%Prevent closing after a 'close' or 'close all'
obj.GuiFigure.HandleVisibility='off';
%Save Propeties upon close
obj.GuiFigure.CloseRequestFcn = @closeFigure;
%Initialize GUI properties
properties2gui();
function gui2properties()
end
function properties2gui()
if ~isempty(obj.N_Step) || ~isempty(obj.N_Scan)|| ~isempty(obj.StepSize)|| ~isempty(obj.Offset)
set(handles.edit_NoStepsPerScan,'Value',obj.N_Step)
set(handles.edit_NoScan,'Value',obj.N_Scan);
set(handles.edit_StepSize,'Value',obj.StepSize);
set(handles.edit_Offset,'Value',obj.Offset);
end
set(handles.Toggle_EnableGalvo,'Value',obj.IsEnable);
if ~isempty(obj.Angle)
if isempty(obj.Word)
obj.angle2word(obj.Angle)
end
set(handles.edit_angle,'Value',obj.Angle)
else
obj.Angle=0;
set(handles.edit_angle,'Value',obj.Angle)
obj.angle2word(obj.Angle)
end
if obj.IsEnable==1
set(handles.Toggle_EnableGalvo,'String','Enable');
set(handles.Toggle_EnableGalvo,'BackgroundColor','green');
else
set(handles.Toggle_EnableGalvo,'String','Disable');
set(handles.Toggle_EnableGalvo,'BackgroundColor',[.8 .8 .8]);
end
end
function closeFigure(~,~)
% gui2properties();
% obj.clear; Ask Keith
delete(obj.GuiFigure);
end
%calculate word based on input angle
function CalAngle(~,~)
Angle=str2double(get(handles.edit_angle,'String'));
if isnan(Angle)
error('Enter a valid angle')
end
obj.angle2word(Angle);
state=get(handles.Toggle_EnableGalvo,'Value');
% turn off the togglebutton if it is already on
if state
set(handles.Toggle_EnableGalvo,'Value',0);
set(handles.Toggle_EnableGalvo,'BackgroundColor',[0.8 0.8 0.8]);%,[0.6 0.8 0])
set(handles.Toggle_EnableGalvo,'String','Disable')
end
end
%Callback function to set angle
function setAngle_Button(~,~)
Angle=str2double(get(handles.edit_angle,'String'));
if isnan(Angle)
error('Enter a valid angle')
end
obj.setAngle();
end
%Callback function to set Sequence
function setParameters_Button(~,~)
%take Scanning Parameters
N_Step=str2double(get(handles.edit_NoStepsPerScan,'String'));
N_Scan=str2double(get(handles.edit_NoScan,'String'));
StepSize=str2double(get(handles.edit_StepSize,'String'));
Offset=str2double(get(handles.edit_Offset,'String'));
if isnan(N_Step) || isnan(N_Scan)|| isnan(StepSize)|| isnan(Offset)
error('Choose proper values for Scanning Parameters')
end
% set Scanning Parameters
obj.N_Step=N_Step;
obj.N_Scan=N_Scan;
obj.StepSize=StepSize;
obj.Offset=Offset;
%set the sequence of Words to move the Galvo Mirror
obj.setSequence();
end
%Callback function for toggle button
function ToggleGalvo(~,~)
state=get(handles.Toggle_EnableGalvo,'Value');
%
% N_Step=str2double(get(handles.edit_NoStepsPerScan,'String'));
% N_Scan=str2double(get(handles.edit_NoScan,'String'));
% StepSize=str2double(get(handles.edit_StepSize,'String'));
% Offset=str2double(get(handles.edit_Offset,'String'));
%
% if isnan(N_Step) || isnan(N_Scan)|| isnan(StepSize)|| isnan(Offset)
% error('Choose proper values for Scanning Parameters')
% end
if state
% obj.Power=str2double(get(handles.SetPower,'String'));
set(handles.Toggle_EnableGalvo,'BackgroundColor','green');%,[0.6 0.8 0])
set(handles.Toggle_EnableGalvo,'String','Enable')
obj.enable();
else
set(handles.Toggle_EnableGalvo,'BackgroundColor',[0.8 0.8 0.8])
set(handles.Toggle_EnableGalvo,'String','Disable')
obj.disable();
end
end
end
|
github
|
LidkeLab/matlab-instrument-control-master
|
errorcheck.m
|
.m
|
matlab-instrument-control-master/@MIC_MCLNanoDrive/errorcheck.m
| 3,188 |
utf_8
|
2abc63fb57985d22013e75228d9714dc
|
function varargout = errorcheck(obj,fname,varargin)
% certain errors throw variable error codes but are specific to axis controls, this is logical branch for that
if obj.LastError ~= obj.ErrorCode.MCL_SUCCESS
displayError(fname,varargin);
end
% Error check function for processing most of the MCL Nano Drive errors
switch obj.LastError
case obj.ErrorCode.MCL_SUCCESS
% nest if statements for when we call this, not sure what
% this needs to be yet
switch fname
case 'MCL_GetProductInfo'
obj.ProductInfo.ADC_resolution=varargin{1}.ADC_resolution;
obj.ProductInfo.DAC_resolution=varargin{1}.DAC_resolution;
obj.ProductInfo.Product_id=varargin{1}.Product_id;
obj.ProductInfo.FirmwareVersion=varargin{1}.FirmwareVersion;
obj.ProductInfo.FirmwareProfile=varargin{1}.FirmwareProfile;
case 'MCL_SingleWriteN'
obj.Position(varargin{2}) = varargin{1};
end
case obj.ErrorCode.MCL_GENERAL_ERROR
error('Some Internal Sanity Check Failed');
case obj.ErrorCode.MCL_DEV_ERROR
error('A problem occurred when transferring data to the Nano-Drive');
case obj.ErrorCode.MCL_DEV_NOT_ATTACHED
error('The Nano-Drive cannot complete the task because it is not attached.');
case obj.ErrorCode.MCL_USAGE_ERROR
error('This library function is not supported by this particular Nano-Drive');
case obj.ErrorCode.MCL_DEV_NOT_READY
error('The Nano-Drive is currently completing or waiting to complete another task');
case obj.ErrorCode.MCL_ARGUMENT_ERROR
error('An argument is out of range or a required pointer is equal to NULL');
case obj.ErrorCode.MCL_INVALID_AXIS
varargout{1} = 'Invalid Axis'; % axis returns as invalid
warning('The Attempted operation on this axis does not exist in the Nano-Drive');
case obj.ErrorCode.MCL_INVALID_HANDLE
error('The handle is not valid, or at least not in this instance of the DLL');
case obj.ErrorCode.MCL_MISC
switch fname
case 'MCL_InitHandle'
error('MCLNanoDrive:NoHandle','Cannot get a handle to the device. Make sure device is on. If on, try ''MCLNanoDrive.libreset''');
case 'MCL_CorrectDriverVersion'
warning('MCLNanoDriveStage:WrongDLL','DLL in use does not match the current driver version');
end
otherwise
switch fname
case 'MCL_GetCalibration'
varargout{1} = obj.LastError; % return correct axis values
obj.LastError = 0;
end
end
end
% I had to make a static function because sometimes MCL will throw variable error codes for a single command
function displayError(fname,varargin)
switch fname
case 'MCL_SingleWriteN'
switch varargin{2}
case 1
dimChar = X;
case 2
dimChar = Y;
case 3
dimChar = Z;
end
disp(obj.LastError);
error('MCLNanoDrive:MoveFailed','Could not move to new %s position',dimChar);
end
end
|
github
|
LidkeLab/matlab-instrument-control-master
|
gui.m
|
.m
|
matlab-instrument-control-master/@MIC_SPTCollect/gui.m
| 23,826 |
utf_8
|
efd104ecb8670653062f168d48d398c1
|
function gui(obj)
% GUI SRcollect Gui for TIRF microscope
% Detailed explanation goes here
h = findall(0,'tag','TIRF-SRcollect.gui');
if ~(isempty(h))
figure(h);
return;
end
%%
xsz=400;
ysz=1000;
xst=100;
yst=50;
pw=.95;
psep=.001;
staticst=10;
editst=110;
guiFig = figure('Units','pixels','Position',[xst yst xsz ysz],...
'MenuBar','none','ToolBar','none','Visible','on',...
'NumberTitle','off','UserData',0,'Tag',...
'SPTCollect.gui','HandleVisibility','off','name','SPTcollect.gui','CloseRequestFcn',@FigureClose);
defaultBackground = get(0,'defaultUicontrolBackgroundColor');
set(guiFig,'Color',defaultBackground);
handles.output = guiFig;
guidata(guiFig,handles);
refh=1;
% File Panel
ph=0.09;
php = ph*ysz;
hFilePanel = uipanel('Parent',guiFig,'Title','FILE','Position',[(1-pw)/2 refh-ph-psep pw ph]);
refh=refh-ph-psep;
uicontrol('Parent',hFilePanel, 'Style', 'edit', 'String', 'Save Directory:','Enable','off','Position', [staticst php-40 100 20]);
handles.Edit_FileDirectory = uicontrol('Parent',hFilePanel, 'Style', 'edit', 'String','Set Auto','Enable','on','BackgroundColor',[1 1 1],'Position', [editst php-40 250 20]);
uicontrol('Parent',hFilePanel, 'Style', 'edit', 'String', 'Base FileName:','Enable','off','Position', [staticst php-65 100 20]);
handles.Edit_FileName = uicontrol('Parent',hFilePanel, 'Style', 'edit', 'String','Set Auto','Enable','on','BackgroundColor',[1 1 1],'Position', [editst php-65 250 20]);
uicontrol('Parent',hFilePanel, 'Style', 'edit', 'String','File type:','Enable','off','Position', [staticst php-90 100 20]);
handles.saveFileType = uicontrol('Parent',hFilePanel, 'Style', 'popupmenu', 'String',{'.mat','.h5'},'Enable','on','BackgroundColor',[1 1 1],'Position', [editst php-90 250 20],'CallBack',@saveFile);
% Camera Panel
ph=0.17;
php = ph*ysz;
hCameraPanel = uipanel('Parent',guiFig,'Title','CAMERA','Position',[(1-pw)/2 refh-ph-psep pw ph]);
refh=refh-ph-psep;
uicontrol('Parent',hCameraPanel, 'Style', 'edit', 'String','Camera Gain:','Enable','off','Position', [staticst php-40 100 20]);
handles.Popup_CameraGain = uicontrol('Parent',hCameraPanel, 'Style', 'popupmenu', 'String',{'Low (Alexa647)','High (FAP/FP)'},'Enable','on','BackgroundColor',[1 1 1],'Position', [editst php-40 250 20],'CallBack',@gain_set);
uicontrol('Parent',hCameraPanel, 'Style', 'edit', 'String','Camera ROI:','Enable','off','Position', [staticst php-70 80 20]);
ROIlist={'Full','Left','Right','Left Center','Right Center','Center Horizontally','Center Horizontally Half','128*16 Center','64*32 low right','64*32 low left','64*16 low right'};
handles.Popup_CameraROI = uicontrol('Parent',hCameraPanel, 'Style', 'popupmenu', 'String',ROIlist,'Enable','on','BackgroundColor',[1 1 1],'Position', [90 php-70 85 20]);
uicontrol('Parent',hCameraPanel, 'Style', 'edit', 'String','IRCamera ROI:','Enable','off','Position', [staticst+180 php-70 80 20]);
ROIlist_IR={'Full','Center 350' ,'Center 256','Center 128'};
handles.Popup_IRCameraROI = uicontrol('Parent',hCameraPanel, 'Style', 'popupmenu', 'String',ROIlist_IR,'Enable','on','BackgroundColor',[1 1 1],'Position', [90+180 php-70 85 20]);
uicontrol('Parent',hCameraPanel, 'Style', 'edit', 'String','Exp. Time Focus:','Enable','off','Position', [staticst php-100 100 20]);
handles.Edit_CameraExpTimeFocusSet = uicontrol('Parent',hCameraPanel, 'Style', 'edit', 'String','0.01','Enable','on','BackgroundColor',[1 1 1],'Position', [editst php-100 50 20]);
% uicontrol('Parent',hCameraPanel, 'Style', 'edit', 'String','Actual:','Enable','off','Position', [175 php-100 100 20]);
% handles.Edit_CameraExpTimeFocusActual = uicontrol('Parent',hCameraPanel, 'Style', 'edit', 'String','','Enable','off','Position', [250 php-100 50 20]);
uicontrol('Parent',hCameraPanel, 'Style', 'edit', 'String','IRCamera Zoom:','Enable','off','Position', [staticst+180 php-100 100 20]);
handles.Popup_CameraDispZoom_IR = uicontrol('Parent',hCameraPanel, 'Style','popupmenu','String',{'50%','100%','200%','400%','1000%'},'Value',2,'Enable','on','BackgroundColor',[1 1 1],'Position', [280 php-100 50 20],'CallBack',@zoom_set_IR);
uicontrol('Parent',hCameraPanel, 'Style', 'edit', 'String','Exp. Time Seq.:','Enable','off','Position', [staticst php-130 100 20]);
handles.Edit_CameraExpTimeSeqSet = uicontrol('Parent',hCameraPanel, 'Style', 'edit', 'String','0.01','Enable','on','BackgroundColor',[1 1 1],'Position', [editst php-130 50 20],'CallBack',@sequence_set);
uicontrol('Parent',hCameraPanel, 'Style', 'edit', 'String','Actual:','Enable','off','Position', [175 php-130 100 20]);
handles.Edit_CameraExpTimeSeqActual = uicontrol('Parent',hCameraPanel, 'Style', 'edit', 'String',num2str(obj.CameraObj.SequenceCycleTime),'Enable','off','Position', [250 php-130 50 20]);
uicontrol('Parent',hCameraPanel, 'Style', 'edit', 'String','Num Frames:','Enable','off','Position', [staticst php-160 100 20]);
handles.Edit_CameraNumFrames = uicontrol('Parent',hCameraPanel, 'Style', 'edit', 'String','2000','Enable','on','BackgroundColor',[1 1 1],'Position', [editst php-160 50 20]);
uicontrol('Parent',hCameraPanel, 'Style', 'edit', 'String','Zoom:','Enable','off','Position', [175 php-160 100 20]);
handles.Popup_CameraDispZoom = uicontrol('Parent',hCameraPanel, 'Style','popupmenu','String',{'50%','100%','200%','400%','1000%'},'Value',4,'Enable','on',...
'BackgroundColor',[1 1 1],'Position', [250 php-160 50 20],'CallBack',@zoom_set);
% Registration Panel
ph=0.213;
php = ph*ysz;
hRegPanel = uipanel('Parent',guiFig,'Title','REGISTRATION','Position',[(1-pw)/2 refh-ph-psep pw ph]);
refh=refh-ph-psep;
uicontrol('Parent',hRegPanel, 'Style', 'edit', 'String','Exp. Time Reg.:','Enable','off','Position', [staticst php-40 100 20]);
handles.Edit_RegExpTime = uicontrol('Parent',hRegPanel, 'Style', 'edit', ...
'String','0.01','Enable','on','BackgroundColor',[1 1 1],...
'Position', [editst php-40 50 20]);
handles.Button_RegLoadRef=uicontrol('Parent',hRegPanel, 'Style', 'pushbutton',...
'String','Load Reference','Enable','on',...
'Position', [staticst php-70 100 20],'Callback',@LoadRef);
handles.Edit_RegFileName = uicontrol('Parent',hRegPanel, 'Style', 'edit', ...
'String','File Name','Enable','on','BackgroundColor',[1 1 1],...
'Position', [editst php-70 250 20]);
handles.Button_RegAlign=uicontrol('Parent',hRegPanel, 'Style', 'pushbutton',...
'String','Align','Enable','on','Position', ...
[staticst php-100 80 20],'Callback',@Align);
handles.Button_RegShowRef=uicontrol('Parent',hRegPanel, 'Style', 'pushbutton', ...
'String','Show Reference','Enable','on','Position', ...
[staticst+80 php-100 100 20],'Callback',@ShowRef);
handles.Button_RegTakeCurrent=uicontrol('Parent',hRegPanel, 'Style', 'pushbutton',...
'String','Take Current','Enable','on','Position', ...
[staticst+180 php-40 90 20],'Callback',@TakeCurrent);
handles.Button_RegCenterStage=uicontrol('Parent',hRegPanel, 'Style', 'pushbutton', ...
'String','Center Stage','Enable','on','Position', ...
[staticst+270 php-40 90 20],'Callback',@CenterStage);
handles.Button_RegTakeReference=uicontrol('Parent',hRegPanel, 'Style', 'pushbutton',...
'String','Take Reference','Enable','on','Position', ...
[staticst+180 php-100 90 20],'Callback',@TakeReference);
handles.Button_RegSaveReference=uicontrol('Parent',hRegPanel, 'Style', 'pushbutton', ...
'String','Save Reference','Enable','on','Position', ...
[staticst+270 php-100 90 20],'Callback',@SaveReference);
BGh=100;
handles.ButtonGroup_RegCollectType=uibuttongroup('Parent',hRegPanel, 'Position', [.02 (php-130-BGh+30)/php .96 BGh/php]);
b1=uicontrol('Parent',handles.ButtonGroup_RegCollectType, 'Style', 'radio', 'tag','None','String','No Registration','Enable','on','Position', [staticst BGh-30 250 20]);
b2=uicontrol('Parent',handles.ButtonGroup_RegCollectType, 'Style', 'radio','tag','Self', 'String','Align to Self (Takes/Saves Reference Image)','Enable','on','Position', [staticst BGh-60 250 20]);
b3=uicontrol('Parent',handles.ButtonGroup_RegCollectType, 'Style', 'radio','tag','Ref','String','Align to Reference','Enable','on','Position', [staticst BGh-90 250 20]);
b4=uicontrol('Parent',handles.ButtonGroup_RegCollectType,'Style','text','String','Reg Camera Type','Position',[staticst+125 BGh-34 140 20]);
b5 = uicontrol('Parent',handles.ButtonGroup_RegCollectType, 'Style', 'popupmenu', 'String',{'Andor Camera','IRCamera'},'Enable','on','BackgroundColor',[1 1 1],...
'Position', [staticst+240 BGh-30 100 20],'CallBack',@RegCamType_set);
b6=uicontrol('Parent',handles.ButtonGroup_RegCollectType,'Style','text','String','Active Stabilization','Position',[staticst+125 BGh-94 210 20]);
b7=uicontrol('Parent',handles.ButtonGroup_RegCollectType,'Style', 'checkbox', 'Value',0,'Position', [staticst+165 BGh-90 15 20],'Callback',@ActiveStabilization);
% LIGHTSOURCE Panel
ph=0.3;
hLampPanel = uipanel('Parent',guiFig,'Title','LIGHT SOURCE','Position',[(1-pw)/2 refh-ph-psep pw ph]);
refh=refh-ph-psep;
uicontrol(hLampPanel,'Style','text','String','On during Focus',...
'Position',[-3 240,60,25]);
uicontrol(hLampPanel,'Style','text','String','On during Aquisition',...
'Position',[-3 180,60,28]);
uicontrol(hLampPanel,'Style','text','String','Low Power',...
'Position',[0 120,60,25]);
uicontrol(hLampPanel,'Style','text','String','High Power',...
'Position',[0 70,60,25]);
uicontrol(hLampPanel,'Style','text','String','[MinPower,MaxPower]',...
'Position',[-1 5,60,35]);
h561Panel=uipanel(hLampPanel,'Title','561 nm','TitlePosition','centertop',...
'Position',[1/5 1/5 1/5 4/5]);
handles.Focus561 = uicontrol(h561Panel,'Style','checkbox',...
'Value',0,'Position',[29 185 130 20]);
handles.Aquisition561 = uicontrol(h561Panel,'Style','checkbox',...
'Value',0,'Position',[29 130 130 20]);
handles.LP561 = uicontrol(h561Panel,'Style','edit',...
'Position',[21 80 30 20],'Callback',@setLaser561Low);
handles.HP561 = uicontrol(h561Panel,'Style','edit',...
'Position',[21 25 30 20]);
% powerString561 = sprintf('[%g, %g] (%s)',obj.Laser561Obj.MinPower,obj.Laser561Obj.MaxPower, obj.Laser561.PowerUnit);
% uicontrol(hLampPanel,'Style','text','String',powerString561,...
% 'Position',[75, 5,60,35]);
h638Panel=uipanel(hLampPanel,'Title','638 nm','TitlePosition','centertop',...
'Position',[2/5 1/5 1/5 4/5]);
handles.Focus638 = uicontrol(h638Panel,'Style','checkbox',...
'Value',0,'Position',[29 185 130 20]);
handles.Aquisition638 = uicontrol(h638Panel,'Style','checkbox',...
'Value',0,'Position',[29 130 130 20]);
handles.LP638 = uicontrol(h638Panel,'Style','edit',...
'Position',[21 80 30 20],'Callback',@setLaser638Low);
handles.HP638 = uicontrol(h638Panel,'Style','edit',...
'Position',[21 25 30 20]);
powerString638 = sprintf('[%g, %g] (%s)',obj.Laser638Obj.MinPower,obj.Laser638Obj.MaxPower, obj.Laser638Obj.PowerUnit);
uicontrol(hLampPanel,'Style','text','String',powerString638,...
'Position',[160 5,60,35]);
hlamp850Panel=uipanel(hLampPanel,'Title','Lamp 850 nm','TitlePosition','centertop',...
'Position',[3/5 1/5 1/5 4/5]);
handles.Focuslamp850 = uicontrol(hlamp850Panel,'Style','checkbox',...
'Value',0,'Position',[29 185 130 20]);
handles.Aquisitionlamp850 = uicontrol(hlamp850Panel,'Style','checkbox',...
'Value',0,'Position',[29 130 130 20]);
handles.LED850lLampPower = uicontrol(hlamp850Panel,'Style','edit',...
'Position',[21 80 30 20],'Callback',@setLamp850Power);
powerString850 = sprintf('[%g, %g] (%s)',obj.Lamp850Obj.MinPower,obj.Lamp850Obj.MaxPower, obj.Lamp850Obj.PowerUnit);
uicontrol(hLampPanel,'Style','text','String',powerString850,...
'Position',[235 5,60,35]);
hX71Panel=uipanel(hLampPanel,'Title','Lamp','TitlePosition','centertop',...
'Position',[4/5 1/5 1/5 4/5]);
handles.FocusIX71Lamp = uicontrol(hX71Panel,'Style','checkbox',...
'Value',0,'Position',[29 185 130 20]);
handles.AquisitionIX71Lamp = uicontrol(hX71Panel,'Style','checkbox',...
'Value',0,'Position',[29 130 130 20]);
handles.IX71LampPower = uicontrol(hX71Panel,'Style','edit',...
'Position',[21 80 30 20],'Callback',@setLampPower);
powerStringLamp = sprintf('[%g, %g] (%s)',obj.LampObj.MinPower,obj.LampObj.MaxPower, obj.LampObj.PowerUnit);
uicontrol(hLampPanel,'Style','text','String',powerStringLamp,...
'Position',[310 5,60,35]);
% CONTROL Panel
ph=0.190;
hControlPanel = uipanel('Parent',guiFig,'Title','CONTROL','Position',[(1-pw)/2 refh-ph-psep pw ph]);
php = ph*ysz;
uicontrol('Parent',hControlPanel, 'Style', 'edit', 'String','Number of Sequences:','Enable','off','Position', [staticst php-40 150 20]);
handles.Edit_ControlNSequence = uicontrol('Parent',hControlPanel, 'Style', 'edit', 'String','20','Enable','on','BackgroundColor',[1 1 1],'Position', [editst+50 php-40 50 20]);
handles.Button_ControlFocusLamp=uicontrol('Parent',hControlPanel, 'Style', 'pushbutton', 'String','Focus Lamp','Enable','on','Position', [staticst php-90 103 35],'BackgroundColor',[1 1 .8],'Callback',@FocusLamp);
handles.Button_ControlFocusLaserLow=uicontrol('Parent',hControlPanel, 'Style', 'pushbutton', 'String','Focus Laser (Low)','Enable','on','Position', [staticst+123 php-90 103 35],'BackgroundColor',[1 .8 .8],'Callback',@FocusLow);
handles.Button_ControlFocusLamp850=uicontrol('Parent',hControlPanel, 'Style', 'pushbutton', 'String','Focus Lamp 850','Enable','on','Position', [staticst+246 php-90 103 35],'BackgroundColor',[1 1 .8],'Callback',@FocusLamp850);
handles.Toggle_LaserLamp=uicontrol('Parent',hControlPanel, 'Style', 'toggle', 'String','Lamp','Enable','on','Position', [staticst php-138 103 35],'BackgroundColor',[1 1 .8],'Callback',@ToggleLamp);
handles.Button_ControlStart=uicontrol('Parent',hControlPanel, 'Style', 'pushbutton', 'String','START (SR)','Enable','on','Position', [staticst php-186 103 35],'BackgroundColor',[0 1 0],'Callback',@Start);
handles.Button_ControlFocusLaserHigh=uicontrol('Parent',hControlPanel, 'Style', 'pushbutton', 'String','Focus Laser (High)','Enable','on','Position', [staticst+123 php-138 103 35],'BackgroundColor',[1 0 0],'Callback',@FocusHigh);
handles.Button_ControlAbort=uicontrol('Parent',hControlPanel, 'Style', 'pushbutton', 'String','ABORT','Enable','on','Position', [staticst+123 php-186 103 35],'BackgroundColor',[1 0 1],'Callback',@Abort);
handles.Button_ControlStart_SPT=uicontrol('Parent',hControlPanel, 'Style', 'pushbutton', 'String','START (SPT+SR)','Enable','on','Position', [staticst+246 php-186 103 35],'BackgroundColor',[0 1 0],'Callback',@Start_SPT);
%% Setup GUI Values
properties2gui();
%% Figure Callbacks
function saveFile(~,~)
file_val=get(handles.saveFileType,'value');
switch file_val
case 1
obj.SaveFileType='mat';
case 2
obj.SaveFileType='h5';
end
end
function LoadRef(~,~)
obj.loadref();
set(handles.Edit_RegFileName,'String',obj.R3DObj.RefImageFile);
end
function Align(~,~)
gui2properties();
obj.align();
end
function ShowRef(~,~)
obj.showref();
end
function TakeCurrent(~,~)
gui2properties();
obj.takecurrent();
end
function CenterStage(~,~)
obj.StageObj.center();
end
function TakeReference(~,~)
gui2properties();
obj.takeref();
end
function SaveReference(~,~)
obj.saveref();
properties2gui();
end
function ToggleLamp(~,~)
gui2properties();
stateLamp1=get(handles.Toggle_LaserLamp,'Value');
if stateLamp1
obj.LampObj.setPower(obj.LampPower);
obj.LampObj.on;
else
obj.LampObj.off;
% pause(obj.LampWait);
end
end
function FocusLamp(~,~)
gui2properties();
obj.focusLamp();
end
function FocusLamp850(~,~)
gui2properties();
obj.focusLamp850();
end
function FocusLow(~,~)
gui2properties();
obj.focusLow();
end
function FocusHigh(~,~)
gui2properties();
obj.focusHigh();
end
function Abort(~,~)
obj.AbortNow=1;
set(handles.Button_ControlStart, 'String','START (SR)','Enable','on');
set(handles.Button_ControlStart_SPT, 'String','START (SPT+SR)','Enable','on');
end
function Start(~,~)
gui2properties();
[temp status]=obj.CameraObj.call_temperature
if status==2
error('Camera is cooling down! Please wait for a few mintues!')
end
set(handles.Button_ControlStart, 'String','Acquiring','Enable','off');
obj.sequenceType='SRCollect';
obj.StartSequence(handles);
set(handles.Button_ControlStart, 'String','START (SR)','Enable','on');
end
function Start_SPT(~,~)
gui2properties();
[temp status]=obj.CameraObj.call_temperature
if status==2
error('Camera is cooling down! Please wait for a few mintues!')
end
set(handles.Button_ControlStart, 'String','Acquiring','Enable','off');
obj.sequenceType='Tracking+SRCollect';
obj.StartSequence(handles);
set(handles.Button_ControlStart, 'String','START (SPT+SR)','Enable','on');
end
function setLampPower(~,~)
gui2properties();
obj.setLampPower();
end
function setLamp850Power(~,~)
gui2properties();
obj.setLampPower();
end
function setLaser561Low(~,~)
obj.Laser561Obj.setPower(str2double(handles.LP561.String));
end
function setLaser638Low(~,~)
obj.Laser638Obj.setPower(str2double(handles.LP638.String));
end
function FigureClose(~,~)
gui2properties();
delete(guiFig);
end
function zoom_set(~,~)
zoom_val = get(handles.Popup_CameraDispZoom,'Value');
switch zoom_val
case 1
obj.CameraObj.DisplayZoom = 0.5;
case 2
obj.CameraObj.DisplayZoom = 1;
case 3
obj.CameraObj.DisplayZoom = 2;
case 4
obj.CameraObj.DisplayZoom = 4;
case 5
obj.CameraObj.DisplayZoom = 10;
end
end
function zoom_set_IR(~,~)
zoom_val = get(handles.Popup_CameraDispZoom_IR,'Value');
switch zoom_val
case 1
obj.IRCameraObj.DisplayZoom = 0.5;
case 2
obj.IRCameraObj.DisplayZoom = 1;
case 3
obj.IRCameraObj.DisplayZoom = 2;
case 4
obj.IRCameraObj.DisplayZoom = 4;
case 5
obj.IRCameraObj.DisplayZoom = 10;
end
end
function gain_set(~,~)
gain_val=get(handles.Popup_CameraGain,'value');
switch gain_val
case 1
obj.CameraEMGainHigh=100;
case 2
obj.CameraEMGainHigh=200;
end
end
function RegCamType_set(~,~)
RegCamType=get(b5,'Value');
switch RegCamType
case 1
obj.RegCamType='Andor Camera';
case 2
obj.RegCamType='IRCamera';
end
obj.set_RegCamType();
end
function ActiveStabilization(~,~)
obj.ActiveRegCheck=get(b7,'Value');
end
function sequence_set(~,~)
gui2properties();
obj.CameraObj.ExpTime_Sequence = obj.ExpTime_Sequence_Set;
obj.CameraObj.AcquisitionType = 'sequence';
obj.CameraObj.setup_acquisition;
set(handles.Edit_CameraExpTimeSeqActual,'String',num2str(obj.CameraObj.SequenceCycleTime));
end
function gui2properties()
%Get GUI values and update to object properties
obj.SaveDir=get(handles.Edit_FileDirectory,'String');
obj.BaseFileName=get(handles.Edit_FileName,'String');
obj.CameraGain=get(handles.Popup_CameraGain,'value');
obj.CameraROI=get(handles.Popup_CameraROI,'value');
obj.IRCameraROI=get(handles.Popup_IRCameraROI,'value');
obj.ExpTime_Focus_Set=str2double(get(handles.Edit_CameraExpTimeFocusSet,'string'));
obj.ExpTime_Sequence_Set=str2double(get(handles.Edit_CameraExpTimeSeqSet,'string'));
obj.NumFrames=str2double(get(handles.Edit_CameraNumFrames,'string'));
obj.R3DObj.ExposureTime=str2double(get(handles.Edit_RegExpTime,'string'));
obj.R3DObj.RefImageFile=get(handles.Edit_RegFileName,'string');
obj.ActiveRegCheck=get(b7,'Value')
obj.focus561Flag=get(handles.Focus561,'Value');
obj.focus638Flag=get(handles.Focus638,'Value');
obj.focusLampFlag=get(handles.FocusIX71Lamp,'Value');
obj.focusLamp850Flag=get(handles.Focuslamp850,'Value');
obj.Laser561Low=str2double(handles.LP561.String);
obj.Laser638Low=str2double(handles.LP638.String);
obj.Laser561High=str2double(handles.HP561.String);
obj.Laser638High=str2double(handles.HP638.String);
obj.LampPower=str2double(handles.IX71LampPower.String);
obj.Lamp850Power=str2double(handles.LED850lLampPower.String);
obj.Laser561Aq=handles.Aquisition561.Value;
obj.Laser638Aq=handles.Aquisition638.Value;
obj.LampAq=handles.AquisitionIX71Lamp.Value;
obj.Lamp850Aq=handles.Aquisitionlamp850.Value;
obj.NumSequences=str2double(get(handles.Edit_ControlNSequence,'string'));
obj.RegType=get(get(handles.ButtonGroup_RegCollectType,'SelectedObject'),'Tag');
end
function properties2gui()
%Set GUI values from object properties
set(handles.Edit_FileDirectory,'String',obj.SaveDir);
set(handles.Edit_FileName,'String',obj.BaseFileName);
set(handles.Popup_CameraGain,'value',obj.CameraGain);
set(handles.Popup_CameraROI,'value',obj.CameraROI);
set(handles.Popup_IRCameraROI,'value',obj.IRCameraROI);
set(handles.Edit_CameraExpTimeFocusSet,'string',num2str(obj.ExpTime_Focus_Set));
set(handles.Edit_CameraExpTimeSeqSet,'string',num2str(obj.ExpTime_Sequence_Set));
% set(handles.Edit_RegExpTime,'string',num2str(obj.R3DObj.ExposureTime));
set(handles.Edit_CameraNumFrames,'string',num2str(obj.NumFrames));
% set(handles.Edit_RegFileName,'string',obj.R3DObj.RefImageFile);
if strcmp(obj.RegCamType,'Andor Camera')
v=1;
elseif strcmp(obj.RegCamType,'IRCamera')
v=2;
end
set(b5,'value',v);
set(b7,'value',obj.ActiveRegCheck);
set(handles.LP561,'string',obj.Laser561Low);
set(handles.LP638,'string',obj.Laser638Low);
set(handles.HP561,'string',obj.Laser561High);
set(handles.HP638,'string',obj.Laser638High);
set(handles.IX71LampPower,'string',obj.LampPower);
set(handles.LED850lLampPower,'string',obj.Lamp850Power);
set(handles.Focus561,'value',obj.focus561Flag);
set(handles.Focus638,'value',obj.focus638Flag);
set(handles.FocusIX71Lamp,'value',obj.focusLampFlag);
set(handles.Focuslamp850,'value',obj.focusLamp850Flag);
set(handles.Edit_ControlNSequence,'string',num2str(obj.NumSequences));
set(handles.Edit_CameraExpTimeSeqActual,'String',num2str(obj.CameraObj.SequenceCycleTime));
switch obj.RegType
case 'None'
set(handles.ButtonGroup_RegCollectType,'SelectedObject',b1);
case 'Self'
set(handles.ButtonGroup_RegCollectType,'SelectedObject',b2);
case 'Ref'
set(handles.ButtonGroup_RegCollectType,'SelectedObject',b3);
end
end
end
|
github
|
LidkeLab/matlab-instrument-control-master
|
setCamProperties.m
|
.m
|
matlab-instrument-control-master/@MIC_AndorCamera/setCamProperties.m
| 5,290 |
utf_8
|
00353ba3ce9c36d6a6457121019fb226
|
function setCamProperties(obj,CamSetting)
%SETCAMERAPROPERTIES Summary of this function goes here
% in: a duplicate CameraSetting structure to be checked and set
% this function sets the camera properties on the camera so that what you
% select on the gui is committed to the API
obj.ReadyForAcq=0;
%obj.CameraParameters=in;
% ADChannel;
% Amp;
% BaselineClamp;
% Cooler;
% Fan;
% HSSpeed;
% PreAmpGain;
% Shutter;
% Trigger;
% VSAmplitudes;
% VSSpeed;
% VerShiftVoltage;
setCamSDK(obj,CamSetting);
obj.get_parameters;
obj.ReadyForAcq=1;
end
function setCamSDK(obj,CamSetting)
% sub function to set the property given the input field, works on case by case basis!
% all of these are copied and pasted from other legacy code so variables
% will have to be renamed shortly!
camFields = fields(CamSetting);
debug = false;
for ii=1:length(camFields)
switch (camFields{ii})
case 'ManualShutter'
obj.CameraSetting.ManualShutter.Bit = CamSetting.ManualShutter.Bit;
case 'EMGain'
obj.LastError = SetEMCCDGain(CamSetting.EMGain.Value);
obj.errorcheck('SetEMCCDGain');
obj.CameraSetting.EMGain.Value=CamSetting.EMGain.Value;
if debug
% check low level behavior
[obj.LastError,EMGainVal] = GetEMCCDGain;
disp(['Check EMGain: set ', num2str(CamSetting.EMGain.Value),' , get ' num2str(EMGainVal)]);
end
case 'ADChannel'
obj.LastError = SetADChannel(CamSetting.ADChannel.Bit);
obj.errorcheck('SetADChannel');
obj.CameraSetting.ADChannel.Bit=CamSetting.ADChannel.Bit;
if debug
% check low level behavior
disp(['Check ADChannel: set ', CamSetting.ADChannel.Desc]);
end
case 'Amp'
obj.LastError = SetOutputAmplifier(CamSetting.Amp.Bit);
obj.errorcheck('SetOutputAmplifier');
obj.CameraSetting.Amp.Bit=CamSetting.Amp.Bit;
if debug
% check low level behavior
disp(['Check Amp: set ', CamSetting.Amp.Desc]);
end
case 'HSSpeed'
AmpBit = CamSetting.Amp.Bit;
obj.LastError = SetHSSpeed(AmpBit,CamSetting.HSSpeed.Bit);
obj.errorcheck('SetHSSpeed');
obj.CameraSetting.HSSpeed.Bit=CamSetting.HSSpeed.Bit;
if debug
% check low level behavior
disp(['Check HSSpeed: set ', CamSetting.HSSpeed.Desc]);
end
case 'BaselineClamp'
obj.LastError = SetBaselineClamp(CamSetting.BaselineClamp.Bit);
obj.errorcheck('SetBaselineClamp');
obj.CameraSetting.BaselineClamp.Bit=CamSetting.BaselineClamp.Bit;
if debug
% check low level behavior
disp(['Check BaselineClamp: set ', CamSetting.BaselineClamp.Desc]);
end
case 'Cooler'
obj.LastError = SetCoolerMode(CamSetting.Cooler.Bit);
obj.errorcheck('SetCoolerMode');
obj.CameraSetting.Cooler.Bit=CamSetting.Cooler.Bit;
case 'Fan'
obj.LastError = SetFanMode(CamSetting.Fan.Bit);
obj.errorcheck('SetFanMode');
obj.CameraSetting.Fan.Bit=CamSetting.Fan.Bit;
case 'PreAmpGain'
obj.LastError = SetPreAmpGain(CamSetting.PreAmpGain.Bit);
obj.errorcheck('SetPreAmpGain');
obj.CameraSetting.PreAmpGain.Bit=CamSetting.PreAmpGain.Bit;
case 'Shutter'
% obj.LastError = SetShutter(value.typ{1},value.mode{1},...
% value.closingtime,value.openingtime);
% obj.errorcheck('SetShutter');
% Set Shutter to Auto (1) or Manual (0)
obj.CameraSetting.ManualShutter.Bit = CamSetting.ManualShutter.Bit;
case 'Trigger'
obj.LastError=SetTriggerMode(CamSetting.Trigger.Bit); % Set trigger mode; 0 for Internal
obj.errorcheck('SetTriggerMode');
obj.CameraSetting.Trigger.Bit=CamSetting.Trigger.Bit;
if debug
% check low level behavior
disp(['Check Trigger: set ', CamSetting.Trigger.Desc]);
end
case 'VSAmplitude' % this is the vertical shift voltage!
obj.LastError = SetVSAmplitude(CamSetting.VSAmplitude.Bit);
obj.errorcheck('SetVSAmplitude');
obj.CameraSetting.VSAmplitude.Bit=CamSetting.VSAmplitude.Bit;
if debug
% check low level behavior
disp(['Check VSAmplitude: set ', CamSetting.VSAmplitude.Desc]);
end
case 'VSSpeed'
obj.LastError = SetVSSpeed(CamSetting.VSSpeed.Bit);
obj.errorcheck('SetVSSpeed');
obj.CameraSetting.VSSpeed.Bit=CamSetting.VSSpeed.Bit;
if debug
% check low level behavior
disp(['Check VSSpeed: set ', CamSetting.VSSpeed.Desc]);
end
case 'FrameTransferMode'
obj.LastError = SetFrameTransferMode(CamSetting.FrameTransferMode.Bit);
obj.errorcheck('SetFrameTransferMode');
obj.CameraSetting.FrameTransferMode.Bit=CamSetting.FrameTransferMode.Bit;
end
end
end
|
github
|
LidkeLab/matlab-instrument-control-master
|
gui.m
|
.m
|
matlab-instrument-control-master/@MIC_RB_PSFEng/gui.m
| 17,913 |
utf_8
|
3ffb4d357fa8f7872686a894b1cd3210
|
function gui( obj )
%GUI Gui for MIC_RB_PSFEng class
% Detailed explanation goes here
%Prevent opening more than one figure for same instrument
if ishandle(obj.GuiFigure)
guiFig = obj.GuiFigure;
figure(obj.GuiFigure);
return
end
%Open figure
guiFig = figure('NumberTitle','off','Resize','off','Units','pixels','MenuBar','none',...
'ToolBar','none','Visible','on', 'Position',[70 600 450 400]);
% Create a property based on GuiFigure
obj.GuiFigure = guiFig;
obj.GuiFigure.Name = sprintf('%s', obj.InstrumentName);
%Prevent closing after a 'close' or 'close all'
obj.GuiFigure.HandleVisibility='off';
%Save Propeties upon close
obj.GuiFigure.CloseRequestFcn = @closeFigure;
%Mouse scroll wheel callback
obj.GuiFigure.WindowScrollWheelFcn = @wheel;
% Laser control
minPower=obj.Laser642.MinPower;
maxPower=obj.Laser642.MaxPower;
unitPower=obj.Laser642.PowerUnit;
% File name and save dir
handles.FilePanel = uipanel(guiFig,'Title','File','FontSize',8,...
'Units','Pixels','Position',[10 280 210 120]);
uicontrol(handles.FilePanel,'Style','text','String','Save Directory',...
'Position',[5,85,130,15],'FontSize',8,'HorizontalAlignment','left');
handles.editSaveDir = uicontrol(handles.FilePanel,'Style','edit',...
'Position',[5,65,200,20],'FontSize',8);
uicontrol(handles.FilePanel,'Style','text','String','File name',...
'Position',[5,50,130,15],'FontSize',8,'HorizontalAlignment','left');
handles.editFileName = uicontrol(handles.FilePanel,'Style','edit',...
'Position',[5,30,200,20],'FontSize',8);
uicontrol(handles.FilePanel,'Style','text','String','Save type',...
'Position',[5,5,130,15],'FontSize',8,'HorizontalAlignment','left');
handles.editSaveType = uicontrol(handles.FilePanel,'Style','popup','String',...
{'mat','h5'},'Position',[75,5,100,20],'FontSize',8);
% laser control
handles.LaserPanel = uipanel(guiFig,'Title','Laser','FontSize',8,...
'Units','Pixels','Position',[10 210 210 70]);
uicontrol(handles.LaserPanel,'Style','text','String',...
['Power limits ' num2str(minPower) ' - ' num2str(maxPower) ' ' unitPower],...
'Position',[5,35,130,15],'FontSize',8,'HorizontalAlignment','left');
uicontrol(handles.LaserPanel,'Style','text','String','Set Power',...
'Position',[5,10,60,15],'FontSize',8,'HorizontalAlignment','left');
handles.SetLaserPower = uicontrol(handles.LaserPanel,'Style','edit',...
'Position',[70 10,60,15],'FontSize',8,'Callback',@setPower);
handles.Toggle_Laser=uicontrol(handles.LaserPanel,'Style','togglebutton',...
'String','Off','Position',[150,10,40,40],...
'BackgroundColor',[0.8 0.8 0.8],'Tag','LaserPowerButton','Callback',@toggleLaser);
% Camera control
handles.CameraPanel = uipanel(guiFig,'Title','Camera','FontSize',8,...
'Units','Pixels','Position',[10 10 210 200]);
handles.CamFocus = uicontrol(handles.CameraPanel,'Style','pushbutton',...
'String','Focus','Position',[5,5,50,30],'FontSize',8,'Callback',@focusCamera);
handles.CamFocusWithI = uicontrol(handles.CameraPanel,'Style','pushbutton',...
'String','Focus with Intensity feedback','Position',[60,5,145,30],'FontSize',8,'Callback',@focusCameraWithFeedback);
uicontrol(handles.CameraPanel,'Style','text','String',...
'ROI','Position',[5,165,50,15],'FontSize',8,'HorizontalAlignment','left');
handles.CamROIpopup = uicontrol(handles.CameraPanel,'Style','popup','String',...
{'center 128','center 256','center 512','center 1024','full'},...
'Position', [60 165 130 15],'FontSize',8,'Callback',@setROI);
uicontrol(handles.CameraPanel,'Style','text','String',...
'Zoom','Position',[5,135,50,15],'FontSize',8,'HorizontalAlignment','left');
handles.CamZoom_popup = uicontrol(handles.CameraPanel,'Style','popupmenu',...
'String',{'50%','100%','200%','400%','1000%'},'Value',4,...
'Position', [60 135 130 15],'FontSize',8,'CallBack',@setZoom);
uicontrol(handles.CameraPanel,'Style','text','String',...
'Acquisition time (s)','Position',[5,100,100,15],'FontSize',8,...
'HorizontalAlignment','left');
handles.CamAcqTime = uicontrol(handles.CameraPanel,'Style','edit',...
'Position',[120,100,70,15],'FontSize',8,'Tag','CamAcqEdit',...
'Callback',@setAcqTime);
% Piezo control
handles.PiezoPanel = uipanel(guiFig,'Title','Piezo','FontSize',8,...
'Units','Pixels','Position',[230 300 210 100]);
minPos=obj.Piezo.MinPosition;
maxPos=obj.Piezo.MaxPosition;
posUnit=obj.Piezo.PositionUnit;
fineStepFrac = 0.01;
coarseStepFrac = 0.1;
fineStep = (maxPos-minPos)*fineStepFrac;
coarseStep = (maxPos-minPos)*coarseStepFrac;
% slider
sliderVertPos = 50;
sliderLeft = 40;
sliderWidth = 130;
sliderHeight = 20;
handles.sliderPosition=uicontrol(handles.PiezoPanel,'Style','slider','Min',minPos,...
'Max',maxPos,'Value',minPos,'SliderStep',[fineStepFrac fineStepFrac],...
'Position', [sliderLeft sliderVertPos sliderWidth sliderHeight],...
'Tag','positionSlider','Callback',@positionSlider);
handles.sliderPosition.KeyPressFcn = @sliderKey;
uicontrol(handles.PiezoPanel,'Style','text','String',...
[num2str(minPos),' ',posUnit],'Position',...
[sliderLeft+15 sliderVertPos+25,30,12],'HorizontalAlignment','left',...
'FontSize',8);
uicontrol(handles.PiezoPanel,'Style','text','String',...
[num2str(maxPos),' ',posUnit],'Position',...
[sliderLeft+80 sliderVertPos+25,40,12],'HorizontalAlignment','left',...
'FontSize',8);
uicontrol(handles.PiezoPanel,'Style','text','String','F','Position',...
[sliderLeft sliderVertPos+25,10,12],'HorizontalAlignment','left',...
'FontSize',8);
uicontrol(handles.PiezoPanel,'Style','text','String','F','Position',...
[sliderLeft+sliderWidth-10 sliderVertPos+25,10,12],'HorizontalAlignment','left',...
'FontSize',8);
% coarse buttons
jogHeight = sliderVertPos;
handles.buttonJogDown = uicontrol(handles.PiezoPanel,'Style','pushbutton','String','<',...
'Position',[sliderLeft-25 jogHeight,20,sliderHeight],'FontSize',16,'Callback',@jogDown);
handles.buttonJogUp = uicontrol(handles.PiezoPanel,'Style','pushbutton','String','>',...
'Position',[sliderLeft+sliderWidth+5 jogHeight,20,sliderHeight],'FontSize',16,'Callback',@jogUp);
uicontrol(handles.PiezoPanel,'Style','text','String','C','Position',...
[sliderLeft-20 sliderVertPos+25,10,12],'HorizontalAlignment','left',...
'FontSize',8);
uicontrol(handles.PiezoPanel,'Style','text','String','C','Position',...
[sliderLeft+sliderWidth+10 sliderVertPos+25,10,12],'HorizontalAlignment','left',...
'FontSize',8);
% set step size and position
uicontrol(handles.PiezoPanel,'Style','text','String','Step size Fine','Position',...
[5 sliderVertPos-20,90,12],'HorizontalAlignment','left',...
'FontSize',8);
handles.editFineStep = uicontrol(handles.PiezoPanel,'Style','edit',...
'Position',[80,sliderVertPos-22,30,15],'FontSize',8,...
'String',num2str(fineStep),'Callback',@setFineStepSize);
uicontrol(handles.PiezoPanel,'Style','text','String','Coarse','Position',...
[125 sliderVertPos-20,40,12],'HorizontalAlignment','left',...
'FontSize',8);
handles.editCoarseStep = uicontrol(handles.PiezoPanel,'Style','edit',...
'Position',[170,sliderVertPos-22,30,15],'FontSize',8,...
'String',num2str(coarseStep));
uicontrol(handles.PiezoPanel,'Style','text','String','Set position','Position',...
[5 sliderVertPos-45,90,12],'HorizontalAlignment','left',...
'FontSize',8);
handles.editPosition = uicontrol(handles.PiezoPanel,'Style','edit',...
'Position',[80,sliderVertPos-48,60,15],'FontSize',8,'Callback',@setPosition);
% set SLM
handles.SLMPanel = uipanel(guiFig,'Title','SLM','FontSize',8,...
'Units','Pixels','Position',[230 160 210 140]);
handles.calPupilPos = uicontrol(handles.SLMPanel,'Style','pushbutton',...
'String','Cal Pupil Position','Position',[5,5,100,30],'FontSize',8,'Callback',@calPupilPos);
handles.optimPSF = uicontrol(handles.SLMPanel,'Style','pushbutton',...
'String','Optimize PSF','Position',[105,5,100,30],'FontSize',8,'Callback',@optimPupil);
uicontrol(handles.SLMPanel,'Style','text','String','# zernike coef to optimize',...
'Position',[5,40,150,15],'FontSize',8);
handles.editNumCoef = uicontrol(handles.SLMPanel,'Style','edit','String','13',...
'Position',[160,40,40,15],'FontSize',8);
% acquire PSF
handles.AcqPanel = uipanel(guiFig,'Title','Acquire PSF','FontSize',8,...
'Units','Pixels','Position',[230 10 210 150]);
uicontrol(handles.AcqPanel,'Style','text','String','Z range ([min step max])',...
'Position',[5,110,140,15],'FontSize',8,'HorizontalAlignment','left');
handles.editZrange = uicontrol(handles.AcqPanel,'Style','edit','String','-1 0.25 1',...
'Position',[140,110,60,15],'FontSize',8,'HorizontalAlignment','center');
uicontrol(handles.AcqPanel,'Style','text','String','Frames per Z position',...
'Position',[5,90,140,15],'FontSize',8,'HorizontalAlignment','left');
handles.editNumFrames = uicontrol(handles.AcqPanel,'Style','edit','String','100',...
'Position',[140,90,60,15],'FontSize',8,'HorizontalAlignment','center');
handles.startZstack = uicontrol(handles.AcqPanel,'Style','pushbutton',...
'String','Start','Position',[5,5,60,30],'FontSize',8,...
'Callback',@startZstack);
% Initialize GUI properties
properties2gui();
% Change some defaults
handles.CamROIpopup.Value = 1;
handles.CamZoom_popup.Value = 4;
handles.CamAcqTime.String = '0.01';
handles.SetLaserPower.String = 1;
gui2properties();
%% callback functions
function closeFigure(~,~)
gui2properties();
delete(obj.GuiFigure);
end
function properties2gui()
% update gui with object properties
% laser
handles.SetLaserPower.String = obj.Laser642.Power;
set(handles.Toggle_Laser,'Value',obj.Laser642.IsOn);
if obj.Laser642.IsOn==1
set(handles.Toggle_Laser,'String','On');
set(handles.Toggle_Laser,'BackgroundColor','red');
else
set(handles.Toggle_Laser,'String','Off');
set(handles.Toggle_Laser,'BackgroundColor',[.8 .8 .8]);
end
% camera
handles.CamAcqTime.String = obj.Camera.ExpTime_Focus;
% piezo
if isempty(obj.Piezo.CurrentPosition) || isnan(obj.Piezo.CurrentPosition)
obj.Piezo.getPosition;
end
handles.sliderPosition.Value = obj.Piezo.CurrentPosition;
handles.editPosition.String = num2str(obj.Piezo.CurrentPosition);
end
function gui2properties()
setPower();
setROI();
setZoom();
setAcqTime();
end
function setPower(~,~)
textValue=str2double(get(handles.SetLaserPower,'String'));
if textValue > obj.Laser642.MaxPower || isnan(textValue)
error('Choose a number for Power between [MinPower,MaxPower]');
end
obj.Laser642.setPower(textValue);
end
function toggleLaser(~,~)
state=get(handles.Toggle_Laser,'Value');
if state
obj.Laser642.on();
set(handles.Toggle_Laser,'BackgroundColor','red');
set(handles.Toggle_Laser,'String','On')
else
set(handles.Toggle_Laser,'BackgroundColor',[0.8 0.8 0.8])
set(handles.Toggle_Laser,'String','Off')
obj.Laser642.off();
end
end
function focusCamera(~,~)
obj.Laser642.on();
obj.Camera.start_focus;
obj.Laser642.off();
end
function focusCameraWithFeedback(~,~)
obj.Laser642.on();
obj.Camera.start_focusWithFeedback;
obj.Laser642.off();
end
function setROI(~,~)
roi_val = handles.CamROIpopup.Value;
switch roi_val
% given as [Xstart Xend Ystart Yend]
case 1
ROI=[961 1088 961 1088];% center 128
case 2
ROI=[897 1152 897 1152];% center 256
case 3
ROI=[769 1280 769 1280];% center 512
case 4
ROI=[513 1536 513 1536]; % center 1024
case 5
ROI=[1 2048 1 2048]; % full 2048
end
obj.Camera.ROI = ROI;
end
function setZoom(~,~)
zoom_val = handles.CamZoom_popup.Value;
switch zoom_val
case 1 % 50%
obj.Camera.DisplayZoom = 0.5;
case 2 % 100%
obj.Camera.DisplayZoom = 1;
case 3 % 200%
obj.Camera.DisplayZoom = 2;
case 4 % 400%
obj.Camera.DisplayZoom = 4;
case 5 % 1000%
obj.Camera.DisplayZoom = 10;
end
end
function setAcqTime(~,~)
Value=str2double(get(handles.CamAcqTime,'String'));
obj.Camera.ExpTime_Capture = Value;
obj.Camera.ExpTime_Focus = Value;
obj.Camera.ExpTime_Sequence = Value;
end
function positionSlider(~,~)
Value=handles.sliderPosition.Value;
obj.Piezo.setPosition(Value)
handles.editPosition.String = num2str(Value);
end
function jogUp(~,~)
stepSize = str2double(handles.editCoarseStep.String);
newPos = obj.Piezo.CurrentPosition + stepSize;
if newPos > obj.Piezo.MaxPosition
warning('Position outside range, moving to maximum position')
newPos = obj.Piezo.MaxPosition;
end
obj.Piezo.setPosition(newPos);
properties2gui()
end
function jogDown(~,~)
stepSize = str2double(handles.editCoarseStep.String);
newPos = obj.Piezo.CurrentPosition - stepSize;
if newPos < obj.Piezo.MinPosition
warning('Position outside range, moving to minimum position')
newPos = obj.Piezo.MinPosition;
end
obj.Piezo.setPosition(newPos);
properties2gui()
end
function setFineStepSize(~,~)
stepSize=str2double(handles.editFineStep.String);
stepPercent = stepSize/(obj.Piezo.MaxPosition-obj.Piezo.MinPosition);
handles.sliderPosition.SliderStep = [stepPercent stepPercent];
end
function setPosition(~,~)
Value=str2double(handles.editPosition.String);
if Value < obj.Piezo.MinPosition
warning('MIC_LinearStage_Abstract:GuiInvPos',...
'Invalid Position (%i %s) Position cannot be smaller then %i %s, moving to minimum position',...
Value, obj.Piezo.PositionUnit, obj.Piezo.MinPosition, obj.Piezo.PositionUnit);
Value = obj.Piezo.MinPosition;
end
if Value > obj.Piezo.MaxPosition
warning('MIC_LinearStage_Abstract:GuiInvPos',...
'Invalid Position (%i %s) Position cannot be larger then %i %s, moving to maximum position',...
Value, obj.Piezo.PositionUnit, obj.Piezo.MaxPosition, obj.Piezo.PositionUnit);
Value = obj.Piezo.MaxPosition;
end
obj.Piezo.setPosition(Value)
handles.sliderPosition.Value = Value;
end
function wheel(~,Event)
point = guiFig.CurrentPoint;
% check whether mouse is over slider
if point(1) < sliderLeft || point(1) > sliderLeft+sliderWidth ...
|| point(2) < sliderBottom || point(2) > sliderVertPos+sliderHeight
return
end
stepSize = str2double(handles.editCoarseJog.String);
step = Event.VerticalScrollCount*-stepSize;
newPos = obj.Piezo.CurrentPosition + step;
if newPos < obj.Piezo.MinPosition || newPos > obj.Piezo.MaxPosition
return
end
obj.Piezo.setPosition(newPos);
properties2gui()
end
function calPupilPos(~,~)
obj.calibratePupilPosition();
end
function optimPupil(~,~)
NumCoef = str2double(handles.editNumCoef.String);
obj.optimizePupil(NumCoef);
end
function startZstack(~,~)
% get save info
SaveDir = handles.editSaveDir.String;
FileName = handles.editFileName.String;
SaveType = handles.editSaveType.String{handles.editSaveType.Value};
TimeStamp = datestr(clock,'yyyy-mm-dd-HH-MM-SS');
% get z range info
ZrangeStr = handles.editZrange.String;
idx = strfind(ZrangeStr,' ');
Zrange = [str2double(ZrangeStr(1:idx(1)-1)),...
str2double(ZrangeStr(idx(1)+1:idx(2)-1)),...
str2double(ZrangeStr(idx(2)+1:end))];
z0=obj.Piezo.CurrentPosition;
z = Zrange(1):Zrange(2):Zrange(3);
dataset=[];
%Setup Camera
obj.Camera.SequenceLength=str2double(handles.editNumFrames.String);
obj.Camera.AcquisitionType = 'sequence';
obj.Camera.setup_acquisition;
%Collect
obj.Laser642.on();
pause(.25);
for ii=1:length(z)
obj.Piezo.setPosition(z0+z(ii))
pause(.1);
sequence=obj.Camera.start_sequence();
dataset=cat(4,dataset,sequence);
end
%Turn off Laser and reset Piezo
obj.Laser642.off();
obj.Piezo.setPosition(z0);
% show data
dipshow(permute(squeeze(mean(dataset,3)),[2,1,3]));
% save data
switch SaveType
case 'mat'
Params.Camera = obj.Camera.exportState();
Params.Piezo = obj.Piezo.exportState();
Params.Laser642 = obj.Laser642.exportState();
Params.SLM = obj.SLM.exportState();
Params.Zrange = Zrange;
Params.NA=obj.NA;
Params.RefrIdx=obj.RefrIdx;
Params.Fobjective=obj.Fobjective;
Params.SLMangle = obj.SLMangle;
Params.PixelSize = obj.PixelSize;
Params.ZCoefOptimized = obj.ZCoefOptimized; %#ok<STRNU>
save(fullfile(SaveDir,[FileName '#' TimeStamp '.mat']),'dataset','Params');
case 'h5'
warning('no h5 saving yet')
end
end
end
|
github
|
LidkeLab/matlab-instrument-control-master
|
gui.m
|
.m
|
matlab-instrument-control-master/@MIC_TIRF_SRcollect/gui.m
| 21,009 |
utf_8
|
93650b7a3e977f739c1540ff8e7a8970
|
function gui(obj)
% GUI SRcollect Gui for TIRF microscope
% Detailed explanation goes here
h = findall(0,'tag','TIRF-SRcollect.gui');
if ~(isempty(h))
figure(h);
return;
end
%%
xsz=400;
ysz=1060;
xst=100;
yst=100;
pw=.95;
psep=.001;
staticst=10;
editst=110;
guiFig = figure('Units','pixels','Position',[xst yst xsz ysz],...
'MenuBar','none','ToolBar','none','Visible','on',...
'NumberTitle','off','UserData',0,'Tag',...
'TIRF-SRcollect.gui','HandleVisibility','off','name','SRcollect.gui','CloseRequestFcn',@FigureClose);
defaultBackground = get(0,'defaultUicontrolBackgroundColor');
set(guiFig,'Color',defaultBackground);
handles.output = guiFig;
guidata(guiFig,handles);
refh=1;
% File Panel
ph=0.09;
php = ph*ysz;
hFilePanel = uipanel('Parent',guiFig,'Title','FILE','Position',[(1-pw)/2 refh-ph-psep pw ph]);
refh=refh-ph-psep;
uicontrol('Parent',hFilePanel, 'Style', 'edit', 'String', 'Save Directory:','Enable','off','Position', [staticst php-40 100 20]);
handles.Edit_FileDirectory = uicontrol('Parent',hFilePanel, 'Style', 'edit', 'String','Set Auto','Enable','on','BackgroundColor',[1 1 1],'Position', [editst php-40 250 20]);
uicontrol('Parent',hFilePanel, 'Style', 'edit', 'String', 'Base FileName:','Enable','off','Position', [staticst php-65 100 20]);
handles.Edit_FileName = uicontrol('Parent',hFilePanel, 'Style', 'edit', 'String','Set Auto','Enable','on','BackgroundColor',[1 1 1],'Position', [editst php-65 250 20]);
uicontrol('Parent',hFilePanel, 'Style', 'edit', 'String','File type:','Enable','off','Position', [staticst php-90 100 20]);
handles.saveFileType = uicontrol('Parent',hFilePanel, 'Style', 'popupmenu', 'String',{'.mat','.h5'},'Enable','on','BackgroundColor',[1 1 1],'Position', [editst php-90 250 20],'CallBack',@saveFile);
% Camera Panel
ph=0.17;
php = ph*ysz;
hCameraPanel = uipanel('Parent',guiFig,'Title','CAMERA','Position',[(1-pw)/2 refh-ph-psep pw ph]);
refh=refh-ph-psep;
uicontrol('Parent',hCameraPanel, 'Style', 'edit', 'String','Camera Gain:','Enable','off','Position', [staticst php-40 100 20]);
handles.Popup_CameraGain = uicontrol('Parent',hCameraPanel, 'Style', 'popupmenu', 'String',{'Low (Alexa647)','High (FAP/FP)'},'Enable','on','BackgroundColor',[1 1 1],'Position', [editst php-40 250 20],'CallBack',@gain_set);
uicontrol('Parent',hCameraPanel, 'Style', 'edit', 'String','Camera ROI:','Enable','off','Position', [staticst php-70 100 20]);
ROIlist={'Full','Left','Right','Left Center','Right Center','Center Horizontally','Left Top','Left Bottom','Right Top','Right Bottom','Top','Bottom','Center256'};
handles.Popup_CameraROI = uicontrol('Parent',hCameraPanel, 'Style', 'popupmenu', 'String',ROIlist,'Enable','on','BackgroundColor',[1 1 1],'Position', [editst php-70 250 20]);
uicontrol('Parent',hCameraPanel, 'Style', 'edit', 'String','Exp. Time Focus:','Enable','off','Position', [staticst php-100 100 20]);
handles.Edit_CameraExpTimeFocusSet = uicontrol('Parent',hCameraPanel, 'Style', 'edit', 'String','0.01','Enable','on','BackgroundColor',[1 1 1],'Position', [editst php-100 50 20]);
uicontrol('Parent',hCameraPanel, 'Style', 'edit', 'String','Actual:','Enable','off','Position', [175 php-100 100 20]);
handles.Edit_CameraExpTimeFocusActual = uicontrol('Parent',hCameraPanel, 'Style', 'edit', 'String','','Enable','off','Position', [250 php-100 50 20]);
uicontrol('Parent',hCameraPanel, 'Style', 'edit', 'String','Exp. Time Seq.:','Enable','off','Position', [staticst php-130 100 20]);
handles.Edit_CameraExpTimeSeqSet = uicontrol('Parent',hCameraPanel, 'Style', 'edit', 'String','0.01','Enable','on','BackgroundColor',[1 1 1],'Position', [editst php-130 50 20],'CallBack',@sequence_set);
uicontrol('Parent',hCameraPanel, 'Style', 'edit', 'String','Actual:','Enable','off','Position', [175 php-130 100 20]);
handles.Edit_CameraExpTimeSeqActual = uicontrol('Parent',hCameraPanel, 'Style', 'edit', 'String',num2str(obj.CameraObj.SequenceCycleTime),'Enable','off','Position', [250 php-130 50 20]);
uicontrol('Parent',hCameraPanel, 'Style', 'edit', 'String','Num Frames:','Enable','off','Position', [staticst php-160 100 20]);
handles.Edit_CameraNumFrames = uicontrol('Parent',hCameraPanel, 'Style', 'edit', 'String','2000','Enable','on','BackgroundColor',[1 1 1],'Position', [editst php-160 50 20]);
uicontrol('Parent',hCameraPanel, 'Style', 'edit', 'String','Zoom:','Enable','off','Position', [175 php-160 100 20]);
handles.Popup_CameraDispZoom = uicontrol('Parent',hCameraPanel, 'Style','popupmenu','String',{'50%','100%','200%','400%','1000%'},'Value',4,'Enable','on','BackgroundColor',[1 1 1],'Position', [250 php-160 50 20],'CallBack',@zoom_set);
% Registration Panel
ph=0.213;
php = ph*ysz;
hRegPanel = uipanel('Parent',guiFig,'Title','REGISTRATION','Position',[(1-pw)/2 refh-ph-psep pw ph]);
refh=refh-ph-psep;
uicontrol('Parent',hRegPanel, 'Style', 'edit', 'String','Exp. Time Reg.:','Enable','off','Position', [staticst php-40 100 20]);
handles.Edit_RegExpTime = uicontrol('Parent',hRegPanel, 'Style', 'edit', ...
'String','0.01','Enable','on','BackgroundColor',[1 1 1],...
'Position', [editst php-40 50 20]);
handles.Button_RegLoadRef=uicontrol('Parent',hRegPanel, 'Style', 'pushbutton',...
'String','Load Reference','Enable','on',...
'Position', [staticst php-70 100 20],'Callback',@LoadRef);
handles.Edit_RegFileName = uicontrol('Parent',hRegPanel, 'Style', 'edit', ...
'String','File Name','Enable','on','BackgroundColor',[1 1 1],...
'Position', [editst php-70 250 20]);
handles.Button_RegAlign=uicontrol('Parent',hRegPanel, 'Style', 'pushbutton',...
'String','Align','Enable','on','Position', ...
[staticst php-100 80 20],'Callback',@Align);
handles.Button_RegShowRef=uicontrol('Parent',hRegPanel, 'Style', 'pushbutton', ...
'String','Show Reference','Enable','on','Position', ...
[staticst+80 php-100 100 20],'Callback',@ShowRef);
handles.Button_RegTakeCurrent=uicontrol('Parent',hRegPanel, 'Style', 'pushbutton',...
'String','Take Current','Enable','on','Position', ...
[staticst+180 php-40 90 20],'Callback',@TakeCurrent);
handles.Button_RegCenterStage=uicontrol('Parent',hRegPanel, 'Style', 'pushbutton', ...
'String','Center Stage','Enable','on','Position', ...
[staticst+270 php-40 90 20],'Callback',@CenterStage);
handles.Button_RegTakeReference=uicontrol('Parent',hRegPanel, 'Style', 'pushbutton',...
'String','Take Reference','Enable','on','Position', ...
[staticst+180 php-100 90 20],'Callback',@TakeReference);
handles.Button_RegSaveReference=uicontrol('Parent',hRegPanel, 'Style', 'pushbutton', ...
'String','Save Reference','Enable','on','Position', ...
[staticst+270 php-100 90 20],'Callback',@SaveReference);
BGh=100;
handles.ButtonGroup_RegCollectType=uibuttongroup('Parent',hRegPanel, 'Position', [.02 (php-130-BGh+30)/php .96 BGh/php]);
b1=uicontrol('Parent',handles.ButtonGroup_RegCollectType, 'Style', 'radio', 'tag','None','String','No Registration','Enable','on','Position', [staticst BGh-30 250 20]);
b2=uicontrol('Parent',handles.ButtonGroup_RegCollectType, 'Style', 'radio','tag','Self', 'String','Align to Self (Takes/Saves Reference Image)','Enable','on','Position', [staticst BGh-60 250 20]);
b3=uicontrol('Parent',handles.ButtonGroup_RegCollectType, 'Style', 'radio','tag','Ref','String','Align to Reference','Enable','on','Position', [staticst BGh-90 250 20]);
% LIGHTSOURCE Panel
ph=0.3;
hLampPanel = uipanel('Parent',guiFig,'Title','LIGHT SOURCE','Position',[(1-pw)/2 refh-ph-psep pw ph]);
refh=refh-ph-psep;
uicontrol(hLampPanel,'Style','text','String','On during Focus',...
'Position',[-3 240,60,25]);
uicontrol(hLampPanel,'Style','text','String','On during Aquisition',...
'Position',[-3 180,60,28]);
uicontrol(hLampPanel,'Style','text','String','Low Power',...
'Position',[0 120,60,25]);
uicontrol(hLampPanel,'Style','text','String','High Power',...
'Position',[0 70,60,25]);
uicontrol(hLampPanel,'Style','text','String','[MinPower,MaxPower]',...
'Position',[-1 5,60,35]);
h405Panel=uipanel(hLampPanel,'Title','405 nm','Position',[1/6 1/6 1/6 5/6]);
handles.Focus405 = uicontrol(h405Panel,'Style','checkbox',...
'Value',0,'Position',[23 190 130 20]);
handles.Aquisition405 = uicontrol(h405Panel,'Style','checkbox',...
'Value',0,'Position',[23 130 130 20]);
handles.LP405 = uicontrol(h405Panel,'Style','edit',...
'Position',[15 80 30 20],'Callback',@setLaser405Low);
handles.HP405 = uicontrol(h405Panel,'Style','edit',...
'Position',[15 25 30 20]);
powerString405 = sprintf('[%g, %g] (%s)',obj.Laser405.MinPower,obj.Laser405.MaxPower, obj.Laser405.PowerUnit);
uicontrol(hLampPanel,'Style','text','String',powerString405,...
'Position',[64, 5,60,35]);
h488Panel=uipanel(hLampPanel,'Title','488 nm','Position',[2/6 1/6 1/6 5/6]);
handles.Focus488 = uicontrol(h488Panel,'Style','checkbox',...
'Value',0,'Position',[23 190 130 20]);
handles.Aquisition488 = uicontrol(h488Panel,'Style','checkbox',...
'Value',0,'Position',[23 130 130 20]);
handles.LP488 = uicontrol(h488Panel,'Style','edit',...
'Position',[15 80 30 20],'Callback',@setLaser488Low);
handles.HP488 = uicontrol(h488Panel,'Style','edit',...
'Position',[15 25 30 20]);
powerString488 = sprintf('[%g, %g] (%s)',obj.Laser488.MinPower,obj.Laser488.MaxPower, obj.Laser488.PowerUnit);
uicontrol(hLampPanel,'Style','text','String',powerString488,...
'Position',[125 5,60,35]);
h561Panel=uipanel(hLampPanel,'Title','561 nm','Position',[3/6 1/6 1/6 5/6]);
handles.Focus561 = uicontrol(h561Panel,'Style','checkbox',...
'Value',0,'Position',[23 190 130 20]);
handles.Aquisition561 = uicontrol(h561Panel,'Style','checkbox',...
'Value',0,'Position',[23 130 130 20]);
handles.LP561 = uicontrol(h561Panel,'Style','edit',...
'Position',[15 80 30 20],'Callback',@setLaser561Low);
handles.HP561 = uicontrol(h561Panel,'Style','edit',...
'Position',[15 25 30 20]);
powerString561 = sprintf('[%g, %g] (%s)',obj.Laser561.MinPower,obj.Laser561.MaxPower, obj.Laser561.PowerUnit);
uicontrol(hLampPanel,'Style','text','String',powerString561,...
'Position',[190 5,60,35]);
h642Panel=uipanel(hLampPanel,'Title','642 nm','Position',[4/6 1/6 1/6 5/6]);
handles.Focus642 = uicontrol(h642Panel,'Style','checkbox',...
'Value',0,'Position',[23 190 130 20]);
handles.Aquisition642 = uicontrol(h642Panel,'Style','checkbox',...
'Value',0,'Position',[23 130 130 20]);
handles.LP642 = uicontrol(h642Panel,'Style','edit',...
'Position',[15 80 30 20],'Callback',@setLaser642Low);
handles.HP642 = uicontrol(h642Panel,'Style','edit',...
'Position',[15 25 30 20]);
powerString642 = sprintf('[%g, %g] (%s)',obj.Laser642.MinPower,obj.Laser642.MaxPower, obj.Laser642.PowerUnit);
uicontrol(hLampPanel,'Style','text','String',powerString642,...
'Position',[250 5,60,35]);
hX71Panel=uipanel(hLampPanel,'Title','Lamp','Position',[5/6 1/6 1/6 5/6]);
handles.FocusIX71Lamp = uicontrol(hX71Panel,'Style','checkbox',...
'Value',0,'Position',[23 190 130 20]);
handles.AquisitionIX71Lamp = uicontrol(hX71Panel,'Style','checkbox',...
'Value',0,'Position',[23 130 130 20]);
handles.IX71LampPower = uicontrol(hX71Panel,'Style','edit',...
'Position',[15 80 30 20],'Callback',@SetLampPower);
powerStringLamp = sprintf('[%g, %g] (%s)',obj.LampObj.MinPower,obj.LampObj.MaxPower, obj.LampObj.PowerUnit);
uicontrol(hLampPanel,'Style','text','String',powerStringLamp,...
'Position',[315 5,60,35]);
% CONTROL Panel
ph=0.190;
hControlPanel = uipanel('Parent',guiFig,'Title','CONTROL','Position',[(1-pw)/2 refh-ph-psep pw ph]);
php = ph*ysz;
uicontrol('Parent',hControlPanel, 'Style', 'edit', 'String','Number of Sequences:','Enable','off','Position', [staticst php-40 150 20]);
handles.Edit_ControlNSequence = uicontrol('Parent',hControlPanel, 'Style', 'edit', 'String','20','Enable','on','BackgroundColor',[1 1 1],'Position', [editst+50 php-40 50 20]);
handles.Button_ControlFocusLamp=uicontrol('Parent',hControlPanel, 'Style', 'pushbutton', 'String','Focus Lamp','Enable','on','Position', [staticst php-90 150 40],'BackgroundColor',[1 1 .8],'Callback',@FocusLamp);
handles.Button_ControlFocusLaserLow=uicontrol('Parent',hControlPanel, 'Style', 'pushbutton', 'String','Focus Laser (Low)','Enable','on','Position', [staticst+200 php-90 150 40],'BackgroundColor',[1 .8 .8],'Callback',@FocusLow);
handles.Toggle_LaserLamp=uicontrol('Parent',hControlPanel, 'Style', 'toggle', 'String','Lamp','Enable','on','Position', [staticst php-138 150 40],'BackgroundColor',[1 1 .8],'Callback',@ToggleLamp);
handles.Button_ControlStart=uicontrol('Parent',hControlPanel, 'Style', 'pushbutton', 'String','START','Enable','on','Position', [staticst php-175 150 30],'BackgroundColor',[0 1 0],'Callback',@Start);
handles.Button_ControlFocusLaserHigh=uicontrol('Parent',hControlPanel, 'Style', 'pushbutton', 'String','Focus Laser (High)','Enable','on','Position', [staticst+200 php-138 150 40],'BackgroundColor',[1 0 0],'Callback',@FocusHigh);
handles.Button_ControlAbort=uicontrol('Parent',hControlPanel, 'Style', 'pushbutton', 'String','ABORT','Enable','on','Position', [staticst+200 php-175 150 30],'BackgroundColor',[1 0 1],'Callback',@Abort);
%% Setup GUI Values
properties2gui();
%% Figure Callbacks
function saveFile(~,~)
file_val=get(handles.saveFileType,'value');
switch file_val
case 1
obj.SaveFileType='mat';
case 2
obj.SaveFileType='h5';
end
end
function LoadRef(~,~)
obj.loadref();
set(handles.Edit_RegFileName,'String',obj.R3DObj.RefImageFile);
end
function Align(~,~)
gui2properties();
obj.align();
end
function ShowRef(~,~)
obj.showref();
end
function TakeCurrent(~,~)
gui2properties();
obj.takecurrent();
end
function CenterStage(~,~)
obj.StageObj.center();
end
function TakeReference(~,~)
gui2properties();
obj.takeref();
end
function SaveReference(~,~)
obj.saveref();
properties2gui();
end
function ToggleLamp(~,~)
gui2properties();
stateLamp1=get(handles.Toggle_LaserLamp,'Value');
if stateLamp1
obj.LampObj.setPower(obj.LampPower);
obj.LampObj.on;
else
obj.LampObj.off;
% pause(obj.LampWait);
end
end
function FocusLamp(~,~)
gui2properties();
obj.focusLamp();
end
function FocusLow(~,~)
gui2properties();
obj.focusLow();
end
function FocusHigh(~,~)
gui2properties();
obj.focusHigh();
end
function Abort(~,~)
obj.AbortNow=1;
set(handles.Button_ControlStart, 'String','START','Enable','on');
end
function Start(~,~)
gui2properties();
set(handles.Button_ControlStart, 'String','Acquiring','Enable','off');
obj.StartSequence(handles);
set(handles.Button_ControlStart, 'String','START','Enable','on');
end
function SetLampPower(~,~)
gui2properties();
obj.setLampPower();
end
function setLaser405Low(~,~)
obj.Laser405.setPower(str2double(handles.LP405.String));
end
function setLaser488Low(~,~)
obj.Laser405.setPower(str2double(handles.LP488.String));
end
function setLaser561Low(~,~)
obj.Laser405.setPower(str2double(handles.LP561.String));
end
function setLaser642Low(~,~)
obj.Laser405.setPower(str2double(handles.LP642.String));
end
function FigureClose(~,~)
gui2properties();
delete(guiFig);
end
function zoom_set(~,~)
zoom_val = get(handles.Popup_CameraDispZoom,'Value');
switch zoom_val
case 1
obj.CameraObj.DisplayZoom = 0.5;
case 2
obj.CameraObj.DisplayZoom = 1;
case 3
obj.CameraObj.DisplayZoom = 2;
case 4
obj.CameraObj.DisplayZoom = 4;
case 5
obj.CameraObj.DisplayZoom = 10;
end
end
function gain_set(~,~)
gain_val=get(handles.Popup_CameraGain,'value');
switch gain_val
case 1
obj.CameraEMGainHigh=100;
case 2
obj.CameraEMGainHigh=200;
end
end
function sequence_set(~,~)
gui2properties();
obj.CameraObj.ExpTime_Sequence = obj.ExpTime_Sequence_Set;
obj.CameraObj.AcquisitionType = 'sequence';
obj.CameraObj.setup_acquisition;
set(handles.Edit_CameraExpTimeSeqActual,'String',num2str(obj.CameraObj.SequenceCycleTime));
end
function gui2properties()
%Get GUI values and update to object properties
obj.SaveDir=get(handles.Edit_FileDirectory,'String');
obj.BaseFileName=get(handles.Edit_FileName,'String');
obj.CameraGain=get(handles.Popup_CameraGain,'value');
obj.CameraROI=get(handles.Popup_CameraROI,'value');
obj.ExpTime_Focus_Set=str2double(get(handles.Edit_CameraExpTimeFocusSet,'string'));
obj.ExpTime_Sequence_Set=str2double(get(handles.Edit_CameraExpTimeSeqSet,'string'));
obj.NumFrames=str2double(get(handles.Edit_CameraNumFrames,'string'));
obj.R3DObj.ExposureTime=str2double(get(handles.Edit_RegExpTime,'string'));
obj.R3DObj.RefImageFile=get(handles.Edit_RegFileName,'string');
obj.focus405Flag=get(handles.Focus405,'Value');
obj.focus488Flag=get(handles.Focus488,'Value');
obj.focus561Flag=get(handles.Focus561,'Value');
obj.focus642Flag=get(handles.Focus642,'Value');
obj.focusLampFlag=get(handles.FocusIX71Lamp,'Value');
obj.Laser405Low=str2double(handles.LP405.String);
obj.Laser488Low=str2double(handles.LP488.String);
obj.Laser561Low=str2double(handles.LP561.String);
obj.Laser642Low=str2double(handles.LP642.String);
obj.Laser405High=str2double(handles.HP405.String);
obj.Laser488High=str2double(handles.HP488.String);
obj.Laser561High=str2double(handles.HP561.String);
obj.Laser642High=str2double(handles.HP642.String);
obj.LampPower=str2double(handles.IX71LampPower.String);
obj.Laser405Aq=handles.Aquisition405.Value;
obj.Laser488Aq=handles.Aquisition488.Value;
obj.Laser561Aq=handles.Aquisition561.Value;
obj.Laser642Aq=handles.Aquisition642.Value;
obj.LampAq=handles.AquisitionIX71Lamp.Value;
obj.NumSequences=str2double(get(handles.Edit_ControlNSequence,'string'));
obj.RegType=get(get(handles.ButtonGroup_RegCollectType,'SelectedObject'),'Tag');
end
function properties2gui()
%Set GUI values from object properties
set(handles.Edit_FileDirectory,'String',obj.SaveDir);
set(handles.Edit_FileName,'String',obj.BaseFileName);
set(handles.Popup_CameraGain,'value',obj.CameraGain);
set(handles.Popup_CameraROI,'value',obj.CameraROI);
set(handles.Edit_CameraExpTimeFocusSet,'string',num2str(obj.ExpTime_Focus_Set));
set(handles.Edit_CameraExpTimeSeqSet,'string',num2str(obj.ExpTime_Sequence_Set));
set(handles.Edit_RegExpTime,'string',num2str(obj.R3DObj.ExposureTime));
set(handles.Edit_CameraNumFrames,'string',num2str(obj.NumFrames));
set(handles.Edit_RegFileName,'string',obj.R3DObj.RefImageFile);
set(handles.LP405,'string',obj.Laser405Low);
set(handles.LP488,'string',obj.Laser488Low);
set(handles.LP561,'string',obj.Laser561Low);
set(handles.LP642,'string',obj.Laser642Low);
set(handles.HP405,'string',obj.Laser405High);
set(handles.HP488,'string',obj.Laser488High);
set(handles.HP561,'string',obj.Laser561High);
set(handles.HP642,'string',obj.Laser642High);
set(handles.IX71LampPower,'string',obj.LampPower);
set(handles.Focus405,'value',obj.focus405Flag);
set(handles.Focus488,'value',obj.focus488Flag);
set(handles.Focus561,'value',obj.focus561Flag);
set(handles.Focus642,'value',obj.focus642Flag);
set(handles.FocusIX71Lamp,'value',obj.focusLampFlag);
set(handles.Edit_ControlNSequence,'string',num2str(obj.NumSequences));
set(handles.Edit_CameraExpTimeSeqActual,'String',num2str(obj.CameraObj.SequenceCycleTime));
switch obj.RegType
case 'None'
set(handles.ButtonGroup_RegCollectType,'SelectedObject',b1);
case 'Self'
set(handles.ButtonGroup_RegCollectType,'SelectedObject',b2);
case 'Ref'
set(handles.ButtonGroup_RegCollectType,'SelectedObject',b3);
end
end
end
|
github
|
vaibhavjoshi16/Matlab-solver-for-adaptive-two-phase-flows-master
|
coarsening.m
|
.m
|
Matlab-solver-for-adaptive-two-phase-flows-master/coarsening.m
| 5,050 |
utf_8
|
19e7e1fc6bd780ce0690c5302041ffbf
|
function [Sol,eta] = coarsening(Sol,eta,theta)
% COARSENING coarsens the current mesh
%
% USAGE
% [Sol,eta] = coarsening(Sol,eta,theta)
%
% INPUT
% Sol: current mesh data
% eta: error indicator for each triangle
% theta: parameter in (0,1).
% We mark minimal number of triangles M such that
% \sum_{T \in M} \eta_T < \theta*\sum\eta_T
%
% OUTPUT
% Sol: new mesh data after coarsening
% eta: new error indicator for each triangle
%
% NOTE
% Only one level coarsening
%
% REFERENCE
% AFEM@matlab Manual --> Algorithms --> Coarsening
%
% L. Chen & C. Zhang 11-15-2006
% Modified by Vaibhav Joshi, Rajeev K. Jaiman
%--------------------------------------------------------------------------
% Construct data structure
%--------------------------------------------------------------------------
N = size(Sol.node,1);
NT = size(Sol.elem,1);
dualEdge = sparse(Sol.elem(:,[1,2,3]),Sol.elem(:,[2,3,1]),[1:NT,1:NT,1:NT]);
valence = accumarray(Sol.elem(:),ones(3*NT,1),[N 1]);
eta_p = accumarray(Sol.elem(:),[eta;eta;eta],[N 1]);
%--------------------------------------------------------------------------
% Mark nodes for coarsen
%--------------------------------------------------------------------------
total = sum(eta_p); maxeta = max(eta_p);
current = 0; marker = uint8(zeros(N,1));
newestNode = unique(Sol.elem(:,1)); % newest vertices of all elements
coarseNode = find(Sol.type==1); % nodes in the initial triangulation
newestNode = setdiff(newestNode,coarseNode);
isGood = (valence(newestNode) == 2) | (valence(newestNode) == 4);
goodNode = newestNode(isGood);
% A node is called 'good' if it can be removed without breaking the mesh
% comformity. A node is 'good' if and only if
% 0. it is not a node of marco elements in the initial triangluation;
% 1. it is the newest node in each of the elements with it as a node;
% 2. if it is an interior node, the valence is 4;
% 3. if it is on the boundary, the valence is 2.
[temp,ix] = sort(eta_p(goodNode));
for i = 1:length(goodNode)
p = goodNode(ix(i));
if (eta_p(p) > 0.2*maxeta), break; end % only coarsen where error small
if (current + eta_p(p) > theta*total), break; end
marker(p) = 1; % mark p to be removed
Sol.type(p) = 0; % node p is non active now
current = current + eta_p(p);
end
if (sum(marker)==0), return; end % no node can be coarsened
%--------------------------------------------------------------------------
% Coarsen the mesh by removing marked nodes
%--------------------------------------------------------------------------
for t = 1:NT
if (Sol.elem(t,1)>0) % otherwise t is already deleted
p = Sol.elem(t,1);
if (marker(p)==1) % p is a marked good point
brother = dualEdge(Sol.elem(t,2),p);
Sol.elem(t,1) = Sol.elem(t,2);
Sol.elem(t,2) = Sol.elem(t,3);
Sol.elem(t,3) = Sol.elem(brother,2);
Sol.elem(brother,1) = 0; % brother is going to be deleted
eta(t) = eta(t) + eta(brother); % new eta = eta_t + eta_brother
end % endif for all markd good nodes
end
end % end of for loop on all elements
%--------------------------------------------------------------------------
% Clear element and eta arrarys
%--------------------------------------------------------------------------
ix = (Sol.elem(:,1) == 0);
Sol.elem(ix,:) = [];
eta(ix,:) = [];
%--------------------------------------------------------------------------
% Update boundary edges
%--------------------------------------------------------------------------
markedNode = goodNode((marker(goodNode)==1)&(valence(goodNode)==2));
Sol.Dirichlet = updatebd(Sol.Dirichlet, markedNode);
Sol.Neumann = updatebd(Sol.Neumann, markedNode);
%--------------------------------------------------------------------------
% End of function COARSENING
%--------------------------------------------------------------------------
%--------------------------------------------------------------------------
% Sub functions called by COARSENING
%--------------------------------------------------------------------------
function bdEdge = updatebd(bdEdge, markedNode)
% UPDATEDBD coarsen the boundary edges
%
% USAGE
% bdEdge = updatebd(bdEdge, markedNode)
%
% INPUT
% bdEdge: old boundary edges
% markedNode: node marked for coarsening
%
% OUTPUT
% bdEdge: new boundary edges after coarsening
%
if (isempty(bdEdge) || isempty(markedNode)), return; end
NB = size(bdEdge,1);
neig = sparse(bdEdge,ones(NB,1)*[2,1],[1:NB,1:NB]);
% skeleton of edges around a node
for k = 1: length(markedNode)
i = neig(markedNode(k),1);
j = neig(markedNode(k),2);
% o --- i --- o --- j --- o
% ^
% noActive(k)
bdEdge(i,2) = bdEdge(j,2);
bdEdge(j,1) = 0;
end
ix = (bdEdge(:,1)==0);
bdEdge(ix,:) = [];
%--------------------------------------------------------------------------
% End of function UPDATEDBD
%--------------------------------------------------------------------------
|
github
|
vaibhavjoshi16/Matlab-solver-for-adaptive-two-phase-flows-master
|
bisection.m
|
.m
|
Matlab-solver-for-adaptive-two-phase-flows-master/bisection.m
| 11,047 |
utf_8
|
76f20349eeb792a7d8eaac98f42ee2a2
|
function [Sol,eta] = bisection(Sol,eta,theta)
% BISECTION refines the triangulation using newest vertex bisection
%
% USAGE
% [Sol,eta] = bisection(Sol,eta,theta)
%
% INPUT
% Sol: current mesh data with all variable data
% eta: error indicator for each triangle
% theta: parameter in (0,1).
% We mark minimal number of triangles M such that
% \sum_{T \in M} \eta_T > \theta*\sum\eta_T
%
% OUTPUT
% Sol: new mesh data with interpolated variable data after refinement
% eta: new error indicator for each triangle
%
% REFERENCE
% Long Chen,
% Short bisection implementation in MATLAB
% Research Notes, 2006
%
% L. Chen & C. Zhang 11-12-2006
%
% Modified by: Vaibhav Joshi, Rajeev K. Jaiman
%--------------------------------------------------------------------------
% Construct data structure
%--------------------------------------------------------------------------
edge = [Sol.elem(:,[1,2]); Sol.elem(:,[1,3]); Sol.elem(:,[2,3])];
edge = unique(sort(edge,2),'rows');
N = size(Sol.node,1);
NT = size(Sol.elem,1);
NE = size(edge,1);
dualEdge = sparse(Sol.elem(:,[1,2,3]),Sol.elem(:,[2,3,1]),[1:NT,1:NT,1:NT]);
d2p = sparse(edge(:,[1,2]),edge(:,[2,1]),[1:NE,1:NE]);
% Detailed explanation can be founded at
% Manual --> Data Structure --> Auxlliary data structure
%--------------------------------------------------------------------------
% Meomery management for node arrary
%--------------------------------------------------------------------------
recycle = find(Sol.type==0);
last = length(recycle);
% Coarsening can create empty spaces in the node array. We collect those
% scattered spaces in recycle arrary and 'last' will point out the last
% empty node index.
% mesh.type array is used to distinguish the type of nodes:
% 0: empty nodes (deleted by coarsening);
% 1: nodes in the initial triangulation or nodes from regular refinement;
% 2: new added nodes due to refinement;
% 5: temporay node (will be deleted when bisection finished).
%--------------------------------------------------------------------------
% Mark triangles according to the error indicator
%--------------------------------------------------------------------------
total = sum(eta);
current = 0;
[temp,ix] = sort(-eta); % sort in descent order
marker = zeros(NE,1);
% initialize for possible new nodes
Sol.node = [Sol.node; zeros(NE,2)];
Sol.type = [Sol.type; uint8(5*ones(NE,1))];
Sol.u = [Sol.u; zeros(NE,2)];
Sol.uPrev = [Sol.uPrev; zeros(NE,2)];
Sol.uAlpha = [Sol.uAlpha; zeros(NE,2)];
Sol.uDot = [Sol.uDot; zeros(NE,2)];
Sol.uDotPrev = [Sol.uDotPrev; zeros(NE,2)];
Sol.uDotAlpha = [Sol.uDotAlpha; zeros(NE,2)];
Sol.p = [Sol.p; zeros(NE,1)];
Sol.pPrev = [Sol.pPrev; zeros(NE,1)];
Sol.phi = [Sol.phi; zeros(NE,1)];
Sol.phiPrev = [Sol.phiPrev; zeros(NE,1)];
Sol.phiAlpha = [Sol.phiAlpha; zeros(NE,1)];
Sol.phiDot = [Sol.phiDot; zeros(NE,1)];
Sol.phiDotPrev = [Sol.phiDotPrev; zeros(NE,1)];
Sol.phiDotAlpha = [Sol.phiDotAlpha; zeros(NE,1)];
for t = 1:NT
if (current > theta*total), break; end % est on marked elem big enough
index = 1;
ct = ix(t);
while (index==1)
base = d2p(Sol.elem(ct,2),Sol.elem(ct,3));
if (marker(base)>0) % base is already marked
index = 0;
else
current = current + eta(ct);
if (last==0)
newNode = N + 1;
N = N+1;
end
if (last>0)
newNode = recycle(last);
last = last-1;
end
marker( d2p(Sol.elem(ct,2),Sol.elem(ct,3)) ) = newNode;
% A new node is added to the mesh. Numerical solution at this
% new added node is approximated by linear interpolation. Type
% of this node is 2 (generated by newest vertex bisection)
Sol.node(newNode,:) = ( Sol.node(Sol.elem(ct,2),:) + ...
Sol.node(Sol.elem(ct,3),:) )/2;
Sol.u(newNode,1) = ( Sol.u(Sol.elem(ct,2),1) + ...
Sol.u(Sol.elem(ct,3),1) )/2;
Sol.uPrev(newNode,1) = ( Sol.uPrev(Sol.elem(ct,2),1) + ...
Sol.uPrev(Sol.elem(ct,3),1) )/2;
Sol.uAlpha(newNode,1) = ( Sol.uAlpha(Sol.elem(ct,2),1) + ...
Sol.uAlpha(Sol.elem(ct,3),1) )/2;
Sol.uDot(newNode,1) = ( Sol.uDot(Sol.elem(ct,2),1) + ...
Sol.uDot(Sol.elem(ct,3),1) )/2;
Sol.uDotPrev(newNode,1) = ( Sol.uDotPrev(Sol.elem(ct,2),1) + ...
Sol.uDotPrev(Sol.elem(ct,3),1) )/2;
Sol.uDotAlpha(newNode,1) = ( Sol.uDotAlpha(Sol.elem(ct,2),1) + ...
Sol.uDotAlpha(Sol.elem(ct,3),1) )/2;
Sol.u(newNode,2) = ( Sol.u(Sol.elem(ct,2),2) + ...
Sol.u(Sol.elem(ct,3),2) )/2;
Sol.uPrev(newNode,2) = ( Sol.uPrev(Sol.elem(ct,2),2) + ...
Sol.uPrev(Sol.elem(ct,3),2) )/2;
Sol.uAlpha(newNode,2) = ( Sol.uAlpha(Sol.elem(ct,2),2) + ...
Sol.uAlpha(Sol.elem(ct,3),2) )/2;
Sol.uDot(newNode,2) = ( Sol.uDot(Sol.elem(ct,2),2) + ...
Sol.uDot(Sol.elem(ct,3),2) )/2;
Sol.uDotPrev(newNode,2) = ( Sol.uDotPrev(Sol.elem(ct,2),2) + ...
Sol.uDotPrev(Sol.elem(ct,3),2) )/2;
Sol.uDotAlpha(newNode,2) = ( Sol.uDotAlpha(Sol.elem(ct,2),2) + ...
Sol.uDotAlpha(Sol.elem(ct,3),2) )/2;
Sol.p(newNode) = ( Sol.p(Sol.elem(ct,2)) + ...
Sol.p(Sol.elem(ct,3)) )/2;
Sol.pPrev(newNode) = ( Sol.pPrev(Sol.elem(ct,2)) + ...
Sol.pPrev(Sol.elem(ct,3)) )/2;
Sol.phi(newNode) = ( Sol.phi(Sol.elem(ct,2)) + ...
Sol.phi(Sol.elem(ct,3)) )/2;
Sol.phiPrev(newNode) = ( Sol.phiPrev(Sol.elem(ct,2)) + ...
Sol.phiPrev(Sol.elem(ct,3)) )/2;
Sol.phiAlpha(newNode) = ( Sol.phiAlpha(Sol.elem(ct,2)) + ...
Sol.phiAlpha(Sol.elem(ct,3)) )/2;
Sol.phiDot(newNode) = ( Sol.phiDot(Sol.elem(ct,2)) + ...
Sol.phiDot(Sol.elem(ct,3)) )/2;
Sol.phiDotPrev(newNode) = ( Sol.phiDotPrev(Sol.elem(ct,2)) + ...
Sol.phiDotPrev(Sol.elem(ct,3)) )/2;
Sol.phiDotAlpha(newNode) = ( Sol.phiDotAlpha(Sol.elem(ct,2)) + ...
Sol.phiDotAlpha(Sol.elem(ct,3)) )/2;
Sol.type(newNode) = 2;
% Find the element which shares the base edge of the current
% element. If it is 0, it means the base of the current element
% is on the boundary.
ct = dualEdge( Sol.elem(ct,3), Sol.elem(ct,2) );
if ( ct == 0 ), index = 0; end
% the while will ended if
% 1. ct==0 means we are on the boundary
% 2. base(ct) is already marked
end
end % end while for recursive marking
end % end of for loop on all elements
% Detailed explanation of the algorithm can be found at
% Manual --> Algorithms --> Bisection
% delete possible empty entries
ix = (Sol.type == 5);
Sol.node(ix,:) = [];
Sol.type(ix) = [];
Sol.u(ix,:) = [];
Sol.uPrev(ix,:) = [];
Sol.uAlpha(ix,:) = [];
Sol.uDot(ix,:) = [];
Sol.uDotPrev(ix,:) = [];
Sol.uDotAlpha(ix,:) = [];
Sol.p(ix) = [];
Sol.pPrev(ix) = [];
Sol.phi(ix) = [];
Sol.phiPrev(ix) = [];
Sol.phiAlpha(ix) = [];
Sol.phiDot(ix) = [];
Sol.phiDotPrev(ix) = [];
Sol.phiDotAlpha(ix) = [];
%--------------------------------------------------------------------------
% Refine marked edges for each triangle
%--------------------------------------------------------------------------
numnew = 2*sum(marker~=0); % number of new elements need to be added
Sol.elem = [Sol.elem; zeros(numnew,3)];
eta = [eta; zeros(numnew,1)];
inew = NT + 1; % index for current new added right child
for t = 1:NT
base = d2p(Sol.elem(t,2),Sol.elem(t,3));
if (marker(base)>0)
p = [Sol.elem(t,:), marker(base)];
% Case 1: divide the current marked triangle
Sol.elem(t,:) = [p(4),p(1),p(2)]; % t is always a left child
Sol.elem(inew,:) = [p(4),p(3),p(1)]; % new is a right child
eta(t) = eta(t)/2; % update error indicators
eta(inew) = eta(t);
inew = inew + 1;
% Case 2: divide the right child, different, careful!!!
right = d2p(p(3),p(1));
if (marker(right)>0)
Sol.elem(inew-1,:) = [marker(right),p(4),p(3)];
Sol.elem(inew,:) = [marker(right),p(1),p(4)];
eta(inew-1) = eta(inew-1)/2;
eta(inew) = eta(inew-1);
inew = inew + 1;
end
% Case 3: divide the left child, similar to the case 1.
left = d2p(p(1),p(2));
if (marker(left)>0)
Sol.elem(t,:) = [marker(left),p(4),p(1)];
Sol.elem(inew,:) = [marker(left),p(2),p(4)];
eta(t) = eta(t)/2;
eta(inew) = eta(t);
inew = inew + 1;
end
end % end of refinement of one element
end % end of for loop on all elements
% delete possible empty entries
Sol.elem = Sol.elem(1:inew-1,:);
eta = eta(1:inew-1,:);
%--------------------------------------------------------------------------
% Update boundary edges
%--------------------------------------------------------------------------
Sol.Dirichlet = updatebd(Sol.Dirichlet,marker,d2p);
Sol.Neumann = updatebd(Sol.Neumann,marker,d2p);
%--------------------------------------------------------------------------
% End of function BISECTION
%--------------------------------------------------------------------------
%--------------------------------------------------------------------------
% Sub functions called by BISECTION
%--------------------------------------------------------------------------
function bdEdge = updatebd(bdEdge,marker,d2p)
% UPDATEDBD refine the boundary edges
%
% USAGE
% bdEdge = updatebd(bdEdge,marker,d2p)
%
% INPUT
% bdEdge: set of boundary edges
% marker: new node index for marked edge
% d2p: index mapping from dual edge to primary edge
%
% OUTPUT
% bdEdge: set of refined boundary edges
%
NB = size(bdEdge,1);
for k = 1:NB
i = bdEdge(k,1);
j = bdEdge(k,2);
if (marker(d2p(i,j)) >0)
bdEdge(k,:) = [i,marker(d2p(i,j))];
bdEdge(size(bdEdge,1)+1,:) = [marker(d2p(i,j)),j];
end
end
%--------------------------------------------------------------------------
% End of function UPDATEDBD
%--------------------------------------------------------------------------
|
github
|
zheng-da/incubator-mxnet-master
|
callmxnet.m
|
.m
|
incubator-mxnet-master/matlab/+mxnet/private/callmxnet.m
| 1,666 |
utf_8
|
23c3a6783ce55cb2598391d3aa27cf4e
|
% Licensed to the Apache Software Foundation (ASF) under one
% or more contributor license agreements. See the NOTICE file
% distributed with this work for additional information
% regarding copyright ownership. The ASF licenses this file
% to you under the Apache License, Version 2.0 (the
% "License"); you may not use this file except in compliance
% with the License. You may obtain a copy of the License at
%
% http://www.apache.org/licenses/LICENSE-2.0
%
% Unless required by applicable law or agreed to in writing,
% software distributed under the License is distributed on an
% "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY
% KIND, either express or implied. See the License for the
% specific language governing permissions and limitations
% under the License.
function callmxnet(func, varargin)
%CALLMXNET call mxnet functions
if ~libisloaded('libmxnet')
cur_pwd = pwd;
mxnet_root = [fileparts(mfilename('fullpath')), '/../../../'];
cd(mxnet_root);
mxnet_root = pwd;
cd(cur_pwd);
assert(exist([mxnet_root, '/lib/libmxnet.so' ], 'file') == 2 || ...
exist([mxnet_root, '/lib/libmxnet.dylib'], 'file') == 2 || ...
exist([mxnet_root, '/lib/libmxnet.dll' ], 'file') == 2, ...
'you need to build mxnet first');
assert(exist([mxnet_root, '/include/mxnet/c_predict_api.h']) == 2, ...
'failed to find c_predict_api.h')
addpath([mxnet_root, '/lib'])
addpath([mxnet_root, '/include/mxnet'])
[err, warn] = loadlibrary('libmxnet', 'c_predict_api.h');
assert(isempty(err));
if warn, warn, end
end
assert(ischar(func))
ret = calllib('libmxnet', func, varargin{:});
assert(ret == 0)
end
|
github
|
zheng-da/incubator-mxnet-master
|
parse_json.m
|
.m
|
incubator-mxnet-master/matlab/+mxnet/private/parse_json.m
| 19,881 |
utf_8
|
9cd6f452886def83ecf848d78f2e903a
|
% Licensed to the Apache Software Foundation (ASF) under one
% or more contributor license agreements. See the NOTICE file
% distributed with this work for additional information
% regarding copyright ownership. The ASF licenses this file
% to you under the Apache License, Version 2.0 (the
% "License"); you may not use this file except in compliance
% with the License. You may obtain a copy of the License at
%
% http://www.apache.org/licenses/LICENSE-2.0
%
% Unless required by applicable law or agreed to in writing,
% software distributed under the License is distributed on an
% "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY
% KIND, either express or implied. See the License for the
% specific language governing permissions and limitations
% under the License.
function data = parse_json(fname,varargin)
%PARSE_JSON parse a JSON (JavaScript Object Notation) file or string
%
% Based on jsonlab (https://github.com/fangq/jsonlab) created by Qianqian Fang. Jsonlab is lisonced under BSD or GPL v3.
global pos inStr len esc index_esc len_esc isoct arraytoken
if(regexp(fname,'^\s*(?:\[.+\])|(?:\{.+\})\s*$','once'))
string=fname;
elseif(exist(fname,'file'))
try
string = fileread(fname);
catch
try
string = urlread(['file://',fname]);
catch
string = urlread(['file://',fullfile(pwd,fname)]);
end
end
else
error('input file does not exist');
end
pos = 1; len = length(string); inStr = string;
isoct=exist('OCTAVE_VERSION','builtin');
arraytoken=find(inStr=='[' | inStr==']' | inStr=='"');
jstr=regexprep(inStr,'\\\\',' ');
escquote=regexp(jstr,'\\"');
arraytoken=sort([arraytoken escquote]);
% String delimiters and escape chars identified to improve speed:
esc = find(inStr=='"' | inStr=='\' ); % comparable to: regexp(inStr, '["\\]');
index_esc = 1; len_esc = length(esc);
opt=varargin2struct(varargin{:});
if(jsonopt('ShowProgress',0,opt)==1)
opt.progressbar_=waitbar(0,'loading ...');
end
jsoncount=1;
while pos <= len
switch(next_char)
case '{'
data{jsoncount} = parse_object(opt);
case '['
data{jsoncount} = parse_array(opt);
otherwise
error_pos('Outer level structure must be an object or an array');
end
jsoncount=jsoncount+1;
end % while
jsoncount=length(data);
if(jsoncount==1 && iscell(data))
data=data{1};
end
if(isfield(opt,'progressbar_'))
close(opt.progressbar_);
end
%%-------------------------------------------------------------------------
function object = parse_object(varargin)
parse_char('{');
object = [];
if next_char ~= '}'
while 1
str = parseStr(varargin{:});
if isempty(str)
error_pos('Name of value at position %d cannot be empty');
end
parse_char(':');
val = parse_value(varargin{:});
object.(valid_field(str))=val;
if next_char == '}'
break;
end
parse_char(',');
end
end
parse_char('}');
if(isstruct(object))
object=struct2jdata(object);
end
%%-------------------------------------------------------------------------
function object = parse_array(varargin) % JSON array is written in row-major order
global pos inStr isoct
parse_char('[');
object = cell(0, 1);
dim2=[];
arraydepth=jsonopt('JSONLAB_ArrayDepth_',1,varargin{:});
pbar=-1;
if(isfield(varargin{1},'progressbar_'))
pbar=varargin{1}.progressbar_;
end
if next_char ~= ']'
if(jsonopt('FastArrayParser',1,varargin{:})>=1 && arraydepth>=jsonopt('FastArrayParser',1,varargin{:}))
[endpos, e1l, e1r]=matching_bracket(inStr,pos);
arraystr=['[' inStr(pos:endpos)];
arraystr=regexprep(arraystr,'"_NaN_"','NaN');
arraystr=regexprep(arraystr,'"([-+]*)_Inf_"','$1Inf');
arraystr(arraystr==sprintf('\n'))=[];
arraystr(arraystr==sprintf('\r'))=[];
%arraystr=regexprep(arraystr,'\s*,',','); % this is slow,sometimes needed
if(~isempty(e1l) && ~isempty(e1r)) % the array is in 2D or higher D
astr=inStr((e1l+1):(e1r-1));
astr=regexprep(astr,'"_NaN_"','NaN');
astr=regexprep(astr,'"([-+]*)_Inf_"','$1Inf');
astr(astr==sprintf('\n'))=[];
astr(astr==sprintf('\r'))=[];
astr(astr==' ')='';
if(isempty(find(astr=='[', 1))) % array is 2D
dim2=length(sscanf(astr,'%f,',[1 inf]));
end
else % array is 1D
astr=arraystr(2:end-1);
astr(astr==' ')='';
[obj, count, errmsg, nextidx]=sscanf(astr,'%f,',[1,inf]);
if(nextidx>=length(astr)-1)
object=obj;
pos=endpos;
parse_char(']');
return;
end
end
if(~isempty(dim2))
astr=arraystr;
astr(astr=='[')='';
astr(astr==']')='';
astr(astr==' ')='';
[obj, count, errmsg, nextidx]=sscanf(astr,'%f,',inf);
if(nextidx>=length(astr)-1)
object=reshape(obj,dim2,numel(obj)/dim2)';
pos=endpos;
parse_char(']');
if(pbar>0)
waitbar(pos/length(inStr),pbar,'loading ...');
end
return;
end
end
arraystr=regexprep(arraystr,'\]\s*,','];');
else
arraystr='[';
end
try
if(isoct && regexp(arraystr,'"','once'))
error('Octave eval can produce empty cells for JSON-like input');
end
object=eval(arraystr);
pos=endpos;
catch
while 1
newopt=varargin2struct(varargin{:},'JSONLAB_ArrayDepth_',arraydepth+1);
val = parse_value(newopt);
object{end+1} = val;
if next_char == ']'
break;
end
parse_char(',');
end
end
end
if(jsonopt('SimplifyCell',0,varargin{:})==1)
try
oldobj=object;
object=cell2mat(object')';
if(iscell(oldobj) && isstruct(object) && numel(object)>1 && jsonopt('SimplifyCellArray',1,varargin{:})==0)
object=oldobj;
elseif(size(object,1)>1 && ismatrix(object))
object=object';
end
catch
end
end
parse_char(']');
if(pbar>0)
waitbar(pos/length(inStr),pbar,'loading ...');
end
%%-------------------------------------------------------------------------
function parse_char(c)
global pos inStr len
pos=skip_whitespace(pos,inStr,len);
if pos > len || inStr(pos) ~= c
error_pos(sprintf('Expected %c at position %%d', c));
else
pos = pos + 1;
pos=skip_whitespace(pos,inStr,len);
end
%%-------------------------------------------------------------------------
function c = next_char
global pos inStr len
pos=skip_whitespace(pos,inStr,len);
if pos > len
c = [];
else
c = inStr(pos);
end
%%-------------------------------------------------------------------------
function newpos=skip_whitespace(pos,inStr,len)
newpos=pos;
while newpos <= len && isspace(inStr(newpos))
newpos = newpos + 1;
end
%%-------------------------------------------------------------------------
function str = parseStr(varargin)
global pos inStr len esc index_esc len_esc
% len, ns = length(inStr), keyboard
if inStr(pos) ~= '"'
error_pos('String starting with " expected at position %d');
else
pos = pos + 1;
end
str = '';
while pos <= len
while index_esc <= len_esc && esc(index_esc) < pos
index_esc = index_esc + 1;
end
if index_esc > len_esc
str = [str inStr(pos:len)];
pos = len + 1;
break;
else
str = [str inStr(pos:esc(index_esc)-1)];
pos = esc(index_esc);
end
nstr = length(str);
switch inStr(pos)
case '"'
pos = pos + 1;
if(~isempty(str))
if(strcmp(str,'_Inf_'))
str=Inf;
elseif(strcmp(str,'-_Inf_'))
str=-Inf;
elseif(strcmp(str,'_NaN_'))
str=NaN;
end
end
return;
case '\'
if pos+1 > len
error_pos('End of file reached right after escape character');
end
pos = pos + 1;
switch inStr(pos)
case {'"' '\' '/'}
str(nstr+1) = inStr(pos);
pos = pos + 1;
case {'b' 'f' 'n' 'r' 't'}
str(nstr+1) = sprintf(['\' inStr(pos)]);
pos = pos + 1;
case 'u'
if pos+4 > len
error_pos('End of file reached in escaped unicode character');
end
str(nstr+(1:6)) = inStr(pos-1:pos+4);
pos = pos + 5;
end
otherwise % should never happen
str(nstr+1) = inStr(pos);
keyboard;
pos = pos + 1;
end
end
error_pos('End of file while expecting end of inStr');
%%-------------------------------------------------------------------------
function num = parse_number(varargin)
global pos inStr isoct
currstr=inStr(pos:min(pos+30,end));
if(isoct~=0)
numstr=regexp(currstr,'^\s*-?(?:0|[1-9]\d*)(?:\.\d+)?(?:[eE][+\-]?\d+)?','end');
[num] = sscanf(currstr, '%f', 1);
delta=numstr+1;
else
[num, one, err, delta] = sscanf(currstr, '%f', 1);
if ~isempty(err)
error_pos('Error reading number at position %d');
end
end
pos = pos + delta-1;
%%-------------------------------------------------------------------------
function val = parse_value(varargin)
global pos inStr len
if(isfield(varargin{1},'progressbar_'))
waitbar(pos/len,varargin{1}.progressbar_,'loading ...');
end
switch(inStr(pos))
case '"'
val = parseStr(varargin{:});
return;
case '['
val = parse_array(varargin{:});
return;
case '{'
val = parse_object(varargin{:});
return;
case {'-','0','1','2','3','4','5','6','7','8','9'}
val = parse_number(varargin{:});
return;
case 't'
if pos+3 <= len && strcmpi(inStr(pos:pos+3), 'true')
val = true;
pos = pos + 4;
return;
end
case 'f'
if pos+4 <= len && strcmpi(inStr(pos:pos+4), 'false')
val = false;
pos = pos + 5;
return;
end
case 'n'
if pos+3 <= len && strcmpi(inStr(pos:pos+3), 'null')
val = [];
pos = pos + 4;
return;
end
end
error_pos('Value expected at position %d');
%%-------------------------------------------------------------------------
function error_pos(msg)
global pos inStr len
poShow = max(min([pos-15 pos-1 pos pos+20],len),1);
if poShow(3) == poShow(2)
poShow(3:4) = poShow(2)+[0 -1]; % display nothing after
end
msg = [sprintf(msg, pos) ': ' ...
inStr(poShow(1):poShow(2)) '<error>' inStr(poShow(3):poShow(4)) ];
error( ['JSONparser:invalidFormat: ' msg] );
%%-------------------------------------------------------------------------
function str = valid_field(str)
global isoct
% From MATLAB doc: field names must begin with a letter, which may be
% followed by any combination of letters, digits, and underscores.
% Invalid characters will be converted to underscores, and the prefix
% "x0x[Hex code]_" will be added if the first character is not a letter.
pos=regexp(str,'^[^A-Za-z]','once');
if(~isempty(pos))
if(~isoct)
str=regexprep(str,'^([^A-Za-z])','x0x${sprintf(''%X'',unicode2native($1))}_','once');
else
str=sprintf('x0x%X_%s',char(str(1)),str(2:end));
end
end
if(isempty(regexp(str,'[^0-9A-Za-z_]', 'once' )))
return;
end
if(~isoct)
str=regexprep(str,'([^0-9A-Za-z_])','_0x${sprintf(''%X'',unicode2native($1))}_');
else
pos=regexp(str,'[^0-9A-Za-z_]');
if(isempty(pos))
return;
end
str0=str;
pos0=[0 pos(:)' length(str)];
str='';
for i=1:length(pos)
str=[str str0(pos0(i)+1:pos(i)-1) sprintf('_0x%X_',str0(pos(i)))];
end
if(pos(end)~=length(str))
str=[str str0(pos0(end-1)+1:pos0(end))];
end
end
%str(~isletter(str) & ~('0' <= str & str <= '9')) = '_';
%%-------------------------------------------------------------------------
function endpos = matching_quote(str,pos)
len=length(str);
while(pos<len)
if(str(pos)=='"')
if(~(pos>1 && str(pos-1)=='\'))
endpos=pos;
return;
end
end
pos=pos+1;
end
error('unmatched quotation mark');
%%-------------------------------------------------------------------------
function [endpos, e1l, e1r, maxlevel] = matching_bracket(str,pos)
global arraytoken
level=1;
maxlevel=level;
endpos=0;
bpos=arraytoken(arraytoken>=pos);
tokens=str(bpos);
len=length(tokens);
pos=1;
e1l=[];
e1r=[];
while(pos<=len)
c=tokens(pos);
if(c==']')
level=level-1;
if(isempty(e1r))
e1r=bpos(pos);
end
if(level==0)
endpos=bpos(pos);
return
end
end
if(c=='[')
if(isempty(e1l))
e1l=bpos(pos);
end
level=level+1;
maxlevel=max(maxlevel,level);
end
if(c=='"')
pos=matching_quote(tokens,pos+1);
end
pos=pos+1;
end
if(endpos==0)
error('unmatched "]"');
end
function opt=varargin2struct(varargin)
%
% opt=varargin2struct('param1',value1,'param2',value2,...)
% or
% opt=varargin2struct(...,optstruct,...)
%
% convert a series of input parameters into a structure
%
% input:
% 'param', value: the input parameters should be pairs of a string and a value
% optstruct: if a parameter is a struct, the fields will be merged to the output struct
%
% output:
% opt: a struct where opt.param1=value1, opt.param2=value2 ...
%
len=length(varargin);
opt=struct;
if(len==0) return; end
i=1;
while(i<=len)
if(isstruct(varargin{i}))
opt=mergestruct(opt,varargin{i});
elseif(ischar(varargin{i}) && i<len)
opt=setfield(opt,lower(varargin{i}),varargin{i+1});
i=i+1;
else
error('input must be in the form of ...,''name'',value,... pairs or structs');
end
i=i+1;
end
function val=jsonopt(key,default,varargin)
%
% val=jsonopt(key,default,optstruct)
%
% setting options based on a struct. The struct can be produced
% by varargin2struct from a list of 'param','value' pairs
%
% authors:Qianqian Fang (fangq<at> nmr.mgh.harvard.edu)
%
% $Id: loadjson.m 371 2012-06-20 12:43:06Z fangq $
%
% input:
% key: a string with which one look up a value from a struct
% default: if the key does not exist, return default
% optstruct: a struct where each sub-field is a key
%
% output:
% val: if key exists, val=optstruct.key; otherwise val=default
%
val=default;
if(nargin<=2) return; end
opt=varargin{1};
if(isstruct(opt))
if(isfield(opt,key))
val=getfield(opt,key);
elseif(isfield(opt,lower(key)))
val=getfield(opt,lower(key));
end
end
function s=mergestruct(s1,s2)
%
% s=mergestruct(s1,s2)
%
% merge two struct objects into one
%
% authors:Qianqian Fang (fangq<at> nmr.mgh.harvard.edu)
% date: 2012/12/22
%
% input:
% s1,s2: a struct object, s1 and s2 can not be arrays
%
% output:
% s: the merged struct object. fields in s1 and s2 will be combined in s.
if(~isstruct(s1) || ~isstruct(s2))
error('input parameters contain non-struct');
end
if(length(s1)>1 || length(s2)>1)
error('can not merge struct arrays');
end
fn=fieldnames(s2);
s=s1;
for i=1:length(fn)
s=setfield(s,fn{i},getfield(s2,fn{i}));
end
function newdata=struct2jdata(data,varargin)
%
% newdata=struct2jdata(data,opt,...)
%
% convert a JData object (in the form of a struct array) into an array
%
% authors:Qianqian Fang (fangq<at> nmr.mgh.harvard.edu)
%
% input:
% data: a struct array. If data contains JData keywords in the first
% level children, these fields are parsed and regrouped into a
% data object (arrays, trees, graphs etc) based on JData
% specification. The JData keywords are
% "_ArrayType_", "_ArraySize_", "_ArrayData_"
% "_ArrayIsSparse_", "_ArrayIsComplex_"
% opt: (optional) a list of 'Param',value pairs for additional options
% The supported options include
% 'Recursive', if set to 1, will apply the conversion to
% every child; 0 to disable
%
% output:
% newdata: the covnerted data if the input data does contain a JData
% structure; otherwise, the same as the input.
%
% examples:
% obj=struct('_ArrayType_','double','_ArraySize_',[2 3],
% '_ArrayIsSparse_',1 ,'_ArrayData_',null);
% ubjdata=struct2jdata(obj);
fn=fieldnames(data);
newdata=data;
len=length(data);
if(jsonopt('Recursive',0,varargin{:})==1)
for i=1:length(fn) % depth-first
for j=1:len
if(isstruct(getfield(data(j),fn{i})))
newdata(j)=setfield(newdata(j),fn{i},jstruct2array(getfield(data(j),fn{i})));
end
end
end
end
if(~isempty(strmatch('x0x5F_ArrayType_',fn)) && ~isempty(strmatch('x0x5F_ArrayData_',fn)))
newdata=cell(len,1);
for j=1:len
ndata=cast(data(j).x0x5F_ArrayData_,data(j).x0x5F_ArrayType_);
iscpx=0;
if(~isempty(strmatch('x0x5F_ArrayIsComplex_',fn)))
if(data(j).x0x5F_ArrayIsComplex_)
iscpx=1;
end
end
if(~isempty(strmatch('x0x5F_ArrayIsSparse_',fn)))
if(data(j).x0x5F_ArrayIsSparse_)
if(~isempty(strmatch('x0x5F_ArraySize_',fn)))
dim=double(data(j).x0x5F_ArraySize_);
if(iscpx && size(ndata,2)==4-any(dim==1))
ndata(:,end-1)=complex(ndata(:,end-1),ndata(:,end));
end
if isempty(ndata)
% All-zeros sparse
ndata=sparse(dim(1),prod(dim(2:end)));
elseif dim(1)==1
% Sparse row vector
ndata=sparse(1,ndata(:,1),ndata(:,2),dim(1),prod(dim(2:end)));
elseif dim(2)==1
% Sparse column vector
ndata=sparse(ndata(:,1),1,ndata(:,2),dim(1),prod(dim(2:end)));
else
% Generic sparse array.
ndata=sparse(ndata(:,1),ndata(:,2),ndata(:,3),dim(1),prod(dim(2:end)));
end
else
if(iscpx && size(ndata,2)==4)
ndata(:,3)=complex(ndata(:,3),ndata(:,4));
end
ndata=sparse(ndata(:,1),ndata(:,2),ndata(:,3));
end
end
elseif(~isempty(strmatch('x0x5F_ArraySize_',fn)))
if(iscpx && size(ndata,2)==2)
ndata=complex(ndata(:,1),ndata(:,2));
end
ndata=reshape(ndata(:),data(j).x0x5F_ArraySize_);
end
newdata{j}=ndata;
end
if(len==1)
newdata=newdata{1};
end
end
|
github
|
vladostan/pulse-master
|
pcamat.m
|
.m
|
pulse-master/ComponentAnalysis/FastICA/pcamat.m
| 12,075 |
utf_8
|
bcb1117d4132558d0d54d8b7b616a902
|
function [E, D] = pcamat(vectors, firstEig, lastEig, s_interactive, ...
s_verbose);
%PCAMAT - Calculates the pca for data
%
% [E, D] = pcamat(vectors, firstEig, lastEig, ...
% interactive, verbose);
%
% Calculates the PCA matrices for given data (row) vectors. Returns
% the eigenvector (E) and diagonal eigenvalue (D) matrices containing the
% selected subspaces. Dimensionality reduction is controlled with
% the parameters 'firstEig' and 'lastEig' - but it can also be done
% interactively by setting parameter 'interactive' to 'on' or 'gui'.
%
% ARGUMENTS
%
% vectors Data in row vectors.
% firstEig Index of the largest eigenvalue to keep.
% Default is 1.
% lastEig Index of the smallest eigenvalue to keep.
% Default is equal to dimension of vectors.
% interactive Specify eigenvalues to keep interactively. Note that if
% you set 'interactive' to 'on' or 'gui' then the values
% for 'firstEig' and 'lastEig' will be ignored, but they
% still have to be entered. If the value is 'gui' then the
% same graphical user interface as in FASTICAG will be
% used. Default is 'off'.
% verbose Default is 'on'.
%
%
% EXAMPLE
% [E, D] = pcamat(vectors);
%
% Note
% The eigenvalues and eigenvectors returned by PCAMAT are not sorted.
%
% This function is needed by FASTICA and FASTICAG
% For historical reasons this version does not sort the eigenvalues or
% the eigen vectors in any ways. Therefore neither does the FASTICA or
% FASTICAG. Generally it seams that the components returned from
% whitening is almost in reversed order. (That means, they usually are,
% but sometime they are not - depends on the EIG-command of matlab.)
% @(#)$Id: pcamat.m,v 1.5 2003/12/15 18:24:32 jarmo Exp $
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
% Default values:
if nargin < 5, s_verbose = 'on'; end
if nargin < 4, s_interactive = 'off'; end
if nargin < 3, lastEig = size(vectors, 1); end
if nargin < 2, firstEig = 1; end
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
% Check the optional parameters;
switch lower(s_verbose)
case 'on'
b_verbose = 1;
case 'off'
b_verbose = 0;
otherwise
error(sprintf('Illegal value [ %s ] for parameter: ''verbose''\n', s_verbose));
end
switch lower(s_interactive)
case 'on'
b_interactive = 1;
case 'off'
b_interactive = 0;
case 'gui'
b_interactive = 2;
otherwise
error(sprintf('Illegal value [ %s ] for parameter: ''interactive''\n', ...
s_interactive));
end
oldDimension = size (vectors, 1);
if ~(b_interactive)
if lastEig < 1 | lastEig > oldDimension
error(sprintf('Illegal value [ %d ] for parameter: ''lastEig''\n', lastEig));
end
if firstEig < 1 | firstEig > lastEig
error(sprintf('Illegal value [ %d ] for parameter: ''firstEig''\n', firstEig));
end
end
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
% Calculate PCA
% Calculate the covariance matrix.
if b_verbose, fprintf ('Calculating covariance...\n'); end
covarianceMatrix = cov(vectors', 1);
% Calculate the eigenvalues and eigenvectors of covariance
% matrix.
[E, D] = eig (covarianceMatrix);
% The rank is determined from the eigenvalues - and not directly by
% using the function rank - because function rank uses svd, which
% in some cases gives a higher dimensionality than what can be used
% with eig later on (eig then gives negative eigenvalues).
rankTolerance = 1e-7;
maxLastEig = sum (diag (D) > rankTolerance);
if maxLastEig == 0,
fprintf (['Eigenvalues of the covariance matrix are' ...
' all smaller than tolerance [ %g ].\n' ...
'Please make sure that your data matrix contains' ...
' nonzero values.\nIf the values are very small,' ...
' try rescaling the data matrix.\n'], rankTolerance);
error ('Unable to continue, aborting.');
end
% Sort the eigenvalues - decending.
eigenvalues = flipud(sort(diag(D)));
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
% Interactive part - command-line
if b_interactive == 1
% Show the eigenvalues to the user
hndl_win=figure;
bar(eigenvalues);
title('Eigenvalues');
% ask the range from the user...
% ... and keep on asking until the range is valid :-)
areValuesOK=0;
while areValuesOK == 0
firstEig = input('The index of the largest eigenvalue to keep? (1) ');
lastEig = input(['The index of the smallest eigenvalue to keep? (' ...
int2str(oldDimension) ') ']);
% Check the new values...
% if they are empty then use default values
if isempty(firstEig), firstEig = 1;end
if isempty(lastEig), lastEig = oldDimension;end
% Check that the entered values are within the range
areValuesOK = 1;
if lastEig < 1 | lastEig > oldDimension
fprintf('Illegal number for the last eigenvalue.\n');
areValuesOK = 0;
end
if firstEig < 1 | firstEig > lastEig
fprintf('Illegal number for the first eigenvalue.\n');
areValuesOK = 0;
end
end
% close the window
close(hndl_win);
end
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
% Interactive part - GUI
if b_interactive == 2
% Show the eigenvalues to the user
hndl_win = figure('Color',[0.8 0.8 0.8], ...
'PaperType','a4letter', ...
'Units', 'normalized', ...
'Name', 'FastICA: Reduce dimension', ...
'NumberTitle','off', ...
'Tag', 'f_eig');
h_frame = uicontrol('Parent', hndl_win, ...
'BackgroundColor',[0.701961 0.701961 0.701961], ...
'Units', 'normalized', ...
'Position',[0.13 0.05 0.775 0.17], ...
'Style','frame', ...
'Tag','f_frame');
b = uicontrol('Parent',hndl_win, ...
'Units','normalized', ...
'BackgroundColor',[0.701961 0.701961 0.701961], ...
'HorizontalAlignment','left', ...
'Position',[0.142415 0.0949436 0.712077 0.108507], ...
'String','Give the indices of the largest and smallest eigenvalues of the covariance matrix to be included in the reduced data.', ...
'Style','text', ...
'Tag','StaticText1');
e_first = uicontrol('Parent',hndl_win, ...
'Units','normalized', ...
'Callback',[ ...
'f=round(str2num(get(gcbo, ''String'')));' ...
'if (f < 1), f=1; end;' ...
'l=str2num(get(findobj(''Tag'',''e_last''), ''String''));' ...
'if (f > l), f=l; end;' ...
'set(gcbo, ''String'', int2str(f));' ...
], ...
'BackgroundColor',[1 1 1], ...
'HorizontalAlignment','right', ...
'Position',[0.284831 0.0678168 0.12207 0.0542535], ...
'Style','edit', ...
'String', '1', ...
'Tag','e_first');
b = uicontrol('Parent',hndl_win, ...
'Units','normalized', ...
'BackgroundColor',[0.701961 0.701961 0.701961], ...
'HorizontalAlignment','left', ...
'Position',[0.142415 0.0678168 0.12207 0.0542535], ...
'String','Range from', ...
'Style','text', ...
'Tag','StaticText2');
e_last = uicontrol('Parent',hndl_win, ...
'Units','normalized', ...
'Callback',[ ...
'l=round(str2num(get(gcbo, ''String'')));' ...
'lmax = get(gcbo, ''UserData'');' ...
'if (l > lmax), l=lmax; fprintf([''The selected value was too large, or the selected eigenvalues were close to zero\n'']); end;' ...
'f=str2num(get(findobj(''Tag'',''e_first''), ''String''));' ...
'if (l < f), l=f; end;' ...
'set(gcbo, ''String'', int2str(l));' ...
], ...
'BackgroundColor',[1 1 1], ...
'HorizontalAlignment','right', ...
'Position',[0.467936 0.0678168 0.12207 0.0542535], ...
'Style','edit', ...
'String', int2str(maxLastEig), ...
'UserData', maxLastEig, ...
'Tag','e_last');
% in the first version oldDimension was used instead of
% maxLastEig, but since the program would automatically
% drop the eigenvalues afte maxLastEig...
b = uicontrol('Parent',hndl_win, ...
'Units','normalized', ...
'BackgroundColor',[0.701961 0.701961 0.701961], ...
'HorizontalAlignment','left', ...
'Position',[0.427246 0.0678168 0.0406901 0.0542535], ...
'String','to', ...
'Style','text', ...
'Tag','StaticText3');
b = uicontrol('Parent',hndl_win, ...
'Units','normalized', ...
'Callback','uiresume(gcbf)', ...
'Position',[0.630697 0.0678168 0.12207 0.0542535], ...
'String','OK', ...
'Tag','Pushbutton1');
b = uicontrol('Parent',hndl_win, ...
'Units','normalized', ...
'Callback',[ ...
'gui_help(''pcamat'');' ...
], ...
'Position',[0.767008 0.0678168 0.12207 0.0542535], ...
'String','Help', ...
'Tag','Pushbutton2');
h_axes = axes('Position' ,[0.13 0.3 0.775 0.6]);
set(hndl_win, 'currentaxes',h_axes);
bar(eigenvalues);
title('Eigenvalues');
uiwait(hndl_win);
firstEig = str2num(get(e_first, 'String'));
lastEig = str2num(get(e_last, 'String'));
% close the window
close(hndl_win);
end
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
% See if the user has reduced the dimension enought
if lastEig > maxLastEig
lastEig = maxLastEig;
if b_verbose
fprintf('Dimension reduced to %d due to the singularity of covariance matrix\n',...
lastEig-firstEig+1);
end
else
% Reduce the dimensionality of the problem.
if b_verbose
if oldDimension == (lastEig - firstEig + 1)
fprintf ('Dimension not reduced.\n');
else
fprintf ('Reducing dimension...\n');
end
end
end
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
% Drop the smaller eigenvalues
if lastEig < oldDimension
lowerLimitValue = (eigenvalues(lastEig) + eigenvalues(lastEig + 1)) / 2;
else
lowerLimitValue = eigenvalues(oldDimension) - 1;
end
lowerColumns = diag(D) > lowerLimitValue;
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
% Drop the larger eigenvalues
if firstEig > 1
higherLimitValue = (eigenvalues(firstEig - 1) + eigenvalues(firstEig)) / 2;
else
higherLimitValue = eigenvalues(1) + 1;
end
higherColumns = diag(D) < higherLimitValue;
% Combine the results from above
selectedColumns = lowerColumns & higherColumns;
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
% print some info for the user
if b_verbose
fprintf ('Selected [ %d ] dimensions.\n', sum (selectedColumns));
end
if sum (selectedColumns) ~= (lastEig - firstEig + 1),
error ('Selected a wrong number of dimensions.');
end
if b_verbose
fprintf ('Smallest remaining (non-zero) eigenvalue [ %g ]\n', eigenvalues(lastEig));
fprintf ('Largest remaining (non-zero) eigenvalue [ %g ]\n', eigenvalues(firstEig));
fprintf ('Sum of removed eigenvalues [ %g ]\n', sum(diag(D) .* ...
(~selectedColumns)));
end
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
% Select the colums which correspond to the desired range
% of eigenvalues.
E = selcol(E, selectedColumns);
D = selcol(selcol(D, selectedColumns)', selectedColumns);
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
% Some more information
if b_verbose
sumAll=sum(eigenvalues);
sumUsed=sum(diag(D));
retained = (sumUsed / sumAll) * 100;
fprintf('[ %g ] %% of (non-zero) eigenvalues retained.\n', retained);
end
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
function newMatrix = selcol(oldMatrix, maskVector);
% newMatrix = selcol(oldMatrix, maskVector);
%
% Selects the columns of the matrix that marked by one in the given vector.
% The maskVector is a column vector.
% 15.3.1998
if size(maskVector, 1) ~= size(oldMatrix, 2),
error ('The mask vector and matrix are of uncompatible size.');
end
numTaken = 0;
for i = 1 : size (maskVector, 1),
if maskVector(i, 1) == 1,
takingMask(1, numTaken + 1) = i;
numTaken = numTaken + 1;
end
end
newMatrix = oldMatrix(:, takingMask);
|
github
|
vladostan/pulse-master
|
icaplot.m
|
.m
|
pulse-master/ComponentAnalysis/FastICA/icaplot.m
| 13,259 |
utf_8
|
dde3e6d852f657a3c1eaacbd03f5dcc7
|
function icaplot(mode, varargin);
%ICAPLOT - plot signals in various ways
%
% ICAPLOT is mainly for plottinf and comparing the mixed signals and
% separated ica-signals.
%
% ICAPLOT has many different modes. The first parameter of the function
% defines the mode. Other parameters and their order depends on the
% mode. The explanation for the more common parameters is in the end.
%
% Classic
% icaplot('classic', s1, n1, range, xrange, titlestr)
%
% Plots the signals in the same manner as the FASTICA and FASTICAG
% programs do. All the signals are plotted in their own axis.
%
% Complot
% icaplot('complot', s1, n1, range, xrange, titlestr)
%
% The signals are plotted on the same axis. This is good for
% visualization of the shape of the signals. The scale of the signals
% has been altered so that they all fit nicely.
%
% Histogram
% icaplot('histogram', s1, n1, range, bins, style)
%
% The histogram of the signals is plotted. The number of bins can be
% specified with 'bins'-parameter. The style for the histograms can
% be either 'bar' (default) of 'line'.
%
% Scatter
% icaplot('scatter', s1, n1, s2, n2, range, titlestr, s1label,
% s2label, markerstr)
%
% A scatterplot is plotted so that the signal 1 is the 'X'-variable
% and the signal 2 is the 'Y'-variable. The 'markerstr' can be used
% to specify the maker used in the plot. The format for 'markerstr'
% is the same as for Matlab's PLOT.
%
% Compare
% icaplot('compare', s1, n1, s2, n2, range, xrange, titlestr,
% s1label, s2label)
%
% This for for comparing two signals. The main used in this context
% would probably be to see how well the separated ICA-signals explain
% the observed mixed signals. The s2 signals are first scaled with
% REGRESS function.
%
% Compare - Sum
% icaplot('sum', s1, n1, s2, n2, range, xrange, titlestr, s1label,
% s2label)
%
% The same as Compare, but this time the signals in s2 (specified by
% n2) are summed together.
%
% Compare - Sumerror
% icaplot('sumerror', s1, n1, s2, n2, range, xrange, titlestr,
% s1label, s2label)
%
% The same as Compare - Sum, but also the 'error' between the signal
% 1 and the summed IC's is plotted.
%
%
% More common parameters
% The signals to be plotted are in matrices s1 and s2. The n1 and n2
% are used to tell the index of the signal or signals to be plotted
% from s1 or s2. If n1 or n2 has a value of 0, then all the signals
% from corresponding matrix will be plotted. The values for n1 and n2
% can also be vectors (like: [1 3 4]) In some casee if there are more
% than 1 signal to be plotted from s1 or s2 then the plot will
% contain as many subplots as are needed.
%
% The range of the signals to be plotted can be limited with
% 'range'-parameter. It's value is a vector ( 10000:15000 ). If range
% is 0, then the whole range will be plotted.
%
% The 'xrange' is used to specify only the labels used on the
% x-axis. The value of 'xrange' is a vector containing the x-values
% for the plots or [start end] for begin and end of the range
% ( 10000:15000 or [10 15] ). If xrange is 0, then value of range
% will be used for x-labels.
%
% You can give a title for the plot with 'titlestr'. Also the
% 's1label' and 's2label' are used to give more meaningfull label for
% the signals.
%
% Lastly, you can omit some of the arguments from the and. You will
% have to give values for the signal matrices (s1, s2) and the
% indexes (n1, n2)
% @(#)$Id: icaplot.m,v 1.2 2003/04/05 14:23:58 jarmo Exp $
switch mode
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
% 'dispsig' is to replace the old DISPSIG
% '' & 'classic' are just another names - '' quite short one :-)
case {'', 'classic', 'dispsig'}
% icaplot(mode, s1, n1, range, xrange, titlestr)
if length(varargin) < 1, error('Not enough arguments.'); end
if length(varargin) < 5, titlestr = '';else titlestr = varargin{5}; end
if length(varargin) < 4, xrange = 0;else xrange = varargin{4}; end
if length(varargin) < 3, range = 0;else range = varargin{3}; end
if length(varargin) < 2, n1 = 0;else n1 = varargin{2}; end
s1 = varargin{1};
range=chkrange(range, s1);
xrange=chkxrange(xrange, range);
n1=chkn(n1, s1);
clf;
numSignals = size(n1, 2);
for i = 1:numSignals,
subplot(numSignals, 1, i);
plot(xrange, s1(n1(i), range));
end
subplot(numSignals,1, 1);
if (~isempty(titlestr))
title(titlestr);
end
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
case 'complot'
% icaplot(mode, s1, n1, range, xrange, titlestr)
if length(varargin) < 1, error('Not enough arguments.'); end
if length(varargin) < 5, titlestr = '';else titlestr = varargin{5}; end
if length(varargin) < 4, xrange = 0;else xrange = varargin{4}; end
if length(varargin) < 3, range = 0;else range = varargin{3}; end
if length(varargin) < 2, n1 = 0;else n1 = varargin{2}; end
s1 = remmean(varargin{1});
range=chkrange(range, s1);
xrange=chkxrange(xrange, range);
n1=chkn(n1, s1);
for i = 1:size(n1, 2)
S1(i, :) = s1(n1(i), range);
end
alpha = mean(max(S1')-min(S1'));
for i = 1:size(n1,2)
S2(i,:) = S1(i,:) - alpha*(i-1)*ones(size(S1(1,:)));
end
plot(xrange, S2');
axis([min(xrange) max(xrange) min(min(S2)) max(max(S2)) ]);
set(gca,'YTick',(-size(S1,1)+1)*alpha:alpha:0);
set(gca,'YTicklabel',fliplr(n1));
if (~isempty(titlestr))
title(titlestr);
end
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
case 'histogram'
% icaplot(mode, s1, n1, range, bins, style)
if length(varargin) < 1, error('Not enough arguments.'); end
if length(varargin) < 5, style = 'bar';else style = varargin{5}; end
if length(varargin) < 4, bins = 10;else bins = varargin{4}; end
if length(varargin) < 3, range = 0;else range = varargin{3}; end
if length(varargin) < 2, n1 = 0;else n1 = varargin{2}; end
s1 = varargin{1};
range = chkrange(range, s1);
n1 = chkn(n1, s1);
numSignals = size(n1, 2);
rows = floor(sqrt(numSignals));
columns = ceil(sqrt(numSignals));
while (rows * columns < numSignals)
columns = columns + 1;
end
switch style
case {'', 'bar'}
for i = 1:numSignals,
subplot(rows, columns, i);
hist(s1(n1(i), range), bins);
title(int2str(n1(i)));
drawnow;
end
case 'line'
for i = 1:numSignals,
subplot(rows, columns, i);
[Y, X]=hist(s1(n1(i), range), bins);
plot(X, Y);
title(int2str(n1(i)));
drawnow;
end
otherwise
fprintf('Unknown style.\n')
end
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
case 'scatter'
% icaplot(mode, s1, n1, s2, n2, range, titlestr, xlabelstr, ylabelstr, markerstr)
if length(varargin) < 4, error('Not enough arguments.'); end
if length(varargin) < 9, markerstr = '.';else markerstr = varargin{9}; end
if length(varargin) < 8, ylabelstr = 'Signal 2';else ylabelstr = varargin{8}; end
if length(varargin) < 7, xlabelstr = 'Signal 1';else xlabelstr = varargin{7}; end
if length(varargin) < 6, titlestr = '';else titlestr = varargin{6}; end
if length(varargin) < 5, range = 0;else range = varargin{5}; end
n2 = varargin{4};
s2 = varargin{3};
n1 = varargin{2};
s1 = varargin{1};
range = chkrange(range, s1);
n1 = chkn(n1, s1);
n2 = chkn(n2, s2);
rows = size(n1, 2);
columns = size(n2, 2);
for r = 1:rows
for c = 1:columns
subplot(rows, columns, (r-1)*columns + c);
plot(s1(n1(r), range),s2(n2(c), range),markerstr);
if (~isempty(titlestr))
title(titlestr);
end
if (rows*columns == 1)
xlabel(xlabelstr);
ylabel(ylabelstr);
else
xlabel([xlabelstr ' (' int2str(n1(r)) ')']);
ylabel([ylabelstr ' (' int2str(n2(c)) ')']);
end
drawnow;
end
end
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
case {'compare', 'sum', 'sumerror'}
% icaplot(mode, s1, n1, s2, n2, range, xrange, titlestr, s1label, s2label)
if length(varargin) < 4, error('Not enough arguments.'); end
if length(varargin) < 9, s2label = 'IC';else s2label = varargin{9}; end
if length(varargin) < 8, s1label = 'Mix';else s1label = varargin{8}; end
if length(varargin) < 7, titlestr = '';else titlestr = varargin{7}; end
if length(varargin) < 6, xrange = 0;else xrange = varargin{6}; end
if length(varargin) < 5, range = 0;else range = varargin{5}; end
s1 = varargin{1};
n1 = varargin{2};
s2 = varargin{3};
n2 = varargin{4};
range = chkrange(range, s1);
xrange = chkxrange(xrange, range);
n1 = chkn(n1, s1);
n2 = chkn(n2, s2);
numSignals = size(n1, 2);
if (numSignals > 1)
externalLegend = 1;
else
externalLegend = 0;
end
rows = floor(sqrt(numSignals+externalLegend));
columns = ceil(sqrt(numSignals+externalLegend));
while (rows * columns < (numSignals+externalLegend))
columns = columns + 1;
end
clf;
for j = 1:numSignals
subplot(rows, columns, j);
switch mode
case 'compare'
plotcompare(s1, n1(j), s2,n2, range, xrange);
[legendtext,legendstyle]=legendcompare(n1(j),n2,s1label,s2label,externalLegend);
case 'sum'
plotsum(s1, n1(j), s2,n2, range, xrange);
[legendtext,legendstyle]=legendsum(n1(j),n2,s1label,s2label,externalLegend);
case 'sumerror'
plotsumerror(s1, n1(j), s2,n2, range, xrange);
[legendtext,legendstyle]=legendsumerror(n1(j),n2,s1label,s2label,externalLegend);
end
if externalLegend
title([titlestr ' (' s1label ' ' int2str(n1(j)) ')']);
else
legend(char(legendtext));
if (~isempty(titlestr))
title(titlestr);
end
end
end
if (externalLegend)
subplot(rows, columns, numSignals+1);
legendsize = size(legendtext, 2);
hold on;
for i=1:legendsize
plot([0 1],[legendsize-i legendsize-i], char(legendstyle(i)));
text(1.5, legendsize-i, char(legendtext(i)));
end
hold off;
axis([0 6 -1 legendsize]);
axis off;
end
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
end
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
function plotcompare(s1, n1, s2, n2, range, xrange);
style=getStyles;
K = regress(s1(n1,:)',s2');
plot(xrange, s1(n1,range), char(style(1)));
hold on
for i=1:size(n2,2)
plotstyle=char(style(i+1));
plot(xrange, K(n2(i))*s2(n2(i),range), plotstyle);
end
hold off
function [legendText, legendStyle]=legendcompare(n1, n2, s1l, s2l, externalLegend);
style=getStyles;
if (externalLegend)
legendText(1)={[s1l ' (see the titles)']};
else
legendText(1)={[s1l ' ', int2str(n1)]};
end
legendStyle(1)=style(1);
for i=1:size(n2, 2)
legendText(i+1) = {[s2l ' ' int2str(n2(i))]};
legendStyle(i+1) = style(i+1);
end
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
function plotsum(s1, n1, s2, n2, range, xrange);
K = diag(regress(s1(n1,:)',s2'));
sigsum = sum(K(:,n2)*s2(n2,:));
plot(xrange, s1(n1, range),'k-', ...
xrange, sigsum(range), 'b-');
function [legendText, legendStyle]=legendsum(n1, n2, s1l, s2l, externalLegend);
if (externalLegend)
legendText(1)={[s1l ' (see the titles)']};
else
legendText(1)={[s1l ' ', int2str(n1)]};
end
legendText(2)={['Sum of ' s2l ': ', int2str(n2)]};
legendStyle={'k-';'b-'};
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
function plotsumerror(s1, n1, s2, n2, range, xrange);
K = diag(regress(s1(n1,:)',s2'));
sigsum = sum(K(:,n2)*s2(n2,:));
plot(xrange, s1(n1, range),'k-', ...
xrange, sigsum(range), 'b-', ...
xrange, s1(n1, range)-sigsum(range), 'r-');
function [legendText, legendStyle]=legendsumerror(n1, n2, s1l, s2l, externalLegend);
if (externalLegend)
legendText(1)={[s1l ' (see the titles)']};
else
legendText(1)={[s1l ' ', int2str(n1)]};
end
legendText(2)={['Sum of ' s2l ': ', int2str(n2)]};
legendText(3)={'"Error"'};
legendStyle={'k-';'b-';'r-'};
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
function style=getStyles;
color = {'k','r','g','b','m','c','y'};
line = {'-',':','-.','--'};
for i = 0:size(line,2)-1
for j = 1:size(color, 2)
style(j + i*size(color, 2)) = strcat(color(j), line(i+1));
end
end
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
function range=chkrange(r, s)
if r == 0
range = 1:size(s, 2);
else
range = r;
end
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
function xrange=chkxrange(xr,r);
if xr == 0
xrange = r;
elseif size(xr, 2) == 2
xrange = xr(1):(xr(2)-xr(1))/(size(r,2)-1):xr(2);
elseif size(xr, 2)~=size(r, 2)
error('Xrange and range have different sizes.');
else
xrange = xr;
end
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
function n=chkn(n,s)
if n == 0
n = 1:size(s, 1);
end
|
github
|
taojiastanford/Automation-of-Calligraphy-master
|
SOMFn.m
|
.m
|
Automation-of-Calligraphy-master/TryAutoencoder/SOMFn.m
| 842,616 |
utf_8
|
2a3d050c1e1d69645129185dadd1a0c7
|
function [Y,Xf,Af] = SOMFn(X,~,~)
%MYNEURALNETWORKFUNCTION neural network simulation function.
%
% Generated by Neural Network Toolbox function genFunction, 10-Dec-2016 10:17:26.
%
% [Y] = myNeuralNetworkFunction(X,~,~) takes these arguments:
%
% X = 1xTS cell, 1 inputs over TS timesteps
% Each X{1,ts} = 400xQ matrix, input #1 at timestep ts.
%
% and returns:
% Y = 1xTS cell of 1 outputs over TS timesteps.
% Each Y{1,ts} = 100xQ matrix, output #1 at timestep ts.
%
% where Q is number of samples (or series) and TS is the number of timesteps.
%#ok<*RPMT0>
% ===== NEURAL NETWORK CONSTANTS =====
% Layer 1
IW1_1 = [0.24178633272214692 0.15493408124054842 0.23612504178814223 0.0045256182211202978 0.012748712401920157 0.08863248005574563 0.37937362795797153 0.15612161991136869 0.30537664832568479 0.071879061486941148 0.16243568805818373 0.32999047034150525 0.082108767890532536 0.16881906280316969 0.60913731337233834 0.39359156542128915 0.0074402169716277743 0.22920302333763787 0.0086213869738671987 0.0040443370674833898 0.0028071179492909159 0.0024999704665222095 0.15518955979715418 0.39681645309618607 0.34111268490252256 0.83988519010185869 0.088191934867215341 0.15627473320421259 0.99637713660300453 0.2364282663645649 0.83797416927376622 0.0028137391378518957 0.0051556873357080785 0.0098810620931575662 0.62110278003404618 0.0084609242058000939 0.0032231279521743135 0.0030666591014973806 0.47016475397414642 0.15737115832028531 0.30334334568888932 0.0034380262641474195 0.69229800186825563 0.24007244299919922 0.54201214655919128 0.15433234087066205 0.15701209983753681 0.080162626888237179 0.085086688977998634 0.010223358390895505 0.45893298149638273 0.085779538456881271 0.16966903821309048 0.15962996617094172 0.078348150383642665 0.76830269598216472 0.082574801013429927 0.30750630259354095 0.0049842211410595907 0.087464008896176212 0.22828964213398653 0.30560727998949794 0.45928690909031766 0.15543153646872349 0.2312835928837132 0.15841692191480095 0.23398314036906859 0.55017606388492735 0.30839592629441254 0.082152991732652864 0.082993352587594146 0.22759267911230324 0.69351860615840932 0.24628336573246973 0.16092606942162449 0.33451449717951504 0.078813087764802711 0.0019420194412632309 0.081940987505168511 0.084769722734209574 0.088488981020948029 0.0019408315214597021 0.24112017787289333 0.0031750010355027719 0.53649506653279677 0.080579871900168534 0.078694528892837179 0.0026935824236224929 0.0040050129780211351 0.99106138048660752 0.45819737200209287 0.46257731831674459 0.15837081573359185 0.080701937540010052 0.61562584821442567 0.083937756072216957 0.082024574145084489 0.078083569610899267 0.69169526720209695 0.15869752585634442 0.079419720047194234 0.084463212776464736 0.23542894828423838 0.67275223417111052 0.14381933414006143 0.082969335835367156 0.0065823475092198838 0.0086353110809332667 0.32244171096317187 0.17088089506371257 0.39608036368996957 0.53587375014589833 0.15905142970451752 0.69071115028855767 0.53249975362037172 0.5370545424499773 0.14895306600731592 0.68684063885570168 0.30573205497849887 0.91639054090391081 0.16301458928331705 0.45699667547609057 0.30832854101598778 0.61979878268407695 0.0091792431927530064 0.43618868382975851 0.23664786649270089 0.0068770849221633009 0.078803293323625068 0.16352331700735645 0.91946391968724273 0.3184425257192266 0.68368249421719229 0.22674420464279327 0.16338638319798596 0.60972165370455067 0.69219011574718237 0.15401517439767085 0.0028386617913967291 0.16604708875482352 0.15197393186050187 0.090235917398972604 0.24322728670825361 0.31766160074676703 0.1524782923742708 0.0095738638395000616 0.4616730029158892 0.15904227208414082 0.21934041373105953 0.15928859320597583 0.081981037735091564 0.3866464277061985 0.00844089666754466 0.079160927257494657 0.079104583044633289 0.083344456520161661 0.1569877535227979 0.30976609614621897 0.15291275193761372 0.0022698955157211009 0.68976840437056919 0.31397556954559513 0.91527880583447385 0.155689513014409 0.15292499048809144 0.0039131305262421973 0.0039350068420204486 0.23816643233848556 0.46089390351080795 0.82629846129701756 0.76851576661529264 0.45886827558261395 0.1575617890551152 0.0062636706791587317 0.31386356197329857 0.0831098638586871 0.47292431551075709 0.15623211265476056 0.40180269954311704 0.08028455688722437 0.0060914284524099024 0.15965667613032378 0.091859824380476754 0.0026966229306905109 0.45356596834086005 0.24274225897842289 0.0048352602755142452 0.0027471162940464712 0.0064889033443027919 0.07916622786144463 0.23717797773929222 0.0048383634592475506 0.15242636056250985 0.31538035079990778 0.15802357094043723 0.085171086480865604 0.094959926346920756 0.0087410054305871229 0.079692636838558248 0.16164175136430792 0.91454565194962067 0.23393911901727776 0.23410960397777281 0.086038749456404842 0.15360277533823627 0.0648750138294511 0.010178814893339464 0.21070300192704472 0.3803811170350152 0.37518935385019175 0.29186719753062007 0.91297233427471358 0.0025296337575194407 0.38089612942862972 0.088347508119167001 0.1563447264095966 0.0067148536777715487 0.080005110218608205 0.078921428163474291 0.31543063873908495 0.012152892727116416 0.077575589926536126 0.39444870339511146 0.15295198183032735 0.0036972674059274485 0.45741934032221709 0.083937901853344002 0.23582971241563314 0.082201146625621391 0.23578843757711573 0.38448836116359036 0.15825044289160578 0.1585073108083429 0.30669738115872425 0.24152448511019439 0.0018960716422917591 0.077260398297845478 0.99505327564621093 0.61208074592593142 0.0044958300570198308 0.0050286775384574076 0.31418081680725612 0.081425689748067381 0.1546828298607133 0.53491269683845433 0.39103871774159027 0.16334894673161723 0.079360190358539584 0.30231872102354984 0.082427348095376884 0.91703333977709856 0.0053204251229292806 0.079874171268608934 0.0041562722742688619 0.08020191509401528 0.99687032065930126 0.8410599402241079 0.15752696066521915 0.61476844815345644 0.98696019907779498 0.45496255952723857 0.91564489308907193 0.081659454848441893 0.45627925995124646 0.0058503055269563242 0.079618977722003229 0.0058039827612010771 0.3796930180033839 0.073233048467651621 0.15916992615404194 0.084181882260793692 0.30762279571504225 0.2215475526765055 0.086224214135707355 0.15579195116970462 0.75370565263066924 0.15822951522369252 0.0023687263568834003 0.14554005827279162 0.0077857109342583022 0.011567398223078907 0.082062096352387481 0.084098292234234331 0.078625953352390587 0.22280529849077266 0.37546561388492783 0.53803190060220119 0.45408902817413549 0.0055904252315255873 0.01000034598092079 0.22921033300734969 0.0032885265069792381 0.083274451715532369 0.16190974735894814 0.1532318054691231 0.54727716027919904 0.15791370807193178 0.15956258766951584 0.0038564678763778771 0.0067177645128923442 0.0045490467345465921 0.15508251434494894 0.085366913359454275 0.085128312479982815 0.16036144146031672 0.006073814968769381 0.15885949186466988 0.15747325595436173 0.15888857118612992 0.16245189852736788 0.38030645320613821 0.010793641855577324 0.31791168731759406 0.0055954717138637774 0.82792965319290723 0.23667632561362978 0.082001244501815646 0.15255228272734633 0.15694563712412826 0.004471822291991466 0.0079644886657404736 0.15864459395201935 0.079241078055024977 0.38401717810111685 0.15722969780142645 0.0026577127448301294 0.39205163456726666 0.16059396109909829 0.0034428489269091806 0.15448833787589769 0.46415436566421481 0.82948241858032223 0.083302445119098956 0.0019632886444268783 0.76820076599077813 0.69955542089925438 0.084905487677372687 0.31035854288942599 0.080821124822294352 0.15686830884498526 0.23116498571764504 0.16325785602477597 0.15618867735563255 0.23344447847057867 0.99434650803522562 0.51781446674286813 0.0059218124770180512 0.22978733344736607 0.45674795829791781 0.15851840413498039 0.83593652338289548 0.39206447581330706 0.15957171363412453 0.15556050624506074 0.68496526835813643 0.15526138334532427 0.92833620227262703 0.081172696892914564 0.0023985759019465808 0.46238003752275336 0.47127286273675739 0.0088123924805830738 0.83832777074632236 0.0067245980552531077 0.083454971638237535 0.75311425433921841 0.004981953427813956 0.90179668491847353 0.0020315527401084006 0.30840252444402116 0.40360197032422418 0.0094959121594931119 0.30875484126090724 0.080819025504444836 0.0810017453152303 0.0022641447177014023 0.38720902239365973 0.0020461491657109885 0.0018490908561729614 0.1534381051698992 0.081814501034614739 0.23763741922145587 0.0021347118636658069 0.45607993449791584 0.0035190060182969259 0.0051598351116225677 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% ===== SIMULATION ========
% Format Input Arguments
isCellX = iscell(X);
if ~isCellX, X = {X}; end;
% Dimensions
TS = size(X,2); % timesteps
% Allocate Outputs
Y = cell(1,TS);
% Time loop
for ts=1:TS
% Input 1
% no processing
% Layer 1
z1 = negdist_apply(IW1_1,X{1,ts});
a1 = compet_apply(z1);
% Output 1
Y{1,ts} = a1;
end
% Final Delay States
Xf = cell(1,0);
Af = cell(1,0);
% Format Output Arguments
if ~isCellX, Y = cell2mat(Y); end
end
% ===== MODULE FUNCTIONS ========
% Negative Distance Weight Function
function z = negdist_apply(w,p,~)
[S,R] = size(w);
Q = size(p,2);
if isa(w,'gpuArray')
z = iNegDistApplyGPU(w,p,R,S,Q);
else
z = iNegDistApplyCPU(w,p,S,Q);
end
end
function z = iNegDistApplyCPU(w,p,S,Q)
z = zeros(S,Q);
if (Q<S)
pt = p';
for q=1:Q
z(:,q) = sum(bsxfun(@minus,w,pt(q,:)).^2,2);
end
else
wt = w';
for i=1:S
z(i,:) = sum(bsxfun(@minus,wt(:,i),p).^2,1);
end
end
z = -sqrt(z);
end
function z = iNegDistApplyGPU(w,p,R,S,Q)
p = reshape(p,1,R,Q);
sd = arrayfun(@iNegDistApplyGPUHelper,w,p);
z = -sqrt(reshape(sum(sd,2),S,Q));
end
function sd = iNegDistApplyGPUHelper(w,p)
sd = (w-p) .^ 2;
end
% Competitive Transfer Function
function a = compet_apply(n,~)
if isempty(n)
a = n;
else
[S,Q] = size(n);
nanInd = any(isnan(n),1);
a = zeros(S,Q,'like',n);
[~,maxRows] = max(n,[],1);
onesInd = maxRows + S*(0:(Q-1));
a(onesInd) = 1;
a(:,nanInd) = NaN;
end
end
|
github
|
zhangchn/otx-master
|
PPCProcessor.m
|
.m
|
otx-master/src/source/Processors/PPCProcessor.m
| 62,175 |
utf_8
|
713d85183996bcd7d3f41e667af270b8
|
/*
PPCProcessor.m
A subclass of ExeProcessor that handles PPC-specific issues.
This file is in the public domain.
*/
#import <Cocoa/Cocoa.h>
#import "PPCProcessor.h"
#import "ArchSpecifics.h"
#import "ListUtils.h"
#import "ObjcAccessors.h"
#import "ObjectLoader.h"
#import "Searchers.h"
#import "SyscallStrings.h"
#import "UserDefaultKeys.h"
extern BOOL gCancel;
@implementation PPCProcessor
// initWithURL:controller:options:
// ----------------------------------------------------------------------------
- (id)initWithURL: (NSURL*)inURL
controller: (id)inController
options: (ProcOptions*)inOptions
{
if ((self = [super initWithURL: inURL
controller: inController options: inOptions]))
{
strncpy(iArchString, "ppc", 4);
iArchSelector = CPU_TYPE_POWERPC;
iFieldWidths.offset = 8;
iFieldWidths.address = 10;
iFieldWidths.instruction = 10;
iFieldWidths.mnemonic = 9;
iFieldWidths.operands = 17;
}
return self;
}
// dealloc
// ----------------------------------------------------------------------------
- (void)dealloc
{
if (iLocalSelves)
{
free(iLocalSelves);
iLocalSelves = NULL;
}
if (iLocalVars)
{
free(iLocalVars);
iLocalVars = NULL;
}
}
// loadDyldDataSection:
// ----------------------------------------------------------------------------
- (void)loadDyldDataSection: (section*)inSect
{
[super loadDyldDataSection: inSect];
if (!iAddrDyldStubBindingHelper)
return;
iAddrDyldFuncLookupPointer = iAddrDyldStubBindingHelper + 24;
}
// codeFromLine:
// ----------------------------------------------------------------------------
- (void)codeFromLine: (Line*)inLine
{
uint32_t theInstruction = (iMachHeader.filetype == MH_OBJECT) ?
*(uint32_t*)((char*)iMachHeaderPtr + (inLine->info.address + iTextOffset)) :
*(uint32_t*)((char*)iMachHeaderPtr + (inLine->info.address - iTextOffset));
inLine->info.codeLength = 4;
uint32_t* intPtr = (uint32_t*)&inLine->info.code[0];
*intPtr = theInstruction;
}
#pragma mark -
// commentForLine:
// ----------------------------------------------------------------------------
- (void)commentForLine: (Line*)inLine;
{
uint32_t theCode = *(uint32_t*)inLine->info.code;
theCode = OSSwapBigToHostInt32(theCode);
char* theDummyPtr = NULL;
char* theSymPtr = NULL;
UInt8 opcode = PO(theCode);
uint32_t localAddy;
iLineCommentCString[0] = 0;
// Examine the primary opcode to see if we need to look for comments.
switch (opcode)
{
case 0x0a: // cmpli | cmplwi UIMM
case 0x0b: // cmpi | cmpwi SIMM
{
SInt16 imm = SIMM(theCode);
// Check for a single printable 7-bit char.
if (imm >= 0x20 && imm < 0x7f)
snprintf(iLineCommentCString, 4, "'%c'", imm);
break;
}
case 0x11: // sc
[self commentForSystemCall];
break;
case 0x10: // bc, bca, bcl, bcla
case 0x12: // b, ba, bl, bla
{
// Check for absolute branches to the ObjC runtime page. Similar to
// the comm page behavior described at
// http://www.opensource.apple.com/darwinsource/10.4.7.ppc/xnu-792.6.76/osfmk/ppc/cpu_capabilities.h
// However, the ObjC runtime page is not really a comm page, and it
// cannot be accessed by bca and bcla instructions, due to their
// 16-bit limitation.
// Deal with absolute branches.
if (AA(theCode))
{
uint32_t target = LI(theCode);
switch (target)
{
case kRTAddress_objc_msgSend:
{
char tempComment[MAX_COMMENT_LENGTH];
strncpy(tempComment, kRTName_objc_msgSend,
strlen(kRTName_objc_msgSend) + 1);
if (iOpts.verboseMsgSends)
[self commentForMsgSend:tempComment fromLine:inLine];
strncpy(iLineCommentCString, tempComment,
strlen(tempComment) + 1);
break;
}
case kRTAddress_objc_assign_ivar:
{
char tempComment[MAX_COMMENT_LENGTH];
strncpy(tempComment, kRTName_objc_assign_ivar,
strlen(kRTName_objc_assign_ivar) + 1);
// Bail if we don't know about the class.
if (!iCurrentClass)
{
strncpy(iLineCommentCString, tempComment,
strlen(tempComment) + 1);
break;
}
if (iRegInfos[5].isValid)
{
objc1_32_ivar theIvar = {0};
objc1_32_class swappedClass = *(objc1_32_class *)iCurrentClass;
#if __LITTLE_ENDIAN__
swap_objc1_32_class(&swappedClass);
#endif
if (!iIsInstanceMethod)
{
if (![self getObjc1MetaClass:&swappedClass fromClass:&swappedClass])
break;
#if __LITTLE_ENDIAN__
swap_objc1_32_class(&swappedClass);
#endif
}
if (![self findIvar:&theIvar inClass:&swappedClass withOffset:iRegInfos[5].value])
{
strncpy(iLineCommentCString, tempComment,
strlen(tempComment) + 1);
break;
}
theSymPtr = [self getPointer:theIvar.ivar_name type:NULL];
if (!theSymPtr)
{
strncpy(iLineCommentCString, tempComment,
strlen(tempComment) + 1);
break;
}
if (iOpts.variableTypes)
{
char theTypeCString[MAX_TYPE_STRING_LENGTH];
theTypeCString[0] = 0;
[self getDescription: theTypeCString
forType: [self getPointer:theIvar.ivar_type type:NULL]];
snprintf(iLineCommentCString, MAX_COMMENT_LENGTH, "%s (%s)%s", tempComment, theTypeCString, theSymPtr);
}
else
snprintf(iLineCommentCString, MAX_COMMENT_LENGTH, "%s %s", tempComment, theSymPtr);
}
else // !mReginfos[5].isValid
snprintf(iLineCommentCString, MAX_COMMENT_LENGTH, "%s", tempComment);
break;
}
case kRTAddress_objc_assign_global:
strncpy(iLineCommentCString, kRTName_objc_assign_global,
strlen(kRTName_objc_assign_global) + 1);
break;
case kRTAddress_objc_assign_strongCast:
strncpy(iLineCommentCString, kRTName_objc_assign_strongCast,
strlen(kRTName_objc_assign_strongCast) + 1);
break;
default:
break;
}
}
else // not an absolute branch
{
// Insert anonymous label or 'return' if there's not a comment yet.
if (iLineCommentCString[0])
break;
uint32_t absoluteAddy;
if (opcode == 0x12)
absoluteAddy =
inLine->info.address + LI(theCode);
else
absoluteAddy =
inLine->info.address + BD(theCode);
FunctionInfo searchKey = {absoluteAddy, NULL, 0, 0};
FunctionInfo* funcInfo = bsearch(&searchKey,
iFuncInfos, iNumFuncInfos, sizeof(FunctionInfo),
(COMPARISON_FUNC_TYPE)Function_Info_Compare);
if (funcInfo && funcInfo->genericFuncNum != 0)
{
snprintf(iLineCommentCString,
ANON_FUNC_BASE_LENGTH + 11, "%s%d",
ANON_FUNC_BASE, funcInfo->genericFuncNum);
break;
}
// FIXME: mCurrentFuncInfoIndex is -1 here when it should not be
funcInfo = &iFuncInfos[iCurrentFuncInfoIndex];
if (!funcInfo->blocks)
break;
uint32_t i;
for (i = 0; i < funcInfo->numBlocks; i++)
{
if (funcInfo->blocks[i].beginAddress != absoluteAddy)
continue;
if (funcInfo->blocks[i].isEpilog)
snprintf(iLineCommentCString, 8, "return;");
break;
}
}
break;
}
case 0x13: // bcctr, bclr, isync
if (SO(theCode) != 528) // bcctr
break;
// Print value of ctr, ignoring the low 2 bits.
if (iCTR.isValid)
snprintf(iLineCommentCString, 10, "0x%x",
iCTR.value & ~3);
break;
case 0x30: // lfs SIMM
case 0x34: // stfs SIMM
case 0x32: // lfd SIMM
case 0x36: // stfd SIMM
{
if (!iRegInfos[RA(theCode)].isValid || RA(theCode) == 0)
break;
if (iRegInfos[RA(theCode)].classPtr)
{ // search instance vars
objc_32_class_ptr classPtr = iRegInfos[RA(theCode)].classPtr;
uint32_t offset = UIMM(theCode);
char *typePtr = NULL;
if (![self getIvarName:&theSymPtr type:&typePtr withOffset:offset inClass:classPtr])
break;
if (theSymPtr)
{
if (iOpts.variableTypes)
{
char theTypeCString[MAX_TYPE_STRING_LENGTH];
theTypeCString[0] = 0;
[self getDescription:theTypeCString forType:typePtr];
snprintf(iLineCommentCString, MAX_COMMENT_LENGTH, "(%s)%s", theTypeCString, theSymPtr);
}
else
snprintf(iLineCommentCString, MAX_COMMENT_LENGTH, "%s", theSymPtr);
}
}
else
{
localAddy = iRegInfos[RA(theCode)].value + SIMM(theCode);
theDummyPtr = [self getPointer:localAddy type:NULL];
if (!theDummyPtr)
break;
if (opcode == 0x32 || opcode == 0x36) // lfd | stfd
{
UInt64 theInt64 = *(UInt64*)theDummyPtr;
theInt64 = OSSwapBigToHostInt64(theInt64);
// dance around printf's type coersion
snprintf(iLineCommentCString,
30, "%lG", *(double*)&theInt64);
}
else // lfs | stfs
{
uint32_t theInt32 = *(uint32_t*)theDummyPtr;
theInt32 = OSSwapBigToHostInt32(theInt32);
// dance around printf's type coersion
snprintf(iLineCommentCString,
30, "%G", *(float*)&theInt32);
}
}
break;
}
case 0x0e: // li | addi SIMM
case 0x18: // ori UIMM
case 0x20: // lwz SIMM
case 0x22: // lbz SIMM
case 0x24: // stw SIMM
case 0x26: // stb SIMM
case 0x28: // lhz SIMM
case 0x2c: // sth SIMM
{
if (!iRegInfos[RA(theCode)].isValid || RA(theCode) == 0)
break;
if (iRegInfos[RA(theCode)].classPtr) // relative to a class
{ // search instance vars
objc_32_class_ptr classPtr = iRegInfos[RA(theCode)].classPtr;
uint32_t offset = UIMM(theCode);
char *typePtr = NULL;
if (![self getIvarName:&theSymPtr type:&typePtr withOffset:offset inClass:classPtr])
break;
if (theSymPtr)
{
if (iOpts.variableTypes)
{
char theTypeCString[MAX_TYPE_STRING_LENGTH];
theTypeCString[0] = 0;
[self getDescription:theTypeCString forType:typePtr];
snprintf(iLineCommentCString, MAX_COMMENT_LENGTH, "(%s)%s", theTypeCString, theSymPtr);
}
else
snprintf(iLineCommentCString, MAX_COMMENT_LENGTH, "%s", theSymPtr);
}
}
else // absolute address
{
if (opcode == 0x18) // ori UIMM
localAddy = iRegInfos[RA(theCode)].value |
UIMM(theCode);
else
localAddy = iRegInfos[RA(theCode)].value +
SIMM(theCode);
UInt8 theType = PointerType;
uint32_t theValue;
theSymPtr = [self getPointer:localAddy type:&theType];
if (theSymPtr)
{
switch (theType)
{
case DataGenericType:
theValue = *(uint32_t*)theSymPtr;
theValue = OSSwapBigToHostInt32(theValue);
theDummyPtr = [self getPointer:theValue type:&theType];
switch (theType)
{
case PointerType:
theSymPtr = theDummyPtr;
break;
default:
theSymPtr = NULL;
break;
}
break;
case DataConstType:
theSymPtr = NULL;
break;
// See http://www.opensource.apple.com/darwinsource/10.4.7.ppc/Csu-58/dyld.s
// They hardcoded the values, we may as well...
case DYLDType:
{
char* dyldComment = NULL;
theValue = *(uint32_t*)theSymPtr;
theValue = OSSwapBigToHostInt32(theValue);
switch(theValue)
{
case kDyldAddress_LaSymBindingEntry:
dyldComment = kDyldName_LaSymBindingEntry;
break;
case kDyldAddress_FuncLookupPointer:
dyldComment = kDyldName_FuncLookupPointer;
break;
default:
break;
}
if (dyldComment)
snprintf(iLineCommentCString, MAX_COMMENT_LENGTH, "%s", dyldComment);
break;
}
case PointerType:
break;
case CFStringType:
{
cfstring_object theCFString = *(cfstring_object*)theSymPtr;
if (theCFString.oc_string.length == 0)
{
theSymPtr = NULL;
break;
}
theCFString.oc_string.chars = OSSwapBigToHostInt32(theCFString.oc_string.chars);
theSymPtr = [self getPointer:theCFString.oc_string.chars type:NULL];
break;
}
case ImpPtrType:
case NLSymType:
{
theValue = *(uint32_t*)theSymPtr;
theValue = OSSwapBigToHostInt32(theValue);
theDummyPtr = [self getPointer:theValue type:NULL];
if (!theDummyPtr)
{
theSymPtr = NULL;
break;
}
theValue = *(uint32_t*)(theDummyPtr + 4);
theValue = OSSwapBigToHostInt32(theValue);
if (theValue != typeid_NSString)
{
theValue = *(uint32_t*)theDummyPtr;
theValue = OSSwapBigToHostInt32(theValue);
theDummyPtr = [self getPointer:theValue type:NULL];
if (!theDummyPtr)
{
theSymPtr = NULL;
break;
}
}
cfstring_object theCFString = *(cfstring_object*)theDummyPtr;
if (theCFString.oc_string.length == 0)
{
theSymPtr = NULL;
break;
}
theCFString.oc_string.chars = OSSwapBigToHostInt32(theCFString.oc_string.chars);
theSymPtr = [self getPointer:theCFString.oc_string.chars type:NULL];
break;
}
case OCGenericType:
case OCStrObjectType:
case OCClassType:
case OCModType:
if (![self getObjc1Description:&theDummyPtr fromObject:theSymPtr type:theType])
break;
if (theDummyPtr)
{
switch (theType)
{
case OCClassType:
iRegInfos[RT(theCode)].classPtr =
(objc_32_class_ptr)theSymPtr;
break;
default:
break;
}
}
theSymPtr = theDummyPtr;
break;
default:
break;
}
if (theSymPtr && !iLineCommentCString[0])
{
if (theType == PStringType)
snprintf(iLineCommentCString, 255,
"%*s", theSymPtr[0], theSymPtr + 1);
else
snprintf(iLineCommentCString, MAX_COMMENT_LENGTH, "%s", theSymPtr);
}
} // if (theSymPtr)
else
{ // Maybe it's a four-char code...
if ((opcode == 0x0e || opcode == 0x18) && // li | addi | ori
localAddy >= 0x20202020 && localAddy < 0x7f7f7f7f)
{
localAddy = OSSwapBigToHostInt32(localAddy);
char* fcc = (char*)&localAddy;
if (fcc[0] >= 0x20 && fcc[0] < 0x7f &&
fcc[1] >= 0x20 && fcc[1] < 0x7f &&
fcc[2] >= 0x20 && fcc[2] < 0x7f &&
fcc[3] >= 0x20 && fcc[3] < 0x7f)
snprintf(iLineCommentCString,
7, "'%.4s'", fcc);
}
}
} // if !(.classPtr)
break;
} // case 0x0e...
default:
break;
}
}
// commentForSystemCall
// ----------------------------------------------------------------------------
// System call number is stored in r0, possible values defined in
// <sys/syscall.h>. Call numbers are indices into a lookup table of handler
// routines. Args being passed to the looked-up handler start at r3 or r4,
// depending on whether it's an indirect SYS_syscall.
- (void)commentForSystemCall
{
if (!iRegInfos[0].isValid ||
iRegInfos[0].value > SYS_MAXSYSCALL)
{
snprintf(iLineCommentCString, 11, "syscall(?)");
return;
}
BOOL isIndirect = (iRegInfos[0].value == SYS_syscall);
uint32_t syscallNumReg = isIndirect ? 3 : 0;
uint32_t syscallArg1Reg = isIndirect ? 4 : 3;
if (!iRegInfos[syscallNumReg].isValid ||
iRegInfos[syscallNumReg].value > SYS_MAXSYSCALL)
{
snprintf(iLineCommentCString, 11, "syscall(?)");
return;
}
const char* theSysString = gSysCalls[iRegInfos[syscallNumReg].value];
if (!theSysString)
return;
char theTempComment[50];
theTempComment[0] = 0;
strncpy(theTempComment, theSysString, strlen(theSysString) + 1);
// Handle various system calls.
switch (iRegInfos[syscallNumReg].value)
{
case SYS_ptrace:
if (iRegInfos[syscallArg1Reg].isValid &&
iRegInfos[syscallArg1Reg].value == PT_DENY_ATTACH)
snprintf(iLineCommentCString, 40, "%s(%s)",
theTempComment, "PT_DENY_ATTACH");
else
snprintf(iLineCommentCString, MAX_COMMENT_LENGTH, "%s", theTempComment);
break;
default:
snprintf(iLineCommentCString, MAX_COMMENT_LENGTH, "%s", theTempComment);
break;
}
}
// selectorForMsgSend:fromLine:
// ----------------------------------------------------------------------------
- (char*)selectorForMsgSend: (char*)outComment
fromLine: (Line*)inLine
{
char* selString = NULL;
uint32_t theCode = *(uint32_t*)inLine->info.code;
theCode = OSSwapBigToHostInt32(theCode);
// Bail if this is not an eligible branch.
if (PO(theCode) != 0x12) // b, bl, ba, bla
return NULL;
// Bail if this is not an objc_msgSend variant.
if (memcmp(outComment, "_objc_msgSend", 13))
return NULL;
UInt8 sendType = [self sendTypeFromMsgSend:outComment];
uint32_t selectorRegNum =
(sendType == sendSuper_stret || sendType == send_stret) ? 5 : 4;
if (!iRegInfos[selectorRegNum].isValid ||
!iRegInfos[selectorRegNum].value)
return NULL;
// Get at the selector.
UInt8 selType = PointerType;
char* selPtr = [self getPointer:iRegInfos[selectorRegNum].value type:&selType];
switch (selType)
{
case PointerType:
selString = selPtr;
break;
case OCGenericType:
if (selPtr)
{
uint32_t selPtrValue = *(uint32_t*)selPtr;
selPtrValue = OSSwapBigToHostInt32(selPtrValue);
selString = [self getPointer:selPtrValue type:NULL];
}
break;
default:
fprintf(stderr, "otx: [PPCProcessor selectorForMsgSend:fromLine:]: "
"unsupported selector type: %d at address: 0x%x\n",
selType, inLine->info.address);
break;
}
return selString;
}
// commentForMsgSend:fromLine:
// ----------------------------------------------------------------------------
- (void)commentForMsgSend: (char*)ioComment
fromLine: (Line*)inLine
{
char* selString = [self selectorForMsgSend:ioComment fromLine:inLine];
// Bail if we couldn't find the selector.
if (!selString)
{
iMissedSelectorCount++;
return;
}
iMatchedSelectorCount++;
UInt8 sendType = [self sendTypeFromMsgSend:ioComment];
// Get the address of the class name string, if this a class method.
uint32_t classNameAddy = 0;
// If *.classPtr is non-NULL, it's not a name string.
if (sendType == sendSuper_stret || sendType == send_stret)
{
if (iRegInfos[4].isValid && !iRegInfos[4].classPtr)
classNameAddy = iRegInfos[4].value;
}
else
{
if (iRegInfos[3].isValid && !iRegInfos[3].classPtr)
classNameAddy = iRegInfos[3].value;
}
char* className = NULL;
char* returnTypeString =
(sendType == sendSuper_stret || sendType == send_stret) ?
"(struct)" : "";
char tempComment[MAX_COMMENT_LENGTH];
tempComment[0] = 0;
if (classNameAddy)
{
// Get at the class name
UInt8 classNameType = PointerType;
char* classNamePtr = [self getPointer:classNameAddy type:&classNameType];
switch (classNameType)
{
// Receiver can be various things in these sections, but we
// only want to display class names as receivers.
case DataGenericType:
case DataConstType:
case CFStringType:
case ImpPtrType:
case OCStrObjectType:
case OCModType:
case PStringType:
case DoubleType:
break;
case NLSymType:
if (classNamePtr)
{
uint32_t namePtrValue = *(uint32_t*)classNamePtr;
namePtrValue = OSSwapBigToHostInt32(namePtrValue);
classNamePtr = [self getPointer:namePtrValue type:&classNameType];
switch (classNameType)
{
case CFStringType:
if (classNamePtr != NULL)
{
cfstring_object classNameCFString = *(cfstring_object*)classNamePtr;
namePtrValue = classNameCFString.oc_string.chars;
namePtrValue = OSSwapBigToHostInt32(namePtrValue);
classNamePtr = [self getPointer:namePtrValue type:NULL];
className = classNamePtr;
}
break;
// Not sure what these are for, but they're out there.
case NLSymType:
case FloatType:
break;
default:
printf("otx: [PPCProcessor commentForMsgSend:fromLine:]: "
"non-lazy symbol pointer points to unrecognized section: %d\n", classNameType);
break;
}
}
break;
case PointerType:
className = classNamePtr;
break;
case OCGenericType:
if (classNamePtr)
{
uint32_t namePtrValue = *(uint32_t*)classNamePtr;
namePtrValue = OSSwapBigToHostInt32(namePtrValue);
className = [self getPointer:namePtrValue type:NULL];
}
break;
case OCClassType:
if (classNamePtr)
[self getObjc1Description:&className fromObject:classNamePtr type:OCClassType];
break;
default:
fprintf(stderr, "otx: [PPCProcessor commentForMsgSend]: "
"unsupported class name type: %d at address: 0x%x\n",
classNameType, inLine->info.address);
break;
}
}
if (className)
{
snprintf(tempComment, MAX_COMMENT_LENGTH,
((sendType == sendSuper || sendType == sendSuper_stret) ?
"+%s[[%s super] %s]" : "+%s[%s %s]"),
returnTypeString, className, selString);
}
else
{
switch (sendType)
{
case send:
case send_rtp:
case send_variadic:
snprintf(tempComment, MAX_COMMENT_LENGTH, "-%s[r3 %s]", returnTypeString, selString);
break;
case sendSuper:
snprintf(tempComment, MAX_COMMENT_LENGTH, "-%s[[r3 super] %s]", returnTypeString, selString);
break;
case send_stret:
snprintf(tempComment, MAX_COMMENT_LENGTH, "-%s[r4 %s]", returnTypeString, selString);
break;
case sendSuper_stret:
snprintf(tempComment, MAX_COMMENT_LENGTH, "-%s[[r4 super] %s]", returnTypeString, selString);
break;
default:
break;
}
}
if (tempComment[0])
strncpy(ioComment, tempComment, strlen(tempComment) + 1);
}
// chooseLine:
// ----------------------------------------------------------------------------
- (void)chooseLine: (Line**)ioLine
{
if (!(*ioLine) || !(*ioLine)->info.isCode ||
!(*ioLine)->alt || !(*ioLine)->alt->chars)
return;
uint32_t theCode = *(uint32_t*)(*ioLine)->info.code;
theCode = OSSwapBigToHostInt32(theCode);
if (PO(theCode) == 18) // b, ba, bl, bla
{
Line* theNewLine = malloc(sizeof(Line));
memcpy(theNewLine, (*ioLine)->alt, sizeof(Line));
theNewLine->chars = malloc(theNewLine->length + 1);
strncpy(theNewLine->chars, (*ioLine)->alt->chars,
theNewLine->length + 1);
// Swap in the verbose line and free the previous verbose lines.
[self deleteLinesBefore:(*ioLine)->alt fromList:&iVerboseLineListHead];
[self replaceLine:*ioLine withLine:theNewLine inList:&iPlainLineListHead];
*ioLine = theNewLine;
}
}
#pragma mark -
// resetRegisters:
// ----------------------------------------------------------------------------
- (void)resetRegisters: (Line*)inLine
{
if (!inLine)
{
fprintf(stderr, "otx: [PPCProcessor resetRegisters]: "
"tried to reset with NULL inLine\n");
return;
}
// Setup the registers with default info. r3 is 'self' at the beginning
// of any Obj-C method, and r12 holds the address of the 1st instruction
// if the function was called indirectly. In the case of direct calls,
// r12 will be overwritten before it is used, if it is used at all.
[self getObjcClassPtr:&iCurrentClass fromMethod:inLine->info.address];
[self getObjc1CatPtr:&iCurrentCat fromMethod:inLine->info.address];
memset(iRegInfos, 0, sizeof(GPRegisterInfo) * 32);
// If we didn't get the class from the method, try to get it from the
// category.
if (!iCurrentClass && iCurrentCat)
{
objc1_32_category swappedCat = *iCurrentCat;
#if __LITTLE_ENDIAN__
swap_objc1_32_category(&swappedCat);
#endif
[self getObjcClassPtr:&iCurrentClass fromName:[self getPointer:swappedCat.class_name type:NULL]];
}
iRegInfos[3].classPtr = iCurrentClass;
iRegInfos[3].catPtr = iCurrentCat;
iRegInfos[3].isValid = YES;
iRegInfos[12].value = iCurrentFuncPtr;
iRegInfos[12].isValid = YES;
iLR = (GPRegisterInfo){0};
iCTR = (GPRegisterInfo){0};
// Try to find out whether this is a class or instance method.
MethodInfo* thisMethod = NULL;
if ([self getObjcMethod:&thisMethod fromAddress:inLine->info.address])
iIsInstanceMethod = thisMethod->inst;
if (iLocalSelves)
{
free(iLocalSelves);
iLocalSelves = NULL;
iNumLocalSelves = 0;
}
if (iLocalVars)
{
free(iLocalVars);
iLocalVars = NULL;
iNumLocalVars = 0;
}
iCurrentFuncInfoIndex++;
if (iCurrentFuncInfoIndex >= iNumFuncInfos)
iCurrentFuncInfoIndex = -1;
}
// updateRegisters:
// ----------------------------------------------------------------------------
// Keep our local copy of the GPRs in sync as much as possible with the
// values that the exe will use at runtime. Assign classPtr and catPtr fields
// in a register's info if its new value points to a class or category.
// http://developer.apple.com/documentation/DeveloperTools/Conceptual/LowLevelABI/Articles/32bitPowerPC.html
// http://developer.apple.com/documentation/DeveloperTools/Conceptual/MachOTopics/Articles/dynamic_code.html
- (void)updateRegisters: (Line*)inLine;
{
if (!inLine)
{
fprintf(stderr, "otx: [PPCProcessor updateRegisters]: "
"tried to update with NULL inLine\n");
return;
}
uint32_t theNewValue;
uint32_t theCode = *(uint32_t*)inLine->info.code;
theCode = OSSwapBigToHostInt32(theCode);
if (IS_BRANCH_LINK(theCode))
{
iLR.value = inLine->info.address + 4;
iLR.isValid = YES;
}
switch (PO(theCode))
{
case 0x07: // mulli SIMM
{
if (!iRegInfos[RA(theCode)].isValid)
{
iRegInfos[RT(theCode)] = (GPRegisterInfo){0};
break;
}
UInt64 theProduct =
(SInt32)iRegInfos[RA(theCode)].value * SIMM(theCode);
iRegInfos[RT(theCode)] = (GPRegisterInfo){0};
iRegInfos[RT(theCode)].value = (uint32_t)(theProduct & 0xffffffff);
iRegInfos[RT(theCode)].isValid = YES;
break;
}
case 0x08: // subfic SIMM
if (!iRegInfos[RA(theCode)].isValid)
{
iRegInfos[RT(theCode)] = (GPRegisterInfo){0};
break;
}
theNewValue = iRegInfos[RA(theCode)].value - SIMM(theCode);
iRegInfos[RT(theCode)] = (GPRegisterInfo){0};
iRegInfos[RT(theCode)].value = theNewValue;
iRegInfos[RT(theCode)].isValid = YES;
break;
case 0x0c: // addic SIMM
case 0x0d: // addic. SIMM
case 0x0e: // addi | li SIMM
if (RA(theCode) == 1 && // current reg is stack pointer (r1)
SIMM(theCode) >= 0) // we're accessing local vars, not args
{
BOOL found = NO;
uint32_t i;
// Check for copied self pointer. This happens mostly in "init"
// methods, as in: "self = [super init]"
if (iLocalSelves) // self was copied to a local variable
{
// If we're accessing a local var copy of self,
// copy that info back to the reg in question.
for (i = 0; i < iNumLocalSelves; i++)
{
if (iLocalSelves[i].offset != UIMM(theCode))
continue;
iRegInfos[RT(theCode)] = iLocalSelves[i].regInfo;
found = YES;
break;
}
}
if (found)
break;
// Check for other local variables.
if (iLocalVars)
{
for (i = 0; i < iNumLocalVars; i++)
{
if (iLocalVars[i].offset != UIMM(theCode))
continue;
iRegInfos[RT(theCode)] = iLocalVars[i].regInfo;
found = YES;
break;
}
}
if (found)
break;
}
// We didn't find any local variables, try immediates.
if (RA(theCode) == 0) // li
{
iRegInfos[RT(theCode)] = (GPRegisterInfo){0};
iRegInfos[RT(theCode)].value = UIMM(theCode);
iRegInfos[RT(theCode)].isValid = YES;
}
else // addi
{
// Update rD if we know what rA is.
if (!iRegInfos[RA(theCode)].isValid)
{
iRegInfos[RT(theCode)] = (GPRegisterInfo){0};
break;
}
iRegInfos[RT(theCode)].classPtr = NULL;
iRegInfos[RT(theCode)].catPtr = NULL;
theNewValue = iRegInfos[RA(theCode)].value + SIMM(theCode);
iRegInfos[RT(theCode)] = (GPRegisterInfo){0};
iRegInfos[RT(theCode)].value = theNewValue;
iRegInfos[RT(theCode)].isValid = YES;
}
break;
case 0x0f: // addis | lis
iRegInfos[RT(theCode)].classPtr = NULL;
iRegInfos[RT(theCode)].catPtr = NULL;
if (RA(theCode) == 0) // lis
{
iRegInfos[RT(theCode)] = (GPRegisterInfo){0};
iRegInfos[RT(theCode)].value = UIMM(theCode) << 16;
iRegInfos[RT(theCode)].isValid = YES;
break;
}
// addis
if (!iRegInfos[RA(theCode)].isValid)
{
iRegInfos[RT(theCode)] = (GPRegisterInfo){0};
break;
}
theNewValue = iRegInfos[RA(theCode)].value +
(SIMM(theCode) << 16);
iRegInfos[RT(theCode)] = (GPRegisterInfo){0};
iRegInfos[RT(theCode)].value = theNewValue;
iRegInfos[RT(theCode)].isValid = YES;
break;
case 0x10: // bcl, bcla
case 0x13: // bclrl, bcctrl
if (!IS_BRANCH_LINK(theCode)) // fall thru if link
break;
case 0x12: // b, ba, bl, bla
{
if (!LK(theCode)) // bl, bla
break;
iRegInfos[3] = (GPRegisterInfo){0};
break;
}
case 0x15: // rlwinm
{
if (!iRegInfos[RT(theCode)].isValid)
{
iRegInfos[RA(theCode)] = (GPRegisterInfo){0};
break;
}
uint32_t rotatedRT =
rotl(iRegInfos[RT(theCode)].value, RB(theCode));
uint32_t theMask = 0x0;
UInt8 i;
for (i = MB(theCode); i <= ME(theCode); i++)
theMask |= 1 << (31 - i);
theNewValue = rotatedRT & theMask;
iRegInfos[RA(theCode)] = (GPRegisterInfo){0};
iRegInfos[RA(theCode)].value = theNewValue;
iRegInfos[RA(theCode)].isValid = YES;
break;
}
case 0x18: // ori
if (!iRegInfos[RT(theCode)].isValid)
{
iRegInfos[RA(theCode)] = (GPRegisterInfo){0};
break;
}
theNewValue =
iRegInfos[RT(theCode)].value | (uint32_t)UIMM(theCode);
iRegInfos[RA(theCode)] = (GPRegisterInfo){0};
iRegInfos[RA(theCode)].value = theNewValue;
iRegInfos[RA(theCode)].isValid = YES;
break;
case 0x1f: // multiple instructions
switch (SO(theCode))
{
case 23: // lwzx
iRegInfos[RT(theCode)] = (GPRegisterInfo){0};
break;
case 8: // subfc
case 40: // subf
if (!iRegInfos[RA(theCode)].isValid ||
!iRegInfos[RB(theCode)].isValid)
{
iRegInfos[RT(theCode)] = (GPRegisterInfo){0};
break;
}
// 2's complement subtraction
theNewValue =
(iRegInfos[RA(theCode)].value ^= 0xffffffff) +
iRegInfos[RB(theCode)].value + 1;
iRegInfos[RT(theCode)] = (GPRegisterInfo){0};
iRegInfos[RT(theCode)].value = theNewValue;
iRegInfos[RT(theCode)].isValid = YES;
break;
case 339: // mfspr
iRegInfos[RT(theCode)] = (GPRegisterInfo){0};
if (SPR(theCode) == LR && // from LR
iLR.isValid)
{ // Copy LR into rD.
iRegInfos[RT(theCode)].value = iLR.value;
iRegInfos[RT(theCode)].isValid = YES;
}
break;
case 444: // or | or.
if (!iRegInfos[RT(theCode)].isValid ||
!iRegInfos[RB(theCode)].isValid)
{
iRegInfos[RA(theCode)] = (GPRegisterInfo){0};
break;
}
theNewValue =
(iRegInfos[RT(theCode)].value |
iRegInfos[RB(theCode)].value);
iRegInfos[RA(theCode)] = (GPRegisterInfo){0};
iRegInfos[RA(theCode)].value = theNewValue;
iRegInfos[RA(theCode)].isValid = YES;
// If we just copied a register, copy the
// remaining fields.
if (RT(theCode) == RB(theCode))
{
iRegInfos[RA(theCode)].classPtr =
iRegInfos[RB(theCode)].classPtr;
iRegInfos[RA(theCode)].catPtr =
iRegInfos[RB(theCode)].catPtr;
}
break;
case 467: // mtspr
if (SPR(theCode) == CTR) // to CTR
{
if (!iRegInfos[RS(theCode)].isValid)
{
iCTR = (GPRegisterInfo){0};
break;
}
iCTR.value = iRegInfos[RS(theCode)].value;
iCTR.isValid = YES;
}
break;
case 24: // slw
if (!iRegInfos[RS(theCode)].isValid ||
!iRegInfos[RB(theCode)].isValid)
{
iRegInfos[RA(theCode)] = (GPRegisterInfo){0};
break;
}
if (SB(iRegInfos[RB(theCode)].value))
{
theNewValue =
iRegInfos[RS(theCode)].value <<
SV(iRegInfos[RB(theCode)].value);
}
else // If RB.5 == 0, RA = 0.
theNewValue = 0;
iRegInfos[RA(theCode)] = (GPRegisterInfo){0};
iRegInfos[RA(theCode)].value = theNewValue;
iRegInfos[RA(theCode)].isValid = YES;
break;
case 536: // srw
if (!iRegInfos[RS(theCode)].isValid ||
!iRegInfos[RB(theCode)].isValid)
{
iRegInfos[RA(theCode)] = (GPRegisterInfo){0};
break;
}
theNewValue =
iRegInfos[RS(theCode)].value >>
SV(iRegInfos[RB(theCode)].value);
iRegInfos[RA(theCode)] = (GPRegisterInfo){0};
iRegInfos[RA(theCode)].value = theNewValue;
iRegInfos[RA(theCode)].isValid = YES;
break;
default:
break;
}
break;
case 0x20: // lwz
case 0x22: // lbz
if (RA(theCode) == 0)
{
iRegInfos[RT(theCode)] = (GPRegisterInfo){0};
iRegInfos[RT(theCode)].value = SIMM(theCode);
iRegInfos[RT(theCode)].isValid = YES;
}
else if (iRegInfos[RA(theCode)].isValid)
{
void *tempPtr = [self getPointer:iRegInfos[RA(theCode)].value + SIMM(theCode) type:NULL];
if (tempPtr)
{
iRegInfos[RT(theCode)] = (GPRegisterInfo){0};
iRegInfos[RT(theCode)].value = *(uint32_t*)tempPtr;
iRegInfos[RT(theCode)].value =
OSSwapBigToHostInt32(iRegInfos[RT(theCode)].value);
iRegInfos[RT(theCode)].isValid = YES;
}
else
iRegInfos[RT(theCode)] = (GPRegisterInfo){0};
}
else if (iLocalVars)
{
uint32_t i;
for (i = 0; i < iNumLocalVars; i++)
{
if (iLocalVars[i].offset == SIMM(theCode))
{
iRegInfos[RT(theCode)] = iLocalVars[i].regInfo;
break;
}
}
}
else
iRegInfos[RT(theCode)] = (GPRegisterInfo){0};
break;
/* case 0x22: // lbz
mRegInfos[RT(theCode)] = (GPRegisterInfo){0};
if (RA(theCode) == 0)
{
mRegInfos[RT(theCode)].value = SIMM(theCode);
mRegInfos[RT(theCode)].isValid = YES;
}
break;*/
case 0x24: // stw
if (!iRegInfos[RT(theCode)].isValid ||
RA(theCode) != 1 ||
SIMM(theCode) < 0)
break;
if (iRegInfos[RT(theCode)].classPtr) // if it's a class
{
iNumLocalSelves++;
iLocalSelves = realloc(iLocalSelves,
iNumLocalSelves * sizeof(VarInfo));
iLocalSelves[iNumLocalSelves - 1] = (VarInfo)
{iRegInfos[RT(theCode)], UIMM(theCode)};
}
else
{
iNumLocalVars++;
iLocalVars = realloc(iLocalVars,
iNumLocalVars * sizeof(VarInfo));
iLocalVars[iNumLocalVars - 1] = (VarInfo)
{iRegInfos[RT(theCode)], UIMM(theCode)};
}
break;
/* case 0x21:
case 0x23:
case 0x25:
case 0x26:
case 0x27:
case 0x28:
case 0x29:
case 0x2a:
case 0x2b:
case 0x2c:
case 0x2d:
case 0x2e:
case 0x2f:
break;*/
default:
break;
}
}
// restoreRegisters:
// ----------------------------------------------------------------------------
- (BOOL)restoreRegisters: (Line*)inLine
{
if (!inLine)
{
fprintf(stderr, "otx: [PPCProcessor restoreRegisters]: "
"tried to restore with NULL inLine\n");
return NO;
}
BOOL needNewLine = NO;
if (iCurrentFuncInfoIndex < 0)
return NO;
// Search current FunctionInfo for blocks that start at this address.
FunctionInfo* funcInfo =
&iFuncInfos[iCurrentFuncInfoIndex];
if (!funcInfo->blocks)
return NO;
uint32_t i;
for (i = 0; i < funcInfo->numBlocks; i++)
{
if (funcInfo->blocks[i].beginAddress !=
inLine->info.address)
continue;
// Update machine state.
MachineState machState =
funcInfo->blocks[i].state;
memcpy(iRegInfos, machState.regInfos,
sizeof(GPRegisterInfo) * 32);
iLR = machState.regInfos[LRIndex];
iCTR = machState.regInfos[CTRIndex];
if (machState.localSelves)
{
if (iLocalSelves)
free(iLocalSelves);
iNumLocalSelves = machState.numLocalSelves;
iLocalSelves = malloc(
sizeof(VarInfo) * iNumLocalSelves);
memcpy(iLocalSelves, machState.localSelves,
sizeof(VarInfo) * iNumLocalSelves);
}
if (machState.localVars)
{
if (iLocalVars)
free(iLocalVars);
iNumLocalVars = machState.numLocalVars;
iLocalVars = malloc(
sizeof(VarInfo) * iNumLocalVars);
memcpy(iLocalVars, machState.localVars,
sizeof(VarInfo) * iNumLocalVars);
}
// Optionally add a blank line before this block.
if (iOpts.separateLogicalBlocks && inLine->chars[0] != '\n' &&
!inLine->info.isFunction)
needNewLine = YES;
break;
} // for (i = 0...)
return needNewLine;
}
// lineIsFunction:
// ----------------------------------------------------------------------------
- (BOOL)lineIsFunction: (Line*)inLine
{
if (!inLine)
return NO;
uint32_t theAddy = inLine->info.address;
if (theAddy == iAddrDyldStubBindingHelper ||
theAddy == iAddrDyldFuncLookupPointer)
return YES;
MethodInfo* theDummyInfo = NULL;
// In Obj-C apps, the majority of funcs will have Obj-C symbols, so check
// those first.
if ([self findClassMethod:&theDummyInfo byAddress:theAddy])
return YES;
if ([self findCatMethod:&theDummyInfo byAddress:theAddy])
return YES;
// If it's not an Obj-C method, maybe there's an nlist.
if ([self findSymbolByAddress:theAddy])
return YES;
// If otool gave us a function name...
if (inLine->prev && !inLine->prev->info.isCode)
return YES;
BOOL isFunction = NO;
uint32_t theCode = *(uint32_t*)inLine->info.code;
theCode = OSSwapBigToHostInt32(theCode);
if ((theCode & 0xfc1fffff) == 0x7c0802a6) // mflr to any reg
{ // Allow for late mflr
BOOL foundUB = NO;
Line* thePrevLine = inLine->prev;
// Walk back to the most recent unconditional branch, looking
// for existing symbols.
while (!foundUB && thePrevLine)
{
// Allow for multiple mflr's
if (thePrevLine->info.isFunction)
return NO;
theCode = *(uint32_t*)thePrevLine->info.code;
theCode = OSSwapBigToHostInt32(theCode);
if ((theCode & 0xfc0007ff) == 0x7c000008) // trap
{
foundUB = YES;
continue;
}
UInt8 opcode = PO(theCode);
if (opcode == 16 || opcode == 18 || opcode == 19)
// bc, bca, bcl, bcla, b, ba, bl, bla, bclr, bclrl and more
{
if (!IS_BRANCH_CONDITIONAL(theCode) &&
theCode != 0x429f0005 && // bcl w/ "always branch"
(theCode & 0x48000001) != 0x48000001) // bl
foundUB = YES;
}
if (!foundUB)
thePrevLine = thePrevLine->prev;
}
if (!thePrevLine)
return YES;
thePrevLine = thePrevLine->next;
// If the code line following the most recent unconditional
// branch is not already recognized, flag it now.
if (thePrevLine == inLine)
isFunction = YES;
else
{
BOOL foundStart = NO;
for (; thePrevLine != inLine;
thePrevLine = thePrevLine->next)
{
if (!thePrevLine->info.isCode)
continue; // not code, keep looking
else if (!thePrevLine->info.isFunction)
{ // not yet recognized, try it
theCode = *(uint32_t*)thePrevLine->info.code;
theCode = OSSwapBigToHostInt32(theCode);
if (theCode == 0x7fe00008 || // ignore traps
theCode == 0x60000000 || // ignore nops
theCode == 0x00000000) // ignore .longs
continue;
else
{
thePrevLine->info.isFunction = YES;
foundStart = YES;
break;
}
}
else // already recognized, bail
{
foundStart = YES;
break;
}
}
if (!foundStart)
isFunction = YES;
}
} // if (theCode == 0x7c0802a6)
return isFunction;
}
// codeIsBlockJump:
// ----------------------------------------------------------------------------
- (BOOL)codeIsBlockJump: (UInt8*)inCode
{
uint32_t theCode = *(uint32_t*)inCode;
theCode = OSSwapBigToHostInt32(theCode);
return IS_BLOCK_BRANCH(theCode);
}
// gatherFuncInfos
// ----------------------------------------------------------------------------
- (void)gatherFuncInfos
{
Line* theLine = iPlainLineListHead;
uint32_t theCode;
uint32_t progCounter = 0;
// Loop thru lines.
while (theLine)
{
if (!(progCounter % (PROGRESS_FREQ * 5)))
{
if (gCancel == YES)
return;
// [NSThread sleepForTimeInterval: 0.0];
}
if (!theLine->info.isCode)
{
theLine = theLine->next;
continue;
}
theCode = *(uint32_t*)theLine->info.code;
theCode = OSSwapBigToHostInt32(theCode);
if (theLine->info.isFunction)
{
iCurrentFuncPtr = theLine->info.address;
[self resetRegisters:theLine];
}
else
[self restoreRegisters:theLine];
[self updateRegisters:theLine];
// Check if we need to save the machine state.
if (IS_BLOCK_BRANCH(theCode) && iCurrentFuncInfoIndex >= 0 &&
PO(theCode) != 0x13) // no new blocks for blr, bctr
{
uint32_t branchTarget = 0;
// Retrieve the branch target.
if (PO(theCode) == 0x12) // b
branchTarget = theLine->info.address + LI(theCode);
else if (PO(theCode) == 0x10) // bc
branchTarget = theLine->info.address + BD(theCode);
// Retrieve current FunctionInfo.
FunctionInfo* funcInfo =
&iFuncInfos[iCurrentFuncInfoIndex];
// 'currentBlock' will point to either an existing block which
// we will update, or a newly allocated block.
BlockInfo* currentBlock = NULL;
Line* endLine = NULL;
BOOL isEpilog = NO;
uint32_t i;
if (funcInfo->blocks)
{ // Blocks exist, find 1st one matching this address.
// This is an exhaustive search, but the speed hit should
// only be an issue with extremely long functions.
for (i = 0; i < funcInfo->numBlocks; i++)
{
if (funcInfo->blocks[i].beginAddress == branchTarget)
{
currentBlock = &funcInfo->blocks[i];
break;
}
}
if (currentBlock)
{ // Determine if the target block is an epilog.
if (currentBlock->endLine == NULL &&
iOpts.returnStatements)
{
// Find the first line of the target block.
Line searchKey = {NULL, 0, NULL, NULL, NULL, {branchTarget, {0}, YES, NO}};
Line* searchKeyPtr = &searchKey;
Line** beginLine = bsearch(&searchKeyPtr, iLineArray, iNumCodeLines, sizeof(Line*),
(COMPARISON_FUNC_TYPE)Line_Address_Compare);
if (beginLine != NULL)
{
// Walk through the block. It's an epilog if it ends
// with 'blr' and contains no 'bl's.
Line* nextLine = *beginLine;
BOOL canBeEpliog = YES;
uint32_t tempCode;
while (nextLine)
{
tempCode = *(uint32_t*)nextLine->info.code;
tempCode = OSSwapBigToHostInt32(tempCode);
if (IS_BRANCH_LINK(tempCode))
canBeEpliog = NO;
if (IS_BLOCK_BRANCH(tempCode))
{
endLine = nextLine;
if (canBeEpliog && IS_BLR(tempCode))
isEpilog = YES;
break;
}
nextLine = nextLine->next;
}
}
// currentBlock->endLine = endLine;
}
}
else
{ // No matching blocks found, so allocate a new one.
funcInfo->numBlocks++;
funcInfo->blocks = realloc(funcInfo->blocks,
sizeof(BlockInfo) * funcInfo->numBlocks);
currentBlock =
&funcInfo->blocks[funcInfo->numBlocks - 1];
*currentBlock = (BlockInfo){0};
}
}
else
{ // No existing blocks, allocate one.
funcInfo->numBlocks++;
funcInfo->blocks = calloc(1, sizeof(BlockInfo));
currentBlock = funcInfo->blocks;
}
// sanity check
if (!currentBlock)
{
fprintf(stderr, "otx: [PPCProcessor gatherFuncInfos] "
"currentBlock is NULL. Flame the dev.\n");
return;
}
// Create a new MachineState.
GPRegisterInfo* savedRegs = malloc(
sizeof(GPRegisterInfo) * 34);
memcpy(savedRegs, iRegInfos, sizeof(GPRegisterInfo) * 32);
savedRegs[LRIndex] = iLR;
savedRegs[CTRIndex] = iCTR;
VarInfo* savedSelves = NULL;
if (iLocalSelves)
{
savedSelves = malloc(
sizeof(VarInfo) * iNumLocalSelves);
memcpy(savedSelves, iLocalSelves,
sizeof(VarInfo) * iNumLocalSelves);
}
VarInfo* savedVars = NULL;
if (iLocalVars)
{
savedVars = malloc(
sizeof(VarInfo) * iNumLocalVars);
memcpy(savedVars, iLocalVars,
sizeof(VarInfo) * iNumLocalVars);
}
MachineState machState =
{savedRegs, savedSelves, iNumLocalSelves,
savedVars, iNumLocalVars};
// Store the new BlockInfo.
BlockInfo blockInfo =
{branchTarget, endLine, isEpilog, machState};
memcpy(currentBlock, &blockInfo, sizeof(BlockInfo));
}
theLine = theLine->next;
progCounter++;
}
iCurrentFuncInfoIndex = -1;
}
#ifdef OTX_DEBUG
// printBlocks:
// ----------------------------------------------------------------------------
- (void)printBlocks: (uint32_t)inFuncIndex;
{
if (!iFuncInfos)
return;
FunctionInfo* funcInfo = &iFuncInfos[inFuncIndex];
if (!funcInfo || !funcInfo->blocks)
return;
uint32_t i, j;
fprintf(stderr, "\nfunction at 0x%x:\n\n", funcInfo->address);
fprintf(stderr, "%d blocks\n", funcInfo->numBlocks);
for (i = 0; i < funcInfo->numBlocks; i++)
{
fprintf(stderr, "\nblock %d at 0x%x:\n\n", i + 1,
funcInfo->blocks[i].beginAddress);
for (j = 0; j < 32; j++)
{
if (!funcInfo->blocks[i].state.regInfos[j].isValid)
continue;
fprintf(stderr, "\t\tr%d: 0x%x\n", j,
funcInfo->blocks[i].state.regInfos[j].value);
}
}
}
#endif // OTX_DEBUG
@end
|
github
|
zhangchn/otx-master
|
Exe32Processor.m
|
.m
|
otx-master/src/source/Processors/Exe32Processor.m
| 71,832 |
utf_8
|
fb7d3166b5926cb8213fe98a8dd69574
|
/*
Exe32Processor.m
This file relies upon, and steals code from, the cctools source code
available from: http://www.opensource.apple.com/darwinsource/
This file is in the public domain.
*/
#import <Cocoa/Cocoa.h>
#import <mach/mach_time.h>
#import "Exe32Processor.h"
#import "ArchSpecifics.h"
#import "ListUtils.h"
#import "ObjcAccessors.h"
#import "ObjectLoader.h"
#import "Searchers.h"
#import "SysUtils.h"
#import "UserDefaultKeys.h"
#import "X86Processor.h"
@implementation Exe32Processor
// Exe32Processor is a base class that handles processor-independent issues.
// PPCProcessor and X86Processor are subclasses that add functionality
// specific to those CPUs. The AppController class creates a new instance of
// one of those subclasses for each processing, and deletes the instance as
// soon as possible. Member variables may or may not be re-initialized before
// destruction. Do not reuse a single instance of those subclasses for
// multiple processings.
// initWithURL:controller:options:
// ----------------------------------------------------------------------------
- (id)initWithURL: (NSURL*)inURL
controller: (id)inController
options: (ProcOptions*)inOptions
{
if (!inURL || !inController || !inOptions)
return nil;
if ((self = [super initWithURL: inURL controller: inController
options: inOptions]) == nil)
return nil;
return self;
}
// dealloc
// ----------------------------------------------------------------------------
- (void)dealloc
{
if (iFuncSyms)
{
free(iFuncSyms);
iFuncSyms = NULL;
}
if (iObjcSects)
{
free(iObjcSects);
iObjcSects = NULL;
}
if (iClassMethodInfos)
{
free(iClassMethodInfos);
iClassMethodInfos = NULL;
}
if (iCatMethodInfos)
{
free(iCatMethodInfos);
iCatMethodInfos = NULL;
}
if (iClassIvars)
{
free(iClassIvars);
iClassIvars = NULL;
}
if (iLineArray)
{
free(iLineArray);
iLineArray = NULL;
}
[self deleteFuncInfos];
[self deleteLinesFromList: iPlainLineListHead];
[self deleteLinesFromList: iVerboseLineListHead];
}
// deleteFuncInfos
// ----------------------------------------------------------------------------
- (void)deleteFuncInfos
{
if (!iFuncInfos)
return;
uint32_t i;
uint32_t j;
FunctionInfo* funcInfo;
BlockInfo* blockInfo;
for (i = 0; i < iNumFuncInfos; i++)
{
funcInfo = &iFuncInfos[i];
if (funcInfo->blocks)
{
for (j = 0; j < funcInfo->numBlocks; j++)
{
blockInfo = &funcInfo->blocks[j];
if (blockInfo->state.regInfos)
{
free(blockInfo->state.regInfos);
blockInfo->state.regInfos = NULL;
}
if (blockInfo->state.localSelves)
{
free(blockInfo->state.localSelves);
blockInfo->state.localSelves = NULL;
}
}
free(funcInfo->blocks);
funcInfo->blocks = NULL;
}
}
free(iFuncInfos);
iFuncInfos = NULL;
}
#pragma mark -
// processExe:
// ----------------------------------------------------------------------------
// The master processing method, designed to be executed in a separate thread.
- (BOOL)processExe: (NSString*)inOutputFilePath
{
if (!iFileArchMagic)
{
fprintf(stderr, "otx: tried to process non-machO file\n");
return NO;
}
iOutputFilePath = inOutputFilePath;
iMachHeaderPtr = NULL;
if (![self loadMachHeader])
{
fprintf(stderr, "otx: failed to load mach header\n");
return NO;
}
[self loadLCommands];
NSMutableDictionary* progDict =
[[NSMutableDictionary alloc] initWithObjectsAndKeys:
[NSNumber numberWithBool: YES], PRNewLineKey,
@"Calling otool", PRDescriptionKey,
nil];
#ifdef OTX_CLI
[iController reportProgress: progDict];
#else
[iController performSelectorOnMainThread: @selector(reportProgress:)
withObject: progDict waitUntilDone: NO];
#endif
[self populateLineLists];
if (gCancel == YES)
return NO;
progDict = [[NSMutableDictionary alloc] initWithObjectsAndKeys:
[NSNumber numberWithBool: YES], PRNewLineKey,
@"Gathering info", PRDescriptionKey,
nil];
#ifdef OTX_CLI
[iController reportProgress: progDict];
#else
[iController performSelectorOnMainThread: @selector(reportProgress:)
withObject: progDict waitUntilDone: NO];
#endif
// Gather info about lines while they're virgin.
[self gatherLineInfos];
if (gCancel == YES)
return NO;
// Find functions and allocate funcInfo's.
[self findFunctions];
if (gCancel == YES)
return NO;
// Gather info about logical blocks. The second pass applies info
// for backward branches.
[self gatherFuncInfos];
if (gCancel == YES)
return NO;
[self gatherFuncInfos];
if (gCancel == YES)
return NO;
uint32_t progCounter = 0;
double progValue = 0.0;
progDict = [[NSMutableDictionary alloc] initWithObjectsAndKeys:
[NSNumber numberWithBool: NO], PRIndeterminateKey,
[NSNumber numberWithDouble: progValue], PRValueKey,
[NSNumber numberWithBool: YES], PRNewLineKey,
@"Generating file", PRDescriptionKey,
nil];
#ifdef OTX_CLI
[iController reportProgress: progDict];
#else
[iController performSelectorOnMainThread: @selector(reportProgress:)
withObject: progDict waitUntilDone: NO];
#endif
Line* theLine = iPlainLineListHead;
// Loop thru lines.
while (theLine)
{
if (!(progCounter % PROGRESS_FREQ))
{
if (gCancel == YES)
return NO;
progValue = (double)progCounter / iNumLines * 100;
progDict = [[NSMutableDictionary alloc] initWithObjectsAndKeys:
[NSNumber numberWithDouble: progValue], PRValueKey,
nil];
#ifdef OTX_CLI
[iController reportProgress: progDict];
#else
[iController performSelectorOnMainThread: @selector(reportProgress:)
withObject: progDict waitUntilDone: NO];
#endif
}
if (theLine->info.isCode)
{
[self processCodeLine:&theLine];
if (iOpts.entabOutput)
[self entabLine:theLine];
}
else
[self processLine:theLine];
theLine = theLine->next;
progCounter++;
}
if (gCancel == YES)
return NO;
progDict = [[NSMutableDictionary alloc] initWithObjectsAndKeys:
[NSNumber numberWithBool: YES], PRIndeterminateKey,
[NSNumber numberWithBool: YES], PRNewLineKey,
@"Writing file", PRDescriptionKey,
nil];
#ifdef OTX_CLI
[iController reportProgress: progDict];
#else
[iController performSelectorOnMainThread: @selector(reportProgress:)
withObject: progDict waitUntilDone: NO];
#endif
// Create output file.
if (![self printLinesFromList: iPlainLineListHead])
{
return NO;
}
if (iOpts.dataSections)
{
if (![self printDataSections])
{
return NO;
}
}
progDict = [[NSMutableDictionary alloc] initWithObjectsAndKeys:
[NSNumber numberWithBool: YES], PRCompleteKey,
nil];
#ifdef OTX_CLI
[iController reportProgress: progDict];
#else
[iController performSelectorOnMainThread: @selector(reportProgress:)
withObject: progDict waitUntilDone: NO];
#endif
return YES;
}
// populateLineLists
// ----------------------------------------------------------------------------
- (BOOL)populateLineLists
{
Line* thePrevVerboseLine = NULL;
Line* thePrevPlainLine = NULL;
// Read __text lines.
[self populateLineList: &iVerboseLineListHead verbosely: YES
fromSection: "__text" afterLine: &thePrevVerboseLine
includingPath: YES];
[self populateLineList: &iPlainLineListHead verbosely: NO
fromSection: "__text" afterLine: &thePrevPlainLine
includingPath: YES];
// Read __coalesced_text lines.
if (iCoalTextSect.size)
{
[self populateLineList: &iVerboseLineListHead verbosely: YES
fromSection: "__coalesced_text" afterLine: &thePrevVerboseLine
includingPath: NO];
[self populateLineList: &iPlainLineListHead verbosely: NO
fromSection: "__coalesced_text" afterLine: &thePrevPlainLine
includingPath: NO];
}
// Read __textcoal_nt lines.
if (iCoalTextNTSect.size)
{
[self populateLineList: &iVerboseLineListHead verbosely: YES
fromSection: "__textcoal_nt" afterLine: &thePrevVerboseLine
includingPath: NO];
[self populateLineList: &iPlainLineListHead verbosely: NO
fromSection: "__textcoal_nt" afterLine: &thePrevPlainLine
includingPath: NO];
}
// Connect the 2 lists.
Line* verboseLine = iVerboseLineListHead;
Line* plainLine = iPlainLineListHead;
while (verboseLine && plainLine)
{
verboseLine->alt = plainLine;
plainLine->alt = verboseLine;
verboseLine = verboseLine->next;
plainLine = plainLine->next;
}
// Optionally insert md5.
if (iOpts.checksum)
[self insertMD5];
return YES;
}
// populateLineList:verbosely:fromSection:afterLine:includingPath:
// ----------------------------------------------------------------------------
- (BOOL)populateLineList: (Line**)inList
verbosely: (BOOL)inVerbose
fromSection: (char*)inSectionName
afterLine: (Line**)inLine
includingPath: (BOOL)inIncludePath
{
char cmdString[MAX_UNIBIN_OTOOL_CMD_SIZE] = "";
NSString* otoolPath = [self pathForTool: @"otool"];
NSUInteger otoolPathLength = [otoolPath length];
size_t archStringLength = strlen(iArchString);
// otool freaks out when somebody says -arch and it's not a unibin.
if (iExeIsFat)
{
// Bail if it won't fit.
if ((otoolPathLength + archStringLength + 7 /* strlen(" -arch ") */) >= MAX_UNIBIN_OTOOL_CMD_SIZE)
return NO;
snprintf(cmdString, MAX_UNIBIN_OTOOL_CMD_SIZE,
"%s -arch %s", [otoolPath UTF8String], iArchString);
}
else
{
// Bail if it won't fit.
if (otoolPathLength >= MAX_UNIBIN_OTOOL_CMD_SIZE)
return NO;
strncpy(cmdString, [otoolPath UTF8String], otoolPathLength);
}
NSString* oPath = [iOFile path];
NSString* otoolString = [NSString stringWithFormat:
@"%s %s -s __TEXT %s \"%@\"%s", cmdString,
(inVerbose) ? "-VQ" : "-vQ", inSectionName, oPath,
(inIncludePath) ? "" : " | sed '1 d'"];
FILE* otoolPipe = popen(UTF8STRING(otoolString), "r");
if (!otoolPipe)
{
fprintf(stderr, "otx: unable to open %s otool pipe\n",
(inVerbose) ? "verbose" : "plain");
return NO;
}
char theCLine[MAX_LINE_LENGTH];
while (fgets(theCLine, MAX_LINE_LENGTH, otoolPipe))
{
// Many thanx to Peter Hosey for the calloc speed test.
// http://boredzo.org/blog/archives/2006-11-26/calloc-vs-malloc
Line* theNewLine = calloc(1, sizeof(Line));
theNewLine->length = strlen(theCLine);
theNewLine->chars = malloc(theNewLine->length + 1);
strncpy(theNewLine->chars, theCLine,
theNewLine->length + 1);
// Add the line to the list.
[self insertLine:theNewLine after:*inLine inList:inList];
*inLine = theNewLine;
}
if (pclose(otoolPipe) == -1)
{
perror((inVerbose) ? "otx: unable to close verbose otool pipe" :
"otx: unable to close plain otool pipe");
return NO;
}
return YES;
}
#pragma mark -
// gatherLineInfos
// ----------------------------------------------------------------------------
// To make life easier as we make changes to the lines, whatever info we need
// is harvested early here.
- (void)gatherLineInfos
{
Line* theLine = iPlainLineListHead;
uint32_t progCounter = 0;
while (theLine)
{
if (!(progCounter % (PROGRESS_FREQ * 5)))
{
if (gCancel == YES)
return;
// [NSThread sleepForTimeInterval: 0.0];
}
if ([self lineIsCode:theLine->chars])
{
theLine->info.isCode = YES;
theLine->info.address = [self addressFromLine:theLine->chars];
[self codeFromLine:theLine]; // FIXME: return a value like the cool kids do.
if (theLine->alt)
{
theLine->alt->info.isCode = theLine->info.isCode;
theLine->alt->info.address = theLine->info.address;
theLine->alt->info.codeLength = theLine->info.codeLength;
memcpy(theLine->alt->info.code, theLine->info.code,
sizeof(theLine->info.code));
}
[self checkThunk:theLine];
}
else // not code...
{
if (strstr(theLine->chars, "(__TEXT,__coalesced_text)"))
iEndOfText = iCoalTextSect.s.addr + iCoalTextSect.s.size;
else if (strstr(theLine->chars, "(__TEXT,__textcoal_nt)"))
iEndOfText = iCoalTextNTSect.s.addr + iCoalTextNTSect.s.size;
}
theLine = theLine->next;
progCounter++;
iNumLines++;
}
iEndOfText = iTextSect.s.addr + iTextSect.s.size;
}
// findFunctions
// ----------------------------------------------------------------------------
- (void)findFunctions
{
// Loop once to flag all funcs.
Line* theLine = iPlainLineListHead;
while (theLine)
{
theLine->info.isFunction = [self lineIsFunction:theLine];
if (theLine->alt)
theLine->alt->info.isFunction = theLine->info.isFunction;
theLine = theLine->next;
}
// Loop again to allocate funcInfo's.
theLine = iPlainLineListHead;
iLineArray = calloc(iNumLines, sizeof(Line*));
iNumCodeLines = 0;
while (theLine)
{
if (theLine->info.isFunction)
{
iNumFuncInfos++;
iFuncInfos = realloc(iFuncInfos,
sizeof(FunctionInfo) * iNumFuncInfos);
uint32_t genericFuncNum = 0;
if (theLine->prev && theLine->prev->info.isCode)
genericFuncNum = ++iCurrentGenericFuncNum;
iFuncInfos[iNumFuncInfos - 1] = (FunctionInfo)
{theLine->info.address, NULL, 0, genericFuncNum};
}
if (theLine->info.isCode)
iLineArray[iNumCodeLines++] = theLine;
theLine = theLine->next;
}
}
// processLine:
// ----------------------------------------------------------------------------
- (void)processLine: (Line*)ioLine;
{
if (!strlen(ioLine->chars))
return;
// otool is inconsistent in printing section headers. Sometimes it
// prints "Contents of (x)" and sometimes just "(x)". We'll take this
// opportunity to use the shorter version in all cases.
char* theContentsString = "Contents of ";
UInt8 theContentsStringLength = strlen(theContentsString);
char* theTextSegString = "(__TEXT,__";
// Kill the "Contents of" if it exists.
if (strstr(ioLine->chars, theContentsString))
{
char theTempLine[MAX_LINE_LENGTH];
theTempLine[0] = '\n';
theTempLine[1] = 0;
strncat(theTempLine, &ioLine->chars[theContentsStringLength],
strlen(&ioLine->chars[theContentsStringLength]));
ioLine->length = strlen(theTempLine);
strncpy(ioLine->chars, theTempLine, ioLine->length + 1);
return;
}
else if (strstr(ioLine->chars, theTextSegString))
{
if (strstr(ioLine->chars, "__coalesced_text)"))
{
iEndOfText = iCoalTextSect.s.addr + iCoalTextSect.s.size;
iCurrentFunctionStart = ioLine->info.address;
}
else if (strstr(ioLine->chars, "__textcoal_nt)"))
{
iEndOfText = iCoalTextNTSect.s.addr + iCoalTextNTSect.s.size;
iCurrentFunctionStart = ioLine->info.address;
}
char theTempLine[MAX_LINE_LENGTH];
theTempLine[0] = '\n';
theTempLine[1] = 0;
strncat(theTempLine, ioLine->chars, strlen(ioLine->chars));
ioLine->length++;
ioLine->chars = (char*)realloc(ioLine->chars, ioLine->length + 1);
strncpy(ioLine->chars, theTempLine, ioLine->length + 1);
return;
}
// If we got here, we have a symbol name.
if (iOpts.demangleCppNames)
{
if (strstr(ioLine->chars, "__Z") == ioLine->chars)
{
char demangledName[MAX_LINE_LENGTH];
// Line should end with ":\n". Terminate over the colon if it exists.
if (ioLine->chars[ioLine->length - 2] == ':')
ioLine->chars[ioLine->length - 2] = 0;
else
ioLine->chars[ioLine->length - 1] = 0;
NSFileHandle* filtWrite = [iCPFiltInputPipe fileHandleForWriting];
NSFileHandle* filtRead = [iCPFiltOutputPipe fileHandleForReading];
NSMutableData* dataToWrite = [NSMutableData dataWithBytes: ioLine->chars
length: strlen(ioLine->chars)];
[dataToWrite appendBytes: "\n"
length: 1];
@try {
[filtWrite writeData: dataToWrite];
}
@catch (NSException* e) {
NSLog(@"otx: [Exe32Processor processLine:] failed to write to c++filt: %@", [e reason]);
}
NSData* readData = nil;
@try {
readData = [filtRead availableData];
}
@catch (NSException* e) {
NSLog(@"otx: [Exe32Processor processLine:] failed to read from c++filt: %@", [e reason]);
}
if (readData != nil)
{
NSUInteger demangledDataLength = [readData length];
NSUInteger demangledStringLength = MIN(demangledDataLength, MAX_LINE_LENGTH - 1);
if (demangledStringLength < demangledDataLength)
NSLog(@"otx: demangled C++ name is too large. Increase MAX_LINE_LENGTH to %lu.\n"
"Name demangling will now go off the rails.", (unsigned long)demangledDataLength);
// Get the string and terminate it.
[readData getBytes: demangledName
length: demangledStringLength];
demangledName[demangledStringLength] = 0;
free(ioLine->chars);
ioLine->length = demangledStringLength;
ioLine->chars = malloc(ioLine->length + 1);
strncpy(ioLine->chars, demangledName, ioLine->length + 1);
}
else
{
NSLog(@"otx: [Exe32Processor processLine:] got nil data from c++filt");
}
}
}
}
// processCodeLine:
// ----------------------------------------------------------------------------
- (void)processCodeLine: (Line**)ioLine;
{
if (!ioLine || !(*ioLine) || !((*ioLine)->chars))
{
fprintf(stderr, "otx: tried to process NULL code line\n");
return;
}
[self chooseLine:ioLine];
size_t theOrigLength = (*ioLine)->length;
char localOffsetString[9] = {0};
char theAddressCString[9] = {0};
char theMnemonicCString[20] = {0};
char addrSpaces[MAX_FIELD_SPACING];
char instSpaces[MAX_FIELD_SPACING];
char mnemSpaces[MAX_FIELD_SPACING];
char opSpaces[MAX_FIELD_SPACING];
char commentSpaces[MAX_FIELD_SPACING];
char theOrigCommentCString[MAX_COMMENT_LENGTH];
char theCommentCString[MAX_COMMENT_LENGTH];
theOrigCommentCString[0] = 0;
theCommentCString[0] = 0;
// Swap in saved registers if necessary
BOOL needNewLine = [self restoreRegisters:*ioLine];
iLineOperandsCString[0] = 0;
char* origFormatString = "%s\t%s\t%s%n";
uint32_t consumedAfterOp = 0;
// The address and mnemonic always exist, separated by a tab.
sscanf((*ioLine)->chars, origFormatString, theAddressCString,
theMnemonicCString, iLineOperandsCString, &consumedAfterOp);
// If we didn't grab everything up to the newline, there's a comment
// remaining. Copy it, starting after the preceding tab.
if (consumedAfterOp && consumedAfterOp < theOrigLength - 1)
{
size_t origCommentLength = theOrigLength - consumedAfterOp - 1;
strncpy(theOrigCommentCString, (*ioLine)->chars + consumedAfterOp + 1,
origCommentLength);
// Add the null terminator.
theOrigCommentCString[origCommentLength - 1] = 0;
}
char theCodeCString[32] = {0};
UInt8* inBuffer = (*ioLine)->info.code;
SInt16 i;
char codeFormatString[61] = "%02x%02x%02x%02x%02x%02x%02x%02x%02x%02x%02x%02x%02x%02x%02x";
if ((*ioLine)->info.codeLength > 15)
{
fprintf(stderr, "otx: surprisingly long instruction of %u bytes at 0x%08x\n", (*ioLine)->info.codeLength, (*ioLine)->info.address);
return;
}
codeFormatString[(*ioLine)->info.codeLength * 4] = 0;
snprintf(theCodeCString, 31, codeFormatString,
inBuffer[0], inBuffer[1], inBuffer[2], inBuffer[3],
inBuffer[4], inBuffer[5], inBuffer[6], inBuffer[7],
inBuffer[8], inBuffer[9], inBuffer[10], inBuffer[11],
inBuffer[12], inBuffer[13], inBuffer[14]);
i = iFieldWidths.instruction - strlen(theCodeCString);
mnemSpaces[i - 1] = 0;
for (; i > 1; i--)
mnemSpaces[i - 2] = 0x20;
i = iFieldWidths.mnemonic - strlen(theMnemonicCString);
opSpaces[i - 1] = 0;
for (; i > 1; i--)
opSpaces[i - 2] = 0x20;
// Fill up commentSpaces based on operands field width.
if (iLineOperandsCString[0] && theOrigCommentCString[0])
{
i = iFieldWidths.operands - strlen(iLineOperandsCString);
commentSpaces[i - 1] = 0;
for (; i > 1; i--)
commentSpaces[i - 2] = 0x20;
}
// Remove "; symbol stub for: "
if (theOrigCommentCString[0])
{
char* theSubstring =
strstr(theOrigCommentCString, "; symbol stub for: ");
if (theSubstring)
snprintf(theCommentCString, MAX_COMMENT_LENGTH, "%s", &theOrigCommentCString[19]);
else
snprintf(theCommentCString, MAX_COMMENT_LENGTH, "%s", theOrigCommentCString);
}
BOOL needFuncName = NO;
char theMethCName[1000];
theMethCName[0] = 0;
// Check if this is the beginning of a function.
if ((*ioLine)->info.isFunction)
{
// Squash the new block flag, just in case.
iEnteringNewBlock = NO;
// New function, new local offset count and current func.
iCurrentFunctionStart = iCurrentFuncPtr = (*ioLine)->info.address;
// Try to build the method name.
MethodInfo* theSwappedInfoPtr = NULL;
MethodInfo theSwappedInfo;
if ([self getObjcMethod:&theSwappedInfoPtr fromAddress:iCurrentFuncPtr])
{
theSwappedInfo = *theSwappedInfoPtr;
char* className = NULL;
char* catName = NULL;
if (iObjcVersion < 2)
{
if (iSwapped)
{
swap_objc1_32_method(&theSwappedInfo.m);
swap_objc1_32_class(&theSwappedInfo.oc_class);
swap_objc1_32_category(&theSwappedInfo.oc_cat);
}
if (theSwappedInfo.oc_cat.category_name)
{
className = [self getPointer:theSwappedInfo.oc_cat.class_name type:NULL];
catName = [self getPointer:theSwappedInfo.oc_cat.category_name type:NULL];
}
else if (theSwappedInfo.oc_class.name)
{
className = [self getPointer:theSwappedInfo.oc_class.name type:NULL];
}
}
else if (iObjcVersion == 2)
{
if (iSwapped)
{
swap_objc2_32_method(&theSwappedInfo.m2);
swap_objc2_32_class(&theSwappedInfo.oc_class2);
}
if (theSwappedInfo.oc_class2.data)
{
objc2_32_class_ro_t* roData = (objc2_32_class_ro_t*)(iObjcConstSect.contents +
(uintptr_t)(theSwappedInfo.oc_class2.data - iObjcConstSect.s.addr));
UInt32 name = roData->name;
if (iSwapped)
name = OSSwapInt32(name);
className = [self getPointer:name type:NULL];
}
}
if (className)
{
char* selName = [self getPointer:theSwappedInfo.m.method_name type:NULL];
if (selName)
{
if (!theSwappedInfo.m.method_types)
return;
char* methTypes = [self getPointer:theSwappedInfo.m.method_types type:NULL];
char returnCType[MAX_TYPE_STRING_LENGTH];
returnCType[0] = 0;
if (methTypes)
{
[self decodeMethodReturnType: methTypes
output: returnCType];
}
else
{
strncpy(returnCType, "???", 4);
}
if (catName)
{
char* methNameFormat = iOpts.returnTypes ?
"\n%1$c(%5$s)[%2$s(%3$s) %4$s]:\n" :
"\n%c[%s(%s) %s]:\n";
snprintf(theMethCName, 1000,
methNameFormat,
(theSwappedInfo.inst) ? '-' : '+',
className, catName, selName, returnCType);
}
else
{
char* methNameFormat = iOpts.returnTypes ?
"\n%1$c(%4$s)[%2$s %3$s]:\n" : "\n%c[%s %s]:\n";
snprintf(theMethCName, 1000,
methNameFormat,
(theSwappedInfo.inst) ? '-' : '+',
className, selName, returnCType);
}
}
}
} // if ([self getObjcMethod:&theSwappedInfoPtr fromAddress:mCurrentFuncPtr])
// Add or replace the method name if possible, else add '\n'.
if ((*ioLine)->prev && (*ioLine)->prev->info.isCode) // prev line is code
{
if (theMethCName[0])
{
Line* theNewLine = malloc(sizeof(Line));
theNewLine->length = strlen(theMethCName);
theNewLine->chars = malloc(theNewLine->length + 1);
strncpy(theNewLine->chars, theMethCName,
theNewLine->length + 1);
[self insertLine:theNewLine before:*ioLine inList:&iPlainLineListHead];
}
else if ((*ioLine)->info.address == iAddrDyldStubBindingHelper)
{
Line* theNewLine = malloc(sizeof(Line));
char* theDyldName = "\ndyld_stub_binding_helper:\n";
theNewLine->length = strlen(theDyldName);
theNewLine->chars = malloc(theNewLine->length + 1);
strncpy(theNewLine->chars, theDyldName, theNewLine->length + 1);
[self insertLine:theNewLine before:*ioLine inList:&iPlainLineListHead];
}
else if ((*ioLine)->info.address == iAddrDyldFuncLookupPointer)
{
Line* theNewLine = malloc(sizeof(Line));
char* theDyldName = "\n__dyld_func_lookup:\n";
theNewLine->length = strlen(theDyldName);
theNewLine->chars = malloc(theNewLine->length + 1);
strncpy(theNewLine->chars, theDyldName, theNewLine->length + 1);
[self insertLine:theNewLine before:*ioLine inList:&iPlainLineListHead];
}
else
needFuncName = YES;
}
else // prev line is not code
{
if (theMethCName[0])
{
Line* theNewLine = malloc(sizeof(Line));
theNewLine->length = strlen(theMethCName);
theNewLine->chars = malloc(theNewLine->length + 1);
strncpy(theNewLine->chars, theMethCName,
theNewLine->length + 1);
[self replaceLine:(*ioLine)->prev withLine:theNewLine inList:&iPlainLineListHead];
}
else
{ // theMethName sux, add '\n' to otool's method name.
char theNewLine[MAX_LINE_LENGTH];
if ((*ioLine)->prev->chars[0] != '\n')
{
theNewLine[0] = '\n';
theNewLine[1] = 0;
}
else
theNewLine[0] = 0;
strncat(theNewLine, (*ioLine)->prev->chars,
(*ioLine)->prev->length);
free((*ioLine)->prev->chars);
(*ioLine)->prev->length = strlen(theNewLine);
(*ioLine)->prev->chars = malloc((*ioLine)->prev->length + 1);
strncpy((*ioLine)->prev->chars, theNewLine,
(*ioLine)->prev->length + 1);
}
}
[self resetRegisters:*ioLine];
} // if ((*ioLine)->info.isFunction)
// Find a comment if necessary.
if (!theCommentCString[0])
{
[self commentForLine:*ioLine];
size_t origCommentLength = strlen(iLineCommentCString);
if (origCommentLength)
{
char tempComment[MAX_COMMENT_LENGTH];
uint32_t i, j = 0;
// Escape newlines, carriage returns and tabs.
for (i = 0; i < origCommentLength; i++)
{
if (iLineCommentCString[i] == '\n')
{
tempComment[j++] = '\\';
tempComment[j++] = 'n';
}
else if (iLineCommentCString[i] == '\r')
{
tempComment[j++] = '\\';
tempComment[j++] = 'r';
}
else if (iLineCommentCString[i] == '\t')
{
tempComment[j++] = '\\';
tempComment[j++] = 't';
}
else
tempComment[j++] = iLineCommentCString[i];
}
// Add the null terminator.
tempComment[j] = 0;
if (iLineOperandsCString[0])
snprintf(theCommentCString, MAX_COMMENT_LENGTH, "%s", tempComment);
else
snprintf(iLineOperandsCString, MAX_COMMENT_LENGTH, "%s", tempComment);
// Fill up commentSpaces based on operands field width.
SInt32 k = (SInt32)(iFieldWidths.operands - strlen(iLineOperandsCString));
commentSpaces[k - 1] = 0;
for (; k > 1; k--)
commentSpaces[k - 2] = 0x20;
}
} // if (!theCommentCString[0])
else // otool gave us a comment.
{
// Optionally modify otool's comment.
if (iOpts.verboseMsgSends)
[self commentForMsgSend:theCommentCString fromLine:*ioLine];
}
// Demangle operands if necessary.
if (iLineOperandsCString[0] && iOpts.demangleCppNames)
{
if (strstr(iLineOperandsCString, "__Z") == iLineOperandsCString)
{
char demangledName[MAX_OPERANDS_LENGTH];
NSFileHandle* filtWrite = [iCPFiltInputPipe fileHandleForWriting];
NSFileHandle* filtRead = [iCPFiltOutputPipe fileHandleForReading];
NSMutableData* dataToWrite = [NSMutableData dataWithBytes: iLineOperandsCString
length: strlen(iLineOperandsCString)];
[dataToWrite appendBytes: "\n"
length: 1];
@try {
[filtWrite writeData: dataToWrite];
}
@catch (NSException* e) {
NSLog(@"otx: [Exe32Processor processCodeLine:] failed to write operands to c++filt: %@", [e reason]);
}
NSData* readData = nil;
@try {
readData = [filtRead availableData];
}
@catch (NSException* e) {
NSLog(@"otx: [Exe32Processor processCodeLine:] failed to read operands from c++filt: %@", [e reason]);
}
if (readData != nil)
{
NSUInteger demangledDataLength = [readData length];
NSUInteger demangledStringLength = MIN(demangledDataLength, MAX_OPERANDS_LENGTH - 1);
if (demangledStringLength < demangledDataLength)
NSLog(@"otx: demangled C++ name is too large. Increase MAX_OPERANDS_LENGTH to %lu.\n"
"Name demangling will now go off the rails.", (unsigned long)demangledDataLength);
[readData getBytes: demangledName
length: demangledStringLength];
// Remove the trailing newline and terminate.
demangledStringLength--;
demangledName[demangledStringLength] = 0;
strncpy(iLineOperandsCString, demangledName, demangledStringLength + 1);
}
else
{
NSLog(@"otx: [Exe32Processor processCodeLine:] got nil operands data from c++filt");
}
}
}
// Demangle comment if necessary.
if (theCommentCString[0] && iOpts.demangleCppNames)
{
if (strstr(theCommentCString, "__Z") == theCommentCString)
{
char demangledName[MAX_COMMENT_LENGTH];
NSFileHandle* filtWrite = [iCPFiltInputPipe fileHandleForWriting];
NSFileHandle* filtRead = [iCPFiltOutputPipe fileHandleForReading];
NSMutableData* dataToWrite = [NSMutableData dataWithBytes: theCommentCString
length: strlen(theCommentCString)];
[dataToWrite appendBytes: "\n"
length: 1];
@try {
[filtWrite writeData: dataToWrite];
}
@catch (NSException* e) {
NSLog(@"otx: [Exe32Processor processCodeLine:] failed to write comment to c++filt: %@", [e reason]);
}
NSData* readData = nil;
@try {
readData = [filtRead availableData];
}
@catch (NSException* e) {
NSLog(@"otx: [Exe32Processor processCodeLine:] failed to read comment from c++filt: %@", [e reason]);
}
if (readData != nil)
{
NSUInteger demangledDataLength = [readData length];
NSUInteger demangledStringLength = MIN(demangledDataLength, MAX_COMMENT_LENGTH - 1);
if (demangledStringLength < demangledDataLength)
NSLog(@"otx: demangled C++ name is too large. Increase MAX_COMMENT_LENGTH to %lu.\n"
"Name demangling will now go off the rails.", (unsigned long)demangledDataLength);
[readData getBytes: demangledName
length: demangledStringLength];
// Remove the trailing newline and terminate.
demangledStringLength--;
demangledName[demangledStringLength] = 0;
strncpy(theCommentCString, demangledName, demangledStringLength + 1);
}
else
{
NSLog(@"otx: [Exe32Processor processCodeLine:] got nil comment data from c++filt");
}
}
}
// Optionally add local offset.
if (iOpts.localOffsets)
{
// Build a right-aligned string with a '+' in it.
snprintf((char*)&localOffsetString, iFieldWidths.offset,
"%6u", ((*ioLine)->info.address - iCurrentFunctionStart));
// Find the space that's followed by a nonspace.
// *Reverse count to optimize for short functions.
for (i = 0; i < 5; i++)
{
if (localOffsetString[i] == 0x20 &&
localOffsetString[i + 1] != 0x20)
{
localOffsetString[i] = '+';
break;
}
}
// Fill up addrSpaces based on offset field width.
i = iFieldWidths.offset - 6;
addrSpaces[i - 1] = 0;
for (; i > 1; i--)
addrSpaces[i - 2] = 0x20;
}
// Fill up instSpaces based on address field width.
i = iFieldWidths.address - 8;
instSpaces[i - 1] = 0;
for (; i > 1; i--)
instSpaces[i - 2] = 0x20;
// Insert a generic function name if needed.
if (needFuncName)
{
FunctionInfo searchKey = {(*ioLine)->info.address, NULL, 0, 0};
FunctionInfo* funcInfo = bsearch(&searchKey,
iFuncInfos, iNumFuncInfos, sizeof(FunctionInfo),
(COMPARISON_FUNC_TYPE)Function_Info_Compare);
// sizeof(UINT32_MAX) + '\n' * 2 + ':' + null term
UInt8 maxlength = ANON_FUNC_BASE_LENGTH + 14;
Line* funcName = calloc(1, sizeof(Line));
funcName->chars = malloc(maxlength);
// Hack Alert: In the case that we have too few funcInfo's, print
// \nAnon???. Of course, we'll still intermittently crash later, but
// when we don't, the output will look pretty.
// Replace "if (funcInfo)" from rev 319 around this...
if (funcInfo)
funcName->length = snprintf(funcName->chars, maxlength,
"\n%s%d:\n", ANON_FUNC_BASE, funcInfo->genericFuncNum);
else
funcName->length = snprintf(funcName->chars, maxlength,
"\n%s???:\n", ANON_FUNC_BASE);
[self insertLine:funcName before:*ioLine inList:&iPlainLineListHead];
}
// Finally, assemble the new string.
char finalFormatCString[MAX_FORMAT_LENGTH];
uint32_t formatMarker = 0;
if (needNewLine)
{
formatMarker++;
finalFormatCString[0] = '\n';
finalFormatCString[1] = 0;
}
else
finalFormatCString[0] = 0;
if (iOpts.localOffsets)
formatMarker += snprintf(&finalFormatCString[formatMarker],
10, "%s", "%s %s");
if (iOpts.showCode)
formatMarker += snprintf(&finalFormatCString[formatMarker],
10, "%s", "%s %s");
if (iLineOperandsCString[0])
{
if (theCommentCString[0])
snprintf(&finalFormatCString[formatMarker],
30, "%s", "%s %s%s %s%s %s%s\n");
else
snprintf(&finalFormatCString[formatMarker],
30, "%s", "%s %s%s %s%s\n");
}
else
snprintf(&finalFormatCString[formatMarker],
30, "%s", "%s %s%s\n");
char theFinalCString[MAX_LINE_LENGTH] = "";
if (iOpts.localOffsets && iOpts.showCode)
snprintf(theFinalCString, MAX_LINE_LENGTH,
finalFormatCString, localOffsetString,
addrSpaces, theAddressCString,
instSpaces, theCodeCString,
mnemSpaces, theMnemonicCString,
opSpaces, iLineOperandsCString,
commentSpaces, theCommentCString);
else if (iOpts.localOffsets)
snprintf(theFinalCString, MAX_LINE_LENGTH,
finalFormatCString, localOffsetString,
addrSpaces, theAddressCString,
instSpaces, theMnemonicCString,
opSpaces, iLineOperandsCString,
commentSpaces, theCommentCString);
else if (iOpts.showCode)
snprintf(theFinalCString, MAX_LINE_LENGTH,
addrSpaces, theAddressCString,
instSpaces, theCodeCString,
mnemSpaces, theMnemonicCString,
opSpaces, iLineOperandsCString,
commentSpaces, theCommentCString);
else
snprintf(theFinalCString, MAX_LINE_LENGTH,
finalFormatCString, theAddressCString,
instSpaces, theMnemonicCString,
opSpaces, iLineOperandsCString,
commentSpaces, theCommentCString);
free((*ioLine)->chars);
if (iOpts.separateLogicalBlocks && iEnteringNewBlock &&
theFinalCString[0] != '\n')
{
(*ioLine)->length = strlen(theFinalCString) + 1;
(*ioLine)->chars = malloc((*ioLine)->length + 1);
(*ioLine)->chars[0] = '\n';
strncpy(&(*ioLine)->chars[1], theFinalCString, (*ioLine)->length);
}
else
{
(*ioLine)->length = strlen(theFinalCString);
(*ioLine)->chars = malloc((*ioLine)->length + 1);
strncpy((*ioLine)->chars, theFinalCString, (*ioLine)->length + 1);
}
// The test above can fail even if mEnteringNewBlock was YES, so we
// should reset it here instead.
iEnteringNewBlock = NO;
[self updateRegisters:*ioLine];
[self postProcessCodeLine:ioLine];
// Possibly prepend a \n to the following line.
if ([self codeIsBlockJump:(*ioLine)->info.code])
iEnteringNewBlock = YES;
}
// addressFromLine:
// ----------------------------------------------------------------------------
- (uint32_t)addressFromLine: (const char*)inLine
{
// sanity check
if ((inLine[0] < '0' || inLine[0] > '9') &&
(inLine[0] < 'a' || inLine[0] > 'f'))
return 0;
uint32_t theAddress = 0;
sscanf(inLine, "%08x", &theAddress);
return theAddress;
}
// lineIsCode:
// ----------------------------------------------------------------------------
// Line is code if first 8 chars are hex numbers and 9th is tab.
- (BOOL)lineIsCode: (const char*)inLine
{
if (strlen(inLine) < 10)
return NO;
UInt16 i;
for (i = 0 ; i < 8; i++)
{
if ((inLine[i] < '0' || inLine[i] > '9') &&
(inLine[i] < 'a' || inLine[i] > 'f'))
return NO;
}
return (inLine[8] == '\t');
}
// chooseLine:
// ----------------------------------------------------------------------------
// Subclasses may override.
- (void)chooseLine: (Line**)ioLine
{}
#pragma mark -
// printDataSections
// ----------------------------------------------------------------------------
// Append data sections to output file.
- (BOOL)printDataSections
{
FILE* outFile = NULL;
if (iOutputFilePath)
outFile = fopen(UTF8STRING(iOutputFilePath), "a");
else
outFile = stdout;
if (!outFile)
{
perror("otx: unable to open output file");
return NO;
}
if (iDataSect.size)
{
if (fprintf(outFile, "\n(__DATA,__data) section\n") < 0)
{
perror("otx: unable to write to output file");
return NO;
}
[self printDataSection: &iDataSect toFile: outFile];
}
if (iCoalDataSect.size)
{
if (fprintf(outFile, "\n(__DATA,__coalesced_data) section\n") < 0)
{
perror("otx: unable to write to output file");
return NO;
}
[self printDataSection: &iCoalDataSect toFile: outFile];
}
if (iCoalDataNTSect.size)
{
if (fprintf(outFile, "\n(__DATA,__datacoal_nt) section\n") < 0)
{
perror("otx: unable to write to output file");
return NO;
}
[self printDataSection: &iCoalDataNTSect toFile: outFile];
}
if (iOutputFilePath)
{
if (fclose(outFile) != 0)
{
perror("otx: unable to close output file");
return NO;
}
}
return YES;
}
// printDataSection:toFile:
// ----------------------------------------------------------------------------
- (void)printDataSection: (section_info*)inSect
toFile: (FILE*)outFile;
{
uint32_t i, j, k, bytesLeft;
uint32_t theDataSize = inSect->size;
char theLineCString[70];
char* theMachPtr = (char*)iMachHeaderPtr;
theLineCString[0] = 0;
for (i = 0; i < theDataSize; i += 16)
{
bytesLeft = theDataSize - i;
if (bytesLeft < 16) // last line
{
theLineCString[0] = 0;
snprintf(theLineCString,
20 ,"%08x |", inSect->s.addr + i);
unsigned char theHexData[17] = {0};
unsigned char theASCIIData[17] = {0};
memcpy(theHexData,
(const void*)(theMachPtr + inSect->s.offset + i), bytesLeft);
memcpy(theASCIIData,
(const void*)(theMachPtr + inSect->s.offset + i), bytesLeft);
j = 10;
for (k = 0; k < bytesLeft; k++)
{
if (!(k % 4))
theLineCString[j++] = 0x20;
snprintf(&theLineCString[j], 4, "%02x", theHexData[k]);
j += 2;
if (theASCIIData[k] < 0x20 || theASCIIData[k] == 0x7f)
theASCIIData[k] = '.';
}
// Append spaces.
for (; j < 48; j++)
theLineCString[j] = 0x20;
// Append ASCII chars.
snprintf(&theLineCString[j], 70, "%s\n", theASCIIData);
}
else // first lines
{
uint32_t* theHexPtr = (uint32_t*)
(theMachPtr + inSect->s.offset + i);
unsigned char theASCIIData[17] = {0};
UInt8 j;
memcpy(theASCIIData,
(const void*)(theMachPtr + inSect->s.offset + i), 16);
for (j = 0; j < 16; j++)
if (theASCIIData[j] < 0x20 || theASCIIData[j] == 0x7f)
theASCIIData[j] = '.';
#if TARGET_RT_LITTLE_ENDIAN
theHexPtr[0] = OSSwapInt32(theHexPtr[0]);
theHexPtr[1] = OSSwapInt32(theHexPtr[1]);
theHexPtr[2] = OSSwapInt32(theHexPtr[2]);
theHexPtr[3] = OSSwapInt32(theHexPtr[3]);
#endif
snprintf(theLineCString, sizeof(theLineCString),
"%08x | %08x %08x %08x %08x %s\n",
inSect->s.addr + i,
theHexPtr[0], theHexPtr[1], theHexPtr[2], theHexPtr[3],
theASCIIData);
}
if (fprintf(outFile, "%s", theLineCString) < 0)
{
perror("otx: [ExeProcessor printDataSection:toFile:]: "
"unable to write to output file");
return;
}
}
}
#pragma mark -
// selectorForMsgSend:fromLine:
// ----------------------------------------------------------------------------
// Subclasses may override.
- (char*)selectorForMsgSend: (char*)outComment
fromLine: (Line*)inLine
{
return NULL;
}
#pragma mark -
// insertMD5
// ----------------------------------------------------------------------------
- (void)insertMD5
{
NSString* md5String = [self generateMD5String];
Line* newLine = calloc(1, sizeof(Line));
const char* utf8String = [md5String UTF8String];
newLine->length = [md5String length];
newLine->chars = malloc(newLine->length + 1);
strncpy(newLine->chars, utf8String, newLine->length + 1);
[self insertLine:newLine after:iPlainLineListHead inList:&iPlainLineListHead];
}
#pragma mark -
// entabLine:
// ----------------------------------------------------------------------------
// A cheap and fast way to entab a line, assuming it contains no tabs already.
// If tabs get added in the future, this WILL break. Single spaces are not
// replaced with tabs, even when possible, since it would save no additional
// bytes. Comments are not entabbed, as that would remove the user's ability
// to search for them in the source code or a hex editor.
- (void)entabLine: (Line*)ioLine;
{
if (!ioLine || !ioLine->chars)
return;
// only need to do this math once...
static uint32_t startOfComment = 0;
if (startOfComment == 0)
{
startOfComment = iFieldWidths.address + iFieldWidths.instruction +
iFieldWidths.mnemonic + iFieldWidths.operands;
if (iOpts.localOffsets)
startOfComment += iFieldWidths.offset;
}
char entabbedLine[MAX_LINE_LENGTH];
size_t theOrigLength = ioLine->length;
// If 1st char is '\n', skip it.
uint32_t firstChar = (ioLine->chars[0] == '\n');
uint32_t i; // old line marker
uint32_t j = 0; // new line marker
if (firstChar)
{
j++;
entabbedLine[0] = '\n';
entabbedLine[1] = 0;
}
else
entabbedLine[0] = 0;
// Inspect 4 bytes at a time.
for (i = firstChar; i < theOrigLength; i += 4)
{
// Don't entab comments.
if (i >= (startOfComment + firstChar) - 4)
{
strncpy(&entabbedLine[j], &ioLine->chars[i],
(theOrigLength - i) + 1);
break;
}
// If fewer than 4 bytes remain, adding any tabs is pointless.
if (i > theOrigLength - 4)
{ // Copy the remainder and split.
while (i < theOrigLength)
entabbedLine[j++] = ioLine->chars[i++];
// Add the null terminator.
entabbedLine[j] = 0;
break;
}
// If the 4th char is not a space, the first 3 chars don't matter.
if (ioLine->chars[i + 3] == 0x20) // 4th char is a space...
{
if (ioLine->chars[i + 2] == 0x20) // 3rd char is a space...
{
if (ioLine->chars[i + 1] == 0x20) // 2nd char is a space...
{
if (ioLine->chars[i] == 0x20) // all 4 chars are spaces!
entabbedLine[j++] = '\t'; // write a tab and split
else // only the 1st char is not a space
{ // copy 1st char and tab
entabbedLine[j++] = ioLine->chars[i];
entabbedLine[j++] = '\t';
}
}
else // 2nd char is not a space
{ // copy 1st 2 chars and tab
entabbedLine[j++] = ioLine->chars[i];
entabbedLine[j++] = ioLine->chars[i + 1];
entabbedLine[j++] = '\t';
}
}
else // 3rd char is not a space
{ // copy 1st 3 chars and tab
entabbedLine[j++] = ioLine->chars[i];
entabbedLine[j++] = ioLine->chars[i + 1];
entabbedLine[j++] = ioLine->chars[i + 2];
entabbedLine[j++] = '\t';
}
}
else // 4th char is not a space
{ // copy all 4 chars
memcpy(&entabbedLine[j], &ioLine->chars[i], 4);
j += 4;
}
// Add the null terminator.
entabbedLine[j] = 0;
}
// Replace the old C string with the new one.
free(ioLine->chars);
ioLine->length = strlen(entabbedLine);
ioLine->chars = malloc(ioLine->length + 1);
strncpy(ioLine->chars, entabbedLine, ioLine->length + 1);
}
- (BOOL)getIvarName:(char **)outName type:(char **)outType withOffset:(uint32_t)offset inClass:(objc_32_class_ptr)classPtr
{
if (iObjcVersion == 1) {
objc1_32_ivar ivar = {0};
objc1_32_class cls = *(objc1_32_class *)classPtr;
#if __BIG_ENDIAN__
swap_objc1_32_class(&cls);
#endif
if (!iIsInstanceMethod)
{
if (![self getObjc1MetaClass:&cls fromClass:&cls])
return NO;
#if __BIG_ENDIAN__
swap_objc1_32_class(&cls);
#endif
}
if (![self findIvar:&ivar inClass:&cls withOffset:offset])
return NO;
char *name = [self getPointer:ivar.ivar_name type:NULL];
char *type = [self getPointer:ivar.ivar_type type:NULL];
if (outName) *outName = name;
if (outType) *outType = type;
return YES;
} else if (iObjcVersion == 2) {
objc2_32_ivar_t* ivar;
if ([self findIvar:&ivar inClass2:(objc2_32_class_t *)classPtr withOffset:offset])
{
char *name = [self getPointer:ivar->name type:NULL];
char *type = [self getPointer:ivar->type type:NULL];
if (outName) *outName = name;
if (outType) *outType = type;
}
return YES;
}
return NO;
}
// getPointer:type: (was get_pointer)
// ----------------------------------------------------------------------------
// Convert a relative ptr to an absolute ptr. Return which data type is being
// referenced in outType.
- (char*)getPointer: (uint32_t)inAddr
type: (UInt8*)outType
{
if (inAddr == 0)
return NULL;
if (outType)
*outType = PointerType;
char* thePtr = NULL;
uint32_t i;
// (__TEXT,__cstring) (char*)
if (inAddr >= iCStringSect.s.addr &&
inAddr < iCStringSect.s.addr + iCStringSect.size)
{
thePtr = (iCStringSect.contents + (inAddr - iCStringSect.s.addr));
// Make sure we're pointing to the beginning of a string,
// not somewhere in the middle.
if (*(thePtr - 1) != 0 && inAddr != iCStringSect.s.addr)
thePtr = NULL;
// Check if this may be a Pascal string. Thanks, Metrowerks.
else if (outType && strlen(thePtr) == thePtr[0] + 1)
*outType = PStringType;
}
else // (__TEXT,__const) (Str255* sometimes)
if (inAddr >= iConstTextSect.s.addr &&
inAddr < iConstTextSect.s.addr + iConstTextSect.size)
{
thePtr = (iConstTextSect.contents + (inAddr - iConstTextSect.s.addr));
if (outType && strlen(thePtr) == thePtr[0] + 1)
*outType = PStringType;
else
thePtr = NULL;
}
else // (__TEXT,__objc_methname) (char*)
if (inAddr >= iObjcMethnameSect.s.addr &&
inAddr < iObjcMethnameSect.s.addr + iObjcMethnameSect.size)
{
thePtr = (iObjcMethnameSect.contents + (inAddr - iObjcMethnameSect.s.addr));
}
else // (__TEXT,__objc_methtype) (char*)
if (inAddr >= iObjcMethtypeSect.s.addr &&
inAddr < iObjcMethtypeSect.s.addr + iObjcMethtypeSect.size)
{
thePtr = (iObjcMethtypeSect.contents + (inAddr - iObjcMethtypeSect.s.addr));
}
else // (__TEXT,__objc_classname) (char*)
if (inAddr >= iObjcClassnameSect.s.addr &&
inAddr < iObjcClassnameSect.s.addr + iObjcClassnameSect.size)
{
thePtr = (iObjcClassnameSect.contents + (inAddr - iObjcClassnameSect.s.addr));
}
else // (__TEXT,__literal4) (float)
if (inAddr >= iLit4Sect.s.addr &&
inAddr < iLit4Sect.s.addr + iLit4Sect.size)
{
thePtr = (char*)(iLit4Sect.contents + (inAddr - iLit4Sect.s.addr));
if (outType)
*outType = FloatType;
}
else // (__TEXT,__literal8) (double)
if (inAddr >= iLit8Sect.s.addr &&
inAddr < iLit8Sect.s.addr + iLit8Sect.size)
{
thePtr = (char*)(iLit8Sect.contents + (inAddr - iLit8Sect.s.addr));
if (outType)
*outType = DoubleType;
}
if (thePtr)
return thePtr;
// (__OBJC,__cstring_object) (objc_string_object)
if (inAddr >= iNSStringSect.s.addr &&
inAddr < iNSStringSect.s.addr + iNSStringSect.size)
{
thePtr = (char*)(iNSStringSect.contents + (inAddr - iNSStringSect.s.addr));
if (outType)
*outType = OCStrObjectType;
}
else // (__OBJC,__class) (objc_class)
if (inAddr >= iClassSect.s.addr &&
inAddr < iClassSect.s.addr + iClassSect.size)
{
thePtr = (char*)(iClassSect.contents + (inAddr - iClassSect.s.addr));
if (outType)
*outType = OCClassType;
}
else // (__OBJC,__meta_class) (objc_class)
if (inAddr >= iMetaClassSect.s.addr &&
inAddr < iMetaClassSect.s.addr + iMetaClassSect.size)
{
thePtr = (char*)(iMetaClassSect.contents + (inAddr - iMetaClassSect.s.addr));
if (outType)
*outType = OCClassType;
}
else // (__OBJC,__module_info) (objc_module)
if (inAddr >= iObjcModSect.s.addr &&
inAddr < iObjcModSect.s.addr + iObjcModSect.size)
{
thePtr = (char*)(iObjcModSect.contents + (inAddr - iObjcModSect.s.addr));
if (outType)
*outType = OCModType;
}
// (__OBJC, ??) (char*)
// __message_refs, __class_refs, __instance_vars, __symbols
for (i = 0; !thePtr && i < iNumObjcSects; i++)
{
if (inAddr >= iObjcSects[i].s.addr &&
inAddr < iObjcSects[i].s.addr + iObjcSects[i].size)
{
thePtr = (char*)(iObjcSects[i].contents + (inAddr - iObjcSects[i].s.addr));
if (outType)
*outType = OCGenericType;
}
}
if (thePtr)
return thePtr;
// (__IMPORT,__pointers) (cf_string_object*)
if (inAddr >= iImpPtrSect.s.addr &&
inAddr < iImpPtrSect.s.addr + iImpPtrSect.size)
{
thePtr = (char*)(iImpPtrSect.contents + (inAddr - iImpPtrSect.s.addr));
if (outType)
*outType = ImpPtrType;
}
if (thePtr)
return thePtr;
// (__DATA,__data) (char**)
if (inAddr >= iDataSect.s.addr &&
inAddr < iDataSect.s.addr + iDataSect.size)
{
thePtr = (char*)(iDataSect.contents + (inAddr - iDataSect.s.addr));
UInt8 theType = DataGenericType;
uint32_t theValue = *(uint32_t*)thePtr;
if (iSwapped)
theValue = OSSwapInt32(theValue);
if (theValue != 0)
{
theType = PointerType;
static uint32_t recurseCount = 0;
while (theType == PointerType)
{
recurseCount++;
if (recurseCount > 5)
{
theType = DataGenericType;
break;
}
thePtr = [self getPointer:theValue type:&theType];
if (!thePtr)
{
theType = DataGenericType;
break;
}
theValue = *(uint32_t*)thePtr;
}
recurseCount = 0;
}
if (outType)
*outType = theType;
}
else // (__DATA,__const) (void*)
if (inAddr >= iConstDataSect.s.addr &&
inAddr < iConstDataSect.s.addr + iConstDataSect.size)
{
thePtr = (char*)(iConstDataSect.contents + (inAddr - iConstDataSect.s.addr));
if (outType)
{
uint32_t theID = *(uint32_t*)thePtr;
if (iSwapped)
theID = OSSwapInt32(theID);
if (theID == typeid_NSString)
*outType = OCStrObjectType;
else
{
theID = *(uint32_t*)(thePtr + 4);
if (iSwapped)
theID = OSSwapInt32(theID);
if (theID == typeid_NSString)
*outType = CFStringType;
else
*outType = DataConstType;
}
}
}
else // (__DATA,__cfstring) (cf_string_object*)
if (inAddr >= iCFStringSect.s.addr &&
inAddr < iCFStringSect.s.addr + iCFStringSect.size)
{
thePtr = (char*)(iCFStringSect.contents + (inAddr - iCFStringSect.s.addr));
if (outType)
*outType = CFStringType;
}
else // (__DATA,__objc_classrefs)
if (inAddr >= iObjcClassRefsSect.s.addr &&
inAddr < iObjcClassRefsSect.s.addr + iObjcClassRefsSect.size)
{
if (inAddr % 4 == 0)
{
UInt32 classRef = *(UInt32*)(iObjcClassRefsSect.contents +
(inAddr - iObjcClassRefsSect.s.addr));
if (classRef &&
classRef >= iObjcDataSect.s.addr &&
classRef < iObjcDataSect.s.addr + iObjcDataSect.s.size)
{
if (iSwapped)
classRef = OSSwapInt32(classRef);
objc2_32_class_t swappedClass = *(objc2_32_class_t*)(iObjcDataSect.contents +
(classRef - iObjcDataSect.s.addr));
if (iSwapped)
swap_objc2_32_class(&swappedClass);
if (swappedClass.data &&
swappedClass.data >= iObjcConstSect.s.addr &&
swappedClass.data < iObjcConstSect.s.addr + iObjcConstSect.s.size)
{
objc2_32_class_ro_t roData = *(objc2_32_class_ro_t*)(iObjcConstSect.contents +
(swappedClass.data - iObjcConstSect.s.addr));
if (iSwapped)
roData.name = OSSwapInt32(roData.name);
thePtr = [self getPointer:roData.name type:NULL];
if (outType)
*outType = OCClassRefType;
}
}
}
}
else // (__DATA,__objc_msgrefs)
if (inAddr >= iObjcMsgRefsSect.s.addr &&
inAddr < iObjcMsgRefsSect.s.addr + iObjcMsgRefsSect.size)
{
objc2_32_message_ref_t ref = *(objc2_32_message_ref_t*)(iObjcMsgRefsSect.contents +
(inAddr - iObjcMsgRefsSect.s.addr));
if (iSwapped)
ref.sel = OSSwapInt32(ref.sel);
thePtr = [self getPointer:ref.sel type:NULL];
if (outType)
*outType = OCMsgRefType;
}
else // (__DATA,__objc_catlist)
if (inAddr >= iObjcCatListSect.s.addr &&
inAddr < iObjcCatListSect.s.addr + iObjcCatListSect.size)
{
}
else // (__DATA,__objc_superrefs)
if (inAddr >= iObjcSuperRefsSect.s.addr &&
inAddr < iObjcSuperRefsSect.s.addr + iObjcSuperRefsSect.size)
{
UInt32 superAddy = *(UInt32*)(iObjcSuperRefsSect.contents +
(inAddr - iObjcSuperRefsSect.s.addr));
if (iSwapped)
superAddy = OSSwapInt32(superAddy);
if (superAddy &&
superAddy >= iObjcDataSect.s.addr &&
superAddy < iObjcDataSect.s.addr + iObjcDataSect.s.size)
{
objc2_32_class_t swappedClass = *(objc2_32_class_t*)(iObjcDataSect.contents +
(superAddy - iObjcDataSect.s.addr));
if (iSwapped)
swap_objc2_32_class(&swappedClass);
if (swappedClass.data &&
swappedClass.data >= iObjcConstSect.s.addr &&
swappedClass.data < iObjcConstSect.s.addr + iObjcConstSect.s.size)
{
objc2_32_class_ro_t* roPtr = (objc2_32_class_ro_t*)(iObjcConstSect.contents +
(swappedClass.data - iObjcConstSect.s.addr));
UInt32 namePtr = roPtr->name;
if (iSwapped)
namePtr = OSSwapInt32(namePtr);
if (namePtr != 0)
{
thePtr = [self getPointer:namePtr type:NULL];
if (outType)
*outType = OCSuperRefType;
}
}
}
}
else // (__DATA,__objc_selrefs)
if (inAddr >= iObjcSelRefsSect.s.addr &&
inAddr < iObjcSelRefsSect.s.addr + iObjcSelRefsSect.size)
{
UInt32 selAddy = *(UInt32*)(iObjcSelRefsSect.contents +
(inAddr - iObjcSelRefsSect.s.addr));
if (iSwapped)
selAddy = OSSwapInt32(selAddy);
if (selAddy != 0)
{
thePtr = [self getPointer:selAddy type:NULL];
if (outType)
*outType = OCSelRefType;
}
}
else
if ((inAddr >= iObjcProtoRefsSect.s.addr && // (__DATA,__objc_protorefs)
inAddr < iObjcProtoRefsSect.s.addr + iObjcProtoRefsSect.size) ||
(inAddr >= iObjcProtoListSect.s.addr && // (__DATA,__objc_protolist)
inAddr < iObjcProtoListSect.s.addr + iObjcProtoListSect.size))
{
UInt32 protoAddy;
UInt8 tempType;
if (inAddr >= iObjcProtoRefsSect.s.addr &&
inAddr < iObjcProtoRefsSect.s.addr + iObjcProtoRefsSect.size)
{
protoAddy = *(UInt32*)(iObjcProtoRefsSect.contents +
(inAddr - iObjcProtoRefsSect.s.addr));
tempType = OCProtoRefType;
}
else
{
protoAddy = *(UInt32*)(iObjcProtoListSect.contents +
(inAddr - iObjcProtoListSect.s.addr));
tempType = OCProtoListType;
}
if (iSwapped)
protoAddy = OSSwapInt32(protoAddy);
if (protoAddy != 0 &&
(protoAddy >= iDataSect.s.addr && protoAddy < (iDataSect.s.addr + iDataSect.size)))
{
objc2_32_protocol_t* proto = (objc2_32_protocol_t*)(iDataSect.contents +
(protoAddy - iDataSect.s.addr));
UInt32 protoName = proto->name;
if (iSwapped)
protoName = OSSwapInt32(protoName);
if (protoName != 0)
{
thePtr = [self getPointer:protoName type:NULL];
if (outType)
*outType = tempType;
}
}
}
else // (__DATA,__nl_symbol_ptr) (cf_string_object*)
if (inAddr >= iNLSymSect.s.addr &&
inAddr < iNLSymSect.s.addr + iNLSymSect.size)
{
thePtr = (char*)(iNLSymSect.contents + (inAddr - iNLSymSect.s.addr));
if (outType)
*outType = NLSymType;
}
else // (__DATA,__dyld) (function ptr)
if (inAddr >= iDyldSect.s.addr &&
inAddr < iDyldSect.s.addr + iDyldSect.size)
{
thePtr = (char*)(iDyldSect.contents + (inAddr - iDyldSect.s.addr));
if (outType)
*outType = DYLDType;
}
// should implement these if they ever contain CFStrings or NSStrings
/* else // (__DATA, __coalesced_data) (?)
if (localAddy >= mCoalDataSect.s.addr &&
localAddy < mCoalDataSect.s.addr + mCoalDataSect.size)
{
}
else // (__DATA, __datacoal_nt) (?)
if (localAddy >= mCoalDataNTSect.s.addr &&
localAddy < mCoalDataNTSect.s.addr + mCoalDataNTSect.size)
{
}*/
return thePtr;
}
#ifdef OTX_DEBUG
// printSymbol:
// ----------------------------------------------------------------------------
// Used for symbol debugging.
- (void)printSymbol: (nlist)inSym
{
fprintf(stderr, "----------------\n\n");
fprintf(stderr, " n_strx = 0x%08x\n", inSym.n_un.n_strx);
fprintf(stderr, " n_type = 0x%02x\n", inSym.n_type);
fprintf(stderr, " n_sect = 0x%02x\n", inSym.n_sect);
fprintf(stderr, " n_desc = 0x%04x\n", inSym.n_desc);
fprintf(stderr, "n_value = 0x%08x (%u)\n\n", inSym.n_value, inSym.n_value);
if ((inSym.n_type & N_STAB) != 0)
{ // too complicated, see <mach-o/stab.h>
fprintf(stderr, "STAB symbol\n");
}
else // not a STAB
{
if ((inSym.n_type & N_PEXT) != 0)
fprintf(stderr, "Private external symbol\n\n");
else if ((inSym.n_type & N_EXT) != 0)
fprintf(stderr, "External symbol\n\n");
UInt8 theNType = inSym.n_type & N_TYPE;
UInt16 theRefType = inSym.n_desc & REFERENCE_TYPE;
fprintf(stderr, "Symbol name: %s\n", (char*)((char *)iMachHeaderPtr + iStringTableOffset + inSym.n_un.n_strx));
fprintf(stderr, "Symbol type: ");
if (theNType == N_ABS)
fprintf(stderr, "Absolute\n");
else if (theNType == N_SECT)
fprintf(stderr, "Defined in section %u\n", inSym.n_sect);
else if (theNType == N_INDR)
fprintf(stderr, "Indirect\n");
else
{
if (theNType == N_UNDF)
fprintf(stderr, "Undefined\n");
else if (theNType == N_PBUD)
fprintf(stderr, "Prebound undefined\n");
switch (theRefType)
{
case REFERENCE_FLAG_UNDEFINED_NON_LAZY:
fprintf(stderr, "REFERENCE_FLAG_UNDEFINED_NON_LAZY\n");
break;
case REFERENCE_FLAG_UNDEFINED_LAZY:
fprintf(stderr, "REFERENCE_FLAG_UNDEFINED_LAZY\n");
break;
case REFERENCE_FLAG_DEFINED:
fprintf(stderr, "REFERENCE_FLAG_DEFINED\n");
break;
case REFERENCE_FLAG_PRIVATE_DEFINED:
fprintf(stderr, "REFERENCE_FLAG_PRIVATE_DEFINED\n");
break;
case REFERENCE_FLAG_PRIVATE_UNDEFINED_NON_LAZY:
fprintf(stderr, "REFERENCE_FLAG_PRIVATE_UNDEFINED_NON_LAZY\n");
break;
case REFERENCE_FLAG_PRIVATE_UNDEFINED_LAZY:
fprintf(stderr, "REFERENCE_FLAG_PRIVATE_UNDEFINED_LAZY\n");
break;
default:
break;
}
}
}
fprintf(stderr, "\n");
}
// printBlocks:
// ----------------------------------------------------------------------------
// Used for block debugging. Subclasses may override.
- (void)printBlocks: (uint32_t)inFuncIndex;
{
if (!iFuncInfos)
return;
FunctionInfo* funcInfo = &iFuncInfos[inFuncIndex];
if (!funcInfo || !funcInfo->blocks)
return;
uint32_t i;
fprintf(stderr, "\nfunction at 0x%x:\n\n", funcInfo->address);
fprintf(stderr, "%d blocks\n", funcInfo->numBlocks);
for (i = 0; i < funcInfo->numBlocks; i++)
{
fprintf(stderr, "\nblock %d at 0x%x:\n\n", i + 1,
funcInfo->blocks[i].beginAddress);
GPRegisterInfo *regInfo = funcInfo->blocks[i].state.regInfos;
if (regInfo[EAX].isValid) fprintf(stderr, "\t\teax: 0x%x\n", regInfo[EAX].value);
if (regInfo[EBX].isValid) fprintf(stderr, "\t\tebx: 0x%x\n", regInfo[EBX].value);
if (regInfo[ECX].isValid) fprintf(stderr, "\t\tecx: 0x%x\n", regInfo[ECX].value);
if (regInfo[EDX].isValid) fprintf(stderr, "\t\tedx: 0x%x\n", regInfo[EDX].value);
if (regInfo[ESP].isValid) fprintf(stderr, "\t\tesp: 0x%x\n", regInfo[ESP].value);
if (regInfo[EBP].isValid) fprintf(stderr, "\t\tebp: 0x%x\n", regInfo[EBP].value);
if (regInfo[ESI].isValid) fprintf(stderr, "\t\tesi: 0x%x\n", regInfo[ESI].value);
if (regInfo[EDI].isValid) fprintf(stderr, "\t\tedi: 0x%x\n", regInfo[EDI].value);
}
}
#endif // OTX_DEBUG
@end
|
github
|
zhangchn/otx-master
|
PPC64Processor.m
|
.m
|
otx-master/src/source/Processors/PPC64Processor.m
| 74,333 |
utf_8
|
6357b279a717e624564964c7ba8e1495
|
/*
PPC64Processor.m
A subclass of Exe64Processor that handles PPC64-specific issues.
This file is in the public domain.
*/
#import <Cocoa/Cocoa.h>
#import "PPC64Processor.h"
#import "PPCProcessor.h"
#import "Arch64Specifics.h"
#import "List64Utils.h"
#import "Objc64Accessors.h"
#import "Object64Loader.h"
#import "Searchers64.h"
#import "SyscallStrings.h"
#import "UserDefaultKeys.h"
@implementation PPC64Processor
// initWithURL:controller:options:
// ----------------------------------------------------------------------------
- (id)initWithURL: (NSURL*)inURL
controller: (id)inController
options: (ProcOptions*)inOptions
{
if ((self = [super initWithURL: inURL
controller: inController options: inOptions]))
{
strncpy(iArchString, "ppc64", 6);
iArchSelector = CPU_TYPE_POWERPC64;
iFieldWidths.offset = 8;
iFieldWidths.address = 18;
iFieldWidths.instruction = 10;
iFieldWidths.mnemonic = 9;
iFieldWidths.operands = 17;
}
return self;
}
// dealloc
// ----------------------------------------------------------------------------
- (void)dealloc
{
if (iLocalSelves)
{
free(iLocalSelves);
iLocalSelves = NULL;
}
if (iLocalVars)
{
free(iLocalVars);
iLocalVars = NULL;
}
}
// loadDyldDataSection:
// ----------------------------------------------------------------------------
- (void)loadDyldDataSection: (section_64*)inSect
{
[super loadDyldDataSection: inSect];
if (!iAddrDyldStubBindingHelper)
return;
iAddrDyldFuncLookupPointer = iAddrDyldStubBindingHelper + 24;
}
// codeFromLine:
// ----------------------------------------------------------------------------
- (void)codeFromLine: (Line64*)inLine
{
uint32_t theInstruction = (iMachHeader.filetype == MH_OBJECT) ?
*(uint32_t*)((char*)iMachHeaderPtr + (inLine->info.address + iTextOffset)) :
*(uint32_t*)((char*)iMachHeaderPtr + (inLine->info.address - iTextOffset));
inLine->info.codeLength = 4;
uint32_t* intPtr = (uint32_t*)&inLine->info.code[0];
*intPtr = theInstruction;
}
#pragma mark -
// commentForLine:
// ----------------------------------------------------------------------------
- (void)commentForLine: (Line64*)inLine;
{
uint32_t theCode = *(uint32_t*)inLine->info.code;
theCode = OSSwapBigToHostInt32(theCode);
char* theDummyPtr = NULL;
char* theSymPtr = NULL;
UInt8 opcode = PO(theCode);
UInt64 localAddy;
iLineCommentCString[0] = 0;
// Examine the primary opcode to see if we need to look for comments.
switch (opcode)
{
case 0x0a: // cmpli | cmplwi UIMM
case 0x0b: // cmpi | cmpwi SIMM
{
SInt16 imm = SIMM(theCode);
// Check for a single printable 7-bit char.
if (imm >= 0x20 && imm < 0x7f)
snprintf(iLineCommentCString, 4, "'%c'", imm);
break;
}
case 0x11: // sc
[self commentForSystemCall];
break;
case 0x10: // bc, bca, bcl, bcla
case 0x12: // b, ba, bl, bla
{
// Check for absolute branches to the ObjC runtime page. Similar to
// the comm page behavior described at
// http://www.opensource.apple.com/darwinsource/10.4.7.ppc/xnu-792.6.76/osfmk/ppc/cpu_capabilities.h
// However, the ObjC runtime page is not really a comm page, and it
// cannot be accessed by bca and bcla instructions, due to their
// 16-bit limitation.
// Deal with absolute branches.
if (AA(theCode))
{
uint32_t target = LI(theCode);
switch (target)
{
case kRTAddress_objc_msgSend:
{
char tempComment[MAX_COMMENT_LENGTH];
strncpy(tempComment, kRTName_objc_msgSend,
strlen(kRTName_objc_msgSend) + 1);
if (iOpts.verboseMsgSends)
[self commentForMsgSend:tempComment fromLine:inLine];
strncpy(iLineCommentCString, tempComment,
strlen(tempComment) + 1);
break;
}
case kRTAddress_objc_assign_ivar:
{
char tempComment[MAX_COMMENT_LENGTH];
strncpy(tempComment, kRTName_objc_assign_ivar,
strlen(kRTName_objc_assign_ivar) + 1);
// Bail if we don't know about the class.
if (!iCurrentClass)
{
strncpy(iLineCommentCString, tempComment,
strlen(tempComment) + 1);
break;
}
if (iRegInfos[5].isValid)
{
objc2_64_ivar_t* theIvar = NULL;
objc2_64_class_t swappedClass = *iCurrentClass;
#if __LITTLE_ENDIAN__
swap_objc2_64_class(&swappedClass);
#endif
if (!iIsInstanceMethod)
{
if (![self getObjcMetaClass:&swappedClass fromClass:&swappedClass])
break;
#if __LITTLE_ENDIAN__
swap_objc2_64_class(&swappedClass);
#endif
}
if (![self findIvar:&theIvar inClass:&swappedClass withOffset:iRegInfos[5].value])
{
strncpy(iLineCommentCString, tempComment, strlen(tempComment) + 1);
break;
}
theSymPtr = [self getPointer:theIvar->name type:NULL];
if (!theSymPtr)
{
strncpy(iLineCommentCString, tempComment, strlen(tempComment) + 1);
break;
}
if (iOpts.variableTypes)
{
char theTypeCString[MAX_TYPE_STRING_LENGTH];
theTypeCString[0] = 0;
[self getDescription:theTypeCString forType:[self getPointer:theIvar->type type:NULL]];
snprintf(iLineCommentCString, MAX_COMMENT_LENGTH, "%s (%s)%s", tempComment, theTypeCString, theSymPtr);
}
else
snprintf(iLineCommentCString, MAX_COMMENT_LENGTH, "%s %s", tempComment, theSymPtr);
}
else // !mReginfos[5].isValid
snprintf(iLineCommentCString, MAX_COMMENT_LENGTH, "%s", tempComment);
break;
}
case kRTAddress_objc_assign_global:
strncpy(iLineCommentCString, kRTName_objc_assign_global,
strlen(kRTName_objc_assign_global) + 1);
break;
case kRTAddress_objc_assign_strongCast:
strncpy(iLineCommentCString, kRTName_objc_assign_strongCast,
strlen(kRTName_objc_assign_strongCast) + 1);
break;
default:
break;
}
}
else // not an absolute branch
{
// Insert anonymous label or 'return' if there's not a comment yet.
if (iLineCommentCString[0])
break;
UInt64 absoluteAddy;
if (opcode == 0x12)
absoluteAddy =
inLine->info.address + LI(theCode);
else
absoluteAddy =
inLine->info.address + BD(theCode);
Function64Info searchKey = {absoluteAddy, NULL, 0, 0};
Function64Info* funcInfo = bsearch(&searchKey,
iFuncInfos, iNumFuncInfos, sizeof(Function64Info),
(COMPARISON_FUNC_TYPE)Function_Info_Compare);
if (funcInfo && funcInfo->genericFuncNum != 0)
{
snprintf(iLineCommentCString,
ANON_FUNC_BASE_LENGTH + 11, "%s%d",
ANON_FUNC_BASE, funcInfo->genericFuncNum);
break;
}
// FIXME: mCurrentFuncInfoIndex is -1 here when it should not be
funcInfo = &iFuncInfos[iCurrentFuncInfoIndex];
if (!funcInfo->blocks)
break;
uint32_t i;
for (i = 0; i < funcInfo->numBlocks; i++)
{
if (funcInfo->blocks[i].beginAddress != absoluteAddy)
continue;
if (funcInfo->blocks[i].isEpilog)
snprintf(iLineCommentCString, 8, "return;");
break;
}
}
break;
}
case 0x13: // bcctr, bclr, isync
if (SO(theCode) != 528) // bcctr
break;
if (iRegInfos[4].messageRefSel != NULL)
{
char* sel = iRegInfos[4].messageRefSel;
strncpy(iLineOperandsCString, " ", 2);
if (iRegInfos[3].className != NULL)
snprintf(iLineCommentCString, MAX_COMMENT_LENGTH, "+[%s %s]", iRegInfos[3].className, sel);
else // Instance method?
if (iRegInfos[3].isValid)
snprintf(iLineCommentCString, MAX_COMMENT_LENGTH, "objc_msgSend(%%r3, %s)", sel);
else
snprintf(iLineCommentCString, MAX_COMMENT_LENGTH, "-[%%r3 %s]", sel);
}
// Print value of ctr, ignoring the low 2 bits.
// if (iCTR.isValid)
// snprintf(iLineCommentCString, 10, "0x%x",
// iCTR.value & ~3);
break;
case 0x30: // lfs SIMM
case 0x34: // stfs SIMM
case 0x32: // lfd SIMM
case 0x36: // stfd SIMM
{
if (!iRegInfos[RA(theCode)].isValid || RA(theCode) == 0)
break;
if (iRegInfos[RA(theCode)].classPtr)
{ // search instance vars
objc2_64_ivar_t* theIvar = NULL;
objc2_64_class_t swappedClass = *iRegInfos[RA(theCode)].classPtr;
#if __LITTLE_ENDIAN__
swap_objc2_64_class(&swappedClass);
#endif
if (!iIsInstanceMethod)
{
if (![self getObjcMetaClass:&swappedClass fromClass:&swappedClass])
break;
#if __LITTLE_ENDIAN__
swap_objc2_64_class(&swappedClass);
#endif
}
if (![self findIvar:&theIvar inClass:&swappedClass withOffset:UIMM(theCode)])
break;
theSymPtr = [self getPointer:theIvar->name type:NULL];
if (theSymPtr)
{
if (iOpts.variableTypes)
{
char theTypeCString[MAX_TYPE_STRING_LENGTH];
theTypeCString[0] = 0;
[self getDescription:theTypeCString forType:[self getPointer:theIvar->type type:NULL]];
snprintf(iLineCommentCString, MAX_COMMENT_LENGTH, "(%s)%s",
theTypeCString, theSymPtr);
}
else
snprintf(iLineCommentCString, MAX_COMMENT_LENGTH, "%s", theSymPtr);
}
}
else
{
localAddy = iRegInfos[RA(theCode)].value + SIMM(theCode);
theDummyPtr = [self getPointer:localAddy type:NULL];
if (!theDummyPtr)
break;
if (opcode == 0x32 || opcode == 0x36) // lfd | stfd
{
UInt64 theInt64 = *(UInt64*)theDummyPtr;
theInt64 = OSSwapBigToHostInt64(theInt64);
// dance around printf's type coersion
snprintf(iLineCommentCString,
30, "%lG", *(double*)&theInt64);
}
else // lfs | stfs
{
uint32_t theInt32 = *(uint32_t*)theDummyPtr;
theInt32 = OSSwapBigToHostInt32(theInt32);
// dance around printf's type coersion
snprintf(iLineCommentCString,
30, "%G", *(float*)&theInt32);
}
}
break;
}
case 0x0e: // li | addi SIMM
case 0x18: // ori UIMM
case 0x20: // lwz SIMM
case 0x22: // lbz SIMM
case 0x24: // stw SIMM
case 0x26: // stb SIMM
case 0x28: // lhz SIMM
case 0x2c: // sth SIMM
{
if (!iRegInfos[RA(theCode)].isValid || RA(theCode) == 0)
break;
if (iRegInfos[RA(theCode)].classPtr) // relative to a class
{ // search instance vars
objc2_64_ivar_t* theIvar = NULL;
objc2_64_class_t swappedClass = *iRegInfos[RA(theCode)].classPtr;
if (![self findIvar:&theIvar inClass:&swappedClass withOffset:UIMM(theCode)])
break;
theSymPtr = [self getPointer:theIvar->name type:NULL];
if (theSymPtr)
{
if (iOpts.variableTypes)
{
char theTypeCString[MAX_TYPE_STRING_LENGTH];
theTypeCString[0] = 0;
[self getDescription:theTypeCString forType:[self getPointer:theIvar->type type:NULL]];
snprintf(iLineCommentCString, MAX_COMMENT_LENGTH, "(%s)%s", theTypeCString, theSymPtr);
}
else
snprintf(iLineCommentCString, MAX_COMMENT_LENGTH, "%s", theSymPtr);
}
}
else // absolute address
{
if (opcode == 0x18) // ori UIMM
localAddy = iRegInfos[RA(theCode)].value | UIMM(theCode);
else
localAddy = iRegInfos[RA(theCode)].value + SIMM(theCode);
UInt8 theType = PointerType;
uint32_t theValue;
theSymPtr = [self getPointer:localAddy type:&theType];
if (theSymPtr)
{
switch (theType)
{
case DataGenericType:
theValue = *(uint32_t*)theSymPtr;
theValue = OSSwapBigToHostInt32(theValue);
theDummyPtr = [self getPointer:theValue type:&theType];
switch (theType)
{
case PointerType:
theSymPtr = theDummyPtr;
break;
default:
theSymPtr = NULL;
break;
}
break;
case DataConstType:
theSymPtr = NULL;
break;
// See http://www.opensource.apple.com/darwinsource/10.4.7.ppc/Csu-58/dyld.s
// They hardcoded the values, we may as well...
case DYLDType:
{
char* dyldComment = NULL;
theValue = *(uint32_t*)theSymPtr;
theValue = OSSwapBigToHostInt32(theValue);
switch(theValue)
{
case kDyldAddress_LaSymBindingEntry:
dyldComment = kDyldName_LaSymBindingEntry;
break;
case kDyldAddress_FuncLookupPointer:
dyldComment = kDyldName_FuncLookupPointer;
break;
default:
break;
}
if (dyldComment)
strcpy(iLineCommentCString, dyldComment);
break;
}
case PointerType:
break;
case CFStringType:
{
cfstring_object_64 theCFString = *(cfstring_object_64*)theSymPtr;
if (theCFString.oc_string.length == 0)
{
theSymPtr = NULL;
break;
}
theCFString.oc_string.chars =
OSSwapBigToHostInt64(theCFString.oc_string.chars);
theSymPtr = [self getPointer:theCFString.oc_string.chars type:NULL];
break;
}
case ImpPtrType:
case NLSymType:
{
theValue = *(uint32_t*)theSymPtr;
theValue = OSSwapBigToHostInt32(theValue);
theDummyPtr = [self getPointer:theValue type:NULL];
if (!theDummyPtr)
{
theSymPtr = NULL;
break;
}
theValue = *(uint32_t*)(theDummyPtr + 4);
theValue = OSSwapBigToHostInt32(theValue);
if (theValue != typeid_NSString)
{
theValue = *(uint32_t*)theDummyPtr;
theValue = OSSwapBigToHostInt32(theValue);
theDummyPtr = [self getPointer:theValue type:NULL];
if (!theDummyPtr)
{
theSymPtr = NULL;
break;
}
}
cfstring_object_64 theCFString = *(cfstring_object_64*)theDummyPtr;
if (theCFString.oc_string.length == 0)
{
theSymPtr = NULL;
break;
}
theCFString.oc_string.chars =
OSSwapBigToHostInt64(theCFString.oc_string.chars);
theSymPtr = [self getPointer:theCFString.oc_string.chars type:NULL];
break;
}
case OCGenericType:
case OCStrObjectType:
case OCClassType:
case OCModType:
if (![self getObjcDescription:&theDummyPtr fromObject:theSymPtr type:theType])
break;
if (theDummyPtr)
{
switch (theType)
{
case OCClassType:
iRegInfos[RT(theCode)].classPtr =
(objc2_64_class_t*)theSymPtr;
break;
default:
break;
}
}
theSymPtr = theDummyPtr;
break;
default:
break;
}
if (theSymPtr && !iLineCommentCString[0])
{
if (theType == PStringType)
snprintf(iLineCommentCString, 255,
"%*s", theSymPtr[0], theSymPtr + 1);
else
snprintf(iLineCommentCString, MAX_COMMENT_LENGTH, "%s", theSymPtr);
}
} // if (theSymPtr)
else
{ // Maybe it's a four-char code...
if ((opcode == 0x0e || opcode == 0x18) && // li | addi | ori
localAddy >= 0x20202020 && localAddy < 0x7f7f7f7f)
{
localAddy = OSSwapBigToHostInt64(localAddy);
char* fcc = (char*)&localAddy;
if (fcc[0] >= 0x20 && fcc[0] < 0x7f &&
fcc[1] >= 0x20 && fcc[1] < 0x7f &&
fcc[2] >= 0x20 && fcc[2] < 0x7f &&
fcc[3] >= 0x20 && fcc[3] < 0x7f)
snprintf(iLineCommentCString,
7, "'%.4s'", fcc);
}
}
} // if !(.classPtr)
break;
} // case 0x0e...
case 0x3a: // ld
{
if (iRegInfos[RA(theCode)].isValid == NO)
break;
UInt64 address = iRegInfos[RA(theCode)].value + DS(theCode);
UInt8 type;
char* symName = NULL;
theSymPtr = [self getPointer:address type:&type];
if (theSymPtr)
{
switch (type)
{
case CFStringType:
[self getObjcDescription:&symName fromObject:theSymPtr type:type];
if (symName)
snprintf(iLineCommentCString, MAX_COMMENT_LENGTH, "%s", symName);
break;
case OCClassRefType:
case OCSuperRefType:
case OCProtoRefType:
case OCProtoListType:
case OCMsgRefType:
case OCSelRefType:
snprintf(iLineCommentCString, MAX_COMMENT_LENGTH, "%s", theSymPtr);
break;
default:
break;
}
}
else
{
if (address >= iDataSect.s.addr && address < (iDataSect.s.addr + iDataSect.size))
{
objc2_64_ivar_t* foundIvar = NULL;
objc2_64_ivar_t* maybeIvar = (objc2_64_ivar_t*)((iDataSect.contents) + (address - iDataSect.s.addr));
if (maybeIvar->offset != 0)
{
UInt64 offset = OSSwapBigToHostInt64(maybeIvar->offset);
if ([self findIvar:&foundIvar inClass:iCurrentClass withOffset:offset])
{
theSymPtr = [self getPointer:foundIvar->name type:NULL];
if (theSymPtr)
{
if (iOpts.variableTypes)
{
char theTypeCString[MAX_TYPE_STRING_LENGTH];
theTypeCString[0] = 0;
[self getDescription:theTypeCString forType:[self getPointer:foundIvar->type type:NULL]];
snprintf(iLineCommentCString, MAX_COMMENT_LENGTH, "(%s)%s", theTypeCString, theSymPtr);
}
else
snprintf(iLineCommentCString, MAX_COMMENT_LENGTH, "%s", theSymPtr);
}
}
}
}
}
break;
}
default:
break;
}
}
// commentForSystemCall
// ----------------------------------------------------------------------------
// System call number is stored in r0, possible values defined in
// <sys/syscall.h>. Call numbers are indices into a lookup table of handler
// routines. Args being passed to the looked-up handler start at r3 or r4,
// depending on whether it's an indirect SYS_syscall.
- (void)commentForSystemCall
{
if (!iRegInfos[0].isValid ||
iRegInfos[0].value > SYS_MAXSYSCALL)
{
snprintf(iLineCommentCString, 11, "syscall(?)");
return;
}
BOOL isIndirect = (iRegInfos[0].value == SYS_syscall);
uint32_t syscallNumReg = isIndirect ? 3 : 0;
uint32_t syscallArg1Reg = isIndirect ? 4 : 3;
if (!iRegInfos[syscallNumReg].isValid ||
iRegInfos[syscallNumReg].value > SYS_MAXSYSCALL)
{
snprintf(iLineCommentCString, 11, "syscall(?)");
return;
}
const char* theSysString = gSysCalls[iRegInfos[syscallNumReg].value];
if (!theSysString)
return;
char theTempComment[50];
theTempComment[0] = 0;
strncpy(theTempComment, theSysString, strlen(theSysString) + 1);
// Handle various system calls.
switch (iRegInfos[syscallNumReg].value)
{
case SYS_ptrace:
if (iRegInfos[syscallArg1Reg].isValid &&
iRegInfos[syscallArg1Reg].value == PT_DENY_ATTACH)
snprintf(iLineCommentCString, 40, "%s(%s)",
theTempComment, "PT_DENY_ATTACH");
else
snprintf(iLineCommentCString, MAX_COMMENT_LENGTH, "%s", theTempComment);
break;
default:
snprintf(iLineCommentCString, MAX_COMMENT_LENGTH, "%s", theTempComment);
break;
}
}
// selectorForMsgSend:fromLine:
// ----------------------------------------------------------------------------
- (char*)selectorForMsgSend: (char*)outComment
fromLine: (Line64*)inLine
{
char* selString = NULL;
uint32_t theCode = *(uint32_t*)inLine->info.code;
theCode = OSSwapBigToHostInt32(theCode);
// Bail if this is not an eligible branch.
if (PO(theCode) != 0x12) // b, bl, ba, bla
return NULL;
// Bail if this is not an objc_msgSend variant.
if (memcmp(outComment, "_objc_msgSend", 13))
return NULL;
UInt8 sendType = [self sendTypeFromMsgSend:outComment];
uint32_t selectorRegNum =
(sendType == sendSuper_stret || sendType == send_stret) ? 5 : 4;
if (!iRegInfos[selectorRegNum].isValid ||
!iRegInfos[selectorRegNum].value)
return NULL;
// Get at the selector.
UInt8 selType = PointerType;
char* selPtr = [self getPointer:iRegInfos[selectorRegNum].value type:&selType];
switch (selType)
{
case PointerType:
selString = selPtr;
break;
case OCGenericType:
if (selPtr)
{
uint32_t selPtrValue = *(uint32_t*)selPtr;
selPtrValue = OSSwapBigToHostInt32(selPtrValue);
selString = [self getPointer:selPtrValue type:NULL];
}
break;
default:
fprintf(stderr, "otx: [PPC64Processor selectorForMsgSend:fromLine:]: "
"unsupported selector type: %d at address: 0x%llx\n",
selType, inLine->info.address);
break;
}
return selString;
}
// commentForMsgSend:fromLine:
// ----------------------------------------------------------------------------
- (void)commentForMsgSend: (char*)ioComment
fromLine: (Line64*)inLine
{
char tempComment[MAX_COMMENT_LENGTH];
tempComment[0] = 0;
if (!strncmp(ioComment, "_objc_msgSend", 13))
{
char* selString = [self selectorForMsgSend:ioComment fromLine:inLine];
// Bail if we couldn't find the selector.
if (!selString)
{
iMissedSelectorCount++;
return;
}
iMatchedSelectorCount++;
UInt8 sendType = [self sendTypeFromMsgSend:ioComment];
// Get the address of the class name string, if this a class method.
UInt64 classNameAddy = 0;
// If *.classPtr is non-NULL, it's not a name string.
if (sendType == sendSuper_stret || sendType == send_stret)
{
if (iRegInfos[4].isValid && !iRegInfos[4].classPtr)
classNameAddy = iRegInfos[4].value;
}
else
{
if (iRegInfos[3].isValid && !iRegInfos[3].classPtr)
classNameAddy = iRegInfos[3].value;
}
char* className = NULL;
char* returnTypeString =
(sendType == sendSuper_stret || sendType == send_stret) ?
"(struct)" : "";
// char tempComment[MAX_COMMENT_LENGTH];
// tempComment[0] = 0;
if (classNameAddy)
{
// Get at the class name
UInt8 classNameType = PointerType;
char* classNamePtr = [self getPointer:classNameAddy type:&classNameType];
switch (classNameType)
{
// Receiver can be a static string or pointer in these sections, but we
// only want to display class names as receivers.
case DataGenericType:
case DataConstType:
case CFStringType:
case ImpPtrType:
case OCStrObjectType:
break;
case NLSymType:
if (classNamePtr)
{
UInt64 namePtrValue = *(UInt64*)classNamePtr;
namePtrValue = OSSwapBigToHostInt64(namePtrValue);
classNamePtr = [self getPointer:namePtrValue type:&classNameType];
switch (classNameType)
{
case CFStringType:
if (classNamePtr != NULL)
{
cfstring_object_64 classNameCFString = *(cfstring_object_64*)classNamePtr;
namePtrValue = classNameCFString.oc_string.chars;
namePtrValue = OSSwapBigToHostInt64(namePtrValue);
classNamePtr = [self getPointer:namePtrValue type:NULL];
className = classNamePtr;
}
break;
// Not sure what these are for, but they're NULL.
case NLSymType:
break;
default:
printf("otx: [PPC64Processor commentForMsgSend:fromLine:]: "
"non-lazy symbol pointer points to unrecognized section: %d\n", classNameType);
break;
}
}
break;
case PointerType:
className = classNamePtr;
break;
case OCGenericType:
if (classNamePtr)
{
uint32_t namePtrValue = *(uint32_t*)classNamePtr;
namePtrValue = OSSwapBigToHostInt32(namePtrValue);
className = [self getPointer:namePtrValue type:NULL];
}
break;
case OCClassType:
if (classNamePtr)
[self getObjcDescription:&className fromObject:classNamePtr type:OCClassType];
break;
default:
fprintf(stderr, "otx: [PPC64Processor commentForMsgSend]: "
"unsupported class name type: %d at address: 0x%llx\n",
classNameType, inLine->info.address);
break;
}
}
if (className)
{
snprintf(tempComment, MAX_COMMENT_LENGTH,
((sendType == sendSuper || sendType == sendSuper_stret) ?
"+%s[[%s super] %s]" : "+%s[%s %s]"),
returnTypeString, className, selString);
}
else
{
switch (sendType)
{
case send:
case send_rtp:
case send_variadic:
snprintf(tempComment, MAX_COMMENT_LENGTH, "-%s[r3 %s]", returnTypeString, selString);
break;
case sendSuper:
snprintf(tempComment, MAX_COMMENT_LENGTH, "-%s[[r3 super] %s]", returnTypeString, selString);
break;
case send_stret:
snprintf(tempComment, MAX_COMMENT_LENGTH, "-%s[r4 %s]", returnTypeString, selString);
break;
case sendSuper_stret:
snprintf(tempComment, MAX_COMMENT_LENGTH, "-%s[[r4 super] %s]", returnTypeString, selString);
break;
default:
break;
}
}
} // if (!strncmp(ioComment, "_objc_msgSend", 13))
else if (!strncmp(ioComment, "_objc_assign_ivar", 17))
{
if (iCurrentClass && iRegInfos[5].isValid)
{
char* theSymPtr = NULL;
objc2_64_ivar_t* theIvar = NULL;
objc2_64_class_t swappedClass = *iCurrentClass;
if (!iIsInstanceMethod)
{
if (![self getObjcMetaClass:&swappedClass fromClass:&swappedClass])
return;
#if __LITTLE_ENDIAN__
swap_objc2_64_class(&swappedClass);
#endif
}
if (![self findIvar:&theIvar inClass:&swappedClass withOffset:iRegInfos[5].value])
return;
theSymPtr = [self getPointer:theIvar->name type:NULL];
if (!theSymPtr)
return;
if (iOpts.variableTypes)
{
char theTypeCString[MAX_TYPE_STRING_LENGTH];
theTypeCString[0] = 0;
[self getDescription:theTypeCString forType:[self getPointer:theIvar->type type:NULL]];
snprintf(tempComment, MAX_COMMENT_LENGTH, " (%s)%s", theTypeCString, theSymPtr);
}
else
snprintf(tempComment, MAX_COMMENT_LENGTH, " %s", theSymPtr);
strncat(ioComment, tempComment, strlen(tempComment));
}
}
}
// chooseLine:
// ----------------------------------------------------------------------------
- (void)chooseLine: (Line64**)ioLine
{
if (!(*ioLine) || !(*ioLine)->info.isCode ||
!(*ioLine)->alt || !(*ioLine)->alt->chars)
return;
uint32_t theCode = *(uint32_t*)(*ioLine)->info.code;
theCode = OSSwapBigToHostInt32(theCode);
if (PO(theCode) == 18) // b, ba, bl, bla
{
Line64* theNewLine = malloc(sizeof(Line64));
memcpy(theNewLine, (*ioLine)->alt, sizeof(Line64));
theNewLine->chars = malloc(theNewLine->length + 1);
strncpy(theNewLine->chars, (*ioLine)->alt->chars,
theNewLine->length + 1);
// Swap in the verbose line and free the previous verbose lines.
[self deleteLinesBefore:(*ioLine)->alt fromList:&iVerboseLineListHead];
[self replaceLine:*ioLine withLine:theNewLine inList:&iPlainLineListHead];
*ioLine = theNewLine;
}
}
#pragma mark -
// resetRegisters:
// ----------------------------------------------------------------------------
- (void)resetRegisters: (Line64*)inLine
{
if (!inLine)
{
fprintf(stderr, "otx: [PPC64Processor resetRegisters]: "
"tried to reset with NULL inLine\n");
return;
}
// Setup the registers with default info. r3 is 'self' at the beginning
// of any Obj-C method, and r12 holds the address of the 1st instruction
// if the function was called indirectly. In the case of direct calls,
// r12 will be overwritten before it is used, if it is used at all.
[self getObjcClassPtr:&iCurrentClass fromMethod:inLine->info.address];
// [self getObjcCatPtr:&iCurrentCat fromMethod:inLine->info.address];
memset(iRegInfos, 0, sizeof(GP64RegisterInfo) * 32);
// If we didn't get the class from the method, try to get it from the
// category.
/* if (!iCurrentClass && iCurrentCat)
{
objc_category swappedCat = *iCurrentCat;
#if __LITTLE_ENDIAN__
swap_objc_category(&swappedCat);
#endif
[self getObjcClassPtr:&iCurrentClass fromName:[self getPointer:swappedCat.class_name type:NULL]];
}*/
iRegInfos[3].classPtr = iCurrentClass;
// iRegInfos[3].catPtr = iCurrentCat;
iRegInfos[3].isValid = YES;
iRegInfos[12].value = iCurrentFuncPtr;
iRegInfos[12].isValid = YES;
iLR = (GP64RegisterInfo){0};
iCTR = (GP64RegisterInfo){0};
// Try to find out whether this is a class or instance method.
Method64Info* thisMethod = NULL;
if ([self getObjcMethod:&thisMethod fromAddress:inLine->info.address])
iIsInstanceMethod = thisMethod->inst;
if (iLocalSelves)
{
free(iLocalSelves);
iLocalSelves = NULL;
iNumLocalSelves = 0;
}
if (iLocalVars)
{
free(iLocalVars);
iLocalVars = NULL;
iNumLocalVars = 0;
}
iCurrentFuncInfoIndex++;
if (iCurrentFuncInfoIndex >= iNumFuncInfos)
iCurrentFuncInfoIndex = -1;
}
// updateRegisters:
// ----------------------------------------------------------------------------
// Keep our local copy of the GPRs in sync as much as possible with the
// values that the exe will use at runtime. Assign classPtr and catPtr fields
// in a register's info if its new value points to a class or category.
// http://developer.apple.com/documentation/DeveloperTools/Conceptual/LowLevelABI/Articles/32bitPowerPC.html
// http://developer.apple.com/documentation/DeveloperTools/Conceptual/MachOTopics/Articles/dynamic_code.html
- (void)updateRegisters: (Line64*)inLine;
{
if (!inLine)
{
fprintf(stderr, "otx: [PPC64Processor updateRegisters]: "
"tried to update with NULL inLine\n");
return;
}
UInt64 theNewValue;
uint32_t theCode = *(uint32_t*)inLine->info.code;
theCode = OSSwapBigToHostInt32(theCode);
if (IS_BRANCH_LINK(theCode))
{
iLR.value = inLine->info.address + 4;
iLR.isValid = YES;
}
switch (PO(theCode))
{
case 0x07: // mulli SIMM
{
if (!iRegInfos[RA(theCode)].isValid)
{
iRegInfos[RT(theCode)] = (GP64RegisterInfo){0};
break;
}
UInt64 theProduct = (SInt32)iRegInfos[RA(theCode)].value * SIMM(theCode);
iRegInfos[RT(theCode)] = (GP64RegisterInfo){0};
iRegInfos[RT(theCode)].value = theProduct & 0xffffffff;
iRegInfos[RT(theCode)].isValid = YES;
break;
}
case 0x08: // subfic SIMM
if (!iRegInfos[RA(theCode)].isValid)
{
iRegInfos[RT(theCode)] = (GP64RegisterInfo){0};
break;
}
theNewValue = iRegInfos[RA(theCode)].value - SIMM(theCode);
iRegInfos[RT(theCode)] = (GP64RegisterInfo){0};
iRegInfos[RT(theCode)].value = theNewValue;
iRegInfos[RT(theCode)].isValid = YES;
break;
case 0x0c: // addic SIMM
case 0x0d: // addic. SIMM
case 0x0e: // addi | li SIMM
if (RA(theCode) == 1 && // current reg is stack pointer (r1)
SIMM(theCode) >= 0) // we're accessing local vars, not args
{
BOOL found = NO;
uint32_t i;
// Check for copied self pointer. This happens mostly in "init"
// methods, as in: "self = [super init]"
if (iLocalSelves) // self was copied to a local variable
{
// If we're accessing a local var copy of self,
// copy that info back to the reg in question.
for (i = 0; i < iNumLocalSelves; i++)
{
if (iLocalSelves[i].offset != UIMM(theCode))
continue;
iRegInfos[RT(theCode)] = iLocalSelves[i].regInfo;
found = YES;
break;
}
}
if (found)
break;
// Check for other local variables.
if (iLocalVars)
{
for (i = 0; i < iNumLocalVars; i++)
{
if (iLocalVars[i].offset != UIMM(theCode))
continue;
iRegInfos[RT(theCode)] = iLocalVars[i].regInfo;
found = YES;
break;
}
}
if (found)
break;
}
// We didn't find any local variables, try immediates.
if (RA(theCode) == 0) // li
{
iRegInfos[RT(theCode)] = (GP64RegisterInfo){0};
iRegInfos[RT(theCode)].value = UIMM(theCode);
iRegInfos[RT(theCode)].isValid = YES;
}
else // addi
{
// Update rD if we know what rA is.
if (!iRegInfos[RA(theCode)].isValid)
{
iRegInfos[RT(theCode)] = (GP64RegisterInfo){0};
break;
}
iRegInfos[RT(theCode)].classPtr = NULL;
iRegInfos[RT(theCode)].className = NULL;
iRegInfos[RT(theCode)].messageRefSel = NULL;
// iRegInfos[RT(theCode)].catPtr = NULL;
theNewValue = iRegInfos[RA(theCode)].value + SIMM(theCode);
UInt8 type;
char* ref = [self getPointer:theNewValue type:&type];
if (type == OCMsgRefType)
iRegInfos[RT(theCode)].messageRefSel = ref;
else if (type == OCClassRefType)
iRegInfos[RT(theCode)].className = ref;
iRegInfos[RT(theCode)].value = theNewValue;
iRegInfos[RT(theCode)].isValid = YES;
}
break;
case 0x0f: // addis | lis
iRegInfos[RT(theCode)].classPtr = NULL;
// iRegInfos[RT(theCode)].catPtr = NULL;
if (RA(theCode) == 0) // lis
{
iRegInfos[RT(theCode)] = (GP64RegisterInfo){0};
iRegInfos[RT(theCode)].value = UIMM(theCode) << 16;
iRegInfos[RT(theCode)].isValid = YES;
break;
}
// addis
if (!iRegInfos[RA(theCode)].isValid)
{
iRegInfos[RT(theCode)] = (GP64RegisterInfo){0};
break;
}
theNewValue = iRegInfos[RA(theCode)].value +
(SIMM(theCode) << 16);
iRegInfos[RT(theCode)] = (GP64RegisterInfo){0};
iRegInfos[RT(theCode)].value = theNewValue;
iRegInfos[RT(theCode)].isValid = YES;
break;
case 0x10: // bcl, bcla
case 0x13: // bclrl, bcctrl
if (!IS_BRANCH_LINK(theCode)) // fall thru if link
break;
case 0x12: // b, ba, bl, bla
{
if (!LK(theCode)) // bl, bla
break;
iRegInfos[3] = (GP64RegisterInfo){0};
break;
}
case 0x15: // rlwinm
{
if (!iRegInfos[RT(theCode)].isValid)
{
iRegInfos[RA(theCode)] = (GP64RegisterInfo){0};
break;
}
UInt64 rotatedRT =
rotl(iRegInfos[RT(theCode)].value, RB(theCode));
uint32_t theMask = 0x0;
UInt8 i;
for (i = MB(theCode); i <= ME(theCode); i++)
theMask |= 1 << (31 - i);
theNewValue = rotatedRT & theMask;
iRegInfos[RA(theCode)] = (GP64RegisterInfo){0};
iRegInfos[RA(theCode)].value = theNewValue;
iRegInfos[RA(theCode)].isValid = YES;
break;
}
case 0x18: // ori
if (!iRegInfos[RT(theCode)].isValid)
{
iRegInfos[RA(theCode)] = (GP64RegisterInfo){0};
break;
}
theNewValue =
iRegInfos[RT(theCode)].value | (uint32_t)UIMM(theCode);
iRegInfos[RA(theCode)] = (GP64RegisterInfo){0};
iRegInfos[RA(theCode)].value = theNewValue;
iRegInfos[RA(theCode)].isValid = YES;
break;
case 0x1e: // rldicl
{
if (!iRegInfos[RT(theCode)].isValid)
{
iRegInfos[RA(theCode)] = (GP64RegisterInfo){0};
break;
}
UInt8 shift = SH(theCode);
UInt8 maskBegin = MB64(theCode);
UInt64 rotatedRT = rotl64(iRegInfos[RT(theCode)].value, shift);
UInt64 theMask = (UInt64)-1 >> maskBegin;
theNewValue = rotatedRT & theMask;
iRegInfos[RA(theCode)] = (GP64RegisterInfo){0};
iRegInfos[RA(theCode)].value = theNewValue;
iRegInfos[RA(theCode)].isValid = YES;
break;
}
case 0x1f: // multiple instructions
switch (SO(theCode))
{
case 21: // ldx
/* if ((RA(theCode) != 0 && !iRegInfos[RA(theCode)].isValid) ||
!iRegInfos[RB(theCode)].isValid)
{
iRegInfos[RT(theCode)] = (GP64RegisterInfo){0};
break;
}
theNewValue = (RA(theCode) == 0) ? 0 :
iRegInfos[RA(theCode)].value + iRegInfos[RB(theCode)].value;*/
iRegInfos[RT(theCode)] = (GP64RegisterInfo){0};
break;
case 23: // lwzx
iRegInfos[RT(theCode)] = (GP64RegisterInfo){0};
break;
case 8: // subfc
case 40: // subf
if (!iRegInfos[RA(theCode)].isValid ||
!iRegInfos[RB(theCode)].isValid)
{
iRegInfos[RT(theCode)] = (GP64RegisterInfo){0};
break;
}
// 2's complement subtraction
theNewValue =
(iRegInfos[RA(theCode)].value ^= 0xffffffff) +
iRegInfos[RB(theCode)].value + 1;
iRegInfos[RT(theCode)] = (GP64RegisterInfo){0};
iRegInfos[RT(theCode)].value = theNewValue;
iRegInfos[RT(theCode)].isValid = YES;
break;
case 266: // add
if (iRegInfos[RA(theCode)].isValid && iRegInfos[RB(theCode)].isValid)
{
iRegInfos[RT(theCode)].value =
iRegInfos[RA(theCode)].value + iRegInfos[RB(theCode)].value;
iRegInfos[RT(theCode)].isValid = YES;
iRegInfos[RT(theCode)].classPtr = NULL;
iRegInfos[RT(theCode)].className = NULL;
iRegInfos[RT(theCode)].messageRefSel = NULL;
}
else
iRegInfos[RT(theCode)] = (GP64RegisterInfo){0};
break;
case 339: // mfspr
iRegInfos[RT(theCode)] = (GP64RegisterInfo){0};
if (SPR(theCode) == LR && // from LR
iLR.isValid)
{ // Copy LR into rD.
iRegInfos[RT(theCode)].value = iLR.value;
iRegInfos[RT(theCode)].isValid = YES;
}
break;
case 444: // or | or.
if (!iRegInfos[RT(theCode)].isValid ||
!iRegInfos[RB(theCode)].isValid)
{
iRegInfos[RA(theCode)] = (GP64RegisterInfo){0};
break;
}
theNewValue =
(iRegInfos[RT(theCode)].value |
iRegInfos[RB(theCode)].value);
iRegInfos[RA(theCode)] = (GP64RegisterInfo){0};
iRegInfos[RA(theCode)].value = theNewValue;
iRegInfos[RA(theCode)].isValid = YES;
// If we just copied a register, copy the
// remaining fields.
if (RT(theCode) == RB(theCode))
{
iRegInfos[RA(theCode)].classPtr =
iRegInfos[RB(theCode)].classPtr;
iRegInfos[RA(theCode)].className =
iRegInfos[RB(theCode)].className;
iRegInfos[RA(theCode)].messageRefSel =
iRegInfos[RB(theCode)].messageRefSel;
// iRegInfos[RA(theCode)].catPtr =
// iRegInfos[RB(theCode)].catPtr;
}
break;
case 467: // mtspr
if (SPR(theCode) == CTR) // to CTR
{
if (!iRegInfos[RS(theCode)].isValid)
{
iCTR = (GP64RegisterInfo){0};
break;
}
iCTR.value = iRegInfos[RS(theCode)].value;
iCTR.isValid = YES;
}
break;
case 24: // slw
if (!iRegInfos[RS(theCode)].isValid ||
!iRegInfos[RB(theCode)].isValid)
{
iRegInfos[RA(theCode)] = (GP64RegisterInfo){0};
break;
}
if (SB(iRegInfos[RB(theCode)].value))
{
theNewValue =
iRegInfos[RS(theCode)].value <<
SV(iRegInfos[RB(theCode)].value);
}
else // If RB.5 == 0, RA = 0.
theNewValue = 0;
iRegInfos[RA(theCode)] = (GP64RegisterInfo){0};
iRegInfos[RA(theCode)].value = theNewValue;
iRegInfos[RA(theCode)].isValid = YES;
break;
case 536: // srw
if (!iRegInfos[RS(theCode)].isValid ||
!iRegInfos[RB(theCode)].isValid)
{
iRegInfos[RA(theCode)] = (GP64RegisterInfo){0};
break;
}
theNewValue =
iRegInfos[RS(theCode)].value >>
SV(iRegInfos[RB(theCode)].value);
iRegInfos[RA(theCode)] = (GP64RegisterInfo){0};
iRegInfos[RA(theCode)].value = theNewValue;
iRegInfos[RA(theCode)].isValid = YES;
break;
default:
// Ideally, we would zero the destination register here. Sadly, because SO values can vary in their formats, we don't know which register is the destination.
break;
}
break;
case 0x20: // lwz
case 0x22: // lbz
if (RA(theCode) == 0)
{
iRegInfos[RT(theCode)] = (GP64RegisterInfo){0};
iRegInfos[RT(theCode)].value = SIMM(theCode);
iRegInfos[RT(theCode)].isValid = YES;
}
else if (iRegInfos[RA(theCode)].isValid)
{
void *tempPtr = [self getPointer:iRegInfos[RA(theCode)].value + SIMM(theCode) type:NULL];
if (tempPtr)
{
iRegInfos[RT(theCode)] = (GP64RegisterInfo){0};
iRegInfos[RT(theCode)].value = *(uint32_t*)tempPtr;
iRegInfos[RT(theCode)].value =
OSSwapBigToHostInt64(iRegInfos[RT(theCode)].value);
iRegInfos[RT(theCode)].isValid = YES;
}
else
iRegInfos[RT(theCode)] = (GP64RegisterInfo){0};
}
else if (iLocalVars)
{
uint32_t i;
for (i = 0; i < iNumLocalVars; i++)
{
if (iLocalVars[i].offset == SIMM(theCode))
{
iRegInfos[RT(theCode)] = iLocalVars[i].regInfo;
break;
}
}
}
else
iRegInfos[RT(theCode)] = (GP64RegisterInfo){0};
break;
/* case 0x22: // lbz
mRegInfos[RT(theCode)] = (GP64RegisterInfo){0};
if (RA(theCode) == 0)
{
mRegInfos[RT(theCode)].value = SIMM(theCode);
mRegInfos[RT(theCode)].isValid = YES;
}
break;*/
case 0x24: // stw
if (!iRegInfos[RT(theCode)].isValid ||
RA(theCode) != 1 ||
SIMM(theCode) < 0)
break;
if (iRegInfos[RT(theCode)].classPtr) // if it's a class
{
iNumLocalSelves++;
iLocalSelves = realloc(iLocalSelves,
iNumLocalSelves * sizeof(Var64Info));
iLocalSelves[iNumLocalSelves - 1] = (Var64Info)
{iRegInfos[RT(theCode)], UIMM(theCode)};
}
else
{
iNumLocalVars++;
iLocalVars = realloc(iLocalVars,
iNumLocalVars * sizeof(Var64Info));
iLocalVars[iNumLocalVars - 1] = (Var64Info)
{iRegInfos[RT(theCode)], UIMM(theCode)};
}
break;
/* case 0x21:
case 0x23:
case 0x25:
case 0x26:
case 0x27:
case 0x28:
case 0x29:
case 0x2a:
case 0x2b:
case 0x2c:
case 0x2d:
case 0x2e:
case 0x2f:
break;*/
case 0x3a: // ld
{
if (RA(theCode) == 0)
{
iRegInfos[RT(theCode)] = (GP64RegisterInfo){0};
iRegInfos[RT(theCode)].value = DS(theCode);
iRegInfos[RT(theCode)].isValid = YES;
}
else if (iRegInfos[RA(theCode)].className != NULL && DS(theCode) == 0)
{
iRegInfos[RT(theCode)] = iRegInfos[RA(theCode)];
}
else if (iRegInfos[RA(theCode)].isValid)
{
iRegInfos[RT(theCode)].classPtr = NULL;
iRegInfos[RT(theCode)].className = NULL;
iRegInfos[RT(theCode)].messageRefSel = NULL;
UInt64 newValue = iRegInfos[RA(theCode)].value + DS(theCode);
iRegInfos[RT(theCode)].value = newValue;
iRegInfos[RT(theCode)].isValid = YES;
UInt8 type;
char* ref = [self getPointer:newValue type:&type];
if (type == OCClassRefType || type == OCSuperRefType)
iRegInfos[RT(theCode)].className = ref;
}
else if (RA(theCode) == 1 && DS(theCode) >= 0)
{
BOOL found = NO;
uint32_t i;
// Check for copied self pointer. This happens mostly in "init"
// methods, as in: "self = [super init]"
if (iLocalSelves) // self was copied to a local variable
{
// If we're accessing a local var copy of self,
// copy that info back to the reg in question.
for (i = 0; i < iNumLocalSelves; i++)
{
if (iLocalSelves[i].offset != UIMM(theCode))
continue;
iRegInfos[RT(theCode)] = iLocalSelves[i].regInfo;
found = YES;
break;
}
}
if (found)
break;
// Check for other local variables.
if (iLocalVars)
{
for (i = 0; i < iNumLocalVars; i++)
{
if (iLocalVars[i].offset != UIMM(theCode))
continue;
iRegInfos[RT(theCode)] = iLocalVars[i].regInfo;
found = YES;
break;
}
}
// We don't know what's being loaded, just zero the receiver.
if (found == NO)
iRegInfos[RT(theCode)] = (GP64RegisterInfo){0};
}
else
iRegInfos[RT(theCode)] = (GP64RegisterInfo){0};
/* else if (iRegInfos[RA(theCode)].isValid)
{
UInt64 address = iRegInfos[RA(theCode)].value + DS(theCode);
UInt8 ptrType = PointerType;
char* sel = [self getPointer:address type:&ptrType];
if (sel != NULL && ptrType == OCMsgRefType)
iRegInfos[RT(theCode)].messageRefSel = sel;
else
iRegInfos[RT(theCode)].messageRefSel = NULL;
iRegInfos[RT(theCode)].classPtr = NULL;
iRegInfos[RT(theCode)].className = NULL;
iRegInfos[RT(theCode)].value = address;
iRegInfos[RT(theCode)].isValid = YES;
}*/
break;
}
case 0x3e: // std
if (!iRegInfos[RT(theCode)].isValid || RA(theCode) != 1 || DS(theCode) < 0)
break;
if (iRegInfos[RT(theCode)].classPtr) // if it's a class
{
iNumLocalSelves++;
iLocalSelves = realloc(iLocalSelves, iNumLocalSelves * sizeof(Var64Info));
iLocalSelves[iNumLocalSelves - 1] = (Var64Info){iRegInfos[RT(theCode)], (uint32_t)DS(theCode)};
}
else
{
iNumLocalVars++;
iLocalVars = realloc(iLocalVars, iNumLocalVars * sizeof(Var64Info));
iLocalVars[iNumLocalVars - 1] = (Var64Info) {iRegInfos[RT(theCode)], (uint32_t)DS(theCode)};
}
break;
default:
break;
}
}
// restoreRegisters:
// ----------------------------------------------------------------------------
- (BOOL)restoreRegisters: (Line64*)inLine
{
if (!inLine)
{
fprintf(stderr, "otx: [PPC64Processor restoreRegisters]: "
"tried to restore with NULL inLine\n");
return NO;
}
BOOL needNewLine = NO;
if (iCurrentFuncInfoIndex < 0)
return NO;
// Search current Function64Info for blocks that start at this address.
Function64Info* funcInfo =
&iFuncInfos[iCurrentFuncInfoIndex];
if (!funcInfo->blocks)
return NO;
uint32_t i;
for (i = 0; i < funcInfo->numBlocks; i++)
{
if (funcInfo->blocks[i].beginAddress !=
inLine->info.address)
continue;
// Update machine state.
Machine64State machState =
funcInfo->blocks[i].state;
memcpy(iRegInfos, machState.regInfos,
sizeof(GP64RegisterInfo) * 32);
iLR = machState.regInfos[LRIndex];
iCTR = machState.regInfos[CTRIndex];
if (machState.localSelves)
{
if (iLocalSelves)
free(iLocalSelves);
iNumLocalSelves = machState.numLocalSelves;
iLocalSelves = malloc(
sizeof(Var64Info) * iNumLocalSelves);
memcpy(iLocalSelves, machState.localSelves,
sizeof(Var64Info) * iNumLocalSelves);
}
if (machState.localVars)
{
if (iLocalVars)
free(iLocalVars);
iNumLocalVars = machState.numLocalVars;
iLocalVars = malloc(
sizeof(Var64Info) * iNumLocalVars);
memcpy(iLocalVars, machState.localVars,
sizeof(Var64Info) * iNumLocalVars);
}
// Optionally add a blank line before this block.
if (iOpts.separateLogicalBlocks && inLine->chars[0] != '\n' &&
!inLine->info.isFunction)
needNewLine = YES;
break;
} // for (i = 0...)
return needNewLine;
}
// lineIsFunction:
// ----------------------------------------------------------------------------
- (BOOL)lineIsFunction: (Line64*)inLine
{
if (!inLine)
return NO;
UInt64 theAddy = inLine->info.address;
if (theAddy == iAddrDyldStubBindingHelper ||
theAddy == iAddrDyldFuncLookupPointer)
return YES;
Method64Info* theDummyInfo = NULL;
// In Obj-C apps, the majority of funcs will have Obj-C symbols, so check
// those first.
if ([self findClassMethod:&theDummyInfo byAddress:theAddy])
return YES;
// if ([self findCatMethod:&theDummyInfo byAddress:theAddy])
// return YES;
// If it's not an Obj-C method, maybe there's an nlist.
if ([self findSymbolByAddress:theAddy])
return YES;
// If otool gave us a function name...
if (inLine->prev && !inLine->prev->info.isCode)
return YES;
BOOL isFunction = NO;
uint32_t theCode = *(uint32_t*)inLine->info.code;
theCode = OSSwapBigToHostInt32(theCode);
if ((theCode & 0xfc1fffff) == 0x7c0802a6) // mflr to any reg
{ // Allow for late mflr
BOOL foundUB = NO;
Line64* thePrevLine = inLine->prev;
// Walk back to the most recent unconditional branch, looking
// for existing symbols.
while (!foundUB && thePrevLine)
{
// Allow for multiple mflr's
if (thePrevLine->info.isFunction)
return NO;
theCode = *(uint32_t*)thePrevLine->info.code;
theCode = OSSwapBigToHostInt32(theCode);
if ((theCode & 0xfc0007ff) == 0x7c000008) // trap
{
foundUB = YES;
continue;
}
UInt8 opcode = PO(theCode);
if (opcode == 16 || opcode == 18 || opcode == 19)
// bc, bca, bcl, bcla, b, ba, bl, bla, bclr, bclrl and more
{
if (!IS_BRANCH_CONDITIONAL(theCode) &&
theCode != 0x429f0005 && // bcl w/ "always branch"
(theCode & 0x48000001) != 0x48000001) // bl
foundUB = YES;
}
if (!foundUB)
thePrevLine = thePrevLine->prev;
}
if (!thePrevLine)
return YES;
thePrevLine = thePrevLine->next;
// If the code line following the most recent unconditional
// branch is not already recognized, flag it now.
if (thePrevLine == inLine)
isFunction = YES;
else
{
BOOL foundStart = NO;
for (; thePrevLine != inLine;
thePrevLine = thePrevLine->next)
{
if (!thePrevLine->info.isCode)
continue; // not code, keep looking
else if (!thePrevLine->info.isFunction)
{ // not yet recognized, try it
theCode = *(uint32_t*)thePrevLine->info.code;
theCode = OSSwapBigToHostInt32(theCode);
if (theCode == 0x7fe00008 || // ignore traps
theCode == 0x60000000 || // ignore nops
theCode == 0x00000000) // ignore .longs
continue;
else
{
thePrevLine->info.isFunction = YES;
foundStart = YES;
break;
}
}
else // already recognized, bail
{
foundStart = YES;
break;
}
}
if (!foundStart)
isFunction = YES;
}
} // if (theCode == 0x7c0802a6)
return isFunction;
}
// codeIsBlockJump:
// ----------------------------------------------------------------------------
- (BOOL)codeIsBlockJump: (UInt8*)inCode
{
uint32_t theCode = *(uint32_t*)inCode;
theCode = OSSwapBigToHostInt32(theCode);
return IS_BLOCK_BRANCH(theCode);
}
// gatherFuncInfos
// ----------------------------------------------------------------------------
- (void)gatherFuncInfos
{
Line64* theLine = iPlainLineListHead;
uint32_t theCode;
uint32_t progCounter = 0;
// Loop thru lines.
while (theLine)
{
if (!(progCounter % (PROGRESS_FREQ * 5)))
{
if (gCancel == YES)
return;
// [NSThread sleepForTimeInterval: 0.0];
}
if (!theLine->info.isCode)
{
theLine = theLine->next;
continue;
}
theCode = *(uint32_t*)theLine->info.code;
theCode = OSSwapBigToHostInt32(theCode);
if (theLine->info.isFunction)
{
iCurrentFuncPtr = theLine->info.address;
[self resetRegisters:theLine];
}
else
[self restoreRegisters:theLine];
[self updateRegisters:theLine];
// Check if we need to save the machine state.
if (IS_BLOCK_BRANCH(theCode) && iCurrentFuncInfoIndex >= 0 &&
PO(theCode) != 0x13) // no new blocks for blr, bctr
{
UInt64 branchTarget = 0;
// Retrieve the branch target.
if (PO(theCode) == 0x12) // b
branchTarget = theLine->info.address + LI(theCode);
else if (PO(theCode) == 0x10) // bc
branchTarget = theLine->info.address + BD(theCode);
// Retrieve current Function64Info.
Function64Info* funcInfo =
&iFuncInfos[iCurrentFuncInfoIndex];
// 'currentBlock' will point to either an existing block which
// we will update, or a newly allocated block.
Block64Info* currentBlock = NULL;
Line64* endLine = NULL;
BOOL isEpilog = NO;
uint32_t i;
if (funcInfo->blocks)
{ // Blocks exist, find 1st one matching this address.
// This is an exhaustive search, but the speed hit should
// only be an issue with extremely long functions.
for (i = 0; i < funcInfo->numBlocks; i++)
{
if (funcInfo->blocks[i].beginAddress == branchTarget)
{
currentBlock = &funcInfo->blocks[i];
break;
}
}
if (currentBlock)
{ // Determine if the target block is an epilog.
if (currentBlock->endLine == NULL &&
iOpts.returnStatements)
{
// Find the first line of the target block.
Line64 searchKey = {NULL, 0, NULL, NULL, NULL, {branchTarget, {0}, YES, NO}};
Line64* searchKeyPtr = &searchKey;
Line64** beginLine = bsearch(&searchKeyPtr, iLineArray, iNumCodeLines, sizeof(Line64*),
(COMPARISON_FUNC_TYPE)Line_Address_Compare);
if (beginLine != NULL)
{
// Walk through the block. It's an epilog if it ends
// with 'blr'.
Line64* nextLine = *beginLine;
uint32_t tempCode;
while (nextLine)
{
tempCode = *(uint32_t*)nextLine->info.code;
tempCode = OSSwapBigToHostInt32(tempCode);
if (IS_BLOCK_BRANCH(tempCode))
{
endLine = nextLine;
if (IS_BLR(tempCode))
isEpilog = YES;
break;
}
nextLine = nextLine->next;
}
}
// currentBlock->endLine = endLine;
}
}
else
{ // No matching blocks found, so allocate a new one.
funcInfo->numBlocks++;
funcInfo->blocks = realloc(funcInfo->blocks,
sizeof(Block64Info) * funcInfo->numBlocks);
currentBlock =
&funcInfo->blocks[funcInfo->numBlocks - 1];
*currentBlock = (Block64Info){0};
}
}
else
{ // No existing blocks, allocate one.
funcInfo->numBlocks++;
funcInfo->blocks = calloc(1, sizeof(Block64Info));
currentBlock = funcInfo->blocks;
}
// sanity check
if (!currentBlock)
{
fprintf(stderr, "otx: [PPC64Processor gatherFuncInfos] "
"currentBlock is NULL. Flame the dev.\n");
return;
}
// Create a new Machine64State.
GP64RegisterInfo* savedRegs = malloc(
sizeof(GP64RegisterInfo) * 34);
memcpy(savedRegs, iRegInfos, sizeof(GP64RegisterInfo) * 32);
savedRegs[LRIndex] = iLR;
savedRegs[CTRIndex] = iCTR;
Var64Info* savedSelves = NULL;
if (iLocalSelves)
{
savedSelves = malloc(
sizeof(Var64Info) * iNumLocalSelves);
memcpy(savedSelves, iLocalSelves,
sizeof(Var64Info) * iNumLocalSelves);
}
Var64Info* savedVars = NULL;
if (iLocalVars)
{
savedVars = malloc(
sizeof(Var64Info) * iNumLocalVars);
memcpy(savedVars, iLocalVars,
sizeof(Var64Info) * iNumLocalVars);
}
Machine64State machState =
{savedRegs, savedSelves, iNumLocalSelves,
savedVars, iNumLocalVars};
// Store the new Block64Info.
Block64Info blockInfo =
{branchTarget, endLine, isEpilog, machState};
memcpy(currentBlock, &blockInfo, sizeof(Block64Info));
}
theLine = theLine->next;
progCounter++;
}
iCurrentFuncInfoIndex = -1;
}
#ifdef OTX_DEBUG
// printBlocks:
// ----------------------------------------------------------------------------
- (void)printBlocks: (uint32_t)inFuncIndex;
{
if (!iFuncInfos)
return;
Function64Info* funcInfo = &iFuncInfos[inFuncIndex];
if (!funcInfo || !funcInfo->blocks)
return;
uint32_t i, j;
fprintf(stderr, "\nfunction at 0x%llx:\n\n", funcInfo->address);
fprintf(stderr, "%d blocks\n", funcInfo->numBlocks);
for (i = 0; i < funcInfo->numBlocks; i++)
{
fprintf(stderr, "\nblock %d at 0x%llx:\n\n", i + 1,
funcInfo->blocks[i].beginAddress);
for (j = 0; j < 32; j++)
{
if (!funcInfo->blocks[i].state.regInfos[j].isValid)
continue;
fprintf(stderr, "\t\tr%d: 0x%llx\n", j,
funcInfo->blocks[i].state.regInfos[j].value);
}
}
}
#endif // OTX_DEBUG
@end
|
github
|
amcorrigan/IA-Lab-master
|
choosePlanes.m
|
.m
|
IA-Lab-master/GUI/choosePlanes.m
| 1,713 |
utf_8
|
8b73f8946c63776dba8f7342c186874b
|
function zvalues = choosePlanes(IL,initSelection,parenth)
% choose selected z planes for modifying the import file.
zidx = find(strcmpi('zslice',IL.ChoiceStruct.Labels),1,'first');
origzvalues = IL.ChoiceStruct.Choices{zidx};
if nargin<3 || isempty(parenth)
parenth = gfigure();
end
set(parenth,'closerequestfcn',@figclosefun)
vbox = uix.VBox('parent',parenth,'padding',20);
uicontrol('parent',vbox,'style','text','String','Select planes:');
lbox = uicontrol('parent',vbox,'style','listbox','Max',100,'min',0,...
'string',arrayfun(@num2str,origzvalues,'uni',false),'value',[]);
if nargin>1 && ~isempty(initSelection)
selinds = any(bsxfun(@eq,origzvalues(:),initSelection(:)'),2);
set(lbox,'value',origzvalues(selinds))
end
temphbox = uix.HBox('parent',vbox);
uicontrol('parent',temphbox,'style','pushbutton','String','Select all',...
'callback',{@selectallcallback,lbox});
uix.Empty('parent',temphbox);
uicontrol('parent',temphbox,'style','pushbutton','String','Finish',...
'callback',@(src,evt)close(parenth));
set(temphbox,'widths',[-1,-2,-2])
set(vbox,'heights',[-1,-5,-1]);
uiwait(parenth);
% get the selected wells, then delete the figure
zinds = get(lbox,'value');
zvalues = origzvalues(zinds);
delete(parenth)
end
function selectallcallback(src,evt,lbox)
numvals = numel(get(lbox,'String')); % need to check this works even in the event of one plane
set(lbox,'value',1:numvals)
end
function figclosefun(src,evt)
if isequal(get(src, 'waitstatus'), 'waiting')
% The GUI is still in UIWAIT, us UIRESUME
uiresume(src);
else
% The GUI is no longer waiting, just close it
delete(src);
end
end
|
github
|
amcorrigan/IA-Lab-master
|
chooseWells.m
|
.m
|
IA-Lab-master/GUI/chooseWells.m
| 1,183 |
utf_8
|
db96ecfe82d88de9511f61be6874106f
|
function wellrowcol = chooseWells(IL,initSelection,parenth)
% find out what choices are available
wellidx = find(strcmpi('well',IL.ChoiceStruct.Labels),1,'first');
[r,c] = wellstr2rowcol(IL.ChoiceStruct.Choices{wellidx});
data = NaN*zeros(IL.PlateDimensions([2,1]));
data(amcSub2Ind(size(data),[r,c])) = 1;
if nargin<3 || isempty(parenth)
parenth = gfigure();
end
set(parenth,'closerequestfcn',@figclosefun)
if nargin<2 || isempty(initSelection)
initSelection = zeros(size(data));
elseif size(initSelection,2)==2 && size(data,2)~=2
temp = initSelection;
initSelection = zeros(size(data));
initSelection(amcSub2Ind(size(data),temp)) = 1;
end
this.WellSelector = PlateShowSelect(data(:,:,[1,1,1]),parenth,initSelection);
uiwait(parenth);
% get the selected wells, then delete the figure
wellinds = this.WellSelector.Status==1;
wellrowcol = findn(wellinds);
delete(parenth)
end
function figclosefun(src,evt)
if isequal(get(src, 'waitstatus'), 'waiting')
% The GUI is still in UIWAIT, us UIRESUME
uiresume(src);
else
% The GUI is no longer waiting, just close it
delete(src);
end
end
|
github
|
amcorrigan/IA-Lab-master
|
getStringGUI.m
|
.m
|
IA-Lab-master/GUI/getStringGUI.m
| 1,184 |
utf_8
|
5fc2dd0f88ca0bf52baa4d95bb53748c
|
function str = getStringGUI(title, msg, varargin)
% get the user to enter a string
if nargin<2 || isempty(msg)
msg = 'Enter some text:';
end
if nargin<1 || isempty(title)
title = 'Get text';
end
fig = gfigure('Name',title,'closerequestfcn',@closereqfun,varargin{:});
vbox = uix.VBox('parent',fig);
texth = uicontrol('style','text','String',msg,'parent',vbox);
edith = uicontrol('style','edit','parent',vbox);
hbox = uix.HBox('parent',vbox);
uix.Empty('parent',hbox);
okbutton = uicontrol('style','pushbutton','String','OK','parent',hbox,...
'callback',{@OKcallback,fig});
set(hbox,'widths',[-4,-1])
set(vbox,'heights',[-2,-2,-1],'spacing',10,'padding',10)
uiwait(fig);
str = get(edith,'String');
delete(fig);
end
function OKcallback(src,evt,fig)
uiresume(fig);
end
function closereqfun(src,evt)
if isequal(get(src, 'waitstatus'), 'waiting')
% The GUI is still in UIWAIT, us UIRESUME
uiresume(src);
else
% The GUI is no longer waiting, just close it
delete(src);
end
end
|
github
|
amcorrigan/IA-Lab-master
|
chooseFields.m
|
.m
|
IA-Lab-master/GUI/chooseFields.m
| 1,820 |
utf_8
|
8cff1357e138e3aeb7e124e10002eb05
|
function fvalues = chooseFields(IL,initSelection,parenth)
% choose selected z planes for modifying the import file.
% This could be completely generalised, nothing field or z specific here
% apart from the choice of label
fidx = find(strcmpi('field',IL.ChoiceStruct.Labels),1,'first');
origfvalues = IL.ChoiceStruct.Choices{fidx};
if nargin<3 || isempty(parenth)
parenth = gfigure();
end
set(parenth,'closerequestfcn',@figclosefun)
vbox = uix.VBox('parent',parenth,'padding',20);
uicontrol('parent',vbox,'style','text','String','Select planes:');
lbox = uicontrol('parent',vbox,'style','listbox','Max',100,'min',0,...
'string',arrayfun(@num2str,origfvalues,'uni',false),'value',[]);
if nargin>1 && ~isempty(initSelection)
selinds = any(bsxfun(@eq,origfvalues(:),initSelection(:)'),2);
set(lbox,'value',origfvalues(selinds))
end
temphbox = uix.HBox('parent',vbox);
uicontrol('parent',temphbox,'style','pushbutton','String','Select all',...
'callback',{@selectallcallback,lbox});
uix.Empty('parent',temphbox);
uicontrol('parent',temphbox,'style','pushbutton','String','Finish',...
'callback',@(src,evt)close(parenth));
set(temphbox,'widths',[-1,-2,-2])
set(vbox,'heights',[-1,-5,-1]);
uiwait(parenth);
% get the selected wells, then delete the figure
finds = get(lbox,'value');
fvalues = origfvalues(finds);
delete(parenth)
end
function selectallcallback(src,evt,lbox)
numvals = numel(get(lbox,'String')); % need to check this works even in the event of one plane
set(lbox,'value',1:numvals)
end
function figclosefun(src,evt)
if isequal(get(src, 'waitstatus'), 'waiting')
% The GUI is still in UIWAIT, us UIRESUME
uiresume(src);
else
% The GUI is no longer waiting, just close it
delete(src);
end
end
|
github
|
amcorrigan/IA-Lab-master
|
prepareForExport.m
|
.m
|
IA-Lab-master/ExportClasses/prepareForExport.m
| 2,849 |
utf_8
|
b51365d0b86be053e25c4b1c4fc72590
|
function stats2 = prepareForExport(stats,include,exclude)
% prepare the statistics structure for export
%
% To export to a csv-type file, each of the fields should contain only
% scalars
% So go through the fields, and if there are non-scalars, replace the field
% with multiple fields, one for each element
fnames = fieldnames(stats);
if nargin<3
if nargin==2 && isstruct(include)
inames = fieldnames(include);
ind = find(strcmpi('exclude',inames),1,'first');
if ~isempty(ind)
exclude = include.(inames{ind});
else
exclude = false(numel(fnames),1);
end
ind = find(strcmpi('include',inames),1,'first');
if ~isempty(ind)
include = include.(inames{ind});
else
include = true(numel(fnames),1);
end
else
exclude = false(numel(fnames),1);
end
end
if nargin<2 || isempty(include)
include = true(numel(fnames),1);
end
if iscell(exclude)
exclude = cellfun(@(x)any(strcmpi(x,exclude)),fnames);
end
if iscell(include)
% cell array of field names supplied
% fstr = include;
include = cellfun(@(x)any(strcmpi(x,include)),fnames);
end
maxSize = zeros(numel(fnames),1);
% skip = false(numel(fnames),1);
skip = exclude(:) | ~include(:);
for ii = 1:numel(fnames)
fieldsize = arrayfun(@(x)numel(x.(fnames{ii})),stats);
maxSize(ii) = max(fieldsize);
maxInd = find(fieldsize==maxSize(ii),1,'first');
if iscell(stats(maxInd).(fnames{ii}))
% for a cell array, check that it's strings inside
if ~ischar(stats(maxInd).(fnames{ii}){1})
skip(ii) = true;
end
elseif ischar(stats(maxInd).(fnames{ii}))
maxSize(ii) = 1; % strings of any length can be accommodated
end
end
trivial = maxSize<=1 & ~skip;
nonTrivial = maxSize>1 & ~skip;
for ii = 1:numel(fnames)
if trivial(ii)
% this syntax is awful!
[stats2(1:numel(stats),1).(fnames{ii})] = stats.(fnames{ii});
elseif nonTrivial(ii)
fmt = ['%s_%0.', num2str(ceil(log10(maxSize(ii)))), 'd'];
for jj = 1:maxSize(ii)
newname = sprintf(fmt,fnames{ii},jj);
tempval = arrayfun(@(x)subarrayfcn(x,fnames{ii},jj),stats,'uni',false);
[stats2(1:numel(stats),1).(newname)] = tempval{:};
end
end
end
if ~exist('stats2','var')
stats2 = struct;
end
end
function val = subarrayfcn(x,fname,ind)
% this function is used by arrayfun above to extract the ind'th element of
% the field fname of the structure x, or NaN if that element doesn't exist
%
% ie
% x.(fname)(ind)
if numel(x.(fname))<ind
val = NaN;
else
val = x.(fname)(ind);
end
end
|
github
|
amcorrigan/IA-Lab-master
|
label2outline.m
|
.m
|
IA-Lab-master/Utilities/label2outline.m
| 3,037 |
utf_8
|
5ecb67916987dd5c80e4bee236a291db
|
function bordxy = label2outline(L,skip,interpfact)
% Currently the interpolation means that there is a bit of a discontinuity
% at the join, this needs tidying up by extending the range of the
% interpolation input
% no real logic behind choosing these factors, just whatever looks nice and
% retains the detail of the label matrix
if nargin<2 || isempty(skip)
skip = 6;
end
if nargin<3 || isempty(interpfact)
interpfact = 2*skip;
end
stats = labelBorder2D(L);
bordxy = cell(numel(stats),1);
for ii = 1:numel(stats)
borderskip = stats(ii).border([(1:skip:end-1),1],:); % make sure circular
if ~isnan(interpfact)
inds = (-1:(size(borderskip,1)+2))';
actinds = mod(inds-1,size(borderskip,1))+1;
bordxy{ii} = interp1(inds,borderskip(actinds,:),...
linspace(1,size(borderskip,1),interpfact*size(borderskip,1))','spline');
else
bordxy{ii} = borderskip;
end
end
end
function stats = labelBorder2D(L)
% return a structure which contains border information for the different
% regions in the label matrix L.
% Absolute means that the centroid isn't subtracted off
% this approach is predicated on having 2D separation. This means that 3D
% overlapping objects or objects without a boundary of zeros separating
% them will cause problems
bw = L>0;
[B,L2] = bwboundaries(bw,8,'noholes');
if max(L2(:))==max(L(:))
cumL = borderLength(B);
stats = regionprops(L2,L,'MeanIntensity');
for ii = 1:numel(stats)
% stats(ii).rawborder = B{ii};
stats(ii).cumL = cumL{ii};
stats(ii).border = B{ii};
end
% rearrange based on the mean region intensity, which should always match
% exactly with the region in the original matrix
ix = [stats.MeanIntensity];
% stats = stats(ix);
stats(ix) = stats;
stats = rmfield(stats,'MeanIntensity');
else
% no clear 2D boundary, so have to do one label at a time
% This also carries the assumption that each region is contiguous.
for ii = 1:max(L(:))
if nnz(L==ii)>0
B = bwboundaries(L==ii,8,'noholes');
if ~iscell(B)
B = {B}; % easier to do this way round..
end
cumL = borderLength(B);
tstats.cumL = cumL{1};
tstats.border = B{1};
stats(ii) = tstats;
else
tstats.cumL = NaN;
tstats.border = NaN;
stats(ii) = tstats;
end
end
end
end
function cumL = borderLength(B)
% return the cumulative length along the border pixels contained in B
if ~iscell(B)
B = {B};
end
cumL = cell(size(B));
for ii = 1:numel(B)
dd = diff(B{ii},1,1);
sL = sqrt(sum(dd.^2,2));% simple addition may be quicker than calling sum
% but MIGHT not alway be in 2D..
cumL{ii} = [0;cumsum(sL)];
end
end
|
github
|
amcorrigan/IA-Lab-master
|
expandCellIndices.m
|
.m
|
IA-Lab-master/Utilities/expandCellIndices.m
| 800 |
utf_8
|
88d51af88990f29b0c4028308028871a
|
function expandIdx = expandCellIndices(cellidx)
% expand the cell indices cellidx into a list of permutations
% use a recursive function?
expandIdx = recurseexpand(cellidx{1},cellidx(2:end));
end
function expandIdx = recurseexpand(currlist,remcellidx)
% for every element of currlist, combine with each element of the next cellidx
% and then call the next level down
try
if isempty(remcellidx)
expandIdx = currlist;
else
initlen = size(currlist,1);
nextlen = numel(remcellidx{1});
newidx = [currlist(ceil((1:(initlen*nextlen))/nextlen),:), repmat(remcellidx{1}(:),[initlen,1])];
expandIdx = recurseexpand(newidx,remcellidx(2:end));
end
catch ME
rethrow(ME)
end
end
|
github
|
amcorrigan/IA-Lab-master
|
matchLabels.m
|
.m
|
IA-Lab-master/Utilities/matchLabels.m
| 865 |
utf_8
|
c436f156ccd8f0e0b607f5edd2c4847b
|
function [Lnew,probvals] = matchLabels(L2,Lseed)
% adjust the values in L2 so that they match those in the seed region.
% Try not to assume that the seed region will be wholely contained within
% L2, but that there is overlap.
%
% also, optionally check for confusion in which region is which, and flag
% this up
L3 = L2;
L3(Lseed==0) = 0;
stats = regionprops(L3,'PixelIdxList');
idxlist = {stats.PixelIdxList}';
% need to remove zeros and then check that the variance is zero and find
% the mean value
% is this any quicker than doing in a loop??
[mu,vv] = cellfun(@(x)meanvarfunction(x,Lseed),idxlist);
probvals = find(vv>0);
mu(probvals) = 0;
mu = [0;mu(:)];
Lnew = mu(L2+1);
end
function [mu,vv] = meanvarfunction(idx,L2)
vals = L2(idx);
vals(vals==0) = [];
mu = mean(vals);
vv = mean(vals.^2) - mu.^2;
end
|
github
|
amcorrigan/IA-Lab-master
|
az_parseXML_ChannelColour_mes.m
|
.m
|
IA-Lab-master/Utilities/az_parseXML_ChannelColour_mes.m
| 3,396 |
utf_8
|
d6908fa960c4fea024cc188e7a861100
|
function o_struct = az_parseXML_ChannelColour_mes(i_fileName)
%
% i_fileName = '\\UK-Image-01\HCB\Technology Eval\Automated confocal\Yokogawa CV7000\CV7000 Demo Data\Corrected Images\Bead 96well_20140827_122725\AssayPlate_BD_#353219\JP_60x_beads_96w_4col.mes'
try
tree = xmlread(i_fileName);
catch
error('Failed to read XML file %s.',i_fileName);
end
% Recurse over child nodes. This could run into problems
% with very deeply nested trees.
try
xmlStruct = parseChildNodes(tree);
catch
error('Unable to parse XML file %s.',i_fileName);
end
%%____________________________________________________________
%%
counter = 0;
for i = 1:length(xmlStruct.Children)
if strcmp(xmlStruct.Children(i).Name, 'bts:ChannelList') == true
for j = 1:length(xmlStruct.Children(i).Children)
if strcmp(xmlStruct.Children(i).Children(j).Name, 'bts:Channel') == true
counter = counter + 1;
o_struct(counter).Ch = uint8(str2double(xmlStruct.Children(i).Children(j).Attributes.Ch));
o_struct(counter).Colour(1) = hex2dec(xmlStruct.Children(i).Children(j).Attributes.Color(4:5))/255;
o_struct(counter).Colour(2) = hex2dec(xmlStruct.Children(i).Children(j).Attributes.Color(6:7))/255;
o_struct(counter).Colour(3) = hex2dec(xmlStruct.Children(i).Children(j).Attributes.Color(8:9))/255;
end;
end;
break;
end;
end;
end
% ----- Local function PARSECHILDNODES -----
function children = parseChildNodes(theNode)
% Recurse over node children.
children = [];
if theNode.hasChildNodes
childNodes = theNode.getChildNodes;
numChildNodes = childNodes.getLength;
allocCell = cell(1, numChildNodes);
children = struct( ...
'Name', allocCell, ...
'Attributes', allocCell, ...
'Children', allocCell);
for count = 1:numChildNodes
theChild = childNodes.item(count-1);
children(count) = makeStructFromNode(theChild);
end
end
end
% ----- Local function MAKESTRUCTFROMNODE -----
function nodeStruct = makeStructFromNode(theNode)
% Create structure of node info.
nodeStruct = struct( ...
'Name', char(theNode.getNodeName), ...
'Attributes', parseAttributes(theNode), ...
'Children', parseChildNodes(theNode));
end
% ----- Local function PARSEATTRIBUTES -----
function attributes = parseAttributes(theNode)
% Create attributes structure.
attributes = [];
if theNode.hasAttributes
theAttributes = theNode.getAttributes;
numAttributes = theAttributes.getLength;
%-- Delete the leading 'dts:' if any
token = 'bts:';
for count = 1:numAttributes
attrib = theAttributes.item(count-1);
%-- Delete the leading 'dts:' if any
aName = char(attrib.getName);
[~,endIndex] = regexp(aName,token);
if ~isempty(endIndex)
tempName = aName(endIndex + 1 : end);
attributes.(tempName) = char(attrib.getValue);
end
end;
end
end
|
github
|
amcorrigan/IA-Lab-master
|
parseChildNodes.m
|
.m
|
IA-Lab-master/Utilities/parseChildNodes.m
| 1,742 |
utf_8
|
aa71c09fe13a05a2507661f5a965daa6
|
function children = parseChildNodes(theNode)
% Recurse over node children.
children = [];
if theNode.hasChildNodes
childNodes = theNode.getChildNodes;
numChildNodes = childNodes.getLength;
allocCell = cell(1, numChildNodes);
children = struct( ...
'Name', allocCell, ...
'Attributes', allocCell, ...
'Children', allocCell);
for count = 1:numChildNodes
theChild = childNodes.item(count-1);
children(count) = makeStructFromNode(theChild);
end
end
end
% ----- Local function MAKESTRUCTFROMNODE -----
function nodeStruct = makeStructFromNode(theNode)
% Create structure of node info.
nodeStruct = struct( ...
'Name', char(theNode.getNodeName), ...
'Attributes', parseAttributes(theNode), ...
'Children', parseChildNodes(theNode));
end
% ----- Local function PARSEATTRIBUTES -----
function attributes = parseAttributes(theNode)
% Create attributes structure.
attributes = [];
if theNode.hasAttributes
theAttributes = theNode.getAttributes;
numAttributes = theAttributes.getLength;
%-- Delete the leading 'dts:' if any
token = 'bts:';
for count = 1:numAttributes
attrib = theAttributes.item(count-1);
%-- Delete the leading 'dts:' if any
aName = char(attrib.getName);
[~,endIndex] = regexp(aName,token);
if ~isempty(endIndex)
tempName = aName(endIndex + 1 : end);
attributes.(tempName) = char(attrib.getValue);
end
end;
end
end
|
github
|
amcorrigan/IA-Lab-master
|
savejson.m
|
.m
|
IA-Lab-master/Utilities/jsonlab/savejson.m
| 19,584 |
utf_8
|
116395347173d949bf39b82ac3bdd794
|
function json=savejson(rootname,obj,varargin)
%
% json=savejson(rootname,obj,filename)
% or
% json=savejson(rootname,obj,opt)
% json=savejson(rootname,obj,'param1',value1,'param2',value2,...)
%
% convert a MATLAB object (cell, struct or array) into a JSON (JavaScript
% Object Notation) string
%
% author: Qianqian Fang (fangq<at> nmr.mgh.harvard.edu)
% created on 2011/09/09
%
% $Id$
%
% input:
% rootname: the name of the root-object, when set to '', the root name
% is ignored, however, when opt.ForceRootName is set to 1 (see below),
% the MATLAB variable name will be used as the root name.
% obj: a MATLAB object (array, cell, cell array, struct, struct array,
% class instance).
% filename: a string for the file name to save the output JSON data.
% opt: a struct for additional options, ignore to use default values.
% opt can have the following fields (first in [.|.] is the default)
%
% opt.FileName [''|string]: a file name to save the output JSON data
% opt.FloatFormat ['%.10g'|string]: format to show each numeric element
% of a 1D/2D array;
% opt.ArrayIndent [1|0]: if 1, output explicit data array with
% precedent indentation; if 0, no indentation
% opt.ArrayToStruct[0|1]: when set to 0, savejson outputs 1D/2D
% array in JSON array format; if sets to 1, an
% array will be shown as a struct with fields
% "_ArrayType_", "_ArraySize_" and "_ArrayData_"; for
% sparse arrays, the non-zero elements will be
% saved to _ArrayData_ field in triplet-format i.e.
% (ix,iy,val) and "_ArrayIsSparse_" will be added
% with a value of 1; for a complex array, the
% _ArrayData_ array will include two columns
% (4 for sparse) to record the real and imaginary
% parts, and also "_ArrayIsComplex_":1 is added.
% opt.ParseLogical [0|1]: if this is set to 1, logical array elem
% will use true/false rather than 1/0.
% opt.SingletArray [0|1]: if this is set to 1, arrays with a single
% numerical element will be shown without a square
% bracket, unless it is the root object; if 0, square
% brackets are forced for any numerical arrays.
% opt.SingletCell [1|0]: if 1, always enclose a cell with "[]"
% even it has only one element; if 0, brackets
% are ignored when a cell has only 1 element.
% opt.ForceRootName [0|1]: when set to 1 and rootname is empty, savejson
% will use the name of the passed obj variable as the
% root object name; if obj is an expression and
% does not have a name, 'root' will be used; if this
% is set to 0 and rootname is empty, the root level
% will be merged down to the lower level.
% opt.Inf ['"$1_Inf_"'|string]: a customized regular expression pattern
% to represent +/-Inf. The matched pattern is '([-+]*)Inf'
% and $1 represents the sign. For those who want to use
% 1e999 to represent Inf, they can set opt.Inf to '$11e999'
% opt.NaN ['"_NaN_"'|string]: a customized regular expression pattern
% to represent NaN
% opt.JSONP [''|string]: to generate a JSONP output (JSON with padding),
% for example, if opt.JSONP='foo', the JSON data is
% wrapped inside a function call as 'foo(...);'
% opt.UnpackHex [1|0]: conver the 0x[hex code] output by loadjson
% back to the string form
% opt.SaveBinary [0|1]: 1 - save the JSON file in binary mode; 0 - text mode.
% opt.Compact [0|1]: 1- out compact JSON format (remove all newlines and tabs)
%
% opt can be replaced by a list of ('param',value) pairs. The param
% string is equivallent to a field in opt and is case sensitive.
% output:
% json: a string in the JSON format (see http://json.org)
%
% examples:
% jsonmesh=struct('MeshNode',[0 0 0;1 0 0;0 1 0;1 1 0;0 0 1;1 0 1;0 1 1;1 1 1],...
% 'MeshTetra',[1 2 4 8;1 3 4 8;1 2 6 8;1 5 6 8;1 5 7 8;1 3 7 8],...
% 'MeshTri',[1 2 4;1 2 6;1 3 4;1 3 7;1 5 6;1 5 7;...
% 2 8 4;2 8 6;3 8 4;3 8 7;5 8 6;5 8 7],...
% 'MeshCreator','FangQ','MeshTitle','T6 Cube',...
% 'SpecialData',[nan, inf, -inf]);
% savejson('jmesh',jsonmesh)
% savejson('',jsonmesh,'ArrayIndent',0,'FloatFormat','\t%.5g')
%
% license:
% BSD or GPL version 3, see LICENSE_{BSD,GPLv3}.txt files for details
%
% -- this function is part of JSONLab toolbox (http://iso2mesh.sf.net/cgi-bin/index.cgi?jsonlab)
%
if(nargin==1)
varname=inputname(1);
obj=rootname;
if(isempty(varname))
varname='root';
end
rootname=varname;
else
varname=inputname(2);
end
if(length(varargin)==1 && ischar(varargin{1}))
opt=struct('filename',varargin{1});
else
opt=varargin2struct(varargin{:});
end
opt.IsOctave=exist('OCTAVE_VERSION','builtin');
if(isfield(opt,'norowbracket'))
warning('Option ''NoRowBracket'' is depreciated, please use ''SingletArray'' and set its value to not(NoRowBracket)');
if(~isfield(opt,'singletarray'))
opt.singletarray=not(opt.norowbracket);
end
end
rootisarray=0;
rootlevel=1;
forceroot=jsonopt('ForceRootName',0,opt);
if((isnumeric(obj) || islogical(obj) || ischar(obj) || isstruct(obj) || ...
iscell(obj) || isobject(obj)) && isempty(rootname) && forceroot==0)
rootisarray=1;
rootlevel=0;
else
if(isempty(rootname))
rootname=varname;
end
end
if((isstruct(obj) || iscell(obj))&& isempty(rootname) && forceroot)
rootname='root';
end
whitespaces=struct('tab',sprintf('\t'),'newline',sprintf('\n'),'sep',sprintf(',\n'));
if(jsonopt('Compact',0,opt)==1)
whitespaces=struct('tab','','newline','','sep',',');
end
if(~isfield(opt,'whitespaces_'))
opt.whitespaces_=whitespaces;
end
nl=whitespaces.newline;
json=obj2json(rootname,obj,rootlevel,opt);
if(rootisarray)
json=sprintf('%s%s',json,nl);
else
json=sprintf('{%s%s%s}\n',nl,json,nl);
end
jsonp=jsonopt('JSONP','',opt);
if(~isempty(jsonp))
json=sprintf('%s(%s);%s',jsonp,json,nl);
end
% save to a file if FileName is set, suggested by Patrick Rapin
filename=jsonopt('FileName','',opt);
if(~isempty(filename))
if(jsonopt('SaveBinary',0,opt)==1)
fid = fopen(filename, 'wb');
fwrite(fid,json);
else
fid = fopen(filename, 'wt');
fwrite(fid,json,'char');
end
fclose(fid);
end
%%-------------------------------------------------------------------------
function txt=obj2json(name,item,level,varargin)
if(iscell(item))
txt=cell2json(name,item,level,varargin{:});
elseif(isstruct(item))
txt=struct2json(name,item,level,varargin{:});
elseif(ischar(item))
txt=str2json(name,item,level,varargin{:});
elseif(isobject(item))
txt=matlabobject2json(name,item,level,varargin{:});
else
txt=mat2json(name,item,level,varargin{:});
end
%%-------------------------------------------------------------------------
function txt=cell2json(name,item,level,varargin)
txt={};
if(~iscell(item))
error('input is not a cell');
end
dim=size(item);
if(ndims(squeeze(item))>2) % for 3D or higher dimensions, flatten to 2D for now
item=reshape(item,dim(1),numel(item)/dim(1));
dim=size(item);
end
len=numel(item);
ws=jsonopt('whitespaces_',struct('tab',sprintf('\t'),'newline',sprintf('\n'),'sep',sprintf(',\n')),varargin{:});
padding0=repmat(ws.tab,1,level);
padding2=repmat(ws.tab,1,level+1);
nl=ws.newline;
bracketlevel=~jsonopt('singletcell',1,varargin{:});
if(len>bracketlevel)
if(~isempty(name))
txt={padding0, '"', checkname(name,varargin{:}),'": [', nl}; name='';
else
txt={padding0, '[', nl};
end
elseif(len==0)
if(~isempty(name))
txt={padding0, '"' checkname(name,varargin{:}) '": []'}; name='';
else
txt={padding0, '[]'};
end
end
for i=1:dim(1)
if(dim(1)>1)
txt(end+1:end+3)={padding2,'[',nl};
end
for j=1:dim(2)
txt{end+1}=obj2json(name,item{i,j},level+(dim(1)>1)+(len>bracketlevel),varargin{:});
if(j<dim(2))
txt(end+1:end+2)={',' nl};
end
end
if(dim(1)>1)
txt(end+1:end+3)={nl,padding2,']'};
end
if(i<dim(1))
txt(end+1:end+2)={',' nl};
end
%if(j==dim(2)) txt=sprintf('%s%s',txt,sprintf(',%s',nl)); end
end
if(len>bracketlevel)
txt(end+1:end+3)={nl,padding0,']'};
end
txt = sprintf('%s',txt{:});
%%-------------------------------------------------------------------------
function txt=struct2json(name,item,level,varargin)
txt={};
if(~isstruct(item))
error('input is not a struct');
end
dim=size(item);
if(ndims(squeeze(item))>2) % for 3D or higher dimensions, flatten to 2D for now
item=reshape(item,dim(1),numel(item)/dim(1));
dim=size(item);
end
len=numel(item);
forcearray= (len>1 || (jsonopt('SingletArray',0,varargin{:})==1 && level>0));
ws=struct('tab',sprintf('\t'),'newline',sprintf('\n'));
ws=jsonopt('whitespaces_',ws,varargin{:});
padding0=repmat(ws.tab,1,level);
padding2=repmat(ws.tab,1,level+1);
padding1=repmat(ws.tab,1,level+(dim(1)>1)+forcearray);
nl=ws.newline;
if(isempty(item))
if(~isempty(name))
txt={padding0, '"', checkname(name,varargin{:}),'": []'};
else
txt={padding0, '[]'};
end
txt = sprintf('%s',txt{:});
return;
end
if(~isempty(name))
if(forcearray)
txt={padding0, '"', checkname(name,varargin{:}),'": [', nl};
end
else
if(forcearray)
txt={padding0, '[', nl};
end
end
for j=1:dim(2)
if(dim(1)>1)
txt(end+1:end+3)={padding2,'[',nl};
end
for i=1:dim(1)
names = fieldnames(item(i,j));
if(~isempty(name) && len==1 && ~forcearray)
txt(end+1:end+5)={padding1, '"', checkname(name,varargin{:}),'": {', nl};
else
txt(end+1:end+3)={padding1, '{', nl};
end
if(~isempty(names))
for e=1:length(names)
txt{end+1}=obj2json(names{e},item(i,j).(names{e}),...
level+(dim(1)>1)+1+forcearray,varargin{:});
if(e<length(names))
txt{end+1}=',';
end
txt{end+1}=nl;
end
end
txt(end+1:end+2)={padding1,'}'};
if(i<dim(1))
txt(end+1:end+2)={',' nl};
end
end
if(dim(1)>1)
txt(end+1:end+3)={nl,padding2,']'};
end
if(j<dim(2))
txt(end+1:end+2)={',' nl};
end
end
if(forcearray)
txt(end+1:end+3)={nl,padding0,']'};
end
txt = sprintf('%s',txt{:});
%%-------------------------------------------------------------------------
function txt=str2json(name,item,level,varargin)
txt={};
if(~ischar(item))
error('input is not a string');
end
item=reshape(item, max(size(item),[1 0]));
len=size(item,1);
ws=struct('tab',sprintf('\t'),'newline',sprintf('\n'),'sep',sprintf(',\n'));
ws=jsonopt('whitespaces_',ws,varargin{:});
padding1=repmat(ws.tab,1,level);
padding0=repmat(ws.tab,1,level+1);
nl=ws.newline;
sep=ws.sep;
if(~isempty(name))
if(len>1)
txt={padding1, '"', checkname(name,varargin{:}),'": [', nl};
end
else
if(len>1)
txt={padding1, '[', nl};
end
end
for e=1:len
val=escapejsonstring(item(e,:));
if(len==1)
obj=['"' checkname(name,varargin{:}) '": ' '"',val,'"'];
if(isempty(name))
obj=['"',val,'"'];
end
txt(end+1:end+2)={padding1, obj};
else
txt(end+1:end+4)={padding0,'"',val,'"'};
end
if(e==len)
sep='';
end
txt{end+1}=sep;
end
if(len>1)
txt(end+1:end+3)={nl,padding1,']'};
end
txt = sprintf('%s',txt{:});
%%-------------------------------------------------------------------------
function txt=mat2json(name,item,level,varargin)
if(~isnumeric(item) && ~islogical(item))
error('input is not an array');
end
ws=struct('tab',sprintf('\t'),'newline',sprintf('\n'),'sep',sprintf(',\n'));
ws=jsonopt('whitespaces_',ws,varargin{:});
padding1=repmat(ws.tab,1,level);
padding0=repmat(ws.tab,1,level+1);
nl=ws.newline;
sep=ws.sep;
if(length(size(item))>2 || issparse(item) || ~isreal(item) || ...
(isempty(item) && any(size(item))) ||jsonopt('ArrayToStruct',0,varargin{:}))
if(isempty(name))
txt=sprintf('%s{%s%s"_ArrayType_": "%s",%s%s"_ArraySize_": %s,%s',...
padding1,nl,padding0,class(item),nl,padding0,regexprep(mat2str(size(item)),'\s+',','),nl);
else
txt=sprintf('%s"%s": {%s%s"_ArrayType_": "%s",%s%s"_ArraySize_": %s,%s',...
padding1,checkname(name,varargin{:}),nl,padding0,class(item),nl,padding0,regexprep(mat2str(size(item)),'\s+',','),nl);
end
else
if(numel(item)==1 && jsonopt('SingletArray',0,varargin{:})==0 && level>0)
numtxt=regexprep(regexprep(matdata2json(item,level+1,varargin{:}),'^\[',''),']','');
else
numtxt=matdata2json(item,level+1,varargin{:});
end
if(isempty(name))
txt=sprintf('%s%s',padding1,numtxt);
else
if(numel(item)==1 && jsonopt('SingletArray',0,varargin{:})==0)
txt=sprintf('%s"%s": %s',padding1,checkname(name,varargin{:}),numtxt);
else
txt=sprintf('%s"%s": %s',padding1,checkname(name,varargin{:}),numtxt);
end
end
return;
end
dataformat='%s%s%s%s%s';
if(issparse(item))
[ix,iy]=find(item);
data=full(item(find(item)));
if(~isreal(item))
data=[real(data(:)),imag(data(:))];
if(size(item,1)==1)
% Kludge to have data's 'transposedness' match item's.
% (Necessary for complex row vector handling below.)
data=data';
end
txt=sprintf(dataformat,txt,padding0,'"_ArrayIsComplex_": ','1', sep);
end
txt=sprintf(dataformat,txt,padding0,'"_ArrayIsSparse_": ','1', sep);
if(size(item,1)==1)
% Row vector, store only column indices.
txt=sprintf(dataformat,txt,padding0,'"_ArrayData_": ',...
matdata2json([iy(:),data'],level+2,varargin{:}), nl);
elseif(size(item,2)==1)
% Column vector, store only row indices.
txt=sprintf(dataformat,txt,padding0,'"_ArrayData_": ',...
matdata2json([ix,data],level+2,varargin{:}), nl);
else
% General case, store row and column indices.
txt=sprintf(dataformat,txt,padding0,'"_ArrayData_": ',...
matdata2json([ix,iy,data],level+2,varargin{:}), nl);
end
else
if(isreal(item))
txt=sprintf(dataformat,txt,padding0,'"_ArrayData_": ',...
matdata2json(item(:)',level+2,varargin{:}), nl);
else
txt=sprintf(dataformat,txt,padding0,'"_ArrayIsComplex_": ','1', sep);
txt=sprintf(dataformat,txt,padding0,'"_ArrayData_": ',...
matdata2json([real(item(:)) imag(item(:))],level+2,varargin{:}), nl);
end
end
txt=sprintf('%s%s%s',txt,padding1,'}');
%%-------------------------------------------------------------------------
function txt=matlabobject2json(name,item,level,varargin)
if numel(item) == 0 %empty object
st = struct();
else
% "st = struct(item);" would produce an inmutable warning, because it
% make the protected and private properties visible. Instead we get the
% visible properties
propertynames = properties(item);
for p = 1:numel(propertynames)
for o = numel(item):-1:1 % aray of objects
st(o).(propertynames{p}) = item(o).(propertynames{p});
end
end
end
txt=struct2json(name,st,level,varargin{:});
%%-------------------------------------------------------------------------
function txt=matdata2json(mat,level,varargin)
ws=struct('tab',sprintf('\t'),'newline',sprintf('\n'),'sep',sprintf(',\n'));
ws=jsonopt('whitespaces_',ws,varargin{:});
tab=ws.tab;
nl=ws.newline;
if(size(mat,1)==1)
pre='';
post='';
level=level-1;
else
pre=sprintf('[%s',nl);
post=sprintf('%s%s]',nl,repmat(tab,1,level-1));
end
if(isempty(mat))
txt='null';
return;
end
floatformat=jsonopt('FloatFormat','%.10g',varargin{:});
%if(numel(mat)>1)
formatstr=['[' repmat([floatformat ','],1,size(mat,2)-1) [floatformat sprintf('],%s',nl)]];
%else
% formatstr=[repmat([floatformat ','],1,size(mat,2)-1) [floatformat sprintf(',\n')]];
%end
if(nargin>=2 && size(mat,1)>1 && jsonopt('ArrayIndent',1,varargin{:})==1)
formatstr=[repmat(tab,1,level) formatstr];
end
txt=sprintf(formatstr,mat');
txt(end-length(nl):end)=[];
if(islogical(mat) && jsonopt('ParseLogical',0,varargin{:})==1)
txt=regexprep(txt,'1','true');
txt=regexprep(txt,'0','false');
end
%txt=regexprep(mat2str(mat),'\s+',',');
%txt=regexprep(txt,';',sprintf('],\n['));
% if(nargin>=2 && size(mat,1)>1)
% txt=regexprep(txt,'\[',[repmat(sprintf('\t'),1,level) '[']);
% end
txt=[pre txt post];
if(any(isinf(mat(:))))
txt=regexprep(txt,'([-+]*)Inf',jsonopt('Inf','"$1_Inf_"',varargin{:}));
end
if(any(isnan(mat(:))))
txt=regexprep(txt,'NaN',jsonopt('NaN','"_NaN_"',varargin{:}));
end
%%-------------------------------------------------------------------------
function newname=checkname(name,varargin)
isunpack=jsonopt('UnpackHex',1,varargin{:});
newname=name;
if(isempty(regexp(name,'0x([0-9a-fA-F]+)_','once')))
return
end
if(isunpack)
isoct=jsonopt('IsOctave',0,varargin{:});
if(~isoct)
newname=regexprep(name,'(^x|_){1}0x([0-9a-fA-F]+)_','${native2unicode(hex2dec($2))}');
else
pos=regexp(name,'(^x|_){1}0x([0-9a-fA-F]+)_','start');
pend=regexp(name,'(^x|_){1}0x([0-9a-fA-F]+)_','end');
if(isempty(pos))
return;
end
str0=name;
pos0=[0 pend(:)' length(name)];
newname='';
for i=1:length(pos)
newname=[newname str0(pos0(i)+1:pos(i)-1) char(hex2dec(str0(pos(i)+3:pend(i)-1)))];
end
if(pos(end)~=length(name))
newname=[newname str0(pos0(end-1)+1:pos0(end))];
end
end
end
%%-------------------------------------------------------------------------
function newstr=escapejsonstring(str)
newstr=str;
isoct=exist('OCTAVE_VERSION','builtin');
if(isoct)
vv=sscanf(OCTAVE_VERSION,'%f');
if(vv(1)>=3.8)
isoct=0;
end
end
if(isoct)
escapechars={'\\','\"','\/','\a','\f','\n','\r','\t','\v'};
for i=1:length(escapechars);
newstr=regexprep(newstr,escapechars{i},escapechars{i});
end
newstr=regexprep(newstr,'\\\\(u[0-9a-fA-F]{4}[^0-9a-fA-F]*)','\$1');
else
escapechars={'\\','\"','\/','\a','\b','\f','\n','\r','\t','\v'};
for i=1:length(escapechars);
newstr=regexprep(newstr,escapechars{i},regexprep(escapechars{i},'\\','\\\\'));
end
newstr=regexprep(newstr,'\\\\(u[0-9a-fA-F]{4}[^0-9a-fA-F]*)','\\$1');
end
|
github
|
amcorrigan/IA-Lab-master
|
loadjson.m
|
.m
|
IA-Lab-master/Utilities/jsonlab/loadjson.m
| 16,843 |
ibm852
|
76e78ae4dcbb1c593583aa12596c6608
|
function data = loadjson(fname,varargin)
%
% data=loadjson(fname,opt)
% or
% data=loadjson(fname,'param1',value1,'param2',value2,...)
%
% parse a JSON (JavaScript Object Notation) file or string
%
% authors:Qianqian Fang (fangq<at> nmr.mgh.harvard.edu)
% created on 2011/09/09, including previous works from
%
% Nedialko Krouchev: http://www.mathworks.com/matlabcentral/fileexchange/25713
% created on 2009/11/02
% François Glineur: http://www.mathworks.com/matlabcentral/fileexchange/23393
% created on 2009/03/22
% Joel Feenstra:
% http://www.mathworks.com/matlabcentral/fileexchange/20565
% created on 2008/07/03
%
% $Id$
%
% input:
% fname: input file name, if fname contains "{}" or "[]", fname
% will be interpreted as a JSON string
% opt: a struct to store parsing options, opt can be replaced by
% a list of ('param',value) pairs - the param string is equivallent
% to a field in opt. opt can have the following
% fields (first in [.|.] is the default)
%
% opt.SimplifyCell [0|1]: if set to 1, loadjson will call cell2mat
% for each element of the JSON data, and group
% arrays based on the cell2mat rules.
% opt.FastArrayParser [1|0 or integer]: if set to 1, use a
% speed-optimized array parser when loading an
% array object. The fast array parser may
% collapse block arrays into a single large
% array similar to rules defined in cell2mat; 0 to
% use a legacy parser; if set to a larger-than-1
% value, this option will specify the minimum
% dimension to enable the fast array parser. For
% example, if the input is a 3D array, setting
% FastArrayParser to 1 will return a 3D array;
% setting to 2 will return a cell array of 2D
% arrays; setting to 3 will return to a 2D cell
% array of 1D vectors; setting to 4 will return a
% 3D cell array.
% opt.ShowProgress [0|1]: if set to 1, loadjson displays a progress bar.
%
% output:
% dat: a cell array, where {...} blocks are converted into cell arrays,
% and [...] are converted to arrays
%
% examples:
% dat=loadjson('{"obj":{"string":"value","array":[1,2,3]}}')
% dat=loadjson(['examples' filesep 'example1.json'])
% dat=loadjson(['examples' filesep 'example1.json'],'SimplifyCell',1)
%
% license:
% BSD or GPL version 3, see LICENSE_{BSD,GPLv3}.txt files for details
%
% -- this function is part of JSONLab toolbox (http://iso2mesh.sf.net/cgi-bin/index.cgi?jsonlab)
%
global pos inStr len esc index_esc len_esc isoct arraytoken
if(regexp(fname,'^\s*(?:\[.*\])|(?:\{.*\})\s*$','once'))
string=fname;
elseif(exist(fname,'file'))
try
string = fileread(fname);
catch
try
string = urlread(['file://',fname]);
catch
string = urlread(['file://',fullfile(pwd,fname)]);
end
end
else
error('input file does not exist');
end
pos = 1; len = length(string); inStr = string;
isoct=exist('OCTAVE_VERSION','builtin');
arraytoken=find(inStr=='[' | inStr==']' | inStr=='"');
jstr=regexprep(inStr,'\\\\',' ');
escquote=regexp(jstr,'\\"');
arraytoken=sort([arraytoken escquote]);
% String delimiters and escape chars identified to improve speed:
esc = find(inStr=='"' | inStr=='\' ); % comparable to: regexp(inStr, '["\\]');
index_esc = 1; len_esc = length(esc);
opt=varargin2struct(varargin{:});
if(jsonopt('ShowProgress',0,opt)==1)
opt.progressbar_=waitbar(0,'loading ...');
end
jsoncount=1;
while pos <= len
switch(next_char)
case '{'
data{jsoncount} = parse_object(opt);
case '['
data{jsoncount} = parse_array(opt);
otherwise
error_pos('Outer level structure must be an object or an array');
end
jsoncount=jsoncount+1;
end % while
jsoncount=length(data);
if(jsoncount==1 && iscell(data))
data=data{1};
end
if(isfield(opt,'progressbar_'))
close(opt.progressbar_);
end
%%-------------------------------------------------------------------------
function object = parse_object(varargin)
parse_char('{');
object = [];
if next_char ~= '}'
while 1
str = parseStr(varargin{:});
if isempty(str)
error_pos('Name of value at position %d cannot be empty');
end
parse_char(':');
val = parse_value(varargin{:});
object.(valid_field(str))=val;
if next_char == '}'
break;
end
parse_char(',');
end
end
parse_char('}');
if(isstruct(object))
object=struct2jdata(object);
end
%%-------------------------------------------------------------------------
function object = parse_array(varargin) % JSON array is written in row-major order
global pos inStr isoct
parse_char('[');
object = cell(0, 1);
dim2=[];
arraydepth=jsonopt('JSONLAB_ArrayDepth_',1,varargin{:});
pbar=-1;
if(isfield(varargin{1},'progressbar_'))
pbar=varargin{1}.progressbar_;
end
if next_char ~= ']'
if(jsonopt('FastArrayParser',1,varargin{:})>=1 && arraydepth>=jsonopt('FastArrayParser',1,varargin{:}))
[endpos, e1l, e1r]=matching_bracket(inStr,pos);
arraystr=['[' inStr(pos:endpos)];
arraystr=regexprep(arraystr,'"_NaN_"','NaN');
arraystr=regexprep(arraystr,'"([-+]*)_Inf_"','$1Inf');
arraystr(arraystr==sprintf('\n'))=[];
arraystr(arraystr==sprintf('\r'))=[];
%arraystr=regexprep(arraystr,'\s*,',','); % this is slow,sometimes needed
if(~isempty(e1l) && ~isempty(e1r)) % the array is in 2D or higher D
astr=inStr((e1l+1):(e1r-1));
astr=regexprep(astr,'"_NaN_"','NaN');
astr=regexprep(astr,'"([-+]*)_Inf_"','$1Inf');
astr(astr==sprintf('\n'))=[];
astr(astr==sprintf('\r'))=[];
astr(astr==' ')='';
if(isempty(find(astr=='[', 1))) % array is 2D
dim2=length(sscanf(astr,'%f,',[1 inf]));
end
else % array is 1D
astr=arraystr(2:end-1);
astr(astr==' ')='';
[obj, count, errmsg, nextidx]=sscanf(astr,'%f,',[1,inf]);
if(nextidx>=length(astr)-1)
object=obj;
pos=endpos;
parse_char(']');
return;
end
end
try
if(~isempty(dim2))
astr=arraystr;
astr(astr=='[')='';
astr(astr==']')='';
astr(astr==' ')='';
[obj, count, errmsg, nextidx]=sscanf(astr,'%f,',inf);
if(nextidx>=length(astr)-1)
object=reshape(obj,dim2,numel(obj)/dim2)';
pos=endpos;
parse_char(']');
if(pbar>0)
waitbar(pos/length(inStr),pbar,'loading ...');
end
return;
end
end
arraystr=regexprep(arraystr,'\]\s*,','];');
catch
end
else
arraystr='[';
end
try
arraystr=regexprep(arraystr,'^\s*\[','{','once');
arraystr=regexprep(arraystr,'\]\s*$','}','once');
if(isoct && regexp(arraystr,'"','once'))
error('Octave eval can produce empty cells for JSON-like input');
end
object=eval(arraystr);
pos=endpos;
catch
while 1
newopt=varargin2struct(varargin{:},'JSONLAB_ArrayDepth_',arraydepth+1);
val = parse_value(newopt);
object{end+1} = val;
if next_char == ']'
break;
end
parse_char(',');
end
end
end
if(jsonopt('SimplifyCell',0,varargin{:})==1)
try
oldobj=object;
object=cell2mat(object')';
if(iscell(oldobj) && isstruct(object) && numel(object)>1 && jsonopt('SimplifyCellArray',1,varargin{:})==0)
object=oldobj;
elseif(size(object,1)>1 && ismatrix(object))
object=object';
end
catch
end
end
parse_char(']');
if(pbar>0)
waitbar(pos/length(inStr),pbar,'loading ...');
end
%%-------------------------------------------------------------------------
function parse_char(c)
global pos inStr len
pos=skip_whitespace(pos,inStr,len);
if pos > len || inStr(pos) ~= c
error_pos(sprintf('Expected %c at position %%d', c));
else
pos = pos + 1;
pos=skip_whitespace(pos,inStr,len);
end
%%-------------------------------------------------------------------------
function c = next_char
global pos inStr len
pos=skip_whitespace(pos,inStr,len);
if pos > len
c = [];
else
c = inStr(pos);
end
%%-------------------------------------------------------------------------
function newpos=skip_whitespace(pos,inStr,len)
newpos=pos;
while newpos <= len && isspace(inStr(newpos))
newpos = newpos + 1;
end
%%-------------------------------------------------------------------------
function str = parseStr(varargin)
global pos inStr len esc index_esc len_esc
% len, ns = length(inStr), keyboard
if inStr(pos) ~= '"'
error_pos('String starting with " expected at position %d');
else
pos = pos + 1;
end
str = '';
while pos <= len
while index_esc <= len_esc && esc(index_esc) < pos
index_esc = index_esc + 1;
end
if index_esc > len_esc
str = [str inStr(pos:len)];
pos = len + 1;
break;
else
str = [str inStr(pos:esc(index_esc)-1)];
pos = esc(index_esc);
end
nstr = length(str);
switch inStr(pos)
case '"'
pos = pos + 1;
if(~isempty(str))
if(strcmp(str,'_Inf_'))
str=Inf;
elseif(strcmp(str,'-_Inf_'))
str=-Inf;
elseif(strcmp(str,'_NaN_'))
str=NaN;
end
end
return;
case '\'
if pos+1 > len
error_pos('End of file reached right after escape character');
end
pos = pos + 1;
switch inStr(pos)
case {'"' '\' '/'}
str(nstr+1) = inStr(pos);
pos = pos + 1;
case {'b' 'f' 'n' 'r' 't'}
str(nstr+1) = sprintf(['\' inStr(pos)]);
pos = pos + 1;
case 'u'
if pos+4 > len
error_pos('End of file reached in escaped unicode character');
end
str(nstr+(1:6)) = inStr(pos-1:pos+4);
pos = pos + 5;
end
otherwise % should never happen
str(nstr+1) = inStr(pos);
keyboard;
pos = pos + 1;
end
end
error_pos('End of file while expecting end of inStr');
%%-------------------------------------------------------------------------
function num = parse_number(varargin)
global pos inStr isoct
currstr=inStr(pos:min(pos+30,end));
if(isoct~=0)
numstr=regexp(currstr,'^\s*-?(?:0|[1-9]\d*)(?:\.\d+)?(?:[eE][+\-]?\d+)?','end');
[num] = sscanf(currstr, '%f', 1);
delta=numstr+1;
else
[num, one, err, delta] = sscanf(currstr, '%f', 1);
if ~isempty(err)
error_pos('Error reading number at position %d');
end
end
pos = pos + delta-1;
%%-------------------------------------------------------------------------
function val = parse_value(varargin)
global pos inStr len
if(isfield(varargin{1},'progressbar_'))
waitbar(pos/len,varargin{1}.progressbar_,'loading ...');
end
switch(inStr(pos))
case '"'
val = parseStr(varargin{:});
return;
case '['
val = parse_array(varargin{:});
return;
case '{'
val = parse_object(varargin{:});
return;
case {'-','0','1','2','3','4','5','6','7','8','9'}
val = parse_number(varargin{:});
return;
case 't'
if pos+3 <= len && strcmpi(inStr(pos:pos+3), 'true')
val = true;
pos = pos + 4;
return;
end
case 'f'
if pos+4 <= len && strcmpi(inStr(pos:pos+4), 'false')
val = false;
pos = pos + 5;
return;
end
case 'n'
if pos+3 <= len && strcmpi(inStr(pos:pos+3), 'null')
val = [];
pos = pos + 4;
return;
end
end
error_pos('Value expected at position %d');
%%-------------------------------------------------------------------------
function error_pos(msg)
global pos inStr len
poShow = max(min([pos-15 pos-1 pos pos+20],len),1);
if poShow(3) == poShow(2)
poShow(3:4) = poShow(2)+[0 -1]; % display nothing after
end
msg = [sprintf(msg, pos) ': ' ...
inStr(poShow(1):poShow(2)) '<error>' inStr(poShow(3):poShow(4)) ];
error( ['JSONparser:invalidFormat: ' msg] );
%%-------------------------------------------------------------------------
function str = valid_field(str)
global isoct
% From MATLAB doc: field names must begin with a letter, which may be
% followed by any combination of letters, digits, and underscores.
% Invalid characters will be converted to underscores, and the prefix
% "x0x[Hex code]_" will be added if the first character is not a letter.
pos=regexp(str,'^[^A-Za-z]','once');
if(~isempty(pos))
if(~isoct)
str=regexprep(str,'^([^A-Za-z])','x0x${sprintf(''%X'',unicode2native($1))}_','once');
else
str=sprintf('x0x%X_%s',char(str(1)),str(2:end));
end
end
if(isempty(regexp(str,'[^0-9A-Za-z_]', 'once' )))
return;
end
if(~isoct)
str=regexprep(str,'([^0-9A-Za-z_])','_0x${sprintf(''%X'',unicode2native($1))}_');
else
pos=regexp(str,'[^0-9A-Za-z_]');
if(isempty(pos))
return;
end
str0=str;
pos0=[0 pos(:)' length(str)];
str='';
for i=1:length(pos)
str=[str str0(pos0(i)+1:pos(i)-1) sprintf('_0x%X_',str0(pos(i)))];
end
if(pos(end)~=length(str))
str=[str str0(pos0(end-1)+1:pos0(end))];
end
end
%str(~isletter(str) & ~('0' <= str & str <= '9')) = '_';
%%-------------------------------------------------------------------------
function endpos = matching_quote(str,pos)
len=length(str);
while(pos<len)
if(str(pos)=='"')
if(~(pos>1 && str(pos-1)=='\'))
endpos=pos;
return;
end
end
pos=pos+1;
end
error('unmatched quotation mark');
%%-------------------------------------------------------------------------
function [endpos, e1l, e1r, maxlevel] = matching_bracket(str,pos)
global arraytoken
level=1;
maxlevel=level;
endpos=0;
bpos=arraytoken(arraytoken>=pos);
tokens=str(bpos);
len=length(tokens);
pos=1;
e1l=[];
e1r=[];
while(pos<=len)
c=tokens(pos);
if(c==']')
level=level-1;
if(isempty(e1r))
e1r=bpos(pos);
end
if(level==0)
endpos=bpos(pos);
return
end
end
if(c=='[')
if(isempty(e1l))
e1l=bpos(pos);
end
level=level+1;
maxlevel=max(maxlevel,level);
end
if(c=='"')
pos=matching_quote(tokens,pos+1);
end
pos=pos+1;
end
if(endpos==0)
error('unmatched "]"');
end
|
github
|
amcorrigan/IA-Lab-master
|
loadubjson.m
|
.m
|
IA-Lab-master/Utilities/jsonlab/loadubjson.m
| 13,774 |
utf_8
|
cf1ef9319b0f46d709ea706a0048f15d
|
function data = loadubjson(fname,varargin)
%
% data=loadubjson(fname,opt)
% or
% data=loadubjson(fname,'param1',value1,'param2',value2,...)
%
% parse a JSON (JavaScript Object Notation) file or string
%
% authors:Qianqian Fang (fangq<at> nmr.mgh.harvard.edu)
% created on 2013/08/01
%
% $Id$
%
% input:
% fname: input file name, if fname contains "{}" or "[]", fname
% will be interpreted as a UBJSON string
% opt: a struct to store parsing options, opt can be replaced by
% a list of ('param',value) pairs - the param string is equivallent
% to a field in opt. opt can have the following
% fields (first in [.|.] is the default)
%
% opt.SimplifyCell [0|1]: if set to 1, loadubjson will call cell2mat
% for each element of the JSON data, and group
% arrays based on the cell2mat rules.
% opt.IntEndian [B|L]: specify the endianness of the integer fields
% in the UBJSON input data. B - Big-Endian format for
% integers (as required in the UBJSON specification);
% L - input integer fields are in Little-Endian order.
% opt.NameIsString [0|1]: for UBJSON Specification Draft 8 or
% earlier versions (JSONLab 1.0 final or earlier),
% the "name" tag is treated as a string. To load
% these UBJSON data, you need to manually set this
% flag to 1.
%
% output:
% dat: a cell array, where {...} blocks are converted into cell arrays,
% and [...] are converted to arrays
%
% examples:
% obj=struct('string','value','array',[1 2 3]);
% ubjdata=saveubjson('obj',obj);
% dat=loadubjson(ubjdata)
% dat=loadubjson(['examples' filesep 'example1.ubj'])
% dat=loadubjson(['examples' filesep 'example1.ubj'],'SimplifyCell',1)
%
% license:
% BSD or GPL version 3, see LICENSE_{BSD,GPLv3}.txt files for details
%
% -- this function is part of JSONLab toolbox (http://iso2mesh.sf.net/cgi-bin/index.cgi?jsonlab)
%
global pos inStr len esc index_esc len_esc isoct arraytoken fileendian systemendian
if(regexp(fname,'[\{\}\]\[]','once'))
string=fname;
elseif(exist(fname,'file'))
fid = fopen(fname,'rb');
string = fread(fid,inf,'uint8=>char')';
fclose(fid);
else
error('input file does not exist');
end
pos = 1; len = length(string); inStr = string;
isoct=exist('OCTAVE_VERSION','builtin');
arraytoken=find(inStr=='[' | inStr==']' | inStr=='"');
jstr=regexprep(inStr,'\\\\',' ');
escquote=regexp(jstr,'\\"');
arraytoken=sort([arraytoken escquote]);
% String delimiters and escape chars identified to improve speed:
esc = find(inStr=='"' | inStr=='\' ); % comparable to: regexp(inStr, '["\\]');
index_esc = 1; len_esc = length(esc);
opt=varargin2struct(varargin{:});
fileendian=upper(jsonopt('IntEndian','B',opt));
[os,maxelem,systemendian]=computer;
jsoncount=1;
while pos <= len
switch(next_char)
case '{'
data{jsoncount} = parse_object(opt);
case '['
data{jsoncount} = parse_array(opt);
otherwise
error_pos('Outer level structure must be an object or an array');
end
jsoncount=jsoncount+1;
end % while
jsoncount=length(data);
if(jsoncount==1 && iscell(data))
data=data{1};
end
%%-------------------------------------------------------------------------
function object = parse_object(varargin)
parse_char('{');
object = [];
type='';
count=-1;
if(next_char == '$')
type=inStr(pos+1); % TODO
pos=pos+2;
end
if(next_char == '#')
pos=pos+1;
count=double(parse_number());
end
if next_char ~= '}'
num=0;
while 1
if(jsonopt('NameIsString',0,varargin{:}))
str = parseStr(varargin{:});
else
str = parse_name(varargin{:});
end
if isempty(str)
error_pos('Name of value at position %d cannot be empty');
end
%parse_char(':');
val = parse_value(varargin{:});
num=num+1;
object.(valid_field(str))=val;
if next_char == '}' || (count>=0 && num>=count)
break;
end
%parse_char(',');
end
end
if(count==-1)
parse_char('}');
end
if(isstruct(object))
object=struct2jdata(object);
end
%%-------------------------------------------------------------------------
function [cid,len]=elem_info(type)
id=strfind('iUIlLdD',type);
dataclass={'int8','uint8','int16','int32','int64','single','double'};
bytelen=[1,1,2,4,8,4,8];
if(id>0)
cid=dataclass{id};
len=bytelen(id);
else
error_pos('unsupported type at position %d');
end
%%-------------------------------------------------------------------------
function [data, adv]=parse_block(type,count,varargin)
global pos inStr isoct fileendian systemendian
[cid,len]=elem_info(type);
datastr=inStr(pos:pos+len*count-1);
if(isoct)
newdata=int8(datastr);
else
newdata=uint8(datastr);
end
id=strfind('iUIlLdD',type);
if(id<=5 && fileendian~=systemendian)
newdata=swapbytes(typecast(newdata,cid));
end
data=typecast(newdata,cid);
adv=double(len*count);
%%-------------------------------------------------------------------------
function object = parse_array(varargin) % JSON array is written in row-major order
global pos inStr
parse_char('[');
object = cell(0, 1);
dim=[];
type='';
count=-1;
if(next_char == '$')
type=inStr(pos+1);
pos=pos+2;
end
if(next_char == '#')
pos=pos+1;
if(next_char=='[')
dim=parse_array(varargin{:});
count=prod(double(dim));
else
count=double(parse_number());
end
end
if(~isempty(type))
if(count>=0)
[object, adv]=parse_block(type,count,varargin{:});
if(~isempty(dim))
object=reshape(object,dim);
end
pos=pos+adv;
return;
else
endpos=matching_bracket(inStr,pos);
[cid,len]=elem_info(type);
count=(endpos-pos)/len;
[object, adv]=parse_block(type,count,varargin{:});
pos=pos+adv;
parse_char(']');
return;
end
end
if next_char ~= ']'
while 1
val = parse_value(varargin{:});
object{end+1} = val;
if next_char == ']'
break;
end
%parse_char(',');
end
end
if(jsonopt('SimplifyCell',0,varargin{:})==1)
try
oldobj=object;
object=cell2mat(object')';
if(iscell(oldobj) && isstruct(object) && numel(object)>1 && jsonopt('SimplifyCellArray',1,varargin{:})==0)
object=oldobj;
elseif(size(object,1)>1 && ismatrix(object))
object=object';
end
catch
end
end
if(count==-1)
parse_char(']');
end
%%-------------------------------------------------------------------------
function parse_char(c)
global pos inStr len
skip_whitespace;
if pos > len || inStr(pos) ~= c
error_pos(sprintf('Expected %c at position %%d', c));
else
pos = pos + 1;
skip_whitespace;
end
%%-------------------------------------------------------------------------
function c = next_char
global pos inStr len
skip_whitespace;
if pos > len
c = [];
else
c = inStr(pos);
end
%%-------------------------------------------------------------------------
function skip_whitespace
global pos inStr len
while pos <= len && isspace(inStr(pos))
pos = pos + 1;
end
%%-------------------------------------------------------------------------
function str = parse_name(varargin)
global pos inStr
bytelen=double(parse_number());
if(length(inStr)>=pos+bytelen-1)
str=inStr(pos:pos+bytelen-1);
pos=pos+bytelen;
else
error_pos('End of file while expecting end of name');
end
%%-------------------------------------------------------------------------
function str = parseStr(varargin)
global pos inStr
% len, ns = length(inStr), keyboard
type=inStr(pos);
if type ~= 'S' && type ~= 'C' && type ~= 'H'
error_pos('String starting with S expected at position %d');
else
pos = pos + 1;
end
if(type == 'C')
str=inStr(pos);
pos=pos+1;
return;
end
bytelen=double(parse_number());
if(length(inStr)>=pos+bytelen-1)
str=inStr(pos:pos+bytelen-1);
pos=pos+bytelen;
else
error_pos('End of file while expecting end of inStr');
end
%%-------------------------------------------------------------------------
function num = parse_number(varargin)
global pos inStr isoct fileendian systemendian
id=strfind('iUIlLdD',inStr(pos));
if(isempty(id))
error_pos('expecting a number at position %d');
end
type={'int8','uint8','int16','int32','int64','single','double'};
bytelen=[1,1,2,4,8,4,8];
datastr=inStr(pos+1:pos+bytelen(id));
if(isoct)
newdata=int8(datastr);
else
newdata=uint8(datastr);
end
if(id<=5 && fileendian~=systemendian)
newdata=swapbytes(typecast(newdata,type{id}));
end
num=typecast(newdata,type{id});
pos = pos + bytelen(id)+1;
%%-------------------------------------------------------------------------
function val = parse_value(varargin)
global pos inStr
switch(inStr(pos))
case {'S','C','H'}
val = parseStr(varargin{:});
return;
case '['
val = parse_array(varargin{:});
return;
case '{'
val = parse_object(varargin{:});
return;
case {'i','U','I','l','L','d','D'}
val = parse_number(varargin{:});
return;
case 'T'
val = true;
pos = pos + 1;
return;
case 'F'
val = false;
pos = pos + 1;
return;
case {'Z','N'}
val = [];
pos = pos + 1;
return;
end
error_pos('Value expected at position %d');
%%-------------------------------------------------------------------------
function error_pos(msg)
global pos inStr len
poShow = max(min([pos-15 pos-1 pos pos+20],len),1);
if poShow(3) == poShow(2)
poShow(3:4) = poShow(2)+[0 -1]; % display nothing after
end
msg = [sprintf(msg, pos) ': ' ...
inStr(poShow(1):poShow(2)) '<error>' inStr(poShow(3):poShow(4)) ];
error( ['JSONparser:invalidFormat: ' msg] );
%%-------------------------------------------------------------------------
function str = valid_field(str)
global isoct
% From MATLAB doc: field names must begin with a letter, which may be
% followed by any combination of letters, digits, and underscores.
% Invalid characters will be converted to underscores, and the prefix
% "x0x[Hex code]_" will be added if the first character is not a letter.
pos=regexp(str,'^[^A-Za-z]','once');
if(~isempty(pos))
if(~isoct)
str=regexprep(str,'^([^A-Za-z])','x0x${sprintf(''%X'',unicode2native($1))}_','once');
else
str=sprintf('x0x%X_%s',char(str(1)),str(2:end));
end
end
if(isempty(regexp(str,'[^0-9A-Za-z_]', 'once' )))
return;
end
if(~isoct)
str=regexprep(str,'([^0-9A-Za-z_])','_0x${sprintf(''%X'',unicode2native($1))}_');
else
pos=regexp(str,'[^0-9A-Za-z_]');
if(isempty(pos))
return;
end
str0=str;
pos0=[0 pos(:)' length(str)];
str='';
for i=1:length(pos)
str=[str str0(pos0(i)+1:pos(i)-1) sprintf('_0x%X_',str0(pos(i)))];
end
if(pos(end)~=length(str))
str=[str str0(pos0(end-1)+1:pos0(end))];
end
end
%str(~isletter(str) & ~('0' <= str & str <= '9')) = '_';
%%-------------------------------------------------------------------------
function endpos = matching_quote(str,pos)
len=length(str);
while(pos<len)
if(str(pos)=='"')
if(~(pos>1 && str(pos-1)=='\'))
endpos=pos;
return;
end
end
pos=pos+1;
end
error('unmatched quotation mark');
%%-------------------------------------------------------------------------
function [endpos, e1l, e1r, maxlevel] = matching_bracket(str,pos)
global arraytoken
level=1;
maxlevel=level;
endpos=0;
bpos=arraytoken(arraytoken>=pos);
tokens=str(bpos);
len=length(tokens);
pos=1;
e1l=[];
e1r=[];
while(pos<=len)
c=tokens(pos);
if(c==']')
level=level-1;
if(isempty(e1r))
e1r=bpos(pos);
end
if(level==0)
endpos=bpos(pos);
return
end
end
if(c=='[')
if(isempty(e1l))
e1l=bpos(pos);
end
level=level+1;
maxlevel=max(maxlevel,level);
end
if(c=='"')
pos=matching_quote(tokens,pos+1);
end
pos=pos+1;
end
if(endpos==0)
error('unmatched "]"');
end
|
github
|
amcorrigan/IA-Lab-master
|
saveubjson.m
|
.m
|
IA-Lab-master/Utilities/jsonlab/saveubjson.m
| 18,302 |
utf_8
|
71eb65f95dee01aa2bf33ff80a5bf80d
|
function json=saveubjson(rootname,obj,varargin)
%
% json=saveubjson(rootname,obj,filename)
% or
% json=saveubjson(rootname,obj,opt)
% json=saveubjson(rootname,obj,'param1',value1,'param2',value2,...)
%
% convert a MATLAB object (cell, struct or array) into a Universal
% Binary JSON (UBJSON) binary string
%
% author: Qianqian Fang (fangq<at> nmr.mgh.harvard.edu)
% created on 2013/08/17
%
% $Id$
%
% input:
% rootname: the name of the root-object, when set to '', the root name
% is ignored, however, when opt.ForceRootName is set to 1 (see below),
% the MATLAB variable name will be used as the root name.
% obj: a MATLAB object (array, cell, cell array, struct, struct array,
% class instance)
% filename: a string for the file name to save the output UBJSON data
% opt: a struct for additional options, ignore to use default values.
% opt can have the following fields (first in [.|.] is the default)
%
% opt.FileName [''|string]: a file name to save the output JSON data
% opt.ArrayToStruct[0|1]: when set to 0, saveubjson outputs 1D/2D
% array in JSON array format; if sets to 1, an
% array will be shown as a struct with fields
% "_ArrayType_", "_ArraySize_" and "_ArrayData_"; for
% sparse arrays, the non-zero elements will be
% saved to _ArrayData_ field in triplet-format i.e.
% (ix,iy,val) and "_ArrayIsSparse_" will be added
% with a value of 1; for a complex array, the
% _ArrayData_ array will include two columns
% (4 for sparse) to record the real and imaginary
% parts, and also "_ArrayIsComplex_":1 is added.
% opt.ParseLogical [1|0]: if this is set to 1, logical array elem
% will use true/false rather than 1/0.
% opt.SingletArray [0|1]: if this is set to 1, arrays with a single
% numerical element will be shown without a square
% bracket, unless it is the root object; if 0, square
% brackets are forced for any numerical arrays.
% opt.SingletCell [1|0]: if 1, always enclose a cell with "[]"
% even it has only one element; if 0, brackets
% are ignored when a cell has only 1 element.
% opt.ForceRootName [0|1]: when set to 1 and rootname is empty, saveubjson
% will use the name of the passed obj variable as the
% root object name; if obj is an expression and
% does not have a name, 'root' will be used; if this
% is set to 0 and rootname is empty, the root level
% will be merged down to the lower level.
% opt.JSONP [''|string]: to generate a JSONP output (JSON with padding),
% for example, if opt.JSON='foo', the JSON data is
% wrapped inside a function call as 'foo(...);'
% opt.UnpackHex [1|0]: conver the 0x[hex code] output by loadjson
% back to the string form
%
% opt can be replaced by a list of ('param',value) pairs. The param
% string is equivallent to a field in opt and is case sensitive.
% output:
% json: a binary string in the UBJSON format (see http://ubjson.org)
%
% examples:
% jsonmesh=struct('MeshNode',[0 0 0;1 0 0;0 1 0;1 1 0;0 0 1;1 0 1;0 1 1;1 1 1],...
% 'MeshTetra',[1 2 4 8;1 3 4 8;1 2 6 8;1 5 6 8;1 5 7 8;1 3 7 8],...
% 'MeshTri',[1 2 4;1 2 6;1 3 4;1 3 7;1 5 6;1 5 7;...
% 2 8 4;2 8 6;3 8 4;3 8 7;5 8 6;5 8 7],...
% 'MeshCreator','FangQ','MeshTitle','T6 Cube',...
% 'SpecialData',[nan, inf, -inf]);
% saveubjson('jsonmesh',jsonmesh)
% saveubjson('jsonmesh',jsonmesh,'meshdata.ubj')
%
% license:
% BSD or GPL version 3, see LICENSE_{BSD,GPLv3}.txt files for details
%
% -- this function is part of JSONLab toolbox (http://iso2mesh.sf.net/cgi-bin/index.cgi?jsonlab)
%
if(nargin==1)
varname=inputname(1);
obj=rootname;
if(isempty(varname))
varname='root';
end
rootname=varname;
else
varname=inputname(2);
end
if(length(varargin)==1 && ischar(varargin{1}))
opt=struct('filename',varargin{1});
else
opt=varargin2struct(varargin{:});
end
opt.IsOctave=exist('OCTAVE_VERSION','builtin');
if(isfield(opt,'norowbracket'))
warning('Option ''NoRowBracket'' is depreciated, please use ''SingletArray'' and set its value to not(NoRowBracket)');
if(~isfield(opt,'singletarray'))
opt.singletarray=not(opt.norowbracket);
end
end
rootisarray=0;
rootlevel=1;
forceroot=jsonopt('ForceRootName',0,opt);
if((isnumeric(obj) || islogical(obj) || ischar(obj) || isstruct(obj) || ...
iscell(obj) || isobject(obj)) && isempty(rootname) && forceroot==0)
rootisarray=1;
rootlevel=0;
else
if(isempty(rootname))
rootname=varname;
end
end
if((isstruct(obj) || iscell(obj))&& isempty(rootname) && forceroot)
rootname='root';
end
json=obj2ubjson(rootname,obj,rootlevel,opt);
if(~rootisarray)
json=['{' json '}'];
end
jsonp=jsonopt('JSONP','',opt);
if(~isempty(jsonp))
json=[jsonp '(' json ')'];
end
% save to a file if FileName is set, suggested by Patrick Rapin
filename=jsonopt('FileName','',opt);
if(~isempty(filename))
fid = fopen(filename, 'wb');
fwrite(fid,json);
fclose(fid);
end
%%-------------------------------------------------------------------------
function txt=obj2ubjson(name,item,level,varargin)
if(iscell(item))
txt=cell2ubjson(name,item,level,varargin{:});
elseif(isstruct(item))
txt=struct2ubjson(name,item,level,varargin{:});
elseif(ischar(item))
txt=str2ubjson(name,item,level,varargin{:});
elseif(isobject(item))
txt=matlabobject2ubjson(name,item,level,varargin{:});
else
txt=mat2ubjson(name,item,level,varargin{:});
end
%%-------------------------------------------------------------------------
function txt=cell2ubjson(name,item,level,varargin)
txt='';
if(~iscell(item))
error('input is not a cell');
end
dim=size(item);
if(ndims(squeeze(item))>2) % for 3D or higher dimensions, flatten to 2D for now
item=reshape(item,dim(1),numel(item)/dim(1));
dim=size(item);
end
bracketlevel=~jsonopt('singletcell',1,varargin{:});
len=numel(item); % let's handle 1D cell first
if(len>bracketlevel)
if(~isempty(name))
txt=[N_(checkname(name,varargin{:})) '[']; name='';
else
txt='[';
end
elseif(len==0)
if(~isempty(name))
txt=[N_(checkname(name,varargin{:})) 'Z']; name='';
else
txt='Z';
end
end
for j=1:dim(2)
if(dim(1)>1)
txt=[txt '['];
end
for i=1:dim(1)
txt=[txt obj2ubjson(name,item{i,j},level+(len>bracketlevel),varargin{:})];
end
if(dim(1)>1)
txt=[txt ']'];
end
end
if(len>bracketlevel)
txt=[txt ']'];
end
%%-------------------------------------------------------------------------
function txt=struct2ubjson(name,item,level,varargin)
txt='';
if(~isstruct(item))
error('input is not a struct');
end
dim=size(item);
if(ndims(squeeze(item))>2) % for 3D or higher dimensions, flatten to 2D for now
item=reshape(item,dim(1),numel(item)/dim(1));
dim=size(item);
end
len=numel(item);
forcearray= (len>1 || (jsonopt('SingletArray',0,varargin{:})==1 && level>0));
if(~isempty(name))
if(forcearray)
txt=[N_(checkname(name,varargin{:})) '['];
end
else
if(forcearray)
txt='[';
end
end
for j=1:dim(2)
if(dim(1)>1)
txt=[txt '['];
end
for i=1:dim(1)
names = fieldnames(item(i,j));
if(~isempty(name) && len==1 && ~forcearray)
txt=[txt N_(checkname(name,varargin{:})) '{'];
else
txt=[txt '{'];
end
if(~isempty(names))
for e=1:length(names)
txt=[txt obj2ubjson(names{e},item(i,j).(names{e}),...
level+(dim(1)>1)+1+forcearray,varargin{:})];
end
end
txt=[txt '}'];
end
if(dim(1)>1)
txt=[txt ']'];
end
end
if(forcearray)
txt=[txt ']'];
end
%%-------------------------------------------------------------------------
function txt=str2ubjson(name,item,level,varargin)
txt='';
if(~ischar(item))
error('input is not a string');
end
item=reshape(item, max(size(item),[1 0]));
len=size(item,1);
if(~isempty(name))
if(len>1)
txt=[N_(checkname(name,varargin{:})) '['];
end
else
if(len>1)
txt='[';
end
end
for e=1:len
val=item(e,:);
if(len==1)
obj=[N_(checkname(name,varargin{:})) '' '',S_(val),''];
if(isempty(name))
obj=['',S_(val),''];
end
txt=[txt,'',obj];
else
txt=[txt,'',['',S_(val),'']];
end
end
if(len>1)
txt=[txt ']'];
end
%%-------------------------------------------------------------------------
function txt=mat2ubjson(name,item,level,varargin)
if(~isnumeric(item) && ~islogical(item))
error('input is not an array');
end
if(length(size(item))>2 || issparse(item) || ~isreal(item) || ...
(isempty(item) && any(size(item))) ||jsonopt('ArrayToStruct',0,varargin{:}))
cid=I_(uint32(max(size(item))));
if(isempty(name))
txt=['{' N_('_ArrayType_'),S_(class(item)),N_('_ArraySize_'),I_a(size(item),cid(1)) ];
else
if(isempty(item))
txt=[N_(checkname(name,varargin{:})),'Z'];
return;
else
txt=[N_(checkname(name,varargin{:})),'{',N_('_ArrayType_'),S_(class(item)),N_('_ArraySize_'),I_a(size(item),cid(1))];
end
end
else
if(isempty(name))
txt=matdata2ubjson(item,level+1,varargin{:});
else
if(numel(item)==1 && jsonopt('SingletArray',0,varargin{:})==0)
numtxt=regexprep(regexprep(matdata2ubjson(item,level+1,varargin{:}),'^\[',''),']','');
txt=[N_(checkname(name,varargin{:})) numtxt];
else
txt=[N_(checkname(name,varargin{:})),matdata2ubjson(item,level+1,varargin{:})];
end
end
return;
end
if(issparse(item))
[ix,iy]=find(item);
data=full(item(find(item)));
if(~isreal(item))
data=[real(data(:)),imag(data(:))];
if(size(item,1)==1)
% Kludge to have data's 'transposedness' match item's.
% (Necessary for complex row vector handling below.)
data=data';
end
txt=[txt,N_('_ArrayIsComplex_'),'T'];
end
txt=[txt,N_('_ArrayIsSparse_'),'T'];
if(size(item,1)==1)
% Row vector, store only column indices.
txt=[txt,N_('_ArrayData_'),...
matdata2ubjson([iy(:),data'],level+2,varargin{:})];
elseif(size(item,2)==1)
% Column vector, store only row indices.
txt=[txt,N_('_ArrayData_'),...
matdata2ubjson([ix,data],level+2,varargin{:})];
else
% General case, store row and column indices.
txt=[txt,N_('_ArrayData_'),...
matdata2ubjson([ix,iy,data],level+2,varargin{:})];
end
else
if(isreal(item))
txt=[txt,N_('_ArrayData_'),...
matdata2ubjson(item(:)',level+2,varargin{:})];
else
txt=[txt,N_('_ArrayIsComplex_'),'T'];
txt=[txt,N_('_ArrayData_'),...
matdata2ubjson([real(item(:)) imag(item(:))],level+2,varargin{:})];
end
end
txt=[txt,'}'];
%%-------------------------------------------------------------------------
function txt=matlabobject2ubjson(name,item,level,varargin)
if numel(item) == 0 %empty object
st = struct();
else
% "st = struct(item);" would produce an inmutable warning, because it
% make the protected and private properties visible. Instead we get the
% visible properties
propertynames = properties(item);
for p = 1:numel(propertynames)
for o = numel(item):-1:1 % aray of objects
st(o).(propertynames{p}) = item(o).(propertynames{p});
end
end
end
txt=struct2ubjson(name,st,level,varargin{:});
%%-------------------------------------------------------------------------
function txt=matdata2ubjson(mat,level,varargin)
if(isempty(mat))
txt='Z';
return;
end
type='';
hasnegtive=(mat<0);
if(isa(mat,'integer') || isinteger(mat) || (isfloat(mat) && all(mod(mat(:),1) == 0)))
if(isempty(hasnegtive))
if(max(mat(:))<=2^8)
type='U';
end
end
if(isempty(type))
% todo - need to consider negative ones separately
id= histc(abs(max(mat(:))),[0 2^7 2^15 2^31 2^63]);
if(isempty(id~=0))
error('high-precision data is not yet supported');
end
key='iIlL';
type=key(id~=0);
end
txt=[I_a(mat(:),type,size(mat))];
elseif(islogical(mat))
logicalval='FT';
if(numel(mat)==1)
txt=logicalval(mat+1);
else
txt=['[$U#' I_a(size(mat),'l') typecast(swapbytes(uint8(mat(:)')),'uint8')];
end
else
if(numel(mat)==1)
txt=['[' D_(mat) ']'];
else
txt=D_a(mat(:),'D',size(mat));
end
end
%txt=regexprep(mat2str(mat),'\s+',',');
%txt=regexprep(txt,';',sprintf('],['));
% if(nargin>=2 && size(mat,1)>1)
% txt=regexprep(txt,'\[',[repmat(sprintf('\t'),1,level) '[']);
% end
if(any(isinf(mat(:))))
txt=regexprep(txt,'([-+]*)Inf',jsonopt('Inf','"$1_Inf_"',varargin{:}));
end
if(any(isnan(mat(:))))
txt=regexprep(txt,'NaN',jsonopt('NaN','"_NaN_"',varargin{:}));
end
%%-------------------------------------------------------------------------
function newname=checkname(name,varargin)
isunpack=jsonopt('UnpackHex',1,varargin{:});
newname=name;
if(isempty(regexp(name,'0x([0-9a-fA-F]+)_','once')))
return
end
if(isunpack)
isoct=jsonopt('IsOctave',0,varargin{:});
if(~isoct)
newname=regexprep(name,'(^x|_){1}0x([0-9a-fA-F]+)_','${native2unicode(hex2dec($2))}');
else
pos=regexp(name,'(^x|_){1}0x([0-9a-fA-F]+)_','start');
pend=regexp(name,'(^x|_){1}0x([0-9a-fA-F]+)_','end');
if(isempty(pos))
return;
end
str0=name;
pos0=[0 pend(:)' length(name)];
newname='';
for i=1:length(pos)
newname=[newname str0(pos0(i)+1:pos(i)-1) char(hex2dec(str0(pos(i)+3:pend(i)-1)))];
end
if(pos(end)~=length(name))
newname=[newname str0(pos0(end-1)+1:pos0(end))];
end
end
end
%%-------------------------------------------------------------------------
function val=N_(str)
val=[I_(int32(length(str))) str];
%%-------------------------------------------------------------------------
function val=S_(str)
if(length(str)==1)
val=['C' str];
else
val=['S' I_(int32(length(str))) str];
end
%%-------------------------------------------------------------------------
function val=I_(num)
if(~isinteger(num))
error('input is not an integer');
end
if(num>=0 && num<255)
val=['U' data2byte(swapbytes(cast(num,'uint8')),'uint8')];
return;
end
key='iIlL';
cid={'int8','int16','int32','int64'};
for i=1:4
if((num>0 && num<2^(i*8-1)) || (num<0 && num>=-2^(i*8-1)))
val=[key(i) data2byte(swapbytes(cast(num,cid{i})),'uint8')];
return;
end
end
error('unsupported integer');
%%-------------------------------------------------------------------------
function val=D_(num)
if(~isfloat(num))
error('input is not a float');
end
if(isa(num,'single'))
val=['d' data2byte(num,'uint8')];
else
val=['D' data2byte(num,'uint8')];
end
%%-------------------------------------------------------------------------
function data=I_a(num,type,dim,format)
id=find(ismember('iUIlL',type));
if(id==0)
error('unsupported integer array');
end
% based on UBJSON specs, all integer types are stored in big endian format
if(id==1)
data=data2byte(swapbytes(int8(num)),'uint8');
blen=1;
elseif(id==2)
data=data2byte(swapbytes(uint8(num)),'uint8');
blen=1;
elseif(id==3)
data=data2byte(swapbytes(int16(num)),'uint8');
blen=2;
elseif(id==4)
data=data2byte(swapbytes(int32(num)),'uint8');
blen=4;
elseif(id==5)
data=data2byte(swapbytes(int64(num)),'uint8');
blen=8;
end
if(nargin>=3 && length(dim)>=2 && prod(dim)~=dim(2))
format='opt';
end
if((nargin<4 || strcmp(format,'opt')) && numel(num)>1)
if(nargin>=3 && (length(dim)==1 || (length(dim)>=2 && prod(dim)~=dim(2))))
cid=I_(uint32(max(dim)));
data=['$' type '#' I_a(dim,cid(1)) data(:)'];
else
data=['$' type '#' I_(int32(numel(data)/blen)) data(:)'];
end
data=['[' data(:)'];
else
data=reshape(data,blen,numel(data)/blen);
data(2:blen+1,:)=data;
data(1,:)=type;
data=data(:)';
data=['[' data(:)' ']'];
end
%%-------------------------------------------------------------------------
function data=D_a(num,type,dim,format)
id=find(ismember('dD',type));
if(id==0)
error('unsupported float array');
end
if(id==1)
data=data2byte(single(num),'uint8');
elseif(id==2)
data=data2byte(double(num),'uint8');
end
if(nargin>=3 && length(dim)>=2 && prod(dim)~=dim(2))
format='opt';
end
if((nargin<4 || strcmp(format,'opt')) && numel(num)>1)
if(nargin>=3 && (length(dim)==1 || (length(dim)>=2 && prod(dim)~=dim(2))))
cid=I_(uint32(max(dim)));
data=['$' type '#' I_a(dim,cid(1)) data(:)'];
else
data=['$' type '#' I_(int32(numel(data)/(id*4))) data(:)'];
end
data=['[' data];
else
data=reshape(data,(id*4),length(data)/(id*4));
data(2:(id*4+1),:)=data;
data(1,:)=type;
data=data(:)';
data=['[' data(:)' ']'];
end
%%-------------------------------------------------------------------------
function bytes=data2byte(varargin)
bytes=typecast(varargin{:});
bytes=bytes(:)';
|
github
|
amcorrigan/IA-Lab-master
|
AddTextToImageWithBorder.m
|
.m
|
IA-Lab-master/Utilities/textimage/AddTextToImageWithBorder.m
| 2,034 |
utf_8
|
98e36284eff76a81ec7ab9b7a1986c24
|
function Image = AddTextToImageWithBorder(Image,String,Position,Color,Font,FontSize,BorderWidth,BorderColor)
% Image = AddTextToImage(Image,String,Position,Color,Font,FontSize,BorderWidth,BorderColor)
%
% Works as AddTextToImage, except also allows for a border of thickness
% BorderWidth pixels and color given by BorderColor. BorderColor should
% be a 1- or 3-element vector giving Y or RGB in the range 0 to 1
% regardless of the image class.
%
% If no border parameters are provided, default is 1 pixel black.
%
% Daniel Warren
% Particle Therapy Cancer Research Institute
% University of Oxford
if ~exist('BorderWidth','var')
BorderWidth = 1;
end
if ~exist('BorderColor','var')
BorderColor = 0;
end
if BorderWidth == 0
Image = AddTextToImage(Image,String,Position,Color,Font,FontSize);
return;
end
% uint8 images go from 0 to 255, whereas double ones go from 0 to 1
if isa(Image, 'uint8')
ScaleFactor = 255;
else
ScaleFactor = 1;
end
% monochrome images need monochrome text, colour images need colour text
if ndims(Image) == 2 %#ok<ISMAT>
BorderColor = mean(BorderColor(:));
end
if ndims(Image) == 3 && numel(BorderColor) == 1
BorderColor = [BorderColor BorderColor BorderColor];
end
Mask = AddTextToImage(false(size(Image(:,:,1))),String,Position,1,Font,FontSize);
ConvElement = double(CircleMask(1+2*BorderWidth,1+2*BorderWidth,BorderWidth+0.5,BorderWidth+0.5,0.5+BorderWidth));
Outline = xor(conv2(double(Mask),ConvElement,'same'),Mask);
Image = AddTextToImage(Image,String,Position,Color,Font,FontSize);
for i = 1:size(Image,3)
tmp = Image(:,:,i);
tmp(Outline) = ScaleFactor*BorderColor(i);
Image(:,:,i) = tmp;
end
end
function out = CircleMask(w,h,cx,cy,r)
% function out = CircleMask(w,h,cx,cy,r)
% Outputs a 1D bitmap of a solid circle of radius r pixels
% centered at pixel (cx,cy) within an matrix of size w x h
% pixels.
[x y] = meshgrid(1:w,1:h);
out = ((x-cx-0.5).^2+(y-cy-0.5).^2) <= r^2;
end
|
github
|
amcorrigan/IA-Lab-master
|
real2rgb.m
|
.m
|
IA-Lab-master/Utilities/sc/real2rgb.m
| 4,918 |
utf_8
|
e3d94e10c8a2aca6dfbb6e867ed707bc
|
function [B lims map] = real2rgb(A, cmap, lims)
%REAL2RGB Converts a real-valued matrix into a truecolor image
%
% Examples:
% B = real2rgb(A, cmap);
% B = real2rgb(A, cmap, lims);
% [B lims map] = real2rgb(...);
%
% This function converts a real-valued matrix into a truecolor image (i.e.
% double array with values between 0 and 1) using the colormap specified
% (either user-defined or the name of a colormap function). The output
% image is suitable for display using IMAGE or IMSHOW, exporting using
% IMWRITE, texture mapping a surface etc.
%
% Colormaps specified by name, e.g. 'hot', can be reversed ('-hot'), made
% to convert linearly to grayscale when printed on a black & white printer
% ('hot*'), or both ('-hot*').
%
% Value limits and a colormap table can be output, for use generating the
% correct colorbar, e.g.:
% [B lims map] = real2rgb(peaks(256), '-hot*');
% hIm = imshow(B);
% set(gcf, 'Colormap', map);
% set(gca, 'CLim', lims);
% set(hIm, 'CDataMapping', 'scaled');
% colorbar;
%
% IN:
% A - MxN real matrix.
% cmap - JxK user-defined colormap, or a string indicating the name
% of the colormap to be used. K = 3 or 4. If K == 4 then
% cmap(1:end-1,4) contains the relative widths of the bins between
% colors. If cmap is a colormap function name then the prefix '-'
% indicates that the colormap is to be reversed, while the suffix
% '*' indicates that the colormap bins are to be rescaled so that
% each bin produces the same change in gray level, such that the
% colormap converts linearly to grayscale when printed in black
% and white.
% lims - 1x2 array of saturation limits to be used on A. Default:
% [min(A(:)) max(A(:))].
%
% OUT:
% B - MxNx3 truecolor image.
% lims - 1x2 array of saturation limits used on A. Same as input lims, if
% given.
% map - 256x3 colormap similar to that used to generate B.
% Copyright: Oliver Woodford, 2009-2010
% Thank you to Peter Nave for reporting a bug whereby colormaps larger than
% 256 entries long are returned.
% Don't do much if A is wrong size
[y x c] = size(A);
if c > 1
error('A can only have 2 dimensions');
end
if y*x*c == 0
% Create an empty array with the correct dimensions
B = zeros(y, x, (c~=0)*3);
return
end
% Generate the colormap
if ischar(cmap)
% If map starts with a '-' sign, invert the colormap
reverseMap = cmap(1) == '-';
% If the map ends with a '*', attempt to make map convert linearly to
% grayscale
grayMap = cmap(end) == '*';
% Extract the map name
cmap = lower(cmap(reverseMap+1:end-grayMap));
% Load the map
try
% Check for a concise table first
map = feval(cmap, Inf);
catch
map = [];
end
if invalid_map(map)
try
% Just load a large table
map = feval(cmap, 256);
catch
error('Colormap ''%s'' not found', cmap);
end
if invalid_map(map)
error('Invalid colormap');
end
end
if reverseMap
% Reverse the map
map = map(end:-1:1,:);
if size(map, 2) == 4
% Shift up the bin lengths
map(1:end-1,4) = map(2:end,4);
end
end
if grayMap && size(map, 1) > 2
% Ensure the map converts linearly to grayscale
map(1:end-1,4) = abs(diff(map(:,1:3) * [0.299; 0.587; 0.114]));
end
else
% Table-based colormap given
map = cmap;
end
% Only work with real doubles
B = reshape(double(real(A)), y*x, c);
% Compute limits and scaled values
maxInd = 1 + (size(map, 1) - 2) * (size(map, 2) ~= 4);
if nargin < 3
lims = [];
end
[B lims] = rescale(B, lims, [0 maxInd]);
% Compute indices and offsets
if size(map, 2) == 4
% Non-linear colormap
bins = map(1:end-1,4);
cbins = cumsum(bins);
bins(bins==0) = 1;
bins = cbins(end) ./ bins;
cbins = [0; cbins(1:end-1) ./ cbins(end); 1+eps];
[ind ind] = histc(B, cbins);
B = (B - cbins(ind)) .* bins(ind);
clear bins cbins
else
% Linear colormap
ind = min(floor(B), maxInd-1);
B = B - ind;
ind = ind + 1;
end
% Compute the output image
B = B(:,[1 1 1]);
B = map(ind,1:3) .* (1 - B) + map(ind+1,1:3) .* B;
B = min(max(B, 0), 1); % Rounding errors can make values slip outside bounds
B = reshape(B, y, x, 3);
if nargout > 2 && (size(map, 1) ~= 256 || size(map, 2) == 4)
% Generate the colormap (for creating a colorbar with)
map = reshape(real2rgb(0:255, map, [0 255]), 256, 3);
end
return
function notmap = invalid_map(map)
notmap = isempty(map) || ndims(map) ~= 2 || size(map, 1) < 1 || size(map, 2) < 3 || size(map, 2) > 4 || ~all(reshape(map(:,1:3) >= 0 & map(:,1:3) <= 1, [], 1));
|
github
|
amcorrigan/IA-Lab-master
|
imsc.m
|
.m
|
IA-Lab-master/Utilities/sc/imsc.m
| 1,299 |
utf_8
|
97cd4a988efe36fe0575539142fc605e
|
%IMSC Wrapper function to SC which replicates display behaviour of IMAGESC
%
% Examples:
% imsc(I, varargin)
% imsc(x, y, I, varargin)
% h = imsc(...)
%
% IN:
% x - 1x2 vector of x-axis bounds. If x(1) > x(2) the image is flipped
% left-right. Default: [1 size(I, 2)].
% y - 1x2 vector of y-axis bounds. If y(1) > y(2) the image is flipped
% up-down. Default: [1 size(I, 1)].
% I - MxNxC input image.
% varargin - Extra input parameters passed to SC. See SC's help for more
% information.
%
% OUT:
% h - Handle of the image graphics object generated.
%
% See also IMAGESC, SC.
% Copyright: Oliver Woodford, 2010
function h = imsc(varargin)
% Check for x, y as first two inputs
if numel(varargin{1}) == 2 && numel(varargin{2}) == 2
% Render
[I clim map] = sc(varargin{3:end});
% Display
h = image(varargin{1}, varargin{2}, I);
else
% Render
[I clim map] = sc(varargin{:});
% Display
h = image(I);
end
% Fix up colormap, if there is one
if ~isempty(clim)
set(h, 'CDataMapping', 'scaled');
ha = get(h, 'Parent');
set(ha, 'CLim', clim);
set(get(ha, 'Parent'), 'Colormap', map);
end
% Don't display the handle if not requested
if nargout < 1
clear h
end
|
github
|
amcorrigan/IA-Lab-master
|
rescale.m
|
.m
|
IA-Lab-master/Utilities/sc/rescale.m
| 1,613 |
utf_8
|
427de5e2419533818c74ea0c8fd7f773
|
function [B lims] = rescale(A, lims, out_lims)
%RESCALE Linearly rescale values in an array
%
% Examples:
% B = rescale(A)
% B = rescale(A, lims)
% B = rescale(A, lims, out_lims)
% [B lims] = rescale(A)
%
% Linearly rescales values in an array, saturating values outside limits.
%
% IN:
% A - Input array of any size and class.
% lims - 1x2 array of saturation limits to be used on A. Default:
% [min(A(:)) max(A(:))].
% out_lims - 1x2 array of output limits the values in lims are to be
% rescaled to. Default: [0 1].
%
% OUT:
% B - size(A) double array.
% lims - 1x2 array of saturation limits used on A. Equal to the input
% lims, if given.
% $Id: rescale.m,v 1.2 2009/04/05 15:09:11 ojw Exp $
% Copyright: Oliver Woodford, 2009
if nargin < 3
out_lims = [0 1];
end
if nargin < 2 || isempty(lims)
M = isfinite(A);
if ~any(reshape(M, numel(M), 1))
% All NaNs, Infs or -Infs
B = double(A > 0);
lims = [0 1];
else
lims = [min(A(M)) max(A(M))];
B = normalize(A, lims, out_lims);
end
clear M
else
B = normalize(A, lims, out_lims);
B = min(max(B, out_lims(1)), out_lims(2));
end
return
function B = normalize(A, lims, out_lims)
if lims(2) == lims(1) || out_lims(1) == out_lims(2)
B = zeros(size(A));
else
B = double(A);
if lims(1)
B = B - lims(1);
end
v = (out_lims(2) - out_lims(1)) / (lims(2) - lims(1));
if v ~= 1
B = B * v;
end
end
if out_lims(1)
B = B + out_lims(1);
end
return
|
github
|
amcorrigan/IA-Lab-master
|
imdisp.m
|
.m
|
IA-Lab-master/Utilities/sc/imdisp.m
| 19,654 |
utf_8
|
c97ad19a7be236223dde28b870a9b800
|
function hIm = imdisp(I, varargin)
%IMDISP Display one or more images nicely
%
% Examples:
% imdisp
% imdisp(I)
% imdisp(I, map)
% imdisp(I, lims)
% imdisp(I, map, lims)
% imdisp(..., param1, value1, param2, value2, ...)
% h = imdisp(...)
%
% This function displays one or more images nicely. Images can be defined
% by arrays or filenames. Multiple images can be input in a cell array or
% stacked along the fourth dimension, and are displayed as a grid of
% subplots (an improvement over MONTAGE). The size of grid is calculated or
% user defined. The figure size is set so that images are magnified by an
% integer value.
%
% If the image grid size is user defined, images not fitting in the grid
% can be scrolled through using the following key presses:
% Up - Back a row.
% Down - Forward a row.
% Left - Back a page (or column if there is only one row).
% Right - Forward a page (or column if there is only one row).
% Shift - 2 x speed.
% Ctrl - 4 x speed.
% Shift + Ctrl - 8 x speed.
%
% This allows fast scrolling through a movie or image stack, e.g.
% imdisp(imstack, 'Size', 1)
% The function can be used as a visual DIR, e.g.
% imdisp()
% to display all images in the current directory on a grid, or
% imdisp({}, 'Size', 1)
% to scroll through them one at a time.
%
% IN:
% I - MxNxCxP array of images, or 1xP cell array. C is 1 for indexed
% images or 3 for RGB images. P is the number of images. If I is a
% cell array then each cell must contain an image. Images can equally
% be defined by filenames. If I is an empty cell array then all the
% images in the current directory are used. Default: {}.
% map - Kx3 colormap to be used with indexed images. Default: gray(256).
% lims - [LOW HIGH] display range for indexed images. Default: [min(I(:))
% max(I(:))].
% Optional parameters - name, value parameter pairs for the following:
% 'Size' - [H W] size of grid to display image on. If only H is given
% then W = H. If either H or W is NaN then the number of rows
% or columns is chosen such that all images fit. If both H
% and W are NaN or the array is empty then the size of grid
% is chosen to fit all images in as large as possible.
% Default: [].
% 'Indices' - 1xL list of indices of images to display. Default: 1:P.
% 'Border' - [TB LR] borders to give each image top and bottom (TB)
% and left and right (LR), to space out images. Borders are
% normalized to the subplot size, i.e. TB = 0.01 gives a
% border 1% of the height of each subplot. If only TB is
% given, LR = TB. Default: 0.01.
% 'DisplayRange' - Same as lims input.
% 'Map' - Kx3 colormap or (additionally from above) name of MATLAB
% colormap, for use with indexed images. Default: gray(256).
%
% OUT:
% h - HxW array of handles to images.
%
% See also IMAGE, IMAGESC, IMSHOW, MONTAGE.
% Copyright: Oliver Woodford 2010
% Parse inputs
[map layout gap indices lims] = parse_inputs(varargin);
if nargin == 0 || (iscell(I) && isempty(I))
% Read in all the images in the directory
I = get_im_names;
if isempty(I)
% No images found
if nargout > 0
hIm = [];
end
return
end
end
% Check if input is filenames
if ischar(I)
[x y c] = size(I);
if (x > 1 && y > 1) || c > 1
I = num2cell(I, 2);
else
I = {I(:)'};
end
end
% Get limits, etc.
if isnumeric(I) || islogical(I)
[y x c n] = size(I);
if isempty(lims)
lims = min_max(I);
elseif isequal(0, lims)
lims = default_limits(I);
elseif c == 3
% Rescale
if ~isfloat(I)
I = single(I);
end
I = min(max((I - lims(1)) ./ (lims(2) - lims(1)), 0), 1);
end
if isfloat(I) && c == 3 && n > 1
I = uint8(I * 256 - 0.5);
lims = round(lims * 256 - 0.5);
end
elseif iscell(I)
n = numel(I);
A = I{1};
if ischar(A)
% Read in the image (or images for multi-frame files)
if n == 1
I = imread_rgb_multi(A);
if iscell(I)
n = numel(I);
A = I{1};
[y x c] = size(A);
else
[y x c n] = size(I);
A = I;
end
else
A = imread_rgb(A);
I{1} = A;
[y x c] = size(A);
end
else
[y x c] = size(A);
end
% Assume all images are the same size and type as the first
if isempty(lims) || isequal(0, lims)
lims = default_limits(A);
end
else
error('I not of recognized type.');
end
% Select indexed images
if ~isequal(indices, -1)
if iscell(I)
I = I(indices);
n = numel(I);
else
I = I(:,:,:,indices);
n = size(I, 4);
end
end
% Get the current figure
hFig = get(0, 'CurrentFigure');
if isempty(hFig)
% Create a new figure
hFig = figure;
end
if n < 2
% Set the colormap
set(hFig, 'Colormap', map);
end
% Display the image(s)
if n == 0
hIm = display_image([], gca, [0 1]);
if nargout == 0
clear hIm % Avoid printing this out
end
return
elseif n == 1
% IMSHOW mode
% Display the single image
hAx = gca;
if iscell(I)
I = I{1};
end
hIm = display_image(I, hAx, lims);
if nargout == 0
clear hIm % Avoid printing this out
end
% Only resize image if it is alone in the figure
if numel(findobj(get(hFig, 'Children'), 'Type', 'axes')) > 1
return
end
% Could still be the first subplot - do another check
axesPos = get(hAx, 'Position');
newAxesPos = [gap(1) gap(end) 1-2*gap(1) 1-2*gap(end)];
if isequal(axesPos, get(hFig, 'DefaultAxesPosition'))
% Default position => not a subplot
% Fill the window
set(hAx, 'Units', 'normalized', 'Position', newAxesPos);
axesPos = newAxesPos;
end
if ~isequal(axesPos, newAxesPos)
% Figure not alone, so don't resize.
return
end
layout = [1 1];
else
% MONTAGE mode
% Compute a good layout
layout = choose_layout(n, y, x, layout);
% Create a data structure to store the data in
num = prod(layout);
state.num = num * ceil(n / num);
hIm = zeros(layout);
hAx = zeros(layout);
% Clear the figure
if n > num
hFig = clf(hFig, 'reset');
else
hFig = clf(hFig);
end
% Set the colormap
set(hFig, 'Colormap', map);
% Set the first lot of images
index = mod(0:num-1, state.num) + 1;
hw = 1 ./ layout;
gap = gap ./ layout;
dims = hw - 2 * gap;
dims = dims([2 1]);
for a = 1:layout(1)
for b = 1:layout(2)
c = index(b + (layout(1) - a) * layout(2));
if c > n
A = [];
elseif iscell(I)
A = I{c};
if ischar(A)
A = imread_rgb(A);
I{c} = A;
end
else
A = I(:,:,:,c);
end
hAx(a,b) = axes('Position', [(b-1)*hw(2)+gap(2) (a-1)*hw(1)+gap(1) dims], 'Units', 'normalized');
hIm(a,b) = display_image(A, hAx(a,b), lims);
end
end
% Check if we need to be able to scroll through images
if n > num
% Intialize rest of data structure
state.hIm = hIm;
state.hAx = hAx;
state.index = 1;
state.layout = layout;
state.n = n;
state.I = I;
% Set the callback for image navigation, and save the image data in the figure
set(hFig, 'KeyPressFcn', @keypress_callback, 'Interruptible', 'off', 'BusyAction', 'cancel', 'UserData', state);
end
% Flip hIm so it matches the layout
hIm = hIm(end:-1:1,:);
if nargout == 0
clear hIm % Avoid printing this out
end
end
if strcmp(get(hFig, 'WindowStyle'), 'docked')
% Figure is docked, so can't resize
return
end
% Set the figure size well
% Compute the image size
ImSz = layout([2 1]) .* [x y] ./ (1 - 2 * gap([end 1]));
% Get the size of the monitor we're on
figPosCur = get(hFig, 'Position');
% Monitor sizes
MonSz = get(0, 'MonitorPositions');
MonOn = size(MonSz, 1);
if MonOn > 1
% Make the origin the top left corner of the primary monitor
correction = 0;
if ispc
for a = 1:MonOn
if isequal(MonSz(a,1:2), [1 1])
correction = MonSz(a,4);
break
end
end
end
% Determine which monitor the centre of the image is on
figCenter = figPosCur(1:2) + figPosCur(3:4) / 2;
figCenter = MonSz - repmat(figCenter, [MonOn 2]);
MonOn = all(sign(figCenter) == repmat([-1 -1 1 1], [MonOn 1]), 2);
MonOn(1) = MonOn(1) | ~any(MonOn);
MonSz = MonSz(MonOn,:);
% Correct the size
MonSz(3:4) = MonSz(3:4) - MonSz(1:2) + 1;
% Correct the origin
if correction
MonSz(2) = correction - MonSz(4) - MonSz(2) + 2;
end
end
% Check if the window is maximized
% This is a hack which may only work on Windows! No matter, though.
if isequal(MonSz([1 3]), figPosCur([1 3]))
% Leave maximized
return
end
% Compute the size to set the window
MaxSz = MonSz(3:4) - [20 120];
RescaleFactor = min(MaxSz ./ ImSz);
if RescaleFactor > 1
% Integer scale for enlarging, but don't make too big
MaxSz = min(MaxSz, [1200 800]);
RescaleFactor = max(floor(min(MaxSz ./ ImSz)), 1);
end
figPosNew = ceil(ImSz * RescaleFactor);
% Don't move the figure if the size isn't changing
if isequal(figPosCur(3:4), figPosNew)
return
end
% Keep the centre of the figure stationary
figPosNew = [floor(figPosCur(1:2)+(figPosCur(3:4)-figPosNew)/2) figPosNew];
% Ensure the figure is in bounds
figPosNew(1:2) = min(max(figPosNew(1:2), MonSz(1:2)+6), MonSz(1:2)+MonSz(3:4)-[6 101]-figPosNew(3:4));
% Set the figure size and position
set(hFig, 'Position', figPosNew);
return
%% Keypress callback
% The function which does all the display stuff
function keypress_callback(fig, event_data)
% Check what key was pressed and update the image index as necessary
switch event_data.Character
case 28 % Left
up = -1; % Back a page
case 29 % Right
up = 1; % Forward a page
case 30 % Up
up = -0.1; % Back a row
case 31 % Down
up = 0.1; % Forward a row
otherwise
% Another key was pressed - ignore it
return
end
% Use control and shift for faster scrolling
if ~isempty(event_data.Modifier)
up = up * (2 ^ (strcmpi(event_data.Modifier, {'shift', 'control'}) * [1; 2]));
end
% Get the state data
state = get(fig, 'UserData');
% Get the current index
index = state.index;
% Get number of images
n = prod(state.layout);
% Generate 12 valid indices
if abs(up) < 1
% Increment by row
index = index + state.layout(2) * (up * 10) - 1;
else
if state.layout(1) == 1
% Increment by column
index = index + up - 1;
else
% Increment by page
index = index + n * up - 1;
end
end
index = mod(index:index+n, state.num) + 1;
% Plot the images
figure(fig);
for a = 1:state.layout(1)
for b = 1:state.layout(2)
% Get the image
c = index(b + (state.layout(1) - a) * state.layout(2));
if c > state.n
% Set the image data
set(state.hIm(a,b), 'CData', []);
elseif iscell(state.I)
A = state.I{c};
if ischar(A)
% Filename - read the image from disk
A = imread_rgb(A);
state.I{c} = A;
end
% Set the image data
set(state.hIm(a,b), 'CData', A);
% Reset the axes limits
if ~isempty(A)
set(state.hAx(a,b), 'XLim', [0.5 size(A, 2)+0.5], 'YLim', [0.5 size(A, 1)+0.5]);
end
else
% Set the image data
set(state.hIm(a,b), 'CData', state.I(:,:,:,c));
end
end
end
drawnow;
% Save the current index
state.index = index(1);
set(fig, 'UserData', state);
return
%% Display the image
function hIm = display_image(A, hAx, lims)
if isempty(A)
hIm = image(zeros(1, 1, 3));
set(hIm, 'CData', []);
else
hIm = image(A);
end
set(hAx, 'Visible', 'off', 'DataAspectRatio', [1 1 1], 'DrawMode', 'fast', 'CLim', lims);
set(get(hAx, 'XLabel'), 'Visible', 'on');
set(get(hAx, 'YLabel'), 'Visible', 'on');
set(get(hAx, 'Title'), 'Visible', 'on');
set(hIm, 'CDataMapping', 'scaled');
return
%% Choose a good layout for the images
function layout = choose_layout(n, y, x, layout)
v = numel(layout);
N = isnan(layout);
if v == 0 || all(N)
% Compute approximate layout
sz = get(0, 'ScreenSize');
sz = sz(3:4) ./ [x y];
layout = ceil(sz([2 1]) ./ sqrt(prod(sz) / n));
% Remove superfluous rows or columns
while 1
switch ([prod(layout - [1 0]) prod(layout - [0 1])] >= n) * [2; 1]
case 0
break;
case 1
layout = layout - [0 1];
case 2
layout = layout - [1 0];
case 3
if min(sz .* (layout - [0 1])) > min(sz .* (layout - [1 0]))
layout = layout - [0 1];
else
layout = layout - [1 0];
end
end
end
elseif v == 1
layout = layout([1 1]);
elseif any(N)
layout(N) = ceil(n / layout(~N));
end
layout = reshape(layout, 1, 2);
return
%% Read image to uint8 rgb array
function A = imread_rgb(name)
try
[A map alpha] = imread(name);
catch
% Format not recognized by imread, so create a red cross (along diagonals)
A = eye(101) | diag(ones(100, 1), 1) | diag(ones(100, 1), -1);
A = (uint8(1) - uint8(A | flipud(A))) * uint8(255);
A = cat(3, zeros(size(A), 'uint8')+uint8(255), A, A);
return
end
A = A(:,:,:,1); % Keep only first frame of multi-frame files
if ~isempty(map)
map = uint8(map * 256 - 0.5); % Convert to uint8 for storage
A = reshape(map(uint32(A)+1,:), [size(A) size(map, 2)]); % Assume indexed from 0
elseif size(A, 3) == 4
if lower(name(end)) == 'f'
% TIFF in CMYK colourspace - convert to RGB
if isfloat(A)
A = A * 255;
else
A = single(A);
end
A = 255 - A;
A(:,:,4) = A(:,:,4) / 255;
A = uint8(A(:,:,1:3) .* A(:,:,[4 4 4]));
else
% Assume 4th channel is an alpha matte
alpha = A(:,:,4);
A = A(:,:,1:3);
end
end
if ~isempty(alpha)
% Apply transprency over a grey checkerboard pattern
if isa(alpha, 'uint8')
alpha = double(alpha) / 255;
end
A = double(A) .* alpha(:,:,ones(1, size(A, 3)));
sqSz = max(size(alpha));
sqSz = floor(max(log(sqSz / 100), 0) * 10 + 1 + min(sqSz, 100) / 20);
grid = repmat(85, ceil(size(alpha) / sqSz));
grid(2:2:end,1:2:end) = 171;
grid(1:2:end,2:2:end) = 171;
grid = kron(grid, ones(sqSz));
alpha = grid(1:size(A, 1),1:size(A, 2)) .* (1 - alpha);
A = uint8(A + alpha(:,:,ones(1, size(A, 3))));
end
return
%% Read (potentially) multi-frame image to uint8 rgb array
function A = imread_rgb_multi(name)
try
% Get file info
info = imfinfo(name);
catch
% Revert to standard case
A = imread_rgb(name);
return
end
if numel(info) < 2
% Single image
A = imread_rgb(name);
return
else
% Multi-frame image
switch lower(info(1).Format)
case 'gif'
[A map] = imread(name, 'frames', 'all');
if ~isempty(map)
map = uint8(map * 256 - 0.5); % Convert to uint8 for storage
A = reshape(map(uint32(A)+1,:), [size(A) size(map, 2)]); % Assume indexed from 0
A = permute(A, [1 2 5 4 3]);
end
case {'tif', 'tiff'}
A = cell(numel(info), 1);
for a = 1:numel(A)
[A{a} map] = imread(name, 'Index', a, 'Info', info);
if ~isempty(map)
map = uint8(map * 256 - 0.5); % Convert to uint8 for storage
A{a} = reshape(map(uint32(A{a})+1,:), [size(A) size(map, 2)]); % Assume indexed from 0
end
if size(A{a}, 3) == 4
% TIFF in CMYK colourspace - convert to RGB
if isfloat(A{a})
A{a} = A{a} * 255;
else
A{a} = single(A{a});
end
A{a} = 255 - A{a};
A{a}(:,:,4) = A{a}(:,:,4) / 255;
A{a} = uint8(A(:,:,1:3) .* A{a}(:,:,[4 4 4]));
end
end
otherwise
% Multi-frame not supported for this format
A = imread_rgb(name);
return
end
end
return
%% Get the names of all images in a directory
function L = get_im_names
D = dir;
n = 0;
L = cell(size(D));
% Go through the directory list
for a = 1:numel(D)
% Check if file is a supported image type
if numel(D(a).name) > 4 && ~D(a).isdir && (any(strcmpi(D(a).name(end-3:end), {'.png', '.tif', '.jpg', '.bmp', '.ppm', '.pgm', '.pbm', '.gif', '.ras'})) || any(strcmpi(D(a).name(end-4:end), {'.tiff', '.jpeg'})))
n = n + 1;
L{n} = D(a).name;
end
end
L = L(1:n);
return
%% Parse inputs
function [map layout gap indices lims] = parse_inputs(inputs)
% Set defaults
map = [];
layout = [];
gap = 0;
indices = -1;
lims = 0;
% Check for map and display range
for b = 1:numel(inputs)
if ~isnumeric(inputs{b})
b = b - 1;
break;
end
if size(inputs{b}, 2) == 3
map = inputs{b};
elseif numel(inputs{b}) < 3
lims = inputs{b};
end
end
% Go through option pairs
for a = b+1:2:numel(inputs)
switch lower(inputs{a})
case 'map'
map = inputs{a+1};
if ischar(map)
map = feval(map, 256);
end
case {'size', 'grid'}
layout = inputs{a+1};
case {'gap', 'border'}
gap = inputs{a+1};
case 'indices'
indices = inputs{a+1};
case {'lims', 'displayrange'}
lims = inputs{a+1};
otherwise
error('Input option %s not recognized', inputs{a});
end
end
if isempty(map)
map = gray(256);
end
return
%% Return default limits for the image type
function lims = default_limits(A)
if size(A, 3) == 1
lims = min_max(A);
else
lims = [0 1];
if ~isfloat(A)
lims = lims * double(intmax(class(A)));
end
end
return
%% Return minimum and maximum values
function lims = min_max(A)
M = isfinite(A);
if all(M(:))
lims = double([min(A(:)) max(A(:))]);
else
lims = double([min(A(M)) max(A(M))]);
end
if isempty(lims)
lims = [0 1];
elseif lims(1) == lims(2)
lims(2) = lims(1) + 1;
end
return
|
github
|
amcorrigan/IA-Lab-master
|
sc.m
|
.m
|
IA-Lab-master/Utilities/sc/sc.m
| 31,219 |
utf_8
|
f247fe4402993a806f759a89a6ddf8a6
|
function [I limits map] = sc(I, varargin)
%SC Display/output truecolor images with a range of colormaps
%
% Examples:
% sc(image)
% sc(image, limits)
% sc(image, map)
% sc(image, limits, map)
% sc(image, map, limits)
% sc(..., col1, mask1, col2, mask2,...)
% out = sc(...)
% [out clim map] = sc(...)
% sc
%
% Generates a truecolor RGB image based on the input values in 'image' and
% any maximum and minimum limits specified, using the colormap specified.
% The image is displayed on screen if there is no output argument.
%
% SC has these advantages over MATLAB image rendering functions:
% - images can be displayed or output; makes combining/overlaying images
% simple.
% - images are rendered/output in truecolor (RGB [0,1]); no nasty
% discretization of the input data.
% - many special, built-in colormaps for viewing various types of data.
% - linearly interpolates user defined linear and non-linear colormaps.
% - no border and automatic, integer magnification (unless figure is
% docked or maximized) for better display.
% - multiple images can be generated simultaneously.
%
% For a demonstration, simply call SC without any input arguments.
%
% If you don't like the display behaviour of SC, e.g. the fixed aspect
% ratio, no border and axes, then you can replicate the behaviour of
% IMAGESC using the wrapper function IMSC.
%
% IN:
% image - MxNxCxP or 3xMxNxP image array. MxN are the dimensions of the
% image(s), C is the number of channels, and P the number of
% images. If P > 1, images can only be exported, not displayed.
% limits - [min max] where values in image less than min will be set to
% min and values greater than max will be set to max.
% map - Kx3 or Kx4 user defined colormap matrix, where the optional 4th
% column is the relative distance between colours along the scale,
% or a string containing the name of the colormap to use to create
% the output image. Default: 'none', which is RGB for 3-channel
% images, grayscale otherwise. Conversion of multi-channel images
% to intensity for intensity-based colormaps is done using the L2
% norm. Most MATLAB colormaps are supported. All named colormaps
% can be reversed by prefixing '-' to the string. This maintains
% integrity of the colorbar. Special, non-MATLAB colormaps are:
% 'hicontrast' - a high contrast colormap for intensity images that
% maintains intensity scale when converted to
% grayscale, for example when printing in black &
% white.
% 'prob' - first channel is plotted as hue, and the other channels
% modulate intensity. Useful for laying probabilites over
% images.
% 'prob_jet' - first channel is plotted as jet colormap, and the other
% channels modulate intensity.
% 'diff' - intensity values are marked blue for > 0 and red for < 0.
% Darker colour means larger absolute value. For multi-
% channel images, the L2 norm of the other channels sets
% green level. 3 channel images are converted to YUV and
% images with more that 3 channels are projected onto the
% principle components first.
% 'compress' - compress many channels to RGB while maximizing
% variance.
% 'contrast' - apply the CONTRAST function to create an approximately
% equal intensity distribution.
% 'flow' - display two channels representing a 2d Cartesian vector as
% hue for angle and intensity for magnitude (darker colour
% indicates a larger magnitude).
% 'phase' - first channel is intensity, second channel is phase in
% radians. Darker colour means greater intensity, hue
% represents phase from 0 to 2 pi.
% 'stereo' - pair of concatenated images used to generate a red/cyan
% anaglyph.
% 'stereo_col' - pair of concatenated RGB images used to generate a
% colour anaglyph.
% 'segment' - given concatenated image and segmentation (index image),
% colour each segment with the mean colour of the image in
% that segment.
% 'rand' - gives an index image a random colormap. Useful for viewing
% segmentations.
% 'rgb2gray' - converts an RGB image to grayscale in the same fashion
% as MATLAB's rgb2gray (in the image processing toolbox).
% col/mask pairs - Pairs of parameters for coloring specific parts of the
% image differently. The first (col) parameter can be
% a MATLAB color specifier, e.g. 'b' or [0.5 0 1], or
% one of the colormaps named above, or an MxNx3 RGB
% image. The second (mask) paramater should be an MxN
% logical array indicating those pixels (true) whose
% color should come from the specified color parameter.
% If there is only one col parameter, without a mask
% pair, then mask = any(isnan(I, 3)), i.e. the mask is
% assumed to indicate the location of NaNs. Note that
% col/mask pairs are applied in order, painting over
% previous pixel values.
%
% OUT:
% out - MxNx3xP truecolour (double) RGB image array in range [0, 1].
% clim - 1x2 vector of limits of the input array mapped to linearly
% [0, 1] in out. [] if this mapping is not available, e.g. if
% output image is multi-spectral.
% map - 256x3 colormap of the output. [] is limits is [].
%
% See also IMAGE, IMAGESC, IMSC, COLORMAP, COLORBAR.
% Copyright: Oliver Woodford, 2007-2010
%% Check for arguments
if nargin == 0
% If there are no input arguments then run the demo
if nargout > 0
error('Output expected from no inputs!');
end
demo; % Run the demo
return
end
%% Size our image(s)
[y x c n] = size(I);
I = reshape(I, y, x, c, n);
%% Check if image is given with RGB colour along the first dimension
if y == 3 && c > 3
% Flip colour to 3rd dimension
I = permute(I, [2 3 1 4]);
[y x c n] = size(I);
end
%% Don't do much if I is empty
if isempty(I)
if nargout == 0
% Clear the current axes if we were supposed to display the image
cla; axis off;
else
% Create an empty array with the correct dimensions
I = zeros(y, x, (c~=0)*3, n);
end
return
end
%% Check for multiple images
% If we have a non-singleton 4th dimension we want to display the images in
% a 3x4 grid and use buttons to cycle through them
if n > 1
% Return transformed images in an YxXx3xN array
A = zeros(y, x, 3, n);
for a = 1:n
A(:,:,:,a) = sc(I(:,:,:,a), varargin{:});
end
I = A;
if nargout == 0
clear I
if n > 12
sz = [3 4];
else
sz = [];
end
imdisp(A, 'Size', sz, 'Border', 0.01);
end
return
end
%% Parse the input arguments coming after I (1st input)
[map limits mask] = parse_inputs(I, varargin, y, x);
%% Call the rendering function
if isnumeric(map) && (size(map, 2) == 3 || size(map, 2) == 4)
% Table-based colormap
[I limits map] = table_wrapper(I, map, limits);
elseif ischar(map)
% Predefined colormap
[I limits map] = colormap_switch(I, map, limits);
else
error('map input invalid.');
end
%% Update any masked pixels
I = reshape(I, y*x, 3);
for a = 1:size(mask, 2)
I(mask{2,a},1) = mask{1,a}(:,1);
I(mask{2,a},2) = mask{1,a}(:,2);
I(mask{2,a},3) = mask{1,a}(:,3);
end
I = reshape(I, [y x 3]); % Reshape to correct size
%% Only display if the output isn't used
if nargout == 0
% Display the image
hIm = imdisp(I, 'Border', 0);
% Set the colormap (if valid)
if ~isempty(limits)
set(gcf, 'Colormap', map);
set(gca, 'CLim', limits);
set(hIm, 'CDataMapping', 'scaled');
end
% Don't print out the matrix if we've forgotten the ";"
clear I
end
return
%% Colormap switch
function [I limits map] = colormap_switch(A, cmap, limits)
% Reshape
[y x c] = size(A);
I = full(real(double(reshape(A, y*x, 1, c))));
% If map starts with a '-' sign, invert the colormap
reverseMap = cmap(1) == '-';
% If the map ends with a '*', attempt to make map convert linearly to
% grayscale
grayMap = cmap(end) == '*';
% Large switch statement for all the colormaps
switch lower(cmap(1+reverseMap:end-grayMap))
%% Prism
case 'prism'
% Similar to the MATLAB internal prism colormap, but only works on
% index images, assigning each index (or rounded float) to a
% different colour
[I limits] = index_im(I);
% Generate prism colormap
map = prism(6);
if reverseMap
map = map(end:-1:1,:); % Reverse the map
end
% Lookup the colours
I = mod(I, 6) + 1;
I = map(I,:);
%% Rand
case 'rand'
% Assigns a random colour to each index
[I limits num_vals] = index_im(I);
% Generate random colormap
map = rand(num_vals, 3);
% Lookup the colours
I = map(I,:);
%% Diff
case 'diff'
% Show positive as blue and negative as red, white is 0
switch c
case 1
I(:,2:3) = 0;
case 2
% Second channel can only have absolute value
I(:,3) = abs(I(:,2));
case 3
% Diff of RGB images - convert to YUV first
I = rgb2yuv(I);
I(:,3) = sqrt(sum(I(:,2:end) .^ 2, 2)) ./ sqrt(2);
otherwise
% Use difference along principle component, and other
% channels to modulate second channel
I = calc_prin_comps(I);
I(:,3) = sqrt(sum(I(:,2:end) .^ 2, 2)) ./ sqrt(c - 1);
I(:,4:end) = [];
end
% Generate limits
if isempty(limits)
limits = [min(I(:,1)) max(I(:,1))];
end
limits = max(abs(limits));
if limits
% Scale
if c > 1
I(:,[1 3]) = I(:,[1 3]) / limits;
else
I = I / (limits * 0.5);
end
else
limits = 1;
end
% Colour
M = I(:,1) > 0;
I(:,2) = -I(:,1) .* ~M;
I(:,1) = I(:,1) .* M;
if reverseMap
% Swap first two channels
I = I(:,[2 1 3]);
end
%I = 1 - I * [1 0.4 1; 0.4 1 1; 1 1 0.4]; % (Green/Red)
I = 1 - I * [1 1 0.4; 0.4 1 1; 1 0.4 1]; % (Blue/Red)
I = min(max(I, 0), 1);
limits = [-limits limits]; % For colorbar
%% Flow
case 'flow'
% Calculate amplitude and phase, and use 'phase'
if c ~= 2
error('''flow'' requires two channels');
end
A = sqrt(sum(I .^ 2, 3));
if isempty(limits)
limits = [min(A) max(A)*2];
else
limits = [0 max(abs(limits)*sqrt(2))*2];
end
I(:,1) = atan2(I(:,2), I(:,1));
I(:,2) = A;
if reverseMap
% Invert the amplitude
I(:,2) = -I(:,2);
limits = -limits([2 1]);
end
I = phase_helper(I, limits, 2); % Last parameter tunes how saturated colors can get
% Set NaNs (unknown flow) to 0
I(isnan(I)) = reverseMap;
limits = []; % This colormap doesn't have a valid colorbar
%% Phase
case 'phase'
% Plot amplitude as intensity and angle as hue
if c < 2
error('''phase'' requires two channels');
end
if isempty(limits)
limits = [min(I(:,1)) max(I(:,1))];
end
if reverseMap
% Invert the phase
I(:,2) = -I(:,2);
end
I = I(:,[2 1]);
if diff(limits)
I = phase_helper(I, limits, 1.3); % Last parameter tunes how saturated colors can get
else
% No intensity - just cycle hsv
I = real2rgb(mod(I(:,1) / (2 * pi), 1), 'hsv');
end
limits = []; % This colormap doesn't have a valid colorbar
%% RGB2Gray
case {'rgb2gray', 'rgb2grey'}
% Compress RGB to greyscale
[I limits] = rgb2gray(I, limits, reverseMap);
%% RGB2YUV
case 'rgb2yuv'
% Convert RGB to YUV - not for displaying or saving to disk!
[I limits] = rgb2yuv(I);
%% YUV2RGB
case 'yuv2rgb'
% Convert YUV to RGB - undo conversion of rgb2yuv
if c ~= 3
error('''yuv2rgb'' requires a 3 channel image');
end
I = I(:,:) * [1 1 1; 0, -0.39465, 2.03211; 1.13983, -0.58060 0];
I = rescale(I, limits);
limits = []; % This colormap doesn't have a valid colorbar
%% Prob
case 'prob'
% Plot first channel as grey variation of 'bled' and modulate
% according to other channels
if c > 1
A = rgb2gray(I(:,:,2:end), [], false);
I = I(:,:,1);
else
A = 0.5;
end
cmap2 = cmap;
cmap2((1:4)+reverseMap) = 'bled';
[I limits] = real2rgb(I, cmap2, limits);
I = rescale(A + I, [-0.1 1.3]);
%% Prob_jet
case 'prob_jet'
% Plot first channel as 'jet' and modulate according to other
% channels
if c > 1
A = rgb2gray(I(:,:,2:end), [], false);
I = I(:,:,1);
else
A = 0.5;
end
cmap2 = cmap;
cmap2(reverseMap+(1:5)) = [];
[I limits] = real2rgb(I, cmap2, limits);
I = rescale(A + I, [0.2 1.8]);
%% Compress
case 'compress'
% Compress to RGB, maximizing variance
% Determine and scale to limits
I = rescale(I, limits);
if reverseMap
% Invert after everything
I = 1 - I;
end
% Zero mean
meanCol = mean(I, 1);
isBsx = exist('bsxfun', 'builtin');
if isBsx
I = bsxfun(@minus, I, meanCol);
else
I = I - meanCol(ones(x*y, 1, 'uint8'),:);
end
% Calculate top 3 principle components
I = calc_prin_comps(I, 3);
% Normalize each channel independently
if isBsx
I = bsxfun(@minus, I, min(I, [], 1));
I = bsxfun(@times, I, 1./max(I, [], 1));
else
for a = 1:3
I(:,a) = I(:,a) - min(I(:,a));
I(:,a) = I(:,a) / max(I(:,a));
end
end
% Put components in order of human eyes' response to channels
I = I(:,[2 1 3]);
limits = []; % This colormap doesn't have a valid colorbar
%% Contrast
case 'contrast'
% Use MATLAB's CONTRAST function to spread the gray levels evenly
[I limits] = intensity(I, limits, 0);
map = contrast(I, 256);
if reverseMap
map = map(end:-1:1,:);
end
I = real2rgb(I, map, [0 1]);
%% Stereo (anaglyph)
case 'stereo'
% Convert 2 colour images to intensity images
% Show first channel as red and second channel as cyan
A = rgb2gray(I(:,1:floor(end/2)), limits, false);
I = rgb2gray(I(:,floor(end/2)+1:end), limits, false);
if reverseMap
I(:,2:3) = A(:,1:2); % Make first image cyan
else
I(:,1) = A(:,1); % Make first image red
end
limits = []; % This colormap doesn't have a valid colorbar
%% Coloured anaglyph
case 'stereo_col'
if c ~= 6
error('''stereo_col'' requires a 6 channel image');
end
I = rescale(I, limits);
% Red channel from one image, green and blue from the other
if reverseMap
I(:,1) = I(:,4); % Make second image red
else
I(:,2:3) = I(:,5:6); % Make first image red
end
I = I(:,1:3);
limits = []; % This colormap doesn't have a valid colorbar
%% Coloured segments
case 'segment'
% Last channel assumed to be an index image. Output each segment as
% a mean of the other channels in the segment.
if c < 2
error('''segment'' requires at least 2 channels');
end
[S num_vals num_vals] = index_im(I(:,end));
% Generate the means
R = 1 ./ (accumarray(S, 1, [num_vals 1]) + 1e-300);
for a = c-1:-1:1
J(:,1,a) = accumarray(S, I(:,a), [num_vals 1]) .* R;
end
if c == 4
J = rescale(J, limits);
limits = [];
else
[J limits map] = table_wrapper(J, 'gray', limits);
end
% Generate the image
I = J(S,:);
%% None
case 'none'
% No colormap - just output the image
if c == 3
I = rescale(I, limits);
limits = [];
if reverseMap
I = 1 - I;
end
else
cmap((1:4)+reverseMap) = 'gray';
[I limits map] = table_wrapper(I, cmap, limits);
end
%% Grey
case 'grey'
cmap(3+reverseMap) = 'a';
[I limits map] = table_wrapper(I, cmap, limits);
%% Colourcube
case {'colorcube2', 'colourcube2'}
% Psychedelic colormap inspired by MATLAB's version
[I limits] = intensity(I, limits, reverseMap); % Intensity map
step = 4;
I = I * (step * (1 - eps));
J = I * step;
K = floor(J);
I = cat(3, mod(K, step)/(step-1), J - floor(K), mod(floor(I), step)/(step-1));
%% Functional colormap
otherwise
[I limits map] = table_wrapper(I, cmap, limits);
end
I = reshape(I, y, x, 3);
% Fix up the colormap
if nargout > 2
if isempty(limits)
map = [];
elseif ~exist('map', 'var')
map = (0:255) * ((limits(2) - limits(1)) / 255) + limits(1);
map = squeeze(colormap_switch(map, cmap, limits));
end
end
return
%% Parse input variables
function [map limits mask] = parse_inputs(I, inputs, y, x)
% Check the first two arguments for the colormap and limits
ninputs = numel(inputs);
map = 'none';
limits = [];
mask = 1;
for a = 1:min(2, ninputs)
if ischar(inputs{a}) && numel(inputs{a}) > 1
% Name of colormap
map = inputs{a};
elseif isnumeric(inputs{a})
[p q r] = size(inputs{a});
if (p * q * r) == 2
% Limits
limits = double(inputs{a});
elseif p > 1 && (q == 3 || q == 4) && r == 1
% Table-based colormap
map = inputs{a};
else
break;
end
else
break;
end
mask = mask + 1;
end
% Check for following inputs
if mask > ninputs
mask = cell(2, 0);
return
end
% Following inputs must either be colour/mask pairs, or a colour for NaNs
if ninputs - mask == 0
mask = cell(2, 1);
mask{1} = inputs{end};
mask{2} = ~all(isfinite(I), 3);
elseif mod(ninputs-mask, 2) == 1
mask = reshape(inputs(mask:end), 2, []);
else
error('Error parsing inputs');
end
% Go through pairs and generate
for a = 1:size(mask, 2)
% Generate any masks from functions
if isa(mask{2,a}, 'function_handle')
mask{2,a} = mask{2,a}(I);
end
if ~islogical(mask{2,a})
error('Mask is not a logical array');
end
if ~isequal(size(mask{2,a}), [y x])
error('Mask does not match image size');
end
if ischar(mask{1,a})
if numel(mask{1,a}) == 1
% Generate colours from MATLAB colour strings
mask{1,a} = rem(floor((strfind('kbgcrmyw', mask{1,a}) - 1) * [0.25 0.5 1]), 2);
else
% Assume it's a colormap name
mask{1,a} = sc(I, mask{1,a});
end
end
mask{1,a} = reshape(mask{1,a}, [], 3);
if size(mask{1,a}, 1) ~= y*x && size(mask{1,a}, 1) ~= 1
error('Replacement color/image of unexpected dimensions');
end
if size(mask{1,a}, 1) ~= 1
mask{1,a} = mask{1,a}(mask{2,a},:);
end
end
return
%% RGB2gray
function [B limits] = rgb2gray(A, limits, reverseMap)
% Compress RGB to grayscale
c = size(A, 3);
B = A;
if c == 3
B = reshape(reshape(B, [], 3) * [0.299; 0.587; 0.114], size(B, 1), size(B, 2));
end
[B limits] = intensity(B, limits, reverseMap);
% Replicate channels
B = B(:,:,[1 1 1]);
return
%% RGB2YUV
function [B limits] = rgb2yuv(A)
% Convert RGB to YUV - not for displaying or saving to disk!
c = size(A, 3);
if c ~= 3
error('rgb2yuv requires a 3 channel image');
end
B = reshape(A, [], c) * [0.299, -0.14713, 0.615; 0.587, -0.28886, -0.51498; 0.114, 0.436, -0.10001];
limits = []; % This colormap doesn't have a valid colorbar
return
%% Phase helper
function I = phase_helper(I, limits, n)
I = squeeze(I);
I(:,1) = mod(I(:,1)/(2*pi), 1);
I(:,2) = I(:,2) - limits(1);
I(:,2) = I(:,2) * (n / (limits(2) - limits(1)));
I(:,3) = n - I(:,2);
I(:,[2 3]) = min(max(I(:,[2 3]), 0), 1);
I = hsv2rgb(reshape(I, [], 1, 3));
return
%% Real2rgb wrapper
function [B limits map] = table_wrapper(A, cmap, limits)
% Convert to intensity
[B limits] = intensity(A, limits, 0);
% Convert to colour using the specified colormap
[B map map] = real2rgb(B, cmap, [0 1]);
return
%% Intensity maps
function [I limits] = intensity(I, limits, reverseMap)
% Squash to 1d using L2 norm
if size(I, 3) > 1
I = sqrt(sum(I .^ 2, 3));
end
% Determine and scale to limits
[I limits] = rescale(I, limits);
if limits(1) == limits(2)
limits(2) = limits(1) + 1;
end
if reverseMap
% Invert after everything
I = 1 - I;
end
return
%% Index images
function [J limits num_vals] = index_im(I)
% Returns an index image
if size(I, 2) ~= 1
error('Index maps only work on single channel images');
end
J = round(I);
rescaled = any(abs(I - J) > 0.01);
if rescaled
% Appears not to be an index image. Rescale over 256 indices
m = min(I);
m = m * (1 - sign(m) * eps);
I = I - m;
I = I * (256 / max(I(:)));
J = ceil(I);
num_vals = 256;
elseif nargout > 2
% Output the number of values
J = J - (min(J) - 1);
num_vals = max(J);
end
% These colormaps don't have valid colorbars
limits = [];
return
%% Calculate principle components
function I = calc_prin_comps(I, numComps)
c = size(I, 3);
I = reshape(I, [], c);
if nargin < 2
numComps = c;
end
% Do SVD
[I S] = svd(I, 0);
% Calculate projection of data onto components
S = diag(S);
S = S(1:numComps)';
if exist('bsxfun', 'builtin')
I = bsxfun(@times, I(:,1:numComps), S);
else
I = I(:,1:numComps) .* S(ones(size(I, 1), 1, 'uint8'),:);
end
return
%% Demo function to show capabilities of sc
function demo
%% Demo gray & lack of border
figure; fig = gcf; Z = peaks(256); sc(Z);
display_text([...
' Lets take a standard, MATLAB, real-valued function:\n\n peaks(256)\n\n'...
' Calling:\n\n figure\n Z = peaks(256);\n sc(Z)\n\n'...
' gives (see figure). SC automatically scales intensity to fill the\n'...
' truecolor range of [0 1].\n\n'...
' If your figure isn''t docked, then the image will have no border, and\n'...
' will be magnified by an integer factor (in this case, 2) so that the\n'...
' image is a reasonable size.']);
%% Demo colour image display
figure(fig); clf;
load mandrill; mandrill = ind2rgb(X, map); sc(mandrill);
display_text([...
' That wasn''t so interesting. The default colormap is ''none'', which\n'...
' produces RGB images given a 3-channel input image, otherwise it produces\n'...
' a grayscale image. So calling:\n\n load mandrill\n'...
' mandrill = ind2rgb(X, map);\n sc(mandrill)\n\n gives (see figure).']);
%% Demo discretization
figure(fig); clf;
subplot(121); sc(Z, 'jet'); label(Z, 'sc(Z, ''jet'')');
subplot(122); imagesc(Z); axis image off; colormap(jet(64)); % Fix the fact we change the default depth
label(Z, 'imagesc(Z); axis image off; colormap(''jet'');');
display_text([...
' However, if we want to display intensity images in color we can use any\n'...
' of the MATLAB colormaps implemented (most of them) to give truecolor\n'...
' images. For example, to use ''jet'' simply call:\n\n'...
' sc(Z, ''jet'')\n\n'...
' The MATLAB alternative, shown on the right, is:\n\n'...
' imagesc(Z)\n axis equal off\n colormap(jet)\n\n'...
' which generates noticeable discretization artifacts.']);
%% Demo intensity colormaps
figure(fig); clf;
subplot(221); sc(Z, 'hsv'); label(Z, 'sc(Z, ''hsv'')');
subplot(222); sc(Z, 'colorcube'); label(Z, 'sc(Z, ''colorcube'')');
subplot(223); sc(Z, 'hicontrast'); label(Z, 'sc(Z, ''hicontrast'')');
subplot(224); sc(Z-round(Z), 'diff'); label(Z, 'sc(Z-round(Z), ''diff'')');
display_text([...
' There are several other intensity colormaps to choose from. Calling:\n\n'...
' help sc\n\n'...
' will give you a list of them. Here are several others demonstrated.']);
%% Demo saturation limits & colormap reversal
figure(fig); clf;
subplot(121); sc(Z, [0 max(Z(:))], '-hot'); label(Z, 'sc(Z, [0 max(Z(:))], ''-hot'')');
subplot(122); sc(mandrill, [-0.5 0.5]); label(mandrill, 'sc(mandrill, [-0.5 0.5])');
display_text([...
' SC can also rescale intensity, given an upper and lower bound provided\n'...
' by the user, and invert most colormaps simply by prefixing a ''-'' to the\n'...
' colormap name. For example:\n\n'...
' sc(Z, [0 max(Z(:))], ''-hot'');\n'...
' sc(mandrill, [-0.5 0.5]);\n\n'...
' Note that the order of the colormap and limit arguments are\n'...
' interchangable.']);
%% Demo prob
load gatlin;
gatlin = X;
figure(fig); clf; im = cat(3, abs(Z)', gatlin(1:256,end-255:end)); sc(im, 'prob');
label(im, 'sc(cat(3, prob, gatlin), ''prob'')');
display_text([...
' SC outputs the recolored data as a truecolor RGB image. This makes it\n'...
' easy to combine colormaps, either arithmetically, or by masking regions.\n'...
' For example, we could combine an image and a probability map\n'...
' arithmetically as follows:\n\n'...
' load gatlin\n'...
' gatlin = X(1:256,end-255:end);\n'...
' prob = abs(Z)'';\n'...
' im = sc(prob, ''hsv'') .* sc(prob, ''gray'') + sc(gatlin, ''rgb2gray'');\n'...
' sc(im, [-0.1 1.3]);\n\n'...
' In fact, that particular colormap has already been implemented in SC.\n'...
' Simply call:\n\n'...
' sc(cat(3, prob, gatlin), ''prob'');']);
%% Demo colorbar
colorbar;
display_text([...
' SC also makes possible the generation of a colorbar in the normal way, \n'...
' with all the colours and data values correct. Simply call:\n\n'...
' colorbar\n\n'...
' The colorbar doesn''t work with all colormaps, but when it does,\n'...
' inverting the colormap (using ''-map'') maintains the integrity of the\n'...
' colorbar (i.e. it works correctly) - unlike if you invert the input data.']);
%% Demo combine by masking
figure(fig); clf;
sc(Z, [0 max(Z(:))], '-hot', sc(Z-round(Z), 'diff'), Z < 0);
display_text([...
' It''s just as easy to combine generated images by masking too. Here''s an\n'...
' example:\n\n'...
' im = cat(4, sc(Z, [0 max(Z(:))], ''-hot''), sc(Z-round(Z), ''diff''));\n'...
' mask = repmat(Z < 0, [1 1 3]);\n'...
' mask = cat(4, mask, ~mask);\n'...
' im = sum(im .* mask, 4);\n'...
' sc(im)\n\n'...
' In fact, SC can also do this for you, by adding image/colormap and mask\n'...
' pairs to the end of the argument list, as follows:\n\n'...
' sc(Z, [0 max(Z(:))], ''-hot'', sc(Z-round(Z), ''diff''), Z < 0);\n\n'...
' A benefit of the latter approach is that you can still display a\n'...
' colorbar for the first colormap.']);
%% Demo user defined colormap
figure(fig); clf; sc(abs(Z), rand(10, 3)); colorbar;
display_text([...
' SC can also use user defined colormaps to display indexed images.\n'...
' These can be defined as a linear colormap. For example:\n\n'...
' sc(abs(Z), rand(10, 3))\n colorbar;\n\n'...
' Note that the colormap is automatically linearly interpolated.']);
%% Demo non-linear user defined colormap
figure(fig); clf; sc(abs(Z), [rand(10, 3) exp((1:10)/2)']); colorbar;
display_text([...
' Non-linear colormaps can also be defined by the user, by including the\n'...
' relative distance between the given colormap points on the colormap\n'...
' scale in the fourth column of the colormap matrix. For example:\n\n'...
' sc(abs(Z), [rand(10, 3) exp((1:10)/2)''])\n colorbar;\n\n'...
' Note that the colormap is still linearly interpolated between points.']);
%% Demo compress
load mri;
mri = D;
figure(fig); clf;
sc(squeeze(mri(:,:,:,1:6)), 'compress');
display_text([...
' SC has many colormaps for displaying multi-dimensional data, including\n'...
' ''flow'' for optic flow fields, ''phase'' for edge maps with phase, and\n'...
' ''stereo'' for generating anaglyphs.\n\n'...
' For images with more than 3 channels, SC can compress these images to RGB\n'...
' while maintaining the maximum amount of variance in the data. For\n'...
' example, this 6 channel image:\n\n'...
' load mri\n mri = D;\n sc(squeeze(mri(:,:,:,1:6), ''compress'')']);
%% Demo texture map
figure(fig); clf;
surf(Z, sc(Z, 'hicontrast'), 'edgecolor', 'none');
display_text([...
' Further benefits of SC outputting the image as an array (on top of being\n'...
' able to combine images) are that the image can be saved straight to disk\n'...
' using imwrite(), or can be used to texture map a surface, thus:\n\n'...
' tex = sc(Z, ''hicontrast'');\n'...
' surf(Z, tex, ''edgecolor'', ''none'');']);
%% Demo multiple images
close(fig); % Only way to get round loss of focus (bug?)
figure(fig); clf; sc(mri, 'bone');
display_text([...
' Finally, SC can process multiple images when passed in as a 4d array,\n'...
' either for export or for display. In the latter case, images are\n'...
' displayed as a montage of up to 12 images. For example:\n\n'...
' sc(mri, ''bone'')']);
display_text([...
' Any additional images can then be viewed by scrolling through them using\n'...
' using the scroll (arrow) keys. Try it and see.']);
clc; fprintf('End of demo.\n');
return
%% Some helper functions for the demo
function display_text(str)
clc;
fprintf([str '\n\n']);
fprintf('Press a key to go on.\n');
figure(gcf);
waitforbuttonpress;
return
function label(im, str)
text(size(im, 2)/2, size(im, 1)+12, str,...
'Interpreter', 'none', 'HorizontalAlignment', 'center', 'VerticalAlignment', 'middle');
return
|
github
|
amcorrigan/IA-Lab-master
|
rescale.m
|
.m
|
IA-Lab-master/Utilities/sc/private/rescale.m
| 1,613 |
utf_8
|
427de5e2419533818c74ea0c8fd7f773
|
function [B lims] = rescale(A, lims, out_lims)
%RESCALE Linearly rescale values in an array
%
% Examples:
% B = rescale(A)
% B = rescale(A, lims)
% B = rescale(A, lims, out_lims)
% [B lims] = rescale(A)
%
% Linearly rescales values in an array, saturating values outside limits.
%
% IN:
% A - Input array of any size and class.
% lims - 1x2 array of saturation limits to be used on A. Default:
% [min(A(:)) max(A(:))].
% out_lims - 1x2 array of output limits the values in lims are to be
% rescaled to. Default: [0 1].
%
% OUT:
% B - size(A) double array.
% lims - 1x2 array of saturation limits used on A. Equal to the input
% lims, if given.
% $Id: rescale.m,v 1.2 2009/04/05 15:09:11 ojw Exp $
% Copyright: Oliver Woodford, 2009
if nargin < 3
out_lims = [0 1];
end
if nargin < 2 || isempty(lims)
M = isfinite(A);
if ~any(reshape(M, numel(M), 1))
% All NaNs, Infs or -Infs
B = double(A > 0);
lims = [0 1];
else
lims = [min(A(M)) max(A(M))];
B = normalize(A, lims, out_lims);
end
clear M
else
B = normalize(A, lims, out_lims);
B = min(max(B, out_lims(1)), out_lims(2));
end
return
function B = normalize(A, lims, out_lims)
if lims(2) == lims(1) || out_lims(1) == out_lims(2)
B = zeros(size(A));
else
B = double(A);
if lims(1)
B = B - lims(1);
end
v = (out_lims(2) - out_lims(1)) / (lims(2) - lims(1));
if v ~= 1
B = B * v;
end
end
if out_lims(1)
B = B + out_lims(1);
end
return
|
github
|
amcorrigan/IA-Lab-master
|
sfm_local_chanvese.m
|
.m
|
IA-Lab-master/ThirdParty/lanktonchanvese/sfm_local_chanvese.m
| 2,172 |
utf_8
|
3a6307d657f860fcd0f80de155397eb3
|
% [seg Lz] = sfm_local_chanvese(img,mask,iterations,lambda,rad,display)
%
% img - any image (2D or 3D). color images will be
% converted to grayscale.
%
% mask - binary image representing initialization.
% (1's foreground, 0's background)
%
% iterations - number of iterations to run
%
% lambda - relative weighting of curve smoothness
% (lambda will ususally be between [0,1])
%
% rad - the radius of the ball used for localization
%
% display - whether or not to display intermediate results
%
% seg - binary map of resulting segmentation
% (1's foreground, 0's background)
%
% Lz - A list of the indexes of points on the zero level set.
%
% --------------------------------------
% written by Shawn Lankton (4/17/2009) - www.shawnlankton.com
%
function [seg Lz] = sfm_local_chanvese(img,mask,iterations,lam,rad,display)
% ensure mex is compiled
if(isempty(which('sfm_local_chanvese_mex')))
compile_sfm_local_chanvese
end
% check for color image and convert to grayscale
if(numel(size(img))==3) %if image is 3D
if(size(img,3)==3) %z dim is 3... probably color
img = rgb2gray(img);%rescale to grayscale
end
end
% mex is expecting img to be a double
img = double(img);
mask = double(mask);
if(any(size(img)~=size(mask)))
error('img and mask must be the same size');
end
% default value of iterations is 100
if(~exist('iterations','var'))
iterations = 100;
end
iterations = double(iterations);
% default value of lambda is 0.1
if(~exist('lam','var'))
lam = 0.1;
end
lam = double(lam);
% default value of rad is 10
if(~exist('rad','var'))
rad = 10;
end
rad = double(rad);
% default value of display is 1
if(~exist('display','var'))
display = 1;
end
display = double(display);
if(display)
clf;
imagesc(img);
end
% perform segmentation
[phi c] = sfm_local_chanvese_mex(img,mask,iterations,display,lam,rad);
% get labelmap from signed distance function
seg = phi<=0;
Lz = uint32(c)+1;
|
github
|
amcorrigan/IA-Lab-master
|
fat_contour.m
|
.m
|
IA-Lab-master/ThirdParty/lanktonchanvese/fat_contour.m
| 571 |
utf_8
|
d41a83dbdb50798bcf825109fc225bb8
|
% FAT_CONTOUR draw a easily visible contour
function [h1 h2] = fat_contour(phi,dashed,c1)
%Coded by: Shawn Lankton
%Function: Display a contour
c2 = 'k';
if(~exist('c1','var')) c1 = 'r'; end
if(~exist('dashed','var')) dashed = false; end
t1 = 4;
t2 = 2;
hold on;
if(dashed)
h1 = contour(phi,[0 0],c1,'linewidth',t1,'linestyle','--');
h2 = contour(phi,[0 0],c2,'linewidth',t2,'linestyle','--');
else
h1 = contour(phi,[0 0],c1,'linewidth',t1);
h2 = contour(phi,[0 0],c2,'linewidth',t2);
end
hold off;
end
|
github
|
amcorrigan/IA-Lab-master
|
AboutWound.m
|
.m
|
IA-Lab-master/Examples/Pellet/AboutWound.m
| 3,125 |
utf_8
|
e11339d283a2565d848bcb30104c1aa5
|
function varargout = AboutWound(varargin)
% ABOUTWOUND MATLAB code for AboutWound.fig
% ABOUTWOUND, by itself, creates a new ABOUTWOUND or raises the existing
% singleton*.
%
% H = ABOUTWOUND returns the handle to a new ABOUTWOUND or the handle to
% the existing singleton*.
%
% ABOUTWOUND('CALLBACK',hObject,eventData,handles,...) calls the local
% function named CALLBACK in ABOUTWOUND.M with the given input arguments.
%
% ABOUTWOUND('Property','Value',...) creates a new ABOUTWOUND or raises the
% existing singleton*. Starting from the left, property value pairs are
% applied to the GUI before AboutWound_OpeningFcn gets called. An
% unrecognized property name or invalid value makes property application
% stop. All inputs are passed to AboutWound_OpeningFcn via varargin.
%
% *See GUI Options on GUIDE's Tools menu. Choose "GUI allows only one
% instance to run (singleton)".
%
% See also: GUIDE, GUIDATA, GUIHANDLES
% Edit the above text to modify the response to help AboutWound
% Last Modified by GUIDE v2.5 12-Dec-2016 10:16:07
% Begin initialization code - DO NOT EDIT
gui_Singleton = 1;
gui_State = struct('gui_Name', mfilename, ...
'gui_Singleton', gui_Singleton, ...
'gui_OpeningFcn', @AboutWound_OpeningFcn, ...
'gui_OutputFcn', @AboutWound_OutputFcn, ...
'gui_LayoutFcn', [] , ...
'gui_Callback', []);
if nargin && ischar(varargin{1})
gui_State.gui_Callback = str2func(varargin{1});
end
if nargout
[varargout{1:nargout}] = gui_mainfcn(gui_State, varargin{:});
else
gui_mainfcn(gui_State, varargin{:});
end
% End initialization code - DO NOT EDIT
end
% --- Executes just before AboutWound is made visible.
function AboutWound_OpeningFcn(hObject, eventdata, handles, varargin)
% This function has no output args, see OutputFcn.
% hObject handle to figure
% eventdata reserved - to be defined in a future version of MATLAB
% handles structure with handles and user data (see GUIDATA)
% varargin command line arguments to AboutWound (see VARARGIN)
anImage = imread('pellet.png');
imshow(anImage, [], 'Parent', handles.axes1, 'InitialMagnification', 'fit');
set(handles.axes1,'xcolor','w','ycolor','w','xtick',[],'ytick',[]);
set(handles.figure1,'Name','About Pellet Explorer')
% Update handles structure
guidata(hObject, handles);
% UIWAIT makes YEAbout wait for user response (see UIRESUME)
% uiwait(handles.figure1);
end
% --- Outputs from this function are returned to the command line.
function varargout = AboutWound_OutputFcn(hObject, eventdata, handles)
% varargout cell array for returning output args (see VARARGOUT);
% hObject handle to figure
% eventdata reserved - to be defined in a future version of MATLAB
% handles structure with handles and user data (see GUIDATA)
% Get default command line output from handles structure
varargout = cell(nargout,1);
end
|
github
|
amcorrigan/IA-Lab-master
|
amcFillNaNs.m
|
.m
|
IA-Lab-master/Examples/Spheroid3D/utilities/amcFillNaNs.m
| 1,083 |
utf_8
|
58043bf2cbc8e1f285c575e09666201e
|
function outim = amcFillNaNs(im,blurScale,maxIts,initScale,epsilon)
% fill in NaNs by iteratively blurring from the edges
if nargin<2 || isempty(blurScale)
blurScale = max(1,0.01*min(size(im,1),size(im,2)));
end
if nargin<3 || isempty(maxIts)
maxIts = 40;
end
if nargin<4 || isempty(initScale)
initScale = 5*blurScale;
end
if nargin<5 || isempty(epsilon)
epsilon = 2e-2;
end
nanreg = isnan(im);
fim = gaussBlurNaNs(im,initScale,nanreg);
while nnz(isnan(fim))>0
fim = gaussBlurNaNs(fim,initScale);
end
outim = im;
outim(nanreg) = fim(nanreg);
for ii = 1:maxIts
fim = gaussFiltND(outim,blurScale*[1,1]);
if max(abs(fim(nanreg)-outim(nanreg))./outim(nanreg))<epsilon
outim(nanreg) = fim(nanreg);
break;
else
outim(nanreg) = fim(nanreg);
end
end
end
function fim = gaussBlurNaNs(im,lscale,bw)
if nargin<3 || isempty(bw)
bw = isnan(im);
end
im(bw) = 0;
num = gaussFiltND(im,lscale*[1,1],0);
denom = gaussFiltND(~bw,lscale*[1,1],0);
fim = num./denom;
end
|
github
|
amcorrigan/IA-Lab-master
|
bwdistsc.m
|
.m
|
IA-Lab-master/Examples/Spheroid3D/utilities/bwdistsc.m
| 18,385 |
utf_8
|
a8192c2781c7f03ef9cf7e9f0b91c769
|
function D=bwdistsc(bw,aspect)
% D=BWDISTSC(BW,ASPECT)
% BWDISTSC computes Euclidean distance transform of the binary 3D image
% BW. For each pixel in BW, the distance transform assignes a number
% that is the distance between that pixel and the nearest nonzero pixel
% of BW. BW may be a single 2D image, 3D array or a cell array of
% 2D slices. ASPECT is 3-component vector defining aspect ratio in
% the dataset BW. If ASPECT is not specified, isotropic aspect
% ratio [1 1 1] is assumed.
%
% BWDISTSC uses fast optimized scanning algorithm and cell-arrays to
% represent internal data, so that it is less demanding to physical
% memory. In many cases BWDISTSC is actually faster than MATLAB's
% optimized kd-tree algorithm used for Euclidean distance
% transform in 3D.
%
% BWDISTSC tries to use MATLAB bwdist for 2D scans if possible, which
% is significantly faster. Otherwise BWDISTSC uses internal algorithm
% to perform 2D scans.
%
% Yuriy Mishchenko JFRC HHMI Chklovskii Lab JUL 2007
% This code is free for use or modifications, just please give credit
% where appropriate. And if you modify code or fix bugs, please drop
% me a message at [email protected].
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
% Scan algorithms below use following Lema: %
% LEMA: let F(X,z) be lower envelope of a family of parabola: %
% F(X,z)=min_{i} [G_i(X)+(z-k_i)^2]; %
% and let H_k(X,z)=A(X)+(z-k)^2 be a parabola. %
% Then for H_k(X,z)==F(X,z) at each X there exist at most %
% two solutions k1<k2 such that H_k12(X,z)=F(X,z), and %
% H_k(X,z)<F(X,z) is restricted to at most k1<k2. %
% Here X is any-dimensional coordinate. %
% %
% Thus, simply scan away from any z such that H_k(X,z)<F(X,z) %
% in either direction as long as H_k(X,z)<F(X,z) and update %
% F(X,z). Note that need to properly choose starting point; %
% starting point is any z such that H_k(X,z)<F(X,z); z==k is %
% usually, but not always the starting point!!! %
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
% parse inputs
if(nargin<2 || isempty(aspect)) aspect=[1 1 1]; end
% determine geometry of data
if(iscell(bw)) shape=[size(bw{1}),length(bw)]; else shape=size(bw); end
% fix to handle 1D & 2D images
if(length(shape)<3) shape(length(shape)+1:3)=1; end
if(length(aspect)<3) aspect(length(aspect)+1:3)=1; end
% allocate space
D=cell(1,shape(3)); for k=1:shape(3) D{k}=zeros(shape(1:2)); end
%%%%%%%%%%%%% scan along XY %%%%%%%%%%%%%%%%
for k=1:shape(3)
if(iscell(bw)) bwXY=bw{k}; else bwXY=bw(:,:,k); end
% initialize arrays
DXY=zeros(shape(1:2));
D1=zeros(shape(1:2));
DK=zeros(shape(1:2));
% if can, use 2D bwdist from image processing toolbox
if(exist('bwdist') && aspect(1)==aspect(2))
D1=aspect(1)^2*bwdist(bwXY).^2;
else % if not, use full XY-scan
%%%%%%%%%%%%%%% X-SCAN %%%%%%%%%%%%%%%
% reference nearest bwXY "on"-pixel in x direction downward:
% scan bottow-up, copy x-reference from previous row unless
% there is bwXY "on"-pixel in that point in current row
xlower=repmat(Inf,shape(1:2));
xlower(1,find(bwXY(1,:)))=1; % fill in first row
for i=2:shape(1)
xlower(i,:)=xlower(i-1,:); % copy previous row
xlower(i,find(bwXY(i,:)))=i;% unless there is pixel
end
% reference nearest bwXY "on"-pixel in x direction upward:
xupper=repmat(Inf,shape(1:2));
xupper(end,find(bwXY(end,:)))=shape(1);
for i=shape(1)-1:-1:1
xupper(i,:)=xupper(i+1,:);
xupper(i,find(bwXY(i,:)))=i;
end
% find points for which distance needs to be updated
idx=find(~bwXY); [x,y]=ind2sub(shape(1:2),idx);
% set distance as the shortest to upward or to downward
DXY(idx)=aspect(1)^2*min((x-xlower(idx)).^2,(x-xupper(idx)).^2);
%%%%%%%%%%%%%%% Y-SCAN %%%%%%%%%%%%%%%
% this will be the envelop
% envelop is initialized at Inf to ensure single scan direction,
% otherwise may end up in infinite loop when trying to find
% starting point
D1=repmat(Inf,shape(1:2));
% these will be the references to parabolas defining the envelop
DK=repmat(Inf,shape(1:2));
% starting points
i0=zeros(shape(1),1);
% convenience x-coords array
x=(1:shape(1))';
for i=1:shape(2)
% need to select starting point for each X:
% * starting point should be below current envelop
% * i0==i is not necessarily a starting point
% * there is at most one starting point
% * there may be no starting point
% i0 is the starting points for each X: i0(X) is the first
% y-index such that parabola from line i is below the envelop
% first guess is the current y-line
i0(:)=i;
% some auxiliary datasets
d0=DXY(:,i);
% L0 indicates for which X starting point had been fixed
L0=isinf(d0) | (d0==0);
while(~isempty(find(~L0,1)))
% reference starting points in DXY
idx=sub2ind(shape(1:2),x(~L0),i0(~L0));
% reduce out trivial points (DXY==0)
L=(DXY(idx)==0);
L0(~L0)=L;
idx=idx(~L);
if(isempty(idx)) continue; end
% these are current best parabolas for starting points
ik=DK(idx);
% these are new values from parabola from line #i
dtmp=d0(~L0)+aspect(2)^2*(i0(~L0)-i).^2;
% these starting points are OK - below the envelop
L=D1(idx)>dtmp; D1(idx(L))=dtmp(L);
% points which are still above the envelop but ik==i0,
% will not get any better, so fix them as well
L=L | (ik==i0(~L0));
% all other points are not OK, need new starting point:
% starting point should be at least below parabola
% beating us at current choice of i0
% solve quadratic equation to find where this happens
ik=(ik-i);
di=(D1(idx(~L))-dtmp(~L))./ik(~L)/2/aspect(2)^2;
% should select next highest index to the equality
di=fix(di)+sign(di);
% the new starting points
idx=find(~L0);
i0(idx(~L))=i0(idx(~L))+di;
% update L0 to indicate which points we've fixed
L0(~L0)=L; L0(idx(~L))=(di==0);
% points that went out of boundaries can't get better;
% fix them as well
idx=idx(~L);
idx=idx((i0(idx)<1) | (i0(idx)>shape(2)));
i0(idx)=i;
L0(idx)=1;
end
% reduce out trivial points DXY(idx)<DXY(:,i)
idx=sub2ind(shape(1:2),x,i0);
L=(DXY(idx)>0) | (i0==i);
idx=idx(L);
% these will keep track along which X should
% keep updating distances
map_lower=L;
map_upper=L;
idx_lower=idx;
idx_upper=idx;
% set trivial pixels D==0 in line #i:
% this has to be done b/s we manually discarded them from L0
D1(d0==0,i)=0;
% scan from starting points for each X,i0 in increments of 1
di=0; % distance from current y-line
eols=2; % end-of-line-scan flag
totlen=prod(shape(1:2));
while(eols)
eols=2;
di=di+1;
% select X which can be updated for di<0;
% i.e. X which had been below envelop all way till now
if(~isempty(idx_lower))
% shift y by -1
idx_lower=idx_lower-shape(1);
% prevent index dropping below 1st
L=(idx_lower>=1);
map_lower(map_lower)=L;
idx_lower=idx_lower(L);
if(~isempty(idx_lower))
dtmp=d0(map_lower)+...
aspect(2)^2*(i0(map_lower)-di-i).^2;
% these pixels are to be updated with i0-di
L=D1(idx_lower)>dtmp & DXY(idx_lower)>0;
map_lower(map_lower)=L;
idx_lower=idx_lower(L);
D1(idx_lower)=dtmp(L);
DK(idx_lower)=i;
end
else % if this is empty, get ready to quit
eols=eols-1;
end
% select X which can be updated for di>0;
% i.e. X which had been below envelop all way till now
if(~isempty(idx_upper))
% shift y by +1
idx_upper=idx_upper+shape(1);
% prevent index from going over array limits
L=(idx_upper<=totlen);
map_upper(map_upper)=L;
idx_upper=idx_upper(L);
if(~isempty(idx_upper))
dtmp=d0(map_upper)+...
aspect(2)^2*(i0(map_upper)+di-i).^2;
% check which pixels are to be updated with i0+di
L=D1(idx_upper)>dtmp & DXY(idx_upper)>0;
map_upper(map_upper)=L;
idx_upper=idx_upper(L);
D1(idx_upper)=dtmp(L);
DK(idx_upper)=i;
end
else % if this is empty, get ready to quit
eols=eols-1;
end
end
end
end
D{k}=D1;
end
%%%%%%%%%%%%% scan along Z %%%%%%%%%%%%%%%%
% this will be the envelop:
% envelop has to be initialized at Inf to ensure single direction of scan,
% otherwise may end up in infinite loop when trying to find starting point
D1=cell(size(D));
for k=1:shape(3) D1{k}=repmat(Inf,shape(1:2)); end
% these will be the references to parabolas defining the envelop
DK=cell(size(D));
for k=1:shape(3) DK{k}=repmat(Inf,shape(1:2)); end
% start building the envelope
for k=1:shape(3)
% need to select starting point for each X:
% * starting point should be below current envelop
% * k0==k is not necessarily a starting point
% * there may be no starting point
% k0 is the starting points for each XY: k0(XY) is the first
% z-index such that parabola from line k is below the envelop
% initial starting point guess is current slice
k0=repmat(k,shape(1:2));
% L0 indicates which starting points had been fixed
L0=isinf(D{k}) | (D{k}==0);
idxtot=find(~L0);
while(~isempty(idxtot))
% because of using cells need to explicitly scan in Z
% to avoid repetitious searches in k0, parse first
ss=getregions(k0(idxtot));
sslen=length(ss);
for kk=1:sslen
% these are starting points @kk which had not been set
idx=idxtot(ss(kk).PixelIdxList);
% reduce out trivial points (D==0)
if(kk~=k)
L=(D{kk}(idx)==0);
L0(idx)=L;
idx=idx(~L);
end
if(isempty(idx)) continue; end
% these are currently best parabolas for slice kk
ik=DK{kk}(idx);
% these are new values for slice kk from parabola from k
dtmp=D{k}(idx)+aspect(3)^2*(kk-k)^2;
% these points are OK - below current envelop
L=D1{kk}(idx)>dtmp; D1{kk}(idx(L))=dtmp(L);
% these points are not OK, but since ik==k0
% can't get any better
L=L | (ik==kk);
% all other points are not OK, need new starting point:
% starting point should be at least below parabola
% beating us at current choice of k0
% solve quadratic equation to find where this happens
ik=(ik-k);
dk=(D1{kk}(idx(~L))-dtmp(~L))./ik(~L)/2/aspect(3)^2;
dk=fix(dk)+sign(dk);
k0(idx(~L))=k0(idx(~L))+dk;
% update starting points that had been set
L0(idx)=L;
L0(idx(~L))=(dk==0);
% points that went out of boundaries can't get better
idx=idx(~L);
idx=idx((k0(idx)<1) | (k0(idx)>shape(3)));
L0(idx)=1;
k0(idx)=k;
end
idxtot=find(~L0);
end
% map_lower/map_upper keeps track of which pixels can be yet updated
% with new distance, i.e. all such XY that had been below envelop for
% all dk up to now for dk<0/dk>0 respectively
map_lower=true(shape(1:2));
map_upper=true(shape(1:2));
% parse different values in k0 to avoid repetitious searching below
ss=getregions(k0);
sslen=length(ss);
% reduce out trivially faulty starting points
for kk=1:sslen
if(kk==k) continue; end
idx=ss(kk).PixelIdxList;
L=D{kk}(idx)>D{k}(idx);
map_lower(idx)=L;
map_upper(idx)=L;
end
% these are maintained to keep fast track of whether maps are empty
idx_lower=find(map_lower);
idx_upper=find(map_upper);
% set trivial pixels D==0 in slice k:
% this has to be done b/s we manually discarded them from L0
D1{k}(D{k}==0)=0;
% scan away from starting points in increments of 1
dk=0; % distance from current xy-slice
eols=2; % end-of-scan flag
while(eols)
eols=2;
dk=dk+1;
if(~isempty(idx_lower))
% prevent index from going over the boundaries
L=(k0(map_lower)-dk>=1);
map_lower(map_lower)=L;
% need to explicitly scan in Z because of using cell-arrays
for kk=1:sslen-dk
% get all XY such that k0-dk==kk
idx=ss(kk+dk).PixelIdxList;
L=map_lower(idx);
idx=idx(L);
if(~isempty(idx))
dtmp=D{k}(idx)+aspect(3)^2*(kk-k)^2;
% these pixels are to be updated with k0-dk
L=D1{kk}(idx)>dtmp & D{kk}(idx)>0;
map_lower(idx)=L;
D1{kk}(idx(L))=dtmp(L);
% ridiculously, but this is faster than
% direct assignment
dtmp=idx(L);
dtmp(:)=k;
DK{kk}(idx(L))=k;
end
end
idx_lower=idx_lower(map_lower(idx_lower));
else
eols=eols-1;
end
if(~isempty(idx_upper))
% prevent index from going over the boundaries
L=(k0(map_upper)+dk<=shape(3));
map_upper(map_upper)=L;
% need to explicitly scan in Z because of using cell-arrays
for kk=dk+1:min(shape(3),sslen+dk)
% get all XY such that k0+dk==kk
idx=ss(kk-dk).PixelIdxList;
L=map_upper(idx);
idx=idx(L);
if(~isempty(idx))
dtmp=D{k}(idx)+aspect(3)^2*(kk-k)^2;
% these pixels are to be updated with k0+dk
L=D1{kk}(idx)>dtmp & D{kk}(idx)>0;
map_upper(idx)=L;
D1{kk}(idx(L))=dtmp(L);
dtmp=idx(L);
dtmp(:)=k;
DK{kk}(idx(L))=dtmp;
end
end
idx_upper=idx_upper(map_upper(idx_upper));
else
eols=eols-1;
end
end
end
% the answer
if(iscell(bw))
D=cell(size(bw));
for k=1:shape(3) D{k}=sqrt(D1{k}); end
else
D=zeros(shape);
for k=1:shape(3) D(:,:,k)=sqrt(D1{k}); end
end
function s=getregions(map)
% this function is replacer for regionprops(map,'PixelIdxList');
% it produces the list of different values along with list of
% indexes of pixels in map with these values; 's' is struct-array
% such that s(i).PixelIdxList contains list of pixels in map
% with value i.
% enable using regionprops if available, faster on 7.3
fregionprops=1;
% version control for using regionprops
v=version; v=str2num(v(1:3));
fregionprops=fregionprops & v>=7.3;
% in later matlab regionprops is actually faster than this code
if(exist('regionprops') & fregionprops)
s=regionprops(map,'PixelIdxList');
return
end
idx=(1:prod(size(map)))';
dtmp=double(map(:));
[dtmp,ind]=sort(dtmp);
idx=idx(ind);
ind=[0;find([diff(dtmp(:));1])];
s=[];
for i=2:length(ind)
if(dtmp(ind(i)))==0 continue; end
s(dtmp(ind(i))).PixelIdxList=idx(ind(i-1)+1:ind(i));
end
|
github
|
amcorrigan/IA-Lab-master
|
nuclearPropertiesFunctionTest.m
|
.m
|
IA-Lab-master/Tests/nuclearPropertiesFunctionTest.m
| 693 |
utf_8
|
ba0a6abfb01ff7b5766b72580e174ee8
|
function tests = nuclearPropertiesFunctionTest
tests = functiontests(localfunctions);
end
function setupOnce(testCase)
parentfolder = fileparts(which('nuclearPropertiesWorkflow.m'));
parser = ParserYokogawa(fullfile(parentfolder,'AssayPlate'));
testCase.TestData.Workflow = nuclearPropertiesWorkflow('tempoutput',parser);
end
function testReproducibleStats(testCase)
imobj = testCase.TestData.Workflow.BatchParser.ParserObj.getAC2DObj('well','E03');
testCase.verifyTrue(iscell(imobj));
testCase.verifyEqual(numel(imobj),1,'Should be 1 image object returned');
imdata = imobj{1}.getDataC2D();
testCase.verifyEqual(numel(imdata),3,'Should be 3 channels');
end
|
github
|
amcorrigan/IA-Lab-master
|
YEAbout.m
|
.m
|
IA-Lab-master/YokoV2/YEAbout.m
| 3,650 |
utf_8
|
80021317baece190475f4d64bdddfe24
|
function varargout = YEAbout(varargin)
% YEABOUT MATLAB code for YEAbout.fig
% YEABOUT, by itself, creates a new YEABOUT or raises the existing
% singleton*.
%
% H = YEABOUT returns the handle to a new YEABOUT or the handle to
% the existing singleton*.
%
% YEABOUT('CALLBACK',hObject,eventData,handles,...) calls the local
% function named CALLBACK in YEABOUT.M with the given input arguments.
%
% YEABOUT('Property','Value',...) creates a new YEABOUT or raises the
% existing singleton*. Starting from the left, property value pairs are
% applied to the GUI before YEAbout_OpeningFcn gets called. An
% unrecognized property name or invalid value makes property application
% stop. All inputs are passed to YEAbout_OpeningFcn via varargin.
%
% *See GUI Options on GUIDE's Tools menu. Choose "GUI allows only one
% instance to run (singleton)".
%
% See also: GUIDE, GUIDATA, GUIHANDLES
% Edit the above text to modify the response to help YEAbout
% Last Modified by GUIDE v2.5 14-Oct-2016 13:34:02
% Begin initialization code - DO NOT EDIT
gui_Singleton = 1;
gui_State = struct('gui_Name', mfilename, ...
'gui_Singleton', gui_Singleton, ...
'gui_OpeningFcn', @YEAbout_OpeningFcn, ...
'gui_OutputFcn', @YEAbout_OutputFcn, ...
'gui_LayoutFcn', [] , ...
'gui_Callback', []);
if nargin && ischar(varargin{1})
gui_State.gui_Callback = str2func(varargin{1});
end
if nargout
[varargout{1:nargout}] = gui_mainfcn(gui_State, varargin{:});
else
gui_mainfcn(gui_State, varargin{:});
end
% End initialization code - DO NOT EDIT
end
% --- Executes just before YEAbout is made visible.
function YEAbout_OpeningFcn(hObject, eventdata, handles, varargin)
% This function has no output args, see OutputFcn.
% hObject handle to figure
% eventdata reserved - to be defined in a future version of MATLAB
% handles structure with handles and user data (see GUIDATA)
% varargin command line arguments to YEAbout (see VARARGIN)
%_______________________________________________
% change Yinhai Icon
% % jFrame = get(hObject,'JavaFrame');
% % jIcon = javax.swing.ImageIcon('\\UK-Image-01\IAGroup\SB\2016\Yoko\Source Code\Artworks\icon_48.png');
% % jFrame.setFigureIcon(jIcon);
% commented this out until any conflict with the licensing agreement is
% clarified
% this isn't necessary, everything is stored in handles
% hAxes = findobj('Tag', 'AxesAbout');
% anImage = imread('\\UK-Image-01\IAGroup\SB\2016\Yoko\Source Code\Artworks\panel.png');
anImage = imread('IALab.png');
imshow(anImage, [], 'Parent', handles.AxesAbout, 'InitialMagnification', 'fit');
set(handles.AxesAbout,'xcolor','w','ycolor','w','xtick',[],'ytick',[]);
set(handles.figure1,'Name','About IALab')
% Update handles structure
guidata(hObject, handles);
% UIWAIT makes YEAbout wait for user response (see UIRESUME)
% uiwait(handles.figure1);
end
% --- Outputs from this function are returned to the command line.
function varargout = YEAbout_OutputFcn(hObject, eventdata, handles)
% varargout cell array for returning output args (see VARARGOUT);
% hObject handle to figure
% eventdata reserved - to be defined in a future version of MATLAB
% handles structure with handles and user data (see GUIDATA)
% Get default command line output from handles structure
varargout = cell(nargout,1);
end
|
github
|
amcorrigan/IA-Lab-master
|
gaussFiltND.m
|
.m
|
IA-Lab-master/Filters/gaussFiltND.m
| 1,751 |
utf_8
|
37578851d6366b2c6b5ba79f53e5a72c
|
function fim = gaussFiltND(im,frad,boundcon,relsiz)
% N-dimensional Gaussian filtering
% This works by permuting the image rather than the
% kernel so that the filtering is always done along the first dimension,
% which seems to be faster for some reason.
if nargin<4 || isempty(relsiz)
relsiz = 6; % size of the filter relative to the Gaussian radius
end
if nargin<3 || isempty(boundcon)
boundcon = 'replicate';
end
if ~isa(im,'double')
im = double(im);
end
% the number of elements of frad explicitly tells us how many dimensions we
% want to filter, so a scalar would mean only the x-dimension is filtered
siz = odd(relsiz.*frad,'up'); % element-wise in case we've specified different relative sizes in each dimension..
% need to work out which dimensions are to be permuted
totdim = numel(size(im)); % assume we won't be daft enough to use this function for low dimensional images..
ndim = numel(frad);
% allow a filter radius of zero to specify no filtering
pvect = 1:totdim;
pvect(1:ndim) = [ndim,1:(ndim-1)];
fim = im;
% work in reverse order
for ii = ndim:-1:1
fim = permute(fim,pvect);
if frad(ii)>0
n = (0.55:0.1:(siz(ii)+0.45))';
m = (1+siz(ii))/2;
temp1 = exp(-((n-m).^2)/(2*frad(ii)^2));
kk = sum(reshape(temp1,[10,numel(temp1)/10]),1)';
kk = kk/sum(kk);
fim = imfilter(fim,kk,boundcon);
end
end
end
function out = odd(x,direction)
if nargin<2
direction = 'up';
end
if ~ischar(direction)
if direction>0
direction = 'up';
else
direction = 'down';
end
end
switch direction
case 'up'
out = ceil((x + 1)/2)*2 - 1;
case 'down'
out = floor((x + 1)/2)*2 - 1;
end
end
|
github
|
amcorrigan/IA-Lab-master
|
amcBilateral2D.m
|
.m
|
IA-Lab-master/Filters/amcBilateral2D.m
| 5,348 |
utf_8
|
c9c7a1e74c52e78500f4ee6e81555d70
|
function fim = amcBilateral2D(im,rdata,sxy,sr,rbins,xydsc)
% fast bilateral filtering, taking advantage of MATLAB's efficiency of
% array indexing
% Adam Corrigan
% if the normalization for r-binning is done only on rg without changing
% im, we don't have to scale then rescale at the end..
% first thing to do is create a 3D image of im separated by intensity
if nargin<4 || isempty(rbins)
rbins = 10;
end
if nargin<5 || isempty(xydsc)
xydsc = 2; % this should really be related to the size of the xy filter
end
if isscalar(xydsc)
xydsc = xydsc*[1,1];
end
if isempty(rdata)
minim = double(min(im(:)));
maxim = double(max(im(:)));
rg = ceil(rbins*(double(im)-minim)/(maxim-minim));
else
minim = double(min(rdata(:)));
maxim = double(max(rdata(:)));
rg = ceil(rbins*(double(rdata)-minim)/(maxim-minim));
end
rg(rg==0) = 1;
rg(rg>rbins) = rbins;
[xx,yy] = amcMakeGrid(im);
insiz = [size(im,1),size(im,2),rbins];
outsiz = ceil(insiz./[xydsc,1]);
if numel(sxy)==1
sxy = [1,1]*sxy;
end
% width of the z-kernel
sb = sr*rbins;
% width of the xy-kernel in downscaled units
scxy = sxy./xydsc;
% % linind = amcSub2Ind(insiz,[xx(:),yy(:),rg(:)]);
loutind = amcSub2Ind(outsiz,[ceil([xx(:),yy(:)]./(ones(numel(xx),1)*xydsc)),rg(:)]);
% % num3 = zeros(size(im,1),size(im,2),rbins);
% % denom3 = zeros(size(num3));
% %
% % for ii = 1:rbins
% % ntemp = zeros(size(im));
% % dtemp = zeros(size(im));
% % ntemp(rg==ii) = im(rg==ii);
% % dtemp(rg==ii) = 1;
% %
% % num3(:,:,ii) = ntemp;
% % denom3(:,:,ii) = dtemp;
% % end
% % d3 = zeros(insiz);
% % n3 = zeros(insiz);
% % d3(linind) = 1;
% % n3(linind) = im(:);
% have to use the 'in' indices here because we may have duplicates in the
% 'out' indices and they need to be summed.
% The two lines below take half the total running time, can we find a
% better way? Perhaps accumarray?
% % scd = blocksum(d3,[xydsc,xydsc,1],1);
% % scn = blocksum(n3,[xydsc,xydsc,1],1);
% This can't deal with NaNs..
% scd = reshape(accumarray(loutind,ones(size(loutind)),[prod(outsiz),1]),outsiz);
% scn = reshape(accumarray(loutind,im(:),[prod(outsiz),1]),outsiz);
inds = ~isnan(im);
scd = reshape(accumarray(loutind(inds),ones(nnz(inds),1),[prod(outsiz),1]),outsiz);
scn = reshape(accumarray(loutind(inds),im(inds),[prod(outsiz),1]),outsiz);
% the rest of the running time is the actual filtering, which might be
% improved
% % fi = dog3split2([scxy,sb]);
% % fnum = gauss3filt(scn,fi);
% % fdenom = gauss3filt(scd,fi);
fnum = gaussFiltND(scn,[scxy,sb]);
fdenom = gaussFiltND(scd,[scxy,sb]);
fim = zeros(insiz(1:2));
fim(inds) = fnum(loutind(inds))./fdenom(loutind(inds));
end
function [x,y,z] = amcMakeGrid(im)
% makegrid (because it uses ndgrid) can be very memory intensive (the
% problem seems to be the permute command (line 48 of ndgrid)
% Do something about this
if numel(im)>3
ss = size(im);
else
ss = im;
end
if numel(ss)==1
ss = ss*ones(1,nargout);
end
if numel(ss)==2 && nargout>2
ss = [ss,1];
end
switch length(ss)
case 2
% [x,y] = ndgrid(1:ss(1),1:ss(2));
x = repmat((1:ss(1))',[1 ss(2)]);
y = repmat((1:ss(2)),[ss(1) 1]);
z = ones(size(x));
case 3
% [x,y,z] = ndgrid(1:ss(1),1:ss(2),1:ss(3));
x = repmat((1:ss(1))',[1 ss(2) ss(3)]);
y = repmat((1:ss(2)),[ss(1) 1 ss(3)]);
z = repmat(permute((1:ss(3)),[1 3 2]),[ss(1) ss(2) 1]);
end
end
function fim = gaussFiltND(im,frad,boundcon,relsiz)
% N-dimensional Gaussian filtering
% This works by permuting the image rather than the
% kernel so that the filtering is always done along the first dimension,
% which seems to be faster for some reason.
if nargin<4 || isempty(relsiz)
relsiz = 6; % size of the filter relative to the Gaussian radius
end
if nargin<3 || isempty(boundcon)
boundcon = 'replicate';
end
if ~isa(im,'double')
im = double(im);
end
% the number of elements of frad explicitly tells us how many dimensions we
% want to filter, so a scalar would mean only the x-dimension is filtered
siz = odd(relsiz.*frad,'up'); % element-wise in case we've specified different relative sizes in each dimension..
% need to work out which dimensions are to be permuted
totdim = numel(size(im)); % assume we won't be daft enough to use this function for low dimensional images..
ndim = numel(frad);
% allow a filter radius of zero to specify no filtering
pvect = 1:totdim;
pvect(1:ndim) = [ndim,1:(ndim-1)];
fim = im;
% work in reverse order
for ii = ndim:-1:1
fim = permute(fim,pvect);
if frad(ii)>0
n = (0.55:0.1:(siz(ii)+0.45))';
m = (1+siz(ii))/2;
temp1 = exp(-((n-m).^2)/(2*frad(ii)^2));
kk = sum(reshape(temp1,[10,numel(temp1)/10]),1)';
kk = kk/sum(kk);
fim = imfilter(fim,kk,boundcon);
end
end
end
function out = odd(x,direction)
if nargin<2
direction = 'up';
end
if ~ischar(direction)
if direction>0
direction = 'up';
else
direction = 'down';
end
end
switch direction
case 'up'
out = ceil((x + 1)/2)*2 - 1;
case 'down'
out = floor((x + 1)/2)*2 - 1;
end
end
|
github
|
amcorrigan/IA-Lab-master
|
bwdistsc.m
|
.m
|
IA-Lab-master/Filters/bwdistsc.m
| 18,385 |
utf_8
|
a8192c2781c7f03ef9cf7e9f0b91c769
|
function D=bwdistsc(bw,aspect)
% D=BWDISTSC(BW,ASPECT)
% BWDISTSC computes Euclidean distance transform of the binary 3D image
% BW. For each pixel in BW, the distance transform assignes a number
% that is the distance between that pixel and the nearest nonzero pixel
% of BW. BW may be a single 2D image, 3D array or a cell array of
% 2D slices. ASPECT is 3-component vector defining aspect ratio in
% the dataset BW. If ASPECT is not specified, isotropic aspect
% ratio [1 1 1] is assumed.
%
% BWDISTSC uses fast optimized scanning algorithm and cell-arrays to
% represent internal data, so that it is less demanding to physical
% memory. In many cases BWDISTSC is actually faster than MATLAB's
% optimized kd-tree algorithm used for Euclidean distance
% transform in 3D.
%
% BWDISTSC tries to use MATLAB bwdist for 2D scans if possible, which
% is significantly faster. Otherwise BWDISTSC uses internal algorithm
% to perform 2D scans.
%
% Yuriy Mishchenko JFRC HHMI Chklovskii Lab JUL 2007
% This code is free for use or modifications, just please give credit
% where appropriate. And if you modify code or fix bugs, please drop
% me a message at [email protected].
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
% Scan algorithms below use following Lema: %
% LEMA: let F(X,z) be lower envelope of a family of parabola: %
% F(X,z)=min_{i} [G_i(X)+(z-k_i)^2]; %
% and let H_k(X,z)=A(X)+(z-k)^2 be a parabola. %
% Then for H_k(X,z)==F(X,z) at each X there exist at most %
% two solutions k1<k2 such that H_k12(X,z)=F(X,z), and %
% H_k(X,z)<F(X,z) is restricted to at most k1<k2. %
% Here X is any-dimensional coordinate. %
% %
% Thus, simply scan away from any z such that H_k(X,z)<F(X,z) %
% in either direction as long as H_k(X,z)<F(X,z) and update %
% F(X,z). Note that need to properly choose starting point; %
% starting point is any z such that H_k(X,z)<F(X,z); z==k is %
% usually, but not always the starting point!!! %
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
% parse inputs
if(nargin<2 || isempty(aspect)) aspect=[1 1 1]; end
% determine geometry of data
if(iscell(bw)) shape=[size(bw{1}),length(bw)]; else shape=size(bw); end
% fix to handle 1D & 2D images
if(length(shape)<3) shape(length(shape)+1:3)=1; end
if(length(aspect)<3) aspect(length(aspect)+1:3)=1; end
% allocate space
D=cell(1,shape(3)); for k=1:shape(3) D{k}=zeros(shape(1:2)); end
%%%%%%%%%%%%% scan along XY %%%%%%%%%%%%%%%%
for k=1:shape(3)
if(iscell(bw)) bwXY=bw{k}; else bwXY=bw(:,:,k); end
% initialize arrays
DXY=zeros(shape(1:2));
D1=zeros(shape(1:2));
DK=zeros(shape(1:2));
% if can, use 2D bwdist from image processing toolbox
if(exist('bwdist') && aspect(1)==aspect(2))
D1=aspect(1)^2*bwdist(bwXY).^2;
else % if not, use full XY-scan
%%%%%%%%%%%%%%% X-SCAN %%%%%%%%%%%%%%%
% reference nearest bwXY "on"-pixel in x direction downward:
% scan bottow-up, copy x-reference from previous row unless
% there is bwXY "on"-pixel in that point in current row
xlower=repmat(Inf,shape(1:2));
xlower(1,find(bwXY(1,:)))=1; % fill in first row
for i=2:shape(1)
xlower(i,:)=xlower(i-1,:); % copy previous row
xlower(i,find(bwXY(i,:)))=i;% unless there is pixel
end
% reference nearest bwXY "on"-pixel in x direction upward:
xupper=repmat(Inf,shape(1:2));
xupper(end,find(bwXY(end,:)))=shape(1);
for i=shape(1)-1:-1:1
xupper(i,:)=xupper(i+1,:);
xupper(i,find(bwXY(i,:)))=i;
end
% find points for which distance needs to be updated
idx=find(~bwXY); [x,y]=ind2sub(shape(1:2),idx);
% set distance as the shortest to upward or to downward
DXY(idx)=aspect(1)^2*min((x-xlower(idx)).^2,(x-xupper(idx)).^2);
%%%%%%%%%%%%%%% Y-SCAN %%%%%%%%%%%%%%%
% this will be the envelop
% envelop is initialized at Inf to ensure single scan direction,
% otherwise may end up in infinite loop when trying to find
% starting point
D1=repmat(Inf,shape(1:2));
% these will be the references to parabolas defining the envelop
DK=repmat(Inf,shape(1:2));
% starting points
i0=zeros(shape(1),1);
% convenience x-coords array
x=(1:shape(1))';
for i=1:shape(2)
% need to select starting point for each X:
% * starting point should be below current envelop
% * i0==i is not necessarily a starting point
% * there is at most one starting point
% * there may be no starting point
% i0 is the starting points for each X: i0(X) is the first
% y-index such that parabola from line i is below the envelop
% first guess is the current y-line
i0(:)=i;
% some auxiliary datasets
d0=DXY(:,i);
% L0 indicates for which X starting point had been fixed
L0=isinf(d0) | (d0==0);
while(~isempty(find(~L0,1)))
% reference starting points in DXY
idx=sub2ind(shape(1:2),x(~L0),i0(~L0));
% reduce out trivial points (DXY==0)
L=(DXY(idx)==0);
L0(~L0)=L;
idx=idx(~L);
if(isempty(idx)) continue; end
% these are current best parabolas for starting points
ik=DK(idx);
% these are new values from parabola from line #i
dtmp=d0(~L0)+aspect(2)^2*(i0(~L0)-i).^2;
% these starting points are OK - below the envelop
L=D1(idx)>dtmp; D1(idx(L))=dtmp(L);
% points which are still above the envelop but ik==i0,
% will not get any better, so fix them as well
L=L | (ik==i0(~L0));
% all other points are not OK, need new starting point:
% starting point should be at least below parabola
% beating us at current choice of i0
% solve quadratic equation to find where this happens
ik=(ik-i);
di=(D1(idx(~L))-dtmp(~L))./ik(~L)/2/aspect(2)^2;
% should select next highest index to the equality
di=fix(di)+sign(di);
% the new starting points
idx=find(~L0);
i0(idx(~L))=i0(idx(~L))+di;
% update L0 to indicate which points we've fixed
L0(~L0)=L; L0(idx(~L))=(di==0);
% points that went out of boundaries can't get better;
% fix them as well
idx=idx(~L);
idx=idx((i0(idx)<1) | (i0(idx)>shape(2)));
i0(idx)=i;
L0(idx)=1;
end
% reduce out trivial points DXY(idx)<DXY(:,i)
idx=sub2ind(shape(1:2),x,i0);
L=(DXY(idx)>0) | (i0==i);
idx=idx(L);
% these will keep track along which X should
% keep updating distances
map_lower=L;
map_upper=L;
idx_lower=idx;
idx_upper=idx;
% set trivial pixels D==0 in line #i:
% this has to be done b/s we manually discarded them from L0
D1(d0==0,i)=0;
% scan from starting points for each X,i0 in increments of 1
di=0; % distance from current y-line
eols=2; % end-of-line-scan flag
totlen=prod(shape(1:2));
while(eols)
eols=2;
di=di+1;
% select X which can be updated for di<0;
% i.e. X which had been below envelop all way till now
if(~isempty(idx_lower))
% shift y by -1
idx_lower=idx_lower-shape(1);
% prevent index dropping below 1st
L=(idx_lower>=1);
map_lower(map_lower)=L;
idx_lower=idx_lower(L);
if(~isempty(idx_lower))
dtmp=d0(map_lower)+...
aspect(2)^2*(i0(map_lower)-di-i).^2;
% these pixels are to be updated with i0-di
L=D1(idx_lower)>dtmp & DXY(idx_lower)>0;
map_lower(map_lower)=L;
idx_lower=idx_lower(L);
D1(idx_lower)=dtmp(L);
DK(idx_lower)=i;
end
else % if this is empty, get ready to quit
eols=eols-1;
end
% select X which can be updated for di>0;
% i.e. X which had been below envelop all way till now
if(~isempty(idx_upper))
% shift y by +1
idx_upper=idx_upper+shape(1);
% prevent index from going over array limits
L=(idx_upper<=totlen);
map_upper(map_upper)=L;
idx_upper=idx_upper(L);
if(~isempty(idx_upper))
dtmp=d0(map_upper)+...
aspect(2)^2*(i0(map_upper)+di-i).^2;
% check which pixels are to be updated with i0+di
L=D1(idx_upper)>dtmp & DXY(idx_upper)>0;
map_upper(map_upper)=L;
idx_upper=idx_upper(L);
D1(idx_upper)=dtmp(L);
DK(idx_upper)=i;
end
else % if this is empty, get ready to quit
eols=eols-1;
end
end
end
end
D{k}=D1;
end
%%%%%%%%%%%%% scan along Z %%%%%%%%%%%%%%%%
% this will be the envelop:
% envelop has to be initialized at Inf to ensure single direction of scan,
% otherwise may end up in infinite loop when trying to find starting point
D1=cell(size(D));
for k=1:shape(3) D1{k}=repmat(Inf,shape(1:2)); end
% these will be the references to parabolas defining the envelop
DK=cell(size(D));
for k=1:shape(3) DK{k}=repmat(Inf,shape(1:2)); end
% start building the envelope
for k=1:shape(3)
% need to select starting point for each X:
% * starting point should be below current envelop
% * k0==k is not necessarily a starting point
% * there may be no starting point
% k0 is the starting points for each XY: k0(XY) is the first
% z-index such that parabola from line k is below the envelop
% initial starting point guess is current slice
k0=repmat(k,shape(1:2));
% L0 indicates which starting points had been fixed
L0=isinf(D{k}) | (D{k}==0);
idxtot=find(~L0);
while(~isempty(idxtot))
% because of using cells need to explicitly scan in Z
% to avoid repetitious searches in k0, parse first
ss=getregions(k0(idxtot));
sslen=length(ss);
for kk=1:sslen
% these are starting points @kk which had not been set
idx=idxtot(ss(kk).PixelIdxList);
% reduce out trivial points (D==0)
if(kk~=k)
L=(D{kk}(idx)==0);
L0(idx)=L;
idx=idx(~L);
end
if(isempty(idx)) continue; end
% these are currently best parabolas for slice kk
ik=DK{kk}(idx);
% these are new values for slice kk from parabola from k
dtmp=D{k}(idx)+aspect(3)^2*(kk-k)^2;
% these points are OK - below current envelop
L=D1{kk}(idx)>dtmp; D1{kk}(idx(L))=dtmp(L);
% these points are not OK, but since ik==k0
% can't get any better
L=L | (ik==kk);
% all other points are not OK, need new starting point:
% starting point should be at least below parabola
% beating us at current choice of k0
% solve quadratic equation to find where this happens
ik=(ik-k);
dk=(D1{kk}(idx(~L))-dtmp(~L))./ik(~L)/2/aspect(3)^2;
dk=fix(dk)+sign(dk);
k0(idx(~L))=k0(idx(~L))+dk;
% update starting points that had been set
L0(idx)=L;
L0(idx(~L))=(dk==0);
% points that went out of boundaries can't get better
idx=idx(~L);
idx=idx((k0(idx)<1) | (k0(idx)>shape(3)));
L0(idx)=1;
k0(idx)=k;
end
idxtot=find(~L0);
end
% map_lower/map_upper keeps track of which pixels can be yet updated
% with new distance, i.e. all such XY that had been below envelop for
% all dk up to now for dk<0/dk>0 respectively
map_lower=true(shape(1:2));
map_upper=true(shape(1:2));
% parse different values in k0 to avoid repetitious searching below
ss=getregions(k0);
sslen=length(ss);
% reduce out trivially faulty starting points
for kk=1:sslen
if(kk==k) continue; end
idx=ss(kk).PixelIdxList;
L=D{kk}(idx)>D{k}(idx);
map_lower(idx)=L;
map_upper(idx)=L;
end
% these are maintained to keep fast track of whether maps are empty
idx_lower=find(map_lower);
idx_upper=find(map_upper);
% set trivial pixels D==0 in slice k:
% this has to be done b/s we manually discarded them from L0
D1{k}(D{k}==0)=0;
% scan away from starting points in increments of 1
dk=0; % distance from current xy-slice
eols=2; % end-of-scan flag
while(eols)
eols=2;
dk=dk+1;
if(~isempty(idx_lower))
% prevent index from going over the boundaries
L=(k0(map_lower)-dk>=1);
map_lower(map_lower)=L;
% need to explicitly scan in Z because of using cell-arrays
for kk=1:sslen-dk
% get all XY such that k0-dk==kk
idx=ss(kk+dk).PixelIdxList;
L=map_lower(idx);
idx=idx(L);
if(~isempty(idx))
dtmp=D{k}(idx)+aspect(3)^2*(kk-k)^2;
% these pixels are to be updated with k0-dk
L=D1{kk}(idx)>dtmp & D{kk}(idx)>0;
map_lower(idx)=L;
D1{kk}(idx(L))=dtmp(L);
% ridiculously, but this is faster than
% direct assignment
dtmp=idx(L);
dtmp(:)=k;
DK{kk}(idx(L))=k;
end
end
idx_lower=idx_lower(map_lower(idx_lower));
else
eols=eols-1;
end
if(~isempty(idx_upper))
% prevent index from going over the boundaries
L=(k0(map_upper)+dk<=shape(3));
map_upper(map_upper)=L;
% need to explicitly scan in Z because of using cell-arrays
for kk=dk+1:min(shape(3),sslen+dk)
% get all XY such that k0+dk==kk
idx=ss(kk-dk).PixelIdxList;
L=map_upper(idx);
idx=idx(L);
if(~isempty(idx))
dtmp=D{k}(idx)+aspect(3)^2*(kk-k)^2;
% these pixels are to be updated with k0+dk
L=D1{kk}(idx)>dtmp & D{kk}(idx)>0;
map_upper(idx)=L;
D1{kk}(idx(L))=dtmp(L);
dtmp=idx(L);
dtmp(:)=k;
DK{kk}(idx(L))=dtmp;
end
end
idx_upper=idx_upper(map_upper(idx_upper));
else
eols=eols-1;
end
end
end
% the answer
if(iscell(bw))
D=cell(size(bw));
for k=1:shape(3) D{k}=sqrt(D1{k}); end
else
D=zeros(shape);
for k=1:shape(3) D(:,:,k)=sqrt(D1{k}); end
end
function s=getregions(map)
% this function is replacer for regionprops(map,'PixelIdxList');
% it produces the list of different values along with list of
% indexes of pixels in map with these values; 's' is struct-array
% such that s(i).PixelIdxList contains list of pixels in map
% with value i.
% enable using regionprops if available, faster on 7.3
fregionprops=1;
% version control for using regionprops
v=version; v=str2num(v(1:3));
fregionprops=fregionprops & v>=7.3;
% in later matlab regionprops is actually faster than this code
if(exist('regionprops') & fregionprops)
s=regionprops(map,'PixelIdxList');
return
end
idx=(1:prod(size(map)))';
dtmp=double(map(:));
[dtmp,ind]=sort(dtmp);
idx=idx(ind);
ind=[0;find([diff(dtmp(:));1])];
s=[];
for i=2:length(ind)
if(dtmp(ind(i)))==0 continue; end
s(dtmp(ind(i))).PixelIdxList=idx(ind(i-1)+1:ind(i));
end
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