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syedsalmanali08/Adaptive-MEMD-master
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memd_adap.m
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.m
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Adaptive-MEMD-master/memd_adap.m
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d9716e1f008803f93c9e5ce8dadcd900
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function q = memd_adap(x, varargin)
%
%MEMD_ADAP is an extension of the standard MEMD proposed by Rehman N. and
% Mandic D.P., 2010. This code has been modified based on the function MEMD (see below).
%
% function MEMD applies the "Multivariate Empirical Mode Decomposition" algorithm (Rehman and Mandic, Proc. Roy. Soc A, 2010)
% to multivariate inputs. We have verified this code by simulations for signals containing 3-16 channels.
%
% Syntax:
%
% imf = MEMD_ADAP(X)
% returns a 3D matrix 'imf(N,M,L)' containing M multivariate IMFs, one IMF per column, computed by applying
% the multivariate EMD algorithm on the N-variate signal (time-series) X of length L.
% - For instance, imf_k = IMF(k,:,:) returns the k-th component (1 <= k <= N) for all of the N-variate IMFs.
%
% For example, for hexavariate inputs (N=6), we obtain a 3D matrix IMF(6, M, L)
% where M is the number of IMFs extracted, and L is the data length.
%
% imf = MEMD(X,num_directions)
% where integer variable num_directions (>= 1) specifies the total number of projections of the signal
% - As a rule of thumb, the minimum value of num_directions should be twice the number of data channels,
% - for instance, num_directions = 6 for a 3-variate signal and num_directions= 16 for an 8-variate signal
% The default number of directions is chosen to be 64 - to extract meaningful IMFs, the number of directions
% should be considerably greater than the dimensionality of the signals
%
% imf = MEMD(X,num_directions,'stopping criteria')
% uses the optional parameter 'stopping criteria' to control the sifting process.
% The available options are
% - 'stop' which uses the standard stopping criterion specified in [2]
% - 'fix_h' which uses the modified version of the stopping criteria specified in [3]
% The default value for the 'stopping criteria' is 'stop'.
%
% The settings num_directions=64 and 'stopping criteria' = 'stop' are defaults.
% Thus imf = MEMD(X) = MEMD(X,64) = MEMD(X,64,'stop') = MEMD(X,[],'stop'),
%
% imf = MEMD(X, num_directions, 'stop', stop_vec)
% computes the IMFs based on the standard stopping criterion whose parameters are given in the 'stop_vec'
% - stop_vec has three elements specifying the threshold and tolerance values used, see [2].
% - the default value for the stopping vector is step_vec = [0.075 0.75 0.075].
% - the option 'stop_vec' is only valid if the parameter 'stopping criteria' is set to 'stop'.
%
% imf = MEMD(X, num_directions, 'fix_h', n_iter)
% computes the IMFs with n_iter (integer variable) specifying the number of consecutive iterations when
% the number of extrema and the number of zero crossings differ at most by one [3].
% - the default value for the parameter n_iter is set to n_iter = 2.
% - the option n_iter is only valid if the parameter 'stopping criteria' = 'fix_h'
%
%
% This code allows to process multivaraite signals having 3-16 channels, using the multivariate EMD algorithm [1].
% - to perform EMD on more than 16 channels, modify the variable 'Max_channels' on line 510 in the code accordingly.
% - to process 1- and 2-dimensional (univariate and bivariate) data using EMD, we recommend the toolbox from
% http://perso.ens-lyon.fr/patrick.flandrin/emd.html
%
% Acknowledgment: Part of this code is based on the bivariate EMD code, publicly available from
% http://perso.ens-lyon.fr/patrick.flandrin/emd.html. We would also like to thank
% Anh Huy Phan from RIKEN for helping us in optimizing the code and making it computationally efficient.
%
%
% Copyright: Naveed ur Rehman and Danilo P. Mandic, Oct-2009
%
%
% [1] Rehman and D. P. Mandic, "Multivariate Empirical Mode Decomposition", Proceedings of the Royal Society A, 2010
% [2] G. Rilling, P. Flandrin and P. Goncalves, "On Empirical Mode Decomposition and its Algorithms", Proc of the IEEE-EURASIP
% Workshop on Nonlinear Signal and Image Processing, NSIP-03, Grado (I), June 2003
% [3] N. E. Huang et al., "A confidence limit for the Empirical Mode Decomposition and Hilbert spectral analysis",
% Proceedings of the Royal Society A, Vol. 459, pp. 2317-2345, 2003
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%%%%%%%%%%%%% Usage %%%%%%%%%%%%%%%
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
% Case 1:
% inp = randn(1000,3);
% imf = memd(inp);
% imf_x = reshape(imf(1,:,:),size(imf,2),length(inp)); % imfs corresponding to 1st component
% imf_y = reshape(imf(2,:,:),size(imf,2),length(inp)); % imfs corresponding to 2nd component
% imf_z = reshape(imf(3,:,:),size(imf,2),length(inp)); % imfs corresponding to 3rd component
% Case 2:
% load syn_hex_inp.mat
% imf = memd(s6,256,'stop',[0.05 0.5 0.05])
global N N_dim;
[x, seq, t, ndir, N_dim, N, sd, sd2, tol, nbit, MAXITERATIONS, stop_crit, stp_cnt] = set_value(x, nargin, varargin{:});
seq_h=seq_generator(ndir/2,N_dim);
r=x; n_imf=1;q = zeros(N_dim,1,N);
while ~stop_emd(r, seq,seq_h,ndir)
% current mode
m = r;
% computation of mean and stopping criterion
if(strcmp(stop_crit,'stop'))
[stop_sift,env_mean] = stop_sifting(m,t,sd,sd2,tol,seq,seq_h,ndir);
else
counter=0;
[stop_sift,env_mean,counter] = stop_sifting_fix(m,t,seq,ndir,stp_cnt,counter);
end
% In case the current mode is so small that machine precision can cause
% spurious extrema to appear
if (max(abs(m))) < (1e-10)*(max(abs(x)))
if ~stop_sift
warning('emd:warning','forced stop of EMD : too small amplitude')
else
disp('forced stop of EMD : too small amplitude')
end
break
end
% sifting loop
while ~stop_sift && nbit<MAXITERATIONS
%sifting
m = m - env_mean;
% computation of mean and stopping criterion
if(strcmp(stop_crit,'stop'))
[stop_sift,env_mean] = stop_sifting(m,t,sd,sd2,tol,seq,seq_h,ndir);
else
[stop_sift,env_mean,counter] = stop_sifting_fix(m,t,seq,ndir,stp_cnt,counter);
end
nbit=nbit+1;
if(nbit==(MAXITERATIONS-1) && nbit > 100)
warning('emd:warning','forced stop of sifting : too many iterations');
end
end
%%%%%%%%%%
% [ref_m,ref_mean]=memd_envp(r,256);
% [reg_m,reg_mean]=memd_envp(r,14);
% err_adap=mse(ref_mean(:,1),env_mean(:,1))
% err_memd=mse(ref_mean(:,1),reg_mean(:,1))
%
% err_adap=mse(ref_mean(:,2),env_mean(:,2))
% err_memd=mse(ref_mean(:,2),reg_mean(:,2))
%
%%%%%%%%%%%
q(:,n_imf,:)=m';
n_imf = n_imf+1;
r = r - m;
if(nbit>20)
v=0;
end
nbit = 0;
end
% Stores the residue
q(:,n_imf,:)=r';
%sprintf('Elapsed time: %f\n',toc);
end
%---------------------------------------------------------------------------------------------------
function stp = stop_emd(r, seq,seq_h, ndir)
global N_dim;
ner = zeros(ndir,1);
[samples,dim]=size(r);
adapDirVec=zeros(dim,ndir);
%dim = 3;
C=cov(r);
[U1,lamd,weightage] = pcacov(C);
weightage;
% U = [U1,-U1];
[Us,S,V]=svd(C);
dirVec = zeros(dim,ndir);
% M=Us*S*V';
%M=S*V';
% lamd=flipud(lamd);
% S=diag(lamd);
% M = V * diag(1./sqrt(diag(S))) * V';
%
% if weightage(1)>=2*(weightage(2))
% M=C;
% else
% M=eye(N_dim);
% end
[Us,S,V]=svd(r);
M=S*V';
M=M(1:N_dim,1:N_dim)';
%M=eye(N_dim,N_dim);
% [coeff,score,latent] = pca(r);
% biplot(coeff)
% figure(1)
% scatter3(r(:,1),r(:,2),r(:,3));
for it=1:ndir/2
if (N_dim~=3) % Multivariate signal (for N_dim ~=3) with hammersley sequence
% Linear normalisation of hammersley sequence in the range of -1.00 - 1.00
b=2*seq_h(1:end,it)-1;
% Find angles corresponding to the normalised sequence
tht = atan2(sqrt(flipud(cumsum(b(N_dim:-1:2).^2))),b(1:N_dim-1)).';
% Find coordinates of unit direction vectors on n-sphere
dir_vec(1:N_dim) = [1 cumprod(sin(tht))];
dir_vec(1:N_dim-1) = cos(tht) .*dir_vec(1:N_dim-1);
else % Trivariate signal with hammersley sequence
% Linear normalisation of hammersley sequence in the range of -1.0 - 1.0
tt = 2*seq_h(1,it)-1;
tt((tt>1))=1;
tt((tt<-1))=-1;
% Normalize angle from 0 - 2*pi
phirad = seq_h(2,it)*2*pi;
st = sqrt(1.0-tt*tt);
dir_vec(1)=st * cos(phirad);
dir_vec(2)=st * sin(phirad);
dir_vec(3)=tt;
end
dirVec_h(:,it)=dir_vec';
end
dirVec_h=realign(dirVec_h);
for it=1:ndir
if (N_dim~=3) % Multivariate signal (for N_dim ~=3) with hammersley sequence
% Linear normalisation of hammersley sequence in the range of -1.00 - 1.00
b=2*seq(1:end,it)-1;
% Find angles corresponding to the normalised sequence
tht = atan2(sqrt(flipud(cumsum(b(N_dim:-1:2).^2))),b(1:N_dim-1)).';
% Find coordinates of unit direction vectors on n-sphere
dir_vec(1:N_dim) = [1 cumprod(sin(tht))];
dir_vec(1:N_dim-1) = cos(tht) .*dir_vec(1:N_dim-1);
else % Trivariate signal with hammersley sequence
% Linear normalisation of hammersley sequence in the range of -1.0 - 1.0
tt = 2*seq(1,it)-1;
tt((tt>1))=1;
tt((tt<-1))=-1;
% Normalize angle from 0 - 2*pi
phirad = seq(2,it)*2*pi;
st = sqrt(1.0-tt*tt);
dir_vec(1)=st * cos(phirad);
dir_vec(2)=st * sin(phirad);
dir_vec(3)=tt;
end
dirVec(:,it)=dir_vec';
end
dirVec=realign(dirVec);
%
% dist=zeros(2*dim,ndir);
%
% for i=1:1:(2*dim)
% for j=1:1:64
% diffVec=U(:,i)-dirVec(:,j);
% dist(i,j)=norm(diffVec);
% end
% end
%
% n=round(ndir*weightage(1)/100);
% n1=round(n/2);
% n1o=n-n1;
% [dist1,ind1]=sort(dist(1,:));
% [dist2,ind2]=sort(dist(2,:));
%
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
% old section begins here....
% if (weightage(1)>=1)
% dirVec(1,2)=0.5;
% dirVec(:,2)=dirVec(:,2)/norm(dirVec(:,2));
%
% dirVec(1,3)=0.5;
% dirVec(:,3)=dirVec(:,3)/norm(dirVec(:,3));
%
% dirVec(1,22)=0.5;
% dirVec(2,22)=0.5;
% dirVec(:,22)=dirVec(:,22)/norm(dirVec(:,22));
%
% end
% %
if (weightage(1)>=(100/(N_dim))*2)
adapDirVec(:,1:ndir/2)=dirVec_h;
adapDirVec(:,ndir/2+1:end)=M*dirVec_h;
else
adapDirVec=M*dirVec;
end
% adapDirVec=M*dirVec;
for i=1:1:ndir
adapDirVec(:,i)=adapDirVec(:,i)/norm(adapDirVec(:,i));
% adapDirVec1(:,i)=adapDirVec1(:,i)/norm(adapDirVec1(:,i));
%projection on revised direction vectors
y = r * adapDirVec(:,i);
% y = r * U(:,i);
% Calculates the extrema of the projected signal using revised
% direction vectors
[indmin, indmax] = local_peaks(y);
ner(i) = length(indmin) + length(indmax);
% ner(i+ndir) = length(indmin) + length(indmax);
end
% old section ends here...
% % % %
figure(1)
[vec,val] = eig(C);
vec=U1;
e1=[zeros(size(vec(:,1))),vec(:,1)]'; e1 = e1/norm(e1)*4;
e2=[zeros(size(vec(:,2))),vec(:,2)]'; e2 = e2/norm(e2)*4;
e3=[zeros(size(vec(:,3))),vec(:,3)]'; e3 = e3/norm(e3)*4;
plot3(r(:,1),r(:,2),r(:,3),'r.');
hold on
plot3(e1(:,1),e1(:,2),e1(:,3),'k','LineWidth',2);
plot3(-1*e1(:,1),-1*e1(:,2),-1*e1(:,3),'k','LineWidth',2);
plot3(e2(:,1),e2(:,2),e2(:,3),'b','LineWidth',2);
plot3(-1*e2(:,1),-1*e2(:,2),-1*e2(:,3),'b','LineWidth',2);
plot3(e3(:,1),e3(:,2),e3(:,3),'g','LineWidth',2);
plot3(-1*e3(:,1),-1*e3(:,2),-1*e3(:,3),'g','LineWidth',2);
%
% [a, b, c] = sphere(128);
% sp = surfl(a, b, c);
% shading interp
% set(sp,'FaceColor',[0.5 0.5 0.5], 'FaceAlpha', 0.5)
% hold on;
% plot3(adapDirVec(1,:),adapDirVec(2,:),adapDirVec(3,:),'bx');
% plot3(dirVec(1,:),dirVec(2,:),dirVec(3,:),'gx');
% figure(2)
% % e1=[zeros(size(vec(:,1))),vec(:,1)]'; e1 = e1/norm(e1)*4;
% % e2=[zeros(size(vec(:,2))),vec(:,2)]'; e2 = e2/norm(e2)*4;
% % e3=[zeros(size(vec(:,3))),vec(:,3)]'; e3 = e3/norm(e3)*4;
% % %plot3(r(:,1),r(:,2),r(:,3),'r');
% % hold on
% % plot3(e1(:,1),e1(:,2),e1(:,3),'k','LineWidth',2);
% % plot3(-1*e1(:,1),-1*e1(:,2),-1*e1(:,3),'k','LineWidth',2);
% % plot3(e2(:,1),e2(:,2),e2(:,3),'b','LineWidth',2);
% % plot3(-1*e2(:,1),-1*e2(:,2),-1*e2(:,3),'b','LineWidth',2);
% % plot3(e3(:,1),e3(:,2),e3(:,3),'g','LineWidth',2);
% % plot3(-1*e3(:,1),-1*e3(:,2),-1*e3(:,3),'g','LineWidth',2);
% %
% % plot3(adapDirVec1(1,:),adapDirVec1(2,:),adapDirVec1(3,:),'bx');
% [a, b, c] = sphere(128);
% sp = surfl(a, b, c);
% shading interp
% set(sp,'FaceColor',[0.5 0.5 0.5], 'FaceAlpha', 0.5)
% hold on;
% plot3(dirVec(1,:),dirVec(2,:),dirVec(3,:),'bx');
% hold off
% close all
% figure(1)
% scatter3(r(:,1),r(:,2),r(:,3))
% figure(2)
% scatter3(dirVec(1,:),dirVec(2,:),dirVec(3,:));
% figure(3)
% scatter3(adapDirVec(1,:),adapDirVec(2,:),adapDirVec(3,:))
% figure(4)
% scatter3(adapDirVec(1,:),adapDirVec(2,:),adapDirVec(3,:))
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
% Stops if the all projected signals have less than 3 extrema
stp = all(ner < 3);
end
%---------------------------------------------------------------------------------------------------
% computes the mean of the envelopes and the mode amplitude estimate
function [env_mean,nem,nzm,amp] = envelope_mean(m,t,seq,seq_h,ndir) %new
global N N_dim;
q=0;
[samples,dim]=size(m);
C=cov(m);
[U1,lamd,weightage] = pcacov(C);
weightage;
dirVec = zeros(dim,ndir);
adapDirVec=zeros(dim,ndir);
adapDirVec1=zeros(dim,ndir);
% M=Us*S*V';
% %M=S*V';
% %M=U1';
% [E, L] = eig(cov(m));
% [L, order] = sort(diag(L), 'descend');
% E = E(:,order);
% m=m*M;
% lamd=flipud(lamd);
% S=diag(lamd);
% M = V * diag(1./diag(sqrt(S))) * V';
% M=diag(1./diag(sqrt(S))) * V';
[Us,S,V]=svd(m);
M=S*V';
M=M(1:N_dim,1:N_dim)';
%M=eye(N_dim,N_dim);
%M1=V*S(1:N_dim,1:N_dim)*V';
NBSYM = 2;
count=0;
env_mean=zeros(length(t),N_dim);
amp = zeros(length(t),1);
nem = zeros(dim,1);nzm = zeros(dim,1);
for it=1:ndir/2
if (N_dim ~=3) % Multivariate signal (for N_dim ~=3) with hammersley sequence
% Linear normalisation of hammersley sequence in the range of -1.00 - 1.00
b=2*seq_h(1:end,it)-1;
% Find angles corresponding to the normalised sequence
tht = atan2(sqrt(flipud(cumsum(b(N_dim:-1:2).^2))),b(1:N_dim-1)).';
% Find coordinates of unit direction vectors on n-sphere
dir_vec(1:N_dim) = [1 cumprod(sin(tht))];
dir_vec(1:N_dim-1) = cos(tht) .*dir_vec(1:N_dim-1);
else % Trivariate signal with hammersley sequence
% Linear normalisation of hammersley sequence in the range of -1.0 - 1.0
tt = 2*seq_h(1,it)-1;
tt((tt>1))=1;
tt((tt<-1))=-1;
% Normalize angle from 0 - 2*pi
phirad = seq_h(2,it)*2*pi;
st = sqrt(1.0-tt*tt);
dir_vec(1)=st * cos(phirad);
dir_vec(2)=st * sin(phirad);
dir_vec(3)=tt;
end
dirVec_h(:,it)=dir_vec';
end
dirVec_h=realign(dirVec_h);
for it=1:ndir
if (N_dim ~=3) % Multivariate signal (for N_dim ~=3) with hammersley sequence
% Linear normalisation of hammersley sequence in the range of -1.00 - 1.00
b=2*seq(1:end,it)-1;
% Find angles corresponding to the normalised sequence
tht = atan2(sqrt(flipud(cumsum(b(N_dim:-1:2).^2))),b(1:N_dim-1)).';
% Find coordinates of unit direction vectors on n-sphere
dir_vec(1:N_dim) = [1 cumprod(sin(tht))];
dir_vec(1:N_dim-1) = cos(tht) .*dir_vec(1:N_dim-1);
else % Trivariate signal with hammersley sequence
% Linear normalisation of hammersley sequence in the range of -1.0 - 1.0
tt = 2*seq(1,it)-1;
tt((tt>1))=1;
tt((tt<-1))=-1;
% Normalize angle from 0 - 2*pi
phirad = seq(2,it)*2*pi;
st = sqrt(1.0-tt*tt);
dir_vec(1)=st * cos(phirad);
dir_vec(2)=st * sin(phirad);
dir_vec(3)=tt;
end
dirVec(:,it)=dir_vec';
end
dirVec=realign(dirVec);
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
% adaptive projection based on SVD
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
% if (weightage(1)>=1)
% dirVec(1,2)=0.5;
% dirVec(:,2)=dirVec(:,2)/norm(dirVec(:,2));
%
% dirVec(1,3)=0.5;
% dirVec(:,3)=dirVec(:,3)/norm(dirVec(:,3));
%
% dirVec(1,22)=0.5;
% dirVec(2,22)=0.5;
% dirVec(:,22)=dirVec(:,22)/norm(dirVec(:,22));
%
% end
% %
if (weightage(1)>=(100/(N_dim))*2)
adapDirVec(:,1:ndir/2)=dirVec_h;
adapDirVec(:,ndir/2+1:end)=M*dirVec_h;
% adapDirVec1(:,1:ndir/2)=dirVec_h;
% adapDirVec1(:,ndir/2+1:end)=M1*dirVec_h;
else
adapDirVec=M*dirVec;
% adapDirVec1=M1*dirVec;
end
% %
% M=eye(N_dim,N_dim);
%adapDirVec=M*dirVec;
for it=1:ndir;
adapDirVec(:,it)=adapDirVec(:,it)/norm(adapDirVec(:,it));
% adapDirVec1(:,it)=adapDirVec1(:,it)/norm(adapDirVec1(:,it));
y(1:N) = m(1:N,:) * adapDirVec(:,it);
% Calculates the extrema of the projected signal
[indmin, indmax] = local_peaks(y);
nem(it) = length(indmin) + length(indmax);
indzer = zero_crossings(y);
nzm(it) = length(indzer);
[tmin,tmax,zmin,zmax,mode] = boundary_conditions(indmin,indmax,t,y,m,NBSYM);
% Calculate multidimensional envelopes using spline interpolation
% Only done if number of extrema of the projected signal exceed 3
if(mode)
env_min = spline(tmin,zmin.',t).';
env_max = spline(tmax,zmax.',t).';
%amp = amp + sqrt(sum((env_max-env_min).^2,2))/2;
amp = amp + sqrt(sum(((env_max-env_min)/2).^2,2));
env_mean = env_mean + (env_max+env_min)/2;
else % if the projected signal has inadequate extrema
count=count+1;
end
%
% if q==1
% figure(1)
% plot(m(:,1))
% hold on
% plot(env_min(:,1))
% plot(env_max(:,1))
%
% close all
%
% end
end
%
% %
% figure(1)
% [vec,val] = eigs(C);
% vec=U1;
% e1=[zeros(size(vec(:,1))),vec(:,1)]'; e1 = e1/norm(e1)*4;
% e2=[zeros(size(vec(:,2))),vec(:,2)]'; e2 = e2/norm(e2)*4;
% e3=[zeros(size(vec(:,3))),vec(:,3)]'; e3 = e3/norm(e3)*4;
% %plot3(m(:,1),m(:,2),m(:,3),'r.');
% hold on
% plot3(e1(:,1),e1(:,2),e1(:,3),'k','LineWidth',2);
% plot3(-1*e1(:,1),-1*e1(:,2),-1*e1(:,3),'k','LineWidth',2);
% plot3(e2(:,1),e2(:,2),e2(:,3),'b','LineWidth',2);
% plot3(-1*e2(:,1),-1*e2(:,2),-1*e2(:,3),'b','LineWidth',2);
% plot3(e3(:,1),e3(:,2),e3(:,3),'g','LineWidth',2);
% plot3(-1*e3(:,1),-1*e3(:,2),-1*e3(:,3),'g','LineWidth',2);
%
% plot3(adapDirVec(1,:),adapDirVec(2,:),adapDirVec(3,:),'bx');
% %plot3(dirVec(1,:),dirVec(2,:),dirVec(3,:),'rx');
%
% hold off
% close all;
% mean_ref=memd_envp(m,256);
% mean_emd=memd_envp(m,20);
% figure(2)
% plot(mean_ref(:,1),'r')
% hold on
% plot(env_mean(:,1),'b')
% plot(mean_emd(:,1),'g')
%
% figure(1)
% vec=U1;
% e1=[zeros(size(vec(:,1))),vec(:,1)]'; e1 = e1/norm(e1)*4;
% e2=[zeros(size(vec(:,2))),vec(:,2)]'; e2 = e2/norm(e2)*4;
% e3=[zeros(size(vec(:,3))),vec(:,3)]'; e3 = e3/norm(e3)*4;
% %plot3(m(:,1),m(:,2),m(:,3),'rx');
% hold on
% plot3(e1(:,1),e1(:,2),e1(:,3),'k','LineWidth',2);
% plot3(-1*e1(:,1),-1*e1(:,2),-1*e1(:,3),'k','LineWidth',2);
% plot3(e2(:,1),e2(:,2),e2(:,3),'b','LineWidth',2);
% plot3(-1*e2(:,1),-1*e2(:,2),-1*e2(:,3),'b','LineWidth',2);
% plot3(e3(:,1),e3(:,2),e3(:,3),'g','LineWidth',2);
% plot3(-1*e3(:,1),-1*e3(:,2),-1*e3(:,3),'g','LineWidth',2);
%
% % figure(2)
% % plot3(e1(:,1),e1(:,2),e1(:,3),'k','LineWidth',2);
% % hold on
% % plot3(-1*e1(:,1),-1*e1(:,2),-1*e1(:,3),'k','LineWidth',2);
% % plot3(e2(:,1),e2(:,2),e2(:,3),'b','LineWidth',2);
% % plot3(-1*e2(:,1),-1*e2(:,2),-1*e2(:,3),'b','LineWidth',2);
% % plot3(e3(:,1),e3(:,2),e3(:,3),'g','LineWidth',2);
% % plot3(-1*e3(:,1),-1*e3(:,2),-1*e3(:,3),'g','LineWidth',2);
% % [a, b, c] = sphere(128);
% % sp = surfl(a, b, c);
% % shading interp
% % set(sp,'FaceColor',[0.5 0.5 0.5], 'FaceAlpha', 0.5)
% % hold on;
% plot3(adapDirVec(1,1:ndir/2),adapDirVec(2,1:ndir/2),adapDirVec(3,1:ndir/2),'bx');
% plot3(adapDirVec(1,ndir/2+1:end),adapDirVec(2,ndir/2+1:end),adapDirVec(3,ndir/2+1:end),'ro');
%
% %plot3(adapDirVec(1,1:ndir),adapDirVec(2,1:ndir),adapDirVec(3,1:ndir),'bx');
%
% figure(2)
% hold on
% plot3(e1(:,1),e1(:,2),e1(:,3),'k','LineWidth',2);
% plot3(-1*e1(:,1),-1*e1(:,2),-1*e1(:,3),'k','LineWidth',2);
% plot3(e2(:,1),e2(:,2),e2(:,3),'b','LineWidth',2);
% plot3(-1*e2(:,1),-1*e2(:,2),-1*e2(:,3),'b','LineWidth',2);
% plot3(e3(:,1),e3(:,2),e3(:,3),'g','LineWidth',2);
% plot3(-1*e3(:,1),-1*e3(:,2),-1*e3(:,3),'g','LineWidth',2);
%
% plot3(adapDirVec1(1,1:ndir/2),adapDirVec1(2,1:ndir/2),adapDirVec1(3,1:ndir/2),'bx');
% plot3(adapDirVec1(1,ndir/2+1:end),adapDirVec1(2,ndir/2+1:end),adapDirVec1(3,ndir/2+1:end),'ro');
%
% %plot3(dirVec(1,:),dirVec(2,:),dirVec(3,:),'rx');
%
% hold off
% close all
ndir1=2*ndir;
ndir1=ndir;
if(ndir1>count)
env_mean = env_mean/(ndir1-count);
amp = amp/(ndir1-count);
else
env_mean = zeros(N,N_dim);
amp = zeros(N,1);
nem = zeros(1,ndir1);
end
close all;
end
%-------------------------------------------------------------------------------
% Stopping criterion
function [stp,env_mean] = stop_sifting(m,t,sd,sd2,tol,seq,seq_h,ndir)
global N N_dim;
try
[env_mean,nem,nzm,amp] = envelope_mean(m,t,seq,seq_h,ndir);
sx = sqrt(sum(env_mean.^2,2));
if(amp) % something is wrong here
sx = sx./amp;
end
stp = ~((mean(sx > sd) > tol | any(sx > sd2)) & any(nem > 2));
catch
env_mean = zeros(N,N_dim);
stp = 1;
end
end
function [stp,env_mean,counter]= stop_sifting_fix(m,t,seq,ndir,stp_count,counter)
global N N_dim;
try
[env_mean,nem,nzm] = envelope_mean(m,t,seq,ndir);
if (all(abs(nzm-nem)>1))
stp = 0;
counter = 0;
else
counter = counter+1;
stp = (counter >= stp_count);
end
catch
env_mean = zeros(N,N_dim);
stp = 1;
end
end
%---------------------------------------------------------------------------------------
% defines new extrema points to extend the interpolations at the edges of the
% signal (mainly mirror symmetry)
function [tmin,tmax,zmin,zmax,mode] = boundary_conditions(indmin,indmax,t,x,z,nbsym)
lx = length(x);
if (length(indmin) + length(indmax) < 3)
mode = 0;
tmin=NaN;tmax=NaN;zmin=NaN;zmax=NaN;
return
else
mode=1; %the projected signal has inadequate extrema
end
% boundary conditions for interpolations :
if indmax(1) < indmin(1)
if x(1) > x(indmin(1))
lmax = fliplr(indmax(2:min(end,nbsym+1)));
lmin = fliplr(indmin(1:min(end,nbsym)));
lsym = indmax(1);
else
lmax = fliplr(indmax(1:min(end,nbsym)));
lmin = [fliplr(indmin(1:min(end,nbsym-1))),1];
lsym = 1;
end
else
if x(1) < x(indmax(1))
lmax = fliplr(indmax(1:min(end,nbsym)));
lmin = fliplr(indmin(2:min(end,nbsym+1)));
lsym = indmin(1);
else
lmax = [fliplr(indmax(1:min(end,nbsym-1))),1];
lmin = fliplr(indmin(1:min(end,nbsym)));
lsym = 1;
end
end
if indmax(end) < indmin(end)
if x(end) < x(indmax(end))
rmax = fliplr(indmax(max(end-nbsym+1,1):end));
rmin = fliplr(indmin(max(end-nbsym,1):end-1));
rsym = indmin(end);
else
rmax = [lx,fliplr(indmax(max(end-nbsym+2,1):end))];
rmin = fliplr(indmin(max(end-nbsym+1,1):end));
rsym = lx;
end
else
if x(end) > x(indmin(end))
rmax = fliplr(indmax(max(end-nbsym,1):end-1));
rmin = fliplr(indmin(max(end-nbsym+1,1):end));
rsym = indmax(end);
else
rmax = fliplr(indmax(max(end-nbsym+1,1):end));
rmin = [lx,fliplr(indmin(max(end-nbsym+2,1):end))];
rsym = lx;
end
end
tlmin = 2*t(lsym)-t(lmin);
tlmax = 2*t(lsym)-t(lmax);
trmin = 2*t(rsym)-t(rmin);
trmax = 2*t(rsym)-t(rmax);
% in case symmetrized parts do not extend enough
if tlmin(1) > t(1) || tlmax(1) > t(1)
if lsym == indmax(1)
lmax = fliplr(indmax(1:min(end,nbsym)));
else
lmin = fliplr(indmin(1:min(end,nbsym)));
end
if lsym == 1
error('bug')
end
lsym = 1;
tlmin = 2*t(lsym)-t(lmin);
tlmax = 2*t(lsym)-t(lmax);
end
if trmin(end) < t(lx) || trmax(end) < t(lx)
if rsym == indmax(end)
rmax = fliplr(indmax(max(end-nbsym+1,1):end));
else
rmin = fliplr(indmin(max(end-nbsym+1,1):end));
end
if rsym == lx
error('bug')
end
rsym = lx;
trmin = 2*t(rsym)-t(rmin);
trmax = 2*t(rsym)-t(rmax);
end
zlmax =z(lmax,:);
zlmin =z(lmin,:);
zrmax =z(rmax,:);
zrmin =z(rmin,:);
tmin = [tlmin t(indmin) trmin];
tmax = [tlmax t(indmax) trmax];
zmin = [zlmin; z(indmin,:); zrmin];
zmax = [zlmax; z(indmax,:); zrmax];
end
function [indmin, indmax] = local_peaks(x)
if(all(x < 1e-5))
x=zeros(1,length(x));
end
m = length(x);
% Calculates the extrema of the projected signal
% Difference between subsequent elements:
dy = diff(x); a = find(dy~=0);
lm = find(diff(a)~=1) + 1;
d = a(lm) - a(lm-1);
a(lm) = a(lm) - floor(d/2);
a(end+1) = m;
ya = x(a);
if(length(ya) > 1)
% Maxima
[pks_max,loc_max]=peaks(ya);
% Minima
[pks_min,loc_min]=peaks(-ya);
if(~isempty(pks_min))
indmin = a(loc_min);
else
indmin = NaN;
end
if(~isempty(pks_max))
indmax = a(loc_max);
else
indmax = NaN;
end
else
indmin=NaN;
indmax=NaN;
end
end
function [pks_max,locs_max] =peaks(X)
dX = sign(diff(X));
locs_max = find((dX(1:end-1) >0) & (dX(2:end) <0)) + 1;
pks_max = X(locs_max);
end
function indzer = zero_crossings(x)
indzer = find(x(1:end-1).*x(2:end)<0);
if any(x == 0)
iz = find( x==0 );
if any(diff(iz)==1)
zer = x == 0;
dz = diff([0 zer 0]);
debz = find(dz == 1);
finz = find(dz == -1)-1;
indz = round((debz+finz)/2);
else
indz = iz;
end
indzer = sort([indzer indz]);
end
end
function seq = hamm(n,base)
seq = zeros(1,n);
if ( 1 < base )
seed = 1:1:n;
base_inv = inv(base);
while ( any ( seed ~= 0 ) )
digit = mod (seed(1:n), base);
seq = seq + digit * base_inv;
base_inv = base_inv / base;
seed = floor (seed / base );
end
else
temp = 1:1:n;
seq = (mod(temp,(-base + 1 ))+0.5)/(-base);
end
end
function [q, seq, t, ndir, N_dim, N, sd, sd2, tol, nbit, MAXITERATIONS, stp_crit, stp_cnt] = set_value(q, narg, varargin)
error(nargchk(1,4,narg));
ndir = [];
stp_crit = [];
stp_vec = [];
stp_cnt = [];
MAXITERATIONS = [];
sd=[];
sd2=[];
tol=[];
prm= [2,3,5,7,11,13,17,19,23,29,31,37,41,43,47,53,59,61,67,71,73,79,83,89,97,101,103,107,109,113,127,131,137,139,149];
% Changes the input vector to double vector
q = double(q);
% Specifies maximum number of channels that can be processed by the code
% Its maximum possible value is 32.
Max_channels = 16;
if(narg==2)
ndir=varargin{1};
end
if(narg==3)
if(~isempty(varargin{1}))
ndir=varargin{1};
else
ndir=64;
end
stp_crit=varargin{2};
end
if(narg==4 && strcmp(varargin{2},'fix_h'))
if(isempty(varargin{1}))
ndir=64;
stp_crit=varargin{2};
stp_cnt = varargin{3};
else
ndir=varargin{1};
stp_crit=varargin{2};
stp_cnt = varargin{3};
end
elseif (narg==4 && strcmp(varargin{2},'stop'))
if(isempty(varargin{1}))
ndir=64;
stp_crit=varargin{2};
stp_vec=varargin{3};
else
ndir=varargin{1};
stp_crit=varargin{2};
stp_vec=varargin{3};
end
elseif (narg==4 && ~xor(strcmp(varargin{2},'fix_h'),strcmp(varargin{2},'stop')))
Nmsgid = generatemsgid('invalid stop_criteria');
error(Nmsgid,'stop_criteria should be either fix_h or stop');
end
%%%%%%%%%%%%%% Rescale input signal if required
if (any(size(q)) == 0)
datamsgid = generatemsgid('emptyDataSet');
error(datamsgid,'Data set cannot be empty.');
end
if size(q,1) < size(q,2)
q=q';
end
%%%%%%%%%%%% Dimension of input signal
N_dim = size(q,2);
if(N_dim < 3 || N_dim > Max_channels)
error('Function only processes the signal having 3 and 16 channels.');
end
%%%%%%%%%%%% Length of input signal
N = size(q,1);
%%%%%%%%%%%%% Check validity of Input parameters
if ~isempty(ndir) && (~isnumeric(ndir) || ~isscalar(ndir) || any(rem(ndir,1)) || (ndir < 6))
Nmsgid = generatemsgid('invalid num_dir');
error(Nmsgid,'num_dir should be an integer greater than or equal to 6.');
end
if ~isempty(stp_crit) && (~ischar(stp_crit) || ~xor(strcmp(stp_crit,'fix_h'),strcmp(stp_crit,'stop')))
Nmsgid = generatemsgid('invalid stop_criteria');
error(Nmsgid,'stop_criteria should be either fix_h or stop');
end
if ~isempty(stp_vec) && (~isnumeric(stp_vec) || length(stp_vec)~=3 || ~strcmp(stp_crit,'stop'))
Nmsgid = generatemsgid('invalid stop_vector');
error(Nmsgid,'stop_vector should be an array with three elements e.g. default is [0.075 0.75 0.075] ');
end
if ~isempty(stp_cnt) && (~isnumeric(stp_cnt) || ~isscalar(stp_cnt) || any(rem(stp_cnt,1)) || (stp_cnt < 0) || ~strcmp(stp_crit,'fix_h'))
Nmsgid = generatemsgid('invalid stop_count');
error(Nmsgid,'stop_count should be a nonnegative integer');
end
if (isempty(ndir))
ndir=64; % default
end
if (isempty(stp_crit))
stp_crit='stop'; % default
end
if (isempty(stp_vec))
stp_vec=[0.075,0.75,0.075]; % default
end
if (isempty(stp_cnt))
stp_cnt=2; % default
end
if(strcmp(stp_crit,'stop'))
sd = stp_vec(1);
sd2 = stp_vec(2);
tol = stp_vec(3);
end
%%%%%%%%%%%%% Initializations for Hammersley function
base(1) = -ndir;
%%%%%%%%%%%%%% Find the pointset for the given input signal
if(N_dim==3)
base(2) = 2;
for it=1:N_dim-1
seq(it,:) = hamm(ndir,base(it));
end
else
for iter = 2 : N_dim
base(iter) = prm(iter-1);
end
for it=1:N_dim
seq(it,:) = hamm(ndir,base(it));
end
end
%%%%%%%%%%%% Define t
t=1:N;
% Counter
nbit=0;
MAXITERATIONS=1000; % default
% tic
end
function [seq] = seq_generator(ndir,N_dim)
prm= [2,3,5,7,11,13,17,19,23,29,31,37,41,43,47,53,59,61,67,71,73,79,83,89,97,101,103,107,109,113,127,131,137,139,149];
base(1) = -ndir;
%%%%%%%%%%%%%% Find the pointset for the given input signal
if(N_dim==3)
base(2) = 2;
for it=1:N_dim-1
seq(it,:) = hamm(ndir,base(it));
end
else
for iter = 2 : N_dim
base(iter) = prm(iter-1);
end
for it=1:N_dim
seq(it,:) = hamm(ndir,base(it));
end
end
end
function [dirvecmod]=realign(dirvec)
[dim, No]=size(dirvec);
for i=1:No
for j=1:dim
if abs(dirvec(j,i))>=0 && abs(dirvec(j,i))<=0.00001
dirvec(j,i)=0.5;
end
end
end
dirvecmod=dirvec;
end
|
github
|
xinghuang2050/Mesoscale-Convective-System-Tracking-master
|
task_assign.m
|
.m
|
Mesoscale-Convective-System-Tracking-master/code/task_assign.m
| 820 |
utf_8
|
cb975819b4a06189edd9aa5341dbd4a1
|
%% for parallel computing
function time_list = task_assign(yr1, mt1, yr2, mt2, array_size, array_id)
total_month = (yr2 - yr1)*12 + (mt2 - mt1) + 1
% eg. if set array_size == total_month --> assign tasks for each month
month_for_each_proc = round(total_month/array_size)
start_day = datenum(sprintf('%d/01/%d', mt1, yr1))
time_list.record_begin_date = datestr(addtodate(start_day, (array_id - 1) * month_for_each_proc, 'month'),'yyyy-mm-dd');
time_list.record_end_date = datestr(addtodate(start_day-1, array_id * month_for_each_proc, 'month'),'yyyy-mm-dd');
time_list.interest_begin_date = datestr(addtodate(start_day, (array_id - 1) * month_for_each_proc - 1, 'month'),'yyyy-mm-dd');
time_list.interest_end_date = datestr(addtodate(start_day-1, array_id * month_for_each_proc+1, 'month'),'yyyy-mm-dd');
end
|
github
|
xinghuang2050/Mesoscale-Convective-System-Tracking-master
|
timestamp_2_date.m
|
.m
|
Mesoscale-Convective-System-Tracking-master/code/utils/timestamp_2_date.m
| 358 |
utf_8
|
62a6f4263cc70cbbd6c55961963a6043
|
function datet = timestamp_2_date(timestamp)
%--dmt = timestamp_2_time(timestamp,timezone)
start_day = datenum(sprintf('%d/01/%d', 1, 0));
%--Defalt UTC timezone=0;
datet = addtodate(start_day, (timestamp- 1) * 3, 'hour');
%--date = addtodate(date,timezone, 'hour');
%--For LST,timezone depends on longitude
%datet = datestr(date,'yyyy-mm-dd-HH');
end
|
github
|
xinghuang2050/Mesoscale-Convective-System-Tracking-master
|
get_grid_area.m
|
.m
|
Mesoscale-Convective-System-Tracking-master/code/utils/get_grid_area.m
| 923 |
utf_8
|
1240546254c42536b13586b04558d536
|
%% area for each grid
function grid_area = get_grid_area(lat_begin,lat_end,...
is_use_pixel)
%% if is_use_pixel == false,grid area with unit 1
% Get surface area for grid cells. https://badc.nerc.ac.uk/help/coordinates/cell-surf-area.html
% grid_area: grid area in km^2
% lat_begin,lat_end: limit of grid, only change in longitude direction
long_grid = 576; % total longitude grid number of CLAUS
lat_grid = 358; % total longitude grid number of CLAUS; =360-2
lat_deg = (-89.75:1/2:89.75); % resolution of CLAUS
grid_area = zeros(lat_grid,1);
R = 6371;
perl = 2*pi/long_grid;
for i = 2:lat_grid+1
phi2 = (lat_deg(i)+lat_deg(i-1))/360.*pi;
phi1 = (lat_deg(i)+lat_deg(i+1))/360.*pi;
grid_area(i-1) = R*R*perl*abs(sin(phi2)-sin(phi1));
end
grid_area=grid_area(lat_begin:lat_end,1);
%% if is_use_pixel == true,grid area with unit 1
if is_use_pixel
grid_area(:)=1;
end
end
|
github
|
adhusch/PaCER-master
|
readMedtronicXMLTrajectory.m
|
.m
|
PaCER-master/lib/Helpers/readMedtronicXMLTrajectory.m
| 4,143 |
utf_8
|
baf2dd0d6838e4474693fc918d647dff
|
%% Read Medtronic Framelink XML Configuration File
%
% Andreas Husch
% Centre Hospitalier de Luxembourg, Dep. of Neurosurgery /
% University of Luxembourg - Luxembourg Centre for Systems Biomedicine
% 2014 - 2017
% [email protected], [email protected]
function config = readMedtronicXMLTrajectory(filepath)
xml = xmlread(filepath);
config = struct();
%% Check Version
configVersion = char(xml.getElementsByTagName('dtd-version').item(0).getFirstChild.getData);
if(~(strcmp(configVersion, '1.0') || strcmp(configVersion, '2.0')))
warning(['Only version 1.0 and 2.0 of the loaded Medtronic File is tested, but the file you specified is Version ' configVersion]);
end
if(strcmp(configVersion, '2.0'))
acPc = xml.getElementsByTagName('reformatSettings_v2').item(0);
surgicalPlans = xml.getElementsByTagName('surgicalPlan_v2');
% Some Medtronic Files are buggy and use the old surgicalPlan tag
% despite reporting v2.. try to fix this
if(surgicalPlans.getLength() == 0)
warning('.xml File reports Version 2.0 but contains no surgicalPlan_v2 tags. Either your file does not contain any plans or it is indicating the wrong version number. Trying to read old v1.0 tags...');
surgicalPlans = xml.getElementsByTagName('surgicalPlan');
end
%% Read the reformat settings specific to Format V2.0
m1Element = acPc.getElementsByTagName('midline1').item(0);
config.M1 = get3DFloatCoordinate(m1Element);
m2Element = acPc.getElementsByTagName('midline2').item(0);
config.M2 = get3DFloatCoordinate(m2Element);
m3Element = acPc.getElementsByTagName('midline3').item(0);
config.M3 = get3DFloatCoordinate(m3Element);
elseif(strcmp(configVersion, '1.0'))
acPc = xml.getElementsByTagName('ACPC').item(0);
surgicalPlans = xml.getElementsByTagName('surgicalPlan');
%% Read the reformat settings specific to Format V1.0
m1Element = acPc.getElementsByTagName('midline').item(0);
config.M1 = get3DFloatCoordinate(m1Element);
m2Element = acPc.getElementsByTagName('midline').item(1);
config.M2 = get3DFloatCoordinate(m2Element);
m3Element = acPc.getElementsByTagName('midline').item(2);
config.M3 = get3DFloatCoordinate(m3Element);
frameRods = xml.getElementsByTagName('frameRods');
frameRod = frameRods.item(0);
for i=0:8
rod = frameRod.getElementsByTagName('rod').item(i);
config.rods(i+1).coord = get3DFloatCoordinate(rod);
end
end
%% Read the reformat settings (== AC/PC/Midline defintions)
acElement = acPc.getElementsByTagName('AC').item(0);
config.AC = get3DFloatCoordinate(acElement);
pcElement = acPc.getElementsByTagName('PC').item(0);
config.PC = get3DFloatCoordinate(pcElement);
%% Read the surgical plans (== trajectories)
% all elementS (lists) that have a guaranted cardinality of 1 can be used with
% item(0) to give the respective element
noTraject = surgicalPlans.getLength();
for i = 0:noTraject-1;
surgicalPlan = surgicalPlans.item(i);
planNameElement = surgicalPlan.getElementsByTagName('name').item(0);
config.trajects(i+1).name = char(planNameElement.getFirstChild.getData);
targetElement = surgicalPlan.getElementsByTagName('target').item(0);
config.trajects(i+1).target = get3DFloatCoordinate(targetElement);
entryElement = surgicalPlan.getElementsByTagName('entry').item(0);
config.trajects(i+1).entry = get3DFloatCoordinate(entryElement);
end
%% Private Helper Functions
function float3 = get3DFloatCoordinate(point3dActive)
x = getFloatCoordinate(point3dActive, 'x');
y = getFloatCoordinate(point3dActive, 'y');
z = getFloatCoordinate(point3dActive, 'z');
float3 = [x;y;z];
end
function float = getFloatCoordinate(point3dActive, strName)
targetPoint3DElement = point3dActive.getElementsByTagName('point3dActive').item(0);
coordElement = targetPoint3DElement.getElementsByTagName(strName).item(0);
coordFloat = coordElement.getElementsByTagName('float').item(0);
float = str2double(coordFloat.getFirstChild.getData);
end
end
|
github
|
adhusch/PaCER-master
|
getIntensityForLabel.m
|
.m
|
PaCER-master/lib/Helpers/getIntensityForLabel.m
| 305 |
utf_8
|
12ccf659452e0929ab0427b2c1acdbf8
|
%% getIntensityForLabel
%
% Florian Bernard
% Centre Hospitalier de Luxembourg, Dep. of Neurosurgery /
% University of Luxembourg - Luxembourg Centre for Systems Biomedicine
% 2014 - 2017
function intensity = getIntensityForLabel(labelNames, label)
intensity = find(strcmp(labelNames, label)) - 1;
end
|
github
|
adhusch/PaCER-master
|
plotSphere.m
|
.m
|
PaCER-master/lib/Helpers/plotSphere.m
| 836 |
utf_8
|
03e3c220056e15a59e8a632549bcd85a
|
%% plotSphere - plot a sphere for given point
%
% Andreas Husch
% Centre Hospitalier de Luxembourg, Dep. of Neurosurgery /
% University of Luxembourg - Luxembourg Centre for Systems Biomedicine
% 2014 - 2017
% [email protected], [email protected]
function graphicsHandle = plotSphere(point, diameter, color, parent, varargin)
if(nargin < 5)
varargin = {};
end
if(nargin < 4)
parent = gca;
end
if(nargin < 3)
color = 'y';
end
[x,y,z] = sphere(); % 10x10 faces (default: 20x20 facess)
x = x .* (diameter/2)+ point(1);
y = y .* (diameter/2)+ point(2);
z = z .* (diameter/2)+ point(3);
graphicsHandle = surf(x,y,z, 'FaceColor', color, 'EdgeColor', 'none', 'Parent', parent, varargin{:});
daspect([1 1 1]);
lighting gouraud;
material shiny;
end
|
github
|
adhusch/PaCER-master
|
CTColormapRGB.m
|
.m
|
PaCER-master/lib/Helpers/CTColormapRGB.m
| 1,410 |
utf_8
|
4f960fcd2146e0c20c858a8fe5217206
|
%% Applying Tone Mapping to CT Data Enabling Simultaneus Display of Bony and Soft-Tissue Structures
%
% Andreas Husch
% Centre Hospitalier de Luxembourg, Dep. of Neurosurgery /
% University of Luxembourg - Luxembourg Centre for Systems Biomedicine
% 2016 - 2017
% [email protected], [email protected]
function CTColormapRGB()
linearColormapR = nan(4096,1);
linearColormapG = nan(4096,1);
linearColormapB = nan(4096,1);
linearColormapR(1:1024) = linspace(1,0,length(1:1024));
linearColormapG(1025:1125) = linspace(0,1,length(1025:1125));
linearColormapB(1126:1525) = linspace(1,0,length(1126:1525));
linearColormapR(1526:4096) = linspace(0,1,length(1526:4096));
% have the neighbor regions overlapping!
linearColormapB(1126:4096) = linspace(0,1,length(1126:4096)); % increase brigthness
linearColormapRGB = [linearColormapR linearColormapG linearColormapB];
colormap(linearColormapRGB)
% %% Plot Transfer Function
% f= figure, plot(-1024:1:3071, linearColormap, 'LineWidth', 5)
% a = gca
% a.XTick = [-1024 0 100 500 3072]
% a.XGrid = 'on'
% xlabel('Data intensity [HU]')
% ylabel('Display Intensity')
% title('Piece-wise Linear Non-Monotic Tone Mapping Transfer Function')
% ChangeInterpreter(gcf,'Latex');
%
% xlim([-1025 3073])
% pos=f.Position;
% pos(3) = 1200;
% pos(4) = 200;
% f.Position = pos;
% a.FontSize = 18;
% cmdStr = Plot2LaTeX(gcf, 'piece-wise-lin-tone-mapping');
% disp(cmdStr);
end
|
github
|
adhusch/PaCER-master
|
scatterMatrix3.m
|
.m
|
PaCER-master/lib/Helpers/scatterMatrix3.m
| 1,025 |
utf_8
|
8cee1b90eb55edf9da58b2576b6a9d71
|
%% scatterSpheres - plot scattered points
%
% Andreas Husch
% Centre Hospitalier de Luxembourg, Dep. of Neurosurgery /
% University of Luxembourg - Luxembourg Centre for Systems Biomedicine
% 2014 - 2017
% [email protected], [email protected]
function h = scatterMatrix3(pointcloud, options, varargin)
fixedArgin = {}; %#ok<NASGU>
if(nargin <= 2)
fixedArgin = {10};
options = {}
else
fixedArgin(1) = varargin(1);
varargin(1) = [];
end
inParse = inputParser;
inParse.KeepUnmatched = true;
inParse.addParameter('numbers',false, @islogical);
inParse.parse(options{:});
nm = size(pointcloud);
if(nm(2) > nm(1) && max(nm) > 3)
pointcloud = pointcloud';
end
h = scatter3(pointcloud(:,1),pointcloud(:,2), pointcloud(:,3),fixedArgin{:}, varargin{:});
if(inParse.Results.numbers)
text(pointcloud(:,1),pointcloud(:,2), pointcloud(:,3),cellstr(num2str((1:size(pointcloud,1))')));
end
end
|
github
|
adhusch/PaCER-master
|
convertMedtronicCoordToLPI.m
|
.m
|
PaCER-master/lib/Helpers/convertMedtronicCoordToLPI.m
| 598 |
utf_8
|
9f5a761f7eb86fb053690473a56e968d
|
%% convertMedtronicCoordToLPI - be careful with that
%
% Andreas Husch
% Centre Hospitalier de Luxembourg, Dept. of Neurosurgery /
% University of Luxembourg - Luxembourg Centre for Systems Biomedicine
% 2014 - 2017
% [email protected], [email protected]
function pointsLPI = convertMedtronicCoordToLPI(pointsInMm, refNii)
refNii.load();
% convert system of Medtronic to LPI [mm] in
% reference image space (origin LPI image corner)
origin = refNii.voxdim .* refNii.voxsize; %RAS corner in [mm]
origin(1) = 0; %LAS corner
pointsLPI = abs(origin - pointsInMm);
end
|
github
|
adhusch/PaCER-master
|
scatterSpheres.m
|
.m
|
PaCER-master/lib/Helpers/scatterSpheres.m
| 668 |
utf_8
|
db0d3a8efa8ea8d4a49077ab404e662a
|
%% scatterSpheres - plot scattered points as spheres
%
% Andreas Husch
% Centre Hospitalier de Luxembourg, Dep. of Neurosurgery /
% University of Luxembourg - Luxembourg Centre for Systems Biomedicine
% 2014 - 2017
% [email protected], [email protected]
function graphicsHandle = scatterSpheres(points, diameter, color, varargin)
if(nargin < 4)
varargin = {};
end
if(nargin < 3)
color = 'y';
end
nm = size(points);
if(nm(1) < nm(2))
points = points';
end
graphicsHandle = hggroup;
for i = 1:length(points);
plotSphere(points(i,:), diameter, color, graphicsHandle, varargin{:});
end
end
|
github
|
adhusch/PaCER-master
|
getFilenameFromWildcard.m
|
.m
|
PaCER-master/lib/Helpers/getFilenameFromWildcard.m
| 445 |
utf_8
|
5030098adb1e4384c041eef41a3eb342
|
%% getFilenameFromWildcard
%
% Florian Bernard
% Centre Hospitalier de Luxembourg, Dep. of Neurosurgery /
% University of Luxembourg - Luxembourg Centre for Systems Biomedicine
% 2014 - 2017
function filepath=getFilenameFromWildcard(folder, wildcard)
theFile=[folder filesep wildcard];
filepath=dir(theFile);
if ( ~isempty(filepath) )
filepath = [filepath(1).name];
else
filepath = [];
end
end
|
github
|
adhusch/PaCER-master
|
readLabels.m
|
.m
|
PaCER-master/lib/Helpers/readLabels.m
| 2,160 |
utf_8
|
ace2564e15a0baa4baa9594bf0eabd5c
|
%% readLabels - read ITK-Snap label file
%
% Florian Bernard, Andreas Husch
% Centre Hospitalier de Luxembourg, Dep. of Neurosurgery /
% University of Luxembourg - Luxembourg Centre for Systems Biomedicine
% 2014 - 2017
% [email protected], [email protected]
function [labelNames, rgbColors, labelId]=readLabels(labelFile)
% if ( Const.fileOperationsDebug )
disp(['Reading label file: ' labelFile]);
% end
if(exist(labelFile, 'file'))
labelFID=fopen(labelFile, 'r');
textscan(labelFID, '%s', 14, 'delimiter','\n');
labelRaw = textscan(labelFID, '%u %d %d %d %u %u %u %q', 'delimiter','\n');
fclose(labelFID);
else
disp('Label File could not be found. Using static labels instead!');
labelFID=[' 0 0 0 0 0 0 0 "Clear Label"+'...
' 1 5 255 0 1 1 1 "SNr+STN_L"+' ...
' 2 0 0 255 1 1 1 "SNr+STN_R"+' ...
' 3 255 21 0 1 1 1 "NR_L"+' ...
' 4 0 255 255 1 1 1 "NR_R"+' ...
' 5 255 255 0 1 1 1 "AC"+' ...
' 6 255 0 255 1 1 1 "SNr_L"+' ...
' 7 255 239 213 1 1 1 "SNr_R"+' ...
' 8 0 0 205 1 1 1 "STN_L"+' ...
' 9 205 133 63 1 1 1 "STN_R"+' ...
' 10 210 180 140 1 1 1 "SNr+STN_LR"' ...
' 11 205 173 0 1 1 1 "MRI_Electrode_Artifact_L"' ...
' 12 0 0 128 1 1 1 "MRI_Electrode_Artifact_R"' ...
' 13 255 19 0 1 1 1 "Arterial System"'];
% read labels
labelRaw = textscan(labelFID, '%u %d %d %d %u %u %u %q', 'delimiter','+');
end
labelId = labelRaw{1};
labelNames=labelRaw{end};
rgbColors=double([labelRaw{2} labelRaw{3} labelRaw{4}]) ./ 255;
% attention: labelNames{1} corresponds to voxels with intensity 0
end
|
github
|
adhusch/PaCER-master
|
CTColormap.m
|
.m
|
PaCER-master/lib/Helpers/CTColormap.m
| 1,207 |
utf_8
|
56575f50923a489156ed62355fa1aa2c
|
%% Applying Tone Mapping to CT Data Enabling Simultaneus Display of Bony and Soft-Tissue Structures
%
% Andreas Husch
% Centre Hospitalier de Luxembourg, Dep. of Neurosurgery /
% University of Luxembourg - Luxembourg Centre for Systems Biomedicine
% 2016 - 2017
% [email protected], [email protected]
function CTColormap()
linearColormap = nan(4096,1);
linearColormap(1:1024) = linspace(1,0,length(1:1024));
linearColormap(1025:1125) = linspace(0,1,length(1025:1125));
linearColormap(1126:1525) = linspace(1,0,length(1126:1525));
linearColormap(1526:4096) = linspace(0,1,length(1526:4096));
linearColormapRGB = [linearColormap linearColormap linearColormap];
colormap(linearColormapRGB)
% %% Plot Transfer Function
% f= figure, plot(-1024:1:3071, linearColormap, 'LineWidth', 5)
% a = gca
% a.XTick = [-1024 0 100 500 3072]
% a.XGrid = 'on'
% xlabel('Data intensity [HU]')
% ylabel('Display Intensity')
% title('Piece-wise Linear Non-Monotic Tone Mapping Transfer Function')
% ChangeInterpreter(gcf,'Latex');
%
% xlim([-1025 3073])
% pos=f.Position;
% pos(3) = 1200;
% pos(4) = 200;
% f.Position = pos;
% a.FontSize = 18;
% cmdStr = Plot2LaTeX(gcf, 'piece-wise-lin-tone-mapping');
% disp(cmdStr);
end
|
github
|
adhusch/PaCER-master
|
getFilepathFromWildcard.m
|
.m
|
PaCER-master/lib/Helpers/getFilepathFromWildcard.m
| 1,917 |
utf_8
|
9cd45f758a63c9ade3b9772da3fe93a8
|
%% getFilepathFromWildcard
%
% Florian Bernard
% Centre Hospitalier de Luxembourg, Dep. of Neurosurgery /
% University of Luxembourg - Luxembourg Centre for Systems Biomedicine
% 2014 - 2017
function filepath=getFilepathFromWildcard(folder, wildcard)
% theFile=[folder filesep wildcard];
% filepath=dir(theFile);
wildcardRegexp = strrep(wildcard, '*', '.*');
allFilepaths=dir(folder);
matchingIndices = [];
for i=1:numel(allFilepaths)
fpName = allFilepaths(i).name;
currIdx = regexpi(fpName, wildcardRegexp);
if ( ~isempty(currIdx) )
matchingIndices(end+1) = i;
end
end
filepath = [];
if ( numel(matchingIndices) >= 1 )
for i=1:numel(matchingIndices)
currFp = allFilepaths(matchingIndices(i));
if ( ~strcmp(currFp.name(1) ,'.'))
filepath = [folder filesep currFp.name];
if ( size(filepath,1) > 1 )
warning(['Multiple matches in folder ' folder ...
' for wildcard ' wildcard ...
' ! The first match that does not begin with . is returned ( '...
filepath ' ).']);
end
return;
end
end
end
% if ( ~isempty(filepath) )
%
% for i=1:numel(filepath)
% if ( ~strcmp(filepath(i).name(1) ,'.') )
% filepath = [folder filesep filepath(i).name];
% if ( size(filepath,1) > 1 )
% warning(['Multiple matches in folder ' folder ...
% ' for wildcard ' wildcard ...
% ' ! The first match that does not begin with . is returned ( '...
% filepath ' ).']);
% end
% return;
% end
% end
% else
% filepath = [];
% end
end
|
github
|
adhusch/PaCER-master
|
rowNorm.m
|
.m
|
PaCER-master/lib/Helpers/rowNorm.m
| 293 |
utf_8
|
e77c17b5f07126023d2f5a3c661d5c9b
|
%% rowNorm - row-wise eucliadian norm
%
% Andreas Husch
% Centre Hospitalier de Luxembourg, Dep. of Neurosurgery /
% University of Luxembourg - Luxembourg Centre for Systems Biomedicine
% 2014 - 2017
% [email protected], [email protected]
function d = rowNorm(A)
d = sqrt(sum(A.*A, 2));
|
github
|
adhusch/PaCER-master
|
createColorImage.m
|
.m
|
PaCER-master/lib/Helpers/createColorImage.m
| 3,659 |
utf_8
|
5caeb71700bcf18c6b404dce6d19b9d2
|
%% createColorImage (RGB) from colormap and indexed image
%
% Andreas Husch
% Centre Hospitalier de Luxembourg, Dept. of Neurosurgery /
% University of Luxembourg - Luxembourg Centre for Systems Biomedicine
% 2009 - 2017
% [email protected], [email protected]
function image = createColorImage(rawImageData, myColormap, lowerLimit, upperLimit)
%cmHumidity = [1,0.600000023841858,0;1,0.623529434204102,0.00267379684373736;1,0.647058844566345,0.00534759368747473;1,0.670588254928589,0.00802139099687338;1,0.694117665290833,0.0106951873749495;1,0.717647075653076,0.0133689846843481;1,0.741176486015320,0.0160427819937468;1,0.764705896377564,0.0187165774405003;1,0.788235306739807,0.0213903747498989;1,0.811764717102051,0.0240641720592976;1,0.835294127464294,0.0267379693686962;1,0.858823537826538,0.0294117648154497;1,0.882352948188782,0.0320855639874935;1,0.905882358551025,0.0347593575716019;1,0.929411768913269,0.0374331548810005;1,0.952941179275513,0.0401069521903992;1,0.976470589637756,0.0427807494997978;1,1,0.0454545468091965;0.990909099578857,0.990909099578857,0.0888429731130600;0.981818199157715,0.981818199157715,0.132231399416924;0.972727298736572,0.972727298736572,0.175619840621948;0.963636338710785,0.963636338710785,0.219008266925812;0.954545438289642,0.954545438289642,0.262396693229675;0.945454537868500,0.945454537868500,0.305785119533539;0.936363637447357,0.936363637447357,0.349173545837402;0.927272737026215,0.927272737026215,0.392561972141266;0.918181836605072,0.918181836605072,0.435950428247452;0.909090936183929,0.909090936183929,0.479338854551315;0.899999976158142,0.899999976158142,0.522727251052856;0.890909075737000,0.890909075737000,0.566115677356720;0.881818175315857,0.881818175315857,0.609504103660584;0.872727274894714,0.872727274894714,0.652892589569092;0.863636374473572,0.863636374473572,0.696281015872955;0.854545474052429,0.854545474052429,0.739669442176819;0.845454573631287,0.845454573631287,0.783057868480682;0.836363673210144,0.836363673210144,0.826446294784546;0.827272713184357,0.827272713184357,0.869834721088409;0.818181812763214,0.818181812763214,0.913223147392273;0.809090912342072,0.809090912342072,0.956611573696137;0.800000011920929,0.800000011920929,1;0.766666650772095,0.766666650772095,1;0.733333349227905,0.733333349227905,1;0.699999988079071,0.699999988079071,1;0.666666686534882,0.666666686534882,1;0.633333325386047,0.633333325386047,1;0.600000023841858,0.600000023841858,1;0.566666662693024,0.566666662693024,1;0.533333361148834,0.533333361148834,1;0.500000000000000,0.500000000000000,1;0.466666668653488,0.466666668653488,1;0.433333337306976,0.433333337306976,1;0.400000005960465,0.400000005960465,1;0.366666674613953,0.366666674613953,1;0.333333343267441,0.333333343267441,1;0.300000011920929,0.300000011920929,1;0.266666680574417,0.266666680574417,1;0.233333334326744,0.233333334326744,1;0.200000002980232,0.200000002980232,1;0.166666671633720,0.166666671633720,1;0.133333340287209,0.133333340287209,1;0.100000001490116,0.100000001490116,1;0.0666666701436043,0.0666666701436043,1;0.0333333350718021,0.0333333350718021,1;0,0,1;];
rawImageData(isnan(rawImageData)) = 0;
colorIndices = round(...
max(...% prevent 0 results
min((double(rawImageData) - double(lowerLimit)) ./ double(upperLimit - lowerLimit),...
1) ...
.* length(myColormap),...
1));
% myColormap = flipud(myColormap);
imageVector = myColormap(colorIndices,:,:);
image = reshape(imageVector, [size(rawImageData) 3]);
end
|
github
|
adhusch/PaCER-master
|
applyFSLTransformToPoints.m
|
.m
|
PaCER-master/lib/FSLTransforms/applyFSLTransformToPoints.m
| 1,115 |
utf_8
|
0b3a327da38862ac66deacd3a588a139
|
%% applyFSLTransformToPoints - transform points in world coordinats of sourceRefImage to
% world coordinates in targetRefImage applying a FSL (FLIRT) transformation
% matrix. world coordinates in PaCER style. (note L/R orientation in plots
% i.e. axis ij vs axis xy!)
%
% Parameters: points - Nx3 matrix
% fslTransMat - FSL transformation matrix (4x4)
% sourceRefImage - Source reference image (NiftiModality or filename)
% targetRefImage - Target reference image (NiftiModality or filename)
%
% Returns: transPoints - Nx3 matrix
%
% Andreas Husch
% Centre Hospitalier de Luxembourg, Dep. of Neurosurgery /
% University of Luxembourg - Luxembourg Centre for Systems Biomedicine
% 2017
% [email protected], [email protected]
function transPoints = applyFSLTransformToPoints(points, fslTransMat, sourceRefImage, targetRefImage)
LtoR = diag([1 1 1]);
pointsR = points * LtoR;
transWorldToWorld = flirtmat2worldmatPaCER(fslTransMat,sourceRefImage,targetRefImage);
transPoints = (inv(transWorldToWorld) * [pointsR ones(length(pointsR), 1)]')' ; %#ok<MINV> %note the inv()!%
end
|
github
|
adhusch/PaCER-master
|
flirtmat2worldmatPaCER.m
|
.m
|
PaCER-master/lib/FSLTransforms/flirtmat2worldmatPaCER.m
| 2,775 |
utf_8
|
4516ba4f2e301c04bd336628ec001913
|
% Simplified version of flirtmat2worldmat removing the various dependencies
% to SPM. Instead using PaCER's Nifti Classes which in turn rely on the
% Nifti Toolbox. Thus it works with .nii.gz files too and has a lot less
% dependencies in general.
% 2017 Andreas Husch.
%
% Based on flirtmat2worldmat by Ged Rigway. See Original
% Text below:
%
% flirtmat2worldmat: convert saved flirt matrix to NIfTI world coords matrix
% flirt matrix is from text file specified in "flirt -omat mat.txt" command
% world matrix maps from NIfTI world coordinates in target to source. Note:
% mat.txt contains a mapping from source to target in FSL's *scaled* coords
% which are not NIfTI world coordinates, and note src-trg directionality!
% worldmat from this script reproduces "img2imgcoord -mm ...".
%
% The script can also return a matrix to map from target to source voxels
% in MATLAB/SPM's one-based convention, or in FSL's zero-based convention
%
% Example:
% [worldmat spmvoxmat fslvoxmat] = flirtmat2worldmat(flirtmat, src, trg);
%
% See also: worldmat2flirtmat, flirtmat_read, flirtmat_write
% Copyright 2009 Ged Ridgway <ged.ridgway gmail.com>
function [worldmat spmvoxmat fslvoxmat] = flirtmat2worldmatPaCER(flirtmat, niiSrc, niiTrg)
if ischar(niiSrc)
niiSrc = NiftiMod(niiSrc, 'isToBeCached', false); %HA: interpreating as filename, loading nii header
end
if ischar(niiTrg)
niiTrg = NiftiMod(niiTrg, 'isToBeCached', false); %HA: interpreating as filename, loading nii header
end
% src = inv(flirtmat) * trg
% srcvox = src.mat \ inv(flirtmat) * trg.mat * trgvox
% BUT, flirt doesn't use src.mat, only absolute values of the
% scaling elements from it,
% AND, if images are not radiological, the x-axis is flipped, see:
% https://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=ind0810&L=FSL&P=185638
% https://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=ind0903&L=FSL&P=R93775
trgscl = nifti2scl(niiTrg.transformationMatrix, niiTrg.voxdim);
srcscl = nifti2scl(niiSrc.transformationMatrix, niiSrc.voxdim);
fslvoxmat = inv(srcscl) * inv(flirtmat) * trgscl;
% AND, Flirt's voxels are zero-based, while SPM's are one-based...
addone = eye(4);
%addone(:, 4) = 1; We DON'T need that it PaCER (would induce off by one
%error)
spmvoxmat = addone * fslvoxmat * inv(addone);
worldmat = niiSrc.transformationMatrix * spmvoxmat * inv(niiTrg.transformationMatrix);
%% Nested Helper
function scl = nifti2scl(mat, voxdim)
scl = diag([sqrt(sum(mat(1:3,1:3).^2)) 1]);
if det(mat) > 0
% neurological, x-axis is flipped, such that [3 2 1 0] and [0 1 2 3]
% have the same *scaled* coordinates:
xflip = diag([-1 1 1 1]);
xflip(1, 4) =voxdim(1)-1;% reflect about centre
scl = scl * xflip;
end
end
end
|
github
|
adhusch/PaCER-master
|
applyFSLTransformToPolyCoeffs.m
|
.m
|
PaCER-master/lib/FSLTransforms/applyFSLTransformToPolyCoeffs.m
| 1,275 |
utf_8
|
b417e27f523f2d03eff0336534447717
|
%% applyFSLTransformToPolyCoeffs - transform polynomial coefficient matrix in world coordinats of sourceRefImage to
% world coordinates in targetRefImage applying a FSL (FLIRT) transformation matrix
%
% Parameters: coeffs - Nx3 matrix, coeffs(end,:) is the bias term (x^0)
% fslTransMat - FSL transformation matrix (4x4)
% sourceRefImage - Source reference image (NiftiModality or filename)
% targetRefImage - Target reference image (NiftiModality or filename)
%
% Returns: transCoeffs - Nx3 matrix
%
% Andreas Husch
% Centre Hospitalier de Luxembourg, Dep. of Neurosurgery /
% University of Luxembourg - Luxembourg Centre for Systems Biomedicine
% 2017
% [email protected], [email protected]
function transCoeffs = applyFSLTransformToPolyCoeffs(coeffs, fslTransMat, sourceRefImage, targetRefImage)
LtoR = diag([1 1 1]);
transWorldToWorld = flirtmat2worldmatPaCER(fslTransMat,sourceRefImage,targetRefImage);
transfWoT = inv(transWorldToWorld); % take inv here
transfWoT(1:3,4) = 0;
transCoef = [coeffs(1:end-1,:)*LtoR ones(length(coeffs(1:end-1,:)), 1)] * (transfWoT)'; % note the transpose!!
transBias = [coeffs(end,:)*LtoR 1] * inv(transWorldToWorld)'; % note the transpose!!
transCoeffs = [transCoef(:,1:3); transBias(:,1:3)];
end
|
github
|
adhusch/PaCER-master
|
NiftiModSPM.m
|
.m
|
PaCER-master/lib/NiftiOOP/NiftiModSPM.m
| 9,088 |
utf_8
|
325d0cc0f4f3e91e49bf08211858340f
|
%% NiftiyModSPM - Base class for all Nifti Objects. Wrapping the SPM Toolbox.
%
% Andreas Husch, Florian Bernard
% Centre Hospitalier de Luxembourg, Dep. of Neurosurgery /
% University of Luxembourg - Luxembourg Centre for Systems Biomedicne
% 2016 - 2017
% [email protected], [email protected]
%
% Andreas Horn
% Charite University Medicine Berlin - Movement Disorders Unit
% 2018
%
% Andreas Husch
% University of Luxembourg - Luxembourg Centre for Systems Biomedicne
% 2018
classdef NiftiModSPM < id & configurable
properties (Access = protected) %references to data objects
header = []; % the nifti header (real data)
data = []; % raw nifti data isLoaded in ram as matlab matrix???
filepathSuffix = [];
end
properties (SetAccess = protected, GetAccess = public) %references to data objects
voxdim = NaN(3,1); % voxel dimensions, P,L,I
voxsize = NaN(3,1); % voxel size, P,L,I in mm
transformationMatrix = NaN(4,4); % matrix that transforms voxel indices to world coordinates in mm
isLoaded; % true = in memory, false = on disk
argParser = [];
niftiFilepathObject = [];
end
properties (Access = public, SetObservable = true) % public access via specific set/get methods
isToBeCached=true; % true => data is kept in memory as long as possible
end
properties (Dependent = true, SetObservable = true, Hidden = true) % create "nifti structure like" interface with "virtual" properties
hdr;
img;
end
properties (Access = public, SetObservable = true, Transient = true, Dependent) % public access via specific set/get methods
%HA: FIXME: Dependent!?
filepath = ''; % full qualified path + filename (normaly a nifti file)
end
methods
function this = NiftiModSPM(niftiFilepathObject, varargin)
if( ~isa(niftiFilepathObject, 'NiftiFilepath'))
niftiFilepathObject = NiftiFilepath(niftiFilepathObject);
end
if ( ~isa(niftiFilepathObject, 'NiftiFilepath') )
error('First argument must be a NiftiFilepath object!');
end
this = this@id(); % call superclass constructor to get an ID
this.isLoaded = false;
lhdr = ea_open_vol(niftiFilepathObject.filepath); % make sure to load header on object conostruction
this.voxdim = lhdr.dim';
this.voxsize= lhdr.voxsize';
this.transformationMatrix = lhdr.mat;
A = lhdr.mat(1:3,1:3);
if(A(~eye(3)))
warning('Transformation contains off-diagnonal elements. Check carefully and consider reordering of data');
end
this.data = [];
this.niftiFilepathObject = niftiFilepathObject;
this.argParser = inputParser();
this.argParser.KeepUnmatched = true;
this.argParser.addOptional('isToBeCached', true);
this.argParser.parse(varargin{:});
args = this.argParser.Results;
this.isToBeCached = args.isToBeCached;
end
function str = toString(this)
[~, str] = fileparts(this.filepath);
end
function value = get.filepath(this)
value = this.niftiFilepathObject.filepath;
end
function [image, header] = load(this)
if( ~this.isLoaded && ~strcmp(this.filepath,'')) % it is not already isLoaded and we were not called with empty string (by Matlab callingn our get functions without command after initiating!)
disp(['Loading ' this.filepath ' from disk using NiftiModSPM...']);
%nifti = ea_load_untouch_nii(this.filepath);
eanifti = ea_load_nii(this.filepath);
this.voxdim = eanifti.dim';
this.voxsize= eanifti.voxsize';
this.header = eanifti; % header should maybe kept all the time ..
this.transformationMatrix = eanifti.mat;
if(this.isToBeCached) % keep data in attributes if caching is enabled
disp('Caching is enabled.');
this.data = eanifti.img;
this.isLoaded = true;
else
disp('Caching is disabled. NOT keeping original volume in memory! Set this.isToBeCached = true to change this behaviour.');
this.data = [];
this.isLoaded = false;
end
header = eanifti; % return data all the time
image = single(eanifti.img);
end
end
function worldCoordinates=getNiftiWorldCoordinatesFromMatlabIdx(this, ...
voxelIdxList,varargin)
% matlab index starts with 1, not 0
worldCoordinates = this.transformationMatrix*[voxelIdxList; ones(1, size(voxelIdxList,2))];
worldCoordinates = worldCoordinates(1:3,:);
end
function voxelIdxList = getMatlabIdxFromNiftiWorldCoordinates(this, worldCoordList,...
varargin)
if ( ~isempty(worldCoordList) && size(worldCoordList,1) ~= 3)
error('worldCoordList needs to be a 3 x N matrix');
end
voxelIdxList = this.transformationMatrix\[worldCoordList; ones(1, size(worldCoordList,2))];
voxelIdxList = voxelIdxList(1:3,:); % matlab index starts with 1, not 0 however SPM already compensated for that by altering the transformationMatrix :-)
end
function passivate(this) % remove data from memory. will be automatically reisLoaded if needed
disp(['Passivating ' this.filepath ' ...']);
this.data = [];
this.isLoaded = false;
end
function image = get.img(this)
if(~this.isLoaded) % load nifti from disk when needed
[image, ~] = this.load();
else
image = this.data;
end
end
function save(this, newFilepath, newImg, isSegmentation, forceFloat)
warning('Saving files is currently not supported by NiftiModSPM');
return;
% this.hdr has been changed during load_nii call (in contrast to
% load_untouch_nii function). however, here we need exactly the
% original header, therefore it is loaded again
nii = ea_load_nii(this.niftiFilepathObject.filepath);
if ( exist('isSegmentation','var') && isSegmentation )
nii.dt(1) = 2; % uint8 is sufficient for segmentation
end
if ( exist('forceFloat','var') && forceFloat )
nii.dt(1) = 16;
end
% %% we won't need below part due to using SPM for loading
% % nii.hdr = this.hdr;
% if ( this.dim(1) ~= nii.dim(1) )
% warning('niftiModality:swapLR', 'Swapping left and right because original and touched header do not agree, make sure to check if the nifti file is as expected!');
% nii.img = newImg(end:-1:1,:,:);
% else
% nii.img = newImg;
% end
% nii.untouch = 1;
%
% disp(['Saving new image data in ' newFilepath ' to disk...']);
%
% [pathstr,filename,ext] = fileparts(newFilepath);
% if(isequal(ext,''))
% newFilepath = [newFilepath, '.nii'];
% elseif(isequal(ext,'.gz'))
% newFilepath = [pathstr filesep filename];
% elseif(~isequal(ext,'.nii'))
% error('NiftiModality:save:WrongFileending','Current Fileending is unkown');
% end
%
% save_untouch_nii(nii, newFilepath);
%
%
% % save zipped file
% gzip(newFilepath); %TODO make this configurable
% delete(newFilepath);
% % this.filepath = newFilepath;
% % newFilepath = [newFilepath, '.gz'];
% % this.niftiFilepathObject = NiftiFilepath(newFilepath);
% %%
end
function header = get.hdr(this)
if(isempty(this.header)) % load nifti from disk when needed
[~, header] = this.load();
% as the header is transformed during load it is not possible
% to load the header only as done below (leads to equal header
% as returned by load_untouch_nii()
% [this.header] = load_nii_hdr(this.filepath);
%
% this.voxdim = this.header.dime.dim(2:4);
% this.voxsize= this.header.dime.pixdim(2:4);
% header = this.header;
else
header = this.header;
end
end
end
end
function test() %#ok<DEFNU>
%%
niiFile = '/Users/fb/cnm/svn/resources/directions_mni.nii.gz';
nii = NiftiModSPM(NiftiFilepath(niiFile));
nii.load();
idx = [1 1 1; 10 10 10; 12 17 99]';
nii.getNiftiWorldCoordinatesFromMatlabIdx(idx)
%%
end
|
github
|
adhusch/PaCER-master
|
checkNiftiHdr.m
|
.m
|
PaCER-master/lib/NiftiOOP/checkNiftiHdr.m
| 1,376 |
utf_8
|
a18ece9916ca8ef02c516582a1afa417
|
%% checkNifti - basic consistency checking of nifti headers according to the nifti-1 standard
%
% Andreas Husch
% University of Luxembourg - Luxembourg Centre for Systems Biomedicine
%
% 2018
%
% [email protected], [email protected]
function checkNiftiHdr(nii)
NIFTI_DOC = ' <a href="https://nifti.nimh.nih.gov/nifti-1/documentation/nifti1fields/nifti1fields_pages/qsform.html">https://nifti.nimh.nih.gov/nifti-1/documentation/nifti1fields/nifti1fields_pages/qsform.html</a>';
if(nii.hdr.hist.qform_code == 0)
warning(['checkNifti: Nifti qform_code = 0, this is discouraged by the Nifti-1 standard. '...
'Please check carefully and refer to ' NIFTI_DOC ' section 5. METHOD 1. Consider '...
'fixing the nifti header of your file before continuing.']);
end
if(nii.hdr.hist.sform_code == nii.hdr.hist.qform_code)
h = nii.hdr.hist;
h.pixdim = nii.hdr.dime.pixdim;
if(~all(all(nii.qform - nii.sform < eps(single(1)))))
warning(['checkNifti: qform_code == sform_code, however the transformation defined in the qform '...
'differes from the sform! This might indicate a serious flaw in the nifti header '...
'and lead to unexpected results as different tools/algorithms might deal differently '...
'with this situation. Fix the nifti header of your file before continuing.']);
end
end
end
|
github
|
adhusch/PaCER-master
|
applyANTSTransformToPolyCoeffs.m
|
.m
|
PaCER-master/lib/ANTSTransforms/applyANTSTransformToPolyCoeffs.m
| 2,177 |
utf_8
|
4a68c10680a6a27c12a525b6924669ae
|
%% applyANTSTransformToPolyCoeffs - transform polynomial coefficient matrix in world coordinats of sourceRefImage to
% world coordinates in targetRefImage applying a ANTS affine transformation
%
% Parameters: coeffs - Nx3 matrix, coeffs(end,:) is the bias term (x^0)
% antsTransformFileStrings - '[antsTransformFile, useInverseFlag]' String with tuples of
% ANTS transformation file(s) names (binary
% .mat) strings and useInverseFlags, if multiple transformations should be concattenated
% pass a cell of transformation tuples. Note that the order is
% ANTs-like, i.e. stacked (last is applied first), and that
% ANTs specifies point transformations in the *inverse*
% direction than non-point transformations, thus useInverseFlag must be 1 for
% a transform from A->B and 0 for a Transform A<-B.
% Refer to ANTs documentation for details.
%
% Returns: transCoeffs - Nx3 matrix
%
% Example: transCoeffs = applyANTSTransformToPolyCoeffs(coeffs,{'[trans_rigid_ct_post_to_t10GenericAffine.mat,1]','[trans_rigid_t1_to_mni0GenericAffine.mat,1]'})
%
% Andreas Husch
% Centre Hospitalier de Luxembourg, Dep. of Neurosurgery /
% University of Luxembourg - Luxembourg Centre for Systems Biomedicine
% 2017
% [email protected], [email protected]
function transCoeffs = applyANTSTransformToPolyCoeffs(coeffs, antsTransformFileStrings)
LtoR = [-1 -1 1];
coeffs = coeffs * diag(LtoR); % LPI / RPI
trans = applyANTSTransformToPoints(coeffs,antsTransformFileStrings);
translation = applyANTSTransformToPoints([0 0 0],antsTransformFileStrings); % valid if center of rotation equals origin of space
transTranslation = applyANTSTransformToPoints(translation,antsTransformFileStrings); % valid if center of rotation equals origin of space
transBias = trans(end,:);% .* LtoR;
transCoef = trans(1:end-1,:);% .* LtoR;
% fix translation of coefs ( not to be translated)
transCoef = transCoef - repmat(translation,length(transCoef),1);
%FIXME document this
transCoeffs = [transCoef; transBias];
transCoeffs = transCoeffs * diag(LtoR);
end
|
github
|
adhusch/PaCER-master
|
applyANTSTransformToPoints.m
|
.m
|
PaCER-master/lib/ANTSTransforms/applyANTSTransformToPoints.m
| 2,485 |
utf_8
|
9499fd0f8a2e46f8ff55225ab1dab63d
|
%% applyANTSTransformToPoints - transform points in world coordinats of a sourceRefImage to
% world coordinates in targetRefImage applying a ANTS affine transformation
%
% Parameters: transPoints - Nx3 matrix of points in world cooridnates
% antsTransformFileStrings - '[antsTransformFile, useInverseFlag]' String with tuples of
% ANTS transformation file(s) names (binary
% .mat) strings and useInverseFlags, if multiple transformations should be concattenated
% pass a cell of transformation tuples. Note that the order is
% ANTs-like, i.e. stacked (last is applied first), and that
% ANTs specifies point transformations in the *inverse*
% direction than non-point transformations, thus useInverseFlag must be 1 for
% a transform from A->B and 0 for a Transform A<-B.
% Refer to ANTs documentation for details.
%
% Returns: Transformed Points
%
% Example: applyANTSTransformToPoints(rand(20,3), {'[trans_1_0GenericAffine.mat,1]','[trans_2_0GenericAffine.mat,1]'})
%
% Andreas Husch
% Centre Hospitalier de Luxembourg, Dep. of Neurosurgery /
% University of Luxembourg - Luxembourg Centre for Systems Biomedicine
% (c) 2017
% [email protected], [email protected]
function transPoints = applyANTSTransformToPoints(points, antsTransformFileStrings)
try
[~, t] = system('echo $ANTSPATH');
antspath = t(1:end-1); % remove line ending
end
if(~isempty(t))
applyTransformsToPointsCmd = [antspath 'antsApplyTransformsToPoints'];
else
applyTransformsToPointsCmd = 'antsApplyTransformsToPoints'; % FIXME: Make multi-os compatabile and find bins automatically
end
tempFile = [tempname() '.csv'];
tempFileOut = [tempname() '.csv'];
fileHandle = fopen(tempFile, 'w');
fprintf(fileHandle, 'x,y,z,t,label,comment\n');
fclose(fileHandle);
dlmwrite(tempFile, [points zeros(size(points,1),3)], '-append');
cmd = [applyTransformsToPointsCmd ' -d 3 -p 1 -i ' tempFile ];
if(iscell(antsTransformFileStrings))
for i=1:length(antsTransformFileStrings)
cmd = [cmd ' -t ' antsTransformFileStrings{i}]; %#ok<AGROW>
end
else
cmd = [cmd ' -t ' antsTransformFileStrings];
end
cmd = [cmd ' -o ' tempFileOut];
if(~ispc)
ret = system(['bash -c "' cmd '"']);
else
ret = system(cmd);
end
assert(ret == 0);
points = dlmread(tempFileOut, ',', 1, 0);
delete(tempFileOut);
delete(tempFile);
transPoints = points(:,1:3);
|
github
|
adhusch/PaCER-master
|
rdir.m
|
.m
|
PaCER-master/external/rdir/rdir.m
| 11,992 |
utf_8
|
4ce6f476106d5c871b653f590cb3db3a
|
function [varargout] = rdir(rootdir,varargin)
% RDIR - Recursive directory listing
%
% D = rdir(ROOT)
% D = rdir(ROOT, TEST)
% D = rdir(ROOT, TEST, RMPATH)
% D = rdir(ROOT, TEST, 1)
% D = rdir(ROOT, '', ...)
% [D, P] = rdir(...)
% rdir(...)
%
%
% *Inputs*
%
% * ROOT
%
% rdir(ROOT) lists the specified files.
% ROOT can be a pathname, filename, or can include both. One can use
% absolute and relative pathnames and wildcards (*). Wildcard can be placed
% anywhere and used many times like 'path*\*.m'
%
% One can also use a double wildcard (**) to match multiple directory
% levels. For example ROOT = 'path\**\*.m' will match all ".m" files in
% "path" and all subdirectories of "path".
%
% NOTE : ".svn" directories created by SubVersion (SVN) or ".git"
% repositories created by git are excluded from the recursive listing.
%
% * TEST
%
% Optional test that can be performed on the returned files.
%
% TEST is a string indicating expression to be evaluated on selected field
% of rdir output.
% All fields (ie name, date, bytes, isdir and datenum) can be used.
%
% Tests are strings similar to what one would use in a "if" statement e.g.
% 'bytes>1024 & datenum>now-7'
%
% One can also use function like "regexp" or "strfind" with string fields
% like "name" and "date" e.g 'regexp(name, 'expr')'. In that case, tests
% that return a non empty value are considered as true.
%
% regexp(name, '(\.m$)|(\.mdl$)')
%
% Test can also be a function handle as used in arrayfun/cellfun, e.g.
% @(f)f.bytes>1024
%
% * RMPATH
%
% Optional path to remove from beginning of "name" field in returned
% output. Specified path must be common to all items found.
%
% If RMPATH = 1 or true, path to remove is part of ROOT before the first
% wildcard.
%
%
% *Outputs*
%
% * D
%
% D is a structure with the same fields as Matlab DIR output.
%
% The "name" field includes the relative path as well as the name to the
% file that was found. Path can be shorten or ommited when using 3rd
% argument RMPATH.
%
% * P
%
% Common path or RMPATH (if specified) for the file list returned in D.
%
% * Screen output
%
% If not output variable is specified then the output is sent to the
% screen.
%
%
% *Versions*
%
% * 1.0 - 2009, Gus Brown
% * 2.0 - 26/05/2011 Thomas Vanaret
% No longer exclude all directories from a simple search (no *);
% Fixing bug on returned path;
% Exclude ".svn" directories;
% Extended test possibilies;
% Subfunctions created;
% * 2.1 - 14/07/2011 Thomas Vanaret
% New argument allowing to remove common path from name;
% Comments review;
% * 2.2 - 20/12/2011 Thomas Vanaret
% Fixing bug on display with 0b files;
% Specific display when no file match filter;
% * 2.3 - 19/01/2014 Thomas Vanaret
% Adding improvements suggested by X. Mo :
% - function handle as TEST input
% - code optimisation (avoiding loop)
% Fixing possible bug when using a wildcard at the beginning;
% Common path as 2nd optionnal output;
%
%
% *Examples*
%
% D = rdir('*.m');
% for ii=1:length(D), disp(D(ii).name); end;
%
% % to find all files in the current directory and sub directories
% D = rdir('**\*')
%
% % If no output is specified then the files are sent to
% % the screen.
% rdir('c:\program files\windows *\*.exe');
% rdir('c:\program files\windows *\**\*.dll');
%
% % Using the test function to find files modified today
% rdir('c:\win*\*','datenum>floor(now)');
% % Using the test function to find files of a certain size
% rdir('c:\program files\win*\*.exe','bytes>1024 & bytes<1048576');
% % Using the test function to find files modified in 2011
% rdir('c:\win*\*','strfind(date, ''2011'')');
%
% % Using the 3rd input to shorten output name
% rdir([matlabroot, '\*.txt'], '', 'C:\Program Files\')
% % Using the 3rd input to shorten output name
% rdir([matlabroot, '\*.txt'], '', 1)
%
%
% See also DIR
%
%--------------------------------------------------------------------------
%% Input validation
% use the current directory if nothing is specified
if ~exist('rootdir','var'),
rootdir = '*';
end
prepath = ''; % the path before the wild card
wildpath = ''; % the path wild card
postpath = rootdir; % the path after the wild card
I = find(rootdir==filesep,1,'last');
% Directory separator for current platform
if filesep == '\'
% On PC, filesep is '\'
anti_filesep = '/';
else
% On UNIX system, filesep is '/'
anti_filesep = '\';
end
if isempty(I) && ~isempty(strfind(rootdir, anti_filesep))
error([mfilename, ':FileSep'],...
'Use correct directory separator "%s".', filesep)
end
%--------------------------------------------------------------------------
%% Split rootdir
% split the file path around the wild card specifiers
if ~isempty(I),
prepath = rootdir(1:I);
postpath = rootdir(I+1:end);
I = find(prepath=='*',1,'first');
if ~isempty(I),
postpath = [prepath(I:end) postpath];
prepath = prepath(1:I-1);
I = find(prepath==filesep,1,'last');
if ~isempty(I),
wildpath = prepath(I+1:end);
prepath = prepath(1:I);
end;
I = find(postpath==filesep,1,'first');
if ~isempty(I),
wildpath = [wildpath postpath(1:I-1)];
postpath = postpath(I:end);
end;
end;
end;
% disp([' "' prepath '" ~ "' wildpath '" ~ "' postpath '" ']);
%--------------------------------------------------------------------------
%% Recursive listing
% Search for matching files until all wildcards have been considered.
if isempty(wildpath)
% If no directory wildcards then just get files and directories list
D = dir([prepath postpath]);
% Exclude ".", ".." and ".svn" directories from the list
excl = isdotdir(D) | isRepoDir(D);
D(excl) = [];
if isdir([prepath postpath]);
fullpath = [prepath postpath];
else
fullpath = prepath;
end
% Place directories on the top of the list
is_dir = [D.isdir]';
D = [D(is_dir); D(~is_dir)];
% Add path before name
for ii = 1:length(D)
D(ii).name = fullfile(fullpath, D(ii).name);
end
% disp(sprintf('Scanning "%s" %g files found',[prepath postpath],length(D)));
elseif strcmp(wildpath,'**')
% A double wildcards directory means recurs down into sub directories
% first look for files in the current directory (remove extra filesep)
D = rdir([prepath postpath(2:end)]);
% then look for sub directories
D_sd = dir([prepath '*']);
% Exclude ".", "..", ".svn" directories and files from the list
excl = isdotdir(D_sd) | isRepoDir(D_sd) | ~([D_sd.isdir]');
D_sd(excl) = [];
% Process each sub directory found
% Performance tweak: avoid growing array within loop (X. Mo)
c_D = arrayfun(@(x) rdir([prepath x.name filesep wildpath postpath]),...
D_sd, 'UniformOutput', false);
D = [D; cell2mat( c_D ) ];
else
% Process directory wild card looking for sub directories that match
D_sd = dir([prepath wildpath]);
% Exclude ".", "..", ".svn" directories and files from the list
excl = isdotdir(D_sd) | isRepoDir(D_sd) | ~([D_sd.isdir]');
D_sd(excl) = [];
if ~isdir(prepath) || ( numel(D_sd)==1 && strcmp(D_sd.name, prepath))
% Fix case like rdir('path*\...') where prepath is not a full directoty
% name OR case were prepath match a unique directory.
% Previous "dir" return then the matching directory name(s).
% prepath is cleaned to use them.
%
% In else case, prepath is a valid path which must be kept.
prepath = '';
end
% Process each directory found
Dt = dir('');
c_D = arrayfun(@(x) rdir([prepath x.name postpath]),...
D_sd, 'UniformOutput', false);
D = [Dt; cell2mat( c_D ) ];
end
%--------------------------------------------------------------------------
%% Apply filter
% If specified, apply the filter to refine the search.
nb_before_filt = length(D);
warning_msg = '';
if (nargin>=2 && ~isempty(varargin{1})),
try
if isa(varargin{1}, 'function_handle')
test_tf = arrayfun(varargin{1}, D);
else
test_tf = evaluate(D, varargin{1});
end
D = D(test_tf);
catch
if isa(varargin{1}, 'function_handle')
test_expr = func2str(varargin{1});
else
test_expr = varargin{1};
end
warning_msg = sprintf('Invalid TEST "%s" : %s', test_expr, lasterr);
end
end
%--------------------------------------------------------------------------
%% Remove path
% If specified, remove given or common path from each returned path.
common_path = '';
if (nargin>=3 && ~isempty(varargin{2})),
arg2 = varargin{2};
if ischar(arg2)
common_path = arg2;
elseif (isnumeric(arg2) || islogical(arg2)) && arg2
common_path = prepath;
end
rm_path = regexptranslate('escape', common_path);
% Check that path is common to all
start = regexp({D.name}', ['^', rm_path]);
% Convert to a logical.
is_common = not( cellfun(@isempty, start) );
if all(is_common)
for k = 1:length(D)
D(k).name = regexprep(D(k).name, ['^', rm_path], '');
end
else
common_path = '';
end
% 19/07/2012 : ajouter common_path en sortie optionnelle
end
%--------------------------------------------------------------------------
%% Display listing if no output variables are specified
% Screen display.
nout = nargout;
if nout == 0
if isempty(D)
if nb_before_filt == 0
fprintf('%s not found.\n', rootdir)
else
fprintf('No item matching filter.\n')
end
else
if ~isempty(common_path)
fprintf('All in : %s\n', common_path)
end
pp = {'' 'k' 'M' 'G' 'T'};
for ii = 1:length(D)
if D(ii).isdir
% Directory item : display name
disp(sprintf(' %29s %-64s','',D(ii).name));
else
% File item : display size, modification date and name
sz = D(ii).bytes;
if sz > 0
ss = min(4,floor(log2(sz)/10));
else
ss = 0;
end
disp(sprintf('%4.0f %1sb %20s %-64s ',...
sz/1024^ss, pp{ss+1}, datestr(D(ii).datenum, 0), D(ii).name));
end
end
end
elseif nout == 1
% send list out
varargout{1} = D;
else
% send list and common path out
varargout{1} = D;
varargout{2} = common_path;
end;
if ~isempty(warning_msg)
warning([mfilename, ':InvalidTest'],...
warning_msg); % ap aff
end
%---------------------------- end of main function ------------------------
%% ------------------------------------------------------------------------
function tf = isRepoDir(d)
% True for ".svn" or ".git" directories.
% d is a structure returned by "dir"
%
is_dir = [d.isdir]';
is_svn = strcmp({d.name}, '.svn')' | strcmp({d.name}, '.git')';
%is_svn = false; % uncomment to disable ".svn" filtering
tf = (is_dir & is_svn);
%---------------------------- end of subfunction --------------------------
%% ------------------------------------------------------------------------
function tf = isdotdir(d)
% True for "." and ".." directories.
% d is a structure returned by "dir"
%
is_dir = [d.isdir]';
is_dot = strcmp({d.name}, '.')';
is_dotdot = strcmp({d.name}, '..')';
tf = (is_dir & (is_dot | is_dotdot) );
%---------------------------- end of subfunction --------------------------
%% ------------------------------------------------------------------------
function tf = evaluate(d, expr)
% True for item where evaluated expression is correct or return a non empty
% cell.
% d is a structure returned by "dir"
%
% Get fields that can be used
name = {d.name}'; %#ok<NASGU>
date = {d.date}'; %#ok<NASGU>
datenum = [d.datenum]'; %#ok<NASGU>
bytes = [d.bytes]'; %#ok<NASGU>
isdir = [d.isdir]'; %#ok<NASGU>
tf = eval(expr); % low risk since done in a dedicated subfunction.
% Convert cell outputs returned by "strfind" or "regexp" filters to a
% logical.
if iscell(tf)
tf = not( cellfun(@isempty, tf) );
end
%---------------------------- end of subfunction --------------------------
%---------------------------- END OF FUNCTION -----------------------------
|
github
|
adhusch/PaCER-master
|
load_nii_ext.m
|
.m
|
PaCER-master/external/NIfTI_20140122/load_nii_ext.m
| 5,337 |
utf_8
|
fa0e831b0a596c3208b21bddc1c6d812
|
% Load NIFTI header extension after its header is loaded using load_nii_hdr.
%
% Usage: ext = load_nii_ext(filename)
%
% filename - NIFTI file name.
%
% Returned values:
%
% ext - Structure of NIFTI header extension, which includes num_ext,
% and all the extended header sections in the header extension.
% Each extended header section will have its esize, ecode, and
% edata, where edata can be plain text, xml, or any raw data
% that was saved in the extended header section.
%
% NIFTI data format can be found on: http://nifti.nimh.nih.gov
%
% - Jimmy Shen ([email protected])
%
function ext = load_nii_ext(filename)
if ~exist('filename','var'),
error('Usage: ext = load_nii_ext(filename)');
end
v = version;
% Check file extension. If .gz, unpack it into temp folder
%
if length(filename) > 2 & strcmp(filename(end-2:end), '.gz')
if ~strcmp(filename(end-6:end), '.img.gz') & ...
~strcmp(filename(end-6:end), '.hdr.gz') & ...
~strcmp(filename(end-6:end), '.nii.gz')
error('Please check filename.');
end
if str2num(v(1:3)) < 7.1 | ~usejava('jvm')
error('Please use MATLAB 7.1 (with java) and above, or run gunzip outside MATLAB.');
elseif strcmp(filename(end-6:end), '.img.gz')
filename1 = filename;
filename2 = filename;
filename2(end-6:end) = '';
filename2 = [filename2, '.hdr.gz'];
tmpDir = tempname;
mkdir(tmpDir);
gzFileName = filename;
filename1 = gunzip(filename1, tmpDir);
filename2 = gunzip(filename2, tmpDir);
filename = char(filename1); % convert from cell to string
elseif strcmp(filename(end-6:end), '.hdr.gz')
filename1 = filename;
filename2 = filename;
filename2(end-6:end) = '';
filename2 = [filename2, '.img.gz'];
tmpDir = tempname;
mkdir(tmpDir);
gzFileName = filename;
filename1 = gunzip(filename1, tmpDir);
filename2 = gunzip(filename2, tmpDir);
filename = char(filename1); % convert from cell to string
elseif strcmp(filename(end-6:end), '.nii.gz')
tmpDir = tempname;
mkdir(tmpDir);
gzFileName = filename;
filename = gunzip(filename, tmpDir);
filename = char(filename); % convert from cell to string
end
end
machine = 'ieee-le';
new_ext = 0;
if findstr('.nii',filename) & strcmp(filename(end-3:end), '.nii')
new_ext = 1;
filename(end-3:end)='';
end
if findstr('.hdr',filename) & strcmp(filename(end-3:end), '.hdr')
filename(end-3:end)='';
end
if findstr('.img',filename) & strcmp(filename(end-3:end), '.img')
filename(end-3:end)='';
end
if new_ext
fn = sprintf('%s.nii',filename);
if ~exist(fn)
msg = sprintf('Cannot find file "%s.nii".', filename);
error(msg);
end
else
fn = sprintf('%s.hdr',filename);
if ~exist(fn)
msg = sprintf('Cannot find file "%s.hdr".', filename);
error(msg);
end
end
fid = fopen(fn,'r',machine);
vox_offset = 0;
if fid < 0,
msg = sprintf('Cannot open file %s.',fn);
error(msg);
else
fseek(fid,0,'bof');
if fread(fid,1,'int32') == 348
if new_ext
fseek(fid,108,'bof');
vox_offset = fread(fid,1,'float32');
end
ext = read_extension(fid, vox_offset);
fclose(fid);
else
fclose(fid);
% first try reading the opposite endian to 'machine'
%
switch machine,
case 'ieee-le', machine = 'ieee-be';
case 'ieee-be', machine = 'ieee-le';
end
fid = fopen(fn,'r',machine);
if fid < 0,
msg = sprintf('Cannot open file %s.',fn);
error(msg);
else
fseek(fid,0,'bof');
if fread(fid,1,'int32') ~= 348
% Now throw an error
%
msg = sprintf('File "%s" is corrupted.',fn);
error(msg);
end
if new_ext
fseek(fid,108,'bof');
vox_offset = fread(fid,1,'float32');
end
ext = read_extension(fid, vox_offset);
fclose(fid);
end
end
end
% Clean up after gunzip
%
if exist('gzFileName', 'var')
rmdir(tmpDir,'s');
end
return % load_nii_ext
%---------------------------------------------------------------------
function ext = read_extension(fid, vox_offset)
ext = [];
if vox_offset
end_of_ext = vox_offset;
else
fseek(fid, 0, 'eof');
end_of_ext = ftell(fid);
end
if end_of_ext > 352
fseek(fid, 348, 'bof');
ext.extension = fread(fid,4)';
end
if isempty(ext) | ext.extension(1) == 0
ext = [];
return;
end
i = 1;
while(ftell(fid) < end_of_ext)
ext.section(i).esize = fread(fid,1,'int32');
ext.section(i).ecode = fread(fid,1,'int32');
ext.section(i).edata = char(fread(fid,ext.section(i).esize-8)');
i = i + 1;
end
ext.num_ext = length(ext.section);
return % read_extension
|
github
|
adhusch/PaCER-master
|
rri_orient.m
|
.m
|
PaCER-master/external/NIfTI_20140122/rri_orient.m
| 2,251 |
utf_8
|
4253fb96b9189a8a4bad49661d9ecac3
|
% Convert image of different orientations to standard Analyze orientation
%
% Usage: nii = rri_orient(nii);
% Jimmy Shen ([email protected]), 26-APR-04
%___________________________________________________________________
function [nii, orient, pattern] = rri_orient(nii, varargin)
if nargin > 1
pattern = varargin{1};
else
pattern = [];
end
if(nargin > 2)
orient = varargin{2};
if(length(find(orient>6)) || length(find(orient<1))) %value checking
orient=[1 2 3]; %set to default if bogus values set
end
else
orient = [1 2 3];
end
dim = double(nii.hdr.dime.dim([2:4]));
if ~isempty(pattern) & ~isequal(length(pattern), prod(dim))
return;
end
% get orient of the current image
%
if isequal(orient, [1 2 3])
orient = rri_orient_ui;
pause(.1);
end
% no need for conversion
%
if isequal(orient, [1 2 3])
return;
end
if isempty(pattern)
pattern = 1:prod(dim);
end
pattern = reshape(pattern, dim);
img = nii.img;
% calculate after flip orient
%
rot_orient = mod(orient + 2, 3) + 1;
% do flip:
%
flip_orient = orient - rot_orient;
for i = 1:3
if flip_orient(i)
pattern = flipdim(pattern, i);
img = flipdim(img, i);
end
end
% get index of orient (do inverse)
%
[tmp rot_orient] = sort(rot_orient);
% do rotation:
%
pattern = permute(pattern, rot_orient);
img = permute(img, [rot_orient 4 5 6]);
% rotate resolution, or 'dim'
%
new_dim = nii.hdr.dime.dim([2:4]);
new_dim = new_dim(rot_orient);
nii.hdr.dime.dim([2:4]) = new_dim;
% rotate voxel_size, or 'pixdim'
%
tmp = nii.hdr.dime.pixdim([2:4]);
tmp = tmp(rot_orient);
nii.hdr.dime.pixdim([2:4]) = tmp;
% re-calculate originator
%
tmp = nii.hdr.hist.originator([1:3]);
tmp = tmp(rot_orient);
flip_orient = flip_orient(rot_orient);
for i = 1:3
if flip_orient(i) & ~isequal(double(tmp(i)), 0)
tmp(i) = int16(double(new_dim(i)) - double(tmp(i)) + 1);
end
end
nii.hdr.hist.originator([1:3]) = tmp;
nii.img = img;
pattern = pattern(:);
return; % rri_orient
|
github
|
adhusch/PaCER-master
|
save_untouch0_nii_hdr.m
|
.m
|
PaCER-master/external/NIfTI_20140122/save_untouch0_nii_hdr.m
| 8,594 |
utf_8
|
7e8b1b327e1924837820f75780d52d01
|
% internal function
% - Jimmy Shen ([email protected])
function save_nii_hdr(hdr, fid)
if ~isequal(hdr.hk.sizeof_hdr,348),
error('hdr.hk.sizeof_hdr must be 348.');
end
write_header(hdr, fid);
return; % save_nii_hdr
%---------------------------------------------------------------------
function write_header(hdr, fid)
% Original header structures
% struct dsr /* dsr = hdr */
% {
% struct header_key hk; /* 0 + 40 */
% struct image_dimension dime; /* 40 + 108 */
% struct data_history hist; /* 148 + 200 */
% }; /* total= 348 bytes*/
header_key(fid, hdr.hk);
image_dimension(fid, hdr.dime);
data_history(fid, hdr.hist);
% check the file size is 348 bytes
%
fbytes = ftell(fid);
if ~isequal(fbytes,348),
msg = sprintf('Header size is not 348 bytes.');
warning(msg);
end
return; % write_header
%---------------------------------------------------------------------
function header_key(fid, hk)
fseek(fid,0,'bof');
% Original header structures
% struct header_key /* header key */
% { /* off + size */
% int sizeof_hdr /* 0 + 4 */
% char data_type[10]; /* 4 + 10 */
% char db_name[18]; /* 14 + 18 */
% int extents; /* 32 + 4 */
% short int session_error; /* 36 + 2 */
% char regular; /* 38 + 1 */
% char hkey_un0; /* 39 + 1 */
% }; /* total=40 bytes */
fwrite(fid, hk.sizeof_hdr(1), 'int32'); % must be 348.
% data_type = sprintf('%-10s',hk.data_type); % ensure it is 10 chars from left
% fwrite(fid, data_type(1:10), 'uchar');
pad = zeros(1, 10-length(hk.data_type));
hk.data_type = [hk.data_type char(pad)];
fwrite(fid, hk.data_type(1:10), 'uchar');
% db_name = sprintf('%-18s', hk.db_name); % ensure it is 18 chars from left
% fwrite(fid, db_name(1:18), 'uchar');
pad = zeros(1, 18-length(hk.db_name));
hk.db_name = [hk.db_name char(pad)];
fwrite(fid, hk.db_name(1:18), 'uchar');
fwrite(fid, hk.extents(1), 'int32');
fwrite(fid, hk.session_error(1), 'int16');
fwrite(fid, hk.regular(1), 'uchar');
fwrite(fid, hk.hkey_un0(1), 'uchar');
return; % header_key
%---------------------------------------------------------------------
function image_dimension(fid, dime)
%struct image_dimension
% { /* off + size */
% short int dim[8]; /* 0 + 16 */
% char vox_units[4]; /* 16 + 4 */
% char cal_units[8]; /* 20 + 8 */
% short int unused1; /* 28 + 2 */
% short int datatype; /* 30 + 2 */
% short int bitpix; /* 32 + 2 */
% short int dim_un0; /* 34 + 2 */
% float pixdim[8]; /* 36 + 32 */
% /*
% pixdim[] specifies the voxel dimensions:
% pixdim[1] - voxel width
% pixdim[2] - voxel height
% pixdim[3] - interslice distance
% ..etc
% */
% float vox_offset; /* 68 + 4 */
% float roi_scale; /* 72 + 4 */
% float funused1; /* 76 + 4 */
% float funused2; /* 80 + 4 */
% float cal_max; /* 84 + 4 */
% float cal_min; /* 88 + 4 */
% int compressed; /* 92 + 4 */
% int verified; /* 96 + 4 */
% int glmax; /* 100 + 4 */
% int glmin; /* 104 + 4 */
% }; /* total=108 bytes */
fwrite(fid, dime.dim(1:8), 'int16');
pad = zeros(1, 4-length(dime.vox_units));
dime.vox_units = [dime.vox_units char(pad)];
fwrite(fid, dime.vox_units(1:4), 'uchar');
pad = zeros(1, 8-length(dime.cal_units));
dime.cal_units = [dime.cal_units char(pad)];
fwrite(fid, dime.cal_units(1:8), 'uchar');
fwrite(fid, dime.unused1(1), 'int16');
fwrite(fid, dime.datatype(1), 'int16');
fwrite(fid, dime.bitpix(1), 'int16');
fwrite(fid, dime.dim_un0(1), 'int16');
fwrite(fid, dime.pixdim(1:8), 'float32');
fwrite(fid, dime.vox_offset(1), 'float32');
fwrite(fid, dime.roi_scale(1), 'float32');
fwrite(fid, dime.funused1(1), 'float32');
fwrite(fid, dime.funused2(1), 'float32');
fwrite(fid, dime.cal_max(1), 'float32');
fwrite(fid, dime.cal_min(1), 'float32');
fwrite(fid, dime.compressed(1), 'int32');
fwrite(fid, dime.verified(1), 'int32');
fwrite(fid, dime.glmax(1), 'int32');
fwrite(fid, dime.glmin(1), 'int32');
return; % image_dimension
%---------------------------------------------------------------------
function data_history(fid, hist)
% Original header structures - ANALYZE 7.5
%struct data_history
% { /* off + size */
% char descrip[80]; /* 0 + 80 */
% char aux_file[24]; /* 80 + 24 */
% char orient; /* 104 + 1 */
% char originator[10]; /* 105 + 10 */
% char generated[10]; /* 115 + 10 */
% char scannum[10]; /* 125 + 10 */
% char patient_id[10]; /* 135 + 10 */
% char exp_date[10]; /* 145 + 10 */
% char exp_time[10]; /* 155 + 10 */
% char hist_un0[3]; /* 165 + 3 */
% int views /* 168 + 4 */
% int vols_added; /* 172 + 4 */
% int start_field; /* 176 + 4 */
% int field_skip; /* 180 + 4 */
% int omax; /* 184 + 4 */
% int omin; /* 188 + 4 */
% int smax; /* 192 + 4 */
% int smin; /* 196 + 4 */
% }; /* total=200 bytes */
% descrip = sprintf('%-80s', hist.descrip); % 80 chars from left
% fwrite(fid, descrip(1:80), 'uchar');
pad = zeros(1, 80-length(hist.descrip));
hist.descrip = [hist.descrip char(pad)];
fwrite(fid, hist.descrip(1:80), 'uchar');
% aux_file = sprintf('%-24s', hist.aux_file); % 24 chars from left
% fwrite(fid, aux_file(1:24), 'uchar');
pad = zeros(1, 24-length(hist.aux_file));
hist.aux_file = [hist.aux_file char(pad)];
fwrite(fid, hist.aux_file(1:24), 'uchar');
fwrite(fid, hist.orient(1), 'uchar');
fwrite(fid, hist.originator(1:5), 'int16');
pad = zeros(1, 10-length(hist.generated));
hist.generated = [hist.generated char(pad)];
fwrite(fid, hist.generated(1:10), 'uchar');
pad = zeros(1, 10-length(hist.scannum));
hist.scannum = [hist.scannum char(pad)];
fwrite(fid, hist.scannum(1:10), 'uchar');
pad = zeros(1, 10-length(hist.patient_id));
hist.patient_id = [hist.patient_id char(pad)];
fwrite(fid, hist.patient_id(1:10), 'uchar');
pad = zeros(1, 10-length(hist.exp_date));
hist.exp_date = [hist.exp_date char(pad)];
fwrite(fid, hist.exp_date(1:10), 'uchar');
pad = zeros(1, 10-length(hist.exp_time));
hist.exp_time = [hist.exp_time char(pad)];
fwrite(fid, hist.exp_time(1:10), 'uchar');
pad = zeros(1, 3-length(hist.hist_un0));
hist.hist_un0 = [hist.hist_un0 char(pad)];
fwrite(fid, hist.hist_un0(1:3), 'uchar');
fwrite(fid, hist.views(1), 'int32');
fwrite(fid, hist.vols_added(1), 'int32');
fwrite(fid, hist.start_field(1),'int32');
fwrite(fid, hist.field_skip(1), 'int32');
fwrite(fid, hist.omax(1), 'int32');
fwrite(fid, hist.omin(1), 'int32');
fwrite(fid, hist.smax(1), 'int32');
fwrite(fid, hist.smin(1), 'int32');
return; % data_history
|
github
|
adhusch/PaCER-master
|
rri_zoom_menu.m
|
.m
|
PaCER-master/external/NIfTI_20140122/rri_zoom_menu.m
| 737 |
utf_8
|
d8151523470b0fba970eb1d98ba56030
|
% Imbed a zoom menu to any figure.
%
% Usage: rri_zoom_menu(fig);
%
% - Jimmy Shen ([email protected])
%
%--------------------------------------------------------------------
function menu_hdl = rri_zoom_menu(fig)
if isnumeric(fig)
menu_hdl = uimenu('Parent',fig, ...
'Label','Zoom on', ...
'Userdata', 1, ...
'Callback','rri_zoom_menu(''zoom'');');
return;
end
zoom_on_state = get(gcbo,'Userdata');
if (zoom_on_state == 1)
zoom on;
set(gcbo,'Userdata',0,'Label','Zoom off');
set(gcbf,'pointer','crosshair');
else
zoom off;
set(gcbo,'Userdata',1,'Label','Zoom on');
set(gcbf,'pointer','arrow');
end
return % rri_zoom_menu
|
github
|
adhusch/PaCER-master
|
rri_select_file.m
|
.m
|
PaCER-master/external/NIfTI_20140122/rri_select_file.m
| 16,599 |
utf_8
|
e349954ca803370f62ceeabdbab5912e
|
function [selected_file, selected_path] = rri_select_file(varargin)
%
% USAGE: [selected_file, selected_path] = ...
% rri_select_file(dir_name, fig_title)
%
% Allow user to select a file from a list of Matlab competible
% file format
%
% Example:
%
% [selected_file, selected_path] = ...
% rri_select_file('/usr','Select Data File');
%
% See Also RRI_GETFILES
% -- Created June 2001 by Wilkin Chau, Rotman Research Institute
%
% use rri_select_file to open & save Matlab recognized format
% -- Modified Dec 2002 by Jimmy Shen, Rotman Research Institute
%
if nargin == 0 | ischar(varargin{1}) % create rri_select_file figure
dir_name = '';
fig_title = 'Select a File';
if nargin > 0
dir_name = varargin{1};
end
if nargin > 1
fig_title = varargin{2};
end
Init(fig_title,dir_name);
uiwait; % wait for user finish
selected_path = getappdata(gcf,'SelectedDirectory');
selected_file = getappdata(gcf,'SelectedFile');
cd (getappdata(gcf,'StartDirectory'));
close(gcf);
return;
end;
% clear the message line,
%
h = findobj(gcf,'Tag','MessageLine');
set(h,'String','');
action = varargin{1}{1};
% change 'File format':
% update 'Files' & 'File selection' based on file pattern
%
if strcmp(action,'EditFilter'),
EditFilter;
% run delete_fig when figure is closing
%
elseif strcmp(action,'delete_fig'),
delete_fig;
% select 'Directories':
% go into the selected dir
% update 'Files' & 'File selection' based on file pattern
%
elseif strcmp(action,'select_dir'),
select_dir;
% select 'Files':
% update 'File selection'
%
elseif strcmp(action,'select_file'),
select_file;
% change 'File selection':
% if it is a file, select that,
% if it is more than a file (*), select those,
% if it is a directory, select based on file pattern
%
elseif strcmp(action,'EditSelection'),
EditSelection;
% clicked 'Select'
%
elseif strcmp(action,'DONE_BUTTON_PRESSED'),
h = findobj(gcf,'Tag','SelectionEdit');
[filepath,filename,fileext] = fileparts(get(h,'String'));
if isempty(filepath) | isempty(filename) | isempty(fileext)
setappdata(gcf,'SelectedDirectory',[]);
setappdata(gcf,'SelectedFile',[]);
else
if ~strcmp(filepath(end),filesep) % not end with filesep
filepath = [filepath filesep]; % add a filesep to filepath
end
setappdata(gcf,'SelectedDirectory',filepath);
setappdata(gcf,'SelectedFile',[filename fileext]);
end
if getappdata(gcf,'ready') % ready to exit
uiresume;
end
% clicked 'cancel'
%
elseif strcmp(action,'CANCEL_BUTTON_PRESSED'),
setappdata(gcf,'SelectedDirectory',[]);
setappdata(gcf,'SelectedFile',[]);
set(findobj(gcf,'Tag','FileList'),'String','');
uiresume;
end;
return;
% --------------------------------------------------------------------
function Init(fig_title,dir_name),
StartDirectory = pwd;
if isempty(StartDirectory),
StartDirectory = filesep;
end;
filter_disp = {'JPEG image (*.jpg)', ...
'TIFF image, compressed (*.tif)', ...
'EPS Level 1 (*.eps)', ...
'Adobe Illustrator 88 (*.ai)', ...
'Enhanced metafile (*.emf)', ...
'Matlab Figure (*.fig)', ...
'Matlab M-file (*.m)', ...
'Portable bitmap (*.pbm)', ...
'Paintbrush 24-bit (*.pcx)', ...
'Portable Graymap (*.pgm)', ...
'Portable Network Graphics (*.png)', ...
'Portable Pixmap (*.ppm)', ...
};
filter_string = {'*.jpg', ...
'*.tif', ...
'*.eps', ...
'*.ai', ...
'*.emf', ...
'*.fig', ...
'*.m', ...
'*.pbm', ...
'*.pcx', ...
'*.pgm', ...
'*.png', ...
'*.ppm', ...
};
% filter_disp = char(filter_disp);
filter_string = char(filter_string);
margine = 0.05;
line_height = 0.07;
char_height = line_height*0.8;
save_setting_status = 'on';
rri_select_file_pos = [];
try
load('pls_profile');
catch
end
if ~isempty(rri_select_file_pos) & strcmp(save_setting_status,'on')
pos = rri_select_file_pos;
else
w = 0.4;
h = 0.6;
x = (1-w)/2;
y = (1-h)/2;
pos = [x y w h];
end
h0 = figure('parent',0, 'Color',[0.8 0.8 0.8], ...
'Units','normal', ...
'Name',fig_title, ...
'NumberTitle','off', ...
'MenuBar','none', ...
'Position', pos, ...
'deleteFcn','rri_select_file({''delete_fig''});', ...
'WindowStyle', 'modal', ...
'Tag','GetFilesFigure', ...
'ToolBar','none');
x = margine;
y = 1 - 1*line_height - margine;
w = 1-2*x;
h = char_height;
pos = [x y w h];
h1 = uicontrol('Parent',h0, ... % Filter Label
'Style','text', ...
'Units','normal', ...
'BackgroundColor',[0.8 0.8 0.8], ...
'fontunit','normal', ...
'FontSize',0.5, ...
'HorizontalAlignment','left', ...
'Position', pos, ...
'String','Choose one of the file format:', ...
'Tag','FilterLabel');
y = 1 - 2*line_height - margine + line_height*0.2;
w = 1-2*x;
pos = [x y w h];
h_filter = uicontrol('Parent',h0, ... % Filter list
'Style','popupmenu', ...
'Units','normal', ...
'BackgroundColor',[1 1 1], ...
'fontunit','normal', ...
'FontSize',0.5, ...
'HorizontalAlignment','left', ...
'Position', pos, ...
'String', filter_disp, ...
'user', filter_string, ...
'value', 1, ...
'Callback','rri_select_file({''EditFilter''});', ...
'Tag','FilterEdit');
y = 1 - 3*line_height - margine;
w = 0.5 - x - margine/2;
pos = [x y w h];
h1 = uicontrol('Parent',h0, ... % Directory Label
'Style','text', ...
'Units','normal', ...
'BackgroundColor',[0.8 0.8 0.8], ...
'fontunit','normal', ...
'FontSize',0.5, ...
'HorizontalAlignment','left', ...
'ListboxTop',0, ...
'Position', pos, ...
'String','Directories', ...
'Tag','DirectoryLabel');
x = 0.5;
y = 1 - 3*line_height - margine;
w = 0.5 - margine;
pos = [x y w h];
h1 = uicontrol('Parent',h0, ... % File Label
'Style','text', ...
'Units','normal', ...
'BackgroundColor',[0.8 0.8 0.8], ...
'fontunit','normal', ...
'FontSize',0.5, ...
'HorizontalAlignment','left', ...
'ListboxTop',0, ...
'Position', pos, ...
'String','Files', ...
'Tag','FileLabel');
x = margine;
y = 4*line_height + margine;
w = 0.5 - x - margine/2;
h = 1 - 7*line_height - 2*margine;
pos = [x y w h];
h_dir = uicontrol('Parent',h0, ... % Directory Listbox
'Style','listbox', ...
'Units','normal', ...
'fontunit','normal', ...
'FontSize',0.08, ...
'HorizontalAlignment','left', ...
'Interruptible', 'off', ...
'ListboxTop',1, ...
'Position', pos, ...
'String', '', ...
'Callback','rri_select_file({''select_dir''});', ...
'Tag','DirectoryList');
x = 0.5;
y = 4*line_height + margine;
w = 0.5 - margine;
h = 1 - 7*line_height - 2*margine;
pos = [x y w h];
h_file = uicontrol('Parent',h0, ... % File Listbox
'Style','listbox', ...
'Units','normal', ...
'fontunit','normal', ...
'FontSize',0.08, ...
'HorizontalAlignment','left', ...
'ListboxTop',1, ...
'Position', pos, ...
'String', '', ...
'Callback','rri_select_file({''select_file''});', ...
'Tag','FileList');
x = margine;
y = 3*line_height + margine - line_height*0.2;
w = 1-2*x;
h = char_height;
pos = [x y w h];
h1 = uicontrol('Parent',h0, ... % Selection Label
'Style','text', ...
'Units','normal', ...
'BackgroundColor',[0.8 0.8 0.8], ...
'fontunit','normal', ...
'FontSize',0.5, ...
'HorizontalAlignment','left', ...
'Position', pos, ...
'String','File you selected:', ...
'Tag','SelectionLabel');
y = 2*line_height + margine;
w = 1-2*x;
pos = [x y w h];
h_select = uicontrol('Parent',h0, ... % Selection Edit
'Style','edit', ...
'Units','normal', ...
'BackgroundColor',[1 1 1], ...
'fontunit','normal', ...
'FontSize',0.5, ...
'HorizontalAlignment','left', ...
'Position', pos, ...
'String', '', ...
'Callback','rri_select_file({''EditSelection''});', ...
'Tag','SelectionEdit');
x = 2*margine;
y = line_height/2 + margine;
w = 0.2;
h = line_height;
pos = [x y w h];
h_done = uicontrol('Parent',h0, ... % DONE
'Units','normal', ...
'fontunit','normal', ...
'FontSize',0.5, ...
'ListboxTop',0, ...
'Position', pos, ...
'HorizontalAlignment','center', ...
'String','Save', ... % 'Select', ...
'Callback','rri_select_file({''DONE_BUTTON_PRESSED''});', ...
'Tag','DONEButton');
x = 1 - x - w;
pos = [x y w h];
h_cancel = uicontrol('Parent',h0, ... % CANCEL
'Units','normal', ...
'fontunit','normal', ...
'FontSize',0.5, ...
'ListboxTop',0, ...
'Position', pos, ...
'HorizontalAlignment','center', ...
'String','Cancel', ...
'Callback','rri_select_file({''CANCEL_BUTTON_PRESSED''});', ...
'Tag','CANCELButton');
if isempty(dir_name)
dir_name = StartDirectory;
end
set(h_select,'string',dir_name);
filter_select = get(h_filter,'value');
filter_pattern = filter_string(filter_select,:);
setappdata(gcf,'FilterPattern',deblank(filter_pattern));
setappdata(gcf,'filter_string',filter_string);
setappdata(gcf,'h_filter', h_filter);
setappdata(gcf,'h_dir', h_dir);
setappdata(gcf,'h_file', h_file);
setappdata(gcf,'h_select', h_select);
setappdata(gcf,'h_done', h_done);
setappdata(gcf,'h_cancel', h_cancel);
setappdata(gcf,'StartDirectory',StartDirectory);
EditSelection;
h_file = getappdata(gcf,'h_file');
if isempty(get(h_file,'string'))
setappdata(gcf,'ready',0);
else
setappdata(gcf,'ready',1);
end
return; % Init
% called by all the actions, to update 'Directories' or 'Files'
% based on filter_pattern. Select first file in filelist.
%
% --------------------------------------------------------------------
function update_dirlist;
filter_path = getappdata(gcf,'curr_dir');
filter_pattern = getappdata(gcf,'FilterPattern');
if exist(filter_pattern) == 2 % user input specific filename
is_single_file = 1; % need manually take path out later
else
is_single_file = 0;
end
% take the file path out from filter_pattern
%
[fpath fname fext] = fileparts(filter_pattern);
filter_pattern = [fname fext];
dir_struct = dir(filter_path);
if isempty(dir_struct)
msg = 'ERROR: Directory not found!';
uiwait(msgbox(msg,'File Selection Error','modal'));
return;
end;
old_pointer = get(gcf,'Pointer');
set(gcf,'Pointer','watch');
dir_list = dir_struct(find([dir_struct.isdir] == 1));
[sorted_dir_names,sorted_dir_index] = sortrows({dir_list.name}');
dir_struct = dir([filter_path filesep filter_pattern]);
if isempty(dir_struct)
sorted_file_names = [];
else
file_list = dir_struct(find([dir_struct.isdir] == 0));
if is_single_file % take out path
tmp = file_list.name;
[fpath fname fext] = fileparts(tmp);
file_list.name = [fname fext];
end
[sorted_file_names,sorted_file_index] = sortrows({file_list.name}');
end;
disp_dir_names = []; % if need full path, use this
% instead of sorted_dir_names
for i=1:length(sorted_dir_names)
tmp = [filter_path filesep sorted_dir_names{i}];
disp_dir_names = [disp_dir_names {tmp}];
end
h = findobj(gcf,'Tag','DirectoryList');
set(h,'String',sorted_dir_names,'Value',1);
h = findobj(gcf,'Tag','FileList');
set(h,'String',sorted_file_names,'value',1);
h_select = getappdata(gcf,'h_select');
if strcmp(filter_path(end),filesep) % filepath end with filesep
filter_path = filter_path(1:end-1); % take filesep out
end
if isempty(sorted_file_names)
set(h_select,'string',[filter_path filesep]);
else
set(h_select,'string',[filter_path filesep sorted_file_names{1}]);
end
set(gcf,'Pointer',old_pointer);
return; % update_dirlist
% change 'File format':
% update 'Files' & 'File selection' based on file pattern
%
% --------------------------------------------------------------------
function EditFilter()
filter_select = get(gcbo,'value');
filter_string = getappdata(gcf,'filter_string');
filter_pattern = filter_string(filter_select,:);
filter_path = getappdata(gcf,'curr_dir');
% update filter_pattern
setappdata(gcf,'FilterPattern',deblank(filter_pattern));
if isempty(filter_path),
filter_path = filesep;
end;
update_dirlist;
h_file = getappdata(gcf,'h_file');
if isempty(get(h_file,'string'))
setappdata(gcf,'ready',0);
else
setappdata(gcf,'ready',1);
end
return; % EditFilter
% select 'Directories':
% go into the selected dir
% update 'Files' & 'File selection' based on file pattern
%
% --------------------------------------------------------------------
function select_dir()
listed_dir = get(gcbo,'String');
selected_dir_idx = get(gcbo,'Value');
selected_dir = listed_dir{selected_dir_idx};
curr_dir = getappdata(gcf,'curr_dir');
% update the selection box
%
try
cd ([curr_dir filesep selected_dir]);
catch
msg = 'ERROR: Cannot access directory';
uiwait(msgbox(msg,'File Selection Error','modal'));
return;
end;
if isempty(pwd)
curr_dir = filesep;
else
curr_dir = pwd;
end;
setappdata(gcf,'curr_dir',curr_dir);
update_dirlist;
h_file = getappdata(gcf,'h_file');
if isempty(get(h_file,'string'))
setappdata(gcf,'ready',0);
else
setappdata(gcf,'ready',1);
end
return; % select_dir
% select 'Files':
% update 'File selection'
%
% --------------------------------------------------------------------
function select_file()
setappdata(gcf,'ready',1);
listed_file = get(gcbo,'String');
selected_file_idx = get(gcbo,'Value');
selected_file = listed_file{selected_file_idx};
curr_dir = getappdata(gcf,'curr_dir');
if strcmp(curr_dir(end),filesep) % filepath end with filesep
curr_dir = curr_dir(1:end-1); % take filesep out
end
h_select = getappdata(gcf,'h_select');
set(h_select,'string',[curr_dir filesep selected_file]);
return; % select_file
% change 'File selection':
% if it is a file, select that,
% if it is more than a file (*), select those,
% if it is a directory, select based on file pattern
%
% --------------------------------------------------------------------
function EditSelection()
filter_string = getappdata(gcf,'filter_string');
h_select = getappdata(gcf,'h_select');
selected_file = get(h_select,'string');
if exist(selected_file) == 7 % if user enter a dir
setappdata(gcf,'ready',0);
setappdata(gcf,'curr_dir',selected_file); % get new dir
update_dirlist;
else
setappdata(gcf,'ready',1);
[fpath fname fext]= fileparts(selected_file);
if exist(fpath) ~=7 % fpath is not a dir
setappdata(gcf,'ready',0);
msg = 'ERROR: Cannot access directory';
uiwait(msgbox(msg,'File Selection Error','modal'));
end
% if the file format user entered is not supported by matlab
if isempty(strmatch(['*',fext],filter_string,'exact'))
setappdata(gcf,'ready',0);
msg = 'ERROR: File format is not supported by Matlab.';
uiwait(msgbox(msg,'File Selection Error','modal'));
end
end
return; % EditSelection
% --------------------------------------------------------------------
function delete_fig()
try
load('pls_profile');
pls_profile = which('pls_profile.mat');
rri_select_file_pos = get(gcbf,'position');
save(pls_profile, '-append', 'rri_select_file_pos');
catch
end
return;
|
github
|
adhusch/PaCER-master
|
clip_nii.m
|
.m
|
PaCER-master/external/NIfTI_20140122/clip_nii.m
| 3,306 |
utf_8
|
a70bdbed5a0813312d4c83f94b99a710
|
% CLIP_NII: Clip the NIfTI volume from any of the 6 sides
%
% Usage: nii = clip_nii(nii, [option])
%
% Inputs:
%
% nii - NIfTI volume.
%
% option - struct instructing how many voxel to be cut from which side.
%
% option.cut_from_L = ( number of voxel )
% option.cut_from_R = ( number of voxel )
% option.cut_from_P = ( number of voxel )
% option.cut_from_A = ( number of voxel )
% option.cut_from_I = ( number of voxel )
% option.cut_from_S = ( number of voxel )
%
% Options description in detail:
% ==============================
%
% cut_from_L: Number of voxels from Left side will be clipped.
%
% cut_from_R: Number of voxels from Right side will be clipped.
%
% cut_from_P: Number of voxels from Posterior side will be clipped.
%
% cut_from_A: Number of voxels from Anterior side will be clipped.
%
% cut_from_I: Number of voxels from Inferior side will be clipped.
%
% cut_from_S: Number of voxels from Superior side will be clipped.
%
% NIfTI data format can be found on: http://nifti.nimh.nih.gov
%
% - Jimmy Shen ([email protected])
%
function nii = clip_nii(nii, opt)
dims = abs(nii.hdr.dime.dim(2:4));
origin = abs(nii.hdr.hist.originator(1:3));
if isempty(origin) | all(origin == 0) % according to SPM
origin = round((dims+1)/2);
end
cut_from_L = 0;
cut_from_R = 0;
cut_from_P = 0;
cut_from_A = 0;
cut_from_I = 0;
cut_from_S = 0;
if nargin > 1 & ~isempty(opt)
if ~isstruct(opt)
error('option argument should be a struct');
end
if isfield(opt,'cut_from_L')
cut_from_L = round(opt.cut_from_L);
if cut_from_L >= origin(1) | cut_from_L < 0
error('cut_from_L cannot be negative or cut beyond originator');
end
end
if isfield(opt,'cut_from_P')
cut_from_P = round(opt.cut_from_P);
if cut_from_P >= origin(2) | cut_from_P < 0
error('cut_from_P cannot be negative or cut beyond originator');
end
end
if isfield(opt,'cut_from_I')
cut_from_I = round(opt.cut_from_I);
if cut_from_I >= origin(3) | cut_from_I < 0
error('cut_from_I cannot be negative or cut beyond originator');
end
end
if isfield(opt,'cut_from_R')
cut_from_R = round(opt.cut_from_R);
if cut_from_R > dims(1)-origin(1) | cut_from_R < 0
error('cut_from_R cannot be negative or cut beyond originator');
end
end
if isfield(opt,'cut_from_A')
cut_from_A = round(opt.cut_from_A);
if cut_from_A > dims(2)-origin(2) | cut_from_A < 0
error('cut_from_A cannot be negative or cut beyond originator');
end
end
if isfield(opt,'cut_from_S')
cut_from_S = round(opt.cut_from_S);
if cut_from_S > dims(3)-origin(3) | cut_from_S < 0
error('cut_from_S cannot be negative or cut beyond originator');
end
end
end
nii = make_nii(nii.img( (cut_from_L+1) : (dims(1)-cut_from_R), ...
(cut_from_P+1) : (dims(2)-cut_from_A), ...
(cut_from_I+1) : (dims(3)-cut_from_S), ...
:,:,:,:,:), nii.hdr.dime.pixdim(2:4), ...
[origin(1)-cut_from_L origin(2)-cut_from_P origin(3)-cut_from_I], ...
nii.hdr.dime.datatype, nii.hdr.hist.descrip);
return;
|
github
|
adhusch/PaCER-master
|
affine.m
|
.m
|
PaCER-master/external/NIfTI_20140122/affine.m
| 16,110 |
utf_8
|
768d2303e551a9584685bdb01abf6f8b
|
% Using 2D or 3D affine matrix to rotate, translate, scale, reflect and
% shear a 2D image or 3D volume. 2D image is represented by a 2D matrix,
% 3D volume is represented by a 3D matrix, and data type can be real
% integer or floating-point.
%
% You may notice that MATLAB has a function called 'imtransform.m' for
% 2D spatial transformation. However, keep in mind that 'imtransform.m'
% assumes y for the 1st dimension, and x for the 2nd dimension. They are
% equivalent otherwise.
%
% In addition, if you adjust the 'new_elem_size' parameter, this 'affine.m'
% is equivalent to 'interp2.m' for 2D image, and equivalent to 'interp3.m'
% for 3D volume.
%
% Usage: [new_img new_M] = ...
% affine(old_img, old_M, [new_elem_size], [verbose], [bg], [method]);
%
% old_img - original 2D image or 3D volume. We assume x for the 1st
% dimension, y for the 2nd dimension, and z for the 3rd
% dimension.
%
% old_M - a 3x3 2D affine matrix for 2D image, or a 4x4 3D affine
% matrix for 3D volume. We assume x for the 1st dimension,
% y for the 2nd dimension, and z for the 3rd dimension.
%
% new_elem_size (optional) - size of voxel along x y z direction for
% a transformed 3D volume, or size of pixel along x y for
% a transformed 2D image. We assume x for the 1st dimension
% y for the 2nd dimension, and z for the 3rd dimension.
% 'new_elem_size' is 1 if it is default or empty.
%
% You can increase its value to decrease the resampling rate,
% and make the 2D image or 3D volume more coarse. It works
% just like 'interp3'.
%
% verbose (optional) - 1, 0
% 1: show transforming progress in percentage
% 2: progress will not be displayed
% 'verbose' is 1 if it is default or empty.
%
% bg (optional) - background voxel intensity in any extra corner that
% is caused by the interpolation. 0 in most cases. If it is
% default or empty, 'bg' will be the average of two corner
% voxel intensities in original data.
%
% method (optional) - 1, 2, or 3
% 1: for Trilinear interpolation
% 2: for Nearest Neighbor interpolation
% 3: for Fischer's Bresenham interpolation
% 'method' is 1 if it is default or empty.
%
% new_img - transformed 2D image or 3D volume
%
% new_M - transformed affine matrix
%
% Example 1 (3D rotation):
% load mri.mat; old_img = double(squeeze(D));
% old_M = [0.88 0.5 3 -90; -0.5 0.88 3 -126; 0 0 2 -72; 0 0 0 1];
% new_img = affine(old_img, old_M, 2);
% [x y z] = meshgrid(1:128,1:128,1:27);
% sz = size(new_img);
% [x1 y1 z1] = meshgrid(1:sz(2),1:sz(1),1:sz(3));
% figure; slice(x, y, z, old_img, 64, 64, 13.5);
% shading flat; colormap(map); view(-66, 66);
% figure; slice(x1, y1, z1, new_img, sz(1)/2, sz(2)/2, sz(3)/2);
% shading flat; colormap(map); view(-66, 66);
%
% Example 2 (2D interpolation):
% load mri.mat; old_img=D(:,:,1,13)';
% old_M = [1 0 0; 0 1 0; 0 0 1];
% new_img = affine(old_img, old_M, [.2 .4]);
% figure; image(old_img); colormap(map);
% figure; image(new_img); colormap(map);
%
% This program is inspired by:
% SPM5 Software from Wellcome Trust Centre for Neuroimaging
% http://www.fil.ion.ucl.ac.uk/spm/software
% Fischer, J., A. del Rio (2004). A Fast Method for Applying Rigid
% Transformations to Volume Data, WSCG2004 Conference.
% http://wscg.zcu.cz/wscg2004/Papers_2004_Short/M19.pdf
%
% - Jimmy Shen ([email protected])
%
function [new_img, new_M] = affine(old_img, old_M, new_elem_size, verbose, bg, method)
if ~exist('old_img','var') | ~exist('old_M','var')
error('Usage: [new_img new_M] = affine(old_img, old_M, [new_elem_size], [verbose], [bg], [method]);');
end
if ndims(old_img) == 3
if ~isequal(size(old_M),[4 4])
error('old_M should be a 4x4 affine matrix for 3D volume.');
end
elseif ndims(old_img) == 2
if ~isequal(size(old_M),[3 3])
error('old_M should be a 3x3 affine matrix for 2D image.');
end
else
error('old_img should be either 2D image or 3D volume.');
end
if ~exist('new_elem_size','var') | isempty(new_elem_size)
new_elem_size = [1 1 1];
elseif length(new_elem_size) < 2
new_elem_size = new_elem_size(1)*ones(1,3);
elseif length(new_elem_size) < 3
new_elem_size = [new_elem_size(:); 1]';
end
if ~exist('method','var') | isempty(method)
method = 1;
elseif ~exist('bresenham_line3d.m','file') & method == 3
error([char(10) char(10) 'Please download 3D Bresenham''s line generation program from:' char(10) char(10) 'http://www.mathworks.com/matlabcentral/fileexchange/loadFile.do?objectId=21057' char(10) char(10) 'to test Fischer''s Bresenham interpolation method.' char(10) char(10)]);
end
% Make compatible to MATLAB earlier than version 7 (R14), which
% can only perform arithmetic on double data type
%
old_img = double(old_img);
old_dim = size(old_img);
if ~exist('bg','var') | isempty(bg)
bg = mean([old_img(1) old_img(end)]);
end
if ~exist('verbose','var') | isempty(verbose)
verbose = 1;
end
if ndims(old_img) == 2
old_dim(3) = 1;
old_M = old_M(:, [1 2 3 3]);
old_M = old_M([1 2 3 3], :);
old_M(3,:) = [0 0 1 0];
old_M(:,3) = [0 0 1 0]';
end
% Vertices of img in voxel
%
XYZvox = [ 1 1 1
1 1 old_dim(3)
1 old_dim(2) 1
1 old_dim(2) old_dim(3)
old_dim(1) 1 1
old_dim(1) 1 old_dim(3)
old_dim(1) old_dim(2) 1
old_dim(1) old_dim(2) old_dim(3) ]';
old_R = old_M(1:3,1:3);
old_T = old_M(1:3,4);
% Vertices of img in millimeter
%
XYZmm = old_R*(XYZvox-1) + repmat(old_T, [1, 8]);
% Make scale of new_M according to new_elem_size
%
new_M = diag([new_elem_size 1]);
% Make translation so minimum vertex is moved to [1,1,1]
%
new_M(1:3,4) = round( min(XYZmm,[],2) );
% New dimensions will be the maximum vertices in XYZ direction (dim_vox)
% i.e. compute dim_vox via dim_mm = R*(dim_vox-1)+T
% where, dim_mm = round(max(XYZmm,[],2));
%
new_dim = ceil(new_M(1:3,1:3) \ ( round(max(XYZmm,[],2))-new_M(1:3,4) )+1)';
% Initialize new_img with new_dim
%
new_img = zeros(new_dim(1:3));
% Mask out any changes from Z axis of transformed volume, since we
% will traverse it voxel by voxel below. We will only apply unit
% increment of mask_Z(3,4) to simulate the cursor movement
%
% i.e. we will use mask_Z * new_XYZvox to replace new_XYZvox
%
mask_Z = diag(ones(1,4));
mask_Z(3,3) = 0;
% It will be easier to do the interpolation if we invert the process
% by not traversing the original volume. Instead, we traverse the
% transformed volume, and backproject each voxel in the transformed
% volume back into the original volume. If the backprojected voxel
% in original volume is within its boundary, the intensity of that
% voxel can be used by the cursor location in the transformed volume.
%
% First, we traverse along Z axis of transformed volume voxel by voxel
%
for z = 1:new_dim(3)
if verbose & ~mod(z,10)
fprintf('%.2f percent is done.\n', 100*z/new_dim(3));
end
% We need to find out the mapping from voxel in the transformed
% volume (new_XYZvox) to voxel in the original volume (old_XYZvox)
%
% The following equation works, because they all equal to XYZmm:
% new_R*(new_XYZvox-1) + new_T == old_R*(old_XYZvox-1) + old_T
%
% We can use modified new_M1 & old_M1 to substitute new_M & old_M
% new_M1 * new_XYZvox == old_M1 * old_XYZvox
%
% where: M1 = M; M1(:,4) = M(:,4) - sum(M(:,1:3),2);
% and: M(:,4) == [T; 1] == sum(M1,2)
%
% Therefore: old_XYZvox = old_M1 \ new_M1 * new_XYZvox;
%
% Since we are traverse Z axis, and new_XYZvox is replaced
% by mask_Z * new_XYZvox, the above formula can be rewritten
% as: old_XYZvox = old_M1 \ new_M1 * mask_Z * new_XYZvox;
%
% i.e. we find the mapping from new_XYZvox to old_XYZvox:
% M = old_M1 \ new_M1 * mask_Z;
%
% First, compute modified old_M1 & new_M1
%
old_M1 = old_M; old_M1(:,4) = old_M(:,4) - sum(old_M(:,1:3),2);
new_M1 = new_M; new_M1(:,4) = new_M(:,4) - sum(new_M(:,1:3),2);
% Then, apply unit increment of mask_Z(3,4) to simulate the
% cursor movement
%
mask_Z(3,4) = z;
% Here is the mapping from new_XYZvox to old_XYZvox
%
M = old_M1 \ new_M1 * mask_Z;
switch method
case 1
new_img(:,:,z) = trilinear(old_img, new_dim, old_dim, M, bg);
case 2
new_img(:,:,z) = nearest_neighbor(old_img, new_dim, old_dim, M, bg);
case 3
new_img(:,:,z) = bresenham(old_img, new_dim, old_dim, M, bg);
end
end; % for z
if ndims(old_img) == 2
new_M(3,:) = [];
new_M(:,3) = [];
end
return; % affine
%--------------------------------------------------------------------
function img_slice = trilinear(img, dim1, dim2, M, bg)
img_slice = zeros(dim1(1:2));
TINY = 5e-2; % tolerance
% Dimension of transformed 3D volume
%
xdim1 = dim1(1);
ydim1 = dim1(2);
% Dimension of original 3D volume
%
xdim2 = dim2(1);
ydim2 = dim2(2);
zdim2 = dim2(3);
% initialize new_Y accumulation
%
Y2X = 0;
Y2Y = 0;
Y2Z = 0;
for y = 1:ydim1
% increment of new_Y accumulation
%
Y2X = Y2X + M(1,2); % new_Y to old_X
Y2Y = Y2Y + M(2,2); % new_Y to old_Y
Y2Z = Y2Z + M(3,2); % new_Y to old_Z
% backproject new_Y accumulation and translation to old_XYZ
%
old_X = Y2X + M(1,4);
old_Y = Y2Y + M(2,4);
old_Z = Y2Z + M(3,4);
for x = 1:xdim1
% accumulate the increment of new_X, and apply it
% to the backprojected old_XYZ
%
old_X = M(1,1) + old_X ;
old_Y = M(2,1) + old_Y ;
old_Z = M(3,1) + old_Z ;
% within boundary of original image
%
if ( old_X > 1-TINY & old_X < xdim2+TINY & ...
old_Y > 1-TINY & old_Y < ydim2+TINY & ...
old_Z > 1-TINY & old_Z < zdim2+TINY )
% Calculate distance of old_XYZ to its neighbors for
% weighted intensity average
%
dx = old_X - floor(old_X);
dy = old_Y - floor(old_Y);
dz = old_Z - floor(old_Z);
x000 = floor(old_X);
x100 = x000 + 1;
if floor(old_X) < 1
x000 = 1;
x100 = x000;
elseif floor(old_X) > xdim2-1
x000 = xdim2;
x100 = x000;
end
x010 = x000;
x001 = x000;
x011 = x000;
x110 = x100;
x101 = x100;
x111 = x100;
y000 = floor(old_Y);
y010 = y000 + 1;
if floor(old_Y) < 1
y000 = 1;
y100 = y000;
elseif floor(old_Y) > ydim2-1
y000 = ydim2;
y010 = y000;
end
y100 = y000;
y001 = y000;
y101 = y000;
y110 = y010;
y011 = y010;
y111 = y010;
z000 = floor(old_Z);
z001 = z000 + 1;
if floor(old_Z) < 1
z000 = 1;
z001 = z000;
elseif floor(old_Z) > zdim2-1
z000 = zdim2;
z001 = z000;
end
z100 = z000;
z010 = z000;
z110 = z000;
z101 = z001;
z011 = z001;
z111 = z001;
x010 = x000;
x001 = x000;
x011 = x000;
x110 = x100;
x101 = x100;
x111 = x100;
v000 = double(img(x000, y000, z000));
v010 = double(img(x010, y010, z010));
v001 = double(img(x001, y001, z001));
v011 = double(img(x011, y011, z011));
v100 = double(img(x100, y100, z100));
v110 = double(img(x110, y110, z110));
v101 = double(img(x101, y101, z101));
v111 = double(img(x111, y111, z111));
img_slice(x,y) = v000*(1-dx)*(1-dy)*(1-dz) + ...
v010*(1-dx)*dy*(1-dz) + ...
v001*(1-dx)*(1-dy)*dz + ...
v011*(1-dx)*dy*dz + ...
v100*dx*(1-dy)*(1-dz) + ...
v110*dx*dy*(1-dz) + ...
v101*dx*(1-dy)*dz + ...
v111*dx*dy*dz;
else
img_slice(x,y) = bg;
end % if boundary
end % for x
end % for y
return; % trilinear
%--------------------------------------------------------------------
function img_slice = nearest_neighbor(img, dim1, dim2, M, bg)
img_slice = zeros(dim1(1:2));
% Dimension of transformed 3D volume
%
xdim1 = dim1(1);
ydim1 = dim1(2);
% Dimension of original 3D volume
%
xdim2 = dim2(1);
ydim2 = dim2(2);
zdim2 = dim2(3);
% initialize new_Y accumulation
%
Y2X = 0;
Y2Y = 0;
Y2Z = 0;
for y = 1:ydim1
% increment of new_Y accumulation
%
Y2X = Y2X + M(1,2); % new_Y to old_X
Y2Y = Y2Y + M(2,2); % new_Y to old_Y
Y2Z = Y2Z + M(3,2); % new_Y to old_Z
% backproject new_Y accumulation and translation to old_XYZ
%
old_X = Y2X + M(1,4);
old_Y = Y2Y + M(2,4);
old_Z = Y2Z + M(3,4);
for x = 1:xdim1
% accumulate the increment of new_X and apply it
% to the backprojected old_XYZ
%
old_X = M(1,1) + old_X ;
old_Y = M(2,1) + old_Y ;
old_Z = M(3,1) + old_Z ;
xi = round(old_X);
yi = round(old_Y);
zi = round(old_Z);
% within boundary of original image
%
if ( xi >= 1 & xi <= xdim2 & ...
yi >= 1 & yi <= ydim2 & ...
zi >= 1 & zi <= zdim2 )
img_slice(x,y) = img(xi,yi,zi);
else
img_slice(x,y) = bg;
end % if boundary
end % for x
end % for y
return; % nearest_neighbor
%--------------------------------------------------------------------
function img_slice = bresenham(img, dim1, dim2, M, bg)
img_slice = zeros(dim1(1:2));
% Dimension of transformed 3D volume
%
xdim1 = dim1(1);
ydim1 = dim1(2);
% Dimension of original 3D volume
%
xdim2 = dim2(1);
ydim2 = dim2(2);
zdim2 = dim2(3);
for y = 1:ydim1
start_old_XYZ = round(M*[0 y 0 1]');
end_old_XYZ = round(M*[xdim1 y 0 1]');
[X Y Z] = bresenham_line3d(start_old_XYZ, end_old_XYZ);
% line error correction
%
% del = end_old_XYZ - start_old_XYZ;
% del_dom = max(del);
% idx_dom = find(del==del_dom);
% idx_dom = idx_dom(1);
% idx_other = [1 2 3];
% idx_other(idx_dom) = [];
%del_x1 = del(idx_other(1));
% del_x2 = del(idx_other(2));
% line_slope = sqrt((del_x1/del_dom)^2 + (del_x2/del_dom)^2 + 1);
% line_error = line_slope - 1;
% line error correction removed because it is too slow
for x = 1:xdim1
% rescale ratio
%
i = round(x * length(X) / xdim1);
if i < 1
i = 1;
elseif i > length(X)
i = length(X);
end
xi = X(i);
yi = Y(i);
zi = Z(i);
% within boundary of the old XYZ space
%
if ( xi >= 1 & xi <= xdim2 & ...
yi >= 1 & yi <= ydim2 & ...
zi >= 1 & zi <= zdim2 )
img_slice(x,y) = img(xi,yi,zi);
% if line_error > 1
% x = x + 1;
% if x <= xdim1
% img_slice(x,y) = img(xi,yi,zi);
% line_error = line_slope - 1;
% end
% end % if line_error
% line error correction removed because it is too slow
else
img_slice(x,y) = bg;
end % if boundary
end % for x
end % for y
return; % bresenham
|
github
|
adhusch/PaCER-master
|
load_untouch_nii_img.m
|
.m
|
PaCER-master/external/NIfTI_20140122/load_untouch_nii_img.m
| 14,756 |
utf_8
|
688b2a42f8071c6402a037c7ca923689
|
% internal function
% - Jimmy Shen ([email protected])
function [img,hdr] = load_untouch_nii_img(hdr,filetype,fileprefix,machine,img_idx,dim5_idx,dim6_idx,dim7_idx,old_RGB,slice_idx)
if ~exist('hdr','var') | ~exist('filetype','var') | ~exist('fileprefix','var') | ~exist('machine','var')
error('Usage: [img,hdr] = load_nii_img(hdr,filetype,fileprefix,machine,[img_idx],[dim5_idx],[dim6_idx],[dim7_idx],[old_RGB],[slice_idx]);');
end
if ~exist('img_idx','var') | isempty(img_idx) | hdr.dime.dim(5)<1
img_idx = [];
end
if ~exist('dim5_idx','var') | isempty(dim5_idx) | hdr.dime.dim(6)<1
dim5_idx = [];
end
if ~exist('dim6_idx','var') | isempty(dim6_idx) | hdr.dime.dim(7)<1
dim6_idx = [];
end
if ~exist('dim7_idx','var') | isempty(dim7_idx) | hdr.dime.dim(8)<1
dim7_idx = [];
end
if ~exist('old_RGB','var') | isempty(old_RGB)
old_RGB = 0;
end
if ~exist('slice_idx','var') | isempty(slice_idx) | hdr.dime.dim(4)<1
slice_idx = [];
end
% check img_idx
%
if ~isempty(img_idx) & ~isnumeric(img_idx)
error('"img_idx" should be a numerical array.');
end
if length(unique(img_idx)) ~= length(img_idx)
error('Duplicate image index in "img_idx"');
end
if ~isempty(img_idx) & (min(img_idx) < 1 | max(img_idx) > hdr.dime.dim(5))
max_range = hdr.dime.dim(5);
if max_range == 1
error(['"img_idx" should be 1.']);
else
range = ['1 ' num2str(max_range)];
error(['"img_idx" should be an integer within the range of [' range '].']);
end
end
% check dim5_idx
%
if ~isempty(dim5_idx) & ~isnumeric(dim5_idx)
error('"dim5_idx" should be a numerical array.');
end
if length(unique(dim5_idx)) ~= length(dim5_idx)
error('Duplicate index in "dim5_idx"');
end
if ~isempty(dim5_idx) & (min(dim5_idx) < 1 | max(dim5_idx) > hdr.dime.dim(6))
max_range = hdr.dime.dim(6);
if max_range == 1
error(['"dim5_idx" should be 1.']);
else
range = ['1 ' num2str(max_range)];
error(['"dim5_idx" should be an integer within the range of [' range '].']);
end
end
% check dim6_idx
%
if ~isempty(dim6_idx) & ~isnumeric(dim6_idx)
error('"dim6_idx" should be a numerical array.');
end
if length(unique(dim6_idx)) ~= length(dim6_idx)
error('Duplicate index in "dim6_idx"');
end
if ~isempty(dim6_idx) & (min(dim6_idx) < 1 | max(dim6_idx) > hdr.dime.dim(7))
max_range = hdr.dime.dim(7);
if max_range == 1
error(['"dim6_idx" should be 1.']);
else
range = ['1 ' num2str(max_range)];
error(['"dim6_idx" should be an integer within the range of [' range '].']);
end
end
% check dim7_idx
%
if ~isempty(dim7_idx) & ~isnumeric(dim7_idx)
error('"dim7_idx" should be a numerical array.');
end
if length(unique(dim7_idx)) ~= length(dim7_idx)
error('Duplicate index in "dim7_idx"');
end
if ~isempty(dim7_idx) & (min(dim7_idx) < 1 | max(dim7_idx) > hdr.dime.dim(8))
max_range = hdr.dime.dim(8);
if max_range == 1
error(['"dim7_idx" should be 1.']);
else
range = ['1 ' num2str(max_range)];
error(['"dim7_idx" should be an integer within the range of [' range '].']);
end
end
% check slice_idx
%
if ~isempty(slice_idx) & ~isnumeric(slice_idx)
error('"slice_idx" should be a numerical array.');
end
if length(unique(slice_idx)) ~= length(slice_idx)
error('Duplicate index in "slice_idx"');
end
if ~isempty(slice_idx) & (min(slice_idx) < 1 | max(slice_idx) > hdr.dime.dim(4))
max_range = hdr.dime.dim(4);
if max_range == 1
error(['"slice_idx" should be 1.']);
else
range = ['1 ' num2str(max_range)];
error(['"slice_idx" should be an integer within the range of [' range '].']);
end
end
[img,hdr] = read_image(hdr,filetype,fileprefix,machine,img_idx,dim5_idx,dim6_idx,dim7_idx,old_RGB,slice_idx);
return % load_nii_img
%---------------------------------------------------------------------
function [img,hdr] = read_image(hdr,filetype,fileprefix,machine,img_idx,dim5_idx,dim6_idx,dim7_idx,old_RGB,slice_idx)
switch filetype
case {0, 1}
fn = [fileprefix '.img'];
case 2
fn = [fileprefix '.nii'];
end
fid = fopen(fn,'r',machine);
if fid < 0,
msg = sprintf('Cannot open file %s.',fn);
error(msg);
end
% Set bitpix according to datatype
%
% /*Acceptable values for datatype are*/
%
% 0 None (Unknown bit per voxel) % DT_NONE, DT_UNKNOWN
% 1 Binary (ubit1, bitpix=1) % DT_BINARY
% 2 Unsigned char (uchar or uint8, bitpix=8) % DT_UINT8, NIFTI_TYPE_UINT8
% 4 Signed short (int16, bitpix=16) % DT_INT16, NIFTI_TYPE_INT16
% 8 Signed integer (int32, bitpix=32) % DT_INT32, NIFTI_TYPE_INT32
% 16 Floating point (single or float32, bitpix=32) % DT_FLOAT32, NIFTI_TYPE_FLOAT32
% 32 Complex, 2 float32 (Use float32, bitpix=64) % DT_COMPLEX64, NIFTI_TYPE_COMPLEX64
% 64 Double precision (double or float64, bitpix=64) % DT_FLOAT64, NIFTI_TYPE_FLOAT64
% 128 uint8 RGB (Use uint8, bitpix=24) % DT_RGB24, NIFTI_TYPE_RGB24
% 256 Signed char (schar or int8, bitpix=8) % DT_INT8, NIFTI_TYPE_INT8
% 511 Single RGB (Use float32, bitpix=96) % DT_RGB96, NIFTI_TYPE_RGB96
% 512 Unsigned short (uint16, bitpix=16) % DT_UNINT16, NIFTI_TYPE_UNINT16
% 768 Unsigned integer (uint32, bitpix=32) % DT_UNINT32, NIFTI_TYPE_UNINT32
% 1024 Signed long long (int64, bitpix=64) % DT_INT64, NIFTI_TYPE_INT64
% 1280 Unsigned long long (uint64, bitpix=64) % DT_UINT64, NIFTI_TYPE_UINT64
% 1536 Long double, float128 (Unsupported, bitpix=128) % DT_FLOAT128, NIFTI_TYPE_FLOAT128
% 1792 Complex128, 2 float64 (Use float64, bitpix=128) % DT_COMPLEX128, NIFTI_TYPE_COMPLEX128
% 2048 Complex256, 2 float128 (Unsupported, bitpix=256) % DT_COMPLEX128, NIFTI_TYPE_COMPLEX128
%
switch hdr.dime.datatype
case 1,
hdr.dime.bitpix = 1; precision = 'ubit1';
case 2,
hdr.dime.bitpix = 8; precision = 'uint8';
case 4,
hdr.dime.bitpix = 16; precision = 'int16';
case 8,
hdr.dime.bitpix = 32; precision = 'int32';
case 16,
hdr.dime.bitpix = 32; precision = 'float32';
case 32,
hdr.dime.bitpix = 64; precision = 'float32';
case 64,
hdr.dime.bitpix = 64; precision = 'float64';
case 128,
hdr.dime.bitpix = 24; precision = 'uint8';
case 256
hdr.dime.bitpix = 8; precision = 'int8';
case 511
hdr.dime.bitpix = 96; precision = 'float32';
case 512
hdr.dime.bitpix = 16; precision = 'uint16';
case 768
hdr.dime.bitpix = 32; precision = 'uint32';
case 1024
hdr.dime.bitpix = 64; precision = 'int64';
case 1280
hdr.dime.bitpix = 64; precision = 'uint64';
case 1792,
hdr.dime.bitpix = 128; precision = 'float64';
otherwise
error('This datatype is not supported');
end
tmp = hdr.dime.dim(2:end);
tmp(find(tmp < 1)) = 1;
hdr.dime.dim(2:end) = tmp;
% move pointer to the start of image block
%
switch filetype
case {0, 1}
fseek(fid, 0, 'bof');
case 2
fseek(fid, hdr.dime.vox_offset, 'bof');
end
% Load whole image block for old Analyze format or binary image;
% otherwise, load images that are specified in img_idx, dim5_idx,
% dim6_idx, and dim7_idx
%
% For binary image, we have to read all because pos can not be
% seeked in bit and can not be calculated the way below.
%
if hdr.dime.datatype == 1 | isequal(hdr.dime.dim(4:8),ones(1,5)) | ...
(isempty(img_idx) & isempty(dim5_idx) & isempty(dim6_idx) & isempty(dim7_idx) & isempty(slice_idx))
% For each frame, precision of value will be read
% in img_siz times, where img_siz is only the
% dimension size of an image, not the byte storage
% size of an image.
%
img_siz = prod(hdr.dime.dim(2:8));
% For complex float32 or complex float64, voxel values
% include [real, imag]
%
if hdr.dime.datatype == 32 | hdr.dime.datatype == 1792
img_siz = img_siz * 2;
end
%MPH: For RGB24, voxel values include 3 separate color planes
%
if hdr.dime.datatype == 128 | hdr.dime.datatype == 511
img_siz = img_siz * 3;
end
img = fread(fid, img_siz, sprintf('*%s',precision));
d1 = hdr.dime.dim(2);
d2 = hdr.dime.dim(3);
d3 = hdr.dime.dim(4);
d4 = hdr.dime.dim(5);
d5 = hdr.dime.dim(6);
d6 = hdr.dime.dim(7);
d7 = hdr.dime.dim(8);
if isempty(slice_idx)
slice_idx = 1:d3;
end
if isempty(img_idx)
img_idx = 1:d4;
end
if isempty(dim5_idx)
dim5_idx = 1:d5;
end
if isempty(dim6_idx)
dim6_idx = 1:d6;
end
if isempty(dim7_idx)
dim7_idx = 1:d7;
end
else
d1 = hdr.dime.dim(2);
d2 = hdr.dime.dim(3);
d3 = hdr.dime.dim(4);
d4 = hdr.dime.dim(5);
d5 = hdr.dime.dim(6);
d6 = hdr.dime.dim(7);
d7 = hdr.dime.dim(8);
if isempty(slice_idx)
slice_idx = 1:d3;
end
if isempty(img_idx)
img_idx = 1:d4;
end
if isempty(dim5_idx)
dim5_idx = 1:d5;
end
if isempty(dim6_idx)
dim6_idx = 1:d6;
end
if isempty(dim7_idx)
dim7_idx = 1:d7;
end
%ROMAN: begin
roman = 1;
if(roman)
% compute size of one slice
%
img_siz = prod(hdr.dime.dim(2:3));
% For complex float32 or complex float64, voxel values
% include [real, imag]
%
if hdr.dime.datatype == 32 | hdr.dime.datatype == 1792
img_siz = img_siz * 2;
end
%MPH: For RGB24, voxel values include 3 separate color planes
%
if hdr.dime.datatype == 128 | hdr.dime.datatype == 511
img_siz = img_siz * 3;
end
% preallocate img
img = zeros(img_siz, length(slice_idx)*length(img_idx)*length(dim5_idx)*length(dim6_idx)*length(dim7_idx) );
currentIndex = 1;
else
img = [];
end; %if(roman)
% ROMAN: end
for i7=1:length(dim7_idx)
for i6=1:length(dim6_idx)
for i5=1:length(dim5_idx)
for t=1:length(img_idx)
for s=1:length(slice_idx)
% Position is seeked in bytes. To convert dimension size
% to byte storage size, hdr.dime.bitpix/8 will be
% applied.
%
pos = sub2ind([d1 d2 d3 d4 d5 d6 d7], 1, 1, slice_idx(s), ...
img_idx(t), dim5_idx(i5),dim6_idx(i6),dim7_idx(i7)) -1;
pos = pos * hdr.dime.bitpix/8;
% ROMAN: begin
if(roman)
% do nothing
else
img_siz = prod(hdr.dime.dim(2:3));
% For complex float32 or complex float64, voxel values
% include [real, imag]
%
if hdr.dime.datatype == 32 | hdr.dime.datatype == 1792
img_siz = img_siz * 2;
end
%MPH: For RGB24, voxel values include 3 separate color planes
%
if hdr.dime.datatype == 128 | hdr.dime.datatype == 511
img_siz = img_siz * 3;
end
end; % if (roman)
% ROMAN: end
if filetype == 2
fseek(fid, pos + hdr.dime.vox_offset, 'bof');
else
fseek(fid, pos, 'bof');
end
% For each frame, fread will read precision of value
% in img_siz times
%
% ROMAN: begin
if(roman)
img(:,currentIndex) = fread(fid, img_siz, sprintf('*%s',precision));
currentIndex = currentIndex +1;
else
img = [img fread(fid, img_siz, sprintf('*%s',precision))];
end; %if(roman)
% ROMAN: end
end
end
end
end
end
end
% For complex float32 or complex float64, voxel values
% include [real, imag]
%
if hdr.dime.datatype == 32 | hdr.dime.datatype == 1792
img = reshape(img, [2, length(img)/2]);
img = complex(img(1,:)', img(2,:)');
end
fclose(fid);
% Update the global min and max values
%
hdr.dime.glmax = double(max(img(:)));
hdr.dime.glmin = double(min(img(:)));
% old_RGB treat RGB slice by slice, now it is treated voxel by voxel
%
if old_RGB & hdr.dime.datatype == 128 & hdr.dime.bitpix == 24
% remove squeeze
img = (reshape(img, [hdr.dime.dim(2:3) 3 length(slice_idx) length(img_idx) length(dim5_idx) length(dim6_idx) length(dim7_idx)]));
img = permute(img, [1 2 4 3 5 6 7 8]);
elseif hdr.dime.datatype == 128 & hdr.dime.bitpix == 24
% remove squeeze
img = (reshape(img, [3 hdr.dime.dim(2:3) length(slice_idx) length(img_idx) length(dim5_idx) length(dim6_idx) length(dim7_idx)]));
img = permute(img, [2 3 4 1 5 6 7 8]);
elseif hdr.dime.datatype == 511 & hdr.dime.bitpix == 96
img = double(img(:));
img = single((img - min(img))/(max(img) - min(img)));
% remove squeeze
img = (reshape(img, [3 hdr.dime.dim(2:3) length(slice_idx) length(img_idx) length(dim5_idx) length(dim6_idx) length(dim7_idx)]));
img = permute(img, [2 3 4 1 5 6 7 8]);
else
% remove squeeze
img = (reshape(img, [hdr.dime.dim(2:3) length(slice_idx) length(img_idx) length(dim5_idx) length(dim6_idx) length(dim7_idx)]));
end
if ~isempty(slice_idx)
hdr.dime.dim(4) = length(slice_idx);
end
if ~isempty(img_idx)
hdr.dime.dim(5) = length(img_idx);
end
if ~isempty(dim5_idx)
hdr.dime.dim(6) = length(dim5_idx);
end
if ~isempty(dim6_idx)
hdr.dime.dim(7) = length(dim6_idx);
end
if ~isempty(dim7_idx)
hdr.dime.dim(8) = length(dim7_idx);
end
return % read_image
|
github
|
adhusch/PaCER-master
|
load_untouch_nii.m
|
.m
|
PaCER-master/external/NIfTI_20140122/load_untouch_nii.m
| 6,182 |
utf_8
|
93108a725d2e357d773c8aa0acf71328
|
% Load NIFTI or ANALYZE dataset, but not applying any appropriate affine
% geometric transform or voxel intensity scaling.
%
% Although according to NIFTI website, all those header information are
% supposed to be applied to the loaded NIFTI image, there are some
% situations that people do want to leave the original NIFTI header and
% data untouched. They will probably just use MATLAB to do certain image
% processing regardless of image orientation, and to save data back with
% the same NIfTI header.
%
% Since this program is only served for those situations, please use it
% together with "save_untouch_nii.m", and do not use "save_nii.m" or
% "view_nii.m" for the data that is loaded by "load_untouch_nii.m". For
% normal situation, you should use "load_nii.m" instead.
%
% Usage: nii = load_untouch_nii(filename, [img_idx], [dim5_idx], [dim6_idx], ...
% [dim7_idx], [old_RGB], [slice_idx])
%
% filename - NIFTI or ANALYZE file name.
%
% img_idx (optional) - a numerical array of image volume indices.
% Only the specified volumes will be loaded. All available image
% volumes will be loaded, if it is default or empty.
%
% The number of images scans can be obtained from get_nii_frame.m,
% or simply: hdr.dime.dim(5).
%
% dim5_idx (optional) - a numerical array of 5th dimension indices.
% Only the specified range will be loaded. All available range
% will be loaded, if it is default or empty.
%
% dim6_idx (optional) - a numerical array of 6th dimension indices.
% Only the specified range will be loaded. All available range
% will be loaded, if it is default or empty.
%
% dim7_idx (optional) - a numerical array of 7th dimension indices.
% Only the specified range will be loaded. All available range
% will be loaded, if it is default or empty.
%
% old_RGB (optional) - a scale number to tell difference of new RGB24
% from old RGB24. New RGB24 uses RGB triple sequentially for each
% voxel, like [R1 G1 B1 R2 G2 B2 ...]. Analyze 6.0 from AnalyzeDirect
% uses old RGB24, in a way like [R1 R2 ... G1 G2 ... B1 B2 ...] for
% each slices. If the image that you view is garbled, try to set
% old_RGB variable to 1 and try again, because it could be in
% old RGB24. It will be set to 0, if it is default or empty.
%
% slice_idx (optional) - a numerical array of image slice indices.
% Only the specified slices will be loaded. All available image
% slices will be loaded, if it is default or empty.
%
% Returned values:
%
% nii structure:
%
% hdr - struct with NIFTI header fields.
%
% filetype - Analyze format .hdr/.img (0);
% NIFTI .hdr/.img (1);
% NIFTI .nii (2)
%
% fileprefix - NIFTI filename without extension.
%
% machine - machine string variable.
%
% img - 3D (or 4D) matrix of NIFTI data.
%
% - Jimmy Shen ([email protected])
%
function nii = load_untouch_nii(filename, img_idx, dim5_idx, dim6_idx, dim7_idx, ...
old_RGB, slice_idx)
if ~exist('filename','var')
error('Usage: nii = load_untouch_nii(filename, [img_idx], [dim5_idx], [dim6_idx], [dim7_idx], [old_RGB], [slice_idx])');
end
if ~exist('img_idx','var') | isempty(img_idx)
img_idx = [];
end
if ~exist('dim5_idx','var') | isempty(dim5_idx)
dim5_idx = [];
end
if ~exist('dim6_idx','var') | isempty(dim6_idx)
dim6_idx = [];
end
if ~exist('dim7_idx','var') | isempty(dim7_idx)
dim7_idx = [];
end
if ~exist('old_RGB','var') | isempty(old_RGB)
old_RGB = 0;
end
if ~exist('slice_idx','var') | isempty(slice_idx)
slice_idx = [];
end
v = version;
% Check file extension. If .gz, unpack it into temp folder
%
if length(filename) > 2 & strcmp(filename(end-2:end), '.gz')
if ~strcmp(filename(end-6:end), '.img.gz') & ...
~strcmp(filename(end-6:end), '.hdr.gz') & ...
~strcmp(filename(end-6:end), '.nii.gz')
error('Please check filename.');
end
if str2num(v(1:3)) < 7.1 | ~usejava('jvm')
error('Please use MATLAB 7.1 (with java) and above, or run gunzip outside MATLAB.');
elseif strcmp(filename(end-6:end), '.img.gz')
filename1 = filename;
filename2 = filename;
filename2(end-6:end) = '';
filename2 = [filename2, '.hdr.gz'];
tmpDir = tempname;
mkdir(tmpDir);
gzFileName = filename;
filename1 = gunzip(filename1, tmpDir);
filename2 = gunzip(filename2, tmpDir);
filename = char(filename1); % convert from cell to string
elseif strcmp(filename(end-6:end), '.hdr.gz')
filename1 = filename;
filename2 = filename;
filename2(end-6:end) = '';
filename2 = [filename2, '.img.gz'];
tmpDir = tempname;
mkdir(tmpDir);
gzFileName = filename;
filename1 = gunzip(filename1, tmpDir);
filename2 = gunzip(filename2, tmpDir);
filename = char(filename1); % convert from cell to string
elseif strcmp(filename(end-6:end), '.nii.gz')
tmpDir = tempname;
mkdir(tmpDir);
gzFileName = filename;
filename = gunzip(filename, tmpDir);
filename = char(filename); % convert from cell to string
end
end
% Read the dataset header
%
[nii.hdr,nii.filetype,nii.fileprefix,nii.machine] = load_nii_hdr(filename);
if nii.filetype == 0
nii.hdr = load_untouch0_nii_hdr(nii.fileprefix,nii.machine);
nii.ext = [];
else
nii.hdr = load_untouch_nii_hdr(nii.fileprefix,nii.machine,nii.filetype);
% Read the header extension
%
nii.ext = load_nii_ext(filename);
end
% Read the dataset body
%
[nii.img,nii.hdr] = load_untouch_nii_img(nii.hdr,nii.filetype,nii.fileprefix, ...
nii.machine,img_idx,dim5_idx,dim6_idx,dim7_idx,old_RGB,slice_idx);
% Perform some of sform/qform transform
%
% nii = xform_nii(nii, tolerance, preferredForm);
nii.untouch = 1;
% Clean up after gunzip
%
if exist('gzFileName', 'var')
% fix fileprefix so it doesn't point to temp location
%
nii.fileprefix = gzFileName(1:end-7);
rmdir(tmpDir,'s');
end
return % load_untouch_nii
|
github
|
adhusch/PaCER-master
|
collapse_nii_scan.m
|
.m
|
PaCER-master/external/NIfTI_20140122/collapse_nii_scan.m
| 6,778 |
utf_8
|
64b1cb0f7cd9e095d3c11ca66453df69
|
% Collapse multiple single-scan NIFTI files into a multiple-scan NIFTI file
%
% Usage: collapse_nii_scan(scan_file_pattern, [collapsed_fileprefix], [scan_file_folder])
%
% Here, scan_file_pattern should look like: 'myscan_0*.img'
% If collapsed_fileprefix is omit, 'multi_scan' will be used
% If scan_file_folder is omit, current file folder will be used
%
% The order of volumes in the collapsed file will be the order of
% corresponding filenames for those selected scan files.
%
% NIFTI data format can be found on: http://nifti.nimh.nih.gov
%
% - Jimmy Shen ([email protected])
%
function collapse_nii_scan(scan_pattern, fileprefix, scan_path)
if ~exist('fileprefix','var')
fileprefix = 'multi_scan';
else
[tmp fileprefix] = fileparts(fileprefix);
end
if ~exist('scan_path','var'), scan_path = pwd; end
pnfn = fullfile(scan_path, scan_pattern);
file_lst = dir(pnfn);
flist = {file_lst.name};
flist = flist(:);
filename = flist{1};
v = version;
% Check file extension. If .gz, unpack it into temp folder
%
if length(filename) > 2 & strcmp(filename(end-2:end), '.gz')
if ~strcmp(filename(end-6:end), '.img.gz') & ...
~strcmp(filename(end-6:end), '.hdr.gz') & ...
~strcmp(filename(end-6:end), '.nii.gz')
error('Please check filename.');
end
if str2num(v(1:3)) < 7.1 | ~usejava('jvm')
error('Please use MATLAB 7.1 (with java) and above, or run gunzip outside MATLAB.');
else
gzFile = 1;
end
else
if ~strcmp(filename(end-3:end), '.img') & ...
~strcmp(filename(end-3:end), '.hdr') & ...
~strcmp(filename(end-3:end), '.nii')
error('Please check filename.');
end
end
nii = load_untouch_nii(fullfile(scan_path,filename));
nii.hdr.dime.dim(5) = length(flist);
if nii.hdr.dime.dim(1) < 4
nii.hdr.dime.dim(1) = 4;
end
hdr = nii.hdr;
filetype = nii.filetype;
if isfield(nii,'ext') & ~isempty(nii.ext)
ext = nii.ext;
[ext, esize_total] = verify_nii_ext(ext);
else
ext = [];
end
switch double(hdr.dime.datatype),
case 1,
hdr.dime.bitpix = int16(1 ); precision = 'ubit1';
case 2,
hdr.dime.bitpix = int16(8 ); precision = 'uint8';
case 4,
hdr.dime.bitpix = int16(16); precision = 'int16';
case 8,
hdr.dime.bitpix = int16(32); precision = 'int32';
case 16,
hdr.dime.bitpix = int16(32); precision = 'float32';
case 32,
hdr.dime.bitpix = int16(64); precision = 'float32';
case 64,
hdr.dime.bitpix = int16(64); precision = 'float64';
case 128,
hdr.dime.bitpix = int16(24); precision = 'uint8';
case 256
hdr.dime.bitpix = int16(8 ); precision = 'int8';
case 512
hdr.dime.bitpix = int16(16); precision = 'uint16';
case 768
hdr.dime.bitpix = int16(32); precision = 'uint32';
case 1024
hdr.dime.bitpix = int16(64); precision = 'int64';
case 1280
hdr.dime.bitpix = int16(64); precision = 'uint64';
case 1792,
hdr.dime.bitpix = int16(128); precision = 'float64';
otherwise
error('This datatype is not supported');
end
if filetype == 2
fid = fopen(sprintf('%s.nii',fileprefix),'w');
if fid < 0,
msg = sprintf('Cannot open file %s.nii.',fileprefix);
error(msg);
end
hdr.dime.vox_offset = 352;
if ~isempty(ext)
hdr.dime.vox_offset = hdr.dime.vox_offset + esize_total;
end
hdr.hist.magic = 'n+1';
save_untouch_nii_hdr(hdr, fid);
if ~isempty(ext)
save_nii_ext(ext, fid);
end
elseif filetype == 1
fid = fopen(sprintf('%s.hdr',fileprefix),'w');
if fid < 0,
msg = sprintf('Cannot open file %s.hdr.',fileprefix);
error(msg);
end
hdr.dime.vox_offset = 0;
hdr.hist.magic = 'ni1';
save_untouch_nii_hdr(hdr, fid);
if ~isempty(ext)
save_nii_ext(ext, fid);
end
fclose(fid);
fid = fopen(sprintf('%s.img',fileprefix),'w');
else
fid = fopen(sprintf('%s.hdr',fileprefix),'w');
if fid < 0,
msg = sprintf('Cannot open file %s.hdr.',fileprefix);
error(msg);
end
save_untouch0_nii_hdr(hdr, fid);
fclose(fid);
fid = fopen(sprintf('%s.img',fileprefix),'w');
end
if filetype == 2 & isempty(ext)
skip_bytes = double(hdr.dime.vox_offset) - 348;
else
skip_bytes = 0;
end
if skip_bytes
fwrite(fid, zeros(1,skip_bytes), 'uint8');
end
glmax = -inf;
glmin = inf;
for i = 1:length(flist)
nii = load_untouch_nii(fullfile(scan_path,flist{i}));
if double(hdr.dime.datatype) == 128
% RGB planes are expected to be in the 4th dimension of nii.img
%
if(size(nii.img,4)~=3)
error(['The NII structure does not appear to have 3 RGB color planes in the 4th dimension']);
end
nii.img = permute(nii.img, [4 1 2 3 5 6 7 8]);
end
% For complex float32 or complex float64, voxel values
% include [real, imag]
%
if hdr.dime.datatype == 32 | hdr.dime.datatype == 1792
real_img = real(nii.img(:))';
nii.img = imag(nii.img(:))';
nii.img = [real_img; nii.img];
end
if nii.hdr.dime.glmax > glmax
glmax = nii.hdr.dime.glmax;
end
if nii.hdr.dime.glmin < glmin
glmin = nii.hdr.dime.glmin;
end
fwrite(fid, nii.img, precision);
end
hdr.dime.glmax = round(glmax);
hdr.dime.glmin = round(glmin);
if filetype == 2
fseek(fid, 140, 'bof');
fwrite(fid, hdr.dime.glmax, 'int32');
fwrite(fid, hdr.dime.glmin, 'int32');
elseif filetype == 1
fid2 = fopen(sprintf('%s.hdr',fileprefix),'w');
if fid2 < 0,
msg = sprintf('Cannot open file %s.hdr.',fileprefix);
error(msg);
end
save_untouch_nii_hdr(hdr, fid2);
if ~isempty(ext)
save_nii_ext(ext, fid2);
end
fclose(fid2);
else
fid2 = fopen(sprintf('%s.hdr',fileprefix),'w');
if fid2 < 0,
msg = sprintf('Cannot open file %s.hdr.',fileprefix);
error(msg);
end
save_untouch0_nii_hdr(hdr, fid2);
fclose(fid2);
end
fclose(fid);
% gzip output file if requested
%
if exist('gzFile', 'var')
if filetype == 1
gzip([fileprefix, '.img']);
delete([fileprefix, '.img']);
gzip([fileprefix, '.hdr']);
delete([fileprefix, '.hdr']);
elseif filetype == 2
gzip([fileprefix, '.nii']);
delete([fileprefix, '.nii']);
end;
end;
return; % collapse_nii_scan
|
github
|
adhusch/PaCER-master
|
rri_orient_ui.m
|
.m
|
PaCER-master/external/NIfTI_20140122/rri_orient_ui.m
| 5,384 |
utf_8
|
e1196b81940d9f93fbdb43c33799e587
|
% Return orientation of the current image:
% orient is orientation 1x3 matrix, in that:
% Three elements represent: [x y z]
% Element value: 1 - Left to Right; 2 - Posterior to Anterior;
% 3 - Inferior to Superior; 4 - Right to Left;
% 5 - Anterior to Posterior; 6 - Superior to Inferior;
% e.g.:
% Standard RAS Orientation: [1 2 3]
% Standard RHOS Orientation: [2 4 3]
% Jimmy Shen ([email protected]), 26-APR-04
%
function orient = rri_orient_ui(varargin)
if nargin == 0
init;
orient_ui_fig = gcf;
uiwait; % wait for user finish
orient = getappdata(gcf, 'orient');
if isempty(orient)
orient = [1 2 3];
end
if ishandle(orient_ui_fig)
close(gcf);
end
return;
end
action = varargin{1};
if strcmp(action, 'done')
click_done;
elseif strcmp(action, 'cancel')
uiresume;
end
return; % rri_orient_ui
%----------------------------------------------------------------------
function init
save_setting_status = 'on';
rri_orient_pos = [];
try
load('pls_profile');
catch
end
try
load('rri_pos_profile');
catch
end
if ~isempty(rri_orient_pos) & strcmp(save_setting_status,'on')
pos = rri_orient_pos;
else
w = 0.35;
h = 0.4;
x = (1-w)/2;
y = (1-h)/2;
pos = [x y w h];
end
handles.figure = figure('Color',[0.8 0.8 0.8], ...
'Units','normal', ...
'Name', 'Convert to standard RAS orientation', ...
'NumberTitle','off', ...
'MenuBar','none', ...
'Position',pos, ...
'WindowStyle', 'normal', ...
'ToolBar','none');
h0 = handles.figure;
Font.FontUnits = 'point';
Font.FontSize = 12;
margin = .1;
line_num = 6;
line_ht = (1 - margin*2) / line_num;
x = margin;
y = 1 - margin - line_ht;
w = 1 - margin * 2;
h = line_ht * .7;
pos = [x y w h];
handles.Ttit = uicontrol('parent', h0, ...
'style','text', ...
'unit', 'normal', ...
Font, ...
'Position',pos, ...
'HorizontalAlignment','left',...
'background', [0.8 0.8 0.8], ...
'string', 'Please input orientation of the current image:');
y = y - line_ht;
w = .2;
pos = [x y w h];
handles.Tx_orient = uicontrol('parent', h0, ...
'style','text', ...
'unit', 'normal', ...
Font, ...
'Position',pos, ...
'HorizontalAlignment','left',...
'background', [0.8 0.8 0.8], ...
'string', 'X Axes:');
y = y - line_ht;
pos = [x y w h];
handles.Ty_orient = uicontrol('parent', h0, ...
'style','text', ...
'unit', 'normal', ...
Font, ...
'Position',pos, ...
'HorizontalAlignment','left',...
'background', [0.8 0.8 0.8], ...
'string', 'Y Axes:');
y = y - line_ht;
pos = [x y w h];
handles.Tz_orient = uicontrol('parent', h0, ...
'style','text', ...
'unit', 'normal', ...
Font, ...
'Position',pos, ...
'HorizontalAlignment','left',...
'background', [0.8 0.8 0.8], ...
'string', 'Z Axes:');
choice = { 'From Left to Right', 'From Posterior to Anterior', ...
'From Inferior to Superior', 'From Right to Left', ...
'From Anterior to Posterior', 'From Superior to Inferior' };
y = 1 - margin - line_ht;
y = y - line_ht;
w = 1 - margin - x - w;
x = 1 - margin - w;
pos = [x y w h];
handles.x_orient = uicontrol('parent', h0, ...
'style','popupmenu', ...
'unit', 'normal', ...
Font, ...
'Position',pos, ...
'HorizontalAlignment','left',...
'string', choice, ...
'value', 1, ...
'background', [1 1 1]);
y = y - line_ht;
pos = [x y w h];
handles.y_orient = uicontrol('parent', h0, ...
'style','popupmenu', ...
'unit', 'normal', ...
Font, ...
'Position',pos, ...
'HorizontalAlignment','left',...
'string', choice, ...
'value', 2, ...
'background', [1 1 1]);
y = y - line_ht;
pos = [x y w h];
handles.z_orient = uicontrol('parent', h0, ...
'style','popupmenu', ...
'unit', 'normal', ...
Font, ...
'Position',pos, ...
'HorizontalAlignment','left',...
'string', choice, ...
'value', 3, ...
'background', [1 1 1]);
x = margin;
y = y - line_ht * 1.5;
w = .3;
pos = [x y w h];
handles.done = uicontrol('parent', h0, ...
'unit', 'normal', ...
Font, ...
'Position',pos, ...
'HorizontalAlignment','center',...
'callback', 'rri_orient_ui(''done'');', ...
'string', 'Done');
x = 1 - margin - w;
pos = [x y w h];
handles.cancel = uicontrol('parent', h0, ...
'unit', 'normal', ...
Font, ...
'Position',pos, ...
'HorizontalAlignment','center',...
'callback', 'rri_orient_ui(''cancel'');', ...
'string', 'Cancel');
setappdata(h0, 'handles', handles);
setappdata(h0, 'orient', [1 2 3]);
return; % init
%----------------------------------------------------------------------
function click_done
handles = getappdata(gcf, 'handles');
x_orient = get(handles.x_orient, 'value');
y_orient = get(handles.y_orient, 'value');
z_orient = get(handles.z_orient, 'value');
orient = [x_orient y_orient z_orient];
test_orient = [orient, orient + 3];
test_orient = mod(test_orient, 3);
if length(unique(test_orient)) ~= 3
msgbox('Please don''t choose same or opposite direction','Error','modal');
return;
end
setappdata(gcf, 'orient', [x_orient y_orient z_orient]);
uiresume;
return; % click_done
|
github
|
adhusch/PaCER-master
|
load_untouch0_nii_hdr.m
|
.m
|
PaCER-master/external/NIfTI_20140122/load_untouch0_nii_hdr.m
| 8,093 |
utf_8
|
3de9ff6a1da47b56ae680e7660eaa041
|
% internal function
% - Jimmy Shen ([email protected])
function hdr = load_nii_hdr(fileprefix, machine)
fn = sprintf('%s.hdr',fileprefix);
fid = fopen(fn,'r',machine);
if fid < 0,
msg = sprintf('Cannot open file %s.',fn);
error(msg);
else
fseek(fid,0,'bof');
hdr = read_header(fid);
fclose(fid);
end
return % load_nii_hdr
%---------------------------------------------------------------------
function [ dsr ] = read_header(fid)
% Original header structures
% struct dsr
% {
% struct header_key hk; /* 0 + 40 */
% struct image_dimension dime; /* 40 + 108 */
% struct data_history hist; /* 148 + 200 */
% }; /* total= 348 bytes*/
dsr.hk = header_key(fid);
dsr.dime = image_dimension(fid);
dsr.hist = data_history(fid);
return % read_header
%---------------------------------------------------------------------
function [ hk ] = header_key(fid)
fseek(fid,0,'bof');
% Original header structures
% struct header_key /* header key */
% { /* off + size */
% int sizeof_hdr /* 0 + 4 */
% char data_type[10]; /* 4 + 10 */
% char db_name[18]; /* 14 + 18 */
% int extents; /* 32 + 4 */
% short int session_error; /* 36 + 2 */
% char regular; /* 38 + 1 */
% char hkey_un0; /* 39 + 1 */
% }; /* total=40 bytes */
%
% int sizeof_header Should be 348.
% char regular Must be 'r' to indicate that all images and
% volumes are the same size.
v6 = version;
if str2num(v6(1))<6
directchar = '*char';
else
directchar = 'uchar=>char';
end
hk.sizeof_hdr = fread(fid, 1,'int32')'; % should be 348!
hk.data_type = deblank(fread(fid,10,directchar)');
hk.db_name = deblank(fread(fid,18,directchar)');
hk.extents = fread(fid, 1,'int32')';
hk.session_error = fread(fid, 1,'int16')';
hk.regular = fread(fid, 1,directchar)';
hk.hkey_un0 = fread(fid, 1,directchar)';
return % header_key
%---------------------------------------------------------------------
function [ dime ] = image_dimension(fid)
%struct image_dimension
% { /* off + size */
% short int dim[8]; /* 0 + 16 */
% /*
% dim[0] Number of dimensions in database; usually 4.
% dim[1] Image X dimension; number of *pixels* in an image row.
% dim[2] Image Y dimension; number of *pixel rows* in slice.
% dim[3] Volume Z dimension; number of *slices* in a volume.
% dim[4] Time points; number of volumes in database
% */
% char vox_units[4]; /* 16 + 4 */
% char cal_units[8]; /* 20 + 8 */
% short int unused1; /* 28 + 2 */
% short int datatype; /* 30 + 2 */
% short int bitpix; /* 32 + 2 */
% short int dim_un0; /* 34 + 2 */
% float pixdim[8]; /* 36 + 32 */
% /*
% pixdim[] specifies the voxel dimensions:
% pixdim[1] - voxel width, mm
% pixdim[2] - voxel height, mm
% pixdim[3] - slice thickness, mm
% pixdim[4] - volume timing, in msec
% ..etc
% */
% float vox_offset; /* 68 + 4 */
% float roi_scale; /* 72 + 4 */
% float funused1; /* 76 + 4 */
% float funused2; /* 80 + 4 */
% float cal_max; /* 84 + 4 */
% float cal_min; /* 88 + 4 */
% int compressed; /* 92 + 4 */
% int verified; /* 96 + 4 */
% int glmax; /* 100 + 4 */
% int glmin; /* 104 + 4 */
% }; /* total=108 bytes */
v6 = version;
if str2num(v6(1))<6
directchar = '*char';
else
directchar = 'uchar=>char';
end
dime.dim = fread(fid,8,'int16')';
dime.vox_units = deblank(fread(fid,4,directchar)');
dime.cal_units = deblank(fread(fid,8,directchar)');
dime.unused1 = fread(fid,1,'int16')';
dime.datatype = fread(fid,1,'int16')';
dime.bitpix = fread(fid,1,'int16')';
dime.dim_un0 = fread(fid,1,'int16')';
dime.pixdim = fread(fid,8,'float32')';
dime.vox_offset = fread(fid,1,'float32')';
dime.roi_scale = fread(fid,1,'float32')';
dime.funused1 = fread(fid,1,'float32')';
dime.funused2 = fread(fid,1,'float32')';
dime.cal_max = fread(fid,1,'float32')';
dime.cal_min = fread(fid,1,'float32')';
dime.compressed = fread(fid,1,'int32')';
dime.verified = fread(fid,1,'int32')';
dime.glmax = fread(fid,1,'int32')';
dime.glmin = fread(fid,1,'int32')';
return % image_dimension
%---------------------------------------------------------------------
function [ hist ] = data_history(fid)
%struct data_history
% { /* off + size */
% char descrip[80]; /* 0 + 80 */
% char aux_file[24]; /* 80 + 24 */
% char orient; /* 104 + 1 */
% char originator[10]; /* 105 + 10 */
% char generated[10]; /* 115 + 10 */
% char scannum[10]; /* 125 + 10 */
% char patient_id[10]; /* 135 + 10 */
% char exp_date[10]; /* 145 + 10 */
% char exp_time[10]; /* 155 + 10 */
% char hist_un0[3]; /* 165 + 3 */
% int views /* 168 + 4 */
% int vols_added; /* 172 + 4 */
% int start_field; /* 176 + 4 */
% int field_skip; /* 180 + 4 */
% int omax; /* 184 + 4 */
% int omin; /* 188 + 4 */
% int smax; /* 192 + 4 */
% int smin; /* 196 + 4 */
% }; /* total=200 bytes */
v6 = version;
if str2num(v6(1))<6
directchar = '*char';
else
directchar = 'uchar=>char';
end
hist.descrip = deblank(fread(fid,80,directchar)');
hist.aux_file = deblank(fread(fid,24,directchar)');
hist.orient = fread(fid, 1,'char')';
hist.originator = fread(fid, 5,'int16')';
hist.generated = deblank(fread(fid,10,directchar)');
hist.scannum = deblank(fread(fid,10,directchar)');
hist.patient_id = deblank(fread(fid,10,directchar)');
hist.exp_date = deblank(fread(fid,10,directchar)');
hist.exp_time = deblank(fread(fid,10,directchar)');
hist.hist_un0 = deblank(fread(fid, 3,directchar)');
hist.views = fread(fid, 1,'int32')';
hist.vols_added = fread(fid, 1,'int32')';
hist.start_field = fread(fid, 1,'int32')';
hist.field_skip = fread(fid, 1,'int32')';
hist.omax = fread(fid, 1,'int32')';
hist.omin = fread(fid, 1,'int32')';
hist.smax = fread(fid, 1,'int32')';
hist.smin = fread(fid, 1,'int32')';
return % data_history
|
github
|
adhusch/PaCER-master
|
load_nii.m
|
.m
|
PaCER-master/external/NIfTI_20140122/load_nii.m
| 6,808 |
utf_8
|
d098a5dbea3cd4ad76cea624ffbef9db
|
% Load NIFTI or ANALYZE dataset. Support both *.nii and *.hdr/*.img
% file extension. If file extension is not provided, *.hdr/*.img will
% be used as default.
%
% A subset of NIFTI transform is included. For non-orthogonal rotation,
% shearing etc., please use 'reslice_nii.m' to reslice the NIFTI file.
% It will not cause negative effect, as long as you remember not to do
% slice time correction after reslicing the NIFTI file. Output variable
% nii will be in RAS orientation, i.e. X axis from Left to Right,
% Y axis from Posterior to Anterior, and Z axis from Inferior to
% Superior.
%
% Usage: nii = load_nii(filename, [img_idx], [dim5_idx], [dim6_idx], ...
% [dim7_idx], [old_RGB], [tolerance], [preferredForm])
%
% filename - NIFTI or ANALYZE file name.
%
% img_idx (optional) - a numerical array of 4th dimension indices,
% which is the indices of image scan volume. The number of images
% scan volumes can be obtained from get_nii_frame.m, or simply
% hdr.dime.dim(5). Only the specified volumes will be loaded.
% All available image volumes will be loaded, if it is default or
% empty.
%
% dim5_idx (optional) - a numerical array of 5th dimension indices.
% Only the specified range will be loaded. All available range
% will be loaded, if it is default or empty.
%
% dim6_idx (optional) - a numerical array of 6th dimension indices.
% Only the specified range will be loaded. All available range
% will be loaded, if it is default or empty.
%
% dim7_idx (optional) - a numerical array of 7th dimension indices.
% Only the specified range will be loaded. All available range
% will be loaded, if it is default or empty.
%
% old_RGB (optional) - a scale number to tell difference of new RGB24
% from old RGB24. New RGB24 uses RGB triple sequentially for each
% voxel, like [R1 G1 B1 R2 G2 B2 ...]. Analyze 6.0 from AnalyzeDirect
% uses old RGB24, in a way like [R1 R2 ... G1 G2 ... B1 B2 ...] for
% each slices. If the image that you view is garbled, try to set
% old_RGB variable to 1 and try again, because it could be in
% old RGB24. It will be set to 0, if it is default or empty.
%
% tolerance (optional) - distortion allowed in the loaded image for any
% non-orthogonal rotation or shearing of NIfTI affine matrix. If
% you set 'tolerance' to 0, it means that you do not allow any
% distortion. If you set 'tolerance' to 1, it means that you do
% not care any distortion. The image will fail to be loaded if it
% can not be tolerated. The tolerance will be set to 0.1 (10%), if
% it is default or empty.
%
% preferredForm (optional) - selects which transformation from voxels
% to RAS coordinates; values are s,q,S,Q. Lower case s,q indicate
% "prefer sform or qform, but use others if preferred not present".
% Upper case indicate the program is forced to use the specificied
% tranform or fail loading. 'preferredForm' will be 's', if it is
% default or empty. - Jeff Gunter
%
% Returned values:
%
% nii structure:
%
% hdr - struct with NIFTI header fields.
%
% filetype - Analyze format .hdr/.img (0);
% NIFTI .hdr/.img (1);
% NIFTI .nii (2)
%
% fileprefix - NIFTI filename without extension.
%
% machine - machine string variable.
%
% img - 3D (or 4D) matrix of NIFTI data.
%
% original - the original header before any affine transform.
%
% Part of this file is copied and modified from:
% http://www.mathworks.com/matlabcentral/fileexchange/1878-mri-analyze-tools
%
% NIFTI data format can be found on: http://nifti.nimh.nih.gov
%
% - Jimmy Shen ([email protected])
%
function nii = load_nii(filename, img_idx, dim5_idx, dim6_idx, dim7_idx, ...
old_RGB, tolerance, preferredForm)
if ~exist('filename','var')
error('Usage: nii = load_nii(filename, [img_idx], [dim5_idx], [dim6_idx], [dim7_idx], [old_RGB], [tolerance], [preferredForm])');
end
if ~exist('img_idx','var') | isempty(img_idx)
img_idx = [];
end
if ~exist('dim5_idx','var') | isempty(dim5_idx)
dim5_idx = [];
end
if ~exist('dim6_idx','var') | isempty(dim6_idx)
dim6_idx = [];
end
if ~exist('dim7_idx','var') | isempty(dim7_idx)
dim7_idx = [];
end
if ~exist('old_RGB','var') | isempty(old_RGB)
old_RGB = 0;
end
if ~exist('tolerance','var') | isempty(tolerance)
tolerance = 0.1; % 10 percent
end
if ~exist('preferredForm','var') | isempty(preferredForm)
preferredForm= 's'; % Jeff
end
v = version;
% Check file extension. If .gz, unpack it into temp folder
%
if length(filename) > 2 & strcmp(filename(end-2:end), '.gz')
if ~strcmp(filename(end-6:end), '.img.gz') & ...
~strcmp(filename(end-6:end), '.hdr.gz') & ...
~strcmp(filename(end-6:end), '.nii.gz')
error('Please check filename.');
end
if str2num(v(1:3)) < 7.1 | ~usejava('jvm')
error('Please use MATLAB 7.1 (with java) and above, or run gunzip outside MATLAB.');
elseif strcmp(filename(end-6:end), '.img.gz')
filename1 = filename;
filename2 = filename;
filename2(end-6:end) = '';
filename2 = [filename2, '.hdr.gz'];
tmpDir = tempname;
mkdir(tmpDir);
gzFileName = filename;
filename1 = gunzip(filename1, tmpDir);
filename2 = gunzip(filename2, tmpDir);
filename = char(filename1); % convert from cell to string
elseif strcmp(filename(end-6:end), '.hdr.gz')
filename1 = filename;
filename2 = filename;
filename2(end-6:end) = '';
filename2 = [filename2, '.img.gz'];
tmpDir = tempname;
mkdir(tmpDir);
gzFileName = filename;
filename1 = gunzip(filename1, tmpDir);
filename2 = gunzip(filename2, tmpDir);
filename = char(filename1); % convert from cell to string
elseif strcmp(filename(end-6:end), '.nii.gz')
tmpDir = tempname;
mkdir(tmpDir);
gzFileName = filename;
filename = gunzip(filename, tmpDir);
filename = char(filename); % convert from cell to string
end
end
% Read the dataset header
%
[nii.hdr,nii.filetype,nii.fileprefix,nii.machine] = load_nii_hdr(filename);
% Read the header extension
%
% nii.ext = load_nii_ext(filename);
% Read the dataset body
%
[nii.img,nii.hdr] = load_nii_img(nii.hdr,nii.filetype,nii.fileprefix, ...
nii.machine,img_idx,dim5_idx,dim6_idx,dim7_idx,old_RGB);
% Perform some of sform/qform transform
%
nii = xform_nii(nii, tolerance, preferredForm);
% Clean up after gunzip
%
if exist('gzFileName', 'var')
% fix fileprefix so it doesn't point to temp location
%
nii.fileprefix = gzFileName(1:end-7);
rmdir(tmpDir,'s');
end
return % load_nii
|
github
|
adhusch/PaCER-master
|
unxform_nii.m
|
.m
|
PaCER-master/external/NIfTI_20140122/unxform_nii.m
| 1,181 |
utf_8
|
a77d113be34b09d588b2eb326a3c65c8
|
% Undo the flipping and rotations performed by xform_nii; spit back only
% the raw img data block. Initial cut will only deal with 3D volumes
% strongly assume we have called xform_nii to write down the steps used
% in xform_nii.
%
% Usage: a = load_nii('original_name');
% manipulate a.img to make array b;
%
% if you use unxform_nii to un-tranform the image (img) data
% block, then nii.original.hdr is the corresponding header.
%
% nii.original.img = unxform_nii(a, b);
% save_nii(nii.original,'newname');
%
% Where, 'newname' is created with data in the same space as the
% original_name data
%
% - Jeff Gunter, 26-JUN-06
%
function outblock = unxform_nii(nii, inblock)
if isempty(nii.hdr.hist.rot_orient)
outblock=inblock;
else
[dummy unrotate_orient] = sort(nii.hdr.hist.rot_orient);
outblock = permute(inblock, unrotate_orient);
end
if ~isempty(nii.hdr.hist.flip_orient)
flip_orient = nii.hdr.hist.flip_orient(unrotate_orient);
for i = 1:3
if flip_orient(i)
outblock = flipdim(outblock, i);
end
end
end;
return;
|
github
|
adhusch/PaCER-master
|
load_untouch_nii_hdr.m
|
.m
|
PaCER-master/external/NIfTI_20140122/load_untouch_nii_hdr.m
| 8,522 |
utf_8
|
2d4bc8c8ffb83b37daf1e8dd87c108e6
|
% internal function
% - Jimmy Shen ([email protected])
function hdr = load_nii_hdr(fileprefix, machine, filetype)
if filetype == 2
fn = sprintf('%s.nii',fileprefix);
if ~exist(fn)
msg = sprintf('Cannot find file "%s.nii".', fileprefix);
error(msg);
end
else
fn = sprintf('%s.hdr',fileprefix);
if ~exist(fn)
msg = sprintf('Cannot find file "%s.hdr".', fileprefix);
error(msg);
end
end
fid = fopen(fn,'r',machine);
if fid < 0,
msg = sprintf('Cannot open file %s.',fn);
error(msg);
else
fseek(fid,0,'bof');
hdr = read_header(fid);
fclose(fid);
end
return % load_nii_hdr
%---------------------------------------------------------------------
function [ dsr ] = read_header(fid)
% Original header structures
% struct dsr
% {
% struct header_key hk; /* 0 + 40 */
% struct image_dimension dime; /* 40 + 108 */
% struct data_history hist; /* 148 + 200 */
% }; /* total= 348 bytes*/
dsr.hk = header_key(fid);
dsr.dime = image_dimension(fid);
dsr.hist = data_history(fid);
% For Analyze data format
%
if ~strcmp(dsr.hist.magic, 'n+1') & ~strcmp(dsr.hist.magic, 'ni1')
dsr.hist.qform_code = 0;
dsr.hist.sform_code = 0;
end
return % read_header
%---------------------------------------------------------------------
function [ hk ] = header_key(fid)
fseek(fid,0,'bof');
% Original header structures
% struct header_key /* header key */
% { /* off + size */
% int sizeof_hdr /* 0 + 4 */
% char data_type[10]; /* 4 + 10 */
% char db_name[18]; /* 14 + 18 */
% int extents; /* 32 + 4 */
% short int session_error; /* 36 + 2 */
% char regular; /* 38 + 1 */
% char dim_info; % char hkey_un0; /* 39 + 1 */
% }; /* total=40 bytes */
%
% int sizeof_header Should be 348.
% char regular Must be 'r' to indicate that all images and
% volumes are the same size.
v6 = version;
if str2num(v6(1))<6
directchar = '*char';
else
directchar = 'uchar=>char';
end
hk.sizeof_hdr = fread(fid, 1,'int32')'; % should be 348!
hk.data_type = deblank(fread(fid,10,directchar)');
hk.db_name = deblank(fread(fid,18,directchar)');
hk.extents = fread(fid, 1,'int32')';
hk.session_error = fread(fid, 1,'int16')';
hk.regular = fread(fid, 1,directchar)';
hk.dim_info = fread(fid, 1,'uchar')';
return % header_key
%---------------------------------------------------------------------
function [ dime ] = image_dimension(fid)
% Original header structures
% struct image_dimension
% { /* off + size */
% short int dim[8]; /* 0 + 16 */
% /*
% dim[0] Number of dimensions in database; usually 4.
% dim[1] Image X dimension; number of *pixels* in an image row.
% dim[2] Image Y dimension; number of *pixel rows* in slice.
% dim[3] Volume Z dimension; number of *slices* in a volume.
% dim[4] Time points; number of volumes in database
% */
% float intent_p1; % char vox_units[4]; /* 16 + 4 */
% float intent_p2; % char cal_units[8]; /* 20 + 4 */
% float intent_p3; % char cal_units[8]; /* 24 + 4 */
% short int intent_code; % short int unused1; /* 28 + 2 */
% short int datatype; /* 30 + 2 */
% short int bitpix; /* 32 + 2 */
% short int slice_start; % short int dim_un0; /* 34 + 2 */
% float pixdim[8]; /* 36 + 32 */
% /*
% pixdim[] specifies the voxel dimensions:
% pixdim[1] - voxel width, mm
% pixdim[2] - voxel height, mm
% pixdim[3] - slice thickness, mm
% pixdim[4] - volume timing, in msec
% ..etc
% */
% float vox_offset; /* 68 + 4 */
% float scl_slope; % float roi_scale; /* 72 + 4 */
% float scl_inter; % float funused1; /* 76 + 4 */
% short slice_end; % float funused2; /* 80 + 2 */
% char slice_code; % float funused2; /* 82 + 1 */
% char xyzt_units; % float funused2; /* 83 + 1 */
% float cal_max; /* 84 + 4 */
% float cal_min; /* 88 + 4 */
% float slice_duration; % int compressed; /* 92 + 4 */
% float toffset; % int verified; /* 96 + 4 */
% int glmax; /* 100 + 4 */
% int glmin; /* 104 + 4 */
% }; /* total=108 bytes */
dime.dim = fread(fid,8,'int16')';
dime.intent_p1 = fread(fid,1,'float32')';
dime.intent_p2 = fread(fid,1,'float32')';
dime.intent_p3 = fread(fid,1,'float32')';
dime.intent_code = fread(fid,1,'int16')';
dime.datatype = fread(fid,1,'int16')';
dime.bitpix = fread(fid,1,'int16')';
dime.slice_start = fread(fid,1,'int16')';
dime.pixdim = fread(fid,8,'float32')';
dime.vox_offset = fread(fid,1,'float32')';
dime.scl_slope = fread(fid,1,'float32')';
dime.scl_inter = fread(fid,1,'float32')';
dime.slice_end = fread(fid,1,'int16')';
dime.slice_code = fread(fid,1,'uchar')';
dime.xyzt_units = fread(fid,1,'uchar')';
dime.cal_max = fread(fid,1,'float32')';
dime.cal_min = fread(fid,1,'float32')';
dime.slice_duration = fread(fid,1,'float32')';
dime.toffset = fread(fid,1,'float32')';
dime.glmax = fread(fid,1,'int32')';
dime.glmin = fread(fid,1,'int32')';
return % image_dimension
%---------------------------------------------------------------------
function [ hist ] = data_history(fid)
% Original header structures
% struct data_history
% { /* off + size */
% char descrip[80]; /* 0 + 80 */
% char aux_file[24]; /* 80 + 24 */
% short int qform_code; /* 104 + 2 */
% short int sform_code; /* 106 + 2 */
% float quatern_b; /* 108 + 4 */
% float quatern_c; /* 112 + 4 */
% float quatern_d; /* 116 + 4 */
% float qoffset_x; /* 120 + 4 */
% float qoffset_y; /* 124 + 4 */
% float qoffset_z; /* 128 + 4 */
% float srow_x[4]; /* 132 + 16 */
% float srow_y[4]; /* 148 + 16 */
% float srow_z[4]; /* 164 + 16 */
% char intent_name[16]; /* 180 + 16 */
% char magic[4]; % int smin; /* 196 + 4 */
% }; /* total=200 bytes */
v6 = version;
if str2num(v6(1))<6
directchar = '*char';
else
directchar = 'uchar=>char';
end
hist.descrip = deblank(fread(fid,80,directchar)');
hist.aux_file = deblank(fread(fid,24,directchar)');
hist.qform_code = fread(fid,1,'int16')';
hist.sform_code = fread(fid,1,'int16')';
hist.quatern_b = fread(fid,1,'float32')';
hist.quatern_c = fread(fid,1,'float32')';
hist.quatern_d = fread(fid,1,'float32')';
hist.qoffset_x = fread(fid,1,'float32')';
hist.qoffset_y = fread(fid,1,'float32')';
hist.qoffset_z = fread(fid,1,'float32')';
hist.srow_x = fread(fid,4,'float32')';
hist.srow_y = fread(fid,4,'float32')';
hist.srow_z = fread(fid,4,'float32')';
hist.intent_name = deblank(fread(fid,16,directchar)');
hist.magic = deblank(fread(fid,4,directchar)');
return % data_history
|
github
|
adhusch/PaCER-master
|
save_nii_ext.m
|
.m
|
PaCER-master/external/NIfTI_20140122/save_nii_ext.m
| 977 |
utf_8
|
b60a98ab7537a883dc3ffef3175f19ae
|
% Save NIFTI header extension.
%
% Usage: save_nii_ext(ext, fid)
%
% ext - struct with NIFTI header extension fields.
%
% NIFTI data format can be found on: http://nifti.nimh.nih.gov
%
% - Jimmy Shen ([email protected])
%
function save_nii_ext(ext, fid)
if ~exist('ext','var') | ~exist('fid','var')
error('Usage: save_nii_ext(ext, fid)');
end
if ~isfield(ext,'extension') | ~isfield(ext,'section') | ~isfield(ext,'num_ext')
error('Wrong header extension');
end
write_ext(ext, fid);
return; % save_nii_ext
%---------------------------------------------------------------------
function write_ext(ext, fid)
fwrite(fid, ext.extension, 'uchar');
for i=1:ext.num_ext
fwrite(fid, ext.section(i).esize, 'int32');
fwrite(fid, ext.section(i).ecode, 'int32');
fwrite(fid, ext.section(i).edata, 'uchar');
end
return; % write_ext
|
github
|
adhusch/PaCER-master
|
view_nii_menu.m
|
.m
|
PaCER-master/external/NIfTI_20140122/view_nii_menu.m
| 14,415 |
utf_8
|
32dd591fa1070721f0255f47f6e02510
|
% Imbed Zoom, Interp, and Info menu to view_nii window.
%
% Usage: view_nii_menu(fig);
%
% - Jimmy Shen ([email protected])
%
%--------------------------------------------------------------------
function menu_hdl = view_nii_menu(fig, varargin)
if isnumeric(fig)
menu_hdl = init(fig);
return;
end
menu_hdl = [];
switch fig
case 'interp'
if nargin > 1
fig = varargin{1};
else
fig = gcbf;
end
nii_menu = getappdata(fig, 'nii_menu');
interp_on_state = get(nii_menu.Minterp,'Userdata');
if (interp_on_state == 1)
opt.useinterp = 1;
view_nii(fig,opt);
set(nii_menu.Minterp,'Userdata',0,'Label','Interp off');
reset_zoom(fig);
else
opt.useinterp = 0;
view_nii(fig,opt);
set(nii_menu.Minterp,'Userdata',1,'Label','Interp on');
reset_zoom(fig);
end
case 'reset_zoom'
if nargin > 1
fig = varargin{1};
else
fig = gcbf;
end
reset_zoom(fig);
case 'orient'
orient;
case 'editvox'
editvox;
case 'img_info'
img_info;
case 'img_hist'
img_hist;
case 'save_disp'
save_disp;
end
return % view_nii_menu
%--------------------------------------------------------------------
function menu_hdl = init(fig)
% search for edit, view menu
%
nii_menu.Mfile = [];
nii_menu.Medit = [];
nii_menu.Mview = [];
menuitems = findobj(fig, 'type', 'uimenu');
for i=1:length(menuitems)
filelabel = get(menuitems(i),'label');
if strcmpi(strrep(filelabel, '&', ''), 'file')
nii_menu.Mfile = menuitems(i);
end
editlabel = get(menuitems(i),'label');
if strcmpi(strrep(editlabel, '&', ''), 'edit')
nii_menu.Medit = menuitems(i);
end
viewlabel = get(menuitems(i),'label');
if strcmpi(strrep(viewlabel, '&', ''), 'view')
nii_menu.Mview = menuitems(i);
end
end
set(fig, 'menubar', 'none');
if isempty(nii_menu.Mfile)
nii_menu.Mfile = uimenu('Parent',fig, ...
'Label','File');
nii_menu.Mfile_save = uimenu('Parent',nii_menu.Mfile, ...
'Label','Save displayed image as ...', ...
'Callback','view_nii_menu(''save_disp'');');
else
nii_menu.Mfile_save = uimenu('Parent',nii_menu.Mfile, ...
'Label','Save displayed image as ...', ...
'separator','on', ...
'Callback','view_nii_menu(''save_disp'');');
end
if isempty(nii_menu.Medit)
nii_menu.Medit = uimenu('Parent',fig, ...
'Label','Edit');
nii_menu.Medit_orient = uimenu('Parent',nii_menu.Medit, ...
'Label','Convert to RAS orientation', ...
'Callback','view_nii_menu(''orient'');');
nii_menu.Medit_editvox = uimenu('Parent',nii_menu.Medit, ...
'Label','Edit voxel value at crosshair', ...
'Callback','view_nii_menu(''editvox'');');
else
nii_menu.Medit_orient = uimenu('Parent',nii_menu.Medit, ...
'Label','Convert to RAS orientation', ...
'separator','on', ...
'Callback','view_nii_menu(''orient'');');
nii_menu.Medit_editvox = uimenu('Parent',nii_menu.Medit, ...
'Label','Edit voxel value at crosshair', ...
'Callback','view_nii_menu(''editvox'');');
end
if isempty(nii_menu.Mview)
nii_menu.Mview = uimenu('Parent',fig, ...
'Label','View');
nii_menu.Mview_info = uimenu('Parent',nii_menu.Mview, ...
'Label','Image Information', ...
'Callback','view_nii_menu(''img_info'');');
nii_menu.Mview_info = uimenu('Parent',nii_menu.Mview, ...
'Label','Volume Histogram', ...
'Callback','view_nii_menu(''img_hist'');');
else
nii_menu.Mview_info = uimenu('Parent',nii_menu.Mview, ...
'Label','Image Information', ...
'separator','on', ...
'Callback','view_nii_menu(''img_info'');');
nii_menu.Mview_info = uimenu('Parent',nii_menu.Mview, ...
'Label','Volume Histogram', ...
'Callback','view_nii_menu(''img_hist'');');
end
nii_menu.Mzoom = rri_zoom_menu(fig);
nii_menu.Minterp = uimenu('Parent',fig, ...
'Label','Interp on', ...
'Userdata', 1, ...
'Callback','view_nii_menu(''interp'');');
setappdata(fig,'nii_menu',nii_menu);
menu_hdl = nii_menu.Minterp;
return % init
%----------------------------------------------------------------
function reset_zoom(fig)
old_handle_vis = get(fig, 'HandleVisibility');
set(fig, 'HandleVisibility', 'on');
nii_view = getappdata(fig, 'nii_view');
nii_menu = getappdata(fig, 'nii_menu');
set(nii_menu.Mzoom,'Userdata',1,'Label','Zoom on');
set(fig,'pointer','arrow');
zoom off;
axes(nii_view.handles.axial_axes);
setappdata(get(gca,'zlabel'), 'ZOOMAxesData', ...
[get(gca, 'xlim') get(gca, 'ylim')])
% zoom reset;
% zoom getlimits;
zoom out;
axes(nii_view.handles.coronal_axes);
setappdata(get(gca,'zlabel'), 'ZOOMAxesData', ...
[get(gca, 'xlim') get(gca, 'ylim')])
% zoom reset;
% zoom getlimits;
zoom out;
axes(nii_view.handles.sagittal_axes);
setappdata(get(gca,'zlabel'), 'ZOOMAxesData', ...
[get(gca, 'xlim') get(gca, 'ylim')])
% zoom reset;
% zoom getlimits;
zoom out;
set(fig, 'HandleVisibility', old_handle_vis);
return; % reset_zoom
%----------------------------------------------------------------
function img_info
nii_view = getappdata(gcbf, 'nii_view');
hdr = nii_view.nii.hdr;
max_value = num2str(double(max(nii_view.nii.img(:))));
min_value = num2str(double(min(nii_view.nii.img(:))));
dim = sprintf('%d %d %d', double(hdr.dime.dim(2:4)));
vox = sprintf('%.3f %.3f %.3f', double(hdr.dime.pixdim(2:4)));
if double(hdr.dime.datatype) == 1
type = '1-bit binary';
elseif double(hdr.dime.datatype) == 2
type = '8-bit unsigned integer';
elseif double(hdr.dime.datatype) == 4
type = '16-bit signed integer';
elseif double(hdr.dime.datatype) == 8
type = '32-bit signed integer';
elseif double(hdr.dime.datatype) == 16
type = '32-bit single float';
elseif double(hdr.dime.datatype) == 64
type = '64-bit double precision';
elseif double(hdr.dime.datatype) == 128
type = '24-bit RGB true color';
elseif double(hdr.dime.datatype) == 256
type = '8-bit signed integer';
elseif double(hdr.dime.datatype) == 511
type = '96-bit RGB true color';
elseif double(hdr.dime.datatype) == 512
type = '16-bit unsigned integer';
elseif double(hdr.dime.datatype) == 768
type = '32-bit unsigned integer';
elseif double(hdr.dime.datatype) == 1024
type = '64-bit signed integer';
elseif double(hdr.dime.datatype) == 1280
type = '64-bit unsigned integer';
end
msg = {};
msg = [msg {''}];
msg = [msg {['Dimension: [', dim, ']']}];
msg = [msg {''}];
msg = [msg {['Voxel Size: [', vox, ']']}];
msg = [msg {''}];
msg = [msg {['Data Type: [', type, ']']}];
msg = [msg {''}];
msg = [msg {['Max Value: [', max_value, ']']}];
msg = [msg {''}];
msg = [msg {['Min Value: [', min_value, ']']}];
msg = [msg {''}];
if isfield(nii_view.nii, 'fileprefix')
if isfield(nii_view.nii, 'filetype') & nii_view.nii.filetype == 2
msg = [msg {['File Name: [', nii_view.nii.fileprefix, '.nii]']}];
msg = [msg {''}];
elseif isfield(nii_view.nii, 'filetype')
msg = [msg {['File Name: [', nii_view.nii.fileprefix, '.img]']}];
msg = [msg {''}];
else
msg = [msg {['File Prefix: [', nii_view.nii.fileprefix, ']']}];
msg = [msg {''}];
end
end
h = msgbox(msg, 'Image Information', 'modal');
set(h,'color',[1 1 1]);
return; % img_info
%----------------------------------------------------------------
function orient
fig = gcbf;
nii_view = getappdata(fig, 'nii_view');
nii = nii_view.nii;
if ~isempty(nii_view.bgimg)
msg = 'You can not modify an overlay image';
h = msgbox(msg, 'Error', 'modal');
return;
end
old_pointer = get(fig,'Pointer');
set(fig,'Pointer','watch');
[nii orient] = rri_orient(nii);
if isequal(orient, [1 2 3]) % do nothing
set(fig,'Pointer',old_pointer);
return;
end
oldopt = view_nii(fig);
opt.command = 'updatenii';
opt.usecolorbar = oldopt.usecolorbar;
opt.usepanel = oldopt.usepanel;
opt.usecrosshair = oldopt.usecrosshair;
opt.usestretch = oldopt.usestretch;
opt.useimagesc = oldopt.useimagesc;
opt.useinterp = oldopt.useinterp;
opt.setarea = oldopt.area;
opt.setunit = oldopt.unit;
opt.setviewpoint = oldopt.viewpoint;
opt.setscanid = oldopt.scanid;
opt.setcbarminmax = oldopt.cbarminmax;
opt.setcolorindex = oldopt.colorindex;
opt.setcolormap = oldopt.colormap;
opt.setcolorlevel = oldopt.colorlevel;
if isfield(oldopt,'highcolor')
opt.sethighcolor = oldopt.highcolor;
end
view_nii(fig, nii, opt);
set(fig,'Pointer',old_pointer);
reset_zoom(fig);
return; % orient
%----------------------------------------------------------------
function editvox
fig = gcbf;
nii_view = getappdata(fig, 'nii_view');
if ~isempty(nii_view.bgimg)
msg = 'You can not modify an overlay image';
h = msgbox(msg, 'Error', 'modal');
return;
end
nii = nii_view.nii;
oldopt = view_nii(fig);
sag = nii_view.imgXYZ.vox(1);
cor = nii_view.imgXYZ.vox(2);
axi = nii_view.imgXYZ.vox(3);
if nii_view.nii.hdr.dime.datatype == 128
imgvalue = [double(nii.img(sag,cor,axi,1,nii_view.scanid)) double(nii.img(sag,cor,axi,2,nii_view.scanid)) double(nii.img(sag,cor,axi,3,nii_view.scanid))];
init_val = sprintf('%7.4g %7.4g %7.4g',imgvalue);
elseif nii_view.nii.hdr.dime.datatype == 511
R = double(nii.img(sag,cor,axi,1,nii_view.scanid)) * (nii_view.nii.hdr.dime.glmax - ...
nii_view.nii.hdr.dime.glmin) + nii_view.nii.hdr.dime.glmin;
G = double(nii.img(sag,cor,axi,2,nii_view.scanid)) * (nii_view.nii.hdr.dime.glmax - ...
nii_view.nii.hdr.dime.glmin) + nii_view.nii.hdr.dime.glmin;
B = double(nii.img(sag,cor,axi,3,nii_view.scanid)) * (nii_view.nii.hdr.dime.glmax - ...
nii_view.nii.hdr.dime.glmin) + nii_view.nii.hdr.dime.glmin;
imgvalue = [R G B];
init_val = sprintf('%7.4g %7.4g %7.4g',imgvalue);
else
imgvalue = double(nii.img(sag,cor,axi,nii_view.scanid));
init_val = sprintf('%.6g',imgvalue);
end
old_pointer = get(fig,'Pointer');
set(fig,'Pointer','watch');
repeat = 1;
while repeat
if nii_view.nii.hdr.dime.datatype == 128 | nii_view.nii.hdr.dime.datatype == 511
init_val = inputdlg({'Replace the current voxel values with 3 new numbers:'}, ...
'Edit voxel value at crosshair', 1, {num2str(init_val)});
else
init_val = inputdlg({'Replace the current voxel value with 1 new number:'}, ...
'Edit voxel value at crosshair', 1, {num2str(init_val)});
end
if isempty(init_val)
set(fig,'Pointer',old_pointer);
return
end
imgvalue = str2num(init_val{1});
if ( (nii_view.nii.hdr.dime.datatype == 128 | nii_view.nii.hdr.dime.datatype == 511) ...
& length(imgvalue) ~= 3 ) | ...
( (nii_view.nii.hdr.dime.datatype ~= 128 & nii_view.nii.hdr.dime.datatype ~= 511) ...
& length(imgvalue) ~= 1 )
% do nothing
else
repeat = 0;
end
end
if nii_view.nii.hdr.dime.datatype == 128
nii.img(sag,cor,axi,1,nii_view.scanid) = imgvalue(1);
nii.img(sag,cor,axi,2,nii_view.scanid) = imgvalue(2);
nii.img(sag,cor,axi,3,nii_view.scanid) = imgvalue(3);
elseif nii_view.nii.hdr.dime.datatype == 511
nii.img(sag,cor,axi,1,nii_view.scanid) = (imgvalue(1) - nii_view.nii.hdr.dime.glmin) ...
/ (nii_view.nii.hdr.dime.glmax - nii_view.nii.hdr.dime.glmin);
nii.img(sag,cor,axi,2,nii_view.scanid) = (imgvalue(2) - nii_view.nii.hdr.dime.glmin) ...
/ (nii_view.nii.hdr.dime.glmax - nii_view.nii.hdr.dime.glmin);
nii.img(sag,cor,axi,3,nii_view.scanid) = (imgvalue(3) - nii_view.nii.hdr.dime.glmin) ...
/ (nii_view.nii.hdr.dime.glmax - nii_view.nii.hdr.dime.glmin);
else
nii.img(sag,cor,axi,nii_view.scanid) = imgvalue;
end
opt.command = 'updatenii';
opt.usecolorbar = oldopt.usecolorbar;
opt.usepanel = oldopt.usepanel;
opt.usecrosshair = oldopt.usecrosshair;
opt.usestretch = oldopt.usestretch;
opt.useimagesc = oldopt.useimagesc;
opt.useinterp = oldopt.useinterp;
opt.setarea = oldopt.area;
opt.setunit = oldopt.unit;
opt.setviewpoint = oldopt.viewpoint;
opt.setscanid = oldopt.scanid;
opt.setcbarminmax = oldopt.cbarminmax;
opt.setcolorindex = oldopt.colorindex;
opt.setcolormap = oldopt.colormap;
opt.setcolorlevel = oldopt.colorlevel;
if isfield(oldopt,'highcolor')
opt.sethighcolor = oldopt.highcolor;
end
view_nii(fig, nii, opt);
set(fig,'Pointer',old_pointer);
reset_zoom(fig);
return; % editvox
%----------------------------------------------------------------
function save_disp
[filename pathname] = uiputfile('*.*', 'Save displayed image as (*.nii or *.img)');
if isequal(filename,0) | isequal(pathname,0)
return;
else
out_imgfile = fullfile(pathname, filename); % original image file
end
old_pointer = get(gcbf,'Pointer');
set(gcbf,'Pointer','watch');
nii_view = getappdata(gcbf, 'nii_view');
nii = nii_view.nii;
try
save_nii(nii, out_imgfile);
catch
msg = 'File can not be saved.';
msgbox(msg, 'File write error', 'modal');
end
set(gcbf,'Pointer',old_pointer);
return; % save_disp
%----------------------------------------------------------------
function img_hist
nii_view = getappdata(gcbf, 'nii_view');
N = hist(double(nii_view.nii.img(:)),256);
x = linspace(double(min(nii_view.nii.img(:))), double(max(nii_view.nii.img(:))), 256);
figure;bar(x,N);
set(gcf, 'number', 'off', 'name', 'Volume Histogram');
set(gcf, 'windowstyle', 'modal'); % no zoom ...
xspan = max(x) - min(x) + 1;
yspan = max(N) + 1;
set(gca, 'xlim', [min(x)-xspan/20, max(x)+xspan/20]);
set(gca, 'ylim', [-yspan/20, max(N)+yspan/20]);
return; % img_hist
|
github
|
adhusch/PaCER-master
|
save_untouch_header_only.m
|
.m
|
PaCER-master/external/NIfTI_20140122/save_untouch_header_only.m
| 2,132 |
utf_8
|
5f0515ef6a35f171bc8371d0f3fd365d
|
% This function is only used to save Analyze or NIfTI header that is
% ended with .hdr and loaded by load_untouch_header_only.m. If you
% have NIfTI file that is ended with .nii and you want to change its
% header only, you can use load_untouch_nii / save_untouch_nii pair.
%
% Usage: save_untouch_header_only(hdr, new_header_file_name)
%
% hdr - struct with NIfTI / Analyze header fields, which is obtained from:
% hdr = load_untouch_header_only(original_header_file_name)
%
% new_header_file_name - NIfTI / Analyze header name ended with .hdr.
% You can either copy original.img(.gz) to new.img(.gz) manually,
% or simply input original.hdr(.gz) in save_untouch_header_only.m
% to overwrite the original header.
%
% - Jimmy Shen ([email protected])
%
function save_untouch_header_only(hdr, filename)
if ~exist('hdr','var') | isempty(hdr) | ~exist('filename','var') | isempty(filename)
error('Usage: save_untouch_header_only(hdr, filename)');
end
v = version;
% Check file extension. If .gz, unpack it into temp folder
%
if length(filename) > 2 & strcmp(filename(end-2:end), '.gz')
if ~strcmp(filename(end-6:end), '.hdr.gz')
error('Please check filename.');
end
if str2num(v(1:3)) < 7.1 | ~usejava('jvm')
error('Please use MATLAB 7.1 (with java) and above, or run gunzip outside MATLAB.');
else
gzFile = 1;
filename = filename(1:end-3);
end
end
[p,f] = fileparts(filename);
fileprefix = fullfile(p, f);
write_hdr(hdr, fileprefix);
% gzip output file if requested
%
if exist('gzFile', 'var')
gzip([fileprefix, '.hdr']);
delete([fileprefix, '.hdr']);
end;
return % save_untouch_header_only
%-----------------------------------------------------------------------------------
function write_hdr(hdr, fileprefix)
fid = fopen(sprintf('%s.hdr',fileprefix),'w');
if isfield(hdr.hist,'magic')
save_untouch_nii_hdr(hdr, fid);
else
save_untouch0_nii_hdr(hdr, fid);
end
fclose(fid);
return % write_hdr
|
github
|
adhusch/PaCER-master
|
pad_nii.m
|
.m
|
PaCER-master/external/NIfTI_20140122/pad_nii.m
| 3,712 |
utf_8
|
0b9de8feba6840e2d8ea1ab1752747c7
|
% PAD_NII: Pad the NIfTI volume from any of the 6 sides
%
% Usage: nii = pad_nii(nii, [option])
%
% Inputs:
%
% nii - NIfTI volume.
%
% option - struct instructing how many voxel to be padded from which side.
%
% option.pad_from_L = ( number of voxel )
% option.pad_from_R = ( number of voxel )
% option.pad_from_P = ( number of voxel )
% option.pad_from_A = ( number of voxel )
% option.pad_from_I = ( number of voxel )
% option.pad_from_S = ( number of voxel )
% option.bg = [0]
%
% Options description in detail:
% ==============================
%
% pad_from_L: Number of voxels from Left side will be padded.
%
% pad_from_R: Number of voxels from Right side will be padded.
%
% pad_from_P: Number of voxels from Posterior side will be padded.
%
% pad_from_A: Number of voxels from Anterior side will be padded.
%
% pad_from_I: Number of voxels from Inferior side will be padded.
%
% pad_from_S: Number of voxels from Superior side will be padded.
%
% bg: Background intensity, which is 0 by default.
%
% NIfTI data format can be found on: http://nifti.nimh.nih.gov
%
% - Jimmy Shen ([email protected])
%
function nii = pad_nii(nii, opt)
dims = abs(nii.hdr.dime.dim(2:4));
origin = abs(nii.hdr.hist.originator(1:3));
if isempty(origin) | all(origin == 0) % according to SPM
origin = round((dims+1)/2);
end
pad_from_L = 0;
pad_from_R = 0;
pad_from_P = 0;
pad_from_A = 0;
pad_from_I = 0;
pad_from_S = 0;
bg = 0;
if nargin > 1 & ~isempty(opt)
if ~isstruct(opt)
error('option argument should be a struct');
end
if isfield(opt,'pad_from_L')
pad_from_L = round(opt.pad_from_L);
if pad_from_L >= origin(1) | pad_from_L < 0
error('pad_from_L cannot be negative');
end
end
if isfield(opt,'pad_from_P')
pad_from_P = round(opt.pad_from_P);
if pad_from_P >= origin(2) | pad_from_P < 0
error('pad_from_P cannot be negative');
end
end
if isfield(opt,'pad_from_I')
pad_from_I = round(opt.pad_from_I);
if pad_from_I >= origin(3) | pad_from_I < 0
error('pad_from_I cannot be negative');
end
end
if isfield(opt,'pad_from_R')
pad_from_R = round(opt.pad_from_R);
if pad_from_R > dims(1)-origin(1) | pad_from_R < 0
error('pad_from_R cannot be negative');
end
end
if isfield(opt,'pad_from_A')
pad_from_A = round(opt.pad_from_A);
if pad_from_A > dims(2)-origin(2) | pad_from_A < 0
error('pad_from_A cannot be negative');
end
end
if isfield(opt,'pad_from_S')
pad_from_S = round(opt.pad_from_S);
if pad_from_S > dims(3)-origin(3) | pad_from_S < 0
error('pad_from_S cannot be negative');
end
end
if isfield(opt,'bg')
bg = opt.bg;
end
end
blk = bg * ones( pad_from_L, dims(2), dims(3) );
nii.img = cat(1, blk, nii.img);
blk = bg * ones( pad_from_R, dims(2), dims(3) );
nii.img = cat(1, nii.img, blk);
dims = size(nii.img);
blk = bg * ones( dims(1), pad_from_P, dims(3) );
nii.img = cat(2, blk, nii.img);
blk = bg * ones( dims(1), pad_from_A, dims(3) );
nii.img = cat(2, nii.img, blk);
dims = size(nii.img);
blk = bg * ones( dims(1), dims(2), pad_from_I );
nii.img = cat(3, blk, nii.img);
blk = bg * ones( dims(1), dims(2), pad_from_S );
nii.img = cat(3, nii.img, blk);
nii = make_nii(nii.img, nii.hdr.dime.pixdim(2:4), ...
[origin(1)+pad_from_L origin(2)+pad_from_P origin(3)+pad_from_I], ...
nii.hdr.dime.datatype, nii.hdr.hist.descrip);
return;
|
github
|
adhusch/PaCER-master
|
load_nii_hdr.m
|
.m
|
PaCER-master/external/NIfTI_20140122/load_nii_hdr.m
| 10,031 |
utf_8
|
e95839e314863f7ee463cc2626dd447c
|
% internal function
% - Jimmy Shen ([email protected])
function [hdr, filetype, fileprefix, machine] = load_nii_hdr(fileprefix)
if ~exist('fileprefix','var'),
error('Usage: [hdr, filetype, fileprefix, machine] = load_nii_hdr(filename)');
end
machine = 'ieee-le';
new_ext = 0;
if findstr('.nii',fileprefix) & strcmp(fileprefix(end-3:end), '.nii')
new_ext = 1;
fileprefix(end-3:end)='';
end
if findstr('.hdr',fileprefix) & strcmp(fileprefix(end-3:end), '.hdr')
fileprefix(end-3:end)='';
end
if findstr('.img',fileprefix) & strcmp(fileprefix(end-3:end), '.img')
fileprefix(end-3:end)='';
end
if new_ext
fn = sprintf('%s.nii',fileprefix);
if ~exist(fn)
msg = sprintf('Cannot find file "%s.nii".', fileprefix);
error(msg);
end
else
fn = sprintf('%s.hdr',fileprefix);
if ~exist(fn)
msg = sprintf('Cannot find file "%s.hdr".', fileprefix);
error(msg);
end
end
fid = fopen(fn,'r',machine);
if fid < 0,
msg = sprintf('Cannot open file %s.',fn);
error(msg);
else
fseek(fid,0,'bof');
if fread(fid,1,'int32') == 348
hdr = read_header(fid);
fclose(fid);
else
fclose(fid);
% first try reading the opposite endian to 'machine'
%
switch machine,
case 'ieee-le', machine = 'ieee-be';
case 'ieee-be', machine = 'ieee-le';
end
fid = fopen(fn,'r',machine);
if fid < 0,
msg = sprintf('Cannot open file %s.',fn);
error(msg);
else
fseek(fid,0,'bof');
if fread(fid,1,'int32') ~= 348
% Now throw an error
%
msg = sprintf('File "%s" is corrupted.',fn);
error(msg);
end
hdr = read_header(fid);
fclose(fid);
end
end
end
if strcmp(hdr.hist.magic, 'n+1')
filetype = 2;
elseif strcmp(hdr.hist.magic, 'ni1')
filetype = 1;
else
filetype = 0;
end
return % load_nii_hdr
%---------------------------------------------------------------------
function [ dsr ] = read_header(fid)
% Original header structures
% struct dsr
% {
% struct header_key hk; /* 0 + 40 */
% struct image_dimension dime; /* 40 + 108 */
% struct data_history hist; /* 148 + 200 */
% }; /* total= 348 bytes*/
dsr.hk = header_key(fid);
dsr.dime = image_dimension(fid);
dsr.hist = data_history(fid);
% For Analyze data format
%
if ~strcmp(dsr.hist.magic, 'n+1') & ~strcmp(dsr.hist.magic, 'ni1')
dsr.hist.qform_code = 0;
dsr.hist.sform_code = 0;
end
return % read_header
%---------------------------------------------------------------------
function [ hk ] = header_key(fid)
fseek(fid,0,'bof');
% Original header structures
% struct header_key /* header key */
% { /* off + size */
% int sizeof_hdr /* 0 + 4 */
% char data_type[10]; /* 4 + 10 */
% char db_name[18]; /* 14 + 18 */
% int extents; /* 32 + 4 */
% short int session_error; /* 36 + 2 */
% char regular; /* 38 + 1 */
% char dim_info; % char hkey_un0; /* 39 + 1 */
% }; /* total=40 bytes */
%
% int sizeof_header Should be 348.
% char regular Must be 'r' to indicate that all images and
% volumes are the same size.
v6 = version;
if str2num(v6(1))<6
directchar = '*char';
else
directchar = 'uchar=>char';
end
hk.sizeof_hdr = fread(fid, 1,'int32')'; % should be 348!
hk.data_type = deblank(fread(fid,10,directchar)');
hk.db_name = deblank(fread(fid,18,directchar)');
hk.extents = fread(fid, 1,'int32')';
hk.session_error = fread(fid, 1,'int16')';
hk.regular = fread(fid, 1,directchar)';
hk.dim_info = fread(fid, 1,'uchar')';
return % header_key
%---------------------------------------------------------------------
function [ dime ] = image_dimension(fid)
% Original header structures
% struct image_dimension
% { /* off + size */
% short int dim[8]; /* 0 + 16 */
% /*
% dim[0] Number of dimensions in database; usually 4.
% dim[1] Image X dimension; number of *pixels* in an image row.
% dim[2] Image Y dimension; number of *pixel rows* in slice.
% dim[3] Volume Z dimension; number of *slices* in a volume.
% dim[4] Time points; number of volumes in database
% */
% float intent_p1; % char vox_units[4]; /* 16 + 4 */
% float intent_p2; % char cal_units[8]; /* 20 + 4 */
% float intent_p3; % char cal_units[8]; /* 24 + 4 */
% short int intent_code; % short int unused1; /* 28 + 2 */
% short int datatype; /* 30 + 2 */
% short int bitpix; /* 32 + 2 */
% short int slice_start; % short int dim_un0; /* 34 + 2 */
% float pixdim[8]; /* 36 + 32 */
% /*
% pixdim[] specifies the voxel dimensions:
% pixdim[1] - voxel width, mm
% pixdim[2] - voxel height, mm
% pixdim[3] - slice thickness, mm
% pixdim[4] - volume timing, in msec
% ..etc
% */
% float vox_offset; /* 68 + 4 */
% float scl_slope; % float roi_scale; /* 72 + 4 */
% float scl_inter; % float funused1; /* 76 + 4 */
% short slice_end; % float funused2; /* 80 + 2 */
% char slice_code; % float funused2; /* 82 + 1 */
% char xyzt_units; % float funused2; /* 83 + 1 */
% float cal_max; /* 84 + 4 */
% float cal_min; /* 88 + 4 */
% float slice_duration; % int compressed; /* 92 + 4 */
% float toffset; % int verified; /* 96 + 4 */
% int glmax; /* 100 + 4 */
% int glmin; /* 104 + 4 */
% }; /* total=108 bytes */
dime.dim = fread(fid,8,'int16')';
dime.intent_p1 = fread(fid,1,'float32')';
dime.intent_p2 = fread(fid,1,'float32')';
dime.intent_p3 = fread(fid,1,'float32')';
dime.intent_code = fread(fid,1,'int16')';
dime.datatype = fread(fid,1,'int16')';
dime.bitpix = fread(fid,1,'int16')';
dime.slice_start = fread(fid,1,'int16')';
dime.pixdim = fread(fid,8,'float32')';
dime.vox_offset = fread(fid,1,'float32')';
dime.scl_slope = fread(fid,1,'float32')';
dime.scl_inter = fread(fid,1,'float32')';
dime.slice_end = fread(fid,1,'int16')';
dime.slice_code = fread(fid,1,'uchar')';
dime.xyzt_units = fread(fid,1,'uchar')';
dime.cal_max = fread(fid,1,'float32')';
dime.cal_min = fread(fid,1,'float32')';
dime.slice_duration = fread(fid,1,'float32')';
dime.toffset = fread(fid,1,'float32')';
dime.glmax = fread(fid,1,'int32')';
dime.glmin = fread(fid,1,'int32')';
return % image_dimension
%---------------------------------------------------------------------
function [ hist ] = data_history(fid)
% Original header structures
% struct data_history
% { /* off + size */
% char descrip[80]; /* 0 + 80 */
% char aux_file[24]; /* 80 + 24 */
% short int qform_code; /* 104 + 2 */
% short int sform_code; /* 106 + 2 */
% float quatern_b; /* 108 + 4 */
% float quatern_c; /* 112 + 4 */
% float quatern_d; /* 116 + 4 */
% float qoffset_x; /* 120 + 4 */
% float qoffset_y; /* 124 + 4 */
% float qoffset_z; /* 128 + 4 */
% float srow_x[4]; /* 132 + 16 */
% float srow_y[4]; /* 148 + 16 */
% float srow_z[4]; /* 164 + 16 */
% char intent_name[16]; /* 180 + 16 */
% char magic[4]; % int smin; /* 196 + 4 */
% }; /* total=200 bytes */
v6 = version;
if str2num(v6(1))<6
directchar = '*char';
else
directchar = 'uchar=>char';
end
hist.descrip = deblank(fread(fid,80,directchar)');
hist.aux_file = deblank(fread(fid,24,directchar)');
hist.qform_code = fread(fid,1,'int16')';
hist.sform_code = fread(fid,1,'int16')';
hist.quatern_b = fread(fid,1,'float32')';
hist.quatern_c = fread(fid,1,'float32')';
hist.quatern_d = fread(fid,1,'float32')';
hist.qoffset_x = fread(fid,1,'float32')';
hist.qoffset_y = fread(fid,1,'float32')';
hist.qoffset_z = fread(fid,1,'float32')';
hist.srow_x = fread(fid,4,'float32')';
hist.srow_y = fread(fid,4,'float32')';
hist.srow_z = fread(fid,4,'float32')';
hist.intent_name = deblank(fread(fid,16,directchar)');
hist.magic = deblank(fread(fid,4,directchar)');
fseek(fid,253,'bof');
hist.originator = fread(fid, 5,'int16')';
return % data_history
|
github
|
adhusch/PaCER-master
|
save_untouch_slice.m
|
.m
|
PaCER-master/external/NIfTI_20140122/save_untouch_slice.m
| 19,683 |
utf_8
|
364468e5dbd3790c1aadf9a768534f1f
|
% Save back to the original image with a portion of slices that was
% loaded by "load_untouch_nii". You can process those slices matrix
% in any way, as long as their dimension is not altered.
%
% Usage: save_untouch_slice(slice, filename, ...
% slice_idx, [img_idx], [dim5_idx], [dim6_idx], [dim7_idx])
%
% slice - a portion of slices that was loaded by "load_untouch_nii".
% This should be a numeric matrix (i.e. only the .img field in the
% loaded structure)
%
% filename - NIfTI or ANALYZE file name.
%
% slice_idx (depending on slice size) - a numerical array of image
% slice indices, which should be the same as that you entered
% in "load_untouch_nii" command.
%
% img_idx (depending on slice size) - a numerical array of image
% volume indices, which should be the same as that you entered
% in "load_untouch_nii" command.
%
% dim5_idx (depending on slice size) - a numerical array of 5th
% dimension indices, which should be the same as that you entered
% in "load_untouch_nii" command.
%
% dim6_idx (depending on slice size) - a numerical array of 6th
% dimension indices, which should be the same as that you entered
% in "load_untouch_nii" command.
%
% dim7_idx (depending on slice size) - a numerical array of 7th
% dimension indices, which should be the same as that you entered
% in "load_untouch_nii" command.
%
% Example:
% nii = load_nii('avg152T1_LR_nifti.nii');
% save_nii(nii, 'test.nii');
% view_nii(nii);
% nii = load_untouch_nii('test.nii','','','','','',[40 51:53]);
% nii.img = ones(91,109,4)*122;
% save_untouch_slice(nii.img, 'test.nii', [40 51:52]);
% nii = load_nii('test.nii');
% view_nii(nii);
%
% - Jimmy Shen ([email protected])
%
function save_untouch_slice(slice, filename, slice_idx, img_idx, dim5_idx, dim6_idx, dim7_idx)
if ~exist('slice','var') | ~isnumeric(slice)
msg = [char(10) '"slice" argument should be a portion of slices that was loaded' char(10)];
msg = [msg 'by "load_untouch_nii.m". This should be a numeric matrix (i.e.' char(10)];
msg = [msg 'only the .img field in the loaded structure).'];
error(msg);
end
if ~exist('filename','var') | ~exist(filename,'file')
error('In order to save back, original NIfTI or ANALYZE file must exist.');
end
if ~exist('slice_idx','var') | isempty(slice_idx) | ~isequal(size(slice,3),length(slice_idx))
msg = [char(10) '"slice_idx" is a numerical array of image slice indices, which' char(10)];
msg = [msg 'should be the same as that you entered in "load_untouch_nii.m"' char(10)];
msg = [msg 'command.'];
error(msg);
end
if ~exist('img_idx','var') | isempty(img_idx)
img_idx = [];
if ~isequal(size(slice,4),1)
msg = [char(10) '"img_idx" is a numerical array of image volume indices, which' char(10)];
msg = [msg 'should be the same as that you entered in "load_untouch_nii.m"' char(10)];
msg = [msg 'command.'];
error(msg);
end
elseif ~isequal(size(slice,4),length(img_idx))
msg = [char(10) '"img_idx" is a numerical array of image volume indices, which' char(10)];
msg = [msg 'should be the same as that you entered in "load_untouch_nii.m"' char(10)];
msg = [msg 'command.'];
error(msg);
end
if ~exist('dim5_idx','var') | isempty(dim5_idx)
dim5_idx = [];
if ~isequal(size(slice,5),1)
msg = [char(10) '"dim5_idx" is a numerical array of 5th dimension indices, which' char(10)];
msg = [msg 'should be the same as that you entered in "load_untouch_nii.m"' char(10)];
msg = [msg 'command.'];
error(msg);
end
elseif ~isequal(size(slice,5),length(img_idx))
msg = [char(10) '"img_idx" is a numerical array of 5th dimension indices, which' char(10)];
msg = [msg 'should be the same as that you entered in "load_untouch_nii.m"' char(10)];
msg = [msg 'command.'];
error(msg);
end
if ~exist('dim6_idx','var') | isempty(dim6_idx)
dim6_idx = [];
if ~isequal(size(slice,6),1)
msg = [char(10) '"dim6_idx" is a numerical array of 6th dimension indices, which' char(10)];
msg = [msg 'should be the same as that you entered in "load_untouch_nii.m"' char(10)];
msg = [msg 'command.'];
error(msg);
end
elseif ~isequal(size(slice,6),length(img_idx))
msg = [char(10) '"img_idx" is a numerical array of 6th dimension indices, which' char(10)];
msg = [msg 'should be the same as that you entered in "load_untouch_nii.m"' char(10)];
msg = [msg 'command.'];
error(msg);
end
if ~exist('dim7_idx','var') | isempty(dim7_idx)
dim7_idx = [];
if ~isequal(size(slice,7),1)
msg = [char(10) '"dim7_idx" is a numerical array of 7th dimension indices, which' char(10)];
msg = [msg 'should be the same as that you entered in "load_untouch_nii.m"' char(10)];
msg = [msg 'command.'];
error(msg);
end
elseif ~isequal(size(slice,7),length(img_idx))
msg = [char(10) '"img_idx" is a numerical array of 7th dimension indices, which' char(10)];
msg = [msg 'should be the same as that you entered in "load_untouch_nii.m"' char(10)];
msg = [msg 'command.'];
error(msg);
end
v = version;
% Check file extension. If .gz, unpack it into temp folder
%
if length(filename) > 2 & strcmp(filename(end-2:end), '.gz')
if ~strcmp(filename(end-6:end), '.img.gz') & ...
~strcmp(filename(end-6:end), '.hdr.gz') & ...
~strcmp(filename(end-6:end), '.nii.gz')
error('Please check filename.');
end
if str2num(v(1:3)) < 7.1 | ~usejava('jvm')
error('Please use MATLAB 7.1 (with java) and above, or run gunzip outside MATLAB.');
elseif strcmp(filename(end-6:end), '.img.gz')
filename1 = filename;
filename2 = filename;
filename2(end-6:end) = '';
filename2 = [filename2, '.hdr.gz'];
tmpDir = tempname;
mkdir(tmpDir);
gzFileName = filename;
filename1 = gunzip(filename1, tmpDir);
filename2 = gunzip(filename2, tmpDir);
filename = char(filename1); % convert from cell to string
elseif strcmp(filename(end-6:end), '.hdr.gz')
filename1 = filename;
filename2 = filename;
filename2(end-6:end) = '';
filename2 = [filename2, '.img.gz'];
tmpDir = tempname;
mkdir(tmpDir);
gzFileName = filename;
filename1 = gunzip(filename1, tmpDir);
filename2 = gunzip(filename2, tmpDir);
filename = char(filename1); % convert from cell to string
elseif strcmp(filename(end-6:end), '.nii.gz')
tmpDir = tempname;
mkdir(tmpDir);
gzFileName = filename;
filename = gunzip(filename, tmpDir);
filename = char(filename); % convert from cell to string
end
end
% Read the dataset header
%
[nii.hdr,nii.filetype,nii.fileprefix,nii.machine] = load_nii_hdr(filename);
if nii.filetype == 0
nii.hdr = load_untouch0_nii_hdr(nii.fileprefix,nii.machine);
else
nii.hdr = load_untouch_nii_hdr(nii.fileprefix,nii.machine,nii.filetype);
end
% Clean up after gunzip
%
if exist('gzFileName', 'var')
% fix fileprefix so it doesn't point to temp location
%
nii.fileprefix = gzFileName(1:end-7);
% rmdir(tmpDir,'s');
end
[p,f] = fileparts(filename);
fileprefix = fullfile(p, f);
% fileprefix = nii.fileprefix;
filetype = nii.filetype;
if ~isequal( nii.hdr.dime.dim(2:3), [size(slice,1),size(slice,2)] )
msg = [char(10) 'The first two dimensions of slice matrix should be the same as' char(10)];
msg = [msg 'the first two dimensions of image loaded by "load_untouch_nii".'];
error(msg);
end
% Save the dataset body
%
save_untouch_slice_img(slice, nii.hdr, filetype, fileprefix, ...
nii.machine, slice_idx,img_idx,dim5_idx,dim6_idx,dim7_idx);
% gzip output file if requested
%
if exist('gzFileName', 'var')
[p,f] = fileparts(gzFileName);
if filetype == 1
gzip([fileprefix, '.img']);
delete([fileprefix, '.img']);
movefile([fileprefix, '.img.gz']);
gzip([fileprefix, '.hdr']);
delete([fileprefix, '.hdr']);
movefile([fileprefix, '.hdr.gz']);
elseif filetype == 2
gzip([fileprefix, '.nii']);
delete([fileprefix, '.nii']);
movefile([fileprefix, '.nii.gz']);
end;
rmdir(tmpDir,'s');
end;
return % save_untouch_slice
%--------------------------------------------------------------------------
function save_untouch_slice_img(slice,hdr,filetype,fileprefix,machine,slice_idx,img_idx,dim5_idx,dim6_idx,dim7_idx)
if ~exist('hdr','var') | ~exist('filetype','var') | ~exist('fileprefix','var') | ~exist('machine','var')
error('Usage: save_untouch_slice_img(slice,hdr,filetype,fileprefix,machine,slice_idx,[img_idx],[dim5_idx],[dim6_idx],[dim7_idx]);');
end
if ~exist('slice_idx','var') | isempty(slice_idx) | hdr.dime.dim(4)<1
slice_idx = [];
end
if ~exist('img_idx','var') | isempty(img_idx) | hdr.dime.dim(5)<1
img_idx = [];
end
if ~exist('dim5_idx','var') | isempty(dim5_idx) | hdr.dime.dim(6)<1
dim5_idx = [];
end
if ~exist('dim6_idx','var') | isempty(dim6_idx) | hdr.dime.dim(7)<1
dim6_idx = [];
end
if ~exist('dim7_idx','var') | isempty(dim7_idx) | hdr.dime.dim(8)<1
dim7_idx = [];
end
% check img_idx
%
if ~isempty(img_idx) & ~isnumeric(img_idx)
error('"img_idx" should be a numerical array.');
end
if length(unique(img_idx)) ~= length(img_idx)
error('Duplicate image index in "img_idx"');
end
if ~isempty(img_idx) & (min(img_idx) < 1 | max(img_idx) > hdr.dime.dim(5))
max_range = hdr.dime.dim(5);
if max_range == 1
error(['"img_idx" should be 1.']);
else
range = ['1 ' num2str(max_range)];
error(['"img_idx" should be an integer within the range of [' range '].']);
end
end
% check dim5_idx
%
if ~isempty(dim5_idx) & ~isnumeric(dim5_idx)
error('"dim5_idx" should be a numerical array.');
end
if length(unique(dim5_idx)) ~= length(dim5_idx)
error('Duplicate index in "dim5_idx"');
end
if ~isempty(dim5_idx) & (min(dim5_idx) < 1 | max(dim5_idx) > hdr.dime.dim(6))
max_range = hdr.dime.dim(6);
if max_range == 1
error(['"dim5_idx" should be 1.']);
else
range = ['1 ' num2str(max_range)];
error(['"dim5_idx" should be an integer within the range of [' range '].']);
end
end
% check dim6_idx
%
if ~isempty(dim6_idx) & ~isnumeric(dim6_idx)
error('"dim6_idx" should be a numerical array.');
end
if length(unique(dim6_idx)) ~= length(dim6_idx)
error('Duplicate index in "dim6_idx"');
end
if ~isempty(dim6_idx) & (min(dim6_idx) < 1 | max(dim6_idx) > hdr.dime.dim(7))
max_range = hdr.dime.dim(7);
if max_range == 1
error(['"dim6_idx" should be 1.']);
else
range = ['1 ' num2str(max_range)];
error(['"dim6_idx" should be an integer within the range of [' range '].']);
end
end
% check dim7_idx
%
if ~isempty(dim7_idx) & ~isnumeric(dim7_idx)
error('"dim7_idx" should be a numerical array.');
end
if length(unique(dim7_idx)) ~= length(dim7_idx)
error('Duplicate index in "dim7_idx"');
end
if ~isempty(dim7_idx) & (min(dim7_idx) < 1 | max(dim7_idx) > hdr.dime.dim(8))
max_range = hdr.dime.dim(8);
if max_range == 1
error(['"dim7_idx" should be 1.']);
else
range = ['1 ' num2str(max_range)];
error(['"dim7_idx" should be an integer within the range of [' range '].']);
end
end
% check slice_idx
%
if ~isempty(slice_idx) & ~isnumeric(slice_idx)
error('"slice_idx" should be a numerical array.');
end
if length(unique(slice_idx)) ~= length(slice_idx)
error('Duplicate index in "slice_idx"');
end
if ~isempty(slice_idx) & (min(slice_idx) < 1 | max(slice_idx) > hdr.dime.dim(4))
max_range = hdr.dime.dim(4);
if max_range == 1
error(['"slice_idx" should be 1.']);
else
range = ['1 ' num2str(max_range)];
error(['"slice_idx" should be an integer within the range of [' range '].']);
end
end
write_image(slice,hdr,filetype,fileprefix,machine,slice_idx,img_idx,dim5_idx,dim6_idx,dim7_idx);
return % save_untouch_slice_img
%---------------------------------------------------------------------
function write_image(slice,hdr,filetype,fileprefix,machine,slice_idx,img_idx,dim5_idx,dim6_idx,dim7_idx)
if filetype == 2
fid = fopen(sprintf('%s.nii',fileprefix),'r+');
if fid < 0,
msg = sprintf('Cannot open file %s.nii.',fileprefix);
error(msg);
end
else
fid = fopen(sprintf('%s.img',fileprefix),'r+');
if fid < 0,
msg = sprintf('Cannot open file %s.img.',fileprefix);
error(msg);
end
end
% Set bitpix according to datatype
%
% /*Acceptable values for datatype are*/
%
% 0 None (Unknown bit per voxel) % DT_NONE, DT_UNKNOWN
% 1 Binary (ubit1, bitpix=1) % DT_BINARY
% 2 Unsigned char (uchar or uint8, bitpix=8) % DT_UINT8, NIFTI_TYPE_UINT8
% 4 Signed short (int16, bitpix=16) % DT_INT16, NIFTI_TYPE_INT16
% 8 Signed integer (int32, bitpix=32) % DT_INT32, NIFTI_TYPE_INT32
% 16 Floating point (single or float32, bitpix=32) % DT_FLOAT32, NIFTI_TYPE_FLOAT32
% 32 Complex, 2 float32 (Use float32, bitpix=64) % DT_COMPLEX64, NIFTI_TYPE_COMPLEX64
% 64 Double precision (double or float64, bitpix=64) % DT_FLOAT64, NIFTI_TYPE_FLOAT64
% 128 uint8 RGB (Use uint8, bitpix=24) % DT_RGB24, NIFTI_TYPE_RGB24
% 256 Signed char (schar or int8, bitpix=8) % DT_INT8, NIFTI_TYPE_INT8
% 511 Single RGB (Use float32, bitpix=96) % DT_RGB96, NIFTI_TYPE_RGB96
% 512 Unsigned short (uint16, bitpix=16) % DT_UNINT16, NIFTI_TYPE_UNINT16
% 768 Unsigned integer (uint32, bitpix=32) % DT_UNINT32, NIFTI_TYPE_UNINT32
% 1024 Signed long long (int64, bitpix=64) % DT_INT64, NIFTI_TYPE_INT64
% 1280 Unsigned long long (uint64, bitpix=64) % DT_UINT64, NIFTI_TYPE_UINT64
% 1536 Long double, float128 (Unsupported, bitpix=128) % DT_FLOAT128, NIFTI_TYPE_FLOAT128
% 1792 Complex128, 2 float64 (Use float64, bitpix=128) % DT_COMPLEX128, NIFTI_TYPE_COMPLEX128
% 2048 Complex256, 2 float128 (Unsupported, bitpix=256) % DT_COMPLEX128, NIFTI_TYPE_COMPLEX128
%
switch hdr.dime.datatype
case 2,
hdr.dime.bitpix = 8; precision = 'uint8';
case 4,
hdr.dime.bitpix = 16; precision = 'int16';
case 8,
hdr.dime.bitpix = 32; precision = 'int32';
case 16,
hdr.dime.bitpix = 32; precision = 'float32';
case 64,
hdr.dime.bitpix = 64; precision = 'float64';
case 128,
hdr.dime.bitpix = 24; precision = 'uint8';
case 256
hdr.dime.bitpix = 8; precision = 'int8';
case 511
hdr.dime.bitpix = 96; precision = 'float32';
case 512
hdr.dime.bitpix = 16; precision = 'uint16';
case 768
hdr.dime.bitpix = 32; precision = 'uint32';
case 1024
hdr.dime.bitpix = 64; precision = 'int64';
case 1280
hdr.dime.bitpix = 64; precision = 'uint64';
otherwise
error('This datatype is not supported');
end
hdr.dime.dim(find(hdr.dime.dim < 1)) = 1;
% move pointer to the start of image block
%
switch filetype
case {0, 1}
fseek(fid, 0, 'bof');
case 2
fseek(fid, hdr.dime.vox_offset, 'bof');
end
if hdr.dime.datatype == 1 | isequal(hdr.dime.dim(4:8),ones(1,5)) | ...
(isempty(img_idx) & isempty(dim5_idx) & isempty(dim6_idx) & isempty(dim7_idx) & isempty(slice_idx))
msg = [char(10) char(10) ' "save_untouch_slice" is used to save back to the original image a' char(10)];
msg = [msg ' portion of slices that were loaded by "load_untouch_nii". You can' char(10)];
msg = [msg ' process those slices matrix in any way, as long as their dimension' char(10)];
msg = [msg ' is not changed.'];
error(msg);
else
d1 = hdr.dime.dim(2);
d2 = hdr.dime.dim(3);
d3 = hdr.dime.dim(4);
d4 = hdr.dime.dim(5);
d5 = hdr.dime.dim(6);
d6 = hdr.dime.dim(7);
d7 = hdr.dime.dim(8);
if isempty(slice_idx)
slice_idx = 1:d3;
end
if isempty(img_idx)
img_idx = 1:d4;
end
if isempty(dim5_idx)
dim5_idx = 1:d5;
end
if isempty(dim6_idx)
dim6_idx = 1:d6;
end
if isempty(dim7_idx)
dim7_idx = 1:d7;
end
%ROMAN: begin
roman = 1;
if(roman)
% compute size of one slice
%
img_siz = prod(hdr.dime.dim(2:3));
% For complex float32 or complex float64, voxel values
% include [real, imag]
%
if hdr.dime.datatype == 32 | hdr.dime.datatype == 1792
img_siz = img_siz * 2;
end
%MPH: For RGB24, voxel values include 3 separate color planes
%
if hdr.dime.datatype == 128 | hdr.dime.datatype == 511
img_siz = img_siz * 3;
end
end; %if(roman)
% ROMAN: end
for i7=1:length(dim7_idx)
for i6=1:length(dim6_idx)
for i5=1:length(dim5_idx)
for t=1:length(img_idx)
for s=1:length(slice_idx)
% Position is seeked in bytes. To convert dimension size
% to byte storage size, hdr.dime.bitpix/8 will be
% applied.
%
pos = sub2ind([d1 d2 d3 d4 d5 d6 d7], 1, 1, slice_idx(s), ...
img_idx(t), dim5_idx(i5),dim6_idx(i6),dim7_idx(i7)) -1;
pos = pos * hdr.dime.bitpix/8;
% ROMAN: begin
if(roman)
% do nothing
else
img_siz = prod(hdr.dime.dim(2:3));
% For complex float32 or complex float64, voxel values
% include [real, imag]
%
if hdr.dime.datatype == 32 | hdr.dime.datatype == 1792
img_siz = img_siz * 2;
end
%MPH: For RGB24, voxel values include 3 separate color planes
%
if hdr.dime.datatype == 128 | hdr.dime.datatype == 511
img_siz = img_siz * 3;
end
end; % if (roman)
% ROMAN: end
if filetype == 2
fseek(fid, pos + hdr.dime.vox_offset, 'bof');
else
fseek(fid, pos, 'bof');
end
% For each frame, fwrite will write precision of value
% in img_siz times
%
fwrite(fid, slice(:,:,s,t,i5,i6,i7), sprintf('*%s',precision));
end
end
end
end
end
end
fclose(fid);
return % write_image
|
github
|
adhusch/PaCER-master
|
load_nii_img.m
|
.m
|
PaCER-master/external/NIfTI_20140122/load_nii_img.m
| 12,328 |
utf_8
|
b1b9dd2838a8f217b10fefdc8a931d5e
|
% internal function
% - Jimmy Shen ([email protected])
function [img,hdr] = load_nii_img(hdr,filetype,fileprefix,machine,img_idx,dim5_idx,dim6_idx,dim7_idx,old_RGB)
if ~exist('hdr','var') | ~exist('filetype','var') | ~exist('fileprefix','var') | ~exist('machine','var')
error('Usage: [img,hdr] = load_nii_img(hdr,filetype,fileprefix,machine,[img_idx],[dim5_idx],[dim6_idx],[dim7_idx],[old_RGB]);');
end
if ~exist('img_idx','var') | isempty(img_idx) | hdr.dime.dim(5)<1
img_idx = [];
end
if ~exist('dim5_idx','var') | isempty(dim5_idx) | hdr.dime.dim(6)<1
dim5_idx = [];
end
if ~exist('dim6_idx','var') | isempty(dim6_idx) | hdr.dime.dim(7)<1
dim6_idx = [];
end
if ~exist('dim7_idx','var') | isempty(dim7_idx) | hdr.dime.dim(8)<1
dim7_idx = [];
end
if ~exist('old_RGB','var') | isempty(old_RGB)
old_RGB = 0;
end
% check img_idx
%
if ~isempty(img_idx) & ~isnumeric(img_idx)
error('"img_idx" should be a numerical array.');
end
if length(unique(img_idx)) ~= length(img_idx)
error('Duplicate image index in "img_idx"');
end
if ~isempty(img_idx) & (min(img_idx) < 1 | max(img_idx) > hdr.dime.dim(5))
max_range = hdr.dime.dim(5);
if max_range == 1
error(['"img_idx" should be 1.']);
else
range = ['1 ' num2str(max_range)];
error(['"img_idx" should be an integer within the range of [' range '].']);
end
end
% check dim5_idx
%
if ~isempty(dim5_idx) & ~isnumeric(dim5_idx)
error('"dim5_idx" should be a numerical array.');
end
if length(unique(dim5_idx)) ~= length(dim5_idx)
error('Duplicate index in "dim5_idx"');
end
if ~isempty(dim5_idx) & (min(dim5_idx) < 1 | max(dim5_idx) > hdr.dime.dim(6))
max_range = hdr.dime.dim(6);
if max_range == 1
error(['"dim5_idx" should be 1.']);
else
range = ['1 ' num2str(max_range)];
error(['"dim5_idx" should be an integer within the range of [' range '].']);
end
end
% check dim6_idx
%
if ~isempty(dim6_idx) & ~isnumeric(dim6_idx)
error('"dim6_idx" should be a numerical array.');
end
if length(unique(dim6_idx)) ~= length(dim6_idx)
error('Duplicate index in "dim6_idx"');
end
if ~isempty(dim6_idx) & (min(dim6_idx) < 1 | max(dim6_idx) > hdr.dime.dim(7))
max_range = hdr.dime.dim(7);
if max_range == 1
error(['"dim6_idx" should be 1.']);
else
range = ['1 ' num2str(max_range)];
error(['"dim6_idx" should be an integer within the range of [' range '].']);
end
end
% check dim7_idx
%
if ~isempty(dim7_idx) & ~isnumeric(dim7_idx)
error('"dim7_idx" should be a numerical array.');
end
if length(unique(dim7_idx)) ~= length(dim7_idx)
error('Duplicate index in "dim7_idx"');
end
if ~isempty(dim7_idx) & (min(dim7_idx) < 1 | max(dim7_idx) > hdr.dime.dim(8))
max_range = hdr.dime.dim(8);
if max_range == 1
error(['"dim7_idx" should be 1.']);
else
range = ['1 ' num2str(max_range)];
error(['"dim7_idx" should be an integer within the range of [' range '].']);
end
end
[img,hdr] = read_image(hdr,filetype,fileprefix,machine,img_idx,dim5_idx,dim6_idx,dim7_idx,old_RGB);
return % load_nii_img
%---------------------------------------------------------------------
function [img,hdr] = read_image(hdr,filetype,fileprefix,machine,img_idx,dim5_idx,dim6_idx,dim7_idx,old_RGB)
switch filetype
case {0, 1}
fn = [fileprefix '.img'];
case 2
fn = [fileprefix '.nii'];
end
fid = fopen(fn,'r',machine);
if fid < 0,
msg = sprintf('Cannot open file %s.',fn);
error(msg);
end
% Set bitpix according to datatype
%
% /*Acceptable values for datatype are*/
%
% 0 None (Unknown bit per voxel) % DT_NONE, DT_UNKNOWN
% 1 Binary (ubit1, bitpix=1) % DT_BINARY
% 2 Unsigned char (uchar or uint8, bitpix=8) % DT_UINT8, NIFTI_TYPE_UINT8
% 4 Signed short (int16, bitpix=16) % DT_INT16, NIFTI_TYPE_INT16
% 8 Signed integer (int32, bitpix=32) % DT_INT32, NIFTI_TYPE_INT32
% 16 Floating point (single or float32, bitpix=32) % DT_FLOAT32, NIFTI_TYPE_FLOAT32
% 32 Complex, 2 float32 (Use float32, bitpix=64) % DT_COMPLEX64, NIFTI_TYPE_COMPLEX64
% 64 Double precision (double or float64, bitpix=64) % DT_FLOAT64, NIFTI_TYPE_FLOAT64
% 128 uint8 RGB (Use uint8, bitpix=24) % DT_RGB24, NIFTI_TYPE_RGB24
% 256 Signed char (schar or int8, bitpix=8) % DT_INT8, NIFTI_TYPE_INT8
% 511 Single RGB (Use float32, bitpix=96) % DT_RGB96, NIFTI_TYPE_RGB96
% 512 Unsigned short (uint16, bitpix=16) % DT_UNINT16, NIFTI_TYPE_UNINT16
% 768 Unsigned integer (uint32, bitpix=32) % DT_UNINT32, NIFTI_TYPE_UNINT32
% 1024 Signed long long (int64, bitpix=64) % DT_INT64, NIFTI_TYPE_INT64
% 1280 Unsigned long long (uint64, bitpix=64) % DT_UINT64, NIFTI_TYPE_UINT64
% 1536 Long double, float128 (Unsupported, bitpix=128) % DT_FLOAT128, NIFTI_TYPE_FLOAT128
% 1792 Complex128, 2 float64 (Use float64, bitpix=128) % DT_COMPLEX128, NIFTI_TYPE_COMPLEX128
% 2048 Complex256, 2 float128 (Unsupported, bitpix=256) % DT_COMPLEX128, NIFTI_TYPE_COMPLEX128
%
switch hdr.dime.datatype
case 1,
hdr.dime.bitpix = 1; precision = 'ubit1';
case 2,
hdr.dime.bitpix = 8; precision = 'uint8';
case 4,
hdr.dime.bitpix = 16; precision = 'int16';
case 8,
hdr.dime.bitpix = 32; precision = 'int32';
case 16,
hdr.dime.bitpix = 32; precision = 'float32';
case 32,
hdr.dime.bitpix = 64; precision = 'float32';
case 64,
hdr.dime.bitpix = 64; precision = 'float64';
case 128,
hdr.dime.bitpix = 24; precision = 'uint8';
case 256
hdr.dime.bitpix = 8; precision = 'int8';
case 511
hdr.dime.bitpix = 96; precision = 'float32';
case 512
hdr.dime.bitpix = 16; precision = 'uint16';
case 768
hdr.dime.bitpix = 32; precision = 'uint32';
case 1024
hdr.dime.bitpix = 64; precision = 'int64';
case 1280
hdr.dime.bitpix = 64; precision = 'uint64';
case 1792,
hdr.dime.bitpix = 128; precision = 'float64';
otherwise
error('This datatype is not supported');
end
hdr.dime.dim(find(hdr.dime.dim < 1)) = 1;
% move pointer to the start of image block
%
switch filetype
case {0, 1}
fseek(fid, 0, 'bof');
case 2
fseek(fid, hdr.dime.vox_offset, 'bof');
end
% Load whole image block for old Analyze format or binary image;
% otherwise, load images that are specified in img_idx, dim5_idx,
% dim6_idx, and dim7_idx
%
% For binary image, we have to read all because pos can not be
% seeked in bit and can not be calculated the way below.
%
if hdr.dime.datatype == 1 | isequal(hdr.dime.dim(5:8),ones(1,4)) | ...
(isempty(img_idx) & isempty(dim5_idx) & isempty(dim6_idx) & isempty(dim7_idx))
% For each frame, precision of value will be read
% in img_siz times, where img_siz is only the
% dimension size of an image, not the byte storage
% size of an image.
%
img_siz = prod(hdr.dime.dim(2:8));
% For complex float32 or complex float64, voxel values
% include [real, imag]
%
if hdr.dime.datatype == 32 | hdr.dime.datatype == 1792
img_siz = img_siz * 2;
end
%MPH: For RGB24, voxel values include 3 separate color planes
%
if hdr.dime.datatype == 128 | hdr.dime.datatype == 511
img_siz = img_siz * 3;
end
img = fread(fid, img_siz, sprintf('*%s',precision));
d1 = hdr.dime.dim(2);
d2 = hdr.dime.dim(3);
d3 = hdr.dime.dim(4);
d4 = hdr.dime.dim(5);
d5 = hdr.dime.dim(6);
d6 = hdr.dime.dim(7);
d7 = hdr.dime.dim(8);
if isempty(img_idx)
img_idx = 1:d4;
end
if isempty(dim5_idx)
dim5_idx = 1:d5;
end
if isempty(dim6_idx)
dim6_idx = 1:d6;
end
if isempty(dim7_idx)
dim7_idx = 1:d7;
end
else
d1 = hdr.dime.dim(2);
d2 = hdr.dime.dim(3);
d3 = hdr.dime.dim(4);
d4 = hdr.dime.dim(5);
d5 = hdr.dime.dim(6);
d6 = hdr.dime.dim(7);
d7 = hdr.dime.dim(8);
if isempty(img_idx)
img_idx = 1:d4;
end
if isempty(dim5_idx)
dim5_idx = 1:d5;
end
if isempty(dim6_idx)
dim6_idx = 1:d6;
end
if isempty(dim7_idx)
dim7_idx = 1:d7;
end
% compute size of one image
%
img_siz = prod(hdr.dime.dim(2:4));
% For complex float32 or complex float64, voxel values
% include [real, imag]
%
if hdr.dime.datatype == 32 | hdr.dime.datatype == 1792
img_siz = img_siz * 2;
end
%MPH: For RGB24, voxel values include 3 separate color planes
%
if hdr.dime.datatype == 128 | hdr.dime.datatype == 511
img_siz = img_siz * 3;
end
% preallocate img
img = zeros(img_siz, length(img_idx)*length(dim5_idx)*length(dim6_idx)*length(dim7_idx) );
currentIndex = 1;
for i7=1:length(dim7_idx)
for i6=1:length(dim6_idx)
for i5=1:length(dim5_idx)
for t=1:length(img_idx)
% Position is seeked in bytes. To convert dimension size
% to byte storage size, hdr.dime.bitpix/8 will be
% applied.
%
pos = sub2ind([d1 d2 d3 d4 d5 d6 d7], 1, 1, 1, ...
img_idx(t), dim5_idx(i5),dim6_idx(i6),dim7_idx(i7)) -1;
pos = pos * hdr.dime.bitpix/8;
if filetype == 2
fseek(fid, pos + hdr.dime.vox_offset, 'bof');
else
fseek(fid, pos, 'bof');
end
% For each frame, fread will read precision of value
% in img_siz times
%
img(:,currentIndex) = fread(fid, img_siz, sprintf('*%s',precision));
currentIndex = currentIndex +1;
end
end
end
end
end
% For complex float32 or complex float64, voxel values
% include [real, imag]
%
if hdr.dime.datatype == 32 | hdr.dime.datatype == 1792
img = reshape(img, [2, length(img)/2]);
img = complex(img(1,:)', img(2,:)');
end
fclose(fid);
% Update the global min and max values
%
hdr.dime.glmax = double(max(img(:)));
hdr.dime.glmin = double(min(img(:)));
% old_RGB treat RGB slice by slice, now it is treated voxel by voxel
%
if old_RGB & hdr.dime.datatype == 128 & hdr.dime.bitpix == 24
% remove squeeze
img = (reshape(img, [hdr.dime.dim(2:3) 3 hdr.dime.dim(4) length(img_idx) length(dim5_idx) length(dim6_idx) length(dim7_idx)]));
img = permute(img, [1 2 4 3 5 6 7 8]);
elseif hdr.dime.datatype == 128 & hdr.dime.bitpix == 24
% remove squeeze
img = (reshape(img, [3 hdr.dime.dim(2:4) length(img_idx) length(dim5_idx) length(dim6_idx) length(dim7_idx)]));
img = permute(img, [2 3 4 1 5 6 7 8]);
elseif hdr.dime.datatype == 511 & hdr.dime.bitpix == 96
img = double(img(:));
img = single((img - min(img))/(max(img) - min(img)));
% remove squeeze
img = (reshape(img, [3 hdr.dime.dim(2:4) length(img_idx) length(dim5_idx) length(dim6_idx) length(dim7_idx)]));
img = permute(img, [2 3 4 1 5 6 7 8]);
else
% remove squeeze
img = (reshape(img, [hdr.dime.dim(2:4) length(img_idx) length(dim5_idx) length(dim6_idx) length(dim7_idx)]));
end
if ~isempty(img_idx)
hdr.dime.dim(5) = length(img_idx);
end
if ~isempty(dim5_idx)
hdr.dime.dim(6) = length(dim5_idx);
end
if ~isempty(dim6_idx)
hdr.dime.dim(7) = length(dim6_idx);
end
if ~isempty(dim7_idx)
hdr.dime.dim(8) = length(dim7_idx);
end
return % read_image
|
github
|
adhusch/PaCER-master
|
bresenham_line3d.m
|
.m
|
PaCER-master/external/NIfTI_20140122/bresenham_line3d.m
| 4,493 |
utf_8
|
c19f06df423676afeb59762ac55c0c2f
|
% Generate X Y Z coordinates of a 3D Bresenham's line between
% two given points.
%
% A very useful application of this algorithm can be found in the
% implementation of Fischer's Bresenham interpolation method in my
% another program that can rotate three dimensional image volume
% with an affine matrix:
% http://www.mathworks.com/matlabcentral/fileexchange/loadFile.do?objectId=21080
%
% Usage: [X Y Z] = bresenham_line3d(P1, P2, [precision]);
%
% P1 - vector for Point1, where P1 = [x1 y1 z1]
%
% P2 - vector for Point2, where P2 = [x2 y2 z2]
%
% precision (optional) - Although according to Bresenham's line
% algorithm, point coordinates x1 y1 z1 and x2 y2 z2 should
% be integer numbers, this program extends its limit to all
% real numbers. If any of them are floating numbers, you
% should specify how many digits of decimal that you would
% like to preserve. Be aware that the length of output X Y
% Z coordinates will increase in 10 times for each decimal
% digit that you want to preserve. By default, the precision
% is 0, which means that they will be rounded to the nearest
% integer.
%
% X - a set of x coordinates on Bresenham's line
%
% Y - a set of y coordinates on Bresenham's line
%
% Z - a set of z coordinates on Bresenham's line
%
% Therefore, all points in XYZ set (i.e. P(i) = [X(i) Y(i) Z(i)])
% will constitute the Bresenham's line between P1 and P1.
%
% Example:
% P1 = [12 37 6]; P2 = [46 3 35];
% [X Y Z] = bresenham_line3d(P1, P2);
% figure; plot3(X,Y,Z,'s','markerface','b');
%
% This program is ported to MATLAB from:
%
% B.Pendleton. line3d - 3D Bresenham's (a 3D line drawing algorithm)
% ftp://ftp.isc.org/pub/usenet/comp.sources.unix/volume26/line3d, 1992
%
% Which is also referenced by:
%
% Fischer, J., A. del Rio (2004). A Fast Method for Applying Rigid
% Transformations to Volume Data, WSCG2004 Conference.
% http://wscg.zcu.cz/wscg2004/Papers_2004_Short/M19.pdf
%
% - Jimmy Shen ([email protected])
%
function [X,Y,Z] = bresenham_line3d(P1, P2, precision)
if ~exist('precision','var') | isempty(precision) | round(precision) == 0
precision = 0;
P1 = round(P1);
P2 = round(P2);
else
precision = round(precision);
P1 = round(P1*(10^precision));
P2 = round(P2*(10^precision));
end
d = max(abs(P2-P1)+1);
X = zeros(1, d);
Y = zeros(1, d);
Z = zeros(1, d);
x1 = P1(1);
y1 = P1(2);
z1 = P1(3);
x2 = P2(1);
y2 = P2(2);
z2 = P2(3);
dx = x2 - x1;
dy = y2 - y1;
dz = z2 - z1;
ax = abs(dx)*2;
ay = abs(dy)*2;
az = abs(dz)*2;
sx = sign(dx);
sy = sign(dy);
sz = sign(dz);
x = x1;
y = y1;
z = z1;
idx = 1;
if(ax>=max(ay,az)) % x dominant
yd = ay - ax/2;
zd = az - ax/2;
while(1)
X(idx) = x;
Y(idx) = y;
Z(idx) = z;
idx = idx + 1;
if(x == x2) % end
break;
end
if(yd >= 0) % move along y
y = y + sy;
yd = yd - ax;
end
if(zd >= 0) % move along z
z = z + sz;
zd = zd - ax;
end
x = x + sx; % move along x
yd = yd + ay;
zd = zd + az;
end
elseif(ay>=max(ax,az)) % y dominant
xd = ax - ay/2;
zd = az - ay/2;
while(1)
X(idx) = x;
Y(idx) = y;
Z(idx) = z;
idx = idx + 1;
if(y == y2) % end
break;
end
if(xd >= 0) % move along x
x = x + sx;
xd = xd - ay;
end
if(zd >= 0) % move along z
z = z + sz;
zd = zd - ay;
end
y = y + sy; % move along y
xd = xd + ax;
zd = zd + az;
end
elseif(az>=max(ax,ay)) % z dominant
xd = ax - az/2;
yd = ay - az/2;
while(1)
X(idx) = x;
Y(idx) = y;
Z(idx) = z;
idx = idx + 1;
if(z == z2) % end
break;
end
if(xd >= 0) % move along x
x = x + sx;
xd = xd - az;
end
if(yd >= 0) % move along y
y = y + sy;
yd = yd - az;
end
z = z + sz; % move along z
xd = xd + ax;
yd = yd + ay;
end
end
if precision ~= 0
X = X/(10^precision);
Y = Y/(10^precision);
Z = Z/(10^precision);
end
return; % bresenham_line3d
|
github
|
adhusch/PaCER-master
|
make_nii.m
|
.m
|
PaCER-master/external/NIfTI_20140122/make_nii.m
| 6,849 |
utf_8
|
3c7c8b81655c111a9ce4b82086bde4f5
|
% Make NIfTI structure specified by an N-D matrix. Usually, N is 3 for
% 3D matrix [x y z], or 4 for 4D matrix with time series [x y z t].
% Optional parameters can also be included, such as: voxel_size,
% origin, datatype, and description.
%
% Once the NIfTI structure is made, it can be saved into NIfTI file
% using "save_nii" command (for more detail, type: help save_nii).
%
% Usage: nii = make_nii(img, [voxel_size], [origin], [datatype], [description])
%
% Where:
%
% img: Usually, img is a 3D matrix [x y z], or a 4D
% matrix with time series [x y z t]. However,
% NIfTI allows a maximum of 7D matrix. When the
% image is in RGB format, make sure that the size
% of 4th dimension is always 3 (i.e. [R G B]). In
% that case, make sure that you must specify RGB
% datatype, which is either 128 or 511.
%
% voxel_size (optional): Voxel size in millimeter for each
% dimension. Default is [1 1 1].
%
% origin (optional): The AC origin. Default is [0 0 0].
%
% datatype (optional): Storage data type:
% 2 - uint8, 4 - int16, 8 - int32, 16 - float32,
% 32 - complex64, 64 - float64, 128 - RGB24,
% 256 - int8, 511 - RGB96, 512 - uint16,
% 768 - uint32, 1792 - complex128
% Default will use the data type of 'img' matrix
% For RGB image, you must specify it to either 128
% or 511.
%
% description (optional): Description of data. Default is ''.
%
% e.g.:
% origin = [33 44 13]; datatype = 64;
% nii = make_nii(img, [], origin, datatype); % default voxel_size
%
% NIFTI data format can be found on: http://nifti.nimh.nih.gov
%
% - Jimmy Shen ([email protected])
%
function nii = make_nii(varargin)
nii.img = varargin{1};
dims = size(nii.img);
dims = [length(dims) dims ones(1,8)];
dims = dims(1:8);
voxel_size = [0 ones(1,7)];
origin = zeros(1,5);
descrip = '';
switch class(nii.img)
case 'uint8'
datatype = 2;
case 'int16'
datatype = 4;
case 'int32'
datatype = 8;
case 'single'
if isreal(nii.img)
datatype = 16;
else
datatype = 32;
end
case 'double'
if isreal(nii.img)
datatype = 64;
else
datatype = 1792;
end
case 'int8'
datatype = 256;
case 'uint16'
datatype = 512;
case 'uint32'
datatype = 768;
otherwise
error('Datatype is not supported by make_nii.');
end
if nargin > 1 & ~isempty(varargin{2})
voxel_size(2:4) = double(varargin{2});
end
if nargin > 2 & ~isempty(varargin{3})
origin(1:3) = double(varargin{3});
end
if nargin > 3 & ~isempty(varargin{4})
datatype = double(varargin{4});
if datatype == 128 | datatype == 511
dims(5) = [];
dims(1) = dims(1) - 1;
dims = [dims 1];
end
end
if nargin > 4 & ~isempty(varargin{5})
descrip = varargin{5};
end
if ndims(nii.img) > 7
error('NIfTI only allows a maximum of 7 Dimension matrix.');
end
maxval = round(double(max(nii.img(:))));
minval = round(double(min(nii.img(:))));
nii.hdr = make_header(dims, voxel_size, origin, datatype, ...
descrip, maxval, minval);
switch nii.hdr.dime.datatype
case 2
nii.img = uint8(nii.img);
case 4
nii.img = int16(nii.img);
case 8
nii.img = int32(nii.img);
case 16
nii.img = single(nii.img);
case 32
nii.img = single(nii.img);
case 64
nii.img = double(nii.img);
case 128
nii.img = uint8(nii.img);
case 256
nii.img = int8(nii.img);
case 511
img = double(nii.img(:));
img = single((img - min(img))/(max(img) - min(img)));
nii.img = reshape(img, size(nii.img));
nii.hdr.dime.glmax = double(max(img));
nii.hdr.dime.glmin = double(min(img));
case 512
nii.img = uint16(nii.img);
case 768
nii.img = uint32(nii.img);
case 1792
nii.img = double(nii.img);
otherwise
error('Datatype is not supported by make_nii.');
end
return; % make_nii
%---------------------------------------------------------------------
function hdr = make_header(dims, voxel_size, origin, datatype, ...
descrip, maxval, minval)
hdr.hk = header_key;
hdr.dime = image_dimension(dims, voxel_size, datatype, maxval, minval);
hdr.hist = data_history(origin, descrip);
return; % make_header
%---------------------------------------------------------------------
function hk = header_key
hk.sizeof_hdr = 348; % must be 348!
hk.data_type = '';
hk.db_name = '';
hk.extents = 0;
hk.session_error = 0;
hk.regular = 'r';
hk.dim_info = 0;
return; % header_key
%---------------------------------------------------------------------
function dime = image_dimension(dims, voxel_size, datatype, maxval, minval)
dime.dim = dims;
dime.intent_p1 = 0;
dime.intent_p2 = 0;
dime.intent_p3 = 0;
dime.intent_code = 0;
dime.datatype = datatype;
switch dime.datatype
case 2,
dime.bitpix = 8; precision = 'uint8';
case 4,
dime.bitpix = 16; precision = 'int16';
case 8,
dime.bitpix = 32; precision = 'int32';
case 16,
dime.bitpix = 32; precision = 'float32';
case 32,
dime.bitpix = 64; precision = 'float32';
case 64,
dime.bitpix = 64; precision = 'float64';
case 128
dime.bitpix = 24; precision = 'uint8';
case 256
dime.bitpix = 8; precision = 'int8';
case 511
dime.bitpix = 96; precision = 'float32';
case 512
dime.bitpix = 16; precision = 'uint16';
case 768
dime.bitpix = 32; precision = 'uint32';
case 1792,
dime.bitpix = 128; precision = 'float64';
otherwise
error('Datatype is not supported by make_nii.');
end
dime.slice_start = 0;
dime.pixdim = voxel_size;
dime.vox_offset = 0;
dime.scl_slope = 0;
dime.scl_inter = 0;
dime.slice_end = 0;
dime.slice_code = 0;
dime.xyzt_units = 0;
dime.cal_max = 0;
dime.cal_min = 0;
dime.slice_duration = 0;
dime.toffset = 0;
dime.glmax = maxval;
dime.glmin = minval;
return; % image_dimension
%---------------------------------------------------------------------
function hist = data_history(origin, descrip)
hist.descrip = descrip;
hist.aux_file = 'none';
hist.qform_code = 0;
hist.sform_code = 0;
hist.quatern_b = 0;
hist.quatern_c = 0;
hist.quatern_d = 0;
hist.qoffset_x = 0;
hist.qoffset_y = 0;
hist.qoffset_z = 0;
hist.srow_x = zeros(1,4);
hist.srow_y = zeros(1,4);
hist.srow_z = zeros(1,4);
hist.intent_name = '';
hist.magic = '';
hist.originator = origin;
return; % data_history
|
github
|
adhusch/PaCER-master
|
verify_nii_ext.m
|
.m
|
PaCER-master/external/NIfTI_20140122/verify_nii_ext.m
| 1,676 |
utf_8
|
db3d32ecba688905185f5ed01b409fd1
|
% Verify NIFTI header extension to make sure that each extension section
% must be an integer multiple of 16 byte long that includes the first 8
% bytes of esize and ecode. If the length of extension section is not the
% above mentioned case, edata should be padded with all 0.
%
% Usage: [ext, esize_total] = verify_nii_ext(ext)
%
% ext - Structure of NIFTI header extension, which includes num_ext,
% and all the extended header sections in the header extension.
% Each extended header section will have its esize, ecode, and
% edata, where edata can be plain text, xml, or any raw data
% that was saved in the extended header section.
%
% esize_total - Sum of all esize variable in all header sections.
%
% NIFTI data format can be found on: http://nifti.nimh.nih.gov
%
% - Jimmy Shen ([email protected])
%
function [ext, esize_total] = verify_nii_ext(ext)
if ~isfield(ext, 'section')
error('Incorrect NIFTI header extension structure.');
elseif ~isfield(ext, 'num_ext')
ext.num_ext = length(ext.section);
elseif ~isfield(ext, 'extension')
ext.extension = [1 0 0 0];
end
esize_total = 0;
for i=1:ext.num_ext
if ~isfield(ext.section(i), 'ecode') | ~isfield(ext.section(i), 'edata')
error('Incorrect NIFTI header extension structure.');
end
ext.section(i).esize = ceil((length(ext.section(i).edata)+8)/16)*16;
ext.section(i).edata = ...
[ext.section(i).edata ...
zeros(1,ext.section(i).esize-length(ext.section(i).edata)-8)];
esize_total = esize_total + ext.section(i).esize;
end
return % verify_nii_ext
|
github
|
adhusch/PaCER-master
|
get_nii_frame.m
|
.m
|
PaCER-master/external/NIfTI_20140122/get_nii_frame.m
| 4,333 |
utf_8
|
8b0cba9d07733a6f82753b0c40b51107
|
% Return time frame of a NIFTI dataset. Support both *.nii and
% *.hdr/*.img file extension. If file extension is not provided,
% *.hdr/*.img will be used as default.
%
% It is a lightweighted "load_nii_hdr", and is equivalent to
% hdr.dime.dim(5)
%
% Usage: [ total_scan ] = get_nii_frame(filename)
%
% filename - NIFTI file name.
%
% Returned values:
%
% total_scan - total number of image scans for the time frame
%
% NIFTI data format can be found on: http://nifti.nimh.nih.gov
%
% - Jimmy Shen ([email protected])
%
function [ total_scan ] = get_nii_frame(filename)
if ~exist('filename','var'),
error('Usage: [ total_scan ] = get_nii_frame(filename)');
end
v = version;
% Check file extension. If .gz, unpack it into temp folder
%
if length(filename) > 2 & strcmp(filename(end-2:end), '.gz')
if ~strcmp(filename(end-6:end), '.img.gz') & ...
~strcmp(filename(end-6:end), '.hdr.gz') & ...
~strcmp(filename(end-6:end), '.nii.gz')
error('Please check filename.');
end
if str2num(v(1:3)) < 7.1 | ~usejava('jvm')
error('Please use MATLAB 7.1 (with java) and above, or run gunzip outside MATLAB.');
elseif strcmp(filename(end-6:end), '.img.gz')
filename1 = filename;
filename2 = filename;
filename2(end-6:end) = '';
filename2 = [filename2, '.hdr.gz'];
tmpDir = tempname;
mkdir(tmpDir);
gzFileName = filename;
filename1 = gunzip(filename1, tmpDir);
filename2 = gunzip(filename2, tmpDir);
filename = char(filename1); % convert from cell to string
elseif strcmp(filename(end-6:end), '.hdr.gz')
filename1 = filename;
filename2 = filename;
filename2(end-6:end) = '';
filename2 = [filename2, '.img.gz'];
tmpDir = tempname;
mkdir(tmpDir);
gzFileName = filename;
filename1 = gunzip(filename1, tmpDir);
filename2 = gunzip(filename2, tmpDir);
filename = char(filename1); % convert from cell to string
elseif strcmp(filename(end-6:end), '.nii.gz')
tmpDir = tempname;
mkdir(tmpDir);
gzFileName = filename;
filename = gunzip(filename, tmpDir);
filename = char(filename); % convert from cell to string
end
end
fileprefix = filename;
machine = 'ieee-le';
new_ext = 0;
if findstr('.nii',fileprefix) & strcmp(fileprefix(end-3:end), '.nii')
new_ext = 1;
fileprefix(end-3:end)='';
end
if findstr('.hdr',fileprefix) & strcmp(fileprefix(end-3:end), '.hdr')
fileprefix(end-3:end)='';
end
if findstr('.img',fileprefix) & strcmp(fileprefix(end-3:end), '.img')
fileprefix(end-3:end)='';
end
if new_ext
fn = sprintf('%s.nii',fileprefix);
if ~exist(fn)
msg = sprintf('Cannot find file "%s.nii".', fileprefix);
error(msg);
end
else
fn = sprintf('%s.hdr',fileprefix);
if ~exist(fn)
msg = sprintf('Cannot find file "%s.hdr".', fileprefix);
error(msg);
end
end
fid = fopen(fn,'r',machine);
if fid < 0,
msg = sprintf('Cannot open file %s.',fn);
error(msg);
else
hdr = read_header(fid);
fclose(fid);
end
if hdr.sizeof_hdr ~= 348
% first try reading the opposite endian to 'machine'
switch machine,
case 'ieee-le', machine = 'ieee-be';
case 'ieee-be', machine = 'ieee-le';
end
fid = fopen(fn,'r',machine);
if fid < 0,
msg = sprintf('Cannot open file %s.',fn);
error(msg);
else
hdr = read_header(fid);
fclose(fid);
end
end
if hdr.sizeof_hdr ~= 348
% Now throw an error
msg = sprintf('File "%s" is corrupted.',fn);
error(msg);
end
total_scan = hdr.dim(5);
% Clean up after gunzip
%
if exist('gzFileName', 'var')
rmdir(tmpDir,'s');
end
return; % get_nii_frame
%---------------------------------------------------------------------
function [ dsr ] = read_header(fid)
fseek(fid,0,'bof');
dsr.sizeof_hdr = fread(fid,1,'int32')'; % should be 348!
fseek(fid,40,'bof');
dsr.dim = fread(fid,8,'int16')';
return; % read_header
|
github
|
adhusch/PaCER-master
|
flip_lr.m
|
.m
|
PaCER-master/external/NIfTI_20140122/flip_lr.m
| 3,484 |
utf_8
|
a0b2d0189d90339a841863efeb60681a
|
% When you load any ANALYZE or NIfTI file with 'load_nii.m', and view
% it with 'view_nii.m', you may find that the image is L-R flipped.
% This is because of the confusion of radiological and neurological
% convention in the medical image before NIfTI format is adopted. You
% can find more details from:
%
% http://www.rotman-baycrest.on.ca/~jimmy/UseANALYZE.htm
%
% Sometime, people even want to convert RAS (standard orientation) back
% to LAS orientation to satisfy the legend programs or processes. This
% program is only written for those purpose. So PLEASE BE VERY CAUTIOUS
% WHEN USING THIS 'FLIP_LR.M' PROGRAM.
%
% With 'flip_lr.m', you can convert any ANALYZE or NIfTI (no matter
% 3D or 4D) file to a flipped NIfTI file. This is implemented simply
% by flipping the affine matrix in the NIfTI header. Since the L-R
% orientation is determined there, so the image will be flipped.
%
% Usage: flip_lr(original_fn, flipped_fn, [old_RGB],[tolerance],[preferredForm])
%
% original_fn - filename of the original ANALYZE or NIfTI (3D or 4D) file
%
% flipped_fn - filename of the L-R flipped NIfTI file
%
% old_RGB (optional) - a scale number to tell difference of new RGB24
% from old RGB24. New RGB24 uses RGB triple sequentially for each
% voxel, like [R1 G1 B1 R2 G2 B2 ...]. Analyze 6.0 from AnalyzeDirect
% uses old RGB24, in a way like [R1 R2 ... G1 G2 ... B1 B2 ...] for
% each slices. If the image that you view is garbled, try to set
% old_RGB variable to 1 and try again, because it could be in
% old RGB24. It will be set to 0, if it is default or empty.
%
% tolerance (optional) - distortion allowed for non-orthogonal rotation
% or shearing in NIfTI affine matrix. It will be set to 0.1 (10%),
% if it is default or empty.
%
% preferredForm (optional) - selects which transformation from voxels
% to RAS coordinates; values are s,q,S,Q. Lower case s,q indicate
% "prefer sform or qform, but use others if preferred not present".
% Upper case indicate the program is forced to use the specificied
% tranform or fail loading. 'preferredForm' will be 's', if it is
% default or empty. - Jeff Gunter
%
% Example: flip_lr('avg152T1_LR_nifti.nii', 'flipped_lr.nii');
% flip_lr('avg152T1_RL_nifti.nii', 'flipped_rl.nii');
%
% You will find that 'avg152T1_LR_nifti.nii' and 'avg152T1_RL_nifti.nii'
% are the same, and 'flipped_lr.nii' and 'flipped_rl.nii' are also the
% the same, but they are L-R flipped from 'avg152T1_*'.
%
% NIFTI data format can be found on: http://nifti.nimh.nih.gov
%
% - Jimmy Shen ([email protected])
%
function flip_lr(original_fn, flipped_fn, old_RGB, tolerance, preferredForm)
if ~exist('original_fn','var') | ~exist('flipped_fn','var')
error('Usage: flip_lr(original_fn, flipped_fn, [old_RGB],[tolerance])');
end
if ~exist('old_RGB','var') | isempty(old_RGB)
old_RGB = 0;
end
if ~exist('tolerance','var') | isempty(tolerance)
tolerance = 0.1;
end
if ~exist('preferredForm','var') | isempty(preferredForm)
preferredForm= 's'; % Jeff
end
nii = load_nii(original_fn, [], [], [], [], old_RGB, tolerance, preferredForm);
M = diag(nii.hdr.dime.pixdim(2:5));
M(1:3,4) = -M(1:3,1:3)*(nii.hdr.hist.originator(1:3)-1)';
M(1,:) = -1*M(1,:);
nii.hdr.hist.sform_code = 1;
nii.hdr.hist.srow_x = M(1,:);
nii.hdr.hist.srow_y = M(2,:);
nii.hdr.hist.srow_z = M(3,:);
save_nii(nii, flipped_fn);
return; % flip_lr
|
github
|
adhusch/PaCER-master
|
save_nii.m
|
.m
|
PaCER-master/external/NIfTI_20140122/save_nii.m
| 9,404 |
utf_8
|
88aa93174482539fe993ac335fb01541
|
% Save NIFTI dataset. Support both *.nii and *.hdr/*.img file extension.
% If file extension is not provided, *.hdr/*.img will be used as default.
%
% Usage: save_nii(nii, filename, [old_RGB])
%
% nii.hdr - struct with NIFTI header fields (from load_nii.m or make_nii.m)
%
% nii.img - 3D (or 4D) matrix of NIFTI data.
%
% filename - NIFTI file name.
%
% old_RGB - an optional boolean variable to handle special RGB data
% sequence [R1 R2 ... G1 G2 ... B1 B2 ...] that is used only by
% AnalyzeDirect (Analyze Software). Since both NIfTI and Analyze
% file format use RGB triple [R1 G1 B1 R2 G2 B2 ...] sequentially
% for each voxel, this variable is set to FALSE by default. If you
% would like the saved image only to be opened by AnalyzeDirect
% Software, set old_RGB to TRUE (or 1). It will be set to 0, if it
% is default or empty.
%
% Tip: to change the data type, set nii.hdr.dime.datatype,
% and nii.hdr.dime.bitpix to:
%
% 0 None (Unknown bit per voxel) % DT_NONE, DT_UNKNOWN
% 1 Binary (ubit1, bitpix=1) % DT_BINARY
% 2 Unsigned char (uchar or uint8, bitpix=8) % DT_UINT8, NIFTI_TYPE_UINT8
% 4 Signed short (int16, bitpix=16) % DT_INT16, NIFTI_TYPE_INT16
% 8 Signed integer (int32, bitpix=32) % DT_INT32, NIFTI_TYPE_INT32
% 16 Floating point (single or float32, bitpix=32) % DT_FLOAT32, NIFTI_TYPE_FLOAT32
% 32 Complex, 2 float32 (Use float32, bitpix=64) % DT_COMPLEX64, NIFTI_TYPE_COMPLEX64
% 64 Double precision (double or float64, bitpix=64) % DT_FLOAT64, NIFTI_TYPE_FLOAT64
% 128 uint RGB (Use uint8, bitpix=24) % DT_RGB24, NIFTI_TYPE_RGB24
% 256 Signed char (schar or int8, bitpix=8) % DT_INT8, NIFTI_TYPE_INT8
% 511 Single RGB (Use float32, bitpix=96) % DT_RGB96, NIFTI_TYPE_RGB96
% 512 Unsigned short (uint16, bitpix=16) % DT_UNINT16, NIFTI_TYPE_UNINT16
% 768 Unsigned integer (uint32, bitpix=32) % DT_UNINT32, NIFTI_TYPE_UNINT32
% 1024 Signed long long (int64, bitpix=64) % DT_INT64, NIFTI_TYPE_INT64
% 1280 Unsigned long long (uint64, bitpix=64) % DT_UINT64, NIFTI_TYPE_UINT64
% 1536 Long double, float128 (Unsupported, bitpix=128) % DT_FLOAT128, NIFTI_TYPE_FLOAT128
% 1792 Complex128, 2 float64 (Use float64, bitpix=128) % DT_COMPLEX128, NIFTI_TYPE_COMPLEX128
% 2048 Complex256, 2 float128 (Unsupported, bitpix=256) % DT_COMPLEX128, NIFTI_TYPE_COMPLEX128
%
% Part of this file is copied and modified from:
% http://www.mathworks.com/matlabcentral/fileexchange/1878-mri-analyze-tools
%
% NIFTI data format can be found on: http://nifti.nimh.nih.gov
%
% - Jimmy Shen ([email protected])
% - "old_RGB" related codes in "save_nii.m" are added by Mike Harms (2006.06.28)
%
function save_nii(nii, fileprefix, old_RGB)
if ~exist('nii','var') | isempty(nii) | ~isfield(nii,'hdr') | ...
~isfield(nii,'img') | ~exist('fileprefix','var') | isempty(fileprefix)
error('Usage: save_nii(nii, filename, [old_RGB])');
end
if isfield(nii,'untouch') & nii.untouch == 1
error('Usage: please use ''save_untouch_nii.m'' for the untouched structure.');
end
if ~exist('old_RGB','var') | isempty(old_RGB)
old_RGB = 0;
end
v = version;
% Check file extension. If .gz, unpack it into temp folder
%
if length(fileprefix) > 2 & strcmp(fileprefix(end-2:end), '.gz')
if ~strcmp(fileprefix(end-6:end), '.img.gz') & ...
~strcmp(fileprefix(end-6:end), '.hdr.gz') & ...
~strcmp(fileprefix(end-6:end), '.nii.gz')
error('Please check filename.');
end
if str2num(v(1:3)) < 7.1 | ~usejava('jvm')
error('Please use MATLAB 7.1 (with java) and above, or run gunzip outside MATLAB.');
else
gzFile = 1;
fileprefix = fileprefix(1:end-3);
end
end
filetype = 1;
% Note: fileprefix is actually the filename you want to save
%
if findstr('.nii',fileprefix) & strcmp(fileprefix(end-3:end), '.nii')
filetype = 2;
fileprefix(end-3:end)='';
end
if findstr('.hdr',fileprefix) & strcmp(fileprefix(end-3:end), '.hdr')
fileprefix(end-3:end)='';
end
if findstr('.img',fileprefix) & strcmp(fileprefix(end-3:end), '.img')
fileprefix(end-3:end)='';
end
write_nii(nii, filetype, fileprefix, old_RGB);
% gzip output file if requested
%
if exist('gzFile', 'var')
if filetype == 1
gzip([fileprefix, '.img']);
delete([fileprefix, '.img']);
gzip([fileprefix, '.hdr']);
delete([fileprefix, '.hdr']);
elseif filetype == 2
gzip([fileprefix, '.nii']);
delete([fileprefix, '.nii']);
end;
end;
if filetype == 1
% So earlier versions of SPM can also open it with correct originator
%
M=[[diag(nii.hdr.dime.pixdim(2:4)) -[nii.hdr.hist.originator(1:3).*nii.hdr.dime.pixdim(2:4)]'];[0 0 0 1]];
save([fileprefix '.mat'], 'M');
end
return % save_nii
%-----------------------------------------------------------------------------------
function write_nii(nii, filetype, fileprefix, old_RGB)
hdr = nii.hdr;
if isfield(nii,'ext') & ~isempty(nii.ext)
ext = nii.ext;
[ext, esize_total] = verify_nii_ext(ext);
else
ext = [];
end
switch double(hdr.dime.datatype),
case 1,
hdr.dime.bitpix = int16(1 ); precision = 'ubit1';
case 2,
hdr.dime.bitpix = int16(8 ); precision = 'uint8';
case 4,
hdr.dime.bitpix = int16(16); precision = 'int16';
case 8,
hdr.dime.bitpix = int16(32); precision = 'int32';
case 16,
hdr.dime.bitpix = int16(32); precision = 'float32';
case 32,
hdr.dime.bitpix = int16(64); precision = 'float32';
case 64,
hdr.dime.bitpix = int16(64); precision = 'float64';
case 128,
hdr.dime.bitpix = int16(24); precision = 'uint8';
case 256
hdr.dime.bitpix = int16(8 ); precision = 'int8';
case 511,
hdr.dime.bitpix = int16(96); precision = 'float32';
case 512
hdr.dime.bitpix = int16(16); precision = 'uint16';
case 768
hdr.dime.bitpix = int16(32); precision = 'uint32';
case 1024
hdr.dime.bitpix = int16(64); precision = 'int64';
case 1280
hdr.dime.bitpix = int16(64); precision = 'uint64';
case 1792,
hdr.dime.bitpix = int16(128); precision = 'float64';
otherwise
error('This datatype is not supported');
end
hdr.dime.glmax = round(double(max(nii.img(:))));
hdr.dime.glmin = round(double(min(nii.img(:))));
if filetype == 2
fid = fopen(sprintf('%s.nii',fileprefix),'w');
if fid < 0,
msg = sprintf('Cannot open file %s.nii.',fileprefix);
error(msg);
end
hdr.dime.vox_offset = 352;
if ~isempty(ext)
hdr.dime.vox_offset = hdr.dime.vox_offset + esize_total;
end
hdr.hist.magic = 'n+1';
save_nii_hdr(hdr, fid);
if ~isempty(ext)
save_nii_ext(ext, fid);
end
else
fid = fopen(sprintf('%s.hdr',fileprefix),'w');
if fid < 0,
msg = sprintf('Cannot open file %s.hdr.',fileprefix);
error(msg);
end
hdr.dime.vox_offset = 0;
hdr.hist.magic = 'ni1';
save_nii_hdr(hdr, fid);
if ~isempty(ext)
save_nii_ext(ext, fid);
end
fclose(fid);
fid = fopen(sprintf('%s.img',fileprefix),'w');
end
ScanDim = double(hdr.dime.dim(5)); % t
SliceDim = double(hdr.dime.dim(4)); % z
RowDim = double(hdr.dime.dim(3)); % y
PixelDim = double(hdr.dime.dim(2)); % x
SliceSz = double(hdr.dime.pixdim(4));
RowSz = double(hdr.dime.pixdim(3));
PixelSz = double(hdr.dime.pixdim(2));
x = 1:PixelDim;
if filetype == 2 & isempty(ext)
skip_bytes = double(hdr.dime.vox_offset) - 348;
else
skip_bytes = 0;
end
if double(hdr.dime.datatype) == 128
% RGB planes are expected to be in the 4th dimension of nii.img
%
if(size(nii.img,4)~=3)
error(['The NII structure does not appear to have 3 RGB color planes in the 4th dimension']);
end
if old_RGB
nii.img = permute(nii.img, [1 2 4 3 5 6 7 8]);
else
nii.img = permute(nii.img, [4 1 2 3 5 6 7 8]);
end
end
if double(hdr.dime.datatype) == 511
% RGB planes are expected to be in the 4th dimension of nii.img
%
if(size(nii.img,4)~=3)
error(['The NII structure does not appear to have 3 RGB color planes in the 4th dimension']);
end
if old_RGB
nii.img = permute(nii.img, [1 2 4 3 5 6 7 8]);
else
nii.img = permute(nii.img, [4 1 2 3 5 6 7 8]);
end
end
% For complex float32 or complex float64, voxel values
% include [real, imag]
%
if hdr.dime.datatype == 32 | hdr.dime.datatype == 1792
real_img = real(nii.img(:))';
nii.img = imag(nii.img(:))';
nii.img = [real_img; nii.img];
end
if skip_bytes
fwrite(fid, zeros(1,skip_bytes), 'uint8');
end
fwrite(fid, nii.img, precision);
% fwrite(fid, nii.img, precision, skip_bytes); % error using skip
fclose(fid);
return; % write_nii
|
github
|
adhusch/PaCER-master
|
rri_file_menu.m
|
.m
|
PaCER-master/external/NIfTI_20140122/rri_file_menu.m
| 3,974 |
utf_8
|
1ec91620ceb4108dde9a63945380028f
|
% Imbed a file menu to any figure. If file menu exist, it will append
% to the existing file menu. This file menu includes: Copy to clipboard,
% print, save, close etc.
%
% Usage: rri_file_menu(fig);
%
% rri_file_menu(fig,0) means no 'Close' menu.
%
% - Jimmy Shen ([email protected])
%
%--------------------------------------------------------------------
function rri_file_menu(action, varargin)
if isnumeric(action)
fig = action;
action = 'init';
end
% clear the message line,
%
h = findobj(gcf,'Tag','MessageLine');
set(h,'String','');
if ~strcmp(action, 'init')
set(gcbf, 'InvertHardcopy','off');
% set(gcbf, 'PaperPositionMode','auto');
end
switch action
case {'init'}
if nargin > 1
init(fig, 1); % no 'close' menu
else
init(fig, 0);
end
case {'print_fig'}
printdlg(gcbf);
case {'copy_fig'}
copy_fig;
case {'export_fig'}
export_fig;
end
return % rri_file_menu
%------------------------------------------------
%
% Create (or append) File menu
%
function init(fig, no_close)
% search for file menu
%
h_file = [];
menuitems = findobj(fig, 'type', 'uimenu');
for i=1:length(menuitems)
filelabel = get(menuitems(i),'label');
if strcmpi(strrep(filelabel, '&', ''), 'file')
h_file = menuitems(i);
break;
end
end
set(fig, 'menubar', 'none');
if isempty(h_file)
if isempty(menuitems)
h_file = uimenu('parent', fig, 'label', 'File');
else
h_file = uimenu('parent', fig, 'label', 'Copy Figure');
end
h1 = uimenu('parent', h_file, ...
'callback','rri_file_menu(''copy_fig'');', ...
'label','Copy to Clipboard');
else
h1 = uimenu('parent', h_file, ...
'callback','rri_file_menu(''copy_fig'');', ...
'separator','on', ...
'label','Copy to Clipboard');
end
h2 = uimenu(h_file, ...
'callback','pagesetupdlg(gcbf);', ...
'label','Page Setup...');
h2 = uimenu(h_file, ...
'callback','printpreview(gcbf);', ...
'label','Print Preview...');
h2 = uimenu('parent', h_file, ...
'callback','printdlg(gcbf);', ...
'label','Print Figure ...');
h2 = uimenu('parent', h_file, ...
'callback','rri_file_menu(''export_fig'');', ...
'label','Save Figure ...');
arch = computer;
if ~strcmpi(arch(1:2),'PC')
set(h1, 'enable', 'off');
end
if ~no_close
h1 = uimenu('parent', h_file, ...
'callback','close(gcbf);', ...
'separator','on', ...
'label','Close');
end
return; % init
%------------------------------------------------
%
% Copy to clipboard
%
function copy_fig
arch = computer;
if(~strcmpi(arch(1:2),'PC'))
error('copy to clipboard can only be used under MS Windows');
return;
end
print -noui -dbitmap;
return % copy_fig
%------------------------------------------------
%
% Save as an image file
%
function export_fig
curr = pwd;
if isempty(curr)
curr = filesep;
end
[selected_file, selected_path] = rri_select_file(curr,'Save As');
if isempty(selected_file) | isempty(selected_path)
return;
end
filename = [selected_path selected_file];
if(exist(filename,'file')==2) % file exist
dlg_title = 'Confirm File Overwrite';
msg = ['File ',filename,' exist. Are you sure you want to overwrite it?'];
response = questdlg(msg,dlg_title,'Yes','No','Yes');
if(strcmp(response,'No'))
return;
end
end
old_pointer = get(gcbf,'pointer');
set(gcbf,'pointer','watch');
try
saveas(gcbf,filename);
catch
msg = 'ERROR: Cannot save file';
set(findobj(gcf,'Tag','MessageLine'),'String',msg);
end
set(gcbf,'pointer',old_pointer);
return; % export_fig
|
github
|
adhusch/PaCER-master
|
reslice_nii.m
|
.m
|
PaCER-master/external/NIfTI_20140122/reslice_nii.m
| 9,817 |
utf_8
|
05783cd4f127a22486db67a9cc89ad2a
|
% The basic application of the 'reslice_nii.m' program is to perform
% any 3D affine transform defined by a NIfTI format image.
%
% In addition, the 'reslice_nii.m' program can also be applied to
% generate an isotropic image from either a NIfTI format image or
% an ANALYZE format image.
%
% The resliced NIfTI file will always be in RAS orientation.
%
% This program only supports real integer or floating-point data type.
% For other data type, the program will exit with an error message
% "Transform of this NIFTI data is not supported by the program".
%
% Usage: reslice_nii(old_fn, new_fn, [voxel_size], [verbose], [bg], ...
% [method], [img_idx], [preferredForm]);
%
% old_fn - filename for original NIfTI file
%
% new_fn - filename for resliced NIfTI file
%
% voxel_size (optional) - size of a voxel in millimeter along x y z
% direction for resliced NIfTI file. 'voxel_size' will use
% the minimum voxel_size in original NIfTI header,
% if it is default or empty.
%
% verbose (optional) - 1, 0
% 1: show transforming progress in percentage
% 2: progress will not be displayed
% 'verbose' is 1 if it is default or empty.
%
% bg (optional) - background voxel intensity in any extra corner that
% is caused by 3D interpolation. 0 in most cases. 'bg'
% will be the average of two corner voxel intensities
% in original image volume, if it is default or empty.
%
% method (optional) - 1, 2, or 3
% 1: for Trilinear interpolation
% 2: for Nearest Neighbor interpolation
% 3: for Fischer's Bresenham interpolation
% 'method' is 1 if it is default or empty.
%
% img_idx (optional) - a numerical array of image volume indices. Only
% the specified volumes will be loaded. All available image
% volumes will be loaded, if it is default or empty.
%
% The number of images scans can be obtained from get_nii_frame.m,
% or simply: hdr.dime.dim(5).
%
% preferredForm (optional) - selects which transformation from voxels
% to RAS coordinates; values are s,q,S,Q. Lower case s,q indicate
% "prefer sform or qform, but use others if preferred not present".
% Upper case indicate the program is forced to use the specificied
% tranform or fail loading. 'preferredForm' will be 's', if it is
% default or empty. - Jeff Gunter
%
% NIFTI data format can be found on: http://nifti.nimh.nih.gov
%
% - Jimmy Shen ([email protected])
%
function reslice_nii(old_fn, new_fn, voxel_size, verbose, bg, method, img_idx, preferredForm)
if ~exist('old_fn','var') | ~exist('new_fn','var')
error('Usage: reslice_nii(old_fn, new_fn, [voxel_size], [verbose], [bg], [method], [img_idx])');
end
if ~exist('method','var') | isempty(method)
method = 1;
end
if ~exist('img_idx','var') | isempty(img_idx)
img_idx = [];
end
if ~exist('verbose','var') | isempty(verbose)
verbose = 1;
end
if ~exist('preferredForm','var') | isempty(preferredForm)
preferredForm= 's'; % Jeff
end
nii = load_nii_no_xform(old_fn, img_idx, 0, preferredForm);
if ~ismember(nii.hdr.dime.datatype, [2,4,8,16,64,256,512,768])
error('Transform of this NIFTI data is not supported by the program.');
end
if ~exist('voxel_size','var') | isempty(voxel_size)
voxel_size = abs(min(nii.hdr.dime.pixdim(2:4)))*ones(1,3);
elseif length(voxel_size) < 3
voxel_size = abs(voxel_size(1))*ones(1,3);
end
if ~exist('bg','var') | isempty(bg)
bg = mean([nii.img(1) nii.img(end)]);
end
old_M = nii.hdr.hist.old_affine;
if nii.hdr.dime.dim(5) > 1
for i = 1:nii.hdr.dime.dim(5)
if verbose
fprintf('Reslicing %d of %d volumes.\n', i, nii.hdr.dime.dim(5));
end
[img(:,:,:,i) M] = ...
affine(nii.img(:,:,:,i), old_M, voxel_size, verbose, bg, method);
end
else
[img M] = affine(nii.img, old_M, voxel_size, verbose, bg, method);
end
new_dim = size(img);
nii.img = img;
nii.hdr.dime.dim(2:4) = new_dim(1:3);
nii.hdr.dime.datatype = 16;
nii.hdr.dime.bitpix = 32;
nii.hdr.dime.pixdim(2:4) = voxel_size(:)';
nii.hdr.dime.glmax = max(img(:));
nii.hdr.dime.glmin = min(img(:));
nii.hdr.hist.qform_code = 0;
nii.hdr.hist.sform_code = 1;
nii.hdr.hist.srow_x = M(1,:);
nii.hdr.hist.srow_y = M(2,:);
nii.hdr.hist.srow_z = M(3,:);
nii.hdr.hist.new_affine = M;
save_nii(nii, new_fn);
return; % reslice_nii
%--------------------------------------------------------------------
function [nii] = load_nii_no_xform(filename, img_idx, old_RGB, preferredForm)
if ~exist('filename','var'),
error('Usage: [nii] = load_nii(filename, [img_idx], [old_RGB])');
end
if ~exist('img_idx','var'), img_idx = []; end
if ~exist('old_RGB','var'), old_RGB = 0; end
if ~exist('preferredForm','var'), preferredForm= 's'; end % Jeff
v = version;
% Check file extension. If .gz, unpack it into temp folder
%
if length(filename) > 2 & strcmp(filename(end-2:end), '.gz')
if ~strcmp(filename(end-6:end), '.img.gz') & ...
~strcmp(filename(end-6:end), '.hdr.gz') & ...
~strcmp(filename(end-6:end), '.nii.gz')
error('Please check filename.');
end
if str2num(v(1:3)) < 7.1 | ~usejava('jvm')
error('Please use MATLAB 7.1 (with java) and above, or run gunzip outside MATLAB.');
elseif strcmp(filename(end-6:end), '.img.gz')
filename1 = filename;
filename2 = filename;
filename2(end-6:end) = '';
filename2 = [filename2, '.hdr.gz'];
tmpDir = tempname;
mkdir(tmpDir);
gzFileName = filename;
filename1 = gunzip(filename1, tmpDir);
filename2 = gunzip(filename2, tmpDir);
filename = char(filename1); % convert from cell to string
elseif strcmp(filename(end-6:end), '.hdr.gz')
filename1 = filename;
filename2 = filename;
filename2(end-6:end) = '';
filename2 = [filename2, '.img.gz'];
tmpDir = tempname;
mkdir(tmpDir);
gzFileName = filename;
filename1 = gunzip(filename1, tmpDir);
filename2 = gunzip(filename2, tmpDir);
filename = char(filename1); % convert from cell to string
elseif strcmp(filename(end-6:end), '.nii.gz')
tmpDir = tempname;
mkdir(tmpDir);
gzFileName = filename;
filename = gunzip(filename, tmpDir);
filename = char(filename); % convert from cell to string
end
end
% Read the dataset header
%
[nii.hdr,nii.filetype,nii.fileprefix,nii.machine] = load_nii_hdr(filename);
% Read the header extension
%
% nii.ext = load_nii_ext(filename);
% Read the dataset body
%
[nii.img,nii.hdr] = ...
load_nii_img(nii.hdr,nii.filetype,nii.fileprefix,nii.machine,img_idx,'','','',old_RGB);
% Perform some of sform/qform transform
%
% nii = xform_nii(nii, preferredForm);
% Clean up after gunzip
%
if exist('gzFileName', 'var')
% fix fileprefix so it doesn't point to temp location
%
nii.fileprefix = gzFileName(1:end-7);
rmdir(tmpDir,'s');
end
hdr = nii.hdr;
% NIFTI can have both sform and qform transform. This program
% will check sform_code prior to qform_code by default.
%
% If user specifys "preferredForm", user can then choose the
% priority. - Jeff
%
useForm=[]; % Jeff
if isequal(preferredForm,'S')
if isequal(hdr.hist.sform_code,0)
error('User requires sform, sform not set in header');
else
useForm='s';
end
end % Jeff
if isequal(preferredForm,'Q')
if isequal(hdr.hist.qform_code,0)
error('User requires sform, sform not set in header');
else
useForm='q';
end
end % Jeff
if isequal(preferredForm,'s')
if hdr.hist.sform_code > 0
useForm='s';
elseif hdr.hist.qform_code > 0
useForm='q';
end
end % Jeff
if isequal(preferredForm,'q')
if hdr.hist.qform_code > 0
useForm='q';
elseif hdr.hist.sform_code > 0
useForm='s';
end
end % Jeff
if isequal(useForm,'s')
R = [hdr.hist.srow_x(1:3)
hdr.hist.srow_y(1:3)
hdr.hist.srow_z(1:3)];
T = [hdr.hist.srow_x(4)
hdr.hist.srow_y(4)
hdr.hist.srow_z(4)];
nii.hdr.hist.old_affine = [ [R;[0 0 0]] [T;1] ];
elseif isequal(useForm,'q')
b = hdr.hist.quatern_b;
c = hdr.hist.quatern_c;
d = hdr.hist.quatern_d;
if 1.0-(b*b+c*c+d*d) < 0
if abs(1.0-(b*b+c*c+d*d)) < 1e-5
a = 0;
else
error('Incorrect quaternion values in this NIFTI data.');
end
else
a = sqrt(1.0-(b*b+c*c+d*d));
end
qfac = hdr.dime.pixdim(1);
i = hdr.dime.pixdim(2);
j = hdr.dime.pixdim(3);
k = qfac * hdr.dime.pixdim(4);
R = [a*a+b*b-c*c-d*d 2*b*c-2*a*d 2*b*d+2*a*c
2*b*c+2*a*d a*a+c*c-b*b-d*d 2*c*d-2*a*b
2*b*d-2*a*c 2*c*d+2*a*b a*a+d*d-c*c-b*b];
T = [hdr.hist.qoffset_x
hdr.hist.qoffset_y
hdr.hist.qoffset_z];
nii.hdr.hist.old_affine = [ [R * diag([i j k]);[0 0 0]] [T;1] ];
elseif nii.filetype == 0 & exist([nii.fileprefix '.mat'],'file')
load([nii.fileprefix '.mat']); % old SPM affine matrix
R=M(1:3,1:3);
T=M(1:3,4);
T=R*ones(3,1)+T;
M(1:3,4)=T;
nii.hdr.hist.old_affine = M;
else
M = diag(hdr.dime.pixdim(2:5));
M(1:3,4) = -M(1:3,1:3)*(hdr.hist.originator(1:3)-1)';
M(4,4) = 1;
nii.hdr.hist.old_affine = M;
end
return % load_nii_no_xform
|
github
|
adhusch/PaCER-master
|
save_untouch_nii.m
|
.m
|
PaCER-master/external/NIfTI_20140122/save_untouch_nii.m
| 6,494 |
utf_8
|
50fa95cbb847654356241a853328f912
|
% Save NIFTI or ANALYZE dataset that is loaded by "load_untouch_nii.m".
% The output image format and file extension will be the same as the
% input one (NIFTI.nii, NIFTI.img or ANALYZE.img). Therefore, any file
% extension that you specified will be ignored.
%
% Usage: save_untouch_nii(nii, filename)
%
% nii - nii structure that is loaded by "load_untouch_nii.m"
%
% filename - NIFTI or ANALYZE file name.
%
% - Jimmy Shen ([email protected])
%
function save_untouch_nii(nii, filename)
if ~exist('nii','var') | isempty(nii) | ~isfield(nii,'hdr') | ...
~isfield(nii,'img') | ~exist('filename','var') | isempty(filename)
error('Usage: save_untouch_nii(nii, filename)');
end
if ~isfield(nii,'untouch') | nii.untouch == 0
error('Usage: please use ''save_nii.m'' for the modified structure.');
end
if isfield(nii.hdr.hist,'magic') & strcmp(nii.hdr.hist.magic(1:3),'ni1')
filetype = 1;
elseif isfield(nii.hdr.hist,'magic') & strcmp(nii.hdr.hist.magic(1:3),'n+1')
filetype = 2;
else
filetype = 0;
end
v = version;
% Check file extension. If .gz, unpack it into temp folder
%
if length(filename) > 2 & strcmp(filename(end-2:end), '.gz')
if ~strcmp(filename(end-6:end), '.img.gz') & ...
~strcmp(filename(end-6:end), '.hdr.gz') & ...
~strcmp(filename(end-6:end), '.nii.gz')
error('Please check filename.');
end
if str2num(v(1:3)) < 7.1 | ~usejava('jvm')
error('Please use MATLAB 7.1 (with java) and above, or run gunzip outside MATLAB.');
else
gzFile = 1;
filename = filename(1:end-3);
end
end
[p,f] = fileparts(filename);
fileprefix = fullfile(p, f);
write_nii(nii, filetype, fileprefix);
% gzip output file if requested
%
if exist('gzFile', 'var')
if filetype == 1
gzip([fileprefix, '.img']);
delete([fileprefix, '.img']);
gzip([fileprefix, '.hdr']);
delete([fileprefix, '.hdr']);
elseif filetype == 2
gzip([fileprefix, '.nii']);
delete([fileprefix, '.nii']);
end;
end;
% % So earlier versions of SPM can also open it with correct originator
% %
% if filetype == 0
% M=[[diag(nii.hdr.dime.pixdim(2:4)) -[nii.hdr.hist.originator(1:3).*nii.hdr.dime.pixdim(2:4)]'];[0 0 0 1]];
% save(fileprefix, 'M');
% elseif filetype == 1
% M=[];
% save(fileprefix, 'M');
%end
return % save_untouch_nii
%-----------------------------------------------------------------------------------
function write_nii(nii, filetype, fileprefix)
hdr = nii.hdr;
if isfield(nii,'ext') & ~isempty(nii.ext)
ext = nii.ext;
[ext, esize_total] = verify_nii_ext(ext);
else
ext = [];
end
switch double(hdr.dime.datatype),
case 1,
hdr.dime.bitpix = int16(1 ); precision = 'ubit1';
case 2,
hdr.dime.bitpix = int16(8 ); precision = 'uint8';
case 4,
hdr.dime.bitpix = int16(16); precision = 'int16';
case 8,
hdr.dime.bitpix = int16(32); precision = 'int32';
case 16,
hdr.dime.bitpix = int16(32); precision = 'float32';
case 32,
hdr.dime.bitpix = int16(64); precision = 'float32';
case 64,
hdr.dime.bitpix = int16(64); precision = 'float64';
case 128,
hdr.dime.bitpix = int16(24); precision = 'uint8';
case 256
hdr.dime.bitpix = int16(8 ); precision = 'int8';
case 512
hdr.dime.bitpix = int16(16); precision = 'uint16';
case 768
hdr.dime.bitpix = int16(32); precision = 'uint32';
case 1024
hdr.dime.bitpix = int16(64); precision = 'int64';
case 1280
hdr.dime.bitpix = int16(64); precision = 'uint64';
case 1792,
hdr.dime.bitpix = int16(128); precision = 'float64';
otherwise
error('This datatype is not supported');
end
% hdr.dime.glmax = round(double(max(nii.img(:))));
% hdr.dime.glmin = round(double(min(nii.img(:))));
if filetype == 2
fid = fopen(sprintf('%s.nii',fileprefix),'w');
if fid < 0,
msg = sprintf('Cannot open file %s.nii.',fileprefix);
error(msg);
end
hdr.dime.vox_offset = 352;
if ~isempty(ext)
hdr.dime.vox_offset = hdr.dime.vox_offset + esize_total;
end
hdr.hist.magic = 'n+1';
save_untouch_nii_hdr(hdr, fid);
if ~isempty(ext)
save_nii_ext(ext, fid);
end
elseif filetype == 1
fid = fopen(sprintf('%s.hdr',fileprefix),'w');
if fid < 0,
msg = sprintf('Cannot open file %s.hdr.',fileprefix);
error(msg);
end
hdr.dime.vox_offset = 0;
hdr.hist.magic = 'ni1';
save_untouch_nii_hdr(hdr, fid);
if ~isempty(ext)
save_nii_ext(ext, fid);
end
fclose(fid);
fid = fopen(sprintf('%s.img',fileprefix),'w');
else
fid = fopen(sprintf('%s.hdr',fileprefix),'w');
if fid < 0,
msg = sprintf('Cannot open file %s.hdr.',fileprefix);
error(msg);
end
save_untouch0_nii_hdr(hdr, fid);
fclose(fid);
fid = fopen(sprintf('%s.img',fileprefix),'w');
end
ScanDim = double(hdr.dime.dim(5)); % t
SliceDim = double(hdr.dime.dim(4)); % z
RowDim = double(hdr.dime.dim(3)); % y
PixelDim = double(hdr.dime.dim(2)); % x
SliceSz = double(hdr.dime.pixdim(4));
RowSz = double(hdr.dime.pixdim(3));
PixelSz = double(hdr.dime.pixdim(2));
x = 1:PixelDim;
if filetype == 2 & isempty(ext)
skip_bytes = double(hdr.dime.vox_offset) - 348;
else
skip_bytes = 0;
end
if double(hdr.dime.datatype) == 128
% RGB planes are expected to be in the 4th dimension of nii.img
%
if(size(nii.img,4)~=3)
error(['The NII structure does not appear to have 3 RGB color planes in the 4th dimension']);
end
nii.img = permute(nii.img, [4 1 2 3 5 6 7 8]);
end
% For complex float32 or complex float64, voxel values
% include [real, imag]
%
if hdr.dime.datatype == 32 | hdr.dime.datatype == 1792
real_img = real(nii.img(:))';
nii.img = imag(nii.img(:))';
nii.img = [real_img; nii.img];
end
if skip_bytes
fwrite(fid, zeros(1,skip_bytes), 'uint8');
end
fwrite(fid, nii.img, precision);
% fwrite(fid, nii.img, precision, skip_bytes); % error using skip
fclose(fid);
return; % write_nii
|
github
|
adhusch/PaCER-master
|
view_nii.m
|
.m
|
PaCER-master/external/NIfTI_20140122/view_nii.m
| 139,608 |
utf_8
|
74f9dea7539a45a7993beb22becf2fa2
|
% VIEW_NII: Create or update a 3-View (Front, Top, Side) of the
% brain data that is specified by nii structure
%
% Usage: status = view_nii([h], nii, [option]) or
% status = view_nii(h, [option])
%
% Where, h is the figure on which the 3-View will be plotted;
% nii is the brain data in NIFTI format;
% option is a struct that configures the view plotted, can be:
%
% option.command = 'init'
% option.command = 'update'
% option.command = 'clearnii'
% option.command = 'updatenii'
% option.command = 'updateimg' (nii is nii.img here)
%
% option.usecolorbar = 0 | [1]
% option.usepanel = 0 | [1]
% option.usecrosshair = 0 | [1]
% option.usestretch = 0 | [1]
% option.useimagesc = 0 | [1]
% option.useinterp = [0] | 1
%
% option.setarea = [x y w h] | [0.05 0.05 0.9 0.9]
% option.setunit = ['vox'] | 'mm'
% option.setviewpoint = [x y z] | [origin]
% option.setscanid = [t] | [1]
% option.setcrosshaircolor = [r g b] | [1 0 0]
% option.setcolorindex = From 1 to 9 (default is 2 or 3)
% option.setcolormap = (Mx3 matrix, 0 <= val <= 1)
% option.setcolorlevel = No more than 256 (default 256)
% option.sethighcolor = []
% option.setcbarminmax = []
% option.setvalue = []
% option.glblocminmax = []
% option.setbuttondown = ''
% option.setcomplex = [0] | 1 | 2
%
% Options description in detail:
% ==============================
%
% 1. command: A char string that can control program.
%
% init: If option.command='init', the program will display
% a 3-View plot on the figure specified by figure h
% or on a new figure. If there is already a 3-View
% plot on the figure, please use option.command =
% 'updatenii' (see detail below); otherwise, the
% new 3-View plot will superimpose on the old one.
% If there is no option provided, the program will
% assume that this is an initial plot. If the figure
% handle is omitted, the program knows that it is
% an initial plot.
%
% update: If there is no command specified, and a figure
% handle of the existing 3-View plot is provided,
% the program will choose option.command='update'
% to update the 3-View plot with some new option
% items.
%
% clearnii: Clear 3-View plot on specific figure
%
% updatenii: If a new nii is going to be loaded on a fig
% that has already 3-View plot on it, use this
% command to clear existing 3-View plot, and then
% display with new nii. So, the new nii will not
% superimpose on the existing one. All options
% for 'init' can be used for 'updatenii'.
%
% updateimg: If a new 3D matrix with the same dimension
% is going to be loaded, option.command='updateimg'
% can be used as a light-weighted 'updatenii, since
% it only updates the 3 slices with new values.
% inputing argument nii should be a 3D matrix
% (nii.img) instead of nii struct. No other option
% should be used together with 'updateimg' to keep
% this command as simple as possible.
%
%
% 2. usecolorbar: If specified and usecolorbar=0, the program
% will not include the colorbar in plot area; otherwise,
% a colorbar will be included in plot area.
%
% 3. usepanel: If specified and usepanel=0, the control panel
% at lower right cornor will be invisible; otherwise,
% it will be visible.
%
% 4. usecrosshair: If specified and usecrosshair=0, the crosshair
% will be invisible; otherwise, it will be visible.
%
% 5. usestretch: If specified and usestretch=0, the 3 slices will
% not be stretched, and will be displayed according to
% the actual voxel size; otherwise, the 3 slices will be
% stretched to the edge.
%
% 6. useimagesc: If specified and useimagesc=0, images data will
% be used directly to match the colormap (like 'image'
% command); otherwise, image data will be scaled to full
% colormap with 'imagesc' command in Matlab.
%
% 7. useinterp: If specified and useinterp=1, the image will be
% displayed using interpolation. Otherwise, it will be
% displayed like mosaic, and each tile stands for a
% pixel. This option does not apply to 'setvalue' option
% is set.
%
%
% 8. setarea: 3-View plot will be displayed on this specific
% region. If it is not specified, program will set the
% plot area to [0.05 0.05 0.9 0.9].
%
% 9. setunit: It can be specified to setunit='voxel' or 'mm'
% and the view will change the axes unit of [X Y Z]
% accordingly.
%
% 10. setviewpoint: If specified, [X Y Z] values will be used
% to set the viewpoint of 3-View plot.
%
% 11. setscanid: If specified, [t] value will be used to display
% the specified image scan in NIFTI data.
%
% 12. setcrosshaircolor: If specified, [r g b] value will be used
% for Crosshair Color. Otherwise, red will be the default.
%
% 13. setcolorindex: If specified, the 3-View will choose the
% following colormap: 2 - Bipolar; 3 - Gray; 4 - Jet;
% 5 - Cool; 6 - Bone; 7 - Hot; 8 - Copper; 9 - Pink;
% If not specified, it will choose 3 - Gray if all data
% values are not less than 0; otherwise, it will choose
% 2 - Bipolar if there is value less than 0. (Contrast
% control can only apply to 3 - Gray colormap.
%
% 14. setcolormap: 3-View plot will use it as a customized colormap.
% It is a 3-column matrix with value between 0 and 1. If
% using MS-Windows version of Matlab, the number of rows
% can not be more than 256, because of Matlab limitation.
% When colormap is used, setcolorlevel option will be
% disabled automatically.
%
% 15. setcolorlevel: If specified (must be no more than 256, and
% cannot be used for customized colormap), row number of
% colormap will be squeezed down to this level; otherwise,
% it will assume that setcolorlevel=256.
%
% 16. sethighcolor: If specified, program will squeeze down the
% colormap, and allocate sethighcolor (an Mx3 matrix)
% to high-end portion of the colormap. The sum of M and
% setcolorlevel should be less than 256. If setcolormap
% option is used, sethighcolor will be inserted on top
% of the setcolormap, and the setcolorlevel option will
% be disabled automatically.
%
% 17. setcbarminmax: if specified, the [min max] will be used to
% set the min and max of the colorbar, which does not
% include any data for highcolor.
%
% 18. setvalue: If specified, setvalue.val (with the same size as
% the source data on solution points) in the source area
% setvalue.idx will be superimposed on the current nii
% image. So, the size of setvalue.val should be equal to
% the size of setvalue.idx. To use this feature, it needs
% single or double nii structure for background image.
%
% 19. glblocminmax: If specified, pgm will use glblocminmax to
% calculate the colormap, instead of minmax of image.
%
% 20. setbuttondown: If specified, pgm will evaluate the command
% after a click or slide action is invoked to the new
% view point.
%
% 21. setcomplex: This option will decide how complex data to be
% displayed: 0 - Real part of complex data; 1 - Imaginary
% part of complex data; 2 - Modulus (magnitude) of complex
% data; If not specified, it will be set to 0 (Real part
% of complex data as default option. This option only apply
% when option.command is set to 'init or 'updatenii'.
%
%
% Additional Options for 'update' command:
% =======================================
%
% option.enablecursormove = [1] | 0
% option.enableviewpoint = 0 | [1]
% option.enableorigin = 0 | [1]
% option.enableunit = 0 | [1]
% option.enablecrosshair = 0 | [1]
% option.enablehistogram = 0 | [1]
% option.enablecolormap = 0 | [1]
% option.enablecontrast = 0 | [1]
% option.enablebrightness = 0 | [1]
% option.enableslider = 0 | [1]
% option.enabledirlabel = 0 | [1]
%
%
% e.g.:
% nii = load_nii('T1'); % T1.img/hdr
% view_nii(nii);
%
% or
%
% h = figure('unit','normal','pos', [0.18 0.08 0.64 0.85]);
% opt.setarea = [0.05 0.05 0.9 0.9];
% view_nii(h, nii, opt);
%
%
% Part of this file is copied and modified from:
% http://www.mathworks.com/matlabcentral/fileexchange/1878-mri-analyze-tools
%
% NIFTI data format can be found on: http://nifti.nimh.nih.gov
%
% - Jimmy Shen ([email protected])
%
function status = view_nii(varargin)
if nargin < 1
error('Please check inputs using ''help view_nii''');
end;
nii = '';
opt = '';
command = '';
usecolorbar = [];
usepanel = [];
usecrosshair = '';
usestretch = [];
useimagesc = [];
useinterp = [];
setarea = [];
setunit = '';
setviewpoint = [];
setscanid = [];
setcrosshaircolor = [];
setcolorindex = '';
setcolormap = 'NA';
setcolorlevel = [];
sethighcolor = 'NA';
setcbarminmax = [];
setvalue = [];
glblocminmax = [];
setbuttondown = '';
setcomplex = 0;
status = [];
if ishandle(varargin{1}) % plot on top of this figure
fig = varargin{1};
if nargin < 2
command = 'update'; % just to get 3-View status
end
if nargin == 2
if ~isstruct(varargin{2})
error('2nd parameter should be either nii struct or option struct');
end
opt = varargin{2};
if isfield(opt,'hdr') & isfield(opt,'img')
nii = opt;
elseif isfield(opt, 'command') & (strcmpi(opt.command,'init') ...
| strcmpi(opt.command,'updatenii') ...
| strcmpi(opt.command,'updateimg') )
error('Option here cannot contain "init", "updatenii", or "updateimg" comand');
end
end
if nargin == 3
nii = varargin{2};
opt = varargin{3};
if ~isstruct(opt)
error('3rd parameter should be option struct');
end
if ~isfield(opt,'command') | ~strcmpi(opt.command,'updateimg')
if ~isstruct(nii) | ~isfield(nii,'hdr') | ~isfield(nii,'img')
error('2nd parameter should be nii struct');
end
if isfield(nii,'untouch') & nii.untouch == 1
error('Usage: please use ''load_nii.m'' to load the structure.');
end
end
end
set(fig, 'menubar', 'none');
elseif ischar(varargin{1}) % call back by event
command = lower(varargin{1});
fig = gcbf;
else % start nii with a new figure
nii = varargin{1};
if ~isstruct(nii) | ~isfield(nii,'hdr') | ~isfield(nii,'img')
error('1st parameter should be either a figure handle or nii struct');
end
if isfield(nii,'untouch') & nii.untouch == 1
error('Usage: please use ''load_nii.m'' to load the structure.');
end
if nargin > 1
opt = varargin{2};
if isfield(opt, 'command') & ~strcmpi(opt.command,'init')
error('Option here must use "init" comand');
end
end
command = 'init';
fig = figure('unit','normal','position',[0.15 0.08 0.70 0.85]);
view_nii_menu(fig);
rri_file_menu(fig);
end
if ~isempty(opt)
if isfield(opt,'command')
command = lower(opt.command);
end
if isempty(command)
command = 'update';
end
if isfield(opt,'usecolorbar')
usecolorbar = opt.usecolorbar;
end
if isfield(opt,'usepanel')
usepanel = opt.usepanel;
end
if isfield(opt,'usecrosshair')
usecrosshair = opt.usecrosshair;
end
if isfield(opt,'usestretch')
usestretch = opt.usestretch;
end
if isfield(opt,'useimagesc')
useimagesc = opt.useimagesc;
end
if isfield(opt,'useinterp')
useinterp = opt.useinterp;
end
if isfield(opt,'setarea')
setarea = opt.setarea;
end
if isfield(opt,'setunit')
setunit = opt.setunit;
end
if isfield(opt,'setviewpoint')
setviewpoint = opt.setviewpoint;
end
if isfield(opt,'setscanid')
setscanid = opt.setscanid;
end
if isfield(opt,'setcrosshaircolor')
setcrosshaircolor = opt.setcrosshaircolor;
if ~isempty(setcrosshaircolor) & (~isnumeric(setcrosshaircolor) | ~isequal(size(setcrosshaircolor),[1 3]) | min(setcrosshaircolor(:))<0 | max(setcrosshaircolor(:))>1)
error('Crosshair Color should be a 1x3 matrix with value between 0 and 1');
end
end
if isfield(opt,'setcolorindex')
setcolorindex = round(opt.setcolorindex);
if ~isnumeric(setcolorindex) | setcolorindex < 1 | setcolorindex > 9
error('Colorindex should be a number between 1 and 9');
end
end
if isfield(opt,'setcolormap')
setcolormap = opt.setcolormap;
if ~isempty(setcolormap) & (~isnumeric(setcolormap) | size(setcolormap,2) ~= 3 | min(setcolormap(:))<0 | max(setcolormap(:))>1)
error('Colormap should be a Mx3 matrix with value between 0 and 1');
end
end
if isfield(opt,'setcolorlevel')
setcolorlevel = round(opt.setcolorlevel);
if ~isnumeric(setcolorlevel) | setcolorlevel > 256 | setcolorlevel < 1
error('Colorlevel should be a number between 1 and 256');
end
end
if isfield(opt,'sethighcolor')
sethighcolor = opt.sethighcolor;
if ~isempty(sethighcolor) & (~isnumeric(sethighcolor) | size(sethighcolor,2) ~= 3 | min(sethighcolor(:))<0 | max(sethighcolor(:))>1)
error('Highcolor should be a Mx3 matrix with value between 0 and 1');
end
end
if isfield(opt,'setcbarminmax')
setcbarminmax = opt.setcbarminmax;
if isempty(setcbarminmax) | ~isnumeric(setcbarminmax) | length(setcbarminmax) ~= 2
error('Colorbar MinMax should contain 2 values: [min max]');
end
end
if isfield(opt,'setvalue')
setvalue = opt.setvalue;
if isempty(setvalue) | ~isstruct(setvalue) | ...
~isfield(opt.setvalue,'idx') | ~isfield(opt.setvalue,'val')
error('setvalue should be a struct contains idx and val');
end
if length(opt.setvalue.idx(:)) ~= length(opt.setvalue.val(:))
error('length of idx and val fields should be the same');
end
if ~strcmpi(class(opt.setvalue.idx),'single')
opt.setvalue.idx = single(opt.setvalue.idx);
end
if ~strcmpi(class(opt.setvalue.val),'single')
opt.setvalue.val = single(opt.setvalue.val);
end
end
if isfield(opt,'glblocminmax')
glblocminmax = opt.glblocminmax;
end
if isfield(opt,'setbuttondown')
setbuttondown = opt.setbuttondown;
end
if isfield(opt,'setcomplex')
setcomplex = opt.setcomplex;
end
end
switch command
case {'init'}
set(fig, 'InvertHardcopy','off');
set(fig, 'PaperPositionMode','auto');
fig = init(nii, fig, setarea, setunit, setviewpoint, setscanid, setbuttondown, ...
setcolorindex, setcolormap, setcolorlevel, sethighcolor, setcbarminmax, ...
usecolorbar, usepanel, usecrosshair, usestretch, useimagesc, useinterp, ...
setvalue, glblocminmax, setcrosshaircolor, setcomplex);
% get status
%
status = get_status(fig);
case {'update'}
nii_view = getappdata(fig,'nii_view');
h = fig;
if isempty(nii_view)
error('The figure should already contain a 3-View plot.');
end
if ~isempty(opt)
% Order of the following update matters.
%
update_shape(h, setarea, usecolorbar, usestretch, useimagesc);
update_useinterp(h, useinterp);
update_useimagesc(h, useimagesc);
update_usepanel(h, usepanel);
update_colorindex(h, setcolorindex);
update_colormap(h, setcolormap);
update_highcolor(h, sethighcolor, setcolorlevel);
update_cbarminmax(h, setcbarminmax);
update_unit(h, setunit);
update_viewpoint(h, setviewpoint);
update_scanid(h, setscanid);
update_buttondown(h, setbuttondown);
update_crosshaircolor(h, setcrosshaircolor);
update_usecrosshair(h, usecrosshair);
% Enable/Disable object
%
update_enable(h, opt);
end
% get status
%
status = get_status(h);
case {'updateimg'}
if ~exist('nii','var')
msg = sprintf('Please input a 3D matrix brain data');
error(msg);
end
% Note: nii is not nii, nii should be a 3D matrix here
%
if ~isnumeric(nii)
msg = sprintf('2nd parameter should be a 3D matrix, not nii struct');
error(msg);
end
nii_view = getappdata(fig,'nii_view');
if isempty(nii_view)
error('The figure should already contain a 3-View plot.');
end
img = nii;
update_img(img, fig, opt);
% get status
%
status = get_status(fig);
case {'updatenii'}
nii_view = getappdata(fig,'nii_view');
if isempty(nii_view)
error('The figure should already contain a 3-View plot.');
end
if ~isstruct(nii) | ~isfield(nii,'hdr') | ~isfield(nii,'img')
error('2nd parameter should be nii struct');
end
if isfield(nii,'untouch') & nii.untouch == 1
error('Usage: please use ''load_nii.m'' to load the structure.');
end
opt.command = 'clearnii';
view_nii(fig, opt);
opt.command = 'init';
view_nii(fig, nii, opt);
% get status
%
status = get_status(fig);
case {'clearnii'}
nii_view = getappdata(fig,'nii_view');
handles = struct2cell(nii_view.handles);
for i=1:length(handles)
if ishandle(handles{i}) % in case already del by parent
delete(handles{i});
end
end
rmappdata(fig,'nii_view');
buttonmotion = get(fig,'windowbuttonmotion');
mymotion = '; view_nii(''move_cursor'');';
buttonmotion = strrep(buttonmotion, mymotion, '');
set(fig, 'windowbuttonmotion', buttonmotion);
case {'axial_image','coronal_image','sagittal_image'}
switch command
case 'axial_image', view = 'axi'; axi = 0; cor = 1; sag = 1;
case 'coronal_image', view = 'cor'; axi = 1; cor = 0; sag = 1;
case 'sagittal_image', view = 'sag'; axi = 1; cor = 1; sag = 0;
end
nii_view = getappdata(fig,'nii_view');
nii_view = get_slice_position(nii_view,view);
if isfield(nii_view, 'disp')
img = nii_view.disp;
else
img = nii_view.nii.img;
end
% CData must be double() for Matlab 6.5 for Windows
%
if axi,
if isfield(nii_view.handles,'axial_bg') & ~isempty(nii_view.handles.axial_bg) & nii_view.useinterp
Saxi = squeeze(nii_view.bgimg(:,:,nii_view.slices.axi));
set(nii_view.handles.axial_bg,'CData',double(Saxi)');
end
if isfield(nii_view.handles,'axial_image'),
if nii_view.nii.hdr.dime.datatype == 128 | nii_view.nii.hdr.dime.datatype == 511
Saxi = squeeze(img(:,:,nii_view.slices.axi,:,nii_view.scanid));
Saxi = permute(Saxi, [2 1 3]);
else
Saxi = squeeze(img(:,:,nii_view.slices.axi,nii_view.scanid));
Saxi = Saxi';
end
set(nii_view.handles.axial_image,'CData',double(Saxi));
end
if isfield(nii_view.handles,'axial_slider'),
set(nii_view.handles.axial_slider,'Value',nii_view.slices.axi);
end;
end
if cor,
if isfield(nii_view.handles,'coronal_bg') & ~isempty(nii_view.handles.coronal_bg) & nii_view.useinterp
Scor = squeeze(nii_view.bgimg(:,nii_view.slices.cor,:));
set(nii_view.handles.coronal_bg,'CData',double(Scor)');
end
if isfield(nii_view.handles,'coronal_image'),
if nii_view.nii.hdr.dime.datatype == 128 | nii_view.nii.hdr.dime.datatype == 511
Scor = squeeze(img(:,nii_view.slices.cor,:,:,nii_view.scanid));
Scor = permute(Scor, [2 1 3]);
else
Scor = squeeze(img(:,nii_view.slices.cor,:,nii_view.scanid));
Scor = Scor';
end
set(nii_view.handles.coronal_image,'CData',double(Scor));
end
if isfield(nii_view.handles,'coronal_slider'),
slider_val = nii_view.dims(2) - nii_view.slices.cor + 1;
set(nii_view.handles.coronal_slider,'Value',slider_val);
end;
end;
if sag,
if isfield(nii_view.handles,'sagittal_bg') & ~isempty(nii_view.handles.sagittal_bg) & nii_view.useinterp
Ssag = squeeze(nii_view.bgimg(nii_view.slices.sag,:,:));
set(nii_view.handles.sagittal_bg,'CData',double(Ssag)');
end
if isfield(nii_view.handles,'sagittal_image'),
if nii_view.nii.hdr.dime.datatype == 128 | nii_view.nii.hdr.dime.datatype == 511
Ssag = squeeze(img(nii_view.slices.sag,:,:,:,nii_view.scanid));
Ssag = permute(Ssag, [2 1 3]);
else
Ssag = squeeze(img(nii_view.slices.sag,:,:,nii_view.scanid));
Ssag = Ssag';
end
set(nii_view.handles.sagittal_image,'CData',double(Ssag));
end
if isfield(nii_view.handles,'sagittal_slider'),
set(nii_view.handles.sagittal_slider,'Value',nii_view.slices.sag);
end;
end;
update_nii_view(nii_view);
if ~isempty(nii_view.buttondown)
eval(nii_view.buttondown);
end
case {'axial_slider','coronal_slider','sagittal_slider'},
switch command
case 'axial_slider', view = 'axi'; axi = 1; cor = 0; sag = 0;
case 'coronal_slider', view = 'cor'; axi = 0; cor = 1; sag = 0;
case 'sagittal_slider', view = 'sag'; axi = 0; cor = 0; sag = 1;
end
nii_view = getappdata(fig,'nii_view');
nii_view = get_slider_position(nii_view);
if isfield(nii_view, 'disp')
img = nii_view.disp;
else
img = nii_view.nii.img;
end
if axi,
if isfield(nii_view.handles,'axial_bg') & ~isempty(nii_view.handles.axial_bg) & nii_view.useinterp
Saxi = squeeze(nii_view.bgimg(:,:,nii_view.slices.axi));
set(nii_view.handles.axial_bg,'CData',double(Saxi)');
end
if isfield(nii_view.handles,'axial_image'),
if nii_view.nii.hdr.dime.datatype == 128 | nii_view.nii.hdr.dime.datatype == 511
Saxi = squeeze(img(:,:,nii_view.slices.axi,:,nii_view.scanid));
Saxi = permute(Saxi, [2 1 3]);
else
Saxi = squeeze(img(:,:,nii_view.slices.axi,nii_view.scanid));
Saxi = Saxi';
end
set(nii_view.handles.axial_image,'CData',double(Saxi));
end
if isfield(nii_view.handles,'axial_slider'),
set(nii_view.handles.axial_slider,'Value',nii_view.slices.axi);
end
end
if cor,
if isfield(nii_view.handles,'coronal_bg') & ~isempty(nii_view.handles.coronal_bg) & nii_view.useinterp
Scor = squeeze(nii_view.bgimg(:,nii_view.slices.cor,:));
set(nii_view.handles.coronal_bg,'CData',double(Scor)');
end
if isfield(nii_view.handles,'coronal_image'),
if nii_view.nii.hdr.dime.datatype == 128 | nii_view.nii.hdr.dime.datatype == 511
Scor = squeeze(img(:,nii_view.slices.cor,:,:,nii_view.scanid));
Scor = permute(Scor, [2 1 3]);
else
Scor = squeeze(img(:,nii_view.slices.cor,:,nii_view.scanid));
Scor = Scor';
end
set(nii_view.handles.coronal_image,'CData',double(Scor));
end
if isfield(nii_view.handles,'coronal_slider'),
slider_val = nii_view.dims(2) - nii_view.slices.cor + 1;
set(nii_view.handles.coronal_slider,'Value',slider_val);
end
end
if sag,
if isfield(nii_view.handles,'sagittal_bg') & ~isempty(nii_view.handles.sagittal_bg) & nii_view.useinterp
Ssag = squeeze(nii_view.bgimg(nii_view.slices.sag,:,:));
set(nii_view.handles.sagittal_bg,'CData',double(Ssag)');
end
if isfield(nii_view.handles,'sagittal_image'),
if nii_view.nii.hdr.dime.datatype == 128 | nii_view.nii.hdr.dime.datatype == 511
Ssag = squeeze(img(nii_view.slices.sag,:,:,:,nii_view.scanid));
Ssag = permute(Ssag, [2 1 3]);
else
Ssag = squeeze(img(nii_view.slices.sag,:,:,nii_view.scanid));
Ssag = Ssag';
end
set(nii_view.handles.sagittal_image,'CData',double(Ssag));
end
if isfield(nii_view.handles,'sagittal_slider'),
set(nii_view.handles.sagittal_slider,'Value',nii_view.slices.sag);
end
end
update_nii_view(nii_view);
if ~isempty(nii_view.buttondown)
eval(nii_view.buttondown);
end
case {'impos_edit'}
nii_view = getappdata(fig,'nii_view');
impos = str2num(get(nii_view.handles.impos,'string'));
if isfield(nii_view, 'disp')
img = nii_view.disp;
else
img = nii_view.nii.img;
end
if isempty(impos) | ~all(size(impos) == [1 3])
msg = 'Please use 3 numbers to represent X,Y and Z';
msgbox(msg,'Error');
return;
end
slices.sag = round(impos(1));
slices.cor = round(impos(2));
slices.axi = round(impos(3));
nii_view = convert2voxel(nii_view,slices);
nii_view = check_slices(nii_view);
impos(1) = nii_view.slices.sag;
impos(2) = nii_view.dims(2) - nii_view.slices.cor + 1;
impos(3) = nii_view.slices.axi;
if isfield(nii_view.handles,'sagittal_slider'),
set(nii_view.handles.sagittal_slider,'Value',impos(1));
end
if isfield(nii_view.handles,'coronal_slider'),
set(nii_view.handles.coronal_slider,'Value',impos(2));
end
if isfield(nii_view.handles,'axial_slider'),
set(nii_view.handles.axial_slider,'Value',impos(3));
end
nii_view = get_slider_position(nii_view);
update_nii_view(nii_view);
if isfield(nii_view.handles,'axial_bg') & ~isempty(nii_view.handles.axial_bg) & nii_view.useinterp
Saxi = squeeze(nii_view.bgimg(:,:,nii_view.slices.axi));
set(nii_view.handles.axial_bg,'CData',double(Saxi)');
end
if isfield(nii_view.handles,'axial_image'),
if nii_view.nii.hdr.dime.datatype == 128 | nii_view.nii.hdr.dime.datatype == 511
Saxi = squeeze(img(:,:,nii_view.slices.axi,:,nii_view.scanid));
Saxi = permute(Saxi, [2 1 3]);
else
Saxi = squeeze(img(:,:,nii_view.slices.axi,nii_view.scanid));
Saxi = Saxi';
end
set(nii_view.handles.axial_image,'CData',double(Saxi));
end
if isfield(nii_view.handles,'axial_slider'),
set(nii_view.handles.axial_slider,'Value',nii_view.slices.axi);
end
if isfield(nii_view.handles,'coronal_bg') & ~isempty(nii_view.handles.coronal_bg) & nii_view.useinterp
Scor = squeeze(nii_view.bgimg(:,nii_view.slices.cor,:));
set(nii_view.handles.coronal_bg,'CData',double(Scor)');
end
if isfield(nii_view.handles,'coronal_image'),
if nii_view.nii.hdr.dime.datatype == 128 | nii_view.nii.hdr.dime.datatype == 511
Scor = squeeze(img(:,nii_view.slices.cor,:,:,nii_view.scanid));
Scor = permute(Scor, [2 1 3]);
else
Scor = squeeze(img(:,nii_view.slices.cor,:,nii_view.scanid));
Scor = Scor';
end
set(nii_view.handles.coronal_image,'CData',double(Scor));
end
if isfield(nii_view.handles,'coronal_slider'),
slider_val = nii_view.dims(2) - nii_view.slices.cor + 1;
set(nii_view.handles.coronal_slider,'Value',slider_val);
end
if isfield(nii_view.handles,'sagittal_bg') & ~isempty(nii_view.handles.sagittal_bg) & nii_view.useinterp
Ssag = squeeze(nii_view.bgimg(nii_view.slices.sag,:,:));
set(nii_view.handles.sagittal_bg,'CData',double(Ssag)');
end
if isfield(nii_view.handles,'sagittal_image'),
if nii_view.nii.hdr.dime.datatype == 128 | nii_view.nii.hdr.dime.datatype == 511
Ssag = squeeze(img(nii_view.slices.sag,:,:,:,nii_view.scanid));
Ssag = permute(Ssag, [2 1 3]);
else
Ssag = squeeze(img(nii_view.slices.sag,:,:,nii_view.scanid));
Ssag = Ssag';
end
set(nii_view.handles.sagittal_image,'CData',double(Ssag));
end
if isfield(nii_view.handles,'sagittal_slider'),
set(nii_view.handles.sagittal_slider,'Value',nii_view.slices.sag);
end
axes(nii_view.handles.axial_axes);
axes(nii_view.handles.coronal_axes);
axes(nii_view.handles.sagittal_axes);
if ~isempty(nii_view.buttondown)
eval(nii_view.buttondown);
end
case 'coordinates',
nii_view = getappdata(fig,'nii_view');
set_image_value(nii_view);
case 'crosshair',
nii_view = getappdata(fig,'nii_view');
if get(nii_view.handles.xhair,'value') == 2 % off
set(nii_view.axi_xhair.lx,'visible','off');
set(nii_view.axi_xhair.ly,'visible','off');
set(nii_view.cor_xhair.lx,'visible','off');
set(nii_view.cor_xhair.ly,'visible','off');
set(nii_view.sag_xhair.lx,'visible','off');
set(nii_view.sag_xhair.ly,'visible','off');
else
set(nii_view.axi_xhair.lx,'visible','on');
set(nii_view.axi_xhair.ly,'visible','on');
set(nii_view.cor_xhair.lx,'visible','on');
set(nii_view.cor_xhair.ly,'visible','on');
set(nii_view.sag_xhair.lx,'visible','on');
set(nii_view.sag_xhair.ly,'visible','on');
set(nii_view.handles.axial_axes,'selected','on');
set(nii_view.handles.axial_axes,'selected','off');
set(nii_view.handles.coronal_axes,'selected','on');
set(nii_view.handles.coronal_axes,'selected','off');
set(nii_view.handles.sagittal_axes,'selected','on');
set(nii_view.handles.sagittal_axes,'selected','off');
end
case 'xhair_color',
old_color = get(gcbo,'user');
new_color = uisetcolor(old_color);
update_crosshaircolor(fig, new_color);
case {'color','contrast_def'}
nii_view = getappdata(fig,'nii_view');
if nii_view.numscan == 1
if get(nii_view.handles.colorindex,'value') == 2
set(nii_view.handles.contrast,'value',128);
elseif get(nii_view.handles.colorindex,'value') == 3
set(nii_view.handles.contrast,'value',1);
end
end
[custom_color_map, custom_colorindex] = change_colormap(fig);
if strcmpi(command, 'color')
setcolorlevel = nii_view.colorlevel;
if ~isempty(custom_color_map) % isfield(nii_view, 'color_map')
setcolormap = custom_color_map; % nii_view.color_map;
else
setcolormap = [];
end
if isfield(nii_view, 'highcolor')
sethighcolor = nii_view.highcolor;
else
sethighcolor = [];
end
redraw_cbar(fig, setcolorlevel, setcolormap, sethighcolor);
if nii_view.numscan == 1 & ...
(custom_colorindex < 2 | custom_colorindex > 3)
contrastopt.enablecontrast = 0;
else
contrastopt.enablecontrast = 1;
end
update_enable(fig, contrastopt);
end
case {'neg_color','brightness','contrast'}
change_colormap(fig);
case {'brightness_def'}
nii_view = getappdata(fig,'nii_view');
set(nii_view.handles.brightness,'value',0);
change_colormap(fig);
case 'hist_plot'
hist_plot(fig);
case 'hist_eq'
hist_eq(fig);
case 'move_cursor'
move_cursor(fig);
case 'edit_change_scan'
change_scan('edit_change_scan');
case 'slider_change_scan'
change_scan('slider_change_scan');
end
return; % view_nii
%----------------------------------------------------------------
function fig = init(nii, fig, area, setunit, setviewpoint, setscanid, buttondown, ...
colorindex, color_map, colorlevel, highcolor, cbarminmax, ...
usecolorbar, usepanel, usecrosshair, usestretch, useimagesc, ...
useinterp, setvalue, glblocminmax, setcrosshaircolor, ...
setcomplex)
% Support data type COMPLEX64 & COMPLEX128
%
if nii.hdr.dime.datatype == 32 | nii.hdr.dime.datatype == 1792
switch setcomplex,
case 0,
nii.img = real(nii.img);
case 1,
nii.img = imag(nii.img);
case 2,
if isa(nii.img, 'double')
nii.img = abs(double(nii.img));
else
nii.img = single(abs(double(nii.img)));
end
end
end
if isempty(area)
area = [0.05 0.05 0.9 0.9];
end
if isempty(setscanid)
setscanid = 1;
else
setscanid = round(setscanid);
if setscanid < 1
setscanid = 1;
end
if setscanid > nii.hdr.dime.dim(5)
setscanid = nii.hdr.dime.dim(5);
end
end
if nii.hdr.dime.datatype == 128 | nii.hdr.dime.datatype == 511
usecolorbar = 0;
elseif isempty(usecolorbar)
usecolorbar = 1;
end
if isempty(usepanel)
usepanel = 1;
end
if isempty(usestretch)
usestretch = 1;
end
if isempty(useimagesc)
useimagesc = 1;
end
if isempty(useinterp)
useinterp = 0;
end
if isempty(colorindex)
tmp = min(nii.img(:,:,:,setscanid));
if min(tmp(:)) < 0
colorindex = 2;
setcrosshaircolor = [1 1 0];
else
colorindex = 3;
end
end
if isempty(color_map) | ischar(color_map)
color_map = [];
else
colorindex = 1;
end
bgimg = [];
if ~isempty(glblocminmax)
minvalue = glblocminmax(1);
maxvalue = glblocminmax(2);
else
minvalue = nii.img(:,:,:,setscanid);
minvalue = double(minvalue(:));
minvalue = min(minvalue(~isnan(minvalue)));
maxvalue = nii.img(:,:,:,setscanid);
maxvalue = double(maxvalue(:));
maxvalue = max(maxvalue(~isnan(maxvalue)));
end
if ~isempty(setvalue)
if ~isempty(glblocminmax)
minvalue = glblocminmax(1);
maxvalue = glblocminmax(2);
else
minvalue = double(min(setvalue.val));
maxvalue = double(max(setvalue.val));
end
bgimg = double(nii.img);
minbg = double(min(bgimg(:)));
maxbg = double(max(bgimg(:)));
bgimg = scale_in(bgimg, minbg, maxbg, 55) + 200; % scale to 201~256
% 56 level for brain structure
%
% highcolor = [zeros(1,3);gray(55)];
highcolor = gray(56);
cbarminmax = [minvalue maxvalue];
if useinterp
% scale signal data to 1~200
%
nii.img = repmat(nan, size(nii.img));
nii.img(setvalue.idx) = setvalue.val;
% 200 level for source image
%
bgimg = single(scale_out(bgimg, cbarminmax(1), cbarminmax(2), 199));
else
bgimg(setvalue.idx) = NaN;
minbg = double(min(bgimg(:)));
maxbg = double(max(bgimg(:)));
bgimg(setvalue.idx) = minbg;
% bgimg must be normalized to [201 256]
%
bgimg = 55 * (bgimg-min(bgimg(:))) / (max(bgimg(:))-min(bgimg(:))) + 201;
bgimg(setvalue.idx) = 0;
% scale signal data to 1~200
%
nii.img = zeros(size(nii.img));
nii.img(setvalue.idx) = scale_in(setvalue.val, minvalue, maxvalue, 199);
nii.img = nii.img + bgimg;
bgimg = [];
nii.img = scale_out(nii.img, cbarminmax(1), cbarminmax(2), 199);
minvalue = double(nii.img(:));
minvalue = min(minvalue(~isnan(minvalue)));
maxvalue = double(nii.img(:));
maxvalue = max(maxvalue(~isnan(maxvalue)));
if ~isempty(glblocminmax) % maxvalue is gray
minvalue = glblocminmax(1);
end
end
colorindex = 2;
setcrosshaircolor = [1 1 0];
end
if isempty(highcolor) | ischar(highcolor)
highcolor = [];
num_highcolor = 0;
else
num_highcolor = size(highcolor,1);
end
if isempty(colorlevel)
colorlevel = 256 - num_highcolor;
end
if usecolorbar
cbar_area = area;
cbar_area(1) = area(1) + area(3)*0.93;
cbar_area(3) = area(3)*0.04;
area(3) = area(3)*0.9; % 90% used for main axes
else
cbar_area = [];
end
% init color (gray) scaling to make sure the slice clim take the
% global clim [min(nii.img(:)) max(nii.img(:))]
%
if isempty(bgimg)
clim = [minvalue maxvalue];
else
clim = [minvalue double(max(bgimg(:)))];
end
if clim(1) == clim(2)
clim(2) = clim(1) + 0.000001;
end
if isempty(cbarminmax)
cbarminmax = [minvalue maxvalue];
end
xdim = size(nii.img, 1);
ydim = size(nii.img, 2);
zdim = size(nii.img, 3);
dims = [xdim ydim zdim];
voxel_size = abs(nii.hdr.dime.pixdim(2:4)); % vol in mm
if any(voxel_size <= 0)
voxel_size(find(voxel_size <= 0)) = 1;
end
origin = abs(nii.hdr.hist.originator(1:3));
if isempty(origin) | all(origin == 0) % according to SPM
origin = (dims+1)/2;
end;
origin = round(origin);
if any(origin > dims) % simulate fMRI
origin(find(origin > dims)) = dims(find(origin > dims));
end
if any(origin <= 0)
origin(find(origin <= 0)) = 1;
end
nii_view.dims = dims;
nii_view.voxel_size = voxel_size;
nii_view.origin = origin;
nii_view.slices.sag = 1;
nii_view.slices.cor = 1;
nii_view.slices.axi = 1;
if xdim > 1, nii_view.slices.sag = origin(1); end
if ydim > 1, nii_view.slices.cor = origin(2); end
if zdim > 1, nii_view.slices.axi = origin(3); end
nii_view.area = area;
nii_view.fig = fig;
nii_view.nii = nii; % image data
nii_view.bgimg = bgimg; % background
nii_view.setvalue = setvalue;
nii_view.minvalue = minvalue;
nii_view.maxvalue = maxvalue;
nii_view.numscan = nii.hdr.dime.dim(5);
nii_view.scanid = setscanid;
Font.FontUnits = 'point';
Font.FontSize = 12;
% create axes for colorbar
%
[cbar_axes cbarminmax_axes] = create_cbar_axes(fig, cbar_area);
if isempty(cbar_area)
nii_view.cbar_area = [];
else
nii_view.cbar_area = cbar_area;
end
% create axes for top/front/side view
%
vol_size = voxel_size .* dims;
[top_ax, front_ax, side_ax] ...
= create_ax(fig, area, vol_size, usestretch);
top_pos = get(top_ax,'position');
front_pos = get(front_ax,'position');
side_pos = get(side_ax,'position');
% Sagittal Slider
%
x = side_pos(1);
y = top_pos(2) + top_pos(4);
w = side_pos(3);
h = (front_pos(2) - y) / 2;
y = y + h;
pos = [x y w h];
if xdim > 1,
slider_step(1) = 1/(xdim);
slider_step(2) = 1.00001/(xdim);
handles.sagittal_slider = uicontrol('Parent',fig, ...
'Style','slider','Units','Normalized', Font, ...
'Position',pos, 'HorizontalAlignment','center',...
'BackgroundColor',[0.5 0.5 0.5],'ForegroundColor',[0 0 0],...
'BusyAction','queue',...
'TooltipString','Sagittal slice navigation',...
'Min',1,'Max',xdim,'SliderStep',slider_step, ...
'Value',nii_view.slices.sag,...
'Callback','view_nii(''sagittal_slider'');');
set(handles.sagittal_slider,'position',pos); % linux66
end
% Coronal Slider
%
x = top_pos(1);
y = top_pos(2) + top_pos(4);
w = top_pos(3);
h = (front_pos(2) - y) / 2;
y = y + h;
pos = [x y w h];
if ydim > 1,
slider_step(1) = 1/(ydim);
slider_step(2) = 1.00001/(ydim);
slider_val = nii_view.dims(2) - nii_view.slices.cor + 1;
handles.coronal_slider = uicontrol('Parent',fig, ...
'Style','slider','Units','Normalized', Font, ...
'Position',pos, 'HorizontalAlignment','center',...
'BackgroundColor',[0.5 0.5 0.5],'ForegroundColor',[0 0 0],...
'BusyAction','queue',...
'TooltipString','Coronal slice navigation',...
'Min',1,'Max',ydim,'SliderStep',slider_step, ...
'Value',slider_val,...
'Callback','view_nii(''coronal_slider'');');
set(handles.coronal_slider,'position',pos); % linux66
end
% Axial Slider
%
% x = front_pos(1) + front_pos(3);
% y = front_pos(2);
% w = side_pos(1) - x;
% h = front_pos(4);
x = top_pos(1);
y = area(2);
w = top_pos(3);
h = top_pos(2) - y;
pos = [x y w h];
if zdim > 1,
slider_step(1) = 1/(zdim);
slider_step(2) = 1.00001/(zdim);
handles.axial_slider = uicontrol('Parent',fig, ...
'Style','slider','Units','Normalized', Font, ...
'Position',pos, 'HorizontalAlignment','center',...
'BackgroundColor',[0.5 0.5 0.5],'ForegroundColor',[0 0 0],...
'BusyAction','queue',...
'TooltipString','Axial slice navigation',...
'Min',1,'Max',zdim,'SliderStep',slider_step, ...
'Value',nii_view.slices.axi,...
'Callback','view_nii(''axial_slider'');');
set(handles.axial_slider,'position',pos); % linux66
end
% plot info view
%
% info_pos = [side_pos([1,3]); top_pos([2,4])];
% info_pos = info_pos(:);
gap = side_pos(1)-(top_pos(1)+top_pos(3));
info_pos(1) = side_pos(1) + gap;
info_pos(2) = area(2);
info_pos(3) = side_pos(3) - gap;
info_pos(4) = top_pos(2) + top_pos(4) - area(2) - gap;
num_inputline = 10;
inputline_space =info_pos(4) / num_inputline;
% for any info_area change, update_usestretch should also be changed
% Image Intensity Value at Cursor
%
x = info_pos(1);
y = info_pos(2);
w = info_pos(3)*0.5;
h = inputline_space*0.6;
pos = [x y w h];
handles.Timvalcur = uicontrol('Parent',fig,'Style','text', ...
'Units','Normalized', Font, ...
'Position',pos, 'HorizontalAlignment', 'left',...
'BackgroundColor', [0.8 0.8 0.8], 'ForegroundColor', [0 0 0],...
'BusyAction','queue',...
'visible','off', ...
'String','Value at cursor:');
if usepanel
set(handles.Timvalcur, 'visible', 'on');
end
x = x + w;
w = info_pos(3)*0.5;
pos = [x y w h];
handles.imvalcur = uicontrol('Parent',fig,'Style','text', ...
'Units','Normalized', Font, ...
'Position',pos, 'HorizontalAlignment', 'right',...
'BackgroundColor', [0.8 0.8 0.8], 'ForegroundColor', [0 0 0],...
'BusyAction','queue',...
'visible','off', ...
'String',' ');
if usepanel
set(handles.imvalcur, 'visible', 'on');
end
% Position at Cursor
%
x = info_pos(1);
y = y + inputline_space;
w = info_pos(3)*0.5;
pos = [x y w h];
handles.Timposcur = uicontrol('Parent',fig,'Style','text', ...
'Units','Normalized', Font, ...
'Position',pos, 'HorizontalAlignment', 'left',...
'BackgroundColor', [0.8 0.8 0.8], 'ForegroundColor', [0 0 0],...
'BusyAction','queue',...
'visible','off', ...
'String','[X Y Z] at cursor:');
if usepanel
set(handles.Timposcur, 'visible', 'on');
end
x = x + w;
w = info_pos(3)*0.5;
pos = [x y w h];
handles.imposcur = uicontrol('Parent',fig,'Style','text', ...
'Units','Normalized', Font, ...
'Position',pos, 'HorizontalAlignment', 'right',...
'BackgroundColor', [0.8 0.8 0.8], 'ForegroundColor', [0 0 0],...
'BusyAction','queue',...
'visible','off', ...
'String',' ','Value',[0 0 0]);
if usepanel
set(handles.imposcur, 'visible', 'on');
end
% Image Intensity Value at Mouse Click
%
x = info_pos(1);
y = y + inputline_space;
w = info_pos(3)*0.5;
pos = [x y w h];
handles.Timval = uicontrol('Parent',fig,'Style','text', ...
'Units','Normalized', Font, ...
'Position',pos, 'HorizontalAlignment', 'left',...
'BackgroundColor', [0.8 0.8 0.8], 'ForegroundColor', [0 0 0],...
'BusyAction','queue',...
'visible','off', ...
'String','Value at crosshair:');
if usepanel
set(handles.Timval, 'visible', 'on');
end
x = x + w;
w = info_pos(3)*0.5;
pos = [x y w h];
handles.imval = uicontrol('Parent',fig,'Style','text', ...
'Units','Normalized', Font, ...
'Position',pos, 'HorizontalAlignment', 'right',...
'BackgroundColor', [0.8 0.8 0.8], 'ForegroundColor', [0 0 0],...
'BusyAction','queue',...
'visible','off', ...
'String',' ');
if usepanel
set(handles.imval, 'visible', 'on');
end
% Viewpoint Position at Mouse Click
%
x = info_pos(1);
y = y + inputline_space;
w = info_pos(3)*0.5;
pos = [x y w h];
handles.Timpos = uicontrol('Parent',fig,'Style','text', ...
'Units','Normalized', Font, ...
'Position',pos, 'HorizontalAlignment', 'left',...
'BackgroundColor', [0.8 0.8 0.8], 'ForegroundColor', [0 0 0],...
'BusyAction','queue',...
'visible','off', ...
'String','[X Y Z] at crosshair:');
if usepanel
set(handles.Timpos, 'visible', 'on');
end
x = x + w + 0.005;
y = y - 0.008;
w = info_pos(3)*0.5;
h = inputline_space*0.9;
pos = [x y w h];
handles.impos = uicontrol('Parent',fig,'Style','edit', ...
'Units','Normalized', Font, ...
'Position',pos, 'HorizontalAlignment', 'right',...
'BackgroundColor', [1 1 1], 'ForegroundColor', [0 0 0],...
'BusyAction','queue',...
'Callback','view_nii(''impos_edit'');', ...
'TooltipString','Viewpoint Location in Axes Unit', ...
'visible','off', ...
'String',' ','Value',[0 0 0]);
if usepanel
set(handles.impos, 'visible', 'on');
end
% Origin Position
%
x = info_pos(1);
y = y + inputline_space*1.2;
w = info_pos(3)*0.5;
h = inputline_space*0.6;
pos = [x y w h];
handles.Torigin = uicontrol('Parent',fig,'Style','text', ...
'Units','Normalized', Font, ...
'Position',pos, 'HorizontalAlignment', 'left',...
'BackgroundColor', [0.8 0.8 0.8], 'ForegroundColor', [0 0 0],...
'BusyAction','queue',...
'visible','off', ...
'String','[X Y Z] at origin:');
if usepanel
set(handles.Torigin, 'visible', 'on');
end
x = x + w;
w = info_pos(3)*0.5;
pos = [x y w h];
handles.origin = uicontrol('Parent',fig,'Style','text', ...
'Units','Normalized', Font, ...
'Position',pos, 'HorizontalAlignment', 'right',...
'BackgroundColor', [0.8 0.8 0.8], 'ForegroundColor', [0 0 0],...
'BusyAction','queue',...
'visible','off', ...
'String',' ','Value',[0 0 0]);
if usepanel
set(handles.origin, 'visible', 'on');
end
if 0
% Voxel Unit
%
x = info_pos(1);
y = y + inputline_space;
w = info_pos(3)*0.5;
pos = [x y w h];
handles.Tcoord = uicontrol('Parent',fig,'Style','text', ...
'Units','Normalized', Font, ...
'Position',pos, 'HorizontalAlignment', 'left',...
'BackgroundColor', [0.8 0.8 0.8], 'ForegroundColor', [0 0 0],...
'BusyAction','queue',...
'visible','off', ...
'String','Axes Unit:');
if usepanel
set(handles.Tcoord, 'visible', 'on');
end
x = x + w + 0.005;
w = info_pos(3)*0.5 - 0.005;
pos = [x y w h];
Font.FontSize = 8;
handles.coord = uicontrol('Parent',fig,'Style','popupmenu', ...
'Units','Normalized', Font, ...
'Position',pos, ...
'BackgroundColor', [1 1 1], 'ForegroundColor', [0 0 0],...
'BusyAction','queue',...
'TooltipString','Choose Voxel or Millimeter',...
'String',{'Voxel','Millimeter'},...
'visible','off', ...
'Callback','view_nii(''coordinates'');');
% 'TooltipString','Choose Voxel, MNI or Talairach Coordinates',...
% 'String',{'Voxel','MNI (mm)','Talairach (mm)'},...
Font.FontSize = 12;
if usepanel
set(handles.coord, 'visible', 'on');
end
end
% Crosshair
%
x = info_pos(1);
y = y + inputline_space;
w = info_pos(3)*0.4;
pos = [x y w h];
handles.Txhair = uicontrol('Parent',fig,'Style','text', ...
'Units','Normalized', Font, ...
'Position',pos, 'HorizontalAlignment', 'left',...
'BackgroundColor', [0.8 0.8 0.8], 'ForegroundColor', [0 0 0],...
'BusyAction','queue',...
'visible','off', ...
'String','Crosshair:');
if usepanel
set(handles.Txhair, 'visible', 'on');
end
x = info_pos(1) + info_pos(3)*0.5;
w = info_pos(3)*0.2;
h = inputline_space*0.7;
pos = [x y w h];
Font.FontSize = 8;
handles.xhair_color = uicontrol('Parent',fig,'Style','push', ...
'Units','Normalized', Font, ...
'Position',pos, 'HorizontalAlignment', 'center',...
'TooltipString','Crosshair Color',...
'User',[1 0 0],...
'String','Color',...
'visible','off', ...
'Callback','view_nii(''xhair_color'');');
if usepanel
set(handles.xhair_color, 'visible', 'on');
end
x = info_pos(1) + info_pos(3)*0.7;
w = info_pos(3)*0.3;
pos = [x y w h];
handles.xhair = uicontrol('Parent',fig,'Style','popupmenu', ...
'Units','Normalized', Font, ...
'Position',pos, ...
'BackgroundColor', [1 1 1], 'ForegroundColor', [0 0 0],...
'BusyAction','queue',...
'TooltipString','Display or Hide Crosshair',...
'String',{'On','Off'},...
'visible','off', ...
'Callback','view_nii(''crosshair'');');
if usepanel
set(handles.xhair, 'visible', 'on');
end
% Histogram & Color
%
x = info_pos(1);
w = info_pos(3)*0.45;
h = inputline_space * 1.5;
pos = [x, y+inputline_space*0.9, w, h];
handles.hist_frame = uicontrol('Parent',fig, ...
'Units','normal', ...
'BackgroundColor',[0.8 0.8 0.8], ...
'Position',pos, ...
'visible','off', ...
'Style','frame');
if usepanel
% set(handles.hist_frame, 'visible', 'on');
end
handles.coord_frame = uicontrol('Parent',fig, ...
'Units','normal', ...
'BackgroundColor',[0.8 0.8 0.8], ...
'Position',pos, ...
'visible','off', ...
'Style','frame');
if usepanel
set(handles.coord_frame, 'visible', 'on');
end
x = info_pos(1) + info_pos(3)*0.475;
w = info_pos(3)*0.525;
h = inputline_space * 1.5;
pos = [x, y+inputline_space*0.9, w, h];
handles.color_frame = uicontrol('Parent',fig, ...
'Units','normal', ...
'BackgroundColor',[0.8 0.8 0.8], ...
'Position',pos, ...
'visible','off', ...
'Style','frame');
if usepanel
set(handles.color_frame, 'visible', 'on');
end
x = info_pos(1) + info_pos(3)*0.025;
y = y + inputline_space*1.2;
w = info_pos(3)*0.2;
h = inputline_space*0.7;
pos = [x y w h];
Font.FontSize = 8;
handles.hist_eq = uicontrol('Parent',fig,'Style','toggle', ...
'Units','Normalized', Font, ...
'Position',pos, 'HorizontalAlignment', 'center',...
'TooltipString','Histogram Equalization',...
'String','Hist EQ',...
'visible','off', ...
'Callback','view_nii(''hist_eq'');');
if usepanel
% set(handles.hist_eq, 'visible', 'on');
end
x = x + w;
w = info_pos(3)*0.2;
pos = [x y w h];
handles.hist_plot = uicontrol('Parent',fig,'Style','push', ...
'Units','Normalized', Font, ...
'Position',pos, 'HorizontalAlignment', 'center',...
'TooltipString','Histogram Plot',...
'String','Hist Plot',...
'visible','off', ...
'Callback','view_nii(''hist_plot'');');
if usepanel
% set(handles.hist_plot, 'visible', 'on');
end
x = info_pos(1) + info_pos(3)*0.025;
w = info_pos(3)*0.4;
pos = [x y w h];
handles.coord = uicontrol('Parent',fig,'Style','popupmenu', ...
'Units','Normalized', Font, ...
'Position',pos, ...
'BackgroundColor', [1 1 1], 'ForegroundColor', [0 0 0],...
'BusyAction','queue',...
'TooltipString','Choose Voxel or Millimeter',...
'String',{'Voxel','Millimeter'},...
'visible','off', ...
'Callback','view_nii(''coordinates'');');
% 'TooltipString','Choose Voxel, MNI or Talairach Coordinates',...
% 'String',{'Voxel','MNI (mm)','Talairach (mm)'},...
if usepanel
set(handles.coord, 'visible', 'on');
end
x = info_pos(1) + info_pos(3)*0.5;
w = info_pos(3)*0.2;
pos = [x y w h];
handles.neg_color = uicontrol('Parent',fig,'Style','toggle', ...
'Units','Normalized', Font, ...
'Position',pos, 'HorizontalAlignment', 'center',...
'TooltipString','Negative Colormap',...
'String','Negative',...
'visible','off', ...
'Callback','view_nii(''neg_color'');');
if usepanel
set(handles.neg_color, 'visible', 'on');
end
if nii.hdr.dime.datatype == 128 | nii.hdr.dime.datatype == 511
set(handles.neg_color, 'enable', 'off');
end
x = info_pos(1) + info_pos(3)*0.7;
w = info_pos(3)*0.275;
pos = [x y w h];
handles.colorindex = uicontrol('Parent',fig,'Style','popupmenu', ...
'Units','Normalized', Font, ...
'Position',pos, ...
'BackgroundColor', [1 1 1], 'ForegroundColor', [0 0 0],...
'BusyAction','queue',...
'TooltipString','Change Colormap',...
'String',{'Custom','Bipolar','Gray','Jet','Cool','Bone','Hot','Copper','Pink'},...
'value', colorindex, ...
'visible','off', ...
'Callback','view_nii(''color'');');
if usepanel
set(handles.colorindex, 'visible', 'on');
end
if nii.hdr.dime.datatype == 128 | nii.hdr.dime.datatype == 511
set(handles.colorindex, 'enable', 'off');
end
x = info_pos(1) + info_pos(3)*0.1;
y = y + inputline_space;
w = info_pos(3)*0.28;
h = inputline_space*0.6;
pos = [x y w h];
Font.FontSize = 8;
handles.Thist = uicontrol('Parent',fig,'Style','text', ...
'Units','Normalized', Font, ...
'Position',pos, 'HorizontalAlignment', 'center',...
'BackgroundColor', [0.8 0.8 0.8], 'ForegroundColor', [0 0 0],...
'BusyAction','queue',...
'visible','off', ...
'String','Histogram');
handles.Tcoord = uicontrol('Parent',fig,'Style','text', ...
'Units','Normalized', Font, ...
'Position',pos, 'HorizontalAlignment', 'center',...
'BackgroundColor', [0.8 0.8 0.8], 'ForegroundColor', [0 0 0],...
'BusyAction','queue',...
'visible','off', ...
'String','Axes Unit');
if usepanel
% set(handles.Thist, 'visible', 'on');
set(handles.Tcoord, 'visible', 'on');
end
x = info_pos(1) + info_pos(3)*0.60;
w = info_pos(3)*0.28;
pos = [x y w h];
handles.Tcolor = uicontrol('Parent',fig,'Style','text', ...
'Units','Normalized', Font, ...
'Position',pos, 'HorizontalAlignment', 'center',...
'BackgroundColor', [0.8 0.8 0.8], 'ForegroundColor', [0 0 0],...
'BusyAction','queue',...
'visible','off', ...
'String','Colormap');
if usepanel
set(handles.Tcolor, 'visible', 'on');
end
if nii.hdr.dime.datatype == 128 | nii.hdr.dime.datatype == 511
set(handles.Tcolor, 'enable', 'off');
end
% Contrast Frame
%
x = info_pos(1);
w = info_pos(3)*0.45;
h = inputline_space * 2;
pos = [x, y+inputline_space*0.8, w, h];
handles.contrast_frame = uicontrol('Parent',fig, ...
'Units','normal', ...
'BackgroundColor',[0.8 0.8 0.8], ...
'Position',pos, ...
'visible','off', ...
'Style','frame');
if usepanel
set(handles.contrast_frame, 'visible', 'on');
end
if colorindex < 2 | colorindex > 3
set(handles.contrast_frame, 'visible', 'off');
end
% Brightness Frame
%
x = info_pos(1) + info_pos(3)*0.475;
w = info_pos(3)*0.525;
pos = [x, y+inputline_space*0.8, w, h];
handles.brightness_frame = uicontrol('Parent',fig, ...
'Units','normal', ...
'BackgroundColor',[0.8 0.8 0.8], ...
'Position',pos, ...
'visible','off', ...
'Style','frame');
if usepanel
set(handles.brightness_frame, 'visible', 'on');
end
% Contrast
%
x = info_pos(1) + info_pos(3)*0.025;
y = y + inputline_space;
w = info_pos(3)*0.4;
h = inputline_space*0.6;
pos = [x y w h];
Font.FontSize = 12;
slider_step(1) = 5/255;
slider_step(2) = 5.00001/255;
handles.contrast = uicontrol('Parent',fig, ...
'Style','slider','Units','Normalized', Font, ...
'Position',pos, 'HorizontalAlignment', 'left',...
'BackgroundColor',[0.5 0.5 0.5],'ForegroundColor',[0 0 0],...
'BusyAction','queue',...
'TooltipString','Change contrast',...
'Min',1,'Max',256,'SliderStep',slider_step, ...
'Value',1, ...
'visible','off', ...
'Callback','view_nii(''contrast'');');
if usepanel
set(handles.contrast, 'visible', 'on');
end
if (nii.hdr.dime.datatype == 128 | nii.hdr.dime.datatype == 511) & nii_view.numscan <= 1
set(handles.contrast, 'enable', 'off');
end
if nii_view.numscan > 1
set(handles.contrast, 'min', 1, 'max', nii_view.numscan, ...
'sliderstep',[1/(nii_view.numscan-1) 1.00001/(nii_view.numscan-1)], ...
'Callback', 'view_nii(''slider_change_scan'');');
elseif colorindex < 2 | colorindex > 3
set(handles.contrast, 'visible', 'off');
elseif colorindex == 2
set(handles.contrast,'value',128);
end
set(handles.contrast,'position',pos); % linux66
% Brightness
%
x = info_pos(1) + info_pos(3)*0.5;
w = info_pos(3)*0.475;
pos = [x y w h];
Font.FontSize = 12;
slider_step(1) = 1/50;
slider_step(2) = 1.00001/50;
handles.brightness = uicontrol('Parent',fig, ...
'Style','slider','Units','Normalized', Font, ...
'Position',pos, 'HorizontalAlignment', 'left',...
'BackgroundColor',[0.5 0.5 0.5],'ForegroundColor',[0 0 0],...
'BusyAction','queue',...
'TooltipString','Change brightness',...
'Min',-1,'Max',1,'SliderStep',slider_step, ...
'Value',0, ...
'visible','off', ...
'Callback','view_nii(''brightness'');');
if usepanel
set(handles.brightness, 'visible', 'on');
end
if nii.hdr.dime.datatype == 128 | nii.hdr.dime.datatype == 511
set(handles.brightness, 'enable', 'off');
end
set(handles.brightness,'position',pos); % linux66
% Contrast text/def
%
x = info_pos(1) + info_pos(3)*0.025;
y = y + inputline_space;
w = info_pos(3)*0.22;
pos = [x y w h];
handles.Tcontrast = uicontrol('Parent',fig,'Style','text', ...
'Units','Normalized', Font, ...
'Position',pos, 'HorizontalAlignment', 'left',...
'BackgroundColor', [0.8 0.8 0.8], 'ForegroundColor', [0 0 0],...
'BusyAction','queue',...
'visible','off', ...
'String','Contrast:');
if usepanel
set(handles.Tcontrast, 'visible', 'on');
end
if (nii.hdr.dime.datatype == 128 | nii.hdr.dime.datatype == 511) & nii_view.numscan <= 1
set(handles.Tcontrast, 'enable', 'off');
end
if nii_view.numscan > 1
set(handles.Tcontrast, 'string', 'Scan ID:');
set(handles.contrast, 'TooltipString', 'Change Scan ID');
elseif colorindex < 2 | colorindex > 3
set(handles.Tcontrast, 'visible', 'off');
end
x = x + w;
w = info_pos(3)*0.18;
pos = [x y w h];
Font.FontSize = 8;
handles.contrast_def = uicontrol('Parent',fig,'Style','push', ...
'Units','Normalized', Font, ...
'Position',pos, 'HorizontalAlignment', 'center',...
'TooltipString','Restore initial contrast',...
'String','Reset',...
'visible','off', ...
'Callback','view_nii(''contrast_def'');');
if usepanel
set(handles.contrast_def, 'visible', 'on');
end
if (nii.hdr.dime.datatype == 128 | nii.hdr.dime.datatype == 511) & nii_view.numscan <= 1
set(handles.contrast_def, 'enable', 'off');
end
if nii_view.numscan > 1
set(handles.contrast_def, 'style', 'edit', 'background', 'w', ...
'TooltipString','Scan (or volume) index in the time series',...
'string', '1', 'Callback', 'view_nii(''edit_change_scan'');');
elseif colorindex < 2 | colorindex > 3
set(handles.contrast_def, 'visible', 'off');
end
% Brightness text/def
%
x = info_pos(1) + info_pos(3)*0.5;
w = info_pos(3)*0.295;
pos = [x y w h];
Font.FontSize = 12;
handles.Tbrightness = uicontrol('Parent',fig,'Style','text', ...
'Units','Normalized', Font, ...
'Position',pos, 'HorizontalAlignment', 'left',...
'BackgroundColor', [0.8 0.8 0.8], 'ForegroundColor', [0 0 0],...
'BusyAction','queue',...
'visible','off', ...
'String','Brightness:');
if usepanel
set(handles.Tbrightness, 'visible', 'on');
end
if nii.hdr.dime.datatype == 128 | nii.hdr.dime.datatype == 511
set(handles.Tbrightness, 'enable', 'off');
end
x = x + w;
w = info_pos(3)*0.18;
pos = [x y w h];
Font.FontSize = 8;
handles.brightness_def = uicontrol('Parent',fig,'Style','push', ...
'Units','Normalized', Font, ...
'Position',pos, 'HorizontalAlignment', 'center',...
'TooltipString','Restore initial brightness',...
'String','Reset',...
'visible','off', ...
'Callback','view_nii(''brightness_def'');');
if usepanel
set(handles.brightness_def, 'visible', 'on');
end
if nii.hdr.dime.datatype == 128 | nii.hdr.dime.datatype == 511
set(handles.brightness_def, 'enable', 'off');
end
% init image handles
%
handles.axial_image = [];
handles.coronal_image = [];
handles.sagittal_image = [];
% plot axial view
%
if ~isempty(nii_view.bgimg)
bg_slice = squeeze(bgimg(:,:,nii_view.slices.axi));
h1 = plot_view(fig, xdim, ydim, top_ax, bg_slice', clim, cbarminmax, ...
handles, useimagesc, colorindex, color_map, ...
colorlevel, highcolor, useinterp, nii_view.numscan);
handles.axial_bg = h1;
else
handles.axial_bg = [];
end
if nii.hdr.dime.datatype == 128 | nii.hdr.dime.datatype == 511
img_slice = squeeze(nii.img(:,:,nii_view.slices.axi,:,setscanid));
img_slice = permute(img_slice, [2 1 3]);
else
img_slice = squeeze(nii.img(:,:,nii_view.slices.axi,setscanid));
img_slice = img_slice';
end
h1 = plot_view(fig, xdim, ydim, top_ax, img_slice, clim, cbarminmax, ...
handles, useimagesc, colorindex, color_map, ...
colorlevel, highcolor, useinterp, nii_view.numscan);
set(h1,'buttondown','view_nii(''axial_image'');');
handles.axial_image = h1;
handles.axial_axes = top_ax;
if size(img_slice,1) == 1 | size(img_slice,2) == 1
set(top_ax,'visible','off');
if isfield(handles,'sagittal_slider') & ishandle(handles.sagittal_slider)
set(handles.sagittal_slider, 'visible', 'off');
end
if isfield(handles,'coronal_slider') & ishandle(handles.coronal_slider)
set(handles.coronal_slider, 'visible', 'off');
end
if isfield(handles,'axial_slider') & ishandle(handles.axial_slider)
set(handles.axial_slider, 'visible', 'off');
end
end
% plot coronal view
%
if ~isempty(nii_view.bgimg)
bg_slice = squeeze(bgimg(:,nii_view.slices.cor,:));
h1 = plot_view(fig, xdim, zdim, front_ax, bg_slice', clim, cbarminmax, ...
handles, useimagesc, colorindex, color_map, ...
colorlevel, highcolor, useinterp, nii_view.numscan);
handles.coronal_bg = h1;
else
handles.coronal_bg = [];
end
if nii.hdr.dime.datatype == 128 | nii.hdr.dime.datatype == 511
img_slice = squeeze(nii.img(:,nii_view.slices.cor,:,:,setscanid));
img_slice = permute(img_slice, [2 1 3]);
else
img_slice = squeeze(nii.img(:,nii_view.slices.cor,:,setscanid));
img_slice = img_slice';
end
h1 = plot_view(fig, xdim, zdim, front_ax, img_slice, clim, cbarminmax, ...
handles, useimagesc, colorindex, color_map, ...
colorlevel, highcolor, useinterp, nii_view.numscan);
set(h1,'buttondown','view_nii(''coronal_image'');');
handles.coronal_image = h1;
handles.coronal_axes = front_ax;
if size(img_slice,1) == 1 | size(img_slice,2) == 1
set(front_ax,'visible','off');
if isfield(handles,'sagittal_slider') & ishandle(handles.sagittal_slider)
set(handles.sagittal_slider, 'visible', 'off');
end
if isfield(handles,'coronal_slider') & ishandle(handles.coronal_slider)
set(handles.coronal_slider, 'visible', 'off');
end
if isfield(handles,'axial_slider') & ishandle(handles.axial_slider)
set(handles.axial_slider, 'visible', 'off');
end
end
% plot sagittal view
%
if ~isempty(nii_view.bgimg)
bg_slice = squeeze(bgimg(nii_view.slices.sag,:,:));
h1 = plot_view(fig, ydim, zdim, side_ax, bg_slice', clim, cbarminmax, ...
handles, useimagesc, colorindex, color_map, ...
colorlevel, highcolor, useinterp, nii_view.numscan);
handles.sagittal_bg = h1;
else
handles.sagittal_bg = [];
end
if nii.hdr.dime.datatype == 128 | nii.hdr.dime.datatype == 511
img_slice = squeeze(nii.img(nii_view.slices.sag,:,:,:,setscanid));
img_slice = permute(img_slice, [2 1 3]);
else
img_slice = squeeze(nii.img(nii_view.slices.sag,:,:,setscanid));
img_slice = img_slice';
end
h1 = plot_view(fig, ydim, zdim, side_ax, img_slice, clim, cbarminmax, ...
handles, useimagesc, colorindex, color_map, ...
colorlevel, highcolor, useinterp, nii_view.numscan);
set(h1,'buttondown','view_nii(''sagittal_image'');');
set(side_ax,'Xdir', 'reverse');
handles.sagittal_image = h1;
handles.sagittal_axes = side_ax;
if size(img_slice,1) == 1 | size(img_slice,2) == 1
set(side_ax,'visible','off');
if isfield(handles,'sagittal_slider') & ishandle(handles.sagittal_slider)
set(handles.sagittal_slider, 'visible', 'off');
end
if isfield(handles,'coronal_slider') & ishandle(handles.coronal_slider)
set(handles.coronal_slider, 'visible', 'off');
end
if isfield(handles,'axial_slider') & ishandle(handles.axial_slider)
set(handles.axial_slider, 'visible', 'off');
end
end
[top1_label, top2_label, side1_label, side2_label] = ...
dir_label(fig, top_ax, front_ax, side_ax);
% store label handles
%
handles.top1_label = top1_label;
handles.top2_label = top2_label;
handles.side1_label = side1_label;
handles.side2_label = side2_label;
% plot colorbar
%
if ~isempty(cbar_axes) & ~isempty(cbarminmax_axes)
if 0
if isempty(color_map)
level = colorlevel + num_highcolor;
else
level = size([color_map; highcolor], 1);
end
end
if isempty(color_map)
level = colorlevel;
else
level = size([color_map], 1);
end
niiclass = class(nii.img);
h1 = plot_cbar(fig, cbar_axes, cbarminmax_axes, cbarminmax, ...
level, handles, useimagesc, colorindex, color_map, ...
colorlevel, highcolor, niiclass, nii_view.numscan);
handles.cbar_image = h1;
handles.cbar_axes = cbar_axes;
handles.cbarminmax_axes = cbarminmax_axes;
end
nii_view.handles = handles; % store handles
nii_view.usepanel = usepanel; % whole panel at low right cornor
nii_view.usestretch = usestretch; % stretch display of voxel_size
nii_view.useinterp = useinterp; % use interpolation
nii_view.colorindex = colorindex; % store colorindex variable
nii_view.buttondown = buttondown; % command after button down click
nii_view.cbarminmax = cbarminmax; % store min max value for colorbar
set_coordinates(nii_view,useinterp); % coord unit
if ~isfield(nii_view, 'axi_xhair') | ...
~isfield(nii_view, 'cor_xhair') | ...
~isfield(nii_view, 'sag_xhair')
nii_view.axi_xhair = []; % top cross hair
nii_view.cor_xhair = []; % front cross hair
nii_view.sag_xhair = []; % side cross hair
end
if ~isempty(color_map)
nii_view.color_map = color_map;
end
if ~isempty(colorlevel)
nii_view.colorlevel = colorlevel;
end
if ~isempty(highcolor)
nii_view.highcolor = highcolor;
end
update_nii_view(nii_view);
if ~isempty(setunit)
update_unit(fig, setunit);
end
if ~isempty(setviewpoint)
update_viewpoint(fig, setviewpoint);
end
if ~isempty(setcrosshaircolor)
update_crosshaircolor(fig, setcrosshaircolor);
end
if ~isempty(usecrosshair)
update_usecrosshair(fig, usecrosshair);
end
nii_menu = getappdata(fig, 'nii_menu');
if ~isempty(nii_menu)
if nii.hdr.dime.datatype == 128 | nii.hdr.dime.datatype == 511
set(nii_menu.Minterp,'Userdata',1,'Label','Interp on','enable','off');
elseif useinterp
set(nii_menu.Minterp,'Userdata',0,'Label','Interp off');
else
set(nii_menu.Minterp,'Userdata',1,'Label','Interp on');
end
end
windowbuttonmotion = get(fig, 'windowbuttonmotion');
windowbuttonmotion = [windowbuttonmotion '; view_nii(''move_cursor'');'];
set(fig, 'windowbuttonmotion', windowbuttonmotion);
return; % init
%----------------------------------------------------------------
function fig = update_img(img, fig, opt)
nii_menu = getappdata(fig,'nii_menu');
if ~isempty(nii_menu)
set(nii_menu.Mzoom,'Userdata',1,'Label','Zoom on');
set(fig,'pointer','arrow');
zoom off;
end
nii_view = getappdata(fig,'nii_view');
change_interp = 0;
if isfield(opt, 'useinterp') & opt.useinterp ~= nii_view.useinterp
nii_view.useinterp = opt.useinterp;
change_interp = 1;
end
setscanid = 1;
if isfield(opt, 'setscanid')
setscanid = round(opt.setscanid);
if setscanid < 1
setscanid = 1;
end
if setscanid > nii_view.numscan
setscanid = nii_view.numscan;
end
end
if isfield(opt, 'glblocminmax') & ~isempty(opt.glblocminmax)
minvalue = opt.glblocminmax(1);
maxvalue = opt.glblocminmax(2);
else
minvalue = img(:,:,:,setscanid);
minvalue = double(minvalue(:));
minvalue = min(minvalue(~isnan(minvalue)));
maxvalue = img(:,:,:,setscanid);
maxvalue = double(maxvalue(:));
maxvalue = max(maxvalue(~isnan(maxvalue)));
end
if isfield(opt, 'setvalue')
setvalue = opt.setvalue;
if isfield(opt, 'glblocminmax') & ~isempty(opt.glblocminmax)
minvalue = opt.glblocminmax(1);
maxvalue = opt.glblocminmax(2);
else
minvalue = double(min(setvalue.val));
maxvalue = double(max(setvalue.val));
end
bgimg = double(img);
minbg = double(min(bgimg(:)));
maxbg = double(max(bgimg(:)));
bgimg = scale_in(bgimg, minbg, maxbg, 55) + 200; % scale to 201~256
cbarminmax = [minvalue maxvalue];
if nii_view.useinterp
% scale signal data to 1~200
%
img = repmat(nan, size(img));
img(setvalue.idx) = setvalue.val;
% 200 level for source image
%
bgimg = single(scale_out(bgimg, cbarminmax(1), cbarminmax(2), 199));
else
bgimg(setvalue.idx) = NaN;
minbg = double(min(bgimg(:)));
maxbg = double(max(bgimg(:)));
bgimg(setvalue.idx) = minbg;
% bgimg must be normalized to [201 256]
%
bgimg = 55 * (bgimg-min(bgimg(:))) / (max(bgimg(:))-min(bgimg(:))) + 201;
bgimg(setvalue.idx) = 0;
% scale signal data to 1~200
%
img = zeros(size(img));
img(setvalue.idx) = scale_in(setvalue.val, minvalue, maxvalue, 199);
img = img + bgimg;
bgimg = [];
img = scale_out(img, cbarminmax(1), cbarminmax(2), 199);
minvalue = double(min(img(:)));
maxvalue = double(max(img(:)));
if isfield(opt,'glblocminmax') & ~isempty(opt.glblocminmax)
minvalue = opt.glblocminmax(1);
end
end
nii_view.bgimg = bgimg;
nii_view.setvalue = setvalue;
else
cbarminmax = [minvalue maxvalue];
end
update_cbarminmax(fig, cbarminmax);
nii_view.cbarminmax = cbarminmax;
nii_view.nii.img = img;
nii_view.minvalue = minvalue;
nii_view.maxvalue = maxvalue;
nii_view.scanid = setscanid;
change_colormap(fig);
% init color (gray) scaling to make sure the slice clim take the
% global clim [min(nii.img(:)) max(nii.img(:))]
%
if isempty(nii_view.bgimg)
clim = [minvalue maxvalue];
else
clim = [minvalue double(max(nii_view.bgimg(:)))];
end
if clim(1) == clim(2)
clim(2) = clim(1) + 0.000001;
end
if strcmpi(get(nii_view.handles.axial_image,'cdatamapping'), 'direct')
useimagesc = 0;
else
useimagesc = 1;
end
if ~isempty(nii_view.bgimg) % with interpolation
Saxi = squeeze(nii_view.bgimg(:,:,nii_view.slices.axi));
if isfield(nii_view.handles,'axial_bg') & ~isempty(nii_view.handles.axial_bg)
set(nii_view.handles.axial_bg,'CData',double(Saxi)');
else
axes(nii_view.handles.axial_axes);
if useimagesc
nii_view.handles.axial_bg = surface(zeros(size(Saxi')),double(Saxi'),'edgecolor','none','facecolor','interp');
else
nii_view.handles.axial_bg = surface(zeros(size(Saxi')),double(Saxi'),'cdatamapping','direct','edgecolor','none','facecolor','interp');
end
order = get(gca,'child');
order(find(order == nii_view.handles.axial_bg)) = [];
order = [order; nii_view.handles.axial_bg];
set(gca, 'child', order);
end
end
if isfield(nii_view.handles,'axial_image'),
if nii_view.nii.hdr.dime.datatype == 128 | nii_view.nii.hdr.dime.datatype == 511
Saxi = squeeze(nii_view.nii.img(:,:,nii_view.slices.axi,:,setscanid));
Saxi = permute(Saxi, [2 1 3]);
else
Saxi = squeeze(nii_view.nii.img(:,:,nii_view.slices.axi,setscanid));
Saxi = Saxi';
end
set(nii_view.handles.axial_image,'CData',double(Saxi));
end
set(nii_view.handles.axial_axes,'CLim',clim);
if ~isempty(nii_view.bgimg)
Scor = squeeze(nii_view.bgimg(:,nii_view.slices.cor,:));
if isfield(nii_view.handles,'coronal_bg') & ~isempty(nii_view.handles.coronal_bg)
set(nii_view.handles.coronal_bg,'CData',double(Scor)');
else
axes(nii_view.handles.coronal_axes);
if useimagesc
nii_view.handles.coronal_bg = surface(zeros(size(Scor')),double(Scor'),'edgecolor','none','facecolor','interp');
else
nii_view.handles.coronal_bg = surface(zeros(size(Scor')),double(Scor'),'cdatamapping','direct','edgecolor','none','facecolor','interp');
end
order = get(gca,'child');
order(find(order == nii_view.handles.coronal_bg)) = [];
order = [order; nii_view.handles.coronal_bg];
set(gca, 'child', order);
end
end
if isfield(nii_view.handles,'coronal_image'),
if nii_view.nii.hdr.dime.datatype == 128 | nii_view.nii.hdr.dime.datatype == 511
Scor = squeeze(nii_view.nii.img(:,nii_view.slices.cor,:,:,setscanid));
Scor = permute(Scor, [2 1 3]);
else
Scor = squeeze(nii_view.nii.img(:,nii_view.slices.cor,:,setscanid));
Scor = Scor';
end
set(nii_view.handles.coronal_image,'CData',double(Scor));
end
set(nii_view.handles.coronal_axes,'CLim',clim);
if ~isempty(nii_view.bgimg)
Ssag = squeeze(nii_view.bgimg(nii_view.slices.sag,:,:));
if isfield(nii_view.handles,'sagittal_bg') & ~isempty(nii_view.handles.sagittal_bg)
set(nii_view.handles.sagittal_bg,'CData',double(Ssag)');
else
axes(nii_view.handles.sagittal_axes);
if useimagesc
nii_view.handles.sagittal_bg = surface(zeros(size(Ssag')),double(Ssag'),'edgecolor','none','facecolor','interp');
else
nii_view.handles.sagittal_bg = surface(zeros(size(Ssag')),double(Ssag'),'cdatamapping','direct','edgecolor','none','facecolor','interp');
end
order = get(gca,'child');
order(find(order == nii_view.handles.sagittal_bg)) = [];
order = [order; nii_view.handles.sagittal_bg];
set(gca, 'child', order);
end
end
if isfield(nii_view.handles,'sagittal_image'),
if nii_view.nii.hdr.dime.datatype == 128 | nii_view.nii.hdr.dime.datatype == 511
Ssag = squeeze(nii_view.nii.img(nii_view.slices.sag,:,:,:,setscanid));
Ssag = permute(Ssag, [2 1 3]);
else
Ssag = squeeze(nii_view.nii.img(nii_view.slices.sag,:,:,setscanid));
Ssag = Ssag';
end
set(nii_view.handles.sagittal_image,'CData',double(Ssag));
end
set(nii_view.handles.sagittal_axes,'CLim',clim);
update_nii_view(nii_view);
if isfield(opt, 'setvalue')
if ~isfield(nii_view,'highcolor') | ~isequal(size(nii_view.highcolor),[56 3])
% 55 level for brain structure (paded 0 for highcolor level 1, i.e. normal level 201, to make 56 highcolor)
%
update_highcolor(fig, [zeros(1,3);gray(55)], []);
end
if nii_view.colorindex ~= 2
update_colorindex(fig, 2);
end
old_color = get(nii_view.handles.xhair_color,'user');
if isequal(old_color, [1 0 0])
update_crosshaircolor(fig, [1 1 0]);
end
% if change_interp
% update_useinterp(fig, nii_view.useinterp);
% end
end
if change_interp
update_useinterp(fig, nii_view.useinterp);
end
return; % update_img
%----------------------------------------------------------------
function [top_pos, front_pos, side_pos] = ...
axes_pos(fig,area,vol_size,usestretch)
set(fig,'unit','pixel');
fig_pos = get(fig,'position');
gap_x = 15/fig_pos(3); % width of vertical scrollbar
gap_y = 15/fig_pos(4); % width of horizontal scrollbar
a = (area(3) - gap_x * 1.3) * fig_pos(3) / (vol_size(1) + vol_size(2)); % no crosshair lost in zoom
b = (area(4) - gap_y * 3) * fig_pos(4) / (vol_size(2) + vol_size(3));
c = min([a b]); % make sure 'ax' is inside 'area'
top_w = vol_size(1) * c / fig_pos(3);
side_w = vol_size(2) * c / fig_pos(3);
top_h = vol_size(2) * c / fig_pos(4);
side_h = vol_size(3) * c / fig_pos(4);
side_x = area(1) + top_w + gap_x * 1.3; % no crosshair lost in zoom
side_y = area(2) + top_h + gap_y * 3;
if usestretch
if a > b % top touched ceiling, use b
d = (area(3) - gap_x * 1.3) / (top_w + side_w); % no crosshair lost in zoom
top_w = top_w * d;
side_w = side_w * d;
side_x = area(1) + top_w + gap_x * 1.3; % no crosshair lost in zoom
else
d = (area(4) - gap_y * 3) / (top_h + side_h);
top_h = top_h * d;
side_h = side_h * d;
side_y = area(2) + top_h + gap_y * 3;
end
end
top_pos = [area(1) area(2)+gap_y top_w top_h];
front_pos = [area(1) side_y top_w side_h];
side_pos = [side_x side_y side_w side_h];
set(fig,'unit','normal');
return; % axes_pos
%----------------------------------------------------------------
function [top_ax, front_ax, side_ax] ...
= create_ax(fig, area, vol_size, usestretch)
cur_fig = gcf; % save h_wait fig
figure(fig);
[top_pos, front_pos, side_pos] = ...
axes_pos(fig,area,vol_size,usestretch);
nii_view = getappdata(fig, 'nii_view');
if isempty(nii_view)
top_ax = axes('position', top_pos);
front_ax = axes('position', front_pos);
side_ax = axes('position', side_pos);
else
top_ax = nii_view.handles.axial_axes;
front_ax = nii_view.handles.coronal_axes;
side_ax = nii_view.handles.sagittal_axes;
set(top_ax, 'position', top_pos);
set(front_ax, 'position', front_pos);
set(side_ax, 'position', side_pos);
end
figure(cur_fig);
return; % create_ax
%----------------------------------------------------------------
function [cbar_axes, cbarminmax_axes] = create_cbar_axes(fig, cbar_area, nii_view)
if isempty(cbar_area) % without_cbar
cbar_axes = [];
cbarminmax_axes = [];
return;
end
cur_fig = gcf; % save h_wait fig
figure(fig);
if ~exist('nii_view', 'var')
nii_view = getappdata(fig, 'nii_view');
end
if isempty(nii_view) | ~isfield(nii_view.handles,'cbar_axes') | isempty(nii_view.handles.cbar_axes)
cbarminmax_axes = axes('position', cbar_area);
cbar_axes = axes('position', cbar_area);
else
cbarminmax_axes = nii_view.handles.cbarminmax_axes;
cbar_axes = nii_view.handles.cbar_axes;
set(cbarminmax_axes, 'position', cbar_area);
set(cbar_axes, 'position', cbar_area);
end
figure(cur_fig);
return; % create_cbar_axes
%----------------------------------------------------------------
function h1 = plot_view(fig, x, y, img_ax, img_slice, clim, ...
cbarminmax, handles, useimagesc, colorindex, color_map, ...
colorlevel, highcolor, useinterp, numscan)
h1 = [];
if x > 1 & y > 1,
axes(img_ax);
nii_view = getappdata(fig, 'nii_view');
if isempty(nii_view)
% set colormap first
%
nii.handles = handles;
nii.handles.axial_axes = img_ax;
nii.colorindex = colorindex;
nii.color_map = color_map;
nii.colorlevel = colorlevel;
nii.highcolor = highcolor;
nii.numscan = numscan;
change_colormap(fig, nii, colorindex, cbarminmax);
if useinterp
if useimagesc
h1 = surface(zeros(size(img_slice)),double(img_slice),'edgecolor','none','facecolor','interp');
else
h1 = surface(zeros(size(img_slice)),double(img_slice),'cdatamapping','direct','edgecolor','none','facecolor','interp');
end
set(gca,'clim',clim);
else
if useimagesc
h1 = imagesc(img_slice,clim);
else
h1 = image(img_slice);
end
set(gca,'clim',clim);
end
else
h1 = nii_view.handles.axial_image;
if ~isequal(get(h1,'parent'), img_ax)
h1 = nii_view.handles.coronal_image;
end
if ~isequal(get(h1,'parent'), img_ax)
h1 = nii_view.handles.sagittal_image;
end
set(h1, 'cdata', double(img_slice));
set(h1, 'xdata', 1:size(img_slice,2));
set(h1, 'ydata', 1:size(img_slice,1));
end
set(img_ax,'YDir','normal','XLimMode','manual','YLimMode','manual',...
'ClimMode','manual','visible','off', ...
'xtick',[],'ytick',[], 'clim', clim);
end
return; % plot_view
%----------------------------------------------------------------
function h1 = plot_cbar(fig, cbar_axes, cbarminmax_axes, cbarminmax, ...
level, handles, useimagesc, colorindex, color_map, ...
colorlevel, highcolor, niiclass, numscan, nii_view)
cbar_image = [1:level]';
% In a uint8 or uint16 indexed image, 0 points to the first row
% in the colormap
%
if 0 % strcmpi(niiclass,'uint8') | strcmpi(niiclass,'uint16')
% we use single for display anyway
ylim = [0, level-1];
else
ylim = [1, level];
end
axes(cbarminmax_axes);
plot([0 0], cbarminmax, 'w');
axis tight;
set(cbarminmax_axes,'YDir','normal', ...
'XLimMode','manual','YLimMode','manual','YColor',[0 0 0], ...
'XColor',[0 0 0],'xtick',[],'YAxisLocation','right');
ylimb = get(cbarminmax_axes,'ylim');
ytickb = get(cbarminmax_axes,'ytick');
ytick=(ylim(2)-ylim(1))*(ytickb-ylimb(1))/(ylimb(2)-ylimb(1))+ylim(1);
axes(cbar_axes);
if ~exist('nii_view', 'var')
nii_view = getappdata(fig, 'nii_view');
end
if isempty(nii_view) | ~isfield(nii_view.handles,'cbar_image') | isempty(nii_view.handles.cbar_image)
% set colormap first
%
nii.handles = handles;
nii.colorindex = colorindex;
nii.color_map = color_map;
nii.colorlevel = colorlevel;
nii.highcolor = highcolor;
nii.numscan = numscan;
change_colormap(fig, nii, colorindex, cbarminmax);
h1 = image([0,1], [ylim(1),ylim(2)], cbar_image);
else
h1 = nii_view.handles.cbar_image;
set(h1, 'cdata', double(cbar_image));
end
set(cbar_axes,'YDir','normal','XLimMode','manual', ...
'YLimMode','manual','YColor',[0 0 0],'XColor',[0 0 0],'xtick',[], ...
'YAxisLocation','right','ylim',ylim,'ytick',ytick,'yticklabel','');
return; % plot_cbar
%----------------------------------------------------------------
function set_coordinates(nii_view,useinterp)
imgPlim.vox = nii_view.dims;
imgNlim.vox = [1 1 1];
if useinterp
xdata_ax = [imgNlim.vox(1) imgPlim.vox(1)];
ydata_ax = [imgNlim.vox(2) imgPlim.vox(2)];
zdata_ax = [imgNlim.vox(3) imgPlim.vox(3)];
else
xdata_ax = [imgNlim.vox(1)-0.5 imgPlim.vox(1)+0.5];
ydata_ax = [imgNlim.vox(2)-0.5 imgPlim.vox(2)+0.5];
zdata_ax = [imgNlim.vox(3)-0.5 imgPlim.vox(3)+0.5];
end
if isfield(nii_view.handles,'axial_image') & ~isempty(nii_view.handles.axial_image)
set(nii_view.handles.axial_axes,'Xlim',xdata_ax);
set(nii_view.handles.axial_axes,'Ylim',ydata_ax);
end;
if isfield(nii_view.handles,'coronal_image') & ~isempty(nii_view.handles.coronal_image)
set(nii_view.handles.coronal_axes,'Xlim',xdata_ax);
set(nii_view.handles.coronal_axes,'Ylim',zdata_ax);
end;
if isfield(nii_view.handles,'sagittal_image') & ~isempty(nii_view.handles.sagittal_image)
set(nii_view.handles.sagittal_axes,'Xlim',ydata_ax);
set(nii_view.handles.sagittal_axes,'Ylim',zdata_ax);
end;
return % set_coordinates
%----------------------------------------------------------------
function set_image_value(nii_view),
% get coordinates of selected voxel and the image intensity there
%
sag = round(nii_view.slices.sag);
cor = round(nii_view.slices.cor);
axi = round(nii_view.slices.axi);
if 0 % isfield(nii_view, 'disp')
img = nii_view.disp;
else
img = nii_view.nii.img;
end
if nii_view.nii.hdr.dime.datatype == 128
imgvalue = [double(img(sag,cor,axi,1,nii_view.scanid)) double(img(sag,cor,axi,2,nii_view.scanid)) double(img(sag,cor,axi,3,nii_view.scanid))];
set(nii_view.handles.imval,'Value',imgvalue);
set(nii_view.handles.imval,'String',sprintf('%7.4g %7.4g %7.4g',imgvalue));
elseif nii_view.nii.hdr.dime.datatype == 511
R = double(img(sag,cor,axi,1,nii_view.scanid)) * (nii_view.nii.hdr.dime.glmax - ...
nii_view.nii.hdr.dime.glmin) + nii_view.nii.hdr.dime.glmin;
G = double(img(sag,cor,axi,2,nii_view.scanid)) * (nii_view.nii.hdr.dime.glmax - ...
nii_view.nii.hdr.dime.glmin) + nii_view.nii.hdr.dime.glmin;
B = double(img(sag,cor,axi,3,nii_view.scanid)) * (nii_view.nii.hdr.dime.glmax - ...
nii_view.nii.hdr.dime.glmin) + nii_view.nii.hdr.dime.glmin;
imgvalue = [double(img(sag,cor,axi,1,nii_view.scanid)) double(img(sag,cor,axi,2,nii_view.scanid)) double(img(sag,cor,axi,3,nii_view.scanid))];
set(nii_view.handles.imval,'Value',imgvalue);
imgvalue = [R G B];
set(nii_view.handles.imval,'String',sprintf('%7.4g %7.4g %7.4g',imgvalue));
else
imgvalue = double(img(sag,cor,axi,nii_view.scanid));
set(nii_view.handles.imval,'Value',imgvalue);
if isnan(imgvalue) | imgvalue > nii_view.cbarminmax(2)
imgvalue = 0;
end
set(nii_view.handles.imval,'String',sprintf('%.6g',imgvalue));
end
% Now update the coordinates of the selected voxel
nii_view = update_imgXYZ(nii_view);
if get(nii_view.handles.coord,'value') == 1,
sag = nii_view.imgXYZ.vox(1);
cor = nii_view.imgXYZ.vox(2);
axi = nii_view.imgXYZ.vox(3);
org = nii_view.origin;
elseif get(nii_view.handles.coord,'value') == 2,
sag = nii_view.imgXYZ.mm(1);
cor = nii_view.imgXYZ.mm(2);
axi = nii_view.imgXYZ.mm(3);
org = [0 0 0];
elseif get(nii_view.handles.coord,'value') == 3,
sag = nii_view.imgXYZ.tal(1);
cor = nii_view.imgXYZ.tal(2);
axi = nii_view.imgXYZ.tal(3);
org = [0 0 0];
end
set(nii_view.handles.impos,'Value',[sag,cor,axi]);
if get(nii_view.handles.coord,'value') == 1,
string = sprintf('%7.0f %7.0f %7.0f',sag,cor,axi);
org_str = sprintf('%7.0f %7.0f %7.0f', org(1), org(2), org(3));
else
string = sprintf('%7.1f %7.1f %7.1f',sag,cor,axi);
org_str = sprintf('%7.1f %7.1f %7.1f', org(1), org(2), org(3));
end;
set(nii_view.handles.impos,'String',string);
set(nii_view.handles.origin, 'string', org_str);
return % set_image_value
%----------------------------------------------------------------
function nii_view = get_slice_position(nii_view,view),
% obtain slices that is in correct unit, then update slices
%
slices = nii_view.slices;
switch view,
case 'sag',
currentpoint = get(nii_view.handles.sagittal_axes,'CurrentPoint');
slices.cor = currentpoint(1,1);
slices.axi = currentpoint(1,2);
case 'cor',
currentpoint = get(nii_view.handles.coronal_axes,'CurrentPoint');
slices.sag = currentpoint(1,1);
slices.axi = currentpoint(1,2);
case 'axi',
currentpoint = get(nii_view.handles.axial_axes,'CurrentPoint');
slices.sag = currentpoint(1,1);
slices.cor = currentpoint(1,2);
end
% update nii_view.slices with the updated slices
%
nii_view.slices.axi = round(slices.axi);
nii_view.slices.cor = round(slices.cor);
nii_view.slices.sag = round(slices.sag);
return % get_slice_position
%----------------------------------------------------------------
function nii_view = get_slider_position(nii_view),
[nii_view.slices.sag,nii_view.slices.cor,nii_view.slices.axi] = deal(0);
if isfield(nii_view.handles,'sagittal_slider'),
if ishandle(nii_view.handles.sagittal_slider),
nii_view.slices.sag = ...
round(get(nii_view.handles.sagittal_slider,'Value'));
end
end
if isfield(nii_view.handles,'coronal_slider'),
if ishandle(nii_view.handles.coronal_slider),
nii_view.slices.cor = ...
round(nii_view.dims(2) - ...
get(nii_view.handles.coronal_slider,'Value') + 1);
end
end
if isfield(nii_view.handles,'axial_slider'),
if ishandle(nii_view.handles.axial_slider),
nii_view.slices.axi = ...
round(get(nii_view.handles.axial_slider,'Value'));
end
end
nii_view = check_slices(nii_view);
return % get_slider_position
%----------------------------------------------------------------
function nii_view = update_imgXYZ(nii_view),
nii_view.imgXYZ.vox = ...
[nii_view.slices.sag,nii_view.slices.cor,nii_view.slices.axi];
nii_view.imgXYZ.mm = ...
(nii_view.imgXYZ.vox - nii_view.origin) .* nii_view.voxel_size;
% nii_view.imgXYZ.tal = mni2tal(nii_view.imgXYZ.mni);
return % update_imgXYZ
%----------------------------------------------------------------
function nii_view = convert2voxel(nii_view,slices),
if get(nii_view.handles.coord,'value') == 1,
% [slices.axi, slices.cor, slices.sag] are in vox
%
nii_view.slices.axi = round(slices.axi);
nii_view.slices.cor = round(slices.cor);
nii_view.slices.sag = round(slices.sag);
elseif get(nii_view.handles.coord,'value') == 2,
% [slices.axi, slices.cor, slices.sag] are in mm
%
xpix = nii_view.voxel_size(1);
ypix = nii_view.voxel_size(2);
zpix = nii_view.voxel_size(3);
nii_view.slices.axi = round(slices.axi / zpix + nii_view.origin(3));
nii_view.slices.cor = round(slices.cor / ypix + nii_view.origin(2));
nii_view.slices.sag = round(slices.sag / xpix + nii_view.origin(1));
elseif get(nii_view.handles.coord,'value') == 3,
% [slices.axi, slices.cor, slices.sag] are in talairach
%
xpix = nii_view.voxel_size(1);
ypix = nii_view.voxel_size(2);
zpix = nii_view.voxel_size(3);
xyz_tal = [slices.sag, slices.cor, slices.axi];
xyz_mni = tal2mni(xyz_tal);
nii_view.slices.axi = round(xyz_mni(3) / zpix + nii_view.origin(3));
nii_view.slices.cor = round(xyz_mni(2) / ypix + nii_view.origin(2));
nii_view.slices.sag = round(xyz_mni(1) / xpix + nii_view.origin(1));
end
return % convert2voxel
%----------------------------------------------------------------
function nii_view = check_slices(nii_view),
img = nii_view.nii.img;
[ SagSize, CorSize, AxiSize, TimeSize ] = size(img);
if nii_view.slices.sag > SagSize, nii_view.slices.sag = SagSize; end;
if nii_view.slices.sag < 1, nii_view.slices.sag = 1; end;
if nii_view.slices.cor > CorSize, nii_view.slices.cor = CorSize; end;
if nii_view.slices.cor < 1, nii_view.slices.cor = 1; end;
if nii_view.slices.axi > AxiSize, nii_view.slices.axi = AxiSize; end;
if nii_view.slices.axi < 1, nii_view.slices.axi = 1; end;
if nii_view.scanid > TimeSize, nii_view.scanid = TimeSize; end;
if nii_view.scanid < 1, nii_view.scanid = 1; end;
return % check_slices
%----------------------------------------------------------------
%
% keep this function small, since it will be called for every click
%
function nii_view = update_nii_view(nii_view)
% add imgXYZ into nii_view struct
%
nii_view = check_slices(nii_view);
nii_view = update_imgXYZ(nii_view);
% update xhair
%
p_axi = nii_view.imgXYZ.vox([1 2]);
p_cor = nii_view.imgXYZ.vox([1 3]);
p_sag = nii_view.imgXYZ.vox([2 3]);
nii_view.axi_xhair = ...
rri_xhair(p_axi, nii_view.axi_xhair, nii_view.handles.axial_axes);
nii_view.cor_xhair = ...
rri_xhair(p_cor, nii_view.cor_xhair, nii_view.handles.coronal_axes);
nii_view.sag_xhair = ...
rri_xhair(p_sag, nii_view.sag_xhair, nii_view.handles.sagittal_axes);
setappdata(nii_view.fig, 'nii_view', nii_view);
set_image_value(nii_view);
return; % update_nii_view
%----------------------------------------------------------------
function hist_plot(fig)
nii_view = getappdata(fig,'nii_view');
if isfield(nii_view, 'disp')
img = nii_view.disp;
else
img = nii_view.nii.img;
end
img = double(img(:));
if length(unique(round(img))) == length(unique(img))
is_integer = 1;
range = max(img) - min(img) + 1;
figure; hist(img, range);
set(gca, 'xlim', [-range/5, max(img)]);
else
is_integer = 0;
figure; hist(img);
end
xlabel('Voxel Intensity');
ylabel('Voxel Numbers for Each Intensity');
set(gcf, 'NumberTitle','off','Name','Histogram Plot');
return; % hist_plot
%----------------------------------------------------------------
function hist_eq(fig)
nii_view = getappdata(fig,'nii_view');
old_pointer = get(fig,'Pointer');
set(fig,'Pointer','watch');
if get(nii_view.handles.hist_eq,'value')
max_img = double(max(nii_view.nii.img(:)));
tmp = double(nii_view.nii.img) / max_img; % normalize for histeq
tmp = histeq(tmp(:));
nii_view.disp = reshape(tmp, size(nii_view.nii.img));
min_disp = min(nii_view.disp(:));
nii_view.disp = (nii_view.disp - min_disp); % range having eq hist
nii_view.disp = nii_view.disp * max_img / max(nii_view.disp(:));
nii_view.disp = single(nii_view.disp);
else
if isfield(nii_view, 'disp')
nii_view.disp = nii_view.nii.img;
else
set(fig,'Pointer',old_pointer);
return;
end
end
% update axial view
%
img_slice = squeeze(double(nii_view.disp(:,:,nii_view.slices.axi)));
h1 = nii_view.handles.axial_image;
set(h1, 'cdata', double(img_slice)');
% update coronal view
%
img_slice = squeeze(double(nii_view.disp(:,nii_view.slices.cor,:)));
h1 = nii_view.handles.coronal_image;
set(h1, 'cdata', double(img_slice)');
% update sagittal view
%
img_slice = squeeze(double(nii_view.disp(nii_view.slices.sag,:,:)));
h1 = nii_view.handles.sagittal_image;
set(h1, 'cdata', double(img_slice)');
% remove disp field if un-check 'histeq' button
%
if ~get(nii_view.handles.hist_eq,'value') & isfield(nii_view, 'disp')
nii_view = rmfield(nii_view, 'disp');
end
update_nii_view(nii_view);
set(fig,'Pointer',old_pointer);
return; % hist_eq
%----------------------------------------------------------------
function [top1_label, top2_label, side1_label, side2_label] = ...
dir_label(fig, top_ax, front_ax, side_ax)
nii_view = getappdata(fig,'nii_view');
top_pos = get(top_ax,'position');
front_pos = get(front_ax,'position');
side_pos = get(side_ax,'position');
top_gap_x = (side_pos(1)-top_pos(1)-top_pos(3)) / (2*top_pos(3));
top_gap_y = (front_pos(2)-top_pos(2)-top_pos(4)) / (2*top_pos(4));
side_gap_x = (side_pos(1)-top_pos(1)-top_pos(3)) / (2*side_pos(3));
side_gap_y = (front_pos(2)-top_pos(2)-top_pos(4)) / (2*side_pos(4));
top1_label_pos = [0, 1]; % rot0
top2_label_pos = [1, 0]; % rot90
side1_label_pos = [1, - side_gap_y]; % rot0
side2_label_pos = [0, 0]; % rot90
if isempty(nii_view)
axes(top_ax);
top1_label = text(double(top1_label_pos(1)),double(top1_label_pos(2)), ...
'== X =>', ...
'vertical', 'bottom', ...
'unit', 'normal', 'fontsize', 8);
axes(top_ax);
top2_label = text(double(top2_label_pos(1)),double(top2_label_pos(2)), ...
'== Y =>', ...
'rotation', 90, 'vertical', 'top', ...
'unit', 'normal', 'fontsize', 8);
axes(side_ax);
side1_label = text(double(side1_label_pos(1)),double(side1_label_pos(2)), ...
'<= Y ==', ...
'horizontal', 'right', 'vertical', 'top', ...
'unit', 'normal', 'fontsize', 8);
axes(side_ax);
side2_label = text(double(side2_label_pos(1)),double(side2_label_pos(2)), ...
'== Z =>', ...
'rotation', 90, 'vertical', 'bottom', ...
'unit', 'normal', 'fontsize', 8);
else
top1_label = nii_view.handles.top1_label;
top2_label = nii_view.handles.top2_label;
side1_label = nii_view.handles.side1_label;
side2_label = nii_view.handles.side2_label;
set(top1_label, 'position', [top1_label_pos 0]);
set(top2_label, 'position', [top2_label_pos 0]);
set(side1_label, 'position', [side1_label_pos 0]);
set(side2_label, 'position', [side2_label_pos 0]);
end
return; % dir_label
%----------------------------------------------------------------
function update_enable(h, opt);
nii_view = getappdata(h,'nii_view');
handles = nii_view.handles;
if isfield(opt,'enablecursormove')
if opt.enablecursormove
v = 'on';
else
v = 'off';
end
set(handles.Timposcur, 'visible', v);
set(handles.imposcur, 'visible', v);
set(handles.Timvalcur, 'visible', v);
set(handles.imvalcur, 'visible', v);
end
if isfield(opt,'enableviewpoint')
if opt.enableviewpoint
v = 'on';
else
v = 'off';
end
set(handles.Timpos, 'visible', v);
set(handles.impos, 'visible', v);
set(handles.Timval, 'visible', v);
set(handles.imval, 'visible', v);
end
if isfield(opt,'enableorigin')
if opt.enableorigin
v = 'on';
else
v = 'off';
end
set(handles.Torigin, 'visible', v);
set(handles.origin, 'visible', v);
end
if isfield(opt,'enableunit')
if opt.enableunit
v = 'on';
else
v = 'off';
end
set(handles.Tcoord, 'visible', v);
set(handles.coord_frame, 'visible', v);
set(handles.coord, 'visible', v);
end
if isfield(opt,'enablecrosshair')
if opt.enablecrosshair
v = 'on';
else
v = 'off';
end
set(handles.Txhair, 'visible', v);
set(handles.xhair_color, 'visible', v);
set(handles.xhair, 'visible', v);
end
if isfield(opt,'enablehistogram')
if opt.enablehistogram
v = 'on';
vv = 'off';
else
v = 'off';
vv = 'on';
end
set(handles.Tcoord, 'visible', vv);
set(handles.coord_frame, 'visible', vv);
set(handles.coord, 'visible', vv);
set(handles.Thist, 'visible', v);
set(handles.hist_frame, 'visible', v);
set(handles.hist_eq, 'visible', v);
set(handles.hist_plot, 'visible', v);
end
if isfield(opt,'enablecolormap')
if opt.enablecolormap
v = 'on';
else
v = 'off';
end
set(handles.Tcolor, 'visible', v);
set(handles.color_frame, 'visible', v);
set(handles.neg_color, 'visible', v);
set(handles.colorindex, 'visible', v);
end
if isfield(opt,'enablecontrast')
if opt.enablecontrast
v = 'on';
else
v = 'off';
end
set(handles.Tcontrast, 'visible', v);
set(handles.contrast_frame, 'visible', v);
set(handles.contrast_def, 'visible', v);
set(handles.contrast, 'visible', v);
end
if isfield(opt,'enablebrightness')
if opt.enablebrightness
v = 'on';
else
v = 'off';
end
set(handles.Tbrightness, 'visible', v);
set(handles.brightness_frame, 'visible', v);
set(handles.brightness_def, 'visible', v);
set(handles.brightness, 'visible', v);
end
if isfield(opt,'enabledirlabel')
if opt.enabledirlabel
v = 'on';
else
v = 'off';
end
set(handles.top1_label, 'visible', v);
set(handles.top2_label, 'visible', v);
set(handles.side1_label, 'visible', v);
set(handles.side2_label, 'visible', v);
end
if isfield(opt,'enableslider')
if opt.enableslider
v = 'on';
else
v = 'off';
end
if isfield(handles,'sagittal_slider') & ishandle(handles.sagittal_slider)
set(handles.sagittal_slider, 'visible', v);
end
if isfield(handles,'coronal_slider') & ishandle(handles.coronal_slider)
set(handles.coronal_slider, 'visible', v);
end
if isfield(handles,'axial_slider') & ishandle(handles.axial_slider)
set(handles.axial_slider, 'visible', v);
end
end
return; % update_enable
%----------------------------------------------------------------
function update_usepanel(fig, usepanel)
if isempty(usepanel)
return;
end
if usepanel
opt.enablecursormove = 1;
opt.enableviewpoint = 1;
opt.enableorigin = 1;
opt.enableunit = 1;
opt.enablecrosshair = 1;
% opt.enablehistogram = 1;
opt.enablecolormap = 1;
opt.enablecontrast = 1;
opt.enablebrightness = 1;
else
opt.enablecursormove = 0;
opt.enableviewpoint = 0;
opt.enableorigin = 0;
opt.enableunit = 0;
opt.enablecrosshair = 0;
% opt.enablehistogram = 0;
opt.enablecolormap = 0;
opt.enablecontrast = 0;
opt.enablebrightness = 0;
end
update_enable(fig, opt);
nii_view = getappdata(fig,'nii_view');
nii_view.usepanel = usepanel;
setappdata(fig,'nii_view',nii_view);
return; % update_usepanel
%----------------------------------------------------------------
function update_usecrosshair(fig, usecrosshair)
if isempty(usecrosshair)
return;
end
if usecrosshair
v=1;
else
v=2;
end
nii_view = getappdata(fig,'nii_view');
set(nii_view.handles.xhair,'value',v);
opt.command = 'crosshair';
view_nii(fig, opt);
return; % update_usecrosshair
%----------------------------------------------------------------
function update_usestretch(fig, usestretch)
nii_view = getappdata(fig,'nii_view');
handles = nii_view.handles;
fig = nii_view.fig;
area = nii_view.area;
vol_size = nii_view.voxel_size .* nii_view.dims;
% Three Axes & label
%
[top_ax, front_ax, side_ax] = ...
create_ax(fig, area, vol_size, usestretch);
dir_label(fig, top_ax, front_ax, side_ax);
top_pos = get(top_ax,'position');
front_pos = get(front_ax,'position');
side_pos = get(side_ax,'position');
% Sagittal Slider
%
x = side_pos(1);
y = top_pos(2) + top_pos(4);
w = side_pos(3);
h = (front_pos(2) - y) / 2;
y = y + h;
pos = [x y w h];
if isfield(handles,'sagittal_slider') & ishandle(handles.sagittal_slider)
set(handles.sagittal_slider,'position',pos);
end
% Coronal Slider
%
x = top_pos(1);
y = top_pos(2) + top_pos(4);
w = top_pos(3);
h = (front_pos(2) - y) / 2;
y = y + h;
pos = [x y w h];
if isfield(handles,'coronal_slider') & ishandle(handles.coronal_slider)
set(handles.coronal_slider,'position',pos);
end
% Axial Slider
%
x = top_pos(1);
y = area(2);
w = top_pos(3);
h = top_pos(2) - y;
pos = [x y w h];
if isfield(handles,'axial_slider') & ishandle(handles.axial_slider)
set(handles.axial_slider,'position',pos);
end
% plot info view
%
% info_pos = [side_pos([1,3]); top_pos([2,4])];
% info_pos = info_pos(:);
gap = side_pos(1)-(top_pos(1)+top_pos(3));
info_pos(1) = side_pos(1) + gap;
info_pos(2) = area(2);
info_pos(3) = side_pos(3) - gap;
info_pos(4) = top_pos(2) + top_pos(4) - area(2) - gap;
num_inputline = 10;
inputline_space =info_pos(4) / num_inputline;
% Image Intensity Value at Cursor
%
x = info_pos(1);
y = info_pos(2);
w = info_pos(3)*0.5;
h = inputline_space*0.6;
pos = [x y w h];
set(handles.Timvalcur,'position',pos);
x = x + w;
w = info_pos(3)*0.5;
pos = [x y w h];
set(handles.imvalcur,'position',pos);
% Position at Cursor
%
x = info_pos(1);
y = y + inputline_space;
w = info_pos(3)*0.5;
pos = [x y w h];
set(handles.Timposcur,'position',pos);
x = x + w;
w = info_pos(3)*0.5;
pos = [x y w h];
set(handles.imposcur,'position',pos);
% Image Intensity Value at Mouse Click
%
x = info_pos(1);
y = y + inputline_space;
w = info_pos(3)*0.5;
pos = [x y w h];
set(handles.Timval,'position',pos);
x = x + w;
w = info_pos(3)*0.5;
pos = [x y w h];
set(handles.imval,'position',pos);
% Viewpoint Position at Mouse Click
%
x = info_pos(1);
y = y + inputline_space;
w = info_pos(3)*0.5;
pos = [x y w h];
set(handles.Timpos,'position',pos);
x = x + w + 0.005;
y = y - 0.008;
w = info_pos(3)*0.5;
h = inputline_space*0.9;
pos = [x y w h];
set(handles.impos,'position',pos);
% Origin Position
%
x = info_pos(1);
y = y + inputline_space*1.2;
w = info_pos(3)*0.5;
h = inputline_space*0.6;
pos = [x y w h];
set(handles.Torigin,'position',pos);
x = x + w;
w = info_pos(3)*0.5;
pos = [x y w h];
set(handles.origin,'position',pos);
if 0
% Axes Unit
%
x = info_pos(1);
y = y + inputline_space;
w = info_pos(3)*0.5;
pos = [x y w h];
set(handles.Tcoord,'position',pos);
x = x + w + 0.005;
w = info_pos(3)*0.5 - 0.005;
pos = [x y w h];
set(handles.coord,'position',pos);
end
% Crosshair
%
x = info_pos(1);
y = y + inputline_space;
w = info_pos(3)*0.4;
pos = [x y w h];
set(handles.Txhair,'position',pos);
x = info_pos(1) + info_pos(3)*0.5;
w = info_pos(3)*0.2;
h = inputline_space*0.7;
pos = [x y w h];
set(handles.xhair_color,'position',pos);
x = info_pos(1) + info_pos(3)*0.7;
w = info_pos(3)*0.3;
pos = [x y w h];
set(handles.xhair,'position',pos);
% Histogram & Color
%
x = info_pos(1);
w = info_pos(3)*0.45;
h = inputline_space * 1.5;
pos = [x, y+inputline_space*0.9, w, h];
set(handles.hist_frame,'position',pos);
set(handles.coord_frame,'position',pos);
x = info_pos(1) + info_pos(3)*0.475;
w = info_pos(3)*0.525;
h = inputline_space * 1.5;
pos = [x, y+inputline_space*0.9, w, h];
set(handles.color_frame,'position',pos);
x = info_pos(1) + info_pos(3)*0.025;
y = y + inputline_space*1.2;
w = info_pos(3)*0.2;
h = inputline_space*0.7;
pos = [x y w h];
set(handles.hist_eq,'position',pos);
x = x + w;
w = info_pos(3)*0.2;
pos = [x y w h];
set(handles.hist_plot,'position',pos);
x = info_pos(1) + info_pos(3)*0.025;
w = info_pos(3)*0.4;
pos = [x y w h];
set(handles.coord,'position',pos);
x = info_pos(1) + info_pos(3)*0.5;
w = info_pos(3)*0.2;
pos = [x y w h];
set(handles.neg_color,'position',pos);
x = info_pos(1) + info_pos(3)*0.7;
w = info_pos(3)*0.275;
pos = [x y w h];
set(handles.colorindex,'position',pos);
x = info_pos(1) + info_pos(3)*0.1;
y = y + inputline_space;
w = info_pos(3)*0.28;
h = inputline_space*0.6;
pos = [x y w h];
set(handles.Thist,'position',pos);
set(handles.Tcoord,'position',pos);
x = info_pos(1) + info_pos(3)*0.60;
w = info_pos(3)*0.28;
pos = [x y w h];
set(handles.Tcolor,'position',pos);
% Contrast Frame
%
x = info_pos(1);
w = info_pos(3)*0.45;
h = inputline_space * 2;
pos = [x, y+inputline_space*0.8, w, h];
set(handles.contrast_frame,'position',pos);
% Brightness Frame
%
x = info_pos(1) + info_pos(3)*0.475;
w = info_pos(3)*0.525;
pos = [x, y+inputline_space*0.8, w, h];
set(handles.brightness_frame,'position',pos);
% Contrast
%
x = info_pos(1) + info_pos(3)*0.025;
y = y + inputline_space;
w = info_pos(3)*0.4;
h = inputline_space*0.6;
pos = [x y w h];
set(handles.contrast,'position',pos);
% Brightness
%
x = info_pos(1) + info_pos(3)*0.5;
w = info_pos(3)*0.475;
pos = [x y w h];
set(handles.brightness,'position',pos);
% Contrast text/def
%
x = info_pos(1) + info_pos(3)*0.025;
y = y + inputline_space;
w = info_pos(3)*0.22;
pos = [x y w h];
set(handles.Tcontrast,'position',pos);
x = x + w;
w = info_pos(3)*0.18;
pos = [x y w h];
set(handles.contrast_def,'position',pos);
% Brightness text/def
%
x = info_pos(1) + info_pos(3)*0.5;
w = info_pos(3)*0.295;
pos = [x y w h];
set(handles.Tbrightness,'position',pos);
x = x + w;
w = info_pos(3)*0.18;
pos = [x y w h];
set(handles.brightness_def,'position',pos);
return; % update_usestretch
%----------------------------------------------------------------
function update_useinterp(fig, useinterp)
if isempty(useinterp)
return;
end
nii_menu = getappdata(fig, 'nii_menu');
if ~isempty(nii_menu)
if get(nii_menu.Minterp,'user')
set(nii_menu.Minterp,'Userdata',0,'Label','Interp off');
else
set(nii_menu.Minterp,'Userdata',1,'Label','Interp on');
end
end
nii_view = getappdata(fig, 'nii_view');
nii_view.useinterp = useinterp;
if ~isempty(nii_view.handles.axial_image)
if strcmpi(get(nii_view.handles.axial_image,'cdatamapping'), 'direct')
useimagesc = 0;
else
useimagesc = 1;
end
elseif ~isempty(nii_view.handles.coronal_image)
if strcmpi(get(nii_view.handles.coronal_image,'cdatamapping'), 'direct')
useimagesc = 0;
else
useimagesc = 1;
end
else
if strcmpi(get(nii_view.handles.sagittal_image,'cdatamapping'), 'direct')
useimagesc = 0;
else
useimagesc = 1;
end
end
if ~isempty(nii_view.handles.axial_image)
img_slice = get(nii_view.handles.axial_image, 'cdata');
delete(nii_view.handles.axial_image);
axes(nii_view.handles.axial_axes);
clim = get(gca,'clim');
if useinterp
if useimagesc
nii_view.handles.axial_image = surface(zeros(size(img_slice)),double(img_slice),'edgecolor','none','facecolor','interp');
else
nii_view.handles.axial_image = surface(zeros(size(img_slice)),double(img_slice),'cdatamapping','direct','edgecolor','none','facecolor','interp');
end
else
if useimagesc
nii_view.handles.axial_image = imagesc('cdata',img_slice);
else
nii_view.handles.axial_image = image('cdata',img_slice);
end
end
set(gca,'clim',clim);
order = get(gca,'child');
order(find(order == nii_view.handles.axial_image)) = [];
order = [order; nii_view.handles.axial_image];
if isfield(nii_view.handles,'axial_bg') & ~isempty(nii_view.handles.axial_bg)
order(find(order == nii_view.handles.axial_bg)) = [];
order = [order; nii_view.handles.axial_bg];
end
set(gca, 'child', order);
if ~useinterp
if isfield(nii_view.handles,'axial_bg') & ~isempty(nii_view.handles.axial_bg)
delete(nii_view.handles.axial_bg);
nii_view.handles.axial_bg = [];
end
end
set(nii_view.handles.axial_image,'buttondown','view_nii(''axial_image'');');
end
if ~isempty(nii_view.handles.coronal_image)
img_slice = get(nii_view.handles.coronal_image, 'cdata');
delete(nii_view.handles.coronal_image);
axes(nii_view.handles.coronal_axes);
clim = get(gca,'clim');
if useinterp
if useimagesc
nii_view.handles.coronal_image = surface(zeros(size(img_slice)),double(img_slice),'edgecolor','none','facecolor','interp');
else
nii_view.handles.coronal_image = surface(zeros(size(img_slice)),double(img_slice),'cdatamapping','direct','edgecolor','none','facecolor','interp');
end
else
if useimagesc
nii_view.handles.coronal_image = imagesc('cdata',img_slice);
else
nii_view.handles.coronal_image = image('cdata',img_slice);
end
end
set(gca,'clim',clim);
order = get(gca,'child');
order(find(order == nii_view.handles.coronal_image)) = [];
order = [order; nii_view.handles.coronal_image];
if isfield(nii_view.handles,'coronal_bg') & ~isempty(nii_view.handles.coronal_bg)
order(find(order == nii_view.handles.coronal_bg)) = [];
order = [order; nii_view.handles.coronal_bg];
end
set(gca, 'child', order);
if ~useinterp
if isfield(nii_view.handles,'coronal_bg') & ~isempty(nii_view.handles.coronal_bg)
delete(nii_view.handles.coronal_bg);
nii_view.handles.coronal_bg = [];
end
end
set(nii_view.handles.coronal_image,'buttondown','view_nii(''coronal_image'');');
end
if ~isempty(nii_view.handles.sagittal_image)
img_slice = get(nii_view.handles.sagittal_image, 'cdata');
delete(nii_view.handles.sagittal_image);
axes(nii_view.handles.sagittal_axes);
clim = get(gca,'clim');
if useinterp
if useimagesc
nii_view.handles.sagittal_image = surface(zeros(size(img_slice)),double(img_slice),'edgecolor','none','facecolor','interp');
else
nii_view.handles.sagittal_image = surface(zeros(size(img_slice)),double(img_slice),'cdatamapping','direct','edgecolor','none','facecolor','interp');
end
else
if useimagesc
nii_view.handles.sagittal_image = imagesc('cdata',img_slice);
else
nii_view.handles.sagittal_image = image('cdata',img_slice);
end
end
set(gca,'clim',clim);
order = get(gca,'child');
order(find(order == nii_view.handles.sagittal_image)) = [];
order = [order; nii_view.handles.sagittal_image];
if isfield(nii_view.handles,'sagittal_bg') & ~isempty(nii_view.handles.sagittal_bg)
order(find(order == nii_view.handles.sagittal_bg)) = [];
order = [order; nii_view.handles.sagittal_bg];
end
set(gca, 'child', order);
if ~useinterp
if isfield(nii_view.handles,'sagittal_bg') & ~isempty(nii_view.handles.sagittal_bg)
delete(nii_view.handles.sagittal_bg);
nii_view.handles.sagittal_bg = [];
end
end
set(nii_view.handles.sagittal_image,'buttondown','view_nii(''sagittal_image'');');
end
if ~useinterp
nii_view.bgimg = [];
end
set_coordinates(nii_view,useinterp);
setappdata(fig, 'nii_view', nii_view);
return; % update_useinterp
%----------------------------------------------------------------
function update_useimagesc(fig, useimagesc)
if isempty(useimagesc)
return;
end
if useimagesc
v='scaled';
else
v='direct';
end
nii_view = getappdata(fig,'nii_view');
handles = nii_view.handles;
if isfield(handles,'cbar_image') & ishandle(handles.cbar_image)
% set(handles.cbar_image,'cdatamapping',v);
end
set(handles.axial_image,'cdatamapping',v);
set(handles.coronal_image,'cdatamapping',v);
set(handles.sagittal_image,'cdatamapping',v);
return; % update_useimagesc
%----------------------------------------------------------------
function update_shape(fig, area, usecolorbar, usestretch, useimagesc)
nii_view = getappdata(fig,'nii_view');
if isempty(usestretch) % no change, get usestretch
stretchchange = 0;
usestretch = nii_view.usestretch;
else % change, set usestretch
stretchchange = 1;
nii_view.usestretch = usestretch;
end
if isempty(area) % no change, get area
areachange = 0;
area = nii_view.area;
elseif ~isempty(nii_view.cbar_area) % change, set area & cbar_area
areachange = 1;
cbar_area = area;
cbar_area(1) = area(1) + area(3)*0.93;
cbar_area(3) = area(3)*0.04;
area(3) = area(3)*0.9; % 90% used for main axes
[cbar_axes cbarminmax_axes] = create_cbar_axes(fig, cbar_area);
nii_view.area = area;
nii_view.cbar_area = cbar_area;
else % change, set area only
areachange = 1;
nii_view.area = area;
end
% Add colorbar
%
if ~isempty(usecolorbar) & usecolorbar & isempty(nii_view.cbar_area)
colorbarchange = 1;
cbar_area = area;
cbar_area(1) = area(1) + area(3)*0.93;
cbar_area(3) = area(3)*0.04;
area(3) = area(3)*0.9; % 90% used for main axes
% create axes for colorbar
%
[cbar_axes cbarminmax_axes] = create_cbar_axes(fig, cbar_area);
nii_view.area = area;
nii_view.cbar_area = cbar_area;
% useimagesc follows axial image
%
if isempty(useimagesc)
if strcmpi(get(nii_view.handles.axial_image,'cdatamap'),'scaled')
useimagesc = 1;
else
useimagesc = 0;
end
end
if isfield(nii_view, 'highcolor') & ~isempty(highcolor)
num_highcolor = size(nii_view.highcolor,1);
else
num_highcolor = 0;
end
if isfield(nii_view, 'colorlevel') & ~isempty(nii_view.colorlevel)
colorlevel = nii_view.colorlevel;
else
colorlevel = 256 - num_highcolor;
end
if isfield(nii_view, 'color_map')
color_map = nii_view.color_map;
else
color_map = [];
end
if isfield(nii_view, 'highcolor')
highcolor = nii_view.highcolor;
else
highcolor = [];
end
% plot colorbar
%
if 0
if isempty(color_map)
level = colorlevel + num_highcolor;
else
level = size([color_map; highcolor], 1);
end
end
if isempty(color_map)
level = colorlevel;
else
level = size([color_map], 1);
end
cbar_image = [1:level]';
niiclass = class(nii_view.nii.img);
h1 = plot_cbar(fig, cbar_axes, cbarminmax_axes, nii_view.cbarminmax, ...
level, nii_view.handles, useimagesc, nii_view.colorindex, ...
color_map, colorlevel, highcolor, niiclass, nii_view.numscan);
nii_view.handles.cbar_image = h1;
nii_view.handles.cbar_axes = cbar_axes;
nii_view.handles.cbarminmax_axes = cbar_axes;
% remove colorbar
%
elseif ~isempty(usecolorbar) & ~usecolorbar & ~isempty(nii_view.cbar_area)
colorbarchange = 1;
area(3) = area(3) / 0.9;
nii_view.area = area;
nii_view.cbar_area = [];
nii_view.handles = rmfield(nii_view.handles,'cbar_image');
delete(nii_view.handles.cbarminmax_axes);
nii_view.handles = rmfield(nii_view.handles,'cbarminmax_axes');
delete(nii_view.handles.cbar_axes);
nii_view.handles = rmfield(nii_view.handles,'cbar_axes');
else
colorbarchange = 0;
end
if colorbarchange | stretchchange | areachange
setappdata(fig,'nii_view',nii_view);
update_usestretch(fig, usestretch);
end
return; % update_shape
%----------------------------------------------------------------
function update_unit(fig, setunit)
if isempty(setunit)
return;
end
if strcmpi(setunit,'mm') | strcmpi(setunit,'millimeter') | strcmpi(setunit,'mni')
v = 2;
% elseif strcmpi(setunit,'tal') | strcmpi(setunit,'talairach')
% v = 3;
elseif strcmpi(setunit,'vox') | strcmpi(setunit,'voxel')
v = 1;
else
v = 1;
end
nii_view = getappdata(fig,'nii_view');
set(nii_view.handles.coord, 'value', v);
set_image_value(nii_view);
return; % update_unit
%----------------------------------------------------------------
function update_viewpoint(fig, setviewpoint)
if isempty(setviewpoint)
return;
end
nii_view = getappdata(fig,'nii_view');
if length(setviewpoint) ~= 3
error('Viewpoint position should contain [x y z]');
end
set(nii_view.handles.impos,'string',num2str(setviewpoint));
opt.command = 'impos_edit';
view_nii(fig, opt);
set(nii_view.handles.axial_axes,'selected','on');
set(nii_view.handles.axial_axes,'selected','off');
set(nii_view.handles.coronal_axes,'selected','on');
set(nii_view.handles.coronal_axes,'selected','off');
set(nii_view.handles.sagittal_axes,'selected','on');
set(nii_view.handles.sagittal_axes,'selected','off');
return; % update_viewpoint
%----------------------------------------------------------------
function update_scanid(fig, setscanid)
if isempty(setscanid)
return;
end
nii_view = getappdata(fig,'nii_view');
if setscanid < 1
setscanid = 1;
end
if setscanid > nii_view.numscan
setscanid = nii_view.numscan;
end
set(nii_view.handles.contrast_def,'string',num2str(setscanid));
set(nii_view.handles.contrast,'value',setscanid);
opt.command = 'updateimg';
opt.setscanid = setscanid;
view_nii(fig, nii_view.nii.img, opt);
return; % update_scanid
%----------------------------------------------------------------
function update_crosshaircolor(fig, new_color)
if isempty(new_color)
return;
end
nii_view = getappdata(fig,'nii_view');
xhair_color = nii_view.handles.xhair_color;
set(xhair_color,'user',new_color);
set(nii_view.axi_xhair.lx,'color',new_color);
set(nii_view.axi_xhair.ly,'color',new_color);
set(nii_view.cor_xhair.lx,'color',new_color);
set(nii_view.cor_xhair.ly,'color',new_color);
set(nii_view.sag_xhair.lx,'color',new_color);
set(nii_view.sag_xhair.ly,'color',new_color);
return; % update_crosshaircolor
%----------------------------------------------------------------
function update_colorindex(fig, colorindex)
if isempty(colorindex)
return;
end
nii_view = getappdata(fig,'nii_view');
nii_view.colorindex = colorindex;
setappdata(fig, 'nii_view', nii_view);
set(nii_view.handles.colorindex,'value',colorindex);
opt.command = 'color';
view_nii(fig, opt);
return; % update_colorindex
%----------------------------------------------------------------
function redraw_cbar(fig, colorlevel, color_map, highcolor)
nii_view = getappdata(fig,'nii_view');
if isempty(nii_view.cbar_area)
return;
end
colorindex = nii_view.colorindex;
if isempty(highcolor)
num_highcolor = 0;
else
num_highcolor = size(highcolor,1);
end
if isempty(colorlevel)
colorlevel=256;
end
if colorindex == 1
colorlevel = size(color_map, 1);
end
% level = colorlevel + num_highcolor;
level = colorlevel;
cbar_image = [1:level]';
cbar_area = nii_view.cbar_area;
% useimagesc follows axial image
%
if strcmpi(get(nii_view.handles.axial_image,'cdatamap'),'scaled')
useimagesc = 1;
else
useimagesc = 0;
end
niiclass = class(nii_view.nii.img);
delete(nii_view.handles.cbar_image);
delete(nii_view.handles.cbar_axes);
delete(nii_view.handles.cbarminmax_axes);
[nii_view.handles.cbar_axes nii_view.handles.cbarminmax_axes] = ...
create_cbar_axes(fig, cbar_area, []);
nii_view.handles.cbar_image = plot_cbar(fig, ...
nii_view.handles.cbar_axes, nii_view.handles.cbarminmax_axes, ...
nii_view.cbarminmax, level, nii_view.handles, useimagesc, ...
colorindex, color_map, colorlevel, highcolor, niiclass, ...
nii_view.numscan, []);
setappdata(fig, 'nii_view', nii_view);
return; % redraw_cbar
%----------------------------------------------------------------
function update_buttondown(fig, setbuttondown)
if isempty(setbuttondown)
return;
end
nii_view = getappdata(fig,'nii_view');
nii_view.buttondown = setbuttondown;
setappdata(fig, 'nii_view', nii_view);
return; % update_buttondown
%----------------------------------------------------------------
function update_cbarminmax(fig, cbarminmax)
if isempty(cbarminmax)
return;
end
nii_view = getappdata(fig, 'nii_view');
if ~isfield(nii_view.handles, 'cbarminmax_axes')
return;
end
nii_view.cbarminmax = cbarminmax;
setappdata(fig, 'nii_view', nii_view);
axes(nii_view.handles.cbarminmax_axes);
plot([0 0], cbarminmax, 'w');
axis tight;
set(nii_view.handles.cbarminmax_axes,'YDir','normal', ...
'XLimMode','manual','YLimMode','manual','YColor',[0 0 0], ...
'XColor',[0 0 0],'xtick',[],'YAxisLocation','right');
ylim = get(nii_view.handles.cbar_axes,'ylim');
ylimb = get(nii_view.handles.cbarminmax_axes,'ylim');
ytickb = get(nii_view.handles.cbarminmax_axes,'ytick');
ytick=(ylim(2)-ylim(1))*(ytickb-ylimb(1))/(ylimb(2)-ylimb(1))+ylim(1);
axes(nii_view.handles.cbar_axes);
set(nii_view.handles.cbar_axes,'YDir','normal','XLimMode','manual', ...
'YLimMode','manual','YColor',[0 0 0],'XColor',[0 0 0],'xtick',[], ...
'YAxisLocation','right','ylim',ylim,'ytick',ytick,'yticklabel','');
return; % update_cbarminmax
%----------------------------------------------------------------
function update_highcolor(fig, highcolor, colorlevel)
nii_view = getappdata(fig,'nii_view');
if ischar(highcolor) & (isempty(colorlevel) | nii_view.colorindex == 1)
return;
end
if ~ischar(highcolor)
nii_view.highcolor = highcolor;
if isempty(highcolor)
nii_view = rmfield(nii_view, 'highcolor');
end
else
highcolor = [];
end
if isempty(colorlevel) | nii_view.colorindex == 1
nii_view.colorlevel = nii_view.colorlevel - size(highcolor,1);
else
nii_view.colorlevel = colorlevel;
end
setappdata(fig, 'nii_view', nii_view);
if isfield(nii_view,'color_map')
color_map = nii_view.color_map;
else
color_map = [];
end
redraw_cbar(fig, nii_view.colorlevel, color_map, highcolor);
change_colormap(fig);
return; % update_highcolor
%----------------------------------------------------------------
function update_colormap(fig, color_map)
if ischar(color_map)
return;
end
nii_view = getappdata(fig,'nii_view');
nii = nii_view.nii;
minvalue = nii_view.minvalue;
if isempty(color_map)
if minvalue < 0
colorindex = 2;
else
colorindex = 3;
end
nii_view = rmfield(nii_view, 'color_map');
setappdata(fig,'nii_view',nii_view);
update_colorindex(fig, colorindex);
return;
else
colorindex = 1;
nii_view.color_map = color_map;
nii_view.colorindex = colorindex;
setappdata(fig,'nii_view',nii_view);
set(nii_view.handles.colorindex,'value',colorindex);
end
colorlevel = nii_view.colorlevel;
if isfield(nii_view, 'highcolor')
highcolor = nii_view.highcolor;
else
highcolor = [];
end
redraw_cbar(fig, colorlevel, color_map, highcolor);
change_colormap(fig);
opt.enablecontrast = 0;
update_enable(fig, opt);
return; % update_colormap
%----------------------------------------------------------------
function status = get_status(h);
nii_view = getappdata(h,'nii_view');
status.fig = h;
status.area = nii_view.area;
if isempty(nii_view.cbar_area)
status.usecolorbar = 0;
else
status.usecolorbar = 1;
width = status.area(3) / 0.9;
status.area(3) = width;
end
if strcmpi(get(nii_view.handles.imval,'visible'), 'on')
status.usepanel = 1;
else
status.usepanel = 0;
end
if get(nii_view.handles.xhair,'value') == 1
status.usecrosshair = 1;
else
status.usecrosshair = 0;
end
status.usestretch = nii_view.usestretch;
if strcmpi(get(nii_view.handles.axial_image,'cdatamapping'), 'direct')
status.useimagesc = 0;
else
status.useimagesc = 1;
end
status.useinterp = nii_view.useinterp;
if get(nii_view.handles.coord,'value') == 1
status.unit = 'vox';
elseif get(nii_view.handles.coord,'value') == 2
status.unit = 'mm';
elseif get(nii_view.handles.coord,'value') == 3
status.unit = 'tal';
end
status.viewpoint = get(nii_view.handles.impos,'value');
status.scanid = nii_view.scanid;
status.intensity = get(nii_view.handles.imval,'value');
status.colorindex = get(nii_view.handles.colorindex,'value');
if isfield(nii_view,'color_map')
status.colormap = nii_view.color_map;
else
status.colormap = [];
end
status.colorlevel = nii_view.colorlevel;
if isfield(nii_view,'highcolor')
status.highcolor = nii_view.highcolor;
else
status.highcolor = [];
end
status.cbarminmax = nii_view.cbarminmax;
status.buttondown = nii_view.buttondown;
return; % get_status
%----------------------------------------------------------------
function [custom_color_map, colorindex] ...
= change_colormap(fig, nii, colorindex, cbarminmax)
custom_color_map = [];
if ~exist('nii', 'var')
nii_view = getappdata(fig,'nii_view');
else
nii_view = nii;
end
if ~exist('colorindex', 'var')
colorindex = get(nii_view.handles.colorindex,'value');
end
if ~exist('cbarminmax', 'var')
cbarminmax = nii_view.cbarminmax;
end
if isfield(nii_view, 'highcolor') & ~isempty(nii_view.highcolor)
highcolor = nii_view.highcolor;
num_highcolor = size(highcolor,1);
else
highcolor = [];
num_highcolor = 0;
end
% if isfield(nii_view, 'colorlevel') & ~isempty(nii_view.colorlevel)
if nii_view.colorlevel < 256
num_color = nii_view.colorlevel;
else
num_color = 256 - num_highcolor;
end
contrast = [];
if colorindex == 3 % for gray
if nii_view.numscan > 1
contrast = 1;
else
contrast = (num_color-1)*(get(nii_view.handles.contrast,'value')-1)/255+1;
contrast = floor(contrast);
end
elseif colorindex == 2 % for bipolar
if nii_view.numscan > 1
contrast = 128;
else
contrast = get(nii_view.handles.contrast,'value');
end
end
if isfield(nii_view,'color_map') & ~isempty(nii_view.color_map)
color_map = nii_view.color_map;
custom_color_map = color_map;
elseif colorindex == 1
[f p] = uigetfile('*.txt', 'Input colormap text file');
if p==0
colorindex = nii_view.colorindex;
set(nii_view.handles.colorindex,'value',colorindex);
return;
end;
try
custom_color_map = load(fullfile(p,f));
loadfail = 0;
catch
loadfail = 1;
end
if loadfail | isempty(custom_color_map) | size(custom_color_map,2)~=3 ...
| min(custom_color_map(:)) < 0 | max(custom_color_map(:)) > 1
msg = 'Colormap should be a Mx3 matrix with value between 0 and 1';
msgbox(msg,'Error in colormap file');
colorindex = nii_view.colorindex;
set(nii_view.handles.colorindex,'value',colorindex);
return;
end
color_map = custom_color_map;
nii_view.color_map = color_map;
end
switch colorindex
case {2}
color_map = bipolar(num_color, cbarminmax(1), cbarminmax(2), contrast);
case {3}
color_map = gray(num_color - contrast + 1);
case {4}
color_map = jet(num_color);
case {5}
color_map = cool(num_color);
case {6}
color_map = bone(num_color);
case {7}
color_map = hot(num_color);
case {8}
color_map = copper(num_color);
case {9}
color_map = pink(num_color);
end
nii_view.colorindex = colorindex;
if ~exist('nii', 'var')
setappdata(fig,'nii_view',nii_view);
end
if colorindex == 3
color_map = [zeros(contrast,3); color_map(2:end,:)];
end
if get(nii_view.handles.neg_color,'value') & isempty(highcolor)
color_map = flipud(color_map);
elseif get(nii_view.handles.neg_color,'value') & ~isempty(highcolor)
highcolor = flipud(highcolor);
end
brightness = get(nii_view.handles.brightness,'value');
color_map = brighten(color_map, brightness);
color_map = [color_map; highcolor];
set(fig, 'colormap', color_map);
return; % change_colormap
%----------------------------------------------------------------
function move_cursor(fig)
nii_view = getappdata(fig, 'nii_view');
if isempty(nii_view)
return;
end
axi = get(nii_view.handles.axial_axes, 'pos');
cor = get(nii_view.handles.coronal_axes, 'pos');
sag = get(nii_view.handles.sagittal_axes, 'pos');
curr = get(fig, 'currentpoint');
if curr(1) >= axi(1) & curr(1) <= axi(1)+axi(3) & ...
curr(2) >= axi(2) & curr(2) <= axi(2)+axi(4)
curr = get(nii_view.handles.axial_axes, 'current');
sag = curr(1,1);
cor = curr(1,2);
axi = nii_view.slices.axi;
elseif curr(1) >= cor(1) & curr(1) <= cor(1)+cor(3) & ...
curr(2) >= cor(2) & curr(2) <= cor(2)+cor(4)
curr = get(nii_view.handles.coronal_axes, 'current');
sag = curr(1,1);
cor = nii_view.slices.cor;
axi = curr(1,2);
elseif curr(1) >= sag(1) & curr(1) <= sag(1)+sag(3) & ...
curr(2) >= sag(2) & curr(2) <= sag(2)+sag(4)
curr = get(nii_view.handles.sagittal_axes, 'current');
sag = nii_view.slices.sag;
cor = curr(1,1);
axi = curr(1,2);
else
set(nii_view.handles.imvalcur,'String',' ');
set(nii_view.handles.imposcur,'String',' ');
return;
end
sag = round(sag);
cor = round(cor);
axi = round(axi);
if sag < 1
sag = 1;
elseif sag > nii_view.dims(1)
sag = nii_view.dims(1);
end
if cor < 1
cor = 1;
elseif cor > nii_view.dims(2)
cor = nii_view.dims(2);
end
if axi < 1
axi = 1;
elseif axi > nii_view.dims(3)
axi = nii_view.dims(3);
end
if 0 % isfield(nii_view, 'disp')
img = nii_view.disp;
else
img = nii_view.nii.img;
end
if nii_view.nii.hdr.dime.datatype == 128
imgvalue = [double(img(sag,cor,axi,1,nii_view.scanid)) double(img(sag,cor,axi,2,nii_view.scanid)) double(img(sag,cor,axi,3,nii_view.scanid))];
set(nii_view.handles.imvalcur,'String',sprintf('%7.4g %7.4g %7.4g',imgvalue));
elseif nii_view.nii.hdr.dime.datatype == 511
R = double(img(sag,cor,axi,1,nii_view.scanid)) * (nii_view.nii.hdr.dime.glmax - ...
nii_view.nii.hdr.dime.glmin) + nii_view.nii.hdr.dime.glmin;
G = double(img(sag,cor,axi,2,nii_view.scanid)) * (nii_view.nii.hdr.dime.glmax - ...
nii_view.nii.hdr.dime.glmin) + nii_view.nii.hdr.dime.glmin;
B = double(img(sag,cor,axi,3,nii_view.scanid)) * (nii_view.nii.hdr.dime.glmax - ...
nii_view.nii.hdr.dime.glmin) + nii_view.nii.hdr.dime.glmin;
imgvalue = [R G B];
set(nii_view.handles.imvalcur,'String',sprintf('%7.4g %7.4g %7.4g',imgvalue));
else
imgvalue = double(img(sag,cor,axi,nii_view.scanid));
if isnan(imgvalue) | imgvalue > nii_view.cbarminmax(2)
imgvalue = 0;
end
set(nii_view.handles.imvalcur,'String',sprintf('%.6g',imgvalue));
end
nii_view.slices.sag = sag;
nii_view.slices.cor = cor;
nii_view.slices.axi = axi;
nii_view = update_imgXYZ(nii_view);
if get(nii_view.handles.coord,'value') == 1,
sag = nii_view.imgXYZ.vox(1);
cor = nii_view.imgXYZ.vox(2);
axi = nii_view.imgXYZ.vox(3);
elseif get(nii_view.handles.coord,'value') == 2,
sag = nii_view.imgXYZ.mm(1);
cor = nii_view.imgXYZ.mm(2);
axi = nii_view.imgXYZ.mm(3);
elseif get(nii_view.handles.coord,'value') == 3,
sag = nii_view.imgXYZ.tal(1);
cor = nii_view.imgXYZ.tal(2);
axi = nii_view.imgXYZ.tal(3);
end
if get(nii_view.handles.coord,'value') == 1,
string = sprintf('%7.0f %7.0f %7.0f',sag,cor,axi);
else
string = sprintf('%7.1f %7.1f %7.1f',sag,cor,axi);
end;
set(nii_view.handles.imposcur,'String',string);
return; % move_cursor
%----------------------------------------------------------------
function change_scan(hdl_str)
fig = gcbf;
nii_view = getappdata(fig,'nii_view');
if strcmpi(hdl_str, 'edit_change_scan') % edit
hdl = nii_view.handles.contrast_def;
setscanid = round(str2num(get(hdl, 'string')));
else % slider
hdl = nii_view.handles.contrast;
setscanid = round(get(hdl, 'value'));
end
update_scanid(fig, setscanid);
return; % change_scan
%----------------------------------------------------------------
function val = scale_in(val, minval, maxval, range)
% scale value into range
%
val = range*(double(val)-double(minval))/(double(maxval)-double(minval))+1;
return; % scale_in
%----------------------------------------------------------------
function val = scale_out(val, minval, maxval, range)
% according to [minval maxval] and range of color levels (e.g. 199)
% scale val back from any thing between 1~256 to a small number that
% is corresonding to [minval maxval].
%
val = (double(val)-1)*(double(maxval)-double(minval))/range+double(minval);
return; % scale_out
|
github
|
adhusch/PaCER-master
|
mat_into_hdr.m
|
.m
|
PaCER-master/external/NIfTI_20140122/mat_into_hdr.m
| 2,608 |
utf_8
|
d53006b93ff90a4a5561d16ff2f4e9a6
|
%MAT_INTO_HDR The old versions of SPM (any version before SPM5) store
% an affine matrix of the SPM Reoriented image into a matlab file
% (.mat extension). The file name of this SPM matlab file is the
% same as the SPM Reoriented image file (.img/.hdr extension).
%
% This program will convert the ANALYZE 7.5 SPM Reoriented image
% file into NIfTI format, and integrate the affine matrix in the
% SPM matlab file into its header file (.hdr extension).
%
% WARNING: Before you run this program, please save the header
% file (.hdr extension) into another file name or into another
% folder location, because all header files (.hdr extension)
% will be overwritten after they are converted into NIfTI
% format.
%
% Usage: mat_into_hdr(filename);
%
% filename: file name(s) with .hdr or .mat file extension, like:
% '*.hdr', or '*.mat', or a single .hdr or .mat file.
% e.g. mat_into_hdr('T1.hdr')
% mat_into_hdr('*.mat')
%
% - Jimmy Shen ([email protected])
%
%-------------------------------------------------------------------------
function mat_into_hdr(files)
pn = fileparts(files);
file_lst = dir(files);
file_lst = {file_lst.name};
file1 = file_lst{1};
[p n e]= fileparts(file1);
for i=1:length(file_lst)
[p n e]= fileparts(file_lst{i});
disp(['working on file ', num2str(i) ,' of ', num2str(length(file_lst)), ': ', n,e]);
process=1;
if isequal(e,'.hdr')
mat=fullfile(pn, [n,'.mat']);
hdr=fullfile(pn, file_lst{i});
if ~exist(mat,'file')
warning(['Cannot find file "',mat , '". File "', n, e, '" will not be processed.']);
process=0;
end
elseif isequal(e,'.mat')
hdr=fullfile(pn, [n,'.hdr']);
mat=fullfile(pn, file_lst{i});
if ~exist(hdr,'file')
warning(['Can not find file "',hdr , '". File "', n, e, '" will not be processed.']);
process=0;
end
else
warning(['Input file must have .mat or .hdr extension. File "', n, e, '" will not be processed.']);
process=0;
end
if process
load(mat);
R=M(1:3,1:3);
T=M(1:3,4);
T=R*ones(3,1)+T;
M(1:3,4)=T;
[h filetype fileprefix machine]=load_nii_hdr(hdr);
h.hist.qform_code=0;
h.hist.sform_code=1;
h.hist.srow_x=M(1,:);
h.hist.srow_y=M(2,:);
h.hist.srow_z=M(3,:);
h.hist.magic='ni1';
fid = fopen(hdr,'w',machine);
save_nii_hdr(h,fid);
fclose(fid);
end
end
return; % mat_into_hdr
|
github
|
adhusch/PaCER-master
|
xform_nii.m
|
.m
|
PaCER-master/external/NIfTI_20140122/xform_nii.m
| 18,107 |
utf_8
|
29a1cff91c944d6a93e5101946a5da4d
|
% internal function
% 'xform_nii.m' is an internal function called by "load_nii.m", so
% you do not need run this program by yourself. It does simplified
% NIfTI sform/qform affine transform, and supports some of the
% affine transforms, including translation, reflection, and
% orthogonal rotation (N*90 degree).
%
% For other affine transforms, e.g. any degree rotation, shearing
% etc. you will have to use the included 'reslice_nii.m' program
% to reslice the image volume. 'reslice_nii.m' is not called by
% any other program, and you have to run 'reslice_nii.m' explicitly
% for those NIfTI files that you want to reslice them.
%
% Since 'xform_nii.m' does not involve any interpolation or any
% slice change, the original image volume is supposed to be
% untouched, although it is translated, reflected, or even
% orthogonally rotated, based on the affine matrix in the
% NIfTI header.
%
% However, the affine matrix in the header of a lot NIfTI files
% contain slightly non-orthogonal rotation. Therefore, optional
% input parameter 'tolerance' is used to allow some distortion
% in the loaded image for any non-orthogonal rotation or shearing
% of NIfTI affine matrix. If you set 'tolerance' to 0, it means
% that you do not allow any distortion. If you set 'tolerance' to
% 1, it means that you do not care any distortion. The image will
% fail to be loaded if it can not be tolerated. The tolerance will
% be set to 0.1 (10%), if it is default or empty.
%
% Because 'reslice_nii.m' has to perform 3D interpolation, it can
% be slow depending on image size and affine matrix in the header.
%
% After you perform the affine transform, the 'nii' structure
% generated from 'xform_nii.m' or new NIfTI file created from
% 'reslice_nii.m' will be in RAS orientation, i.e. X axis from
% Left to Right, Y axis from Posterior to Anterior, and Z axis
% from Inferior to Superior.
%
% NOTE: This function should be called immediately after load_nii.
%
% Usage: [ nii ] = xform_nii(nii, [tolerance], [preferredForm])
%
% nii - NIFTI structure (returned from load_nii)
%
% tolerance (optional) - distortion allowed for non-orthogonal rotation
% or shearing in NIfTI affine matrix. It will be set to 0.1 (10%),
% if it is default or empty.
%
% preferredForm (optional) - selects which transformation from voxels
% to RAS coordinates; values are s,q,S,Q. Lower case s,q indicate
% "prefer sform or qform, but use others if preferred not present".
% Upper case indicate the program is forced to use the specificied
% tranform or fail loading. 'preferredForm' will be 's', if it is
% default or empty. - Jeff Gunter
%
% NIFTI data format can be found on: http://nifti.nimh.nih.gov
%
% - Jimmy Shen ([email protected])
%
function nii = xform_nii(nii, tolerance, preferredForm)
% save a copy of the header as it was loaded. This is the
% header before any sform, qform manipulation is done.
%
nii.original.hdr = nii.hdr;
if ~exist('tolerance','var') | isempty(tolerance)
tolerance = 0.1;
elseif(tolerance<=0)
tolerance = eps;
end
if ~exist('preferredForm','var') | isempty(preferredForm)
preferredForm= 's'; % Jeff
end
% if scl_slope field is nonzero, then each voxel value in the
% dataset should be scaled as: y = scl_slope * x + scl_inter
% I bring it here because hdr will be modified by change_hdr.
%
if nii.hdr.dime.scl_slope ~= 0 & ...
ismember(nii.hdr.dime.datatype, [2,4,8,16,64,256,512,768]) & ...
(nii.hdr.dime.scl_slope ~= 1 | nii.hdr.dime.scl_inter ~= 0)
nii.img = ...
nii.hdr.dime.scl_slope * double(nii.img) + nii.hdr.dime.scl_inter;
if nii.hdr.dime.datatype == 64
nii.hdr.dime.datatype = 64;
nii.hdr.dime.bitpix = 64;
else
nii.img = single(nii.img);
nii.hdr.dime.datatype = 16;
nii.hdr.dime.bitpix = 32;
end
nii.hdr.dime.glmax = max(double(nii.img(:)));
nii.hdr.dime.glmin = min(double(nii.img(:)));
% set scale to non-use, because it is applied in xform_nii
%
nii.hdr.dime.scl_slope = 0;
end
% However, the scaling is to be ignored if datatype is DT_RGB24.
% If datatype is a complex type, then the scaling is to be applied
% to both the real and imaginary parts.
%
if nii.hdr.dime.scl_slope ~= 0 & ...
ismember(nii.hdr.dime.datatype, [32,1792])
nii.img = ...
nii.hdr.dime.scl_slope * double(nii.img) + nii.hdr.dime.scl_inter;
if nii.hdr.dime.datatype == 32
nii.img = single(nii.img);
end
nii.hdr.dime.glmax = max(double(nii.img(:)));
nii.hdr.dime.glmin = min(double(nii.img(:)));
% set scale to non-use, because it is applied in xform_nii
%
nii.hdr.dime.scl_slope = 0;
end
% There is no need for this program to transform Analyze data
%
if nii.filetype == 0 & exist([nii.fileprefix '.mat'],'file')
load([nii.fileprefix '.mat']); % old SPM affine matrix
R=M(1:3,1:3);
T=M(1:3,4);
T=R*ones(3,1)+T;
M(1:3,4)=T;
nii.hdr.hist.qform_code=0;
nii.hdr.hist.sform_code=1;
nii.hdr.hist.srow_x=M(1,:);
nii.hdr.hist.srow_y=M(2,:);
nii.hdr.hist.srow_z=M(3,:);
elseif nii.filetype == 0
nii.hdr.hist.rot_orient = [];
nii.hdr.hist.flip_orient = [];
return; % no sform/qform for Analyze format
end
hdr = nii.hdr;
[hdr,orient]=change_hdr(hdr,tolerance,preferredForm);
% flip and/or rotate image data
%
if ~isequal(orient, [1 2 3])
old_dim = hdr.dime.dim([2:4]);
% More than 1 time frame
%
if ndims(nii.img) > 3
pattern = 1:prod(old_dim);
else
pattern = [];
end
if ~isempty(pattern)
pattern = reshape(pattern, old_dim);
end
% calculate for rotation after flip
%
rot_orient = mod(orient + 2, 3) + 1;
% do flip:
%
flip_orient = orient - rot_orient;
for i = 1:3
if flip_orient(i)
if ~isempty(pattern)
pattern = flipdim(pattern, i);
else
nii.img = flipdim(nii.img, i);
end
end
end
% get index of orient (rotate inversely)
%
[tmp rot_orient] = sort(rot_orient);
new_dim = old_dim;
new_dim = new_dim(rot_orient);
hdr.dime.dim([2:4]) = new_dim;
new_pixdim = hdr.dime.pixdim([2:4]);
new_pixdim = new_pixdim(rot_orient);
hdr.dime.pixdim([2:4]) = new_pixdim;
% re-calculate originator
%
tmp = hdr.hist.originator([1:3]);
tmp = tmp(rot_orient);
flip_orient = flip_orient(rot_orient);
for i = 1:3
if flip_orient(i) & ~isequal(tmp(i), 0)
tmp(i) = new_dim(i) - tmp(i) + 1;
end
end
hdr.hist.originator([1:3]) = tmp;
hdr.hist.rot_orient = rot_orient;
hdr.hist.flip_orient = flip_orient;
% do rotation:
%
if ~isempty(pattern)
pattern = permute(pattern, rot_orient);
pattern = pattern(:);
if hdr.dime.datatype == 32 | hdr.dime.datatype == 1792 | ...
hdr.dime.datatype == 128 | hdr.dime.datatype == 511
tmp = reshape(nii.img(:,:,:,1), [prod(new_dim) hdr.dime.dim(5:8)]);
tmp = tmp(pattern, :);
nii.img(:,:,:,1) = reshape(tmp, [new_dim hdr.dime.dim(5:8)]);
tmp = reshape(nii.img(:,:,:,2), [prod(new_dim) hdr.dime.dim(5:8)]);
tmp = tmp(pattern, :);
nii.img(:,:,:,2) = reshape(tmp, [new_dim hdr.dime.dim(5:8)]);
if hdr.dime.datatype == 128 | hdr.dime.datatype == 511
tmp = reshape(nii.img(:,:,:,3), [prod(new_dim) hdr.dime.dim(5:8)]);
tmp = tmp(pattern, :);
nii.img(:,:,:,3) = reshape(tmp, [new_dim hdr.dime.dim(5:8)]);
end
else
nii.img = reshape(nii.img, [prod(new_dim) hdr.dime.dim(5:8)]);
nii.img = nii.img(pattern, :);
nii.img = reshape(nii.img, [new_dim hdr.dime.dim(5:8)]);
end
else
if hdr.dime.datatype == 32 | hdr.dime.datatype == 1792 | ...
hdr.dime.datatype == 128 | hdr.dime.datatype == 511
nii.img(:,:,:,1) = permute(nii.img(:,:,:,1), rot_orient);
nii.img(:,:,:,2) = permute(nii.img(:,:,:,2), rot_orient);
if hdr.dime.datatype == 128 | hdr.dime.datatype == 511
nii.img(:,:,:,3) = permute(nii.img(:,:,:,3), rot_orient);
end
else
nii.img = permute(nii.img, rot_orient);
end
end
else
hdr.hist.rot_orient = [];
hdr.hist.flip_orient = [];
end
nii.hdr = hdr;
return; % xform_nii
%-----------------------------------------------------------------------
function [hdr, orient] = change_hdr(hdr, tolerance, preferredForm)
orient = [1 2 3];
affine_transform = 1;
% NIFTI can have both sform and qform transform. This program
% will check sform_code prior to qform_code by default.
%
% If user specifys "preferredForm", user can then choose the
% priority. - Jeff
%
useForm=[]; % Jeff
if isequal(preferredForm,'S')
if isequal(hdr.hist.sform_code,0)
error('User requires sform, sform not set in header');
else
useForm='s';
end
end % Jeff
if isequal(preferredForm,'Q')
if isequal(hdr.hist.qform_code,0)
error('User requires qform, qform not set in header');
else
useForm='q';
end
end % Jeff
if isequal(preferredForm,'s')
if hdr.hist.sform_code > 0
useForm='s';
elseif hdr.hist.qform_code > 0
useForm='q';
end
end % Jeff
if isequal(preferredForm,'q')
if hdr.hist.qform_code > 0
useForm='q';
elseif hdr.hist.sform_code > 0
useForm='s';
end
end % Jeff
if isequal(useForm,'s')
R = [hdr.hist.srow_x(1:3)
hdr.hist.srow_y(1:3)
hdr.hist.srow_z(1:3)];
T = [hdr.hist.srow_x(4)
hdr.hist.srow_y(4)
hdr.hist.srow_z(4)];
if det(R) == 0 | ~isequal(R(find(R)), sum(R)')
hdr.hist.old_affine = [ [R;[0 0 0]] [T;1] ];
R_sort = sort(abs(R(:)));
R( find( abs(R) < tolerance*min(R_sort(end-2:end)) ) ) = 0;
hdr.hist.new_affine = [ [R;[0 0 0]] [T;1] ];
if det(R) == 0 | ~isequal(R(find(R)), sum(R)')
msg = [char(10) char(10) ' Non-orthogonal rotation or shearing '];
msg = [msg 'found inside the affine matrix' char(10)];
msg = [msg ' in this NIfTI file. You have 3 options:' char(10) char(10)];
msg = [msg ' 1. Using included ''reslice_nii.m'' program to reslice the NIfTI' char(10)];
msg = [msg ' file. I strongly recommand this, because it will not cause' char(10)];
msg = [msg ' negative effect, as long as you remember not to do slice' char(10)];
msg = [msg ' time correction after using ''reslice_nii.m''.' char(10) char(10)];
msg = [msg ' 2. Using included ''load_untouch_nii.m'' program to load image' char(10)];
msg = [msg ' without applying any affine geometric transformation or' char(10)];
msg = [msg ' voxel intensity scaling. This is only for people who want' char(10)];
msg = [msg ' to do some image processing regardless of image orientation' char(10)];
msg = [msg ' and to save data back with the same NIfTI header.' char(10) char(10)];
msg = [msg ' 3. Increasing the tolerance to allow more distortion in loaded' char(10)];
msg = [msg ' image, but I don''t suggest this.' char(10) char(10)];
msg = [msg ' To get help, please type:' char(10) char(10) ' help reslice_nii.m' char(10)];
msg = [msg ' help load_untouch_nii.m' char(10) ' help load_nii.m'];
error(msg);
end
end
elseif isequal(useForm,'q')
b = hdr.hist.quatern_b;
c = hdr.hist.quatern_c;
d = hdr.hist.quatern_d;
if 1.0-(b*b+c*c+d*d) < 0
if abs(1.0-(b*b+c*c+d*d)) < 1e-5
a = 0;
else
error('Incorrect quaternion values in this NIFTI data.');
end
else
a = sqrt(1.0-(b*b+c*c+d*d));
end
qfac = hdr.dime.pixdim(1);
if qfac==0, qfac = 1; end
i = hdr.dime.pixdim(2);
j = hdr.dime.pixdim(3);
k = qfac * hdr.dime.pixdim(4);
R = [a*a+b*b-c*c-d*d 2*b*c-2*a*d 2*b*d+2*a*c
2*b*c+2*a*d a*a+c*c-b*b-d*d 2*c*d-2*a*b
2*b*d-2*a*c 2*c*d+2*a*b a*a+d*d-c*c-b*b];
T = [hdr.hist.qoffset_x
hdr.hist.qoffset_y
hdr.hist.qoffset_z];
% qforms are expected to generate rotation matrices R which are
% det(R) = 1; we'll make sure that happens.
%
% now we make the same checks as were done above for sform data
% BUT we do it on a transform that is in terms of voxels not mm;
% after we figure out the angles and squash them to closest
% rectilinear direction. After that, the voxel sizes are then
% added.
%
% This part is modified by Jeff Gunter.
%
if det(R) == 0 | ~isequal(R(find(R)), sum(R)')
% det(R) == 0 is not a common trigger for this ---
% R(find(R)) is a list of non-zero elements in R; if that
% is straight (not oblique) then it should be the same as
% columnwise summation. Could just as well have checked the
% lengths of R(find(R)) and sum(R)' (which should be 3)
%
hdr.hist.old_affine = [ [R * diag([i j k]);[0 0 0]] [T;1] ];
R_sort = sort(abs(R(:)));
R( find( abs(R) < tolerance*min(R_sort(end-2:end)) ) ) = 0;
R = R * diag([i j k]);
hdr.hist.new_affine = [ [R;[0 0 0]] [T;1] ];
if det(R) == 0 | ~isequal(R(find(R)), sum(R)')
msg = [char(10) char(10) ' Non-orthogonal rotation or shearing '];
msg = [msg 'found inside the affine matrix' char(10)];
msg = [msg ' in this NIfTI file. You have 3 options:' char(10) char(10)];
msg = [msg ' 1. Using included ''reslice_nii.m'' program to reslice the NIfTI' char(10)];
msg = [msg ' file. I strongly recommand this, because it will not cause' char(10)];
msg = [msg ' negative effect, as long as you remember not to do slice' char(10)];
msg = [msg ' time correction after using ''reslice_nii.m''.' char(10) char(10)];
msg = [msg ' 2. Using included ''load_untouch_nii.m'' program to load image' char(10)];
msg = [msg ' without applying any affine geometric transformation or' char(10)];
msg = [msg ' voxel intensity scaling. This is only for people who want' char(10)];
msg = [msg ' to do some image processing regardless of image orientation' char(10)];
msg = [msg ' and to save data back with the same NIfTI header.' char(10) char(10)];
msg = [msg ' 3. Increasing the tolerance to allow more distortion in loaded' char(10)];
msg = [msg ' image, but I don''t suggest this.' char(10) char(10)];
msg = [msg ' To get help, please type:' char(10) char(10) ' help reslice_nii.m' char(10)];
msg = [msg ' help load_untouch_nii.m' char(10) ' help load_nii.m'];
error(msg);
end
else
R = R * diag([i j k]);
end % 1st det(R)
else
affine_transform = 0; % no sform or qform transform
end
if affine_transform == 1
voxel_size = abs(sum(R,1));
inv_R = inv(R);
originator = inv_R*(-T)+1;
orient = get_orient(inv_R);
% modify pixdim and originator
%
hdr.dime.pixdim(2:4) = voxel_size;
hdr.hist.originator(1:3) = originator;
% set sform or qform to non-use, because they have been
% applied in xform_nii
%
hdr.hist.qform_code = 0;
hdr.hist.sform_code = 0;
end
% apply space_unit to pixdim if not 1 (mm)
%
space_unit = get_units(hdr);
if space_unit ~= 1
hdr.dime.pixdim(2:4) = hdr.dime.pixdim(2:4) * space_unit;
% set space_unit of xyzt_units to millimeter, because
% voxel_size has been re-scaled
%
hdr.dime.xyzt_units = char(bitset(hdr.dime.xyzt_units,1,0));
hdr.dime.xyzt_units = char(bitset(hdr.dime.xyzt_units,2,1));
hdr.dime.xyzt_units = char(bitset(hdr.dime.xyzt_units,3,0));
end
hdr.dime.pixdim = abs(hdr.dime.pixdim);
return; % change_hdr
%-----------------------------------------------------------------------
function orient = get_orient(R)
orient = [];
for i = 1:3
switch find(R(i,:)) * sign(sum(R(i,:)))
case 1
orient = [orient 1]; % Left to Right
case 2
orient = [orient 2]; % Posterior to Anterior
case 3
orient = [orient 3]; % Inferior to Superior
case -1
orient = [orient 4]; % Right to Left
case -2
orient = [orient 5]; % Anterior to Posterior
case -3
orient = [orient 6]; % Superior to Inferior
end
end
return; % get_orient
%-----------------------------------------------------------------------
function [space_unit, time_unit] = get_units(hdr)
switch bitand(hdr.dime.xyzt_units, 7) % mask with 0x07
case 1
space_unit = 1e+3; % meter, m
case 3
space_unit = 1e-3; % micrometer, um
otherwise
space_unit = 1; % millimeter, mm
end
switch bitand(hdr.dime.xyzt_units, 56) % mask with 0x38
case 16
time_unit = 1e-3; % millisecond, ms
case 24
time_unit = 1e-6; % microsecond, us
otherwise
time_unit = 1; % second, s
end
return; % get_units
|
github
|
adhusch/PaCER-master
|
make_ana.m
|
.m
|
PaCER-master/external/NIfTI_20140122/make_ana.m
| 5,455 |
utf_8
|
2f62999cbcad72129c892135ff492a1e
|
% Make ANALYZE 7.5 data structure specified by a 3D or 4D matrix.
% Optional parameters can also be included, such as: voxel_size,
% origin, datatype, and description.
%
% Once the ANALYZE structure is made, it can be saved into ANALYZE 7.5
% format data file using "save_untouch_nii" command (for more detail,
% type: help save_untouch_nii).
%
% Usage: ana = make_ana(img, [voxel_size], [origin], [datatype], [description])
%
% Where:
%
% img: a 3D matrix [x y z], or a 4D matrix with time
% series [x y z t]. When image is in RGB format,
% make sure that the size of 4th dimension is
% always 3 (i.e. [R G B]). In that case, make
% sure that you must specify RGB datatype to 128.
%
% voxel_size (optional): Voxel size in millimeter for each
% dimension. Default is [1 1 1].
%
% origin (optional): The AC origin. Default is [0 0 0].
%
% datatype (optional): Storage data type:
% 2 - uint8, 4 - int16, 8 - int32, 16 - float32,
% 64 - float64, 128 - RGB24
% Default will use the data type of 'img' matrix
% For RGB image, you must specify it to 128.
%
% description (optional): Description of data. Default is ''.
%
% e.g.:
% origin = [33 44 13]; datatype = 64;
% ana = make_ana(img, [], origin, datatype); % default voxel_size
%
% ANALYZE 7.5 format: http://www.rotman-baycrest.on.ca/~jimmy/ANALYZE75.pdf
%
% - Jimmy Shen ([email protected])
%
function ana = make_ana(varargin)
ana.img = varargin{1};
dims = size(ana.img);
dims = [4 dims ones(1,8)];
dims = dims(1:8);
voxel_size = [0 ones(1,3) zeros(1,4)];
origin = zeros(1,5);
descrip = '';
switch class(ana.img)
case 'uint8'
datatype = 2;
case 'int16'
datatype = 4;
case 'int32'
datatype = 8;
case 'single'
datatype = 16;
case 'double'
datatype = 64;
otherwise
error('Datatype is not supported by make_ana.');
end
if nargin > 1 & ~isempty(varargin{2})
voxel_size(2:4) = double(varargin{2});
end
if nargin > 2 & ~isempty(varargin{3})
origin(1:3) = double(varargin{3});
end
if nargin > 3 & ~isempty(varargin{4})
datatype = double(varargin{4});
if datatype == 128 | datatype == 511
dims(5) = [];
dims = [dims 1];
end
end
if nargin > 4 & ~isempty(varargin{5})
descrip = varargin{5};
end
if ndims(ana.img) > 4
error('NIfTI only allows a maximum of 4 Dimension matrix.');
end
maxval = round(double(max(ana.img(:))));
minval = round(double(min(ana.img(:))));
ana.hdr = make_header(dims, voxel_size, origin, datatype, ...
descrip, maxval, minval);
ana.filetype = 0;
ana.ext = [];
ana.untouch = 1;
switch ana.hdr.dime.datatype
case 2
ana.img = uint8(ana.img);
case 4
ana.img = int16(ana.img);
case 8
ana.img = int32(ana.img);
case 16
ana.img = single(ana.img);
case 64
ana.img = double(ana.img);
case 128
ana.img = uint8(ana.img);
otherwise
error('Datatype is not supported by make_ana.');
end
return; % make_ana
%---------------------------------------------------------------------
function hdr = make_header(dims, voxel_size, origin, datatype, ...
descrip, maxval, minval)
hdr.hk = header_key;
hdr.dime = image_dimension(dims, voxel_size, datatype, maxval, minval);
hdr.hist = data_history(origin, descrip);
return; % make_header
%---------------------------------------------------------------------
function hk = header_key
hk.sizeof_hdr = 348; % must be 348!
hk.data_type = '';
hk.db_name = '';
hk.extents = 0;
hk.session_error = 0;
hk.regular = 'r';
hk.hkey_un0 = '0';
return; % header_key
%---------------------------------------------------------------------
function dime = image_dimension(dims, voxel_size, datatype, maxval, minval)
dime.dim = dims;
dime.vox_units = 'mm';
dime.cal_units = '';
dime.unused1 = 0;
dime.datatype = datatype;
switch dime.datatype
case 2,
dime.bitpix = 8; precision = 'uint8';
case 4,
dime.bitpix = 16; precision = 'int16';
case 8,
dime.bitpix = 32; precision = 'int32';
case 16,
dime.bitpix = 32; precision = 'float32';
case 64,
dime.bitpix = 64; precision = 'float64';
case 128
dime.bitpix = 24; precision = 'uint8';
otherwise
error('Datatype is not supported by make_ana.');
end
dime.dim_un0 = 0;
dime.pixdim = voxel_size;
dime.vox_offset = 0;
dime.roi_scale = 1;
dime.funused1 = 0;
dime.funused2 = 0;
dime.cal_max = 0;
dime.cal_min = 0;
dime.compressed = 0;
dime.verified = 0;
dime.glmax = maxval;
dime.glmin = minval;
return; % image_dimension
%---------------------------------------------------------------------
function hist = data_history(origin, descrip)
hist.descrip = descrip;
hist.aux_file = 'none';
hist.orient = 0;
hist.originator = origin;
hist.generated = '';
hist.scannum = '';
hist.patient_id = '';
hist.exp_date = '';
hist.exp_time = '';
hist.hist_un0 = '';
hist.views = 0;
hist.vols_added = 0;
hist.start_field = 0;
hist.field_skip = 0;
hist.omax = 0;
hist.omin = 0;
hist.smax = 0;
hist.smin = 0;
return; % data_history
|
github
|
adhusch/PaCER-master
|
extra_nii_hdr.m
|
.m
|
PaCER-master/external/NIfTI_20140122/extra_nii_hdr.m
| 7,830 |
utf_8
|
853f39f00cbf133e90d0f2cf08d79488
|
% Decode extra NIFTI header information into hdr.extra
%
% Usage: hdr = extra_nii_hdr(hdr)
%
% hdr can be obtained from load_nii_hdr
%
% NIFTI data format can be found on: http://nifti.nimh.nih.gov
%
% - Jimmy Shen ([email protected])
%
function hdr = extra_nii_hdr(hdr)
switch hdr.dime.datatype
case 1
extra.NIFTI_DATATYPES = 'DT_BINARY';
case 2
extra.NIFTI_DATATYPES = 'DT_UINT8';
case 4
extra.NIFTI_DATATYPES = 'DT_INT16';
case 8
extra.NIFTI_DATATYPES = 'DT_INT32';
case 16
extra.NIFTI_DATATYPES = 'DT_FLOAT32';
case 32
extra.NIFTI_DATATYPES = 'DT_COMPLEX64';
case 64
extra.NIFTI_DATATYPES = 'DT_FLOAT64';
case 128
extra.NIFTI_DATATYPES = 'DT_RGB24';
case 256
extra.NIFTI_DATATYPES = 'DT_INT8';
case 512
extra.NIFTI_DATATYPES = 'DT_UINT16';
case 768
extra.NIFTI_DATATYPES = 'DT_UINT32';
case 1024
extra.NIFTI_DATATYPES = 'DT_INT64';
case 1280
extra.NIFTI_DATATYPES = 'DT_UINT64';
case 1536
extra.NIFTI_DATATYPES = 'DT_FLOAT128';
case 1792
extra.NIFTI_DATATYPES = 'DT_COMPLEX128';
case 2048
extra.NIFTI_DATATYPES = 'DT_COMPLEX256';
otherwise
extra.NIFTI_DATATYPES = 'DT_UNKNOWN';
end
switch hdr.dime.intent_code
case 2
extra.NIFTI_INTENT_CODES = 'NIFTI_INTENT_CORREL';
case 3
extra.NIFTI_INTENT_CODES = 'NIFTI_INTENT_TTEST';
case 4
extra.NIFTI_INTENT_CODES = 'NIFTI_INTENT_FTEST';
case 5
extra.NIFTI_INTENT_CODES = 'NIFTI_INTENT_ZSCORE';
case 6
extra.NIFTI_INTENT_CODES = 'NIFTI_INTENT_CHISQ';
case 7
extra.NIFTI_INTENT_CODES = 'NIFTI_INTENT_BETA';
case 8
extra.NIFTI_INTENT_CODES = 'NIFTI_INTENT_BINOM';
case 9
extra.NIFTI_INTENT_CODES = 'NIFTI_INTENT_GAMMA';
case 10
extra.NIFTI_INTENT_CODES = 'NIFTI_INTENT_POISSON';
case 11
extra.NIFTI_INTENT_CODES = 'NIFTI_INTENT_NORMAL';
case 12
extra.NIFTI_INTENT_CODES = 'NIFTI_INTENT_FTEST_NONC';
case 13
extra.NIFTI_INTENT_CODES = 'NIFTI_INTENT_CHISQ_NONC';
case 14
extra.NIFTI_INTENT_CODES = 'NIFTI_INTENT_LOGISTIC';
case 15
extra.NIFTI_INTENT_CODES = 'NIFTI_INTENT_LAPLACE';
case 16
extra.NIFTI_INTENT_CODES = 'NIFTI_INTENT_UNIFORM';
case 17
extra.NIFTI_INTENT_CODES = 'NIFTI_INTENT_TTEST_NONC';
case 18
extra.NIFTI_INTENT_CODES = 'NIFTI_INTENT_WEIBULL';
case 19
extra.NIFTI_INTENT_CODES = 'NIFTI_INTENT_CHI';
case 20
extra.NIFTI_INTENT_CODES = 'NIFTI_INTENT_INVGAUSS';
case 21
extra.NIFTI_INTENT_CODES = 'NIFTI_INTENT_EXTVAL';
case 22
extra.NIFTI_INTENT_CODES = 'NIFTI_INTENT_PVAL';
case 23
extra.NIFTI_INTENT_CODES = 'NIFTI_INTENT_LOGPVAL';
case 24
extra.NIFTI_INTENT_CODES = 'NIFTI_INTENT_LOG10PVAL';
case 1001
extra.NIFTI_INTENT_CODES = 'NIFTI_INTENT_ESTIMATE';
case 1002
extra.NIFTI_INTENT_CODES = 'NIFTI_INTENT_LABEL';
case 1003
extra.NIFTI_INTENT_CODES = 'NIFTI_INTENT_NEURONAME';
case 1004
extra.NIFTI_INTENT_CODES = 'NIFTI_INTENT_GENMATRIX';
case 1005
extra.NIFTI_INTENT_CODES = 'NIFTI_INTENT_SYMMATRIX';
case 1006
extra.NIFTI_INTENT_CODES = 'NIFTI_INTENT_DISPVECT';
case 1007
extra.NIFTI_INTENT_CODES = 'NIFTI_INTENT_VECTOR';
case 1008
extra.NIFTI_INTENT_CODES = 'NIFTI_INTENT_POINTSET';
case 1009
extra.NIFTI_INTENT_CODES = 'NIFTI_INTENT_TRIANGLE';
case 1010
extra.NIFTI_INTENT_CODES = 'NIFTI_INTENT_QUATERNION';
case 1011
extra.NIFTI_INTENT_CODES = 'NIFTI_INTENT_DIMLESS';
otherwise
extra.NIFTI_INTENT_CODES = 'NIFTI_INTENT_NONE';
end
extra.NIFTI_INTENT_NAMES = hdr.hist.intent_name;
if hdr.hist.sform_code > 0
switch hdr.hist.sform_code
case 1
extra.NIFTI_SFORM_CODES = 'NIFTI_XFORM_SCANNER_ANAT';
case 2
extra.NIFTI_SFORM_CODES = 'NIFTI_XFORM_ALIGNED_ANAT';
case 3
extra.NIFTI_SFORM_CODES = 'NIFTI_XFORM_TALAIRACH';
case 4
extra.NIFTI_SFORM_CODES = 'NIFTI_XFORM_MNI_152';
otherwise
extra.NIFTI_SFORM_CODES = 'NIFTI_XFORM_UNKNOWN';
end
extra.NIFTI_QFORM_CODES = 'NIFTI_XFORM_UNKNOWN';
elseif hdr.hist.qform_code > 0
extra.NIFTI_SFORM_CODES = 'NIFTI_XFORM_UNKNOWN';
switch hdr.hist.qform_code
case 1
extra.NIFTI_QFORM_CODES = 'NIFTI_XFORM_SCANNER_ANAT';
case 2
extra.NIFTI_QFORM_CODES = 'NIFTI_XFORM_ALIGNED_ANAT';
case 3
extra.NIFTI_QFORM_CODES = 'NIFTI_XFORM_TALAIRACH';
case 4
extra.NIFTI_QFORM_CODES = 'NIFTI_XFORM_MNI_152';
otherwise
extra.NIFTI_QFORM_CODES = 'NIFTI_XFORM_UNKNOWN';
end
else
extra.NIFTI_SFORM_CODES = 'NIFTI_XFORM_UNKNOWN';
extra.NIFTI_QFORM_CODES = 'NIFTI_XFORM_UNKNOWN';
end
switch bitand(hdr.dime.xyzt_units, 7) % mask with 0x07
case 1
extra.NIFTI_SPACE_UNIT = 'NIFTI_UNITS_METER';
case 2
extra.NIFTI_SPACE_UNIT = 'NIFTI_UNITS_MM'; % millimeter
case 3
extra.NIFTI_SPACE_UNIT = 'NIFTI_UNITS_MICRO';
otherwise
extra.NIFTI_SPACE_UNIT = 'NIFTI_UNITS_UNKNOWN';
end
switch bitand(hdr.dime.xyzt_units, 56) % mask with 0x38
case 8
extra.NIFTI_TIME_UNIT = 'NIFTI_UNITS_SEC';
case 16
extra.NIFTI_TIME_UNIT = 'NIFTI_UNITS_MSEC';
case 24
extra.NIFTI_TIME_UNIT = 'NIFTI_UNITS_USEC'; % microsecond
otherwise
extra.NIFTI_TIME_UNIT = 'NIFTI_UNITS_UNKNOWN';
end
switch hdr.dime.xyzt_units
case 32
extra.NIFTI_SPECTRAL_UNIT = 'NIFTI_UNITS_HZ';
case 40
extra.NIFTI_SPECTRAL_UNIT = 'NIFTI_UNITS_PPM'; % part per million
case 48
extra.NIFTI_SPECTRAL_UNIT = 'NIFTI_UNITS_RADS'; % radians per second
otherwise
extra.NIFTI_SPECTRAL_UNIT = 'NIFTI_UNITS_UNKNOWN';
end
% MRI-specific spatial and temporal information
%
dim_info = hdr.hk.dim_info;
extra.NIFTI_FREQ_DIM = bitand(dim_info, 3);
extra.NIFTI_PHASE_DIM = bitand(bitshift(dim_info, -2), 3);
extra.NIFTI_SLICE_DIM = bitand(bitshift(dim_info, -4), 3);
% Check slice code
%
switch hdr.dime.slice_code
case 1
extra.NIFTI_SLICE_ORDER = 'NIFTI_SLICE_SEQ_INC'; % sequential increasing
case 2
extra.NIFTI_SLICE_ORDER = 'NIFTI_SLICE_SEQ_DEC'; % sequential decreasing
case 3
extra.NIFTI_SLICE_ORDER = 'NIFTI_SLICE_ALT_INC'; % alternating increasing
case 4
extra.NIFTI_SLICE_ORDER = 'NIFTI_SLICE_ALT_DEC'; % alternating decreasing
case 5
extra.NIFTI_SLICE_ORDER = 'NIFTI_SLICE_ALT_INC2'; % ALT_INC # 2
case 6
extra.NIFTI_SLICE_ORDER = 'NIFTI_SLICE_ALT_DEC2'; % ALT_DEC # 2
otherwise
extra.NIFTI_SLICE_ORDER = 'NIFTI_SLICE_UNKNOWN';
end
% Check NIFTI version
%
if ~isempty(hdr.hist.magic) & strcmp(hdr.hist.magic(1),'n') & ...
( strcmp(hdr.hist.magic(2),'i') | strcmp(hdr.hist.magic(2),'+') ) & ...
str2num(hdr.hist.magic(3)) >= 1 & str2num(hdr.hist.magic(3)) <= 9
extra.NIFTI_VERSION = str2num(hdr.hist.magic(3));
else
extra.NIFTI_VERSION = 0;
end
% Check if data stored in the same file (*.nii) or separate
% files (*.hdr/*.img)
%
if isempty(hdr.hist.magic)
extra.NIFTI_ONEFILE = 0;
else
extra.NIFTI_ONEFILE = strcmp(hdr.hist.magic(2), '+');
end
% Swap has been taken care of by checking whether sizeof_hdr is
% 348 (machine is 'ieee-le' or 'ieee-be' etc)
%
% extra.NIFTI_NEEDS_SWAP = (hdr.dime.dim(1) < 0 | hdr.dime.dim(1) > 7);
% Check NIFTI header struct contains a 5th (vector) dimension
%
if hdr.dime.dim(1) > 4 & hdr.dime.dim(6) > 1
extra.NIFTI_5TH_DIM = hdr.dime.dim(6);
else
extra.NIFTI_5TH_DIM = 0;
end
hdr.extra = extra;
return; % extra_nii_hdr
|
github
|
adhusch/PaCER-master
|
rri_xhair.m
|
.m
|
PaCER-master/external/NIfTI_20140122/rri_xhair.m
| 2,208 |
utf_8
|
b3ae9df90d43e5d9538b6b135fa8af20
|
% rri_xhair: create a pair of full_cross_hair at point [x y] in
% axes h_ax, and return xhair struct
%
% Usage: xhair = rri_xhair([x y], xhair, h_ax);
%
% If omit xhair, rri_xhair will create a pair of xhair; otherwise,
% rri_xhair will update the xhair. If omit h_ax, current axes will
% be used.
%
% 24-nov-2003 jimmy ([email protected])
%
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
function xhair = rri_xhair(varargin)
if nargin == 0
error('Please enter a point position as first argument');
return;
end
if nargin > 0
p = varargin{1};
if ~isnumeric(p) | length(p) ~= 2
error('Invalid point position');
return;
else
xhair = [];
end
end
if nargin > 1
xhair = varargin{2};
if ~isempty(xhair)
if ~isstruct(xhair)
error('Invalid xhair struct');
return;
elseif ~isfield(xhair,'lx') | ~isfield(xhair,'ly')
error('Invalid xhair struct');
return;
elseif ~ishandle(xhair.lx) | ~ishandle(xhair.ly)
error('Invalid xhair struct');
return;
end
lx = xhair.lx;
ly = xhair.ly;
else
lx = [];
ly = [];
end
end
if nargin > 2
h_ax = varargin{3};
if ~ishandle(h_ax)
error('Invalid axes handle');
return;
elseif ~strcmp(lower(get(h_ax,'type')), 'axes')
error('Invalid axes handle');
return;
end
else
h_ax = gca;
end
x_range = get(h_ax,'xlim');
y_range = get(h_ax,'ylim');
if ~isempty(xhair)
set(lx, 'ydata', [p(2) p(2)]);
set(ly, 'xdata', [p(1) p(1)]);
set(h_ax, 'selected', 'on');
set(h_ax, 'selected', 'off');
else
figure(get(h_ax,'parent'));
axes(h_ax);
xhair.lx = line('xdata', x_range, 'ydata', [p(2) p(2)], ...
'zdata', [11 11], 'color', [1 0 0], 'hittest', 'off');
xhair.ly = line('xdata', [p(1) p(1)], 'ydata', y_range, ...
'zdata', [11 11], 'color', [1 0 0], 'hittest', 'off');
end
set(h_ax,'xlim',x_range);
set(h_ax,'ylim',y_range);
return;
|
github
|
adhusch/PaCER-master
|
save_untouch_nii_hdr.m
|
.m
|
PaCER-master/external/NIfTI_20140122/save_untouch_nii_hdr.m
| 8,514 |
utf_8
|
582f82c471a9a8826eda59354f61dd1a
|
% internal function
% - Jimmy Shen ([email protected])
function save_nii_hdr(hdr, fid)
if ~isequal(hdr.hk.sizeof_hdr,348),
error('hdr.hk.sizeof_hdr must be 348.');
end
write_header(hdr, fid);
return; % save_nii_hdr
%---------------------------------------------------------------------
function write_header(hdr, fid)
% Original header structures
% struct dsr /* dsr = hdr */
% {
% struct header_key hk; /* 0 + 40 */
% struct image_dimension dime; /* 40 + 108 */
% struct data_history hist; /* 148 + 200 */
% }; /* total= 348 bytes*/
header_key(fid, hdr.hk);
image_dimension(fid, hdr.dime);
data_history(fid, hdr.hist);
% check the file size is 348 bytes
%
fbytes = ftell(fid);
if ~isequal(fbytes,348),
msg = sprintf('Header size is not 348 bytes.');
warning(msg);
end
return; % write_header
%---------------------------------------------------------------------
function header_key(fid, hk)
fseek(fid,0,'bof');
% Original header structures
% struct header_key /* header key */
% { /* off + size */
% int sizeof_hdr /* 0 + 4 */
% char data_type[10]; /* 4 + 10 */
% char db_name[18]; /* 14 + 18 */
% int extents; /* 32 + 4 */
% short int session_error; /* 36 + 2 */
% char regular; /* 38 + 1 */
% char dim_info; % char hkey_un0; /* 39 + 1 */
% }; /* total=40 bytes */
fwrite(fid, hk.sizeof_hdr(1), 'int32'); % must be 348.
% data_type = sprintf('%-10s',hk.data_type); % ensure it is 10 chars from left
% fwrite(fid, data_type(1:10), 'uchar');
pad = zeros(1, 10-length(hk.data_type));
hk.data_type = [hk.data_type char(pad)];
fwrite(fid, hk.data_type(1:10), 'uchar');
% db_name = sprintf('%-18s', hk.db_name); % ensure it is 18 chars from left
% fwrite(fid, db_name(1:18), 'uchar');
pad = zeros(1, 18-length(hk.db_name));
hk.db_name = [hk.db_name char(pad)];
fwrite(fid, hk.db_name(1:18), 'uchar');
fwrite(fid, hk.extents(1), 'int32');
fwrite(fid, hk.session_error(1), 'int16');
fwrite(fid, hk.regular(1), 'uchar'); % might be uint8
% fwrite(fid, hk.hkey_un0(1), 'uchar');
% fwrite(fid, hk.hkey_un0(1), 'uint8');
fwrite(fid, hk.dim_info(1), 'uchar');
return; % header_key
%---------------------------------------------------------------------
function image_dimension(fid, dime)
% Original header structures
% struct image_dimension
% { /* off + size */
% short int dim[8]; /* 0 + 16 */
% float intent_p1; % char vox_units[4]; /* 16 + 4 */
% float intent_p2; % char cal_units[8]; /* 20 + 4 */
% float intent_p3; % char cal_units[8]; /* 24 + 4 */
% short int intent_code; % short int unused1; /* 28 + 2 */
% short int datatype; /* 30 + 2 */
% short int bitpix; /* 32 + 2 */
% short int slice_start; % short int dim_un0; /* 34 + 2 */
% float pixdim[8]; /* 36 + 32 */
% /*
% pixdim[] specifies the voxel dimensions:
% pixdim[1] - voxel width
% pixdim[2] - voxel height
% pixdim[3] - interslice distance
% pixdim[4] - volume timing, in msec
% ..etc
% */
% float vox_offset; /* 68 + 4 */
% float scl_slope; % float roi_scale; /* 72 + 4 */
% float scl_inter; % float funused1; /* 76 + 4 */
% short slice_end; % float funused2; /* 80 + 2 */
% char slice_code; % float funused2; /* 82 + 1 */
% char xyzt_units; % float funused2; /* 83 + 1 */
% float cal_max; /* 84 + 4 */
% float cal_min; /* 88 + 4 */
% float slice_duration; % int compressed; /* 92 + 4 */
% float toffset; % int verified; /* 96 + 4 */
% int glmax; /* 100 + 4 */
% int glmin; /* 104 + 4 */
% }; /* total=108 bytes */
fwrite(fid, dime.dim(1:8), 'int16');
fwrite(fid, dime.intent_p1(1), 'float32');
fwrite(fid, dime.intent_p2(1), 'float32');
fwrite(fid, dime.intent_p3(1), 'float32');
fwrite(fid, dime.intent_code(1), 'int16');
fwrite(fid, dime.datatype(1), 'int16');
fwrite(fid, dime.bitpix(1), 'int16');
fwrite(fid, dime.slice_start(1), 'int16');
fwrite(fid, dime.pixdim(1:8), 'float32');
fwrite(fid, dime.vox_offset(1), 'float32');
fwrite(fid, dime.scl_slope(1), 'float32');
fwrite(fid, dime.scl_inter(1), 'float32');
fwrite(fid, dime.slice_end(1), 'int16');
fwrite(fid, dime.slice_code(1), 'uchar');
fwrite(fid, dime.xyzt_units(1), 'uchar');
fwrite(fid, dime.cal_max(1), 'float32');
fwrite(fid, dime.cal_min(1), 'float32');
fwrite(fid, dime.slice_duration(1), 'float32');
fwrite(fid, dime.toffset(1), 'float32');
fwrite(fid, dime.glmax(1), 'int32');
fwrite(fid, dime.glmin(1), 'int32');
return; % image_dimension
%---------------------------------------------------------------------
function data_history(fid, hist)
% Original header structures
%struct data_history
% { /* off + size */
% char descrip[80]; /* 0 + 80 */
% char aux_file[24]; /* 80 + 24 */
% short int qform_code; /* 104 + 2 */
% short int sform_code; /* 106 + 2 */
% float quatern_b; /* 108 + 4 */
% float quatern_c; /* 112 + 4 */
% float quatern_d; /* 116 + 4 */
% float qoffset_x; /* 120 + 4 */
% float qoffset_y; /* 124 + 4 */
% float qoffset_z; /* 128 + 4 */
% float srow_x[4]; /* 132 + 16 */
% float srow_y[4]; /* 148 + 16 */
% float srow_z[4]; /* 164 + 16 */
% char intent_name[16]; /* 180 + 16 */
% char magic[4]; % int smin; /* 196 + 4 */
% }; /* total=200 bytes */
% descrip = sprintf('%-80s', hist.descrip); % 80 chars from left
% fwrite(fid, descrip(1:80), 'uchar');
pad = zeros(1, 80-length(hist.descrip));
hist.descrip = [hist.descrip char(pad)];
fwrite(fid, hist.descrip(1:80), 'uchar');
% aux_file = sprintf('%-24s', hist.aux_file); % 24 chars from left
% fwrite(fid, aux_file(1:24), 'uchar');
pad = zeros(1, 24-length(hist.aux_file));
hist.aux_file = [hist.aux_file char(pad)];
fwrite(fid, hist.aux_file(1:24), 'uchar');
fwrite(fid, hist.qform_code, 'int16');
fwrite(fid, hist.sform_code, 'int16');
fwrite(fid, hist.quatern_b, 'float32');
fwrite(fid, hist.quatern_c, 'float32');
fwrite(fid, hist.quatern_d, 'float32');
fwrite(fid, hist.qoffset_x, 'float32');
fwrite(fid, hist.qoffset_y, 'float32');
fwrite(fid, hist.qoffset_z, 'float32');
fwrite(fid, hist.srow_x(1:4), 'float32');
fwrite(fid, hist.srow_y(1:4), 'float32');
fwrite(fid, hist.srow_z(1:4), 'float32');
% intent_name = sprintf('%-16s', hist.intent_name); % 16 chars from left
% fwrite(fid, intent_name(1:16), 'uchar');
pad = zeros(1, 16-length(hist.intent_name));
hist.intent_name = [hist.intent_name char(pad)];
fwrite(fid, hist.intent_name(1:16), 'uchar');
% magic = sprintf('%-4s', hist.magic); % 4 chars from left
% fwrite(fid, magic(1:4), 'uchar');
pad = zeros(1, 4-length(hist.magic));
hist.magic = [hist.magic char(pad)];
fwrite(fid, hist.magic(1:4), 'uchar');
return; % data_history
|
github
|
adhusch/PaCER-master
|
expand_nii_scan.m
|
.m
|
PaCER-master/external/NIfTI_20140122/expand_nii_scan.m
| 1,333 |
utf_8
|
748da05d09c1a005401c67270c4b94ab
|
% Expand a multiple-scan NIFTI file into multiple single-scan NIFTI files
%
% Usage: expand_nii_scan(multi_scan_filename, [img_idx], [path_to_save])
%
% NIFTI data format can be found on: http://nifti.nimh.nih.gov
%
% - Jimmy Shen ([email protected])
%
function expand_nii_scan(filename, img_idx, newpath)
v = version;
% Check file extension. If .gz, unpack it into temp folder
%
if length(filename) > 2 & strcmp(filename(end-2:end), '.gz')
if ~strcmp(filename(end-6:end), '.img.gz') & ...
~strcmp(filename(end-6:end), '.hdr.gz') & ...
~strcmp(filename(end-6:end), '.nii.gz')
error('Please check filename.');
end
if str2num(v(1:3)) < 7.1 | ~usejava('jvm')
error('Please use MATLAB 7.1 (with java) and above, or run gunzip outside MATLAB.');
else
gzFile = 1;
end
end
if ~exist('newpath','var') | isempty(newpath), newpath = pwd; end
if ~exist('img_idx','var') | isempty(img_idx), img_idx = 1:get_nii_frame(filename); end
for i=img_idx
nii_i = load_untouch_nii(filename, i);
fn = [nii_i.fileprefix '_' sprintf('%04d',i)];
pnfn = fullfile(newpath, fn);
if exist('gzFile', 'var')
pnfn = [pnfn '.nii.gz'];
end
save_untouch_nii(nii_i, pnfn);
end
return; % expand_nii_scan
|
github
|
adhusch/PaCER-master
|
load_untouch_header_only.m
|
.m
|
PaCER-master/external/NIfTI_20140122/load_untouch_header_only.m
| 7,068 |
utf_8
|
8996c72db42b01029c92a4ecd88f4b21
|
% Load NIfTI / Analyze header without applying any appropriate affine
% geometric transform or voxel intensity scaling. It is equivalent to
% hdr field when using load_untouch_nii to load dataset. Support both
% *.nii and *.hdr file extension. If file extension is not provided,
% *.hdr will be used as default.
%
% Usage: [header, ext, filetype, machine] = load_untouch_header_only(filename)
%
% filename - NIfTI / Analyze file name.
%
% Returned values:
%
% header - struct with NIfTI / Analyze header fields.
%
% ext - NIfTI extension if it is not empty.
%
% filetype - 0 for Analyze format (*.hdr/*.img);
% 1 for NIFTI format in 2 files (*.hdr/*.img);
% 2 for NIFTI format in 1 file (*.nii).
%
% machine - a string, see below for details. The default here is 'ieee-le'.
%
% 'native' or 'n' - local machine format - the default
% 'ieee-le' or 'l' - IEEE floating point with little-endian
% byte ordering
% 'ieee-be' or 'b' - IEEE floating point with big-endian
% byte ordering
% 'vaxd' or 'd' - VAX D floating point and VAX ordering
% 'vaxg' or 'g' - VAX G floating point and VAX ordering
% 'cray' or 'c' - Cray floating point with big-endian
% byte ordering
% 'ieee-le.l64' or 'a' - IEEE floating point with little-endian
% byte ordering and 64 bit long data type
% 'ieee-be.l64' or 's' - IEEE floating point with big-endian byte
% ordering and 64 bit long data type.
%
% Part of this file is copied and modified from:
% http://www.mathworks.com/matlabcentral/fileexchange/1878-mri-analyze-tools
%
% NIFTI data format can be found on: http://nifti.nimh.nih.gov
%
% - Jimmy Shen ([email protected])
%
function [hdr, ext, filetype, machine] = load_untouch_header_only(filename)
if ~exist('filename','var')
error('Usage: [header, ext, filetype, machine] = load_untouch_header_only(filename)');
end
v = version;
% Check file extension. If .gz, unpack it into temp folder
%
if length(filename) > 2 & strcmp(filename(end-2:end), '.gz')
if ~strcmp(filename(end-6:end), '.img.gz') & ...
~strcmp(filename(end-6:end), '.hdr.gz') & ...
~strcmp(filename(end-6:end), '.nii.gz')
error('Please check filename.');
end
if str2num(v(1:3)) < 7.1 | ~usejava('jvm')
error('Please use MATLAB 7.1 (with java) and above, or run gunzip outside MATLAB.');
elseif strcmp(filename(end-6:end), '.img.gz')
filename1 = filename;
filename2 = filename;
filename2(end-6:end) = '';
filename2 = [filename2, '.hdr.gz'];
tmpDir = tempname;
mkdir(tmpDir);
gzFileName = filename;
filename1 = gunzip(filename1, tmpDir);
filename2 = gunzip(filename2, tmpDir);
filename = char(filename1); % convert from cell to string
elseif strcmp(filename(end-6:end), '.hdr.gz')
filename1 = filename;
filename2 = filename;
filename2(end-6:end) = '';
filename2 = [filename2, '.img.gz'];
tmpDir = tempname;
mkdir(tmpDir);
gzFileName = filename;
filename1 = gunzip(filename1, tmpDir);
filename2 = gunzip(filename2, tmpDir);
filename = char(filename1); % convert from cell to string
elseif strcmp(filename(end-6:end), '.nii.gz')
tmpDir = tempname;
mkdir(tmpDir);
gzFileName = filename;
filename = gunzip(filename, tmpDir);
filename = char(filename); % convert from cell to string
end
end
% Read the dataset header
%
[hdr, filetype, fileprefix, machine] = load_nii_hdr(filename);
if filetype == 0
hdr = load_untouch0_nii_hdr(fileprefix, machine);
ext = [];
else
hdr = load_untouch_nii_hdr(fileprefix, machine, filetype);
% Read the header extension
%
ext = load_nii_ext(filename);
end
% Set bitpix according to datatype
%
% /*Acceptable values for datatype are*/
%
% 0 None (Unknown bit per voxel) % DT_NONE, DT_UNKNOWN
% 1 Binary (ubit1, bitpix=1) % DT_BINARY
% 2 Unsigned char (uchar or uint8, bitpix=8) % DT_UINT8, NIFTI_TYPE_UINT8
% 4 Signed short (int16, bitpix=16) % DT_INT16, NIFTI_TYPE_INT16
% 8 Signed integer (int32, bitpix=32) % DT_INT32, NIFTI_TYPE_INT32
% 16 Floating point (single or float32, bitpix=32) % DT_FLOAT32, NIFTI_TYPE_FLOAT32
% 32 Complex, 2 float32 (Use float32, bitpix=64) % DT_COMPLEX64, NIFTI_TYPE_COMPLEX64
% 64 Double precision (double or float64, bitpix=64) % DT_FLOAT64, NIFTI_TYPE_FLOAT64
% 128 uint8 RGB (Use uint8, bitpix=24) % DT_RGB24, NIFTI_TYPE_RGB24
% 256 Signed char (schar or int8, bitpix=8) % DT_INT8, NIFTI_TYPE_INT8
% 511 Single RGB (Use float32, bitpix=96) % DT_RGB96, NIFTI_TYPE_RGB96
% 512 Unsigned short (uint16, bitpix=16) % DT_UNINT16, NIFTI_TYPE_UNINT16
% 768 Unsigned integer (uint32, bitpix=32) % DT_UNINT32, NIFTI_TYPE_UNINT32
% 1024 Signed long long (int64, bitpix=64) % DT_INT64, NIFTI_TYPE_INT64
% 1280 Unsigned long long (uint64, bitpix=64) % DT_UINT64, NIFTI_TYPE_UINT64
% 1536 Long double, float128 (Unsupported, bitpix=128) % DT_FLOAT128, NIFTI_TYPE_FLOAT128
% 1792 Complex128, 2 float64 (Use float64, bitpix=128) % DT_COMPLEX128, NIFTI_TYPE_COMPLEX128
% 2048 Complex256, 2 float128 (Unsupported, bitpix=256) % DT_COMPLEX128, NIFTI_TYPE_COMPLEX128
%
switch hdr.dime.datatype
case 1,
hdr.dime.bitpix = 1; precision = 'ubit1';
case 2,
hdr.dime.bitpix = 8; precision = 'uint8';
case 4,
hdr.dime.bitpix = 16; precision = 'int16';
case 8,
hdr.dime.bitpix = 32; precision = 'int32';
case 16,
hdr.dime.bitpix = 32; precision = 'float32';
case 32,
hdr.dime.bitpix = 64; precision = 'float32';
case 64,
hdr.dime.bitpix = 64; precision = 'float64';
case 128,
hdr.dime.bitpix = 24; precision = 'uint8';
case 256
hdr.dime.bitpix = 8; precision = 'int8';
case 511
hdr.dime.bitpix = 96; precision = 'float32';
case 512
hdr.dime.bitpix = 16; precision = 'uint16';
case 768
hdr.dime.bitpix = 32; precision = 'uint32';
case 1024
hdr.dime.bitpix = 64; precision = 'int64';
case 1280
hdr.dime.bitpix = 64; precision = 'uint64';
case 1792,
hdr.dime.bitpix = 128; precision = 'float64';
otherwise
error('This datatype is not supported');
end
tmp = hdr.dime.dim(2:end);
tmp(find(tmp < 1)) = 1;
hdr.dime.dim(2:end) = tmp;
% Clean up after gunzip
%
if exist('gzFileName', 'var')
rmdir(tmpDir,'s');
end
return % load_untouch_header_only
|
github
|
adhusch/PaCER-master
|
bipolar.m
|
.m
|
PaCER-master/external/NIfTI_20140122/bipolar.m
| 2,145 |
utf_8
|
295f87ece96ca4c5dff8dce4cd912a34
|
%BIPOLAR returns an M-by-3 matrix containing a blue-red colormap, in
% in which red stands for positive, blue stands for negative,
% and white stands for 0.
%
% Usage: cmap = bipolar(M, lo, hi, contrast); or cmap = bipolar;
%
% cmap: output M-by-3 matrix for BIPOLAR colormap.
% M: number of shades in the colormap. By default, it is the
% same length as the current colormap.
% lo: the lowest value to represent.
% hi: the highest value to represent.
%
% Inspired from the LORETA PASCAL program:
% http://www.unizh.ch/keyinst/NewLORETA
%
% [email protected]
%
%----------------------------------------------------------------
function cmap = bipolar(M, lo, hi, contrast)
if ~exist('contrast','var')
contrast = 128;
end
if ~exist('lo','var')
lo = -1;
end
if ~exist('hi','var')
hi = 1;
end
if ~exist('M','var')
cmap = colormap;
M = size(cmap,1);
end
steepness = 10 ^ (1 - (contrast-1)/127);
pos_infs = 1e-99;
neg_infs = -1e-99;
doubleredc = [];
doublebluec = [];
if lo >= 0 % all positive
if lo == 0
lo = pos_infs;
end
for i=linspace(hi/M, hi, M)
t = exp(log(i/hi)*steepness);
doubleredc = [doubleredc; [(1-t)+t,(1-t)+0,(1-t)+0]];
end
cmap = doubleredc;
elseif hi <= 0 % all negative
if hi == 0
hi = neg_infs;
end
for i=linspace(abs(lo)/M, abs(lo), M)
t = exp(log(i/abs(lo))*steepness);
doublebluec = [doublebluec; [(1-t)+0,(1-t)+0,(1-t)+t]];
end
cmap = flipud(doublebluec);
else
if hi > abs(lo)
maxc = hi;
else
maxc = abs(lo);
end
for i=linspace(maxc/M, hi, round(M*hi/(hi-lo)))
t = exp(log(i/maxc)*steepness);
doubleredc = [doubleredc; [(1-t)+t,(1-t)+0,(1-t)+0]];
end
for i=linspace(maxc/M, abs(lo), round(M*abs(lo)/(hi-lo)))
t = exp(log(i/maxc)*steepness);
doublebluec = [doublebluec; [(1-t)+0,(1-t)+0,(1-t)+t]];
end
cmap = [flipud(doublebluec); doubleredc];
end
return; % bipolar
|
github
|
adhusch/PaCER-master
|
save_nii_hdr.m
|
.m
|
PaCER-master/external/NIfTI_20140122/save_nii_hdr.m
| 9,270 |
utf_8
|
f97c194f5bfc667eb4f96edf12be02a7
|
% internal function
% - Jimmy Shen ([email protected])
function save_nii_hdr(hdr, fid)
if ~exist('hdr','var') | ~exist('fid','var')
error('Usage: save_nii_hdr(hdr, fid)');
end
if ~isequal(hdr.hk.sizeof_hdr,348),
error('hdr.hk.sizeof_hdr must be 348.');
end
if hdr.hist.qform_code == 0 & hdr.hist.sform_code == 0
hdr.hist.sform_code = 1;
hdr.hist.srow_x(1) = hdr.dime.pixdim(2);
hdr.hist.srow_x(2) = 0;
hdr.hist.srow_x(3) = 0;
hdr.hist.srow_y(1) = 0;
hdr.hist.srow_y(2) = hdr.dime.pixdim(3);
hdr.hist.srow_y(3) = 0;
hdr.hist.srow_z(1) = 0;
hdr.hist.srow_z(2) = 0;
hdr.hist.srow_z(3) = hdr.dime.pixdim(4);
hdr.hist.srow_x(4) = (1-hdr.hist.originator(1))*hdr.dime.pixdim(2);
hdr.hist.srow_y(4) = (1-hdr.hist.originator(2))*hdr.dime.pixdim(3);
hdr.hist.srow_z(4) = (1-hdr.hist.originator(3))*hdr.dime.pixdim(4);
end
write_header(hdr, fid);
return; % save_nii_hdr
%---------------------------------------------------------------------
function write_header(hdr, fid)
% Original header structures
% struct dsr /* dsr = hdr */
% {
% struct header_key hk; /* 0 + 40 */
% struct image_dimension dime; /* 40 + 108 */
% struct data_history hist; /* 148 + 200 */
% }; /* total= 348 bytes*/
header_key(fid, hdr.hk);
image_dimension(fid, hdr.dime);
data_history(fid, hdr.hist);
% check the file size is 348 bytes
%
fbytes = ftell(fid);
if ~isequal(fbytes,348),
msg = sprintf('Header size is not 348 bytes.');
warning(msg);
end
return; % write_header
%---------------------------------------------------------------------
function header_key(fid, hk)
fseek(fid,0,'bof');
% Original header structures
% struct header_key /* header key */
% { /* off + size */
% int sizeof_hdr /* 0 + 4 */
% char data_type[10]; /* 4 + 10 */
% char db_name[18]; /* 14 + 18 */
% int extents; /* 32 + 4 */
% short int session_error; /* 36 + 2 */
% char regular; /* 38 + 1 */
% char dim_info; % char hkey_un0; /* 39 + 1 */
% }; /* total=40 bytes */
fwrite(fid, hk.sizeof_hdr(1), 'int32'); % must be 348.
% data_type = sprintf('%-10s',hk.data_type); % ensure it is 10 chars from left
% fwrite(fid, data_type(1:10), 'uchar');
pad = zeros(1, 10-length(hk.data_type));
hk.data_type = [hk.data_type char(pad)];
fwrite(fid, hk.data_type(1:10), 'uchar');
% db_name = sprintf('%-18s', hk.db_name); % ensure it is 18 chars from left
% fwrite(fid, db_name(1:18), 'uchar');
pad = zeros(1, 18-length(hk.db_name));
hk.db_name = [hk.db_name char(pad)];
fwrite(fid, hk.db_name(1:18), 'uchar');
fwrite(fid, hk.extents(1), 'int32');
fwrite(fid, hk.session_error(1), 'int16');
fwrite(fid, hk.regular(1), 'uchar'); % might be uint8
% fwrite(fid, hk.hkey_un0(1), 'uchar');
% fwrite(fid, hk.hkey_un0(1), 'uint8');
fwrite(fid, hk.dim_info(1), 'uchar');
return; % header_key
%---------------------------------------------------------------------
function image_dimension(fid, dime)
% Original header structures
% struct image_dimension
% { /* off + size */
% short int dim[8]; /* 0 + 16 */
% float intent_p1; % char vox_units[4]; /* 16 + 4 */
% float intent_p2; % char cal_units[8]; /* 20 + 4 */
% float intent_p3; % char cal_units[8]; /* 24 + 4 */
% short int intent_code; % short int unused1; /* 28 + 2 */
% short int datatype; /* 30 + 2 */
% short int bitpix; /* 32 + 2 */
% short int slice_start; % short int dim_un0; /* 34 + 2 */
% float pixdim[8]; /* 36 + 32 */
% /*
% pixdim[] specifies the voxel dimensions:
% pixdim[1] - voxel width
% pixdim[2] - voxel height
% pixdim[3] - interslice distance
% pixdim[4] - volume timing, in msec
% ..etc
% */
% float vox_offset; /* 68 + 4 */
% float scl_slope; % float roi_scale; /* 72 + 4 */
% float scl_inter; % float funused1; /* 76 + 4 */
% short slice_end; % float funused2; /* 80 + 2 */
% char slice_code; % float funused2; /* 82 + 1 */
% char xyzt_units; % float funused2; /* 83 + 1 */
% float cal_max; /* 84 + 4 */
% float cal_min; /* 88 + 4 */
% float slice_duration; % int compressed; /* 92 + 4 */
% float toffset; % int verified; /* 96 + 4 */
% int glmax; /* 100 + 4 */
% int glmin; /* 104 + 4 */
% }; /* total=108 bytes */
fwrite(fid, dime.dim(1:8), 'int16');
fwrite(fid, dime.intent_p1(1), 'float32');
fwrite(fid, dime.intent_p2(1), 'float32');
fwrite(fid, dime.intent_p3(1), 'float32');
fwrite(fid, dime.intent_code(1), 'int16');
fwrite(fid, dime.datatype(1), 'int16');
fwrite(fid, dime.bitpix(1), 'int16');
fwrite(fid, dime.slice_start(1), 'int16');
fwrite(fid, dime.pixdim(1:8), 'float32');
fwrite(fid, dime.vox_offset(1), 'float32');
fwrite(fid, dime.scl_slope(1), 'float32');
fwrite(fid, dime.scl_inter(1), 'float32');
fwrite(fid, dime.slice_end(1), 'int16');
fwrite(fid, dime.slice_code(1), 'uchar');
fwrite(fid, dime.xyzt_units(1), 'uchar');
fwrite(fid, dime.cal_max(1), 'float32');
fwrite(fid, dime.cal_min(1), 'float32');
fwrite(fid, dime.slice_duration(1), 'float32');
fwrite(fid, dime.toffset(1), 'float32');
fwrite(fid, dime.glmax(1), 'int32');
fwrite(fid, dime.glmin(1), 'int32');
return; % image_dimension
%---------------------------------------------------------------------
function data_history(fid, hist)
% Original header structures
%struct data_history
% { /* off + size */
% char descrip[80]; /* 0 + 80 */
% char aux_file[24]; /* 80 + 24 */
% short int qform_code; /* 104 + 2 */
% short int sform_code; /* 106 + 2 */
% float quatern_b; /* 108 + 4 */
% float quatern_c; /* 112 + 4 */
% float quatern_d; /* 116 + 4 */
% float qoffset_x; /* 120 + 4 */
% float qoffset_y; /* 124 + 4 */
% float qoffset_z; /* 128 + 4 */
% float srow_x[4]; /* 132 + 16 */
% float srow_y[4]; /* 148 + 16 */
% float srow_z[4]; /* 164 + 16 */
% char intent_name[16]; /* 180 + 16 */
% char magic[4]; % int smin; /* 196 + 4 */
% }; /* total=200 bytes */
% descrip = sprintf('%-80s', hist.descrip); % 80 chars from left
% fwrite(fid, descrip(1:80), 'uchar');
pad = zeros(1, 80-length(hist.descrip));
hist.descrip = [hist.descrip char(pad)];
fwrite(fid, hist.descrip(1:80), 'uchar');
% aux_file = sprintf('%-24s', hist.aux_file); % 24 chars from left
% fwrite(fid, aux_file(1:24), 'uchar');
pad = zeros(1, 24-length(hist.aux_file));
hist.aux_file = [hist.aux_file char(pad)];
fwrite(fid, hist.aux_file(1:24), 'uchar');
fwrite(fid, hist.qform_code, 'int16');
fwrite(fid, hist.sform_code, 'int16');
fwrite(fid, hist.quatern_b, 'float32');
fwrite(fid, hist.quatern_c, 'float32');
fwrite(fid, hist.quatern_d, 'float32');
fwrite(fid, hist.qoffset_x, 'float32');
fwrite(fid, hist.qoffset_y, 'float32');
fwrite(fid, hist.qoffset_z, 'float32');
fwrite(fid, hist.srow_x(1:4), 'float32');
fwrite(fid, hist.srow_y(1:4), 'float32');
fwrite(fid, hist.srow_z(1:4), 'float32');
% intent_name = sprintf('%-16s', hist.intent_name); % 16 chars from left
% fwrite(fid, intent_name(1:16), 'uchar');
pad = zeros(1, 16-length(hist.intent_name));
hist.intent_name = [hist.intent_name char(pad)];
fwrite(fid, hist.intent_name(1:16), 'uchar');
% magic = sprintf('%-4s', hist.magic); % 4 chars from left
% fwrite(fid, magic(1:4), 'uchar');
pad = zeros(1, 4-length(hist.magic));
hist.magic = [hist.magic char(pad)];
fwrite(fid, hist.magic(1:4), 'uchar');
return; % data_history
|
github
|
adhusch/PaCER-master
|
cylinder2P.m
|
.m
|
PaCER-master/external/cylinder2P/cylinder2P.m
| 2,223 |
utf_8
|
ac7fd8dba2e4a89a99014e478c5886dc
|
% CYLINDER: A function to draw a N-sided cylinder based on the
% generator curve in the vector R.
%
% Usage: [X, Y, Z] = cylinder(R, N)
%
% Arguments: R - The vector of radii used to define the radius of
% the different segments of the cylinder.
% N - The number of points around the circumference.
%
% Returns: X - The x-coordinates of each facet in the cylinder.
% Y - The y-coordinates of each facet in the cylinder.
% Z - The z-coordinates of each facet in the cylinder.
%
% Author: Luigi Barone
% Date: 9 September 2001
% Modified: Per Sundqvist July 2004
function [X, Y, Z] = cylinder2P(R, N,r1,r2)
% The parametric surface will consist of a series of N-sided
% polygons with successive radii given by the array R.
% Z increases in equal sized steps from 0 to 1.
% Set up an array of angles for the polygon.
theta = linspace(0,2*pi,N);
m = length(R); % Number of radius values
% supplied.
if m == 1 % Only one radius value supplied.
R = [R; R]; % Add a duplicate radius to make
m = 2; % a cylinder.
end
X = zeros(m, N); % Preallocate memory.
Y = zeros(m, N);
Z = zeros(m, N);
v=(r2-r1)/sqrt((r2-r1)*(r2-r1)'); %Normalized vector;
%cylinder axis described by: r(t)=r1+v*t for 0<t<1
R2=rand(1,3); %linear independent vector (of v)
x2=v-R2/(R2*v'); %orthogonal vector to v
x2=x2/sqrt(x2*x2'); %orthonormal vector to v
x3=cross(v,x2); %vector orthonormal to v and x2
x3=x3/sqrt(x3*x3');
r1x=r1(1);r1y=r1(2);r1z=r1(3);
r2x=r2(1);r2y=r2(2);r2z=r2(3);
vx=v(1);vy=v(2);vz=v(3);
x2x=x2(1);x2y=x2(2);x2z=x2(3);
x3x=x3(1);x3y=x3(2);x3z=x3(3);
time=linspace(0,1,m);
for j = 1 : m
t=time(j);
X(j, :) = r1x+(r2x-r1x)*t+R(j)*cos(theta)*x2x+R(j)*sin(theta)*x3x;
Y(j, :) = r1y+(r2y-r1y)*t+R(j)*cos(theta)*x2y+R(j)*sin(theta)*x3y;
Z(j, :) = r1z+(r2z-r1z)*t+R(j)*cos(theta)*x2z+R(j)*sin(theta)*x3z;
end
%surf(X, Y, Z);
|
github
|
adhusch/PaCER-master
|
tracking.m
|
.m
|
PaCER-master/external/GUI Layout Toolbox 2.3.1/layout/+uix/tracking.m
| 5,988 |
utf_8
|
fccbfb28138da702922a5a605bcb423c
|
function varargout = tracking( varargin )
%tracking Track anonymized usage data
%
% tracking(p,v,id) tracks usage to the property p for the product version
% v and identifier id. No personally identifiable information is tracked.
%
% r = tracking(...) returns the server response r, for debugging purposes.
%
% tracking('on') turns tracking on. tracking('off') turns tracking off.
% tracking('query') returns the tracking state.
% tracking('spoof') sets the tracking settings -- domain, language,
% client, MATLAB version, operating system version -- to spoof values.
% tracking('reset') sets the tracking settings to normal values.
%
% [t,s] = tracking('query') returns the tracking state t and settings s.
% Copyright 2016 The MathWorks, Inc.
% $Revision: 1435 $ $Date: 2016-11-17 17:50:34 +0000 (Thu, 17 Nov 2016) $
persistent STATE USERNAME DOMAIN LANGUAGE CLIENT MATLAB OS
if isempty( STATE )
STATE = getpref( 'Tracking', 'State', 'on' );
if strcmp( STATE, 'snooze' ) % deprecated
setpref( 'Tracking', 'State', 'on' )
STATE = 'on';
end
if ispref( 'Tracking', 'Date' ) % deprecated
rmpref( 'Tracking', 'Date' )
end
USERNAME = getenv( 'USERNAME' );
reset()
end % initialize
switch nargin
case 1
switch varargin{1}
case {'on','off'}
STATE = varargin{1};
setpref( 'Tracking', 'State', varargin{1} ) % persist
case 'spoof'
spoof()
case 'reset'
reset()
case 'query'
varargout{1} = STATE;
varargout{2} = query();
otherwise
error( 'tracking:InvalidArgument', ...
'Valid options are ''on'', ''off'' and ''query''.' )
end
case 3
switch nargout
case 0
if strcmp( STATE, 'off' ), return, end
uri = 'https://www.google-analytics.com/collect';
track( uri, varargin{:} );
case 1
uri = 'https://www.google-analytics.com/debug/collect';
varargout{1} = track( uri, varargin{:} );
otherwise
nargoutchk( 0, 1 )
end
otherwise
narginchk( 3, 3 )
end % switch
function reset()
%reset Set normal settings
DOMAIN = lower( getenv( 'USERDOMAIN' ) );
LANGUAGE = char( java.util.Locale.getDefault() );
CLIENT = getpref( 'Tracking', 'Client', uuid() );
MATLAB = matlab();
OS = os();
end % reset
function spoof()
%spoof Set spoof settings
DOMAIN = randomDomain();
LANGUAGE = randomLanguage();
CLIENT = randomClient();
MATLAB = randomMatlab();
OS = randomOs();
end % spoof
function s = query()
%query Return settings
s.Username = USERNAME;
s.Domain = DOMAIN;
s.Language = LANGUAGE;
s.Client = CLIENT;
s.Matlab = MATLAB;
s.Os = OS;
end % query
function varargout = track( uri, p, v, s )
%track Do tracking
a = sprintf( '%s/%s (%s)', MATLAB, v, OS );
if isdeployed()
ds = 'deployed';
elseif strcmp( DOMAIN, 'mathworks' )
ds = DOMAIN;
else
ds = 'unknown';
end
pv = {'v', '1', 'tid', p, 'ua', escape( a ), 'ul', LANGUAGE, ...
'cid', CLIENT, 'ht', 'pageview', ...
'dp', sprintf( '/%s', s ), 'ds', ds};
[varargout{1:nargout}] = urlread( uri, 'Post', pv );
end % track
end % tracking
function s = randomDomain()
%randomDomain Random domain string
switch randi( 4 )
case 1
s = 'mathworks';
otherwise
s = hash( uuid() );
end
end % randomDomain
function s = randomLanguage()
%randomLanguage Random language string
lo = java.util.Locale.getAvailableLocales();
s = char( lo(randi( numel( lo ) )) );
end % randomLanguage
function s = randomClient()
%randomClient Random client identifier
s = uuid();
end % randomClient
function s = matlab()
%matlab MATLAB version string
v = ver( 'MATLAB' );
s = v.Release;
s(s=='('|s==')') = [];
end % matlab
function s = randomMatlab()
%randomMatlab Random MATLAB version string
releases = {'R2014b' 'R2015a' 'R2015b' 'R2016a' 'R2016b'};
s = releases{randi( numel( releases ) )};
end % randomMatlab
function s = os()
%os Operating system string
if ispc()
s = sprintf( 'Windows NT %s', ...
char( java.lang.System.getProperty( 'os.version' ) ) );
elseif isunix()
s = 'Linux x86_64';
elseif ismac()
s = sprintf( 'Macintosh; Intel OS X %s', ...
strrep( char( java.lang.System.getProperty( 'os.version' ) ), ' ', '_' ) );
else
s = 'unknown';
end
end % os
function s = randomOs()
%randomOs Random operating system string
switch randi( 3 )
case 1
versions = [5.1 5.2 6 6.1 6.2 6.3 10];
s = sprintf( 'Windows NT %.1f', ...
versions(randi( numel( versions ) )) );
case 2
s = 'Linux x86_64';
case 3
s = sprintf( 'Macintosh; Intel OS X 10_%d', ...
randi( [10 12] ) );
end
end % randomOs
function s = escape( s )
%escape Escape string
s = char( java.net.URLEncoder.encode( s, 'UTF-8' ) );
end % escape
function h = hash( s )
%hash Hash string
%
% See also: rptgen.hash
persistent MD5
if isempty( MD5 )
MD5 = java.security.MessageDigest.getInstance( 'MD5' );
end
MD5.update( uint8( s(:) ) );
h = typecast( MD5.digest, 'uint8' );
h = dec2hex( h )';
h = lower( h(:) )';
end % hash
function s = uuid()
%uuid Unique identifier
s = char( java.util.UUID.randomUUID() );
end % uuid
|
github
|
adhusch/PaCER-master
|
Text.m
|
.m
|
PaCER-master/external/GUI Layout Toolbox 2.3.1/layout/+uix/Text.m
| 15,451 |
utf_8
|
8acacfb7d4da6e4b084f28ff1ebc6855
|
classdef Text < matlab.mixin.SetGet
%uix.Text Text control
%
% t = uix.Text(p1,v1,p2,v2,...) constructs a text control and sets
% parameter p1 to value v1, etc.
%
% A text control adds functionality to a uicontrol of Style text:
% * Set VerticalAlignment to 'top', 'middle' or 'bottom'
% * Fire a Callback when the user clicks on the text
%
% See also: uicontrol
% Copyright 2009-2015 The MathWorks, Inc.
% $Revision: 1435 $ $Date: 2016-11-17 17:50:34 +0000 (Thu, 17 Nov 2016) $
properties( Dependent )
BackgroundColor
end
properties( Dependent, SetAccess = private )
BeingDeleted
end
properties( Dependent )
Callback
DeleteFcn
Enable
end
properties( Dependent, SetAccess = private )
Extent
end
properties( Dependent )
FontAngle
FontName
FontSize
FontUnits
FontWeight
ForegroundColor
HandleVisibility
HorizontalAlignment
Parent
Position
String
Tag
TooltipString
end
properties( Dependent, SetAccess = private )
Type
end
properties( Dependent )
UIContextMenu
Units
UserData
VerticalAlignment
Visible
end
properties( Access = private )
Container % container
Checkbox % checkbox, used for label
Screen % text, used for covering checkbox
VerticalAlignment_ = 'top' % backing for VerticalAlignment
Dirty = false % flag
FigureObserver % observer
FigureListener % listener
end
properties( Constant, Access = private )
Margin = checkBoxLabelOffset() % checkbox size
end
methods
function obj = Text( varargin )
%uix.Text Text control
%
% t = uix.Text(p1,v1,p2,v2,...) constructs a text control and
% sets parameter p1 to value v1, etc.
% Create graphics
container = uicontainer( 'Parent', [], ...
'Units', get( 0, 'DefaultUicontrolUnits' ), ...
'Position', get( 0, 'DefaultUicontrolPosition' ), ...
'SizeChangedFcn', @obj.onResized );
checkbox = uicontrol( 'Parent', container, ...
'HandleVisibility', 'off', ...
'Style', 'checkbox', 'Units', 'pixels', ...
'HorizontalAlignment', 'center', ...
'Enable', 'inactive' );
screen = uicontrol( 'Parent', container, ...
'HandleVisibility', 'off', ...
'Style', 'text', 'Units', 'pixels' );
% Create observers and listeners
figureObserver = uix.FigureObserver( container );
figureListener = event.listener( figureObserver, ...
'FigureChanged', @obj.onFigureChanged );
% Store properties
obj.Container = container;
obj.Checkbox = checkbox;
obj.Screen = screen;
obj.FigureObserver = figureObserver;
obj.FigureListener = figureListener;
% Set properties
if nargin > 0
try
assert( rem( nargin, 2 ) == 0, 'uix:InvalidArgument', ...
'Parameters and values must be provided in pairs.' )
set( obj, varargin{:} )
catch e
delete( obj )
e.throwAsCaller()
end
end
end % constructor
function delete( obj )
%delete Destructor
delete( obj.Container )
end % destructor
end % structors
methods
function value = get.BackgroundColor( obj )
value = obj.Checkbox.BackgroundColor;
end % get.BackgroundColor
function set.BackgroundColor( obj, value )
obj.Container.BackgroundColor = value;
obj.Checkbox.BackgroundColor = value;
obj.Screen.BackgroundColor = value;
end % set.BackgroundColor
function value = get.BeingDeleted( obj )
value = obj.Checkbox.BeingDeleted;
end % get.BeingDeleted
function value = get.Callback( obj )
value = obj.Checkbox.Callback;
end % get.Callback
function set.Callback( obj, value )
obj.Checkbox.Callback = value;
end % set.Callback
function value = get.DeleteFcn( obj )
value = obj.Checkbox.DeleteFcn;
end % get.DeleteFcn
function set.DeleteFcn( obj, value )
obj.Checkbox.DeleteFcn = value;
end % set.DeleteFcn
function value = get.Enable( obj )
value = obj.Checkbox.Enable;
end % get.Enable
function set.Enable( obj, value )
obj.Checkbox.Enable = value;
end % set.Enable
function value = get.Extent( obj )
value = obj.Checkbox.Extent;
end % get.Extent
function value = get.FontAngle( obj )
value = obj.Checkbox.FontAngle;
end % get.FontAngle
function set.FontAngle( obj, value )
% Set
obj.Checkbox.FontAngle = value;
% Mark as dirty
obj.setDirty()
end % set.FontAngle
function value = get.FontName( obj )
value = obj.Checkbox.FontName;
end % get.FontName
function set.FontName( obj, value )
% Set
obj.Checkbox.FontName = value;
% Mark as dirty
obj.setDirty()
end % set.FontName
function value = get.FontSize( obj )
value = obj.Checkbox.FontSize;
end % get.FontSize
function set.FontSize( obj, value )
% Set
obj.Checkbox.FontSize = value;
% Mark as dirty
obj.setDirty()
end % set.FontSize
function value = get.FontUnits( obj )
value = obj.Checkbox.FontUnits;
end % get.FontUnits
function set.FontUnits( obj, value )
obj.Checkbox.FontUnits = value;
end % set.FontUnits
function value = get.FontWeight( obj )
value = obj.Checkbox.FontWeight;
end % get.FontWeight
function set.FontWeight( obj, value )
% Set
obj.Checkbox.FontWeight = value;
% Mark as dirty
obj.setDirty()
end % set.FontWeight
function value = get.ForegroundColor( obj )
value = obj.Checkbox.ForegroundColor;
end % get.ForegroundColor
function set.ForegroundColor( obj, value )
obj.Checkbox.ForegroundColor = value;
end % set.ForegroundColor
function value = get.HandleVisibility( obj )
value = obj.Container.HandleVisibility;
end % get.HandleVisibility
function set.HandleVisibility( obj, value )
obj.Container.HandleVisibility = value;
end % set.HandleVisibility
function value = get.HorizontalAlignment( obj )
value = obj.Checkbox.HorizontalAlignment;
end % get.HorizontalAlignment
function set.HorizontalAlignment( obj, value )
% Set
obj.Checkbox.HorizontalAlignment = value;
% Mark as dirty
obj.setDirty()
end % set.HorizontalAlignment
function value = get.Parent( obj )
value = obj.Container.Parent;
end % get.Parent
function set.Parent( obj, value )
obj.Container.Parent = value;
end % set.Parent
function value = get.Position( obj )
value = obj.Container.Position;
end % get.Position
function set.Position( obj, value )
obj.Container.Position = value;
end % set.Position
function value = get.String( obj )
value = obj.Checkbox.String;
end % get.String
function set.String( obj, value )
% Set
obj.Checkbox.String = value;
% Mark as dirty
obj.setDirty()
end % set.String
function value = get.Tag( obj )
value = obj.Checkbox.Tag;
end % get.Tag
function set.Tag( obj, value )
obj.Checkbox.Tag = value;
end % set.Tag
function value = get.TooltipString( obj )
value = obj.Checkbox.TooltipString;
end % get.TooltipString
function set.TooltipString( obj, value )
obj.Checkbox.TooltipString = value;
end % set.TooltipString
function value = get.Type( obj )
value = obj.Checkbox.Type;
end % get.Type
function value = get.UIContextMenu( obj )
value = obj.Checkbox.UIContextMenu;
end % get.UIContextMenu
function set.UIContextMenu( obj, value )
obj.Checkbox.UIContextMenu = value;
end % set.UIContextMenu
function value = get.Units( obj )
value = obj.Container.Units;
end % get.Units
function set.Units( obj, value )
obj.Container.Units = value;
end % set.Units
function value = get.UserData( obj )
value = obj.Checkbox.UserData;
end % get.UserData
function set.UserData( obj, value )
obj.Checkbox.UserData = value;
end % set.UserData
function value = get.VerticalAlignment( obj )
value = obj.VerticalAlignment_;
end % get.VerticalAlignment
function set.VerticalAlignment( obj, value )
% Check
assert( ischar( value ) && ...
any( strcmp( value, {'top','middle','bottom'} ) ), ...
'uix:InvalidPropertyValue', ...
'Property ''VerticalAlignment'' must be ''top'', ''middle'' or ''bottom''.' )
% Set
obj.VerticalAlignment_ = value;
% Mark as dirty
obj.setDirty()
end % set.VerticalAlignment
function value = get.Visible( obj )
value = obj.Container.Visible;
end % get.Visible
function set.Visible( obj, value )
obj.Container.Visible = value;
end % set.Visible
end % accessors
methods( Access = private )
function onResized( obj, ~, ~ )
%onResized Event handler
% Rooted, so redraw
obj.redraw()
end % onResized
function onFigureChanged( obj, ~, eventData )
% If rooted, redraw
if isempty( eventData.OldFigure ) && ...
~isempty( eventData.NewFigure ) && obj.Dirty
obj.redraw()
end
end % onFigureChanged
end % event handlers
methods( Access = private )
function setDirty( obj )
%setDirty Mark as dirty
%
% t.setDirty() marks the text control t as dirty. If the text
% control is rooted then it is redrawn immediately. If not
% then the redraw is queued for when it is next rooted.
if isempty( obj.FigureObserver.Figure )
obj.Dirty = true; % set flag
else
obj.Dirty = false; % unset flag
obj.redraw() % redraw
end
end % setDirty
function redraw( obj )
%redraw Redraw
%
% t.redraw() redraws the text control t. Note that this
% requires the text control to be rooted. Methods should
% request redraws using setDirty, rather than calling redraw
% directly.
c = obj.Container;
b = obj.Checkbox;
s = obj.Screen;
bo = hgconvertunits( ancestor( obj, 'figure' ), ...
[0 0 1 1], 'normalized', 'pixels', c ); % bounds
m = obj.Margin;
e = b.Extent;
switch b.HorizontalAlignment
case 'left'
x = 1 - m;
case 'center'
x = 1 + bo(3)/2 - e(3)/2 - m;
case 'right'
x = 1 + bo(3) - e(3) - m;
end
w = e(3) + m;
switch obj.VerticalAlignment_
case 'top'
y = 1 + bo(4) - e(4);
case 'middle'
y = 1 + bo(4)/2 - e(4)/2;
case 'bottom'
y = 1;
end
h = e(4);
b.Position = [x y w h];
s.Position = [x y m h];
end % redraw
end % helpers
end % classdef
function o = checkBoxLabelOffset()
%checkBoxLabelOffset Horizontal offset to checkbox label
if verLessThan( 'MATLAB', '8.6' ) % R2015b
o = 18;
else
o = 16;
end
end % margin
|
github
|
adhusch/PaCER-master
|
loadIcon.m
|
.m
|
PaCER-master/external/GUI Layout Toolbox 2.3.1/layout/+uix/loadIcon.m
| 3,228 |
utf_8
|
15fc42b7b92439d8ef2b48cac7828dbd
|
function cdata = loadIcon( filename, bgcol )
%loadIcon Load an icon and set the transparent color
%
% cdata = uix.loadIcon(filename) loads the icon from the specified
% filename. For PNG files with transparency, the transparent pixels are
% set to NaN. For other files, pixels that are pure green are set to
% transparent (i.e., "green screen"). The resulting cdata is an RGB
% double array.
%
% cdata = uix.loadIcon(filename,bgcol) tries to merge the color data with
% the specified background colour bgcol. Fully transparent pixels are
% still set to NaN, but partially transparent pixels are merged with the
% background.
%
% See also: imread
% Copyright 2009-2016 The MathWorks, Inc.
% $Revision: 1436 $ $Date: 2016-11-17 17:53:29 +0000 (Thu, 17 Nov 2016) $
% Check inputs
narginchk( 1, 2 )
if nargin < 2
bgcol = get( 0, 'DefaultUIControlBackgroundColor' );
end
% First try normally
thisDir = fileparts( mfilename( 'fullpath' ) );
iconDir = fullfile( thisDir, 'Resources' );
if exist( filename, 'file' )
[cdata, map, alpha] = imread( filename );
elseif exist( fullfile( iconDir, filename ), 'file' )
[cdata, map, alpha] = imread( fullfile( iconDir, filename ) );
else
error( 'uix:FileNotFound', 'Cannot open file ''%s''.', filename )
end
% Convert indexed images to RGB
if ~isempty( map )
cdata = ind2rgb( cdata, map );
end
% Convert to double before applying transparency
cdata = convertToDouble( cdata );
% Handle transparency
[rows, cols, ~] = size( cdata );
if ~isempty( alpha )
% Transparency specified
alpha = convertToDouble( alpha );
f = find( alpha==0 );
if ~isempty( f )
cdata(f) = NaN;
cdata(f + rows*cols) = NaN;
cdata(f + 2*rows*cols) = NaN;
end
% Now blend partial alphas
f = find( alpha(:)>0 & alpha(:)<1 );
if ~isempty(f)
cdata(f) = cdata(f).*alpha(f) + bgcol(1)*(1-alpha(f));
cdata(f + rows*cols) = cdata(f + rows*cols).*alpha(f) + bgcol(2)*(1-alpha(f));
cdata(f + 2*rows*cols) = cdata(f + 2*rows*cols).*alpha(f) + bgcol(3)*(1-alpha(f));
end
else
% Do a "green screen", treating anything pure-green as transparent
f = find( cdata(:,:,1)==0 & cdata(:,:,2)==1 & cdata(:,:,3)==0 );
cdata(f) = NaN;
cdata(f + rows*cols) = NaN;
cdata(f + 2*rows*cols) = NaN;
end
end % uix.loadIcon
% -------------------------------------------------------------------------
function cdata = convertToDouble( cdata )
%convertToDouble Convert image data to double in the range [0,1]
%
% cdata = convertToDouble(cData)
switch lower( class( cdata ) )
case 'double'
% do nothing
case 'single'
cdata = double( cdata );
case 'uint8'
cdata = double( cdata ) / 255;
case 'uint16'
cdata = double( cdata ) / 65535;
case 'int8'
cdata = ( double( cdata ) + 128 ) / 255;
case 'int16'
cdata = ( double( cdata ) + 32768 ) / 65535;
otherwise
error( 'uix:InvalidArgument', ...
'Image data of type ''%s'' is not supported.', class( cdata ) )
end
end % convertToDouble
|
github
|
adhusch/PaCER-master
|
ChildObserver.m
|
.m
|
PaCER-master/external/GUI Layout Toolbox 2.3.1/layout/+uix/ChildObserver.m
| 9,050 |
utf_8
|
ca853750869b05d4214ddf3474a93712
|
classdef ( Hidden, Sealed ) ChildObserver < handle
%uix.ChildObserver Child observer
%
% co = uix.ChildObserver(o) creates a child observer for the graphics
% object o. A child observer raises events when objects are added to
% and removed from the property Children of o.
%
% See also: uix.Node
% Copyright 2009-2016 The MathWorks, Inc.
% $Revision: 1436 $ $Date: 2016-11-17 17:53:29 +0000 (Thu, 17 Nov 2016) $
properties( Access = private )
Root % root node
end
events( NotifyAccess = private )
ChildAdded % child added
ChildRemoved % child removed
end
methods
function obj = ChildObserver( oRoot )
%uix.ChildObserver Child observer
%
% co = uix.ChildObserver(o) creates a child observer for the
% graphics object o. A child observer raises events when
% objects are added to and removed from the property Children
% of o.
% Check
assert( iscontent( oRoot ) && ...
isequal( size( oRoot ), [1 1] ), 'uix.InvalidArgument', ...
'Object must be a graphics object.' )
% Create root node
nRoot = uix.Node( oRoot );
childAddedListener = event.listener( oRoot, ...
'ObjectChildAdded', ...
@(~,e)obj.addChild(nRoot,e.Child) );
childAddedListener.Recursive = true;
nRoot.addprop( 'ChildAddedListener' );
nRoot.ChildAddedListener = childAddedListener;
childRemovedListener = event.listener( oRoot, ...
'ObjectChildRemoved', ...
@(~,e)obj.removeChild(nRoot,e.Child) );
childRemovedListener.Recursive = true;
nRoot.addprop( 'ChildRemovedListener' );
nRoot.ChildRemovedListener = childRemovedListener;
% Add children
oChildren = hgGetTrueChildren( oRoot );
for ii = 1:numel( oChildren )
obj.addChild( nRoot, oChildren(ii) )
end
% Store properties
obj.Root = nRoot;
end % constructor
end % structors
methods( Access = private )
function addChild( obj, nParent, oChild )
%addChild Add child object to parent node
%
% co.addChild(np,oc) adds the child object oc to the parent
% node np, either as part of construction of the child
% observer co, or in response to an ObjectChildAdded event on
% an object of interest to co. This may lead to ChildAdded
% events being raised on co.
% Create child node
nChild = uix.Node( oChild );
nParent.addChild( nChild )
if iscontent( oChild )
% Add Internal PreSet property listener
internalPreSetListener = event.proplistener( oChild, ...
findprop( oChild, 'Internal' ), 'PreSet', ...
@(~,~)obj.preSetInternal(nChild) );
nChild.addprop( 'InternalPreSetListener' );
nChild.InternalPreSetListener = internalPreSetListener;
% Add Internal PostSet property listener
internalPostSetListener = event.proplistener( oChild, ...
findprop( oChild, 'Internal' ), 'PostSet', ...
@(~,~)obj.postSetInternal(nChild) );
nChild.addprop( 'InternalPostSetListener' );
nChild.InternalPostSetListener = internalPostSetListener;
else
% Add ObjectChildAdded listener
childAddedListener = event.listener( oChild, ...
'ObjectChildAdded', ...
@(~,e)obj.addChild(nChild,e.Child) );
nChild.addprop( 'ChildAddedListener' );
nChild.ChildAddedListener = childAddedListener;
% Add ObjectChildRemoved listener
childRemovedListener = event.listener( oChild, ...
'ObjectChildRemoved', ...
@(~,e)obj.removeChild(nChild,e.Child) );
nChild.addprop( 'ChildRemovedListener' );
nChild.ChildRemovedListener = childRemovedListener;
end
% Raise ChildAdded event
if iscontent( oChild ) && oChild.Internal == false
notify( obj, 'ChildAdded', uix.ChildEvent( oChild ) )
end
% Add grandchildren
if ~iscontent( oChild )
oGrandchildren = hgGetTrueChildren( oChild );
for ii = 1:numel( oGrandchildren )
obj.addChild( nChild, oGrandchildren(ii) )
end
end
end % addChild
function removeChild( obj, nParent, oChild )
%removeChild Remove child object from parent node
%
% co.removeChild(np,oc) removes the child object oc from the
% parent node np, in response to an ObjectChildRemoved event
% on an object of interest to co. This may lead to
% ChildRemoved events being raised on co.
% Get child node
nChildren = nParent.Children;
tf = oChild == [nChildren.Object];
nChild = nChildren(tf);
% Raise ChildRemoved event(s)
notifyChildRemoved( nChild )
% Delete child node
delete( nChild )
function notifyChildRemoved( nc )
% Process child nodes
ngc = nc.Children;
for ii = 1:numel( ngc )
notifyChildRemoved( ngc(ii) )
end
% Process this node
oc = nc.Object;
if iscontent( oc ) && oc.Internal == false
notify( obj, 'ChildRemoved', uix.ChildEvent( oc ) )
end
end % notifyChildRemoved
end % removeChild
function preSetInternal( ~, nChild )
%preSetInternal Perform property PreSet tasks
%
% co.preSetInternal(n) caches the previous value of the
% property Internal of the object referenced by the node n, to
% enable PostSet tasks to identify whether the value changed.
% This is necessary since Internal AbortSet is false.
oldInternal = nChild.Object.Internal;
nChild.addprop( 'OldInternal' );
nChild.OldInternal = oldInternal;
end % preSetInternal
function postSetInternal( obj, nChild )
%postSetInternal Perform property PostSet tasks
%
% co.postSetInternal(n) raises a ChildAdded or ChildRemoved
% event on the child observer co in response to a change of
% the value of the property Internal of the object referenced
% by the node n.
% Retrieve old and new values
oChild = nChild.Object;
newInternal = oChild.Internal;
oldInternal = nChild.OldInternal;
% Clean up node
delete( findprop( nChild, 'OldInternal' ) )
% Raise event
switch newInternal
case oldInternal % no change
% no event
case true % false to true
notify( obj, 'ChildRemoved', uix.ChildEvent( oChild ) )
case false % true to false
notify( obj, 'ChildAdded', uix.ChildEvent( oChild ) )
end
end % postSetInternal
end % event handlers
end % classdef
function tf = iscontent( o )
%iscontent True for graphics that can be Contents (and can be Children)
%
% uix.ChildObserver needs to determine which objects can be Contents,
% which is equivalent to can be Children if HandleVisibility is 'on' and
% Internal is false. Prior to R2016a, this condition could be checked
% using isgraphics. From R2016a, isgraphics returns true for a wider
% range of objects, including some that can never by Contents, e.g.,
% JavaCanvas. Therefore this function checks whether an object is of type
% matlab.graphics.internal.GraphicsBaseFunctions, which is what isgraphics
% did prior to R2016a.
tf = isa( o, 'matlab.graphics.internal.GraphicsBaseFunctions' ) &&...
isprop( o, 'Position' );
end % iscontent
|
github
|
adhusch/PaCER-master
|
Empty.m
|
.m
|
PaCER-master/external/GUI Layout Toolbox 2.3.1/layout/+uix/Empty.m
| 2,730 |
utf_8
|
8370636fc1b842d73a35d3f44fb23483
|
function obj = Empty( varargin )
%uix.Empty Create an empty space
%
% obj = uix.Empty() creates an empty space that can be used to add gaps
% between elements in layouts.
%
% obj = uix.Empty(param,value,...) also sets one or more property
% values.
%
% See the <a href="matlab:doc uix.Empty">documentation</a> for more detail and the list of properties.
%
% Examples:
% >> f = figure();
% >> box = uix.HBox( 'Parent', f );
% >> uicontrol( 'Parent', box, 'Background', 'r' )
% >> uix.Empty( 'Parent', box )
% >> uicontrol( 'Parent', box, 'Background', 'b' )
% Copyright 2009-2016 The MathWorks, Inc.
% $Revision: 1436 $ $Date: 2016-11-17 17:53:29 +0000 (Thu, 17 Nov 2016) $
% Create uicontainer
obj = matlab.ui.container.internal.UIContainer( 'Tag', 'empty', varargin{:} );
% Create property for Parent listener
p = addprop( obj, 'ParentListener' );
p.Hidden = true;
% Create Parent listener
obj.ParentListener = event.proplistener( obj, ...
findprop( obj, 'Parent' ), 'PostSet', @(~,~)onParentChanged(obj) );
% Create property for Parent color listener
p = addprop( obj, 'ParentColorListener' );
p.Hidden = true;
% Initialize color and listener
updateColor( obj )
updateListener( obj )
end % uix.Empty
function onParentChanged( obj )
%onParentColorChanged Event handler
% Update color and listener
updateColor( obj )
updateListener( obj )
end % onParentChanged
function onParentColorChanged( obj )
%onParentColorChanged Event handler
% Update color
updateColor( obj )
end % onParentColorChanged
function name = getColorProperty( obj )
%getColorProperty Get color property
names = {'Color','BackgroundColor'}; % possible names
for ii = 1:numel( names ) % loop over possible names
name = names{ii};
if isprop( obj, name )
return
end
end
error( 'Cannot find color property for %s.', class( obj ) )
end % getColorProperty
function updateColor( obj )
%updateColor Set uicontainer BackgroundColor to match Parent
parent = obj.Parent;
if isempty( parent ), return, end
property = getColorProperty( parent );
color = parent.( property );
try
obj.BackgroundColor = color;
catch e
warning( e.identifier, e.message ) % rethrow as warning
end
end % updateColor
function updateListener( obj )
%updateListener Create listener to parent color property
parent = obj.Parent;
if isempty( parent )
obj.ParentColorListener = [];
else
property = getColorProperty( parent );
obj.ParentColorListener = event.proplistener( parent, ...
findprop( parent, property ), 'PostSet', ...
@(~,~)onParentColorChanged(obj) );
end
end % updateListener
|
github
|
adhusch/PaCER-master
|
guideApp.m
|
.m
|
PaCER-master/external/GUI Layout Toolbox 2.3.1/layoutdoc/Examples/guideApp.m
| 4,073 |
utf_8
|
f1e03beaed00662522eda571d8c8f409
|
function varargout = guideApp(varargin)
% GUIDEAPP MATLAB code for guideApp.fig
% GUIDEAPP, by itself, creates a new GUIDEAPP or raises the existing
% singleton*.
%
% H = GUIDEAPP returns the handle to a new GUIDEAPP or the handle to
% the existing singleton*.
%
% GUIDEAPP('CALLBACK',hObject,eventData,handles,...) calls the local
% function named CALLBACK in GUIDEAPP.M with the given input arguments.
%
% GUIDEAPP('Property','Value',...) creates a new GUIDEAPP or raises the
% existing singleton*. Starting from the left, property value pairs are
% applied to the GUI before guideApp_OpeningFcn gets called. An
% unrecognized property name or invalid value makes property application
% stop. All inputs are passed to guideApp_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
% Copyright 2009-2013 The MathWorks Ltd.
% Edit the above text to modify the response to help guideApp
% Last Modified by GUIDE v2.5 21-Jul-2010 07:36:25
% Begin initialization code - DO NOT EDIT
gui_Singleton = 1;
gui_State = struct('gui_Name', mfilename, ...
'gui_Singleton', gui_Singleton, ...
'gui_OpeningFcn', @guideApp_OpeningFcn, ...
'gui_OutputFcn', @guideApp_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 guideApp is made visible.
function guideApp_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 guideApp (see VARARGIN)
% Choose default command line output for guideApp
handles.output = hObject;
% Update handles structure
guidata(hObject, handles);
% Put a layout in the panel
g = uix.GridFlex( 'Parent', handles.uipanel1, ...
'Units', 'Normalized', 'Position', [0 0 1 1], ...
'Spacing', 5 );
uix.BoxPanel( 'Parent', g, 'Title', 'Panel 1' );
uix.BoxPanel( 'Parent', g, 'Title', 'Panel 2' );
uix.BoxPanel( 'Parent', g, 'Title', 'Panel 3' );
uix.BoxPanel( 'Parent', g, 'Title', 'Panel 4' );
g.Heights = [-1 -1];
% UIWAIT makes guideApp wait for user response (see UIRESUME)
% uiwait(handles.figure1);
% --- Outputs from this function are returned to the command line.
function varargout = guideApp_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 pushbutton1.
function pushbutton1_Callback(hObject, eventdata, handles)
% hObject handle to pushbutton1 (see GCBO)
% eventdata reserved - to be defined in a future version of MATLAB
% handles structure with handles and user data (see GUIDATA)
% --- Executes on button press in pushbutton2.
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)
% --- Executes on button press in pushbutton3.
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)
|
github
|
adhusch/PaCER-master
|
inpolyhedron.m
|
.m
|
PaCER-master/external/inpolyhedron/inpolyhedron.m
| 22,966 |
utf_8
|
8c8cced0d59898757b46be18e1459504
|
function IN = inpolyhedron(varargin)
%INPOLYHEDRON Tests if points are inside a 3D triangulated (faces/vertices) surface
%
% IN = INPOLYHEDRON(FV,QPTS) tests if the query points (QPTS) are inside
% the patch/surface/polyhedron defined by FV (a structure with fields
% 'vertices' and 'faces'). QPTS is an N-by-3 set of XYZ coordinates. IN
% is an N-by-1 logical vector which will be TRUE for each query point
% inside the surface. By convention, surface normals point OUT from the
% object (see FLIPNORMALS option below if to reverse this convention).
%
% INPOLYHEDRON(FACES,VERTICES,...) takes faces/vertices separately, rather than in
% an FV structure.
%
% IN = INPOLYHEDRON(..., X, Y, Z) voxelises a mask of 3D gridded query points
% rather than an N-by-3 array of points. X, Y, and Z coordinates of the grid
% supplied in XVEC, YVEC, and ZVEC respectively. IN will return as a 3D logical
% volume with SIZE(IN) = [LENGTH(YVEC) LENGTH(XVEC) LENGTH(ZVEC)], equivalent to
% syntax used by MESHGRID. INPOLYHEDRON handles this input faster and with a lower
% memory footprint than using MESHGRID to make full X, Y, Z query points matrices.
%
% INPOLYHEDRON(...,'PropertyName',VALUE,'PropertyName',VALUE,...) tests query
% points using the following optional property values:
%
% TOL - Tolerance on the tests for "inside" the surface. You can think of
% tol as the distance a point may possibly lie above/below the surface, and still
% be perceived as on the surface. Due to numerical rounding nothing can ever be
% done exactly here. Defaults to ZERO. Note that in the current implementation TOL
% only affects points lying above/below a surface triangle (in the Z-direction).
% Points coincident with a vertex in the XY plane are considered INside the surface.
% More formal rules can be implemented with input/feedback from users.
%
% GRIDSIZE - Internally, INPOLYHEDRON uses a divide-and-conquer algorithm to
% split all faces into a chessboard-like grid of GRIDSIZE-by-GRIDSIZE regions.
% Performance will be a tradeoff between a small GRIDSIZE (few iterations, more
% data per iteration) and a large GRIDSIZE (many iterations of small data
% calculations). The sweet-spot has been experimentally determined (on a win64
% system) to be correlated with the number of faces/vertices. You can overwrite
% this automatically computed choice by specifying a GRIDSIZE parameter.
%
% FACENORMALS - By default, the normals to the FACE triangles are computed as the
% cross-product of the first two triangle edges. You may optionally specify face
% normals here if they have been pre-computed.
%
% FLIPNORMALS - (Defaults FALSE). To match a wider convention, triangle
% face normals are presumed to point OUT from the object's surface. If
% your surface normals are defined pointing IN, then you should set the
% FLIPNORMALS option to TRUE to use the reverse of this convention.
%
% Example:
% tmpvol = zeros(20,20,20); % Empty voxel volume
% tmpvol(5:15,8:12,8:12) = 1; % Turn some voxels on
% tmpvol(8:12,5:15,8:12) = 1;
% tmpvol(8:12,8:12,5:15) = 1;
% fv = isosurface(tmpvol, 0.99); % Create the patch object
% fv.faces = fliplr(fv.faces); % Ensure normals point OUT
% % Test SCATTERED query points
% pts = rand(200,3)*12 + 4; % Make some query points
% in = inpolyhedron(fv, pts); % Test which are inside the patch
% figure, hold on, view(3) % Display the result
% patch(fv,'FaceColor','g','FaceAlpha',0.2)
% plot3(pts(in,1),pts(in,2),pts(in,3),'bo','MarkerFaceColor','b')
% plot3(pts(~in,1),pts(~in,2),pts(~in,3),'ro'), axis image
% % Test STRUCTURED GRID of query points
% gridLocs = 3:2.1:19;
% [x,y,z] = meshgrid(gridLocs,gridLocs,gridLocs);
% in = inpolyhedron(fv, gridLocs,gridLocs,gridLocs);
% figure, hold on, view(3) % Display the result
% patch(fv,'FaceColor','g','FaceAlpha',0.2)
% plot3(x(in), y(in), z(in),'bo','MarkerFaceColor','b')
% plot3(x(~in),y(~in),z(~in),'ro'), axis image
%
% See also: UNIFYMESHNORMALS (on the <a href="http://www.mathworks.com/matlabcentral/fileexchange/loadFile.do?objectId=43013">file exchange</a>)
% TODO-list
% - Optmise overall memory footprint. (need examples with MEM errors)
% - Implement an "ignore these" step to speed up calculations for:
% * Query points outside the convex hull of the faces/vertices input
% - Get a better/best gridSize calculation. User feedback?
% - Detect cases where X-rays or Y-rays would be better than Z-rays?
%
% Author: Sven Holcombe
% - 10 Jun 2012: Version 1.0
% - 28 Aug 2012: Version 1.1 - Speedup using accumarray
% - 07 Nov 2012: Version 2.0 - BEHAVIOUR CHANGE
% Query points coincident with a VERTEX are now IN an XY triangle
% - 18 Aug 2013: Version 2.1 - Gridded query point handling with low memory footprint.
% - 10 Sep 2013: Version 3.0 - BEHAVIOUR CHANGE
% NEW CONVENTION ADOPTED to expect face normals pointing IN
% Vertically oriented faces are now ignored. Speeds up
% computation and fixes bug where presence of vertical faces
% produced NaN distance from a query pt to facet, making all
% query points under facet erroneously NOT IN polyhedron.
% - 25 Sep 2013: Version 3.1 - Dropped nested unique call which was made
% mostly redundant via v2.1 gridded point handling. Also
% refreshed grid size selection via optimisation.
% - 25 Feb 2014: Version 3.2 - Fixed indeterminate behaviour for query
% points *exactly* in line with an "overhanging" vertex.
% - 11 Nov 2016: Version 3.3 - Used quoted semicolons ':' inside function
% handle calls to conform with new 2015b interpreter
%%
% FACETS is an unpacked arrangement of faces/vertices. It is [3-by-3-by-N],
% with 3 1-by-3 XYZ coordinates of N faces.
[facets, qPts, options] = parseInputs(varargin{:});
numFaces = size(facets,3);
if ~options.griddedInput % SCATTERED QUERY POINTS
numQPoints = size(qPts,1);
else % STRUCTURED QUERY POINTS
numQPoints = prod(cellfun(@numel,qPts(1:2)));
end
% Precompute 3d normals to all facets (triangles). Do this via the cross
% product of the first edge vector with the second. Normalise the result.
allEdgeVecs = facets([2 3 1],:,:) - facets(:,:,:);
if isempty(options.facenormals)
allFacetNormals = bsxfun(@times, allEdgeVecs(1,[2 3 1],:), allEdgeVecs(2,[3 1 2],:)) - ...
bsxfun(@times, allEdgeVecs(2,[2 3 1],:), allEdgeVecs(1,[3 1 2],:));
allFacetNormals = bsxfun(@rdivide, allFacetNormals, sqrt(sum(allFacetNormals.^2,2)));
else
allFacetNormals = permute(options.facenormals,[3 2 1]);
end
if options.flipnormals
allFacetNormals = -allFacetNormals;
end
% We use a Z-ray intersection so we don't even need to consider facets that
% are purely vertically oriented (have zero Z-component).
isFacetUseful = allFacetNormals(:,3,:) ~= 0;
%% Setup grid referencing system
% Function speed can be thought of as a function of grid size. A small number of grid
% squares means iterating over fewer regions (good) but with more faces/qPts to
% consider each time (bad). For any given mesh/queryPt configuration, there will be a
% sweet spot that minimises computation time. There will also be a constraint from
% memory available - low grid sizes means considering many queryPt/faces at once,
% which will require a larger memory footprint. Here we will let the user specify
% gridsize directly, or we will estimate the optimum size based on prior testing.
if ~isempty(options.gridsize)
gridSize = options.gridsize;
else
% Coefficients (with 95% confidence bounds):
p00 = -47; p10 = 12.83; p01 = 20.89;
p20 = 0.7578; p11 = -6.511; p02 = -2.586;
p30 = -0.1802; p21 = 0.2085; p12 = 0.7521;
p03 = 0.09984; p40 = 0.005815; p31 = 0.007775;
p22 = -0.02129; p13 = -0.02309;
GSfit = @(x,y)p00 + p10*x + p01*y + p20*x^2 + p11*x*y + p02*y^2 + p30*x^3 + p21*x^2*y + p12*x*y^2 + p03*y^3 + p40*x^4 + p31*x^3*y + p22*x^2*y^2 + p13*x*y^3;
gridSize = min(150 ,max(1, ceil(GSfit(log(numQPoints),log(numFaces)))));
if isnan(gridSize), gridSize = 1; end
end
%% Find candidate qPts -> triangles pairs
% We have a large set of query points. For each query point, find potential
% triangles that would be pierced by vertical rays through the qPt. First,
% a simple filter by XY bounding box
% Calculate the bounding box of each facet
minFacetCoords = permute(min(facets(:,1:2,:),[],1),[3 2 1]);
maxFacetCoords = permute(max(facets(:,1:2,:),[],1),[3 2 1]);
% Set rescale values to rescale all vertices between 0(-eps) and 1(+eps)
scalingOffsetsXY = min(minFacetCoords,[],1) - eps;
scalingRangeXY = max(maxFacetCoords,[],1) - scalingOffsetsXY + 2*eps;
% Based on scaled min/max facet coords, get the [lowX lowY highX highY] "grid" index
% of all faces
lowToHighGridIdxs = floor(bsxfun(@rdivide, ...
bsxfun(@minus, ... % Use min/max coordinates of each facet (+/- the tolerance)
[minFacetCoords-options.tol maxFacetCoords+options.tol],...
[scalingOffsetsXY scalingOffsetsXY]),...
[scalingRangeXY scalingRangeXY]) * gridSize) + 1;
% Build a grid of cells. In each cell, place the facet indices that encroach into
% that grid region. Similarly, each query point will be assigned to a grid region.
% Note that query points will be assigned only one grid region, facets can cover many
% regions. Furthermore, we will add a tolerance to facet region assignment to ensure
% a query point will be compared to facets even if it falls only on the edge of a
% facet's bounding box, rather than inside it.
cells = cell(gridSize);
[unqLHgrids,~,facetInds] = unique(lowToHighGridIdxs,'rows');
tmpInds = accumarray(facetInds(isFacetUseful),find(isFacetUseful),[size(unqLHgrids,1),1],@(x){x});
for xi = 1:gridSize
xyMinMask = xi >= unqLHgrids(:,1) & xi <= unqLHgrids(:,3);
for yi = 1:gridSize
cells{yi,xi} = cat(1,tmpInds{xyMinMask & yi >= unqLHgrids(:,2) & yi <= unqLHgrids(:,4)});
% The above line (with accumarray) is faster with equiv results than:
% % cells{yi,xi} = find(ismember(facetInds, xyInds));
end
end
% With large number of facets, memory may be important:
clear lowToHightGridIdxs LHgrids facetInds tmpInds xyMinMask minFacetCoords maxFacetCoords
%% Compute edge unit vectors and dot products
% Precompute the 2d unit vectors making up each facet's edges in the XY plane.
allEdgeUVecs = bsxfun(@rdivide, allEdgeVecs(:,1:2,:), sqrt(sum(allEdgeVecs(:,1:2,:).^2,2)));
% Precompute the inner product between edgeA.edgeC, edgeB.edgeA, edgeC.edgeB
allEdgeEdgeDotPs = sum(allEdgeUVecs .* -allEdgeUVecs([3 1 2],:,:),2) - 1e-9;
%% Gather XY query locations
% Since query points are most likely given as a (3D) grid of query locations, we only
% need to consider the unique XY locations when asking which facets a vertical ray
% through an XY location would pierce.
if ~options.griddedInput % SCATTERED QUERY POINTS
qPtsXY = @(varargin)qPts(:,1:2);
qPtsXYZViaUnqIndice = @(ind)qPts(ind,:);
outPxIndsViaUnqIndiceMask = @(ind,mask)ind(mask);
outputSize = [size(qPts,1),1];
reshapeINfcn = @(INMASK)INMASK;
minFacetDistanceFcn = @minFacetToQptDistance;
else % STRUCTURED QUERY POINTS
[xmat,ymat] = meshgrid(qPts{1:2});
qPtsXY = [xmat(:) ymat(:)];
% A standard set of Z locations will be shifted around by different
% unqQpts XY coordinates.
zCoords = qPts{3}(:) * [0 0 1];
qPtsXYZViaUnqIndice = @(ind)bsxfun(@plus, zCoords, [qPtsXY(ind,:) 0]);
% From a given indice and mask, we will turn on/off the IN points under
% that indice based on the mask. The easiest calculation is to setup
% the IN matrix as a numZpts-by-numUnqPts mask. At the end, we must
% unpack/reshape this 2D mask to a full 3D logical mask
numZpts = size(zCoords,1);
baseZinds = 1:numZpts;
outPxIndsViaUnqIndiceMask = @(ind,mask)(ind-1)*numZpts + baseZinds(mask);
outputSize = [numZpts, size(qPtsXY,1)];
reshapeINfcn = @(INMASK)reshape(INMASK', cellfun(@numel, qPts([2 1 3])));
minFacetDistanceFcn = @minFacetToQptsDistance;
end
% Start with every query point NOT inside the polyhedron. We will
% iteratively find those query points that ARE inside.
IN = false(outputSize);
% Determine with grids each query point falls into.
qPtGridXY = floor(bsxfun(@rdivide, bsxfun(@minus, qPtsXY(':',':'), scalingOffsetsXY),...
scalingRangeXY) * gridSize) + 1;
[unqQgridXY,~,qPtGridInds] = unique(qPtGridXY,'rows');
% We need only consider grid indices within those already set up
ptsToConsidMask = ~any(qPtGridXY<1 | qPtGridXY>gridSize, 2);
if ~any(ptsToConsidMask)
IN = reshapeINfcn(IN);
return;
end
% Build the reference list
cellQptContents = accumarray(qPtGridInds(ptsToConsidMask),find(ptsToConsidMask), [],@(x){x});
gridsToCheck = unqQgridXY(~any(unqQgridXY<1 | unqQgridXY>gridSize, 2),:);
cellQptContents(cellfun('isempty',cellQptContents)) = [];
gridIndsToCheck = sub2ind(size(cells), gridsToCheck(:,2), gridsToCheck(:,1));
% For ease of multiplication, reshape qPt XY coords to [1-by-2-by-1-by-N]
qPtsXY = permute(qPtsXY(':',':'),[4 2 3 1]);
% There will be some grid indices with query points but without facets.
emptyMask = cellfun('isempty',cells(gridIndsToCheck))';
for i = find(~emptyMask)
% We get all the facet coordinates (ie, triangle vertices) of triangles
% that intrude into this grid location. The size is [3-by-2-by-N], for
% the [3vertices-by-XY-by-Ntriangles]
allFacetInds = cells{gridIndsToCheck(i)};
candVerts = facets(:,1:2,allFacetInds);
% We need the XY coordinates of query points falling into this grid.
allqPtInds = cellQptContents{i};
queryPtsXY = qPtsXY(:,:,:,allqPtInds);
% Get unit vectors pointing from each triangle vertex to my query point(s)
vert2ptVecs = bsxfun(@minus, queryPtsXY, candVerts);
vert2ptUVecs = bsxfun(@rdivide, vert2ptVecs, sqrt(sum(vert2ptVecs.^2,2)));
% Get unit vectors pointing around each triangle (along edge A, edge B, edge C)
edgeUVecs = allEdgeUVecs(:,:,allFacetInds);
% Get the inner product between edgeA.edgeC, edgeB.edgeA, edgeC.edgeB
edgeEdgeDotPs = allEdgeEdgeDotPs(:,:,allFacetInds);
% Get inner products between each edge unit vec and the UVs from qPt to vertex
edgeQPntDotPs = sum(bsxfun(@times, edgeUVecs, vert2ptUVecs),2);
qPntEdgeDotPs = sum(bsxfun(@times,vert2ptUVecs, -edgeUVecs([3 1 2],:,:)),2);
% If both inner products 2 edges to the query point are greater than the inner
% product between the two edges themselves, the query point is between the V
% shape made by the two edges. If this is true for all 3 edge pair, the query
% point is inside the triangle.
resultIN = all(bsxfun(@gt, edgeQPntDotPs, edgeEdgeDotPs) & bsxfun(@gt, qPntEdgeDotPs, edgeEdgeDotPs),1);
resultONVERTEX = any(any(isnan(vert2ptUVecs),2),1);
result = resultIN | resultONVERTEX;
qPtHitsTriangles = any(result,3);
% If NONE of the query points pierce ANY triangles, we can skip forward
if ~any(qPtHitsTriangles), continue, end
% In the next step, we'll need to know the indices of ALL the query points at
% each of the distinct XY coordinates. Let's get their indices into "qPts" as a
% cell of length M, where M is the number of unique XY points we had found.
for ptNo = find(qPtHitsTriangles(:))'
% Which facets does it pierce?
piercedFacetInds = allFacetInds(result(1,1,:,ptNo));
% Get the 1-by-3-by-N set of triangle normals that this qPt pierces
piercedTriNorms = allFacetNormals(:,:,piercedFacetInds);
% Pick the first vertex as the "origin" of a plane through the facet. Get the
% vectors from each query point to each facet origin
facetToQptVectors = bsxfun(@minus, ...
qPtsXYZViaUnqIndice(allqPtInds(ptNo)),...
facets(1,:,piercedFacetInds));
% Calculate how far you need to go up/down to pierce the facet's plane.
% Positive direction means "inside" the facet, negative direction means
% outside.
facetToQptDists = bsxfun(@rdivide, ...
sum(bsxfun(@times,piercedTriNorms,facetToQptVectors),2), ...
abs(piercedTriNorms(:,3,:)));
% Since it's possible for two triangles sharing the same vertex to
% be the same distance away, I want to sum up all the distances of
% triangles that are closest to the query point. Simple case: The
% closest triangle is unique Edge case: The closest triangle is one
% of many the same distance and direction away. Tricky case: The
% closes triangle has another triangle the equivalent distance
% but facing the opposite direction
IN( outPxIndsViaUnqIndiceMask(allqPtInds(ptNo), ...
minFacetDistanceFcn(facetToQptDists)<options.tol...
)) = true;
end
end
% If they provided X,Y,Z vectors of query points, our output is currently a
% 2D mask and must be reshaped to [LEN(Y) LEN(X) LEN(Z)].
IN = reshapeINfcn(IN);
%% Called subfunctions
% vertices = [
% 0.9046 0.1355 -0.0900
% 0.8999 0.3836 -0.0914
% 1.0572 0.2964 -0.0907
% 0.8735 0.1423 -0.1166
% 0.8685 0.4027 -0.1180
% 1.0337 0.3112 -0.1173
% 0.9358 0.1287 -0.0634
% 0.9313 0.3644 -0.0647
% 1.0808 0.2816 -0.0641
% ];
% faces = [
% 1 2 5
% 1 5 4
% 2 3 6
% 2 6 5
% 3 1 4
% 3 4 6
% 6 4 5
% 2 1 8
% 8 1 7
% 3 2 9
% 9 2 8
% 1 3 7
% 7 3 9
% 7 9 8
% ];
% point = [vertices(3,1),vertices(3,2),1.5];
function closestTriDistance = minFacetToQptDistance(facetToQptDists)
% FacetToQptDists is a 1pt-by-1-by-Nfacets array of how far you need to go
% up/down to pierce each facet's plane. If the Qpt was directly over an
% "overhang" vertex, then two facets with opposite orientation will be
% equally distant from the Qpt, with one distance positive and one
% negative. In such cases, it is impossible for the Qpt to actually be
% "inside" this pair of facets, so their distance is updated to Inf.
[~,minInd] = min(abs(facetToQptDists),[],3);
while any( abs(facetToQptDists + facetToQptDists(minInd)) < 1e-15 )
% Since the above comparison is made every time, but the below variable
% setting is done only in the rare case that a query point coincides
% with an overhang vertex, it is more efficient to re-compute the
% equality when it's true, rather than store the result every time.
facetToQptDists( abs(facetToQptDists) - abs(facetToQptDists(minInd)) < 1e-15) = inf;
if ~any(isfinite(facetToQptDists))
break;
end
[~,minInd] = min(abs(facetToQptDists),[],3);
end
closestTriDistance = facetToQptDists(minInd);
function closestTriDistance = minFacetToQptsDistance(facetToQptDists)
% As above, but facetToQptDists is an Mpts-by-1-by-Nfacets array.
% The multi-point version is a little more tricky. While below is quite a
% bit slower when the while loop is entered, it is very rarely entered and
% very fast to make just the initial comparison.
[minVals,minInds] = min(abs(facetToQptDists),[],3);
while any(...
any(abs(bsxfun(@plus,minVals,facetToQptDists))<1e-15,3) & ...
any(abs(bsxfun(@minus,minVals,facetToQptDists))<1e-15,3))
maskP = abs(bsxfun(@plus,minVals,facetToQptDists))<1e-15;
maskN = abs(bsxfun(@minus,minVals,facetToQptDists))<1e-15;
mustAlterMask = any(maskP,3) & any(maskN,3);
for i = find(mustAlterMask)'
facetToQptDists(i,:,maskP(i,:,:) | maskN(i,:,:)) = inf;
end
[newMv,newMinInds] = min(abs(facetToQptDists(mustAlterMask,:,:)),[],3);
minInds(mustAlterMask) = newMinInds(:);
minVals(mustAlterMask) = newMv(:);
end
% Below is a tiny speedup on basically a sub2ind call.
closestTriDistance = facetToQptDists((minInds-1)*size(facetToQptDists,1) + (1:size(facetToQptDists,1))');
%% Input handling subfunctions
function [facets, qPts, options] = parseInputs(varargin)
% Gather FACES and VERTICES
if isstruct(varargin{1}) % inpolyhedron(FVstruct, ...)
if ~all(isfield(varargin{1},{'vertices','faces'}))
error( 'Structure FV must have "faces" and "vertices" fields' );
end
faces = varargin{1}.faces;
vertices = varargin{1}.vertices;
varargin(1) = []; % Chomp off the faces/vertices
else % inpolyhedron(FACES, VERTICES, ...)
faces = varargin{1};
vertices = varargin{2};
varargin(1:2) = []; % Chomp off the faces/vertices
end
% Unpack the faces/vertices into [3-by-3-by-N] facets. It's better to
% perform this now and have FACETS only in memory in the main program,
% rather than FACETS, FACES and VERTICES
facets = vertices';
facets = permute(reshape(facets(:,faces'), 3, 3, []),[2 1 3]);
% Extract query points
if length(varargin)<2 || ischar(varargin{2}) % inpolyhedron(F, V, [x(:) y(:) z(:)], ...)
qPts = varargin{1};
varargin(1) = []; % Chomp off the query points
else % inpolyhedron(F, V, xVec, yVec, zVec, ...)
qPts = varargin(1:3);
% Chomp off the query points and tell the world that it's gridded input.
varargin(1:3) = [];
varargin = [varargin {'griddedInput',true}];
end
% Extract configurable options
options = parseOptions(varargin{:});
% Check if face normals are unified
if options.testNormals
options.normalsAreUnified = checkNormalUnification(faces);
end
function options = parseOptions(varargin)
IP = inputParser;
if verLessThan('matlab', 'R2013b')
fcn = 'addParamValue';
else
fcn = 'addParameter';
end
IP.(fcn)('gridsize',[], @(x)isscalar(x) && isnumeric(x))
IP.(fcn)('tol', 0, @(x)isscalar(x) && isnumeric(x))
IP.(fcn)('tol_ang', 1e-5, @(x)isscalar(x) && isnumeric(x))
IP.(fcn)('facenormals',[]);
IP.(fcn)('flipnormals',false);
IP.(fcn)('griddedInput',false);
IP.(fcn)('testNormals',false);
IP.parse(varargin{:});
options = IP.Results;
|
github
|
adhusch/PaCER-master
|
PaCER.m
|
.m
|
PaCER-master/src/PaCER.m
| 3,530 |
utf_8
|
c451064c9339950b31e5cd87229324dc
|
%% PaCER - Precise and Convenient Electrode Reconstruction for Deep Brain Stimulation
%
% Andreas Husch
% Centre Hospitalier de Luxembourg (CHL), Dept. of Neurosurgery /
% University of Luxembourg - Luxembourg Centre for Systems Biomedicine (LCSB)
% (c) 2016 - 2017
% [email protected], [email protected]
function [elecModels, elecPointCloudsStruct, intensityProfiles, skelSkelmms] = PaCER(niiCT, varargin)
%% Optional Arguments and Default Values
argParser = inputParser();
argParser.KeepUnmatched = true;
argParser.addOptional('finalDegree', 3, @(x)(isnumeric(x) && (x >= 1)));
argParser.addOptional('displayProfiles', false); % optional plot of intensity profiles
argParser.addOptional('displayMPR', false); % optional MPR plot of orthogonal oblique resampling along the trajceotry
argParser.addOptional('noMask', false); % for phantom studies where no brain is present in data
argParser.addParameter('brainMask', ''); % for manually providing a brain mask (binary segmentation image file path)
argParser.addOptional('reverseDir', false); % for special cases with I-S flip
argParser.addOptional('contactDetectionMethod', 'contactAreaCenter', @(x)(ismember(x, {'peak', 'peakWaveCenter', 'contactAreaCenter'}))); % default contactAreaCenter, if peak, automatic fallback to contactAreaCenter for "bad quality data"
argParser.addParameter('electrodeType', '', @(x)(ismember(x, {'', 'Medtronic 3387', 'Medtronic 3389', 'Boston Vercise Directional'})));
argParser.addOptional('medtronicXMLPlan', '', @(x)(ischar(x)));
argParser.parse(varargin{:});
args = argParser.Results;
%% profe contactDetectionMethod contactAreaCenter if electrodeType is set manually
if(~isempty(args.electrodeType))
args.contactDetectionMethod = 'contactAreaCenter';
end
%% Checks
assert(logical(license('test', 'image_toolbox')), 'It seems this system does not have the Image Processing Toolbox installed. PaCER requires the Image Processing Toolbox to continue.')
if(~isa(niiCT, 'NiftiMod') && ~isa(niiCT, 'NiftiModSPM') )
disp('First parameter is not a nifti object. Intrepretating as filename and tring to load a nifti file with that name from disk...');
niiCT = NiftiMod(niiCT);
end
if(max(niiCT.voxsize) > 1)
warning('Slice thickness is greater than 1 mm! Independent contact detection is most likly not possible. Forcing contactAreaCenter based method.');
args.contactDetectionMethod = 'contactAreaCenter';
elseif(max(niiCT.voxsize) > 0.7)
warning('Slice thickness is greater than 0.7 mm! Independet contact detection might not work reliable in this case. However, for certain electrode types with large contacts spacings you might be lucky.');
end
%% Run Algorithm
disp(['===================== Processing ' niiCT.filepath ' =====================']);
disp(['Voxel size: ' num2str(niiCT.voxsize')]);
elecPointCloudsStruct = extractElectrodePointclouds(niiCT, varargin{:}); % preprocessing
elecModels = {};
intensityProfiles = {};
skelSkelmms = {};
for i=1:length(elecPointCloudsStruct)
disp('------------- Processing Electrode -------------');
% Preprocessing and "1st pass" model
initialR3polynomial = electrodePointCloudModelEstimate(elecPointCloudsStruct(i).pointCloudWorld , elecPointCloudsStruct(i).pixelValues, args.reverseDir); % internally always degree 8
% Refitting ("2nd and 3rd pass")
[elecModels{i}, intensityProfiles{i}, skelSkelmms{i}] = refitElec(initialR3polynomial,elecPointCloudsStruct(i).pointCloudWorld, elecPointCloudsStruct(i).pixelValues, args); %#ok<AGROW>
end
end
|
github
|
adhusch/PaCER-master
|
electrodePointCloudModelEstimate.m
|
.m
|
PaCER-master/src/Functions/electrodePointCloudModelEstimate.m
| 3,487 |
utf_8
|
b769436b1ae7533365eace1e82be1f19
|
%% electrodePointCloudModelEstimate - extract skeleton points from given pointcloud and subsequently fit a polynomial
%
% PARAMETERS
% varargin{1} = pixelValues list got from reference image of the segmentation. When given used for intensity based
% weightig of cenroid calculation.
% varargin{2} = reverse Z direction (for special cases, e.g. certain phantom studies)
%
% Andreas Husch
% Centre Hospitalier de Luxembourg / Luxembourg Centre for Systems
% Biomedicine, University of Luxembourg
% 2014 - 2017
% [email protected]
function [r3polynomial, tPerMm, skeleton, totalLengthMm] = electrodePointCloudModelEstimate(elecPointCloudMm, varargin)
revDir = false;
INTERNAL_DEGREE = 8; % fixed, determined as sufficient by AIC analysis
if(nargin < 2)
USE_REF_IMAGE_WEIGHTING=false;
warning('No Reference image for intensity weighting given! Accuracy is thus limited to voxel size!');
pixelValues = [];
else
USE_REF_IMAGE_WEIGHTING=true;
pixelValues = varargin{1};
if(nargin == 3)
revDir = varargin{2};
end
end
%% Axial centers based skeletonization
zPlanes = unique(elecPointCloudMm(:,3));
tol = 0;
if ~(length(zPlanes) < length(elecPointCloudMm))
warning('CT planes in Z direction are not exactly aligned. Trying with 0.1 mm tolerance')
tol = 0.1;
zPlanes = uniquetol(elecPointCloudMm(:,3), tol / max(abs(elecPointCloudMm(:,3)))); % trying with tolerance
end
assert(length(zPlanes) < length(elecPointCloudMm), 'Couln''t find CT planes in z direction. Check that the CT scan was not acquired oblique!');
skeleton = [];%skeleton = NaN(length(zPlanes),3); length is unknown a-priori because of possible "non planes"
sumInPlane = []; %sumInPlane = NaN(length(zPlanes),1);
for i=1:length(zPlanes)
inPlanePoints = elecPointCloudMm( abs(elecPointCloudMm(:,3) - zPlanes(i)) <= tol ,:);
if(size(inPlanePoints,1) > 1)
if(USE_REF_IMAGE_WEIGHTING)
inPlaneIntensities = single(pixelValues(abs(elecPointCloudMm(:,3) - zPlanes(i)) <= tol)); % pixelValues MUST be same order than elecPointCloudMm!
skeleton(end+1,:) = inPlanePoints' * inPlaneIntensities / sum(inPlaneIntensities)'; %#ok<AGROW>
sumInPlane(end+1) = sum(inPlaneIntensities); %#ok<AGROW>
else
skeleton(end+1,:) = mean(inPlanePoints); %#ok<AGROW>
end
%else
% ignore pseudo slices with just one plane, so do nothing
end
end
%% Filter Skeleton for valid Points
% see bar(sumInPlane) to get a feeling
filter = sumInPlane < (median(sumInPlane) / 1.5);
if(sum(filter) > 0)
disp('Applied axial skeleton filter because of low intensity planes')
skeleton = skeleton(~filter,:);
end
if(isequal(skeleton(1,:) , [0 0 0]))
error('Empty skeleton. Was the CT image aquired in axial flow?')
end
%% Approximate parameterized polynomial ([x y z] = f(t))
if(length(skeleton) < INTERNAL_DEGREE + 1)
warning(['electrodePointCloudModelEstimate: less data points ' num2str(length(skeleton)) ...
'than internal poly. degree (' num2str(INTERNAL_DEGREE) '). Lowering degree but take care']);
INTERNAL_DEGREE = length(skeleton) - 1;
end
if(revDir)
[r3polynomial, tPerMm] = fitParamPolyToSkeleton(flipud(skeleton), INTERNAL_DEGREE); % note degree (8)
else
[r3polynomial, tPerMm] = fitParamPolyToSkeleton(skeleton, INTERNAL_DEGREE); % note degree (8)
end
totalLengthMm = polyArcLength3(r3polynomial, 0, 1); % for backwards compatibility
end
|
github
|
adhusch/PaCER-master
|
TestElectrodes.m
|
.m
|
PaCER-master/src/Classes/TestElectrodes.m
| 27,501 |
utf_8
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f74d6c10a2c77ffc6f772de40bb4bb6b
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%% TestElectrodes - Class representing a Ben's Gun configuration of Test Electrodes (up to rotation!)
% note that the precise rotation depends on the kinematics of the
% sterotactic frame/the micro drive device
%
% Andreas Husch
% Centre Hospitalier de Luxembourg, Dep. of Neurosurgery /
% University of Luxembourg - Luxembourg Centre for Systems Biomedicne
% 2014 - 2017
% [email protected], [email protected]
classdef TestElectrodes < Trajectory & plotable3D & plotableImage & configurable & id
properties (SetAccess = protected, GetAccess=public, SetObservable = true)
originalEntryPoint = NaN(3,1);
originalTargetPoint = NaN(3,1);
marker = 'x'; %default circle
color = [0.2 1 0.4]; %default
diameter = 4; % groesse
lineStyle = '--';
show2DProjection = 1; % variable {0,1} die angibt, ob 2D plots angezeigt werden oder nicht
%INHERITED
%plotHandleHashMap (from plotableImage)
trajectoryChangedListener = event.listener.empty();
end
properties(Access=public, SetObservable, AbortSet)
obliqueViewRadius = 80;
currentDepthValue = 0; % 0= we ar at target; -x means we are x mm above the target; +x means the depth is x + target in mm
end
properties (SetAccess = public, GetAccess=public, SetObservable = true)
intersections = zeros(2,5) ; %TODO: [tg1, tg2] for all electrodes %center, medial, lateral, posterior, anterior. Set NaN for unused Electrodes. (Replace by Dep. Prop. that filtes NaN)
ELECTRODE_DISTANCE = 2.0; %[mm], distance from posterior, anterior, lateral, medial to center electrode
ELECTRODE_RECORDED_INTERSECTION_COLOR = 'r';
ELECTRODE_INTERSECTION_COLOR = 'g';
ELECTRODE_COLOR = [0 1 1]; %lightblue
ELECTRODE_PLOT_EXTENSION_MM = 15; %[mm], define how long the plottet electrode lines should be extended beyond the target/entry points;
DISPLAY_TARGET_POINTS = false;
end
properties (SetAccess = protected, GetAccess = public, ... %dependent props.
Dependent = true)
electrodesEntryPoints = {}; %center, right, left, posterior, anterior.
electrodesTargetPoints = {}; %center, right, left, posterior, anterior.
end
properties (Access = private)
electrodesOffsets;
electrodesOffsetsDirection;
end
properties(SetAccess = private, GetAccess = public, Dependent = true)
% to control ObliqueView
trajectoryLength = 0;
end
events
SliderValueChanged; %OBSOLET
end
methods
function this = TestElectrodes(varargin)
if(nargin == 2)
entryPoint = varargin{1};
targetPoint = varargin{2};
if(sum(size(entryPoint) ~= [3 1]) ||sum(size(targetPoint) ~= [3 1]))
warning('TestElectrodes: entryPoint and TargetPoint MUST be 3x1 vectors!'); %#ok<WNTAG>
if(size(entryPoint) ~= [3 1]) %#ok<BDSCA>
entryPoint = entryPoint';
end
if(size(targetPoint) ~= [3 1]) %#ok<BDSCA>
targetPoint = targetPoint';
end
end
this.entryPoint = entryPoint;
this.targetPoint = targetPoint;
this.originalEntryPoint = this.entryPoint;
this.originalTargetPoint = this.targetPoint;
this.currentDepthValue = -this.trajectoryLength;
end
addlistener(this, 'ELECTRODE_COLOR', 'PostSet', @this.updatePlot3D);
this.trajectoryChangedListener = this.addlistener('trajectoryChanged', @this.onUpdatePlots);
end
function electrodesEntryPoints = get.electrodesEntryPoints(this)
centralpoint = repmat(this.entryPoint, 1, 5); % x y z for 5 electrodes
offsets = this.getElectrodesOffsets();
electrodesEntryPoints = centralpoint + offsets;
end
function electrodesTargetPoints = get.electrodesTargetPoints(this)
centralpoint = repmat(this.targetPoint, 1, 5); % x y z for 5 electrodes
offsets = this.getElectrodesOffsets();
electrodesTargetPoints = centralpoint + offsets;
% electrodesTargetPoints = mat2cell(centralpoint + offsets, ...
% 3,ones(length(centralpoint),1));
end
function trajectoryLength = get.trajectoryLength(this)
trajectoryLength = this.entryPoint-this.targetPoint;
trajectoryLength = ceil(sqrt(dot(trajectoryLength, trajectoryLength)));
end
function obliqueViewRadius = get.obliqueViewRadius(this)
obliqueViewRadius = this.obliqueViewRadius;
end
function set.obliqueViewRadius(this, value)
if(value < 0)
disp(strcat('Testelectrodes:set.obliqueViewRadius:Radius have to be greater than 0'));
else
this.obliqueViewRadius = value;
end;
end
function pointCloud = getIntersectionPointCloud(this)
% 3d-point = Target + rg * tg1
pointCloudTg1 = this.electrodesTargetPoints + repmat(this.direction,1,5) .* repmat(this.intersections(1,:),3,1);
% 3d-point = Target + rg * tg2
pointCloudTg2 = this.electrodesTargetPoints + repmat(this.direction,1,5) .* repmat(this.intersections(2,:),3,1);
pointCloud = [pointCloudTg1 pointCloudTg2]; % TODO Remove Electrodes with no Intersection
end
function disableTrajectoryChangedEvent(this)
this.trajectoryChangedListener.delete();
end
function enableTrajectoryChangedEvent(this)
this.trajectoryChangedListener = this.addlistener('trajectoryChanged', @this.onUpdatePlots);
end
end
methods (Access = private)
function [offsets, B] = getElectrodesOffsets(this)
if(~isempty(this.electrodesOffsets) && ~isnan(this.electrodesOffsets(1,1)) &&isequal(this.direction, this.electrodesOffsetsDirection))
offsets = this.electrodesOffsets;
else
config = this.ELECTRODE_DISTANCE * ...
[0 0 0; % 5-dice configuration, FIXME: should be ortogonal 2mm to center electrode
0 1 0; % note that config is transposed!
0 -1 0;
0 0 -1;
0 0 1];
e1 = [1; 0; 0]; % <-> l-r TODO: replace this by direction vecotrs from frame
e2 = [0; 1; 0]; % <-> a-p
b1 = this.direction; %MUST be normalized!
if(all(eq(abs(round(b1)), [1;0;0])))
b2 = [0; 1; 0];
b3 = [0; 0; 1];
else
b2 = e1 - dot(b1,e1) * b1;
b2 = b2 / norm(b2);
b3 = e2 - dot(b1, e2) * b1 - dot(b2,e2) * b2;
b3 = b3 / norm(b3);
end
B = [b1,b2,b3]; %new BASE (b2,b3 forming a plane ortogonal to our electrode)
offsets = B * config';
this.electrodesOffsets = offsets;
this.electrodesOffsetsDirection = this.direction;
end
end
function [base,directionVec] = getElectrodePoints(this)
base = this.electrodesTargetPoints;
directionVec = (this.electrodesEntryPoints-base);
end%fcn-getElectrodePoints
end
methods % graphical methods
function graphicsHandle = initPlot3D(this, parentAxes)
if(this.plotHandleHashMap3D.isKey(parentAxes))
warning('TestElectrodes:initPlot3DcalledMoreThanOnce', 'initPlot3D was called more than once for the same axes and the same object!');
graphicsHandle = this.plotHandleHashMap3D(parentAxes);
return;
end
% set(0,'DefaultLineLineSmoothing','on'); %enable line smoothing for all objects that support it
% create a group object and group all plots to this "parent" handle
graphicsHandle = hggroup('Parent', parentAxes);
d = this.electrodesTargetPoints;
e = this.electrodesEntryPoints;
tg = this.getIntersectionPointCloud;
set(parentAxes, 'NextPlot', 'add');
if(this.DISPLAY_TARGET_POINTS)
graphicsHandles.targetPoints = plot3(d(1,:),d(2,:),d(3,:), 'b*', 'Parent', graphicsHandle,'Clipping','on');
set(graphicsHandles.targetPoints, 'Parent', graphicsHandle);
end
graphicsHandles.entryPoints = plot3(e(1,:),e(2,:),e(3,:), 'g*', 'Parent', graphicsHandle,'Clipping','on');
set(graphicsHandles.entryPoints, 'Parent', graphicsHandle);
graphicsHandles.intersectionPoints = plot3(tg(1,:),tg(2,:),tg(3,:), 'r*', 'Parent', graphicsHandle,'Clipping','on');
set(graphicsHandles.intersectionPoints, 'Parent', graphicsHandle);
% plot trajectories XX mm beyoned the target point and before the entry point
dPlusXX = d + repmat(this.direction,1,5) * this.ELECTRODE_PLOT_EXTENSION_MM;
eMinusXX = e - repmat(this.direction,1,5) * this.ELECTRODE_PLOT_EXTENSION_MM;
graphicsHandles.electrodes = ...
line([eMinusXX(1,:); dPlusXX(1,:)], ...
[eMinusXX(2,:); dPlusXX(2,:)], ...
[eMinusXX(3,:); dPlusXX(3,:)], ...
'LineWidth', 1.0,...
'Color', this.ELECTRODE_COLOR,...
'Parent', graphicsHandle);
set(graphicsHandles.electrodes , 'Parent', graphicsHandle);
% mark lateral (left)
graphicsHandles.electrodes = ...
line([eMinusXX(1,3); dPlusXX(1,3)], ...
[eMinusXX(2,3); dPlusXX(2,3)], ...
[eMinusXX(3,3); dPlusXX(3,3)], ...
'LineWidth', 1.0,...
'Color', this.ELECTRODE_COLOR,...
'Parent', graphicsHandle);
set(graphicsHandles.electrodes , 'Parent', graphicsHandle);
graphicsHandles.recordedIntersections = ...
line([tg(1,1:5); tg(1,6:10)], ...
[tg(2,1:5); tg(2,6:10)], ...
[tg(3,1:5); tg(3,6:10)], ...
'LineWidth', 3.0,...
'Color', this.ELECTRODE_RECORDED_INTERSECTION_COLOR ,...
'Parent', graphicsHandle);
set(graphicsHandles.recordedIntersections , 'Parent', graphicsHandle);
this.plotHandleHashMap3D(double(parentAxes)) = double(graphicsHandle);
end%fcn-initPlot3D
%TODO: dragging points implementieren
function graphicsHandle = initPlotAxial(this, ax, CurrentPositionObject)
% create a group object and group all plots to this "parent" handle
graphicsHandle = hggroup('Parent', ax);
% keyVal = ['axial',this.String,ax];
keyVal = ax;
% [base, direcVec] = this.getElectrodePoints;
% curPosInMM = repmat(CurrentPositionObject.currentImagePosInMmA,1,5);
% factor = repmat(((curPosInMM - base(3,:))./direcVec(3,:)),3,1);
curPosInMM = CurrentPositionObject.currentImagePosInMmA;
base = this.targetPoint;
direcVec = this.entryPoint - base;
factor = ((curPosInMM - base(3))./direcVec(3));
projectionPoint = base + factor.*direcVec;
%if abfrage wenn projection < targetPoint, dann p = t oder
%keine projektion
pointStart = [this.entryPoint(1) this.targetPoint(1)];
pointEnd = [this.entryPoint(2) this.targetPoint(2)];
projectionPointStart = [this.entryPoint(1) projectionPoint(1)];
projectionPointEnd = [this.entryPoint(2) projectionPoint(2)];
posLineColor = [0 1 1];
%check wheather we are within entry-target or >taget
if(projectionPoint(2) < min(this.targetPoint(2),this.entryPoint(2)))%note it starts from left-bottom-corner
projectionPointStart = [this.targetPoint(1) projectionPoint(1)];
projectionPointEnd = [this.targetPoint(2) projectionPoint(2)];
posLineColor = [1 0 0];
elseif(projectionPoint(2) > max(this.entryPoint(2),this.targetPoint(2)))
projectionPointStart = [this.entryPoint(1) projectionPoint(1)];
projectionPointEnd = [this.entryPoint(2) projectionPoint(2)];
posLineColor = [1 0 0];
end%if
%start to plot what needs to be plotted
handle.CurrentPositionObject = CurrentPositionObject;
% this.plotHandleHashMap(1.0) = CurrentPositionObject;
this.onOrthogonalProjectionPlot(keyVal, graphicsHandle, pointStart, pointEnd, projectionPointStart, projectionPointEnd, posLineColor, handle);
end%fcn-initPlotAxial
function graphicsHandle = initPlotCoronal(this, ax, CurrentPositionObject)
% create a group object and group all plots to this "parent" handle
graphicsHandle = hggroup('Parent', ax);
% keyVal = ['coronal',this.String,ax];
keyVal = ax;
% [base, direcVec] = this.getElectrodePoints;
% curPosInMM = repmat(CurrentPositionObject.currentImagePosInMmC,1,5);
% factor = repmat(((curPosInMM - base(2,:))./direcVec(2,:)),3,1);
% projectionPoint = base + factor.*direcVec;
curPosInMM = CurrentPositionObject.currentImagePosInMmC;
base = this.targetPoint;
direcVec = this.entryPoint - base;
factor = ((curPosInMM - base(2))./direcVec(2));
projectionPoint = base + factor.*direcVec;
pointStart = [this.entryPoint(1) this.targetPoint(1)];
pointEnd = [this.entryPoint(3) this.targetPoint(3)];
projectionPointStart = [this.entryPoint(1) projectionPoint(1)];
projectionPointEnd = [this.entryPoint(3) projectionPoint(3)];
posLineColor = [0 1 1];
%check wheather we are within entry-target or >taget
if(projectionPoint(3) < min(this.targetPoint(3),this.entryPoint(3)))%note it starts from left-bottom-corner
projectionPointStart = [this.targetPoint(1) projectionPoint(1)];
projectionPointEnd = [this.targetPoint(3) projectionPoint(3)];
posLineColor = [1 0 0];
elseif(projectionPoint(3) > max(this.entryPoint(3),this.targetPoint(3)))
projectionPointStart = [this.entryPoint(1) projectionPoint(1)];
projectionPointEnd = [this.entryPoint(3) projectionPoint(3)];
posLineColor = [1 0 0];
end%if
%start to plot what needs to be plotted
handle.CurrentPositionObject = CurrentPositionObject;
% this.plotHandleHashMap(1.0) = CurrentPositionObject;
this.onOrthogonalProjectionPlot(keyVal, graphicsHandle, pointStart, pointEnd, projectionPointStart, projectionPointEnd, posLineColor, handle);
end%fcn-initPlotCoronal
function graphicsHandle = initPlotSagital(this,ax, CurrentPositionObject)
% create a group object and group all plots to this "parent" handle
graphicsHandle = hggroup('Parent', ax);
% keyVal = ['sagital',this.String,ax];
keyVal = ax;
% [base, direcVec] = this.getElectrodePoints;
% curPosInMM = repmat(CurrentPositionObject.currentImagePosInMmS,1,5);
% factor = repmat(((curPosInMM - base(1,:))./direcVec(1,:)),3,1);
% projectionPoint = base + factor.*direcVec;
curPosInMM = CurrentPositionObject.currentImagePosInMmS;
base = this.targetPoint;
direcVec = this.entryPoint - base;
factor = ((curPosInMM - base(1))./direcVec(1));
projectionPoint = base + factor.*direcVec;
pointStart = [this.entryPoint(2) this.targetPoint(2)];
pointEnd = [this.entryPoint(3) this.targetPoint(3)];
projectionPointStart = [this.entryPoint(2) projectionPoint(2)];
projectionPointEnd = [this.entryPoint(3) projectionPoint(3)];
posLineColor = [0 1 1];
%check wheather we are within entry-target or >taget
if(projectionPoint(3) < min(this.targetPoint(3),this.entryPoint(3)))%note it starts from left-bottom-corner
projectionPointStart = [this.targetPoint(2) projectionPoint(2)];
projectionPointEnd = [this.targetPoint(3) projectionPoint(3)];
posLineColor = [1 0 0];
elseif(projectionPoint(3) > max(this.entryPoint(3),this.targetPoint(3)))
projectionPointStart = [this.entryPoint(2) projectionPoint(2)];
projectionPointEnd = [this.entryPoint(3) projectionPoint(3)];
posLineColor = [1 0 0];
end%if
% Start to Plot what needs to be plotted
handle.CurrentPositionObject = CurrentPositionObject;
% this.plotHandleHashMap(1.0) = CurrentPositionObject;
this.onOrthogonalProjectionPlot(keyVal, graphicsHandle, pointStart, pointEnd, projectionPointStart, projectionPointEnd, posLineColor, handle);
end%fcn-initPlotSagital
% 'Callback' is called from inherited 2D-plot-methods (see plotableImage) to start
% plotting
function onOrthogonalProjectionPlot(this, keyVal, graphicsHandle, pointStart, pointEnd, projectionPointStart, projectionPointEnd, posLineColor, handle)
if(this.show2DProjection)
%check if exists a handle for this axes. if yes only change
%currentPosition line
if(isKey(this.plotHandleHashMap,double(keyVal)))
%kill old handle (graphic in axes)
value = values(this.plotHandleHashMap,{double(keyVal)});
try
handlesFromHgGroup = get(value{1}.ProjectionHandle, 'Children'); %two-childs: first->curPosLine, second->electrode
hgGroup = value{1}.ProjectionHandle;
% update the line
handlesFromHgGroup(1).XData = projectionPointStart;
handlesFromHgGroup(1).YData = projectionPointEnd;
catch
end
else%if not perform whole plot
% TODO:add- on these two points for dragging/moving
% them and so change the trajectory
graphicsHandles.entryPoint = line(pointStart(1),pointEnd(1), 'Marker', ...
'o','Color',this.color,'LineStyle','none',...
'MarkerSize', this.diameter, 'Parent', graphicsHandle);
% set(graphicsHandles.entryPoint, 'Parent', graphicsHandle);
graphicsHandles.targetPoint = line(pointStart(2),pointEnd(2), 'Marker', ...
'o','Color',this.color,'LineStyle','none',...
'MarkerSize', this.diameter, 'Parent', graphicsHandle);
% set(graphicsHandles.targetPoint, 'Parent', graphicsHandle);
graphicsHandles.electrode = line(pointStart,pointEnd, 'Marker', ...
this.marker,'Color',this.color,'LineStyle',this.lineStyle,...
'MarkerSize', this.diameter, 'Parent', graphicsHandle);
% set(graphicsHandles.electrode, 'Parent', graphicsHandle);
graphicsHandles.currentPosLine = line(projectionPointStart,projectionPointEnd, 'Marker', ...
this.marker,'Color',posLineColor,'LineStyle','-',...
'MarkerSize', this.diameter, 'Parent', graphicsHandle);
% set(graphicsHandles.currentPosLine, 'Parent', graphicsHandle);
handle.ProjectionHandle = graphicsHandle;
this.plotHandleHashMap(double(keyVal)) = handle; %speichere hggroup in HashMap
end%if
set(keyVal, 'DataAspectRatio',[1 1 1], ...
'PlotBoxAspectRatioMode','auto');
set(keyVal, 'Position', [0 0 1 1]); %fill whole axis
% if show2DProjection-Flag ist not set, kill all
else
% this.onHelpDeleteItemsInHashMap({keyVal});
end%if
end%fcn-onOrthogonalProjectionPlot
function onUpdatePlots(this, ~, ~)
this.updatePlot3D;
this.updatePlot2D;
end%fcn-onUpdatePlots
%TODO: think about removing this configurable part. not needed
%anymore
function panel = getConfigPanel(this, varargin)
% stepSize = 0.5;
% if(this.trajectoryLength > 0)
% sliderStepSize = [stepSize, stepSize] / this.trajectoryLength;
% else
% error('TestElectrodes:getConfigPanel', 'trajectory lenght have to be greater than zero');
% end%if
parent = findArg('Parent', varargin{:});
panel = uiextras.Panel('Parent',parent,'Title','TestElectrode','Padding', 3);
vBox = uiextras.VBox('Parent',double(panel), 'Spacing', 3);
%horizontal box for checkboxes
checkBoxBox = uiextras.HBox('Parent', vBox, 'Spacing', 3);
uicontrol('Parent',checkBoxBox,'Style','checkbox', ...
'Callback', @this.onCheckBoxTestElectrodeClicked, ...
'String', '2D-Projection', ...
'Value', this.show2DProjection);
HBoxBox = uiextras.HBox('Parent', vBox, 'Spacing', 2);
uicontrol('Parent', HBoxBox,'Style','pushbutton',...
'String', 'transfrom',...
'Callback', @this.onTransformationClicked);
uicontrol('Parent', HBoxBox,'Style','pushbutton',...
'String', 'save',...
'Callback', @this.onSaveClicked);
% uicontrol('Parent', vBox,'Style','slider', ...
% 'Min', 0, 'Max', this.trajectoryLength, 'SliderStep', [0.1 0.5] ./ this.trajectoryLength, ...
% 'Value', 0, 'Callback', @this.sliderMoved);
% set(HBoxBox,'sizes',[-1,-1]);
end%fcn-getConfigPanel
function onCheckBoxTestElectrodeClicked(this, src, ~)
val = get(src, 'Value');
if(isequal(val,1))
this.show2DProjection = 1;
this.updatePlot2D();
else
this.show2DProjection = 0;
this.onHelpDeleteItemsInHashMap();
end%if
end%fcn-onCheckBoxTestElectrodeClicked
function onTransformationClicked(this, ~ ,~)
[fileName,pathName] = uigetfile({'*.nii*'},'Select the target System (only RigidMni and RigidIntraCT)');
[folder, ~, ~] = fileparts(fullfile(pathName, fileName));
[folderWithoutRefSys, ref] = fileparts(folder);
if(~(isequal(ref,'rigidMni') || isequal(ref,'rigidIntraCT')))
HintWindow('At the moment there is only a transformation between RigidMni and RigidIntraCT possible. Please choose a target Image from either one of this Reference-Systems');
return
end%if
[~,patId] = fileparts(folderWithoutRefSys);
% if !=reverse % transfrom from RigidIntraCT -> RigidMni
reverse = 1 - isequal(ref,'rigidMni');
points2RigidMni = {this.entryPoint, this.targetPoint};
transformedPointsInMmfromRigidIntraCtToRigidMni = transformPointsFromRigidIntraCTToRigidMni(patId, points2RigidMni,reverse);
[entry, target] = transformedPointsInMmfromRigidIntraCtToRigidMni{:};
this.entryPoint = entry;
this.targetPoint = target;
end%fcn-onTransformationClicked
function onSaveClicked(this, ~, ~)
[fileName, pathName] = uiputfile({[this.toString, '.ele']},'Select Path to store the trajectory');
save(fullfile(pathName,fileName), 'this'); % save as mat-file
end%fcn-onSaveClicked
function delete(this) %HN:if an testelectrode is deleted, so this method guarantees that all plots will be deleted$added 16.4.14
delete@plotableImage(this); % call superclass destructor
delete@plotable3D(this); % call superclass destructor
% delete@Trajectory(this);
end%
end
methods(Access=public)
function onHelpDeleteItemsInHashMap(this, keyVal)
if(nargin < 2)
keyVal = this.plotHandleHashMap.keys();
end%if
if(isKey(this.plotHandleHashMap,keyVal))
value = values(this.plotHandleHashMap,keyVal);
for i=1:length(value)
try
handlesFromHgGroup = get(value{i}.ProjectionHandle, 'Children'); %two-childs: first->curPosLine, second->electrode
% handlesFromHgGroup = get(value{1}.ProjectionHandle; %two-childs: first->curPosLine, second->electrode
delete(handlesFromHgGroup);
catch e
disp(['TestElectrodes:onHelpDeleteItemsInHashMap:CantGetItem']);
end%try/catch
end%for
% remove(this.plotHandleHashMap, keyVal);
end%if
end%fcn-onHelpDeleteItemsInHashMap
end%methods-private
end%class
%%
function test()
elec = TestElectrodes([0; 150; 200], [80;111; 67]); %RAI
elec.intersections = [1 12 2 0 -5; 10 6 6 6 6]; % =[tg1c tg1a tg1p tg1l tg1r; tg2c tg2a tg2p tg2l tg2r]
elec.initPlot3D(gca);
nii = NiftiSegmentationSubvolume('segmentation_swan_fb.nii');
nii.initPlot3D(gca);
nii.pointCloudInMm('SNr+STN_L')
% d = elec.electrodesTargetPoints
% e = elec.electrodesEntryPoints
% tg = elec.getIntersectionPointCloud
% scatter3(d(1,:),d(2,:),d(3,:), 'b*')
% camtarget(d(:,1));
% hold on
% scatter3(e(1,:),e(2,:),e(3,:), 'g*')
%
% scatter3(tg(1,:),tg(2,:),tg(3,:), 'r')
% parentAxes = gca;
% line([tg(1,1:5); tg(1,6:10)], ...
% [tg(2,1:5); tg(2,6:10)], ...
% [tg(3,1:5); tg(3,6:10)], ...
% 'LineWidth', 2.0,...
% 'Color', 'r',...
% 'Parent', parentAxes)
end
|
github
|
adhusch/PaCER-master
|
runTestSuite.m
|
.m
|
PaCER-master/test/base/runTestSuite.m
| 5,712 |
utf_8
|
4381df966d287763eddc417175f5b48c
|
function [results, resultTable] = runTestSuite(testNames)
% This function runs all tests (i.e. files starting with 'test' in the
% CBTDIR/test/ folder and returns the status.
% It can distinguish between skipped and Failed tests. A test is considered
% to be skipped if it throws a COBRA:RequirementsNotMet error.
%
% INPUTS:
%
% testNames: only run tests matching the regexp given in testNames.
%
% OUTPUTS:
%
% results: A structure array with one entry per test and the following fields:
%
% - `.passed`: true if the test passed otherwise false
% - `.skipped`: true if the test was skipped otherwise false
% - `.failed`: true if the test failed, or was skipped, otherwise false
% - `.status`: a string representing the status of the test ('failed','skipped' or'passed')
% - `.fileName`: the fileName of the test
% - `.time`: the duration of the test (if passed otherwise NaN)
% - `.statusMessage`: Informative string about potential problems
% - `.Error`: Error message received from a failed or skipped test
% resultTable: A Table with details of the results.
%
% Author:
% - Thomas Pfau Jan 2018.
%
% NOTE:
% this function has been adapted from
% https://github.com/opencobra/cobratoolbox/blob/master/test/runTestSuite.m
% [5395578]
global PACERDIR
if ~exist('testNames','var')
testNames = '.*';
end
% go to the test directory.
testDir = [PACERDIR filesep 'test'];
currentDir = cd(testDir);
% get all names of test files
testFiles = rdir(['suite' filesep '**' filesep 'test*.m']);
testFileNames = {testFiles.name};
testFileNames = testFileNames(~cellfun(@(x) isempty(regexp(x,testNames,'ONCE')),testFileNames));
% save the current globals (all tests should have the same environment when
% starting) and path
environment = getEnvironment();
% save the current warning state
warnstate = warning();
% run the tests and show outputs.
for i = 1:numel(testFileNames)
% shut down any existing parpool.
try
% test if there is a parpool that we should shut down before the next test.
p = gcp('nocreate');
delete(p);
catch
% do nothing
end
% reset the globals
restoreEnvironment(environment)
% reset the warning state
warning(warnstate);
[~,file,ext] = fileparts(testFileNames{i});
testName = file;
fprintf('****************************************************\n\n');
fprintf('Running %s\n\n',testName);
results(i) = runScriptFile([file ext]);
fprintf('\n\n%s %s!\n',testName,results(i).status);
if ~results(i).passed
if results(i).skipped
fprintf('Reason:\n%s\n',results(i).statusMessage);
else
trace = results(i).Error.getReport();
tracePerLine = strsplit(trace,'\n');
testSuitePosition = find(cellfun(@(x) ~isempty(strfind(x, 'runTestSuite')),tracePerLine));
trace = sprintf(strjoin(tracePerLine(1:(testSuitePosition-7)),'\n')); % Remove the testSuiteTrace.
fprintf('Reason:\n%s\n',trace);
end
end
fprintf('\n\n****************************************************\n');
end
% create a table from the fields
resultTable= table({results.fileName}',{results.status}',[results.passed]',[results.skipped]',...
[results.failed]',[results.time]',{results.statusMessage}',...
'VariableNames',{'TestName','Status','Passed','Skipped','Failed','Time','Details'});
% change back to the original directory.
cd(currentDir)
end
function globals = getGlobals()
% Get all values of current globals in a struct.
% USAGE:
% globals = getGlobals()
%
% OUTPUT:
%
% globals: a struct of all global variables
globals = struct();
globalvars = who('global');
for i = 1:numel(globalvars)
globals.(globalvars{i}) = getGlobalValue(globalvars{i});
end
end
function resetGlobals(globals)
% Reset all global variables to a value stored in the input struct (all
% variables not present will be deleted.
% USAGE:
% resetGlobals(globals)
%
% INPUT:
% globals: A struct with 1 field per global variable.
globalvars = who('global');
globalsToDelete = setdiff(globalvars,fieldnames(globals));
for i = 1:numel(globalsToDelete)
clearGlobal(globalsToDelete{i});
end
% Note: we cannot clean functions as this would remove profiling information
% for everything else, check, if it changed
globalNames = fieldnames(globals);
for i = 1:numel(globalNames)
% set the global to the old value.
setGlobal(globalNames{i},globals.(globalNames{i}));
end
end
function setGlobal(globalName,globalValue)
% Safely set a global Variable to a specific value.
%
% USAGE:
% setGlobal(globalName,globalValue)
%
% INPUTS:
% globalName: A string representing the name of the global variable
% globalValue: The value to set the global variable to
eval([ globalName '_val = globalValue;']);
eval(['global ' globalName]);
eval([globalName ' = ' globalName '_val;']);
end
function clearGlobal(globalName)
% Safely clear a global variable.
%
% USAGE:
% clearGlobal(globalName)
%
% INPUTS:
% globalName: The name of the global variable to clear.
clearvars('-global',globalName);
end
function value = getGlobalValue(globalName)
% Safely get the Value of a global variable.
%
% USAGE:
% getGlobalValue(globalName)
%
% INPUTS:
% globalName: The name of the global variable to get the value for
eval(['global ' globalName]);
eval(['value = ' globalName ';']);
end
|
github
|
adhusch/PaCER-master
|
runScriptFile.m
|
.m
|
PaCER-master/test/base/runScriptFile.m
| 2,635 |
utf_8
|
153f68ed0516be2fe70535bcb1c9fe22
|
function result = runScriptFile(fileName)
% This function runs the test in fileName
% It can distinguish between skipped and Failed tests. A test is considered
% to be skipped if it throws a COBRA:RequirementsNotMet error.
%
% OUTPUTS:
%
% result: A structure array with the following fields:
%
% - `.passed`: true if the test passed otherwise false
% - `.skipped`: true if the test was skipped otherwise false
% - `.failed`: true if the test failed, or was skipped, otherwise false
% - `.status`: a string representing the status of the test ('failed','skipped' or'passed')
% - `.fileName`: the fileName of the test
% - `.time`: the duration of the test (if passed otherwise NaN)
% - `.statusMessage`: Informative string about potential problems.
% - `.Error`: Error message received from a failed or skipped test
%
% .. Author: - Thomas Pfau Jan 2018.
%
% NOTE:
% this function has been adapted from
% https://github.com/opencobra/cobratoolbox/blob/master/test/runScriptFile.m
% [b58da0c]
global CBT_MISSING_REQUIREMENTS_ERROR_ID
COBRA_TESTSUITE_TESTFILE = fileName;
% get the timinig (and hope these values are not overwritten.
COBRA_TESTSUITE_STARTTIME = clock();
try
% run the file
executefile(fileName);
catch ME
% vatch errors and interpret them
clearvars -except ME COBRA_TESTSUITE_STARTTIME COBRA_TESTSUITE_TESTFILE CBT_MISSING_REQUIREMENTS_ERROR_ID
scriptTime = etime(clock(), COBRA_TESTSUITE_STARTTIME);
result = struct('status', 'failed', 'failed', true, 'passed', false, 'skipped', false, 'fileName', ...
COBRA_TESTSUITE_TESTFILE, 'time', scriptTime, 'statusMessage', 'fail', 'Error', ME);
if strcmp(ME.identifier, CBT_MISSING_REQUIREMENTS_ERROR_ID)
% requirement missing, so the test was skipped.
result.status = 'skipped';
result.skipped = true;
result.failed = false;
result.statusMessage = ME.message;
else
% actual error in the test.
result.skipped = false;
result.status = 'failed';
result.statusMessage = ME.message;
end
return
end
% get the timinig.
scriptTime = etime(clock(), COBRA_TESTSUITE_STARTTIME);
result = struct('status', 'passed', 'failed', false, 'passed', true, 'skipped', false, 'fileName', ...
COBRA_TESTSUITE_TESTFILE, 'time', scriptTime, 'statusMessage', 'success', 'Error', MException('', ''));
end
function executefile(fileName)
% runs a script file (used to separate workspaces)
run(fileName)
end
|
github
|
timy/texmacs-master
|
struct2tree.m
|
.m
|
texmacs-master/plugins/octave/octave/convert/struct2tree.m
| 1,242 |
utf_8
|
9f26e9205c9c9067a4bfb8553933311a
|
###############################################################################
##
## MODULE : struct2tree.m
## DESCRIPTION : Convert an Octave structure to a Scheme tree
## COPYRIGHT : (C) 2002 Michael Graffam [email protected]
##
## This software falls under the GNU general public license version 3 or later.
## It comes WITHOUT ANY WARRANTY WHATSOEVER. For details, see the file LICENSE
## in the root directory or <http://www.gnu.org/licenses/gpl-3.0.html>.
function ret= struct2tree (n,name)
global TMCOLORS;
global TMCOLIDX;
# Make sure name is defined
if ((nargin<2))
name= with_mode_math ("(big \"triangleup\")");
endif
keycolor= deblank (TMCOLORS(1,:));
valcolor= deblank (TMCOLORS(TMCOLIDX,:));
colored_name= with_color (keycolor, name);
ret=["(tree ", colored_name, " "];
for [val, key] = n
colored_key= with_color (keycolor, dquote (key));
colored_val= with_color (valcolor, obj2scm(val));
switch (typeinfo (val))
case {"struct", "scalar struct"}
## Itemize the new struct, and switch the key color
ret1= struct2tree (val, key);
otherwise
ret1= colored_val;
endswitch
ret= [ret,ret1];
endfor
ret= [ret,")"];
endfunction
|
github
|
timy/texmacs-master
|
list2scm.m
|
.m
|
texmacs-master/plugins/octave/octave/convert/list2scm.m
| 482 |
utf_8
|
baf6d9f7b9af571a525917a5b65e83ca
|
## Released under the GNU General Public License, see www.gnu.org
## Copyright (C) 2002 by the Free Software Foundation
## Written by Michael Graffam [email protected]
##
## Convert an Octave list to a Scheme expression
## Created: Sept 2002
function ret= list2scm (L,c)
if (nargin<2)
c=1;
endif
ret= "(enumerate-numeric (document";
len= length(L);
for i=1:len
ret= [ret, " (concat (item) ", obj2scm(nth(L,i),c),")"];
endfor
ret= [ret,"))"];
endfunction
|
github
|
timy/texmacs-master
|
num2scm.m
|
.m
|
texmacs-master/plugins/octave/octave/convert/num2scm.m
| 1,513 |
utf_8
|
d77aec1970ad05ef2e853a573ee7227e
|
###############################################################################
##
## MODULE : with_mode_math.m
## DESCRIPTION : with mode math
## COPYRIGHT : (C) 2002 Michael Graffam [email protected]
## 2020 Darcy Shen
##
## This software falls under the GNU general public license version 3 or later.
## It comes WITHOUT ANY WARRANTY WHATSOEVER. For details, see the file LICENSE
## in the root directory or <http://www.gnu.org/licenses/gpl-3.0.html>.
function ret= num2scm (n)
switch (typeinfo (n))
case ("complex scalar")
real_str= num2str (real (n));
imag_str= num2str (abs (imag (n)));
if (imag (n) >= 0)
op= "+";
else
op= "-";
endif
if (real (n) != 0)
ret= with_mode_math ([real_str, op, imag_str, "<cdot><b-i>"]);
elseif (imag (n) < 0)
ret= with_mode_math ([op, imag_str, "<cdot><b-i>"]);
else
ret= with_mode_math ([imag_str, "<cdot><b-i>"]);
endif
case ("int32 scalar")
ret= with_mode_math (int2str (n));
case ("int64 scalar")
ret= with_mode_math (int2str (n));
case ("scalar")
if (isfloat (n) && n == 0.0)
ret= with_mode_math (dquote ("0.0"));
else
tmp= disp (n);
ret= with_mode_math (dquote (strtrim (tmp)));
endif
case ("bool")
if (n)
ret= with_mode_math ("true");
else
ret= with_mode_math ("false");
endif
otherwise
ret= "";
endswitch
endfunction
|
github
|
timy/texmacs-master
|
struct2scm.m
|
.m
|
texmacs-master/plugins/octave/octave/convert/struct2scm.m
| 740 |
utf_8
|
bfdc4117310dc51f3e569ac9d8208d2f
|
###############################################################################
##
## MODULE : struct2scm.m
## DESCRIPTION : Convert an Octave structure to Scheme
## COPYRIGHT : (C) 2002 Michael Graffam [email protected]
##
## This software falls under the GNU general public license version 3 or later.
## It comes WITHOUT ANY WARRANTY WHATSOEVER. For details, see the file LICENSE
## in the root directory or <http://www.gnu.org/licenses/gpl-3.0.html>.
function ret= struct2scm (n,a,b)
global TMSTRUCT;
if (TMSTRUCT) # Bullets!
if ((nargin<2)||(a<6))
a= 1;
endif
ret= struct2bullet (n, a);
else # Tree
if (nargin<3)
b= "name";
endif
ret= struct2tree (n, b);
endif
endfunction
|
github
|
timy/texmacs-master
|
mat2scm.m
|
.m
|
texmacs-master/plugins/octave/octave/convert/mat2scm.m
| 794 |
utf_8
|
eec54a59f5ad49b67922cc197ec17461
|
###############################################################################
##
## MODULE : mat2scm.m
## DESCRIPTION : Convert a matrix to a Scheme expression
## COPYRIGHT : (C) 2002 Michael Graffam [email protected]
## 2020 Darcy Shen
##
## This software falls under the GNU general public license version 3 or later.
## It comes WITHOUT ANY WARRANTY WHATSOEVER. For details, see the file LICENSE
## in the root directory or <http://www.gnu.org/licenses/gpl-3.0.html>.
function ret= mat2scm (M)
ret= "(matrix (tformat (table";
[r,c]= size(M);
for i=1:r
ret= [ret,"(row "];
for j=1:c
ret= [ret, "(cell ", num2scm(M(i,j)), ") "];
endfor
ret= [ret,") "];
endfor
ret= [ret,")))"];
ret= with_mode_math (ret, true);
endfunction
|
github
|
timy/texmacs-master
|
cell2scm.m
|
.m
|
texmacs-master/plugins/octave/octave/convert/cell2scm.m
| 647 |
utf_8
|
7583547dffe3aba68bac4cb9a4cd7372
|
###############################################################################
##
## MODULE : cell2scm.m
## DESCRIPTION : Convert an Octave cell to scheme code
## COPYRIGHT : (C) 2020 Darcy Shen
##
## This software falls under the GNU general public license version 3 or later.
## It comes WITHOUT ANY WARRANTY WHATSOEVER. For details, see the file LICENSE
## in the root directory or <http://www.gnu.org/licenses/gpl-3.0.html>.
function ret= cell2scm (param)
len= length (param);
ret= "(enumerate-numeric (document";
for i= 1:len
ret= [ret, " (concat (item) ", obj2scm(param{i}),")"];
endfor
ret= [ret,"))"];
endfunction
|
github
|
timy/texmacs-master
|
obj2scm.m
|
.m
|
texmacs-master/plugins/octave/octave/convert/obj2scm.m
| 1,225 |
utf_8
|
4a7f8bb4794fa65a39d1f4e9cf87f4ec
|
###############################################################################
##
## MODULE : obj2scm.m
## DESCRIPTION : Convert an Octave object to a Scheme expression
## COPYRIGHT : (C) 2002 Michael Graffam [email protected]
## 2004 Joris van der Hoeven
##
## This software falls under the GNU general public license version 3 or later.
## It comes WITHOUT ANY WARRANTY WHATSOEVER. For details, see the file LICENSE
## in the root directory or <http://www.gnu.org/licenses/gpl-3.0.html>.
function ret= obj2scm (n,c)
if (nargin<2)
c= 0;
endif
switch (typeinfo (n))
case {"range", "matrix", "complex matrix", "bool matrix", "char matrix", "diagonal matrix"}
ret= mat2scm (n);
case {"int32 scalar", "int64 scalar", "complex scalar", "scalar", "bool"}
ret= num2scm (n);
case {"scalar struct", "struct"}
ret= struct2scm (n, c+1, with_mode_math ("(big \"triangleup\")"));
case ("list")
ret= list2scm (n, c);
case ("cell")
ret= cell2scm (n);
case {"sq_string", "string"}
[r, c]= size(n);
if (r == 1)
ret = "";
else
ret= str2scm (n);
endif
otherwise
ret= "";
endswitch
endfunction
|
github
|
timy/texmacs-master
|
struct2bullet.m
|
.m
|
texmacs-master/plugins/octave/octave/convert/struct2bullet.m
| 1,118 |
utf_8
|
2857daa18a2fbcd0e77cfc9ea5343323
|
## Released under the GNU General Public License, see www.gnu.org
## Copyright (C) 2002 by the Free Software Foundation
## Written by Michael Graffam [email protected]
##
## Convert an Octave structure to a Scheme bulleted list
## Created: Sept 2002
function tmp= struct2bullet (n,c)
global TMCOLORS;
global TMCOLIDX;
# Constrain c to 1:TMCOLIDX, and insure it is defined
if ((nargin<2) || (c>TMCOLIDX))
c=1;
endif
color= deblank (TMCOLORS(c,:)); ## Pick a color, any color
## Use arrows first then we itemize with bullets
if (c==1)
tmp= "(itemize-arrow (document ";
else
tmp= "(itemize (document ";
endif
for [val, key]= n
switch (typeinfo (val))
case {"struct", "scalar struct"}
## Itemize the new struct, and switch the key color
tmp1= ["(concat (item) ", with_color (color, dquote ([key, " = "])), " ", struct2bullet (val, c+1), ")"];
otherwise
tmp1= ["(concat (item) ", with_color (color, dquote ([key, " = "])), " ", obj2scm (val, c), ")"];
endswitch
tmp= [tmp, tmp1];
endfor
tmp= [tmp, "))"];
endfunction
|
github
|
timy/texmacs-master
|
str2scm.m
|
.m
|
texmacs-master/plugins/octave/octave/convert/str2scm.m
| 758 |
utf_8
|
d80e929f7aa82b79b73977108110b0e0
|
###############################################################################
##
## MODULE : obj2scm.m
## DESCRIPTION : Convert an Octave string to a Scheme string
## COPYRIGHT : (C) 2002 Michael Graffam [email protected]
## 2021 Darcy Shen [email protected]
##
## This software falls under the GNU general public license version 3 or later.
## It comes WITHOUT ANY WARRANTY WHATSOEVER. For details, see the file LICENSE
## in the root directory or <http://www.gnu.org/licenses/gpl-3.0.html>.
function ret= str2scm (n)
[r, c]= size(n);
ret= "(stack (tformat (table";
for i=1:r
ret= [ret,"(row "];
ret= [ret, "(cell ", dquote(n(i, :)), ") "];
ret= [ret,") "];
endfor
ret= [ret,")))"];
endfunction
|
github
|
timy/texmacs-master
|
flush_prompt.m
|
.m
|
texmacs-master/plugins/octave/octave/protocol/flush_prompt.m
| 503 |
utf_8
|
55ae70ad994f54a989f1a1c22455d00e
|
###############################################################################
##
## MODULE : flush_prompt.m
## DESCRIPTION : change the prompt
## COPYRIGHT : (C) 2020 Darcy Shen
##
## This software falls under the GNU general public license version 3 or later.
## It comes WITHOUT ANY WARRANTY WHATSOEVER. For details, see the file LICENSE
## in the root directory or <http://www.gnu.org/licenses/gpl-3.0.html>.
function flush_prompt (prompt)
flush_any (["prompt#", prompt]);
endfunction
|
github
|
timy/texmacs-master
|
flush_scheme.m
|
.m
|
texmacs-master/plugins/octave/octave/protocol/flush_scheme.m
| 515 |
utf_8
|
5943dbd50416e4434044bc7886fbe853
|
###############################################################################
##
## MODULE : flush_scheme.m
## DESCRIPTION : flush scheme content to stdout
## COPYRIGHT : (C) 2020 Darcy Shen
##
## This software falls under the GNU general public license version 3 or later.
## It comes WITHOUT ANY WARRANTY WHATSOEVER. For details, see the file LICENSE
## in the root directory or <http://www.gnu.org/licenses/gpl-3.0.html>.
function flush_scheme (scheme)
flush_any (["scheme:", scheme]);
endfunction
|
github
|
timy/texmacs-master
|
flush_verbatim.m
|
.m
|
texmacs-master/plugins/octave/octave/protocol/flush_verbatim.m
| 526 |
utf_8
|
5367c26aea9aed1e687ae1252beda0a8
|
###############################################################################
##
## MODULE : flush_verbatim.m
## DESCRIPTION : flush verbatim content to stdout
## COPYRIGHT : (C) 2020 Darcy Shen
##
## This software falls under the GNU general public license version 3 or later.
## It comes WITHOUT ANY WARRANTY WHATSOEVER. For details, see the file LICENSE
## in the root directory or <http://www.gnu.org/licenses/gpl-3.0.html>.
function flush_verbatim (content)
flush_any (["verbatim:", content]);
endfunction
|
github
|
timy/texmacs-master
|
flush_file.m
|
.m
|
texmacs-master/plugins/octave/octave/protocol/flush_file.m
| 496 |
utf_8
|
ef97a2e40cab4118a779f72ea0d89122
|
###############################################################################
##
## MODULE : flush_file.m
## DESCRIPTION : flush file to TeXmacs
## COPYRIGHT : (C) 2020 Darcy Shen
##
## This software falls under the GNU general public license version 3 or later.
## It comes WITHOUT ANY WARRANTY WHATSOEVER. For details, see the file LICENSE
## in the root directory or <http://www.gnu.org/licenses/gpl-3.0.html>.
function flush_file (path)
flush_any (["file:", path]);
endfunction
|
github
|
timy/texmacs-master
|
with_color.m
|
.m
|
texmacs-master/plugins/octave/octave/protocol/with_color.m
| 527 |
utf_8
|
27e4ab8c5e08e9436e428422e3ec6dc2
|
###############################################################################
##
## MODULE : with_color.m
## DESCRIPTION : with color
## COPYRIGHT : (C) 2020 Darcy Shen
##
## This software falls under the GNU general public license version 3 or later.
## It comes WITHOUT ANY WARRANTY WHATSOEVER. For details, see the file LICENSE
## in the root directory or <http://www.gnu.org/licenses/gpl-3.0.html>.
function ret= with_color (color, content)
ret= sprintf('(with "color" "%s" %s)', color, content);
endfunction
|
github
|
timy/texmacs-master
|
flush_any.m
|
.m
|
texmacs-master/plugins/octave/octave/protocol/flush_any.m
| 590 |
utf_8
|
c0b082f9a81bca5f55192f54b096d9f4
|
###############################################################################
##
## MODULE : flush_any.m
## DESCRIPTION : flush any content to stdout
## COPYRIGHT : (C) 2020 Darcy Shen
##
## This software falls under the GNU general public license version 3 or later.
## It comes WITHOUT ANY WARRANTY WHATSOEVER. For details, see the file LICENSE
## in the root directory or <http://www.gnu.org/licenses/gpl-3.0.html>.
function flush_any (output)
DATA_BEGIN= 2;
DATA_END= 5;
surrounded= sprintf ("%c%s%c", DATA_BEGIN, output, DATA_END);
printf (surrounded);
endfunction
|
github
|
timy/texmacs-master
|
with_mode_math.m
|
.m
|
texmacs-master/plugins/octave/octave/protocol/with_mode_math.m
| 662 |
utf_8
|
5a4afc1c0e0510d43dd6f4cfac9c7fef
|
###############################################################################
##
## MODULE : with_mode_math.m
## DESCRIPTION : with mode math
## COPYRIGHT : (C) 2020 Darcy Shen
##
## This software falls under the GNU general public license version 3 or later.
## It comes WITHOUT ANY WARRANTY WHATSOEVER. For details, see the file LICENSE
## in the root directory or <http://www.gnu.org/licenses/gpl-3.0.html>.
function ret= with_mode_math (content, math_display= false)
if (math_display)
ret= sprintf('(with "mode" "math" "math-display" "true" %s)', content);
else
ret= sprintf('(with "mode" "math" %s)', content);
endif
endfunction
|
github
|
timy/texmacs-master
|
tmplot.m
|
.m
|
texmacs-master/plugins/octave/octave/tm/tmplot.m
| 2,044 |
utf_8
|
59b6600858a421ac723e61e580be5e93
|
###############################################################################
##
## MODULE : tmplot.m
## DESCRIPTION : TeXmacs plotting interface
## v 0.5 Aug 2018
## v 0.6 Nov 2019 - added Windows compatibility, added plot
## windows visibility, switched form sleep
## (obsolete) to pause
## COPYRIGHT : (C) 2003 Michael Graffam [email protected]
## 2018-2019 Lorenzo Lunelli
## 2020 Darcy Shen
##
## This software falls under the GNU general public license version 3 or later.
## It comes WITHOUT ANY WARRANTY WHATSOEVER. For details, see the file LICENSE
## in the root directory or <http://www.gnu.org/licenses/gpl-3.0.html>.
function ret= tmplot ()
ret= false;
# Set the platform dependent $TEXMACS_OCTAVE_TMP
if (ispc ())
TEXMACS_OCTAVE_TMP= [getenv("TEMP"), filesep, "tmplot.eps"];
else
TEXMACS_OCTAVE_TMP= ["/tmp", filesep, "tmplot.eps"];
endif
global TEXMACS_OCTAVE_PLUGIN_CONTROL;
h= gcf ();
# Set the visibility of the plotting
if (bitget (TEXMACS_OCTAVE_PLUGIN_CONTROL, 2) == 0) # check bit 2 state (figure visibility off)
set (h, "visible", "off");
endif
if (bitget (TEXMACS_OCTAVE_PLUGIN_CONTROL, 2) == 1) # check bit 2 state (figure visibility on)
set (h, "visible", "on");
endif
if (sizeof (get (h, "currentaxes")) != 0) # there is a figure with a plot
if (bitget (TEXMACS_OCTAVE_PLUGIN_CONTROL, 1) == 1) # check bit 1 state (plotting mode): interactive mode, only show the figure
pause (0.1); # this seems to be necessary on Linux
refresh (h);
refresh (h); # Cygwin: this seems to be necessary to update the image (the same behavior happens in octave)
else
if (exist (TEXMACS_OCTAVE_TMP) == 2)
delete (TEXMACS_OCTAVE_TMP);
endif
print (h, TEXMACS_OCTAVE_TMP, "-deps", "-color");
flush_file (TEXMACS_OCTAVE_TMP);
ret= true;
endif
endif
endfunction
|
github
|
timy/texmacs-master
|
complete.m
|
.m
|
texmacs-master/plugins/octave/octave/tm/complete.m
| 723 |
utf_8
|
717c8f0732da48821fa9dbcf165a6660
|
###############################################################################
##
## MODULE : complete.m
## DESCRIPTION : Tab Completion
## COPYRIGHT : (C) 2021 Darcy Shen
##
## This software falls under the GNU general public license version 3 or later.
## It comes WITHOUT ANY WARRANTY WHATSOEVER. For details, see the file LICENSE
## in the root directory or <http://www.gnu.org/licenses/gpl-3.0.html>.
function ret= complete (key)
lf= lookfor (key);
ret = ["(tuple ", "\"", key, "\""];
for cmd=lf
if length(cmd{1}) > length(key) && starts_with (cmd{1}, key)
part= substr(cmd{1}, length(key) + 1);
ret= [ret, " ", "\"", part, "\""];
endif
endfor
ret = [ret, ")"];
endfunction
|
github
|
timy/texmacs-master
|
tmmod.m
|
.m
|
texmacs-master/plugins/octave/octave/tm/tmmod.m
| 3,264 |
utf_8
|
d297d88f96d7f5d2387e3cd45e228a25
|
###############################################################################
##
## MODULE : tmmod.m
## DESCRIPTION : This function set the environment variable that determines the
## octave plugin behavior (presently, only the interactive use of
## octave plots in TeXmacs)
## COPYRIGHT : (C) 2018-2019 Lorenzo Lunelli
## (C) 2020 Darcy Shen
##
## This software falls under the GNU general public license version 3 or later.
## It comes WITHOUT ANY WARRANTY WHATSOEVER. For details, see the file LICENSE
## in the root directory or <http://www.gnu.org/licenses/gpl-3.0.html>.
function info= tmmod (choice)
# 1 Sept 2018: bit 1 controls the plotting mode (0 normal, 1 interactive)
# 1 Nov 2019: bit 2 controls visibility of octave figure during drawing (0 hidden, 1 visible)
global TEXMACS_OCTAVE_PLUGIN_CONTROL; # 28-August 2018: now using global variables - 1 Sept 2018: changed variable name
if (nargin>0) # change the plugin mode
if (strcmpi (choice,'i') || choice==1) # ----------------------------- INTERACTIVE MODE -------------------------
TEXMACS_OCTAVE_PLUGIN_CONTROL= bitset (TEXMACS_OCTAVE_PLUGIN_CONTROL,2,1); # set bit 2 to 1, figures are visible
TEXMACS_OCTAVE_PLUGIN_CONTROL= bitset (TEXMACS_OCTAVE_PLUGIN_CONTROL,1,1); # set bit 1 (the lowest) to 1
message= "-- TeXmacs OctaveX plugin: set interactive plotting mode";
message= char (message,"-- in some cases you need to use 'refresh()' to update the octave window");
message= char (message,"-- use tmfig to load a figure in the document");
message= char (message,"-- use tmmod('n'|'i')) to change plotting mode");
elseif (strcmpi (choice,'n') || choice==0) # ----------------------------- NORMAL MODE --------------------------
TEXMACS_OCTAVE_PLUGIN_CONTROL=bitset(TEXMACS_OCTAVE_PLUGIN_CONTROL,1,0); # set bit 1 (the lowest) to 0
if (any (strcmp("qt", graphics_toolkit()))) # Lorenzo added 1-9-2019, check if qt graphic toolkit is active
TEXMACS_OCTAVE_PLUGIN_CONTROL=bitset(TEXMACS_OCTAVE_PLUGIN_CONTROL,2,0); # set bit 2 to 0: figures are hidden
endif
message= "-- TeXmacs OctaveX plugin: set normal plotting mode";
message= char(message,"-- use tmmod('n'|'i') to change plotting mode");
elseif (strcmpi (choice,'_v_')) # --------------- figures are visible --------------------------------------------
TEXMACS_OCTAVE_PLUGIN_CONTROL= bitset(TEXMACS_OCTAVE_PLUGIN_CONTROL,2,1); # set bit 2 to 1
message= "Octave figure visible";
elseif (strcmpi (choice,'_h_')) # --------------- figures are hidden ---------------------------------------------
TEXMACS_OCTAVE_PLUGIN_CONTROL= bitset(TEXMACS_OCTAVE_PLUGIN_CONTROL,2,0); # set bit 2 to 0
message= "Octave figure hidden";
else
message= 'please use a valid option';
endif
else # check the plotting mode
if (bitget (TEXMACS_OCTAVE_PLUGIN_CONTROL,1)==0) # check bit 1 state (plotting mode)
message= "current plotting mode is normal";
endif
if (bitget (TEXMACS_OCTAVE_PLUGIN_CONTROL,1)==1) # check bit 1 state (plotting mode)
message= "current plotting mode is interactive";
endif
endif
info= message;
endfunction
|
github
|
timy/texmacs-master
|
plot_cmds.m
|
.m
|
texmacs-master/plugins/octave/octave/tm/plot_cmds.m
| 1,125 |
utf_8
|
1502426e3fcad2b3b79f3928e1f043f9
|
###############################################################################
##
## MODULE : plot_cmds.m
## DESCRIPTION : Return a list of plot cmds
## COPYRIGHT : (C) 2021 Darcy Shen
##
## This software falls under the GNU general public license version 3 or later.
## It comes WITHOUT ANY WARRANTY WHATSOEVER. For details, see the file LICENSE
## in the root directory or <http://www.gnu.org/licenses/gpl-3.0.html>.
function ret= plot_cmds()
octave_home= OCTAVE_HOME();
ind= 0;
ret= cell();
for x= strsplit (path(), pathsep)
p = x{1};
if (starts_with (p, octave_home) &&
(ends_with (p, ["m", filesep, "plot", filesep, "appearance"]) ||
ends_with (p, ["m", filesep, "plot", filesep, "draw"]) ||
ends_with (p, ["m", filesep, "image"])))
files= glob ([p, filesep, "*.m"]);
[r, c]= size(files);
for i=1:r
name= substr (files{i}, length(p)+2);
if (ends_with (name, ".m") && !starts_with (name, "__"))
ind= ind+1;
ret{ind}= substr (name, 1, length (name) - 2);
endif
endfor
endif
endfor
endfunction
|
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