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poll_for_data_preproc.m
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function poll_for_data_preproc(SubjectID, sessionN, cfg)
% every 2 sec look for a file with a name template in a directory
% send New Data even to the listener
%listener will print got it and the volume number
% SubjectID='Phantom';
% sessionN=3;
ft_defaults
%ft_hastoolbox('spm8', 1);
if nargin <= 2
cfg = [];
end
% cfg.inputDir='C:\Users\eust_abbondanza\Documents\realtime\20130429_19720216VLRZ\Ser0003\';
% cfg.NrOfVols=50;
% cfg.TimeOut=6.0;
% cfg.output='C:\Documents\realtime\TEST\';
% % % cfg.maskpath='C:\Users\eust_abbondanza\Documents\MATLAB\attend'
% % % cfg.datapath='C:\Documents\realtime\';
% % % cfg.protocolpath='C:\Users\eust_abbondanza\Documents\MATLAB\';
%cfg.Classifier=2; %1 for SVM from PR tollbox, 2 for EN classifier
%cfg.blockDurVol=8;
%Cfg.name_templates='prepScan_*.nii';
%files = dir(fullfile(Cfg.inputDir,Cfg.name_templates));
%first non-dummy volume
%param = spm_normalise(cfg.mytemplate, cfg.ref_image, cfg.matname, defaults.normalise.estimate.weight,'',defaults.normalise.estimate);
if ~isfield(cfg, 'numDummy')
cfg.numDummy = 5; % number of dummy scans to drop
end
if ~isfield(cfg, 'NrOfVols')
cfg.NrOfVols=170;
end
if ~isfield(cfg, 'smoothFWHM')
cfg.smoothFWHM = 0; %8;
end
if ~isfield(cfg, 'correctMotion')
cfg.correctMotion = 1; %1;
end
if ~isfield(cfg, 'normalize2EPI')
cfg.normalize2EPI = 0; %1;
end
if ~isfield(cfg, 'correctSliceTime')
cfg.correctSliceTime = 1; %1;
end
if ~isfield(cfg, 'maskpath')
cfg.maskpath='C:\Users\eust_abbondanza\Documents\MATLAB\attend';
end
if ~isfield(cfg, 'Classifier')
cfg.Classifier=2; %1 for SVM from PR tollbox, 2 for EN classifier
end
if ~isfield(cfg, 'whichEcho')
cfg.whichEcho = 1;
else
if cfg.whichEcho < 1
error '"whichEcho" configuration field must be >= 1';
end
end
hist_file=sprintf('history_%s.mat', SubjectID);
if ~exist(hist_file, 'file')
history = struct('S',[], 'RRM', [], 'motion', []);
else
load(hist_file);
end
numTotal=cfg.numDummy+1;
numTrial = cfg.NrOfVols*(sessionN-1);
numProper = 0;
motEst = [];
waiting_time=0;
while 1 %length(files)
GrabVol=tic;
pause(0.2);
name_template=sprintf('Analyze%05d.hdr', numTotal);
%start timer
%after 1.5 sec check if there is a volume with a number
%close timer
target=dir(fullfile(cfg.inputDir,name_template));
if isempty(target)
fprintf('\nNo new data\n');
time=toc(GrabVol);
waiting_time=waiting_time +time
if waiting_time>cfg.TimeOut
break
end
else
% notify(H, 'NewData');
fprintf('\nAvailable volume %i\n', numTotal)
fname=fullfile(cfg.inputDir,name_template);
vol_hdr=spm_vol(fname);
% vol_vol=spm_read_vols(vol_hdr);
% dat=vol_vol(maskvol_vol>0);
dat=spm_read_vols(vol_hdr);
S=[];
S.TR=cfg.TR;
S.voxels=vol_hdr.dim;
S.voxdim=[3.0000 3.0000 3.600]; %vol_hdr.pixdim(1:3)
S.mat0=vol_hdr.mat;
S.numEchos=1;
S.vx=vol_hdr.dim(1);
S.vy=vol_hdr.dim(2);
S.vz=vol_hdr.dim(3);
inds=[(1:2:S.vz) (2:2:S.vz)];
S.deltaT = (0:(S.vz-1))*S.TR/S.vz;
S.deltaT(inds) = S.deltaT;
if isempty(S)
warning('No protocol information found!')
% restart loop
pause(0.5);
continue;
end
if cfg.whichEcho > S.numEchos
warning('Selected echo number exceeds the number of echos in the protocol.');
grabEcho = S.numEchos;
fprintf(1,'Will grab echo #%i of %i\n', grabEcho, S.numEchos);
else
grabEcho = 1;
end
% Prepare smoothing kernels based on configuration and voxel size
if cfg.smoothFWHM > 0
[smKernX, smKernY, smKernZ, smOff] = ft_omri_smoothing_kernel(cfg.smoothFWHM, S.voxdim);%ft_omri_smoothing_kernel(cfg.smoothFWHM, S.voxdim);
smKern = convn(smKernX'*smKernY, reshape(smKernZ, 1, 1, length(smKernZ)));
else
smKernX = [];
smKernY = [];
smKernZ = [];
smKern = [];
smOff = [0 0 0];
end
% store current info structure in history
numTrial = numTrial + 1;
history(numTrial).S = S;
disp(S)
fprintf(1,'Starting to process\n');
% numTotal = cfg.numDummy * S.numEchos;
% Loop this as long as the experiment runs with the same protocol (= data keeps coming in)
% determine number of samples available in buffer / wait for more than numTotal
% threshold.nsamples = numTotal + S.numEchos - 1;
%CHECK FUNCTION !!!!!!!!!!!!!!!
% % % newNum = ft_poll_buffer(cfg.input, threshold, 500);
% % %
% % % if newNum.nsamples < numTotal
% % % % scanning seems to have stopped - re-read header to continue with next trial
% % % break;
% % % end
% % % if newNum.nsamples < numTotal + S.numEchos
% % % % timeout -- go back to start of (inner) loop
% % % continue;
% % % end
% % %
% % % % this is necessary for ft_read_data
% % % hdr.nSamples = newNum.nsamples;
% % %
index = (cfg.numDummy + numProper) * S.numEchos + grabEcho;
fprintf('\nTrying to read %i. proper scan at sample index %d\n', numProper+1, index);
GrabSampleT = tic;
% % % try
% % % % read data from buffer (only the last scan)
% % % dat = ft_read_data(cfg.input, 'header', hdr, 'begsample', index, 'endsample', index);
% % % catch
% % % warning('Problems reading data - going back to poll operation...');
% % % continue;
% % % end
numProper = numProper + 1;
rawScan = single(reshape(dat, S.voxels));
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
% slice timing correction
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
if cfg.correctSliceTime
if numProper == 1
fprintf(1,'Initialising slice-time correction model...\n');
STM = ft_omri_slice_time_init(rawScan, S.TR, S.deltaT);
else
fprintf('%-30s','Slice time correction...');
tic;
[STM, procScan] = ft_omri_slice_time_apply(STM, rawScan);
toc
end
end
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
% motion correction
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
if cfg.correctMotion
doneHere = 0;
if numProper == 1
RRM=[];
for i=1:length(history)
if isequal(history(i).S, S)
fprintf(1,'Will realign scans to reference model from trial %i session ...\n', i);
% protocol the same => re-use realignment reference
RRM = history(i).RRM;
break;
end
end
% none found - setup new one
if isempty(RRM)
flags = struct('mat', S.mat0);
fprintf(1,'Setting up first num-dummy scan as reference volume...\n');
RRM = ft_omri_align_init(rawScan, flags); %RRM = ft_omri_align_init(rawScan, flags);
motEst = zeros(1,6);
curSixDof = zeros(1,6);
history(numTrial).RRM = RRM;
procScan = single(rawScan); % procScan = single(rawScan);
doneHere = 1;
end
end
if ~doneHere
fprintf('%-30s','Registration...');
tic;
[RRM, M, Mabs, procScan] = ft_omri_align_scan(RRM, procScan); % [RRM, M, Mabs, procScan] = ft_omri_align_scan(RRM, rawScan);
toc
curSixDof = hom2six(M);
motEst = [motEst; curSixDof.*[1 1 1 180/pi 180/pi 180/pi]];
end
else
procScan = single(procScan); % procScan = single(rawScan);
motEst = [motEst; zeros(1,6)];
end
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
% slice timing correction
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
% if cfg.correctSliceTime
% if numProper == 1
% fprintf(1,'Initialising slice-time correction model...\n');
% STM = ft_omri_slice_time_init(procScan, S.TR, S.deltaT);
% else
% fprintf('%-30s','Slice time correction...');
% tic;
% [STM, procScan] = ft_omri_slice_time_apply(STM, procScan);
% toc
% end
% end
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
% smoothing
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
if cfg.smoothFWHM > 0
fprintf('%-30s','Smoothing...');
tic;
% MATLAB convolution
%Vsm = convn(procScan,smKern);
%procScan = Vsm((1+smOff(1)):(end-smOff(1)), (1+smOff(2)):(end-smOff(2)), (1+smOff(3)):(end-smOff(3)));
% specialised MEX file
procScan = ft_omri_smooth_volume(single(procScan), smKernX, smKernY, smKernZ);
toc
end
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
% done with pre-processing, write output
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
if cfg.correctMotion
procSample = [single(procScan(:)) ; single(curSixDof')];
else
procSample = single(procScan(:));
% procSample = procScan(:);
end
procScan=flip(procScan, 2);
% procScan=spm_write_sn(procScan,param,defaults.normalise.write);
filename=sprintf('prepScan_%i.nii', numProper);
V=[];
run_path=sprintf('%s\\Ser%04d', cfg.dataPath, sessionN);
if ~exist(run_path, 'dir')
mkdir(run_path)
end
% if cfg.normalize2MNI==0
% procScan=flip(procScan, 2);
% end
V.fname=fullfile(run_path, filename);
V.pixdim=S.voxdim;
V.dt=[4 0];
V.x=S.vx;
V.y=S.vy;
V.z=S.vz;
V.mat=S.mat0;
V.dim=S.voxels;
% V.size=S.size;
% V.numEchos=S.numEchos;
V.TR=S.TR;
% V.deltaT=S.deltaT;
V.n=[1 1];
V.pinfo=[1 0 352]';
V=spm_create_vol(V);
spm_write_vol(V, procScan); %spm_create_vol
% V=spm_vol(Analyze_file)
% V=spm_write_vol(V, procScan)
% ft_write_data(cfg.output1, procSample, 'header', hdrOut, 'append', true);
%evr.sample = numProper;
%ft_write_event(cfg.output, evr);
fprintf('Done -- total time = %f\n', toc(GrabSampleT));
fprintf('Volume processed in %f\n', toc(GrabVol));
subplot(4,1,1);
plot(motEst(:,1:3));
subplot(4,1,2);
plot(motEst(:,4:6));
subplot(4,1,3);
slcImg = reshape(dat, [S.vx S.vy*S.vz]);
imagesc(slcImg);
colormap(gray);
subplot(4,1,4);
slcImg = reshape(procScan, [S.vx S.vy*S.vz]);
imagesc(slcImg);
colormap(gray);
% force Matlab to update the figure
drawnow
if numTotal==cfg.NrOfVols
% save('mot_corr_params.mat', 'RRM');
% save('motEstim.mat', 'motEst');
% save('SixDof.mat', 'curSixDof');
fname_hist=fullfile(cfg.output, sprintf('history_%s.mat', SubjectID));
save(fname_hist, 'history');
break;
else
numTotal = numTotal + S.numEchos;
end
% time=toc;
%write event
%addlistener(input_dir_search,'NewVol',my_omri_pipeline) %the listener gets the signal and starts the preprocessing, event.listener
%read event and print data received
end
end