Working implementation with multiple contrast output. Need to test wh…

…ether batch system works as expected. Note that input images are no longer denoising method specific.

hmri_denoising.m

@@ -1,15 +1,14 @@
-function varargout = hmri_denoising(job)
+function varargout = hmri_denoising(jobsubj)
 
 % retrieve effective acquisition & processing parameters
-jobsubj = job.subj;
-denoisedout = get_denoising_params(jobsubj);
+denoising_params = get_denoising_params(jobsubj);
 protocolfield = fieldnames(jobsubj.denoisingtype);
 denoising_protocol = protocolfield{1};
 
 % execute the chosen denoising method and define output
 switch denoising_protocol
     case 'lcpca_denoise'
-        [output_mag, output_phase] = hmri_calc_lcpcadenoise(denoisedout);
+        [output_mag, output_phase] = hmri_calc_lcpcadenoise(denoising_params);
         varargout{1} = output_mag;
         varargout{2} = output_phase;
 end
@@ -61,20 +60,22 @@
 [v,r] = spm('Ver');
 denoising_params.SPMver = sprintf('%s (%s)', v, r);
 
+% Load input data
+denoising_params.mag_img = cellstr(char(spm_file(jobsubj.mag_img,'number','')));
+denoising_params.phase_img = cellstr(char(spm_file(jobsubj.phase_img,'number','')));
+denoising_params.phase_bool = any(~cellfun(@isempty, denoising_params.phase_img));
+denoising_params.mag_bool = any(~cellfun(@isempty, denoising_params.mag_img));
+
+% processing can continue if only magnitude images were entered but
+% only warn that optional phase img are missing
+if ~denoising_params.phase_bool || ~isfield(jobsubj,'phase_img')
+    hmri_log('Warning: No (optional) phase images were entered, denoising will continue with only magnitude images', denoising_params.defflags);
+end
+
 % Denoising method-specific parameters
 % Load all the batch entered and possibly user-modified parameters
 switch denoising_protocol
     case 'lcpca_denoise'
-        denoising_params.mag_img = cellstr(char(spm_file(jobsubj.denoisingtype.(denoising_protocol).mag_img,'number','')));
-        denoising_params.phase_img = cellstr(char(spm_file(jobsubj.denoisingtype.(denoising_protocol).phase_img,'number','')));
-        denoising_params.phase_bool = any(~cellfun(@isempty, denoising_params.phase_img));
-        denoising_params.mag_bool = any(~cellfun(@isempty, denoising_params.mag_img));
-
-        % processing can continue if only magnitude images were entered but
-        % only warn that optional phase img are missing
-        if ~denoising_params.phase_bool || ~isfield(jobsubj.denoisingtype.(denoising_protocol),'phase_img')
-            hmri_log('Warning: No (optional) phase images were entered, Lcpca-denoising continues with only magnitude images', denoising_params.defflags);
-        end
 
         dnstruct = jobsubj.denoisingtype.lcpca_denoise;
         denoising_params.ngbsize = dnstruct.ngbsize;

hmri_run_denoising.m

@@ -8,17 +8,24 @@
 
 end
 
-function out = hmri_denoising_local(job)
+function out = hmri_denoising_local(jobsubj)
 
-% Get denoising protocol
-dntype=fieldnames(job.subj.denoisingtype);
+% concatenate all contrasts into jobsubj.mag_img and phase_img
+contrasts = {'pdw','t1w','mtw'};
+jobsubj.mag_img = {};
+jobsubj.phase_img = {};
+for c = 1:length(contrasts)
+    con = contrasts{c};
+    jobsubj.mag_img = [jobsubj.mag_img; jobsubj.(con).mag_img];
+    jobsubj.phase_img = [jobsubj.phase_img; jobsubj.(con).phase_img];
+end
 
 % Case indir versus outdir
 try
-    outpath = job.subj.output.outdir{1}; % case outdir
+    outpath = jobsubj.output.outdir{1}; % case outdir
     if ~exist(outpath,'dir'); mkdir(outpath); end
 catch
-    Pin = char(job.subj.denoisingtype.(dntype{1}).mag_input);
+    Pin = char(jobsubj.mag_img);
     outpath = fileparts(Pin(1,:)); % case indir
 end
 
@@ -52,41 +59,41 @@
 supplpath = fullfile(outpath, 'Results', 'Supplementary');
 if ~exist(supplpath,'dir'); mkdir(supplpath); end
 
-% save all these paths in the job.subj structure
-job.subj.path.dnrespath = respath;
-job.subj.path.respath = respath;
-job.subj.path.supplpath = supplpath;
+% save all these paths in the jobsubj structure
+jobsubj.path.dnrespath = respath;
+jobsubj.path.respath = respath;
+jobsubj.path.supplpath = supplpath;
 
 % save log file location
-job.subj.log.logfile = fullfile(supplpath, 'hMRI_denoising_logfile.log');
-job.subj.log.flags = struct('LogFile',struct('Enabled',true,'FileName','hMRI_denoising_logfile.log','LogDir',supplpath), ...
-    'PopUp',job.subj.popup,'ComWin',true);
-flags = job.subj.log.flags;
+jobsubj.log.logfile = fullfile(supplpath, 'hMRI_denoising_logfile.log');
+jobsubj.log.flags = struct('LogFile',struct('Enabled',true,'FileName','hMRI_denoising_logfile.log','LogDir',supplpath), ...
+    'PopUp',jobsubj.popup,'ComWin',true);
+flags = jobsubj.log.flags;
 flags.PopUp = false;
 hmri_log(sprintf('\t============ DENOISING MODULE - %s.m (%s) ============', mfilename, datetime('now')),flags);
 
 if newrespath
     hmri_log(sprintf(['WARNING: existing results from previous run(s) were found, \n' ...
-        'the output directory has been modified. It is now:\n%s\n'],outpath),job.subj.log.flags);
+        'the output directory has been modified. It is now:\n%s\n'],outpath),jobsubj.log.flags);
 else
     hmri_log(sprintf('INFO: the output directory is:\n%s\n',outpath),flags);
 end
 
 % check basic requirements and error if basic requirements fail
-check_params.mag_input = cellstr(char(spm_file(job.subj.denoisingtype.(dntype{1}).mag_input,'number','')));
-check_params.phase_input = cellstr(char(spm_file(job.subj.denoisingtype.(dntype{1}).phase_input,'number','')));
-check_params.phase_bool = any(~cellfun(@isempty, check_params.phase_input));
-check_params.mag_bool = any(~cellfun(@isempty, check_params.mag_input));
+check_params.mag_img = cellstr(char(spm_file(jobsubj.mag_img,'number','')));
+check_params.mag_bool = any(~cellfun(@isempty, check_params.mag_img));
+check_params.phase_img = cellstr(char(spm_file(jobsubj.phase_img,'number','')));
+check_params.phase_bool = any(~cellfun(@isempty, check_params.phase_img));
 
 % Issue an error and abort in cases of non-existent magnitude image data and
 % non-equal number of non-empty phase and magnitude images
-if ~check_params.mag_bool || ~isfield(job.subj.denoisingtype.(dntype{1}),'mag_input')
+if ~check_params.mag_bool || ~isfield(jobsubj,'mag_img')
     msg = 'No magnitude images were entered, aborting! Please check your input data and try again!';
     hmri_log(msg, flags);
     error(msg)
 end
 
-if check_params.phase_bool && (length(check_params.mag_input) ~= length(check_params.phase_input))
+if check_params.phase_bool && (length(check_params.mag_img) ~= length(check_params.phase_img))
     msg = 'The number of phase and magnitude images are different, please check your input data and try again!';
     hmri_log(msg, flags);
     error(msg)
@@ -95,47 +102,31 @@
 % save SPM version (slight differences may appear in the results depending
 % on the SPM version!)
 [v,r] = spm('Ver');
-job.SPMver = sprintf('%s (%s)', v, r);
+jobsubj.SPMver = sprintf('%s (%s)', v, r);
 
 % save original job to supplementary directory
-spm_jsonwrite(fullfile(supplpath,'hMRI_denoising_job.json'),job,struct('indent','\t'));
+spm_jsonwrite(fullfile(supplpath,'hMRI_denoising_job.json'),jobsubj,struct('indent','\t'));
 
 % run the denoising and collect the results
 hmri_log(sprintf('\t============ %s - %s.m (%s) ============',"APPLYING DENOISING", mfilename, datetime('now')),flags);
 
-% concatenate all contrasts into jobsubj.denoisingtype.(denoising_protocol).mag_img and phase_img
-contrasts = {'mtw','pdw','t1w'};
-jobsubj.denoisingtype.(dntype{1}).mag_img = {};
-jobsubj.denoisingtype.(dntype{1}).phase_img = {};
-for c = 1:length(contrasts)
-    con = contrasts{c};
-
-    jobsubj.denoisingtype.(dntype{1}).mag_img = 
-        [jobsubj.denoisingtype.(dntype{1}).mag_img;
-        jobsubj.denoisingtype.(dntype{1}).(con).mag_img];
-
-    jobsubj.denoisingtype.(dntype{1}).phase_img = 
-        [jobsubj.denoisingtype.(dntype{1}).phase_img;
-        jobsubj.denoisingtype.(dntype{1}).(con).phase_img];
-end
-
 % run the denoising
-[output_mag, output_phase] = hmri_denoising(job);
+[output_mag, output_phase] = hmri_denoising(jobsubj);
 
 % assign output dependencies to denoised output images of separate contrasts
 iMag = 1;
 iPhase = 1;
 for c = 1:length(contrasts)
     con = contrasts{c};
 
-    nMag = length(jobsubj.denoisingtype.(dntype{1}).(con).mag_img);
+    nMag = length(jobsubj.(con).mag_img);
     idxstr = ['DenoisedMagnitude' con];
-    out.subj.(idxstr) = output_mag(iMag:iMag+nMag);
+    out.(idxstr) = output_mag(iMag:iMag+nMag-1);
     iMag = iMag + nMag;
 
-    nPhase = length(jobsubj.denoisingtype.(dntype{1}).(con).phase_img);
+    nPhase = length(jobsubj.(con).phase_img);
     idxstr = ['DenoisedPhase' con];
-    out.subj.(idxstr) = output_phase(iPhase:iPhase+nPhase);
+    out.(idxstr) = output_phase(iPhase:iPhase+nPhase-1);
     iPhase = iPhase + nPhase;
 end
 

tbx_cfg_hmri.m

@@ -10,7 +10,7 @@
 % Bogdan Draganski & Ferath Kherif, 2011
 % ======================================================================
 
-if ~isdeployed, 
+if ~isdeployed
     hMRIpath = fileparts(mfilename('fullpath'));
     addpath(hMRIpath);
     addpath(fullfile(hMRIpath, 'config'));
@@ -43,6 +43,6 @@
     'and will include a number of (as yet unspecified) extensions in ',...
     'future updates.  Please report any bugs or problems to [email protected].']
     }';
-hmri.values  = {tbx_scfg_hmri_config tbx_scfg_hmri_dicom_import tbx_scfg_hmri_autoreorient tbx_scfg_hmri_imperf_spoil tbx_scfg_hmri_B1_create tbx_scfg_hmri_create tbx_scfg_hmri_quality tbx_scfg_hmri_proc tbx_scfg_hmri_QUIQI tbx_scfg_hmri_denoising};
+hmri.values  = {tbx_scfg_hmri_config tbx_scfg_hmri_dicom_import tbx_scfg_hmri_denoising tbx_scfg_hmri_autoreorient tbx_scfg_hmri_imperf_spoil tbx_scfg_hmri_B1_create tbx_scfg_hmri_create tbx_scfg_hmri_quality tbx_scfg_hmri_proc tbx_scfg_hmri_QUIQI};
 end
 

tbx_scfg_hmri_denoising.m

@@ -80,7 +80,8 @@
 mag_img.help    = {'Select the (required) magnitude images to be denoised'};
 mag_img.filter  = 'image';
 mag_img.ufilter = '.*';
-mag_img.num     = [1 Inf];
+mag_img.num     = [0 Inf];
+mag_img.val     = {''};
 
 % ---------------------------------------------------------------------
 % Phase input images
@@ -99,22 +100,28 @@
 % ---------------------------------------------------------------------
 mtw      = cfg_branch;
 mtw.tag  = 'mtw';
-mtw.name = 'MTw input';
+mtw.name = 'MTw input (optional)';
 mtw.help = {'Input Magnitude/Phase images from MTw data'};
 mtw.val  = {mag_img phase_img};
 
-pdw      = cfg_branch;
-pdw.tag  = 't1w';
-pdw.name = 'T1w input';
-pdw.help = {'Input Magnitude/Phase images from PDw data'};
-pdw.val  = {mag_img phase_img};
-
 t1w      = cfg_branch;
-t1w.tag  = 'pdw';
-t1w.name = 'PDw input';
+t1w.tag  = 't1w';
+t1w.name = 'T1w input (optional)';
 t1w.help = {'Input Magnitude/Phase images from T1w data'};
 t1w.val  = {mag_img phase_img};
 
+% PDw is required input
+pdw_mag_img = mag_img;
+pdw_mag_img.num = [1 Inf];
+pdw_mag_img.val = {};
+
+pdw      = cfg_branch;
+pdw.tag  = 'pdw';
+pdw.name = 'PDw input';
+pdw.help = {'Input Magnitude/Phase images from PDw data', ...
+    'If you only have one kind of weighting, please put them here.'};
+pdw.val  = {pdw_mag_img phase_img};
+
 % ---------------------------------------------------------------------
 % Standard deviation parameter
 % ---------------------------------------------------------------------
@@ -152,7 +159,7 @@
 denoisinginput_lcpca.help = {'Input Magnitude/Phase images for Lcpca-denoising'
     ['Regarding processing parameters, you can either stick with metadata and standard ' ...
     'defaults parameters (recommended) or select your own hmri_denoising_local_defaults_*.m customised defaults file.']};
-denoisinginput_lcpca.val  = {mtw pdw t1w DNparameters std ngbsize};
+denoisinginput_lcpca.val  = {DNparameters std ngbsize};
 
 % ---------------------------------------------------------------------
 % menu denoisingtype
@@ -211,7 +218,7 @@
 subj.tag        = 'subj';
 subj.name       = 'Subject';
 subj.help       = {'Specify a subject for denoising.'};
-subj.val        = {output denoisingtype popup};
+subj.val        = {output pdw t1w mtw denoisingtype popup};
 
 % ---------------------------------------------------------------------
 % data Data
@@ -251,7 +258,7 @@
 
 % iterate to generate dependency tags for outputs
 nsub = numel(job.subj);
-contrasts = {'mtw','pdw','t1w'};
+contrasts = {'pdw','t1w','mtw'};
 ncon = length(contrasts);
 dep = repmat(cfg_dep,1,2*ncon*nsub);
 for i=1:nsub
@@ -261,15 +268,15 @@
 
         % define variables and initialize cfg_dep for magnitude images
         cdep            = cfg_dep;
-        cdep.sname      = sprintf('lcpcaDenoised_%s_magnitude',con);
+        cdep.sname      = sprintf('Denoised_%s_magnitude',con);
         idxstr = ['DenoisedMagnitude' con];
         cdep.src_output = substruct('.','subj','()',{i},'.',idxstr,'()',{':'});
         cdep.tgt_spec   = cfg_findspec({{'filter','image','strtype','e'}});
         dep((i-1)*ncon+k) = cdep;
 
         % define variables and initialize cfg_dep for phase images
         cdep            = cfg_dep;
-        cdep.sname      = sprintf('lcpcaDenoised_%s_phase',con);
+        cdep.sname      = sprintf('Denoised_%s_phase',con);
         idxstr = ['DenoisedPhase' con];
         cdep.src_output = substruct('.','subj','()',{i},'.',idxstr,'()',{':'});
         cdep.tgt_spec   = cfg_findspec({{'filter','image','strtype','e'}});