[BUG FIX] - Osprey GUI - Crash for MEGA data - Gaelle Doucet

GUI generated job crashes for MEGA data. This was related to the edit target and include metabolite cells. Additionally, fixed process plots for dcm plots. Release preparation.
schorschinho · Jun 24, 2022 · a9d1296 · a9d1296
1 parent 6062789
commit a9d1296
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Showing 20 changed files with 69 additions and 54 deletions.
diff --git a/GUI/Osprey.m b/GUI/Osprey.m
@@ -30,7 +30,7 @@
 logoFcn = @()imread('osprey.png', 'BackgroundColor', gui.colormap.Background);
 logoBanner = uiw.utility.loadIcon(logoFcn);
 % Here the intro banner is created
-gui.d = uiw.dialog.About('Name', 'Osprey','Version','2.2.0','Date', 'April 12, 2022',...
+gui.d = uiw.dialog.About('Name', 'Osprey','Version','2.3.0','Date', 'June 24, 2022',...
 'Timeout', 3,'CustomText', 'Osprey is provided by Johns Hopkins University.',...
 'ContactInfo', '[email protected]','LogoCData', logoBanner);
 

diff --git a/GUI/osp_Toolbox_Check.m b/GUI/osp_Toolbox_Check.m
@@ -32,7 +32,7 @@
 %       2020-05-15: First version of the code.
 %% % 1. SAVE OSPREY VERSION%%%
 %%% 1. SAVE OSPREY VERSION%%%
-OspreyVersion = 'Osprey 2.2.0';
+OspreyVersion = 'Osprey 2.3.0';
 fprintf(['Timestamp %s ' OspreyVersion '  ' Module '\n'], datestr(now,'mmmm dd, yyyy HH:MM:SS'));
 hasSPM = 1; % For the compiled GUI
 %% % 2. GET SPMPATH AND TOOLBOXES%%%

diff --git a/GUI/osp_onLoad.m b/GUI/osp_onLoad.m
@@ -65,7 +65,7 @@
     osp_iniLoadWindow(gui);
     gui.layout.b_load.Enable = 'off';
     gui.layout.b_proc.Enable = 'on';
-    if MRSCont.flags.hasSPM == 1
+    if MRSCont.flags.hasSPM == 1 &&  ~isempty(MRSCont.files_nii)
         gui.layout.b_coreg.Enable = 'on';
     end
     gui.layout.ListBox.Enable = 'on';

diff --git a/fit/OspreyFit.m b/fit/OspreyFit.m
@@ -81,7 +81,7 @@
     if MRSCont.flags.hasRef
         refFitTime = tic;
         % Loop over all the datasets here
-        for kk = 1:MRSCont.nDatasets
+        for kk = 1:MRSCont.nDatasets(1)
             [~] = printLog('OspreyFitRef',kk,1,MRSCont.nDatasets,progressText,MRSCont.flags.isGUI ,MRSCont.flags.isMRSI);
             if ~(MRSCont.flags.didFit == 1 && MRSCont.flags.speedUp && isfield(MRSCont, 'fit') && (kk > length(MRSCont.fit.results.ref.fitParams))) || ~strcmp(MRSCont.ver.Osp,MRSCont.ver.CheckOsp)
                 [MRSCont] = osp_fitWater(MRSCont, kk, 'ref');
@@ -101,7 +101,7 @@
     if MRSCont.flags.hasWater
         waterFitTime = tic;
         % Loop over all the datasets here
-        for kk = 1:MRSCont.nDatasets
+        for kk = 1:MRSCont.nDatasets(1)
             [~] = printLog('OspreyFitWater',kk,1,MRSCont.nDatasets,progressText,MRSCont.flags.isGUI ,MRSCont.flags.isMRSI);
             if ~(MRSCont.flags.didFit == 1 && MRSCont.flags.speedUp && isfield(MRSCont, 'fit') && (kk > length(MRSCont.fit.results.w.fitParams))) || ~strcmp(MRSCont.ver.Osp,MRSCont.ver.CheckOsp)
                 [MRSCont] = osp_fitWater(MRSCont, kk, 'w');

diff --git a/fit/osp_fitHERCULES.m b/fit/osp_fitHERCULES.m
@@ -32,7 +32,7 @@
 else
     progressText = '';
 end
-for kk = 1:MRSCont.nDatasets
+for kk = 1:MRSCont.nDatasets(1)
     [~] = printLog('OspreyFit',kk,1,MRSCont.nDatasets,progressText,MRSCont.flags.isGUI ,MRSCont.flags.isMRSI); 
     %%% 1. DETERMINE THE FITTING STYLE %%%
     % Extract fit options

diff --git a/fit/osp_fitHERMES.m b/fit/osp_fitHERMES.m
@@ -32,7 +32,7 @@
 else
     progressText = '';
 end
-for kk = 1:MRSCont.nDatasets
+for kk = 1:MRSCont.nDatasets(1)
     [~] = printLog('OspreyFit',kk,1,MRSCont.nDatasets,progressText,MRSCont.flags.isGUI ,MRSCont.flags.isMRSI); 
     %%% 1. DETERMINE THE FITTING STYLE %%%
     % Extract fit options

diff --git a/fit/osp_fitInitialise.m b/fit/osp_fitInitialise.m
@@ -155,7 +155,7 @@
         end
 
         % Determine the scaling factor between data and basis set for each dataset
-        for kk = 1:MRSCont.nDatasets
+        for kk = 1:MRSCont.nDatasets(1)
             if ~MRSCont.flags.isMRSI  && ~MRSCont.flags.isPRIAM
                 if ~MRSCont.flags.isUnEdited
                     dataToScale   = op_takesubspec(MRSCont.processed.metab{kk},1);

diff --git a/fit/osp_fitUnEdited.m b/fit/osp_fitUnEdited.m
@@ -41,7 +41,7 @@
     basisSet_mm = fit_selectMetabs(basisSet_mm, metabList_mm, 1);
 end
 
-for kk = 1:MRSCont.nDatasets
+for kk = 1:MRSCont.nDatasets(1)
 
 
     % ----- Osprey fit pipeline -----

diff --git a/job/CreateOspreyJob.mlapp b/job/CreateOspreyJob.mlapp
diff --git a/job/CreateOspreyJob_app.m b/job/CreateOspreyJob_app.m
@@ -404,7 +404,6 @@ function H2OReferenceButtonPushed(app, event)
         % Button pushed function: H2OShortTEButton
         function H2OShortTEButtonPushed(app, event)
             info = 'Please select the water short-TE file to read';
-            [fname,pathname]=uigetfile('*.*',info);
 
             ndata = app.NumberofdatasetsEditField.Value;
 
@@ -492,7 +491,7 @@ function StatcsvFileButtonPushed(app, event)
 
             csvfiles = spm_select(ndata,'any',info,{},pwd,'.csv','1');
 
-            app.StatcsvEditField.Value = svfiles(1,:);
+            app.StatcsvEditField.Value = csvfiles(1,:);
         end
 
         % Button pushed function: basissetfileButton

diff --git a/job/OspreyJob.m b/job/OspreyJob.m
@@ -256,7 +256,7 @@
         error('Invalid job file! A job file needs to specify an output folder.');
     end
     if isfield(jobStruct, 'file_stat')
-        outputFolder = jobStruct.file_stat{1};
+        file_stat = jobStruct.file_stat{1};
     else
         '';
     end
@@ -307,10 +307,13 @@
         MRSCont.opts.ECC.mm = str2num(jobStruct.ECCmm);
     end
     if isfield(jobStruct,'MM3coModel')
-        MRSCont.opts.fit.coMM3 = jobStruct.MM3coModel;
+        opts.fit.coMM3 = jobStruct.MM3coModel;
     end
     if isfield(jobStruct,'FWHMMM3co')
-        MRSCont.opts.fit.FWHMcoMM3= num2str(jobStruct.FWHMMM3co);
+        opts.fit.FWHMcoMM3= str2num(jobStruct.FWHMMM3co);
+        if isempty(opts.fit.FWHMcoMM3) || strcmp(opts.fit.FWHMcoMM3,' ')
+            opts.fit.FWHMcoMM3 = 14;
+        end
     end
     if isfield(jobStruct,'saveLCM')
         MRSCont.opts.saveLCM = str2num(jobStruct.saveLCM);
@@ -445,6 +448,11 @@
             MRSCont.opts.fit.coMM3 = 'none';
             MRSCont.opts.fit.FWHMcoMM3 = 14;
         end
+        if isfield(MRSCont.opts.fit, 'FWHMcoMM3')
+            if isempty(MRSCont.opts.fit.FWHMcoMM3)
+                MRSCont.opts.fit.FWHMcoMM3 = 14;
+            end
+        end
         if ~isfield(MRSCont.opts.fit, 'GAP')
             MRSCont.opts.fit.GAP.A = [];
             MRSCont.opts.fit.GAP.diff1 = [];
@@ -703,7 +711,7 @@
 %%% 7. SET FLAGS AND VERSION %%%
 MRSCont.flags.didJob        = 1;
 MRSCont.loadedJob           = jobFile;
-MRSCont.ver.Osp             = 'Osprey 2.2.0';
+MRSCont.ver.Osp             = 'Osprey 2.3.0';
 
 
 %%% 8. CHECK IF OUTPUT STRUCTURE ALREADY EXISTS IN OUTPUT FOLDER %%%

diff --git a/job/osp_create_job_file.m b/job/osp_create_job_file.m
@@ -32,11 +32,11 @@
 fprintf(fid,'\n\t%s',['"seqType": "' app.SequenceTypeDropDown.Value '",']);
 
 if strcmp(app.SequenceTypeDropDown.Value,'MEGA')
-    fprintf(fid,'\n\t%s',['"editTarget": "' app.EditingTargetsDropDown.Value '",']);
+    fprintf(fid,'\n\t%s',['"editTarget": ["' app.EditingTargetsDropDown.Value '"],']);
 end
 if strcmp(app.SequenceTypeDropDown.Value,'HERMES') || strcmp(app.SequenceTypeDropDown.Value,'HERCULES')
     if strcmp(app.EditingTargetsDropDown.Value, 'GABA, GSH')
-        fprintf(fid,'\n\t%s',['"editTarget": "''GABA'',''GSH''",']);
+        fprintf(fid,'\n\t%s',['"editTarget": ["GABA","GSH"],']);
     end
 end
 
@@ -107,7 +107,7 @@
         fprintf(fid,'%s','],');
 
     otherwise
-        fprintf(fid,'\n\t%s',['"includeMetabs": "' app.IncludedMetabolitesDropDown.Value '",']);
+        fprintf(fid,'\n\t%s',['"includeMetabs": ["' app.IncludedMetabolitesDropDown.Value '"],']);
 end
 
 fprintf(fid,'\n\t%s',['"style": "' app.FittingStyleDropDown.Value '",']);

diff --git a/libraries/FID-A/fitTools/fitModels/Osprey/fit_Osprey.m b/libraries/FID-A/fitTools/fitModels/Osprey/fit_Osprey.m
@@ -181,7 +181,7 @@
         [fitParamsStep2] = fit_OspreyPrelimStep2(dataToFitRef, resBasisSet, minKnotSpacingPPM, fitRangePPM, fitParamsStep1, refFWHM,fitOpts.GAP);    
     end
 else
-    if fitOpts.GaussLBMM 
+    if fitOpts.GaussLBMM && resBasisSet.nMM == 1 % We only want to use a separate gaussian parameter for the single MM functions
         [fitParamsStep2] = fit_OspreyPrelimStep2MMExp(dataToFitRef, resBasisSet, minKnotSpacingPPM, fitRangePPM, fitParamsStep1, refFWHM,fitOpts.GAP); 
     else
         [fitParamsStep2] = fit_OspreyPrelimStep2(dataToFitRef, resBasisSet, minKnotSpacingPPM, fitRangePPM, fitParamsStep1, refFWHM,fitOpts.GAP);   

diff --git a/libraries/FID-A/processingTools/op_rmempty.m b/libraries/FID-A/processingTools/op_rmempty.m
@@ -16,29 +16,30 @@
 
 function [out]=op_rmempty(in)
 
-if in.flags.averaged
-    error('ERROR:  Spectra have already been averaged!  Aborting!');
-end
-
-% If the standard deviation of an FID is ~0, this FID row is empty.
-% Find the indices of the averages with non-zero standard deviations -
-% these are the ones that will be 
-idx_nonzeroFID = find(std(in.fids,0,1)>1e-40);
-nonzero_fids = in.fids(:,idx_nonzeroFID);
-
-%re-calculate Specs using fft
-nonzero_specs=fftshift(fft(nonzero_fids,[],in.dims.t),in.dims.t);
-
-%recalculate the sz vector
-sz=size(nonzero_fids);
-
-% 
-%FILLING IN DATA STRUCTURES
-out=in;
-out.fids=nonzero_fids;
-out.specs=nonzero_specs;
-out.sz=sz;
-out.averages=sz(2);
-
-%FILLING IN THE FLAGS
-out.flags=in.flags;
+if ~in.flags.averaged
+
+    % If the standard deviation of an FID is ~0, this FID row is empty.
+    % Find the indices of the averages with non-zero standard deviations -
+    % these are the ones that will be 
+    idx_nonzeroFID = find(std(in.fids,0,1)>1e-40);
+    nonzero_fids = in.fids(:,idx_nonzeroFID);
+
+    %re-calculate Specs using fft
+    nonzero_specs=fftshift(fft(nonzero_fids,[],in.dims.t),in.dims.t);
+
+    %recalculate the sz vector
+    sz=size(nonzero_fids);
+
+    % 
+    %FILLING IN DATA STRUCTURES
+    out=in;
+    out.fids=nonzero_fids;
+    out.specs=nonzero_specs;
+    out.sz=sz;
+    out.averages=sz(2);
+
+    %FILLING IN THE FLAGS
+    out.flags=in.flags;
+else
+    out = in;
+end
diff --git a/plot/osp_plotLoad.m b/plot/osp_plotLoad.m
@@ -296,6 +296,9 @@
 else if MRSCont.flags.isMEGA && (strcmp(which, 'w') || strcmp(which, 'ref')|| strcmp(which, 'mm_ref'))
     axesHandles.A = gca();
     nAvgs = dataToPlot.averages;
+    if nAvgs > dataToPlot.sz(dataToPlot.dims.averages)
+        nAvgs =dataToPlot.sz(dataToPlot.dims.averages);
+    end
     % Loop over all averages
     for rr = 1:nAvgs
         plot(axesHandles.A, dataToPlot.ppm, real(dataToPlot.specs(:,rr)) + rr*stag, 'k', 'LineWidth', 0.5, 'Color',MRSCont.colormap.Foreground);

diff --git a/plot/osp_plotRaincloud.m b/plot/osp_plotRaincloud.m
@@ -94,9 +94,9 @@
 if ~strcmp(quant,'Quality')
     ind = find(strcmp(MRSCont.overview.FitSpecNamesStruct.metab,model));  
     quant_ind = [basis ind(1)];
-    names_list = MRSCont.quantify.names.metab{quant_ind};
+    names_list = MRSCont.quantify.names.metab{quant_ind(2)};
     idx_1  = find(strcmp(names_list,metab));
-    metabolite_conc = MRSCont.quantify.tables.metab.(quant).(['Voxel_' num2str(VoxelIndex)]){quant_ind};
+    metabolite_conc = MRSCont.quantify.tables.metab.(quant).(['Voxel_' num2str(VoxelIndex)]){quant_ind(2)};
     ConcData = metabolite_conc{:,idx_1};  
 else
    quality = {'SNR','FWHM','freqShift'};

diff --git a/plot/osp_plotScatter.m b/plot/osp_plotScatter.m
@@ -74,9 +74,9 @@
 ind = find(strcmp(MRSCont.overview.FitSpecNamesStruct.metab,model));
 quant_ind = [basis ind(1)];
 
-names_list = MRSCont.quantify.names.metab{quant_ind};
+names_list = MRSCont.quantify.names.metab{quant_ind(2)};
 idx_1  = find(strcmp(names_list,metab));
-metabolite_conc = MRSCont.quantify.tables.metab.(quant).(['Voxel_' num2str(VoxelIndex)]){quant_ind};
+metabolite_conc = MRSCont.quantify.tables.metab.(quant).(['Voxel_' num2str(VoxelIndex)]){quant_ind(2)};
 ConcData = metabolite_conc{:,idx_1}; 
 
 
@@ -89,7 +89,7 @@
 if ischar(corrData)
     metabFlag = 1;
     idx_1  = find(strcmp(names_list,corrData));
-    metabolite_conc = MRSCont.quantify.tables.metab.(quant).(['Voxel_' num2str(VoxelIndex)]){quant_ind};
+    metabolite_conc = MRSCont.quantify.tables.metab.(quant).(['Voxel_' num2str(VoxelIndex)]){quant_ind(2)};
     corrData = metabolite_conc{:,idx_1};  
 end
 

diff --git a/process/OspreyProcess.m b/process/OspreyProcess.m
@@ -155,6 +155,10 @@
                     raw_w.flags.averaged    = 1;
                     raw_w.dims.averages     = 0;
                 end
+
+                if raw_w.subspecs > 1
+                    raw_w = combine_water_subspecs(raw_w);
+                end
                 if ~MRSCont.flags.isMRSI
                     [raw_w,~]                       = op_eccKlose(raw_w, raw_w);        % Klose eddy current correction
                 else

diff --git a/utilities/CompileOspreyStandalone.m b/utilities/CompileOspreyStandalone.m
@@ -168,7 +168,7 @@ function CompileOspreyStandalone(OutputDir,SPM12Dir,WidgetsDir,GUILayoutDir)
     'OutputDir',OutputDirHBCD,...
     'ExecutableIcon',fullfile(OspreyDir, 'graphics','osprey.gif'),...
     'ExecutableSplashScreen',fullfile(OspreyDir, 'graphics','osprey.gif'),...
-    'ExecutableVersion','2.2.0',...
+    'ExecutableVersion','2.3.0',...
     'ExecutableName','OspreyHBCD',...
     'AdditionalFiles',{ fullfile(SPM12Dir),...
                        fullfile(OspreyDir,'coreg'),...
@@ -225,7 +225,7 @@ function CompileOspreyStandalone(OutputDir,SPM12Dir,WidgetsDir,GUILayoutDir)
     'OutputDir',OutputDirCmd,...
     'ExecutableIcon',fullfile(OspreyDir, 'graphics','osprey.gif'),...
     'ExecutableSplashScreen',fullfile(OspreyDir, 'graphics','osprey.gif'),...
-    'ExecutableVersion','2.2.0',...
+    'ExecutableVersion','2.3.0',...
     'ExecutableName','OspreyCMD',...
     'AdditionalFiles',{ fullfile(SPM12Dir),...
                        fullfile(OspreyDir,'coreg'),...
@@ -264,7 +264,7 @@ function CompileOspreyStandalone(OutputDir,SPM12Dir,WidgetsDir,GUILayoutDir)
         'OutputDir',OutputDirGUI,...
         'ExecutableIcon',fullfile(OspreyDir, 'graphics','osprey.gif'),...
         'ExecutableSplashScreen',fullfile(OspreyDir, 'graphics','osprey.gif'),...
-        'ExecutableVersion','2.2.0',...
+        'ExecutableVersion','2.3.0',...
         'ExecutableName','Osprey',...
         'AdditionalFiles',{fullfile(WidgetsDir),...
                            fullfile(GUILayoutDir),...

diff --git a/utilities/osp_CheckRunPreviousModule.m b/utilities/osp_CheckRunPreviousModule.m
@@ -74,7 +74,7 @@
 end
 
 %Do the toolbox check here
-OspreyVersion = 'Osprey 2.2.0';
+OspreyVersion = 'Osprey 2.3.0';
 hasSPM = 1;
 [hasSPM,OspreyVersion ] = osp_Toolbox_Check (module,MRSCont.flags.isGUI);