Merge pull request #452 from schorschinho/develop

Prepare v2.3.0 release

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);
 

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%%%

GUI/osp_iniFitWindow.m

@@ -290,11 +290,11 @@ function osp_iniFitWindow(gui)
             waterFitRangeString = ['Fitting range: ' num2str(MRSCont.opts.fit.rangeWater(1)) ' to ' num2str(MRSCont.opts.fit.rangeWater(2)) ' ppm'];
             % Where are the metabolite names stored?
             if strcmp(gui.fit.Style, 'ref') || strcmp(gui.fit.Style, 'w')
-                basisSetNames = MRSCont.fit.resBasisSet.(gui.fit.Style).(['np_sw_' num2str(MRSCont.processed.metab{1}.sz(1)) '_' num2str(MRSCont.processed.metab{1}.spectralwidth)]){1,1}.name;
+                basisSetNames = MRSCont.fit.resBasisSet.(gui.fit.Style).(['np_sw_' num2str(round(MRSCont.processed.metab{1}.sz(1))) '_' num2str(round(MRSCont.processed.metab{1}.spectralwidth))]){1,1}.name;
             else if strcmp(gui.fit.Style, 'conc')
-                    basisSetNames = MRSCont.fit.resBasisSet.(gui.fit.Style).(['np_sw_' num2str(MRSCont.processed.metab{1}.sz(1)) '_' num2str(MRSCont.processed.metab{1}.spectralwidth)]){1,1}.name;
+                    basisSetNames = MRSCont.fit.resBasisSet.(gui.fit.Style).(['np_sw_' num2str(round(MRSCont.processed.metab{1}.sz(1))) '_' num2str(round(MRSCont.processed.metab{1}.spectralwidth))]){1,1}.name;
                 else
-                    basisSetNames = MRSCont.fit.resBasisSet.(gui.fit.Style).(['np_sw_' num2str(MRSCont.processed.metab{1}.sz(1)) '_' num2str(MRSCont.processed.metab{1}.spectralwidth)]){1,end}.name;
+                    basisSetNames = MRSCont.fit.resBasisSet.(gui.fit.Style).(['np_sw_' num2str(round(MRSCont.processed.metab{1}.sz(1))) '_' num2str(round(MRSCont.processed.metab{1}.spectralwidth))]){1,end}.name;
                 end
             end
              % Larger fonts for the results

GUI/osp_onCoreg.m

@@ -40,6 +40,7 @@ function osp_onCoreg( ~, ~ ,gui)
             end
         end
     end
+    set(gui.layout.tabs,'SelectionChangedFcn','');
     gui.layout.tabs.Selection  = 4;
 %%% 2. CALL OSPREYCOREG %%%    
     [gui,MRSCont] = osp_processingWindow(gui,MRSCont);  
@@ -51,4 +52,5 @@ function osp_onCoreg( ~, ~ ,gui)
     osp_iniCoregWindow(gui);
     gui.layout.b_coreg.Enable = 'off';
     gui.layout.b_segm.Enable = 'on';
+    set(gui.layout.tabs,'SelectionChangedFcn',{@osp_SelectionChangedFcn,gui});
 end % onCoreg

GUI/osp_onFit.m

@@ -27,6 +27,8 @@ function osp_onFit( ~, ~ ,gui)
 %%% 1. DELETE OLD PLOTS %%%
     MRSCont = getappdata(gui.figure,'MRSCont'); % Get MRSCont from hidden container in gui class  
     set(gui.figure,'HandleVisibility','off');
+    set(gui.layout.tabs,'SelectionChangedFcn','');
+    set(gui.layout.fitTab, 'SelectionChangedFcn','');
     gui.layout.tabs.Selection  = 3;
     [gui,MRSCont] = osp_processingWindow(gui,MRSCont);
 %%% 2. CALL OSPREYFIT %%%
@@ -101,4 +103,6 @@ function osp_onFit( ~, ~ ,gui)
     osp_iniFitWindow(gui);
     gui.layout.b_fit.Enable = 'off';
     gui.layout.b_quant.Enable = 'on';
+    set(gui.layout.tabs,'SelectionChangedFcn',{@osp_SelectionChangedFcn,gui});
+    set(gui.layout.fitTab, 'SelectionChangedFcn',{@osp_FitTabChangeFcn,gui});
 end % onFit

GUI/osp_onLoad.m

@@ -27,6 +27,7 @@
 %%% 1. INITIALIZE DATA %%%
     MRSCont = getappdata(gui.figure,'MRSCont'); % Get MRSCont from hidden container in gui class
     set(gui.figure,'HandleVisibility','off');
+    set(gui.layout.tabs,'SelectionChangedFcn','');
     gui.layout.tabs.Selection  = 1;
     [gui,MRSCont] = osp_processingWindow(gui,MRSCont);
 %%% 2. CALL OSPREYLOAD %%%
@@ -64,9 +65,9 @@
     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';
-
+    set(gui.layout.tabs,'SelectionChangedFcn',{@osp_SelectionChangedFcn,gui});
 end % onLoad

GUI/osp_onProc.m

@@ -27,6 +27,7 @@ function osp_onProc( ~, ~ ,gui)
 %%% 1. INITIALIZE %%%
     MRSCont = getappdata(gui.figure,'MRSCont');  % Get MRSCont from hidden container in gui class 
     set(gui.figure,'HandleVisibility','off');
+    set(gui.layout.tabs,'SelectionChangedFcn','');
     gui.layout.tabs.TabEnables{2} = 'on';
     gui.layout.tabs.Selection  = 2;
     [gui,MRSCont] = osp_processingWindow(gui,MRSCont);
@@ -42,4 +43,5 @@ function osp_onProc( ~, ~ ,gui)
     osp_iniProcessWindow(gui);
     gui.layout.b_proc.Enable = 'off';
     gui.layout.b_fit.Enable = 'on';
+    set(gui.layout.tabs,'SelectionChangedFcn',{@osp_SelectionChangedFcn,gui});
 end % onProc

GUI/osp_onQuant.m

@@ -27,6 +27,8 @@ function osp_onQuant( ~, ~ ,gui)
 %%% 1. INITIALIZE %%%
     MRSCont = getappdata(gui.figure,'MRSCont'); % Get MRSCont from hidden container in gui class
     set(gui.figure,'HandleVisibility','off');
+    set(gui.layout.tabs,'SelectionChangedFcn','');
+    set(gui.layout.quantifyTab, 'SelectionChangedFcn','');
     gui.layout.tabs.Selection  = 5;
     [gui,MRSCont] = osp_processingWindow(gui,MRSCont);
 %%% 2. CALL OSPREYQUANTIFY %%%    
@@ -75,4 +77,6 @@ function osp_onQuant( ~, ~ ,gui)
     set(gui.controls.pop_whichcorrOvCorr,'callback',{@osp_pop_whichcorrOvCorr_Call,gui});
     gui.layout.b_quant.Enable = 'off';
     set(gui.figure,'HandleVisibility','on');
+    set(gui.layout.tabs,'SelectionChangedFcn',{@osp_SelectionChangedFcn,gui});
+    set(gui.layout.quantifyTab, 'SelectionChangedFcn',{@osp_QuantTabChangeFcn,gui});
 end % onQuant

GUI/osp_onRightBasis.m

@@ -36,7 +36,7 @@ function osp_onRightBasis( ~, ~ ,gui)
         gui.fit.Style = 'conc';
     end
 
-    if gui.controls.act_basis < length(MRSCont.fit.resBasisSet.(gui.fit.Style).(['np_sw_' num2str(MRSCont.processed.metab{1}.sz(1)) '_' num2str(MRSCont.processed.metab{1}.spectralwidth)]))
+    if gui.controls.act_basis < length(MRSCont.fit.resBasisSet.(gui.fit.Style).(['np_sw_' num2str(round(MRSCont.processed.metab{1}.sz(1))) '_' num2str(round(MRSCont.processed.metab{1}.spectralwidth))]))
         gui.controls.act_basis = gui.controls.act_basis + 1;
 
         setappdata(gui.figure,'MRSCont',MRSCont); % Write MRSCont into hidden container in gui class

GUI/osp_onSeg.m

@@ -40,6 +40,7 @@ function osp_onSeg( ~, ~ ,gui)
             end
         end
     end
+    set(gui.layout.tabs,'SelectionChangedFcn','');
     gui.layout.tabs.Selection  = 4;
     [gui,MRSCont] = osp_processingWindow(gui,MRSCont);
 %%% 2. CALL OSPREYSEG %%%    
@@ -61,4 +62,5 @@ function osp_onSeg( ~, ~ ,gui)
         gui.pop_distrOvQuantControls.String = gui.quant.Names.Quants;
         gui.pop_corrOvQuantControls.String = gui.quant.Names.Quants;
     end
+    set(gui.layout.tabs,'SelectionChangedFcn',{@osp_SelectionChangedFcn,gui});
 end % onSeg

exampledata/ima/jobIMA.m

@@ -153,11 +153,11 @@
 % Select the metabolites to be included in the basis set as a cell array,
 % with entries separates by commas.
 % With default Osprey basis sets, you can select the following metabolites:
-% Ala, Asc, Asp, bHB, bHG, Cit, Cr, CrCH2, EtOH, GABA, GPC, GSH, Glc, Gln,
+% Ala, Asc, Asp, bHB, bHG, Cit, Cr, Cystat, CrCH2, EtOH, GABA, GPC, GSH, Glc, Gln,
 % Glu, Gly, H2O, mI, Lac, NAA, NAAG, PCh, PCr, PE, Phenyl, sI, Ser,
 % Tau, Tyros, MM09, MM12, MM14, MM17, MM20, Lip09, Lip13, Lip20.
 % If you enter 'default', the basis set will include all of the above
-% except for Ala, bHB, bHG, Cit, EtOH, Glc, Gly, Phenyl, Ser, and Tyros.
+% except for Ala, bHB, bHG, Cit, Cystat, EtOH, Glc, Gly, Phenyl, Ser, and Tyros.
 opts.fit.includeMetabs      = {'default'};      % OPTIONS:    - {'default'}
                                                 %             - {'full'}
                                                 %             - {custom} 

exampledata/nifti-mrs/jobNIfTIMRS.m

@@ -148,11 +148,11 @@
 % Select the metabolites to be included in the basis set as a cell array,
 % with entries separates by commas.
 % With default Osprey basis sets, you can select the following metabolites:
-% Ala, Asc, Asp, bHB, bHG, Cit, Cr, CrCH2, EtOH, GABA, GPC, GSH, Glc, Gln,
+% Ala, Asc, Asp, bHB, bHG, Cit, Cr, Cystat, CrCH2, EtOH, GABA, GPC, GSH, Glc, Gln,
 % Glu, Gly, H2O, mI, Lac, NAA, NAAG, PCh, PCr, PE, Phenyl, sI, Ser,
 % Tau, Tyros, MM09, MM12, MM14, MM17, MM20, Lip09, Lip13, Lip20.
 % If you enter 'default', the basis set will include all of the above
-% except for Ala, bHB, bHG, Cit, EtOH, Glc, Gly, Phenyl, Ser, and Tyros.
+% except for Ala, bHB, bHG, Cit, Cystat, EtOH, Glc, Gly, Phenyl, Ser, and Tyros.
 opts.fit.includeMetabs      = {'default'};      % OPTIONS:    - {'default'}
                                                 %             - {custom}                                     
 

exampledata/p/jobP.m

@@ -150,7 +150,7 @@
 % Select the metabolites to be included in the basis set as a cell array,
 % with entries separates by commas.
 % With default Osprey basis sets, you can select the following metabolites:
-% Ala, Asc, Asp, bHB, bHG, Cit, Cr, CrCH2, EtOH, GABA, GPC, GSH, Glc, Gln,
+% Ala, Asc, Asp, bHB, bHG, Cit, Cr, Cystat, CrCH2, EtOH, GABA, GPC, GSH, Glc, Gln,
 % Glu, Gly, H2O, mI, Lac, NAA, NAAG, PCh, PCr, PE, Phenyl, sI, Ser,
 % Tau, Tyros, MM09, MM12, MM14, MM17, MM20, Lip09, Lip13, Lip20.
 % If you enter 'default', the basis set will include all of the above

exampledata/rda/jobRDA.m

@@ -152,11 +152,11 @@
 % Select the metabolites to be included in the basis set as a cell array,
 % with entries separates by commas.
 % With default Osprey basis sets, you can select the following metabolites:
-% Ala, Asc, Asp, bHB, bHG, Cit, Cr, CrCH2, EtOH, GABA, GPC, GSH, Glc, Gln,
+% Ala, Asc, Asp, bHB, bHG, Cit, Cr, Cystat, CrCH2, EtOH, GABA, GPC, GSH, Glc, Gln,
 % Glu, Gly, H2O, mI, Lac, NAA, NAAG, PCh, PCr, PE, Phenyl, sI, Ser,
 % Tau, Tyros, MM09, MM12, MM14, MM17, MM20, Lip09, Lip13, Lip20.
 % If you enter 'default', the basis set will include all of the above
-% except for Ala, bHB, bHG, Cit, EtOH, Glc, Gly, Phenyl, Ser, and Tyros.
+% except for Ala, bHB, bHG, Cit, Cystat, EtOH, Glc, Gly, Phenyl, Ser, and Tyros.
 opts.fit.includeMetabs      = {'default'};      % OPTIONS:    - {'default'}
                                                 %             - {'full'}
                                                 %             - {custom} 

exampledata/sdat/MEGA/jobSDAT_MEGA.m

@@ -150,11 +150,11 @@
 % Select the metabolites to be included in the basis set as a cell array,
 % with entries separates by commas.
 % With default Osprey basis sets, you can select the following metabolites:
-% Ala, Asc, Asp, bHB, bHG, Cit, Cr, CrCH2, EtOH, GABA, GPC, GSH, Glc, Gln,
+% Ala, Asc, Asp, bHB, bHG, Cit, Cr, Cystat, CrCH2, EtOH, GABA, GPC, GSH, Glc, Gln,
 % Glu, Gly, H2O, mI, Lac, NAA, NAAG, PCh, PCr, PE, Phenyl, sI, Ser,
 % Tau, Tyros, MM09, MM12, MM14, MM17, MM20, Lip09, Lip13, Lip20.
 % If you enter 'default', the basis set will include all of the above
-% except for Ala, bHB, bHG, Cit, EtOH, Glc, Gly, Phenyl, Ser, and Tyros.
+% except for Ala, bHB, bHG, Cit, Cystat, EtOH, Glc, Gly, Phenyl, Ser, and Tyros.
 opts.fit.includeMetabs      = {'default'};      % OPTIONS:    - {'default'}
                                                 %             - {'full'}
                                                 %             - {custom}

exampledata/sdat/MEGA/jobSDAT_MEGA_Multidataset.m

@@ -150,11 +150,11 @@
 % Select the metabolites to be included in the basis set as a cell array,
 % with entries separates by commas.
 % With default Osprey basis sets, you can select the following metabolites:
-% Ala, Asc, Asp, bHB, bHG, Cit, Cr, CrCH2, EtOH, GABA, GPC, GSH, Glc, Gln,
+% Ala, Asc, Asp, bHB, bHG, Cit, Cr, Cystat, CrCH2, EtOH, GABA, GPC, GSH, Glc, Gln,
 % Glu, Gly, H2O, mI, Lac, NAA, NAAG, PCh, PCr, PE, Phenyl, sI, Ser,
 % Tau, Tyros, MM09, MM12, MM14, MM17, MM20, Lip09, Lip13, Lip20.
 % If you enter 'default', the basis set will include all of the above
-% except for Ala, bHB, bHG, Cit, EtOH, Glc, Gly, Phenyl, Ser, and Tyros.
+% except for Ala, bHB, bHG, Cit, Cystat, EtOH, Glc, Gly, Phenyl, Ser, and Tyros.
 opts.fit.includeMetabs      = {'default'};      % OPTIONS:    - {'default'}
                                                 %             - {'full'}
                                                 %             - {custom}

exampledata/sdat/UnEdited/jobSDAT.m

@@ -147,11 +147,11 @@
 % Select the metabolites to be included in the basis set as a cell array,
 % with entries separates by commas.
 % With default Osprey basis sets, you can select the following metabolites:
-% Ala, Asc, Asp, bHB, bHG, Cit, Cr, CrCH2, EtOH, GABA, GPC, GSH, Glc, Gln,
+% Ala, Asc, Asp, bHB, bHG, Cit, Cr, Cystat, CrCH2, EtOH, GABA, GPC, GSH, Glc, Gln,
 % Glu, Gly, H2O, mI, Lac, NAA, NAAG, PCh, PCr, PE, Phenyl, sI, Ser,
 % Tau, Tyros, MM09, MM12, MM14, MM17, MM20, Lip09, Lip13, Lip20.
 % If you enter 'default', the basis set will include all of the above
-% except for Ala, bHB, bHG, Cit, EtOH, Glc, Gly, Phenyl, Ser, and Tyros.
+% except for Ala, bHB, bHG, Cit, Cystat, EtOH, Glc, Gly, Phenyl, Ser, and Tyros.
 opts.fit.includeMetabs      = {'default'};      % OPTIONS:    - {'default'}
                                                 %             - {custom}
 

exampledata/sdat/UnEdited/jobSDAT_LCModel.m

@@ -149,11 +149,11 @@
 % Select the metabolites to be included in the basis set as a cell array,
 % with entries separates by commas.
 % With default Osprey basis sets, you can select the following metabolites:
-% Ala, Asc, Asp, bHB, bHG, Cit, Cr, CrCH2, EtOH, GABA, GPC, GSH, Glc, Gln,
+% Ala, Asc, Asp, bHB, bHG, Cit, Cr, Cystat, CrCH2, EtOH, GABA, GPC, GSH, Glc, Gln,
 % Glu, Gly, H2O, mI, Lac, NAA, NAAG, PCh, PCr, PE, Phenyl, sI, Ser,
 % Tau, Tyros, MM09, MM12, MM14, MM17, MM20, Lip09, Lip13, Lip20.
 % If you enter 'default', the basis set will include all of the above
-% except for Ala, bHB, bHG, Cit, EtOH, Glc, Gly, Phenyl, Ser, and Tyros.
+% except for Ala, bHB, bHG, Cit, Cystat, EtOH, Glc, Gly, Phenyl, Ser, and Tyros.
 opts.fit.includeMetabs      = {'default'};      % OPTIONS:    - {'default'}
                                                 %             - {custom}
 

exampledata/twix/jobTwix.m

@@ -152,11 +152,11 @@
 % Select the metabolites to be included in the basis set as a cell array,
 % with entries separates by commas.
 % With default Osprey basis sets, you can select the following metabolites:
-% Ala, Asc, Asp, bHB, bHG, Cit, Cr, CrCH2, EtOH, GABA, GPC, GSH, Glc, Gln,
+% Ala, Asc, Asp, bHB, bHG, Cit, Cr, Cystat, CrCH2, EtOH, GABA, GPC, GSH, Glc, Gln,
 % Glu, Gly, H2O, mI, Lac, NAA, NAAG, PCh, PCr, PE, Phenyl, sI, Ser,
 % Tau, Tyros, MM09, MM12, MM14, MM17, MM20, Lip09, Lip13, Lip20.
 % If you enter 'default', the basis set will include all of the above
-% except for Ala, bHB, bHG, Cit, EtOH, Glc, Gly, Phenyl, Ser, and Tyros.
+% except for Ala, bHB, bHG, Cit, Cystat, EtOH, Glc, Gly, Phenyl, Ser, and Tyros.
 opts.fit.includeMetabs      = {'default'};      % OPTIONS:    - {'default'}
                                                 %             - {'full'}
                                                 %             - {custom} 

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');