Release v.2.5.0

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','2.4.0','Date', 'August 8, 2022',...
+gui.d = uiw.dialog.About('Name', 'Osprey','Version','2.5.0','Date', 'April 7, 2023',...
 'Timeout', 3,'CustomText', 'Osprey is provided by Johns Hopkins University.',...
 'ContactInfo', 'gabamrs@gmail.com','LogoCData', logoBanner);
 
@@ -74,7 +74,7 @@
     set(gui.Buttons, 'ButtonSize', [300 60]);
     % Create Job
     gui.CreateJob = uicontrol('Parent', gui.Buttons,'Style','PushButton','String','Create Job','ForegroundColor', gui.colormap.Foreground,...
-                               'TooltipString', 'Create a OspreyJob .m-file');
+                               'TooltipString', 'Create a OspreyJob .json-file');
     set(gui.CreateJob,'Units','Normalized','Position',[0.1 0.9 0.8 0.08], 'FontSize', 16, 'FontName', gui.font, 'FontWeight', 'Bold');
     set(gui.CreateJob,'Callback',{@onCreateJob});
     % JobFile input button

GUI/OspreyGUI.m

@@ -134,6 +134,7 @@
             gui.controls.act_y = 1;
             gui.controls.act_z = 1;
             gui.controls.act_basis = 1;
+            gui.overview.Selected.Spec = 1;
         %Names for each selection
             gui.load.Names.Spec = {'metabolites'};
         %Inital number of datasets
@@ -155,7 +156,11 @@
                     if strcmp(sprintf('\n'),MRSCont.raw{1,gui.controls.Selected}.seq(end)) %Clean up Sequence Name if needed
                         gui.load.Names.Seq = MRSCont.raw{1,gui.controls.Selected}.seq(1:end-1);
                     else
-                        gui.load.Names.Seq = MRSCont.raw{1,gui.controls.Selected}.seq;
+                        if iscell(MRSCont.raw{1,gui.controls.Selected}.seq)
+                            gui.load.Names.Seq = MRSCont.raw{1,gui.controls.Selected}.seq{1,1};
+                        else
+                            gui.load.Names.Seq = MRSCont.raw{1,gui.controls.Selected}.seq
+                        end
                     end
                 else
                     if MRSCont.flags.isUnEdited
@@ -200,10 +205,9 @@
                 end
             end
 
-            if gui.controls.nExperiments > 1
-                gui.info.nXvoxels = gui.controls.nExperiments;
-                gui.info.nExperiments = gui.controls.nExperiments;
-            end
+            gui.info.nXvoxels = gui.controls.nExperiments;
+            gui.info.nExperiments = gui.controls.nExperiments;
+
             if MRSCont.flags.didProcess %Get variables regarding the processing
                 gui.process.Number = length(fieldnames(MRSCont.processed));
                 gui.info.nYvoxels = MRSCont.processed.metab{1, 1}.subspecs;
@@ -272,7 +276,10 @@
             %Version check and updating log file
             MRSCont.flags.isGUI = 1;
             outputFolder = MRSCont.outputFolder;
-
+
+            %Add cosmetics
+            MRSCont.opts.cosmetics.LB = 0;
+            MRSCont.opts.cosmetics.Zoom = 2.75;
             %% Create the overall figure            
             gui.figure = figure('Name', 'Osprey', 'Tag', 'Osprey', 'NumberTitle', 'off', 'Visible', 'on','Menu', 'none',...
                                 'ToolBar', 'none', 'HandleVisibility', 'on', 'Renderer', 'painters', 'Color', gui.colormap.Background);
@@ -413,7 +420,10 @@
                 'ForegroundColor',gui.colormap.Foreground, 'HighlightColor',gui.colormap.Foreground, 'ShadowColor',gui.colormap.Foreground,'Tag','SubjectListPanel');
             gui.layout.fileList = MRSCont.files(1,:);
             if ~MRSCont.flags.moved
-                [~, ~] = osp_detDataType(MRSCont);
+                try
+                    [~, ~] = osp_detDataType(MRSCont);
+                catch
+                end
             end
             SepFileList = cell(1,MRSCont.nDatasets(1));
             gui.layout.RedFileList = cell(1,MRSCont.nDatasets(1));
@@ -537,10 +547,18 @@
             close(gui.controls.waitbar);
         %% Here we add callback listeners triggered on selection changes
             set(gui.layout.tabs,'SelectionChangedFcn',{@osp_SelectionChangedFcn,gui});
-            set(gui.layout.rawTab, 'SelectionChangedFcn',{@osp_RawTabChangeFcn,gui});
-            set(gui.layout.proTab,'SelectionChangedFcn',{@osp_ProTabChangeFcn,gui});
-            set(gui.layout.fitTab, 'SelectionChangedFcn',{@osp_FitTabChangeFcn,gui});
-            set(gui.layout.quantifyTab, 'SelectionChangedFcn',{@osp_QuantTabChangeFcn,gui});
+            if MRSCont.flags.didLoad
+                set(gui.layout.rawTab, 'SelectionChangedFcn',{@osp_RawTabChangeFcn,gui});
+            end
+            if MRSCont.flags.didProcess
+                set(gui.layout.proTab,'SelectionChangedFcn',{@osp_ProTabChangeFcn,gui});
+            end
+            if MRSCont.flags.didFit
+                set(gui.layout.fitTab, 'SelectionChangedFcn',{@osp_FitTabChangeFcn,gui});
+            end
+            if MRSCont.flags.didQuantify
+                set(gui.layout.quantifyTab, 'SelectionChangedFcn',{@osp_QuantTabChangeFcn,gui});
+            end
             set(gui.layout.ListBox,'Callback', {@osp_onListSelection,gui},'KeyPressFcn',{@osp_WindowKeyDown,gui}, 'KeyReleaseFcn', {@osp_WindowKeyUp,gui});
 
         end

GUI/osp_OverviewTabChangedFcn.m

@@ -28,9 +28,9 @@ function osp_OverviewTabChangedFcn(src,~,gui)
     switch NewValue
        case 1
             osp_updateSpecsOvWindow(gui);
-            set(gui.controls.pop_specsOvPlot, 'value',gui.process.Selected)
+            set(gui.controls.pop_specsOvPlot, 'value',gui.overview.Selected.Spec)
        case 2
-            splt_string =  strsplit(gui.controls.pop_specsOvPlot.String{gui.process.Selected});
+            splt_string =  strsplit(gui.controls.pop_specsOvPlot.String{gui.overview.Selected.Spec});
             if length(splt_string) > 1
                 if strcmp(splt_string{2},'ref') || strcmp(splt_string{2},'w')
                     gui.process.Selected = find(contains(gui.controls.pop_meanOvPlot.String,splt_string{2}));
@@ -39,7 +39,7 @@ function osp_OverviewTabChangedFcn(src,~,gui)
                 end
             end
             osp_updatemeanOvWindow(gui);
-            set(gui.controls.pop_meanOvPlot, 'value',gui.process.Selected)
+            set(gui.controls.pop_meanOvPlot, 'value',gui.overview.Selected.Spec)
        case 3
             set(gui.layout.overviewTab, 'selection', 3);
        case 4

GUI/osp_ProTabChangeFcn.m

@@ -28,14 +28,22 @@ function osp_ProTabChangeFcn(src,~,gui)
     % User selected tab refreshs plot
     gui.process.Selected = src.Selection;
 
-    if MRSCont.processed.(gui.process.Names{gui.process.Selected}){gui.controls.Selected}.dims.extras > 0
-        gui.info.nXvoxels = MRSCont.processed.(gui.process.Names{gui.process.Selected}){gui.controls.Selected}.sz(MRSCont.processed.(gui.process.Names{gui.process.Selected}){gui.controls.Selected}.dims.extras);
+    if isfield(MRSCont,'processed')
+        if MRSCont.processed.(gui.process.Names{gui.process.Selected}){gui.controls.Selected}.dims.extras > 0
+            gui.info.nXvoxels = MRSCont.processed.(gui.process.Names{gui.process.Selected}){gui.controls.Selected}.sz(MRSCont.processed.(gui.process.Names{gui.process.Selected}){gui.controls.Selected}.dims.extras);
+        else
+            gui.info.nXvoxels = 1;
+        end   
     else
         gui.info.nXvoxels = 1;
-    end            
+    end
     gui.controls.act_x = 1;
-    if MRSCont.processed.(gui.process.Names{gui.process.Selected}){gui.controls.Selected}.dims.subSpecs > 0
-        gui.info.nYvoxels = MRSCont.processed.(gui.process.Names{gui.process.Selected}){gui.controls.Selected}.sz(MRSCont.processed.(gui.process.Names{gui.process.Selected}){gui.controls.Selected}.dims.subSpecs);
+    if isfield(MRSCont,'processed')
+        if MRSCont.processed.(gui.process.Names{gui.process.Selected}){gui.controls.Selected}.dims.subSpecs > 0
+            gui.info.nYvoxels = MRSCont.processed.(gui.process.Names{gui.process.Selected}){gui.controls.Selected}.sz(MRSCont.processed.(gui.process.Names{gui.process.Selected}){gui.controls.Selected}.dims.subSpecs);
+        else
+            gui.info.nYvoxels = MRSCont.nDatasets(2);
+        end
     else
         gui.info.nYvoxels = MRSCont.nDatasets(2);
     end

GUI/osp_Toolbox_Check.m

@@ -32,123 +32,125 @@
 %       2020-05-15: First version of the code.
 %% % 1. SAVE OSPREY VERSION%%%
 %%% 1. SAVE OSPREY VERSION%%%
-OspreyVersion = 'Osprey 2.4.0';
+OspreyVersion = 'Osprey 2.5.0';
 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%%%
-warning('off','MATLAB:javaclasspath:jarAlreadySpecified');
-addons = matlab.addons.installedAddons;
-available = cellstr(table2cell(addons(:,1)));
-for tl = 1 : size(addons,1)
-    try
-        matlab.addons.enableAddon(addons.Name{tl});
-    catch
+if ~(ismcc || isdeployed)
+    warning('off','MATLAB:javaclasspath:jarAlreadySpecified');
+    addons = matlab.addons.installedAddons;
+    available = cellstr(table2cell(addons(:,1)));
+    for tl = 1 : size(addons,1)
+        try
+            matlab.addons.enableAddon(addons.Name{tl});
+        catch
+        end
     end
-end
-addons = matlab.addons.installedAddons;
-lic = strcmp({'Enabled'}, addons.Properties.VariableNames);
-if ~isempty(lic)
-    enabled = table2cell(addons(:,lic==1));
-else
-    enabled = table2cell(addons(:,1));
-end
-
-[settingsFolder,~,~] = fileparts(which('OspreySettings.m'));
-allFolders      = strsplit(settingsFolder, filesep);
-ospFolder       = strjoin(allFolders(1:end-1), filesep); % parent folder (= Osprey folder)
-
-% Get SPM folder and check if SPM12 is installed
-spmversion = fileparts(which(fullfile('spm.m')));
-if isempty(spmversion)
-    hasSPM = 0;
-elseif strcmpi(spmversion(end-3:end),'spm8')
-    available{end+1} = 'SPM8';
-    enabled{end+1} = false;
-    hasSPM = 0;
-else
-    available{end+1} = 'SPM12';
-    enabled{end+1} = true;
-    hasSPM = 1;
-end 
-
-try
+    addons = matlab.addons.installedAddons;
+    lic = strcmp({'Enabled'}, addons.Properties.VariableNames);
     if ~isempty(lic)
-        available(find(cellfun(@(a)~isempty(a)&&a<1,enabled)), :) = [];
-    end    
-
-    %%% 3. CHECK AVAILABILTY %%%
-    switch Module
-        case 'OspreyGUI'
-            ModuleString = 'fully run \bfOsprey';
-            neededGlobal = {'Optimization Toolbox', 'Statistics and Machine Learning Toolbox','SPM12'};
-            neededSpecific = {'Widgets Toolbox', 'GUI Layout Toolbox'};
-        case 'OspreyProcess'
-            ModuleString = 'run \bfOspreyProcess';
-            neededGlobal = {'Optimization Toolbox', 'Statistics and Machine Learning Toolbox','SPM12'};
-            neededSpecific = {'Optimization Toolbox', 'Statistics and Machine Learning Toolbox'}; 
-        case 'OspreyFit'
-            ModuleString = 'run \bfOspreyFit';
-            neededGlobal = {'Optimization Toolbox', 'Statistics and Machine Learning Toolbox','SPM12'};
-            neededSpecific = {'Optimization Toolbox', 'Statistics and Machine Learning Toolbox'};
-        case 'OspreyCoreg'
-            ModuleString = 'run \bfOspreyCoreg';
-            neededGlobal = {'Optimization Toolbox', 'Statistics and Machine Learning Toolbox','SPM12'};
-            neededSpecific = {'SPM12'};
-        case 'OspreySeg'
-            ModuleString = 'run \bfOspreySeg';
-            neededGlobal = {'Optimization Toolbox', 'Statistics and Machine Learning Toolbox','SPM12'};
-            neededSpecific = {'SPM12'};        
-        otherwise
-            ModuleString = ['run \bf' Module];
-            neededGlobal = {'Optimization Toolbox', 'Statistics and Machine Learning Toolbox','SPM12'};
-            neededSpecific = cellstr({});
+        enabled = table2cell(addons(:,lic==1));
+    else
+        enabled = table2cell(addons(:,1));
     end
 
-    %To account for the re-naming of new downloads of the Widget Toolbox
-    %for Matlab versions earlier than 2020b, while maintaining
-    %functionality for older downloads, we need to check for all naming
-    %conventions of the Widgets Toolbox HZ
-    for tb = 1 : length(available)
-        if contains(available{tb},'Widgets Toolbox')
-            available{tb} = 'Widgets Toolbox';
+    [settingsFolder,~,~] = fileparts(which('OspreySettings.m'));
+    allFolders      = strsplit(settingsFolder, filesep);
+    ospFolder       = strjoin(allFolders(1:end-1), filesep); % parent folder (= Osprey folder)
+
+    % Get SPM folder and check if SPM12 is installed
+    spmversion = fileparts(which(fullfile('spm.m')));
+    if isempty(spmversion)
+        hasSPM = 0;
+    elseif strcmpi(spmversion(end-3:end),'spm8')
+        available{end+1} = 'SPM8';
+        enabled{end+1} = false;
+        hasSPM = 0;
+    else
+        available{end+1} = 'SPM12';
+        enabled{end+1} = true;
+        hasSPM = 1;
+    end 
+
+    try
+        if ~isempty(lic)
+            available(find(cellfun(@(a)~isempty(a)&&a<1,enabled)), :) = [];
+        end    
+
+        %%% 3. CHECK AVAILABILTY %%%
+        switch Module
+            case 'OspreyGUI'
+                ModuleString = 'fully run \bfOsprey';
+                neededGlobal = {'Optimization Toolbox', 'Statistics and Machine Learning Toolbox','SPM12'};
+                neededSpecific = {'Widgets Toolbox', 'GUI Layout Toolbox'};
+            case 'OspreyProcess'
+                ModuleString = 'run \bfOspreyProcess';
+                neededGlobal = {'Optimization Toolbox', 'Statistics and Machine Learning Toolbox','SPM12'};
+                neededSpecific = {'Optimization Toolbox', 'Statistics and Machine Learning Toolbox'}; 
+            case 'OspreyFit'
+                ModuleString = 'run \bfOspreyFit';
+                neededGlobal = {'Optimization Toolbox', 'Statistics and Machine Learning Toolbox','SPM12'};
+                neededSpecific = {'Optimization Toolbox', 'Statistics and Machine Learning Toolbox'};
+            case 'OspreyCoreg'
+                ModuleString = 'run \bfOspreyCoreg';
+                neededGlobal = {'Optimization Toolbox', 'Statistics and Machine Learning Toolbox','SPM12'};
+                neededSpecific = {'SPM12'};
+            case 'OspreySeg'
+                ModuleString = 'run \bfOspreySeg';
+                neededGlobal = {'Optimization Toolbox', 'Statistics and Machine Learning Toolbox','SPM12'};
+                neededSpecific = {'SPM12'};        
+            otherwise
+                ModuleString = ['run \bf' Module];
+                neededGlobal = {'Optimization Toolbox', 'Statistics and Machine Learning Toolbox','SPM12'};
+                neededSpecific = cellstr({});
         end
-    end
-    missingSpecific = setdiff(neededSpecific,available);
-    missing = setdiff(neededGlobal,available); 
-
-    %%% 4. CREATE WARNING MESSAGES %%%
-    if ~ToolChecked
-        warningMsg = cellstr({});
-        warning_count = 1;
-        if ~isempty(missing) || ~isempty(missingSpecific)
-            opts.Interpreter = 'tex';
-            opts.WindowStyle = 'modal';
-            warningMsg{1} = ['The following toolboxes are missing to ' ModuleString '\rm:'];
-            for i = 1 : length(missing)
-                warningMsg{i+1} = ['\bf' missing{i} '\rm'];
+
+        %To account for the re-naming of new downloads of the Widget Toolbox
+        %for Matlab versions earlier than 2020b, while maintaining
+        %functionality for older downloads, we need to check for all naming
+        %conventions of the Widgets Toolbox HZ
+        for tb = 1 : length(available)
+            if contains(available{tb},'Widgets Toolbox')
+                available{tb} = 'Widgets Toolbox';
             end
-            warning_count = warning_count +length(missing) + 1;
-            warningMsg{warning_count} = ['Please install them to ' ModuleString '\rm'];
-            warning_count = warning_count + 1;
-            if ~isempty(missingSpecific)
-                warningMsg{warning_count} = ['The following toolboxes are missing to run ' Module ':']; 
-                warningc = ['Please install and include the following toolboxes to use ' Module ':'];
-                for i = 1 : length(missingSpecific)
-                    warningMsg{warning_count + i} = ['\bf' missingSpecific{i} '\rm'];
-                    warningc = [warningc ' ' missingSpecific{i}];
+        end
+        missingSpecific = setdiff(neededSpecific,available);
+        missing = setdiff(neededGlobal,available); 
+
+        %%% 4. CREATE WARNING MESSAGES %%%
+        if ~ToolChecked
+            warningMsg = cellstr({});
+            warning_count = 1;
+            if ~isempty(missing) || ~isempty(missingSpecific)
+                opts.Interpreter = 'tex';
+                opts.WindowStyle = 'modal';
+                warningMsg{1} = ['The following toolboxes are missing to ' ModuleString '\rm:'];
+                for i = 1 : length(missing)
+                    warningMsg{i+1} = ['\bf' missing{i} '\rm'];
                 end
-                warningMsg{warning_count + length(missingSpecific) + 1} = ['Please install them to use \bf' Module '\rm'];
+                warning_count = warning_count +length(missing) + 1;
+                warningMsg{warning_count} = ['Please install them to ' ModuleString '\rm'];
+                warning_count = warning_count + 1;
+                if ~isempty(missingSpecific)
+                    warningMsg{warning_count} = ['The following toolboxes are missing to run ' Module ':']; 
+                    warningc = ['Please install and include the following toolboxes to use ' Module ':'];
+                    for i = 1 : length(missingSpecific)
+                        warningMsg{warning_count + i} = ['\bf' missingSpecific{i} '\rm'];
+                        warningc = [warningc ' ' missingSpecific{i}];
+                    end
+                    warningMsg{warning_count + length(missingSpecific) + 1} = ['Please install them to use \bf' Module '\rm'];
+                    warndlg(warningMsg,'Missing Toolboxes',opts);
+                    error(warningc);
+                end    
                 warndlg(warningMsg,'Missing Toolboxes',opts);
-                error(warningc);
-            end    
-            warndlg(warningMsg,'Missing Toolboxes',opts);
+            end
         end
-    end
-
-catch %If the MATLAB version pre-dates the inmplementation of matlab.addons.installedAddons
-    warningMsg = cellstr({});
-    warningMsg{1} = 'Your current MATLAB version does not allow the automated toolbox check. We assume that all required toolboxes are available.';
-    warndlg(warningMsg,'Automated toolbox check not working.',opts);
-end   
-warning('on','MATLAB:javaclasspath:jarAlreadySpecified');
+
+    catch %If the MATLAB version pre-dates the inmplementation of matlab.addons.installedAddons
+        warningMsg = cellstr({});
+        warningMsg{1} = 'Your current MATLAB version does not allow the automated toolbox check. We assume that all required toolboxes are available.';
+        warndlg(warningMsg,'Automated toolbox check not working.',opts);
+    end   
+    warning('on','MATLAB:javaclasspath:jarAlreadySpecified');
+end
 end