Merge pull request #427 from schorschinho/develop

Prepare v.2.2.0 release

.github/ISSUE_TEMPLATE/bug_report.md

@@ -1,7 +1,7 @@
 ---
 name: Bug report
 about: Create a report to help us improve Osprey
-title: "[BUG]"
+title: "[BUG] - Description of Issue - function with main changes - Submitter"
 labels: bug
 assignees: ''
 

.github/ISSUE_TEMPLATE/feature_request.md

@@ -1,7 +1,7 @@
 ---
 name: Feature request
 about: Suggest a function that Osprey should have
-title: "[FEATURE REQUEST]"
+title: "[FEATURE REQUEST] - Description of feature - function with main changes - Submitter"
 labels: enhancement, help wanted
 assignees: ''
 

GUI/Osprey.m

@@ -16,7 +16,7 @@
 %   HISTORY:
 %       2019-07-11: First version of the code.
 %% Check for available add-ons
-  [~] = osp_Toolbox_Check ('OspreyGUI',0);
+  [~,~] = osp_Toolbox_Check ('OspreyGUI',0);
 %% Set up Layout
 %Here we set up the color layout
 %default colormap and fonts
@@ -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','2.0.0','Date', 'April 12, 2022',...
+gui.d = uiw.dialog.About('Name', 'Osprey','Version','2.2.0','Date', 'April 12, 2022',...
 'Timeout', 3,'CustomText', 'Osprey is provided by Johns Hopkins University.',...
 'ContactInfo', '[email protected]','LogoCData', logoBanner);
 
@@ -79,7 +79,7 @@
     set(gui.CreateJob,'Callback',{@onCreateJob});
     % JobFile input button
     gui.LoadJob = uicontrol('Parent', gui.Buttons,'Style','PushButton','String','Load Job file','ForegroundColor', gui.colormap.Foreground,...
-                               'TooltipString', 'Load a Job (.m or .csv-file)');
+                               'TooltipString', 'Load a Job (.m, .json or .csv-file) Osprey Standalone Supports .json and .csv files only');
     set(gui.LoadJob,'Units','Normalized','Position',[0.1 0.75 0.8 0.08], 'FontSize', 16, 'FontName', gui.font, 'FontWeight', 'Bold');
     set(gui.LoadJob,'Callback',{@onLoadJob});
     % MRSCont input button
@@ -161,7 +161,7 @@ function onCreateJob( ~, ~) %Callback Create Job button
 
 function onLoadJob( ~, ~) %Callback Load Job button
     % User wants to quit out of the application
-    gui.out =  uipickfiles('FilterSpec',[ospFolder], 'REFilter', '\.m$|\.csv$','NumFiles',1,'Prompt','Select Osprey job file (.m or .csv-file)');
+    gui.out =  uipickfiles('FilterSpec',[ospFolder], 'REFilter', '\.m$|\.csv$|\.json$','NumFiles',1,'Prompt','Select Osprey job file (.m, .json or .csv-file)');
     if iscell(gui.out)
         loadJob(gui);
     end

GUI/OspreyGUI.m

@@ -87,17 +87,17 @@
                 end
             end
             diary off
+
+            % This is for the compiled GUI
+            MRSCont.flags.hasSPM = 1; 
+
         % Toolbox check
             if isfield(MRSCont.flags,'isToolChecked')
                 [MRSCont.flags.hasSPM,MRSCont.ver.CheckOsp] = osp_Toolbox_Check ('OspreyGUI',MRSCont.flags.isToolChecked);
             else
                 [MRSCont.flags.hasSPM,MRSCont.ver.CheckOsp] = osp_Toolbox_Check ('OspreyGUI',0);
                 MRSCont.flags.isToolChecked = 1;
             end
-            if MRSCont.flags.hasSPM
-                load(fullfile(gui.folder.ospFolder,'GUI','SPMpath.mat'),'SPMpath')
-                gui.folder.spmversion = SPMpath;
-            end
 
     % Show warning if the version is different
        if ~strcmp(MRSCont.ver.Osp,MRSCont.ver.CheckOsp)  
@@ -150,7 +150,7 @@
         end
 
         %Setting up remaining values in dependence of the conducted processing steps
-            if MRSCont.flags.didLoadData %Get variables regarding the loading
+            if MRSCont.flags.didLoad %Get variables regarding the loading
                 if ~isempty(MRSCont.raw{1,gui.controls.Selected}.seq)
                     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);
@@ -266,7 +266,7 @@
                 end
 
             end
-            gui.waitbar.overall = MRSCont.flags.didLoadData+MRSCont.flags.didProcess+MRSCont.flags.didFit+MRSCont.flags.didCoreg+MRSCont.flags.didSeg+MRSCont.flags.didQuantify+MRSCont.flags.didOverview;
+            gui.waitbar.overall = MRSCont.flags.didLoad+MRSCont.flags.didProcess+MRSCont.flags.didFit+MRSCont.flags.didCoreg+MRSCont.flags.didSeg+MRSCont.flags.didQuantify+MRSCont.flags.didOverview;
             gui.waitbar.step = 1/ gui.waitbar.overall;
 
             %Version check and updating log file
@@ -333,7 +333,7 @@
             gui.layout.b_load = uicontrol('Parent', gui.layout.p2,'Style','PushButton','String','Load data','Enable','on','ForegroundColor', gui.colormap.Foreground);
             set(gui.layout.b_load,'Units','Normalized','Position',[0.1 0.75 0.8 0.08], 'FontSize', 16, 'FontName', gui.font, 'FontWeight', 'Bold','Tag','LoadButton');
 
-            if  (MRSCont.flags.didLoadData == 1  && isfield(MRSCont, 'raw')) 
+            if  (MRSCont.flags.didLoad == 1  && isfield(MRSCont, 'raw')) 
                 sz_raw = size(MRSCont.raw);
                 if  (gui.controls.nDatasets(1) >= sz_raw(end))
                     gui.layout.b_load.Enable = 'off';
@@ -346,7 +346,7 @@
             set(gui.layout.b_proc,'Units','Normalized','Position',[0.1 0.75 0.8 0.08], 'FontSize', 16, 'FontName', gui.font, 'FontWeight', 'Bold','Tag','ProcButton');
             if (MRSCont.flags.didProcess == 1  && isfield(MRSCont, 'raw') && (gui.controls.nDatasets(1) >= length(MRSCont.processed.metab)))
                 gui.layout.b_proc.Enable = 'off';
-            else if ~(MRSCont.flags.didLoadData == 1  && isfield(MRSCont, 'raw') && (gui.controls.nDatasets(1) >= sz_raw(end)))
+            else if ~(MRSCont.flags.didLoad == 1  && isfield(MRSCont, 'raw') && (gui.controls.nDatasets(1) >= sz_raw(end)))
                     gui.layout.b_proc.Enable = 'off';
                 end
             end
@@ -364,7 +364,7 @@
         % Coregister button
             gui.layout.b_coreg = uicontrol('Parent', gui.layout.p2,'Style','PushButton','String','CoRegister','Enable','off','ForegroundColor', gui.colormap.Foreground);
             set(gui.layout.b_coreg,'Units','Normalized','Position',[0.1 0.59 0.8 0.08], 'FontSize', 16, 'FontName', gui.font, 'FontWeight', 'Bold','Tag','CoregButton');
-            if MRSCont.flags.hasSPM == 1 && ~isempty(MRSCont.files_nii) && ~(MRSCont.flags.didCoreg == 1  && isfield(MRSCont, 'coreg') && (gui.controls.nDatasets(1) >= length(MRSCont.coreg.vol_image))) && (MRSCont.flags.didLoadData == 1  && isfield(MRSCont, 'raw') && (gui.controls.nDatasets(1) >= length(MRSCont.raw)))               
+            if MRSCont.flags.hasSPM == 1 && ~isempty(MRSCont.files_nii) && ~(MRSCont.flags.didCoreg == 1  && isfield(MRSCont, 'coreg') && (gui.controls.nDatasets(1) >= length(MRSCont.coreg.vol_image))) && (MRSCont.flags.didLoad == 1  && isfield(MRSCont, 'raw') && (gui.controls.nDatasets(1) >= length(MRSCont.raw)))               
                 if ~(isfield(MRSCont.flags,'addImages') && (MRSCont.flags.addImages == 0) && MRSCont.flags.moved)
                     gui.layout.b_coreg.Enable = 'on';
                 end
@@ -411,14 +411,14 @@
             gui.layout.controlPanel = uix.Panel('Parent', gui.layout.leftMenu, 'Title', 'MRS Container','BackgroundColor',gui.colormap.Background);
             set(gui.layout.controlPanel,'Units','Normalized','Position',[0.5 0 0.66 0.1], 'FontSize', 16, 'FontName', gui.font, 'FontWeight', 'Bold',...
                 'ForegroundColor',gui.colormap.Foreground, 'HighlightColor',gui.colormap.Foreground, 'ShadowColor',gui.colormap.Foreground,'Tag','SubjectListPanel');
-            gui.layout.fileList = MRSCont.files;
+            gui.layout.fileList = MRSCont.files(1,:);
             if ~MRSCont.flags.moved
                 [~, ~] = osp_detDataType(MRSCont);
             end
-            SepFileList = cell(1,length(MRSCont.files));
-            gui.layout.RedFileList = cell(1,length(MRSCont.files));
-            gui.layout.OnlyFileList = cell(1,length(MRSCont.files));
-            for i = 1 : length(MRSCont.files) %find last two subfolders and file names
+            SepFileList = cell(1,MRSCont.nDatasets(1));
+            gui.layout.RedFileList = cell(1,MRSCont.nDatasets(1));
+            gui.layout.OnlyFileList = cell(1,MRSCont.nDatasets(1));
+            for i = 1 : MRSCont.nDatasets(1) %find last two subfolders and file names
                 SepFileList{i} =  split(gui.layout.fileList(i), filesep);
                 if length(SepFileList{i}) == 1
                     SepFileList{i} =  split(gui.layout.fileList(i), '\');
@@ -470,7 +470,7 @@
         % been completed:
             gui.controls.waitbar = waitbar(0,'Start','Name','Loading your MRS Container');
             waitbar(0,gui.controls.waitbar,'Loading your raw spectra')
-            if (MRSCont.flags.didLoadData == 1  && isfield(MRSCont, 'raw') && (gui.controls.nDatasets(1) >= sz_raw(end))) % Was data loaded at all that can be looked at?
+            if (MRSCont.flags.didLoad == 1  && isfield(MRSCont, 'raw') && (gui.controls.nDatasets(1) >= sz_raw(end))) % Was data loaded at all that can be looked at?
                 set(gui.layout.tabs, 'Visible','on');
                 osp_iniLoadWindow(gui);
                 if MRSCont.flags.isMRSI
@@ -528,7 +528,7 @@
                 set(gui.controls.b_save_meanOvTab,'Callback',{@osp_onPrint,gui});
             end
             gui.layout.tabs.Selection  = 1;
-            if ~MRSCont.flags.didLoadData %Turn of Listbox if data has not been loaded
+            if ~MRSCont.flags.didLoad %Turn of Listbox if data has not been loaded
                 gui.layout.ListBox.Enable = 'off';
             end
             set(gui.layout.tabs, 'Visible','on');

GUI/osp_OverviewTabChangedFcn.m

@@ -35,7 +35,7 @@ function osp_OverviewTabChangedFcn(src,~,gui)
                 if strcmp(splt_string{2},'ref') || strcmp(splt_string{2},'w')
                     gui.process.Selected = find(contains(gui.controls.pop_meanOvPlot.String,splt_string{2}));
                 else
-                    gui.process.Selected = find(contains(gui.controls.pop_meanOvPlot.String,splt_string{3}));
+                    gui.process.Selected = find(contains(gui.controls.pop_meanOvPlot.String,splt_string{1}));
                 end
             end
             osp_updatemeanOvWindow(gui);

GUI/osp_Toolbox_Check.m

@@ -30,10 +30,13 @@
 %
 %   HISTORY:
 %       2020-05-15: First version of the code.
-%%
-%%% 1. GET SPMPATH AND TOOLBOXES%%%
-OspreyVersion = 'Osprey 2.0.0';
+%% % 1. SAVE OSPREY VERSION%%%
+%%% 1. SAVE OSPREY VERSION%%%
+OspreyVersion = 'Osprey 2.2.0';
 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)
@@ -42,6 +45,7 @@
     catch
     end
 end
+addons = matlab.addons.installedAddons;
 lic = strcmp({'Enabled'}, addons.Properties.VariableNames);
 if ~isempty(lic)
     enabled = table2cell(addons(:,lic==1));
@@ -53,24 +57,8 @@
 allFolders      = strsplit(settingsFolder, filesep);
 ospFolder       = strjoin(allFolders(1:end-1), filesep); % parent folder (= Osprey folder)
 
-% SPM
-if isfile(fullfile(ospFolder,'GUI','SPMpath.mat')) % Load path to SPM
-    load(fullfile(ospFolder,'GUI','SPMpath.mat'),'SPMpath')
-    if exist(SPMpath, 'dir')
-        spmversion = SPMpath;
-    else  %This isn't the right SPM path (maybe it was copied from another machine)
-        spmversion = uipickfiles('FilterSpec',ospFolder,'REFilter', '\','NumFiles',1,'Prompt','Select your SPM-folder (Will be saved in SPMpath.mat file in the GUI folder)');
-        spmversion = spmversion{1};
-        SPMpath = spmversion;
-        save(fullfile(ospFolder,'GUI','SPMpath.mat'),'SPMpath');
-    end
-else %Set path to SPM
-    spmversion = uipickfiles('FilterSpec',ospFolder,'REFilter', '\','NumFiles',1,'Prompt','Select your SPM-folder (Will be saved in SPMpath.mat file in the GUI folder)');
-    spmversion = spmversion{1};
-    SPMpath = spmversion;
-    save(fullfile(ospFolder,'GUI','SPMpath.mat'),'SPMpath');
-end
-% Check if SPM12 is installed
+% 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')
@@ -81,15 +69,14 @@
     available{end+1} = 'SPM12';
     enabled{end+1} = true;
     hasSPM = 1;
-    rmpath(genpath([spmversion filesep 'external' filesep 'fieldtrip' filesep 'external' filesep 'stats' filesep 'finv.m']));
 end 
 
 try
     if ~isempty(lic)
         available(find(cellfun(@(a)~isempty(a)&&a<1,enabled)), :) = [];
     end    
 
-    %%% 2. CHECK AVAILABILTY %%%
+    %%% 3. CHECK AVAILABILTY %%%
     switch Module
         case 'OspreyGUI'
             ModuleString = 'fully run \bfOsprey';
@@ -129,39 +116,39 @@
     missingSpecific = setdiff(neededSpecific,available);
     missing = setdiff(neededGlobal,available); 
 
-    %%% 3. CREATE WARNING MESSAGES %%%
+    %%% 4. CREATE WARNING MESSAGES %%%
     if ~ToolChecked
-        warning = cellstr({});
+        warningMsg = cellstr({});
         warning_count = 1;
         if ~isempty(missing) || ~isempty(missingSpecific)
             opts.Interpreter = 'tex';
             opts.WindowStyle = 'modal';
-            warning{1} = ['The following toolboxes are missing to ' ModuleString '\rm:'];
+            warningMsg{1} = ['The following toolboxes are missing to ' ModuleString '\rm:'];
             for i = 1 : length(missing)
-                warning{i+1} = ['\bf' missing{i} '\rm'];
+                warningMsg{i+1} = ['\bf' missing{i} '\rm'];
             end
             warning_count = warning_count +length(missing) + 1;
-            warning{warning_count} = ['Please install them to ' ModuleString '\rm'];
+            warningMsg{warning_count} = ['Please install them to ' ModuleString '\rm'];
             warning_count = warning_count + 1;
             if ~isempty(missingSpecific)
-                warning{warning_count} = ['The following toolboxes are missing to run ' Module ':']; 
+                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)
-                    warning{warning_count + i} = ['\bf' missingSpecific{i} '\rm'];
+                    warningMsg{warning_count + i} = ['\bf' missingSpecific{i} '\rm'];
                     warningc = [warningc ' ' missingSpecific{i}];
                 end
-                warning{warning_count + length(missingSpecific) + 1} = ['Please install them to use \bf' Module '\rm'];
-                warndlg(warning,'Missing Toolboxes',opts);
+                warningMsg{warning_count + length(missingSpecific) + 1} = ['Please install them to use \bf' Module '\rm'];
+                warndlg(warningMsg,'Missing Toolboxes',opts);
                 error(warningc);
             end    
-            warndlg(warning,'Missing Toolboxes',opts);
+            warndlg(warningMsg,'Missing Toolboxes',opts);
         end
     end
 
 catch %If the MATLAB version pre-dates the inmplementation of matlab.addons.installedAddons
-    warning = cellstr({});
-    warning{1} = 'Your current MATLAB version does not allow the automated toolbox check. We assume that all required toolboxes are available.';
-    warndlg(warning,'Automated toolbox check not working.',opts);
+    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

GUI/osp_WindowKeyDown.m

@@ -35,15 +35,15 @@ function osp_WindowKeyDown(~,EventData,gui)
         OldValue = get( gui.layout.ListBox,'value');
         gui.controls.KeyPress = 1;
         if OldValue == 1
-            set(gui.layout.ListBox, 'value', MRSCont.nDatasets );
+            set(gui.layout.ListBox, 'value', MRSCont.nDatasets(1));
         else
             set(gui.layout.ListBox, 'value', OldValue-1 );
         end
     end
     if strcmp(EventData.Key, 'downarrow') % scrolling down
         OldValue = get( gui.layout.ListBox,'value');
         gui.controls.KeyPress = 1;
-        if OldValue == MRSCont.nDatasets
+        if OldValue == MRSCont.nDatasets(1)
             set(gui.layout.ListBox, 'value', 1 );
         else
             set(gui.layout.ListBox, 'value', OldValue+1 );

GUI/osp_iniCoregWindow.m

@@ -26,6 +26,7 @@ function osp_iniCoregWindow(gui)
 %       2020-01-16: First version of the code.
 %%% 1. GET HANDLES %%%
 % This function creates the initial coreg/seg window
+    warning('off','MATLAB:handle_graphics:exceptions:SceneNode');
     MRSCont = getappdata(gui.figure,'MRSCont'); % Get MRSCont from hidden container in gui class
     gui.layout.tabs.TabEnables{4} = 'on';
     gui.layout.tabs.Selection  = 4;
@@ -179,5 +180,6 @@ function osp_iniCoregWindow(gui)
             close(h(ff))
         end
     end
+    warning('on','MATLAB:handle_graphics:exceptions:SceneNode');
     setappdata(gui.figure,'MRSCont',MRSCont); % Write MRSCont into hidden container in gui class
 end

GUI/osp_iniLoadWindow.m

@@ -66,12 +66,6 @@ function osp_iniLoadWindow(gui)
                  gui.load.Names.Spec{3} = 'reference';
                 gui.load.Names.Spec{4} = 'MM reference';
                 gui.load.Names.Spec{5} = 'water';
-            otherwise
-                gui.controls.Number = gui.controls.Number + 4;
-                gui.load.Names.Spec{2} = 'spectra 1';
-                 gui.load.Names.Spec{3} = 'spectra 2';
-                gui.load.Names.Spec{4} = 'spectra 3';
-                gui.load.Names.Spec{5} = 'spectra 4';
         end
 
         gui.layout.tabs.TabEnables{1} = 'on';
@@ -345,7 +339,6 @@ function osp_iniLoadWindow(gui)
  %%% 4. VISUALIZATION PART OF THIS TAB %%%
  %osp_plotLoad is used to visualize the raw data. Number of subplots
  %depends on the number of subspectra of the seuqence
-        temp = figure( 'Visible', 'off' );
         switch gui.load.Names.Spec{t}
             case 'metabolites'
                 temp = osp_plotLoad(MRSCont, gui.controls.Selected,'mets');

GUI/osp_onGit.m

@@ -23,5 +23,9 @@ function osp_onGit( ~, ~)
 %       2020-01-16: First version of the code.
 %%% 1. Visit websites %%%
 
-web('https://github.com/schorschinho/osprey', '-browser'); %Github Link
+try
+    web('https://github.com/schorschinho/osprey', '-browser'); %Github Link
+catch
+    system('open "https://github.com/schorschinho/osprey"'); %for compiled Osprey
+end
 end