v1.80.1

-- If no data files were found in group folder because all the potential ones had errors display all the files not loaded in the error files listbox instead of displaying completely empty GUI.

* DataTree, v1.15.1
-- Avoid loading snirf files from derived data folder such as derivatives/homer.
-- Error check measurement list in DataClass. Make sure that for source/detector pair the number of channels is equal to number of data types that is number of wavelengths or for derived data number of Hb types * number of conditions.

* Utils, v1.7.1
-- Avoid loading snirf files from derived data folder such as derivatives/homer. Extend excluded folders in findTypeFiles.m to check for files in derived folder

Author: jayd1860

DataTree/AcquiredData/DataFiles/DataFilesClass.m

@@ -15,6 +15,7 @@
 
     properties (Access = private)
         lookupTable
+        excludedFolders
     end
 
     methods
@@ -38,6 +39,7 @@
 
             obj.logger = logger;
             obj.lookupTable = [];
+            obj.excludedFolders = {};
 
             skipconfigfile = false;
             askToFixNameConflicts = [];
@@ -74,7 +76,7 @@
             obj.rootdir = filesepStandard(obj.rootdir,'full');           
 
             % Configuration parameters
-            obj.config = struct('RegressionTestActive','','AskToFixNameConflicts',1);
+            obj.config = struct('RegressionTestActive','',  'AskToFixNameConflicts',1, 'DerivedDataDir','');
             if skipconfigfile==false
                 str = cfg.GetValue('Regression Test Active');
                 if strcmp(str,'true')
@@ -96,6 +98,18 @@
                 obj.config.SuppressErrorChecking = true;                
             end
 
+            [p, f] = fileparts(cfg.GetValue('Output Folder Name'));
+            if isempty(p)
+                obj.config.DerivedDataDir = f;
+            else
+                obj.config.DerivedDataDir = p;
+            end
+            obj.excludedFolders = {...
+                [obj.rootdir, obj.config.DerivedDataDir];
+                [obj.rootdir, 'fw'];
+                [obj.rootdir, 'imagerecon'];
+                [obj.rootdir, 'anatomical'];
+                };
             if nargin==0
                 return;
             end
@@ -222,6 +236,14 @@ function FindDataSet(obj, iFormat, iPattern, parentdir)
                 return
             end
             parentdir = filesepStandard(parentdir);
+            
+            % Check if folder is excluded, if yes don't search there
+            for ii = 1:length(obj.excludedFolders)
+                if includes(parentdir, obj.excludedFolders{ii})
+                    return;
+                end
+            end
+            
             pattern = obj.dirFormats.choices{iFormat}{iPattern};
 
             dirs = mydir([parentdir, pattern], obj.rootdir);
@@ -307,9 +329,9 @@ function ErrorCheckFinal(obj)
             obj.ErrorCheckName();
 
             % Find all acquisition files in group folder
-            fileNames = findTypeFiles(obj.rootdir, ['.', obj.filetype]);
+            fileNames = findTypeFiles(obj.rootdir, ['.', obj.filetype], obj.excludedFolders);
 
-            % Make alist of all files excluded from current data set  
+            % Make a list of all files excluded from current data set  
             for ii = 1:length(fileNames)
                 filefound = false;
 

DataTree/AcquiredData/Snirf/DataClass.m

@@ -289,6 +289,8 @@
             if ~exist('params','var')
                 params = propnames(obj);
             end
+            
+            % Check dataTimeSeries
             if ismember('dataTimeSeries',params)
                 if obj.IsEmpty()
                     err = -2;
@@ -304,6 +306,8 @@
                     err = 5;
                 end
             end
+            
+            % Check time 
             if ismember('time',params)
                 if isempty(obj.time)
                     err = -6;
@@ -313,6 +317,25 @@
                     err = 7;
                 end
             end
+            
+            % Check measurement list
+            if ismember('measurementList',params)
+                ml = sortrows(obj.GetMeasurementList('matrix'));
+                nDatatypes = length(unique(ml(:,4))) * length(unique(ml(:,3)));
+                i = 1;
+                while i <= size(ml,1)
+                    k = find(ml(:,1)==ml(i,1) & ml(:,2)==ml(i,2));
+                    if length(k) < nDatatypes
+                        err = -7;
+                    elseif length(k) > nDatatypes
+                        err = -8;
+                    end
+                    if err < 0
+                        break
+                    end
+                    i = i+length(k);
+                end
+            end
         end
 
     end

DataTree/DataTreeClass.m

@@ -267,6 +267,8 @@ function FindAndLoadGroups(obj, groupDirs, fmt, procStreamCfgFile, options)
                     while dataInit.GetError() < 0
                         dataInit = FindFiles(obj.dirnameGroups{kk}, fmt, options);
                         if isempty(dataInit) || dataInit.IsEmpty()
+                            obj.filesErr = dataInit.filesErr;
+                            ErrorCheckLoadedFiles(obj);
                             return;
                         end
                         dataInitPrev(iter) = dataInit;
@@ -374,6 +376,7 @@ function LoadGroup(obj, iGroup, procStreamCfgFile, options)
             %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
             obj.AcqData2Group(iGroup);
             if isempty(obj.groups)
+                obj.ErrorCheckLoadedFiles();
                 return
             end
 

DataTree/Version.txt

@@ -1 +1 @@
-1.15.0
+1.15.1

MainGUI/MainGUI.m

@@ -84,13 +84,17 @@ function MainGUI_EnableDisableGUI(handles, val)
 
 % Processing element panel
 set(handles.listboxGroupTree, 'enable', val);
-set(handles.listboxFilesErr, 'enable', val);
+if strcmp(get(handles.listboxFilesErr, 'visible'), 'on')
+    set(handles.listboxFilesErr, 'enable','on');
+else
+    set(handles.listboxFilesErr, 'enable',val);
+end
 set(handles.pushbuttonHideErrors, 'enable',val);
 set(handles.radiobuttonProcTypeGroup, 'enable', val);
 set(handles.radiobuttonProcTypeSubj, 'enable', val);
 set(handles.radiobuttonProcTypeSess, 'enable', val);
 set(handles.radiobuttonProcTypeRun, 'enable', val);
-set(handles.textStatus, 'enable', val);
+set(handles.textStatus, 'enable','on');
 
 % Data plot panel
 set(handles.textPanLeftRight, 'enable', val);
@@ -153,12 +157,17 @@ function MainGUI_EnableDisablePlotEditMode(handles, val)
 
 % Processing element panel
 set(handles.listboxGroupTree, 'enable', val);
-set(handles.listboxFilesErr, 'enable', val);
+if strcmp(get(handles.listboxFilesErr, 'visible'), 'on')
+    set(handles.listboxFilesErr, 'enable','on');
+else
+    set(handles.listboxFilesErr, 'enable',val);
+end
+set(handles.textStatus, 'enable','on');
+set(handles.pushbuttonHideErrors, 'enable',val);
 set(handles.radiobuttonProcTypeGroup, 'enable', val);
 set(handles.radiobuttonProcTypeSubj, 'enable', val);
 set(handles.radiobuttonProcTypeSess, 'enable', val);
 set(handles.radiobuttonProcTypeRun, 'enable', val);
-set(handles.textStatus, 'enable', val);
 
 % Control
 set(handles.pushbuttonCalcProcStream, 'enable', val);
@@ -246,6 +255,7 @@ function MainGUI_EnableDisablePlotEditMode(handles, val)
 % Load date files into group tree object
 maingui.dataTree = LoadDataTree(maingui.groupDirs, maingui.format, procStreamFile);
 if maingui.dataTree.IsEmpty()
+    DisplayGroupTree(handles);
     return;
 end
 if ~isempty(maingui.unitTest)
@@ -367,7 +377,7 @@ function DisplayGroupTree(handles)
 % Initialize listboxGroupTree params struct
 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
 maingui.listboxGroupTreeParams = struct('listMaps',struct('names',{{}}, 'idxs', []), ...
-                                        'views', struct('GROUP',1, 'SUBJS',2, 'SESS',3, 'NOSESS',4, 'RUNS',5), ...
+                                        'views',struct('GROUP',1, 'SUBJS',2, 'SESS',3, 'NOSESS',4, 'RUNS',5), ...
                                         'viewSetting',0);
 
 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
@@ -379,13 +389,16 @@ function DisplayGroupTree(handles)
 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
 % Determine the best view for the data files 
 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
-[viewSetting, views] = SetView(handles, nSubjs, nSess, nRuns);
+[viewSetting, ~] = SetView(handles, nSubjs, nSess, nRuns);
 
 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
 % Set listbox used for displaying valid data
 % Get the GUI listboxGroupTree setting 
 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
-listboxGroup = maingui.listboxGroupTreeParams.listMaps(viewSetting).names;
+listboxGroup = {};
+if viewSetting <= length(maingui.listboxGroupTreeParams.listMaps)
+    listboxGroup = maingui.listboxGroupTreeParams.listMaps(viewSetting).names;
+end
 
 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
 % Set listbox used for displaying files that did not load correctly
@@ -417,8 +430,16 @@ function DisplayGroupTree(handles)
     if nFilesFailed > 0 || nFilesWarning > 0
         set(handles.textStatus, 'foregroundcolor',maingui.errcolor);
         if nFilesFailed > 0
-            set(handles.listboxFilesErr, 'visible','on', 'value',1, 'string',listboxFilesErr)
+            set(handles.listboxFilesErr, 'visible','on', 'enable','on','value',1, 'string',listboxFilesErr)
             set(handles.pushbuttonHideErrors, 'visible','on');
+            if nFileSuccess==0
+                set(handles.pushbuttonHideErrors, 'visible','off');
+                p1 = get(handles.listboxGroupTree, 'position');
+                p2 = get(handles.listboxFilesErr, 'position');
+                offset_y = p1(4)/2;
+                set(handles.listboxGroupTree, 'position',[p1(1), p1(2)+offset_y, p1(3), offset_y])
+                set(handles.listboxFilesErr, 'position',[p2(1), p2(2), p2(3), p2(4)+offset_y])
+            end
         else
             set(handles.listboxFilesErr, 'visible','off');
             set(handles.pushbuttonHideErrors, 'visible','off');
@@ -436,6 +457,9 @@ function DisplayGroupTree(handles)
         set(handles.listboxGroupTree, 'position', [pos1(1) pos2(2) pos1(3) .98-pos2(2)]);
     end
 end
+if nFileSuccess==0
+    return
+end
 
 % Select initial data tree processing element in the 'Current Processing Element' panel
 idx = [1,1,1,1];

MainGUI/MapGroupTree2List.m

@@ -5,7 +5,10 @@
 % a linear index used to select a listbox entry
 
 viewSetting = maingui.listboxGroupTreeParams.viewSetting;
-idxs = maingui.listboxGroupTreeParams.listMaps(viewSetting).idxs;
+idxs = [];
+if viewSetting <= length(maingui.listboxGroupTreeParams.listMaps)
+    idxs = maingui.listboxGroupTreeParams.listMaps(viewSetting).idxs;
+end
 
 % Convert processing element tuple index to a scalar
 scalar0 = index2scalar(iGroup, iSubj, iSess, iRun);

Utils/Shared/Version.txt

@@ -1 +1 @@
-1.7.0
+1.7.1

Utils/Shared/findTypeFiles.m

@@ -35,6 +35,9 @@
             if strcmp(files(ii).name, exclList{kk})
                 exclFlag = true;
             end
+            if ~isempty(pathsubtract(files(ii).folder, exclList{kk}))
+                exclFlag = true;
+            end
         end
         if exclFlag==true
             continue;
@@ -137,3 +140,29 @@
 
 
 
+% ----------------------------------------------------------------
+function diff = pathsubtract(p2_0, p1_0, options)
+if ~exist('options','var')
+    options = '';
+end
+if optionExists(options, 'nochange')
+    option = '';
+else
+    option = 'full';
+end
+p1 = filesepStandard(p1_0, option);
+p2 = filesepStandard(p2_0, option);
+if isempty(p1)
+    p1 = p1_0;
+end
+if isempty(p2)
+    p2 = p2_0;
+end
+k = strfind(p2, p1);
+if ~isempty(k) && k(1)==1
+    diff = p2(k(1)+length(p1):end);
+elseif ~isempty(k)
+    diff = p2(1:k(1)-1);
+else
+    diff = '';
+end

Version.txt

@@ -1 +1 @@
-1.80.0
+1.80.1