BUNPC
diff --git a/‎DataTree/AcquiredData/Snirf/DataClass.m
Lines changed: 23 additions & 12 deletions b/‎DataTree/AcquiredData/Snirf/DataClass.m
Lines changed: 23 additions & 12 deletions
diff --git a/‎DataTree/setpaths.m
Lines changed: 152 additions & 11 deletions b/‎DataTree/setpaths.m
Lines changed: 152 additions & 11 deletions
diff --git a/‎Utils/OpenFileGUI.fig renamed to ‎Utils/Shared/OpenFileGUI.fig b/‎Utils/OpenFileGUI.fig renamed to ‎Utils/Shared/OpenFileGUI.fig
diff --git a/‎Utils/OpenFileGUI.m renamed to ‎Utils/Shared/OpenFileGUI.m
Lines changed: 2 additions & 0 deletions b/‎Utils/OpenFileGUI.m renamed to ‎Utils/Shared/OpenFileGUI.m
Lines changed: 2 additions & 0 deletions
diff --git a/‎Utils/submodules/findTypeFiles.m renamed to ‎Utils/Shared/findTypeFiles.m b/‎Utils/submodules/findTypeFiles.m renamed to ‎Utils/Shared/findTypeFiles.m
diff --git a/‎Utils/isblankline.m renamed to ‎Utils/Shared/isblankline.m b/‎Utils/isblankline.m renamed to ‎Utils/Shared/isblankline.m
diff --git a/‎Utils/isuppercase.m renamed to ‎Utils/Shared/isuppercase.m b/‎Utils/isuppercase.m renamed to ‎Utils/Shared/isuppercase.m
diff --git a/‎Utils/isvalidfuncname.m renamed to ‎Utils/Shared/isvalidfuncname.m b/‎Utils/isvalidfuncname.m renamed to ‎Utils/Shared/isvalidfuncname.m
diff --git a/‎Utils/submodules/syncSubmodules.m
Lines changed: 10 additions & 10 deletions b/‎Utils/submodules/syncSubmodules.m
Lines changed: 10 additions & 10 deletions
diff --git a/‎Version.txt
Lines changed: 1 addition & 1 deletion b/‎Version.txt
Lines changed: 1 addition & 1 deletion
@@ -8,6 +8,7 @@
 
     properties
         cache
+        diagnostic
     end
 
     methods
@@ -50,6 +51,7 @@
             % Set SNIRF fomat properties
             obj.measurementList = MeasListClass().empty();
             obj.cache = struct('measurementListMatrix',[]);
+            obj.diagnostic = false;
 
             if nargin==0
                 return;
@@ -620,10 +622,10 @@ function SaveHdf5(obj, fileobj, location)
 
                 elseif nWavelengths > 0 && nCond > 0
 
-                    for iS = 1:length(srcs)
-                        for iD = 1:length(dets)
-                            for iWl = 1:nWavelengths
-                                for iCond = 1:nCond
+                    for iCond = 1:nCond
+                        for iS = 1:length(srcs)
+                            for iD = 1:length(dets)
+                                for iWl = 1:nWavelengths
 
                                     k = find(measurementListFull(:,1)==srcs(iS) & measurementListFull(:,2)==dets(iD) & measurementListFull(:,3)==iCond &  measurementListFull(:,4)==wavelengths(iWl));
                                     if ~isempty(k)
@@ -658,10 +660,10 @@ function SaveHdf5(obj, fileobj, location)
 
                 elseif nDataTypeLabels > 0 && nCond > 0
 
-                    for iS = 1:length(srcs)
-                        for iD = 1:length(dets)
-                            for iHbType = 1:length(hbTypes)
-                                for iCond = 1:nCond
+                    for iCond = 1:nCond
+                        for iS = 1:length(srcs)
+                            for iD = 1:length(dets)
+                                for iHbType = 1:length(hbTypes)
 
                                     k = find(measurementListFull(:,1)==srcs(iS) & measurementListFull(:,2)==dets(iD) & measurementListFull(:,3)==iCond &  measurementListFull(:,4)==iHbType);
                                     if ~isempty(k)
@@ -688,7 +690,7 @@ function SaveHdf5(obj, fileobj, location)
                                 k = find(measurementListFull(:,1)==srcs(iS) & measurementListFull(:,2)==dets(iD) & measurementListFull(:,4)==wavelengths(iWl));
                                 if ~isempty(k)
                                     iSDPair = find(measurementListSDpairs(:,1)==srcs(iS) & measurementListSDpairs(:,2)==dets(iD));
-                                    d(:, iWl, iSDPair) = obj.dataTimeSeries(:,k); %#ok<*FNDSB>
+                                    d(:, iSDPair, iWl) = obj.dataTimeSeries(:,k); %#ok<*FNDSB>
                                     order(kk) = k;
                                     kk = kk+1;
                                 end
@@ -707,7 +709,7 @@ function SaveHdf5(obj, fileobj, location)
                                     k = find(measurementListFull(:,1)==srcs(iS) & measurementListFull(:,2)==dets(iD) & measurementListFull(:,3)==iCond &  measurementListFull(:,4)==wavelengths(iWl));
                                     if ~isempty(k)
                                         iSDPair = find(measurementListSDpairs(:,1)==srcs(iS) & measurementListSDpairs(:,2)==dets(iD));
-                                        d(:, iWl, iSDPair, iCond) = obj.dataTimeSeries(:,k);
+                                        d(:, iSDPair, iWl, iCond) = obj.dataTimeSeries(:,k);
                                         order(kk) = k;
                                         kk = kk+1;
                                     end
@@ -726,7 +728,7 @@ function SaveHdf5(obj, fileobj, location)
                                 k = find(measurementListFull(:,1)==srcs(iS) & measurementListFull(:,2)==dets(iD) & measurementListFull(:,4)==iHbType);
                                 if ~isempty(k)
                                     iSDPair = find(measurementListSDpairs(:,1)==srcs(iS) & measurementListSDpairs(:,2)==dets(iD));
-                                    d(:, iHbType, iSDPair) = obj.dataTimeSeries(:,k);
+                                    d(:, iSDPair, iHbType) = obj.dataTimeSeries(:,k);
                                     order(kk) = k;
                                     kk = kk+1;
                                 end
@@ -745,7 +747,7 @@ function SaveHdf5(obj, fileobj, location)
                                     k = find(measurementListFull(:,1)==srcs(iS) & measurementListFull(:,2)==dets(iD) & measurementListFull(:,3)==iCond &  measurementListFull(:,4)==iHbType);
                                     if ~isempty(k)
                                         iSDPair = find(measurementListSDpairs(:,1)==srcs(iS) & measurementListSDpairs(:,2)==dets(iD));
-                                        d(:, iHbType, iSDPair, iCond) = obj.dataTimeSeries(:,k);
+                                        d(:, iSDPair, iHbType, iCond) = obj.dataTimeSeries(:,k);
                                         order(kk) = k;
                                         kk = kk+1;
                                     end
@@ -768,7 +770,16 @@ function SaveHdf5(obj, fileobj, location)
                 ml(order) = ml;
             end
 
+            obj.SimulateErrors(d);
+        end
+        
+        
 
+        % ---------------------------------------------------------
+        function d = SimulateErrors(obj, d)
+            if obj.diagnostic == false
+                return
+            end
             d = simulateDataError(d);
         end
 
 
@@ -36,7 +36,7 @@ function setpaths(options)
     appNameInclList = {};
     exclSearchList  = {'.git','Data','Docs','*_install','*.app'};
 
-    appThis         = filesepStandard_startup(pwd);
+    appThis         = filesepStandard(pwd);
     appThisPaths    = findDotMFolders(appThis, exclSearchList);
     if addremove == 0
         if ~isempty(which('deleteNamespace.m'))
@@ -53,8 +53,8 @@ function setpaths(options)
     for ii = 1:length(appNameExclList)
         foo = which([appNameExclList{ii}, '.m'],'-all');
         for jj = 1:length(foo)
-            p = filesepStandard_startup(fileparts(foo{jj}));
-            if pathscompare_startup(appThis, p)
+            p = filesepStandard(fileparts(foo{jj}));
+            if pathscompare(appThis, p)
                 continue
             end
             fprintf('Exclude paths for %s\n', p);
@@ -67,11 +67,11 @@ function setpaths(options)
         foo = which([appNameInclList{ii}, '.m'],'-all');
         for jj = 1:length(foo)
             if jj > 1
-                p = filesepStandard_startup(fileparts(foo{jj}));
+                p = filesepStandard(fileparts(foo{jj}));
                 appExclList = [appExclList; p]; %#ok<AGROW>
                 fprintf('Exclude paths for %s\n', p);
             else
-                p = filesepStandard_startup(fileparts(foo{jj}));
+                p = filesepStandard(fileparts(foo{jj}));
                 appInclList = [appInclList; p]; %#ok<AGROW>
                 fprintf('Include paths for %s\n', p);
             end
@@ -97,7 +97,7 @@ function setpaths(options)
     % Add back all search paths for all other apps except for current app
     for ii = 1:length(appInclList)
         % This app's path has already been added
-        if pathscompare_startup(appInclList{ii}, appThis)
+        if pathscompare(appInclList{ii}, appThis)
             continue;
         end
         foo = findDotMFolders(appInclList{ii}, exclSearchList);
@@ -119,9 +119,6 @@ function setpaths(options)
 
 end
 
-appnames = [appname; dependencies()];
-PrintSystemInfo([], appnames)
-
 cd(currdir);
 
 
@@ -184,15 +181,15 @@ function removeSearchPaths(app)
 r = version('-release');
 msg = sprintf('Removing search paths for %s ...', appname);
 h = waitbar(0, msg);
-p = str2cell_startup(p, delimiter);
+p = str2cell(p, delimiter);
 for kk = 1:length(p)
     if mod(kk,100)==0
         waitbar(kk/length(p), h);
     end
     if ~isempty(strfind(lower(p{kk}), 'matlab')) && ~isempty(strfind(p{kk}, r))
         continue;
     end
-    if ~isempty(strfind(filesepStandard_startup(p{kk}), app))
+    if ~isempty(strfind(filesepStandard(p{kk}), app))
         rmpath(p{kk});
     end
 end
@@ -268,3 +265,147 @@ function   addDependenciesSearchPaths()
 end
 C(kk:end) = [];
 
+
+
+
+% -------------------------------------------------------------------------
+function dotmfolders = findDotMFolders(subdir, exclList)
+global MAXPATHLENGTH
+MAXPATHLENGTH = 8;
+
+dotmfolders = {};
+
+if ~exist('subdir','var')
+    subdir = pwd;
+end
+if ~exist('exclList','var')
+    exclList = {};
+end
+
+if ~iscell(exclList)
+    exclList = {exclList};
+end
+
+subdirFullpath = filesepStandard(subdir,'full');
+
+if ~ispathvalid(subdirFullpath, 'dir')
+    fprintf('Warning: folder %s doesn''t exist\n', subdirFullpath);
+    return;
+end
+
+% If current subjdir is in the exclList then go back to curr dir and exit
+if isExcluded(subdirFullpath, exclList)
+    return;
+end
+
+dirs = dir([subdirFullpath, '*']);
+if isempty(dirs)
+    return;
+end
+
+if isdotmfolder(subdirFullpath)
+    dotmfolders = {filesepStandard(subdirFullpath, 'nameonly')};
+end
+
+for ii = 1:length(dirs)
+    if ~dirs(ii).isdir
+        continue;
+    end
+    if dirs(ii).name(1) == '.'
+        continue;
+    end
+    dotmfolders = [dotmfolders; findDotMFolders([subdirFullpath, dirs(ii).name], exclList)]; %#ok<AGROW>
+end
+
+
+
+
+
+% -------------------------------------------------------------------------
+function b = isdotmfolder(folder)
+global MAXPATHLENGTH
+b = false;
+if ~ispathvalid(folder, 'dir')
+    return
+end
+if isempty(dir([folder,'/*.m']))
+    % Exceptions to rule that 'dotm' folder must have at least one '.m' file: 
+    % it is a an executable folder (i.e. '/bin')
+    if ~isempty(strfind(folder, '/bin/')) %#ok<*STREMP>
+        b = true;
+        return
+    end
+    return;
+else
+    rootdir = which('findDotMFolders');
+    rootdir = fileparts(rootdir);
+    rootdir = pathsubtract(rootdir, 'Utils/submodules','nochange');
+    p = pathsubtract(folder, rootdir);
+    if length(find(p=='/')) > MAXPATHLENGTH
+        return
+    end
+end
+b = true;
+
+
+
+
+% -------------------------------------------------------------------------
+function b = isExcluded(pname, exclList)
+b = true;
+if pname(end)=='/'
+    pname(end) = '';
+end
+if ~ispathvalid(pname,'dir')
+    return;
+end
+[~,f,e] = fileparts(pname);
+for ii = 1:length(exclList)
+    [c,d] = str2cell(exclList{ii},'*');
+    if isempty(d) && strcmp(c{1}, [f,e])
+        return;
+    end
+
+    % Get list of all folders matching exclList{ii} pattern, whether it be
+    % a single folder name or a wildcard pattern
+    for jj = 1:length(c)
+        k = strfind(c{jj}, [f,e]);
+        if isempty(k)
+            break;
+        end
+    end
+    if ~isempty(k)
+        return;
+    end
+end
+b = false;
+
+
+
+% -------------------------------------------------------------------------
+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
+
@@ -315,6 +315,8 @@ function dummyfunc(~, ~, ~)
 function listboxFilesFolders_KeyPressFcn(hObject, eventdata, handles)
 if strcmp(eventdata.Key, 'downarrow') || strcmp(eventdata.Key, 'uparrow')
     setappdata(hObject, 'keypress',1)
+elseif strcmp(eventdata.Key, 'home') || strcmp(eventdata.Key, 'end')
+    setappdata(hObject, 'keypress',1)
 elseif strcmp(eventdata.Key, 'return')
     editFilename_Callback(handles.editFilename, 1, handles);
 end
 
@@ -106,16 +106,16 @@
 if ~exist('peerlessonly','var')
     peerlessonly = false;
 end
-f1_1 = findTypeFiles(repo1.path, '.m');
-f1_2 = findTypeFiles(repo1.path, '.txt');
-f1_2 = findTypeFiles(repo1.path, '.cfg');
-f1_3 = findTypeFiles(repo1.path, '.numberfiles');
-f2_1 = findTypeFiles(repo2.path, '.m');
-f2_2 = findTypeFiles(repo2.path, '.cfg');
-f2_3 = findTypeFiles(repo2.path, '.numberfiles');
-f1 = [f1_1; f1_2; f1_3];
-f2 = [f2_1; f2_2; f2_3];
 
+fileTypes = {'.m','.txt','.cfg','.numberfiles','.fig'};
+for iRepo = 1:2
+    for iFt = 1:length(fileTypes)
+        if eval( sprintf('~exist(''f%d'',''var'')', iRepo) )
+            eval( sprintf('f%d = {};', iRepo) )
+        end
+        eval( sprintf('f%d = [f%d; findTypeFiles(repo%d.path, fileTypes{iFt})];', iRepo, iRepo, iRepo) )
+    end
+end
 q = 0;
 for kk = 1:length(f2)
 
@@ -152,7 +152,7 @@
         % repo1, then ADD f2 to repo1
         if repo2.datetime.num > repo1.datetime.num  
 
-            p = pathsubtract(f2{kk}, repo2.path);
+            p = pathsubtract_startup(f2{kk}, repo2.path);
             q = makeChange('add',  f2{kk}, [repo1.path, p], repo1, preview, q);
             identical = false;
 
 
@@ -1,3 +1,3 @@
-1.52.0
+1.54.0