v2.42.0

-- Make condition names loading work. Display actual condition names in GUI, change condition edit boxes to condition popupmenu types. Do image recon based on the displayed condition. Pass currently selected condition to ImageRecon gui.
-- Fix another bug in image recon display where the cortex display turns all red when switching between sensitivity and Hb Conc image recon displays. Add function turnOffAllOtherPatches in setImageDisplay_EmptyImage.m to turn off visibility for all patches other than the one being displayed

* DataTree, v1.14.2
-- Fix events TSV file naming bug. Add TSV file name method TreeNode.GetStimTsvFilename() to use for all events TSV file naming. Add config param "Replace TSV File Tabs with Spaces" to handle events TSV errors when file  is a mix of spaces and tabs.
-- Fixes to setpaths for running DataTree standalone

* Utils, v1.6.0
-- Fix some bugs in events TSV stim loading error handling. Add config param "Replace TSV File Tabs with Spaces" to handle events TSV errors when file  is a mix of spaces and tabs.
-- Add method ConfigFileClass.GetValueOptions for getting all available value options for a param.

AtlasViewerGUI.m

@@ -2712,7 +2712,7 @@ function menuItemSetMCParams_Callback(~, ~, ~)
 
 
 % --------------------------------------------------------------------
-function pushbuttonCalcMetrics_new_Callback(hObject, eventdata, handles)
+function pushbuttonCalcMetrics_new_Callback(~, ~, handles)
 global atlasViewer
 
 imgrecon     = atlasViewer.imgrecon;
@@ -2740,9 +2740,9 @@ function pushbuttonCalcMetrics_new_Callback(hObject, eventdata, handles)
 
 
 % --------------------------------------------------------------------
-function menuItemImageReconGUI_Callback(hObject, eventdata, handles)
-global atlasViewer
-ImageRecon();
+function menuItemImageReconGUI_Callback(~, ~, handles)
+iCond = get(handles.editCondition,'value');
+ImageRecon(iCond);
 
 
 
@@ -2809,53 +2809,9 @@ function menuItemOverlayHbConc_Callback(~, ~, ~)
 
 
 % --------------------------------------------------------------------
-function editCondition_Callback(hObject, ~, handles)
-global atlasViewer
-
-hbconc = atlasViewer.hbconc;
-imgrecon  = atlasViewer.imgrecon;
-fwmodel   = atlasViewer.fwmodel;
-pialsurf  = atlasViewer.pialsurf;
-probe     = atlasViewer.probe;
-
-condstr = get(hObject, 'string');
-if isempty(condstr)
-    set(hObject, 'string', num2str(hbconc.iCond));
-    return;
-end
-if ~isnumber(condstr)
-    set(hObject, 'string', num2str(hbconc.iCond));
-    return;
-end
-cond = str2num(condstr);
-if floor(str2num(condstr))~=cond
-    set(hObject, 'string', num2str(hbconc.iCond));
-    return;
-end
-if (cond < 1) | (cond > size(hbconc.HbConcRaw,4))
-    set(hObject, 'string', num2str(hbconc.iCond));
-    return;
-end
-if hbconc.iCond == cond    
-    return;
-end
-val = get(handles.popupmenuImageDisplay,'value');
-if val ~= hbconc.menuoffset+1 & val ~= hbconc.menuoffset+2
-    return;
-end
-
-hbconc = calcHbConc(hbconc, probe);
-hbconc = calcHbConcCmThreshold(hbconc);
-set(hbconc.handles.editColormapThreshold, ...
-    'string',sprintf('%0.2g %0.2g', hbconc.cmThreshold(1,1), hbconc.cmThreshold(1,2)));
-
-% Turn off the other object displays that share the Image Display panel
-fwmodel = showFwmodelDisplay(fwmodel, [], 'off');
-imgrecon = showImgReconDisplay(imgrecon, [], 'off','off','off','off');
-
-hbconc = displayHbConc(hbconc, pialsurf, probe, fwmodel, imgrecon);
-
-atlasViewer.hbconc = hbconc;
+function editCondition_Callback(hObject, ~, ~)
+iCond = get(hObject, 'value');
+ImageRecon(iCond);
 
 
 

AtlasViewerGUI_enableDisable.m

@@ -18,14 +18,19 @@ function AtlasViewerGUI_enableDisable(handles)
 end
 
 
-if isempty(digpts.refpts.pos) | isempty(refpts.pos) | isempty(headsurf.mesh.vertices)
+if isempty(digpts.refpts.pos) || isempty(refpts.pos) || isempty(headsurf.mesh.vertices)
     set(handles.menuItemRegisterAtlasToDigpts,'enable','off')
 else
     set(handles.menuItemRegisterAtlasToDigpts,'enable','on')
 end
 
 % Set the GUI controls for post-probe-registration controls, 
 % like fw model, image recon, hb overlay, 
-fwmodel = updateGuiControls_AfterProbeRegistration(probe, fwmodel, imgrecon, labelssurf);
+updateGuiControls_AfterProbeRegistration(probe, fwmodel, imgrecon, labelssurf);
 
+if ~isempty(atlasViewer.dataTree)
+    set(handles.editCondition, 'string',atlasViewer.dataTree.currElem.CondNames, 'value',1,'enable','on');
+else
+    set(handles.editCondition, 'enable','off');
+end
 

Group/DataTree/AcquiredData/DataFiles/SnirfFile2Tsv.m

@@ -48,11 +48,4 @@
     writeTsv(dst, tsv);
 end
 
-% Remove stim from
-% if optionExists(options, 'removeStim')
-%     s.Load();
-%     s.stim = StimClass().empty();
-%     s.Save();
-% end
-
 

Group/DataTree/AppSettings.cfg

@@ -40,4 +40,7 @@ No
 % Quiet Mode # On, Off
 Off
 
+% Replace TSV File Tabs with Spaces # auto-replace, ask me, don't replace and don't ask me
+ask me
+
 % END

Group/DataTree/TreeNodeClass.m

@@ -548,6 +548,17 @@ function ReloadStim(obj)
 
 
 
+        % ----------------------------------------------------------------------------------
+        function fnameTsv = GetStimTsvFilename(obj)
+            fnameTsv = [];
+            if isempty(obj.acquired)
+                return;
+            end
+            fnameTsv = obj.acquired.GetStimTsvFilename();
+        end
+
+
+
         % ----------------------------------------------------------------------------------
         function EditStim(obj, waitForInput)
             if ~exist('waitForInput','var')
@@ -558,10 +569,9 @@ function EditStim(obj, waitForInput)
                 return;
             end
             filenameData = [obj.path, obj.GetFilename()];
-            [p1,f1] = fileparts(filenameData);
 
             % From data file name get events TSV file and load in matlab editor
-            filenameEvents = [p1, '/', f1, '_events.tsv'];
+            filenameEvents = obj.GetStimTsvFilename();
             if ~ispathvalid(filenameEvents)
                 obj.logger.Write('Events TSV file for %s doesn''t exist.\n', filenameData);
                 obj.ExportStim();

Group/DataTree/Version.txt

@@ -1 +1 @@
-1.14.1
+1.14.2

Group/DataTree/setpaths.m

@@ -33,6 +33,10 @@ function setpaths(addremove)
     % Add libraries on which DataTreeClass depends
     d = addDependenciesSearchPaths();
 
+    if ~isempty(which('setNamespace.m'))
+        setNamespace(appname);
+    end
+
     % Start logger only after adding library paths. Logger is in the Utils libary. 
     logger = Logger('setpaths');
 
@@ -127,15 +131,14 @@ function setpaths(addremove)
 
     warning('on','MATLAB:rmpath:DirNotFound');
 
-    PrintSystemInfo(logger, ['DataTreeClass'; d]);
+    PrintSystemInfo(logger, [appname; d]);
     logger.CurrTime('Setpaths completed on ');
     logger.Close();
     cd(currdir);
 
 catch ME
 
-    printStack(ME)
-    if exist('logger','var')
+    if exist('logger','var') && isa(logger, 'Logger')
         logger.Close();
     end
     cd(currdir);
@@ -180,7 +183,7 @@ function addSearchPaths(appPaths)
     else
         delimiter = ':';
     end        
-    appPaths = str2cell(p, delimiter);
+    appPaths = str2cell_startup(p, delimiter);
 end
 for kk = 1:length(appPaths)
     if strfind(appPaths{kk}, '.git')
@@ -225,28 +228,23 @@ function removeSearchPaths(app)
 
 % ----------------------------------------------------
 function   d = addDependenciesSearchPaths()
-if exist([pwd, '/Utils/submodules'],'dir')
-    addpath([pwd, '/Utils/submodules'],'-end');
-end
-d = dependencies();
-for ii = 1:length(d)
-    rootpath = findFolder(pwd, d{ii});
-    rootpath(rootpath=='\') = '/';
-    if ispathvalid_startup([rootpath, '/Shared'],'dir')
-        rootpath = [rootpath, '/Shared'];
-    end
-    if ~exist(rootpath,'dir')
+submodules = downloadDependencies();
+d = cell(size(submodules,1),1);
+for ii = 1:size(submodules)    
+    submodulespath = [filesepStandard_startup(pwd), submodules{ii,end}];
+    if ~exist(submodulespath,'dir')
         printMethod(sprintf('ERROR: Could not find required dependency %s\n', d{ii}));
         continue;
     end
-    addSearchPaths(rootpath);
+    printMethod(sprintf('Adding searchpaths for submodule %s\n', submodulespath));
+    addSearchPaths(submodulespath);
+    d{ii,1} = submodules{ii,end};
 end
 
 
 
-
 % -----------------------------------------------------------------------------
-function [C,k] = str2cell(str, delimiters, options)
+function [C,k] = str2cell_startup(str, delimiters, options)
 
 % Option tells weather to keep leading whitespaces. 
 % (Trailing whitespaces are always removed)
@@ -310,6 +308,55 @@ function printMethod(msg)
 
 
 
+% -------------------------------------------------------------------------
+function submodules = parseGitSubmodulesFile(repo)
+submodules = cell(0,3);
+
+if ~exist('repo','var') || isempty(repo)
+    repo = pwd;
+end
+currdir = pwd;
+if repo(end) ~= '/' && repo(end) ~= '\'
+    repo = [repo, '/'];
+end
+
+filename = [repo, '.gitmodules'];
+if ~exist(filename, 'file')
+    return;
+end
+cd(repo);
+
+fid = fopen(filename, 'rt');
+strs = textscan(fid, '%s');
+strs = strs{1};
+kk = 1;
+for ii = 1:length(strs)
+    if strcmp(strs{ii}, '[submodule')
+        jj = 1;
+        while ~strcmp(strs{ii+jj}, '[submodule')
+            if ii+jj+2>length(strs)
+                break;
+            end
+            if strcmp(strs{ii+jj}, 'path')
+                submodules{kk,2} = [pwd, '/', strs{ii+jj+2}];
+            end
+            if strcmp(strs{ii+jj}, 'path')
+                submodules{kk,3} = strs{ii+jj+2};
+            end
+            if strcmp(strs{ii+jj}, 'url')
+                submodules{kk,1} = strs{ii+jj+2};
+            end
+            jj = jj+1;
+        end
+        kk = kk+1;
+    end
+end
+fclose(fid);
+cd(currdir);
+
+
+
+
 % -------------------------------------------------------------------------
 function dirpath = findFolder(repo, dirname)
 dirpath = '';
@@ -351,9 +398,9 @@ function printMethod(msg)
     exclList = {exclList};
 end
 
-subdirFullpath = filesepStandard(subdir,'full');
+subdirFullpath = filesepStandard_startup(subdir,'full');
 
-if ~ispathvalid(subdirFullpath, 'dir')
+if ~ispathvalid_startup(subdirFullpath, 'dir')
     logger.Write('Warning: folder %s doesn''t exist\n', subdirFullpath);
     return;
 end
@@ -369,7 +416,7 @@ function printMethod(msg)
 end
 
 if isdotmfolder(subdirFullpath)
-    dotmfolders = {filesepStandard(subdirFullpath, 'nameonly')};
+    dotmfolders = {filesepStandard_startup(subdirFullpath, 'nameonly')};
 end
 
 for ii = 1:length(dirs)
@@ -390,7 +437,7 @@ function printMethod(msg)
 function b = isdotmfolder(folder)
 global MAXPATHLENGTH
 b = false;
-if ~ispathvalid(folder, 'dir')
+if ~ispathvalid_startup(folder, 'dir')
     return
 end
 if isempty(dir([folder,'/*.m']))
@@ -421,7 +468,7 @@ function printMethod(msg)
 if pname(end)=='/'
     pname(end) = '';
 end
-if ~ispathvalid(pname,'dir')
+if ~ispathvalid_startup(pname,'dir')
     return;
 end
 [~,f,e] = fileparts(pname);
@@ -452,13 +499,13 @@ function printMethod(msg)
 if ~exist('options','var')
     options = '';
 end
-if optionExists(options, 'nochange')
+if optionExists_startup(options, 'nochange')
     option = '';
 else
     option = 'full';
 end
-p1 = filesepStandard(p1_0, option);
-p2 = filesepStandard(p2_0, option);
+p1 = filesepStandard_startup(p1_0, option);
+p2 = filesepStandard_startup(p2_0, option);
 if isempty(p1)
     p1 = p1_0;
 end
@@ -481,7 +528,7 @@ function printMethod(msg)
 
 %
 % Usage:
-%    pathname = filesepStandard(pathname, options)
+%    pathname = filesepStandard_startup(pathname, options)
 %
 % Takes a pathname as argument and replaces any non-standard file/folder
 % separators with standard ones, that is '/'. It also gets rid of redundant
@@ -490,7 +537,7 @@ function printMethod(msg)
 % Example:
 %
 %   >> pathname = 'C:\dir1\\\dir2\\dir3\test1/\test2/'
-%   >> pathname = filesepStandard(pathname)
+%   >> pathname = filesepStandard_startup(pathname)
 %
 %   pathname =
 %
@@ -754,8 +801,8 @@ function printMethod(msg)
     path1 = lower(path1);
     path2 = lower(path2);
 end
-p1 = str2cell(path1,{'\','/'});
-p2 = str2cell(path2,{'\','/'});
+p1 = str2cell_startup(path1,{'\','/'});
+p2 = str2cell_startup(path2,{'\','/'});
 if length(p1) ~= length(p2)
     return;
 end

HbConc/calcHbConc.m

@@ -35,8 +35,7 @@
 end
 
 % Get condition 
-str = get(hbconc.handles.editCondition, 'string');
-hbconc.iCond = str2num(str);
+hbconc.iCond = get(hbconc.handles.editCondition, 'value');
 iCond = hbconc.iCond;
 if iCond<1 | iCond>size(hbconc.HbConcRaw,4)
     hbconc.HbO = [];