v1.79.2

-- Add more standalone startup function to setpaths.m to be able to independent of any startup code search paths except current folder
-- Chnage default value of config param Load Stim From TSV File from no to yes.

* 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.
-- 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.

AppSettings.cfg

@@ -11,9 +11,6 @@ don't ask again
 one processing element per file
 
 % Load Stim From TSV File # Yes, No
-No
-
-% Replace TSV File Tabs with Spaces # Yes, No
-No
+Yes
 
 % END

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
-
 

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

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();

DataTree/Version.txt

@@ -1,2 +1 @@
-1.14.1
-
+1.14.2

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

Utils/Shared/ConfigFileClass.m

@@ -375,6 +375,9 @@ function AddParam(obj, name, val, valOptions, iF)
             else
                 valOptions = strtrim_improve(obj.linestr(ii:jj));
                 valOptions = split(valOptions,', ');
+                for ii = 1:length(valOptions)
+                    valOptions{ii} = strtrim_improve(valOptions{ii});
+                end
             end
         end
 
@@ -416,7 +419,28 @@ function AddParam(obj, name, val, valOptions, iF)
             end
         end
 
-         % -------------------------------------------------------------------------------------------------
+
+
+        % -------------------------------------------------------------------------------------------------
+        function valOptions = GetValueOptions(obj, paramName)
+            valOptions = '';
+            if nargin<2
+                return;
+            end
+            if ~ischar(paramName)
+                return;
+            end
+            for ii = 1:length(obj.params)
+                if strcmpi(obj.params(ii).name, paramName)
+                    valOptions = obj.params(ii).valOptions;
+                    break;
+                end
+            end
+        end
+
+
+
+        % -------------------------------------------------------------------------------------------------
         function val = GetMultiValues(obj, paramName)
             val = '';
             if nargin<2
@@ -435,11 +459,24 @@ function AddParam(obj, name, val, valOptions, iF)
             end
         end
 
+
+
         % -------------------------------------------------------------------------------------------------
-        function SetValue(obj, paramName, val)
+        function SetValue(obj, paramName, val, autosave)
             if nargin<3
                 return;
             end
+            if ~exist('autosave','var')
+                autosave = 0;
+            end
+            if ischar(autosave) 
+                if strcmpi(autosave,'autosave')
+                    autosave = true;
+                end
+            else
+                autosave = false;
+            end
+
             if ~ischar(paramName)
                 return;
             end
@@ -448,6 +485,10 @@ function SetValue(obj, paramName, val)
                     obj.params(ii).val{1} = val;
                 end
             end
+
+            if autosave
+                obj.Save();
+            end
         end
 
 

Utils/Shared/Version.txt

@@ -1 +1 @@
-1.5.1
+1.6.0