1.77.0 -- Fix stim events TSV issue with conditions names with spaces…

… - we should be able to handle that. (#170)

* v1.77.0

Utils, v1.5.0
-- Fix stim events TSV issue with conditions names with spaces - we should be able to handle that. Change rule to handle spaces and how error reporting is done in readTsv.

DataTree, v1.12.1
-- Don't load events TSV files twice - once in SnirfClass and once in AcqDataClass its superclass.

AppSettings.cfg

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

DataTree/AcquiredData/AcqDataClass.m

@@ -92,7 +92,6 @@
             if ~ischar(fileobj)
                 fileobj = '';
             end
-            obj.LoadBids(fileobj);           
         end
 
 
@@ -162,7 +161,11 @@ function Initialize(obj)
             if isempty(file)
                 return
             end
-            obj.bids.stim = readTsv([filesepStandard(p), file(1).name],'numstr2num');
+            [obj.bids.stim, err] = readTsv([filesepStandard(p), file(1).name],'numstr2num');
+%             if err < 0
+%                 obj.SetError(-8);
+%                 return;
+%             end
             if isempty(obj.bids.stim)
                 return
             end

DataTree/AcquiredData/Snirf/SnirfClass.m

@@ -455,7 +455,10 @@ function SortStims(obj)
         function err = LoadStim(obj, fileobj)
             err = 0;
 
-            if obj.LoadStimOverride(obj.GetFilename())                
+            if obj.LoadStimOverride(obj.GetFilename())
+%                 if obj.GetError()<0
+%                     err = -1;
+%                 end
                 return
             end
 

DataTree/Examples/EditStimExample.m

@@ -82,7 +82,7 @@ function EditStimExample(dataSetDir)
 
 pause(2);
 
-obj.EditStim();
+obj.EditStim(1);
 
 obj.ClosePlots();
 dataTree.ReloadStim();

DataTree/TreeNodeClass.m

@@ -549,7 +549,10 @@ function ReloadStim(obj)
 
 
         % ----------------------------------------------------------------------------------
-        function EditStim(obj)
+        function EditStim(obj, waitForInput)
+            if ~exist('waitForInput','var')
+                waitForInput = 0;
+            end
             if isempty(obj.acquired)
                 MenuBox(sprintf('%s level processing does not have stims. Please select a run to edit stim marks\n', [upper(obj.type(1)), obj.type(2:end)]));
                 return;
@@ -578,7 +581,9 @@ function EditStim(obj)
                 end
                 editorTab = editorTabs(ii);
                 editorTab.makeActive;
-                % MenuBox('Please edit TSV stim file and save it, then click the ''OK'' button.');
+                if waitForInput
+                    MenuBox('Please edit TSV stim file and save it, then click the ''OK'' button.');
+                end
             else
                 if ispc()
                     cmd = sprintf('start notepad %s', filenameEvents);
@@ -588,7 +593,9 @@ function EditStim(obj)
                     cmd = sprintf('open -a TextEdit %s', filenameEvents);
                     obj.logger.Write('cmd:  "%s"', cmd);
                     system(cmd);                    
-                    % MenuBox(sprintf('The events file associated with the current processing element is\n%s\n Open the file in a text editor to modify stim marks', filenameEvents));
+                    if waitForInput
+                        MenuBox(sprintf('The events file associated with the current processing element is\n%s\n Open the file in a text editor to modify stim marks', filenameEvents));
+                    end
                 end
             end
         end

DataTree/Version.txt

@@ -1 +1 @@
-1.12.0
+1.12.1

Utils/Shared/MenuBox.m

@@ -47,7 +47,7 @@
 if ~exist('textLineWidth','var') || isempty(textLineWidth)
     textLineWidth = 70;
 end
-if ~exist('options','var')
+if ~exist('options','var') || isempty(options)
     options = '';
 end
 
@@ -78,7 +78,7 @@
 
 
 % Initial X size and position of text
-Wtext = 70;
+Wtext = textLineWidth;
 
 nNewLines = length(find(msg == sprintf('\n')))+4; %#ok<SPRINTFN>
 nLines = ceil(length(msg) / Wtext)*1.5;
@@ -186,6 +186,9 @@
             uicontrol('parent',hf, 'style','text', 'string',bttns{k}, 'units','characters', 'position',[p(1)+4, p(2), p(3), p(4)], ...
                 'horizontalalignment','left', 'fontsize',fs(2), 'userdata',2, 'backgroundcolor',[1.0, 1.0, 1.0]);
         else
+            if nbttns==1
+                p(1) = floor(Wfig/2 - Wbttn/2);
+            end
             uicontrol('parent',hf, 'style',selectionStyle, 'string',bttns{k}, 'units','characters', 'position',[p(1), p(2), p(3), p(4)+Hbttn/2], ...
                 'tag',sprintf('%d', k), 'fontsize',fs(2), 'callback',@pushbuttonGroup_Callback, 'userdata',2, 'backgroundcolor',[1.0, 1.0, 1.0]);
         end

Utils/Shared/Version.txt

@@ -1 +1 @@
-1.4.6
+1.5.0

Utils/Shared/tsv/readTsv.m

@@ -1,4 +1,8 @@
-function [tsv, tabReplacefFlag] = readTsv(filename, option)
+function [tsv, err] = readTsv(filename, option)
+global cfg
+cfg = InitConfig(cfg);
+err = 0;
+
 tsv = struct([]);
 if ~exist('filename', 'var')
     filename = '';
@@ -20,9 +24,9 @@
     numstr2num = true;
 end
 fid = fopen(filename, 'rt');
-kk = 1;
+nLines = 0;
 ncols = 0;
-tabReplacefFlag = false;
+tabReplacefFlag = [];
 while 1
     line = fgetl(fid);
     if line==-1
@@ -32,25 +36,32 @@
         continue;
     end
 
+    nLines = nLines+1;
+
     % Get rid of any non-ascii characters from read line
     if ischar(line)
         line(line>130) = '';
         line(line<9) = '';
     end
 
     delimiter = findDelimiter(strtrim(line), ncols);
+    c = str2cell(strtrim(line), delimiter);
+    if ncols == 0
+        ncols = length(c);
+    end
+
+    % Check for errors
+    if errorCheck([f,e], nLines, c, ncols, delimiter)<0
+        err = -1;
+        return;
+    end
 
-    % If delimiter contains non-tab spaces then raise flag that 
+    % If delimiter contains non-tab spaces then raise flag that
     % they need to be replaces by tabs in a tav file
     if ~isempty(find(strcmp(delimiter,' ')))
-        fprintf('WARNING: file %s uses space separators instead of tabs. This could confuse some applitions\n', filename);
-        tabReplacefFlag = true;
+        tabReplacefFlag = [tabReplacefFlag, nLines];
     end
 
-    c = str2cell(strtrim(line), delimiter);
-    if ncols == 0
-        ncols = length(c);
-    end
     if isempty(tsv)
         tsv = cell(1,length(c));
     end
@@ -61,17 +72,24 @@
             end
         end
     end
-    tsv(kk,:) = c;
-    kk = kk+1;
+    tsv(nLines,:) = c;
 end
 fclose(fid);
 
-
 % If delimiter contains non-tab spaces then raise flag that
-% they need to be replaces by tabs in a tav file
-if tabReplacefFlag
-    fprintf('Rewriting file %s to replace space separators with tabs\n', filename);
-    writeTsv(filename, tsv);
+% they need to be replaces by tabs in a tsv file
+if ~isempty(tabReplacefFlag)
+    fprintf('WARNING: File  "%s"  uses space separators instead of tabs at lines:  [ %s ]. This could confuse some applications\n', ...
+        [f,e], num2str(tabReplacefFlag));
+    val = '';
+    if ~isempty(cfg)
+        val = cfg.GetValue('Replace TSV File Tabs with Spaces');
+    end
+    if strcmpi(val, 'Yes')
+        printMethod(sprintf('Rewriting file %s to replace space separators with tabs\n', filename));
+        copyfile(filename, [filename, '.orig']);
+        writeTsv(filename, tsv);
+    end
 end
 
 
@@ -97,15 +115,59 @@
         delimiter = sprintf('\t');
     elseif ntabs==0 && nspaces>0 && nspaces+1==ncols
         delimiter = sprintf(' ');
-    elseif ntabs>0 && nspaces>0
-        if ntabs+1 == ncols
-            delimiter = sprintf(' ');
-        elseif nspaces+1 == ncols
-            delimiter = sprintf('\t');
-        else
-            delimiter = {sprintf('\t'), ' '};
+    elseif ntabs>0 && nspaces>0 && nspaces+1==ncols
+        delimiter = {sprintf('\t'), ' '};
+    elseif ntabs>0
+        delimiter = sprintf('\t');
+    end
+end
+
+
+
+
+% -----------------------------------------------------------
+function err = errorCheck(filename, nLines, c, ncols, delimiter)
+err = 0;
+errmsg = '';
+if length(c) ~= ncols
+    errmsg{1} = sprintf('ERROR: Found %d data columns in line %d of %s which does not match number of columns in file (%d)\n\n', ...
+        length(c), nLines, filename, ncols);
+    for ii = 1:length(c)
+        errmsg{ii+1} = sprintf('col %d:    "', ii);
+        c2 = str2cell(c{ii}, {delimiter, sprintf('\t')});
+        for jj = 1:length(c2)
+            errmsg{ii+1} = [errmsg{ii+1}, sprintf('%s    ', c2{jj})];
         end
+        errmsg{ii+1} = [errmsg{ii+1}, sprintf('"\n')];
     end
 end
+if ~isempty(errmsg)
+    errmsgLen = length([errmsg{:}]);
+    if errmsgLen > 70 
+        errmsgLen = 100;
+    end
+    MenuBox(errmsg,{},[],errmsgLen);
+    err = -1;
+end
+printMethod(errmsg);
+
+
+
+% -------------------------------------------------------------------------
+function printMethod(msg)
+global logger
+if isempty(msg)
+    return;
+end
+if isa(logger', 'Logger')
+    try
+        logger.Write(msg);
+    catch
+        fprintf(msg);
+    end
+else
+    fprintf(msg);
+end
+
 
 

Version.txt

@@ -1 +1 @@
-1.76.0
+1.77.0