v1.9.2

-- Made displaying of rejected stims work in data axes of main GUI.
-- Added motion correction unit test
-- Cleaned up, streamlined and improved many aspects of unit testing.

Author: jayd1860

DataTree/DataFiles/DeleteSnirfFiles.m

@@ -0,0 +1,26 @@
+function DeleteSnirfFiles(snirffiles0)
+
+if ~exist('snirffiles0','var')
+    snirffiles0 = SnirfFilesClass().files;
+end
+
+snirffiles = mydir('');
+if iscell(snirffiles0)
+    for ii=1:length(snirffiles0)
+        snirffiles(ii) = mydir(snirffiles0{ii});
+    end
+elseif ischar(snirffiles0)
+    snirffiles = mydir(snirffiles0);
+elseif isa(snirffiles0, 'FileClass')
+    snirffiles = snirffiles0;
+end
+
+for ii=1:length(snirffiles)
+    if snirffiles(ii).isdir
+        continue;
+    end
+    fprintf('Deleting %s\n', [snirffiles(ii).pathfull, '/', snirffiles(ii).filename]);
+    delete([snirffiles(ii).pathfull, '/', snirffiles(ii).filename]);
+    pause(0.25);
+end
+

DataTree/GroupClass.m

@@ -327,7 +327,7 @@ function Load(obj)
 
         % ----------------------------------------------------------------------------------
         function Save(obj, options)
-            if ~exist('optionsstr','var')
+            if ~exist('options','var')
                 options = 'acquired:derived';
             end
             options_s = obj.parseSaveOptions(options);

DataTree/ProcStream/FuncCallClass.m

@@ -105,6 +105,25 @@ function Copy(obj, obj2, reg)
         end
 
 
+        % ------------------------------------------------------------
+        function idx = GetParamIdx(obj, key)
+            idx = [];
+            if ~exist('key','var') || isempty(key)
+                key=1;
+            end
+            if ischar(key)
+                for ii=1:length(obj.paramIn)
+                    if strcmp(key, obj.paramIn(ii).name)
+                        idx=ii;
+                        break;
+                    end
+                end
+            elseif iswholenum(key) && (key <= length(obj.paramIn))
+                idx = key;
+            end
+        end
+        
+        
         % ------------------------------------------------------------
         function phelp = GetParamHelp(obj, key)
             phelp = '';
@@ -450,25 +469,6 @@ function AddUsageInfo(obj, reg)
     %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
     methods (Access = 'private')
 
-        % ------------------------------------------------------------
-        function idx = GetParamIdx(obj, key)
-            idx = [];
-            if ~exist('key','var') || isempty(key)
-                key=1;
-            end
-            if ischar(key)
-                for ii=1:length(obj.paramIn)
-                    if strcmp(key, obj.paramIn(ii).name)
-                        idx=ii;
-                        break;
-                    end
-                end
-            elseif iswholenum(key) && (key <= length(obj.paramIn))
-                idx = key;
-            end
-        end
-        
-        
     end
 end
 

DataTree/ProcStream/ProcInputClass.m

@@ -8,6 +8,7 @@
         CondName2Subj;           % Used by group processing stream
         CondName2Run;            % Used by subject processing stream      
         tIncMan;                 % Manually include/excluded time points
+        stimValSettings;         % Derived stim values 
         misc;
         changeFlag;              % Flag specifying if procInput+acquisition data is out 
                                  %    of sync with procResult (currently not implemented)
@@ -26,6 +27,7 @@
             obj.misc = [];
             obj.changeFlag = 0;
             obj.config = struct('procStreamCfgFile','');
+            obj.stimValSettings = struct('none',0, 'incl',1, 'excl_manual',-1, 'excl_auto',-2);
             if nargin==0
                 return;
             end
@@ -353,13 +355,31 @@ function LoadVars(obj, vars)
                 eval( sprintf('obj.misc.%s = vars.%s;', fields{ii}, fields{ii}) );
             end
         end
-
+        
+    end
+        
+    
+    
+    methods
+        
+        % ----------------------------------------------------------------------------------
+        function vals = GetStimValSettings(obj)
+            vals = obj.stimValSettings;
+        end
+        
+        
+        % ----------------------------------------------------------------------------------
+        function s = GetStims(obj)
+            s = [];
+        end
+        
 
         % ----------------------------------------------------------------------------------
         function SetTincMan(obj, val)
             obj.tIncMan = val;
         end
-                
+        
+        
         % ----------------------------------------------------------------------------------
         function val = GetTincMan(obj)
              val = obj.tIncMan;

DataTree/RunClass.m

@@ -34,9 +34,9 @@
                 obj.acquired = SnirfClass(obj.name);
             end            
             obj.CondName2Group = [];
-            obj.Load();            
+            obj.Load();
         end
-                
+
 
 
         % ----------------------------------------------------------------------------------
@@ -255,9 +255,17 @@ function SetStims_MatInput(obj,s,t,CondNames)
 
         % ----------------------------------------------------------------------------------
         function s = GetStims(obj)
+            % First look in derived data, then acquired
+            
+            % Proc stream output 
             s = obj.procStream.output.GetStims();
             if isempty(s)
-                s = obj.acquired.GetStims();
+                % Proc stream input
+                s = obj.procStream.input.GetStims();
+                if isempty(s)
+                    % Acquired data
+                    s = obj.acquired.GetStims();
+                end
             end
         end
 
@@ -436,6 +444,13 @@ function RenameCondition(obj, oldname, newname)
             obj.acquired.RenameCondition(oldname, newname);
         end
 
+        
+        % ----------------------------------------------------------------------------------
+        function vals = GetStimValSettings(obj)
+            vals = obj.procStream.input.GetStimValSettings();
+        end        
+        
+        
     end
 
 end

Homer3.m

@@ -831,52 +831,46 @@ function DisplayStim(handles)
 
 %%% Plot stim marks. This has to be done before plotting exclude time
 %%% patches because stim legend doesn't work otherwise.
-if ~isempty(procElem.GetStims())
-    t  = procElem.acquired.GetTime();
-    s  = procElem.acquired.GetStims();
-    
-    % Plot included and excluded stims
-    yrange = GetAxesYRangeForStimPlot(hAxes);
-    hLg=[];
-    idxLg=[];
-    kk=1;
-    CondColTbl = procElem.CondColTbl;
-    for iS = 1:size(s,2)
-        iCond         = procElem.CondName2Group(iS);
-        lstS          = find(s(:,iS)  ~=  0);
-        lstExclS_Auto = [];
-        lstExclS_Man  = find(s(:,iS)  == -1);
-        
-        for iS2=1:length(lstS)
-            if ~isempty(find(lstS(iS2) == lstExclS_Auto))
-                hl = plot(t(lstS(iS2))*[1 1],yrange,'-.');
-                set(hl,'linewidth',1);
-                set(hl,'color',CondColTbl(iCond,:));
-            elseif ~isempty(find(lstS(iS2) == lstExclS_Man))
-                hl = plot(t(lstS(iS2))*[1 1],yrange,'--');
-                set(hl,'linewidth',1);
-                set(hl,'color',CondColTbl(iCond,:));
-            else
-                hl = plot(t(lstS(iS2))*[1 1],yrange,'-');
-                set(hl,'linewidth',1);
-                set(hl,'color',CondColTbl(iCond,:));
-            end
-        end
-        
-        % Get handles and indices of each stim condition
-        % for legend display
-        if ~isempty(lstS)
-            % We don't want dashed lines appearing in legend, so
-            % we draw invisible solid stims over all stims to
-            % trick the legend into only showing solid lines.
-            hLg(kk) = plot(t(lstS(iS2))*[1 1],yrange,'-', 'linewidth',4, 'visible','off');
-            set(hLg(kk),'color',CondColTbl(iCond,:));
-            idxLg(kk) = iCond;
-            kk=kk+1;
+t          = procElem.GetTime();
+s          = procElem.GetStims();
+stimVals   = procElem.GetStimValSettings();
+CondColTbl = procElem.CondColTbl;
+
+% Plot included and excluded stims
+yrange = GetAxesYRangeForStimPlot(hAxes);
+hLg=[];
+idxLg=[];
+kk=1;
+for iCond = 1:size(s,2)
+    iCondGroup = procElem.CondName2Group(iCond);
+    iS = find(s(:,iCond) ~= stimVals.none);
+    for ii=1:length(iS)
+        linestyle = '';
+        if     s(iS(ii),iCond) == stimVals.excl_auto
+            linestyle = '-.';
+        elseif s(iS(ii),iCond) == stimVals.excl_manual
+            linestyle = '--';
+        elseif s(iS(ii),iCond) == stimVals.incl
+            linestyle = '-';
         end
+        hl = plot(t(iS(ii))*[1 1], yrange, linestyle);
+        set(hl, 'linewidth',1);
+        set(hl, 'color',CondColTbl(iCondGroup,:));
+    end
+    
+    % Get handles and indices of each stim condition
+    % for legend display
+    if ~isempty(iS)
+        % We don't want dashed lines appearing in legend, so
+        % we draw invisible solid stims over all stims to
+        % trick the legend into only showing solid lines.
+        hLg(kk) = plot(t(iS(1))*[1 1],yrange,'-', 'linewidth',4, 'visible','off');
+        set(hLg(kk),'color',CondColTbl(iCondGroup,:));
+        idxLg(kk) = iCondGroup;
+        kk=kk+1;
     end
-    DisplayCondLegend(hLg, idxLg);
 end
+DisplayCondLegend(hLg, idxLg);
 hold off
 set(hAxes,'ygrid','on');
 
@@ -888,6 +882,12 @@ function DisplayCondLegend(hLg, idxLg)
 dataTree = hmr.dataTree;
 procElem = dataTree.currElem;
 
+if isempty(hLg)
+    return;    
+end
+if isempty(idxLg)
+    return;    
+end
 [idxLg, k] = sort(idxLg);
 CondNamesAll = procElem.CondNamesAll;
 if ishandles(hLg)

StimEdit/stimGUI_Display.m

@@ -26,8 +26,9 @@ function stimGUI_Display(handles)
 CondColTbl     = stimEdit.dataTree.group.CondColTbl();
 t              = stimEdit.dataTree.currElem.GetTime();
 s              = stimEdit.dataTree.currElem.GetStims();
+stimVals       = stimEdit.dataTree.currElem.GetStimValSettings();
 
-[lstR,lstC] = find(abs(s)==1);
+[lstR,lstC] = find(abs(s) ~= stimVals.none);
 [lstR,k] = sort(lstR);
 lstC = lstC(k);
 nStim = length(lstR);
@@ -37,11 +38,14 @@ function stimGUI_Display(handles)
 hLg=[];
 kk=1;
 for ii=1:nStim
-    if(s(lstR(ii),lstC(ii))==1)
-        Lines(ii).handle = plot([1 1]*t(lstR(ii)), yy,'-', 'parent',handles.axes1);
-    elseif(s(lstR(ii),lstC(ii))==-1)
-        Lines(ii).handle = plot([1 1]*t(lstR(ii)), yy,'--', 'parent',handles.axes1);
+    if(s(lstR(ii),lstC(ii))==stimVals.incl)
+        linestyle = '-';
+    elseif(s(lstR(ii),lstC(ii))==stimVals.excl_manual)
+        linestyle = '--';
+    elseif(s(lstR(ii),lstC(ii))==stimVals.excl_auto)
+        linestyle = '-.';
     end
+    Lines(ii).handle = plot([1 1]*t(lstR(ii)), yy, linestyle, 'parent',handles.axes1);
 
     iCond = stimEdit.dataTree.currElem.CondName2Group(lstC(ii));
     Lines(ii).color = CondColTbl(iCond,1:3);