adding preference option for annot timestamp format

bento/annotations/setAnnotSaveType.m

@@ -0,0 +1,20 @@
+function setAnnotSaveType(source)
+%
+% (C) Ann Kennedy, 2019
+% California Institute of Technology
+% Licensing: https://github.com/annkennedy/bento/blob/master/LICENSE.txt
+
+
+
+gui=guidata(source);
+answer = questdlg('Units for saved annotations:', ...
+	'Set annotation save format', ...
+	'Frames','Time (seconds)','Frames');
+
+switch answer
+    case 'Frames'
+        gui.annot.saveAsTime = false;
+    otherwise
+        gui.annot.saveAsTime = true;
+end
+guidata(gui.h0,gui);

bento/gui/setActiveMouse.m

@@ -33,7 +33,7 @@
         case 'Yes'
             gui.allData(mOld).(sessOld)(trOld).annot = gui.data.annot;
 			suggestedName = ['mouse' num2str(mOld) '_' sessOld '_' num2str(trOld,'%03d') '.annot'];
-            saveAnnotSheetTxt(gui.data.io.movie.fid,gui.data,suggestedName);
+            saveAnnotSheetTxt(gui.data.io.movie.fid,gui.data,suggestedName,0,gui.annot.saveAsTime);
             gui.annot.modified = 0;
         case 'No'
             gui.allData(mOld).(sessOld)(trOld).annot = gui.data.annot;

bento/popups/edit annotations/Manager_applyLabelChanges.m

@@ -29,7 +29,7 @@ function Manager_applyLabelChanges(source,~)
 
     dat     = data(m).(sess)(trial);
 	suggestedName = ['mouse' num2str(m) '_' sess '_' num2str(trial,'%03d') '.annot'];
-    saveAnnotSheetTxt(gui.data.io.movie.fid,dat,suggestedName);
+    saveAnnotSheetTxt(gui.data.io.movie.fid,dat,suggestedName,0,gui.annot.saveAsTime);
 end
 gui = setActiveMouse(gui,m,sess,trial,0);
 guidata(gui.h0,gui);

bento/saving data/makeBehaviorSummary.m

@@ -1,12 +1,12 @@
-function [M,channelSummary] = makeBehaviorSummary(channel,tmin,tmax,FR,frameFlag)
+function [M,channelSummary] = makeBehaviorSummary(channel,tmin,tmax,FR,saveAsTime)
 %
 % (C) Ann Kennedy, 2019
 % California Institute of Technology
 % Licensing: https://github.com/annkennedy/bento/blob/master/LICENSE.txt
 
-% set a default value of frameFlag
-if(~exist('frameFlag','var'))
-    frameFlag = false;
+% set a default value of saveAsTime
+if(~exist('saveAsTime','var'))
+    saveAsTime = false;
 end
 
 M = {};
@@ -20,12 +20,12 @@
         M{1,count*3-2} = fields{f};
         M(2,(count-1)*3+(1:3)) = {'Start','Stop','Duration'};
 
-        if(frameFlag) % save in frames
-            M(2+(1:size(channel.(fields{f}),1)),count*3-[2 1]) = num2cell(channel.(fields{f}));
-            delta = 1;
-        else % save in seconds (default)
+        if(saveAsTime) % save in seconds
             M(2+(1:size(channel.(fields{f}),1)),count*3-[2 1]) = num2cell(channel.(fields{f})/FR);
             delta = 1/FR;
+        else            % save in frames (default)
+            M(2+(1:size(channel.(fields{f}),1)),count*3-[2 1]) = num2cell(channel.(fields{f}));
+            delta = 1;
         end
         delta = delta + channel.(fields{f})(:,2) - channel.(fields{f})(:,1);
         M(2+(1:size(channel.(fields{f}),1)),count*3) = num2cell(delta);

bento/saving data/quickSave.m

@@ -22,9 +22,9 @@ function quickSave(source,~)
     suggestedName = ['mouse' num2str(m) '_' sess '_' num2str(tr,'%03d') '.annot'];
 end
 if(isfield(trial.io.movie,'fid')) %save the file too
-    fname = saveAnnotSheetTxt(trial.io.movie.fid,gui.data,suggestedName,0,0);
+    fname = saveAnnotSheetTxt(trial.io.movie.fid,gui.data,suggestedName,0,gui.annot.saveAsTime);
 else
-    fname = saveAnnotSheetTxt([],gui.data,suggestedName,0,0);
+    fname = saveAnnotSheetTxt([],gui.data,suggestedName,0,gui.annot.saveAsTime);
 end
 
 gui.annot.modified = 0;

bento/saving data/saveAnnot.m

@@ -1,12 +1,12 @@
-function saveAnnot(filename,annot,tmin,tmax,FR,movieNames,stim,frameFlag)
+function saveAnnot(filename,annot,tmin,tmax,FR,movieNames,stim,saveAsTime)
 %
 % (C) Ann Kennedy, 2019
 % California Institute of Technology
 % Licensing: https://github.com/annkennedy/bento/blob/master/LICENSE.txt
 
 % set a default value of frameFlag
-if(~exist('frameFlag','var'))
-    frameFlag = false;
+if(~exist('saveAsTime','var'))
+    saveAsTime = false;
 end
 
 fid = fopen(filename,'w');
@@ -49,17 +49,17 @@ function saveAnnot(filename,annot,tmin,tmax,FR,movieNames,stim,frameFlag)
 for c = 1:length(channels)
     Ch = channels{c};
 
-    [M,summaries.(Ch)] = makeBehaviorSummary(annot.(Ch),tmin,tmax,FR,frameFlag);
+    [M,summaries.(Ch)] = makeBehaviorSummary(annot.(Ch),tmin,tmax,FR,saveAsTime);
     if(isempty(M))
         M{1,1} = '';
         continue;
     end
     %convert from frames to times, to avoid future tragedies
-    if(frameFlag)
-        if(~any(cellfun(@any,cellfun(@(x)rem(x,1),{M{:}},'uniformOutput',false))))
-            M(cellfun(@isnumeric,M)) = cellfun(@(x) x/FR,M(cellfun(@isnumeric,M)),'uniformoutput',false);
-        end
-    end
+%     if(saveAsTime)
+%         if(~any(cellfun(@any,cellfun(@(x)rem(x,1),{M{:}},'uniformOutput',false))))
+%             M(cellfun(@isnumeric,M)) = cellfun(@(x) x/FR,M(cellfun(@isnumeric,M)),'uniformoutput',false);
+%         end
+%     end
 
     fprintf(fid,'%s----------\n',channels{c});
     for beh = 1:3:size(M,2)

bento/saving data/saveAnnotSheetTxt.m

@@ -1,4 +1,4 @@
-function filename = saveAnnotSheetTxt(movieNames,trial,suggestedName,promptOverride,frameFlag)
+function filename = saveAnnotSheetTxt(movieNames,trial,suggestedName,promptOverride,saveAsTime)
 %
 % (C) Ann Kennedy, 2019
 % California Institute of Technology
@@ -33,8 +33,8 @@
 end
 
 % set a default value of frameFlag
-if(~exist('frameFlag','var'))
-    frameFlag = false;
+if(~exist('saveAsTime','var'))
+    saveAsTime = false;
 end
 
 
@@ -49,7 +49,7 @@
 
 annot = trial.annot;
 stim  = trial.stim;
-saveAnnot(filename,annot,tmin,tmax,FR,movieNames,stim,frameFlag);
+saveAnnot(filename,annot,tmin,tmax,FR,movieNames,stim,saveAsTime);
 
 
 

bento/scripts/fixAnnotFromFront.m

@@ -105,7 +105,7 @@ function fixAnnotFromFront(pth)
     disp('   saving...');
     fname = strrep(fname,'.annot','_TS.annot');
     fname = strrep(fname,'.txt','_TS.annot');
-    saveAnnot(fname,annot,tmin,tmax,FR,{movieNames},stim,0);
+    saveAnnot(fname,annot,tmin,tmax,FR,{movieNames},stim,0,1);
     disp('   done!');
 end
 

bento/scripts/fixAnnotFromTop.m

@@ -104,7 +104,7 @@ function fixAnnotFromTop(pth)
     disp('   saving...');
     fname = strrep(fname,'.annot','_TS.annot');
     fname = strrep(fname,'.txt','_TS.annot');
-    saveAnnot(fname,annot,tmin,tmax,FR,{movieNames},stim,0);
+    saveAnnot(fname,annot,tmin,tmax,FR,{movieNames},stim,0, 1);
     disp('   done!');
 end
 

bento/startup/drawAnnot.m

@@ -12,6 +12,7 @@
 annot.activeBeh     = '';
 annot.modified      = 0;
 annot.highlighting  = 0;
+annot.saveAsTime    = false;
 annot.prev          = [];
 annot.bhv           = struct();
 annot.show          = struct();

bento/startup/menu_setup.m

@@ -31,6 +31,7 @@
                  '>Set annotation &hotkeys^h',...
                  '>Fix annot timing',...
                  '>Change annot framerate',...
+                 '>Preferences...',...
              '&Display',...
                  '>Select &traces to show^t',...
                  '>Select a&nnotations to show^n',...
@@ -58,6 +59,7 @@
                 'setAnnotHotkeys(gcf,[])',...
                 'bumpAnnot(gcf)',...
                 'launchAnnoChanger(gcf)',...
+                'setAnnotSaveType(gcf)',...
              '','pickUnits(gcf)','pickAnnot(gcf)',...
              '','setScatterDims(gcf)',...
                 'clearScatterDims(gcf)',...