concat position, veloc, viewangle and similar vectors for all trials

Author: stephprince

diamond-maze-behavior/calcDiamondMetricsBySess.m

@@ -11,11 +11,18 @@
 disp(['Calculating session metrics for ' animalID num2str(index(1)) ' ' num2str(index(2)) ' ' num2str(index(3))]);
 
 if ~exist(filename) || makenewfiles
+    %% concatenate trial position, velocity, and viewAngle data
+    concatTrialData = concatTrialBehavior(trialdata,sessdata.params.trainingtype)
+    fnamesBehavior = fieldnames(concatTrialData);
+    for fieldIdx = 1:length(fnamesBehavior)
+        behaviorDataDiamondBySess.(fnamesBehavior{fieldIdx}) = concatTrialData.(fnamesBehavior{fieldIdx});
+    end
+
     %% concatenate trial outputs
-    concatTrialData = concatTrialOutcomes(trialdata,sessdata.params.trainingtype);
-    fnamesOutcomes = fieldnames(concatTrialData);
+    concatTrialResults = concatTrialOutcomes(trialdata,sessdata.params.trainingtype);
+    fnamesOutcomes = fieldnames(concatTrialResults);
     for fieldIdx = 1:length(fnamesOutcomes)
-        behaviorDataDiamondBySess.(fnamesOutcomes{fieldIdx}) = concatTrialData.(fnamesOutcomes{fieldIdx});
+        behaviorDataDiamondBySess.(fnamesOutcomes{fieldIdx}) = concatTrialResults.(fnamesOutcomes{fieldIdx});
     end
 
     %% get percent correct

diamond-maze-behavior/calcSessionPerformance.m

@@ -45,8 +45,11 @@
 for typeIdx = 1:length(trialTypes)
     trialsSinceCorrect = [];
     correctTrials = find(output.(['sessOutcomes' trialTypes{typeIdx}]) == 1);
-    incorrectIntervals = [correctTrials, [correctTrials(2:end)-1; length(output.(['sessOutcomes' trialTypes{typeIdx}]))]];
     if ~isempty(correctTrials)
+        incorrectIntervals = [correctTrials, [correctTrials(2:end)-1; length(output.(['sessOutcomes' trialTypes{typeIdx}]))]];
+        if incorrectIntervals(1,1) ~= 1 %if the intervals don't start at the first trial
+          incorrectIntervals = [1, incorrectIntervals(1,1)-1; incorrectIntervals];
+        end
         for i = 1:size(incorrectIntervals,1)
             startToEnd = incorrectIntervals(i,:);
             countsSinceLast = [startToEnd(1):startToEnd(2)]-startToEnd(1);

diamond-maze-behavior/concatDiamondMazeSessions.m

@@ -16,32 +16,38 @@
         for fieldIdx = 1:length(fnamesAll)
             allsessdata(animals(anIdx)).(track).(fnamesAll{fieldIdx}) = [];
         end
-        
+
         %loop through sessions and concatenate data
         sesscounter = 1; %keep track of how many sessions on each track there are
         for sessIdx = 1:size(inclsess,1)
             %initialize variabls
             sessindex = indices.behaviorindex(inclsess(sessIdx),:);
             sessdata = behaviordata.bySession{sessindex(1)}{sessindex(2)}{sessindex(3)};
             trialdata = behaviordata.byTrial{sessindex(1)}{sessindex(2)}{sessindex(3)};
-            
+
             %hacky way to get choice 1 side for now bc I was dumb and forgot to include it in the raw data structure
             if sessindex(2) > 190922 && sessindex(2) < 191030
                 sessdata.trainingtype = 'choice1side_short';
             end
 
             if strcmp(sessdata.trainingtype,track)
+
+                %combine all the fields where there is one value per trial/session
                 for fieldIdx = 1:length(fnames)
                     if isfield(sessdata, fnamesAll{fieldIdx})
                         allsessdata(animals(anIdx)).(track).(fnamesAll{fieldIdx}) = [allsessdata(animals(anIdx)).(track).(fnamesAll{fieldIdx}); sessdata.(fnamesAll{fieldIdx})];
                     end
                 end
-                
+
+                %combine fields where there are multiple values per trial (ex. viewAngle, positionX, positionY)
+
+
+
                 %sessinfo structure so you can index into trials easily
                 sessInfo = [repmat([sessindex(1:3), sesscounter],sessdata.numTrialsAll,1), [1:sessdata.numTrialsAll]'];
-                allsessdata(animals(anIdx)).(track).sessInfo = [allsessdata(animals(anIdx)).(track).sessInfo; sessInfo]; 
+                allsessdata(animals(anIdx)).(track).sessInfo = [allsessdata(animals(anIdx)).(track).sessInfo; sessInfo];
                 sesscounter = sesscounter + 1;
             end
         end
     end
-end
+end

diamond-maze-behavior/concatTrialBehavior.m

@@ -0,0 +1,21 @@
+function output = concatTrialBehavior(trialdata,tracktype)
+%SP 191121
+% this function concatenate data from trials like position, view angle, etc.
+
+%% get variables to concatenate
+fnames = fieldnames(trialdata{1});
+counter = 1;
+for fieldIdx = 1:length(fnames)
+    if size(trialdata{1}.(fnames{fieldIdx}),2) == size(trialdata{1}.time,2) %checking which fieldnames are behavior data vectors
+      fnames2concat{counter} = fnames{fieldIdx};
+      counter = counter + 1;
+    end
+end
+
+%% loop through trials to concatenate data
+trialcounter = 1; trialInfo = [];
+for trialIdx = 1:size(trialdata,2)
+    for fieldIdx = 1:length(fnames2concat)
+      output.(fnames{fieldIdx}){trialcounter} = trialdata{trialIdx}.(fnames{fieldIdx}); %change data structure so will be able to concat sessions
+    end
+end

diamond-maze-behavior/concatTrialOutcomes.m

@@ -11,7 +11,7 @@
 for trialIdx = 1:size(trialdata,2) 
     %% get info from trialdata structure
     %trial duration
-    dur = trialdata{trialIdx}.trialdur;
+    dur = trialdata{trialIdx}.trialdurRaw;
 
     % get start and reward locations
     %finds what the directions/locations are and map to number (ie,1 = north, 2 = east, 3 = south, 4 = west (like a compass lol))

diamond-maze-behavior/plotContinuousAltPerformance.m

@@ -21,10 +21,10 @@
 
     %% plot percent correct trials for each session
     trackdata.trialsSinceCorrectAll
-    plotDiamondTrackMetricsBySession(trackdata,animal,track,dirs,plotInfo,'perCorrect');
-    plotDiamondTrackMetricsBySession(trackdata,animal,track,dirs,plotInfo,'perIncorrect');
-    plotDiamondTrackMetricsBySession(trackdata,animal,track,dirs,plotInfo,'numCorrect');
-    plotDiamondTrackMetricsBySession(trackdata,animal,track,dirs,plotInfo,'numTrials');
+    % plotDiamondTrackMetricsBySession(trackdata,animal,track,dirs,plotInfo,'perCorrect');
+    % plotDiamondTrackMetricsBySession(trackdata,animal,track,dirs,plotInfo,'perIncorrect');
+    % plotDiamondTrackMetricsBySession(trackdata,animal,track,dirs,plotInfo,'numCorrect');
+    % plotDiamondTrackMetricsBySession(trackdata,animal,track,dirs,plotInfo,'numTrials');
 
 end
 

diamond-maze-behavior/resampleDiamondMazeTrials.m

@@ -14,7 +14,7 @@
 end
 
 %sets time window for resampling to constant sampling rate (in time)
-newTrialSampSize = round(trialdata.trialdur/params.constSampRateTime); %find out how many samples should be in new vect
+newTrialSampSize = round(trialdata.trialdurRaw/params.constSampRateTime); %find out how many samples should be in new vect
 newTimes = trialdata.timeRaw(1):params.constSampRateTime:((newTrialSampSize*params.constSampRateTime)+trialdata.timeRaw(1)); %get times from start to end with const time window
 for i = 1:length(fnames2resample)
   resampledVect = interp1(trialdata.timeRaw,trialdata.([fnames2resample{i} 'Raw']),newTimes,'linear','extrap'); %added extrap to get rid of accidental nan values in the data
@@ -33,11 +33,11 @@
   startingValue = trialdata.([fnames2findsteppoints{i} 'Raw'])(1);
   endingValue = trialdata.([fnames2findsteppoints{i} 'Raw'])(end);
   oldValues = [startingValue; trialdata.([fnames2findsteppoints{i} 'Raw'])(oldInds); endingValue]; %gets values at each of the indices for stepping through
-  
+
   %make new vector with step functions with step occurring at each ind
   output.(fnames2findsteppoints{i}) = zeros(size(output.(fnames2findsteppoints{i})))+startingValue;
   for stepIdx = 1:length(oldValues(2:end-1))    %only include value where switch occurred, starting value was already initialized
-    
+
     if stepIdx == length(oldValues(2:end-1))
       inds2change = newInds(stepIdx):length(output.(fnames2findsteppoints{i})); %if last indics then go to end with final value
     else