Merge pull request #9 from maljoras/development

bug fixes

+fish/+stimulus/@Presenter/Presenter.m

@@ -85,7 +85,10 @@ function initProgressBar(self)
                                     'Name',sprintf('%s progress..',class(self)));
 
         set(self.progressBarH,'CloseRequestFcn',@closereqfun);
+      else
+        self.closeProgressBar();
       end
+
     end
 
 

+fish/+stimulus/PresenterTrackTextures.m

@@ -168,7 +168,7 @@ function reset(self)
       end
 
       if any(self.stmVelThres)
-        v = self.trackVelocity;
+        v = sqrt(sum(self.trackVelocity.^2,2));
         stmmsk = stmmsk &  v>self.stmVelThres(1);
         if length(self.stmVelThres)>1
           stmmsk = stmmsk &  v<self.stmVelThres(2);

+fish/@Tracker/Tracker.m

@@ -384,13 +384,14 @@
       opts = [];
       opts.nfish = 4;
       opts.fishlength = 100;
-      opts.fishwidth = 30;
+      opts.fishwidth = 50;
       opts.stmif = 1;
       opts.stimulus.presenter = 'fish.stimulus.PresenterCalibration';
       opts.stimulus.screen =   screenIdx;
       opts.classifier.timeToInit = Inf; 
       opts.detector.inverted = 1;
       opts.tracks.useDagResults = 0;
+      opts.tracks.initBackground = 0;
 
       ft = fish.Tracker({camIdx,''},opts);
 
@@ -400,7 +401,7 @@
 
       if plotif>1
         ft.setDisplay(1);
-        ft.setDisplay('tracks',1);      
+        ft.setDisplay('tracks',1,'stimulusProgress',0);      
       else
         ft.setDisplay(0);
       end
@@ -410,6 +411,7 @@
       ft.stimulusPresenter.width = 50; % maybe needs to be adjusted
       ft.stimulusPresenter.tmax = 30;
       ft.stimulusPresenter.freq = 0.2;
+
 
       fish.helper.verbose(['\n\n****** \tStarting calibration. ' ...
                           'Make sure that the IR filter is NOT ' ...
@@ -422,9 +424,8 @@
 
       res = ft.getTrackingResults();
 
-      pos = ft.deleteInvisible(res,'pos');
-      bbox = ft.deleteInvisible(res,'bbox');
-
+      pos = permute(ft.interpolateInvisible(res,'centroid'),[1,3,2]);
+      bbox = ft.interpolateInvisible(res,'bbox');
       [screenBoundingBox,xyframe] = getCalibrationBox(pos,bbox,ft.videoHandler.frameSize);
 
       if plotif
@@ -661,20 +662,22 @@ function initBackgroundAndObjects(self)
 
       else
         % init background  
-        n = min(self.videoHandler.history,floor(self.videoHandler.timeRange(2)*self.videoHandler.frameRate));
-        n = min(n,500);
-        self.videoHandler.reset(); % resets reader to timerange(1)
-        self.videoHandler.resetBkg();
-        self.videoHandler.initialize(0);
-        self.videoHandler.computeSegments = false;
-
-        for i = 1:n
-          self.videoHandler.step();
-          fish.helper.verbose('%1.1f%%\r',i/n*100); % some output
+        if self.opts.tracks.initBackground
+          n = min(self.videoHandler.history,floor(self.videoHandler.timeRange(2)*self.videoHandler.frameRate));
+          n = min(n,500);
+          self.videoHandler.reset(); % resets reader to timerange(1)
+          self.videoHandler.resetBkg();
+          self.videoHandler.initialize(0);
+          self.videoHandler.computeSegments = false;
+
+          for i = 1:n
+            self.videoHandler.step();
+            fish.helper.verbose('%1.1f%%\r',i/n*100); % some output
+          end
+          self.videoHandler.computeSegments = true;
+          self.videoHandler.reset();
         end
-        self.videoHandler.computeSegments = true;
-        self.videoHandler.reset();
-
+
       end
     end
 
@@ -815,12 +818,21 @@ function initTracking(self)
       self.nFramesForSingleUpdate = floor(1.5* self.nFramesForUniqueUpdate);
       self.maxFramesPerBatch = self.nFramesForSingleUpdate + 50;
 
+
       if ~isinf(self.opts.classifier.timeToInit)
         self.nFramesForInit = min(max(ceil(self.opts.classifier.timeToInit*self.avgTimeScale),1),200);
       else
         self.nFramesForInit = Inf; % disables the classifier
       end
-
+
+      fish.helper.verbose('nFramesForInit: %d',self.nFramesForInit);
+      fish.helper.verbose('nFramesAfterCrossing: %d',self.nFramesAfterCrossing);
+      fish.helper.verbose('nFramesForUniqueUpdate: %d',self.nFramesForUniqueUpdate);
+      fish.helper.verbose('nFramesForSingleUpdate: %d',self.nFramesForSingleUpdate);
+
+      fish.helper.verbose('clpMovAvgTau: %d',self.clpMovAvgTau);
+      fish.helper.verbose('minBatchN: %d',self.minBatchN );
+
     end
 
 
@@ -2535,7 +2547,7 @@ function checkVideoHandler(self)
 
       def.opts.detector.adjustThresScale = 0.95;   
       doc.detector.adjustThresScale = {'0.8..1 : reduce when detections too noisy (useKNN=0)',''};
-      
+
 
       %% reader
       def.opts.reader(1).resizeif = false;
@@ -2632,7 +2644,7 @@ function checkVideoHandler(self)
       def.opts.tracks.tauVelocity = 1; 
       doc.tracks.tauVelocity = {'Time constant to compute the ' 'velocity [avgBLC]'};
 
-
+      def.opts.tracks.initBackground = 1;
 
       %% dag
       def.opts.dag.probScale = 0.5;

+fish/@Tracker/private/generateResults.m

@@ -63,7 +63,6 @@ function generateResults(self)
       tmp(tidx,:,:,:,:,:) = field; 
       self.res.(f{1}).tracks.(f2{1}) = tmp;
     end
-    self.res.(f{1}).tracks = rmfield(self.res.(f{1}).tracks,'t');
 
     self.res.(f{1}).t = t;
     self.res.(f{1}).tabs = nan(size(t));

+fish/@Tracker/private/getCalibrationBox.m

@@ -6,7 +6,10 @@
   offset = ceil(size(pos,1)/10); 
   pos = pos(offset+1:end-offset,:,:);
   bbox = bbox(offset+1:end-offset,:,:);
-
+  dmsk = isnan(pos(:,1));
+  pos(dmsk,:,:) = [];
+  bbox(dmsk,:,:) = [];
+
   mpos = squeeze(nanmean(pos,1));
 
   % NOTE: For simplicity we assume that the screen is rectangular and

exps/texturesinregions.m

@@ -5,8 +5,8 @@
 PLOT =0
 TEST = 0;
 
-path = '/data/videos/onlinelearning';
-VIDID = 
+path = '/data/videos/onlinelearning/new';
+VIDID = 2;
 
 if LOAD && ~exist('ft','var')
 
@@ -24,9 +24,9 @@
   opts.stimulus.presenter = 'fish.stimulus.PresenterTrackTextureRegions';
   opts.detector.adjustThresScale = 1.05;
 
-  opts.fishwidth = 25;
-  opts.fishlength =  90;
-
+  opts.fishwidth = 35;
+  opts.fishlength = 150;
+  opts.detector.history = 5000;
 
   ft = fish.Tracker({0,videoFile},opts);
 end
@@ -35,9 +35,9 @@
 if COMPUTE
 
   if ~exist('sbbox','var')
-    %sbbox = fish.Tracker.calibrateStimulusScreen();
+    %sbbox = fish.Tracker.calibrateStimulusScreen(0,1);
     %sbbox =  [115,90,1550,1214];
-    sbbox = [114,69,1557,1226];
+    sbbox = [147,71,1555,1237];
   end
   opts = [];
   opts.avgVelocity = 5;
@@ -51,14 +51,14 @@
   ostm.usePredFishId = false;
 
   ostm.stmCol= parula(ft.nfish);
-  ostm.stmOnInt= 1; % in sec
+  ostm.stmOnInt= 2; % in sec
   ostm.stmOnIntCV= 0.1;   
 
-  ostm.stmOffInt= 5; % in sec
+  ostm.stmOffInt= 4; % in sec
   ostm.stmOffIntCV= 0.5; 
 
   ostm.stmSize = ft.fishlength;  
-  ostm.regSizeFactorScale = [0,0.5,1.5];
+  ostm.regSizeFactorScale = [0,1,2];
   ostm.stmSizeFactor = 1;  
   ostm.xRegions = [1/3,2/3];
 
@@ -67,7 +67,7 @@
 
   ostm.stmShiftOriSTD = -1; % random;
   ostm.stmShiftCV = 2;  
-  ostm.stmSizeFactorCV = 0.5;
+  ostm.stmSizeFactorCV = 0.25;
 
   ostm.stmVelThres = [2];
   ostm.stmBorderThres = 0.05;
@@ -76,11 +76,11 @@
 
   ostm.colBackground = [0,0,0];
   ostm.colBorder = [1,1,1];
-  ostm.borderWidth = 0.0;
+  ostm.borderWidth = 0.00;
 
 
   ostm.adaptationTime = 30;
-  ostm.tmax = 3600*5;
+  ostm.tmax = 3600*2;