Merge pull request #18 from gardner-lab/Liberti

Liberti
gardner-lab · Jan 23, 2020 · 4bdcb27 · 4bdcb27
2 parents b00b8d1 + ab00ded
commit 4bdcb27
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Showing 3 changed files with 16 additions and 9 deletions.
diff --git a/Analysis Pipeline/FS_Plot_ROI.m b/Analysis Pipeline/FS_Plot_ROI.m
@@ -14,7 +14,8 @@
 n = 1; % How much to interpolate by?
 roi_ave.samp_rate = 30;
 ave_fs=roi_ave.samp_rate*n; % multiply by a variable 'n' if you want to interpolate
-save_dir='roi';
+date = datestr(now);
+save_dir=['roi_',date];
 template=[];
 per=2;
 max_row=5;
@@ -28,7 +29,7 @@
 crop_correct=0;
 counteri = 1;
 ring = 0; % subtract ring around ROI ( local backgrounds)
-resize = 0.3
+resize = 0.3;
 
 
 nparams=length(varargin);
@@ -111,8 +112,8 @@
 
 
 
-
-mov_data = double(mov_data2);
+disp(['resizing video by a factor of', num2str(resize)]);
+mov_data = imresize(double(mov_data2),resize);
 
 % Check For Dropped Frames:
 if any(G >.25) %0.05 for 30fps
@@ -156,7 +157,7 @@
 						[yCoordinates, xCoordinates] = GetRing(round(ROIS.coordinates{j}*resize),rows,columns);
 						annul=mov_data(yCoordinates,xCoordinates,k);
 						roi_t(j,k)=mean(tmp(:));
-                        ring_t(j,k) = mean(annul(:));
+                        ring_t(j,k) = median(annul(:));
                 else    
 			roi_t(j,k)=mean(tmp(:));
 
@@ -190,13 +191,15 @@
 
         if ring ==1;
 %         tmp=roi_t(j,:) - ring_t(j,:); 
-        tmp = roi_t(j,:)-smooth(ring_t(j,:),12)';
+        tmp = roi_t(j,:)-smooth(ring_t(j,:),5)';
         tmp(:,1:10) = roi_t(j,1:10)-ring_t(j,1:10);
+        tmp = tmp+min(smooth(ring_t(j,:),5)); % add back the min...
         else
 		tmp=roi_t(j,:);
         end
 
         tmp = tmp(:,(1:size(timevec,2)));
+
 		if baseline==0
 			norm_fact=mean(tmp,3);
 		elseif baseline==1

diff --git a/Analysis Pipeline/FS_tiff.m b/Analysis Pipeline/FS_tiff.m
@@ -18,7 +18,7 @@ function FS_tiff(videodata,varargin)
 
 
 
-  filename = 'G.tiff';
+  filename = 'G';
 format_switch = 1;
   nparams=length(varargin);
 

diff --git a/Analysis Pipeline/GetRing.m b/Analysis Pipeline/GetRing.m
@@ -3,12 +3,16 @@
   G = boundary(ROI_dat);
   G2 = round(G*1);
 
-  scalF = 1.5;
+  scalF = 2.5;
   scalF2 = scalF-1;
+
+  moat = 2;
+  scalF3 = moat-1;
 
 
   h = poly2mask(ROI_dat(G,1)*scalF-mean(ROI_dat(G,1))*scalF2 ,ROI_dat(G,2)*scalF -mean(ROI_dat(G,2)*scalF2),row,col);
-  h2 = poly2mask(ROI_dat(G,1),ROI_dat(G,2),row,col);
+  h2 = poly2mask(ROI_dat(G,1)*moat-mean(ROI_dat(G,1))*scalF3 ,ROI_dat(G,2)*moat -mean(ROI_dat(G,2)*scalF3),row,col);
+%   h2 = poly2mask(ROI_dat(G,1)+moat,ROI_dat(G,2),row,col);
 
   h3 = h-h2;
   % figure(); imagesc(h3)