change default ring and resize value options

gardner-lab · Aug 2, 2019 · f34cede · f34cede
1 parent f3db44a
commit f34cede
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Showing 4 changed files with 21 additions and 13 deletions.
diff --git a/Analysis Pipeline/FS_AV_Parse.m b/Analysis Pipeline/FS_AV_Parse.m
@@ -25,7 +25,7 @@ function FS_AV_Parse(DIR,varargin)
 gif_dir=[pwd,'/gif'];
 error_dir =[pwd,'/error'];
 plot_spectrogram =0;
-resize_factor = 0.3;
+resize_factor = 1;
 
 if exist(mat_dir,'dir') rmdir(mat_dir,'s'); end
 if exist(gif_dir,'dir') rmdir(gif_dir,'s'); end

diff --git a/Analysis Pipeline/FS_Plot_ROI.m b/Analysis Pipeline/FS_Plot_ROI.m
@@ -28,7 +28,7 @@
 crop_correct=0;
 counteri = 1;
 ring = 0; % subtract ring around ROI ( local backgrounds)
-
+resize = 0.3
 
 
 nparams=length(varargin);
@@ -126,6 +126,8 @@
 
 roi_n=length(ROIS.coordinates);
 roi_t=zeros(roi_n,frames);
+ring_t=zeros(roi_n,frames);
+
 ave_time=0:1/ave_fs:length(mic_data)/fs;
 [path,file,ext]=fileparts(mov_listing{i});
 save_file=[ file '_roi' ];
@@ -147,14 +149,15 @@
 		fprintf(1,formatstring,round((j/roi_n)*100));
 
 		for k=1:frames
-			tmp=mov_data(ROIS.coordinates{j}(:,2),ROIS.coordinates{j}(:,1),k);
+			tmp=mov_data(round(ROIS.coordinates{j}(:,2)*resize),round(ROIS.coordinates{j}(:,1)*resize),k);
 
 				if ring == 1;
 
-						[yCoordinates, xCoordinates] = GetRing(ROIS.coordinates{j},rows,columns);
+						[yCoordinates, xCoordinates] = GetRing(round(ROIS.coordinates{j}*resize),rows,columns);
 						annul=mov_data(yCoordinates,xCoordinates,k);
-						roi_t(j,k)=mean(tmp(:))-mean(annul(:));
-else
+						roi_t(j,k)=mean(tmp(:));
+                        ring_t(j,k) = mean(annul(:));
+                else    
 			roi_t(j,k)=mean(tmp(:));
 
 		end
@@ -174,7 +177,7 @@
 
 %------[ Background and Neuropil]--------%
 
-[Bgnd, Npil] = FS_neuropil(mov_data,ROIS);
+[Bgnd, Npil] = FS_neuropil(mov_data,ROIS,resize);
 
 roi_ave.Bgnd{counteri}=interp1(timevec,Bgnd,ave_time,'spline');
 roi_ave.Npil{counteri}=interp1(timevec,Npil,ave_time,'spline');
@@ -185,8 +188,14 @@
 	for j=1:roi_n
 clear tmp; clear dff; clear yy2; clear yy;
 
-
+        if ring ==1;
+%         tmp=roi_t(j,:) - ring_t(j,:); 
+        tmp = roi_t(j,:)-smooth(ring_t(j,:),12)';
+        tmp(:,1:10) = roi_t(j,1:10)-ring_t(j,1:10);
+        else
 		tmp=roi_t(j,:);
+        end
+
         tmp = tmp(:,(1:size(timevec,2)));
 		if baseline==0
 			norm_fact=mean(tmp,3);

diff --git a/Analysis Pipeline/GetRing.m b/Analysis Pipeline/GetRing.m
@@ -3,7 +3,7 @@
   G = boundary(ROI_dat);
   G2 = round(G*1);
 
-  scalF = 1.1;
+  scalF = 1.5;
   scalF2 = scalF-1;
 
 
@@ -14,7 +14,6 @@
   % figure(); imagesc(h3)
 
 
-
   [yCoordinates, xCoordinates] = find(h3);
 
   % figure(); plot(ROI.coordinates{1}(:,1),ROI.coordinates{1}(:,2)); hold on; plot(xCoordinates,yCoordinates,'*');

diff --git a/Analysis Pipeline/helpers/FS_neuropil.m b/Analysis Pipeline/helpers/FS_neuropil.m
@@ -1,4 +1,4 @@
-function [Bgnd, Npil] = FS_neuropil(out_mov,ROI)
+function [Bgnd, Npil] = FS_neuropil(out_mov,ROI,resize)
 % Extract Neuropil
 
 % d09/24/17
@@ -8,9 +8,9 @@
 % Make indexes for the ROI coordinates
   for i = 1:size(ROI.coordinates,2);
   if i == 1;
-    X2 = [ROI.coordinates{i}(:,2),ROI.coordinates{i}(:,1)];
+    X2 = [round(ROI.coordinates{i}(:,2)*resize),round(ROI.coordinates{i}(:,1)*resize)];
     else
-    X = [ROI.coordinates{i}(:,2),ROI.coordinates{i}(:,1)];
+    X = [round(ROI.coordinates{i}(:,2)*resize),round(ROI.coordinates{i}(:,1)*resize)];
     X2 = cat(1,X2,X);
   end
   end