required changes for fast merging

@Sources2D/Sources2D.m

@@ -49,21 +49,21 @@ function updateSpatial(obj, Y)
         end
 
         %% update temporal components
-        function Y_res = updateTemporal(obj, Y)
-            [obj.C, obj.f, Y_res, obj.P, obj.S] = update_temporal_components(...
+        function updateTemporal(obj, Y)
+            [obj.C, obj.f, obj.P, obj.S] = update_temporal_components(...
                 Y, obj.A, obj.b, obj.C, obj.f, obj.P, obj.options);
         end
 
         %% update temporal components in parallel
-        function Y_res = updateTemporalParallel(obj, Y)
-            [obj.C, obj.f, Y_res, obj.P, obj.S] = update_temporal_components_parallel(...
+        function updateTemporalParallel(obj, Y)
+            [obj.C, obj.f, obj.P, obj.S] = update_temporal_components_parallel(...
                 Y, obj.A, obj.b, obj.C, obj.f, obj.P, obj.options);
         end
 
         %% merge found components
-        function [nr, merged_ROIs] = merge(obj, Y_res)
+        function [nr, merged_ROIs] = merge(obj, Y)
             [obj.A, obj.C, nr, merged_ROIs, obj.P, obj.S] = merge_components(...
-                Y_res,obj.A, obj.b, obj.C, obj.f, obj.P,obj.S, obj.options);
+                Y,obj.A, obj.b, obj.C, obj.f, obj.P,obj.S, obj.options);
         end
 
         %% compute the residual

CNMFSetParms.m

@@ -63,6 +63,7 @@
     'resparse       ' % number of times that the solution is resparsened (default: 0)
     % MERGING (merge_ROIs.m)
     'merge_thr      ' % merging threshold (default: 0.85)
+    'fast_merge     ' % flag for using fast merging (default 1)
     % VIDEO (make_patch_video.m)
     'ind            ' % indeces of components to be shown (deafult: 1:4)
     'skip_frame     ' % skip frames when showing the video (default: 1 (no skipping))
@@ -213,6 +214,7 @@
     {0}
     % MERGING (merge_ROIs.m)
     {0.85}
+    {1}
     % VIDEO (make_patch_video.m)
     {[1:4]}
     {1}

demo_script.m

@@ -50,13 +50,13 @@
 [A,b] = update_spatial_components(Yr,Cin,fin,Ain,P,options);
 
 %% update temporal components
-
-[C,f,Y_res,P,S] = update_temporal_components(Yr,A,b,Cin,fin,P,options);
+% consider using update_temporal_components_parallel for increased speed
+[C,f,P,S] = update_temporal_components(Yr,A,b,Cin,fin,P,options);
 
 %% merge found components
-
-[Am,Cm,K_m,merged_ROIs,P,Sm] = merge_components(Y_res,A,b,C,f,P,S,options);
-
+tic;
+[Am,Cm,K_m,merged_ROIs,P,Sm] = merge_components(Yr,A,b,C,f,P,S,options);
+toc;
 display_merging = 1; % flag for displaying merging example
 if display_merging
     i = 1; randi(length(merged_ROIs));
@@ -78,7 +78,7 @@
 
 %% repeat
 [A2,b2] = update_spatial_components(Yr,Cm,f,Am,P,options);
-[C2,f2,Y_res,P,S2] = update_temporal_components(Yr,A2,b2,Cm,f,P,options);
+[C2,f2,P,S2] = update_temporal_components(Yr,A2,b2,Cm,f,P,options);
 [C_df,~,S_df] = extract_DF_F(Yr,[A2,b2],[C2;f2],S2,K_m+1); % extract DF/F values (optional)
 
 %% do some plotting

demo_script_class.m

@@ -53,12 +53,12 @@
 updateSpatial(obj, Yr);
 
 %% update temporal components
-Y_res = updateTemporal(obj, Yr);
+updateTemporal(obj, Yr);
 
 %% merge found components
 Apr = obj.A;    % store non-merged components
 Cpr = obj.C;
-[K_m, merged_ROIs] = merge(obj, Y_res);
+[K_m, merged_ROIs] = merge(obj, Yr);
 display_merging = 1; % flag for displaying merging example
 if display_merging
     i = 1; randi(length(merged_ROIs));
@@ -80,7 +80,7 @@
 
 %% repeat
 updateSpatial(obj, Yr);
-Y_res = updateTemporal(obj, Yr);
+updateTemporal(obj, Yr);
 [C_df, ~, S_df] = extractDF_F(obj, Yr, K_m+1);
 
 %% do some plotting