made a function for classifying components

CNMFSetParms.m

@@ -83,6 +83,8 @@
     'make_gif           ' % save animation (default: 0)
     'save_avi           ' % save video (default: 0)
     'pause_time         ' % time to pause between each component (default: Inf, user has to click)
+    % CLASSIFY COMPONENTS (classify components.m)
+    'cl_thr             ' % overlap threshold for energy for a component to be classified as true (default: 0.8)
     ];
 
 [m,n] = size(Names);
@@ -239,6 +241,8 @@
     {0}
     {0}
     {Inf}
+    % CLASSIFY COMPONENTS (classify_components.m)
+    {0.8}
     ];
 
 for j = 1:m

run_CNMF_patches.m

@@ -207,17 +207,10 @@
 end
 fprintf(' done. \n');
 %% classify components
-ff = false(1,size(Am,2));
-for i = 1:size(Am,2)
-    a1 = Am(:,i);
-    a2 = Am(:,i).*Pm.active_pixels(:);
-    if sum(a2.^2) >= cl_thr^2*sum(a1.^2)
-        ff(i) = true;
-    end
-end
-
+ff = classify_components(Am,Pm,options);
 A = Am(:,ff);
 C = Cm(ff,:);
+
 %% update spatial components
 fprintf('Updating spatial components...');
 % FIRST COMPUTE A TEMPORAL BACKGROUND

utilities/classify_components.m

@@ -0,0 +1,36 @@
+function ff = classify_components(A,P,options)
+
+% Classify components based on their spatial overlap with the active pixels
+% Each component is classified as true if when restricted to the active
+% pixels retains at least options.cl_thr of its l_2 norm
+
+% INPUTS
+% A         : set of spatial components (d x K)
+% P         : parameter structure (must include P.active_pixels) obtained from preprocess_data.m
+% options   : options structure (optional) for reading the energy threshold
+
+% OUTPUT
+% ff        : K x 1 binary vector classifying the components
+
+% Author: Eftychios A. Pnevmatikakis
+%           Simons Foundation, 2016
+
+defoptions = CNMFSetParms;
+if nargin < 3 || isempty(options)
+    options = defoptions;
+end
+
+if ~isfield(options,'cl_thr') || isempty(options.cl_thr)
+    cl_thr = defoptions.cl_thr;
+else
+    cl_thr = options.cl_thr;
+end
+
+ff = false(1,size(A,2));
+for i = 1:size(A,2)
+    a1 = A(:,i);
+    a2 = A(:,i).*P.active_pixels(:);
+    if sum(a2.^2) >= cl_thr^2*sum(a1.^2)
+        ff(i) = true;
+    end
+end