bug fixing

flatironinstitute · Dec 1, 2015 · 5070336 · 5070336
1 parent 1d5ddd6
commit 5070336
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Showing 2 changed files with 10 additions and 3 deletions.
diff --git a/ca_source_extraction/merge_rois.py b/ca_source_extraction/merge_rois.py
@@ -14,8 +14,10 @@
 from update_spatial_components import update_spatial_components
 from update_temporal_components import update_temporal_components
 import warnings
+from scipy.ndimage.morphology import generate_binary_structure, iterate_structure
+
 #%%
-def mergeROIS(Y_res,A,b,C,f,d1,d2,P_,thr=0.8,mx=50,sn=None,deconv_method='spgl1',min_size=3,max_size=8,dist=3):
+def mergeROIS(Y_res,A,b,C,f,d1,d2,P_,thr=0.8,mx=50,sn=None,deconv_method='spgl1',min_size=3,max_size=8,dist=3,method_exp = 'ellipse', expandCore = iterate_structure(generate_binary_structure(2,1), 2).astype(int)):
     """
     merging of spatially overlapping components that have highly correlated tmeporal activity
     % The correlation threshold for merging overlapping components is user specified in P.merge_thr (default value 0.85)
@@ -100,7 +102,7 @@ def mergeROIS(Y_res,A,b,C,f,d1,d2,P_,thr=0.8,mx=50,sn=None,deconv_method='spgl1'
 
             cc,_,_,Ptemp = update_temporal_components(np.asarray(Y_res[ff,:]),A_merged[ff,i],b[ff],aa_2,f,p=p,deconv_method=deconv_method)  
 
-            aa,bb,cc = update_spatial_components(np.asarray(Y_res),cc,f,A_merged[:,i],d1=d1,d2=d2,sn=sn,min_size=min_size,max_size=max_size,dist=dist)
+            aa,bb,cc = update_spatial_components(np.asarray(Y_res),cc,f,A_merged[:,i],d1=d1,d2=d2,sn=sn,min_size=min_size,max_size=max_size,dist=dist,method = method_exp, expandCore =expandCore)
 
             A_merged[:,i] = aa.tocsr();        
 

diff --git a/ca_source_extraction/update_spatial_components.py b/ca_source_extraction/update_spatial_components.py
@@ -142,7 +142,12 @@ def determine_search_location(A, d1, d2, method = 'ellipse', min_size = 3, max_s
     elif method == 'dilate':
         for i in range(nr):
             A_temp = np.reshape(A[:,i].todense(),(d2,d1))
-            A_temp = grey_dilation(A_temp, footprint = expandCore)
+            if len(expandCore)> 0:
+                A_temp = grey_dilation(A_temp, footprint = expandCore)
+            else:
+                A_temp = grey_dilation(A_temp, (1,1))            
+
+#            A_temp = grey_dilation(A_temp, footprint = expandCore)
             IND[:,i] = np.squeeze(np.reshape(A_temp,(d,1)))>0
     else:
         IND = True*np.ones((d,nr))