maxthr=global_params['max_thr'], extract_cc=True, se=None, ss=None, dview=dview) A_thr_bin = A_thr > 0 size_neurons = A_thr_bin.sum(0) idx_size_neurons = np.where((size_neurons > min_size_neuro) & (size_neurons < max_size_neuro))[0] #A_thr = A_thr[:,idx_size_neuro] print(A_thr.shape) #%% duplicates_gt, indeces_keep_gt, indeces_remove_gt, D_gt, overlap_gt = detect_duplicates_and_subsets( A_gt_thr_bin[:, idx_size_neurons_gt].reshape( [dims[0], dims[1], -1], order='F').transpose([2, 0, 1]) * 1., predictions=None, r_values=None, dist_thr=0.1, min_dist=10, thresh_subset=0.6) idx_components_gt = idx_size_neurons_gt.copy() if len(duplicates_gt) > 0: if plot_on: pl.figure() pl.subplot(1, 3, 1) pl.imshow(A_gt_thr_bin[:, idx_size_neurons_gt].reshape( [dims[0], dims[1], -1], order='F').transpose( [2, 0, 1])[np.array(duplicates_gt).flatten()].sum(0)) pl.colorbar() pl.subplot(1, 3, 2)
A_gt_thr_bin = A_gt_thr > 0 size_neurons_gt = A_gt_thr_bin.sum(0) idx_size_neurons_gt = np.where((size_neurons_gt>min_size_neuro) & (size_neurons_gt < max_size_neuro) )[0] print(A_gt_thr.shape) #%% filter for size found neurons A_thr = cm.source_extraction.cnmf.spatial.threshold_components(A.tocsc()[:,:].toarray(), dims, medw=None, thr_method='max', maxthr=global_params['max_thr'], extract_cc=True, se=None, ss=None, dview=dview) A_thr_bin = A_thr > 0 size_neurons = A_thr_bin.sum(0) idx_size_neurons = np.where((size_neurons>min_size_neuro) & (size_neurons<max_size_neuro))[0] #A_thr = A_thr[:,idx_size_neuro] print(A_thr.shape) #%% duplicates_gt, indeces_keep_gt, indeces_remove_gt, D_gt, overlap_gt = detect_duplicates_and_subsets( A_gt_thr_bin[:,idx_size_neurons_gt].reshape([dims[0],dims[1],-1],order = 'F').transpose([2,0,1])*1., predictions = None, r_values = None, dist_thr=0.1, min_dist = 10,thresh_subset = 0.6) idx_components_gt = idx_size_neurons_gt.copy() if len(duplicates_gt) > 0: if plot_on: pl.figure() pl.subplot(1,3,1) pl.imshow(A_gt_thr_bin[:,idx_size_neurons_gt].reshape([dims[0],dims[1],-1],order = 'F').transpose([2,0,1])[np.array(duplicates_gt).flatten()].sum(0)) pl.colorbar() pl.subplot(1,3,2) pl.imshow(A_gt_thr_bin[:,idx_size_neurons_gt].reshape([dims[0],dims[1],-1],order = 'F').transpose([2,0,1])[np.array(indeces_keep_gt)[:]].sum(0)) pl.colorbar() pl.subplot(1,3,3) pl.imshow(A_gt_thr_bin[:,idx_size_neurons_gt].reshape([dims[0],dims[1],-1],order = 'F').transpose([2,0,1])[np.array(indeces_remove_gt)[:]].sum(0))