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Commit 2199c143 authored by Valentyna Zinchenko's avatar Valentyna Zinchenko
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cleaned up

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1 merge request!2Merge versioning and scripts into master
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scripts/attributes/genes.py
+ 1
− 4
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...@@ -52,10 +52,7 @@ def get_cell_expression(segm_data, all_genes): ...@@ -52,10 +52,7 @@ def get_cell_expression(segm_data, all_genes):
genes_in_cell = all_genes[tuple([slice(0,None),] + list(bb))] genes_in_cell = all_genes[tuple([slice(0,None),] + list(bb))]
for gene in range(num_genes): for gene in range(num_genes):
gene_expr = genes_in_cell[gene] gene_expr = genes_in_cell[gene]
try: gene_expr_sum = np.sum(gene_expr[cell_masked]>0)
gene_expr_sum = np.sum(gene_expr[cell_masked]>0)
except:
print(gene_expr.shape, cell_masked.shape)
cells_expression[cell_idx, gene] = gene_expr_sum / cell_size cells_expression[cell_idx, gene] = gene_expr_sum / cell_size
return labels, cells_expression return labels, cells_expression
......
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