From c08565cb71d30f2240c5a8bddd58a4aaf0188e34 Mon Sep 17 00:00:00 2001
From: Constantin Pape <c.pape@gmx.net>
Date: Fri, 7 Jun 2019 14:19:50 +0200
Subject: [PATCH] PEP8
---
scripts/attributes/genes.py | 26 ++++++++++++--------------
1 file changed, 12 insertions(+), 14 deletions(-)
diff --git a/scripts/attributes/genes.py b/scripts/attributes/genes.py
index 49822ab..15e64ff 100755
--- a/scripts/attributes/genes.py
+++ b/scripts/attributes/genes.py
@@ -7,11 +7,10 @@ from vigra.sampling import resize
def get_bbs(data):
- shape = data.shape
num_cells = (np.max(data)).astype('int') + 1
cells_bbs = [[] for i in range(num_cells)]
mins_and_maxs = extractRegionFeatures(data.astype('float32'), data.astype('uint32'),
- features = ['Coord<Maximum >', 'Coord<Minimum >'])
+ features=['Coord<Maximum >', 'Coord<Minimum >'])
mins = mins_and_maxs['Coord<Minimum >'].astype('uint32')
maxs = mins_and_maxs['Coord<Maximum >'].astype('uint32') + 1
for cell in range(num_cells):
@@ -31,7 +30,7 @@ def get_cell_sizes(data):
for z in range(Z):
for x in range(X):
for y in range(Y):
- label = data[z,x,y]
+ label = data[z, x, y]
cell_sizes[label] += 1
cell_sizes = np.array(cell_sizes)
return cell_sizes
@@ -45,21 +44,22 @@ def get_cell_expression(segm_data, all_genes):
cell_bbs = get_bbs(segm_data)
for cell_idx in range(len(labels)):
cell_label = labels[cell_idx]
- if cell_label == 0: continue
+ if cell_label == 0:
+ continue
cell_size = cell_sizes[cell_label]
bb = cell_bbs[cell_label]
- cell_masked = (segm_data[bb]==cell_label)
- genes_in_cell = all_genes[tuple([slice(0,None),] + list(bb))]
+ cell_masked = (segm_data[bb] == cell_label)
+ genes_in_cell = all_genes[tuple([slice(0, None)] + list(bb))]
for gene in range(num_genes):
gene_expr = genes_in_cell[gene]
- gene_expr_sum = np.sum(gene_expr[cell_masked]>0)
+ gene_expr_sum = np.sum(gene_expr[cell_masked] > 0)
cells_expression[cell_idx, gene] = gene_expr_sum / cell_size
return labels, cells_expression
def write_genes_table(segm_file, genes_file, table_file, labels):
DSET = 't00000/s00/4/cells'
- NEW_SHAPE = (570,518,550)
+ NEW_SHAPE = (570, 518, 550)
GENES_DSET = 'genes'
NAMES_DSET = 'gene_names'
@@ -73,17 +73,15 @@ def write_genes_table(segm_file, genes_file, table_file, labels):
gene_names = [i.decode('utf-8') for i in f[NAMES_DSET]]
num_genes = len(gene_names)
- downsampled_data = resize(segment_data.astype("float32"), shape = NEW_SHAPE, order=0).astype('uint16')
+ downsampled_data = resize(segment_data.astype("float32"), shape=NEW_SHAPE, order=0).astype('uint16')
avail_labels, expression = get_cell_expression(downsampled_data, all_genes)
with open(genes_table_file, 'w') as genes_table:
csv_writer = csv.writer(genes_table, delimiter='\t')
- _ = csv_writer.writerow(['label_id',] + gene_names)
+ _ = csv_writer.writerow(['label_id'] + gene_names)
for label in labels:
if label in avail_labels:
idx = avail_labels.index(label)
- _ = csv_writer.writerow([label, ] + list(expression[idx]))
+ _ = csv_writer.writerow([label] + list(expression[idx]))
else:
- _ = csv_writer.writerow([label, ] + [0] * num_genes)
-
-
+ _ = csv_writer.writerow([label] + [0] * num_genes)
--
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