From ac241ce3505f580e8e533c89e2460bcc15dff41f Mon Sep 17 00:00:00 2001
From: Constantin Pape <c.pape@gmx.net>
Date: Tue, 9 Jul 2019 19:27:31 +0200
Subject: [PATCH] Update nucleus mapping test
---
test/attributes/test_cell_nucleus_mapping.py | 16 ++++++----------
1 file changed, 6 insertions(+), 10 deletions(-)
diff --git a/test/attributes/test_cell_nucleus_mapping.py b/test/attributes/test_cell_nucleus_mapping.py
index b530d5e..aa1002d 100644
--- a/test/attributes/test_cell_nucleus_mapping.py
+++ b/test/attributes/test_cell_nucleus_mapping.py
@@ -15,7 +15,7 @@ sys.path.append('../..')
class TestCellNucleusMapping(unittest.TestCase):
tmp_folder = 'tmp'
- def _tearDown(self):
+ def tearDown(self):
try:
rmtree(self.tmp_folder)
except OSError:
@@ -53,15 +53,11 @@ class TestCellNucleusMapping(unittest.TestCase):
table = pandas.read_csv(output_path, sep='\t')
assert len(table) == max_id + 1
- # base_path = '../../data/0.0.0/tables/sbem-6dpf-1-whole-segmented-cells-labels/default.csv'
- # base_table = pandas.read_csv(base_path, sep='\t')
-
- # seg_key = 't00000/s00/2/cells'
- # tissue_path = '../../data/rawdata/sbem-6dpf-1-whole-segmented-tissue-labels.h5'
- # tissue_key = 't00000/s00/0/cells'
- # self.check_result(table, base_table,
- # seg_path, seg_key,
- # tissue_path, tissue_key)
+ # make sure each nucleus is mapped only once
+ nucleus_ids = table['nucleus_id'].values
+ nucleus_ids, id_counts = np.unique(nucleus_ids, return_counts=True)
+ nucleus_ids, id_counts = nucleus_ids[1:], id_counts[1:]
+ self.assertEqual(id_counts.sum(), id_counts.size)
if __name__ == '__main__':
--
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