From eddbc834f2c3af153a6b9519d02187971c1dbec5 Mon Sep 17 00:00:00 2001
From: Constantin Pape <constantin.pape@iwr.uni-heidelberg.de>
Date: Tue, 11 Jun 2019 15:50:32 +0200
Subject: [PATCH] Add test for morphology attributes
---
.gitignore | 1 +
scripts/attributes/master.py | 2 +-
test/attributes/test_morphology.py | 60 ++++++++++++++++++++++++++++++
3 files changed, 62 insertions(+), 1 deletion(-)
create mode 100644 test/attributes/test_morphology.py
diff --git a/.gitignore b/.gitignore
index 8d98bb0..bfcdccd 100644
--- a/.gitignore
+++ b/.gitignore
@@ -1,2 +1,3 @@
*.h5
__pycache__/
+tmp*
diff --git a/scripts/attributes/master.py b/scripts/attributes/master.py
index e466b7f..ce8a00a 100644
--- a/scripts/attributes/master.py
+++ b/scripts/attributes/master.py
@@ -50,7 +50,7 @@ def make_cell_tables(folder, name, tmp_folder, resolution,
if not os.path.exists(aux_gene_path):
raise RuntimeError("Can't find auxiliary gene file")
gene_out = os.path.join(table_folder, 'genes.csv')
- # write_genes_table(seg_path, aux_gene_path, gene_out, label_ids)
+ write_genes_table(seg_path, aux_gene_path, gene_out, label_ids)
# make table with morphology
morpho_out = os.path.join(table_folder, 'morphology.csv')
diff --git a/test/attributes/test_morphology.py b/test/attributes/test_morphology.py
new file mode 100644
index 0000000..f92f87e
--- /dev/null
+++ b/test/attributes/test_morphology.py
@@ -0,0 +1,60 @@
+import unittest
+import sys
+import os
+import numpy as np
+sys.path.append('../..')
+
+
+# check new version of gene mapping against original
+class TestMorphologyAttributes(unittest.TestCase):
+ test_file = 'test_table.csv'
+
+ def tearDown(self):
+ try:
+ os.remove(self.test_file)
+ except OSError:
+ pass
+
+ def load_table(self, table_file):
+ table = np.genfromtxt(table_file, delimiter='\t', skip_header=1,
+ dtype='float32')
+ return table
+
+ def test_nucleus_morphology(self):
+ from scripts.attributes.morphology import write_morphology_nuclei
+
+ # compute and load the morpho table
+ seg_path = '../../data/0.0.0/segmentations/em-segmented-nuclei-labels.h5'
+ table_in_path = '../../data/0.0.0/tables/em-segmented-nuclei-labels/default.csv'
+ table_out_path = self.test_file
+ print("Start computation ...")
+ write_morphology_nuclei(seg_path, table_in_path, table_out_path)
+ table = self.load_table(table_out_path)
+
+ # load original table, make sure new and old table agree
+ original_table_file = '../../data/0.0.0/tables/em-segmented-nuclei-labels/morphology.csv'
+ original_table = self.load_table(original_table_file)
+ self.assertEqual(table.shape, original_table.shape)
+ self.assertTrue(np.allclose(table, original_table))
+
+ def test_cell_morphology(self):
+ from scripts.attributes.morphology import write_morphology_cells
+
+ # compute and load the morpho table
+ seg_path = '../../data/0.0.0/segmentations/em-segmented-cells-labels.h5'
+ mapping_path = '../../data/0.0.0/tables/em-segmented-cells-labels/objects.csv'
+ table_in_path = '../../data/0.0.0/tables/em-segmented-cells-labels/default.csv'
+ table_out_path = self.test_file
+ print("Start computation ...")
+ write_morphology_cells(seg_path, table_in_path, mapping_path, table_out_path)
+ table = self.load_table(table_out_path)
+
+ # load original table, make sure new and old table agree
+ original_table_file = '../../data/0.0.0/tables/em-segmented-cells-labels/morphology.csv'
+ original_table = self.load_table(original_table_file)
+ self.assertEqual(table.shape, original_table.shape)
+ self.assertTrue(np.allclose(table, original_table))
+
+
+if __name__ == '__main__':
+ unittest.main()
--
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