From 1a6b131da57bb7cbfe1969f4b0c71b30247f9316 Mon Sep 17 00:00:00 2001
From: Christopher Rhodes <christopher.rhodes@embl.de>
Date: Mon, 30 Oct 2023 10:19:41 +0100
Subject: [PATCH] Clean test showing that modified HDF5 isn't providing correct
results
---
.../examples/test_modify_object_classifier.py | 19 ++++++++++++-------
1 file changed, 12 insertions(+), 7 deletions(-)
diff --git a/extensions/chaeo/examples/test_modify_object_classifier.py b/extensions/chaeo/examples/test_modify_object_classifier.py
index 2cabba44..647f9461 100644
--- a/extensions/chaeo/examples/test_modify_object_classifier.py
+++ b/extensions/chaeo/examples/test_modify_object_classifier.py
@@ -7,17 +7,22 @@ import numpy as np
from extensions.chaeo.accessors import MonoPatchStack, MonoPatchStackFromFile
from extensions.chaeo.models import PatchStackObjectClassifier
-def modify_ilastik_object_classifier(template_ilp: Path, lane=0):
- where = template_ilp.parent
+
+def modify_ilastik_object_classifier(template_ilp: Path, lane: int = 0):
+ proj_dir = template_ilp.parent
proj_name = template_ilp.stem
- new_ilp = shutil.copy(template_ilp, where / ('mod_' + proj_name + '.ilp'))
+ proj_new_ilp = shutil.copy(template_ilp, proj_dir / ('mod_' + proj_name + '.ilp'))
- with h5py.File(where / new_ilp, 'r+') as h5:
+ with h5py.File(where / proj_new_ilp, 'r+') as h5:
# delete ObjectExtraction / RegionFeatures / 0000
# delete ObjectClassification/ClassifierForests
- for key in [f'ObjectExtraction/RegionFeatures/{lane:04d}', 'ObjectExtraction/ClassifierForests']:
- if (key) in h5.keys():
+ keys_to_delete = [
+ f'ObjectExtraction/RegionFeatures/{lane:04d}',
+ 'ObjectExtraction/ClassifierForests'
+ ]
+ for key in keys_to_delete:
+ if key in h5.keys():
del h5[key]
assert key not in h5.keys()
@@ -33,7 +38,7 @@ def modify_ilastik_object_classifier(template_ilp: Path, lane=0):
h5[f'{key}/filePath'] = rel_pa
assert h5[f'{key}/filePath'][()] == rel_pa.encode()
- return new_ilp
+ return proj_new_ilp
if __name__ == '__main__':
--
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