From 4da7a11950c9e60f800b714db977d5dd90c8d8dd Mon Sep 17 00:00:00 2001
From: Christopher Rhodes <christopher.rhodes@embl.de>
Date: Mon, 30 Oct 2023 10:19:25 +0100
Subject: [PATCH] Clean test showing that modified HDF5 isn't providing correct
results
---
.../examples/test_modify_object_classifier.py | 53 +++++++++++++++++++
1 file changed, 53 insertions(+)
create mode 100644 extensions/chaeo/examples/test_modify_object_classifier.py
diff --git a/extensions/chaeo/examples/test_modify_object_classifier.py b/extensions/chaeo/examples/test_modify_object_classifier.py
new file mode 100644
index 00000000..2cabba44
--- /dev/null
+++ b/extensions/chaeo/examples/test_modify_object_classifier.py
@@ -0,0 +1,53 @@
+from pathlib import Path
+import shutil
+
+import h5py
+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
+ proj_name = template_ilp.stem
+ new_ilp = shutil.copy(template_ilp, where / ('mod_' + proj_name + '.ilp'))
+
+ with h5py.File(where / 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():
+ del h5[key]
+ assert key not in h5.keys()
+
+ # make links to input data relative
+ for gk in ['Raw Data', 'Segmentation Image']:
+ key = f'Input Data/infos/lane{lane:04d}/{gk}'
+ assert h5[f'{key}/location'][()] == 'FileSystem'.encode()
+ pa = Path(h5[f'{key}/filePath'][()].decode())
+ assert pa.is_absolute()
+ rel_pa = pa.name
+ assert (where / rel_pa).exists()
+ del h5[f'{key}/filePath']
+ h5[f'{key}/filePath'] = rel_pa
+ assert h5[f'{key}/filePath'][()] == rel_pa.encode()
+
+ return new_ilp
+
+
+if __name__ == '__main__':
+ where = Path('c:/Users/rhodes/projects/proj0011-plankton-seg/exp0009/output/labeled_patches-20231030-0001')
+ where_ilp = where / 'auto_obj_before.ilp'
+ new_ilp = modify_ilastik_object_classifier(where_ilp)
+ model = PatchStackObjectClassifier({'project_file': where / new_ilp})
+
+ raw = MonoPatchStackFromFile(where / 'zstack_train_raw.tif')
+ mask = MonoPatchStackFromFile(where / 'zstack_train_mask.tif')
+ labels = MonoPatchStackFromFile(where / f'zstack_train_label.tif')
+
+ result, _ = model.infer(raw, mask)
+ assert isinstance(result, MonoPatchStack)
+
+ print(f'Unique labels in truth set: {np.unique(labels.data)}')
+ print(f'Unique labels in inferred set: {np.unique(result.data)}')
\ No newline at end of file
--
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