From 9dd27213e4c22f7acbfc94318947db7042cb0a1b Mon Sep 17 00:00:00 2001
From: Christopher Rhodes <christopher.rhodes@embl.de>
Date: Mon, 30 Oct 2023 11:03:32 +0100
Subject: [PATCH] Wrong key name, needed to delete tree from
ObjectClassification group
---
.../examples/test_modify_object_classifier.py | 2 +-
...nsfer_labels_to_ilastik_object_classifier.py | 17 +++++++++--------
2 files changed, 10 insertions(+), 9 deletions(-)
diff --git a/extensions/chaeo/examples/test_modify_object_classifier.py b/extensions/chaeo/examples/test_modify_object_classifier.py
index 11ac90e7..1c5343e5 100644
--- a/extensions/chaeo/examples/test_modify_object_classifier.py
+++ b/extensions/chaeo/examples/test_modify_object_classifier.py
@@ -19,7 +19,7 @@ def modify_ilastik_object_classifier(template_ilp: Path, lane: int = 0):
# delete ObjectClassification/ClassifierForests
keys_to_delete = [
f'ObjectExtraction/RegionFeatures/{lane:04d}',
- 'ObjectExtraction/ClassifierForests'
+ 'ObjectClassification/ClassifierForests'
]
for key in keys_to_delete:
if key in h5.keys():
diff --git a/extensions/chaeo/examples/transfer_labels_to_ilastik_object_classifier.py b/extensions/chaeo/examples/transfer_labels_to_ilastik_object_classifier.py
index d723ee7a..78418b8b 100644
--- a/extensions/chaeo/examples/transfer_labels_to_ilastik_object_classifier.py
+++ b/extensions/chaeo/examples/transfer_labels_to_ilastik_object_classifier.py
@@ -114,6 +114,7 @@ def generate_ilastik_object_classifier(
return new_ilp
+
def compare_object_maps(truth: GenericImageDataAccessor, inferred: GenericImageDataAccessor) -> pd.DataFrame:
"""
Compare two object maps to assess classification results
@@ -150,16 +151,16 @@ def compare_object_maps(truth: GenericImageDataAccessor, inferred: GenericImageD
if __name__ == '__main__':
root = Path('c:/Users/rhodes/projects/proj0011-plankton-seg/')
template_ilp = root / 'exp0014/template_obj.ilp'
- where_patch_stack = root / 'exp0009/output/labeled_patches-20231030-0001'
+ where_patch_stack = root / 'exp0009/output/labeled_patches-20231030-0002'
# auto-populate an object classifier
- # auto_ilp = generate_ilastik_object_classifier(
- # template_ilp,
- # where_patch_stack,
- # stack_name='train',
- # proj_name='auto_obj_before'
- # )
- auto_ilp = 'auto_obj_before.ilp'
+ auto_ilp = generate_ilastik_object_classifier(
+ template_ilp,
+ where_patch_stack,
+ stack_name='train',
+ proj_name='auto_obj_before'
+ )
+ # auto_ilp = 'auto_obj_before.ilp'
def infer_and_compare_training_set(ilp, suffix):
# infer object labels from the same data used to train the classifier
--
GitLab