Merge pull request #38 from neuro-ml/dev

fixed orientation for cl-detection
neuro-ml · Jun 8, 2023 · 4b3cbf8 · 4b3cbf8
2 parents d4fdeb5 + 0a0a37c
commit 4b3cbf8
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Showing 2 changed files with 4 additions and 3 deletions.
diff --git a/amid/__version__.py b/amid/__version__.py
@@ -1 +1 @@
-__version__ = '0.11.0'
+__version__ = '0.11.1'
diff --git a/amid/cl_detection.py b/amid/cl_detection.py
@@ -3,7 +3,7 @@
 
 import numpy as np
 import SimpleITK
-from connectome import Source, Transform, meta
+from connectome import Apply, Source, Transform, meta
 from connectome.interface.nodes import Silent
 from deli import load
 from imops import crop_to_box
@@ -85,7 +85,8 @@ def spacing(i, _points):
 
     @classmethod
     def normalizer(cls):
-        return CropPadding()
+        # align the points' and image's axes
+        return Apply(points=lambda pts: {name: pt[::-1] for name, pt in pts.items()}) >> CropPadding()
 
 
 class CropPadding(Transform):