From b54bfadd6c24920458b1da91f9936d1a04474c0e Mon Sep 17 00:00:00 2001
From: Christopher Rhodes <christopher.rhodes@embl.de>
Date: Mon, 19 Feb 2024 13:53:36 +0100
Subject: [PATCH] Test coverage of patch stack object classification
---
model_server/extensions/ilastik/models.py | 21 ++++++++++---------
.../extensions/ilastik/tests/test_ilastik.py | 8 +++++--
2 files changed, 17 insertions(+), 12 deletions(-)
diff --git a/model_server/extensions/ilastik/models.py b/model_server/extensions/ilastik/models.py
index 2cd56349..9a6de5e8 100644
--- a/model_server/extensions/ilastik/models.py
+++ b/model_server/extensions/ilastik/models.py
@@ -189,7 +189,10 @@ class PatchStackObjectClassifier(IlastikObjectClassifierFromSegmentationModel):
def infer(self, input_acc: PatchStack, segmentation_acc: PatchStack) -> (np.ndarray, dict):
assert segmentation_acc.is_mask()
- assert input_acc.chroma == 1
+ if not input_acc.chroma == 1:
+ raise InvalidInputImageError('Object classifier expects only monochrome patches')
+ if not input_acc.nz == 1:
+ raise InvalidInputImageError('Object classifier expects only 2d patches')
tagged_input_data = vigra.taggedView(input_acc.pczyx, 'tczyx')
tagged_seg_data = vigra.taggedView(segmentation_acc.pczyx, 'tczyx')
@@ -205,14 +208,12 @@ class PatchStackObjectClassifier(IlastikObjectClassifierFromSegmentationModel):
assert len(obmaps) == 1, 'ilastik generated more than one object map'
- # for some reason ilastik scrambles these axes to Z(1)YX(1)
- assert obmaps[0].shape == (input_acc.nz, 1, input_acc.hw[0], input_acc.hw[1], 1)
- yxz = np.moveaxis(
- obmaps[0][:, 0, :, :, 0],
- [1, 2, 0],
- [0, 1, 2]
+ # for some reason ilastik scrambles these axes to P(1)YX(1); unclear which should be Z and C
+ assert obmaps[0].shape == (input_acc.count, 1, input_acc.hw[0], input_acc.hw[1], 1)
+ pyxcz = np.moveaxis(
+ obmaps[0],
+ [0, 1, 2, 3, 4],
+ [0, 4, 1, 2, 3]
)
- assert yxz.shape[0:2] == input_acc.hw
- assert yxz.shape[2] == input_acc.nz
- return PatchStack(data=yxz), {'success': True}
+ return PatchStack(data=pyxcz), {'success': True}
\ No newline at end of file
diff --git a/model_server/extensions/ilastik/tests/test_ilastik.py b/model_server/extensions/ilastik/tests/test_ilastik.py
index c21e338d..5f765ba7 100644
--- a/model_server/extensions/ilastik/tests/test_ilastik.py
+++ b/model_server/extensions/ilastik/tests/test_ilastik.py
@@ -292,5 +292,9 @@ class TestIlastikObjectClassification(unittest.TestCase):
def test_classify_patches(self):
raw_patches = self.roiset.get_raw_patches()
patch_masks = self.roiset.get_patch_masks()
- res = self.object_classifier.infer(raw_patches, patch_masks)
- self.assertEqual(0, 1)
+ res_patches, _ = self.object_classifier.infer(raw_patches, patch_masks)
+ self.assertEqual(res_patches.count, self.roiset.count)
+ for pi in range(0, res_patches.count): # assert that there is only one nonzero label per patch
+ unique = np.unique(res_patches.iat(pi))
+ self.assertEqual(len(unique), 2)
+ self.assertEqual(unique[0], 0)
--
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