From f1ceaefba7ee7dcdfd166baef18cf4de1a938fbe Mon Sep 17 00:00:00 2001
From: Christopher Rhodes <christopher.rhodes@embl.de>
Date: Wed, 10 Apr 2024 15:07:43 +0200
Subject: [PATCH] Handle sporadic ilastik error when patches are close in size
to largest filters
---
model_server/extensions/ilastik/models.py | 7 ++++++-
1 file changed, 6 insertions(+), 1 deletion(-)
diff --git a/model_server/extensions/ilastik/models.py b/model_server/extensions/ilastik/models.py
index 30e7a45e..db7ba835 100644
--- a/model_server/extensions/ilastik/models.py
+++ b/model_server/extensions/ilastik/models.py
@@ -128,11 +128,16 @@ class IlastikPixelClassifierModel(IlastikModel, SemanticSegmentationModel):
"""
Iterative over a patch stack, call inference separately on each cropped patch
"""
+ from ilastik.applets.featureSelection.opFeatureSelection import FeatureSelectionConstraintError
+
nc = len(self.labels)
data = np.zeros((img.count, *img.hw, nc, img.nz), dtype=float) # interpret as PYXCZ
for i in range(0, img.count):
sl = img.get_slice_at(i)
- data[i][sl[0], sl[1], :, sl[3]] = self.infer(img.iat(i, crop=True))[0].data
+ try:
+ data[i][sl[0], sl[1], :, sl[3]] = self.infer(img.iat(i, crop=True))[0].data
+ except FeatureSelectionConstraintError: # occurs occasionally on small patches
+ continue
return PatchStack(data), {'success': True}
def label_pixel_class(self, img: GenericImageDataAccessor, px_class: int = 0, px_prob_threshold=0.5, **kwargs):
--
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