From 9331b28a3396a0bb900d7fbf875cfe4c1ccdbaa7 Mon Sep 17 00:00:00 2001
From: Christopher Rhodes <christopher.rhodes@embl.de>
Date: Mon, 5 Aug 2024 11:43:35 +0200
Subject: [PATCH] Corrected Gaussian smoothing in pixel map
---
model_server/extensions/ilastik/models.py | 10 ++++++----
1 file changed, 6 insertions(+), 4 deletions(-)
diff --git a/model_server/extensions/ilastik/models.py b/model_server/extensions/ilastik/models.py
index 5e7a0a75..fe2a7052 100644
--- a/model_server/extensions/ilastik/models.py
+++ b/model_server/extensions/ilastik/models.py
@@ -107,7 +107,7 @@ class IlastikPixelClassifierParams(IlastikParams):
class IlastikPixelClassifierModel(IlastikModel, SemanticSegmentationModel):
model_id = 'ilastik_pixel_classification'
operations = ['segment', ]
-
+
def __init__(self, params: IlastikPixelClassifierParams, **kwargs):
super(IlastikPixelClassifierModel, self).__init__(params, **kwargs)
@@ -169,7 +169,7 @@ class IlastikPixelClassifierModel(IlastikModel, SemanticSegmentationModel):
pxmap, _ = self.infer(img)
sig = self.params['px_smoothing']
if sig > 0.0:
- proc = smooth(img.data, sig)
+ proc = smooth(pxmap.data, sig)
else:
proc = pxmap.data
mask = proc[:, :, self.params['px_class'], :] > self.params['px_prob_threshold']
@@ -317,9 +317,11 @@ class IlastikObjectClassifierFromPixelPredictionsModel(IlastikModel, ImageToImag
"""
if not img.shape == pxmap.shape:
raise InvalidInputImageError('Expecting input image and pixel probabilities to be the same shape')
+ if not pxmap.data.min() >= 0.0 and pxmap.data.max() <= 1.0:
+ raise InvalidInputImageError('Pixel probability values must be between 0.0 and 1.0')
pxch = kwargs.get('pixel_classification_channel', 0)
- pxtr = kwargs.get('pixel_classification_threshold', 0.5)
- mask = pxmap.get_mono(pxch).apply(lambda x: x > pxtr)
+ pxtr = kwargs('pixel_classification_threshold', 0.5)
+ mask = InMemoryDataAccessor(pxmap.get_one_channel_data(pxch).data > pxtr)
obmap, _ = self.infer(img, mask)
return obmap
--
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