From e2b759e42a862312e66ac16fffdbd911d5d44eae Mon Sep 17 00:00:00 2001
From: Christopher Rhodes <christopher.rhodes@embl.de>
Date: Wed, 17 Apr 2024 12:31:51 +0200
Subject: [PATCH] Disabled generation of ilastik object model that receives
segmentation masks from one that receives pixel probabilities; this was
causing inaccurate results
---
model_server/extensions/ilastik/models.py | 20 -------------------
.../extensions/ilastik/tests/test_ilastik.py | 16 ---------------
2 files changed, 36 deletions(-)
diff --git a/model_server/extensions/ilastik/models.py b/model_server/extensions/ilastik/models.py
index af3b1edc..90edcec5 100644
--- a/model_server/extensions/ilastik/models.py
+++ b/model_server/extensions/ilastik/models.py
@@ -266,26 +266,6 @@ class IlastikObjectClassifierFromPixelPredictionsModel(IlastikModel, ImageToImag
obmap, _ = self.infer(img, mask)
return obmap
- def make_instance_segmentation_model(self, px_ch: int):
- """
- Generate an instance segmentation model, i.e. one that takes binary masks instead of pixel probabilities as a
- second input.
- :param px_ch: channel of pixel probability map to use
- :return:
- InstanceSegmentationModel object
- """
- class _Mod(self.__class__, InstanceSegmentationModel):
- def label_instance_class(
- self, img: GenericImageDataAccessor, mask: GenericImageDataAccessor, **kwargs
- ) -> GenericImageDataAccessor:
- if mask.dtype == 'bool':
- norm_mask = 1.0 * mask.data
- else:
- norm_mask = mask.data / np.iinfo(mask.dtype).max
- norm_mask_acc = InMemoryDataAccessor(norm_mask.astype('float32'))
- return super().label_instance_class(img, norm_mask_acc, pixel_classification_channel=px_ch)
- return _Mod(params={'project_file': self.project_file})
-
class Error(Exception):
diff --git a/model_server/extensions/ilastik/tests/test_ilastik.py b/model_server/extensions/ilastik/tests/test_ilastik.py
index a30c4cba..7a3a9c38 100644
--- a/model_server/extensions/ilastik/tests/test_ilastik.py
+++ b/model_server/extensions/ilastik/tests/test_ilastik.py
@@ -163,22 +163,6 @@ class TestIlastikPixelClassification(unittest.TestCase):
)
self.assertEqual(objmap.data.max(), 2)
- def test_make_seg_obj_model_from_pxmap_obj(self):
- self.test_run_pixel_classifier()
- fp = czifile['path']
- pxmap_model = ilm.IlastikObjectClassifierFromPixelPredictionsModel(
- {'project_file': ilastik_classifiers['pxmap_to_obj']}
- )
- seg_model = pxmap_model.make_instance_segmentation_model(px_ch=0)
- objmap = seg_model.label_instance_class(self.mono_image, self.mask)
-
- self.assertTrue(
- write_accessor_data_to_file(
- output_path / f'obmap_seg_from_pxmap_{fp.stem}.tif',
- objmap,
- )
- )
- self.assertEqual(objmap.data.max(), 2)
def test_run_object_classifier_from_segmentation(self):
self.test_run_pixel_classifier()
--
GitLab