From c3a8f9153b3b50ad5c556c32b55643fd2e79595f Mon Sep 17 00:00:00 2001
From: Christopher Rhodes <christopher.rhodes@embl.de>
Date: Mon, 25 Mar 2024 12:44:46 +0100
Subject: [PATCH] Generate an InstanceSegmentationModel from an
IlastikObjectClassifierFromPixelPredictionsModel given binarization
parameters
---
model_server/extensions/ilastik/models.py | 18 +++++++++++++++++-
.../extensions/ilastik/tests/test_ilastik.py | 17 +++++++++++++++++
2 files changed, 34 insertions(+), 1 deletion(-)
diff --git a/model_server/extensions/ilastik/models.py b/model_server/extensions/ilastik/models.py
index ac322e85..d3cc0d93 100644
--- a/model_server/extensions/ilastik/models.py
+++ b/model_server/extensions/ilastik/models.py
@@ -235,11 +235,27 @@ class IlastikObjectClassifierFromPixelPredictionsModel(IlastikModel, ImageToImag
if not img.shape == pxmap.shape:
raise InvalidInputImageError('Expecting input image and pixel probabilities to be the same shape')
pxch = kwargs.get('pixel_classification_channel', 0)
- pxtr = kwargs('pixel_classification_threshold', 0.5)
+ pxtr = kwargs.get('pixel_classification_threshold', 0.5)
mask = InMemoryDataAccessor(pxmap.get_one_channel_data(pxch).data > pxtr)
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:
+ return super().label_instance_class(img, mask, pixel_classification_channel=px_ch)
+ return _Mod(params={'project_file': self.project_file})
+
+
class Error(Exception):
pass
diff --git a/model_server/extensions/ilastik/tests/test_ilastik.py b/model_server/extensions/ilastik/tests/test_ilastik.py
index 21e3d9af..15bca41d 100644
--- a/model_server/extensions/ilastik/tests/test_ilastik.py
+++ b/model_server/extensions/ilastik/tests/test_ilastik.py
@@ -136,6 +136,23 @@ 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()
fp = czifile['path']
--
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