Disabled generation of ilastik object model that receives segmentation masks...

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

@@ -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):

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()