Now that RoiSet is in base, remove dependency on ilastik in its test; tests...

Now that RoiSet is in base, remove dependency on ilastik in its test; tests now open segmentation mask from file

model_server/extensions/chaeo/conf/testing.py

@@ -8,6 +8,7 @@ multichannel_zstack = {
     'h': 512,
     'c': 5,
     'z': 7,
+    'mask_path': root / 'testing' / 'zmask-test-stack-mask.tif',
 }
 
 pixel_classifier = {

tests/test_roiset.py

@@ -15,27 +15,10 @@ from model_server.base.models import DummyInstanceSegmentationModel
 class BaseTestRoiSetMonoProducts(object):
 
     def setUp(self) -> None:
-
-        # need test data incl obj map
+        # set up test raw data and segmentation from file
         self.stack = generate_file_accessor(multichannel_zstack['path'])
-        self.stack_ch_seg = self.stack.get_one_channel_data(pipeline_params['segmentation_channel'])
         self.stack_ch_pa = self.stack.get_one_channel_data(pipeline_params['patches_channel'])
-
-        self.pxmodel = IlastikPixelClassifierModel(
-            {'project_file': pixel_classifier['path']},
-        )
-        mip = InMemoryDataAccessor(
-            self.stack_ch_seg.data.max(axis=-1, keepdims=True)
-        )
-        pxmap, _ = self.pxmodel.infer(mip)
-
-        write_accessor_data_to_file(output_path / 'pxmap.tif', pxmap)
-        self.seg_mask = InMemoryDataAccessor(
-            pxmap.get_one_channel_data(
-                pipeline_params['pxmap_channel']
-            ).data > pipeline_params['pxmap_threshold']
-        )
-        write_accessor_data_to_file(output_path / 'seg_mask.tif', self.seg_mask)
+        self.seg_mask = generate_file_accessor(multichannel_zstack['mask_path'])
 
 class TestRoiSetMonoProducts(BaseTestRoiSetMonoProducts, unittest.TestCase):