Can load and use simple binary threshold classifier instead of ilastik pixel classifier

tests/test_ilastik/test_roiset_workflow.py

@@ -64,27 +64,40 @@ class BaseTestRoiSetMonoProducts(object):
             'deproject_channel': 0,
         }
 
-    def _get_models(self): # tests can either use model objects directly, or load in API via project file string
-        fp_px = classifiers['px']['path'].__str__()
-        fp_ob = classifiers['seg_to_obj']['path'].__str__()
+    # def _get_models(self): # tests can either use model objects directly, or load in API via project file string
+    #     fp_px = classifiers['px']['path'].__str__()
+    #     fp_ob = classifiers['seg_to_obj']['path'].__str__()
+    #     return {
+    #         'pixel_classifier_segmentation': {
+    #             'name': 'ilastik_px_mod',
+    #             'project_file': fp_px,
+    #             'model': ilm.IlastikPixelClassifierModel(
+    #                 {
+    #                     'project_file': fp_px,
+    #                     'px_class': 0,
+    #                     'px_prob_threshold': 0.5,
+    #                 },
+    #             ),
+    #         },
+    #         'object_classifier': {
+    #             'name': 'ilastik_ob_mod',
+    #             'project_file': fp_ob,
+    #             'model': ilm.IlastikObjectClassifierFromSegmentationModel(
+    #                 {'project_file': fp_ob},
+    #             )
+    #         },
+    #     }
+
+    def _get_models(self):
+        from model_server.base.models import BinaryThresholdSegmentationModel, PermissiveInstanceSegmentationModel
         return {
             'pixel_classifier_segmentation': {
-                'name': 'ilastik_px_mod',
-                'project_file': fp_px,
-                'model': ilm.IlastikPixelClassifierModel(
-                    {
-                        'project_file': fp_px,
-                        'px_class': 0,
-                        'px_prob_threshold': 0.5,
-                    },
-                ),
+                'name': 'min_px_mod',
+                'model': BinaryThresholdSegmentationModel({'tr': 1e4}),
             },
             'object_classifier': {
-                'name': 'ilastik_ob_mod',
-                'project_file': fp_ob,
-                'model': ilm.IlastikObjectClassifierFromSegmentationModel(
-                    {'project_file': fp_ob},
-                )
+                'name': 'min_ob_mod',
+                'model': PermissiveInstanceSegmentationModel()
             },
         }
 
@@ -115,17 +128,18 @@ class TestRoiSetWorkflow(BaseTestRoiSetMonoProducts, unittest.TestCase):
             {f'{k}_': v['model'] for k, v in self._get_models().items()},
             **params.dict()
         )
-        self.assertEqual(trace.pop('annotated_patches_2d').count, 13)
-        self.assertEqual(trace.pop('patches_2d').count, 13)
+        self.assertEqual(trace.pop('annotated_patches_2d').count, 26)
+        self.assertEqual(trace.pop('patches_2d').count, 26)
         trace.write_interm(Path(output_path) / 'trace', 'roiset_worfklow_trace', skip_first=False, skip_last=False)
         self.assertTrue('ob_id' in trace.keys())
-        self.assertEqual(len(trace['labeled'].unique()[0]), 14)
-        self.assertEqual(rois.count, 13)
+        self.assertEqual(len(trace['labeled'].unique()[0]), 51)
+        self.assertEqual(rois.count, 26)
         self.assertEqual(len(trace['ob_id'].unique()[0]), 2)
 
 
 class TestRoiSetWorkflowOverApi(conf.TestServerBaseClass, BaseTestRoiSetMonoProducts):
 
+    # TODO: rename app
     app_name = 'tests.test_ilastik.test_roiset_workflow:app'
     input_data = data['multichannel_zstack_raw']
 
@@ -143,11 +157,16 @@ class TestRoiSetWorkflowOverApi(conf.TestServerBaseClass, BaseTestRoiSetMonoProd
         return self.assertPutSuccess(f'accessors/read_from_file/{fname}')
 
     def test_load_pixel_classifier(self):
+        # mid = self.assertPutSuccess(
+        #     'ilastik/seg/load/',
+        #     body={'project_file': self._get_models()['pixel_classifier_segmentation']['project_file']},
+        # )['model_id']
         mid = self.assertPutSuccess(
-            'ilastik/seg/load/',
-            body={'project_file': self._get_models()['pixel_classifier_segmentation']['project_file']},
+            'models/seg/binary_threshold/load/',
+            body={'tr': 1e4},
         )['model_id']
-        self.assertTrue(mid.startswith('IlastikPixelClassifierModel'))
+        # self.assertTrue(mid.startswith('IlastikPixelClassifierModel'))
+        self.assertTrue(mid.startswith('BinaryThresholdSegmentationModel'))
         return mid
 
     def test_load_object_classifier(self):