Confirms that ilastik pixel classification already works with multichannel input

model_server/conf/testing.py

@@ -57,6 +57,8 @@ ilastik_classifiers = {
     'px': root / 'ilastik' / 'demo_px.ilp',
     'pxmap_to_obj': root / 'ilastik' / 'demo_obj.ilp',
     'seg_to_obj': root / 'ilastik' / 'demo_obj_seg.ilp',
+    'px_color_zstack': root / 'ilastik' / 'px_color_zstack.ilp',
+    'ob_color_zstack': root / 'ilastik' / 'ob_color_zstack.ilp',
 }
 
 roiset_test_data = {

model_server/extensions/ilastik/tests/test_ilastik.py

@@ -320,6 +320,34 @@ class TestIlastikOverApi(TestServerBaseClass):
         self.assertEqual(resp_infer.status_code, 200, resp_infer.content.decode())
 
 
+class TestIlastikOnMultichannelInputs(TestServerBaseClass):
+    def setUp(self) -> None:
+        super(TestIlastikOnMultichannelInputs, self).setUp()
+        self.pa_px_classifier = ilastik_classifiers['px_color_zstack']
+        self.pa_ob_classifier = ilastik_classifiers['ob_color_zstack']
+        self.input_image = generate_file_accessor(roiset_test_data['multichannel_zstack']['path'])
+
+    def _copy_input_file_to_server(self):
+        from shutil import copyfile
+
+        pa_data = roiset_test_data['multichannel_zstack']['path']
+        resp = self._get('paths')
+        pa = resp.json()['inbound_images']
+        outpath = pathlib.Path(pa) / pa_data.name
+        copyfile(
+            czifile['path'],
+            outpath
+        )
+
+    def test_classify_pixels(self):
+        self.assertGreater(self.input_image.chroma, 1)
+        mod = ilm.IlastikPixelClassifierModel(params={'project_file': self.pa_px_classifier})
+        pxmap = mod.infer(self.input_image)[0]
+        self.assertEqual(pxmap.hw, self.input_image.hw)
+
+
+
+
 class TestIlastikObjectClassification(unittest.TestCase):
     def setUp(self):
         stack = generate_file_accessor(roiset_test_data['multichannel_zstack']['path'])