ilastik functional checks passed; confirmed accurate image outputs

conf/testing.py

 from pathlib import Path
 
 root = Path('c:/Users/rhodes/projects/proj0015-model-server/resources')
-filename = 'Selection--W0000--P0001-T0001.czi'
+filename = 'D3-selection-01.czi'
 czifile = {
     'filename': filename,
     'path': root / 'testdata' / filename,
-    'w': 1024,
-    'h': 1024,
-    'c': 4,
+    'w': 1274,
+    'h': 1274,
+    'c': 5,
     'z': 1,
 }
 
 ilastik = {
-    'pixel_classifier': root / 'testdata' / 'pix02.ilp',
-    'object_classifier': root / 'testdata' / 'obj01.ilp',
+    'pixel_classifier': root / 'testdata' / 'ilastik' / 'demo_px.ilp',
+    'object_classifier': root / 'testdata' / 'ilastik' / 'demo_obj.ilp',
 }
 
 output_path = root / 'testing_output'

model_server/ilastik.py

@@ -23,8 +23,6 @@ class IlastikImageToImageModel(ImageToImageModel):
         # self.operator = None
         super().__init__(autoload, params)
 
-    def __del__(self):
-        self.shell.closeCurrentProject()
 
     def load(self):
         os.environ["LAZYFLOW_THREADS"] = "8"
@@ -39,18 +37,10 @@ class IlastikImageToImageModel(ImageToImageModel):
             raise ParameterExpectedError(
                 f'Ilastik project file {self.project_file} does not describe an instance of {shell.workflow.__class__}'
             )
-        # self.operator = self.get_top_level_operator(shell.workflow)
         self.shell = shell
 
         return True
 
-    # @staticmethod
-    # def get_top_level_operator(workflow):
-    #     if isinstance(workflow, PixelClassificationWorkflow):
-    #         return workflow.pcApplet.topLevelOperator
-    #     elif isinstance(workflow, ObjectClassificationWorkflow):
-    #         return workflow.objectClassificationApplet.topLevelOperator
-
 
 class IlastikPixelClassifierModel(IlastikImageToImageModel):
     workflow = PixelClassificationWorkflow

model_server/image.py

@@ -77,7 +77,7 @@ class CziImageFileAccessor(GenericImageFileAccessor):
             raise FileAccessorError(f'Unable to access CZI data in {fpath}')
 
         sd = {ch: cf.shape[cf.axes.index(ch)] for ch in cf.axes}
-        if sd['S'] > 1 or sd['T'] > 1:
+        if (sd.get('S') and (sd['S'] > 1)) or (sd.get('T') and (sd['T'] > 1)):
             raise DataShapeError(f'Cannot handle image with multiple positions or time points: {sd}')
 
         idx = {k: sd[k] for k in ['X', 'Y', 'C', 'Z']}

model_server/workflow.py

@@ -34,7 +34,7 @@ def infer_image_to_image(fpi, model, where_output, **kwargs) -> dict:
     # TODO: assert outdata format
 
     # write output to file
-    outpath = where_output / (fpi.stem + '.tif')
+    outpath = where_output / (model.model_id + '_' + fpi.stem + '.tif')
     write_accessor_data_to_file(outpath, outdata)
     dt_fo = time() - t0
 

tests/test_ilastik.py

@@ -10,8 +10,6 @@ class TestIlastikPixelClassification(unittest.TestCase):
     def setUp(self) -> None:
         self.cf = CziImageFileAccessor(czifile['path'])
 
-    # def tearDown(self) -> None:
-    #     pass
 
     def test_faulthandler(self): # recreate error that is messing up ilastik
         import io
@@ -43,7 +41,7 @@ class TestIlastikPixelClassification(unittest.TestCase):
         self.assertEqual(pxmap.shape, (w, h, 2, 1))
 
     def test_run_pixel_classifier(self):
-        channel = 2
+        channel = 0
         model = IlastikPixelClassifierModel({'project_file': ilastik['pixel_classifier']})
         cf = CziImageFileAccessor(czifile['path'])
         mono_image = cf.get_one_channel_data(channel)
@@ -65,6 +63,19 @@ class TestIlastikPixelClassification(unittest.TestCase):
             )
         )
 
+        self.mono_image = mono_image
+        self.pxmap = pxmap
+
     def test_run_object_classifier(self):
+        self.test_run_pixel_classifier()
+        fp = czifile['path']
         model = IlastikObjectClassifierModel({'project_file': ilastik['object_classifier']})
+        objmap, _ = model.infer(self.mono_image, self.pxmap)
 
+        self.assertTrue(
+            write_accessor_data_to_file(
+                output_path / f'obmap_{fp.stem}.tif',
+                objmap,
+            )
+        )
+        self.assertEqual(objmap.data.max(), 3)

tests/test_image.py

@@ -20,9 +20,9 @@ class TestCziImageFileAccess(unittest.TestCase):
         self.assertEqual(cf.shape[1], czifile['w'])
 
     def test_write_single_channel_tif(self):
-        ch = 2
+        ch = 4
         cf = CziImageFileAccessor(czifile['path'])
-        mono = cf.get_one_channel_data(2)
+        mono = cf.get_one_channel_data(ch)
         self.assertTrue(
             write_accessor_data_to_file(
                 output_path / f'{cf.fpath.stem}_ch{ch}.tif',