Test covering annotated multichannel z-stacks, too

model_server/extensions/chaeo/tests/test_zstack.py

@@ -257,7 +257,7 @@ class TestRoiSetMultichannelProducts(BaseTestRoiSetMonoProducts, unittest.TestCa
     def test_multichannel_to_mono_2d_patches(self):
 
         files = export_multichannel_patches_from_zstack(
-            output_path / 'test_multichannel_to_mono_2d_patches',
+            output_path / 'multichannel' / 'mono_2d_patches',
             self.roiset,
             white_channel=3,
             draw_bounding_box=True,
@@ -267,7 +267,7 @@ class TestRoiSetMultichannelProducts(BaseTestRoiSetMonoProducts, unittest.TestCa
 
     def test_multichannnel_to_mono_2d_patches_rgb_bbox(self):
         files = export_multichannel_patches_from_zstack(
-            output_path / 'multichannnel_to_mono_2d_patches_rgb_bbox',
+            output_path / 'multichannel' / 'mono_2d_patches_rgb_bbox',
             self.roiset,
             white_channel=3,
             draw_bounding_box=True,
@@ -278,7 +278,7 @@ class TestRoiSetMultichannelProducts(BaseTestRoiSetMonoProducts, unittest.TestCa
 
     def test_multichannnel_to_rgb_2d_patches_bbox(self):
         files = export_multichannel_patches_from_zstack(
-            output_path / 'multichannnel_to_rgb_2d_patches_bbox',
+            output_path / 'multichannel' / 'rgb_2d_patches_bbox',
             self.roiset,
             white_channel=4,
             rgb_overlay_channels=(3, None, None),
@@ -291,7 +291,7 @@ class TestRoiSetMultichannelProducts(BaseTestRoiSetMonoProducts, unittest.TestCa
 
     def test_multichannnel_to_rgb_2d_patches_contour(self):
         files = export_multichannel_patches_from_zstack(
-            output_path / 'multichannnel_to_rgb_2d_patches_contour',
+            output_path / 'multichannel' / 'rgb_2d_patches_contour',
             self.roiset,
             rgb_overlay_channels=(3, None, None),
             draw_contour=True,
@@ -303,12 +303,22 @@ class TestRoiSetMultichannelProducts(BaseTestRoiSetMonoProducts, unittest.TestCa
         self.assertEqual(result.get_one_channel_data(2).data.max(), 0)  # blue channel is black
 
     def test_multichannel_to_multichannel_tif_patches(self):
-        # roiset = self._setup_multichannel_tests()
         files = export_multichannel_patches_from_zstack(
-            output_path / 'multichannel_to_multichannel_tif_patches',
+            output_path / 'multichannel' / 'multichannel_tif_patches',
             self.roiset,
         )
         result = generate_file_accessor(Path(files[0]['location']) / files[0]['patch_filename'])
         self.assertEqual(result.chroma, 5)
 
+    def test_multichannel_annotated_zstack(self):
+        self.roiset.export_annotated_zstack(
+            output_path / 'multichannel' / 'annotated_zstack',
+            'test_multichannel_annotated_zstack',
 
+        )
+        # files = export_multichannel_patches_from_zstack(
+        #     output_path / 'multichannel_to_multichannel_tif_patches',
+        #     self.roiset,
+        # )
+        # result = generate_file_accessor(Path(files[0]['location']) / files[0]['patch_filename'])
+        # self.assertEqual(result.chroma, 5)

model_server/extensions/chaeo/zmask.py

@@ -203,9 +203,7 @@ class RoiSet(object):
             return Multichannel3dPatchStack(patches)
 
     def export_annotated_zstack(self, where, prefix='zstack', **kwargs):
-        annotated = InMemoryDataAccessor(draw_boxes_on_3d_image(self, **kwargs)
-            # draw_boxes_on_3d_image(self.acc_raw.data, self.zmask_meta, **kwargs)  # TODO remove zmask_meta ref
-        )
+        annotated = InMemoryDataAccessor(draw_boxes_on_3d_image(self, **kwargs))
         success = write_accessor_data_to_file(where / (prefix + '.tif'), annotated)
         return {'location': where.__str__(), 'filename': prefix + '.tif'}