Cleaned up patch export functino

extensions/chaeo/products.py

@@ -56,7 +56,6 @@ def export_patches_from_zstack(
 
         assert len(patch.shape) == 4
         assert patch.shape[2] == stack.chroma
-        # assert patch.shape[3] == 1 # should not get to zstacks by this point
 
         if rescale_clip is not None:
             patch = rescale(patch, rescale_clip)
@@ -68,10 +67,6 @@ def export_patches_from_zstack(
             y1 = rbb['y1']
 
             for zi in range(0, patch.shape[3]):
-                # pilimg = Image.fromarray(patch[:, :, 0, zi])  # drawing modifies array in-place
-                # draw = ImageDraw.Draw(pilimg)
-                # draw.rectangle([(x0, y0), (x1, y1)], outline='white', width=kwargs.get('linewidth', 1))
-                # patch[:, :, 0, zi] = np.array(pilimg)
                 patch[:, :, 0, zi] = draw_box_on_patch(
                     patch[:, :, 0, zi],
                     ((x0, y0), (x1, y1)),

extensions/chaeo/tests/test_zstack.py

@@ -26,13 +26,12 @@ class TestZStackDerivedDataProducts(unittest.TestCase):
         self.obmap = InMemoryDataAccessor(self.pxmap.data > pipeline_params['threshold'])
         # write_accessor_data_to_file(output_path / 'obmap.tif', self.obmap)
 
-    def test_zmask_makes_correct_boxes(self, mask_type='boxes', filters=None, expand_box_by=None):
+    def test_zmask_makes_correct_boxes(self, mask_type='boxes', **kwargs):
         zmask, meta = build_zmask_from_object_mask(
             self.obmap.get_one_channel_data(0),
             self.stack.get_one_channel_data(0),
             mask_type=mask_type,
-            filters=filters,
-            expand_box_by=expand_box_by,
+            **kwargs,
         )
         zmask_acc = InMemoryDataAccessor(zmask)
         self.assertTrue(zmask_acc.is_mask())