Removed solidity from features, this was no longer being used and was...

Removed solidity from features, this was no longer being used and was triggering convex hull warnings

model_server/base/roiset.py

@@ -44,7 +44,6 @@ class RoiFilterRange(BaseModel):
 
 class RoiFilter(BaseModel):
     area: Union[RoiFilterRange, None] = None
-    solidity: Union[RoiFilterRange, None] = None
 
 
 class RoiSetMetaParams(BaseModel):
@@ -164,38 +163,21 @@ class RoiSet(object):
         :return: pd.DataFrame
         """
         # build dataframe of objects, assign z index to each object
+
         if acc_obj_ids.nz == 1:  # deproject objects' z-coordinates from argmax of raw image
-            argmax = acc_raw.data.argmax(axis=3, keepdims=True)[:, :, 0, 0].astype('uint16')
-            df = (
-                pd.DataFrame(
-                    regionprops_table(
-                        acc_obj_ids.data[:, :, 0, 0],
-                        intensity_image=argmax,
-                        properties=('label', 'area', 'intensity_mean', 'solidity', 'bbox', 'centroid')
-                    )
-                )
-                .rename(
-                    columns={'bbox-0': 'y0', 'bbox-1': 'x0', 'bbox-2': 'y1', 'bbox-3': 'x1', }
-                )
-            )
+            df = pd.DataFrame(regionprops_table(
+                acc_obj_ids.data[:, :, 0, 0],
+                intensity_image=acc_raw.data.argmax(axis=3, keepdims=True)[:, :, 0, 0].astype('uint16'),
+                properties=('label', 'area', 'intensity_mean', 'bbox', 'centroid')
+            )).rename(columns={'bbox-0': 'y0', 'bbox-1': 'x0', 'bbox-2': 'y1', 'bbox-3': 'x1'})
             df['zi'] = df['intensity_mean'].round().astype('int')
-        else:  # objects' z-coordinates come from arg of max count in object identities map
-            df = (
-                pd.DataFrame(
-                    regionprops_table(
-                        acc_obj_ids.data[:, :, 0, :],
-                        properties=('label', 'area', 'solidity', 'bbox', 'centroid')
-                    )
-                )
-                .rename(
-                    columns={'bbox-0': 'y0', 'bbox-1': 'x0', 'bbox-2': 'y1', 'bbox-3': 'x1', }
-                )
-            )
-            def _get_zi_from_obj_map_counts(la):
-                return (acc_obj_ids.data == la).sum(axis=(0, 1, 2)).argmax()
-
-            df['zi'] = df['label'].apply(_get_zi_from_obj_map_counts)
 
+        else:  # objects' z-coordinates come from arg of max count in object identities map
+            df = pd.DataFrame(regionprops_table(
+                acc_obj_ids.data[:, :, 0, :],
+                properties=('label', 'area', 'bbox', 'centroid')
+            )).rename(columns={'bbox-0': 'y0', 'bbox-1': 'x0', 'bbox-2': 'z0', 'bbox-3': 'y1', 'bbox-4': 'x1', 'bbox-5': 'z1'})
+            df['zi'] = df['label'].apply(lambda x: (acc_obj_ids.data == x).sum(axis=(0, 1, 2)).argmax())
 
         # compute expanded bounding boxes
         h, w, c, nz = acc_raw.shape
@@ -272,7 +254,7 @@ class RoiSet(object):
         query_str = 'label > 0'  # always true
         if filters is not None:  # parse filters
             for k, val in filters.dict(exclude_unset=True).items():
-                assert k in ('area', 'solidity')
+                assert k in ('area')
                 vmin = val['min']
                 vmax = val['max']
                 assert vmin >= 0

tests/test_roiset.py

@@ -279,11 +279,6 @@ class TestRoiSetFromZmask(unittest.TestCase):
         is_2d = all([self._label_is_2d(id_map.data, la) for la in labels])
         self.assertTrue(is_2d)
 
-    def test_3d_zmask(self):
-        write_accessor_data_to_file(output_path / 'roiset_from_3d' / 'raw.tif', self.roiset.acc_raw)
-        # write_accessor_data_to_file(output_path / 'roiset_from_3d' / 'ob_ids.tif', self.roiset.acc_obj_ids)
-        write_accessor_data_to_file(output_path / 'roiset_from_3d' / 'zmask.tif', self.zmask)
-
     def test_create_roiset_from_3d_obj_ids(self):
         id_map = _get_label_ids(self.seg_mask_3d, allow_3d=True, connect_3d=False)
         self.assertEqual(self.stack_ch_pa.shape, id_map.shape)