Bugfix kwargs and variable name and add unit tests for write_annotati…

…ons.py (#438)

python/neuroglancer/write_annotations.py

@@ -107,21 +107,21 @@ def add_point(self, point: Sequence[int], id: Optional[int] = None, **kwargs):
 
         self.lower_bound = np.minimum(self.lower_bound, point)
         self.upper_bound = np.maximum(self.upper_bound, point)
-        self._add_obj(point, id, kwargs)
+        self._add_obj(point, id, **kwargs)
 
     def add_axis_aligned_bounding_box(self, point_a: Sequence[int], point_b: Sequence[int], id: Optional[int] = None, **kwargs):
         if self.annotation_type != 'axis_aligned_bounding_box':
             raise ValueError(
                 f'Expected annotation type axis_aligned_bounding_box, but received: {self.annotation_type}'
             )
-        self._add_two_point_obj(point_a, point_b, id, kwargs)
+        self._add_two_point_obj(point_a, point_b, id, **kwargs)
 
     def add_line(self, point_a: Sequence[int], point_b: Sequence[int], id: Optional[int] = None, **kwargs):
         if self.annotation_type != 'line':
             raise ValueError(
                 f'Expected annotation type line, but received: {self.annotation_type}'
             )
-        self._add_two_point_obj(point_a, point_b, id, kwargs)
+        self._add_two_point_obj(point_a, point_b, id, **kwargs)
 
     def _add_two_point_obj(self, point_a: Sequence[int], point_b: Sequence[int], id: Optional[int] = None, **kwargs):
         if len(point_a) != self.coordinate_space.rank:
@@ -137,11 +137,11 @@ def _add_two_point_obj(self, point_a: Sequence[int], point_b: Sequence[int], id:
         self.lower_bound = np.minimum(self.lower_bound, point_a)
         self.upper_bound = np.maximum(self.upper_bound, point_b)
         coords = np.concatenate((point_a, point_b))
-        self._add_obj(coords, id, kwargs)
+        self._add_obj(coords, id, **kwargs)
 
     def _add_obj(self, coords: Sequence[int], id: Optional[int], **kwargs):
         encoded = np.zeros(shape=(), dtype=self.dtype)
-        encoded[()]['geometry'] = point
+        encoded[()]['geometry'] = coords
 
         for i, p in enumerate(self.properties):
             if p.id in kwargs:

python/tests/write_annotations_test.py

@@ -0,0 +1,48 @@
+# @license
+# Copyright 2023 Google Inc.
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#
+#      http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+
+from __future__ import absolute_import
+
+import os
+import pathlib
+
+import neuroglancer
+from neuroglancer import write_annotations
+
+
+def test_annotation_writer_axis_aligned_bounding_box(tmp_path: pathlib.Path):
+  dim_dict = {'names': ['x', 'y'], 'units': ['m', 'm'], 'scales': [1, 1]}
+  coordinate_space = neuroglancer.CoordinateSpace(**dim_dict)
+  writer = write_annotations.AnnotationWriter(
+      coordinate_space=coordinate_space,
+      annotation_type='axis_aligned_bounding_box')
+  writer.add_axis_aligned_bounding_box([2, 5], [3, 6])
+  writer.write(tmp_path)
+  assert os.path.exists(os.path.join(tmp_path, 'info'))
+  assert os.path.exists(os.path.join(tmp_path, 'spatial0'))
+  assert os.path.exists(os.path.join(tmp_path, 'by_id'))
+
+
+def test_annotation_writer_point(tmp_path: pathlib.Path):
+  dim_dict = {'names': ['x', 'y'], 'units': ['m', 'm'], 'scales': [1, 1]}
+  coordinate_space = neuroglancer.CoordinateSpace(**dim_dict)
+  writer = write_annotations.AnnotationWriter(
+      coordinate_space=coordinate_space,
+      annotation_type='point')
+  writer.add_point([2, 5])
+  writer.write(tmp_path)
+  assert os.path.exists(os.path.join(tmp_path, 'info'))
+  assert os.path.exists(os.path.join(tmp_path, 'spatial0'))
+  assert os.path.exists(os.path.join(tmp_path, 'by_id'))
+