Support linking to multiple camera devices

README.md

@@ -71,7 +71,7 @@ pe = PoseEstimation(
     source_software_version='2.2b8',
     nodes=['front_left_paw', 'front_right_paw'],
     edges=np.array([[0, 1]], dtype='uint8'),
-    # devices=[camera1, camera2],  # this is not yet supported
+    devices=[camera1, camera2],
 )
 
 behavior_pm = nwbfile.create_processing_module(

spec/ndx-pose.extensions.yaml

@@ -115,3 +115,7 @@ groups:
   - neurodata_type_inc: PoseEstimationSeries
     doc: Estimated position data for each body part.
     quantity: '*'
+  links:
+  - target_type: Device
+    doc: Cameras used to record the videos.
+    quantity: '*'

src/pynwb/ndx_pose/pose.py

@@ -60,14 +60,14 @@ class PoseEstimation(MultiContainerInterface):
             'type': PoseEstimationSeries,
             'attr': 'pose_estimation_series'
         },
-        # {
-        #     'add': 'add_device',
-        #     'get': 'get_devices',
-        #     'type': Device,
-        #     'attr': 'devices'
-        #     # TODO prevent these from being children / add better support for links
-        #     # may require update to HDMF to add a key 'child': False
-        # }
+        {
+            'add': 'add_device',
+            'get': 'get_devices',
+            'type': Device,
+            'attr': 'devices'
+            # TODO prevent these from being children / add better support for links
+            # may require update to HDMF to add a key 'child': False
+        }
     ]
 
     __nwbfields__ = ('description', 'original_videos', 'labeled_videos', 'dimensions', 'scorer', 'source_software',
@@ -112,9 +112,9 @@ class PoseEstimation(MultiContainerInterface):
          'doc': ("Array of pairs of indices corresponding to edges between nodes. Index values correspond to row "
                  "indices of the 'nodes' field. Index values use 0-indexing."),
          'default': None},
-        # {'name': 'devices', 'type': ('array_data', 'data'),
-        #  'doc': ('Cameras used to record the videos.'),
-        #  'default': None},
+        {'name': 'devices', 'type': ('array_data', 'data'),
+         'doc': ('Cameras used to record the videos.'),
+         'default': None},
         allow_positional=AllowPositional.ERROR
     )
     def __init__(self, **kwargs):
@@ -123,7 +123,7 @@ def __init__(self, **kwargs):
         dimensions, scorer = popargs('dimensions', 'scorer', kwargs)
         source_software, source_software_version = popargs('source_software', 'source_software_version', kwargs)
         nodes, edges = popargs('nodes', 'edges', kwargs)
-        # devices = popargs('devices', kwargs)
+        devices = popargs('devices', kwargs)
         call_docval_func(super().__init__, kwargs)
         self.pose_estimation_series = pose_estimation_series
         self.description = description
@@ -135,15 +135,15 @@ def __init__(self, **kwargs):
         self.source_software_version = source_software_version
         self.nodes = nodes
         self.edges = edges
-        # self.devices = devices
+        self.devices = devices
 
         # TODO include calibration images for 3D estimates?
 
-        # if original_videos is not None and (devices is None or len(original_videos) != len(devices)):
-        #     raise ValueError("The number of original videos should equal the number of camera devices.")
-        # if labeled_videos is not None and (devices is None or len(labeled_videos) != len(devices)):
-        #     raise ValueError("The number of labeled videos should equal the number of camera devices.")
-        # if dimensions is not None and (devices is None or len(dimensions) != len(devices)):
-        #     raise ValueError("The number of dimensions should equal the number of camera devices.")
+        if original_videos is not None and (devices is None or len(original_videos) != len(devices)):
+            raise ValueError("The number of original videos should equal the number of camera devices.")
+        if labeled_videos is not None and (devices is None or len(labeled_videos) != len(devices)):
+            raise ValueError("The number of labeled videos should equal the number of camera devices.")
+        if dimensions is not None and (devices is None or len(dimensions) != len(devices)):
+            raise ValueError("The number of dimensions should equal the number of camera devices.")
 
         # TODO validate nodes and edges correspondence, convert edges to uint

src/pynwb/tests/integration/hdf5/test_pose.py

@@ -170,7 +170,7 @@ def test_roundtrip(self):
             source_software_version='2.2b8',
             nodes=['front_left_paw', 'front_right_paw'],
             edges=np.array([[0, 1]], dtype='uint8'),
-            # devices=[self.nwbfile.devices['camera1'], self.nwbfile.devices['camera2']],
+            devices=[self.nwbfile.devices['camera1'], self.nwbfile.devices['camera2']],
         )
 
         behavior_pm = self.nwbfile.create_processing_module(
@@ -189,9 +189,9 @@ def test_roundtrip(self):
             self.assertEqual(len(read_pe.pose_estimation_series), 2)
             self.assertContainerEqual(read_pe.pose_estimation_series['front_left_paw'], pose_estimation_series[0])
             self.assertContainerEqual(read_pe.pose_estimation_series['front_right_paw'], pose_estimation_series[1])
-            # self.assertEqual(len(read_pe.devices), 2)
-            # self.assertContainerEqual(read_pe.devices['camera1'], self.nwbfile.devices['camera1'])
-            # self.assertContainerEqual(read_pe.devices['camera2'], self.nwbfile.devices['camera2'])
+            self.assertEqual(len(read_pe.devices), 2)
+            self.assertContainerEqual(read_pe.devices['camera1'], self.nwbfile.devices['camera1'])
+            self.assertContainerEqual(read_pe.devices['camera2'], self.nwbfile.devices['camera2'])
 
 
 # NOTE it is recommended to add links to devices in the constructor of PoseEstimation. however,

src/pynwb/tests/test_example_usage.py

@@ -62,7 +62,7 @@ def test_example_usage():
         source_software_version='2.2b8',
         nodes=['front_left_paw', 'front_right_paw'],
         edges=np.array([[0, 1]], dtype='uint8'),
-        # devices=[camera1, camera2],  # this is not yet supported
+        devices=[camera1, camera2],
     )
 
     behavior_pm = nwbfile.create_processing_module(

src/pynwb/tests/unit/test_pose.py

@@ -93,7 +93,7 @@ def test_constructor(self):
             source_software_version='2.2b8',
             nodes=['front_left_paw', 'front_right_paw'],
             edges=np.array([[0, 1]], dtype='uint8'),
-            # devices=[self.nwbfile.devices['camera1'], self.nwbfile.devices['camera2']],
+            devices=[self.nwbfile.devices['camera1'], self.nwbfile.devices['camera2']],
         )
 
         self.assertEqual(pe.name, 'PoseEstimation')
@@ -109,6 +109,6 @@ def test_constructor(self):
         self.assertEqual(pe.source_software_version, '2.2b8')
         self.assertEqual(pe.nodes, ['front_left_paw', 'front_right_paw'])
         np.testing.assert_array_equal(pe.edges, np.array([[0, 1]], dtype='uint8'))
-        # self.assertEqual(len(pe.devices), 2)
-        # self.assertIs(pe.devices['camera1'], self.nwbfile.devices['camera1'])
-        # self.assertIs(pe.devices['camera2'], self.nwbfile.devices['camera2'])
+        self.assertEqual(len(pe.devices), 2)
+        self.assertIs(pe.devices['camera1'], self.nwbfile.devices['camera1'])
+        self.assertIs(pe.devices['camera2'], self.nwbfile.devices['camera2'])

src/spec/create_extension_spec.py

@@ -142,14 +142,13 @@ def main():
                 quantity='?',
             ),
         ],
-        # TODO: collections of multiple links is currently buggy in PyNWB/HDMF
-        # links=[
-        #     NWBLinkSpec(
-        #         target_type='Device',
-        #         doc='Cameras used to record the videos.',
-        #         quantity='*',
-        #     ),
-        # ],
+        links=[
+            NWBLinkSpec(
+                target_type='Device',
+                doc='Cameras used to record the videos.',
+                quantity='*',
+            ),
+        ],
     )
 
     new_data_types = [pose_estimation_series, pose_estimation]