Add NWB support III - provenance writing (#17)

* added tests for provenance writting

* MyPy compliance

sleap_io/io/nwb.py

@@ -109,6 +109,21 @@ def write_labels_to_nwb(
         https://pynwb.readthedocs.io/en/stable/pynwb.file.html#pynwb.file.NWBFile
 
         Defaults to None and default values are used to generate the nwb file.
+
+        pose_estimation_metadata (dict): This argument has a dual purpose:
+
+        1) It can be used to pass time information about the video which is
+        necessary for synchronizing frames in pose estimation tracking to other
+        modalities. Either the video timestamps can be passed to
+        This can be used to pass the timestamps with the key `video_timestamps`
+        or the sampling rate with key`video_sample_rate`.
+
+        e.g. pose_estimation_metadata["video_timestamps"] = np.array(timestamps)
+        or   pose_estimation_metadata["video_sample_rate] = 15  # In Hz
+
+        2) The other use of this dictionary is to ovewrite sleap-io default
+        arguments for the PoseEstimation container.
+        see https://github.com/rly/ndx-pose for a full list or arguments.
     """
 
     nwb_file_kwargs = nwb_file_kwargs or dict()
@@ -129,7 +144,6 @@ def write_labels_to_nwb(
     )
 
     nwbfile = NWBFile(**nwb_file_kwargs)
-
     nwbfile = append_labels_data_to_nwb(labels, nwbfile, pose_estimation_metadata)
 
     with NWBHDF5IO(str(nwbfile_path), "w") as io:
@@ -145,12 +159,33 @@ def append_labels_data_to_nwb(
         labels (Labels): A general labels object
         nwbfile (NWBFile): And in-memory nwbfile where the data is to be appended.
 
+        pose_estimation_metadata (dict): This argument has a dual purpose:
+
+        1) It can be used to pass time information about the video which is
+        necessary for synchronizing frames in pose estimation tracking to other
+        modalities. Either the video timestamps can be passed to
+        This can be used to pass the timestamps with the key `video_timestamps`
+        or the sampling rate with key`video_sample_rate`.
+
+        e.g. pose_estimation_metadata["video_timestamps"] = np.array(timestamps)
+        or   pose_estimation_metadata["video_sample_rate] = 15  # In Hz
+
+        2) The other use of this dictionary is to ovewrite sleap-io default
+        arguments for the PoseEstimation container.
+        see https://github.com/rly/ndx-pose for a full list or arguments.
+
     Returns:
         NWBFile: An in-memory nwbfile with the data from the labels object appended.
     """
 
     pose_estimation_metadata = pose_estimation_metadata or dict()
 
+    # Extract default metadata
+    provenance = labels.provenance
+    default_metadata = dict(scorer=str(provenance))
+    sleap_version = provenance.get("sleap_version", None)
+    default_metadata["source_software_version"] = sleap_version
+
     labels_data_df = _extract_predicted_instances_data(labels)
 
     # For every video create a processing module
@@ -162,20 +197,27 @@ def append_labels_data_to_nwb(
             processing_module_name, nwbfile
         )
 
+        # Propagate video metadata
+        default_metadata["original_videos"] = [f"{video.filename}"]  # type: ignore
+        default_metadata["labeled_videos"] = [f"{video.filename}"]  # type: ignore
+
+        # Overwrite default with the user provided metadata
+        default_metadata.update(pose_estimation_metadata)
+
+        # For every track in that video create a PoseEstimation container
         name_of_tracks_in_video = (
             labels_data_df[video.filename]
             .columns.get_level_values("track_name")
             .unique()
         )
 
-        # For every track in that video create a PoseEstimation container
         for track_index, track_name in enumerate(name_of_tracks_in_video):
             pose_estimation_container = build_pose_estimation_container_for_track(
                 labels_data_df,
                 labels,
                 track_name,
                 video,
-                pose_estimation_metadata,
+                default_metadata,
             )
             nwb_processing_module.add(pose_estimation_container)
 
@@ -260,19 +302,14 @@ def build_pose_estimation_container_for_track(
     )
 
     # Arrange and mix metadata
-
     pose_estimation_container_kwargs = dict(
         name=f"track={track_name}",
         description=f"Estimated positions of {skeleton.name} in video {video_path.name}",
         pose_estimation_series=pose_estimation_series_list,
         nodes=skeleton.node_names,
         edges=np.array(skeleton.edge_inds).astype("uint64"),
         source_software="SLEAP",
-        original_videos=[f"{video.filename}"],
-        labeled_videos=[f"{video.filename}"],
         # dimensions=np.array([[video.backend.height, video.backend.width]]),
-        # scorer=str(labels.provenance),
-        # source_software_version=f"{sleap.__version__}
     )
 
     pose_estimation_container_kwargs.update(**pose_estimation_metadata)
@@ -302,28 +339,32 @@ def build_track_pose_estimation_list(
 
     pose_estimation_series_list: List[PoseEstimationSeries] = []
     for node_name in name_of_nodes_in_track:
-        # Add predicted instances only
 
-        data_for_node = track_data_df[
-            node_name,
-        ]
+        # Drop data with missing values
+        data_for_node = track_data_df[node_name].dropna(axis="index", how="any")
 
-        data_for_node_cleaned = data_for_node.dropna(axis="index", how="any")
-        node_trajectory = data_for_node_cleaned[["x", "y"]].to_numpy()
-        confidence = data_for_node_cleaned["score"].to_numpy()
+        node_trajectory = data_for_node[["x", "y"]].to_numpy()
+        confidence = data_for_node["score"].to_numpy()
+
+        reference_frame = (
+            "The coordinates are in (x, y) relative to the top-left of the image. "
+            "Coordinates refer to the midpoint of the pixel. "
+            "That is, t the midpoint of the top-left pixel is at (0, 0), whereas "
+            "the top-left corner of that same pixel is at (-0.5, -0.5)."
+        )
 
         pose_estimation_kwargs = dict(
             name=f"{node_name}",
             description=f"Sequential trajectory of {node_name}.",
             data=node_trajectory,
             unit="pixels",
-            reference_frame="No reference.",
+            reference_frame=reference_frame,
             confidence=confidence,
             confidence_definition="Point-wise confidence scores.",
         )
 
-        # Add timestamps or rate if timestamps are uniform
-        frames = data_for_node_cleaned.index.values
+        # Add timestamps or only rate if the timestamps are uniform
+        frames = data_for_node.index.values
         timestamps_for_data = timestamps[frames]
         sample_periods = np.diff(timestamps_for_data)
         if sample_periods.size == 0:
@@ -334,6 +375,8 @@ def build_track_pose_estimation_list(
             rate = 1 / sample_periods[0] if uniform_samples else None
 
         if rate:
+            # Video sample rates are ints but nwb expect floats
+            rate = float(int(rate))
             pose_estimation_kwargs.update(rate=rate)
         else:
             pose_estimation_kwargs.update(timestamps=timestamps_for_data)

tests/fixtures/slp.py

@@ -29,4 +29,4 @@ def slp_predictions():
 @pytest.fixture
 def slp_predictions_with_provenance():
     """The slp file generated with the collab tutorial and sleap version 1.27"""
-    return "tests/data/slp/tutorial_predictions_version_1.2.7_with_provenance.slp"
+    return "tests/data/slp/predictions_1.2.7_provenance_and_tracking.slp"

tests/io/test_nwb.py

@@ -87,6 +87,39 @@ def test_typical_case_append_with_metadata_propagation(nwbfile, slp_typical):
     assert extracted_dimensions == expected_dimensions
 
 
+def test_provenance_writing(nwbfile, slp_predictions_with_provenance):
+    labels = load_slp(slp_predictions_with_provenance)
+    nwbfile = append_labels_data_to_nwb(labels, nwbfile)
+
+    # Extract processing module
+    video_index = 0
+    video = labels.videos[video_index]
+    video_path = Path(video.filename)
+    processing_module_name = f"SLEAP_VIDEO_{video_index:03}_{video_path.stem}"
+    processing_module = nwbfile.processing[processing_module_name]
+
+    # Test that the provenance information is propagated
+    for pose_estimation_container in processing_module.data_interfaces.values():
+        assert pose_estimation_container.scorer == str(labels.provenance)
+
+
+def test_default_metadata_overwriting(nwbfile, slp_predictions_with_provenance):
+    labels = load_slp(slp_predictions_with_provenance)
+    pose_estimation_metadata = {"scorer": "overwritten_value"}
+    nwbfile = append_labels_data_to_nwb(labels, nwbfile, pose_estimation_metadata)
+
+    # Extract processing module
+    video_index = 0
+    video = labels.videos[video_index]
+    video_path = Path(video.filename)
+    processing_module_name = f"SLEAP_VIDEO_{video_index:03}_{video_path.stem}"
+    processing_module = nwbfile.processing[processing_module_name]
+
+    # Test that the value of scorer was overwritten
+    for pose_estimation_container in processing_module.data_interfaces.values():
+        assert pose_estimation_container.scorer == "overwritten_value"
+
+
 def test_complex_case_append(nwbfile, slp_predictions):
     labels = load_slp(slp_predictions)
     nwbfile = append_labels_data_to_nwb(labels, nwbfile)