Merge pull request #110 from catalystneuro/keypoint

Switch keypoint timestamps to rate
catalystneuro · Apr 25, 2024 · 47c681e · 47c681e
2 parents 7540d94 + ae9e085
commit 47c681e
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Showing 2 changed files with 12 additions and 3 deletions.
diff --git a/src/datta_lab_to_nwb/markowitz_gillis_nature_2023/rawfiberphotometryinterface.py b/src/datta_lab_to_nwb/markowitz_gillis_nature_2023/rawfiberphotometryinterface.py
@@ -175,10 +175,20 @@ def add_to_nwbfile(self, nwbfile: NWBFile, metadata: dict) -> None:
             coordinates=(0.260, 2.550, -2.40),  # (AP, ML, DV)
         )
 
+        keypoint_sessions = [
+            "keypoint-dls-dlight-9",
+            "keypoint-dls-dlight-10",
+            "keypoint-dls-dlight-11",
+            "keypoint-dls-dlight-12",
+            "keypoint-dls-dlight-13",
+        ]
         skip = (
             self.source_data["tdt_path"] is None
             or not Path(self.source_data["tdt_path"]).exists()
-            or not (Path(self.source_data["tdt_path"]).parent / "alignment_df.parquet").exists()
+            or (
+                not (Path(self.source_data["tdt_path"]).parent / "alignment_df.parquet").exists()
+                and self.source_data["session_id"] not in keypoint_sessions
+            )
         )
         if skip:
             excitation_sources_table.add_row(peak_wavelength=470.0, source_type="LED")

diff --git a/src/datta_lab_to_nwb/markowitz_gillis_nature_2023_keypoint/keypointinterface.py b/src/datta_lab_to_nwb/markowitz_gillis_nature_2023_keypoint/keypointinterface.py
@@ -50,7 +50,6 @@ def add_to_nwbfile(self, nwbfile: NWBFile, metadata: dict) -> None:
         SAMPLING_RATE = metadata["Constants"]["VIDEO_SAMPLING_RATE"]
         keypoint_dict = joblib.load(self.source_data["file_path"])
         raw_keypoints = keypoint_dict["positions_median"]
-        timestamps = H5DataIO(np.arange(raw_keypoints.shape[0]) / SAMPLING_RATE, compression=True)
 
         index_to_name = metadata["Keypoint"]["index_to_name"]
         camera_names = ["bottom", "side1", "side2", "side3", "side4", "top"]  # as confirmed by email with authors
@@ -64,7 +63,7 @@ def add_to_nwbfile(self, nwbfile: NWBFile, metadata: dict) -> None:
                 name=keypoint_name,
                 description=f"Keypoint corresponding to {keypoint_name}",
                 data=H5DataIO(raw_keypoints[:, keypoint_index, :], compression=True),
-                timestamps=timestamps,
+                rate=SAMPLING_RATE,
                 unit="mm",
                 reference_frame=metadata["Keypoint"]["reference_frame"],
             )