Merge pull request #105 from LorenFrankLab/add_pos_post

Add pos post

Author: edeno

src/trodes_to_nwb/convert_position.py

@@ -785,13 +785,18 @@ def add_position(
 
     epoch_to_camera_ids = pd.concat(df).set_index("epoch").sort_index()
 
-    position = Position(name="position")
-
     # Make a processing module for behavior and add to the nwbfile
     if not "behavior" in nwb_file.processing:
         nwb_file.create_processing_module(
             name="behavior", description="Contains all behavior-related data"
         )
+
+    if "position" not in nwb_file.processing["behavior"].data_interfaces:
+        position = Position(name="position")
+        nwb_file.processing["behavior"].add(position)
+    else:
+        position = nwb_file.processing["behavior"]["position"]
+
     # get epoch data to seperate dio timestamps into epochs
     if (not ptp_enabled) and (not len(nwb_file.epochs)):
         raise ValueError(
@@ -903,8 +908,6 @@ def add_position(
             )
         )
 
-    nwb_file.processing["behavior"].add(position)
-
 
 def convert_h264_to_mp4(file: str, video_directory: str) -> str:
     """

src/trodes_to_nwb/tests/test_convert_position.py

@@ -5,6 +5,7 @@
 import pandas as pd
 import pytest
 from pynwb import NWBHDF5IO, TimeSeries
+from pynwb.behavior import BehavioralEvents, Position
 
 from trodes_to_nwb import convert, convert_rec_header, convert_yaml
 from trodes_to_nwb.convert_dios import add_dios
@@ -207,7 +208,7 @@ def test_correct_timestamps_for_camera_to_mcu_lag():
     np.allclose(corrected_camera_systime, expected_corrected_camera_systime)
 
 
-def test_add_position():
+def test_add_position(prior_position=False):
     probe_metadata = [data_path / "tetrode_12.5.yml"]
 
     # make session_df
@@ -226,8 +227,17 @@ def test_add_position():
     # make nwb file
     nwbfile = convert_yaml.initialize_nwb(metadata, rec_header)
 
+    # Optional test: add position data to nwbfile before running add_position
+    if prior_position:
+        nwbfile.create_processing_module(
+            name="behavior", description="Contains all behavior-related data"
+        )
+        position = Position(name="position")
+        nwbfile.processing["behavior"].add(position)
+
     # run add_position and prerequisite functions
     convert_yaml.add_cameras(nwbfile, metadata)
+
     add_position(nwbfile, metadata, session_df, rec_header)
 
     # Check that the objects were properly added
@@ -294,6 +304,10 @@ def test_add_position():
     os.remove(filename)
 
 
+def test_add_position_preexisting():
+    test_add_position(prior_position=True)
+
+
 from trodes_to_nwb.convert_position import read_trodes_datafile