Merge pull request #619 from catalystneuro/add_radius_as_scaling

Add radius as conversion (scaling) instead of adding the scaled data in `FicTrac`

CHANGELOG.md

@@ -14,6 +14,7 @@
 * Added alignment methods to `FicTracDataInterface`.  [PR #607](https://github.com/catalystneuro/neuroconv/pull/607)
 * Added alignment methods support to `MockRecordingInterface` [PR #611](https://github.com/catalystneuro/neuroconv/pull/611)
 * Added `NeuralynxNvtInterface`, which can read position tracking NVT files. [PR #580](https://github.com/catalystneuro/neuroconv/pull/580)
+* Adding radius as a conversion factor in `FicTracDataInterface`.  [PR #619](https://github.com/catalystneuro/neuroconv/pull/619)
 
 ### Fixes
 * Remove `starting_time` reset to default value (0.0) when adding the rate and updating the `photon_series_kwargs` or `roi_response_series_kwargs`, in `add_photon_series` or `add_fluorescence_traces`. [PR #595](https://github.com/catalystneuro/neuroconv/pull/595)

src/neuroconv/datainterfaces/behavior/fictrac/fictracdatainterface.py

@@ -154,7 +154,8 @@ def __init__(
         file_path : a string or a path
             Path to the .dat file (the output of fictrac)
         radius : float, optional
-            The radius of the ball in meters. If provided the data will be converted to meters and stored as such.
+            The radius of the ball in meters. If provided the radius is stored as a conversion factor
+            and the units are set to meters. If not provided the units are set to radians.
         verbose : bool, default: True
             controls verbosity. ``True`` by default.
         """
@@ -220,7 +221,7 @@ def add_to_nwbfile(
             column_in_dat_file = data_dict["column_in_dat_file"]
             data = fictrac_data_df[column_in_dat_file].to_numpy()
             if self.radius is not None:
-                data = data * self.radius
+                spatial_series_kwargs["conversion"] = self.radius
                 units = "meters"
             else:
                 units = "radians"
@@ -237,8 +238,8 @@ def add_to_nwbfile(
             spatial_series = SpatialSeries(**spatial_series_kwargs)
             position_container.add_spatial_series(spatial_series)
 
-        # Add the compass direction container to the processing module
-        processing_module = get_module(nwbfile=nwbfile, name="Behavior")
+        # Add the container to the processing module
+        processing_module = get_module(nwbfile=nwbfile, name="behavior")
         processing_module.add_data_interface(position_container)
 
     def get_original_timestamps(self):

tests/test_on_data/test_behavior_interfaces.py

@@ -47,7 +47,7 @@ def check_read_nwb(self, nwbfile_path: str):  # This is currently structured to
         with NWBHDF5IO(path=nwbfile_path, mode="r", load_namespaces=True) as io:
             nwbfile = io.read()
 
-            fictrac_position_container = nwbfile.processing["Behavior"].data_interfaces["FicTrac"]
+            fictrac_position_container = nwbfile.processing["behavior"].data_interfaces["FicTrac"]
             assert isinstance(fictrac_position_container, Position)
 
             assert len(fictrac_position_container.spatial_series) == 10
@@ -63,6 +63,7 @@ def check_read_nwb(self, nwbfile_path: str):  # This is currently structured to
 
                 expected_units = "radians"
                 assert spatial_series.unit == expected_units
+                assert spatial_series.conversion == 1.0
 
 
 class TestFicTracDataInterfaceWithRadius(DataInterfaceTestMixin, unittest.TestCase):
@@ -81,7 +82,7 @@ def check_read_nwb(self, nwbfile_path: str):  # This is currently structured to
         with NWBHDF5IO(path=nwbfile_path, mode="r", load_namespaces=True) as io:
             nwbfile = io.read()
 
-            fictrac_position_container = nwbfile.processing["Behavior"].data_interfaces["FicTrac"]
+            fictrac_position_container = nwbfile.processing["behavior"].data_interfaces["FicTrac"]
             assert isinstance(fictrac_position_container, Position)
 
             assert len(fictrac_position_container.spatial_series) == 10
@@ -96,6 +97,7 @@ def check_read_nwb(self, nwbfile_path: str):  # This is currently structured to
                 assert reference_frame == spatial_series.reference_frame
                 expected_units = "meters"
                 assert spatial_series.unit == expected_units
+                assert spatial_series.conversion == self.interface.radius
 
 
 class TestFicTracDataInterfaceTiming(TemporalAlignmentMixin, unittest.TestCase):