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Add radius as conversion (scaling) instead of adding the scaled data in FicTrac #619

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merged 6 commits into from
Oct 30, 2023
Merged

Add radius as conversion (scaling) instead of adding the scaled data in FicTrac #619

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f194ec2
add radius as scaling instead of adding scaled data
h-mayorquin Oct 27, 2023
1a07257
Change log
h-mayorquin Oct 27, 2023
60469e0
best practice name for behavior module
h-mayorquin Oct 27, 2023
3646bac
correct docstring
h-mayorquin Oct 27, 2023
ceac3e9
fix tests
h-mayorquin Oct 28, 2023
7495597
Merge branch 'main' into add_radius_as_scaling
CodyCBakerPhD Oct 30, 2023
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1 change: 1 addition & 0 deletions CHANGELOG.md
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Original file line number Diff line number Diff line change
Expand Up @@ -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)
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9 changes: 5 additions & 4 deletions src/neuroconv/datainterfaces/behavior/fictrac/fictracdatainterface.py
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Expand Up @@ -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.
"""
Expand Down Expand Up @@ -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"
Expand All @@ -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):
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6 changes: 4 additions & 2 deletions tests/test_on_data/test_behavior_interfaces.py
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Expand Up @@ -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
Expand All @@ -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):
Expand All @@ -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
Expand All @@ -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):
Expand Down