allensdk.brain_observatory.ecephys.lfp_subsampling.subsampling module¶
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allensdk.brain_observatory.ecephys.lfp_subsampling.subsampling.
remove_lfp_noise
(lfp, surface_channel, channel_numbers, channel_max=384, channel_limit=380)[source]¶ Subtract mean of channels out of brain to remove noise
- lfp : numpy.ndarray
- 2D array of LFP values (time x channels)
- surface_channel : int
- Surface channel (relative to original probe)
- channel_numbers : numpy.ndarray
- Channel numbers in ‘lfp’ array (relative to original probe)
Returns:
- lfp_noise_removed : numpy.ndarray
- New 2D array of LFP values
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allensdk.brain_observatory.ecephys.lfp_subsampling.subsampling.
remove_lfp_offset
(lfp, sampling_frequency, cutoff_frequency, filter_order)[source]¶ High-pass filters LFP data to remove offset
- lfp : numpy.ndarray
- 2D array of LFP values (time x channels)
- sampling_frequency : float
- Sampling frequency in Hz
- cutoff_frequency : float
- Cutoff frequency for highpass filter
- filter_order : int
- Butterworth filter order
Returns:
- lfp_filtered : numpy.ndarray
- New 2D array of LFP values
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allensdk.brain_observatory.ecephys.lfp_subsampling.subsampling.
select_channels
(total_channels, surface_channel, surface_padding, start_channel_offset, channel_stride, channel_order, noisy_channels=array([], dtype=float64), remove_noisy_channels=False, reference_channels=array([], dtype=float64), remove_references=False)[source]¶ Selects a subset of channels for spatial downsampling
- total_channels : int
- Number of channels in the original data file
- surface_channel : int
- Index of channel at brain surface
- surface_padding : int
- Number of channels above surface to save
- start_channel_offset : int
- First channel to save
- channel_stride : int
- Number of channels to skip in output
- channel_order : np.ndarray
- Actual order of LFP channels (needed to account for the bug in NPX extraction)
- noisy_channels : numpy.ndarray
- Array indicating noisy channels
- remove_noisy_channels : bool
- Flag to remove noisy channels
- reference_channels : numpy.ndarray
- Array indicating refence channels
- remove_references : bool
- Flag to remove reference channels
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allensdk.brain_observatory.ecephys.lfp_subsampling.subsampling.
subsample_lfp
(lfp_raw, selected_channels, subsampling_factor)[source]¶ Subsamples LFP data
- lfp_raw : numpy.ndarray
- 2D array of LFP values (time x channels)
- selected_channels : numpy.ndarray
- Indices of channels to select (spatial subsampling)
- downsampling_factor : int
- Factor by which to subsample in time
Returns:
- lfp_subsampled : numpy.ndarray
- New 2D array of LFP values
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allensdk.brain_observatory.ecephys.lfp_subsampling.subsampling.
subsample_timestamps
(timestamps, subsampling_factor)[source]¶ Subsamples an array of timestamps
- timestamps : numpy.ndarray
- 1D array of timestamp values
- downsampling_factor : int
- Factor by which to subsample the timestamps
Returns:
- timestamps_sub : numpy.ndarray
- New 1D array of timestamps