diff --git a/src/pyflask/manageNeuroconv/manage_neuroconv.py b/src/pyflask/manageNeuroconv/manage_neuroconv.py index fd529f902..bd066916b 100644 --- a/src/pyflask/manageNeuroconv/manage_neuroconv.py +++ b/src/pyflask/manageNeuroconv/manage_neuroconv.py @@ -1665,11 +1665,11 @@ def generate_test_data(output_path: str): """ Autogenerate the data formats needed for the tutorial pipeline. - Consists of a single-probe single-segment SpikeGLX recording (both AP and LF bands) as well as Phy spiking data. + Consists of a single-probe single-segment SpikeGLX recording (both AP and LF bands) as well as Phy sorting data. """ - import spikeinterface + import spikeinterface as si from spikeinterface.exporters import export_to_phy - from spikeinterface.preprocessing import bandpass_filter, resample, scale + from spikeinterface.preprocessing import bandpass_filter, decimate, scale base_path = Path(output_path) spikeglx_output_folder = base_path / "spikeglx" @@ -1684,8 +1684,8 @@ def generate_test_data(output_path: str): lf_sampling_frequency = 2_500.0 downsample_factor = int(ap_sampling_frequency / lf_sampling_frequency) - # Generate synthetic spiking and voltage traces with waveforms around them - artificial_ap_band_in_uV, spiking = spikeinterface.generate_ground_truth_recording( + # Generate synthetic sorting and voltage traces with waveforms around them + artificial_ap_band_in_uV, sorting = si.generate_ground_truth_recording( durations=[duration_in_s], sampling_frequency=ap_sampling_frequency, num_channels=number_of_channels, @@ -1699,7 +1699,7 @@ def generate_test_data(output_path: str): int16_artificial_ap_band.set_channel_gains(conversion_factor_to_uV) unscaled_artificial_lf_filter = bandpass_filter(recording=unscaled_artificial_ap_band, freq_min=0.5, freq_max=1_000) - unscaled_artificial_lf_band = resample(recording=unscaled_artificial_lf_filter, resample_rate=2_500) + unscaled_artificial_lf_band = decimate(recording=unscaled_artificial_lf_filter, decimation_factor=downsample_factor) int16_artificial_lf_band = unscaled_artificial_lf_band.astype(dtype="int16") int16_artificial_lf_band.set_channel_gains(conversion_factor_to_uV) @@ -1710,8 +1710,8 @@ def generate_test_data(output_path: str): # Make .bin files ap_file_path.parent.mkdir(parents=True, exist_ok=True) - spikeinterface.write_binary_recording(recording=int16_artificial_ap_band, file_paths=[ap_file_path]) - spikeinterface.write_binary_recording(recording=int16_artificial_lf_band, file_paths=[lf_file_path]) + si.write_binary_recording(recording=int16_artificial_ap_band, file_paths=[ap_file_path]) + si.write_binary_recording(recording=int16_artificial_lf_band, file_paths=[lf_file_path]) # Make .meta files ap_meta_content = _format_spikeglx_meta_file(bin_file_path=ap_file_path) @@ -1723,12 +1723,12 @@ def generate_test_data(output_path: str): io.write(lf_meta_content) # Make Phy folder - waveform_extractor = spikeinterface.extract_waveforms( - recording=artificial_ap_band_in_uV, sorting=spiking, mode="memory" + sorting_analyzer = si.create_sorting_analyzer( + sorting=sorting, recording=artificial_ap_band_in_uV, mode="memory", sparse=False ) export_to_phy( - waveform_extractor=waveform_extractor, output_folder=phy_output_folder, remove_if_exists=True, copy_binary=False + sorting_analyzer=sorting_analyzer, output_folder=phy_output_folder, remove_if_exists=True, copy_binary=False )