fix bug spatial filter #4175 #4286
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oliche
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Dec 31, 2025
zm711
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Jan 1, 2026
| from copy import deepcopy | ||
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| import spikeinterface as si | ||
| import spikeinterface.full as si |
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Why switch from core to full. This is super heavy and probably not necessary right? This is a bit of a poorly explained part of our importing.
import spikeinterface as siis equivalent to
import spikeinterface.core as siwhich is a faster import.
alejoe91
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Jan 2, 2026
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| if Path(folder_path).is_file(): | ||
| folder_path = Path(folder_path).parent |
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Why do we need this? :)
One can either pass the root folder or a direct path the the cbin file with the cbin_file_path arg
| gain = scipy.signal.fftconvolve(np.abs(traces), window[:, None], mode="same", axes=0) | ||
| # default value for epsilon is relative to the rms, loosely matching the IBL 1e-8 for an input in Volts | ||
| if epsilon is None: | ||
| epsilon = np.std(traces - np.mean(traces)) * 0.003 |
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maybe the 0.003 should also be an argument? epsilon_factor?
| local_path = si.download_dataset(remote_path="spikeglx/Noise4Sam_g0") | ||
| si_recording = se.read_spikeglx(local_path, stream_id="imec0.ap") | ||
| si_recording = spre.astype(si_recording, "float") | ||
| recording_ps = si.phase_shift(si_recording) |
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Suggested change
| recording_ps = si.phase_shift(si_recording) | |
| recording_ps = spre.phase_shift(si_recording) |
| si_recording = se.read_spikeglx(local_path, stream_id="imec0.ap") | ||
| si_recording = spre.astype(si_recording, "float") | ||
| recording_ps = si.phase_shift(si_recording) | ||
| recording_hp = si.highpass_filter(recording_ps, freq_min=300, filter_order=3) |
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Suggested change
| recording_hp = si.highpass_filter(recording_ps, freq_min=300, filter_order=3) | |
| recording_hp = spre.highpass_filter(recording_ps, freq_min=300, filter_order=3) |
| si_recording = spre.astype(si_recording, "float") | ||
| recording_ps = si.phase_shift(si_recording) | ||
| recording_hp = si.highpass_filter(recording_ps, freq_min=300, filter_order=3) | ||
| recording_hps = si.highpass_spatial_filter(recording_hp) |
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Suggested change
| recording_hps = si.highpass_spatial_filter(recording_hp) | |
| recording_hps = spre.highpass_spatial_filter(recording_hp) |
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Fixed the main bug: all of the processing has to be done in float, even if only to reconvert to int at the end of the module.
I have also improved a few things:
neurodspmodule doesn't exist anymore