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Clarify docstrings in neuropixels_utils #3895

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Merged
samuelgarcia merged 5 commits into from
May 7, 2025
Merged

Clarify docstrings in neuropixels_utils #3895

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6b7f3da
Clarify docstrings in neuropixels_utils
alejoe91 Apr 30, 2025
ef02007
num_adcs -> num_channels_per_adc
alejoe91 May 2, 2025
8bcecf7
Merge branch 'main' into improve-np-utils-docs
alejoe91 May 2, 2025
0a2dcfa
fix get_neuropixels_channel_groups
alejoe91 May 2, 2025
0e02f7f
Merge branch 'improve-np-utils-docs' of github.com:alejoe91/spikeinte…
alejoe91 May 2, 2025
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8 changes: 5 additions & 3 deletions src/spikeinterface/extractors/neoextractors/spikeglx.py
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Original file line number Diff line number Diff line change
Expand Up @@ -87,11 +87,13 @@ def __init__(
self.set_probe(probe, in_place=True)

# load num_channels_per_adc depending on probe type
ptype = probe.annotations["probe_type"]
model_name = probe.annotations.get("model_name", None)
if model_name is None:
model_name = probe.annotations["probe_name"]

if ptype in [21, 24]: # NP2.0
if "2.0" in model_name: # Neuropixels 2.0
num_channels_per_adc = 16
num_cycles_in_adc = 16 # TODO: Check this.
num_cycles_in_adc = 16
total_channels = 384
else: # NP1.0
num_channels_per_adc = 12
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10 changes: 5 additions & 5 deletions src/spikeinterface/extractors/neuropixels_utils.py
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Expand Up @@ -28,8 +28,8 @@ def get_neuropixels_sample_shifts(
Neuropixels probes typically have 384 channels.
num_channels_per_adc : int, default: 12
Number of channels assigned to each ADC on the probe.
Neuropixels 1.0 probes have 12 ADCs, each handling 32 channels.
Neuropixels 2.0 probes have 16 ADCs.
Neuropixels 1.0 probes have 32 ADCs, each handling 12 channels.
Neuropixels 2.0 probes have 24 ADCs, each handling 16 channels.
num_cycles : int or None, default: None
Number of cycles in the ADC sampling sequence.
Neuropixels 1.0 probes have 13 cycles for AP (action potential) signals
Expand Down Expand Up @@ -57,7 +57,7 @@ def get_neuropixels_sample_shifts(
return sample_shifts


def get_neuropixels_channel_groups(num_channels=384, num_adcs=12):
def get_neuropixels_channel_groups(num_channels=384, num_channels_per_adc=12):
"""
Returns groups of simultaneously sampled channels on a Neuropixels probe.

Expand Down Expand Up @@ -85,8 +85,8 @@ def get_neuropixels_channel_groups(num_channels=384, num_adcs=12):
All currently available Neuropixels variants have 384 channels.
num_channels_per_adc : int, default: 12
The number of channels per ADC on the probe.
Neuropixels 1.0 probes have 12 ADCs.
Neuropixels 2.0 probes have 16 ADCs.
Neuropixels 1.0 probes have 32 ADCs, each handling 12 channels.
Neuropixels 2.0 probes have 24 ADCs, each handling 16 channels.

Returns
-------
Expand Down