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Add mux_index contact annotation #368

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Add mux_index contact annotation #368

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18 changes: 10 additions & 8 deletions src/probeinterface/neuropixels_tools.py
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Original file line number Diff line number Diff line change
Expand Up @@ -317,13 +317,18 @@ def _make_npx_probe_from_description(probe_description, model_name, elec_ids, sh
# annotate each contact with its mux channel
num_adcs, num_channels_per_adc, mux_table = make_mux_table_array(mux_info)
num_contacts = positions.shape[0]
# mux channel: which adc is used for each contact
mux_channels = np.zeros(num_contacts, dtype="int64")
# mux index: order of sampling of the contact in the adc group
mux_index = np.zeros(num_contacts, dtype="int64")
for adc_idx, mux_channels_per_adc in enumerate(mux_table):
mux_channels_per_adc = mux_channels_per_adc[mux_channels_per_adc < num_contacts]
mux_channels[mux_channels_per_adc] = adc_idx
mux_index[mux_channels_per_adc] = np.arange(len(mux_channels_per_adc))
probe.annotate(num_adcs=num_adcs)
probe.annotate(num_channels_per_adc=num_channels_per_adc)
probe.annotate_contacts(mux_channels=mux_channels)
probe.annotate_contacts(mux_index=mux_index)

return probe

Expand Down Expand Up @@ -1044,20 +1049,17 @@ def read_openephys(
pt_metadata = np_probe_info["pt_metadata"]
mux_info = np_probe_info["mux_info"]

probe = _make_npx_probe_from_description(
pt_metadata, probe_part_number, elec_ids, shank_ids=shank_ids, mux_info=mux_info
)

# check if subset of channels
chans_saved = get_saved_channel_indices_from_openephys_settings(settings_file, stream_name=stream_name)

# if a recording state is found, slice probe
if chans_saved is not None:
positions = positions[chans_saved]
if shank_ids is not None:
shank_ids = np.array(shank_ids)[chans_saved]
if elec_ids is not None:
elec_ids = np.array(elec_ids)[chans_saved]
probe = probe.get_slice(chans_saved)

probe = _make_npx_probe_from_description(
pt_metadata, probe_part_number, elec_ids, shank_ids=shank_ids, mux_info=mux_info
)
probe.serial_number = np_probe_info["serial_number"]
probe.name = np_probe_info["name"]

Expand Down