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Add num_adcs, num_channels_per_adc, num_readout_channels, adc_bit_depth annotations to NP probes #356

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Merged
merged 1 commit into from
Jul 29, 2025
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Add num_adcs, num_channels_per_adc, num_readout_channels, adc_bit_depth annotations to NP probes #356

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40 changes: 26 additions & 14 deletions src/probeinterface/neuropixels_tools.py
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Original file line number Diff line number Diff line change
Expand Up @@ -128,15 +128,19 @@ def make_mux_table_array(mux_information) -> np.array:

# mux_information looks like (num_adcs num_channels_per_adc)(int int int ...)(int int int ...)...(int int int ...)
# First split on ')(' to get a list of the information in the brackets, and remove the leading data
adc_info = mux_information.split(")(")[0]
split_mux = mux_information.split(")(")[1:]

# The first element is the number of ADCs and the number of channels per ADC
num_adcs, num_channels_per_adc = map(int, adc_info[1:].split(","))

# Then remove the brackets, and split using " " to get each integer as a list
mux_channels = [
np.array(each_mux.replace("(", "").replace(")", "").split(" ")).astype("int") for each_mux in split_mux
]
mux_channels_array = np.transpose(np.array(mux_channels))

return mux_channels_array
return num_adcs, num_channels_per_adc, mux_channels_array


def get_probe_contour_vertices(shank_width, tip_length, probe_length) -> list:
Expand Down Expand Up @@ -225,7 +229,7 @@ def read_imro(file_path: Union[str, Path]) -> Probe:
return _read_imro_string(imro_str, imDatPrb_pn)


def _make_npx_probe_from_description(probe_description, model_name, elec_ids, shank_ids, mux_table=None) -> Probe:
def _make_npx_probe_from_description(probe_description, model_name, elec_ids, shank_ids, mux_info=None) -> Probe:
# used by _read_imro_string and for generating the NP library

# compute position
Expand Down Expand Up @@ -302,14 +306,23 @@ def _make_npx_probe_from_description(probe_description, model_name, elec_ids, sh
# wire it
probe.set_device_channel_indices(np.arange(positions.shape[0]))

# set other key metadata annotations
probe.annotate(
adc_bit_depth=probe_description["adc_bit_depth"],
num_readout_channels=probe_description["num_readout_channels"],
)

# annotate with MUX table
if mux_table is not None:
if mux_info is not None:
# 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_channels = 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
probe.annotate(num_adcs=num_adcs)
probe.annotate(num_channels_per_adc=num_channels_per_adc)
probe.annotate_contacts(mux_channels=mux_channels)

return probe
Expand Down Expand Up @@ -343,7 +356,7 @@ def _read_imro_string(imro_str: str, imDatPrb_pn: Optional[str] = None) -> Probe
probe_type = probe_type_num_chans.split(",")[0][1:]

probe_features = _load_np_probe_features()
pt_metadata, fields, mux_table = get_probe_metadata_from_probe_features(probe_features, imDatPrb_pn)
pt_metadata, fields, mux_info = get_probe_metadata_from_probe_features(probe_features, imDatPrb_pn)

# fields = probe_description["fields_in_imro_table"]
contact_info = {k: [] for k in fields}
Expand All @@ -369,7 +382,7 @@ def _read_imro_string(imro_str: str, imDatPrb_pn: Optional[str] = None) -> Probe
else:
shank_ids = None

probe = _make_npx_probe_from_description(pt_metadata, imDatPrb_pn, elec_ids, shank_ids, mux_table)
probe = _make_npx_probe_from_description(pt_metadata, imDatPrb_pn, elec_ids, shank_ids, mux_info)

# scalar annotations
probe.annotate(
Expand Down Expand Up @@ -405,9 +418,10 @@ def get_probe_metadata_from_probe_features(probe_features: dict, imDatPrb_pn: st

Returns
-------
probe_metadata, imro_field
probe_metadata, imro_field, mux_information
Dictionary of probe metadata.
Tuple of fields included in the `imro_table_fields`.
Mux table information, if available, as a string.
"""

probe_metadata = probe_features["neuropixels_probes"].get(imDatPrb_pn)
Expand Down Expand Up @@ -440,15 +454,13 @@ def get_probe_metadata_from_probe_features(probe_features: dict, imDatPrb_pn: st
imro_fields = tuple(imro_fields_list)

# Read MUX table information
mux_table = None
mux_information = None

if "z_mux_tables" in probe_features:
mux_table_format_type = probe_metadata.get("mux_table_format_type", None)
mux_information = probe_features["z_mux_tables"].get(mux_table_format_type, None)
if mux_information is not None:
mux_table = make_mux_table_array(mux_information)

return probe_metadata, imro_fields, mux_table
return probe_metadata, imro_fields, mux_information


def write_imro(file: str | Path, probe: Probe):
Expand Down Expand Up @@ -862,7 +874,7 @@ def read_openephys(
positions = np.array([xpos, ypos]).T

probe_part_number = np_probe.get("probe_part_number", None)
pt_metadata, _, mux_table = get_probe_metadata_from_probe_features(probe_features, probe_part_number)
pt_metadata, _, mux_info = get_probe_metadata_from_probe_features(probe_features, probe_part_number)

shank_pitch = pt_metadata["shank_pitch_um"]

Expand Down Expand Up @@ -926,7 +938,7 @@ def read_openephys(
"dock": dock,
"serial_number": probe_serial_number,
"part_number": probe_part_number,
"mux_table": mux_table,
"mux_info": mux_info,
}
# Sequentially assign probe names
if "custom_probe_name" in np_probe.attrib and np_probe.attrib["custom_probe_name"] != probe_serial_number:
Expand Down Expand Up @@ -1024,7 +1036,7 @@ def read_openephys(
shank_ids = np_probe_info["shank_ids"]
elec_ids = np_probe_info["elec_ids"]
pt_metadata = np_probe_info["pt_metadata"]
mux_table = np_probe_info["mux_table"]
mux_info = np_probe_info["mux_info"]

# check if subset of channels
chans_saved = get_saved_channel_indices_from_openephys_settings(settings_file, stream_name=stream_name)
Expand All @@ -1038,7 +1050,7 @@ def read_openephys(
elec_ids = np.array(elec_ids)[chans_saved]

probe = _make_npx_probe_from_description(
pt_metadata, probe_part_number, elec_ids, shank_ids=shank_ids, mux_table=mux_table
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