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fix: gate has_spikegadgets_neuropixels_probes on supported variants #478

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fix: gate has_spikegadgets_neuropixels_probes on supported variants #478

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c65b081
fix: gate `has_spikegadgets_neuropixels_probes` on supported variants
Nov 12, 2026
5eb4b39
remove non-existent code reference in comments
Nov 12, 2026
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135 changes: 74 additions & 61 deletions src/probeinterface/neuropixels_tools.py
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Original file line number Diff line number Diff line change
Expand Up @@ -1835,6 +1835,55 @@ def _spikegadgets_channel_index_np2_1shank(channel_index: int) -> int:
return row * COLS_PER_SHANK + col_on_shank


# Dispatch keyed by SpikeConfiguration (device, deviceSubType) attributes
# (see Trodes `configuration.cpp:2495-2520` and `5246-5291`). Each entry
# gives the HardwareConfiguration `Device` name to filter on, the catalogue
# part number to build the full probe from, the per-probe horizontal shift
# (um) used when plotting multi-probe ProbeGroups, and (optionally) a
# function remapping Trodes' ``channelsOn`` bit position (channel_index, equal to
# ``electrode_id[1:] - 1`` in the .rec XML) to a probeinterface catalogue
# contact index. The remap is None when Trodes' ordering already matches
# the catalogue's (NP1.0 standard).
#
# All NP1.0 staggered catalogue variants (NP1000, NP1001, NP1010-NP1014,
# PRB_1_2_0480_2, PRB_1_4_0480_1, PRB_1_4_0480_1_C) share identical 2D
# geometry, so NP1000 is the canonical pick. All NP2.0 4-shank catalogue
# variants (NP2010, NP2013, NP2014, NP2020, NP2021) share identical 2D
# geometry, so NP2014 is the canonical pick. model_name and description
# are cleared on the sliced probe in both cases because the XML does not
# carry a part-number field.
_SPIKEGADGETS_NEUROPIXELS_FORMATS = {
("neuropixels1", "10"): {
"hardware_device_name": "NeuroPixels1",
"part_number": "NP1000",
"multi_probe_plot_offset_um": 250.0,
"channel_index_to_catalogue_index": None,
},
("neuropixels2", "1_SHANK"): {
"hardware_device_name": "NeuroPixels2",
"part_number": "NP2000",
"multi_probe_plot_offset_um": 250.0,
"channel_index_to_catalogue_index": _spikegadgets_channel_index_np2_1shank,
},
("neuropixels2", "4_SHANK"): {
"hardware_device_name": "NeuroPixels2",
"part_number": "NP2014",
"multi_probe_plot_offset_um": 1000.0,
"channel_index_to_catalogue_index": _spikegadgets_channel_index_np2_4shank,
},
}


def _spikegadgets_neuropixels_dispatch_key(sconf) -> tuple[str, str]:
# Older NP1.0 recordings predate the device/deviceSubType attributes, so
# missing values fall back to NP1.0 standard.
sconf_device = (sconf.attrib.get("device", "") if sconf is not None else "").lower() or "neuropixels1"
sconf_subtype = sconf.attrib.get("deviceSubType", "") if sconf is not None else ""
if sconf_device == "neuropixels1" and not sconf_subtype:
sconf_subtype = "10"
return (sconf_device, sconf_subtype)


def read_spikegadgets_neuropixels(file: str | Path, raise_error: bool = True) -> ProbeGroup:
"""
Find active channels of the given Neuropixels probe from a SpikeGadgets .rec file.
Expand Down Expand Up @@ -1863,63 +1912,19 @@ def read_spikegadgets_neuropixels(file: str | Path, raise_error: bool = True) ->
probe_group : ProbeGroup object

"""
# Dispatch keyed by SpikeConfiguration (device, deviceSubType) attributes
# (see Trodes `configuration.cpp:2495-2520` and `5246-5291`). Each entry
# gives the HardwareConfiguration `Device` name to filter on, the catalogue
# part number to build the full probe from, the per-probe horizontal shift
# (um) used when plotting multi-probe ProbeGroups, and (optionally) a
# function remapping Trodes' ``channelsOn`` bit position (channel_index, equal to
# ``electrode_id[1:] - 1`` in the .rec XML) to a probeinterface catalogue
# contact index. The remap is None when Trodes' ordering already matches
# the catalogue's (NP1.0 standard).
#
# All NP1.0 staggered catalogue variants (NP1000, NP1001, NP1010-NP1014,
# PRB_1_2_0480_2, PRB_1_4_0480_1, PRB_1_4_0480_1_C) share identical 2D
# geometry, so NP1000 is the canonical pick. All NP2.0 4-shank catalogue
# variants (NP2010, NP2013, NP2014, NP2020, NP2021) share identical 2D
# geometry, so NP2014 is the canonical pick. model_name and description
# are cleared on the sliced probe in both cases because the XML does not
# carry a part-number field.
spikegadgets_neuropixels_formats = {
("neuropixels1", "10"): {
"hardware_device_name": "NeuroPixels1",
"part_number": "NP1000",
"multi_probe_plot_offset_um": 250.0,
"channel_index_to_catalogue_index": None,
},
("neuropixels2", "1_SHANK"): {
"hardware_device_name": "NeuroPixels2",
"part_number": "NP2000",
"multi_probe_plot_offset_um": 250.0,
"channel_index_to_catalogue_index": _spikegadgets_channel_index_np2_1shank,
},
("neuropixels2", "4_SHANK"): {
"hardware_device_name": "NeuroPixels2",
"part_number": "NP2014",
"multi_probe_plot_offset_um": 1000.0,
"channel_index_to_catalogue_index": _spikegadgets_channel_index_np2_4shank,
},
}

header_txt = parse_spikegadgets_header(file)
root = ElementTree.fromstring(header_txt)
hconf = root.find("HardwareConfiguration")
sconf = root.find("SpikeConfiguration")

# Older NP1.0 recordings predate the device/deviceSubType attributes, so
# missing values fall back to NP1.0 standard.
sconf_device = (sconf.attrib.get("device", "") if sconf is not None else "").lower() or "neuropixels1"
sconf_subtype = sconf.attrib.get("deviceSubType", "") if sconf is not None else ""
if sconf_device == "neuropixels1" and not sconf_subtype:
sconf_subtype = "10"
dispatch_key = (sconf_device, sconf_subtype)
if dispatch_key not in spikegadgets_neuropixels_formats:
dispatch_key = _spikegadgets_neuropixels_dispatch_key(sconf)
if dispatch_key not in _SPIKEGADGETS_NEUROPIXELS_FORMATS:
raise ValueError(
f"Unsupported SpikeGadgets Neuropixels variant device={sconf_device!r} "
f"deviceSubType={sconf_subtype!r}; supported: "
f"{sorted(spikegadgets_neuropixels_formats)}"
f"Unsupported SpikeGadgets Neuropixels variant device={dispatch_key[0]!r} "
f"deviceSubType={dispatch_key[1]!r}; supported: "
f"{sorted(_SPIKEGADGETS_NEUROPIXELS_FORMATS)}"
)
fmt = spikegadgets_neuropixels_formats[dispatch_key]
fmt = _SPIKEGADGETS_NEUROPIXELS_FORMATS[dispatch_key]

probe_configs = [d for d in hconf if d.attrib.get("name") == fmt["hardware_device_name"]]
n_probes = len(probe_configs)
Expand Down Expand Up @@ -2049,14 +2054,21 @@ def read_spikegadgets(*args, **kwargs) -> ProbeGroup:
def has_spikegadgets_neuropixels_probes(file: str | Path) -> bool:
"""
Return True if the SpikeGadgets ``.rec`` file describes at least one
Neuropixels probe.
Neuropixels probe readable by :func:`read_spikegadgets_neuropixels`.

Detection requires two conditions on the ``.rec`` XML header:

Detection scans the ``HardwareConfiguration`` block of the ``.rec`` XML
header for ``Device`` entries whose ``name`` attribute matches a known
Neuropixels source name (``"NeuroPixels1"`` or ``"NeuroPixels2"``). The
presence of any such entry is the ground-truth signal that the file
contains Neuropixels probe geometry, independent of what other hardware
the headstage is also streaming.
1. The ``HardwareConfiguration`` block contains an entry (``Device`` or
``SourceOptions``) whose ``name`` attribute matches a known Neuropixels
source name (``"NeuroPixels1"`` or ``"NeuroPixels2"``).
2. The ``SpikeConfiguration`` ``(device, deviceSubType)`` pair is a
variant that :func:`read_spikegadgets_neuropixels` supports.

Condition 2 matters because other headstages, such as NRIC (Pixie384)
recordings, also carry Neuropixels-named ``SourceOptions`` gain blocks
although their geometry is not Neuropixels; without it, callers gating
on this helper would trigger an unsupported-variant ``ValueError`` in the
reader.

Intended use: callers that route heterogeneous SpikeGadgets recordings
(mixing tetrodes, Neuropixels, etc.) can gate the call to
Expand Down Expand Up @@ -2084,10 +2096,11 @@ def has_spikegadgets_neuropixels_probes(file: str | Path) -> bool:
if hconf is None:
return False

for device in hconf:
if device.attrib.get("name") in neuropixels_source_names:
return True
return False
if not any(child.attrib.get("name") in neuropixels_source_names for child in hconf):
return False

sconf = root.find("SpikeConfiguration")
return _spikegadgets_neuropixels_dispatch_key(sconf) in _SPIKEGADGETS_NEUROPIXELS_FORMATS


def parse_spikegadgets_header(file: str | Path) -> str:
Expand Down
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