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Add MSH SpikeGadgets fixture to CI #1855

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Add MSH SpikeGadgets fixture to CI #1855

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9af8c88
more improvements spikegadgets
h-mayorquin May 21, 2026
1c14f96
improve warning and comments messages, I have a Zach on my shoulder
h-mayorquin May 21, 2026
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23 changes: 22 additions & 1 deletion neo/rawio/spikegadgetsrawio.py
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Original file line number Diff line number Diff line change
Expand Up @@ -177,9 +177,30 @@ def _intan_hwchans_in_binary_order(self, sconf, num_ephy_channels, num_ephy_chan
intan_chans_per_chip = int(sconf.attrib.get("chanPerChip", 32)) # RHD2132 default for legacy files
hw_chans_in_xml = [int(schan.attrib["hwChan"]) for trode in sconf for schan in trode]

if intan_chans_per_chip > num_ephy_channels:
# chanPerChip larger than the total channel count is structurally impossible
# for any real Intan chip layout. Reported in #1830 with the example value
# 1645402192, suspected to come from a Trodes header-write bug.
self.logger.warning(
f"SpikeGadgets chanPerChip={intan_chans_per_chip} exceeds "
f"num_ephy_channels={num_ephy_channels}; treating as invalid "
f"and falling back to XML document order. This could indicate "
f"a bug; verify that channel order matches your expectation, "
f"and please open an issue at "
f"https://github.com/NeuralEnsemble/python-neo/issues if you "
f"encounter this. See PR #1830 for an earlier report."
)

channels_fit_chip_layout = intan_chans_per_chip > 0 and num_ephy_channels % intan_chans_per_chip == 0
if not channels_fit_chip_layout:
return hw_chans_in_xml
# The Trodes always write the data so the binary
# stream is hwChan-ascending for every SpikeGadgets device. Source:
# `Trodes/src-threads/recordThread.cpp` lines ~281-298 in the
# canonical Trodes repo at https://bitbucket.org/mkarlsso/trodes
# (checked May 2026). The correct ordering for the fallback path
# is therefore hwChan ascending; sort rather than trust XML
# document order in case the user reordered the xml
return sorted(hw_chans_in_xml)

# Reproduce the chip-interleaved hwChan sequence (local-channel outer, chip inner)
# so that hwchans_in_binary_order[i] is the hwChan whose data lives at byte pair i.
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1 change: 1 addition & 0 deletions neo/test/rawiotest/test_spikegadgetsrawio.py
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Expand Up @@ -18,6 +18,7 @@ class TestSpikeGadgetsRawIO(
"spikegadgets/W122_06_09_2019_1_fromSD.rec",
"spikegadgets/SpikeGadgets_test_data_2xNpix1.0_20240318_173658.rec",
"spikegadgets/neuropixels2_4shank/20260122_134412_merged_cropped_1min_NP2.rec",
"spikegadgets/msh_1024ch/msh_1024ch.rec",
]

def test_parse_header_missing_channels(self):
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