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Added support for missing channels in SpikeGadgets #1593

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Added support for missing channels in SpikeGadgets #1593

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6ba3d96
added support for missing channels
pauladkisson Nov 1, 2024
5df9d8d
added test for header
pauladkisson Nov 4, 2024
33ebfcd
added note to docstring
pauladkisson Nov 11, 2024
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25 changes: 16 additions & 9 deletions neo/rawio/spikegadgetsrawio.py
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Original file line number Diff line number Diff line change
Expand Up @@ -81,7 +81,7 @@ def __init__(self, filename="", selected_streams=None):
def _source_name(self):
return self.filename

def _produce_ephys_channel_ids(self, n_total_channels, n_channels_per_chip):
def _produce_ephys_channel_ids(self, n_total_channels, n_channels_per_chip, missing_hw_chans):
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"""Compute the channel ID labels for subset of spikegadgets recordings
The ephys channels in the .rec file are stored in the following order:
hwChan ID of channel 0 of first chip, hwChan ID of channel 0 of second chip, ..., hwChan ID of channel 0 of Nth chip,
Expand All @@ -94,14 +94,18 @@ def _produce_ephys_channel_ids(self, n_total_channels, n_channels_per_chip):
This doesn't work for all types of spikegadgets
see: https://github.com/NeuralEnsemble/python-neo/issues/1517

If there are any missing hardware channels, they must be specified in missing_hw_chans.
See: https://github.com/NeuralEnsemble/python-neo/issues/1592
"""
ephys_channel_ids_list = []
for hw_channel in range(n_channels_per_chip):
hw_channel_list = [
hw_channel + chip * n_channels_per_chip for chip in range(int(n_total_channels / n_channels_per_chip))
]
ephys_channel_ids_list.append(hw_channel_list)
return [channel for channel_list in ephys_channel_ids_list for channel in channel_list]
for local_hw_channel in range(n_channels_per_chip):
n_chips = int(n_total_channels / n_channels_per_chip)
for chip in range(n_chips):
global_hw_chan = local_hw_channel + chip * n_channels_per_chip
if global_hw_chan in missing_hw_chans:
continue
ephys_channel_ids_list.append(local_hw_channel + chip * n_channels_per_chip)
return ephys_channel_ids_list

def _parse_header(self):
# parse file until "</Configuration>"
Expand All @@ -126,7 +130,8 @@ def _parse_header(self):
sconf = root.find("SpikeConfiguration")

self._sampling_rate = float(hconf.attrib["samplingRate"])
num_ephy_channels = int(hconf.attrib["numChannels"])
num_ephy_channels_xml = int(hconf.attrib["numChannels"])
num_ephy_channels = num_ephy_channels_xml

# check for agreement with number of channels in xml
sconf_channels = np.sum([len(x) for x in sconf])
Expand Down Expand Up @@ -220,7 +225,9 @@ def _parse_header(self):
# we can only produce these channels for a subset of spikegadgets setup. If this criteria isn't
# true then we should just use the raw_channel_ids and let the end user sort everything out
if num_ephy_channels % num_chan_per_chip == 0:
channel_ids = self._produce_ephys_channel_ids(num_ephy_channels, num_chan_per_chip)
all_hw_chans = [int(schan.attrib["hwChan"]) for trode in sconf for schan in trode]
missing_hw_chans = set(range(num_ephy_channels)) - set(all_hw_chans)
channel_ids = self._produce_ephys_channel_ids(num_ephy_channels_xml, num_chan_per_chip, missing_hw_chans)
raw_channel_ids = False
else:
raw_channel_ids = True
Expand Down
33 changes: 33 additions & 0 deletions neo/test/rawiotest/test_spikegadgetsrawio.py
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Original file line number Diff line number Diff line change
Expand Up @@ -2,6 +2,7 @@

from neo.rawio.spikegadgetsrawio import SpikeGadgetsRawIO
from neo.test.rawiotest.common_rawio_test import BaseTestRawIO
from numpy.testing import assert_array_equal


class TestSpikeGadgetsRawIO(
Expand All @@ -16,6 +17,38 @@ class TestSpikeGadgetsRawIO(
"spikegadgets/SpikeGadgets_test_data_2xNpix1.0_20240318_173658.rec",
]

class TestSpikeGadgetsRawIOHeaderOnly(unittest.TestCase):
def setUp(self):
filename = "/Volumes/T7/CatalystNeuro/Jadhav/stubbed_files/SL18_D19_S01_F01_BOX_SLP_20230503_112642_stubbed.rec"
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something tells me this line won't work for the CI

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Yes, this will need to be updated once the test file is up on the gin repo.

self.rawio = SpikeGadgetsRawIO(filename=filename)

def test_parse_header(self):
self.rawio.parse_header()
assert_array_equal(
self.rawio.header['signal_channels']['id'],
[
'ECU_Ain1', 'ECU_Ain2', 'ECU_Ain3', 'ECU_Ain4', 'ECU_Ain5', 'ECU_Ain6',
'ECU_Ain7', 'ECU_Ain8', 'ECU_Aout1', 'ECU_Aout2', 'ECU_Aout3', 'ECU_Aout4', '0',
'32', '96', '160', '192', '224', '1', '33', '65', '97', '161', '193', '225', '2', '34',
'98', '162', '194', '226', '3', '35', '67', '99', '163', '195', '227', '4', '36',
'100', '164', '196', '228', '5', '37', '69', '101', '165', '197', '229', '6', '38',
'102', '166', '198', '230', '7', '39', '71', '103', '167', '199', '231', '8', '40',
'72', '104', '136', '168', '200', '232', '9', '41', '73', '105', '137', '169', '201',
'233', '10', '42', '74', '106', '138', '170', '202', '234', '11', '43', '75', '107',
'139', '171', '203', '235', '12', '44', '76', '108', '140', '172', '204', '236', '13',
'45', '77', '109', '141', '173', '205', '237', '14', '46', '78', '110', '142', '174',
'206', '238', '15', '47', '79', '111', '143', '175', '207', '239', '80', '144', '176',
'208', '240', '17', '49', '81', '145', '177', '209', '241', '82', '146', '178', '210',
'242', '19', '51', '83', '147', '179', '211', '243', '84', '148', '180', '212', '244',
'21', '53', '85', '149', '181', '213', '245', '86', '150', '182', '214', '246', '23',
'55', '87', '151', '183', '215', '247', '24', '56', '88', '152', '184', '216', '248',
'25', '57', '89', '121', '153', '185', '217', '249', '26', '58', '90', '154', '186',
'218', '250', '27', '59', '91', '123', '155', '187', '219', '251', '28', '60', '92',
'156', '188', '220', '252', '29', '61', '93', '125', '157', '189', '221', '253', '30',
'62', '94', '158', '190', '222', '254', '31', '63', '95', '127', '159', '191', '223',
'255',
]
)

if __name__ == "__main__":
unittest.main()