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Num hw chan resolution #85

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merged 5 commits into from
Feb 3, 2024
Merged

Num hw chan resolution #85

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e5d2c90
define number of ephys channels based on the spike configuration
samuelbray32 Jan 25, 2024
68a41e5
limit maximum number of channels to the requested hwChannels when req…
samuelbray32 Jan 25, 2024
567278a
Allow specification of iterator stream based on name
samuelbray32 Jan 26, 2024
4562bba
linting
samuelbray32 Jan 26, 2024
a82f1d7
Merge branch 'main' into num_hwChan_resolution
edeno Feb 3, 2024
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2 changes: 2 additions & 0 deletions src/trodes_to_nwb/convert_ephys.py
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Original file line number Diff line number Diff line change
Expand Up @@ -87,6 +87,8 @@ def __init__(
else:
self.nwb_hw_channel_order = nwb_hw_channel_order

if stream_index == 3 and len(self.nwb_hw_channel_order) < self.n_channel:
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self.n_channel = len(self.nwb_hw_channel_order)
"""split excessively large iterators into smaller ones
"""
iterator_size = [neo_io._raw_memmap.shape[0] for neo_io in self.neo_io]
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9 changes: 9 additions & 0 deletions src/trodes_to_nwb/spike_gadgets_raw_io.py
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Expand Up @@ -101,6 +101,15 @@ def _parse_header(self):

self._sampling_rate = float(hconf.attrib["samplingRate"])
num_ephy_channels = int(hconf.attrib["numChannels"])
# check for agreement with number of channels in xml
sconf_channels = np.sum([len(x) for x in sconf])
if sconf_channels < num_ephy_channels:
num_ephy_channels = sconf_channels
if sconf_channels > num_ephy_channels:
raise ValueError(
"SpikeGadgets: the number of channels in the spike configuration is larger than the number of channels in the hardware configuration"
)

try:
num_chan_per_chip = int(sconf.attrib["chanPerChip"])
except KeyError:
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