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Fix electrode selection in Axona raw recording #1520

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Fix electrode selection in Axona raw recording #1520

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15c5d9f
fixed channels selection in AxonaRawIO
Aug 5, 2024
547c8ae
add author name and affiliation
Aug 5, 2024
0d4b92e
update fix neo/rawio/axonarawio.py
Dec 4, 2024
e6685be
Merge branch 'master' into fix_axonarawio
zm711 Dec 5, 2024
03affe4
switch function to private version.
zm711 Dec 5, 2024
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2 changes: 2 additions & 0 deletions doc/source/authors.rst
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Original file line number Diff line number Diff line change
Expand Up @@ -88,6 +88,7 @@ and may not be the current affiliation of a contributor.
* Téo Lohrer
* Anthony Pinto [41]
* Xin Niu
* Letizia Signorelli [42]

1. Centre de Recherche en Neuroscience de Lyon, CNRS UMR5292 - INSERM U1028 - Universite Claude Bernard Lyon 1
2. Unité de Neuroscience, Information et Complexité, CNRS UPR 3293, Gif-sur-Yvette, France
Expand Down Expand Up @@ -130,6 +131,7 @@ and may not be the current affiliation of a contributor.
39. Massachusetts General Hospital, Department of Molecular Biology
40. Plexon Inc.
41. Paris Brain Institute
42. Centre for Molecular Medicine Norway (NCMM), University of Oslo, Norway



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22 changes: 18 additions & 4 deletions neo/rawio/axonarawio.py
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Expand Up @@ -374,8 +374,7 @@ def _get_analogsignal_chunk(self, block_index, seg_index, i_start, i_stop, strea
if channel_indexes is None:
channel_indexes = [i for i in range(bin_dict["num_channels"])]
elif isinstance(channel_indexes, slice):
channel_indexes_all = [i for i in range(bin_dict["num_channels"])]
channel_indexes = channel_indexes_all[channel_indexes]
channel_indexes = self.get_active_channels()
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num_samples = i_stop - i_start

Expand Down Expand Up @@ -558,6 +557,20 @@ def get_active_tetrode(self):
tetrode_id = int(key.strip("collectMask_"))
active_tetrodes.append(tetrode_id)
return active_tetrodes

def get_active_channels(self):
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public or private? what do you think?

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I advice to make things private by default and move away from it when you have a good reason to.

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That's how I was leaning too. I don't see why the user would run this function.

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Yes, I agree with making them private

"""
Returns the ID numbers of the active channels as a list.
E.g.: [20,21,22,23] for tetrode 6 active.
"""
active_tetrodes = self.get_active_tetrode()
active_channels = []

for tetrode in active_tetrodes:
chan = self._get_channel_from_tetrode(tetrode)
active_channels.append(chan)

return np.concatenate(active_channels)
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what's the benefit of concat? I need to doublecheck what is chan is it a list of all channels from a tetrode. If that is the case I would call it channels or chans instead so we know it's plural.

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Yes, chan is a list of all channels from a tetrode, so I agree to call it channels or chans.

Since I was using this function only for the _get_analogsignal_chunk function and it needed the list of active channels as an array I returned directly active_channels as an array. But we can also do it in _get_analogsignal_chunk and keep this function consistent with get_active_tetrodes and return directly active_channels


def _get_channel_from_tetrode(self, tetrode):
"""
Expand Down Expand Up @@ -629,12 +642,13 @@ def _get_signal_chan_header(self):
gain_list = self._get_channel_gain()
offset = 0 # What is the offset?

first_channel = (active_tetrode_set[0] - 1)*elec_per_tetrode
sig_channels = []
for itetr in range(num_active_tetrode):

for ielec in range(elec_per_tetrode):
cntr = (itetr * elec_per_tetrode) + ielec
ch_name = f"{itetr + 1}{letters[ielec]}"
cntr = (itetr * elec_per_tetrode) + ielec + first_channel
ch_name = "{}{}".format(itetr + active_tetrode_set[0], letters[ielec])
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Suggested change
ch_name = "{}{}".format(itetr + active_tetrode_set[0], letters[ielec])
ch_name = f"{itetr + active_tetrode_set[0]}{letters[ielec]}"

we try to keep the codebase on f-strings since they are faster and easier to read :)

chan_id = str(cntr)
gain = gain_list[cntr]
stream_id = "0"
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