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Axonarawio #958

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merged 70 commits into from
Apr 12, 2021
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a3988ee
added placeholder for axonarawio.py and temporary notebook for testing
sbuergers Mar 6, 2021
2e4f80b
some progress - reading data with BinConverter help and starting on .…
sbuergers Mar 8, 2021
e1b52b7
added first draft of sig_channels
sbuergers Mar 8, 2021
87352bf
first draft - check if I can use AxonaRawIO
sbuergers Mar 9, 2021
0271f32
some minor additions
sbuergers Mar 9, 2021
d0c0adf
added axonarawio to neo.rawio.__init__.py
sbuergers Mar 9, 2021
0cb868d
added axonarawio.py to neo/rawio/__init__.py
sbuergers Mar 9, 2021
dc9bfbf
first scaffolding for reading raw cont data
sbuergers Mar 9, 2021
49e3d57
added comparison of two methods for reading cont data using mmap
sbuergers Mar 9, 2021
7a1e89b
added way of reading data using np.memmap for comparison
sbuergers Mar 9, 2021
6b532ec
cleaned up notebook and settled on np.memmap for raw signal
sbuergers Mar 10, 2021
75bd006
implemented reading raw continous data with get_analogsignal_chunk
sbuergers Mar 10, 2021
8be3bd1
added timing checks + looking for faster get_analogsignal_chunk
sbuergers Mar 10, 2021
1399f1d
trying hopefully faster implementation for get_analogsignal_chunk
sbuergers Mar 10, 2021
fdd6659
trying to test hopefully faster implementation of get_analogsignal_chunk
sbuergers Mar 10, 2021
962569c
fixed base index vector to read cont. data
sbuergers Mar 10, 2021
4d95f28
fixed selecting arbitrary chunk of cont data
sbuergers Mar 10, 2021
bef055e
some minor changes
sbuergers Mar 11, 2021
3fada9e
some changes to adjust toward new baserawio
sbuergers Mar 15, 2021
e7b3f2e
found better implementation of reading cont signals
sbuergers Mar 15, 2021
55785a6
implemented new method for reading cont data
sbuergers Mar 15, 2021
1b879a2
added check for reading cont data using axonarawio
sbuergers Mar 15, 2021
d19cb34
adjusted helper methods
sbuergers Mar 15, 2021
f9ad898
somewhat checking adjustments of helper methods
sbuergers Mar 15, 2021
c19936b
started exploring unit data files
sbuergers Mar 16, 2021
22379b5
linting or comment changes
sbuergers Mar 16, 2021
d09815c
copied over updated annotatiosn from examplerawio.py where applicable
sbuergers Mar 16, 2021
687969f
adjusted get_channel_gain (still unverified if correct)
sbuergers Mar 16, 2021
6d50833
starting to explore remaining pieces for python-neo .bin implmementation
sbuergers Mar 17, 2021
9841f64
added slightly more detailed notes about data formats
sbuergers Mar 18, 2021
1959530
added more thorough description of what data should be supported
sbuergers Mar 18, 2021
14cc0f0
small clean-up of notebook
sbuergers Mar 18, 2021
454dfd7
filled in methods related to signal dur or len
sbuergers Mar 18, 2021
60d349e
added test_axonarawio.py
sbuergers Mar 19, 2021
2865c61
adjusted desc and filled spiking and event information with None
sbuergers Mar 19, 2021
28a6f1f
added axonaio.py
sbuergers Mar 19, 2021
55fb3b7
added test_axonaio.py
sbuergers Mar 19, 2021
ef4e283
changed files_to_download to only include base filename
sbuergers Mar 19, 2021
0a89ab4
added axonaio to io.__init__
sbuergers Mar 19, 2021
ca62a2c
check if AxonaIO works
sbuergers Mar 19, 2021
e56b64f
removed specific example tests for test_axonaio
sbuergers Mar 19, 2021
2af6a9b
added gain factor for conversion to uV for .bin data
sbuergers Mar 19, 2021
0f8b958
added notes and fixed equation for uV conversion
sbuergers Mar 19, 2021
fe4b646
checking conversion factor for getting uV
sbuergers Mar 19, 2021
cacb924
Update neo/io/axonaio.py
sbuergers Mar 20, 2021
44f5e1a
remove default val for filename
sbuergers Mar 21, 2021
61e0825
Merge branch 'axonarawio' of https://github.com/catalystneuro/python-…
sbuergers Mar 21, 2021
14ed2f1
removed variable assignment that already has it as default val
sbuergers Mar 22, 2021
4853b5e
rewrite desc
sbuergers Mar 23, 2021
9ae6586
allow base filename, set and bin extensions as user input
sbuergers Mar 23, 2021
7b16ed7
made channel_memory_offset global variable
sbuergers Mar 23, 2021
4e7dcfb
ensure chan_id is a str
sbuergers Mar 23, 2021
a720f41
ensure stream_id is a str
sbuergers Mar 23, 2021
2d2c110
create class variable for channel_memory_offset (remapping of chan ids)
sbuergers Mar 23, 2021
e1cc140
made ecephys data type instance variable
sbuergers Mar 23, 2021
4192f82
check code modifications
sbuergers Mar 23, 2021
2d70529
remove jupyter notebook
sbuergers Mar 23, 2021
83d5bdd
minor annotation adjustments
sbuergers Mar 23, 2021
6535674
remove None from first index in channel_memory_offset
sbuergers Mar 23, 2021
7e05f2e
count channel ids from 0 upwards instead of 1
sbuergers Mar 23, 2021
2bda34b
explicitly load set and bin file in test_axonaio.py
sbuergers Mar 24, 2021
76fecd0
Steffen and Sam do some debug.
samuelgarcia Apr 9, 2021
6f6c697
Merge pull request #1 from samuelgarcia/axonarawio
sbuergers Apr 9, 2021
79a486c
automatically get sampling rate from .set file
sbuergers Apr 9, 2021
dfa9375
added additional annotations, including tetrode per channel
sbuergers Apr 9, 2021
1362162
debugged new additions - tests pass
sbuergers Apr 9, 2021
3884860
pep8 adherence in axonarawio
sbuergers Apr 9, 2021
d74f267
removed #eof
sbuergers Apr 9, 2021
74ac209
fix pep8 from pep8speaks complaints
sbuergers Apr 9, 2021
d1498d9
final pep8 fixes
sbuergers Apr 9, 2021
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7 changes: 7 additions & 0 deletions neo/io/__init__.py
Original file line number Diff line number Diff line change
Expand Up @@ -19,6 +19,7 @@
* :attr:`AsciiSignalIO`
* :attr:`AsciiSpikeTrainIO`
* :attr:`AxographIO`
* :attr:`AxonaIO`
* :attr:`AxonIO`
* :attr:`BCI2000IO`
* :attr:`BlackrockIO`
Expand Down Expand Up @@ -77,6 +78,10 @@

.. autoattribute:: extensions

.. autoclass:: neo.io.AxonaIO

.. autoattribute:: extensions

.. autoclass:: neo.io.AxonIO

.. autoattribute:: extensions
Expand Down Expand Up @@ -250,6 +255,7 @@
from neo.io.asciisignalio import AsciiSignalIO
from neo.io.asciispiketrainio import AsciiSpikeTrainIO
from neo.io.axographio import AxographIO
from neo.io.axonaio import AxonaIO
from neo.io.axonio import AxonIO
from neo.io.blackrockio import BlackrockIO
from neo.io.blkio import BlkIO
Expand Down Expand Up @@ -295,6 +301,7 @@
AsciiSignalIO,
AsciiSpikeTrainIO,
AxographIO,
AxonaIO,
AxonIO,
BCI2000IO,
BlackrockIO,
Expand Down
13 changes: 13 additions & 0 deletions neo/io/axonaio.py
Original file line number Diff line number Diff line change
@@ -0,0 +1,13 @@
from neo.io.basefromrawio import BaseFromRaw
from neo.rawio.axonarawio import AxonaRawIO


class AxonaIO(AxonaRawIO, BaseFromRaw):
name = 'Axona IO'
description = "Read raw continuous data (.bin and .set files)"

def __init__(self, filename):
AxonaRawIO.__init__(self, filename=filename)
BaseFromRaw.__init__(self, filename)

# eof
7 changes: 7 additions & 0 deletions neo/rawio/__init__.py
Original file line number Diff line number Diff line change
Expand Up @@ -13,6 +13,7 @@
Classes:

* :attr:`AxographRawIO`
* :attr:`AxonaRawIO`
* :attr:`AxonRawIO`
* :attr:`BlackrockRawIO`
* :attr:`BrainVisionRawIO`
Expand Down Expand Up @@ -40,6 +41,10 @@

.. autoattribute:: extensions

.. autoclass:: neo.rawio.AxonaRawIO

.. autoattribute:: extensions

.. autoclass:: neo.rawio.AxonRawIO

.. autoattribute:: extensions
Expand Down Expand Up @@ -128,6 +133,7 @@
import os

from neo.rawio.axographrawio import AxographRawIO
from neo.rawio.axonarawio import AxonaRawIO
from neo.rawio.axonrawio import AxonRawIO
from neo.rawio.blackrockrawio import BlackrockRawIO
from neo.rawio.brainvisionrawio import BrainVisionRawIO
Expand All @@ -153,6 +159,7 @@

rawiolist = [
AxographRawIO,
AxonaRawIO,
AxonRawIO,
BlackrockRawIO,
BrainVisionRawIO,
Expand Down
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