Code

Axonarawio#958

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samuelgarcia merged 70 commits intoNeuralEnsemble:masterNeuralEnsemble/python-neo:masterfrom catalystneuro:axonarawiocatalystneuro/python-neo:axonarawioCopy head branch name to clipboardApr 12, 2021

+432

Commits

Commits on Mar 11, 2021

• added placeholder for axonarawio.py and temporary notebook for testing

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• some progress - reading data with BinConverter help and starting on .set file

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• added first draft of sig_channels

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• first draft - check if I can use AxonaRawIO

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• some minor additions

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• added axonarawio to neo.rawio.__init__.py

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• added axonarawio.py to neo/rawio/__init__.py

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• first scaffolding for reading raw cont data

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• added comparison of two methods for reading cont data using mmap

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• added way of reading data using np.memmap for comparison

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• cleaned up notebook and settled on np.memmap for raw signal

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• implemented reading raw continous data with get_analogsignal_chunk

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• added timing checks + looking for faster get_analogsignal_chunk

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• trying hopefully faster implementation for get_analogsignal_chunk

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• trying to test hopefully faster implementation of get_analogsignal_chunk

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• fixed base index vector to read cont. data

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• fixed selecting arbitrary chunk of cont data

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• some minor changes

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Commits on Mar 15, 2021

• some changes to adjust toward new baserawio

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• found better implementation of reading cont signals

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• implemented new method for reading cont data

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• added check for reading cont data using axonarawio

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• adjusted helper methods

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• somewhat checking adjustments of helper methods

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Commits on Mar 16, 2021

• started exploring unit data files

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• linting or comment changes

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• copied over updated annotatiosn from examplerawio.py where applicable

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• adjusted get_channel_gain (still unverified if correct)

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Commits on Mar 17, 2021

• starting to explore remaining pieces for python-neo .bin implmementation

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Commits on Mar 18, 2021

• added slightly more detailed notes about data formats

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• added more thorough description of what data should be supported

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• small clean-up of notebook

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• filled in methods related to signal dur or len

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Commits on Mar 19, 2021

• added test_axonarawio.py

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• adjusted desc and filled spiking and event information with None

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• added axonaio.py

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• added test_axonaio.py

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• changed files_to_download to only include base filename

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• added axonaio to io.__init__

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• check if AxonaIO works

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• removed specific example tests for test_axonaio

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• added gain factor for conversion to uV for .bin data

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• added notes and fixed equation for uV conversion

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• checking conversion factor for getting uV

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Commits on Mar 20, 2021

• Update neo/io/axonaio.py

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Commits on Mar 21, 2021

• remove default val for filename

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• Merge branch 'axonarawio' of https://github.com/catalystneuro/python-neo into axonarawio

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Commits on Mar 22, 2021

• removed variable assignment that already has it as default val

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Commits on Mar 23, 2021

• rewrite desc

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• allow base filename, set and bin extensions as user input

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• made channel_memory_offset global variable

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• ensure chan_id is a str

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• ensure stream_id is a str

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• create class variable for channel_memory_offset (remapping of chan ids)

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• made ecephys data type instance variable

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• check code modifications

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• remove jupyter notebook

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• minor annotation adjustments

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• remove None from first index in channel_memory_offset

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• count channel ids from 0 upwards instead of 1

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Commits on Mar 24, 2021

• explicitly load set and bin file in test_axonaio.py

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Commits on Apr 9, 2021

• Steffen and Sam do some debug.

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• Merge pull request #1 from samuelgarcia/axonarawio

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• automatically get sampling rate from .set file

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• added additional annotations, including tetrode per channel

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• debugged new additions - tests pass

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• pep8 adherence in axonarawio

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• removed #eof

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• fix pep8 from pep8speaks complaints

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• final pep8 fixes

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