Axonarawio (#958)

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

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

* added first draft of sig_channels

* first draft - check if I can use AxonaRawIO

* some minor additions

* added axonarawio to neo.rawio.__init__.py

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

* first scaffolding for reading raw cont data

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

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

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

* implemented reading raw continous data with get_analogsignal_chunk

* added timing checks + looking for faster get_analogsignal_chunk

* trying hopefully faster implementation for get_analogsignal_chunk

* trying to test hopefully faster implementation of get_analogsignal_chunk

* fixed base index vector to read cont. data

* fixed selecting arbitrary chunk of cont data

* some minor changes

* some changes to adjust toward new baserawio

* found better implementation of reading cont signals

* implemented new method for reading cont data

* added check for reading cont data using axonarawio

* adjusted helper methods

* somewhat checking adjustments of helper methods

* started exploring unit data files

* linting or comment changes

* copied over updated annotatiosn from examplerawio.py where applicable

* adjusted get_channel_gain (still unverified if correct)

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

* added slightly more detailed notes about data formats

* added more thorough description of what data should be supported

* small clean-up of notebook

* filled in methods related to signal dur or len

* added test_axonarawio.py

* adjusted desc and filled spiking and event information with None

* added axonaio.py

* added test_axonaio.py

* changed files_to_download to only include base filename

* added axonaio to io.__init__

* check if AxonaIO works

* removed specific example tests for test_axonaio

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

* added notes and fixed equation for uV conversion

* checking conversion factor for getting uV

* Update neo/io/axonaio.py

remove default val for filename, bc filename has to be specified

Co-authored-by: Alessio Buccino <[email protected]>

* remove default val for filename

* removed variable assignment that already has it as default val

* rewrite desc

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

* made channel_memory_offset global variable

* ensure chan_id is a str

* ensure stream_id is a str

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

* made ecephys data type instance variable

* check code modifications

* remove jupyter notebook

* minor annotation adjustments

* remove None from first index in channel_memory_offset

* count channel ids from 0 upwards instead of 1

* explicitly load set and bin file in test_axonaio.py

* Steffen and Sam do some debug.

* automatically get sampling rate from .set file

* added additional annotations, including tetrode per channel

* debugged new additions - tests pass

* pep8 adherence in axonarawio

* removed #eof

* fix pep8 from pep8speaks complaints

* final pep8 fixes

Co-authored-by: Alessio Buccino <[email protected]>
Co-authored-by: Samuel Garcia <[email protected]>

Author: 3 people

doc/source/authors.rst

@@ -56,6 +56,7 @@ and may not be the current affiliation of a contributor.
 * Shashwat Sridhar
 * Alessio Buccino [23]
 * Regimantas Jurkus [13]
+* Steffen Buergers [24]
 
 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
@@ -80,6 +81,7 @@ and may not be the current affiliation of a contributor.
 21. Institut des Neurosciences Paris-Saclay, CNRS UMR 9197 - Université Paris-Sud, Gif-sur-Yvette, France
 22. Neurtex Brain Research Institute, Dallas, TX, USAs
 23. Bio Engineering Laboratory, DBSSE, ETH, Basel, Switzerland
+24. CatalystNeuro
 
 If we've somehow missed you off the list we're very sorry - please let us know.
 

neo/io/__init__.py

@@ -19,6 +19,7 @@
 * :attr:`AsciiSignalIO`
 * :attr:`AsciiSpikeTrainIO`
 * :attr:`AxographIO`
+* :attr:`AxonaIO`
 * :attr:`AxonIO`
 * :attr:`BCI2000IO`
 * :attr:`BlackrockIO`
@@ -77,6 +78,10 @@
 
     .. autoattribute:: extensions
 
+.. autoclass:: neo.io.AxonaIO
+
+    .. autoattribute:: extensions
+
 .. autoclass:: neo.io.AxonIO
 
     .. autoattribute:: extensions
@@ -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
@@ -295,6 +301,7 @@
     AsciiSignalIO,
     AsciiSpikeTrainIO,
     AxographIO,
+    AxonaIO,
     AxonIO,
     BCI2000IO,
     BlackrockIO,

neo/io/axonaio.py

@@ -0,0 +1,11 @@
+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)

neo/rawio/__init__.py

@@ -13,6 +13,7 @@
 Classes:
 
 * :attr:`AxographRawIO`
+* :attr:`AxonaRawIO`
 * :attr:`AxonRawIO`
 * :attr:`BlackrockRawIO`
 * :attr:`BrainVisionRawIO`
@@ -41,6 +42,10 @@
 
     .. autoattribute:: extensions
 
+.. autoclass:: neo.rawio.AxonaRawIO
+
+    .. autoattribute:: extensions
+
 .. autoclass:: neo.rawio.AxonRawIO
 
     .. autoattribute:: extensions
@@ -133,6 +138,7 @@
 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
@@ -159,6 +165,7 @@
 
 rawiolist = [
     AxographRawIO,
+    AxonaRawIO,
     AxonRawIO,
     BlackrockRawIO,
     BrainVisionRawIO,