Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Add NWBIO #796

Merged
merged 90 commits into from
Jul 22, 2021
Merged
Show file tree
Hide file tree
Changes from all commits
Commits
Show all changes
90 commits
Select commit Hold shift + click to select a range
01d333a
Synchronisation avec le projet original
msenoville Oct 31, 2017
54aa47f
test nwb
legouee Mar 13, 2019
bcfe5c6
Add NWB class
legouee Mar 13, 2019
dc3518e
NWB Files names
legouee Mar 13, 2019
412af76
nwbrawio file
legouee Mar 13, 2019
01faf3b
remove form to adding hdmf with version pynwb=1.0.0 to pynwb=1.0.1
legouee Mar 19, 2019
1f3e220
NWB support updates
legouee Jul 1, 2019
b42a92d
nwbio files
legouee Jul 12, 2019
73931e8
Read NWB files and tests
legouee Jul 18, 2019
752f9d1
update
msenoville Sep 5, 2019
7402e99
Updates
legouee Sep 6, 2019
3298018
after recent modification
legouee Sep 18, 2019
9c10d7f
Segment and AnalogSignals
legouee Sep 19, 2019
c13213c
Without print
legouee Sep 26, 2019
2242cbd
Writing part
legouee Oct 2, 2019
6c93c16
Writing part
legouee Oct 14, 2019
d2d9509
commit before switching to another branch
legouee Oct 24, 2019
032c986
commit for unuseful files...
legouee Oct 24, 2019
896e6ba
neo udpates...
legouee Oct 24, 2019
3f5ae4d
Support reading and writing a .nwb file
legouee Oct 31, 2019
205a298
Several blocks and segments
legouee Nov 22, 2019
d90ec09
minor modif
legouee Nov 22, 2019
1e5d449
NWB files with several blocks
legouee Nov 29, 2019
5fbde3e
Modifications segments
legouee Dec 2, 2019
c7b3448
Merge branch 'NWB_updated' of https://github.com/legouee/python-neo i…
msenoville Dec 10, 2019
34daf70
save modifs
msenoville Dec 10, 2019
2d8540f
improvement of of reading of multiple blocks
msenoville Dec 11, 2019
0435541
Commit before pull
legouee Dec 11, 2019
f98ba35
trying to merge
legouee Dec 11, 2019
047dedd
Several blocks
legouee Dec 11, 2019
3dbb381
Writing function
legouee Dec 12, 2019
c4bd09f
writing part
legouee Dec 13, 2019
39fc11d
Improvements writing several blocks - wip
legouee Dec 18, 2019
78a026c
Neo SpikeTrain Epoch
legouee Jan 27, 2020
68f3d63
Calcium imaging data
legouee Feb 17, 2020
244282b
Calcium imaging data test
legouee Feb 21, 2020
f1fb32e
NWB
legouee Feb 28, 2020
6750534
fix 'rescale' method for Event and Epoch
apdavison Mar 4, 2020
1583966
wip
apdavison Mar 4, 2020
5d2b090
Store Neo Epochs in epochs group, Spiketrains in units group.
apdavison Mar 5, 2020
d742b64
Store global annotations appropriately, handle "stimulus" group
apdavison Mar 5, 2020
b886965
temporarily remove incomplete calcium image data handling code, so as…
apdavison Mar 5, 2020
47d56ec
Remove unused imports
apdavison Mar 5, 2020
f7dcd82
group read and write methods (and rename "_handle_X" to "_read_X" for…
apdavison Mar 5, 2020
0c2d336
wip lazy loading
apdavison Mar 5, 2020
a196868
implement lazy loading
apdavison Mar 6, 2020
f970de9
Merge branch 'master' into nwb2
apdavison Mar 6, 2020
785e3b2
fix NWB tests to download data files, so they should work on CI system
apdavison Mar 6, 2020
1ab49c7
delete some old files
apdavison Mar 6, 2020
b10d69c
Add pynwb to testing requirements
apdavison Mar 6, 2020
d7344ce
More test fixes
apdavison Mar 6, 2020
cb13915
Python 2.7 fix
apdavison Mar 6, 2020
85b6c57
PyNWB doesn't support Python 2.7
apdavison Mar 6, 2020
e090b42
Revert some unintentional changes
apdavison Mar 6, 2020
7c581f5
fix some pep8 warnings
apdavison Mar 6, 2020
45a7c68
Added NWBIO example
apdavison Mar 6, 2020
bbcda25
NWBIO: be more careful with file modes
apdavison Aug 31, 2020
e4d36b3
[NWBIO] better handling of dict-valued annotations
apdavison Aug 31, 2020
112828d
[NWBIO] Start adding support for writing to NWB groups other than "ac…
apdavison Aug 31, 2020
b14952b
[nwbio] handle subclasses of TimeSeries
apdavison Sep 28, 2020
3d5cf26
load now handles slices of irregularly sampled data
bendichter Dec 6, 2020
7bad76a
Merge pull request #5 from bendichter/nwb_fix
apdavison Dec 6, 2020
71eb24e
Merge branch 'master' into nwb2
apdavison Dec 6, 2020
7755125
Merge branch 'master' into nwb2
apdavison Feb 3, 2021
e123ee0
handle unexpected units, such as "n/a" !
apdavison Feb 3, 2021
9136df9
fix shape of AnalogSignalProxy in NWBIO
apdavison Feb 3, 2021
3bab725
Be more forgiving of weird lines when loading ascii files
apdavison Feb 3, 2021
c017c70
Merge branch 'master' into nwb2
apdavison Apr 19, 2021
89dc0d7
replace annotation "nwb_type" with "nwb_neurodata_type" to more close…
apdavison Jun 28, 2021
a69c4cb
update links in NWBIO docstring
apdavison Jun 28, 2021
c87fcd8
fix recently appeared bug (due to changes in h5py?) where boolean ind…
apdavison Jun 28, 2021
2961059
Make "session_start_time" a required block annotation for NWB
apdavison Jun 28, 2021
f5d0d6f
Add a "block_index" argument to `NWBIO.read_block()`
apdavison Jun 28, 2021
a5befa7
Validate NWB files after writing them
apdavison Jun 28, 2021
0bfe1a7
Merge branch 'master' into nwb2
apdavison Jun 29, 2021
3e89a13
remove deprecated ChannelIndex and Unit from NWBIO
apdavison Jun 29, 2021
0c74e2a
partially integrated NWB testing into common framework
apdavison Jun 29, 2021
084967d
Removed example NWB notebook following discussion in #796
apdavison Jun 29, 2021
ac26693
Apply suggestions from code review
apdavison Jul 8, 2021
5b73c97
PR suggestions
legouee Jul 8, 2021
73582d1
Apply suggestions from code review
legouee Jul 8, 2021
eabe094
Merge pull request #7 from legouee/PR-correct
apdavison Jul 8, 2021
0e27757
handle differences in float precision when obtaining unit prefixes
apdavison Jul 9, 2021
2cca447
Switch testing of NWB to use BaseTestIO
apdavison Jul 9, 2021
f4e6e2b
pep8 reformatting
JuliaSprenger Jul 22, 2021
c5a8983
more pep8 reformatting
JuliaSprenger Jul 22, 2021
0f61b0b
[nwbio] guess fix for typo
JuliaSprenger Jul 22, 2021
4b25e7c
[nwbio] add missing docstrings
JuliaSprenger Jul 22, 2021
b968ab8
[nwbio] more pep8
JuliaSprenger Jul 22, 2021
16e9f7d
[nwbio] remove unused import
JuliaSprenger Jul 22, 2021
File filter

Filter by extension

Filter by extension


Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
7 changes: 7 additions & 0 deletions neo/io/__init__.py
Original file line number Diff line number Diff line change
Expand Up @@ -44,6 +44,7 @@
* :attr:`NeuroScopeIO`
* :attr:`NeuroshareIO`
* :attr:`NixIO`
* :attr:`NWBIO`
* :attr:`OpenEphysIO`
* :attr:`OpenEphysBinaryIO`
* :attr:`PhyIO`
Expand Down Expand Up @@ -184,6 +185,10 @@

.. autoattribute:: extensions

.. autoclass:: neo.io.NWBIO

.. autoattribute:: extensions

.. autoclass:: neo.io.OpenEphysIO

.. autoattribute:: extensions
Expand Down Expand Up @@ -292,6 +297,7 @@
from neo.io.neuroscopeio import NeuroScopeIO
from neo.io.nixio import NixIO
from neo.io.nixio_fr import NixIO as NixIOFr
from neo.io.nwbio import NWBIO
from neo.io.openephysio import OpenEphysIO
from neo.io.openephysbinaryio import OpenEphysBinaryIO
from neo.io.phyio import PhyIO
Expand Down Expand Up @@ -340,6 +346,7 @@
NeuroExplorerIO,
NeuroScopeIO,
NeuroshareIO,
NWBIO,
OpenEphysIO,
OpenEphysBinaryIO,
PhyIO,
Expand Down
3 changes: 2 additions & 1 deletion neo/io/asciisignalio.py
Original file line number Diff line number Diff line change
Expand Up @@ -195,7 +195,8 @@ def read_segment(self, lazy=False):
delimiter=self.delimiter,
usecols=self.usecols,
skip_header=self.skiprows,
dtype='f')
dtype='f',
invalid_raise=False)
if len(sig.shape) == 1:
sig = sig[:, np.newaxis]
elif self.method == 'csv':
Expand Down
Loading