diff --git a/neo/io/__init__.py b/neo/io/__init__.py index f72175eba..e3cdf3bcf 100644 --- a/neo/io/__init__.py +++ b/neo/io/__init__.py @@ -42,7 +42,7 @@ * :attr:`NeuroshareIO` * :attr:`NixIO` * :attr:`NSDFIO` -* :attr:`OpenEphysIO` +* :attr:`OldOpenEphysIO` * :attr:`PickleIO` * :attr:`PlexonIO` * :attr:`RawBinarySignalIO` @@ -171,7 +171,7 @@ .. autoattribute:: extensions -.. autoclass:: neo.io.OpenEphysIO +.. autoclass:: neo.io.OldOpenEphysIO .. autoattribute:: extensions @@ -267,7 +267,7 @@ from neo.io.nixio import NixIO from neo.io.nixio_fr import NixIO as NixIOFr from neo.io.nsdfio import NSDFIO -from neo.io.openephysio import OpenEphysIO +from neo.io.oldopenephysio import OldOpenEphysIO from neo.io.pickleio import PickleIO from neo.io.plexonio import PlexonIO from neo.io.rawbinarysignalio import RawBinarySignalIO @@ -310,7 +310,7 @@ NeuroScopeIO, NeuroshareIO, NSDFIO, - OpenEphysIO, + OldOpenEphysIO, PickleIO, PlexonIO, RawBinarySignalIO, diff --git a/neo/io/openephysio.py b/neo/io/oldopenephysio.py similarity index 69% rename from neo/io/openephysio.py rename to neo/io/oldopenephysio.py index 1c9333151..aceff1a58 100644 --- a/neo/io/openephysio.py +++ b/neo/io/oldopenephysio.py @@ -1,8 +1,8 @@ from neo.io.basefromrawio import BaseFromRaw -from neo.rawio.openephysrawio import OpenEphysRawIO +from neo.rawio.oldopenephysrawio import OldOpenEphysRawIO -class OpenEphysIO(OpenEphysRawIO, BaseFromRaw): +class OldOpenEphysIO(OldOpenEphysRawIO, BaseFromRaw): _prefered_signal_group_mode = 'group-by-same-units' mode = 'dir' diff --git a/neo/rawio/__init__.py b/neo/rawio/__init__.py index c9f29f85f..ba9ed3e0d 100644 --- a/neo/rawio/__init__.py +++ b/neo/rawio/__init__.py @@ -23,7 +23,7 @@ * :attr:`NeuroExplorerRawIO` * :attr:`NeuroScopeRawIO` * :attr:`NIXRawIO` -* :attr:`OpenEphysRawIO` +* :attr:`OldOpenEphysRawIO` * :attr:`PlexonRawIO` * :attr:`RawBinarySignalRawIO` * :attr:`RawMCSRawIO` @@ -77,7 +77,7 @@ .. autoattribute:: extensions -.. autoclass:: neo.rawio.OpenEphysRawIO +.. autoclass:: neo.rawio.OldOpenEphysRawIO .. autoattribute:: extensions @@ -124,7 +124,7 @@ from neo.rawio.neuroexplorerrawio import NeuroExplorerRawIO from neo.rawio.neuroscoperawio import NeuroScopeRawIO from neo.rawio.nixrawio import NIXRawIO -from neo.rawio.openephysrawio import OpenEphysRawIO +from neo.rawio.oldopenephysrawio import OldOpenEphysRawIO from neo.rawio.plexonrawio import PlexonRawIO from neo.rawio.rawbinarysignalrawio import RawBinarySignalRawIO from neo.rawio.rawmcsrawio import RawMCSRawIO @@ -145,7 +145,7 @@ NeuroExplorerRawIO, NeuroScopeRawIO, NIXRawIO, - OpenEphysRawIO, + OldOpenEphysRawIO, PlexonRawIO, RawBinarySignalRawIO, RawMCSRawIO, diff --git a/neo/rawio/openephysrawio.py b/neo/rawio/oldopenephysrawio.py similarity index 97% rename from neo/rawio/openephysrawio.py rename to neo/rawio/oldopenephysrawio.py index 930b6ec54..8c0c55399 100644 --- a/neo/rawio/openephysrawio.py +++ b/neo/rawio/oldopenephysrawio.py @@ -1,5 +1,9 @@ """ -This module implement OpenEphys format. +This module implement the "old" OpenEphys binary flat format. + +See +https://open-ephys.atlassian.net/wiki/spaces/OEW/pages/65667095/Flat+binary+format+old+version + Author: Samuel Garcia """ @@ -17,13 +21,17 @@ HEADER_SIZE = 1024 -class OpenEphysRawIO(BaseRawIO): +class OldOpenEphysRawIO(BaseRawIO): """ - OpenEphys GUI software offers several data formats, see - https://open-ephys.atlassian.net/wiki/spaces/OEW/pages/491632/Data+format - - This class implements the legacy OpenEphys format here - https://open-ephys.atlassian.net/wiki/spaces/OEW/pages/65667092/Open+Ephys+format + This module implement the "old" OpenEphys binary flat format. + + See + https://open-ephys.atlassian.net/wiki/spaces/OEW/pages/65667095/Flat+binary+format+old+version + + Since 2017 OpenEphys have a "new" binary flat format which is more efficient. + You should use it. + + This class is kept in neo to be able to read old datasets. The OpenEphys group already proposes some tools here: https://github.com/open-ephys/analysis-tools/blob/master/OpenEphys.py diff --git a/neo/test/iotest/test_openephysio.py b/neo/test/iotest/test_oldopenephysio.py similarity index 67% rename from neo/test/iotest/test_openephysio.py rename to neo/test/iotest/test_oldopenephysio.py index a73d6fb9d..c5fe68065 100644 --- a/neo/test/iotest/test_openephysio.py +++ b/neo/test/iotest/test_oldopenephysio.py @@ -6,19 +6,19 @@ import quantities as pq -from neo.io import OpenEphysIO +from neo.io import OldOpenEphysIO from neo.test.iotest.common_io_test import BaseTestIO -from neo.test.rawiotest.test_openephysrawio import TestOpenEphysRawIO +from neo.test.rawiotest.test_oldopenephysrawio import TestOldOpenEphysRawIO class TestOpenEphysIO(BaseTestIO, unittest.TestCase, ): - ioclass = OpenEphysIO + ioclass = OldOpenEphysIO files_to_test = ['OpenEphys_SampleData_1', # 'OpenEphys_SampleData_2_(multiple_starts)', # This not implemented this raise error # 'OpenEphys_SampleData_3', ] - files_to_download = TestOpenEphysRawIO.files_to_download + files_to_download = TestOldOpenEphysRawIO.files_to_download if __name__ == "__main__": diff --git a/neo/test/rawiotest/test_openephysrawio.py b/neo/test/rawiotest/test_oldopenephysrawio.py similarity index 95% rename from neo/test/rawiotest/test_openephysrawio.py rename to neo/test/rawiotest/test_oldopenephysrawio.py index 8553ea777..14a733585 100644 --- a/neo/test/rawiotest/test_openephysrawio.py +++ b/neo/test/rawiotest/test_oldopenephysrawio.py @@ -1,11 +1,11 @@ import unittest -from neo.rawio.openephysrawio import OpenEphysRawIO +from neo.rawio.oldopenephysrawio import OldOpenEphysRawIO from neo.test.rawiotest.common_rawio_test import BaseTestRawIO -class TestOpenEphysRawIO(BaseTestRawIO, unittest.TestCase, ): - rawioclass = OpenEphysRawIO +class TestOldOpenEphysRawIO(BaseTestRawIO, unittest.TestCase, ): + rawioclass = OldOpenEphysRawIO entities_to_test = ['OpenEphys_SampleData_1', # 'OpenEphys_SampleData_2_(multiple_starts)', # This not implemented this raise error # 'OpenEphys_SampleData_3',