From bed7a6ef0ad4691166e6642ede32b817d494c30c Mon Sep 17 00:00:00 2001 From: Ben Dichter Date: Wed, 7 Feb 2024 09:52:12 -0800 Subject: [PATCH 1/4] try new structure for conversion examples --- .../conversion_example_gallery.rst | 6 ++++-- docs/conversion_examples_gallery/recording/alphaomega.rst | 4 ++-- docs/conversion_examples_gallery/recording/axona.rst | 4 ++-- docs/index.rst | 2 +- 4 files changed, 9 insertions(+), 7 deletions(-) rename docs/{conversion_examples_gallery => }/conversion_example_gallery.rst (95%) diff --git a/docs/conversion_examples_gallery/conversion_example_gallery.rst b/docs/conversion_example_gallery.rst similarity index 95% rename from docs/conversion_examples_gallery/conversion_example_gallery.rst rename to docs/conversion_example_gallery.rst index b6dd7c658e..99f5aa15c7 100644 --- a/docs/conversion_examples_gallery/conversion_example_gallery.rst +++ b/docs/conversion_example_gallery.rst @@ -1,5 +1,6 @@ .. _conversion_gallery: + Conversion Gallery ================== @@ -12,11 +13,12 @@ Extracellular electrophysiology Recording ~~~~~~~~~ +.. include:: conversion_examples_gallery/recording/alphaomega.rst +.. include:: conversion_examples_gallery/recording/axona.rst + .. toctree:: :maxdepth: 1 - AlphaOmega - Axona Biocam Blackrock European Data Format (EDF) diff --git a/docs/conversion_examples_gallery/recording/alphaomega.rst b/docs/conversion_examples_gallery/recording/alphaomega.rst index f354963662..598faf1254 100644 --- a/docs/conversion_examples_gallery/recording/alphaomega.rst +++ b/docs/conversion_examples_gallery/recording/alphaomega.rst @@ -1,5 +1,5 @@ -AlphaOmega conversion ---------------------- +AlphaOmega +^^^^^^^^^^ Install NeuroConv with the additional dependencies necessary for reading AlphaOmega data. diff --git a/docs/conversion_examples_gallery/recording/axona.rst b/docs/conversion_examples_gallery/recording/axona.rst index 61b1ff5ff2..4445b26d7d 100644 --- a/docs/conversion_examples_gallery/recording/axona.rst +++ b/docs/conversion_examples_gallery/recording/axona.rst @@ -1,5 +1,5 @@ -Axona data conversion ---------------------- +Axona +^^^^^ Install NeuroConv with the additional dependencies necessary for reading Axona data. diff --git a/docs/index.rst b/docs/index.rst index 24027490c7..783f264e04 100644 --- a/docs/index.rst +++ b/docs/index.rst @@ -28,7 +28,7 @@ Features: :caption: Contents user_guide/user_guide - conversion_examples_gallery/conversion_example_gallery + conversion_example_gallery catalogue/catalogue developer_guide api From 89da6384a726299e5a19be32f258a90b8ed68bbf Mon Sep 17 00:00:00 2001 From: Ben Dichter Date: Wed, 7 Feb 2024 10:07:18 -0800 Subject: [PATCH 2/4] alter page nav for example conversions --- docs/conf.py | 5 +++++ docs/conversion_example_gallery.rst | 2 +- 2 files changed, 6 insertions(+), 1 deletion(-) diff --git a/docs/conf.py b/docs/conf.py index c241239a8c..b11805e23d 100644 --- a/docs/conf.py +++ b/docs/conf.py @@ -112,3 +112,8 @@ def setup(app): # This makes the data-interfaces signatures display on the docs "format-request-form": ("https://github.com/catalystneuro/neuroconv/issues/new?assignees=&labels=enhancement" "%2Cdata+interfaces&template=format_request.yml&title=%5BNew+Format%5D%3A+", "") } + +html_sidebars = { + "conversion_example_gallery": ["page-toc", "edit-this-page", "sourcelink"] +} + diff --git a/docs/conversion_example_gallery.rst b/docs/conversion_example_gallery.rst index 99f5aa15c7..2a800bbe87 100644 --- a/docs/conversion_example_gallery.rst +++ b/docs/conversion_example_gallery.rst @@ -1,5 +1,5 @@ .. _conversion_gallery: - +:html_theme.sidebar_secondary.remove: Conversion Gallery ================== From 65c75348451e0c2051f7148a1b630b9d1606e210 Mon Sep 17 00:00:00 2001 From: "pre-commit-ci[bot]" <66853113+pre-commit-ci[bot]@users.noreply.github.com> Date: Wed, 7 Feb 2024 18:08:53 +0000 Subject: [PATCH 3/4] [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci --- docs/conf.py | 1 - 1 file changed, 1 deletion(-) diff --git a/docs/conf.py b/docs/conf.py index b11805e23d..5235b797d2 100644 --- a/docs/conf.py +++ b/docs/conf.py @@ -116,4 +116,3 @@ def setup(app): # This makes the data-interfaces signatures display on the docs html_sidebars = { "conversion_example_gallery": ["page-toc", "edit-this-page", "sourcelink"] } - From e4accc683b07d1e93cab70b95177559cb07e28c2 Mon Sep 17 00:00:00 2001 From: Ben Dichter Date: Fri, 16 Feb 2024 14:17:20 +0000 Subject: [PATCH 4/4] fix call signatures that are broken --- docs/conversion_example_gallery.rst | 142 ++++++++---------- .../behavior/audio.rst | 4 +- .../behavior/deeplabcut.rst | 4 +- .../behavior/fictrac.rst | 4 +- .../behavior/lightningpose.rst | 4 +- .../behavior/neuralynx_nvt.rst | 4 +- .../behavior/sleap.rst | 4 +- .../behavior/video.rst | 6 +- .../imaging/brukertiff.rst | 4 +- .../imaging/hdf5imaging.rst | 4 +- .../imaging/micromanagertiff.rst | 4 +- .../imaging/miniscope.rst | 4 +- .../imaging/scanbox.rst | 4 +- .../imaging/scanimage.rst | 4 +- .../imaging/tiff.rst | 4 +- .../recording/abf.rst | 4 +- .../recording/biocam.rst | 4 +- .../recording/blackrock.rst | 5 +- .../recording/edf.rst | 4 +- .../recording/intan.rst | 5 +- .../recording/maxone.rst | 4 +- .../recording/mcsraw.rst | 4 +- .../recording/mearec.rst | 4 +- .../recording/neuralynx.rst | 4 +- .../recording/neuroscope.rst | 4 +- .../recording/openephys.rst | 4 +- .../recording/plexon.rst | 4 +- .../recording/spike2.rst | 4 +- .../recording/spikegadgets.rst | 4 +- .../recording/spikeglx.rst | 4 +- .../recording/tdt.rst | 4 +- .../segmentation/caiman.rst | 2 +- .../segmentation/cnmfe.rst | 2 +- .../segmentation/extract.rst | 2 +- .../segmentation/suite2p.rst | 2 +- .../sorting/blackrock.rst | 4 +- .../sorting/cellexplorer.rst | 4 +- .../sorting/kilosort.rst | 4 +- .../sorting/neuralynx.rst | 4 +- .../sorting/neuroscope.rst | 4 +- .../sorting/phy.rst | 4 +- .../sorting/plexon.rst | 4 +- docs/conversion_examples_gallery/text/csv.rst | 4 +- .../text/excel.rst | 6 +- 44 files changed, 146 insertions(+), 166 deletions(-) diff --git a/docs/conversion_example_gallery.rst b/docs/conversion_example_gallery.rst index 2a800bbe87..f8cff915ac 100644 --- a/docs/conversion_example_gallery.rst +++ b/docs/conversion_example_gallery.rst @@ -1,122 +1,104 @@ .. _conversion_gallery: :html_theme.sidebar_secondary.remove: +################## Conversion Gallery -================== +################## The examples here are guaranteed to be running correctly with our testing suite. Their aim is to be a showcase of the library capabilities and to get you to hit the ground running with your own conversion. +******************************* Extracellular electrophysiology -------------------------------- +******************************* Recording -~~~~~~~~~ +--------- .. include:: conversion_examples_gallery/recording/alphaomega.rst .. include:: conversion_examples_gallery/recording/axona.rst - -.. toctree:: - :maxdepth: 1 - - Biocam - Blackrock - European Data Format (EDF) - Intan - MaxOne - MCSRaw - MEArec - Neuralynx - NeuroScope - OpenEphys - Plexon - Spike2 - Spikegadgets - SpikeGLX - Tucker-Davis Technologies (TDT) +.. include:: conversion_examples_gallery/recording/biocam.rst +.. include:: conversion_examples_gallery/recording/blackrock.rst +.. include:: conversion_examples_gallery/recording/edf.rst +.. include:: conversion_examples_gallery/recording/intan.rst +.. include:: conversion_examples_gallery/recording/maxone.rst +.. include:: conversion_examples_gallery/recording/mcsraw.rst +.. include:: conversion_examples_gallery/recording/mearec.rst +.. include:: conversion_examples_gallery/recording/neuralynx.rst +.. include:: conversion_examples_gallery/recording/neuroscope.rst +.. include:: conversion_examples_gallery/recording/openephys.rst +.. include:: conversion_examples_gallery/recording/plexon.rst +.. include:: conversion_examples_gallery/recording/spike2.rst +.. include:: conversion_examples_gallery/recording/spikegadgets.rst +.. include:: conversion_examples_gallery/recording/spikeglx.rst +.. include:: conversion_examples_gallery/recording/tdt.rst Sorting -~~~~~~~ - -.. toctree:: - :maxdepth: 1 +------- - Blackrock - Cell Explorer - KiloSort - Neuralynx - NeuroScope - Phy - Plexon +.. include:: conversion_examples_gallery/sorting/blackrock.rst +.. include:: conversion_examples_gallery/sorting/cellexplorer.rst +.. include:: conversion_examples_gallery/sorting/kilosort.rst +.. include:: conversion_examples_gallery/sorting/neuralynx.rst +.. include:: conversion_examples_gallery/sorting/neuroscope.rst +.. include:: conversion_examples_gallery/sorting/phy.rst +.. include:: conversion_examples_gallery/sorting/plexon.rst +******************************* Intracellular electrophysiology -------------------------------- +******************************* -.. toctree:: - :maxdepth: 1 - - ABF +.. include:: conversion_examples_gallery/recording/abf.rst +****************** Optical physiology ------------------- +****************** Imaging -~~~~~~~ +------- -.. toctree:: - :maxdepth: 1 +.. include:: conversion_examples_gallery/imaging/brukertiff.rst +.. include:: conversion_examples_gallery/imaging/hdf5imaging.rst +.. include:: conversion_examples_gallery/imaging/micromanagertiff.rst +.. include:: conversion_examples_gallery/imaging/miniscope.rst +.. include:: conversion_examples_gallery/imaging/scanbox.rst +.. include:: conversion_examples_gallery/imaging/scanimage.rst +.. include:: conversion_examples_gallery/imaging/tiff.rst - Bruker - HDF5 - Micro-Manager - Miniscope - Scanbox - ScanImage - Tiff Segmentation -~~~~~~~~~~~~ - -.. toctree:: - :maxdepth: 1 +------------ - Caiman - CNMFE - EXTRACT - Suite2P +.. include:: conversion_examples_gallery/segmentation/caiman.rst +.. include:: conversion_examples_gallery/segmentation/cnmfe.rst +.. include:: conversion_examples_gallery/segmentation/extract.rst +.. include:: conversion_examples_gallery/segmentation/suite2p.rst +******** Behavior --------- - -.. toctree:: - :maxdepth: 1 - - Audio - DeepLabCut - FicTrac - LightningPose - SLEAP - Videos +******** +.. include:: conversion_examples_gallery/behavior/audio.rst +.. include:: conversion_examples_gallery/behavior/deeplabcut.rst +.. include:: conversion_examples_gallery/behavior/fictrac.rst +.. include:: conversion_examples_gallery/behavior/lightningpose.rst +.. include:: conversion_examples_gallery/behavior/sleap.rst +.. include:: conversion_examples_gallery/behavior/video.rst +.. include:: conversion_examples_gallery/behavior/neuralynx_nvt.rst Text ---- -.. toctree:: - :maxdepth: 1 - - CSV - Excel +.. include:: conversion_examples_gallery/text/csv.rst +.. include:: conversion_examples_gallery/text/excel.rst +***************************** Common interface combinations ------------------------------ - -.. toctree:: - :maxdepth: 1 +***************************** - combinations/spikeglx_and_phy - combinations/tiff_and_suite2p - combinations/ecephys_pose_estimation +.. include:: conversion_examples_gallery/combinations/spikeglx_and_phy.rst +.. include:: conversion_examples_gallery/combinations/tiff_and_suite2p.rst +.. include:: conversion_examples_gallery/combinations/ecephys_pose_estimation.rst .. note:: If you do not see the format you need, feel free to :format-request-form:`request it<>` or diff --git a/docs/conversion_examples_gallery/behavior/audio.rst b/docs/conversion_examples_gallery/behavior/audio.rst index 3ec1d3181a..7c835deefd 100644 --- a/docs/conversion_examples_gallery/behavior/audio.rst +++ b/docs/conversion_examples_gallery/behavior/audio.rst @@ -1,5 +1,5 @@ -Audio data conversion ---------------------- +Audio +----- Install NeuroConv with the additional dependencies necessary for reading audio data. diff --git a/docs/conversion_examples_gallery/behavior/deeplabcut.rst b/docs/conversion_examples_gallery/behavior/deeplabcut.rst index cad525be54..560f6258c4 100644 --- a/docs/conversion_examples_gallery/behavior/deeplabcut.rst +++ b/docs/conversion_examples_gallery/behavior/deeplabcut.rst @@ -1,5 +1,5 @@ -DeepLabCut data conversion --------------------------- +DeepLabCut +---------- Install NeuroConv with the additional dependencies necessary for reading DeepLabCut data. diff --git a/docs/conversion_examples_gallery/behavior/fictrac.rst b/docs/conversion_examples_gallery/behavior/fictrac.rst index 82a7c65802..23c7efd33f 100644 --- a/docs/conversion_examples_gallery/behavior/fictrac.rst +++ b/docs/conversion_examples_gallery/behavior/fictrac.rst @@ -1,5 +1,5 @@ -FicTrac data conversion --------------------------- +FicTrac +------- Install NeuroConv with the additional dependencies necessary for reading `FicTrac `_ data. diff --git a/docs/conversion_examples_gallery/behavior/lightningpose.rst b/docs/conversion_examples_gallery/behavior/lightningpose.rst index b8c1a66e3b..762d47ad31 100644 --- a/docs/conversion_examples_gallery/behavior/lightningpose.rst +++ b/docs/conversion_examples_gallery/behavior/lightningpose.rst @@ -1,5 +1,5 @@ -LightningPose data conversion --------------------------- +LightningPose +------------- Install NeuroConv with the additional dependencies necessary for reading LightningPose data. diff --git a/docs/conversion_examples_gallery/behavior/neuralynx_nvt.rst b/docs/conversion_examples_gallery/behavior/neuralynx_nvt.rst index b57f34672e..5a9ccc71ea 100644 --- a/docs/conversion_examples_gallery/behavior/neuralynx_nvt.rst +++ b/docs/conversion_examples_gallery/behavior/neuralynx_nvt.rst @@ -1,5 +1,5 @@ -Neuralynx NVT data conversion ------------------------------ +Neuralynx NVT +------------- Neuralynx NVT files contain information about position tracking. This interface requires no additional dependencies, so you can install NeuroConv using: diff --git a/docs/conversion_examples_gallery/behavior/sleap.rst b/docs/conversion_examples_gallery/behavior/sleap.rst index e9cd6d30cd..8904dc52f3 100644 --- a/docs/conversion_examples_gallery/behavior/sleap.rst +++ b/docs/conversion_examples_gallery/behavior/sleap.rst @@ -1,5 +1,5 @@ -SLEAP data conversion ---------------------- +SLEAP +----- Install NeuroConv with the additional dependencies necessary for reading SLEAP data. diff --git a/docs/conversion_examples_gallery/behavior/video.rst b/docs/conversion_examples_gallery/behavior/video.rst index f51c86183f..5f525e6ed9 100644 --- a/docs/conversion_examples_gallery/behavior/video.rst +++ b/docs/conversion_examples_gallery/behavior/video.rst @@ -1,5 +1,5 @@ -Video data conversion (multimedia formats) ------------------------------------------- +Video (multimedia formats) +-------------------------- Install NeuroConv with the additional dependencies necessary for reading multimedia data. @@ -7,7 +7,7 @@ Install NeuroConv with the additional dependencies necessary for reading multime pip install neuroconv[video] -This interface can handle conversions from avi, mov, mp4, wmv, flv and most FFmpeg_ supported formats to NWB using the +This interface can handle conversions from .avi, .mov, .mp4, .wmv, .flv and most FFmpeg_-supported formats to NWB using the :py:class:`~neuroconv.datainterfaces.behavior.video.videodatainterface.VideoInterface` class. .. _FFmpeg: https://ffmpeg.org/ diff --git a/docs/conversion_examples_gallery/imaging/brukertiff.rst b/docs/conversion_examples_gallery/imaging/brukertiff.rst index c8983dc9a7..05e97146f9 100644 --- a/docs/conversion_examples_gallery/imaging/brukertiff.rst +++ b/docs/conversion_examples_gallery/imaging/brukertiff.rst @@ -1,5 +1,5 @@ -Bruker TIFF data conversion ---------------------------- +Bruker TIFF +^^^^^^^^^^^ Install NeuroConv with the additional dependencies necessary for reading Bruker TIFF data. diff --git a/docs/conversion_examples_gallery/imaging/hdf5imaging.rst b/docs/conversion_examples_gallery/imaging/hdf5imaging.rst index 6332bb953f..f39e082201 100644 --- a/docs/conversion_examples_gallery/imaging/hdf5imaging.rst +++ b/docs/conversion_examples_gallery/imaging/hdf5imaging.rst @@ -1,5 +1,5 @@ -HDF5 data conversion --------------------- +HDF5 Imaging +^^^^^^^^^^^^ Install NeuroConv with the additional dependencies necessary for reading HDF5 data. diff --git a/docs/conversion_examples_gallery/imaging/micromanagertiff.rst b/docs/conversion_examples_gallery/imaging/micromanagertiff.rst index 1f71c7868f..3fd3efb423 100644 --- a/docs/conversion_examples_gallery/imaging/micromanagertiff.rst +++ b/docs/conversion_examples_gallery/imaging/micromanagertiff.rst @@ -1,5 +1,5 @@ -Micro-Manager TIFF data conversion ----------------------------------- +Micro-Manager TIFF +^^^^^^^^^^^^^^^^^^ Install NeuroConv with the additional dependencies necessary for reading Micro-Manager TIFF data. diff --git a/docs/conversion_examples_gallery/imaging/miniscope.rst b/docs/conversion_examples_gallery/imaging/miniscope.rst index 5e16ea793d..7376f96708 100644 --- a/docs/conversion_examples_gallery/imaging/miniscope.rst +++ b/docs/conversion_examples_gallery/imaging/miniscope.rst @@ -1,5 +1,5 @@ -Miniscope data conversion -------------------------- +Miniscope +^^^^^^^^^ Install NeuroConv with the additional dependencies necessary for reading Miniscope data. diff --git a/docs/conversion_examples_gallery/imaging/scanbox.rst b/docs/conversion_examples_gallery/imaging/scanbox.rst index 4e9211a174..a1e5e680a2 100644 --- a/docs/conversion_examples_gallery/imaging/scanbox.rst +++ b/docs/conversion_examples_gallery/imaging/scanbox.rst @@ -1,5 +1,5 @@ -Scanbox data conversion ------------------------ +Scanbox +^^^^^^^ Install NeuroConv with the additional dependencies necessary for reading Scanbox data. diff --git a/docs/conversion_examples_gallery/imaging/scanimage.rst b/docs/conversion_examples_gallery/imaging/scanimage.rst index d60a7826ea..41a15b16fd 100644 --- a/docs/conversion_examples_gallery/imaging/scanimage.rst +++ b/docs/conversion_examples_gallery/imaging/scanimage.rst @@ -1,5 +1,5 @@ -ScanImage data conversion -------------------------- +ScanImage +^^^^^^^^^ Install NeuroConv with the additional dependencies necessary for reading ScanImage data. diff --git a/docs/conversion_examples_gallery/imaging/tiff.rst b/docs/conversion_examples_gallery/imaging/tiff.rst index f6e88bd6ed..c98f44c005 100644 --- a/docs/conversion_examples_gallery/imaging/tiff.rst +++ b/docs/conversion_examples_gallery/imaging/tiff.rst @@ -1,5 +1,5 @@ -TIFF data conversion --------------------- +TIFF +^^^^ Install NeuroConv with the additional dependencies necessary for reading TIFF data. diff --git a/docs/conversion_examples_gallery/recording/abf.rst b/docs/conversion_examples_gallery/recording/abf.rst index 1ef4967ac8..25faceb9df 100644 --- a/docs/conversion_examples_gallery/recording/abf.rst +++ b/docs/conversion_examples_gallery/recording/abf.rst @@ -1,5 +1,5 @@ -ABF data conversion -------------------- +ABF +--- Install NeuroConv with the additional dependencies necessary for reading ABF data. diff --git a/docs/conversion_examples_gallery/recording/biocam.rst b/docs/conversion_examples_gallery/recording/biocam.rst index 1cfa78d078..9cbfc8b18e 100644 --- a/docs/conversion_examples_gallery/recording/biocam.rst +++ b/docs/conversion_examples_gallery/recording/biocam.rst @@ -1,5 +1,5 @@ -Biocam conversion ------------------ +Biocam +^^^^^^ Install NeuroConv with the additional dependencies necessary for reading Biocam data. diff --git a/docs/conversion_examples_gallery/recording/blackrock.rst b/docs/conversion_examples_gallery/recording/blackrock.rst index 281561d1dc..d2d08c3ba2 100644 --- a/docs/conversion_examples_gallery/recording/blackrock.rst +++ b/docs/conversion_examples_gallery/recording/blackrock.rst @@ -1,6 +1,5 @@ -Blackrock data conversion -------------------------- - +Blackrock recording +^^^^^^^^^^^^^^^^^^^ Install NeuroConv with the additional dependencies necessary for reading Blackrock data. .. code-block:: bash diff --git a/docs/conversion_examples_gallery/recording/edf.rst b/docs/conversion_examples_gallery/recording/edf.rst index eb6b8da74a..e237f1ee47 100644 --- a/docs/conversion_examples_gallery/recording/edf.rst +++ b/docs/conversion_examples_gallery/recording/edf.rst @@ -1,5 +1,5 @@ -European Data Format (EDF) conversion -------------------------------------- +European Data Format (EDF) +^^^^^^^^^^^^^^^^^^^^^^^^^^ Install NeuroConv with the additional dependencies necessary for reading EDF data. diff --git a/docs/conversion_examples_gallery/recording/intan.rst b/docs/conversion_examples_gallery/recording/intan.rst index 356be532b4..bd659dcf38 100644 --- a/docs/conversion_examples_gallery/recording/intan.rst +++ b/docs/conversion_examples_gallery/recording/intan.rst @@ -1,6 +1,5 @@ -Intan data conversion ---------------------- - +Intan +^^^^^ Install NeuroConv with the additional dependencies necessary for reading Intan data. .. code-block:: bash diff --git a/docs/conversion_examples_gallery/recording/maxone.rst b/docs/conversion_examples_gallery/recording/maxone.rst index ea6221feb4..1bc4acd381 100644 --- a/docs/conversion_examples_gallery/recording/maxone.rst +++ b/docs/conversion_examples_gallery/recording/maxone.rst @@ -1,5 +1,5 @@ -MaxOne conversion ------------------ +MaxOne +^^^^^^ Install NeuroConv with the additional dependencies necessary for reading MaxOne data. diff --git a/docs/conversion_examples_gallery/recording/mcsraw.rst b/docs/conversion_examples_gallery/recording/mcsraw.rst index 2d454c593d..adc9add2fe 100644 --- a/docs/conversion_examples_gallery/recording/mcsraw.rst +++ b/docs/conversion_examples_gallery/recording/mcsraw.rst @@ -1,5 +1,5 @@ -MCSRaw conversion ------------------ +MCSRaw +^^^^^^ Install NeuroConv with the additional dependencies necessary for reading MCSRaw data. diff --git a/docs/conversion_examples_gallery/recording/mearec.rst b/docs/conversion_examples_gallery/recording/mearec.rst index 4a3a881eb5..2e93a32f3a 100644 --- a/docs/conversion_examples_gallery/recording/mearec.rst +++ b/docs/conversion_examples_gallery/recording/mearec.rst @@ -1,5 +1,5 @@ -MEArec conversion ------------------ +MEArec +^^^^^^ Install NeuroConv with the additional dependencies necessary for reading MEArec data. diff --git a/docs/conversion_examples_gallery/recording/neuralynx.rst b/docs/conversion_examples_gallery/recording/neuralynx.rst index 7d5bf2856f..c689c70ec1 100644 --- a/docs/conversion_examples_gallery/recording/neuralynx.rst +++ b/docs/conversion_examples_gallery/recording/neuralynx.rst @@ -1,5 +1,5 @@ -Neuralynx data conversion -------------------------- +Neuralynx +^^^^^^^^^ Install NeuroConv with the additional dependencies necessary for reading Neuralynx data. diff --git a/docs/conversion_examples_gallery/recording/neuroscope.rst b/docs/conversion_examples_gallery/recording/neuroscope.rst index 9ecc8e62ab..58c2bc7385 100644 --- a/docs/conversion_examples_gallery/recording/neuroscope.rst +++ b/docs/conversion_examples_gallery/recording/neuroscope.rst @@ -1,5 +1,5 @@ -NeuroScope data conversion --------------------------- +NeuroScope +^^^^^^^^^^ Install NeuroConv with the additional dependencies necessary for reading NeuroScope data. diff --git a/docs/conversion_examples_gallery/recording/openephys.rst b/docs/conversion_examples_gallery/recording/openephys.rst index f318734453..ec5a4a3f0c 100644 --- a/docs/conversion_examples_gallery/recording/openephys.rst +++ b/docs/conversion_examples_gallery/recording/openephys.rst @@ -1,5 +1,5 @@ -OpenEphys data conversion -------------------------- +OpenEphys +^^^^^^^^^ Install NeuroConv with the additional dependencies necessary for reading OpenEphys data. diff --git a/docs/conversion_examples_gallery/recording/plexon.rst b/docs/conversion_examples_gallery/recording/plexon.rst index 5a73bb978a..b8e6fac9c5 100644 --- a/docs/conversion_examples_gallery/recording/plexon.rst +++ b/docs/conversion_examples_gallery/recording/plexon.rst @@ -1,5 +1,5 @@ -Plexon Recording Conversion ---------------------------- +Plexon +^^^^^^ Install NeuroConv with the additional dependencies necessary for reading Plexon acquisition data. diff --git a/docs/conversion_examples_gallery/recording/spike2.rst b/docs/conversion_examples_gallery/recording/spike2.rst index 93990a959e..e12cbebba6 100644 --- a/docs/conversion_examples_gallery/recording/spike2.rst +++ b/docs/conversion_examples_gallery/recording/spike2.rst @@ -1,5 +1,5 @@ -Spike2 data conversion ----------------------- +Spike2 +^^^^^^ Install NeuroConv with the additional dependencies necessary for reading Spike2 data by CED. diff --git a/docs/conversion_examples_gallery/recording/spikegadgets.rst b/docs/conversion_examples_gallery/recording/spikegadgets.rst index a5302b8833..2b59889ac9 100644 --- a/docs/conversion_examples_gallery/recording/spikegadgets.rst +++ b/docs/conversion_examples_gallery/recording/spikegadgets.rst @@ -1,5 +1,5 @@ -Spikegadgets data conversion ----------------------------- +Spikegadgets +^^^^^^^^^^^^ Install NeuroConv with the additional dependencies necessary for reading Spikegadgets data. diff --git a/docs/conversion_examples_gallery/recording/spikeglx.rst b/docs/conversion_examples_gallery/recording/spikeglx.rst index 9bb0515604..18564c3f58 100644 --- a/docs/conversion_examples_gallery/recording/spikeglx.rst +++ b/docs/conversion_examples_gallery/recording/spikeglx.rst @@ -1,5 +1,5 @@ -SpikeGLX data conversion ------------------------- +SpikeGLX +^^^^^^^^ Install NeuroConv with the additional dependencies necessary for reading SpikeGLX data. diff --git a/docs/conversion_examples_gallery/recording/tdt.rst b/docs/conversion_examples_gallery/recording/tdt.rst index 9de1292938..49ce82106c 100644 --- a/docs/conversion_examples_gallery/recording/tdt.rst +++ b/docs/conversion_examples_gallery/recording/tdt.rst @@ -1,5 +1,5 @@ -Tucker-Davis Technologies (TDT) data conversion ------------------------------------------------ +Tucker-Davis Technologies (TDT) +^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ Install NeuroConv with the additional dependencies necessary for reading TDT data. diff --git a/docs/conversion_examples_gallery/segmentation/caiman.rst b/docs/conversion_examples_gallery/segmentation/caiman.rst index 495506fd88..46df0d3189 100644 --- a/docs/conversion_examples_gallery/segmentation/caiman.rst +++ b/docs/conversion_examples_gallery/segmentation/caiman.rst @@ -1,5 +1,5 @@ CaImAn ------- +^^^^^^ Install NeuroConv with the additional dependencies necessary for reading CaImAn data. diff --git a/docs/conversion_examples_gallery/segmentation/cnmfe.rst b/docs/conversion_examples_gallery/segmentation/cnmfe.rst index 1a74bd2508..dde57adc03 100644 --- a/docs/conversion_examples_gallery/segmentation/cnmfe.rst +++ b/docs/conversion_examples_gallery/segmentation/cnmfe.rst @@ -1,5 +1,5 @@ CNMFE ------ +^^^^^ Install NeuroConv with the additional dependencies necessary for reading CNMF-E data. diff --git a/docs/conversion_examples_gallery/segmentation/extract.rst b/docs/conversion_examples_gallery/segmentation/extract.rst index 3d80207840..35236ef7d9 100644 --- a/docs/conversion_examples_gallery/segmentation/extract.rst +++ b/docs/conversion_examples_gallery/segmentation/extract.rst @@ -1,5 +1,5 @@ EXTRACT -------- +^^^^^^^ Install NeuroConv with the additional dependencies necessary for reading EXTRACT data. diff --git a/docs/conversion_examples_gallery/segmentation/suite2p.rst b/docs/conversion_examples_gallery/segmentation/suite2p.rst index 619f04a0b0..11b8fa9302 100644 --- a/docs/conversion_examples_gallery/segmentation/suite2p.rst +++ b/docs/conversion_examples_gallery/segmentation/suite2p.rst @@ -1,5 +1,5 @@ suite2p -------- +^^^^^^^ Install NeuroConv with the additional dependencies necessary for reading suite2p data. diff --git a/docs/conversion_examples_gallery/sorting/blackrock.rst b/docs/conversion_examples_gallery/sorting/blackrock.rst index ddd8a1bfd7..03a2a116fa 100644 --- a/docs/conversion_examples_gallery/sorting/blackrock.rst +++ b/docs/conversion_examples_gallery/sorting/blackrock.rst @@ -1,5 +1,5 @@ -Blackrock sorting data conversion ---------------------------------- +Blackrock sorting +^^^^^^^^^^^^^^^^^ Install NeuroConv with the additional dependencies necessary for reading Blackrock sorting data. diff --git a/docs/conversion_examples_gallery/sorting/cellexplorer.rst b/docs/conversion_examples_gallery/sorting/cellexplorer.rst index 62d298d12f..1f46e289a8 100644 --- a/docs/conversion_examples_gallery/sorting/cellexplorer.rst +++ b/docs/conversion_examples_gallery/sorting/cellexplorer.rst @@ -1,5 +1,5 @@ -CellExplorer data conversion ------------------------------ +CellExplorer +^^^^^^^^^^^^ Install NeuroConv with the additional dependencies necessary for reading CellExplorer data. diff --git a/docs/conversion_examples_gallery/sorting/kilosort.rst b/docs/conversion_examples_gallery/sorting/kilosort.rst index fb3e3e42c9..49e9f81750 100644 --- a/docs/conversion_examples_gallery/sorting/kilosort.rst +++ b/docs/conversion_examples_gallery/sorting/kilosort.rst @@ -1,5 +1,5 @@ -KiloSort data conversion ------------------------- +KiloSort +^^^^^^^^ Install NeuroConv with the additional dependencies necessary for reading kilosort data. diff --git a/docs/conversion_examples_gallery/sorting/neuralynx.rst b/docs/conversion_examples_gallery/sorting/neuralynx.rst index 1c537ba82b..ba7dfad1db 100644 --- a/docs/conversion_examples_gallery/sorting/neuralynx.rst +++ b/docs/conversion_examples_gallery/sorting/neuralynx.rst @@ -1,5 +1,5 @@ -Neuralynx data conversion -------------------------- +Neuralynx sorting +^^^^^^^^^^^^^^^^^ Install NeuroConv with the additional dependencies necessary for reading neuralynx data. diff --git a/docs/conversion_examples_gallery/sorting/neuroscope.rst b/docs/conversion_examples_gallery/sorting/neuroscope.rst index e001f99449..7f42643148 100644 --- a/docs/conversion_examples_gallery/sorting/neuroscope.rst +++ b/docs/conversion_examples_gallery/sorting/neuroscope.rst @@ -1,5 +1,5 @@ -NeuroScope sorting data conversion ----------------------------------- +NeuroScope sorting +^^^^^^^^^^^^^^^^^^ Install NeuroConv with the additional dependencies necessary for reading neuroscope data. diff --git a/docs/conversion_examples_gallery/sorting/phy.rst b/docs/conversion_examples_gallery/sorting/phy.rst index b5dcbac192..56aaae8394 100644 --- a/docs/conversion_examples_gallery/sorting/phy.rst +++ b/docs/conversion_examples_gallery/sorting/phy.rst @@ -1,5 +1,5 @@ -Phy sorting data conversion ---------------------------- +Phy sorting +^^^^^^^^^^^ Install NeuroConv with the additional dependencies necessary for reading Phy data. diff --git a/docs/conversion_examples_gallery/sorting/plexon.rst b/docs/conversion_examples_gallery/sorting/plexon.rst index ec7db83066..209d271af5 100644 --- a/docs/conversion_examples_gallery/sorting/plexon.rst +++ b/docs/conversion_examples_gallery/sorting/plexon.rst @@ -1,5 +1,5 @@ -Plexon sorting data conversion ------------------------------- +Plexon sorting +^^^^^^^^^^^^^^ Install NeuroConv with the additional dependencies necessary for reading Plexon data. diff --git a/docs/conversion_examples_gallery/text/csv.rst b/docs/conversion_examples_gallery/text/csv.rst index 16853848dc..a8840240bd 100644 --- a/docs/conversion_examples_gallery/text/csv.rst +++ b/docs/conversion_examples_gallery/text/csv.rst @@ -1,5 +1,5 @@ -Comma-Separated Values (CSV) files ----------------------------------- +Comma-Separated Values (CSV) +---------------------------- Install NeuroConv. No extra dependencies are necessary for reading CSV. diff --git a/docs/conversion_examples_gallery/text/excel.rst b/docs/conversion_examples_gallery/text/excel.rst index bb0d4a0488..7eb9e093a7 100644 --- a/docs/conversion_examples_gallery/text/excel.rst +++ b/docs/conversion_examples_gallery/text/excel.rst @@ -1,5 +1,5 @@ -Excel data conversion ---------------------- +Excel +----- Install NeuroConv with the additional dependencies necessary for reading Excel data. @@ -7,7 +7,7 @@ Install NeuroConv with the additional dependencies necessary for reading Excel d pip install neuroconv[excel] -Convert Excel data to NWB using +Convert Excel files (.xls, .xlsx) to NWB using :py:class:`~neuroconv.datainterfaces.text.excel.exceltimeintervalsinterface.ExcelTimeIntervalsInterface`. The Excel file must contain a header row that contains at least the column names "start_time" and "stop_time".