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208 changes: 123 additions & 85 deletions README.rst
Original file line number Diff line number Diff line change
@@ -1,110 +1,148 @@
.. -*- rest -*-
.. vim:syntax=rst

.. image:: https://codecov.io/gh/nipy/nibabel/branch/master/graph/badge.svg
:target: https://codecov.io/gh/nipy/nibabel
.. Following contents should be copied from LONG_DESCRIPTION in NiBabel/info.py

.. image:: https://zenodo.org/badge/DOI/10.5281/zenodo.591597.svg
:target: https://doi.org/10.5281/zenodo.591597
.. image:: doc/pics/logo.png
:target: https://nipy.org/nibabel
:alt: NiBabel logo

.. image:: https://repology.org/badge/version-for-repo/aur/python:nibabel.svg?header=Arch%20%28%41%55%52%29
:target: https://repology.org/project/python:nibabel/versions
:alt: Arch (AUR)
Read and write access to common neuroimaging file formats, including: ANALYZE_ (plain, SPM99, SPM2 and later),
GIFTI_, NIfTI1_, NIfTI2_, `CIFTI-2`_, MINC1_, MINC2_, `AFNI BRIK/HEAD`_, ECAT_ and Philips PAR/REC
In addition, NiBabel also supports FreeSurfer_'s MGH_, geometry, annotation and morphometry files,
and provides some limited support for DICOM_.

.. image:: https://repology.org/badge/version-for-repo/debian_unstable/nibabel.svg?header=Debian%20Unstable
:target: https://repology.org/project/nibabel/versions
:alt: Debian Unstable package
NiBabel's API gives full or selective access to header information (metadata), and image
data is made available via NumPy arrays. For more information, see NiBabel's `documentation site`_
and `API reference`_.

.. image:: https://repology.org/badge/version-for-repo/gentoo_ovl_science/nibabel.svg?header=Gentoo%20%28%3A%3Ascience%29
:target: https://repology.org/project/nibabel/versions
:alt: Gentoo (::science)

.. image:: https://repology.org/badge/version-for-repo/nix_unstable/python:nibabel.svg?header=nixpkgs%20unstable
:target: https://repology.org/project/python:nibabel/versions
:alt: nixpkgs unstable

.. Following contents should be from LONG_DESCRIPTION in nibabel/info.py


=======
NiBabel
=======

Read / write access to some common neuroimaging file formats

This package provides read +/- write access to some common medical and
neuroimaging file formats, including: ANALYZE_ (plain, SPM99, SPM2 and later),
GIFTI_, NIfTI1_, NIfTI2_, `CIFTI-2`_, MINC1_, MINC2_, `AFNI BRIK/HEAD`_, MGH_ and
ECAT_ as well as Philips PAR/REC. We can read and write FreeSurfer_ geometry,
annotation and morphometry files. There is some very limited support for
DICOM_. NiBabel is the successor of PyNIfTI_.

.. _ANALYZE: http://www.grahamwideman.com/gw/brain/analyze/formatdoc.htm
.. _API reference: https://nipy.org/nibabel/api.html
.. _AFNI BRIK/HEAD: https://afni.nimh.nih.gov/pub/dist/src/README.attributes
.. _NIfTI1: http://nifti.nimh.nih.gov/nifti-1/
.. _NIfTI2: http://nifti.nimh.nih.gov/nifti-2/
.. _ANALYZE: http://www.grahamwideman.com/gw/brain/analyze/formatdoc.htm
.. _CIFTI-2: https://www.nitrc.org/projects/cifti/
.. _DICOM: http://medical.nema.org/
.. _documentation site: http://nipy.org/NiBabel
.. _ECAT: http://xmedcon.sourceforge.net/Docs/Ecat
.. _Freesurfer: https://surfer.nmr.mgh.harvard.edu
.. _GIFTI: https://www.nitrc.org/projects/gifti
.. _MGH: https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/MghFormat
.. _MINC1:
https://en.wikibooks.org/wiki/MINC/Reference/MINC1_File_Format_Reference
.. _MINC2:
https://en.wikibooks.org/wiki/MINC/Reference/MINC2.0_File_Format_Reference
.. _PyNIfTI: http://niftilib.sourceforge.net/pynifti/
.. _GIFTI: https://www.nitrc.org/projects/gifti
.. _MGH: https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/MghFormat
.. _ECAT: http://xmedcon.sourceforge.net/Docs/Ecat
.. _Freesurfer: https://surfer.nmr.mgh.harvard.edu
.. _DICOM: http://medical.nema.org/

The various image format classes give full or selective access to header
(meta) information and access to the image data is made available via NumPy
arrays.

Website
=======

Current documentation on nibabel can always be found at the `NIPY nibabel
website <http://nipy.org/nibabel>`_.
.. _NIfTI1: http://nifti.nimh.nih.gov/nifti-1/
.. _NIfTI2: http://nifti.nimh.nih.gov/nifti-2/

Mailing Lists
=============
.. list-table::
:widths: 20 80
:header-rows: 0

* - Code
-
.. image:: https://img.shields.io/badge/code%20style-black-000000.svg
:target: https://github.com/psf/black
:alt: code style: black
.. image:: https://img.shields.io/badge/%20imports-isort-%231674b1?style=flat&labelColor=ef8336
:target: https://pycqa.github.io/isort/
:alt: imports: isort
.. image:: https://img.shields.io/badge/pre--commit-enabled-brightgreen?logo=pre-commit&logoColor=white
:target: https://github.com/pre-commit/pre-commit
:alt: pre-commit
.. image:: https://codecov.io/gh/nipy/NiBabel/branch/master/graph/badge.svg
:target: https://codecov.io/gh/nipy/NiBabel
:alt: codecov badge
.. image:: https://img.shields.io/librariesio/github/nipy/NiBabel
:target: https://libraries.io/github/nipy/NiBabel
:alt: Libraries.io dependency status for GitHub repo

* - Status
-
.. image:: https://github.com/nipy/NiBabel/actions/workflows/stable.yml/badge.svg
:target: https://github.com/nipy/NiBabel/actions/workflows/stable.yml
:alt: stable tests
.. image:: https://github.com/nipy/NiBabel/actions/workflows/pages/pages-build-deployment/badge.svg
:target: https://github.com/nipy/NiBabel/actions/workflows/pages/pages-build-deployment
:alt: documentation build

* - Packaging
-
.. image:: https://img.shields.io/pypi/v/nibabel.svg
:target: https://pypi.python.org/pypi/nibabel/
:alt: PyPI version
.. image:: https://img.shields.io/pypi/format/nibabel.svg
:target: https://pypi.org/project/nibabel/
:alt: PyPI Format
.. image:: https://img.shields.io/pypi/pyversions/nibabel.svg
:target: https://pypi.python.org/pypi/nibabel/
:alt: PyPI - Python Version
.. image:: https://img.shields.io/pypi/implementation/nibabel.svg
:target: https://pypi.python.org/pypi/nibabel/
:alt: PyPI - Implementation
.. image:: https://img.shields.io/pypi/dm/nibabel.svg
:target: https://pypistats.org/packages/nibabel/
:alt: PyPI - Downloads

* - Distribution
-
.. image:: https://repology.org/badge/version-for-repo/aur/python:nibabel.svg?header=Arch%20%28%41%55%52%29
:target: https://repology.org/project/python:nibabel/versions
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I would consider PyPI and conda primary distribution channels

Suggested change
.. image:: https://repology.org/badge/version-for-repo/aur/python:nibabel.svg?header=Arch%20%28%41%55%52%29
:target: https://repology.org/project/python:nibabel/versions
.. image:: https://img.shields.io/conda/vn/conda-forge/nibabel
:target: https://anaconda.org/conda-forge/nibabel
:alt: Conda (channel only)
.. image:: https://img.shields.io/pypi/v/nibabel.svg
:target: https://pypi.python.org/pypi/nibabel/
:alt: PyPI version
.. image:: https://repology.org/badge/version-for-repo/aur/python:nibabel.svg?header=Arch%20%28%41%55%52%29
:target: https://repology.org/project/python:nibabel/versions

:alt: Arch (AUR)
.. image:: https://repology.org/badge/version-for-repo/debian_unstable/nibabel.svg?header=Debian%20Unstable
:target: https://repology.org/project/nibabel/versions
:alt: Debian Unstable package
.. image:: https://repology.org/badge/version-for-repo/gentoo_ovl_science/nibabel.svg?header=Gentoo%20%28%3A%3Ascience%29
:target: https://repology.org/project/nibabel/versions
:alt: Gentoo (::science)
.. image:: https://repology.org/badge/version-for-repo/nix_unstable/python:nibabel.svg?header=nixpkgs%20unstable
:target: https://repology.org/project/python:nibabel/versions
:alt: nixpkgs unstable
* - License & DOI
-
.. image:: https://img.shields.io/pypi/l/nibabel.svg
:target: https://github.com/nipy/nibabel/blob/master/COPYING
:alt: License
.. image:: https://zenodo.org/badge/DOI/10.5281/zenodo.591597.svg
:target: https://doi.org/10.5281/zenodo.591597
:alt: Zenodo DOI

Installation
============

To install NiBabel's `current release`_ with ``pip``, run::

pip install nibabel

To install the latest development version, run::

pip install git+https://github.com/nipy/nibabel

For more information on previous releases, see the `release archive`_.

.. _current release: https://pypi.python.org/pypi/NiBabel
.. _release archive: https://github.com/nipy/NiBabel/releases

Mailing List
============

Please send any questions or suggestions to the `neuroimaging mailing list
<https://mail.python.org/mailman/listinfo/neuroimaging>`_.

Code
====

Install nibabel with::

pip install nibabel

You may also be interested in:

* the `nibabel code repository`_ on Github;
* documentation_ for all releases and current development tree;
* download the `current release`_ from pypi;
* download `current development version`_ as a zip file;
* downloads of all `available releases`_.

.. _nibabel code repository: https://github.com/nipy/nibabel
.. _Documentation: http://nipy.org/nibabel
.. _current release: https://pypi.python.org/pypi/nibabel
.. _current development version: https://github.com/nipy/nibabel/archive/master.zip
.. _available releases: https://github.com/nipy/nibabel/releases

License
=======

Nibabel is licensed under the terms of the MIT license. Some code included
with nibabel is licensed under the BSD license. Please see the COPYING file
in the nibabel distribution.
NiBabel is licensed under the terms of the `MIT license`_. Some code included
with NiBabel is licensed under the `BSD license`_. For more information,
please see the COPYING_ file.

Citing nibabel
==============
.. _BSD license: https://opensource.org/licenses/BSD-3-Clause
.. _COPYING: https://github.com/nipy/nibabel/blob/master/COPYING
.. _MIT license: https://github.com/nipy/nibabel/blob/master/COPYING#nibabel

Please see the `available releases`_ for the release of nibabel that you are
using. Recent releases have a Zenodo_ `Digital Object Identifier`_ badge at
the top of the release notes. Click on the badge for more information.
Citation
========

Recent NiBabel releases have a Zenodo_ `Digital Object Identifier`_ (DOI) badge at
the top of the release notes. Click on the badge for more information.

.. _zenodo: https://zenodo.org
.. _Digital Object Identifier: https://en.wikipedia.org/wiki/Digital_object_identifier
.. _zenodo: https://zenodo.org
Binary file added doc/pics/logo.png
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