.. bmiptools documentation master file, created by
   sphinx-quickstart on Fri Jun  3 07:27:22 2022.
   You can adapt this file completely to your liking, but it should at least
   contain the root `toctree` directive.


Welcome to bmiptools's documentation!
=====================================


.. toctree::
   :maxdepth: 2

   bmiptools

.. toctree::
   :maxdepth: 2
   :caption: Usage:

   Usage/installation.rst
   Usage/basic api usage.rst
   Usage/advanced api usage.rst
   Usage/GUI usage.rst

.. toctree::
   :maxdepth: 2
   :caption: Plugins:

   Plugins/general.rst
   Plugins/standardizer.rst
   Plugins/histogram matcher.rst
   Plugins/denoiser.rst
   Plugins/denoiserDNN.rst
   Plugins/destriper.rst
   Plugins/flatter.rst
   Plugins/decharger.rst
   Plugins/registrator.rst
   Plugins/affine.rst
   Plugins/cropper.rst
   Plugins/equalizer.rst

.. toctree::
   :maxdepth: 2
   :caption: Visualization:

   Visualization/basic visualization.rst
   Visualization/change coordinate system.rst

.. toctree::
   :maxdepth: 2
   :caption: Developer:

   Developer/general conventions.rst
   Developer/plugin structure.rst
   Developer/guipi.rst
   Developer/plugin installation.rst
   Developer/contribute.rst
   Developer/api references.rst

.. toctree::
   :maxdepth: 2
   :caption: Miscellaneous:

   Miscellaneous/basic stack-pipeline.rst
   Miscellaneous/create custom plugin.rst
   Miscellaneous/destriper optimization.rst
   Miscellaneous/decharger optimization.rst


Indices and tables
==================


* :ref:`genindex`
* :ref:`modindex`
* :ref:`search`