API Reference
=============

The following section outlines the API of shimming-toolbox.

.. contents::
   :local:
   :depth: 1
..

Fieldmapping
------------

.. automodule:: shimmingtoolbox.prepare_fieldmap
    :members:

.. automodule:: shimmingtoolbox.unwrap.unwrap_phase
   :members:

.. automodule:: shimmingtoolbox.unwrap.prelude
   :members:

Masking
-------

.. automodule:: shimmingtoolbox.masking.shapes
    :members:

.. automodule:: shimmingtoolbox.masking.threshold
    :members:

.. automodule:: shimmingtoolbox.masking.mask_utils
    :members:

Coils
-----

.. automodule:: shimmingtoolbox.coils.coil
    :members:
    :special-members: __init__

.. automodule:: shimmingtoolbox.coils.spherical_harmonics
    :members:

.. automodule:: shimmingtoolbox.coils.spher_harm_basis
    :members:

.. automodule:: shimmingtoolbox.coils.coordinates
    :members:

.. automodule:: shimmingtoolbox.coils.biot_savart
   :members:

Shim
----

.. automodule:: shimmingtoolbox.shim.sequencer
   :members:

.. automodule:: shimmingtoolbox.shim.b1shim
   :members:

Optimizer
---------

.. automodule:: shimmingtoolbox.optimizer.basic_optimizer
   :members:
   :special-members: __init__

.. automodule:: shimmingtoolbox.optimizer.lsq_optimizer
   :members:
   :special-members: __init__
   :show-inheritance:
   :inherited-members:

Image manipulation
------------------

.. automodule:: shimmingtoolbox.image
   :members:

Numerical model
---------------

.. automodule:: shimmingtoolbox.simulate.numerical_model
   :members:

Miscellaneous
-------------

.. automodule:: shimmingtoolbox.dicom_to_nifti
   :members:

.. automodule:: shimmingtoolbox.load_nifti
   :members:

.. automodule:: shimmingtoolbox.download
   :members:

.. automodule:: shimmingtoolbox.pmu
   :members:

.. automodule:: shimmingtoolbox.utils
   :members: