Parameters settings
===================

The PyStack3D workflow parameters are defined in a ``params.toml`` file that is structured as follows:

* The first parameters are related to the **general** parameters that specify the conditions of the **workflow** execution.

* The following 'encapsulated' parameters are related to the conditions of each **process step** execution.

To illustrate each of the process step we will consider hereafter the `synthetic test case <https://github.com/CEA-MetroCarac/pystack3d/blob/main/examples/ex_synthetic_stack.py>`_ obtained by adding defects to an original stack (which is named 'target' in what follows) composed of 300 x 300 x 300 voxels. The defects to be removed corresponds to:

    - curtaining effects in some slices

    - a background effect (defined from a polynom x*y*z),

    - shifts along the x-axis (for slices in [20-70])

    - changes in brightness (for slices in [70-100])

    - a non-uniform sampling (inter-slice distance *dz* changing from 0.01 to 0.02 at slice 100)


.. figure:: _static/synth_use_case_3D.png
    :width: 100%
    :align: center


.. figure:: _static/synth_use_case.png
    :width: 70%
    :align: center

    Illustration of the synthetic use case: 3D visualisations and cut-planes corresponding to Z=83 and Y=150.


.. toctree::
    :titlesonly:

    general.rst
    cropping.rst
    bkg_removal.rst
    intensity_rescaling.rst
    registration.rst
    destriping.rst
    resampling.rst
    cropping_final.rst