.. _extensions:

:tocdepth: 3

=======
Scripts
=======


Image
=====

The module contains scripts to read, convert, write, and process medical images. 
Beside standard image processing tools, many algorithm are added to create 
finite element simulation models. The image processor is able to run SimpleITK 
scripts. Visual interactions are possible via a 3D Slicer bridge which allows
to call 3D Slicer from medtool. 

.. automodule:: mic
.. automodule:: mic_mpi
.. automodule:: ctcal
.. automodule:: imgToFe
.. automodule:: pfeToH5
.. automodule:: medtoolSlicerBridge


Mesh
====
The meshing module contains interfaces to freely available meshing software as well as 
specialized meshing algorithm. They are designed to create high-quality meshes 
which are usually used for simulation models. A unstructured (finite element) 
mesh converter allows to convert between different file formats. 

.. automodule:: isosurfRun
.. automodule:: dpMesher
.. automodule:: cgal3dMesher
.. automodule:: bom
.. automodule:: gmshMesher
.. automodule:: fec



Material
========

Computational homogenization is a method to model hierarchical materials. Information of a 
micro-structural level is used to compute an equivalent stiffness and strength which is 
used in macroscopic models. 

.. image:: images/mia-multi1.png 

This information has to be computed and mapped from CT images to Finite Element material cards. 
medtool supports Abaqus/Calculix and Ensight '.case' (Paraview) format.  

.. automodule:: miamultiDoc
.. automodule:: ctxmultiDoc


Boundary
========

This module provides scripts for the computational homogenization. Example problem
template for classical boundary conditions are provided. A boundary condition generation 
creates coupling conditions needed for the individual boundary condition types. 

.. automodule:: cbc
.. automodule:: cbcex


Solve
=====

The solve module provids interfaces to commercial and freely available 
finite element solver. An efficient linear micro FE solver (ParOSol) is 
available for Linux.  


.. automodule:: ccxRun
.. automodule:: cgxRun
.. automodule:: abqRun
.. automodule:: parosolRun


Post
====

The post-processing algorithm which are prived are mainly designed for computational homogenization 
task but can also be used for the automated reading of information from FE result files. 

.. automodule:: abqFuReader
.. automodule:: abqSeReader
.. automodule:: abqFuAvg
.. automodule:: abqSeAvg
.. automodule:: historyReader
.. automodule:: fieldReader

.. automodule:: ccxSeReader

.. automodule:: pfeFuRead
.. automodule:: pfeSeRead
.. automodule:: pfeToXmf

.. automodule:: FuAnalyzer
.. automodule:: FuAnalyzerNL
.. automodule:: SeAnalyzer


Analyze
=======

.. automodule:: mia
.. automodule:: hma
.. automodule:: dxa
.. automodule:: gda


Publish
=======

.. automodule:: rem
.. automodule:: XYPlot


Fabricate
=========


.. automodule:: fevox


Extras
======

.. automodule:: paf
.. automodule:: paf2
.. automodule:: mcsv
.. automodule:: userRun
.. automodule:: mgv
.. automodule:: info

Archive
=======

These modules are no longer being developed or compiled. 
It is recommended to switch to new *medtool* modules with similar functionalities.

.. automodule:: itkDicom
.. automodule:: marcher
.. automodule:: stiffErr
.. automodule:: stiffRegr
.. automodule:: stiffOut
.. automodule:: sop
.. automodule:: miastiffDoc
.. automodule:: stiffModel