Newer
Older
|pipeline|_ |coverage|_ |pypi|_
.. |pipeline| image:: https://iffgit.fz-juelich.de/empyre/empyre/badges/master/pipeline.svg
.. _pipeline: https://iffgit.fz-juelich.de/empyre/empyre/commits/master
.. |coverage| image:: https://iffgit.fz-juelich.de/empyre/empyre/badges/master/coverage.svg
.. _coverage: https://iffgit.fz-juelich.de/empyre/empyre
.. |pypi| image:: https://badge.fury.io/py/empyre.svg
.. _pypi: https://pypi.org/project/empyre/
EMPyRe is an open source framework for constructing and solving hyperdimensional inverse problems and visualizing the corresponding input and output data. it has
its roots in the reconstruction of three-dimensional magnetization distributions from magnetic phase images generated by electron holography but is meant to be
extendable for many other problems that are based on forward models that are expressable as a combination of linear subproblems. EMPyRe is purely Python
package, so all platforms should be supported.
Installation
------------
EMPyRe is available on the `Python Package Index <http://pypi.python.org/pypi>`_ and can be simply be installed via `pip <http://pypi.python.org/pypi/pip>`_:
.. code-block:: bash
Per default, only the strictly required libraries are installed, but there are a few additional dependencies that will unlock additional capabilites of EMPYRE.
* ``io`` will install the `HyperSpy <https://hyperspy.org/>`_ package that is used for loading and saving additional file formats.
Due to this `issue <https://github.com/hyperspy/hyperspy/issues/2315>`_, a pip install of hyperspy is currently not possible. Please use
`conda <https://docs.conda.io/en/latest/>`_ to install HyperSpy, instead.
* ``fftw`` will install `PyFFTW <https://github.com/pyFFTW/pyFFTW>`_ to speed up Fourier transforms used in some forward models.
* ``colors`` will install the `cmocean <https://matplotlib.org/cmocean/>`_, whose ``balance`` color map is used as a default for the ``imshow`` commmand, if available.
* ``all`` will install all of the dependencies listed above.
You can choose these settings by using, *e.g.*:
.. code-block:: bash
Structure
---------
EMPyRe has several dedicated submodules which are fully documented `here <https://empyre.iffgit.fz-juelich.de/empyre/>`_!
* The ``fields`` submodule provides the ``Field`` container class for multidimensional scalar or vector fields and is the fundamental data structure used in EMPyRe.
* The ``vis`` submodule enables the plotting of ``Field`` objects, based on and similar in syntax to the commonly known `matplotlib <https://matplotlib.org/>`_ framework.
* The ``models`` submodule provides tools for constructing forward models that describe processes in Electron Microscopy.
* The ``reconstruct`` submodule is a collection of tools for solving the inverse problems corresponding to the constructed forward models and diagnostic tools for their assessment.
* The ``io`` submodule is used to load and save ``Field`` objects and the models generated by the ``models`` subpackage.
License
-------
EMPyRe is licensed under `GPLv3 <https://iffgit.fz-juelich.de/empyre/empyre/-/blob/master/LICENSE>`_.