Metadata-Version: 2.1
Name: espm
Version: 0.2.0
Summary: Electron SPectro-Microscopy Python Library
Home-page: https://github.com/adriente/espm
Author: Adrien Teurtie, Nathanael Perraudin
Author-email: nathanael.perraudin@sdsc.ethz.ch
License: MIT
Classifier: Development Status :: 5 - Production/Stable
Classifier: Intended Audience :: Science/Research
Classifier: Intended Audience :: End Users/Desktop
Classifier: Intended Audience :: Developers
Classifier: Natural Language :: English
Classifier: License :: OSI Approved :: GNU General Public License v3 (GPLv3)
Classifier: Operating System :: MacOS :: MacOS X
Classifier: Operating System :: POSIX :: Linux
Classifier: Programming Language :: C
Classifier: Programming Language :: Python :: 3.6
Classifier: Programming Language :: Python :: 3.7
Classifier: Programming Language :: Python :: 3.8
Classifier: Topic :: Scientific/Engineering :: Mathematics
Classifier: Topic :: Scientific/Engineering
Requires-Python: >=3.7
Description-Content-Type: text/markdown
Requires-Dist: hyperspy
Requires-Dist: tqdm
Requires-Dist: lmfit
Requires-Dist: scikit-learn
Provides-Extra: dev
Requires-Dist: flake8 ; extra == 'dev'
Requires-Dist: pytest ; extra == 'dev'
Requires-Dist: jupyterlab ; extra == 'dev'
Requires-Dist: twine ; extra == 'dev'
Requires-Dist: setuptools ; extra == 'dev'
Requires-Dist: wheel ; extra == 'dev'
Requires-Dist: sphinx ; extra == 'dev'
Requires-Dist: numpydoc ; extra == 'dev'
Requires-Dist: sphinxcontrib-bibtex ; extra == 'dev'
Requires-Dist: sphinx-gallery ; extra == 'dev'
Requires-Dist: memory-profiler ; extra == 'dev'
Requires-Dist: sphinx-rtd-theme ; extra == 'dev'
Requires-Dist: sphinx-copybutton ; extra == 'dev'
Requires-Dist: nbsphinx ; extra == 'dev'
Requires-Dist: pandoc ; extra == 'dev'

espm: The Electron Spectro-Microscopy Python Library
=====================================================

.. image:: https://readthedocs.org/projects/espm/badge/?version=latest
    :target: https://espm.readthedocs.io/en/latest/?badge=latest
    :alt: Documentation Status

This library contains algorithms to perform non-negative matrix factorization with 
diverse regularisation (e.g. Laplacian or L1) and contraints (e.g. simplex).

It is specialized for Electron Microscopy applications. It contains code to create artificial 
Energy dispersive X-ray spectroscopy (EDXS) data and to perform hyperspectral unmixing on 
EDXS spectrum images.

Installation
------------

You can install this package from PyPi using::

    $ pip install espm

If you want to develop, please use the option::

    $ git clone https://github.com/adriente/espm.git
    $ cd espm
    $ pip install cython
    $ pip install -e ".[dev]" 

Getting started
---------------
Try the api.ipynb notebook in the `notebooks` folder.


Documentation
-------------

The documentation is available at https://espm.readthedocs.io/en/latest/

You can get started with the following notebooks:

* https://espm.readthedocs.io/en/latest/introduction/notebooks/api.html
* https://espm.readthedocs.io/en/latest/introduction/notebooks/toy-problem.html

CITING
------

If you use this library, please cite the following paper::

    @article{teurtrie2023espm,
    title={espm: A Python library for the simulation of STEM-EDXS datasets},
    author={Teurtrie, Adrien and Perraudin, Nathana{\"e}l and Holvoet, Thomas and Chen, Hui and Alexander, Duncan TL and Obozinski, Guillaume and H{\'e}bert, C{\'e}cile},
    journal={Ultramicroscopy},
    pages={113719},
    year={2023},
    publisher={Elsevier}
    }
