espm 1.1.2

Electron SPectro-Microscopy Python Library

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

The espm package is designed for simulation and physics-guided NMF decomposition of hyperspectral data. Even though the package is mainly centered around electron spectro-microscopy applications, custom models can be implemented for other type of data. Currently espm supports the simulation and analysis of simultaneous scanning transmission electron microscopy and energy dispersive X-ray spectroscopy (STEM / EDXS). In future implementation, we will try to extend the package to support electron energy loss spectroscopy (EELS).

This library is integrated as much as possible in the hyperspy <https://hyperspy.org> and scikit-learn <https://scikit-learn.org> frameworks.

The main components of the package are:

• The simulation of STEM-EDXS datasets using :mod:espm.datasets which combines :mod:espm.weights for the simulation of spatial distributions and :mod:èspm.models for the simulation of spectra.
• The hyperspectral unmixing of STEM-EDXS spectrum images using :mod:espm.estimators. This module contains algorithms to perform non-negative matrix factorization with diverse regularisation (e.g. Laplacian or L1) and contraints (e.g. simplex).
• The :mod:espm.models module can also be used to perform a physics-guided decomposition of STEM-EDXS datasets.

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]" 

If you get issues regarding pandoc when using make doc, you can install it using::

$ sudo apt-get install pandoc

or::

$ conda install pandoc

Recommended Installation

We recommend to install the package in a virtual environment using conda::

$ conda create -n espm python=3.11
$ conda activate espm
$ pip install espm

We also recommend that you install the following packages in the same environment::

$ pip install pyqt5
$ pip install hyperspy_gui_traitsui
$ pip install hyperspy_gui_ipywidgets

It is especially useful for the interactive plotting in the notebooks.

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:

• Simulate STEM-EDXS data : https://espm.readthedocs.io/en/latest/introduction/notebooks/generate_data.ipynb
• Physics-guided decomposition (ESpM-NMF) STEM-EDXS data : https://espm.readthedocs.io/en/latest/introduction/notebooks/api.html
• Tests of the ESpM-NMF with a toy dataset : 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}
}