EMPyRe - Electron Microscopy Reconstruction
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 and can be simply be installed via pip:
$ pip install empyre
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 tvtk & HyperSpy packages that are used for loading and saving additional file formats.fftw
will install PyFFTW to speed up Fourier transforms used in some forward models.colors
will install the cmocean, whosebalance
color map is used as a default for theimshow
commmand, if available.3d
will install the mayavi package for 3D plotting capabilities.tests
will install all dependencies that are needed to test the package (usually not necessary for the average user).all
will install all of the dependencies listed above.
You can choose these settings by using, e.g.:
$ pip install empyre[all]
Structure
EMPyRe has several dedicated modules which are fully documented here!
The
fields
module provides theField
container class for multidimensional scalar or vector fields and is the fundamental data structure used in EMPyRe.The
vis
module enables the plotting ofField
objects, based on and similar in syntax to the commonly known matplotlib framework.The
models
module provides tools for constructing forward models that describe processes in Electron Microscopy.The
reconstruct
module is a collection of tools for solving the inverse problems corresponding to the constructed forward models and diagnostic tools for their assessment.The
io
module is used to load and saveField
objects and the models generated by themodels
subpackage.The
utils
module, which houses utility functionality used throughout EMPyRe.
License
EMPyRe is licensed under GPLv3.