Electron Microscopy Pix (EMPix)

empix is a Python library that contains tools for analyzing electron microscopy data that are not available in hyperspy.

Visit the empix website for a web version of the installation instructions, the reference guide, and the examples archive.

The source code can be found in the empix GitHub repository.

Table of contents

• Instructions for installing and uninstalling empix
  • Installing empix
    • Installing empix using pip
    • Installing empix using conda
  • Uninstalling empix
• Learning how to use empix

Instructions for installing and uninstalling empix

Installing empix

For all installation scenarios, first open up the appropriate command line interface. On Unix-based systems, you could open e.g. a terminal. On Windows systems you could open e.g. an Anaconda Prompt as an administrator.

Installing empix using pip

Before installing empix, make sure that you have activated the (virtual) environment in which you intend to install said package. After which, simply run the following command:

pip install empix

The above command will install the latest stable version of empix.

To install the latest development version from the main branch of the empix GitHub repository, one must first clone the repository by running the following command:

git clone https://github.com/mrfitzpa/empix.git

Next, change into the root of the cloned repository, and then run the following command:

pip install .

Note that you must include the period as well. The above command executes a standard installation of empix.

Optionally, for additional features in empix, one can install additional dependencies upon installing empix. To install a subset of additional dependencies (along with the standard installation), run the following command from the root of the repository:

pip install .[<selector>]

where <selector> can be one of the following:

• tests: to install the dependencies necessary for running unit tests;
• examples: to install the dependencies necessary for executing files stored in <root>/examples, where <root> is the root of the repository;
• docs: to install the dependencies necessary for documentation generation;
• all: to install all of the above optional dependencies.

Alternatively, one can run:

pip install empix[<selector>]

elsewhere in order to install the latest stable version of empix, along with the subset of additional dependencies specified by <selector>.

Installing empix using conda

To install empix using the conda package manager, run the following command:

conda install -c conda-forge empix

The above command will install the latest stable version of empix.

Uninstalling empix

If empix was installed using pip, then to uninstall, run the following command:

pip uninstall empix

If empix was installed using conda, then to uninstall, run the following command:

conda remove empix

Learning how to use empix

For those new to the empix library, it is recommended that they take a look at the Examples page, which contain code examples that show how one can use the empix library. While going through the examples, readers can consult the empix reference guide to understand what each line of code is doing.