wsp_tools

Utilities for TEM data analysis and simulation.

Features:

• Single Image TIE
• Lorentz TEM simulations
• spatial modes
• a matplotlib.pyplot wrapper
• an implementation of the CIELAB colorspace
• a scipy.constants wrapper that allows arbitrary units (i.e., using nanometers instead of meters)

Installation

Pip

As of version 1.3.1, wsp_tools is available on PyPi, and can be installed with pip:

python -m pip install wsp-tools

GitHub

wsp_tools can also be installed directly from GitHub via

pip install -e git+https://github.com/McMorranLab/wsp_tools#egg=wsp-tools

Installing in editable mode -e ensures that pip freeze records the install url, not just the version.

You can specify the commit or tag to install, via

pip install -e git+https://github.com/McMorranLab/wsp_tools@{commit id or tag number}#egg=wsp_tools

Documentation

As of version 1.3.1, documentation is available at https://mcmorranlab.github.io/wsp_tools/.

As of version 1.0.94, wsp_tools includes a helper function docs(outdir="."), which uses pdoc3 to auto-generate html documentation and save it to an outdir of your choice, thus avoiding the need to clone this repository just to see the documentation. For example:

import wsp_tools
wsp_tools.docs("~/Desktop") # generates docs in the folder ~/Desktop/wsp_tools

Tests

Tests are split into two subdirectories:

1. tests These are typical unit tests, that assert that functions return the right shape, beam parameters return the right values, etc. Run with pytest.
2. devtests These are tests of the actual functionality, that require a trained eye to evaluate. For example, a function test_bessel() will generate a bessel beam using wsp_tools.bessel(), but rather than asserting a unit test, will just plot the bessel beam so the developer can manually assert whether it looks correct. Run as normal .py scripts.

The rationale for devtests is that this package is math-heavy, so it's highly possible for the code to run fine, but be wrong. The easiest way to test for this is to check base cases where the developer knows what to look for.