Software projects


Below are some of my software projects. You can click on cards to go directly to the GitHub repository.

GitHub cards provided by gh-card.

General purpose software

hakyll-images - Hakyll utilities to deal with images

hakyll-images is suite of utilities to deal with images in the context of Hakyll.

hakyll-images, at this time, allows to compress JPEG images by re-encoding them at a lower quality. Further features are planned, namely image-resizing and image-scaling.

pandoc-plot - A Pandoc filter to generate figures directly in documents, using your plotting toolkit of choice

pandoc-plot is a Pandoc filter that allows to keep documents and figures always in sync. Write plotting code to make a figure in your Markdown , and pandoc-plot will generate the figure for you and embed it in the document. This way, your documents and figures are always up-to-date with each other.

pandoc-plot supports many plotting toolkits, including matplotlib, MATLAB, GNU Octave, ggplot2, Julia’s Plots.jl, and many more! See the website for examples and documentation.

Scientific software

crystals - Data structures for crystallography

crystals is a fully-tested Python package containing data structures representing abstract crystals. Parsing from structure files (e.g. CIF, PDB) is made easy, as is symmetry-determination through the SPGLIB package.

Here’s a quick example:

>>> from crystals import Crystal
>>> vo2 = Crystal.from_database('vo2-m1')
>>> print(vo2)	   # Short string representation
< Crystal object with following unit cell:
    Atom O  @ (0.90, 0.79, 0.80)
    Atom O  @ (0.90, 0.71, 0.30)
    Atom O  @ (0.61, 0.31, 0.71)
    Atom O  @ (0.39, 0.69, 0.29)
    Atom O  @ (0.61, 0.19, 0.21)
    Atom O  @ (0.10, 0.29, 0.70)
    Atom O  @ (0.10, 0.21, 0.20)
    Atom O  @ (0.39, 0.81, 0.79)
    Atom V  @ (0.76, 0.03, 0.97)
    Atom V  @ (0.76, 0.48, 0.47)
    ... omitting 2 atoms ...
Lattice parameters:
    a=5.743Å, b=4.517Å, c=5.375Å
    α=90.000°, β=122.600°, γ=90.000°
Chemical composition:
    O: 66.667%
    V: 33.333%
    (...omitted...)\crystals\cifs\vo2-m1.cif >
>>> print(vo2.symmetry())
{'international_symbol': 'P2_1/c', 
'hall_symbol': '-P 2ybc', 
'hm_symbol': 'P121/c1',
'international_number': 14, 
'hall_number': 81, 
'international_full': 'P 1 2_1/c 1', 
'pointgroup': 'C2h'}

To install from PyPI:

> python -m pip install crystals

For Anaconda users, crystals is also available on the conda-forge channel:

> conda install -c conda-forge crystals

iris-ued - Interactive exploration of ultrafast electron scattering data

Overview of the GUI component of iris. Two GUI instances show the two types of datasets. On the top left, Bragg peak dynamics for photoexcited single-crystal data is shown. On the bottom right, azimuthally-averaged polycrystalline diffraction data is presented. Integration regions can be interactively dragged, updating the time-series shown below in real-time.

Ultrafast electron diffractometer generates huge amounts of data in the forms of image stacks. While processing this data is generally straightforward, the sheer size of datasets is always a problem. Even once the data is combined into a single time-series of images, we are still looking at multiple gigabytes of data.

Iris allows us to interactively look at this data by slicing diffraction patterns (and powder patterns) through time. Making use of our baseline-removal routine based on the dual-tree complex wavelet transform, we can look at publication-quality data minutes after data collection is complete. While each new experiment ultimately requires different tools, our investigations always start with Iris.

The latest version of Iris includes a plug-in manager. You can write your own plug-in to interact with raw, unprocessed ultrafast electron diffraction data and explore it.

To install from PyPI:

> python -m pip install iris-ued

For Anaconda users, iris-ued is also available on the conda-forge channel:

> conda install -c conda-forge iris-ued

npstreams - Streaming operations on NumPy arrays

npstreams is an open-source Python package for streaming NumPy array operations. The goal is to provide tested routines that operate on streams of arrays instead of dense arrays.

Streaming reduction operations (sums, averages, etc.) can be implemented in constant memory, which in turns allows for easy parallelization. Some routines in npstreams are parallelized in this way. In our experience, this approach has resulted in huge speedups when working with images; the images are read one-by-one from disk and combined/processed in a streaming fashion, in parallel.

To install from PyPI:

> python -m pip install npstreams

For Anaconda users, npstreams is also available on the conda-forge channel:

> conda install -c conda-forge npstreams

scikit-ued - Algorithms and data structures related to ultrafast electron scattering

scikit-ued is a fully-tested Python package containing routines and algorithms related to (ultrafast) electron diffraction. The package aims to provide software to deal with simulation, structure manipulation, image-analysis, baseline-determination, and more.

To install from PyPI:

> python -m pip install scikit-ued

For Anaconda users, scikit-ued is also available on the conda-forge channel:

> conda install -c conda-forge scikit-ued