Software
I have written some open-source software, some to scratch an itch, and some as part of my research.
Currently Active Projects
Pymorph: Python Morphology Toolbox
This is a Python image morphology toolbox which I have adopted (i.e., taken over maintaining).
- Includes basic operations such as
- erode
- dilate
- open
- tophat opening
- watershed
- ...
License: BSD.
gitcms
This is the system behind this website. It is a django based content managed system, where all the content is stored on flat text files. I use git to manage those text files and publish on the website.
License: Affero GPL.
Jug
Jug is a task based framework for running embarassingly parallel code in Python. You can also think of it as a light-weight python-based map-reduce environment.
License: MIT.
Dormant Projects
These are projects that work but which I am not too interested in pursuing write now, but which I might revive in the future.
ncreduce: No Copy Reduce Operations for Numpy
This improves on the speed of reduce-type operations in numpy. The code works great for its purpose, and I still resort to it everytime that ndarray.sum shows up in my profiles as a time hog (surprisingly often). However, it is too large (the binary is huge).
I learned a lot about numpy's internals while doing it and I developed this technique for writing fast clean C++ to work on numpy code.
License: GPL.
Bits & Pieces
These are little projects that are helpful, but not part of anything larger.
FASTA Python Reader
Parses FASTA files in Python. As a major feature, it correctly handles comments (which many programmes do not). As a major mis-feature, it was one of the first Python classes that I wrote and it shows.
License: MIT