chmutil

Utility package to run Cascaded Hierarchical Model (CHM) jobs on clusters.

For more information visit our wiki page

Tools

• createchmjob.py -- Creates a set of CHM jobs to process a set of images on various compute clusters (Gordon, Comet, & Rocce)
• checkchmjob.py -- Checks status of jobs generated by createchmjob.py script
• createchmtrainjob.py -- Creates a CHM train job, runnable on various compute clusters (Comet & Rocce), which teaches CHM how to segment a desired feature. The output from this job is a trained model that is needed as an input for createchmjob.py
• createchmimage.py -- Simple image conversion utility
• createprobmapoverlay.py -- Overlays semi-transparent colored probability maps over base image
• mergetiles.py -- Merges a set of image tiles in a directory into single image
• chmrunner.py -- Internal tool that runs a CHM task created by createchmjob.py
• mergetilerunner.py -- Internal tool that runs Merge task created by createchmjob.py

Dependencies

• argparse
• configparser
• Pillow
• CHM singularity image (not required to build this software, but is needed to run the jobs)

Compatibility

• Should work on Python 2.7 & 3+ on Linux distributions

Installation

pip install chmutil

Usage

# creates a job assuming images are in ./images and ./trainedmodel has
# chm model
createchmjob.py ./images ./trainedmodel myrun --cluster rocce

License

See LICENSE.txt

Bugs

Please report them here

Credits

This package was created with Cookiecutter and the audreyr/cookiecutter-pypackage project template.