Utility package to run CHM jobs on clusters
Utility package to run Cascaded Hierarchical Model (CHM) jobs on clusters.
- 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
- Should work on Python 2.7 & 3+ on Linux distributions
pip install chmutil
# creates a job assuming images are in ./images and ./trainedmodel has # chm model createchmjob.py ./images ./trainedmodel myrun --cluster rocce
Please report them here
- Try number two to get comet configuration to load singularity 2.3.2. See issue 76 below.
- Fixed typo in history notes which caused pypi not to render project description properly
- Added –gentiles flag to createchmimage.py to generate tiles from image that can be viewed in probability map viewer. Issue #42
- Added –rawthreshold flag to createprobmapoverlay.py which lets caller specify exact pixel intensity value instead of percentage as offered with –threshpc. Issue #41
- Added virtual_free to requirements for SGE jobs submitted by createchmtrainjob.py to rocce cluster. Issue #40
- Added –detailed option to checkchmjob.py. Issue #6
- Added –addprobmap to createprobmapoverlay.py to enable additional probability maps to be overlayed. Issue #25
- Added createchmtrainjob.py script that creates a CHM train job. Issue #19
- Fixed incorrect script names in readme.txt generated by createchmjob.py. Issue #20
- First release on PyPI.
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