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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