Package: chmutil
chmutilUtility package to runCascaded Hierarchical Model (CHM)jobs on clusters.For more information visit our wiki pageToolscreatechmjob.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 bycreatechmjob.pyscriptcreatechmtrainjob.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 forcreatechmjob.pycreatechmimage.py– Simple image conversion utilitycreateprobmapoverlay.py– Overlays semi-transparent colored probability maps over base imagemergetiles.py– Merges a set of image tiles in a directory into single imagechmrunner.py– Internal tool that runs a CHM task created bycreatechmjob.pymergetilerunner.py– Internal tool that runs Merge task created bycreatechmjob.pyDependenciesargparseconfigparserPillowCHM singularity image(not required to build this software, but is needed to run the jobs)CompatibilityShould work on Python 2.7 & 3+ on Linux distributionsInstallationpip install chmutilUsage# creates a job assuming images are in ./images and ./trainedmodel has
# chm model
createchmjob.py ./images ./trainedmodel myrun --cluster rocceLicenseSeeLICENSE.txtBugsPlease report themhereCreditsThis package was created withCookiecutterand theaudreyr/cookiecutter-pypackageproject template.History0.8.4 (2018-03-20)Try number two to get comet configuration to load singularity 2.3.2.
See issue 76 below.0.8.3 (2018-03-16)Added –dontdeletescratch option to createtrainingmrcstack.py to skip
deletion of scratchdir.Issue #78Updated comet configuration to load singularity 2.3.2.Issue #760.8.2 (2017-07-27)Fixed typo in history notes which caused pypi not to render project description properly0.8.1 (2017-07-27)Fixed bug in createtrainingmrcstack.py which caused program to fail due
to incorrect call to get_image_path_list().Issue #48Increased required memory for merge tasks on Rocce cluster from 10 to
20 gigabytes of ram and added virtual_free constraint to handle
gigapixel images.Issue #490.8.0 (2017-06-23)Added –gentifs to createchmjob.py to generate tif probability map imagesIssue #43Fixed bug in checkchmjob.py –detailed where ram value was incorrectIssue #44Added information about input images to checkchmjob.py –detailedIssue #280.7.0 (2017-06-09)Added –gentiles flag to createchmimage.py to generate tiles from
image that can be viewed in probability map viewer.Issue #42Added –rawthreshold flag to createprobmapoverlay.py which
lets caller specify exact pixel intensity value instead of
percentage as offered with –threshpc.Issue #41Added virtual_free to requirements for SGE jobs submitted
by createchmtrainjob.py to rocce cluster.Issue #400.6.0 (2017-03-03)Added –detailed option to checkchmjob.py.Issue #6Added –addprobmap to createprobmapoverlay.py to enable
additional probability maps to be overlayed.Issue #25Added createchmtrainjob.py script that creates a CHM
train job.Issue #19Fixed incorrect script names in readme.txt generated by
createchmjob.py.Issue #200.5.1 (2017-01-12)Fixed account not being put into runjobs.gordon and runmerge.gordon.Issue #11Fixed errors in checking job status examples in readme.txt
created by createchmjob.py.Issue #120.5.0 (2017-01-11)First release on PyPI.