chmutil 0.8.4

Utility package to run CHM jobs on clusters

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.

History

0.8.4 (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 #78

• Updated comet configuration to load singularity 2.3.2. Issue #76

0.8.2 (2017-07-27)

• Fixed typo in history notes which caused pypi not to render project description properly

0.8.1 (2017-07-27)

• Fixed bug in createtrainingmrcstack.py which caused program to fail due to incorrect call to get_image_path_list(). Issue #48

• Increased 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 #49

0.8.0 (2017-06-23)

• Added –gentifs to createchmjob.py to generate tif probability map images Issue #43

• Fixed bug in checkchmjob.py –detailed where ram value was incorrect Issue #44

• Added information about input images to checkchmjob.py –detailed Issue #28

0.7.0 (2017-06-09)

• Added –gentiles flag to createchmimage.py to generate tiles from image that can be viewed in probability map viewer. Issue #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

0.6.0 (2017-03-03)

• 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

0.5.1 (2017-01-12)

• Fixed account not being put into runjobs.gordon and runmerge.gordon. Issue #11

• Fixed errors in checking job status examples in readme.txt created by createchmjob.py. Issue #12

0.5.0 (2017-01-11)

• First release on PyPI.