Skip to main content

Utility package to run CHM jobs on clusters

Project description


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

For more information visit our wiki page


  • – Creates a set of CHM jobs to process a set of images on various compute clusters (Gordon, Comet, & Rocce)

  • – Checks status of jobs generated by script

  • – 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

  • – Simple image conversion utility

  • – Overlays semi-transparent colored probability maps over base image

  • – Merges a set of image tiles in a directory into single image

  • – Internal tool that runs a CHM task created by

  • – Internal tool that runs Merge task created by



  • 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 ./images ./trainedmodel myrun --cluster rocce




Please report them here


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


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 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 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 to generate tif probability map images Issue #43

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

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

0.7.0 (2017-06-09)

  • Added –gentiles flag to to generate tiles from image that can be viewed in probability map viewer. Issue #42

  • Added –rawthreshold flag to 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 to rocce cluster. Issue #40

0.6.0 (2017-03-03)

  • Added –detailed option to Issue #6

  • Added –addprobmap to to enable additional probability maps to be overlayed. Issue #25

  • Added script that creates a CHM train job. Issue #19

  • Fixed incorrect script names in readme.txt generated by 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 Issue #12

0.5.0 (2017-01-11)

  • First release on PyPI.

Project details

Download files

Download the file for your platform. If you're not sure which to choose, learn more about installing packages.

Source Distribution

chmutil-0.8.4.tar.gz (80.5 kB view hashes)

Uploaded source

Built Distribution

chmutil-0.8.4-py2.py3-none-any.whl (83.5 kB view hashes)

Uploaded py2 py3

Supported by

AWS AWS Cloud computing and Security Sponsor Datadog Datadog Monitoring Fastly Fastly CDN Google Google Download Analytics Microsoft Microsoft PSF Sponsor Pingdom Pingdom Monitoring Sentry Sentry Error logging StatusPage StatusPage Status page