Metadata-Version: 1.1
Name: chmutil
Version: 0.7.0
Summary: Utility package to run CHM jobs on clusters
Home-page: https://github.com/CRBS/chmutil
Author: Christopher Churas
Author-email: churas@ncmir.ucsd.edu
License: UNKNOWN
Description: ===============================
        chmutil
        ===============================
        
        
        .. image:: https://img.shields.io/pypi/v/chmutil.svg
                   :target: https://pypi.python.org/pypi/chmutil
        
        .. image:: https://pyup.io/repos/github/crbs/chmutil/shield.svg
                :target: https://pyup.io/repos/github/crbs/chmutil
        
        .. image:: https://travis-ci.org/CRBS/chmutil.svg?branch=master
               :target: https://travis-ci.org/CRBS/chmutil
        
        .. image:: https://coveralls.io/repos/github/CRBS/chmutil/badge.svg?branch=master
           :target: https://coveralls.io/github/CRBS/chmutil?branch=master
        
        Utility package to run `Cascaded Hierarchical Model (CHM) <https://www.sci.utah.edu/software/chm.html>`_ jobs on clusters.
        
        `For more information visit our wiki page <https://github.com/CRBS/chmutil/wiki>`_
        
        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 <https://pypi.python.org/pypi/argparse>`_
        
        * `configparser <https://pypi.python.org/pypi/configparser>`_
        
        * `Pillow <https://pypi.python.org/pypi/Pillow>`_
        
        * `CHM singularity image <https://github.com/crbs/chm_singularity>`_ (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 <https://github.com/CRBS/chmutil/issues>`_
        
        
        Credits
        ---------
        
        This package was created with Cookiecutter_ and the `audreyr/cookiecutter-pypackage`_ project template.
        
        .. _NCMIR: https://ncmir.ucsd.edu/
        .. _LICENSE.txt: https://github.com/CRBS/chmutil/blob/master/LICENSE.txt
        .. _Cookiecutter: https://github.com/audreyr/cookiecutter
        .. _`audreyr/cookiecutter-pypackage`: https://github.com/audreyr/cookiecutter-pypackage
        
        
        
        =======
        History
        =======
        
        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 <https://github.com/CRBS/chmutil/issues/42>`_
        
        * Added --rawthreshold flag to createprobmapoverlay.py which 
          lets caller specify exact pixel intensity value instead of
          percentage as offered with --threshpc.
          `Issue #41 <https://github.com/CRBS/chmutil/issues/41>`_
        
        * Added virtual_free to requirements for SGE jobs submitted
          by createchmtrainjob.py to rocce cluster. 
          `Issue #40 <https://github.com/CRBS/chmutil/issues/40>`_
        
        0.6.0 (2017-03-03)
        ------------------
        
        * Added --detailed option to checkchmjob.py. 
          `Issue #6 <https://github.com/CRBS/chmutil/issues/6>`_
        
        * Added --addprobmap to createprobmapoverlay.py to enable
          additional probability maps to be overlayed. 
          `Issue #25 <https://github.com/CRBS/chmutil/issues/25>`_
        
        * Added createchmtrainjob.py script that creates a CHM
          train job. 
          `Issue #19 <https://github.com/CRBS/chmutil/issues/19>`_
        
        * Fixed incorrect script names in readme.txt generated by
          createchmjob.py. 
          `Issue #20 <https://github.com/CRBS/chmutil/issues/20>`_
        
        0.5.1 (2017-01-12)
        ------------------
        
        * Fixed account not being put into runjobs.gordon and runmerge.gordon.
          `Issue #11 <https://github.com/CRBS/chmutil/issues/11>`_
        
        * Fixed errors in checking job status examples in readme.txt 
          created by createchmjob.py.
          `Issue #12 <https://github.com/CRBS/chmutil/issues/12>`_
        
        0.5.0 (2017-01-11)
        ------------------
        
        * First release on PyPI.
        
        
Keywords: chmutil
Platform: UNKNOWN
Classifier: Development Status :: 2 - Pre-Alpha
Classifier: Intended Audience :: Developers
Classifier: Natural Language :: English
Classifier: Programming Language :: Python :: 2.7
Classifier: Programming Language :: Python :: 3.3
Classifier: Programming Language :: Python :: 3.4
Classifier: Programming Language :: Python :: 3.5
