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chmutil-0.8.4
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مشاهده بیشترتوضیحات
Utility package to run CHM jobs on clusters
| ویژگی | مقدار |
|---|---|
| سیستم عامل | - |
| نام فایل | chmutil-0.8.4 |
| نام | chmutil |
| نسخه کتابخانه | 0.8.4 |
| نگهدارنده | [] |
| ایمیل نگهدارنده | [] |
| نویسنده | Christopher Churas |
| ایمیل نویسنده | churas@ncmir.ucsd.edu |
| آدرس صفحه اصلی | https://github.com/CRBS/chmutil |
| آدرس اینترنتی | https://pypi.org/project/chmutil/ |
| مجوز | - |
===============================
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.
.. _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
=======
0.8.4 (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 <https://github.com/CRBS/chmutil/issues/78>`_
* Updated comet configuration to load singularity 2.3.2.
`Issue #76 <https://github.com/CRBS/chmutil/issues/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 <https://github.com/CRBS/chmutil/issues/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 <https://github.com/CRBS/chmutil/issues/49>`_
0.8.0 (2017-06-23)
------------------
* Added --gentifs to createchmjob.py to generate tif probability map images
`Issue #43 <https://github.com/CRBS/chmutil/issues/43>`_
* Fixed bug in checkchmjob.py --detailed where ram value was incorrect
`Issue #44 <https://github.com/CRBS/chmutil/issues/44>`_
* Added information about input images to checkchmjob.py --detailed
`Issue #28 <https://github.com/CRBS/chmutil/issues/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 <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.
نیازمندی
| مقدار | نام |
|---|---|
| - | argparse |
| - | configparser |
| - | Pillow |
نحوه نصب
نصب پکیج whl chmutil-0.8.4:
pip install chmutil-0.8.4.whl
نصب پکیج tar.gz chmutil-0.8.4:
pip install chmutil-0.8.4.tar.gz