A plug-in to meassure model accuracy on test data
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.. image:: https://badge.fury.io/py/dice_coeff.svg :target: https://badge.fury.io/py/dice_coeff
.. image:: https://travis-ci.org/FNNDSC/dice_coeff.svg?branch=master :target: https://travis-ci.org/FNNDSC/dice_coeff
.. image:: https://img.shields.io/badge/python-3.5%2B-blue.svg :target: https://badge.fury.io/py/pl-dice_coeff
.. contents:: Table of Contents
An app to calculate model testing accuracy by dice coefficient
.. code::
python dice_coeff.py \
[-v <level>] [--verbosity <level>] \
[--version] \
[--man] \
[--meta] \
[--prediction <prediction dir>] \
[--ground_truth <ground truth dir>] \
<inputDir>
<outputDir>
dice_coeff.py is a ChRIS-based application that...
.. code::
[-v <level>] [--verbosity <level>]
Verbosity level for app. Not used currently.
[--version]
If specified, print version number.
[--man]
If specified, print (this) man page.
[--meta]
If specified, print plugin meta data.
[--prediction <prediction dir>]
The directory where the predicted images are stored.
[--ground_truth <ground truth dir>]
The directory where the ground truth images are stored.
This plugin can be run in two modes: natively as a python package or as a containerized docker image.
Using PyPI
To run from PyPI, simply do a
.. code:: bash
pip install dice_coeff
and run with
.. code:: bash
dice_coeff.py --man --predition pred --ground_truth gt /tmp /tmp
to get inline help. The app should also understand being called with only two positional arguments
.. code:: bash
dice_coeff.py --prediction pred_dir_name --ground_truth grnd_trh_dir_name /some/input/directory /destination/directory
Using ``docker run``
To run using docker, be sure to assign an "input" directory to /incoming and an output directory to /outgoing. Make sure that the $(pwd)/out directory is world writable!
Now, prefix all calls with
.. code:: bash
docker run --rm -v $(pwd)/out:/outgoing \
fnndsc/pl-dice_coeff dice_coeff.py \
Thus, getting inline help is:
.. code:: bash
mkdir in out && chmod 777 out
docker run --rm -v $(pwd)/in:/incoming -v $(pwd)/out:/outgoing \
fnndsc/pl-dice_coeff dice_coeff.py \
--man \
--prediction pred \
--ground_truth gt \
/incoming /outgoing
Content type
Image
Digest
Size
389.2 MB
Last updated
over 6 years ago
docker pull sandip117/pl-dice_coeff