first commit

.gitignore

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+*~
+*.DS_Store
+*.egg-info
+__pycache__
+docs/build
+.coverage
+htmlcov
+.docker
+.idea/

Dockerfile

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+# Docker file for mriseg ChRIS plugin app
+#
+# Build with
+#
+#   docker build -t <name> .
+#
+# For example if building a local version, you could do:
+#
+#   docker build -t local/pl-mriseg .
+#
+# In the case of a proxy (located at 192.168.13.14:3128), do:
+#
+#    docker build --build-arg http_proxy=http://192.168.13.14:3128 --build-arg UID=$UID -t local/pl-mriseg .
+#
+# To run an interactive shell inside this container, do:
+#
+#   docker run -ti --entrypoint /bin/bash local/pl-mriseg
+#
+# To pass an env var HOST_IP to container, do:
+#
+#   docker run -ti -e HOST_IP=$(ip route | grep -v docker | awk '{if(NF==11) print $9}') --entrypoint /bin/bash local/pl-mriseg
+#
+
+
+
+FROM fnndsc/ubuntu-python3:latest
+MAINTAINER fnndsc "[email protected]"
+
+ENV APPROOT="/usr/src/mriseg"
+COPY ["mriseg", "${APPROOT}"]
+COPY ["requirements.txt", "${APPROOT}"]
+
+WORKDIR $APPROOT
+
+RUN pip install --upgrade pip
+RUN pip install -r requirements.txt
+
+CMD ["mriseg.py", "--help"]

LICENSE

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+MIT License
+
+Copyright (c) 2017 FNNDSC / BCH
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all
+copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+SOFTWARE.

README.rst

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+pl-mriseg
+================================
+
+.. image:: https://badge.fury.io/py/mriseg.svg
+    :target: https://badge.fury.io/py/mriseg
+
+.. image:: https://travis-ci.org/FNNDSC/mriseg.svg?branch=master
+    :target: https://travis-ci.org/FNNDSC/mriseg
+
+.. image:: https://img.shields.io/badge/python-3.5%2B-blue.svg
+    :target: https://badge.fury.io/py/pl-mriseg
+
+.. contents:: Table of Contents
+
+
+Abstract
+--------
+
+An app to perform 3D segmentation on Brain MRI data
+
+
+Synopsis
+--------
+
+.. code::
+
+    python mriseg.py                                           \
+        [-v <level>] [--verbosity <level>]                          \
+        [--version]                                                 \
+        [--man]                                                     \
+        [--meta]                                                    \
+        <inputDir>
+        <outputDir> 
+
+Description
+-----------
+
+``mriseg.py`` is a ChRIS-based application that...
+
+Agruments
+---------
+
+.. 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.
+
+
+Run
+----
+
+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 mriseg
+
+and run with
+
+.. code:: bash
+
+    mriseg.py --man /tmp /tmp
+
+to get inline help. The app should also understand being called with only two positional arguments
+
+.. code:: bash
+
+    mriseg.py /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-mriseg mriseg.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-mriseg mriseg.py                        \
+            --man                                                       \
+            /incoming /outgoing
+
+Examples
+--------
+
+
+
+
+

mriseg/mriseg.py

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+#!/usr/bin/env python                                            
+#
+# mriseg ds ChRIS plugin app
+#
+# (c) 2016-2019 Fetal-Neonatal Neuroimaging & Developmental Science Center
+#                   Boston Children's Hospital
+#
+#              http://childrenshospital.org/FNNDSC/
+#                        [email protected]
+#
+
+
+import os
+import sys
+sys.path.append(os.path.dirname(__file__))
+
+# import the Chris app superclass
+from chrisapp.base import ChrisApp
+
+
+Gstr_title = """
+
+Generate a title from 
+http://patorjk.com/software/taag/#p=display&f=Doom&t=mriseg
+
+"""
+
+Gstr_synopsis = """
+
+(Edit this in-line help for app specifics. At a minimum, the 
+flags below are supported -- in the case of DS apps, both
+positional arguments <inputDir> and <outputDir>; for FS apps
+only <outputDir> -- and similarly for <in> <out> directories
+where necessary.)
+
+    NAME
+
+       mriseg.py 
+
+    SYNOPSIS
+
+        python mriseg.py                                         \\
+            [-h] [--help]                                               \\
+            [--json]                                                    \\
+            [--man]                                                     \\
+            [--meta]                                                    \\
+            [--savejson <DIR>]                                          \\
+            [-v <level>] [--verbosity <level>]                          \\
+            [--version]                                                 \\
+            <inputDir>                                                  \\
+            <outputDir> 
+
+    BRIEF EXAMPLE
+
+        * Bare bones execution
+
+            mkdir in out && chmod 777 out
+            python mriseg.py   \\
+                                in    out
+
+    DESCRIPTION
+
+        `mriseg.py` ...
+
+    ARGS
+
+        [-h] [--help]
+        If specified, show help message and exit.
+        
+        [--json]
+        If specified, show json representation of app and exit.
+        
+        [--man]
+        If specified, print (this) man page and exit.
+
+        [--meta]
+        If specified, print plugin meta data and exit.
+        
+        [--savejson <DIR>] 
+        If specified, save json representation file to DIR and exit. 
+        
+        [-v <level>] [--verbosity <level>]
+        Verbosity level for app. Not used currently.
+        
+        [--version]
+        If specified, print version number and exit. 
+
+"""
+
+
+class Mriseg(ChrisApp):
+    """
+    An app to perform 3D segmentation on Brain MRI data.
+    """
+    AUTHORS                 = 'Sandip Samal ([email protected])'
+    SELFPATH                = os.path.dirname(os.path.abspath(__file__))
+    SELFEXEC                = os.path.basename(__file__)
+    EXECSHELL               = 'python3'
+    TITLE                   = '3D segmentation app'
+    CATEGORY                = ''
+    TYPE                    = 'ds'
+    DESCRIPTION             = 'An app to perform 3D segmentation on Brain MRI data'
+    DOCUMENTATION           = 'http://wiki'
+    VERSION                 = '0.1'
+    ICON                    = '' # url of an icon image
+    LICENSE                 = 'Opensource (MIT)'
+    MAX_NUMBER_OF_WORKERS   = 1  # Override with integer value
+    MIN_NUMBER_OF_WORKERS   = 1  # Override with integer value
+    MAX_CPU_LIMIT           = '' # Override with millicore value as string, e.g. '2000m'
+    MIN_CPU_LIMIT           = '' # Override with millicore value as string, e.g. '2000m'
+    MAX_MEMORY_LIMIT        = '' # Override with string, e.g. '1Gi', '2000Mi'
+    MIN_MEMORY_LIMIT        = '' # Override with string, e.g. '1Gi', '2000Mi'
+    MIN_GPU_LIMIT           = 0  # Override with the minimum number of GPUs, as an integer, for your plugin
+    MAX_GPU_LIMIT           = 0  # Override with the maximum number of GPUs, as an integer, for your plugin
+
+    # Use this dictionary structure to provide key-value output descriptive information
+    # that may be useful for the next downstream plugin. For example:
+    #
+    # {
+    #   "finalOutputFile":  "final/file.out",
+    #   "viewer":           "genericTextViewer",
+    # }
+    #
+    # The above dictionary is saved when plugin is called with a ``--saveoutputmeta``
+    # flag. Note also that all file paths are relative to the system specified
+    # output directory.
+    OUTPUT_META_DICT = {}
+
+    def define_parameters(self):
+        """
+        Define the CLI arguments accepted by this plugin app.
+        Use self.add_argument to specify a new app argument.
+        """
+
+    def run(self, options):
+        """
+        Define the code to be run by this plugin app.
+        """
+        print(Gstr_title)
+        print('Version: %s' % self.get_version())
+
+    def show_man_page(self):
+        """
+        Print the app's man page.
+        """
+        print(Gstr_synopsis)
+
+
+# ENTRYPOINT
+if __name__ == "__main__":
+    chris_app = Mriseg()
+    chris_app.launch()

mriseg/tests/test_mriseg.py

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+
+from unittest import TestCase
+from unittest import mock
+from mriseg.mriseg import Mriseg
+
+
+class MrisegTests(TestCase):
+    """
+    Test Mriseg.
+    """
+    def setUp(self):
+        self.app = Mriseg()
+
+    def test_run(self):
+        """
+        Test the run code.
+        """
+        args = []
+        if self.app.TYPE == 'ds':
+            args.append('inputdir') # you may want to change this inputdir mock
+        args.append('outputdir')  # you may want to change this outputdir mock
+
+        # you may want to add more of your custom defined optional arguments to test
+        # your app with
+        # eg.
+        # args.append('--custom-int')
+        # args.append(10)
+
+        options = self.app.parse_args(args)
+        self.app.run(options)
+
+        # write your own assertions
+        self.assertEqual(options.outputdir, 'outputdir')