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‎.gitignore

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build/
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develop-eggs/
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dist/
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downloads/
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eggs/
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lib/
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lib64/
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*.egg
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# PyInstaller
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# Usually these files are written by a python script from a template
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# before PyInstaller builds the exe, so as to inject date/other infos into it.
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# Usually these files are written by a python script from a template
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# before PyInstaller builds the exe, so as to inject date/other infos into it.
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*.manifest
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*.spec
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# PyBuilder
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target/
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#Temporal files
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*~
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#PyCharm Project
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.idea/
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#reference code
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devdoc/

‎CHANGES.rst

Whitespace-only changes.

‎Makefile

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.PHONY: help clean clean-pyc clean-build list test test-all coverage docs release sdist install develop install_deps
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help:
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@echo "clean-build - remove build artifacts"
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@echo "clean-pyc - remove Python file artifacts"
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@echo "lint - check style with flake8"
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@echo "test - run tests quickly with the default Python"
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@echo "testall - run tests on every Python version with tox"
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@echo "coverage - check code coverage quickly with the default Python"
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@echo "docs - generate Sphinx HTML documentation, including API docs"
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@echo "release - package and upload a release"
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@echo "sdist - package"
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@echo "install - install"
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@echo "develop - install in development mode"
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install: install_deps
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python setup.py install
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develop: install_deps
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python setup.py develop
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install_deps:
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./install_deps.py requirements.txt
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clean: clean-build clean-pyc
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clean-build:
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rm -fr build/
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rm -fr dist/
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rm -fr *.egg-info
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clean-pyc:
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find . -name '*.pyc' -exec rm -f {} +
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find . -name '*.pyo' -exec rm -f {} +
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find . -name '*~' -exec rm -f {} +
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lint:
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flake8 boyle test
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test:
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py.test
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test-all:
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tox
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coverage:
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coverage run --source boyle setup.py test
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coverage report -m
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coverage html
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open htmlcov/index.html
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docs:
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rm -f docs/boyle.rst
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rm -f docs/modules.rst
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sphinx-apidoc -o docs/ boyle
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$(MAKE) -C docs clean
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$(MAKE) -C docs html
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open docs/_build/html/index.html
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release: clean
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python setup.py sdist upload
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python setup.py bdist_wheel upload
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sdist: clean
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python setup.py sdist
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python setup.py bdist_wheel upload
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ls -l dist

‎README.md

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‎README.rst

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.. -*- mode: rst -*-
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boyle
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=====
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Medical Image Conversion and Input/Output Tools
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Named after Robert Boyle (1627-1691), known as the first modern chemist, although he believed in the transmutation of metals to be a possibility following the alchemical tradition.
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.. image:: https://secure.travis-ci.org/alexsavio/boyle.png?branch=master
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:target: https://travis-ci.org/alexsavio/boyle
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.. image:: https://coveralls.io/repos/alexsavio/boyle/badge.png
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:target: https://coveralls.io/r/alexsavio/boyle
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Dependencies
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============
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Please see the requirements.txt file.
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Install
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=======
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Before installing it, you need all the requirements installed.
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These are listed in the requirements.txt files.
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The best way to install them is running the following command:
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for r in \`cat boyle/requirements.txt\`; do pip install $r; done
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This package uses distutils, which is the default way of installing
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python modules. To install in your home directory, use::
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python setup.py install --user
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To install for all users on Unix/Linux::
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python setup.py build
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sudo python setup.py install
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Development
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===========
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Code
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----
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Github
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~~~~~~
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You can check the latest sources with the command::
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git clone https://www.github.com/Neurita/boyle.git
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or if you have write privileges::
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git clone [email protected]:Neurita/boyle.git
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If you are going to create patches for this project, create a branch for it
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from the master branch.
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The stable releases are tagged in the repository.
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Testing
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-------
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TODO

‎boyle/__init__.py

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from .logger import setup_logging
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setup_logging()

‎boyle/commands.py

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# coding=utf-8
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#------------------------------------------------------------------------------
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#Author: Alexandre Manhaes Savio
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#Grupo de Inteligencia Computational <www.ehu.es/ccwintco>
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#Universidad del Pais Vasco UPV/EHU
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#License: 3-Clause BSD
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#2013, Alexandre Manhaes Savio
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#Use this at your own risk!
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#------------------------------------------------------------------------------
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import subprocess
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import logging
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log = logging.getLogger(__name__)
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def check_call(cmd_args):
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"""
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Calls the command
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Parameters
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----------
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cmd_args: list of str
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Command name to call and its arguments in a list.
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Returns
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-------
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Command output
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"""
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p = subprocess.Popen(cmd_args, stdout=subprocess.PIPE)
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(output, err) = p.communicate()
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return output
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def condor_call(cmd, shell=True):
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"""
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Tries to submit cmd to HTCondor, if it does not succeed, it will
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be called with subprocess.call.
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Parameters
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----------
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cmd: string
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Command to be submitted
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Returns
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-------
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"""
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log.info(cmd)
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ret = condor_submit(cmd)
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if ret != 0:
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subprocess.call(cmd, shell=shell)
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def condor_submit(cmd):
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"""
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Submits cmd to HTCondor queue
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Parameters
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----------
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cmd: string
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Command to be submitted
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Returns
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-------
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int
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returncode value from calling the submission command.
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"""
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try:
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is_running = subprocess.call('condor_status', shell=True) == 0
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except Exception as exc:
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log.exception('Could not find a running instance of HTCondor.')
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raise
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sub_cmd = 'condor_qsub -shell n -b y -r y -N ' \
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+ cmd.split()[0] + ' -m n'
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log.info('Calling: ' + sub_cmd)
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return subprocess.call(sub_cmd + ' ' + cmd, shell=True)
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# if [ $scriptmode -ne 1 ] ; then
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# sge_command="$qsub_cmd -V -cwd -shell n -b y -r y $queueCmd $pe_options -M $mailto -N $JobName -m $MailOpts $LogOpts $sge_arch $sge_hol
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# d"
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# else
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# sge_command="$qsub_cmd $LogOpts $sge_arch $sge_hold"
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# fi
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# if [ $verbose -eq 1 ] ; then
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# echo sge_command: $sge_command >&2
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# echo executing: $@ >&2
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# fi
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# exec $sge_command $@ | awk '{print $3}'
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‎boyle/config.py

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import os
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import logging
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from collections import OrderedDict
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#Known two-part file extensions
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ALLOWED_EXTS = {'.gz': {'.nii'}}
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LOG_LEVEL = logging.INFO
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#Acceptable extensions for DICOM files
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DICOM_FILE_EXTENSIONS = ['.IMA', '.DICOM', '.DCM']
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DICOM_FILE_EXTENSIONS.extend([x.lower() for x in DICOM_FILE_EXTENSIONS])
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OUTPUT_DICOM_EXTENSION = '.dcm'
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#MACUTO-DATA PATH
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TESTDATA_PATH = os.path.join(os.path.dirname(__file__), '..', 'macuto-data')
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#DICOM field weights for dicom.comparison
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DICOM_FIELD_WEIGHTS = OrderedDict([('PatientID', 1),
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('PatientName', 1),
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('PatientAddress', 0.5),
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('PatientSex', 0.2),
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('AcquisitionDate', 0.2),
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('PatientBirthDate', 0.3)])

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