Revision ed19f0bd5f10867fd51849ff2a875b57fabc9761 authored by Joost van Griethuysen on 10 January 2018, 17:37:44 UTC, committed by Joost van Griethuysen on 10 January 2018, 17:37:44 UTC
Add a function (`LoadJSONParams`) in the featureextractor, which accepts a JSON formatted string. This string will then be validated similar to a parameter file and if successful, used to customize the extraction.
1 parent fb7590c
setup.py
#!/usr/bin/env python
from distutils import sysconfig
import platform
import sys
import numpy
from setuptools import Extension, setup
from setuptools.command.test import test as TestCommand
import versioneer
# Check if current PyRadiomics is compatible with current python installation (> 2.6, 64 bits)
if sys.version_info < (2, 6, 0):
raise Exception("pyradiomics > 0.9.7 requires python 2.6 or later")
if platform.architecture()[0].startswith('32'):
raise Exception('PyRadiomics requires 64 bits python')
with open('requirements.txt', 'r') as fp:
requirements = list(filter(bool, (line.strip() for line in fp)))
with open('requirements-dev.txt', 'r') as fp:
dev_requirements = list(filter(bool, (line.strip() for line in fp)))
with open('requirements-setup.txt', 'r') as fp:
setup_requirements = list(filter(bool, (line.strip() for line in fp)))
class NoseTestCommand(TestCommand):
"""Command to run unit tests using nose driver after in-place build"""
user_options = TestCommand.user_options + [
("args=", None, "Arguments to pass to nose"),
]
def initialize_options(self):
self.args = []
TestCommand.initialize_options(self)
def finalize_options(self):
TestCommand.finalize_options(self)
if self.args:
self.args = __import__('shlex').split(self.args)
def run_tests(self):
# Run nose ensuring that argv simulates running nosetests directly
nose_args = ['nosetests']
nose_args.extend(self.args)
__import__('nose').run_exit(argv=nose_args)
commands = versioneer.get_cmdclass()
commands['test'] = NoseTestCommand
incDirs = [sysconfig.get_python_inc(), numpy.get_include()]
ext = [Extension("radiomics._cmatrices", ["radiomics/src/_cmatrices.c", "radiomics/src/cmatrices.c"],
include_dirs=incDirs),
Extension("radiomics._cshape", ["radiomics/src/_cshape.c", "radiomics/src/cshape.c"],
include_dirs=incDirs)]
setup(
name='pyradiomics',
url='http://github.com/Radiomics/pyradiomics#readme',
author='pyradiomics community',
author_email='pyradiomics@googlegroups.com',
version=versioneer.get_version(),
cmdclass=commands,
packages=['radiomics', 'radiomics.scripts'],
ext_modules=ext,
zip_safe=False,
package_data={'radiomics': ['schemas/paramSchema.yaml', 'schemas/schemaFuncs.py']},
entry_points={
'console_scripts': [
'pyradiomics=radiomics.scripts.commandline:main',
'pyradiomicsbatch=radiomics.scripts.commandlinebatch:main'
]},
description='Radiomics features library for python',
license='BSD License',
classifiers=[
'Development Status :: 5 - Production/Stable',
'Environment :: Console',
'Intended Audience :: Developers',
'Intended Audience :: Science/Research',
'License :: OSI Approved :: BSD License',
'Operating System :: OS Independent',
'Programming Language :: C',
'Programming Language :: Python :: 2',
'Programming Language :: Python :: 2.7',
'Programming Language :: Python :: 3.4',
'Programming Language :: Python :: 3.5',
'Topic :: Scientific/Engineering :: Bio-Informatics',
],
keywords='radiomics cancerimaging medicalresearch computationalimaging',
install_requires=requirements,
test_suite='nose.collector',
tests_require=dev_requirements,
setup_requires=setup_requirements
)
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