def configuration(parent_package='', top_path=None):
from numpy.distutils.misc_util import Configuration, get_numpy_include_dirs
config = Configuration('restoration', parent_package, top_path)
config.add_data_dir('tests')
cython(['_unwrap_1d.pyx'], working_path=base_path)
cython(['_unwrap_2d.pyx'], working_path=base_path)
cython(['_unwrap_3d.pyx'], working_path=base_path)
cython(['_denoise_cy.pyx'], working_path=base_path)
cython(['_nl_means_denoising.pyx'], working_path=base_path)
config.add_extension('_unwrap_1d', sources=['_unwrap_1d.c'],
include_dirs=[get_numpy_include_dirs()])
unwrap_sources_2d = ['_unwrap_2d.c', 'unwrap_2d_ljmu.c']
config.add_extension('_unwrap_2d', sources=unwrap_sources_2d,
include_dirs=[get_numpy_include_dirs()])
unwrap_sources_3d = ['_unwrap_3d.c', 'unwrap_3d_ljmu.c']
config.add_extension('_unwrap_3d', sources=unwrap_sources_3d,
include_dirs=[get_numpy_include_dirs()])
config.add_extension('_denoise_cy', sources=['_denoise_cy.c'],
include_dirs=[get_numpy_include_dirs(), '../_shared'])
config.add_extension('_nl_means_denoising',
sources=['_nl_means_denoising.c'],
include_dirs=[get_numpy_include_dirs()])
return config
def configuration(parent_package="", top_path=None):
from numpy.distutils.misc_util import Configuration, get_numpy_include_dirs
config = Configuration("measure", parent_package, top_path)
config.add_data_dir("tests")
cython(["_ccomp.pyx"], working_path=base_path)
cython(["_find_contours_cy.pyx"], working_path=base_path)
cython(["_moments_cy.pyx"], working_path=base_path)
cython(["_marching_cubes_classic_cy.pyx"], working_path=base_path)
cython(["_marching_cubes_lewiner_cy.pyx"], working_path=base_path)
cython(["_pnpoly.pyx"], working_path=base_path)
config.add_extension("_ccomp", sources=["_ccomp.c"], include_dirs=[get_numpy_include_dirs()])
config.add_extension("_find_contours_cy", sources=["_find_contours_cy.c"], include_dirs=[get_numpy_include_dirs()])
config.add_extension("_moments_cy", sources=["_moments_cy.c"], include_dirs=[get_numpy_include_dirs()])
config.add_extension(
"_marching_cubes_classic_cy", sources=["_marching_cubes_classic_cy.c"], include_dirs=[get_numpy_include_dirs()]
)
config.add_extension(
"_marching_cubes_lewiner_cy", sources=["_marching_cubes_lewiner_cy.c"], include_dirs=[get_numpy_include_dirs()]
)
config.add_extension("_pnpoly", sources=["_pnpoly.c"], include_dirs=[get_numpy_include_dirs(), "../_shared"])
return config
def configuration(parent_package='', top_path=None):
from numpy.distutils.misc_util import Configuration, get_numpy_include_dirs
config = Configuration('measure', parent_package, top_path)
config.add_data_dir('tests')
cython(['_ccomp.pyx'], working_path=base_path)
cython(['_find_contours_cy.pyx'], working_path=base_path)
cython(['_moments_cy.pyx'], working_path=base_path)
cython(['_marching_cubes_cy.pyx'], working_path=base_path)
cython(['_pnpoly.pyx'], working_path=base_path)
config.add_extension('_ccomp', sources=['_ccomp.c'],
include_dirs=[get_numpy_include_dirs()])
config.add_extension('_find_contours_cy', sources=['_find_contours_cy.c'],
include_dirs=[get_numpy_include_dirs()])
config.add_extension('_moments_cy', sources=['_moments_cy.c'],
include_dirs=[get_numpy_include_dirs()])
config.add_extension('_marching_cubes_cy',
sources=['_marching_cubes_cy.c'],
include_dirs=[get_numpy_include_dirs()])
config.add_extension('_pnpoly', sources=['_pnpoly.c'],
include_dirs=[get_numpy_include_dirs(), '../_shared'])
return config
def configuration(parent_package='', top_path=None):
from numpy.distutils.misc_util import Configuration, get_numpy_include_dirs
config = Configuration('io', parent_package, top_path)
config.add_data_dir('tests')
config.add_data_files('_plugins/*.ini')
# This function tries to create C files from the given .pyx files. If
# it fails, we build the checked-in .c files.
cython(['_plugins/_colormixer.pyx', '_plugins/_histograms.pyx'],
working_path=base_path)
config.add_extension('_plugins._colormixer',
sources=['_plugins/_colormixer.c'],
include_dirs=[get_numpy_include_dirs()])
config.add_extension('_plugins._histograms',
sources=['_plugins/_histograms.c'],
include_dirs=[get_numpy_include_dirs()])
config.add_extension('_plugins._tifffile',
sources=['_plugins/tifffile.c'],
include_dirs=[get_numpy_include_dirs()])
return config
def configuration(parent_package='', top_path=None):
from numpy.distutils.misc_util import Configuration, get_numpy_include_dirs
config = Configuration('filter', parent_package, top_path)
config.add_data_dir('tests')
# This function tries to create C files from the given .pyx files. If
# it fails, try to build with pre-generated .c files.
cython(['median.pyx'], working_path=base_path)
cython(['tvdenoise.pyx'], working_path=base_path)
cython(['shock.pyx'], working_path=base_path)
cython(['nlmeans.pyx'], working_path=base_path)
cython(['perdecomp.pyx'], working_path=base_path)
config.add_extension('median', sources=['median.c'],
include_dirs=[get_numpy_include_dirs()])
config.add_extension('tvdenoise', sources=['tvdenoise.c'],
include_dirs=[get_numpy_include_dirs()])
config.add_extension('shock', sources=['shock.c'],
include_dirs=[get_numpy_include_dirs()])
config.add_extension('nlmeans', sources=['nlmeans.c'],
include_dirs=[get_numpy_include_dirs()])
config.add_extension('perdecomp', sources=['perdecomp.c'],
include_dirs=[get_numpy_include_dirs()])
return config
def configuration(parent_package='', top_path=None):
from numpy.distutils.misc_util import Configuration, get_numpy_include_dirs
from numpy.distutils.system_info import get_info
from distutils.sysconfig import get_python_inc
config = Configuration('spatial', parent_package, top_path)
config.add_data_dir('tests')
qhull_src = ['geom2.c', 'geom.c', 'global.c', 'io.c', 'libqhull.c',
'mem.c', 'merge.c', 'poly2.c', 'poly.c', 'qset.c',
'random.c', 'rboxlib.c', 'stat.c', 'user.c', 'usermem.c',
'userprintf.c', 'userprintf_rbox.c']
qhull_src = [join('qhull', 'src', x) for x in qhull_src]
inc_dirs = [get_python_inc()]
if inc_dirs[0] != get_python_inc(plat_specific=1):
inc_dirs.append(get_python_inc(plat_specific=1))
inc_dirs.append(get_numpy_include_dirs())
cfg = dict(get_info('lapack_opt'))
cfg.setdefault('include_dirs', []).extend(inc_dirs)
cfg.setdefault('define_macros', []).append(('qh_QHpointer','1'))
config.add_extension('qhull',
sources=['qhull.c'] + qhull_src,
**cfg)
config.add_extension('ckdtree', sources=['ckdtree.c']) # FIXME: cython
config.add_extension('_distance_wrap',
sources=[join('src', 'distance_wrap.c')],
depends=[join('src', 'distance_impl.h')],
include_dirs=[get_numpy_include_dirs()])
return config
def configuration(parent_package='', top_path=None):
from numpy.distutils.misc_util import Configuration, get_numpy_include_dirs
config = Configuration('filter', parent_package, top_path)
config.add_data_dir('tests')
config.add_data_dir('rank/tests')
cython(['_ctmf.pyx'], working_path=base_path)
cython(['rank/core_cy.pyx'], working_path=base_path)
cython(['rank/generic_cy.pyx'], working_path=base_path)
cython(['rank/percentile_cy.pyx'], working_path=base_path)
cython(['rank/bilateral_cy.pyx'], working_path=base_path)
config.add_extension('_ctmf', sources=['_ctmf.c'],
include_dirs=[get_numpy_include_dirs()])
config.add_extension('rank.core_cy', sources=['rank/core_cy.c'],
include_dirs=[get_numpy_include_dirs()])
config.add_extension('rank.generic_cy', sources=['rank/generic_cy.c'],
include_dirs=[get_numpy_include_dirs()])
config.add_extension(
'rank.percentile_cy', sources=['rank/percentile_cy.c'],
include_dirs=[get_numpy_include_dirs()])
config.add_extension(
'rank.bilateral_cy', sources=['rank/bilateral_cy.c'],
include_dirs=[get_numpy_include_dirs()])
return config
def configuration(parent_package='', top_path=None):
from numpy.distutils.misc_util import Configuration, get_numpy_include_dirs
from numpy.distutils.misc_util import get_info as get_misc_info
from numpy.distutils.system_info import get_info as get_sys_info
from distutils.sysconfig import get_python_inc
config = Configuration('spatial', parent_package, top_path)
config.add_data_dir('tests')
# qhull
qhull_src = ['geom2.c', 'geom.c', 'global.c', 'io.c', 'libqhull.c',
'mem.c', 'merge.c', 'poly2.c', 'poly.c', 'qset.c',
'random.c', 'rboxlib.c', 'stat.c', 'user.c', 'usermem.c',
'userprintf.c', 'userprintf_rbox.c']
qhull_src = [join('qhull', 'src', x) for x in qhull_src]
inc_dirs = [get_python_inc()]
if inc_dirs[0] != get_python_inc(plat_specific=1):
inc_dirs.append(get_python_inc(plat_specific=1))
inc_dirs.append(get_numpy_include_dirs())
cfg = dict(get_sys_info('lapack_opt'))
cfg.setdefault('include_dirs', []).extend(inc_dirs)
cfg.setdefault('define_macros', []).append(('qh_QHpointer','1'))
config.add_extension('qhull',
sources=['qhull.c'] + qhull_src,
**cfg)
# cKDTree
ckdtree_src = ['ckdtree_query.cxx',
'ckdtree_globals.cxx',
'ckdtree_cpp_exc.cxx']
ckdtree_src = [join('ckdtree', 'src', x) for x in ckdtree_src]
ckdtree_headers = ['ckdtree_decl.h',
'ckdtree_exc.h',
'ckdtree_methods.h',
'ckdtree_utils.h']
ckdtree_headers = [join('ckdtree', 'src', x) for x in ckdtree_headers]
ckdtree_dep = ['ckdtree.cxx'] + ckdtree_headers + ckdtree_src
config.add_extension('ckdtree',
sources=[join('ckdtree', 'ckdtree.cxx')] + ckdtree_src,
depends=ckdtree_dep,
include_dirs=inc_dirs + [join('ckdtree','src')])
# _distance_wrap
config.add_extension('_distance_wrap',
sources=[join('src', 'distance_wrap.c')],
depends=[join('src', 'distance_impl.h')],
include_dirs=[get_numpy_include_dirs()],
extra_info=get_misc_info("npymath"))
return config
def configuration(parent_package="", top_path=None):
from numpy.distutils.misc_util import Configuration, get_numpy_include_dirs
config = Configuration("feature", parent_package, top_path)
config.add_data_dir("tests")
cython(["_texture.pyx"], working_path=base_path)
cython(["_template.pyx"], working_path=base_path)
config.add_extension("_texture", sources=["_texture.c"], include_dirs=[get_numpy_include_dirs(), "../_shared"])
config.add_extension("_template", sources=["_template.c"], include_dirs=[get_numpy_include_dirs(), "../_shared"])
return config
def configuration(parent_package='', top_path=None):
from numpy.distutils.misc_util import Configuration, get_numpy_include_dirs
config = Configuration('feature', parent_package, top_path)
config.add_data_dir('tests')
cython(['corner_cy.pyx'], working_path=base_path)
cython(['censure_cy.pyx'], working_path=base_path)
cython(['orb_cy.pyx'], working_path=base_path)
cython(['brief_cy.pyx'], working_path=base_path)
cython(['_texture.pyx'], working_path=base_path)
cython(['_hessian_det_appx.pyx'], working_path=base_path)
cython(['_hoghistogram.pyx'], working_path=base_path)
cython(['_haar.pyx'], working_path=base_path)
config.add_extension('corner_cy', sources=['corner_cy.c'],
include_dirs=[get_numpy_include_dirs()])
config.add_extension('censure_cy', sources=['censure_cy.c'],
include_dirs=[get_numpy_include_dirs()])
config.add_extension('orb_cy', sources=['orb_cy.c'],
include_dirs=[get_numpy_include_dirs()])
config.add_extension('brief_cy', sources=['brief_cy.c'],
include_dirs=[get_numpy_include_dirs()])
config.add_extension('_texture', sources=['_texture.c'],
include_dirs=[get_numpy_include_dirs(), '../_shared'])
config.add_extension('_hessian_det_appx', sources=['_hessian_det_appx.c'],
include_dirs=[get_numpy_include_dirs()])
config.add_extension('_hoghistogram', sources=['_hoghistogram.c'],
include_dirs=[get_numpy_include_dirs(), '../_shared'])
config.add_extension('_haar', sources=['_haar.cpp'],
include_dirs=[get_numpy_include_dirs(), '../_shared'],
language="c++")
return config
def configuration(parent_package='', top_path=None):
from numpy.distutils.misc_util import Configuration, get_numpy_include_dirs
config = Configuration('filter', parent_package, top_path)
config.add_data_dir('tests')
cython(['_ctmf.pyx'], working_path=base_path)
cython(['_denoise.pyx'], working_path=base_path)
config.add_extension('_ctmf', sources=['_ctmf.c'],
include_dirs=[get_numpy_include_dirs()])
config.add_extension('_denoise', sources=['_denoise.c'],
include_dirs=[get_numpy_include_dirs(), '../_shared'])
return config
def configuration(parent_package = '', top_path = None):
from numpy.distutils.misc_util import Configuration, get_numpy_include_dirs
config = Configuration('cluster', parent_package, top_path)
config.add_data_dir('tests')
config.add_extension('_vq',
sources=[join('src', 'vq_module.c'), join('src', 'vq.c')],
include_dirs = [get_numpy_include_dirs()])
config.add_extension('_hierarchy_wrap',
sources=[join('src', 'hierarchy_wrap.c'), join('src', 'hierarchy.c')],
include_dirs = [get_numpy_include_dirs()])
return config
def configuration(parent_package='', top_path=None):
from numpy.distutils.misc_util import Configuration, get_numpy_include_dirs
config = Configuration('feature', parent_package, top_path)
config.add_data_dir('tests')
cython(['_greycomatrix.pyx'], working_path=base_path)
cython(['_template.pyx'], working_path=base_path)
config.add_extension('_greycomatrix', sources=['_greycomatrix.c'],
include_dirs=[get_numpy_include_dirs()])
config.add_extension('_template', sources=['_template.c'],
include_dirs=[get_numpy_include_dirs()])
return config
def configuration(parent_package='', top_path=None):
from numpy.distutils.misc_util import Configuration, get_numpy_include_dirs
config = Configuration('morphology', parent_package, top_path)
config.add_data_dir('tests')
cython(['ccomp.pyx'], working_path=base_path)
cython(['cmorph.pyx'], working_path=base_path)
config.add_extension('ccomp', sources=['ccomp.c'],
include_dirs=[get_numpy_include_dirs()])
config.add_extension('cmorph', sources=['cmorph.c'],
include_dirs=[get_numpy_include_dirs()])
return config
def configuration(parent_package='', top_path=None):
from numpy.distutils.misc_util import Configuration, get_numpy_include_dirs
config = Configuration('measure', parent_package, top_path)
config.add_data_dir('tests')
cython(['_find_contours.pyx'], working_path=base_path)
cython(['_moments.pyx'], working_path=base_path)
config.add_extension('_find_contours', sources=['_find_contours.c'],
include_dirs=[get_numpy_include_dirs()])
config.add_extension('_moments', sources=['_moments.c'],
include_dirs=[get_numpy_include_dirs()])
return config
def configuration(parent_package="", top_path=None):
from numpy.distutils.misc_util import Configuration, get_numpy_include_dirs
from numpy.distutils.system_info import get_info
from distutils.sysconfig import get_python_inc
config = Configuration("spatial", parent_package, top_path)
config.add_data_dir("tests")
config.add_data_dir("benchmarks")
qhull_src = [
"geom2.c",
"geom.c",
"global.c",
"io.c",
"libqhull.c",
"mem.c",
"merge.c",
"poly2.c",
"poly.c",
"qset.c",
"random.c",
"rboxlib.c",
"stat.c",
"user.c",
"usermem.c",
"userprintf.c",
"userprintf_rbox.c",
]
qhull_src = [join("qhull", "src", x) for x in qhull_src]
inc_dirs = [get_python_inc()]
if inc_dirs[0] != get_python_inc(plat_specific=1):
inc_dirs.append(get_python_inc(plat_specific=1))
inc_dirs.append(get_numpy_include_dirs())
cfg = dict(get_info("lapack_opt"))
cfg.setdefault("include_dirs", []).extend(inc_dirs)
cfg.setdefault("define_macros", []).append(("qh_QHpointer", "1"))
config.add_extension("qhull", sources=["qhull.c"] + qhull_src, **cfg)
config.add_extension("ckdtree", sources=["ckdtree.c"]) # FIXME: cython
config.add_extension(
"_distance_wrap", sources=[join("src", "distance_wrap.c")], include_dirs=[get_numpy_include_dirs()]
)
return config
def pkgconfig(*packages, **kw):
flag_map = {'-I': 'include_dirs', '-L': 'library_dirs', '-l': 'libraries'}
for token in commands.getoutput("pkg-config --libs --cflags %s" % ' '.join(packages)).split():
kw.setdefault(flag_map.get(token[:2]), []).append(token[2:])
try:
kw["libraries"].append("boost_python")
except:
kw["libraries"] = ["boost_python"]
try:
kw["library_dirs"].append(boost_library_dir)
except:
pass
try:
kw["include_dirs"].append(boost_inc_dir)
except:
pass
if not kw.has_key("extra_compile_args"):
kw["extra_compile_args"] = []
kw["include_dirs"].append(misc_util.get_numpy_include_dirs()[0])
#kw["extra_compile_args"].append('-std=c++0x')
if cpp_11_support:
kw["extra_compile_args"].append("-std=c++0x")
if debug:
kw["extra_compile_args"].append('-O0')
kw["extra_compile_args"].append('-g')
return kw
def configuration(parent_package='', top_path=None):
from numpy.distutils.misc_util import Configuration, get_numpy_include_dirs
from skimage._build import cython
config = Configuration('resample', parent_package, top_path)
config.add_data_dir('tests')
cython(['_resample.pyx'], working_path=base_path)
config.add_extension(
'_resample',
sources=['_resample.c'],
include_dirs=[get_numpy_include_dirs()],
extra_compile_args=[
"-fopenmp",
"-pthread",
"-O6",
"-march=native",
"-mtune=native",
"-funroll-all-loops",
"-fomit-frame-pointer",
"-march=native",
"-mtune=native",
"-msse4",
"-ftree-vectorize",
"-ftree-vectorizer-verbose=5",
],
extra_link_args=['-fopenmp'],
)
return config
def configuration(parent_package='', top_path=None):
from numpy.distutils.misc_util import Configuration, get_numpy_include_dirs
config = Configuration('segmentation', parent_package, top_path)
cython(['_felzenszwalb_cy.pyx',
'_quickshift_cy.pyx',
'_slic.pyx'], working_path=base_path)
config.add_extension('_felzenszwalb_cy', sources=['_felzenszwalb_cy.c'],
include_dirs=[get_numpy_include_dirs()])
config.add_extension('_quickshift_cy', sources=['_quickshift_cy.c'],
include_dirs=[get_numpy_include_dirs()])
config.add_extension('_slic', sources=['_slic.c'],
include_dirs=[get_numpy_include_dirs()])
return config
def configuration(parent_package='',top_path=None):
from numpy.distutils.misc_util import Configuration, get_numpy_include_dirs
from numpy.distutils.system_info import get_info, system_info
config = Configuration('labs', parent_package, top_path)
# fff library
config.add_include_dirs(os.path.join(LIBS,'fff'))
config.add_include_dirs(os.path.join(LIBS,'fff_python_wrapper'))
config.add_include_dirs(get_numpy_include_dirs())
sources = [os.path.join(LIBS,'fff','*.c')]
sources.append(os.path.join(LIBS,'fff_python_wrapper','*.c'))
config.add_library('cstat', sources=sources)
# Subpackages
config.add_subpackage('bindings')
config.add_subpackage('glm')
config.add_subpackage('group')
config.add_subpackage('spatial_models')
config.add_subpackage('utils')
config.add_subpackage('viz_tools')
config.add_subpackage('datasets')
config.add_subpackage('tests')
config.make_config_py() # installs __config__.py
return config
def build_extensions(self):
from numpy.distutils.misc_util import get_numpy_include_dirs
for e in self.extensions:
e.include_dirs.extend(get_numpy_include_dirs())
build_ext.build_extensions(self)
def check_numpy(_, options, package):
"""See if the NumPy extension has been installed.
"""
if options.disable_numpy:
options.excluded_features.append("-x HAS_NUMPY")
return options
try:
import numpy
# Try to find numpy/arrayobject.h.
from numpy.distutils.misc_util import get_numpy_include_dirs
include_dirs = get_numpy_include_dirs()
for inc_dir in include_dirs:
header = os.path.join(inc_dir, 'numpy', 'arrayobject.h')
if os.access(header, os.F_OK):
break
else:
print ('NumPy has been installed, '
'but its headers are not in the standard location.\n'
'%s will be build without support for NumPy.\n'
'(Linux users may have to install a development package)\n'
) % (package,)
raise ImportError
print 'Found NumPy-%s.\n' % numpy.__version__
options.extra_defines.append('HAS_NUMPY')
options.extra_include_dirs.extend(include_dirs)
except ImportError:
options.excluded_features.append("-x HAS_NUMPY")
print ("Failed to find NumPy: "
"%s will be build without support for NumPy.\n"
) % (package,)
return options
def configuration(parent_package='', top_path=None):
from numpy.distutils.misc_util import Configuration, get_numpy_include_dirs
from skimage._build import cython
config = Configuration('zmuv', parent_package, top_path)
cython(['zmuv.pyx'], working_path=base_path)
config.add_extension(
'zmuv',
sources=['zmuv.c'],
include_dirs=[get_numpy_include_dirs()],
extra_compile_args=[
"-fopenmp",
"-pthread",
"-O3",
#"-march=native",
#"-mtune=native",
#"-funroll-all-loops",
#"-fomit-frame-pointer",
#"-msse4",
#"-ftree-vectorize",
#"-ftree-vectorizer-verbose=5",
#"-ffast-math",
#"-ftree-loop-distribution",
#"-funroll-loops",
#"-ftracer",
#"-ftree-parallelize-loops=4",
#"-foptimize-register-move",
#"-funswitch-loops",
],
extra_link_args=['-fopenmp'],
)
return config
def configuration(parent_package='', top_path=None):
from numpy.distutils.misc_util import Configuration, get_numpy_include_dirs
config = Configuration('graph', parent_package, top_path)
config.add_data_dir('tests')
# This function tries to create C files from the given .pyx files. If
# it fails, try to build with pre-generated .c files.
cython(['_ncut_cy.pyx', 'rag.pyx', 'graph_merge.pyx'], working_path=base_path)
config.add_extension('_ncut_cy', sources=['_ncut_cy.c'],
include_dirs=[get_numpy_include_dirs()])
config.add_extension('rag', sources=['rag.c'],
include_dirs=[get_numpy_include_dirs()])
config.add_extension('graph_merge', sources=['graph_merge.c'],
include_dirs=[get_numpy_include_dirs()])
return config
def configuration(parent_package='', top_path=None):
from numpy.distutils.misc_util import Configuration, get_numpy_include_dirs
config = Configuration('transform', parent_package, top_path)
config.add_data_dir('tests')
cython(['_hough_transform.pyx'], working_path=base_path)
cython(['_project.pyx'], working_path=base_path)
config.add_extension('_hough_transform', sources=['_hough_transform.c'],
include_dirs=[get_numpy_include_dirs()])
config.add_extension('_project', sources=['_project.c'],
include_dirs=[get_numpy_include_dirs()])
return config
def configuration(parent_package='', top_path=None):
from numpy.distutils.misc_util import Configuration, get_numpy_include_dirs
from numpy.distutils.system_info import get_info
from distutils.sysconfig import get_python_inc
config = Configuration('spatial_016', parent_package, top_path)
inc_dirs = [get_python_inc()]
if inc_dirs[0] != get_python_inc(plat_specific=1):
inc_dirs.append(get_python_inc(plat_specific=1))
inc_dirs.append(get_numpy_include_dirs())
ckdtree_src = ['ckdtree_query.cxx',
'ckdtree_globals.cxx',
'ckdtree_cpp_exc.cxx']
ckdtree_src = [join('ckdtree', 'src', x) for x in ckdtree_src]
ckdtree_headers = ['ckdtree_decl.h',
'ckdtree_exc.h',
'ckdtree_methods.h',
'ckdtree_utils.h']
ckdtree_headers = [join('ckdtree', 'src', x) for x in ckdtree_headers]
ckdtree_dep = ['ckdtree.cxx'] + ckdtree_headers + ckdtree_src
config.add_extension('ckdtree',
sources=[join('ckdtree', 'ckdtree.cxx')] + ckdtree_src,
depends=ckdtree_dep,
include_dirs=inc_dirs + [join('ckdtree','src')])
return config
def configure_extensions():
if os.path.exists('MANIFEST'):
os.remove('MANIFEST')
# search for all cython files and build them as modules
# in the corresponding subpackage
packages = setuptools.find_packages('.')
exts = []
for package in packages:
working_path = os.path.join(*package.split('.'))
pyx_paths = glob.glob(os.path.join(working_path, '*.pyx'))
pyx_files = [path.split('/')[-1] for path in pyx_paths]
for pyx_file in pyx_files:
name = pyx_file[:-4]
full_path = os.path.join(working_path, pyx_file)
e = Extension(package + "." + name, [full_path],
include_dirs=get_numpy_include_dirs())
exts.append(e)
return exts
def configuration(parent_package = '', top_path = None):
from numpy.distutils.misc_util import Configuration, get_numpy_include_dirs
from numpy.distutils.system_info import get_info
config = Configuration('spatial', parent_package, top_path)
config.add_data_dir('tests')
qhull_src = ['geom.c', 'geom2.c', 'global.c', 'io.c', 'mem.c',
'merge.c', 'poly.c', 'poly2.c', 'qset.c', 'user.c',
'stat.c', 'qhull.c']
config.add_library('qhull',
sources=[join('qhull', 'src', x) for x in qhull_src],
# XXX: GCC dependency!
#extra_compiler_args=['-fno-strict-aliasing'],
)
lapack = dict(get_info('lapack_opt'))
try:
libs = ['qhull'] + lapack.pop('libraries')
except KeyError:
libs = ['qhull']
config.add_extension('qhull',
sources=['qhull.c'],
libraries=libs,
**lapack)
config.add_extension('ckdtree', sources=['ckdtree.c']) # FIXME: cython
config.add_extension('_distance_wrap',
sources=[join('src', 'distance_wrap.c'), join('src', 'distance.c')],
include_dirs = [get_numpy_include_dirs()])
return config
def setup_package():
# Assemble additional setup commands
cmdclass = versioneer.get_cmdclass()
cmdclass['docs'] = sphinx_builder()
cmdclass['doctest'] = sphinx_builder()
cmdclass['test'] = PyTest
# Some helper variables
version = versioneer.get_version()
docs_path = os.path.join(__location__, "doc")
docs_build_path = os.path.join(docs_path, "_build")
install_reqs = get_install_requirements("requirements.txt")
command_options = {
'docs': {'project': ('setup.py', MAIN_PACKAGE),
'version': ('setup.py', version.split('-', 1)[0]),
'release': ('setup.py', version),
'build_dir': ('setup.py', docs_build_path),
'config_dir': ('setup.py', docs_path),
'source_dir': ('setup.py', docs_path)},
'doctest': {'project': ('setup.py', MAIN_PACKAGE),
'version': ('setup.py', version.split('-', 1)[0]),
'release': ('setup.py', version),
'build_dir': ('setup.py', docs_build_path),
'config_dir': ('setup.py', docs_path),
'source_dir': ('setup.py', docs_path),
'builder': ('setup.py', 'doctest')},
'test': {'test_suite': ('setup.py', 'test'),
'cov': ('setup.py', 'puq')}}
if JUNIT_XML:
command_options['test']['junitxml'] = ('setup.py', 'junit.xml')
if COVERAGE_XML:
command_options['test']['cov_xml'] = ('setup.py', True)
if COVERAGE_HTML:
command_options['test']['cov_html'] = ('setup.py', True)
from numpy.distutils.misc_util import get_numpy_include_dirs
incdirs = get_numpy_include_dirs()
setup(name=MAIN_PACKAGE,
version=version,
url=URL,
description=DESCRIPTION,
author=AUTHOR,
author_email=EMAIL,
license=LICENSE,
long_description=read('README.rst'),
classifiers=CLASSIFIERS,
test_suite='tests',
packages=setuptools.find_packages(exclude=['tests', 'tests.*']),
install_requires=install_reqs,
setup_requires=['six'],
cmdclass=cmdclass,
tests_require=['pytest-cov', 'pytest'],
command_options=command_options,
entry_points={'console_scripts': CONSOLE_SCRIPTS},
zip_safe=False,
package_data={'puq': ['spgrid_cache.hdf5']},
)
def configuration(parent_package='', top_path=None):
from numpy.distutils.misc_util import Configuration, get_numpy_include_dirs
config = Configuration('_shared', parent_package, top_path)
config.add_data_dir('tests')
cython(['geometry.pyx'], working_path=base_path)
cython(['interpolation.pyx'], working_path=base_path)
cython(['transform.pyx'], working_path=base_path)
config.add_extension('geometry', sources=['geometry.c'])
config.add_extension('interpolation', sources=['interpolation.c'],
include_dirs=[get_numpy_include_dirs()])
config.add_extension('transform', sources=['transform.c'],
include_dirs=[get_numpy_include_dirs()])
return config
def configuration(parent_package='', top_path=None):
from numpy.distutils.misc_util import Configuration, get_numpy_include_dirs
config = Configuration('cluster', parent_package, top_path)
config.add_data_dir('tests')
config.add_extension('_vq',
sources=[('_vq.c')],
include_dirs=[get_numpy_include_dirs()])
config.add_extension('_hierarchy',
sources=[('_hierarchy.c')],
include_dirs=[get_numpy_include_dirs()])
config.add_extension('_optimal_leaf_ordering',
sources=[('_optimal_leaf_ordering.c')],
include_dirs=[get_numpy_include_dirs()])
return config
def configuration(parent_package='', top_path=None):
from numpy.distutils.misc_util import Configuration, get_numpy_include_dirs
config = Configuration('ext', parent_package, top_path)
c_files = [f for f in os.listdir(config.local_path or '.')
if f.endswith('.c') and not f.endswith('poly_operator.c')]
config.ext_modules.append(CExtension(
'libsupreme_',
c_files,
path=config.local_path,
include_dirs=[get_numpy_include_dirs()]),
)
config.add_extension('poly_operator', sources=['poly_operator.c', 'polygon.c'],
include_dirs=[get_numpy_include_dirs()])
return config
def configuration(parent_package='', top_path=None):
from numpy.distutils.misc_util import Configuration, get_numpy_include_dirs
config = Configuration('weno', parent_package, top_path)
config.add_extension(
'reconstruct',
sources=['reconstruct.c'],
include_dirs=[get_numpy_include_dirs()],
extra_compile_args=['-std=c99']) # to support 'restrict' with gcc
return config
def configuration(parent_package='', top_path=None):
from numpy.distutils.misc_util import Configuration, get_numpy_include_dirs
config = Configuration('pyfunt', parent_package, top_path)
config.add_subpackage('examples')
config.add_extension('im2col_cyt',
sources=[('im2col_cyt.c')],
include_dirs=[get_numpy_include_dirs()])
return config
def configuration(parent_package='', top_path=None):
from numpy.distutils.misc_util import Configuration, get_numpy_include_dirs
config = Configuration('segmentation', parent_package, top_path)
cython(['_felzenszwalb_cy.pyx'], working_path=base_path)
config.add_extension('_felzenszwalb_cy',
sources=['_felzenszwalb_cy.c'],
include_dirs=[get_numpy_include_dirs()])
cython(['_quickshift.pyx'], working_path=base_path)
config.add_extension('_quickshift',
sources=['_quickshift.c'],
include_dirs=[get_numpy_include_dirs()])
cython(['_slic.pyx'], working_path=base_path)
config.add_extension('_slic',
sources=['_slic.c'],
include_dirs=[get_numpy_include_dirs()])
return config
def get_extensions():
from numpy.distutils.misc_util import get_numpy_include_dirs
from pathlib import Path
extensions = [
Extension(
'waveforms.math.npufunc',
['src/multi_type_logit.c'],
include_dirs=get_numpy_include_dirs(),
library_dirs=[
str(Path(p).parent / 'lib') for p in get_numpy_include_dirs()
],
libraries=["npymath"],
# extra_compile_args=['-std=c99'],
),
# cythonize("waveforms/math/prime.pyx"),
]
return extensions
def configuration(parent_package='', top_path=None):
from numpy.distutils.misc_util import Configuration, get_numpy_include_dirs
from numpy.distutils.system_info import get_info
from distutils.sysconfig import get_python_inc
config = Configuration('spatial', parent_package, top_path)
config.add_data_dir('tests')
qhull_src = [
'geom2.c', 'geom.c', 'global.c', 'io.c', 'libqhull.c', 'mem.c',
'merge.c', 'poly2.c', 'poly.c', 'qset.c', 'random.c', 'rboxlib.c',
'stat.c', 'user.c', 'usermem.c', 'userprintf.c'
]
config.add_library(
'qhull',
sources=[join('qhull', 'src', x) for x in qhull_src],
include_dirs=[get_python_inc(),
get_numpy_include_dirs()],
# XXX: GCC dependency!
#extra_compiler_args=['-fno-strict-aliasing'],
)
lapack = dict(get_info('lapack_opt'))
try:
libs = ['qhull'] + lapack.pop('libraries')
except KeyError:
libs = ['qhull']
config.add_extension('qhull',
sources=['qhull.c'],
libraries=libs,
**lapack)
config.add_extension('ckdtree', sources=['ckdtree.c']) # FIXME: cython
config.add_extension(
'_distance_wrap',
sources=[join('src', 'distance_wrap.c'),
join('src', 'distance.c')],
include_dirs=[get_numpy_include_dirs()])
return config
def configuration(parent_package='', top_path=None):
from numpy.distutils.misc_util import Configuration, get_numpy_include_dirs
config = Configuration('_shared', parent_package, top_path)
config.add_data_dir('tests')
cython(['geometry.pyx'], working_path=base_path)
cython(['interpolation.pyx'], working_path=base_path)
cython(['transform.pyx'], working_path=base_path)
config.add_extension('geometry', sources=['geometry.c'])
config.add_extension('interpolation',
sources=['interpolation.c'],
include_dirs=[get_numpy_include_dirs()])
config.add_extension('transform',
sources=['transform.c'],
include_dirs=[get_numpy_include_dirs()])
return config
def configuration(parent_package='', top_path=None):
from numpy.distutils.system_info import get_info
from numpy.distutils.misc_util import Configuration, get_numpy_include_dirs
config = Configuration('cluster', parent_package, top_path)
blas_opt = get_info('lapack_opt')
config.add_data_dir('tests')
config.add_extension('_vq',
sources=[('_vq.c')],
include_dirs=[get_numpy_include_dirs()],
extra_info=blas_opt)
config.add_extension('_hierarchy',
sources=[('_hierarchy.c')],
include_dirs=[get_numpy_include_dirs()])
return config
def configuration(parent_package='', top_path=None):
from numpy.distutils.misc_util import Configuration, get_numpy_include_dirs
config = Configuration('feature', parent_package, top_path)
config.add_data_dir('tests')
cython(['_cascade.pyx'], working_path=base_path)
cython(['corner_cy.pyx'], working_path=base_path)
cython(['censure_cy.pyx'], working_path=base_path)
cython(['orb_cy.pyx'], working_path=base_path)
cython(['brief_cy.pyx'], working_path=base_path)
cython(['_texture.pyx'], working_path=base_path)
cython(['_hessian_det_appx.pyx'], working_path=base_path)
cython(['_hoghistogram.pyx'], working_path=base_path)
cython(['_haar.pyx'], working_path=base_path)
config.add_extension('_cascade',
sources=['_cascade.cpp'],
include_dirs=[get_numpy_include_dirs()],
language="c++")
config.add_extension('corner_cy',
sources=['corner_cy.c'],
include_dirs=[get_numpy_include_dirs()])
config.add_extension('censure_cy',
sources=['censure_cy.c'],
include_dirs=[get_numpy_include_dirs()])
config.add_extension('orb_cy',
sources=['orb_cy.c'],
include_dirs=[get_numpy_include_dirs()])
config.add_extension('brief_cy',
sources=['brief_cy.c'],
include_dirs=[get_numpy_include_dirs()])
config.add_extension('_texture',
sources=['_texture.c'],
include_dirs=[get_numpy_include_dirs(), '../_shared'])
config.add_extension('_hessian_det_appx',
sources=['_hessian_det_appx.c'],
include_dirs=[get_numpy_include_dirs()])
config.add_extension('_hoghistogram',
sources=['_hoghistogram.c'],
include_dirs=[get_numpy_include_dirs(), '../_shared'])
config.add_extension('_haar',
sources=['_haar.cpp'],
include_dirs=[get_numpy_include_dirs(), '../_shared'],
language="c++")
return config
def configuration(parent_package='', top_path=None):
from numpy.distutils.misc_util import Configuration, get_numpy_include_dirs
config = Configuration('graph', parent_package, top_path)
config.add_data_dir('tests')
# This function tries to create C files from the given .pyx files. If
# it fails, try to build with pre-generated .c files.
cython(['_spath.pyx', '_mcp.pyx', 'heap.pyx'], working_path=base_path)
config.add_extension('_spath',
sources=['_spath.c'],
include_dirs=[get_numpy_include_dirs()])
config.add_extension('_mcp',
sources=['_mcp.c'],
include_dirs=[get_numpy_include_dirs()])
config.add_extension('heap',
sources=['heap.c'],
include_dirs=[get_numpy_include_dirs()])
return config
def configuration(parent_package='', top_path=None):
from numpy.distutils.misc_util import Configuration, get_numpy_include_dirs
config = Configuration('LUT', parent_package, top_path)
config.add_extension('lut',
sources=['lut.c'],
include_dirs=[get_numpy_include_dirs()],
extra_compile_args=['-O3', '-fno-exceptions'],
extra_link_args=linkArgs)
return config
def configuration(parent_package = '', top_path = None):
from numpy.distutils.misc_util import Configuration, get_numpy_include_dirs
config = Configuration('cModels', parent_package, top_path)
config.add_extension('gauss_app',
sources=['gauss_ap.c'],
include_dirs = [get_numpy_include_dirs()],
extra_compile_args = ['-O3', '-fno-exceptions', '-ffast-math', '-march=nocona', '-mtune=nocona'],
extra_link_args=linkArgs)
return config
def configuration(parent_package='', top_path=None):
from numpy.distutils.misc_util import Configuration, get_numpy_include_dirs
config = Configuration('nurbs', parent_package, top_path)
config.add_extension('_Bas', ['_Bas.c'],
include_dirs=[get_numpy_include_dirs()],
)
config.add_data_dir('doc')
return config
def configuration(parent_package='', top_path=None):
from numpy.distutils.misc_util import \
Configuration, get_numpy_include_dirs
config = Configuration('samplers', parent_package, top_path)
config.add_extension('libsampler',
sources=['libsampler.cpp'],
include_dirs=[get_numpy_include_dirs()])
return config
def configuration(parent_package='', top_path=None):
from numpy.distutils.misc_util import Configuration, get_numpy_include_dirs
nxheader = join(
get_numpy_include_dirs()[0],
'numpy',
)
confgr = Configuration('hydroclimpy', parent_package, top_path)
#
confgr.add_data_files('hydroclimpyrc', 'hydroclimpyrc.template')
confgr.add_subpackage('stats')
return confgr
def configuration(parent_package = '', top_path = None):
from numpy.distutils.misc_util import Configuration, get_numpy_include_dirs
config = Configuration('astigmatism', parent_package, top_path)
config.add_extension('astiglookup',
sources=['astiglookup.c'],
include_dirs = [get_numpy_include_dirs()],
extra_compile_args = ['-O3', '-fno-exceptions', '-march=native', '-mtune=native'],
extra_link_args=linkArgs)
return config
def configuration(parent_package='', top_path=None):
from numpy.distutils.misc_util import Configuration, get_numpy_include_dirs
config = Configuration('io', parent_package, top_path)
config.add_data_files('_plugins/*.ini')
# This function tries to create C files from the given .pyx files. If
# it fails, we build the checked-in .c files.
cython(['_plugins/_colormixer.pyx', '_plugins/_histograms.pyx'],
working_path=base_path)
config.add_extension('_plugins._colormixer',
sources=['_plugins/_colormixer.c'],
include_dirs=[get_numpy_include_dirs()])
config.add_extension('_plugins._histograms',
sources=['_plugins/_histograms.c'],
include_dirs=[get_numpy_include_dirs()])
return config
def configuration(parent_package='', top_path=None):
from numpy.distutils.misc_util import Configuration, get_numpy_include_dirs
config = Configuration('feature', parent_package, top_path)
config.add_data_files('orb_descriptor_positions.txt')
cython(['corner_cy.pyx',
'censure_cy.pyx',
'orb_cy.pyx',
'_texture.pyx',
'_hoghistogram.pyx',
'_sift.pyx',
], working_path=base_path)
# _haar uses c++, so it must be cythonized separately
cython(['_cascade.pyx',
'_haar.pyx'], working_path=base_path)
config.add_extension('_cascade', sources=['_cascade.cpp'],
include_dirs=[get_numpy_include_dirs()],
language="c++")
config.add_extension('corner_cy', sources=['corner_cy.c'],
include_dirs=[get_numpy_include_dirs()])
config.add_extension('censure_cy', sources=['censure_cy.c'],
include_dirs=[get_numpy_include_dirs()])
config.add_extension('orb_cy', sources=['orb_cy.c'],
include_dirs=[get_numpy_include_dirs()])
config.add_extension('_texture', sources=['_texture.c'],
include_dirs=[get_numpy_include_dirs(), '../_shared'])
config.add_extension('_hoghistogram', sources=['_hoghistogram.c'],
include_dirs=[get_numpy_include_dirs(), '../_shared'])
config.add_extension('_haar', sources=['_haar.cpp'],
include_dirs=[get_numpy_include_dirs(), '../_shared'],
language="c++")
config.add_extension('_sift', sources=['_sift.c'],
include_dirs=[get_numpy_include_dirs(), '../_shared'])
# pythran submodules
pythran.config.logger.setLevel(logging.INFO)
ext = pythran.dist.PythranExtension(
'skimage.feature.brief_cy',
sources=["skimage/feature/brief_pythran.py"],
config=['compiler.blas=none'])
config.ext_modules.append(ext)
ext = pythran.dist.PythranExtension(
'skimage.feature._hessian_det_appx',
sources=["skimage/feature/_hessian_det_appx_pythran.py"],
config=['compiler.blas=none'])
config.ext_modules.append(ext)
return config
def configuration(parent_package = '', top_path = None):
from numpy.distutils.misc_util import Configuration, get_numpy_include_dirs
config = Configuration('sensicam', parent_package, top_path)
config.add_extension('_sensicam',
sources=["sensicam.i","Cam.cpp"],
libraries=["senntcam"],
library_dirs = ["."],
include_dirs = [get_numpy_include_dirs(), '.'],
extra_compile_args = ['-O3'])
return config
def configuration(parent_package='', top_path=None):
from numpy.distutils.misc_util import Configuration, get_numpy_include_dirs
config = Configuration('draw', parent_package, top_path)
cython(['_draw.pyx'], working_path=base_path)
config.add_extension('_draw',
sources=['_draw.c'],
include_dirs=[get_numpy_include_dirs(), '../_shared'])
return config
def configuration(parent_package = '', top_path = None):
from numpy.distutils.misc_util import Configuration, get_numpy_include_dirs
config = Configuration('countdir', parent_package, top_path)
if not sys.platform == 'win32':
config.add_extension('countdir',
sources=['countdir.c'],
include_dirs = [get_numpy_include_dirs()],
extra_compile_args = ['-O3', '-fno-exceptions', '-ffast-math', '-march=nocona', '-mtune=nocona'],
extra_link_args=linkArgs)
return config
def configuration(parent_package='', top_path=None):
from numpy.distutils.misc_util import Configuration, get_numpy_include_dirs
config = Configuration('cluster', parent_package, top_path)
config.add_data_dir('tests')
config.add_extension(
'_vq',
sources=[join('src', 'vq_module.c'),
join('src', 'vq.c')],
include_dirs=[get_numpy_include_dirs()],
define_macros=DEFINE_MACROS)
config.add_extension(
'_hierarchy_wrap',
sources=[join('src', 'hierarchy_wrap.c'),
join('src', 'hierarchy.c')],
include_dirs=[get_numpy_include_dirs()],
define_macros=DEFINE_MACROS)
return config
def configuration(parent_package='', top_path=None):
from numpy.distutils.misc_util import Configuration, get_numpy_include_dirs
config = Configuration()
cython(['snrm2_.pyx'], working_path=base_path)
config.add_extension('snrm2_', sources=['snrm2_.c'],
include_dirs=[get_numpy_include_dirs()],
libraries=['blas'],
)
return config
def configuration(parent_package='', top_path=None):
from numpy.distutils.misc_util import Configuration, get_numpy_include_dirs
config = Configuration('feature', parent_package, top_path)
config.add_data_dir('tests')
cython(['corner_cy.pyx'], working_path=base_path)
cython(['_brief_cy.pyx'], working_path=base_path)
cython(['_texture.pyx'], working_path=base_path)
cython(['_template.pyx'], working_path=base_path)
config.add_extension('corner_cy', sources=['corner_cy.c'],
include_dirs=[get_numpy_include_dirs()])
config.add_extension('_brief_cy', sources=['_brief_cy.c'],
include_dirs=[get_numpy_include_dirs()])
config.add_extension('_texture', sources=['_texture.c'],
include_dirs=[get_numpy_include_dirs(), '../_shared'])
config.add_extension('_template', sources=['_template.c'],
include_dirs=[get_numpy_include_dirs(), '../_shared'])
return config
def configuration(parent_package='', top_path=None):
from numpy.distutils.misc_util import Configuration, get_numpy_include_dirs
config = Configuration('resolve', parent_package, top_path)
config.add_extension('operators',
sources=['operators.c'],
include_dirs=[get_numpy_include_dirs()])
config.add_data_dir('tests')
return config
def configuration(parent_package = '', top_path = None):
from numpy.distutils.misc_util import Configuration, get_numpy_include_dirs
from glob import glob
config = Configuration('abf', parent_package, top_path)
config.add_extension('abf',
sources=['abf.cpp', 'axon/AxAbfFio32/*.cpp', 'axon/Common/*.cpp', 'axon/Common/*.c'],
include_dirs = [get_numpy_include_dirs()] + getBoostInclude(),
extra_compile_args = ['-O3', '-fno-exceptions', '-D__UNIX__','-D__STF__'])
return config
def configuration(parent_package='', top_path=None):
from numpy.distutils.misc_util import Configuration, get_numpy_include_dirs
config = Configuration('filter', parent_package, top_path)
config.add_data_dir('tests')
cython(['_ctmf.pyx'], working_path=base_path)
config.add_extension('_ctmf', sources=['_ctmf.c'],
include_dirs=[get_numpy_include_dirs()])
return config
def configuration(parent_package='', top_path=None):
from numpy.distutils.misc_util import Configuration, get_numpy_include_dirs
config = Configuration('transform', parent_package, top_path)
cython(['_hough_transform.pyx', '_warps_cy.pyx', '_radon_transform.pyx'],
working_path=base_path)
config.add_extension('_hough_transform',
sources=['_hough_transform.c'],
include_dirs=[get_numpy_include_dirs()])
config.add_extension('_warps_cy',
sources=['_warps_cy.c'],
include_dirs=[get_numpy_include_dirs(), '../_shared'])
config.add_extension('_radon_transform',
sources=['_radon_transform.c'],
include_dirs=[get_numpy_include_dirs()])
return config
def configuration(parent_package='', top_path=None):
from numpy.distutils.misc_util import Configuration, get_numpy_include_dirs
config = Configuration('measure', parent_package, top_path)
config.add_data_dir('tests')
cython(['_find_contours.pyx'], working_path=base_path)
cython(['_moments.pyx'], working_path=base_path)
cython(['_marching_cubes_cy.pyx'], working_path=base_path)
config.add_extension('_find_contours',
sources=['_find_contours.c'],
include_dirs=[get_numpy_include_dirs()])
config.add_extension('_moments',
sources=['_moments.c'],
include_dirs=[get_numpy_include_dirs()])
config.add_extension('_marching_cubes_cy',
sources=['_marching_cubes_cy.c'],
include_dirs=[get_numpy_include_dirs()])
return config
