def test_optional_package():
pkg, have_pkg, _ = optional_package('fake_pkg')
npt.assert_raises(TripWireError, pkg)
assert_false(have_pkg)
pkg, have_pkg, _ = optional_package('os')
assert_true(isinstance(pkg, ModuleType))
npt.assert_equal(pkg.__name__, 'os')
assert_true(have_pkg)
def get_info(verbose=False):
"""Return dict describing the context of this package.
Parameters
------------
pkg_path : str
path containing __init__.py for package
Returns
----------
context : dict
with named parameters of interest
"""
from fury.optpkg import optional_package
from os.path import dirname
import sys
import numpy
import scipy
import vtk
mpl, have_mpl, _ = optional_package('matplotlib')
dipy, have_dipy, _ = optional_package('dipy')
info = dict(fury_version=__version__,
pkg_path=dirname(__file__),
commit_hash=__revision_id__,
sys_version=sys.version,
sys_executable=sys.executable,
sys_platform=sys.platform,
numpy_version=numpy.__version__,
scipy_version=scipy.__version__,
vtk_version=vtk.vtkVersion.GetVTKVersion())
d_mpl = dict(matplotlib_version=mpl.__version__) if have_mpl else {}
d_dipy = dict(dipy_version=dipy.__version__) if have_dipy else {}
info.update(d_mpl)
info.update(d_dipy)
if verbose:
print('\n'.join(['{0}: {1}'.format(k, v) for k, v in info.items()]))
return info
from warnings import warn
import json
from os.path import join as pjoin
import numpy as np
import vtk
from fury.data import DATA_DIR
# Allow import, but disable doctests if we don't have matplotlib
from fury.optpkg import optional_package
cm, have_matplotlib, _ = optional_package('matplotlib.cm')
def colormap_lookup_table(scale_range=(0, 1),
hue_range=(0.8, 0),
saturation_range=(1, 1),
value_range=(0.8, 0.8)):
"""Lookup table for the colormap.
Parameters
----------
scale_range : tuple
It can be anything e.g. (0, 1) or (0, 255). Usually it is the mininum
and maximum value of your data. Default is (0, 1).
hue_range : tuple of floats
HSV values (min 0 and max 1). Default is (0.8, 0).
saturation_range : tuple of floats
HSV values (min 0 and max 1). Default is (1, 1).
value_range : tuple of floats
HSV value (min 0 and max 1). Default is (0.8, 0.8).
import numpy.testing as npt
from scipy.ndimage.measurements import center_of_mass
from scipy.signal import convolve
from fury import shaders
from fury import actor, window, primitive as fp
from fury.actor import grid
from fury.decorators import skip_osx, skip_win
from fury.utils import shallow_copy, rotate
from fury.testing import assert_greater, assert_greater_equal
from fury.primitive import prim_sphere
# Allow import, but disable doctests if we don't have dipy
from fury.optpkg import optional_package
# dipy, have_dipy, _ = optional_package('dipy')
matplotlib, have_matplotlib, _ = optional_package('matplotlib')
# if have_dipy:
# from dipy.data import get_sphere
# from dipy.reconst.shm import sh_to_sf_matrix
# from dipy.tracking.streamline import (center_streamlines,
# transform_streamlines)
# from dipy.align.tests.test_streamlinear import fornix_streamlines
# from dipy.reconst.dti import color_fa, fractional_anisotropy
if have_matplotlib:
import matplotlib.pyplot as plt
from fury.convert import matplotlib_figure_to_numpy
class Sphere():
vertices = None
import os
import numpy as np
from fury import actor, window
import numpy.testing as npt
from fury.tmpdirs import InTemporaryDirectory
from fury.decorators import xvfb_it
from tempfile import mkstemp
# Allow import, but disable doctests if we don't have dipy
from fury.optpkg import optional_package
dipy, have_dipy, _ = optional_package('dipy')
if have_dipy:
from dipy.tracking.streamline import (center_streamlines,
transform_streamlines)
from dipy.align.tests.test_streamlinear import fornix_streamlines
from dipy.reconst.dti import color_fa, fractional_anisotropy
from dipy.data import get_sphere
use_xvfb = os.environ.get('TEST_WITH_XVFB', False)
skip_it = use_xvfb == 'skip'
@npt.dec.skipif(skip_it)
@xvfb_it
def test_slicer():
renderer = window.renderer()
data = (255 * np.random.rand(50, 50, 50))
affine = np.eye(4)
import pytest
import numpy as np
import numpy.testing as npt
from scipy.ndimage.measurements import center_of_mass
from fury import shaders
from fury import actor, window
from fury.actor import grid
from fury.primitive import prim_sphere
from fury.utils import shallow_copy, rotate
from fury.testing import assert_greater, assert_greater_equal
# Allow import, but disable doctests if we don't have dipy
from fury.optpkg import optional_package
dipy, have_dipy, _ = optional_package('dipy')
matplotlib, have_matplotlib, _ = optional_package('matplotlib')
if have_dipy:
from dipy.data import get_sphere
from dipy.tracking.streamline import (center_streamlines,
transform_streamlines)
from dipy.align.tests.test_streamlinear import fornix_streamlines
from dipy.reconst.dti import color_fa, fractional_anisotropy
if have_matplotlib:
import matplotlib.pyplot as plt
from fury.convert import matplotlib_figure_to_numpy
def test_slicer(verbose=False):
#!/usr/bin/python3 -u
from dipy.tracking.utils import length
from fury import actor, window
from fury.optpkg import optional_package
from nibabel.streamlines.tck import TckFile
from nibabel.streamlines.trk import TrkFile
from PIL import Image
import itertools
import json
import nibabel as nib
import numpy as np
import os
xvfbwrapper, has_xvfbwrapper, setup_module = optional_package('xvfbwrapper')
if has_xvfbwrapper:
from xvfbwrapper import Xvfb
_VIEW_PARAMS = [{
'view': 'axial',
'cam_pos': (-5.58, 84.98, 467.47),
'focal_pnt': (-8.92, -16.15, 4.47),
'view_up': (0.00, 1.00, -0.21)
}, {
'view': 'sagittal_left',
'cam_pos': (-482.32, 3.58, -6.28),
'focal_pnt': (-8.92, -16.15, 4.47),
'view_up': (0.00, 0.00, 1.00)
}, {
'view': 'coronal',
-----
this file is copied (with minor modifications) from the Nibabel.
https://github.com/nipy/nibabel. See COPYING file distributed along with
the Nibabel package for the copyright and license terms.
"""
import functools
import warnings
import re
from fury import __version__
from fury.optpkg import optional_package
# packaging.version.parse is a third-party utility but is used by setuptools
# (so probably already installed) and is conformant to the current PEP 440.
# But just if it is not the case, we use distutils
packaging, have_pkg, _ = optional_package('setuptools.extern.packaging')
_LEADING_WHITE = re.compile(r'^(\s*)')
class ExpiredDeprecationError(RuntimeError):
"""Error for expired deprecation.
Error raised when a called function or method has passed out of its
deprecation period.
"""
pass
