def data_install_msgs():
from nipy.utils import make_datasource, DataError
for name in ('templates', 'data'):
try:
make_datasource('nipy', name)
except DataError, exception:
log.warn('%s\n%s' % ('_'*80, exception))
def check_pkg_install(archive):
''' Check that source package installs so that NIPY can read it
Parameters
----------
archive : string
filename of source archive
Returns
-------
None
'''
# extract package name from archive
pth, fname = os.path.split(archive)
fname, ext = os.path.splitext(fname)
pkg_match = pkg_re.search(fname)
if not pkg_match:
raise OSError('Could not get package name from %s' % archive)
pkg_name = pkg_match.groups()[0]
archive = os.path.abspath(archive)
with InTemporaryDirectory() as tmpdir:
extract_archive(archive, tmpdir)
out_dirs = glob('*')
if not out_dirs:
raise OSError('No directory created by package unpack')
if len(out_dirs) > 1:
raise OSError('Expecting only one directory, got %s' %
';'.join(out_dirs))
os.chdir(out_dirs[0])
caller('python setup.py install --prefix=%s' % tmpdir)
# check that nipy finds the directory and initializes it correctly
repo = make_datasource('share', 'nipy', 'nipy', pkg_name,
data_path=[tmpdir])
def check_pkg_install(archive):
''' Check that source package installs so that NIPY can read it
Parameters
----------
archive : string
filename of source archive
Returns
-------
None
'''
# extract package name from archive
pth, fname = os.path.split(archive)
fname, ext = os.path.splitext(fname)
pkg_match = pkg_re.search(fname)
if not pkg_match:
raise OSError('Could not get package name from %s' % archive)
pkg_name = pkg_match.groups()[0]
archive = os.path.abspath(archive)
with InTemporaryDirectory() as tmpdir:
extract_archive(archive, tmpdir)
out_dirs = glob('*')
if not out_dirs:
raise OSError('No directory created by package unpack')
if len(out_dirs) > 1:
raise OSError('Expecting only one directory, got %s' %
';'.join(out_dirs))
os.chdir(out_dirs[0])
caller('python setup.py install --prefix=%s' % tmpdir)
# check that nipy finds the directory and initializes it correctly
repo = make_datasource('share',
'nipy',
'nipy',
pkg_name,
data_path=[tmpdir])
"""Create a nifti image from a numpy array and an affine transform."""
import os
import numpy as np
from nipy.core.api import fromarray, Affine
from nipy.io.api import save_image, load_image
from nipy.utils import make_datasource
# Make the templates datasource
templates = make_datasource('nipy', 'templates')
# Load an image to get the array and affine
filename = templates.get_filename('ICBM152', '2mm', 'T1.nii.gz')
assert os.path.exists(filename)
# Use one of our test files to get an array and affine (as numpy array) from.
img = load_image(filename)
arr = np.asarray(img)
affine_array = img.coordmap.affine.copy()
################################################################################
# START HERE
################################################################################
# 1) Create a CoordinateMap from the affine transform which specifies
# the mapping from input to output coordinates.
# Specify the axis order of the input coordinates
