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# emacs: -*- mode: python; py-indent-offset: 4; indent-tabs-mode: nil -*-
# vi: set ft=python sts=4 ts=4 sw=4 et:
"""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
input_coords = ['k', 'j', 'i']
output_coords = ['z','y','x']
#or
innames = ('kji')
outnames = ('zyx')
# either way works
# Build a CoordinateMap to create the image with
affine_coordmap = Affine.from_params(innames, outnames, affine_array)
# 2) Create a nipy image from the array and CoordinateMap
# Create new image
newimg = fromarray(arr, innames=innames, outnames=outnames,
coordmap=affine_coordmap)
################################################################################
# END HERE, for testing purposes only.
################################################################################
# Imports used just for development and testing. Users typically
# would not uses these when creating an image.
from tempfile import mkstemp
from nipy.testing import assert_equal
# We use a temporary file for this example so as to not create junk
# files in the nipy directory.
fd, name = mkstemp(suffix='.nii.gz')
tmpfile = open(name)
# Save the nipy image to the specified filename
save_image(newimg, tmpfile.name)
# Reload and verify the affine was saved correctly.
tmpimg = load_image(tmpfile.name)
assert_equal(tmpimg.affine, affine_coordmap.affine)
assert_equal(np.mean(tmpimg), np.mean(img))
assert_equal(np.std(tmpimg), np.std(img))
assert_equal(np.asarray(tmpimg), np.asarray(img))
# cleanup our tempfile
tmpfile.close()
os.unlink(name)
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