"""Create a nifti image from a numpy array and an affine transform."""

from os import path

import numpy as np

from neuroimaging.core.api import fromarray, save_image, load_image, \
    Affine, CoordinateMap

# Imports used just for development and testing.  User's typically
# would not uses these when creating an image.
from tempfile import NamedTemporaryFile
from neuroimaging.testing import assert_equal

# Load an image to get the array and affine
fn = path.join(path.expanduser('~'), '.nipy', 'tests', 'data', 
               'avg152T1.nii.gz')

if not path.exists(fn):
    raise IOError('file does not exists: %s\n' % fn)


# Use one of our test files to get an array and affine from.
img = load_image(fn)
arr = np.asarray(img)
affine = img.affine.copy()

# We use a temporary file for this example so as to not create junk
# files in the nipy directory.
tmpfile = NamedTemporaryFile(suffix='.nii.gz')

#
# 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 affine
axes_names = ['x', 'y', 'z']

# Build a CoordinateMap to create the image with
coordmap = CoordinateMap.from_affine(Affine(affine), names=axes_names, 
                                     shape=arr.shape)

# 2) Create a nipy image from the array and CoordinateMap

# Create new image
newimg = fromarray(arr, names=axes_names, coordmap=coordmap)

# 3) Save the nipy image to the specified filename
save_image(newimg, tmpfile.name)

#
# END HERE
#

# Reload and verify the affine was saved correctly.
tmpimg = load_image(tmpfile.name)
assert_equal(tmpimg.affine, 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))

Add example for creating an image from an array and an affine.
Add example for creating an image from an array and an affine.