old_contents: """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.data import template_pjoin
  
  # Load an image to get the array and affine
  filename = template_pjoin('avg152T1.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)
  
  
new_contents: """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.data_files import get_data_file
  
  # Load an image to get the array and affine
  filename = get_data_file('avg152T1.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)
  
  
subject: Fix example