Code snippet to shift nii data by specified number of voxels along specified axis

shiftVolByVoxel.py

# -*- coding: utf-8 -*-
"""
Created on Thu Mar 30 11:55:27 2017

@author: marian
"""
import os
import numpy as np
from nibabel import load, save, Nifti1Image

# %% Set parameters
# set path to volume that shoudl be shifted
pathIn = '/home/marian/Documents/Testing/hausdorfTests/hdSphere2Vox_innBrdr.nii.gz'
# set the number of voxels by which volume should be shifted
shift = 2
# set the axis along which the shift should occur
axis = 2

# %% Load Data
nii = load(pathIn)
basename = nii.get_filename().split(os.extsep, 1)[0]
dirname = os.path.dirname(nii.get_filename())

orig = nii.get_data()  # original data
data = nii.get_data()

borders = np.where(data > 0)
borders = list(borders)

borders[axis] = borders[axis]+shift
data = np.zeros((data.shape))
data[borders] = 1
data = data.astype('int')

# %% save shifted vol as nifti
out = Nifti1Image(data, header=nii.header, affine=nii.affine)
save(out, basename + "_shiftedVox"+str(shift)+"Axis"+str(axis)+".nii.gz")