sitk_attempt.py

import SimpleITK as sitk
import numpy as np
mask_file = '/data/ct-cspine/test_set_w_masks_2019_05_01/cspine_fx_seg/Cspine_fx_seg/5616571.nrrd'
array_file = '/data/ct-cspine/processed-studies/data_20180524_161757/anonymized_data/images/test/5616571.npy'

def projectImage(reference, moving, interpolate = 'linear'):
    # projects moving image onto reference image space
    # use  interpolate = 'NN' for segmentation masks
    resample = sitk.ResampleImageFilter()
    resample.SetReferenceImage(reference)
    if interpolate == 'linear':
        resample.SetInterpolator(sitk.sitkLinear)
    elif interpolate == 'NN':
        resample.SetInterpolator(sitk.sitkNearestNeighbor)
    resampledimg = resample.Execute(moving)
    return resampledimg

image = np.load(array_file)
mask_sitk  = sitk.ReadImage(mask_file)
sitk_image = sitk.GetImageFromArray(image)  # also fails if you pass image.T
#You can do:

#nearest neighbor interpolation for 1 or 0 masks
alignedmask = projectImage(sitk_image, mask_sitk, interpolate = 'NN')

alignedmasknpy = sitk.GetArrayFromImage(alignedmask).T
mask_arr = sitk.GetArrayFromImage(mask_sitk)
imgnpy = sitk.GetArrayFromImage(sitk_image).T
print(alignedmasknpy.max())
print(mask_arr.max())