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"""
Utils for datasets
"""
import numpy as np
import numpy as np
import SimpleITK as sitk
def read_nii_bysitk(input_fid, peel_info = False):
""" read nii to numpy through simpleitk
peelinfo: taking direction, origin, spacing and metadata out
"""
img_obj = sitk.ReadImage(input_fid)
img_np = sitk.GetArrayFromImage(img_obj)
if peel_info:
info_obj = {
"spacing": img_obj.GetSpacing(),
"origin": img_obj.GetOrigin(),
"direction": img_obj.GetDirection(),
"array_size": img_np.shape
}
return img_np, info_obj
else:
return img_np
def convert_to_sitk(input_mat, peeled_info):
"""
write a numpy array to sitk image object with essential meta-data
"""
nii_obj = sitk.GetImageFromArray(input_mat)
if peeled_info:
nii_obj.SetSpacing( peeled_info["spacing"] )
nii_obj.SetOrigin( peeled_info["origin"] )
nii_obj.SetDirection(peeled_info["direction"] )
return nii_obj
def np2itk(img, ref_obj):
"""
img: numpy array
ref_obj: reference sitk object for copying information from
"""
itk_obj = sitk.GetImageFromArray(img)
itk_obj.SetSpacing( ref_obj.GetSpacing() )
itk_obj.SetOrigin( ref_obj.GetOrigin() )
itk_obj.SetDirection( ref_obj.GetDirection() )
return itk_obj
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