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377b913 | 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 | """Minimal NIfTI-1 writer (.nii.gz), dependency-free. Fallback for when
SimpleITK/nibabel are unavailable. Pairs with read_nifti.read_nii."""
import gzip
import struct
import numpy as np
def write_nii(path, vol, spacing=(1.0, 1.0, 1.0)):
vol = np.asarray(vol, dtype=np.float32)
assert vol.ndim == 3, "expected a 3D volume"
nx, ny, nz = vol.shape
hdr = bytearray(348)
struct.pack_into("<i", hdr, 0, 348) # sizeof_hdr
struct.pack_into("<8h", hdr, 40, 3, nx, ny, nz, 1, 1, 1, 1) # dim
struct.pack_into("<h", hdr, 70, 16) # datatype = FLOAT32
struct.pack_into("<h", hdr, 72, 32) # bitpix
struct.pack_into("<8f", hdr, 76, 0.0, float(spacing[0]), float(spacing[1]),
float(spacing[2]), 1.0, 1.0, 1.0, 1.0) # pixdim
struct.pack_into("<f", hdr, 108, 352.0) # vox_offset
struct.pack_into("<f", hdr, 112, 1.0) # scl_slope
struct.pack_into("<h", hdr, 252, 1) # qform_code
struct.pack_into("<h", hdr, 254, 1) # sform_code
# simple diagonal sform
struct.pack_into("<4f", hdr, 280, float(spacing[0]), 0, 0, 0)
struct.pack_into("<4f", hdr, 296, 0, float(spacing[1]), 0, 0)
struct.pack_into("<4f", hdr, 312, 0, 0, float(spacing[2]), 0)
hdr[344:348] = b"n+1\x00" # magic
data = np.ascontiguousarray(vol.transpose(2, 1, 0)).astype("<f4").tobytes(order="C")
# NIfTI stores fastest-varying first (x), so write in Fortran order of (nx,ny,nz)
data = np.asfortranarray(vol).astype("<f4").tobytes(order="F")
with gzip.open(path, "wb") as f:
f.write(bytes(hdr) + b"\x00\x00\x00\x00" + data)
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