def axis_align_dwi(dwi, outfile=None, precision=5):
dwi_hdr = get_hdr(dwi)
spcdir_orig = matrix(find_spc_dir(dwi_hdr))
print(spcdir_orig)
sizes = diag([linalg.norm(spcdir_orig[0,:]),linalg.norm(spcdir_orig[1,:]),linalg.norm(spcdir_orig[2,:])])
print(sizes)
R = get_numpy_rotation(spcdir_orig)
print(R)
spcdir_new = matrix.round(sizes *R*linalg.inv(sizes)*spcdir_orig,4)
print(spcdir_new)
mf_orig = find_mf(dwi_hdr)
print(mf_orig)
mf_new = matrix.round(R * matrix(mf_orig),4)
print(mf_new)
mf_new = [','.join(map(str, x)) for x in mf_new.tolist()]
newline = 'measurement frame: (%s) (%s) (%s)\n' % (mf_new[0], mf_new[1],
mf_new[2])
dwi_new = splitext(dwi)[0] + '_axisaligned.nhdr' if not outfile else \
outfile
t('unu save -f nrrd -e gzip -i %s -o %s' % (dwi, dwi_new))
replace_line_in_file(dwi_new, 'measurement frame:', newline)
newline = 'space directions: (%s) (%s) (%s) none\n' % (','.join(map(str, spcdir_new[0])),
','.join(map(str, spcdir_new[1])),
','.join(map(str, spcdir_new[2])))
replace_line_in_file(dwi_new, 'space directions:', newline)
def axis_align_3d(image, outfile=None):
img_hdr = get_hdr(image)
spcdir_orig = matrix(find_spc_dir(img_hdr))
print(spcdir_orig)
sizes = diag([linalg.norm(spcdir_orig[0,:]),linalg.norm(spcdir_orig[1,:]),linalg.norm(spcdir_orig[2,:])])
print(sizes)
R = get_numpy_rotation(spcdir_orig)
print(R)
spcdir_new = matrix.round(sizes *R*linalg.inv(sizes)*spcdir_orig,4)
print(spcdir_new)
image_new = splitext(image)[0] + '_axisaligned.nhdr' if not outfile else \
outfile
t('unu save -f nrrd -e gzip -i %s -o %s' % (image, image_new))
newline = 'space directions: (%s) (%s) (%s)\n' % (','.join(map(str, spcdir_new[0])),
','.join(map(str, spcdir_new[1])),
','.join(map(str, spcdir_new[2])))
replace_line_in_file(image_new, 'space directions:', newline)
