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_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_dwi(dwi, hdr_out, outfile=None, precision=5):
# hdr_out= hdr.copy()
spcdir_orig = hdr_out['space directions'][0:3, 0:3]
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,
precision)
print(spcdir_new)
mf_orig = hdr_out['measurement frame']
print(mf_orig)
mf_new = matrix.round(R @ matrix(mf_orig), precision)
print(mf_new)
hdr_out['space directions'][0:3, 0:3] = array(spcdir_new)
hdr_out['measurement frame'] = array(mf_new)
nrrd.write(outfile, dwi, header=hdr_out, compression_level=1)
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)
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)
