Should as_closest_canonical drop scanner anat q/sform_code? #1427
Description
The current reordering of as_closest_canonical causes sform and qform codes to change.
When converting a dicom to nifti with dcm2niix, we'll get sform and qform codes 1 for NIFTI_XFORM_SCANNER_ANAT.
git clone https://github.com/effigies/nitest-dicom.git
cd nitest-dicom.git
dcm2niix -f test -o . 4d_multiframe_with_derived.dcm
pythonimport nibabel as nib
nii = nib.load("test.nii")
niiacc = nib.as_closest_canonical(nii)
print(nii.header['sform_code'])
print(nii.header['qform_code'])
print(niiacc.header['sform_code'])
print(niiacc.header['qform_code'])1
1
2
0
This is counter-intuitive to me because if we do the dcm2niix conversion flipping the rows (dcm2niix -y n -f test -o . 4d_multiframe_with_derived.dcm), for example, we'd still get scanner anat. Should I thus not expect that as_closest_canonical would maintain those as well?
Ok, it seems that the thing is that as_closest_canonical is a wrapper to as_reoriented, which does return self.__class__(t_arr, new_aff, self.header). Since the new_aff is checked against the header, and those will obviously differ, upon object instantiation the sforms and qforms are changed.
I take it'd be safe to assume that, if is_closest_canonical is called on an image with qform and sform set to 1, that it should keep it that way?
So instead of:
# Get the image class to transform the data for us
img = img.as_reoriented(io_orientation(img.affine))
# however, the affine may not be diagonal
if enforce_diag and not _aff_is_diag(img.affine):
raise OrientationError('Transformed affine is not diagonal')
return imgone would do:
orig_sform_code = img.get_sform(coded=True)[1]
orig_qform_code = img.get_qform(coded=True)[1]
# Get the image class to transform the data for us
img = img.as_reoriented(io_orientation(img.affine))
# however, the affine may not be diagonal
if enforce_diag and not _aff_is_diag(img.affine):
raise OrientationError('Transformed affine is not diagonal')
# if sform and qform were 1 before:
if (orig_sform_code == 1) and (orig_qform_code ==1):
img.set_sform(img.get_sform(), orig_sform_code)
img.set_qform(img.get_qform(), orig_qform_code)
return img