def multicoil_convert(self):
"""GE specific multicoil converesion. requires partial volume and missing slices check."""
log.debug('multicoil recon')
mr.partial_vol_check(self)
stacks = []
group_id = 0
for group in self._dcm_groups:
group_id += 1
log.debug('multicoil - %2s, %s dicom' %
(str(group_id), str(len(group))))
num_positions = len(set([d.SliceLocation for d in group]))
if num_positions != self.num_slices:
raise DicomError('coil %s has %s unique positions; expected %s' %
(group_id, num_positions, self.num_slices))
stack = dcmstack.DicomStack()
for dcm in group:
meta = MetaExtractor(dcm)
stack.add_dcm(dcm, meta)
nii_wrp = stack.to_nifti_wrapper()
stacks.append(nii_wrp)
try:
nii_wrp = dcmstack.dcmmeta.NiftiWrapper.from_sequence(stacks)
except dcmstack.InvalidStackError as e:
raise DicomError(
'cannot reconstruct %s: %s' %
(self.filepath, e)) # XXX FAIL! unexpected for recon to fail
# raise NIMSDicomError('cannot reconstruct %s: %s' % (self.filepath, e), log_level=logging.ERROR)
del self._dcm_groups, self._dcm_list, stacks, stack, dcm
nii = nii_wrp.nii_img
self.data = {'': nii.get_data()}
self.qto_xyz = nii.get_affine()
del nii_wrp, nii
mr.post_convert(self)
def multicoil_convert(self):
"""GE specific multicoil converesion. requires partial volume and missing slices check."""
log.debug('multicoil recon')
mr.partial_vol_check(self)
stacks = []
group_id = 0
for group in self._dcm_groups:
group_id += 1
log.debug('multicoil - %2s, %s dicom' % (str(group_id), str(len(group))))
num_positions = len(set([d.SliceLocation for d in group]))
if num_positions != self.num_slices:
raise DicomError('coil %s has %s unique positions; expected %s' % (group_id, num_positions, self.num_slices))
stack = dcmstack.DicomStack()
for dcm in group:
meta = MetaExtractor(dcm)
stack.add_dcm(dcm, meta)
nii_wrp = stack.to_nifti_wrapper()
stacks.append(nii_wrp)
try:
nii_wrp = dcmstack.dcmmeta.NiftiWrapper.from_sequence(stacks)
except dcmstack.InvalidStackError as e:
raise DicomError('cannot reconstruct %s: %s' % (self.filepath, e)) # XXX FAIL! unexpected for recon to fail
# raise NIMSDicomError('cannot reconstruct %s: %s' % (self.filepath, e), log_level=logging.ERROR)
del self._dcm_groups, self._dcm_list, stacks, stack, dcm
nii = nii_wrp.nii_img
self.data = {'': nii.get_data()}
self.qto_xyz = nii.get_affine()
del nii_wrp, nii
mr.post_convert(self)
def fastcard_convert(self):
"""GE fast card conversion."""
log.debug('fast card')
stacks = []
group_id = 0
def _split_list(l, size):
return [l[i:i + size] for i in range(0, len(l), size)]
dcm_groups = _split_list(self._dcm_list, self.total_num_slices / 5)
for group in dcm_groups:
group_id += 1
num_positions = len(set([d.SliceLocation for d in group]))
if num_positions != self.num_slices:
raise DicomError('volume %s has %s unique positions; expected %s' %
(group_id, num_positions, self.num_slices))
stack = dcmstack.DicomStack()
for d in group:
meta = MetaExtractor(d)
stack.add_dcm(d, meta)
nii_wrp = stack.to_nifti_wrapper()
stacks.append(nii_wrp)
try:
nii_wrp = dcmstack.dcmmeta.NiftiWrapper.from_sequence(stacks)
except dcmstack.InvalidStackError as e:
raise DicomError('cannot reconstruct %s: %s' % (self.filepath, str(e)))
nii = nii_wrp.nii_img
self.data = {'': nii.get_data()}
self.qto_xyz = nii.get_affine()
mr.post_convert(self)
def fastcard_convert(self):
"""GE fast card conversion."""
log.debug('fast card')
stacks = []
group_id = 0
def _split_list(l, size):
return [l[i:i+size] for i in range(0, len(l), size)]
dcm_groups = _split_list(self._dcm_list, self.total_num_slices / 5)
for group in dcm_groups:
group_id += 1
num_positions = len(set([d.SliceLocation for d in group]))
if num_positions != self.num_slices:
raise DicomError('volume %s has %s unique positions; expected %s' % (group_id, num_positions, self.num_slices))
stack = dcmstack.DicomStack()
for d in group:
meta = MetaExtractor(d)
stack.add_dcm(d, meta)
nii_wrp = stack.to_nifti_wrapper()
stacks.append(nii_wrp)
try:
nii_wrp = dcmstack.dcmmeta.NiftiWrapper.from_sequence(stacks)
except dcmstack.InvalidStackError as e:
raise DicomError('cannot reconstruct %s: %s' % (self.filepath, str(e)))
nii = nii_wrp.nii_img
self.data = {'': nii.get_data()}
self.qto_xyz = nii.get_affine()
mr.post_convert(self)
