def calculate(self, acqs):
if acqs.is_sorted() is False:
print('WARNING: acquisitions may be in a wrong order')
if self.handle is not None:
pygadgetron.deleteObject(self.handle)
self.handle = pygadgetron.cGT_CoilSensitivities('')
_check_status(self.handle)
_set_int_par\
(self.handle, 'coil_sensitivity', 'smoothness', self.smoothness)
handle = pygadgetron.cGT_computeCoilSensitivities\
(self.handle, acqs.handle)
_check_status(handle)
pygadgetron.deleteDataHandle(handle)
def calculate(self, data, method=None):
'''
Calculates coil sensitivity maps from coil images or sorted
acquisitions.
data : either AcquisitionData or CoilImages
method: either SRSS (Square Root of the Sum of Squares, default) or
Inati
'''
if isinstance(data, AcquisitionData):
if data.is_sorted() is False:
print('WARNING: acquisitions may be in a wrong order')
if self.handle is not None:
pyiutil.deleteDataHandle(self.handle)
self.handle = pygadgetron.cGT_CoilSensitivities('')
check_status(self.handle)
if method is not None:
method_name, parm_list = name_and_parameters(method)
parm = parse_arglist(parm_list)
else:
method_name = 'SRSS'
parm = {}
if isinstance(data, AcquisitionData):
assert data.handle is not None
_set_int_par\
(self.handle, 'coil_sensitivity', 'smoothness', self.smoothness)
try_calling(pygadgetron.cGT_computeCoilSensitivities\
(self.handle, data.handle))
elif isinstance(data, CoilImageData):
assert data.handle is not None
if method_name == 'Inati':
if not HAVE_ISMRMRDTOOLS:
raise error('Inati method requires ismrmrd-python-tools')
nz = data.number()
for z in range(nz):
ci = numpy.squeeze(data.as_array(z))
(csm, rho) = coils.calculate_csm_inati_iter(ci)
self.append(csm.astype(numpy.complex64))
elif method_name == 'SRSS':
if 'niter' in parm:
nit = int(parm['niter'])
_set_int_par\
(self.handle, 'coil_sensitivity', 'smoothness', nit)
try_calling(pygadgetron.cGT_computeCSMsFromCIs\
(self.handle, data.handle))
else:
raise error('Unknown method %s' % method_name)
else:
raise error('Cannot calculate coil sensitivities from %s' % \
repr(type(data)))
def append(self, csm):
'''
Appends a coil sensitivity map to self.
csm: Numpy ndarray with csm values
'''
if self.handle is None:
self.handle = pygadgetron.cGT_CoilSensitivities('')
check_status(self.handle)
shape = csm.shape
nc = shape[0]
if csm.ndim == 4:
nz = shape[1]
iy = 2
else:
nz = 1
iy = 1
ny = shape[iy]
nx = shape[iy + 1]
re = csm.real.copy()
im = csm.imag.copy()
handle = pygadgetron.cGT_appendCSM\
(self.handle, nx, ny, nz, nc, re.ctypes.data, im.ctypes.data)
check_status(handle)
pyiutil.deleteDataHandle(handle)
def read(self, file):
if self.handle is not None:
pyiutil.deleteDataHandle(self.handle)
self.handle = pygadgetron.cGT_CoilSensitivities(file)
check_status(self.handle)
def read(self, file):
if self.handle is not None:
pygadgetron.deleteObject(self.handle)
self.handle = pygadgetron.cGT_CoilSensitivities(file)
_check_status(self.handle)