def get_direction_matrix(self):
"""Each row gives a vector dictating the direction of the axis in LPS physical space."""
arr = numpy.ndarray((3, 3), dtype=numpy.float32)
try_calling(
pysirf.cSIRF_GeomInfo_get_direction_matrix(self.handle,
arr.ctypes.data))
return arr
def axpby(self, a, b, y, out=None, **kwargs):
'''
Addition for data containers.
Returns the sum of the container data with another container
data viewed as vectors.
y: DataContainer
out: DataContainer to store the result to.
'''
# if isinstance(other , ( Number, int, float, numpy.float32 )):
# tmp = other + numpy.zeros(self.as_array().shape)
# other = self.copy()
# other.fill(tmp)
assert_validities(self, y)
alpha = numpy.asarray([a.real, a.imag], dtype=numpy.float32)
beta = numpy.asarray([b.real, b.imag], dtype=numpy.float32)
if out is None:
z = self.same_object()
z.handle = pysirf.cSIRF_axpby \
(alpha.ctypes.data, self.handle, beta.ctypes.data, y.handle)
else:
assert_validities(self, out)
z = out
try_calling(pysirf.cSIRF_axpbyAlt \
(alpha.ctypes.data, self.handle, beta.ctypes.data, y.handle, z.handle))
check_status(z.handle)
return z
def get_index_to_physical_point_matrix(self):
"""Get the 4x4 affine matrix that converts an index to a point in LPS physical space."""
arr = numpy.ndarray((4, 4), dtype=numpy.float32)
try_calling(
pysirf.cSIRF_GeomInfo_get_index_to_physical_point_matrix(
self.handle, arr.ctypes.data))
return arr
def set_properties(self, prop):
'''
Assigns specified values to specified gadget properties.
prop: a string with comma-separated list of property value assignments
prop_name=prop_value
'''
try_calling(pygadgetron.cGT_setGadgetProperties(self.handle, prop))
def as_array(self):
'''
Returns all self's images as a 3D Numpy ndarray.
'''
assert self.handle is not None
if self.number() < 1:
return numpy.ndarray((0, 0, 0), dtype=numpy.float32)
dim = numpy.ndarray((4, ), dtype=numpy.int32)
image = Image(self)
pygadgetron.cGT_getImageDim(image.handle, dim.ctypes.data)
nx = dim[0]
ny = dim[1]
nz = dim[2]
nc = dim[3]
nz = nz * nc * self.number()
if self.is_real():
array = numpy.ndarray((nz, ny, nx), dtype=numpy.float32)
try_calling(pygadgetron.cGT_getImagesDataAsFloatArray\
(self.handle, array.ctypes.data))
return array
else:
z = numpy.ndarray((nz, ny, nx), dtype=numpy.complex64)
try_calling(pygadgetron.cGT_getImagesDataAsCmplxArray\
(self.handle, z.ctypes.data))
return z
def subtract(self, other, out=None):
'''
Overloads - for data containers.
Returns the difference of the container data with another container
data viewed as vectors.
other: DataContainer
'''
if not isinstance(other, (DataContainer, Number)):
return NotImplemented
if isinstance(other, Number):
tmp = other + numpy.zeros(self.shape, self.dtype)
other = self.copy()
other.fill(tmp)
assert_validities(self, other)
pl_one = numpy.asarray([1.0, 0.0], dtype=numpy.float32)
mn_one = numpy.asarray([-1.0, 0.0], dtype=numpy.float32)
if out is None:
z = self.same_object()
z.handle = pysirf.cSIRF_axpby \
(pl_one.ctypes.data, self.handle, mn_one.ctypes.data, other.handle)
check_status(z.handle)
else:
assert_validities(self, out)
z = out
try_calling(pysirf.cSIRF_axpbyAlt \
(pl_one.ctypes.data, self.handle, mn_one.ctypes.data, other.handle, z.handle))
return z
def process(self):
'''
Processes the input with the gadget chain.
'''
if self.input_data is None:
raise error('no input data')
try_calling(pygadgetron.cGT_reconstructImages\
(self.handle, self.input_data.handle))
def add_gadget(self, id, gadget):
'''
Adds a gadget to the chain.
id : gadget id (string)
writer: Gadget
'''
assert isinstance(gadget, Gadget)
try_calling(pygadgetron.cGT_addGadget(self.handle, id, gadget.handle))
def set_coil_sensitivity_maps(self, csm):
'''
Specifies the coil sensitivity maps to be used by the model.
csm: CoilSensitivityData
'''
assert_validity(csm, CoilSensitivityData)
try_calling(pygadgetron.cGT_setAcquisitionModelParameter \
(self.handle, 'coil_sensitivity_maps', csm.handle))
def fill(self, data):
'''
Fills self's acquisitions with specified values.
data: Python Numpy array
'''
assert self.handle is not None
try_calling(pygadgetron.cGT_fillAcquisitionsData\
(self.handle, data.ctypes.data, 1))
def set_property(self, prop, value):
'''
Assigns specified value to specified gadget property.
prop : property name (string)
value: property value (string)
'''
try_calling(pygadgetron.cGT_setGadgetProperty(self.handle, prop,
value))
def calculate(self, acqs):
'''
Calculates coil images from a given sorted acquisitions.
acqs: AcquisitionData
'''
assert_validity(acqs, AcquisitionData)
if acqs.is_sorted() is False:
print('WARNING: acquisitions may be in a wrong order')
try_calling(pygadgetron.cGT_computeCoilImages\
(self.handle, acqs.handle))
def sort(self):
'''
Sorts acquisitions with respect to (in this order):
- repetition
- slice
- kspace_encode_step_1
'''
assert self.handle is not None
try_calling(pygadgetron.cGT_sortAcquisitions(self.handle))
self.sorted = True
def set_storage_scheme(scheme):
'''Sets acquisition data storage scheme.
scheme = 'file' (default):
all acquisition data generated from now on will be kept in
scratch files deleted after the user's script terminates
scheme = 'memory':
all acquisition data generated from now on will be kept in RAM
(avoid if data is very large)
'''
try_calling(pygadgetron.cGT_setAcquisitionsStorageScheme(scheme))
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:
try:
from ismrmrdtools import coils
except:
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 set_gadget_property(self, id, prop, value):
'''
Assigns specified value to specified gadget property.
id : gadget id
prop : property name (string)
value: property value (string)
'''
if type(value) == type('abc'):
v = value
else:
v = repr(value).lower()
hg = _parameterHandle(self.handle, 'gadget_chain', id)
try_calling(pygadgetron.cGT_setGadgetProperty(hg, prop, v))
pyiutil.deleteDataHandle(hg)
def as_array(self, select='image'):
'''
Returns selected self's acquisitions as a 3D Numpy ndarray.
'''
assert self.handle is not None
na = self.number()
ny, nc, ns = self.dimensions(select)
if select == 'all': # return all
return_all = 1
else: # return only image-related
return_all = 0
z = numpy.ndarray((ny, nc, ns), dtype=numpy.complex64)
try_calling(pygadgetron.cGT_acquisitionsDataAsArray\
(self.handle, z.ctypes.data, return_all))
return z
def fill(self, data):
'''
Fills self's image data with specified values.
data: Python Numpy array
'''
assert self.handle is not None
if self.is_real():
if data.dtype != numpy.float32:
data = data.astype(numpy.float32)
try_calling(pygadgetron.cGT_setImagesDataAsFloatArray\
(self.handle, data.ctypes.data))
else:
if data.dtype != numpy.complex64:
data = data.astype(numpy.complex64)
try_calling(pygadgetron.cGT_setImagesDataAsCmplxArray\
(self.handle, data.ctypes.data))
def conjugate(self, out=None):
''' Computes complex conjugate of self.
Use y = x.conjugate() to get the conjugated copy of x.
Use x.conjugate(out=x) to conjugate in-place.
'''
assert self.handle is not None
if out is self:
try_calling(pysirf.cSIRF_conjugate(self.handle))
return
elif out is None:
x = self.same_object()
else:
x = out
x.handle = pysirf.cSIRF_conjugated(self.handle)
check_status(x.handle)
if out is None:
return x
def divide(self, other, out=None):
'''
Returns the elementwise ratio of this and another container
data viewed as vectors.
other: DataContainer
out: DataContainer to store the result to.
'''
if not isinstance (other, ( DataContainer , Number )):
return NotImplemented
if isinstance(other , Number ):
tmp = other + numpy.zeros(self.shape, self.dtype)
other = self.copy()
other.fill(tmp)
assert_validities(self, other)
if out is None:
out = self.same_object()
out.handle = pysirf.cSIRF_ratio(self.handle, other.handle)
check_status(out.handle)
#out = self.copy()
else:
assert_validities(self, out)
try_calling(pysirf.cSIRF_divide(self.handle, other.handle, out.handle))
return out
def axpby(self, a, b, y, out=None, **kwargs):
'''
Addition for data containers.
Returns the sum of the container data with another container
data viewed as vectors.
a: multiplier to self, can be a number or a DataContainer
b: multiplier to y, can be a number or a DataContainer
y: DataContainer
out: DataContainer to store the result to.
'''
# splits axpby in 3 steps if a and b are not numbers as
# pysirf.cSIRF_axpby requires them as numbers
if not (isinstance(a, Number) and isinstance(b, Number)):
if out is None:
out = y.multiply(b)
else:
y.multiply(b, out=out)
tmp = self.multiply(a)
out.add(tmp, out=out)
return out
assert_validities(self, y)
alpha = numpy.asarray([a.real, a.imag], dtype=numpy.float32)
beta = numpy.asarray([b.real, b.imag], dtype=numpy.float32)
if out is None:
z = self.same_object()
z.handle = pysirf.cSIRF_axpby \
(alpha.ctypes.data, self.handle, beta.ctypes.data, y.handle)
else:
assert_validities(self, out)
z = out
try_calling(pysirf.cSIRF_axpbyAlt \
(alpha.ctypes.data, self.handle, beta.ctypes.data, y.handle, z.handle))
check_status(z.handle)
return z
def write(self, filename):
'''
Writes to file.
'''
assert self.handle is not None
try_calling(pysirf.cSIRF_write(self.handle, filename))
def push_back(self, handle):
"""Push back new data handle."""
try_calling(pysirf.cSIRF_DataHandleVector_push_back(self.handle, handle))
check_status(self.handle)
def reorient(self, geom_info):
"""Reorient image. Requires that dimensions match."""
if not isinstance(geom_info, GeometricalInfo):
raise AssertionError()
try_calling(
pysirf.cSIRF_ImageData_reorient(self.handle, geom_info.handle))
def sapyb(self, a, y, b, out=None, **kwargs):
'''
Addition for data containers. Can be in place.
Returns the sum of the container data with another container
data viewed as vectors.
a: multiplier to self, can be a number or a DataContainer
b: multiplier to y, can be a number or a DataContainer
y: DataContainer
out: DataContainer to store the result to, can be self or y.
'''
assert_validities(self, y)
if out is not None:
assert_validities(self, out)
z = out
else:
z = self.same_object()
if isinstance(a, Number):
alpha = numpy.asarray([a.real, a.imag], dtype=numpy.float32)
if isinstance(b, Number):
#a is scalar, b is scalar
beta = numpy.asarray([b.real, b.imag], dtype=numpy.float32)
if out is None:
z.handle = pysirf.cSIRF_axpby(alpha.ctypes.data,
self.handle,
beta.ctypes.data, y.handle)
else:
try_calling(
pysirf.cSIRF_axpbyAlt(alpha.ctypes.data, self.handle,
beta.ctypes.data, y.handle,
z.handle))
else:
#a is scalar, b is array
one = numpy.asarray([1.0, 0.0], dtype=numpy.float32)
tmp = y.multiply(b)
if out is None:
z.handle = pysirf.cSIRF_axpby(alpha.ctypes.data,
self.handle, one.ctypes.data,
tmp.handle)
else:
try_calling(
pysirf.cSIRF_axpbyAlt(alpha.ctypes.data, self.handle,
one.ctypes.data, tmp.handle,
z.handle))
else:
assert_validities(self, a)
if isinstance(b, Number):
#a is array, b is scalar
one = numpy.asarray([1.0, 0.0], dtype=numpy.float32)
beta = numpy.asarray([b.real, b.imag], dtype=numpy.float32)
tmp = self.multiply(a)
if out is None:
z.handle = pysirf.cSIRF_axpby(one.ctypes.data, tmp.handle,
beta.ctypes.data, y.handle)
else:
try_calling(
pysirf.cSIRF_axpbyAlt(one.ctypes.data, tmp.handle,
beta.ctypes.data, y.handle,
z.handle))
else:
#a is array, b is array
assert_validities(self, b)
if out is None:
try:
z.handle = pysirf.cSIRF_xapyb(self.handle, a.handle,
y.handle, b.handle)
check_status(z.handle)
except error as e:
if 'NotImplemented' in str(e):
tmp = self.multiply(a)
z = y.multiply(b)
z.add(tmp, out=z)
else:
raise RuntimeError(str(e))
else:
try:
try_calling(
pysirf.cSIRF_xapybAlt(self.handle, a.handle,
y.handle, b.handle,
z.handle))
except error as e:
if 'NotImplemented' in str(e):
tmp = self.multiply(a)
y.multiply(b, out=z)
z.add(tmp, out=z)
else:
raise RuntimeError(str(e))
check_status(z.handle)
return z
def get_size(self):
"""Size is the number of voxels in each dimension."""
arr = numpy.ndarray((3, ), dtype=numpy.int32)
try_calling(
pysirf.cSIRF_GeomInfo_get_size(self.handle, arr.ctypes.data))
return tuple(arr)
def get_spacing(self):
"""Spacing is the physical distance between voxels in each dimension."""
arr = numpy.ndarray((3, ), dtype=numpy.float32)
try_calling(
pysirf.cSIRF_GeomInfo_get_spacing(self.handle, arr.ctypes.data))
return tuple(arr)
def get_offset(self):
"""Offset is the LPS coordinate of the centre of the first voxel."""
arr = numpy.ndarray((3, ), dtype=numpy.float32)
try_calling(
pysirf.cSIRF_GeomInfo_get_offset(self.handle, arr.ctypes.data))
return tuple(arr)
def print_info(self):
"""Print the geom info"""
try_calling(pysirf.cSIRF_GeomInfo_print(self.handle))
def fill(self, image):
try_calling(pysirf.cSIRF_fillImageFromImage(self.handle, image.handle))
