def get_asm_attn(sino, attn, acq_model):
"""Get attn ASM from sino, attn image and acq model."""
asm_attn = pet.AcquisitionSensitivityModel(attn, acq_model)
# temporary fix pending attenuation offset fix in STIR:
# converting attenuation into 'bin efficiency'
asm_attn.set_up(sino)
bin_eff = pet.AcquisitionData(sino)
bin_eff.fill(1.0)
asm_attn.unnormalise(bin_eff)
asm_attn = pet.AcquisitionSensitivityModel(bin_eff)
return asm_attn
def main():
"""Do main."""
# Acq model and template sino
acq_model = pet.AcquisitionModelUsingRayTracingMatrix()
acq_data = pet.AcquisitionData(sino_file)
# If norm is present
asm_norm = None
if norm_e8_file:
# create acquisition sensitivity model from ECAT8 normalisation data
asm_norm = pet.AcquisitionSensitivityModel(norm_e8_file)
# If attenuation is present
asm_attn = None
if attn_im_file:
attn_image = pet.ImageData(attn_im_file)
if trans:
attn_image = resample_attn_image(attn_image)
asm_attn = pet.AcquisitionSensitivityModel(attn_image, acq_model)
# temporary fix pending attenuation offset fix in STIR:
# converting attenuation into 'bin efficiency'
asm_attn.set_up(acq_data)
bin_eff = pet.AcquisitionData(acq_data)
bin_eff.fill(1.0)
print('applying attenuation (please wait, may take a while)...')
asm_attn.unnormalise(bin_eff)
asm_attn = pet.AcquisitionSensitivityModel(bin_eff)
# Get ASM dependent on attn and/or norm
if asm_norm and asm_attn:
print("AcquisitionSensitivityModel contains norm and attenuation...")
asm = pet.AcquisitionSensitivityModel(asm_norm, asm_attn)
elif asm_norm:
print("AcquisitionSensitivityModel contains norm...")
asm = asm_norm
elif asm_attn:
print("AcquisitionSensitivityModel contains attenuation...")
asm = asm_attn
else:
raise ValueError("Need norm and/or attn")
# only need to project again if normalisation is added
# (since attenuation has already been projected)
if asm_norm:
asm_attn.set_up(acq_data)
bin_eff = pet.AcquisitionData(acq_data)
bin_eff.fill(1.0)
print('getting sinograms for multiplicative factors...')
asm.set_up(acq_data)
asm.unnormalise(bin_eff)
print('writing multiplicative sinogram: ' + outp_file)
bin_eff.write(outp_file)
def get_acquisition_model(uMap, templ_sino):
"""Create acquisition model"""
am = pet.AcquisitionModelUsingRayTracingMatrix()
am.set_num_tangential_LORs(5)
# Set up sensitivity due to attenuation
asm_attn = pet.AcquisitionSensitivityModel(uMap, am)
asm_attn.set_up(templ_sino)
bin_eff = pet.AcquisitionData(templ_sino)
bin_eff.fill(1.0)
asm_attn.unnormalise(bin_eff)
asm_attn = pet.AcquisitionSensitivityModel(bin_eff)
am.set_acquisition_sensitivity(asm_attn)
am.set_up(templ_sino, uMap)
return am
def main():
# direct all engine's messages to files
msg_red = PET.MessageRedirector('info.txt', 'warn.txt', 'errr.txt')
PET.AcquisitionData.set_storage_scheme('memory')
# Create the Scatter Estimator
# We can use a STIR parameter file like this
# par_file_path = os.path.join(os.path.dirname(__file__), '..', '..', 'parameter_files')
# se = PET.ScatterEstimator(PET.existing_filepath(par_file_path, 'scatter_estimation.par'))
# However, we will just use all defaults here, and set variables below.
se = PET.ScatterEstimator()
prompts = PET.AcquisitionData(raw_data_file)
se.set_input(prompts)
se.set_attenuation_image(PET.ImageData(mu_map_file))
if randoms_data_file is None:
randoms = None
else:
randoms = PET.AcquisitionData(randoms_data_file)
se.set_randoms(randoms)
if not(norm_file is None):
se.set_asm(PET.AcquisitionSensitivityModel(norm_file))
if not(acf_file is None):
se.set_attenuation_correction_factors(PET.AcquisitionData(acf_file))
# could set number of iterations if you want to
se.set_num_iterations(1)
print("number of scatter iterations that will be used: %d" % se.get_num_iterations())
se.set_output_prefix(output_prefix)
se.set_up()
se.process()
scatter_estimate = se.get_output()
## show estimated scatter data
scatter_estimate_as_array = scatter_estimate.as_array()
show_2D_array('Scatter estimate', scatter_estimate_as_array[0, 0, :, :])
## let's draw some profiles to check
# we will average over all sinograms to reduce noise
PET_plot_functions.plot_sinogram_profile(prompts, randoms=randoms, scatter=scatter_estimate)
#%% Settings for reconstruction
# set acq_model
acq_model = Pet.AcquisitionModelUsingRayTracingMatrix()
acq_model.set_num_tangential_LORs(5)
# set recon, OSEM
recon = Pet.OSMAPOSLReconstructor()
num_subsets = 7
num_subiterations = 4
recon.set_num_subsets(num_subsets)
recon.set_num_subiterations(num_subiterations)
# definitions for detector sensitivity modelling
asm_norm = Pet.AcquisitionSensitivityModel(norm_file)
acq_model.set_acquisition_sensitivity(asm_norm)
#%% redirect STIR messages to some files
# you can check these if things go wrong
msg_red = Pet.MessageRedirector('info.txt', 'warn.txt')
#%% List of sino and rand
list_sino = [
f for f in os.listdir(working_folder + '/sino/') if f.endswith(".hs")
]
list_rando = [
f for f in os.listdir(working_folder + '/rando/') if f.endswith(".hs")
]
#%% NAC reconstruction
def main():
## PET.AcquisitionData.set_storage_scheme('memory')
# no info printing from the engine, warnings and errors sent to stdout
msg_red = PET.MessageRedirector()
# Create a template Acquisition Model
#acq_template = AcquisitionData('Siemens mMR', 1, 0, 1)
acq_template = PET.AcquisitionData(
acq_template_filename) #q.get_uniform_copy()
# create the attenuation image
atten_image = PET.ImageData(acq_template)
image_size = atten_image.dimensions()
voxel_size = atten_image.voxel_sizes()
# create a cylindrical water phantom
water_cyl = PET.EllipticCylinder()
water_cyl.set_length(image_size[0] * voxel_size[0])
water_cyl.set_radii((image_size[1]*voxel_size[1]*0.25, \
image_size[2]*voxel_size[2]*0.25))
water_cyl.set_origin((image_size[0] * voxel_size[0] * 0.5, 0, 0))
# add the shape to the image
atten_image.add_shape(water_cyl, scale=9.687E-02)
# z-pixel coordinate of the xy-crossection to show
z = int(image_size[0] * 0.5)
# show the phantom image
atten_image_array = atten_image.as_array()
show_2D_array('Attenuation image', atten_image_array[z, :, :])
# Create the activity image
act_image = atten_image.clone()
act_image.fill(0.0)
# create the activity cylinder
act_cyl = PET.EllipticCylinder()
act_cyl.set_length(image_size[0] * voxel_size[0])
act_cyl.set_radii((image_size[1] * voxel_size[1] * 0.125, \
image_size[2] * voxel_size[2] * 0.125))
act_cyl.set_origin((0, image_size[1] * voxel_size[1] * 0.06, \
image_size[2] * voxel_size[2] * 0.06))
# add the shape to the image
act_image.add_shape(act_cyl, scale=1)
# z-pixel coordinate of the xy-crossection to show
z = int(image_size[0] * 0.5)
# show the phantom image
act_image_array = act_image.as_array()
show_2D_array('Activity image', act_image_array[z, :, :])
# Create the Single Scatter Simulation model
sss = PET.SingleScatterSimulator()
# Set the attenuation image
sss.set_attenuation_image(atten_image)
# set-up the scatter simulator
sss.set_up(acq_template, act_image)
# Simulate!
sss_data = sss.forward(act_image)
# show simulated scatter data
simulated_scatter_as_array = sss_data.as_array()
show_2D_array('scatter simulation', simulated_scatter_as_array[0, 0, :, :])
sss_data.write(output_file)
## let's also compute the unscattered counts (at the same low resolution) and compare
acq_model = PET.AcquisitionModelUsingRayTracingMatrix()
asm = PET.AcquisitionSensitivityModel(atten_image, acq_model)
acq_model.set_acquisition_sensitivity(asm)
acq_model.set_up(acq_template, act_image)
#unscattered_data = acq_template.get_uniform_copy()
unscattered_data = acq_model.forward(act_image)
simulated_unscatter_as_array = unscattered_data.as_array()
show_2D_array('unscattered simulation',
simulated_unscatter_as_array[0, 0, :, :])
plt.figure()
ax = plt.subplot(111)
plt.plot(simulated_unscatter_as_array[0, 4, 0, :], label='unscattered')
plt.plot(simulated_scatter_as_array[0, 4, 0, :], label='scattered')
ax.legend()
plt.show()
#%% settings for reconstruction
# set acq_model
acq_model = Pet.AcquisitionModelUsingRayTracingMatrix()
acq_model.set_num_tangential_LORs(5)
# set recon, OSEM
recon = Pet.OSMAPOSLReconstructor()
num_subsets = 7
num_subiterations = 4
recon.set_num_subsets(num_subsets)
recon.set_num_subiterations(num_subiterations)
# definitions for attenuation
attn_acq_model = Pet.AcquisitionModelUsingRayTracingMatrix()
asm_attn = Pet.AcquisitionSensitivityModel(attn_image, attn_acq_model)
# definitions for detector sensitivity modelling
asm_norm = Pet.AcquisitionSensitivityModel(norm_file)
acq_model.set_acquisition_sensitivity(asm_norm)
#%% for-loop, reconstruction of time intervals
tprint('Start Recon')
for i in range(len(time_intervals)-1):
print('Begin reconstruction: Frame {}'.format(i))
# listmode-to-sinogram
lm2sino.set_time_interval(time_intervals[i], time_intervals[i+1])
lm2sino.set_up()
lm2sino.process()
data_path = '/home/edo/scratch/code/PETMR/install/share/sirf/NEMA'
os.chdir(os.path.abspath(data_path))
acq_data = pet.AcquisitionData('NEMA_sino_0-{}s.hs'.format(seconds))
# fix a problem with the header which doesn't allow
# to do algebra with randoms and sinogram
# rand_arr = pet.AcquisitionData('{}/sino_randoms_f1g1d0b0.hs'.format(data_path)).as_array()
rand_arr = pet.AcquisitionData('NEMA_randoms_0-{}s.hs'.format(seconds))
rand = acq_data * 0
rand.fill(rand_arr)
image = acq_data.create_uniform_image(1., (127, 220, 220))
image.initialise(dim=(127, 220, 220), vsize=(2.03125, 1.7080754, 1.7080754))
attns = pet.ImageData('mu_map.hv')
asm_norm = pet.AcquisitionSensitivityModel('norm.n.hdr')
def get_asm_attn(sino, attn, acq_model):
"""Get attn ASM from sino, attn image and acq model."""
asm_attn = pet.AcquisitionSensitivityModel(attn, acq_model)
# temporary fix pending attenuation offset fix in STIR:
# converting attenuation into 'bin efficiency'
asm_attn.set_up(sino)
bin_eff = pet.AcquisitionData(sino)
bin_eff.fill(1.0)
asm_attn.unnormalise(bin_eff)
asm_attn = pet.AcquisitionSensitivityModel(bin_eff)
return asm_attn
def main():
###########################################################################
# Parse input files
###########################################################################
if trans_pattern is None:
raise AssertionError("--trans missing")
if sino_pattern is None:
raise AssertionError("--sino missing")
trans_files = sorted(glob(trans_pattern))
sino_files = sorted(glob(sino_pattern))
attn_files = sorted(glob(attn_pattern))
rand_files = sorted(glob(rand_pattern))
num_ms = len(sino_files)
# Check some sinograms found
if num_ms == 0:
raise AssertionError("No sinograms found!")
# Should have as many trans as sinos
if num_ms != len(trans_files):
raise AssertionError("#trans should match #sinos. "
"#sinos = " + str(num_ms) + ", #trans = " +
str(len(trans_files)))
# If any rand, check num == num_ms
if len(rand_files) > 0 and len(rand_files) != num_ms:
raise AssertionError("#rand should match #sinos. "
"#sinos = " + str(num_ms) + ", #rand = " +
str(len(rand_files)))
# For attn, there should be 0, 1 or num_ms images
if len(attn_files) > 1 and len(attn_files) != num_ms:
raise AssertionError("#attn should be 0, 1 or #sinos")
###########################################################################
# Read input
###########################################################################
if trans_type == "tm":
trans = [reg.AffineTransformation(file) for file in trans_files]
elif trans_type == "disp":
trans = [
reg.NiftiImageData3DDisplacement(file) for file in trans_files
]
elif trans_type == "def":
trans = [reg.NiftiImageData3DDeformation(file) for file in trans_files]
else:
raise error("Unknown transformation type")
sinos_raw = [pet.AcquisitionData(file) for file in sino_files]
attns = [pet.ImageData(file) for file in attn_files]
rands = [pet.AcquisitionData(file) for file in rand_files]
# Loop over all sinograms
sinos = [0] * num_ms
for ind in range(num_ms):
# If any sinograms contain negative values
# (shouldn't be the case), set them to 0
sino_arr = sinos_raw[ind].as_array()
if (sino_arr < 0).any():
print("Input sinogram " + str(ind) +
" contains -ve elements. Setting to 0...")
sinos[ind] = sinos_raw[ind].clone()
sino_arr[sino_arr < 0] = 0
sinos[ind].fill(sino_arr)
else:
sinos[ind] = sinos_raw[ind]
# If rebinning is desired
segs_to_combine = 1
if args['--numSegsToCombine']:
segs_to_combine = int(args['--numSegsToCombine'])
views_to_combine = 1
if args['--numViewsToCombine']:
views_to_combine = int(args['--numViewsToCombine'])
if segs_to_combine * views_to_combine > 1:
sinos[ind] = sinos[ind].rebin(segs_to_combine, views_to_combine)
# only print first time
if ind == 0:
print(f"Rebinned sino dimensions: {sinos[ind].dimensions()}")
###########################################################################
# Initialise recon image
###########################################################################
if initial_estimate:
image = pet.ImageData(initial_estimate)
else:
# Create image based on ProjData
image = sinos[0].create_uniform_image(0.0, (nxny, nxny))
# If using GPU, need to make sure that image is right size.
if use_gpu:
dim = (127, 320, 320)
spacing = (2.03125, 2.08626, 2.08626)
# elif non-default spacing desired
elif args['--dxdy']:
dim = image.dimensions()
dxdy = float(args['--dxdy'])
spacing = (image.voxel_sizes()[0], dxdy, dxdy)
if use_gpu or args['--dxdy']:
image.initialise(dim=dim, vsize=spacing)
image.fill(0.0)
###########################################################################
# Set up resamplers
###########################################################################
resamplers = [get_resampler(image, trans=tran) for tran in trans]
###########################################################################
# Resample attenuation images (if necessary)
###########################################################################
resampled_attns = None
if len(attns) > 0:
resampled_attns = [0] * num_ms
# if using GPU, dimensions of attn and recon images have to match
ref = image if use_gpu else None
for i in range(len(attns)):
# if we only have 1 attn image, then we need to resample into
# space of each gate. However, if we have num_ms attn images, then
# assume they are already in the correct position, so use None as
# transformation.
tran = trans[i] if len(attns) == 1 else None
# If only 1 attn image, then resample that. If we have num_ms attn
# images, then use each attn image of each frame.
attn = attns[0] if len(attns) == 1 else attns[i]
resam = get_resampler(attn, ref=ref, trans=tran)
resampled_attns[i] = resam.forward(attn)
###########################################################################
# Set up acquisition models
###########################################################################
print("Setting up acquisition models...")
if not use_gpu:
acq_models = num_ms * [pet.AcquisitionModelUsingRayTracingMatrix()]
else:
acq_models = num_ms * [pet.AcquisitionModelUsingNiftyPET()]
for acq_model in acq_models:
acq_model.set_use_truncation(True)
acq_model.set_cuda_verbosity(verbosity)
# If present, create ASM from ECAT8 normalisation data
asm_norm = None
if norm_file:
asm_norm = pet.AcquisitionSensitivityModel(norm_file)
# Loop over each motion state
for ind in range(num_ms):
# Create attn ASM if necessary
asm_attn = None
if resampled_attns:
asm_attn = get_asm_attn(sinos[ind], resampled_attns[i],
acq_models[ind])
# Get ASM dependent on attn and/or norm
asm = None
if asm_norm and asm_attn:
if ind == 0:
print("ASM contains norm and attenuation...")
asm = pet.AcquisitionSensitivityModel(asm_norm, asm_attn)
elif asm_norm:
if ind == 0:
print("ASM contains norm...")
asm = asm_norm
elif asm_attn:
if ind == 0:
print("ASM contains attenuation...")
asm = asm_attn
if asm:
acq_models[ind].set_acquisition_sensitivity(asm)
if len(rands) > 0:
acq_models[ind].set_background_term(rands[ind])
# Set up
acq_models[ind].set_up(sinos[ind], image)
###########################################################################
# Set up reconstructor
###########################################################################
print("Setting up reconstructor...")
# Create composition operators containing acquisition models and resamplers
C = [
CompositionOperator(am, res, preallocate=True)
for am, res in zip(*(acq_models, resamplers))
]
# Configure the PDHG algorithm
if args['--normK'] and not args['--onlyNormK']:
normK = float(args['--normK'])
else:
kl = [KullbackLeibler(b=sino, eta=(sino * 0 + 1e-5)) for sino in sinos]
f = BlockFunction(*kl)
K = BlockOperator(*C)
# Calculate normK
print("Calculating norm of the block operator...")
normK = K.norm(iterations=10)
print("Norm of the BlockOperator ", normK)
if args['--onlyNormK']:
exit(0)
# Optionally rescale sinograms and BlockOperator using normK
scale_factor = 1. / normK if args['--normaliseDataAndBlock'] else 1.0
kl = [
KullbackLeibler(b=sino * scale_factor, eta=(sino * 0 + 1e-5))
for sino in sinos
]
f = BlockFunction(*kl)
K = BlockOperator(*C) * scale_factor
# If preconditioned
if precond:
def get_nonzero_recip(data):
"""Get the reciprocal of a datacontainer. Voxels where input == 0
will have their reciprocal set to 1 (instead of infinity)"""
inv_np = data.as_array()
inv_np[inv_np == 0] = 1
inv_np = 1. / inv_np
data.fill(inv_np)
tau = K.adjoint(K.range_geometry().allocate(1))
get_nonzero_recip(tau)
tmp_sigma = K.direct(K.domain_geometry().allocate(1))
sigma = 0. * tmp_sigma
get_nonzero_recip(sigma[0])
def precond_proximal(self, x, tau, out=None):
"""Modify proximal method to work with preconditioned tau"""
pars = {
'algorithm':
FGP_TV,
'input':
np.asarray(x.as_array() / tau.as_array(), dtype=np.float32),
'regularization_parameter':
self.lambdaReg,
'number_of_iterations':
self.iterationsTV,
'tolerance_constant':
self.tolerance,
'methodTV':
self.methodTV,
'nonneg':
self.nonnegativity,
'printingOut':
self.printing
}
res, info = regularisers.FGP_TV(pars['input'],
pars['regularization_parameter'],
pars['number_of_iterations'],
pars['tolerance_constant'],
pars['methodTV'], pars['nonneg'],
self.device)
if out is not None:
out.fill(res)
else:
out = x.copy()
out.fill(res)
out *= tau
return out
FGP_TV.proximal = precond_proximal
print("Will run proximal with preconditioned tau...")
# If not preconditioned
else:
sigma = float(args['--sigma'])
# If we need to calculate default tau
if args['--tau']:
tau = float(args['--tau'])
else:
tau = 1 / (sigma * normK**2)
if regularisation == 'none':
G = IndicatorBox(lower=0)
elif regularisation == 'FGP_TV':
r_iterations = float(args['--reg_iters'])
r_tolerance = 1e-7
r_iso = 0
r_nonneg = 1
r_printing = 0
device = 'gpu' if use_gpu else 'cpu'
G = FGP_TV(r_alpha, r_iterations, r_tolerance, r_iso, r_nonneg,
r_printing, device)
else:
raise error("Unknown regularisation")
if precond:
def PDHG_new_update(self):
"""Modify the PDHG update to allow preconditioning"""
# save previous iteration
self.x_old.fill(self.x)
self.y_old.fill(self.y)
# Gradient ascent for the dual variable
self.operator.direct(self.xbar, out=self.y_tmp)
self.y_tmp *= self.sigma
self.y_tmp += self.y_old
self.f.proximal_conjugate(self.y_tmp, self.sigma, out=self.y)
# Gradient descent for the primal variable
self.operator.adjoint(self.y, out=self.x_tmp)
self.x_tmp *= -1 * self.tau
self.x_tmp += self.x_old
self.g.proximal(self.x_tmp, self.tau, out=self.x)
# Update
self.x.subtract(self.x_old, out=self.xbar)
self.xbar *= self.theta
self.xbar += self.x
PDHG.update = PDHG_new_update
# Get filename
outp_file = outp_prefix
if descriptive_fname:
if len(attn_files) > 0:
outp_file += "_wAC"
if norm_file:
outp_file += "_wNorm"
if use_gpu:
outp_file += "_wGPU"
outp_file += "_Reg-" + regularisation
if regularisation == 'FGP_TV':
outp_file += "-alpha" + str(r_alpha)
outp_file += "-riters" + str(r_iterations)
if args['--normK']:
outp_file += '_userNormK' + str(normK)
else:
outp_file += '_calcNormK' + str(normK)
if args['--normaliseDataAndBlock']:
outp_file += '_wDataScale'
else:
outp_file += '_noDataScale'
if not precond:
outp_file += "_sigma" + str(sigma)
outp_file += "_tau" + str(tau)
else:
outp_file += "_wPrecond"
outp_file += "_nGates" + str(len(sino_files))
if resamplers is None:
outp_file += "_noMotion"
pdhg = PDHG(f=f,
g=G,
operator=K,
sigma=sigma,
tau=tau,
max_iteration=num_iters,
update_objective_interval=update_obj_fn_interval,
x_init=image,
log_file=outp_file + ".log")
def callback_save(iteration, objective_value, solution):
"""Callback function to save images"""
if (iteration + 1) % save_interval == 0:
out = solution if not nifti else reg.NiftiImageData(solution)
out.write(outp_file + "_iters" + str(iteration + 1))
pdhg.run(iterations=num_iters,
callback=callback_save,
verbose=True,
very_verbose=True)
if visualisations:
# show reconstructed image
out = pdhg.get_output()
out_arr = out.as_array()
z = out_arr.shape[0] // 2
show_2D_array('Reconstructed image', out.as_array()[z, :, :])
pylab.show()
