def main():
# direct all engine's messages to files
msg_red = MessageRedirector('info.txt', 'warn.txt', 'errr.txt')
# select acquisition data storage scheme
AcquisitionData.set_storage_scheme(storage)
# create listmode-to-sinograms converter object
lm2sino = ListmodeToSinograms()
# set input, output and template files
lm2sino.set_input(list_file)
lm2sino.set_output_prefix(sino_file)
lm2sino.set_template(tmpl_file)
# set interval
lm2sino.set_time_interval(interval[0], interval[1])
# set flags such that we only get the delayed coincidences
lm2sino.flag_on('store_delayeds')
lm2sino.flag_off('store_prompts')
# set up the converter
lm2sino.set_up()
# convert
lm2sino.process()
# get access to the sinograms
delayeds_acq_data = lm2sino.get_output()
# estimate the randoms from the delayeds via Maximum Likelihood estimation
# This will take at least a few seconds
randoms_estimate_acq_data = lm2sino.estimate_randoms()
# copy the acquisition data into Python arrays
delayeds_acq_array = delayeds_acq_data.as_array()
randoms_estimate_acq_array = randoms_estimate_acq_data.as_array()
acq_dim = delayeds_acq_array.shape
print('acquisition data dimensions: %dx%dx%dx%d' % acq_dim)
print(
'The total number of delayed coincidences and estimated randoms have to be very similar.'
)
print('Let us check this:')
print('total delayeds: %.1f, total estimated randoms: %.1f' %
(delayeds_acq_array.sum(), randoms_estimate_acq_array.sum()))
print(
'Max values should be somewhat similar, but this depends on statistics of course.'
)
print('max delayeds: %f, max estimated randoms: %f' %
(delayeds_acq_array.max(), randoms_estimate_acq_array.max()))
print('A single sinogram (this will look very different for noisy data)')
z = acq_dim[1] // 2
if show_plot:
show_3D_array(np.stack((delayeds_acq_array[0, z, :, :],
randoms_estimate_acq_array[0, z, :, :])),
titles=('raw delayeds', ' estimated randoms'))
pylab.show()
def main():
# MR
# specify the MR raw data source
input_data = MR.AcquisitionData(input_file)
# pre-process acquisitions
processed_data = MR.preprocess_acquisition_data(input_data)
# perform reconstruction
recon = MR.FullySampledReconstructor()
recon.set_input(processed_data)
recon.process()
complex_image = recon.get_output()
# PET
# convert MR image into PET image
image_arr = abs(complex_image.as_array()) # image as Python array
image = PET.ImageData() # empty PET ImageData object
image.initialise(image_arr.shape[::-1]) # set image shape
image.fill(image_arr) # fill image with values
# apply filter that zeroes the image outside a cylinder of the same
# diameter as the image xy-section size
filter = PET.TruncateToCylinderProcessor()
filter.set_input(image)
filter.process()
processed_image = filter.get_output()
# shortcuts for the above 3 lines
# image is intact
## processed_image = filter.process(image)
# image is modified
## filter.apply(image)
# display image
pUtil.show_3D_array(image.as_array(), \
suptitle = 'MR Image', label = 'slice', show = False)
pUtil.show_3D_array(processed_image.as_array(), \
suptitle = 'PET Processed Image', label = 'slice')
# set a portion of bin efficiencies to zero;
bin_efficiencies_array = bin_efficiencies.as_array()
bin_efficiencies_array[0, :, 5:20, :] = 0
bin_efficiencies.fill(bin_efficiencies_array)
#%% Create a new acquisition model
am2 = pet.AcquisitionModelUsingRayTracingMatrix()
am2.set_num_tangential_LORs(5)
am2.set_up(templ, image)
# now include the bin efficiencies in our acquisition model
asm = pet.AcquisitionSensitivityModel(bin_efficiencies)
am2.set_acquisition_sensitivity(asm)
am2.set_up(templ, image)
#%% forward project the image again with this acquisition model and display
acquired_data = am2.forward(image)
acquisition_array = acquired_data.as_array()
show_3D_array(acquisition_array[0, :, :, :])
#%% Let us reconstruct this data with the original acquisition model (without bin efficiencies)
obj_fun.set_acquisition_data(acquired_data)
obj_fun.set_acquisition_model(am)
reconstructed_image.fill(1)
recon.set_up(reconstructed_image)
recon.set_num_subiterations(10)
recon.reconstruct(reconstructed_image)
#%% display
# we fix the max for the colour scale related to the true max
cmax = image.as_array().max() * 1.2
reconstructed_array = reconstructed_image.as_array()
plt.figure()
imshow(reconstructed_array[slice_num, :, :, ], [0, cmax],
'reconstructed image with original acquisition model')
def main():
# locate the k-space raw data file
input_file = existing_filepath(data_path, data_file)
# acquisition data will be read from an HDF file input_file
acq_data = AcquisitionData(input_file)
print('---\n acquisition data norm: %e' % acq_data.norm())
# pre-process acquisition data
print('---\n pre-processing acquisition data...')
processed_data = preprocess_acquisition_data(acq_data)
print('---\n processed acquisition data norm: %e' % processed_data.norm())
# perform reconstruction to obtain a meaningful ImageData object
# (cannot be obtained in any other way at present)
recon = FullySampledReconstructor()
recon.set_input(processed_data)
recon.process()
complex_images = recon.get_output()
print('---\n reconstructed images norm: %e' % complex_images.norm())
for i in range(complex_images.number()):
complex_image = complex_images.image(i)
print('--- image %d' % i)
for p in [ \
'version', 'flags', 'data_type', 'channels', \
'slice', 'repetition', \
'image_type', 'image_index', 'image_series_index' \
]:
form = p + ' %d'
print(form % complex_image.info(p))
print('matrix size:'),
print(complex_image.matrix_size())
print('patient_table_position:'),
print(complex_image.patient_table_position())
ind = complex_images.get_info('image_index')
print('image indices:')
print(ind)
ptp = complex_images.get_info('patient_table_position')
print('patient table positions:')
print(ptp)
# sort processed acquisition data;
# sorting currently performed with respect to (in this order):
# - repetition
# - slice
# - kspace encode step 1
print('---\n sorting acquisition data...')
processed_data.sort()
# compute coil sensitivity maps
print('---\n computing coil sensitivity maps...')
csms = CoilSensitivityData()
csms.calculate(processed_data)
# alternatively, coil sensitivity maps can be computed from
# CoilImageData - see coil_sensitivity_maps.py
# create acquisition model based on the acquisition parameters
# stored in processed_data and image parameters stored in complex_images
## acq_model = AcquisitionModel(processed_data, complex_images)
acq_model = AcquisitionModel()
acq_model.set_up(processed_data, complex_images)
acq_model.set_coil_sensitivity_maps(csms)
# use the acquisition model (forward projection) to produce simulated
# acquisition data
simulated_acq_data = acq_model.forward(complex_images)
print('---\n reconstructed images forward projection norm %e'\
% simulated_acq_data.norm())
if output_file is not None:
simulated_acq_data.write(output_file)
# get simulated acquisition data as a Python ndarray
simulated_acq_array = simulated_acq_data.as_array()
# display simulated acquisition data
# simulated_acq_array = numpy.transpose(simulated_acq_array,(1,2,0))
simulated_acq_array = numpy.transpose(simulated_acq_array, (1, 0, 2))
title = 'Simulated acquisition data (magnitude)'
show_3D_array(simulated_acq_array, power = 0.2, suptitle = title, \
xlabel = 'samples', ylabel = 'readouts', label = 'coil')
# backproject simulated acquisition data
backprojected_data = acq_model.backward(simulated_acq_data)
# show backprojected data
backprojected_array = backprojected_data.as_array()
title = 'Backprojected data (magnitude)'
show_3D_array(abs(backprojected_array), suptitle = title, \
xlabel = 'samples', ylabel = 'readouts', label = 'slice')
#%% create a shape
shape = pet.EllipticCylinder()
# define its size (in mm)
shape.set_length(50)
shape.set_radii((30, 40))
# centre of shape in (x,y,z) coordinates where (0,0,0) is centre of first plane
shape.set_origin((60, -30, 20))
#%% add the shape to the image
# first set the image values to 0
image.fill(0)
image.add_shape(shape, scale=1)
#%% add same shape at different location and with different intensity
shape.set_origin((-60, -30, 40))
image.add_shape(shape, scale=0.75)
#%% show the phantom image as a sequence of transverse images
show_3D_array(image.as_array())
#%% forward project this image and display all sinograms
acquired_data = am.forward(image)
acquisition_array = acquired_data.as_array()
show_3D_array(acquisition_array)
#%% Show every 8th view
# Doing this here with a complicated one-liner...
show_3D_array(
acquisition_array[:, range(0, acquisition_array.shape[1], 8), :].transpose(
1, 0, 2))
# You could now of course try the animation of the previous demo...
def main():
# locate the k-space raw data file
input_file = existing_filepath(data_path, data_file)
# acquisition data will be read from an HDF file input_file
acq_data = AcquisitionData(input_file)
print('---\n acquisition data norm: %e' % acq_data.norm())
# pre-process acquisition data
print('---\n pre-processing acquisition data...')
processed_data = preprocess_acquisition_data(acq_data)
print('---\n processed acquisition data norm: %e' % processed_data.norm())
# perform reconstruction to obtain a meaningful ImageData object
# (cannot be obtained in any other way at present)
recon = FullySampledReconstructor()
recon.set_input(processed_data)
recon.process()
complex_images = recon.get_output()
print('---\n reconstructed images norm: %e' % complex_images.norm())
# sort processed acquisition data;
# sorting currently performed with respect to (in this order):
# - repetition
# - slice
# - kspace encode step 1
print('---\n sorting acquisition data...')
processed_data.sort()
# compute coil sensitivity maps
print('---\n computing coil sensitivity maps...')
csms = CoilSensitivityData()
csms.calculate(processed_data)
# alternatively, coil sensitivity maps can be computed from
# CoilImageData - see coil_sensitivity_maps.py
# create acquisition model based on the acquisition parameters
# stored in processed_data and image parameters stored in complex_images
acq_model = AcquisitionModel(processed_data, complex_images)
acq_model.set_coil_sensitivity_maps(csms)
# use the acquisition model (forward projection) to produce simulated
# acquisition data
simulated_acq_data = acq_model.forward(complex_images)
print('---\n reconstructed images forward projection norm %e'\
% simulated_acq_data.norm())
# get simulated acquisition data as a Python ndarray
simulated_acq_array = simulated_acq_data.as_array()
# display simulated acquisition data
# simulated_acq_array = numpy.transpose(simulated_acq_array,(1,2,0))
simulated_acq_array = numpy.transpose(simulated_acq_array, (1, 0, 2))
title = 'Simulated acquisition data (magnitude)'
show_3D_array(simulated_acq_array, power = 0.2, suptitle = title, \
xlabel = 'samples', ylabel = 'readouts', label = 'coil')
# backproject simulated acquisition data
backprojected_data = acq_model.backward(simulated_acq_data)
# show backprojected data
backprojected_array = backprojected_data.as_array()
title = 'Backprojected data (magnitude)'
show_3D_array(abs(backprojected_array), suptitle = title, \
xlabel = 'samples', ylabel = 'readouts', label = 'slice')
def main():
# Acquisitions will be read from this HDF file
input_file = existing_filepath(data_path, data_file)
# Initially we create a container that points to the h5 file. Data is
# not read from file until the gadgetron is called using
# the 'process' method.
# Create an acquisition container of type pGadgetron.AcquisitionData
print('---\n reading in file %s...' % input_file)
acq_data = AcquisitionData(input_file)
# Pre-process this input data using three preparation gadgets
# from gadgetron.
# List gadgets to use (not all may be required for this test data).
prep_gadgets = ['NoiseAdjustGadget', 'AsymmetricEchoAdjustROGadget', \
'RemoveROOversamplingGadget' ]
# Call gadgetron by using the 'process' method. This runs the gadgets
# specified in prep_gadgets, returning an instance
# of an mGadgetron.AcquisitionsContainer
preprocessed_data = acq_data.process(prep_gadgets)
# Extract sorted k-space, permute dimensions and display
acq_array = preprocessed_data.as_array(0)
[ns, nc, nro] = preprocessed_data.dimensions() # [nx ncoil ny]
acq_array = numpy.transpose(acq_array, (1, 0, 2))
title = 'Acquisition data (magnitude)'
show_3D_array(acq_array, power = 0.2, \
suptitle = title, title_size = 16, \
xlabel = 'samples', ylabel = 'readouts', label = 'coil')
# Perform reconstruction of the preprocessed data.
# 1) Create a recon object for the desired reconstruction.
# In this demo, the recon object is created using the class
# Reconstructor(). A simpler class is available in the SIRF code
# for a GRAPPA reconstruction:
# recon = CartesianGRAPPAReconstructor()
recon_gadgets = [
'AcquisitionAccumulateTriggerGadget', 'BucketToBufferGadget',
'GenericReconCartesianReferencePrepGadget',
'GRAPPA:GenericReconCartesianGrappaGadget',
'GenericReconFieldOfViewAdjustmentGadget',
'GenericReconImageArrayScalingGadget', 'ImageArraySplitGadget'
]
recon = Reconstructor(recon_gadgets)
# 2) The GRAPPA gadget can compute G-factors in addition to
# reconstructed images. We can set a gadget property as below if the gadget
# has been identified with a label. In the above list of recon_gadgets,
# the 4th is labelled 'GRAPPA' and we can use this label as below:
recon.set_gadget_property('GRAPPA', 'send_out_gfactor', True)
# If the chain had been set using
# recon = CartesianGRAPPAReconstructor(), an alternative method
# would be available:
# recon.compute_gfactors(True)
# 3) set the reconstruction input to be the data we just preprocessed.
recon.set_input(preprocessed_data)
# 4) Run the reconstruction using 'process' to call gadgetron.
print('---\n reconstructing...\n')
recon.process()
# Output
# Reconstructed data sits in memory. We need to first get data
# for both the reconstructed images and g-factors, before extracting the
# data as Python arrays.
# Get image and gfactor data as objects of type mGadgetron.ImageData
# (Note this syntax may change in the future with the addition of a
# method '.get_gfactor'.)
image_data = recon.get_output('image')
gfact_data = recon.get_output('gfactor')
# Return as Python matrices the data pointed to by the containers.
# Note the image data is complex.
image_as_3D_array = image_data.as_array()
maxv = numpy.amax(abs(image_as_3D_array))
title = 'Reconstructed image data (magnitude)'
show_3D_array(abs(image_as_3D_array), \
suptitle = title, title_size = 16, \
xlabel = 'samples', ylabel = 'readouts', label = 'slice', \
scale = (0, maxv))
gfactor_as_3D_array = gfact_data.as_array()
maxv = numpy.amax(abs(gfactor_as_3D_array))
title = 'G-factor data (magnitude)'
show_3D_array(abs(gfactor_as_3D_array),
suptitle = title, title_size = 16, \
xlabel = 'samples', ylabel = 'readouts', label = 'slice', \
scale = (0, maxv))
# set a portion of bin efficiencies to zero;
bin_efficiencies_array = bin_efficiencies.as_array()
bin_efficiencies_array[:, 5:20, :] = 0
bin_efficiencies.fill(bin_efficiencies_array)
#%% Create a new acquisition model
am2 = pet.AcquisitionModelUsingRayTracingMatrix()
am2.set_num_tangential_LORs(5)
am2.set_up(templ, image)
# now include the bin efficiencies in our acquisition model
asm = pet.AcquisitionSensitivityModel(bin_efficiencies)
am2.set_acquisition_sensitivity(asm)
am2.set_up(templ, image)
#%% forward project the image again with this acquisition model and display
acquired_data = am2.forward(image)
acquisition_array = acquired_data.as_array()
show_3D_array(acquisition_array)
#%% Let us reconstruct this data with the original acquisition model (without bin efficiencies)
obj_fun.set_acquisition_data(acquired_data)
obj_fun.set_acquisition_model(am)
reconstructed_image.fill(1)
recon.set_up(reconstructed_image)
recon.set_num_subiterations(10)
recon.reconstruct(reconstructed_image)
#%% display
# we fix the max for the colour scale related to the true max
cmax = image.as_array().max() * 1.2
reconstructed_array = reconstructed_image.as_array()
plt.figure()
imshow(reconstructed_array[slice, :, :, ], [0, cmax],
'reconstructed image with original acquisition model')
