def run_shooting(xml_parameters):
print('[ run_shooting function ]')
print('')
"""
Create the template object
"""
t_list, t_name, t_name_extension, t_noise_variance, multi_object_attachment = \
create_template_metadata(xml_parameters.template_specifications)
print("Object list:", t_list)
template = DeformableMultiObject()
template.object_list = t_list
template.update()
"""
Reading Control points and momenta
"""
# if not (os.path.exists(Settings().output_dir)): Settings().output_dir
if not xml_parameters.initial_control_points is None:
control_points = read_2D_array(xml_parameters.initial_control_points)
else:
raise ArgumentError('Please specify a path to control points to perform a shooting')
if not xml_parameters.initial_momenta is None:
momenta = read_3D_array(xml_parameters.initial_momenta)
else:
raise ArgumentError('Please specify a path to momenta to perform a shooting')
template_data_numpy = template.get_points()
template_data_torch = Variable(torch.from_numpy(template_data_numpy))
momenta_torch = Variable(torch.from_numpy(momenta))
control_points_torch = Variable(torch.from_numpy(control_points))
exp = Exponential()
exp.set_initial_control_points(control_points_torch)
exp.set_initial_template_data(template_data_torch)
exp.number_of_time_points = 10
exp.kernel = kernel_factory.factory(xml_parameters.deformation_kernel_type, xml_parameters.deformation_kernel_width)
exp.set_use_rk2(xml_parameters.use_rk2)
for i in range(len(momenta_torch)):
exp.set_initial_momenta(momenta_torch[i])
exp.update()
deformedPoints = exp.get_template_data()
names = [elt + "_"+ str(i) for elt in t_name]
exp.write_flow(names, t_name_extension, template)
exp.write_control_points_and_momenta_flow("Shooting_"+str(i))
def _exp_parallelize(control_points, initial_momenta, projected_momenta,
xml_parameters):
objects_list, objects_name, objects_name_extension, _, _ = create_template_metadata(
xml_parameters.template_specifications)
template = DeformableMultiObject()
template.object_list = objects_list
template.update()
template_data = template.get_points()
template_data_torch = Variable(
torch.from_numpy(template_data).type(Settings().tensor_scalar_type))
geodesic = Geodesic()
geodesic.concentration_of_time_points = xml_parameters.concentration_of_time_points
geodesic.set_kernel(
kernel_factory.factory(xml_parameters.deformation_kernel_type,
xml_parameters.deformation_kernel_width))
geodesic.set_use_rk2(xml_parameters.use_rk2)
# Those are mandatory parameters.
assert xml_parameters.tmin != -float(
"inf"), "Please specify a minimum time for the geodesic trajectory"
assert xml_parameters.tmax != float(
"inf"), "Please specify a maximum time for the geodesic trajectory"
geodesic.tmin = xml_parameters.tmin
geodesic.tmax = xml_parameters.tmax
if xml_parameters.t0 is None:
geodesic.t0 = geodesic.tmin
else:
geodesic.t0 = xml_parameters.t0
geodesic.set_momenta_t0(initial_momenta)
geodesic.set_control_points_t0(control_points)
geodesic.set_template_data_t0(template_data_torch)
geodesic.update()
# We write the flow of the geodesic
geodesic.write("Regression", objects_name, objects_name_extension,
template)
# Now we transport!
parallel_transport_trajectory = geodesic.parallel_transport(
projected_momenta)
# Getting trajectory caracteristics:
times = geodesic._get_times()
control_points_traj = geodesic._get_control_points_trajectory()
momenta_traj = geodesic._get_momenta_trajectory()
template_data_traj = geodesic._get_template_data_trajectory()
exponential = Exponential()
exponential.number_of_time_points = xml_parameters.number_of_time_points
exponential.set_kernel(
kernel_factory.factory(xml_parameters.deformation_kernel_type,
xml_parameters.deformation_kernel_width))
exponential.set_use_rk2(xml_parameters.use_rk2)
# We save this trajectory, and the corresponding shape trajectory
for i, (time, cp, mom, transported_mom, td) in enumerate(
zip(times, control_points_traj, momenta_traj,
parallel_transport_trajectory, template_data_traj)):
# Writing the momenta/cps
write_2D_array(
cp.data.numpy(),
"control_Points_tp_" + str(i) + "__age_" + str(time) + ".txt")
write_3D_array(mom.data.numpy(),
"momenta_tp_" + str(i) + "__age_" + str(time) + ".txt")
write_3D_array(
transported_mom.data.numpy(),
"transported_momenta_tp_" + str(i) + "__age_" + str(time) + ".txt")
# Shooting from the geodesic:
exponential.set_initial_template_data(td)
exponential.set_initial_control_points(cp)
exponential.set_initial_momenta(transported_mom)
exponential.update()
# Uncomment for massive writing, useful for debugging.
# dir = "exp_"+str(i)+"_"+str(time)
# if not(os.path.isdir(os.path.join(Settings().output_dir, dir))):
# os.mkdir(os.path.join(Settings().output_dir, dir))
# exponential.write_flow([os.path.join(dir, elt) for elt in objects_name],
# objects_name_extension,
# template)
# exponential.write_control_points_and_momenta_flow(os.path.join(dir, "cp_and_mom"))
parallel_td = exponential.get_template_data()
template.set_points(parallel_td)
names = [
objects_name[k] + "_parallel_curve_tp_" + str(i) + "__age_" +
str(time) + "_" + objects_name_extension[k]
for k in range(len(objects_name))
]
template.write(names)