def process_frames(self, data):
import numpy as np
self.pars['input'] = np.nan_to_num(data[0])
# Running Ccpi-RGLTK modules on GPU
if (self.parameters['method'] == 'ROF_TV'):
(im_res,
infogpu) = ROF_TV(self.pars['input'],
self.pars['regularisation_parameter'],
self.pars['number_of_iterations'],
self.pars['time_marching_parameter'],
self.pars['tolerance_constant'], self.device)
if (self.parameters['method'] == 'FGP_TV'):
(im_res, infogpu) = FGP_TV(self.pars['input'],
self.pars['regularisation_parameter'],
self.pars['number_of_iterations'],
self.pars['tolerance_constant'],
self.pars['methodTV'],
self.pars['nonneg'], self.device)
if (self.parameters['method'] == 'SB_TV'):
(im_res, infogpu) = SB_TV(self.pars['input'],
self.pars['regularisation_parameter'],
self.pars['number_of_iterations'],
self.pars['tolerance_constant'],
self.pars['methodTV'], self.device)
if (self.parameters['method'] == 'TGV'):
(im_res,
infogpu) = TGV(self.pars['input'],
self.pars['regularisation_parameter'],
self.pars['alpha1'], self.pars['alpha0'],
self.pars['number_of_iterations'],
self.pars['LipshitzConstant'],
self.pars['tolerance_constant'], self.device)
if (self.parameters['method'] == 'LLT_ROF'):
(im_res,
infogpu) = LLT_ROF(self.pars['input'],
self.pars['regularisation_parameter'],
self.pars['regularisation_parameterLLT'],
self.pars['number_of_iterations'],
self.pars['time_marching_parameter'],
self.pars['tolerance_constant'], self.device)
if (self.parameters['method'] == 'NDF'):
(im_res, infogpu) = NDF(
self.pars['input'], self.pars['regularisation_parameter'],
self.pars['edge_parameter'], self.pars['number_of_iterations'],
self.pars['time_marching_parameter'],
self.pars['penalty_type'], self.pars['tolerance_constant'],
self.device)
if (self.parameters['method'] == 'DIFF4th'):
(im_res,
infogpu) = Diff4th(self.pars['input'],
self.pars['regularisation_parameter'],
self.pars['edge_parameter'],
self.pars['number_of_iterations'],
self.pars['time_marching_parameter'],
self.pars['tolerance_constant'], self.device)
#print "calling process frames", data[0].shape
return im_res
def test_SB_TV_CPU(self):
# set parameters
Im, input, ref = self.getPars()
# call routine
sb_cpu, info = SB_TV(input, 0.02, 150, 0.0, 0, 'cpu')
rms = rmse(Im, sb_cpu)
# now test that it generates some expected output
self.assertAlmostEqual(rms, 0.02, delta=0.01)
a.set_title('Noisy Image')
imgplot = plt.imshow(u0,cmap="gray")
# set parameters
pars = {'algorithm' : SB_TV, \
'input' : u0,\
'regularisation_parameter':0.02, \
'number_of_iterations' :250 ,\
'tolerance_constant':0.0,\
'methodTV': 0}
print ("#############SB-TV CPU####################")
start_time = timeit.default_timer()
(sb_cpu, info_vec_cpu) = SB_TV(pars['input'],
pars['regularisation_parameter'],
pars['number_of_iterations'],
pars['tolerance_constant'],
pars['methodTV'], 'cpu')
Qtools = QualityTools(Im, sb_cpu)
pars['rmse'] = Qtools.rmse()
txtstr = printParametersToString(pars)
txtstr += "%s = %.3fs" % ('elapsed time',timeit.default_timer() - start_time)
print (txtstr)
a=fig.add_subplot(1,4,2)
# these are matplotlib.patch.Patch properties
props = dict(boxstyle='round', facecolor='wheat', alpha=0.75)
# place a text box in upper left in axes coords
def process_frames(self, data):
import numpy as np
#input_temp = data[0]
#indices = np.where(np.isnan(input_temp))
#input_temp[indices] = 0.0
#self.pars['input'] = input_temp
input_temp = np.nan_to_num(data[0])
input_temp[input_temp > 10**15] = 0.0
self.pars['input'] = input_temp
#self.pars['input'] = np.nan_to_num(data[0])
# Running Ccpi-RGLTK modules on GPU
if (self.parameters['method'] == 'ROF_TV'):
(im_res,
infogpu) = ROF_TV(self.pars['input'],
self.pars['regularisation_parameter'],
self.pars['number_of_iterations'],
self.pars['time_marching_parameter'],
self.pars['tolerance_constant'], self.device)
if (self.parameters['method'] == 'FGP_TV'):
(im_res, infogpu) = FGP_TV(self.pars['input'],
self.pars['regularisation_parameter'],
self.pars['number_of_iterations'],
self.pars['tolerance_constant'],
self.pars['methodTV'],
self.pars['nonneg'], self.device)
if (self.parameters['method'] == 'SB_TV'):
(im_res, infogpu) = SB_TV(self.pars['input'],
self.pars['regularisation_parameter'],
self.pars['number_of_iterations'],
self.pars['tolerance_constant'],
self.pars['methodTV'], self.device)
if (self.parameters['method'] == 'TGV'):
(im_res,
infogpu) = TGV(self.pars['input'],
self.pars['regularisation_parameter'],
self.pars['alpha1'], self.pars['alpha0'],
self.pars['number_of_iterations'],
self.pars['LipshitzConstant'],
self.pars['tolerance_constant'], self.device)
if (self.parameters['method'] == 'LLT_ROF'):
(im_res,
infogpu) = LLT_ROF(self.pars['input'],
self.pars['regularisation_parameter'],
self.pars['regularisation_parameterLLT'],
self.pars['number_of_iterations'],
self.pars['time_marching_parameter'],
self.pars['tolerance_constant'], self.device)
if (self.parameters['method'] == 'NDF'):
(im_res, infogpu) = NDF(
self.pars['input'], self.pars['regularisation_parameter'],
self.pars['edge_parameter'], self.pars['number_of_iterations'],
self.pars['time_marching_parameter'],
self.pars['penalty_type'], self.pars['tolerance_constant'],
self.device)
if (self.parameters['method'] == 'DIFF4th'):
(im_res,
infogpu) = Diff4th(self.pars['input'],
self.pars['regularisation_parameter'],
self.pars['edge_parameter'],
self.pars['number_of_iterations'],
self.pars['time_marching_parameter'],
self.pars['tolerance_constant'], self.device)
if (self.parameters['method'] == 'NLTV'):
pars_NLTV = {'algorithm' : PatchSelect, \
'input' : self.pars['input'],\
'searchwindow': 9, \
'patchwindow': 2,\
'neighbours' : 17 ,\
'edge_parameter':self.pars['edge_parameter']}
H_i, H_j, Weights = PatchSelect(pars_NLTV['input'],
pars_NLTV['searchwindow'],
pars_NLTV['patchwindow'],
pars_NLTV['neighbours'],
pars_NLTV['edge_parameter'],
self.device)
parsNLTV_init = {'algorithm' : NLTV, \
'input' : pars_NLTV['input'],\
'H_i': H_i, \
'H_j': H_j,\
'H_k' : 0,\
'Weights' : Weights,\
'regularisation_parameter': self.pars['regularisation_parameter'],\
'iterations': self.pars['number_of_iterations']}
im_res = NLTV(parsNLTV_init['input'], parsNLTV_init['H_i'],
parsNLTV_init['H_j'], parsNLTV_init['H_k'],
parsNLTV_init['Weights'],
parsNLTV_init['regularisation_parameter'],
parsNLTV_init['iterations'])
del H_i, H_j, Weights
#print "calling process frames", data[0].shape
return im_res
def test_SB_TV_CPU_vs_GPU(self):
filename = os.path.join("lena_gray_512.tif")
plt = TiffReader()
# read image
Im = plt.imread(filename)
Im = np.asarray(Im, dtype='float32')
Im = Im / 255
perc = 0.05
u0 = Im + np.random.normal(loc=0, scale=perc * Im, size=np.shape(Im))
u_ref = Im + np.random.normal(
loc=0, scale=0.01 * Im, size=np.shape(Im))
# map the u0 u0->u0>0
# f = np.frompyfunc(lambda x: 0 if x < 0 else x, 1,1)
u0 = u0.astype('float32')
u_ref = u_ref.astype('float32')
print("%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%")
print("____________SB-TV bench___________________")
print("%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%")
# set parameters
pars = {'algorithm' : SB_TV, \
'input' : u0,\
'regularisation_parameter':0.04, \
'number_of_iterations' :150 ,\
'tolerance_constant':1e-05,\
'methodTV': 0 ,\
'printingOut': 0
}
print("#############SB-TV CPU####################")
start_time = timeit.default_timer()
sb_cpu = SB_TV(pars['input'], pars['regularisation_parameter'],
pars['number_of_iterations'],
pars['tolerance_constant'], pars['methodTV'],
pars['printingOut'], 'cpu')
rms = rmse(Im, sb_cpu)
pars['rmse'] = rms
txtstr = printParametersToString(pars)
txtstr += "%s = %.3fs" % ('elapsed time',
timeit.default_timer() - start_time)
print(txtstr)
print("##############SB TV GPU##################")
start_time = timeit.default_timer()
try:
sb_gpu = SB_TV(pars['input'], pars['regularisation_parameter'],
pars['number_of_iterations'],
pars['tolerance_constant'], pars['methodTV'],
pars['printingOut'], 'gpu')
except ValueError as ve:
self.assertTrue(True)
return
rms = rmse(Im, sb_gpu)
pars['rmse'] = rms
pars['algorithm'] = SB_TV
txtstr = printParametersToString(pars)
txtstr += "%s = %.3fs" % ('elapsed time',
timeit.default_timer() - start_time)
print(txtstr)
print("--------Compare the results--------")
tolerance = 1e-05
diff_im = np.zeros(np.shape(sb_cpu))
diff_im = abs(sb_cpu - sb_gpu)
diff_im[diff_im > tolerance] = 1
self.assertLessEqual(diff_im.sum(), 1)
def ADMM(
self,
projdata, # tomographic projection data in 2D (sinogram) or 3D array
InitialObject=0, # initialise reconstruction with an array
iterationsADMM=15, # the number of outer ADMM iterations
rho_const=1000.0, # augmented Lagrangian parameter
alpha=1.0, # over-relaxation parameter (ADMM)
regularisation=None, # enable regularisation with CCPi - RGL toolkit
regularisation_parameter=0.01, # regularisation parameter if regularisation is not None
regularisation_parameter2=0.01, # 2nd regularisation parameter (LLT_ROF method)
regularisation_iterations=100, # the number of INNER iterations for regularisation
tolerance_regul=0.0, # tolerance to stop inner (regularisation) iterations / e.g. 1e-06
time_marching_parameter=0.0025, # gradient step parameter (ROF_TV, LLT_ROF, NDF, DIFF4th) penalties
TGV_alpha1=1.0, # TGV specific parameter for the 1st order term
TGV_alpha2=2.0, # TGV specific parameter for the 2st order term
TGV_LipschitzConstant=12.0, # TGV specific parameter for convergence
edge_param=0.01, # edge (noise) threshold parameter for NDF and DIFF4th
NDF_penalty=1, # NDF specific penalty type: 1 - Huber, 2 - Perona-Malik, 3 - Tukey Biweight
NLTV_H_i=0, # NLTV-specific penalty type, the array of i-related indices
NLTV_H_j=0, # NLTV-specific penalty type, the array of j-related indices
NLTV_Weights=0, # NLTV-specific penalty type, the array of Weights
methodTV=0 # 0/1 - isotropic/anisotropic TV
):
def ADMM_Ax(x):
data_upd = self.Atools.A_optomo(x)
x_temp = self.Atools.A_optomo.transposeOpTomo(data_upd)
x_upd = x_temp + self.rho_const * x
return x_upd
def ADMM_Atb(b):
b = self.Atools.A_optomo.transposeOpTomo(b)
return b
self.rho_const = rho_const
(data_dim, rec_dim) = np.shape(self.Atools.A_optomo)
# The dependency on the CCPi-RGL toolkit for regularisation
if regularisation is not None:
if ((regularisation != 'ROF_TV') and (regularisation != 'FGP_TV')
and (regularisation != 'SB_TV')
and (regularisation != 'LLT_ROF')
and (regularisation != 'TGV') and (regularisation != 'NDF')
and (regularisation != 'Diff4th')
and (regularisation != 'NLTV')):
raise (
'Unknown regularisation method, select: ROF_TV, FGP_TV, SB_TV, LLT_ROF, TGV, NDF, Diff4th, NLTV'
)
else:
from ccpi.filters.regularisers import ROF_TV, FGP_TV, SB_TV, LLT_ROF, TGV, NDF, Diff4th, NLTV
# initialise the solution and other ADMM variables
if (np.size(InitialObject) == rec_dim):
# the object has been initialised with an array
X = InitialObject.ravel()
del InitialObject
else:
X = np.zeros(rec_dim, 'float32')
denomN = 1.0 / np.size(X)
z = np.zeros(rec_dim, 'float32')
u = np.zeros(rec_dim, 'float32')
b_to_solver_const = self.Atools.A_optomo.transposeOpTomo(
projdata.ravel())
# Outer ADMM iterations
for iter in range(0, iterationsADMM):
X_old = X
# solving quadratic problem using linalg solver
A_to_solver = scipy.sparse.linalg.LinearOperator(
(rec_dim, rec_dim), matvec=ADMM_Ax, rmatvec=ADMM_Atb)
b_to_solver = b_to_solver_const + self.rho_const * (z - u)
outputSolver = scipy.sparse.linalg.gmres(A_to_solver,
b_to_solver,
tol=self.tolerance,
maxiter=20)
X = np.float32(outputSolver[0]) # get gmres solution
if (self.nonnegativity == 1):
X[X < 0.0] = 0.0
# ADMM iterations stopping criteria
nrm = LA.norm(X - X_old) * denomN
if nrm > self.tolerance:
# z-update with relaxation
zold = z.copy()
x_hat = alpha * X + (1.0 - alpha) * zold
if (self.geom == '2D'):
x_prox_reg = (x_hat + u).reshape(
[self.ObjSize, self.ObjSize])
if (self.geom == '3D'):
x_prox_reg = (x_hat + u).reshape(
[self.DetectorsDimV, self.ObjSize, self.ObjSize])
# Apply regularisation using CCPi-RGL toolkit. The proximal operator of the chosen regulariser
if (regularisation == 'ROF_TV'):
# Rudin - Osher - Fatemi Total variation method
(z, info_vec) = ROF_TV(x_prox_reg,
regularisation_parameter,
regularisation_iterations,
time_marching_parameter,
tolerance_regul, self.device)
if (regularisation == 'FGP_TV'):
# Fast-Gradient-Projection Total variation method
(z, info_vec) = FGP_TV(x_prox_reg,
regularisation_parameter,
regularisation_iterations,
tolerance_regul, methodTV, 0,
self.device)
if (regularisation == 'SB_TV'):
# Split Bregman Total variation method
(z, info_vec) = SB_TV(x_prox_reg, regularisation_parameter,
regularisation_iterations,
tolerance_regul, methodTV,
self.device)
if (regularisation == 'LLT_ROF'):
# Lysaker-Lundervold-Tai + ROF Total variation method
(z,
info_vec) = LLT_ROF(x_prox_reg, regularisation_parameter,
regularisation_parameter2,
regularisation_iterations,
time_marching_parameter,
tolerance_regul, self.device)
if (regularisation == 'TGV'):
# Total Generalised Variation method
(z, info_vec) = TGV(x_prox_reg, regularisation_parameter,
TGV_alpha1, TGV_alpha2,
regularisation_iterations,
TGV_LipschitzConstant, tolerance_regul,
self.device)
if (regularisation == 'NDF'):
# Nonlinear isotropic diffusion method
(z, info_vec) = NDF(x_prox_reg, regularisation_parameter,
edge_param, regularisation_iterations,
time_marching_parameter, NDF_penalty,
tolerance_regul, self.device)
if (regularisation == 'DIFF4th'):
# Anisotropic diffusion of higher order
(z,
info_vec) = Diff4th(x_prox_reg, regularisation_parameter,
edge_param, regularisation_iterations,
time_marching_parameter,
tolerance_regul, self.device)
if (regularisation == 'NLTV'):
# Non-local Total Variation / 2D only
z = NLTV(x_prox_reg, NLTV_H_i, NLTV_H_j, NLTV_H_i,
NLTV_Weights, regularisation_parameter,
regularisation_iterations)
z = z.ravel()
# update u variable
u = u + (x_hat - z)
else:
print('ADMM stopped at iteration', iter)
break
if (self.geom == '2D'):
return X.reshape([self.ObjSize, self.ObjSize])
if (self.geom == '3D'):
return X.reshape([self.DetectorsDimV, self.ObjSize, self.ObjSize])
def FISTA(
self,
projdata, # tomographic projection data in 2D (sinogram) or 3D array
weights=None, # raw projection data for PWLS model
lambdaR_L1=0.0, # regularisation parameter for GH data model
alpha_ring=50, # GH data model convergence accelerator (use carefully !)
huber_data_threshold=0.0, # threshold parameter for __Huber__ data fidelity
student_data_threshold=0.0, # threshold parameter for __Students't__ data fidelity
InitialObject=None, # initialise reconstruction with an array
lipschitz_const=5e+06, # can be a given value or calculated using Power method
iterationsFISTA=100, # the number of OUTER FISTA iterations
regularisation=None, # enable regularisation with CCPi - RGL toolkit
regularisation_parameter=0.01, # regularisation parameter if regularisation is not None
regularisation_parameter2=0.01, # 2nd regularisation parameter (LLT_ROF method)
regularisation_iterations=100, # the number of INNER iterations for regularisation
tolerance_regul=0.0, # tolerance to stop inner (regularisation) iterations / e.g. 1e-06
time_marching_parameter=0.0025, # gradient step parameter (ROF_TV, LLT_ROF, NDF, DIFF4th) penalties
TGV_alpha1=1.0, # TGV specific parameter for the 1st order term
TGV_alpha2=2.0, # TGV specific parameter for the 2st order term
TGV_LipschitzConstant=12.0, # TGV specific parameter for convergence
edge_param=0.01, # edge (noise) threshold parameter for NDF and DIFF4th
NDF_penalty='Huber', # NDF specific penalty type: Huber (default), Perona, Tukey
NLTV_H_i=0, # NLTV-specific penalty type, the array of i-related indices
NLTV_H_j=0, # NLTV-specific penalty type, the array of j-related indices
NLTV_Weights=0, # NLTV-specific penalty type, the array of Weights
methodTV=0 # 0/1 - TV specific isotropic/anisotropic choice
):
L_const_inv = 1.0 / lipschitz_const # inverted Lipschitz constant
if (self.geom == '2D'):
# 2D reconstruction
# initialise the solution
if (np.size(InitialObject) == self.ObjSize**2):
# the object has been initialised with an array
X = InitialObject
del InitialObject
else:
X = np.zeros((self.ObjSize, self.ObjSize),
'float32') # initialise with zeros
r = np.zeros(
(self.DetectorsDimH, 1),
'float32') # 1D array of sparse "ring" variables (GH)
if (self.geom == '3D'):
# initialise the solution
if (np.size(InitialObject) == self.ObjSize**3):
# the object has been initialised with an array
X = InitialObject
del InitialObject
else:
X = np.zeros((self.DetectorsDimV, self.ObjSize, self.ObjSize),
'float32') # initialise with zeros
r = np.zeros(
(self.DetectorsDimV, self.DetectorsDimH),
'float32') # 2D array of sparse "ring" variables (GH)
if (self.OS_number > 1):
regularisation_iterations = (int)(regularisation_iterations /
self.OS_number)
if (NDF_penalty == 'Huber'):
NDF_penalty = 1
elif (NDF_penalty == 'Perona'):
NDF_penalty = 2
elif (NDF_penalty == 'Tukey'):
NDF_penalty = 3
else:
raise ("For NDF_penalty choose Huber, Perona or Tukey")
# The dependency on the CCPi-RGL toolkit for regularisation
if regularisation is not None:
if ((regularisation != 'ROF_TV') and (regularisation != 'FGP_TV')
and (regularisation != 'SB_TV')
and (regularisation != 'LLT_ROF')
and (regularisation != 'TGV') and (regularisation != 'NDF')
and (regularisation != 'Diff4th')
and (regularisation != 'NLTV')):
raise (
'Unknown regularisation method, select: ROF_TV, FGP_TV, SB_TV, LLT_ROF, TGV, NDF, Diff4th, NLTV'
)
else:
from ccpi.filters.regularisers import ROF_TV, FGP_TV, SB_TV, LLT_ROF, TGV, NDF, Diff4th, NLTV
#****************************************************************************#
# FISTA (model-based modification) algorithm begins here:
t = 1.0
denomN = 1.0 / np.size(X)
X_t = np.copy(X)
r_x = r.copy()
# Outer FISTA iterations
for iter in range(0, iterationsFISTA):
r_old = r
# Do G-H fidelity pre-calculations using the full projections dataset for OS version
if ((self.OS_number > 1) and (lambdaR_L1 > 0.0) and (iter > 0)):
if (self.geom == '2D'):
vec = np.zeros((self.DetectorsDimH))
else:
vec = np.zeros((self.DetectorsDimV, self.DetectorsDimH))
for sub_ind in range(self.OS_number):
#select a specific set of indeces for the subset (OS)
indVec = self.Atools.newInd_Vec[sub_ind, :]
if (indVec[self.Atools.NumbProjBins - 1] == 0):
indVec = indVec[:-1] #shrink vector size
if (self.geom == '2D'):
res = self.Atools.forwprojOS(
X_t, sub_ind) - projdata[indVec, :]
res[:,
0:None] = res[:, 0:None] + alpha_ring * r_x[:, 0]
vec = vec + (1.0 / self.OS_number) * res.sum(axis=0)
else:
res = self.Atools.forwprojOS(
X_t, sub_ind) - projdata[:, indVec, :]
for ang_index in range(len(indVec)):
res[:,
ang_index, :] = res[:,
ang_index, :] + alpha_ring * r_x
vec = res.sum(axis=1)
if (self.geom == '2D'):
r[:, 0] = r_x[:, 0] - np.multiply(L_const_inv, vec)
else:
r = r_x - np.multiply(L_const_inv, vec)
# loop over subsets (OS)
for sub_ind in range(self.OS_number):
X_old = X
t_old = t
if (self.OS_number > 1):
#select a specific set of indeces for the subset (OS)
indVec = self.Atools.newInd_Vec[sub_ind, :]
if (indVec[self.Atools.NumbProjBins - 1] == 0):
indVec = indVec[:-1] #shrink vector size
if (self.OS_number > 1):
# OS-reduced residuals
if (self.geom == '2D'):
if (self.datafidelity == 'LS'):
# 2D Least-squares (LS) data fidelity - OS (linear)
res = self.Atools.forwprojOS(
X_t, sub_ind) - projdata[indVec, :]
elif (self.datafidelity == 'PWLS'):
# 2D Penalised Weighted Least-squares - OS data fidelity (approximately linear)
res = np.multiply(
weights[indVec, :],
(self.Atools.forwprojOS(X_t, sub_ind) -
projdata[indVec, :]))
else:
raise (
"Choose the data fidelity term: LS, PWLS")
# ring removal part for Group-Huber (GH) fidelity (2D)
if ((lambdaR_L1 > 0.0) and (iter > 0)):
res[:,
0:None] = res[:,
0:None] + alpha_ring * r_x[:,
0]
else: # 3D
if (self.datafidelity == 'LS'):
# 3D Least-squares (LS) data fidelity - OS (linear)
res = self.Atools.forwprojOS(
X_t, sub_ind) - projdata[:, indVec, :]
elif (self.datafidelity == 'PWLS'):
# 3D Penalised Weighted Least-squares - OS data fidelity (approximately linear)
res = np.multiply(
weights[:, indVec, :],
(self.Atools.forwprojOS(X_t, sub_ind) -
projdata[:, indVec, :]))
else:
raise (
"Choose the data fidelity term: LS, PWLS")
# GH - fidelity part (3D)
if ((lambdaR_L1 > 0.0) and (iter > 0)):
for ang_index in range(len(indVec)):
res[:,
ang_index, :] = res[:,
ang_index, :] + alpha_ring * r_x
else: # non-OS (classical all-data approach)
if (self.datafidelity == 'LS'):
# full residual for LS fidelity
res = self.Atools.forwproj(X_t) - projdata
elif (self.datafidelity == 'PWLS'):
# full gradient for the PWLS fidelity
res = np.multiply(
weights, (self.Atools.forwproj(X_t) - projdata))
else:
raise ("Choose the data fidelity term: LS, PWLS")
if ((self.geom == '2D') and (lambdaR_L1 > 0.0)
and (iter > 0)): # GH 2D part
res[0:None, :] = res[0:None, :] + alpha_ring * r_x[:,
0]
vec = res.sum(axis=0)
r[:, 0] = r_x[:, 0] - np.multiply(L_const_inv, vec)
if ((self.geom == '3D') and (lambdaR_L1 > 0.0)
and (iter > 0)): # GH 3D part
for ang_index in range(self.angles_number):
res[:,
ang_index, :] = res[:,
ang_index, :] + alpha_ring * r_x
vec = res.sum(axis=1)
r = r_x - np.multiply(L_const_inv, vec)
if (huber_data_threshold > 0.0):
# apply Huber penalty
multHuber = np.ones(np.shape(res))
multHuber[(np.where(
np.abs(res) > huber_data_threshold))] = np.divide(
huber_data_threshold,
np.abs(res[(np.where(
np.abs(res) > huber_data_threshold))]))
if (self.OS_number > 1):
# OS-Huber-gradient
grad_fidelity = self.Atools.backprojOS(
np.multiply(multHuber, res), sub_ind)
else:
# full Huber gradient
grad_fidelity = self.Atools.backproj(
np.multiply(multHuber, res))
elif (student_data_threshold > 0.0):
# apply Students't penalty
multStudent = np.ones(np.shape(res))
multStudent = np.divide(2.0,
student_data_threshold**2 + res**2)
if (self.OS_number > 1):
# OS-Students't-gradient
grad_fidelity = self.Atools.backprojOS(
np.multiply(multStudent, res), sub_ind)
else:
# full Students't gradient
grad_fidelity = self.Atools.backproj(
np.multiply(multStudent, res))
else:
if (self.OS_number > 1):
# OS reduced gradient
grad_fidelity = self.Atools.backprojOS(res, sub_ind)
else:
# full gradient
grad_fidelity = self.Atools.backproj(res)
X = X_t - L_const_inv * grad_fidelity
if (self.nonnegativity == 1):
X[X < 0.0] = 0.0
# The proximal operator of the chosen regulariser
if (regularisation == 'ROF_TV'):
# Rudin - Osher - Fatemi Total variation method
(X, info_vec) = ROF_TV(X, regularisation_parameter,
regularisation_iterations,
time_marching_parameter,
tolerance_regul, self.device)
if (regularisation == 'FGP_TV'):
# Fast-Gradient-Projection Total variation method
(X, info_vec) = FGP_TV(X, regularisation_parameter,
regularisation_iterations,
tolerance_regul, methodTV, 0,
self.device)
if (regularisation == 'SB_TV'):
# Split Bregman Total variation method
(X, info_vec) = SB_TV(X, regularisation_parameter,
regularisation_iterations,
tolerance_regul, methodTV,
self.device)
if (regularisation == 'LLT_ROF'):
# Lysaker-Lundervold-Tai + ROF Total variation method
(X, info_vec) = LLT_ROF(X, regularisation_parameter,
regularisation_parameter2,
regularisation_iterations,
time_marching_parameter,
tolerance_regul, self.device)
if (regularisation == 'TGV'):
# Total Generalised Variation method
(X, info_vec) = TGV(X, regularisation_parameter,
TGV_alpha1, TGV_alpha2,
regularisation_iterations,
TGV_LipschitzConstant, tolerance_regul,
self.device)
if (regularisation == 'NDF'):
# Nonlinear isotropic diffusion method
(X, info_vec) = NDF(X, regularisation_parameter,
edge_param, regularisation_iterations,
time_marching_parameter, NDF_penalty,
tolerance_regul, self.device)
if (regularisation == 'Diff4th'):
# Anisotropic diffusion of higher order
(X, info_vec) = Diff4th(X, regularisation_parameter,
edge_param,
regularisation_iterations,
time_marching_parameter,
tolerance_regul, self.device)
if (regularisation == 'NLTV'):
# Non-local Total Variation
X = NLTV(X, NLTV_H_i, NLTV_H_j, NLTV_H_i, NLTV_Weights,
regularisation_parameter,
regularisation_iterations)
t = (1.0 + np.sqrt(1.0 + 4.0 * t**2)) * 0.5
# updating t variable
X_t = X + ((t_old - 1.0) / t) * (X - X_old) # updating X
if ((lambdaR_L1 > 0.0) and (iter > 0)):
r = np.maximum((np.abs(r) - lambdaR_L1), 0.0) * np.sign(
r) # soft-thresholding operator for ring vector
r_x = r + ((t_old - 1.0) / t) * (r - r_old) # updating r
# stopping criteria
nrm = LA.norm(X - X_old) * denomN
if nrm < self.tolerance:
print('FISTA stopped at iteration', iter)
break
return X
imgplot = plt.imshow(noisyVol[10, :, :], cmap="gray")
# set parameters
pars = {'algorithm' : SB_TV, \
'input' : noisyVol,\
'regularisation_parameter':0.04, \
'number_of_iterations' :100 ,\
'tolerance_constant':1e-05,\
'methodTV': 0 ,\
'printingOut': 0
}
print("#############SB TV GPU####################")
start_time = timeit.default_timer()
sb_gpu3D = SB_TV(pars['input'], pars['regularisation_parameter'],
pars['number_of_iterations'], pars['tolerance_constant'],
pars['methodTV'], pars['printingOut'], 'gpu')
rms = rmse(idealVol, sb_gpu3D)
pars['rmse'] = rms
txtstr = printParametersToString(pars)
txtstr += "%s = %.3fs" % ('elapsed time', timeit.default_timer() - start_time)
print(txtstr)
a = fig.add_subplot(1, 2, 2)
# these are matplotlib.patch.Patch properties
props = dict(boxstyle='round', facecolor='wheat', alpha=0.75)
# place a text box in upper left in axes coords
a.text(0.15,
0.25,
def FISTA(
self,
projdata, # tomographic projection data in 2D (sinogram) or 3D array
weights=None, # raw projection data for PWLS model
InitialObject=0, # initialise reconstruction with an array
lipschitz_const=5e+06, # can be a given value or calculated using Power method
iterationsFISTA=100, # the number of OUTER FISTA iterations
regularisation=None, # enable regularisation with CCPi - RGL toolkit
regularisation_parameter=0.01, # regularisation parameter if regularisation is not None
regularisation_parameter2=0.01, # 2nd regularisation parameter (LLT_ROF method)
regularisation_iterations=100, # the number of INNER iterations for regularisation
time_marching_parameter=0.0025, # gradient step parameter (ROF_TV, LLT_ROF, NDF, DIFF4th) penalties
tolerance_regul=1e-06, # tolerance to stop regularisation
TGV_alpha1=1.0, # TGV specific parameter for the 1st order term
TGV_alpha2=0.8, # TGV specific parameter for the 2st order term
TGV_LipschitzConstant=12.0, # TGV specific parameter for convergence
edge_param=0.01, # edge (noise) threshold parameter for NDF and DIFF4th
NDF_penalty=1, # NDF specific penalty type: 1 - Huber, 2 - Perona-Malik, 3 - Tukey Biweight
NLTV_H_i=0, # NLTV-specific penalty type, the array of i-related indices
NLTV_H_j=0, # NLTV-specific penalty type, the array of j-related indices
NLTV_Weights=0, # NLTV-specific penalty type, the array of Weights
methodTV=0, # 0/1 - isotropic/anisotropic TV
nonneg=0 # 0/1 disabled/enabled nonnegativity (for FGP_TV currently)
):
L_const_inv = 1.0 / lipschitz_const # inverted Lipschitz constant
if (self.geom == '2D'):
# 2D reconstruction
# initialise the solution
if (np.size(InitialObject) == self.ObjSize**2):
# the object has been initialised with an array
X = InitialObject
del InitialObject
else:
X = np.zeros((self.ObjSize, self.ObjSize), 'float32')
if (self.geom == '3D'):
# initialise the solution
if (np.size(InitialObject) == self.ObjSize**3):
# the object has been initialised with an array
X = InitialObject
del InitialObject
else:
X = np.zeros((self.ObjSize, self.ObjSize, self.ObjSize),
'float32')
if (self.OS_number > 1):
regularisation_iterations = (int)(regularisation_iterations /
self.OS_number)
# The dependency on the CCPi-RGL toolkit for regularisation
if regularisation is not None:
if ((regularisation != 'ROF_TV') and (regularisation != 'FGP_TV')
and (regularisation != 'SB_TV')
and (regularisation != 'LLT_ROF')
and (regularisation != 'TGV') and (regularisation != 'NDF')
and (regularisation != 'DIFF4th')
and (regularisation != 'NLTV')):
raise (
'Unknown regularisation method, select: ROF_TV, FGP_TV, SB_TV, LLT_ROF, TGV, NDF, DIFF4th, NLTV'
)
else:
from ccpi.filters.regularisers import ROF_TV, FGP_TV, SB_TV, LLT_ROF, TGV, NDF, DIFF4th, NLTV
#****************************************************************************#
# FISTA algorithm begins here:
t = 1.0
denomN = 1.0 / np.size(X)
X_t = np.copy(X)
# Outer FISTA iterations
for iter in range(0, iterationsFISTA):
for sub_ind in range(self.OS_number):
# loop over subsets
X_old = X
t_old = t
if (self.OS_number > 1):
#select a specific set of indeces for the subset (OS)
indVec = self.Atools.newInd_Vec[sub_ind, :]
if (indVec[self.Atools.NumbProjBins - 1] == 0):
indVec = indVec[:-1] #shrink vector size
if (self.datafidelity == 'LS'):
# Least-squares data fidelity (linear)
if (self.OS_number > 1):
# OS-reduced gradient for LS fidelity
if (self.geom == '2D'):
grad_fidelity = self.Atools.backprojOS(
self.Atools.forwprojOS(X_t, sub_ind) -
projdata[indVec, :], sub_ind)
else:
grad_fidelity = self.Atools.backprojOS(
self.Atools.forwprojOS(X_t, sub_ind) -
projdata[:, indVec, :], sub_ind)
else:
# full gradient for LS fidelity
grad_fidelity = self.Atools.backproj(
self.Atools.forwproj(X_t) - projdata)
elif (self.datafidelity == 'PWLS'):
# Penalised Weighted Least-squares data fidelity (approximately linear)
if (self.OS_number > 1):
# OS-reduced gradient for PWLS fidelity
if (self.geom == '2D'):
grad_fidelity = self.Atools.backprojOS(
np.multiply(
weights[indVec, :],
(self.Atools.forwprojOS(X_t, sub_ind) -
projdata[indVec, :])), sub_ind)
else:
grad_fidelity = self.Atools.backprojOS(
np.multiply(
weights[:, indVec, :],
(self.Atools.forwprojOS(X_t, sub_ind) -
projdata[:, indVec, :])), sub_ind)
else:
# full gradient for PWLS fidelity
grad_fidelity = self.Atools.backproj(
np.multiply(
weights,
(self.Atools.forwproj(X_t) - projdata)))
else:
raise ("Choose the data fidelity term: LS, PWLS")
X = X_t - L_const_inv * grad_fidelity
# stopping criteria
nrm = LA.norm(X - X_old) * denomN
if nrm > self.tolerance:
# The proximal operator of the chosen regulariser
if (regularisation == 'ROF_TV'):
# Rudin - Osher - Fatemi Total variation method
X = ROF_TV(X, regularisation_parameter,
regularisation_iterations,
time_marching_parameter, self.device)
if (regularisation == 'FGP_TV'):
# Fast-Gradient-Projection Total variation method
X = FGP_TV(X, regularisation_parameter,
regularisation_iterations, tolerance_regul,
methodTV, nonneg, 0, self.device)
if (regularisation == 'SB_TV'):
# Split Bregman Total variation method
X = SB_TV(X, regularisation_parameter,
regularisation_iterations, tolerance_regul,
methodTV, 0, self.device)
if (regularisation == 'LLT_ROF'):
# Lysaker-Lundervold-Tai + ROF Total variation method
X = LLT_ROF(X, regularisation_parameter,
regularisation_parameter2,
regularisation_iterations,
time_marching_parameter, self.device)
if (regularisation == 'TGV'):
# Total Generalised Variation method (2D only currently)
X = TGV(X, regularisation_parameter, TGV_alpha1,
TGV_alpha2, regularisation_iterations,
TGV_LipschitzConstant,
'cpu') # till gpu version is fixed
if (regularisation == 'NDF'):
# Nonlinear isotropic diffusion method
X = NDF(X, regularisation_parameter, edge_param,
regularisation_iterations,
time_marching_parameter, NDF_penalty,
self.device)
if (regularisation == 'DIFF4th'):
# Anisotropic diffusion of higher order
X = DIFF4th(X, regularisation_parameter, edge_param,
regularisation_iterations,
time_marching_parameter, self.device)
if (regularisation == 'NLTV'):
# Non-local Total Variation
X = NLTV(X, NLTV_H_i, NLTV_H_j, NLTV_H_i, NLTV_Weights,
regularisation_parameter,
regularisation_iterations)
t = (1.0 + np.sqrt(1.0 + 4.0 * t**2)) * 0.5
# updating t variable
X_t = X + ((t_old - 1.0) / t) * (X - X_old) # updating X
else:
#print('FISTA stopped at iteration', iter)
break
#****************************************************************************#
return X