From d0de394cc4d2be254fc6b1c7c89571b58f7bd30d Mon Sep 17 00:00:00 2001
From: Edoardo Pasca <edo.paskino@gmail.com>
Date: Thu, 19 Oct 2017 13:00:32 +0100
Subject: progress in pythonization
---
src/Python/test_reconstructor-os.py | 66 ++++++++++++++++++++++++-------------
1 file changed, 44 insertions(+), 22 deletions(-)
diff --git a/src/Python/test_reconstructor-os.py b/src/Python/test_reconstructor-os.py
index 6f3721f..3ee92fa 100644
--- a/src/Python/test_reconstructor-os.py
+++ b/src/Python/test_reconstructor-os.py
@@ -139,7 +139,10 @@ if True:
## additional for
proj_geomSUB = proj_geom.copy()
- fistaRecon.residual2 = numpy.zeros(numpy.shape(self.pars['input_sinogram']))
+ fistaRecon.residual2 = numpy.zeros(numpy.shape(fistaRecon.pars['input_sinogram']))
+ residual2 = fistaRecon.residual2
+ sino_updt_FULL = residual.copy()
+
print ("starting iterations")
## % Outer FISTA iterations loop
for i in range(fistaRecon.getParameter('number_of_iterations')):
@@ -153,11 +156,23 @@ if True:
# hence additional work is required one solution is to work with a full
# sinogram at times
- ## https://github.com/vais-ral/CCPi-FISTA_Reconstruction/issues/4
- if (lambdaR_L1 > 0) :
- sino_id2, sino_updt2 = astra.creators.create_sino3d_gpu(
- X, proj_geom, vol_geom)
- astra.matlab.data3d('delete', sino_id2)
+
+ SlicesZ, anglesNumb, Detectors = \
+ numpy.shape(fistaRecon.getParameter('input_sinogram')) ## https://github.com/vais-ral/CCPi-FISTA_Reconstruction/issues/4
+ if (i > 1 and lambdaR_L1 > 0) :
+ for kkk in range(anglesNumb):
+
+ residual2[:,kkk,:] = (weights[:,kkk,:]).squeeze() * \
+ ((sino_updt_FULL[:,kkk,:]).squeeze() - \
+ (sino[:,kkk,:]).squeeze() -\
+ (alpha_ring * r_x)
+ )
+ r_old = fistaRecon.r.copy()
+ vec = residual.sum(axis = 1)
+ #if SlicesZ > 1:
+ # vec = vec[:,1,:] # 1 or 0?
+ r_x = fistaRecon.r_x
+ fistaRecon.r = (r_x - (1./L_const) * vec).copy()
# subset loop
counterInd = 1
@@ -165,8 +180,7 @@ if True:
print ("Subset {0}".format(ss))
X_old = X.copy()
t_old = t
- r_old = fistaRecon.r.copy()
-
+
# the number of projections per subset
numProjSub = fistaRecon.getParameter('os_bins')[ss]
CurrSubIndices = fistaRecon.getParameter('os_indices')\
@@ -198,27 +212,35 @@ if True:
## RING REMOVAL
residual = fistaRecon.residual
- residual2 = fistaRecon.residual2
lambdaR_L1 , alpha_ring , weights , L_const= \
fistaRecon.getParameter(['ring_lambda_R_L1',
'ring_alpha' , 'weights',
'Lipschitz_constant'])
- r_x = fistaRecon.r_x
- SlicesZ, anglesNumb, Detectors = \
- numpy.shape(fistaRecon.getParameter('input_sinogram'))
+ sino_updt_Sub = numpy.zeros(numpy.shape(self.pars['input_sinogram']))
if lambdaR_L1 > 0 :
print ("ring removal")
-## % the ring removal part (Group-Huber fidelity)
-## % first 2 iterations do additional work reconstructing whole dataset to ensure
-## % the stablility
-## if (i < 3)
-## [sino_id2, sino_updt2] = astra_create_sino3d_cuda(X_t, proj_geom, vol_geom);
-## astra_mex_data3d('delete', sino_id2);
-## else
-## [sino_id, sino_updt] = astra_create_sino3d_cuda(X_t, proj_geomSUB, vol_geom);
-## end
+ geometry_type = fistaRecon.getParameter('projector_geometry')['type']
+ if geometry_type == 'parallel' or \
+ geometry_type == 'fanflat' or \
+ geometry_type == 'fanflat_vec' :
+ # here
+ for kkk in range(SlicesZ):
+ sino_id, sinoT[kkk] = \
+ astra.creators.create_sino3d_gpu(
+ X_t[kkk:kkk+1], proj_geomSUB, vol_geom)
+ sino_updt_Sub[kkk] = sinoT.T.copy()
+ astra.matlab.data3d('delete', sino_id)
+
+## % if geometry is 2D use slice-by-slice projection-backprojection routine
+## for kkk = 1:SlicesZ
+## [sino_id, sinoT] = astra_create_sino_cuda(X_t(:,:,kkk), proj_geomSUB, vol_geom);
+## sino_updt_Sub(:,:,kkk) = sinoT';
+## astra_mex_data2d('delete', sino_id);
+## end
+
+##
## https://github.com/vais-ral/CCPi-FISTA_Reconstruction/issues/4
if i < 3:
pass
@@ -254,7 +276,7 @@ if True:
if i < 3:
residual[:,kkk,:] = residual2[:,indC,:].squeeze()
else:
- residual(:,kkk,:) = \
+ residual[:,kkk,:] = \
weights[:,indC,:].squeeze() * sino_updt[:,kkk,:].squeeze() - \
sino[:,indC,:].squeeze() - alpha_ring * fistaRecon.r_x
#squeeze(weights(:,indC,:)).* \
--
cgit v1.2.3
From 98443072f33a1f46eb8ea5ab27741a6400970afa Mon Sep 17 00:00:00 2001
From: Edoardo Pasca <edo.paskino@gmail.com>
Date: Thu, 19 Oct 2017 14:56:20 +0100
Subject: further progress
---
src/Python/test_reconstructor-os.py | 88 +++++++++++++++++++++++--------------
1 file changed, 54 insertions(+), 34 deletions(-)
diff --git a/src/Python/test_reconstructor-os.py b/src/Python/test_reconstructor-os.py
index 3ee92fa..8820db7 100644
--- a/src/Python/test_reconstructor-os.py
+++ b/src/Python/test_reconstructor-os.py
@@ -176,6 +176,23 @@ if True:
# subset loop
counterInd = 1
+ geometry_type = fistaRecon.getParameter('projector_geometry')['type']
+ if geometry_type == 'parallel' or \
+ geometry_type == 'fanflat' or \
+ geometry_type == 'fanflat_vec' :
+
+ for kkk in range(SlicesZ):
+ sino_id, sinoT[kkk] = \
+ astra.creators.create_sino3d_gpu(
+ X_t[kkk:kkk+1], proj_geomSUB, vol_geom)
+ sino_updt_Sub[kkk] = sinoT.T.copy()
+
+ else:
+ sino_id, sino_updt_Sub = \
+ astra.creators.create_sino3d_gpu(X_t, proj_geomSUB, vol_geom)
+
+ astra.matlab.data3d('delete', sino_id)
+
for ss in range(fistaRecon.getParameter('subsets')):
print ("Subset {0}".format(ss))
X_old = X.copy()
@@ -186,29 +203,29 @@ if True:
CurrSubIndices = fistaRecon.getParameter('os_indices')\
[counterInd:counterInd+numProjSub-1]
proj_geomSUB['ProjectionAngles'] = angles[CurrSubIndeces]
+
+ shape = list(numpy.shape(fistaRecon.getParameter('input_sinogram')))
+ shape[1] = numProjSub
+ sino_updt_Sub = numpy.zeros(shape)
+
+ if geometry_type == 'parallel' or \
+ geometry_type == 'fanflat' or \
+ geometry_type == 'fanflat_vec' :
+
+ for kkk in range(SlicesZ):
+ sino_id, sinoT = astra.creators.create_sino3d_gpu (
+ X_t[kkk:kkk+1] , proj_geomSUB, vol_geom)
+ sino_updt_Sub[kkk] = sinoT.T.copy()
+
+ else:
+ # for 3D geometry (watch the GPU memory overflow in ASTRA < 1.8)
+ sino_id, sino_updt_Sub = \
+ astra.creators.create_sino3d_gpu (X_t, proj_geomSUB, vol_geom)
+
+ astra.matlab.data3d('delete', sino_id)
+
-## if fistaRecon.getParameter('projector_geometry')['type'] == 'parallel' or \
-## fistaRecon.getParameter('projector_geometry')['type'] == 'fanflat' or \
-## fistaRecon.getParameter('projector_geometry')['type'] == 'fanflat_vec' :
-## # if the geometry is parallel use slice-by-slice
-## # projection-backprojection routine
-## #sino_updt = zeros(size(sino),'single');
-## proj_geomT = proj_geom.copy()
-## proj_geomT['DetectorRowCount'] = 1
-## vol_geomT = vol_geom.copy()
-## vol_geomT['GridSliceCount'] = 1;
-## sino_updt = numpy.zeros(numpy.shape(sino), dtype=numpy.float)
-## for kkk in range(SlicesZ):
-## sino_id, sino_updt[kkk] = \
-## astra.creators.create_sino3d_gpu(
-## X_t[kkk:kkk+1], proj_geom, vol_geom)
-## astra.matlab.data3d('delete', sino_id)
-## else:
-## # for divergent 3D geometry (watch the GPU memory overflow in
-## # ASTRA versions < 1.8)
-## #[sino_id, sino_updt] = astra_create_sino3d_cuda(X_t, proj_geom, vol_geom);
-## sino_id, sino_updt = astra.creators.create_sino3d_gpu(
-## X_t, proj_geom, vol_geom)
+
## RING REMOVAL
residual = fistaRecon.residual
@@ -217,20 +234,23 @@ if True:
fistaRecon.getParameter(['ring_lambda_R_L1',
'ring_alpha' , 'weights',
'Lipschitz_constant'])
- sino_updt_Sub = numpy.zeros(numpy.shape(self.pars['input_sinogram']))
if lambdaR_L1 > 0 :
print ("ring removal")
- geometry_type = fistaRecon.getParameter('projector_geometry')['type']
- if geometry_type == 'parallel' or \
- geometry_type == 'fanflat' or \
- geometry_type == 'fanflat_vec' :
- # here
- for kkk in range(SlicesZ):
- sino_id, sinoT[kkk] = \
- astra.creators.create_sino3d_gpu(
- X_t[kkk:kkk+1], proj_geomSUB, vol_geom)
- sino_updt_Sub[kkk] = sinoT.T.copy()
- astra.matlab.data3d('delete', sino_id)
+ residualSub = numpy.zeros(shape)
+## for a chosen subset
+## for kkk = 1:numProjSub
+## indC = CurrSubIndeces(kkk);
+## residualSub(:,kkk,:) = squeeze(weights(:,indC,:)).*(squeeze(sino_updt_Sub(:,kkk,:)) - (squeeze(sino(:,indC,:)) - alpha_ring.*r_x));
+## sino_updt_FULL(:,indC,:) = squeeze(sino_updt_Sub(:,kkk,:)); % filling the full sinogram
+## end
+ for kkk in range(numProjSub):
+ indC = CurrSubIndices[kkk]
+ residualSub[:,kkk,:] = weights[:,indC,:].squeeze() * \
+ (sino_updt_Sub[:,kkk,:].squeeze() - \
+ sino[:,indC,:].squeeze() - alpha_ring * r_x)
+ # filling the full sinogram
+ sino_updt_FULL[:,indC,:] = sino_updt_Sub[:,kkk,:].squeeze()
+
## % if geometry is 2D use slice-by-slice projection-backprojection routine
## for kkk = 1:SlicesZ
--
cgit v1.2.3
From d2ce1b74b4ecad5cdecb29207181e09ef0f6013a Mon Sep 17 00:00:00 2001
From: Edoardo Pasca <edo.paskino@gmail.com>
Date: Thu, 19 Oct 2017 15:09:06 +0100
Subject: finished first draft
---
src/Python/test_reconstructor-os.py | 136 ++++++------------------------------
1 file changed, 21 insertions(+), 115 deletions(-)
diff --git a/src/Python/test_reconstructor-os.py b/src/Python/test_reconstructor-os.py
index 8820db7..f6d7d4b 100644
--- a/src/Python/test_reconstructor-os.py
+++ b/src/Python/test_reconstructor-os.py
@@ -250,102 +250,34 @@ if True:
sino[:,indC,:].squeeze() - alpha_ring * r_x)
# filling the full sinogram
sino_updt_FULL[:,indC,:] = sino_updt_Sub[:,kkk,:].squeeze()
-
-
-## % if geometry is 2D use slice-by-slice projection-backprojection routine
-## for kkk = 1:SlicesZ
-## [sino_id, sinoT] = astra_create_sino_cuda(X_t(:,:,kkk), proj_geomSUB, vol_geom);
-## sino_updt_Sub(:,:,kkk) = sinoT';
-## astra_mex_data2d('delete', sino_id);
-## end
-
-##
-## https://github.com/vais-ral/CCPi-FISTA_Reconstruction/issues/4
- if i < 3:
- pass
- else:
- sino_id, sino_updt = astra.creators.create_sino3d_gpu(
- X_t, proj_geomSUB, vol_geom)
-## sino_id, sino_updt = astra.creators.create_sino3d_gpu(
-## X, proj_geom, vol_geom)
-## astra.matlab.data3d('delete', sino_id)
-
- for kkk in range(anglesNumb):
-
- residual2[:,kkk,:] = (weights[:,kkk,:]).squeeze() * \
- ((sino_updt2[:,kkk,:]).squeeze() - \
- (sino[:,kkk,:]).squeeze() -\
- (alpha_ring * r_x)
- )
- shape = list(numpy.shape(fistaRecon.getParameter('input_sinogram')))
- shape[1] = numProjSub
- fistaRecon.residual = numpy.zeros(shape)
- if fistaRecon.residual.__hash__() != residual.__hash__():
- residual = fistaRecon.residual
-## for kkk = 1:numProjSub
-## indC = CurrSubIndeces(kkk);
-## if (i < 3)
-## residual(:,kkk,:) = squeeze(residual2(:,indC,:));
-## else
-## residual(:,kkk,:) = squeeze(weights(:,indC,:)).*(squeeze(sino_updt(:,kkk,:)) - (squeeze(sino(:,indC,:)) - alpha_ring.*r_x));
-## end
-## end
- for kk in range(numProjSub):
- indC = fistaRecon.getParameter('os_indices')[kkk]
- if i < 3:
- residual[:,kkk,:] = residual2[:,indC,:].squeeze()
- else:
- residual[:,kkk,:] = \
- weights[:,indC,:].squeeze() * sino_updt[:,kkk,:].squeeze() - \
- sino[:,indC,:].squeeze() - alpha_ring * fistaRecon.r_x
- #squeeze(weights(:,indC,:)).* \
- # (squeeze(sino_updt(:,kkk,:)) - \
- #(squeeze(sino(:,indC,:)) - alpha_ring.*r_x));
-
-
-
- vec = residual.sum(axis = 1)
- #if SlicesZ > 1:
- # vec = vec[:,1,:].squeeze()
- fistaRecon.r = (r_x - (1./L_const) * vec).copy()
- objective[i] = (0.5 * (residual ** 2).sum())
-## % the ring removal part (Group-Huber fidelity)
-## for kkk = 1:anglesNumb
-## residual(:,kkk,:) = squeeze(weights(:,kkk,:)).*
-## (squeeze(sino_updt(:,kkk,:)) -
-## (squeeze(sino(:,kkk,:)) - alpha_ring.*r_x));
-## end
-## vec = sum(residual,2);
-## if (SlicesZ > 1)
-## vec = squeeze(vec(:,1,:));
-## end
-## r = r_x - (1./L_const).*vec;
-## objective(i) = (0.5*sum(residual(:).^2)); % for the objective function output
-
-
+ else:
+ #PWLS model
+ residualSub = weights[:,CurrSubIndices,:] * \
+ ( sino_updt_Sub - sino[:,CurrSubIndices,:].squeeze() )
+ objective[i] = 0.5 * numpy.linalg.norm(residualSub)
- # Projection/Backprojection Routine
- if fistaRecon.getParameter('projector_geometry')['type'] == 'parallel' or \
- fistaRecon.getParameter('projector_geometry')['type'] == 'fanflat' or\
- fistaRecon.getParameter('projector_geometry')['type'] == 'fanflat_vec':
- x_temp = numpy.zeros(numpy.shape(X),dtype=numpy.float32)
- print ("Projection/Backprojection Routine")
+ if geometry_type == 'parallel' or \
+ geometry_type == 'fanflat' or \
+ geometry_type == 'fanflat_vec' :
+ # if geometry is 2D use slice-by-slice projection-backprojection
+ # routine
+ x_temp = numpy.zeros(numpy.shape(X), dtype=numpy.float32)
for kkk in range(SlicesZ):
x_id, x_temp[kkk] = \
astra.creators.create_backprojection3d_gpu(
- residual[kkk:kkk+1],
- proj_geomT, vol_geomT)
- astra.matlab.data3d('delete', x_id)
+ residualSub[kkk:kkk+1],
+ proj_geomSUB, vol_geom)
+
else:
x_id, x_temp = \
astra.creators.create_backprojection3d_gpu(
- residual, proj_geom, vol_geom)
+ residualSub, proj_geomSUB, vol_geom)
- X = X_t - (1/L_const) * x_temp
- astra.matlab.data3d('delete', sino_id)
astra.matlab.data3d('delete', x_id)
+ X = X_t - (1/L_const) * x_temp
+
## REGULARIZATION
@@ -364,12 +296,9 @@ if True:
fistaRecon.r = numpy.max(
numpy.abs(fistaRecon.r) - lambdaR_L1 , 0) * \
numpy.sign(fistaRecon.r)
- t = (1 + numpy.sqrt(1 + 4 * t**2))/2
- X_t = X + (((t_old -1)/t) * (X - X_old))
-
- if lambdaR_L1 > 0:
- fistaRecon.r_x = fistaRecon.r + \
- (((t_old-1)/t) * (fistaRecon.r - r_old))
+ # updating r
+ r_x = fistaRecon.r + ((t_old-1)/t) * (fistaRecon.r - r_old)
+
if fistaRecon.getParameter('region_of_interest') is None:
string = 'Iteration Number {0} | Objective {1} \n'
@@ -382,30 +311,7 @@ if True:
string = 'Iteration Number {0} | RMS Error {1} | Objective {2} \n'
print (string.format(i,Resid_error[i], objective[i]))
-## if (lambdaR_L1 > 0)
-## r = max(abs(r)-lambdaR_L1, 0).*sign(r); % soft-thresholding operator for ring vector
-## end
-##
-## t = (1 + sqrt(1 + 4*t^2))/2; % updating t
-## X_t = X + ((t_old-1)/t).*(X - X_old); % updating X
-##
-## if (lambdaR_L1 > 0)
-## r_x = r + ((t_old-1)/t).*(r - r_old); % updating r
-## end
-##
-## if (show == 1)
-## figure(10); imshow(X(:,:,slice), [0 maxvalplot]);
-## if (lambdaR_L1 > 0)
-## figure(11); plot(r); title('Rings offset vector')
-## end
-## pause(0.01);
-## end
-## if (strcmp(X_ideal, 'none' ) == 0)
-## Resid_error(i) = RMSE(X(ROI), X_ideal(ROI));
-## fprintf('%s %i %s %s %.4f %s %s %f \n', 'Iteration Number:', i, '|', 'Error RMSE:', Resid_error(i), '|', 'Objective:', objective(i));
-## else
-## fprintf('%s %i %s %s %f \n', 'Iteration Number:', i, '|', 'Objective:', objective(i));
-## end
+
else:
fistaRecon = FISTAReconstructor(proj_geom,
vol_geom,
--
cgit v1.2.3
From 903175ed67f7645fa35edf4623b27999d6cb990f Mon Sep 17 00:00:00 2001
From: Edoardo Pasca <edo.paskino@gmail.com>
Date: Fri, 20 Oct 2017 17:04:26 +0100
Subject: Further development
---
src/Python/ccpi/fista/FISTAReconstructor.py | 24 ++++++
src/Python/test_reconstructor-os.py | 112 ++++++++++++++--------------
2 files changed, 81 insertions(+), 55 deletions(-)
diff --git a/src/Python/ccpi/fista/FISTAReconstructor.py b/src/Python/ccpi/fista/FISTAReconstructor.py
index fda9cf0..85bfac5 100644
--- a/src/Python/ccpi/fista/FISTAReconstructor.py
+++ b/src/Python/ccpi/fista/FISTAReconstructor.py
@@ -583,3 +583,27 @@ class FISTAReconstructor():
string = 'Iteration Number {0} | RMS Error {1} | Objective {2} \n'
print (string.format(i,Resid_error[i], self.objective[i]))
return (X , X_t, t)
+
+ def os_iterate(self, Xin=None):
+ print ("FISTA Reconstructor: iterate")
+
+ if Xin is None:
+ if self.getParameter('initialize'):
+ X = self.initialize()
+ else:
+ N = vol_geom['GridColCount']
+ X = numpy.zeros((N,N,SlicesZ), dtype=numpy.float)
+ else:
+ # copy by reference
+ X = Xin
+ # store the output volume in the parameters
+ self.setParameter(output_volume=X)
+ X_t = X.copy()
+
+ # some useful constants
+ proj_geom , vol_geom, sino , \
+ SlicesZ, weights , alpha_ring ,
+ lambdaR_L1 , L_const = self.getParameter(
+ ['projector_geometry' , 'output_geometry',
+ 'input_sinogram', 'SlicesZ' , 'weights', 'ring_alpha' ,
+ 'ring_lambda_R_L1', 'Lipschitz_constant'])
diff --git a/src/Python/test_reconstructor-os.py b/src/Python/test_reconstructor-os.py
index f6d7d4b..aee70a4 100644
--- a/src/Python/test_reconstructor-os.py
+++ b/src/Python/test_reconstructor-os.py
@@ -122,10 +122,13 @@ if True:
X_t = X.copy()
print ("initialized")
proj_geom , vol_geom, sino , \
- SlicesZ = fistaRecon.getParameter(['projector_geometry' ,
- 'output_geometry',
- 'input_sinogram',
- 'SlicesZ'])
+ SlicesZ, weights , alpha_ring = fistaRecon.getParameter(
+ ['projector_geometry' , 'output_geometry',
+ 'input_sinogram', 'SlicesZ' , 'weights', 'ring_alpha'])
+ lambdaR_L1 , alpha_ring , weights , L_const= \
+ fistaRecon.getParameter(['ring_lambda_R_L1',
+ 'ring_alpha' , 'weights',
+ 'Lipschitz_constant'])
#fistaRecon.setParameter(number_of_iterations = 3)
iterFISTA = fistaRecon.getParameter('number_of_iterations')
@@ -136,12 +139,13 @@ if True:
t = 1
+
## additional for
proj_geomSUB = proj_geom.copy()
fistaRecon.residual2 = numpy.zeros(numpy.shape(fistaRecon.pars['input_sinogram']))
residual2 = fistaRecon.residual2
- sino_updt_FULL = residual.copy()
+ sino_updt_FULL = fistaRecon.residual.copy()
print ("starting iterations")
## % Outer FISTA iterations loop
@@ -156,7 +160,8 @@ if True:
# hence additional work is required one solution is to work with a full
# sinogram at times
-
+ r_old = fistaRecon.r.copy()
+ t_old = t
SlicesZ, anglesNumb, Detectors = \
numpy.shape(fistaRecon.getParameter('input_sinogram')) ## https://github.com/vais-ral/CCPi-FISTA_Reconstruction/issues/4
if (i > 1 and lambdaR_L1 > 0) :
@@ -167,8 +172,8 @@ if True:
(sino[:,kkk,:]).squeeze() -\
(alpha_ring * r_x)
)
- r_old = fistaRecon.r.copy()
- vec = residual.sum(axis = 1)
+
+ vec = fistaRecon.residual.sum(axis = 1)
#if SlicesZ > 1:
# vec = vec[:,1,:] # 1 or 0?
r_x = fistaRecon.r_x
@@ -227,56 +232,53 @@ if True:
- ## RING REMOVAL
- residual = fistaRecon.residual
-
- lambdaR_L1 , alpha_ring , weights , L_const= \
- fistaRecon.getParameter(['ring_lambda_R_L1',
- 'ring_alpha' , 'weights',
- 'Lipschitz_constant'])
- if lambdaR_L1 > 0 :
- print ("ring removal")
- residualSub = numpy.zeros(shape)
-## for a chosen subset
-## for kkk = 1:numProjSub
-## indC = CurrSubIndeces(kkk);
-## residualSub(:,kkk,:) = squeeze(weights(:,indC,:)).*(squeeze(sino_updt_Sub(:,kkk,:)) - (squeeze(sino(:,indC,:)) - alpha_ring.*r_x));
-## sino_updt_FULL(:,indC,:) = squeeze(sino_updt_Sub(:,kkk,:)); % filling the full sinogram
-## end
- for kkk in range(numProjSub):
- indC = CurrSubIndices[kkk]
- residualSub[:,kkk,:] = weights[:,indC,:].squeeze() * \
- (sino_updt_Sub[:,kkk,:].squeeze() - \
- sino[:,indC,:].squeeze() - alpha_ring * r_x)
- # filling the full sinogram
- sino_updt_FULL[:,indC,:] = sino_updt_Sub[:,kkk,:].squeeze()
+ ## RING REMOVAL
+ residual = fistaRecon.residual
+
+
+ if lambdaR_L1 > 0 :
+ print ("ring removal")
+ residualSub = numpy.zeros(shape)
+ ## for a chosen subset
+ ## for kkk = 1:numProjSub
+ ## indC = CurrSubIndeces(kkk);
+ ## residualSub(:,kkk,:) = squeeze(weights(:,indC,:)).*(squeeze(sino_updt_Sub(:,kkk,:)) - (squeeze(sino(:,indC,:)) - alpha_ring.*r_x));
+ ## sino_updt_FULL(:,indC,:) = squeeze(sino_updt_Sub(:,kkk,:)); % filling the full sinogram
+ ## end
+ for kkk in range(numProjSub):
+ indC = CurrSubIndices[kkk]
+ residualSub[:,kkk,:] = weights[:,indC,:].squeeze() * \
+ (sino_updt_Sub[:,kkk,:].squeeze() - \
+ sino[:,indC,:].squeeze() - alpha_ring * r_x)
+ # filling the full sinogram
+ sino_updt_FULL[:,indC,:] = sino_updt_Sub[:,kkk,:].squeeze()
- else:
- #PWLS model
- residualSub = weights[:,CurrSubIndices,:] * \
- ( sino_updt_Sub - sino[:,CurrSubIndices,:].squeeze() )
- objective[i] = 0.5 * numpy.linalg.norm(residualSub)
+ else:
+ #PWLS model
+ residualSub = weights[:,CurrSubIndices,:] * \
+ ( sino_updt_Sub - sino[:,CurrSubIndices,:].squeeze() )
+ objective[i] = 0.5 * numpy.linalg.norm(residualSub)
- if geometry_type == 'parallel' or \
- geometry_type == 'fanflat' or \
- geometry_type == 'fanflat_vec' :
- # if geometry is 2D use slice-by-slice projection-backprojection
- # routine
- x_temp = numpy.zeros(numpy.shape(X), dtype=numpy.float32)
- for kkk in range(SlicesZ):
-
- x_id, x_temp[kkk] = \
- astra.creators.create_backprojection3d_gpu(
- residualSub[kkk:kkk+1],
- proj_geomSUB, vol_geom)
-
- else:
- x_id, x_temp = \
- astra.creators.create_backprojection3d_gpu(
- residualSub, proj_geomSUB, vol_geom)
+ if geometry_type == 'parallel' or \
+ geometry_type == 'fanflat' or \
+ geometry_type == 'fanflat_vec' :
+ # if geometry is 2D use slice-by-slice projection-backprojection
+ # routine
+ x_temp = numpy.zeros(numpy.shape(X), dtype=numpy.float32)
+ for kkk in range(SlicesZ):
+
+ x_id, x_temp[kkk] = \
+ astra.creators.create_backprojection3d_gpu(
+ residualSub[kkk:kkk+1],
+ proj_geomSUB, vol_geom)
+
+ else:
+ x_id, x_temp = \
+ astra.creators.create_backprojection3d_gpu(
+ residualSub, proj_geomSUB, vol_geom)
- astra.matlab.data3d('delete', x_id)
- X = X_t - (1/L_const) * x_temp
+ astra.matlab.data3d('delete', x_id)
+ X = X_t - (1/L_const) * x_temp
--
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