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-rw-r--r--demos/Demo_Phantom3D_Cone.m4
-rw-r--r--demos/Demo_Phantom3D_Parallel.m24
-rw-r--r--main_func/FISTA_REC.m43
3 files changed, 44 insertions, 27 deletions
diff --git a/demos/Demo_Phantom3D_Cone.m b/demos/Demo_Phantom3D_Cone.m
index 6419386..3a9178b 100644
--- a/demos/Demo_Phantom3D_Cone.m
+++ b/demos/Demo_Phantom3D_Cone.m
@@ -17,8 +17,8 @@ angles = 0:1.5:360; % angles vector in degrees
angles_rad = angles*(pi/180); % conversion to radians
det_size = round(sqrt(2)*N); % detector size
% in order to run functions you have to go to the directory:
-cd /home/algol/Documents/MATLAB/TomoPhantom/functions/
-TomoPhantom = buildPhantom3D(modelNo,N); % generate 3D phantom
+pathTP = '/home/algol/Documents/MATLAB/TomoPhantom/functions/models/Phantom3DLibrary.dat'; % path to TomoPhantom parameters file
+TomoPhantom = buildPhantom3D(modelNo,N,pathTP); % generate 3D phantom
%%
% using ASTRA-toolbox to set the projection geometry (cone beam)
% eg: astra.create_proj_geom('cone', 1.0 (resol), 1.0 (resol), detectorRowCount, detectorColCount, angles, originToSource, originToDetector)
diff --git a/demos/Demo_Phantom3D_Parallel.m b/demos/Demo_Phantom3D_Parallel.m
index ac9827c..6a54450 100644
--- a/demos/Demo_Phantom3D_Parallel.m
+++ b/demos/Demo_Phantom3D_Parallel.m
@@ -10,19 +10,35 @@ addpath('../supp/');
%%
% build 3D phantom using TomoPhantom and generate projection data
-modelNo = 3; % see Phantom3DLibrary.dat file in TomoPhantom
+modelNo = 2; % see Phantom3DLibrary.dat file in TomoPhantom
N = 256; % x-y-z size (cubic image)
angles = 1:0.5:180; % angles vector in degrees
angles_rad = angles*(pi/180); % conversion to radians
det_size = round(sqrt(2)*N); % detector size
% in order to run functions you have to go to the directory:
-cd /home/algol/Documents/MATLAB/TomoPhantom/functions/
-TomoPhantom = buildPhantom3D(modelNo,N); % generate 3D phantom
-sino_tomophan3D = buildSino3D(modelNo, N, det_size, single(angles)); % generate data
+pathTP = '/home/algol/Documents/MATLAB/TomoPhantom/functions/models/Phantom3DLibrary.dat'; % path to TomoPhantom parameters file
+TomoPhantom = buildPhantom3D(modelNo,N,pathTP); % generate 3D phantom
+sino_tomophan3D = buildSino3D(modelNo, N, det_size, single(angles),pathTP); % generate ideal data
+% Adding noise and distortions if required
+sino_artifacts = sino_add_artifacts(sino_tomophan3D,'rings');
+%
%%
% using ASTRA-toolbox to set the projection geometry (parallel beam)
proj_geom = astra_create_proj_geom('parallel', 1, det_size, angles_rad);
vol_geom = astra_create_vol_geom(N,N);
+%%
+fprintf('%s\n', 'Reconstructing with FBP using ASTRA-toolbox ...');
+for i = 1:k
+vol_id = astra_mex_data2d('create', '-vol', vol_geom, 0);
+proj_id = astra_mex_data2d('create', '-proj3d', proj_geom, sino_artifacts(:,:,k));
+cfg = astra_struct('FBP_CUDA');
+cfg.ProjectionDataId = proj_id;
+cfg.ReconstructionDataId = vol_id;
+cfg.option.MinConstraint = 0;
+alg_id = astra_mex_algorithm('create', cfg);
+astra_mex_algorithm('iterate', alg_id, 15);
+reconASTRA_3D = astra_mex_data2d('get', vol_id);
+end
%%
fprintf('%s\n', 'Reconstruction using FISTA-LS without regularization...');
clear params
diff --git a/main_func/FISTA_REC.m b/main_func/FISTA_REC.m
index d177748..bdaeb18 100644
--- a/main_func/FISTA_REC.m
+++ b/main_func/FISTA_REC.m
@@ -487,7 +487,7 @@ else
% Ordered Subsets (OS) FISTA reconstruction routine (normally one order of magnitude faster than the classical version)
t = 1;
X_t = X;
- proj_geomSUB = proj_geom;
+ proj_geomSUB = proj_geom;
r = zeros(Detectors,SlicesZ, 'single'); % 2D array (for 3D data) of sparse "ring" vectors
r_x = r; % another ring variable
@@ -495,7 +495,7 @@ else
sino_updt_FULL = zeros(size(sino),'single');
% Outer FISTA iterations loop
- for i = 1:iterFISTA
+ for i = 1:iterFISTA
if ((i > 1) && (lambdaR_L1 > 0))
% in order to make Group-Huber fidelity work with ordered subsets
@@ -517,31 +517,31 @@ else
% subsets loop
counterInd = 1;
- if (strcmp(proj_geom.type,'parallel') || strcmp(proj_geom.type,'fanflat') || strcmp(proj_geom.type,'fanflat_vec'))
- % 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
- else
- % for 3D geometry (watch the GPU memory overflow in earlier ASTRA versions < 1.8)
- [sino_id, sino_updt_Sub] = astra_create_sino3d_cuda(X_t, proj_geomSUB, vol_geom);
- astra_mex_data3d('delete', sino_id);
- end
for ss = 1:subsets
X_old = X;
- t_old = t;
+ t_old = t;
numProjSub = binsDiscr(ss); % the number of projections per subset
+ sino_updt_Sub = zeros(Detectors, numProjSub, SlicesZ,'single');
CurrSubIndeces = IndicesReorg(counterInd:(counterInd + numProjSub - 1)); % extract indeces attached to the subset
proj_geomSUB.ProjectionAngles = angles(CurrSubIndeces);
- sino_updt_Sub = zeros(Detectors, numProjSub, SlicesZ,'single');
+
+ if (strcmp(proj_geom.type,'parallel') || strcmp(proj_geom.type,'fanflat') || strcmp(proj_geom.type,'fanflat_vec'))
+ % 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
+ else
+ % for 3D geometry (watch the GPU memory overflow in earlier ASTRA versions < 1.8)
+ [sino_id, sino_updt_Sub] = astra_create_sino3d_cuda(X_t, proj_geomSUB, vol_geom);
+ astra_mex_data3d('delete', sino_id);
+ end
if (lambdaR_L1 > 0)
% Group-Huber fidelity (ring removal)
-
residualSub = zeros(Detectors, numProjSub, SlicesZ,'single'); % residual for a chosen subset
for kkk = 1:numProjSub
indC = CurrSubIndeces(kkk);
@@ -551,8 +551,6 @@ else
elseif (studentt > 0)
% student t data fidelity
-
-
% artifacts removal with Students t penalty
residualSub = squeeze(weights(:,CurrSubIndeces,:)).*(sino_updt_Sub - squeeze(sino(:,CurrSubIndeces,:)));
@@ -566,8 +564,11 @@ else
objective(i) = ff; % for the objective function output
else
% PWLS model
-
+ residualSub = squeeze(weights(:,CurrSubIndeces,:)).*(sino_updt_Sub - squeeze(sino(:,CurrSubIndeces,:)));
+ objective(i) = 0.5*norm(residualSub(:)); % for the objective function output
+ end
+ % perform backprojection of a subset
if (strcmp(proj_geom.type,'parallel') || strcmp(proj_geom.type,'fanflat') || strcmp(proj_geom.type,'fanflat_vec'))
% if geometry is 2D use slice-by-slice projection-backprojection routine
x_temp = zeros(size(X),'single');
@@ -579,7 +580,7 @@ else
astra_mex_data3d('delete', id);
end
- X = X_t - (1/L_const).*x_temp;
+ X = X_t - (1/L_const).*x_temp;
% ----------------Regularization part------------------------%
if (lambdaFGP_TV > 0)
generated by cgit v1.2.3 (git 2.25.1) at 2024-11-08 09:47:37 +0000