diff options
| -rw-r--r-- | demos/Demo_Phantom3D_Cone.m | 4 | ||||
| -rw-r--r-- | demos/Demo_Phantom3D_Parallel.m | 24 | ||||
| -rw-r--r-- | main_func/FISTA_REC.m | 35 |
3 files changed, 48 insertions, 15 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..1e4228d 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 @@ -531,16 +531,29 @@ else 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 @@ -551,8 +564,7 @@ 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 +578,13 @@ 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 +596,7 @@ 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) |