diff options
| -rw-r--r-- | demos/DemoRD1.m | 100 | ||||
| -rw-r--r-- | demos/Demo_Phantom3D_Cone.m | 5 | ||||
| -rw-r--r-- | demos/Demo_Phantom3D_Parallel.m | 79 | ||||
| -rw-r--r-- | demos/Demo_RealData3D_Parallel.m (renamed from demos/DemoRD2.m) | 16 | ||||
| -rw-r--r-- | main_func/FISTA_REC.m | 4 | ||||
| -rw-r--r-- | main_func/regularizers_CPU/FGP_TV.c | 6 | ||||
| -rw-r--r-- | supp/sino_add_artifacts.m | 33 |
7 files changed, 117 insertions, 126 deletions
diff --git a/demos/DemoRD1.m b/demos/DemoRD1.m deleted file mode 100644 index 5bb5f6b..0000000 --- a/demos/DemoRD1.m +++ /dev/null @@ -1,100 +0,0 @@ -% Demonstration of tomographic reconstruction from neutron tomography -% dataset (basalt sample) using Student t data fidelity -clear all -close all - -% adding paths -addpath('../data/'); -addpath('../main_func/'); addpath('../main_func/regularizers_CPU/'); -addpath('../supp/'); - -load('sino_basalt.mat') % load real neutron data - -size_det = size(sino_basalt, 1); % detector size -angSize = size(sino_basalt,2); % angles dim -recon_size = 650; % reconstruction size - -FBP = iradon(sino_basalt, rad2deg(angles),recon_size); -figure; imshow(FBP , [0, 0.45]); title ('FBP reconstruction'); -%% -% set projection/reconstruction geometry here -Z_slices = 1; -det_row_count = Z_slices; -proj_geom = astra_create_proj_geom('parallel3d', 1, 1, det_row_count, size_det, angles); -vol_geom = astra_create_vol_geom(recon_size,recon_size,Z_slices); -%% -fprintf('%s\n', 'Reconstruction using FISTA-LS without regularization...'); -clear params -params.proj_geom = proj_geom; % pass geometry to the function -params.vol_geom = vol_geom; -params.sino = sino_basalt; -params.iterFISTA = 50; -params.show = 0; -params.maxvalplot = 0.6; params.slice = 1; - -tic; [X_fista] = FISTA_REC(params); toc; -figure; imshow(X_fista , [0, 0.45]); title ('FISTA-LS reconstruction'); -%% -fprintf('%s\n', 'Reconstruction using FISTA-LS-TV...'); -clear params -params.proj_geom = proj_geom; % pass geometry to the function -params.vol_geom = vol_geom; -params.sino = sino_basalt; -params.iterFISTA = 60; -params.Regul_LambdaTV = 0.0003; % TV regularization parameter -params.show = 0; -params.maxvalplot = 0.6; params.slice = 1; - -tic; [X_fista_TV] = FISTA_REC(params); toc; -figure; imshow(X_fista_TV , [0, 0.45]); title ('FISTA-LS-TV reconstruction'); -%% -%% -fprintf('%s\n', 'Reconstruction using FISTA-GH-TV...'); -clear params -params.proj_geom = proj_geom; % pass geometry to the function -params.vol_geom = vol_geom; -params.sino = sino_basalt; -params.iterFISTA = 60; -params.Regul_LambdaTV = 0.0003; % TV regularization parameter -params.Ring_LambdaR_L1 = 0.001; % Soft-Thresh L1 ring variable parameter -params.Ring_Alpha = 20; % acceleration for ring variable -params.show = 0; -params.maxvalplot = 0.6; params.slice = 1; - -tic; [X_fista_GH_TV] = FISTA_REC(params); toc; -figure; imshow(X_fista_GH_TV , [0, 0.45]); title ('FISTA-GH-TV reconstruction'); -%% -%% -fprintf('%s\n', 'Reconstruction using FISTA-Student-TV...'); -clear params -params.proj_geom = proj_geom; % pass geometry to the function -params.vol_geom = vol_geom; -params.sino = sino_basalt; -params.iterFISTA = 50; -params.L_const = 3500; % Lipshitz constant -params.Regul_LambdaTV = 0.0003; % TV regularization parameter -params.fidelity = 'student'; % choosing Student t penalty -params.show = 1; -params.initialize = 1; % warm start with SIRT -params.maxvalplot = 0.6; params.slice = 1; - -tic; [X_fistaStudentTV] = FISTA_REC(params); toc; -figure; imshow(X_fistaStudentTV , [0, 0.45]); title ('FISTA-Student-TV reconstruction'); -%% - -fprintf('%s\n', 'Segmentation using OTSU method ...'); -level = graythresh(X_fista); -Segm_FISTA = im2bw(X_fista,level); -figure; imshow(Segm_FISTA, []); title ('Segmented FISTA-LS reconstruction'); - -level = graythresh(X_fista_TV); -Segm_FISTA_TV = im2bw(X_fista_TV,level); -figure; imshow(Segm_FISTA_TV, []); title ('Segmented FISTA-LS-TV reconstruction'); - -level = graythresh(X_fista_GH_TV); -BW_FISTA_GH_TV = im2bw(X_fista_GH_TV,level); -figure; imshow(BW_FISTA_GH_TV, []); title ('Segmented FISTA-GH-TV reconstruction'); - -level = graythresh(X_fistaStudentTV); -BW_FISTA_Student_TV = im2bw(X_fistaStudentTV,level); -figure; imshow(BW_FISTA_Student_TV, []); title ('Segmented FISTA-Student-LS reconstruction');
\ No newline at end of file diff --git a/demos/Demo_Phantom3D_Cone.m b/demos/Demo_Phantom3D_Cone.m index 3a9178b..a8f2c92 100644 --- a/demos/Demo_Phantom3D_Cone.m +++ b/demos/Demo_Phantom3D_Cone.m @@ -8,7 +8,6 @@ addpath('../data/'); addpath('../main_func/'); addpath('../main_func/regularizers_CPU/'); addpath('../main_func/regularizers_GPU/NL_Regul/'); addpath('../main_func/regularizers_GPU/Diffus_HO/'); addpath('../supp/'); - %% % build 3D phantom using TomoPhantom modelNo = 3; % see Phantom3DLibrary.dat file in TomoPhantom @@ -16,9 +15,11 @@ N = 256; % x-y-z size (cubic image) 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: + +%---------TomoPhantom routines---------% 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 6a54450..402bdd2 100644 --- a/demos/Demo_Phantom3D_Parallel.m +++ b/demos/Demo_Phantom3D_Parallel.m @@ -9,48 +9,74 @@ addpath('../main_func/'); addpath('../main_func/regularizers_CPU/'); addpath('.. addpath('../supp/');
%%
-% build 3D phantom using TomoPhantom and generate projection data
+% Main reconstruction/data generation parameters
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:
+
+%---------TomoPhantom routines---------%
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');
+sino_tomophan3D = sino_add_artifacts(sino_tomophan3D,'rings');
+% adding Poisson noise
+dose = 3e9; % photon flux (controls noise level)
+multifactor = max(sino_tomophan3D(:));
+dataExp = dose.*exp(-sino_tomophan3D/multifactor); % noiseless raw data
+dataRaw = astra_add_noise_to_sino(dataExp, dose); % pre-log noisy raw data (weights)
+sino3D_log = log(dose./max(dataRaw,1))*multifactor; %log corrected data -> sinogram
+clear dataExp sino_tomophan3D
%
%%
+%-------------Astra toolbox------------%
+% one can generate data using ASTRA toolbox
+proj_geom = astra_create_proj_geom('parallel', 1, det_size, angles_rad);
+vol_geom = astra_create_vol_geom(N,N);
+sino_ASTRA3D = zeros(det_size, length(angles), N, 'single');
+for i = 1:N
+[sino_id, sinoT] = astra_create_sino_cuda(TomoPhantom(:,:,i), proj_geom, vol_geom);
+sino_ASTRA3D(:,:,i) = sinoT';
+astra_mex_data2d('delete', sino_id);
+end
+%--------------------------------------%
+%%
% 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
+reconASTRA_3D = zeros(size(TomoPhantom),'single');
+for k = 1:N
vol_id = astra_mex_data2d('create', '-vol', vol_geom, 0);
-proj_id = astra_mex_data2d('create', '-proj3d', proj_geom, sino_artifacts(:,:,k));
+proj_id = astra_mex_data2d('create', '-sino', proj_geom, sino3D_log(:,:,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);
+astra_mex_algorithm('iterate', alg_id, 1);
+rec = astra_mex_data2d('get', vol_id);
+reconASTRA_3D(:,:,k) = single(rec);
end
+figure; imshow(reconASTRA_3D(:,:,128), [0 1.3]);
%%
-fprintf('%s\n', 'Reconstruction using FISTA-LS without regularization...');
+%%
+fprintf('%s\n', 'Reconstruction using OS-FISTA-PWLS without regularization...');
clear params
% define parameters
params.proj_geom = proj_geom; % pass geometry to the function
params.vol_geom = vol_geom;
-params.sino = single(sino_tomophan3D); % sinogram
-params.iterFISTA = 5; %max number of outer iterations
+params.sino = single(sino3D_log); % sinogram
+params.iterFISTA = 12; %max number of outer iterations
params.X_ideal = TomoPhantom; % ideal phantom
+params.weights = dataRaw./max(dataRaw(:)); % statistical weight for PWLS
+params.subsets = 12; % the number of subsets
params.show = 1; % visualize reconstruction on each iteration
-params.subsets = 12;
-params.slice = round(N/2); params.maxvalplot = 1;
+params.slice = 1; params.maxvalplot = 1.3;
tic; [X_FISTA, output] = FISTA_REC(params); toc;
error_FISTA = output.Resid_error; obj_FISTA = output.objective;
@@ -63,4 +89,33 @@ subplot(1,2,2); imshow(Resid3D(:,:,params.slice),[0 0.1]); title('residual'); c figure(3);
subplot(1,2,1); plot(error_FISTA); title('RMSE plot');
subplot(1,2,2); plot(obj_FISTA); title('Objective plot');
+%%
+%%
+fprintf('%s\n', 'Reconstruction using OS-FISTA-GH without FGP-TV regularization...');
+clear params
+% define parameters
+params.proj_geom = proj_geom; % pass geometry to the function
+params.vol_geom = vol_geom;
+params.sino = single(sino3D_log); % sinogram
+params.iterFISTA = 15; %max number of outer iterations
+params.X_ideal = TomoPhantom; % ideal phantom
+params.weights = dataRaw./max(dataRaw(:)); % statistical weight for PWLS
+params.subsets = 8; % the number of subsets
+params.Regul_Lambda_FGPTV = 0.003; % TV regularization parameter for FGP-TV
+params.Ring_LambdaR_L1 = 0.02; % Soft-Thresh L1 ring variable parameter
+params.Ring_Alpha = 21; % to boost ring removal procedure
+params.show = 1; % visualize reconstruction on each iteration
+params.slice = 1; params.maxvalplot = 1.3;
+tic; [X_FISTA_GH_TV, output] = FISTA_REC(params); toc;
+
+error_FISTA_GH_TV = output.Resid_error; obj_FISTA_GH_TV = output.objective;
+fprintf('%s %.4f\n', 'Min RMSE for FISTA-PWLS reconstruction is:', min(error_FISTA_GH_TV(:)));
+
+Resid3D = (TomoPhantom - X_FISTA_GH_TV).^2;
+figure(2);
+subplot(1,2,1); imshow(X_FISTA_GH_TV(:,:,params.slice),[0 params.maxvalplot]); title('FISTA-LS reconstruction'); colorbar;
+subplot(1,2,2); imshow(Resid3D(:,:,params.slice),[0 0.1]); title('residual'); colorbar;
+figure(3);
+subplot(1,2,1); plot(error_FISTA_GH_TV); title('RMSE plot');
+subplot(1,2,2); plot(obj_FISTA_GH_TV); title('Objective plot');
%%
\ No newline at end of file diff --git a/demos/DemoRD2.m b/demos/Demo_RealData3D_Parallel.m index 717a55d..e4c9eb0 100644 --- a/demos/DemoRD2.m +++ b/demos/Demo_RealData3D_Parallel.m @@ -11,12 +11,12 @@ addpath('../supp/'); load('DendrRawData.mat') % load raw data of 3D dendritic set angles_rad = angles*(pi/180); % conversion to radians -size_det = size(data_raw3D,1); % detectors dim +det_size = size(data_raw3D,1); % detectors dim angSize = size(data_raw3D, 2); % angles dim slices_tot = size(data_raw3D, 3); % no of slices recon_size = 950; % reconstruction size -Sino3D = zeros(size_det, angSize, slices_tot, 'single'); % log-corrected sino +Sino3D = zeros(det_size, angSize, slices_tot, 'single'); % log-corrected sino % normalizing the data for jj = 1:slices_tot sino = data_raw3D(:,:,jj); @@ -30,10 +30,8 @@ Weights3D = single(data_raw3D); % weights for PW model clear data_raw3D %% % set projection/reconstruction geometry here -Z_slices = 5; -det_row_count = Z_slices; -proj_geom = astra_create_proj_geom('parallel3d', 1, 1, det_row_count, size_det, angles_rad); -vol_geom = astra_create_vol_geom(recon_size,recon_size,Z_slices); +proj_geom = astra_create_proj_geom('parallel', 1, det_size, angles_rad); +vol_geom = astra_create_vol_geom(recon_size,recon_size); %% fprintf('%s\n', 'Reconstruction using FBP...'); FBP = iradon(Sino3D(:,:,10), angles,recon_size); @@ -50,7 +48,7 @@ params.iterFISTA = 12; params.weights = Weights3D; params.subsets = 16; % the number of ordered subsets params.show = 1; -params.maxvalplot = 2.5; params.slice = 2; +params.maxvalplot = 2.5; params.slice = 1; tic; [X_fista, outputFISTA] = FISTA_REC(params); toc; figure; imshow(X_fista(:,:,params.slice) , [0, 2.5]); title ('FISTA-OS-PWLS reconstruction'); @@ -76,13 +74,13 @@ params.proj_geom = proj_geom; % pass geometry to the function params.vol_geom = vol_geom; params.sino = Sino3D; params.iterFISTA = 12; -params.Regul_Lambda_FGPTV = 0.005; % TV regularization parameter for FGP-TV +% params.Regul_Lambda_FGPTV = 0.005; % TV regularization parameter for FGP-TV params.Ring_LambdaR_L1 = 0.002; % Soft-Thresh L1 ring variable parameter params.Ring_Alpha = 21; % to boost ring removal procedure params.weights = Weights3D; params.subsets = 16; % the number of ordered subsets params.show = 1; -params.maxvalplot = 2.5; params.slice = 2; +params.maxvalplot = 2.5; params.slice = 1; tic; [X_fista_GH_TV, outputGHTV] = FISTA_REC(params); toc; figure; imshow(X_fista_GH_TV(:,:,params.slice) , [0, 2.5]); title ('FISTA-OS-GH-TV reconstruction'); diff --git a/main_func/FISTA_REC.m b/main_func/FISTA_REC.m index 1e4228d..3d22b97 100644 --- a/main_func/FISTA_REC.m +++ b/main_func/FISTA_REC.m @@ -685,6 +685,10 @@ else counterInd = counterInd + numProjSub; end + if (i == 1) + r_old = r; + end + % working with a 'ring vector' if (lambdaR_L1 > 0) r = max(abs(r)-lambdaR_L1, 0).*sign(r); % soft-thresholding operator for ring vector diff --git a/main_func/regularizers_CPU/FGP_TV.c b/main_func/regularizers_CPU/FGP_TV.c index 66442c9..30cea1a 100644 --- a/main_func/regularizers_CPU/FGP_TV.c +++ b/main_func/regularizers_CPU/FGP_TV.c @@ -66,7 +66,7 @@ void mexFunction( A = (float *) mxGetData(prhs[0]); /*noisy image (2D/3D) */ lambda = (float) mxGetScalar(prhs[1]); /* regularization parameter */ iter = 50; /* default iterations number */ - epsil = 0.001; /* default tolerance constant */ + epsil = 0.0001; /* default tolerance constant */ methTV = 0; /* default isotropic TV penalty */ if ((nrhs == 3) || (nrhs == 4) || (nrhs == 5)) iter = (int) mxGetScalar(prhs[2]); /* iterations number */ @@ -89,7 +89,7 @@ void mexFunction( tk = 1.0f; tkp1=1.0f; - count = 1; + count = 0; re_old = 0.0f; if (number_of_dims == 2) { @@ -128,7 +128,7 @@ void mexFunction( } re = sqrt(re)/sqrt(re1); if (re < epsil) count++; - if (count > 3) { + if (count > 4) { Obj_func_CALC2D(A, D, funcvalA, lambda, dimX, dimY); break; } diff --git a/supp/sino_add_artifacts.m b/supp/sino_add_artifacts.m new file mode 100644 index 0000000..f601914 --- /dev/null +++ b/supp/sino_add_artifacts.m @@ -0,0 +1,33 @@ +function sino_artifacts = sino_add_artifacts(sino,artifact_type) +% function to add various distortions to the sinogram space, current +% version includes: random rings and zingers (streaks) +% Input: +% 1. sinogram +% 2. artifact type: 'rings' or 'zingers' (streaks) + + +[Detectors, anglesNumb, SlicesZ] = size(sino); +fprintf('%s %i %s %i %s %i %s \n', 'Sinogram has a dimension of', Detectors, 'detectors;', anglesNumb, 'projections;', SlicesZ, 'vertical slices.'); + +sino_artifacts = sino; + +if (strcmp(artifact_type,'rings')) + fprintf('%s \n', 'Adding rings...'); + NumRings = round(Detectors/20); % Number of rings relatively to the size of Detectors + IntenOff = linspace(0.05,0.5,NumRings); % the intensity of rings in the selected range + + for k = 1:SlicesZ + % generate random indices to propagate rings + RandInd = randperm(Detectors,Detectors); + for jj = 1:NumRings + ind_c = RandInd(jj); + sino_artifacts(ind_c,1:end,k) = sino_artifacts(ind_c,1:end,k) + IntenOff(jj).*sino_artifacts(ind_c,1:end,k); % generate a constant offset + end + + end +elseif (strcmp(artifact_type,'zingers')) + fprintf('%s \n', 'Adding zingers...'); +else + fprintf('%s \n', 'Nothing selected, the same sinogram returned...'); +end +end
\ No newline at end of file |