Initial revision

1 files changed, 130 insertions, 0 deletions

diff --git a/demo/DemoRD2.m b/demo/DemoRD2.m
new file mode 100644
index 0000000..a8ac2ca
--- /dev/null
+++ b/demo/DemoRD2.m
@@ -0,0 +1,130 @@
+% Demonstration of tomographic 3D reconstruction from X-ray synchrotron 
+% dataset (dendrites) using various data fidelities 
+% clear all
+% close all 
+% 
+% % adding paths
+ addpath('data/'); 
+ addpath('main_func/'); 
+ addpath('supp/'); 
+
+load('sino3D_dendrites.mat') % load 3D normalized sinogram
+angles_rad = angles*(pi/180); % conversion to radians
+
+angSize = size(Sino3D,1); % angles dim
+size_det = size(Sino3D, 2); % detector size
+recon_size = 850; % reconstruction size
+
+FBP = iradon(Sino3D(:,:,10)', angles,recon_size);
+figure; imshow(FBP , [0, 3]); title ('FBP reconstruction');
+
+%%
+fprintf('%s\n', 'Reconstruction using FISTA-LS without regularization...');
+clear params
+params.sino = Sino3D;
+params.N  = recon_size;
+params.angles = angles_rad;
+params.iterFISTA  = 80;
+params.precondition  = 1; % switch on preconditioning
+params.show = 0;
+params.maxvalplot = 2.5; params.slice = 10;
+
+tic; [X_fista] = FISTA_REC(params); toc;
+figure; imshow(X_fista(:,:,10) , [0, 2.5]); title ('FISTA-LS reconstruction');
+%%
+fprintf('%s\n', 'Reconstruction using FISTA-LS-TV...');
+clear params
+params.sino = Sino3D;
+params.N  = recon_size;
+params.angles = angles_rad;
+params.iterFISTA  = 100;
+params.lambdaTV = 0.001; % TV regularization parameter for FISTA-TV
+params.tol = 1.0e-04;
+params.iterTV = 20;
+params.precondition  = 1; % switch on preconditioning
+params.show = 0;
+params.maxvalplot = 2.5; params.slice = 10;
+
+tic; [X_fista_TV] = FISTA_REC(params); toc;
+figure; imshow(X_fista_TV(:,:,10) , [0, 2.5]); title ('FISTA-LS-TV reconstruction');
+%%
+%%
+fprintf('%s\n', 'Reconstruction using FISTA-GH-TV...');
+clear params
+params.sino = Sino3D;
+params.N  = recon_size;
+params.angles = angles_rad;
+params.iterFISTA  = 100;
+params.lambdaTV = 0.001; % TV regularization parameter for FISTA-TV
+params.tol = 1.0e-04;
+params.iterTV = 20;
+params.lambdaR_L1 = 0.001; % Soft-Thresh L1 ring variable parameter
+params.alpha_ring = 20; % to boost ring removal procedure
+params.precondition  = 1; % switch on preconditioning
+params.show = 0;
+params.maxvalplot = 2.5; params.slice = 10;
+
+tic; [X_fista_GH_TV] = FISTA_REC(params); toc;
+figure; imshow(X_fista_GH_TV(:,:,10) , [0, 2.5]); title ('FISTA-GH-TV reconstruction');
+%%
+%%
+fprintf('%s\n', 'Reconstruction using FISTA-GH-TV-LLT...');
+clear params
+params.sino = Sino3D;
+params.N  = recon_size;
+params.angles = angles_rad;
+params.iterFISTA  = 100;
+params.lambdaTV = 0.001; % TV regularization parameter for FISTA-TV
+params.tol = 1.0e-04;
+params.iterTV = 20;
+params.lambdaHO = 35;  % regularization parameter for LLT problem
+params.tauHO = 0.00011; % time-step parameter for explicit scheme
+params.iterHO = 70; % the max number of TV iterations   
+params.lambdaR_L1 = 0.001; % Soft-Thresh L1 ring variable parameter
+params.alpha_ring = 20; % to boost ring removal procedure
+params.precondition  = 1; % switch on preconditioning
+params.show = 0;
+params.maxvalplot = 2.5; params.slice = 10;
+
+tic; [X_fista_GH_TVLLT] = FISTA_REC(params); toc;
+figure; imshow(X_fista_GH_TVLLT(:,:,10) , [0, 2.5]); title ('FISTA-GH-TV-LLT reconstruction');
+%%
+%%
+% fprintf('%s\n', 'Reconstruction using FISTA-Student-TV...');
+% %%%%<<<< Not stable with this dataset! Requires more work >>>> %%%%%
+% clear params
+% params.sino = Sino3D(:,:,15);
+% params.N  = 950;
+% params.angles = angles_rad;
+% params.iterFISTA  = 150;
+% params.L_const = 30; % Lipshitz constant
+% params.lambdaTV = 0.009; % TV regularization parameter for FISTA-TV
+% params.tol = 1.0e-04;
+% params.iterTV = 20;
+% params.fidelity = 'student'; % choosing Student t penalty
+% % params.precondition  = 1; % switch on preconditioning
+% params.show = 1;
+% params.maxvalplot = 2.5; params.slice = 1;
+% 
+% tic; [X_fistaStudentTV] = FISTA_REC(params); toc;
+% figure; imshow(X_fistaStudentTV , [0, 2.5]); title ('FISTA-Student-TV reconstruction');
+%%
+slice = 10; % if 3D reconstruction
+
+fprintf('%s\n', 'Segmentation using OTSU method ...');
+level = graythresh(X_fista(:,:,slice));
+Segm_FISTA = im2bw(X_fista(:,:,slice),level);
+figure; imshow(Segm_FISTA, []); title ('Segmented FISTA-LS reconstruction');
+
+level = graythresh(X_fista_TV(:,:,slice));
+Segm_FISTA_TV = im2bw(X_fista_TV(:,:,slice),level);
+figure; imshow(Segm_FISTA_TV, []); title ('Segmented FISTA-LS-TV reconstruction');
+
+level = graythresh(X_fista_GH_TV(:,:,slice));
+BW_FISTA_GH_TV = im2bw(X_fista_GH_TV(:,:,slice),level);
+figure; imshow(BW_FISTA_GH_TV, []); title ('Segmented FISTA-GH-TV reconstruction');
+
+level = graythresh(X_fista_GH_TVLLT(:,:,slice));
+BW_FISTA_GH_TVLLT = im2bw(X_fista_GH_TVLLT(:,:,slice),level);
+figure; imshow(BW_FISTA_GH_TVLLT, []); title ('Segmented FISTA-GH-TV-LLT reconstruction');
+%%
\ No newline at end of file