Major reorganization, updated routines

1 files changed, 126 insertions, 0 deletions

diff --git a/demos/DemoRD2.m b/demos/DemoRD2.m
new file mode 100644
index 0000000..ab4da96
--- /dev/null
+++ b/demos/DemoRD2.m
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+% Demonstration of tomographic 3D reconstruction from X-ray synchrotron
+% dataset (dendrites) using various data fidelities
+% warning: can take up to 15-20 minutes to run for the whole 3D data
+clear all
+close all
+%%
+% % adding paths
+addpath('../data/');
+addpath('../main_func/');
+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
+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
+% normalizing the data
+for  jj = 1:slices_tot
+    sino = data_raw3D(:,:,jj);
+    for ii = 1:angSize
+        Sino3D(:,ii,jj) = log((flats_ar(:,jj)-darks_ar(:,jj))./(single(sino(:,ii)) - darks_ar(:,jj)));
+    end
+end
+
+Sino3D = Sino3D.*1000;
+Weights3D = single(data_raw3D); % weights for PW model
+clear data_raw3D
+%%
+% set projection/reconstruction geometry here
+Z_slices = 20;
+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);
+%%
+fprintf('%s\n', 'Reconstruction using FBP...');
+FBP = iradon(Sino3D(:,:,10), angles,recon_size);
+figure; imshow(FBP , [0, 3]); title ('FBP reconstruction');
+%%
+fprintf('%s\n', 'Reconstruction using FISTA-PWLS without regularization...');
+clear params
+params.proj_geom = proj_geom; % pass geometry to the function
+params.vol_geom = vol_geom;
+params.sino = Sino3D;
+params.L_const = 7.6789e+08; % found quickly for one slice first
+params.iterFISTA  = 30;
+params.weights = Weights3D;
+params.show = 1;
+params.maxvalplot = 2.5; params.slice = 4;
+
+tic; [X_fista, output] = FISTA_REC(params); toc;
+figure; imshow(X_fista(:,:,1) , [0, 2.5]); title ('FISTA-PWLS reconstruction');
+%%
+fprintf('%s\n', 'Reconstruction using FISTA-PWLS-TV...');
+clear params
+params.proj_geom = proj_geom; % pass geometry to the function
+params.vol_geom = vol_geom;
+params.sino = Sino3D;
+params.iterFISTA  = 40;
+params.L_const = 7.6789e+08; 
+params.Regul_LambdaTV = 0.005; % TV regularization parameter for FISTA-TV
+params.weights = Weights3D;
+params.show = 1;
+params.maxvalplot = 2.5; params.slice = 10;
+
+tic; [X_fista_TV] = FISTA_REC(params); toc;
+figure; imshow(X_fista_TV(:,:,1) , [0, 2.5]); title ('FISTA-PWLS-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 = Sino3D;
+params.iterFISTA  = 40;
+params.Regul_LambdaTV = 0.005; % TV regularization parameter for FISTA-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.show = 1;
+params.maxvalplot = 2.5; params.slice = 10;
+
+tic; [X_fista_GH_TV] = FISTA_REC(params); toc;
+figure; imshow(X_fista_GH_TV(:,:,1) , [0, 2.5]); title ('FISTA-GH-TV reconstruction');
+%%
+%%
+fprintf('%s\n', 'Reconstruction using FISTA-GH-TV-LLT...');
+clear params
+params.proj_geom = proj_geom; % pass geometry to the function
+params.vol_geom = vol_geom;
+params.sino = Sino3D;
+params.iterFISTA  = 40;
+params.Regul_LambdaTV = 0.005; % TV regularization parameter for FISTA-TV
+params.Regul_LambdaHO = 200;  % regularization parameter for LLT problem
+params.Regul_tauHO = 0.0005; % time-step parameter for the explicit scheme
+params.Regul_iterHO = 250; % the max number of TV iterations
+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.show = 1;
+params.maxvalplot = 2.5; params.slice = 10;
+
+tic; [X_fista_GH_TVLLT] = FISTA_REC(params); toc;
+figure; imshow(X_fista_GH_TVLLT(:,:,1) , [0, 2.5]); title ('FISTA-GH-TV-LLT reconstruction');
+%%
+%%
+% fprintf('%s\n', 'Reconstruction using FISTA-Student-TV...');
+% clear params
+% params.sino = Sino3D(:,:,10);
+% params.N  = recon_size;
+% params.angles = angles_rad;
+% params.iterFISTA  = 100;
+% params.L_const = 0.01; % Lipshitz constant
+% params.lambdaTV = 0.006; % TV regularization parameter for FISTA-TV
+% params.tol = 1.0e-04;
+% params.iterTV = 20;
+% params.fidelity = 'student'; % choosing Student t penalty
+% params.weights = Weights3D(:,:,10);
+% params.show = 0;
+% params.maxvalplot = 2.5; params.slice = 1;
+% 
+% tic; [X_fistaStudentTV] = FISTA_REC(params); toc;
+% figure; imshow(X_fistaStudentTV(:,:,1), [0, 2.5]); title ('FISTA-Student-TV reconstruction');
+%%