cleaning stage, leaving only FGP/ROF and related compilers, demos

3 files changed, 0 insertions, 171 deletions

diff --git a/Wrappers/Matlab/supp/sino_add_artifacts.m b/Wrappers/Matlab/supp/sino_add_artifacts.m
deleted file mode 100644
index f601914..0000000
--- a/Wrappers/Matlab/supp/sino_add_artifacts.m
+++ /dev/null
@@ -1,33 +0,0 @@
-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
diff --git a/Wrappers/Matlab/supp/studentst.m b/Wrappers/Matlab/supp/studentst.m
deleted file mode 100644
index 99fed1e..0000000
--- a/Wrappers/Matlab/supp/studentst.m
+++ /dev/null
@@ -1,47 +0,0 @@
-function [f,g,h,s,k] = studentst(r,k,s)
-% Students T penalty with 'auto-tuning'
-%
-% use:
-%   [f,g,h,{k,{s}}] = studentst(r)     - automatically fits s and k
-%   [f,g,h,{k,{s}}] = studentst(r,k)   - automatically fits s
-%   [f,g,h,{k,{s}}] = studentst(r,k,s) - use given s and k
-%
-% input:
-%   r - residual as column vector
-%   s - scale (optional)
-%   k - degrees of freedom (optional)
-% 
-% output:
-%   f - misfit (scalar)
-%   g - gradient (column vector)
-%   h - positive approximation of the Hessian (column vector, Hessian is a diagonal matrix)
-%   s,k - scale and degrees of freedom
-%
-% Tristan van Leeuwen, 2012.
-% tleeuwen@eos.ubc.ca
-
-% fit both s and k
-if nargin == 1
-    opts = optimset('maxFunEvals',1e2);
-    tmp = fminsearch(@(x)st(r,x(1),x(2)),[1;2],opts);
-    s   = tmp(1);
-    k   = tmp(2);
-end
-
-
-if nargin == 2
-    opts = optimset('maxFunEvals',1e2);
-    tmp = fminsearch(@(x)st(r,x,k),[1],opts);
-    s   = tmp(1);
-end
-
-% evaulate penalty
-[f,g,h] = st(r,s,k);
-
-
-function [f,g,h] = st(r,s,k)
-n = length(r);
-c = -n*(gammaln((k+1)/2) - gammaln(k/2) - .5*log(pi*s*k));
-f = c + .5*(k+1)*sum(log(1 + conj(r).*r/(s*k)));
-g = (k+1)*r./(s*k + conj(r).*r);
-h = (k+1)./(s*k + conj(r).*r);
diff --git a/Wrappers/Matlab/supp/zing_rings_add.m b/Wrappers/Matlab/supp/zing_rings_add.m
deleted file mode 100644
index d197b1f..0000000
--- a/Wrappers/Matlab/supp/zing_rings_add.m
+++ /dev/null
@@ -1,91 +0,0 @@
-%  uncomment this part of script to generate data with different noise characterisitcs
-
-fprintf('%s\n', 'Generating Projection Data...');
-
-% Creating RHS (b) - the sinogram (using a strip projection model)
-% vol_geom = astra_create_vol_geom(N, N);
-% proj_geom = astra_create_proj_geom('parallel', 1.0, P, theta_rad);
-% proj_id_temp = astra_create_projector('strip', proj_geom, vol_geom);
-% [sinogram_id, sinogramIdeal] = astra_create_sino(phantom, proj_id_temp);
-% astra_mex_data2d('delete',sinogram_id);
-% astra_mex_algorithm('delete',proj_id_temp);
-
-%%
-% inverse crime data generation
-[sino_id, sinogramIdeal] = astra_create_sino3d_cuda(phantom, proj_geom, vol_geom);
-astra_mex_data3d('delete', sino_id);
-
-% [id,x] = astra_create_backprojection3d_cuda(sinogramIdeal, proj_geom, vol_geom);
-% astra_mex_data3d('delete', id);
-%%
-%
-% % adding Gaussian noise
-% eta = 0.04;  % Relative noise level
-% E = randn(size(sinogram));
-% sinogram = sinogram + eta*norm(sinogram,'fro')*E/norm(E,'fro');  % adding noise to the sinogram
-% sinogram(sinogram<0) = 0;
-% clear E;
-
-%%
-% adding zingers
-val_offset = 0;
-sino_zing = sinogramIdeal';
-vec1 = [60, 80, 80, 70, 70, 90, 90, 40, 130, 145, 155, 125];
-vec2 = [350, 450, 190, 500, 250, 530, 330, 230, 550, 250, 450, 195];
-for jj = 1:length(vec1)
-    for i1 = -2:2
-        for j1 = -2:2
-            sino_zing(vec1(jj)+i1, vec2(jj)+j1) = val_offset;
-        end
-    end
-end
-
-% adding stripes into the signogram
-sino_zing_rings = sino_zing;
-coeff = linspace2(0.01,0.15,180);
-vmax = max(sinogramIdeal(:));
-sino_zing_rings(1:180,120) = sino_zing_rings(1:180,120) + vmax*0.13;
-sino_zing_rings(80:180,209) = sino_zing_rings(80:180,209) + vmax*0.14;
-sino_zing_rings(50:110,210) = sino_zing_rings(50:110,210) + vmax*0.12;
-sino_zing_rings(1:180,211) = sino_zing_rings(1:180,211) + vmax*0.14;
-sino_zing_rings(1:180,300) = sino_zing_rings(1:180,300) + vmax*coeff(:);
-sino_zing_rings(1:180,301) = sino_zing_rings(1:180,301) + vmax*0.14;
-sino_zing_rings(10:100,302) = sino_zing_rings(10:100,302) + vmax*0.15;
-sino_zing_rings(90:180,350) = sino_zing_rings(90:180,350) + vmax*0.11;
-sino_zing_rings(60:140,410) = sino_zing_rings(60:140,410) + vmax*0.12;
-sino_zing_rings(1:180,411) = sino_zing_rings(1:180,411) + vmax*0.14;
-sino_zing_rings(1:180,412) = sino_zing_rings(1:180,412) + vmax*coeff(:);
-sino_zing_rings(1:180,413) = sino_zing_rings(1:180,413) + vmax*coeff(:);
-sino_zing_rings(1:180,500) = sino_zing_rings(1:180,500) - vmax*0.12;
-sino_zing_rings(1:180,501) = sino_zing_rings(1:180,501) - vmax*0.12;
-sino_zing_rings(1:180,550) = sino_zing_rings(1:180,550) + vmax*0.11;
-sino_zing_rings(1:180,551) = sino_zing_rings(1:180,551) + vmax*0.11;
-sino_zing_rings(1:180,552) = sino_zing_rings(1:180,552) + vmax*0.11;
-
-sino_zing_rings(sino_zing_rings < 0) = 0;
-%%
-
-% adding Poisson noise
-dose = 50000;
-multifactor = 0.002;
-
-dataExp = dose.*exp(-sino_zing_rings*multifactor); % noiseless raw data
-dataPnoise = astra_add_noise_to_sino(dataExp, dose); % pre-log noisy raw data (weights)
-sino_zing_rings = log(dose./max(dataPnoise,1))/multifactor; %log corrected data -> sinogram
-Dweights = dataPnoise'; % statistical weights
-sino_zing_rings = sino_zing_rings';
-clear dataPnoise dataExp 
-
-% w = dose./exp(sinogram*multifactor); % getting back raw data from log-cor
-
-% figure(1);
-% set(gcf, 'Position', get(0,'Screensize'));
-% subplot(1,2,1); imshow(phantom,[0 0.6]); title('Ideal Phantom'); colorbar;
-% subplot(1,2,2); imshow(sinogram,[0 180]);  title('Noisy Sinogram');  colorbar;
-% colormap(cmapnew);
-
-% figure;
-% set(gcf, 'Position', get(0,'Screensize'));
-% subplot(1,2,1); imshow(sinogramIdeal,[0 180]);  title('Ideal Sinogram');  colorbar;
-% imshow(sino_zing_rings,[0 180]); title('Noisy Sinogram with zingers and stripes');  colorbar;
-% colormap(cmapnew);
\ No newline at end of file