summaryrefslogtreecommitdiffstats
path: root/Wrappers/Matlab
diff options
context:
space:
mode:
authorDaniil Kazantsev <dkazanc@hotmail.com>2018-05-30 10:08:01 +0100
committerDaniil Kazantsev <dkazanc@hotmail.com>2018-05-30 10:08:01 +0100
commit4992d79f8d10749f8e9c32c6dae33bfddd239fbc (patch)
treed327d19f48c8dd96a52ec4f028947e8227efb204 /Wrappers/Matlab
parent44f1bf583985a173ef8ac7a0ed4aa95dc07f2f7a (diff)
downloadregularization-4992d79f8d10749f8e9c32c6dae33bfddd239fbc.tar.gz
regularization-4992d79f8d10749f8e9c32c6dae33bfddd239fbc.tar.bz2
regularization-4992d79f8d10749f8e9c32c6dae33bfddd239fbc.tar.xz
regularization-4992d79f8d10749f8e9c32c6dae33bfddd239fbc.zip
LLT-ROF model added
Diffstat (limited to 'Wrappers/Matlab')
-rw-r--r--Wrappers/Matlab/demos/demoMatlab_3Ddenoise.m68
-rw-r--r--Wrappers/Matlab/demos/demoMatlab_denoise.m20
-rw-r--r--Wrappers/Matlab/mex_compile/compileCPU_mex_Linux.m22
-rw-r--r--Wrappers/Matlab/mex_compile/compileCPU_mex_WINDOWS.m22
-rw-r--r--Wrappers/Matlab/mex_compile/compileGPU_mex.m21
-rw-r--r--Wrappers/Matlab/mex_compile/regularisers_CPU/LLT_ROF.c81
-rw-r--r--Wrappers/Matlab/mex_compile/regularisers_GPU/LLT_ROF_GPU.cpp81
7 files changed, 293 insertions, 22 deletions
diff --git a/Wrappers/Matlab/demos/demoMatlab_3Ddenoise.m b/Wrappers/Matlab/demos/demoMatlab_3Ddenoise.m
index 9a65e37..5cc47b3 100644
--- a/Wrappers/Matlab/demos/demoMatlab_3Ddenoise.m
+++ b/Wrappers/Matlab/demos/demoMatlab_3Ddenoise.m
@@ -6,11 +6,13 @@ addpath(Path1);
addpath(Path2);
N = 512;
-slices = 30;
+slices = 15;
vol3D = zeros(N,N,slices, 'single');
+Ideal3D = zeros(N,N,slices, 'single');
Im = double(imread('lena_gray_512.tif'))/255; % loading image
for i = 1:slices
vol3D(:,:,i) = Im + .05*randn(size(Im));
+Ideal3D(:,:,i) = Im;
end
vol3D(vol3D < 0) = 0;
figure; imshow(vol3D(:,:,15), [0 1]); title('Noisy image');
@@ -23,39 +25,71 @@ tau_rof = 0.0025; % time-marching constant
iter_rof = 300; % number of ROF iterations
tic; u_rof = ROF_TV(single(vol3D), lambda_reg, iter_rof, tau_rof); toc;
energyfunc_val_rof = TV_energy(single(u_rof),single(vol3D),lambda_reg, 1); % get energy function value
-figure; imshow(u_rof(:,:,15), [0 1]); title('ROF-TV denoised volume (CPU)');
+rmse_rof = (RMSE(Ideal3D(:),u_rof(:)));
+fprintf('%s %f \n', 'RMSE error for ROF is:', rmse_rof);
+figure; imshow(u_rof(:,:,7), [0 1]); title('ROF-TV denoised volume (CPU)');
%%
% fprintf('Denoise a volume using the ROF-TV model (GPU) \n');
% tau_rof = 0.0025; % time-marching constant
% iter_rof = 300; % number of ROF iterations
% tic; u_rofG = ROF_TV_GPU(single(vol3D), lambda_reg, iter_rof, tau_rof); toc;
-% figure; imshow(u_rofG(:,:,15), [0 1]); title('ROF-TV denoised volume (GPU)');
+% rmse_rofG = (RMSE(Ideal3D(:),u_rofG(:)));
+% fprintf('%s %f \n', 'RMSE error for ROF is:', rmse_rofG);
+% figure; imshow(u_rofG(:,:,7), [0 1]); title('ROF-TV denoised volume (GPU)');
%%
fprintf('Denoise a volume using the FGP-TV model (CPU) \n');
iter_fgp = 300; % number of FGP iterations
epsil_tol = 1.0e-05; % tolerance
tic; u_fgp = FGP_TV(single(vol3D), lambda_reg, iter_fgp, epsil_tol); toc;
energyfunc_val_fgp = TV_energy(single(u_fgp),single(vol3D),lambda_reg, 1); % get energy function value
-figure; imshow(u_fgp(:,:,15), [0 1]); title('FGP-TV denoised volume (CPU)');
+rmse_fgp = (RMSE(Ideal3D(:),u_fgp(:)));
+fprintf('%s %f \n', 'RMSE error for FGP-TV is:', rmse_fgp);
+figure; imshow(u_fgp(:,:,7), [0 1]); title('FGP-TV denoised volume (CPU)');
%%
% fprintf('Denoise a volume using the FGP-TV model (GPU) \n');
% iter_fgp = 300; % number of FGP iterations
% epsil_tol = 1.0e-05; % tolerance
% tic; u_fgpG = FGP_TV_GPU(single(vol3D), lambda_reg, iter_fgp, epsil_tol); toc;
-% figure; imshow(u_fgpG(:,:,15), [0 1]); title('FGP-TV denoised volume (GPU)');
+% rmse_fgpG = (RMSE(Ideal3D(:),u_fgpG(:)));
+% fprintf('%s %f \n', 'RMSE error for FGP-TV is:', rmse_fgpG);
+% figure; imshow(u_fgpG(:,:,7), [0 1]); title('FGP-TV denoised volume (GPU)');
%%
fprintf('Denoise a volume using the SB-TV model (CPU) \n');
iter_sb = 150; % number of SB iterations
epsil_tol = 1.0e-05; % tolerance
tic; u_sb = SB_TV(single(vol3D), lambda_reg, iter_sb, epsil_tol); toc;
energyfunc_val_sb = TV_energy(single(u_sb),single(vol3D),lambda_reg, 1); % get energy function value
-figure; imshow(u_sb(:,:,15), [0 1]); title('SB-TV denoised volume (CPU)');
+rmse_sb = (RMSE(Ideal3D(:),u_sb(:)));
+fprintf('%s %f \n', 'RMSE error for SB-TV is:', rmse_sb);
+figure; imshow(u_sb(:,:,7), [0 1]); title('SB-TV denoised volume (CPU)');
%%
% fprintf('Denoise a volume using the SB-TV model (GPU) \n');
% iter_sb = 150; % number of SB iterations
% epsil_tol = 1.0e-05; % tolerance
% tic; u_sbG = SB_TV_GPU(single(vol3D), lambda_reg, iter_sb, epsil_tol); toc;
-% figure; imshow(u_sbG(:,:,15), [0 1]); title('SB-TV denoised volume (GPU)');
+% rmse_sbG = (RMSE(Ideal3D(:),u_sbG(:)));
+% fprintf('%s %f \n', 'RMSE error for SB-TV is:', rmse_sbG);
+% figure; imshow(u_sbG(:,:,7), [0 1]); title('SB-TV denoised volume (GPU)');
+%%
+fprintf('Denoise a volume using the ROF-LLT model (CPU) \n');
+lambda_ROF = lambda_reg; % ROF regularisation parameter
+lambda_LLT = lambda_reg*0.35; % LLT regularisation parameter
+iter_LLT = 300; % iterations
+tau_rof_llt = 0.0025; % time-marching constant
+tic; u_rof_llt = LLT_ROF(single(vol3D), lambda_ROF, lambda_LLT, iter_LLT, tau_rof_llt); toc;
+rmse_rof_llt = (RMSE(Ideal3D(:),u_rof_llt(:)));
+fprintf('%s %f \n', 'RMSE error for ROF-LLT is:', rmse_rof_llt);
+figure; imshow(u_rof_llt(:,:,7), [0 1]); title('ROF-LLT denoised volume (CPU)');
+%%
+% fprintf('Denoise a volume using the ROF-LLT model (GPU) \n');
+% lambda_ROF = lambda_reg; % ROF regularisation parameter
+% lambda_LLT = lambda_reg*0.35; % LLT regularisation parameter
+% iter_LLT = 300; % iterations
+% tau_rof_llt = 0.0025; % time-marching constant
+% tic; u_rof_llt_g = LLT_ROF_GPU(single(vol3D), lambda_ROF, lambda_LLT, iter_LLT, tau_rof_llt); toc;
+% rmse_rof_llt = (RMSE(Ideal3D(:),u_rof_llt_g(:)));
+% fprintf('%s %f \n', 'RMSE error for ROF-LLT is:', rmse_rof_llt);
+% figure; imshow(u_rof_llt_g(:,:,7), [0 1]); title('ROF-LLT denoised volume (GPU)');
%%
fprintf('Denoise a volume using Nonlinear-Diffusion model (CPU) \n');
iter_diff = 300; % number of diffusion iterations
@@ -63,7 +97,9 @@ lambda_regDiff = 0.025; % regularisation for the diffusivity
sigmaPar = 0.015; % edge-preserving parameter
tau_param = 0.025; % time-marching constant
tic; u_diff = NonlDiff(single(vol3D), lambda_regDiff, sigmaPar, iter_diff, tau_param, 'Huber'); toc;
-figure; imshow(u_diff(:,:,15), [0 1]); title('Diffusion denoised volume (CPU)');
+rmse_diff = (RMSE(Ideal3D(:),u_diff(:)));
+fprintf('%s %f \n', 'RMSE error for Diffusion is:', rmse_diff);
+figure; imshow(u_diff(:,:,7), [0 1]); title('Diffusion denoised volume (CPU)');
%%
% fprintf('Denoise a volume using Nonlinear-Diffusion model (GPU) \n');
% iter_diff = 300; % number of diffusion iterations
@@ -71,7 +107,9 @@ figure; imshow(u_diff(:,:,15), [0 1]); title('Diffusion denoised volume (CPU)');
% sigmaPar = 0.015; % edge-preserving parameter
% tau_param = 0.025; % time-marching constant
% tic; u_diff_g = NonlDiff_GPU(single(vol3D), lambda_regDiff, sigmaPar, iter_diff, tau_param, 'Huber'); toc;
-% figure; imshow(u_diff_g(:,:,15), [0 1]); title('Diffusion denoised volume (GPU)');
+% rmse_diff = (RMSE(Ideal3D(:),u_diff_g(:)));
+% fprintf('%s %f \n', 'RMSE error for Diffusion is:', rmse_diff);
+% figure; imshow(u_diff_g(:,:,7), [0 1]); title('Diffusion denoised volume (GPU)');
%%
fprintf('Denoise using Fourth-order anisotropic diffusion model (CPU) \n');
iter_diff = 300; % number of diffusion iterations
@@ -79,7 +117,9 @@ lambda_regDiff = 3.5; % regularisation for the diffusivity
sigmaPar = 0.02; % edge-preserving parameter
tau_param = 0.0015; % time-marching constant
tic; u_diff4 = Diffusion_4thO(single(vol3D), lambda_regDiff, sigmaPar, iter_diff, tau_param); toc;
-figure; imshow(u_diff4(:,:,15), [0 1]); title('Diffusion 4thO denoised volume (CPU)');
+rmse_diff4 = (RMSE(Ideal3D(:),u_diff4(:)));
+fprintf('%s %f \n', 'RMSE error for Anis.Diff of 4th order is:', rmse_diff4);
+figure; imshow(u_diff4(:,:,7), [0 1]); title('Diffusion 4thO denoised volume (CPU)');
%%
% fprintf('Denoise using Fourth-order anisotropic diffusion model (GPU) \n');
% iter_diff = 300; % number of diffusion iterations
@@ -87,7 +127,9 @@ figure; imshow(u_diff4(:,:,15), [0 1]); title('Diffusion 4thO denoised volume (C
% sigmaPar = 0.02; % edge-preserving parameter
% tau_param = 0.0015; % time-marching constant
% tic; u_diff4_g = Diffusion_4thO_GPU(single(vol3D), lambda_regDiff, sigmaPar, iter_diff, tau_param); toc;
-% figure; imshow(u_diff4_g(:,:,15), [0 1]); title('Diffusion 4thO denoised volume (GPU)');
+% rmse_diff4 = (RMSE(Ideal3D(:),u_diff4_g(:)));
+% fprintf('%s %f \n', 'RMSE error for Anis.Diff of 4th order is:', rmse_diff4);
+% figure; imshow(u_diff4_g(:,:,7), [0 1]); title('Diffusion 4thO denoised volume (GPU)');
%%
%>>>>>>>>>>>>>> MULTI-CHANNEL priors <<<<<<<<<<<<<<< %
@@ -105,7 +147,7 @@ iter_fgp = 300; % number of FGP iterations
epsil_tol = 1.0e-05; % tolerance
eta = 0.2; % Reference image gradient smoothing constant
tic; u_fgp_dtv = FGP_dTV(single(vol3D), single(vol3D_ref), lambda_reg, iter_fgp, epsil_tol, eta); toc;
-figure; imshow(u_fgp_dtv(:,:,15), [0 1]); title('FGP-dTV denoised volume (CPU)');
+figure; imshow(u_fgp_dtv(:,:,7), [0 1]); title('FGP-dTV denoised volume (CPU)');
%%
fprintf('Denoise a volume using the FGP-dTV model (GPU) \n');
@@ -121,5 +163,5 @@ iter_fgp = 300; % number of FGP iterations
epsil_tol = 1.0e-05; % tolerance
eta = 0.2; % Reference image gradient smoothing constant
tic; u_fgp_dtv_g = FGP_dTV_GPU(single(vol3D), single(vol3D_ref), lambda_reg, iter_fgp, epsil_tol, eta); toc;
-figure; imshow(u_fgp_dtv_g(:,:,15), [0 1]); title('FGP-dTV denoised volume (GPU)');
+figure; imshow(u_fgp_dtv_g(:,:,7), [0 1]); title('FGP-dTV denoised volume (GPU)');
%%
diff --git a/Wrappers/Matlab/demos/demoMatlab_denoise.m b/Wrappers/Matlab/demos/demoMatlab_denoise.m
index 3f0ca54..d11bc63 100644
--- a/Wrappers/Matlab/demos/demoMatlab_denoise.m
+++ b/Wrappers/Matlab/demos/demoMatlab_denoise.m
@@ -79,6 +79,26 @@ figure; imshow(u_tgv, [0 1]); title('TGV denoised image (CPU)');
% fprintf('%s %f \n', 'RMSE error for TGV is:', rmseTGV_gpu);
% figure; imshow(u_tgv_gpu, [0 1]); title('TGV denoised image (GPU)');
%%
+fprintf('Denoise using the ROF-LLT model (CPU) \n');
+lambda_ROF = lambda_reg; % ROF regularisation parameter
+lambda_LLT = lambda_reg*0.45; % LLT regularisation parameter
+iter_LLT = 1; % iterations
+tau_rof_llt = 0.0025; % time-marching constant
+tic; u_rof_llt = LLT_ROF(single(u0), lambda_ROF, lambda_LLT, iter_LLT, tau_rof_llt); toc;
+rmseROFLLT = (RMSE(u_rof_llt(:),Im(:)));
+fprintf('%s %f \n', 'RMSE error for TGV is:', rmseROFLLT);
+figure; imshow(u_rof_llt, [0 1]); title('ROF-LLT denoised image (CPU)');
+%%
+% fprintf('Denoise using the ROF-LLT model (GPU) \n');
+% lambda_ROF = lambda_reg; % ROF regularisation parameter
+% lambda_LLT = lambda_reg*0.45; % LLT regularisation parameter
+% iter_LLT = 500; % iterations
+% tau_rof_llt = 0.0025; % time-marching constant
+% tic; u_rof_llt_g = LLT_ROF_GPU(single(u0), lambda_ROF, lambda_LLT, iter_LLT, tau_rof_llt); toc;
+% rmseROFLLT_g = (RMSE(u_rof_llt_g(:),Im(:)));
+% fprintf('%s %f \n', 'RMSE error for TGV is:', rmseROFLLT_g);
+% figure; imshow(u_rof_llt_g, [0 1]); title('ROF-LLT denoised image (GPU)');
+%%
fprintf('Denoise using Nonlinear-Diffusion model (CPU) \n');
iter_diff = 800; % number of diffusion iterations
lambda_regDiff = 0.025; % regularisation for the diffusivity
diff --git a/Wrappers/Matlab/mex_compile/compileCPU_mex_Linux.m b/Wrappers/Matlab/mex_compile/compileCPU_mex_Linux.m
index 8acc1b7..064b416 100644
--- a/Wrappers/Matlab/mex_compile/compileCPU_mex_Linux.m
+++ b/Wrappers/Matlab/mex_compile/compileCPU_mex_Linux.m
@@ -14,44 +14,60 @@ cd regularisers_CPU
Pathmove = sprintf(['..' fsep 'installed' fsep], 1i);
-fprintf('%s \n', 'Compiling CPU regularisers...');
+fprintf('%s \n', '<<<<<<<<<<<Compiling CPU regularisers>>>>>>>>>>>>>');
+
+fprintf('%s \n', 'Compiling ROF-TV...');
mex ROF_TV.c ROF_TV_core.c utils.c CFLAGS="\$CFLAGS -fopenmp -Wall -std=c99" LDFLAGS="\$LDFLAGS -fopenmp"
movefile('ROF_TV.mex*',Pathmove);
+fprintf('%s \n', 'Compiling FGP-TV...');
mex FGP_TV.c FGP_TV_core.c utils.c CFLAGS="\$CFLAGS -fopenmp -Wall -std=c99" LDFLAGS="\$LDFLAGS -fopenmp"
movefile('FGP_TV.mex*',Pathmove);
+fprintf('%s \n', 'Compiling SB-TV...');
mex SB_TV.c SB_TV_core.c utils.c CFLAGS="\$CFLAGS -fopenmp -Wall -std=c99" LDFLAGS="\$LDFLAGS -fopenmp"
movefile('SB_TV.mex*',Pathmove);
+fprintf('%s \n', 'Compiling dFGP-TV...');
mex FGP_dTV.c FGP_dTV_core.c utils.c CFLAGS="\$CFLAGS -fopenmp -Wall -std=c99" LDFLAGS="\$LDFLAGS -fopenmp"
movefile('FGP_dTV.mex*',Pathmove);
+fprintf('%s \n', 'Compiling TNV...');
mex TNV.c TNV_core.c utils.c CFLAGS="\$CFLAGS -fopenmp -Wall -std=c99" LDFLAGS="\$LDFLAGS -fopenmp"
movefile('TNV.mex*',Pathmove);
+fprintf('%s \n', 'Compiling NonLinear Diffusion...');
mex NonlDiff.c Diffusion_core.c utils.c CFLAGS="\$CFLAGS -fopenmp -Wall -std=c99" LDFLAGS="\$LDFLAGS -fopenmp"
movefile('NonlDiff.mex*',Pathmove);
+fprintf('%s \n', 'Compiling Anisotropic diffusion of higher order...');
mex Diffusion_4thO.c Diffus4th_order_core.c utils.c CFLAGS="\$CFLAGS -fopenmp -Wall -std=c99" LDFLAGS="\$LDFLAGS -fopenmp"
movefile('Diffusion_4thO.mex*',Pathmove);
+fprintf('%s \n', 'Compiling TGV...');
mex TGV.c TGV_core.c utils.c CFLAGS="\$CFLAGS -fopenmp -Wall -std=c99" LDFLAGS="\$LDFLAGS -fopenmp"
movefile('TGV.mex*',Pathmove);
+fprintf('%s \n', 'Compiling ROF-LLT...');
+mex LLT_ROF.c LLT_ROF_core.c utils.c CFLAGS="\$CFLAGS -fopenmp -Wall -std=c99" LDFLAGS="\$LDFLAGS -fopenmp"
+movefile('LLT_ROF.mex*',Pathmove);
+
+fprintf('%s \n', 'Compiling additional tools...');
mex TV_energy.c utils.c CFLAGS="\$CFLAGS -fopenmp -Wall -std=c99" LDFLAGS="\$LDFLAGS -fopenmp"
movefile('TV_energy.mex*',Pathmove);
%############Inpainters##############%
+fprintf('%s \n', 'Compiling Nonlinear/Linear diffusion inpainting...');
mex NonlDiff_Inp.c Diffusion_Inpaint_core.c utils.c CFLAGS="\$CFLAGS -fopenmp -Wall -std=c99" LDFLAGS="\$LDFLAGS -fopenmp"
movefile('NonlDiff_Inp.mex*',Pathmove);
+fprintf('%s \n', 'Compiling Nonlocal marching method for inpaiting...');
mex NonlocalMarching_Inpaint.c NonlocalMarching_Inpaint_core.c utils.c CFLAGS="\$CFLAGS -fopenmp -Wall -std=c99" LDFLAGS="\$LDFLAGS -fopenmp"
movefile('NonlocalMarching_Inpaint.mex*',Pathmove);
-delete SB_TV_core* ROF_TV_core* FGP_TV_core* FGP_dTV_core* TNV_core* utils* Diffusion_core* Diffus4th_order_core* TGV_core* CCPiDefines.h
+delete SB_TV_core* ROF_TV_core* FGP_TV_core* FGP_dTV_core* TNV_core* utils* Diffusion_core* Diffus4th_order_core* TGV_core* LLT_ROF_core* CCPiDefines.h
delete Diffusion_Inpaint_core* NonlocalMarching_Inpaint_core*
-fprintf('%s \n', 'Regularisers successfully compiled!');
+fprintf('%s \n', '<<<<<<< Regularisers successfully compiled! >>>>>>>');
pathA2 = sprintf(['..' fsep '..' fsep], 1i);
cd(pathA2);
diff --git a/Wrappers/Matlab/mex_compile/compileCPU_mex_WINDOWS.m b/Wrappers/Matlab/mex_compile/compileCPU_mex_WINDOWS.m
index ea1ad7d..1b59dc2 100644
--- a/Wrappers/Matlab/mex_compile/compileCPU_mex_WINDOWS.m
+++ b/Wrappers/Matlab/mex_compile/compileCPU_mex_WINDOWS.m
@@ -5,7 +5,7 @@
% not sure if openmp is enabled after the compilation.
% Here I present two ways how software can be compiled, if you have some
-% other suggestions please contact me at dkazanc@hotmail.com
+% other suggestions/remarks please contact me at dkazanc@hotmail.com
% >>>>>>>>>>>>>>>>>>>>>>>>>>>>>
fsep = '/';
@@ -22,38 +22,54 @@ cd regularisers_CPU
Pathmove = sprintf(['..' fsep 'installed' fsep], 1i);
-fprintf('%s \n', 'Compiling CPU regularisers...');
+fprintf('%s \n', '<<<<<<<<<<<Compiling CPU regularisers>>>>>>>>>>>>>');
+
+fprintf('%s \n', 'Compiling ROF-TV...');
mex ROF_TV.c ROF_TV_core.c utils.c COMPFLAGS="\$COMPFLAGS -fopenmp -Wall -std=c99"
movefile('ROF_TV.mex*',Pathmove);
+fprintf('%s \n', 'Compiling FGP-TV...');
mex FGP_TV.c FGP_TV_core.c utils.c COMPFLAGS="\$COMPFLAGS -fopenmp -Wall -std=c99"
movefile('FGP_TV.mex*',Pathmove);
+fprintf('%s \n', 'Compiling SB-TV...');
mex SB_TV.c SB_TV_core.c utils.c COMPFLAGS="\$COMPFLAGS -fopenmp -Wall -std=c99"
movefile('SB_TV.mex*',Pathmove);
+fprintf('%s \n', 'Compiling dFGP-TV...');
mex FGP_dTV.c FGP_dTV_core.c utils.c COMPFLAGS="\$COMPFLAGS -fopenmp -Wall -std=c99"
movefile('FGP_dTV.mex*',Pathmove);
+fprintf('%s \n', 'Compiling TNV...');
mex TNV.c TNV_core.c utils.c COMPFLAGS="\$COMPFLAGS -fopenmp -Wall -std=c99"
movefile('TNV.mex*',Pathmove);
+fprintf('%s \n', 'Compiling NonLinear Diffusion...');
mex NonlDiff.c Diffusion_core.c utils.c COMPFLAGS="\$COMPFLAGS -fopenmp -Wall -std=c99"
movefile('NonlDiff.mex*',Pathmove);
+fprintf('%s \n', 'Compiling Anisotropic diffusion of higher order...');
mex Diffusion_4thO.c Diffus4th_order_core.c utils.c COMPFLAGS="\$COMPFLAGS -fopenmp -Wall -std=c99"
movefile('Diffusion_4thO.mex*',Pathmove);
+fprintf('%s \n', 'Compiling TGV...');
mex TGV.c TGV_core.c utils.c COMPFLAGS="\$COMPFLAGS -fopenmp -Wall -std=c99"
movefile('TGV.mex*',Pathmove);
+fprintf('%s \n', 'Compiling ROF-LLT...');
+mex LLT_ROF.c LLT_ROF_core.c utils.c COMPFLAGS="\$COMPFLAGS -fopenmp -Wall -std=c99"
+movefile('LLT_ROF.mex*',Pathmove);
+
+fprintf('%s \n', 'Compiling additional tools...');
mex TV_energy.c utils.c COMPFLAGS="\$COMPFLAGS -fopenmp -Wall -std=c99"
movefile('TV_energy.mex*',Pathmove);
%############Inpainters##############%
+fprintf('%s \n', 'Compiling Nonlinear/Linear diffusion inpainting...');
mex NonlDiff_Inp.c Diffusion_Inpaint_core.c utils.c COMPFLAGS="\$COMPFLAGS -fopenmp -Wall -std=c99"
movefile('NonlDiff_Inp.mex*',Pathmove);
+fprintf('%s \n', 'Compiling Nonlocal marching method for inpaiting...');
mex NonlocalMarching_Inpaint.c NonlocalMarching_Inpaint_core.c utils.c COMPFLAGS="\$COMPFLAGS -fopenmp -Wall -std=c99"
movefile('NonlocalMarching_Inpaint.mex*',Pathmove);
@@ -87,6 +103,8 @@ fprintf('%s \n', 'Regularisers successfully compiled!');
% movefile('Diffusion_4thO.mex*',Pathmove);
% mex C:\TDMGCC\lib\gcc\x86_64-w64-mingw32\5.1.0\libgomp.a CXXFLAGS="$CXXFLAGS -std=c++11 -fopenmp" TGV.c TGV_core.c utils.c
% movefile('TGV.mex*',Pathmove);
+% mex C:\TDMGCC\lib\gcc\x86_64-w64-mingw32\5.1.0\libgomp.a CXXFLAGS="$CXXFLAGS -std=c++11 -fopenmp" LLT_ROF.c LLT_ROF_core.c utils.c
+% movefile('LLT_ROF.mex*',Pathmove);
% mex C:\TDMGCC\lib\gcc\x86_64-w64-mingw32\5.1.0\libgomp.a CXXFLAGS="$CXXFLAGS -std=c++11 -fopenmp" TV_energy.c utils.c
% movefile('TV_energy.mex*',Pathmove);
% mex C:\TDMGCC\lib\gcc\x86_64-w64-mingw32\5.1.0\libgomp.a CXXFLAGS="$CXXFLAGS -std=c++11 -fopenmp" NonlDiff_Inp.c Diffusion_Inpaint_core.c utils.c
diff --git a/Wrappers/Matlab/mex_compile/compileGPU_mex.m b/Wrappers/Matlab/mex_compile/compileGPU_mex.m
index 003c6ec..e0311ea 100644
--- a/Wrappers/Matlab/mex_compile/compileGPU_mex.m
+++ b/Wrappers/Matlab/mex_compile/compileGPU_mex.m
@@ -9,8 +9,8 @@
% Tested on Ubuntu 16.04/MATLAB 2016b/cuda7.5/gcc4.9
-% It HAS NOT been tested on Windows, please contact me if you'll be able to
-% install software on Windows and I greatefully include it into the release.
+% Installation HAS NOT been tested on Windows, please contact me if you'll be able to
+% install software on Windows and I gratefully include it into the master release.
fsep = '/';
@@ -24,36 +24,49 @@ cd regularisers_GPU
Pathmove = sprintf(['..' fsep 'installed' fsep], 1i);
-fprintf('%s \n', 'Compiling GPU regularisers (CUDA)...');
+fprintf('%s \n', '<<<<<<<<<<<Compiling GPU regularisers (CUDA)>>>>>>>>>>>>>');
+
+fprintf('%s \n', 'Compiling ROF-TV...');
!/usr/local/cuda/bin/nvcc -O0 -c TV_ROF_GPU_core.cu -Xcompiler -fPIC -I~/SOFT/MATLAB9/extern/include/
mex -g -I/usr/local/cuda-7.5/include -L/usr/local/cuda-7.5/lib64 -lcudart -lcufft -lmwgpu ROF_TV_GPU.cpp TV_ROF_GPU_core.o
movefile('ROF_TV_GPU.mex*',Pathmove);
+fprintf('%s \n', 'Compiling FGP-TV...');
!/usr/local/cuda/bin/nvcc -O0 -c TV_FGP_GPU_core.cu -Xcompiler -fPIC -I~/SOFT/MATLAB9/extern/include/
mex -g -I/usr/local/cuda-7.5/include -L/usr/local/cuda-7.5/lib64 -lcudart -lcufft -lmwgpu FGP_TV_GPU.cpp TV_FGP_GPU_core.o
movefile('FGP_TV_GPU.mex*',Pathmove);
+fprintf('%s \n', 'Compiling SB-TV...');
!/usr/local/cuda/bin/nvcc -O0 -c TV_SB_GPU_core.cu -Xcompiler -fPIC -I~/SOFT/MATLAB9/extern/include/
mex -g -I/usr/local/cuda-7.5/include -L/usr/local/cuda-7.5/lib64 -lcudart -lcufft -lmwgpu SB_TV_GPU.cpp TV_SB_GPU_core.o
movefile('SB_TV_GPU.mex*',Pathmove);
+fprintf('%s \n', 'Compiling TGV...');
!/usr/local/cuda/bin/nvcc -O0 -c TGV_GPU_core.cu -Xcompiler -fPIC -I~/SOFT/MATLAB9/extern/include/
mex -g -I/usr/local/cuda-7.5/include -L/usr/local/cuda-7.5/lib64 -lcudart -lcufft -lmwgpu TGV_GPU.cpp TGV_GPU_core.o
movefile('TGV_GPU.mex*',Pathmove);
+fprintf('%s \n', 'Compiling dFGP-TV...');
!/usr/local/cuda/bin/nvcc -O0 -c dTV_FGP_GPU_core.cu -Xcompiler -fPIC -I~/SOFT/MATLAB9/extern/include/
mex -g -I/usr/local/cuda-7.5/include -L/usr/local/cuda-7.5/lib64 -lcudart -lcufft -lmwgpu FGP_dTV_GPU.cpp dTV_FGP_GPU_core.o
movefile('FGP_dTV_GPU.mex*',Pathmove);
+fprintf('%s \n', 'Compiling NonLinear Diffusion...');
!/usr/local/cuda/bin/nvcc -O0 -c NonlDiff_GPU_core.cu -Xcompiler -fPIC -I~/SOFT/MATLAB9/extern/include/
mex -g -I/usr/local/cuda-7.5/include -L/usr/local/cuda-7.5/lib64 -lcudart -lcufft -lmwgpu NonlDiff_GPU.cpp NonlDiff_GPU_core.o
movefile('NonlDiff_GPU.mex*',Pathmove);
+fprintf('%s \n', 'Compiling Anisotropic diffusion of higher order...');
!/usr/local/cuda/bin/nvcc -O0 -c Diffus_4thO_GPU_core.cu -Xcompiler -fPIC -I~/SOFT/MATLAB9/extern/include/
mex -g -I/usr/local/cuda-7.5/include -L/usr/local/cuda-7.5/lib64 -lcudart -lcufft -lmwgpu Diffusion_4thO_GPU.cpp Diffus_4thO_GPU_core.o
movefile('Diffusion_4thO_GPU.mex*',Pathmove);
-delete TV_ROF_GPU_core* TV_FGP_GPU_core* TV_SB_GPU_core* dTV_FGP_GPU_core* NonlDiff_GPU_core* Diffus_4thO_GPU_core* TGV_GPU_core* CCPiDefines.h
+fprintf('%s \n', 'Compiling ROF-LLT...');
+!/usr/local/cuda/bin/nvcc -O0 -c LLT_ROF_GPU_core.cu -Xcompiler -fPIC -I~/SOFT/MATLAB9/extern/include/
+mex -g -I/usr/local/cuda-7.5/include -L/usr/local/cuda-7.5/lib64 -lcudart -lcufft -lmwgpu LLT_ROF_GPU.cpp LLT_ROF_GPU_core.o
+movefile('LLT_ROF_GPU.mex*',Pathmove);
+
+delete TV_ROF_GPU_core* TV_FGP_GPU_core* TV_SB_GPU_core* dTV_FGP_GPU_core* NonlDiff_GPU_core* Diffus_4thO_GPU_core* TGV_GPU_core* LLT_ROF_GPU_core* CCPiDefines.h
fprintf('%s \n', 'All successfully compiled!');
pathA2 = sprintf(['..' fsep '..' fsep], 1i);
diff --git a/Wrappers/Matlab/mex_compile/regularisers_CPU/LLT_ROF.c b/Wrappers/Matlab/mex_compile/regularisers_CPU/LLT_ROF.c
new file mode 100644
index 0000000..81b717d
--- /dev/null
+++ b/Wrappers/Matlab/mex_compile/regularisers_CPU/LLT_ROF.c
@@ -0,0 +1,81 @@
+/*
+ * This work is part of the Core Imaging Library developed by
+ * Visual Analytics and Imaging System Group of the Science Technology
+ * Facilities Council, STFC
+ *
+ * Copyright 2017 Daniil Kazantsev
+ * Copyright 2017 Srikanth Nagella, Edoardo Pasca
+ *
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * You may obtain a copy of the License at
+ * http://www.apache.org/licenses/LICENSE-2.0
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ */
+#include "matrix.h"
+#include "mex.h"
+#include "LLT_ROF_core.h"
+
+/* C-OMP implementation of Lysaker, Lundervold and Tai (LLT) model [1] combined with Rudin-Osher-Fatemi [2] TV regularisation penalty.
+*
+* This penalty can deliver visually pleasant piecewise-smooth recovery if regularisation parameters are selected well.
+* The rule of thumb for selection is to start with lambdaLLT = 0 (just the ROF-TV model) and then proceed to increase
+* lambdaLLT starting with smaller values.
+*
+* Input Parameters:
+* 1. U0 - original noise image/volume
+* 2. lambdaROF - ROF-related regularisation parameter
+* 3. lambdaLLT - LLT-related regularisation parameter
+* 4. tau - time-marching step
+* 5. iter - iterations number (for both models)
+*
+* Output:
+* Filtered/regularised image
+*
+* References:
+* [1] Lysaker, M., Lundervold, A. and Tai, X.C., 2003. Noise removal using fourth-order partial differential equation with applications to medical magnetic resonance images in space and time. IEEE Transactions on image processing, 12(12), pp.1579-1590.
+* [2] Rudin, Osher, Fatemi, "Nonlinear Total Variation based noise removal algorithms"
+*/
+
+void mexFunction(
+ int nlhs, mxArray *plhs[],
+ int nrhs, const mxArray *prhs[])
+
+{
+ int number_of_dims, iterationsNumb, dimX, dimY, dimZ;
+ const int *dim_array;
+ float *Input, *Output=NULL, lambdaROF, lambdaLLT, tau;
+
+ dim_array = mxGetDimensions(prhs[0]);
+ number_of_dims = mxGetNumberOfDimensions(prhs[0]);
+
+ if ((nrhs < 3) || (nrhs > 5)) mexErrMsgTxt("At least 3 parameters is required, all parameters are: Image(2D/3D), Regularisation parameter (ROF), Regularisation parameter (LTT), iterations number, time-marching parameter");
+
+ /*Handling Matlab input data*/
+ Input = (float *) mxGetData(prhs[0]);
+ lambdaROF = (float) mxGetScalar(prhs[1]); /* ROF regularization parameter */
+ lambdaLLT = (float) mxGetScalar(prhs[2]); /* ROF regularization parameter */
+ iterationsNumb = 250;
+ tau = 0.0025;
+
+ if (mxGetClassID(prhs[0]) != mxSINGLE_CLASS) {mexErrMsgTxt("The input image must be in a single precision"); }
+ if ((nrhs == 4) || (nrhs == 5)) iterationsNumb = (int) mxGetScalar(prhs[3]); /* iterations number */
+ if (nrhs == 5) tau = (float) mxGetScalar(prhs[4]); /* marching step parameter */
+
+ /*Handling Matlab output data*/
+ dimX = dim_array[0]; dimY = dim_array[1]; dimZ = dim_array[2];
+
+ /* output arrays*/
+ if (number_of_dims == 2) {
+ dimZ = 1; /*2D case*/
+ /* output image/volume */
+ Output = (float*)mxGetPr(plhs[0] = mxCreateNumericArray(2, dim_array, mxSINGLE_CLASS, mxREAL));
+ }
+ if (number_of_dims == 3) Output = (float*)mxGetPr(plhs[0] = mxCreateNumericArray(3, dim_array, mxSINGLE_CLASS, mxREAL));
+
+ LLT_ROF_CPU_main(Input, Output, lambdaROF, lambdaLLT, iterationsNumb, tau, dimX, dimY, dimZ);
+} \ No newline at end of file
diff --git a/Wrappers/Matlab/mex_compile/regularisers_GPU/LLT_ROF_GPU.cpp b/Wrappers/Matlab/mex_compile/regularisers_GPU/LLT_ROF_GPU.cpp
new file mode 100644
index 0000000..37563b0
--- /dev/null
+++ b/Wrappers/Matlab/mex_compile/regularisers_GPU/LLT_ROF_GPU.cpp
@@ -0,0 +1,81 @@
+/*
+ * This work is part of the Core Imaging Library developed by
+ * Visual Analytics and Imaging System Group of the Science Technology
+ * Facilities Council, STFC
+ *
+ * Copyright 2017 Daniil Kazantsev
+ * Copyright 2017 Srikanth Nagella, Edoardo Pasca
+ *
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * You may obtain a copy of the License at
+ * http://www.apache.org/licenses/LICENSE-2.0
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ */
+#include "matrix.h"
+#include "mex.h"
+#include "LLT_ROF_GPU_core.h"
+
+/* CUDA implementation of Lysaker, Lundervold and Tai (LLT) model [1] combined with Rudin-Osher-Fatemi [2] TV regularisation penalty.
+*
+* This penalty can deliver visually pleasant piecewise-smooth recovery if regularisation parameters are selected well.
+* The rule of thumb for selection is to start with lambdaLLT = 0 (just the ROF-TV model) and then proceed to increase
+* lambdaLLT starting with smaller values.
+*
+* Input Parameters:
+* 1. U0 - original noise image/volume
+* 2. lambdaROF - ROF-related regularisation parameter
+* 3. lambdaLLT - LLT-related regularisation parameter
+* 4. tau - time-marching step
+* 5. iter - iterations number (for both models)
+*
+* Output:
+* Filtered/regularised image
+*
+* References:
+* [1] Lysaker, M., Lundervold, A. and Tai, X.C., 2003. Noise removal using fourth-order partial differential equation with applications to medical magnetic resonance images in space and time. IEEE Transactions on image processing, 12(12), pp.1579-1590.
+* [2] Rudin, Osher, Fatemi, "Nonlinear Total Variation based noise removal algorithms"
+*/
+
+void mexFunction(
+ int nlhs, mxArray *plhs[],
+ int nrhs, const mxArray *prhs[])
+
+{
+ int number_of_dims, iterationsNumb, dimX, dimY, dimZ;
+ const int *dim_array;
+ float *Input, *Output=NULL, lambdaROF, lambdaLLT, tau;
+
+ dim_array = mxGetDimensions(prhs[0]);
+ number_of_dims = mxGetNumberOfDimensions(prhs[0]);
+
+ if ((nrhs < 3) || (nrhs > 5)) mexErrMsgTxt("At least 3 parameters is required, all parameters are: Image(2D/3D), Regularisation parameter (ROF), Regularisation parameter (LTT), iterations number, time-marching parameter");
+
+ /*Handling Matlab input data*/
+ Input = (float *) mxGetData(prhs[0]);
+ lambdaROF = (float) mxGetScalar(prhs[1]); /* ROF regularization parameter */
+ lambdaLLT = (float) mxGetScalar(prhs[2]); /* ROF regularization parameter */
+ iterationsNumb = 250;
+ tau = 0.0025;
+
+ if (mxGetClassID(prhs[0]) != mxSINGLE_CLASS) {mexErrMsgTxt("The input image must be in a single precision"); }
+ if ((nrhs == 4) || (nrhs == 5)) iterationsNumb = (int) mxGetScalar(prhs[3]); /* iterations number */
+ if (nrhs == 5) tau = (float) mxGetScalar(prhs[4]); /* marching step parameter */
+
+ /*Handling Matlab output data*/
+ dimX = dim_array[0]; dimY = dim_array[1]; dimZ = dim_array[2];
+
+ /* output arrays*/
+ if (number_of_dims == 2) {
+ dimZ = 1; /*2D case*/
+ /* output image/volume */
+ Output = (float*)mxGetPr(plhs[0] = mxCreateNumericArray(2, dim_array, mxSINGLE_CLASS, mxREAL));
+ }
+ if (number_of_dims == 3) Output = (float*)mxGetPr(plhs[0] = mxCreateNumericArray(3, dim_array, mxSINGLE_CLASS, mxREAL));
+
+ LLT_ROF_GPU_main(Input, Output, lambdaROF, lambdaLLT, iterationsNumb, tau, dimX, dimY, dimZ);
+} \ No newline at end of file