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authorDaniil Kazantsev <dkazanc3@googlemail.com>2018-04-16 15:29:57 +0100
committerGitHub <noreply@github.com>2018-04-16 15:29:57 +0100
commit3d17b516f269921f5c8fb4eb54cec49f732e27d5 (patch)
treeb6dd09825750854bf6c87cee8e544c2278ac5586 /Wrappers
parent7ae26b005c5f3d9ca0181ab1cf06b6ee8df5ed69 (diff)
parent57727584760e6b1a980071587e1f1e8910c7d6a3 (diff)
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Merge pull request #50 from vais-ral/SB_TV
Split Bregman method
Diffstat (limited to 'Wrappers')
-rw-r--r--Wrappers/Matlab/demos/demoMatlab_3Ddenoise.m34
-rw-r--r--Wrappers/Matlab/demos/demoMatlab_denoise.m33
-rw-r--r--Wrappers/Matlab/mex_compile/compileCPU_mex.m5
-rw-r--r--Wrappers/Matlab/mex_compile/compileGPU_mex.m16
-rw-r--r--Wrappers/Matlab/mex_compile/regularisers_CPU/SB_TV.c89
-rw-r--r--Wrappers/Matlab/mex_compile/regularisers_GPU/SB_TV_GPU.cpp89
-rw-r--r--Wrappers/Python/ccpi/filters/regularisers.py23
-rw-r--r--Wrappers/Python/demos/demo_cpu_regularisers.py103
-rw-r--r--Wrappers/Python/demos/demo_cpu_vs_gpu_regularisers.py90
-rw-r--r--Wrappers/Python/demos/demo_gpu_regularisers.py102
-rw-r--r--Wrappers/Python/setup-regularisers.py.in1
-rw-r--r--Wrappers/Python/src/cpu_regularisers.pyx58
-rw-r--r--Wrappers/Python/src/gpu_regularisers.pyx75
13 files changed, 673 insertions, 45 deletions
diff --git a/Wrappers/Matlab/demos/demoMatlab_3Ddenoise.m b/Wrappers/Matlab/demos/demoMatlab_3Ddenoise.m
index dc49d9c..fb55097 100644
--- a/Wrappers/Matlab/demos/demoMatlab_3Ddenoise.m
+++ b/Wrappers/Matlab/demos/demoMatlab_3Ddenoise.m
@@ -14,35 +14,47 @@ end
vol3D(vol3D < 0) = 0;
figure; imshow(vol3D(:,:,15), [0 1]); title('Noisy image');
+
+lambda_reg = 0.03; % regularsation parameter for all methods
%%
fprintf('Denoise a volume using the ROF-TV model (CPU) \n');
-lambda_rof = 0.03; % regularisation parameter
tau_rof = 0.0025; % time-marching constant
iter_rof = 300; % number of ROF iterations
-tic; u_rof = ROF_TV(single(vol3D), lambda_rof, iter_rof, tau_rof); toc;
+tic; u_rof = ROF_TV(single(vol3D), lambda_reg, iter_rof, tau_rof); toc;
figure; imshow(u_rof(:,:,15), [0 1]); title('ROF-TV denoised volume (CPU)');
%%
% fprintf('Denoise a volume using the ROF-TV model (GPU) \n');
-% lambda_rof = 0.03; % regularisation parameter
% tau_rof = 0.0025; % time-marching constant
% iter_rof = 300; % number of ROF iterations
-% tic; u_rofG = ROF_TV_GPU(single(vol3D), lambda_rof, iter_rof, tau_rof); toc;
+% 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)');
%%
fprintf('Denoise a volume using the FGP-TV model (CPU) \n');
-lambda_fgp = 0.03; % regularisation parameter
iter_fgp = 300; % number of FGP iterations
epsil_tol = 1.0e-05; % tolerance
-tic; u_fgp = FGP_TV(single(vol3D), lambda_fgp, iter_fgp, epsil_tol); toc;
+tic; u_fgp = FGP_TV(single(vol3D), lambda_reg, iter_fgp, epsil_tol); toc;
figure; imshow(u_fgp(:,:,15), [0 1]); title('FGP-TV denoised volume (CPU)');
%%
% fprintf('Denoise a volume using the FGP-TV model (GPU) \n');
-% lambda_fgp = 0.03; % regularisation parameter
% iter_fgp = 300; % number of FGP iterations
% epsil_tol = 1.0e-05; % tolerance
-% tic; u_fgpG = FGP_TV_GPU(single(vol3D), lambda_fgp, iter_fgp, epsil_tol); toc;
+% 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)');
%%
+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;
+figure; imshow(u_sb(:,:,15), [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)');
+%%
+
+%>>>>>>>>>>>>>> MULTI-CHANNEL priors <<<<<<<<<<<<<<< %
fprintf('Denoise a volume using the FGP-dTV model (CPU) \n');
% create another volume (reference) with slightly less amount of noise
@@ -53,11 +65,10 @@ end
vol3D_ref(vol3D_ref < 0) = 0;
% vol3D_ref = zeros(size(Im),'single'); % pass zero reference (dTV -> TV)
-lambda_fgp = 0.03; % regularisation parameter
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_fgp, iter_fgp, epsil_tol, eta); toc;
+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)');
%%
fprintf('Denoise a volume using the FGP-dTV model (GPU) \n');
@@ -70,10 +81,9 @@ end
vol3D_ref(vol3D_ref < 0) = 0;
% vol3D_ref = zeros(size(Im),'single'); % pass zero reference (dTV -> TV)
-lambda_fgp = 0.03; % regularisation parameter
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_fgp, iter_fgp, epsil_tol, eta); toc;
+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)');
%% \ No newline at end of file
diff --git a/Wrappers/Matlab/demos/demoMatlab_denoise.m b/Wrappers/Matlab/demos/demoMatlab_denoise.m
index 145f2ff..129bedc 100644
--- a/Wrappers/Matlab/demos/demoMatlab_denoise.m
+++ b/Wrappers/Matlab/demos/demoMatlab_denoise.m
@@ -8,45 +8,55 @@ Im = double(imread('lena_gray_512.tif'))/255; % loading image
u0 = Im + .05*randn(size(Im)); u0(u0 < 0) = 0;
figure; imshow(u0, [0 1]); title('Noisy image');
+lambda_reg = 0.03; % regularsation parameter for all methods
%%
fprintf('Denoise using the ROF-TV model (CPU) \n');
-lambda_rof = 0.03; % regularisation parameter
tau_rof = 0.0025; % time-marching constant
iter_rof = 2000; % number of ROF iterations
-tic; u_rof = ROF_TV(single(u0), lambda_rof, iter_rof, tau_rof); toc;
+tic; u_rof = ROF_TV(single(u0), lambda_reg, iter_rof, tau_rof); toc;
figure; imshow(u_rof, [0 1]); title('ROF-TV denoised image (CPU)');
%%
% fprintf('Denoise using the ROF-TV model (GPU) \n');
-% lambda_rof = 0.03; % regularisation parameter
% tau_rof = 0.0025; % time-marching constant
% iter_rof = 2000; % number of ROF iterations
-% tic; u_rofG = ROF_TV_GPU(single(u0), lambda_rof, iter_rof, tau_rof); toc;
+% tic; u_rofG = ROF_TV_GPU(single(u0), lambda_reg, iter_rof, tau_rof); toc;
% figure; imshow(u_rofG, [0 1]); title('ROF-TV denoised image (GPU)');
%%
fprintf('Denoise using the FGP-TV model (CPU) \n');
-lambda_fgp = 0.03; % regularisation parameter
iter_fgp = 1000; % number of FGP iterations
epsil_tol = 1.0e-06; % tolerance
-tic; u_fgp = FGP_TV(single(u0), lambda_fgp, iter_fgp, epsil_tol); toc;
+tic; u_fgp = FGP_TV(single(u0), lambda_reg, iter_fgp, epsil_tol); toc;
figure; imshow(u_fgp, [0 1]); title('FGP-TV denoised image (CPU)');
%%
% fprintf('Denoise using the FGP-TV model (GPU) \n');
-% lambda_fgp = 0.03; % regularisation parameter
% iter_fgp = 1000; % number of FGP iterations
% epsil_tol = 1.0e-05; % tolerance
-% tic; u_fgpG = FGP_TV_GPU(single(u0), lambda_fgp, iter_fgp, epsil_tol); toc;
+% tic; u_fgpG = FGP_TV_GPU(single(u0), lambda_reg, iter_fgp, epsil_tol); toc;
% figure; imshow(u_fgpG, [0 1]); title('FGP-TV denoised image (GPU)');
%%
+fprintf('Denoise using the SB-TV model (CPU) \n');
+iter_sb = 150; % number of SB iterations
+epsil_tol = 1.0e-06; % tolerance
+tic; u_sb = SB_TV(single(u0), lambda_reg, iter_sb, epsil_tol); toc;
+figure; imshow(u_sb, [0 1]); title('SB-TV denoised image (CPU)');
+%%
+% fprintf('Denoise using the SB-TV model (GPU) \n');
+% iter_sb = 150; % number of SB iterations
+% epsil_tol = 1.0e-06; % tolerance
+% tic; u_sbG = SB_TV_GPU(single(u0), lambda_reg, iter_sb, epsil_tol); toc;
+% figure; imshow(u_sbG, [0 1]); title('SB-TV denoised image (GPU)');
+%%
+%>>>>>>>>>>>>>> MULTI-CHANNEL priors <<<<<<<<<<<<<<< %
+
fprintf('Denoise using the FGP-dTV model (CPU) \n');
% create another image (reference) with slightly less amount of noise
u_ref = Im + .01*randn(size(Im)); u_ref(u_ref < 0) = 0;
% u_ref = zeros(size(Im),'single'); % pass zero reference (dTV -> TV)
-lambda_fgp = 0.03; % regularisation parameter
iter_fgp = 1000; % number of FGP iterations
epsil_tol = 1.0e-06; % tolerance
eta = 0.2; % Reference image gradient smoothing constant
-tic; u_fgp_dtv = FGP_dTV(single(u0), single(u_ref), lambda_fgp, iter_fgp, epsil_tol, eta); toc;
+tic; u_fgp_dtv = FGP_dTV(single(u0), single(u_ref), lambda_reg, iter_fgp, epsil_tol, eta); toc;
figure; imshow(u_fgp_dtv, [0 1]); title('FGP-dTV denoised image (CPU)');
%%
% fprintf('Denoise using the FGP-dTV model (GPU) \n');
@@ -54,10 +64,9 @@ figure; imshow(u_fgp_dtv, [0 1]); title('FGP-dTV denoised image (CPU)');
% u_ref = Im + .01*randn(size(Im)); u_ref(u_ref < 0) = 0;
% % u_ref = zeros(size(Im),'single'); % pass zero reference (dTV -> TV)
%
-% lambda_fgp = 0.03; % regularisation parameter
% iter_fgp = 1000; % number of FGP iterations
% epsil_tol = 1.0e-06; % tolerance
% eta = 0.2; % Reference image gradient smoothing constant
-% tic; u_fgp_dtvG = FGP_dTV_GPU(single(u0), single(u_ref), lambda_fgp, iter_fgp, epsil_tol, eta); toc;
+% tic; u_fgp_dtvG = FGP_dTV_GPU(single(u0), single(u_ref), lambda_reg, iter_fgp, epsil_tol, eta); toc;
% figure; imshow(u_fgp_dtvG, [0 1]); title('FGP-dTV denoised image (GPU)');
%%
diff --git a/Wrappers/Matlab/mex_compile/compileCPU_mex.m b/Wrappers/Matlab/mex_compile/compileCPU_mex.m
index 71f345a..c3c82ff 100644
--- a/Wrappers/Matlab/mex_compile/compileCPU_mex.m
+++ b/Wrappers/Matlab/mex_compile/compileCPU_mex.m
@@ -11,10 +11,13 @@ movefile ROF_TV.mex* ../installed/
mex FGP_TV.c FGP_TV_core.c utils.c CFLAGS="\$CFLAGS -fopenmp -Wall -std=c99" LDFLAGS="\$LDFLAGS -fopenmp"
movefile FGP_TV.mex* ../installed/
+mex SB_TV.c SB_TV_core.c utils.c CFLAGS="\$CFLAGS -fopenmp -Wall -std=c99" LDFLAGS="\$LDFLAGS -fopenmp"
+movefile SB_TV.mex* ../installed/
+
mex FGP_dTV.c FGP_dTV_core.c utils.c CFLAGS="\$CFLAGS -fopenmp -Wall -std=c99" LDFLAGS="\$LDFLAGS -fopenmp"
movefile FGP_dTV.mex* ../installed/
-delete ROF_TV_core* FGP_TV_core* FGP_dTV_core* utils* CCPiDefines.h
+delete SB_TV_core* ROF_TV_core* FGP_TV_core* FGP_dTV_core* utils* CCPiDefines.h
fprintf('%s \n', 'All successfully compiled!');
diff --git a/Wrappers/Matlab/mex_compile/compileGPU_mex.m b/Wrappers/Matlab/mex_compile/compileGPU_mex.m
index f58e9bc..3dbeb8a 100644
--- a/Wrappers/Matlab/mex_compile/compileGPU_mex.m
+++ b/Wrappers/Matlab/mex_compile/compileGPU_mex.m
@@ -1,13 +1,13 @@
% execute this mex file in Matlab once
-%>>>>>>>>>>>>>>Important<<<<<<<<<<<<<<<<<<<
+%>>>>>>>>>>>>>>>>>Important<<<<<<<<<<<<<<<<<<<
% In order to compile CUDA modules one needs to have nvcc-compiler
-% installed (see CUDA SDK)
-% check it under MATLAB with !nvcc --version
-% In the code bellow we provide a full path to nvcc compiler
+% installed (see CUDA SDK), check it under MATLAB with !nvcc --version
+
+% In the code bellow we provide a full explicit path to nvcc compiler
% ! paths to matlab and CUDA sdk can be different, modify accordingly !
-% tested on Ubuntu 16.04/MATLAB 2016b
+% tested on Ubuntu 16.04/MATLAB 2016b/cuda7.5/gcc4.9
copyfile ../../../Core/regularisers_GPU/ regularisers_GPU/
copyfile ../../../Core/CCPiDefines.h regularisers_GPU/
@@ -23,11 +23,15 @@ movefile ROF_TV_GPU.mex* ../installed/
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* ../installed/
+!/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* ../installed/
+
!/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* ../installed/
-delete TV_ROF_GPU_core* TV_FGP_GPU_core* dTV_FGP_GPU_core* CCPiDefines.h
+delete TV_ROF_GPU_core* TV_FGP_GPU_core* TV_SB_GPU_core* dTV_FGP_GPU_core* CCPiDefines.h
fprintf('%s \n', 'All successfully compiled!');
cd ../../
diff --git a/Wrappers/Matlab/mex_compile/regularisers_CPU/SB_TV.c b/Wrappers/Matlab/mex_compile/regularisers_CPU/SB_TV.c
new file mode 100644
index 0000000..d284cac
--- /dev/null
+++ b/Wrappers/Matlab/mex_compile/regularisers_CPU/SB_TV.c
@@ -0,0 +1,89 @@
+/*
+ * 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 "SB_TV_core.h"
+
+/* C-OMP implementation of Split Bregman - TV denoising-regularisation model (2D/3D) [1]
+*
+* Input Parameters:
+* 1. Noisy image/volume
+* 2. lambda - regularisation parameter
+* 3. Number of iterations [OPTIONAL parameter]
+* 4. eplsilon - tolerance constant [OPTIONAL parameter]
+* 5. TV-type: 'iso' or 'l1' [OPTIONAL parameter]
+* 6. print information: 0 (off) or 1 (on) [OPTIONAL parameter]
+*
+* Output:
+* 1. Filtered/regularized image
+*
+* This function is based on the Matlab's code and paper by
+* [1]. Goldstein, T. and Osher, S., 2009. The split Bregman method for L1-regularized problems. SIAM journal on imaging sciences, 2(2), pp.323-343.
+*/
+
+void mexFunction(
+ int nlhs, mxArray *plhs[],
+ int nrhs, const mxArray *prhs[])
+
+{
+ int number_of_dims, iter, dimX, dimY, dimZ, methTV, printswitch;
+ const int *dim_array;
+ float *Input, *Output=NULL, lambda, epsil;
+
+ number_of_dims = mxGetNumberOfDimensions(prhs[0]);
+ dim_array = mxGetDimensions(prhs[0]);
+
+ /*Handling Matlab input data*/
+ if ((nrhs < 2) || (nrhs > 6)) mexErrMsgTxt("At least 2 parameters is required, all parameters are: Image(2D/3D), Regularization parameter, Regularization parameter, iterations number, tolerance, penalty type ('iso' or 'l1'), print switch");
+
+ Input = (float *) mxGetData(prhs[0]); /*noisy image (2D/3D) */
+ lambda = (float) mxGetScalar(prhs[1]); /* regularization parameter */
+ iter = 100; /* default iterations number */
+ epsil = 0.0001; /* default tolerance constant */
+ methTV = 0; /* default isotropic TV penalty */
+ printswitch = 0; /*default print is switched, off - 0 */
+
+ if (mxGetClassID(prhs[0]) != mxSINGLE_CLASS) {mexErrMsgTxt("The input image must be in a single precision"); }
+
+ if ((nrhs == 3) || (nrhs == 4) || (nrhs == 5) || (nrhs == 6)) iter = (int) mxGetScalar(prhs[2]); /* iterations number */
+ if ((nrhs == 4) || (nrhs == 5) || (nrhs == 6)) epsil = (float) mxGetScalar(prhs[3]); /* tolerance constant */
+ if ((nrhs == 5) || (nrhs == 6)) {
+ char *penalty_type;
+ penalty_type = mxArrayToString(prhs[4]); /* choosing TV penalty: 'iso' or 'l1', 'iso' is the default */
+ if ((strcmp(penalty_type, "l1") != 0) && (strcmp(penalty_type, "iso") != 0)) mexErrMsgTxt("Choose TV type: 'iso' or 'l1',");
+ if (strcmp(penalty_type, "l1") == 0) methTV = 1; /* enable 'l1' penalty */
+ mxFree(penalty_type);
+ }
+ if (nrhs == 6) {
+ printswitch = (int) mxGetScalar(prhs[5]);
+ if ((printswitch != 0) && (printswitch != 1)) mexErrMsgTxt("Print can be enabled by choosing 1 or off - 0");
+ }
+
+ /*Handling Matlab output data*/
+ dimX = dim_array[0]; dimY = dim_array[1]; dimZ = dim_array[2];
+
+ if (number_of_dims == 2) {
+ dimZ = 1; /*2D case*/
+ 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));
+
+ /* running the function */
+ SB_TV_CPU_main(Input, Output, lambda, iter, epsil, methTV, printswitch, dimX, dimY, dimZ);
+}
diff --git a/Wrappers/Matlab/mex_compile/regularisers_GPU/SB_TV_GPU.cpp b/Wrappers/Matlab/mex_compile/regularisers_GPU/SB_TV_GPU.cpp
new file mode 100644
index 0000000..60847d9
--- /dev/null
+++ b/Wrappers/Matlab/mex_compile/regularisers_GPU/SB_TV_GPU.cpp
@@ -0,0 +1,89 @@
+/*
+ * 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 "TV_SB_GPU_core.h"
+
+/* CUDA mex-file for implementation of Split Bregman - TV denoising-regularisation model (2D/3D) [1]
+*
+* Input Parameters:
+* 1. Noisy image/volume
+* 2. lambda - regularisation parameter
+* 3. Number of iterations [OPTIONAL parameter]
+* 4. eplsilon - tolerance constant [OPTIONAL parameter]
+* 5. TV-type: 'iso' or 'l1' [OPTIONAL parameter]
+* 6. print information: 0 (off) or 1 (on) [OPTIONAL parameter]
+*
+* Output:
+* 1. Filtered/regularized image
+*
+* This function is based on the Matlab's code and paper by
+* [1]. Goldstein, T. and Osher, S., 2009. The split Bregman method for L1-regularized problems. SIAM journal on imaging sciences, 2(2), pp.323-343.
+*/
+
+void mexFunction(
+ int nlhs, mxArray *plhs[],
+ int nrhs, const mxArray *prhs[])
+
+{
+ int number_of_dims, iter, dimX, dimY, dimZ, methTV, printswitch;
+ const int *dim_array;
+ float *Input, *Output=NULL, lambda, epsil;
+
+ number_of_dims = mxGetNumberOfDimensions(prhs[0]);
+ dim_array = mxGetDimensions(prhs[0]);
+
+ /*Handling Matlab input data*/
+ if ((nrhs < 2) || (nrhs > 6)) mexErrMsgTxt("At least 2 parameters is required, all parameters are: Image(2D/3D), Regularization parameter, Regularization parameter, iterations number, tolerance, penalty type ('iso' or 'l1'), print switch");
+
+ Input = (float *) mxGetData(prhs[0]); /*noisy image (2D/3D) */
+ lambda = (float) mxGetScalar(prhs[1]); /* regularization parameter */
+ iter = 100; /* default iterations number */
+ epsil = 0.0001; /* default tolerance constant */
+ methTV = 0; /* default isotropic TV penalty */
+ printswitch = 0; /*default print is switched, off - 0 */
+
+ if (mxGetClassID(prhs[0]) != mxSINGLE_CLASS) {mexErrMsgTxt("The input image must be in a single precision"); }
+
+ if ((nrhs == 3) || (nrhs == 4) || (nrhs == 5) || (nrhs == 6)) iter = (int) mxGetScalar(prhs[2]); /* iterations number */
+ if ((nrhs == 4) || (nrhs == 5) || (nrhs == 6)) epsil = (float) mxGetScalar(prhs[3]); /* tolerance constant */
+ if ((nrhs == 5) || (nrhs == 6)) {
+ char *penalty_type;
+ penalty_type = mxArrayToString(prhs[4]); /* choosing TV penalty: 'iso' or 'l1', 'iso' is the default */
+ if ((strcmp(penalty_type, "l1") != 0) && (strcmp(penalty_type, "iso") != 0)) mexErrMsgTxt("Choose TV type: 'iso' or 'l1',");
+ if (strcmp(penalty_type, "l1") == 0) methTV = 1; /* enable 'l1' penalty */
+ mxFree(penalty_type);
+ }
+ if (nrhs == 6) {
+ printswitch = (int) mxGetScalar(prhs[5]);
+ if ((printswitch != 0) && (printswitch != 1)) mexErrMsgTxt("Print can be enabled by choosing 1 or off - 0");
+ }
+
+ /*Handling Matlab output data*/
+ dimX = dim_array[0]; dimY = dim_array[1]; dimZ = dim_array[2];
+
+ if (number_of_dims == 2) {
+ dimZ = 1; /*2D case*/
+ 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));
+
+ /* running the function */
+ TV_SB_GPU_main(Input, Output, lambda, iter, epsil, methTV, printswitch, dimX, dimY, dimZ);
+}
diff --git a/Wrappers/Python/ccpi/filters/regularisers.py b/Wrappers/Python/ccpi/filters/regularisers.py
index 376cc9c..50c4374 100644
--- a/Wrappers/Python/ccpi/filters/regularisers.py
+++ b/Wrappers/Python/ccpi/filters/regularisers.py
@@ -2,8 +2,8 @@
script which assigns a proper device core function based on a flag ('cpu' or 'gpu')
"""
-from ccpi.filters.cpu_regularisers_cython import TV_ROF_CPU, TV_FGP_CPU, dTV_FGP_CPU
-from ccpi.filters.gpu_regularisers import TV_ROF_GPU, TV_FGP_GPU, dTV_FGP_GPU
+from ccpi.filters.cpu_regularisers_cython import TV_ROF_CPU, TV_FGP_CPU, TV_SB_CPU, dTV_FGP_CPU
+from ccpi.filters.gpu_regularisers import TV_ROF_GPU, TV_FGP_GPU, TV_SB_GPU, dTV_FGP_GPU
def ROF_TV(inputData, regularisation_parameter, iterations,
time_marching_parameter,device='cpu'):
@@ -42,6 +42,25 @@ def FGP_TV(inputData, regularisation_parameter,iterations,
else:
raise ValueError('Unknown device {0}. Expecting gpu or cpu'\
.format(device))
+def SB_TV(inputData, regularisation_parameter, iterations,
+ tolerance_param, methodTV, printM, device='cpu'):
+ if device == 'cpu':
+ return TV_SB_CPU(inputData,
+ regularisation_parameter,
+ iterations,
+ tolerance_param,
+ methodTV,
+ printM)
+ elif device == 'gpu':
+ return TV_SB_GPU(inputData,
+ regularisation_parameter,
+ iterations,
+ tolerance_param,
+ methodTV,
+ printM)
+ else:
+ raise ValueError('Unknown device {0}. Expecting gpu or cpu'\
+ .format(device))
def FGP_dTV(inputData, refdata, regularisation_parameter, iterations,
tolerance_param, eta_const, methodTV, nonneg, printM, device='cpu'):
if device == 'cpu':
diff --git a/Wrappers/Python/demos/demo_cpu_regularisers.py b/Wrappers/Python/demos/demo_cpu_regularisers.py
index 00beb0b..0e4355b 100644
--- a/Wrappers/Python/demos/demo_cpu_regularisers.py
+++ b/Wrappers/Python/demos/demo_cpu_regularisers.py
@@ -12,7 +12,7 @@ import matplotlib.pyplot as plt
import numpy as np
import os
import timeit
-from ccpi.filters.regularisers import ROF_TV, FGP_TV, FGP_dTV
+from ccpi.filters.regularisers import ROF_TV, FGP_TV, SB_TV, FGP_dTV
from qualitymetrics import rmse
###############################################################################
def printParametersToString(pars):
@@ -141,13 +141,60 @@ a.text(0.15, 0.25, txtstr, transform=a.transAxes, fontsize=14,
imgplot = plt.imshow(fgp_cpu, cmap="gray")
plt.title('{}'.format('CPU results'))
+print ("%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%")
+print ("_______________SB-TV (2D)__________________")
+print ("%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%")
+
+## plot
+fig = plt.figure(3)
+plt.suptitle('Performance of SB-TV regulariser using the CPU')
+a=fig.add_subplot(1,2,1)
+a.set_title('Noisy Image')
+imgplot = plt.imshow(u0,cmap="gray")
+
+# set parameters
+pars = {'algorithm' : SB_TV, \
+ 'input' : u0,\
+ 'regularisation_parameter':0.04, \
+ 'number_of_iterations' :150 ,\
+ 'tolerance_constant':1e-06,\
+ 'methodTV': 0 ,\
+ 'printingOut': 0
+ }
+
+print ("#############SB TV CPU####################")
+start_time = timeit.default_timer()
+sb_cpu = SB_TV(pars['input'],
+ pars['regularisation_parameter'],
+ pars['number_of_iterations'],
+ pars['tolerance_constant'],
+ pars['methodTV'],
+ pars['printingOut'],'cpu')
+
+
+rms = rmse(Im, sb_cpu)
+pars['rmse'] = rms
+
+txtstr = printParametersToString(pars)
+txtstr += "%s = %.3fs" % ('elapsed time',timeit.default_timer() - start_time)
+print (txtstr)
+a=fig.add_subplot(1,2,2)
+
+# these are matplotlib.patch.Patch properties
+props = dict(boxstyle='round', facecolor='wheat', alpha=0.75)
+# place a text box in upper left in axes coords
+a.text(0.15, 0.25, txtstr, transform=a.transAxes, fontsize=14,
+ verticalalignment='top', bbox=props)
+imgplot = plt.imshow(sb_cpu, cmap="gray")
+plt.title('{}'.format('CPU results'))
+
print ("%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%")
print ("_____________FGP-dTV (2D)__________________")
print ("%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%")
## plot
-fig = plt.figure(3)
+fig = plt.figure(4)
plt.suptitle('Performance of FGP-dTV regulariser using the CPU')
a=fig.add_subplot(1,2,1)
a.set_title('Noisy Image')
@@ -223,7 +270,7 @@ print ("_______________ROF-TV (3D)_________________")
print ("%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%")
## plot
-fig = plt.figure(4)
+fig = plt.figure(5)
plt.suptitle('Performance of ROF-TV regulariser using the CPU')
a=fig.add_subplot(1,2,1)
a.set_title('Noisy 15th slice of a volume')
@@ -263,7 +310,7 @@ print ("_______________FGP-TV (3D)__________________")
print ("%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%")
## plot
-fig = plt.figure(5)
+fig = plt.figure(6)
plt.suptitle('Performance of FGP-TV regulariser using the CPU')
a=fig.add_subplot(1,2,1)
a.set_title('Noisy Image')
@@ -307,13 +354,59 @@ a.text(0.15, 0.25, txtstr, transform=a.transAxes, fontsize=14,
imgplot = plt.imshow(fgp_cpu3D[10,:,:], cmap="gray")
plt.title('{}'.format('Recovered volume on the CPU using FGP-TV'))
+print ("%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%")
+print ("_______________SB-TV (3D)_________________")
+print ("%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%")
+
+## plot
+fig = plt.figure(7)
+plt.suptitle('Performance of SB-TV regulariser using the CPU')
+a=fig.add_subplot(1,2,1)
+a.set_title('Noisy Image')
+imgplot = plt.imshow(noisyVol[10,:,:],cmap="gray")
+
+# set parameters
+pars = {'algorithm' : SB_TV, \
+ 'input' : noisyVol,\
+ 'regularisation_parameter':0.04, \
+ 'number_of_iterations' :150 ,\
+ 'tolerance_constant':0.00001,\
+ 'methodTV': 0 ,\
+ 'printingOut': 0
+ }
+
+print ("#############SB TV CPU####################")
+start_time = timeit.default_timer()
+sb_cpu3D = SB_TV(pars['input'],
+ pars['regularisation_parameter'],
+ pars['number_of_iterations'],
+ pars['tolerance_constant'],
+ pars['methodTV'],
+ pars['printingOut'],'cpu')
+
+rms = rmse(idealVol, sb_cpu3D)
+pars['rmse'] = rms
+
+txtstr = printParametersToString(pars)
+txtstr += "%s = %.3fs" % ('elapsed time',timeit.default_timer() - start_time)
+print (txtstr)
+a=fig.add_subplot(1,2,2)
+
+# these are matplotlib.patch.Patch properties
+props = dict(boxstyle='round', facecolor='wheat', alpha=0.75)
+# place a text box in upper left in axes coords
+a.text(0.15, 0.25, txtstr, transform=a.transAxes, fontsize=14,
+ verticalalignment='top', bbox=props)
+imgplot = plt.imshow(sb_cpu3D[10,:,:], cmap="gray")
+plt.title('{}'.format('Recovered volume on the CPU using SB-TV'))
+
print ("%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%")
print ("_______________FGP-dTV (3D)__________________")
print ("%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%")
## plot
-fig = plt.figure(6)
+fig = plt.figure(8)
plt.suptitle('Performance of FGP-dTV regulariser using the CPU')
a=fig.add_subplot(1,2,1)
a.set_title('Noisy Image')
diff --git a/Wrappers/Python/demos/demo_cpu_vs_gpu_regularisers.py b/Wrappers/Python/demos/demo_cpu_vs_gpu_regularisers.py
index 310cf75..d8e2da7 100644
--- a/Wrappers/Python/demos/demo_cpu_vs_gpu_regularisers.py
+++ b/Wrappers/Python/demos/demo_cpu_vs_gpu_regularisers.py
@@ -12,7 +12,7 @@ import matplotlib.pyplot as plt
import numpy as np
import os
import timeit
-from ccpi.filters.regularisers import ROF_TV, FGP_TV, FGP_dTV
+from ccpi.filters.regularisers import ROF_TV, FGP_TV, SB_TV, FGP_dTV
from qualitymetrics import rmse
###############################################################################
def printParametersToString(pars):
@@ -218,13 +218,99 @@ if (diff_im.sum() > 1):
else:
print ("Arrays match")
+print ("%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%")
+print ("____________SB-TV bench___________________")
+print ("%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%")
+
+## plot
+fig = plt.figure(3)
+plt.suptitle('Comparison of SB-TV regulariser using CPU and GPU implementations')
+a=fig.add_subplot(1,4,1)
+a.set_title('Noisy Image')
+imgplot = plt.imshow(u0,cmap="gray")
+
+# set parameters
+pars = {'algorithm' : SB_TV, \
+ 'input' : u0,\
+ 'regularisation_parameter':0.04, \
+ 'number_of_iterations' :150 ,\
+ 'tolerance_constant':1e-05,\
+ 'methodTV': 0 ,\
+ 'printingOut': 0
+ }
+
+print ("#############SB-TV CPU####################")
+start_time = timeit.default_timer()
+sb_cpu = SB_TV(pars['input'],
+ pars['regularisation_parameter'],
+ pars['number_of_iterations'],
+ pars['tolerance_constant'],
+ pars['methodTV'],
+ pars['printingOut'],'cpu')
+
+
+rms = rmse(Im, sb_cpu)
+pars['rmse'] = rms
+
+txtstr = printParametersToString(pars)
+txtstr += "%s = %.3fs" % ('elapsed time',timeit.default_timer() - start_time)
+print (txtstr)
+a=fig.add_subplot(1,4,2)
+
+# these are matplotlib.patch.Patch properties
+props = dict(boxstyle='round', facecolor='wheat', alpha=0.75)
+# place a text box in upper left in axes coords
+a.text(0.15, 0.25, txtstr, transform=a.transAxes, fontsize=14,
+ verticalalignment='top', bbox=props)
+imgplot = plt.imshow(sb_cpu, cmap="gray")
+plt.title('{}'.format('CPU results'))
+
+
+print ("##############SB TV GPU##################")
+start_time = timeit.default_timer()
+sb_gpu = SB_TV(pars['input'],
+ pars['regularisation_parameter'],
+ pars['number_of_iterations'],
+ pars['tolerance_constant'],
+ pars['methodTV'],
+ pars['printingOut'],'gpu')
+
+rms = rmse(Im, sb_gpu)
+pars['rmse'] = rms
+pars['algorithm'] = SB_TV
+txtstr = printParametersToString(pars)
+txtstr += "%s = %.3fs" % ('elapsed time',timeit.default_timer() - start_time)
+print (txtstr)
+a=fig.add_subplot(1,4,3)
+
+# these are matplotlib.patch.Patch properties
+props = dict(boxstyle='round', facecolor='wheat', alpha=0.75)
+# place a text box in upper left in axes coords
+a.text(0.15, 0.25, txtstr, transform=a.transAxes, fontsize=14,
+ verticalalignment='top', bbox=props)
+imgplot = plt.imshow(sb_gpu, cmap="gray")
+plt.title('{}'.format('GPU results'))
+
+print ("--------Compare the results--------")
+tolerance = 1e-05
+diff_im = np.zeros(np.shape(rof_cpu))
+diff_im = abs(sb_cpu - sb_gpu)
+diff_im[diff_im > tolerance] = 1
+a=fig.add_subplot(1,4,4)
+imgplot = plt.imshow(diff_im, vmin=0, vmax=1, cmap="gray")
+plt.title('{}'.format('Pixels larger threshold difference'))
+if (diff_im.sum() > 1):
+ print ("Arrays do not match!")
+else:
+ print ("Arrays match")
+
print ("%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%")
print ("____________FGP-dTV bench___________________")
print ("%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%")
## plot
-fig = plt.figure(3)
+fig = plt.figure(4)
plt.suptitle('Comparison of FGP-dTV regulariser using CPU and GPU implementations')
a=fig.add_subplot(1,4,1)
a.set_title('Noisy Image')
diff --git a/Wrappers/Python/demos/demo_gpu_regularisers.py b/Wrappers/Python/demos/demo_gpu_regularisers.py
index 24a3c88..25d8d85 100644
--- a/Wrappers/Python/demos/demo_gpu_regularisers.py
+++ b/Wrappers/Python/demos/demo_gpu_regularisers.py
@@ -12,7 +12,7 @@ import matplotlib.pyplot as plt
import numpy as np
import os
import timeit
-from ccpi.filters.regularisers import ROF_TV, FGP_TV, FGP_dTV
+from ccpi.filters.regularisers import ROF_TV, FGP_TV, SB_TV, FGP_dTV
from qualitymetrics import rmse
###############################################################################
def printParametersToString(pars):
@@ -139,12 +139,59 @@ a.text(0.15, 0.25, txtstr, transform=a.transAxes, fontsize=14,
imgplot = plt.imshow(fgp_gpu, cmap="gray")
plt.title('{}'.format('GPU results'))
+
print ("%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%")
-print ("____________FGP-dTV bench___________________")
+print ("____________SB-TV bench___________________")
print ("%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%")
## plot
fig = plt.figure(3)
+plt.suptitle('Performance of the SB-TV regulariser using the GPU')
+a=fig.add_subplot(1,2,1)
+a.set_title('Noisy Image')
+imgplot = plt.imshow(u0,cmap="gray")
+
+# set parameters
+pars = {'algorithm' : SB_TV, \
+ 'input' : u0,\
+ 'regularisation_parameter':0.04, \
+ 'number_of_iterations' :150 ,\
+ 'tolerance_constant':1e-06,\
+ 'methodTV': 0 ,\
+ 'printingOut': 0
+ }
+
+print ("##############SB TV GPU##################")
+start_time = timeit.default_timer()
+sb_gpu = SB_TV(pars['input'],
+ pars['regularisation_parameter'],
+ pars['number_of_iterations'],
+ pars['tolerance_constant'],
+ pars['methodTV'],
+ pars['printingOut'],'gpu')
+
+rms = rmse(Im, sb_gpu)
+pars['rmse'] = rms
+pars['algorithm'] = SB_TV
+txtstr = printParametersToString(pars)
+txtstr += "%s = %.3fs" % ('elapsed time',timeit.default_timer() - start_time)
+print (txtstr)
+a=fig.add_subplot(1,2,2)
+
+# these are matplotlib.patch.Patch properties
+props = dict(boxstyle='round', facecolor='wheat', alpha=0.75)
+# place a text box in upper left in axes coords
+a.text(0.15, 0.25, txtstr, transform=a.transAxes, fontsize=14,
+ verticalalignment='top', bbox=props)
+imgplot = plt.imshow(sb_gpu, cmap="gray")
+plt.title('{}'.format('GPU results'))
+
+print ("%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%")
+print ("____________FGP-dTV bench___________________")
+print ("%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%")
+
+## plot
+fig = plt.figure(4)
plt.suptitle('Performance of the FGP-dTV regulariser using the GPU')
a=fig.add_subplot(1,2,1)
a.set_title('Noisy Image')
@@ -219,7 +266,7 @@ print ("_______________ROF-TV (3D)_________________")
print ("%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%")
## plot
-fig = plt.figure(4)
+fig = plt.figure(5)
plt.suptitle('Performance of ROF-TV regulariser using the GPU')
a=fig.add_subplot(1,2,1)
a.set_title('Noisy 15th slice of a volume')
@@ -259,7 +306,7 @@ print ("_______________FGP-TV (3D)__________________")
print ("%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%")
## plot
-fig = plt.figure(5)
+fig = plt.figure(6)
plt.suptitle('Performance of FGP-TV regulariser using the GPU')
a=fig.add_subplot(1,2,1)
a.set_title('Noisy Image')
@@ -302,13 +349,58 @@ a.text(0.15, 0.25, txtstr, transform=a.transAxes, fontsize=14,
imgplot = plt.imshow(fgp_gpu3D[10,:,:], cmap="gray")
plt.title('{}'.format('Recovered volume on the GPU using FGP-TV'))
+print ("%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%")
+print ("_______________SB-TV (3D)__________________")
+print ("%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%")
+
+## plot
+fig = plt.figure(7)
+plt.suptitle('Performance of SB-TV regulariser using the GPU')
+a=fig.add_subplot(1,2,1)
+a.set_title('Noisy Image')
+imgplot = plt.imshow(noisyVol[10,:,:],cmap="gray")
+
+# set parameters
+pars = {'algorithm' : SB_TV, \
+ 'input' : noisyVol,\
+ 'regularisation_parameter':0.04, \
+ 'number_of_iterations' :100 ,\
+ 'tolerance_constant':1e-05,\
+ 'methodTV': 0 ,\
+ 'printingOut': 0
+ }
+
+print ("#############SB TV GPU####################")
+start_time = timeit.default_timer()
+sb_gpu3D = SB_TV(pars['input'],
+ pars['regularisation_parameter'],
+ pars['number_of_iterations'],
+ pars['tolerance_constant'],
+ pars['methodTV'],
+ pars['printingOut'],'gpu')
+
+rms = rmse(idealVol, sb_gpu3D)
+pars['rmse'] = rms
+
+txtstr = printParametersToString(pars)
+txtstr += "%s = %.3fs" % ('elapsed time',timeit.default_timer() - start_time)
+print (txtstr)
+a=fig.add_subplot(1,2,2)
+
+# these are matplotlib.patch.Patch properties
+props = dict(boxstyle='round', facecolor='wheat', alpha=0.75)
+# place a text box in upper left in axes coords
+a.text(0.15, 0.25, txtstr, transform=a.transAxes, fontsize=14,
+ verticalalignment='top', bbox=props)
+imgplot = plt.imshow(sb_gpu3D[10,:,:], cmap="gray")
+plt.title('{}'.format('Recovered volume on the GPU using SB-TV'))
print ("%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%")
print ("_______________FGP-dTV (3D)________________")
print ("%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%")
## plot
-fig = plt.figure(6)
+fig = plt.figure(8)
plt.suptitle('Performance of FGP-dTV regulariser using the GPU')
a=fig.add_subplot(1,2,1)
a.set_title('Noisy Image')
diff --git a/Wrappers/Python/setup-regularisers.py.in b/Wrappers/Python/setup-regularisers.py.in
index c7ebb5c..0681cc4 100644
--- a/Wrappers/Python/setup-regularisers.py.in
+++ b/Wrappers/Python/setup-regularisers.py.in
@@ -36,6 +36,7 @@ extra_include_dirs += [os.path.join(".." , ".." , "Core"),
os.path.join(".." , ".." , "Core", "regularisers_CPU"),
os.path.join(".." , ".." , "Core", "regularisers_GPU" , "TV_FGP" ) ,
os.path.join(".." , ".." , "Core", "regularisers_GPU" , "TV_ROF" ) ,
+ os.path.join(".." , ".." , "Core", "regularisers_GPU" , "TV_SB" ) ,
os.path.join(".." , ".." , "Core", "regularisers_GPU" , "dTV_FGP" ) ,
"."]
diff --git a/Wrappers/Python/src/cpu_regularisers.pyx b/Wrappers/Python/src/cpu_regularisers.pyx
index 1661375..417670d 100644
--- a/Wrappers/Python/src/cpu_regularisers.pyx
+++ b/Wrappers/Python/src/cpu_regularisers.pyx
@@ -20,6 +20,7 @@ cimport numpy as np
cdef extern float TV_ROF_CPU_main(float *Input, float *Output, float lambdaPar, int iterationsNumb, float tau, int dimX, int dimY, int dimZ);
cdef extern float TV_FGP_CPU_main(float *Input, float *Output, float lambdaPar, int iterationsNumb, float epsil, int methodTV, int nonneg, int printM, int dimX, int dimY, int dimZ);
+cdef extern float SB_TV_CPU_main(float *Input, float *Output, float lambdaPar, int iterationsNumb, float epsil, int methodTV, int printM, int dimX, int dimY, int dimZ);
cdef extern float dTV_FGP_CPU_main(float *Input, float *InputRef, float *Output, float lambdaPar, int iterationsNumb, float epsil, float eta, int methodTV, int nonneg, int printM, int dimX, int dimY, int dimZ);
@@ -125,6 +126,63 @@ def TV_FGP_3D(np.ndarray[np.float32_t, ndim=3, mode="c"] inputData,
printM,
dims[2], dims[1], dims[0])
return outputData
+
+#***************************************************************#
+#********************** Total-variation SB *********************#
+#***************************************************************#
+#*************** Total-variation Split Bregman (SB)*************#
+def TV_SB_CPU(inputData, regularisation_parameter, iterationsNumb, tolerance_param, methodTV, printM):
+ if inputData.ndim == 2:
+ return TV_SB_2D(inputData, regularisation_parameter, iterationsNumb, tolerance_param, methodTV, printM)
+ elif inputData.ndim == 3:
+ return TV_SB_3D(inputData, regularisation_parameter, iterationsNumb, tolerance_param, methodTV, printM)
+
+def TV_SB_2D(np.ndarray[np.float32_t, ndim=2, mode="c"] inputData,
+ float regularisation_parameter,
+ int iterationsNumb,
+ float tolerance_param,
+ int methodTV,
+ int printM):
+
+ cdef long dims[2]
+ dims[0] = inputData.shape[0]
+ dims[1] = inputData.shape[1]
+
+ cdef np.ndarray[np.float32_t, ndim=2, mode="c"] outputData = \
+ np.zeros([dims[0],dims[1]], dtype='float32')
+
+ #/* Run SB-TV iterations for 2D data */
+ SB_TV_CPU_main(&inputData[0,0], &outputData[0,0], regularisation_parameter,
+ iterationsNumb,
+ tolerance_param,
+ methodTV,
+ printM,
+ dims[0], dims[1], 1)
+
+ return outputData
+
+def TV_SB_3D(np.ndarray[np.float32_t, ndim=3, mode="c"] inputData,
+ float regularisation_parameter,
+ int iterationsNumb,
+ float tolerance_param,
+ int methodTV,
+ int printM):
+ cdef long dims[3]
+ dims[0] = inputData.shape[0]
+ dims[1] = inputData.shape[1]
+ dims[2] = inputData.shape[2]
+
+ cdef np.ndarray[np.float32_t, ndim=3, mode="c"] outputData = \
+ np.zeros([dims[0], dims[1], dims[2]], dtype='float32')
+
+ #/* Run SB-TV iterations for 3D data */
+ SB_TV_CPU_main(&inputData[0,0,0], &outputData[0,0,0], regularisation_parameter,
+ iterationsNumb,
+ tolerance_param,
+ methodTV,
+ printM,
+ dims[2], dims[1], dims[0])
+ return outputData
#****************************************************************#
#**************Directional Total-variation FGP ******************#
#****************************************************************#
diff --git a/Wrappers/Python/src/gpu_regularisers.pyx b/Wrappers/Python/src/gpu_regularisers.pyx
index 18efdcd..36eec95 100644
--- a/Wrappers/Python/src/gpu_regularisers.pyx
+++ b/Wrappers/Python/src/gpu_regularisers.pyx
@@ -20,6 +20,7 @@ cimport numpy as np
cdef extern void TV_ROF_GPU_main(float* Input, float* Output, float lambdaPar, int iter, float tau, int N, int M, int Z);
cdef extern void TV_FGP_GPU_main(float *Input, float *Output, float lambdaPar, int iter, float epsil, int methodTV, int nonneg, int printM, int N, int M, int Z);
+cdef extern void TV_SB_GPU_main(float *Input, float *Output, float lambdaPar, int iter, float epsil, int methodTV, int printM, int N, int M, int Z);
cdef extern void dTV_FGP_GPU_main(float *Input, float *InputRef, float *Output, float lambdaPar, int iterationsNumb, float epsil, float eta, int methodTV, int nonneg, int printM, int N, int M, int Z);
# Total-variation Rudin-Osher-Fatemi (ROF)
@@ -62,6 +63,27 @@ def TV_FGP_GPU(inputData,
methodTV,
nonneg,
printM)
+# Total-variation Split Bregman (SB)
+def TV_SB_GPU(inputData,
+ regularisation_parameter,
+ iterations,
+ tolerance_param,
+ methodTV,
+ printM):
+ if inputData.ndim == 2:
+ return SBTV2D(inputData,
+ regularisation_parameter,
+ iterations,
+ tolerance_param,
+ methodTV,
+ printM)
+ elif inputData.ndim == 3:
+ return SBTV3D(inputData,
+ regularisation_parameter,
+ iterations,
+ tolerance_param,
+ methodTV,
+ printM)
# Directional Total-variation Fast-Gradient-Projection (FGP)
def dTV_FGP_GPU(inputData,
refdata,
@@ -197,7 +219,60 @@ def FGPTV3D(np.ndarray[np.float32_t, ndim=3, mode="c"] inputData,
dims[2], dims[1], dims[0]);
return outputData
+#***************************************************************#
+#********************** Total-variation SB *********************#
+#***************************************************************#
+#*************** Total-variation Split Bregman (SB)*************#
+def SBTV2D(np.ndarray[np.float32_t, ndim=2, mode="c"] inputData,
+ float regularisation_parameter,
+ int iterations,
+ float tolerance_param,
+ int methodTV,
+ int printM):
+
+ cdef long dims[2]
+ dims[0] = inputData.shape[0]
+ dims[1] = inputData.shape[1]
+
+ cdef np.ndarray[np.float32_t, ndim=2, mode="c"] outputData = \
+ np.zeros([dims[0],dims[1]], dtype='float32')
+
+ # Running CUDA code here
+ TV_SB_GPU_main(&inputData[0,0], &outputData[0,0],
+ regularisation_parameter,
+ iterations,
+ tolerance_param,
+ methodTV,
+ printM,
+ dims[0], dims[1], 1);
+
+ return outputData
+def SBTV3D(np.ndarray[np.float32_t, ndim=3, mode="c"] inputData,
+ float regularisation_parameter,
+ int iterations,
+ float tolerance_param,
+ int methodTV,
+ int printM):
+
+ cdef long dims[3]
+ dims[0] = inputData.shape[0]
+ dims[1] = inputData.shape[1]
+ dims[2] = inputData.shape[2]
+
+ cdef np.ndarray[np.float32_t, ndim=3, mode="c"] outputData = \
+ np.zeros([dims[0],dims[1],dims[2]], dtype='float32')
+
+ # Running CUDA code here
+ TV_SB_GPU_main(&inputData[0,0,0], &outputData[0,0,0],
+ regularisation_parameter ,
+ iterations,
+ tolerance_param,
+ methodTV,
+ printM,
+ dims[2], dims[1], dims[0]);
+
+ return outputData
#****************************************************************#
#**************Directional Total-variation FGP ******************#
#****************************************************************#