Merge pull request #73 from vais-ral/NLTV

Nonlocal TV method added (CPU version)

5 files changed, 221 insertions, 7 deletions

diff --git a/Wrappers/Matlab/demos/demoMatlab_denoise.m b/Wrappers/Matlab/demos/demoMatlab_denoise.m
index d11bc63..54b8bac 100644
--- a/Wrappers/Matlab/demos/demoMatlab_denoise.m
+++ b/Wrappers/Matlab/demos/demoMatlab_denoise.m
@@ -135,7 +135,21 @@ figure; imshow(u_diff4, [0 1]); title('Diffusion 4thO denoised image (CPU)');
 % tic; u_diff4_g = Diffusion_4thO_GPU(single(u0), lambda_regDiff, sigmaPar, iter_diff, tau_param); toc; 
 % figure; imshow(u_diff4_g, [0 1]); title('Diffusion 4thO denoised image (GPU)');
 %%
-
+fprintf('Weights pre-calculation for Non-local TV (takes time on CPU) \n');
+SearchingWindow = 7;
+PatchWindow = 2;
+NeighboursNumber = 15; % the number of neibours to include
+h = 0.23; % edge related parameter for NLM
+[H_i, H_j, Weights] = PatchSelect(single(u0), SearchingWindow, PatchWindow, NeighboursNumber, h);
+%%
+fprintf('Denoise using Non-local Total Variation (CPU) \n');
+iter_nltv = 2; % number of nltv iterations
+lambda_nltv = 0.085; % regularisation parameter for nltv
+tic; u_nltv = Nonlocal_TV(single(u0), H_i, H_j, 0, Weights, lambda_nltv, iter_nltv); toc; 
+rmse_nltv = (RMSE(u_nltv(:),Im(:)));
+fprintf('%s %f \n', 'RMSE error for Non-local Total Variation is:', rmse_nltv);
+figure; imshow(u_nltv, [0 1]); title('Non-local Total Variation denoised image (CPU)');
+%%
 %>>>>>>>>>>>>>> MULTI-CHANNEL priors <<<<<<<<<<<<<<< %
 
 fprintf('Denoise using the FGP-dTV model (CPU) \n');
diff --git a/Wrappers/Matlab/mex_compile/compileCPU_mex_Linux.m b/Wrappers/Matlab/mex_compile/compileCPU_mex_Linux.m
index 767d811..72a828e 100644
--- a/Wrappers/Matlab/mex_compile/compileCPU_mex_Linux.m
+++ b/Wrappers/Matlab/mex_compile/compileCPU_mex_Linux.m
@@ -52,6 +52,12 @@ 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 NonLocal-TV...');
+mex PatchSelect.c PatchSelect_core.c utils.c CFLAGS="\$CFLAGS -fopenmp -Wall -std=c99" LDFLAGS="\$LDFLAGS -fopenmp"
+mex Nonlocal_TV.c Nonlocal_TV_core.c utils.c CFLAGS="\$CFLAGS -fopenmp -Wall -std=c99" LDFLAGS="\$LDFLAGS -fopenmp"
+movefile('Nonlocal_TV.mex*',Pathmove);
+movefile('PatchSelect.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);
@@ -66,6 +72,7 @@ mex NonlocalMarching_Inpaint.c NonlocalMarching_Inpaint_core.c utils.c CFLAGS="\
 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* LLT_ROF_core* CCPiDefines.h
+delete PatchSelect_core* Nonlocal_TV_core*
 delete Diffusion_Inpaint_core* NonlocalMarching_Inpaint_core*
 fprintf('%s \n', '<<<<<<< Regularisers successfully compiled! >>>>>>>');
 
diff --git a/Wrappers/Matlab/mex_compile/compileCPU_mex_WINDOWS.m b/Wrappers/Matlab/mex_compile/compileCPU_mex_WINDOWS.m
index 1b59dc2..6f7541c 100644
--- a/Wrappers/Matlab/mex_compile/compileCPU_mex_WINDOWS.m
+++ b/Wrappers/Matlab/mex_compile/compileCPU_mex_WINDOWS.m
@@ -60,6 +60,12 @@ 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 NonLocal-TV...');
+mex PatchSelect.c PatchSelect_core.c utils.c COMPFLAGS="\$COMPFLAGS -fopenmp -Wall -std=c99"
+mex Nonlocal_TV.c Nonlocal_TV_core.c utils.c COMPFLAGS="\$COMPFLAGS -fopenmp -Wall -std=c99"
+movefile('Nonlocal_TV.mex*',Pathmove);
+movefile('PatchSelect.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);
@@ -73,9 +79,7 @@ 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);
 
-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 Diffusion_Inpaint_core* NonlocalMarching_Inpaint_core*
-fprintf('%s \n', 'Regularisers successfully compiled!');
+
 %%
 %%% The second approach to compile using TDM-GCC which follows this
 %%% discussion:
@@ -105,15 +109,24 @@ fprintf('%s \n', 'Regularisers successfully compiled!');
 % 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" PatchSelect.c PatchSelect_core.c utils.c
+% mex C:\TDMGCC\lib\gcc\x86_64-w64-mingw32\5.1.0\libgomp.a CXXFLAGS="$CXXFLAGS -std=c++11 -fopenmp" Nonlocal_TV.c Nonlocal_TV_core.c utils.c
+% movefile('Nonlocal_TV.mex*',Pathmove);
+% movefile('PatchSelect.mex*',Pathmove);
 % mex C:\TDMGCC\lib\gcc\x86_64-w64-mingw32\5.1.0\libgomp.a CXXFLAGS="$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="$CXXFLAGS -std=c++11 -fopenmp" NonlDiff_Inp.c Diffusion_Inpaint_core.c utils.c
 % movefile('NonlDiff_Inp.mex*',Pathmove);
 % mex C:\TDMGCC\lib\gcc\x86_64-w64-mingw32\5.1.0\libgomp.a CXXFLAGS="$CXXFLAGS -std=c++11 -fopenmp" NonlocalMarching_Inpaint.c NonlocalMarching_Inpaint_core.c utils.c
 % 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 Diffusion_Inpaint_core* NonlocalMarching_Inpaint_core*
-% fprintf('%s \n', 'Regularisers successfully compiled!');
+
+
+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 PatchSelect_core* Nonlocal_TV_core*
+delete Diffusion_Inpaint_core* NonlocalMarching_Inpaint_core*
+fprintf('%s \n', 'Regularisers successfully compiled!');
+
+
 %%
 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
 
diff --git a/Wrappers/Matlab/mex_compile/regularisers_CPU/Nonlocal_TV.c b/Wrappers/Matlab/mex_compile/regularisers_CPU/Nonlocal_TV.c
new file mode 100644
index 0000000..014c0a0
--- /dev/null
+++ b/Wrappers/Matlab/mex_compile/regularisers_CPU/Nonlocal_TV.c
@@ -0,0 +1,88 @@
+/*
+ * This work is part of the Core Imaging Library developed by
+ * Visual Analytics and Imaging System Group of the Science Technology
+ * Facilities Council, STFC and Diamond Light Source Ltd. 
+ *
+ * Copyright 2017 Daniil Kazantsev
+ * Copyright 2017 Srikanth Nagella, Edoardo Pasca
+ * Copyright 2018 Diamond Light Source Ltd. 
+ *
+ * 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 "Nonlocal_TV_core.h"
+
+#define EPS 1.0000e-9
+
+/* Matlab wrapper for C-OMP implementation of non-local regulariser
+ * Weights and associated indices must be given as an input.
+ * Gauss-Seidel fixed point iteration requires ~ 3 iterations, so the main effort
+ * goes in pre-calculation of weights and selection of patches
+ *
+ *
+ * Input Parameters:
+ * 1. 2D/3D grayscale image/volume
+ * 2. AR_i - indeces of i neighbours
+ * 3. AR_j - indeces of j neighbours
+ * 4. AR_k - indeces of k neighbours (0 - for 2D case)
+ * 5. Weights_ij(k) - associated weights 
+ * 6. regularisation parameter
+ * 7. iterations number 
+ 
+ * Output:
+ * 1. denoised image/volume 	
+ * Elmoataz, Abderrahim, Olivier Lezoray, and Sébastien Bougleux. "Nonlocal discrete regularization on weighted graphs: a framework for image and manifold processing." IEEE Trans. Image Processing 17, no. 7 (2008): 1047-1060.
+ */
+
+void mexFunction(
+        int nlhs, mxArray *plhs[],
+        int nrhs, const mxArray *prhs[])
+{
+    long number_of_dims,  dimX, dimY, dimZ;
+    int IterNumb, NumNeighb = 0;
+    unsigned short *H_i, *H_j, *H_k;
+    const int  *dim_array;
+    const int  *dim_array2;
+    float *A_orig, *Output=NULL, *Weights, lambda;
+    
+    dim_array = mxGetDimensions(prhs[0]);
+    dim_array2 = mxGetDimensions(prhs[1]);
+    number_of_dims = mxGetNumberOfDimensions(prhs[0]);
+    
+    /*Handling Matlab input data*/
+    A_orig  = (float *) mxGetData(prhs[0]); /* a 2D image or a set of 2D images (3D stack) */
+    H_i  = (unsigned short *) mxGetData(prhs[1]); /* indeces of i neighbours */
+    H_j  = (unsigned short *) mxGetData(prhs[2]); /* indeces of j neighbours */
+    H_k  = (unsigned short *) mxGetData(prhs[3]); /* indeces of k neighbours */
+    Weights = (float *) mxGetData(prhs[4]); /* weights for patches */
+    lambda = (float) mxGetScalar(prhs[5]); /* regularisation parameter */
+    IterNumb = (int) mxGetScalar(prhs[6]); /* the number of iterations */
+ 
+    dimX = dim_array[0]; dimY = dim_array[1]; dimZ = dim_array[2];   
+         
+    /*****2D INPUT *****/
+    if (number_of_dims == 2) {
+        dimZ = 0;   
+        NumNeighb = dim_array2[2];
+        Output = (float*)mxGetPr(plhs[0] = mxCreateNumericArray(2, dim_array, mxSINGLE_CLASS, mxREAL));  
+        }
+    /*****3D INPUT *****/
+    /****************************************************/
+    if (number_of_dims == 3) {
+        NumNeighb = dim_array2[3];
+        Output = (float*)mxGetPr(plhs[0] = mxCreateNumericArray(3, dim_array, mxSINGLE_CLASS, mxREAL));
+    }
+    
+    /* run the main function here */
+    Nonlocal_TV_CPU_main(A_orig, Output, H_i, H_j, H_k, Weights, dimX, dimY, dimZ, NumNeighb, lambda, IterNumb);
+}
diff --git a/Wrappers/Matlab/mex_compile/regularisers_CPU/PatchSelect.c b/Wrappers/Matlab/mex_compile/regularisers_CPU/PatchSelect.c
new file mode 100644
index 0000000..f942539
--- /dev/null
+++ b/Wrappers/Matlab/mex_compile/regularisers_CPU/PatchSelect.c
@@ -0,0 +1,92 @@
+/*
+ * This work is part of the Core Imaging Library developed by
+ * Visual Analytics and Imaging System Group of the Science Technology
+ * Facilities Council, STFC and Diamond Light Source Ltd. 
+ *
+ * Copyright 2017 Daniil Kazantsev
+ * Copyright 2017 Srikanth Nagella, Edoardo Pasca
+ * Copyright 2018 Diamond Light Source Ltd. 
+ *
+ * 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 "PatchSelect_core.h"
+
+/* C-OMP implementation of non-local weight pre-calculation for non-local priors
+ * Weights and associated indices are stored into pre-allocated arrays and passed
+ * to the regulariser
+ *
+ *
+ * Input Parameters:
+ * 1. 2D/3D grayscale image/volume
+ * 2. Searching window (half-size of the main bigger searching window, e.g. 11)
+ * 3. Similarity window (half-size of the patch window, e.g. 2)
+ * 4. The number of neighbours to take (the most prominent after sorting neighbours will be taken)
+ * 5. noise-related parameter to calculate non-local weights
+ *
+ * Output [2D]:
+ * 1. AR_i - indeces of i neighbours
+ * 2. AR_j - indeces of j neighbours
+ * 3. Weights_ij - associated weights
+ *
+ * Output [3D]:
+ * 1. AR_i - indeces of i neighbours
+ * 2. AR_j - indeces of j neighbours
+ * 3. AR_k - indeces of j neighbours
+ * 4. Weights_ijk - associated weights
+ */
+/**************************************************/
+void mexFunction(
+        int nlhs, mxArray *plhs[],
+        int nrhs, const mxArray *prhs[])
+{
+    int number_of_dims,  SearchWindow, SimilarWin, NumNeighb;
+    mwSize dimX, dimY, dimZ;
+    unsigned short *H_i=NULL, *H_j=NULL, *H_k=NULL;
+    const int  *dim_array;
+    float *A, *Weights = NULL, h;
+    int dim_array2[3]; /* for 2D data */
+    int dim_array3[4]; /* for 3D data */
+    
+    dim_array = mxGetDimensions(prhs[0]);
+    number_of_dims = mxGetNumberOfDimensions(prhs[0]);
+    
+    /*Handling Matlab input data*/
+    A  = (float *) mxGetData(prhs[0]); /* a 2D or 3D image/volume */
+    SearchWindow = (int) mxGetScalar(prhs[1]);    /* Large Searching window */
+    SimilarWin = (int) mxGetScalar(prhs[2]);    /* Similarity window (patch-search)*/
+    NumNeighb = (int) mxGetScalar(prhs[3]); /* the total number of neighbours to take */
+    h = (float) mxGetScalar(prhs[4]); /* NLM parameter */
+
+    dimX = dim_array[0]; dimY = dim_array[1]; dimZ = dim_array[2];
+    dim_array2[0] = dimX; dim_array2[1] = dimY; dim_array2[2] = NumNeighb;  /* 2D case */
+    dim_array3[0] = dimX; dim_array3[1] = dimY; dim_array3[2] = dimZ; dim_array3[3] = NumNeighb;  /* 3D case */
+    
+    /****************2D INPUT ***************/
+    if (number_of_dims == 2) {
+        dimZ = 0;               
+        H_i = (unsigned short*)mxGetPr(plhs[0] = mxCreateNumericArray(3, dim_array2, mxUINT16_CLASS, mxREAL));
+        H_j = (unsigned short*)mxGetPr(plhs[1] = mxCreateNumericArray(3, dim_array2, mxUINT16_CLASS, mxREAL));
+        Weights = (float*)mxGetPr(plhs[2] = mxCreateNumericArray(3, dim_array2, mxSINGLE_CLASS, mxREAL));
+        }
+    /****************3D INPUT ***************/
+    if (number_of_dims == 3) {        
+        H_i = (unsigned short*)mxGetPr(plhs[0] = mxCreateNumericArray(4, dim_array3, mxUINT16_CLASS, mxREAL));
+        H_j = (unsigned short*)mxGetPr(plhs[1] = mxCreateNumericArray(4, dim_array3, mxUINT16_CLASS, mxREAL));
+        H_k = (unsigned short*)mxGetPr(plhs[2] = mxCreateNumericArray(4, dim_array3, mxUINT16_CLASS, mxREAL));
+        Weights = (float*)mxGetPr(plhs[3] = mxCreateNumericArray(4, dim_array3, mxSINGLE_CLASS, mxREAL));        
+    }
+    
+    PatchSelect_CPU_main(A, H_i, H_j, H_k, Weights, (long)(dimX), (long)(dimY), (long)(dimZ), SearchWindow, SimilarWin, NumNeighb, h, 0); 
+    
+ }