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authorDaniil Kazantsev <dkazanc@hotmail.com>2018-05-03 23:18:47 +0100
committerDaniil Kazantsev <dkazanc@hotmail.com>2018-05-03 23:18:47 +0100
commit66b101901f29776486009d165221d03a57316a0e (patch)
tree1e142d6400f09b7d4f61bfab1260b9399b3d7628
parent9d0dd9704173a50226cb2d46c5418b8172b25f69 (diff)
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4th order diffusion added
-rw-r--r--Core/CMakeLists.txt2
-rw-r--r--Core/regularisers_CPU/Diffus4th_order_core.c250
-rw-r--r--Core/regularisers_CPU/Diffus4th_order_core.h55
-rw-r--r--Core/regularisers_GPU/Diffus_4thO_GPU_core.cu278
-rw-r--r--Core/regularisers_GPU/Diffus_4thO_GPU_core.h8
-rw-r--r--Readme.md3
-rw-r--r--Wrappers/Matlab/demos/demoMatlab_3Ddenoise.m16
-rw-r--r--Wrappers/Matlab/demos/demoMatlab_denoise.m21
-rw-r--r--Wrappers/Matlab/mex_compile/compileCPU_mex.m5
-rw-r--r--Wrappers/Matlab/mex_compile/compileGPU_mex.m12
-rw-r--r--Wrappers/Matlab/mex_compile/regularisers_CPU/Diffusion_4thO.c76
-rw-r--r--Wrappers/Matlab/mex_compile/regularisers_GPU/Diffusion_4thO_GPU.cpp76
-rw-r--r--Wrappers/Python/ccpi/filters/regularisers.py22
-rw-r--r--Wrappers/Python/demos/demo_cpu_regularisers.py311
-rw-r--r--Wrappers/Python/demos/demo_cpu_regularisers3D.py366
-rw-r--r--Wrappers/Python/demos/demo_cpu_vs_gpu_regularisers.py92
-rw-r--r--Wrappers/Python/demos/demo_gpu_regularisers.py285
-rw-r--r--Wrappers/Python/demos/demo_gpu_regularisers3D.py367
-rw-r--r--Wrappers/Python/setup-regularisers.py.in1
-rw-r--r--Wrappers/Python/src/cpu_regularisers.pyx43
-rw-r--r--Wrappers/Python/src/gpu_regularisers.pyx60
21 files changed, 1825 insertions, 524 deletions
diff --git a/Core/CMakeLists.txt b/Core/CMakeLists.txt
index 86d69b2..7529d72 100644
--- a/Core/CMakeLists.txt
+++ b/Core/CMakeLists.txt
@@ -77,6 +77,7 @@ add_library(cilreg SHARED
${CMAKE_CURRENT_SOURCE_DIR}/regularisers_CPU/FGP_TV_core.c
${CMAKE_CURRENT_SOURCE_DIR}/regularisers_CPU/SB_TV_core.c
${CMAKE_CURRENT_SOURCE_DIR}/regularisers_CPU/Diffusion_core.c
+ ${CMAKE_CURRENT_SOURCE_DIR}/regularisers_CPU/Diffus4th_order_core.c
#${CMAKE_CURRENT_SOURCE_DIR}/regularisers_CPU/LLT_model_core.c
#${CMAKE_CURRENT_SOURCE_DIR}/regularisers_CPU/PatchBased_Regul_core.c
#${CMAKE_CURRENT_SOURCE_DIR}/regularisers_CPU/TGV_PD_core.c
@@ -129,6 +130,7 @@ if (CUDA_FOUND)
${CMAKE_CURRENT_SOURCE_DIR}/regularisers_GPU/TV_SB_GPU_core.cu
${CMAKE_CURRENT_SOURCE_DIR}/regularisers_GPU/dTV_FGP_GPU_core.cu
${CMAKE_CURRENT_SOURCE_DIR}/regularisers_GPU/NonlDiff_GPU_core.cu
+ ${CMAKE_CURRENT_SOURCE_DIR}/regularisers_GPU/Diffus_4thO_GPU_core.cu
)
if (UNIX)
message ("I'd install into ${CMAKE_INSTALL_PREFIX}/lib")
diff --git a/Core/regularisers_CPU/Diffus4th_order_core.c b/Core/regularisers_CPU/Diffus4th_order_core.c
new file mode 100644
index 0000000..069a42e
--- /dev/null
+++ b/Core/regularisers_CPU/Diffus4th_order_core.c
@@ -0,0 +1,250 @@
+/*
+ * 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 "Diffus4th_order_core.h"
+#include "utils.h"
+
+#define EPS 1.0e-7
+
+/* C-OMP implementation of fourth-order diffusion scheme [1] for piecewise-smooth recovery (2D/3D case)
+ * The minimisation is performed using explicit scheme.
+ *
+ * Input Parameters:
+ * 1. Noisy image/volume
+ * 2. lambda - regularization parameter
+ * 3. Edge-preserving parameter (sigma)
+ * 4. Number of iterations, for explicit scheme >= 150 is recommended
+ * 5. tau - time-marching step for the explicit scheme
+ *
+ * Output:
+ * [1] Regularized image/volume
+ *
+ * This function is based on the paper by
+ * [1] Hajiaboli, M.R., 2011. An anisotropic fourth-order diffusion filter for image noise removal. International Journal of Computer Vision, 92(2), pp.177-191.
+ */
+
+float Diffus4th_CPU_main(float *Input, float *Output, float lambdaPar, float sigmaPar, int iterationsNumb, float tau, int dimX, int dimY, int dimZ)
+{
+ int i,DimTotal;
+ float sigmaPar2;
+ float *W_Lapl=NULL;
+ sigmaPar2 = sigmaPar*sigmaPar;
+ DimTotal = dimX*dimY*dimZ;
+
+ W_Lapl = calloc(DimTotal, sizeof(float));
+
+ /* copy into output */
+ copyIm(Input, Output, dimX, dimY, dimZ);
+
+ if (dimZ == 1) {
+ /* running 2D diffusion iterations */
+ for(i=0; i < iterationsNumb; i++) {
+ /* Calculating weighted Laplacian */
+ Weighted_Laplc2D(W_Lapl, Output, sigmaPar2, dimX, dimY);
+ /* Perform iteration step */
+ Diffusion_update_step2D(Output, Input, W_Lapl, lambdaPar, sigmaPar2, tau, dimX, dimY);
+ }
+ }
+ else {
+ /* running 3D diffusion iterations */
+ for(i=0; i < iterationsNumb; i++) {
+ /* Calculating weighted Laplacian */
+ Weighted_Laplc3D(W_Lapl, Output, sigmaPar2, dimX, dimY, dimZ);
+ /* Perform iteration step */
+ Diffusion_update_step3D(Output, Input, W_Lapl, lambdaPar, sigmaPar2, tau, dimX, dimY, dimZ);
+ }
+ }
+ free(W_Lapl);
+ return *Output;
+}
+/********************************************************************/
+/***************************2D Functions*****************************/
+/********************************************************************/
+float Weighted_Laplc2D(float *W_Lapl, float *U0, float sigma, int dimX, int dimY)
+{
+ int i,j,i1,i2,j1,j2,index;
+ float gradX, gradX_sq, gradY, gradY_sq, gradXX, gradYY, gradXY, xy_2, denom, V_norm, V_orth, c, c_sq;
+
+ #pragma omp parallel for shared(W_Lapl) private(i,j,i1,i2,j1,j2,index,gradX, gradX_sq, gradY, gradY_sq, gradXX, gradYY, gradXY, xy_2, denom, V_norm, V_orth, c, c_sq)
+ for(i=0; i<dimX; i++) {
+ /* symmetric boundary conditions */
+ i1 = i+1; if (i1 == dimX) i1 = i-1;
+ i2 = i-1; if (i2 < 0) i2 = i+1;
+ for(j=0; j<dimY; j++) {
+ /* symmetric boundary conditions */
+ j1 = j+1; if (j1 == dimY) j1 = j-1;
+ j2 = j-1; if (j2 < 0) j2 = j+1;
+
+ index = j*dimX+i;
+
+ gradX = 0.5f*(U0[j*dimX+i2] - U0[j*dimX+i1]);
+ gradX_sq = pow(gradX,2);
+
+ gradY = 0.5f*(U0[j2*dimX+i] - U0[j1*dimX+i]);
+ gradY_sq = pow(gradY,2);
+
+ gradXX = U0[j*dimX+i2] + U0[j*dimX+i1] - 2*U0[index];
+ gradYY = U0[j2*dimX+i] + U0[j1*dimX+i] - 2*U0[index];
+
+ gradXY = 0.25f*(U0[j2*dimX+i2] + U0[j1*dimX+i1] - U0[j1*dimX+i2] - U0[j2*dimX+i1]);
+ xy_2 = 2.0f*gradX*gradY*gradXY;
+
+ denom = gradX_sq + gradY_sq;
+
+ if (denom <= EPS) {
+ V_norm = (gradXX*gradX_sq + xy_2 + gradYY*gradY_sq)/EPS;
+ V_orth = (gradXX*gradY_sq - xy_2 + gradYY*gradX_sq)/EPS;
+ }
+ else {
+ V_norm = (gradXX*gradX_sq + xy_2 + gradYY*gradY_sq)/denom;
+ V_orth = (gradXX*gradY_sq - xy_2 + gradYY*gradX_sq)/denom;
+ }
+
+ c = 1.0f/(1.0f + denom/sigma);
+ c_sq = c*c;
+
+ W_Lapl[index] = c_sq*V_norm + c*V_orth;
+ }
+ }
+ return *W_Lapl;
+}
+
+float Diffusion_update_step2D(float *Output, float *Input, float *W_Lapl, float lambdaPar, float sigmaPar2, float tau, int dimX, int dimY)
+{
+ int i,j,i1,i2,j1,j2,index;
+ float gradXXc, gradYYc;
+
+ #pragma omp parallel for shared(Output, Input, W_Lapl) private(i,j,i1,i2,j1,j2,index,gradXXc,gradYYc)
+ for(i=0; i<dimX; i++) {
+ /* symmetric boundary conditions */
+ i1 = i+1; if (i1 == dimX) i1 = i-1;
+ i2 = i-1; if (i2 < 0) i2 = i+1;
+ for(j=0; j<dimY; j++) {
+ /* symmetric boundary conditions */
+ j1 = j+1; if (j1 == dimY) j1 = j-1;
+ j2 = j-1; if (j2 < 0) j2 = j+1;
+ index = j*dimX+i;
+
+ gradXXc = W_Lapl[j*dimX+i2] + W_Lapl[j*dimX+i1] - 2*W_Lapl[index];
+ gradYYc = W_Lapl[j2*dimX+i] + W_Lapl[j1*dimX+i] - 2*W_Lapl[index];
+
+ Output[index] += tau*(-lambdaPar*(gradXXc + gradYYc) - (Output[index] - Input[index]));
+ }
+ }
+ return *Output;
+}
+/********************************************************************/
+/***************************3D Functions*****************************/
+/********************************************************************/
+float Weighted_Laplc3D(float *W_Lapl, float *U0, float sigma, int dimX, int dimY, int dimZ)
+{
+ int i,j,k,i1,i2,j1,j2,k1,k2,index;
+ float gradX, gradX_sq, gradY, gradY_sq, gradXX, gradYY, gradXY, xy_2, denom, V_norm, V_orth, c, c_sq, gradZ, gradZ_sq, gradZZ, gradXZ, gradYZ, xyz_1, xyz_2;
+
+ #pragma omp parallel for shared(W_Lapl) private(i,j,k,i1,i2,j1,j2,k1,k2,index,gradX, gradX_sq, gradY, gradY_sq, gradXX, gradYY, gradXY, xy_2, denom, V_norm, V_orth, c, c_sq, gradZ, gradZ_sq, gradZZ, gradXZ, gradYZ, xyz_1, xyz_2)
+ for(i=0; i<dimX; i++) {
+ /* symmetric boundary conditions */
+ i1 = i+1; if (i1 == dimX) i1 = i-1;
+ i2 = i-1; if (i2 < 0) i2 = i+1;
+ for(j=0; j<dimY; j++) {
+ /* symmetric boundary conditions */
+ j1 = j+1; if (j1 == dimY) j1 = j-1;
+ j2 = j-1; if (j2 < 0) j2 = j+1;
+
+ for(k=0; k<dimZ; k++) {
+ /* symmetric boundary conditions */
+ k1 = k+1; if (k1 == dimZ) k1 = k-1;
+ k2 = k-1; if (k2 < 0) k2 = k+1;
+
+ index = (dimX*dimY)*k + j*dimX+i;
+
+ gradX = 0.5f*(U0[(dimX*dimY)*k + j*dimX+i2] - U0[(dimX*dimY)*k + j*dimX+i1]);
+ gradX_sq = pow(gradX,2);
+
+ gradY = 0.5f*(U0[(dimX*dimY)*k + j2*dimX+i] - U0[(dimX*dimY)*k + j1*dimX+i]);
+ gradY_sq = pow(gradY,2);
+
+ gradZ = 0.5f*(U0[(dimX*dimY)*k2 + j*dimX+i] - U0[(dimX*dimY)*k1 + j*dimX+i]);
+ gradZ_sq = pow(gradZ,2);
+
+ gradXX = U0[(dimX*dimY)*k + j*dimX+i2] + U0[(dimX*dimY)*k + j*dimX+i1] - 2*U0[index];
+ gradYY = U0[(dimX*dimY)*k + j2*dimX+i] + U0[(dimX*dimY)*k + j1*dimX+i] - 2*U0[index];
+ gradZZ = U0[(dimX*dimY)*k2 + j*dimX+i] + U0[(dimX*dimY)*k1 + j*dimX+i] - 2*U0[index];
+
+ gradXY = 0.25f*(U0[(dimX*dimY)*k + j2*dimX+i2] + U0[(dimX*dimY)*k + j1*dimX+i1] - U0[(dimX*dimY)*k + j1*dimX+i2] - U0[(dimX*dimY)*k + j2*dimX+i1]);
+ gradXZ = 0.25f*(U0[(dimX*dimY)*k2 + j*dimX+i2] - U0[(dimX*dimY)*k2+j*dimX+i1] - U0[(dimX*dimY)*k1+j*dimX+i2] + U0[(dimX*dimY)*k1+j*dimX+i1]);
+ gradYZ = 0.25f*(U0[(dimX*dimY)*k2 +j2*dimX+i] - U0[(dimX*dimY)*k2+j1*dimX+i] - U0[(dimX*dimY)*k1+j2*dimX+i] + U0[(dimX*dimY)*k1+j1*dimX+i]);
+
+ xy_2 = 2.0f*gradX*gradY*gradXY;
+ xyz_1 = 2.0f*gradX*gradZ*gradXZ;
+ xyz_2 = 2.0f*gradY*gradZ*gradYZ;
+
+ denom = gradX_sq + gradY_sq + gradZ_sq;
+
+ if (denom <= EPS) {
+ V_norm = (gradXX*gradX_sq + gradYY*gradY_sq + gradZZ*gradZ_sq + xy_2 + xyz_1 + xyz_2)/EPS;
+ V_orth = ((gradY_sq + gradZ_sq)*gradXX + (gradX_sq + gradZ_sq)*gradYY + (gradX_sq + gradY_sq)*gradZZ - xy_2 - xyz_1 - xyz_2)/EPS;
+ }
+ else {
+ V_norm = (gradXX*gradX_sq + gradYY*gradY_sq + gradZZ*gradZ_sq + xy_2 + xyz_1 + xyz_2)/denom;
+ V_orth = ((gradY_sq + gradZ_sq)*gradXX + (gradX_sq + gradZ_sq)*gradYY + (gradX_sq + gradY_sq)*gradZZ - xy_2 - xyz_1 - xyz_2)/denom;
+ }
+
+ c = 1.0f/(1.0f + denom/sigma);
+ c_sq = c*c;
+
+ W_Lapl[index] = c_sq*V_norm + c*V_orth;
+ }
+ }
+ }
+ return *W_Lapl;
+}
+
+float Diffusion_update_step3D(float *Output, float *Input, float *W_Lapl, float lambdaPar, float sigmaPar2, float tau, int dimX, int dimY, int dimZ)
+{
+ int i,j,i1,i2,j1,j2,index, k,k1,k2;
+ float gradXXc, gradYYc, gradZZc;
+
+ #pragma omp parallel for shared(Output, Input, W_Lapl) private(i,j,i1,i2,j1,j2,k,k1,k2,index,gradXXc,gradYYc,gradZZc)
+ for(i=0; i<dimX; i++) {
+ /* symmetric boundary conditions */
+ i1 = i+1; if (i1 == dimX) i1 = i-1;
+ i2 = i-1; if (i2 < 0) i2 = i+1;
+ for(j=0; j<dimY; j++) {
+ /* symmetric boundary conditions */
+ j1 = j+1; if (j1 == dimY) j1 = j-1;
+ j2 = j-1; if (j2 < 0) j2 = j+1;
+
+ for(k=0; k<dimZ; k++) {
+ /* symmetric boundary conditions */
+ k1 = k+1; if (k1 == dimZ) k1 = k-1;
+ k2 = k-1; if (k2 < 0) k2 = k+1;
+
+ index = (dimX*dimY)*k + j*dimX+i;
+
+ gradXXc = W_Lapl[(dimX*dimY)*k + j*dimX+i2] + W_Lapl[(dimX*dimY)*k + j*dimX+i1] - 2*W_Lapl[index];
+ gradYYc = W_Lapl[(dimX*dimY)*k + j2*dimX+i] + W_Lapl[(dimX*dimY)*k + j1*dimX+i] - 2*W_Lapl[index];
+ gradZZc = W_Lapl[(dimX*dimY)*k2 + j*dimX+i] + W_Lapl[(dimX*dimY)*k1 + j*dimX+i] - 2*W_Lapl[index];
+
+ Output[index] += tau*(-lambdaPar*(gradXXc + gradYYc + gradZZc) - (Output[index] - Input[index]));
+ }
+ }
+ }
+ return *Output;
+}
diff --git a/Core/regularisers_CPU/Diffus4th_order_core.h b/Core/regularisers_CPU/Diffus4th_order_core.h
new file mode 100644
index 0000000..7b8fc08
--- /dev/null
+++ b/Core/regularisers_CPU/Diffus4th_order_core.h
@@ -0,0 +1,55 @@
+/*
+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 <math.h>
+#include <stdlib.h>
+#include <memory.h>
+#include <stdio.h>
+#include "omp.h"
+#include "utils.h"
+#include "CCPiDefines.h"
+
+/* C-OMP implementation of fourth-order diffusion scheme [1] for piecewise-smooth recovery (2D/3D case)
+ * The minimisation is performed using explicit scheme.
+ *
+ * Input Parameters:
+ * 1. Noisy image/volume
+ * 2. lambda - regularization parameter
+ * 3. Edge-preserving parameter (sigma)
+ * 4. Number of iterations, for explicit scheme >= 150 is recommended
+ * 5. tau - time-marching step for explicit scheme
+ *
+ * Output:
+ * [1] Regularized image/volume
+ *
+ * This function is based on the paper by
+ * [1] Hajiaboli, M.R., 2011. An anisotropic fourth-order diffusion filter for image noise removal. International Journal of Computer Vision, 92(2), pp.177-191.
+ */
+
+#ifdef __cplusplus
+extern "C" {
+#endif
+CCPI_EXPORT float Diffus4th_CPU_main(float *Input, float *Output, float lambdaPar, float sigmaPar, int iterationsNumb, float tau, int dimX, int dimY, int dimZ);
+CCPI_EXPORT float Weighted_Laplc2D(float *W_Lapl, float *U0, float sigma, int dimX, int dimY);
+CCPI_EXPORT float Diffusion_update_step2D(float *Output, float *Input, float *W_Lapl, float lambdaPar, float sigmaPar2, float tau, int dimX, int dimY);
+CCPI_EXPORT float Weighted_Laplc3D(float *W_Lapl, float *U0, float sigma, int dimX, int dimY, int dimZ);
+CCPI_EXPORT float Diffusion_update_step3D(float *Output, float *Input, float *W_Lapl, float lambdaPar, float sigmaPar2, float tau, int dimX, int dimY, int dimZ);
+#ifdef __cplusplus
+}
+#endif
diff --git a/Core/regularisers_GPU/Diffus_4thO_GPU_core.cu b/Core/regularisers_GPU/Diffus_4thO_GPU_core.cu
new file mode 100644
index 0000000..fd586ef
--- /dev/null
+++ b/Core/regularisers_GPU/Diffus_4thO_GPU_core.cu
@@ -0,0 +1,278 @@
+ /*
+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 "Diffus_4thO_GPU_core.h"
+
+/* CUDA implementation of fourth-order diffusion scheme [1] for piecewise-smooth recovery (2D/3D case)
+ * The minimisation is performed using explicit scheme.
+ *
+ * Input Parameters:
+ * 1. Noisy image/volume
+ * 2. lambda - regularization parameter
+ * 3. Edge-preserving parameter (sigma)
+ * 4. Number of iterations, for explicit scheme >= 150 is recommended
+ * 5. tau - time-marching step for explicit scheme
+ *
+ * Output:
+ * [1] Regularized image/volume
+ *
+ * This function is based on the paper by
+ * [1] Hajiaboli, M.R., 2011. An anisotropic fourth-order diffusion filter for image noise removal. International Journal of Computer Vision, 92(2), pp.177-191.
+ */
+
+#define CHECK(call) \
+{ \
+ const cudaError_t error = call; \
+ if (error != cudaSuccess) \
+ { \
+ fprintf(stderr, "Error: %s:%d, ", __FILE__, __LINE__); \
+ fprintf(stderr, "code: %d, reason: %s\n", error, \
+ cudaGetErrorString(error)); \
+ exit(1); \
+ } \
+}
+
+#define BLKXSIZE 8
+#define BLKYSIZE 8
+#define BLKZSIZE 8
+
+#define BLKXSIZE2D 16
+#define BLKYSIZE2D 16
+#define EPS 1.0e-7
+#define idivup(a, b) ( ((a)%(b) != 0) ? (a)/(b)+1 : (a)/(b) )
+/********************************************************************/
+/***************************2D Functions*****************************/
+/********************************************************************/
+__global__ void Weighted_Laplc2D_kernel(float *W_Lapl, float *U0, float sigma, int dimX, int dimY)
+{
+ int i1,i2,j1,j2;
+ float gradX, gradX_sq, gradY, gradY_sq, gradXX, gradYY, gradXY, xy_2, denom, V_norm, V_orth, c, c_sq;
+
+ int i = blockDim.x * blockIdx.x + threadIdx.x;
+ int j = blockDim.y * blockIdx.y + threadIdx.y;
+
+ int index = i + dimX*j;
+
+ if ((i >= 0) && (i < dimX) && (j >= 0) && (j < dimY)) {
+
+ /* boundary conditions (Neumann reflections) */
+ i1 = i+1; if (i1 == dimX) i1 = i-1;
+ i2 = i-1; if (i2 < 0) i2 = i+1;
+ j1 = j+1; if (j1 == dimY) j1 = j-1;
+ j2 = j-1; if (j2 < 0) j2 = j+1;
+
+ gradX = 0.5f*(U0[j*dimX+i2] - U0[j*dimX+i1]);
+ gradX_sq = powf(gradX,2);
+
+ gradY = 0.5f*(U0[j2*dimX+i] - U0[j1*dimX+i]);
+ gradY_sq = powf(gradY,2);
+
+ gradXX = U0[j*dimX+i2] + U0[j*dimX+i1] - 2*U0[index];
+ gradYY = U0[j2*dimX+i] + U0[j1*dimX+i] - 2*U0[index];
+
+ gradXY = 0.25f*(U0[j2*dimX+i2] + U0[j1*dimX+i1] - U0[j1*dimX+i2] - U0[j2*dimX+i1]);
+ xy_2 = 2.0f*gradX*gradY*gradXY;
+
+ denom = gradX_sq + gradY_sq;
+
+ if (denom <= EPS) {
+ V_norm = (gradXX*gradX_sq + xy_2 + gradYY*gradY_sq)/EPS;
+ V_orth = (gradXX*gradY_sq - xy_2 + gradYY*gradX_sq)/EPS;
+ }
+ else {
+ V_norm = (gradXX*gradX_sq + xy_2 + gradYY*gradY_sq)/denom;
+ V_orth = (gradXX*gradY_sq - xy_2 + gradYY*gradX_sq)/denom;
+ }
+
+ c = 1.0f/(1.0f + denom/sigma);
+ c_sq = c*c;
+
+ W_Lapl[index] = c_sq*V_norm + c*V_orth;
+ }
+ return;
+}
+
+__global__ void Diffusion_update_step2D_kernel(float *Output, float *Input, float *W_Lapl, float lambdaPar, float sigmaPar2, float tau, int dimX, int dimY)
+{
+ int i1,i2,j1,j2;
+ float gradXXc, gradYYc;
+
+ int i = blockDim.x * blockIdx.x + threadIdx.x;
+ int j = blockDim.y * blockIdx.y + threadIdx.y;
+
+ int index = i + dimX*j;
+
+ if ((i >= 0) && (i < dimX) && (j >= 0) && (j < dimY)) {
+
+ /* boundary conditions (Neumann reflections) */
+ i1 = i+1; if (i1 == dimX) i1 = i-1;
+ i2 = i-1; if (i2 < 0) i2 = i+1;
+ j1 = j+1; if (j1 == dimY) j1 = j-1;
+ j2 = j-1; if (j2 < 0) j2 = j+1;
+
+ gradXXc = W_Lapl[j*dimX+i2] + W_Lapl[j*dimX+i1] - 2*W_Lapl[index];
+ gradYYc = W_Lapl[j2*dimX+i] + W_Lapl[j1*dimX+i] - 2*W_Lapl[index];
+
+ Output[index] += tau*(-lambdaPar*(gradXXc + gradYYc) - (Output[index] - Input[index]));
+ }
+ return;
+}
+/********************************************************************/
+/***************************3D Functions*****************************/
+/********************************************************************/
+__global__ void Weighted_Laplc3D_kernel(float *W_Lapl, float *U0, float sigma, int dimX, int dimY, int dimZ)
+{
+ int i1,i2,j1,j2,k1,k2;
+ float gradX, gradX_sq, gradY, gradY_sq, gradXX, gradYY, gradXY, xy_2, denom, V_norm, V_orth, c, c_sq, gradZ, gradZ_sq, gradZZ, gradXZ, gradYZ, xyz_1, xyz_2;
+
+ int i = blockDim.x * blockIdx.x + threadIdx.x;
+ int j = blockDim.y * blockIdx.y + threadIdx.y;
+ int k = blockDim.z * blockIdx.z + threadIdx.z;
+
+ if ((i >= 0) && (i < dimX) && (j >= 0) && (j < dimY) && (k >= 0) && (k < dimZ)) {
+
+ /* boundary conditions (Neumann reflections) */
+ i1 = i+1; if (i1 == dimX) i1 = i-1;
+ i2 = i-1; if (i2 < 0) i2 = i+1;
+ j1 = j+1; if (j1 == dimY) j1 = j-1;
+ j2 = j-1; if (j2 < 0) j2 = j+1;
+ k1 = k+1; if (k1 == dimZ) k1 = k-1;
+ k2 = k-1; if (k2 < 0) k2 = k+1;
+
+ int index = (dimX*dimY)*k + j*dimX+i;
+
+ gradX = 0.5f*(U0[(dimX*dimY)*k + j*dimX+i2] - U0[(dimX*dimY)*k + j*dimX+i1]);
+ gradX_sq = pow(gradX,2);
+
+ gradY = 0.5f*(U0[(dimX*dimY)*k + j2*dimX+i] - U0[(dimX*dimY)*k + j1*dimX+i]);
+ gradY_sq = pow(gradY,2);
+
+ gradZ = 0.5f*(U0[(dimX*dimY)*k2 + j*dimX+i] - U0[(dimX*dimY)*k1 + j*dimX+i]);
+ gradZ_sq = pow(gradZ,2);
+
+ gradXX = U0[(dimX*dimY)*k + j*dimX+i2] + U0[(dimX*dimY)*k + j*dimX+i1] - 2*U0[index];
+ gradYY = U0[(dimX*dimY)*k + j2*dimX+i] + U0[(dimX*dimY)*k + j1*dimX+i] - 2*U0[index];
+ gradZZ = U0[(dimX*dimY)*k2 + j*dimX+i] + U0[(dimX*dimY)*k1 + j*dimX+i] - 2*U0[index];
+
+ gradXY = 0.25f*(U0[(dimX*dimY)*k + j2*dimX+i2] + U0[(dimX*dimY)*k + j1*dimX+i1] - U0[(dimX*dimY)*k + j1*dimX+i2] - U0[(dimX*dimY)*k + j2*dimX+i1]);
+ gradXZ = 0.25f*(U0[(dimX*dimY)*k2 + j*dimX+i2] - U0[(dimX*dimY)*k2+j*dimX+i1] - U0[(dimX*dimY)*k1+j*dimX+i2] + U0[(dimX*dimY)*k1+j*dimX+i1]);
+ gradYZ = 0.25f*(U0[(dimX*dimY)*k2 +j2*dimX+i] - U0[(dimX*dimY)*k2+j1*dimX+i] - U0[(dimX*dimY)*k1+j2*dimX+i] + U0[(dimX*dimY)*k1+j1*dimX+i]);
+
+ xy_2 = 2.0f*gradX*gradY*gradXY;
+ xyz_1 = 2.0f*gradX*gradZ*gradXZ;
+ xyz_2 = 2.0f*gradY*gradZ*gradYZ;
+
+ denom = gradX_sq + gradY_sq + gradZ_sq;
+
+ if (denom <= EPS) {
+ V_norm = (gradXX*gradX_sq + gradYY*gradY_sq + gradZZ*gradZ_sq + xy_2 + xyz_1 + xyz_2)/EPS;
+ V_orth = ((gradY_sq + gradZ_sq)*gradXX + (gradX_sq + gradZ_sq)*gradYY + (gradX_sq + gradY_sq)*gradZZ - xy_2 - xyz_1 - xyz_2)/EPS;
+ }
+ else {
+ V_norm = (gradXX*gradX_sq + gradYY*gradY_sq + gradZZ*gradZ_sq + xy_2 + xyz_1 + xyz_2)/denom;
+ V_orth = ((gradY_sq + gradZ_sq)*gradXX + (gradX_sq + gradZ_sq)*gradYY + (gradX_sq + gradY_sq)*gradZZ - xy_2 - xyz_1 - xyz_2)/denom;
+ }
+
+ c = 1.0f/(1.0f + denom/sigma);
+ c_sq = c*c;
+
+ W_Lapl[index] = c_sq*V_norm + c*V_orth;
+ }
+ return;
+}
+__global__ void Diffusion_update_step3D_kernel(float *Output, float *Input, float *W_Lapl, float lambdaPar, float sigmaPar2, float tau, int dimX, int dimY, int dimZ)
+{
+ int i1,i2,j1,j2,k1,k2;
+ float gradXXc, gradYYc, gradZZc;
+
+ int i = blockDim.x * blockIdx.x + threadIdx.x;
+ int j = blockDim.y * blockIdx.y + threadIdx.y;
+ int k = blockDim.z * blockIdx.z + threadIdx.z;
+
+ if ((i >= 0) && (i < dimX) && (j >= 0) && (j < dimY) && (k >= 0) && (k < dimZ)) {
+
+ /* boundary conditions (Neumann reflections) */
+ i1 = i+1; if (i1 == dimX) i1 = i-1;
+ i2 = i-1; if (i2 < 0) i2 = i+1;
+ j1 = j+1; if (j1 == dimY) j1 = j-1;
+ j2 = j-1; if (j2 < 0) j2 = j+1;
+ k1 = k+1; if (k1 == dimZ) k1 = k-1;
+ k2 = k-1; if (k2 < 0) k2 = k+1;
+
+ int index = (dimX*dimY)*k + j*dimX+i;
+
+ gradXXc = W_Lapl[(dimX*dimY)*k + j*dimX+i2] + W_Lapl[(dimX*dimY)*k + j*dimX+i1] - 2*W_Lapl[index];
+ gradYYc = W_Lapl[(dimX*dimY)*k + j2*dimX+i] + W_Lapl[(dimX*dimY)*k + j1*dimX+i] - 2*W_Lapl[index];
+ gradZZc = W_Lapl[(dimX*dimY)*k2 + j*dimX+i] + W_Lapl[(dimX*dimY)*k1 + j*dimX+i] - 2*W_Lapl[index];
+
+ Output[index] += tau*(-lambdaPar*(gradXXc + gradYYc + gradZZc) - (Output[index] - Input[index]));
+ }
+ return;
+}
+/*%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%*/
+/********************* MAIN HOST FUNCTION ******************/
+/*%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%*/
+extern "C" void Diffus4th_GPU_main(float *Input, float *Output, float lambdaPar, float sigmaPar, int iterationsNumb, float tau, int N, int M, int Z)
+{
+ int dimTotal, dev = 0;
+ CHECK(cudaSetDevice(dev));
+ float *d_input, *d_output, *d_W_Lapl;
+ float sigmaPar2;
+ sigmaPar2 = sigmaPar*sigmaPar;
+ dimTotal = N*M*Z;
+
+ CHECK(cudaMalloc((void**)&d_input,dimTotal*sizeof(float)));
+ CHECK(cudaMalloc((void**)&d_output,dimTotal*sizeof(float)));
+ CHECK(cudaMalloc((void**)&d_W_Lapl,dimTotal*sizeof(float)));
+
+ CHECK(cudaMemcpy(d_input,Input,dimTotal*sizeof(float),cudaMemcpyHostToDevice));
+ CHECK(cudaMemcpy(d_output,Input,dimTotal*sizeof(float),cudaMemcpyHostToDevice));
+
+ if (Z == 1) {
+ /*2D case */
+ dim3 dimBlock(BLKXSIZE2D,BLKYSIZE2D);
+ dim3 dimGrid(idivup(N,BLKXSIZE2D), idivup(M,BLKYSIZE2D));
+
+ for(int n=0; n < iterationsNumb; n++) {
+ /* Calculating weighted Laplacian */
+ Weighted_Laplc2D_kernel<<<dimGrid,dimBlock>>>(d_W_Lapl, d_output, sigmaPar2, N, M);
+ CHECK(cudaDeviceSynchronize());
+ /* Perform iteration step */
+ Diffusion_update_step2D_kernel<<<dimGrid,dimBlock>>>(d_output, d_input, d_W_Lapl, lambdaPar, sigmaPar2, tau, N, M);
+ CHECK(cudaDeviceSynchronize());
+ }
+ }
+ else {
+ /*3D case*/
+ dim3 dimBlock(BLKXSIZE,BLKYSIZE,BLKZSIZE);
+ dim3 dimGrid(idivup(N,BLKXSIZE), idivup(M,BLKYSIZE),idivup(Z,BLKZSIZE));
+ for(int n=0; n < iterationsNumb; n++) {
+ /* Calculating weighted Laplacian */
+ Weighted_Laplc3D_kernel<<<dimGrid,dimBlock>>>(d_W_Lapl, d_output, sigmaPar2, N, M, Z);
+ CHECK(cudaDeviceSynchronize());
+ /* Perform iteration step */
+ Diffusion_update_step3D_kernel<<<dimGrid,dimBlock>>>(d_output, d_input, d_W_Lapl, lambdaPar, sigmaPar2, tau, N, M, Z);
+ CHECK(cudaDeviceSynchronize());
+ }
+ }
+ CHECK(cudaMemcpy(Output,d_output,dimTotal*sizeof(float),cudaMemcpyDeviceToHost));
+ CHECK(cudaFree(d_input));
+ CHECK(cudaFree(d_output));
+ CHECK(cudaFree(d_W_Lapl));
+}
diff --git a/Core/regularisers_GPU/Diffus_4thO_GPU_core.h b/Core/regularisers_GPU/Diffus_4thO_GPU_core.h
new file mode 100644
index 0000000..6314c1f
--- /dev/null
+++ b/Core/regularisers_GPU/Diffus_4thO_GPU_core.h
@@ -0,0 +1,8 @@
+#ifndef __Diff_4thO_GPU_H__
+#define __Diff_4thO_GPU_H__
+#include "CCPiDefines.h"
+#include <stdio.h>
+
+extern "C" CCPI_EXPORT void Diffus4th_GPU_main(float *Input, float *Output, float lambdaPar, float sigmaPar, int iterationsNumb, float tau, int N, int M, int Z);
+
+#endif
diff --git a/Readme.md b/Readme.md
index d114deb..356cacf 100644
--- a/Readme.md
+++ b/Readme.md
@@ -20,6 +20,7 @@
2. Fast-Gradient-Projection (FGP) Total Variation **2D/3D CPU/GPU** (Ref. *2*)
3. Split-Bregman (SB) Total Variation **2D/3D CPU/GPU** (Ref. *5*)
4. Linear and nonlinear diffusion (explicit PDE minimisation scheme) **2D/3D CPU/GPU** (Ref. *7*)
+5. Anisotropic Fourth-Order Diffusion (explicit PDE minimisation) **2D/3D CPU/GPU** (Ref. *8*)
### Multi-channel (denoising):
1. Fast-Gradient-Projection (FGP) Directional Total Variation **2D/3D CPU/GPU** (Ref. *3,4,2*)
@@ -66,6 +67,8 @@
*7. [Black, M.J., Sapiro, G., Marimont, D.H. and Heeger, D., 1998. Robust anisotropic diffusion. IEEE Transactions on image processing, 7(3), pp.421-432.](https://doi.org/10.1109/83.661192)*
+*8. [Hajiaboli, M.R., 2011. An anisotropic fourth-order diffusion filter for image noise removal. International Journal of Computer Vision, 92(2), pp.177-191.](https://doi.org/10.1007/s11263-010-0330-1)*
+
### License:
[Apache License, Version 2.0](http://www.apache.org/licenses/LICENSE-2.0)
diff --git a/Wrappers/Matlab/demos/demoMatlab_3Ddenoise.m b/Wrappers/Matlab/demos/demoMatlab_3Ddenoise.m
index c087433..ccd47f1 100644
--- a/Wrappers/Matlab/demos/demoMatlab_3Ddenoise.m
+++ b/Wrappers/Matlab/demos/demoMatlab_3Ddenoise.m
@@ -74,6 +74,22 @@ figure; imshow(u_diff(:,:,15), [0 1]); title('Diffusion denoised volume (CPU)');
% 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)');
%%
+fprintf('Denoise using Fourth-order anisotropic diffusion model (CPU) \n');
+iter_diff = 300; % number of diffusion iterations
+lambda_regDiff = 3.5; % regularisation for the diffusivity
+sigmaPar = 0.02; % edge-preserving parameter
+tau_param = 0.0025; % 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)');
+%%
+% fprintf('Denoise using Fourth-order anisotropic diffusion model (GPU) \n');
+% iter_diff = 300; % number of diffusion iterations
+% lambda_regDiff = 3.5; % regularisation for the diffusivity
+% sigmaPar = 0.02; % edge-preserving parameter
+% tau_param = 0.0025; % 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)');
+%%
%>>>>>>>>>>>>>> MULTI-CHANNEL priors <<<<<<<<<<<<<<< %
fprintf('Denoise a volume using the FGP-dTV model (CPU) \n');
diff --git a/Wrappers/Matlab/demos/demoMatlab_denoise.m b/Wrappers/Matlab/demos/demoMatlab_denoise.m
index d93f477..30ad79d 100644
--- a/Wrappers/Matlab/demos/demoMatlab_denoise.m
+++ b/Wrappers/Matlab/demos/demoMatlab_denoise.m
@@ -53,8 +53,8 @@ figure; imshow(u_sb, [0 1]); title('SB-TV denoised image (CPU)');
%%
fprintf('Denoise using Nonlinear-Diffusion model (CPU) \n');
iter_diff = 800; % number of diffusion iterations
-lambda_regDiff = 0.06; % regularisation for the diffusivity
-sigmaPar = 0.04; % edge-preserving parameter
+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(u0), lambda_regDiff, sigmaPar, iter_diff, tau_param, 'Huber'); toc;
figure; imshow(u_diff, [0 1]); title('Diffusion denoised image (CPU)');
@@ -67,6 +67,23 @@ figure; imshow(u_diff, [0 1]); title('Diffusion denoised image (CPU)');
% tic; u_diff_g = NonlDiff_GPU(single(u0), lambda_regDiff, sigmaPar, iter_diff, tau_param, 'Huber'); toc;
% figure; imshow(u_diff_g, [0 1]); title('Diffusion denoised image (GPU)');
%%
+fprintf('Denoise using Fourth-order anisotropic diffusion model (CPU) \n');
+iter_diff = 800; % number of diffusion iterations
+lambda_regDiff = 3.5; % regularisation for the diffusivity
+sigmaPar = 0.02; % edge-preserving parameter
+tau_param = 0.005; % time-marching constant
+tic; u_diff4 = Diffusion_4thO(single(u0), lambda_regDiff, sigmaPar, iter_diff, tau_param); toc;
+figure; imshow(u_diff4, [0 1]); title('Diffusion 4thO denoised image (CPU)');
+%%
+% fprintf('Denoise using Fourth-order anisotropic diffusion model (GPU) \n');
+% iter_diff = 800; % number of diffusion iterations
+% lambda_regDiff = 3.5; % regularisation for the diffusivity
+% sigmaPar = 0.02; % edge-preserving parameter
+% tau_param = 0.005; % time-marching constant
+% 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)');
+%%
+
%>>>>>>>>>>>>>> MULTI-CHANNEL priors <<<<<<<<<<<<<<< %
fprintf('Denoise using the FGP-dTV model (CPU) \n');
diff --git a/Wrappers/Matlab/mex_compile/compileCPU_mex.m b/Wrappers/Matlab/mex_compile/compileCPU_mex.m
index b232f33..19eb301 100644
--- a/Wrappers/Matlab/mex_compile/compileCPU_mex.m
+++ b/Wrappers/Matlab/mex_compile/compileCPU_mex.m
@@ -31,6 +31,9 @@ movefile('TNV.mex*',Pathmove);
mex NonlDiff.c Diffusion_core.c utils.c CFLAGS="\$CFLAGS -fopenmp -Wall -std=c99" LDFLAGS="\$LDFLAGS -fopenmp"
movefile('NonlDiff.mex*',Pathmove);
+mex Diffusion_4thO.c Diffus4th_order_core.c utils.c CFLAGS="\$CFLAGS -fopenmp -Wall -std=c99" LDFLAGS="\$LDFLAGS -fopenmp"
+movefile('Diffusion_4thO.mex*',Pathmove);
+
mex TV_energy.c utils.c CFLAGS="\$CFLAGS -fopenmp -Wall -std=c99" LDFLAGS="\$LDFLAGS -fopenmp"
movefile('TV_energy.mex*',Pathmove);
@@ -41,7 +44,7 @@ movefile('NonlDiff_Inp.mex*',Pathmove);
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* CCPiDefines.h
+delete SB_TV_core* ROF_TV_core* FGP_TV_core* FGP_dTV_core* TNV_core* utils* Diffusion_core* Diffus4th_order_core* CCPiDefines.h
delete Diffusion_Inpaint_core* NonlocalMarching_Inpaint_core*
fprintf('%s \n', 'Regularisers successfully compiled!');
diff --git a/Wrappers/Matlab/mex_compile/compileGPU_mex.m b/Wrappers/Matlab/mex_compile/compileGPU_mex.m
index 46d85a6..6b69c34 100644
--- a/Wrappers/Matlab/mex_compile/compileGPU_mex.m
+++ b/Wrappers/Matlab/mex_compile/compileGPU_mex.m
@@ -42,5 +42,13 @@ movefile('FGP_dTV_GPU.mex*',Pathmove);
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);
-delete TV_ROF_GPU_core* TV_FGP_GPU_core* TV_SB_GPU_core* dTV_FGP_GPU_core* NonlDiff_GPU_core* CCPiDefines.h
-fprintf('%s \n', 'All successfully compiled!'); \ No newline at end of file
+!/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* CCPiDefines.h
+fprintf('%s \n', 'All successfully compiled!');
+
+pathA2 = sprintf(['..' filesep '..' filesep], 1i);
+cd(pathA2);
+cd demos \ No newline at end of file
diff --git a/Wrappers/Matlab/mex_compile/regularisers_CPU/Diffusion_4thO.c b/Wrappers/Matlab/mex_compile/regularisers_CPU/Diffusion_4thO.c
new file mode 100644
index 0000000..81c0600
--- /dev/null
+++ b/Wrappers/Matlab/mex_compile/regularisers_CPU/Diffusion_4thO.c
@@ -0,0 +1,76 @@
+/*
+ * 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 "Diffus4th_order_core.h"
+
+/* C-OMP implementation of fourth-order diffusion scheme [1] for piecewise-smooth recovery (2D/3D case)
+ * The minimisation is performed using explicit scheme.
+ *
+ * Input Parameters:
+ * 1. Noisy image/volume [REQUIRED]
+ * 2. lambda - regularization parameter [REQUIRED]
+ * 3. Edge-preserving parameter (sigma) [REQUIRED]
+ * 4. Number of iterations, for explicit scheme >= 150 is recommended [OPTIONAL, default 300]
+ * 5. tau - time-marching step for the explicit scheme [OPTIONAL, default 0.015]
+ *
+ * Output:
+ * [1] Regularized image/volume
+ *
+ * This function is based on the paper by
+ * [1] Hajiaboli, M.R., 2011. An anisotropic fourth-order diffusion filter for image noise removal. International Journal of Computer Vision, 92(2), pp.177-191.
+ */
+
+void mexFunction(
+ int nlhs, mxArray *plhs[],
+ int nrhs, const mxArray *prhs[])
+
+{
+ int number_of_dims, iter_numb, dimX, dimY, dimZ;
+ const int *dim_array;
+ float *Input, *Output=NULL, lambda, tau, sigma;
+
+ dim_array = mxGetDimensions(prhs[0]);
+ number_of_dims = mxGetNumberOfDimensions(prhs[0]);
+
+ /*Handling Matlab input data*/
+ Input = (float *) mxGetData(prhs[0]);
+ lambda = (float) mxGetScalar(prhs[1]); /* regularization parameter */
+ sigma = (float) mxGetScalar(prhs[2]); /* Edge-preserving parameter */
+ iter_numb = 300; /* iterations number */
+ tau = 0.01; /* marching step parameter */
+
+ if (mxGetClassID(prhs[0]) != mxSINGLE_CLASS) {mexErrMsgTxt("The input image must be in a single precision"); }
+ if ((nrhs < 3) || (nrhs > 5)) mexErrMsgTxt("At least 3 parameters is required, all parameters are: Image(2D/3D), Regularisation parameter, Edge-preserving parameter, iterations number, time-marching constant");
+ if ((nrhs == 4) || (nrhs == 5)) iter_numb = (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));
+
+ Diffus4th_CPU_main(Input, Output, lambda, sigma, iter_numb, tau, dimX, dimY, dimZ);
+} \ No newline at end of file
diff --git a/Wrappers/Matlab/mex_compile/regularisers_GPU/Diffusion_4thO_GPU.cpp b/Wrappers/Matlab/mex_compile/regularisers_GPU/Diffusion_4thO_GPU.cpp
new file mode 100644
index 0000000..0edc067
--- /dev/null
+++ b/Wrappers/Matlab/mex_compile/regularisers_GPU/Diffusion_4thO_GPU.cpp
@@ -0,0 +1,76 @@
+/*
+ * 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 "Diffus_4thO_GPU_core.h"
+
+/* CUDA implementation of fourth-order diffusion scheme [1] for piecewise-smooth recovery (2D/3D case)
+ * The minimisation is performed using explicit scheme.
+ *
+ * Input Parameters:
+ * 1. Noisy image/volume [REQUIRED]
+ * 2. lambda - regularization parameter [REQUIRED]
+ * 3. Edge-preserving parameter (sigma) [REQUIRED]
+ * 4. Number of iterations, for explicit scheme >= 150 is recommended [OPTIONAL, default 300]
+ * 5. tau - time-marching step for the explicit scheme [OPTIONAL, default 0.015]
+ *
+ * Output:
+ * [1] Regularized image/volume
+ *
+ * This function is based on the paper by
+ * [1] Hajiaboli, M.R., 2011. An anisotropic fourth-order diffusion filter for image noise removal. International Journal of Computer Vision, 92(2), pp.177-191.
+ */
+
+void mexFunction(
+ int nlhs, mxArray *plhs[],
+ int nrhs, const mxArray *prhs[])
+
+{
+ int number_of_dims, iter_numb, dimX, dimY, dimZ;
+ const int *dim_array;
+ float *Input, *Output=NULL, lambda, tau, sigma;
+
+ dim_array = mxGetDimensions(prhs[0]);
+ number_of_dims = mxGetNumberOfDimensions(prhs[0]);
+
+ /*Handling Matlab input data*/
+ Input = (float *) mxGetData(prhs[0]);
+ lambda = (float) mxGetScalar(prhs[1]); /* regularization parameter */
+ sigma = (float) mxGetScalar(prhs[2]); /* Edge-preserving parameter */
+ iter_numb = 300; /* iterations number */
+ tau = 0.01; /* marching step parameter */
+
+ if (mxGetClassID(prhs[0]) != mxSINGLE_CLASS) {mexErrMsgTxt("The input image must be in a single precision"); }
+ if ((nrhs < 3) || (nrhs > 5)) mexErrMsgTxt("At least 3 parameters is required, all parameters are: Image(2D/3D), Regularisation parameter, Edge-preserving parameter, iterations number, time-marching constant");
+ if ((nrhs == 4) || (nrhs == 5)) iter_numb = (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));
+
+ Diffus4th_GPU_main(Input, Output, lambda, sigma, iter_numb, tau, dimX, dimY, dimZ);
+} \ No newline at end of file
diff --git a/Wrappers/Python/ccpi/filters/regularisers.py b/Wrappers/Python/ccpi/filters/regularisers.py
index a07b39a..0b79dac 100644
--- a/Wrappers/Python/ccpi/filters/regularisers.py
+++ b/Wrappers/Python/ccpi/filters/regularisers.py
@@ -2,8 +2,9 @@
script which assigns a proper device core function based on a flag ('cpu' or 'gpu')
"""
-from ccpi.filters.cpu_regularisers import TV_ROF_CPU, TV_FGP_CPU, TV_SB_CPU, dTV_FGP_CPU, TNV_CPU, NDF_CPU, NDF_INPAINT_CPU, NVM_INPAINT_CPU
-from ccpi.filters.gpu_regularisers import TV_ROF_GPU, TV_FGP_GPU, TV_SB_GPU, dTV_FGP_GPU, NDF_GPU
+from ccpi.filters.cpu_regularisers import TV_ROF_CPU, TV_FGP_CPU, TV_SB_CPU, dTV_FGP_CPU, TNV_CPU, NDF_CPU, Diff4th_CPU
+from ccpi.filters.gpu_regularisers import TV_ROF_GPU, TV_FGP_GPU, TV_SB_GPU, dTV_FGP_GPU, NDF_GPU, Diff4th_GPU
+from ccpi.filters.cpu_regularisers import NDF_INPAINT_CPU, NVM_INPAINT_CPU
def ROF_TV(inputData, regularisation_parameter, iterations,
time_marching_parameter,device='cpu'):
@@ -110,6 +111,23 @@ def NDF(inputData, regularisation_parameter, edge_parameter, iterations,
else:
raise ValueError('Unknown device {0}. Expecting gpu or cpu'\
.format(device))
+def DIFF4th(inputData, regularisation_parameter, edge_parameter, iterations,
+ time_marching_parameter, device='cpu'):
+ if device == 'cpu':
+ return Diff4th_CPU(inputData,
+ regularisation_parameter,
+ edge_parameter,
+ iterations,
+ time_marching_parameter)
+ elif device == 'gpu':
+ return Diff4th_GPU(inputData,
+ regularisation_parameter,
+ edge_parameter,
+ iterations,
+ time_marching_parameter)
+ else:
+ raise ValueError('Unknown device {0}. Expecting gpu or cpu'\
+ .format(device))
def NDF_INP(inputData, maskData, regularisation_parameter, edge_parameter, iterations,
time_marching_parameter, penalty_type):
return NDF_INPAINT_CPU(inputData, maskData, regularisation_parameter,
diff --git a/Wrappers/Python/demos/demo_cpu_regularisers.py b/Wrappers/Python/demos/demo_cpu_regularisers.py
index 986e3e9..51e7fb5 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, SB_TV, FGP_dTV, TNV, NDF
+from ccpi.filters.regularisers import ROF_TV, FGP_TV, SB_TV, FGP_dTV, TNV, NDF, DIFF4th
from qualitymetrics import rmse
###############################################################################
def printParametersToString(pars):
@@ -221,9 +221,9 @@ imgplot = plt.imshow(u0,cmap="gray")
# set parameters
pars = {'algorithm' : NDF, \
'input' : u0,\
- 'regularisation_parameter':0.06, \
- 'edge_parameter':0.04,\
- 'number_of_iterations' :1000 ,\
+ 'regularisation_parameter':0.025, \
+ 'edge_parameter':0.015,\
+ 'number_of_iterations' :500 ,\
'time_marching_parameter':0.025,\
'penalty_type':1
}
@@ -255,11 +255,56 @@ plt.title('{}'.format('CPU results'))
print ("%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%")
-print ("_____________FGP-dTV (2D)__________________")
+print ("___Anisotropic Diffusion 4th Order (2D)____")
print ("%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%")
## plot
fig = plt.figure(5)
+plt.suptitle('Performance of DIFF4th 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' : DIFF4th, \
+ 'input' : u0,\
+ 'regularisation_parameter':3.5, \
+ 'edge_parameter':0.02,\
+ 'number_of_iterations' :500 ,\
+ 'time_marching_parameter':0.005
+ }
+
+print ("#############DIFF4th CPU################")
+start_time = timeit.default_timer()
+diff4_cpu = DIFF4th(pars['input'],
+ pars['regularisation_parameter'],
+ pars['edge_parameter'],
+ pars['number_of_iterations'],
+ pars['time_marching_parameter'],'cpu')
+
+rms = rmse(Im, diff4_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(diff4_cpu, cmap="gray")
+plt.title('{}'.format('CPU results'))
+
+
+print ("%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%")
+print ("_____________FGP-dTV (2D)__________________")
+print ("%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%")
+
+## plot
+fig = plt.figure(6)
plt.suptitle('Performance of FGP-dTV regulariser using the CPU')
a=fig.add_subplot(1,2,1)
a.set_title('Noisy Image')
@@ -311,7 +356,7 @@ print ("__________Total nuclear Variation__________")
print ("%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%")
## plot
-fig = plt.figure(6)
+fig = plt.figure(7)
plt.suptitle('Performance of TNV regulariser using the CPU')
a=fig.add_subplot(1,2,1)
a.set_title('Noisy Image')
@@ -355,257 +400,3 @@ a.text(0.15, 0.25, txtstr, transform=a.transAxes, fontsize=14,
verticalalignment='top', bbox=props)
imgplot = plt.imshow(tnv_cpu[3,:,:], cmap="gray")
plt.title('{}'.format('CPU results'))
-
-
-# Uncomment to test 3D regularisation performance
-#%%
-"""
-slices = 20
-perc = 0.05
-
-noisyVol = np.zeros((slices,N,M),dtype='float32')
-noisyRef = np.zeros((slices,N,M),dtype='float32')
-idealVol = np.zeros((slices,N,M),dtype='float32')
-
-for i in range (slices):
- noisyVol[i,:,:] = Im + np.random.normal(loc = 0 , scale = perc * Im , size = np.shape(Im))
- noisyRef[i,:,:] = Im + np.random.normal(loc = 0 , scale = 0.01 * Im , size = np.shape(Im))
- idealVol[i,:,:] = Im
-
-
-print ("%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%")
-print ("_______________ROF-TV (3D)_________________")
-print ("%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%")
-
-## plot
-fig = plt.figure(7)
-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')
-imgplot = plt.imshow(noisyVol[10,:,:],cmap="gray")
-
-# set parameters
-pars = {'algorithm': ROF_TV, \
- 'input' : noisyVol,\
- 'regularisation_parameter':0.04,\
- 'number_of_iterations': 500,\
- 'time_marching_parameter': 0.0025
- }
-print ("#############ROF TV CPU####################")
-start_time = timeit.default_timer()
-rof_cpu3D = ROF_TV(pars['input'],
- pars['regularisation_parameter'],
- pars['number_of_iterations'],
- pars['time_marching_parameter'],'cpu')
-rms = rmse(idealVol, rof_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(rof_cpu3D[10,:,:], cmap="gray")
-plt.title('{}'.format('Recovered volume on the CPU using ROF-TV'))
-
-
-print ("%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%")
-print ("_______________FGP-TV (3D)__________________")
-print ("%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%")
-
-## plot
-fig = plt.figure(8)
-plt.suptitle('Performance of FGP-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' : FGP_TV, \
- 'input' : noisyVol,\
- 'regularisation_parameter':0.04, \
- 'number_of_iterations' :300 ,\
- 'tolerance_constant':0.00001,\
- 'methodTV': 0 ,\
- 'nonneg': 0 ,\
- 'printingOut': 0
- }
-
-print ("#############FGP TV CPU####################")
-start_time = timeit.default_timer()
-fgp_cpu3D = FGP_TV(pars['input'],
- pars['regularisation_parameter'],
- pars['number_of_iterations'],
- pars['tolerance_constant'],
- pars['methodTV'],
- pars['nonneg'],
- pars['printingOut'],'cpu')
-
-
-rms = rmse(idealVol, fgp_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(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(9)
-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 ("________________NDF (3D)___________________")
-print ("%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%")
-
-## plot
-fig = plt.figure(10)
-plt.suptitle('Performance of NDF regulariser using the CPU')
-a=fig.add_subplot(1,2,1)
-a.set_title('Noisy volume')
-imgplot = plt.imshow(noisyVol[10,:,:],cmap="gray")
-
-# set parameters
-pars = {'algorithm' : NDF, \
- 'input' : noisyVol,\
- 'regularisation_parameter':0.06, \
- 'edge_parameter':0.04,\
- 'number_of_iterations' :1000 ,\
- 'time_marching_parameter':0.025,\
- 'penalty_type': 1
- }
-
-print ("#############NDF CPU################")
-start_time = timeit.default_timer()
-ndf_cpu3D = NDF(pars['input'],
- pars['regularisation_parameter'],
- pars['edge_parameter'],
- pars['number_of_iterations'],
- pars['time_marching_parameter'],
- pars['penalty_type'])
-
-rms = rmse(idealVol, ndf_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(ndf_cpu3D[10,:,:], cmap="gray")
-plt.title('{}'.format('Recovered volume on the CPU using NDF iterations'))
-
-print ("%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%")
-print ("_______________FGP-dTV (3D)__________________")
-print ("%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%")
-
-## plot
-fig = plt.figure(11)
-plt.suptitle('Performance of FGP-dTV 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' : FGP_dTV,\
- 'input' : noisyVol,\
- 'refdata' : noisyRef,\
- 'regularisation_parameter':0.04, \
- 'number_of_iterations' :300 ,\
- 'tolerance_constant':0.00001,\
- 'eta_const':0.2,\
- 'methodTV': 0 ,\
- 'nonneg': 0 ,\
- 'printingOut': 0
- }
-
-print ("#############FGP dTV CPU####################")
-start_time = timeit.default_timer()
-fgp_dTV_cpu3D = FGP_dTV(pars['input'],
- pars['refdata'],
- pars['regularisation_parameter'],
- pars['number_of_iterations'],
- pars['tolerance_constant'],
- pars['eta_const'],
- pars['methodTV'],
- pars['nonneg'],
- pars['printingOut'],'cpu')
-
-
-rms = rmse(idealVol, fgp_dTV_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(fgp_dTV_cpu3D[10,:,:], cmap="gray")
-plt.title('{}'.format('Recovered volume on the CPU using FGP-dTV'))
-"""
-#%%
diff --git a/Wrappers/Python/demos/demo_cpu_regularisers3D.py b/Wrappers/Python/demos/demo_cpu_regularisers3D.py
new file mode 100644
index 0000000..0f47ea9
--- /dev/null
+++ b/Wrappers/Python/demos/demo_cpu_regularisers3D.py
@@ -0,0 +1,366 @@
+#!/usr/bin/env python3
+# -*- coding: utf-8 -*-
+"""
+Created on Thu Feb 22 11:39:43 2018
+
+Demonstration of 3D CPU regularisers
+
+@authors: Daniil Kazantsev, Edoardo Pasca
+"""
+
+import matplotlib.pyplot as plt
+import numpy as np
+import os
+import timeit
+from ccpi.filters.regularisers import ROF_TV, FGP_TV, SB_TV, FGP_dTV, TNV, NDF, DIFF4th
+from qualitymetrics import rmse
+###############################################################################
+def printParametersToString(pars):
+ txt = r''
+ for key, value in pars.items():
+ if key== 'algorithm' :
+ txt += "{0} = {1}".format(key, value.__name__)
+ elif key == 'input':
+ txt += "{0} = {1}".format(key, np.shape(value))
+ elif key == 'refdata':
+ txt += "{0} = {1}".format(key, np.shape(value))
+ else:
+ txt += "{0} = {1}".format(key, value)
+ txt += '\n'
+ return txt
+###############################################################################
+#%%
+filename = os.path.join(".." , ".." , ".." , "data" ,"lena_gray_512.tif")
+
+# read image
+Im = plt.imread(filename)
+Im = np.asarray(Im, dtype='float32')
+
+Im = Im/255
+perc = 0.05
+u0 = Im + np.random.normal(loc = 0 ,
+ scale = perc * Im ,
+ size = np.shape(Im))
+u_ref = Im + np.random.normal(loc = 0 ,
+ scale = 0.01 * Im ,
+ size = np.shape(Im))
+(N,M) = np.shape(u0)
+# map the u0 u0->u0>0
+# f = np.frompyfunc(lambda x: 0 if x < 0 else x, 1,1)
+u0 = u0.astype('float32')
+u_ref = u_ref.astype('float32')
+
+# change dims to check that modules work with non-squared images
+"""
+M = M-100
+u_ref2 = np.zeros([N,M],dtype='float32')
+u_ref2[:,0:M] = u_ref[:,0:M]
+u_ref = u_ref2
+del u_ref2
+
+u02 = np.zeros([N,M],dtype='float32')
+u02[:,0:M] = u0[:,0:M]
+u0 = u02
+del u02
+
+Im2 = np.zeros([N,M],dtype='float32')
+Im2[:,0:M] = Im[:,0:M]
+Im = Im2
+del Im2
+"""
+
+# Uncomment to test 3D regularisation performance
+#%%
+slices = 20
+
+noisyVol = np.zeros((slices,N,M),dtype='float32')
+noisyRef = np.zeros((slices,N,M),dtype='float32')
+idealVol = np.zeros((slices,N,M),dtype='float32')
+
+for i in range (slices):
+ noisyVol[i,:,:] = Im + np.random.normal(loc = 0 , scale = perc * Im , size = np.shape(Im))
+ noisyRef[i,:,:] = Im + np.random.normal(loc = 0 , scale = 0.01 * Im , size = np.shape(Im))
+ idealVol[i,:,:] = Im
+
+
+print ("%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%")
+print ("_______________ROF-TV (3D)_________________")
+print ("%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%")
+
+## plot
+fig = plt.figure(1)
+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')
+imgplot = plt.imshow(noisyVol[10,:,:],cmap="gray")
+
+# set parameters
+pars = {'algorithm': ROF_TV, \
+ 'input' : noisyVol,\
+ 'regularisation_parameter':0.04,\
+ 'number_of_iterations': 500,\
+ 'time_marching_parameter': 0.0025
+ }
+print ("#############ROF TV CPU####################")
+start_time = timeit.default_timer()
+rof_cpu3D = ROF_TV(pars['input'],
+ pars['regularisation_parameter'],
+ pars['number_of_iterations'],
+ pars['time_marching_parameter'],'cpu')
+rms = rmse(idealVol, rof_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(rof_cpu3D[10,:,:], cmap="gray")
+plt.title('{}'.format('Recovered volume on the CPU using ROF-TV'))
+
+
+print ("%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%")
+print ("_______________FGP-TV (3D)__________________")
+print ("%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%")
+
+## plot
+fig = plt.figure(2)
+plt.suptitle('Performance of FGP-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' : FGP_TV, \
+ 'input' : noisyVol,\
+ 'regularisation_parameter':0.04, \
+ 'number_of_iterations' :300 ,\
+ 'tolerance_constant':0.00001,\
+ 'methodTV': 0 ,\
+ 'nonneg': 0 ,\
+ 'printingOut': 0
+ }
+
+print ("#############FGP TV CPU####################")
+start_time = timeit.default_timer()
+fgp_cpu3D = FGP_TV(pars['input'],
+ pars['regularisation_parameter'],
+ pars['number_of_iterations'],
+ pars['tolerance_constant'],
+ pars['methodTV'],
+ pars['nonneg'],
+ pars['printingOut'],'cpu')
+
+
+rms = rmse(idealVol, fgp_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(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(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(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 ("________________NDF (3D)___________________")
+print ("%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%")
+
+## plot
+fig = plt.figure(4)
+plt.suptitle('Performance of NDF regulariser using the CPU')
+a=fig.add_subplot(1,2,1)
+a.set_title('Noisy volume')
+imgplot = plt.imshow(noisyVol[10,:,:],cmap="gray")
+
+# set parameters
+pars = {'algorithm' : NDF, \
+ 'input' : noisyVol,\
+ 'regularisation_parameter':0.025, \
+ 'edge_parameter':0.015,\
+ 'number_of_iterations' :500 ,\
+ 'time_marching_parameter':0.025,\
+ 'penalty_type': 1
+ }
+
+print ("#############NDF CPU################")
+start_time = timeit.default_timer()
+ndf_cpu3D = NDF(pars['input'],
+ pars['regularisation_parameter'],
+ pars['edge_parameter'],
+ pars['number_of_iterations'],
+ pars['time_marching_parameter'],
+ pars['penalty_type'])
+
+rms = rmse(idealVol, ndf_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(ndf_cpu3D[10,:,:], cmap="gray")
+plt.title('{}'.format('Recovered volume on the CPU using NDF iterations'))
+
+
+print ("%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%")
+print ("___Anisotropic Diffusion 4th Order (2D)____")
+print ("%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%")
+
+## plot
+fig = plt.figure(5)
+plt.suptitle('Performance of Diff4th regulariser using the CPU')
+a=fig.add_subplot(1,2,1)
+a.set_title('Noisy volume')
+imgplot = plt.imshow(noisyVol[10,:,:],cmap="gray")
+
+# set parameters
+pars = {'algorithm' : DIFF4th, \
+ 'input' : noisyVol,\
+ 'regularisation_parameter':3.5, \
+ 'edge_parameter':0.02,\
+ 'number_of_iterations' :300 ,\
+ 'time_marching_parameter':0.005
+ }
+
+print ("#############DIFF4th CPU################")
+start_time = timeit.default_timer()
+diff4th_cpu3D = DIFF4th(pars['input'],
+ pars['regularisation_parameter'],
+ pars['edge_parameter'],
+ pars['number_of_iterations'],
+ pars['time_marching_parameter'])
+
+rms = rmse(idealVol, diff4th_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(diff4th_cpu3D[10,:,:], cmap="gray")
+plt.title('{}'.format('Recovered volume on the CPU using DIFF4th iterations'))
+
+
+print ("%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%")
+print ("_______________FGP-dTV (3D)__________________")
+print ("%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%")
+
+## plot
+fig = plt.figure(6)
+plt.suptitle('Performance of FGP-dTV 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' : FGP_dTV,\
+ 'input' : noisyVol,\
+ 'refdata' : noisyRef,\
+ 'regularisation_parameter':0.04, \
+ 'number_of_iterations' :300 ,\
+ 'tolerance_constant':0.00001,\
+ 'eta_const':0.2,\
+ 'methodTV': 0 ,\
+ 'nonneg': 0 ,\
+ 'printingOut': 0
+ }
+
+print ("#############FGP dTV CPU####################")
+start_time = timeit.default_timer()
+fgp_dTV_cpu3D = FGP_dTV(pars['input'],
+ pars['refdata'],
+ pars['regularisation_parameter'],
+ pars['number_of_iterations'],
+ pars['tolerance_constant'],
+ pars['eta_const'],
+ pars['methodTV'],
+ pars['nonneg'],
+ pars['printingOut'],'cpu')
+
+
+rms = rmse(idealVol, fgp_dTV_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(fgp_dTV_cpu3D[10,:,:], cmap="gray")
+plt.title('{}'.format('Recovered volume on the CPU using FGP-dTV'))
+#%%
diff --git a/Wrappers/Python/demos/demo_cpu_vs_gpu_regularisers.py b/Wrappers/Python/demos/demo_cpu_vs_gpu_regularisers.py
index 05db23e..2910c65 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, SB_TV, FGP_dTV, NDF
+from ccpi.filters.regularisers import ROF_TV, FGP_TV, SB_TV, FGP_dTV, NDF, DIFF4th
from qualitymetrics import rmse
###############################################################################
def printParametersToString(pars):
@@ -207,7 +207,7 @@ plt.title('{}'.format('GPU results'))
print ("--------Compare the results--------")
tolerance = 1e-05
-diff_im = np.zeros(np.shape(rof_cpu))
+diff_im = np.zeros(np.shape(fgp_cpu))
diff_im = abs(fgp_cpu - fgp_gpu)
diff_im[diff_im > tolerance] = 1
a=fig.add_subplot(1,4,4)
@@ -293,7 +293,7 @@ plt.title('{}'.format('GPU results'))
print ("--------Compare the results--------")
tolerance = 1e-05
-diff_im = np.zeros(np.shape(rof_cpu))
+diff_im = np.zeros(np.shape(sb_cpu))
diff_im = abs(sb_cpu - sb_gpu)
diff_im[diff_im > tolerance] = 1
a=fig.add_subplot(1,4,4)
@@ -379,7 +379,7 @@ plt.title('{}'.format('GPU results'))
print ("--------Compare the results--------")
tolerance = 1e-05
-diff_im = np.zeros(np.shape(rof_cpu))
+diff_im = np.zeros(np.shape(ndf_cpu))
diff_im = abs(ndf_cpu - ndf_gpu)
diff_im[diff_im > tolerance] = 1
a=fig.add_subplot(1,4,4)
@@ -391,13 +391,93 @@ else:
print ("Arrays match")
+print ("%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%")
+print ("___Anisotropic Diffusion 4th Order (2D)____")
+print ("%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%")
+
+## plot
+fig = plt.figure(5)
+plt.suptitle('Comparison of Diff4th 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' : DIFF4th, \
+ 'input' : u0,\
+ 'regularisation_parameter':3.5, \
+ 'edge_parameter':0.02,\
+ 'number_of_iterations' :500 ,\
+ 'time_marching_parameter':0.005
+ }
+
+print ("#############Diff4th CPU####################")
+start_time = timeit.default_timer()
+diff4th_cpu = Diff4th(pars['input'],
+ pars['regularisation_parameter'],
+ pars['edge_parameter'],
+ pars['number_of_iterations'],
+ pars['time_marching_parameter'],'cpu')
+
+rms = rmse(Im, diff4th_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(diff4th_cpu, cmap="gray")
+plt.title('{}'.format('CPU results'))
+
+print ("##############Diff4th GPU##################")
+start_time = timeit.default_timer()
+diff4th_gpu = Diff4th(pars['input'],
+ pars['regularisation_parameter'],
+ pars['edge_parameter'],
+ pars['number_of_iterations'],
+ pars['time_marching_parameter'], 'gpu')
+
+rms = rmse(Im, diff4th_gpu)
+pars['rmse'] = rms
+pars['algorithm'] = Diff4th
+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(diff4th_gpu, cmap="gray")
+plt.title('{}'.format('GPU results'))
+
+print ("--------Compare the results--------")
+tolerance = 1e-05
+diff_im = np.zeros(np.shape(diff4th_cpu))
+diff_im = abs(diff4th_cpu - diff4th_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(5)
+fig = plt.figure(6)
plt.suptitle('Comparison of FGP-dTV regulariser using CPU and GPU implementations')
a=fig.add_subplot(1,4,1)
a.set_title('Noisy Image')
@@ -475,7 +555,7 @@ plt.title('{}'.format('GPU results'))
print ("--------Compare the results--------")
tolerance = 1e-05
-diff_im = np.zeros(np.shape(rof_cpu))
+diff_im = np.zeros(np.shape(fgp_dtv_cpu))
diff_im = abs(fgp_dtv_cpu - fgp_dtv_gpu)
diff_im[diff_im > tolerance] = 1
a=fig.add_subplot(1,4,4)
diff --git a/Wrappers/Python/demos/demo_gpu_regularisers.py b/Wrappers/Python/demos/demo_gpu_regularisers.py
index f3ed50c..8432696 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, SB_TV, FGP_dTV, NDF
+from ccpi.filters.regularisers import ROF_TV, FGP_TV, SB_TV, FGP_dTV, NDF, DIFF4th
from qualitymetrics import rmse
###############################################################################
def printParametersToString(pars):
@@ -219,9 +219,9 @@ imgplot = plt.imshow(u0,cmap="gray")
# set parameters
pars = {'algorithm' : NDF, \
'input' : u0,\
- 'regularisation_parameter':0.06, \
- 'edge_parameter':0.04,\
- 'number_of_iterations' :1000 ,\
+ 'regularisation_parameter':0.025, \
+ 'edge_parameter':0.015,\
+ 'number_of_iterations' :500 ,\
'time_marching_parameter':0.025,\
'penalty_type': 1
}
@@ -253,246 +253,34 @@ plt.title('{}'.format('GPU results'))
print ("%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%")
-print ("____________FGP-dTV bench___________________")
+print ("___Anisotropic Diffusion 4th Order (2D)____")
print ("%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%")
## plot
fig = plt.figure(5)
-plt.suptitle('Performance of the FGP-dTV regulariser using the GPU')
+plt.suptitle('Performance of DIFF4th 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' : FGP_dTV, \
+pars = {'algorithm' : DIFF4th, \
'input' : u0,\
- 'refdata' : u_ref,\
- 'regularisation_parameter':0.04, \
- 'number_of_iterations' :2000 ,\
- 'tolerance_constant':1e-06,\
- 'eta_const':0.2,\
- 'methodTV': 0 ,\
- 'nonneg': 0 ,\
- 'printingOut': 0
- }
-
-print ("##############FGP dTV GPU##################")
-start_time = timeit.default_timer()
-fgp_dtv_gpu = FGP_dTV(pars['input'],
- pars['refdata'],
- pars['regularisation_parameter'],
- pars['number_of_iterations'],
- pars['tolerance_constant'],
- pars['eta_const'],
- pars['methodTV'],
- pars['nonneg'],
- pars['printingOut'],'gpu')
-
-rms = rmse(Im, fgp_dtv_gpu)
-pars['rmse'] = rms
-pars['algorithm'] = FGP_dTV
-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(fgp_dtv_gpu, cmap="gray")
-plt.title('{}'.format('GPU results'))
-
-
-# Uncomment to test 3D regularisation performance
-#%%
-"""
-N = 512
-slices = 20
-
-filename = os.path.join(".." , ".." , ".." , "data" ,"lena_gray_512.tif")
-Im = plt.imread(filename)
-Im = np.asarray(Im, dtype='float32')
-
-Im = Im/255
-perc = 0.05
-
-noisyVol = np.zeros((slices,N,N),dtype='float32')
-noisyRef = np.zeros((slices,N,N),dtype='float32')
-idealVol = np.zeros((slices,N,N),dtype='float32')
-
-for i in range (slices):
- noisyVol[i,:,:] = Im + np.random.normal(loc = 0 , scale = perc * Im , size = np.shape(Im))
- noisyRef[i,:,:] = Im + np.random.normal(loc = 0 , scale = 0.01 * Im , size = np.shape(Im))
- idealVol[i,:,:] = Im
-
-print ("%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%")
-print ("_______________ROF-TV (3D)_________________")
-print ("%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%")
-
-## plot
-fig = plt.figure(6)
-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')
-imgplot = plt.imshow(noisyVol[10,:,:],cmap="gray")
-
-# set parameters
-pars = {'algorithm': ROF_TV, \
- 'input' : noisyVol,\
- 'regularisation_parameter':0.04,\
- 'number_of_iterations': 500,\
- 'time_marching_parameter': 0.0025
+ 'regularisation_parameter':3.5, \
+ 'edge_parameter':0.02,\
+ 'number_of_iterations' :500 ,\
+ 'time_marching_parameter':0.005
}
-print ("#############ROF TV GPU####################")
+
+print ("#############DIFF4th CPU################")
start_time = timeit.default_timer()
-rof_gpu3D = ROF_TV(pars['input'],
- pars['regularisation_parameter'],
- pars['number_of_iterations'],
- pars['time_marching_parameter'],'gpu')
-rms = rmse(idealVol, rof_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(rof_gpu3D[10,:,:], cmap="gray")
-plt.title('{}'.format('Recovered volume on the GPU using ROF-TV'))
-
-print ("%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%")
-print ("_______________FGP-TV (3D)__________________")
-print ("%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%")
-
-## plot
-fig = plt.figure(7)
-plt.suptitle('Performance of FGP-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' : FGP_TV, \
- 'input' : noisyVol,\
- 'regularisation_parameter':0.04, \
- 'number_of_iterations' :300 ,\
- 'tolerance_constant':0.00001,\
- 'methodTV': 0 ,\
- 'nonneg': 0 ,\
- 'printingOut': 0
- }
-
-print ("#############FGP TV GPU####################")
-start_time = timeit.default_timer()
-fgp_gpu3D = FGP_TV(pars['input'],
- pars['regularisation_parameter'],
- pars['number_of_iterations'],
- pars['tolerance_constant'],
- pars['methodTV'],
- pars['nonneg'],
- pars['printingOut'],'gpu')
-
-rms = rmse(idealVol, fgp_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(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(8)
-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 ("_______________NDF-TV (3D)_________________")
-print ("%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%")
-
-## plot
-fig = plt.figure(9)
-plt.suptitle('Performance of NDF 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' : NDF, \
- 'input' : noisyVol,\
- 'regularisation_parameter':0.06, \
- 'edge_parameter':0.04,\
- 'number_of_iterations' :1000 ,\
- 'time_marching_parameter':0.025,\
- 'penalty_type': 1
- }
-
-print ("#############NDF GPU####################")
-start_time = timeit.default_timer()
-ndf_gpu3D = NDF(pars['input'],
+diff4_gpu = DIFF4th(pars['input'],
pars['regularisation_parameter'],
pars['edge_parameter'],
pars['number_of_iterations'],
- pars['time_marching_parameter'],
- pars['penalty_type'],'gpu')
-
-rms = rmse(idealVol, ndf_gpu3D)
+ pars['time_marching_parameter'],'gpu')
+
+rms = rmse(Im, diff4_gpu)
pars['rmse'] = rms
txtstr = printParametersToString(pars)
@@ -505,49 +293,48 @@ 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(ndf_gpu3D[10,:,:], cmap="gray")
-plt.title('{}'.format('Recovered volume on the GPU using NDF'))
-
+imgplot = plt.imshow(diff4_gpu, cmap="gray")
+plt.title('{}'.format('GPU results'))
print ("%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%")
-print ("_______________FGP-dTV (3D)________________")
+print ("____________FGP-dTV bench___________________")
print ("%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%")
## plot
-fig = plt.figure(10)
-plt.suptitle('Performance of FGP-dTV regulariser using the GPU')
+fig = plt.figure(6)
+plt.suptitle('Performance of the FGP-dTV regulariser using the GPU')
a=fig.add_subplot(1,2,1)
a.set_title('Noisy Image')
-imgplot = plt.imshow(noisyVol[10,:,:],cmap="gray")
+imgplot = plt.imshow(u0,cmap="gray")
# set parameters
pars = {'algorithm' : FGP_dTV, \
- 'input' : noisyVol,\
- 'refdata' : noisyRef,\
+ 'input' : u0,\
+ 'refdata' : u_ref,\
'regularisation_parameter':0.04, \
- 'number_of_iterations' :300 ,\
- 'tolerance_constant':0.00001,\
+ 'number_of_iterations' :2000 ,\
+ 'tolerance_constant':1e-06,\
'eta_const':0.2,\
'methodTV': 0 ,\
'nonneg': 0 ,\
'printingOut': 0
}
-print ("#############FGP TV GPU####################")
+print ("##############FGP dTV GPU##################")
start_time = timeit.default_timer()
-fgp_dTV_gpu3D = FGP_dTV(pars['input'],
+fgp_dtv_gpu = FGP_dTV(pars['input'],
pars['refdata'],
pars['regularisation_parameter'],
pars['number_of_iterations'],
pars['tolerance_constant'],
- pars['eta_const'],
+ pars['eta_const'],
pars['methodTV'],
pars['nonneg'],
pars['printingOut'],'gpu')
-
-rms = rmse(idealVol, fgp_dTV_gpu3D)
+
+rms = rmse(Im, fgp_dtv_gpu)
pars['rmse'] = rms
-
+pars['algorithm'] = FGP_dTV
txtstr = printParametersToString(pars)
txtstr += "%s = %.3fs" % ('elapsed time',timeit.default_timer() - start_time)
print (txtstr)
@@ -558,7 +345,5 @@ 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(fgp_dTV_gpu3D[10,:,:], cmap="gray")
-plt.title('{}'.format('Recovered volume on the GPU using FGP-dTV'))
-"""
-#%%
+imgplot = plt.imshow(fgp_dtv_gpu, cmap="gray")
+plt.title('{}'.format('GPU results'))
diff --git a/Wrappers/Python/demos/demo_gpu_regularisers3D.py b/Wrappers/Python/demos/demo_gpu_regularisers3D.py
new file mode 100644
index 0000000..022df95
--- /dev/null
+++ b/Wrappers/Python/demos/demo_gpu_regularisers3D.py
@@ -0,0 +1,367 @@
+#!/usr/bin/env python3
+# -*- coding: utf-8 -*-
+"""
+Created on Thu Feb 22 11:39:43 2018
+
+Demonstration of GPU regularisers
+
+@authors: Daniil Kazantsev, Edoardo Pasca
+"""
+
+import matplotlib.pyplot as plt
+import numpy as np
+import os
+import timeit
+from ccpi.filters.regularisers import ROF_TV, FGP_TV, SB_TV, FGP_dTV, NDF, DIFF4th
+from qualitymetrics import rmse
+###############################################################################
+def printParametersToString(pars):
+ txt = r''
+ for key, value in pars.items():
+ if key== 'algorithm' :
+ txt += "{0} = {1}".format(key, value.__name__)
+ elif key == 'input':
+ txt += "{0} = {1}".format(key, np.shape(value))
+ elif key == 'refdata':
+ txt += "{0} = {1}".format(key, np.shape(value))
+ else:
+ txt += "{0} = {1}".format(key, value)
+ txt += '\n'
+ return txt
+###############################################################################
+#%%
+filename = os.path.join(".." , ".." , ".." , "data" ,"lena_gray_512.tif")
+
+# read image
+Im = plt.imread(filename)
+Im = np.asarray(Im, dtype='float32')
+
+Im = Im/255
+perc = 0.05
+u0 = Im + np.random.normal(loc = 0 ,
+ scale = perc * Im ,
+ size = np.shape(Im))
+u_ref = Im + np.random.normal(loc = 0 ,
+ scale = 0.01 * Im ,
+ size = np.shape(Im))
+(N,M) = np.shape(u0)
+# map the u0 u0->u0>0
+# f = np.frompyfunc(lambda x: 0 if x < 0 else x, 1,1)
+u0 = u0.astype('float32')
+u_ref = u_ref.astype('float32')
+"""
+M = M-100
+u_ref2 = np.zeros([N,M],dtype='float32')
+u_ref2[:,0:M] = u_ref[:,0:M]
+u_ref = u_ref2
+del u_ref2
+
+u02 = np.zeros([N,M],dtype='float32')
+u02[:,0:M] = u0[:,0:M]
+u0 = u02
+del u02
+
+Im2 = np.zeros([N,M],dtype='float32')
+Im2[:,0:M] = Im[:,0:M]
+Im = Im2
+del Im2
+"""
+
+#%%
+slices = 20
+
+filename = os.path.join(".." , ".." , ".." , "data" ,"lena_gray_512.tif")
+Im = plt.imread(filename)
+Im = np.asarray(Im, dtype='float32')
+
+Im = Im/255
+perc = 0.05
+
+noisyVol = np.zeros((slices,N,N),dtype='float32')
+noisyRef = np.zeros((slices,N,N),dtype='float32')
+idealVol = np.zeros((slices,N,N),dtype='float32')
+
+for i in range (slices):
+ noisyVol[i,:,:] = Im + np.random.normal(loc = 0 , scale = perc * Im , size = np.shape(Im))
+ noisyRef[i,:,:] = Im + np.random.normal(loc = 0 , scale = 0.01 * Im , size = np.shape(Im))
+ idealVol[i,:,:] = Im
+
+print ("%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%")
+print ("_______________ROF-TV (3D)_________________")
+print ("%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%")
+
+## plot
+fig = plt.figure(1)
+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')
+imgplot = plt.imshow(noisyVol[10,:,:],cmap="gray")
+
+# set parameters
+pars = {'algorithm': ROF_TV, \
+ 'input' : noisyVol,\
+ 'regularisation_parameter':0.04,\
+ 'number_of_iterations': 500,\
+ 'time_marching_parameter': 0.0025
+ }
+print ("#############ROF TV GPU####################")
+start_time = timeit.default_timer()
+rof_gpu3D = ROF_TV(pars['input'],
+ pars['regularisation_parameter'],
+ pars['number_of_iterations'],
+ pars['time_marching_parameter'],'gpu')
+rms = rmse(idealVol, rof_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(rof_gpu3D[10,:,:], cmap="gray")
+plt.title('{}'.format('Recovered volume on the GPU using ROF-TV'))
+
+print ("%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%")
+print ("_______________FGP-TV (3D)__________________")
+print ("%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%")
+
+## plot
+fig = plt.figure(2)
+plt.suptitle('Performance of FGP-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' : FGP_TV, \
+ 'input' : noisyVol,\
+ 'regularisation_parameter':0.04, \
+ 'number_of_iterations' :300 ,\
+ 'tolerance_constant':0.00001,\
+ 'methodTV': 0 ,\
+ 'nonneg': 0 ,\
+ 'printingOut': 0
+ }
+
+print ("#############FGP TV GPU####################")
+start_time = timeit.default_timer()
+fgp_gpu3D = FGP_TV(pars['input'],
+ pars['regularisation_parameter'],
+ pars['number_of_iterations'],
+ pars['tolerance_constant'],
+ pars['methodTV'],
+ pars['nonneg'],
+ pars['printingOut'],'gpu')
+
+rms = rmse(idealVol, fgp_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(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(3)
+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 ("_______________NDF-TV (3D)_________________")
+print ("%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%")
+
+## plot
+fig = plt.figure(4)
+plt.suptitle('Performance of NDF 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' : NDF, \
+ 'input' : noisyVol,\
+ 'regularisation_parameter':0.025, \
+ 'edge_parameter':0.015,\
+ 'number_of_iterations' :500 ,\
+ 'time_marching_parameter':0.025,\
+ 'penalty_type': 1
+ }
+
+print ("#############NDF GPU####################")
+start_time = timeit.default_timer()
+ndf_gpu3D = NDF(pars['input'],
+ pars['regularisation_parameter'],
+ pars['edge_parameter'],
+ pars['number_of_iterations'],
+ pars['time_marching_parameter'],
+ pars['penalty_type'],'gpu')
+
+rms = rmse(idealVol, ndf_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(ndf_gpu3D[10,:,:], cmap="gray")
+plt.title('{}'.format('Recovered volume on the GPU using NDF'))
+
+
+print ("%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%")
+print ("___Anisotropic Diffusion 4th Order (3D)____")
+print ("%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%")
+
+## plot
+fig = plt.figure(5)
+plt.suptitle('Performance of DIFF4th 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' : DIFF4th, \
+ 'input' : noisyVol,\
+ 'regularisation_parameter':3.5, \
+ 'edge_parameter':0.02,\
+ 'number_of_iterations' :300 ,\
+ 'time_marching_parameter':0.005
+ }
+
+print ("#############DIFF4th CPU################")
+start_time = timeit.default_timer()
+diff4_gpu3D = DIFF4th(pars['input'],
+ pars['regularisation_parameter'],
+ pars['edge_parameter'],
+ pars['number_of_iterations'],
+ pars['time_marching_parameter'],'gpu')
+
+rms = rmse(idealVol, diff4_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(diff4_gpu3D[10,:,:], cmap="gray")
+plt.title('{}'.format('GPU results'))
+
+
+print ("%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%")
+print ("_______________FGP-dTV (3D)________________")
+print ("%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%")
+
+## plot
+fig = plt.figure(6)
+plt.suptitle('Performance of FGP-dTV 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' : FGP_dTV, \
+ 'input' : noisyVol,\
+ 'refdata' : noisyRef,\
+ 'regularisation_parameter':0.04, \
+ 'number_of_iterations' :300 ,\
+ 'tolerance_constant':0.00001,\
+ 'eta_const':0.2,\
+ 'methodTV': 0 ,\
+ 'nonneg': 0 ,\
+ 'printingOut': 0
+ }
+
+print ("#############FGP TV GPU####################")
+start_time = timeit.default_timer()
+fgp_dTV_gpu3D = FGP_dTV(pars['input'],
+ pars['refdata'],
+ pars['regularisation_parameter'],
+ pars['number_of_iterations'],
+ pars['tolerance_constant'],
+ pars['eta_const'],
+ pars['methodTV'],
+ pars['nonneg'],
+ pars['printingOut'],'gpu')
+
+rms = rmse(idealVol, fgp_dTV_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(fgp_dTV_gpu3D[10,:,:], cmap="gray")
+plt.title('{}'.format('Recovered volume on the GPU using FGP-dTV'))
+#%%
diff --git a/Wrappers/Python/setup-regularisers.py.in b/Wrappers/Python/setup-regularisers.py.in
index f55c6fe..76dfecf 100644
--- a/Wrappers/Python/setup-regularisers.py.in
+++ b/Wrappers/Python/setup-regularisers.py.in
@@ -40,6 +40,7 @@ extra_include_dirs += [os.path.join(".." , ".." , "Core"),
os.path.join(".." , ".." , "Core", "regularisers_GPU" , "TV_SB" ) ,
os.path.join(".." , ".." , "Core", "regularisers_GPU" , "NDF" ) ,
os.path.join(".." , ".." , "Core", "regularisers_GPU" , "dTV_FGP" ) ,
+ os.path.join(".." , ".." , "Core", "regularisers_GPU" , "DIFF4th" ) ,
"."]
if platform.system() == 'Windows':
diff --git a/Wrappers/Python/src/cpu_regularisers.pyx b/Wrappers/Python/src/cpu_regularisers.pyx
index c934f1d..7dc3396 100644
--- a/Wrappers/Python/src/cpu_regularisers.pyx
+++ b/Wrappers/Python/src/cpu_regularisers.pyx
@@ -22,6 +22,7 @@ cdef extern float TV_ROF_CPU_main(float *Input, float *Output, float lambdaPar,
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 Diffusion_CPU_main(float *Input, float *Output, float lambdaPar, float sigmaPar, int iterationsNumb, float tau, int penaltytype, int dimX, int dimY, int dimZ);
+cdef extern float Diffus4th_CPU_main(float *Input, float *Output, float lambdaPar, float sigmaPar, int iterationsNumb, float tau, int dimX, int dimY, int dimZ);
cdef extern float TNV_CPU_main(float *Input, float *u, float lambdaPar, int maxIter, float tol, 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);
@@ -322,6 +323,48 @@ def NDF_3D(np.ndarray[np.float32_t, ndim=3, mode="c"] inputData,
return outputData
+#****************************************************************#
+#*************Anisotropic Fourth-Order diffusion*****************#
+#****************************************************************#
+def Diff4th_CPU(inputData, regularisation_parameter, edge_parameter, iterationsNumb, time_marching_parameter):
+ if inputData.ndim == 2:
+ return Diff4th_2D(inputData, regularisation_parameter, edge_parameter, iterationsNumb, time_marching_parameter, penalty_type)
+ elif inputData.ndim == 3:
+ return Diff4th_3D(inputData, regularisation_parameter, edge_parameter, iterationsNumb, time_marching_parameter, penalty_type)
+
+def Diff4th_2D(np.ndarray[np.float32_t, ndim=2, mode="c"] inputData,
+ float regularisation_parameter,
+ float edge_parameter,
+ int iterationsNumb,
+ float time_marching_parameter):
+ 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 Anisotropic Fourth-Order diffusion for 2D data
+ Diffus4th_CPU_main(&inputData[0,0], &outputData[0,0], regularisation_parameter, edge_parameter, iterationsNumb, time_marching_parameter, dims[1], dims[0], 1)
+ return outputData
+
+def Diff4th_3D(np.ndarray[np.float32_t, ndim=3, mode="c"] inputData,
+ float regularisation_parameter,
+ float edge_parameter,
+ int iterationsNumb,
+ float time_marching_parameter):
+ 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 Anisotropic Fourth-Order diffusion for 3D data
+ Diffus4th_CPU_main(&inputData[0,0,0], &outputData[0,0,0], regularisation_parameter, edge_parameter, iterationsNumb, time_marching_parameter, dims[2], dims[1], dims[0])
+
+ return outputData
#*********************Inpainting WITH****************************#
#***************Nonlinear (Isotropic) Diffusion******************#
#****************************************************************#
diff --git a/Wrappers/Python/src/gpu_regularisers.pyx b/Wrappers/Python/src/gpu_regularisers.pyx
index 7eab5d5..b67e62b 100644
--- a/Wrappers/Python/src/gpu_regularisers.pyx
+++ b/Wrappers/Python/src/gpu_regularisers.pyx
@@ -23,6 +23,7 @@ cdef extern void TV_FGP_GPU_main(float *Input, float *Output, float lambdaPar, i
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 NonlDiff_GPU_main(float *Input, float *Output, float lambdaPar, float sigmaPar, int iterationsNumb, float tau, int penaltytype, 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);
+cdef extern void Diffus4th_GPU_main(float *Input, float *Output, float lambdaPar, float sigmaPar, int iterationsNumb, float tau, int N, int M, int Z);
# Total-variation Rudin-Osher-Fatemi (ROF)
def TV_ROF_GPU(inputData,
@@ -135,7 +136,26 @@ def NDF_GPU(inputData,
edge_parameter,
iterations,
time_marching_parameter,
- penalty_type)
+ penalty_type)
+# Anisotropic Fourth-Order diffusion
+def Diff4th_GPU(inputData,
+ regularisation_parameter,
+ edge_parameter,
+ iterations,
+ time_marching_parameter):
+ if inputData.ndim == 2:
+ return Diff4th_2D(inputData,
+ regularisation_parameter,
+ edge_parameter,
+ iterations,
+ time_marching_parameter)
+ elif inputData.ndim == 3:
+ return Diff4th_3D(inputData,
+ regularisation_parameter,
+ edge_parameter,
+ iterations,
+ time_marching_parameter)
+
#****************************************************************#
#********************** Total-variation ROF *********************#
#****************************************************************#
@@ -403,3 +423,41 @@ def NDF_GPU_3D(np.ndarray[np.float32_t, ndim=3, mode="c"] inputData,
NonlDiff_GPU_main(&inputData[0,0,0], &outputData[0,0,0], regularisation_parameter, edge_parameter, iterationsNumb, time_marching_parameter, penalty_type, dims[2], dims[1], dims[0])
return outputData
+#****************************************************************#
+#************Anisotropic Fourth-Order diffusion******************#
+#****************************************************************#
+def Diff4th_2D(np.ndarray[np.float32_t, ndim=2, mode="c"] inputData,
+ float regularisation_parameter,
+ float edge_parameter,
+ int iterationsNumb,
+ float time_marching_parameter):
+ 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 Anisotropic Fourth-Order diffusion for 2D data
+ # Running CUDA code here
+ Diffus4th_GPU_main(&inputData[0,0], &outputData[0,0], regularisation_parameter, edge_parameter, iterationsNumb, time_marching_parameter, dims[1], dims[0], 1)
+ return outputData
+
+def Diff4th_3D(np.ndarray[np.float32_t, ndim=3, mode="c"] inputData,
+ float regularisation_parameter,
+ float edge_parameter,
+ int iterationsNumb,
+ float time_marching_parameter):
+ 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 Anisotropic Fourth-Order diffusion for 3D data
+ # Running CUDA code here
+ Diffus4th_GPU_main(&inputData[0,0,0], &outputData[0,0,0], regularisation_parameter, edge_parameter, iterationsNumb, time_marching_parameter, dims[2], dims[1], dims[0])
+
+ return outputData