From 4cb85a3009859ebb6369f27d6e3d775469da50a2 Mon Sep 17 00:00:00 2001
From: dkazanc <dkazanc@hotmail.com>
Date: Wed, 15 May 2019 11:06:31 +0100
Subject: fix to cmakelists file
---
build/run.sh | 16 ++++++++--------
demos/Matlab_demos/demoMatlab_denoise.m | 2 +-
src/Core/CMakeLists.txt | 1 -
3 files changed, 9 insertions(+), 10 deletions(-)
diff --git a/build/run.sh b/build/run.sh
index 2404d1b..bcea14b 100755
--- a/build/run.sh
+++ b/build/run.sh
@@ -10,20 +10,20 @@ export CIL_VERSION=19.04
# install Python modules without CUDA
#cmake ../ -DBUILD_PYTHON_WRAPPER=ON -DBUILD_MATLAB_WRAPPER=OFF -DBUILD_CUDA=OFF -DCMAKE_BUILD_TYPE=Release -DCMAKE_INSTALL_PREFIX=./install
# install Python modules with CUDA
-cmake ../ -DBUILD_PYTHON_WRAPPER=ON -DBUILD_MATLAB_WRAPPER=OFF -DBUILD_CUDA=ON -DCMAKE_BUILD_TYPE=Release -DCMAKE_INSTALL_PREFIX=./install
+# cmake ../ -DBUILD_PYTHON_WRAPPER=ON -DBUILD_MATLAB_WRAPPER=OFF -DBUILD_CUDA=ON -DCMAKE_BUILD_TYPE=Release -DCMAKE_INSTALL_PREFIX=./install
# install Matlab modules without CUDA
-#cmake ../ -DBUILD_PYTHON_WRAPPER=OFF -DMatlab_ROOT_DIR=/dls_sw/apps/matlab/r2014a/ -DBUILD_MATLAB_WRAPPER=ON -DBUILD_CUDA=OFF -DCMAKE_BUILD_TYPE=Release -DCMAKE_INSTALL_PREFIX=./install
+# cmake ../ -DBUILD_PYTHON_WRAPPER=OFF -DMatlab_ROOT_DIR=/dls_sw/apps/matlab/r2014a/ -DBUILD_MATLAB_WRAPPER=ON -DBUILD_CUDA=OFF -DCMAKE_BUILD_TYPE=Release -DCMAKE_INSTALL_PREFIX=./install
# install Matlab modules with CUDA
-# cmake ../ -DBUILD_PYTHON_WRAPPER=OFF -DMatlab_ROOT_DIR=/dls_sw/apps/matlab/r2014a/ -DBUILD_MATLAB_WRAPPER=ON -DBUILD_CUDA=ON -DCMAKE_BUILD_TYPE=Release -DCMAKE_INSTALL_PREFIX=./install
+cmake ../ -DBUILD_PYTHON_WRAPPER=OFF -DMatlab_ROOT_DIR=/dls_sw/apps/matlab/r2014a/ -DBUILD_MATLAB_WRAPPER=ON -DBUILD_CUDA=ON -DCMAKE_BUILD_TYPE=Release -DCMAKE_INSTALL_PREFIX=./install
# cmake ../ -DBUILD_PYTHON_WRAPPER=OFF -DMatlab_ROOT_DIR=/home/algol/SOFT/MATLAB9/ -DBUILD_MATLAB_WRAPPER=ON -DBUILD_CUDA=ON -DCMAKE_BUILD_TYPE=Release -DCMAKE_INSTALL_PREFIX=./install
make install
############### Python(linux)###############
-cp install/lib/libcilreg.so install/python/ccpi/filters
-cd install/python
-export LD_LIBRARY_PATH=${LD_LIBRARY_PATH}:../lib
-spyder
+#cp install/lib/libcilreg.so install/python/ccpi/filters
+#cd install/python
+#export LD_LIBRARY_PATH=${LD_LIBRARY_PATH}:../lib
+#spyder
############### Matlab(linux)###############
# export LD_PRELOAD=/home/algol/anaconda3/lib/libstdc++.so.6 # if there is libstdc error in matlab
# PATH="/path/to/mex/:$PATH" LD_LIBRARY_PATH="/path/to/library:$LD_LIBRARY_PATH" matlab
-# PATH="/home/kjy41806/Documents/SOFT/CCPi-Regularisation-Toolkit/build_proj/install/matlab/:$PATH" LD_LIBRARY_PATH="/home/kjy41806/Documents/SOFT/CCPi-Regularisation-Toolkit/build_proj/install/lib:$LD_LIBRARY_PATH" matlab
+PATH="/home/kjy41806/Documents/SOFT/CCPi-Regularisation-Toolkit/build_proj/install/matlab/:$PATH" LD_LIBRARY_PATH="/home/kjy41806/Documents/SOFT/CCPi-Regularisation-Toolkit/build_proj/install/lib:$LD_LIBRARY_PATH" matlab
#PATH="/home/algol/Documents/DEV/CCPi-Regularisation-Toolkit/build_proj/install/matlab/:$PATH" LD_LIBRARY_PATH="/home/algol/Documents/DEV/CCPi-Regularisation-Toolkit/build_proj/install/lib:$LD_LIBRARY_PATH" /home/algol/SOFT/MATLAB9/bin/matlab
diff --git a/demos/Matlab_demos/demoMatlab_denoise.m b/demos/Matlab_demos/demoMatlab_denoise.m
index 5af927f..12d5570 100644
--- a/demos/Matlab_demos/demoMatlab_denoise.m
+++ b/demos/Matlab_demos/demoMatlab_denoise.m
@@ -2,9 +2,9 @@
clear; close all
fsep = '/';
-Path1 = sprintf(['..' fsep '..' fsep 'src' fsep 'Matlab' fsep 'mex_compile' fsep 'installed'], 1i);
Path2 = sprintf(['..' fsep 'data' fsep], 1i);
Path3 = sprintf(['..' fsep '..' fsep 'src' fsep 'Matlab' fsep 'supp'], 1i);
+Path1 = sprintf(['..' fsep '..' fsep 'src' fsep 'Matlab' fsep 'mex_compile' fsep 'installed'], 1i);
addpath(Path1);
addpath(Path2);
addpath(Path3);
diff --git a/src/Core/CMakeLists.txt b/src/Core/CMakeLists.txt
index 8aec749..eea0d63 100644
--- a/src/Core/CMakeLists.txt
+++ b/src/Core/CMakeLists.txt
@@ -68,7 +68,6 @@ add_library(cilreg SHARED
${CMAKE_CURRENT_SOURCE_DIR}/regularisers_CPU/SB_TV_core.c
${CMAKE_CURRENT_SOURCE_DIR}/regularisers_CPU/TGV_core.c
${CMAKE_CURRENT_SOURCE_DIR}/regularisers_CPU/Diffusion_core.c
- ${CMAKE_CURRENT_SOURCE_DIR}/regularisers_CPU/MASK_merge_core.c
${CMAKE_CURRENT_SOURCE_DIR}/regularisers_CPU/Diffus4th_order_core.c
${CMAKE_CURRENT_SOURCE_DIR}/regularisers_CPU/LLT_ROF_core.c
${CMAKE_CURRENT_SOURCE_DIR}/regularisers_CPU/ROF_TV_core.c
--
cgit v1.2.3
From baa8a9208e6d4d685c08cc50699864865292159a Mon Sep 17 00:00:00 2001
From: dkazanc <dkazanc@hotmail.com>
Date: Wed, 15 May 2019 11:20:29 +0100
Subject: modified run
---
build/run.sh | 18 +++++++++---------
1 file changed, 9 insertions(+), 9 deletions(-)
diff --git a/build/run.sh b/build/run.sh
index bcea14b..521272c 100755
--- a/build/run.sh
+++ b/build/run.sh
@@ -6,24 +6,24 @@ rm -r ../build_proj
mkdir ../build_proj
cd ../build_proj/
#make clean
-export CIL_VERSION=19.04
+export CIL_VERSION=19.05
# install Python modules without CUDA
-#cmake ../ -DBUILD_PYTHON_WRAPPER=ON -DBUILD_MATLAB_WRAPPER=OFF -DBUILD_CUDA=OFF -DCMAKE_BUILD_TYPE=Release -DCMAKE_INSTALL_PREFIX=./install
+# cmake ../ -DBUILD_PYTHON_WRAPPER=ON -DBUILD_MATLAB_WRAPPER=OFF -DBUILD_CUDA=OFF -DCMAKE_BUILD_TYPE=Release -DCMAKE_INSTALL_PREFIX=./install
# install Python modules with CUDA
-# cmake ../ -DBUILD_PYTHON_WRAPPER=ON -DBUILD_MATLAB_WRAPPER=OFF -DBUILD_CUDA=ON -DCMAKE_BUILD_TYPE=Release -DCMAKE_INSTALL_PREFIX=./install
+cmake ../ -DBUILD_PYTHON_WRAPPER=ON -DBUILD_MATLAB_WRAPPER=OFF -DBUILD_CUDA=ON -DCMAKE_BUILD_TYPE=Release -DCMAKE_INSTALL_PREFIX=./install
# install Matlab modules without CUDA
# cmake ../ -DBUILD_PYTHON_WRAPPER=OFF -DMatlab_ROOT_DIR=/dls_sw/apps/matlab/r2014a/ -DBUILD_MATLAB_WRAPPER=ON -DBUILD_CUDA=OFF -DCMAKE_BUILD_TYPE=Release -DCMAKE_INSTALL_PREFIX=./install
# install Matlab modules with CUDA
-cmake ../ -DBUILD_PYTHON_WRAPPER=OFF -DMatlab_ROOT_DIR=/dls_sw/apps/matlab/r2014a/ -DBUILD_MATLAB_WRAPPER=ON -DBUILD_CUDA=ON -DCMAKE_BUILD_TYPE=Release -DCMAKE_INSTALL_PREFIX=./install
+# cmake ../ -DBUILD_PYTHON_WRAPPER=OFF -DMatlab_ROOT_DIR=/dls_sw/apps/matlab/r2014a/ -DBUILD_MATLAB_WRAPPER=ON -DBUILD_CUDA=ON -DCMAKE_BUILD_TYPE=Release -DCMAKE_INSTALL_PREFIX=./install
# cmake ../ -DBUILD_PYTHON_WRAPPER=OFF -DMatlab_ROOT_DIR=/home/algol/SOFT/MATLAB9/ -DBUILD_MATLAB_WRAPPER=ON -DBUILD_CUDA=ON -DCMAKE_BUILD_TYPE=Release -DCMAKE_INSTALL_PREFIX=./install
make install
############### Python(linux)###############
-#cp install/lib/libcilreg.so install/python/ccpi/filters
-#cd install/python
-#export LD_LIBRARY_PATH=${LD_LIBRARY_PATH}:../lib
-#spyder
+cp install/lib/libcilreg.so install/python/ccpi/filters
+cd install/python
+export LD_LIBRARY_PATH=${LD_LIBRARY_PATH}:../lib
+spyder
############### Matlab(linux)###############
# export LD_PRELOAD=/home/algol/anaconda3/lib/libstdc++.so.6 # if there is libstdc error in matlab
# PATH="/path/to/mex/:$PATH" LD_LIBRARY_PATH="/path/to/library:$LD_LIBRARY_PATH" matlab
-PATH="/home/kjy41806/Documents/SOFT/CCPi-Regularisation-Toolkit/build_proj/install/matlab/:$PATH" LD_LIBRARY_PATH="/home/kjy41806/Documents/SOFT/CCPi-Regularisation-Toolkit/build_proj/install/lib:$LD_LIBRARY_PATH" matlab
+# PATH="/home/kjy41806/Documents/SOFT/CCPi-Regularisation-Toolkit/build_proj/install/matlab/:$PATH" LD_LIBRARY_PATH="/home/kjy41806/Documents/SOFT/CCPi-Regularisation-Toolkit/build_proj/install/lib:$LD_LIBRARY_PATH" matlab
#PATH="/home/algol/Documents/DEV/CCPi-Regularisation-Toolkit/build_proj/install/matlab/:$PATH" LD_LIBRARY_PATH="/home/algol/Documents/DEV/CCPi-Regularisation-Toolkit/build_proj/install/lib:$LD_LIBRARY_PATH" /home/algol/SOFT/MATLAB9/bin/matlab
--
cgit v1.2.3
From d8168df8b3235284c0917a9a123aeb36a9a3becc Mon Sep 17 00:00:00 2001
From: dkazanc <dkazanc@hotmail.com>
Date: Wed, 15 May 2019 11:26:25 +0100
Subject: mask segm bits removed from Cython
---
src/Python/ccpi/filters/regularisers.py | 13 +------------
src/Python/src/cpu_regularisers.pyx | 31 -------------------------------
2 files changed, 1 insertion(+), 43 deletions(-)
diff --git a/src/Python/ccpi/filters/regularisers.py b/src/Python/ccpi/filters/regularisers.py
index 2fee8b3..0b5b2ee 100644
--- a/src/Python/ccpi/filters/regularisers.py
+++ b/src/Python/ccpi/filters/regularisers.py
@@ -2,7 +2,7 @@
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, Diff4th_CPU, TGV_CPU, LLT_ROF_CPU, PATCHSEL_CPU, NLTV_CPU, MASK_CORR_CPU
+from ccpi.filters.cpu_regularisers import TV_ROF_CPU, TV_FGP_CPU, TV_SB_CPU, dTV_FGP_CPU, TNV_CPU, NDF_CPU, Diff4th_CPU, TGV_CPU, LLT_ROF_CPU, PATCHSEL_CPU, NLTV_CPU
try:
from ccpi.filters.gpu_regularisers import TV_ROF_GPU, TV_FGP_GPU, TV_SB_GPU, dTV_FGP_GPU, NDF_GPU, Diff4th_GPU, TGV_GPU, LLT_ROF_GPU, PATCHSEL_GPU
gpu_enabled = True
@@ -212,15 +212,4 @@ def NDF_INP(inputData, maskData, regularisation_parameter, edge_parameter, itera
def NVM_INP(inputData, maskData, SW_increment, iterations):
return NVM_INPAINT_CPU(inputData, maskData, SW_increment, iterations)
-
-def MASK_CORR(maskdata, select_classes, total_classesNum, CorrectionWindow, device='cpu'):
- if device == 'cpu':
- return MASK_CORR_CPU(maskdata, select_classes, total_classesNum, CorrectionWindow)
- elif device == 'gpu' and gpu_enabled:
- return MASK_CORR_CPU(maskdata, select_classes, total_classesNum, CorrectionWindow)
- else:
- if not gpu_enabled and device == 'gpu':
- raise ValueError ('GPU is not available')
- raise ValueError('Unknown device {0}. Expecting gpu or cpu'\
- .format(device))
diff --git a/src/Python/src/cpu_regularisers.pyx b/src/Python/src/cpu_regularisers.pyx
index 9855eca..904b4f5 100644
--- a/src/Python/src/cpu_regularisers.pyx
+++ b/src/Python/src/cpu_regularisers.pyx
@@ -24,7 +24,6 @@ cdef extern float SB_TV_CPU_main(float *Input, float *Output, float *infovector,
cdef extern float LLT_ROF_CPU_main(float *Input, float *Output, float *infovector, float lambdaROF, float lambdaLLT, int iterationsNumb, float tau, float epsil, int dimX, int dimY, int dimZ);
cdef extern float TGV_main(float *Input, float *Output, float *infovector, float lambdaPar, float alpha1, float alpha0, int iterationsNumb, float L2, float epsil, int dimX, int dimY, int dimZ);
cdef extern float Diffusion_CPU_main(float *Input, float *Output, float *infovector, float lambdaPar, float sigmaPar, int iterationsNumb, float tau, int penaltytype, float epsil, int dimX, int dimY, int dimZ);
-cdef extern float Mask_merge_main(unsigned char *MASK, unsigned char *MASK_upd, unsigned char *CORRECTEDRegions, unsigned char *SelClassesList, int SelClassesList_length, int classesNumb, int CorrectionWindow, int dimX, int dimY, int dimZ);
cdef extern float Diffus4th_CPU_main(float *Input, float *Output, float *infovector, float lambdaPar, float sigmaPar, int iterationsNumb, float tau, float epsil, int dimX, int dimY, int dimZ);
cdef extern float dTV_FGP_CPU_main(float *Input, float *InputRef, float *Output, float *infovector, float lambdaPar, int iterationsNumb, float epsil, float eta, int methodTV, int nonneg, 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);
@@ -707,36 +706,6 @@ def NVM_INP_2D(np.ndarray[np.float32_t, ndim=2, mode="c"] inputData,
return (outputData, maskData_upd)
-##############################################################################
-#****************************************************************#
-#********Mask (segmented image) correction module **************#
-#****************************************************************#
-def MASK_CORR_CPU(maskData, select_classes, total_classesNum, CorrectionWindow):
- if maskData.ndim == 2:
- return MASK_CORR_CPU_2D(maskData, select_classes, total_classesNum, CorrectionWindow)
- elif maskData.ndim == 3:
- return 0
-
-def MASK_CORR_CPU_2D(np.ndarray[np.uint8_t, ndim=2, mode="c"] maskData,
- np.ndarray[np.uint8_t, ndim=1, mode="c"] select_classes,
- int total_classesNum,
- int CorrectionWindow):
-
- cdef long dims[2]
- dims[0] = maskData.shape[0]
- dims[1] = maskData.shape[1]
-
- select_classes_length = select_classes.shape[0]
-
- cdef np.ndarray[np.uint8_t, ndim=2, mode="c"] mask_upd = \
- np.zeros([dims[0],dims[1]], dtype='uint8')
- cdef np.ndarray[np.uint8_t, ndim=2, mode="c"] corr_regions = \
- np.zeros([dims[0],dims[1]], dtype='uint8')
-
- # Run the function to process given MASK
- Mask_merge_main(&maskData[0,0], &mask_upd[0,0], &corr_regions[0,0], &select_classes[0], select_classes_length,
- total_classesNum, CorrectionWindow, dims[1], dims[0], 1)
- return (mask_upd,corr_regions)
##############################################################################
--
cgit v1.2.3
From 1207b14fa2fac7f8b83280d75884ad3a62e57e75 Mon Sep 17 00:00:00 2001
From: dkazanc <dkazanc@hotmail.com>
Date: Wed, 15 May 2019 12:04:29 +0100
Subject: rerun
---
build/run.sh | 2 +-
1 file changed, 1 insertion(+), 1 deletion(-)
diff --git a/build/run.sh b/build/run.sh
index 521272c..c243b12 100755
--- a/build/run.sh
+++ b/build/run.sh
@@ -6,7 +6,7 @@ rm -r ../build_proj
mkdir ../build_proj
cd ../build_proj/
#make clean
-export CIL_VERSION=19.05
+export CIL_VERSION=19.06
# install Python modules without CUDA
# cmake ../ -DBUILD_PYTHON_WRAPPER=ON -DBUILD_MATLAB_WRAPPER=OFF -DBUILD_CUDA=OFF -DCMAKE_BUILD_TYPE=Release -DCMAKE_INSTALL_PREFIX=./install
# install Python modules with CUDA
--
cgit v1.2.3