Merge pull request #122 from vais-ral/matlab_fix

fix to cmakelists file
TomographicImaging · May 15, 2019 · 5fb5be3 · 5fb5be3
2 parents e871292 + 1207b14
commit 5fb5be3
Show file tree

Hide file tree

Showing 5 changed files with 5 additions and 48 deletions.
diff --git a/build/run.sh b/build/run.sh
@@ -6,13 +6,13 @@ rm -r ../build_proj
 mkdir ../build_proj
 cd ../build_proj/
 #make clean
-export CIL_VERSION=19.04
+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
+# 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
 # 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=/home/algol/SOFT/MATLAB9/ -DBUILD_MATLAB_WRAPPER=ON -DBUILD_CUDA=ON -DCMAKE_BUILD_TYPE=Release -DCMAKE_INSTALL_PREFIX=./install

diff --git 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
@@ -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

diff --git 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
@@ -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)
 
 ##############################################################################