Merge pull request #33 from dkazanc/cmaking

CMake interface, major restructure of the package. Updated demos.

CMakeLists.txt

@@ -0,0 +1,37 @@
+#   Copyright 2017 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.
+
+cmake_minimum_required (VERSION 3.0)
+
+project(TomoPhantom)
+#https://stackoverflow.com/questions/13298504/using-cmake-with-setup-py
+
+# The version number.
+set (CIL_VERSION_MAJOR 0)
+set (CIL_VERSION_MINOR 11)
+set (CIL_VERSION_PATCH 0)
+
+set (CIL_VERSION '${CIL_VERSION_MAJOR}.${CIL_VERSION_MINOR}.${CIL_VERSION_PATCH}' CACHE INTERNAL "Core Imaging Library version" FORCE)
+
+# set the Python variables for the Conda environment
+#include(${CMAKE_SOURCE_DIR}/CMake/FindAnacondaEnvironment.cmake)
+
+set(CMAKE_BUILD_TYPE "Release")
+
+option (BUILD_MATLAB_WRAPPER "Build Matlab Wrappers" OFF)
+option (BUILD_PYTHON_WRAPPER "Build Python Wrappers" ON)
+option (CONDA_BUILD "Conda Build" OFF)
+
+add_subdirectory(Core)
+add_subdirectory(Wrappers)

Core/CCPiDefines.h

@@ -0,0 +1,47 @@
+/**
+# -*- coding: utf-8 -*-
+#   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 2018 CCPi
+
+#   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.
+
+#   Code is derived from code developed by Prof. Brian Bay
+*/
+
+#ifndef CCPIDEFINES_H
+#define CCPIDEFINES_H
+
+#if defined(_WIN32) || defined(__WIN32__)
+  #if defined(cilDVC_EXPORTS) ||  defined(CCPiNexusWidget_EXPORTS) || defined(CCPi_EXPORTS)//  add by CMake 
+    #define  CCPI_EXPORT __declspec(dllexport)
+    #define EXPIMP_TEMPLATE
+  #else
+    #define  CCPI_EXPORT __declspec(dllimport)
+    #define EXPIMP_TEMPLATE extern
+  #endif  CCPi_EXPORTS 
+#elif defined(linux) || defined(__linux) || defined(__APPLE__)
+ #define CCPI_EXPORT
+#endif
+
+//	Revised:
+
+#define DAY_REV 25
+#define MONTH_REV "Nov"
+#define YEAR_REV 2017
+
+#define VERSION 1.30
+
+#endif

Core/CMakeLists.txt

@@ -0,0 +1,118 @@
+#   Copyright 2018 Edoardo Pasca
+#cmake_minimum_required (VERSION 3.0)
+
+project(RGL_core)
+#https://stackoverflow.com/questions/13298504/using-cmake-with-setup-py
+
+# The version number.
+
+#set (CIL_VERSION $ENV{CIL_VERSION} CACHE INTERNAL "Core Imaging Library version" FORCE)
+
+# conda orchestrated build
+message("CIL_VERSION ${CIL_VERSION}")
+#include (GenerateExportHeader)
+
+
+find_package(OpenMP REQUIRED)
+if (OPENMP_FOUND)
+    set (CMAKE_C_FLAGS "${CMAKE_C_FLAGS} ${OpenMP_C_FLAGS}")
+    set (CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} ${OpenMP_CXX_FLAGS}")
+    set (CMAKE_EXE_LINKER_FLAGS "${CMAKE_EXE_LINKER_FLAGS} ${OpenMP_EXE_LINKER_FLAGS} ${OpenMP_CXX_FLAGS}")
+   set (CMAKE_SHARED_LINKER_FLAGS "${CMAKE_EXE_LINKER_FLAGS} ${OpenMP_SHARED_LINKER_FLAGS} ${OpenMP_CXX_FLAGS}")
+   set (CMAKE_STATIC_LINKER_FLAGS "${CMAKE_EXE_LINKER_FLAGS} ${OpenMP_STATIC_LINKER_FLAGS} ${OpenMP_CXX_FLAGS}")
+
+endif()
+
+## Build the regularisers package as a library
+message("Creating Regularisers as a shared library")
+
+message("CMAKE_CXX_FLAGS ${CMAKE_CXX_FLAGS}")
+message("CMAKE_C_FLAGS ${CMAKE_C_FLAGS}")
+message("CMAKE_EXE_LINKER_FLAGS ${CMAKE_EXE_LINKER_FLAGS}")
+message("CMAKE_SHARED_LINKER_FLAGS ${CMAKE_SHARED_LINKER_FLAGS}")
+message("CMAKE_STATIC_LINKER_FLAGS ${CMAKE_STATIC_LINKER_FLAGS}")
+
+set(CMAKE_BUILD_TYPE "Release")
+
+if(WIN32)
+  set (FLAGS "/DWIN32 /EHsc /DCCPi_EXPORTS")
+  set (CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} ${FLAGS}")
+  set (CMAKE_C_FLAGS "${CMAKE_CXX_FLAGS} ${FLAGS}")
+  set (CMAKE_EXE_LINKER_FLAGS "${CMAKE_EXE_LINKER_FLAGS} /NODEFAULTLIB:MSVCRT.lib")
+
+  set (EXTRA_LIBRARIES)
+
+  message("library lib: ${LIBRARY_LIB}")
+
+elseif(UNIX)
+   set (FLAGS "-O2 -funsigned-char -Wall  -Wl,--no-undefined  -DCCPiReconstructionIterative_EXPORTS ")  
+   set (CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} ${FLAGS}")
+   set (CMAKE_C_FLAGS "${CMAKE_CXX_FLAGS} ${FLAGS}")
+   if (OPENMP_FOUND)
+     set (EXTRA_LIBRARIES 
+		"gomp"
+		"m"
+		)
+    else()
+       set (EXTRA_LIBRARIES 
+		"m"
+		)
+    endif()
+endif()
+message("CMAKE_CXX_FLAGS ${CMAKE_CXX_FLAGS}")
+
+## Build the regularisers package as a library
+message("Adding regularisers as a shared library")
+
+#set(CMAKE_C_COMPILER /apps/pgi/linux86-64/17.4/bin/pgcc)
+#set(CMAKE_C_FLAGS "-acc -Minfo -ta=tesla:cc20 -openmp")
+#set(CMAKE_C_FLAGS "-acc -Minfo -ta=multicore -openmp -fPIC")
+add_library(ctomophantom "SHARED"
+	    ${CMAKE_CURRENT_SOURCE_DIR}/TomoP2DModel_core.c
+	    ${CMAKE_CURRENT_SOURCE_DIR}/TomoP2DModelSino_core.c
+	    ${CMAKE_CURRENT_SOURCE_DIR}/TomoP3DModel_core.c
+	    ${CMAKE_CURRENT_SOURCE_DIR}/utils.c
+	    ${CMAKE_CURRENT_SOURCE_DIR}/TomoP2DSinoNum_core.c
+		)
+#add_library(ctomophantom_static "STATIC"
+#	    ${CMAKE_CURRENT_SOURCE_DIR}/TomoP2DModel_core.c
+#	    ${CMAKE_CURRENT_SOURCE_DIR}/TomoP2DModelSino_core.c
+#	    ${CMAKE_CURRENT_SOURCE_DIR}/TomoP3DModel_core.c
+#	    ${CMAKE_CURRENT_SOURCE_DIR}/utils.c
+#	    ${CMAKE_CURRENT_SOURCE_DIR}/TomoP2DSinoNum_core.c
+#	    )
+target_link_libraries(ctomophantom ${EXTRA_LIBRARIES} )
+include_directories(ctomophantom PUBLIC 
+                      ${LIBRARY_INC}/include 
+					  ${CMAKE_CURRENT_SOURCE_DIR}
+		              )
+
+## Install
+
+set(INSTALL_BIN_DIR ${CMAKE_INSTALL_PREFIX}/bin)
+set(INSTALL_LIB_DIR ${CMAKE_INSTALL_PREFIX}/lib)
+set(INSTALL_INCLUDE_DIR ${CMAKE_INSTALL_PREFIX}/include)
+
+if (UNIX)
+message ("I'd install into ${CMAKE_INSTALL_PREFIX}/lib")
+install(TARGETS ctomophantom
+	LIBRARY DESTINATION lib
+	CONFIGURATIONS ${CMAKE_BUILD_TYPE} 
+	)
+elseif(WIN32)
+message ("I'd install into ${CMAKE_INSTALL_PREFIX} lib bin")
+  install(TARGETS ctomophantom 
+	RUNTIME DESTINATION bin
+	ARCHIVE DESTINATION lib
+	CONFIGURATIONS ${CMAKE_BUILD_TYPE} 
+	)
+endif()
+
+
+#install(TARGETS ctomophantom
+#	LIBRARY  DESTINATION "${INSTALL_LIB_DIR}" COMPONENT lib
+#	PUBLIC_HEADER DESTINATION "${INSTALL_INCLUDE_DIR}" COMPONENT dev
+#	RUNTIME  DESTINATION "${INSTALL_BIN_DIR}" COMPONENT bin
+#	ARCHIVE  DESTINATION "${INSTALL_LIB_DIR}" COMPONENT lib
+#   CONFIGURATIONS ${CMAKE_BUILD_TYPE}
+#	)

functions/TomoP2DModelSino_core.c → Core/TomoP2DModelSino_core.c

@@ -12,12 +12,7 @@
  * limitations under the License.
  */
 
-#include <math.h>
-#include <stdlib.h>
-#include <memory.h>
-#include <stdio.h>
-#include "omp.h"
-#include "utils.h"
+#include "TomoP2DModelSino_core.h"
 
 #define M_PI 3.14159265358979323846
 #define EPS 0.000000001
@@ -38,9 +33,9 @@
  */
 
 /* function to build a single sinogram - object */
-float TomoP2DObjectSino_core(float *A, long N, long P, float *Th, long AngTot, int CenTypeIn, char *Object, float C0, float x0, float y0, float a, float b, float phi_rot, long tt)
+float TomoP2DObjectSino_core(float *A, int N, int P, float *Th, int AngTot, int CenTypeIn, char *Object, float C0, float x0, float y0, float a, float b, float phi_rot, int tt)
 {
-    long i, j;
+    int i, j;
     float *Tomorange_X_Ar=NULL, Tomorange_Xmin, Tomorange_Xmax, Sinorange_Pmax, Sinorange_Pmin, H_p, H_x, C1, a22, b22, phi_rot_radian;
     float *Sinorange_P_Ar=NULL, *AnglesRad=NULL;
     float AA5, sin_2, cos_2, delta1, delta_sq, first_dr, AA2, AA3, AA6, under_exp, x00, y00;
@@ -373,7 +368,7 @@ float TomoP2DModelSino_core(float *A, int ModelSelected, int N, int P, float *Th
                                     //mexErrMsgTxt("b (object size) must be positive in [0,2] range");
                                     break; }
                                 //printf("\nObject : %s \nC0 : %f \nx0 : %f \ny0 : %f \na : %f \nb : %f \n", tmpstr2, C0, x0, y0,  a, b);
-                               TomoP2DObjectSino_core(A, (long)N, (long)P, Th, (long)AngTot, CenTypeIn, tmpstr2, C0, x0, y0, b, a, -psi_gr1, 0l);
+                               TomoP2DObjectSino_core(A, N, P, Th, AngTot, CenTypeIn, tmpstr2, C0, x0, y0, b, a, -psi_gr1, 0);
                             }
                         }
                         else {
@@ -433,14 +428,14 @@ float TomoP2DModelSino_core(float *A, int ModelSelected, int N, int P, float *Th
                                 float b_step = (b1 - b)/(steps-1);
                                 float phi_rot_step = (psi_gr1_1 - psi_gr1)/(steps-1);
 
-                                long tt;
+                                int tt;
                                 float x_t, y_t, a_t, b_t, C_t, phi_t, d_step;
                                 /* initialize */
                                 x_t = x0; y_t = y0; a_t = a; b_t = b; C_t = C0; phi_t = psi_gr1; d_step = d_dist;
                                 /*loop over time frames*/
                                 for(tt=0; tt < steps; tt++) {
 
-                                    TomoP2DObjectSino_core(A, (long)N, (long)P, Th, (long)AngTot, CenTypeIn, tmpstr2, C_t, -y_t, x_t, b_t, a_t, -phi_t, tt);                                                         
+                                    TomoP2DObjectSino_core(A, N, P, Th, AngTot, CenTypeIn, tmpstr2, C_t, -y_t, x_t, b_t, a_t, -phi_t, tt);                                                         
 
                                     /* calculating new coordinates of an object */
                                     if (distance != 0.0f) {

functions/TomoP2DModelSino_core.h → Core/TomoP2DModelSino_core.h

@@ -17,6 +17,7 @@ limitations under the License.
 #include <memory.h>
 #include <stdio.h>
 #include "omp.h"
+#include "CCPiDefines.h"
 
-float TomoP2DModelSino_core(float *A, int ModelSelected, int N, int P, float *Th, int AngTot, int CenTypeIn, char* ModelParametersFilename);
-float TomoP2DObjectSino_core(float *A, long N, long P, float *Th, long AngTot, int CenTypeIn, char* Obj, float C0, float x0, float y0, float a, float b, float phi_rot, long tt);
+CCPI_EXPORT float TomoP2DModelSino_core(float *A, int ModelSelected, int N, int P, float *Th, int AngTot, int CenTypeIn, char* ModelParametersFilename);
+CCPI_EXPORT float TomoP2DObjectSino_core(float *A, int N, int P, float *Th, int AngTot, int CenTypeIn, char* Obj, float C0, float x0, float y0, float a, float b, float phi_rot, int tt);

functions/TomoP2DModel_core.c → Core/TomoP2DModel_core.c

@@ -12,12 +12,7 @@
  * limitations under the License.
  */
 
-#include <math.h>
-#include <stdlib.h>
-#include <memory.h>
-#include <stdio.h>
-#include "omp.h"
-#include "utils.h"
+#include "TomoP2DModel_core.h"
 
 #define M_PI 3.14159265358979323846
 #define MAXCHAR 1000
@@ -40,18 +35,18 @@
  */
 
 /* function to build a single object */
-float TomoP2DObject_core(float *A, long N, char *Object,
+float TomoP2DObject_core(float *A, int N, char *Object,
         float C0, /* intensity */
         float x0, /* x0 position */
         float y0, /* y0 position */
         float a , /* a - size object */
         float b , /* b - size object */
         float phi_rot, /* phi - rotation angle */
-        long tt /* time frame loop */)
+        int tt /* time frame loop */)
 {
     printf ("Base C0 %.2e x0 %.2e y0 %.2e a %.2e b %.2e phi %.2e\n" , C0, x0, y0, a, b, phi_rot);                            
 
-    long i, j;
+    int i, j;
     float *Tomorange_X_Ar=NULL, Tomorange_Xmin, Tomorange_Xmax, H_x, C1, a2, b2, phi_rot_radian, sin_phi, cos_phi;
     float *Xdel = NULL, *Ydel = NULL, T;
     Tomorange_X_Ar = malloc(N*sizeof(float));
@@ -236,7 +231,7 @@ float TomoP2DModel_core(float *A, int ModelSelected, int N, char *ModelParameter
                                     //mexErrMsgTxt("Cannot find 'Object' string in parameters file");
                                     break; }   
                                 printf ("C0 %.2e x0 %.2e y0 %.2e a %.2e b %.2e phi %.2e\n" , C0, x0, y0, a, b, psi_gr1);                            
-                                TomoP2DObject_core(A, (long)N, tmpstr2, C0, y0, x0, a, b, psi_gr1, 0l); /* python */
+                                TomoP2DObject_core(A, N, tmpstr2, C0, y0, x0, a, b, psi_gr1, 0); /* python */
                             }
                         }
                         else {
@@ -292,14 +287,14 @@ float TomoP2DModel_core(float *A, int ModelSelected, int N, char *ModelParameter
                                 float b_step = (b1 - b)/(steps-1);
                                 float phi_rot_step = (psi_gr1_1 - psi_gr1)/(steps-1);
 
-                                long tt;
+                                int tt;
                                 float x_t, y_t, a_t, b_t, C_t, phi_t, d_step;
                                 /* initialize */
                                 x_t = x0; y_t = y0; a_t = a; b_t = b; C_t = C0; phi_t = psi_gr1; d_step = d_dist;
                                 /*loop over time frames*/
                                 for(tt=0; tt < steps; tt++) {
 
-                                     TomoP2DObject_core(A, (long)N, tmpstr2, C_t, x_t, -y_t, a_t, b_t, phi_t, tt); /* python */
+                                     TomoP2DObject_core(A, N, tmpstr2, C_t, x_t, -y_t, a_t, b_t, phi_t, tt); /* python */
 
                                     /* calculating new coordinates of an object */
                                     if (distance != 0.0f) {

functions/TomoP2DModel_core.h → Core/TomoP2DModel_core.h

@@ -12,12 +12,14 @@ See the License for the specific language governing permissions and
 limitations under the License.
 */
 
-#include <matrix.h>
+//#include <matrix.h>
 #include <math.h>
 #include <stdlib.h>
 #include <memory.h>
 #include <stdio.h>
 #include "omp.h"
+#include "CCPiDefines.h"
 
-float TomoP2DModel_core(float *A, int ModelSelected, int N, char *ModelParametersFilename);
-float TomoP2DObject_core(float *A, long N,  char *Object, float C0, float x0, float y0, float a, float b, float phi_rot, long tt);
+
+CCPI_EXPORT float TomoP2DModel_core(float *A, int ModelSelected, int N, char *ModelParametersFilename);
+CCPI_EXPORT float TomoP2DObject_core(float *A, int N,  char *Object, float C0, float x0, float y0, float a, float b, float phi_rot, int tt);

functions/TomoP2DSinoNum_core.h → Core/TomoP2DSinoNum_core.h

@@ -17,7 +17,8 @@ limitations under the License.
 #include <memory.h>
 #include <stdio.h>
 #include "omp.h"
+#include "CCPiDefines.h"
 
-float TomoP2DSinoNum_core(float *Sinogram, float *Phantom, int dimX, int DetSize, float *Theta, int ThetaLength, int sys);
-float BilinearInterpolation(float *Phantom_pad, float *B, int DetSize, float ct, float st);
-float padding(float *Phantom, float *Phantom_pad, int DetSize, int PhantSize, int padXY, int sys);
+CCPI_EXPORT float TomoP2DSinoNum_core(float *Sinogram, float *Phantom, int dimX, int DetSize, float *Theta, int ThetaLength, int sys);
+CCPI_EXPORT float BilinearInterpolation(float *Phantom_pad, float *B, int DetSize, float ct, float st);
+CCPI_EXPORT float padding(float *Phantom, float *Phantom_pad, int DetSize, int PhantSize, int padXY, int sys);