Merge branch 'master' into tutorial

Author: jessdtate

Superbuild/Superbuild.cmake

@@ -70,6 +70,11 @@ OPTION(BUILD_TESTING "Build with tests." ON)
 # Configure python
 OPTION(BUILD_WITH_PYTHON "Build with python support." ON)
 
+###########################################
+# Configure python
+OPTION(WITH_TETGEN "Build Tetgen." ON)
+MARK_AS_ADVANCED(WITH_TETGEN)
+
 ###########################################
 # Configure Windows executable to run with
 # or without the console
@@ -122,34 +127,34 @@ MARK_AS_ADVANCED(REGENERATE_MODULE_FACTORY_CODE)
 
 SET( SCIRun_DEPENDENCIES )
 
+MACRO(ADD_EXTERNAL cmake_file external)
+  INCLUDE( ${cmake_file} )
+  LIST(APPEND SCIRun_DEPENDENCIES ${external})
+ENDMACRO()
+
 SET(SUPERBUILD_DIR ${CMAKE_CURRENT_SOURCE_DIR} CACHE INTERNAL "" FORCE)
 SET(SCIRUN_SOURCE_DIR ${CMAKE_CURRENT_SOURCE_DIR}/../src CACHE INTERNAL "" FORCE)
 SET(SCIRUN_BINARY_DIR ${CMAKE_BINARY_DIR}/SCIRun CACHE INTERNAL "" FORCE)
 
 IF(BUILD_TESTING)
-  INCLUDE( ${SUPERBUILD_DIR}/TestDataConfig.cmake )
-  LIST(APPEND SCIRun_DEPENDENCIES SCIRunTestData_external)
+  ADD_EXTERNAL( ${SUPERBUILD_DIR}/TestDataConfig.cmake SCIRunTestData_external )
 ENDIF()
 
-INCLUDE( ${SUPERBUILD_DIR}/ZlibExternal.cmake )
-LIST(APPEND SCIRun_DEPENDENCIES Zlib_external)
-
-INCLUDE( ${SUPERBUILD_DIR}/SQLiteExternal.cmake )
-LIST(APPEND SCIRun_DEPENDENCIES SQLite_external)
-
-INCLUDE( ${SUPERBUILD_DIR}/LibPNGExternal.cmake )
-LIST(APPEND SCIRun_DEPENDENCIES LibPNG_external)
+ADD_EXTERNAL( ${SUPERBUILD_DIR}/ZlibExternal.cmake Zlib_external )
+ADD_EXTERNAL( ${SUPERBUILD_DIR}/SQLiteExternal.cmake SQLite_external )
+ADD_EXTERNAL( ${SUPERBUILD_DIR}/LibPNGExternal.cmake LibPNG_external )
+ADD_EXTERNAL( ${SUPERBUILD_DIR}/TeemExternal.cmake Teem_external )
 
 IF(BUILD_WITH_PYTHON)
-  INCLUDE( ${SUPERBUILD_DIR}/PythonExternal.cmake )
-  LIST(APPEND SCIRun_DEPENDENCIES Python_external)
+  ADD_EXTERNAL( ${SUPERBUILD_DIR}/PythonExternal.cmake Python_external )
 ENDIF()
 
-INCLUDE( ${SUPERBUILD_DIR}/BoostExternal.cmake )
-LIST(APPEND SCIRun_DEPENDENCIES Boost_external)
+IF(WITH_TETGEN)
+  MESSAGE(STATUS "Configuring Tetgen library under GPL. The SCIRun InterfaceWithTetGen module can be disabled by setting the CMake build variable WITH_TETGEN to OFF.")
+  ADD_EXTERNAL( ${SUPERBUILD_DIR}/TetgenExternal.cmake Tetgen_external )
+ENDIF()
 
-INCLUDE( ${SUPERBUILD_DIR}/TeemExternal.cmake )
-LIST(APPEND SCIRun_DEPENDENCIES Teem_external)
+ADD_EXTERNAL( ${SUPERBUILD_DIR}/BoostExternal.cmake Boost_external )
 
 ###########################################
 # Download external data sources
@@ -171,13 +176,15 @@ SET(SCIRUN_CACHE_ARGS
     "-DBUILD_HEADLESS:BOOL=${BUILD_HEADLESS}"
     "-DSCIRUN_TEST_RESOURCE_DIR:PATH=${SCIRUN_TEST_RESOURCE_DIR}"
     "-DBUILD_WITH_PYTHON:BOOL=${BUILD_WITH_PYTHON}"
+    "-DWITH_TETGEN:BOOL=${WITH_TETGEN}"
     "-DREGENERATE_MODULE_FACTORY_CODE:BOOL=${REGENERATE_MODULE_FACTORY_CODE}"
     "-DGENERATE_MODULE_FACTORY_CODE:BOOL=${GENERATE_MODULE_FACTORY_CODE}"
     "-DZlib_DIR:PATH=${Zlib_DIR}"
     "-DLibPNG_DIR:PATH=${LibPNG_DIR}"
     "-DSQLite_DIR:PATH=${SQLite_DIR}"
     "-DBoost_DIR:PATH=${Boost_DIR}"
     "-DTeem_DIR:PATH=${Teem_DIR}"
+    "-DTetgen_DIR:PATH=${Tetgen_DIR}"
 )
 
 IF(BUILD_WITH_PYTHON)
@@ -187,6 +194,12 @@ IF(BUILD_WITH_PYTHON)
   )
 ENDIF()
 
+IF(WITH_TETGEN)
+  LIST(APPEND SCIRUN_CACHE_ARGS
+    "-DTetgen_DIR:PATH=${Tetgen_DIR}"
+  )
+ENDIF()
+
 IF(WIN32)
   LIST(APPEND SCIRUN_CACHE_ARGS
     "-DSCIRUN_SHOW_CONSOLE:BOOL=${SCIRUN_SHOW_CONSOLE}"

Superbuild/TetgenConfig.cmake.in

@@ -0,0 +1,4 @@
+set(TETGEN_INCLUDE "@TETGEN_INCLUDE@")
+set(TETGEN_LIBRARY_DIR "@TETGEN_LIBRARY_DIR@")
+set(TETGEN_LIBRARY "@TETGEN_LIBRARY@")
+set(TETGEN_USE_FILE "@TETGEN_USE_FILE@")

src/Externals/sqlite/CMakeLists.txt Superbuild/TetgenExternal.cmakesrc/Externals/sqlite/CMakeLists.txt renamed to Superbuild/TetgenExternal.cmake

@@ -1,4 +1,3 @@
-#
 #  For more information, please see: http://software.sci.utah.edu
 # 
 #  The MIT License
@@ -24,26 +23,31 @@
 #  LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
 #  FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER
 #  DEALINGS IN THE SOFTWARE.
-#
 
-PROJECT(SQLite)
-
-###########################################
-# Source files for SQLite
-SET( SQLITE_SRCS
-	sqlite3.h
-	sqlite3ext.h
-	sqlite3.c
+SET_PROPERTY(DIRECTORY PROPERTY "EP_BASE" ${ep_base})
+ExternalProject_Add(Tetgen_external
+  URL "http://www.tetgen.org/1.5/src/tetgen1.5.0.tar.gz"
+  PATCH_COMMAND ""
+  INSTALL_COMMAND ""
+  CMAKE_CACHE_ARGS
+    -DCMAKE_VERBOSE_MAKEFILE:BOOL=${CMAKE_VERBOSE_MAKEFILE}
+    -DCMAKE_BUILD_TYPE:STRING=${CMAKE_BUILD_TYPE}
+    -DCMAKE_POSITION_INDEPENDENT_CODE:BOOL=ON
+    #-DTETLIBRARY
 )
 
-ADD_DEFINITIONS(-DSQLITE_ENABLE_COLUMN_METADATA)
-
-###########################################
-# Set the name of the library
-SET(SCI_SQLITE_LIBRARY sqlite CACHE INTERNAL "SQLite Library name." FORCE)
+ExternalProject_Get_Property(Tetgen_external SOURCE_DIR)
+ExternalProject_Get_Property(Tetgen_external BINARY_DIR)
+ExternalProject_Get_Property(Tetgen_external INSTALL_DIR)
+SET(TETGEN_INCLUDE ${SOURCE_DIR})
+SET(TETGEN_LIBRARY_DIR ${BINARY_DIR})
+SET(TETGEN_USE_FILE ${INSTALL_DIR}/UseTetgen.cmake)
+# see Tetgen CMakeLists.txt file
+SET(TETGEN_LIBRARY "tet")
+SET(Tetgen_DIR ${INSTALL_DIR} CACHE PATH "")
 
-###########################################
-# Include directory of SQLite
-SET(SCI_SQLITE_INCLUDE ${CMAKE_CURRENT_SOURCE_DIR} CACHE INTERNAL "SQLite include directories" FORCE)
+# Boost is special case - normally this should be handled in external library repo
+CONFIGURE_FILE(${SUPERBUILD_DIR}/TetgenConfig.cmake.in ${INSTALL_DIR}/TetgenConfig.cmake @ONLY)
+CONFIGURE_FILE(${SUPERBUILD_DIR}/UseTetgen.cmake ${TETGEN_USE_FILE} COPYONLY)
 
-ADD_LIBRARY(${SCI_SQLITE_LIBRARY} STATIC ${SQLITE_SRCS})
+MESSAGE(STATUS "Tetgen_DIR: ${Tetgen_DIR}")

Superbuild/UseTetgen.cmake

@@ -0,0 +1,2 @@
+include_directories(${TETGEN_INCLUDE})
+link_directories(${TETGEN_LIBRARY_DIR})

src/.gitignore

@@ -1,2 +1 @@
 CMakeLists.txt.user
-*.svn-base

src/CMakeLists.txt

@@ -206,61 +206,40 @@ IF(BUILD_TESTING)
 ENDIF()
 
 #########################################################################
-## Python
-#
-#OPTION(BUILD_WITH_PYTHON "Build with python support." OFF)
-#
-#IF(BUILD_WITH_PYTHON)
-#  MESSAGE(STATUS "Configuring Python")
-#  SET(PythonLibs_FIND_VERSION "3.2")
-#  FIND_PACKAGE(PythonLibs REQUIRED)
-#  IF(NOT PYTHONLIBS_FOUND)
-#    MESSAGE(FATAL_ERROR "Python 3.3 or 3.2 not found. Set PYTHON_INCLUDE_DIR and PYT#HON_LIBRARY to the correct Python installation.")
-#  ENDIF()
-#
-#  ADD_DEFINITIONS(-DBOOST_PYTHON_STATIC_LIB)
-#  ADD_DEFINITIONS(-DBUILD_WITH_PYTHON)
-#ENDIF(BUILD_WITH_PYTHON)
+# External projects
 
+MACRO(CONFIG_STANDARD_EXTERNAL name config_file directory)
+  FIND_PACKAGE(${name} CONFIGS ${config_file} HINTS ${directory} NO_SYSTEM_ENVIRONMENT_PATH)
+  IF(NOT ${name}_FOUND)
+    MESSAGE(FATAL_ERROR "${name} library not found in ${directory}")
+  ENDIF()
+ENDMACRO()
 
-FIND_PACKAGE(Zlib CONFIGS ZlibConfig.cmake HINTS ${Zlib_DIR} NO_SYSTEM_ENVIRONMENT_PATH)
-IF(NOT Zlib_FOUND)
-  MESSAGE(FATAL_ERROR "Zlib library not found in ${Zlib_DIR}")
-ENDIF()
+CONFIG_STANDARD_EXTERNAL( Zlib ZlibConfig.cmake ${Zlib_DIR} )
 INCLUDE(${ZLIB_USE_FILE})
 
-FIND_PACKAGE(LibPNG CONFIGS LibPNGConfig.cmake HINTS ${LibPNG_DIR} NO_SYSTEM_ENVIRONMENT_PATH)
-IF(NOT LibPNG_FOUND)
-  MESSAGE(FATAL_ERROR "Png library not found in ${LibPNG_DIR}")
-ENDIF()
+CONFIG_STANDARD_EXTERNAL( LibPNG LibPNGConfig.cmake ${LibPNG_DIR} )
 INCLUDE(${PNG_USE_FILE})
 
-FIND_PACKAGE(SQLite CONFIGS SQLiteConfig.cmake HINTS ${SQLite_DIR} NO_SYSTEM_ENVIRONMENT_PATH)
-IF(NOT SQLite_FOUND)
-  MESSAGE(FATAL_ERROR "SQLite library not found in ${SQLite_DIR}")
-ENDIF()
+CONFIG_STANDARD_EXTERNAL( SQLite SQLiteConfig.cmake ${SQLite_DIR} )
 INCLUDE(${SQLITE_USE_FILE})
 
-FIND_PACKAGE(Teem CONFIGS TeemConfig.cmake HINTS ${Teem_DIR} NO_SYSTEM_ENVIRONMENT_PATH)
-IF(NOT Teem_FOUND)
-  MESSAGE(FATAL_ERROR "Teem library not found in ${Teem_DIR}")
-ENDIF()
+CONFIG_STANDARD_EXTERNAL( Teem TeemConfig.cmake ${Teem_DIR} )
 INCLUDE(${Teem_USE_FILE})
 
 IF(BUILD_WITH_PYTHON)
-  FIND_PACKAGE(Python CONFIGS PythonConfig.cmake HINTS ${Python_DIR} NO_SYSTEM_ENVIRONMENT_PATH)
-  IF(NOT Python_FOUND)
-    MESSAGE(FATAL_ERROR "Python library not found in ${Python_DIR}")
-  ENDIF()
+  CONFIG_STANDARD_EXTERNAL( Python PythonConfig.cmake ${Python_DIR} )
   INCLUDE(${SCI_PYTHON_USE_FILE})
 ENDIF()
 
-FIND_PACKAGE(Boost CONFIGS BoostConfig.cmake HINTS ${Boost_DIR} NO_SYSTEM_ENVIRONMENT_PATH)
-IF(NOT Boost_FOUND)
-  MESSAGE(FATAL_ERROR "Boost library not found in ${Boost_DIR}")
-ENDIF()
+CONFIG_STANDARD_EXTERNAL( Boost BoostConfig.cmake ${Boost_DIR} )
 INCLUDE(${SCI_BOOST_USE_FILE})
 
+IF(WITH_TETGEN)
+  CONFIG_STANDARD_EXTERNAL( Tetgen TetgenConfig.cmake ${Tetgen_DIR} )
+  INCLUDE(${TETGEN_USE_FILE})
+ENDIF()
+
 ########################################################################
 # Custom compiler flags and definitions
 
@@ -356,45 +335,11 @@ ENDIF()
 # ENDIF()
 
 ########################################################################
-# Download external data sources
-
-#OPTION(DOWNLOAD_TOOLKITS "Download toolkit repositories." ON)
-#MARK_AS_ADVANCED(DOWNLOAD_TOOLKITS)
-#IF(DOWNLOAD_TOOLKITS)
-#  INCLUDE(${CMAKE_CURRENT_SOURCE_DIR}/CMake/ToolkitsConfig.cmake)
-#  EXTERNAL_TOOLKIT(BrainStimulator)
-#  EXTERNAL_TOOLKIT(FwdInvToolkit)
-#ENDIF()
-#
-#########################################################################
-## Configure zlib external project
-#
-#INCLUDE(${CMAKE_CURRENT_SOURCE_DIR}/CMake/ZlibConfig.cmake)
-#EXTERNAL_ZLIB_LIBRARY(GIT)
-#
-#
-##########################################################################
-## Configure Boost external project
-#
-#INCLUDE(${CMAKE_CURRENT_SOURCE_DIR}/CMake/BoostConfig.cmake)
-#EXTERNAL_BOOST_LIBRARY(GIT)
-#
-#
-#########################################################################
-## Configure teem external project
-#
-#INCLUDE(${CMAKE_CURRENT_SOURCE_DIR}/CMake/TeemConfig.cmake)
-#EXTERNAL_TEEM_LIBRARY(GIT)
+# Configure tetgen module build
 
-
-########################################################################
-# Configure tetgen external project
-
-OPTION(WITH_TETGEN "Build Tetgen." ON)
-MARK_AS_ADVANCED(WITH_TETGEN)
 IF(WITH_TETGEN)
   ADD_DEFINITIONS(-DWITH_TETGEN)
-ENDIF(WITH_TETGEN)
+ENDIF()
 
 ########################################################################
 # Configure CPM and Spire - http://github.com/iauns/cpm
@@ -610,7 +555,7 @@ INCLUDE_DIRECTORIES(
   ${SCIRun_SOURCE_DIR}/Externals/log4cpp/include
   ${SCI_TEEM_INCLUDE}
   ${SCI_ZLIB_INCLUDE}
-  ${SCI_TETGEN_INCLUDE}
+  #${SCI_TETGEN_INCLUDE}
 )
 
 INCLUDE_DIRECTORIES(SYSTEM ${SCI_BOOST_INCLUDE})
@@ -911,25 +856,16 @@ IF(BUILD_TESTING)
   ENDIF()
 ENDIF()
 
-#SET_PROPERTY(TARGET Boost_external   PROPERTY FOLDER "Externals")
 SET_PROPERTY(TARGET ${CPM_LIBRARIES} PROPERTY FOLDER "Externals")
 SET_PROPERTY(TARGET ${SCI_LOG4CPP_LIBRARY} PROPERTY FOLDER "Externals")
-#SET_PROPERTY(TARGET sqlite PROPERTY FOLDER "Externals")
 SET_PROPERTY(TARGET cleaver PROPERTY FOLDER "Externals")
-#SET_PROPERTY(TARGET Zlib_external   PROPERTY FOLDER "Externals")
-#SET_PROPERTY(TARGET Teem_external   PROPERTY FOLDER "Externals")
 SET_PROPERTY(TARGET xml2 PROPERTY FOLDER "Externals")
 
 IF(BUILD_WITH_PYTHON)
   SET_PROPERTY(TARGET Core_Python         PROPERTY FOLDER "Core")
   SET_PROPERTY(TARGET SCIRunPythonAPI PROPERTY FOLDER "Dataflow/Engine")
 ENDIF()
 
-IF(WITH_TETGEN)
-  SET_PROPERTY(TARGET tetgen         PROPERTY FOLDER "Externals")
-  SET_PROPERTY(TARGET tetlib         PROPERTY FOLDER "Externals")
-ENDIF()
-
 ########################################################################
 # Custom CMake settings for CPack
 

src/Core/Algorithms/Legacy/DataIO/CMakeLists.txt

@@ -32,11 +32,13 @@ SET(Core_Algorithms_Legacy_DataIO_SRCS
   DataIOAlgo.cc
   #MRCReader.cc
   ObjToFieldReader.cc
+  VTKToTriSurfReader.cc
   #StreamData/StreamACQFile.cc
 )
 
 SET(Core_Algorithms_Legacy_DataIO_HEADERS
   ObjToFieldReader.h
+  VTKToTriSurfReader.h
   DataIOAlgo.h
 )