Teem fix

CMakeLists.txt

@@ -1,5 +1,4 @@
 cmake_minimum_required(VERSION 2.8.9) #2.8.9 needed for ExternalProject Simplification
-cmake_policy(VERSION 2.8.9)
 
 set(PRIMARY_PROJECT_NAME UKFTractography)
 
@@ -19,13 +18,37 @@ set(PRIMARY_PROJECT_NAME UKFTractography)
 #                   Phase II: Build the ${PRIMARY_PROJECT_NAME}, referencing the support
 #                             packages built in Phase I.
 #-----------------------------------------------------------------------------
-option(${PRIMARY_PROJECT_NAME}_SUPERBUILD "Build ${PRIMARY_PROJECT_NAME} and the projects it depends on via SuperBuild.cmake." ON)
+
+#-----------------------------------------------------------------------------
+set(EXTENSION_NAME  UKFTractography)
+set(EXTENSION_HOMEPAGE "http://www.nitrc.org/plugins/mwiki/index.php/ukftractography:MainPage")
+set(EXTENSION_CATEGORY "Diffusion.Tractography")
+set(EXTENSION_CONTRIBUTORS "Yogesh Rathi, Stefan Lienhard, Yinpeng Li, Martin Styner, Ipek Oguz, Yundi Shi, Christian Baumgartner, Ryan Eckbo, Kent Williams, Hans Johnson, Peter Savadjiev, Carl-Fredrik Westin")
+set(EXTENSION_MAJOR_VERSION 1)
+set(EXTENSION_MINOR_VERSION 2)
+set(EXTENSION_PATCH_VERSION 0)
+set(EXTENSION_STATUS "Alpha")
+set(EXTENSION_DEPENDS "Eigen")
+set(EXTENSION_DESCRIPTION "This module traces fibers in a DWI Volume using the multiple tensor unscented Kalman Filter methology. ")
+set(EXTENSION_LICENSE_SHORT_DESCRIPTION "Quadratic Programming Library QuadProg++ has LGPL or GPL")
+set(EXTENSION_ICONURL "http://viewvc.slicer.org/viewvc.cgi/Slicer4/trunk/Extensions/Testing/CLIExtensionTemplate/CLIExtensionTemplate.png?revision=19437&view=co")
+set(EXTENSION_SCREENSHOTURLS "http://wiki.slicer.org/slicerWiki/images/a/ab/Slicer-r19441-CLIExtensionTemplate-screenshot.png http://wiki.slicer.org/slicerWiki/images/1/1e/Slicer-r19441-CLIExtensionTemplate-screenshot-2.png")
+
+#-----------------------------------------------------------------------------
+if(${PRIMARY_PROJECT_NAME}_BUILD_SLICER_EXTENSION)
+  set(default_superbuild_value OFF)
+else()
+  set(default_superbuild_value ON)
+endif()
+
+#-----------------------------------------------------------------------------
+option(${PRIMARY_PROJECT_NAME}_SUPERBUILD "Build ${PRIMARY_PROJECT_NAME} and the projects it depends on via SuperBuild.cmake." ${default_superbuild_value})
 mark_as_advanced(${PRIMARY_PROJECT_NAME}_SUPERBUILD)
 
 #-----------------------------------------------------------------------------
 # Superbuild script
 #-----------------------------------------------------------------------------
-if(${PRIMARY_PROJECT_NAME}_SUPERBUILD AND NOT ${PRIMARY_PROJECT_NAME}_BUILD_SLICER_EXTENSION)
+if(${PRIMARY_PROJECT_NAME}_SUPERBUILD)
   project(SuperBuild_${PRIMARY_PROJECT_NAME})  # <- NOTE: Project name for pre-requisites is different form main project
   include("${CMAKE_CURRENT_SOURCE_DIR}/SuperBuild.cmake")
   return()

Common.cmake

@@ -10,6 +10,10 @@ enable_language(CXX)
 include(CMakeDependentOption)
 include(Artichoke)
 
+#-----------------------------------------------------------------------------
+# Build option(s)
+#-----------------------------------------------------------------------------
+
 option(${PRIMARY_PROJECT_NAME}_INSTALL_DEVELOPMENT "Install development support include and libraries for external packages." OFF)
 mark_as_advanced(${PRIMARY_PROJECT_NAME}_INSTALL_DEVELOPMENT)
 
@@ -25,10 +29,6 @@ if(NOT CMAKE_BUILD_TYPE AND NOT CMAKE_CONFIGURATION_TYPES)
   set_property(CACHE CMAKE_BUILD_TYPE PROPERTY STRINGS "Debug" "Release" "MinSizeRel" "RelWithDebInfo")
 endif()
 
-#-----------------------------------------------------------------------------
-# Build option(s)
-#-----------------------------------------------------------------------------
-
 #-----------------------------------------------------------------------------
 # Update CMake module path
 #------------------------------------------------------------------------------
@@ -71,31 +71,15 @@ if(NOT COMMAND SETIFEMPTY)
   endmacro()
 endif()
 
-#
-# if you're building as a Slicer extension, this stuff
-# overrides the defaults being set up for the Extension.
-if(UKFTractography_SUPERBUILD AND NOT ${PRIMARY_PROJECT_NAME}_BUILD_SLICER_EXTENSION)
-
-  #-----------------------------------------------------------------------------
-  SETIFEMPTY(CMAKE_LIBRARY_OUTPUT_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}/lib)
-  SETIFEMPTY(CMAKE_ARCHIVE_OUTPUT_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}/lib)
-  SETIFEMPTY(CMAKE_RUNTIME_OUTPUT_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}/bin)
-
-  #-----------------------------------------------------------------------------
-  SETIFEMPTY(CMAKE_INSTALL_LIBRARY_DESTINATION lib)
-  SETIFEMPTY(CMAKE_INSTALL_ARCHIVE_DESTINATION lib)
-  SETIFEMPTY(CMAKE_INSTALL_RUNTIME_DESTINATION bin)
-
-  set(SlicerExecutionModel_DEFAULT_CLI_INSTALL_RUNTIME_DESTINATION ${CMAKE_INSTALL_RUNTIME_DESTINATION})
-  set(SlicerExecutionModel_DEFAULT_CLI_INSTALL_LIBRARY_DESTINATION ${CMAKE_INSTALL_LIBRARY_DESTINATION})
-  set(SlicerExecutionModel_DEFAULT_CLI_INSTALL_ARCHIVE_DESTINATION ${CMAKE_INSTALL_ARCHIVE_DESTINATION})
-endif()
-
-# these apparently need to be set to something; 
-SETIFEMPTY(SlicerExecutionModel_DEFAULT_CLI_INSTALL_RUNTIME_DESTINATION bin)
-SETIFEMPTY(SlicerExecutionModel_DEFAULT_CLI_INSTALL_LIBRARY_DESTINATION lib)
-SETIFEMPTY(SlicerExecutionModel_DEFAULT_CLI_INSTALL_ARCHIVE_DESTINATION lib)
+#-----------------------------------------------------------------------------
+SETIFEMPTY(CMAKE_LIBRARY_OUTPUT_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}/lib)
+SETIFEMPTY(CMAKE_ARCHIVE_OUTPUT_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}/lib)
+SETIFEMPTY(CMAKE_RUNTIME_OUTPUT_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}/bin)
 
+#-----------------------------------------------------------------------------
+SETIFEMPTY(CMAKE_INSTALL_LIBRARY_DESTINATION lib)
+SETIFEMPTY(CMAKE_INSTALL_ARCHIVE_DESTINATION lib)
+SETIFEMPTY(CMAKE_INSTALL_RUNTIME_DESTINATION bin)
 
 #-------------------------------------------------------------------------
 # Augment compiler flags
@@ -108,13 +92,6 @@ if("${CMAKE_CXX_COMPILER}${CMAKE_CXX_COMPILER_ARG1}" MATCHES ".*clang.*")
   set(CMAKE_COMPILER_IS_CLANGXX ON CACHE BOOL "compiler is CLang")
 endif()
 
-set(CMAKE_C_FLAGS  "${CMAKE_C_FLAGS} ${ITK_REQUIRED_C_FLAGS}")
-set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} ${ITK_REQUIRED_CXX_FLAGS}")
-set(CMAKE_EXE_LINKER_FLAGS "${CMAKE_EXE_LINKER_FLAGS} ${ITK_REQUIRED_LINK_FLAGS}")
-set(CMAKE_SHARED_LINKER_FLAGS "${CMAKE_SHARED_LINKER_FLAGS} ${ITK_REQUIRED_LINK_FLAGS}")
-set(CMAKE_MODULE_LINKER_FLAGS "${CMAKE_MODULE_LINKER_FLAGS} ${ITK_REQUIRED_LINK_FLAGS}")
-
-
 #-----------------------------------------------------------------------------
 # Add needed flag for gnu on linux like enviroments to build static common libs
 # suitable for linking with shared object libs.
@@ -127,3 +104,9 @@ if(CMAKE_SYSTEM_PROCESSOR STREQUAL "x86_64")
   endif()
 endif()
 
+set(CMAKE_C_FLAGS  "${CMAKE_C_FLAGS} ${ITK_REQUIRED_C_FLAGS}" CACHE STRING "CMake C Flags" FORCE)
+set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} ${ITK_REQUIRED_CXX_FLAGS}" CACHE STRING "CMake CXX Flags" FORCE)
+set(CMAKE_EXE_LINKER_FLAGS "${CMAKE_EXE_LINKER_FLAGS} ${ITK_REQUIRED_LINK_FLAGS}" CACHE STRING "CMake Linker Flags" FORCE)
+set(CMAKE_SHARED_LINKER_FLAGS "${CMAKE_SHARED_LINKER_FLAGS} ${ITK_REQUIRED_LINK_FLAGS}" CACHE STRING "CMake shared linker Flags" FORCE)
+set(CMAKE_MODULE_LINKER_FLAGS "${CMAKE_MODULE_LINKER_FLAGS} ${ITK_REQUIRED_LINK_FLAGS}" CACHE STRING "CMake module linker Flags" FORCE)
+

CompressedSensing/CMakeLists.txt

@@ -1,48 +1,17 @@
-cmake_minimum_required(VERSION 2.8.7)
+
+#-----------------------------------------------------------------------------
 find_package(Boost REQUIRED)
 include_directories(${Boost_INCLUDE_DIRS})
 message("Boost_INCLUDE_DIRS=${Boost_INCLUDE_DIRS}")
-#-----------------------------------------------------------------------------
-set(MODULE_NAME CompressedSensing)
 
 #-----------------------------------------------------------------------------
-if(NOT Slicer_SOURCE_DIR AND NOT UKFTractography_SuperBuild)
-  find_package(Slicer REQUIRED)
-  include(${Slicer_USE_FILE})
-endif()
-
-if(NOT SlicerExecutionModel_FOUND)
-find_package(SlicerExecutionModel REQUIRED)
-include(${SlicerExecutionModel_USE_FILE})
-endif()
-
-if(NOT Teem_FOUND)
-find_package(Teem REQUIRED)
-include(${Teem_USE_FILE})
-endif()
-
-if(NOT ITK_FOUND)
-find_package(ITK REQUIRED)
-include(${ITK_USE_FILE})
-endif()
-
-if(NOT GenerateCLP_FOUND)
-find_package(GenerateCLP REQUIRED)
-include(${GenerateCLP_USE_FILE})
-endif()
-
-if(NOT VTK_FOUND)
-find_package(VTK REQUIRED)
-include(${VTK_USE_FILE})
-endif()
+set(MODULE_NAME CompressedSensing)
 
 #-----------------------------------------------------------------------------
 set(MODULE_INCLUDE_DIRECTORIES
-    ${Teem_INCLUDE_DIRS}
-    ${CMAKE_CURRENT_SOURCE_DIR}
- )
-
-include_directories( ${MODULE_INCLUDE_DIRECTORIES} )
+  ${Teem_INCLUDE_DIRS}
+  ${CMAKE_CURRENT_SOURCE_DIR}
+  )
 
 set(MODULE_SRCS
   CompressedSensing.cxx
@@ -59,10 +28,10 @@ set(MODULE_SRCS
   )
 
 set(MODULE_TARGET_LIBRARIES
-    ${ITK_LIBRARIES}
-    ${CMAKE_THREAD_LIBS_INIT}
-    ${TEEM_LIB}
-    ${VTK_LIBRARIES}
+  ${ITK_LIBRARIES}
+  ${CMAKE_THREAD_LIBS_INIT}
+  ${TEEM_LIB} ${ZLIB_LIBRARIES}
+  ${VTK_LIBRARIES}
   )
 
 #-----------------------------------------------------------------------------

CompressedSensing/Testing/CMakeLists.txt

@@ -12,4 +12,4 @@ add_test(NAME fibertractdispersion
   --writeUnCompressed
   --inputFiberBundle     ${BASELINE}/1T_fiber.vtk
   --outputFiberBundle ${TESTING_RESULTS_DIRECTORY}/${CLP}_1T_fiber.vtk
-)
+  )