COMP: Add JPEG & TIFF BUILDS, pass to DCMTK build

DWIConvert/CMakeLists.txt

@@ -3,8 +3,6 @@ project (DWIConvert)
 #-----------------------------------------------------------------------------
 enable_testing()
 
-find_package(ITK 4 REQUIRED)
-
 set(CMAKE_MODULE_PATH ${CMAKE_CURRENT_LIST_DIR} ${CMAKE_MODULE_PATH})
 
 set(DWIConvertSupportLib_SRCS

SuperBuild/EP_Autoconf_Utils.cmake

@@ -0,0 +1,12 @@
+#
+# Building external projects via ExternalProject requires passing along some important CMkae variables into the autoconf configuration.
+get_filename_component(CMAKE_CURRENT_LIST_FILENAME ${CMAKE_CURRENT_LIST_FILE} NAME_WE)
+if(${CMAKE_CURRENT_LIST_FILENAME}_FILE_INCLUDED)
+  return()
+endif()
+set(${CMAKE_CURRENT_LIST_FILENAME}_FILE_INCLUDED 1)
+
+macro(AutoConf_FLAGS varname lang additional_flags)
+  string(TOUPPER CONF ${CMAKE_BUILD_TYPE})
+  set(${varname} "${CMAKE_${lang}_FLAGS} ${CMAKE_${lang}_FLAGS_${CONF}} ${additional_flags}")
+endmacro()

SuperBuild/External_DCMTK.cmake

@@ -31,7 +31,7 @@ if(DEFINED ${extProjName}_DIR AND NOT EXISTS ${${extProjName}_DIR})
 endif()
 
 # Set dependency list
-set(${proj}_DEPENDENCIES "")
+set(${proj}_DEPENDENCIES TIFF)
 
 # Include dependent projects if any
 SlicerMacroCheckExternalProjectDependency(${proj})
@@ -57,19 +57,27 @@ if(NOT ( DEFINED "${extProjName}_DIR" OR ( DEFINED "${USE_SYSTEM_${extProjName}}
   ### --- Project specific additions here
   set(${proj}_CMAKE_OPTIONS
       -DDCMTK_WITH_DOXYGEN:BOOL=OFF
-      -DDCMTK_WITH_ZLIB:BOOL=OFF # see CTK github issue #25
+      -DDCMTK_WITH_ZLIB:BOOL=ON # see CTK github issue #25
       -DDCMTK_WITH_OPENSSL:BOOL=OFF # see CTK github issue #25
       -DDCMTK_WITH_PNG:BOOL=OFF # see CTK github issue #25
-      -DDCMTK_WITH_TIFF:BOOL=OFF  # see CTK github issue #25
+      -DDCMTK_WITH_TIFF:BOOL=ON  # see CTK github issue #25
       -DDCMTK_WITH_XML:BOOL=OFF  # see CTK github issue #25
       -DDCMTK_WITH_ICONV:BOOL=OFF  # see CTK github issue #178
       -DDCMTK_FORCE_FPIC_ON_UNIX:BOOL=ON
       -DDCMTK_OVERWRITE_WIN32_COMPILER_FLAGS:BOOL=OFF
       -DDCMTK_WITH_WRAP:BOOL=OFF   # CTK does not build on Mac with this option turned ON due to library dependencies missing
+#      -DTIFF_DIR:PATH=${TIFF_DIR}
+      -DTIFF_LIBRARY:FILEPATH=${TIFF_LIBRARY}
+      -DTIFF_INCLUDE_DIR:PATH=${TIFF_INCLUDE_DIR}
+      -DJPEG_LIBRARY:FILEPATH=${JPEG_LIBRARY}
+      -DJPEG_INCLUDE_DIR:PATH=${JPEG_INCLUDE_DIR}
   )
   ### --- End Project specific additions
-  set(${proj}_REPOSITORY ${git_protocol}://github.com/commontk/DCMTK.git)
-  set(${proj}_GIT_TAG "d06e2b7d9bafb23df4e969482a68b50fc75aaaa9")
+#  set(${proj}_REPOSITORY ${git_protocol}://github.com/commontk/DCMTK.git)
+#  set(${proj}_GIT_TAG "d06e2b7d9bafb23df4e969482a68b50fc75aaaa9")
+  set(${proj}_REPOSITORY https://github.com/InsightSoftwareConsortium/DCMTK.git)
+  set(${proj}_GIT_TAG AddProperConfig)
+
   ExternalProject_Add(${proj}
     GIT_REPOSITORY ${${proj}_REPOSITORY}
     GIT_TAG ${${proj}_GIT_TAG}
@@ -93,7 +101,7 @@ if(NOT ( DEFINED "${extProjName}_DIR" OR ( DEFINED "${USE_SYSTEM_${extProjName}}
     DEPENDS
       ${${proj}_DEPENDENCIES}
   )
-  set(${extProjName}_DIR ${CMAKE_BINARY_DIR}/${proj}-install)
+  set(${extProjName}_DIR ${CMAKE_BINARY_DIR}/${proj}-install/lib/cmake/dcmtk)
 else()
   if(${USE_SYSTEM_${extProjName}})
     find_package(${extProjName} REQUIRED)

SuperBuild/External_DoubleConvert.cmake

@@ -63,7 +63,7 @@ if(NOT ( DEFINED "${extProjName}_DIR" OR ( DEFINED "${USE_SYSTEM_${extProjName}}
     )
   ### --- End Project specific additions
   set(${proj}_REPOSITORY ${git_protocol}://github.com/BRAINSia/double-conversion.git)
-  set(${proj}_GIT_TAG 9014759697ed334753a8334e09ec8c01f9c53830)
+  set(${proj}_GIT_TAG e5e143791e4815ac19b10570e010d83d55c2c25b)
   ExternalProject_Add(${proj}
     GIT_REPOSITORY ${${proj}_REPOSITORY}
     GIT_TAG ${${proj}_GIT_TAG}
@@ -81,7 +81,7 @@ if(NOT ( DEFINED "${extProjName}_DIR" OR ( DEFINED "${USE_SYSTEM_${extProjName}}
     DEPENDS
       ${${proj}_DEPENDENCIES}
   )
-  set(${extProjName}_DIR ${CMAKE_BINARY_DIR}/${proj}-install/lib/cmake/ITK-4.4)
+  set(${extProjName}_DIR ${CMAKE_BINARY_DIR}/${proj}-install/lib/cmake/double-conversion)
 else()
   if(${USE_SYSTEM_${extProjName}})
     find_package(${extProjName} ${ITK_VERSION_MAJOR} REQUIRED)

SuperBuild/External_ITKv4.cmake

@@ -33,7 +33,7 @@ endif()
 # Set dependency list
 set(${proj}_DEPENDENCIES "")
 if(${PROJECT_NAME}_BUILD_DICOM_SUPPORT)
-  list(APPEND ${proj}_DEPENDENCIES DCMTK)
+  list(APPEND ${proj}_DEPENDENCIES DCMTK JPEG TIFF)
 endif()
 
 # Include dependent projects if any
@@ -57,6 +57,7 @@ if(NOT ( DEFINED "${extProjName}_DIR" OR ( DEFINED "${USE_SYSTEM_${extProjName}}
     set(${proj}_DCMTK_ARGS
       -DITK_USE_SYSTEM_DCMTK:BOOL=ON
       -DDCMTK_DIR:PATH=${DCMTK_DIR}
+      -DModule_ITKDCMTK:BOOL=ON
       -DModule_ITKIODCMTK:BOOL=ON
       )
   endif()
@@ -104,6 +105,8 @@ if(NOT ( DEFINED "${extProjName}_DIR" OR ( DEFINED "${USE_SYSTEM_${extProjName}}
       set(git_protocol "git")
   endif()
 
+  find_package(ZLIB REQUIRED)
+
   set(${proj}_CMAKE_OPTIONS
       -DBUILD_TESTING:BOOL=OFF
       -DBUILD_EXAMPLES:BOOL=OFF
@@ -117,14 +120,27 @@ if(NOT ( DEFINED "${extProjName}_DIR" OR ( DEFINED "${USE_SYSTEM_${extProjName}}
       -DKWSYS_USE_MD5:BOOL=ON # Required by SlicerExecutionModel
       -DITK_WRAPPING:BOOL=OFF #${BUILD_SHARED_LIBS} ## HACK:  QUICK CHANGE
       -DITK_USE_SYSTEM_DCMTK:BOOL=${${PROJECT_NAME}_BUILD_DICOM_SUPPORT}
+
+      -DITK_USE_SYSTEM_TIFF:BOOL=ON
+      -DTIFF_LIBRARY:FILEPATH=${TIFF_LIBRARY}
+      -DTIFF_INCLUDE_DIR:PATH=${TIFF_INCLUDE_DIR}
+
+      -DITK_USE_SYSTEM_JPEG:BOOL=ON
+      -DJPEG_LIBRARY:FILEPATH=${JPEG_LIBRARY}
+      -DJPEG_INCLUDE_DIR:PATH=${JPEG_INCLUDE_DIR}
+
+      -DITK_USE_SYSTEM_ZLIB:BOOL=ON
+      -DZLIB_INCLUDE_DIRS:STRING=${ZLIB_INCLUDE_DIRS}
+      -DZLIB_LIBRARIES:STRING=${ZLIB_LIBRARIES}
       ${${proj}_DCMTK_ARGS}
       ${${proj}_WRAP_ARGS}
       ${${proj}_FFTWF_ARGS}
       ${${proj}_FFTWD_ARGS}
     )
   ### --- End Project specific additions
-  set(${proj}_REPOSITORY ${git_protocol}://itk.org/ITK.git)
-  set(${proj}_GIT_TAG 7533cafcee0ad15c1b0b3e492e3a5aacc37b4258) #2013-03-01 Provide const correct API
+
+  set(${proj}_REPOSITORY https://github.com/Chaircrusher/ITK.git)
+  set(${proj}_GIT_TAG DCMTK_NO_MODULE)
   ExternalProject_Add(${proj}
     GIT_REPOSITORY ${${proj}_REPOSITORY}
     GIT_TAG ${${proj}_GIT_TAG}

SuperBuild/External_JPEG.cmake

@@ -0,0 +1,94 @@
+# Make sure this file is included only once by creating globally unique varibles
+# based on the name of this included file.
+get_filename_component(CMAKE_CURRENT_LIST_FILENAME ${CMAKE_CURRENT_LIST_FILE} NAME_WE)
+if(${CMAKE_CURRENT_LIST_FILENAME}_FILE_INCLUDED)
+  return()
+endif()
+set(${CMAKE_CURRENT_LIST_FILENAME}_FILE_INCLUDED 1)
+
+include(${CMAKE_CURRENT_LIST_DIR}/EP_Autoconf_Utils.cmake)
+
+## External_${extProjName}.cmake files can be recurisvely included,
+## and cmake variables are global, so when including sub projects it
+## is important make the extProjName and proj variables
+## appear to stay constant in one of these files.
+## Store global variables before overwriting (then restore at end of this file.)
+ProjectDependancyPush(CACHED_extProjName ${extProjName})
+ProjectDependancyPush(CACHED_proj ${proj})
+
+# Make sure that the ExtProjName/IntProjName variables are unique globally
+# even if other External_${ExtProjName}.cmake files are sourced by
+# SlicerMacroCheckExternalProjectDependency
+set(extProjName JPEG) #The find_package known name
+set(proj        JPEG) #This local name
+set(${extProjName}_REQUIRED_VERSION "")  #If a required version is necessary, then set this, else leave blank
+
+#if(${USE_SYSTEM_${extProjName}})
+#  unset(${extProjName}_DIR CACHE)
+#endif()
+
+# Sanity checks
+if(DEFINED ${extProjName}_DIR AND NOT EXISTS ${${extProjName}_DIR})
+  message(FATAL_ERROR "${extProjName}_DIR variable is defined but corresponds to non-existing directory (${${extProjName}_DIR})")
+endif()
+
+# Set dependency list
+set(${proj}_DEPENDENCIES "")
+
+# Include dependent projects if any
+SlicerMacroCheckExternalProjectDependency(${proj})
+
+if(NOT ( DEFINED "${extProjName}_DIR" OR ( DEFINED "${USE_SYSTEM_${extProjName}}" AND NOT "${USE_SYSTEM_${extProjName}}" ) ) )
+
+
+  set(${proj}_URL
+    "http://www.infai.org/jpeg/files?get=jpegsrc.v09a.tar.gz")
+  set(${proj}_MD5 "546c94c044a3f546927c955e31316dd5")
+
+  AutoConf_FLAGS(${proj}_CFLAGS C "")
+  AutoConf_FLAGS(${proj}_CXXFLAGS CXX "")
+
+  ExternalProject_Add(${proj}
+    URL ${${proj}_URL}
+    URL_MD5 ${${proj}_MD5}
+    SOURCE_DIR ${proj}
+    BINARY_DIR ${proj}-build
+    INSTALL_DIR ${proj}-install
+    ${cmakeversion_external_update} "${cmakeversion_external_update_value}"
+    CMAKE_GENERATOR ${gen}
+    CONFIGURE_COMMAND <SOURCE_DIR>/configure --prefix=<INSTALL_DIR>
+    --enable-shared=No
+    --enable-static=Yes
+    CC=${CMAKE_C_COMPILER}
+    CXX=${CMAKE_CXX_COMPILER}
+    "CFLAGS=${${proj}_CFLAGS}"
+    "CXXFLAGS=${${proj}_CXXFLAGS}"
+    DEPENDS
+    ${${proj}_DEPENDENCIES}
+  )
+  set(${extProjName}_DIR
+    ${CMAKE_BINARY_DIR}/${proj}-install)
+  set(${extProjName}_INCLUDE_DIR
+    ${CMAKE_BINARY_DIR}/${proj}-install/include)
+  set(${extProjName}_LIB_DIR
+    ${CMAKE_BINARY_DIR}/${proj}-install/lib)
+  set(${extProjName}_LIBRARY
+    ${${extProjName}_LIB_DIR}/libjpeg.a)
+
+else()
+  if(${USE_SYSTEM_${extProjName}})
+    find_package(${extProjName} ${${extProjName}_REQUIRED_VERSION} REQUIRED)
+    if(NOT ${extProjName}_DIR)
+      message(FATAL_ERROR "To use the system ${extProjName}, set ${extProjName}_DIR")
+    endif()
+    message("USING the system ${extProjName}, set ${extProjName}_DIR=${${extProjName}_DIR}")
+  endif()
+  # The project is provided using ${extProjName}_DIR, nevertheless since other
+  # project may depend on ${extProjName}, let's add an 'empty' one
+  SlicerMacroEmptyExternalProject(${proj} "${${proj}_DEPENDENCIES}")
+endif()
+
+list(APPEND ${CMAKE_PROJECT_NAME}_SUPERBUILD_EP_VARS ${extProjName}_DIR:PATH)
+
+ProjectDependancyPop(CACHED_extProjName extProjName)
+ProjectDependancyPop(CACHED_proj proj)

SuperBuild/External_OpenJPEG.cmake

@@ -0,0 +1,107 @@
+# Make sure this file is included only once by creating globally unique varibles
+# based on the name of this included file.
+get_filename_component(CMAKE_CURRENT_LIST_FILENAME ${CMAKE_CURRENT_LIST_FILE} NAME_WE)
+if(${CMAKE_CURRENT_LIST_FILENAME}_FILE_INCLUDED)
+  return()
+endif()
+set(${CMAKE_CURRENT_LIST_FILENAME}_FILE_INCLUDED 1)
+
+## External_${extProjName}.cmake files can be recurisvely included,
+## and cmake variables are global, so when including sub projects it
+## is important make the extProjName and proj variables
+## appear to stay constant in one of these files.
+## Store global variables before overwriting (then restore at end of this file.)
+ProjectDependancyPush(CACHED_extProjName ${extProjName})
+ProjectDependancyPush(CACHED_proj ${proj})
+
+# Make sure that the ExtProjName/IntProjName variables are unique globally
+# even if other External_${ExtProjName}.cmake files are sourced by
+# SlicerMacroCheckExternalProjectDependency
+set(extProjName OpenJPEG) #The find_package known name
+set(proj        OpenJPEG) #This local name
+set(${extProjName}_REQUIRED_VERSION "")  #If a required version is necessary, then set this, else leave blank
+
+#if(${USE_SYSTEM_${extProjName}})
+#  unset(${extProjName}_DIR CACHE)
+#endif()
+
+# Sanity checks
+if(DEFINED ${extProjName}_DIR AND NOT EXISTS ${${extProjName}_DIR})
+  message(FATAL_ERROR "${extProjName}_DIR variable is defined but corresponds to non-existing directory (${${extProjName}_DIR})")
+endif()
+
+# Set dependency list
+set(${proj}_DEPENDENCIES "")
+
+# Include dependent projects if any
+SlicerMacroCheckExternalProjectDependency(${proj})
+
+if(NOT ( DEFINED "${extProjName}_DIR" OR ( DEFINED "${USE_SYSTEM_${extProjName}}" AND NOT "${USE_SYSTEM_${extProjName}}" ) ) )
+  #message(STATUS "${__indent}Adding project ${proj}")
+
+  # Set CMake OSX variable to pass down the external project
+  set(CMAKE_OSX_EXTERNAL_PROJECT_ARGS)
+  if(APPLE)
+    list(APPEND CMAKE_OSX_EXTERNAL_PROJECT_ARGS
+      -DCMAKE_OSX_ARCHITECTURES=${CMAKE_OSX_ARCHITECTURES}
+      -DCMAKE_OSX_SYSROOT=${CMAKE_OSX_SYSROOT}
+      -DCMAKE_OSX_DEPLOYMENT_TARGET=${CMAKE_OSX_DEPLOYMENT_TARGET})
+  endif()
+
+  ### --- Project specific additions here
+  set(${proj}_CMAKE_OPTIONS
+      -DCMAKE_INSTALL_PREFIX:PATH=${CMAKE_CURRENT_BINARY_DIR}/${proj}-install
+      -DBUILD_EXAMPLES:BOOL=OFF
+      -DBUILD_TESTING:BOOL=OFF
+    )
+
+  ### --- End Project specific additions
+  if(NOT DEFINED git_protocol)
+      set(git_protocol "git")
+  endif()
+
+  set(${proj}_REPOSITORY "http://openjpeg.googlecode.com/svn/trunk")
+  set(${proj}_SVN_REVISION 2292) #2013-01-30 New Repository.
+  ExternalProject_Add(${proj}
+    SVN_REPOSITORY ${${proj}_REPOSITORY}
+    SVN_REVISION -r ${${proj}_SVN_REVISION}
+    SOURCE_DIR ${proj}
+    BINARY_DIR ${proj}-build
+    ${cmakeversion_external_update} "${cmakeversion_external_update_value}"
+    CMAKE_GENERATOR ${gen}
+    CMAKE_ARGS
+      -Wno-dev
+      --no-warn-unused-cli
+      ${CMAKE_OSX_EXTERNAL_PROJECT_ARGS}
+      ${COMMON_EXTERNAL_PROJECT_ARGS}
+      ${${proj}_CMAKE_OPTIONS}
+## We really do want to install in order to limit # of include paths INSTALL_COMMAND ""
+    DEPENDS
+    ${${proj}_DEPENDENCIES}
+  )
+  set(${extProjName}_DIR
+    ${CMAKE_BINARY_DIR}/${proj}-install/openjpeg-2.0)
+  set(${extProjName}_INCLUDE_DIR
+    ${CMAKE_BINARY_DIR}/${proj}-install/include/openjpeg-2.0)
+  set(${extProjName}_LIB_DIR
+    ${CMAKE_BINARY_DIR}/${proj}-install/lib)
+  set(${extProjName}_LIBRARY
+    ${${extProjName}_LIB_DIR}/libopenjp2.a)
+
+else()
+  if(${USE_SYSTEM_${extProjName}})
+    find_package(${extProjName} ${${extProjName}_REQUIRED_VERSION} REQUIRED)
+    if(NOT ${extProjName}_DIR)
+      message(FATAL_ERROR "To use the system ${extProjName}, set ${extProjName}_DIR")
+    endif()
+    message("USING the system ${extProjName}, set ${extProjName}_DIR=${${extProjName}_DIR}")
+  endif()
+  # The project is provided using ${extProjName}_DIR, nevertheless since other
+  # project may depend on ${extProjName}, let's add an 'empty' one
+  SlicerMacroEmptyExternalProject(${proj} "${${proj}_DEPENDENCIES}")
+endif()
+
+list(APPEND ${CMAKE_PROJECT_NAME}_SUPERBUILD_EP_VARS ${extProjName}_DIR:PATH)
+
+ProjectDependancyPop(CACHED_extProjName extProjName)
+ProjectDependancyPop(CACHED_proj proj)