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Fix issue #124 (GET /studies/ID/media fails for certain dicom file)
author Sebastien Jodogne <s.jodogne@gmail.com>
date Thu, 10 Jan 2019 20:55:28 +0100
parents 85999ed092c5
children 0c2a8d5e0097
line wrap: on
line source

if (NOT DEFINED ENABLE_DCMTK_NETWORKING)
    set(ENABLE_DCMTK_NETWORKING ON)
endif()

if (STATIC_BUILD OR NOT USE_SYSTEM_DCMTK)
  if (USE_DCMTK_360)
    SET(DCMTK_VERSION_NUMBER 360)
    SET(DCMTK_PACKAGE_VERSION "3.6.0")
    SET(DCMTK_SOURCES_DIR ${CMAKE_BINARY_DIR}/dcmtk-3.6.0)
    SET(DCMTK_URL "http://www.orthanc-server.com/downloads/third-party/dcmtk-3.6.0.zip")
    SET(DCMTK_MD5 "219ad631b82031806147e4abbfba4fa4")
  else()
    SET(DCMTK_VERSION_NUMBER 362)
    SET(DCMTK_PACKAGE_VERSION "3.6.2")
    SET(DCMTK_SOURCES_DIR ${CMAKE_BINARY_DIR}/dcmtk-3.6.2)
    SET(DCMTK_URL "http://www.orthanc-server.com/downloads/third-party/dcmtk-3.6.2.tar.gz")
    SET(DCMTK_MD5 "d219a4152772985191c9b89d75302d12")

    macro(DCMTK_UNSET)
    endmacro()

    macro(DCMTK_UNSET_CACHE)
    endmacro()

    set(DCMTK_BINARY_DIR ${DCMTK_SOURCES_DIR}/)
    set(DCMTK_CMAKE_INCLUDE ${DCMTK_SOURCES_DIR}/)
    set(DCMTK_WITH_THREADS ON)
    
    add_definitions(-DDCMTK_INSIDE_LOG4CPLUS=1)
  endif()
  
  if (IS_DIRECTORY "${DCMTK_SOURCES_DIR}")
    set(FirstRun OFF)
  else()
    set(FirstRun ON)
  endif()

  DownloadPackage(${DCMTK_MD5} ${DCMTK_URL} "${DCMTK_SOURCES_DIR}")

  
  if (FirstRun)
    if (USE_DCMTK_360)
      # If using DCMTK 3.6.0, backport the "private.dic" file from DCMTK
      # 3.6.2. This adds support for more private tags, and fixes some
      # import problems with Philips MRI Achieva.
      if (USE_DCMTK_362_PRIVATE_DIC)
        message("Using the dictionary of private tags from DCMTK 3.6.2")
        configure_file(
          ${ORTHANC_ROOT}/Resources/Patches/dcmtk-3.6.2-private.dic
          ${DCMTK_SOURCES_DIR}/dcmdata/data/private.dic
          COPYONLY)
      else()
        message("Using the dictionary of private tags from DCMTK 3.6.0")
      endif()
      
      # Patches specific to DCMTK 3.6.0
      message("Applying patch to solve vulnerability in DCMTK 3.6.0")
      execute_process(
        COMMAND ${PATCH_EXECUTABLE} -p0 -N -i
        ${ORTHANC_ROOT}/Resources/Patches/dcmtk-3.6.0-dulparse-vulnerability.patch
        WORKING_DIRECTORY ${CMAKE_BINARY_DIR}
        RESULT_VARIABLE Failure
        )

      if (Failure)
        message(FATAL_ERROR "Error while patching a file")
      endif()

      # This patch is not needed anymore thanks to the following commit
      # (information sent by Jorg Riesmeier on Twitter on 2017-07-19):
      # http://git.dcmtk.org/?p=dcmtk.git;a=commit;h=8df1f5e517b8629ae09088d0935c2a8dd333c76f
      message("Applying patch for speed in DCMTK 3.6.0")
      execute_process(
        COMMAND ${PATCH_EXECUTABLE} -p0 -N -i
        ${ORTHANC_ROOT}/Resources/Patches/dcmtk-3.6.0-speed.patch
        WORKING_DIRECTORY ${CMAKE_BINARY_DIR}
        RESULT_VARIABLE Failure
        )

      if (Failure)
        message(FATAL_ERROR "Error while patching a file")
      endif()

    else()
      # "3.6.2 CXX11 fails on Linux; patch suggestions included"
      # https://forum.dcmtk.org/viewtopic.php?f=3&t=4637
      message("Applying patch to detect mathematic primitives in DCMTK 3.6.2 with C++11")
      execute_process(
        COMMAND ${PATCH_EXECUTABLE} -p0 -N -i
        ${ORTHANC_ROOT}/Resources/Patches/dcmtk-3.6.2-cmath.patch
        WORKING_DIRECTORY ${CMAKE_BINARY_DIR}
        RESULT_VARIABLE Failure
        )

      if (Failure)
        message(FATAL_ERROR "Error while patching a file")
      endif()
    endif()
  else()
    message("The patches for DCMTK have already been applied")
  endif()


  # C_CHAR_UNSIGNED *must* be set before calling "GenerateDCMTKConfigure.cmake"
  IF (CMAKE_CROSSCOMPILING)
    if (CMAKE_COMPILER_IS_GNUCXX AND
        CMAKE_SYSTEM_NAME STREQUAL "Windows")  # MinGW
      SET(C_CHAR_UNSIGNED 1 CACHE INTERNAL "Whether char is unsigned.")

    elseif(CMAKE_SYSTEM_NAME STREQUAL "Emscripten")  # WebAssembly or asm.js

      # Check out "../WebAssembly/ArithmeticTests/" to regenerate the
      # "arith.h" file
      configure_file(
        ${ORTHANC_ROOT}/Resources/WebAssembly/arith.h
        ${DCMTK_SOURCES_DIR}/config/include/dcmtk/config/arith.h
        COPYONLY)

      UNSET(C_CHAR_UNSIGNED CACHE)
      SET(C_CHAR_UNSIGNED 0 CACHE INTERNAL "")

    else()
      message(FATAL_ERROR "Support your platform here")
    endif()
  ENDIF()

  
  if ("${CMAKE_SYSTEM_VERSION}" STREQUAL "LinuxStandardBase")
    SET(DCMTK_ENABLE_CHARSET_CONVERSION "iconv" CACHE STRING "")
    SET(HAVE_SYS_GETTID 0 CACHE INTERNAL "")

    execute_process(
      COMMAND ${PATCH_EXECUTABLE} -p0 -N -i
      ${ORTHANC_ROOT}/Resources/Patches/dcmtk-3.6.2-linux-standard-base.patch
      WORKING_DIRECTORY ${CMAKE_BINARY_DIR}
      RESULT_VARIABLE Failure
      )

    if (FirstRun AND Failure)
      message(FATAL_ERROR "Error while patching a file")
    endif()
  endif()

  SET(DCMTK_SOURCE_DIR ${DCMTK_SOURCES_DIR})
  include(${DCMTK_SOURCES_DIR}/CMake/CheckFunctionWithHeaderExists.cmake)
  include(${DCMTK_SOURCES_DIR}/CMake/GenerateDCMTKConfigure.cmake)


  if (CMAKE_SYSTEM_NAME STREQUAL "Emscripten")  # WebAssembly or
    # asm.js The macros below are not properly discovered by DCMTK
    # when using WebAssembly. Check out "../WebAssembly/arith.h" for
    # how we produced these values. This step MUST be after
    # "GenerateDCMTKConfigure" and before the generation of
    # "osconfig.h".
    UNSET(SIZEOF_VOID_P   CACHE)
    UNSET(SIZEOF_CHAR     CACHE)
    UNSET(SIZEOF_DOUBLE   CACHE)
    UNSET(SIZEOF_FLOAT    CACHE)
    UNSET(SIZEOF_INT      CACHE)
    UNSET(SIZEOF_LONG     CACHE)
    UNSET(SIZEOF_SHORT    CACHE)
    UNSET(SIZEOF_VOID_P   CACHE)

    SET(SIZEOF_VOID_P 4   CACHE INTERNAL "")
    SET(SIZEOF_CHAR 1     CACHE INTERNAL "")
    SET(SIZEOF_DOUBLE 8   CACHE INTERNAL "")
    SET(SIZEOF_FLOAT 4    CACHE INTERNAL "")
    SET(SIZEOF_INT 4      CACHE INTERNAL "")
    SET(SIZEOF_LONG 4     CACHE INTERNAL "")
    SET(SIZEOF_SHORT 2    CACHE INTERNAL "")
    SET(SIZEOF_VOID_P 4   CACHE INTERNAL "")
  endif()


  set(DCMTK_PACKAGE_VERSION_SUFFIX "")
  set(DCMTK_PACKAGE_VERSION_NUMBER ${DCMTK_VERSION_NUMBER})

  CONFIGURE_FILE(
    ${DCMTK_SOURCES_DIR}/CMake/osconfig.h.in
    ${DCMTK_SOURCES_DIR}/config/include/dcmtk/config/osconfig.h)

  if (NOT USE_DCMTK_360)
    if (${CMAKE_SYSTEM_NAME} STREQUAL "Windows")
      link_libraries(netapi32)  # For NetWkstaUserGetInfo@12
      link_libraries(iphlpapi)  # For GetAdaptersInfo@8

      # Configure Wine if cross-compiling for Windows
      if (CMAKE_COMPILER_IS_GNUCXX)
        include(${DCMTK_SOURCES_DIR}/CMake/dcmtkUseWine.cmake)
        FIND_PROGRAM(WINE_WINE_PROGRAM wine)
        FIND_PROGRAM(WINE_WINEPATH_PROGRAM winepath)
        list(APPEND DCMTK_TRY_COMPILE_REQUIRED_CMAKE_FLAGS "-DCMAKE_EXE_LINKER_FLAGS=-static")
      endif()
    endif()

    # This step must be after the generation of "osconfig.h"
    if (NOT CMAKE_SYSTEM_NAME STREQUAL "Emscripten")
      INSPECT_FUNDAMENTAL_ARITHMETIC_TYPES()
    endif()
  endif()

  AUX_SOURCE_DIRECTORY(${DCMTK_SOURCES_DIR}/dcmdata/libsrc DCMTK_SOURCES)
  AUX_SOURCE_DIRECTORY(${DCMTK_SOURCES_DIR}/ofstd/libsrc DCMTK_SOURCES)

  if (ENABLE_DCMTK_NETWORKING)
    AUX_SOURCE_DIRECTORY(${DCMTK_SOURCES_DIR}/dcmnet/libsrc DCMTK_SOURCES)
    include_directories(
      ${DCMTK_SOURCES_DIR}/dcmnet/include
      )
  endif()

  if (ENABLE_DCMTK_JPEG)
    AUX_SOURCE_DIRECTORY(${DCMTK_SOURCES_DIR}/dcmjpeg/libsrc DCMTK_SOURCES)
    AUX_SOURCE_DIRECTORY(${DCMTK_SOURCES_DIR}/dcmjpeg/libijg8 DCMTK_SOURCES)
    AUX_SOURCE_DIRECTORY(${DCMTK_SOURCES_DIR}/dcmjpeg/libijg12 DCMTK_SOURCES)
    AUX_SOURCE_DIRECTORY(${DCMTK_SOURCES_DIR}/dcmjpeg/libijg16 DCMTK_SOURCES)
    include_directories(
      ${DCMTK_SOURCES_DIR}/dcmjpeg/include
      ${DCMTK_SOURCES_DIR}/dcmjpeg/libijg8
      ${DCMTK_SOURCES_DIR}/dcmjpeg/libijg12
      ${DCMTK_SOURCES_DIR}/dcmjpeg/libijg16
      ${DCMTK_SOURCES_DIR}/dcmimgle/include
      )
    list(REMOVE_ITEM DCMTK_SOURCES 
      ${DCMTK_SOURCES_DIR}/dcmjpeg/libsrc/ddpiimpl.cc

      # Disable support for encoding JPEG (modification in Orthanc 1.0.1)
      ${DCMTK_SOURCES_DIR}/dcmjpeg/libsrc/djcodece.cc
      ${DCMTK_SOURCES_DIR}/dcmjpeg/libsrc/djencsv1.cc
      ${DCMTK_SOURCES_DIR}/dcmjpeg/libsrc/djencbas.cc
      ${DCMTK_SOURCES_DIR}/dcmjpeg/libsrc/djencpro.cc
      ${DCMTK_SOURCES_DIR}/dcmjpeg/libsrc/djenclol.cc
      ${DCMTK_SOURCES_DIR}/dcmjpeg/libsrc/djencode.cc
      ${DCMTK_SOURCES_DIR}/dcmjpeg/libsrc/djencext.cc
      ${DCMTK_SOURCES_DIR}/dcmjpeg/libsrc/djencsps.cc
      )
  endif()


  if (ENABLE_DCMTK_JPEG_LOSSLESS)
    AUX_SOURCE_DIRECTORY(${DCMTK_SOURCES_DIR}/dcmjpls/libsrc DCMTK_SOURCES)
    AUX_SOURCE_DIRECTORY(${DCMTK_SOURCES_DIR}/dcmjpls/libcharls DCMTK_SOURCES)
    include_directories(
      ${DCMTK_SOURCES_DIR}/dcmjpeg/include
      ${DCMTK_SOURCES_DIR}/dcmjpls/include
      ${DCMTK_SOURCES_DIR}/dcmjpls/libcharls
      )
    list(REMOVE_ITEM DCMTK_SOURCES 
      ${DCMTK_SOURCES_DIR}/dcmjpls/libsrc/djcodece.cc

      # Disable support for encoding JPEG-LS (modification in Orthanc 1.0.1)
      ${DCMTK_SOURCES_DIR}/dcmjpls/libsrc/djencode.cc
      )
    list(APPEND DCMTK_SOURCES 
      ${DCMTK_SOURCES_DIR}/dcmjpeg/libsrc/djrplol.cc
      )
  endif()


  # Source for the logging facility of DCMTK
  AUX_SOURCE_DIRECTORY(${DCMTK_SOURCES_DIR}/oflog/libsrc DCMTK_SOURCES)
  if (${CMAKE_SYSTEM_NAME} STREQUAL "Linux" OR
      ${CMAKE_SYSTEM_NAME} STREQUAL "Darwin" OR
      ${CMAKE_SYSTEM_NAME} STREQUAL "FreeBSD" OR
      ${CMAKE_SYSTEM_NAME} STREQUAL "kFreeBSD" OR
      ${CMAKE_SYSTEM_NAME} STREQUAL "OpenBSD" OR
      ${CMAKE_SYSTEM_NAME} STREQUAL "Emscripten")
    list(REMOVE_ITEM DCMTK_SOURCES 
      ${DCMTK_SOURCES_DIR}/oflog/libsrc/clfsap.cc
      ${DCMTK_SOURCES_DIR}/oflog/libsrc/windebap.cc
      ${DCMTK_SOURCES_DIR}/oflog/libsrc/winsock.cc
      )

  elseif (${CMAKE_SYSTEM_NAME} STREQUAL "Windows")
    list(REMOVE_ITEM DCMTK_SOURCES 
      ${DCMTK_SOURCES_DIR}/oflog/libsrc/unixsock.cc
      ${DCMTK_SOURCES_DIR}/oflog/libsrc/clfsap.cc
      )

    if (CMAKE_COMPILER_IS_GNUCXX AND
        USE_DCMTK_360)
      # This is a patch for MinGW64
      execute_process(
        COMMAND ${PATCH_EXECUTABLE} -p0 -N -i
        ${ORTHANC_ROOT}/Resources/Patches/dcmtk-3.6.0-mingw64.patch
        WORKING_DIRECTORY ${CMAKE_BINARY_DIR}
        RESULT_VARIABLE Failure
        )

      if (Failure AND FirstRun)
        message(FATAL_ERROR "Error while patching a file")
      endif()
    endif()
  endif()


  if (NOT USE_DCMTK_360 AND
      ORTHANC_SANDBOXED)
    configure_file(
      ${ORTHANC_ROOT}/Resources/WebAssembly/dcdict.h
      ${DCMTK_SOURCES_DIR}/dcmdata/include/dcmtk/dcmdata/dcdict.h
      COPYONLY)
    
    configure_file(
      ${ORTHANC_ROOT}/Resources/WebAssembly/dcdict.cc
      ${DCMTK_SOURCES_DIR}/dcmdata/libsrc/dcdict.cc
      COPYONLY)
  endif()

  
  list(REMOVE_ITEM DCMTK_SOURCES 
    ${DCMTK_SOURCES_DIR}/dcmdata/libsrc/mkdictbi.cc
    ${DCMTK_SOURCES_DIR}/dcmdata/libsrc/mkdeftag.cc
    )

  #set_source_files_properties(${DCMTK_SOURCES}
  #  PROPERTIES COMPILE_DEFINITIONS
  #  "PACKAGE_VERSION=\"${DCMTK_PACKAGE_VERSION}\";PACKAGE_VERSION_NUMBER=\"${DCMTK_VERSION_NUMBER}\"")

  # This fixes crashes related to the destruction of the DCMTK OFLogger
  # http://support.dcmtk.org/docs-snapshot/file_macros.html
  add_definitions(
    -DLOG4CPLUS_DISABLE_FATAL=1
    -DDCMTK_VERSION_NUMBER=${DCMTK_VERSION_NUMBER}
    )

  if (NOT ENABLE_DCMTK_LOG)
    # Disable logging internal to DCMTK
    # https://groups.google.com/d/msg/orthanc-users/v2SzzAmY948/VxT1QVGiBAAJ
    add_definitions(
      -DDCMTK_LOG4CPLUS_DISABLE_FATAL=1
      -DDCMTK_LOG4CPLUS_DISABLE_ERROR=1
      -DDCMTK_LOG4CPLUS_DISABLE_WARN=1
      -DDCMTK_LOG4CPLUS_DISABLE_INFO=1
      -DDCMTK_LOG4CPLUS_DISABLE_DEBUG=1
      )
  endif()

  include_directories(
    #${DCMTK_SOURCES_DIR}
    ${DCMTK_SOURCES_DIR}/config/include
    ${DCMTK_SOURCES_DIR}/ofstd/include
    ${DCMTK_SOURCES_DIR}/oflog/include
    ${DCMTK_SOURCES_DIR}/dcmdata/include
    )

  source_group(ThirdParty\\Dcmtk REGULAR_EXPRESSION ${DCMTK_SOURCES_DIR}/.*)

  set(DCMTK_BUNDLES_LOG4CPLUS 1)

  if (STANDALONE_BUILD)
    set(DCMTK_USE_EMBEDDED_DICTIONARIES 1)
    set(DCMTK_DICTIONARIES
      DICTIONARY_DICOM ${DCMTK_SOURCES_DIR}/dcmdata/data/dicom.dic
      DICTIONARY_PRIVATE ${DCMTK_SOURCES_DIR}/dcmdata/data/private.dic
      DICTIONARY_DICONDE ${DCMTK_SOURCES_DIR}/dcmdata/data/diconde.dic
      )
  else()
    set(DCMTK_USE_EMBEDDED_DICTIONARIES 0)
  endif()

else()
  # The following line allows to manually add libraries at the
  # command-line, which is necessary for Ubuntu/Debian packages
  set(tmp "${DCMTK_LIBRARIES}")
  include(FindDCMTK)
  list(APPEND DCMTK_LIBRARIES "${tmp}")

  include_directories(${DCMTK_INCLUDE_DIRS})

  add_definitions(
    -DHAVE_CONFIG_H=1
    )

  if (EXISTS "${DCMTK_config_INCLUDE_DIR}/cfunix.h")
    set(DCMTK_CONFIGURATION_FILE "${DCMTK_config_INCLUDE_DIR}/cfunix.h")
  elseif (EXISTS "${DCMTK_config_INCLUDE_DIR}/osconfig.h")  # This is for Arch Linux
    set(DCMTK_CONFIGURATION_FILE "${DCMTK_config_INCLUDE_DIR}/osconfig.h")
  elseif (EXISTS "${DCMTK_INCLUDE_DIRS}/dcmtk/config/osconfig.h")  # This is for Debian Buster
    set(DCMTK_CONFIGURATION_FILE "${DCMTK_INCLUDE_DIRS}/dcmtk/config/osconfig.h")
  else()
    message(FATAL_ERROR "Please install libdcmtk*-dev")
  endif()

  message("DCMTK configuration file: ${DCMTK_CONFIGURATION_FILE}")
  
  # Autodetection of the version of DCMTK
  file(STRINGS
    "${DCMTK_CONFIGURATION_FILE}" 
    DCMTK_VERSION_NUMBER1 REGEX
    ".*PACKAGE_VERSION .*")    

  string(REGEX REPLACE
    ".*PACKAGE_VERSION.*\"([0-9]*)\\.([0-9]*)\\.([0-9]*)\"$"
    "\\1\\2\\3" 
    DCMTK_VERSION_NUMBER 
    ${DCMTK_VERSION_NUMBER1})

  set(DCMTK_USE_EMBEDDED_DICTIONARIES 0)
endif()


add_definitions(-DDCMTK_VERSION_NUMBER=${DCMTK_VERSION_NUMBER})
message("DCMTK version: ${DCMTK_VERSION_NUMBER}")


add_definitions(-DDCMTK_USE_EMBEDDED_DICTIONARIES=${DCMTK_USE_EMBEDDED_DICTIONARIES})
if (NOT DCMTK_USE_EMBEDDED_DICTIONARIES)
  # Lookup for DICOM dictionaries, if none is specified by the user
  if (DCMTK_DICTIONARY_DIR STREQUAL "")
    find_path(DCMTK_DICTIONARY_DIR_AUTO dicom.dic
      /usr/share/dcmtk
      /usr/share/libdcmtk1
      /usr/share/libdcmtk2
      /usr/share/libdcmtk3
      /usr/share/libdcmtk4
      /usr/share/libdcmtk5
      /usr/share/libdcmtk6
      /usr/share/libdcmtk7
      /usr/share/libdcmtk8
      /usr/share/libdcmtk9
      /usr/share/libdcmtk10
      /usr/share/libdcmtk11
      /usr/share/libdcmtk12
      /usr/share/libdcmtk13
      /usr/share/libdcmtk14
      /usr/share/libdcmtk15
      /usr/share/libdcmtk16
      /usr/share/libdcmtk17
      /usr/share/libdcmtk18
      /usr/share/libdcmtk19
      /usr/share/libdcmtk20
      /usr/local/share/dcmtk
      )

    if (${DCMTK_DICTIONARY_DIR_AUTO} MATCHES "DCMTK_DICTIONARY_DIR_AUTO-NOTFOUND")
      message(FATAL_ERROR "Cannot locate the DICOM dictionary on this system")
    endif()

    message("Autodetected path to the DICOM dictionaries: ${DCMTK_DICTIONARY_DIR_AUTO}")
    add_definitions(-DDCMTK_DICTIONARY_DIR="${DCMTK_DICTIONARY_DIR_AUTO}")
  else()
    add_definitions(-DDCMTK_DICTIONARY_DIR="${DCMTK_DICTIONARY_DIR}")
  endif()
endif()