# HG changeset patch
# User Sebastien Jodogne <s.jodogne@gmail.com>
# Date 1402040530 -7200
# Node ID 9ee2e7a5efaf7c7ee04b941f90dc6b220fe2b117
# Parent  dcd8a3e4d298f1138e0792e29d701ebbeacc5b30
support of JPEG images

diff -r dcd8a3e4d298 -r 9ee2e7a5efaf CMakeLists.txt
--- a/CMakeLists.txt	Thu Jun 05 21:32:55 2014 +0200
+++ b/CMakeLists.txt	Fri Jun 06 09:42:10 2014 +0200
@@ -18,7 +18,8 @@
 SET(DCMTK_DICTIONARY_DIR "" CACHE PATH "Directory containing the DCMTK dictionaries \"dicom.dic\" and \"private.dic\" (only when using system version of DCMTK)") 
 SET(ALLOW_DOWNLOADS OFF CACHE BOOL "Allow CMake to download packages")
 SET(UNIT_TESTS_WITH_HTTP_CONNEXIONS ON CACHE BOOL "Allow unit tests to make HTTP requests")
-SET(ENABLE_JPEG_LOSSLESS CACHE BOOL "Enable JPEG Lossless decompression")
+SET(ENABLE_JPEG ON CACHE BOOL "Enable JPEG decompression")
+SET(ENABLE_JPEG_LOSSLESS ON CACHE BOOL "Enable JPEG-LS (Lossless) decompression")
 
 # Advanced parameters to fine-tune linking against system libraries
 SET(USE_SYSTEM_JSONCPP ON CACHE BOOL "Use the system version of JsonCpp")
@@ -204,6 +205,13 @@
 endif()
 
 
+if (ENABLE_JPEG)
+  add_definitions(-DORTHANC_JPEG_ENABLED=1)
+else()
+  add_definitions(-DORTHANC_JPEG_ENABLED=0)
+endif()
+
+
 if (ENABLE_JPEG_LOSSLESS)
   add_definitions(-DORTHANC_JPEG_LOSSLESS_ENABLED=1)
 else()
diff -r dcd8a3e4d298 -r 9ee2e7a5efaf OrthancServer/Internals/DicomImageDecoder.cpp
--- a/OrthancServer/Internals/DicomImageDecoder.cpp	Thu Jun 05 21:32:55 2014 +0200
+++ b/OrthancServer/Internals/DicomImageDecoder.cpp	Fri Jun 06 09:42:10 2014 +0200
@@ -256,16 +256,18 @@
     {
       target.SetFormat(PixelFormat_RGB24);
     }
-    else if (bitsStored == 16 && samplesPerPixel == 1 && !isSigned)
+    else if (bitsStored >= 9 && bitsStored <= 16 && samplesPerPixel == 1 && !isSigned)
     {
       target.SetFormat(PixelFormat_Grayscale16);
     }
-    else if (bitsStored == 16 && samplesPerPixel == 1 && isSigned)
+    else if (bitsStored >= 9 && bitsStored <= 16 && samplesPerPixel == 1 && isSigned)
     {
       target.SetFormat(PixelFormat_SignedGrayscale16);
     }
     else
     {
+      LOG(WARNING) << "Unsupported DICOM image: " << bitsStored << "bpp, " 
+      << samplesPerPixel << " channels, " << (isSigned ? "signed" : "unsigned");
       throw OrthancException(ErrorCode_NotImplemented);
     }
   }
diff -r dcd8a3e4d298 -r 9ee2e7a5efaf Resources/CMake/DcmtkConfiguration.cmake
--- a/Resources/CMake/DcmtkConfiguration.cmake	Thu Jun 05 21:32:55 2014 +0200
+++ b/Resources/CMake/DcmtkConfiguration.cmake	Fri Jun 06 09:42:10 2014 +0200
@@ -1,166 +1,181 @@
-# 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/libdcmtk2
-    )
-
-  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()
-
-
-
-if (STATIC_BUILD OR NOT USE_SYSTEM_DCMTK)
-  SET(DCMTK_VERSION_NUMBER 360)
-  SET(DCMTK_SOURCES_DIR ${CMAKE_BINARY_DIR}/dcmtk-3.6.0)
-  DownloadPackage(
-    "219ad631b82031806147e4abbfba4fa4"
-    "http://www.montefiore.ulg.ac.be/~jodogne/Orthanc/ThirdPartyDownloads/dcmtk-3.6.0.zip" 
-    "${DCMTK_SOURCES_DIR}")
-
-  IF(CMAKE_CROSSCOMPILING)
-    SET(C_CHAR_UNSIGNED 1 CACHE INTERNAL "Whether char is unsigned.")
-  ENDIF()
-  SET(DCMTK_SOURCE_DIR ${CMAKE_BINARY_DIR}/dcmtk-3.6.0)
-  include(${DCMTK_SOURCES_DIR}/CMake/CheckFunctionWithHeaderExists.cmake)
-  include(${DCMTK_SOURCES_DIR}/CMake/GenerateDCMTKConfigure.cmake)
-
-  if ("${CMAKE_SYSTEM_VERSION}" STREQUAL "LinuxStandardBase")
-    set(HAVE_SSTREAM 1)
-    set(HAVE_PROTOTYPE_BZERO 1)
-    set(HAVE_PROTOTYPE_GETHOSTNAME 1)
-    set(HAVE_PROTOTYPE_GETSOCKOPT 1)
-    set(HAVE_PROTOTYPE_SETSOCKOPT 1)
-    set(HAVE_PROTOTYPE_CONNECT 1)
-    set(HAVE_PROTOTYPE_BIND 1)
-    set(HAVE_PROTOTYPE_ACCEPT 1)
-    set(HAVE_PROTOTYPE_SETSOCKNAME 1)
-    set(HAVE_PROTOTYPE_GETSOCKNAME 1)
-  endif()
-
-  CONFIGURE_FILE(
-    ${DCMTK_SOURCES_DIR}/CMake/osconfig.h.in
-    ${DCMTK_SOURCES_DIR}/config/include/dcmtk/config/osconfig.h)
-
-  AUX_SOURCE_DIRECTORY(${DCMTK_SOURCES_DIR}/dcmnet/libsrc DCMTK_SOURCES)
-  AUX_SOURCE_DIRECTORY(${DCMTK_SOURCES_DIR}/dcmdata/libsrc DCMTK_SOURCES)
-  AUX_SOURCE_DIRECTORY(${DCMTK_SOURCES_DIR}/ofstd/libsrc DCMTK_SOURCES)
-
-  if (ENABLE_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)
-    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")
-    list(REMOVE_ITEM DCMTK_SOURCES 
-      ${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 
-      ${DCMTK_SOURCES_DIR}/oflog/libsrc/unixsock.cc
-      )
-
-    if (${CMAKE_COMPILER_IS_GNUCXX})
-      # This is a patch for MinGW64
-      execute_process(
-        COMMAND patch -p0 -i ${CMAKE_SOURCE_DIR}/Resources/Patches/dcmtk-mingw64.patch
-        WORKING_DIRECTORY ${CMAKE_BINARY_DIR}
-        )
-    endif()
-
-  endif()
-
-  list(REMOVE_ITEM DCMTK_SOURCES 
-    ${DCMTK_SOURCES_DIR}/dcmdata/libsrc/mkdictbi.cc
-    ${DCMTK_SOURCES_DIR}/dcmdata/libsrc/mkdeftag.cc
-    ${DCMTK_SOURCES_DIR}/dcmdata/libsrc/dcdictbi.cc
-    )
-
-  # This fixes crashes related to the destruction of the DCMTK OFLogger
-  # http://support.dcmtk.org/docs-snapshot/file_macros.html
-  add_definitions(
-    -DLOG4CPLUS_DISABLE_FATAL=1
-    -DDCMTK_VERSION_NUMBER=360
-    )
-
-  include_directories(
-    #${DCMTK_SOURCES_DIR}
-    ${DCMTK_SOURCES_DIR}/config/include
-    ${DCMTK_SOURCES_DIR}/dcmnet/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)
-    add_definitions(-DDCMTK_USE_EMBEDDED_DICTIONARIES=1)
-  else()
-    add_definitions(-DDCMTK_USE_EMBEDDED_DICTIONARIES=0)
-  endif()
-
-  set(DCMTK_DICTIONARIES
-    DICTIONARY_DICOM ${DCMTK_SOURCES_DIR}/dcmdata/data/dicom.dic
-    DICTIONARY_PRIVATE ${DCMTK_SOURCES_DIR}/dcmdata/data/private.dic
-    DICTIONARY_DICONDE ${DCMTK_SOURCES_DIR}/dcmdata/data/diconde.dic
-    )
-
-else()
-  # The following line allows to manually add libraries at the
-  # command-line, which is necessary for Ubuntu/Debian packages
-  set(tmp "${DCMTK_LIBRARIES}")
-  include(FindDCMTK)
-  list(APPEND DCMTK_LIBRARIES "${tmp}")
-
-  include_directories(${DCMTK_INCLUDE_DIR})
-  link_libraries(${DCMTK_LIBRARIES})
-
-  add_definitions(
-    -DHAVE_CONFIG_H=1
-    )
-
-  if (EXISTS "${DCMTK_DIR}/config/cfunix.h")
-    set(DCMTK_CONFIGURATION_FILE "${DCMTK_DIR}/config/cfunix.h")
-  elseif (EXISTS "${DCMTK_DIR}/config/osconfig.h")  # This is for Arch Linux
-    set(DCMTK_CONFIGURATION_FILE "${DCMTK_DIR}/config/osconfig.h")
-  else()
-    message(FATAL_ERROR "Please install libdcmtk1-dev")
-  endif()
-
-  # Autodetection of the version of DCMTK
-  file(STRINGS
-    "${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 
-    ${DCMTK_VERSION_NUMBER1})
-
-  add_definitions(-DDCMTK_USE_EMBEDDED_DICTIONARIES=0)
-
-endif()
-
-add_definitions(-DDCMTK_VERSION_NUMBER=${DCMTK_VERSION_NUMBER})
-message("DCMTK version: ${DCMTK_VERSION_NUMBER}")
+# 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/libdcmtk2
+    )
+
+  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()
+
+
+
+if (STATIC_BUILD OR NOT USE_SYSTEM_DCMTK)
+  SET(DCMTK_VERSION_NUMBER 360)
+  SET(DCMTK_SOURCES_DIR ${CMAKE_BINARY_DIR}/dcmtk-3.6.0)
+  DownloadPackage(
+    "219ad631b82031806147e4abbfba4fa4"
+    "http://www.montefiore.ulg.ac.be/~jodogne/Orthanc/ThirdPartyDownloads/dcmtk-3.6.0.zip" 
+    "${DCMTK_SOURCES_DIR}")
+
+  IF(CMAKE_CROSSCOMPILING)
+    SET(C_CHAR_UNSIGNED 1 CACHE INTERNAL "Whether char is unsigned.")
+  ENDIF()
+  SET(DCMTK_SOURCE_DIR ${CMAKE_BINARY_DIR}/dcmtk-3.6.0)
+  include(${DCMTK_SOURCES_DIR}/CMake/CheckFunctionWithHeaderExists.cmake)
+  include(${DCMTK_SOURCES_DIR}/CMake/GenerateDCMTKConfigure.cmake)
+
+  if ("${CMAKE_SYSTEM_VERSION}" STREQUAL "LinuxStandardBase")
+    set(HAVE_SSTREAM 1)
+    set(HAVE_PROTOTYPE_BZERO 1)
+    set(HAVE_PROTOTYPE_GETHOSTNAME 1)
+    set(HAVE_PROTOTYPE_GETSOCKOPT 1)
+    set(HAVE_PROTOTYPE_SETSOCKOPT 1)
+    set(HAVE_PROTOTYPE_CONNECT 1)
+    set(HAVE_PROTOTYPE_BIND 1)
+    set(HAVE_PROTOTYPE_ACCEPT 1)
+    set(HAVE_PROTOTYPE_SETSOCKNAME 1)
+    set(HAVE_PROTOTYPE_GETSOCKNAME 1)
+  endif()
+
+  CONFIGURE_FILE(
+    ${DCMTK_SOURCES_DIR}/CMake/osconfig.h.in
+    ${DCMTK_SOURCES_DIR}/config/include/dcmtk/config/osconfig.h)
+
+  AUX_SOURCE_DIRECTORY(${DCMTK_SOURCES_DIR}/dcmnet/libsrc DCMTK_SOURCES)
+  AUX_SOURCE_DIRECTORY(${DCMTK_SOURCES_DIR}/dcmdata/libsrc DCMTK_SOURCES)
+  AUX_SOURCE_DIRECTORY(${DCMTK_SOURCES_DIR}/ofstd/libsrc DCMTK_SOURCES)
+
+
+  if (ENABLE_JPEG_LOSSLESS)
+    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
+      ${DCMTK_SOURCES_DIR}/dcmjpeg/libijg16
+      )
+  endif()
+
+
+  if (ENABLE_JPEG_LOSSLESS)
+    AUX_SOURCE_DIRECTORY(${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)
+    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")
+    list(REMOVE_ITEM DCMTK_SOURCES 
+      ${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 
+      ${DCMTK_SOURCES_DIR}/oflog/libsrc/unixsock.cc
+      )
+
+    if (${CMAKE_COMPILER_IS_GNUCXX})
+      # This is a patch for MinGW64
+      execute_process(
+        COMMAND patch -p0 -i ${CMAKE_SOURCE_DIR}/Resources/Patches/dcmtk-mingw64.patch
+        WORKING_DIRECTORY ${CMAKE_BINARY_DIR}
+        )
+    endif()
+
+  endif()
+
+  list(REMOVE_ITEM DCMTK_SOURCES 
+    ${DCMTK_SOURCES_DIR}/dcmdata/libsrc/mkdictbi.cc
+    ${DCMTK_SOURCES_DIR}/dcmdata/libsrc/mkdeftag.cc
+    ${DCMTK_SOURCES_DIR}/dcmdata/libsrc/dcdictbi.cc
+    )
+
+  # This fixes crashes related to the destruction of the DCMTK OFLogger
+  # http://support.dcmtk.org/docs-snapshot/file_macros.html
+  add_definitions(
+    -DLOG4CPLUS_DISABLE_FATAL=1
+    -DDCMTK_VERSION_NUMBER=360
+    )
+
+  include_directories(
+    #${DCMTK_SOURCES_DIR}
+    ${DCMTK_SOURCES_DIR}/config/include
+    ${DCMTK_SOURCES_DIR}/dcmnet/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)
+    add_definitions(-DDCMTK_USE_EMBEDDED_DICTIONARIES=1)
+  else()
+    add_definitions(-DDCMTK_USE_EMBEDDED_DICTIONARIES=0)
+  endif()
+
+  set(DCMTK_DICTIONARIES
+    DICTIONARY_DICOM ${DCMTK_SOURCES_DIR}/dcmdata/data/dicom.dic
+    DICTIONARY_PRIVATE ${DCMTK_SOURCES_DIR}/dcmdata/data/private.dic
+    DICTIONARY_DICONDE ${DCMTK_SOURCES_DIR}/dcmdata/data/diconde.dic
+    )
+
+else()
+  # The following line allows to manually add libraries at the
+  # command-line, which is necessary for Ubuntu/Debian packages
+  set(tmp "${DCMTK_LIBRARIES}")
+  include(FindDCMTK)
+  list(APPEND DCMTK_LIBRARIES "${tmp}")
+
+  include_directories(${DCMTK_INCLUDE_DIR})
+  link_libraries(${DCMTK_LIBRARIES})
+
+  add_definitions(
+    -DHAVE_CONFIG_H=1
+    )
+
+  if (EXISTS "${DCMTK_DIR}/config/cfunix.h")
+    set(DCMTK_CONFIGURATION_FILE "${DCMTK_DIR}/config/cfunix.h")
+  elseif (EXISTS "${DCMTK_DIR}/config/osconfig.h")  # This is for Arch Linux
+    set(DCMTK_CONFIGURATION_FILE "${DCMTK_DIR}/config/osconfig.h")
+  else()
+    message(FATAL_ERROR "Please install libdcmtk1-dev")
+  endif()
+
+  # Autodetection of the version of DCMTK
+  file(STRINGS
+    "${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 
+    ${DCMTK_VERSION_NUMBER1})
+
+  add_definitions(-DDCMTK_USE_EMBEDDED_DICTIONARIES=0)
+
+endif()
+
+add_definitions(-DDCMTK_VERSION_NUMBER=${DCMTK_VERSION_NUMBER})
+message("DCMTK version: ${DCMTK_VERSION_NUMBER}")
diff -r dcd8a3e4d298 -r 9ee2e7a5efaf UnitTestsSources/JpegLossless.cpp
--- a/UnitTestsSources/JpegLossless.cpp	Thu Jun 05 21:32:55 2014 +0200
+++ b/UnitTestsSources/JpegLossless.cpp	Fri Jun 06 09:42:10 2014 +0200
@@ -79,12 +79,13 @@
   }
 #else
   DcmFileFormat fileformat;
-  //if (fileformat.loadFile("IM-0001-1001-0001.dcm").good())
-  ASSERT_TRUE(fileformat.loadFile("tata.dcm").good());
-
+  ASSERT_TRUE(fileformat.loadFile("IM-0001-1001-0001.dcm").good());
+  //ASSERT_TRUE(fileformat.loadFile("tata.dcm").good());
+  //ASSERT_TRUE(fileformat.loadFile("RG2_JPLY").good());
+  
   DcmDataset& dataset = *fileformat.getDataset();
 
-  ASSERT_TRUE(DicomImageDecoder::IsJpegLossless(dataset));
+  //ASSERT_TRUE(DicomImageDecoder::IsJpegLossless(dataset));
 
   ImageBuffer image;
   //DicomImageDecoder::DecodeJpegLossless(image, dataset, 0);