ENH: Update GDCM to version 2.8.6.

.travis.yml

@@ -39,7 +39,7 @@ matrix:
  osx_image: xcode8.3
  compiler: clang
  env:
- - SDK_INSTALL_PREFIX="$HOME/uroot/usr/local"
+ - SDK_INSTALL_PREFIX="$HOME/sdk-0.15/usr/local"
  - DYLD_LIBRARY_PATH="$SDK_INSTALL_PREFIX/lib"
  - DYLD_FRAMEWORK_PATH="/usr/local/opt/qt5/lib"
 
@@ -55,13 +55,13 @@ matrix:
  - PATH="$QTDIR/bin:$PATH"
  - LDFLAGS=-L$QTDIR/lib
  - CPPFLAGS=-I$QTDIR/include
- - wget -nv --directory-prefix=$HOME http:https://trueta.udg.edu/apt/macosx/devel/0.14/starviewer-sdk-macosx-0.14-4.tar.xz
- - mkdir ~/uroot
- - tar xf ~/starviewer-sdk-macosx-0.14-4.tar.xz -C ~/uroot
+ - wget -nv --directory-prefix=$HOME http:https://trueta.udg.edu/apt/macos/devel/0.15/starviewer-sdk-macos-0.15-0.tar.xz
+ - mkdir ~/sdk-0.15
+ - tar xf ~/starviewer-sdk-macos-0.15-0.tar.xz -C ~/sdk-0.15
 
  script:
  - cd starviewer
  - qmake
- - make -j3 | sed 's/\/Applications\/Xcode\.app\/Contents\/Developer/[xcode]/g' | sed -E 's/\/(Users|home)\/travis\/uroot/[uroot]/g'
+ - make -j3 | sed 's/\/Applications\/Xcode\.app\/Contents\/Developer/[xcode]/g' | sed -E 's/\/(Users|home)\/travis\/sdk-0.15/[sdk]/g'
  - cd tests/auto
  - ./autotests -silent

Dockerfile

@@ -13,12 +13,12 @@ RUN apt-get install -qq libwrap0 libwrap0-dev zlib1g zlib1g-dev libssl-dev
 RUN rm -rf /var/lib/apt/lists/*
 RUN unset DEBIAN_FRONTEND
 
-RUN wget -nv --directory-prefix=/ http:https://trueta.udg.edu/apt/ubuntu/devel/0.14/starviewer-sdk-linux-0.14-4.tar.xz
-RUN mkdir /sdk-0.14
-RUN tar xf /starviewer-sdk-linux-0.14-4.tar.xz -C /sdk-0.14
+RUN wget -nv --directory-prefix=/ http:https://trueta.udg.edu/apt/ubuntu/devel/0.15/starviewer-sdk-linux-0.15-0.tar.xz
+RUN mkdir /sdk-0.15
+RUN tar xf /starviewer-sdk-linux-0.15-0.tar.xz -C /sdk-0.15
 
-ENV SDK_INSTALL_PREFIX /sdk-0.14/usr/local
-ENV LD_LIBRARY_PATH /sdk-0.14/usr/local/lib:/sdk-0.14/usr/local/lib/x86_64-linux-gnu
+ENV SDK_INSTALL_PREFIX /sdk-0.15/usr/local
+ENV LD_LIBRARY_PATH /sdk-0.15/usr/local/lib:/sdk-0.15/usr/local/lib/x86_64-linux-gnu
 
 WORKDIR /starviewer/starviewer
 CMD ["bash"]

appveyor.yml

@@ -1,4 +1,4 @@
-version: 0.14-{build}-{branch}
+version: 0.15-{build}-{branch}
 
 environment:
  SDK_INSTALL_PREFIX: C:\
@@ -19,18 +19,18 @@ install:
 - ps: |
  # Setup precompiled SDK
 
- $source = "http:https://trueta.udg.edu/apt/windows/devel/0.14/starviewer-sdk-win$env:BITS-0.14-5.7z"
- $destination = "c:\starviewer-sdk-win$env:BITS-0.14-5.7z"
+ $source = "http:https://trueta.udg.edu/apt/windows/devel/0.15/starviewer-sdk-win$env:BITS-0.15-0.7z"
+ $destination = "c:\starviewer-sdk-win$env:BITS-0.15-0.7z"
  Invoke-WebRequest $source -OutFile $destination
 
  7z x $destination -oc:\ > 7z-output.txt
 
- $env:PATH = "$env:QTDIR\bin;c:\vtk\7.0.0\bin;c:\gdcm\2.6.4\bin;c:\ThreadWeaver\5.3.0\bin;$env:PATH"
+ $env:PATH = "$env:QTDIR\bin;c:\vtk\7.0.0\bin;c:\gdcm\2.8.6\bin;c:\ThreadWeaver\5.3.0\bin;$env:PATH"
 
 
  # Setup jom
 
- $source = "http:https://ftp.fau.de/qtproject/official_releases/jom/jom_1_1_0.zip"
+ $source = "http:https://ftp.fau.de/qtproject/official_releases/jom/jom_1_1_2.zip"
  $destination = "c:\jom.zip"
  Invoke-WebRequest $source -OutFile $destination
 

sdk/library_versions.txt

@@ -8,5 +8,5 @@ Si existeix vol dir que cal aplicar tots els patch que hi hagi en aquest directo
 - DCMTK 3.6.1-20120515
 - ITK 4.10.0
 - VTK 7.0.0
-- gdcm 2.6.4
+- gdcm 2.8.6
 - ThreadWeaver 5.3.0

sdk/patches/gdcm/makeGdcmReaderRethrowExceptionOnError_ticket_1487.patch

@@ -1,15 +1,23 @@
---- gdcm-2.0.19/Source/DataStructureAndEncodingDefinition/gdcmReader.cxx Tue Jun 12 12:16:11 2012
-+++ gdcm-2.0.19_with_modifications/Source/DataStructureAndEncodingDefinition/gdcmReader.cxx Tue Jun 12 11:39:31 2012
-@@ -657,6 +657,7 @@
+diff --git a/Source/DataStructureAndEncodingDefinition/gdcmReader.cxx b/Source/DataStructureAndEncodingDefinition/gdcmReader.cxx
+index 5c5edf7..93c2a61 100644
+--- a/Source/DataStructureAndEncodingDefinition/gdcmReader.cxx
++++ b/Source/DataStructureAndEncodingDefinition/gdcmReader.cxx
+@@ -671,11 +671,13 @@ bool Reader::InternalReadCommon(const T_Caller &caller)
+ {
+ gdcmDebugMacro( "No way this is DICOM" );
+ success = false;
++ throw ex;
+ }
+ }
  #else
  gdcmDebugMacro( ex.what() ); (void)ex;
  success = false;
 + throw ex;
  #endif /* GDCM_SUPPORT_BROKEN_IMPLEMENTATION */
  }
  catch( Exception &ex )
-@@ -664,11 +665,13 @@
-  (void)ex; //to avoid unreferenced variable warning on release
+@@ -683,11 +685,13 @@ bool Reader::InternalReadCommon(const T_Caller &caller)
+  (void)ex; //to avoid unreferenced variable warning on release
  gdcmDebugMacro( ex.what() );
  success = false;
 + throw ex;
@@ -22,8 +30,8 @@
  }
 
  //if( success ) assert( Stream->eof() );
-@@ -679,11 +682,13 @@
-  (void)ex; //to avoid unreferenced variable warning on release
+@@ -698,11 +702,13 @@ bool Reader::InternalReadCommon(const T_Caller &caller)
+  (void)ex; //to avoid unreferenced variable warning on release
  gdcmDebugMacro( ex.what() );
  success = false;
 + throw ex;
@@ -34,5 +42,5 @@
  success = false;
 + throw;
  }
-  // if( !success )
- //  {
+
+ // FIXME : call this function twice...

sdk/patches/gdcm/makeStringstreamThrowExceptionOnBadAlloc_ticket_1610.patch

@@ -63,7 +63,7 @@ diff -upr gdcm-2.4.3/Source/MediaStorageAndFileFormat/gdcmRLECodec.cxx gdcm-2.4.
  delete[] mybuffer;
  std::stringstream os;
 + os.exceptions(std::ostream::failbit | std::ostream::badbit);
- SetLength( llen );
+ SetLength( (unsigned long)llen );
  #if !defined(NDEBUG)
  const unsigned int * const dimensions = this->GetDimensions();
 @@ -610,6 +611,7 @@ bool RLECodec::Decode(DataElement const
@@ -72,5 +72,5 @@ diff -upr gdcm-2.4.3/Source/MediaStorageAndFileFormat/gdcmRLECodec.cxx gdcm-2.4.
  std::stringstream os;
 + os.exceptions(std::ostream::failbit | std::ostream::badbit);
  bool r = DecodeByStreams(is, os);
- assert( r ); (void)r; //warning removal
- std::string str = os.str();
+ if( !r )
+ {

sdk/scripts/unix/config/gdcm.sh

@@ -3,7 +3,7 @@
 # Call vtk configuration script to make sure VTKCMAKEDIR is set
 . "$SCRIPTS_ROOT/config/vtk.sh"
 
-SOURCE_DIR="$SOURCE_DIR_BASE/GDCM-2.6.4"
+SOURCE_DIR="$SOURCE_DIR_BASE/GDCM-2.8.6"
 
 if [ $BUILD_TYPE = debug ]
 then
@@ -21,9 +21,10 @@ fi
 CMAKE_OPTIONS="-DCMAKE_BUILD_TYPE:STRING=$CMAKE_BUILD_TYPE \
  -DCMAKE_INSTALL_PREFIX:PATH=$SDK_INSTALL_PREFIX \
  -DGDCM_BUILD_SHARED_LIBS:BOOL=TRUE \
+ -DGDCM_BUILD_DOCBOOK_MANPAGES:BOOL=FALSE \
  -DGDCM_USE_VTK:BOOL=TRUE \
  -DVTK_DIR:PATH=$VTKCMAKEDIR"
 
-GDCMCMAKEDIR="$SDK_INSTALL_PREFIX/lib/gdcm-2.6"
+GDCMCMAKEDIR="$SDK_INSTALL_PREFIX/lib/gdcm-2.8"
 GDCMLIBDIR="$SDK_INSTALL_PREFIX/lib"
-GDCMINCLUDEDIR="$SDK_INSTALL_PREFIX/include/gdcm-2.6"
+GDCMINCLUDEDIR="$SDK_INSTALL_PREFIX/include/gdcm-2.8"

sdk/scripts/unix/sdk_download.sh

@@ -48,9 +48,9 @@ do
  'https://www.vtk.org/files/release/7.0/VTK-7.0.0.tar.gz'
  ;;
  gdcm)
- download_and_verify bbf7eeda622cf18499bd162f3b06d0c937a5379f6f3d1445d57b3d4d0070f97e \
- 'gdcm-2.6.4.tar.gz' \
- 'https://github.com/malaterre/GDCM/archive/v2.6.4.tar.gz'
+ download_and_verify f4e611c74ea2b16c9aa28d7fdf3a8678ce926909606705b7cd08c9a5b05d34fc \
+ 'GDCM-2.8.6.tar.gz' \
+ 'https://github.com/malaterre/GDCM/archive/v2.8.6.tar.gz'
  ;;
  itk)
  download_and_verify ea0011fc99a6303427b236c3ceaf54688224350ce1a216b64c9771ab3194b15f \

sdk/scripts/unix/sdk_extract.sh

@@ -29,7 +29,7 @@ do
  tar -C "${SOURCE_DIR_BASE}" -xvf "${DOWNLOAD_PREFIX}/VTK-7.0.0.tar.gz"
  ;;
  gdcm)
- tar -C "${SOURCE_DIR_BASE}" -xvf "${DOWNLOAD_PREFIX}/gdcm-2.6.4.tar.gz"
+ tar -C "${SOURCE_DIR_BASE}" -xvf "${DOWNLOAD_PREFIX}/GDCM-2.8.6.tar.gz"
  ;;
  itk)
  tar -C "${SOURCE_DIR_BASE}" -xvf "${DOWNLOAD_PREFIX}/InsightToolkit-4.10.0.tar.xz"

sdk/scripts/windows/config/gdcm.cmd

@@ -1,26 +1,27 @@
 REM Call vtk configuration script to make sure VtkDir is set
 call "%ScriptsRoot%\config\vtk.cmd"
 
-set SourceDir=%SourceDirPrefix%\gdcm-2.6.4
-set BuildDir=%BuildDirPrefix%\gdcm-2.6.4
+set SourceDir=%SourceDirPrefix%\GDCM-2.8.6
+set BuildDir=%BuildDirPrefix%\GDCM-2.8.6
 
 if %BuildType% == debug (
  set CMakeBuildType=Debug
  set BuildDir=%BuildDir%-deb
- set InstallPrefix=%SdkInstallPrefix%/gdcm/2.6.4d
+ set InstallPrefix=%SdkInstallPrefix%/gdcm/2.8.6d
 )
 if %BuildType% == release (
  set CMakeBuildType=RelWithDebInfo
  set BuildDir=%BuildDir%-rel
- set InstallPrefix=%SdkInstallPrefix%/gdcm/2.6.4
+ set InstallPrefix=%SdkInstallPrefix%/gdcm/2.8.6
 )
 
 REM ============== Nothing should need to be changed below this line ==============
 
 set CMakeOptions=-DCMAKE_BUILD_TYPE:STRING=%CMakeBuildType% ^
  -DCMAKE_INSTALL_PREFIX:PATH="%InstallPrefix%" ^
  -DGDCM_BUILD_SHARED_LIBS:BOOL=TRUE ^
+ -DGDCM_BUILD_DOCBOOK_MANPAGES:BOOL=FALSE ^
  -DGDCM_USE_VTK:BOOL=TRUE ^
  -DVTK_DIR="%VtkDir%"
 
-set GdcmDir=%InstallPrefix%/lib/gdcm-2.6
+set GdcmDir=%InstallPrefix%/lib/gdcm-2.8

sdk/scripts/windows/config/setup.cmd

@@ -5,7 +5,7 @@ REM List of libs to build. Possible values: zlib, dcmtk, vtk, gdcm, itk, ecm, th
 set Libs=zlib dcmtk vtk gdcm itk ecm threadweaver
 
 REM Global prefix of the Starviewer SDK files.
-set Prefix=D:\starviewer-sdk-0.14
+set Prefix=E:\starviewer-sdk-0.15
 
 REM Where the libraries are downloaded.
 set DownloadPrefix=%Prefix%\downloads
@@ -24,17 +24,20 @@ set SdkInstallPrefix=%Prefix%\%Arch%
 
 REM The path where Qt is installed.
 if %Arch% == 32 (
- set QtInstallPrefix=%SystemDrive%\Qt\5.6\msvc2015
+ set QtInstallPrefix=%SystemDrive%\Qt\5.6.3\msvc2015
 ) else (
- set QtInstallPrefix=%SystemDrive%\Qt\5.6\msvc2015_64
+ set QtInstallPrefix=%SystemDrive%\Qt\5.6.3\msvc2015_64
 )
 
 REM How to call CMake.
 set CMakeGenerator=-G "NMake Makefiles"
-set CMake="%ProgramFiles(x86)%\CMake\bin\cmake.exe" %CMakeGenerator%
+set CMake="%ProgramFiles%\CMake\bin\cmake.exe" %CMakeGenerator%
 
 REM How to call git.
 set Git="%ProgramFiles%\Git\bin\git.exe"
 
 REM Needed by CMake to find Qt.
 set CMAKE_PREFIX_PATH=%QtInstallPrefix%
+
+REM How to call jom.
+set Jom="%SystemDrive%\Qt\Tools\QtCreator\bin\jom.exe"

sdk/scripts/windows/libs/cmakebuild.cmd

@@ -15,7 +15,7 @@ if exist "%PatchesRoot%\%BuildLib%" (
 )
 
 %CMake% -Wno-dev %CMakeOptions% "%SourceDir%"
-nmake
-nmake install
+%Jom% -j2
+%Jom% install
 
 popd