sync upstream patches

CMake/ExportConfiguration/GDCMConfig.cmake.in

@@ -37,9 +37,9 @@ get_filename_component(SELF_DIR "${CMAKE_CURRENT_LIST_FILE}" PATH)
 if(EXISTS ${SELF_DIR}/GDCMTargets.cmake)
   # This is an install tree
   include(${SELF_DIR}/GDCMTargets.cmake)
-  get_filename_component(GDCM_INCLUDE_ROOT "${SELF_DIR}/../../@GDCM_INSTALL_INCLUDE_DIR@" ABSOLUTE)
+  get_filename_component(GDCM_INCLUDE_ROOT "${SELF_DIR}/../../../@GDCM_INSTALL_INCLUDE_DIR@" ABSOLUTE)
   set(GDCM_INCLUDE_DIRS ${GDCM_INCLUDE_ROOT})
-  get_filename_component(GDCM_LIB_ROOT "${SELF_DIR}/../../@GDCM_INSTALL_LIB_DIR@" ABSOLUTE)
+  get_filename_component(GDCM_LIB_ROOT "${SELF_DIR}/../../../@GDCM_INSTALL_LIB_DIR@" ABSOLUTE)
   set(GDCM_LIBRARY_DIRS ${GDCM_LIB_ROOT})
 else()
   if(EXISTS ${SELF_DIR}/GDCMExports.cmake)

Source/Common/gdcmSystem.cxx

@@ -461,6 +461,10 @@ std::wstring System::ConvertToUNC(const char *utf8path)
 #endif
 }
 
+#ifndef PATH_MAX
+#define PATH_MAX 4096
+#endif
+
 // return size of file; also returns zero if no file exists
 size_t System::FileSize(const char* filename)
 {

Source/DataDictionary/gdcmGlobal.cxx

@@ -138,6 +138,10 @@ bool Global::Prepend(const char *path)
 #define PATH_MAX 4096
 #endif
 
+#ifndef PATH_MAX
+#define PATH_MAX 4096
+#endif
+
 const char *Global::Locate(const char *resfile) const
 {
 #ifdef _WIN32

Utilities/doxygen/CMakeLists.txt

@@ -160,6 +160,7 @@ if(GDCM_DOCUMENTATION)
     install(FILES
       ${CMAKE_CURRENT_BINARY_DIR}/latex/gdcm-${GDCM_VERSION}.pdf
       DESTINATION ${GDCM_INSTALL_DOC_DIR}
+      RENAME gdcm-${GDCM_MAJOR_VERSION}.pdf
     )
     add_dependencies(DoxygenDoc GDCMDoxygenPDF)
   else()

Utilities/doxygen/vtk/CMakeLists.txt

@@ -22,7 +22,7 @@ mark_as_advanced(VTK_DIR)
     set (QT_TAG_FILE "${CMAKE_CURRENT_BINARY_DIR}/Qt.tag")
   endif ()
   set(BUILD_DOXYGEN ON)
-  set(DOCUMENTATION_DOWNLOAD_VTK_TAGFILE ON)
+  set(DOCUMENTATION_DOWNLOAD_VTK_TAGFILE OFF)
   set(DOCUMENTATION_HTML_TARZ ON)
   set(DOXYGEN_PROJECT_NAME "vtkgdcm")
   if(VTK_SOURCE_DIR)
@@ -35,8 +35,8 @@ mark_as_advanced(VTK_DIR)
       # sudo apt-get install vtk-doc
   if(EXISTS "/usr/share/doc/vtk-doc/html")
   set(DOXYGEN_SOURCE_DIR "/usr/share/doc/vtk-doc/html")
-  elseif(EXISTS "/usr/share/doc/vtk6-doc/doxygen")
-  set(DOXYGEN_SOURCE_DIR "/usr/share/doc/vtk6-doc/doxygen")
+  elseif(EXISTS "/usr/share/doc/vtk9/doxygen")
+  set(DOXYGEN_SOURCE_DIR "/usr/share/doc/vtk9/doxygen")
   else()
   message(ERROR "DOXYGEN_SOURCE_DIR need to be set.")
   endif()
@@ -97,7 +97,7 @@ mark_as_advanced(VTK_DIR)
     get_filename_component(DOT_PATH ${DOT} PATH)
   endif()
 
-  set(TAGFILES "\"${CMAKE_CURRENT_BINARY_DIR}/vtkNightlyDoc.tag=http://www.vtk.org/doc/nightly/html\"")
+  #set(TAGFILES "\"${CMAKE_CURRENT_BINARY_DIR}/vtkNightlyDoc.tag=http://www.vtk.org/doc/nightly/html\"")
   if(INCLUDE_QT_DOCUMENTATION)
     set (TAGFILES "${TAGFILES} \"${QT_TAG_FILE}=http://doc.trolltech.com/4.2\"")
   endif()

Utilities/doxygen/vtk/doc_makeall.sh.in

@@ -42,7 +42,7 @@ export PROJECT_NAME=@DOXYGEN_PROJECT_NAME@
 # Example:
 #   PATH_TO_VTK_DOX_SCRIPTS=@CMAKE_CURRENT_SOURCE_DIR@
 #
-export PATH_TO_VTK_DOX_SCRIPTS="@DOXYGEN_SOURCE_DIR@"
+export PATH_TO_VTK_DOX_SCRIPTS=/usr/share/vtk9/doxygen/
 
 export PATH_TO_VTKGDCM_FINAL_PATH="@VTKGDCM_FINAL_PATH@"
 
@@ -169,12 +169,12 @@ cd "${DOXTEMP}" || echoexit "Cannot find Doxygen output directory: ${DOXTEMP}"
 # Convert the VTK headers to the Doxygen format.
 echo "Convert the VTK headers to the Doxygen format."
 if test "x$PERL_PROG" != "xNOTFOUND" ; then
-    $PERL_PROG "$PATH_TO_VTK_DOX_SCRIPTS/doc_header2doxygen.pl" \
+    $PERL_PROG "$PATH_TO_VTK_DOX_SCRIPTS/doc_header2doxygen.pl"  \
         --to "$INTERMEDIATE_DOX_DIR" \
         --relativeto "@DOXYGEN_SOURCE_LOCATIONS_DIR@" \
         @DOXYGEN_SOURCE_LOCATIONS@ || echoexit "Problem converting VTK headers"
     if test "x@DOXYGEN_BINARY_LOCATIONS_DIR@" != "x"; then
-      $PERL_PROG "$PATH_TO_VTK_DOX_SCRIPTS/doc_header2doxygen.pl" \
+    $PERL_PROG "$PATH_TO_VTK_DOX_SCRIPTS/doc_header2doxygen.pl" \
         --to "$INTERMEDIATE_DOX_DIR" \
         --relativeto "@DOXYGEN_BINARY_LOCATIONS_DIR@" \
         @DOXYGEN_BINARY_LOCATIONS@ || echoexit "Problem converting VTK headers"
@@ -186,13 +186,16 @@ echo "Convert the VTK headers to the Doxygen format - done"
 # Build the full-text index.
 echo "Build the full-text index."
 if test "x$PERL_PROG" != "xNOTFOUND" ; then
+   cp "$PATH_TO_VTK_DOX_SCRIPTS/doc_index.stop" doc_index.stop
+
     $PERL_PROG "$PATH_TO_VTK_DOX_SCRIPTS/doc_index.pl" \
         --project "$PROJECT_NAME" \
-        --stop  "$PATH_TO_VTK_DOX_SCRIPTS/doc_index.stop" \
+        --stop  "doc_index.stop" \
         --store "doc_""$PROJECT_NAME""_index.dox" \
         --to "$INTERMEDIATE_DOX_DIR" \
         @DOXYGEN_SOURCE_LOCATIONS@ \
         @DOXYGEN_BINARY_LOCATIONS@ || echoexit "Problem building full-text index"
+   rm -f doc_index.stop
 fi
 echo "Build the full-text index - done"
 
@@ -201,7 +204,7 @@ echo "Build the full-text index - done"
 #  # demos that use that class.
 
 #  if test "x$PERL_PROG" != "xNOTFOUND" ; then
-#      $PERL_PROG $PATH_TO_VTK_DOX_SCRIPTS/doc_class2example.pl \
+#      gzip -dc $PATH_TO_VTK_DOX_SCRIPTS/doc_class2example.pl | $PERL_PROG - \
 #          --datamatch "\W((VTK|ParaView)_DATA_ROOT|(VTK|MedVIP)Data|(vtk)?GetDataRoot|ExpandDataFileName)\W" \
 #          --dataicon "paper-clip.gif" \
 #          --dirmatch "^demos$" \

Utilities/doxygen/vtk/doxyfile.in

@@ -23,6 +23,7 @@ PDF_HYPERLINKS       = YES
 HAVE_DOT             = YES
 #HAVE_DOT            = NO
 DOT_PATH             = "@DOT_PATH@"
+DOT_IMAGE_FORMAT     = svg
 CLASS_GRAPH          = YES
 COLLABORATION_GRAPH  = YES
 TEMPLATE_RELATIONS   = YES

debian/upstream/metadata

@@ -1,14 +0,0 @@
-Reference:
- Author: >
-  David Rodríguez González and Trevor Carpenter and Jano I. van Hemert
-  and Joanna Wardlaw
- Title: An open source toolkit for medical imaging de-identification
- Journal: European Radiology
- Year: 2010
- Volume: 20
- Number: 8
- Pages: 1896-1904
- DOI: 10.1007/s00330-010-1745-3
- PMID: 20204640
- URL: http://www.springerlink.com/content/j20844338623m167
- eprint: http://www.springerlink.com/content/j20844338623m167/fulltext.pdf