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commit 600fd4e1ba92eed61c6892920dff5dde50b62a82 Author: Gert Wollny <[email protected]> Date: Sat Jan 30 20:57:57 2016 +0100 Imported Upstream version 2.6.3 --- .travis.yml | 62 +++++++++++++++++----- AUTHORS | 2 +- CMake/FindJavaProperties.cmake | 2 +- CMake/FindOpenJPEG.cmake | 1 + CMake/FindUUID.cmake | 8 +-- CMake/UseCSharp.cmake | 9 +++- CMake/UseJavaTest.cmake | 14 +++-- CMake/UsePythonTest.cmake | 27 ++++++++-- CMakeLists.txt | 2 +- Copyright.txt | 2 +- Examples/Csharp/DecompressImage.cs | 5 ++ Examples/Java/CMakeLists.txt | 10 ++-- Examples/Python/ConvertNumpy.py | 4 +- README.txt | 20 +++---- Source/Common/CMakeLists.txt | 6 +++ Source/Common/gdcmBoxRegion.cxx | 2 +- Source/Common/gdcmConfigure.h.in | 1 + Source/Common/gdcmDummyValueGenerator.cxx | 2 +- Source/Common/gdcmSystem.cxx | 57 ++------------------ .../gdcmDataSet.h | 19 ++++--- .../DataStructureAndEncodingDefinition/gdcmVR.cxx | 9 ++-- Source/DataStructureAndEncodingDefinition/gdcmVR.h | 15 +++++- .../MediaStorageAndFileFormat/gdcmImageHelper.cxx | 4 +- .../MediaStorageAndFileFormat/gdcmJPEGLSCodec.cxx | 2 +- Source/MediaStorageAndFileFormat/gdcmJSON.cxx | 32 +++++++---- Source/MediaStorageAndFileFormat/gdcmRLECodec.cxx | 2 +- Source/MediaStorageAndFileFormat/gdcmSegment.cxx | 2 +- .../MediaStorageAndFileFormat/gdcmSerieHelper.cxx | 2 +- .../MediaStorageAndFileFormat/gdcmStringFilter.cxx | 1 + .../gdcmSurfaceReader.cxx | 2 +- .../MediaStorageAndFileFormat/gdcmXMLPrinter.cxx | 1 + Testing/Source/Common/Cxx/TestByteSwap.cxx | 2 +- Testing/Source/Common/Cxx/TestSystem1.cxx | 2 +- Testing/Source/Common/Python/CMakeLists.txt | 8 ++- Testing/Source/Common/Python/TestDirectory.py | 2 +- Testing/Source/Common/Python/TestTesting.py | 2 +- .../Java/CMakeLists.txt | 11 ++-- .../Python/CMakeLists.txt | 7 ++- .../Python/TestReader.py | 14 ++--- .../Python/TestTag.py | 2 +- .../Cxx/TestPhotometricInterpretation.cxx | 2 +- .../Python/CMakeLists.txt | 23 +++++--- .../Python/TestAnonymizer.py | 22 ++++---- .../Python/TestDCMTKMD5.py | 8 +-- .../Python/TestIPPSorter.py | 2 +- .../Python/TestImageReader.py | 8 +-- .../Python/TestKakaduDecompressionMD5.py | 10 ++-- .../Python/TestModifyFields.py | 14 ++--- .../Python/TestOrientation.py | 10 ++-- .../Python/TestPythonFilter.py | 12 ++--- .../Python/TestStringFilter.py | 12 ++--- .../Cxx/TestFindPatientRootQuery.cxx | 2 +- .../Cxx/TestFindStudyRootQuery.cxx | 2 +- Utilities/VTK/CMakeLists.txt | 6 ++- .../VTK/Testing/Python/TestvtkGDCMImageWriter.py | 2 +- .../Python/TestvtkGDCMThreadedImageReader.py | 6 +-- .../Python/TestvtkGDCMThreadedImageReader2.py | 2 +- Utilities/VTK/vtkGDCMThreadedImageReader.cxx | 8 +-- Utilities/doxygen/CMakeLists.txt | 35 +++++++++++- Utilities/doxygen/man/gdcm2pnm.xml | 2 +- Utilities/doxygen/man/gdcm2vtk.xml | 2 +- Utilities/doxygen/man/gdcmanon.xml | 2 +- Utilities/doxygen/man/gdcmconv.xml | 2 +- Utilities/doxygen/man/gdcmdiff.xml | 2 +- Utilities/doxygen/man/gdcmdump.xml | 2 +- Utilities/doxygen/man/gdcmgendir.xml | 2 +- Utilities/doxygen/man/gdcmimg.xml | 2 +- Utilities/doxygen/man/gdcminfo.xml | 2 +- Utilities/doxygen/man/gdcmpap3.xml | 2 +- Utilities/doxygen/man/gdcmpdf.xml | 2 +- Utilities/doxygen/man/gdcmraw.xml | 2 +- Utilities/doxygen/man/gdcmscanner.xml | 2 +- Utilities/doxygen/man/gdcmscu.xml | 2 +- Utilities/doxygen/man/gdcmtar.xml | 2 +- Utilities/doxygen/man/gdcmviewer.xml | 2 +- Utilities/doxygen/man/gdcmxml.xml | 2 +- Utilities/doxygen/vtk/CMakeLists.txt | 8 ++- Utilities/gdcmopenjpeg-v1/libopenjpeg/t2.c | 6 ++- Utilities/gdcmzlib/gzio.c | 4 +- Wrapping/Csharp/gdcm.i | 6 +++ Wrapping/Java/CMakeLists.txt | 15 +++--- Wrapping/Java/gdcm.i | 17 ++++++ Wrapping/Python/CMakeLists.txt | 7 +++ Wrapping/Python/TestWrap.py | 15 ++++++ Wrapping/Python/gdcmPythonFilter.h | 2 +- Wrapping/Python/gdcmswig.i | 13 ++++- appveyor.yml | 52 ++++++++++++------ 87 files changed, 468 insertions(+), 274 deletions(-) diff --git a/.travis.yml b/.travis.yml index 9c3b659..5657d4b 100644 --- a/.travis.yml +++ b/.travis.yml @@ -1,3 +1,5 @@ +# https://docs.travis-ci.com/user/environment-variables/#Default-Environment-Variables +# https://github.com/travis-ci/travis-ci/issues/3505 language: cpp # Use the faster container-based infrastructure. sudo: false @@ -5,33 +7,44 @@ env: global: # The next declaration is the encrypted COVERITY_SCAN_TOKEN, created # via the "travis encrypt" command using the project repo's public key - - secure: "ClIqhtIIfQPhil8GH9bnJg70rvJfuYs7Z2Aq2SrdwQsIFNvvfFD5pVxQiaYbZI3nxNclggQ50BmGB96e6jLxbbd/xlIOjcU19W2nzyP6LGkXFHDHm8FwhqqDNpfYvirAOfqgjqf7khRe3ajF33jhrLrhb5QOO5640N93pdChu1sAvI0LZv8JFIUcN7A7To3+WYc7H4CK3U8B2V8nzqcBSHDZNBGAdeVdmldwrlBtQeWBg5wJAEzzUHn0x+kltqvuoPYi2ShpaUkEfHeUWYhOT1uoyXNRAqHXiM1jhiw3JCkqaf7sUKLzyx0ozjTnYntNMggtBzavKjuYg6RhdlNdNbdsi2nxrycCOyCZcF+d4limq+yDMqoP7g/DnPag7XFgjkG/ThULPu+pEK/6nV1NqGNWFu1CqgAwPW7hGbIUADPsMEb+Bz2L2KUof2wU1cdvGK4fzsM9Qpdipbagghn4b5eGtvyBzY [...] + - secure: ClIqhtIIfQPhil8GH9bnJg70rvJfuYs7Z2Aq2SrdwQsIFNvvfFD5pVxQiaYbZI3nxNclggQ50BmGB96e6jLxbbd/xlIOjcU19W2nzyP6LGkXFHDHm8FwhqqDNpfYvirAOfqgjqf7khRe3ajF33jhrLrhb5QOO5640N93pdChu1sAvI0LZv8JFIUcN7A7To3+WYc7H4CK3U8B2V8nzqcBSHDZNBGAdeVdmldwrlBtQeWBg5wJAEzzUHn0x+kltqvuoPYi2ShpaUkEfHeUWYhOT1uoyXNRAqHXiM1jhiw3JCkqaf7sUKLzyx0ozjTnYntNMggtBzavKjuYg6RhdlNdNbdsi2nxrycCOyCZcF+d4limq+yDMqoP7g/DnPag7XFgjkG/ThULPu+pEK/6nV1NqGNWFu1CqgAwPW7hGbIUADPsMEb+Bz2L2KUof2wU1cdvGK4fzsM9Qpdipbagghn4b5eGtvyBzYz [...] # -m32 is not supported # no poppler, openjpeg, uuid, json # no swig + +# using debian-sid I get: +# /usr/bin/ld: BFD (GNU Binutils for Ubuntu) 2.22 internal error, aborting at +# ../../bfd/reloc.c line 443 in bfd_get_reloc_size matrix: fast_finish: true include: - compiler: gcc os: linux env: + - CFLAGS="-g -O2" + - CXXFLAGS="-g -O2" + - B_NAME=default + - compiler: gcc + os: linux + addons: {apt: {packages: [default-jdk, mono-devel, swig, libcharls-dev, libvtk5-dev, libopenjpeg-dev, libexpat-dev, libz-dev, uuid-dev, python-all-dev, libpoppler-dev, xsltproc, dcmtk]}} + env: - CFLAGS="-Wall -Wextra -m64" - CXXFLAGS="-Wall -Wextra -m64" - - CMAKE_EXTRA="-DGDCM_USE_SYSTEM_OPENSSL:BOOL=ON -DGDCM_WRAP_PYTHON:BOOL=OFF -DGDCM_WRAP_CSHARP:BOOL=OFF -DGDCM_WRAP_JAVA:BOOL=OFF -DGDCM_WRAP_PHP:BOOL=OFF -DGDCM_USE_SYSTEM_EXPAT:BOOL=ON -DGDCM_USE_SYSTEM_JSON:BOOL=OFF -DGDCM_USE_SYSTEM_LIBXML2:BOOL=ON -DGDCM_USE_SYSTEM_OPENJPEG:BOOL=OFF -DGDCM_USE_SYSTEM_POPPLER:BOOL=OFF -DGDCM_USE_SYSTEM_UUID:BOOL=OFF -DGDCM_USE_SYSTEM_ZLIB:BOOL=ON" + - CMAKE_EXTRA="-DGDCM_USE_SYSTEM_OPENSSL:BOOL=ON -DGDCM_WRAP_PYTHON:BOOL=ON -DGDCM_WRAP_CSHARP:BOOL=ON -DGDCM_WRAP_JAVA:BOOL=ON -DGDCM_WRAP_PHP:BOOL=OFF -DGDCM_USE_SYSTEM_EXPAT:BOOL=ON -DGDCM_USE_SYSTEM_JSON:BOOL=OFF -DGDCM_USE_SYSTEM_LIBXML2:BOOL=ON -DGDCM_USE_SYSTEM_OPENJPEG:BOOL=ON -DGDCM_USE_SYSTEM_POPPLER:BOOL=ON -DGDCM_USE_SYSTEM_UUID:BOOL=ON -DGDCM_USE_SYSTEM_ZLIB:BOOL=ON -DGDCM_WEAK_SWIG_CHECK:BOOL=ON -DGDCM_LEGACY_SILENT:BOOL=ON" - B_NAME=system - compiler: clang os: linux env: - - CFLAGS="-Wall -Wextra -m64 -fsanitize=address,undefined,shift" - - CXXFLAGS="-g -Wall -Wextra -m64 -fsanitize=address,undefined,shift" + - CFLAGS="-g -O0 -Wall -Wextra -m64 -fsanitize=address,undefined,shift" + - CXXFLAGS="-g -O0 -Wall -Wextra -m64 -fsanitize=address,undefined,shift" - B_NAME=fsanitize - compiler: clang os: osx env: - CFLAGS="-Wall -Wextra" # -m64 -fsanitize=address,undefined - CXXFLAGS="-Wall -Wextra" # -m64 -fsanitize=address,undefined - - B_NAME=fsanitize + - B_NAME=default before_install: #- env @@ -39,25 +52,50 @@ before_install: #- swig -version # do not run the full test suite for now - mv Testing/Data Testing/Data.old + - if [ "$B_NAME" == "system" ]; then wget http://kakadusoftware.com/wp-content/uploads/2014/06/KDU77_Demo_Apps_for_Linux-x86-64_150710.zip; fi + - if [ "$B_NAME" == "system" ]; then unzip KDU77_Demo_Apps_for_Linux-x86-64_150710.zip; fi + - if [ "$B_NAME" == "system" ]; then export PATH=$PATH:$PWD/KDU77_Demo_Apps_for_Linux-x86-64_150710; fi install: true -before_script: true -script: - - cmake -Wno-dev -G "Unix Makefiles" -DCMAKE_BUILD_TYPE:STRING=None -DGDCM_BUILD_TESTING:BOOL=ON -DGDCM_BUILD_APPLICATIONS:BOOL=ON -DGDCM_BUILD_SHARED_LIBS:BOOL=ON -DGDCM_ALLOW_INSOURCE_BUILD:BOOL=ON -DBUILDNAME:STRING=${TRAVIS_OS_NAME}-${TRAVIS_BRANCH}-${B_NAME} ${CMAKE_EXTRA} . +before_script: + - cmake -Wno-dev -G "Unix Makefiles" -DCMAKE_BUILD_TYPE:STRING=None -DGDCM_BUILD_TESTING:BOOL=ON -DGDCM_BUILD_APPLICATIONS:BOOL=ON -DGDCM_BUILD_SHARED_LIBS:BOOL=ON -DBUILDNAME:STRING=${TRAVIS_OS_NAME}-${TRAVIS_BRANCH}-${B_NAME} ${CMAKE_EXTRA} . - ctest -D ExperimentalStart +script: - ctest -D ExperimentalBuild -j2 - ctest -D ExperimentalTest -j2 || true +after_success: - ctest -D ExperimentalSubmit || true - -after_success: true + # prefer after_success since before_deploy is not called (conditions unmet) + - cpack -G TGZ + - cpack -G TBZ2 after_failure: true + +before_deploy: +- VTAG=$(echo $TRAVIS_TAG | cut -f2 -dv) +deploy: + edge: true + provider: releases + api_key: + secure: R5+dbibdcgPHq6cAPC8uepifDuS3yjZu2dBB2oSeQtBZTAeN1VIfJMrF8TeQDqj2GC28RHxXm4BHwdJ2FUpBXjOS2eUE6Mto1Rbbvfi63MREnFPIAWkNyLtR2Jxq/Gzb8X05PbCWGwCNvX9eeo+qcWTpczuQvJ+/bds7MyRsk45+sUc+j7rglAbxewgijsXebCkObwaXmhqTYJwrvf2lyEnA2Jo1gL2WmK6iPjHvTOVS9JfBMqVRmlk7j8efnqag8fMCzNp1Ess5wBy5Jf58qvVs7RuuBi16s7vOOBtb9xVjcDB1KaAxc/dDQGQhRkrveBtH18ZpFrArOj6DBPbupS3+xuU4ywdYbCuGnvdpRFafBc+iNU4M81crkFUDmSPEQChBnL4wwpaYaQ1LlgdlF0r9/Rlu2/iqKe4t7rdZnkQqQ/3SNNf+x4AKnGmaSGasV/VUXstTGVrtl7hsDMzSdrVCXODao0SR [...] + file: + - GDCM-$VTAG-Linux-x86_64.tar.gz + - GDCM-$VTAG-Linux-x86_64.tar.bz2 + skip_cleanup: true + on: + repo: malaterre/GDCM + condition: $B_NAME = default + all_branches: true + tags: true + +# final after_script: true addons: coverity_scan: project: - name: "malaterre/GDCM" + name: malaterre/GDCM description: "Grassroots DICOM" notification_email: [email protected] - build_command_prepend: cmake -G "Unix Makefiles" -DCMAKE_BUILD_TYPE:STRING=RelWithDebInfo -DGDCM_BUILD_SHARED_LIBS:BOOL=ON -DGDCM_ALLOW_INSOURCE_BUILD:BOOL=ON .. + build_command_prepend: cmake -G "Unix Makefiles" -DCMAKE_BUILD_TYPE:STRING=RelWithDebInfo + -DGDCM_BUILD_SHARED_LIBS:BOOL=ON .. build_command: cmake --build . branch_pattern: coverity_scan diff --git a/AUTHORS b/AUTHORS index b7516bc..e37e40b 100644 --- a/AUTHORS +++ b/AUTHORS @@ -18,7 +18,7 @@ GDCM 2.x: Jean-Pierre Roux : Developer, maintain gdcmDataExtra Christina Rossmanith : Contributor (Siemens CSA) Christopher W Treml : Contributor (C#) - Joel Spaltenstein : Developer (MacOSX) + Joel Spaltenstein : Developer (Mac OS X) GDCM 1.x (Developpers and contributors, alphabetical order) diff --git a/CMake/FindJavaProperties.cmake b/CMake/FindJavaProperties.cmake index b60eb5d..10f28cf 100644 --- a/CMake/FindJavaProperties.cmake +++ b/CMake/FindJavaProperties.cmake @@ -57,7 +57,7 @@ if(${current_list_path}/GetSystemProperty.java IS_NEWER_THAN ${CMAKE_BINARY_DIR} #message("${current_list_path}/GetSystemProperty.java") #message("${CMAKE_CURRENT_BINARY_DIR}/GetSystemProperty.class") execute_process( - COMMAND ${Java_JAVAC_EXECUTABLE} -source 1.5 -target 1.5 + COMMAND ${Java_JAVAC_EXECUTABLE} -source ${GDCM_JAVA_SOURCE_VERSION} -target ${GDCM_JAVA_TARGET_VERSION} ${current_list_path}/GetSystemProperty.java -d ${CMAKE_BINARY_DIR} WORKING_DIRECTORY ${CMAKE_BINARY_DIR} ) diff --git a/CMake/FindOpenJPEG.cmake b/CMake/FindOpenJPEG.cmake index 26b169f..010f22c 100644 --- a/CMake/FindOpenJPEG.cmake +++ b/CMake/FindOpenJPEG.cmake @@ -20,6 +20,7 @@ # Try first to locate a cmake config file find_package(OpenJPEG QUIET NO_MODULE) +mark_as_advanced(OpenJPEG_DIR) if( NOT OpenJPEG_DIR ) set(OPENJPEG_MAJOR_VERSION 1) # FIXME ? diff --git a/CMake/FindUUID.cmake b/CMake/FindUUID.cmake index 45c7244..f72ddca 100644 --- a/CMake/FindUUID.cmake +++ b/CMake/FindUUID.cmake @@ -7,18 +7,14 @@ # also defined, but not for general use are # UUID_LIBRARY, where to find the UUID library. # -# Copyright (c) 2006-2011 Mathieu Malaterre <[email protected]> +# Copyright (c) 2006-2016 Mathieu Malaterre <[email protected]> # # Redistribution and use is allowed according to the terms of the New # BSD license. # For details see the accompanying COPYING-CMAKE-SCRIPTS file. # -# On MacOSX we have: -# $ nm -g /usr/lib/libSystem.dylib | grep uuid_generate -# 000b3aeb T _uuid_generate -# 0003e67e T _uuid_generate_random -# 000b37a1 T _uuid_generate_time +# On Mac OS X the uuid functions are in the System library. if(APPLE) set(UUID_LIBRARY_VAR System) else() diff --git a/CMake/UseCSharp.cmake b/CMake/UseCSharp.cmake index 3216b84..ed49a44 100644 --- a/CMake/UseCSharp.cmake +++ b/CMake/UseCSharp.cmake @@ -56,11 +56,16 @@ endif() if(WIN32) # There is a subttle issue when compiling on 64bits platform using a 32bits compiler # See bug ID: 3510023 (BadImageFormatException: An attempt was made to load a progr) - set(CSC_ACCEPTS_PLATFORM_FLAG 0) if(CMAKE_CSHARP_COMPILER) execute_process(COMMAND "${CMAKE_CSHARP_COMPILER}" "/?" OUTPUT_VARIABLE CSC_HELP) + # get version (no /version, so use /help output): + if("${CSC_HELP}" MATCHES "Compiler version") + string(REGEX REPLACE ".*Compiler version ([0-9\\.]+).*" "\\1" VERSION_STRING + "${CSC_HELP}") + message(STATUS "Comp version: ${VERSION_STRING}") + endif() # when cmd locale is in French it displays: "/platform:<chaine>" in english: "/platform:<string>" # so only regex match in /platform: if("${CSC_HELP}" MATCHES "/platform:") @@ -175,7 +180,7 @@ macro(CSHARP_LINK_LIBRARIES name) ARGS ${CSHARP_EXECUTABLE_${name}_ARGS} WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR} #DEPENDS ${csharp_cs_sources} - COMMENT "Create HelloWorld.exe" + COMMENT "Create ${name}.exe" ) #message("DEBUG2:${csharp_libraries_depends}") diff --git a/CMake/UseJavaTest.cmake b/CMake/UseJavaTest.cmake index a48998a..ea2ca65 100644 --- a/CMake/UseJavaTest.cmake +++ b/CMake/UseJavaTest.cmake @@ -18,6 +18,10 @@ # UseCSharp.cmake macro(ADD_JAVA_TEST TESTNAME FILENAME) + set(_sep ":") + if(WIN32) + set(_sep "\\;") + endif() get_source_file_property(loc ${FILENAME}.class LOCATION) get_source_file_property(pyenv ${FILENAME}.class RUNTIMEPATH) get_source_file_property(theclasspath ${FILENAME}.class CLASSPATH) @@ -36,7 +40,7 @@ macro(ADD_JAVA_TEST TESTNAME FILENAME) endif() else() if(pyenv) - set(pyenv ${pyenv}:${LIBRARY_OUTPUT_PATH}) + set(pyenv ${pyenv}${_sep}${LIBRARY_OUTPUT_PATH}) else() set(pyenv ${LIBRARY_OUTPUT_PATH}) endif() @@ -55,7 +59,7 @@ macro(ADD_JAVA_TEST TESTNAME FILENAME) set(ld_library_path ${theld_library_path}) endif() if(pyenv) - set(ld_library_path ${ld_library_path}:${pyenv}) + set(ld_library_path ${ld_library_path}${_sep}${pyenv}) endif() file(WRITE ${CMAKE_CURRENT_BINARY_DIR}/${TESTNAME}.cmake @@ -63,18 +67,20 @@ macro(ADD_JAVA_TEST TESTNAME FILENAME) if(UNIX) set(ENV{LD_LIBRARY_PATH} ${ld_library_path}) set(ENV{DYLD_LIBRARY_PATH} ${ld_library_path}) - #set(ENV{CLASSPATH} ${pyenv}/gdcm.jar:.) - message(\"pyenv: ${pyenv}\") + #set(ENV{CLASSPATH} ${pyenv}/gdcm.jar${_sep}.) + #message(\"pyenv: ${pyenv}\") else() #set(the_path $ENV{PATH}) set(ENV{PATH} ${ld_library_path}) endif() + message(\"ld_library_path: ${ld_library_path}\") message(\"loc: ${loc}\") message(\"loc2: ${loc2}\") message(\"classpath: ${classpath}\") message(\"java runtime: ${Java_JAVA_EXECUTABLE}\") #message( \"wo_semicolumn: ${wo_semicolumn}\" ) execute_process( + #COMMAND ${Java_JAVA_EXECUTABLE} -Djava.library.path=\"${GDCM_LIBRARY_DIR}\" -classpath \"${classpath}\" ${loc2} ${wo_semicolumn} COMMAND ${Java_JAVA_EXECUTABLE} -classpath \"${classpath}\" ${loc2} ${wo_semicolumn} WORKING_DIRECTORY \"${EXECUTABLE_OUTPUT_PATH}\" RESULT_VARIABLE import_res diff --git a/CMake/UsePythonTest.cmake b/CMake/UsePythonTest.cmake index b9eca5a..7bf576c 100644 --- a/CMake/UsePythonTest.cmake +++ b/CMake/UsePythonTest.cmake @@ -24,6 +24,10 @@ find_package(PythonInterp REQUIRED) mark_as_advanced(PYTHON_EXECUTABLE) macro(ADD_PYTHON_TEST TESTNAME FILENAME) + set(_sep ":") + if(WIN32) + set(_sep "\\;") + endif() get_source_file_property(loc ${FILENAME} LOCATION) get_source_file_property(pyenv ${FILENAME} PYTHONPATH) if(CMAKE_CONFIGURATION_TYPES) @@ -38,7 +42,7 @@ macro(ADD_PYTHON_TEST TESTNAME FILENAME) endif() else() if(pyenv) - set(pyenv ${pyenv}:${LIBRARY_OUTPUT_PATH}) + set(pyenv ${pyenv}${_sep}${LIBRARY_OUTPUT_PATH}) else() set(pyenv ${LIBRARY_OUTPUT_PATH}) endif() @@ -46,9 +50,11 @@ macro(ADD_PYTHON_TEST TESTNAME FILENAME) string(REGEX REPLACE ";" " " wo_semicolumn "${ARGN}") file(WRITE ${CMAKE_CURRENT_BINARY_DIR}/${TESTNAME}.cmake " - set(ENV{PYTHONPATH} ${pyenv}:\$ENV{PYTHONPATH}) - set(ENV{LD_LIBRARY_PATH} ${pyenv}:\$ENV{LD_LIBRARY_PATH}) - message(\"${pyenv}\") + set(ENV{PYTHONPATH} ${pyenv}${_sep}\$ENV{PYTHONPATH}) + set(ENV{LD_LIBRARY_PATH} ${pyenv}${_sep}\$ENV{LD_LIBRARY_PATH}) + message(\"pyenv is: ${pyenv}\") + message(\"py_exec is: ${PYTHON_EXECUTABLE}\") + message(\"py_found is: ${PYTHONINTERP_FOUND}\") execute_process( COMMAND ${PYTHON_EXECUTABLE} ${loc} ${wo_semicolumn} RESULT_VARIABLE import_res @@ -58,9 +64,20 @@ macro(ADD_PYTHON_TEST TESTNAME FILENAME) # Pass the output back to ctest if(import_output) - message(\"\${import_output}\") + message(\"import_output is: \${import_output}\") endif() if(import_res) + message(\"Import res: \${import_res}\") + message(\"py_exec is: \${PYTHON_EXECUTABLE}\") + message(\"loc is: \${loc}\") + message(\"wo is: \${wo_semicolumn}\") + execute_process( + COMMAND ${PYTHON_EXECUTABLE} -v ${loc} ${wo_semicolumn} + RESULT_VARIABLE import2_res + OUTPUT_VARIABLE import2_output + ERROR_VARIABLE import2_output + ) + message(\"\${import2_output}\") message(SEND_ERROR \"\${import_res}\") endif() " diff --git a/CMakeLists.txt b/CMakeLists.txt index e33645a..a5175ff 100644 --- a/CMakeLists.txt +++ b/CMakeLists.txt @@ -32,7 +32,7 @@ set(GDCM_PACKAGE_CONTACT "GDCM Developers <[email protected] #---------------------------------------------------------------------------- set(GDCM_MAJOR_VERSION 2) set(GDCM_MINOR_VERSION 6) -set(GDCM_BUILD_VERSION 2) +set(GDCM_BUILD_VERSION 3) set(GDCM_VERSION "${GDCM_MAJOR_VERSION}.${GDCM_MINOR_VERSION}.${GDCM_BUILD_VERSION}") # let advanced user the option to define GDCM_API_VERSION: diff --git a/Copyright.txt b/Copyright.txt index 0f5435f..9623a3a 100644 --- a/Copyright.txt +++ b/Copyright.txt @@ -2,7 +2,7 @@ Program: GDCM (Grassroots DICOM). A DICOM library -Copyright (c) 2006-2011 Mathieu Malaterre +Copyright (c) 2006-2016 Mathieu Malaterre Copyright (c) 1993-2005 CREATIS (CREATIS = Centre de Recherche et d'Applications en Traitement de l'Image) All rights reserved. diff --git a/Examples/Csharp/DecompressImage.cs b/Examples/Csharp/DecompressImage.cs index c5800b8..c1cb802 100644 --- a/Examples/Csharp/DecompressImage.cs +++ b/Examples/Csharp/DecompressImage.cs @@ -34,6 +34,11 @@ public class DecompressImage return 1; } + // check that one can access a Fragment from C#: + var de = reader.GetFile().GetDataSet().GetDataElement(new Tag(0x7fe0, 0x0010)); + var sq = de.GetSequenceOfFragments(); + sq.GetFragment(0); + Image image = new Image(); Image ir = reader.GetImage(); diff --git a/Examples/Java/CMakeLists.txt b/Examples/Java/CMakeLists.txt index a36a8c0..aa86a72 100644 --- a/Examples/Java/CMakeLists.txt +++ b/Examples/Java/CMakeLists.txt @@ -19,13 +19,13 @@ set(examples ) foreach(example ${examples}) add_custom_command( - OUTPUT ${EXECUTABLE_OUTPUT_PATH}/${example}.class - COMMAND ${Java_JAVAC_EXECUTABLE} ARGS -source ${GDCM_JAVA_SOURCE_VERSION} -target ${GDCM_JAVA_TARGET_VERSION} ${CMAKE_CURRENT_SOURCE_DIR}/${example}.java -d ${EXECUTABLE_OUTPUT_PATH} -classpath ${LIBRARY_OUTPUT_PATH}/gdcm.jar + OUTPUT ${GDCM_EXECUTABLE_DIR}/${example}.class + COMMAND ${Java_JAVAC_EXECUTABLE} ARGS -source ${GDCM_JAVA_SOURCE_VERSION} -target ${GDCM_JAVA_TARGET_VERSION} ${CMAKE_CURRENT_SOURCE_DIR}/${example}.java -d ${GDCM_EXECUTABLE_DIR} -classpath ${GDCM_LIBRARY_DIR}/gdcm.jar WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR} DEPENDS ${CMAKE_CURRENT_SOURCE_DIR}/${example}.java COMMENT "javac ${example}.java" ) - list(APPEND classfilesdep ${EXECUTABLE_OUTPUT_PATH}/${example}.class) + list(APPEND classfilesdep ${GDCM_EXECUTABLE_DIR}/${example}.class) endforeach() # 3. ok now add the target @@ -38,7 +38,7 @@ add_dependencies(GDCMJavaExample GDCMJavaJar) if(BUILD_TESTING) if(GDCM_DATA_ROOT) - set_source_files_properties(${EXECUTABLE_OUTPUT_PATH}/HelloSimple.class PROPERTIES CLASSPATH "${EXECUTABLE_OUTPUT_PATH}/gdcm.jar") - ADD_JAVA_TEST(TestHelloSimpleJava ${EXECUTABLE_OUTPUT_PATH}/HelloSimple ${GDCM_DATA_ROOT}/012345.002.050.dcm) + set_source_files_properties(${GDCM_EXECUTABLE_DIR}/HelloSimple.class PROPERTIES CLASSPATH "${GDCM_LIBRARY_DIR}/gdcm.jar") + ADD_JAVA_TEST(TestHelloSimpleJava ${GDCM_EXECUTABLE_DIR}/HelloSimple ${GDCM_DATA_ROOT}/012345.002.050.dcm) endif() endif() diff --git a/Examples/Python/ConvertNumpy.py b/Examples/Python/ConvertNumpy.py index e9db128..608912f 100644 --- a/Examples/Python/ConvertNumpy.py +++ b/Examples/Python/ConvertNumpy.py @@ -27,8 +27,8 @@ import numpy def get_gdcm_to_numpy_typemap(): """Returns the GDCM Pixel Format to numpy array type mapping.""" - _gdcm_np = {gdcm.PixelFormat.UINT8 :numpy.int8, - gdcm.PixelFormat.INT8 :numpy.uint8, + _gdcm_np = {gdcm.PixelFormat.UINT8 :numpy.uint8, + gdcm.PixelFormat.INT8 :numpy.int8, #gdcm.PixelFormat.UINT12 :numpy.uint12, #gdcm.PixelFormat.INT12 :numpy.int12, gdcm.PixelFormat.UINT16 :numpy.uint16, diff --git a/README.txt b/README.txt index 45b588c..0305a04 100644 --- a/README.txt +++ b/README.txt @@ -12,23 +12,23 @@ Just a quick note on the build process of GDCM. GDCM build process make use of the cmake software(*). This allow us: 1. To get rid of the autoconf/autotools insanity 2. Transparently generate Unix Makefiles, NMake Makefiles, -VS8/9/10 Solution, XCode 2.1... -3. Automatic nightly testing, one of the most important thing -for a robust library/software devlpt process. GDCM devpt is develop +VS8/9/10 Solution, Xcode projects, etc. +3. Automatic nightly testing, one of the most important things +for a robust library/software development process. GDCM development is develop based on the XP definition, and to preserve backward compatibility make sure that code is working from one release to another: each night -we configure, we build and we test GDCM. The result are then send to +we configure, we build and we test GDCM. The result are then sent to the dashboard located at: - http://public.kitware.com/dashboard.php?name=gdcm + https://open.cdash.org/index.php?project=GDCM -A continuous dashboard make also sure that any commit did not introduce -any error on another plateform, a warning or broke a test... +A continuous dashboard also makes sure that any commit did not introduce +any error on another platform, a warning or a broken test... Therefore you should be able to use GDCM from the bleeding edge without -knowing too much on what is going on. All you need to do is have a look -at the GDCM dashboard, and if your plateform is 'green' then you can -update your git copy and compile safely knowing that there are very few chances +knowing too much about what is going on. All you need to do is have a look +at the GDCM dashboard, and if your platform is 'green' then you can +update your git copy and compile safely knowing that there is very little chance that something won't work. Cheers ! diff --git a/Source/Common/CMakeLists.txt b/Source/Common/CMakeLists.txt index a3b4218..b2ea721 100644 --- a/Source/Common/CMakeLists.txt +++ b/Source/Common/CMakeLists.txt @@ -55,6 +55,12 @@ check_function_exists(lround GDCM_HAVE_LROUND) #include(CheckSymbolExists) CHECK_FUNCTION_EXISTS(gettimeofday GDCM_HAVE_GETTIMEOFDAY) +# json-c API changed: +if(GDCM_USE_SYSTEM_JSON) + set(CMAKE_REQUIRED_INCLUDES ${JSON_INCLUDE_DIRS}) + set(CMAKE_REQUIRED_LIBRARIES ${JSON_LIBRARIES}) + CHECK_SYMBOL_EXISTS(json_object_object_get_ex "json.h" GDCM_HAVE_JSON_OBJECT_OBJECT_GET_EX) +endif() include(CheckCXXSourceCompiles) CHECK_CXX_SOURCE_COMPILES( diff --git a/Source/Common/gdcmBoxRegion.cxx b/Source/Common/gdcmBoxRegion.cxx index f0d4960..b675a0d 100644 --- a/Source/Common/gdcmBoxRegion.cxx +++ b/Source/Common/gdcmBoxRegion.cxx @@ -102,7 +102,7 @@ size_t BoxRegion::Area() const // multiplication exceed range of unsigned return 0; } - return tmp * C; + return (size_t)(tmp * C); } unsigned int BoxRegion::GetXMin() const diff --git a/Source/Common/gdcmConfigure.h.in b/Source/Common/gdcmConfigure.h.in index 0f7ded0..41e1772 100644 --- a/Source/Common/gdcmConfigure.h.in +++ b/Source/Common/gdcmConfigure.h.in @@ -122,6 +122,7 @@ #cmakedefine GDCM_HAVE__SNPRINTF #cmakedefine GDCM_HAVE_LROUND #cmakedefine GDCM_HAVE_GETTIMEOFDAY +#cmakedefine GDCM_HAVE_JSON_OBJECT_OBJECT_GET_EX // MM: I have a feeling that if GDCM_HAVE_WCHAR_IFSTREAM, then UNICODE filename // are expected to be specified as UTF-16, but if no API exist for UTF-16 diff --git a/Source/Common/gdcmDummyValueGenerator.cxx b/Source/Common/gdcmDummyValueGenerator.cxx index e7867ce..8e76f55 100644 --- a/Source/Common/gdcmDummyValueGenerator.cxx +++ b/Source/Common/gdcmDummyValueGenerator.cxx @@ -29,7 +29,7 @@ const char* DummyValueGenerator::Generate(const char *input) if( input ) { // Cannot use MD5 as it has been broken multiple time (2005) - b = MD5::Compute(input, strlen(input), digest); + b = MD5::Compute(input, (unsigned long)strlen(input), digest); //b = SHA1::Compute(input, strlen(input), digest); } diff --git a/Source/Common/gdcmSystem.cxx b/Source/Common/gdcmSystem.cxx index 1f4c863..c975cdb 100644 --- a/Source/Common/gdcmSystem.cxx +++ b/Source/Common/gdcmSystem.cxx @@ -2,7 +2,7 @@ Program: GDCM (Grassroots DICOM). A DICOM library - Copyright (c) 2006-2011 Mathieu Malaterre + Copyright (c) 2006-2016 Mathieu Malaterre All rights reserved. See Copyright.txt or http://gdcm.sourceforge.net/Copyright.html for details. @@ -43,9 +43,7 @@ #define snprintf _snprintf #endif #ifdef __APPLE__ -#include <CoreFoundation/CFBase.h> -#include <CoreFoundation/CFBundle.h> -#include <CoreFoundation/CFURL.h> +#include <CoreFoundation/CoreFoundation.h> #endif // __APPLE__ #if defined(_WIN32) && (defined(_MSC_VER) || defined(__WATCOMC__) ||defined(__BORLANDC__) || defined(__MINGW32__)) @@ -398,51 +396,6 @@ size_t System::FileSize(const char* filename) return size2; } -#if 0 -const char *System::GetCurrentDataDirectory() -{ -#ifdef _WIN32 - static char path[MAX_PATH]; - gdcm::Filename fn( GetCurrentProcessFileName() ); - if ( !fn.IsEmpty() ) - { - std::string str = fn.GetPath(); - str += "/../" GDCM_INSTALL_DATA_DIR; - strcpy(path, str.c_str()); - return path; - } -#else - - static char path[PATH_MAX]; - -#ifdef __APPLE__ - Boolean success = false; - CFURLRef pathURL = CFBundleCopyResourcesDirectoryURL(CFBundleGetMainBundle()); - if (pathURL != NULL) - { - success = CFURLGetFileSystemRepresentation(pathURL, true /*resolveAgainstBase*/, (unsigned char*) path, PATH_MAX); - CFRelease(pathURL); - } - if (success) - { - strncat(path, "/" GDCM_INSTALL_DATA_DIR, PATH_MAX); - return path; - } -#endif - - gdcm::Filename fn( GetCurrentProcessFileName() ); - if ( !fn.IsEmpty() ) - { - std::string str = fn.GetPath(); - str += "/../" GDCM_INSTALL_DATA_DIR; - strcpy(path, str.c_str()); - return path; - } -#endif - return 0; -} -#endif - /* * TODO: * check cygwin @@ -450,9 +403,6 @@ const char *System::GetCurrentDataDirectory() * check solaris * check hpux * check os2: DosGetInfoBlocks / DosQueryModuleName - * check macosx : - * ProcessSerialNumber psn = {kNoProcess, kCurrentProcess}; - * GetProcessInformation -> FSMakeFSSpec * ... */ const char *System::GetCurrentProcessFileName() @@ -464,7 +414,6 @@ const char *System::GetCurrentProcessFileName() return buf; } #elif defined(__APPLE__) - // _NSGetExecutablePath() static char buf[PATH_MAX]; Boolean success = false; CFURLRef pathURL = CFBundleCopyExecutableURL(CFBundleGetMainBundle()); @@ -544,7 +493,7 @@ const char *System::GetCurrentResourcesDirectory() } if (success) { - strncat(path, "/" GDCM_INSTALL_DATA_DIR, PATH_MAX); + strlcat(path, "/" GDCM_INSTALL_DATA_DIR, PATH_MAX); return path; } #endif diff --git a/Source/DataStructureAndEncodingDefinition/gdcmDataSet.h b/Source/DataStructureAndEncodingDefinition/gdcmDataSet.h index 82745a2..198ef58 100644 --- a/Source/DataStructureAndEncodingDefinition/gdcmDataSet.h +++ b/Source/DataStructureAndEncodingDefinition/gdcmDataSet.h @@ -149,19 +149,24 @@ public: /// Replace a dataelement with another one void Replace(const DataElement& de) { ConstIterator it = DES.find(de); - // detect loop: - gdcmAssertAlwaysMacro( &*it != &de ); - if( it != DES.end() ) DES.erase(de); + if( it != DES.end() ) + { + // detect loop: + gdcmAssertAlwaysMacro( &*it != &de ); + DES.erase(it); + } DES.insert(de); } /// Only replace a DICOM attribute when it is missing or empty void ReplaceEmpty(const DataElement& de) { ConstIterator it = DES.find(de); - // detect loop: - gdcmAssertAlwaysMacro( &*it != &de ); if( it != DES.end() && it->IsEmpty() ) - DES.erase(de); - DES.insert(de); + { + // detect loop: + gdcmAssertAlwaysMacro( &*it != &de ); + DES.erase(it); + } + DES.insert(de); } /// Completely remove a dataelement from the dataset SizeType Remove(const Tag& tag) { diff --git a/Source/DataStructureAndEncodingDefinition/gdcmVR.cxx b/Source/DataStructureAndEncodingDefinition/gdcmVR.cxx index e0ea954..824801e 100644 --- a/Source/DataStructureAndEncodingDefinition/gdcmVR.cxx +++ b/Source/DataStructureAndEncodingDefinition/gdcmVR.cxx @@ -307,11 +307,14 @@ VR::VRType VR::GetVRTypeFromFile(const char *vr) std::lower_bound(start, end, vr, MySort()); if( (*p)[0] != vr[0] || (*p)[1] != vr[1] ) { - if( vr[0] >= 'A' && vr[0] <= 'Z' - && vr[1] >= 'A' && vr[1] <= 'Z' ) + // https://groups.google.com/d/msg/comp.protocols.dicom/0ata_3lpjF4/xlkjOKRGBwAJ + // http://dicom.nema.org/medical/dicom/current/output/chtml/part05/chapter_E.html + if( vr[0] >= ' ' && vr[0] <= '~' + && vr[1] >= ' ' && vr[1] <= '~' ) // FIXME Control Char LF/FF/CR TAB and ESC should be accepted { // newly added VR ? - return VR::VL32; + // we are not capable of preserving the original VR. this is accepted behavior + return VR::UN; } return VR::INVALID; } diff --git a/Source/DataStructureAndEncodingDefinition/gdcmVR.h b/Source/DataStructureAndEncodingDefinition/gdcmVR.h index 8c6d513..fddb94e 100644 --- a/Source/DataStructureAndEncodingDefinition/gdcmVR.h +++ b/Source/DataStructureAndEncodingDefinition/gdcmVR.h @@ -152,8 +152,19 @@ public: is.read(vr, 2); VRField = GetVRTypeFromFile(vr); assert( VRField != VR::VR_END ); - //assert( VRField != VR::INVALID ); - if( VRField == VR::INVALID ) throw Exception( "INVALID VR" ); + if( VRField == VR::INVALID ) + { + // \0\2 Data/TheralysGDCM120Bug.dcm + // \0\0 Data/MR_Philips_Intera_PrivateSequenceExplicitVR_in_SQ_2001_e05f_item_wrong_lgt_use_NOSHADOWSEQ.dcm + // \0\4 Data/BugGDCM2_UndefItemWrongVL.dcm + // \44\0 Data/gdcm-MR-PHILIPS-16-Multi-Seq.dcm + // \0\20 Data/ExplicitVRforPublicElementsImplicitVRforShadowElements.dcm + // \0\3 Data/DMCPACS_ExplicitImplicit_BogusIOP.dcm + // \0\4 Data/THERALYS-12-MONO2-Uncompressed-Even_Length_Tag.dcm + // \0\4 Data/PrivateGEImplicitVRBigEndianTransferSyntax16Bits.dcm + // \0\4 Data/GE_DLX-8-MONO2-PrivateSyntax.dcm + throw Exception( "INVALID VR" ); + } if( VRField & VL32 ) { #if 0 diff --git a/Source/MediaStorageAndFileFormat/gdcmImageHelper.cxx b/Source/MediaStorageAndFileFormat/gdcmImageHelper.cxx index e7bfd00..72109a0 100644 --- a/Source/MediaStorageAndFileFormat/gdcmImageHelper.cxx +++ b/Source/MediaStorageAndFileFormat/gdcmImageHelper.cxx @@ -961,7 +961,7 @@ std::vector<double> ImageHelper::GetRescaleInterceptSlopeValue(File const & f) { interceptslope[0] = el_ri.GetValue(); interceptslope[1] = el_rs.GetValue(); - gdcmWarningMacro( "PMS Modality LUT found for MR Image Storage: [" << interceptslope[0] << "," << interceptslope[1] << "]" ); + gdcmWarningMacro( "PMS Modality LUT loaded for MR Image Storage: [" << interceptslope[0] << "," << interceptslope[1] << "]" ); } } else @@ -970,7 +970,7 @@ std::vector<double> ImageHelper::GetRescaleInterceptSlopeValue(File const & f) if( GetRescaleInterceptSlopeValueFromDataSet(ds, dummy) ) { // for everyone else, read your DCS, and set: ForceRescaleInterceptSlope = true if needed - gdcmDebugMacro( "Modality LUT found for MR Image Storage: [" << dummy[0] << "," << dummy[1] << "]" ); + gdcmDebugMacro( "Modality LUT unused for MR Image Storage: [" << dummy[0] << "," << dummy[1] << "]" ); } } #endif diff --git a/Source/MediaStorageAndFileFormat/gdcmJPEGLSCodec.cxx b/Source/MediaStorageAndFileFormat/gdcmJPEGLSCodec.cxx index a56d6b1..abd0b09 100644 --- a/Source/MediaStorageAndFileFormat/gdcmJPEGLSCodec.cxx +++ b/Source/MediaStorageAndFileFormat/gdcmJPEGLSCodec.cxx @@ -564,7 +564,7 @@ bool JPEGLSCodec::AppendRowEncode( std::ostream & , const char * , size_t ) bool JPEGLSCodec::AppendFrameEncode( std::ostream & out, const char * data, size_t datalen ) { const unsigned int * dimensions = this->GetDimensions(); - const PixelFormat & pf = this->GetPixelFormat(); + const PixelFormat & pf = this->GetPixelFormat(); (void)pf; assert( datalen == dimensions[0] * dimensions[1] * pf.GetPixelSize() ); std::vector<BYTE> rgbyteCompressed; diff --git a/Source/MediaStorageAndFileFormat/gdcmJSON.cxx b/Source/MediaStorageAndFileFormat/gdcmJSON.cxx index 9059914..b88bcea 100644 --- a/Source/MediaStorageAndFileFormat/gdcmJSON.cxx +++ b/Source/MediaStorageAndFileFormat/gdcmJSON.cxx @@ -21,6 +21,16 @@ #include <json.h> #endif +#ifdef GDCM_HAVE_JSON_OBJECT_OBJECT_GET_EX +// https://github.com/json-c/json-c/issues/142 +static inline json_object * json_object_object_get_old(json_object * obj, const char * name) { + json_object * sub; + return json_object_object_get_ex(obj, name, & sub) ? sub : NULL; +} +#else +#define json_object_object_get_old json_object_object_get +#endif + /* * Implementation is done based on Sup166, which may change in the future. */ @@ -576,14 +586,14 @@ static void ProcessJSONElement( const char *tag_str, json_object * obj, DataElem { json_type jtype = json_object_get_type( obj ); assert( jtype == json_type_object ); - json_object * jvr = json_object_object_get(obj, "VR"); + json_object * jvr = json_object_object_get_old(obj, "VR"); const char * vr_str = json_object_get_string ( jvr ); de.GetTag().ReadFromContinuousString( tag_str ); const char * pc_str = 0; if( de.GetTag().IsPrivate() && !de.GetTag().IsPrivateCreator() ) { - json_object * jprivatecreator = json_object_object_get(obj, "PrivateCreator"); + json_object * jprivatecreator = json_object_object_get_old(obj, "PrivateCreator"); pc_str = json_object_get_string ( jprivatecreator ); assert( pc_str ); } @@ -595,11 +605,11 @@ static void ProcessJSONElement( const char *tag_str, json_object * obj, DataElem if( vrtype == VR::SQ ) { - json_object * jvalue = json_object_object_get(obj, "Value"); + json_object * jvalue = json_object_object_get_old(obj, "Value"); json_type jvaluetype = json_object_get_type( jvalue ); assert( jvaluetype != json_type_null && jvaluetype == json_type_array ); #ifndef NDEBUG - json_object * jseq = json_object_object_get(obj, "Sequence"); + json_object * jseq = json_object_object_get_old(obj, "Sequence"); json_type jsqtype = json_object_get_type( jseq ); assert( jsqtype == json_type_null ); #endif @@ -655,9 +665,9 @@ static void ProcessJSONElement( const char *tag_str, json_object * obj, DataElem with the value of "null". For example: "Value": [ null ] */ - json_object * jvalue = json_object_object_get(obj, "Value"); + json_object * jvalue = json_object_object_get_old(obj, "Value"); #ifndef NDEBUG - json_object * jpn = json_object_object_get(obj, "PersonName"); + json_object * jpn = json_object_object_get_old(obj, "PersonName"); json_type jpntype = json_object_get_type( jpn ); assert( jpntype == json_type_null ); #endif @@ -686,9 +696,9 @@ static void ProcessJSONElement( const char *tag_str, json_object * obj, DataElem case VR::PN: { json_object * jopn[3]; - jopn[0] = json_object_object_get(value, "Alphabetic"); - jopn[1]= json_object_object_get(value, "Ideographic"); - jopn[2]= json_object_object_get(value, "Phonetic"); + jopn[0] = json_object_object_get_old(value, "Alphabetic"); + jopn[1]= json_object_object_get_old(value, "Ideographic"); + jopn[2]= json_object_object_get_old(value, "Phonetic"); for( int i = 0; i < 3; ++i ) { const char *tmp = json_object_get_string ( jopn[i] ); @@ -740,9 +750,9 @@ static void ProcessJSONElement( const char *tag_str, json_object * obj, DataElem } else { - json_object * jvaluebin = json_object_object_get(obj, "InlineBinary"); + json_object * jvaluebin = json_object_object_get_old(obj, "InlineBinary"); json_type jvaluebintype = json_object_get_type( jvaluebin ); - json_object * jvalue = json_object_object_get(obj, "Value"); + json_object * jvalue = json_object_object_get_old(obj, "Value"); json_type jvaluetype = json_object_get_type( jvalue ); //const char * dummy = json_object_to_json_string ( jvalue ); assert( jvaluetype == json_type_array || jvaluetype == json_type_null ); diff --git a/Source/MediaStorageAndFileFormat/gdcmRLECodec.cxx b/Source/MediaStorageAndFileFormat/gdcmRLECodec.cxx index b91db2f..157432f 100644 --- a/Source/MediaStorageAndFileFormat/gdcmRLECodec.cxx +++ b/Source/MediaStorageAndFileFormat/gdcmRLECodec.cxx @@ -628,7 +628,7 @@ bool RLECodec::Decode(DataElement const &in, DataElement &out) const unsigned long len = GetBufferLength(); unsigned long pos = 0; // Each RLE Frame store a 2D frame. len is the 3d length - const unsigned long nframes = sf->GetNumberOfFragments(); + const size_t nframes = sf->GetNumberOfFragments(); const size_t zdim = Dimensions[2]; if( nframes != zdim ) { diff --git a/Source/MediaStorageAndFileFormat/gdcmSegment.cxx b/Source/MediaStorageAndFileFormat/gdcmSegment.cxx index eb75c68..90f16d3 100644 --- a/Source/MediaStorageAndFileFormat/gdcmSegment.cxx +++ b/Source/MediaStorageAndFileFormat/gdcmSegment.cxx @@ -192,7 +192,7 @@ void Segment::SetSegmentAlgorithmName(const char * name) void Segment::ComputeSurfaceCount() { - SurfaceCount = Surfaces.size(); + SurfaceCount = (unsigned long)Surfaces.size(); } unsigned long Segment::GetSurfaceCount() diff --git a/Source/MediaStorageAndFileFormat/gdcmSerieHelper.cxx b/Source/MediaStorageAndFileFormat/gdcmSerieHelper.cxx index 1667c55..b87372d 100644 --- a/Source/MediaStorageAndFileFormat/gdcmSerieHelper.cxx +++ b/Source/MediaStorageAndFileFormat/gdcmSerieHelper.cxx @@ -148,7 +148,7 @@ void SerieHelper::AddFileName(std::string const &filename) } } -bool CompareDicomString(const std::string &s1, const char *s2, int op) +static bool CompareDicomString(const std::string &s1, const char *s2, int op) { // s2 is the string from the DICOM reference e.g. : 'MONOCHROME1' std::string s1_even = s1; //Never change input parameter diff --git a/Source/MediaStorageAndFileFormat/gdcmStringFilter.cxx b/Source/MediaStorageAndFileFormat/gdcmStringFilter.cxx index b290a4c..6efce54 100644 --- a/Source/MediaStorageAndFileFormat/gdcmStringFilter.cxx +++ b/Source/MediaStorageAndFileFormat/gdcmStringFilter.cxx @@ -221,6 +221,7 @@ bool StringFilter::ExecuteQuery(std::string const & query_const, } if( state != 2 ) { + free( query ); return false; } free( query ); diff --git a/Source/MediaStorageAndFileFormat/gdcmSurfaceReader.cxx b/Source/MediaStorageAndFileFormat/gdcmSurfaceReader.cxx index b7621f0..bc0ffec 100644 --- a/Source/MediaStorageAndFileFormat/gdcmSurfaceReader.cxx +++ b/Source/MediaStorageAndFileFormat/gdcmSurfaceReader.cxx @@ -29,7 +29,7 @@ SurfaceReader::~SurfaceReader() unsigned long SurfaceReader::GetNumberOfSurfaces() const { - return Segments.size(); + return (unsigned long)Segments.size(); } bool SurfaceReader::Read() diff --git a/Source/MediaStorageAndFileFormat/gdcmXMLPrinter.cxx b/Source/MediaStorageAndFileFormat/gdcmXMLPrinter.cxx index 1d7ca08..a024ba4 100644 --- a/Source/MediaStorageAndFileFormat/gdcmXMLPrinter.cxx +++ b/Source/MediaStorageAndFileFormat/gdcmXMLPrinter.cxx @@ -499,6 +499,7 @@ void XMLPrinter::PrintDataSet(const DataSet &ds, const TransferSyntax & ts, std: } } */ + delete[] bulkData; } else { diff --git a/Testing/Source/Common/Cxx/TestByteSwap.cxx b/Testing/Source/Common/Cxx/TestByteSwap.cxx index a997fda..88b511a 100644 --- a/Testing/Source/Common/Cxx/TestByteSwap.cxx +++ b/Testing/Source/Common/Cxx/TestByteSwap.cxx @@ -136,7 +136,7 @@ int TestByteSwap(int , char *[]) uint16_t array[] = { 0x1234 }; gdcm::ByteSwap<uint16_t>::SwapRangeFromSwapCodeIntoSystem(array, - gdcm::SwapCode::BigEndian,2); + gdcm::SwapCode::BigEndian,1); if ( array[0] != 0x3412 ) { std::cerr << std::hex << "array: " << array[0] << std::endl; diff --git a/Testing/Source/Common/Cxx/TestSystem1.cxx b/Testing/Source/Common/Cxx/TestSystem1.cxx index ab6f7e1..b6b6d23 100644 --- a/Testing/Source/Common/Cxx/TestSystem1.cxx +++ b/Testing/Source/Common/Cxx/TestSystem1.cxx @@ -96,7 +96,7 @@ int TestSystem1(int, char *[]) if( size2 != size4 ) { std::cerr << "size_t is diff from std::streamsize: " << size2 << " " << size4 << std::endl; - return 1; + //return 1; } char datetime[22]; diff --git a/Testing/Source/Common/Python/CMakeLists.txt b/Testing/Source/Common/Python/CMakeLists.txt index 11cf827..629709f 100644 --- a/Testing/Source/Common/Python/CMakeLists.txt +++ b/Testing/Source/Common/Python/CMakeLists.txt @@ -2,9 +2,13 @@ # gdcm-python set(GDCM_PYTHON_TEST_SRCS TestTesting - TestDirectory ) - +if(GDCM_DATA_ROOT) + set(GDCM_PYTHON_TEST_SRCS + ${GDCM_PYTHON_TEST_SRCS} + TestDirectory + ) +endif() # Loop over files and create executables foreach(name ${GDCM_PYTHON_TEST_SRCS}) diff --git a/Testing/Source/Common/Python/TestDirectory.py b/Testing/Source/Common/Python/TestDirectory.py index ac15e31..9edfdf1 100644 --- a/Testing/Source/Common/Python/TestDirectory.py +++ b/Testing/Source/Common/Python/TestDirectory.py @@ -34,4 +34,4 @@ for file in dir.GetFilenames(): print(file) # Test succeed ? -#sys.exit(sucess != 1) +#sys.exit(success != 1) diff --git a/Testing/Source/Common/Python/TestTesting.py b/Testing/Source/Common/Python/TestTesting.py index 2a10150..65ef70f 100644 --- a/Testing/Source/Common/Python/TestTesting.py +++ b/Testing/Source/Common/Python/TestTesting.py @@ -26,4 +26,4 @@ print(t.GetFileName(10000)) print(t.GetDataRoot()) # Test succeed ? -#sys.exit(sucess != 1) +#sys.exit(success != 1) diff --git a/Testing/Source/DataStructureAndEncodingDefinition/Java/CMakeLists.txt b/Testing/Source/DataStructureAndEncodingDefinition/Java/CMakeLists.txt index eb76a05..46e27ce 100644 --- a/Testing/Source/DataStructureAndEncodingDefinition/Java/CMakeLists.txt +++ b/Testing/Source/DataStructureAndEncodingDefinition/Java/CMakeLists.txt @@ -14,15 +14,16 @@ set(classfilesdep) foreach(example ${GDCM_JAVA_TEST_SRCS}) add_custom_command( - OUTPUT ${EXECUTABLE_OUTPUT_PATH}/${example}.class - COMMAND ${Java_JAVAC_EXECUTABLE} ARGS ${CMAKE_CURRENT_SOURCE_DIR}/${example}.java -d ${EXECUTABLE_OUTPUT_PATH} -source ${GDCM_JAVA_SOURCE_VERSION} -target ${GDCM_JAVA_TARGET_VERSION} -classpath ${LIBRARY_OUTPUT_PATH}/gdcm.jar + OUTPUT ${GDCM_EXECUTABLE_DIR}/${example}.class + COMMAND ${Java_JAVAC_EXECUTABLE} ARGS ${CMAKE_CURRENT_SOURCE_DIR}/${example}.java -d ${GDCM_EXECUTABLE_DIR} -source ${GDCM_JAVA_SOURCE_VERSION} -target ${GDCM_JAVA_TARGET_VERSION} -classpath ${GDCM_LIBRARY_DIR}/gdcm.jar WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR} DEPENDS ${CMAKE_CURRENT_SOURCE_DIR}/${example}.java COMMENT "javac ${example}.java" ) - list(APPEND classfilesdep ${EXECUTABLE_OUTPUT_PATH}/${example}.class) - set_source_files_properties(${EXECUTABLE_OUTPUT_PATH}/${example}.class PROPERTIES CLASSPATH "${EXECUTABLE_OUTPUT_PATH}/gdcm.jar") - ADD_JAVA_TEST(${example}Java ${EXECUTABLE_OUTPUT_PATH}/${example}) + list(APPEND classfilesdep ${GDCM_EXECUTABLE_DIR}/${example}.class) + set(GDCM_LIBRARY_DIR2 ${LIBRARY_OUTPUT_PATH}/\${BUILD_TYPE}) + set_source_files_properties(${GDCM_EXECUTABLE_DIR}/${example}.class PROPERTIES CLASSPATH "${GDCM_LIBRARY_DIR2}/gdcm.jar") + ADD_JAVA_TEST(${example}Java ${GDCM_EXECUTABLE_DIR}/${example}) endforeach() # 3. ok now add the target diff --git a/Testing/Source/DataStructureAndEncodingDefinition/Python/CMakeLists.txt b/Testing/Source/DataStructureAndEncodingDefinition/Python/CMakeLists.txt index 225c63f..89d9e38 100644 --- a/Testing/Source/DataStructureAndEncodingDefinition/Python/CMakeLists.txt +++ b/Testing/Source/DataStructureAndEncodingDefinition/Python/CMakeLists.txt @@ -1,9 +1,14 @@ # Define the tests for gdcm-python # gdcm-python set(GDCM_PYTHON_TEST_SRCS - TestReader TestTag ) +if(GDCM_DATA_ROOT) + set(GDCM_PYTHON_TEST_SRCS + ${GDCM_PYTHON_TEST_SRCS} + TestReader + ) +endif() # Loop over files and create executables foreach(name ${GDCM_PYTHON_TEST_SRCS}) diff --git a/Testing/Source/DataStructureAndEncodingDefinition/Python/TestReader.py b/Testing/Source/DataStructureAndEncodingDefinition/Python/TestReader.py index b765dd7..6df8f2f 100644 --- a/Testing/Source/DataStructureAndEncodingDefinition/Python/TestReader.py +++ b/Testing/Source/DataStructureAndEncodingDefinition/Python/TestReader.py @@ -12,22 +12,22 @@ # ############################################################################ -import gdcm import os,sys +import gdcm def TestRead(filename, verbose = False): r = gdcm.Reader() r.SetFileName( filename ) - sucess = r.Read() + success = r.Read() #if verbose: print r.GetFile() if verbose: print(r.GetFile().GetDataSet()) - return sucess + return success if __name__ == "__main__": - sucess = 0 + success = 0 try: filename = os.sys.argv[1] - sucess += TestRead( filename, True ) + success += TestRead( filename, True ) except: # loop over all files: gdcm.Trace.DebugOff() @@ -36,8 +36,8 @@ if __name__ == "__main__": nfiles = t.GetNumberOfFileNames() for i in range(0,nfiles): filename = t.GetFileName(i) - sucess += TestRead( filename ) + success += TestRead( filename ) # Test succeed ? - sys.exit(sucess == 0) + sys.exit(success == 0) diff --git a/Testing/Source/DataStructureAndEncodingDefinition/Python/TestTag.py b/Testing/Source/DataStructureAndEncodingDefinition/Python/TestTag.py index e4c3a06..fad1ac0 100644 --- a/Testing/Source/DataStructureAndEncodingDefinition/Python/TestTag.py +++ b/Testing/Source/DataStructureAndEncodingDefinition/Python/TestTag.py @@ -12,8 +12,8 @@ # ############################################################################ -import gdcm import os,sys +import gdcm if __name__ == "__main__": o1 = gdcm.Tag(0x0000,0x0000) diff --git a/Testing/Source/MediaStorageAndFileFormat/Cxx/TestPhotometricInterpretation.cxx b/Testing/Source/MediaStorageAndFileFormat/Cxx/TestPhotometricInterpretation.cxx index 63c8210..4a065c3 100644 --- a/Testing/Source/MediaStorageAndFileFormat/Cxx/TestPhotometricInterpretation.cxx +++ b/Testing/Source/MediaStorageAndFileFormat/Cxx/TestPhotometricInterpretation.cxx @@ -19,7 +19,7 @@ int TestPhotometricInterpretation(int, char *[]) { gdcm::PhotometricInterpretation pi; int end = gdcm::PhotometricInterpretation::PI_END; - for( int i = 0; i < end; ++i) + for( int i = 1; i < end; ++i) { const char *pistr = gdcm::PhotometricInterpretation::GetPIString( (gdcm::PhotometricInterpretation::PIType)i ); if( strlen( pistr ) % 2 ) diff --git a/Testing/Source/MediaStorageAndFileFormat/Python/CMakeLists.txt b/Testing/Source/MediaStorageAndFileFormat/Python/CMakeLists.txt index ecd0336..2f63974 100644 --- a/Testing/Source/MediaStorageAndFileFormat/Python/CMakeLists.txt +++ b/Testing/Source/MediaStorageAndFileFormat/Python/CMakeLists.txt @@ -1,25 +1,32 @@ # Define the tests for gdcm-python # gdcm-python set(GDCM_PYTHON_TEST_SRCS - TestScanner - TestImageReader - TestUIDGenerator - TestModifyFields - TestAnonymizer + #TestPythonFilter #TestStringFilter - TestOrientation TestIPPSorter - #TestPythonFilter + TestOrientation + TestUIDGenerator + ) +if(GDCM_DATA_ROOT) + set(GDCM_PYTHON_TEST_SRCS + ${GDCM_PYTHON_TEST_SRCS} + TestAnonymizer + TestModifyFields + TestImageReader + TestScanner ) +endif() if(BUILD_APPLICATIONS) if(DCMTK_DCMDUMP_EXECUTABLE) if(UNIX) + if(GDCM_DATA_ROOT) set(GDCM_PYTHON_TEST_SRCS ${GDCM_PYTHON_TEST_SRCS} TestDCMTKMD5 # need dcmdrle and dcmdjpeg ) endif() endif() + endif() endif() # Loop over files and create executables @@ -33,7 +40,9 @@ find_package(KAKADU) if(BUILD_APPLICATIONS) if(KDU_EXPAND_EXECUTABLE) if(UNIX) + if(GDCM_DATA_ROOT) ADD_PYTHON_TEST(TestKakaduDecompressionMD5Python TestKakaduDecompressionMD5.py ${KDU_EXPAND_EXECUTABLE}) endif() endif() + endif() endif() diff --git a/Testing/Source/MediaStorageAndFileFormat/Python/TestAnonymizer.py b/Testing/Source/MediaStorageAndFileFormat/Python/TestAnonymizer.py index 5e8344e..81d4bce 100644 --- a/Testing/Source/MediaStorageAndFileFormat/Python/TestAnonymizer.py +++ b/Testing/Source/MediaStorageAndFileFormat/Python/TestAnonymizer.py @@ -18,8 +18,8 @@ import os,sys def TestAnonymizer(filename, verbose = False): r = gdcm.Reader() r.SetFileName( filename ) - sucess = r.Read() - if( not sucess ): return 1 + success = r.Read() + if( not success ): return 1 #print r.GetFile().GetDataSet() ano = gdcm.Anonymizer() @@ -31,8 +31,8 @@ def TestAnonymizer(filename, verbose = False): # 3. Make a tag empty ano.Empty( gdcm.Tag(0x0008,0x0070) ) # Call the main function: - sucess = ano.RemovePrivateTags() # do it ! - if( not sucess ): return 1 + success = ano.RemovePrivateTags() # do it ! + if( not success ): return 1 # Check we can also change value from binary field #ano.Replace( gdcm.Tag(0x0010,0x0010), "16", gdcm. ) @@ -55,27 +55,27 @@ def TestAnonymizer(filename, verbose = False): w.SetFileName( outfilename ) w.SetFile( r.GetFile() ) w.SetCheckFileMetaInformation( False ) - sucess = w.Write() - if( not sucess ): return 1 + success = w.Write() + if( not success ): return 1 if verbose: print("Success to write: %s"%outfilename) - return sucess + return success if __name__ == "__main__": - sucess = 0 + success = 0 try: filename = os.sys.argv[1] - sucess += TestAnonymizer( filename, True ) + success += TestAnonymizer( filename, True ) except: # loop over all files: t = gdcm.Testing() nfiles = t.GetNumberOfFileNames() for i in range(0,nfiles): filename = t.GetFileName(i) - sucess += TestAnonymizer( filename ) + success += TestAnonymizer( filename ) # Test succeed ? - sys.exit(sucess == 0) + sys.exit(success == 0) diff --git a/Testing/Source/MediaStorageAndFileFormat/Python/TestDCMTKMD5.py b/Testing/Source/MediaStorageAndFileFormat/Python/TestDCMTKMD5.py index b72d791..29e1be8 100644 --- a/Testing/Source/MediaStorageAndFileFormat/Python/TestDCMTKMD5.py +++ b/Testing/Source/MediaStorageAndFileFormat/Python/TestDCMTKMD5.py @@ -172,10 +172,10 @@ def TestDCMTKMD5( filename, verbose = False ): return 1 if __name__ == "__main__": - sucess = 0 + success = 0 try: filename = os.sys.argv[1] - sucess += TestDCMTKMD5( filename, True ) + success += TestDCMTKMD5( filename, True ) except: # loop over all files: t = gdcm.Testing() @@ -184,7 +184,7 @@ if __name__ == "__main__": nfiles = t.GetNumberOfFileNames() for i in range(0,nfiles): filename = t.GetFileName(i) - sucess += TestDCMTKMD5( filename ) + success += TestDCMTKMD5( filename ) # Test succeed ? - sys.exit(sucess) + sys.exit(success) diff --git a/Testing/Source/MediaStorageAndFileFormat/Python/TestIPPSorter.py b/Testing/Source/MediaStorageAndFileFormat/Python/TestIPPSorter.py index 6283041..4e7751e 100644 --- a/Testing/Source/MediaStorageAndFileFormat/Python/TestIPPSorter.py +++ b/Testing/Source/MediaStorageAndFileFormat/Python/TestIPPSorter.py @@ -16,7 +16,7 @@ import gdcm import os,sys if __name__ == "__main__": - sucess = 0 + success = 0 s = gdcm.IPPSorter() # black box test: if not s.Sort([]): diff --git a/Testing/Source/MediaStorageAndFileFormat/Python/TestImageReader.py b/Testing/Source/MediaStorageAndFileFormat/Python/TestImageReader.py index aeba8af..dbc45f0 100644 --- a/Testing/Source/MediaStorageAndFileFormat/Python/TestImageReader.py +++ b/Testing/Source/MediaStorageAndFileFormat/Python/TestImageReader.py @@ -23,10 +23,10 @@ def TestImageRead(filename, verbose = False): return success if __name__ == "__main__": - sucess = 0 + success = 0 try: filename = os.sys.argv[1] - sucess += TestImageRead( filename, True ) + success += TestImageRead( filename, True ) except: # loop over all files: gdcm.Trace.DebugOff() @@ -36,7 +36,7 @@ if __name__ == "__main__": for i in range(0,nfiles): #print t.GetFileName(i) filename = t.GetFileName(i) - sucess += TestImageRead( filename ) + success += TestImageRead( filename ) # Test succeed ? - sys.exit(sucess == 0) + sys.exit(success == 0) diff --git a/Testing/Source/MediaStorageAndFileFormat/Python/TestKakaduDecompressionMD5.py b/Testing/Source/MediaStorageAndFileFormat/Python/TestKakaduDecompressionMD5.py index cf45e42..9b7e38c 100644 --- a/Testing/Source/MediaStorageAndFileFormat/Python/TestKakaduDecompressionMD5.py +++ b/Testing/Source/MediaStorageAndFileFormat/Python/TestKakaduDecompressionMD5.py @@ -67,17 +67,17 @@ def TestKakadu(filename, kdu_expand): return retval if __name__ == "__main__": - sucess = 0 + success = 0 #try: # filename = os.sys.argv[1] - # sucess += TestKakadu( filename ) + # success += TestKakadu( filename ) #except: # loop over all files: #t = gdcm.Testing() #nfiles = t.GetNumberOfFileNames() #for i in range(0,nfiles): # filename = t.GetFileName(i) - # sucess += TestKakadu( filename ) + # success += TestKakadu( filename ) d = gdcm.Directory() tempdir = gdcm.Testing.GetTempDirectory() j2ksubdir = 'TestImageChangeTransferSyntax2' # FIXME hardcoded ! @@ -89,7 +89,7 @@ if __name__ == "__main__": files = d.GetFilenames() for i in range(0,nfiles): filename = files[i] - sucess += TestKakadu( filename, os.sys.argv[1] ) + success += TestKakadu( filename, os.sys.argv[1] ) # Test succeed ? - sys.exit(sucess) + sys.exit(success) diff --git a/Testing/Source/MediaStorageAndFileFormat/Python/TestModifyFields.py b/Testing/Source/MediaStorageAndFileFormat/Python/TestModifyFields.py index eda3cda..675ef7d 100644 --- a/Testing/Source/MediaStorageAndFileFormat/Python/TestModifyFields.py +++ b/Testing/Source/MediaStorageAndFileFormat/Python/TestModifyFields.py @@ -19,7 +19,7 @@ def TestModifyFields(filename): outfilename = filename + ".rewrite" r = gdcm.Reader() r.SetFileName( filename ) - sucess = r.Read() + success = r.Read() #print r.GetFile().GetDataSet() ds = r.GetFile().GetDataSet() @@ -63,22 +63,22 @@ def TestModifyFields(filename): #w = gdcm.Writer() #w.SetFileName( outfilename ) #w.SetFile( r.GetFile() ) - #sucess = w.Write() - return sucess + #success = w.Write() + return success if __name__ == "__main__": - sucess = 0 + success = 0 try: filename = os.sys.argv[1] - sucess += TestModifyFields( filename, True ) + success += TestModifyFields( filename, True ) except: # loop over all files: t = gdcm.Testing() nfiles = t.GetNumberOfFileNames() for i in range(0,nfiles): filename = t.GetFileName(i) - sucess += TestModifyFields( filename ) + success += TestModifyFields( filename ) # Test succeed ? - sys.exit(sucess == 0) + sys.exit(success == 0) diff --git a/Testing/Source/MediaStorageAndFileFormat/Python/TestOrientation.py b/Testing/Source/MediaStorageAndFileFormat/Python/TestOrientation.py index 8f3dcc7..5f23743 100644 --- a/Testing/Source/MediaStorageAndFileFormat/Python/TestOrientation.py +++ b/Testing/Source/MediaStorageAndFileFormat/Python/TestOrientation.py @@ -16,7 +16,7 @@ import gdcm import os,sys if __name__ == "__main__": - sucess = True + success = True ori1 = (1,0,0,0,1,0) ori2 = (1,0,0,0,0,1) @@ -25,15 +25,15 @@ if __name__ == "__main__": label1 = gdcm.Orientation.GetLabel( gdcm.Orientation.GetType( ori1 ) ) if label1 != 'AXIAL': print("Found:",label1) - sucess = False + success = False label2 = gdcm.Orientation.GetLabel( gdcm.Orientation.GetType( ori2 ) ) if label2 != 'CORONAL': print("Found:",label2) - sucess = False + success = False label3 = gdcm.Orientation.GetLabel( gdcm.Orientation.GetType( ori3 ) ) if label3 != 'SAGITTAL': print("Found:",label3) - sucess = False + success = False image = gdcm.Image() image.SetNumberOfDimensions(2) @@ -53,4 +53,4 @@ if __name__ == "__main__": #print dircos.Cross() # Test succeed ? - sys.exit(sucess == False) + sys.exit(success == False) diff --git a/Testing/Source/MediaStorageAndFileFormat/Python/TestPythonFilter.py b/Testing/Source/MediaStorageAndFileFormat/Python/TestPythonFilter.py index eaac6fb..6250469 100644 --- a/Testing/Source/MediaStorageAndFileFormat/Python/TestPythonFilter.py +++ b/Testing/Source/MediaStorageAndFileFormat/Python/TestPythonFilter.py @@ -18,8 +18,8 @@ import os,sys def TestPythonFilter(filename, verbose = False): r = gdcm.Reader() r.SetFileName( filename ) - sucess = r.Read() - if( not sucess ): return 1 + success = r.Read() + if( not success ): return 1 file = r.GetFile() ds = file.GetDataSet() @@ -46,10 +46,10 @@ def TestPythonFilter(filename, verbose = False): return 0 if __name__ == "__main__": - sucess = 0 + success = 0 try: filename = os.sys.argv[1] - sucess += TestPythonFilter( filename, True ) + success += TestPythonFilter( filename, True ) except: # loop over all files: gdcm.Trace.WarningOff() @@ -57,8 +57,8 @@ if __name__ == "__main__": nfiles = t.GetNumberOfFileNames() for i in range(0,nfiles): filename = t.GetFileName(i) - sucess += TestPythonFilter( filename ) + success += TestPythonFilter( filename ) # Test succeed ? - sys.exit(sucess == 0) + sys.exit(success == 0) diff --git a/Testing/Source/MediaStorageAndFileFormat/Python/TestStringFilter.py b/Testing/Source/MediaStorageAndFileFormat/Python/TestStringFilter.py index f1b8490..cd47e3b 100644 --- a/Testing/Source/MediaStorageAndFileFormat/Python/TestStringFilter.py +++ b/Testing/Source/MediaStorageAndFileFormat/Python/TestStringFilter.py @@ -18,8 +18,8 @@ import os,sys def TestStringFilter(filename, verbose = False): r = gdcm.Reader() r.SetFileName( filename ) - sucess = r.Read() - if( not sucess ): return 1 + success = r.Read() + if( not success ): return 1 file = r.GetFile() ds = file.GetDataSet() @@ -45,10 +45,10 @@ def TestStringFilter(filename, verbose = False): return 0 if __name__ == "__main__": - sucess = 0 + success = 0 try: filename = os.sys.argv[1] - sucess += TestStringFilter( filename, True ) + success += TestStringFilter( filename, True ) except: # loop over all files: gdcm.Trace.WarningOff() @@ -56,8 +56,8 @@ if __name__ == "__main__": nfiles = t.GetNumberOfFileNames() for i in range(0,nfiles): filename = t.GetFileName(i) - sucess += TestStringFilter( filename ) + success += TestStringFilter( filename ) # Test succeed ? - sys.exit(sucess == 0) + sys.exit(success == 0) diff --git a/Testing/Source/MessageExchangeDefinition/Cxx/TestFindPatientRootQuery.cxx b/Testing/Source/MessageExchangeDefinition/Cxx/TestFindPatientRootQuery.cxx index caf4e87..2c227e3 100644 --- a/Testing/Source/MessageExchangeDefinition/Cxx/TestFindPatientRootQuery.cxx +++ b/Testing/Source/MessageExchangeDefinition/Cxx/TestFindPatientRootQuery.cxx @@ -248,6 +248,6 @@ int TestFindPatientRootQuery(int , char *[]) } } - //std::cout << "sucess" << std::endl; + //std::cout << "success" << std::endl; return 0; } diff --git a/Testing/Source/MessageExchangeDefinition/Cxx/TestFindStudyRootQuery.cxx b/Testing/Source/MessageExchangeDefinition/Cxx/TestFindStudyRootQuery.cxx index eb72c4e..1dcba0e 100644 --- a/Testing/Source/MessageExchangeDefinition/Cxx/TestFindStudyRootQuery.cxx +++ b/Testing/Source/MessageExchangeDefinition/Cxx/TestFindStudyRootQuery.cxx @@ -213,6 +213,6 @@ int TestFindStudyRootQuery(int , char *[]) } } - //std::cout << "sucess" << std::endl; + //std::cout << "success" << std::endl; return 0; } diff --git a/Utilities/VTK/CMakeLists.txt b/Utilities/VTK/CMakeLists.txt index 5ab4bda..e8eb0c8 100644 --- a/Utilities/VTK/CMakeLists.txt +++ b/Utilities/VTK/CMakeLists.txt @@ -648,6 +648,10 @@ if(GDCM_WRAP_JAVA) if(EXISTS ${VTK_JAVA_JAR}) # http://bugs.debian.org/cgi-bin/bugreport.cgi?bug=533193 set(GDCM_VTK_JAVA_JAR ${VTK_JAVA_JAR}) + else() + find_file(VTK_JAVA_JAR NAMES vtk.jar vtk6.jar vtk5.jar + PATHS ${vtkWrappingJava_RUNTIME_LIBRARY_DIRS}) + set(GDCM_VTK_JAVA_JAR ${VTK_JAVA_JAR}) endif() if(EXISTS /usr/lib/jni/libvtkCommonJava.so) # http://bugs.debian.org/cgi-bin/bugreport.cgi?bug=533198 @@ -678,7 +682,7 @@ if(GDCM_WRAP_JAVA) #COMMAND ${Java_JAVAC_EXECUTABLE} ARGS -cp ${GDCM_VTK_JAVA_JAR} "vtk/*.java" # No such thing as -cp for javac only java is listed: # http://java.sun.com/j2se/1.5.0/docs/tooldocs/windows/classpath.html - COMMAND ${Java_JAVAC_EXECUTABLE} ARGS ${jflags} -source 1.5 -target 1.5 -classpath ${GDCM_VTK_JAVA_JAR} "vtk/*.java" + COMMAND ${Java_JAVAC_EXECUTABLE} ARGS ${jflags} -source ${GDCM_JAVA_SOURCE_VERSION} -target ${GDCM_JAVA_TARGET_VERSION} -classpath ${GDCM_VTK_JAVA_JAR} "vtk/*.java" COMMAND ${Java_JAR_EXECUTABLE} ARGS -cvfm ${LIBRARY_OUTPUT_PATH}/${PROJECT_NAME}.jar ${CMAKE_CURRENT_SOURCE_DIR}/manifest.txt vtk/*.class WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}/java DEPENDS ${VTKGDCM_NAME}Java diff --git a/Utilities/VTK/Testing/Python/TestvtkGDCMImageWriter.py b/Utilities/VTK/Testing/Python/TestvtkGDCMImageWriter.py index 7474939..1b2a346 100644 --- a/Utilities/VTK/Testing/Python/TestvtkGDCMImageWriter.py +++ b/Utilities/VTK/Testing/Python/TestvtkGDCMImageWriter.py @@ -42,4 +42,4 @@ if __name__ == "__main__": writer.Write() # Test succeed ? - #sys.exit(sucess != 1) + #sys.exit(success != 1) diff --git a/Utilities/VTK/Testing/Python/TestvtkGDCMThreadedImageReader.py b/Utilities/VTK/Testing/Python/TestvtkGDCMThreadedImageReader.py index acb1be3..a20f039 100644 --- a/Utilities/VTK/Testing/Python/TestvtkGDCMThreadedImageReader.py +++ b/Utilities/VTK/Testing/Python/TestvtkGDCMThreadedImageReader.py @@ -35,8 +35,8 @@ def ExecuteInformation(reader, filename, dimz = 1): #print reader r = gdcm.ImageReader() r.SetFileName( reffile ) - sucess = r.Read() - assert sucess + success = r.Read() + assert success #print r.GetImage().Print() image = r.GetImage() assert image.GetNumberOfDimensions() == 2 or image.GetNumberOfDimensions() == 3 @@ -118,4 +118,4 @@ if __name__ == "__main__": # Test succeed ? - #sys.exit(sucess != 1) + #sys.exit(success != 1) diff --git a/Utilities/VTK/Testing/Python/TestvtkGDCMThreadedImageReader2.py b/Utilities/VTK/Testing/Python/TestvtkGDCMThreadedImageReader2.py index 163f031..b41b088 100644 --- a/Utilities/VTK/Testing/Python/TestvtkGDCMThreadedImageReader2.py +++ b/Utilities/VTK/Testing/Python/TestvtkGDCMThreadedImageReader2.py @@ -92,4 +92,4 @@ if __name__ == "__main__": print(r.GetOutput()) # Test succeed ? - #sys.exit(sucess != 1) + #sys.exit(success != 1) diff --git a/Utilities/VTK/vtkGDCMThreadedImageReader.cxx b/Utilities/VTK/vtkGDCMThreadedImageReader.cxx index 90042d8..93e281e 100644 --- a/Utilities/VTK/vtkGDCMThreadedImageReader.cxx +++ b/Utilities/VTK/vtkGDCMThreadedImageReader.cxx @@ -2,7 +2,7 @@ Program: GDCM (Grassroots DICOM). A DICOM library - Copyright (c) 2006-2011 Mathieu Malaterre + Copyright (c) 2006-2016 Mathieu Malaterre All rights reserved. See Copyright.txt or http://gdcm.sourceforge.net/Copyright.html for details. @@ -39,7 +39,6 @@ #endif #ifdef __APPLE__ -// For some reason sysconf + _SC_NPROCESSORS_ONLN is documented on macosx tiger, but it does not compile #include <sys/types.h> #include <sys/sysctl.h> #endif @@ -450,8 +449,11 @@ void vtkGDCMThreadedImageReader::ReadFiles(unsigned int nfiles, const char *file const unsigned int nprocs = (unsigned int)sysconf( _SC_NPROCESSORS_ONLN ); #else #ifdef __APPLE__ - int count = 1; + int32_t count = 1; size_t size = sizeof(count); + + // hw.ncpu is deprecated and should be replaced with hw.logicalcpu one day. + // hw.logicalcpu exists since at least 10.8, but maybe not earlier... int res = sysctlbyname("hw.ncpu",&count,&size,NULL,0); if( res == -1 ) { diff --git a/Utilities/doxygen/CMakeLists.txt b/Utilities/doxygen/CMakeLists.txt index 055cf3a..cf8f616 100644 --- a/Utilities/doxygen/CMakeLists.txt +++ b/Utilities/doxygen/CMakeLists.txt @@ -247,10 +247,41 @@ set(MANPAGES_XML find_package(LibXslt) # need an XSLT 1.0 processor, use xsltproc, maybe add more implementations later if(LIBXSLT_XSLTPROC_EXECUTABLE) + set(XSLT_PROCESSOR ${LIBXSLT_XSLTPROC_EXECUTABLE}) +# http://docbook.sourceforge.net/release/xsl/current/doc/manpages/man.output.quietly.html + set(XSLT_PROCESSOR_ARG --param man.output.quietly 1) + # User can change the behavior at cmake time: + if(NOT DEFINED GDCM_MANPAGES_USE_NONET) + set(GDCM_MANPAGES_USE_NONET FALSE) + # By default I want nonet on Debian: + if(EXISTS /etc/xml/catalog) + set(GDCM_MANPAGES_USE_NONET TRUE) + endif() + endif() + if(GDCM_MANPAGES_USE_NONET) + list(APPEND XSLT_PROCESSOR_ARG --nonet) + endif() +else() + find_program(MSXSL_EXECUTABLE + msxsl + ) + if(MSXSL_EXECUTABLE) + set(XSLT_PROCESSOR ${MSXSL_EXECUTABLE}) + set(XSLT_PROCESSOR_ARG "-pi") +# msxsl.exe -pi gdcmimg.xml +# +#Error occurred while executing stylesheet 'http://docbook.sourceforge.net/release/xsl-ns/current/manpages/docbook.xsl'. +# +#Code: 0x80004005 +#Namespace 'http://exslt.org/common' does not contain any functions. +# -> http://stackoverflow.com/a/16605034/136285 ?? + endif() +endif() +if(XSLT_PROCESSOR) foreach(docbook ${MANPAGES_XML}) add_custom_command( OUTPUT ${CMAKE_CURRENT_BINARY_DIR}/${docbook}.1 - COMMAND ${LIBXSLT_XSLTPROC_EXECUTABLE} ${CMAKE_CURRENT_SOURCE_DIR}/man/${docbook}.xml + COMMAND ${XSLT_PROCESSOR} ${XSLT_PROCESSOR_ARG} ${CMAKE_CURRENT_SOURCE_DIR}/man/${docbook}.xml DEPENDS ${CMAKE_CURRENT_SOURCE_DIR}/man/${docbook}.xml ) list(APPEND MANPAGES @@ -267,5 +298,5 @@ install(FILES DESTINATION ${GDCM_INSTALL_MAN_DIR}/man1 COMPONENT DebugDevel ) else() - message(WARNING "Cannot build man page from docbook (need xsltproc)") + message(WARNING "Cannot build man page from docbook (need an XSL processor)") endif() diff --git a/Utilities/doxygen/man/gdcm2pnm.xml b/Utilities/doxygen/man/gdcm2pnm.xml index 5ccb02c..ba6e660 100644 --- a/Utilities/doxygen/man/gdcm2pnm.xml +++ b/Utilities/doxygen/man/gdcm2pnm.xml @@ -1,5 +1,5 @@ <?xml version='1.0' encoding='UTF-8' standalone='no'?> -<?xml-stylesheet type="text/xsl" href="http://docbook.sourceforge.net/release/xsl/current/manpages/docbook.xsl"; ?> +<?xml-stylesheet type="text/xsl" href="http://docbook.sourceforge.net/release/xsl-ns/current/manpages/docbook.xsl"; ?> <refentry xmlns="http://docbook.org/ns/docbook"; version="5.0" xmlns:xlink="http://www.w3.org/1999/xlink";> <info> <author><personname><firstname>Mathieu</firstname><surname>Malaterre</surname></personname><contrib>Main developer</contrib></author> diff --git a/Utilities/doxygen/man/gdcm2vtk.xml b/Utilities/doxygen/man/gdcm2vtk.xml index ff5ad6f..f8a1986 100644 --- a/Utilities/doxygen/man/gdcm2vtk.xml +++ b/Utilities/doxygen/man/gdcm2vtk.xml @@ -1,5 +1,5 @@ <?xml version='1.0' encoding='UTF-8' standalone='no'?> -<?xml-stylesheet type="text/xsl" href="http://docbook.sourceforge.net/release/xsl/current/manpages/docbook.xsl"; ?> +<?xml-stylesheet type="text/xsl" href="http://docbook.sourceforge.net/release/xsl-ns/current/manpages/docbook.xsl"; ?> <refentry xmlns="http://docbook.org/ns/docbook"; version="5.0" xmlns:xlink="http://www.w3.org/1999/xlink";> <info> <author><personname><firstname>Mathieu</firstname><surname>Malaterre</surname></personname><contrib>Main developer</contrib></author> diff --git a/Utilities/doxygen/man/gdcmanon.xml b/Utilities/doxygen/man/gdcmanon.xml index 49ff84c..d681acf 100644 --- a/Utilities/doxygen/man/gdcmanon.xml +++ b/Utilities/doxygen/man/gdcmanon.xml @@ -1,5 +1,5 @@ <?xml version='1.0' encoding='UTF-8' standalone='no'?> -<?xml-stylesheet type="text/xsl" href="http://docbook.sourceforge.net/release/xsl/current/manpages/docbook.xsl"; ?> +<?xml-stylesheet type="text/xsl" href="http://docbook.sourceforge.net/release/xsl-ns/current/manpages/docbook.xsl"; ?> <refentry xmlns="http://docbook.org/ns/docbook"; version="5.0" xmlns:xlink="http://www.w3.org/1999/xlink";> <info> <author><personname><firstname>Mathieu</firstname><surname>Malaterre</surname></personname><contrib>Main developer</contrib></author> diff --git a/Utilities/doxygen/man/gdcmconv.xml b/Utilities/doxygen/man/gdcmconv.xml index e207c76..9f495bc 100644 --- a/Utilities/doxygen/man/gdcmconv.xml +++ b/Utilities/doxygen/man/gdcmconv.xml @@ -1,5 +1,5 @@ <?xml version='1.0' encoding='UTF-8' standalone='no'?> -<?xml-stylesheet type="text/xsl" href="http://docbook.sourceforge.net/release/xsl/current/manpages/docbook.xsl"; ?> +<?xml-stylesheet type="text/xsl" href="http://docbook.sourceforge.net/release/xsl-ns/current/manpages/docbook.xsl"; ?> <refentry xmlns="http://docbook.org/ns/docbook"; version="5.0" xmlns:xlink="http://www.w3.org/1999/xlink";> <info> <author><personname><firstname>Mathieu</firstname><surname>Malaterre</surname></personname><contrib>Main developer</contrib></author> diff --git a/Utilities/doxygen/man/gdcmdiff.xml b/Utilities/doxygen/man/gdcmdiff.xml index ccd35b9..8635707 100644 --- a/Utilities/doxygen/man/gdcmdiff.xml +++ b/Utilities/doxygen/man/gdcmdiff.xml @@ -1,5 +1,5 @@ <?xml version='1.0' encoding='UTF-8' standalone='no'?> -<?xml-stylesheet type="text/xsl" href="http://docbook.sourceforge.net/release/xsl/current/manpages/docbook.xsl"; ?> +<?xml-stylesheet type="text/xsl" href="http://docbook.sourceforge.net/release/xsl-ns/current/manpages/docbook.xsl"; ?> <refentry xmlns="http://docbook.org/ns/docbook"; version="5.0" xmlns:xlink="http://www.w3.org/1999/xlink";> <info> <author><personname><firstname>Mathieu</firstname><surname>Malaterre</surname></personname><contrib>Main developer</contrib></author> diff --git a/Utilities/doxygen/man/gdcmdump.xml b/Utilities/doxygen/man/gdcmdump.xml index fe7de6d..9ae5698 100644 --- a/Utilities/doxygen/man/gdcmdump.xml +++ b/Utilities/doxygen/man/gdcmdump.xml @@ -1,5 +1,5 @@ <?xml version="1.0" encoding="utf-8"?> -<?xml-stylesheet type="text/xsl" href="http://docbook.sourceforge.net/release/xsl/current/manpages/docbook.xsl"; ?> +<?xml-stylesheet type="text/xsl" href="http://docbook.sourceforge.net/release/xsl-ns/current/manpages/docbook.xsl"; ?> <refentry xmlns="http://docbook.org/ns/docbook"; version="5.0" xmlns:xlink="http://www.w3.org/1999/xlink";> <info> <author><personname><firstname>Mathieu</firstname><surname>Malaterre</surname></personname><contrib>Main developer</contrib></author> diff --git a/Utilities/doxygen/man/gdcmgendir.xml b/Utilities/doxygen/man/gdcmgendir.xml index 4e75d72..207b649 100644 --- a/Utilities/doxygen/man/gdcmgendir.xml +++ b/Utilities/doxygen/man/gdcmgendir.xml @@ -1,5 +1,5 @@ <?xml version='1.0' encoding='UTF-8' standalone='no'?> -<?xml-stylesheet type="text/xsl" href="http://docbook.sourceforge.net/release/xsl/current/manpages/docbook.xsl"; ?> +<?xml-stylesheet type="text/xsl" href="http://docbook.sourceforge.net/release/xsl-ns/current/manpages/docbook.xsl"; ?> <refentry xmlns="http://docbook.org/ns/docbook"; version="5.0" xmlns:xlink="http://www.w3.org/1999/xlink";> <info> <author><personname><firstname>Mathieu</firstname><surname>Malaterre</surname></personname><contrib>Main developer</contrib></author> diff --git a/Utilities/doxygen/man/gdcmimg.xml b/Utilities/doxygen/man/gdcmimg.xml index 2911ce9..7fb7e16 100644 --- a/Utilities/doxygen/man/gdcmimg.xml +++ b/Utilities/doxygen/man/gdcmimg.xml @@ -1,5 +1,5 @@ <?xml version='1.0' encoding='UTF-8' standalone='no'?> -<?xml-stylesheet type="text/xsl" href="http://docbook.sourceforge.net/release/xsl/current/manpages/docbook.xsl"; ?> +<?xml-stylesheet type="text/xsl" href="http://docbook.sourceforge.net/release/xsl-ns/current/manpages/docbook.xsl"; ?> <refentry xmlns="http://docbook.org/ns/docbook"; version="5.0" xmlns:xlink="http://www.w3.org/1999/xlink";> <info> <author><personname><firstname>Mathieu</firstname><surname>Malaterre</surname></personname><contrib>Main developer</contrib></author> diff --git a/Utilities/doxygen/man/gdcminfo.xml b/Utilities/doxygen/man/gdcminfo.xml index 3affa95..3c80686 100644 --- a/Utilities/doxygen/man/gdcminfo.xml +++ b/Utilities/doxygen/man/gdcminfo.xml @@ -1,5 +1,5 @@ <?xml version='1.0' encoding='UTF-8' standalone='no'?> -<?xml-stylesheet type="text/xsl" href="http://docbook.sourceforge.net/release/xsl/current/manpages/docbook.xsl"; ?> +<?xml-stylesheet type="text/xsl" href="http://docbook.sourceforge.net/release/xsl-ns/current/manpages/docbook.xsl"; ?> <refentry xmlns="http://docbook.org/ns/docbook"; version="5.0" xmlns:xlink="http://www.w3.org/1999/xlink";> <info> <author><personname><firstname>Mathieu</firstname><surname>Malaterre</surname></personname><contrib>Main developer</contrib></author> diff --git a/Utilities/doxygen/man/gdcmpap3.xml b/Utilities/doxygen/man/gdcmpap3.xml index 0b8bc58..0b87e6a 100644 --- a/Utilities/doxygen/man/gdcmpap3.xml +++ b/Utilities/doxygen/man/gdcmpap3.xml @@ -1,5 +1,5 @@ <?xml version='1.0' encoding='UTF-8' standalone='no'?> -<?xml-stylesheet type="text/xsl" href="http://docbook.sourceforge.net/release/xsl/current/manpages/docbook.xsl"; ?> +<?xml-stylesheet type="text/xsl" href="http://docbook.sourceforge.net/release/xsl-ns/current/manpages/docbook.xsl"; ?> <refentry xmlns="http://docbook.org/ns/docbook"; version="5.0" xmlns:xlink="http://www.w3.org/1999/xlink";> <info> <author><personname><firstname>Mathieu</firstname><surname>Malaterre</surname></personname><contrib>Main developer</contrib></author> diff --git a/Utilities/doxygen/man/gdcmpdf.xml b/Utilities/doxygen/man/gdcmpdf.xml index 961d214..77655bf 100644 --- a/Utilities/doxygen/man/gdcmpdf.xml +++ b/Utilities/doxygen/man/gdcmpdf.xml @@ -1,5 +1,5 @@ <?xml version='1.0' encoding='UTF-8' standalone='no'?> -<?xml-stylesheet type="text/xsl" href="http://docbook.sourceforge.net/release/xsl/current/manpages/docbook.xsl"; ?> +<?xml-stylesheet type="text/xsl" href="http://docbook.sourceforge.net/release/xsl-ns/current/manpages/docbook.xsl"; ?> <refentry xmlns="http://docbook.org/ns/docbook"; version="5.0" xmlns:xlink="http://www.w3.org/1999/xlink";> <info> <author><personname><firstname>Mathieu</firstname><surname>Malaterre</surname></personname><contrib>Main developer</contrib></author> diff --git a/Utilities/doxygen/man/gdcmraw.xml b/Utilities/doxygen/man/gdcmraw.xml index 6b3d316..2d406cb 100644 --- a/Utilities/doxygen/man/gdcmraw.xml +++ b/Utilities/doxygen/man/gdcmraw.xml @@ -1,5 +1,5 @@ <?xml version='1.0' encoding='UTF-8' standalone='no'?> -<?xml-stylesheet type="text/xsl" href="http://docbook.sourceforge.net/release/xsl/current/manpages/docbook.xsl"; ?> +<?xml-stylesheet type="text/xsl" href="http://docbook.sourceforge.net/release/xsl-ns/current/manpages/docbook.xsl"; ?> <refentry xmlns="http://docbook.org/ns/docbook"; version="5.0" xmlns:xlink="http://www.w3.org/1999/xlink";> <info> <author><personname><firstname>Mathieu</firstname><surname>Malaterre</surname></personname><contrib>Main developer</contrib></author> diff --git a/Utilities/doxygen/man/gdcmscanner.xml b/Utilities/doxygen/man/gdcmscanner.xml index 047d23a..9eaab42 100644 --- a/Utilities/doxygen/man/gdcmscanner.xml +++ b/Utilities/doxygen/man/gdcmscanner.xml @@ -1,5 +1,5 @@ <?xml version='1.0' encoding='UTF-8' standalone='no'?> -<?xml-stylesheet type="text/xsl" href="http://docbook.sourceforge.net/release/xsl/current/manpages/docbook.xsl"; ?> +<?xml-stylesheet type="text/xsl" href="http://docbook.sourceforge.net/release/xsl-ns/current/manpages/docbook.xsl"; ?> <refentry xmlns="http://docbook.org/ns/docbook"; version="5.0" xmlns:xlink="http://www.w3.org/1999/xlink";> <info> <author><personname><firstname>Mathieu</firstname><surname>Malaterre</surname></personname><contrib>Main developer</contrib></author> diff --git a/Utilities/doxygen/man/gdcmscu.xml b/Utilities/doxygen/man/gdcmscu.xml index 083baa7..8471ef1 100644 --- a/Utilities/doxygen/man/gdcmscu.xml +++ b/Utilities/doxygen/man/gdcmscu.xml @@ -1,5 +1,5 @@ <?xml version='1.0' encoding='UTF-8' standalone='no'?> -<?xml-stylesheet type="text/xsl" href="http://docbook.sourceforge.net/release/xsl/current/manpages/docbook.xsl"; ?> +<?xml-stylesheet type="text/xsl" href="http://docbook.sourceforge.net/release/xsl-ns/current/manpages/docbook.xsl"; ?> <refentry xmlns="http://docbook.org/ns/docbook"; version="5.0" xmlns:xlink="http://www.w3.org/1999/xlink";> <info> <author><personname><firstname>Mathieu</firstname><surname>Malaterre</surname></personname><contrib>Main developer</contrib></author> diff --git a/Utilities/doxygen/man/gdcmtar.xml b/Utilities/doxygen/man/gdcmtar.xml index ac36457..2e0efe0 100644 --- a/Utilities/doxygen/man/gdcmtar.xml +++ b/Utilities/doxygen/man/gdcmtar.xml @@ -1,5 +1,5 @@ <?xml version='1.0' encoding='UTF-8' standalone='no'?> -<?xml-stylesheet type="text/xsl" href="http://docbook.sourceforge.net/release/xsl/current/manpages/docbook.xsl"; ?> +<?xml-stylesheet type="text/xsl" href="http://docbook.sourceforge.net/release/xsl-ns/current/manpages/docbook.xsl"; ?> <refentry xmlns="http://docbook.org/ns/docbook"; version="5.0" xmlns:xlink="http://www.w3.org/1999/xlink";> <info> <author><personname><firstname>Mathieu</firstname><surname>Malaterre</surname></personname><contrib>Main developer</contrib></author> diff --git a/Utilities/doxygen/man/gdcmviewer.xml b/Utilities/doxygen/man/gdcmviewer.xml index 985e15e..1857c2a 100644 --- a/Utilities/doxygen/man/gdcmviewer.xml +++ b/Utilities/doxygen/man/gdcmviewer.xml @@ -1,5 +1,5 @@ <?xml version='1.0' encoding='UTF-8' standalone='no'?> -<?xml-stylesheet type="text/xsl" href="http://docbook.sourceforge.net/release/xsl/current/manpages/docbook.xsl"; ?> +<?xml-stylesheet type="text/xsl" href="http://docbook.sourceforge.net/release/xsl-ns/current/manpages/docbook.xsl"; ?> <refentry xmlns="http://docbook.org/ns/docbook"; version="5.0" xmlns:xlink="http://www.w3.org/1999/xlink";> <info> <author><personname><firstname>Mathieu</firstname><surname>Malaterre</surname></personname><contrib>Main developer</contrib></author> diff --git a/Utilities/doxygen/man/gdcmxml.xml b/Utilities/doxygen/man/gdcmxml.xml index 2803fbd..ad4e53a 100644 --- a/Utilities/doxygen/man/gdcmxml.xml +++ b/Utilities/doxygen/man/gdcmxml.xml @@ -1,5 +1,5 @@ <?xml version='1.0' encoding='UTF-8' standalone='no'?> -<?xml-stylesheet type="text/xsl" href="http://docbook.sourceforge.net/release/xsl/current/manpages/docbook.xsl"; ?> +<?xml-stylesheet type="text/xsl" href="http://docbook.sourceforge.net/release/xsl-ns/current/manpages/docbook.xsl"; ?> <refentry xmlns="http://docbook.org/ns/docbook"; version="5.0" xmlns:xlink="http://www.w3.org/1999/xlink";> <info> <author><personname><firstname>Mathieu</firstname><surname>Malaterre</surname></personname><contrib>Main developer</contrib></author> diff --git a/Utilities/doxygen/vtk/CMakeLists.txt b/Utilities/doxygen/vtk/CMakeLists.txt index 83a9fbd..7f1432c 100644 --- a/Utilities/doxygen/vtk/CMakeLists.txt +++ b/Utilities/doxygen/vtk/CMakeLists.txt @@ -31,7 +31,13 @@ mark_as_advanced(VTK_DIR) set(DOXYGEN_SOURCE_DIR "${VTK_SOURCE_DIR}/Utilities/Doxygen") else() # sudo apt-get install vtk-doc - set(DOXYGEN_SOURCE_DIR "/usr/share/doc/vtk-doc/html/") + 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") + else() + message(WARNING "DOXYGEN_SOURCE_DIR need to be set.") + endif() endif() set(DOXYGEN_PROJECT_SOURCE_DIR "${vtkgdcm_SOURCE_DIR}") set(VTK_DOXYGEN_HOME "${vtkgdcm_SOURCE_DIR}/VTK/Utilities/Doxygen") diff --git a/Utilities/gdcmopenjpeg-v1/libopenjpeg/t2.c b/Utilities/gdcmopenjpeg-v1/libopenjpeg/t2.c index 48463c9..550dde9 100644 --- a/Utilities/gdcmopenjpeg-v1/libopenjpeg/t2.c +++ b/Utilities/gdcmopenjpeg-v1/libopenjpeg/t2.c @@ -714,7 +714,11 @@ int t2_decode_packets(opj_t2_t *t2, unsigned char *src, int len, int tileno, opj } else { e = 0; } - if(e == -999) return -999; + if(e == -999) + { + pi_destroy(pi, cp, tileno); + return -999; + } /* progression in resolution */ image->comps[pi[pino].compno].resno_decoded = (e > 0) ? diff --git a/Utilities/gdcmzlib/gzio.c b/Utilities/gdcmzlib/gzio.c index 7e90f49..5cf50e0 100644 --- a/Utilities/gdcmzlib/gzio.c +++ b/Utilities/gdcmzlib/gzio.c @@ -256,7 +256,7 @@ int ZEXPORT gzsetparams (file, level, strategy) /* =========================================================================== Read a byte from a gz_stream; update next_in and avail_in. Return EOF for end of file. - IN assertion: the stream s has been sucessfully opened for reading. + IN assertion: the stream s has been successfully opened for reading. */ local int get_byte(s) gz_stream *s; @@ -281,7 +281,7 @@ local int get_byte(s) mode to transparent if the gzip magic header is not present; set s->err to Z_DATA_ERROR if the magic header is present but the rest of the header is incorrect. - IN assertion: the stream s has already been created sucessfully; + IN assertion: the stream s has already been created successfully; s->stream.avail_in is zero for the first time, but may be non-zero for concatenated .gz files. */ diff --git a/Wrapping/Csharp/gdcm.i b/Wrapping/Csharp/gdcm.i index 437f47b..b1a0dda 100644 --- a/Wrapping/Csharp/gdcm.i +++ b/Wrapping/Csharp/gdcm.i @@ -239,6 +239,7 @@ public class"; #include "gdcmBoxRegion.h" #include "gdcmImageRegionReader.h" #include "gdcmJSON.h" +#include "gdcmFileDecompressLookupTable.h" using namespace gdcm; %} @@ -356,6 +357,7 @@ EXTEND_CLASS_PRINT(gdcm::VM) %template (FilenamesType) std::vector<std::string>; %include "gdcmDirectory.h" EXTEND_CLASS_PRINT(gdcm::Directory) +%clear FilenamesType; %include "gdcmObject.h" %include "gdcmValue.h" EXTEND_CLASS_PRINT(gdcm::Value) @@ -441,6 +443,7 @@ EXTEND_CLASS_PRINT(gdcm::SequenceOfItems) %include "gdcmDataSet.h" EXTEND_CLASS_PRINT(gdcm::DataSet) //%include "gdcmString.h" +//%include "gdcmCodeString.h" //%include "gdcmTransferSyntax.h" %include "gdcmPhotometricInterpretation.h" EXTEND_CLASS_PRINT(gdcm::PhotometricInterpretation) @@ -537,6 +540,8 @@ EXTEND_CLASS_PRINT(gdcm::Pixmap) EXTEND_CLASS_PRINT(gdcm::Image) %include "gdcmFragment.h" EXTEND_CLASS_PRINT(gdcm::Fragment) +// convert SWIGTYPE_p_std__vectorT_gdcm__Fragment_t__size_type +%template() std::vector< gdcm::Fragment >; %include "gdcmPDBElement.h" EXTEND_CLASS_PRINT(gdcm::PDBElement) %include "gdcmPDBHeader.h" @@ -865,3 +870,4 @@ EXTEND_CLASS_PRINT(gdcm::BoxRegion) %include "gdcmImageRegionReader.h" %clear char* inreadbuffer; %include "gdcmJSON.h" +%include "gdcmFileDecompressLookupTable.h" diff --git a/Wrapping/Java/CMakeLists.txt b/Wrapping/Java/CMakeLists.txt index 12454d6..a1f46b3 100644 --- a/Wrapping/Java/CMakeLists.txt +++ b/Wrapping/Java/CMakeLists.txt @@ -1,6 +1,3 @@ -# TODO: -# SWIG is really a pain in the neck to use, a better alternative is Py++ which is using -# gccxml for the C++ parser and allow a full ANSI C++ support find_package(SWIG REQUIRED) include(${SWIG_USE_FILE}) option(GDCM_AUTOLOAD_GDCMJNI "Automatically load gdcmjni" ON) @@ -17,13 +14,12 @@ include_directories( # $ export JAVA_HOME=/usr/lib/j2sdk1.6-sun/ # $ export JAVA_HOME=/usr/lib/jvm/java-1.5.0-sun/ -find_package(Java 1.5 REQUIRED) # javac, jar +find_package(Java 1.7 REQUIRED) # javac, jar find_package(JNI REQUIRED) include_directories( ${JNI_INCLUDE_DIRS} ) set_source_files_properties(gdcm.i PROPERTIES CPLUSPLUS ON) -#include(${GDCM_SOURCE_DIR}/CMake/UseSWIGExtra.cmake) set(GDCM_JAVA_HOME ${CMAKE_CURRENT_BINARY_DIR}/java/gdcm) file(MAKE_DIRECTORY ${GDCM_JAVA_HOME}) @@ -70,7 +66,7 @@ if(CMAKE_COMPILER_IS_GNUCXX) endif() add_custom_command( - OUTPUT ${LIBRARY_OUTPUT_PATH}/gdcm.jar + OUTPUT ${GDCM_LIBRARY_DIR}/gdcm.jar # 1. run the custom command only when the gdcmJAVA_wrap.cxx has been generated # (which means all *.java should be there) Some compiler are picky about Java # version. For instance covariant return type was only added to Java 5, so to @@ -81,7 +77,7 @@ add_custom_command( # 2. now that the *.class have been generated construct the jar file. We can # only rely on the gdcm.java / gdcm.class to build dependencie, I am pretty # sure it will break parallel builds... oh well - COMMAND ${Java_JAR_EXECUTABLE} ARGS cvf ${LIBRARY_OUTPUT_PATH}/gdcm.jar gdcm/*.class + COMMAND ${Java_JAR_EXECUTABLE} ARGS cvf ${GDCM_LIBRARY_DIR}/gdcm.jar gdcm/*.class WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}/java DEPENDS "${swig_generated_file_fullname}" COMMENT "javac *.java; jar cvf -> gdcm.jar" @@ -89,14 +85,15 @@ add_custom_command( # 3. ok now add the target add_custom_target(GDCMJavaJar ALL - DEPENDS ${LIBRARY_OUTPUT_PATH}/gdcm.jar + DEPENDS ${GDCM_LIBRARY_DIR}/gdcm.jar COMMENT "building gdcm.jar" ) if(NOT GDCM_INSTALL_NO_LIBRARIES) install_swig_module(gdcmjni Java) + set(GDCM_LIBRARY_DIR2 ${LIBRARY_OUTPUT_PATH}/\${BUILD_TYPE}) # because gdcm.jar is constructed with custom commands, it need the INSTALL(FILES signature: - install(FILES ${LIBRARY_OUTPUT_PATH}/gdcm.jar + install(FILES ${GDCM_LIBRARY_DIR2}/gdcm.jar DESTINATION ${GDCM_INSTALL_JARMODULE_DIR} COMPONENT JavaModule ) endif() diff --git a/Wrapping/Java/gdcm.i b/Wrapping/Java/gdcm.i index 90edb5c..772996e 100644 --- a/Wrapping/Java/gdcm.i +++ b/Wrapping/Java/gdcm.i @@ -33,6 +33,7 @@ #include "gdcmSwapCode.h" #include "gdcmEvent.h" #include "gdcmProgressEvent.h" +#include "gdcmFileNameEvent.h" #include "gdcmAnonymizeEvent.h" #include "gdcmDirectory.h" #ifdef GDCM_BUILD_TESTING @@ -89,6 +90,7 @@ #include "gdcmUUIDGenerator.h" //#include "gdcmConstCharWrapper.h" #include "gdcmScanner.h" +#include "gdcmStrictScanner.h" #include "gdcmAttribute.h" #include "gdcmSubject.h" #include "gdcmCommand.h" @@ -147,6 +149,7 @@ #include "gdcmDecoder.h" #include "gdcmCodec.h" #include "gdcmImageCodec.h" +#include "gdcmRLECodec.h" #include "gdcmJPEGCodec.h" #include "gdcmJPEGLSCodec.h" #include "gdcmJPEG2000Codec.h" @@ -189,6 +192,7 @@ #include "gdcmBoxRegion.h" #include "gdcmImageRegionReader.h" #include "gdcmJSON.h" +#include "gdcmFileDecompressLookupTable.h" using namespace gdcm; %} @@ -310,6 +314,12 @@ EXTEND_CLASS_PRINT(gdcm::PrivateTag) return dynamic_cast<ProgressEvent*>(event); } }; +%include "gdcmFileNameEvent.h" +%extend gdcm::FileNameEvent { + static FileNameEvent *Cast(Event *event) { + return dynamic_cast<FileNameEvent*>(event); + } +}; //%feature("director") AnonymizeEvent; %include "gdcmAnonymizeEvent.h" %extend gdcm::AnonymizeEvent { @@ -508,6 +518,8 @@ EXTEND_CLASS_PRINT(gdcm::Pixmap) EXTEND_CLASS_PRINT(gdcm::Image) %include "gdcmFragment.h" EXTEND_CLASS_PRINT(gdcm::Fragment) +// convert SWIGTYPE_p_std__vectorT_gdcm__Fragment_t__size_type +%template() std::vector< gdcm::Fragment >; %include "gdcmPDBElement.h" EXTEND_CLASS_PRINT(gdcm::PDBElement) %include "gdcmPDBHeader.h" @@ -652,6 +664,9 @@ $1 = JNU_GetStringNativeChars(jenv, $input); %template(SmartPtrScan) gdcm::SmartPointer<gdcm::Scanner>; %include "gdcmScanner.h" EXTEND_CLASS_PRINT(gdcm::Scanner) +%template(SmartPtrStrictScan) gdcm::SmartPointer<gdcm::StrictScanner>; +%include "gdcmStrictScanner.h" +EXTEND_CLASS_PRINT(gdcm::StrictScanner) %template(SmartPtrAno) gdcm::SmartPointer<gdcm::Anonymizer>; //%ignore gdcm::Anonymizer::Anonymizer; @@ -776,6 +791,7 @@ EXTEND_CLASS_PRINT(gdcm::ModuleEntry) //%include "gdcmCodec.h" %feature("director") ImageCodec; %include "gdcmImageCodec.h" +%include "gdcmRLECodec.h" %include "gdcmJPEGCodec.h" %include "gdcmJPEGLSCodec.h" %include "gdcmJPEG2000Codec.h" @@ -852,3 +868,4 @@ EXTEND_CLASS_PRINT(gdcm::BoxRegion) //EXTEND_CLASS_PRINT(gdcm::ImageRegionReader) %clear signed char* inreadbuffer; %include "gdcmJSON.h" +%include "gdcmFileDecompressLookupTable.h" diff --git a/Wrapping/Python/CMakeLists.txt b/Wrapping/Python/CMakeLists.txt index d019607..3bf7247 100644 --- a/Wrapping/Python/CMakeLists.txt +++ b/Wrapping/Python/CMakeLists.txt @@ -20,7 +20,11 @@ include_regular_expression("^(gdcm).*$") # http://sourceforge.net/mailarchive/message.php?msg_id=29294773 # 2.0.6 cannot be used because of a serious typemap bug in 2.0.5 # http://sourceforge.net/mailarchive/message.php?msg_id=29305946 +if(GDCM_WEAK_SWIG_CHECK) +find_package(SWIG 2.0.4 REQUIRED) +else() find_package(SWIG 2.0.7 REQUIRED) +endif() mark_as_advanced(SWIG_DIR SWIG_EXECUTABLE SWIG_VERSION) include(${SWIG_USE_FILE}) @@ -109,6 +113,9 @@ if(WIN32 AND NOT CYGWIN) set_target_properties(${SWIG_MODULE_${GDCM_PYTHON_IMPLEMENTATION_NAME}_REAL_NAME} PROPERTIES SUFFIX ".pyd") # shared libs on windows needs to be fully resolved SWIG_LINK_LIBRARIES(${GDCM_PYTHON_IMPLEMENTATION_NAME} ${PYTHON_LIBRARIES}) + message(STATUS "Will use pyd extension" ) +else() + message(STATUS "Will NOT use pyd extension" ) endif() set_target_properties(${SWIG_MODULE_${GDCM_PYTHON_IMPLEMENTATION_NAME}_REAL_NAME} PROPERTIES LINK_INTERFACE_LIBRARIES "") diff --git a/Wrapping/Python/TestWrap.py b/Wrapping/Python/TestWrap.py index a77bf0a..abd0255 100755 --- a/Wrapping/Python/TestWrap.py +++ b/Wrapping/Python/TestWrap.py @@ -49,12 +49,14 @@ blacklist = ( "GroupDict" "DictConverter" # Information thingy : +"Tables" "MacroEntry" "XMLDictReader" "TableReader" "Table" "XMLPrivateDictReader" # Common +"Configure" "LegacyMacro" "Swapper" "SmartPointer" @@ -180,6 +182,19 @@ blacklist = ( "SOPClassExtendedNegociationSub" "FindPatientRootQuery" "ServiceClassApplicationInformation" +"ModalityPerformedProcedureStepSetQuery" +"NormalizedMessageFactory" +"NormalizedNetworkFunctions" +"NSetMessages" +"WLMFindQuery" +"ModalityPerformedProcedureStepCreateQuery" +"BaseNormalizedMessage" +"NCreateMessages" +"NActionMessages" +"NGetMessages" +"BaseQuery" +"NEventReportMessages" +"NDeleteMessages" ) def processonedir(dirname): diff --git a/Wrapping/Python/gdcmPythonFilter.h b/Wrapping/Python/gdcmPythonFilter.h index 2874aeb..e255b66 100644 --- a/Wrapping/Python/gdcmPythonFilter.h +++ b/Wrapping/Python/gdcmPythonFilter.h @@ -34,7 +34,7 @@ public: PythonFilter(); ~PythonFilter(); - void UseDictAlways(bool use) {} + void UseDictAlways(bool ) {} // Allow user to pass in there own dicts void SetDicts(const Dicts &dicts); diff --git a/Wrapping/Python/gdcmswig.i b/Wrapping/Python/gdcmswig.i index b290737..7bf0027 100644 --- a/Wrapping/Python/gdcmswig.i +++ b/Wrapping/Python/gdcmswig.i @@ -33,6 +33,7 @@ #include "gdcmSwapCode.h" #include "gdcmEvent.h" #include "gdcmProgressEvent.h" +#include "gdcmFileNameEvent.h" #include "gdcmAnonymizeEvent.h" #include "gdcmDirectory.h" #ifdef GDCM_BUILD_TESTING @@ -89,6 +90,7 @@ #include "gdcmUUIDGenerator.h" //#include "gdcmConstCharWrapper.h" #include "gdcmScanner.h" +#include "gdcmStrictScanner.h" #include "gdcmAttribute.h" #include "gdcmSubject.h" #include "gdcmCommand.h" @@ -148,6 +150,7 @@ #include "gdcmDecoder.h" #include "gdcmCodec.h" #include "gdcmImageCodec.h" +#include "gdcmRLECodec.h" #include "gdcmJPEGCodec.h" #include "gdcmJPEGLSCodec.h" #include "gdcmJPEG2000Codec.h" @@ -190,6 +193,7 @@ #include "gdcmBoxRegion.h" #include "gdcmImageRegionReader.h" #include "gdcmJSON.h" +#include "gdcmFileDecompressLookupTable.h" using namespace gdcm; %} @@ -290,7 +294,6 @@ EXTEND_CLASS_PRINT(gdcm::VM) %template (FilenamesType) std::vector<std::string>; %include "gdcmDirectory.h" EXTEND_CLASS_PRINT(gdcm::Directory) -//%clear FilenameType; %clear FilenamesType; %include "gdcmObject.h" %include "gdcmValue.h" @@ -433,6 +436,9 @@ EXTEND_CLASS_PRINT(gdcm::Pixmap) EXTEND_CLASS_PRINT(gdcm::Image) %include "gdcmFragment.h" EXTEND_CLASS_PRINT(gdcm::Fragment) +// convert SWIGTYPE_p_std__vectorT_gdcm__Fragment_t__size_type +//%template() std::vector< gdcm::Fragment >; +// -> error: ‘type_name’ is not a member of ‘swig::traits<gdcm::Fragment>’ (swig 3.0.7) %include "gdcmPDBElement.h" EXTEND_CLASS_PRINT(gdcm::PDBElement) %include "gdcmPDBHeader.h" @@ -536,6 +542,9 @@ EXTEND_CLASS_PRINT(gdcm::Dicts) %template(SmartPtrScan) gdcm::SmartPointer<gdcm::Scanner>; %include "gdcmScanner.h" EXTEND_CLASS_PRINT(gdcm::Scanner) +%template(SmartPtrStrictScan) gdcm::SmartPointer<gdcm::StrictScanner>; +%include "gdcmStrictScanner.h" +EXTEND_CLASS_PRINT(gdcm::StrictScanner) %template(SmartPtrAno) gdcm::SmartPointer<gdcm::Anonymizer>; //%ignore gdcm::Anonymizer::Anonymizer; @@ -724,6 +733,7 @@ EXTEND_CLASS_PRINT(gdcm::ModuleEntry) //%include "gdcmCodec.h" %feature("director") ImageCodec; %include "gdcmImageCodec.h" +%include "gdcmRLECodec.h" %include "gdcmJPEGCodec.h" %include "gdcmJPEGLSCodec.h" %include "gdcmJPEG2000Codec.h" @@ -785,3 +795,4 @@ EXTEND_CLASS_PRINT(gdcm::BoxRegion) %include "gdcmImageRegionReader.h" %clear char* inreadbuffer; %include "gdcmJSON.h" +%include "gdcmFileDecompressLookupTable.h" diff --git a/appveyor.yml b/appveyor.yml index 6860569..9322396 100644 --- a/appveyor.yml +++ b/appveyor.yml @@ -2,14 +2,24 @@ # http://www.appveyor.com/docs/appveyor-yml # Set build version format here instead of in the admin panel. -version: 2.6.2.{build} +version: 2.6.3.{build} # http://www.appveyor.com/docs/build-cache#caching-chocolatey-packages # https://github.com/kvirc/KVIrc/blob/master/.appveyor.yml cache: - C:\ProgramData\chocolatey\bin -> appveyor.yml - C:\ProgramData\chocolatey\lib -> appveyor.yml - - 'c:\Program Files\NSIS' + - 'C:\Program Files (x86)\NSIS' + +## http://www.appveyor.com/docs/installed-software#python +## Python 2.7; 32-bit version +# - python: C:\Python27;C:\Python27\Scripts +## Python 2.7; 64-bit version +# - python: C:\Python27-x64;C:\Python27-x64\Scripts +## Python 3.4; 32-bit version +# - python: C:\Python34;C:\Python34\Scripts +## Python 3.4; 64-bit version +# - python: C:\Python34-x64;C:\Python34-x64\Scripts environment: matrix: @@ -17,10 +27,14 @@ environment: CONFIG: Release B_NAME: Windows-x86 DO_REL: true + PYTHONHOME: C:\Python27 + JAVA_HOME: C:\Program Files (x86)\Java\jdk1.7.0 - VS_GEN: Visual Studio 10 2010 Win64 CONFIG: Release B_NAME: Windows-x86_64 DO_REL: true + PYTHONHOME: C:\Python34-x64 + JAVA_HOME: C:\Program Files\Java\jdk1.8.0 # - VS_GEN: Visual Studio 14 2015 Win64 # CONFIG: Release # B_NAME: Win64 @@ -49,6 +63,7 @@ branches: # scripts that are called at very beginning, before repo cloning init: # Print environment info ( set / systeminfo) + - set PATH=%JAVA_HOME%\bin;%PYTHONHOME%;%PATH% - msbuild /version - cmake --version - python --version @@ -57,29 +72,39 @@ init: - del c:\programdata\chocolatey\bin\cpack.exe # scripts that run after cloning repository +# https://www.appveyor.com/docs/build-configuration#powershell install: # Fetch submodules #- git submodule update --init --recursive - - choco install swig + # PowerShell + #- ps: (New-Object Net.WebClient).DownloadFile('http://download.microsoft.com/download/f/2/6/f263ac46-1fe9-4ae9-8fd3-21102100ebf5/msxsl.exe', "$env:appveyor_build_folder\msxsl.exe") + #- msxsl -? --> code return is 1 !! + # chocolatey: + - ps: | + if (Test-Path "C:/ProgramData/chocolatey/bin/swig.exe") { + echo "using swig from cache" + } else { + choco install -y swig > $null + } - swig -version # https://chocolatey.org/packages/nsis.install/ - ps: | - if (Test-Path "c:/Program Files/NSIS/makensis.exe") { + if (Test-Path "C:/Program Files (x86)/NSIS/makensis.exe") { echo "using nsis from cache" } else { - choco install nsis.install -pre -version 2.46.0.20150406 + choco install -y nsis.install -pre -version 2.46.0.20150406 } - # Set VC variables for the platform - # - if %PLATFORM% == x64 call "C:\Program Files (x86)\Microsoft Visual Studio 12.0\VC\bin\x86_amd64\vcvarsx86_amd64.bat" - # - if %PLATFORM% == x86 call "C:\Program Files (x86)\Microsoft Visual Studio 12.0\VC\bin\vcvars32.bat" + - cmd: SET PATH=%PATH%;C:\Program Files (x86)\NSIS on_failure: # Display error log file if generated - - if exist C:\ProgramData\chocolatey\logs\chocolatey.log type C:\ProgramData\chocolatey\logs\chocolatey.log + - dir C:\projects\gdcm\bin + - dir C:\projects\gdcm\bin\Release + #- if exist C:\ProgramData\chocolatey\logs\chocolatey.log type C:\ProgramData\chocolatey\logs\chocolatey.log # scripts to run before build before_build: - - cmake -Wno-dev -G"%VS_GEN%" -DCMAKE_BUILD_TYPE=%CONFIG% -DGDCM_BUILD_TESTING:BOOL=ON -DGDCM_BUILD_APPLICATIONS:BOOL=ON -DGDCM_BUILD_SHARED_LIBS:BOOL=ON -DBUILDNAME:STRING=%COMPUTERNAME%-%B_NAME% -DGDCM_WRAP_CSHARP:BOOL=ON -DGDCM_WRAP_JAVA:BOOL=ON -DGDCM_WRAP_PYTHON:BOOL=ON -DGDCM_USE_PVRG:BOOL=ON -DGDCM_JAVA_SOURCE_VERSION:STRING=1.7 -DGDCM_JAVA_TARGET_VERSION:STRING=1.7 -DCPACK_SYSTEM_NAME:STRING=%B_NAME% . + - cmake -Wno-dev -G"%VS_GEN%" -DCMAKE_BUILD_TYPE=%CONFIG% -DGDCM_BUILD_TESTING:BOOL=ON -DGDCM_BUILD_APPLICATIONS:BOOL=ON -DGDCM_BUILD_EXAMPLES:BOOL=ON -DGDCM_BUILD_SHARED_LIBS:BOOL=ON -DBUILDNAME:STRING=%COMPUTERNAME%-%branch%-%B_NAME% -DGDCM_WRAP_CSHARP:BOOL=ON -DGDCM_WRAP_JAVA:BOOL=ON -DGDCM_WRAP_PYTHON:BOOL=ON -DGDCM_USE_PVRG:BOOL=ON -DGDCM_LEGACY_SILENT:BOOL=ON -DCPACK_SYSTEM_NAME:STRING=%B_NAME% . - ctest -D ExperimentalStart -C %CONFIG% # scripts to run after build @@ -88,18 +113,13 @@ after_build: - cpack -G NSIS -C %CONFIG% # create binary zip - cpack -G ZIP -C %CONFIG% - # on github it does make sense to do source package + # no need for source release on github # to run your custom scripts instead of automatic MSBuild build_script: # Do not run Test=Update/Configure, only Start/Build/Test/Submit (TODO: Coverage) - ctest -D ExperimentalBuild -j %NUMBER_OF_PROCESSORS% -C %CONFIG% -Q -# scripts to run before tests -#before_test: -# - echo %APPVEYOR_REPO_TAG_NAME% -# - echo %APPVEYOR_REPO_TAG_NAME:~1% - # scripts to run after tests after_test: -- Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-med/gdcm.git _______________________________________________ debian-med-commit mailing list [email protected] http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
