From defe64d274b7404256f18e3d6c31ebbfecedb70a Mon Sep 17 00:00:00 2001 From: Hans Johnson Date: Mon, 22 Oct 2018 19:33:09 -0500 Subject: [PATCH 1/4] COMP: HD5 changed API for printing Errors. --- BRAINSConstellationDetector/src/LLSModel.cxx | 16 ++++++++-------- BRAINSConstellationDetector/src/fcsv_to_hdf5.cxx | 8 ++++---- 2 files changed, 12 insertions(+), 12 deletions(-) diff --git a/BRAINSConstellationDetector/src/LLSModel.cxx b/BRAINSConstellationDetector/src/LLSModel.cxx index 9cec9449ed..1ad502a2cd 100644 --- a/BRAINSConstellationDetector/src/LLSModel.cxx +++ b/BRAINSConstellationDetector/src/LLSModel.cxx @@ -191,25 +191,25 @@ ::Write() // catch failure caused by the H5File operations catch( H5::FileIException & error ) { - error.printError(); + error.printErrorStack(); return -1; } // catch failure caused by the DataSet operations catch( H5::DataSetIException & error ) { - error.printError(); + error.printErrorStack(); return -1; } // catch failure caused by the DataSpace operations catch( H5::DataSpaceIException & error ) { - error.printError(); + error.printErrorStack(); return -1; } // catch failure caused by the DataType operations catch( H5::DataTypeIException & error ) { - error.printError(); + error.printErrorStack(); return -1; } return 0; @@ -385,25 +385,25 @@ ::Read() // catch failure caused by the H5File operations catch( H5::FileIException & error ) { - error.printError(); + error.printErrorStack(); return -1; } // catch failure caused by the DataSet operations catch( H5::DataSetIException & error ) { - error.printError(); + error.printErrorStack(); return -1; } // catch failure caused by the DataSpace operations catch( H5::DataSpaceIException & error ) { - error.printError(); + error.printErrorStack(); return -1; } // catch failure caused by the DataType operations catch( H5::DataTypeIException & error ) { - error.printError(); + error.printErrorStack(); return -1; } return 0; diff --git a/BRAINSConstellationDetector/src/fcsv_to_hdf5.cxx b/BRAINSConstellationDetector/src/fcsv_to_hdf5.cxx index 14a916fbc5..fc13f02ed2 100644 --- a/BRAINSConstellationDetector/src/fcsv_to_hdf5.cxx +++ b/BRAINSConstellationDetector/src/fcsv_to_hdf5.cxx @@ -470,28 +470,28 @@ int main(int argc, char* argv[]) // catch failure caused by the H5File operations catch( H5::FileIException& error ) { - error.printError(); + error.printErrorStack(); return -1; } // catch failure caused by the DataSet operations catch( H5::DataSetIException& error ) { - error.printError(); + error.printErrorStack(); return -1; } // catch failure caused by the DataSpace operations catch( H5::DataSpaceIException& error ) { - error.printError(); + error.printErrorStack(); return -1; } // catch failure caused by the DataSpace operations catch( H5::DataTypeIException& error ) { - error.printError(); + error.printErrorStack(); return -1; } } From 2e49e437d3c0e6546aa673beb54400d1bf0bf7d4 Mon Sep 17 00:00:00 2001 From: Hans Johnson Date: Mon, 22 Oct 2018 19:35:06 -0500 Subject: [PATCH 2/4] COMP: Remove unused variables. --- .../src/landmarksConstellationDetector.h | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/BRAINSConstellationDetector/src/landmarksConstellationDetector.h b/BRAINSConstellationDetector/src/landmarksConstellationDetector.h index d15c59251b..e6e58771b5 100644 --- a/BRAINSConstellationDetector/src/landmarksConstellationDetector.h +++ b/BRAINSConstellationDetector/src/landmarksConstellationDetector.h @@ -286,7 +286,7 @@ class landmarksConstellationDetector RigidTransformType::Pointer m_TmspBasedOnReflectionCrossCorrelation; SImageType::PointType m_CenterOfHeadMassEMSP; - SImageType::PointType m_BestCenter; + //SImageType::PointType m_BestCenter; SImageType::Pointer m_VolumeRoughAlignedWithHoughEye; SImageType::Pointer m_OriginalInputImage; SImageType::Pointer m_VolumeMSP; @@ -316,8 +316,8 @@ class landmarksConstellationDetector SImageType::PointType m_LEPoint; // in input space SImageType::PointType m_REPoint; - SImageType::PointType m_ReferencePointAC; - SImageType::PointType m_ReferencePointPC; + //SImageType::PointType m_ReferencePointAC; + //SImageType::PointType m_ReferencePointPC; SImageType::PointType m_CenterOfHeadMass; // Store linear model parameters From 0934f136c23c12ffdf8833928f7b9ea7de674ce9 Mon Sep 17 00:00:00 2001 From: Hans Johnson Date: Mon, 22 Oct 2018 19:40:18 -0500 Subject: [PATCH 3/4] COMP: ITKv5 updates for JPEG2000. --- CMake/FindITKUtil.cmake | 1 + SuperBuild/External_ITKv5.cmake | 3 ++- 2 files changed, 3 insertions(+), 1 deletion(-) diff --git a/CMake/FindITKUtil.cmake b/CMake/FindITKUtil.cmake index 00dda9af30..94178f2766 100644 --- a/CMake/FindITKUtil.cmake +++ b/CMake/FindITKUtil.cmake @@ -34,6 +34,7 @@ macro(FindITKUtil ITK_VAR_PREFIX ) ITKIOGDCM ITKIOGIPL ITKIOJPEG + ITKIOJPEG2000 ITKIOLSM ITKIOMeta ITKIONIFTI diff --git a/SuperBuild/External_ITKv5.cmake b/SuperBuild/External_ITKv5.cmake index a06f27c40e..5f4c75903a 100644 --- a/SuperBuild/External_ITKv5.cmake +++ b/SuperBuild/External_ITKv5.cmake @@ -39,7 +39,8 @@ if(NOT DEFINED ITK_DIR AND NOT ${CMAKE_PROJECT_NAME}_USE_SYSTEM_${proj}) endif() set(${CMAKE_PROJECT_NAME}_${proj}_GIT_REPOSITORY ${git_protocol}://itk.org/ITK.git) - set(${CMAKE_PROJECT_NAME}_${proj}_GIT_TAG f5e254b6680e6e52f6caf8d6eb2321c8829eedf3 ) # 20180905 ITKv5b01 + set(${CMAKE_PROJECT_NAME}_${proj}_GIT_TAG 465a69bc633aed484bcd46f323d93e32d4feed8d ) # 20181022 + set(EXTERNAL_PROJECT_OPTIONAL_CMAKE_CACHE_ARGS) if(NOT ${CMAKE_PROJECT_NAME}ITKV3_COMPATIBILITY AND CMAKE_CL_64) From 787f26527aa5c1c8554116f1bb61818dc53273a2 Mon Sep 17 00:00:00 2001 From: Hans Johnson Date: Mon, 22 Oct 2018 19:45:36 -0500 Subject: [PATCH 4/4] ENH: Updated packages for improved C++11. --- SuperBuild/External_ANTs.cmake | 2 +- SuperBuild/External_DCMTK.cmake | 10 +++++----- SuperBuild/External_OpenCV.cmake | 6 ++++-- SuperBuild/External_RTK.cmake | 3 ++- SuperBuild/External_TBB.cmake | 6 +++--- 5 files changed, 15 insertions(+), 12 deletions(-) diff --git a/SuperBuild/External_ANTs.cmake b/SuperBuild/External_ANTs.cmake index 1d80d9ff4f..1457165c04 100644 --- a/SuperBuild/External_ANTs.cmake +++ b/SuperBuild/External_ANTs.cmake @@ -38,7 +38,7 @@ if(${SUPERBUILD_TOPLEVEL_PROJECT}_USE_QT) endif() ### --- End Project specific additions set(${proj}_REPOSITORY "https://github.com/stnava/ANTs.git") -set(${proj}_GIT_TAG c3a2857a0805b9b1e3abde1f7bae446453f0e713) # 20180422 +set(${proj}_GIT_TAG 23003843bd0e0a9a83c7df0d688359dcf3c67460) # 20181017 ExternalProject_Add(${proj} ${${proj}_EP_ARGS} GIT_REPOSITORY ${${proj}_REPOSITORY} diff --git a/SuperBuild/External_DCMTK.cmake b/SuperBuild/External_DCMTK.cmake index e81028a14b..70277a42e5 100644 --- a/SuperBuild/External_DCMTK.cmake +++ b/SuperBuild/External_DCMTK.cmake @@ -60,12 +60,12 @@ if(NOT DEFINED DCMTK_DIR AND NOT ${CMAKE_PROJECT_NAME}_USE_SYSTEM_${proj}) ) ExternalProject_SetIfNotDefined( - ${CMAKE_PROJECT_NAME}_${proj}_GIT_TAG - # Include patches for: - # * DCMTK_ENABLE_CXX11 support on Linux + # Official DCMTK master as of 20180621 + # http://git.dcmtk.org/?p=dcmtk.git;a=commit;h=29f9de10c2e8576147f16475b156bba98d14ba7d + # plus the following patch: # * Set CMP0067 to ensure try_compile work as expected - # * Fix template parameter in dcmiod/iodimage - "54004ba20077c626ff4e3042b1d4a5b36eda5e0e" # v3.6.3_20180205 + ${CMAKE_PROJECT_NAME}_${proj}_GIT_TAG + "e79118cd2f40b77654630a56bbb17fe0bccc354c" # v3.6.3_20180621 QUIET ) diff --git a/SuperBuild/External_OpenCV.cmake b/SuperBuild/External_OpenCV.cmake index d9140a2630..fbbf5b444d 100644 --- a/SuperBuild/External_OpenCV.cmake +++ b/SuperBuild/External_OpenCV.cmake @@ -43,6 +43,8 @@ if(NOT ( DEFINED "USE_SYSTEM_${extProjName}" AND "${USE_SYSTEM_${extProjName}}" -DWITH_JPEG:BOOL=OFF -DWITH_TIFF:BOOL=OFF -DWITH_PNG:BOOL=OFF + + -DENABLE_CXX11:BOOL=ON #Will be required for OpenCV4 ## The following might cause build issues, here for testing #-- OUTDATED -DENABLE_SSE:BOOL=ON #-- OUTDATED -DENABLE_SSE2:BOOL=ON @@ -106,8 +108,8 @@ if(NOT ( DEFINED "USE_SYSTEM_${extProjName}" AND "${USE_SYSTEM_${extProjName}}" ### --- End Project specific additions #set(${proj}_REPOSITORY "${git_protocol}://github.com/Itseez/opencv") #set(${proj}_GIT_TAG "2.4.9") # USE THIS FOR UPDATED VERSION - set(${proj}_REPOSITORY "${git_protocol}://github.com/BRAINSia/opencv.git") # USE THIS FOR UPDATED VERSION - set(${proj}_GIT_TAG 71f42810808b78c1b85682058694db6e9bccaea5) # "20160127 + set(${proj}_REPOSITORY "${git_protocol}://github.com/opencv/opencv.git") + set(${proj}_GIT_TAG 3.4.2) # 20181017 #set(${proj}_GIT_TAG "20140630_Upstream") # USE THIS FOR UPDATED VERSION for GCC 4.4.7 on RHEL6 ExternalProject_Add(${proj} ${${proj}_EP_ARGS} diff --git a/SuperBuild/External_RTK.cmake b/SuperBuild/External_RTK.cmake index b58979c59a..5c4e6677c8 100644 --- a/SuperBuild/External_RTK.cmake +++ b/SuperBuild/External_RTK.cmake @@ -28,7 +28,8 @@ set(${proj}_CMAKE_OPTIONS ) ### --- End Project specific additions set(${proj}_REPOSITORY "https://github.com/SimonRit/RTK.git") -set(${proj}_GIT_TAG 125063515aa50208816e62d3e25042c0535859ee) # 20180421 +#set(${proj}_REPOSITORY "https://github.com/hjmjohnson/RTK.git") +set(${proj}_GIT_TAG 219f1cf25ec624a3beb0cc2ee5bd72e95013a120) #2018-10-20 ExternalProject_Add(${proj} ${${proj}_EP_ARGS} GIT_REPOSITORY ${${proj}_REPOSITORY} diff --git a/SuperBuild/External_TBB.cmake b/SuperBuild/External_TBB.cmake index 5e35fe71dc..52cc37225a 100644 --- a/SuperBuild/External_TBB.cmake +++ b/SuperBuild/External_TBB.cmake @@ -20,13 +20,13 @@ set(${proj}_CMAKE_OPTIONS ) set(${proj}_REPOSITORY ${git_protocol}://github.com/01org/tbb.git) -set(${proj}_GIT_TAG 2018_U2) # +set(${proj}_GIT_TAG 2018_U6) # 20181017 ExternalProject_Add(${proj} ${${proj}_EP_ARGS} GIT_REPOSITORY ${${proj}_REPOSITORY} GIT_TAG ${${proj}_GIT_TAG} SOURCE_DIR ${SOURCE_DOWNLOAD_CACHE}/${proj} - BINARY_DIR tbb_downloaded/2018_U2 + BINARY_DIR tbb_downloaded/${${proj}_GIT_TAG} DOWNLOAD_COMMAND "" #, no download CONFIGURE_COMMAND "" #, no config BUILD_COMMAND "" #, no build @@ -56,7 +56,7 @@ include(${CMAKE_CURRENT_LIST_DIR}/tbb_cmake/TBBGet.cmake) include(${CMAKE_CURRENT_LIST_DIR}/tbb_cmake/TBBBuild.cmake) tbb_get(TBB_ROOT TBB_LOCAL_SRC_DIR SAVE_TO ${SOURCE_DOWNLOAD_CACHE}/${proj} - RELEASE_TAG 2018_U2 + RELEASE_TAG ${${proj}_GIT_TAG} SYSTEM_NAME ${CMAKE_SYSTEM_NAME} CONFIG_DIR TBB_DIR SOURCE_CODE)