New upstream version 1.8.0+dfsg.1 (1afde37a) · Commits · Debian Med / plastimatch

CMakeLists.txt

+48 −28

Original line number	Diff line number	Diff line
		@@ -5,15 +5,16 @@
		##-----------------------------------------------------------------------------
		project (plastimatch)

		## The version here should be equal to the "most recent release"
		# The version here should be equal to the "most recent release"
		set (PLM_VERSION_MAJOR "1")
		set (PLM_VERSION_MINOR "7")
		set (PLM_VERSION_PATCH "4")
		set (PLM_VERSION_MINOR "8")
		set (PLM_VERSION_PATCH "0")

		##-----------------------------------------------------------------------------
		## Set up CMake defaults
		##-----------------------------------------------------------------------------
		cmake_minimum_required (VERSION 2.8.12)
		# CMAKE_CXX_STANDARD was introduced in 3.1.3
		cmake_minimum_required (VERSION 3.1.3)

		# CMP0003: Libraries linked via full path no longer produce linker search
		# paths.
		@@ -35,9 +36,13 @@ endif ()
		if (POLICY CMP0054)
		cmake_policy (SET CMP0054 NEW)
		endif ()
		# Fix behavior of CMAKE_CXX_STANDARD when targeting macOS.
		if (POLICY CMP0025)
		cmake_policy(SET CMP0025 NEW)
		endif ()

		##-----------------------------------------------------------------------------
		## CMake include files
		## CMake path
		##-----------------------------------------------------------------------------
		set (CMAKE_MODULE_PATH "${CMAKE_SOURCE_DIR}/cmake" ${CMAKE_MODULE_PATH})

		@@ -47,11 +52,17 @@ set (CMAKE_MODULE_PATH "${CMAKE_SOURCE_DIR}/cmake" ${CMAKE_MODULE_PATH})
		include (PreventInSourceBuilds)

		##-----------------------------------------------------------------------------
		## Macros and functions used in this script
		## Misc macros and functions used in this script
		##-----------------------------------------------------------------------------
		include (PlmMacros)
		include (SuperbuildOptions)

		##-----------------------------------------------------------------------------
		## Set C++ compiler standard
		##-----------------------------------------------------------------------------
		sb_set(CMAKE_CXX_STANDARD 11)
		sb_set(CMAKE_CXX_STANDARD_REQUIRED ON)

		##-----------------------------------------------------------------------------
		## Define default build type as Release
		##-----------------------------------------------------------------------------
		@@ -96,6 +107,8 @@ sb_option (PLM_CONFIG_PREFER_PATCHED_ITK
		"Prefer to use the patched version of certain ITK files" ON)
		sb_option (PLM_CONFIG_VOL_LIST
		"Native support for volumes with irregular slice thicknesses" OFF)
		sb_option (PLM_CONFIG_HARDEN_XFORM_BY_DEFAULT
		"By default, harden linear transforms rather than resample" OFF)

		# Plastimatch legacy options
		sb_option (PLM_CONFIG_LEGACY_BSPLINE_EXTEND
		@@ -239,6 +252,13 @@ if (WIN32 AND NOT CYGWIN AND NOT MINGW)
		)
		endif ()

		##-----------------------------------------------------------------------------
		## Disable spurious warnings on GCC
		##-----------------------------------------------------------------------------
		if (CMAKE_COMPILER_IS_GNUCC)
		add_compile_options (-Wno-cpp)
		endif ()

		##-----------------------------------------------------------------------------
		## Compile with -fPIC is needed for amd64 and other platforms
		##-----------------------------------------------------------------------------
		@@ -247,10 +267,10 @@ plm_set_pic_flags ()
		##-----------------------------------------------------------------------------
		## Extra paths
		##-----------------------------------------------------------------------------
		set (PLM_TESTING_SOURCE_DIR "${CMAKE_SOURCE_DIR}/Testing")
		set (PLM_TESTING_DATA_DIR "${CMAKE_SOURCE_DIR}/Testing/Data")
		set (PLM_TESTING_DOWNLOAD_DATA_DIR "${CMAKE_BINARY_DIR}/TestData")
		set (PLM_BUILD_TESTING_DIR "${CMAKE_BINARY_DIR}/Testing")
		set (PLM_TESTING_SOURCE_DIR "${PLM_SOURCE_DIR}/Testing")
		set (PLM_TESTING_DATA_DIR "${PLM_SOURCE_DIR}/Testing/Data")
		set (PLM_TESTING_DOWNLOAD_DATA_DIR "${PLM_BINARY_DIR}/TestData")
		set (PLM_BUILD_TESTING_DIR "${PLM_BINARY_DIR}/Testing")

		##-----------------------------------------------------------------------------
		## Set the math library
		@@ -342,7 +362,7 @@ find_package (wxWidgets)
		##-----------------------------------------------------------------------------
		if (NOT LIBLBFGS_FOUND)
		add_subdirectory (libs/liblbfgs-1.9)
		sb_set (LIBLBFGS_INCLUDE_DIR "${CMAKE_SOURCE_DIR}/libs/liblbfgs-1.9/include")
		sb_set (LIBLBFGS_INCLUDE_DIR "${PLM_SOURCE_DIR}/libs/liblbfgs-1.9/include")
		sb_set (LIBLBFGS_LIBRARIES lbfgs)
		link_directories (${CMAKE_CURRENT_BINARY_DIR}/libs/liblbfgs-1.9)
		sb_set (LIBLBFGS_FOUND TRUE)
		@@ -353,7 +373,7 @@ endif ()
		##-----------------------------------------------------------------------------
		if (NOT SQLITE_FOUND AND NOT PLM_CONFIG_DEBIAN_BUILD)
		add_subdirectory (libs/sqlite-3.6.21)
		set (SQLITE_INCLUDE_DIR "${CMAKE_SOURCE_DIR}/libs/sqlite-3.6.21")
		set (SQLITE_INCLUDE_DIR "${PLM_SOURCE_DIR}/libs/sqlite-3.6.21")
		set (SQLITE_LIBRARIES sqlite3)
		set (SQLITE_FOUND TRUE)
		endif ()
		@@ -361,13 +381,13 @@ endif ()
		#-----------------------------------------------------------------------------
		## Only use local devillard
		##-----------------------------------------------------------------------------
		sb_set (DEVILLARD_INCLUDE_DIR "${CMAKE_SOURCE_DIR}/libs/devillard")
		sb_set (DEVILLARD_INCLUDE_DIR "${PLM_SOURCE_DIR}/libs/devillard")
		add_subdirectory (libs/devillard)

		##-----------------------------------------------------------------------------
		## Only use local inih
		##-----------------------------------------------------------------------------
		sb_set (INIH_INCLUDE_DIR "${CMAKE_SOURCE_DIR}/libs/inih-r29")
		sb_set (INIH_INCLUDE_DIR "${PLM_SOURCE_DIR}/libs/inih-r29")
		add_subdirectory (libs/inih-r29)

		##-----------------------------------------------------------------------------
		@@ -375,7 +395,7 @@ add_subdirectory (libs/inih-r29)
		##-----------------------------------------------------------------------------
		# We can't use debian's lua 5.1 because it doesn't contain lobject.h
		#add_subdirectory (libs/lua-5.1.4)
		#set (LUA_INCLUDE_DIR "${CMAKE_SOURCE_DIR}/libs/lua-5.1.4/src")
		#set (LUA_INCLUDE_DIR "${PLM_SOURCE_DIR}/libs/lua-5.1.4/src")
		#link_directories (${CMAKE_CURRENT_BINARY_DIR}/libs/lua-5.1.4)

		# for history, etc in plastimatch tty mode
		@@ -392,12 +412,12 @@ sb_set (SPECFUN_FOUND TRUE)
		##-----------------------------------------------------------------------------
		## Only use local msinttypes
		##-----------------------------------------------------------------------------
		sb_set (MSINTTYPES_INCLUDE_DIR "${CMAKE_SOURCE_DIR}/libs")
		sb_set (MSINTTYPES_INCLUDE_DIR "${PLM_SOURCE_DIR}/libs")

		##-----------------------------------------------------------------------------
		## Only use local nkidecompress
		##-----------------------------------------------------------------------------
		sb_set (NKIDECOMPRESS_INCLUDE_DIR "${CMAKE_SOURCE_DIR}/libs/nkidecompress")
		sb_set (NKIDECOMPRESS_INCLUDE_DIR "${PLM_SOURCE_DIR}/libs/nkidecompress")
		add_subdirectory (libs/nkidecompress)

		##-----------------------------------------------------------------------------
		@@ -513,7 +533,7 @@ set (PLM_BASIC_VERSION_STRING
		"${PLM_VERSION_MAJOR}.${PLM_VERSION_MINOR}.${PLM_VERSION_PATCH}")
		set (PLASTIMATCH_VERSION_STRING
		"${PLM_VERSION_MAJOR}.${PLM_VERSION_MINOR}.${PLM_VERSION_PATCH}")
		if (EXISTS "${CMAKE_SOURCE_DIR}/.git" AND GIT_FOUND)
		if (EXISTS "${PLM_SOURCE_DIR}/.git" AND GIT_FOUND)
		if (GIT_EXECUTABLE MATCHES "[wW][sS][lL].*")
		set (GIT_EXECUTABLE "wsl;git")
		endif ()
		@@ -521,7 +541,7 @@ if (EXISTS "${CMAKE_SOURCE_DIR}/.git" AND GIT_FOUND)
		COMMAND
		#${GIT_EXECUTABLE} rev-list --first-parent --count HEAD
		${GIT_EXECUTABLE} ${GIT_EXECUTABLE_EXTRA} describe --always
		WORKING_DIRECTORY "${CMAKE_SOURCE_DIR}"
		WORKING_DIRECTORY "${PLM_SOURCE_DIR}"
		RESULT_VARIABLE git_result
		OUTPUT_VARIABLE git_output
		ERROR_VARIABLE git_error
		@@ -606,7 +626,7 @@ endif ()
		##-----------------------------------------------------------------------------
		## Only use local rapidjson
		##-----------------------------------------------------------------------------
		set (RAPIDJSON_DIR "${CMAKE_SOURCE_DIR}/libs/rapidjson-2015-03-22")
		set (RAPIDJSON_DIR "${PLM_SOURCE_DIR}/libs/rapidjson-2015-03-22")
		if (EXISTS "${RAPIDJSON_DIR}" AND IS_DIRECTORY "${RAPIDJSON_DIR}")
		set (RAPIDJSON_INCLUDE_DIR
		"${RAPIDJSON_DIR}/include"
		@@ -694,7 +714,7 @@ endif ()

		# Add sample directory/files to Install Only for windows users
		if (WIN32 OR WIN64)
		set (PLM_WINDOWS_INSTALL_DIR "${CMAKE_SOURCE_DIR}/extra/windows-install")
		set (PLM_WINDOWS_INSTALL_DIR "${PLM_SOURCE_DIR}/extra/windows-install")
		install (DIRECTORY "${PLM_WINDOWS_INSTALL_DIR}/sample" DESTINATION bin)
		install (FILES "${PLM_WINDOWS_INSTALL_DIR}/launch_cmd_prompt.bat" DESTINATION bin)
		endif ()
		@@ -796,9 +816,9 @@ macro (PLM_ADD_TEST PLM_TEST_NAME PLM_TEST_COMMAND PARMS)
		-DPLM_BUILD_TESTING_DIR=${PLM_BUILD_TESTING_DIR}
		"-DPARMS=${TMP_PARMS}"
		${EXTRA_PARMS}
		-P ${CMAKE_SOURCE_DIR}/cmake/RUN_CTEST.cmake
		-P ${PLM_SOURCE_DIR}/cmake/RUN_CTEST.cmake
		)
		# message (STATUS "${CMAKE_COMMAND} -DPLM_TEST_NAME=${PLM_TEST_NAME} ${PLM_ITK_LIBRARY_PATH_HACK} ${PLM_PLASTIMATCH_PATH_HACK} ${PLM_FFTW_PATH_HACK} -DPLM_TEST_COMMAND=${PLM_TEST_COMMAND} -DPLM_TESTING_SOURCE_DIR=${PLM_TESTING_SOURCE_DIR} -DPLM_BUILD_TESTING_DIR=${PLM_BUILD_TESTING_DIR} \"-DPARMS=${TMP_PARMS}\" ${EXTRA_PARMS} -P ${CMAKE_SOURCE_DIR}/cmake/RUN_CTEST.cmake")
		# message (STATUS "${CMAKE_COMMAND} -DPLM_TEST_NAME=${PLM_TEST_NAME} ${PLM_ITK_LIBRARY_PATH_HACK} ${PLM_PLASTIMATCH_PATH_HACK} ${PLM_FFTW_PATH_HACK} -DPLM_TEST_COMMAND=${PLM_TEST_COMMAND} -DPLM_TESTING_SOURCE_DIR=${PLM_TESTING_SOURCE_DIR} -DPLM_BUILD_TESTING_DIR=${PLM_BUILD_TESTING_DIR} \"-DPARMS=${TMP_PARMS}\" ${EXTRA_PARMS} -P ${PLM_SOURCE_DIR}/cmake/RUN_CTEST.cmake")
		endmacro ()

		# Figure out which tests to ignore
		@@ -806,11 +826,11 @@ endmacro ()
		# in either directory. MSVC uses the one in ${CMAKE_BINARY_DIR}.
		configure_file (
		${PLM_TESTING_SOURCE_DIR}/CTestCustom.cmake.in
		${CMAKE_BINARY_DIR}/CTestCustom.cmake
		${PLM_BINARY_DIR}/CTestCustom.cmake
		@ONLY)
		configure_file (
		${PLM_TESTING_SOURCE_DIR}/CTestCustom.cmake.in
		${CMAKE_BINARY_DIR}/Testing/CTestCustom.cmake
		${PLM_BINARY_DIR}/Testing/CTestCustom.cmake
		@ONLY)

		if (PLM_BUILD_TESTING)
		@@ -818,10 +838,10 @@ if (PLM_BUILD_TESTING)
		add_subdirectory (Testing)

		# Copy the lconv script
		if (EXISTS "${CMAKE_SOURCE_DIR}/extra/devtools/run_lcov.sh")
		if (EXISTS "${PLM_SOURCE_DIR}/extra/devtools/run_lcov.sh")
		configure_file (
		"${CMAKE_SOURCE_DIR}/extra/devtools/run_lcov.sh"
		"${CMAKE_BINARY_DIR}/run_lcov.sh"
		"${PLM_SOURCE_DIR}/extra/devtools/run_lcov.sh"
		"${PLM_BINARY_DIR}/run_lcov.sh"
		COPYONLY)
		endif ()
		endif ()

Testing/CMakeLists.txt

+281 −75

File changed.

Preview size limit exceeded, changes collapsed.

Testing/Data/itk-affine-a.tfm

0 → 100644

+5 −0

Original line number	Diff line number	Diff line
		#Insight Transform File V1.0
		#Transform 0
		Transform: AffineTransform_double_3_3
		Parameters: 0.925416578398323 0.1631759111665347 0.3420201433256686 0.018028311236297216 0.8825641192593854 -0.46984631039295405 -0.3785223063697923 0.4409696105298823 0.8137976813493736 2.257079707543866 31.926954809339303 -19.37976129358149
		FixedParameters: 0 0 0

cmake/FindDCMTK_wrap.cmake

+2 −8

Original line number	Diff line number	Diff line
		@@ -8,16 +8,10 @@ if (DCMTK_wrap_FIND_REQUIRED)
		list (APPEND DCMTK_EXTRA_ARGS REQUIRED)
		endif ()

		# if (DCMTK_DIR AND EXISTS "${DCMTK_DIR}/DCMTKConfig.cmake")
		# find_package (DCMTK NO_MODULE ${EXTRA_ARGS})
		# else ()
		# find_package (DCMTK_legacy ${EXTRA_ARGS})
		# endif ()

		find_package (DCMTK NO_MODULE ${EXTRA_ARGS})
		find_package (DCMTK NO_MODULE ${DCMTK_EXTRA_ARGS})
		if (NOT DCMTK_FOUND)
		message (STATUS "Searching for DCMTK using legacy method")
		find_package (DCMTK_legacy ${EXTRA_ARGS})
		find_package (DCMTK_legacy ${DCMTK_EXTRA_ARGS})
		endif ()

		# The DCMTK 3.6.2 DCMTKConfig.cmake seems to be broken on windows

cmake/HandleITK.cmake

+2 −2

Original line number	Diff line number	Diff line
		@@ -40,8 +40,8 @@ elseif (${ITK_VERSION_MAJOR} VERSION_EQUAL "4")
		"Fatal Error. ITK 4 must be 4.1 or greater")
		endif ()
		else ()
		message (FATAL_ERROR
		"Fatal Error. ITK version should be either 3.X or 4.X")
		message (AUTHOR_WARNING
		"Warning. ITK version greater than 4.X is not tested")
		endif ()
		message (STATUS "ITK_VERSION = ${ITK_VERSION} found")