itk: use external dependencies (#7963)

* itk: use external dependencies

* disable test

* Update xmake.lua

* Update xmake.lua

* use static hdf5

* fix bsd

packages/i/itk/patch/linux.patch

@@ -1,22 +0,0 @@
-diff --git a/Modules/ThirdParty/MINC/src/libminc/libcommon/ParseArgv.c b/Modules/ThirdParty/MINC/src/libminc/libcommon/ParseArgv.c
-index 260f574..15d80dd 100644
---- a/Modules/ThirdParty/MINC/src/libminc/libcommon/ParseArgv.c
-+++ b/Modules/ThirdParty/MINC/src/libminc/libcommon/ParseArgv.c
-@@ -315,7 +315,7 @@ ParseArgv(argcPtr, argv, argTable, flags)
-          }
-          break;
-       case ARGV_FUNC: {
--         int (*handlerProc)() =  (int (*)())(uintptr_t)infoPtr->src;
-+         int (*handlerProc)(void *, const char *, char *) = (int (*)(void *, const char *, char *))(uintptr_t)infoPtr->src;
- 		
-          if ((*handlerProc)(infoPtr->dst, infoPtr->key,
-                             argv[srcIndex])) {
-@@ -325,7 +325,7 @@ ParseArgv(argcPtr, argv, argTable, flags)
-          break;
-       }
-       case ARGV_GENFUNC: {
--         int (*handlerProc)() = (int (*)())(uintptr_t)infoPtr->src;
-+         int (*handlerProc)(void *, const char *, int, char **) = (int (*)(void *, const char *, int, char **))(uintptr_t)infoPtr->src;
- 
-          argc = (*handlerProc)(infoPtr->dst, infoPtr->key,
-                                argc, argv+srcIndex);

packages/i/itk/patches/hdf5.patch

@@ -0,0 +1,45 @@
+diff --git a/Modules/ThirdParty/HDF5/CMakeLists.txt b/Modules/ThirdParty/HDF5/CMakeLists.txt
+index dcaa2fa..cc4d6ea 100644
+--- a/Modules/ThirdParty/HDF5/CMakeLists.txt
++++ b/Modules/ThirdParty/HDF5/CMakeLists.txt
+@@ -39,7 +39,6 @@ if(NOT ITK_BINARY_DIR)
+ endif()
+ ")
+ 
+-  if(BUILD_SHARED_LIBS)
+     if (TARGET hdf5-shared)
+       set(ITKHDF5_LIBRARIES hdf5_cpp-shared hdf5-shared hdf5_hl-shared)
+     elseif(TARGET hdf5::hdf5-shared)
+@@ -49,7 +48,6 @@ endif()
+     else()
+       set(ITKHDF5_LIBRARIES ${HDF5_C_SHARED_LIBRARY} ${HDF5_CXX_SHARED_LIBRARY} ${HDF5_CXX_LIBRARY_NAMES} ${HDF5_HL_SHARED_LIBRARY} ${HDF5_LIBRARIES})
+     endif()
+-  else()
+     if (TARGET hdf5-static)
+       set(ITKHDF5_LIBRARIES hdf5_cpp-static hdf5-static hdf5_hl-static)
+     elseif(TARGET hdf5::hdf5-static)
+@@ -59,7 +57,6 @@ endif()
+     else()
+       set(ITKHDF5_LIBRARIES ${HDF5_C_STATIC_LIBRARY} ${HDF5_CXX_STATIC_LIBRARY} ${HDF5_CXX_LIBRARY_NAMES} ${HDF5_HL_STATIC_LIBRARY} ${HDF5_LIBRARIES})
+     endif()
+-  endif()
+ 
+   set(ITKHDF5_INCLUDE_DIRS
+     ${ITKHDF5_BINARY_DIR}/src # itk_hdf5.h and itk_H5Cpp.h
+diff --git a/Modules/ThirdParty/HDF5/itk-module-init.cmake b/Modules/ThirdParty/HDF5/itk-module-init.cmake
+index 93604eb..74cc73c 100644
+--- a/Modules/ThirdParty/HDF5/itk-module-init.cmake
++++ b/Modules/ThirdParty/HDF5/itk-module-init.cmake
+@@ -3,11 +3,7 @@ mark_as_advanced(ITK_USE_SYSTEM_HDF5)
+ 
+ if(ITK_USE_SYSTEM_HDF5)
+   set(HDF5_NO_MODULE 1)
+-  if(ITK_BUILD_SHARED_LIBS)
+-    find_package(HDF5 QUIET NO_MODULE COMPONENTS CXX C HL shared)
+-  else()
+-    find_package(HDF5 QUIET NO_MODULE COMPONENTS CXX C HL static)
+-  endif()
++  find_package(HDF5 CONFIG REQUIRED)
+ 
+   if(NOT HDF5_FOUND)
+     find_package(HDF5 REQUIRED COMPONENTS CXX C HL)

packages/i/itk/xmake.lua

@@ -1,5 +1,4 @@
 package("itk")
-
     set_homepage("https://itk.org/")
     set_description("ITK is an open-source, cross-platform library that provides developers with an extensive suite of software tools for image analysis.")
     set_license("Apache-2.0")
@@ -9,51 +8,73 @@ package("itk")
     add_versions("5.2.1", "192d41bcdd258273d88069094f98c61c38693553fd751b54f8cda308439555db")
     add_versions("5.4.4", "d2092cd018a7b9d88e8c3dda04acb7f9345ab50619b79800688c7bc3afcca82a")
 
-    add_deps("cmake", "eigen")
+    add_patches(">5.0", "patches/hdf5.patch", "47594e3f5885a11dc214768d6fd6e54c014e1f335d24c7209a837a43f4a22631")
+
+    add_configs("opencv", {description = "Build ITKVideoBridgeOpenCV module.", default = false, type = "boolean"})
+    add_configs("vtk", {description = "Build ITKVtkGlue module.", default = false, type = "boolean"})
+
+    add_deps("cmake", "double-conversion", "eigen", "expat", "gdcm", "libjpeg", "libminc", "libpng", "libtiff", "vxl", "zlib")
+    add_deps("hdf5", {configs = {cpplib = true}})
     if is_plat("windows") then
         add_syslinks("shell32", "advapi32")
     elseif is_plat("linux") then
         add_extsources("apt::libinsighttoolkit5-dev", "pacman::itk")
-        add_patches("5.4.4", "patch/linux.patch", "e3971fb669bc20135310d912dd7272ce038a4745f35e21dec6e1e676a5045b94")
         add_syslinks("dl", "pthread")
+    elseif is_plat("bsd") then
+        add_syslinks("execinfo")
+    elseif is_plat("macosx") then
+        add_extsources("brew::itk")
     elseif is_plat("mingw") and is_subhost("msys") then
         add_extsources("pacman::itk")
     end
 
-    on_load("windows", "linux", "macosx", function (package)
+    on_load(function (package)
         local ver = package:version():major() .. "." .. package:version():minor()
         package:add("includedirs", "include/ITK-" .. ver)
-        local libs = {"ITKWatersheds", "ITKVideoIO", "ITKVideoCore", "ITKVTK", "ITKTestKernel", "ITKRegistrationMethodsv4", "ITKRegionGrowing", "ITKQuadEdgeMeshFiltering", "ITKOptimizersv4", "ITKMarkovRandomFieldsClassifiers", "itklbfgs", "ITKKLMRegionGrowing", "ITKIOVTK", "ITKIOTransformMatlab", "ITKIOTransformInsightLegacy", "ITKIOTransformHDF5", "ITKIOTransformBase", "ITKTransformFactory", "ITKIOStimulate", "ITKIOSpatialObjects", "ITKIOXML", "ITKIOSiemens", "ITKIOPNG", "itkpng", "ITKIONRRD", "ITKNrrdIO", "ITKIONIFTI", "ITKIOMeta", "ITKIOMeshVTK", "ITKIOMeshOFF", "ITKIOMeshOBJ", "ITKIOMeshGifti", "ITKIOMeshFreeSurfer", "ITKIOMeshBYU", "ITKIOMeshBase", "ITKIOMRC", "ITKIOMINC", "itkminc2", "ITKIOLSM", "ITKIOTIFF", "itktiff", "ITKIOJPEG2000", "itkopenjpeg", "ITKIOJPEG", "itkjpeg", "ITKIOHDF5", "ITKIOGIPL", "ITKIOGE", "ITKIOIPL", "ITKIOGDCM", "ITKIOCSV", "ITKIOBruker", "ITKIOBioRad", "ITKIOBMP", "ITKPDEDeformableRegistration", "ITKgiftiio", "ITKniftiio", "ITKznz", "gdcmMSFF", "gdcmDICT", "ITKEXPAT", "ITKDiffusionTensorImage", "ITKDenoising", "ITKDeformableMesh", "ITKDICOMParser", "ITKConvolution", "ITKFFT", "ITKColormap", "ITKBiasCorrection", "ITKPolynomials", "ITKOptimizers", "ITKImageFeature", "ITKSmoothing", "ITKIOImageBase", "ITKFastMarching", "ITKQuadEdgeMesh", "ITKMathematicalMorphology", "ITKLabelMap", "ITKPath", "ITKSpatialObjects", "ITKMetaIO", "itkzlib", "ITKMesh", "ITKTransform", "ITKStatistics", "itkNetlibSlatec", "ITKCommon", "itkvcl", "itkvnl_algo", "itkvnl", "itkv3p_netlib", "itksys", "itkdouble-conversion"}
+        local libs = { "ITKBiasCorrection", "ITKColormap", "ITKCommon", "ITKConvolution", "ITKDICOMParser", "ITKDeformableMesh", "ITKDenoising", "ITKDiffusionTensorImage", "ITKFFT", "ITKFastMarching", "ITKIOBMP", "ITKIOBioRad", "ITKIOBruker", "ITKIOCSV", "ITKIOGDCM", "ITKIOGE", "ITKIOGIPL", "ITKIOHDF5", "ITKIOIPL", "ITKIOImageBase", "ITKIOJPEG", "ITKIOJPEG2000", "ITKIOLSM", "ITKIOMINC", "ITKIOMRC", "ITKIOMeshBYU", "ITKIOMeshBase", "ITKIOMeshFreeSurfer", "ITKIOMeshGifti", "ITKIOMeshOBJ", "ITKIOMeshOFF", "ITKIOMeshVTK", "ITKIOMeta", "ITKIONIFTI", "ITKIONRRD", "ITKIOPNG", "ITKIOSiemens", "ITKIOSpatialObjects", "ITKIOStimulate", "ITKIOTIFF", "ITKIOTransformBase", "ITKIOTransformHDF5", "ITKIOTransformInsightLegacy", "ITKIOTransformMatlab", "ITKIOVTK", "ITKIOXML", "ITKImageFeature", "ITKImageIntensity", "ITKKLMRegionGrowing", "ITKLabelMap", "ITKMarkovRandomFieldsClassifiers", "ITKMathematicalMorphology", "ITKMesh", "ITKMetaIO", "ITKNrrdIO", "ITKOptimizers", "ITKOptimizersv4", "ITKPDEDeformableRegistration", "ITKPath", "ITKPolynomials", "ITKQuadEdgeMesh", "ITKQuadEdgeMeshFiltering", "ITKRegionGrowing", "ITKRegistrationMethodsv4", "ITKSmoothing", "ITKSpatialObjects", "ITKStatistics", "ITKTestKernel", "ITKTransform", "ITKTransformFactory", "ITKVNLInstantiation", "ITKVTK", "ITKVtkGlue", "ITKVideoCore", "ITKVideoIO", "ITKVideoBridgeOpenCV", "ITKWatersheds", "ITKgiftiio", "ITKniftiio", "ITKznz", "itkNetlibSlatec", "itklbfgs", "itkopenjpeg", "itksys" }
         for _, lib in ipairs(libs) do
             package:add("links", lib .. "-" .. ver)
         end
-        if package:is_plat("windows", "macosx") and package:config("shared") then
-            package:add("deps", "hdf5", {configs = {shared = true, cpplib = true}})
-        else
-            package:add("deps", "hdf5", {configs = {cpplib = true}})
+        if package:config("opencv") then
+            package:add("deps", "opencv")
+        end
+        if package:config("vtk") then
+            package:add("deps", "vtk")
         end
     end)
 
-    on_install("windows|!arm64", "linux", "macosx", function (package)
+    on_install("windows|!arm64", "linux", "macosx", "bsd", function (package)
+        io.replace("Modules/ThirdParty/GoogleTest/itk-module.cmake", "DEPENDS", "DEPENDS\n  EXCLUDE_FROM_DEFAULT", {plain = true})
         local configs = {"-DITK_SKIP_PATH_LENGTH_CHECKS=ON",
                          "-DBUILD_TESTING=OFF",
                          "-DBUILD_EXAMPLES=OFF",
                          "-DITK_WRAPPING=OFF",
+                         "-DDO_NOT_BUILD_ITK_TEST_DRIVER=ON",
+                         "-DITK_USE_SYSTEM_DOUBLECONVERSION=ON",
                          "-DITK_USE_SYSTEM_EIGEN=ON",
+                         "-DITK_USE_SYSTEM_EXPAT=ON",
+                         "-DITK_USE_SYSTEM_GDCM=ON",
+                         "-DITK_USE_SYSTEM_GOOGLETEST=ON",
                          "-DITK_USE_SYSTEM_HDF5=ON",
+                         "-DITK_USE_SYSTEM_JPEG=ON",
+                         "-DITK_USE_SYSTEM_MINC=ON",
+                         "-DITK_USE_SYSTEM_PNG=ON",
+                         "-DITK_USE_SYSTEM_TIFF=ON",
+                         "-DITK_USE_SYSTEM_VXL=ON",
+                         "-DITK_USE_SYSTEM_ZLIB=ON",
         }
-        table.insert(configs, "-DCMAKE_BUILD_TYPE=" .. (package:debug() and "Debug" or "Release"))
+        table.insert(configs, "-DCMAKE_BUILD_TYPE=" .. (package:is_debug() and "Debug" or "Release"))
         table.insert(configs, "-DBUILD_SHARED_LIBS=" .. (package:config("shared") and "ON" or "OFF"))
+        table.insert(configs, "-DModule_ITKVideoBridgeOpenCV=" .. (package:config("opencv") and "ON" or "OFF"))
+        table.insert(configs, "-DModule_ITKVtkGlue=" .. (package:config("vtk") and "ON" or "OFF"))
         table.insert(configs, "-DCMAKE_CXX_STANDARD=" .. (package:version():ge("5.4.0") and "17" or "14"))
         if package:config("pic") ~= false then
             table.insert(configs, "-DCMAKE_POSITION_INDEPENDENT_CODE=ON")
         end
         if package:is_plat("windows") then
             table.insert(configs, "-DITK_MSVC_STATIC_RUNTIME_LIBRARY=" .. (package:has_runtime("MT", "MTd") and "ON" or "OFF"))
-            import("package.tools.cmake").install(package, configs, {builddir = path.join(os.tmpdir(), "itk_build")})
-        else
-            import("package.tools.cmake").install(package, configs)
         end
+        import("package.tools.cmake").install(package, configs)
     end)
 
     on_test(function (package)