CMakeLists.txt

@@ -8,9 +8,7 @@ project (plastimatch)
 ## 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 "0")
-#set (PLM_RELEASE_VERSION FALSE)
-set (PLM_RELEASE_VERSION TRUE)
+set (PLM_VERSION_PATCH "3")
 
 ##-----------------------------------------------------------------------------
 ##  Set up CMake defaults
@@ -67,18 +65,23 @@ sb_variable (CMAKE_BUILD_TYPE)
 ##-----------------------------------------------------------------------------
 ##  Define plastimatch configuration variables
 ##-----------------------------------------------------------------------------
-sb_option (PLM_CONFIG_DISABLE_CUDA "Set to ON to build without CUDA" OFF)
-option (PLM_CONFIG_DISABLE_DCMTK "Set to ON to build without DCMTK" OFF)
-option (PLM_CONFIG_DISABLE_FATM "Set to ON to build without FATM" ON)
-option (PLM_CONFIG_DISABLE_MONDOSHOT "Disable building mondoshot" ON)
-sb_option (PLM_CONFIG_DISABLE_OPENCL "Set to ON to build without OpenCL" OFF)
-sb_option (PLM_CONFIG_DISABLE_OPENMP "Set to ON to build without OpenMP" OFF)
-option (PLM_CONFIG_DISABLE_PLASTIMATCH "Disable building plastimatch" OFF)
-option (PLM_CONFIG_DISABLE_QT "Set to ON to build without QT" OFF)
-sb_option (PLM_CONFIG_DISABLE_SSE2 "Set to ON to build without SSE" OFF)
-option (PLM_CONFIG_ENABLE_MATLAB "Set to ON to build Matlab plugins" OFF)
-
-option (PLM_CONFIG_BUILD_QT_PLUGINS "Build QT4 Designer Plugins?" OFF)
+sb_option (PLM_CONFIG_ENABLE_CUDA "Set to ON to allow build with CUDA" ON)
+option (PLM_CONFIG_ENABLE_DCMTK "Set to ON to allow build with DCMTK" ON)
+option (PLM_CONFIG_ENABLE_FATM "Set to ON to allow building fatm" OFF)
+option (PLM_CONFIG_ENABLE_MONDOSHOT "Set to ON to allow building mondoshot" OFF)
+sb_option (PLM_CONFIG_ENABLE_OPENCL "Set to ON to allow build with OpenCL" ON)
+sb_option (PLM_CONFIG_ENABLE_OPENMP "Set to ON to allow build with OpenMP" ON)
+sb_option (PLM_CONFIG_ENABLE_OPT4D "Set to ON to allow build with Opt4D" OFF)
+option (PLM_CONFIG_ENABLE_PLASTIMATCH "Set to ON to allow building plastimatch" ON)
+option (PLM_CONFIG_ENABLE_QT "Set to ON to allow build with QT" ON)
+sb_option (PLM_CONFIG_ENABLE_SSE2 "Set to ON to allow build with SSE" ON)
+option (PLM_CONFIG_ENABLE_MATLAB "Set to ON to allow build of Matlab plugins" OFF)
+sb_option (PLM_CONFIG_ENABLE_VISCOUS
+  "Set to ON to allow build of experimental viscous fluid registration algorithm" OFF)
+sb_option (PLM_CONFIG_ENABLE_PLASTIMATCH_QT
+  "Set to ON to allow build of experimental plastimatch_qt executable" OFF)
+
+option (PLM_CONFIG_BUILD_QT_PLUGINS "Set to ON to allow build of QT4 Designer Plugins" OFF)
 sb_option (PLM_CONFIG_DEBIAN_BUILD "Set to ON to configure build for debian" OFF)
 option (PLM_CONFIG_LIBRARY_BUILD "Set to ON to build only libraries" OFF)
 option (PLM_CONFIG_NOMANIFEST
@@ -89,10 +92,6 @@ option (PLM_CONFIG_ENABLE_SUPERBUILD
 # Plastimatch software configuration options
 option (PLM_CONFIG_CLANG_COMPLETE
   "Generate .clang_complete for hipster Vim-ers" OFF)
-option (PLM_CONFIG_DISABLE_VISCOUS
-  "Disable experimental viscous fluid registration algorithm" ON)
-option (PLM_CONFIG_ENABLE_PLASTIMATCH_QT
-  "Enable experimental plastimatch_qt executable" OFF)
 sb_option (PLM_CONFIG_PREFER_PATCHED_ITK
   "Prefer to use the patched version of certain ITK files" ON)
 sb_option (PLM_CONFIG_VOL_LIST
@@ -103,12 +102,20 @@ sb_option (PLM_CONFIG_LEGACY_BSPLINE_EXTEND
   "Use legacy code for extending b-spline domain" OFF)
 sb_option (PLM_CONFIG_LEGACY_BSPLINE_XFORM_IO
   "Use legacy code for reading and writing b-spline xform files" OFF)
+sb_option (PLM_CONFIG_LEGACY_CUDA_DELAYLOAD
+  "Use legacy code for verifying CUDA runtime" ON)
+sb_option (PLM_CONFIG_LEGACY_DRR_CUDA_TEXTURE
+  "Use legacy 1D texture for CUDA DRR generation" OFF)
 sb_option (PLM_CONFIG_LEGACY_MI_METRIC
   "For ITK metrics, the legacy implementation of the mi metric is Viola-Wells to Mattes" OFF)
 sb_option (PLM_CONFIG_LEGACY_PROJ_GEO
   "Use legacy method for specifying projection geometry" ON)
+sb_option (PLM_CONFIG_LEGACY_RAY_TRACE_EXACT
+  "Use legacy algorithm for exact ray tracing" OFF)
 
 # Compile and link options
+sb_option (PLM_CUDA_ALL_DEVICES
+  "Generate GPU code for all compute capabilities?" OFF)
 sb_option (BUILD_SHARED_LIBS "Build plastimatch as shared library" OFF)
 
 # Choose whether to build against included and/or superbuild libraries
@@ -133,7 +140,7 @@ sb_option (PLM_CONFIG_INSTALL_LIBRARIES "Include libraries in install" ON)
 option (PLM_PACKAGE_32BIT
     "Set this when building 32-bit packages on a 64-bit machine" OFF)
 option (PLM_PACKAGE_NSIS "Set to ON when packaging binaries with NSIS" OFF)
-option (PLM_PACKAGE_WIX "Set to ON when packaging binaries with WIX" OFF)
+option (PLM_PACKAGE_WIX "Set to ON when packaging binaries with WIX" ON)
 sb_option (PLM_PACKAGE_LEGACY_CMAKE_CONFIG
     "Use the old code for creating PlastimatchConfig.cmake and friends" OFF)
 
@@ -144,8 +151,8 @@ endif ()
 
 # Override some options if library build is selected
 if (PLM_CONFIG_LIBRARY_BUILD)
-  set (PLM_CONFIG_DISABLE_FATM ON)
-  set (PLM_CONFIG_DISABLE_MONDOSHOT ON)
+  set (PLM_CONFIG_ENABLE_FATM OFF)
+  set (PLM_CONFIG_ENABLE_MONDOSHOT OFF)
 endif ()
 
 ##-----------------------------------------------------------------------------
@@ -267,19 +274,11 @@ find_library (LIBDL_FOUND dl)
 ## it will have a working version of DCMTKConfig.cmake.
 ## In this case, we can use the modern find_package variant.
 ## Otherwise we use the old hacked version of FindDCMTK.cmake.
-if (NOT PLM_CONFIG_DISABLE_DCMTK)
+if (PLM_CONFIG_ENABLE_DCMTK)
   if (PLM_SYSTEM_DCMTK STREQUAL "YES")
-    if (DCMTK_DIR AND EXISTS "${DCMTK_DIR}/DCMTKConfig.cmake")
-      find_package (DCMTK NO_MODULE REQUIRED)
-    else ()
-      find_package (DCMTK_legacy REQUIRED)
-    endif ()
+    find_package (DCMTK_wrap REQUIRED)
   elseif (PLM_SYSTEM_DCMTK STREQUAL "PREFERRED")
-    if (DCMTK_DIR AND EXISTS "${DCMTK_DIR}/DCMTKConfig.cmake")
-      find_package (DCMTK NO_MODULE QUIET)
-    else ()
-      find_package (DCMTK_legacy QUIET)
-    endif ()
+    find_package (DCMTK_wrap QUIET)
   endif ()
 
   if (NOT DCMTK_FOUND AND NOT PLM_SYSTEM_DCMTK STREQUAL "YES")
@@ -292,6 +291,8 @@ if (NOT PLM_CONFIG_DISABLE_DCMTK)
       message (STATUS "DCMTK not found.")
     endif ()
   endif ()
+else ()
+  set (DCMTK_FOUND FALSE)
 endif ()
 
 # Workaround for CMake bug in FindDCMTK.  This was fixed some time between
@@ -317,10 +318,10 @@ else ()
   set (MATLAB_FOUND false)
 endif ()
 find_package (Octave)
-if (NOT PLM_CONFIG_DISABLE_OPENCL)
+if (PLM_CONFIG_ENABLE_OPENCL)
   find_package (OpenCL)
 endif ()
-if (NOT PLM_CONFIG_DISABLE_OPENMP)
+if (PLM_CONFIG_ENABLE_OPENMP)
   find_package (OpenMP)
 endif ()
 if (PLM_CONFIG_DEBIAN_BUILD)
@@ -328,8 +329,8 @@ if (PLM_CONFIG_DEBIAN_BUILD)
 else ()
   find_package (SQLite)
 endif ()
-if (NOT PLM_CONFIG_DISABLE_SSE2)
-  find_package (SSE)           # SSE Extensions for CPU
+if (PLM_CONFIG_ENABLE_SSE2)
+  find_package (SSE)
 else ()
   set (SSE2_FOUND false)
 endif ()
@@ -402,14 +403,14 @@ add_subdirectory (libs/nkidecompress)
 ##-----------------------------------------------------------------------------
 ##  Special CUDA processing
 ##-----------------------------------------------------------------------------
-if (PLM_CONFIG_DISABLE_CUDA)
-  set (CUDA_FOUND false)
-else ()
+if (PLM_CONFIG_ENABLE_CUDA)
   find_package (CUDA_wrap)
   set (CUDA_FOUND ${CUDA_FOUND} CACHE BOOL "Did we find cuda?")
   if (CUDA_FOUND)
     cuda_include_directories (${CMAKE_CURRENT_SOURCE_DIR})
   endif ()
+else ()
+  set (CUDA_FOUND false)
 endif ()
 
 ##-----------------------------------------------------------------------------
@@ -512,33 +513,38 @@ 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 (NOT PLM_RELEASE_VERSION)
-  set (PLASTIMATCH_VERSION_STRING "${PLASTIMATCH_VERSION_STRING}-dev")
-endif ()
 if (EXISTS "${CMAKE_SOURCE_DIR}/.git" AND GIT_FOUND)
+  if (GIT_EXECUTABLE MATCHES "[wW][sS][lL].*")
+    set (GIT_EXECUTABLE "wsl;git")
+  endif ()
   execute_process (
     COMMAND
     #${GIT_EXECUTABLE} rev-list --first-parent --count HEAD
-    ${GIT_EXECUTABLE} describe --always
+    ${GIT_EXECUTABLE} ${GIT_EXECUTABLE_EXTRA} describe --always
     WORKING_DIRECTORY "${CMAKE_SOURCE_DIR}"
     RESULT_VARIABLE git_result
-    OUTPUT_VARIABLE git_version
+    OUTPUT_VARIABLE git_output
     ERROR_VARIABLE git_error
     OUTPUT_STRIP_TRAILING_WHITESPACE
     )
   if (${git_result} EQUAL 0)
-    set (PLASTIMATCH_VERSION_STRING "${PLASTIMATCH_VERSION_STRING} (${git_version})")
+    string (REGEX MATCH "[^-]*-([0-9]+)-.*" junk ${git_output})
+    set (PLM_VERSION_TWEAK "${CMAKE_MATCH_1}")
+    set (PLASTIMATCH_VERSION_STRING "${git_output}")
   endif ()
-  message (STATUS "Plastimatch version is ${git_version}")
 endif ()
+message (STATUS "Plastimatch version is ${PLASTIMATCH_VERSION_STRING}")
 
 ##-----------------------------------------------------------------------------
 ##  ITK
 ##-----------------------------------------------------------------------------
+set (FIND_LIBRARY_USE_LIB64 true)
 if (PLM_SYSTEM_ITK STREQUAL "YES")
-  find_package (ITK REQUIRED)
+  find_package (ITK REQUIRED
+    PATHS "/usr/lib64/cmake/InsightToolkit")
 elseif (PLM_SYSTEM_ITK STREQUAL "PREFERRED")
-  find_package (ITK QUIET)
+  find_package (ITK QUIET
+    PATHS "/usr/lib64/cmake/InsightToolkit")
 endif ()
 if (NOT ITK_FOUND AND NOT PLM_SYSTEM_ITK STREQUAL "YES")
   message (STATUS "ITK will be downloaded and built.")
@@ -547,6 +553,7 @@ endif ()
 
 if (ITK_FOUND)
   include (HandleITK)
+  include (HandleVXL)
 endif ()
 
 ##-----------------------------------------------------------------------------
@@ -593,12 +600,12 @@ endif ()
 ##-----------------------------------------------------------------------------
 ##  QT
 ##-----------------------------------------------------------------------------
-if (PLM_CONFIG_DISABLE_QT)
-  set (QT4_FOUND false)
-  set (QT5_FOUND false)
-else ()
+if (PLM_CONFIG_ENABLE_QT)
   find_package (Qt4 4.6.3 QUIET COMPONENTS QtCore QtGui QtDesigner)
   find_package (Qt5 QUIET COMPONENTS Core Gui Designer Network Widgets)
+else ()
+  set (QT4_FOUND false)
+  set (QT5_FOUND false)
 endif ()
 
 if (QT4_FOUND)
@@ -653,10 +660,24 @@ endif ()
 ##-----------------------------------------------------------------------------
 find_package (LibYAML)
 
+##-----------------------------------------------------------------------------
+##  Opt4D
+##-----------------------------------------------------------------------------
+if (PLM_CONFIG_ENABLE_OPT4D)
+  set (opt4D_DIR "${opt4D_DIR}" CACHE PATH "Path to opt4D build directory")
+  find_package (opt4D)
+  if (NOT opt4D_FOUND)
+    message (STATUS "Opt4D will be downloaded and built.")
+    include (SuperBuild/External_opt4D.cmake)
+  endif ()
+else ()
+  set (opt4D_FOUND FALSE)
+endif ()
+
 ##-----------------------------------------------------------------------------
 ##  Configure include files
 ##-----------------------------------------------------------------------------
-set (PLM_BUILD_SHARED_LIBS ${BUILD_SHARED_LIBS})
+sb_set (PLM_BUILD_SHARED_LIBS ${BUILD_SHARED_LIBS})
 
 ##-----------------------------------------------------------------------------
 ##  Subdirectories
@@ -667,10 +688,13 @@ add_subdirectory (src)
 ##  Additional install files
 ##-----------------------------------------------------------------------------
 if (ITK_FOUND)
-  file (GLOB DLLFILES "${ITK_DIR}/bin/release/*.dll")
+  set (DLL_PATTERNS "ITKCommon*.dll" "ITKIO*.dll" "ITKOptimizers*.dll" "ITKStatistics*.dll" "ITKTransform*.dll")
+  foreach (p ${DLL_PATTERNS})
+    file (GLOB DLLFILES "${ITK_DIR}/bin/release/${p}")
     if (DLLFILES)
       install (FILES ${DLLFILES} DESTINATION bin)
     endif ()
+  endforeach ()
 endif ()
 
 #Add QT dlls to Install
@@ -849,7 +873,7 @@ endif ()
 ##    ...from within your build directory
 ##-----------------------------------------------------------------------------
 # Choose generator
-if (PLM_PACKAGE_WIX)
+if (WIN32 AND PLM_PACKAGE_WIX)
   set (CPACK_GENERATOR "WIX")
 elseif (PLM_PACKAGE_NSIS)
   set (CPACK_GENERATOR "NSIS")
@@ -867,12 +891,13 @@ set (CPACK_MONOLITHIC_INSTALL 1)
 set (CPACK_INSTALL_PREFIX "")
 set (CPACK_PACKAGE_CONTACT "plastimatch@googlegroups.com")
 set (CPACK_PACKAGE_NAME "plastimatch")
+set (CPACK_PACKAGE_INSTALL_DIRECTORY "Plastimatch")
 set (CPACK_PACKAGE_DESCRIPTION_SUMMARY "Plastimatch - A Medical Imaging Application")
 set (CPACK_PACKAGE_VENDOR "Plastimatch Dev Team")
 set (CPACK_PACKAGE_VERSION_MAJOR "${PLM_VERSION_MAJOR}")
 set (CPACK_PACKAGE_VERSION_MINOR "${PLM_VERSION_MINOR}")
 set (CPACK_PACKAGE_VERSION_PATCH "${PLM_VERSION_PATCH}")
-set (CPACK_PACKAGE_VERSION_TWEAK ${PLASTIMATCH_REPOSITORY_VERSION})
+set (CPACK_PACKAGE_VERSION_TWEAK "${PLM_VERSION_TWEAK}")
 set (CPACK_SOURCE_IGNORE_FILES
   "/\\\\.git"
   "/\\\\.svn"
@@ -893,6 +918,31 @@ set (CPACK_WIX_LICENSE_RTF  "${PLM_WINDOWS_INSTALL_DIR}/License.rtf")
 set (CPACK_WIX_UI_BANNER  "${PLM_WINDOWS_INSTALL_DIR}/plm_logo.jpg")
 set (CPACK_WIX_UI_DIALOG  "${PLM_WINDOWS_INSTALL_DIR}/plm_logo_GUI.jpg")
 
+set (CPACK_WIX_EXTRA_SOURCES
+    "${PLM_SOURCE_DIR}/extra/wix/cmake_extra_dialog.wxs"
+    "${PLM_SOURCE_DIR}/extra/wix/install_dir.wxs"
+    "${PLM_SOURCE_DIR}/extra/wix/start_menu.wxs"
+    )
+set (CPACK_WIX_PATCH_FILE
+    "${PLM_SOURCE_DIR}/extra/wix/patch_path_env.xml"
+#    "${PLM_SOURCE_DIR}/extra/wix/patch_start_menu.xml"
+    )
+set (CPACK_WIX_UI_REF "CMakeUI_InstallDir")
+if (CPACK_GENERATOR STREQUAL "WIX")
+  set (CPACK_PACKAGE_NAME "Plastimatch")
+  if (CPACK_PACKAGE_VERSION_TWEAK AND CPACK_PACKAGE_VERSION_TWEAK GREATER "0")
+    set (CPACK_PACKAGE_VERSION "${CPACK_PACKAGE_VERSION_MAJOR}.${CPACK_PACKAGE_VERSION_MINOR}.${CPACK_PACKAGE_VERSION_PATCH}.${CPACK_PACKAGE_VERSION_TWEAK}")
+    if (CMAKE_SIZEOF_VOID_P EQUAL 8)
+      set (CPACK_SYSTEM_NAME "win64")
+    else ()
+      set (CPACK_SYSTEM_NAME "win32")
+    endif ()
+    set (CPACK_PACKAGE_FILE_NAME "${CPACK_PACKAGE_NAME}-${CPACK_PACKAGE_VERSION}-${CPACK_SYSTEM_NAME}")
+  endif ()
+  set_property (INSTALL "bin/launch_cmd_prompt.bat"
+    PROPERTY CPACK_START_MENU_SHORTCUTS "Plastimatch Command Prompt")
+endif ()
+
 # ZIP stuff
 if (CPACK_GENERATOR STREQUAL "ZIP")
   set (CPACK_SET_DESTDIR ON)

LICENSE.TXT

-Plastimatch and uno-2-3-reg are distributed under BSD-style licenses.
+Plastimatch is distributed under a BSD-style license.
 
-Please see src/plastimatch/LICENSE.TXT and src/uno-2-3-reg/LICENSE.txt 
-for license details.
+Please see src/plastimatch/LICENSE.TXT for details.
 

SuperBuild/External_opt4D.cmake

+##-----------------------------------------------------------------------------
+##  Download opt4D from internet and compile
+##-----------------------------------------------------------------------------
+set (proj opt4D)
+
+if(NOT DEFINED git_protocol)
+  set(git_protocol "git")
+endif()
+
+set (opt4D_GIT_REPOSITORY "${git_protocol}://gitlab.com/gregsharp/opt4D.git")
+set (opt4D_GIT_TAG "2e5a9edcdc472c427ccfc2c567499a7405f02e47")
+
+ExternalProject_Add (${proj}
+  GIT_REPOSITORY "${opt4D_GIT_REPOSITORY}"
+  GIT_TAG ${opt4D_GIT_TAG}
+  SOURCE_DIR ${proj}
+  BINARY_DIR ${proj}-build
+  CMAKE_GENERATOR ${gen}
+  CMAKE_ARGS
+  -DCMAKE_BUILD_TYPE:STRING=${CMAKE_BUILD_TYPE}
+  -DCMAKE_CXX_COMPILER:FILEPATH=${CMAKE_CXX_COMPILER}
+  -DCMAKE_CXX_FLAGS:STRING=${CMAKE_CXX_FLAGS}
+  -DCMAKE_C_COMPILER:FILEPATH=${CMAKE_C_COMPILER}
+  -DCMAKE_C_FLAGS:STRING=${CMAKE_C_FLAGS}
+  #    -DCMAKE_CXX_STANDARD:STRING=${CMAKE_CXX_STANDARD}
+  -DCMAKE_CXX_STANDARD_REQUIRED:BOOL=${CMAKE_CXX_STANDARD_REQUIRED}
+  -DCMAKE_CXX_EXTENSIONS:BOOL=${CMAKE_CXX_EXTENSIONS}
+  -DBUILD_EXAMPLES:BOOL=OFF
+  -DBUILD_SHARED_LIBS:BOOL=ON
+  -DBUILD_TESTING:BOOL=OFF
+  -DModule_ITKReview:BOOL=ON
+  INSTALL_COMMAND ""
+  )
+
+set (opt4D_DIR ${CMAKE_BINARY_DIR}/${proj}-build)

Testing/CMakeLists.txt

@@ -822,6 +822,7 @@ set_tests_properties (demons-cuda-a-check PROPERTIES DEPENDS demons-cuda-a)
 ##   drr-d       gauss-4.mha (negative spacing), uniform
 ##   drr-cuda    gauss-1.mha, uniform
 ##   drr-opencl  gauss-1.mha, uniform
+##   pcmd-drr-a  same as drr-a, but with plastimatch front end
 ## -------------------------------------------------------------------------
 plm_add_test (
   "drr-a"
@@ -943,6 +944,26 @@ set_tests_properties (drr-opencl PROPERTIES DEPENDS gauss-1)
 set_tests_properties (drr-opencl-stats PROPERTIES DEPENDS drr-opencl)
 set_tests_properties (drr-opencl-check PROPERTIES DEPENDS drr-opencl-stats)
 
+plm_add_test (
+  "plm-drr-a"
+  ${PLM_PLASTIMATCH_PATH}/plastimatch
+  "drr;-a;20;-O;${PLM_BUILD_TESTING_DIR}/plm-drr-a/out_;-I;${PLM_BUILD_TESTING_DIR}/gauss-1.mha"
+  )
+plm_add_test (
+  "plm-drr-a-stats"
+  ${PLM_PLASTIMATCH_PATH}/plastimatch
+  "stats;${PLM_BUILD_TESTING_DIR}/plm-drr-a/out_0010.pfm"
+  )
+plmtest_check_interval ("plm-drr-a-check"
+  "${PLM_BUILD_TESTING_DIR}/plm-drr-a-stats.stdout.txt"
+  "MAX *([-0-9.]*)"
+  "0.045"
+  "0.055"
+  )
+set_tests_properties (plm-drr-a PROPERTIES DEPENDS gauss-1)
+set_tests_properties (plm-drr-a-stats PROPERTIES DEPENDS plm-drr-a)
+set_tests_properties (plm-drr-a-check PROPERTIES DEPENDS plm-drr-a-stats)
+
 ## -------------------------------------------------------------------------
 ## fdk - all tests using fdk filtered backprojection
 ##   fdk-cpu-a     CPU reconstruction of synthetic data, flavor a

Testing/CTestCustom.cmake.in

@@ -58,6 +58,9 @@ if (OPENCL_FOUND)
   endif ()
 endif ()
 
+# OpenCL tests disabled/issue #30
+set (RUN_OPENCL_TESTS OFF)
+
 # In ITK 3.20.1 (official release), masked registration is broken
 if (NOT ${ITK_VERSION} VERSION_GREATER "3.20.1")
 set (CTEST_CUSTOM_TESTS_IGNORE

cmake/CheckNullptr.cmake

+######################################################
+##  Check if nullptr is supported by the compiler
+##  Returns: HAVE_NULLPTR
+######################################################
+include (CheckCXXSourceCompiles)
+set (NULLPTR_TEST_SOURCE "int main() {(void)nullptr;}")
+check_cxx_source_compiles ("${NULLPTR_TEST_SOURCE}" HAVE_NULLPTR)
+if (NOT HAVE_NULLPTR)
+  unset (HAVE_NULLPTR CACHE)
+  push_var (CMAKE_REQUIRED_FLAGS)
+  set (CMAKE_REQUIRED_FLAGS "-std=c++11")
+  check_cxx_source_compiles ("${NULLPTR_TEST_SOURCE}" HAVE_NULLPTR)
+  pop_var (CMAKE_REQUIRED_FLAGS)
+  if (HAVE_NULLPTR)
+    set (CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -std=c++11")
+  endif ()
+endif ()

cmake/FindAdvantech.cmake

-# Detect development libraries for Advantech I/O card.
-# These variables are set:
-#
-#   ADVANTECH_FOUND
-#   ADVANTECH_INCLUDE_DIR
-#   ADVANTECH_LIBRARIES
-#
-# Only works on Windows
-
-if (ADVANTECH_INCLUDE_DIR)
-  # Already in cache, be silent
-  set (Advantech_FIND_QUIETLY TRUE)
-endif ()
-
-FIND_PATH (ADVANTECH_INCLUDE_DIR "Driver.h"
-  "C:/Program Files/Advantech/Adsapi/Include"
-  DOC "Path to ADVANTECH include files.")
-
-FIND_PATH (ADVANTECH_LIBRARY_PATH "ADSDEV.lib"
-  "C:/Program Files/Advantech/Adsapi/Lib"
-  DOC "Path to ADVANTECH libraries.")
-
-FIND_LIBRARY(ADVANTECH_ADS841_LIB ADS841 ${ADVANTECH_LIBRARY_PATH})
-FIND_LIBRARY(ADVANTECH_Adsapi32_LIB Adsapi32 ${ADVANTECH_LIBRARY_PATH})
-FIND_LIBRARY(ADVANTECH_Adsapi32bcb_LIB Adsapi32bcb ${ADVANTECH_LIBRARY_PATH})
-FIND_LIBRARY(ADVANTECH_Adscomm_LIB Adscomm ${ADVANTECH_LIBRARY_PATH})
-FIND_LIBRARY(ADVANTECH_ADSDEV_LIB ADSDEV ${ADVANTECH_LIBRARY_PATH})
-FIND_LIBRARY(ADVANTECH_adsdnet_LIB adsdnet ${ADVANTECH_LIBRARY_PATH})
-
-if (ADVANTECH_Adscomm_LIB AND ADVANTECH_Adsapi32_LIB)
-  set (ADVANTECH_LIBRARIES ${ADVANTECH_Adscomm_LIB} ${ADVANTECH_Adsapi32_LIB})
-else ()
-  set (ADVANTECH_LIBRARIES)
-endif ()
-
-INCLUDE (FindPackageHandleStandardArgs)
-FIND_PACKAGE_HANDLE_STANDARD_ARGS (Advantech DEFAULT_MSG 
-  ADVANTECH_LIBRARIES ADVANTECH_INCLUDE_DIR)
-
-MARK_AS_ADVANCED (
-  ADVANTECH_ADS841_LIB
-  ADVANTECH_Adsapi32_LIB
-  ADVANTECH_Adsapi32bcb_LIB
-  ADVANTECH_Adscomm_LIB
-  ADVANTECH_ADSDEV_LIB
-  ADVANTECH_adsdnet_LIB)

cmake/FindBitflow.cmake

-# Bitflow lib and include path
-# These variables are set:
-#
-#   BITFLOW_FOUND
-#   BITFLOW_INCLUDE_DIR
-#   BITFLOW_LIBRARIES
-#
-# Only works on Windows
-
-if (BITFLOW_INCLUDE_DIR)
-  # Already in cache, be silent
-  set (Bitflow_FIND_QUIETLY TRUE)
-endif ()
-
-FIND_PATH (BITFLOW_SDK_DIR "include/BFApi.h" "C:/BitFlow SDK 4.00"
-  DOC "Path to Bitflow SDK")
-
-FIND_PATH (BITFLOW_INCLUDE_DIR "BFApi.h" 
-  "${BITFLOW_SDK_DIR}/include"
-  "C:/BitFlow SDK 4.00/include"
-  DOC "Path to Bitflow include files")
-FIND_PATH (BITFLOW_LIBRARY_PATH "BFD.lib"
-  "${BITFLOW_SDK_DIR}/lib"
-  "C:/BitFlow SDK 4.00/lib"
-  DOC "Path to Bitflow libraries.")
-
-FIND_LIBRARY (BITFLOW_BFD_LIB BFD ${BITFLOW_LIBRARY_PATH})
-FIND_LIBRARY (BITFLOW_R2D_LIB R2d ${BITFLOW_LIBRARY_PATH})
-FIND_LIBRARY (BITFLOW_DISPSURF_LIB DispSurf ${BITFLOW_LIBRARY_PATH})
-
-if (BITFLOW_BFD_LIB AND BITFLOW_R2D_LIB AND BITFLOW_DISPSURF_LIB)
-  set (BITFLOW_LIBRARIES 
-    ${BITFLOW_BFD_LIB} ${BITFLOW_R2D_LIB} ${BITFLOW_DISPSURF_LIB})
-else ()
-  set (BITFLOW_LIBRARIES)
-endif ()
-
-INCLUDE (FindPackageHandleStandardArgs)
-FIND_PACKAGE_HANDLE_STANDARD_ARGS (Bitflow DEFAULT_MSG 
-  BITFLOW_LIBRARIES BITFLOW_INCLUDE_DIR)
-
-MARK_AS_ADVANCED (
-  BITFLOW_INCLUDE_DIR
-  BITFLOW_LIBRARY_PATH
-  BITFLOW_BFD_LIB
-  BITFLOW_R2D_LIB
-  BITFLOW_DISPSURF_LIB)

cmake/FindCUDA_wrap.cmake

 # - Wrapper around FindCUDA
 
+macro (set_compute_capabilities)
+  # JAS 2010.12.09
+  #   Build code for all known compute capabilities by default.
+  #   When developing, it is sometimes nice to turn this off in order
+  #   to speed up the build processes (since you only have 1 GPU in your machine).
+  if (PLM_CUDA_ALL_DEVICES)
+    message (STATUS "CUDA Build Level: ALL Compute Capabilities")
+
+    if (CUDA_VERSION_MAJOR LESS "7")
+      message (STATUS " Compute Cap 1: [X]")
+      set (CUDA_NVCC_FLAGS ${CUDA_NVCC_FLAGS}
+	-gencode arch=compute_11,code=sm_11
+	-gencode arch=compute_12,code=sm_12
+	-gencode arch=compute_13,code=sm_13
+	)
+      if (CUDA_VERSION_MINOR LESS "5")
+	set (CUDA_NVCC_FLAGS ${CUDA_NVCC_FLAGS}
+	  -gencode arch=compute_10,code=sm_10)
+      endif ()
+    else()
+      message (STATUS " Compute Cap 1: [ ]")
+    endif()
+
+    if (CUDA_VERSION_MAJOR GREATER "2" AND CUDA_VERSION_MAJOR LESS "9")
+      message (STATUS " Compute Cap 2: [X]")
+      set (CUDA_NVCC_FLAGS ${CUDA_NVCC_FLAGS}
+	-gencode arch=compute_20,code=sm_20
+	)
+    else()
+      message (STATUS " Compute Cap 2: [ ]")
+    endif()
+
+    if (CUDA_VERSION_MAJOR GREATER "4")
+      message (STATUS " Compute Cap 3: [X]")
+      set (CUDA_NVCC_FLAGS ${CUDA_NVCC_FLAGS}
+	-gencode arch=compute_30,code=sm_30
+	)
+    else()
+      message (STATUS " Compute Cap 3: [ ]")
+    endif()
+
+    if (CUDA_VERSION_MAJOR GREATER "5")
+      message (STATUS " Compute Cap 5: [X]")
+      set (CUDA_NVCC_FLAGS ${CUDA_NVCC_FLAGS}
+	-gencode arch=compute_50,code=sm_50
+	-gencode arch=compute_50,code=compute_50
+	)
+    else()
+      message (STATUS " Compute Cap 5: [ ]")
+    endif()
+
+    if (CUDA_VERSION_MAJOR GREATER "7")
+      message (STATUS " Compute Cap 6: [X]")
+      set (CUDA_NVCC_FLAGS ${CUDA_NVCC_FLAGS}
+	-gencode arch=compute_60,code=sm_60
+	-gencode arch=compute_60,code=compute_60
+	)
+    else()
+      message (STATUS " Compute Cap 6: [ ]")
+    endif()
+
+    if (CUDA_VERSION_MAJOR GREATER "8")
+      message (STATUS " Compute Cap 7: [X]")
+      set (CUDA_NVCC_FLAGS ${CUDA_NVCC_FLAGS}
+	-gencode arch=compute_70,code=sm_70
+	-gencode arch=compute_70,code=compute_70
+	)
+    else()
+      message (STATUS " Compute Cap 7: [ ]")
+    endif()
+  else ()
+    message (STATUS "CUDA Build Level: Build system Compute Capability ONLY!")
+  endif ()
+endmacro ()
+
 if (MINGW)
   # Cuda doesn't work with mingw at all
   set (CUDA_FOUND FALSE)
@@ -59,13 +134,18 @@ if (CUDA_CXX_FLAGS)
   list (APPEND CUDA_NVCC_FLAGS --compiler-options ${CUDA_CXX_FLAGS})
 endif ()
 
-set (CUDA_FOUND ${CUDA_FOUND} CACHE BOOL "Did we find cuda?")
+#set (CUDA_FOUND ${CUDA_FOUND} CACHE BOOL "Did we find cuda?")
+
+if (CUDA_FOUND)
+  message (STATUS "CUDA Version ${CUDA_VERSION}")
+else ()
+  message (STATUS "CUDA Not found")
+endif ()
 
 if (CUDA_FOUND)
   cuda_include_directories (
     ${CMAKE_CURRENT_SOURCE_DIR}
     )
-endif ()
 
   # GCS 2012-05-22 -- viscous fluid registration requires CUDA SDK.
   if (NOT CUDA_SDK_ROOT_DIR)
@@ -95,6 +175,19 @@ endif ()
   #   This script will modify CUDA_NVCC_FLAGS if system default is not gcc-4.3
   include (nvcc-check)
 
+  # Make nvcc less whiny
+  if (CUDA_VERSION_MAJOR GREATER "5")
+    set (CUDA_NVCC_FLAGS ${CUDA_NVCC_FLAGS}
+      --Wno-deprecated-gpu-targets)
+  endif ()
+
+  if (CUDA_VERSION_MAJOR EQUAL "9"
+      AND CMAKE_COMPILER_IS_GNUCC
+      AND NOT CMAKE_CXX_COMPILER_VERSION VERSION_LESS 7.0)
+    list (APPEND CUDA_NVCC_FLAGS
+      --compiler-options -D__GNUC__=6)
+  endif ()
+  
   # GCS 2017-10-24: Let CUDA work with gcc 6 and CUDA 8
   if (CUDA_VERSION_MAJOR EQUAL "8"
       AND CMAKE_COMPILER_IS_GNUCC
@@ -103,66 +196,7 @@ if (CUDA_VERSION_MAJOR EQUAL "8"
       --compiler-options -D__GNUC__=5)
   endif ()
 
-# JAS 2010.12.09
-#   Build code for all known compute capabilities by default.
-#   When developing, it is sometimes nice to turn this off in order
-#   to speed up the build processes (since you only have 1 GPU in your machine).
-set (PLM_CUDA_ALL_DEVICES ON CACHE BOOL 
-  "Generate GPU code for all compute capabilities?")
-if (PLM_CUDA_ALL_DEVICES)
-  message (STATUS "CUDA Build Level: ALL Compute Capabilities")
-
-    if (CUDA_VERSION_MAJOR LESS "7")
-	message (STATUS "  >> Generation 1: [X]")
-	set (CUDA_NVCC_FLAGS ${CUDA_NVCC_FLAGS}
-	    -gencode arch=compute_11,code=sm_11
-	    -gencode arch=compute_12,code=sm_12
-	    -gencode arch=compute_13,code=sm_13
-	    )
-	if (CUDA_VERSION_MAJOR EQUAL "6")
-	    set (CUDA_NVCC_FLAGS ${CUDA_NVCC_FLAGS}
-		--Wno-deprecated-gpu-targets)
-	    if (CUDA_VERSION_MINOR LESS "5")
-		set (CUDA_NVCC_FLAGS ${CUDA_NVCC_FLAGS}
-		    -gencode arch=compute_10,code=sm_10)
-	    endif ()
-	else ()
-	    set (CUDA_NVCC_FLAGS ${CUDA_NVCC_FLAGS}
-		-gencode arch=compute_10,code=sm_10)
-	endif ()
-    else()
-	message (STATUS "  >> Generation 1: [ ]")
-    endif()
-    if (CUDA_VERSION_MAJOR GREATER "2")
-	message (STATUS "  >> Generation 2: [X]")
-	set (CUDA_NVCC_FLAGS ${CUDA_NVCC_FLAGS}
-            -gencode arch=compute_20,code=sm_20
-	    )
-    else()
-	message (STATUS "  >> Generation 2: [ ]")
-    endif()
-
-    if (CUDA_VERSION_MAJOR GREATER "4")
-	message (STATUS "  >> Generation 3: [X]")
-	set (CUDA_NVCC_FLAGS ${CUDA_NVCC_FLAGS}
-            -gencode arch=compute_30,code=sm_30
-	    )
-    else()
-	message (STATUS "  >> Generation 3: [ ]")
-    endif()
-
-    if (CUDA_VERSION_MAJOR GREATER "5")
-	message (STATUS "  >> Generation 5: [X]")
-	set (CUDA_NVCC_FLAGS ${CUDA_NVCC_FLAGS}
-	    -gencode arch=compute_50,code=sm_50
-	    -gencode arch=compute_50,code=compute_50
-	    )
-    else()
-	message (STATUS "  >> Generation 5: [ ]")
-    endif()
+  # Choose compute capabilities
+  set_compute_capabilities ()
 
-    #MESSAGE(STATUS "<<-->>: CUDA_NVCC_FLAGS set to \"${CUDA_NVCC_FLAGS}\"")
-else ()
-    message (STATUS "CUDA Build Level: Build system Compute Capability ONLY!")
 endif ()
-

cmake/FindDCMTK_legacy.cmake

 # - find DCMTK libraries
 #
 
-#  DCMTK_INCLUDE_DIR   - Directories to include to use DCMTK
+#  DCMTK_INCLUDE_DIRS  - Directories to include to use DCMTK
 #  DCMTK_LIBRARIES     - Files to link against to use DCMTK
 #  DCMTK_FOUND         - If false, don't try to use DCMTK
 #  DCMTK_DIR           - (optional) Source directory for DCMTK
@@ -54,7 +54,7 @@ else ()
   message (STATUS "Looking for SSL - not found")
 endif ()
 
-find_path (DCMTK_INCLUDE_DIR
+find_path (DCMTK_INCLUDE_DIRS
   NAMES dcmtk/config/osconfig.h
   HINTS
   ${DCMTK_DIR}/include
@@ -155,7 +155,7 @@ find_library (DCMTK_ofstd_LIBRARY
   /usr/local/dicom/lib
 )
 
-if (DCMTK_INCLUDE_DIR 
+if (DCMTK_INCLUDE_DIRS
     AND DCMTK_dcmnet_LIBRARY
     AND DCMTK_ofstd_LIBRARY
     AND DCMTK_dcmdata_LIBRARY
@@ -222,8 +222,8 @@ if (DCMTK_INCLUDE_DIR
   # Dcmtk must be linked with libwrap if the original package was 
   # built with libwrap support.  
   set (NEED_LIBWRAP_CHECK TRUE)
-  if (EXISTS "${DCMTK_INCLUDE_DIR}/dcmtk/config/osconfig.h")
-    file (STRINGS "${DCMTK_INCLUDE_DIR}/dcmtk/config/osconfig.h"
+  if (EXISTS "${DCMTK_INCLUDE_DIRS}/dcmtk/config/osconfig.h")
+    file (STRINGS "${DCMTK_INCLUDE_DIRS}/dcmtk/config/osconfig.h"
       DCMTK_UNDEF_TCPWRAPPER
       REGEX "#undef WITH_TCPWRAPPER")
     if (NOT ${DCMTK_UNDEF_TCPWRAPPER} STREQUAL "")
@@ -247,3 +247,4 @@ if (DCMTK_INCLUDE_DIR
     set (DCMTK_LIBRARIES ${DCMTK_LIBRARIES} netapi32 ws2_32)
   endif ()
 endif ()
+

cmake/FindDCMTK_wrap.cmake

-# - Wrapper around FindDCMTK
-
-## If it is a modern version of DCMTK, such as found in Slicer build, 
-## it will have a working version of DCMTKConfig.cmake.
-## Otherwise we use the old hacked version of FindDCMTK.cmake.
-if (DCMTK_DIR)
-  if (EXISTS "${DCMTK_DIR}/DCMTKConfig.cmake")
-    find_package (DCMTK NO_MODULE)
-  endif ()
+##-----------------------------------------------------------------------------
+##  See COPYRIGHT.TXT and LICENSE.TXT for copyright and license information
+##-----------------------------------------------------------------------------
+if (DCMTK_wrap_FIND_QUIETLY)
+  list (APPEND DCMTK_EXTRA_ARGS QUIET)
 endif ()
-if (NOT DCMTK_FOUND)
-  find_package (DCMTK)
+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 ()
 
-
-## Get the version string (?)
-if (DCMTK_FOUND)
-  # Basic version information
-  if (DCMTK_VERSION_MAJOR)
-    set (DCMTK_VERSION_STRING "${DCMTK_VERSION_MAJOR}.${DCMTK_VERSION_MINOR}.${DCMTK_VERSION_PATCH}")
-  endif ()
-
-  if (NOT DCMTK_VERSION_STRING)
-    if (EXISTS "${DCMTK_INCLUDE_DIR}/dcmtk/dcmdata/dcuid.h")
-      file (STRINGS "${DCMTK_INCLUDE_DIR}/dcmtk/dcmdata/dcuid.h" 
-	DCMTK_VERSION_STRING
-	REGEX "^#define OFFIS_DCMTK_VERSION_STRING *\"([^\"]*)\"")
-    endif ()
-  endif ()
-  if (NOT DCMTK_VERSION_STRING)
-    if (EXISTS "${DCMTK_INCLUDE_DIR}/dcmtk/config/osconfig.h")
-      file (STRINGS "${DCMTK_INCLUDE_DIR}/dcmtk/config/osconfig.h"
-	DCMTK_VERSION_STRING
-	REGEX "^#define PACKAGE_VERSION *\"([^\"]*)\"")
-    endif ()
-  endif ()
-  if (NOT DCMTK_VERSION_STRING)
-    if (EXISTS "${DCMTK_INCLUDE_DIR}/dcmtk/config/cfunix.h")
-      file (STRINGS "${DCMTK_INCLUDE_DIR}/dcmtk/config/cfunix.h"
-        DCMTK_VERSION_STRING
-        REGEX "^#define PACKAGE_VERSION *\"([^\"]*)\"")
-    endif ()
-  endif ()
-
-  if (DCMTK_VERSION_STRING)
-    # GCS: The below doesn't seem to work on Mac CMake 2.6.4.
-    #  SET (DCMTK_VERSION_STRING "${CMAKE_MATCH_1}")
-    string (REGEX REPLACE "[^\"]*\"([^\"]*)\".*" "\\1"
-      DCMTK_VERSION_STRING "${DCMTK_VERSION_STRING}")
-  endif ()
+find_package (DCMTK NO_MODULE ${EXTRA_ARGS})
+if (NOT DCMTK_FOUND)
+  message (STATUS "Searching for DCMTK using legacy method")
+  find_package (DCMTK_legacy ${EXTRA_ARGS})
 endif ()
 
-
-if (DCMTK_FOUND)
-  message (STATUS "DCMTK version ${DCMTK_VERSION_STRING}")
-else ()
-  message (STATUS "DCMTK not found")
-endif ()
+# The DCMTK 3.6.2 DCMTKConfig.cmake seems to be broken on windows
+string (REPLACE "DCMTK_INCLUDE_DIRS-NOTFOUND;" "" DCMTK_INCLUDE_DIRS
+  "${DCMTK_INCLUDE_DIRS}")