Commit 1f5351c4 authored by Gregory Sharp's avatar Gregory Sharp
Browse files

New upstream version 1.7.3+dfsg.1

parent ad976fbe

CMakeLists.txt

100644 → 100755
+159 −109
Original line number Diff line number Diff line
@@ -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

+2 −3
Original line number Diff line number Diff line 
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

0 → 100755
+35 −0
Original line number Diff line number Diff line 
##-----------------------------------------------------------------------------

##  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

+4544 −4523
Original line number Diff line number Diff line
@@ -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

+3 −0
Original line number Diff line number Diff line
@@ -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