Merge branch 'develop'

.ExternalData/README.rst

@@ -0,0 +1,6 @@
+.ExternalData
+=============
+
+The ITK ``.ExternalData`` directory is an object store for the
+CMake ExternalData module that ITK uses to manage test input
+and baseline data.

.travis.yml

@@ -20,5 +20,5 @@ before_script:
   - cd SimpleElastix-build
 
 script:
-  - cmake ../SimpleElastix/SuperBuild
+  - cmake ../SimpleElastix/SuperBuild -DBUILD_TESTING=OFF # Not enough time
   - make --jobs=2

CMake/CTestCustom.cmake.in

@@ -65,7 +65,7 @@ SET(CTEST_CUSTOM_WARNING_EXCEPTION
   "warning: lowering visibility of .* to match its type"
 
   # Warning from SWIG with self member type
-  "sitkCommand.* Warning 314.*self.*is a python keyword"
+  "sitkCommand.* [wW]arning 314.*self.*is a python keyword"
 
   # Warning from RH5 gcc 4.1.2
   "tr1/mu_iterate.h.* warning: unused parameter '__tuple'"

CMake/FindGTest.cmake

@@ -0,0 +1,211 @@
+#.rst:
+# FindGTest
+# ---------
+#
+# Locate the Google C++ Testing Framework.
+#
+# Defines the following variables:
+#
+# ::
+#
+#    GTEST_FOUND - Found the Google Testing framework
+#    GTEST_INCLUDE_DIRS - Include directories
+#
+#
+#
+# Also defines the library variables below as normal variables.  These
+# contain debug/optimized keywords when a debugging library is found.
+#
+# ::
+#
+#    GTEST_BOTH_LIBRARIES - Both libgtest & libgtest-main
+#    GTEST_LIBRARIES - libgtest
+#    GTEST_MAIN_LIBRARIES - libgtest-main
+#
+#
+#
+# Accepts the following variables as input:
+#
+# ::
+#
+#    GTEST_ROOT - (as a CMake or environment variable)
+#                 The root directory of the gtest install prefix
+#
+#
+#
+# ::
+#
+#    GTEST_MSVC_SEARCH - If compiling with MSVC, this variable can be set to
+#                        "MD" or "MT" to enable searching a GTest build tree
+#                        (defaults: "MD")
+#
+#
+#
+# Example Usage:
+#
+# ::
+#
+#     enable_testing()
+#     find_package(GTest REQUIRED)
+#     include_directories(${GTEST_INCLUDE_DIRS})
+#
+#
+#
+# ::
+#
+#     add_executable(foo foo.cc)
+#     target_link_libraries(foo ${GTEST_BOTH_LIBRARIES})
+#
+#
+#
+# ::
+#
+#     add_test(AllTestsInFoo foo)
+#
+#
+#
+#
+#
+# If you would like each Google test to show up in CTest as a test you
+# may use the following macro.  NOTE: It will slow down your tests by
+# running an executable for each test and test fixture.  You will also
+# have to rerun CMake after adding or removing tests or test fixtures.
+#
+# GTEST_ADD_TESTS(executable extra_args ARGN)
+#
+# ::
+#
+#     executable = The path to the test executable
+#     extra_args = Pass a list of extra arguments to be passed to
+#                  executable enclosed in quotes (or "" for none)
+#     ARGN =       A list of source files to search for tests & test
+#                  fixtures. Or AUTO to find them from executable target.
+#
+#
+#
+# ::
+#
+#   Example:
+#      set(FooTestArgs --foo 1 --bar 2)
+#      add_executable(FooTest FooUnitTest.cc)
+#      GTEST_ADD_TESTS(FooTest "${FooTestArgs}" AUTO)
+
+#=============================================================================
+# Copyright 2009 Kitware, Inc.
+# Copyright 2009 Philip Lowman <[email protected]>
+# Copyright 2009 Daniel Blezek <[email protected]>
+#
+# Distributed under the OSI-approved BSD License (the "License");
+# see accompanying file Copyright.txt for details.
+#
+# This software is distributed WITHOUT ANY WARRANTY; without even the
+# implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.
+# See the License for more information.
+#=============================================================================
+# (To distribute this file outside of CMake, substitute the full
+#  License text for the above reference.)
+#
+# Thanks to Daniel Blezek <[email protected]> for the GTEST_ADD_TESTS code
+
+function(GTEST_ADD_TESTS executable extra_args)
+    if(NOT ARGN)
+        message(FATAL_ERROR "Missing ARGN: Read the documentation for GTEST_ADD_TESTS")
+    endif()
+    if(ARGN STREQUAL "AUTO")
+        # obtain sources used for building that executable
+        get_property(ARGN TARGET ${executable} PROPERTY SOURCES)
+    endif()
+    set(gtest_case_name_regex ".*\\( *([A-Za-z_0-9]+) *, *([A-Za-z_0-9]+) *\\).*")
+    set(gtest_test_type_regex "(TYPED_TEST|TEST_?[FP]?)")
+    foreach(source ${ARGN})
+        file(READ "${source}" contents)
+        string(REGEX MATCHALL "${gtest_test_type_regex} *\\(([A-Za-z_0-9 ,]+)\\)" found_tests ${contents})
+        foreach(hit ${found_tests})
+          string(REGEX MATCH "${gtest_test_type_regex}" test_type ${hit})
+
+          # Parameterized tests have a different signature for the filter
+          if("x${test_type}" STREQUAL "xTEST_P")
+            string(REGEX REPLACE ${gtest_case_name_regex}  "*/\\1.\\2/*" test_name ${hit})
+          elseif("x${test_type}" STREQUAL "xTEST_F" OR "x${test_type}" STREQUAL "xTEST")
+            string(REGEX REPLACE ${gtest_case_name_regex} "\\1.\\2" test_name ${hit})
+          elseif("x${test_type}" STREQUAL "xTYPED_TEST")
+            string(REGEX REPLACE ${gtest_case_name_regex} "\\1/*.\\2" test_name ${hit})
+          else()
+            message(WARNING "Could not parse GTest ${hit} for adding to CTest.")
+            continue()
+          endif()
+          add_test(NAME ${test_name} COMMAND ${executable} --gtest_filter=${test_name} ${extra_args})
+        endforeach()
+    endforeach()
+endfunction()
+
+function(_gtest_append_debugs _endvar _library)
+    if(${_library} AND ${_library}_DEBUG)
+        set(_output optimized ${${_library}} debug ${${_library}_DEBUG})
+    else()
+        set(_output ${${_library}})
+    endif()
+    set(${_endvar} ${_output} PARENT_SCOPE)
+endfunction()
+
+function(_gtest_find_library _name)
+    find_library(${_name}
+        NAMES ${ARGN}
+        HINTS
+            ENV GTEST_ROOT
+            ${GTEST_ROOT}
+        PATH_SUFFIXES ${_gtest_libpath_suffixes}
+    )
+    mark_as_advanced(${_name})
+endfunction()
+
+#
+
+if(NOT DEFINED GTEST_MSVC_SEARCH)
+    set(GTEST_MSVC_SEARCH MD)
+endif()
+
+set(_gtest_libpath_suffixes lib)
+if(MSVC)
+    if(GTEST_MSVC_SEARCH STREQUAL "MD")
+        list(APPEND _gtest_libpath_suffixes
+            msvc/gtest-md/Debug
+            msvc/gtest-md/Release)
+    elseif(GTEST_MSVC_SEARCH STREQUAL "MT")
+        list(APPEND _gtest_libpath_suffixes
+            msvc/gtest/Debug
+            msvc/gtest/Release)
+    endif()
+endif()
+
+
+find_path(GTEST_INCLUDE_DIR gtest/gtest.h
+    HINTS
+        $ENV{GTEST_ROOT}/include
+        ${GTEST_ROOT}/include
+)
+mark_as_advanced(GTEST_INCLUDE_DIR)
+
+if(MSVC AND GTEST_MSVC_SEARCH STREQUAL "MD")
+    # The provided /MD project files for Google Test add -md suffixes to the
+    # library names.
+    _gtest_find_library(GTEST_LIBRARY            gtest-md  gtest)
+    _gtest_find_library(GTEST_LIBRARY_DEBUG      gtest-mdd gtestd)
+    _gtest_find_library(GTEST_MAIN_LIBRARY       gtest_main-md  gtest_main)
+    _gtest_find_library(GTEST_MAIN_LIBRARY_DEBUG gtest_main-mdd gtest_maind)
+else()
+    _gtest_find_library(GTEST_LIBRARY            gtest)
+    _gtest_find_library(GTEST_LIBRARY_DEBUG      gtestd)
+    _gtest_find_library(GTEST_MAIN_LIBRARY       gtest_main)
+    _gtest_find_library(GTEST_MAIN_LIBRARY_DEBUG gtest_maind)
+endif()
+
+include(FindPackageHandleStandardArgs)
+FIND_PACKAGE_HANDLE_STANDARD_ARGS(GTest DEFAULT_MSG GTEST_LIBRARY GTEST_INCLUDE_DIR GTEST_MAIN_LIBRARY)
+
+if(GTEST_FOUND)
+    set(GTEST_INCLUDE_DIRS ${GTEST_INCLUDE_DIR})
+    _gtest_append_debugs(GTEST_LIBRARIES      GTEST_LIBRARY)
+    _gtest_append_debugs(GTEST_MAIN_LIBRARIES GTEST_MAIN_LIBRARY)
+    set(GTEST_BOTH_LIBRARIES ${GTEST_LIBRARIES} ${GTEST_MAIN_LIBRARIES})
+endif()

CMake/FindLuaInterp.cmake

@@ -0,0 +1,45 @@
+#.rst:
+# FindLuaInterp
+# --------
+#
+# Find Lua Interpreter
+#
+# ::
+#
+#   LUA_EXECUTABLE     - the full path to lua
+#   LUA_EXECUTABLE_FOUND          - If false, don't attempt to use lua
+#   LUA_EXECUTABLE_VERSION_STRING - version of lua found
+
+find_program(LUA_EXECUTABLE
+  NAMES lua
+  )
+
+if(LUA_EXECUTABLE)
+  ### LUA_VERSION
+  execute_process(
+    COMMAND ${LUA_EXECUTABLE} -v
+    OUTPUT_VARIABLE
+      LUA_EXECUTABLE_VERSION_STRING
+    ERROR_VARIABLE
+      LUA_EXECUTABLE_VERSION_STRING
+    RESULT_VARIABLE
+      LUA_VERSION_RESULT_VARIABLE
+    OUTPUT_STRIP_TRAILING_WHITESPACE
+    ERROR_STRIP_TRAILING_WHITESPACE
+    )
+  if (NOT LUA_VERSION_RESULT_VARIABLE)
+    string( REGEX MATCH "([0-9]*)([.])([0-9]*)([.]*)([0-9]*)"
+      LUA_EXECUTABLE_VERSION
+      ${LUA_EXECUTABLE_VERSION_STRING} )
+  endif()
+endif()
+
+
+# handle the QUIETLY and REQUIRED arguments and set LUA_FOUND to TRUE if
+# all listed variables are TRUE
+include(FindPackageHandleStandardArgs)
+find_package_handle_standard_args(Lua
+                                  REQUIRED_VARS LUA_EXECUTABLE
+                                  VERSION_VAR LUA_VERSION_STRING)
+
+mark_as_advanced(LUA_EXECUTABLE)

CMake/FindPythonVirtualEnv.cmake

@@ -0,0 +1,53 @@
+#.rst:
+# FindPythonVirtualEnv
+# --------
+#
+# Find Python's VirtualEnv Utility
+#
+# ::
+#
+#   PYTHON_VIRTUALENV_SCRIPT           - the full path to virtualenv
+#   PYTHON_VIRTUALENV_SCRIPT_FOUND     - If false, don't attempt to use lua
+#   PYTHON_VIRTUALENV_VERSION_STRING   - version of lua found
+
+find_program(PYTHON_VIRTUALENV_SCRIPT
+  NAMES virtualenv.py virtualenv
+  )
+
+if(PYTHON_VIRTUALENV_SCRIPT)
+
+  if ("${PYTHON_EXECUTABLE}" STREQUAL "")
+    find_package(PythonInterp REQUIRED)
+  endif()
+
+  ### PYTHON_VIRTUALENV_VERSION
+  execute_process(
+    COMMAND ${PYTHON_EXECUTABLE} ${PYTHON_VIRTUALENV_SCRIPT} --version
+    OUTPUT_VARIABLE
+      PYTHON_VIRTUALENV_VERSION_STRING
+    ERROR_VARIABLE
+      PYTHON_VIRTUALENV_VERSION_STRING
+    RESULT_VARIABLE
+      PYTHON_VIRTUALENV_VERSION_RESULT_VARIABLE
+    OUTPUT_STRIP_TRAILING_WHITESPACE
+    ERROR_STRIP_TRAILING_WHITESPACE
+    )
+  if (PYTHON_VIRTUALENV_VERSION_RESULT_VARIABLE)
+    message(ERROR "Unable to determing PythonVirtualEnv version!\n${PYTHON_VIRTUALENV_VERSION_STRING}")
+    set(PYTHON_VIRTUALENV_VERSION_STRING "")
+  else()
+    string( REGEX MATCH "([0-9]*)([.])([0-9]*)([.]*)([0-9]*)"
+      PYTHON_VIRTUALENV_VERSION
+      ${PYTHON_VIRTUALENV_VERSION_STRING} )
+  endif()
+endif()
+
+
+# handle the QUIETLY and REQUIRED arguments and set PYTHON_VIRTUALENV_FOUND to TRUE if
+# all listed variables are TRUE
+include(FindPackageHandleStandardArgs)
+find_package_handle_standard_args(PythonVirtualEnv
+                                  REQUIRED_VARS PYTHON_VIRTUALENV_SCRIPT
+                                  VERSION_VAR PYTHON_VIRTUALENV_VERSION_STRING)
+
+mark_as_advanced(PYTHON_VIRTUALENV_SCRIPT)

CMake/UseCSharp.cmake

@@ -76,6 +76,9 @@ macro( CSHARP_ADD_PROJECT type name )
         FILE( GLOB it_glob ${it} )
         list( APPEND sources ${it} )
         list( APPEND sources_dep ${it_glob} )
+      elseif( IS_ABSOLUTE ${it} )
+        list( APPEND sources ${it} )
+        list( APPEND sources_dep ${it} )
       endif( )
     endif ( )
   endforeach( )