.gitignore

@@ -36,10 +36,25 @@
 .DS_Store
 
 # IDEs
-.idea
+.idea/
 cmake-build-*
 .kdev4
 .vscode
 
+# Temporary structure
+temporary*/
+
 # Source
 Documentation/build
+
+# SuperBench output
+TransformParameters.*
+registration_driver.log
+
+# Dropbox sync
+.dropbox.attr
+
+# Images
+*.nii.gz
+*.mhd
+*.raw
\ No newline at end of file

.travis.yml

-language: cpp
+language:
+  - cpp
+  - python
 
 env:
   global:
@@ -30,84 +32,89 @@ matrix:
       compiler: gcc
       addons:
         apt:
-          sources:
-            - ubuntu-toolchain-r-test
-          packages:
-            - g++-4.9
-      env:
-         - GCC="CC=gcc-4.9 && CXX=g++-4.9"
+          sources: ubuntu-toolchain-r-test
+          packages: [g++-5, python3, python3-pip, libinsighttoolkit4*]
+      env: PYTHON=3.5 GCC="CC=gcc-5 && CXX=g++-5"
     - os: linux
       dist: trusty
       sudo: required
       compiler: gcc
       addons:
         apt:
-          sources:
-            - ubuntu-toolchain-r-test
-          packages:
-            - g++-5
-      env:
-         - GCC="CC=gcc-5 && CXX=g++-5"
+          sources: ubuntu-toolchain-r-test
+          packages: [g++-6, python3, python3-pip, libinsighttoolkit4*]
+      env: PYTHON=3.5 GCC="CC=gcc-6 && CXX=g++-6"
     - os: linux
       dist: trusty
       sudo: required
       compiler: gcc
       addons:
         apt:
-          sources:
-            - ubuntu-toolchain-r-test
-          packages:
-            - g++-6
-      env:
-         - GCC="CC=gcc-6 && CXX=g++-6"
-    - os: linux
-      dist: trusty
-      sudo: required
-      compiler: gcc
-      addons:
-        apt:
-          sources:
-            - ubuntu-toolchain-r-test
-          packages:
-            - g++-7
-      env:
-         - GCC="CC=gcc-7 && CXX=g++-7"
+          sources: ubuntu-toolchain-r-test
+          packages: [g++-7, python3, python3-pip, libinsighttoolkit4*]
+      env: PYTHON=3.5 GCC="CC=gcc-7 && CXX=g++-7"
     - os: osx
       compiler: clang
+      osx_image: xcode8.3
+      env: PYTHON=3.5 CPP=14 CLANG
     - os: osx
       compiler: gcc
+      osx_image: xcode8.3
+      env: PYTHON=3.5 CPP=14 CLANG
 
 before_install:
+  - root=$PWD
   - if [[ "$TRAVIS_OS_NAME" == "linux" ]]; then eval ${GCC}; fi;
-
-before_script:
   - mkdir -p ${SUPERELASTIX_BUILD_DIR}
   - mkdir -p ${ExternalData_OBJECT_STORES}
-  - if [[ "$TRAVIS_OS_NAME" == "linux" && ! -e "${ExternalData_OBJECT_STORES}/${CMAKE_DOWNLOAD_FILE}" ]]; then (cd ${ExternalData_OBJECT_STORES} && curl -sSO https://cmake.org/files/v3.6/${CMAKE_DOWNLOAD_FILE}); fi; 
+  - if [[ "$TRAVIS_OS_NAME" == "linux" && ! -e "${ExternalData_OBJECT_STORES}/${CMAKE_DOWNLOAD_FILE}" ]]; then (cd ${ExternalData_OBJECT_STORES} && curl -sSO https://cmake.org/files/v3.6/${CMAKE_DOWNLOAD_FILE}); fi;
   - if [[ "$TRAVIS_OS_NAME" == "linux" ]]; then sudo bash "${ExternalData_OBJECT_STORES}/${CMAKE_DOWNLOAD_FILE}" --prefix=/usr/local --exclude-subdir; fi
   - if [[ "$TRAVIS_OS_NAME" == "linux" ]]; then cmake --version; fi
+  - if [[ "$TRAVIS_OS_NAME" == "osx" ]]; then
+   brew upgrade python &&
+   curl https://bootstrap.pypa.io/get-pip.py | python3 &&
+   brew list python | grep pip; fi
 
-script:
+install:
   - if [[ ! -e ${ITK_BUILD_DIR}/ITKConfig.cmake ]]; then
       rm -rf ${ITK_SOURCE_DIR} {ITK_BUILD_DIR} &&
       git clone ${ITK_URL} ${ITK_SOURCE_DIR} &&
       cd ${ITK_SOURCE_DIR} &&
-      git checkout v4.12.2 &&
+      git checkout v4.13.0 &&
       mkdir -p ${ITK_BUILD_DIR} &&
       cd ${ITK_BUILD_DIR} &&
       cmake -DBUILD_EXAMPLES=OFF -DBUILD_TESTING=OFF -DCMAKE_BUILD_TYPE=Release -DCMAKE_POSITION_INDEPENDENT_CODE:BOOL=ON -DCMAKE_VISIBILITY_INLINES_HIDDEN:BOOL=ON -DBUILD_SHARED_LIBS:BOOL=OFF -DCMAKE_SKIP_RPATH:BOOL=ON -DITK_LEGACY_REMOVE:BOOL=ON -DITK_USE_KWSTYLE:BOOL=OFF -DITK_BUILD_DEFAULT_MODULES:BOOL=ON -DModule_ITKReview:BOOL=ON ${ITK_SOURCE_DIR} &&
-      make --jobs=4; fi
-  - if [[ ! -e ${ELASTIX_BUILD_DIR}/ElastixConfig.cmake ]]; then
+      make --jobs=2 && 
+      touch ${HOME_DIR}/built_cache; fi
+  - if [[ ! -e ${ELASTIX_BUILD_DIR}/ElastixConfig.cmake && ! -e ${HOME_DIR}/built_cache ]]; then
       rm -rf ${ELASTIX_SOURCE_DIR} ${ELASTIX_BUILD_DIR} &&
       git clone ${ELASTIX_URL} ${ELASTIX_SOURCE_DIR} &&
       cd ${ELASTIX_SOURCE_DIR} &&
-      git checkout e8354222396c6bd78e9fe6d5a39e4ecac4bb0d52 &&
+      git checkout 0ce6c24a2b74c0132f1a53848321f1c7a92162ea &&
       mkdir -p ${ELASTIX_BUILD_DIR} &&
       cd ${ELASTIX_BUILD_DIR} &&
       cmake -DBUILD_TESTING:BOOL=OFF -DELASTIX_BUILD_EXECUTABLE:BOOL=OFF -DITK_DIR=${ITK_BUILD_DIR} -DCMAKE_BUILD_TYPE=Release ${ELASTIX_SOURCE_DIR} &&
-      make --jobs=4 && 
+      make --jobs=2 && 
       touch ${HOME_DIR}/built_cache; fi
   - cd ${SUPERELASTIX_BUILD_DIR}
   - if [[ ! -e ${HOME_DIR}/built_cache ]]; then
       cmake -DBUILD_APPLICATIONS_EXTERNAL_PROJECT:BOOL=ON -DBUILD_TESTING:BOOL=ON -DCMAKE_BUILD_TYPE=Release -DUSE_SYSTEM_ITK:BOOL=ON -DITK_DIR=${ITK_BUILD_DIR} -DUSE_SYSTEM_ELASTIX:BOOL=ON -DElastix_DIR=${ELASTIX_BUILD_DIR} ${SUPERELASTIX_SOURCE_DIR} && 
-      make --jobs=4; fi
+      make --jobs=2; fi
+
+#before_script:
+#  - cd $root
+#  - mkdir temp
+#  - python3 --version && pip3 --version
+#  - sudo pip3 install -U pip
+#  - pip3 install --user -r requirements.txt
+#  - sudo pip3 install --ignore-installed nose pytest pytest-cov coverage codecov codacy-coverage
+
+script: sleep 1 # disable default call ./configure && make && make test
+#  - nosetests Tools -v --exe --with-doctest --with-xunit --with-coverage --cover-package=Tools
+#  - nosetests ContinuousRegistration -v --exe --with-doctest --with-xunit --with-coverage --cover-package=ContinuousRegistration  --ignore-files=submit_jobs.py
+#  - py.test Tools -v --doctest-modules
+#  - py.test ContinuousRegistration -v --doctest-modules --ignore=ContinuousRegistration/Source/submit_jobs.py
+#  - coverage run --source Tools -m py.test Tools -v --doctest-modules
+#  - coverage run --source ContinuousRegistration -m py.test ContinuousRegistration -v --doctest-modules --ignore=ContinuousRegistration/Source/submit_jobs.py
+#  - coverage report
+#  - codecov
\ No newline at end of file

Applications/CommandLineInterface/CMakeLists.txt

@@ -35,7 +35,10 @@ find_package(Boost COMPONENTS program_options filesystem system regex REQUIRED Q
 include_directories( ${Boost_INCLUDE_DIR} )
 
 # Compile executable
-include_directories( "${CMAKE_CURRENT_SOURCE_DIR}/include" )
+include_directories(  
+  "${CMAKE_CURRENT_SOURCE_DIR}/include"
+  "${CMAKE_CURRENT_BINARY_DIR}/Applications"  # For selxGitRevisionSha.h
+)
 add_executable( SuperElastix ${COMMANDLINE_SOURCE_FILES} ${COMMANDLINE_HEADER_FILES} )
 target_link_libraries( SuperElastix ${SUPERELASTIX_LIBRARIES} ${Boost_LIBRARIES} ${ITK_LIBRARIES} ${ELASTIX_LIBRARIES} )
 

Applications/CommandLineInterface/Demo/Scripts_Linux/1A_SuperElastix_elastix_NC.sh

-../SuperElastix --conf ../Configuration/elastix_Bspline_NC.json --graphout 1B_graph_elastix_NC.dot --in FixedImage=../Data/coneA2d64.mhd MovingImage=../Data/coneB2d64.mhd --out ResultImage=1A_image_elastix_NC.mhd
+../SuperElastix --conf ../Configuration/elastix_Bspline_NC.json --graphout 1B_graph_elastix_NC.dot --in FixedImage=../Data/coneA2d64.mhd MovingImage=../Data/coneB2d64.mhd --out ResultImage=1A_image_elastix_NC.mhd --loglevel trace

Applications/CommandLineInterface/Demo/Scripts_Linux/1B_SuperElastix_elastix_MSD.sh

-../SuperElastix --conf ../Configuration/elastix_Bspline_MSD.json --graphout 1B_graph_elastix_MSD.dot --in FixedImage=../Data/coneA2d64.mhd MovingImage=../Data/coneB2d64.mhd --out ResultImage=1B_image_elastix_MSD.mhd
+../SuperElastix --conf ../Configuration/elastix_Bspline_MSD.json --graphout 1B_graph_elastix_MSD.dot --in FixedImage=../Data/coneA2d64.mhd MovingImage=../Data/coneB2d64.mhd --out ResultImage=1B_image_elastix_MSD.mhd  --loglevel trace

Applications/CommandLineInterface/Demo/Scripts_Linux/2A_SuperElastix_itkv4_NC.sh

-../SuperElastix --conf ../Configuration/itkv4_SVF_ANTsCC.json --graphout 2A_graph_itkv4_NC.dot --in FixedImage=../Data/coneA2d64.mhd MovingImage=../Data/coneB2d64.mhd --out ResultImage=2A_image_itkv4_NC.mhd ResultDisplacementField=2A_deformation_itkv4_NC.mhd
+../SuperElastix --conf ../Configuration/itkv4_SVF_ANTsCC.json --graphout 2A_graph_itkv4_NC.dot --in FixedImage=../Data/coneA2d64.mhd MovingImage=../Data/coneB2d64.mhd --out ResultImage=2A_image_itkv4_NC.mhd ResultDisplacementField=2A_deformation_itkv4_NC.mhd  --loglevel trace

Applications/CommandLineInterface/Demo/Scripts_Linux/2B_SuperElastix_itkv4_MSD.sh

-../SuperElastix --conf ../Configuration/itkv4_SVF_MSD.json --graphout 2B_graph_itkv4_MSD.dot --in FixedImage=../Data/coneA2d64.mhd MovingImage=../Data/coneB2d64.mhd --out ResultImage=2B_image_itkv4_MSD.mhd ResultDisplacementField=2B_deformation_itkv4_MSD.mhd
+../SuperElastix --conf ../Configuration/itkv4_SVF_MSD.json --graphout 2B_graph_itkv4_MSD.dot --in FixedImage=../Data/coneA2d64.mhd MovingImage=../Data/coneB2d64.mhd --out ResultImage=2B_image_itkv4_MSD.mhd ResultDisplacementField=2B_deformation_itkv4_MSD.mhd  --loglevel trace

Applications/CommandLineInterface/Demo/Scripts_Linux/IdentityTransformRegistration.sh

 #!/bin/bash
-../SuperElastix --conf ../Configuration/IdentityTransformRegistration.json --in FixedImage=../Data/coneA2d64.mhd MovingImage=../Data/coneB2d64.mhd --out DisplacementField=IdentityDeformationField.mhd
+../SuperElastix --conf ../Configuration/IdentityTransformRegistration.json --in FixedImage=../Data/coneA2d64.mhd MovingImage=../Data/coneB2d64.mhd --out DisplacementField=IdentityDeformationField.mhd --log-level trace

Applications/CommandLineInterface/Demo/Scripts_Linux/elastix3d.sh

 # data from Namic - Deformable registration speed optimization http://www.insight-journal.org/midas/collection/view/29
-../SuperElastix --conf ../Configuration/elastix3d.json --loglevel debug --in FixedImage=N012_S03_tof3d_multi_slab.mha MovingImage=N026_S02_tof3d_multi_slab.mha --out ResultImage=elastix3d_warped.mhd ResultDisplacementField=elastix3d_displacement.mhd
+../SuperElastix --conf ../Configuration/elastix3d.json --loglevel debug --in FixedImage=N012_S03_tof3d_multi_slab.mha MovingImage=N026_S02_tof3d_multi_slab.mha --out ResultImage=elastix3d_warped.mhd ResultDisplacementField=elastix3d_displacement.mhd --log-level trace

Applications/CommandLineInterface/src/selxSuperElastix.cxx

@@ -21,6 +21,7 @@
 #include "selxAnyFileReader.h"
 #include "selxAnyFileWriter.h"
 #include "selxLogger.h"
+#include "selxGitInfo.h"
 
 #include <boost/algorithm/string.hpp>
 #include <boost/filesystem.hpp>
@@ -93,6 +94,7 @@ main( int ac, char * av[] )
     boost::program_options::options_description desc("Allowed options");
     desc.add_options()
       ( "help", "produce help message" )
+      ( "revision-sha", "produce git revision SHA-1 hash of SuperElastix source" )
       ("conf", boost::program_options::value< VectorOfPathsType >(&configurationPaths)->required()->multitoken(), "Configuration file: single or multiple Blueprints [.xml|.json]")
       ("in", boost::program_options::value< VectorOfStringsType >(&inputPairs)->multitoken(), "Input data: images, labels, meshes, etc. Usage arg: <name>=<path> (or multiple pairs)")
       ("out", boost::program_options::value< VectorOfStringsType >(&outputPairs)->multitoken(), "Output data: images, labels, meshes, etc. Usage arg: <name>=<path> (or multiple pairs)")
@@ -105,7 +107,14 @@ main( int ac, char * av[] )
 
     if( vm.count( "help" ) )
     {
-      std::cout << desc << "\n";
+      std::cout
+        << "SuperElastix GIT Revision SHA-1: " << selx::GitInfo::GetRevisionSha() << '\n'
+        << desc << std::endl;
+      return 0;
+    }
+    if (vm.count("revision-sha"))
+    {
+      std::cout << selx::GitInfo::GetRevisionSha() << std::endl;
       return 0;
     }
     boost::program_options::notify(vm);

Applications/CommandLineInterface/test/integration.cmake

@@ -17,22 +17,80 @@
 #
 #=========================================================================
 
-add_integration_test(
-  NAME SuperElastixIntegrationTest
-  DRIVER SuperElastix
-  ARGUMENTS --conf ${CMAKE_SOURCE_DIR}/Testing/Data/Configuration/itkv4_SVF_ANTsCC.json --in FixedImage=${CMAKE_BINARY_DIR}/Testing/Data/Input/coneA2d64.mhd MovingImage=${CMAKE_BINARY_DIR}/Testing/Data/Input/coneB2d64.mhd --out ResultImage=2A_image_itkv4_NC.mhd ResultDisplacementField=2A_deformation_itkv4_NC.mhd
-)
+# Integration tests are "short" tests that typically test a combination of components by using the SuperElastix commandline interface with a configuration file.
 
-# Possible grand challenge CMake interface:
-# 
-# add_grand_challenge_submission( 
-#   NAME username
-#   DRIVER GrandChallengeDriver
-#   ARGUMENTS ...
-# )
-#  
-# The CMake mechanism would be similar to that of integration tests, except
-# we would allow users to write their own driver and/or use an executable that 
-# contains additional functionality for saving results. The macro would also
-# invoke a script that uploads results and configurition files to website.
+#Application Demo 1A: should match <source>/Applications/CommandLineInterface/Demo/Scripts_[Linux|Windows]/
+add_test(NAME Integration_Demo_1A COMMAND SuperElastix
+  --logfile ${SUPERELASTIX_OUTPUT_DATA_DIR}/Integration_Demo_1A.log 
+  --loglevel trace
+  --conf ${SUPERELASTIX_CONFIGURATION_DATA_DIR}/elastix_Bspline_NC.json
+  --graphout ${SUPERELASTIX_OUTPUT_DATA_DIR}/Integration_Demo_1A.dot 
+  --in FixedImage=${SUPERELASTIX_INPUT_DATA_DIR}/coneA2d64.mhd 
+       MovingImage=${SUPERELASTIX_INPUT_DATA_DIR}/coneB2d64.mhd
+  --out ResultImage=${SUPERELASTIX_OUTPUT_DATA_DIR}/Integration_Demo_1A_image_elastix_NC.mhd)
 
+#Application Demo 1B: should match <source>/Applications/CommandLineInterface/Demo/Scripts_[Linux|Windows]/
+add_test(NAME Integration_Demo_1B COMMAND SuperElastix
+  --logfile ${SUPERELASTIX_OUTPUT_DATA_DIR}/Integration_Demo_1B.log 
+  --loglevel trace
+  --conf ${SUPERELASTIX_CONFIGURATION_DATA_DIR}/elastix_Bspline_MSD.json
+  --graphout ${SUPERELASTIX_OUTPUT_DATA_DIR}/Integration_Demo_1B.dot 
+  --in FixedImage=${SUPERELASTIX_INPUT_DATA_DIR}/coneA2d64.mhd 
+       MovingImage=${SUPERELASTIX_INPUT_DATA_DIR}/coneB2d64.mhd
+  --out ResultImage=${SUPERELASTIX_OUTPUT_DATA_DIR}/Integration_Demo_1B_image_elastix_MSD.mhd)
+
+#Application Demo 2A: should match <source>/Applications/CommandLineInterface/Demo/Scripts_[Linux|Windows]/
+add_test(NAME Integration_Demo_2A COMMAND SuperElastix
+  --logfile ${SUPERELASTIX_OUTPUT_DATA_DIR}/Integration_Demo_2A.log 
+  --loglevel trace
+  --conf ${SUPERELASTIX_CONFIGURATION_DATA_DIR}/itkv4_SVF_ANTsCC.json
+  --graphout ${SUPERELASTIX_OUTPUT_DATA_DIR}/Integration_Demo_2A.dot 
+  --in FixedImage=${SUPERELASTIX_INPUT_DATA_DIR}/coneA2d64.mhd 
+       MovingImage=${SUPERELASTIX_INPUT_DATA_DIR}/coneB2d64.mhd
+  --out ResultImage=${SUPERELASTIX_OUTPUT_DATA_DIR}/Integration_Demo_2A_image_itkv4_NC.mhd
+        ResultDisplacementField=${SUPERELASTIX_OUTPUT_DATA_DIR}/Integration_Demo_2A_deformation_itkv4_NC.mhd)
+
+#Application Demo 2B: should match <source>/Applications/CommandLineInterface/Demo/Scripts_[Linux|Windows]/
+add_test(NAME Integration_Demo_2B COMMAND SuperElastix
+  --logfile ${SUPERELASTIX_OUTPUT_DATA_DIR}/Integration_Demo_2B.log 
+  --loglevel trace
+  --conf ${SUPERELASTIX_CONFIGURATION_DATA_DIR}/itkv4_SVF_MSD.json
+  --graphout ${SUPERELASTIX_OUTPUT_DATA_DIR}/Integration_Demo_2B.dot 
+  --in FixedImage=${SUPERELASTIX_INPUT_DATA_DIR}/coneA2d64.mhd 
+       MovingImage=${SUPERELASTIX_INPUT_DATA_DIR}/coneB2d64.mhd
+  --out ResultImage=${SUPERELASTIX_OUTPUT_DATA_DIR}/Integration_Demo_2B_image_itkv4_MSD.mhd
+        ResultDisplacementField=${SUPERELASTIX_OUTPUT_DATA_DIR}/Integration_Demo_2B_deformation_itkv4_MSD.mhd)
+
+add_test(NAME Integration_WarpByItkTransform COMMAND SuperElastix
+  --logfile ${SUPERELASTIX_OUTPUT_DATA_DIR}/Integration_WarpByItkTransform.log 
+  --loglevel trace
+  --conf ${SUPERELASTIX_CONFIGURATION_DATA_DIR}/itk_warper.json
+  --graphout ${SUPERELASTIX_OUTPUT_DATA_DIR}/Integration_WarpByItkTransform.dot 
+  --in FixedAndMovingImageSource=${SUPERELASTIX_INPUT_DATA_DIR}/coneA2d64.mhd 
+       TransformSource=${SUPERELASTIX_INPUT_DATA_DIR}/ItkAffine2Dtransform.tfm 
+  --out ResultImageSink=${SUPERELASTIX_OUTPUT_DATA_DIR}/Integration_WarpByItkTransform.mhd)
+
+add_test(NAME Integration_ComposeBlueprintElastix COMMAND SuperElastix
+  --logfile ${SUPERELASTIX_OUTPUT_DATA_DIR}/Integration_ComposeBlueprintElastix.log 
+  --loglevel trace
+  --conf ${SUPERELASTIX_CONFIGURATION_DATA_DIR}/elastix_Base.json
+  --conf ${SUPERELASTIX_CONFIGURATION_DATA_DIR}/elastix_Blueprint_Bspline_MSD.json
+  --graphout ${SUPERELASTIX_OUTPUT_DATA_DIR}/Integration_ComposeBlueprintElastix.dot 
+  --in FixedImage=${SUPERELASTIX_INPUT_DATA_DIR}/coneA2d64.mhd 
+       MovingImage=${SUPERELASTIX_INPUT_DATA_DIR}/coneB2d64.mhd 
+  --out ResultImage=${SUPERELASTIX_OUTPUT_DATA_DIR}/Integration_ComposeBlueprintElastix.mhd)
+  
+add_test(NAME Integration_ComposeBlueprintItk COMMAND SuperElastix
+  --logfile ${SUPERELASTIX_OUTPUT_DATA_DIR}/Integration_ComposeBlueprintElastix.log 
+  --loglevel trace
+  --conf ${SUPERELASTIX_CONFIGURATION_DATA_DIR}/itkv4_Base.json
+  --conf ${SUPERELASTIX_CONFIGURATION_DATA_DIR}/itkv4_Affine_MSD.json
+  --conf ${SUPERELASTIX_CONFIGURATION_DATA_DIR}/itk_TransformSink.json
+  --graphout ${SUPERELASTIX_OUTPUT_DATA_DIR}/Integration_ComposeBlueprintItk.dot 
+  --in FixedImage=${SUPERELASTIX_INPUT_DATA_DIR}/coneA2d64.mhd 
+       MovingImage=${SUPERELASTIX_INPUT_DATA_DIR}/coneB2d64.mhd 
+  --out ResultImage=${SUPERELASTIX_OUTPUT_DATA_DIR}/Integration_ComposeBlueprintItk.mhd
+        ResultDisplacementField=${SUPERELASTIX_OUTPUT_DATA_DIR}/Integration_ComposeBlueprintItk_def.mhd
+        ResultTransform=Integration_ComposeBlueprintItk.tfm)
+  
+  
\ No newline at end of file

CMake/selxApplications.cmake

@@ -51,7 +51,7 @@ macro( _selxapplications_initialize )
 
     message( STATUS "  ${APPLICATION}" )
 
-    option( "USE_${APPLICATION}" OFF )
+    option( "USE_${APPLICATION}" ON )
     set( "${APPLICATION}_CMAKE_FILE" ${CMAKE_SOURCE_DIR}/${APPLICATION_CMAKE_FILE} )
     set( "${APPLICATION}_IS_ENABLED" FALSE )
 

CMakeLists.txt

@@ -77,6 +77,17 @@ if( ${CMAKE_CXX_COMPILER_ID} STREQUAL MSVC )
       "Please move the build directory to a directory with a shorter path."
     )
   endif()
+  
+  # Avoid many warnings, originating mainly from NiftyReg
+  add_definitions(-D_CRT_SECURE_NO_WARNINGS)
+  # Avoid many warnings, originating mainly from GoogleTest
+  add_definitions(-D_SILENCE_TR1_NAMESPACE_DEPRECATION_WARNING)
+  
+
+  if( ${CMAKE_CONFIGURATION_TYPES} STREQUAL "Debug" )
+    # For a Visual C++ Debug build, use 64-bit toolset, to avoid link errors.
+    set(CMAKE_GENERATOR_TOOLSET "host=x64" CACHE STRING "SuperElastix Visual C++ Debug uses 64-bit toolset" FORCE)
+  endif()
 
   # Explicitly add INCREMENTAL linking option to command lines.
   # http://www.cmake.org/pipermail/cmake/2010-February/035174.html
@@ -125,7 +136,7 @@ include_directories( ${Boost_INCLUDE_DIRS} )
 # ---------------------------------------------------------------------
 # SuperElastix configuration 
 
-option( BUILD_APPLICATIONS "Build applications." OFF )
+option( BUILD_APPLICATIONS "Build applications." ON )
 
 mark_as_advanced( BUILD_SHARED_LIBS )
 option( BUILD_SHARED_LIBS "Build shared libraries." OFF )
@@ -141,7 +152,30 @@ _selxmodules_initialize()
 enable_modules()
 message( STATUS "Enabling modules ... Done" )
 
+# Originally based on the answer by Naszta at
+# https://stackoverflow.com/questions/6526451/how-to-include-git-commit-number-into-a-c-executable
+find_package(Git)
+if(GIT_FOUND)
+  execute_process(
+    COMMAND ${GIT_EXECUTABLE} rev-parse HEAD
+    WORKING_DIRECTORY "${CMAKE_CURRENT_SOURCE_DIR}"
+    OUTPUT_VARIABLE SELX_GIT_REVISION_SHA
+    ERROR_QUIET
+    OUTPUT_STRIP_TRAILING_WHITESPACE)
+  else()
+    set(SELX_GIT_REVISION_SHA 0)
+endif()
+
+configure_file(${CMAKE_CURRENT_SOURCE_DIR}/Modules/Core/selxGitRevisionSha.h.in ${CMAKE_CURRENT_BINARY_DIR}/ModuleCore/selxGitRevisionSha.h @ONLY)
+
 include( ${ModuleFilter_SOURCE_DIR}/CompiledLibraryComponents.cmake )
+mark_as_advanced( COMPILED_LIBRARY_CONFIG_DIR )
+set( COMPILED_LIBRARY_CONFIG_DIR ${PROJECT_BINARY_DIR} CACHE PATH "Path where a custom selxCompiledLibraryComponents.h can be found. Defaults to automatic generated file in ${PROJECT_BINARY_DIR}")
+include_directories(${COMPILED_LIBRARY_CONFIG_DIR})
+list( APPEND SUPERELASTIX_INCLUDE_DIRS ${COMPILED_LIBRARY_CONFIG_DIR} )
+    
+option( BUILD_UNIT_TESTS "Also build tests that take a long time to run." ON )
+
 
 # Build applications
 if( ${BUILD_APPLICATIONS} )
@@ -154,16 +188,6 @@ endif()
 
 # TODO: Functionality to disable default modules/applications
 
-# ---------------------------------------------------------------------
-# SuperBench
-
-option( BUILD_SUPERBENCH "Build SuperBench continuous challenge framework." OFF )
-mark_as_advanced( BUILD_SUPERBENCH )
-
-if( BUILD_SUPERBENCH )
-  add_subdirectory( SuperBench )
-endif()
-
 # ---------------------------------------------------------------------
 # Testing
 

CTest.cmake

@@ -23,30 +23,45 @@ set(CTEST_BINARY_DIRECTORY ".")
 
 set(CTEST_SITE "lkeb-selx01")
 
-find_package( Git REQUIRED )
+if(NOT DEFINED CTEST_GIT_COMMAND)
+  find_program(CTEST_GIT_COMMAND NAMES git git.cmd)
+endif()
+set(CTEST_GIT_UPDATE_CUSTOM "${CTEST_GIT_COMMAND}" pull origin)
 
-execute_process (
-    COMMAND ${GIT_EXECUTABLE} rev-parse --short HEAD
-    WORKING_DIRECTORY ${CTEST_SOURCE_DIRECTORY}
-    OUTPUT_VARIABLE SELX_GIT_COMMIT_SHA 
-)
-execute_process (
-    COMMAND ${GIT_EXECUTABLE} name-rev --name-only HEAD
-    WORKING_DIRECTORY ${CTEST_SOURCE_DIRECTORY}
-    OUTPUT_VARIABLE SELX_GIT_BRANCH_NAME 
-)
+if ("$ENV{CHANGE_AUTHOR}" STREQUAL "")
+  set(CTEST_BUILD_NAME "$ENV{BRANCH_NAME}")
+else()
+  set(CTEST_BUILD_NAME "$ENV{BRANCH_NAME};$ENV{CHANGE_AUTHOR}")
+endif()
+set(CTEST_BUILD_NAME "${CTEST_BUILD_NAME};Test")
 
-set(CTEST_BUILD_NAME "${SELX_GIT_BRANCH_NAME};Tests;commit=SHA\\:${SELX_GIT_COMMIT_SHA}")
 
 set(CTEST_CMAKE_GENERATOR "Unix Makefiles")
 set(CTEST_BUILD_CONFIGURATION Release)
-set(CTEST_BUILD_FLAGS "-j2")
+set(CTEST_BUILD_FLAGS "-j4")
 
-set(CTEST_CONFIGURE_COMMAND "${CMAKE_COMMAND} -DCMAKE_BUILD_TYPE:STRING=${CTEST_BUILD_CONFIGURATION} --build ${CTEST_BINARY_DIRECTORY}")
-set(CTEST_CONFIGURE_COMMAND "${CTEST_CONFIGURE_COMMAND} -DWITH_TESTING:BOOL=ON ${CTEST_BUILD_OPTIONS}")
-set(CTEST_CONFIGURE_COMMAND "${CTEST_CONFIGURE_COMMAND} \"-G${CTEST_CMAKE_GENERATOR}\"")
-set(CTEST_CONFIGURE_COMMAND "${CTEST_CONFIGURE_COMMAND} \"${CTEST_SOURCE_DIRECTORY}\"")
+string(CONCAT CTEST_CONFIGURE_COMMAND "${CMAKE_COMMAND}"
+    " -DCMAKE_BUILD_TYPE:STRING=${CTEST_BUILD_CONFIGURATION}"
+    " --build ${CTEST_BINARY_DIRECTORY}"
+    " ${CTEST_BUILD_OPTIONS}"
+    " \"-G${CTEST_CMAKE_GENERATOR}\""
+    " \"${CTEST_SOURCE_DIRECTORY}\"")
 
-ctest_start("Nightly")
-ctest_test()
-ctest_submit( PARTS Test )
+# Tells CTest to not do a git pull, but to still record what version of the software it's building and testing
+# As explained by mail, by Zack Galbreath
+set(CTEST_UPDATE_VERSION_ONLY 1)
+
+# For CDash integration with GitHub: https://blog.kitware.com/cdash-integration-with-github
+set(CTEST_CHANGE_ID $ENV{CHANGE_ID})
+
+ctest_start("Continuous")
+# Added ctest_update() to ensure that the commit SHA will be passed to CDash, and GitHub.
+ctest_update()
+ctest_test(RETURN_VALUE RES)
+ctest_submit( PARTS Test Update )
+
+if (RES)
+  message(FATAL_ERROR "Unit tests have return code != 0")
+else (RES)
+  message(STATUS "Unit tests have return code ${RES}")
+endif(RES)

CTestConfig.cmake

@@ -8,7 +8,7 @@
 
 set(CTEST_PROJECT_NAME "SuperElastix")
 set(CTEST_NIGHTLY_START_TIME "00:00:00 EST")
-set(CTEST_DROP_METHOD "https")
-set(CTEST_DROP_SITE "my.cdash.org")
+set(CTEST_DROP_METHOD "http")
+set(CTEST_DROP_SITE "trunk.cdash.org")
 set(CTEST_DROP_LOCATION "/submit.php?project=SuperElastix")
 set(CTEST_DROP_SITE_CDASH TRUE)

ContinuousRegistration/README.md

+# What is this?
+The `Submissions` directory contains all submissions for the [Continuous Registration Challenge](https://continuousregistration.grand-challenge.org/). The `Source` directory contains code for running the submissions on several different data sets.
+
+# How to participate
+Open a pull request that creates a directory under `Submissions` which contains your parameter files and a `README.md` file that describes your implementation.
+
+# How to run registrations
+`make_registration_scripts.py` in `Source` generate shell scripts or batch scripts for running the registrations. Each script will register one pair of images. The following command will generate shell scripts for all submissions for POPI, DIRLAB, and EMPIRE data sets:
+```bash
+python make_registration_scripts.py \
+      --superelastix /path/to/superelastix/build/tree/SuperElastix-build/bin/superelastix \
+      --submissions-directory /path/to/superelastix/source/tree/ContinuousRegistration/Submissions \
+      --output-directory /tmp \
+      --popi-input-directory /path/to/POPI \
+      --dirlab-input-directory /path/to/DIRLAB \
+      --empire-input-directory /path/to/EMPIRE \
+      --lpba40-input-directory /path/to/LPBA40 \
+      --ibsr18-input-directory /path/to/IBSR18 \
+      --cumc12-input-directory /path/to/CUMC12 \
+      --hbia-input-directory /path/to/HistoBIA
+```
+
+This generates shell scripts to running the registrations, one for each registration. For example, on Linux you can navigate to the output directory and run
+```bash
+find . -name "*.sh" -exec chmod +x "{}" \;
+find . -name "*.sh" -exec "{}" \;
+find . -name "*.sh" -exec echo "nohup {} &" \; > parallel.sh;
+```
+
+to recursively find scripts, make them executable, and run them.

ContinuousRegistration/Source/__init__.py

+import numpy as np
+
+# parse the numpy versions
+np_version = [int(i) for i in np.version.full_version.split('.')]
+# comparing strings does not work for version lower 1.10
+if np_version >= [1, 14]:
+    np.set_printoptions(legacy='1.13')
\ No newline at end of file

ContinuousRegistration/Source/compose_displacement_fields.json

+{
+    "Components": [
+        {
+            "Name": "DisplacementField",
+            "NameOfClass": "ItkDisplacementFieldSourceComponent",
+            "Dimensionality": "3"
+        },
+
+        {
+            "Name": "WarpingDisplacementField",
+            "NameOfClass": "ItkDisplacementFieldSourceComponent",
+            "Dimensionality": "3"
+        },
+        {
+            "Name": "DisplacementFieldComposer",
+            "NameOfClass": "ItkDisplacementFieldComposerComponent",
+            "Dimensionality": "3"
+        },
+        {
+            "Name": "DisplacementFieldSink",
+            "NameOfClass": "ItkDisplacementFieldSinkComponent",
+            "Dimensionality": "3"
+        }
+    ],
+	"Connections": [
+        {
+            "Out": "DisplacementField",
+            "In": "DisplacementFieldComposer",
+            "NameOfInterface": "itkDisplacementFieldInterface"
+        },
+        {
+            "Out": "WarpingDisplacementField",
+            "In": "DisplacementFieldComposer",
+            "NameOfInterface": "itkWarpingDisplacementFieldInterface"
+        },
+        {
+            "Out": "DisplacementFieldComposer",
+            "In": "DisplacementFieldSink"
+        }
+    ]
+}

ContinuousRegistration/Source/crc.sh

+#!/bin/bash -eux
+# This file serves as an example on how to run registrations locally on Linux and macOS
+# using the Python scripts in this directory. Adapt the parameters to your own needs.
+
+python --version
+
+# Parameters
+SUPERELASTIX_SOURCE_DIR=/Users/kasper/Development/SuperElastix
+SUPERELASTIX_BUILD_DIR=/Users/kasper/Development/build/SuperElastixRelease
+CRC_INPUT_DIR=/Users/kasper/Development/SuperBenchData
+CRC_OUTPUT_DIR=/Users/kasper/Data/SuperBench
+CRC_MASK_DIR=/Users/kasper/Development/SuperBenchMask
+CRC_MAX_NUM_REG_PER_DATASET=8
+CRC_DATASETS="--hammers-input-directory $CRC_INPUT_DIR/HAMMERS --popi-input-directory $CRC_INPUT_DIR/POPI/MedPhys11 --popi-mask-directory $CRC_MASK_DIR/POPI --dirlab-input-directory $CRC_INPUT_DIR/DIRLAB --dirlab-mask-directory $CRC_MASK_DIR/DIRLAB --spread-input-directory $CRC_INPUT_DIR/SPREAD  --mgh10-input-directory $CRC_INPUT_DIR/MGH10 --cumc12-input-directory $CRC_INPUT_DIR/CUMC12 --ibsr18-input-directory $CRC_INPUT_DIR/IBSR18 --lpba40-input-directory $CRC_INPUT_DIR/LPBA40"
+CRC_BLUEPRINT_FILE_NAME="--blueprint-file-name NiftyRegAffineBSpline.json" # Leave empty to run registrations for all blueprints
+
+pushd $SUPERELASTIX_SOURCE_DIR
+
+# Generate shell scripts
+python -m ContinuousRegistration.Source.make_registration_scripts --superelastix $SUPERELASTIX_BUILD_DIR/SuperElastix-build/bin/SuperElastix --submissions-directory $SUPERELASTIX_SOURCE_DIR/ContinuousRegistration/Submissions --output-directory $CRC_OUTPUT_DIR $CRC_DATASETS $CRC_BLUEPRINT_FILE_NAME --max-number-of-registrations-per-dataset $CRC_MAX_NUM_REG_PER_DATASET
+
+# Register images serially
+# find $CRC_OUTPUT_DIR -type f -name "*.sh" -exec "{}" \;
+
+# Register images in parallel
+find $CRC_OUTPUT_DIR -type f -name "*.sh" | parallel -j6 bash
+
+# Evaluate registrations, generate visualizations, and generate leaderboard
+python -m ContinuousRegistration.Source.make_evaluation --superelastix $SUPERELASTIX_BUILD_DIR/SuperElastix-build/bin/SuperElastix --submissions-directory $SUPERELASTIX_SOURCE_DIR/ContinuousRegistration/Submissions --output-directory $CRC_OUTPUT_DIR $CRC_DATASETS $CRC_BLUEPRINT_FILE_NAME --max-number-of-registrations-per-dataset $CRC_MAX_NUM_REG_PER_DATASET --make-image-checkerboards True --make-label-checkerboards True --make-difference-images True
+python -m ContinuousRegistration.Source.make_leaderboard --superelastix $SUPERELASTIX_BUILD_DIR/SuperElastix-build/bin/SuperElastix --submissions-directory $SUPERELASTIX_SOURCE_DIR/ContinuousRegistration/Submissions --output-directory $CRC_OUTPUT_DIR $CRC_DATASETS $CRC_BLUEPRINT_FILE_NAME --max-number-of-registrations-per-dataset $CRC_MAX_NUM_REG_PER_DATASET
+
+popd

ContinuousRegistration/Source/dirlab_image_information.csv

+id,x_size,y_size,z_size,x_spacing,y_spacing,z_spacing
+1,256,256,94,0.97,0.97,2.5
+2,256,256,112,1.16,1.16,2.5
+3,256,256,104,1.15,1.15,2.5
+4,256,256,99,1.13,1.13,2.5
+5,256,256,106,1.10,1.10,2.5
+6,512,512,128,0.97,0.97,2.5
+7,512,512,136,0.97,0.97,2.5
+8,512,512,128,0.97,0.97,2.5
+9,512,512,128,0.97,0.97,2.5
+10,512,512,120,0.97,0.97,2.5
\ No newline at end of file

ContinuousRegistration/Source/make_evaluation.py

+import os, json, datetime
+from ContinuousRegistration.Source.make_registration_scripts import parser
+from ContinuousRegistration.Source.util import logging, load_submissions, write_json
+from ContinuousRegistration.Source.datasets import load_datasets
+
+def run(parameters):
+    submissions = load_submissions(parameters)
+    datasets = load_datasets(parameters)
+
+    results = {}
+    for team_name, blueprint_file_names in submissions.items():
+        for blueprint_file_name in blueprint_file_names:
+            if not team_name in results:
+                results[team_name] = {}
+
+            blueprint_name, blueprint_ext = os.path.splitext(os.path.basename(blueprint_file_name))
+            if not blueprint_name in results[team_name]:
+                results[team_name][blueprint_name] = {}
+
+            logging.info('Loading blueprint %s/%s.' % (team_name, os.path.basename(blueprint_name)))
+            blueprint = json.load(open(blueprint_file_name))
+            for dataset_name in blueprint['Datasets']:
+                if not dataset_name in datasets:
+                    continue
+
+                dataset = datasets[dataset_name]
+                results[team_name][blueprint_name][dataset_name] = []
+
+                for file_names in dataset.generator():
+                    output_directory = os.path.join(parameters.output_directory, team_name, blueprint_name)
+
+                    logging.info('Evaluating registration for blueprint %s and images %s.', blueprint_name, file_names['image_file_names'])
+                    try:
+                        results[team_name][blueprint_name][dataset.name].append(dataset.evaluate(
+                            parameters.superelastix, file_names, output_directory))
+
+                        if hasattr(parameters, 'make_images') and parameters.make_images:
+                            dataset.make_images(parameters.superelastix, file_names, output_directory)
+
+                        if hasattr(parameters, 'make_labels') and parameters.make_labels:
+                            dataset.make_labels(parameters.superelastix, file_names, output_directory)
+
+                        if hasattr(parameters, 'make_difference_images') and parameters.make_difference_images:
+                            dataset.make_difference_images(parameters.superelastix, file_names, output_directory)
+
+                        if hasattr(parameters, 'make_checkerboards') and parameters.make_checkerboards:
+                            dataset.make_checkerboards(parameters.superelastix, file_names, output_directory)
+
+                        if hasattr(parameters, 'make_image_checkerboards') and parameters.make_image_checkerboards:
+                            dataset.make_image_checkerboards(parameters.superelastix, file_names, output_directory)
+
+                        if hasattr(parameters, 'make_label_checkerboards') and parameters.make_label_checkerboards and dataset.name in ["CUMC12", "IBSR18", "LPBA40", "MGH10"]:
+                            dataset.make_label_checkerboards(parameters.superelastix, file_names, output_directory)
+                    except Exception as e:
+                        logging.error('Error during evaluation of %s\'s blueprint %s and dataset %s: %s'
+                                      % (team_name, blueprint_name, dataset.name, str(e)))
+
+    write_json(os.path.join(parameters.output_directory,
+                            'results.json'), results)
+
+    return results
+
+
+if __name__ == '__main__':
+    parser.add_argument('--make-images', '-mi', type=bool, default=False, help="Warp moving images.")
+    parser.add_argument('--make-labels', '-ml', type=bool, default=False, help="Warp moving labels.")
+    parser.add_argument('--make-difference-images', '-mdi', type=bool, default=False, help="Warp moving images and subtract from fixed images.")
+    parser.add_argument('--make-checkerboards', '-mc', type=bool, default=False, help="Warp checkerboard pattern.")
+    parser.add_argument('--make-image-checkerboards', '-mic', type=bool, default=False,
+                        help="Warp moving images and make checkerboard with fixed and warped moving image.")
+    parser.add_argument('--make-label-checkerboards', '-mlc', type=bool, default=False,
+                        help="Warp moving labels and make checkerboard with fixed and warped moving label.")
+    run(parser.parse_args())

ContinuousRegistration/Source/make_leaderboard.py

+import glob, os
+from ContinuousRegistration.Source.make_registration_scripts import parser, load_datasets, load_submissions
+from ContinuousRegistration.Source.util import logging, load_results_from_json, get_script_path
+from datetime import datetime
+import numpy as np
+import json
+import subprocess
+
+date = datetime.now().strftime('%d-%m-%Y')
+
+def run(parameters):
+    result_file_names = glob.glob(os.path.join(parameters.output_directory, 'results*'))
+
+    # Most recent first
+    result_file_names.sort(reverse=True)
+
+    if not result_file_names:
+        raise Exception('No result JSON files found in %s.' % parameters.output_directory)
+
+    logging.info('Loading results from %s.' % result_file_names[0])
+    results, result_names = load_results_from_json(result_file_names[0])
+    datasets = load_datasets(parameters)
+
+    for dataset_name, dataset in datasets.items():
+        if not dataset_name in result_names:
+            # This dataset was not evaluated
+            continue
+
+        make_dataset_results(dataset_name, result_names, results)
+
+def make_dataset_results(dataset_name, result_names, results):
+    table = '<!DOCTYPE html>'
+    table += '<html>'
+
+    table += '<head>'
+    table += '<link href="https://rawgit.com/tristen/tablesort/gh-pages/tablesort.css" rel="stylesheet">'
+    table += '<link href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css" rel="stylesheet" integrity="sha384-BVYiiSIFeK1dGmJRAkycuHAHRg32OmUcww7on3RYdg4Va+PmSTsz/K68vbdEjh4u" crossorigin="anonymous">'
+    table += '<script src="https://rawgit.com/tristen/tablesort/gh-pages/dist/tablesort.min.js"></script>'
+    table += '<style>'
+    table += 'table { width: 100%; } th, td { padding: 5px; text-align: left; }'
+    table += 'font-size: small'
+    table += '</style>'
+    table += '</head>'
+
+    table += '<body>'
+    table += '<table id="leaderboard-%s" class="sort">' % dataset_name
+
+    # Add table header
+    table += '<thead>'
+    table += '<tr>'
+    table += '<th role="columnheader">Team</th>'
+    table += '<th role="columnheader">Blueprint</th>'
+    table += '<th role="columnheader">Date</th>'
+
+    # Try to get blueprint commit hash
+    try:
+        repo_commit = subprocess.check_output(['git', 'describe', '--always'],
+                                              cwd=parameters.source_directory)
+    except subprocess.CalledProcessError as e:
+        repo_commit = None
+        logging.error('Error (exit code {0}): {1}'.format(e.returncode, e.output))
+    except Exception as e:
+        repo_commit = None
+        logging.error('Error reading commit hash from source directory "%s".' % parameters.source_directory)
+
+    if repo_commit:
+        table += '<th role="columnheader">Blueprint Commit</th>'
+        table += '<th role="columnheader">Repo Commit</th>'
+
+    table += '<th role="columnheader">Completed</th>'
+
+    for result_name in result_names[dataset_name]:
+        table += '<th role="columnheader">%s</th>' % result_name
+
+    table += '</tr>'
+    table += '</thead>'
+    table += '<tbody>'
+
+    for team_name, team_results in results.items():
+        for blueprint_name, blueprint_results in team_results.items():
+            if parameters.blueprint_file_name is not None and not blueprint_name \
+                    in [os.path.splitext(blueprint_file_name)[0] for blueprint_file_name in parameters.blueprint_file_name]:
+                # User requested specific blueprints and this blueprint is not one of them
+                continue
+
+            blueprint_file_name_json = os.path.join(parameters.submissions_directory, team_name, blueprint_name + '.json')
+            blueprint_file_name_xml = os.path.join(parameters.submissions_directory, team_name,blueprint_name + '.xml')
+            if os.path.isfile(blueprint_file_name_json):
+                blueprint = json.load(open(blueprint_file_name_json))
+            elif os.path.isfile(blueprint_file_name_xml):
+                raise NotImplementedError('Cannot read xml blueprints yet.')
+            else:
+                raise Exception('Could not load blueprint.')
+
+            if dataset_name not in blueprint['Datasets']:
+                continue
+
+            make_blueprint_results(dataset_name, team_name, blueprint_name, blueprint_results, result_names)
+
+            table += '<tr>'
+            table += '<td>%s</td>' % team_name
+            table += '<td><a href="%s">%s</a></td>' % ('leaderboard-' + dataset_name + '-' + team_name + '-' + blueprint_name + '.html', blueprint_name)
+            table += '<td>%s</td>' % date
+
+            if repo_commit:
+                table += '<td>%s</td>' % repo_commit
+
+                # Try to get blueprint commit hash
+                try:
+                    table += '<td>%s</td>' % subprocess.check_output(['git', 'describe', '--always'],
+                                                                     cwd=parameters.source_directory)
+                except subprocess.CalledProcessError as e:
+                    table += '<td></td>'
+                    logging.error('Error (exit code {0}): {1}'.format(e.returncode, e.output))
+
+            if dataset_name in blueprint_results \
+                and 'result' in blueprint_results[dataset_name] \
+                and not np.isnan(blueprint_results[dataset_name]['result']).all():
+                    result = blueprint_results[dataset_name]['result']
+                    table += '<td>%s/%s</td>' % (len(~np.isnan(result)), len(result))
+                    means = np.nanmean(result, axis=0)
+                    stds = np.nanstd(result, axis=0)
+                    for mean, std in zip(means, stds):
+                        table += '<td>%.2f \pm %.2f</td>' % (mean, std)
+            else:
+                table += '<td>0</td>'
+                for result_name in result_names[dataset_name]:
+                    table += '<td>N/A</td>'
+
+            table += '</tr>'
+
+    table += '</tbody>'
+    table += '</table>'
+
+    table += '<script>new Tablesort(document.getElementById("leaderboard-%s"));</script>' % dataset_name
+
+    table += '</body>'
+    table += '</html>'
+
+    table_file = open(os.path.join(parameters.output_directory,
+                                   'leaderboard-' + dataset_name + '.html'), "w")
+
+    table_file.write(table)
+    table_file.close()
+
+def make_blueprint_results(dataset_name, team_name, blueprint_name, blueprint_results, result_names):
+    blueprint_table = '<!DOCTYPE html>'
+    blueprint_table += '<html>'
+
+    blueprint_table += '<head>'
+    blueprint_table += '<link href="https://rawgit.com/tristen/tablesort/gh-pages/tablesort.css" rel="stylesheet">'
+    blueprint_table += '<link href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css" rel="stylesheet" integrity="sha384-BVYiiSIFeK1dGmJRAkycuHAHRg32OmUcww7on3RYdg4Va+PmSTsz/K68vbdEjh4u" crossorigin="anonymous">'
+    blueprint_table += '<script src="https://rawgit.com/tristen/tablesort/gh-pages/dist/tablesort.min.js"></script>'
+    blueprint_table += '<style>'
+    blueprint_table += 'table { width: 100%; } th, td { padding: 5px; text-align: left; }'
+    blueprint_table += '</style>'
+    blueprint_table += '</head>'
+
+    blueprint_table += '<body>'
+    blueprint_table += '<a href="leaderboard-' + dataset_name + '.html">Back</a>'
+    blueprint_table += '<table id="leaderboard-%s" class="sort">' % dataset_name
+
+    # Add table header
+    blueprint_table += '<thead>'
+    blueprint_table += '<tr>'
+    blueprint_table += '<th role="columnheader">Team</th>'
+    blueprint_table += '<th role="columnheader">Blueprint</th>'
+    blueprint_table += '<th role="columnheader">DisplacementField</th>'
+    blueprint_table += '<th role="columnheader">Date</th>'
+
+    for result_name in result_names[dataset_name]:
+        blueprint_table += '<th role="columnheader">%s</th>' % result_name
+    blueprint_table += '</tr>'
+
+    if dataset_name in blueprint_results \
+            and 'result' in blueprint_results[dataset_name]:
+
+        for result_name, results in zip(blueprint_results[dataset_name]['name'], blueprint_results[dataset_name]['result']):
+            blueprint_table += '<tr>'
+            blueprint_table += '<td>%s</td>' % team_name
+            blueprint_table += '<td>%s</td>' % blueprint_name
+            blueprint_table += '<td>%s</td>' % result_name
+            blueprint_table += '<td>%s</td>' % date
+
+            for result in results:
+                blueprint_table += '<td>%.2f</td>' % result
+            blueprint_table += '</tr>'
+
+    # Add table footer
+    blueprint_table += '</tbody>'
+    blueprint_table += '</table>'
+    blueprint_table += '<a href="leaderboard-' + dataset_name + '.html">Back</a>'
+
+    blueprint_table += '<script>new Tablesort(document.getElementById("leaderboard-%s"));</script>' % dataset_name
+
+    blueprint_table += '</body>'
+    blueprint_table += '</html>'
+
+    f = open(os.path.join(parameters.output_directory,
+                          'leaderboard-' + dataset_name + '-' + team_name + '-' + blueprint_name + '.html'), "w")
+
+    f.write(blueprint_table)
+    f.close()
+
+if __name__ == '__main__':
+    parameters = parser.parse_args()
+
+    if not os.path.exists(parameters.output_directory):
+        raise Exception('Output directory %s not found.' % parameters.output_directory)
+
+    run(parameters)

ContinuousRegistration/Source/make_registration_scripts.py

+import os, json, argparse
+from ContinuousRegistration.Source.datasets import logging, load_datasets
+from ContinuousRegistration.Source.util import load_submissions
+
+parser = argparse.ArgumentParser(description='Continuous Registration Challenge command line interface.')
+parser.add_argument('--superelastix', '-selx', required=True,
+                    help="Path to SuperElastix executable.")
+parser.add_argument('--submissions-directory', '-sd', required=True,
+                    help='Directory with parameter files.')
+parser.add_argument('--output-directory', '-od', required=True,
+                    help="Directory where results will be saved.")
+parser.add_argument('--make-shell-scripts', '-mss', type=bool, default=True,
+                    help="Generate shell scripts (default: True).")
+parser.add_argument('--make-batch-scripts', '-mbs', type=bool, default=False,
+                    help="Generate shell scripts (default: False).")
+parser.add_argument('--brain2d-input-directory', '-b2d')
+parser.add_argument('--lung2d-input-directory', '-l2d')
+parser.add_argument('--cumc12-input-directory', '-cid')
+parser.add_argument('--dirlab-input-directory', '-did')
+parser.add_argument('--dirlab-mask-directory', '-dmd', default=None)
+parser.add_argument('--empire-input-directory', '-eid')
+parser.add_argument('--hammers-input-directory', '-hid')
+parser.add_argument('--ibsr18-input-directory', '-iid')
+parser.add_argument('--lpba40-input-directory', '-lid')
+parser.add_argument('--spread-input-directory', '-sid')
+parser.add_argument('--popi-input-directory', '-pid')
+parser.add_argument('--popi-mask-directory', '-pmd', default=None)
+parser.add_argument('--mgh10-input-directory', '-mid')
+parser.add_argument('--hbia-input-directory', '-hbiaid')
+parser.add_argument('--team-name', '-tn', action='append',
+                    help="If specified, only generated shell scripts for these teams.")
+parser.add_argument('--blueprint-file-name', '-bfn', action='append',
+                    help="If specified, only generated shell scripts for this blueprint.")
+parser.add_argument('--max-number-of-registrations-per-dataset', '-mnorpd', type=int, default=8)
+parser.add_argument('--source-directory', '-srcd', default='.')
+
+
+def run(parameters):
+
+    if not parameters.make_shell_scripts and not parameters.make_batch_scripts:
+        logging.error('Neither --make-shell-scripts or --make-batch-scripts were True. Nothing to do.')
+        quit()
+
+    submissions = load_submissions(parameters)
+    datasets = load_datasets(parameters)
+
+    for team_name, blueprint_file_names in submissions.items():
+        for blueprint_file_name in blueprint_file_names:
+            logging.info('Loading blueprint %s.' % blueprint_file_name)
+            blueprint = json.load(open(blueprint_file_name))
+
+            if not 'Datasets' in blueprint:
+                logging.error('Missing key \'Datasets\' in blueprint %s. '
+                              'Blueprint must specify on which datasets it should be evaluated. '
+                              'Example: { Datasets: [\"SPREAD\", \"POPI\", \"LPBA40\"] }. '
+                              'Skipping blueprint.' % blueprint_file_name)
+                continue
+
+            for dataset_name in blueprint['Datasets']:
+                if not dataset_name in datasets:
+                    continue
+
+                dataset = datasets[dataset_name]
+
+                blueprint_name, blueprint_ext = os.path.splitext(os.path.basename(blueprint_file_name))
+                for file_names in dataset.generator():
+                    logging.info('Generating registration scripts for blueprint "%s" and images %s.',
+                                 blueprint_name, file_names['image_file_names'])
+                    dir_name = os.path.dirname(file_names['disp_field_file_names'][0])
+                    blueprint_output_directory = os.path.join(parameters.output_directory,
+                                                              team_name, blueprint_name,
+                                                              dir_name)
+
+                    if not os.path.exists(blueprint_output_directory):
+                        os.makedirs(blueprint_output_directory)
+
+                    output_directory = os.path.join(parameters.output_directory,
+                                                    team_name, blueprint_name)
+
+                    if parameters.make_shell_scripts:
+                        dataset.make_shell_scripts(parameters.superelastix,
+                                                   blueprint_file_name, file_names,
+                                                   output_directory)
+
+                    if parameters.make_batch_scripts:
+                        dataset.make_batch_scripts(parameters.superelastix,
+                                                   blueprint_file_name,
+                                                   file_names, output_directory)
+
+
+if __name__ == '__main__':
+    parameters = parser.parse_args()
+
+    if not os.path.isfile(parameters.superelastix):
+        raise Exception('Could not find SuperElastix '
+                        + parameters.superelastix + ".")
+
+    if not os.path.exists(parameters.submissions_directory):
+        raise Exception('Could not find submission directory '
+                        + parameters.submissions_directory + ".")
+
+    if not os.path.exists(parameters.output_directory):
+        os.mkdir(parameters.output_directory)
+
+    run(parameters)
+

ContinuousRegistration/Source/metrics.py

+import numpy as np
+import SimpleITK as sitk
+from ContinuousRegistration.Source.util import warp_image, warp_point_set, compose_displacement_fields
+from ContinuousRegistration.Source.util import logging
+
+def tre(superelastix, point_sets, deformation_field_file_names):
+    try:
+        point_set_fixed0_to_moving1 = warp_point_set(superelastix, point_sets[0], deformation_field_file_names[0])
+        point_set_fixed1_to_moving0 = warp_point_set(superelastix, point_sets[1], deformation_field_file_names[1])
+    except Exception:
+        logging.error('Failed to compute tre for image pair (%s, %s).' % deformation_field_file_names)
+        return (
+            {'1. TRE': np.NaN},
+            {'1. TRE': np.NaN}
+        )
+
+    return (
+        {'1. TRE': np.nanmean(np.sqrt(np.nansum((point_set_fixed0_to_moving1 - point_sets[1]) ** 2, -1)))},
+        {'1. TRE': np.nanmean(np.sqrt(np.nansum((point_set_fixed1_to_moving0 - point_sets[0]) ** 2, -1)))}
+    )
+
+