- CMAKE_MINIMUM_REQUIRED(VERSION 3.0)
+ cmake_minimum_required(VERSION 3.0)
## ========================
## == Project definition ==
## ========================
- SET(prj_NAME FrontAlgorithms)
- SET(prj_MAJOR_VERSION 0)
- SET(prj_MINOR_VERSION 1)
- SET(prj_RELEASE_VERSION 0)
- SET(_subdirs lib plugins examples)
- SET(_policies CMP0015 CMP0020 CMP0042)
+ set(prj_MAJ_VERSION 0)
+ set(prj_MIN_VERSION 1)
+ set(prj_REL_VERSION 0)
+ set(prj_VERSION "${prj_MAJ_VERSION}.${prj_MIN_VERSION}.${prj_REL_VERSION}")
+ set(prj_SHORT_VERSION "${prj_MAJ_VERSION}")
+ project(fpa VERSION ${prj_VERSION})
## ==========================
## == Some useful policies ==
## ==========================
- FOREACH(_p ${_policies})
- IF(POLICY ${_p})
- CMAKE_POLICY(SET ${_p} NEW)
- ENDIF(POLICY ${_p})
- ENDFOREACH(_p)
+ set(_policies CMP0015 CMP0020 CMP0042 CMP0053)
+ foreach(_p ${_policies})
+ if(POLICY ${_p})
+ cmake_policy(SET ${_p} NEW)
+ endif(POLICY ${_p})
+ endforeach(_p)
- ## ===========================
- ## == Project configuration ==
- ## ===========================
+ ## ===============================
+ ## == Some basic configurations ==
+ ## ===============================
- PROJECT(${prj_NAME})
- SET(
- prj_VERSION
- "${prj_MAJOR_VERSION}.${prj_MINOR_VERSION}.${prj_RELEASE_VERSION}"
- )
- SET(prj_SHORT_VERSION "${prj_MAJOR_VERSION}")
-
- ## =====================================
- ## == Functions, packages and options ==
- ## =====================================
-
- INCLUDE(cmake/BaseConfig.cmake)
- OPTION(USE_cpPlugins "Build cpPlugins-based code" OFF)
- IF(USE_cpPlugins)
- FIND_PACKAGE(cpPlugins)
- MARK_AS_ADVANCED(CLEAR cpPlugins_DIR)
- ENDIF(USE_cpPlugins)
- INCLUDE(cmake/KitwareTools.cmake)
- INCLUDE(cmake/QtTools.cmake)
- INCLUDE(cmake/Functions.cmake)
+ include(cmake/fpaBaseConfig.cmake)
+
+ ## ==============
+ ## == Find ITK ==
+ ## ==============
+
+ find_package(ITK CONFIG REQUIRED)
+ include(${ITK_USE_FILE})
+
+ ## =========================
+ ## == Installation values ==
+ ## =========================
+
+ set(config_install_dir "lib/cmake/${PROJECT_NAME}")
+ set(include_install_dir "include")
+ set(generated_dir "${CMAKE_CURRENT_BINARY_DIR}/generated")
+ set(version_config "${generated_dir}/${PROJECT_NAME}ConfigVersion.cmake")
+ set(project_config "${generated_dir}/${PROJECT_NAME}Config.cmake")
+ set(targets_export_name "${PROJECT_NAME}Targets")
+ set(namespace "${PROJECT_NAME}::")
## ===========================
## == Build different parts ==
## ===========================
- FOREACH(_s ${_subdirs})
- SUBDIRS(${_s})
- ENDFOREACH(_s)
-subdirs(lib)
++subdirs(examples lib)
+
+ ## ===============================
+ ## == Global installation rules ==
+ ## ===============================
+
+ include(CMakePackageConfigHelpers)
+ write_basic_package_version_file(
+ "${version_config}" COMPATIBILITY SameMajorVersion
+ )
+ configure_package_config_file(
+ "cmake/${PROJECT_NAME}Config.cmake.in"
+ "${project_config}"
+ INSTALL_DESTINATION "${config_install_dir}"
+ )
+ install(
+ FILES
+ "${project_config}"
+ "${version_config}"
+ "${CMAKE_CURRENT_SOURCE_DIR}/cmake/fpaBaseConfig.cmake"
+ DESTINATION "${config_install_dir}"
+ )
+ #install(
+ # EXPORT "${targets_export_name}"
+ # NAMESPACE "${namespace}"
+ # DESTINATION "${config_install_dir}"
+ # )
## eof - $RCSfile$
- OPTION(BUILD_Examples "Build simple examples?" OFF)
-
- IF(BUILD_Examples)
-OPTION(BUILD_EXAMPLES "Build cpPlugins-free examples." OFF)
-IF(BUILD_EXAMPLES)
-- SET(
++option(BUILD_EXAMPLES "Build cpPlugins-free examples." OFF)
++if(BUILD_EXAMPLES)
++ set(
_examples
- RegionGrow_00
- FastMarching_00
- MoriRegionGrow_00
- Skeleton_00
+ RegionGrow_Tautology
+ RegionGrow_BinaryThreshold
+ RegionGrow_Mori
+ Dijkstra_Maurer
+ #CreateMoriInputImage
+ #BronchiiInitialSegmentationWithMori
+ #BronchiiInitialSegmentationWithBinaryThresholdRegionGrow
)
- OPTION(BUILD_EXAMPLE_SANDBOX "Build sandbox example." OFF)
- IF(BUILD_EXAMPLE_SANDBOX)
- LIST(APPEND _examples sandbox)
- ENDIF(BUILD_EXAMPLE_SANDBOX)
-- INCLUDE_DIRECTORIES(
- ${PROJECT_SOURCE_DIR}/libs
- ${PROJECT_BINARY_DIR}/libs
++ option(BUILD_EXAMPLE_SANDBOX "Build sandbox example." OFF)
++ if(BUILD_EXAMPLE_SANDBOX)
++ list(APPEND _examples sandbox)
++ endif(BUILD_EXAMPLE_SANDBOX)
++ include_directories(
+ ${PROJECT_SOURCE_DIR}/lib
+ ${PROJECT_BINARY_DIR}/lib
)
- FOREACH(_example ${_examples})
- ADD_EXECUTABLE(fpa_example_${_example} ${_example}.cxx)
- TARGET_LINK_LIBRARIES(fpa_example_${_example} ${ITK_LIBRARIES} ${VTK_LIBRARIES})
- ENDFOREACH(_example)
- ENDIF(BUILD_Examples)
- FOREACH(_e ${_examples})
- ADD_EXECUTABLE(fpa_example_${_e} ${_e}.cxx)
- TARGET_LINK_LIBRARIES(fpa_example_${_e} ${ITK_LIBRARIES})
- ENDFOREACH(_e)
-ENDIF(BUILD_EXAMPLES)
++ foreach(_e ${_examples})
++ add_executable(fpa_example_${_e} ${_e}.cxx)
++ target_link_libraries(fpa_example_${_e} ${ITK_LIBRARIES})
++ endforeach(_e)
++endif(BUILD_EXAMPLES)
## eof - $RCSfile$
--- /dev/null
- if( argc < 7 + VDim )
+ #include <chrono>
+ #include <iomanip>
+ #include <itkCommand.h>
+ #include <itkImage.h>
+ #include <itkImageFileReader.h>
+ #include <itkImageFileWriter.h>
+ #include <itkBinaryThresholdImageFilter.h>
+
+ #include <fpa/Image/MoriRegionGrow.h>
+
+ // -------------------------------------------------------------------------
+ static const unsigned int VDim = 3;
+ typedef short TPixel;
+ typedef itk::Image< TPixel, VDim > TImage;
+ typedef itk::ImageFileReader< TImage > TReader;
+ typedef itk::ImageFileWriter< TImage > TWriter;
+ typedef fpa::Image::MoriRegionGrow< TImage, TImage > TFilter;
+ typedef itk::BinaryThresholdImageFilter< TImage, TImage > TThreshold;
+
+ // -------------------------------------------------------------------------
+ class ShowProgressObject
+ {
+ public:
+ ShowProgressObject( itk::ProcessObject* o )
+ {
+ this->m_Process = o;
+ }
+ void ShowProgress( )
+ {
+ std::cerr
+ << "\rProgress " << std::fixed << std::setprecision( 2 )
+ << ( this->m_Process->GetProgress( ) * 100 )
+ << " %" << std::flush;
+ }
+ itk::ProcessObject::Pointer m_Process;
+ };
+
+ // -------------------------------------------------------------------------
+ int main( int argc, char* argv[] )
+ {
+ // Get arguments
- << " input_image output_image auxiliary_image lower upper delta";
++ if( argc < 6 + VDim )
+ {
+ std::cerr
+ << "Usage: " << argv[ 0 ]
- std::string auxiliary_image_filename = argv[ 3 ];
- TPixel lower = std::atof( argv[ 4 ] );
- TPixel upper = std::atof( argv[ 5 ] );
- TPixel delta = std::atof( argv[ 6 ] );
++ << " input_image output_image lower upper delta";
+ for( unsigned int i = 0; i < VDim; ++i )
+ std::cerr << " s_" << i;
+ std::cerr << std::endl;
+ return( 1 );
+
+ } // fi
+ std::string input_image_filename = argv[ 1 ];
+ std::string output_image_filename = argv[ 2 ];
- pnt[ i ] = std::atof( argv[ i + 7 ] );
++ TPixel lower = std::atof( argv[ 3 ] );
++ TPixel upper = std::atof( argv[ 4 ] );
++ TPixel delta = std::atof( argv[ 5 ] );
+
+ TReader::Pointer reader = TReader::New( );
+ reader->SetFileName( input_image_filename );
+ try
+ {
+ reader->Update( );
+ }
+ catch( std::exception& err )
+ {
+ std::cerr << "ERROR: " << err.what( ) << std::endl;
+ return( 1 );
+
+ } // yrt
+
+ TFilter::Pointer filter = TFilter::New( );
+ filter->SetInput( reader->GetOutput( ) );
+ filter->SetThresholdRange( lower, upper, delta );
+ TImage::PointType pnt;
+ for( int i = 0; i < VDim; ++i )
-
- TWriter::Pointer aux_writer = TWriter::New( );
- aux_writer->SetInput( filter->GetOutput( ) );
- aux_writer->SetFileName( auxiliary_image_filename );
++ pnt[ i ] = std::atof( argv[ i + 6 ] );
+
+ TImage::IndexType seed;
+ if( !( reader->GetOutput( )->TransformPhysicalPointToIndex( pnt, seed ) ) )
+ {
+ std::cerr << "ERROR: seed outside image." << std::endl;
+ return( 1 );
+
+ } // fi
+ filter->AddSeed( seed );
+
+ // to test ProgressReporter
+ /* TODO
+ ShowProgressObject progressWatch( filter );
+ typedef itk::SimpleMemberCommand< ShowProgressObject > CommandType;
+ CommandType::Pointer command = CommandType::New();
+ command->SetCallbackFunction( &progressWatch,
+ &ShowProgressObject::ShowProgress );
+ filter->AddObserver( itk::ProgressEvent( ), command );
+ */
+ std::chrono::time_point< std::chrono::system_clock > start, end;
+ start = std::chrono::system_clock::now( );
+ filter->Update( );
+ end = std::chrono::system_clock::now( );
+ std::chrono::duration< double > elapsed_seconds = end - start;
+
+ TThreshold::Pointer threshold = TThreshold::New( );
+ threshold->SetInput( filter->GetOutput( ) );
+ threshold->SetInsideValue( 255 );
+ threshold->SetOutsideValue( 0 );
+ threshold->SetLowerThreshold( 0 );
+ threshold->SetUpperThreshold( filter->GetOptimumThreshold( ) );
+
+ TWriter::Pointer writer = TWriter::New( );
+ writer->SetInput( threshold->GetOutput( ) );
+ writer->SetFileName( output_image_filename );
- aux_writer->Update( );
+ try
+ {
+ writer->Update( );
+ }
+ catch( std::exception& err )
+ {
+ std::cerr << "ERROR: " << err.what( ) << std::endl;
+ return( 1 );
+
+ } // yrt
+
+ // Show data
+ TFilter::TCurve curve = filter->GetCurve( );
+ for( TFilter::TCurveData data: curve )
+ {
+ std::cout << data.XValue << " " << data.YValue << " " << data.Diff1 << std::endl;
+ }
+ std::cout
+ << std::endl
+ << "# Opt: "
+ << curve[ filter->GetOptimumThreshold( ) ].XValue
+ << "("
+ << filter->GetOptimumThreshold( )
+ << ")"
+ << std::endl;
+ std::cout << "Time: " << elapsed_seconds.count( ) << "s" << std::endl;
+ return( 0 );
+ }
+
+ // eof - $RCSfile$