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Francois Budin
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Merge pull request #13 from jeanyves-yang/master
MedianFilter
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‎Exercices/MedianFilter/CMakeLists.txt

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cmake_minimum_required(VERSION 2.8)
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project(MedianFilter)
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# Find SlicerExecutionModel
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find_package(SlicerExecutionModel REQUIRED)
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include(${SlicerExecutionModel_USE_FILE})
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include(${GenerateCLP_USE_FILE})
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# Find ITK
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find_package(ITK REQUIRED)
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include(${ITK_USE_FILE})
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set(MedianFilter_SOURCE MedianFilter.cxx)
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SEMMacroBuildCLI(
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NAME MedianFilter
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EXECUTABLE_ONLY
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TARGET_LIBRARIES ${ITK_LIBRARIES}
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)
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option(BUILD_TESTING "Build the testing tree" ON)
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IF(BUILD_TESTING)
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include(CTest)
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ADD_SUBDIRECTORY(Testing)
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ENDIF(BUILD_TESTING)
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‎Exercices/MedianFilter/MedianFilter.cxx

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/*=============================================================================
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Licensed under the Apache License, Version 2.0 (the "License");
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you may not use this file except in compliance with the License.
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You may obtain a copy of the License at
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http://www.apache.org/licenses/LICENSE-2.0
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Unless required by applicable law or agreed to in writing, software
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distributed under the License is distributed on an "AS IS" BASIS,
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WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
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See the License for the specific language governing permissions and
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limitations under the License.
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=============================================================================*/
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#include "itkImage.h"
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#include "itkImageFileReader.h"
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#include "itkImageFileWriter.h"
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#include "itkMedianImageFilter.h"
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#include "MedianFilterCLP.h"
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#include "stdlib.h"
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#include "itkImageIOBase.h"
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void GetImageType ( std::string fileName , itk::ImageIOBase::IOComponentType &componentType )
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{
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typedef itk::Image< unsigned char, 3 > ImageType ;
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itk::ImageFileReader<ImageType>::Pointer imageReader = itk::ImageFileReader< ImageType >::New() ;
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imageReader->SetFileName( fileName.c_str() ) ;
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imageReader->UpdateOutputInformation() ;
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componentType = imageReader->GetImageIO()->GetComponentType() ;
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}
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template< class TImage >
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int ReadImage( const char* fileName , typename TImage::Pointer& image )
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{
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typedef TImage ImageType ;
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typedef itk::ImageFileReader< ImageType > ImageReaderType ;
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typename ImageReaderType::Pointer reader = ImageReaderType::New() ;
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reader->SetFileName( fileName ) ;
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try
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{
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reader->Update() ;
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}
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catch( itk::ExceptionObject& e )
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{
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std::cerr << e.what() << std::endl ;
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return 1 ;
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}
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image = reader->GetOutput() ;
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return 0 ;
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}
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/* Creates the Median Filter and the output image with the input type. */
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template< class ComponentType >
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int MedianFilter( std::string inputFileName , std::string outputFileName , int radius )
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{
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typedef itk::Image< ComponentType , 3 > ImageType ;
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typedef itk::MedianImageFilter < ImageType , ImageType > FilterType ;
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typename FilterType::Pointer medianFilter = FilterType::New() ;
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typename FilterType::InputSizeType filterRadius ;
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typename ImageType::Pointer image = ImageType::New() ;
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if( radius < 1 )
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{
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std::cout << "Radius value must be non-zero positive integer." << std::endl ;
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return EXIT_FAILURE ;
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}
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if( ReadImage< ImageType >( inputFileName.c_str() , image ) )
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{
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std::cout << "Image could not be read." << std::endl ;
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return EXIT_FAILURE ;
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}
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filterRadius.Fill( radius ) ;
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medianFilter->SetRadius( filterRadius ) ;
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medianFilter->SetInput( image ) ;
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typedef itk::ImageFileWriter< ImageType > WriterType ;
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typename WriterType::Pointer writer = WriterType::New() ;
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writer->SetInput( medianFilter->GetOutput() ) ;
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writer->SetFileName( outputFileName ) ;
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writer->Update() ;
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return EXIT_SUCCESS ;
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}
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int main( int argc , char *argv[] )
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{
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PARSE_ARGS ;
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itk::ImageIOBase::IOPixelType pixelType ;
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itk::ImageIOBase::IOComponentType componentType ;
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try
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{
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GetImageType( input , componentType ) ;
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/* Apply the Median Filter according to the type of the input file */
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switch( componentType )
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{
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case itk::ImageIOBase::UCHAR:
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{
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return MedianFilter< unsigned char >( input , output , radius ) ;
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break ;
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}
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case itk::ImageIOBase::CHAR:
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{
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return MedianFilter< char >( input , output , radius ) ;
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break ;
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}
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case itk::ImageIOBase::USHORT:
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{
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return MedianFilter< unsigned short >( input , output , radius ) ;
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break ;
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}
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case itk::ImageIOBase::SHORT:
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{
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return MedianFilter< short >( input , output , radius ) ;
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break ;
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}
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case itk::ImageIOBase::UINT:
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{
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return MedianFilter< unsigned int >( input , output , radius ) ;
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break ;
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}
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case itk::ImageIOBase::INT:
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{
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return MedianFilter< int >( input , output , radius ) ;
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break ;
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}
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case itk::ImageIOBase::ULONG:
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{
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return MedianFilter< unsigned long >( input , output , radius ) ;
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break ;
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}
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case itk::ImageIOBase::LONG:
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{
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return MedianFilter< long >( input , output , radius ) ;
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break ;
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}
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case itk::ImageIOBase::FLOAT:
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{
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return MedianFilter< float >( input , output , radius ) ;
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break ;
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}
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case itk::ImageIOBase::DOUBLE:
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{
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return MedianFilter< double >( input , output , radius ) ;
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break ;
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}
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default:
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case itk::ImageIOBase::UNKNOWNCOMPONENTTYPE:
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{
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std::cerr << "Unknown and unsupported component type!" << std::endl ;
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return EXIT_FAILURE ;
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}
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}
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}
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catch( itk::ExceptionObject &excep )
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{
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std::cerr << argv[0] << ": exception caught !" << std::endl ;
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std::cerr << excep << std::endl ;
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return EXIT_FAILURE ;
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}
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return EXIT_SUCCESS ;
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}

‎Exercices/MedianFilter/MedianFilter.xml

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<?xml version="1.0" encoding="utf-8"?>
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<executable>
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<category>Filtering.Arithmetic</category>
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<title>Median Image Filtering</title>
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<description>Median filter of a image</description>
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<parameters>
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<label>IO</label>
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<description>Input/Output parameters</description>
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<image>
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<name>input</name>
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<label>image input</label>
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<channel>image</channel>
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<index>0</index>
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<description>image input</description>
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</image>
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<image>
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<name>output</name>
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<label>image output</label>
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<channel>image</channel>
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<index>1</index>
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<description>image output</description>
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</image>
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<integer>
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<name>radius</name>
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<longflag>radius</longflag>
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<flag>r</flag>
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<label>radius</label>
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<description>radius value</description>
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<constraints>
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<minimum>1</minimum>
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</constraints>
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</integer>
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</parameters>
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</executable>
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‎Exercices/MedianFilter/Testing/CMakeLists.txt

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set(Data Data)
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set(TEMP_DIR ${MedianFilter_BINARY_DIR}/Testing/Temporary )
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set(SOURCE_DIR ${CMAKE_CURRENT_SOURCE_DIR}/${Data} )
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set(BaselineRadius2 ${SOURCE_DIR}/baselineT2Radius2.nrrd )
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set(BaselineRadius4 ${SOURCE_DIR}/baselineT2Radius4.nrrd )
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set(DummyOutput ${SOURCE_DIR}/DummyOutput.nrrd )
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set(Input ${SOURCE_DIR}/inputT2.nrrd )
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include_directories( ${CMAKE_SOURCE_DIR} )
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add_executable(MedianFilterTest MedianFilterTest.cxx)
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target_link_libraries(MedianFilterTest MedianFilterLib)
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set( RadiusValue2 ${TEMP_DIR}/RadiusValue2.nrrd )
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set( RadiusValue4 ${TEMP_DIR}/RadiusValue4.nrrd )
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# Test checking that the program cannot run without arguments
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add_test(NAME OpenFileTest COMMAND $<TARGET_FILE:MedianFilter>)
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set_tests_properties(OpenFileTest PROPERTIES WILL_FAIL true )
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# Test checking that the radius value cannot go below 1
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add_test(NAME RadiusLimitMin COMMAND $<TARGET_FILE:MedianFilter>
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${Input}
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${DummyOutput}
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-r 0
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)
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set_tests_properties( RadiusLimitMin PROPERTIES WILL_FAIL true )
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#Test checking that a wrong input will prevent the program from running
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add_test(NAME MedianFilterWrongInputFileName COMMAND $<TARGET_FILE:MedianFilter>
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WrongInput.nrrd
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${DummyOutput}
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-r 20
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)
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set_tests_properties( MedianFilterWrongInputFileName PROPERTIES WILL_FAIL true )
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# Tests checking that that the output image is what is expected
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add_test(NAME MedianFilterRadiusValue2 COMMAND $<TARGET_FILE:MedianFilterTest>
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--compare
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${BaselineRadius2}
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${RadiusValue2}
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ModuleEntryPoint
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${Input}
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${RadiusValue2}
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-r 2
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)
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add_test(NAME MedianFilterRadiusValue4 COMMAND $<TARGET_FILE:MedianFilterTest>
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--compare
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${BaselineRadius4}
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${RadiusValue4}
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ModuleEntryPoint
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${Input}
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${RadiusValue4}
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-r 4
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)
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# Test for the command --help
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add_test(NAME PrintHelp COMMAND $<TARGET_FILE:MedianFilter> --help)

‎Exercices/MedianFilter/Testing/Data/baselineT2Radius2.nrrd

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‎Exercices/MedianFilter/Testing/Data/baselineT2Radius4.nrrd

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‎Exercices/MedianFilter/Testing/Data/inputT2.nrrd

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‎Exercices/MedianFilter/Testing/MedianFilterTest.cxx

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#include "itkTestMain.h"
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#ifdef WIN32
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#define MODULE_IMPORT __declspec(dllimport)
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#else
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#define MODULE_IMPORT
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#endif
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extern "C" MODULE_IMPORT int ModuleEntryPoint(int, char * []);
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void RegisterTests()
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{
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StringToTestFunctionMap["ModuleEntryPoint"] = ModuleEntryPoint;
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}

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