ITK  5.0.0
Insight Segmentation and Registration Toolkit
SphinxExamples/src/Segmentation/LevelSets/SegmentWithGeodesicActiveContourLevelSet/Code.cxx
/*=========================================================================
*
* Copyright Insight Software Consortium
*
* Licensed under the Apache License, Version 2.0 (the "License");
* you may not use this file except in compliance with the License.
* You may obtain a copy of the License at
*
* http://www.apache.org/licenses/LICENSE-2.0.txt
*
* Unless required by applicable law or agreed to in writing, software
* distributed under the License is distributed on an "AS IS" BASIS,
* WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
* See the License for the specific language governing permissions and
* limitations under the License.
*
*=========================================================================*/
int main( int argc, char* argv[] )
{
if( argc != 11 )
{
std::cerr << "Usage: " << argv[0];
std::cerr << " <InputFileName> <OutputFileName>";
std::cerr << " <seedX> <seedY> <InitialDistance>";
std::cerr << " <Sigma> <SigmoidAlpha> <SigmoidBeta>";
std::cerr << " <PropagationScaling> <NumberOfIterations>" << std::endl;
return EXIT_FAILURE;
}
const char * inputFileName = argv[1];
const char * outputFileName = argv[2];
const int seedPosX = atoi( argv[3] );
const int seedPosY = atoi( argv[4] );
const double initialDistance = atof( argv[5] );
const double sigma = atof( argv[6] );
const double alpha = atof( argv[7] );
const double beta = atof( argv[8] );
const double propagationScaling = atof( argv[9] );
const double numberOfIterations = atoi( argv[10] );
const double seedValue = - initialDistance;
constexpr unsigned int Dimension = 2;
using InputPixelType = float;
using OutputPixelType = unsigned char;
ReaderType::Pointer reader = ReaderType::New();
reader->SetFileName( inputFileName );
SmoothingFilterType::Pointer smoothing = SmoothingFilterType::New();
smoothing->SetTimeStep( 0.125 );
smoothing->SetNumberOfIterations( 5 );
smoothing->SetConductanceParameter( 9.0 );
smoothing->SetInput( reader->GetOutput() );
GradientFilterType::Pointer gradientMagnitude = GradientFilterType::New();
gradientMagnitude->SetSigma( sigma );
gradientMagnitude->SetInput( smoothing->GetOutput() );
SigmoidFilterType::Pointer sigmoid = SigmoidFilterType::New();
sigmoid->SetOutputMinimum( 0.0 );
sigmoid->SetOutputMaximum( 1.0 );
sigmoid->SetAlpha( alpha );
sigmoid->SetBeta( beta );
sigmoid->SetInput( gradientMagnitude->GetOutput() );
FastMarchingFilterType::Pointer fastMarching = FastMarchingFilterType::New();
GeodesicActiveContourFilterType::Pointer geodesicActiveContour = GeodesicActiveContourFilterType::New();
geodesicActiveContour->SetPropagationScaling( propagationScaling );
geodesicActiveContour->SetCurvatureScaling( 1.0 );
geodesicActiveContour->SetAdvectionScaling( 1.0 );
geodesicActiveContour->SetMaximumRMSError( 0.02 );
geodesicActiveContour->SetNumberOfIterations( numberOfIterations );
geodesicActiveContour->SetInput( fastMarching->GetOutput() );
geodesicActiveContour->SetFeatureImage( sigmoid->GetOutput() );
ThresholdingFilterType::Pointer thresholder = ThresholdingFilterType::New();
thresholder->SetLowerThreshold( -1000.0 );
thresholder->SetUpperThreshold( 0.0 );
thresholder->SetOutsideValue( itk::NumericTraits< OutputPixelType >::min() );
thresholder->SetInsideValue( itk::NumericTraits< OutputPixelType >::max() );
thresholder->SetInput( geodesicActiveContour->GetOutput() );
using NodeContainer = FastMarchingFilterType::NodeContainer;
using NodeType = FastMarchingFilterType::NodeType;
seedPosition[0] = seedPosX;
seedPosition[1] = seedPosY;
NodeContainer::Pointer seeds = NodeContainer::New();
NodeType node;
node.SetValue( seedValue );
node.SetIndex( seedPosition );
seeds->Initialize();
seeds->InsertElement( 0, node );
fastMarching->SetTrialPoints( seeds );
fastMarching->SetSpeedConstant( 1.0 );
CastFilterType::Pointer caster1 = CastFilterType::New();
CastFilterType::Pointer caster2 = CastFilterType::New();
CastFilterType::Pointer caster3 = CastFilterType::New();
CastFilterType::Pointer caster4 = CastFilterType::New();
WriterType::Pointer writer1 = WriterType::New();
WriterType::Pointer writer2 = WriterType::New();
WriterType::Pointer writer3 = WriterType::New();
WriterType::Pointer writer4 = WriterType::New();
caster1->SetInput( smoothing->GetOutput() );
writer1->SetInput( caster1->GetOutput() );
writer1->SetFileName("GeodesicActiveContourImageFilterOutput1.png");
caster1->SetOutputMinimum( itk::NumericTraits< OutputPixelType >::min() );
caster1->SetOutputMaximum( itk::NumericTraits< OutputPixelType >::max() );
writer1->Update();
caster2->SetInput( gradientMagnitude->GetOutput() );
writer2->SetInput( caster2->GetOutput() );
writer2->SetFileName("GeodesicActiveContourImageFilterOutput2.png");
caster2->SetOutputMinimum( itk::NumericTraits< OutputPixelType >::min() );
caster2->SetOutputMaximum( itk::NumericTraits< OutputPixelType >::max() );
writer2->Update();
caster3->SetInput( sigmoid->GetOutput() );
writer3->SetInput( caster3->GetOutput() );
writer3->SetFileName("GeodesicActiveContourImageFilterOutput3.png");
caster3->SetOutputMinimum( itk::NumericTraits< OutputPixelType >::min() );
caster3->SetOutputMaximum( itk::NumericTraits< OutputPixelType >::max() );
writer3->Update();
caster4->SetInput( fastMarching->GetOutput() );
writer4->SetInput( caster4->GetOutput() );
writer4->SetFileName("GeodesicActiveContourImageFilterOutput4.png");
caster4->SetOutputMinimum( itk::NumericTraits< OutputPixelType >::min() );
caster4->SetOutputMaximum( itk::NumericTraits< OutputPixelType >::max() );
fastMarching->SetOutputSize(
reader->GetOutput()->GetBufferedRegion().GetSize() );
WriterType::Pointer writer = WriterType::New();
writer->SetFileName( outputFileName );
writer->SetInput( thresholder->GetOutput() );
try
{
writer->Update();
}
catch( itk::ExceptionObject & error )
{
std::cerr << "Error: " << error << std::endl;
return EXIT_FAILURE;
}
std::cout << std::endl;
std::cout << "Max. no. iterations: " << geodesicActiveContour->GetNumberOfIterations() << std::endl;
std::cout << "Max. RMS error: " << geodesicActiveContour->GetMaximumRMSError() << std::endl;
std::cout << std::endl;
std::cout << "No. elpased iterations: " << geodesicActiveContour->GetElapsedIterations() << std::endl;
std::cout << "RMS change: " << geodesicActiveContour->GetRMSChange() << std::endl;
try
{
writer4->Update();
}
catch( itk::ExceptionObject & error )
{
std::cerr << "Error: " << error << std::endl;
return EXIT_FAILURE;
}
using InternalWriterType = itk::ImageFileWriter< InputImageType >;
InternalWriterType::Pointer mapWriter = InternalWriterType::New();
mapWriter->SetInput( fastMarching->GetOutput() );
mapWriter->SetFileName("GeodesicActiveContourImageFilterOutput4.mha");
try
{
mapWriter->Update();
}
catch( itk::ExceptionObject & error )
{
std::cerr << "Error: " << error << std::endl;
return EXIT_FAILURE;
}
InternalWriterType::Pointer speedWriter = InternalWriterType::New();
speedWriter->SetInput( sigmoid->GetOutput() );
speedWriter->SetFileName("GeodesicActiveContourImageFilterOutput3.mha");
try
{
speedWriter->Update();
}
catch( itk::ExceptionObject & error )
{
std::cerr << "Error: " << error << std::endl;
return EXIT_FAILURE;
}
InternalWriterType::Pointer gradientWriter = InternalWriterType::New();
gradientWriter->SetInput( gradientMagnitude->GetOutput() );
gradientWriter->SetFileName("GeodesicActiveContourImageFilterOutput2.mha");
try
{
gradientWriter->Update();
}
catch( itk::ExceptionObject & error )
{
std::cerr << "Error: " << error << std::endl;
return EXIT_FAILURE;
}
return EXIT_SUCCESS;
}