ITK  4.9.0
Insight Segmentation and Registration Toolkit
Examples/Filtering/OtsuThresholdImageFilter.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.
*
*=========================================================================*/
// Software Guide : BeginCommandLineArgs
// INPUTS: {BrainProtonDensitySlice.png}
// OUTPUTS: {OtsuThresholdImageFilterOutput.png}
// ARGUMENTS: 255 0
// Software Guide : EndCommandLineArgs
// Software Guide : BeginLatex
//
// This example illustrates how to use the \doxygen{OtsuThresholdImageFilter}.
//
// Software Guide : EndLatex
// Software Guide : BeginCodeSnippet
// Software Guide : EndCodeSnippet
#include "itkImage.h"
int main( int argc, char * argv[] )
{
if( argc < 5 )
{
std::cerr << "Usage: " << argv[0];
std::cerr << " inputImageFile outputImageFile ";
std::cerr << " insideValue outsideValue " << std::endl;
return EXIT_FAILURE;
}
// Software Guide : BeginLatex
//
// The next step is to decide which pixel types to use for the input and output
// images, and to define the image dimension.
//
// Software Guide : EndLatex
// Software Guide : BeginCodeSnippet
typedef unsigned char InputPixelType;
typedef unsigned char OutputPixelType;
const unsigned int Dimension = 2;
// Software Guide : EndCodeSnippet
// Software Guide : BeginLatex
//
// The input and output image types are now defined using their respective
// pixel types and dimensions.
//
// Software Guide : EndLatex
// Software Guide : BeginCodeSnippet
// Software Guide : EndCodeSnippet
// Software Guide : BeginLatex
//
// The filter type can be instantiated using the input and output image
// types defined above.
//
// Software Guide : EndLatex
// Software Guide : BeginCodeSnippet
InputImageType, OutputImageType > FilterType;
// Software Guide : EndCodeSnippet
// Software Guide : BeginLatex
//
// An \doxygen{ImageFileReader} class is also instantiated in order to read
// image data from a file. (See Section \ref{sec:IO} on page
// \pageref{sec:IO} for more information about reading
// and writing data.)
//
// Software Guide : EndLatex
// Software Guide : BeginCodeSnippet
// Software Guide : EndCodeSnippet
// Software Guide : BeginLatex
//
// An \doxygen{ImageFileWriter} is instantiated in order to write the output
// image to a file.
//
// Software Guide : EndLatex
// Software Guide : BeginCodeSnippet
// Software Guide : EndCodeSnippet
// Software Guide : BeginLatex
//
// Both the filter and the reader are created by invoking their \code{New()}
// methods and assigning the result to \doxygen{SmartPointer}s.
//
// Software Guide : EndLatex
// Software Guide : BeginCodeSnippet
ReaderType::Pointer reader = ReaderType::New();
FilterType::Pointer filter = FilterType::New();
// Software Guide : EndCodeSnippet
WriterType::Pointer writer = WriterType::New();
writer->SetInput( filter->GetOutput() );
reader->SetFileName( argv[1] );
// Software Guide : BeginLatex
//
// The image obtained with the reader is passed as input to the
// \code{OtsuThresholdImageFilter}.
//
// \index{itk::Otsu\-Threshold\-Image\-Filter!SetInput()}
// \index{itk::FileImageReader!GetOutput()}
//
// Software Guide : EndLatex
// Software Guide : BeginCodeSnippet
filter->SetInput( reader->GetOutput() );
// Software Guide : EndCodeSnippet
// Software Guide : BeginLatex
//
// The method \code{SetOutsideValue()} defines the intensity value to be
// assigned to those pixels whose intensities are outside the range defined
// by the lower and upper thresholds. The method \code{SetInsideValue()}
// defines the intensity value to be assigned to pixels with intensities
// falling inside the threshold range.
//
// \index{itk::Otsu\-Threshold\-Image\-Filter!SetOutsideValue()}
// \index{itk::Otsu\-Threshold\-Image\-Filter!SetInsideValue()}
// \index{SetOutsideValue()!itk::Otsu\-Threshold\-Image\-Filter}
// \index{SetInsideValue()!itk::Otsu\-Threshold\-Image\-Filter}
//
// Software Guide : EndLatex
const OutputPixelType outsideValue = atoi( argv[3] );
const OutputPixelType insideValue = atoi( argv[4] );
// Software Guide : BeginCodeSnippet
filter->SetOutsideValue( outsideValue );
filter->SetInsideValue( insideValue );
// Software Guide : EndCodeSnippet
// Software Guide : BeginLatex
//
// Execution of the filter is triggered by invoking the \code{Update()}
// method, which we wrap in a \code{try/catch} block. If the filter's
// output has been passed as input to subsequent filters, the \code{Update()}
// call on any downstream filters in the pipeline will indirectly trigger
// the update of this filter.
//
// Software Guide : EndLatex
// Software Guide : BeginCodeSnippet
try
{
filter->Update();
}
catch( itk::ExceptionObject & excp )
{
std::cerr << "Exception thrown " << excp << std::endl;
}
// Software Guide : EndCodeSnippet
// Software Guide : BeginLatex
//
// We can now retrieve the internally-computed threshold value with the
// \code{GetThreshold()} method and print it to the console.
//
// Software Guide : EndLatex
// Software Guide : BeginCodeSnippet
int threshold = filter->GetThreshold();
std::cout << "Threshold = " << threshold << std::endl;
// Software Guide : EndCodeSnippet
// Software Guide : BeginLatex
//
// \begin{figure}
// \center
// \includegraphics[width=0.44\textwidth]{BrainProtonDensitySlice}
// \includegraphics[width=0.44\textwidth]{OtsuThresholdImageFilterOutput}
// \itkcaption[OtsuThresholdImageFilter output]{Effect of the
// OtsuThresholdImageFilter on a slice from a MRI proton density image of
// the brain.}
// \label{fig:OtsuThresholdImageFilterInputOutput}
// \end{figure}
//
// Figure \ref{fig:OtsuThresholdImageFilterInputOutput} illustrates the
// effect of this filter on a MRI proton density image of the brain. This
// figure shows the limitations of this filter for performing segmentation
// by itself. These limitations are particularly noticeable in noisy images
// and in images lacking spatial uniformity as is the case with MRI due to
// field bias.
//
// \relatedClasses
// \begin{itemize}
// \item \doxygen{ThresholdImageFilter}
// \end{itemize}
//
// Software Guide : EndLatex
writer->SetFileName( argv[2] );
try
{
writer->Update();
}
catch( itk::ExceptionObject & excp )
{
std::cerr << "Exception thrown " << excp << std::endl;
}
return EXIT_SUCCESS;
}