# AVIMultiChannelRAndGAndNIRVegetationIndexImageFilter.cxxΒΆ

Example usage:

./AVIMultiChannelRAndGAndNIRVegetationIndexImageFilter Input/verySmallFSATSW.tif \
Output/AVIMultiChannelRAndGAndNIRVegetationIndex.tif \
Output/pretty_FSATSW.png \
Output/pretty_AVIMultiChannelRAndGAndNIRVegetationIndex.png \
3 \
2 \
4


Example source code (AVIMultiChannelRAndGAndNIRVegetationIndexImageFilter.cxx):

// \index{otb::VegetationIndex}
//
//
// The following example illustrates the use of the
// itk::UnaryFunctorImageFilter with the
// use of the Angular Vegetation Index (AVI).
// The equation for the Angular Vegetation Index involves the gren, red
// and near infra-red bands. $\lambda_1$, $\lambda_2$ and $\lambda_3$ are the mid-band
// wavelengths for the green, red and NIR bands and $\tan^{-1}$ is the arctangent function.
//
// The AVI expression is
//
//
// \mathbf{A_1} = \frac{\lambda_3-\lambda_2}{\lambda_2}
//
//
// \mathbf{A_2} = \frac{\lambda_2-\lambda_1}{\lambda_2}
//
//
//
// \mathbf{AVI} = \tan^{-1}\left({\frac{A_1}{NIR-R}}\right) + \tan^{-1}\left({\frac{A_2}{G-R}}\right)
//
//
// For more details, refer to Plummer work \cite{AVI}.
//
//
// Let's look at the minimal code required to use this
// algorithm.

#include "otbVegetationIndicesFunctor.h"
#include "itkUnaryFunctorImageFilter.h"

#include "otbImage.h"
#include "otbImageFileWriter.h"
#include "itkRescaleIntensityImageFilter.h"
#include "otbVectorRescaleIntensityImageFilter.h"
#include "otbMultiChannelExtractROI.h"
#include "itkThresholdImageFilter.h"

int main(int argc, char* argv[])
{
if (argc < 8)
{
std::cerr << "Missing Parameters " << std::endl;
std::cerr << "Usage: " << argv[0];
std::cerr << " inputImage , outputImage , prettyInput , prettyOutput , redChannel , greenChannel , nirChannel ," << std::endl;
return 1;
}

// The image types are now defined using pixel types and
// dimension. The input image is defined as an \doxygen{otb}{VectorImage},
// the output is a \doxygen{otb}{Image}.

const unsigned int Dimension = 2;
using InputPixelType         = double;
using OutputPixelType        = float;
using InputImageType         = otb::VectorImage<InputPixelType, Dimension>;
using OutputImageType        = otb::Image<OutputPixelType, Dimension>;

// We instantiate reader and writer types
using WriterType = otb::ImageFileWriter<OutputImageType>;

// The AVI (Angular Vegetation Index) is
// instantiated using the image pixel types as template parameters.

using FunctorType = otb::Functor::AVI<InputPixelType, OutputPixelType>;

// The
// \doxygen{itk}{UnaryFunctorImageFilter}
// type is defined using the image types and the AVI functor as
// template parameters. We then instantiate the filter itself.

using AVIImageFilterTypeType = itk::UnaryFunctorImageFilter<InputImageType, OutputImageType, FunctorType>;

AVIImageFilterTypeType::Pointer filter = AVIImageFilterTypeType::New();

WriterType::Pointer writer = WriterType::New();

//  Now the input image is set and a name is given to the output image.

writer->SetFileName(argv[2]);

// The three used index bands (red, green and NIR) are declared.

filter->GetFunctor().SetBandIndex(CommonBandNames::RED, ::atoi(argv[5]));
filter->GetFunctor().SetBandIndex(CommonBandNames::GREEN, ::atoi(argv[6]));
filter->GetFunctor().SetBandIndex(CommonBandNames::NIR, ::atoi(argv[7]));

// the filter output is linked to the writer input.

writer->SetInput(filter->GetOutput());

//  The invocation of the \code{Update()} method on the writer triggers the
//  execution of the pipeline.  It is recommended to place update calls in a
//  \code{try/catch} block in case errors occur and exceptions are thrown.

try
{
writer->Update();
}
catch (itk::ExceptionObject& excep)
{
std::cerr << "Exception caught !" << std::endl;
std::cerr << excep << std::endl;
}
catch (...)
{
std::cout << "Unknown exception !" << std::endl;
return EXIT_FAILURE;
}

// Pretty image creation for the printing
using OutputPrettyImageType       = otb::Image<unsigned char, Dimension>;
using OutputVectorPrettyImageType = otb::VectorImage<unsigned char, Dimension>;
using WriterVectorPrettyType      = otb::ImageFileWriter<OutputVectorPrettyImageType>;
using WriterPrettyType            = otb::ImageFileWriter<OutputPrettyImageType>;
using ChannelExtractorType        = otb::MultiChannelExtractROI<unsigned char, unsigned char>;

ChannelExtractorType::Pointer   selecter         = ChannelExtractorType::New();
WriterVectorPrettyType::Pointer vectPrettyWriter = WriterVectorPrettyType::New();

OutputVectorPrettyImageType::PixelType minimum, maximum;
minimum.Fill(0);
maximum.Fill(255);
vectRescaler->SetOutputMinimum(minimum);
vectRescaler->SetOutputMaximum(maximum);
//  vectRescaler->SetClampThreshold(1);

selecter->SetInput(vectRescaler->GetOutput());
selecter->SetChannel(3);
selecter->SetChannel(2);
selecter->SetChannel(1);

vectPrettyWriter->SetFileName(argv[3]);
vectPrettyWriter->SetInput(selecter->GetOutput());

using ThresholderType = itk::ThresholdImageFilter<OutputImageType>;

ThresholderType::Pointer thresholder = ThresholderType::New();
thresholder->SetInput(filter->GetOutput());
thresholder->SetOutsideValue(1.0);
thresholder->ThresholdOutside(-1.0, 0.05);
thresholder->Update();

WriterPrettyType::Pointer prettyWriter = WriterPrettyType::New();
rescaler->SetInput(thresholder->GetOutput());
rescaler->SetOutputMinimum(0);
rescaler->SetOutputMaximum(255);
prettyWriter->SetFileName(argv[4]);
prettyWriter->SetInput(rescaler->GetOutput());

try
{
prettyWriter->Update();
vectPrettyWriter->Update();
}
catch (itk::ExceptionObject& excep)
{
std::cerr << "Exception caught !" << std::endl;
std::cerr << excep << std::endl;
}
catch (...)
{
std::cout << "Unknown exception !" << std::endl;
return EXIT_FAILURE;
}

return EXIT_SUCCESS;

// Let's now run this example using as input the image
// \code{verySmallFSATSW.tif} provided in the
// directory \code{Examples/Data}.
//
//
// \begin{figure} \center
// \includegraphics[width=0.24\textwidth]{pretty_FSATSW.eps}
// \includegraphics[width=0.24\textwidth]{pretty_AVIMultiChannelRAndGAndNIRVegetationIndex.eps}
// \itkcaption[AVI Example]{AVI result on the right with the left image in input.}
// \label{fig:AVIMultiChannelRAndGAndNIRIndexImageFilter}
// \end{figure}
}