ITK  5.2.0
Insight Toolkit
Examples/SpatialObjects/DTITubeSpatialObject.cxx
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*
* Copyright NumFOCUS
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* 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
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* http://www.apache.org/licenses/LICENSE-2.0.txt
*
* Unless required by applicable law or agreed to in writing, software
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// Software Guide : BeginLatex
//
// \index{itk::DTITubeSpatialObject}
//
// \doxygen{DTITubeSpatialObject} derives from \doxygen{TubeSpatialObject}.
// It represents a fiber tracts from Diffusion Tensor Imaging.
// A DTITubeSpatialObject is described as a list of centerline points which
// have a position, a radius, normals, the fractional anisotropy (FA) value,
// the ADC value, the geodesic anisotropy (GA) value, the eigenvalues and
// vectors as well as the full tensor matrix.
//
// Let's start by including the appropriate header file.
//
// Software Guide : EndLatex
// Software Guide : BeginCodeSnippet
// Software Guide : EndCodeSnippet
int
main(int, char *[])
{
// Software Guide : BeginLatex
//
// DTITubeSpatialObject is templated over the dimension of the space. A
// DTITubeSpatialObject contains a list of DTITubeSpatialObjectPoints.
//
// First we define some type definitions and we create the tube.
//
// Software Guide : EndLatex
unsigned int i;
// Software Guide : BeginCodeSnippet
using DTITubeType = itk::DTITubeSpatialObject<3>;
using DTITubePointType = DTITubeType::DTITubePointType;
DTITubeType::Pointer dtiTube = DTITubeType::New();
// Software Guide : EndCodeSnippet
// Software Guide : BeginLatex
//
// We create a point list and we set:
// \begin{enumerate}
// \item The position of each point in the local coordinate system using the
// \code{SetPositionInObjectSpace()} method.
// \item The radius of the tube at this position using
// \code{SetRadiusInObjectSpace()}. \item The FA value using
// \code{AddField(DTITubePointType::FA)}. \item The ADC value using
// \code{AddField(DTITubePointType::ADC)}. \item The GA value using
// \code{AddField(DTITubePointType::GA)}. \item The full tensor matrix
// supposed to be symmetric definite positive value using
// \code{SetTensorMatrix()}. \item The color of the point is set to red in
// our case. \end{enumerate}
//
// Software Guide : EndLatex
// Software Guide : BeginCodeSnippet
DTITubeType::DTITubePointListType list;
for (i = 0; i < 5; ++i)
{
DTITubePointType p;
PointType pnt;
pnt[0] = i;
pnt[1] = i + 1;
pnt[2] = i + 2;
p.SetPositionInObjectSpace(pnt);
p.SetRadiusInObjectSpace(1);
p.AddField(
i);
DTITubeSpatialObjectPointField::ADC,
2 * i);
p.AddField(
3 * i);
p.AddField("Lambda1", 4 * i);
p.AddField("Lambda2", 5 * i);
p.AddField("Lambda3", 6 * i);
auto * v = new float[6];
for (unsigned int k = 0; k < 6; k++)
{
v[k] = k;
}
p.SetTensorMatrix(v);
delete[] v;
p.SetColor(1, 0, 0, 1);
list.push_back(p);
}
// Software Guide : EndCodeSnippet
// Software Guide : BeginLatex
//
// Next, we create the tube and set its name using \code{SetName()}. We also
// set its identification number with \code{SetId()} and, at the end, we add
// the list of points previously created.
//
// Software Guide : EndLatex
// Software Guide : BeginCodeSnippet
dtiTube->GetProperty().SetName("DTITube");
dtiTube->SetId(1);
dtiTube->SetPoints(list);
dtiTube->Update();
// Software Guide : EndCodeSnippet
// Software Guide : BeginLatex
//
// The \code{GetPoints()} method return a reference to the internal list of
// points of the object.
//
// Software Guide : EndLatex
// Software Guide : BeginCodeSnippet
DTITubeType::DTITubePointListType pointList = dtiTube->GetPoints();
std::cout << "Number of points representing the fiber tract: ";
std::cout << pointList.size() << std::endl;
// Software Guide : EndCodeSnippet
// Software Guide : BeginLatex
//
// Then we can access the points using STL iterators.
// \code{GetPositionInObjectSpace()}
// and \code{GetColor()} functions return respectively the position and the
// color of the point.
//
// Software Guide : EndLatex
// Software Guide : BeginCodeSnippet
DTITubeType::DTITubePointListType::const_iterator it =
dtiTube->GetPoints().begin();
i = 0;
while (it != dtiTube->GetPoints().end())
{
std::cout << std::endl;
std::cout << "Point #" << i << std::endl;
std::cout << "Position: " << (*it).GetPositionInObjectSpace()
<< std::endl;
std::cout << "Radius: " << (*it).GetRadiusInObjectSpace() << std::endl;
std::cout << "FA: "
DTITubeSpatialObjectPointField::FA)
<< std::endl;
std::cout << "ADC: "
DTITubeSpatialObjectPointField::ADC)
<< std::endl;
std::cout << "GA: "
DTITubeSpatialObjectPointField::GA)
<< std::endl;
std::cout << "Lambda1: " << (*it).GetField("Lambda1") << std::endl;
std::cout << "Lambda2: " << (*it).GetField("Lambda2") << std::endl;
std::cout << "Lambda3: " << (*it).GetField("Lambda3") << std::endl;
std::cout << "TensorMatrix: " << (*it).GetTensorMatrix()[0] << " : ";
std::cout << (*it).GetTensorMatrix()[1] << " : ";
std::cout << (*it).GetTensorMatrix()[2] << " : ";
std::cout << (*it).GetTensorMatrix()[3] << " : ";
std::cout << (*it).GetTensorMatrix()[4] << " : ";
std::cout << (*it).GetTensorMatrix()[5] << std::endl;
std::cout << "Color = " << (*it).GetColor() << std::endl;
++it;
++i;
}
// Software Guide : EndCodeSnippet
return EXIT_SUCCESS;
}
itk::DTITubeSpatialObject
Representation of a tube based on the spatial object classes.
Definition: itkDTITubeSpatialObject.h:42
itkDTITubeSpatialObject.h
itk::GTest::TypedefsAndConstructors::Dimension2::PointType
ImageBaseType::PointType PointType
Definition: itkGTestTypedefsAndConstructors.h:51
itk::DTITubeSpatialObjectPointEnums::DTITubeSpatialObjectPointField::FA
itk::DTITubeSpatialObjectPointEnums
Contains all enum classes used by DTITubeSpatialObjectPoint class.
Definition: itkDTITubeSpatialObjectPoint.h:31
itk::DTITubeSpatialObjectPointEnums::DTITubeSpatialObjectPointField::GA
itk::FixedArray::size
SizeType size() const