Examples/SpatialObjects/DTITubeSpatialObject.cxx

/*=========================================================================
 *
 *  Copyright NumFOCUS
 *
 *  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
 *
 *         https://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 : 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
#include "itkDTITubeSpatialObject.h"
// 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
 
  // Software Guide : BeginCodeSnippet
  using DTITubeType = itk::DTITubeSpatialObject<3>;
  using DTITubePointType = DTITubeType::DTITubePointType;
  using PointType = DTITubeType::PointType;
 
  auto 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 (unsigned int 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(
      itk::DTITubeSpatialObjectPointEnums::DTITubeSpatialObjectPointField::FA,
      i);
    p.AddField(itk::DTITubeSpatialObjectPointEnums::
                 DTITubeSpatialObjectPointField::ADC,
               2 * i);
    p.AddField(
      itk::DTITubeSpatialObjectPointEnums::DTITubeSpatialObjectPointField::GA,
      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
  const 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
  {
    unsigned int i = 0;
    for (auto & currentPoint : dtiTube->GetPoints())
    {
      std::cout << std::endl;
      std::cout << "Point #" << i << std::endl;
      std::cout << "Position: " << currentPoint.GetPositionInObjectSpace()
                << std::endl;
      std::cout << "Radius: " << currentPoint.GetRadiusInObjectSpace()
                << std::endl;
      std::cout << "FA: "
                << currentPoint.GetField(itk::DTITubeSpatialObjectPointEnums::
                                           DTITubeSpatialObjectPointField::FA)
                << std::endl;
      std::cout << "ADC: "
                << currentPoint.GetField(
                     itk::DTITubeSpatialObjectPointEnums::
                       DTITubeSpatialObjectPointField::ADC)
                << std::endl;
      std::cout << "GA: "
                << currentPoint.GetField(itk::DTITubeSpatialObjectPointEnums::
                                           DTITubeSpatialObjectPointField::GA)
                << std::endl;
      std::cout << "Lambda1: " << currentPoint.GetField("Lambda1")
                << std::endl;
      std::cout << "Lambda2: " << currentPoint.GetField("Lambda2")
                << std::endl;
      std::cout << "Lambda3: " << currentPoint.GetField("Lambda3")
                << std::endl;
      std::cout << "TensorMatrix: " << currentPoint.GetTensorMatrix()[0]
                << " : ";
      std::cout << currentPoint.GetTensorMatrix()[1] << " : ";
      std::cout << currentPoint.GetTensorMatrix()[2] << " : ";
      std::cout << currentPoint.GetTensorMatrix()[3] << " : ";
      std::cout << currentPoint.GetTensorMatrix()[4] << " : ";
      std::cout << currentPoint.GetTensorMatrix()[5] << std::endl;
      std::cout << "Color = " << currentPoint.GetColor() << std::endl;
 
      ++i;
    }
  }
  // Software Guide : EndCodeSnippet
 
  return EXIT_SUCCESS;
}