mitkDicomSR_GantryTiltInformation.cpp

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/*===================================================================

The Medical Imaging Interaction Toolkit (MITK)

Copyright (c) German Cancer Research Center,
Division of Medical and Biological Informatics.
All rights reserved.

This software is distributed WITHOUT ANY WARRANTY; without
even the implied warranty of MERCHANTABILITY or FITNESS FOR
A PARTICULAR PURPOSE.

See LICENSE.txt or http://www.mitk.org for details.

===================================================================*/

#include <mitkDicomSeriesReader.h>

namespace mitk
{
  DicomSeriesReader::GantryTiltInformation::GantryTiltInformation()
    : m_ShiftUp(0.0), m_ShiftRight(0.0), m_ShiftNormal(0.0), m_ITKAssumedSliceSpacing(0.0), m_NumberOfSlicesApart(1)
  {
  }

#define doublepoint(x)                                                                                                 \
  Point3Dd x;                                                                                                          \
  x[0] = x##f[0];                                                                                                      \
  x[1] = x##f[1];                                                                                                      \
  x[2] = x##f[2];

#define doublevector(x)                                                                                                \
  Vector3Dd x;                                                                                                         \
  x[0] = x##f[0];                                                                                                      \
  x[1] = x##f[1];                                                                                                      \
  x[2] = x##f[2];

  DicomSeriesReader::GantryTiltInformation::GantryTiltInformation(const Point3D &origin1f,
                                                                  const Point3D &origin2f,
                                                                  const Vector3D &rightf,
                                                                  const Vector3D &upf,
                                                                  unsigned int numberOfSlicesApart)
    : m_ShiftUp(0.0), m_ShiftRight(0.0), m_ShiftNormal(0.0), m_NumberOfSlicesApart(numberOfSlicesApart)
  {
    assert(numberOfSlicesApart);

    doublepoint(origin1);
    doublepoint(origin2);
    doublevector(right);
    doublevector(up);

    // determine if slice 1 (imagePosition1 and imageOrientation1) and slice 2 can be in one orthogonal slice stack:
    // calculate a line from origin 1, directed along the normal of slice (calculated as the cross product of
    // orientation
    // 1)
    // check if this line passes through origin 2

    /*
       Determine if line (imagePosition2 + l * normal) contains imagePosition1.
       Done by calculating the distance of imagePosition1 from line (imagePosition2 + l *normal)

       E.g. http://mathworld.wolfram.com/Point-LineDistance3-Dimensional.html

       squared distance = | (pointAlongNormal - origin2) x (origin2 - origin1) | ^ 2
       /
       |pointAlongNormal - origin2| ^ 2

       ( x meaning the cross product )
    */

    Vector3Dd normal = itk::CrossProduct(right, up);
    Point3Dd pointAlongNormal = origin2 + normal;

    double numerator = itk::CrossProduct(pointAlongNormal - origin2, origin2 - origin1).GetSquaredNorm();
    double denominator = (pointAlongNormal - origin2).GetSquaredNorm();

    double distance = sqrt(numerator / denominator);

    if (distance > 0.001) // mitk::eps is too small; 1/1000 of a mm should be enough to detect tilt
    {
      MITK_DEBUG << "  Series seems to contain a tilted (or sheared) geometry";
      MITK_DEBUG << "  Distance of expected slice origin from actual slice origin: " << distance;
      MITK_DEBUG << "    ==> storing this shift for later analysis:";
      MITK_DEBUG << "    v right: " << right;
      MITK_DEBUG << "    v up: " << up;
      MITK_DEBUG << "    v normal: " << normal;

      Point3Dd projectionRight = projectPointOnLine(origin1, origin2, right);
      Point3Dd projectionNormal = projectPointOnLine(origin1, origin2, normal);

      m_ShiftRight = (projectionRight - origin2).GetNorm();
      m_ShiftNormal = (projectionNormal - origin2).GetNorm();

      /*
         now also check to which side the image is shifted.

         Calculation e.g. from
         http://mathworld.wolfram.com/Point-PlaneDistance.html
      */

      Point3Dd testPoint = origin1;
      Vector3Dd planeNormal = up;

      double signedDistance =
        (planeNormal[0] * testPoint[0] + planeNormal[1] * testPoint[1] + planeNormal[2] * testPoint[2] -
         (planeNormal[0] * origin2[0] + planeNormal[1] * origin2[1] + planeNormal[2] * origin2[2])) /
        sqrt(planeNormal[0] * planeNormal[0] + planeNormal[1] * planeNormal[1] + planeNormal[2] * planeNormal[2]);

      m_ShiftUp = signedDistance;

      m_ITKAssumedSliceSpacing = (origin2 - origin1).GetNorm();
      // How do we now this is assumed? See header documentation for ITK code references
      // double itkAssumedSliceSpacing = sqrt( m_ShiftUp * m_ShiftUp + m_ShiftNormal * m_ShiftNormal );

      MITK_DEBUG << "    shift normal: " << m_ShiftNormal;
      MITK_DEBUG << "    shift normal assumed by ITK: " << m_ITKAssumedSliceSpacing;
      MITK_DEBUG << "    shift up: " << m_ShiftUp;
      MITK_DEBUG << "    shift right: " << m_ShiftRight;

      MITK_DEBUG << "    tilt angle (deg): " << atan(m_ShiftUp / m_ShiftNormal) * 180.0 / 3.1415926535;
    }
  }

  Point3D DicomSeriesReader::GantryTiltInformation::projectPointOnLine(Point3Dd p,
                                                                       Point3Dd lineOrigin,
                                                                       Vector3Dd lineDirection)
  {
    Vector3Dd lineOriginToP = p - lineOrigin;
    double innerProduct = lineOriginToP * lineDirection;

    double factor = innerProduct / lineDirection.GetSquaredNorm();
    Point3Dd projection = lineOrigin + factor * lineDirection;

    return projection;
  }

  double DicomSeriesReader::GantryTiltInformation::GetTiltCorrectedAdditionalSize() const { return fabs(m_ShiftUp); }
  double DicomSeriesReader::GantryTiltInformation::GetTiltAngleInDegrees() const
  {
    return atan(fabs(m_ShiftUp) / m_ShiftNormal) * 180.0 / 3.1415926535;
  }

  double DicomSeriesReader::GantryTiltInformation::GetMatrixCoefficientForCorrectionInWorldCoordinates() const
  {
    // so many mm need to be shifted per slice!
    return m_ShiftUp / static_cast<double>(m_NumberOfSlicesApart);
  }

  double DicomSeriesReader::GantryTiltInformation::GetRealZSpacing() const
  {
    return m_ShiftNormal / static_cast<double>(m_NumberOfSlicesApart);
  }

  bool DicomSeriesReader::GantryTiltInformation::IsSheared() const
  {
    return (fabs(m_ShiftRight) > 0.001 || fabs(m_ShiftUp) > 0.001);
  }

  bool DicomSeriesReader::GantryTiltInformation::IsRegularGantryTilt() const
  {
    return (fabs(m_ShiftRight) < 0.001 && fabs(m_ShiftUp) > 0.001);
  }

} // end namespace mitk