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Libs/Optimize/Domain/ImageDomain.h

Namespaces

Name
shapeworks
User usage reporting (telemetry)

Classes

Name
class shapeworks::ImageDomain

Source code

#pragma once

#include <itkImage.h>
#include <itkImageRegionConstIteratorWithIndex.h>
#include <itkImageToVTKImageFilter.h>
#include <itkZeroCrossingImageFilter.h>
#include <vtkContourFilter.h>
#include <vtkMassProperties.h>

#include <chrono>
#include <fstream>

#include "ParticleRegionDomain.h"

// we have to undef foreach here because both Qt and OpenVDB define foreach
#undef foreach
#ifndef Q_MOC_RUN
#include <openvdb/math/Math.h>
#include <openvdb/math/Transform.h>
#include <openvdb/openvdb.h>
#include <openvdb/tools/GridOperators.h>
#include <openvdb/tools/Interpolation.h>
#include <openvdb/tools/SignedFloodFill.h>
#endif

namespace shapeworks {
template <class T>
class ImageDomain : public ParticleRegionDomain {
 public:
  using Pointer = std::shared_ptr<ImageDomain>;

  using ImageType = itk::Image<T, DIMENSION>;

  using PointType = ParticleRegionDomain::PointType;

  void SetImage(ImageType* I, double narrow_band) {
    this->m_FixedDomain = false;
    // this->Modified();

    openvdb::initialize();  // It is safe to initialize multiple times.

    // Set a large background value, so that we quickly catch particles outside or on the edge the narrow band.
    // (Downside: its more difficult to display the correct location of the point of failure.)
    m_VDBImage = openvdb::FloatGrid::create(1e8);
    m_VDBImage->setGridClass(openvdb::GRID_LEVEL_SET);
    auto vdbAccessor = m_VDBImage->getAccessor();

    // Save properties of the Image needed for the optimizer
    m_Size = I->GetRequestedRegion().GetSize();
    m_Spacing = I->GetSpacing();
    m_Origin = I->GetOrigin();
    m_Index = I->GetRequestedRegion().GetIndex();

    // Transformation from index space to world space
    openvdb::math::Mat4f mat;
    mat.setIdentity();
    mat.postScale(openvdb::Vec3f(m_Spacing[0], m_Spacing[1], m_Spacing[2]));
    mat.postTranslate(openvdb::Vec3f(m_Origin[0], m_Origin[1], m_Origin[2]));
    const auto xform = openvdb::math::Transform::createLinearTransform(mat);
    m_VDBImage->setTransform(xform);

    itk::ImageRegionIterator<ImageType> it(I, I->GetRequestedRegion());
    it.GoToBegin();

    while (!it.IsAtEnd()) {
      const auto idx = it.GetIndex();
      const auto pixel = it.Get();
      if (abs(pixel) > narrow_band) {
        ++it;
        continue;
      }
      const auto coord = openvdb::Coord(idx[0], idx[1], idx[2]);
      vdbAccessor.setValue(coord, pixel);
      ++it;
    }

    typename ImageType::PointType l0;
    I->TransformIndexToPhysicalPoint(m_Index, l0);
    for (unsigned int i = 0; i < DIMENSION; i++) m_Index[i] += m_Size[i] - 1;

    typename ImageType::PointType u0;
    I->TransformIndexToPhysicalPoint(m_Index, u0);

    // Cast points to higher precision if needed.  Parent class uses doubles
    // because they are compared directly with points in the particle system,
    // which are always double precision.
    PointType l;
    PointType u;

    for (unsigned int i = 0; i < DIMENSION; i++) {
      l[i] = static_cast<double>(l0[i]);
      u[i] = static_cast<double>(u0[i]);
    }

    this->SetLowerBound(l);
    this->SetUpperBound(u);

    // Precompute and save values that are used in parts of the optimizer
    this->SetupImageForCrossingPointUpdate(I);  // this->UpdateZeroCrossingPoint(I);
    this->UpdateSurfaceArea(I);
  }

  inline double GetSurfaceArea() const override {
    throw std::runtime_error("Surface area is not computed currently.");
    return m_SurfaceArea;
  }

  inline PointType GetOrigin() const { return m_Origin; }

  inline typename ImageType::SizeType GetSize() const { return m_Size; }

  inline typename ImageType::SpacingType GetSpacing() const { return m_Spacing; }

  inline typename ImageType::RegionType::IndexType GetIndex() const { return m_Index; }

  inline PointType GetValidLocationNear(PointType p) const override {
    // todo why is this function ignoring the argument? Also see Optimize::AddSinglePoint
    return m_ZeroCrossingPoint;
  }

  inline T Sample(const PointType& p) const {
    if (this->IsInsideBuffer(p)) {
      const auto coord = this->ToVDBCoord(p);
      return openvdb::tools::BoxSampler::sample(m_VDBImage->tree(), coord);
    } else {
      std::ostringstream message;
      message << "Domain " << m_DomainID << ": " << m_DomainName << " : Distance transform queried for a Point, " << p
              << ", outside the given image domain. Consider increasing the padding in grooming or the narrow band optimization parameter";
      throw std::runtime_error(message.str());
    }
  }

  inline double GetMaxDiameter() const override {
    double bestRadius = 0;
    double maxdim = 0;
    for (unsigned int i = 0; i < ImageType::ImageDimension; i++) {
      if (GetSize()[i] > maxdim) {
        maxdim = GetSize()[i];
        bestRadius = maxdim * GetSpacing()[i];
      }
    }
    return bestRadius;
  }

  void DeleteImages() override { m_VDBImage = 0; }

  // Updates zero crossing points. Raster scans candidate zero crossing points, and finds one that does not violate any
  // constraints.
  void UpdateZeroCrossingPoint() override {
    for (size_t i = 0; i < m_possible_zero_crossings.size(); i++) {
      this->m_ZeroCrossingPoint = m_possible_zero_crossings[i];
      if (!this->GetConstraints()->isAnyViolated(this->m_ZeroCrossingPoint)) {
        // std::cout << "Chosen initial point " << this->m_ZeroCrossingPoint << std::endl;
        break;
      }
    }

    if (this->GetConstraints()->isAnyViolated(this->m_ZeroCrossingPoint)) {
      std::cerr << "A particle initialization violates at least one constraint. Make sure at least one point satisfies "
                   "all constraints"
                << std::endl;
    }
  }

 protected:
  openvdb::FloatGrid::Ptr GetVDBImage() const { return m_VDBImage; }

  ImageDomain() {}
  virtual ~ImageDomain(){};

  void PrintSelf(std::ostream& os, itk::Indent indent) const {
    ParticleRegionDomain::PrintSelf(os, indent);
    os << indent << "VDB Active Voxels = " << m_VDBImage->activeVoxelCount() << std::endl;
  }

  inline openvdb::math::Transform::Ptr transform() const { return this->m_VDBImage->transformPtr(); }

  // Converts a coordinate from an ITK Image point in world space to the corresponding
  // coordinate in OpenVDB Index space. Raises an exception if the narrow band is not
  // sufficiently large to sample the point.
  inline openvdb::Vec3R ToVDBCoord(const PointType& p) const {
    const auto worldCoord = openvdb::Vec3R(p[0], p[1], p[2]);
    const auto idxCoord = this->transform()->worldToIndex(worldCoord);

    // Make sure the coordinate is part of the narrow band
    if (m_VDBImage->tree().isValueOff(
            openvdb::Coord::round(idxCoord))) {  // `isValueOff` requires an integer coordinate
      // If multiple threads crash here at the same time, the error message displayed is just "terminate called
      // recursively", which isn't helpful. So we std::cerr the error to make sure its printed to the console.
      std::cerr << "Sampled point outside the narrow band: " << p << std::endl;

      std::ostringstream message;
      message << "Attempt to sample at a point outside the narrow band: " << p
              << ". Consider increasing the narrow band";
      throw std::runtime_error(message.str());
    }

    return idxCoord;
  }

 private:
  openvdb::FloatGrid::Ptr m_VDBImage;
  typename ImageType::SizeType m_Size;
  typename ImageType::SpacingType m_Spacing;
  PointType m_Origin;
  PointType m_ZeroCrossingPoint;
  typename ImageType::RegionType::IndexType m_Index;  // Index defining the corner of the region
  double m_SurfaceArea;
  std::vector<PointType> m_possible_zero_crossings;

  // Computes possible zero crossing points. Later on, one can find the ones that do not violate constraints.
  void SetupImageForCrossingPointUpdate(ImageType* I) {
    typename itk::ZeroCrossingImageFilter<ImageType, ImageType>::Pointer zc =
        itk::ZeroCrossingImageFilter<ImageType, ImageType>::New();
    zc->SetInput(I);
    zc->Update();
    typename itk::ImageRegionConstIteratorWithIndex<ImageType> zcIt(zc->GetOutput(),
                                                                    zc->GetOutput()->GetRequestedRegion());

    for (zcIt.GoToReverseBegin(); !zcIt.IsAtReverseEnd(); --zcIt) {
      if (zcIt.Get() == 1.0) {
        PointType pos;
        I->TransformIndexToPhysicalPoint(zcIt.GetIndex(), pos);
        this->m_ZeroCrossingPoint = pos;
        m_possible_zero_crossings.push_back(pos);
      }
    }
  }

  void UpdateSurfaceArea(ImageType* I) {
    // TODO: This code has been copied from Optimize.cpp. It does not work
    /*
    typename itk::ImageToVTKImageFilter < ImageType > ::Pointer itk2vtkConnector;
    itk2vtkConnector = itk::ImageToVTKImageFilter < ImageType > ::New();
    itk2vtkConnector->SetInput(I);
    vtkSmartPointer < vtkContourFilter > ls = vtkSmartPointer < vtkContourFilter > ::New();
    ls->SetInputData(itk2vtkConnector->GetOutput());
    ls->SetValue(0, 0.0);
    ls->Update();
    vtkSmartPointer < vtkMassProperties > mp = vtkSmartPointer < vtkMassProperties > ::New();
    mp->SetInputData(ls->GetOutput());
    mp->Update();
    m_SurfaceArea = mp->GetSurfaceArea();
    */
  }
};

}  // end namespace shapeworks

Updated on 2024-07-12 at 20:10:35 +0000