mitkPlanarFigureReader.cpp

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

The Medical Imaging Interaction Toolkit (MITK)

Copyright (c) German Cancer Research Center (DKFZ)
All rights reserved.

Use of this source code is governed by a 3-clause BSD license that can be
found in the LICENSE file.

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

#include "mitkPlanarFigureReader.h"

#include "mitkPlanarAngle.h"
#include "mitkPlanarArrow.h"
#include "mitkPlanarBezierCurve.h"
#include "mitkPlanarCircle.h"
#include "mitkPlanarCross.h"
#include "mitkPlanarDoubleEllipse.h"
#include "mitkPlanarEllipse.h"
#include "mitkPlanarFourPointAngle.h"
#include "mitkPlanarLine.h"
#include "mitkPlanarPolygon.h"
#include "mitkPlanarRectangle.h"
#include "mitkPlanarSubdivisionPolygon.h"
#include "mitkPlaneGeometry.h"

#include "mitkBasePropertySerializer.h"
#include <mitkLocaleSwitch.h>

#include <itksys/SystemTools.hxx>
#include <tinyxml.h>

mitk::PlanarFigureReader::PlanarFigureReader()
  : PlanarFigureSource(), FileReader(), m_FileName(""), m_FilePrefix(""), m_FilePattern(""), m_Success(false)
{
  this->SetNumberOfRequiredOutputs(1);
  this->SetNumberOfIndexedOutputs(1);
  this->SetNthOutput(0, this->MakeOutput(0));

  m_CanReadFromMemory = true;

  // this->Modified();
  // this->GetOutput()->Modified();
  // this->GetOutput()->ReleaseData();
}

mitk::PlanarFigureReader::~PlanarFigureReader()
{
}

void mitk::PlanarFigureReader::GenerateData()
{
  mitk::LocaleSwitch localeSwitch("C");
  m_Success = false;
  this->SetNumberOfIndexedOutputs(0); // reset all outputs, we add new ones depending on the file content

  TiXmlDocument document;

  if (m_ReadFromMemory)
  {
    if (m_MemoryBuffer == nullptr || m_MemorySize == 0)
    {
      // check
      itkWarningMacro(<< "Sorry, memory buffer has not been set!");
      return;
    }
    if (m_MemoryBuffer[m_MemorySize - 1] == '\0')
    {
      document.Parse(m_MemoryBuffer);
    }
    else
    {
      auto tmpArray = new char[(int)m_MemorySize + 1];
      tmpArray[m_MemorySize] = '\0';
      memcpy(tmpArray, m_MemoryBuffer, m_MemorySize);

      document.Parse(m_MemoryBuffer);

      delete[] tmpArray;
    }
  }
  else
  {
    if (m_FileName.empty())
    {
      itkWarningMacro(<< "Sorry, filename has not been set!");
      return;
    }
    if (this->CanReadFile(m_FileName.c_str()) == false)
    {
      itkWarningMacro(<< "Sorry, can't read file " << m_FileName << "!");
      return;
    }
    if (!document.LoadFile(m_FileName))
    {
      MITK_ERROR << "Could not open/read/parse " << m_FileName << ". TinyXML reports: '" << document.ErrorDesc()
                 << "'. "
                 << "The error occurred in row " << document.ErrorRow() << ", column " << document.ErrorCol() << ".";
      return;
    }
  }

  int fileVersion = 1;
  TiXmlElement *versionObject = document.FirstChildElement("Version");
  if (versionObject != nullptr)
  {
    if (versionObject->QueryIntAttribute("FileVersion", &fileVersion) != TIXML_SUCCESS)
    {
      MITK_WARN << m_FileName << " does not contain version information! Trying version 1 format." << std::endl;
    }
  }
  else
  {
    MITK_WARN << m_FileName << " does not contain version information! Trying version 1 format." << std::endl;
  }
  if (fileVersion !=
      1) // add file version selection and version specific file parsing here, if newer file versions are created
  {
    MITK_WARN << "File version > 1 is not supported by this reader.";
    return;
  }

  /* file version 1 reader code */
  for (TiXmlElement *pfElement = document.FirstChildElement("PlanarFigure"); pfElement != nullptr;
       pfElement = pfElement->NextSiblingElement("PlanarFigure"))
  {
    std::string type = pfElement->Attribute("type");

    mitk::PlanarFigure::Pointer planarFigure = nullptr;
    if (type == "PlanarAngle")
    {
      planarFigure = mitk::PlanarAngle::New();
    }
    else if (type == "PlanarCircle")
    {
      planarFigure = mitk::PlanarCircle::New();
    }
    else if (type == "PlanarEllipse")
    {
      planarFigure = mitk::PlanarEllipse::New();
    }
    else if (type == "PlanarCross")
    {
      planarFigure = mitk::PlanarCross::New();
    }
    else if (type == "PlanarFourPointAngle")
    {
      planarFigure = mitk::PlanarFourPointAngle::New();
    }
    else if (type == "PlanarLine")
    {
      planarFigure = mitk::PlanarLine::New();
    }
    else if (type == "PlanarPolygon")
    {
      planarFigure = mitk::PlanarPolygon::New();
    }
    else if (type == "PlanarSubdivisionPolygon")
    {
      planarFigure = mitk::PlanarSubdivisionPolygon::New();
    }
    else if (type == "PlanarRectangle")
    {
      planarFigure = mitk::PlanarRectangle::New();
    }
    else if (type == "PlanarArrow")
    {
      planarFigure = mitk::PlanarArrow::New();
    }
    else if (type == "PlanarDoubleEllipse")
    {
      planarFigure = mitk::PlanarDoubleEllipse::New();
    }
    else if (type == "PlanarBezierCurve")
    {
      planarFigure = mitk::PlanarBezierCurve::New();
    }
    else
    {
      // unknown type
      MITK_WARN << "encountered unknown planar figure type '" << type << "'. Skipping this element.";
      continue;
    }

    // Read properties of the planar figure
    for (TiXmlElement *propertyElement = pfElement->FirstChildElement("property"); propertyElement != nullptr;
         propertyElement = propertyElement->NextSiblingElement("property"))
    {
      const char *keya = propertyElement->Attribute("key");
      const std::string key(keya ? keya : "");

      const char *typea = propertyElement->Attribute("type");
      const std::string type(typea ? typea : "");

      // hand propertyElement to specific reader
      std::stringstream propertyDeserializerClassName;
      propertyDeserializerClassName << type << "Serializer";

      const std::list<itk::LightObject::Pointer> readers =
        itk::ObjectFactoryBase::CreateAllInstance(propertyDeserializerClassName.str().c_str());
      if (readers.size() < 1)
      {
        MITK_ERROR << "No property reader found for " << type;
      }
      if (readers.size() > 1)
      {
        MITK_WARN << "Multiple property readers found for " << type << ". Using arbitrary first one.";
      }

      for (auto iter = readers.cbegin(); iter != readers.cend(); ++iter)
      {
        if (auto *reader = dynamic_cast<BasePropertySerializer *>(iter->GetPointer()))
        {
          const BaseProperty::Pointer property = reader->Deserialize(propertyElement->FirstChildElement());
          if (property.IsNotNull())
          {
            planarFigure->GetPropertyList()->ReplaceProperty(key, property);
          }
          else
          {
            MITK_ERROR << "There were errors while loading property '" << key << "' of type " << type
                       << ". Your data may be corrupted";
          }
          break;
        }
      }
    }

    // If we load a planarFigure, it has definitely been placed correctly.
    // If we do not set this property here, we cannot load old planarFigures
    // without messing up the interaction (PF-Interactor needs this property.
    planarFigure->GetPropertyList()->SetBoolProperty("initiallyplaced", true);

    // Which features (length or circumference etc) a figure has is decided by whether it is closed or not
    // the function SetClosed has to be called in case of PlanarPolygons to ensure they hold the correct feature
    auto *planarPolygon = dynamic_cast<PlanarPolygon *>(planarFigure.GetPointer());
    if (planarPolygon != nullptr)
    {
      bool isClosed = false;
      planarFigure->GetPropertyList()->GetBoolProperty("closed", isClosed);
      planarPolygon->SetClosed(isClosed);
    }

    // Read geometry of containing plane
    TiXmlElement *geoElement = pfElement->FirstChildElement("Geometry");
    if (geoElement != nullptr)
    {
      try
      {
        // Create plane geometry
        mitk::PlaneGeometry::Pointer planeGeo = mitk::PlaneGeometry::New();

        // Extract and set plane transform parameters
        const DoubleList transformList =
          this->GetDoubleAttributeListFromXMLNode(geoElement->FirstChildElement("transformParam"), "param", 12);

        typedef mitk::BaseGeometry::TransformType TransformType;
        TransformType::ParametersType parameters;
        parameters.SetSize(12);

        unsigned int i;
        DoubleList::const_iterator it;
        for (it = transformList.cbegin(), i = 0; it != transformList.cend(); ++it, ++i)
        {
          parameters.SetElement(i, *it);
        }

        typedef mitk::BaseGeometry::TransformType TransformType;
        TransformType::Pointer affineGeometry = TransformType::New();
        affineGeometry->SetParameters(parameters);
        planeGeo->SetIndexToWorldTransform(affineGeometry);

        // Extract and set plane bounds
        const DoubleList boundsList =
          this->GetDoubleAttributeListFromXMLNode(geoElement->FirstChildElement("boundsParam"), "bound", 6);

        typedef mitk::BaseGeometry::BoundsArrayType BoundsArrayType;

        BoundsArrayType bounds;
        for (it = boundsList.cbegin(), i = 0; it != boundsList.cend(); ++it, ++i)
        {
          bounds[i] = *it;
        }

        planeGeo->SetBounds(bounds);

        // Extract and set spacing and origin
        const Vector3D spacing = this->GetVectorFromXMLNode(geoElement->FirstChildElement("Spacing"));
        planeGeo->SetSpacing(spacing);

        const Point3D origin = this->GetPointFromXMLNode(geoElement->FirstChildElement("Origin"));
        planeGeo->SetOrigin(origin);
        planarFigure->SetPlaneGeometry(planeGeo);
      }
      catch (...)
      {
      }
    }
    TiXmlElement *cpElement = pfElement->FirstChildElement("ControlPoints");
    bool first = true;
    if (cpElement != nullptr)
      for (TiXmlElement *vertElement = cpElement->FirstChildElement("Vertex"); vertElement != nullptr;
           vertElement = vertElement->NextSiblingElement("Vertex"))
      {
        int id = 0;
        mitk::Point2D::ValueType x = 0.0;
        mitk::Point2D::ValueType y = 0.0;
        if (vertElement->QueryIntAttribute("id", &id) == TIXML_WRONG_TYPE)
          return; // TODO: can we do a better error handling?
        if (vertElement->QueryDoubleAttribute("x", &x) == TIXML_WRONG_TYPE)
          return; // TODO: can we do a better error handling?
        if (vertElement->QueryDoubleAttribute("y", &y) == TIXML_WRONG_TYPE)
          return; // TODO: can we do a better error handling?
        Point2D p;
        p.SetElement(0, x);
        p.SetElement(1, y);
        if (first == true) // needed to set m_FigurePlaced to true
        {
          planarFigure->PlaceFigure(p);
          first = false;
        }
        planarFigure->SetControlPoint(id, p, true);
      }

    // Calculate feature quantities of this PlanarFigure
    planarFigure->EvaluateFeatures();

    // Make sure that no control point is currently selected
    planarFigure->DeselectControlPoint();

    // \TODO: what about m_FigurePlaced and m_SelectedControlPoint ??
    this->SetNthOutput(this->GetNumberOfOutputs(), planarFigure); // add planarFigure as new output of this filter
  }

  m_Success = true;
}

mitk::Point3D mitk::PlanarFigureReader::GetPointFromXMLNode(TiXmlElement *e)
{
  if (e == nullptr)
    throw std::invalid_argument("node invalid"); // TODO: can we do a better error handling?
  mitk::Point3D point;
  mitk::ScalarType p(-1.0);
  if (e->QueryDoubleAttribute("x", &p) == TIXML_WRONG_TYPE)
    throw std::invalid_argument("node malformatted"); // TODO: can we do a better error handling?
  point.SetElement(0, p);
  if (e->QueryDoubleAttribute("y", &p) == TIXML_WRONG_TYPE)
    throw std::invalid_argument("node malformatted"); // TODO: can we do a better error handling?
  point.SetElement(1, p);
  if (e->QueryDoubleAttribute("z", &p) == TIXML_WRONG_TYPE)
    throw std::invalid_argument("node malformatted"); // TODO: can we do a better error handling?
  point.SetElement(2, p);
  return point;
}

mitk::Vector3D mitk::PlanarFigureReader::GetVectorFromXMLNode(TiXmlElement *e)
{
  if (e == nullptr)
    throw std::invalid_argument("node invalid"); // TODO: can we do a better error handling?
  mitk::Vector3D vector;
  mitk::ScalarType p(-1.0);
  if (e->QueryDoubleAttribute("x", &p) == TIXML_WRONG_TYPE)
    throw std::invalid_argument("node malformatted"); // TODO: can we do a better error handling?
  vector.SetElement(0, p);
  if (e->QueryDoubleAttribute("y", &p) == TIXML_WRONG_TYPE)
    throw std::invalid_argument("node malformatted"); // TODO: can we do a better error handling?
  vector.SetElement(1, p);
  if (e->QueryDoubleAttribute("z", &p) == TIXML_WRONG_TYPE)
    throw std::invalid_argument("node malformatted"); // TODO: can we do a better error handling?
  vector.SetElement(2, p);
  return vector;
}

mitk::PlanarFigureReader::DoubleList mitk::PlanarFigureReader::GetDoubleAttributeListFromXMLNode(
  TiXmlElement *e, const char *attributeNameBase, unsigned int count)
{
  DoubleList list;

  if (e == nullptr)
    throw std::invalid_argument("node invalid"); // TODO: can we do a better error handling?

  for (unsigned int i = 0; i < count; ++i)
  {
    mitk::ScalarType p(-1.0);
    std::stringstream attributeName;
    attributeName << attributeNameBase << i;

    if (e->QueryDoubleAttribute(attributeName.str().c_str(), &p) == TIXML_WRONG_TYPE)
      throw std::invalid_argument("node malformatted"); // TODO: can we do a better error handling?
    list.push_back(p);
  }

  return list;
}

void mitk::PlanarFigureReader::GenerateOutputInformation()
{
}

int mitk::PlanarFigureReader::CanReadFile(const char *name)
{
  if (std::string(name).empty())
    return false;

  return (itksys::SystemTools::LowerCase(itksys::SystemTools::GetFilenameLastExtension(name)) ==
          ".pf"); // assume, we can read all .pf files

  // TiXmlDocument document(name);
  // if (document.LoadFile() == false)
  //  return false;
  // return (document.FirstChildElement("PlanarFigure") != nullptr);
}

bool mitk::PlanarFigureReader::CanReadFile(const std::string filename, const std::string, const std::string)
{
  if (filename.empty())
    return false;

  return (itksys::SystemTools::LowerCase(itksys::SystemTools::GetFilenameLastExtension(filename)) ==
          ".pf"); // assume, we can read all .pf files

  // TiXmlDocument document(filename);
  // if (document.LoadFile() == false)
  //  return false;
  // return (document.FirstChildElement("PlanarFigure") != nullptr);
}

void mitk::PlanarFigureReader::ResizeOutputs(const unsigned int &num)
{
  unsigned int prevNum = this->GetNumberOfOutputs();
  this->SetNumberOfIndexedOutputs(num);
  for (unsigned int i = prevNum; i < num; ++i)
  {
    this->SetNthOutput(i, this->MakeOutput(i).GetPointer());
  }
}