mitk::ProportionalTimeGeometry::Pointer mitk::ProportionalTimeGeometryToXML::FromXML(TiXmlElement *timeGeometryElement)
{
if (!timeGeometryElement)
{
MITK_ERROR << "Cannot deserialize ProportionalTimeGeometry from nullptr.";
return nullptr;
}
int numberOfTimeSteps = 0;
if (TIXML_SUCCESS != timeGeometryElement->QueryIntAttribute("NumberOfTimeSteps", &numberOfTimeSteps))
{
MITK_WARN << "<ProportionalTimeGeometry> found without NumberOfTimeSteps attribute. Counting...";
}
// might be missing!
TimePointType firstTimePoint;
std::string firstTimePoint_s;
TimePointType stepDuration;
std::string stepDuration_s;
try
{
if (TIXML_SUCCESS == timeGeometryElement->QueryStringAttribute("FirstTimePoint", &firstTimePoint_s))
{
firstTimePoint = boost::lexical_cast<double>(firstTimePoint_s);
}
else
{
firstTimePoint = -std::numeric_limits<TimePointType>::max();
}
if (TIXML_SUCCESS == timeGeometryElement->QueryStringAttribute("StepDuration", &stepDuration_s))
{
stepDuration = boost::lexical_cast<double>(stepDuration_s);
}
else
{
stepDuration = std::numeric_limits<TimePointType>::infinity();
}
}
catch (boost::bad_lexical_cast &e)
{
MITK_ERROR << "Could not parse string as number: " << e.what();
return nullptr;
}
// list of all geometries with their time steps
std::multimap<TimeStepType, BaseGeometry::Pointer> allReadGeometries;
int indexForUnlabeledTimeStep(-1);
for (TiXmlElement *currentElement = timeGeometryElement->FirstChildElement(); currentElement != nullptr;
currentElement = currentElement->NextSiblingElement())
{
// different geometries could have been inside a ProportionalTimeGeometry.
// By now, we only support Geometry3D
std::string tagName = currentElement->Value();
if (tagName == "Geometry3D")
{
Geometry3D::Pointer restoredGeometry = Geometry3DToXML::FromXML(currentElement);
if (restoredGeometry.IsNotNull())
{
int timeStep(-1);
if (TIXML_SUCCESS != currentElement->QueryIntAttribute("TimeStep", &timeStep))
{
timeStep = indexForUnlabeledTimeStep--; // decrement index for next one
MITK_WARN << "Found <Geometry3D> without 'TimeStep' attribute in <ProportionalTimeGeometry>. No guarantees "
"on order anymore.";
}
if (allReadGeometries.count(static_cast<TimeStepType>(timeStep)) > 0)
{
MITK_WARN << "Found <Geometry3D> tags with identical 'TimeStep' attribute in <ProportionalTimeGeometry>. No "
"guarantees on order anymore.";
}
allReadGeometries.insert(std::make_pair(static_cast<TimeStepType>(timeStep), restoredGeometry.GetPointer()));
}
}
else
{
MITK_WARN << "Found unsupported tag <" << tagName << "> inside <ProportionalTimeGeometry>. Ignoring.";
}
}
// now add all BaseGeometries that were read to a new instance
// of ProportionalTimeGeometry
ProportionalTimeGeometry::Pointer newTimeGeometry = ProportionalTimeGeometry::New();
newTimeGeometry->SetFirstTimePoint(firstTimePoint);
newTimeGeometry->SetStepDuration(stepDuration);
newTimeGeometry->ReserveSpaceForGeometries(allReadGeometries.size());
TimeStepType t(0);
for (auto entry : allReadGeometries)
{
// We add items with newly assigned time steps.
// This avoids great confusion when a file contains
// bogus numbers.
newTimeGeometry->SetTimeStepGeometry(entry.second, t++);
}
// Need to re-calculate global bounding box.
// This is neither stored in a file, nor done by SetTimeStepGeometry
newTimeGeometry->UpdateBoundingBox();
return newTimeGeometry;
}
mitk::BaseGeometry::Pointer mitk::PointSetReaderService::ReadGeometry(TiXmlElement *parentElement)
{
TiXmlElement *geometryElem = parentElement->FirstChildElement("geometry3d");
if (!geometryElem)
return nullptr;
// data to generate
AffineTransform3D::MatrixType matrix;
AffineTransform3D::OffsetType offset;
bool isImageGeometry(false);
unsigned int frameOfReferenceID(0);
BaseGeometry::BoundsArrayType bounds;
bool somethingMissing(false);
// find data in xml structure
TiXmlElement *imageGeometryElem = geometryElem->FirstChildElement("image_geometry");
if (imageGeometryElem)
{
std::string igs = imageGeometryElem->GetText();
isImageGeometry = igs == "true" || igs == "TRUE" || igs == "1";
}
else
somethingMissing = true;
TiXmlElement *frameOfReferenceElem = geometryElem->FirstChildElement("frame_of_reference_id");
if (frameOfReferenceElem)
{
frameOfReferenceID = atoi(frameOfReferenceElem->GetText());
}
else
somethingMissing = true;
TiXmlElement *indexToWorldElem = geometryElem->FirstChildElement("index_to_world");
if (indexToWorldElem)
{
TiXmlElement *matrixElem = indexToWorldElem->FirstChildElement("matrix3x3");
TiXmlElement *offsetElem = indexToWorldElem->FirstChildElement("offset");
if (indexToWorldElem && offsetElem)
{
TiXmlElement *col0 = matrixElem->FirstChildElement("column_0");
TiXmlElement *col1 = matrixElem->FirstChildElement("column_1");
TiXmlElement *col2 = matrixElem->FirstChildElement("column_2");
if (col0 && col1 && col2)
{
somethingMissing |= TIXML_SUCCESS != col0->QueryDoubleAttribute("x", &matrix[0][0]);
somethingMissing |= TIXML_SUCCESS != col0->QueryDoubleAttribute("y", &matrix[1][0]);
somethingMissing |= TIXML_SUCCESS != col0->QueryDoubleAttribute("z", &matrix[2][0]);
somethingMissing |= TIXML_SUCCESS != col1->QueryDoubleAttribute("x", &matrix[0][1]);
somethingMissing |= TIXML_SUCCESS != col1->QueryDoubleAttribute("y", &matrix[1][1]);
somethingMissing |= TIXML_SUCCESS != col1->QueryDoubleAttribute("z", &matrix[2][1]);
somethingMissing |= TIXML_SUCCESS != col2->QueryDoubleAttribute("x", &matrix[0][2]);
somethingMissing |= TIXML_SUCCESS != col2->QueryDoubleAttribute("y", &matrix[1][2]);
somethingMissing |= TIXML_SUCCESS != col2->QueryDoubleAttribute("z", &matrix[2][2]);
}
else
somethingMissing = true;
somethingMissing |= TIXML_SUCCESS != offsetElem->QueryDoubleAttribute("x", &offset[0]);
somethingMissing |= TIXML_SUCCESS != offsetElem->QueryDoubleAttribute("y", &offset[1]);
somethingMissing |= TIXML_SUCCESS != offsetElem->QueryDoubleAttribute("z", &offset[2]);
}
else
somethingMissing = true;
TiXmlElement *boundsElem = geometryElem->FirstChildElement("bounds");
if (boundsElem)
{
TiXmlElement *minBoundsElem = boundsElem->FirstChildElement("min");
TiXmlElement *maxBoundsElem = boundsElem->FirstChildElement("max");
if (minBoundsElem && maxBoundsElem)
{
somethingMissing |= TIXML_SUCCESS != minBoundsElem->QueryDoubleAttribute("x", &bounds[0]);
somethingMissing |= TIXML_SUCCESS != minBoundsElem->QueryDoubleAttribute("y", &bounds[2]);
somethingMissing |= TIXML_SUCCESS != minBoundsElem->QueryDoubleAttribute("z", &bounds[4]);
somethingMissing |= TIXML_SUCCESS != maxBoundsElem->QueryDoubleAttribute("x", &bounds[1]);
somethingMissing |= TIXML_SUCCESS != maxBoundsElem->QueryDoubleAttribute("y", &bounds[3]);
somethingMissing |= TIXML_SUCCESS != maxBoundsElem->QueryDoubleAttribute("z", &bounds[5]);
}
else
somethingMissing = true;
}
else
somethingMissing = true;
}
else
somethingMissing = true;
if (somethingMissing)
{
MITK_ERROR << "XML structure of geometry inside a PointSet file broken. Refusing to build Geometry3D";
return nullptr;
}
else
{
Geometry3D::Pointer g = Geometry3D::New();
g->SetImageGeometry(isImageGeometry);
g->SetFrameOfReferenceID(frameOfReferenceID);
g->SetBounds(bounds);
AffineTransform3D::Pointer transform = AffineTransform3D::New();
transform->SetMatrix(matrix);
transform->SetOffset(offset);
g->SetIndexToWorldTransform(transform);
return g.GetPointer();
}
}