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();
}
}
bool
RenderingManager
::InitializeViews( const Geometry3D * dataGeometry, RequestType type, bool preserveRoughOrientationInWorldSpace )
{
MITK_DEBUG << "initializing views";
bool boundingBoxInitialized = false;
Geometry3D::ConstPointer geometry = dataGeometry;
if (dataGeometry && preserveRoughOrientationInWorldSpace)
{
// clone the input geometry
Geometry3D::Pointer modifiedGeometry = dynamic_cast<Geometry3D*>( dataGeometry->Clone().GetPointer() );
assert(modifiedGeometry.IsNotNull());
// construct an affine transform from it
AffineGeometryFrame3D::TransformType::Pointer transform = AffineGeometryFrame3D::TransformType::New();
assert( modifiedGeometry->GetIndexToWorldTransform() );
transform->SetMatrix( modifiedGeometry->GetIndexToWorldTransform()->GetMatrix() );
transform->SetOffset( modifiedGeometry->GetIndexToWorldTransform()->GetOffset() );
// get transform matrix
AffineGeometryFrame3D::TransformType::MatrixType::InternalMatrixType& oldMatrix =
const_cast< AffineGeometryFrame3D::TransformType::MatrixType::InternalMatrixType& > ( transform->GetMatrix().GetVnlMatrix() );
AffineGeometryFrame3D::TransformType::MatrixType::InternalMatrixType newMatrix(oldMatrix);
// get offset and bound
Vector3D offset = modifiedGeometry->GetIndexToWorldTransform()->GetOffset();
Geometry3D::BoundsArrayType oldBounds = modifiedGeometry->GetBounds();
Geometry3D::BoundsArrayType newBounds = modifiedGeometry->GetBounds();
// get rid of rotation other than pi/2 degree
for ( unsigned int i = 0; i < 3; ++i )
{
// i-th column of the direction matrix
Vector3D currentVector;
currentVector[0] = oldMatrix(0,i);
currentVector[1] = oldMatrix(1,i);
currentVector[2] = oldMatrix(2,i);
// matchingRow will store the row that holds the biggest
// value in the column
unsigned int matchingRow = 0;
// maximum value in the column
float max = std::numeric_limits<float>::min();
// sign of the maximum value (-1 or 1)
int sign = 1;
// iterate through the column vector
for (unsigned int dim = 0; dim < 3; ++dim)
{
if ( fabs(currentVector[dim]) > max )
{
matchingRow = dim;
max = fabs(currentVector[dim]);
if(currentVector[dim]<0)
sign = -1;
else
sign = 1;
}
}
// in case we found a negative maximum,
// we negate the column and adjust the offset
// (in order to run through the dimension in the opposite direction)
if(sign == -1)
{
currentVector *= sign;
offset += modifiedGeometry->GetAxisVector(i);
}
// matchingRow is now used as column index to place currentVector
// correctly in the new matrix
vnl_vector<ScalarType> newMatrixColumn(3);
newMatrixColumn[0] = currentVector[0];
newMatrixColumn[1] = currentVector[1];
newMatrixColumn[2] = currentVector[2];
newMatrix.set_column( matchingRow, newMatrixColumn );
// if a column is moved, we also have to adjust the bounding
// box accordingly, this is done here
newBounds[2*matchingRow ] = oldBounds[2*i ];
newBounds[2*matchingRow+1] = oldBounds[2*i+1];
}
// set the newly calculated bounds array
modifiedGeometry->SetBounds(newBounds);
// set new offset and direction matrix
AffineGeometryFrame3D::TransformType::MatrixType newMatrixITK( newMatrix );
transform->SetMatrix( newMatrixITK );
transform->SetOffset( offset );
modifiedGeometry->SetIndexToWorldTransform( transform );
geometry = modifiedGeometry;
}
int warningLevel = vtkObject::GetGlobalWarningDisplay();
vtkObject::GlobalWarningDisplayOff();
if ( (geometry.IsNotNull() ) && (const_cast< mitk::BoundingBox * >(
geometry->GetBoundingBox())->GetDiagonalLength2() > mitk::eps) )
{
boundingBoxInitialized = true;
}
if (geometry.IsNotNull() )
{ // make sure bounding box has an extent bigger than zero in any direction
// clone the input geometry
Geometry3D::Pointer modifiedGeometry = dynamic_cast<Geometry3D*>( dataGeometry->Clone().GetPointer() );
assert(modifiedGeometry.IsNotNull());
Geometry3D::BoundsArrayType newBounds = modifiedGeometry->GetBounds();
for( unsigned int dimension = 0; ( 2 * dimension ) < newBounds.Size() ; dimension++ )
{
//check for equality but for an epsilon
if( Equal( newBounds[ 2 * dimension ], newBounds[ 2 * dimension + 1 ] ) )
{
newBounds[ 2 * dimension + 1 ] += 1;
}
}
// set the newly calculated bounds array
modifiedGeometry->SetBounds(newBounds);
geometry = modifiedGeometry;
}
RenderWindowList::iterator it;
for ( it = m_RenderWindowList.begin(); it != m_RenderWindowList.end(); ++it )
{
mitk::BaseRenderer *baseRenderer =
mitk::BaseRenderer::GetInstance( it->first );
baseRenderer->GetDisplayGeometry()->SetConstrainZoomingAndPanning(m_ConstrainedPaddingZooming);
int id = baseRenderer->GetMapperID();
if ( ((type == REQUEST_UPDATE_ALL)
|| ((type == REQUEST_UPDATE_2DWINDOWS) && (id == 1))
|| ((type == REQUEST_UPDATE_3DWINDOWS) && (id == 2)))
)
{
this->InternalViewInitialization( baseRenderer, geometry,
boundingBoxInitialized, id );
}
}
if ( m_TimeNavigationController != NULL )
{
if ( boundingBoxInitialized )
{
m_TimeNavigationController->SetInputWorldGeometry( geometry );
}
m_TimeNavigationController->Update();
}
this->RequestUpdateAll( type );
vtkObject::SetGlobalWarningDisplay( warningLevel );
// Inform listeners that views have been initialized
this->InvokeEvent( mitk::RenderingManagerViewsInitializedEvent() );
return boundingBoxInitialized;
}
mitk::Geometry3D::Pointer mitk::Geometry3DToXML::FromXML( TiXmlElement* geometryElement )
{
if (!geometryElement)
{
MITK_ERROR << "Cannot deserialize Geometry3D from nullptr.";
return nullptr;
}
AffineTransform3D::MatrixType matrix;
AffineTransform3D::OffsetType offset;
bool isImageGeometry(false);
unsigned int frameOfReferenceID(0);
BaseGeometry::BoundsArrayType bounds;
if ( TIXML_SUCCESS != geometryElement->QueryUnsignedAttribute("FrameOfReferenceID", &frameOfReferenceID) )
{
MITK_WARN << "Missing FrameOfReference for Geometry3D.";
}
if ( TIXML_SUCCESS != geometryElement->QueryBoolAttribute("ImageGeometry", &isImageGeometry) )
{
MITK_WARN << "Missing bool ImageGeometry for Geometry3D.";
}
// matrix
if ( TiXmlElement* matrixElem = geometryElement->FirstChildElement("IndexToWorld")->ToElement() )
{
bool matrixComplete = true;
for ( unsigned int r = 0; r < 3; ++r )
{
for ( unsigned int c = 0; c < 3; ++c )
{
std::stringstream element_namer;
element_namer << "m_" << r << "_" << c;
std::string string_value;
if (TIXML_SUCCESS == matrixElem->QueryStringAttribute(element_namer.str().c_str(),
&string_value))
{
try
{
matrix[r][c] = boost::lexical_cast<double>(string_value);
}
catch (boost::bad_lexical_cast& e)
{
MITK_ERROR << "Could not parse '" << string_value << "' as number: " << e.what();
return nullptr;
}
}
else
{
matrixComplete = false;
}
}
}
if ( !matrixComplete )
{
MITK_ERROR << "Could not parse all Geometry3D matrix coefficients!";
return nullptr;
}
} else
{
MITK_ERROR << "Parse error: expected Matrix3x3 child below Geometry3D node";
return nullptr;
}
// offset
if ( TiXmlElement* offsetElem = geometryElement->FirstChildElement("Offset")->ToElement() )
{
bool vectorComplete = true;
std::string offset_string[3];
vectorComplete &= TIXML_SUCCESS == offsetElem->QueryStringAttribute("x", &offset_string[0]);
vectorComplete &= TIXML_SUCCESS == offsetElem->QueryStringAttribute("y", &offset_string[1]);
vectorComplete &= TIXML_SUCCESS == offsetElem->QueryStringAttribute("z", &offset_string[2]);
if ( !vectorComplete )
{
MITK_ERROR << "Could not parse complete Geometry3D offset!";
return nullptr;
}
for ( unsigned int d = 0; d < 3; ++d )
try
{
offset[d] = boost::lexical_cast<double>(offset_string[d]);
}
catch ( boost::bad_lexical_cast& e )
{
MITK_ERROR << "Could not parse '" << offset_string[d] << "' as number: " << e.what();
return nullptr;
}
}
else
{
MITK_ERROR << "Parse error: expected Offset3D child below Geometry3D node";
return nullptr;
}
// bounds
if ( TiXmlElement* boundsElem = geometryElement->FirstChildElement("Bounds")->ToElement() )
{
bool vectorsComplete(true);
std::string bounds_string[6];
if ( TiXmlElement* minElem = boundsElem->FirstChildElement("Min")->ToElement() )
{
vectorsComplete &= TIXML_SUCCESS == minElem->QueryStringAttribute("x", &bounds_string[0]);
vectorsComplete &= TIXML_SUCCESS == minElem->QueryStringAttribute("y", &bounds_string[2]);
vectorsComplete &= TIXML_SUCCESS == minElem->QueryStringAttribute("z", &bounds_string[4]);
} else
{
vectorsComplete = false;
}
if ( TiXmlElement* maxElem = boundsElem->FirstChildElement("Max")->ToElement() )
{
vectorsComplete &= TIXML_SUCCESS == maxElem->QueryStringAttribute("x", &bounds_string[1]);
vectorsComplete &= TIXML_SUCCESS == maxElem->QueryStringAttribute("y", &bounds_string[3]);
vectorsComplete &= TIXML_SUCCESS == maxElem->QueryStringAttribute("z", &bounds_string[5]);
} else
{
vectorsComplete = false;
}
if ( !vectorsComplete )
{
MITK_ERROR << "Could not parse complete Geometry3D bounds!";
return nullptr;
}
for (unsigned int d = 0; d < 6; ++d)
try
{
bounds[d] = boost::lexical_cast<double>(bounds_string[d]);
}
catch (boost::bad_lexical_cast& e)
{
MITK_ERROR << "Could not parse '" << bounds_string[d] << "' as number: " << e.what();
return nullptr;
}
}
// build GeometryData from matrix/offset
AffineTransform3D::Pointer newTransform = AffineTransform3D::New();
newTransform->SetMatrix(matrix);
newTransform->SetOffset(offset);
Geometry3D::Pointer newGeometry = Geometry3D::New();
newGeometry->SetFrameOfReferenceID(frameOfReferenceID);
newGeometry->SetImageGeometry(isImageGeometry);
newGeometry->SetIndexToWorldTransform(newTransform);
newGeometry->SetBounds(bounds);
return newGeometry;
}