bool BrainAnnotationTreeItem::addData(const Surface& tSurface, const Annotation& tAnnotation)
{
//Create color from annotation data if annotation is not empty
if(!tAnnotation.isEmpty()) {
QByteArray arrayColorsAnnot;
arrayColorsAnnot.resize(tAnnotation.getVertices().rows() * 3 * (int)sizeof(float));
float *rawArrayColors = reinterpret_cast<float *>(arrayColorsAnnot.data());
QList<FSLIB::Label> qListLabels;
QList<RowVector4i> qListLabelRGBAs;
tAnnotation.toLabels(tSurface, qListLabels, qListLabelRGBAs);
for(int i = 0; i<qListLabels.size(); i++) {
FSLIB::Label label = qListLabels.at(i);
for(int j = 0; j<label.vertices.rows(); j++) {
rawArrayColors[label.vertices(j)*3+0] = qListLabelRGBAs.at(i)(0)/255.0;
rawArrayColors[label.vertices(j)*3+1] = qListLabelRGBAs.at(i)(1)/255.0;
rawArrayColors[label.vertices(j)*3+2] = qListLabelRGBAs.at(i)(2)/255.0;
}
}
//Add data which is held by this BrainAnnotationTreeItem
QVariant data;
data.setValue(arrayColorsAnnot);
this->setData(data, BrainAnnotationTreeItemRoles::AnnotColors);
data.setValue(qListLabels);
this->setData(data, BrainAnnotationTreeItemRoles::LabeList);
data.setValue(tAnnotation.getLabelIds());
this->setData(data, BrainAnnotationTreeItemRoles::LabeIds);
//Add annotation meta information as item children
BrainTreeMetaItem *itemAnnotFileName = new BrainTreeMetaItem(BrainTreeMetaItemTypes::AnnotFileName, tAnnotation.fileName());
itemAnnotFileName->setEditable(false);
*this<<itemAnnotFileName;
data.setValue(tAnnotation.fileName());
itemAnnotFileName->setData(data, BrainAnnotationTreeItemRoles::AnnotFileName);
BrainTreeMetaItem *itemAnnotPath = new BrainTreeMetaItem(BrainTreeMetaItemTypes::AnnotFilePath, tAnnotation.filePath());
itemAnnotPath->setEditable(false);
*this<<itemAnnotPath;
data.setValue(tAnnotation.filePath());
itemAnnotFileName->setData(data, BrainAnnotationTreeItemRoles::AnnotFilePath);
}
return true;
}
BrainObject::BrainObject(const Surface &tSurface, const Annotation &tAnnotation, Qt3DCore::QEntity *parent)
: Renderable3DEntity(tSurface.rr(), tSurface.nn(), tSurface.tris(), -tSurface.offset(), parent)
, m_sFilePath(tSurface.filePath())
, m_sSurfFileName(tSurface.fileName())
, m_iHemi(tSurface.hemi())
, m_sSurf(tSurface.surf())
, m_vecCurv(tSurface.curv())
, m_vecOffset(tSurface.offset())
, m_ColorGyri(QColor(125,125,125))
, m_ColorSulci(QColor(50,50,50))
, m_matVert(tSurface.rr())
, m_matTris(tSurface.tris())
, m_matNorm(tSurface.nn())
, m_sAnnotFilePath(tAnnotation.fileName())
{
//Create color from curvature information
m_matColorsOrig.resize(m_matVert.rows(), m_matVert.cols());
for(int i = 0; i<m_matVert.rows() ; i++) {
if(m_vecCurv[i] >= 0) {
m_matColorsOrig(i, 0) = m_ColorSulci.redF();
m_matColorsOrig(i, 1) = m_ColorSulci.greenF();
m_matColorsOrig(i, 2) = m_ColorSulci.blueF();
} else {
m_matColorsOrig(i, 0) = m_ColorGyri.redF();
m_matColorsOrig(i, 1) = m_ColorGyri.greenF();
m_matColorsOrig(i, 2) = m_ColorGyri.blueF();
}
}
//Create color from annotation data if annotation is not empty
if(tAnnotation.getVertices().rows() != 0) {
tAnnotation.toLabels(tSurface, m_qListLabels, m_qListLabelRGBAs);
m_matColorsAnnot.resize(m_matVert.rows(), m_matVert.cols());
for(int i = 0; i<m_qListLabels.size(); i++) {
FSLIB::Label label = m_qListLabels.at(i);
for(int j = 0; j<label.vertices.rows(); j++) {
m_matColorsAnnot(label.vertices(j), 0) = m_qListLabelRGBAs.at(i)(0)/255.0;
m_matColorsAnnot(label.vertices(j), 1) = m_qListLabelRGBAs.at(i)(1)/255.0;
m_matColorsAnnot(label.vertices(j), 2) = m_qListLabelRGBAs.at(i)(2)/255.0;
}
}
}
}
QPair<QByteArray, QByteArray> RtSourceLocDataWorker::performVisualizationTypeCalculation(const VectorXd& sourceColorSamples)
{
QPair<QByteArray, QByteArray> colorPair;
colorPair.first = m_arraySurfaceVertColorLeftHemi;
colorPair.second = m_arraySurfaceVertColorRightHemi;
//NOTE: This function is called for every new sample point and therefore must be kept highly efficient!
if(sourceColorSamples.rows() != m_vecVertNoLeftHemi.rows() + m_vecVertNoRightHemi.rows()) {
qDebug() << "RtSourceLocDataWorker::performVisualizationTypeCalculation - number of rows in sample (" << sourceColorSamples.rows() << ") do not not match with idx/no number of rows in vertex (" << m_vecVertNoLeftHemi.rows() + m_vecVertNoRightHemi.rows() << "). Returning...";
return colorPair;
}
//Cut out left and right hemisphere from source data
VectorXd sourceColorSamplesLeftHemi = sourceColorSamples.segment(0,m_vecVertNoLeftHemi.rows());
VectorXd sourceColorSamplesRightHemi = sourceColorSamples.segment(m_vecVertNoLeftHemi.rows()+1,m_vecVertNoRightHemi.rows());
//Generate color data for vertices
switch(m_iVisualizationType) {
case Data3DTreeModelItemRoles::VertexBased: {
if(!m_bSurfaceDataIsInit) {
qDebug() << "RtSourceLocDataWorker::performVisualizationTypeCalculation - Surface data was not initialized. Returning ...";
return colorPair;
}
//Left hemisphere
QByteArray arrayCurrentVertColorLeftHemi = m_arraySurfaceVertColorLeftHemi;
float *rawArrayCurrentVertColorLeftHemi = reinterpret_cast<float *>(arrayCurrentVertColorLeftHemi.data());
//Create final QByteArray with colors based on the current anatomical information
for(int i = 0; i < m_vecVertNoLeftHemi.rows(); ++i) {
VectorXd vecActivationLeftHemi(1);
vecActivationLeftHemi(0) = sourceColorSamplesLeftHemi(i);
if(vecActivationLeftHemi(0) >= m_vecThresholds.x()) {
QByteArray sourceColorSamplesColorLeftHemi = transformDataToColor(vecActivationLeftHemi);
const float *rawSourceColorSamplesColorLeftHemi = reinterpret_cast<const float *>(sourceColorSamplesColorLeftHemi.data());
rawArrayCurrentVertColorLeftHemi[m_vecVertNoLeftHemi(i)*3+0] = rawSourceColorSamplesColorLeftHemi[0];
rawArrayCurrentVertColorLeftHemi[m_vecVertNoLeftHemi(i)*3+1] = rawSourceColorSamplesColorLeftHemi[1];
rawArrayCurrentVertColorLeftHemi[m_vecVertNoLeftHemi(i)*3+2] = rawSourceColorSamplesColorLeftHemi[2];
}
}
colorPair.first = arrayCurrentVertColorLeftHemi;
//Right hemisphere
QByteArray arrayCurrentVertColorRightHemi = m_arraySurfaceVertColorRightHemi;
float *rawArrayCurrentVertColorRightHemi = reinterpret_cast<float *>(arrayCurrentVertColorRightHemi.data());
//Create final QByteArray with colors based on the current anatomical information
for(int i = 0; i < m_vecVertNoRightHemi.rows(); ++i) {
VectorXd vecActivationRightHemi(1);
vecActivationRightHemi(0) = sourceColorSamplesRightHemi(i);
if(vecActivationRightHemi(0) >= m_vecThresholds.x()) {
QByteArray sourceColorSamplesColorRightHemi = transformDataToColor(vecActivationRightHemi);
const float *rawSourceColorSamplesColorRightHemi = reinterpret_cast<const float *>(sourceColorSamplesColorRightHemi.data());
rawArrayCurrentVertColorRightHemi[m_vecVertNoRightHemi(i)*3+0] = rawSourceColorSamplesColorRightHemi[0];
rawArrayCurrentVertColorRightHemi[m_vecVertNoRightHemi(i)*3+1] = rawSourceColorSamplesColorRightHemi[1];
rawArrayCurrentVertColorRightHemi[m_vecVertNoRightHemi(i)*3+2] = rawSourceColorSamplesColorRightHemi[2];
}
}
colorPair.second = arrayCurrentVertColorRightHemi;
return colorPair;
}
case Data3DTreeModelItemRoles::AnnotationBased: {
if(!m_bAnnotationDataIsInit) {
qDebug() << "RtSourceLocDataWorker::performVisualizationTypeCalculation - Annotation data was not initialized. Returning ...";
return colorPair;
}
//Find maximum actiavtion for each label
QMap<qint32, double> vecLabelActivationLeftHemi;
for(int i = 0; i < m_vecVertNoLeftHemi.rows(); ++i) {
//Find out label for source
qint32 labelIdxLeftHemi = m_mapLabelIdSourcesLeftHemi[m_vecVertNoLeftHemi(i)];
if(abs(sourceColorSamplesLeftHemi(i)) > abs(vecLabelActivationLeftHemi[labelIdxLeftHemi]))
vecLabelActivationLeftHemi.insert(labelIdxLeftHemi, sourceColorSamplesLeftHemi(i));
}
QMap<qint32, double> vecLabelActivationRightHemi;
for(int i = 0; i < m_vecVertNoRightHemi.rows(); ++i) {
//Find out label for source
qint32 labelIdxRightHemi = m_mapLabelIdSourcesRightHemi[m_vecVertNoRightHemi(i)];
if(abs(sourceColorSamplesRightHemi(i)) > abs(vecLabelActivationRightHemi[labelIdxRightHemi]))
vecLabelActivationRightHemi.insert(labelIdxRightHemi, sourceColorSamplesRightHemi(i));
}
//Color all labels respectivley to their activation
//Left hemisphere
QByteArray arrayCurrentVertColorLeftHemi;
//arrayCurrentVertColor.resize(m_arraySurfaceVertColor.size());
arrayCurrentVertColorLeftHemi = m_arraySurfaceVertColorLeftHemi;
float *rawArrayCurrentVertColorLeftHemi = reinterpret_cast<float *>(arrayCurrentVertColorLeftHemi.data());
for(int i = 0; i<m_lLabelsLeftHemi.size(); i++) {
FSLIB::Label labelLeftHemi = m_lLabelsLeftHemi.at(i);
//Transform label activations to rgb colors
VectorXd vecActivationLeftHemi(1);
vecActivationLeftHemi(0) = vecLabelActivationLeftHemi[labelLeftHemi.label_id];
//Check if value is bigger than lower threshold. If not, don't plot activation
if(vecActivationLeftHemi(0) >= m_vecThresholds.x()) {
QByteArray arrayLabelColorsLeftHemi = transformDataToColor(vecActivationLeftHemi);
float *rawArrayLabelColorsLeftHemi = reinterpret_cast<float *>(arrayLabelColorsLeftHemi.data());
for(int j = 0; j<labelLeftHemi.vertices.rows(); j++) {
rawArrayCurrentVertColorLeftHemi[labelLeftHemi.vertices(j)*3+0] = rawArrayLabelColorsLeftHemi[0];
rawArrayCurrentVertColorLeftHemi[labelLeftHemi.vertices(j)*3+1] = rawArrayLabelColorsLeftHemi[1];
rawArrayCurrentVertColorLeftHemi[labelLeftHemi.vertices(j)*3+2] = rawArrayLabelColorsLeftHemi[2];
}
}
}
colorPair.first = arrayCurrentVertColorLeftHemi;
//Right hemisphere
QByteArray arrayCurrentVertColorRightHemi;
//arrayCurrentVertColor.resize(m_arraySurfaceVertColor.size());
arrayCurrentVertColorRightHemi = m_arraySurfaceVertColorRightHemi;
float *rawArrayCurrentVertColorRightHemi = reinterpret_cast<float *>(arrayCurrentVertColorRightHemi.data());
for(int i = 0; i<m_lLabelsRightHemi.size(); i++) {
FSLIB::Label labelRightHemi = m_lLabelsRightHemi.at(i);
//Transform label activations to rgb colors
VectorXd vecActivationRightHemi(1);
vecActivationRightHemi(0) = vecLabelActivationRightHemi[labelRightHemi.label_id];
//Check if value is bigger than lower threshold. If not, don't plot activation
if(vecActivationRightHemi(0) >= m_vecThresholds.x()) {
QByteArray arrayLabelColorsRightHemi = transformDataToColor(vecActivationRightHemi);
float *rawArrayLabelColorsRightHemi = reinterpret_cast<float *>(arrayLabelColorsRightHemi.data());
for(int j = 0; j<labelRightHemi.vertices.rows(); j++) {
rawArrayCurrentVertColorRightHemi[labelRightHemi.vertices(j)*3+0] = rawArrayLabelColorsRightHemi[0];
rawArrayCurrentVertColorRightHemi[labelRightHemi.vertices(j)*3+1] = rawArrayLabelColorsRightHemi[1];
rawArrayCurrentVertColorRightHemi[labelRightHemi.vertices(j)*3+2] = rawArrayLabelColorsRightHemi[2];
}
}
}
colorPair.second = arrayCurrentVertColorRightHemi;
return colorPair;
}
case Data3DTreeModelItemRoles::SmoothingBased: {
//TODO: Smooth here!
break;
}
}
return colorPair;
}
