Ejemplo n.º 1
0
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;
}
Ejemplo n.º 2
0
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;
            }
        }
    }
}
Ejemplo n.º 3
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;
}