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#include <stdio.h>
#include <QtCore>
#include "CiftiXMLElements.h"
#include "iostream"
#include "CiftiXMLReader.h"
void parseCiftiXML(QXmlStreamReader &xml, CiftiRootElement &rootElement)
{
while (!xml.atEnd() && !xml.hasError()) {
xml.readNext();
QString test = xml.name().toString();
if(xml.isStartElement())
{
QString elementName = xml.name().toString();
if(elementName == "CIFTI") {
QXmlStreamAttributes attributes = xml.attributes();
if(attributes.hasAttribute("Version")) rootElement.m_version = attributes.value("Version").toString();
else xml.raiseError("Cifti XML Header missing Version String.");
if(attributes.hasAttribute("NumberOfMatrices")) rootElement.m_numberOfMatrices = attributes.value("NumberOfMatrices").toString().toULong();
else xml.raiseError("Cifti XML Header missing number of matrices.");
}
else if(elementName == "Matrix") {
rootElement.m_matrices.push_back(CiftiMatrixElement());
parseMatrixElement(xml,rootElement.m_matrices.back());
}
else std::cout << "unknown element: " << elementName.toAscii().data() << std::endl;
}
}
if(xml.hasError())
{
std::cout << "XML error: " << xml.errorString().toAscii().data() << std::endl;
}
else if(xml.atEnd())
{
;//std::cout << "Reached end, done" << std::endl;
}
}
void parseMatrixElement(QXmlStreamReader &xml, CiftiMatrixElement &matrixElement)
{
QString test = xml.name().toString();
while (!(xml.isEndElement() && (xml.name().toString() == "Matrix")) && !xml.hasError()) {// && xml.name() == "Matrix") {
xml.readNext();
QString test2 = xml.name().toString();
if(xml.isStartElement())
{
QString elementName = xml.name().toString();
if(elementName == "MetaData")
{
parseMetaData(xml,matrixElement.m_userMetaData);
}
else if(elementName == "LabelTable") {
parseLabelTable(xml,matrixElement.m_labelTable);
}
else if(elementName == "MatrixIndicesMap")
{
matrixElement.m_matrixIndicesMap.push_back(CiftiMatrixIndicesMapElement());
parseMatrixIndicesMap(xml,matrixElement.m_matrixIndicesMap.back());
}
else if(elementName == "Volume")
{
matrixElement.m_volume.push_back(CiftiVolume());
parseVolume(xml,matrixElement.m_volume.back());
}
else std::cout << "unknown element: " << elementName.toAscii().data() << std::endl;
}
}
QString test2=xml.name().toString();
//check end element
if(!xml.hasError()) if(!xml.isEndElement() || (xml.name().toString() != "Matrix"))
xml.raiseError("Matrix end tag not found.");
}
void parseMetaData(QXmlStreamReader &xml, QHash<QString, QString> &userMetaData)
{
while (!(xml.isEndElement() && (xml.name().toString() == "MetaData")) && !xml.hasError()) {// && xml.name() == "MetaData") {
xml.readNext();
if(xml.isStartElement())
{
QString elementName = xml.name().toString();
if(elementName == "MD")
{
parseMetaDataElement(xml,userMetaData);
}
else std::cout << "unknown element: " << elementName.toAscii().data() << std::endl;
}
}
//check for end element
if(!xml.isEndElement() || (xml.name().toString() != "MetaData"))
xml.raiseError("MetaData end tag not found.");
}
void parseMetaDataElement(QXmlStreamReader &xml, QHash<QString,QString> &userMetaData)
{
QString name;
QString value;
QString test;
while (!(xml.isEndElement() && (xml.name().toString() == "MD")) && !xml.hasError()) {
test = xml.name().toString();
xml.readNext();
if(xml.isStartElement())
{
QString elementName = xml.name().toString();
if(elementName == "Name")
{
xml.readNext();
if(xml.tokenType() != QXmlStreamReader::Characters) {
return;
}
name = xml.text().toString();
xml.readNext();
if(!xml.isEndElement())
xml.raiseError("End element for meta data name tag not found.");
}
else if(elementName == "Value")
{
xml.readNext();
if(xml.tokenType() != QXmlStreamReader::Characters) {
return;
}
value = xml.text().toString();
xml.readNext();
if(!xml.isEndElement())
xml.raiseError("End element for meta data value tag not found.");
}
else std::cout << "unknown element: " << elementName.toAscii().data() << std::endl;
}
}
userMetaData.insert(name,value);
if(!xml.isEndElement() || (xml.name().toString() != "MD"))
xml.raiseError("End element for MD tag not found");
}
void parseLabelTable(QXmlStreamReader &xml, std::vector<CiftiLabelElement> &labelTable)
{
while (!(xml.isEndElement() && (xml.name().toString() == "LabelTable"))&& !xml.hasError()) {// && xml.name() == "Matrix") {
xml.readNext();
if(xml.isStartElement())
{
QString elementName = xml.name().toString();
if(elementName == "Label")
{
labelTable.push_back(CiftiLabelElement());
parseLabel(xml,labelTable.back());
}
else std::cout << "unknown element: " << elementName.toAscii().data() << std::endl;
}
}
//check end element
if(!xml.isEndElement() || (xml.name().toString() != "LabelTable"))
{
xml.raiseError("End element for label table not found.");
}
}
void parseLabel(QXmlStreamReader &xml, CiftiLabelElement &label)
{
if(!(xml.name().toString() == "Label")) xml.raiseError("Error parsing Label\n");
QXmlStreamAttributes attributes = xml.attributes();
//get attribute values
if(attributes.hasAttribute("Key")) label.m_key = attributes.value("Key").toString().toULongLong();
else xml.raiseError("Label does not contain Key value\n");
if(attributes.hasAttribute("Red")) label.m_red = attributes.value("Red").toString().toFloat();
else xml.raiseError("Label does not contain Red value\n");
if(attributes.hasAttribute("Green")) label.m_green = attributes.value("Green").toString().toFloat();
else xml.raiseError("Label does not contain Green value\n");
if(attributes.hasAttribute("Blue")) label.m_blue = attributes.value("Blue").toString().toFloat();
else xml.raiseError("Label does not contain Blue value\n");
if(attributes.hasAttribute("Alpha")) label.m_alpha = attributes.value("Alpha").toString().toFloat();
else xml.raiseError("Label does not contain Alpha value\n");
if(attributes.hasAttribute("X")) label.m_x = attributes.value("X").toString().toFloat();
else xml.raiseError("Label does not contain X value\n");
if(attributes.hasAttribute("Y")) label.m_y = attributes.value("Y").toString().toFloat();
else xml.raiseError("Label does not contain Y value\n");
if(attributes.hasAttribute("Z")) label.m_z = attributes.value("Z").toString().toFloat();
else xml.raiseError("Label does not contain Z value\n");
//get Label Text
xml.readNext();
if(xml.tokenType() != QXmlStreamReader::Characters) {
return;
}
label.m_text = xml.text().toString();
//get end element
xml.readNext();
if(!xml.isEndElement())
{
xml.raiseError("End element for label not found.");
}
}
void parseMatrixIndicesMap(QXmlStreamReader &xml, CiftiMatrixIndicesMapElement &matrixIndicesMap)
{
QXmlStreamAttributes attributes = xml.attributes();
//get attribute values
if(attributes.hasAttribute("AppliesToMatrixDimension"))
{
QStringList values = attributes.value("AppliesToMatrixDimension").toString().split(',');
for(int i = 0;i<values.size();i++)
matrixIndicesMap.m_appliesToMatrixDimension.push_back(values.at(i).toInt());
}
else xml.raiseError("MatrixIndicesMap does not contain AppliesToMatrixDimension value\n");
if(attributes.hasAttribute("IndicesMapToDataType")) {
QString indicesMapToDataType = attributes.value("IndicesMapToDataType").toString();
if(indicesMapToDataType == "CIFTI_INDEX_TYPE_BRAIN_MODELS") matrixIndicesMap.m_indicesMapToDataType = CIFTI_INDEX_TYPE_BRAIN_MODELS;
else if(indicesMapToDataType == "CIFTI_TYPE_FIBERS") matrixIndicesMap.m_indicesMapToDataType = CIFTI_INDEX_TYPE_FIBERS;
else if(indicesMapToDataType == "CIFTI_INDEX_TYPE_PARCELS") matrixIndicesMap.m_indicesMapToDataType = CIFTI_INDEX_TYPE_PARCELS;
else if(indicesMapToDataType == "CIFTI_INDEX_TYPE_TIME_POINTS") matrixIndicesMap.m_indicesMapToDataType = CIFTI_INDEX_TYPE_TIME_POINTS;
else xml.raiseError("Error, unrecognized value for BrainModel, indicesMapToDataType.");
}
else xml.raiseError("MatrixIndicesMap does not contain IndicesMapToDataType value\n");
if(attributes.hasAttribute("TimeStep")) matrixIndicesMap.m_timeStep = attributes.value("TimeStep").toString().toFloat();
//else xml.raiseError("MatrixIndicesMap does not contain timeStep Value.");
if(attributes.hasAttribute("TimeStepUnits"))
{
QString timeStepUnits = attributes.value("TimeStepUnits").toString();
if(timeStepUnits == "NIFTI_UNITS_SEC")
{
matrixIndicesMap.m_timeStepUnits = NIFTI_UNITS_SEC;
}
else if(timeStepUnits == "NIFTI_UNITS_MSEC")
{
matrixIndicesMap.m_timeStepUnits = NIFTI_UNITS_MSEC;
}
else if(timeStepUnits == "NIFTI_UNITS_USEC")
{
matrixIndicesMap.m_timeStepUnits = NIFTI_UNITS_USEC;
}
}
while (!xml.isEndElement() && !xml.hasError()) {
xml.readNext();
if(xml.isStartElement())
{
QString elementName = xml.name().toString();
if(elementName == "BrainModel")
{
matrixIndicesMap.m_brainModels.push_back(CiftiBrainModelElement());
parseBrainModel(xml,matrixIndicesMap.m_brainModels.back());
xml.readNext();//read next element after brainmodel end element
}
else std::cout << "unknown element: " << elementName.toAscii().data() << std::endl;
}
}
}
void parseBrainModel(QXmlStreamReader &xml, CiftiBrainModelElement &brainModel)
{
QXmlStreamAttributes attributes = xml.attributes();
//get attribute values
if(attributes.hasAttribute("IndexOffset")) brainModel.m_indexOffset = attributes.value("IndexOffset").toString().toULongLong();
else xml.raiseError("BrainModel does not contain required IndexOffset attribute\n");
if(attributes.hasAttribute("IndexCount")) brainModel.m_indexCount = attributes.value("IndexCount").toString().toULongLong();
else xml.raiseError("BrainModel does not contain required IndexCount attribute\n");
if(attributes.hasAttribute("ModelType"))
{
QString modelType = attributes.value("ModelType").toString();
if(modelType == "CIFTI_MODEL_TYPE_SURFACE")
{
brainModel.m_modelType = CIFTI_MODEL_TYPE_SURFACE;
}
else if(modelType == "CIFTI_MODEL_TYPE_VOXELS")
{
brainModel.m_modelType = CIFTI_MODEL_TYPE_VOXELS;
}
else xml.raiseError("BrainModel contains unrecognized model type");
}
else xml.raiseError("BrainModel does not contain required ModelType attribute\n");
if(attributes.hasAttribute("BrainStructure"))
{
QString brainStructure = attributes.value("BrainStructure").toString();
brainModel.m_brainStructure = attributes.value("BrainStructure").toString();
}
if(attributes.hasAttribute("SurfaceNumberOfNodes")) brainModel.m_surfaceNumberOfNodes = attributes.value("SurfaceNumberOfNodes").toString().toULongLong();
else brainModel.m_surfaceNumberOfNodes = 0;
//else xml.raiseError("BrainModel does not contain require SurfaceNumberOfNodes attribute\n");
while (!(xml.isEndElement() && (xml.name().toString() == "BrainModel")) && !xml.hasError()) {
xml.readNext();
if(xml.isStartElement())
{
QString elementName = xml.name().toString();
if(elementName == "NodeIndices")
{
//get node Indices
xml.readNext();
if(xml.tokenType() != QXmlStreamReader::Characters) {
return;
}
QString nodeIndices = xml.text().toString();
QStringList list = nodeIndices.split(QRegExp("\\D+"),QString::SkipEmptyParts);
for(int i = 0;i<list.count();i++)
{
brainModel.m_nodeIndices.push_back(list[i].toULongLong());
}
//get end element
xml.readNext();
if(!xml.isEndElement())
{
xml.raiseError("End element for NodeIndices not found.");
}
}
else if(elementName == "VoxelIndicesIJK")
{
//get voxel Indices IJK
xml.readNext();
if(xml.tokenType() != QXmlStreamReader::Characters) {
return;
}
QString voxelIndicesIJK = xml.text().toString();
QStringList list = voxelIndicesIJK.split(QRegExp("\\D+"),QString::SkipEmptyParts);
if(list.count()%3) std::cout << voxelIndicesIJK.toAscii().data() << std::endl << list[list.count()-3].toULongLong() << list[list.count()-2].toULongLong() << list[list.count()-1].toULongLong() << std::endl;
for(int i = 0;i<list.count();i++)
{
brainModel.m_voxelIndicesIJK.push_back(list[i].toULongLong());
}
//get end element
xml.readNext();
if(!xml.isEndElement()|| (xml.name().toString() != "VoxelIndicesIJK"))
{
xml.raiseError("End element for VoxelIndicesIJK not found.");
}
}
else std::cout << "unknown element: " << elementName.toAscii().data() << std::endl;
}
}
//get end element for BrainModel
while(!(xml.isEndElement() && (xml.name().toString() == "BrainModel"))&& !xml.hasError()) xml.readNext();
if(!xml.isEndElement() || (xml.name().toString() != "BrainModel"))
{
xml.raiseError("End element for brain Model not found.");
}
}
void parseVolume(QXmlStreamReader &xml, CiftiVolume &volume)
{
QXmlStreamAttributes attributes = xml.attributes();
//get attribute values
if(attributes.hasAttribute("VolumeDimensions"))
{
QStringList list = attributes.value("VolumeDimensions").toString().split(',');
for(int i=0;i<3;i++)
{
volume.m_volumeDimensions[i]=list[i].toUInt();
}
}
else xml.raiseError("Volume does not contain required VolumeDimensions attribute\n");
while (!(xml.isEndElement() && (xml.name().toString() == "Volume")) && !xml.hasError()) {
xml.readNext();
if(xml.isStartElement())
{
QString elementName = xml.name().toString();
if(elementName == "TransformationMatrixVoxelIndicesIJKtoXYZ")
{
volume.m_transformationMatrixVoxelIndicesIJKtoXYZ.push_back(TransformationMatrixVoxelIndicesIJKtoXYZ());
parseTransformationMatrixVoxelIndicesIJKtoXYZ(xml,volume.m_transformationMatrixVoxelIndicesIJKtoXYZ.back());
}
else std::cout << "unknown element: " << elementName.toAscii().data() << std::endl;
}
}
//check end element for Volume
if(!xml.isEndElement())
{
xml.raiseError("End element for Volume not found.");
}
}
void parseTransformationMatrixVoxelIndicesIJKtoXYZ(QXmlStreamReader &xml, TransformationMatrixVoxelIndicesIJKtoXYZ &transform)
{
QXmlStreamAttributes attributes = xml.attributes();
//get attribute values
if(attributes.hasAttribute("DataSpace"))
{
QString dataSpace = attributes.value("DataSpace").toString();
if(dataSpace == "NIFTI_XFORM_UNKNOWN") transform.m_dataSpace = NIFTI_XFORM_UNKNOWN;
else if(dataSpace == "NIFTI_XFORM_SCANNER_ANAT") transform.m_dataSpace = NIFTI_XFORM_SCANNER_ANAT;
else if(dataSpace == "NIFTI_XFORM_ALIGNED_ANAT") transform.m_dataSpace = NIFTI_XFORM_ALIGNED_ANAT;
else if(dataSpace == "NIFTI_XFORM_TALAIRACH") transform.m_dataSpace = NIFTI_XFORM_TALAIRACH;
else if(dataSpace == "NIFTI_XFORM_MNI_152") transform.m_dataSpace = NIFTI_XFORM_MNI_152;
else xml.raiseError("Volume contains unknown or unsupported data space.");
}
else xml.raiseError("TransformationMatrixVoxelIndicesIJKtoXYZ does not contain dataSpace.");
if(attributes.hasAttribute("TransformedSpace"))
{
QString transformedSpace = attributes.value("TransformedSpace").toString();
if(transformedSpace == "NIFTI_XFORM_UNKNOWN") transform.m_transformedSpace = NIFTI_XFORM_UNKNOWN;
else if(transformedSpace == "NIFTI_XFORM_SCANNER_ANAT") transform.m_transformedSpace = NIFTI_XFORM_SCANNER_ANAT;
else if(transformedSpace == "NIFTI_XFORM_ALIGNED_ANAT") transform.m_transformedSpace = NIFTI_XFORM_ALIGNED_ANAT;
else if(transformedSpace == "NIFTI_XFORM_TALAIRACH") transform.m_transformedSpace = NIFTI_XFORM_TALAIRACH;
else if(transformedSpace == "NIFTI_XFORM_MNI_152") transform.m_transformedSpace = NIFTI_XFORM_MNI_152;
else xml.raiseError("Volume contains unknown or unsupported transformed space.");
}
else xml.raiseError("TransformationMatrixVoxelIndicesIJKtoXYZ does not contain transformedSpace.");
if(attributes.hasAttribute("UnitsXYZ"))
{
QString unitsXYZ = attributes.value("UnitsXYZ").toString();
if(unitsXYZ == "NIFTI_UNITS_MM") transform.m_unitsXYZ = NIFTI_UNITS_MM;
else if(unitsXYZ == "NIFTI_UNITS_MICRON") transform.m_unitsXYZ = NIFTI_UNITS_MICRON;
else xml.raiseError("Volume contains unknown or unsupported spatial XYZ coordinates.");
}
else xml.raiseError("TransformationMatrixVoxelIndicesIJKtoXYZ does not contain UnitsXYZ.");
xml.readNext();
if(xml.tokenType() != QXmlStreamReader::Characters) {
xml.raiseError("Error reading Transformation matrix.");
}
QString voxelIndicesString = xml.text().toString();
QStringList voxelIndices = voxelIndicesString.split(QRegExp("\\s+"),QString::SkipEmptyParts);
for(int i = 0;i<16;i++)
transform.m_transform[i] = voxelIndices.at(i).toFloat();
//get end element for TransformationMatrixVoxelIndicesIJKtoXYZ
while(!xml.isEndElement() && !xml.hasError()) xml.readNext();
if(!xml.isEndElement())
{
xml.raiseError("End element for TransformationMatrixVoxelIndicesIJKtoXYZ not found.");
}
}
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