cxToolFileParser.cpp

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#include "cxToolFileParser.h"
 
#include <QFile>
#include <QDir>
#include "cxLogger.h"
#include "cxFrame3D.h"
#include "cxTransformFile.h"
#include "cxEnumConversion.h"
 
namespace cx {
 
Transform3D ToolFileParser::ToolInternalStructure::getCalibrationAsSSC() const
{
        //vtkMatrix4x4Ptr M = vtkMatrix4x4Ptr::New();
        //mCalibration.ExportTransform(*(M.GetPointer()));
        //Transform3D sMt = Transform3D::fromVtkMatrix(M);
        //return sMt;
        return mCalibration;
}
 
void ToolFileParser::ToolInternalStructure::setCalibration(const Transform3D& cal)
{
        mCalibration = cal;
        //mCalibration.ImportTransform(*cal.getVtkMatrix());
}
 
void ToolFileParser::ToolInternalStructure::saveCalibrationToFile()
{
        QString filename = mCalibrationFilename;
        //      QFile calibrationFile;
        if (!filename.isEmpty() && QFile::exists(filename))
        {
                //Calibration file exists, overwrite
                //              calibrationFile.setFileName(mCalibrationFilename);
        }
        else
        {
                //Make a new file, use rom file name as base name
                filename = mSROMFilename.remove(".rom", Qt::CaseInsensitive);
                filename.append(".cal");
                //              calibrationFile.setFileName(calibrationFileName);
        }
 
        TransformFile file(filename);
        file.write(this->getCalibrationAsSSC());
        //
        //      Transform3D sMt = this->getCalibrationAsSSC();
        //
        //      if (!calibrationFile.open(QIODevice::WriteOnly | QIODevice::Truncate))
        //      {
        //              reportError("Could not open " + mUid + "s calibrationfile: " + calibrationFile.fileName());
        //              return;
        //      }
        //
        //      QTextStream streamer(&calibrationFile);
        //      streamer << qstring_cast(sMt);
        //      streamer << endl;
        //
        //      calibrationFile.close();
 
        report("Replaced calibration in " + filename);
}
 
bool ToolFileParser::ToolInternalStructure::verify()
{
        bool retval = true;
        QString verificationError("Internal verification of tool " + mUid + " failed! REASON: ");
        if (!mIsPointer && !mIsReference && !mIsProbe)
        {
                //    reportError(verificationError+" Tag <tool>::<type> is invalid ["+qstring_cast(mType)+"]. Valid types: [pointer, usprobe, reference]");
                reportError(
                                        verificationError
                                        + " Tag <tool>::<type> is invalid, must be one one of pointer/probe/reference ");
                retval = false;
        }
        if (mUid.isEmpty())
        {
                reportError(verificationError + " Tag <tool>::<uid> is empty. Give tool a unique id.");
                retval = false;
        }
        if (mTrackerType == tsNONE)
        {
                reportError(
                                        verificationError + " Tag <sensor>::<type> is invalid ["
                                        + qstring_cast(mTrackerType)
                                        + "]. Valid types: [polaris, spectra, vicra, aurora, micron (NOT SUPPORTED YET)]");
                retval = false;
        }
        if ((mTrackerType == tsAURORA) && (mPortNumber >= 4))
        {
                reportError(
                                        verificationError + " Tag <sensor>::<portnumber> is invalid ["
                                        + qstring_cast(mPortNumber)
                                        + "]. Valid numbers: [0, 1, 2, 3]");
                retval = false;
        }
        if ((mTrackerType == tsAURORA) && (mChannelNumber >= 1))
        {
                reportError(
                                        verificationError + " Tag <sensor>::<channelnumber> is invalid ["
                                        + qstring_cast(mChannelNumber) + "]. Valid numbers: [0, 1]");
                retval = false;
        }
        QDir dir;
        if (!mSROMFilename.isEmpty() && !dir.exists(mSROMFilename))
        {
                reportError(
                                        verificationError + " Tag <sensor>::<rom_file> is invalid [" + mSROMFilename
                                        + "]. Valid path: relative path to existing rom file.");
                retval = false;
        }
        if (!mCalibrationFilename.isEmpty() && !dir.exists(mCalibrationFilename))
        {
                reportError(
                                        verificationError + " Tag <calibration>::<cal_file> is invalid ["
                                        + mCalibrationFilename
                                        + "]. Valid path: relative path to existing calibration file.");
                retval = false;
        }
        if (!mTransformSaveFileName.isEmpty() && !dir.exists(mTransformSaveFileName))
        {
                reportError(verificationError + " Logging folder is invalid. Contact programmer! :)");
                retval = false;
        }
        if (!mLoggingFolderName.isEmpty() && !dir.exists(mLoggingFolderName))
        {
                reportError(verificationError + " Logging folder is invalid. Contact programmer! :)");
                retval = false;
        }
 
        return retval;
}
 
ToolFileParser::ToolFileParser(QString absoluteToolFilePath, QString loggingFolder) :
        mToolFilePath(absoluteToolFilePath), mLoggingFolder(loggingFolder), mToolTag("tool"), mToolTypeTag("type"),
        mToolIdTag("id"), mToolNameTag("name"), mToolDescriptionTag("description"), mToolManufacturerTag("manufacturer"),
        mToolClinicalAppTag("clinical_app"), mToolGeoFileTag("geo_file"), mToolPicFileTag("pic_file"),
        mToolDocFileTag("doc_file"), mToolInstrumentTag("instrument"), mToolInstrumentTypeTag("type"),
        mToolInstrumentIdTag("id"), mToolInstrumentNameTag("name"), mToolInstrumentManufacturerTag("manufacturer"),
        mToolInstrumentScannerIdTag("scannerid"), mToolInstrumentDescriptionTag("description"),
        mToolSensorTag("sensor"), mToolSensorTypeTag("type"), mToolSensorIdTag("id"),
        mToolSensorNameTag("name"), mToolSensorWirelessTag("wireless"), mToolSensorDOFTag("DOF"),
        mToolSensorPortnumberTag("portnumber"), mToolSensorChannelnumberTag("channelnumber"),
        mToolSensorReferencePointTag("reference_point"), mToolSensorManufacturerTag("manufacturer"),
        mToolSensorDescriptionTag("description"), mToolSensorRomFileTag("rom_file"), mToolCalibrationTag("calibration"),
        mToolCalibrationFileTag("cal_file"),
        mToolOpenigtlinkImageIdTag("openigtlinkimageid"), mToolOpenigtlinkTransformIdTag("openigtlinktransformid")
{
}
 
ToolFileParser::~ToolFileParser()
{
}
 
ToolFileParser::ToolInternalStructurePtr ToolFileParser::getTool()
{
        ToolInternalStructurePtr retval;
 
        QFile toolFile(mToolFilePath);
        QString toolFolderAbsolutePath = QFileInfo(toolFile).dir().absolutePath() + "/";
        QDomNode toolNode = this->getToolNode(mToolFilePath);
        ToolInternalStructurePtr internalStructure = ToolInternalStructurePtr(new ToolInternalStructure());
        //    ToolFileParser::ToolInternalStructure internalStructure;
        if (toolNode.isNull())
        {
                report(
                                        "Could not read the <tool> tag of file: " + mToolFilePath
                                        + ", this is not a tool file, skipping.");
                return retval;
        }
 
        QDomElement toolTypeElement = toolNode.firstChildElement(mToolTypeTag);
        QString toolTypeText = toolTypeElement.text();
 
        internalStructure->mIsReference = toolTypeText.contains("reference", Qt::CaseInsensitive);
        internalStructure->mIsPointer = toolTypeText.contains("pointer", Qt::CaseInsensitive);
        internalStructure->mIsProbe = toolTypeText.contains("usprobe", Qt::CaseInsensitive);
 
        //    if (toolTypeText.contains("reference", Qt::CaseInsensitive))
        //    {
        //      internalStructure.mType = Tool::TOOL_REFERENCE;
        //    } else if (toolTypeText.contains("pointer", Qt::CaseInsensitive))
        //    {
        //      internalStructure.mType = Tool::TOOL_POINTER;
        //    } else if (toolTypeText.contains("usprobe", Qt::CaseInsensitive))
        //    {
        //      internalStructure.mType = Tool::TOOL_US_PROBE;
        //    } else
        //    {
        //      internalStructure.mType = Tool::TOOL_NONE;
        //    }
 
        QDomElement toolIdElement = toolNode.firstChildElement(mToolIdTag);
        QString toolIdText = toolIdElement.text();
        internalStructure->mUid = toolIdText;
 
        QDomElement toolNameElement = toolNode.firstChildElement(mToolNameTag);
        QString toolNameText = toolNameElement.text();
        internalStructure->mName = toolNameText;
 
        QDomElement toolClinicalAppElement = toolNode.firstChildElement(mToolClinicalAppTag);
        QString toolClinicalAppText = toolClinicalAppElement.text();
        QStringList applicationList = toolClinicalAppText.split(" ");
        foreach(QString string, applicationList)
        {
                if (string.isEmpty())
                        continue;
                string = string.toLower();
                internalStructure->mClinicalApplications.push_back(string);
        }
 
        QDomElement toolGeofileElement = toolNode.firstChildElement(mToolGeoFileTag);
        QString toolGeofileText = toolGeofileElement.text();
        if (!toolGeofileText.isEmpty())
                toolGeofileText = toolFolderAbsolutePath + toolGeofileText;
        internalStructure->mGraphicsFileName = toolGeofileText;
 
        QDomElement toolPicfileElement = toolNode.firstChildElement(mToolPicFileTag);
        QString toolPicfileText = toolPicfileElement.text();
        if (!toolPicfileText.isEmpty())
                toolPicfileText = toolFolderAbsolutePath + toolPicfileText;
        internalStructure->mPictureFileName = toolPicfileText;
 
        QDomElement toolImageIdfileElement = toolNode.firstChildElement(mToolOpenigtlinkImageIdTag);
        QString toolImageIdfileText = toolImageIdfileElement.text();
        internalStructure->mOpenigtlinkImageId = toolImageIdfileText;
 
        QDomElement toolTransformIdfileElement = toolNode.firstChildElement(mToolOpenigtlinkTransformIdTag);
        QString toolTransformIdfileText = toolTransformIdfileElement.text();
        internalStructure->mOpenigtlinkTransformId = toolTransformIdfileText;
 
        QDomElement toolInstrumentElement = toolNode.firstChildElement(mToolInstrumentTag);
        if (toolInstrumentElement.isNull())
        {
                reportError(
                                        "Could not find the <instrument> tag under the <tool> tag. Aborting this tool.");
                return retval;
        }
        QDomElement toolInstrumentIdElement = toolInstrumentElement.firstChildElement(mToolInstrumentIdTag);
        QString toolInstrumentIdText = toolInstrumentIdElement.text();
        internalStructure->mInstrumentId = toolInstrumentIdText;
 
        QDomElement toolInstrumentScannerIdElement = toolInstrumentElement.firstChildElement(mToolInstrumentScannerIdTag);
        QString toolInstrumentScannerIdText = toolInstrumentScannerIdElement.text();
        internalStructure->mInstrumentScannerId = toolInstrumentScannerIdText;
 
        QDomElement toolSensorElement = toolNode.firstChildElement(mToolSensorTag);
        if (toolSensorElement.isNull())
        {
                reportError("Could not find the <sensor> tag under the <tool> tag. Aborting this tool.");
                return retval;
        }
        QDomElement toolSensorTypeElement = toolSensorElement.firstChildElement(mToolSensorTypeTag);
        QString toolSensorTypeText = toolSensorTypeElement.text();
        internalStructure->mTrackerType = string2enum<TRACKING_SYSTEM>(toolSensorTypeText);
 
        QDomElement toolSensorWirelessElement = toolSensorElement.firstChildElement(mToolSensorWirelessTag);
        QString toolSensorWirelessText = toolSensorWirelessElement.text();
        if (toolSensorWirelessText.contains("yes", Qt::CaseInsensitive))
                internalStructure->mWireless = true;
        else if (toolSensorWirelessText.contains("no", Qt::CaseInsensitive))
                internalStructure->mWireless = false;
 
        QDomElement toolSensorDOFElement = toolSensorElement.firstChildElement(mToolSensorDOFTag);
        QString toolSensorDOFText = toolSensorDOFElement.text();
        if (toolSensorDOFText.contains("5", Qt::CaseInsensitive))
                internalStructure->m5DOF = true;
        else if (toolSensorDOFText.contains("6", Qt::CaseInsensitive))
                internalStructure->m5DOF = false;
 
        QDomElement toolSensorPortnumberElement = toolSensorElement.firstChildElement(mToolSensorPortnumberTag);
        QString toolSensorPortnumberText = toolSensorPortnumberElement.text();
        internalStructure->mPortNumber = toolSensorPortnumberText.toUInt();
 
        QDomElement toolSensorChannelnumberElement = toolSensorElement.firstChildElement(mToolSensorChannelnumberTag);
        QString toolSensorChannelnumberText = toolSensorChannelnumberElement.text();
        internalStructure->mChannelNumber = toolSensorChannelnumberText.toUInt();
 
        QDomNodeList toolSensorReferencePointList = toolSensorElement.elementsByTagName(mToolSensorReferencePointTag);
        for (int j = 0; j < toolSensorReferencePointList.count(); j++)
        {
                QDomNode node = toolSensorReferencePointList.item(j);
                if (!node.hasAttributes())
                {
                        reportWarning("Found reference point without id attribute. Skipping.");
                        continue;
                }
                QString id = node.toElement().attribute("id");
                QString toolSensorReferencePointText = node.toElement().text();
                Vector3D vector = Vector3D::fromString(toolSensorReferencePointText);
                internalStructure->mReferencePoints[id] = vector;
        }
 
        QDomElement toolSensorRomFileElement = toolSensorElement.firstChildElement(mToolSensorRomFileTag);
        QString toolSensorRomFileText = toolSensorRomFileElement.text();
        if (!toolSensorRomFileText.isEmpty())
                toolSensorRomFileText = toolFolderAbsolutePath + toolSensorRomFileText;
        internalStructure->mSROMFilename = toolSensorRomFileText;
 
        QDomElement toolCalibrationElement = toolNode.firstChildElement(mToolCalibrationTag);
        if (toolCalibrationElement.isNull())
        {
                reportError(
                                        "Could not find the <calibration> tag under the <tool> tag. Aborting this tool.");
                return retval;
        }
        QDomElement toolCalibrationFileElement = toolCalibrationElement.firstChildElement(mToolCalibrationFileTag);
        QString toolCalibrationFileText = toolCalibrationFileElement.text();
        if (!toolCalibrationFileText.isEmpty())
                toolCalibrationFileText = toolFolderAbsolutePath + toolCalibrationFileText;
        internalStructure->mCalibrationFilename = toolCalibrationFileText;
        internalStructure->mCalibration = this->readCalibrationFile(internalStructure->mCalibrationFilename);
 
        internalStructure->mTransformSaveFileName = mLoggingFolder;
        internalStructure->mLoggingFolderName = mLoggingFolder;
        retval = internalStructure;
 
        return retval;
}
 
QDomNode ToolFileParser::getToolNode(QString toolAbsoluteFilePath)
{
        QDomNode retval;
        QFile toolFile(toolAbsoluteFilePath);
        if (!mToolDoc.setContent(&toolFile))
        {
                reportError("Could not set the xml content of the tool file " + toolAbsoluteFilePath);
                return retval;
        }
        //there can only be one tool defined in every tool.xml-file, that's why we say ...item(0)
        retval = mToolDoc.elementsByTagName(mToolTag).item(0);
        return retval;
}
 
Transform3D ToolFileParser::readCalibrationFile(QString absoluteFilePath)
{
        bool ok = true;
        TransformFile file(absoluteFilePath);
        Transform3D retval = file.read(&ok);
 
        if (ok)
        {
                retval = Frame3D::create(retval).transform(); // clean rotational parts, transform should now be pure rotation+translation
        }
 
        return retval;
}
 
/*
QString ToolFileParser::getTemplatesAbsoluteFilePath()
{
        QString retval = DataLocations::getRootConfigPath() + "/tool/TEMPLATE_tool.xml";
        return retval;
}
*/
 
}