cxToolFileParser.cpp

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#include "cxToolFileParser.h"

#include <QFile>
#include <QDir>
#include "cxLogger.h"
#include "cxEnumConverter.h"
#include "cxFrame3D.h"
#include "cxTransformFile.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")
{
}

ToolFileParser::~ToolFileParser()
{
}

ToolFileParser::ToolInternalStructure ToolFileParser::getTool()
{
    ToolInternalStructure retval;

    QFile toolFile(mToolFilePath);
    QString toolFolderAbsolutePath = QFileInfo(toolFile).dir().absolutePath() + "/";
    QDomNode toolNode = this->getToolNode(mToolFilePath);
    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 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.toInt();

    QDomElement toolSensorChannelnumberElement = toolSensorElement.firstChildElement(mToolSensorChannelnumberTag);
    QString toolSensorChannelnumberText = toolSensorChannelnumberElement.text();
    internalStructure.mChannelNumber = toolSensorChannelnumberText.toInt();

    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;
        }
        bool ok;
        int id = node.toElement().attribute("id").toInt(&ok);
        if (!ok)
        {
            reportWarning("Attribute id of a reference point was not an int. Skipping.");
            continue;
        }
        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;
}
*/

}