cxToolConfigurationParser.cpp

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/*=========================================================================
This file is part of CustusX, an Image Guided Therapy Application.

Copyright (c) 2008-2014, SINTEF Department of Medical Technology
All rights reserved.

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modification, are permitted provided that the following conditions are met:

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   this list of conditions and the following disclaimer.

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   may be used to endorse or promote products derived from this software 
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#include "cxToolConfigurationParser.h"

#include <QFile>
#include <QDir>
#include <QFileInfo>
#include <QTextStream>
#include "cxLogger.h"
#include "cxTypeConversions.h"
#include "cxEnumConverter.h"
#include "cxDataLocations.h"
#include "cxProfile.h"
#include "cxFrame3D.h"
#include "cxTransformFile.h"

namespace cx
{

ConfigurationFileParser::ConfigurationFileParser(QString absoluteConfigFilePath, QString loggingFolder) :
                                mConfigurationFilePath(absoluteConfigFilePath), mLoggingFolder(loggingFolder), mConfigTag(
                                                                "configuration"), mConfigTrackerTag("tracker"), mConfigTrackerToolFile("toolfile"), mTypeAttribute(
                                                                "type"), mClinicalAppAttribute("clinical_app"), mReferenceAttribute("reference")
{
        this->setConfigDocument(mConfigurationFilePath);
}

ConfigurationFileParser::~ConfigurationFileParser()
{
}

QString ConfigurationFileParser::getApplicationapplication()
{
        if (!this->isConfigFileValid())
                return "";

        QDomNode configNode = mConfigureDoc.elementsByTagName(mConfigTag).at(0);
        QString retval = configNode.toElement().attribute(mClinicalAppAttribute);
        return retval;
}

std::vector<IgstkTracker::InternalStructure> ConfigurationFileParser::getTrackers()
{
        std::vector<IgstkTracker::InternalStructure> retval;

        if (!this->isConfigFileValid())
                return retval;

        QDomNodeList trackerNodes = mConfigureDoc.elementsByTagName(mConfigTrackerTag);
        for (int i = 0; i < trackerNodes.count(); ++i)
        {
                IgstkTracker::InternalStructure internalStructure;
                QString trackerType = trackerNodes.at(i).toElement().attribute(mTypeAttribute);
                internalStructure.mType = string2enum<TRACKING_SYSTEM>(trackerType);
                internalStructure.mLoggingFolderName = mLoggingFolder;

                retval.push_back(internalStructure);
        }

        if (retval.size() > 1)
                reportError(
                                                "Config file " + mConfigurationFilePath
                                                                                + " has a invalid number of tracking systems, we only support 1 tracking system atm!");

        return retval;
}

std::vector<QString> ConfigurationFileParser::getAbsoluteToolFilePaths()
{
        std::vector<QString> retval;

        if (!this->isConfigFileValid())
                return retval;

        QDomNodeList toolFileNodes = mConfigureDoc.elementsByTagName(mConfigTrackerToolFile);
        for (int i = 0; i < toolFileNodes.count(); ++i)
        {
                QString absoluteToolFilePath = this->getAbsoluteToolFilePath(toolFileNodes.at(i).toElement());
                if (absoluteToolFilePath.isEmpty())
                        continue;

                retval.push_back(absoluteToolFilePath);
        }

        return retval;
}

QString ConfigurationFileParser::getAbsoluteReferenceFilePath()
{
        QString retval;

        if (!this->isConfigFileValid())
                return retval;

//  QFile configFile(mConfigurationFilePath);
//  QString configFolderAbsolutePath = QFileInfo(configFile).dir().absolutePath()+"/";
//  std::cout << "configFolderAbsolutePath " << configFolderAbsolutePath << std::endl;

        QDomNodeList toolFileNodes = mConfigureDoc.elementsByTagName(mConfigTrackerToolFile);
        for (int i = 0; i < toolFileNodes.count(); ++i)
        {
                QString reference = toolFileNodes.at(i).toElement().attribute(mReferenceAttribute);
                if (reference.contains("yes", Qt::CaseInsensitive))
                {
//      std::cout << "Found yes..." << std::endl;
                        retval = this->getAbsoluteToolFilePath(toolFileNodes.at(i).toElement());
                }
        }
        return retval;
}

QString ConfigurationFileParser::getTemplatesAbsoluteFilePath()
{
        QString retval = DataLocations::getRootConfigPath() + "/tool/TEMPLATE_configuration.xml";
        return retval;
}

QString ConfigurationFileParser::convertToRelativeToolFilePath(QString configFilename, QString absoluteToolFilePath)
{
        foreach (QString root, profile()->getAllRootConfigPaths())
        {
                QString configPath = getToolPathFromRoot(root);
                if (!absoluteToolFilePath.contains(configPath))
                        continue;
                absoluteToolFilePath.replace(configPath, "");
                if (absoluteToolFilePath.startsWith("/"))
                        absoluteToolFilePath.remove(0, 1);
                return absoluteToolFilePath;
        }

        // file not in any of the standard locations: return absolute
        return absoluteToolFilePath;
}

QString ConfigurationFileParser::getToolPathFromRoot(QString root)
{
        return root + "/tool/Tools/";
}

void ConfigurationFileParser::saveConfiguration(Configuration& config)
{
        QDomDocument doc;
        doc.appendChild(doc.createProcessingInstruction("xml version =", "\"1.0\""));

        QDomElement configNode = doc.createElement("configuration");
        configNode.setAttribute("clinical_app", config.mClinical_app);

        TrackersAndToolsMap::iterator it1 = config.mTrackersAndTools.begin();
        for (; it1 != config.mTrackersAndTools.end(); ++it1)
        {
                QString trackerType = enum2string(it1->first);
                QDomElement trackerTagNode = doc.createElement("tracker");
                trackerTagNode.setAttribute("type", trackerType);

                ToolFilesAndReferenceVector::iterator it2 = it1->second.begin();
                for (; it2 != it1->second.end(); ++it2)
                {
                        QString absoluteToolFilePath = it2->first;
                        QString relativeToolFilePath = convertToRelativeToolFilePath(config.mFileName, absoluteToolFilePath);

                        ToolFileParser toolparser(absoluteToolFilePath);
                        QString toolTrackerType = enum2string(toolparser.getTool().mTrackerType);
                        if (!trackerType.contains(enum2string(toolparser.getTool().mTrackerType), Qt::CaseInsensitive))
                        {
                                reportWarning("When saving configuration, skipping tool " + relativeToolFilePath + " of type "
                                                                                                + toolTrackerType + " because tracker is set to " + trackerType);
                                continue;
                        }

                        QDomElement toolFileNode = doc.createElement("toolfile");
                        toolFileNode.appendChild(doc.createTextNode(relativeToolFilePath));
                        toolFileNode.setAttribute("reference", (it2->second ? "yes" : "no"));
                        trackerTagNode.appendChild(toolFileNode);
                }
                configNode.appendChild(trackerTagNode);
        }

        doc.appendChild(configNode);

        //write to file
        QFile file(config.mFileName);
        QDir().mkpath(QFileInfo(config.mFileName).absolutePath());

        if (!file.open(QIODevice::WriteOnly))
        {
                reportWarning("Could not open file " + file.fileName() + ", aborting writing of config.");
                return;
        }
        QTextStream stream(&file);
        doc.save(stream, 4);
        reportSuccess("Configuration file " + file.fileName() + " is written.");
}

void ConfigurationFileParser::setConfigDocument(QString configAbsoluteFilePath)
{
        QFile configFile(configAbsoluteFilePath);
        if (!configFile.exists())
        {
//    reportDebug("Configfile "+configAbsoluteFilePath+" does not exist.");
                return;
        }

        if (!mConfigureDoc.setContent(&configFile))
        {
                reportError("Could not set the xml content of the config file " + configAbsoluteFilePath);
                return;
        }
}

bool ConfigurationFileParser::isConfigFileValid()
{
        //there can only be one config defined in every config.xml-file, that's why we say ...item(0)
        QDomNode configNode = mConfigureDoc.elementsByTagName(mConfigTag).item(0);
        if (configNode.isNull())
        {
                //reportDebug("Configuration file \""+mConfigurationFilePath+"\" does not contain the tag <"+mConfigTag+">.");
                return false;
        }
        return true;
}

QString ConfigurationFileParser::findXmlFileWithDirNameInPath(QString path)
{
        QDir dir(path);
        QStringList filter;
        filter << dir.dirName() + ".xml";
        QStringList filepaths = dir.entryList(filter);
        if (!filepaths.isEmpty())
                return dir.absoluteFilePath(filter[0]);
        return "";
}

QString ConfigurationFileParser::searchForExistingToolFilePath(QString relativeToolFilePath)
{
        // remove old-style paths (<= v3.7.0)
        relativeToolFilePath.replace("../Tools/", "");

        foreach (QString root, profile()->getAllRootConfigPaths())
        {
                QString configPath = this->getToolPathFromRoot(root);
                QFileInfo guess(configPath + "/" + relativeToolFilePath);
                if (guess.exists())
                        return guess.canonicalFilePath();
        }
        return "";
}

QString ConfigurationFileParser::getAbsoluteToolFilePath(QDomElement toolfileelement)
{
        QString relativeToolFilePath = toolfileelement.text();
        if (relativeToolFilePath.isEmpty())
                return "";

        QString absoluteToolFilePath = this->searchForExistingToolFilePath(relativeToolFilePath);

        QFileInfo info(absoluteToolFilePath);
        if (!info.exists())
                reportError(QString("Tool file %1 in configuration %2 not found. Skipping.")
                                        .arg(relativeToolFilePath)
                                        .arg(mConfigurationFilePath));

        if (info.isDir())
                absoluteToolFilePath = this->findXmlFileWithDirNameInPath(absoluteToolFilePath);
        return absoluteToolFilePath;
}
//----------------------------------------------------------------------------------------------------------------------

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()
{
}

IgstkTool::InternalStructure ToolFileParser::getTool()
{
        IgstkTool::InternalStructure retval;

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

QString ToolFileParser::getTemplatesAbsoluteFilePath()
{
        QString retval = DataLocations::getRootConfigPath() + "/tool/TEMPLATE_tool.xml";
        return retval;
}

igstk::Transform ToolFileParser::readCalibrationFile(QString absoluteFilePath)
{
        igstk::Transform retval;

        bool ok = true;
        TransformFile file(absoluteFilePath);
        Transform3D M = file.read(&ok);

        if (ok)
        {
                M = Frame3D::create(M).transform(); // clean rotational parts, transform should now be pure rotation+translation
                retval.ImportTransform(*M.getVtkMatrix());
        }

        return retval;
}

//----------------------------------------------------------------------------------------------------------------------

}//namespace cx