cxToolConfigurationParser.cpp

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/*=========================================================================
This file is part of CustusX, an Image Guided Therapy Application.
                 
Copyright (c) SINTEF Department of Medical Technology.
All rights reserved.
                 
CustusX is released under a BSD 3-Clause license.
                 
See Lisence.txt (https://github.com/SINTEFMedtek/CustusX/blob/master/License.txt) for details.
=========================================================================*/
 
#include "cxToolConfigurationParser.h"
 
#include <QFile>
#include <QDir>
#include <QFileInfo>
#include <QTextStream>
#include "cxLogger.h"
#include "cxTypeConversions.h"
#include "cxEnumConversion.h"
#include "cxDataLocations.h"
#include "cxProfile.h"
#include "cxFrame3D.h"
#include "cxTransformFile.h"
 
namespace cx
{
 
// names of necessary tags in the configuration file
#define CONFIG_TAG "configuration"
#define CONFIG_TRACKER_TAG "tracker"
#define CONFIG_TRACKER_TOOL_FILE "toolfile"
#define CONFIG_TRACKINGSYSTEMIMPLEMENTATION_TAG "trackingsystemimplementation"
 
// names of necessary attributes in the configuration file
#define TYPE_ATTRIBUTE "type"
#define CLINICAL_APP_ATTRIBUTE "clinical_app"
#define REFERENCE_ATTRIBUTE "reference"
#define OPENIGTLINK_TRANSFORM_ID_ATTRIBUTE "openigtlinktransformid"
#define OPENIGTLINK_IMAGE_ID_ATTRIBUTE "openigtlinkimageid"
#define OPENIGTLINK_APPLY_REF_TO_TOOLS_ATTRIBUTE "openigtlinkApplyRefToTools"
 
ConfigurationFileParser::ConfigurationFileParser(QString absoluteConfigFilePath, QString loggingFolder) :
                                mConfigurationFilePath(absoluteConfigFilePath), mLoggingFolder(loggingFolder)
{
        this->setConfigDocument(mConfigurationFilePath);
}
 
ConfigurationFileParser::~ConfigurationFileParser()
{
}
 
QString ConfigurationFileParser::getApplicationapplication()
{
        if (!this->isConfigFileValid())
                return "";
 
        QDomNode configNode = mConfigureDoc.elementsByTagName(CONFIG_TAG).at(0);
        QString retval = configNode.toElement().attribute(CLINICAL_APP_ATTRIBUTE);
        return retval;
}
 
QString ConfigurationFileParser::getTrackingSystemImplementation()
{
        QString retval;
 
        QDomNodeList trackingsystemImplementationNodes = mConfigureDoc.elementsByTagName(CONFIG_TRACKINGSYSTEMIMPLEMENTATION_TAG);
        for (int i = 0; i < trackingsystemImplementationNodes.count(); ++i)
        {
                retval = trackingsystemImplementationNodes.at(i).toElement().attribute(TYPE_ATTRIBUTE);
        }
 
        if (trackingsystemImplementationNodes.count() == 0)
        {
                //CX_LOG_DEBUG() << "Cannot find " << CONFIG_TRACKINGSYSTEMIMPLEMENTATION_TAG << " tag. Selecting " << TRACKING_SYSTEM_IMPLEMENTATION_IGSTK;
                retval = TRACKING_SYSTEM_IMPLEMENTATION_IGSTK;//Revert to igstk implementation for old config files
        }
        else if(trackingsystemImplementationNodes.count() > 1)
        {
                CX_LOG_ERROR() << "ConfigurationFileParser::getTrackingSystemImplementation(): Config file: " << mConfigurationFilePath
                                                                         << " has more the one tracking system implementation. Only one is currently supported.";
        }
 
        return retval;
}
 
std::vector<ToolFileParser::TrackerInternalStructure> ConfigurationFileParser::getTrackers()
{
    std::vector<ToolFileParser::TrackerInternalStructure> retval;
 
        if (!this->isConfigFileValid())
                return retval;
 
        QDomNodeList trackerNodes = mConfigureDoc.elementsByTagName(CONFIG_TRACKER_TAG);
        for (int i = 0; i < trackerNodes.count(); ++i)
        {
        ToolFileParser::TrackerInternalStructure internalStructure;
                QString trackerType = trackerNodes.at(i).toElement().attribute(TYPE_ATTRIBUTE);
                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(CONFIG_TRACKER_TOOL_FILE);
        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(CONFIG_TRACKER_TOOL_FILE);
        for (int i = 0; i < toolFileNodes.count(); ++i)
        {
                QString reference = toolFileNodes.at(i).toElement().attribute(REFERENCE_ATTRIBUTE);
                if (reference.contains("yes", Qt::CaseInsensitive))
                {
//      std::cout << "Found yes..." << std::endl;
                        retval = this->getAbsoluteToolFilePath(toolFileNodes.at(i).toElement());
                }
        }
        return retval;
}
 
std::vector<ConfigurationFileParser::ToolStructure> ConfigurationFileParser::getToolListWithMetaInformation()
{
        std::vector<ToolStructure> retval;
 
        if (!this->isConfigFileValid())
                return retval;
        bool applyRefToTools = this->getApplyRefToTools();
 
        QDomNodeList toolFileNodes = mConfigureDoc.elementsByTagName(CONFIG_TRACKER_TOOL_FILE);
        for (int i = 0; i < toolFileNodes.count(); ++i)
        {
                ToolStructure toolStructure;
                toolStructure.mAbsoluteToolFilePath = this->getAbsoluteToolFilePath(toolFileNodes.at(i).toElement());
                toolStructure.mOpenIGTLinkTransformId = toolFileNodes.at(i).toElement().attribute(OPENIGTLINK_TRANSFORM_ID_ATTRIBUTE);
                toolStructure.mOpenIGTLinkImageId = toolFileNodes.at(i).toElement().attribute(OPENIGTLINK_IMAGE_ID_ATTRIBUTE);
                toolStructure.mApplyRefToTool = applyRefToTools;
 
                QString reference = toolFileNodes.at(i).toElement().attribute(REFERENCE_ATTRIBUTE);
                if (reference.contains("yes", Qt::CaseInsensitive))
                        toolStructure.mReference = true;
                else
                        toolStructure.mReference = false;
                retval.push_back(toolStructure);
        }
        return retval;
}
 
QString ConfigurationFileParser::getTemplatesAbsoluteFilePath()
{
        QString retval = DataLocations::getRootConfigPath() + "/tool/TEMPLATE_configuration.xml";
        return retval;
}
 
bool ConfigurationFileParser::getApplyRefToTools()
{
        bool retval = false;
        if (!this->isConfigFileValid())
                return retval;
 
        QDomNodeList trackingsystemImplementationNodes = mConfigureDoc.elementsByTagName(CONFIG_TRACKINGSYSTEMIMPLEMENTATION_TAG);
        for (int i = 0; i < trackingsystemImplementationNodes.count(); ++i)
        {
                QString applyRef = trackingsystemImplementationNodes.at(i).toElement().attribute(OPENIGTLINK_APPLY_REF_TO_TOOLS_ATTRIBUTE);
                if (applyRef.contains("yes", Qt::CaseInsensitive))
                        retval = true;
        }
        //Is it neccesary to check for number of tracking system implementations here?
        //This is done in ConfigurationFileParser::getTrackingSystemImplementation()
        if(trackingsystemImplementationNodes.count() > 1)
        {
                CX_LOG_ERROR() << "ConfigurationFileParser::getApplyRefToTools(): Config file: " << mConfigurationFilePath
                                           << " has more the one tracking system implementation. Only one is currently supported.";
        }
        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(CONFIG_TAG);
        configNode.setAttribute(CLINICAL_APP_ATTRIBUTE, config.mClinical_app);
 
        QDomElement trackingsystemImplementationNode = doc.createElement(CONFIG_TRACKINGSYSTEMIMPLEMENTATION_TAG);
        trackingsystemImplementationNode.setAttribute(TYPE_ATTRIBUTE, config.mTrackingSystemImplementation);
 
        if (config.mTrackingSystemImplementation.contains(TRACKING_SYSTEM_IMPLEMENTATION_IGTLINK, Qt::CaseInsensitive))
                trackingsystemImplementationNode.setAttribute(OPENIGTLINK_APPLY_REF_TO_TOOLS_ATTRIBUTE, (config.mApplyRefToTools ? "yes" : "no"));
 
        configNode.appendChild(trackingsystemImplementationNode);
 
        TrackersAndToolsMap::iterator it1 = config.mTrackersAndTools.begin();
        for (; it1 != config.mTrackersAndTools.end(); ++it1)
        {
                QString trackingSystemName = enum2string(it1->first);
                if(trackingSystemName.isEmpty())
                {
                        CX_LOG_WARNING() << "trackingSystemName is empty.";
                        trackingSystemName="";
                }
                QDomElement trackerTagNode = doc.createElement(CONFIG_TRACKER_TAG);
                trackerTagNode.setAttribute(TYPE_ATTRIBUTE, trackingSystemName);
 
                ToolStructureVector::iterator it2 = it1->second.begin();
                for (; it2 != it1->second.end(); ++it2)
                {
                        QString absoluteToolFilePath = it2->mAbsoluteToolFilePath;
                        QString relativeToolFilePath = convertToRelativeToolFilePath(config.mFileName, absoluteToolFilePath);
 
                        ToolFileParser toolparser(absoluteToolFilePath);
                        QString toolTrackerType = enum2string(toolparser.getTool()->mTrackerType);
 
                        if (!trackingSystemName.contains(enum2string(toolparser.getTool()->mTrackerType), Qt::CaseInsensitive))
                        {
                                reportWarning("When saving configuration, skipping tool " + relativeToolFilePath + " of type "
                                                                                                + toolTrackerType + " because trackingSystemName is set to " + trackingSystemName);
                                continue;
                        }
 
                        QDomElement toolFileNode = doc.createElement(CONFIG_TRACKER_TOOL_FILE);
                        toolFileNode.appendChild(doc.createTextNode(relativeToolFilePath));
                        createToolFileNode(it2, toolFileNode, toolparser);
                        trackerTagNode.appendChild(toolFileNode);
                }
                trackingsystemImplementationNode.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::createToolFileNode(ToolStructureVector::iterator iter, QDomElement &toolFileNode, ToolFileParser &toolparser)
{
        toolFileNode.setAttribute(REFERENCE_ATTRIBUTE, (iter->mReference ? "yes" : "no"));
        //Use OpenIGTLink id values from tool config file if present
        QString transformId = iter->mOpenIGTLinkTransformId;
        QString imageId = iter->mOpenIGTLinkImageId;
        //Otherwise use id values from tool  file
        if(transformId.isEmpty())
                transformId = toolparser.getTool()->mOpenigtlinkTransformId;
        if(imageId.isEmpty())
                imageId = toolparser.getTool()->mOpenigtlinkImageId;
        if(!transformId.isEmpty())
                toolFileNode.setAttribute(OPENIGTLINK_TRANSFORM_ID_ATTRIBUTE, transformId);
        if(!imageId.isEmpty())
                toolFileNode.setAttribute(OPENIGTLINK_IMAGE_ID_ATTRIBUTE, imageId);
}
 
void ConfigurationFileParser::setConfigDocument(QString configAbsoluteFilePath)
{
        QFile configFile(configAbsoluteFilePath);
        if (!configFile.exists())
        {
//    reportDebug("Configfile "+configAbsoluteFilePath+" does not exist.");
                return;
        }
 
        QString errorMessage;
        int errorInLine = 0;
        if (!mConfigureDoc.setContent(&configFile, &errorMessage, &errorInLine))
        {
                reportError("Could not set the xml content of the config file " + configAbsoluteFilePath);
                CX_LOG_ERROR() << "Qt error message: " << errorMessage << " in line: " << errorInLine;
                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(CONFIG_TAG).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;
}
//----------------------------------------------------------------------------------------------------------------------
 
 
//----------------------------------------------------------------------------------------------------------------------
 
}//namespace cx