cxPatientData.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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   this list of conditions and the following disclaimer in the documentation 
   and/or other materials provided with the distribution.

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   may be used to endorse or promote products derived from this software 
   without specific prior written permission.

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AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE 
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#include "cxPatientData.h"

#include <QDomDocument>
#include <QFile>
#include <QDir>
#include <QTimer>
#include <QTextStream>
#include <QApplication>

#include "cxTime.h"
#include "cxLogger.h"
#include "cxUtilHelpers.h"
#include "cxCustomMetaImage.h"
#include "cxMesh.h"

#include "cxSettings.h"

#include <vtkPolyData.h>
#include <vtkPointData.h>

#include "cxDataManager.h"
#include "cxImage.h"
#include "cxTypeConversions.h"
#include "cxConfig.h"
#include "cxSessionStorageService.h"
#include "cxXMLNodeWrapper.h"
#include "cxDataFactory.h"

namespace cx
{


PatientData::PatientData(DataServicePtr dataManager, SessionStorageServicePtr session) :
        mDataManager(dataManager),
        mSession(session)
{
        connect(mSession.get(), &SessionStorageService::sessionChanged, this, &PatientData::patientChanged);
        connect(mSession.get(), &SessionStorageService::cleared, this, &PatientData::onCleared);
//      connect(mSession.get(), &SessionStorageService::cleared, this, &PatientData::cleared);
        connect(mSession.get(), &SessionStorageService::isLoading, this, &PatientData::onSessionLoad);
        connect(mSession.get(), &SessionStorageService::isSaving, this, &PatientData::onSessionSave);
}

PatientData::~PatientData()
{}

QString PatientData::getActivePatientFolder() const
{
        return mSession->getRootFolder();
}

bool PatientData::isPatientValid() const
{
        return mSession->isValid();
}

void PatientData::onCleared()
{
        mDataManager->clear();
}

void PatientData::onSessionLoad(QDomElement &node)
{
        XMLNodeParser root(node);
        QDomElement dataManagerNode = root.descend("managers/datamanager").node().toElement();

        if (!dataManagerNode.isNull())
                mDataManager->parseXml(dataManagerNode, mSession->getRootFolder());
}

void PatientData::onSessionSave(QDomElement &node)
{
        XMLNodeAdder root(node);
        QDomElement managerNode = root.descend("managers").node().toElement();

        mDataManager->addXml(managerNode);

        // save position transforms into the mhd files.
        // This hack ensures data files can be used in external programs without an explicit export.
        DataManager::ImagesMap images = mDataManager->getImages();
        for (DataManager::ImagesMap::iterator iter = images.begin(); iter != images.end(); ++iter)
        {
                CustomMetaImagePtr customReader = CustomMetaImage::create(
                                                mSession->getRootFolder() + "/" + iter->second->getFilename());
                customReader->setTransform(iter->second->get_rMd());
        }

}

void PatientData::autoSave()
{
        if (settings()->value("Automation/autoSave").toBool())
                mSession->save();
}

void PatientData::exportPatient(bool niftiFormat)
{
        QString targetFolder = mSession->getRootFolder() + "/Export/"
                                        + QDateTime::currentDateTime().toString(timestampSecondsFormat());

        DataManager::ImagesMap images = mDataManager->getImages();
        for (DataManager::ImagesMap::iterator iter = images.begin(); iter != images.end(); ++iter)
        {
                iter->second->save(targetFolder);
        }

        DataManager::MeshMap meshes = mDataManager->getMeshes();
        for (DataManager::MeshMap::iterator iter = meshes.begin(); iter != meshes.end(); ++iter)
        {
                MeshPtr mesh = iter->second;

                Transform3D rMd = mesh->get_rMd();
                if (niftiFormat)
                {
                        rMd = rMd * createTransformRotateZ(M_PI); // convert back to NIFTI format
                        report("Nifti export: rotated data " + mesh->getName() + " 180* around Z-axis.");
                }

                vtkPolyDataPtr poly = mesh->getTransformedPolyData(rMd);
                // create a copy with the SAME UID as the original. Do not load this one into the datamanager!
                mesh = mDataManager->getDataFactory()->createSpecific<Mesh>(mesh->getUid(), mesh->getName());
                mesh->setVtkPolyData(poly);
                mesh->setFilename("Images");
                mesh->save(targetFolder);
        }

        report("Exported patient data to " + targetFolder + ".");
}

DataPtr PatientData::importData(QString fileName, QString &infoText)
{
        if (fileName.isEmpty())
        {
                QString text = "Import canceled";
                report(text);
                infoText = "<font color=red>" + text + "</font>";
                return DataPtr();
        }

        QFileInfo fileInfo(fileName);
        QString strippedFilename = changeExtension(fileInfo.fileName(), "");
        QString uid = strippedFilename + "_" + QDateTime::currentDateTime().toString(timestampSecondsFormat());

        if (mDataManager->getData(uid))
        {
                QString text = "Data with uid " + uid + " already exists. Import canceled.";
                reportWarning(text);
                infoText = "<font color=red>" + text + "</font>";
                return DataPtr();
        }

        // Read files before copy
        DataPtr data = mDataManager->loadData(uid, fileName);
        if (!data)
        {
                QString text = "Error with data file: " + fileName + " Import canceled.";
                reportWarning(text);
                infoText = "<font color=red>" + text + "</font>";
                return DataPtr();
        }
        data->setAcquisitionTime(QDateTime::currentDateTime());

        data->save(mSession->getRootFolder());

        // remove redundant line breaks
        infoText = infoText.split("<br>", QString::SkipEmptyParts).join("<br>");

        return data;
}

void PatientData::removeData(QString uid)
{
        mDataManager->removeData(uid, this->getActivePatientFolder());
}

} // namespace cx