cxNIfTIReader.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 "cxNIfTIReader.h"

#include <QFileInfo>
#include "vtkNIFTIImageReader.h"
#include "vtkMatrix4x4.h"
#include "vtkImageData.h"
#include "cxRegistrationTransform.h"
#include "cxTypeConversions.h"
#include "cxErrorObserver.h"
#include "cxImage.h"
#include "cxPatientModelService.h"

namespace cx
{

NIfTIReader::NIfTIReader(PatientModelServicePtr patientModelService) :
        FileReaderWriterImplService("NIfTIReader", Image::getTypeName(), "", "nii", patientModelService)
{
        sform_matrix = vtkMatrix4x4Ptr::New();
}

NIfTIReader::~NIfTIReader()
{
}


bool NIfTIReader::readInto(ImagePtr image, QString path)
{
        if (!image)
                return false;

        vtkImageDataPtr raw = this->loadVtkImageData(path);
        if(!raw)
                return false;

        Transform3D rMd(sform_matrix);
        image->setVtkImageData(raw);
        image->get_rMd_History()->setRegistration(rMd);

        return true;
}


bool NIfTIReader::readInto(DataPtr data, QString filename)
{
        return this->readInto(boost::dynamic_pointer_cast<Image>(data), filename);
}

vtkImageDataPtr NIfTIReader::loadVtkImageData(QString filename)
{
        vtkNIFTIImageReaderPtr reader = vtkNIFTIImageReaderPtr::New();
        reader->SetFileName(cstring_cast(filename));
        reader->ReleaseDataFlagOn();
        reader->Update();

        sform_matrix = reader->GetSFormMatrix();

        if (!ErrorObserver::checkedRead(reader, filename))
                return vtkImageDataPtr();

        return reader->GetOutput();
}

bool NIfTIReader::isNull()
{
        return false;
}

QString NIfTIReader::canReadDataType() const
{
        return Image::getTypeName();
}

bool NIfTIReader::canRead(const QString &type, const QString &filename)
{
        return this->canReadInternal(type, filename);
}

DataPtr NIfTIReader::read(const QString &uid, const QString &filename)
{
        ImagePtr image(new Image(uid, vtkImageDataPtr()));
        this->readInto(image, filename);
        return image;
}

std::vector<DataPtr> NIfTIReader::read(const QString &filename)
{
        std::vector<DataPtr> retval;
        ImagePtr image = boost::dynamic_pointer_cast<Image>(this->createData(Image::getTypeName(), filename));

        vtkImageDataPtr raw = this->loadVtkImageData(filename);
        if(!raw)
                return retval;

        Transform3D rMd(sform_matrix);
        image->setVtkImageData(raw);
        image->get_rMd_History()->setRegistration(rMd);


        retval.push_back(image);
        return retval;
}

QString NIfTIReader::canWriteDataType() const
{
        return "";
}

bool NIfTIReader::canWrite(const QString &type, const QString &filename) const
{
        return this->canWriteInternal(type, filename);
}

void NIfTIReader::write(cx::DataPtr data, const QString &filename)
{
}

} //namespace cx