cxDataReaderWriter.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.

THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" 
AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE 
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#include "cxDataReaderWriter.h"

#include <sstream>
#include <vtkImageData.h>
#include <vtkMetaImageReader.h>
#include <vtkSmartPointer.h>
#include <vtkMetaImageWriter.h>

#include <vtkPolyData.h>
#include <vtkPolyDataReader.h>
#include <vtkXMLPolyDataReader.h>
#include <vtkPolyDataWriter.h>
#include <vtkSTLReader.h>
#include <vtkImageChangeInformation.h>
#include "vtkMINCImageReader.h"
#include "vtkTransform.h"
#include "vtkCommand.h"
#include <vtkPNGReader.h>
#include <vtkNIFTIImageReader.h>
#include <vtkNIFTIImageHeader.h>

#include <QtCore>
#include <QDomDocument>
#include <QFileInfo>
#include <QFile>
#include <QTextStream>
#include <QDir>

#include "cxTransform3D.h"
#include "cxRegistrationTransform.h"
#include "cxLogger.h"
#include "cxTypeConversions.h"
#include "cxUtilHelpers.h"
#include "cxVideoSource.h"
#include "cxCustomMetaImage.h"
#include "cxConfig.h"

#include "cxImageLUT2D.h"
#include "cxImageTF3D.h"
#include "cxErrorObserver.h"


typedef vtkSmartPointer<class vtkPNGReader> vtkPNGReaderPtr;

namespace cx
{

//-----
vtkImageDataPtr MetaImageReader::loadVtkImageData(QString filename)
{
        vtkMetaImageReaderPtr reader = vtkMetaImageReaderPtr::New();
        reader->SetFileName(cstring_cast(filename));
        reader->ReleaseDataFlagOn();

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

        vtkImageChangeInformationPtr zeroer = vtkImageChangeInformationPtr::New();
        zeroer->SetInputConnection(reader->GetOutputPort());
        zeroer->SetOutputOrigin(0, 0, 0);
        zeroer->Update();
        return zeroer->GetOutput();
}

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

bool MetaImageReader::readInto(ImagePtr image, QString filename)
{
        if (!image)
                return false;

        CustomMetaImagePtr customReader = CustomMetaImage::create(filename);
        Transform3D rMd = customReader->readTransform();

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

        image->setVtkImageData(raw);
        image->get_rMd_History()->setRegistration(rMd);
        image->setModality(customReader->readModality());
        image->setImageType(customReader->readImageType());

        bool ok1 = true;
        bool ok2 = true;
        double level = customReader->readKey("WindowLevel").toDouble(&ok1);
        double window = customReader->readKey("WindowWidth").toDouble(&ok2);

        if (ok1 && ok2)
        {
                image->setInitialWindowLevel(window, level);
                image->resetTransferFunctions();
        }

        return true;
}

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

void MetaImageReader::saveImage(ImagePtr image, const QString& filename)
{
        vtkMetaImageWriterPtr writer = vtkMetaImageWriterPtr::New();
        writer->SetInputData(image->getBaseVtkImageData());
        writer->SetFileDimensionality(3);
        writer->SetFileName(cstring_cast(filename));
        QDir().mkpath(QFileInfo(filename).path());

//      std::cout << "SAVING MHD COMPRESSED " << filename << std::endl;
//      writer->SetCompression(true);
        writer->SetCompression(false);
//      writer->Update(); // caused writing of (null).0 files - not necessary
        writer->Write();

        writer = 0;

        CustomMetaImagePtr customReader = CustomMetaImage::create(filename);
        customReader->setTransform(image->get_rMd());
        customReader->setModality(image->getModality());
        customReader->setImageType(image->getImageType());
        customReader->setKey("WindowLevel", qstring_cast(image->getInitialWindowLevel()));
        customReader->setKey("WindowWidth", qstring_cast(image->getInitialWindowWidth()));
        customReader->setKey("Creator", QString("CustusX_%1").arg(CustusX_VERSION_STRING));
}


NIfTIReader::NIfTIReader() :
        DataReader()
{
        sform_matrix = vtkMatrix4x4Ptr::New();
}

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);
}

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

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

bool PNGImageReader::readInto(ImagePtr image, QString filename)
{
        if (!image)
                return false;
        vtkImageDataPtr raw = this->loadVtkImageData(filename);
        if(!raw)
                return false;
        image->setVtkImageData(raw);
        return true;
}

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

vtkImageDataPtr PNGImageReader::loadVtkImageData(QString filename)
{
        vtkPNGReaderPtr pngReader = vtkPNGReaderPtr::New();
        pngReader->SetFileName(filename.toStdString().c_str());
        pngReader->Update();
        return pngReader->GetOutput();
}


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

bool PolyDataMeshReader::readInto(MeshPtr mesh, QString filename)
{
        if (!mesh)
                return false;
        vtkPolyDataPtr raw = this->loadVtkPolyData(filename);
        if(!raw)
                return false;
        mesh->setVtkPolyData(raw);
        return true;
}
//-----
vtkPolyDataPtr PolyDataMeshReader::loadVtkPolyData(QString fileName)
{
        vtkPolyDataReaderPtr reader = vtkPolyDataReaderPtr::New();
        reader->SetFileName(cstring_cast(fileName));

        if (!ErrorObserver::checkedRead(reader, fileName))
                return vtkPolyDataPtr();

        vtkPolyDataPtr polyData = reader->GetOutput();
        return polyData;
}

DataPtr PolyDataMeshReader::load(const QString& uid, const QString& filename)
{
        MeshPtr mesh(new Mesh(uid));
        this->readInto(mesh, filename);
        return mesh;
}



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

bool XMLPolyDataMeshReader::readInto(MeshPtr mesh, QString filename)
{
        if (!mesh)
                return false;
        vtkPolyDataPtr raw = this->loadVtkPolyData(filename);
        if(!raw)
                return false;
        mesh->setVtkPolyData(raw);
        return true;
}
//-----
vtkPolyDataPtr XMLPolyDataMeshReader::loadVtkPolyData(QString fileName)
{
        vtkXMLPolyDataReaderPtr reader = vtkXMLPolyDataReaderPtr::New();
        reader->SetFileName(cstring_cast(fileName));

        if (!ErrorObserver::checkedRead(reader, fileName))
                return vtkPolyDataPtr();

        vtkPolyDataPtr polyData = reader->GetOutput();
        return polyData;
}

DataPtr XMLPolyDataMeshReader::load(const QString& uid, const QString& filename)
{
        MeshPtr mesh(new Mesh(uid));
        this->readInto(mesh, filename);
        return mesh;
}



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

bool StlMeshReader::readInto(MeshPtr mesh, QString filename)
{
        if (!mesh)
                return false;
        vtkPolyDataPtr raw = this->loadVtkPolyData(filename);
        if(!raw)
                return false;
        mesh->setVtkPolyData(raw);
        return true;
}


vtkPolyDataPtr StlMeshReader::loadVtkPolyData(QString fileName)
{
        vtkSTLReaderPtr reader = vtkSTLReaderPtr::New();
        reader->SetFileName(cstring_cast(fileName));

        if (!ErrorObserver::checkedRead(reader, fileName))
                return vtkPolyDataPtr();

        vtkPolyDataPtr polyData = reader->GetOutput();
        return polyData;
}

DataPtr StlMeshReader::load(const QString& uid, const QString& filename)
{
        MeshPtr mesh(new Mesh(uid));
        this->readInto(mesh, filename);
        return mesh;
}



DataReaderWriter::DataReaderWriter()
{
        mDataReaders.insert(DataReaderPtr(new MetaImageReader()));
        mDataReaders.insert(DataReaderPtr(new NIfTIReader()));
        mDataReaders.insert(DataReaderPtr(new PolyDataMeshReader()));
        mDataReaders.insert(DataReaderPtr(new XMLPolyDataMeshReader()));
        mDataReaders.insert(DataReaderPtr(new StlMeshReader()));
        mDataReaders.insert(DataReaderPtr(new PNGImageReader()));
}

DataReaderPtr DataReaderWriter::findReader(const QString& path, const QString& type)
{
        for (DataReadersType::iterator iter = mDataReaders.begin(); iter != mDataReaders.end(); ++iter)
        {
                if ((*iter)->canLoad(type, path))
                        return *iter;
        }
        return DataReaderPtr();
}

vtkImageDataPtr DataReaderWriter::loadVtkImageData(QString filename)
{
        DataReaderPtr reader = this->findReader(filename);
        if (reader)
                return reader->loadVtkImageData(filename);
        return vtkImageDataPtr();
}

vtkPolyDataPtr DataReaderWriter::loadVtkPolyData(QString filename)
{
        DataReaderPtr reader = this->findReader(filename);
        if (reader)
                return reader->loadVtkPolyData(filename);
        return vtkPolyDataPtr();
}

QString DataReaderWriter::findDataTypeFromFile(QString filename)
{
        DataReaderPtr reader = this->findReader(filename);
        if (reader)
                return reader->canLoadDataType();
        return "";
}

void DataReaderWriter::readInto(DataPtr data, QString path)
{
        DataReaderPtr reader = this->findReader(path, data->getType());
        if (reader)
                reader->readInto(data, path);

        if(data)
        {
                QFileInfo fileInfo(qstring_cast(path));
                data->setName(changeExtension(fileInfo.fileName(), ""));
                data->setFilename(path); // need path even when not set explicitly: nice for testing
        }

}




} // namespace cx