cxDicomImageReader.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 
IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE 
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=========================================================================*/

#include "cxDicomImageReader.h"

#include "cxVolumeHelpers.h"
#include "dcvrpn.h"
#include "cxLogger.h"

namespace cx
{

DicomImageReaderPtr DicomImageReader::createFromFile(QString filename)
{
        DicomImageReaderPtr retval(new DicomImageReader);
        if (retval->loadFile(filename))
                return retval;
        else
                return DicomImageReaderPtr();
}

DicomImageReader::DicomImageReader() :
        mDataset(NULL)
{
}

bool DicomImageReader::loadFile(QString filename)
{
        mFilename = filename;
        OFCondition status = mFileFormat.loadFile(filename.toLatin1().data());
        if( !status.good() )
        {
                return false;
        }

        mDataset = mFileFormat.getDataset();
        return true;
}

ctkDICOMItemPtr DicomImageReader::item() const
{
        return this->wrapInCTK(mDataset);
}

double DicomImageReader::getDouble(const DcmTagKey& tag, const unsigned long pos, const OFBool searchIntoSub) const
{
        double retval = 0;
        OFCondition condition;
        condition = mDataset->findAndGetFloat64(tag, retval, pos, searchIntoSub);
        if (!condition.good())
        {
                QString tagName = this->item()->TagDescription(tag);
                this->error(QString("Failed to get tag %1/%2").arg(tagName).arg(pos));
        }
        return retval;
}

DicomImageReader::WindowLevel DicomImageReader::getWindowLevel() const
{
        WindowLevel retval;
        retval.center = this->getDouble(DCM_WindowCenter, 0, OFTrue);
        retval.width = this->getDouble(DCM_WindowWidth, 0, OFTrue);
        return retval;
}

bool DicomImageReader::isLocalizerImage() const
{
        //DICOM standard PS3.3 section C.7.6.1.1.2 Image Type
        //http://dicom.nema.org/medical/dicom/current/output/html/part03.html#sect_C.7.6.1.1.2
        bool retval = false;

        OFCondition condition;
        OFString value;
        condition = mDataset->findAndGetOFString(DCM_ImageType, value, 2, OFTrue);
        if (condition.good())
        {
                QString imageSpesialization(value.c_str());
                if (imageSpesialization.compare("LOCALIZER", Qt::CaseSensitive) == 0)
                        retval = true;
        }
        return retval;
}

int DicomImageReader::getNumberOfFrames() const
{
        int numberOfFrames = this->item()->GetElementAsInteger(DCM_NumberOfFrames);
        if (numberOfFrames==0)
        {
                unsigned short rows = 0;
                unsigned short columns = 0;
                mDataset->findAndGetUint16(DCM_Rows, rows, 0, OFTrue);
                mDataset->findAndGetUint16(DCM_Columns, columns, 0, OFTrue);
                if (rows*columns > 0)
                        numberOfFrames = 1; // seems like we have a 2D image
        }
        return numberOfFrames;
}

Transform3D DicomImageReader::getImageTransformPatient() const
{
        Vector3D pos;
        Vector3D e_x;
        Vector3D e_y;

        for (int i=0; i<3; ++i)
        {
                OFCondition condition;
                e_x[i] = this->getDouble(DCM_ImageOrientationPatient, i, OFTrue);
                e_y[i] = this->getDouble(DCM_ImageOrientationPatient, i+3, OFTrue);
                pos[i] = this->getDouble(DCM_ImagePositionPatient, i, OFTrue);
        }

        Transform3D retval = cx::createTransformIJC(e_x, e_y, pos);
        return retval;
}

ctkDICOMItemPtr DicomImageReader::wrapInCTK(DcmItem* item) const
{
        if (!item)
                return ctkDICOMItemPtr();
        ctkDICOMItemPtr retval(new ctkDICOMItem);
        retval->InitializeFromItem(item);
        return retval;
}

void DicomImageReader::error(QString message) const
{
        reportError(QString("Dicom convert: [%1] in %2").arg(message).arg(mFilename));
}

vtkImageDataPtr DicomImageReader::createVtkImageData()
{
        DicomImage dicomImage(mFilename.toLatin1().data()); //, CIF_MayDetachPixelData );
        const DiPixel *pixels = dicomImage.getInterData();
        if (!pixels)
        {
                this->error("Found no pixel data");
                return vtkImageDataPtr();
        }

        vtkImageDataPtr data = vtkImageDataPtr::New();

        data->SetSpacing(this->getSpacing().data());

        Eigen::Array3i dim = this->getDim(dicomImage);
        data->SetExtent(0, dim[0]-1, 0, dim[1]-1, 0, dim[2]-1);

        int samplesPerPixel = pixels->getPlanes();
        int scalarSize = dim.prod() * samplesPerPixel;
        int pixelDepth = dicomImage.getDepth();

        switch (pixels->getRepresentation())
        {
        case EPR_Uint8:
//              std::cout << "  VTK_UNSIGNED_CHAR" << std::endl;
                data->AllocateScalars(VTK_UNSIGNED_CHAR, samplesPerPixel);
                break;
        case EPR_Uint16:
//              std::cout << "  VTK_UNSIGNED_SHORT" << std::endl;
                data->AllocateScalars(VTK_UNSIGNED_SHORT, samplesPerPixel);
                break;
        case EPR_Uint32:
                this->error("DICOM EPR_Uint32 not supported");
                return vtkImageDataPtr();
                break;
        case EPR_Sint8:
//              std::cout << "  VTK_CHAR" << std::endl;
                data->AllocateScalars(VTK_CHAR, samplesPerPixel);
                break;
        case EPR_Sint16:
//              std::cout << "  VTK_SHORT" << std::endl;
                data->AllocateScalars(VTK_SHORT, samplesPerPixel);
                break;
        case EPR_Sint32:
                this->error("DICOM EPR_Sint32 not supported");
                return vtkImageDataPtr();
                break;
        }

        int bytesPerPixel = data->GetScalarSize() * samplesPerPixel;

        memcpy(data->GetScalarPointer(), pixels->getData(), pixels->getCount()*bytesPerPixel);
        if (pixels->getCount()!=scalarSize)
                this->error("Mismatch in pixel counts");
        setDeepModified(data);
        return data;
}

Eigen::Array3d DicomImageReader::getSpacing() const
{
        Eigen::Array3d spacing;
        spacing[0] = this->getDouble(DCM_PixelSpacing, 0, OFTrue);
        spacing[1] = this->getDouble(DCM_PixelSpacing, 1, OFTrue);
        spacing[2] = this->getDouble(DCM_SliceThickness, 0, OFTrue);
//      std::cout << "  spacing: " << spacing << std::endl;
        return spacing;
}

Eigen::Array3i DicomImageReader::getDim(const DicomImage& dicomImage) const
{
        Eigen::Array3i dim;
        dim[0] = dicomImage.getWidth();
        dim[1] = dicomImage.getHeight();
        dim[2] = dicomImage.getFrameCount();
        return dim;
}

QString DicomImageReader::getPatientName() const
{
        QString rawName = this->item()->GetElementAsString(DCM_PatientName);
        return this->formatPatientName(rawName);
}

QString DicomImageReader::formatPatientName(QString rawName) const
{
        // ripped from ctkDICOMModel

        OFString dicomName = rawName.toStdString().c_str();
        OFString formattedName;
        OFString lastName, firstName, middleName, namePrefix, nameSuffix;
        OFCondition l_error = DcmPersonName::getNameComponentsFromString(dicomName,
                                                                                                                                         lastName, firstName, middleName, namePrefix, nameSuffix);
        if (l_error.good())
        {
                formattedName.clear();
                /* concatenate name components per this convention
   * Last, First Middle, Suffix (Prefix)
   * */
                if (!lastName.empty())
                {
                        formattedName += lastName;
                        if ( !(firstName.empty() && middleName.empty()) )
                        {
                                formattedName += ",";
                        }
                }
                if (!firstName.empty())
                {
                        formattedName += " ";
                        formattedName += firstName;
                }
                if (!middleName.empty())
                {
                        formattedName += " ";
                        formattedName += middleName;
                }
                if (!nameSuffix.empty())
                {
                        formattedName += ", ";
                        formattedName += nameSuffix;
                }
                if (!namePrefix.empty())
                {
                        formattedName += " (";
                        formattedName += namePrefix;
                        formattedName += ")";
                }
        }
        return QString(formattedName.c_str());
}


} // namespace cx