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/*
//
// Copyright 2004-2012, 2013 SRI International
//
// Copyright 1997-2009 Torsten Rohlfing
//
// This file is part of the Computational Morphometry Toolkit.
//
// http://www.nitrc.org/projects/cmtk/
//
// The Computational Morphometry Toolkit is free software: you can
// redistribute it and/or modify it under the terms of the GNU General Public
// License as published by the Free Software Foundation, either version 3 of
// the License, or (at your option) any later version.
//
// The Computational Morphometry Toolkit is distributed in the hope that it
// will be useful, but WITHOUT ANY WARRANTY; without even the implied
// warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
// GNU General Public License for more details.
//
// You should have received a copy of the GNU General Public License along
// with the Computational Morphometry Toolkit. If not, see
// <http://www.gnu.org/licenses/>.
//
// $Revision: 5436 $
//
// $LastChangedDate: 2018-12-10 19:01:20 -0800 (Mon, 10 Dec 2018) $
//
// $LastChangedBy: torstenrohlfing $
//
*/
#ifndef __cmtkDICOM_h_included_
#define __cmtkDICOM_h_included_
#include <cmtkconfig.h>
#include <Base/cmtkScalarImage.h>
#include <dcmtk/dcmdata/dcdeftag.h>
#include <dcmtk/dcmimgle/didocu.h>
#include <dcmtk/dcmimgle/diutils.h>
#include <memory>
namespace
cmtk
{
/** \addtogroup IO */
//@{
/** Reader/writer class for DICOM images.
*/
class DICOM
{
public:
/// This class.
typedef DICOM Self;
/// Default constructor.
DICOM() : m_Dataset( NULL ) {}
/// Read file constructor.
DICOM( const std::string& path ) { this->InitFromFile( path ); }
/// Read object from DICOM file.
void InitFromFile( const std::string& path );
/// Get image dimensions (number of pixels per axis).
const FixedVector<3,int> GetDims() const;
/// Get image pixel size.
const FixedVector<3,double> GetPixelSize() const;
/// Get image origin in scanner coordinates.
const FixedVector<3,double> GetImageOrigin() const;
/// Get image orientation of the i and j grid axes.
const FixedArray< 2, FixedVector<3,double> > GetImageOrientation() const;
/** Get pixel data array.
* The pixel data type is determined automatically based on bits allocated and signed vs. unsigned representation.
*
* If the RescaleSlope or RescaleIntercept tags are present, intensity rescaling is applied.
*
* If a padding value is defined in the DICOM file, this value is also set as padding in the output array.
*
*\warning As a side effect, this function releases the pixel data array pointer from the DICOM object, i.e.,
* this function can only be called ONCE for each object.
*/
TypedArray::SmartPtr GetPixelDataArray( const size_t pixelDataLength );
/// Demosaic (if necessary) the image and return slice normal vector.
const FixedVector<3,double> DemosaicAndGetNormal( const FixedArray< 2, FixedVector<3,double> >& imageOrientation /*!< Image orientation vectors (read-only, for default normal computation)*/,
const FixedVector<3,Types::Coordinate>& deltas /*!< Pixel size - this is needed for computing image origin coordinates from image center location */,
FixedVector<3,int>& dims /*!< Image dimensions - these may be modified if the image is a mosaic */,
TypedArray::SmartPtr& pixelDataArray /*!< Pixel data array - a new array will be returned if the image is a mosaic.*/,
FixedVector<3,double>& imageOrigin /*!< True image origin from CSA header if this is a mosaic file. */);
/// Get const DICOM dataset.
const DcmDataset& Dataset() const
{
return *(this->m_Dataset);
}
/// Get DICOM dataset.
DcmDataset& Dataset()
{
return *(this->m_Dataset);
}
/// Get const DICOM document.
const DiDocument& Document() const
{
return *(this->m_Document);
}
/// Get DICOM document.
DiDocument& Document()
{
return *(this->m_Document);
}
/** Read ScalarImage from DICOM file.
*/
static ScalarImage* Read( const char *path );
private:
/// Path of this DICOM file.
std::string m_Path;
/// Pointer to the DICOM dataset object
DcmDataset* m_Dataset;
/// Pointer to the DICOM document object
std::auto_ptr<DiDocument> m_Document;
/// Parse private Siemens CSA data.
void ParseSiemensCSA( const DcmTagKey& tagKey /*!< DCM tag with the Siemens CSA header data */,
int& unmosaicImageCols /*!< Return demosaiced image columns */,
int& unmosaicImageRows /*!< Return demosaiced image rows */,
int& slices /*!< Return demosaiced image slices */,
FixedVector<3,double>& sliceNormal /*!< Return demosaiced image slice normal */,
FixedVector<3,double>& imageOrigin /*!< Return demosaiced image origin */ );
};
//@}
} // namespace cmtk
#endif // #ifndef __cmtkDICOM_h_included_
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