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/*
//
// Copyright 2004-2014 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: 4497 $
//
// $LastChangedDate: 2012-08-24 13:46:21 -0700 (Fri, 24 Aug 2012) $
//
// $LastChangedBy: torstenrohlfing $
//
*/
#ifndef __cmtkImageStackDICOM_h_included_
#define __cmtkImageStackDICOM_h_included_
#include <cmtkconfig.h>
#include <IO/cmtkImageFileDICOM.h>
#include <System/cmtkSmartPtr.h>
#include <System/cmtkSmartConstPtr.h>
#include <Base/cmtkUniformVolume.h>
#include <mxml.h>
#include <vector>
namespace
cmtk
{
/** \addtogroup IO */
//@{
/// Class handling a stack of DICOM image files.
class ImageStackDICOM : public std::vector<ImageFileDICOM::SmartConstPtr>
{
public:
/// This class.
typedef ImageStackDICOM Self;
/// Smart pointer to this class.
typedef SmartPointer<Self> SmartPtr;
/// Smart pointer to const object of this class.
typedef SmartConstPointer<Self> SmartConstPtr;
/// Enum type to select DICOM information to be embedded into output images as "description".
typedef enum
{
/// No embedding.
EMBED_NONE = 0,
/// Embed StudyID plus Date.
EMBED_STUDYID_STUDYDATE = 1,
/// Embed patient name.
EMBED_PATIENTNAME = 2,
/// Embed series description.
EMBED_SERIESDESCR = 3
} EmbedInfoEnum;
/// Constructor.
ImageStackDICOM( const Types::Coordinate tolerance = 0 /*!< Tolerance for floating point comparisons, e.g., when testing for uniform pixel/slice spacings.*/ ) : m_Tolerance( tolerance ) {}
/// Add new DICOM image file to this stack.
void AddImageFile( ImageFileDICOM::SmartConstPtr& image );
/// Match new image file against this volume stack.
bool Match ( const ImageFileDICOM& newImage /*!< New image - test whether this belongs with the ones already in this stack.*/,
const Types::Coordinate numericalTolerance = 0, /*!< Numerical comparison tolerance; values with absolute difference less than this threshold are considered equal. */
const bool disableCheckOrientation = false /*!< Flag for disabling the checking of image orientation vectors.*/,
const bool ignoreAcquisitionNumber = false /*!< When this flag is set, the AcquisitionNumber DICOM tag is ignore for matching images*/ ) const;
/// Write XML sidecar file.
void WriteXML( const std::string& name /*!< Sidecar XML file name. */, const cmtk::UniformVolume& volume /*!< Previously written image volume - provides information about coordinate system etc. */,
const bool includeIdentifiers = false /*!< If this is set, protected "identifiers" such as device serial numbers will also be included in the XML output.*/ ) const;
/// Write to image file.
cmtk::UniformVolume::SmartConstPtr WriteImage ( const std::string& name /*!< File name and path for new image.*/, const Self::EmbedInfoEnum embedInfo /*!< Flag for selecting information embedded into image description.*/ ) const;
/// Print stack information.
void print() const;
private:
/// Stored floating point tolerance.
Types::Coordinate m_Tolerance;
/// Assemble slice times vector from current set of slices.
std::vector<double> AssembleSliceTimes() const;
/// Generate custom whitespaces for XML output.
static const char *WhitespaceWriteMiniXML( mxml_node_t*, int where);
};
//@}
} // namespace cmtk
#endif // #ifndef __cmtkImageStackDICOM_h_included_
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