/*
//
//  Copyright 2004-2014, 2022 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 <IO/cmtkImageOperationXMLOptions.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 ImageOperationXMLOptions &outputOptions /*!< Various XML output options that may be set.*/) const;

    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 bool dryRun = false /*!< If this is set, do not actually write the image file. */) 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_
