cmtkStudy.h

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/*
//
//  Copyright 1997-2009 Torsten Rohlfing
//
//  Copyright 2004-2011 SRI International
//
//  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: 2752 $
//
//  $LastChangedDate: 2011-01-17 11:33:31 -0800 (Mon, 17 Jan 2011) $
//
//  $LastChangedBy: torstenrohlfing $
//
*/

#ifndef __cmtkStudy_h_included_
#define __cmtkStudy_h_included_

#include <cmtkconfig.h>

#include <Base/cmtkMacros.h>
#include <Base/cmtkVolume.h>
#include <Base/cmtkUniformVolume.h>
#include <Base/cmtkAffineXform.h>
#include <Base/cmtkWarpXform.h>
#include <Base/cmtkLandmarkList.h>
#include <Base/cmtkSegmentationLabel.h>

#include <IO/cmtkFileFormat.h>

namespace
cmtk
{


enum
{
  PALETTE_GRAY = 0,
  PALETTE_RED = 1,
  PALETTE_GREEN = 2,
  PALETTE_BLUE = 3,
  PALETTE_RAINBOW = 4,
  PALETTE_LABELS = 5
};

class Study
{
  cmtkGetSetMacroString(FileSystemPath);

  cmtkGetSetMacroString(Name);

  cmtkGetSetMacroString(Description);

  cmtkGetSetMacroString(Modality);

  cmtkGetSetMacro(UniformVolume::SmartPtr,Volume);

  cmtkGetSetMacro(LandmarkList::SmartPtr,LandmarkList);

  DataGrid::IndexType m_Dims;

  cmtkGetSetMacro3Array(Types::Coordinate,Calibration);

  cmtkGetSetMacro(Types::DataItem,MinimumValue);

  cmtkGetSetMacro(Types::DataItem,MaximumValue);

  cmtkGetSetMacro(bool,Padding);

  cmtkGetSetMacro(Types::DataItem,PaddingValue);

  cmtkGetSetMacro(bool,HaveUserColorMap);

  cmtkGetSetMacro(char,StandardColormap);

  cmtkGetSetMacro(bool,ReverseColormap);

  cmtkGetSetMacro(Types::DataItem,Black);

  cmtkGetSetMacro(Types::DataItem,White);

  cmtkGetSetMacro(double,Gamma);

  cmtkGetSetMacro(unsigned int,DisplayedImageIndex);

  cmtkGetSetMacro(unsigned int,ZoomFactor);

  cmtkGetSetMacro(int,SliceNormal);

public:
  typedef SmartPointer<Study> SmartPtr;

  Study();

  Study( const char* fileSystemPath, const char* name = NULL );

  virtual ~Study();

  virtual void UpdateFromVolume();

  virtual bool ReadVolume( const bool reRead = false, const char* orientation = NULL );

  const char* SetMakeName( const char* name = NULL , const int suffix = 0  );

  static Study* Read( const char* path );

  virtual void CopyColormap( const Study* other );

  void SetFromLabelMap( const SegmentationLabelMap& lblMap ) 
  {
    this->m_HaveUserColorMap = true;
    UserLabelMap = lblMap;
  }

  const SegmentationLabelMap& GetUserLabelMap() const 
  {
    return UserLabelMap; 
  }
  
private:
  SegmentationLabelMap UserLabelMap;
};


} // namespace cmtk

#endif // #ifndef __cmtkStudy_h_included_