cmtkVolumeFromSlices.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 __cmtkVolumeFromSlices_h_included_
#define __cmtkVolumeFromSlices_h_included_

#include <cmtkconfig.h>

#include <Base/cmtkTypes.h>
#include <Base/cmtkVolume.h>
#include <Base/cmtkUniformVolume.h>
#include <Base/cmtkScalarImage.h>

#include <stdio.h>


#define CMTK_MAX_CALIB_ERROR 1e-5

#define CMTK_MAX_ANGLE_ERROR 1e-3

#define CMTK_MAX_LOCALIZE_ERROR 1e-2


namespace
cmtk
{


class VolumeFromSlices 
{
public:
  VolumeFromSlices() : VolumeDataArray( NULL ) {}

  virtual ~VolumeFromSlices() {}

protected:
  void InitSequence( const ScalarImage* image, const unsigned int numberOfSlices );

  virtual char* AllocDataArray( const int bytesperpixel, const int data_size ) const;

  virtual TypedArray::SmartPtr EncapDataArray( const ScalarDataType dtype, void *const data, const int data_size ) const;
  
  const char* FillPlane ( unsigned int& plane, const ScalarImage* image );

  UniformVolume::SmartPtr FinishVolume( Types::Coordinate& sliceOffset, int& sliceDirection );

  UniformVolume::SmartPtr FinishVolume () 
  {
    Types::Coordinate dummy_c;
    int dummy_i;
    
    return FinishVolume( dummy_c, dummy_i );
  }
  
  virtual UniformVolume::SmartPtr ConstructVolume( const DataGrid::IndexType& Dims, const UniformVolume::CoordinateVectorType& Size, const Types::Coordinate *Points[3], TypedArray::SmartPtr& Data ) const;

  const char* CheckImage ( const int plane, const ScalarImage* image, const unsigned int frame = 0 );

  virtual void HandleError ( const char* message ) const 
  {
    fputs ( message, stderr );
  }
  
private:
  DataGrid::IndexType Dims;

  UniformVolume::CoordinateVectorType Size;

  Types::Coordinate* Points[3];

  unsigned int DataSize;

  char *RawData;

  TypedArray::SmartPtr VolumeDataArray;

  int BytesPerPixel;

  bool SignBit;

  ScalarDataType DataType;

  Types::Coordinate Spacing[2];

  ScalarImage::SpaceVectorType FirstImagePosition;

  ScalarImage::SpaceVectorType ImagePosition;

  ScalarImage::SpaceVectorType ImageOrientation[2];

  int IncX;

  int IncY;

  int BlockSize;

  ScalarImage::SpaceVectorType IncrementVector;

  bool Padding;

  union {
    unsigned char int8;
    unsigned short int16;
    unsigned int int32;
  } PaddingValue;
};


} // namespace cmtk

#endif // #ifndef __cmtkVolumeFromSlices_h_included_