itkMRCHeaderObject.h

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/*=========================================================================

  Program:   Insight Segmentation & Registration Toolkit
  Module:    $RCSfile: itkMRCHeaderObject.h,v $
  Language:  C++
  Date:      $Date: 2010-06-16 18:23:47 $
  Version:   $Revision: 1.3 $

  Copyright (c) Insight Software Consortium. All rights reserved.
  See ITKCopyright.txt or http://www.itk.org/HTML/Copyright.htm for details.

     This software is distributed WITHOUT ANY WARRANTY; without even
     the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR
     PURPOSE.  See the above copyright notices for more information.

=========================================================================*/

#ifndef __itkMRCHeaderObject_h
#define __itkMRCHeaderObject_h


#include "itkLightObject.h"
#include "itkByteSwapper.h"
#include "itkIntTypes.h"

namespace itk
{

const char * const magicMAP = "MAP ";


class ITK_EXPORT MRCHeaderObject :
  public itk::LightObject
{
public:
  typedef MRCHeaderObject               Self;
  typedef LightObject                   Superclass;
  typedef SmartPointer<Self>            Pointer;
  typedef SmartPointer<const Self>      ConstPointer;


  struct Header
    {

    int32_t mode;

    int32_t nxstart;
    int32_t nystart;
    int32_t nzstart;


    int32_t mx;
    int32_t my;
    int32_t mz;

    float   xlen;
    float   ylen;
    float   zlen;


    float   alpha;
    float   beta;
    float   gamma;


    // These need to be set for proper scaling of
    // non byte data.
    // These two values specify the structure of data in the
    // extended header; their meaning depend on whether the
    // extended header has the Agard format, a series of
    // 4-byte integers then real numbers, or has data
    // produced by SerialEM, a series of short integers.
    // SerialEM stores a float as two shorts, s1 and s2, by:
    // value = (sign of s1)*(|s1|*256 + (|s2| modulo 256))
    // * 2**((sign of s2) * (|s2|/256))

    int16_t   nint;        // Number of integers per section (Agard format) or
                           // number of bytes per section (SerialEM format)
    int16_t   nreal;       // Number of reals per section (Agard format) or
      // flags for which types of short data (SerialEM format):
    // 1 = tilt angle * 100  (2 bytes)
    // 2 = piece coordinates for montage  (6 bytes)
    // 4 = Stage position * 25    (4 bytes)
    // 8 = Magnification / 100 (2 bytes)
    // 16 = Intensity * 25000  (2 bytes)
    // 32 = Exposure dose in e-/A2, a float in 4 bytes
    // 128, 512: Reserved for 4-byte items
    // 64, 256, 1024: Reserved for 2-byte items
    // If the number of bytes implied by these flags does
    // not add up to the value in nint, then nint and nreal
    // are interpreted as ints and reals per section

    int8_t    notused2[28];

    // Explanation of type of data.
    int16_t   idtype;      // ( 0 = mono, 1 = tilt, 2 = tilts, 3 = lina, 4 = lins)
    int16_t   lens;
    int16_t   nd1;         // for idtype = 1, nd1 = axis (1, 2, or 3)
    int16_t   nd2;
    int16_t   vd1;         // vd1 = 100. * tilt increment
    int16_t   vd2;         // vd2 = 100. * starting angle

    // Used to rotate model to match new rotated image.
    float   tiltangles[6];   // 0,1,2 = original:  3,4,5 = current


    // NEW-STYLE MRC image2000 HEADER - IMOD 2.6.20 and above:
    float   xorg;            // Origin of image.  Used to auto translate model
    float   yorg;            // to match a new image that has been translated.
    float   zorg;


    float   rms;

    // ALL HEADERS:
    };

  struct FeiExtendedHeader
    {

    float magnification; 

    };

  enum {MRCHEADER_MODE_UINT8 = 0,
        MRCHEADER_MODE_IN16 = 1,
        MRCHEADER_MODE_FLOAT = 2,
        MRCHEADER_MODE_COMPLEX_INT16 = 3,
        MRCHEADER_MODE_COMPLEX_FLOAT = 4,
        MRCHEADER_MODE_UINT16 = 6,
        MRCHEADER_MODE_RGB_BYTE = 16};

  enum {MRCHEADER_MAP_X = 1,
        MRCHEADER_MAP_Y = 2,
        MRCHEADER_MAP_Z = 3};

public:


  itkNewMacro(Self);


  itkTypeMacro(MRCHeaderObject, LightObject);


  void DeepCopy(ConstPointer h);

  bool SetHeader(const Header *buffer);
  const Header & GetHeader() const;

  bool SetExtendedHeader(const void *buffer);


  size_t GetExtendedHeaderSize(void) const;

  size_t GetHeaderSize(void) const { return sizeof(Header); }

  bool IsOriginalHeaderBigEndian(void) const;

  Header                  m_Header;   // FIXME : This should be private and should have Get/Set Methods.

protected:

  MRCHeaderObject(void);
  ~MRCHeaderObject(void);

  void swapHeader(bool bigEndian);

  void PrintSelf(std::ostream& os, Indent indent) const;

private:
  MRCHeaderObject(const Self&); //purposely not implemented
  void operator=(const Self&); //purposely not implemented

  size_t                  m_ExtendedHeaderSize;
  void                *   m_ExtendedHeader;

  FeiExtendedHeader   *   m_ExtendedFeiHeader;

  bool                    m_BigEndianHeader;

};

} // namespace itk

#endif