itkMRCHeaderObject.h

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/*=========================================================================
 *
 *  Copyright Insight Software Consortium
 *
 *  Licensed under the Apache License, Version 2.0 (the "License");
 *  you may not use this file except in compliance with the License.
 *  You may obtain a copy of the License at
 *
 *         http://www.apache.org/licenses/LICENSE-2.0.txt
 *
 *  Unless required by applicable law or agreed to in writing, software
 *  distributed under the License is distributed on an "AS IS" BASIS,
 *  WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
 *  See the License for the specific language governing permissions and
 *  limitations under the License.
 *
 *=========================================================================*/
#ifndef itkMRCHeaderObject_h
#define itkMRCHeaderObject_h
#include "ITKIOMRCExport.h"

#include "itkObjectFactory.h"
#include "itkLightObject.h"
#include "itkIntTypes.h"

namespace itk
{

class ITKIOMRC_EXPORT MRCHeaderObject:
  public 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);

  SizeValueType GetExtendedHeaderSize() const;

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

  bool IsOriginalHeaderBigEndian() const;

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

protected:

  MRCHeaderObject();
  ~MRCHeaderObject();

  void swapHeader(bool bigEndian);

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

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

  SizeValueType m_ExtendedHeaderSize;
  void *        m_ExtendedHeader;

  FeiExtendedHeader *m_ExtendedFeiHeader;

  bool m_BigEndianHeader;
};
} // namespace itk

#endif