itkMRCHeaderObject.h

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/*=========================================================================
 *
 *  Copyright NumFOCUS
 *
 *  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
 *
 *         https://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:
  ITK_DISALLOW_COPY_AND_MOVE(MRCHeaderObject);

  using Self = MRCHeaderObject;
  using Superclass = LightObject;
  using Pointer = SmartPointer<Self>;
  using ConstPointer = SmartPointer<const Self>;

  struct Header
  {
    int32_t nx; 
    int32_t ny; 
    int32_t nz; 

    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;
 
    int32_t mapc; 
    int32_t mapr; 
    int32_t maps; 
 
    // These need to be set for proper scaling of
    // non byte data.
    float amin;  
    float amax;  
    float amean; 
 
    int16_t ispg;   
    int16_t nsymbt; 
 
    int32_t next;    
    int16_t creatid; 
 
    int8_t notused1[30]; 
 
    // 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;
 
    char cmap[4];  
    char stamp[4]; 
    float rms;
 
    // ALL HEADERS:
    int32_t nlabl;         
    char    label[10][80]; 
  };

  struct FeiExtendedHeader
  {
    float atilt;     
    float btilt;     
    float xstage;    
    float ystage;    
    float zstage;    
    float xshift;    
    float yshift;    
    float defocus;   
    float exptime;   
    float meanint;   
    float tiltaxis;  
    float pixelsize; 
    float magnification;
    char  notused[76]; 
  };

  enum
  {
    MRCHEADER_MODE_UINT8 = 0,
    MRCHEADER_MODE_INT8 = 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);

  itkOverrideGetNameOfClassMacro(MRCHeaderObject);
 
  void
  DeepCopy(ConstPointer h);

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

  bool
  SetExtendedHeader(const void * buffer);

  SizeValueType
  GetExtendedHeaderSize() const;

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

  bool
  IsOriginalHeaderBigEndian() const;

  Header m_Header{}; // FIXME : This should be private and
                     // should have Get/Set Methods.
 
protected:
  MRCHeaderObject();
  ~MRCHeaderObject() override;

  void
  swapHeader(bool bigEndian);

  void
  PrintSelf(std::ostream & os, Indent indent) const override;
 
private:
  SizeValueType m_ExtendedHeaderSize{ 0 };
  void *        m_ExtendedHeader{ nullptr };
 
  FeiExtendedHeader * m_ExtendedFeiHeader{ nullptr };
 
  bool m_BigEndianHeader{};
};
} // namespace itk
 
#endif