imp doc wiki groups imp at salilab.org | contact

ImageHeader.h

Go to the documentation of this file.

/**
 *  \file ImageHeader.h
 *  \brief Header for EM images. Compatible with Spider and Xmipp formats
 *  \author Javier Velazquez-Muriel
 *  Copyright 2007-2010 IMP Inventors. All rights reserved.
*/

#ifndef IMPEM_IMAGE_HEADER_H
#define IMPEM_IMAGE_HEADER_H

#include "em_config.h"
#include "SpiderHeader.h"
#include <IMP/algebra/Matrix2D.h>
#include <IMP/algebra/utility.h>
#include <IMP/algebra/endian.h>
#include <cstdio>
#include <iostream>
#include <fstream>
#include <cstring>

IMPEM_BEGIN_NAMESPACE

// Class to deal with the header of Electron Microscopy images in IMP.
/**
 * (Compatible with Xmipp and Spider formats)
 */
class IMPEMEXPORT ImageHeader
{
public:
  //! Types of initialization of ImageHeader
  typedef enum { IMG_BYTE = 0, IMG_IMPEM  = 1,
                 IMG_INT  = 9, /*IMG_SHORT  = , IMG_UCHAR = ,*/
                 VOL_BYTE = 2,  VOL_IMPEM  = 3,
                 VOL_INT  = 10 , /*VOL_SHORT  = , VOL_UCHAR =, */
                 IMG_FOURIER = -1, VOL_FOURIER = -3
               } img_type;

  //! Constructor.
  ImageHeader() {
    clear();
    header_.fIform=(float)IMG_IMPEM;
  }

  //! Constructor. The type of image can be specified
  ImageHeader(img_type im) {
    clear();
    header_.fIform=(float)im;
  }

  //! Constructor. The type of image can be specified
  ImageHeader(float im) {
    clear();
    header_.fIform=im;
  }

  //! Get the type of image
  float get_image_type() const {
    return header_.fIform;
  }

  //! Set the type of image
  /**
   * param[in] im type of image. Available values:
   * IMG_BYTE = 0, IMG_IMPEM  = 1,IMG_INT  = 9, VOL_BYTE = 2,  VOL_IMPEM  = 3,
   * VOL_INT  = 10 , IMG_FOURIER = -1, VOL_FOURIER = -3
   * \note No check is done for correctness of the value
   */
  //! Set the type of image
  void set_image_type(img_type im) {
    this->set_image_type((float)im);
  }

  //! Set the type of image
  /**
   * param[in] im type of image. Available values:
   */
  void set_image_type(float im) {
    header_.fIform=im;
  }

#ifndef SWIG
  //! Output operator
  friend std::ostream& operator<<(std::ostream& out, const ImageHeader& I) {
    out << "Image type   : ";
    switch ((int) I.header_.fIform) {
    case IMG_BYTE:
      out << "2D Byte image";
      break;
    case IMG_IMPEM:
      out << "2D IMP EM image";
      break;
    case IMG_INT:
      out << "2D INT image";
      break;
    case VOL_BYTE:
      out << "3D Byte volume";
      break;
    case VOL_IMPEM:
      out << "3D IMP EM volume";
      break;
    case VOL_INT:
      out << "3D INT volume";
      break;
    case IMG_FOURIER:
      out << "2D Fourier image";
      break;
    case VOL_FOURIER:
      out << "3D Fourier volume";
      break;
    }
    out << std::endl;
    out << "Reversed     : ";
    if (I.reversed_) {
      out << "TRUE" << std::endl;
    } else {
      out << "FALSE" << std::endl;
    }
    out << "dimensions   : " << I.header_.fNslice << " x "
    << I.header_.fNrow   << " x "  << I.header_.fNcol
    << " (slices x rows x columns) " << std::endl;

    out << "Euler angles (ZYZ convention): " << std::endl;
    out << "  Phi   (rotation around Z axis) = " <<
           I.header_.fPhi << std::endl;
    out << "  Theta (tilt, rotation around new Y axis) = " <<
            I.header_.fTheta << std::endl;
    out << "  Psi   (third rotation around new Z axis) = " <<
            I.header_.fPsi << std::endl;
    out << "Origin Offsets : " << std::endl;
    out << "  Xoff  (origin offset in X-direction) = " <<
            I.header_.fXoff << std::endl;
    out << "  Yoff  (origin offset in Y-direction) = " <<
            I.header_.fYoff << std::endl;
    if (I.header_.fFlag == 1.0f || I.header_.fFlag == 2.0f) {
      out << "  Phi1   = " << I.header_.fPhi1 ;
      out << "  theta1 = " << I.header_.fTheta1 ;
      out << "  Psi1   = " << I.header_.fPsi1 << std::endl;
    }
    if (I.header_.fFlag == 2.0f) {
      out << "  Phi2   = " << I.header_.fPhi2 ;
      out << "  theta2 = " << I.header_.fTheta2 ;
      out << "  Psi2   = " << I.header_.fPsi2 << std::endl;
    }
    out << "Date         : " << I.get_date() << std::endl;
    out << "Time         : " << I.get_time() << std::endl;
    out << "Title        : " << I.get_title() << std::endl;
    out << "Header size  : " << I.get_header_size() << std::endl;
    out << "Weight  : " << I.get_Weight() << std::endl;
    return out;
  }
#endif

  //! Prints a reduced set of information (debugging purposes)
  void print_hard(std::ostream& out) const;

  //! Shows only the projection parameters
  inline void show_projection_params(std::ostream& out) const {
    out << "(Phi,Theta,Psi) = ( " << header_.fPhi << " , " << header_.fTheta
        << " , " << header_.fPsi << " ) " << " (y,x) = ( " << header_.fYoff
        << " , " << header_.fXoff << " ) " <<  std::endl;
  }

  //! Reads the header of a EM image
  // \note reversed is only used in case that the type_check is skipped
  int read(const String filename, bool skip_type_check = false,
           bool force_reversed = false, bool skip_extra_checkings = false);

  //! Reads the header of a EM image from an input file stream
  bool read(std::ifstream& f, bool skip_type_check = false,
            bool force_reversed = false, bool skip_extra_checkings = false);

  //! Writes the header of a EM image
  void write(const String &filename, bool force_reversed = false);

  //! Writes the header of a EM image to an output file stream
  void write(std::ofstream& f, bool force_reversed = false);

  //! Clear header data and sets a consistent header
  void clear();

  //! Sets a consistent header
  void set_header();

  //! Interaction with data
  bool get_reversed() const {
    return reversed_;
  }

  //! Interaction with data
  void set_reversed(bool value) {
    reversed_=value;
  }

  //! get header size
  int get_header_size() const {
    return (int) header_.fNcol *(int) header_.fLabrec * sizeof(float);
  }

  //! Get number of slices
  float get_number_of_slices()  const {
    return header_.fNslice;
  }

  //! Set number of slices
  void set_number_of_slices(float n) {
    header_.fNslice = n;
  }

  //! Get number of rows
  float get_number_of_rows() const {
    return header_.fNrow;
  }

  //! Set number of rows
  void set_number_of_rows(float n) {
    header_.fNrow = n;
  }

  //! Get number columns
  float get_number_of_columns() const {
    return header_.fNcol;
  }

  //! Get number columns
  void set_number_of_columns(float n) {
    header_.fNcol = n;
  }

  //! get rotation angle. (Xmipp compatibility)
  float get_old_rot() const {
    return header_.fAngle1;
  }

  //! set rotation angle. (Xmipp compatibility)
  void set_old_rot(float value) {
    header_.fAngle1= value;
  }

  //! get rotation angle. (Xmipp compatibility)
  float get_fAngle1() const {
    return header_.fAngle1;
  }

  //! set rotation angle. (Xmipp compatibility)
  void set_fAngle1(float value) {
    header_.fAngle1= value;
  }

  float  get_Scale() const {
    return header_.fScale;
  }

  void set_Scale(float value) {
    header_.fScale=value;
  }

  /* For Maximum-Likelihood refinement (Xmipp compatibility:
  not currently used)
  */

  float get_Flip() const {
    return header_.Flip;
  }

  /* For Maximum-Likelihood refinement (Xmipp compatibility:
  not currently used)
  */
  void set_Flip(float value) {
    header_.Flip=value;
  }

  float get_Weight() const {
    return header_.Weight;
  }

  void set_Weight(float value) {
    header_.Weight=value;
  }

  float get_fNrec() const {
    return header_.fNrec;
  }

  void set_fNrec(float value) {
    header_.fNrec = value;
  }

  float get_fNlabel() const {
    return header_.fNlabel;
  }

  void set_fNlabel(float value) {
    header_.fNlabel=value;
  }

  float get_fIform() const {
    return header_.fIform;
  }

  void set_fIform(float value) {
    header_.fIform = value;
  }

  float get_fImami() const {
    return header_.fImami;
  }

  void set_fImami(float value) {
    header_.fImami=value;
  }

  float get_fFmax() const {
    return header_.fFmax;
  }

  void set_fFmax(float value) {
    header_.fFmax= value;
  }

  float get_fFmin() const {
    return header_.fFmin;
  }

  void set_fFmin(float value) {
    header_.fFmin=value;
  }

  float get_fAv() const {
    return header_.fAv;
  }

  void set_fAv(float value) {
    header_.fAv=value;
  }

  float get_fSig() const {
    return header_.fSig;
  }

  void set_fSig(float value) {
    header_.fSig=value;
  }

  float get_fIhist()  const {
    return header_.fIhist;
  }

  void set_fIhist(float value) {
    header_.fIhist=value;
  }

  float get_fLabrec() const {
    return header_.fLabrec;
  }

  void set_fLabrec(float value) {
    header_.fLabrec=value;
  }

  float get_fIangle() const {
    return header_.fIangle;
  }

  void set_fIangle(float value) {
    header_.fIangle=value;
  }

  float get_xorigin() const {
    return header_.fXoff;
  }

  void set_xorigin(float value) {
    header_.fXoff = value;
  }

  float get_yorigin() const {
    return header_.fYoff;
  }

  void set_yorigin(float value) {
    header_.fYoff = value;
  }

  float get_zorigin() const {
    return header_.fZoff;
  }

  void set_zorigin(float value) {
    header_.fZoff = value;
  }

  float get_object_pixel_size() const {
    return header_.fScale;
  }

  void set_object_pixel_size(float value) {
    header_.fScale = value;
  }

  float get_fLabbyt() const {
    return header_.fLabbyt;
  }

  void set_fLabbyt(float value) {
    header_.fLabbyt=value;
  }

  float get_fLenbyt() const {
    return header_.fLenbyt;
  }

  void set_fLenbyt(float value) {
    header_.fLenbyt=value;
  }

  IMP::algebra::Matrix2D< double > get_fGeo_matrix();

  // Origin offsets
  void set_origin_offsets(float Yoff, float Xoff);
  void set_origin_offsets(float Zoff, float Yoff, float Xoff);

  // Euler angles
  void set_euler_angles(float Phi, float Theta, float Psi);
  void set_euler_angles1(float Phi1, float Theta1, float Psi1);
  void set_euler_angles2(float Phi2, float Theta2, float Psi2);


  //! Gets the fFlag.
  /** fFlag contains the number of triads of Euler angles stored
      in the header (up to three).
      set_euler_angles2 makes fFlag=2, set_euler_angles1 makes
      fFlag=max(fFlag, 1), set_euler_angles does not change fFlag
  */
  float get_fFlag() const {
    return header_.fFlag;
  }


  //! Sets the fFlag.
  /** fFlag contains the number of triads of Euler angles stored
      in the header (up to three).
      set_euler_angles2 makes fFlag=2, set_euler_angles1 makes
      fFlag=max(fFlag, 1), set_euler_angles does not change fFlag
  */
  void set_fFlag(float value) {
    header_.fFlag = value;
  }

  template<typename T>
  void get_euler_angles(T& Phi, T& Theta, T& Psi) const {
    Phi = (T) header_.fPhi;
    Theta = (T) header_.fTheta;
    Psi = (T) header_.fPsi;
  }

  template<typename T>
  void get_euler_angles1(T& Phi1, T& Theta1, T& Psi1) const {
    Phi1 = (T) header_.fPhi1;
    Theta1 = (T) header_.fTheta1;
    Psi1 = (T) header_.fPsi1;
  }

  template<typename T>
  void get_euler_angles2(T& Phi2, T& Theta2, T& Psi2) const {
    Phi2 = (T) header_.fPhi2;
    Theta2 = (T) header_.fTheta2;
    Psi2 = (T) header_.fPsi2;
  }

  template<typename T>
  void get_origin_offsets(T &Yoff, T &Xoff) const   {
    Yoff =  (T) header_.fYoff;
    Xoff =  (T) header_.fXoff;
  }

  template<typename T>
  void get_origin_offsets(T &Zoff,T &Yoff,T &Xoff) const {
    Zoff =  (T) header_.fZoff;
    Yoff =  (T) header_.fYoff;
    Xoff =  (T) header_.fXoff;
  }

  void set_Phi(float value) {
    header_.fIangle = 1;
    header_.fPhi=value;
  }

  float get_Phi() const {
    return header_.fPhi;
  }

  void set_Theta(float value) {
    header_.fIangle = 1;
    header_.fTheta=value;
  }

  float get_Theta() const {
    return header_.fTheta;
  }

  void set_Psi(float value) {
    header_.fIangle = 1;
    header_.fPsi=value;
  }

  float get_Psi() const {
    return header_.fPsi;
  }

  void set_Phi1(float value) {
    header_.fFlag = 1.f;
    header_.fPhi1=value;
  }

  float get_Phi1() const {
    return header_.fPhi1;
  }

  void set_Theta1(float value) {
    header_.fFlag = 1.f;
    header_.fTheta1=value;
  }

  float get_Theta1() const {
    return header_.fTheta1;
  }

  void set_Psi1(float value) {
    header_.fFlag = 1.f;
    header_.fPsi1=value;
  }

  float get_Psi1() const {
    return header_.fPsi1;
  }

  void set_Phi2(float value) {
    header_.fFlag = 2.f;
    header_.fPhi2=value;
  }

  float get_Phi2() const {
    return header_.fPhi2;
  }

  void set_Theta2(float value) {
    header_.fFlag = 2.f;
    header_.fTheta2=value;
  }

  float get_Theta2() const {
    return header_.fTheta2;
  }

  void set_Psi2(float value) {
    header_.fFlag = 2.f;
    header_.fPsi2=value;
  }

  float get_Psi2() const {
    return header_.fPsi2;
  }

  bool is_normalized() const {
    if(std::abs(this->get_fAv()) <1e-6 &&
       std::abs(this->get_fSig()-1.0) < 1e-6) {
      return true;
    }
    return false;
  }

  // Date and Time
  char* get_date() const;
  char* get_time() const;
  void set_date();
  void set_time();

  //! Set info about the image dimension in the header
  void set_dimensions(float Ydim, float Xdim);
  //! Get info about the image dimension from the header
  void get_dimensions(float& Ydim, float& Xdim) const;
  //! Set info about volume dimension in the header
  void set_dimensions(float Zdim,float Ydim, float Xdim);
  //! Get info about volume dimension from the header
  void get_dimensions(float& Zdim,float& Ydim, float& Xdim) const;

  // Title
  char* get_title() const;

  //! Set title of image in the header
  void set_title(String newName);

private:

  // The header is directly in format Spider with a couple of additions
  SpiderHeader header_;
  bool reversed_;
}; // ImageHeader

IMPEM_END_NAMESPACE

#endif /* IMPEM_IMAGE_HEADER_H */

---