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IMP Reference Guide  develop.d247202c1c,2019/10/23
The Integrative Modeling Platform
IMP::em::ImageHeader Class Reference

Class to deal with the header of Electron Microscopy images in IMP. More...

#include <IMP/em/ImageHeader.h>

Detailed Description

Class to deal with the header of Electron Microscopy images in IMP.

Note
Compatible with SPIDER format

Definition at line 28 of file ImageHeader.h.

Public Types

enum  img_type {
  IMG_BYTE = 0, IMG_IMPEM = 1, IMG_INT = 9, VOL_BYTE = 2,
  VOL_IMPEM = 3, VOL_INT = 10, IMG_FOURIER = -1, VOL_FOURIER = -3
}
 Types of initialization of ImageHeader. More...
 

Public Member Functions

 ImageHeader (img_type im)
 
 ImageHeader (float im)
 
void clear ()
 Clear header data and sets a consistent header. More...
 
void do_show (std::ostream &out) const
 
algebra::Vector3D get_euler_angles () const
 
algebra::Vector3D get_euler_angles1 () const
 
algebra::Vector3D get_euler_angles2 () const
 
float get_fAngle1 () const
 get rotation angle. (Xmipp compatibility) More...
 
float get_fAv () const
 
float get_fFlag () const
 Gets the fFlag. More...
 
float get_fFmax () const
 
float get_fFmin () const
 
double get_fGeo_matrix (unsigned int i, unsigned int j) const
 
float get_fIangle () const
 
float get_fIform () const
 
float get_fIhist () const
 
float get_fImami () const
 
float get_fLabbyt () const
 
float get_fLabrec () const
 
float get_fLenbyt () const
 
float get_Flip () const
 
float get_fNlabel () const
 
float get_fNrec () const
 
float get_fSig () const
 
float get_image_type () const
 
unsigned int get_number_of_columns () const
 
unsigned int get_number_of_rows () const
 
unsigned int get_number_of_slices () const
 
float get_object_pixel_size () const
 
float get_old_rot () const
 get rotation angle. (Xmipp compatibility) More...
 
algebra::Vector3D get_origin () const
 
bool get_reversed () const
 Interaction with data. More...
 
float get_Scale () const
 
float get_Weight () const
 
bool is_normalized () const
 
void print_hard (std::ostream &out) const
 Prints a reduced set of information (debugging purposes) More...
 
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. More...
 
bool read (std::ifstream &f, 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. More...
 
void set_date ()
 
void set_euler_angles (const algebra::Vector3D &euler)
 
void set_euler_angles1 (const algebra::Vector3D &euler)
 
void set_euler_angles2 (const algebra::Vector3D &euler)
 
void set_fAngle1 (float value)
 set rotation angle. (Xmipp compatibility) More...
 
void set_fAv (float value)
 
void set_fFlag (float value)
 
void set_fFmax (float value)
 
void set_fFmin (float value)
 
void set_fIangle (float value)
 
void set_fIform (float value)
 
void set_fIhist (float value)
 
void set_fImami (float value)
 
void set_fLabbyt (float value)
 
void set_fLabrec (float value)
 
void set_fLenbyt (float value)
 
void set_Flip (float value)
 
void set_fNlabel (float value)
 
void set_fNrec (float value)
 
void set_fSig (float value)
 
void set_header ()
 Sets a consistent header. More...
 
void set_image_type (img_type im)
 Set the type of image. More...
 
void set_image_type (float im)
 
void set_number_of_columns (unsigned int n)
 
void set_number_of_rows (unsigned int n)
 
void set_number_of_slices (unsigned int n)
 
void set_object_pixel_size (float value)
 
void set_old_rot (float value)
 set rotation angle. (Xmipp compatibility) More...
 
void set_origin (const algebra::Vector3D &v)
 
void set_origin (const algebra::Vector2D &v)
 
void set_reversed (bool value)
 
void set_Scale (float value)
 
void set_time ()
 
void set_title (String newName)
 Set title of image in the header. More...
 
void set_Weight (float value)
 
void show (std::ostream &out=std::cout) const
 
void show_projection_params (std::ostream &out) const
 Shows only the projection parameters. More...
 
void write (const String &filename, bool force_reversed=false)
 Writes the header of a EM image. More...
 
void write (std::ofstream &f, bool force_reversed=false)
 Writes the header of a EM image to an output file stream. More...
 

Member Enumeration Documentation

Types of initialization of ImageHeader.

Definition at line 31 of file ImageHeader.h.

Member Function Documentation

void IMP::em::ImageHeader::clear ( )

Clear header data and sets a consistent header.

float IMP::em::ImageHeader::get_fAngle1 ( ) const

get rotation angle. (Xmipp compatibility)

Definition at line 190 of file ImageHeader.h.

float IMP::em::ImageHeader::get_fFlag ( ) const

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

Definition at line 279 of file ImageHeader.h.

float IMP::em::ImageHeader::get_old_rot ( ) const

get rotation angle. (Xmipp compatibility)

Definition at line 184 of file ImageHeader.h.

bool IMP::em::ImageHeader::get_reversed ( ) const

Interaction with data.

Definition at line 161 of file ImageHeader.h.

void IMP::em::ImageHeader::print_hard ( std::ostream &  out) const

Prints a reduced set of information (debugging purposes)

int IMP::em::ImageHeader::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.

bool IMP::em::ImageHeader::read ( std::ifstream &  f,
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.

void IMP::em::ImageHeader::set_fAngle1 ( float  value)

set rotation angle. (Xmipp compatibility)

Definition at line 193 of file ImageHeader.h.

void IMP::em::ImageHeader::set_header ( )

Sets a consistent header.

void IMP::em::ImageHeader::set_image_type ( img_type  im)

Set the type of image.

Parameters
[in]imtype 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

Definition at line 66 of file ImageHeader.h.

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void IMP::em::ImageHeader::set_old_rot ( float  value)

set rotation angle. (Xmipp compatibility)

Definition at line 187 of file ImageHeader.h.

void IMP::em::ImageHeader::set_title ( String  newName)

Set title of image in the header.

void IMP::em::ImageHeader::show_projection_params ( std::ostream &  out) const

Shows only the projection parameters.

Definition at line 132 of file ImageHeader.h.

void IMP::em::ImageHeader::write ( const String filename,
bool  force_reversed = false 
)

Writes the header of a EM image.

void IMP::em::ImageHeader::write ( std::ofstream &  f,
bool  force_reversed = false 
)

Writes the header of a EM image to an output file stream.


The documentation for this class was generated from the following file: