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

enum IMP::em::ImageHeader::img_type

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]

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

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.

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

• ImageHeader.h