#include <IMP/em/DensityHeader.h>

Public Member Functions
void	compute_xyz_top (bool force=false)
	Compute the farthest point of the grid. More...

int	get_data_type () const
	Get the number of bits that used to store the density of a single voxel.

bool	get_has_resolution () const
	Return if the resolution has been set.

int	get_number_of_voxels () const

int	get_nx () const
	Get the number of voxels in the x dimension.

int	get_ny () const
	Get the number of voxels in the y dimension.

int	get_nz () const
	Get the number of voxels in the z dimension.

float	get_origin (int i) const
	Returns the origin on the map. More...

float	get_resolution () const
	Returns the resolution of the map.

float	get_spacing () const

emreal	get_top (int ind) const
	gets the upper bound of the grid More...

float	get_xorigin () const
	Returns the origin on the map (x-coordinate)

float	get_yorigin () const
	Returns the origin on the map (y-coordinate)

float	get_zorigin () const
	Returns the origin on the map (z-coordinate)

bool	is_top_calculated () const
	True if the top coodinates (bounding-box) are calculated.

void	set_data_type (int data_type)

void	set_resolution (float resolution)
	Sets the resolution of the map.

void	set_xorigin (float x)
	Sets the origin on the map (x-coordinate). More...

void	set_yorigin (float y)
	Sets the origin on the map (y-coordinate) More...

void	set_zorigin (float z)
	Sets the origin on the map (z-coordinate) More...

void	show (std::ostream &out=std::cout) const

void	update_cell_dimensions ()

void	update_map_dimensions (int nnx, int nny, int nnz)

Public Attributes
float	alpha

float	Aperture

float	Astigmatism

float	AstigmatismAngle

float	beta

float	CCDArea

char	comments [COMMENT_FIELD_NUM_OF][COMMENT_FIELD_SINGLE_SIZE]
	text comments More...

float	CountsPerElectron

float	Cs

float	Defocus

float	dmax

float	dmean

float	dmin

float	EnergyOffset

float	EnergySlitwidth

float	Exposuretime

float	FocusIncrement

float	gamma

float	Intensity

int	ispg

int	lswap

int	machinestamp

int	magic

float	Magnification

char	map [MAP_FIELD_SIZE]

int	mapc

int	mapr

int	maps

float	MarkerX

float	MarkerY

float	Microscope

int	mx

int	my

int	mz

int	nlabl

int	nsymbt

int	nxstart
	number of first columns in map (x-dimension)

int	nystart
	number of first columns in map (y-dimension)

int	nzstart
	number of first columns in map (z-dimension)

float	Objectpixelsize_

float	Pixelsize

float	Postmagnification

float	rms

float	Tiltangle

float	Tiltaxis

int	user [USER_FIELD_SIZE]

float	voltage

float	xlen

float	ylen

float	zlen

Static Public Attributes
static const unsigned short	COMMENT_FIELD_NUM_OF = 10

static const unsigned short	COMMENT_FIELD_SINGLE_SIZE = 80

static const unsigned short	MAP_FIELD_SIZE = 4

static const unsigned short	USER_FIELD_SIZE = 25

Protected Attributes
int	data_type_

bool	is_resolution_set_

int	nx_

int	ny_

int	nz_

float	resolution_

bool	top_calculated_

float	xorigin_

float	xtop_

float	yorigin_

float	ytop_

float	zorigin_

float	ztop_

Detailed Description

Definition at line 25 of file DensityHeader.h.

Member Function Documentation

void IMP::em::DensityHeader::compute_xyz_top ( bool force = false )

/param[in] force if true then the top point is calculated even if it has already been calcualted.

float IMP::em::DensityHeader::get_origin ( int i ) const

Parameters

[in] i the relevant coordinate (0:x, 1:y, 2:z)

Exceptions

ValueException if the value of i is out of range.

Definition at line 152 of file DensityHeader.h.

float IMP::em::DensityHeader::get_spacing ( ) const

Note: Use DensityMap::update_voxel_size() to set the spacing value.

Definition at line 140 of file DensityHeader.h.

emreal IMP::em::DensityHeader::get_top ( int ind ) const

Parameters

[in] ind The dimension index x:=0,y:=1,z:=2

Returns: the coordinate value in angstroms

Definition at line 41 of file DensityHeader.h.

void IMP::em::DensityHeader::set_xorigin ( float x )

Note: This is an absolute position in space.

Definition at line 168 of file DensityHeader.h.

void IMP::em::DensityHeader::set_yorigin ( float y )

Note: This is an absolute position in space.

Definition at line 176 of file DensityHeader.h.

void IMP::em::DensityHeader::set_zorigin ( float z )

Note: This is an absolute position in space.

Definition at line 184 of file DensityHeader.h.

void IMP::em::DensityHeader::update_cell_dimensions ( )

Update the cell dimensions of the map multiplying the number of voxels along each direction by the Objectpixelsize

void IMP::em::DensityHeader::update_map_dimensions	(	int	nnx,
		int	nny,
		int	nnz
	)

Update the dimensions of the map to be (nnx,nny,nnz) The origin of the map does not change /param[in] nnx the new number of voxels on the X axis /param[in] nny the new number of voxels on the Y axis /param[in] nnz the new number of voxels on the Z axis

Member Data Documentation

char IMP::em::DensityHeader::comments[COMMENT_FIELD_NUM_OF][COMMENT_FIELD_SINGLE_SIZE]

Definition at line 98 of file DensityHeader.h.

int IMP::em::DensityHeader::data_type_

protected

How many bits are used to store the density of a single voxel (used in MRC format)

Definition at line 213 of file DensityHeader.h.

int IMP::em::DensityHeader::magic

magic byte for machine platform (~endian), OS-9=0, VAX=1, Convex=2, SGI=3, Sun=4, Mac(Motorola)=5, PC,IntelMac=6

Definition at line 101 of file DensityHeader.h.

int IMP::em::DensityHeader::mapc

Axes corresponding to columns (mapc), rows (mapr) and sections (maps) (1,2,3 for x,y,z)

Definition at line 88 of file DensityHeader.h.

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

DensityHeader.h

Public Member Functions

Public Attributes

Static Public Attributes

Protected Attributes

Detailed Description

Member Function Documentation

Member Data Documentation