IMP::em::DensityHeader Class Reference

#include <IMP/em/DensityHeader.h>

Detailed Description

Definition at line 25 of file 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. More...
bool	get_has_resolution () const
	Return if the resolution has been set. More...
int	get_number_of_voxels () const
int	get_nx () const
	Get the number of voxels in the x dimension. More...
int	get_ny () const
	Get the number of voxels in the y dimension. More...
int	get_nz () const
	Get the number of voxels in the z dimension. More...
float	get_origin (int i) const
	Returns the origin on the map. More...
float	get_resolution () const
	Returns the resolution of the map. More...
float	get_spacing () const
double	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) More...
float	get_yorigin () const
	Returns the origin on the map (y-coordinate) More...
float	get_zorigin () const
	Returns the origin on the map (z-coordinate) More...
bool	is_top_calculated () const
	True if the top coordinates (bounding-box) are calculated. More...
void	set_data_type (int data_type)
void	set_resolution (float resolution)
	Sets the resolution of the map. More...
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) More...
int	nystart
	number of first columns in map (y-dimension) More...
int	nzstart
	number of first columns in map (z-dimension) More...
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_

Member Function Documentation

void IMP::em::DensityHeader::compute_xyz_top

(

bool

force = false

)

Compute the farthest point of the grid.

Parameters

[in]

force

if true then the top point is calculated even if it has already been calculated.

int IMP::em::DensityHeader::get_data_type

(

)

const

Get the number of bits that used to store the density of a single voxel.

Definition at line 201 of file DensityHeader.h.

bool IMP::em::DensityHeader::get_has_resolution

(

)

const

Return if the resolution has been set.

Definition at line 132 of file DensityHeader.h.

int IMP::em::DensityHeader::get_nx

(

)

const

Get the number of voxels in the x dimension.

Definition at line 194 of file DensityHeader.h.

int IMP::em::DensityHeader::get_ny

(

)

const

Get the number of voxels in the y dimension.

Definition at line 196 of file DensityHeader.h.

int IMP::em::DensityHeader::get_nz

(

)

const

Get the number of voxels in the z dimension.

Definition at line 198 of file DensityHeader.h.

float IMP::em::DensityHeader::get_origin

(

int

i

)

const

Returns the origin on the map.

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_resolution

(

)

const

Returns the resolution of the map.

Definition at line 126 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.

double IMP::em::DensityHeader::get_top

(

int

ind

)

const

gets the upper bound of the grid

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.

float IMP::em::DensityHeader::get_xorigin

(

)

const

Returns the origin on the map (x-coordinate)

Definition at line 142 of file DensityHeader.h.

float IMP::em::DensityHeader::get_yorigin

(

)

const

Returns the origin on the map (y-coordinate)

Definition at line 144 of file DensityHeader.h.

float IMP::em::DensityHeader::get_zorigin

(

)

const

Returns the origin on the map (z-coordinate)

Definition at line 146 of file DensityHeader.h.

bool IMP::em::DensityHeader::is_top_calculated

(

)

const

True if the top coordinates (bounding-box) are calculated.

Definition at line 189 of file DensityHeader.h.

void IMP::em::DensityHeader::set_resolution

(

float

resolution

)

Sets the resolution of the map.

Definition at line 134 of file DensityHeader.h.

void IMP::em::DensityHeader::set_xorigin

(

float

x

)

Sets the origin on the map (x-coordinate).

Note

This is an absolute position in space.

Definition at line 168 of file DensityHeader.h.

void IMP::em::DensityHeader::set_yorigin

(

float

y

)

Sets the origin on the map (y-coordinate)

Note

This is an absolute position in space.

Definition at line 176 of file DensityHeader.h.

void IMP::em::DensityHeader::set_zorigin

(

float

z

)

Sets the origin on the map (z-coordinate)

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

Parameters

[in]	nnx	the new number of voxels on the X axis
[in]	nny	the new number of voxels on the Y axis
[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]

text comments

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.

int IMP::em::DensityHeader::nxstart

number of first columns in map (x-dimension)

Definition at line 77 of file DensityHeader.h.

int IMP::em::DensityHeader::nystart

number of first columns in map (y-dimension)

Definition at line 79 of file DensityHeader.h.

int IMP::em::DensityHeader::nzstart

number of first columns in map (z-dimension)

Definition at line 81 of file DensityHeader.h.

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

• DensityHeader.h