IMP logo
IMP Reference Guide  develop.29b24c6ad6,2021/05/15
The Integrative Modeling Platform
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
 
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) 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]forceif 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]ithe relevant coordinate (0:x, 1:y, 2:z)
Exceptions
ValueExceptionif 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.

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

gets the upper bound of the grid

Parameters
[in]indThe 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]nnxthe new number of voxels on the X axis
[in]nnythe new number of voxels on the Y axis
[in]nnzthe 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.


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