Public Member Functions | |
void | compute_xyz_top (bool force=false) |
Compute the farthest point of the grid. | |
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. | |
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 | |
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_number_of_voxels (int nx, int ny, int nz) |
void | set_resolution (float resolution) |
Sets the resolution of the map. | |
void | set_xorigin (float x) |
Sets the origin on the map (x-coordinate). | |
void | set_yorigin (float y) |
Sets the origin on the map (y-coordinate). | |
void | set_zorigin (float z) |
Sets the origin on the map (z-coordinate). | |
void | show (std::ostream &out=std::cout) const |
void | update_cell_dimensions () |
void | update_map_dimensions (int nnx, int nny, int nnz) |
Data Fields | |
float | alpha |
float | Aperture |
float | Astigmatism |
float | AstigmatismAngle |
float | beta |
float | CCDArea |
char | comments [COMMENT_FIELD_NUM_OF][COMMENT_FIELD_SINGLE_SIZE] |
text comments | |
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 | |
COMMENT_FIELD_NUM_OF = _IMP_em.DensityHeader_COMMENT_FIELD_NUM_OF | |
static const unsigned short | COMMENT_FIELD_NUM_OF = 10 |
COMMENT_FIELD_SINGLE_SIZE = _IMP_em.DensityHeader_COMMENT_FIELD_SINGLE_SIZE | |
static const unsigned short | COMMENT_FIELD_SINGLE_SIZE = 80 |
MAP_FIELD_SIZE = _IMP_em.DensityHeader_MAP_FIELD_SIZE | |
static const unsigned short | MAP_FIELD_SIZE = 4 |
USER_FIELD_SIZE = _IMP_em.DensityHeader_USER_FIELD_SIZE | |
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_ |
Friends | |
std::ostream & | operator<< (std::ostream &s, const DensityHeader &v) |
void IMP::em::DensityHeader::compute_xyz_top | ( | bool | force = false |
) |
Compute the farthest point of the grid.
/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 |
Returns the origin on the map.
[in] | i | the relevant coordinate (0:x, 1:y, 2:z) |
ValueException | if the value of i is out of range. |
float IMP::em::DensityHeader::get_spacing | ( | ) | const |
emreal IMP::em::DensityHeader::get_top | ( | int | ind | ) | const |
gets the upper bound of the grid
[in] | ind | The dimension index x:=0,y:=1,z:=2 |
void IMP::em::DensityHeader::set_number_of_voxels | ( | int | nx, | |
int | ny, | |||
int | nz | |||
) |
void IMP::em::DensityHeader::set_xorigin | ( | float | x | ) |
Sets the origin on the map (x-coordinate).
void IMP::em::DensityHeader::set_yorigin | ( | float | y | ) |
Sets the origin on the map (y-coordinate).
void IMP::em::DensityHeader::set_zorigin | ( | float | z | ) |
Sets the origin on the map (z-coordinate).
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
char IMP::em::DensityHeader::comments[COMMENT_FIELD_NUM_OF][COMMENT_FIELD_SINGLE_SIZE] |
text comments
int IMP::em::DensityHeader::data_type_ [protected] |
How many bits are used to store the density of a single voxel (used in MRC format)
magic byte for machine platform (~endian), OS-9=0, VAX=1, Convex=2, SGI=3, Sun=4, Mac(Motorola)=5, PC,IntelMac=6
Axes corresponding to columns (mapc), rows (mapr) and sections (maps) (1,2,3 for x,y,z)