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)
