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IMP Reference Guide
2.21.0
The Integrative Modeling Platform
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#include <IMP/em/DensityHeader.h>
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 |
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_ |
| void IMP::em::DensityHeader::compute_xyz_top | ( | bool | force = false | ) |
Compute the farthest point of the grid.
| [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.
| [in] | i | the relevant coordinate (0:x, 1:y, 2:z) |
| 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 |
Definition at line 140 of file DensityHeader.h.
| double 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 |
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).
Definition at line 168 of file DensityHeader.h.
| void IMP::em::DensityHeader::set_yorigin | ( | float | y | ) |
Sets the origin on the map (y-coordinate)
Definition at line 176 of file DensityHeader.h.
| void IMP::em::DensityHeader::set_zorigin | ( | float | z | ) |
Sets the origin on the map (z-coordinate)
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
| [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 |
| char IMP::em::DensityHeader::comments[COMMENT_FIELD_NUM_OF][COMMENT_FIELD_SINGLE_SIZE] |
text comments
Definition at line 98 of file DensityHeader.h.
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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.