IMP Reference Guide
2.14.0
The Integrative Modeling Platform
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Class for handling density maps. More...
#include <IMP/em/DensityMap.h>
Class for handling density maps.
Definition at line 93 of file DensityMap.h.
Public Member Functions | |
DensityMap (std::string name="DensityMap%1%") | |
DensityMap (const DensityHeader &header, std::string name="DensityMap%1%") | |
Construct a density map as instructed in the input header. More... | |
void | add (const DensityMap *other) |
Sums two grids; the result is kept in the map. More... | |
void | add (Float d) |
Add a number to every voxel in the map. More... | |
void | calc_all_voxel2loc () |
Calculates the coordinates that correspond to all voxels. More... | |
emreal | calcRMS () |
Calculates RMSD and mean of a map values as stored in the header. More... | |
void | copy_map (const DensityMap *other) |
Copy map into this map. More... | |
algebra::Vector3D | get_centroid (emreal threshold=0.0) const |
Get the centroid of all voxels with density above a given threshold. More... | |
DensityMap * | get_cropped (float threshold) |
Create and return a new cropped map. More... | |
DensityMap * | get_cropped (const algebra::BoundingBox3D &bb) |
Create and return a new cropped map with the given bounding box extent. More... | |
int | get_dim_index_by_location (const algebra::Vector3D &v, int ind) const |
Calculate dimension index of a given location. More... | |
int | get_dim_index_by_location (float loc_val, int ind) const |
const DensityHeader * | get_header () const |
Returns a read-only pointer to the header of the map. More... | |
DensityHeader * | get_header_writable () |
Returns a pointer to the header of the map in a writable version. More... | |
algebra::Vector3D | get_location_by_voxel (long index) const |
Calculate the location of a given voxel. More... | |
float | get_location_in_dim_by_voxel (long index, int dim) const |
Calculate the location of a given voxel in a given dimension. More... | |
std::string | get_locations_string (float t) |
Print the locations of all voxels with value above a given threshold. More... | |
emreal | get_max_value () const |
Returns the value of the voxel with the highest density. More... | |
float | get_maximum_value_in_xy_plane (int z_ind) |
Get the maximum value in a XY plane indicated by a Z index. More... | |
float | get_maximum_value_in_xz_plane (int y_ind) |
Get the maximum value in a XZ plane indicated by a Y index. More... | |
float | get_maximum_value_in_yz_plane (int x_ind) |
Get the maximum value in a YZ plane indicated by a X index. More... | |
emreal | get_min_value () const |
Returns the value of the voxel with the lowest density. More... | |
long | get_number_of_voxels () const |
Get the number of map voxels. More... | |
algebra::Vector3D | get_origin () const |
bool | get_rms_calculated () const |
Float | get_spacing () const |
Get the voxel size of the map. More... | |
algebra::Vector3D | get_top () const |
virtual std::string | get_type_name () const |
emreal | get_value (float x, float y, float z) const |
Gets the value of the voxel located at (x,y,z) More... | |
emreal | get_value (const algebra::Vector3D &point) const |
emreal | get_value (long index) const |
Gets the value of the voxel at a given index. More... | |
virtual ::IMP::VersionInfo | get_version_info () const |
Get information about the module and version of the object. More... | |
long | get_voxel_by_location (float x, float y, float z) const |
Calculate the voxel of a given location. More... | |
long | get_voxel_by_location (const algebra::Vector3D &v) const |
Calculate the voxel of a given location. More... | |
bool | is_normalized () const |
bool | is_part_of_volume (float x, float y, float z) const |
Checks whether a given point is in the grid. More... | |
bool | is_part_of_volume (const algebra::Vector3D &v) const |
Checks whether a given point is in the grid. More... | |
bool | is_xyz_ind_part_of_volume (int ix, int iy, int iz) const |
int | lower_voxel_shift (emreal loc, emreal kdist, emreal orig, int ndim) const |
void | multiply (float factor) |
Multiply in place each voxel in the map by the input factor. More... | |
void | pad (int nx, int ny, int nz, float val=0.0) |
Increase the dimension of the map. More... | |
DensityMap * | pad_margin (int mrg_x, int mrg_y, int mrg_z, float val=0.0) |
Create a new padded map. More... | |
void | pick_max (const DensityMap *other) |
Pick the max value between two corresponding voxels between two maps. More... | |
void | reset_data (float value=0.0) |
Set the density voxels to some value and reset the management flags. More... | |
bool | same_dimensions (const DensityMap *other) const |
Checks if two maps have the same dimensions. More... | |
bool | same_origin (const DensityMap *other) const |
Checks if two maps have the same origin. More... | |
bool | same_voxel_size (const DensityMap *other) const |
Checks if two maps have the same voxel size. More... | |
void | set_origin (float x, float y, float z) |
Sets the origin of the header. More... | |
void | set_origin (const IMP::algebra::Vector3D &v) |
void | set_value (long index, emreal value) |
Set the value of the voxel at a given index. More... | |
void | set_value (float x, float y, float z, emreal value) |
Set the value of the voxel at given coordinates. More... | |
void | set_void_map (int nx, int ny, int nz) |
Set the map dimension and reset all voxels to 0. More... | |
void | std_normalize () |
Normalize the density voxels according to standard deviation (stdv). More... | |
void | update_voxel_size (float new_apix) |
Update the voxel size of the map. More... | |
int | upper_voxel_shift (emreal loc, emreal kdist, emreal orig, int ndim) const |
long | xyz_ind2voxel (int x, int y, int z) const |
Calculate the voxel of a given xyz index. More... | |
Public Member Functions inherited from IMP::Object | |
virtual void | clear_caches () |
CheckLevel | get_check_level () const |
LogLevel | get_log_level () const |
void | set_check_level (CheckLevel l) |
void | set_log_level (LogLevel l) |
Set the logging level used in this object. More... | |
void | set_was_used (bool tf) const |
void | show (std::ostream &out=std::cout) const |
const std::string & | get_name () const |
void | set_name (std::string name) |
Protected Member Functions | |
void | allocated_data () |
void | float2real (float *f_data, boost::scoped_array< emreal > &r_data) |
void | real2float (emreal *r_data, boost::scoped_array< float > &f_data) |
void | reset_all_voxel2loc () |
void | update_header () |
update the header values – still in work More... | |
Protected Member Functions inherited from IMP::Object | |
Object (std::string name) | |
Construct an object with the given name. More... | |
virtual void | do_destroy () |
Protected Attributes | |
boost::scoped_array< emreal > | data_ |
bool | data_allocated_ |
DensityHeader | header_ |
bool | loc_calculated_ |
true if the locations have already been computed More... | |
bool | normalized_ |
bool | rms_calculated_ |
boost::scoped_array< float > | x_loc_ |
boost::scoped_array< float > | y_loc_ |
boost::scoped_array< float > | z_loc_ |
Friends | |
DensityMap * | read_map (std::string filename, MapReaderWriter *reader) |
void | write_map (DensityMap *m, std::string filename, MapReaderWriter *writer) |
Related Functions | |
(Note that these are not member functions.) | |
void | add_to_map (DensityMap *dm, const Particles &pis) |
Rasterize the particles into an existing density map. More... | |
DensityMap * | create_density_map (algebra::DenseGrid3D< float > &grid) |
Return a density map with the values taken from the grid. More... | |
DensityMap * | create_density_map (algebra::DenseGrid3D< double > &grid) |
Return a density map with the values taken from the grid. More... | |
DensityMap * | get_binarized_interior (DensityMap *dmap) |
Return a binarized map with 1 for voxels that are internal in the input map. More... | |
double | get_density (const DensityMap *m, const algebra::Vector3D &v) |
Get density value at point v, interpolating linearly from the sample values. More... | |
DensityMap * | get_resampled (DensityMap *input, double scaling) |
Get a resampled version of the map. More... | |
DensityMap * | get_transformed (const DensityMap *input, const algebra::Transformation3D &tr, double threshold) |
Return a new density map containing a rotated version of the old one. More... | |
DensityMap * | get_transformed (DensityMap *input, const algebra::Transformation3D &tr) |
Return a new density map containing a rotated version of the old one. More... | |
void | get_transformed_into (const DensityMap *source, const algebra::Transformation3D &tr, DensityMap *into, bool calc_rms=true) |
Rotate a density map into another map. More... | |
DensityMap * | read_map (std::string filename, MapReaderWriter *reader) |
Read a density map from a file (using the given reader) and return it. More... | |
DensityMap * | read_map (std::string filename) |
Read a density map from a file and return it. More... | |
void | write_map (DensityMap *m, std::string filename, MapReaderWriter *writer) |
Write a density map to a file using the given writer. More... | |
void | write_map (DensityMap *m, std::string filename) |
Write a density map to a file. More... | |
IMP::em::DensityMap::DensityMap | ( | const DensityHeader & | header, |
std::string | name = "DensityMap%1%" |
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) |
Construct a density map as instructed in the input header.
void IMP::em::DensityMap::add | ( | const DensityMap * | other | ) |
Sums two grids; the result is kept in the map.
[in] | other | the other map |
void IMP::em::DensityMap::add | ( | Float | d | ) |
Add a number to every voxel in the map.
[in] | d | Value to add |
void IMP::em::DensityMap::calc_all_voxel2loc | ( | ) |
Calculates the coordinates that correspond to all voxels.
emreal IMP::em::DensityMap::calcRMS | ( | ) |
Calculates RMSD and mean of a map values as stored in the header.
The header stores whether the map is normalized.
void IMP::em::DensityMap::copy_map | ( | const DensityMap * | other | ) |
Copy map into this map.
algebra::Vector3D IMP::em::DensityMap::get_centroid | ( | emreal | threshold = 0.0 | ) | const |
Get the centroid of all voxels with density above a given threshold.
[in] | threshold | the input threshold |
DensityMap* IMP::em::DensityMap::get_cropped | ( | float | threshold | ) |
Create and return a new cropped map.
The margins are determined to be the bounding box with density values below the input
[in] | threshold | used for cropping |
DensityMap* IMP::em::DensityMap::get_cropped | ( | const algebra::BoundingBox3D & | bb | ) |
Create and return a new cropped map with the given bounding box extent.
[in] | bb | the bounding box |
int IMP::em::DensityMap::get_dim_index_by_location | ( | const algebra::Vector3D & | v, |
int | ind | ||
) | const |
Calculate dimension index of a given location.
[in] | v | The position (in angstroms) |
[in] | ind | dimension index (X:0,Y:1 or Z:2) |
const DensityHeader* IMP::em::DensityMap::get_header | ( | ) | const |
Returns a read-only pointer to the header of the map.
Definition at line 243 of file DensityMap.h.
DensityHeader* IMP::em::DensityMap::get_header_writable | ( | ) |
Returns a pointer to the header of the map in a writable version.
Definition at line 246 of file DensityMap.h.
algebra::Vector3D IMP::em::DensityMap::get_location_by_voxel | ( | long | index | ) | const |
Calculate the location of a given voxel.
[in] | index | The voxel index |
Definition at line 168 of file DensityMap.h.
float IMP::em::DensityMap::get_location_in_dim_by_voxel | ( | long | index, |
int | dim | ||
) | const |
Calculate the location of a given voxel in a given dimension.
[in] | index | The voxel index |
[in] | dim | The dimension of interest (x:=0,y:=1,z:=2) |
std::string IMP::em::DensityMap::get_locations_string | ( | float | t | ) |
Print the locations of all voxels with value above a given threshold.
emreal IMP::em::DensityMap::get_max_value | ( | ) | const |
Returns the value of the voxel with the highest density.
float IMP::em::DensityMap::get_maximum_value_in_xy_plane | ( | int | z_ind | ) |
Get the maximum value in a XY plane indicated by a Z index.
float IMP::em::DensityMap::get_maximum_value_in_xz_plane | ( | int | y_ind | ) |
Get the maximum value in a XZ plane indicated by a Y index.
float IMP::em::DensityMap::get_maximum_value_in_yz_plane | ( | int | x_ind | ) |
Get the maximum value in a YZ plane indicated by a X index.
emreal IMP::em::DensityMap::get_min_value | ( | ) | const |
Returns the value of the voxel with the lowest density.
long IMP::em::DensityMap::get_number_of_voxels | ( | ) | const |
Get the number of map voxels.
Float IMP::em::DensityMap::get_spacing | ( | ) | const |
Get the voxel size of the map.
Definition at line 407 of file DensityMap.h.
emreal IMP::em::DensityMap::get_value | ( | float | x, |
float | y, | ||
float | z | ||
) | const |
Gets the value of the voxel located at (x,y,z)
[in] | x | The position (in angstroms) of the x coordinate |
[in] | y | The position (in angstroms) of the y coordinate |
[in] | z | The position (in angstroms) of the z coordinate |
IndexException | The point is not covered by the grid. |
emreal IMP::em::DensityMap::get_value | ( | long | index | ) | const |
Gets the value of the voxel at a given index.
[in] | index | voxel number in physical sense, NOT logical |
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virtual |
Get information about the module and version of the object.
Reimplemented from IMP::Object.
Definition at line 412 of file DensityMap.h.
long IMP::em::DensityMap::get_voxel_by_location | ( | float | x, |
float | y, | ||
float | z | ||
) | const |
Calculate the voxel of a given location.
[in] | x | The position (in angstroms) of the x coordinate |
[in] | y | The position (in angstroms) of the y coordinate |
[in] | z | The position (in angstroms) of the z coordinate |
long IMP::em::DensityMap::get_voxel_by_location | ( | const algebra::Vector3D & | v | ) | const |
Calculate the voxel of a given location.
[in] | v | The position (in angstroms) |
Definition at line 155 of file DensityMap.h.
bool IMP::em::DensityMap::is_part_of_volume | ( | float | x, |
float | y, | ||
float | z | ||
) | const |
Checks whether a given point is in the grid.
[in] | x | The position (in angstroms) of the x coordinate |
[in] | y | The position (in angstroms) of the y coordinate |
[in] | z | The position (in angstroms) of the z coordinate |
bool IMP::em::DensityMap::is_part_of_volume | ( | const algebra::Vector3D & | v | ) | const |
Checks whether a given point is in the grid.
[in] | v | The position (in angstroms) |
Definition at line 190 of file DensityMap.h.
void IMP::em::DensityMap::multiply | ( | float | factor | ) |
Multiply in place each voxel in the map by the input factor.
The result is kept in the map.
[in] | factor | the multiplication factor |
void IMP::em::DensityMap::pad | ( | int | nx, |
int | ny, | ||
int | nz, | ||
float | val = 0.0 |
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) |
Increase the dimension of the map.
The function pads zeroes to the right-upper section on the map. The original content of the map will be in the lower XYZ part of the map.
[in] | nx | the number of voxels on the X axis |
[in] | ny | the number of voxels on the Y axis |
[in] | nz | the number of voxels on the Z axis |
[in] | val | all additional voxels will have this value |
UsageException | if the input numbers of x/y/z voxels are smaller than those currently in the map |
DensityMap* IMP::em::DensityMap::pad_margin | ( | int | mrg_x, |
int | mrg_y, | ||
int | mrg_z, | ||
float | val = 0.0 |
||
) |
Create a new padded map.
Given this map of size [nx,ny,nz], the new map is of size [2*mrg_x+nx,2*mrg_y+ny,2*mrg_z+nz]. The new map will consist of the values of the old map, with a padded margin on all sides.
[in] | mrg_x | number of margin voxels to add on both right and left on the X axis |
[in] | mrg_y | number of margin voxels to add on both right and left on the Y axis |
[in] | mrg_z | number of margin voxels to add on both right and left on the Z axis |
[in] | val | ignored |
UsageException | if the input numbers of x/y/z voxels are smaller than those currently in the map |
void IMP::em::DensityMap::pick_max | ( | const DensityMap * | other | ) |
Pick the max value between two corresponding voxels between two maps.
The result is kept in the map.
[in] | other | the other map |
void IMP::em::DensityMap::reset_data | ( | float | value = 0.0 | ) |
Set the density voxels to some value and reset the management flags.
[in] | value | all of the density voxels will have this value |
bool IMP::em::DensityMap::same_dimensions | ( | const DensityMap * | other | ) | const |
Checks if two maps have the same dimensions.
[in] | other | the map to compare with |
bool IMP::em::DensityMap::same_origin | ( | const DensityMap * | other | ) | const |
Checks if two maps have the same origin.
[in] | other | the map to compare with |
bool IMP::em::DensityMap::same_voxel_size | ( | const DensityMap * | other | ) | const |
Checks if two maps have the same voxel size.
[in] | other | the map to compare with |
void IMP::em::DensityMap::set_origin | ( | float | x, |
float | y, | ||
float | z | ||
) |
Sets the origin of the header.
x | the new x (angstroms) |
y | the new y (angstroms) |
z | the new z (angstroms) |
void IMP::em::DensityMap::set_value | ( | long | index, |
emreal | value | ||
) |
Set the value of the voxel at a given index.
[in] | index | voxel number in physical sense, NOT logical |
[in] | value | value |
void IMP::em::DensityMap::set_value | ( | float | x, |
float | y, | ||
float | z, | ||
emreal | value | ||
) |
Set the value of the voxel at given coordinates.
void IMP::em::DensityMap::set_void_map | ( | int | nx, |
int | ny, | ||
int | nz | ||
) |
Set the map dimension and reset all voxels to 0.
[in] | nx | x-dimension (voxels) |
[in] | ny | y-dimension (voxels) |
[in] | nz | z-dimension (voxels) |
void IMP::em::DensityMap::std_normalize | ( | ) |
Normalize the density voxels according to standard deviation (stdv).
The mean is subtracted from the map, which is then divided by the stdv. The normalization flag is set to avoid repeated computation.
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protected |
update the header values – still in work
void IMP::em::DensityMap::update_voxel_size | ( | float | new_apix | ) |
Update the voxel size of the map.
long IMP::em::DensityMap::xyz_ind2voxel | ( | int | x, |
int | y, | ||
int | z | ||
) | const |
Calculate the voxel of a given xyz index.
[in] | x | The voxel index on the x axis of the grid |
[in] | y | The voxel index on the y axis of the grid |
[in] | z | The voxel index on the z axis of the grid |
Definition at line 137 of file DensityMap.h.
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Rasterize the particles into an existing density map.
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Return a density map with the values taken from the grid.
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related |
Return a density map with the values taken from the grid.
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Return a binarized map with 1 for voxels that are internal in the input map.
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Get density value at point v, interpolating linearly from the sample values.
The resulting function is C0 over R3.
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Get a resampled version of the map.
The spacing is multiplied by scaling, i.e. scaling values greater than 1 increase the voxel size.
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Return a new density map containing a rotated version of the old one.
Only voxels whose value is above threshold are considered when computing the bounding box of the new map (set IMP::em::get_bounding_box()).
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Return a new density map containing a rotated version of the old one.
The dimension of the new map is the same as the old one.
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related |
Rotate a density map into another map.
[in] | source | the map to transform |
[in] | tr | transform the from density map by this transformation |
[out] | into | the map to transform into |
[in] | calc_rms | if true RMS is calculated on the transformed map |
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Read a density map from a file (using the given reader) and return it.
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related |
Read a density map from a file and return it.
Guess the file type from the file name. The file formats supported are:
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related |
Write a density map to a file using the given writer.
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related |
Write a density map to a file.
Guess the file type from the file name. The file formats supported are:
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true if the locations have already been computed
Definition at line 458 of file DensityMap.h.
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Locations (centers) for each of the voxels of the map (they are precomputed and each one is of size nvox, where nvox is the size of the map)
Definition at line 456 of file DensityMap.h.