IMP  2.0.0
The Integrative Modeling Platform
IMP::em::MapDistanceTransform Class Reference

Class for getting the distance from the map envelope. More...

#include <IMP/em/MapDistanceTransform.h>

+ Inheritance diagram for IMP::em::MapDistanceTransform:

Public Member Functions

 MapDistanceTransform (IMP::em::DensityMap *map, float density_threshold, float max_distance)
 
float get_distance_from_envelope (const IMP::algebra::Vector3D &v) const
 
- Public Member Functions inherited from IMP::em::DensityMap
 DensityMap (std::string name="DensityMap%1%")
 
 DensityMap (const DensityHeader &header, std::string name="DensityMap%1%")
 Construct a density map as intructed in the input header.
 
void add (const DensityMap *other)
 
void calc_all_voxel2loc ()
 Calculates the coordinates that correspond to all voxels.
 
emreal calcRMS ()
 Calculates RMSD and mean of a map values are stored in the header. More...
 
void copy_map (const DensityMap *other)
 copy map into this map
 
algebra::Vector3D get_centroid (emreal threshold=0.0) const
 
DensityMapget_cropped (float threshold)
 Create a new cropped map. More...
 
DensityMapget_cropped (const algebra::BoundingBox3D &bb)
 Create a new cropped map with the 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 DensityHeaderget_header () const
 
DensityHeaderget_header_writable ()
 Returns a pointer to the header of the map in a writable version.
 
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)
 
emreal get_max_value () const
 Returns the the value of the voxel with the highest density.
 
float get_maximum_value_in_xy_plane (int z_ind)
 Get the maximum value in a XY plane indicated by a Z index.
 
float get_maximum_value_in_xz_plane (int y_ind)
 Get the maximum value in a XZ plane indicated by a Y index.
 
float get_maximum_value_in_yz_plane (int x_ind)
 Get the maximum value in a YZ plane indicated by a X index.
 
emreal get_min_value () const
 Returns the the value of the voxel with the lowest density.
 
long get_number_of_voxels () const
 number of map voxels
 
algebra::Vector3D get_origin () const
 
bool get_rms_calculated () const
 
Float get_spacing () const
 Updated the voxel size of the map. More...
 
algebra::Vector3D get_top () 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...
 
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 the voxel of a given location. More...
 
bool is_part_of_volume (const algebra::Vector3D &v) const
 Checks whether a given point is in the grid the voxel of a given location. 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)
 
void pad (int nx, int ny, int nz, float val=0.0)
 
DensityMappad_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)
 
void release ()
 
void reset_data (float value=0.0)
 Set the density voxels to some calue and reset the managment 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 a given index. 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 ()
 Normailze the density voxles according to standard deviation (stdv). More...
 
void update_voxel_size (float new_apix)
 Updated the voxel size of the map.
 
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 indexes. More...
 
- Public Member Functions inherited from IMP::base::Object
virtual void clear_caches ()
 
virtual IMP::base::VersionInfo get_version_info () const =0
 Get information about the module and version of the object.
 
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 Attributes

float max_distance_
 
std::vector< long > neighbors_
 
- Protected Attributes inherited from IMP::em::DensityMap
boost::scoped_array< emreal > data_
 
bool data_allocated_
 
DensityHeader header_
 
bool loc_calculated_
 true if the locations have already been computed
 
bool normalized_
 
bool rms_calculated_
 
boost::scoped_array< float > x_loc_
 
boost::scoped_array< float > y_loc_
 
boost::scoped_array< float > z_loc_
 

Additional Inherited Members

- Protected Member Functions inherited from IMP::em::DensityMap
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
 

Detailed Description

The class creates and stores a conversion of density map into a distance transform. The envelope voxels (that are determined using density_threshold) are zero distance. The rest of the voxels hold the distance to the closest envelop voxel. Positive distance means inside the object, negative - outside.

Definition at line 25 of file MapDistanceTransform.h.

Constructor & Destructor Documentation

IMP::em::MapDistanceTransform::MapDistanceTransform ( IMP::em::DensityMap map,
float  density_threshold,
float  max_distance 
)

init the distance transform

Parameters
[in]map- input density map
[in]density_threshold- a threshold that detemines the envelope of the map
[in]max_distance- how far from the envelope to compute the transform

Member Function Documentation

float IMP::em::MapDistanceTransform::get_distance_from_envelope ( const IMP::algebra::Vector3D v) const

get the distance from object envelope (-max_float is returned if the point is outside the grid)

Definition at line 41 of file MapDistanceTransform.h.

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