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IMP Reference Guide
2.19.0
The Integrative Modeling Platform
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Class for getting the distance from the map envelope. More...
#include <IMP/em/MapDistanceTransform.h>
Inheritance diagram for IMP::em::MapDistanceTransform:Class for getting the distance from the map envelope.
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 envelope voxel. Positive distance means inside the object, negative - outside.
Definition at line 25 of file MapDistanceTransform.h.
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 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... | |
| double | 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 (double 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 (Particles ps, double distance, bool inverse=false, bool keep_map_dimensions=false) |
| Create and return a new cropped map based on particles. 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... | |
| double | 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... | |
| double | 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 override |
| double | get_value (float x, float y, float z) const |
| Gets the value of the voxel located at (x,y,z) More... | |
| double | get_value (const algebra::Vector3D &point) const |
| double | get_value (long index) const |
| Gets the value of the voxel at a given index. More... | |
| virtual ::IMP::VersionInfo | get_version_info () const override |
| 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 (double loc, double kdist, double 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, double value) |
| Set the value of the voxel at a given index. More... | |
| void | set_value (float x, float y, float z, double 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 (double loc, double kdist, double 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 Attributes | |
| float | max_distance_ |
| std::vector< long > | neighbors_ |
| Protected Attributes inherited from IMP::em::DensityMap | |
| boost::scoped_array< double > | 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_ |
Additional Inherited Members | |
| Protected Member Functions inherited from IMP::em::DensityMap | |
| void | allocated_data () |
| void | float2real (float *f_data, boost::scoped_array< double > &r_data) |
| void | real2float (double *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 () |
| Related Functions inherited from IMP::em::DensityMap | |
| 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::MapDistanceTransform::MapDistanceTransform | ( | IMP::em::DensityMap * | map, |
| float | density_threshold, | ||
| float | max_distance | ||
| ) |
init the distance transform
| [in] | map | input density map |
| [in] | density_threshold | a threshold that determines the envelope of the map |
| [in] | max_distance | how far from the envelope to compute the transform |
| 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 40 of file MapDistanceTransform.h.
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