Class for sampling a density map from particles.
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| | SampledDensityMap (KernelType kt=GAUSSIAN) |
| | Creates a new density map for sampled map. More...
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| SampledDensityMap (const DensityHeader &header, KernelType kt=GAUSSIAN) |
| | The size of the map is determined by the header and the data is allocated.
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| | SampledDensityMap (const kernel::ParticlesTemp &ps, emreal resolution, emreal voxel_size, IMP::FloatKey mass_key=IMP::atom::Mass::get_mass_key(), int sig_cuttoff=3, KernelType kt=GAUSSIAN) |
| | Generate a sampled density map from the particles. More...
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KernelParameters * | get_kernel_params () |
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float | get_minimum_resampled_value () |
| | Get minimum density value between voxels that correspond to particles.
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const kernel::Particles & | get_sampled_particles () const |
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FloatKey | get_weight_key () const |
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const core::XYZRs & | get_xyzr_particles () const |
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| void | project (const kernel::ParticlesTemp &ps, int x_margin, int y_margin, int z_margin, algebra::Vector3D shift=algebra::Vector3D(0., 0., 0.), FloatKey mass_key=atom::Mass::get_mass_key()) |
| | Project particles on the grid by their mass value. More...
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| virtual void | resample () |
| | Resample beads on an EM grid. More...
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void | set_particles (const kernel::ParticlesTemp &ps, IMP::FloatKey mass_key=IMP::atom::Mass::get_mass_key()) |
| | setting particles in case they were not set by the constructor
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| DensityMap (std::string name="DensityMap%1%") |
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| DensityMap (const DensityHeader &header, std::string name="DensityMap%1%") |
| | Construct a density map as intructed in the input header.
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| void | add (const DensityMap *other) |
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void | calc_all_voxel2loc () |
| | Calculates the coordinates that correspond to all voxels.
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| emreal | calcRMS () |
| | Calculates RMSD and mean of a map values are stored in the header. More...
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void | copy_map (const DensityMap *other) |
| | copy map into this map
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| algebra::Vector3D | get_centroid (emreal threshold=0.0) const |
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| DensityMap * | get_cropped (float threshold) |
| | Create a new cropped map. More...
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| DensityMap * | get_cropped (const algebra::BoundingBox3D &bb) |
| | Create a new cropped map with the bounding box extent. More...
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| int | get_dim_index_by_location (const algebra::Vector3D &v, int ind) const |
| | Calculate dimension index of a given location. More...
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int | get_dim_index_by_location (float loc_val, int ind) const |
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const DensityHeader * | get_header () const |
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DensityHeader * | get_header_writable () |
| | Returns a pointer to the header of the map in a writable version.
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| algebra::Vector3D | get_location_by_voxel (long index) const |
| | Calculate the location of a given voxel. More...
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| float | get_location_in_dim_by_voxel (long index, int dim) const |
| | Calculate the location of a given voxel in a given dimension. More...
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| std::string | get_locations_string (float t) |
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emreal | get_max_value () const |
| | Returns the the value of the voxel with the highest density.
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float | get_maximum_value_in_xy_plane (int z_ind) |
| | Get the maximum value in a XY plane indicated by a Z index.
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float | get_maximum_value_in_xz_plane (int y_ind) |
| | Get the maximum value in a XZ plane indicated by a Y index.
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float | get_maximum_value_in_yz_plane (int x_ind) |
| | Get the maximum value in a YZ plane indicated by a X index.
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emreal | get_min_value () const |
| | Returns the the value of the voxel with the lowest density.
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long | get_number_of_voxels () const |
| | number of map voxels
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algebra::Vector3D | get_origin () const |
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bool | get_rms_calculated () const |
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| Float | get_spacing () const |
| | Updated the voxel size of the map. More...
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algebra::Vector3D | get_top () const |
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virtual std::string | get_type_name () const |
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| emreal | get_value (float x, float y, float z) const |
| | Gets the value of the voxel located at (x,y,z) More...
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emreal | get_value (const algebra::Vector3D &point) const |
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| emreal | get_value (long index) const |
| | Gets the value of the voxel at a given index. More...
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virtual ::IMP::base::VersionInfo | get_version_info () const |
| | Get information about the module and version of the object.
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| long | get_voxel_by_location (float x, float y, float z) const |
| | Calculate the voxel of a given location. More...
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| long | get_voxel_by_location (const algebra::Vector3D &v) const |
| | Calculate the voxel of a given location. More...
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bool | is_normalized () const |
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| 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...
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| 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...
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bool | is_xyz_ind_part_of_volume (int ix, int iy, int iz) const |
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int | lower_voxel_shift (emreal loc, emreal kdist, emreal orig, int ndim) const |
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| void | multiply (float factor) |
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| void | pad (int nx, int ny, int nz, float val=0.0) |
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| DensityMap * | pad_margin (int mrg_x, int mrg_y, int mrg_z, float val=0.0) |
| | Create a new padded map. More...
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| void | pick_max (const DensityMap *other) |
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void | release () |
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| void | reset_data (float value=0.0) |
| | Set the density voxels to some calue and reset the managment flags. More...
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| bool | same_dimensions (const DensityMap *other) const |
| | Checks if two maps have the same dimensions. More...
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| bool | same_origin (const DensityMap *other) const |
| | Checks if two maps have the same origin. More...
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| bool | same_voxel_size (const DensityMap *other) const |
| | Checks if two maps have the same voxel size. More...
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| void | set_origin (float x, float y, float z) |
| | Sets the origin of the header. More...
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void | set_origin (const IMP::algebra::Vector3D &v) |
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| void | set_value (long index, emreal value) |
| | Set the value of the voxel at a given index. More...
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| void | set_value (float x, float y, float z, emreal value) |
| | Set the value of the voxel at a given index. More...
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| void | set_void_map (int nx, int ny, int nz) |
| | Set the map dimension and reset all voxels to 0. More...
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| void | std_normalize () |
| | Normailze the density voxles according to standard deviation (stdv). More...
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void | update_voxel_size (float new_apix) |
| | Updated the voxel size of the map.
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int | upper_voxel_shift (emreal loc, emreal kdist, emreal orig, int ndim) const |
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| long | xyz_ind2voxel (int x, int y, int z) const |
| | Calculate the voxel of a given xyz indexes. More...
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| virtual void | clear_caches () |
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| virtual void | do_destroy () |
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CheckLevel | get_check_level () const |
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LogLevel | get_log_level () const |
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| void | set_check_level (CheckLevel l) |
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| void | set_log_level (LogLevel l) |
| | Set the logging level used in this object. More...
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| void | set_was_used (bool tf) const |
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void | show (std::ostream &out=std::cout) const |
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const std::string & | get_name () const |
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void | set_name (std::string name) |
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Inheritance diagram for IMP::em::SampledDensityMap: