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VolumetricData Class Reference

Volumetric data class for potential maps, electron density maps, etc. More...

#include <VolumetricData.h>

List of all members.

Public Methods

VolumetricData (const char *name, const float *origin, const float *xaxis, const float *yaxis, const float *zaxis, int xs, int ys, int zs, float *dataptr)

constructors for both single- and double-precision axes. More...

VolumetricData (const char *name, const double *origin, const double *xaxis, const double *yaxis, const double *zaxis, int xs, int ys, int zs, float *dataptr)

constructor for double precision origin/axes info. More...

~VolumetricData ()

destructor. More...

ptrdiff_t gridsize () const

return total number of gridpoints. More...

void datarange (float &min, float &max)

return min/max data values. More...

void set_name (const char *name)

Sets data name to an internal copy of the provided string. More...

float mean ()

return the mean value of the density map, implemented via O(1) access to a cached value. More...

float sigma ()

return the standard deviation (sigma) of the density map, implemented via O(1) access to a cached value. More...

double integral ()

return integral of map as product of mean() times total volume. More...

void cell_lengths (float *xl, float *yl, float *zl) const

return cell side lengths. More...

void cell_axes (float *xax, float *yax, float *zax) const

return cell axes. More...

void cell_axes (double *xax, double *yax, double *zax) const

return cell axes. More...

void cell_dirs (float *xax, float *yax, float *zax) const

return cell axes directions. More...

double cell_volume () const

return cell volume. More...

void set_volume_axes (float *xax, float *yax, float *zax)

set volume/cell lengths. More...

void set_volume_axes (double *xax, double *yax, double *zax)

void scale_volume (double scalex, double scaley, double scalez)

scale volume/cell lengths. More...

void set_volume_origin (float *org)

set volume origin. More...

void set_volume_origin (double *org)

void voxel_coord_from_cartesian_coord (const float *carcoord, float *voxcoord, int shiftflag) const

return volumetric coordinate from cartesian coordinate. More...

ptrdiff_t voxel_index_from_coord (float xpos, float ypos, float zpos) const

return index of the voxel nearest to a cartesian coordinate. More...

float voxel_value (int x, int y, int z) const

return voxel at requested index, no safety checks. More...

float voxel_value_safe (int x, int y, int z) const

return voxel, after safely clamping index to valid range. More...

float voxel_value_interpolate (float xv, float yv, float zv) const

return interpolated value from 8 nearest neighbor voxels. More...

float voxel_value_from_coord (float xpos, float ypos, float zpos) const

return voxel value based on cartesian coordinates. More...

float voxel_value_interpolate_from_coord (float xpos, float ypos, float zpos) const

return interpolated value of voxel, based on cartesian coords. More...

float voxel_value_from_coord_safe (float xpos, float ypos, float zpos) const

return voxel value based on cartesian coordinates. safe versions return zero if coordinates are outside the map. More...

float voxel_value_interpolate_from_coord_safe (float xpos, float ypos, float zpos) const

return interpolated value of voxel, based on cartesian coords. this safe version returns zero if the coordinates are outside the map. More...

const float * access_volume_gradient ()

get read-only access to the gradient. More...

void set_volume_gradient (float *gradient)

provide the volume gradient. More...

void compute_volume_gradient (void)

(re)compute the volume gradient. More...

void voxel_gradient_fast (int x, int y, int z, float *grad) const

return gradient at requested index, no safety checks. More...

void voxel_gradient_safe (int x, int y, int z, float *grad) const

return gradient, after safely clamping index to valid range. More...

void voxel_gradient_interpolate (const float *voxcoord, float *gradient) const

interpolate the gradient between the eight neighboring voxels. More...

void voxel_gradient_from_coord (const float *coord, float *gradient) const

return voxel gradient based on cartesian coordinates. More...

void voxel_gradient_interpolate_from_coord (const float *coord, float *gradient) const

return interpolated voxel gradient for cartesian coordinate. More...

void voxel_coord (int x, int y, int z, float &gx, float &gy, float &gz) const

get the cartesian coordinate of a voxel given its x,y,z indices. More...

void voxel_coord (ptrdiff_t i, float &x, float &y, float &z) const

get the cartesian coordinate of a voxel given its 1-D index. More...

void pad (int padxm, int padxp, int padym, int padyp, int padzm, int padzp)

add or remove voxels in the given axis directions. More...

void crop (double crop_minx, double crop_miny, double crop_minz, double crop_maxx, double crop_maxy, double crop_maxz)

crop a volumetric data to a given set of cartesian coordinates. More...

void clamp (float min_value, float max_value)

clamp out of range voxel values. More...

void scale_by (float ff)

scales voxel data by given amount. More...

void scalar_add (float ff)

add scalar value to to all voxels. More...

void rescale_voxel_value_range (float min_value, float max_value)

rescale voxel data to a given range. More...

void downsample ()

decimate/dowmnsample voxels by 2 in each dimension (x8 total reduction). More...

void supersample ()

refine/supersample voxels by 2 in each dimension (x8 total increase). More...

void sigma_scale ()

Transform map to a sigma scale, so that isovalues in VMD correspond to number of sigmas above the mean. More...

void binmask (float threshold=0.0f)

Make a binary mask out of a map, i.e. map values > threshold are set to 1, and all others are set to 0. More...

void gaussian_blur (double sigma)

Guassian blur by sigma. More...

void mdff_potential (float threshold)

Create a potential for use with MDFF. More...

Public Attributes

double origin [3]

origin of volume (x=0, y=0, z=0 corner). More...

double xaxis [3]

direction and length for X axis (non-unit). More...

double yaxis [3]

direction and length for Y axis (non-unit). More...

double zaxis [3]

direction and length for Z axis (non-unit). More...

int xsize

int ysize

int zsize

number of samples along each axis. More...

char * name

human-readable volume dataset identifier. More...

float * data

raw data, total of xsize*ysize*zsize voxels stored x varying fastest, then y, then z. More...

Detailed Description

Volumetric data class for potential maps, electron density maps, etc.

Definition at line 35 of file VolumetricData.h.

Constructor & Destructor Documentation

VolumetricData::VolumetricData ( const char * name,

const float * origin,

const float * xaxis,

const float * yaxis,

const float * zaxis,

int xs,

int ys,

int zs,

float * dataptr

)

constructors for both single- and double-precision axes.

Definition at line 41 of file VolumetricData.C.
References data, name, NULL, origin, stringdup, xaxis, xsize, yaxis, ysize, zaxis, and zsize.

VolumetricData::VolumetricData ( const char * name,

const double * origin,

const double * xaxis,

const double * yaxis,

const double * zaxis,

int xs,

int ys,

int zs,

float * dataptr

)

constructor for double precision origin/axes info.

Definition at line 68 of file VolumetricData.C.
References data, name, NULL, origin, stringdup, xaxis, xsize, yaxis, ysize, zaxis, and zsize.

VolumetricData::~VolumetricData ( )

destructor.

Definition at line 95 of file VolumetricData.C.
References data, and name.

Member Function Documentation

const float * VolumetricData::access_volume_gradient ( )

get read-only access to the gradient.

Definition at line 415 of file VolumetricData.C.
References compute_volume_gradient, and NULL.
Referenced by IsoSurface::DoCellGeneral, and IsoSurface::DoGridPosNorms.

void VolumetricData::binmask ( float threshold = 0.0f )

Make a binary mask out of a map, i.e. map values > threshold are set to 1, and all others are set to 0.

Definition at line 1030 of file VolumetricData.C.
References data, gridsize, and threshold.
Referenced by density_binmask.

void VolumetricData::cell_axes ( double * xax,

double * yax,

double * zax

) const

return cell axes.

Definition at line 172 of file VolumetricData.C.
References xaxis, xsize, yaxis, ysize, zaxis, and zsize.

void VolumetricData::cell_axes ( float * xax,

float * yax,

float * zax

) const

return cell axes.

Definition at line 138 of file VolumetricData.C.
References xaxis, xsize, yaxis, ysize, zaxis, and zsize.
Referenced by cell_dirs, cell_volume, IsoSurface::compute, VolMapCreateCoulombPotentialMSM::compute_frame, VolMapCreateCoulombPotential::compute_frame, VolMapCreateOccupancy::compute_frame, VolMapCreateDensity::compute_frame, VolMapCreateMask::compute_frame, density_info, volmap_write_dx_file, voxel_coord, and voxel_coord.

void VolumetricData::cell_dirs ( float * xax,

float * yax,

float * zax

) const

return cell axes directions.

Definition at line 206 of file VolumetricData.C.
References cell_axes, and cell_lengths.
Referenced by IsoSurface::compute.

void VolumetricData::cell_lengths ( float * xl,

float * yl,

float * zl

) const

return cell side lengths.

Definition at line 112 of file VolumetricData.C.
References dot_prod, xaxis, xsize, yaxis, ysize, zaxis, and zsize.
Referenced by cell_dirs, and compute_volume_gradient.

double VolumetricData::cell_volume ( ) const

return cell volume.

Definition at line 227 of file VolumetricData.C.
References cell_axes.
Referenced by density_info, and integral.

void VolumetricData::clamp ( float min_value,

float max_value

)

clamp out of range voxel values.

Definition at line 693 of file VolumetricData.C.
References data, and gridsize.
Referenced by density_clamp.

void VolumetricData::compute_volume_gradient ( void )

(re)compute the volume gradient.

Definition at line 442 of file VolumetricData.C.
References cell_lengths, clamp_int, data, gridsize, voxel_value, xsize, ysize, and zsize.
Referenced by access_volume_gradient, BaseMolecule::add_volume_data, and vmd_measure_volinterior.

void VolumetricData::crop ( double crop_minx,

double crop_miny,

double crop_minz,

double crop_maxx,

double crop_maxy,

double crop_maxz

)

crop a volumetric data to a given set of cartesian coordinates.

Definition at line 674 of file VolumetricData.C.
References origin, pad, xaxis, xsize, yaxis, ysize, zaxis, and zsize.
Referenced by density_crop.

void VolumetricData::datarange ( float & min,

float & max

)

return min/max data values.

Definition at line 1116 of file VolumetricData.C.
Referenced by BaseMolecule::add_volume_data, density_info, AtomColor::find, VolumeTexture::generateContourLineTexture, histogram, and GraphicsFltkMenu::update_molchooser.

void VolumetricData::downsample ( )

decimate/dowmnsample voxels by 2 in each dimension (x8 total reduction).

Definition at line 792 of file VolumetricData.C.
References data, n, xaxis, xsize, yaxis, ysize, zaxis, and zsize.
Referenced by density_downsample.

void VolumetricData::gaussian_blur ( double sigma )

Guassian blur by sigma.

Definition at line 1051 of file VolumetricData.C.
References GaussianBlur::blur, data, GaussianBlur::get_image, sigma, xsize, ysize, and zsize.
Referenced by density_smooth.

ptrdiff_t VolumetricData::gridsize ( ) const [inline]

return total number of gridpoints.

Definition at line 59 of file VolumetricData.h.
References xsize, ysize, and zsize.
Referenced by add, BaseMolecule::add_volume_data, average, binmask, clamp, VolMapCreateILS::compute, compute_volume_gradient, countIsoGrids, histogram, init_from_identity, init_from_intersection, init_from_union, markIsoGrid, mdff_potential, multiply, normalize_pmap, process_pmap, rescale_voxel_value_range, scalar_add, scale_by, segment_volume, sigma_scale, subtract, vmd_volmap_compare, vol_com, and vol_probability.

double VolumetricData::integral ( )

return integral of map as product of mean() times total volume.

Definition at line 1190 of file VolumetricData.C.
References cell_volume, mean, xsize, ysize, and zsize.
Referenced by density_info.

void VolumetricData::mdff_potential ( float threshold )

Create a potential for use with MDFF.

Definition at line 1073 of file VolumetricData.C.
References data, gridsize, and threshold.
Referenced by density_mdff_potential.

float VolumetricData::mean ( )

return the mean value of the density map, implemented via O(1) access to a cached value.

Definition at line 1159 of file VolumetricData.C.
Referenced by density_info, integral, and sigma_scale.

void VolumetricData::pad ( int padxm,

int padxp,

int padym,

int padyp,

int padzm,

int padzp

)

add or remove voxels in the given axis directions.

Definition at line 601 of file VolumetricData.C.
References data, MAX, MIN, origin, vec_scaled_add, xaxis, xsize, yaxis, ysize, zaxis, and zsize.
Referenced by crop, and density_trim.

void VolumetricData::rescale_voxel_value_range ( float min_value,

float max_value

)

rescale voxel data to a given range.

Definition at line 767 of file VolumetricData.C.
References data, and gridsize.
Referenced by density_range.

void VolumetricData::scalar_add ( float ff )

add scalar value to to all voxels.

Definition at line 749 of file VolumetricData.C.
References data, and gridsize.
Referenced by density_sadd.

void VolumetricData::scale_by ( float ff )

scales voxel data by given amount.

Definition at line 724 of file VolumetricData.C.
References data, and gridsize.
Referenced by density_smult.

void VolumetricData::scale_volume ( double scalex,

double scaley,

double scalez

) [inline]

scale volume/cell lengths.

Definition at line 124 of file VolumetricData.h.
References xaxis, yaxis, and zaxis.
Referenced by text_cmd_mol.

void VolumetricData::set_name ( const char * name )

Sets data name to an internal copy of the provided string.

Definition at line 104 of file VolumetricData.C.
References name.
Referenced by VolMapCreateCoulombPotentialMSM::compute_init, VolMapCreateCoulombPotential::compute_init, VolMapCreateDistance::compute_init, VolMapCreateOccupancy::compute_init, VolMapCreateInterp::compute_init, VolMapCreateDensity::compute_init, VolMapCreateMask::compute_init, and VolMapCreateILS::write_map.

void VolumetricData::set_volume_axes ( double * xax,

double * yax,

double * zax

) [inline]

Definition at line 108 of file VolumetricData.h.
References xaxis, yaxis, and zaxis.

void VolumetricData::set_volume_axes ( float * xax,

float * yax,

float * zax

) [inline]

set volume/cell lengths.

Definition at line 93 of file VolumetricData.h.
References xaxis, yaxis, and zaxis.
Referenced by text_cmd_mol.

void VolumetricData::set_volume_gradient ( float * gradient )

provide the volume gradient.

Definition at line 424 of file VolumetricData.C.
References NULL, xsize, ysize, and zsize.
Referenced by BaseMolecule::add_volume_data.

void VolumetricData::set_volume_origin ( double * org ) [inline]

Definition at line 147 of file VolumetricData.h.
References origin.

void VolumetricData::set_volume_origin ( float * org ) [inline]

set volume origin.

Definition at line 140 of file VolumetricData.h.
References origin.
Referenced by text_cmd_mol.

float VolumetricData::sigma ( )

return the standard deviation (sigma) of the density map, implemented via O(1) access to a cached value.

Definition at line 1176 of file VolumetricData.C.
Referenced by density_info, gaussian_blur, and sigma_scale.

void VolumetricData::sigma_scale ( )

Transform map to a sigma scale, so that isovalues in VMD correspond to number of sigmas above the mean.

Definition at line 1009 of file VolumetricData.C.
References data, gridsize, mean, and sigma.
Referenced by density_sigma.

void VolumetricData::supersample ( )

refine/supersample voxels by 2 in each dimension (x8 total increase).

Definition at line 845 of file VolumetricData.C.
References cubic_interp, data, xsize, ysize, and zsize.
Referenced by density_supersample.

void VolumetricData::voxel_coord ( ptrdiff_t i,

float & x,

float & y,

float & z

) const [inline]

get the cartesian coordinate of a voxel given its 1-D index.

Definition at line 221 of file VolumetricData.h.
References cell_axes, origin, xsize, ysize, and z.

void VolumetricData::voxel_coord ( int x,

int y,

int z,

float & gx,

float & gy,

float & gz

) const [inline]

get the cartesian coordinate of a voxel given its x,y,z indices.

Definition at line 210 of file VolumetricData.h.
References cell_axes, origin, and z.
Referenced by add, average, multiply, subtract, and vol_com.

void VolumetricData::voxel_coord_from_cartesian_coord ( const float * carcoord,

float * voxcoord,

int shiftflag

) const

return volumetric coordinate from cartesian coordinate.

Definition at line 242 of file VolumetricData.C.
References Matrix4::inverse, Matrix4::multpoint3d, origin, xaxis, xsize, yaxis, ysize, zaxis, and zsize.
Referenced by colvarproxy_vmd::compute_voldata, voxel_gradient_from_coord, voxel_gradient_interpolate_from_coord, voxel_index_from_coord, voxel_value_interpolate_from_coord, and voxel_value_interpolate_from_coord_safe.

void VolumetricData::voxel_gradient_fast ( int x,

int y,

int z,

float * grad

) const [inline]

return gradient at requested index, no safety checks.

Definition at line 192 of file VolumetricData.h.
References xsize, ysize, and z.

void VolumetricData::voxel_gradient_from_coord ( const float * coord,

float * gradient

) const

return voxel gradient based on cartesian coordinates.

Definition at line 570 of file VolumetricData.C.
References voxel_coord_from_cartesian_coord, and voxel_gradient_safe.

void VolumetricData::voxel_gradient_interpolate ( const float * voxcoord,

float * gradient

) const

interpolate the gradient between the eight neighboring voxels.

Definition at line 531 of file VolumetricData.C.
References vec_lerp, voxel_gradient_safe, and z.
Referenced by colvarproxy_vmd::compute_voldata, and voxel_gradient_interpolate_from_coord.

void VolumetricData::voxel_gradient_interpolate_from_coord ( const float * coord,

float * gradient

) const

return interpolated voxel gradient for cartesian coordinate.

Definition at line 582 of file VolumetricData.C.
References NAN, voxel_coord_from_cartesian_coord, voxel_gradient_interpolate, xsize, ysize, and zsize.

void VolumetricData::voxel_gradient_safe ( int x,

int y,

int z,

float * grad

) const

return gradient, after safely clamping index to valid range.

Definition at line 518 of file VolumetricData.C.
References xsize, ysize, z, and zsize.
Referenced by voxel_gradient_from_coord, and voxel_gradient_interpolate.

ptrdiff_t VolumetricData::voxel_index_from_coord ( float xpos,

float ypos,

float zpos

) const

return index of the voxel nearest to a cartesian coordinate.

Definition at line 280 of file VolumetricData.C.
References voxel_coord_from_cartesian_coord, xsize, ysize, and zsize.
Referenced by atomsel_gridindex_array, voxel_value_from_coord, and voxel_value_from_coord_safe.

float VolumetricData::voxel_value ( int x,

int y,

int z

) const [inline]

return voxel at requested index, no safety checks.

Definition at line 162 of file VolumetricData.h.
References data, xsize, ysize, and z.
Referenced by compute_volume_gradient, and volmap_write_dx_file.

float VolumetricData::voxel_value_from_coord ( float xpos,

float ypos,

float zpos

) const

return voxel value based on cartesian coordinates.

Definition at line 343 of file VolumetricData.C.
References data, NAN, and voxel_index_from_coord.
Referenced by atomsel_volume_array, and multiply.

float VolumetricData::voxel_value_from_coord_safe ( float xpos,

float ypos,

float zpos

) const

return voxel value based on cartesian coordinates. safe versions return zero if coordinates are outside the map.

Definition at line 375 of file VolumetricData.C.
References data, and voxel_index_from_coord.
Referenced by add, average, and subtract.

float VolumetricData::voxel_value_interpolate ( float xv,

float yv,

float zv

) const

return interpolated value from 8 nearest neighbor voxels.

Definition at line 312 of file VolumetricData.C.
References voxel_value_safe, and z.
Referenced by colvarproxy_vmd::compute_voldata, VolumeTexture::generateContourLineTexture, voxel_value_interpolate_from_coord, and voxel_value_interpolate_from_coord_safe.

float VolumetricData::voxel_value_interpolate_from_coord ( float xpos,

float ypos,

float zpos

) const

return interpolated value of voxel, based on cartesian coords.

Definition at line 353 of file VolumetricData.C.
References NAN, voxel_coord_from_cartesian_coord, voxel_value_interpolate, xsize, ysize, and zsize.
Referenced by atomsel_interp_volume_array, and multiply.

float VolumetricData::voxel_value_interpolate_from_coord_safe ( float xpos,

float ypos,

float zpos

) const

return interpolated value of voxel, based on cartesian coords. this safe version returns zero if the coordinates are outside the map.

Definition at line 386 of file VolumetricData.C.
References voxel_coord_from_cartesian_coord, voxel_value_interpolate, xsize, ysize, and zsize.
Referenced by add, average, and subtract.

float VolumetricData::voxel_value_safe ( int x,

int y,

int z

) const

return voxel, after safely clamping index to valid range.

Definition at line 301 of file VolumetricData.C.
References data, xsize, ysize, z, and zsize.
Referenced by voxel_value_interpolate.

Member Data Documentation

float* VolumetricData::data

raw data, total of xsize*ysize*zsize voxels stored x varying fastest, then y, then z.

Definition at line 43 of file VolumetricData.h.
Referenced by add, VolMapCreateILS::add_map_to_molecule, average, binmask, cc_threaded, clamp, VolMapCreate::combo_begin, VolMapCreate::combo_export, VolMapCreateILS::compute, VolMapCreate::compute_all, compute_volume_gradient, countIsoGrids, IsoContour::DoCell, IsoSurface::DoCellGeneral, IsoSurface::DoGridPosNorms, downsample, gaussian_blur, VolumeTexture::generateChargeTexture, VolumeTexture::generateColorScaleTexture, VolumeTexture::generateHSVTexture, histogram, init_from_identity, init_from_intersection, init_from_union, init_new_volume_molecule, markIsoGrid, mdff_cc, mdff_potential, multiply, normalize_pmap, pad, process_pmap, py_mol_get_volumetric, RaycastGrid, rescale_voxel_value_range, scalar_add, scale_by, segment_volume, Segmentation::Segmentation, sigma_scale, subtract, supersample, vmd_cuda_calc_density, vmd_cuda_compare_sel_refmap, vmd_measure_volinterior, vmd_volmap_compare, vmd_volmap_new_fromtype, vol_com, vol_probability, VolIn_CleanGrid, volin_threaded, volin_threaded_prob, volmap_write_dx_file, VolumetricData, voxel_value, voxel_value_from_coord, voxel_value_from_coord_safe, voxel_value_safe, MolFilePlugin::write_volumetric, and ~VolumetricData.

char* VolumetricData::name

human-readable volume dataset identifier.

Definition at line 42 of file VolumetricData.h.
Referenced by VolMapCreateILS::add_map_to_molecule, BaseMolecule::add_volume_data, mdff_cc, SaveTrajectoryFltkMenu::molchooser_activate_selection, set_name, GraphicsFltkMenu::update_molchooser, vmd_measure_volinterior, vmd_volmap_new_fromtype, GraphicsFltkMenu::volindex_update, volmap_write_dx_file, VolumetricData, MolFilePlugin::write_volumetric, and ~VolumetricData.

double VolumetricData::origin[3]

origin of volume (x=0, y=0, z=0 corner).

Definition at line 37 of file VolumetricData.h.
Referenced by VolMapCreateILS::add_map_to_molecule, calc_density_bounds_overlapping_map, VolMapCreateCoulombPotentialMSM::compute_frame, VolMapCreateCoulombPotential::compute_frame, VolMapCreateDistance::compute_frame, VolMapCreateOccupancy::compute_frame, VolMapCreateInterp::compute_frame, VolMapCreateDensity::compute_frame, VolMapCreateMask::compute_frame, VolMapCreate::compute_init, DrawMolecule::cov, CreateEmptyGrid, CreateProbGrid, crop, density_info, density_rotate, IsoContour::DoCell, IsoSurface::DoCellGeneral, IsoSurface::DoGridPosNorms, init_from_identity, init_from_intersection, init_from_union, init_new_volume_molecule, mdff_cc, normalize_pmap, pad, prepare_texture_coordinates, process_pmap, py_mol_get_volumetric, segment_volume, IsoSurface::set_color_voltex_rgb3fv, set_volume_origin, text_cmd_mol, vmd_cuda_calc_density, vmd_measure_volinterior, vmd_volmap_compare, vmd_volmap_new_fromtype, vol_move, vol_moveto, volmap_write_dx_file, VolumetricData, voxel_coord, voxel_coord, voxel_coord_from_cartesian_coord, and MolFilePlugin::write_volumetric.

double VolumetricData::xaxis[3]

direction and length for X axis (non-unit).

Definition at line 38 of file VolumetricData.h.
Referenced by VolMapCreateILS::add_map_to_molecule, calc_density_bounds_overlapping_map, cell_axes, cell_lengths, IsoContour::compute, VolMapCreate::compute_init, DrawMolecule::cov, CreateEmptyGrid, CreateProbGrid, crop, density_rotate, downsample, init_from_identity, init_from_intersection, init_from_union, init_new_volume_molecule, mdff_cc, normalize_pmap, pad, prepare_texture_coordinates, process_pmap, py_mol_get_volumetric, DrawMolecule::scale_factor, scale_volume, segment_volume, set_volume_axes, text_cmd_mol, vmd_cuda_calc_density, vmd_cuda_compare_sel_refmap, vmd_measure_volinterior, vmd_volmap_compare, vmd_volmap_new_fromtype, vol_move, VolumetricData, voxel_coord_from_cartesian_coord, and MolFilePlugin::write_volumetric.

int VolumetricData::xsize

Definition at line 41 of file VolumetricData.h.
Referenced by VolMapCreateILS::add_map_to_molecule, calc_density_bounds_overlapping_map, cc_threaded, cell_axes, cell_lengths, VolMapCreate::combo_addframe, VolMapCreate::combo_begin, VolMapCreate::combo_export, VolMapCreateILS::compute, IsoSurface::compute, IsoContour::compute, VolMapCreate::compute_all, VolMapCreateCoulombPotentialMSM::compute_frame, VolMapCreateCoulombPotential::compute_frame, VolMapCreateDistance::compute_frame, VolMapCreateOccupancy::compute_frame, VolMapCreateInterp::compute_frame, VolMapCreateDensity::compute_frame, VolMapCreateMask::compute_frame, VolMapCreate::compute_init, colvarproxy_vmd::compute_voldata, compute_volume_gradient, CreateEmptyGrid, CreateProbGrid, crop, density_info, IsoContour::DoCell, IsoSurface::DoCellGeneral, IsoSurface::DoGridPosNorms, downsample, gaussian_blur, VolumeTexture::generateChargeTexture, VolumeTexture::generateColorScaleTexture, VolumeTexture::generateContourLineTexture, VolumeTexture::generateHSVTexture, gridsize, init_from_identity, init_from_intersection, init_from_union, init_new_volume_molecule, integral, mdff_cc, normalize_pmap, pad, process_pmap, py_mol_get_volumetric, RaycastGrid, segment_volume, Segmentation::Segmentation, IsoSurface::set_color_voltex_rgb3fv, set_volume_gradient, supersample, vmd_cuda_calc_density, vmd_cuda_compare_sel_refmap, vmd_measure_volinterior, vmd_volmap_compare, vmd_volmap_new_fromtype, VolIn_CleanGrid, volin_threaded, volin_threaded_prob, volmap_write_dx_file, VolumetricData, voxel_coord, voxel_coord, voxel_coord_from_cartesian_coord, voxel_gradient_fast, voxel_gradient_interpolate_from_coord, voxel_gradient_safe, voxel_index_from_coord, voxel_value, voxel_value_interpolate_from_coord, voxel_value_interpolate_from_coord_safe, voxel_value_safe, and MolFilePlugin::write_volumetric.

double VolumetricData::yaxis[3]

direction and length for Y axis (non-unit).

Definition at line 39 of file VolumetricData.h.
Referenced by VolMapCreateILS::add_map_to_molecule, calc_density_bounds_overlapping_map, cell_axes, cell_lengths, IsoContour::compute, VolMapCreate::compute_init, DrawMolecule::cov, CreateEmptyGrid, CreateProbGrid, crop, density_rotate, downsample, init_from_identity, init_from_intersection, init_from_union, init_new_volume_molecule, mdff_cc, normalize_pmap, pad, prepare_texture_coordinates, process_pmap, py_mol_get_volumetric, DrawMolecule::scale_factor, scale_volume, segment_volume, set_volume_axes, text_cmd_mol, vmd_cuda_calc_density, vmd_cuda_compare_sel_refmap, vmd_measure_volinterior, vmd_volmap_compare, vmd_volmap_new_fromtype, vol_move, VolumetricData, voxel_coord_from_cartesian_coord, and MolFilePlugin::write_volumetric.

int VolumetricData::ysize

Definition at line 41 of file VolumetricData.h.
Referenced by VolMapCreateILS::add_map_to_molecule, calc_density_bounds_overlapping_map, cc_threaded, cell_axes, cell_lengths, VolMapCreate::combo_addframe, VolMapCreate::combo_begin, VolMapCreate::combo_export, VolMapCreateILS::compute, IsoSurface::compute, IsoContour::compute, VolMapCreate::compute_all, VolMapCreateCoulombPotentialMSM::compute_frame, VolMapCreateCoulombPotential::compute_frame, VolMapCreateDistance::compute_frame, VolMapCreateOccupancy::compute_frame, VolMapCreateInterp::compute_frame, VolMapCreateDensity::compute_frame, VolMapCreateMask::compute_frame, VolMapCreate::compute_init, colvarproxy_vmd::compute_voldata, compute_volume_gradient, CreateEmptyGrid, CreateProbGrid, crop, density_info, IsoContour::DoCell, IsoSurface::DoCellGeneral, IsoSurface::DoGridPosNorms, downsample, gaussian_blur, VolumeTexture::generateChargeTexture, VolumeTexture::generateColorScaleTexture, VolumeTexture::generateContourLineTexture, VolumeTexture::generateHSVTexture, gridsize, init_from_identity, init_from_intersection, init_from_union, init_new_volume_molecule, integral, mdff_cc, normalize_pmap, pad, process_pmap, py_mol_get_volumetric, RaycastGrid, segment_volume, Segmentation::Segmentation, IsoSurface::set_color_voltex_rgb3fv, set_volume_gradient, supersample, vmd_cuda_calc_density, vmd_cuda_compare_sel_refmap, vmd_measure_volinterior, vmd_volmap_compare, vmd_volmap_new_fromtype, VolIn_CleanGrid, volin_threaded, volin_threaded_prob, volmap_write_dx_file, VolumetricData, voxel_coord, voxel_coord, voxel_coord_from_cartesian_coord, voxel_gradient_fast, voxel_gradient_interpolate_from_coord, voxel_gradient_safe, voxel_index_from_coord, voxel_value, voxel_value_interpolate_from_coord, voxel_value_interpolate_from_coord_safe, voxel_value_safe, and MolFilePlugin::write_volumetric.

double VolumetricData::zaxis[3]

direction and length for Z axis (non-unit).

Definition at line 40 of file VolumetricData.h.
Referenced by VolMapCreateILS::add_map_to_molecule, calc_density_bounds_overlapping_map, cell_axes, cell_lengths, IsoContour::compute, VolMapCreate::compute_init, DrawMolecule::cov, CreateEmptyGrid, CreateProbGrid, crop, density_rotate, downsample, init_from_identity, init_from_intersection, init_from_union, init_new_volume_molecule, mdff_cc, normalize_pmap, pad, prepare_texture_coordinates, process_pmap, py_mol_get_volumetric, DrawMolecule::scale_factor, scale_volume, segment_volume, set_volume_axes, text_cmd_mol, vmd_cuda_calc_density, vmd_cuda_compare_sel_refmap, vmd_measure_volinterior, vmd_volmap_compare, vmd_volmap_new_fromtype, vol_move, VolumetricData, voxel_coord_from_cartesian_coord, and MolFilePlugin::write_volumetric.

int VolumetricData::zsize

number of samples along each axis.

Definition at line 41 of file VolumetricData.h.
Referenced by VolMapCreateILS::add_map_to_molecule, calc_density_bounds_overlapping_map, cc_threaded, cell_axes, cell_lengths, VolMapCreate::combo_addframe, VolMapCreate::combo_begin, VolMapCreate::combo_export, IsoSurface::compute, IsoContour::compute, VolMapCreate::compute_all, VolMapCreateCoulombPotentialMSM::compute_frame, VolMapCreateCoulombPotential::compute_frame, VolMapCreateDistance::compute_frame, VolMapCreateOccupancy::compute_frame, VolMapCreateInterp::compute_frame, VolMapCreateDensity::compute_frame, VolMapCreateMask::compute_frame, VolMapCreate::compute_init, colvarproxy_vmd::compute_voldata, compute_volume_gradient, CreateEmptyGrid, CreateProbGrid, crop, density_info, IsoSurface::DoGridPosNorms, downsample, gaussian_blur, VolumeTexture::generateChargeTexture, VolumeTexture::generateColorScaleTexture, VolumeTexture::generateContourLineTexture, VolumeTexture::generateHSVTexture, gridsize, init_from_identity, init_from_intersection, init_from_union, init_new_volume_molecule, integral, mdff_cc, normalize_pmap, pad, process_pmap, py_mol_get_volumetric, RaycastGrid, segment_volume, Segmentation::Segmentation, IsoSurface::set_color_voltex_rgb3fv, set_volume_gradient, supersample, vmd_cuda_calc_density, vmd_cuda_compare_sel_refmap, vmd_measure_volinterior, vmd_volmap_compare, vmd_volmap_new_fromtype, VolIn_CleanGrid, volin_threaded, volin_threaded_prob, volmap_write_dx_file, VolumetricData, voxel_coord_from_cartesian_coord, voxel_gradient_interpolate_from_coord, voxel_gradient_safe, voxel_index_from_coord, voxel_value_interpolate_from_coord, voxel_value_interpolate_from_coord_safe, voxel_value_safe, and MolFilePlugin::write_volumetric.

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

Generated on Fri Jan 23 01:53:15 2026 for VMD (current) by

Public Methods
	VolumetricData (const char name, const float origin, const float xaxis, const float yaxis, const float zaxis, int xs, int ys, int zs, float dataptr)
	constructors for both single- and double-precision axes. More...
	VolumetricData (const char name, const double origin, const double xaxis, const double yaxis, const double zaxis, int xs, int ys, int zs, float dataptr)
	constructor for double precision origin/axes info. More...
	~VolumetricData ()
	destructor. More...
ptrdiff_t	gridsize () const
	return total number of gridpoints. More...
void	datarange (float &min, float &max)
	return min/max data values. More...
void	set_name (const char *name)
	Sets data name to an internal copy of the provided string. More...
float	mean ()
	return the mean value of the density map, implemented via O(1) access to a cached value. More...
float	sigma ()
	return the standard deviation (sigma) of the density map, implemented via O(1) access to a cached value. More...
double	integral ()
	return integral of map as product of mean() times total volume. More...
void	cell_lengths (float xl, float yl, float *zl) const
	return cell side lengths. More...
void	cell_axes (float xax, float yax, float *zax) const
	return cell axes. More...
void	cell_axes (double xax, double yax, double *zax) const
	return cell axes. More...
void	cell_dirs (float xax, float yax, float *zax) const
	return cell axes directions. More...
double	cell_volume () const
	return cell volume. More...
void	set_volume_axes (float xax, float yax, float *zax)
	set volume/cell lengths. More...
void	set_volume_axes (double xax, double yax, double *zax)
void	scale_volume (double scalex, double scaley, double scalez)
	scale volume/cell lengths. More...
void	set_volume_origin (float *org)
	set volume origin. More...
void	set_volume_origin (double *org)
void	voxel_coord_from_cartesian_coord (const float carcoord, float voxcoord, int shiftflag) const
	return volumetric coordinate from cartesian coordinate. More...
ptrdiff_t	voxel_index_from_coord (float xpos, float ypos, float zpos) const
	return index of the voxel nearest to a cartesian coordinate. More...
float	voxel_value (int x, int y, int z) const
	return voxel at requested index, no safety checks. More...
float	voxel_value_safe (int x, int y, int z) const
	return voxel, after safely clamping index to valid range. More...
float	voxel_value_interpolate (float xv, float yv, float zv) const
	return interpolated value from 8 nearest neighbor voxels. More...
float	voxel_value_from_coord (float xpos, float ypos, float zpos) const
	return voxel value based on cartesian coordinates. More...
float	voxel_value_interpolate_from_coord (float xpos, float ypos, float zpos) const
	return interpolated value of voxel, based on cartesian coords. More...
float	voxel_value_from_coord_safe (float xpos, float ypos, float zpos) const
	return voxel value based on cartesian coordinates. safe versions return zero if coordinates are outside the map. More...
float	voxel_value_interpolate_from_coord_safe (float xpos, float ypos, float zpos) const
	return interpolated value of voxel, based on cartesian coords. this safe version returns zero if the coordinates are outside the map. More...
const float *	access_volume_gradient ()
	get read-only access to the gradient. More...
void	set_volume_gradient (float *gradient)
	provide the volume gradient. More...
void	compute_volume_gradient (void)
	(re)compute the volume gradient. More...
void	voxel_gradient_fast (int x, int y, int z, float *grad) const
	return gradient at requested index, no safety checks. More...
void	voxel_gradient_safe (int x, int y, int z, float *grad) const
	return gradient, after safely clamping index to valid range. More...
void	voxel_gradient_interpolate (const float voxcoord, float gradient) const
	interpolate the gradient between the eight neighboring voxels. More...
void	voxel_gradient_from_coord (const float coord, float gradient) const
	return voxel gradient based on cartesian coordinates. More...
void	voxel_gradient_interpolate_from_coord (const float coord, float gradient) const
	return interpolated voxel gradient for cartesian coordinate. More...
void	voxel_coord (int x, int y, int z, float &gx, float &gy, float &gz) const
	get the cartesian coordinate of a voxel given its x,y,z indices. More...
void	voxel_coord (ptrdiff_t i, float &x, float &y, float &z) const
	get the cartesian coordinate of a voxel given its 1-D index. More...
void	pad (int padxm, int padxp, int padym, int padyp, int padzm, int padzp)
	add or remove voxels in the given axis directions. More...
void	crop (double crop_minx, double crop_miny, double crop_minz, double crop_maxx, double crop_maxy, double crop_maxz)
	crop a volumetric data to a given set of cartesian coordinates. More...
void	clamp (float min_value, float max_value)
	clamp out of range voxel values. More...
void	scale_by (float ff)
	scales voxel data by given amount. More...
void	scalar_add (float ff)
	add scalar value to to all voxels. More...
void	rescale_voxel_value_range (float min_value, float max_value)
	rescale voxel data to a given range. More...
void	downsample ()
	decimate/dowmnsample voxels by 2 in each dimension (x8 total reduction). More...
void	supersample ()
	refine/supersample voxels by 2 in each dimension (x8 total increase). More...
void	sigma_scale ()
	Transform map to a sigma scale, so that isovalues in VMD correspond to number of sigmas above the mean. More...
void	binmask (float threshold=0.0f)
	Make a binary mask out of a map, i.e. map values > threshold are set to 1, and all others are set to 0. More...
void	gaussian_blur (double sigma)
	Guassian blur by sigma. More...
void	mdff_potential (float threshold)
	Create a potential for use with MDFF. More...
Public Attributes
double	origin [3]
	origin of volume (x=0, y=0, z=0 corner). More...
double	xaxis [3]
	direction and length for X axis (non-unit). More...
double	yaxis [3]
	direction and length for Y axis (non-unit). More...
double	zaxis [3]
	direction and length for Z axis (non-unit). More...
int	xsize
int	ysize
int	zsize
	number of samples along each axis. More...
char *	name
	human-readable volume dataset identifier. More...
float *	data
	raw data, total of xsizeysizezsize voxels stored x varying fastest, then y, then z. More...