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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)

constructor. More...

~VolumetricData ()

destructor. More...

int gridsize () const

return total number of gridpoints. More...

void set_name (const char *name)

Sets data name to an internal copy of the provided string. 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_dirs (float *xax, float *yax, float *zax) const

return cell axes directions. More...

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

return volumetric coordinate from cartesian coordinate. More...

int 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...

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...

Public Attributes

char * name

human-readable volume dataset identifier. More...

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...

float * data

raw data, total of xsize*ysize*zsize voxels. More...

float * gradient

negated normalized volume gradient map. More...

float datamin

float datamax

min and max data values. More...

Detailed Description

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

Definition at line 27 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

)

constructor.

Definition at line 36 of file VolumetricData.C.
References data, datamax, datamin, gradient, name, NULL, origin, stringdup, xaxis, xsize, yaxis, ysize, zaxis, and zsize.

VolumetricData::~VolumetricData ( )

destructor.

Definition at line 70 of file VolumetricData.C.
References data, gradient, and name.

Member Function Documentation

void VolumetricData::cell_axes ( float * xax,

float * yax,

float * zax

) const

return cell axes.

Definition at line 112 of file VolumetricData.C.
References xaxis, xsize, yaxis, ysize, zaxis, and zsize.
Referenced by cell_dirs, IsoSurface::compute, VolMapCreateCoulombPotentialMSM::compute_frame, VolMapCreateCoulombPotential::compute_frame, VolMapCreateOccupancy::compute_frame, VolMapCreateDensity::compute_frame, VolMapCreateMask::compute_frame, and volmap_write_dx_file.

void VolumetricData::cell_dirs ( float * xax,

float * yax,

float * zax

) const

return cell axes directions.

Definition at line 146 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 86 of file VolumetricData.C.
References dot_prod, xaxis, xsize, yaxis, ysize, zaxis, and zsize.
Referenced by cell_dirs, and compute_volume_gradient.

void VolumetricData::compute_volume_gradient ( void )

(re)compute the volume gradient.

Definition at line 300 of file VolumetricData.C.
References cell_lengths, clamp_int, gradient, voxel_value, xsize, ysize, and zsize.
Referenced by BaseMolecule::add_volume_data, and QuickSurf::calc_surf.

int VolumetricData::gridsize ( ) const [inline]

return total number of gridpoints.

Definition at line 48 of file VolumetricData.h.
References xsize, ysize, and zsize.
Referenced by VolMapCreateILS::compute, and vmd_volmap_compare.

void VolumetricData::set_name ( const char * name )

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

Definition at line 78 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::voxel_coord_from_cartesian_coord ( const float * carcoord,

float * voxcoord,

int shiftflag

) const

return volumetric coordinate from cartesian coordinate.

Definition at line 168 of file VolumetricData.C.
References Matrix4::inverse, Matrix4::multpoint3d, origin, xaxis, xsize, yaxis, ysize, zaxis, and zsize.
Referenced by voxel_gradient_from_coord, voxel_gradient_interpolate_from_coord, voxel_index_from_coord, and voxel_value_interpolate_from_coord.

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 88 of file VolumetricData.h.
References gradient, xsize, and ysize.

void VolumetricData::voxel_gradient_from_coord ( const float * coord,

float * gradient

) const

return voxel gradient based on cartesian coordinates.

Definition at line 410 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 371 of file VolumetricData.C.
References vec_lerp, and voxel_gradient_safe.
Referenced by 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 422 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 358 of file VolumetricData.C.
References gradient, xsize, ysize, and zsize.
Referenced by voxel_gradient_from_coord, and voxel_gradient_interpolate.

int 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 206 of file VolumetricData.C.
References voxel_coord_from_cartesian_coord, xsize, ysize, and zsize.
Referenced by atomsel_gridindex_array, and voxel_value_from_coord.

float VolumetricData::voxel_value ( int x,

int y,

int z

) const [inline]

return voxel at requested index, no safety checks.

Definition at line 69 of file VolumetricData.h.
References data, xsize, and ysize.
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 269 of file VolumetricData.C.
References data, NAN, and voxel_index_from_coord.
Referenced by atomsel_volume_array.

float VolumetricData::voxel_value_interpolate ( float xv,

float yv,

float zv

) const

return interpolated value from 8 nearest neighbor voxels.

Definition at line 238 of file VolumetricData.C.
References voxel_value_safe.
Referenced by VolumeTexture::generateContourLineTexture, and voxel_value_interpolate_from_coord.

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 279 of file VolumetricData.C.
References NAN, voxel_coord_from_cartesian_coord, voxel_value_interpolate, xsize, ysize, and zsize.
Referenced by atomsel_interp_volume_array.

float VolumetricData::voxel_value_safe ( int x,

int y,

int z

) const

return voxel, after safely clamping index to valid range.

Definition at line 227 of file VolumetricData.C.
References data, xsize, ysize, and zsize.
Referenced by voxel_value_interpolate.

Member Data Documentation

float* VolumetricData::data

raw data, total of xsize*ysize*zsize voxels.

Definition at line 35 of file VolumetricData.h.
Referenced by VolMapCreateILS::add_map_to_molecule, VolMapCreate::combo_begin, VolMapCreate::combo_export, VolMapCreateILS::compute, VolMapCreate::compute_all, IsoContour::DoCell, IsoSurface::DoCellGeneral, IsoSurface::DoGridPosNorms, VolumeTexture::generateChargeTexture, VolumeTexture::generateColorScaleTexture, VolumeTexture::generateHSVTexture, vmd_volmap_compare, vmd_volmap_new_fromtype, volmap_write_dx_file, VolumetricData, voxel_value, voxel_value_from_coord, voxel_value_safe, and ~VolumetricData.

float VolumetricData::datamax

min and max data values.

Definition at line 37 of file VolumetricData.h.
Referenced by BaseMolecule::add_volume_data, AtomColor::find, VolumeTexture::generateContourLineTexture, GraphicsFltkMenu::update_molchooser, and VolumetricData.

float VolumetricData::datamin

Definition at line 37 of file VolumetricData.h.
Referenced by BaseMolecule::add_volume_data, AtomColor::find, VolumeTexture::generateContourLineTexture, GraphicsFltkMenu::update_molchooser, and VolumetricData.

float* VolumetricData::gradient

negated normalized volume gradient map.

Definition at line 36 of file VolumetricData.h.
Referenced by compute_volume_gradient, VolumetricData, voxel_gradient_fast, voxel_gradient_safe, and ~VolumetricData.

char* VolumetricData::name

human-readable volume dataset identifier.

Definition at line 29 of file VolumetricData.h.
Referenced by VolMapCreateILS::add_map_to_molecule, BaseMolecule::add_volume_data, SaveTrajectoryFltkMenu::molchooser_activate_selection, set_name, GraphicsFltkMenu::update_molchooser, vmd_volmap_new_fromtype, GraphicsFltkMenu::volindex_update, volmap_write_dx_file, VolumetricData, and ~VolumetricData.

double VolumetricData::origin[3]

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

Definition at line 30 of file VolumetricData.h.
Referenced by VolMapCreateILS::add_map_to_molecule, 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, IsoContour::DoCell, IsoSurface::DoCellGeneral, IsoSurface::DoGridPosNorms, prepare_texture_coordinates, IsoSurface::set_color_voltex_rgb3fv, vmd_volmap_compare, vmd_volmap_new_fromtype, volmap_write_dx_file, VolumetricData, and voxel_coord_from_cartesian_coord.

double VolumetricData::xaxis[3]

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

Definition at line 31 of file VolumetricData.h.
Referenced by VolMapCreateILS::add_map_to_molecule, cell_axes, cell_lengths, IsoContour::compute, VolMapCreate::compute_init, DrawMolecule::cov, prepare_texture_coordinates, DrawMolecule::scale_factor, vmd_volmap_compare, vmd_volmap_new_fromtype, VolumetricData, and voxel_coord_from_cartesian_coord.

int VolumetricData::xsize

Definition at line 34 of file VolumetricData.h.
Referenced by VolMapCreateILS::add_map_to_molecule, 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, compute_volume_gradient, IsoContour::DoCell, IsoSurface::DoCellGeneral, IsoSurface::DoGridPosNorms, VolumeTexture::generateChargeTexture, VolumeTexture::generateColorScaleTexture, VolumeTexture::generateContourLineTexture, VolumeTexture::generateHSVTexture, gridsize, IsoSurface::set_color_voltex_rgb3fv, vmd_volmap_compare, vmd_volmap_new_fromtype, volmap_write_dx_file, VolumetricData, 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, and voxel_value_safe.

double VolumetricData::yaxis[3]

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

Definition at line 32 of file VolumetricData.h.
Referenced by VolMapCreateILS::add_map_to_molecule, cell_axes, cell_lengths, IsoContour::compute, VolMapCreate::compute_init, DrawMolecule::cov, prepare_texture_coordinates, DrawMolecule::scale_factor, vmd_volmap_compare, vmd_volmap_new_fromtype, VolumetricData, and voxel_coord_from_cartesian_coord.

int VolumetricData::ysize

Definition at line 34 of file VolumetricData.h.
Referenced by VolMapCreateILS::add_map_to_molecule, 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, compute_volume_gradient, IsoContour::DoCell, IsoSurface::DoCellGeneral, IsoSurface::DoGridPosNorms, VolumeTexture::generateChargeTexture, VolumeTexture::generateColorScaleTexture, VolumeTexture::generateContourLineTexture, VolumeTexture::generateHSVTexture, gridsize, IsoSurface::set_color_voltex_rgb3fv, vmd_volmap_compare, vmd_volmap_new_fromtype, volmap_write_dx_file, VolumetricData, 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, and voxel_value_safe.

double VolumetricData::zaxis[3]

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

Definition at line 33 of file VolumetricData.h.
Referenced by VolMapCreateILS::add_map_to_molecule, cell_axes, cell_lengths, IsoContour::compute, VolMapCreate::compute_init, DrawMolecule::cov, prepare_texture_coordinates, DrawMolecule::scale_factor, vmd_volmap_compare, vmd_volmap_new_fromtype, VolumetricData, and voxel_coord_from_cartesian_coord.

int VolumetricData::zsize

number of samples along each axis.

Definition at line 34 of file VolumetricData.h.
Referenced by VolMapCreateILS::add_map_to_molecule, 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, compute_volume_gradient, IsoSurface::DoGridPosNorms, VolumeTexture::generateChargeTexture, VolumeTexture::generateColorScaleTexture, VolumeTexture::generateContourLineTexture, VolumeTexture::generateHSVTexture, gridsize, IsoSurface::set_color_voltex_rgb3fv, vmd_volmap_compare, vmd_volmap_new_fromtype, 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, and voxel_value_safe.

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

Generated on Sat May 26 01:49:35 2012 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)
	constructor. More...
	~VolumetricData ()
	destructor. More...
int	gridsize () const
	return total number of gridpoints. More...
void	set_name (const char *name)
	Sets data name to an internal copy of the provided string. 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_dirs (float xax, float yax, float *zax) const
	return cell axes directions. More...
void	voxel_coord_from_cartesian_coord (const float carcoord, float voxcoord, int shiftflag) const
	return volumetric coordinate from cartesian coordinate. More...
int	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...
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...
Public Attributes
char *	name
	human-readable volume dataset identifier. More...
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...
float *	data
	raw data, total of xsizeysizezsize voxels. More...
float *	gradient
	negated normalized volume gradient map. More...
float	datamin
float	datamax
	min and max data values. More...