sphview: Visualise one or several 3D point sets

In obreschkow/simstar: Reading, processing and visualising astrophysical N-body simulation data

Description

Produces a raster image visualising particle positions in 3D N-body/SPH data.

Usage

sphview(
  x,
  species = NULL,
  value = NULL,
  valrange = NULL,
  fix.brightness = TRUE,
  weight = NULL,
  colspecies = c("#ff0010", "#0515ff", "green", "orange", "yellow", "purple"),
  colscale = cooltools::spectrumcolors(1000),
  center = NULL,
  width = NULL,
  aspect = 1,
  thickness = NULL,
  subsampling = 1,
  screen = TRUE,
  pngfile = NULL,
  pdffile = NULL,
  rotation = 1,
  ngrid = 300,
  title = NULL,
  title.origin = NULL,
  lum = 1,
  shadows = 1,
  freeze.lum = FALSE,
  sigma = NULL,
  kde = TRUE,
  arrows = TRUE,
  arrow.origin = NULL,
  arrow.length = NULL,
  arrow.lwd = 1.5,
  scale = TRUE,
  scale.origin = NULL,
  scale.length = NULL,
  scale.lwd = 1.5,
  length.unit = "",
  xlab = NULL,
  ylab = NULL,
  cex = 1,
  text.offset = 0,
  text.col = "white"
)

Arguments

x	n-by-3 matrix, representing the 3D-coordinates of n particles.
species	optional argument specifying different particle species. This must be either a n-element vector giving the integer species indices of each particle or a 6-element vector giving the number of particles of each type (see Npart or NumPart_ThisFile in Gadget header). Different species can be displayed with different colors. If not given, all particles will be assumed to be of the first species (normally gas in Gadget).
value	optional n-element vector specifying a particle property (e.g. temperatures) to be shown in color. This overwrites the colors set by species.
valrange	2-vector specifying the range of values covered by the colors in the vector colorscale.
fix.brightness	logical flag specifying whether the brightness of value-plots should scale with density.
weight	optional n-element vector, specifying the weight of different particles.
colspecies	vector of colors, specifying the color of the species given in the optional species vector.
colscale	vector of colors used to shown the particle property given by the optional vectors value.
center	optional 3-vector specifying the coordinate at the center of the plot. The default is the geometric center (= center of mass, if all particle masses are equal).
width	optional horizontal range of the image in the length units of x. The default corresponds to the full range of particle positions.
aspect	aspect ratio (= width/height).
thickness	optional thickness in length units of x of the slice to be plotted. If not given, all particles are shown.
subsampling	fraction of particles to be used (if 1, all particles are used, if <1 a random subsample is drawn)
screen	logical flag specifying whether the images is displayed on the screen.
pngfile	optional png-filename to save the image as raster image.
pdffile	optional pdf-filename to save the image as pdf-file.
rotation	either an integer (1-6), a 3-vector or a 3-by-3 matrix, specifying a rotation of the 3D particle positions. In case of an integer: 1=(x,y)-plane, 2=(y,z)-plane, 3=(x,y)-plane, 4=(qmax,qmin)-plane, 5=(qmax,qmid)-plane, 6=(qmid,qmin)-plane, where qmax/qmid/qmin are the eigenvectors of the particle-quadrupole, associated with the maximum/middle/minimum eigenvalues, respectively. If rotation is a vector, its direction specifies the rotation axis and its norm the rotation angle in radians in the positive geometric sense.
ngrid	optional number of grid cells per side in the output image. If the image is not square ngrid is interpreted as the geometric mean between the horizontal and the vertical number of pixels, such that the total number of pixels remains about ngrid^2.
title	Text to be added to the figure.
title.origin	optional 2-vector specifying the position of the title
lum	overall luminosity scaling factor (default 1).
shadows	differential luminosity scaling factor for darker regions (default 1).
freeze.lum	logical flag (default FALSE). If set to TRUE, the luminosity will not be adjusted as a function of the visible particles. This is normally needed to avoid flickering in animations.
sigma	smoothing scale in simulation units. The default is NULL, meaning that a value is picked automatically. If a vector is provided, the different elements will be interpreted as corresponding to different species.
kde	logical flag, specifying whether the particles are smoothed using an adaptive kernel density estimator. If a vector is provided, the different elements will be interpreted as corresponding to different species.
arrows	logical flag, specifying if axis-arrows are drawn
arrow.origin	optional 2-vector specifying the bottom left corner of the arrows
arrow.length	optional number specifying the length of the arrows
arrow.lwd	line width of arrows
scale	logical flag, specifying if a length scale is shown
scale.origin	optional 2-vector specifying the right end of the length scale
scale.length	optional number specifying the length of the length scale (is always rounded to one significant digit)
scale.lwd	line width of length scale
length.unit	character string of length unit (e.g. "m" or "kpc")
xlab	label on horizontal arrow (only shown if arrows=TRUE).
ylab	label on vertical arrow (only shown if arrows=TRUE).
cex	text size
text.offset	optional extra offset for the arrow and scale labels
text.col	color of text, arrows and scale

Value

Returns a list of items

rgb	ngrid-by-ngrid-by-3 array of containig the rgb colour data between 0 and 1
radius	positive real number specifying the radius of the image along the horizontal and vertical axes, in the units of the particle positions
rotationmatrix	rotation matrix applied to the input data, i.e. the projection was x = (x%*%rot)[,1:2]

Author(s)

Danail Obreschkow

Examples

# Example of 2x1e4 particles in a triaxial ellipsoid
x.red = t(t(cooltools::runif3(1e4))*c(3,2,1))
x.blue = abs(t(t(cooltools::runif3(1e4,r=c(0.5,1)))*c(3,2,1)))
sphview(rbind(x.red,x.blue), species=c(rep(1,1e4),rep(2,1e4)), center=0)

obreschkow/simstar documentation built on Jan. 29, 2022, 2:16 p.m.