read.hxsurf: Read Amira surface (aka HxSurface or HyperSurface) files into...

In nat: NeuroAnatomy Toolbox for Analysis of 3D Image Data

Read Amira surface (aka HxSurface or HyperSurface) files into hxsurf object

Description

Read Amira surface (aka HxSurface or HyperSurface) files into hxsurf object

Usage

read.hxsurf(
  filename,
  RegionNames = NULL,
  RegionChoice = "both",
  FallbackRegionCol = "grey",
  Verbose = FALSE
)

Arguments

filename	Character vector defining path to file
RegionNames	Character vector specifying which regions should be read from file. Default value of NULL => all regions.
RegionChoice	Whether the Inner or Outer material, or both (default), should define the material of the patch. See details.
FallbackRegionCol	Colour to set regions when no colour is defined
Verbose	Print status messages during parsing when TRUE

Details

Note that when RegionChoice="both" or RegionChoice=c("Inner", "Outer") both polygons in inner and outer regions will be added to named regions. To understand the significance of this, consider two adjacent regions, A and B, with a shared surface. For the polygons in both A and B, Amira will have a patch with (say) InnerRegion A and OuterRegion B. This avoids duplication in the file. However, it might be convenient to add these polygons to both regions when we read them into R, so that regions A and B in our R object are both closed surfaces. To achieve this when RegionChoice="both", read.hxsurf adds these polygons to region B (as well as region A) but swaps the order of the vertices defining the polygon to ensure that the surface directionality is correct.

As a rule of thumb, stick with RegionChoice="both". If you get more regions than you wanted, then try switching to RegionChoice="Inner" or RegionChoice="Outer".

Value

A list with S3 class hxsurf with elements

Vertices

A data.frame with columns X, Y, Z, PointNo

Regions

A list with 3 column data.frames specifying triplets of vertices for each region (with reference to PointNo column in Vertices element)

RegionList

Character vector of region names (should match names of Regions element)

RegionColourList

Character vector specifying default colour to plot each region in R's rgb format

See Also

plot3d.hxsurf, rgb

Other amira: amiratype(), is.amiramesh(), read.amiramesh(), write.hxsurf()

Other hxsurf: as.hxsurf(), as.mesh3d(), materials(), plot3d.hxsurf(), subset.hxsurf(), write.hxsurf()

Examples

## Not run: 
read.hxsurf("my.surf", RegionChoice="both")

## End(Not run)

nat documentation built on Aug. 18, 2025, 5:20 p.m.