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

In alexanderbates/catnat: Analyse neuronal morphology and connectivity (extends catmaid and nat)

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

Description

Read Amira surface (aka HxSurface or HyperSurface) files into hxsurf object. Modified version of similar nat function, nat::read.hxsurf()

Usage

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

Arguments

filename	file path from which to read
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
...	additional arguments passed to methods

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

someneuronlist with cell sidedness in the metadata

alexanderbates/catnat documentation built on Sept. 5, 2023, 4:51 a.m.