getSurface: Remove artificial surface layers from processed CT data

In troyhill/coreCT: Programmatic Analysis of Sediment Cores Using Computed Tomography Imaging

Description

Identifies and removes artificial surface layers from processed CT data

Usage

getSurface(x, material = "particulates", threshold = 0.40, 
start = "top", thickness = 0.625)

Arguments

x	dataframe created by conv
material	material used for determining where the surface begins
threshold	decimal fraction of total area, used to determine the surface layer. Surface slices where material exceeds threshold value are removed.
start	should core be processed from the top, bottom, or both?
thickness	CT image thickness (mm)

Details

Identifies and removes artificial surface layers from processed CT data. Areas can be removed from one or both ends of the core (set by start), based on exceeding a threshold proportion of material (e.g., 75

Value

value getSurface shortens the output of conv to remove artificial surface layers. The output is thus a subset of the input, and identical in structure to the /codeconv output.

See Also

conv

Examples

### Not run:
## Not run: data(core_426)
ct.slope <- unique(extractHeader(core_426$hdr, "RescaleSlope"))
ct.int   <- unique(extractHeader(core_426$hdr, "RescaleIntercept")) 
# convert raw units to Hounsfield units
HU_426 <- lapply(core_426$img, function(x) x*ct.slope + ct.int)

materials <- conv(HU_426)
head(materials[, 1:6], 20)

materials2 <- getSurface(materials)
head(materials2[, 1:6])

## End(Not run)

troyhill/coreCT documentation built on Feb. 6, 2021, 7:16 p.m.