conv: Convert a matrix of semi-processed DICOM images to mass and...

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

Description

Converts raw CT units to material classes for each CT slice, directly replicating Earl Davey's manual classification approach. This method is deprecated as of coreCT version 1.3.0.

Usage

conv(mat.list, upperLim = 3045, lowerLim = -1025, 
pixelA, thickness = 0.625, # all in mm 
airHU = -850.3233, airSD = 77.6953, 
SiHU = 271.7827, SiSD = 39.2814,
glassHU = 1345.0696, glassSD = 45.4129,
waterHU = 63.912, waterSD = 14.1728,
densities = c(0.0012, 1, 1.23, 2.2))

Arguments

mat.list	list of DICOM images for a sediment core (values in Hounsfield Units)
upperLim	upper bound cutoff for pixels (Hounsfield Units)
lowerLim	lower bound cutoff for pixels (Hounsfield Units)
pixelA	pixel area (mm2)
thickness	CT image thickness (mm)
airHU	mean value for air-filled calibration rod (Hounsfield Units)
airSD	standard deviation for air-filled calibration rod
SiHU	mean value for colloidal silica calibration rod
SiSD	standard deviation for colloidal Si calibration rod
glassHU	mean value for glass calibration rod
glassSD	standard deviation for glass calibration rod
waterHU	mean value for water filled calibration rod
waterSD	standard deviation for water filled calibration rod
densities	numeric vector of known cal rod densities. Format must be c(air, water, Si, glass)

Details

Calculates average Hounsfield units, cross-sectional areas (cm2), volumes (cm3), and masses (g) of material classes for each CT slice. This function assumes that core walls and all non-sediment material have been removed from the raw DICOM imagery. This function converts data from raw x-ray attenuation values to Hounsfield Units, and then uses user-defined calibration rod inputs to categorize sediment components: air, roots and rhizomes, peat, water, particulates, sand, and rock/shell.

Value

value conv returns a dataframe with one row per CT slice. Values returned are the average Hounsfield Unit value, the area (cm2), volume (cm3), and mass (grams) of 7 material classes: gas, peat, roots and rhizomes, particulates, sand, water, and rock/shell. If <code>rootData = TRUE</code>, data for specified root size classes are also returned. See <code>rootSize</code> for more detail on those values.

See Also

rootSize operates similarly.

Examples

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, pixelA = 0.0596)

## Not run: 
# plot using "ggplot" package after transforming with "reshape2" package
mass.long <- reshape2::melt(materials, id.vars = c("depth"), 
   measure.vars = grep(".g", names(materials)))
ggplot2::ggplot(data = mass.long, ggplot2::aes(y = -depth, x = value, 
   color = variable)) + ggplot2::geom_point() + ggplot2::theme_classic() + 
   ggplot2::xlab("mass per section (g)")

## End(Not run)

coreCT documentation built on Feb. 5, 2021, 5:06 p.m.