conv: Convert a matrix of semi-processed DICOM images to mass and volume of material classes. This is a deprecated version.

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)

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.

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.

Examples

Run this code

# NOT RUN {
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)")
# }
# NOT RUN {
# }