convert: 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. This version accommodates calibration curves with >4 calibrants, and uses density thresholds converted to Hounsfield Units using the calibration curve (rather than direct calibration rod values) to partition sediment components.

Usage

convert(mat.list, upperLim = 3045, lowerLim = -1025, 
pixelA, thickness = 0.625, # all in mm 
means     = c(-850.3233, 63.912, 271.7827, 1345.0696),
sds       = c(77.6953, 14.1728, 39.2814, 45.4129),
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	slice thickness for computed tomography image series (mm)
means	mean values (units = Hounsfield Units) for calibration rods used.
sds	standard deviations (units = Hounsfield Units) for calibration rods used. Must be in the same order as means.
densities	numeric vector of known cal rod densities. Must be in the same order as means and sds.

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. The input style for calibration rods ensures sediment components are partitioned following the density divisions in Davey et al. 2011. Calibration rods and are used to develop the calibration curve. Separately, the densities used for partitioning in Davey et al. 2011 (0.0012, 1, 1.23, 2.2 g/cm3) are converted to Hounsfield Units and used for partitioning sediment components. The standard deviation for the calibration rod nearest to the target value is used for the standard deviation for the division between two sediment components.

Value

value convert 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>getRoots</code> for more detail on those values.

See Also

getRoots 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 <- convert(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.