inst/doc/Using_coreCT.R

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

## ---- echo = FALSE, message=FALSE, warning=FALSE, results = "hide"------------
library(coreCT)
# extract metadata and convert raw values to Hounsfield Units
ct.slope <- unique(extractHeader(core_426$hdr, "RescaleSlope"))
ct.int   <- unique(extractHeader(core_426$hdr, "RescaleIntercept")) 
HU_426 <- lapply(core_426$img, function(x) x*ct.slope + ct.int)

# Use coreCT::conv to convert Hounsfield Units to densities and quantify component masses, volumes
materials <- convert(HU_426, pixelA = voxDims("core_426")$pixelArea.mm2, thickness = voxDims("core_426")$thickness.mm)

plot(-depth ~ peat.cm3, data = materials, xlab = "Peat volume (cm3; per slice)", ylab = "Depth (cm)")

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materials <- convertDir("core_426", rootData = FALSE)

plot(-depth ~ peat.cm3, data = materials, xlab = "Peat volume (cm3; per slice)", ylab = "Depth (cm)")

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HUfreq <- coreHist("core_426")

names(HUfreq)
HUfreq$splits

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rootChars <- getRootsDir("core_426", diameter.classes = c(1, 2.5, 10))

plot(-depth ~ structures, data = rootChars, xlab = "Root structures (per slice)", ylab = "Depth (cm)")