convDir {coreCT} | R Documentation |
Convert a directory of raw DICOM images to material classes
Description
Calculates the area and volume of material classes for each CT slice in a directory. This approach directly replicates Earl Davey's manual classification approach. This method is deprecated as of coreCT version 1.3.0.
Usage
convDir(directory = file.choose(), upperLim = 3045, lowerLim = -1025,
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),
rootData = TRUE,
diameter.classes = c(1, 2, 2.5, 10),
class.names = diameter.classes,
pixel.minimum = 4)
Arguments
directory |
a character string that can be a matrix of DICOM images or the address of an individual DICOM file in a folder of DICOM images. The default action is <code>file.choose()</code>; a browser menu appears so the user can select the the desired directory by identifying a single DICOM file in the folder of images. |
upperLim |
upper bound cutoff for pixels (Hounsfield Units) |
lowerLim |
lower bound cutoff for pixels (Hounsfield Units) |
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) |
rootData |
if TRUE, |
diameter.classes |
if rootData is TRUE, this argument provides an integer vector of diameter cut points used by |
class.names |
placeholder, not used presently |
pixel.minimum |
minimum number of pixels needed for a clump to be identified as a root |
Details
Calculates the area and volume of material classes for each CT slice in a directory. Unlike conv
, convDir
accepts a folder of raw values and makes the conversion to Hounsfield Units using the metadata associated with the DICOM images.
Value
value convDir
returns a dataframe with one row per CT slice. Values returned are the area and volume of seven material classes: gas, peat, roots and rhizomes, rock and shell, fine mineral particles, sand, and water. If rootData = TRUE
, the output will also contain data on the abundance (number of particles), volume (cm3), and external surface area (cm2) of the root size classes specified in the diameter.classes
argument.
See Also
convDir
is a wrapper for conv
. rootSizeDir
operates similarly.
Examples
materials <- convDir("core_426", rootData = FALSE)
## 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)