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Create Regions of Interest (ROI) Graphic

Source: R/plot_ROI.R
plot_ROI.Rd

Create ROI graphic with data extracted from the data imported via read_RF2R. This function is used internally by analyse_IRSAR.RF but might be of use to work with reduced data from spatially resolved measurements. The plot dimensions mimic the original image dimensions

Usage

plot_ROI(
  object,
  exclude_ROI = c(1),
  dist_thre = -Inf,
  dim.CCD = NULL,
  bg_image = NULL,
  plot = TRUE,
  ...
)

Arguments

object

RLum.Analysis, RLum.Results or a list of such objects (required): data input. Please note that to avoid function errors, only input created by the functions read_RF2R or extract_ROI is accepted

exclude_ROI

numeric (with default): option to remove particular ROIs from the analysis. Those ROIs are plotted but not coloured and not taken into account in distance analysis. NULL excludes nothing.

dist_thre

numeric (optional): euclidean distance threshold in pixel distance. All ROI for which the euclidean distance is smaller are marked. This helps to identify ROIs that might be affected by signal cross-talk. Note: the distance is calculated from the centre of an ROI, e.g., the threshold should include consider the ROIs or grain radius.

dim.CCD

numeric (optional): metric x and y for the recorded (chip) surface in µm. For instance c(8192,8192), if set additional x and y-axes are shown

bg_image

RLum.Data.Image (optional): background image object please note that the dimensions are not checked.

plot

logical (with default): enable or disable plot output to use the function only to extract the ROI data

...

further parameters to manipulate the plot. On top of all arguments of graphics::plot.default the following arguments are supported: lwd.ROI, lty.ROI, col.ROI, col.pixel, text.labels, text.offset, grid (TRUE/FALSE), legend (TRUE/FALSE), legend.text, legend.pos

Value

An ROI plot and an RLum.Results object with a matrix containing the extracted ROI data and a object produced by stats::dist containing the euclidean distance between the ROIs.

Function version

0.2.0

See also

read_RF2R, analyse_IRSAR.RF

Author

Sebastian Kreutzer, Institute of Geography, Heidelberg University (Germany) , RLum Developer Team

How to cite

Kreutzer, S., 2024. plot_ROI(): Create Regions of Interest (ROI) Graphic. Function version 0.2.0. In: Kreutzer, S., Burow, C., Dietze, M., Fuchs, M.C., Schmidt, C., Fischer, M., Friedrich, J., Mercier, N., Philippe, A., Riedesel, S., Autzen, M., Mittelstrass, D., Gray, H.J., Galharret, J., Colombo, M., 2024. Luminescence: Comprehensive Luminescence Dating Data Analysis. R package version 0.9.26. https://r-lum.github.io/Luminescence/

Examples


## simple example
file <- system.file("extdata", "RF_file.rf", package = "Luminescence")
temp <- read_RF2R(file)
plot_ROI(temp)


## in combination with extract_ROI()
m <- matrix(runif(100,0,255), ncol = 10, nrow = 10)
roi <- matrix(c(2.,4,2,5,6,7,3,1,1), ncol = 3)
t <- extract_ROI(object = m, roi = roi)
plot_ROI(t, bg_image = m)