Full_SizeExtractR_Workflow: Run the full SizeExtractR workflow - a series of nested...

In liamlachs/SizeExtractR: Extracts object size metrics from scaled images analysed in SizeExtractR ImageJ protocols

Description

Run the full SizeExtractR workflow - a series of nested functions to extract all sizes.

Usage

Full_SizeExtractR_Workflow(
  path,
  known.calibration.length,
  include.calibrations
)

Arguments

path	A Directory path within which holds the text files outputted from SizeExtractR imageJ tools and protocol. The directory path should be given in double quotes in the same format as that returned by the function getwd()
known.calibration.length	a numerical value of the length of calibration lengths from image analyses (in user-defined units, e.g. centimeters).
include.calibrations	logical. Determines whether or not to include the calibration-length ROIs alongside the ROIs of interest.

Value

Returns a calibrated dataset of size metrics, that includes user defined variables based on 1) the directory structure, and 2) the ROI labels used in image analyses.

All relevant interactive checks are also undertaken to determine whether the exported database is correct or not.

Examples

# Set directory within which all text files are located
mypath = paste0(.libPaths()[1],"/SizeExtractR/TextFiles")

# Run the function

Database.cal.SizeOnly = Full_SizeExtractR_Workflow(mypath, 1, FALSE)

# Show dataset
if(length(Database.cal.SizeOnly) > 0){
  head(Database.cal.SizeOnly)
  colnames(Database.cal.SizeOnly)
  hist(Database.cal.SizeOnly$Area, xlab = bquote(Egg~Area~(cm^2)), main = "Size Only Dataset")
}

liamlachs/SizeExtractR documentation built on Feb. 13, 2022, 9:46 p.m.