defunct code/readIJResults.R

In ornelles/virustiter: Virus Titer and Related Functions for Fluorescent Micrographs

#' Read Results from ImageJ Multiwell "Fluorescent Cell Count"
#'
#' Legacy code to read results from ImageJ code that performs the work now done in
#' \code{parseImages}. 
#'
#' @param f	Path to ImageJ results file, single character vector.
#' @param SEP Character used to separate directory and filename in ImageJ
#'   results file.
#'
#' @details
#'
#' Not recommended to use this any more. It has not been well maintained
#' since early 2016. At last incarnation, this program expects variables
#' from ImageJ as "Area", "Mean gray value", "Center of Mass", "Display
#' label", and "Inverted Y coordinates". "Label" must be of the form
#' "xnn/filename" where xnn is the well such as "A01" or "b2". The ImageJ
#' results file should have the multiplicity as an x or moi value and a
#' unit indicator (unit) coded as 1, 2, 3 or 4 for "VP per cell", "IU per
#' cell", "ul per cell", "ml per cell".
#'
#' @export
#'
readIJResults <- function(f, SEP = NULL)
{
# coded vector of units from ImageJ, note that the "per well" units were
# converted to per cell in the ImageJ code

	unitList <- c("VP", "IU", "ul", "ml")	# used in "1 IU = 2.5 VP, etc.

# read data from ImageJ results file and adjust ImageJ names
	if (is.null(SEP))
		SEP <- .Platform$file.sep
	df <- read.table(f, header = TRUE)
	names(df) <- tolower(names(df))
	sel <- which(names(df) == "mean")
	names(df)[sel] <- "mfi"
	sel <- which(names(df) == "label")
	names(df)[sel] <- "file"


# extract unit string from first entry in Image J Results file
	if("unit" %in% names(df))
		unit <- unitList[df$unit[1]]
	else
		unit <- "none"

# extract well, row, column and file name information such as "a01/file001.tif"
	txt <- strsplit(as.character(df$file), SEP)
	if (!all(sapply(txt, length) == 2))
		stop("encountered file label with more than one separator, ", SEP)
	txt <- unlist(txt)
	v <- txt[seq(1,length(txt),2)]
	row <- well.info(v)$row				# row, checks for only letters
	column <- well.info(v)$column		# column, checks for sensible numbers
	well <- well.info(v)$well			# well, a01 format returned
	dname <- basename(dirname(f))		# parent directory name
	fname <- txt[seq(2,length(txt),2)]	# Image file name
	fname <- gsub("\\..*$", "", fname)	# file name without extension

# assemble first part of data.frame
	df <- data.frame(df[1], fname = fname, dir = dname, well = well,
		row = row, column = factor(column), df[-1], unit)

# Extract x/moi values from Image J results file and
# verify that each well is unique.
	if (!(any(c("x", "moi") %in% names(df))))
		stop("The ImageJ results file must have 'x' or 'moi' values")
	if ("x" %in% names(df))
		xx <- with(df, tapply(x, well, unique))		# xx holds an array of x values
	else # "moi" %in% names(df)
		xx <- with(df, tapply(moi, well, unique))		# xx holds an array of x values
	tally <- sapply(xx, length)					# count unique 'x' values
	if (length(tally) == 1)
		warning("only a single x/moi value was found: ", xx[1])
	if(!all(tally == 1))
		warning("multiple x/moi values found: ", names(which(tally > 1)))

# assign type to each well as standard or control if x==0
	type <- rep("standard", nrow(df))
	control.wells <- names(which(xx == 0))
	type[df$well %in% control.wells] <- "control"

# assemble and return data.frame, changed "mean" to "mfi"
	df <- data.frame(df, type = type)
	return(df)
}