R/hiQuantAdjust.R

In jtheorell/pixMed: Summation of pixel intensities above threshold in png images and tiff movies

#' Relate the intensities in each previously medMad-normalized movie frame to
#' all other frames
#'
#' This function takes a set of image frames, or a set of tiff-movies, that have
#' previously been normalized with the medMadNormSum function, and uses the
#' highQuants portion of the medMadNormSum output to relate them to each other.
#' This is used both to make the individual movie meaningful, but can also be
#' used to make a set of movies, e.g. where both controls and interesting
#' samples are present, relate to each other, so that the top intensity in all
#' the movies dictates the values in all movies.
#'
#' @param medMadNormImages A vector of TIFF movie file names, e.g. generated
#' with list.files(). The input should have been normalized with the
#' \code{\link{medMadNormSum}}function.
#' @param medMadOutput The output from the \code{\link{medMadNormSum}} function
#' for the run that generated the medMadNormImages.
#' @param outDir Directory where the normalized tiff movies will be saved.
#' Default is to save a new tiff file in the current directory, with the same
#' name as the old file, but with the extension "adjusted_final".
#' @importFrom tiff readTIFF writeTIFF
#' @return The adjusted tiff movies, saved to the outDir.
#'
#' @examples
#'
#' #Load example data.
#' data(testMovie)
#'
#' #Run medMadNormSumRes with the output in the current directory
#' medMadNormSumRes <- medMadNormSum(testMovie)
#'
#' #Now run the final function
#' hiQuantAdjust("Test_normalized.tif", medMadNormSumRes)
#' @export hiQuantAdjust

hiQuantAdjust <- function(medMadNormImages, medMadOutput,
                          outDir = "."){
    maxQuant <- max(unlist(medMadOutput$highQuants))
    lapply(seq_along(medMadNormImages), function(x){
        longName <- medMadNormImages[[x]]
        shortName <- gsub("|\\.tif", "", basename(longName))
        message(paste0(shortName, " currently processed"))
        images <- readTIFF(longName, all = TRUE)
        there <- paste0(outDir, "/", shortName, "_adjusted_final.tif")
        hiQuantNormCoFunc(images, medMadOutput$highQuants[[x]], maxQuant, there)
    })
}

hiQuantNormCoFunc <- function(images, highQuants, maxQuant, there){
    normQuants <- highQuants/maxQuant
    normTifs <- lapply(seq_along(images), function(y){
        normTif <- round(images[[y]]*normQuants[y], digits = 1)
    })
    writeTIFF(normTifs, where = there)
}