R/zeiss.r

In hmbotelho/htmrenamer: File Renaming Tools for High Throughput Microscopy

#' Zeiss renamer GUI
#'
#' Displays the renamer tool GUI for Zeiss Zen Blue exports.
#' The actual renaming process is performed by function rename_zeiss().
#'
#' @return Null
#'
#' @seealso
#' \code{\link{rename_zeiss}} is the function which implements the actual renaming algorithm.\cr
#' \code{\link{rename_leica_gui}} for the Leica renamer GUI.\cr
#'
#' @export
#' @importFrom gWidgets2 addSpace gbutton ggroup glabel gprogressbar gspinbutton gtext gwindow insert svalue
#' @importFrom tcltk tk_choose.dir tk_choose.files
#' @import utils
#' 
rename_zeiss_gui <- function(){

    # library(gWidgets2tcltk)
    # library(utils)

    #####################################################################################################
    # Initialize variables
    #####################################################################################################
    sourcefolder <- "<not specified>"
    targetfolder <- "<not specified>"
    infile <- "<not specified>"
    plate <- "96 well"



    #####################################################################################################
    # Construct dialog box
    #####################################################################################################

    # Launch dialog box
    mainWindow <- gWidgets2::gwindow(paste0("Zeiss File Renamer Tool    -    htmrenamer v", utils::packageVersion("htmrenamer")))
    size(mainWindow) <- c(300,660)

    # Define groups
    groupMainWindow    <- gWidgets2::ggroup(spacing = 0, horizontal = FALSE, container = mainWindow)
    groupTopButtons    <- gWidgets2::ggroup(spacing = 1, container = groupMainWindow)
    groupWellLayout    <- gWidgets2::ggroup(spacing = 1, horizontal = FALSE, container = groupMainWindow)
    groupWellLayoutR   <- gWidgets2::ggroup(spacing = 1, container = groupWellLayout)
    groupWellLayoutC   <- gWidgets2::ggroup(spacing = 1, container = groupWellLayout)
    groupLabels1       <- gWidgets2::ggroup(spacing = 1, container = groupMainWindow)
    groupLabels2       <- gWidgets2::ggroup(spacing = 1, container = groupMainWindow)
    groupLabels3       <- gWidgets2::ggroup(spacing = 1, container = groupMainWindow)
    groupLabels4       <- gWidgets2::ggroup(spacing = 1, container = groupMainWindow)
    groupLog           <- gWidgets2::ggroup(horizontal = FALSE, container = groupMainWindow)
    groupProgressBar   <- gWidgets2::ggroup(spacing = 1, horizontal = FALSE, container = groupMainWindow)
    groupBottomButtons <- gWidgets2::ggroup(horizontal = FALSE, container = groupMainWindow)


    # Generate top buttons
    gWidgets2::gbutton("Select Input Folder", container = groupTopButtons, handler = function(h,...) {
        sourcefolder <<- if(Sys.info()["sysname"] == "Windows"){
                            utils::choose.dir(default = getwd(), caption = "Where are the raw images?")
                         } else{
                            tcltk::tk_choose.dir(default = getwd(), caption = "Where are the raw images?")
                         }
        gWidgets2::svalue(labelsourcefolder) <- sourcefolder
        print(paste0("Input folder: ", sourcefolder))
    })
    gWidgets2::gbutton("Select Output Folder", container = groupTopButtons, handler = function(h,...) {
        targetfolder <<- if(Sys.info()["sysname"] == "Windows"){
            utils::choose.dir(default = getwd(), caption = "Where do you want to save the images?")
        } else{
            tcltk::tk_choose.dir(default = getwd(), caption = "Where do you want to save the images?")
        }
        gWidgets2::svalue(labeltargetfolder) <- targetfolder
        print(paste0("Output folder: ", targetfolder))
    })
    gWidgets2::gbutton("Select Microscope Infile", container = groupTopButtons, handler = function(h,...) {
        infile <<- if(Sys.info()["sysname"] == "Windows"){
                        utils::choose.files(default = "", caption = "Select the in-file", multi = FALSE)
                   } else{
                        tcltk::tk_choose.files(default = "", caption = "Select the in-file", multi = FALSE)
                   }
        gWidgets2::svalue(labelInFile) <- infile
        print(paste0("In-file: ", infile))
    })
    gWidgets2::addSpace(groupTopButtons, 3)


    # Generate spin buttons
    gWidgets2::addSpace(groupWellLayout, 3)
    gWidgets2::glabel("Number of Rows:        ", container = groupWellLayoutR)
    numrow <- gWidgets2::gspinbutton(from = 1,to = 32, by = 1, value = 8, container = groupWellLayoutR, handler = function(h, ...){
        plate <<- paste0(gWidgets2::svalue(numrow) * gWidgets2::svalue(numcol), " well")
        gWidgets2::svalue(labelPlateType) <- plate
    })
    gWidgets2::glabel("Number of Columns: ", container = groupWellLayoutC)
    numcol <- gWidgets2::gspinbutton(from = 1,to = 48, by = 1, value = 12, container = groupWellLayoutC, handler = function(h, ...){
        plate <<- paste0(gWidgets2::svalue(numrow) * gWidgets2::svalue(numcol), " well")
        gWidgets2::svalue(labelPlateType) <- plate
    })


    # Generate text labels (folder & filenames)
    gWidgets2::addSpace(groupLabels1, 3)
    gWidgets2::glabel("Input Folder:   ", container = groupLabels1)
    labelsourcefolder <- gWidgets2::glabel(sourcefolder, container = groupLabels1)
    gWidgets2::addSpace(groupLabels1, 3)
    gWidgets2::addSpace(groupLabels2, 3)
    gWidgets2::glabel("Output Folder:", container = groupLabels2)
    labeltargetfolder <- gWidgets2::glabel(targetfolder, container = groupLabels2)
    gWidgets2::addSpace(groupLabels2, 3)
    gWidgets2::addSpace(groupLabels3, 3)
    gWidgets2::glabel("Mic-In File:      ", container = groupLabels3)
    labelInFile <- gWidgets2::glabel(infile, container = groupLabels3)
    gWidgets2::addSpace(groupLabels3, 3)
    gWidgets2::addSpace(groupLabels4, 3)
    gWidgets2::glabel("Plate type:       ", container = groupLabels4)
    labelPlateType <- gWidgets2::glabel(plate, container = groupLabels4)
    gWidgets2::addSpace(groupLabels4, 3)


    # Generate log window
    logWindow <<- gWidgets2::gtext("May 2022\nHugo Botelho\nhmbotelho@fc.ul.pt\n\nTo use this tool you first need to export your *.czi files using 'File Export > TIFF' in the Zeiss Zen program.\n\nA typical exported file has a name like 'image_s01t1.tif'\n\n", container = groupLog, width = 100, height = 300)


    # Generate progress bar
    ProgressBar <<- gWidgets2::gprogressbar(value=0, container = groupProgressBar)


    # This button triggers all file-related actions
    gWidgets2::gbutton("Start renaming", container = groupBottomButtons, handler = function(h,...) {
        if (sourcefolder == "<not specified>"){
            gWidgets2::insert(logWindow,"No input folder!\n")
        } else if (targetfolder == "<not specified>"){
            gWidgets2::insert(logWindow,"No output folder!\n")
        } else if (infile == "<not specified>"){
            gWidgets2::insert(logWindow,"No infile!\n")
        } else {
            gWidgets2::insert(logWindow,"Starting Transfer !\n")

            rename_zeiss(sourcefolder     = sourcefolder,
                         targetfolder     = targetfolder,
                         infilepath       = infile,
                         numrow           = gWidgets2::svalue(numrow),
                         numcol           = gWidgets2::svalue(numcol),
                         REGEXvalidimages = "^.*?s.*?t.*?\\.tif$",
                         REGEXscenenum    = "^.*/.*_s(.*)t.*\\.tif$",
                         REGEXtimenum     = "^.*/.*_s.*t(.*)\\.tif$",
                         printMessages    = TRUE, 
                         printFiles       = TRUE,
                         printToGUI       = TRUE,
                         move             = FALSE)

            gWidgets2::insert(logWindow,"\nRenaming Ended\n")
        }
    })


}










#' Zeiss renamer
#'
#' Renaming of Zeiss TIF files exported with Zen Blue according to a microscope infile. See \code{\link{newinfile.df}} or \code{\link{newinfile.char}} for a description of the infile structure.
#' @param sourcefolder character, the folder with raw images.
#' @param targetfolder character, folder where to place renamed files. A subfolder with the same name as the infile will be created by the function and must not exist previously.
#' @param infilepath character, location of the microscope infile
#' @param numrow integer, number of rows in the multi well plate
#' @param numcol integer, number of columns in the multi well plate
#' @param REGEXvalidimages character, regular expression matching all files which should be renamed
#' @param REGEXscenenum character, regular expression capturing (\code{(\1)}) the scene number (i.e. well number)
#' @param REGEXtimenum character, regular expression capturing (\code{(\1)}) the time number in a time lapse
#' @param printMessages, logical, print messages in the console?
#' @param printFiles, logical, print file-by-file progress in the console?
#' @param printToGUI logical, print messages to the renamer GUI?
#' @param move logical, move (rather than copy) raw images?
#'
#' @return Renamed files, metadata and log file
#'
#' @return Null
#'
#' @seealso
#' \code{\link{rename_zeiss_gui}} for interacting with this function using a GUI.
#'
#' @export
#' @importFrom gWidgets2 svalue
#' 
rename_zeiss <- function(sourcefolder, targetfolder, infilepath, numrow, numcol, REGEXvalidimages = "^.*?s.*?t.*?\\.tif$", REGEXscenenum = "^.*/.*_s(.*)t.*\\.tif$", REGEXtimenum = "^.*/.*_s.*t(.*)\\.tif$", printMessages = TRUE, printFiles = TRUE, printToGUI = FALSE, move = FALSE){

    # read Infile
    infilename   <- gsub("(.+?)\\.[^\\.]+$", "\\1", basename(infilepath))
    InFile <- read.infile.df(infilepath)



    targetsubfolder <- paste0(targetfolder, "/", infilename)

    # Read raw image folder and store all filenames in a data.frame
    allimages <- list.files(sourcefolder, pattern = REGEXvalidimages, full.names = TRUE, recursive = TRUE)

    renamer <- data.frame(oldname   = allimages,
                          newname   = character(length(allimages)),
                          basepath  = targetsubfolder,
                          platename = infilename,
                          scenenum  = character(length(allimages)),
                          wellnum   = character(length(allimages)),
                          timenum   = character(length(allimages)),
                          stringsAsFactors = FALSE)


    # Fill data.frame with scene numbers
    renamer$scenenum <- gsub(REGEXscenenum, "\\1", renamer$oldname)


    # Fill data.frame with well numbers
    well2scene <- data.frame(wellnum  = 1:(numrow*numcol),
                             scenenum = as.numeric(t(matrix_snake(1:(numrow*numcol), numrow, numcol, byrow=FALSE))))
    renamer$wellnum <- sapply(renamer$scenenum, function(x){
        formatC(
            x     = well2scene[which(well2scene$scenenum == as.numeric(x)), "wellnum"],
            width = 3,
            flag  = "0"
        )

    })


    # Fill data.frame with time numbers
    renamer$timenum   <- formatC(x     = sapply(renamer$oldname, function(x) as.numeric(gsub(REGEXtimenum, "\\1", x)) - 1),
                                 flag  = "0",
                                 width = 4)


    # Exclude files which are not mentioned in the InFile
    files.within.infile <- sapply(renamer$wellnum, function(x) x %in% InFile$WellNum)
    renamer <- renamer[files.within.infile,]

    # Fill data.frame with the path of the renamed files
    renamer$newname  <- apply(renamer, 1, function(x){

        temp         <- InFile[which(InFile$WellNum == x["wellnum"]),]

        wellpath     <- paste0("W0", temp[1,"WellNum"], "--", temp[1,"data1"], "--", temp[1,"data2"])
        pospath      <- paste0("P001--", temp[1,"data1"], "--", temp[1,"data2"])
        filename     <- paste0(infilename, "--", temp[1, "data1"], "--", temp[1, "data2"], "--W0", temp[1, "WellNum"], "--P001--T", x["timenum"], "--C00.tif")

        paste(targetsubfolder, wellpath, pospath, filename, sep = "/")
    })



    ## Sanity check
    # Check if all wells are properly annotated
    files.no.annotation <- renamer[which(renamer == "", arr.ind = TRUE)[1], "oldname"]
    if(!is.null(nrow(files.no.annotation))){
        msg <- paste0("Missing annotation for ", length(files.no.annotation), " files. Consider checking the number of rows and columns, as well as the infile. These are the files affected: ", paste(files.no.annotation, collapse = " ; "))

        echo(msg, printToGUI = printToGUI, printToConsole = printMessages)
        stop(msg)
    }



    # Create target subfolder
    dir.create(targetsubfolder, showWarnings = FALSE, recursive = TRUE)
    LogFile <- file(paste0(targetsubfolder, "/renamer.log"), "w")


    ## Go through the list and copy files
    ## Write log file as the files are renamed
    totalcopies <- nrow(renamer)
    copiedfiles <- 0

    cat("Raw Filename|Renamed Filename", file= LogFile, sep="\n", append=TRUE)
    for(i in 1:nrow(renamer)){

        OldFile <- renamer[i, "oldname"]
        NewFile <- renamer[i, "newname"]

        copiedfiles <- copiedfiles + 1
        progress <- copiedfiles / totalcopies * 100
        progressTxt <- paste0(substr(formatC(progress, mode = "character"), 1, 5), "%")

        if (file.exists(OldFile)){
            if(!dir.exists(dirname(NewFile))){
                dir.create(dirname(NewFile), recursive = TRUE)
            }
            file.copy(OldFile, NewFile, overwrite = TRUE)

            # Make sure the file has been copied correctly
            while(file.size(OldFile) != file.size(NewFile)){
                file.copy(OldFile, NewFile, overwrite = TRUE)
                msg <- paste0(progressTxt, "   Copy error! Retry copy: ", NewFile)
                echo(msg, printToGUI = printToGUI, printToConsole = printMessages)
            }

            # Delete OldFile, if required
            if(move) file.remove(OldFile)

            msg <- paste0(progressTxt, "   Renamed file: ", NewFile)
            echo(msg, printToGUI = printToGUI, printToConsole = printFiles)
            cat(paste0(OldFile, "|", NewFile), file= LogFile, sep="\n", append=TRUE)
            if(printToGUI) gWidgets2::svalue(ProgressBar) <- progress

        } else{
            msg <- paste0("File does not exist: ", OldFile, "\n")
            warning(msg)
            echo(msg, printToGUI = printToGUI, printToConsole = printMessages)
            if(printToGUI) gWidgets2::svalue(ProgressBar) <<- progress
        }

    }

    close(LogFile)
    print("Renaming Ended")

}