R/getImagesValues.R

In gitdemont/IFC: Tools for Imaging Flow Cytometry

################################################################################
# This file is released under the GNU General Public License, Version 3, GPL-3 #
# Copyright (C) 2020 Yohann Demont                                             #
#                                                                              #
# It is part of IFC package, please cite:                                      #
# -IFC: An R Package for Imaging Flow Cytometry                                #
# -YEAR: 2020                                                                  #
# -COPYRIGHT HOLDERS: Yohann Demont, Gautier Stoll, Guido Kroemer,             #
#                     Jean-Pierre Marolleau, Loïc Garçon,                      #
#                     INSERM, UPD, CHU Amiens                                  #
#                                                                              #
# DISCLAIMER:                                                                  #
# -You are using this package on your own risk!                                #
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# -This program is distributed in the hope that it will be useful, but WITHOUT #
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# You should have received a copy of the GNU General Public License            #
# along with IFC. If not, see <http://www.gnu.org/licenses/>.                  #
################################################################################

#' @title RIF/CIF Image Values Extraction
#' @name getImagesValues
#' @description
#' Extracts the image values from RIF or CIF as what can be found in DAF files
#' @param fileName path to file.
#' @param offsets Object of class `IFC_offset`. If missing, the default, 'offsets' will be extracted from 'fileName'.\cr
#' This param is not mandatory but it may allow to save time when exporting repeated image value on same file.
#' @param objects integer vector, IDEAS objects ids numbers to extract.\cr
#' If missing, the default, images values from all objects will be extracted.
#' @param display_progress whether to display a progress bar. Default is FALSE.
#' @param fast when no 'offsets' are provided whether to fast extract 'objects' or not. Default is TRUE.\cr
#' Meaning that 'objects' will be extracted expecting that 'objects' are stored in ascending order.\cr
#' Only apply when 'offsets' are not provided.\cr
#' Note that a warning will be sent if an object is found at an unexpected order.
#' @param ... other arguments to be passed.
#' @return A data.frame is returned.
#' @keywords internal
getImagesValues <- function(fileName, offsets, objects, display_progress = FALSE, fast = TRUE, ...) {
  dots = list(...)
  if(missing(fileName)) stop("'fileName' can't be missing")
  tmp = duplicated(fileName)
  if(any(tmp)) {
    warning(paste0("duplicated files have been removed from 'fileName': ","\n-", paste0(fileName[tmp],collapse="\n-")))
    fileName = fileName[!tmp]
  }
  if(length(fileName) != 1) stop("'fileName' should be of length 1")
  fileName = normalizePath(fileName, winslash = "/", mustWork = TRUE)
  title_progress = basename(fileName)
  display_progress = as.logical(display_progress); assert(display_progress, len = 1, alw = c(TRUE, FALSE))
  IFD = getIFD(fileName = fileName, offsets = "first", trunc_bytes = 8, force_trunc = FALSE, verbose = FALSE, verbosity = 1, bypass = FALSE, ...)
  bits = IFD[[1]]$tags$`258`$map
  tmp = read_xml(getFullTag(IFD = IFD, which = 1, tag = "33027", raw = TRUE), options=c("HUGE","RECOVER","NOENT","NOBLANKS","NSCLEAN"))
  in_use = as.logical(as.numeric(strsplit(xml_text(xml_find_first(tmp, "//Imaging//ChannelInUseIndicators_0_11")), " ", useBytes = TRUE, fixed=TRUE)[[1]]))
  rm(tmp)
  chan_number = sum(in_use)
  
  compute_offsets = TRUE
  if(!missing(offsets)) {
    if(!("IFC_offset" %in% class(offsets))) {
      warning("provided offsets do not match with expected ones, offsets will be recomputed", immediate. = TRUE, call. = FALSE)
    } else {
      if(attr(offsets, "checksum") != checksumXIF(fileName)) {
        warning("provided offsets do not match with expected ones, offsets will be recomputed", immediate. = TRUE, call. = FALSE)
      } else {
        compute_offsets = FALSE
      }
    }
  }
  if(compute_offsets) {
    offsets = suppressMessages(getOffsets(fileName = fileName, fast = fast, display_progress = display_progress))
  }
  
  # check objects to extract
  nobj = as.integer(attr(x = offsets, which = "obj_count"))
  
  if(missing(objects)) {
    objects = as.integer(0:(nobj - 1))
  } else {
    objects = na.omit(as.integer(objects))
    tokeep = (objects >= 0) & (objects < nobj)
    if(length(tokeep) == 0) {
      warning("getImagesValues: No objects to extract, check the objects you provided.", immediate. = TRUE, call. = FALSE)
      return(data.frame())
    }
    if(!all(tokeep)) {
      warning("Some objects that are not in ", fileName, " have been automatically removed from extraction process:\n", paste0(objects[!tokeep], collapse=", "))
      objects = objects[tokeep]
    }
  }
  
  # extract objects
  sel = subsetOffsets(offsets = offsets, objects = objects, image_type = "img")
  sel = split(sel, ceiling(seq_along(sel)/20))
  L=length(sel)
  if(L == 0) {
    warning("ExtractMasks_toMatrix: No objects to extract, check the objects you provided.", immediate. = TRUE, call. = FALSE)
    return(NULL)
  }
  
  if(display_progress) {
    pb = newPB(min = 0, max = L, initial = 0, style = 3)
    on.exit(endPB(pb))
    ans = lapply(1:L, FUN=function(i) {
      setPB(pb, value = i, title = title_progress, label = "extracting images values (binary)")
      t(sapply(#getIFD(fileName = fileName, offsets = subsetOffsets(offsets = offsets, objects = sel[[i]], image_type = "img"), trunc_bytes = 12,
               #        force_trunc = FALSE, verbose = FALSE, verbosity = 1, bypass = TRUE, ...), FUN = function(ifd) {
        sel[[i]], FUN = function(off) {
          ifd = cpp_getTAGS(fname = fileName, offset = off, trunc_bytes = 12, force_trunc = TRUE, verbose = FALSE)
          c(ifd$infos$OBJECT_ID, # id
            ifd$curr_IFD_offset, # imgIFD
            ifd$next_IFD_offset, # mskIFD
            bits,                # spIFD
            ifd$tags$`256`$map,  # w
            ifd$tags$`257`$map,  # l
            ifd$tags$`33012`$map,# fs
            ifd$tags$`33016`$map,# cl
            ifd$tags$`33017`$map,# ct
            ifd$tags$`33071`$map,# objCenterX
            ifd$tags$`33072`$map,# objCenterY
            ifd$tags$`33053`$map[1:chan_number],# bgstd
            ifd$tags$`33052`$map[1:chan_number],# bgmean
            ifd$tags$`33054`$map[1:chan_number],# satcount
            ifd$tags$`33055`$map[1:chan_number])# satpercent
        }))
    })
  } else {
    ans = lapply(1:L, FUN=function(i) {
      t(sapply(#getIFD(fileName = fileName, offsets = subsetOffsets(offsets = offsets, objects = sel[[i]], image_type = "img"), trunc_bytes = 12,
               #        force_trunc = FALSE, verbose = FALSE, verbosity = 1, bypass = TRUE, ...), FUN = function(ifd) {
        sel[[i]], FUN = function(off) {
          ifd = cpp_getTAGS(fname = fileName, offset = off, trunc_bytes = 12, force_trunc = TRUE, verbose = FALSE)
          c(ifd$infos$OBJECT_ID, # id
            ifd$curr_IFD_offset, # imgIFD
            ifd$next_IFD_offset, # mskIFD
            bits,                # spIFD
            ifd$tags$`256`$map,  # w
            ifd$tags$`257`$map,  # l
            ifd$tags$`33012`$map,# fs
            ifd$tags$`33016`$map,# cl
            ifd$tags$`33017`$map,# ct
            ifd$tags$`33071`$map,# objCenterX
            ifd$tags$`33072`$map,# objCenterY
            ifd$tags$`33053`$map[1:chan_number],# bgstd
            ifd$tags$`33052`$map[1:chan_number],# bgmean
            ifd$tags$`33054`$map[1:chan_number],# satcount
            ifd$tags$`33055`$map[1:chan_number])# satpercent
        }))
    })
  }
  if(L>1) {
    ans = do.call(what="rbind", args=ans)
  } else {
    ans = ans[[1]]
  }
  images=as.data.frame(ans, stringsAsFactors = FALSE)
  N = c("id","imgIFD","mskIFD","spIFD","w","l","fs","cl","ct","objCenterX","objCenterY",
        paste0("bgstd",(1:chan_number)),
        paste0("bgmean",(1:chan_number)),
        paste0("satcount",(1:chan_number)),
        paste0("satpercent",(1:chan_number)))
  if(ncol(images) != length(N)) images = cbind(images, matrix(0, ncol = length(N) - ncol(images), nrow = nrow(images)))
  colnames(images) <- N
  rownames(images) <- num_to_string(1:nrow(images))
  if(!all(objects == images$id)) warning("Extracted object_ids differ from expected ones. Concider running with 'fast' = FALSE", call. = FALSE, immediate. = TRUE)
  class(images) <- c("data.frame", "IFC_images")
  return(images)
}