R/checksumDAF.R

In IFC: Tools for Imaging Flow Cytometry

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# 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                                  #
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#' @title DAF File Checksum 
#' @description 
#' This function returns CIF checksum computed from images values found in DAF
#' Checksum is the sum of img IFDs (Image Field Directory) offsets of objects 0, 1, 2, 3 and 4.
#' @param fileName path to file.
#' @param endianness The endian-ness ("big" or "little") of the target system for the file. Default is .Platform$endian.\cr
#' Endianness describes the bytes order of data stored within the files. This parameter may not be modified.
#' @param ... other arguments to be passed.
#' @keywords internal
checksumDAF <- function(fileName, endianness = .Platform$endian, ...) {
  # TODO ask AMNIS how checksum is computed
  if(missing(fileName)) stop("'fileName' can't be missing")
  file_extension = getFileExt(fileName)
  assert(file_extension, len = 1, alw = "daf")
  if(!file.exists(fileName)) stop(paste("can't find",fileName,sep=" "))
  assert(endianness, len = 1, alw= c("big", "little"))
  fileName = enc2native(normalizePath(fileName, winslash = "/", mustWork = FALSE))
  toskip=cpp_scanFirst(fileName, charToRaw('</Assay>'), start = 0, end = 0)
  if(toskip == 0) stop(paste0(fileName, "\ndoes not seem to be well formatted: </Assay> not found")) 
  toskip = toskip + nchar("</Assay>") - 1
  tmp=read_xml(readBin(con = fileName, what = "raw", n = toskip), options=c("HUGE","RECOVER","NOENT","NOBLANKS","NSCLEAN"))
  
  ##### extracts obj_count / chan_number
  obj_count = as.integer(xml_attr(xml_find_first(tmp, "//SOD"), attr = "objcount"))
  chan_number = as.integer(xml_attr(xml_find_first(tmp, "//ChannelPresets"), attr = "count"))
  
  ##### check binary
  is_binary=as.logical(na.omit(xml_attr(xml_find_first(tmp, "//Assay"), attr = "binaryfeatures")))
  if(length(is_binary)==0) {is_binary=FALSE}
  
  ##### initialize values
  warn = TRUE
  obj = c(0,1,2,3,4)
  i_image = 0
  images = c()
  if(is_binary) {
    ##### open daf for binary extraction
    toread=file(description = fileName, open = "rb")
    on.exit(close(toread))
    
    ##### extracts important values
    seek(toread,toskip+3)
    feat_version=cpp_int32_to_uint32(readBin(toread, "integer", size = 4, n = 1, endian = endianness))
    feat_number=cpp_int32_to_uint32(readBin(toread, "integer", size = 4, n = 1, endian = endianness))
    obj_number=cpp_int32_to_uint32(readBin(toread, "integer", size = 4, n = 1, endian = endianness))
    if(obj_count != obj_number) stop("mismatch between expected object count and features values stored")
    
    ##### extracts images values
    seek(toread, toskip + feat_number*(obj_number*8 + 4) + 15)
    SO_number=cpp_int32_to_uint32(readBin(toread, "integer", size = 4, n = 1, endian = endianness)) # number of SO
    if(SO_number != obj_number) stop("mismatch between expected object count and images numbers stored")
    
    ##### start extracting id + img/msk offsets
    while((length(obj) != 0) && (i_image < SO_number)) {
      i_image = i_image + 1
      id = cpp_int32_to_uint32(readBin(toread, "integer", size = 4, n = 1, endian = endianness))
      imgIFD = cpp_int32_to_uint32(readBin(toread, "integer", size = 4, n = 1, endian = endianness))
      readBin(toread, "raw", size = 1, n = 84 + 8 * 4 * chan_number, endian = endianness) # not used for checksumDAF
      if(id %in% obj) {
        if(warn) if(id != obj[1]) { # ensure it is stored in ascending order
          warning("raw object are not stored in expected order")
          warn = FALSE
        }
        obj = setdiff(obj, id)
        images = sum(images, imgIFD)
      } else { # ensure it is stored in ascending order
        if(warn) { 
          warning("raw object are not stored in expected order")
          warn = FALSE
        }
      }
    }
  } else {
    #####  keep on reading xml
    nodes = xml_find_all(tmp, "//SO")
    SO_number = length(nodes)
    if(SO_number != obj_count) stop("mismatch between expected object count and images numbers stored")
    
    ##### loop over xml SO nodes for id and img/msk offsets
    while((length(obj) != 0) && (i_image < SO_number)) {
      i_image = i_image + 1
      val = as.numeric(xml_attrs(nodes[[i_image]])[1:2])
      if(val[1] %in% obj) {
        if(warn) if(val[1] != obj[1]) { # ensure it is stored in ascending order
          warning("raw object are not stored in expected order")
          warn = FALSE
        }
        obj = setdiff(obj, val[1])
        images = sum(images, val[2])
      } else { # ensure it is stored in ascending order
        if(warn) { 
          warning("raw object are not stored in expected order")
          warn = FALSE
        }
      }
    }
  }
  return(images)
}