R/getInfo.R
In gitdemont/IFC: Tools for Imaging Flow Cytometry
Defines functions
getInfo
Documented in
getInfo
################################################################################
# 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! #
# -We do not guarantee privacy nor confidentiality. #
# -This program is distributed in the hope that it will be useful, but WITHOUT #
# ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or #
# FITNESS FOR A PARTICULAR PURPOSE. In no event shall the copyright holders or #
# contributors be liable for any direct, indirect, incidental, special, #
# exemplary, or consequential damages (including, but not limited to, #
# procurement of substitute goods or services; loss of use, data, or profits; #
# or business interruption) however caused and on any theory of liability, #
# whether in contract, strict liability, or tort (including negligence or #
# otherwise) arising in any way out of the use of this software, even if #
# advised of the possibility of such damage. #
# #
# You should have received a copy of the GNU General Public License #
# along with IFC. If not, see <http://www.gnu.org/licenses/>. #
################################################################################
#' @title IFC File Information Extraction
#' @description
#' Retrieves rich information from RIF, CIF and DAF files.
#' @param fileName path to file..
#' @param from whether to extract information from 'acquisition' or 'analysis'. Default is 'analysis'.
#' @param verbose whether to display information (use for debugging purpose). Default is FALSE.
#' @param verbosity quantity of information print to console when verbose is TRUE; 1: normal, 2: rich. Default is 1.
#' @param warn whether to send warning message when trying to read 'analysis' information from a 'rif' file. Default is TRUE.
#' @param force_default when display information can't be retrieved whether to use default values. Default is TRUE.
#' @param cifdir the path of the directory to initially look to cif file. Default is dirname(fileName). Only apply when 'fileName' is a .daf file.
#' @param ntry number of times \code{\link{getInfo}} will be allowed to find corresponding cif file. Default is +Inf. Only apply when 'fileName' is a .daf file.
#' If cif can't be found, but 'ntry' is reached, then an error will be thrown.
#' @param ... other arguments to be passed.
#' @examples
#' if(requireNamespace("IFCdata", quietly = TRUE)) {
#' ## use a daf file
#' file_daf <- system.file("extdata", "example.daf", package = "IFCdata")
#' info <- getInfo(fileName = file_daf, from = "analysis")
#' ## show some information
#' print(info$Images)
#' } else {
#' message(sprintf('Please run `install.packages("IFCdata", repos = "%s", type = "source")` %s',
#' 'https://gitdemont.github.io/IFCdata/',
#' 'to install extra files required to run this example.'))
#' }
#' @return a list of information (open .daf file in an text editor for more details) about input fileName of class `IFC_info` and `acquistion` or `analysis`, whose members are:\cr
#' -objcount, number of object in file,\cr
#' -date, date of file creation,\cr
#' -instrument, instrument identification,\cr
#' -sw_raw, version of software for raw data,\cr
#' -sw_processed, version of software for processed data,\cr
#' -channelwidth, default channel width in pixel,\cr
#' -in_use, channels used,\cr
#' -brightfield, whether brightfield is applied on channels and its intensity,\cr
#' -illumination, laser illumination parameters,\cr
#' -collectionmode, the collection mode,\cr
#' -magnification, magnification used,\cr
#' -coremode, the core mode,\cr
#' -evmode, the high gain mode,\cr
#' -CrossTalkMatrix. compensation matrix applied,\cr
#' -ChannelPresets, channel preset,\cr
#' -ImageDisplaySettings, image display settings,\cr
#' -Images, information about colors, range and channels,\cr
#' -masks, masks defined,\cr
#' -ViewingModes, modes of visualization,\cr
#' -checksum, checksum computed,\cr
#' -Origin_rif, character vector of path of rif used to create cif, if input file was a cif,\cr
#' -Merged_rif, character vector of path of files used to create rif, if input file was a merged,\cr
#' -XIF_type, character definig XIF type,\cr
#' -XIF_test, integer defining XIF type,\cr
#' -checksum, integer corresponding to file checksum,\cr
#' -fileName, path of fileName input,\cr
#' -fileName_image, path of fileName_image.
#' @export
getInfo <- function(fileName,
from = c("acquisition","analysis")[2],
verbose = FALSE,
verbosity = 1,
warn = TRUE,
force_default = TRUE,
cifdir = dirname(fileName),
ntry = +Inf,
...) {
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")
if(!file.exists(fileName)) stop(paste0("can't find ",fileName))
file_extension = getFileExt(fileName)
assert(file_extension, len = 1, alw = c("daf", "cif", "rif"))
fileName = enc2native(normalizePath(fileName, winslash = "/", mustWork = FALSE))
assert(from, len = 1, alw = c("acquisition","analysis"))
verbose = as.logical(verbose); assert(verbose, len = 1, alw = c(TRUE, FALSE))
verbosity = as.integer(verbosity); assert(verbosity, len = 1, alw = c(1, 2))
warn = as.logical(warn); assert(warn, len = 1, alw = c(TRUE, FALSE))
force_default = as.logical(force_default); assert(force_default, len = 1, alw = c(TRUE, FALSE))
cifdir = na.omit(as.character(cifdir)); assert(cifdir, len = 1, typ = "character")
ntry = na.omit(as.numeric(ntry)); assert(ntry, len = 1, typ = "numeric")
if(ntry < 0) ntry = 0
if(warn & file_extension == "rif" & from == "analysis") warning("Only information from 'acquisition' can be retrieved from 'rif' file", call. = FALSE, immediate. = TRUE)
if(file_extension == "daf") {
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_daf = read_xml(readBin(con = fileName, what = "raw", n = toskip), options=c("HUGE","RECOVER","NOENT","NOBLANKS","NSCLEAN"))
cname = xml_attr(xml_find_first(tmp_daf, "//SOD"), attr = "file")
fcs = xml_attr(xml_find_first(tmp_daf, "//FCS"), attr = "file")
if(!is.na(fcs)) stop("can't extract information from .daf generated from .fcs")
found = FALSE
checksum = checksumDAF(fileName)
fileName_image = file.path(cifdir, paste0(splitf(cname)[c("short","ext")], collapse = ".")) # look in cifdir 1st
if(file.exists(fileName_image)) {
if(checksumXIF(fileName_image) == checksum) found = TRUE
} else {
fileName_image = cname
}
if((!found) && file.exists(fileName_image)) {
if(checksumXIF(fileName_image) == checksum) found = TRUE
}
while((interactive() && (ntry > 0) && (!found))) {
message(paste0("daf file does not refer to: ", fileName_image))
old_wd = getwd()
on.exit(setwd(old_wd), add= TRUE)
setwd(dirname(fileName))
if(.Platform$OS.type == "windows") {
fileName_image = choose.files(caption = paste0("Looking for: ", basename(cname)), multi = FALSE, filters = cbind("Compensated Image File (*.cif)", "*.cif"))
} else {
fileName_image = file.choose()
}
if(file.exists(fileName_image)) if(getFileExt(fileName_image)=="cif") if(checksumXIF(fileName_image) == checksum) {
found = TRUE
break;
}
ntry = ntry - 1
}
if(!found) stop("can't extract information")
fileName_image = normalizePath(fileName_image, winslash = "/")
IFD = getIFD(fileName = fileName_image, offsets = "first", trunc_bytes = 8, force_trunc = FALSE, verbose = verbose, verbosity = verbosity, bypass = TRUE, ...)
}
if(file_extension == "cif" | file_extension == "rif") {
fileName_image = fileName
IFD = getIFD(fileName = fileName_image, offsets = "first", trunc_bytes = 8, force_trunc = FALSE, verbose = verbose, verbosity = verbosity, bypass = TRUE, ...)
}
Origin_rif = character()
Merged_rif = character()
xif_type = IFDtype(IFD[[1]])
if(!is.null(IFD[[1]]$tags[["33026"]])) {
if(IFD[[1]]$tags[["33026"]]$byt != 0) Origin_rif = strsplit(as.character(getFullTag(IFD = IFD, which = 1, tag="33026")), "|", fixed = TRUE)[[1]]
}
if(!is.null(IFD[[1]]$tags[["33030"]])) {
if(IFD[[1]]$tags[["33030"]]$byt != 0) Merged_rif = strsplit(as.character(getFullTag(IFD = IFD, which = 1, tag="33030")), "|", fixed = TRUE)[[1]]
}
if(file_extension == "daf" & from == "acquisition") file_extension = "cif"
tmp_acq = read_xml(getFullTag(IFD = IFD, which = 1, tag = "33027", raw = TRUE), options=c("HUGE","RECOVER","NOENT","NOBLANKS","NSCLEAN"))
acquisition = list("Illumination"=lapply(as_list(xml_find_first(tmp_acq, "//Illumination")), unlist),
"Fluidics"=lapply(as_list(xml_find_first(tmp_acq, "//Fluidics")), unlist),
"Imaging"=lapply(as_list(xml_find_first(tmp_acq, "//Imaging")), unlist),
"Display"=lapply(as_list(xml_find_first(tmp_acq, "//Display")), unlist))
infos = list("objcount" = IFD[[1]]$tags[["33018"]]$map, # should not exceed 4 bytes
"date"=getFullTag(IFD = IFD, which = 1, "33004"),
"instrument"=getFullTag(IFD = IFD, which = 1, "33006"),
"sw_raw"=suppressWarnings(getFullTag(IFD = IFD, which = 1, "33069")),
"sw_process"=getFullTag(IFD = IFD, which = 1, "33066"))
# determines channelwidth, very important for objectExtract() when force_width = TRUE
# prefer using channelwidth extracted from ifd dedicated tag (=tag 33009) rather than the one from parsing ASSISTdb (=tag 33064)
# TODO ask AMNIS the rules for extracting channelwidth
channelwidth1 = IFD[[1]]$tags[["33009"]]$map # should not exceed 4 bytes
tmp_ins = read_xml(getFullTag(IFD = IFD, which = 1, tag ="33064", raw = TRUE), options = c("HUGE","RECOVER","NOENT","NOBLANKS","NSCLEAN"))
channelwidth2 = as.numeric(xml_text(xml_find_first(tmp_ins, xpath = "//ChannelWidth")))
tryCatch({
# information in acquisition db
lasers_nodes = grep("Filter", grep("ExLaser", names(acquisition[["Illumination"]]), value = TRUE), value = TRUE, invert = TRUE)
lasers_on = acquisition$Illumination[grep("PowerOn", lasers_nodes, value = TRUE)]
lasers_on = as.logical(as.integer(unlist(lasers_on[order(as.integer(gsub("\\D+", "", names(lasers_on))))])))
lasers_power = acquisition$Illumination[grep("IntensityWatts", lasers_nodes, value = TRUE)]
lasers_power = as.numeric(sprintf("%.2f", as.numeric(unlist(lasers_power[order(as.integer(gsub("\\D+", "", names(lasers_power))))]))))
if(length(lasers_power) != length(lasers_on)) lasers_power = rep(NA, length(lasers_on))
# information in instrument db
ins_lasers = lapply(as_list(xml_find_first(tmp_ins, "Illumination")), unlist)
lasers_nodes = grep("ExLaser", names(ins_lasers), value = TRUE)
lasers_present = ins_lasers[grep("Filter|LAF", grep("Present", lasers_nodes, value = TRUE), value = TRUE, invert = TRUE)]
lasers_present = as.logical(as.integer(unlist(lasers_present[order(as.integer(gsub("\\D+", "", names(lasers_present))))])))
if(length(lasers_present) != length(lasers_on)) lasers_present = rep(NA, length(lasers_on))
lasers_wavelength = ins_lasers[grep("Wavelength", lasers_nodes, value = TRUE)]
lasers_wavelength = as.integer(unlist(lasers_wavelength[order(as.integer(gsub("\\D+", "", names(lasers_wavelength))))]))
if(length(lasers_wavelength) != length(lasers_on)) lasers_wavelength = rep(NA, length(lasers_on))
lasers_minpow = ins_lasers[grep("MinPower", lasers_nodes, value = TRUE)]
lasers_minpow = as.numeric(unlist(lasers_minpow[order(as.integer(gsub("\\D+", "", names(lasers_minpow))))]))
if(length(lasers_minpow) != length(lasers_on)) lasers_minpow = rep(NA, length(lasers_on))
lasers_maxpow = ins_lasers[grep("MaxPower", lasers_nodes, value = TRUE)]
lasers_maxpow = as.numeric(unlist(lasers_maxpow[order(as.integer(gsub("\\D+", "", names(lasers_maxpow))))]))
if(length(lasers_maxpow) != length(lasers_on)) lasers_maxpow = rep(NA, length(lasers_on))
illumination = data.frame("installed" = lasers_present,
"wavelength" = lasers_wavelength,
"powered" = lasers_on,
"power" = lasers_power,
"min" = lasers_minpow,
"max" = lasers_maxpow, stringsAsFactors = FALSE)
}, error = function(e) {
illumination = data.frame(matrix(NA, ncol = 6, nrow = 0))
colnames(illumination) = c("installed","wavelength", "powered" ,"power" ,"min","max")
})
infos$channelwidth = channelwidth1
if(length(channelwidth1)==0) infos$channelwidth = channelwidth2
if(length(channelwidth1)!=0) if(is.na(channelwidth1)) infos$channelwidth = channelwidth2
if(length(channelwidth1)!=0) if(channelwidth1==0) infos$channelwidth = channelwidth2
infos$in_use = as.logical(as.numeric(unlist(strsplit(acquisition$Imaging[["ChannelInUseIndicators_0_11"]], " ", useBytes = TRUE, fixed=TRUE))))
infos$brightfield = list("channel"=as.logical(as.numeric(unlist(strsplit(acquisition$Illumination[["BfLedIndicators_0_11"]], " ", useBytes = TRUE, fixed=TRUE)))),
"power"= as.logical(as.numeric(acquisition$Illumination[["BFOnOff"]])),
"intensity" = as.numeric(acquisition$Illumination[["BFIntensity"]]))
infos$illumination = illumination
# TODO ask AMNIS, if collectionmode is the good variable that determines default information
infos$collectionmode = as.numeric(acquisition$Illumination[["CollectionMode"]])
infos$magnification = as.numeric(acquisition$Imaging[["Magnification"]])
infos$coremode = as.numeric(acquisition$Fluidics[["CoreMode"]])
infos$evmode = as.numeric(acquisition$Imaging[["EVModeEnabled"]])
if(from == "analysis" & file_extension != "rif") {
if(length(IFD[[1]]$tags[["33020"]]$map)!=0) {
cross = getFullTag(IFD = IFD, which = 1, tag = "33020")
infos$CrossTalkMatrix = matrix(cross, nrow = sqrt(length(cross)), byrow = TRUE)
} else {
infos$CrossTalkMatrix = NULL
}
} else {
if(length(acquisition$Imaging$InspireCrossTalkMatrix) == 0) {
if(length(IFD[[1]]$tags[["33020"]]$map)!=0) {
cross = getFullTag(IFD = IFD, which = 1, tag = "33020")
infos$CrossTalkMatrix = matrix(cross, nrow = sqrt(length(cross)), byrow = TRUE)
} else {
infos$CrossTalkMatrix = NULL
}
} else {
infos$CrossTalkMatrix = matrix(as.numeric(strsplit(x = acquisition$Imaging$InspireCrossTalkMatrix, split=" ", fixed = TRUE)[[1]]), nrow = length(infos$in_use), byrow = TRUE)
}
}
if(file_extension == "daf") {
tmp_last = tmp_daf
} else {
if(getFileExt(fileName) == "daf") rm(tmp_daf)
if(length(acquisition$Imaging[["DafFile"]])!=0) {
if(acquisition$Imaging[["DafFile"]]!="") {
tmp_last = read_xml(acquisition$Imaging[["DafFile"]], options=c("HUGE","RECOVER","NOENT","NOBLANKS","NSCLEAN"))
force_default = FALSE
} else {
if(!force_default) stop("can't determine acquisition information")
}
} else {
if(!force_default) stop("can't determine acquisition information")
}
if(force_default) {
node = lapply(1:12, FUN=function(i) {
im = buildImage(physicalChannel = i, MODE = infos$collectionmode, BF = infos$brightfield$channel[i])
im$physicalChannel = im$physicalChannel - 1
as.character(xml_new_node("image", im))
})
tmp_last = read_xml(paste0("<Images>",paste0(node, collapse=""),"</Images>"), options=c("HUGE","RECOVER","NOENT","NOBLANKS","NSCLEAN"))
}
}
infos = c(infos, list("ChannelPresets" = to_list_node(xml_find_all(tmp_last, "//ChannelPresets")),
"ImageDisplaySettings" = to_list_node(xml_find_all(tmp_last, "//ImageDisplaySettings")),
"Images" = as.data.frame(do.call(what = "rbind", args = xml_attrs(xml_find_all(tmp_last, "//image"))), stringsAsFactors = FALSE),
"masks" = as.data.frame(do.call(what="rbind", xml_attrs(xml_find_all(tmp_last, "//mask"))), stringsAsFactors=FALSE)),
"ViewingModes" = to_list_node(xml_find_all(tmp_last, "//ViewingModes")),
"Origin_rif" = list(Origin_rif),
"Merged_rif" = list(Merged_rif),
"XIF_type" = attr(xif_type, "label"),
"XIF_test" = testXIF(fileName_image),
"checksum" = checksumXIF(fileName_image),
"fileName" = fileName,
"fileName_image" = normalizePath(fileName_image, winslash = "/"))
for(i in c("physicalChannel","xmin","xmax","xmid","ymid","scalemin","scalemax")) if(i %in% names(infos$Images)) infos$Images[, i] = as.integer(infos$Images[, i])
infos$Images$physicalChannel = infos$Images$physicalChannel + 1L
infos$Images = infos$Images[order(infos$Images$physicalChannel), ]
infos$Images$gamma = apply(infos$Images[,c("xmin", "xmax", "xmid", "ymid")], 1, cpp_computeGamma)
infos$Images[,"color"] = map_color(infos$Images[,"color"])
if("saturation"%in%names(infos$Images)) infos$Images[,"saturation"] = map_color(infos$Images[,"saturation"])
if(ncol(infos$masks) == 0) infos$masks = data.frame(type = "C", name = "MC", def = paste0(sprintf("M%02i", infos$Images$physicalChannel), collapse="|Or|"))
class(infos$masks) <- c(class(infos$masks), "IFC_masks")
if(length(infos$ViewingModes) != 0) names(infos$ViewingModes) = sapply(infos$ViewingModes, FUN=function(x) x$name)
attr(infos, "class") <- c("IFC_info",from)
return(infos)
}
gitdemont/IFC documentation built on Feb. 20, 2025, 12:55 a.m.
R Package Documentation
Browse R Packages
We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
Defines functions getInfo
Documented in getInfo
################################################################################
# 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! #
# -We do not guarantee privacy nor confidentiality. #
# -This program is distributed in the hope that it will be useful, but WITHOUT #
# ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or #
# FITNESS FOR A PARTICULAR PURPOSE. In no event shall the copyright holders or #
# contributors be liable for any direct, indirect, incidental, special, #
# exemplary, or consequential damages (including, but not limited to, #
# procurement of substitute goods or services; loss of use, data, or profits; #
# or business interruption) however caused and on any theory of liability, #
# whether in contract, strict liability, or tort (including negligence or #
# otherwise) arising in any way out of the use of this software, even if #
# advised of the possibility of such damage. #
# #
# You should have received a copy of the GNU General Public License #
# along with IFC. If not, see <http://www.gnu.org/licenses/>. #
################################################################################
#' @title IFC File Information Extraction
#' @description
#' Retrieves rich information from RIF, CIF and DAF files.
#' @param fileName path to file..
#' @param from whether to extract information from 'acquisition' or 'analysis'. Default is 'analysis'.
#' @param verbose whether to display information (use for debugging purpose). Default is FALSE.
#' @param verbosity quantity of information print to console when verbose is TRUE; 1: normal, 2: rich. Default is 1.
#' @param warn whether to send warning message when trying to read 'analysis' information from a 'rif' file. Default is TRUE.
#' @param force_default when display information can't be retrieved whether to use default values. Default is TRUE.
#' @param cifdir the path of the directory to initially look to cif file. Default is dirname(fileName). Only apply when 'fileName' is a .daf file.
#' @param ntry number of times \code{\link{getInfo}} will be allowed to find corresponding cif file. Default is +Inf. Only apply when 'fileName' is a .daf file.
#' If cif can't be found, but 'ntry' is reached, then an error will be thrown.
#' @param ... other arguments to be passed.
#' @examples
#' if(requireNamespace("IFCdata", quietly = TRUE)) {
#' ## use a daf file
#' file_daf <- system.file("extdata", "example.daf", package = "IFCdata")
#' info <- getInfo(fileName = file_daf, from = "analysis")
#' ## show some information
#' print(info$Images)
#' } else {
#' message(sprintf('Please run `install.packages("IFCdata", repos = "%s", type = "source")` %s',
#' 'https://gitdemont.github.io/IFCdata/',
#' 'to install extra files required to run this example.'))
#' }
#' @return a list of information (open .daf file in an text editor for more details) about input fileName of class `IFC_info` and `acquistion` or `analysis`, whose members are:\cr
#' -objcount, number of object in file,\cr
#' -date, date of file creation,\cr
#' -instrument, instrument identification,\cr
#' -sw_raw, version of software for raw data,\cr
#' -sw_processed, version of software for processed data,\cr
#' -channelwidth, default channel width in pixel,\cr
#' -in_use, channels used,\cr
#' -brightfield, whether brightfield is applied on channels and its intensity,\cr
#' -illumination, laser illumination parameters,\cr
#' -collectionmode, the collection mode,\cr
#' -magnification, magnification used,\cr
#' -coremode, the core mode,\cr
#' -evmode, the high gain mode,\cr
#' -CrossTalkMatrix. compensation matrix applied,\cr
#' -ChannelPresets, channel preset,\cr
#' -ImageDisplaySettings, image display settings,\cr
#' -Images, information about colors, range and channels,\cr
#' -masks, masks defined,\cr
#' -ViewingModes, modes of visualization,\cr
#' -checksum, checksum computed,\cr
#' -Origin_rif, character vector of path of rif used to create cif, if input file was a cif,\cr
#' -Merged_rif, character vector of path of files used to create rif, if input file was a merged,\cr
#' -XIF_type, character definig XIF type,\cr
#' -XIF_test, integer defining XIF type,\cr
#' -checksum, integer corresponding to file checksum,\cr
#' -fileName, path of fileName input,\cr
#' -fileName_image, path of fileName_image.
#' @export
getInfo <- function(fileName,
from = c("acquisition","analysis")[2],
verbose = FALSE,
verbosity = 1,
warn = TRUE,
force_default = TRUE,
cifdir = dirname(fileName),
ntry = +Inf,
...) {
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")
if(!file.exists(fileName)) stop(paste0("can't find ",fileName))
file_extension = getFileExt(fileName)
assert(file_extension, len = 1, alw = c("daf", "cif", "rif"))
fileName = enc2native(normalizePath(fileName, winslash = "/", mustWork = FALSE))
assert(from, len = 1, alw = c("acquisition","analysis"))
verbose = as.logical(verbose); assert(verbose, len = 1, alw = c(TRUE, FALSE))
verbosity = as.integer(verbosity); assert(verbosity, len = 1, alw = c(1, 2))
warn = as.logical(warn); assert(warn, len = 1, alw = c(TRUE, FALSE))
force_default = as.logical(force_default); assert(force_default, len = 1, alw = c(TRUE, FALSE))
cifdir = na.omit(as.character(cifdir)); assert(cifdir, len = 1, typ = "character")
ntry = na.omit(as.numeric(ntry)); assert(ntry, len = 1, typ = "numeric")
if(ntry < 0) ntry = 0
if(warn & file_extension == "rif" & from == "analysis") warning("Only information from 'acquisition' can be retrieved from 'rif' file", call. = FALSE, immediate. = TRUE)
if(file_extension == "daf") {
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_daf = read_xml(readBin(con = fileName, what = "raw", n = toskip), options=c("HUGE","RECOVER","NOENT","NOBLANKS","NSCLEAN"))
cname = xml_attr(xml_find_first(tmp_daf, "//SOD"), attr = "file")
fcs = xml_attr(xml_find_first(tmp_daf, "//FCS"), attr = "file")
if(!is.na(fcs)) stop("can't extract information from .daf generated from .fcs")
found = FALSE
checksum = checksumDAF(fileName)
fileName_image = file.path(cifdir, paste0(splitf(cname)[c("short","ext")], collapse = ".")) # look in cifdir 1st
if(file.exists(fileName_image)) {
if(checksumXIF(fileName_image) == checksum) found = TRUE
} else {
fileName_image = cname
}
if((!found) && file.exists(fileName_image)) {
if(checksumXIF(fileName_image) == checksum) found = TRUE
}
while((interactive() && (ntry > 0) && (!found))) {
message(paste0("daf file does not refer to: ", fileName_image))
old_wd = getwd()
on.exit(setwd(old_wd), add= TRUE)
setwd(dirname(fileName))
if(.Platform$OS.type == "windows") {
fileName_image = choose.files(caption = paste0("Looking for: ", basename(cname)), multi = FALSE, filters = cbind("Compensated Image File (*.cif)", "*.cif"))
} else {
fileName_image = file.choose()
}
if(file.exists(fileName_image)) if(getFileExt(fileName_image)=="cif") if(checksumXIF(fileName_image) == checksum) {
found = TRUE
break;
}
ntry = ntry - 1
}
if(!found) stop("can't extract information")
fileName_image = normalizePath(fileName_image, winslash = "/")
IFD = getIFD(fileName = fileName_image, offsets = "first", trunc_bytes = 8, force_trunc = FALSE, verbose = verbose, verbosity = verbosity, bypass = TRUE, ...)
}
if(file_extension == "cif" | file_extension == "rif") {
fileName_image = fileName
IFD = getIFD(fileName = fileName_image, offsets = "first", trunc_bytes = 8, force_trunc = FALSE, verbose = verbose, verbosity = verbosity, bypass = TRUE, ...)
}
Origin_rif = character()
Merged_rif = character()
xif_type = IFDtype(IFD[[1]])
if(!is.null(IFD[[1]]$tags[["33026"]])) {
if(IFD[[1]]$tags[["33026"]]$byt != 0) Origin_rif = strsplit(as.character(getFullTag(IFD = IFD, which = 1, tag="33026")), "|", fixed = TRUE)[[1]]
}
if(!is.null(IFD[[1]]$tags[["33030"]])) {
if(IFD[[1]]$tags[["33030"]]$byt != 0) Merged_rif = strsplit(as.character(getFullTag(IFD = IFD, which = 1, tag="33030")), "|", fixed = TRUE)[[1]]
}
if(file_extension == "daf" & from == "acquisition") file_extension = "cif"
tmp_acq = read_xml(getFullTag(IFD = IFD, which = 1, tag = "33027", raw = TRUE), options=c("HUGE","RECOVER","NOENT","NOBLANKS","NSCLEAN"))
acquisition = list("Illumination"=lapply(as_list(xml_find_first(tmp_acq, "//Illumination")), unlist),
"Fluidics"=lapply(as_list(xml_find_first(tmp_acq, "//Fluidics")), unlist),
"Imaging"=lapply(as_list(xml_find_first(tmp_acq, "//Imaging")), unlist),
"Display"=lapply(as_list(xml_find_first(tmp_acq, "//Display")), unlist))
infos = list("objcount" = IFD[[1]]$tags[["33018"]]$map, # should not exceed 4 bytes
"date"=getFullTag(IFD = IFD, which = 1, "33004"),
"instrument"=getFullTag(IFD = IFD, which = 1, "33006"),
"sw_raw"=suppressWarnings(getFullTag(IFD = IFD, which = 1, "33069")),
"sw_process"=getFullTag(IFD = IFD, which = 1, "33066"))
# determines channelwidth, very important for objectExtract() when force_width = TRUE
# prefer using channelwidth extracted from ifd dedicated tag (=tag 33009) rather than the one from parsing ASSISTdb (=tag 33064)
# TODO ask AMNIS the rules for extracting channelwidth
channelwidth1 = IFD[[1]]$tags[["33009"]]$map # should not exceed 4 bytes
tmp_ins = read_xml(getFullTag(IFD = IFD, which = 1, tag ="33064", raw = TRUE), options = c("HUGE","RECOVER","NOENT","NOBLANKS","NSCLEAN"))
channelwidth2 = as.numeric(xml_text(xml_find_first(tmp_ins, xpath = "//ChannelWidth")))
tryCatch({
# information in acquisition db
lasers_nodes = grep("Filter", grep("ExLaser", names(acquisition[["Illumination"]]), value = TRUE), value = TRUE, invert = TRUE)
lasers_on = acquisition$Illumination[grep("PowerOn", lasers_nodes, value = TRUE)]
lasers_on = as.logical(as.integer(unlist(lasers_on[order(as.integer(gsub("\\D+", "", names(lasers_on))))])))
lasers_power = acquisition$Illumination[grep("IntensityWatts", lasers_nodes, value = TRUE)]
lasers_power = as.numeric(sprintf("%.2f", as.numeric(unlist(lasers_power[order(as.integer(gsub("\\D+", "", names(lasers_power))))]))))
if(length(lasers_power) != length(lasers_on)) lasers_power = rep(NA, length(lasers_on))
# information in instrument db
ins_lasers = lapply(as_list(xml_find_first(tmp_ins, "Illumination")), unlist)
lasers_nodes = grep("ExLaser", names(ins_lasers), value = TRUE)
lasers_present = ins_lasers[grep("Filter|LAF", grep("Present", lasers_nodes, value = TRUE), value = TRUE, invert = TRUE)]
lasers_present = as.logical(as.integer(unlist(lasers_present[order(as.integer(gsub("\\D+", "", names(lasers_present))))])))
if(length(lasers_present) != length(lasers_on)) lasers_present = rep(NA, length(lasers_on))
lasers_wavelength = ins_lasers[grep("Wavelength", lasers_nodes, value = TRUE)]
lasers_wavelength = as.integer(unlist(lasers_wavelength[order(as.integer(gsub("\\D+", "", names(lasers_wavelength))))]))
if(length(lasers_wavelength) != length(lasers_on)) lasers_wavelength = rep(NA, length(lasers_on))
lasers_minpow = ins_lasers[grep("MinPower", lasers_nodes, value = TRUE)]
lasers_minpow = as.numeric(unlist(lasers_minpow[order(as.integer(gsub("\\D+", "", names(lasers_minpow))))]))
if(length(lasers_minpow) != length(lasers_on)) lasers_minpow = rep(NA, length(lasers_on))
lasers_maxpow = ins_lasers[grep("MaxPower", lasers_nodes, value = TRUE)]
lasers_maxpow = as.numeric(unlist(lasers_maxpow[order(as.integer(gsub("\\D+", "", names(lasers_maxpow))))]))
if(length(lasers_maxpow) != length(lasers_on)) lasers_maxpow = rep(NA, length(lasers_on))
illumination = data.frame("installed" = lasers_present,
"wavelength" = lasers_wavelength,
"powered" = lasers_on,
"power" = lasers_power,
"min" = lasers_minpow,
"max" = lasers_maxpow, stringsAsFactors = FALSE)
}, error = function(e) {
illumination = data.frame(matrix(NA, ncol = 6, nrow = 0))
colnames(illumination) = c("installed","wavelength", "powered" ,"power" ,"min","max")
})
infos$channelwidth = channelwidth1
if(length(channelwidth1)==0) infos$channelwidth = channelwidth2
if(length(channelwidth1)!=0) if(is.na(channelwidth1)) infos$channelwidth = channelwidth2
if(length(channelwidth1)!=0) if(channelwidth1==0) infos$channelwidth = channelwidth2
infos$in_use = as.logical(as.numeric(unlist(strsplit(acquisition$Imaging[["ChannelInUseIndicators_0_11"]], " ", useBytes = TRUE, fixed=TRUE))))
infos$brightfield = list("channel"=as.logical(as.numeric(unlist(strsplit(acquisition$Illumination[["BfLedIndicators_0_11"]], " ", useBytes = TRUE, fixed=TRUE)))),
"power"= as.logical(as.numeric(acquisition$Illumination[["BFOnOff"]])),
"intensity" = as.numeric(acquisition$Illumination[["BFIntensity"]]))
infos$illumination = illumination
# TODO ask AMNIS, if collectionmode is the good variable that determines default information
infos$collectionmode = as.numeric(acquisition$Illumination[["CollectionMode"]])
infos$magnification = as.numeric(acquisition$Imaging[["Magnification"]])
infos$coremode = as.numeric(acquisition$Fluidics[["CoreMode"]])
infos$evmode = as.numeric(acquisition$Imaging[["EVModeEnabled"]])
if(from == "analysis" & file_extension != "rif") {
if(length(IFD[[1]]$tags[["33020"]]$map)!=0) {
cross = getFullTag(IFD = IFD, which = 1, tag = "33020")
infos$CrossTalkMatrix = matrix(cross, nrow = sqrt(length(cross)), byrow = TRUE)
} else {
infos$CrossTalkMatrix = NULL
}
} else {
if(length(acquisition$Imaging$InspireCrossTalkMatrix) == 0) {
if(length(IFD[[1]]$tags[["33020"]]$map)!=0) {
cross = getFullTag(IFD = IFD, which = 1, tag = "33020")
infos$CrossTalkMatrix = matrix(cross, nrow = sqrt(length(cross)), byrow = TRUE)
} else {
infos$CrossTalkMatrix = NULL
}
} else {
infos$CrossTalkMatrix = matrix(as.numeric(strsplit(x = acquisition$Imaging$InspireCrossTalkMatrix, split=" ", fixed = TRUE)[[1]]), nrow = length(infos$in_use), byrow = TRUE)
}
}
if(file_extension == "daf") {
tmp_last = tmp_daf
} else {
if(getFileExt(fileName) == "daf") rm(tmp_daf)
if(length(acquisition$Imaging[["DafFile"]])!=0) {
if(acquisition$Imaging[["DafFile"]]!="") {
tmp_last = read_xml(acquisition$Imaging[["DafFile"]], options=c("HUGE","RECOVER","NOENT","NOBLANKS","NSCLEAN"))
force_default = FALSE
} else {
if(!force_default) stop("can't determine acquisition information")
}
} else {
if(!force_default) stop("can't determine acquisition information")
}
if(force_default) {
node = lapply(1:12, FUN=function(i) {
im = buildImage(physicalChannel = i, MODE = infos$collectionmode, BF = infos$brightfield$channel[i])
im$physicalChannel = im$physicalChannel - 1
as.character(xml_new_node("image", im))
})
tmp_last = read_xml(paste0("<Images>",paste0(node, collapse=""),"</Images>"), options=c("HUGE","RECOVER","NOENT","NOBLANKS","NSCLEAN"))
}
}
infos = c(infos, list("ChannelPresets" = to_list_node(xml_find_all(tmp_last, "//ChannelPresets")),
"ImageDisplaySettings" = to_list_node(xml_find_all(tmp_last, "//ImageDisplaySettings")),
"Images" = as.data.frame(do.call(what = "rbind", args = xml_attrs(xml_find_all(tmp_last, "//image"))), stringsAsFactors = FALSE),
"masks" = as.data.frame(do.call(what="rbind", xml_attrs(xml_find_all(tmp_last, "//mask"))), stringsAsFactors=FALSE)),
"ViewingModes" = to_list_node(xml_find_all(tmp_last, "//ViewingModes")),
"Origin_rif" = list(Origin_rif),
"Merged_rif" = list(Merged_rif),
"XIF_type" = attr(xif_type, "label"),
"XIF_test" = testXIF(fileName_image),
"checksum" = checksumXIF(fileName_image),
"fileName" = fileName,
"fileName_image" = normalizePath(fileName_image, winslash = "/"))
for(i in c("physicalChannel","xmin","xmax","xmid","ymid","scalemin","scalemax")) if(i %in% names(infos$Images)) infos$Images[, i] = as.integer(infos$Images[, i])
infos$Images$physicalChannel = infos$Images$physicalChannel + 1L
infos$Images = infos$Images[order(infos$Images$physicalChannel), ]
infos$Images$gamma = apply(infos$Images[,c("xmin", "xmax", "xmid", "ymid")], 1, cpp_computeGamma)
infos$Images[,"color"] = map_color(infos$Images[,"color"])
if("saturation"%in%names(infos$Images)) infos$Images[,"saturation"] = map_color(infos$Images[,"saturation"])
if(ncol(infos$masks) == 0) infos$masks = data.frame(type = "C", name = "MC", def = paste0(sprintf("M%02i", infos$Images$physicalChannel), collapse="|Or|"))
class(infos$masks) <- c(class(infos$masks), "IFC_masks")
if(length(infos$ViewingModes) != 0) names(infos$ViewingModes) = sapply(infos$ViewingModes, FUN=function(x) x$name)
attr(infos, "class") <- c("IFC_info",from)
return(infos)
}
R Package Documentation
Browse R Packages
We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
Embedding an R snippet on your website
Add the following code to your website.
For more information on customizing the embed code, read Embedding Snippets.