R/ChidRecordings.R

In LAAC-LSCP/ChildRecordsR: ChildRecordsR Reliability Analysis

utils::globalVariables(c('segment_offset',
                         'segment_onset',
                         'child_id',
                         'age_in_day',
                         'speaker_type',
                         'experiment',
                         'range_offset',
                         'duration',
                         'voc',
                         'indicator',
                         'ICC',
                         'corpus',
                         'pr',
                         'Freq',
                         'rec',
                         'rater',
                         'coeff.val after',
                         'coeff.name',
                         'conf.inf',
                         'conf.sup',
                         'weight',
                         'indic'))



#' Building childrecordings class
#'
#' Main class of the package. Help to check data integrity and provide data
#' organization. Only provide the path folder of the childrecordings project.
#' Provid some integrity check such as missing files or missing meta
#'
#' @param path path to the childrecoding project folder
#' @return  A ChildRecordings class containing meta data path
#' 
#' @export
#' 
#' @importFrom utils read.csv
#'
#' @examples
#' 
#' \dontrun{
#' 
#' library(ChildRecordsR)
#' path = "/mnt/94707AA4707A8CAC/CNRS/corpus/vandam-daylong-demo"
#' CR = ChildRecordings(path)
#'
#' }


ChildRecordings <- function(path) {

  ### Metadata
  annotations <- utils::read.csv(file.path(path, "metadata", "annotations.csv"), stringsAsFactors = F)
  recordings <- utils::read.csv(file.path(path, "metadata", "recordings.csv"), stringsAsFactors = F)
  children <- utils::read.csv(file.path(path, "metadata", "children.csv"), stringsAsFactors = F)
  
  all.meta <- merge(recordings, annotations, by = "recording_filename")
  all.meta <- merge(all.meta, children, by= "child_id")

  error.conversion <- all.meta[ nchar(all.meta$error)>=1 & !is.na(nchar(all.meta$error)),]
  all.meta <- all.meta[is.na(all.meta$error) | all.meta$error=="",]

  ### Check data test
  ## Meta file
  ## referenced files
  n.referenced.file.raw <-length(unique(all.meta$raw_filename))
  path.referenced.file.raw <- paste0(all.meta$set,"/raw/",all.meta$raw_filename)

  n.referenced.file.annotation <-length(unique(all.meta$annotation_filename))
  path.referenced.file.annotation <- paste0(all.meta$set,"/converted/",all.meta$annotation_filename)

  n.referenced.file =  n.referenced.file.annotation

  ## Files
  path.file <- list.files(file.path(path, "annotations"), recursive = T)
  n.file <- length(path.file)

  # Check file
  files.missing <- path.referenced.file.annotation[!path.referenced.file.annotation %in% path.file]
  files.unreferenced <- path.file[!(path.file %in% path.referenced.file.annotation |path.file %in% path.referenced.file.raw)]

  # check time start
  test <- is.na(all.meta$start_time)
  nbr.start.time <- sum(test)
  missing.start.time <- all.meta[test, ]$annotation_filename

  # check empty file
  vec_files = file.path(all.meta$set, "converted", all.meta$annotation_filename)
  empty.files <- c()
  
  for (file in vec_files){
    
    iter_file = file.path(path, 'annotations', file)
    if (!file.exists(iter_file)) {
      empty.files <- c(empty.files, file)
    }
  }

  value <- list(annotations = annotations,
                recordings = recordings,
                children = children,
                all.meta = all.meta,
                path = paste0(path,"/"),
                integrity_test = list("nbr.file"=n.file,
                                      "referenced.file"= n.referenced.file,
                                      "files.missing"=files.missing,
                                      "files.unreferenced"=files.unreferenced,
                                      "missing.start.time"=missing.start.time,
                                      "empty.files"=empty.files,
                                      "error.conversion"=error.conversion)
  )
  
  attr(value, "class") <- "ChildRecordings"

  print.ChildRecordings(value)
  invisible(value)
}


#' @export

print.ChildRecordings <- function(ChildRecordings){

  # Meta file
  nbr.file <- ChildRecordings$integrity_test$nbr.file
  coders <- unique(ChildRecordings$all.meta$set)
  referenced.file <- ChildRecordings$integrity_test$referenced.file
  files.missing <- ChildRecordings$integrity_test$files.missing
  files.unreferenced <- ChildRecordings$integrity_test$files.unreferenced
  error.conversion <- ChildRecordings$integrity_test$error.conversion

  # check time start
  missing.start.time <- ChildRecordings$integrity_test$missing.start.time

  # check empty file
  empty.files <- ChildRecordings$integrity_test$empty.files

  ### Print Info summary
  cat("###############################################\n")
  cat("Hello Wellcome to the ChildRecordings R Project \n\n")

  cat("Your ChildRecording project path contained : \n",
      nbr.file," annotations files \n",
      referenced.file, " are referenced in the metadata \n",
      length(coders), " coders were found : ",  coders, "\n")

  if(length(files.missing)==0 & length(files.unreferenced)==0){
    cat("\n All files seems to be present and referenced in the metadata (good news ;) )\n")
  }

  cat("\n")
  if(length(files.missing)!=0 ){
    cat(" ", length(files.missing), " file(s) seem(s) to be missing in the annotations folders")
    cat("\t more infos in ChildRecordings$integrity_test$files.missing \n")
  }

  if(length(files.unreferenced)!=0 ){
    cat( length(files.unreferenced), " file(s) seem(s) to be unreferenced in the metadata \n")
    cat("\t more infos in  ChildRecordings$integrity_test$files.unreferenced \n")
  }

  cat("\n")
  if(length(missing.start.time)!=0){
    cat(" ", length(missing.start.time), " metadata don't have a start recording time (a.k.a start.time) \n" )
    cat("\t therefore time indicators will not be built for those files \n")
    cat("\t more infos in ChildRecordings$integrity_test$missing.start.time \n")
  }

  if(length(empty.files)!=0){
    cat(" ", length(empty.files), " files are empty \n" )
    cat("\t This should normally mean that no annotation were provided by annotator \n")
    cat("\t more infos in ChildRecordings$integrity_test$empty.files \n")
  }

  if (nrow(error.conversion)!=0){
    cat(" ", nrow(error.conversion), " files with conversion error\n" )
    cat("\t This should normally mean that your conversion fail \n")
    cat("\t Those files are remove from package analysis \n")
    cat("\t more infos in ChildRecordings$integrity_test$error.conversion \n")
  }
}