R/Tracks.as.dataframe.R

In marionlouveaux/mamut2r: Import of MaMuT xml files into R

#' Convert MaMuT xml Tracks tags to a dataframe
#'
#' @param MaMuT_XML .xml MaMuT Fiji plugin file converted to list with readMaMuT()
#' @importFrom dplyr bind_rows
#' @importFrom dplyr mutate
#' @importFrom tibble as.tibble
#'
#' @export
#' @return Dataframe containing the spot ID, its name, its visibility, its radius, quality, source and position (x, y, z, t).
#' Tracks.as.dataframe()

Tracks.as.dataframe <- function(MaMuT_XML){
  AllTracks <- MaMuT_XML$Model$AllTracks

  names(AllTracks)
  id_alltrack <- which(names(AllTracks) == "Track")

  for (i in 1:length(id_alltrack)){
    names(AllTracks)[id_alltrack[i]] <- paste0(names(AllTracks)[id_alltrack[i]], "_", i)
  }

  Tracks_df <- NULL
  for (i in id_alltrack){

    Tracks <- AllTracks[[i]]
    names(Tracks)
    id_edge <- which(names(Tracks) == "Edge")

    for (index in 1:length(id_edge)){
      names(Tracks)[id_edge[index]] <- paste0(names(Tracks)[id_edge[index]], "_", index)
    }

    Tracks_df_tmp <- NULL
    for (index in 1:length(id_edge)){
      Tracks_df_tmp <- data.frame(rbind(Tracks_df_tmp, Tracks[[index]]), stringsAsFactors = FALSE)
    }

    TRACK_NAME <- Tracks$.attrs["name"]
    TRACK_ID <- Tracks$.attrs["TRACK_ID"]
    TRACK_INDEX <- Tracks$.attrs["TRACK_INDEX"]

    Tracks_df_tmp <- cbind(Tracks_df_tmp, data.frame(TRACK_NAME, TRACK_ID, TRACK_INDEX, stringsAsFactors = FALSE), row.names = NULL)

    Tracks_df_tmp <- Tracks_df_tmp %>%
      mutate(SPOT_SOURCE_ID=as.integer(SPOT_SOURCE_ID),
           SPOT_TARGET_ID=as.integer(SPOT_TARGET_ID),
           VELOCITY=as.numeric(VELOCITY),
           DISPLACEMENT=as.numeric(DISPLACEMENT))

    Tracks_df <- Tracks_df %>%
      bind_rows(Tracks_df_tmp) %>%
    as.tibble()
  }
return(Tracks_df)
}