R/visumot_check.R

In grrchrr/VisumotR: Visualizing Motility on Images

#' @title visumot_check
#' @description Gives a summary that allows to check the linking between a passed dataframe
#'  and images in a frame-wise manner.
#' @details To be written...
#' @examples To be written...

#' @export
visumot_check <- function(df, images, stack_time=FALSE, dimensions=2){
  #' @param df dataframe of the form: \code{df(track, time, X, Y, (Z,) mapping_parameters, ...)}
  #' @param images \code{vector}: filenames of images ordered by frames/time
  #' @param stack \code{logical}: default: \code{FALSE}, single image file provided if time-resolved imagestack is used, set: \code{TRUE}
  #' #' @param dimensions \code{numeric}: specify whether the images are 2D or 3D. 
  #' If 3D is selected data is assumed to be in the form: \code{df(track, time, X, Y, Z, mapping paramters, ...)}
  
  # add frames to dataframe
  df <- df %>% mutate(frame=match(time, sort(unique(time)))) %>% distinct(frame, time) 
  
  if(dimensions == 3 & stack_time == TRUE){
    stop("When using 3D data, supply individual time/frame resolved Z-stacks and set stack_time=FALSE")
  } 
  
  if (length(images)==nrow(df)){
    if(stack_time==TRUE){
      message('Image stack has same number of slices as timepoints in the dataset.')
      return(df)
    } else {
      message('Same number of images as timepoints in the dataset.')
      return(df %>% mutate(image=images))
    }
  } else {
    message('VisumotR detected differing number of timepoints in the dataset and images. Please check your dataset and image files or be careful.')
  }
  
  
  
}