R/Extr_Morphometrics.R

In vrrenske/shinyspots: Visualization and Analysis of Bacterial Cell Segmentation and Fluorescence Data

##8-11-2017

##Renske van Raaphorst

##Extracting Morphometrics Data


##########################################################


##Dependencies:
    #library(R.matlab)


extr_Morphometrics_cellList <- function(morphpath){
  if (!requireNamespace("R.matlab", quietly = TRUE)) {
    inp <- readline("Package 'R.matlab' needed for this function to work. Press 'y' to install, or any other key to cancel.")
    if(inp=="y"|inp=="Y"){utils::install.packages("R.matlab")}else{stop("Canceled")}
  }
  morphdata <- R.matlab::readMat(morphpath)
  framenum <- 2*(1:(length(morphdata$frame)/2))
  for(u in framenum){
    cellListf <- data.frame(t(data.frame(morphdata$frame[u])))
    if(nrow(cellListf)!=0){
      cellListf$frame <- u/2
      if(u==2){
        cellList <- cellListf
      }
      else{
        cellList <- rbind(cellList, cellListf)
      }
    }
  }

  cellList <- cellList[cellList$area>24,]
  return(cellList)
}


spotrExtractMorphMESH <- function(cellList){

  if("length"%in%colnames(cellList)!=T){
      MESH <- do.call('rbind', lapply(c(1:nrow(cellList)), function(x) extrMorphCell(cellList[x,], l=FALSE) ))
      M1 <- MESH[MESH$numpoint==MESH$pole1,]
      M2 <- MESH[MESH$numpoint==MESH$pole2,]
      M1 <- M1[order(M1$cell,M1$frame),]
      M2 <- M2[order(M2$cell, M2$frame),]
      M1$max.length <- sqrt((M1$X-M2$X)^2+(M1$Y-M2$Y)^2)
      MESH <- merge(MESH, M1[,c("cell", "frame", "max.length")])
  }else{MESH <- do.call('rbind', lapply(c(1:nrow(cellList)), function(x) extrMorphCell(cellList[x,], l=TRUE)))}
  return(MESH)

}

extrMorphCell <- function(cell, l = TRUE){
  print(c(cell$cellID, cell$frame))
  meshcell <- data.frame(cell$Xcont, cell$Ycont, cell$cellID, cell$area, cell$pole1, cell$pole2, cell$frame)

  #meshcell <- data.frame(cell$Xcont[1], cell$Ycont[1], cell$cellID[1], cell$area[1],
                     #    cell$pole1[1], cell$pole2[1], cell$frame[1])
  colnames(meshcell) <- c("X", "Y", "cell", "area", "pole1", "pole2", "frame")
  if(l==TRUE){
    meshcell$max.length <- cell$length
    meshcell$max.width <- cell$width
  }
  meshcell$numpoint <- 1:nrow(meshcell)
  return(meshcell)
}



#' @export
extr_Morphometrics <- function(morphpath, mag, turncells = TRUE, cellList=FALSE){
  C <- extr_Morphometrics_cellList(morphpath)
  M <- spotrExtractMorphMESH(C)
  listM <- list()
  if(cellList==TRUE){
    listM$cellList <- C
  }
  if(turncells==TRUE){
    listM$mesh <- meshTurn(M)
  }
  if(turncells==FALSE){
    listM$mesh <- M
  }

  if(!missing(mag)){
    if(is.numeric(unlist(get(magnificationList,envir=magEnv)[mag]))==FALSE){
      stop("Magnification conversion factor not recognized. Please use addPixels2um('pixelName', pixelsize) to add your conversion factor")
    }
    if(turncells==TRUE){
      listM$mesh$Xrot_micron <- listM$mesh$X_rot * unlist(get(magnificationList, envir=magEnv)[mag])
      listM$mesh$Yrot_micron <- listM$mesh$Y_rot * unlist(get(magnificationList, envir=magEnv)[mag])
      listM$mesh$maxwum <- listM$mesh$max.width * unlist(get(magnificationList, envir=magEnv)[mag])
    }
    listM$mesh$max_um <- listM$mesh$max.length * unlist(get(magnificationList, envir=magEnv)[mag])
    listM$mesh$area_um <- listM$mesh$area *  unlist(get(magnificationList, envir=magEnv)[mag])^2
    listM$pixel2um <- unlist(get(magnificationList, envir=magEnv)[mag])
  }
  listM$mesh$num <- listM$mesh$numpoint
  listM$mesh$numpoint <- NULL
  return(listM)
}