R/arrays.R

In sje30/sjemea: Multi electrode analysis

get.array.info <- function(data) {
  ## Array-specific information; maybe this could go in a file, rather
  ## than be read-in separately.  Useful for the HDF5 functions.
  
  pos <- data$epos;  rownames(pos) <- data$names
  array <- data$array

  if (array == 'MCS_8x8_100um') {
    ## e.g. Demas2003
    xlim <- ylim <- c(50, 850)
    spacing <- 100
    corr.breaks <- c(0, 150, 250, 350, 450, 550, 650, 1000)
  }

  if (array == 'MCS_8x8_200um') {
    ## e.g. Sun2008
    xlim <- ylim <- c(50, 1700) ## TODO SPOT: make.sun.layout()
    spacing <- 200
    corr.breaks <- c(0, 150, 250, 350, 450, 550, 650, 1000, 2000)  
  }

  if (array == 'EJC1_hex_60um') {
    ## e.g. Torborg2004,Feller2003.
    xlim <- ylim <- c(-300, 300)
    spacing <- 60
    corr.breaks <-  c(0, seq(35, by=70, length=9))
  }


  
  if (array == 'stanford_hex_60um') {
    ## e.g. Wong1993
    xlim <- ylim <- c(-300, 300)
    spacing <- 60
    corr.breaks <-  c(0, seq(35, by=70, length=9))
  }

  
  if (array == 'litke_hex_60um') {
    xlim <- c(-1000, 1000)
    ylim <- c(-500, 500)
    spacing <- 60
    corr.breaks <- c(0, 0.001, seq(from=50, to=2050, by=50))
  }

  if ( any(grep('^Axion', array))) {
    ## e.g. Neurotox ongoing project.
    xlim <- c(0, 8000)
    ylim <- c(0, 6000)
    spacing <- 200
    corr.breaks <-  0                   #TODO; by default, do no breaks!
  }

  if (array == "APS_64x64_42um") {
    spacing      <- 42
    xlim <- ylim <- c(0, 64*spacing)
    max.dist     <- sqrt(2*(64*spacing)^2)
    corr.breaks  <- seq(from=0, to=max.dist, by=50)
  }



  ## HACK for HDF5: the arrayname (stored in array) is a string, which
  ## can either be stored as a character vector or as an array.  R was
  ## getting confused about this, and all.equal() was failing...
  ## Need a clearer example...
  
  array <- as.character(array)
  layout <- list(xlim = xlim, ylim = ylim, spacing = spacing, 
                 pos = pos, array=array)
  class(layout) <- "mealayout"
  list(layout=layout, corr.breaks=corr.breaks)
}