## ----include = FALSE, echo = FALSE, results='hide'----------------------------
if(identical(Sys.getenv("IEEGIO_PKGDOWN", unset = ""), "")) {
  knitr::opts_chunk$set(
    collapse = TRUE,
    comment = "#>",
    eval = FALSE
  )
} else {
  options("rgl.useNULL" = TRUE)
  library(ieegio)
  library(rgl)
  knitr::opts_chunk$set(
    collapse = TRUE,
    comment = "#>"
  )
  rgl::setupKnitr(autoprint = FALSE)
  cache_dir <- tools::R_user_dir("ieegio", "cache")
  dir.create(cache_dir, showWarnings = FALSE, recursive = TRUE)
  cache_dir <- normalizePath(cache_dir, mustWork = TRUE)
  options("ieegio.extract_path", cache_dir)
}


## ----sample-------------------------------------------------------------------
#  library(ieegio)
#  
#  # volume file
#  nifti_file <- ieegio_sample_data("brain.demosubject.nii.gz")
#  
#  # geometry
#  geom_file <- ieegio_sample_data(
#    "gifti/icosahedron3d/geometry.gii")
#  
#  # measurements
#  shape_file <- ieegio_sample_data(
#    "gifti/icosahedron3d/rand.gii"
#  )
#  
#  # time series
#  ts_file <- ieegio_sample_data(
#    "gifti/icosahedron3d/ts.gii")
#  

## ----read_volume--------------------------------------------------------------
#  volume <- read_volume(nifti_file)
#  volume

## ----plot_volume, fig.width=8, fig.height=3, out.width="95%"------------------
#  par(mfrow = c(1, 3), mar = c(0, 0, 3.1, 0))
#  
#  ras_position <- c(-50, -10, 15)
#  
#  ras_str <- paste(sprintf("%.0f", ras_position), collapse = ",")
#  
#  for(which in c("coronal", "axial", "sagittal")) {
#    plot(x = volume, position = ras_position, crosshair_gap = 10,
#         crosshair_lty = 2, zoom = 3, which = which,
#         main = sprintf("%s T1RAS=[%s]", which, ras_str))
#  }
#  

## ----read_surface-------------------------------------------------------------
#  library(ieegio)
#  # geometry
#  geometry <- read_surface(geom_file)
#  
#  # measurements
#  measurement <- read_surface(shape_file)
#  
#  # time series
#  time_series <- read_surface(ts_file)

## ----merge--------------------------------------------------------------------
#  merged <- merge(geometry, measurement, time_series)
#  print(merged)

## ----plot_surface, webgl = TRUE, out.width="70%", fig.width = 7---------------
#  # plot the first column in measurements section
#  plot(merged, name = list("measurements", 1))

## ----time_series, webgl = TRUE, out.width="100%", fig.width = 7---------------
#  ts_demean <- apply(
#    merged$time_series$value,
#    MARGIN = 1L,
#    FUN = function(x) {
#      x - mean(x)
#    }
#  )
#  merged$time_series$value <- t(ts_demean)
#  plot(
#    merged, name = "time_series",
#    col = c(
#      "#053061", "#2166ac", "#4393c3",
#      "#92c5de", "#d1e5f0", "#ffffff",
#      "#fddbc7", "#f4a582", "#d6604d",
#      "#b2182b", "#67001f"
#    )
#  )