Reading Isomap data into R

isomap_data.R

### Swiss Roll

# Install the R.matlab package:
# install.packages("R.matlab")

# downloads and reads Swiss Roll data
# returns a list:
# X.data a 3 x 20000 matrix of the column-stored X, Y, Z data
# Y.data a 2 x 20000 matrix of what I assume is the unrolled data coordinates
read_isoswiss <- function(url = "http://web.mit.edu/cocosci/isomap/swiss_roll_data.mat") {
  if (!requireNamespace("R.matlab", quietly = TRUE)) {
    stop("Library 'R.matlab' needed for this function to work. Please install it.",
         call. = FALSE)
  }
  f <- gzcon(base::url(url, "rb"))
  res <- R.matlab::readMat(f)
  close(f)
  res
}

# install the snedata package and make use of a private function
# remotes::install_github("jlmelville/snedata")
# Returns data frame:
# each row is an observation, with x, y, z coordinate and color string value (helpful for visualization)
read_isoswiss_df <- function(url = "http://web.mit.edu/cocosci/isomap/swiss_roll_data.mat") {
  if (!requireNamespace("snedata", quietly = TRUE)) {
    stop("Github library 'snedata' needed for this function to work. Please install it.",
         call. = FALSE)
  }
  swiss_list <- read_isoswiss()
  swiss_roll <- data.frame(t(swiss_list$X.data))
  swiss_roll <- cbind(swiss_roll, snedata:::linear_color_map(swiss_list$Y.data[1, ]))
  colnames(swiss_roll) <- c("x", "y", "z", "color")
  swiss_roll
}

# plot the cross-section
plot(isoswiss_roll$x, isoswiss_roll$y, col = isoswiss_roll$color, cex = 0.1)

### Faces

# Two extra problems here:
# 1. Dataset no longer exists on the Stanford website
# 2. Data was Z compressed, which is a pain to uncompress via R (you need to use an external program).

# Procedure:
# 1. Download the dataset via the wayback machine:
# https://web.archive.org/web/20160913051505/http://isomap.stanford.edu/face_data.mat.Z
# 2. uncompress manually (e.g. using 7-zip)
# 3. Run the code below

library(R.matlab)
facesl <- readMat(con = "wherever-you-downloaded-and-decompressed/face_data.mat")
isofaces <- t(facesl$images)
colnames(isofaces) <- paste0('px', 1:4096)
isofaces <- data.frame(isofaces)
# pose1 and pose2 relate to the angle of the head, either could be used to color the manifold the faces lie on
isofaces <- cbind(isofaces, pose1 = facesl$poses[1, ], pose2 = facesl$poses[2, ])

# displays face in row i of the dataframe
view_isoface <- function(df, i) {
  graphics::image(matrix(as.numeric(df[i, 1:4096]), nrow = 64, ncol = 64, byrow = TRUE)[, 64:1], 
                  col = grDevices::gray(1:255 / 255))
}