Accessing calibration hypercube data

[dlebauer]

On April 15 we captured hyperspectral images of target objects at 15 min intervals throughout the day. See also terraref/computing-pipeline#289

Here is a picture of the calibration targets:

This is how you can get started extracting data from the VNIR files:

(you will want to get some files close in time to where you have validation measurements)

library(ncdf4)
library(dplyr)

hsi_calibration_dir <- '/data/terraref/sites/ua-mac/Level_1/hyperspectral/2017-04-15'
hsi_calibration_files <- dir(hsi_calibration_dir, 
                             recursive = TRUE,
                             full.names = TRUE)

fileinfo <- bind_rows(lapply(hsi_calibration_files, file.info)) %>%
  mutate(size_gb = size/1073741824)

calibration_nc <- nc_open(hsi_calibration_files[200])
a <- calibration_nc$var$rfl_img


#calibration_nc$dim$x$len 1600
#calibration_nc$dim$y$len
x_length <- round(calibration_nc$dim$x$len / 10)
y_length <- round(calibration_nc$dim$y$len * 3/4)

xstart <- ceiling(calibration_nc$dim$x$len / 2) - floor(x_length / 2) + 1

ystart <- ceiling(calibration_nc$dim$y$len / 2) - floor(y_length / 2) + 1


rfl <- ncvar_get(calibration_nc, 'rfl_img', 
          #start = c(1, xstart, ystart), 
          #count = c(955, x_length, y_length)
          start = c(1, 100, 100),
          count = c(calibration_nc$dim$wavelength$len, 160, 1324)
          )
x <- ncvar_get(calibration_nc, 'x', start = 100, count = 160)
y <- ncvar_get(calibration_nc, 'y', start = 100, count = 1324)

lambda <- calibration_nc$dim$wavelength$vals
for(i in 1 + 0:10*95){
  image(rfl[i,,],
        xlab = 'x (m)', ylab = 'y (m)',
        col = rainbow(n=100),
        main = paste('wavelength', 
                      udunits2::ud.convert(lambda[i],'m','nm')))
}