buildBrick: Read and Pre-Process Hyperspectral Image

Description

Retrieve the raw data from the ENVI file, simultaneously read the header file and build a Brick containing all the layers (spectral bands) of the hyperspectral image. Optionally, do pre-processing steps on row data, such as: radiometric correction using the Dark Object Subtraction (DOS) method, set up the spatial extents using the coordinates of a reference layer and inputs of the camera, convert the row values (digital numbers) to spectral features such as radiance or reflectance.

Usage

buildBrick(
  path,
  path_hdr = sub(".dat", ".hdr", path, fixed = TRUE),
  hFOV = NULL,
  vFOV = NULL,
  height = NULL,
  ref_layer = 1,
  spectral_feature = c("raw", "radiance", "reflectance"),
  reflectance_method = c("irradiance", "white_panel"),
  dark_path = NULL,
  dark_quantile = 0.25,
  white_path = NULL
)

Arguments

path

A character giving the path for the ENVI file (.dat).

path_hdr

(Optional, character) The path for the header file (.hdr).

hFOV

(Optional, numeric) The horizontal Field Of View (in degrees) of the camera. Note: this is used to calculate the spatial extent. See Details.

vFOV

(Optional, numeric) The vertical Field Of View (in degrees) of the camera. Note: this is used to calculate the spatial extent. See Details.

height

(Optional, numeric) The flight altitude (in meters). Note: this is be used to calculate the spatial extent. See Details.

ref_layer

(Optional, integer) The reference layer (spectral band) to be used to set up the geographic location of the image.

spectral_feature

A character giving the name of the spectral feature to be loaded. Must be one of the three: "raw" (digital numbers), "radiance", "reflectance". See Details.

reflectance_method

A character for selecting the method to calculate the reflectance values. It must be one of the following: "irradiance" or "white_panel". See Details.

dark_path

(Optional) A character giving the path for the ENVI file containing the dark reference raw values, a.k.a. noisy energy, for DOS calibration. See Details.

dark_quantile

A numeric value used to calculate the quantile of the dark reference raw values of each spectral band. Default is 0.25. This will be used for the DOS radiometric correction.

white_path

(Optional) A character giving the path for the ENVI file containing the white panel. See Details.

Value

A RasterBrick object (from the package raster).

Details

The geographical coordinates (xy) registered in the header file are automatically retrieved. If the arguments hFOV, vFOV and height are passed, buildBrick will automatically compute the UTM zone and the spatial extent, and set up the coordinate reference system.

"radiance" is obtained by multiplying the raw values of each spectral band by the respective "gain" values registered in the header file (if available).

If "reflectance" is passed as value for the argument spectral_feature, then the value of the next argument, reflectance_method, will be used to calculate the reflectance values. The "irradiance" method consists of using the solar irradiance values registered in the header file (if available) at each spectral band as reference for the radiance values reaching the camera sensor. If "white_panel" is chosen, then the path for the ENVI file containing the image of the white panel must be passed as value for the respective argument. Note that buildBrick will consider value of the white panel as the maximum.

Make sure that the header file (.hdr) has the same name as the ENVI (.dat) file when pointing them at the arguments dark_path or white_path.

Examples

Run this code

# NOT RUN {
# Point to an ENVI data
path <- system.file('exdata', 'obory.dat', package = 'hyperbrick')
# First, let's check the header file
# There are 81 bands. First two are noisy.
# Irradiance is available.
path_hdr <- system.file('exdata', 'obory.hdr', package = 'hyperbrick')
readLines(path_hdr)

# Example 1 - raw values
path <- system.file('exdata', 'obory.dat', package = 'hyperbrick')
b <- buildBrick(path)
print(b)
plot(b, 35)

# Example 2 - set up CRS and compute radiance
br <- buildBrick(path, hFOV = 36.8, vFOV = 36.8, height = 45,
                ref_layer = 35, spectral_feature = 'radiance')
print(br)
plot(br, 35)

# Example 3 - DOS correction
dpath <- system.file('exdata', 'obory_dark.dat', package = 'hyperbrick')
brd <- buildBrick(path, hFOV = 36.8, vFOV = 36.8, height = 45,
                  ref_layer = 35, spectral_feature = 'radiance',
                  dark_path = dpath)
print(brd)
plot(brd, 35)

# Example 4 - compute reflectance
bre <- buildBrick(path, hFOV = 36.8, vFOV = 36.8, height = 45,
                  ref_layer = 35, spectral_feature = 'reflectance',
                  reflectance_method = "irradiance",
                  dark_path = dpath)
print(bre)
plot(bre, 35)

# Example 5 - there is a white-reference panel in this image
idmax <- which.max(bre[[35]])
plot(bre, 35, asp = 0)
points(xyFromCell(bre[[35]], idmax), pch = 3)

bre2 <- buildBrick(path, hFOV = 36.8, vFOV = 36.8, height = 45,
                   ref_layer = 35, spectral_feature = 'reflectance',
                   reflectance_method = "white_panel",
                   white_path = path, dark_path = dpath)
print(bre2)
plot(bre2, 35)

# }