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Create masked raster from multiband image

Source: R/create_masked_raster.R
create_masked_raster.Rd

This function creates a masked raster by removing non-vegetation pixels based on NDVI and NIR threshold values. It supports processing single files, multiple files in a directory, or a list of file paths. Threshold values can be specified as single values or as a data frame with site-specific thresholds. The function assumes that the input layers are stacked in wavelength order and saves the masked raster to the specified output directory.

Usage

create_masked_raster(
  input,
  output_dir = tempdir(),
  ndvi_threshold = NULL,
  nir_threshold = NULL,
  ndvi_threshold_df = NULL,
  nir_threshold_df = NULL,
  red_band_index = 3,
  nir_band_index = 5,
  make_plot = FALSE,
  return_raster = FALSE
)

Arguments

input

A directory containing multiple ENVI or TIF files, a single file, or a character vector of file paths.

output_dir

A directory where the masked raster(s) will be saved.

ndvi_threshold

Numeric. NDVI threshold for masking (pixels with NDVI values below this are masked as non-vegetation).

nir_threshold

Numeric. NIR threshold for masking (pixels with NIR values below this are masked as shadows).

ndvi_threshold_df

Optional. A data frame with two columns: site (site identifiers) and threshold (NDVI threshold values for each site). The site values must match the beginning of the input file names.

nir_threshold_df

Optional. A data frame with two columns: site (site identifiers) and threshold (NIR threshold values for each site). The site values must match the beginning of the input file names.

red_band_index

Integer. The index (layer number) of the red band in the input raster. Default is 3.

nir_band_index

Integer. The index (layer number) of the NIR band in the input raster. Default is 5.

make_plot

Logical. If TRUE, a plot of the masked raster is generated for verification. Default is FALSE.

return_raster

Logical. If TRUE, the masked raster object is returned. Default is FALSE.

Value

Saves masked raster(s) as TIF files in the specified output_dir. If return_raster = TRUE, the function returns the masked raster object as a terra raster.

Examples


input <- system.file("extdata/multiband_image", package = "saltbush")
output_dir <- tempdir()
create_masked_raster(input,
                    output_dir,
                    ndvi_threshold = 0.02,
                   nir_threshold = 0.04,
                     red_band_index = 3,
                     nir_band_index = 5)
#> [1] "Files found: /home/runner/work/_temp/Library/saltbush/extdata/multiband_image/multiband_image.tif"
#> [1] "Masked raster saved to: /tmp/RtmpMzyNnD/multiband_image_masked.tif"