Prepare a mosaic — mosaic_prepare • pliman

Prepare an SpatRaster object to be analyzed in pliman. This includes cropping the original mosaic, aligning it, and cropping the aligned object. The resulting object is an object of class Image that can be further analyzed.

Usage

mosaic_prepare(
  mosaic,
  r = 3,
  g = 2,
  b = 1,
  re = 4,
  nir = 5,
  crop_mosaic = TRUE,
  align = TRUE,
  crop_aligned = TRUE,
  rescale = TRUE,
  coef = 0,
  viewer = "mapview",
  max_pixels = 5e+05,
  show = "rgb",
  index = "R"
)

Arguments

mosaic: A mosaic of class SpatRaster, generally imported with mosaic_input().
r, g, b, re, nir: The red, green, blue, red-edge, and near-infrared bands of the image, respectively. By default, the function assumes a BGR as input (b = 1, g = 2, r = 3). If a multispectral image is provided up to seven bands can be used to compute built-in indexes. There are no limitation of band numbers if the index is computed using the band name.
crop_mosaic: Logical, whether to crop the mosaic interactively before aligning it (default: FALSE).
align: Logical, whether to align the mosaic interactively (default: TRUE).
crop_aligned: Logical, whether to crop the aligned mosaic interactively (default: TRUE).
rescale: Rescale the final values? If TRUE the final values are rescaled so that the maximum value is 1.
coef: An addition coefficient applied to the resulting object. This is useful to adjust the brightness of the final image. Defaults to 0.
viewer: The viewer option. If not provided, the value is retrieved using get_pliman_viewer(). This option controls the type of viewer to use for interactive plotting. The available options are "base" and "mapview". If set to "base", the base R graphics system is used for interactive plotting. If set to "mapview", the mapview package is used. To set this argument globally for all functions in the package, you can use the set_pliman_viewer() function. For example, you can run set_pliman_viewer("mapview") to set the viewer option to "mapview" for all functions.
max_pixels: Maximum number of pixels to render in the map or plot (default: 500000).
show: The display option for the map view. Options are "rgb" for RGB view and "index" for index view.
index: The index to use for the index view. Defaults to "B".

Value

A prepared object of class Image.

Examples

if (interactive() && requireNamespace("EBImage")) {
library(pliman)
mosaic <- mosaic_input(system.file("ex/elev.tif", package="terra"))
mosaic_prepare(mosaic)
}
#> Warning: The current raster is in the lat/lon coordinate system, which may result in processing errors when trying to segment individuals in the `mosaic_analyze()` function. It is highly suggested to reproject the raster using mosaic_project() with EPSG:32632
#> class       : SpatRaster 
#> dimensions  : 90, 95, 1  (nrow, ncol, nlyr)
#> resolution  : 0.008333333, 0.008333333  (x, y)
#> extent      : 5.741667, 6.533333, 49.44167, 50.19167  (xmin, xmax, ymin, ymax)
#> coord. ref. : lon/lat WGS 84 (EPSG:4326) 
#> source      : elev.tif 
#> name        : elevation 
#> min value   :       141 
#> max value   :       547 
#> 
#> Listening on http://127.0.0.1:6534
#> Error in st_bbox.default(x): no st_bbox method available for object of class NULL