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Identify colour classes in an image for adjacency analyses

Source: R/classify.R
classify.Rd

Classify image pixels into discrete colour classes.

Usage

classify(
  imgdat,
  method = c("kMeans", "kMedoids"),
  kcols = NULL,
  refID = NULL,
  interactive = FALSE,
  plotnew = FALSE,
  col = "red",
  ...
)

Arguments

imgdat

(required) image data. Either a single image, or a series of images stored in a list. Preferably the result of getimg().

method

methods for image segmentation/classification.

  • 'kMeans': k-means clustering (default)

  • 'kMedoids': k-medoids clustering, using the partitioning-around-medoids ('pam') algorithm for large datasets.

kcols

the number of discrete colour classes present in the input image(s). Can be a single integer when only a single image is present, or if kcols is identical for all images. When passing a list of images, kcols can also be a vector the same length as imgdat, or a data.frame with two columns specifying image file names and corresponding kcols. This argument can optionally be disregarded when interactive = TRUE, and kcols will be inferred from the number of selections.

refID

either the numeric index or name of a 'reference' image, for use when passing a list of images. Other images will be k-means classified using centres identified in the single reference image, thus helping to ensure that homologous pattern elements will be reliably classified between images, if so desired.

interactive

interactively specify the colour-category 'centers', for k-means clustering. When TRUE, the user is asked to click a number of points (equal to kcols, if specified, otherwise user-determined) that represent the distinct colours of interest. If a reference image is specified, it will be the only image presented.

plotnew

Should plots be opened in a new window when interactive = TRUE? Defaults to FALSE.

col

the color of the marker points, when interactive = TRUE.

...

additional graphical parameters when interactive = TRUE. Also see graphics::par().

Value

A matrix, or list of matrices, of class rimg containing the colour class classifications ID at each pixel location. The RGB values corresponding to cluster centres (i.e. colour classes) are stored as object attributes.

Details

You can customise the type of parallel processing used by this function with the future::plan() function. This works on all operating systems, as well as high performance computing (HPC) environment. Similarly, you can customise the way progress is shown with the progressr::handlers() functions (progress bar, acoustic feedback, nothing, etc.)

Note

Since the kmeans process draws on random numbers to find initial cluster centres when interactive = FALSE, use set.seed() if reproducible cluster ID's are desired between runs.

See also

stats::kmeans

Author

Thomas E. White thomas.white026@gmail.com

Examples

# Single image
papilio <- getimg(system.file("testdata/images/butterflies/papilio.png", package = "pavo"))
papilio_class <- classify(papilio, kcols = 4)
#> Image classification in progress...

# Multiple images, with interactive classification and a reference image
snakes <- getimg(system.file("testdata/images/snakes", package = "pavo"))
#> 2 files found; importing images.
if (interactive()) {
  snakes_class <- classify(snakes, refID = "snake_01", interactive = TRUE)
}