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Utilities for working with image objects

Source: R/utils_objects.R
utils_objects.Rd

  • object_id() get the object identification in an image.

  • object_coord() get the object coordinates and (optionally) draw a bounding rectangle around multiple objects in an image.

  • object_contour() returns the coordinates (x and y) for the contours of each object in the image.

  • object_isolate() isolates an object from an image.

Usage

object_coord(
  img,
  id = NULL,
  index = "NB",
  watershed = TRUE,
  invert = FALSE,
  opening = FALSE,
  closing = FALSE,
  filter = FALSE,
  fill_hull = FALSE,
  threshold = "Otsu",
  edge = 2,
  extension = NULL,
  tolerance = NULL,
  object_size = "medium",
  parallel = FALSE,
  workers = NULL,
  plot = TRUE
)

object_contour(
  img,
  pattern = NULL,
  dir_original = NULL,
  center = FALSE,
  index = "NB",
  invert = FALSE,
  opening = FALSE,
  closing = FALSE,
  filter = FALSE,
  fill_hull = FALSE,
  threshold = "Otsu",
  watershed = TRUE,
  extension = NULL,
  tolerance = NULL,
  object_size = "medium",
  parallel = FALSE,
  workers = NULL,
  plot = TRUE,
  verbose = TRUE
)

object_isolate(img, id = NULL, parallel = FALSE, workers = NULL, ...)

object_id(img, parallel = FALSE, workers = NULL, ...)

Arguments

img

An image of class Image or a list of Image objects.

id

  • For object_coord(), a vector (or scalar) of object id to compute the bounding rectangle. Object ids can be obtained with object_id(). Set id = "all" to compute the coordinates for all objects in the image. If id = NULL (default) a bounding rectangle is drawn including all the objects.

  • For object_isolate(), a scalar that identifies the object to be extracted.

index

The index to produce a binary image used to compute bounding rectangle coordinates. See image_binary() for more details.

watershed

If TRUE (default) performs watershed-based object detection. This will detect objects even when they are touching one other. If FALSE, all pixels for each connected set of foreground pixels are set to a unique object. This is faster but is not able to segment touching objects.

invert

Inverts the binary image, if desired. Defaults to FALSE.

opening, closing, filter

Morphological operations (brush size)

  • opening performs an erosion followed by a dilation. This helps to remove small objects while preserving the shape and size of larger objects.

  • closing performs a dilatation followed by an erosion. This helps to fill small holes while preserving the shape and size of larger objects.

  • filter performs median filtering in the binary image. Provide a positive integer > 1 to indicate the size of the median filtering. Higher values are more efficient to remove noise in the background but can dramatically impact the perimeter of objects, mainly for irregular perimeters such as leaves with serrated edges.

Hierarchically, the operations are performed as opening > closing > filter. The value declared in each argument will define the brush size.

fill_hull

Fill holes in the objects? Defaults to FALSE.

threshold

By default (threshold = "Otsu"), a threshold value based on Otsu's method is used to reduce the grayscale image to a binary image. If a numeric value is informed, this value will be used as a threshold. Inform any non-numeric value different than "Otsu" to iteratively chosen the threshold based on a raster plot showing pixel intensity of the index.

edge

The number of pixels in the edge of the bounding rectangle. Defaults to 2.

extension, tolerance, object_size

Controls the watershed segmentation of objects in the image. See analyze_objects() for more details.

parallel

Processes the images asynchronously (in parallel) in separate R sessions running in the background on the same machine. It may speed up the processing time when image is a list. The number of sections is set up to 50% of available cores.

workers

A positive numeric scalar or a function specifying the maximum number of parallel processes that can be active at the same time.

plot

Shows the image with bounding rectangles? Defaults to TRUE.

pattern

A pattern of file name used to identify images to be imported. For example, if pattern = "im" all images in the current working directory that the name matches the pattern (e.g., img1.-, image1.-, im2.-) will be imported as a list. Providing any number as pattern (e.g., pattern = "1") will select images that are named as 1.-, 2.-, and so on. An error will be returned if the pattern matches any file that is not supported (e.g., img1.pdf).

dir_original

The directory containing the original images. Defaults to NULL, which means that the current working directory will be considered.

center

If TRUE returns the object contours centered on the origin.

verbose

If TRUE (default) a summary is shown in the console.

...

  • For object_isolate(), further arguments passed on to object_coord().

  • For object_id(), further arguments passed on to analyze_objects().

Value

  • object_id() An image of class "Image" containing the object's identification.

  • object_coord() A list with the coordinates for the bounding rectangles. If id = "all" or a numeric vector, a list with a vector of coordinates is returned.

  • object_isolate() An image of class "Image" containing the isolated object.

Examples

if (interactive() && requireNamespace("EBImage")) {
library(pliman)
img <- image_pliman("la_leaves.jpg")
# Get the object's (leaves) identification
object_id(img)

# Get the coordinates and draw a bounding rectangle around leaves 1 and 3
object_coord(img, id = c(1, 3))

# Isolate leaf 3
isolated <- object_isolate(img, id = 3)
plot(isolated)

}