IndexedImage-class {EBImage}R Documentation

Defintion of class 'IndexedImage'

Description

The class IndexedImage is used to store the results of functions that index image into separate objects using integer 1-based indexing. Such an image is essentially the same as Image in the gray scale mode. The class was defined to ensure correct types in calls to other object detection and processing routines.

Class Definition

    ## S4 class definition
    setClass( "IndexedImage", contains="Image" )

Creating objects

Objects of this class are not supposed to be created directly, rather as the result of calls to watershed or propagate, or other functions that index objects in images.

Details

No accessor methods are defined for this class, however all of the parents' ones are available, i.e. those of Image and array.

One coersion routine is defined in addition, which simply sets the class attribute to Image:

    ## S4 method for signature 'x=IndexedImage'
    as.Image(x, ...)

When used with IndexedImage's display by default normalizes the image.

Author(s)

Oleg Sklyar, osklyar@ebi.ac.uk, 2007

See Also

Image, watershed, getFeatures

Examples

  ## load images
  f <- paste( system.file(package="EBImage"), "images/Gene1_G.tif", sep="/" )
  ii = readImage(f)
  ## normalize images
  ii = normalize(ii, separate=TRUE)
  ## segment
  mask = thresh(ii, 25, 25, 0.02)
  ## refine segmentation with morphology filters
  mk3 = morphKern(3)
  mk5 = morphKern(5)
  mask = dilate(erode(closing(mask, mk5), mk3), mk5)
  ## index objects with 'watershed'
  io = watershed( distmap(mask), 1.5, 1)

  class(io)

[Package EBImage version 2.2.0 Index]