getFeatures {EBImage} | R Documentation

## Feature extraction for objects in indexed images

### Description

Functions to extract numerical descriptors for objects in indexed images. The functions here call a set of individual feature extraction routines for every feature set like hull, texture (Haralick), edge, moment features etc.

### Usage

      ## S4 method for signature 'IndexedImage':
      getFeatures(x, ref, N=12, R=30, apply.Gaussian=TRUE, nc=256, ...)
      ## S4 method for signature 'IndexedImage':
      features(x, ...)

### Arguments

`x` | An object of `IndexedImage` (like those obtained from `propagate` or `watershed`.
`ref` | A reference image containing images of the objects in Grayscale mode (intensity values)!
`N` | Passed to `zernikeMoments`. Integer value defining the degree of the Zernike polynomials, which in turn defines the number of features calculated. Defaults to 12.
`R` | Passed to `zernikeMoments`. Defines the radius of the circle around an object centre from which the features are calculated. It also defines the standard deviation for the 2D Gausian applied at the centre of an object. See details. Defaults to 30.
`apply.Gaussian` | Passed to `zernikeMoments`. A logical value that specifies if a local 2D Gaussian modification should be applied to every object at its centre. Defaults to `TRUE`.
`nc` | Passed to `haralickFeatures`. A numeric value. Specifies the number of gray levels to separate `ref` into when calculating the co-occurrence matrix. Here defaults to 256.
`...` | Reserved.

### Details

`ref` can be missing in calls to `getFeatures`. In this case texture and other intensity-dependent features will be omitted.

### Value

`getFeatures` calculates feature matrices and returns an object of `IndexedImage` with its `features` slot set. The typical use would be to re-assign the result to the original image itself, i.e. `x <- getFeatures(x, a)`.
`features` extracts the content of the `features` slot of the `IndexedImage`. If it is empty, the function calls `getFeatures` without a reference image and returns the generated feature set. In this case the `features` slot of the original image is not updated.

### Author(s)

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

### See Also

`IndexedImage, propagate, paintObjects, stackObjects, hullFeatures, haralickFeatures, moments, edgeFeatures, zernikeMoments`

### 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)
      ft = hullFeatures(io)
      mf = moments(io, ii)   ## need these for intensity and size
      for ( i in seq_along(ft) ) ft[[i]] = cbind(ft[[i]], mf[[i]])
      io = rmObjects(io, lapply(ft, function(x)
             which(x[,"h.s"] < 150 | x[,"int"] < 50 | 0.3 * x[,"h.p"] < x[,"h.edge"] )
           ))
      io = getFeatures(io, ii)
      str( features(io) )

[Package EBImage version 2.2.0 Index]