Image {EBImage}R Documentation

Image class

Description

The package EBImage uses the class Image to store and process images. Images are stored as multi-dimensional arrays containing the pixel intensities. The class Image extends the base class array and uses the colormode slot to store how the color information of the multi-dimensional data is handled.

The colormode slot could be either Grayscale or Color. In both modes, the two first dimensions of the underlying array are understood to be the spatial dimensions of the image. In the Grayscale mode, the remaining dimensions contain other images. In the the Color mode, the third dimension contains the red, green and blue channels of the image and the remaining dimensions contain other images.

All methods of the package EBImage works either with Image objects or multi-dimensional arrays but in the latter case, the color mode is assumed to be Grayscale.

Usage

  Image(data, dim, colormode)
  as.Image(x)
  is.Image(x)
  as.raster.Image(y)

  colorMode(y)	
  colorMode(y) <- value

  imageData(y)
  imageData(y) <- value	

  getFrame(y, i, type='total')
  getNumberOfFrames(y, type='total')  	

Arguments

data

A vector or array containing the pixel intensities of an image. If missing, a default 1x1 null array is used.

dim

A vector containing the final dimensions of an Image object. If missing, equals to dim(data).

colormode

A numeric or a character string containing the color mode which could be either Grayscale or Color. If missing, equals to Grayscale.

x

An R object.

y

An Image object or an array.

i

A numeric.

value

For colorMode, a numeric or a character string containing the color mode which could be either Grayscale or Color. For imageData, an Image object or an array.

type

A character string containing total or render. Default is total.

Details

Depending of type, getNumberOfFrames returns the total number of frames contained in the object y or the number of renderable frames. The total number of frames is independent of the color mode and is equal to the product of all the dimensions except the two first ones. The number of renderable frames is equal to the total number of frames in the Grayscale color mode and is equal to the product of all the dimensions except the three first ones in the Color color mode.

getFrame returns the i-th frame contained in the image y. If type is total, the function is unaware of the color mode and returns an xy-plane. If render, the function returns the i-th image as shown by the display function.

Value

Image and as.Image return a new Image object.

is.Image returns TRUE if x is an Image object and FALSE otherwise.

as.raster.Image coerces an Image object to a raster object.

colorMode returns the color mode of y and colorMode<- changes the color mode of y.

imageData returns the array contained in an Image object.

Author(s)

Oleg Sklyar, osklyar@ebi.ac.uk, 2005-2007

See Also

readImage, display

Examples

  s1 = exp(12i*pi*seq(-1, 1, length=300)^2)
  y = Image(outer(Im(s1), Re(s1)))
  if (interactive()) display(normalize(y))

  x = Image(rnorm(300*300*3),dim=c(300,300,3), colormode='Color')
  if (interactive()) display(x)	

  w = matrix(seq(0, 1, len=300), nc=300, nr=300)
  m = abind(w, t(w), along=3)
  z = Image(m, colormode='Color')
  if (interactive()) display(normalize(z))

  y = Image(c('red', 'violet', '#ff51a5', 'yellow'), dim=c(71, 71))
  if (interactive()) display(y)

  ## colorMode example
  x = readImage(system.file('images', 'nuclei.tif', package='EBImage'))
  x = x[,,1:3]
  if (interactive()) display(x, title='Cell nuclei')
  colorMode(x)=Color
  if (interactive()) display(x, title='Cell nuclei in RGB')

[Package EBImage version 3.10.0 Index]