Image-class {EBImage} | R Documentation |
The class Image
enables the storage and manipulation of image data for
grayscale and true color (RGB) images in R
. The class is based on
(derived from) array
and inherits all its properties and methods,
e.g. mathematical operations, subsetting, histograms etc. Image processing and
analysis routines are defined as S4 methods for objects of the class Image
.
The class is defined as follows:
## S4 class definition setClass( "Image", representation ( colormode = "integer", filename = "character", compression = "character", resolution = "numeric", features = "list" ), contains = "array" )
Additionally, two constants are defined and exported that can be used to specify or test image data type:
Grayscale = as.integer(0) TrueColor = as.integer(1)
Objects can be created using new("Image")
supplying slot data
as necessary. Additionally, wrapper functions are defined to simplify the
construction of Image
objects in different situations: the default
constructor, Image
, the readImage
constructor that
creates an object from reading image files and the copy
constructor.
Accessor methods are class methods that are defined to retrieve data values from objects of a given class or to assigne those. These should be used instead of directly referring to the slots. Unfortunately, R does not have a concept of private or protected class members: all slots have "public" access in terms of other object-oriented languages. Therefore, data encapsulation in sense of hiding the particular structure of the class is impossible. At the same time, it is still recommended to use accessor functions instead of directly accessing slots. One can also assume that any slot that does not have an accessor method should not be accessed directly by the user.
The following accessor methods are defined as S4 methods for class Image
:
colorMode(x)
, colorMode(x) <- value
value
is one of the constants above.
Default: Grayscale
. compression(x)
, compression(x) <- value
character
are 'NONE', 'LZW',
'ZIP', 'JPEG', 'BZIP'
and 'GROUP4'
. Some of these may be
unavailable on your system if ImageMagick
was compiles without
their support. Default: 'LZW'
. features(x)
list
or matrices with descriptors of detected objects.
If object detection was executed on the image, an empty list is
returned. Otherwise, the number of elements matches the number of
frames in the image. Default: list()
. fileName(x)
, fileName(x) <- value
'no-name'
. imageData(x)
, imageData(x) <- value
colorMode()
. resolution(x)
, resolution(x) <- value
x
and y
dimensions. Generally resolution
is understood in pixel-per-inch (ppi) or dots-per-inch (dpi), however
some microscopes can save these values in images in different units.
It is the responsibility of the user to identify the unit and keep the
units comparable between different images in the same project if
required: the package does not take care of this. The default values
are equal for both directions, 2.5e+6 dpi.
Image data are stored as 3D arrays with first two dimensions specifying
frame size and third the number of frames. A single 2D image has the number of
frames 1. In subsetting, the value of drop
parameter is set to
FALSE
, thus image dimensionality is preserved at 3.
Image
is derived from array
, therefore, the data is stored
in arrays. Image
can store either grayscale or true color data at the
moment. Grayscale data is stored in numeric
arrays, whereas true
color data is stored in integer
arrays. Correspondingly, the data
is created with array(as.numeric(val),dim(val))
for grayscale and
array(as.integer(val),dim(val))
for true color images. Grayscale values
are assumed to be in the range [0,1]
, although this is not a requirement
in sense of data storage. Although, many image processing functions will
assume data in this range or will generate invalid results for the data out of
this range.
Oleg Sklyar, osklyar@ebi.ac.uk, 2005-2007
Image, IndexedImage, display, channel,
image,Image-method, show,Image-method,
## New Grayscale image of a black-to-white vertical gradient w <- 120 a <- Image((0:(w^2))/w^2, c(w,w)) if ( interactive() ) display(a) print(a) ## Converts image to TrueColor b <- a colorMode(b) <- TrueColor print(b) ## Fills values with intensities over 0.5 (50%) with red b[ a > 0.5 ] = as.integer(255) if ( interactive() ) display(b)