ANTsR (version 1.0)

Extract: Extract/Replace regions an antsImage

Description

Set of methods to extract a numeric vector from an antsImage. Set of methods to replace the pixels in an antsImage using a numeric vector.

Usage

img[ mask ]
img[ lst ]
img[ mask , region ]
img[ row , col , slice , time ]
img[ mask ] <- vect
img[ lst ] <- vect
img[ mask , region ] <- vect
img[ row , col , slice , time ] <- vect

Arguments

img

Image object of S4 class 'antsImage' to be indexed.

mask

logical vector/matrix/array to be used as mask while extracting pixel values from the image. 1/TRUEs return corresponding pixel values ; 0/FALSEs return NA. The vector provided will be 'matched' against the image-region column-wise meaning that first column of image-region is extracted using first column-length values from the vector, second column is extracted using the next column-length values from the vector and so on. Default: entire region is extracted.

region

antsRegion with in the antsImage to be considered for extraction. An antsRegion object can be created using new. Default: largest-possible-region( entire image ) in the image.

lst

list of named arguments containing names 'mask' and 'region'. lst$mask is used as 'mask' and lst$region is used as 'region'.

vect

numeric vector of length equal to number of pixels in the 'region' considered. Depending on the mask, the values in the numeric vector will replace the corresponding pixel values in the image indexed by the region. Only the values corresponding to 1/TRUE in the 'mask' are used. Image pixels corresponding to 0/FALSE in the 'mask' are left unchanged. This vector is matched against the image-region column-wise meaning that the first column of the image-region gets its values from the first column-length values in this vector, second column of the image-region gets its values from the second column-length values in this vector and so on.

row

numeric vector used to select the 'row' dimension of the image. Use 'NULL' to access the entire 'row' of the image.

col

numeric vector used to select the 'column' dimensin of the image. Use 'NULL' to access the entire 'column' of the image.

slice

numeric vector used to select the 'slice' dimension of the image. Use 'NULL' to access the all 'slice's of the image.

time

numeric vector used to select the 'time' dimension of the image. Use 'NULL' to access all the 'time's of the image.

Value

Extractors : numeric vector of dimensions equal to that of 'region' considered or number of 'pixels' considered -- Success ; NA -- Failure Mutators : Modified S4 object of class antsImage -- Success ; Original S4 object of class antsImage -- Failure

Details

img[mask]

Image-region considered is the largest-possible-region( entire image ) of the image.

img[row,col,slice,time]

Number of indices must match the number of dimensions of the image. A 2D image requires and allows indices 'row' and 'col' only. A 3D image requires and allows indices 'row', 'col' and 'slice' only. A 4D image requires and allows indices 'row', 'col', 'slice' and 'time'.

Examples

# NOT RUN {
# extract a vector from an image 'img' of class 'antsImage' by considering only the region starting at index (1,1,1) with size (10,10,10) ;
# here the first 10 elements of vect correspond to first column ( row = 1:10 , col = 1 , slice = 1 ) of image-region, next 10 elements come from
# second column ( row = 1:10 , col = 2 , slice = 1 ) of the image-region and so on
reg = new( "antsRegion" , index = c(1,1,1) , size = c(10,10,10) )
vect = img[ NULL , region = reg ] # OR
vect = img[ list( mask = NULL , region = reg ) ]
# set the values of pixels in the square ( row = 1:10 , col = 1:10 , slice = 3 ) using the vector c(1:100) ; 
# here the first column ( row = 1:10 , col = 1 , slice = 3 ) of image gets values c(1:10), second column ( row = 1:10 , col = 2 , slice = 3 ) gets
# values c(11:20) and so on
img[ 1:10 , 1:10 , 3 ] <- c(1:100)
# }