ANTsR (version 0.3.3)

plot.antsImage: Plotting an image slice or multi-slice with optional color overlay.

Description

This is a plotting utility for antsImage types with a background and color overlay option. Useful for displaying statistical results overlaid on a background image.

Usage

"plot"(x, y, color.img = "white", color.overlay = c("jet", "red", "blue", "green", "yellow"), axis = 2, slices, colorbar = missing(y), title.colorbar, title.img, color.colorbar, window.img, window.overlay, quality = 2, outname = NA, alpha = 1, newwindow = FALSE, nslices = 10, domainImageMap = NA, ncolumns = 4, useAbsoluteScale = FALSE, doCropping = TRUE, ...)

Arguments

x

the reference image on which to overlay.

y

image or list of images to use as overlays.

color.img

color for main image.

color.overlay

the color for the overlay , e.g c('blue','red') length of this list should match the image list.

axis

the axis to slice (1 , 2 or 3)

slices

vector of slices to plot (e.g., c(10, 15, 20))

colorbar

make colorbar?

title.colorbar

title for colorbar

title.img

title for main image

color.colorbar

color scale to use for colorbar

window.img

lower and upper thresholds for display of main image

window.overlay

lower and upper thresholds for display of overlay. if you set window.overlay = c( 0, 100 ) and useAbsoluteScale=T then the image overlay will map into that range. otherswise, the min and max of the image will be used.

quality

integer quality magnification factor 1 => large (e.g. 10)

outname

name of output file if you want to write result to file, e.g. plot.jpg.

alpha

opacity

newwindow

boolean controlling if we open a new device for this plot

nslices

number of slices to view

domainImageMap

this input antsImage or list contains a reference image (domainImage) and optional reference mapping named domainMap. these will be used to map the input image(s) to this antsImage space before plotting. this is useful for non-standard image orientations.

ncolumns

number of columns in plot

useAbsoluteScale

boolean determines whether dynamic range is maximized when visualizing overlays

doCropping

apply cropping, defaults to TRUE

...

other parameters

Value

output is plot to standard R window

Examples

img <- makeImage(c(4,4), rnorm(4*4))
mask <- makeImage(c(4,4),
   as.matrix(c(0,0,0,0,
            0,1,1,0,
            0,1,1,0,
            0,0,0,0), nrow=4))
plot(img, list(mask))
## Not run: 
#   mnit<-getANTsRData('mni')
#   mnit<-antsImageRead(mnit)
#   mniafn<-getANTsRData('mnia')
#   mnia<-antsImageRead(mniafn)
#   mnia<-thresholdImage(mnia,22,25)
#   mnia<-smoothImage(mnia,1.5)
#   mnia2<-antsImageRead(mniafn)
#   mnia2<-thresholdImage(mnia2,1,4)
#   mnia2<-smoothImage(mnia2,1.5)
#   ofn<-paste(tempfile(),'.png',sep='')
#   # write directly to a file
#   plot( mnit, list(mnia,mnia2), slices=seq(50, 140, by=5),
#     window.overlay = c(0.25,1), axis=2,
#     color.overlay=c('red','blue'), outname = ofn )
# ## End(Not run)