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

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.

# S3 method for class 'antsImage'
plot(
  x,
  y = NULL,
  color.img = "white",
  color.overlay = c("jet", "red", "blue", "green", "yellow", "viridis", "magma",
    "plasma", "inferno"),
  axis = 2,
  slices,
  colorbar = FALSE,
  title.colorbar,
  title.img,
  title.line = NA,
  color.colorbar,
  window.img,
  window.overlay,
  quality = 2,
  outname = NA,
  alpha = 1,
  direction = 1,
  begin = 0,
  end = 1,
  newwindow = FALSE,
  nslices = 10,
  domainImageMap = NULL,
  ncolumns = 4,
  useAbsoluteScale = FALSE,
  doCropping = TRUE,
  text,
  ...
)

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 (not displayed when file is saved with outname)
title.line: title vertical displacement (irrelevant when a file is saved with outname)
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
direction: Sets the order of colors in the scale. If 1, the default, colors are ordered from darkest to lightest. If -1, the order of colors is reversed.
begin: The (corrected) hue in [0,1] at which the viridis colormap begins.
end: The (corrected) hue in [0,1] at which the viridis colormap ends
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
text: vector containing x, y, label, cex and color values passed to text command, e.g. txt=list(x=0,y=0,label='my text',cex=2,col='red')
...: other parameters

Value

output is plot to standard R window

Author

Avants BB

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))
txt <- list(x = 2.5, y = 1.5, label = "my text", cex = 4, col = "red")
plot(img, list(mask), text = txt)

testthat::expect_error(plot(multi_component_image))

if (FALSE) { # \dontrun{

img <- antsImageRead(getANTsRData("r16"))
betaVals <- rnorm(prod(dim(img)), 0, 20)
betaImg <- makeImage(dim(img), betaVals) %>% smoothImage(3.5)
betaImg[abs(betaImg) < 1.5] <- 0
plot(img, betaImg, window.img = range(img), window.overlay = range(betaImg))

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
)
} # }