getShift | R Documentation |
Determine the optimal x-y shift to align the target image with the (nuclear) mask.
getShift(mask, target, parscale = c(25, 25), FUN = idiff, value = FALSE)
mask |
An object mask with connected pixels having the same integer value. |
target |
A fluorescent |
parscale |
A numeric vector of length 2 used as the
|
FUN |
Function to be minimized over |
value |
Logical value (default |
This optimization function FUN
accepts three arguments
(x, mask, target
) where x
is a numeric vector of
length two representing the x and y position in the integer
Image
mask (mask
) and the Image
object
(target
). FUN
must return a single value
representing the difference between the two images. The
optim
function minimizes FUN
with respect to
x[1]
and x[2]
. The default function is designed
to align nuclear masks with predominantly nuclear signals and
should be replaced for other localization patterns.
The argument parscale
is used by optim
to scale the
parameters in x
such that a unit change in the parameter
amounts to unit change in the optimizing function empirically,
c(25, 25)
seems to be in the middle of a robust range.
If value = FALSE
, a list of subpixel translations named "dx"
and "dy"
that can be applied to the argument target
with
translate
to maximize the alignment between mask and target.
If value = TRUE
, a list of values of the shift required for each
image.
path <- system.file("extdata", "by_folder/b2", package = "virustiter")
x <- getImages(path)
getShift(nucMask(x$nuc[[1]]), x$tgt[[1]], value = TRUE)
getShift(nucMask(x$nuc[[1]]), x$tgt[[1]])
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