MRIaggr-outline: Outline a region on a slice
In bozenne/MRIaggr: Management, Display, and Processing of Medical Imaging Data

Description Usage Arguments Details Value Examples

Tool for graphical definition of a spatial region on an image.

1 2	outline(n=50,sequential = TRUE, min_dist = 1, col = c("blue","red","grey"), pch = 20, cex = c(0.75,1,0.75))

`n`	maximum number of points to define the outline. integer.
`sequential`	should the region edge be updated on the graphical device after each point ? logical.
`min_dist`	if the distance between the new point and the initial point is inferior to `min_dist`, then the definition of the region ends. numeric. Only active if `sequential` is `TRUE`.
`col`	the colors in which the user-defined edge points, the interpolated edge points and the interior points should be ploted. character vector of size 3.
`pch`	the symbol with which the observations will be displayed. positive integer.
`cex`	the expansion factor used to plot the edge points, the interpolated edge points and the interior points. positive numeric vector of size 3.

FUNCTION:
This function uses the locator function to obtain the coordinates of the cursor. It enable a point by point definition of a region where a linear interpolation is used between user-defined points to define the edge of the region.
In the non sequential mode, the definition of the points stop if the number of points exceed n or using Echap. In the sequential mode, the definition of the points stop if the number of points exceed n or if the new point is close enough to the initial point.

After defining the edge, the region is filled.

A list of two elements :

[[edge]] : a data.frame containing the position ("i" "j") of the edge of the region, the edge number ("edge"), whether its user-specified point or interpolated point ("points") and whether it was removed for the filling precedure ("valid").
[[surface]] : a data.frame containing the position ("i" "j") of the points belonging to the region.

## Not run:  
## load a MRIaggr object
data("MRIaggr.Pat1_red", package = "MRIaggr")
num <- 3

## display 1
multiplot(MRIaggr.Pat1_red, param = "T2_FLAIR_t2",              
             num = num, legend = FALSE, window = FALSE)

## outline on display 1
res <- outline(sequential=TRUE,min_dist=3)

## display the results
multiplot(MRIaggr.Pat1_red, param = "T2_FLAIR_t2",              
             num = num, legend = FALSE,
             index1 = data.frame(k = num, res$edge[,c("i","j")]),
             index2 = data.frame(k = num, res$surface[,c("i","j")]),
             window = FALSE)

carto <- selectContrast(MRIaggr.Pat1_red, param = c("MASK_T2_FLAIR_t2","index"),
             num = num, coords = TRUE)
carto <- merge(carto, cbind(res$surface, outline = TRUE), all = TRUE)
carto[is.na(carto$outline),"outline"] <- FALSE
head(carto)

## display the results next to MASK_T2_FLAIR_t2
multiplot(MRIaggr.Pat1_red, param = "T2_FLAIR_t2",              
             num = num, legend = FALSE,
             index1 = carto[carto$MASK_T2_FLAIR_t2,c("i","j","k")],
             index2 = carto[carto$outline,c("i","j","k")],
             window = FALSE)

## End(Not run)