profoundSegimGroup: Create Segmentation Groups
In ProFound: Photometry Tools

Description Usage Arguments Details Value Author(s) See Also Examples

Given an input segmentation map, returns a map of groups of touching segments as well as the IDs of segments within each group.

1	profoundSegimGroup(segim = NULL)

segim

Integer matrix; required, the segmentation map.

To use this function you will need to have EBImage installed. Since this can be a bit cumbersome on some platforms (given its dependencies) this is only listed as a suggested package. You can have a go at installing it by running:

> source("http://bioconductor.org/biocLite.R")

> biocLite("EBImage")

Linux users might also need to install some non-standard graphics libraries (depending on your install). If you do not have them already, you should look to install **jpeg** and **tiff** libraries (these are apparently technically not entirely free, hence not coming by default on some strictly open source Linux variants).

profoundSegimGroup uses the bwlabel function from EBImage.

A list containting the following structures:

`groupim`	An map of the unique groups identified in the input segim, where the groupID is the same as the lowest valued segID in the group.
`groupsegID`	A data.frame of lists giving the segIDs of segments in each group.

The data.frame returned by groupsegID is a slightly unusal structure to see in R, but it allows for a compact manner of storing uneven vectors of grouped segments. E.g. you might have a massive group containing 30 other segments and many groups containing a single segment. Padding a normal matrix out to accommodate the larger figure would be quite inefficient. It contains the following:

`groupID`	Group ID, which can be matched against values in groupim
`segID`	An embedded list of segmentation IDs for segments in the group. I.e. each list element of segID is a vector (see Examples for clarity).
`Ngroup`	The total number of segments that are in the group.
`Npix`	The total number of pixels that are in the group.

Aaron Robotham

profoundSegimNear, ~~~

## Not run: 
image=readFITS(system.file("extdata", 'VIKING/mystery_VIKING_Z.fits', package="ProFound"))
profound=profoundProFound(image, skycut=1.5, magzero=30, verbose=TRUE)

#Look for nearby (in this case touching) neighbours

group=profoundSegimGroup(profound$segim)

#Look at the first few rows (groups 1:5):

group$groupsegID[1:5,]

#To access the embedded vectors you have to use unlist:

unlist(group$groupsegID[1,2])

#We can check to see which segments are in group number 1:

profoundSegimPlot(image$imDat, profound$segim)
magimage(group$groupim==1, col=c(NA,'red'), add=TRUE)

## End(Not run)