mincIO.putSlice-methods: Methods to Transfer a Slice into a MincVolumeIO Object

In jnikelski/rmincIO: Package for reading and writing MINC2 files

Description

Move a 2D slice, as held within a MincSlice object, into a MincVolumeIO object.

Usage

## S4 method for signature 'MincSlice,MincVolumeIO'
mincIO.putSlice(mincSlice, mincVolume, sliceNo)

Arguments

mincSlice	The name of the MincSlice object.
mincVolume	The name of the MincVolumeIO object, to which the slice is to be written.
sliceNo	A slice number, within the MincVolumeIO object, to which the slice is to be written. This is not a required argument; by default, the slice number recorded within the MincSlice object is used. Thus, only use this argument if you wish to write the slice back to a different slice from which it was originally retrieved.
...	Other yet to be defined parameters.

Details

The primary purpose of this method is to permit the re-insertion of newly modified slices into a MincVolumeIO volume, prior to writing the volume out. Now of course, the other major use-case would consist of creating a new, empty volume with mincIO.makeNewVolume, and then inserting newly created slices into this volume. Note that as it's currently not possible to create an empty slice (well, not easily, at least), one could simply create an empty volume and then mincIO.getSliceX/Y/Z any slice, which would then serve as the template empty slice. Clearly, in this case, the sliceNo argument would need to be specified in order to write the modified template slices to different positions within the volume.

Value

A newly updated MincVolumeIO object.

Methods

mincSlice = "MincSlice", mincVolume = "MincVolumeIO"

Only one method/signature.

Author(s)

Jim Nikelski [e-mail]

See Also

mincIO.getSliceXYZ MincSlice

Examples

## Not run: 
\dontshow{
# clear debug flag and get full volume pathname
# ... dunno why zzz.R debug setting is not passed
    R_DEBUG_rmincIO <- 0      
    volDir <- system.file("packageData/volumes", package="rmincIO")
}
# modify a slice and then put it back
v305PET <- file.path(volDir, "average305_PET_t1_tal_lin.mnc")
vol <- mincIO.readVolume(v305PET)            # read the 3D volume
sx <- mincIO.getSliceX(vol, 60)              # extract an axial slice
sx[10,20] <- 0                               # modify the slice
updatedVol <- mincIO.putSlice(sx, vol)       # put the slice back into the volume

## End(Not run)

jnikelski/rmincIO documentation built on May 19, 2019, 2:58 p.m.