WIP: trying to allow scaling of diameter by xform

* this works ok when reg is a function, but fails when reg is actually a reglist object (one of whose elements is a function)

R/xform.R

@@ -1,63 +1,79 @@
 #' Transform the 3D location of objects such as neurons
-#' 
-#' \code{xform} is designed to operate on a variety of data types, especially 
-#' objects encapsulating neurons. \code{xform} depends on two specialised 
-#' downstream functions \code{\link{xformpoints}} and \code{\link{xformimage}}. 
+#'
+#' \code{xform} is designed to operate on a variety of data types, especially
+#' objects encapsulating neurons. \code{xform} depends on two specialised
+#' downstream functions \code{\link{xformpoints}} and \code{\link{xformimage}}.
 #' These are user visible any contain some useful documentation, but should only
-#' be required for expert use; in almost all circumstances, you should use only 
+#' be required for expert use; in almost all circumstances, you should use only
 #' \code{xform}.
-#' 
+#'
 #' @section Registrations:
-#'   
-#'   When \code{reg} is a character vector, xform's specialised downstream 
-#'   functions will check to see if it defines a path to one (or more) 
+#'
+#'   When \code{reg} is a character vector, xform's specialised downstream
+#'   functions will check to see if it defines a path to one (or more)
 #'   registrations on disk. These can be of two classes
-#'   
+#'
 #'   \itemize{
-#'   
+#'
 #'   \item CMTK registrations
-#'   
-#'   \item \code{\link{reglist}} objects saved in R's \code{RDS} format (see 
-#'   \code{\link{readRDS}}) which can contain any sequence of registrations 
+#'
+#'   \item \code{\link{reglist}} objects saved in R's \code{RDS} format (see
+#'   \code{\link{readRDS}}) which can contain any sequence of registrations
 #'   supported by nat.
-#'   
+#'
 #'   }
-#'   
+#'
 #'   If the path does indeed point to a CMTK registration, this method will hand
 #'   off to \code{xformpoints.cmtkreg} or \code{xformimages.cmtkreg}. In this
 #'   case, the character vector may optionally have an attribute, 'swap', a
 #'   logical vector of the same length indicating whether the transformation
 #'   direction should be swapped. At the moment only CMTK registration files are
 #'   supported.
-#'   
-#'   If \code{reg} is a character vector of length >=1 defining a sequence of 
+#'
+#'   If \code{reg} is a character vector of length >=1 defining a sequence of
 #'   registration files on disk they should proceed from sample to reference.
-#'   
-#'   Where \code{reg} is a function, it should have a signature like 
-#'   \code{myfun(x,), ...} where the \code{...} \strong{must} be provided in 
-#'   order to swallow any arguments passed from higher level functions that are 
-#'   not relevant to this particular transformation function.
-
-#' @details Methods are provided for some specialised S3 classes. Further 
-#'   methods can of course be constructed for user-defined S3 classes. However 
-#'   this will probably not be necessary if the \code{xyzmatrix} and 
-#'   \code{`xyzmatrix<-`} generics are suitably overloaded \emph{and} the S3 
+#'
+#'   Where \code{reg} is a function, it should have a signature like
+#'   \code{myfun(x,), ...} where the \code{...} \strong{must} be provided in
+#'   order to swallow any arguments passed from higher level functions that are
+#'   not relevant to this particular transformation function. Note that
+#'   functions can be supplied that expect an Nx3 matrix of points OR a
+#'   \code{neuron} as input. In the latter case, the function can be used to
+#'   scale the neuron's diameter as well as the point locations. See examples.
+#'
+#' @details Methods are provided for some specialised S3 classes. Further
+#'   methods can of course be constructed for user-defined S3 classes. However
+#'   this will probably not be necessary if the \code{xyzmatrix} and
+#'   \code{`xyzmatrix<-`} generics are suitably overloaded \emph{and} the S3
 #'   object inherits from \code{list}.
-#'   
+#'
 #'   Note that given the behaviour of the \code{xyzmatrix} functions, the
 #'   \code{xform.data.frame} method will transform the x,y,z or X,Y,Z columns of
 #'   a data.frame if the data.frame has more than 3 columns, erroring out if no
 #'   such unique columns exist.
-#'   
+#'
 #' @param x an object to transform
-#' @param reg A registration defined by a matrix, a function, a \code{cmtkreg} 
-#'   object, or a character vector specifying a path to one or more 
+#' @param reg A registration defined by a matrix, a function, a \code{cmtkreg}
+#'   object, or a character vector specifying a path to one or more
 #'   registrations on disk (see Registrations section).
-#' @param ... additional arguments passed to methods and eventually to 
+#' @param ... additional arguments passed to methods and eventually to
 #'   \code{\link{xformpoints}}
 #' @export
 #' @rdname xform
 #' @seealso \code{\link{xformpoints}}
+#' 
+#' @examples 
+#' ## using an affine matrix
+#' scalemat=t(rgl::scaleMatrix(1,2,3))
+#' scaled=xform(Cell07PNs[1:3], scalemat)
+#' 
+#' ## using a function
+#' # doesn't scale radius
+#' tnm=xform(Cell07PNs[1:3], function(x, ...) x=x*1e3)
+#' head(tnm[[1]][['d']])
+#' # does scale radius
+#' tnm2=xform(Cell07PNs[1:3], function(x, ...) x=x*rep(1e3, 4))
+#' head(tnm2[[1]][['d']])
 xform<-function(x, reg, ...) UseMethod('xform')
 
 #' @details TODO get this to work for matrices with more than 3 columns by
@@ -116,7 +132,21 @@ xform.shape3d<-xform.list
 
 #' @export
 #' @rdname xform
-xform.neuron<-xform.list
+xform.neuron<-function(x, reg, FallBackToAffine=TRUE, na.action='error', ...){
+  if(is.function(reg)) {
+    # as a special case if we are passed a function, see if we can 
+    # apply it directly to neuron. This is a bit hacky but lets us
+    # more easily scale
+    tx <- try(reg(x, FallBackToAffine=TRUE, na.action='error', ...))
+    if(!inherits(tx, 'try-error')) 
+      return(tx)
+  }
+  points=xyzmatrix(x)
+  pointst=xformpoints(reg, points, FallBackToAffine=FallBackToAffine, 
+                      na.action=na.action, ...)
+  xyzmatrix(x)<-pointst
+  x
+}
 
 #' @export
 #' @rdname xform