From f21cc8e81ed501a1934c9dce68326c5441f782f4 Mon Sep 17 00:00:00 2001
From: Gregory Jefferis <jefferis@gmail.com>
Date: Fri, 26 Jun 2020 23:52:28 +0100
Subject: [PATCH] Document and fix collate field

---
 DESCRIPTION        |  2 ++
 NAMESPACE          |  1 +
 R/elastix_io.R     |  2 +-
 man/xformpoints.Rd | 17 +++++++++++++----
 4 files changed, 17 insertions(+), 5 deletions(-)

diff --git a/DESCRIPTION b/DESCRIPTION
index 5b7bbc7e..808b9909 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -63,6 +63,8 @@ Collate:
     'dist3D_Segment_to_Segment.R'
     'neuron.R'
     'dotprops.R'
+    'elastix.R'
+    'elastix_io.R'
     'geometry.R'
     'graph-nodes.R'
     'hxsurf.R'
diff --git a/NAMESPACE b/NAMESPACE
index 73fe8d86..a1fff03a 100644
--- a/NAMESPACE
+++ b/NAMESPACE
@@ -183,6 +183,7 @@ S3method(xformimage,reglist)
 S3method(xformpoints,character)
 S3method(xformpoints,cmtkreg)
 S3method(xformpoints,default)
+S3method(xformpoints,elastixreg)
 S3method(xformpoints,reglist)
 S3method(xformpoints,tpsreg)
 S3method(xyzmatrix,default)
diff --git a/R/elastix_io.R b/R/elastix_io.R
index 78198062..b48db9d2 100644
--- a/R/elastix_io.R
+++ b/R/elastix_io.R
@@ -9,7 +9,7 @@ read.elastixreg <- function(x, ...) {
   l
 }
 
-#' internal function to read the elastix files into an R list
+# internal function to read the elastix files into an R list
 read.elastix<-function(con, CheckLabel=TRUE){
   
   l=list()
diff --git a/man/xformpoints.Rd b/man/xformpoints.Rd
index 0979b5fd..81bb977d 100644
--- a/man/xformpoints.Rd
+++ b/man/xformpoints.Rd
@@ -1,6 +1,7 @@
 % Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/xformpoints.R
-\name{xformpoints}
+% Please edit documentation in R/elastix.R, R/xformpoints.R
+\name{xformpoints.elastixreg}
+\alias{xformpoints.elastixreg}
 \alias{xformpoints}
 \alias{xformpoints.character}
 \alias{xformpoints.cmtkreg}
@@ -8,6 +9,14 @@
 \alias{xformpoints.default}
 \title{Transform 3D points using a registration, affine matrix or function}
 \usage{
+\method{xformpoints}{elastixreg}(
+  reg,
+  points,
+  transformtype = c("warp", "affine"),
+  direction = NULL,
+  ...
+)
+
 xformpoints(reg, points, ...)
 
 \method{xformpoints}{character}(reg, points, ...)
@@ -33,8 +42,6 @@ path(s) to registrations on disk (see details).}
 
 \item{points}{Nx3 matrix of points}
 
-\item{...}{Additional arguments passed to methods}
-
 \item{transformtype}{Which transformation to use when the CMTK file contains
 both warp (default) and affine}
 
@@ -42,6 +49,8 @@ both warp (default) and affine}
 space (called \strong{inverse} by CMTK) or from reference to sample space
 (called \strong{forward} by CMTK). Default (when \code{NULL} is inverse).}
 
+\item{...}{Additional arguments passed to methods}
+
 \item{FallBackToAffine}{Whether to use the affine transformation for points
 that fail to transform under a warping transformation.}
 }