From 15fd982907c9a310d329ecab5515e2f7bb627b25 Mon Sep 17 00:00:00 2001
From: aoles <andrzej.oles@gmail.com>
Date: Fri, 8 Sep 2017 11:09:02 +0200
Subject: [PATCH] version 4.19.9 - correct way of checking for out-of-bounds
 points in `floodFill` (fixes https://github.com/aoles/EBImage/issues/23) -
 improved interace to `floodFill` for single-frame images (see
 https://github.com/aoles/EBImage/issues/21)

---
 DESCRIPTION      |  2 +-
 R/floodFill.R    | 35 +++++++++++++++++++----------------
 man/floodFill.Rd |  9 ++++-----
 3 files changed, 24 insertions(+), 22 deletions(-)

diff --git a/DESCRIPTION b/DESCRIPTION
index 5dd3cdb..9930616 100755
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -1,5 +1,5 @@
 Package: EBImage
-Version: 4.19.8
+Version: 4.19.9
 Title: Image processing and analysis toolbox for R
 Encoding: UTF-8
 Author: Andrzej Oleś, Gregoire Pau, Mike Smith, Oleg Sklyar, Wolfgang Huber, with contributions from Joseph Barry and Philip A. Marais
diff --git a/R/floodFill.R b/R/floodFill.R
index 5d22907..6d54f5f 100644
--- a/R/floodFill.R
+++ b/R/floodFill.R
@@ -15,34 +15,37 @@
 # LGPL license wording: http://www.gnu.org/licenses/lgpl.html
 
 ## - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
-floodFill = function(x, pt, col, tolerance=0) {
+floodFill = function(x, pts, col, tolerance=0) {
   validImage(x)
   nf = numberOfFrames(x, 'render')
   nc = numberOfChannels(x)
   
   ## make sure that `pt` and `col` are lists of length matching the number of frames
-  if ( is.list(pt) ) {
-    if ( length(pt) != nf ) stop("length of 'pt' must match the number of 'render' frames")
-  } else {
-    pt = rep(list(pt), nf)
-  }
-  if ( is.list(col) ) {
-    if ( length(col) != nf ) stop("length of 'col' must match the number of 'render' frames")
-  } else {
-    col = rep(list(col), nf)
+  format_as_list = function(x, nf) {
+    if ( is.list(x) )
+      if ( length(x)==nf )
+        return(x)
+      else if ( nf > 1L)
+        stop(sprintf("length of '%s' must match the number of 'render' frames"), deparse(substitute(x)))
+    rep(list(x), nf) 
   }
+  pts = format_as_list(pts, nf)
+  col = format_as_list(col, nf)
   
   for (i in seq_len(nf) ) {
-    pti = pt[[i]]
+    pti = pts[[i]]
     if ( is.list(pti) )
-      pti = unlist(pti, use.names=FALSE)
+      if ( is.data.frame(pti) ) 
+        pti = as.matrix(pti)
+      else 
+        pti = unlist(pti, use.names=FALSE)
     storage.mode(pti) = "integer"
-    if ( any(pti<1L) || any(pti>dim(x)[1:2]) )
-      stop("coordinates of starting point(s) 'pt' must be inside image boundaries")
     if ( !is.matrix(pti) || dim(pti)[2L]!=2L )
       pti = matrix(pti, nrow=length(pti)/2, ncol=2L, byrow=TRUE)
     np = dim(pti)[1L]
-    pt[[i]] = pti
+    if ( any( pti<1L ) || any( pti>rep(dim(x)[1:2], each=np) ) )
+      stop("coordinates of starting point(s) 'pts' must be inside image boundaries")
+    pts[[i]] = pti
     
     cli = col[[i]]
     cli = if ( is.character(cli) )
@@ -54,7 +57,7 @@ floodFill = function(x, pt, col, tolerance=0) {
     col[[i]] = cli
   }
   
-  return( .Call(C_floodFill, x, pt, col, as.numeric(tolerance)))
+  return( .Call(C_floodFill, x, pts, col, as.numeric(tolerance)))
 }
 
 ## - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
diff --git a/man/floodFill.Rd b/man/floodFill.Rd
index 831e41e..84f4fd4 100644
--- a/man/floodFill.Rd
+++ b/man/floodFill.Rd
@@ -9,16 +9,15 @@
 }
 
 \usage{
-floodFill(x, pt, col, tolerance=0)
+floodFill(x, pts, col, tolerance=0)
 }
 
 \arguments{
   \item{x}{An \code{Image} object or an array.}
 
-  \item{pt}{Coordinates of the start filling points provided as a matrix where rows represent points and columns are the x and y cordinates. For image stacks different points for each frame can be specified by providing a list whose length matches the number of 'render' frames.}
+  \item{pts}{Coordinates of the start filling points given as either of the following: a vector of the form \code{c(x1, y1, x2, y2, ...)}, a list of points, a matrix or data frame where rows represent points and columns are the x and y coordinates. For image stacks different points for each frame can be specified by providing them in a list of length matching the number of 'render' frames.}
 
-  \item{col}{Fill color. This argument should be a numeric for Grayscale images
-    and an R color for Color images. Values are recycled such that their length matches the number of points in `pt`. Can be a list similarly as `pt`.}
+  \item{col}{Fill color. This argument should be a numeric for Grayscale images and an R color for Color images. Values are recycled such that their length matches the number of points in \code{pts}. Can be a list of length matching the number of 'render' frames similarly as \code{pts}.}
 
   \item{tolerance}{Color tolerance used during the fill.}
 }
@@ -30,7 +29,7 @@ floodFill(x, pt, col, tolerance=0)
 
 \details{
   Flood fill is performed using the fast scan line algorithm. Filling
-  starts at \code{pt} and grows in connected areas where the absolute
+  starts at \code{pts} and grows in connected areas where the absolute
   difference of the pixels intensities (or colors) remains below
   \code{tolerance}.
 }