version 4.19.8

- allow multiple points and colors to be passed to `floodFill` (#21) From: aoles <[email protected]> git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/EBImage@131904 bc3139a8-67e5-0310-9ffc-ced21a209358
aoles · Aug 11, 2017 · ea841b0 · ea841b0
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diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,5 +1,5 @@
 Package: EBImage
-Version: 4.19.7
+Version: 4.19.8
 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/Image.R b/R/Image.R
@@ -45,12 +45,11 @@ Image = function(data = array(0, dim=c(1,1)), dim, colormode) {
       else
         parseColorMode(colormode)
 
-    if (missing(dim)) {
+    if (missing(dim))
       dim = setdim(data)
 
-      if ( colormode==Color )
-        dim = c(dim[1:2], 3L, dim[-(1:2)])
-    }
+    if ( colormode==Color )
+      dim = c(dim[1:2], 3L, dim[-(1:2)])  
 
     dimnames = dimnames(data)
     data = col2rgb(data)/255
@@ -507,6 +506,10 @@ numberOfFrames = function(y, type = c('total', 'render')) {
     .Call(C_numberOfFrames, y, type)
 }
 
+numberOfChannels = function(y, d = dim(y), cm = colorMode(y)) {
+  if ( cm==Grayscale || is.na(d[3L]) ) 1L else d[3L]
+}
+
 ## - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
 showImage = function (object, short=FALSE) {
   nd = dim(object)

diff --git a/R/display.R b/R/display.R
@@ -207,13 +207,10 @@ displayWidget <- function(x, title, embed = !interactiveMode(), tempDir = tempfi
     imageData(x) = abind(x, Image(0, fd), along = 3L)
   }
 
-  nf = numberOfFrames(x, type='render')
-  colormode = colorMode(x)
-
   x = clipImage(x) ## clip the image and change storage mode to double
   x = transpose(x)
 
-  frames = seq_len(nf)
+  frames = seq_len(numberOfFrames(x, type='render'))
   dependencies = NULL
 
   if ( isTRUE(embed) ) {

diff --git a/R/floodFill.R b/R/floodFill.R
@@ -17,15 +17,44 @@
 ## - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
 floodFill = function(x, pt, col, tolerance=0) {
   validImage(x)
-
-  n = numberOfFrames(x, 'total')
-  if ( is.list(pt) ) pt = unlist(pt, use.names=FALSE)
-  pt = as.integer(pt)
-  if ( is.character(col) ) col = as.numeric(col2rgb(col)/255)
-  col = if ( typeof(x)=="double" ) as.double(col) else as.integer(col)
-  if ( any( pt<1L || pt>dim(x)[1:2] ) ) stop("coordinates 'pt' of the starting point(s) must be inside the image boundaries")
-
-  return( .Call(C_floodFill, x, matrix(pt, nrow=n, ncol=2L, byrow=TRUE), matrix(col, nrow=n, ncol=1L), as.numeric(tolerance)))
+  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)
+  }
+
+  for (i in seq_len(nf) ) {
+    pti = pt[[i]]
+    if ( is.list(pti) )
+      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
+
+    cli = col[[i]]
+    cli = if ( is.character(cli) )
+      unlist(lapply(cli, function(col) rep_len(col2rgb(col, alpha=TRUE)/255, nc)))
+    else 
+      rep(cli, each=nc)
+    storage.mode(cli) = storage.mode(x) 
+    cli = matrix(rep_len(cli, np * nc), nrow=np, ncol=nc, byrow=TRUE)
+    col[[i]] = cli
+  }
+
+  return( .Call(C_floodFill, x, pt, col, as.numeric(tolerance)))
 }
 
 ## - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

diff --git a/man/bwlabel.Rd b/man/bwlabel.Rd
@@ -60,7 +60,7 @@ bwlabel(x)
   nbnuclei = apply(z, 3, max)
   cat('Number of nuclei=', paste(nbnuclei, collapse=','),'\n')
 
-  ## recolor nuclei in colors
+  ## paint nuclei in color
   cols = c('black', sample(rainbow(max(z))))
   zrainbow = Image(cols[1+z], dim=dim(z))
   display(zrainbow, title='Cell nuclei (recolored)')

diff --git a/man/floodFill.Rd b/man/floodFill.Rd
@@ -15,10 +15,10 @@ floodFill(x, pt, col, tolerance=0)
 \arguments{
   \item{x}{An \code{Image} object or an array.}
 
-  \item{pt}{Coordinates of the start filling point.}
+  \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{col}{Fill color. This argument should be a numeric for Grayscale images
-    and an R color for Color 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{tolerance}{Color tolerance used during the fill.}
 }
@@ -41,15 +41,33 @@ floodFill(x, pt, col, tolerance=0)
 
 \examples{
   x = readImage(system.file("images", "shapes.png", package="EBImage"))
+
+  ## fill a shape with 50% shade of gray
   y = floodFill(x, c(67, 146), 0.5)
   display(y)
-
-  y = channel(y, 'rgb')
-  y = floodFill(y, c(48, 78), 'red')
-  y = floodFill(y, c(156, 52), 'orange')	
+  
+  ## fill with color
+  y = toRGB(y)
+  y = floodFill(y, c(48, 78), 'orange')	
   display(y)
-
+
+  ## fill multiple shapes with different colors
+  y = y[110:512,1:130,]
+  points = rbind(c(50, 50), c(100, 50), c(150, 50))
+  colors = c("red", "green", "blue")
+  y = floodFill(y, points, colors)
+  display(y)
+
+  ## area fill
   x = readImage(system.file("images", "sample.png", package="EBImage"))
-  y = floodFill(x, c(226, 121), 1, tolerance=0.1)
+  y = floodFill(x, rbind(c(200, 400), c(200, 325)), 1, tolerance=0.1)
+  display(y)
+
+  ## application to image stacks
+  f = system.file("images", "nuclei.tif", package="EBImage")
+  x = readImage(f)[1:250,1:250,]
+  x = opening(thresh(x, 12, 12), makeBrush(5, shape='disc'))
+  xy = lapply(getFrames(bwlabel(x)), function(x) computeFeatures.moment(x)[,1:2])
+  y = floodFill(toRGB(x), xy, c("red", "green", "blue"))
   display(y)
 }
diff --git a/src/floodFill.cpp b/src/floodFill.cpp
@@ -24,38 +24,46 @@ template <class T> void _bwlabel(T *, int *, XYPoint);
 
 /* -------------------------------------------------------------------------- */
 SEXP
-floodFill(SEXP x, SEXP point, SEXP col, SEXP tol) {
-  int i, nz, *dim, *pts;
+floodFill(SEXP x, SEXP _pts, SEXP _col, SEXP _tol) {
+  int i, p, c, nf, np, nc, *dim, *pts;
+  double tol = REAL(_tol)[0];
   XYPoint pt;
-  SEXP res;
-
+  SEXP res, points, colors;
   // check image validity
-  validImage(x,0);
-  nz = getNumberOfFrames(x, 0);
+  validImage(x, 0);
+  nf = getNumberOfFrames(x, 1);
+  nc = getNumberOfChannels(x, COLOR_MODE(x));
   dim = INTEGER(GET_DIM(x));
   XYPoint size(dim[0], dim[1]);
   if (size.x <= 0 || size.y <= 0) error("image must have positive dimensions");
-  if (LENGTH(point) != 2*nz) error("point must have a size of two times the number of frames");
-  if (LENGTH(col) != nz) error("color must have the same size as the number of frames");
+  if (LENGTH(_pts) != nf) error("length of points list must match the number of 'render' frames");
+  if (LENGTH(_col) != nf) error("length of color list must match the number of 'render' frames");
 
   // initialize result
   PROTECT(res = Rf_duplicate(x));
 
-  pts = INTEGER(point);
-
-  // do the job over images
-  for (i=0; i<nz; i++) {
-    pt.x = pts[i]-1;
-    pt.y = pts[nz+i]-1;
-
-    switch (TYPEOF(res)) {
-      case LGLSXP:
-      case INTSXP:
-        _floodFill<int>(&(INTEGER(res)[i*size.x*size.y]), size, pt, INTEGER(col)[i], REAL(tol)[0]);
-        break;
-      case REALSXP:
-        _floodFill<double>(&(REAL(res)[i*size.x*size.y]), size, pt, REAL(col)[i], REAL(tol)[0]);
-        break;
+  // iterate over images
+  for (i=0; i<nf; i++) {
+    points = VECTOR_ELT(_pts, i);
+    colors = VECTOR_ELT(_col, i);
+    np = INTEGER(GET_DIM(points))[0];
+    pts = INTEGER(points);
+    // iterate over points
+    for (p=0; p<np; p++) {
+      pt.x = pts[p]-1;
+      pt.y = pts[np+p]-1;
+      // iterate over channels
+      for (c=0; c<nc; c++) {
+        switch (TYPEOF(res)) {
+        case LGLSXP:
+        case INTSXP:
+          _floodFill<int>(&(INTEGER(res)[(i*nc+c)*size.x*size.y]), size, pt, INTEGER(colors)[c*np+p], tol);
+          break;
+        case REALSXP:
+          _floodFill<double>(&(REAL(res)[(i*nc+c)*size.x*size.y]), size, pt, REAL(colors)[c*np+p], tol);
+          break;
+        }
+      }
     }
   }
 
@@ -386,4 +394,3 @@ _fillHullT(T *_m, const XYPoint &srcsize) {
   delete[] canvas;
   delete[] bbox;
 }
-
diff --git a/tests/test.Rout.save b/tests/test.Rout.save
@@ -700,7 +700,7 @@ checking 'blackTopHat' ........................ PASS (af7e8fad58a0f587) 202411.9
 checking 'selfComplementaryTopHat' ............ PASS (729954d933215c8d) 2151192
 checking 'distmap' ............................ PASS (8ba0b0fb6770e8a3) 3856630
 checking 'watershed' .......................... PASS (0bd6a31bc6197067) 1443978
-checking 'floodFill' .......................... PASS (45775cc98ccde7d0) 1055560
+checking 'floodFill' .......................... PASS (7a8a06c4be73e522) 2057384
 checking 'fillHull' ........................... PASS (d3904950b8acdb73) 1096352
 checking 'propagate' .......................... PASS (6c610fe4376714f6) 1613920
 checking 'toRGB' .............................. PASS (57b9a77f5a12af4f) 8499672

diff --git a/vignettes/EBImage-introduction.Rmd b/vignettes/EBImage-introduction.Rmd
@@ -646,12 +646,12 @@ display(filled_logo)
 
 ```{r floodFill-logo, fig.width=dim(logo)[1L]/.dpi, fig.height=dim(logo)[2L]/.dpi, dpi=.dpi}
 rgblogo = toRGB(logo)
-rgblogo = floodFill(rgblogo, c(50, 50), "red")
-rgblogo = floodFill(rgblogo, c(100, 50), "green")
-rgblogo = floodFill(rgblogo, c(150, 50), "blue")
+points = rbind(c(50, 50), c(100, 50), c(150, 50))
+colors = c("red", "green", "blue")
+rgblogo = floodFill(rgblogo, points, colors)
 display( rgblogo )
 ```{r floodFill-img, fig.width=dim(img)[1L]/.dpi, fig.height=dim(img)[2L]/.dpi, dpi=.dpi/2}
-display( floodFill(img, c(444, 222), col=0.2, tolerance=0.2) )
+display(floodFill(img, rbind(c(200, 300), c(444, 222)), col=0.2, tolerance=0.2))
 ```
 
 ## Highlighting objects