[Vennerable-commits] r50 - in pkg/Vennerable: R inst/doc tests

noreply at r-forge.r-project.org noreply at r-forge.r-project.org
Sat Sep 12 14:11:56 CEST 2009 

Author: js229
Date: 2009-09-12 14:11:50 +0200 (Sat, 12 Sep 2009)
New Revision: 50

Added:
   pkg/Vennerable/tests/bug06492CEuler.R
Modified:
   pkg/Vennerable/R/02TissueDrawing.R
   pkg/Vennerable/R/Circles.R
   pkg/Vennerable/inst/doc/TissueDrawingTest.Rnw
   pkg/Vennerable/inst/doc/TissueDrawingTest.pdf
   pkg/Vennerable/inst/doc/Venn.Rnw
   pkg/Vennerable/tests/bugellipseear.R
   pkg/Vennerable/tests/bugjoiningcircles.R
   pkg/Vennerable/tests/facelabeltwocircles.R
Log:
fix ear bugs (by avoiding ear calcs mostly) and introduce midpoint centroids for face midpoints

Modified: pkg/Vennerable/R/02TissueDrawing.R
===================================================================
--- pkg/Vennerable/R/02TissueDrawing.R	2009-09-12 11:06:17 UTC (rev 49)
+++ pkg/Vennerable/R/02TissueDrawing.R	2009-09-12 12:11:50 UTC (rev 50)
@@ -344,6 +344,13 @@
 .join.arcs <- function(object1,object2) {
 	# assumes they do join and have same radius centre and hand (and as a side effect will have the same bb)
 	visibility <- c(object1 at visible,object2 at visible);stopifnot(visibility[1]==visibility[2])
+	if (!fequal((object1 at toTheta - object2 at fromTheta) %% (2 * pi),0)) {
+		stop(sprintf("Sectors joined at different thetas %g %g\n",object1 at toTheta, object2 at fromTheta))
+	}
+	if (object1 at toTheta <= 0 & object2 at fromTheta > 0 ) {
+		object2 at fromTheta <- object2 at fromTheta - 2*pi # not used but you get the idea
+		object2 at toTheta <- object2 at toTheta - 2 *pi
+	}
 	newEdge <- object1; 
 	newEdge at toTheta <- object2 at toTheta
 	newEdge at to <- object2 at to
@@ -496,6 +503,18 @@
 }
 )
 
+
+.face.midplace <- function(drawing,faceName) {
+	# try forming the centroid of the points at the midplace of each edge
+#	browser()
+#	edgeClasses <- .faceEdgeClasses(drawing,faceName)
+#	stopifnot( (length(edgeClasses)==2 & all(edgeClasses=="VDedgeSector")))
+	edges <- .face.to.faceEdges(drawing,faceName)
+	midpoints <- t(sapply(edges,.midpoint))
+	midpoints.centroid <- matrix(apply(midpoints,2,mean),ncol=2,byrow=TRUE)
+	midpoints.centroid
+}
+
 ########################################
 # if a point is on an edge, we will split want to the edge into two
 #
@@ -650,6 +669,18 @@
 	edges
 }
 
+.faceEdgeClasses <- function(drawing,faceName,type="face") { 
+	if (type=="set") {
+		edges <- drawing at setList[[faceName]]
+	} else {
+		edges <- drawing at faceList[[faceName]] 
+	}
+	unsigned.edges <- sub("^-","",edges); 
+	res <- sapply(drawing at edgeList[unsigned.edges],function(x)as.character(class(x)))
+	res
+}
+
+
 renameFaces <- function(drawing,oldName,newName) {
 	stopifnot(length(oldName) == length(newName)) 
 	oldFaceNames <- names(drawing at faceList) 
@@ -948,6 +979,7 @@
 }
 
 .polygon.area <- function(xy) {
+	# this area is negative for clockwise polygons, sigh
 	xy1 <- xy; xy2 <- xy[ c(2:nrow(xy),1),]
 	x1 <- xy1[,1];y1 <-xy1[,2];x2<-xy2[,1];y2<- xy2[,2]
 	det <- x1*y2 - x2*y1
@@ -1059,6 +1091,15 @@
 	if (.is.point.within.face(drawing,faceName,faceCentroid)) {
 		return(faceCentroid)
 	}
+#browser()
+	# hmm. try the midpoint of each edge and form the centroid of those
+	# will be exactly what we want for two intersceting circle sectors
+	aPoint <- 	.face.midplace(drawing,faceName)
+	if (.is.point.within.face(drawing,faceName,aPoint )) {
+		return(aPoint )
+	}
+
+
 	if (FALSE) { # old method 
 	# find a point on the edge which is ideally not a node
 	amidpoint <- .find.point.on.face(drawing,faceName)
@@ -1086,7 +1127,7 @@
 	ear.triangle <- .find.triangle.within.face(drawing,faceName)
 	earCentroid <- .polygon.centroid(ear.triangle)
 	if (!	.is.point.within.face(drawing,faceName,earCentroid )) {
-		stop("Ear method failed in face %s\n",faceName)
+		stop(sprintf("Ear method failed in face %s\n",faceName))
 	}
 	return(earCentroid)
 }
@@ -1463,7 +1504,7 @@
 		x <- f1[1]+r*cos(theta)
 		y <- f1[2]+r*sin(theta)
 		
-	points.xy <- cbind(x,y)
+	points.xy <- cbind(x,y)	
 	rownames(points.xy) <- paste("e",letters[Set],1:nrow(points.xy),sep="")
 	newTissueFromPolygon(points.xy=points.xy,Set=Set)
 }
@@ -1473,6 +1514,11 @@
 newTissueFromPolygon <- function(points.xy,Set=1) {
 	points.xy <- 	.removeDuplicates (points.xy)
 	if (nrow(points.xy)<3) {stop("Not enough distince points for a polygon")}
+	isclockwise <- (.polygon.area(points.xy) < 0) 
+	if (!isclockwise) {
+		points.xy <- points.xy[nrow(points.xy):1,]
+	}
+
 	frompoint <- points.xy[1,,drop=FALSE]
 	if (!is.null(rownames(frompoint))) {
 		from = rownames(frompoint) ; 
@@ -2088,7 +2134,6 @@
 }
 
 remove.nonintersectionpoints <- function(drawing) {
-
 	for (fname in .faceNames(drawing)) {
 		edgesbySet <- list()
 		for (setname in names(drawing at setList)) {
@@ -2148,7 +2193,7 @@
 	outedge <-getEdge (drawing,outpos) 
 	if (inedge at to != outedge at from) { stop(sprintf("Edges do not joint at single point: %s,%s\n",inedge at to,outedge at from))}
 	if (class(inedge) != class(outedge)) { stop(sprintf("Cant join edges of different classes")) }
-	if (class(inedge) != "VDedgeLines") {stop(sprintf("Cant join edges of non edgeLine classes")) }
+	#if (class(inedge) != "VDedgeLines") {stop(sprintf("Cant join edges of non edgeLine classes")) }
 
 
 	newEdge <- joinEdges(inedge,outedge)

Modified: pkg/Vennerable/R/Circles.R
===================================================================
--- pkg/Vennerable/R/Circles.R	2009-09-12 11:06:17 UTC (rev 49)
+++ pkg/Vennerable/R/Circles.R	2009-09-12 12:11:50 UTC (rev 50)
@@ -19,7 +19,7 @@
 	centres <- matrix(c(-d/2,0,d/2,0),ncol=2,byrow=TRUE)
 	VDC1 <- newTissueFromCircle(centres[1,],radius=r[1],Set=1); 
 	VDC2 <- newTissueFromCircle(centres[2,],radius=r[2],Set=2); 
-	TM <- addSetToDrawing (drawing1=VDC1,drawing2=VDC2,set2Name="Set2")
+	TM <- addSetToDrawing (drawing1=VDC1,drawing2=VDC2,set2Name="Set2",remove.points=TRUE)
 	new("CircleDrawing",TM,V,radii=r,centres=centres)
 }
 setMethod("VisibleRange","CircleDrawing",function(object){

Modified: pkg/Vennerable/inst/doc/TissueDrawingTest.Rnw
===================================================================
--- pkg/Vennerable/inst/doc/TissueDrawingTest.Rnw	2009-09-12 11:06:17 UTC (rev 49)
+++ pkg/Vennerable/inst/doc/TissueDrawingTest.Rnw	2009-09-12 12:11:50 UTC (rev 50)
@@ -78,7 +78,7 @@
 A \texttt{VDedgeSector} object inherits from a \texttt{VDedgeDrawn} one.
 A sector is a segment of a circle, defined by two points, 
 together with the convention that a right-handed sector goes clockwise (Figure \ref{fig:vds}).
-Angles are all interpreted in the same way as \texttt{acos2} ie clockwise from the line $y=0$.
+Angles are all interpreted in the same way as \texttt{atan2}, ie clockwise from the line $y=0$.
 The angles of the beginning $\theta_f$ and end $\theta_t$ of the segment obey $2\pi\geq \theta_f >  0$ and $\theta_f>\theta_t>-2*pi$.
 
 

Modified: pkg/Vennerable/inst/doc/TissueDrawingTest.pdf
===================================================================
--- pkg/Vennerable/inst/doc/TissueDrawingTest.pdf	2009-09-12 11:06:17 UTC (rev 49)
+++ pkg/Vennerable/inst/doc/TissueDrawingTest.pdf	2009-09-12 12:11:50 UTC (rev 50)
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[TRUNCATED]

To get the complete diff run:
    svnlook diff /svnroot/vennerable -r 50

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