abscondment-rubyvor 0.1.2

data/History.txt

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+=== 0.1.2 / 2009-04-24
+
+* Compilation fixes for OSX. Thanks to jpemberthy and febuiles!
+
+=== 0.1.1 / 2009-01-15
+
+* LibXML require conflict fix.
+
+=== 0.1.0 / 2009-01-13
+
+* Configurable handling of "no neighbors" case.
+* Tests for "no neighbors" case.
+
+=== 0.0.9 / 2009-01-01
+
+Happy New Year!
+* New speed improvements.
+* Additional visualization tweaks.
+* More tests.
+
+=== 0.0.8 / 2008-12-23
+
+* Several C warning fixes (more ISO C compliance unused variables, etc)
+* Moved minimum_spanning_tree computation into C, yielding large speed gain.
+* Basic SVG visualization.
+
+=== 0.0.7 / 2008-12-12
+
+* Bugfix: there are cases where performing a Delaunay triangulation on a set of points will not yield a complete nearest neighbor graph. This causes computation of the minimum spanning tree and clustering to fail for these nodes (they always appear as disconnected from the main graph).
+
+* To fix this, the nn_graph function now treats any point that is excluded from Delaunay triangulation as having *all* other points as nearest neighbors. This is a naive approach, but is a good fix while a more efficient solution is considered.
+
+=== 0.0.6 / 2008-12-11
+
+* Implementation of cluster_by_size to partition points into N clusters.
+
+=== 0.0.5 / 2008-12-10
+
+* Beginnings of clustering and useful graph algorithms.
+* Some refactoring of C methods.
+
+=== 0.0.4 / 2008-12-04
+
+* Fixed 64-bit segfaults due to improper definition of the myrealloc() function.
+
+=== 0.0.3 / 2008-12-03
+
+* Fixed a segfault by using rb_ary_push instead of direct pointer manipulation. Much simpler.
+
+=== 0.0.2 / 2008-12-03
+
+* Computations succeed on a naive Point class, returning raw values for the associated Voronoi Diagram and Delaunay triangulation.
+
+=== 0.0.1 / 2008-12-01
+
+* Initial release. Nothing works.

data/Manifest.txt

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+History.txt
+Manifest.txt
+README.txt
+Rakefile
+ext/Doc
+ext/edgelist.c
+ext/extconf.rb
+ext/geometry.c
+ext/heap.c
+ext/memory.c
+ext/output.c
+ext/rb_cComputation.c
+ext/rb_cPoint.c
+ext/rb_cPriorityQueue.c
+ext/ruby_vor_c.c
+ext/ruby_vor_c.h
+ext/vdefs.h
+ext/voronoi.c
+lib/ruby_vor.rb
+lib/ruby_vor/computation.rb
+lib/ruby_vor/geo_ruby_extensions.rb
+lib/ruby_vor/point.rb
+lib/ruby_vor/priority_queue.rb
+lib/ruby_vor/version.rb
+lib/ruby_vor/visualizer.rb
+rubyvor.gemspec
+test/test_computation.rb
+test/test_point.rb
+test/test_priority_queue.rb
+test/test_voronoi_interface.rb

data/README.txt

@@ -0,0 +1,76 @@
+= rubyvor
+
+Efficient Voronoi diagrams and Delaunay trianglation for Ruby
+
+== Description
+
+RubyVor provides efficient computation of Voronoi diagrams and
+Delaunay triangulation for a set of Ruby points. It is intended to
+function as a complemenet to GeoRuby. These structures can be used to
+compute a nearest-neighbor graph for a set of points. This graph can
+in turn be used for proximity-based clustering of the input points.
+
+== Usage:
+
+require 'lib/ruby_vor'
+require 'pp'
+
+points = [
+  RubyVor::Point.new(120, 290),
+  RubyVor::Point.new(110, 120),
+  RubyVor::Point.new(160, 90.2),
+  RubyVor::Point.new(3.14159265, 3.14159265)
+]
+
+# Compute the diagram & triangulation
+comp = RubyVor::VDDT::Computation.from_points(points)
+
+puts "The nearest-neighbor graph:"
+pp comp.nn_graph
+
+puts "\nThe minimum-spanning tree:"
+pp comp.minimum_spanning_tree
+
+#
+# Visualize these things as SVGs
+#
+
+# Just the triangulation
+RubyVor::Visualizer.make_svg(comp, :name => 'tri.svg')
+
+# Just the MST
+RubyVor::Visualizer.make_svg(comp, :name => 'mst.svg', :triangulation => false, :mst => true)
+
+# Voronoi diagram and the triangulation
+RubyVor::Visualizer.make_svg(comp, :name => 'dia.svg', :voronoi_diagram => true)
+
+
+== LICENSE:
+
+Original public-domain C code (by Steven Fortune; http://ect.bell-labs.com/who/sjf/) and
+memory-management fixes for said C code (by Derek Bradley; http://www.derekbradley.ca)
+used (and released under the MIT-LICENSE) with permission.
+
+
+(The MIT License)
+
+Copyright (c) 2008 Brendan Ribera <brendan.ribera+rubyvor@gmail.com>
+
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in
+all copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT.  IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
+THE SOFTWARE.

data/Rakefile

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+# -*- ruby -*-
+
+require 'rubygems'
+require 'hoe'
+require './lib/ruby_vor/version.rb'
+
+EXT = "ext/voronoi_interface.#{Hoe::DLEXT}"
+
+Hoe.new('rubyvor', RubyVor::VERSION) do |p|
+  p.developer('Brendan Ribera', 'brendan.ribera+rubyvor@gmail.com')  
+  p.url = 'http://github.com/bribera/rubyvor'
+
+  # C extension goodness
+  p.spec_extras[:extensions] = "ext/extconf.rb"
+  p.clean_globs << EXT << 'ext/*.o' << 'ext/Makefile'
+end
+
+desc "Compile extensions"
+task :compile => EXT
+task :test => :compile
+
+file EXT => ['ext/extconf.rb', 'ext/ruby_vor_c.c'] do
+  Dir.chdir 'ext' do
+    ruby 'extconf.rb'
+    sh 'make'
+  end    
+end
+
+desc "Prepare for github upload"
+task :github do
+  system "git ls-files | egrep -v \"\\.gitignore\" > Manifest.txt"
+  system "rake debug_gem | egrep -v \"^\\(in\" > rubyvor.gemspec"
+end
+
+task :gem => :github

data/ext/Doc

@@ -0,0 +1,30 @@
+voronoi - compute Voronoi diagram or Delaunay triangulation
+SYNOPSIS
+	voronoi [-s -t] <pointfile >outputfile
+
+Voronoi reads the standard input for a set of points in the plane and writes either
+the Voronoi diagram or the Delaunay triangulation to the standard output.
+Each input line should consist of two real numbers, separated by white space.
+
+If option
+	-t 
+is present, the Delaunay triangulation is produced. 
+Each output line is a triple
+	i j k
+which are the indices of the three points in a Delaunay triangle. Points are
+numbered starting at 0. If this option is not present, the
+Voronoi diagram is produced.  There are four output record types.
+	s a b
+indicates that an input point at coordinates 
+	l a b c
+indicates a line with equation ax + by = c.
+	v a b
+indicates a vertex at  a b.
+	e l v1 v2
+indicates a Voronoi segment which is a subsegment of line number l;
+with endpoints numbered v1 and v2.  If v1 or v2 is -1, the line
+extends to infinity.
+
+AUTHOR
+Steve J. Fortune (1987) A Sweepline Algorithm for Voronoi Diagrams,
+Algorithmica 2, 153-174.

data/ext/edgelist.c

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+
+/*** EDGELIST.C ***/
+
+#include "vdefs.h"
+
+static int ELhashsize ;
+static Halfedge * ELleftend, * ELrightend, ** ELhash ;
+static Freelist hfl ;
+static int ntry, totalsearch ;
+
+void
+ELinitialize(void)
+{
+    int i ;
+
+    freeinit(&hfl, sizeof(Halfedge)) ;
+    ELhashsize = 2 * rubyvorState.sqrt_nsites ;
+    ELhash = (Halfedge **)myalloc( sizeof(*ELhash) * ELhashsize) ;
+    for (i = 0  ; i < ELhashsize  ; i++)
+    {
+        ELhash[i] = (Halfedge *)NULL ;
+    }
+    ELleftend = HEcreate((Edge *)NULL, 0) ;
+    ELrightend = HEcreate((Edge *)NULL, 0) ;
+    ELleftend->ELleft = (Halfedge *)NULL ;
+    ELleftend->ELright = ELrightend ;
+    ELrightend->ELleft = ELleftend ;
+    ELrightend->ELright = (Halfedge *)NULL ;
+    ELhash[0] = ELleftend ;
+    ELhash[ELhashsize-1] = ELrightend ;
+}
+
+Halfedge *
+HEcreate(Edge * e, int pm)
+{
+    Halfedge * answer ;
+
+    answer = (Halfedge *)getfree(&hfl) ;
+    answer->ELedge = e ;
+    answer->ELpm = pm ;
+    answer->PQnext = (Halfedge *)NULL ;
+    answer->vertex = (Site *)NULL ;
+    answer->ELrefcnt = 0 ;
+    return (answer) ;
+}
+
+void
+ELinsert(Halfedge * lb, Halfedge * new)
+{
+    new->ELleft = lb ;
+    new->ELright = lb->ELright ;
+    (lb->ELright)->ELleft = new ;
+    lb->ELright = new ;
+}
+
+/* Get entry from hash table, pruning any deleted nodes */
+
+Halfedge *
+ELgethash(int b)
+{
+    Halfedge * he ;
+
+    if ((b < 0) || (b >= ELhashsize))
+    {
+        return ((Halfedge *)NULL) ;
+    }
+    he = ELhash[b] ;
+    if ((he == (Halfedge *)NULL) || (he->ELedge != (Edge *)DELETED))
+    {
+        return (he) ;
+    }
+    /* Hash table points to deleted half edge.  Patch as necessary. */
+    ELhash[b] = (Halfedge *)NULL ;
+    if ((--(he->ELrefcnt)) == 0)
+    {
+        makefree((Freenode *)he, (Freelist *)&hfl) ;
+    }
+    return ((Halfedge *)NULL) ;
+}
+
+Halfedge *
+ELleftbnd(Point * p)
+{
+    int i, bucket ;
+    Halfedge * he ;
+
+    /* Use hash table to get close to desired halfedge */
+    bucket = (p->x - rubyvorState.xmin) / rubyvorState.deltax * ELhashsize ;
+    if (bucket < 0)
+    {
+        bucket = 0 ;
+    }
+    if (bucket >= ELhashsize)
+    {
+        bucket = ELhashsize - 1 ;
+    }
+    he = ELgethash(bucket) ;
+    if  (he == (Halfedge *)NULL)
+    {
+        for (i = 1 ; 1 ; i++)
+        {
+            if ((he = ELgethash(bucket-i)) != (Halfedge *)NULL)
+            {
+                break ;
+            }
+            if ((he = ELgethash(bucket+i)) != (Halfedge *)NULL)
+            {
+                break ;
+            }
+        }
+        totalsearch += i ;
+    }
+    ntry++ ;
+    /* Now search linear list of halfedges for the corect one */
+    if (he == ELleftend || (he != ELrightend && right_of(he,p)))
+    {
+        do  {
+            he = he->ELright ;
+        } while (he != ELrightend && right_of(he,p)) ;
+        he = he->ELleft ;
+    }
+    else
+    {
+        do  {
+            he = he->ELleft ;
+        } while (he != ELleftend && !right_of(he,p)) ;
+    }
+    /*** Update hash table and reference counts ***/
+    if ((bucket > 0) && (bucket < ELhashsize-1))
+    {
+        if (ELhash[bucket] != (Halfedge *)NULL)
+        {
+            (ELhash[bucket]->ELrefcnt)-- ;
+        }
+        ELhash[bucket] = he ;
+        (ELhash[bucket]->ELrefcnt)++ ;
+    }
+    return (he) ;
+}
+
+/*** This delete routine can't reclaim node, since pointers from hash
+ : table may be present.
+ ***/
+
+void
+ELdelete(Halfedge * he)
+{
+    (he->ELleft)->ELright = he->ELright ;
+    (he->ELright)->ELleft = he->ELleft ;
+    he->ELedge = (Edge *)DELETED ;
+}
+
+Halfedge *
+ELright(Halfedge * he)
+{
+    return (he->ELright) ;
+}
+
+Halfedge *
+ELleft(Halfedge * he)
+{
+    return (he->ELleft) ;
+}
+
+Site *
+leftreg(Halfedge * he)
+{
+    if (he->ELedge == (Edge *)NULL)
+    {
+        return(rubyvorState.bottomsite) ;
+    }
+    return (he->ELpm == le ? he->ELedge->reg[le] :
+            he->ELedge->reg[re]) ;
+}
+
+Site *
+rightreg(Halfedge * he)
+{
+    if (he->ELedge == (Edge *)NULL)
+    {
+        return(rubyvorState.bottomsite) ;
+    }
+    return (he->ELpm == le ? he->ELedge->reg[re] :
+            he->ELedge->reg[le]) ;
+}
+
+/*
+ * Semi-hacky way to access these static variables. Placing them inside rubyvorState
+ * causes pointer issues that I don't want to debug, and they're only accessed briefly
+ * inside of voronoi.c.  Since we're just doing pointer comparison there, this is an
+ * acceptable compromise.
+ */
+
+Halfedge *
+getELleftend(void)
+{
+    return(ELleftend);
+}
+
+Halfedge *
+getELrightend(void)
+{
+    return(ELrightend);
+}

data/ext/extconf.rb

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+require 'mkmf'
+dir_config('ruby_vor_c')
+create_makefile('ruby_vor_c')

data/ext/geometry.c

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+
+/*** GEOMETRY.C ***/
+
+#include <math.h>
+#include "vdefs.h"
+
+static Freelist efl;
+
+void
+geominit(void)
+{
+    freeinit(&efl, sizeof(Edge)) ;
+    rubyvorState.nvertices = rubyvorState.nedges = 0 ;
+    rubyvorState.sqrt_nsites = sqrt(rubyvorState.nsites+4) ;
+    rubyvorState.deltay = rubyvorState.ymax - rubyvorState.ymin ;
+    rubyvorState.deltax = rubyvorState.xmax - rubyvorState.xmin ;
+}
+
+Edge *
+bisect(Site * s1, Site * s2)
+{
+    float dx, dy, adx, ady ;
+    Edge * newedge ;
+
+    newedge = (Edge *)getfree(&efl) ;
+    newedge->reg[0] = s1 ;
+    newedge->reg[1] = s2 ;
+    ref(s1) ;
+    ref(s2) ;
+    newedge->ep[0] = newedge->ep[1] = (Site *)NULL ;
+    dx = s2->coord.x - s1->coord.x ;
+    dy = s2->coord.y - s1->coord.y ;
+    adx = dx>0 ? dx : -dx ;
+    ady = dy>0 ? dy : -dy ;
+    newedge->c = s1->coord.x * dx + s1->coord.y * dy + (dx*dx +
+dy*dy) * 0.5 ;
+    if (adx > ady)
+    {
+        newedge->a = 1.0 ;
+        newedge->b = dy/dx ;
+        newedge->c /= dx ;
+    }
+    else
+    {
+        newedge->b = 1.0 ;
+        newedge->a = dx/dy ;
+        newedge->c /= dy ;
+    }
+    newedge->edgenbr = rubyvorState.nedges ;
+    out_bisector(newedge) ;
+    rubyvorState.nedges++ ;
+    return (newedge) ;
+}
+
+Site *
+intersect(Halfedge * el1, Halfedge * el2)
+{
+    Edge * e1, * e2, * e ;
+    Halfedge * el ;
+    float d, xint, yint ;
+    int right_of_site ;
+    Site * v ;
+
+    e1 = el1->ELedge ;
+    e2 = el2->ELedge ;
+    if ((e1 == (Edge*)NULL) || (e2 == (Edge*)NULL))
+    {
+        return ((Site *)NULL) ;
+    }
+    if (e1->reg[1] == e2->reg[1])
+    {
+        return ((Site *)NULL) ;
+    }
+    d = (e1->a * e2->b) - (e1->b * e2->a) ;
+    if ((-1.0e-10 < d) && (d < 1.0e-10))
+    {
+        return ((Site *)NULL) ;
+    }
+    xint = (e1->c * e2->b - e2->c * e1->b) / d ;
+    yint = (e2->c * e1->a - e1->c * e2->a) / d ;
+    if ((e1->reg[1]->coord.y < e2->reg[1]->coord.y) ||
+        (e1->reg[1]->coord.y == e2->reg[1]->coord.y &&
+        e1->reg[1]->coord.x < e2->reg[1]->coord.x))
+    {
+        el = el1 ;
+        e = e1 ;
+    }
+    else
+    {
+        el = el2 ;
+        e = e2 ;
+    }
+    right_of_site = (xint >= e->reg[1]->coord.x) ;
+    if ((right_of_site && (el->ELpm == le)) ||
+       (!right_of_site && (el->ELpm == re)))
+    {
+        return ((Site *)NULL) ;
+    }
+    v = (Site *)getfree(&(rubyvorState.sfl)) ;
+    v->refcnt = 0 ;
+    v->coord.x = xint ;
+    v->coord.y = yint ;
+    return (v) ;
+}
+
+/*** returns 1 if p is to right of halfedge e ***/
+
+int
+right_of(Halfedge * el, Point * p)
+{
+    Edge * e ;
+    Site * topsite ;
+    int right_of_site, above, fast ;
+    float dxp, dyp, dxs, t1, t2, t3, yl ;
+
+    e = el->ELedge ;
+    topsite = e->reg[1] ;
+    right_of_site = (p->x > topsite->coord.x) ;
+    if (right_of_site && (el->ELpm == le))
+    {
+        return (1) ;
+    }
+    if(!right_of_site && (el->ELpm == re))
+    {
+        return (0) ;
+    }
+    if (e->a == 1.0)
+    {
+        dyp = p->y - topsite->coord.y ;
+        dxp = p->x - topsite->coord.x ;
+        fast = 0 ;
+        if ((!right_of_site & (e->b < 0.0)) ||
+         (right_of_site & (e->b >= 0.0)))
+        {
+            fast = above = (dyp >= e->b*dxp) ;
+        }
+        else
+        {
+            above = ((p->x + p->y * e->b) > (e->c)) ;
+            if (e->b < 0.0)
+            {
+                above = !above ;
+            }
+            if (!above)
+            {
+                fast = 1 ;
+            }
+        }
+        if (!fast)
+        {
+            dxs = topsite->coord.x - (e->reg[0])->coord.x ;
+            above = (e->b * (dxp*dxp - dyp*dyp))
+                    <
+                    (dxs * dyp * (1.0 + 2.0 * dxp /
+                    dxs + e->b * e->b)) ;
+            if (e->b < 0.0)
+            {
+                above = !above ;
+            }
+        }
+    }
+    else  /*** e->b == 1.0 ***/
+    {
+        yl = e->c - e->a * p->x ;
+        t1 = p->y - yl ;
+        t2 = p->x - topsite->coord.x ;
+        t3 = yl - topsite->coord.y ;
+        above = ((t1*t1) > ((t2 * t2) + (t3 * t3))) ;
+    }
+    return (el->ELpm == le ? above : !above) ;
+}
+
+void
+endpoint(Edge * e, int lr, Site * s)
+{
+    e->ep[lr] = s ;
+    ref(s) ;
+    if (e->ep[re-lr] == (Site *)NULL)
+    {
+        return ;
+    }
+    out_ep(e) ;
+    deref(e->reg[le]) ;
+    deref(e->reg[re]) ;
+    makefree((Freenode *)e, (Freelist *) &efl) ;
+}
+
+float
+dist(Site * s, Site * t)
+{
+    float dx,dy ;
+
+    dx = s->coord.x - t->coord.x ;
+    dy = s->coord.y - t->coord.y ;
+    return (sqrt(dx*dx + dy*dy)) ;
+}
+
+void
+makevertex(Site * v)
+{
+    v->sitenbr = rubyvorState.nvertices++ ;
+    out_vertex(v) ;
+}
+
+void
+deref(Site * v)
+{
+    if (--(v->refcnt) == 0 )
+    {
+        makefree((Freenode *)v, (Freelist *)&(rubyvorState.sfl)) ;
+    }
+}
+
+void
+ref(Site * v)
+{
+    ++(v->refcnt) ;
+}
+