Cluster adjacent Vornoi polygons of same category - r

We have a set of points, each with (x,y) coordinates and a category C. We have built the Voronoi diagram based on these points and would now like to "cluster" adjacent polygons when they are of a particular category. Is there a ready-made algorithm / R package for doing this ?
If not, our current thinking is to go back to the Delaunay triangulation and brute-force our way to the solution : consider each vertix V, find the vertix v of each edge going into V and see if they are the same category, if so aggregate the polygons.
Is there a better way to do that ? Is there an R package that could do that ? If not, which R package implementing Delaunay would have the best result data-structure to do this ?

Note: I wouldn't call this cluster analysis. If you stick to this keyword, you will not find anything useful to you. What you apparently want to do is merge adjacent Voronoi cells, but that's about it.
Your Voronoi cell / Delaunay triangulation algorithm should give you information of all the edges. What you probably want to do is iterate over all edges, and when both cells have the same category, merge them.
Trivial code; and heavily application dependant (what is "same category"?), so you probably won't find a "libary" for it.

You can use a convex hull on the points and remove all points inside a same category. Then repeat the voronoi diagram. BTW. I know nothing about R.

Related

If i already know the Voronoi vertices points, how can i create a polygon from the list?

I'm trying to create this in Gamemaker. I already know the Voronoi vertices but i'm stuck with how to create polygons for each seed object. I need them to be independent so i can split it up later to apply texture mapping to them.
I've tried delaunay already but it doesn't seem as accurate as my voronoi generation. But being that the cicrumradius is the voronoi vertices anyways i feel like i don't need it. The problem with the Delaunay is that it only returns the points near the center of the diagram and doesn't return any points towards the Borders of the Box. The only good thing is that delaunay did skip an extra step and made it easier to return if the the seeds x and y are within the circumradius then just add them to the list of vertices
Is there any way to make a polygon from a plot of points from a data structure?
Pick the midpoint of each edge and the distance to each site then sort the result and pick the first and second (when they are equal) and save them into polygons. For the borders there is of course only 1 edge.
Duplicate:Getting polygons from voronoi edges

How to use the function r.cost to get the least-cost path between two polygons?

I am a beginner in GRASS but I would like to get the least-cost path between two polygons. More exactely, I would like to get the smallest cost from any point situated at the edge of one polygon (polygon A) to any point situated at the edge of another polygon (polygon B).
Until now, I used the function CostDistance and CostPath of ArcGIS by using a cost raster where each cell had a cost value, a shapefile for the first polygon, and a shapefile for the second polygon. I would like to do the same thing with GRASS. I think that the function r.cost allows to do this. But I don't know how to specify in parameters the two polygons in GRASS ?
Have you got an example of how to use r.cost with two polygons in R with package spgrass6?
Thanks very much for your help.
If the use of GRASS is not mandatory and sticking with R is sufficient, you should check the marmap package. Section 2.4 of the vignette (vignette("marmap")) is entitled:
2.4 Using bathymetric data for least-cost path analysis
The marmap package allows for computation of least-cost path constrained within a range of depth/altitude between any number of points. The two key functions here are trans.mat() to create a transition matrix similar to the cost-raster you mention. Then, lc.dist() computes the least-cost distance and allows to plot the path between points.
Detailed examples are provided in the marmap vignette.

Determine the points in the boundary of a given region in 2D

What is a good way to determine the points in the boundary of a given region in 2D?
Suppose that you are given a nested list with lists of two coordinates, e.g.
{ {x1,y1}, {x2,y2}, {x3,y3} }
Of course the actual nested list would have a lot more points than 3, which are associated to a given region in the plane. The nested list, for example, could determine a disk in the plane. Then, the output should be a nested list corresponding to a circle.
I don't want any image recognition stuff applied to a possible plot. I would like operations on the nested list.
This answer is based on #andand comment. The credit is all his.
If I have a nested list called "region", with lists of the 2d coordinates, I would get the "convex hull" of it writing
Needs["ComputationalGeometry`"]
regionhull = ConvexHull[ region ]
But "ConvexHull" gives us the indices of the lists within the nested list, in counterclockwise order, corresponding to the convex boundary of the region. Thus, an adittional step is needed, to make the needed output:
regionboundary = region[[ regionhull ]]
But still, this answer is incomplete. It seems to me that a "concave hull" algorithm would be the more general solution. Would anyone know anything about the concave hull in Mathematica? I may post an additional question for that.
Below, I show a figure to understand the concave and convex hull algorithms extracted from
https://gis.stackexchange.com/questions/1200/concave-hull-definition-algorithms-and-practical-solutions
A tutorial for the "Computational Geometry Package" is found at
http://reference.wolfram.com/mathematica/ComputationalGeometry/tutorial/ComputationalGeometry.html
** Addendum **
The package "alphahull" can solve the problem of finding the boundary of a concave region. Its description is found here:
http://cran.r-project.org/web/packages/alphahull/vignettes/alphahull.pdf
Sounds like you want some kind of interpolation technique. http://en.wikipedia.org/wiki/Interpolation

How to construct a mesh from given edge points?

I have some points on the edge(left image), and I want to construct a mesh(right), Is there any good algorithm to achieve it? many thanks!
image can see here http://ww3.sinaimg.cn/large/6a2c8e2bjw1dk8jr3t7eaj.jpg
To begin with, see Delauney triangulation. Look at this project: http://people.sc.fsu.edu/~jburkardt/c_src/triangulate/triangulate.html.
Edited because my original had too few details on edge-flipping, and when I tried to provided those details I found the TRIANGULATE project.
If the region is flat or quasi-flat look for Ear Clipping approach (http://www.geometrictools.com/Documentation/TriangulationByEarClipping.pdf). In the case of curved surface you need point inside the region and therefore you may need Constrained Delaunay Triangulation (otherwise some edges may not be included in the triangulation).
There is delaunayn function in geometry package for R language (see doc)
It takes an array of boundary points (as in your case) to create a Delaunay mesh on it.
You could also save your geometry into some well-known format, and use one of mesh generators.

A simple algorithm for polygon intersection

I'm looking for a very simple algorithm for computing the polygon intersection/clipping.
That is, given polygons P, Q, I wish to find polygon T which is contained in P and in Q, and I wish T to be maximal among all possible polygons.
I don't mind the run time (I have a few very small polygons), I can also afford getting an approximation of the polygons' intersection (that is, a polygon with less points, but which is still contained in the polygons' intersection).
But it is really important for me that the algorithm will be simple (cheaper testing) and preferably short (less code).
edit: please note, I wish to obtain a polygon which represent the intersection. I don't need only a boolean answer to the question of whether the two polygons intersect.
I understand the original poster was looking for a simple solution, but unfortunately there really is no simple solution.
Nevertheless, I've recently created an open-source freeware clipping library (written in Delphi, C++ and C#) which clips all kinds of polygons (including self-intersecting ones). This library is pretty simple to use: https://github.com/AngusJohnson/Clipper2
You could use a Polygon Clipping algorithm to find the intersection between two polygons. However these tend to be complicated algorithms when all of the edge cases are taken into account.
One implementation of polygon clipping that you can use your favorite search engine to look for is Weiler-Atherton. wikipedia article on Weiler-Atherton
Alan Murta has a complete implementation of a polygon clipper GPC.
Edit:
Another approach is to first divide each polygon into a set of triangles, which are easier to deal with. The Two-Ears Theorem by Gary H. Meisters does the trick. This page at McGill does a good job of explaining triangle subdivision.
If you use C++, and don't want to create the algorithm yourself, you can use Boost.Geometry. It uses an adapted version of the Weiler-Atherton algorithm mentioned above.
You have not given us your representation of a polygon. So I am choosing (more like suggesting) one for you :)
Represent each polygon as one big convex polygon, and a list of smaller convex polygons which need to be 'subtracted' from that big convex polygon.
Now given two polygons in that representation, you can compute the intersection as:
Compute intersection of the big convex polygons to form the big polygon of the intersection. Then 'subtract' the intersections of all the smaller ones of both to get a list of subracted polygons.
You get a new polygon following the same representation.
Since convex polygon intersection is easy, this intersection finding should be easy too.
This seems like it should work, but I haven't given it more deeper thought as regards to correctness/time/space complexity.
Here's a simple-and-stupid approach: on input, discretize your polygons into a bitmap. To intersect, AND the bitmaps together. To produce output polygons, trace out the jaggy borders of the bitmap and smooth the jaggies using a polygon-approximation algorithm. (I don't remember if that link gives the most suitable algorithms, it's just the first Google hit. You might check out one of the tools out there to convert bitmap images to vector representations. Maybe you could call on them without reimplementing the algorithm?)
The most complex part would be tracing out the borders, I think.
Back in the early 90s I faced something like this problem at work, by the way. I muffed it: I came up with a (completely different) algorithm that would work on real-number coordinates, but seemed to run into a completely unfixable plethora of degenerate cases in the face of the realities of floating-point (and noisy input). Perhaps with the help of the internet I'd have done better!
I have no very simple solution, but here are the main steps for the real algorithm:
Do a custom double linked list for the polygon vertices and
edges. Using std::list won't do because you must swap next and
previous pointers/offsets yourself for a special operation on the
nodes. This is the only way to have simple code, and this will give
good performance.
Find the intersection points by comparing each pair of edges. Note
that comparing each pair of edge will give O(N²) time, but improving
the algorithm to O(N·logN) will be easy afterwards. For some pair of
edges (say a→b and c→d), the intersection point is found by using
the parameter (from 0 to 1) on edge a→b, which is given by
tₐ=d₀/(d₀-d₁), where d₀ is (c-a)×(b-a) and d₁ is (d-a)×(b-a). × is
the 2D cross product such as p×q=pₓ·qᵧ-pᵧ·qₓ. After having found tₐ,
finding the intersection point is using it as a linear interpolation
parameter on segment a→b: P=a+tₐ(b-a)
Split each edge adding vertices (and nodes in your linked list)
where the segments intersect.
Then you must cross the nodes at the intersection points. This is
the operation for which you needed to do a custom double linked
list. You must swap some pair of next pointers (and update the
previous pointers accordingly).
Then you have the raw result of the polygon intersection resolving algorithm. Normally, you will want to select some region according to the winding number of each region. Search for polygon winding number for an explanation on this.
If you want to make a O(N·logN) algorithm out of this O(N²) one, you must do exactly the same thing except that you do it inside of a line sweep algorithm. Look for Bentley Ottman algorithm. The inner algorithm will be the same, with the only difference that you will have a reduced number of edges to compare, inside of the loop.
The way I worked about the same problem
breaking the polygon into line segments
find intersecting line using IntervalTrees or LineSweepAlgo
finding a closed path using GrahamScanAlgo to find a closed path with adjacent vertices
Cross Reference 3. with DinicAlgo to Dissolve them
note: my scenario was different given the polygons had a common vertice. But Hope this can help
If you do not care about predictable run time you could try by first splitting your polygons into unions of convex polygons and then pairwise computing the intersection between the sub-polygons.
This would give you a collection of convex polygons such that their union is exactly the intersection of your starting polygons.
If the polygons are not aligned then they have to be aligned. I would do this by finding the centre of the polygon (average in X, average in Y) then incrementally rotating the polygon by matrix transformation, project the points to one of the axes and use the angle of minimum stdev to align the shapes (you could also use principal components). For finding the intersection, a simple algorithm would be define a grid of points. For each point maintain a count of points inside one polygon, or the other polygon or both (union) (there are simple & fast algorithms for this eg. http://wiki.unity3d.com/index.php?title=PolyContainsPoint). Count the points polygon1 & polygon2, divide by the amount of points in polygon1 or Polygon2 and you have a rough (depending on the grid sampling) estimate of proportion of polygons overlap. The intersection area would be given by the points corresponding to an AND operation.
eg.
function get_polygon_intersection($arr, $user_array)
{
$maxx = -999; // choose sensible limits for your application
$maxy = -999;
$minx = 999;
$miny = 999;
$intersection_count = 0;
$not_intersected = 0;
$sampling = 20;
// find min, max values of polygon (min/max variables passed as reference)
get_array_extent($arr, $maxx, $maxy, $minx, $miny);
get_array_extent($user_array, $maxx, $maxy, $minx, $miny);
$inc_x = $maxx-$minx/$sampling;
$inc_y = $maxy-$miny/$sampling;
// see if x,y is within poly1 and poly2 and count
for($i=$minx; $i<=$maxx; $i+= $inc_x)
{
for($j=$miny; $j<=$maxy; $j+= $inc_y)
{
$in_arr = pt_in_poly_array($arr, $i, $j);
$in_user_arr = pt_in_poly_array($user_array, $i, $j);
if($in_arr && $in_user_arr)
{
$intersection_count++;
}
else
{
$not_intersected++;
}
}
}
// return score as percentage intersection
return 100.0 * $intersection_count/($not_intersected+$intersection_count);
}
This can be a huge approximation depending on your polygons, but here's one :
Compute the center of mass for each
polygon.
Compute the min or max or average
distance from each point of the
polygon to the center of mass.
If C1C2 (where C1/2 is the center of the first/second polygon) >= D1 + D2 (where D1/2 is the distance you computed for first/second polygon) then the two polygons "intersect".
Though, this should be very efficient as any transformation to the polygon applies in the very same way to the center of mass and the center-node distances can be computed only once.

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