I'm implementing an algorithm in which I need manipulate a mesh, adding and deleting edges quickly and iterating quickly over the edges adjacent to a vertex in CCW or CW order.
The winged-edge structure is used in the description of the algorithm I'm working from, but I can't find any concise descriptions of how to perform those operations on this data structure.
I've learned about it in University but that was a while ago.
In response to this question i've searched the web too for any good documentation, found none that is good, but we can go through a quick example for CCW and CW order and insertion/deletion here.
Have a look at this table and graphic:
from this page:
http://www.cs.mtu.edu/~shene/COURSES/cs3621/NOTES/model/winged-e.html
The table gives only the entry for one edge a, in a real table you have this row for every edge. You can see you get the:
left predecessor,
left successor,
right predecessor,
right successor
but here comes the critical point: it gives them relative to the direction of the edge which is X->Y in this case, and when it is right-traversed (e->a->c).
So for the CW-order of going through the graph this is very easy to read: edge a left has right-successor c and then you look into the row for edge c.
Ok, this table is easy to read for CW-order traversal; for CCW you have to think "from which edge did i come from when i walked this edge backwards". Effectively you get the next edge in CCW-order by taking the left-traverse-predecessor in this case b and continue with the row-entry for edge b in the same manner.
Now insertion and deletion: It is clear that you cant just remove the edge and think that the graph would still consist of only triangles; during deletion you have to join two vertices, for example X and Y in the graphic. To do this you first have to make sure that everywhere the edge a is referred-to we have to fix that reference.
So where can a be referred-to? only in the edges b,c,d and e (all other edges are too far away to know a) plus in the vertex->edge-table if you have that (but let's only consider the edges-table in this example).
As an example of how we have to fix edges lets take a look at c. Like a, c has a left and right pre- and successor (so 4 edges), which one of those is a? We cannot know that without checking because the table-entry for c can have the node Y in either its Start- or End-Node. So we have to check which one it is, let's assume we find that c has Y in its Start-Node, we then have to check whether a is c's right predecessor (which it is and which we find out by looking at c's entry and comparing it to a) OR whether it is c's right successor. "Successor??" you might ask? Yes because remember the two "left-traverse"-columns are relative to going the edge backward. So, now we have found that a is c's right predecessor and we can fix that reference by inserting a's right predecessor. Continue with the other 3 edges and you are done with the edges-table. Fixing an additional Node->Vertices is trivial of course, just look into the entries for X and Y and delete a there.
Adding edges is basically the reverse of this fix-up of 4 other edges BUT with a little twist. Lets call the node which we want to split Z (it will be split into X and Y). You have to take care that you split it in the right direction because you can have either d and e combined in a node or e and c (like if the new edge is horizontal instead of the vertical a in the graphic)! You first have to find out between which 2 edges of the soon-to-be X and between which 2 edges of Y the new edge is added: You just choose which edges shall be on one node and which on the other node: In this example graphic: choose that you want b, c and the 2 edges to the north in between them on one node, and it follows that the other edges are on the other node which will become X. You then find by vector-subtraction that the new edge a has to be between b and c, not between say c and one of the 2 edges in the north. The vector-subtraction is the desired position of the new X minus the desired position of Y.
Related
jgrapht supports the idea of putting a wehight(a cost) on an edge/vertex between two nodes. This can be achieved using the class DefaultWeightedEdge.
In my graph I do have the requirement to not find the shortest path but the cheapest one. The cheapest path might be longer/have more hops nodes to travel then the shortest path.
Therefor, one can use the DijkstraShortestPath algorithm to achieve this.
However, my use case is a bit more complex: It needs to also evaluate costs on actions that need to be executed when arriving at a node.
Let's say, you have a graph like a chess board(8x8 fields, each field beeing a node). All the edges have a weight of 1. To move in a car from left bottom to the diagonal corner(right upper), there are many paths with the cost of 16. You can take a diagonal path in a zic zac style, or you can first travel all nodes to the right and then all nodes upwards.
The difference is: When taking a zic zac, you need to rotate yourself in the direction of moving. You rotate 16 times.
When moving first all to the right and then upwards, you need to rotate only once (maybe twice, depending on your start orientation).
So the zic zac path is, from a Djikstra point of view, perfect. From a logical point of view, it's the worst.
Long story short: How can I put some costs on a node or edge depending on the previous edge/node in that path? I did not find anything related in the source code of jgrapht.
Or is there a better algorithm to use?
This is not a JGraphT issue but a graph algorithm issue. You need to think about how to encode this problem and formalize that in more detail
Incorporating weights on vertices is in general easy. Say that every vertex represents visiting a customer, which takes a_i time. This can be encoded in the graph by adding a_i/2 to the cost of every incoming arc in node i, as well as a_i/2 to the cost of every outgoing arc.
A cost function where the cost of traveling from j to k dependents on the arc (i,j) you used to travel to j is more complicated.
Approach a.: Use a dynamic programming (labeling) algorithm. This is perhaps the easiest. You can define your cost function as a recursive function, where the cost of traversing an arc depends on the cost of the previous arc.
Approach b.: With some tricks you may be able to encode the costs in the graph by adding extra nodes to it. Here's an example:
Given a graph with vertices {a,b,c,d,e}, with arcs: (a,e), (e,b), (c,e), (e,d). This graph represents a crossroad with vertex e being in the middle. Going from a->e->b (straight) is free, however, a turn from a->e->d takes additional time. Similar for c->e->d (straight) is free and c->e->b (turning) should be penalized.
Decouple vertex e in 4 new vertices: e1,e2,e3,e4.
Add the following arcs:
(a,e1), (e3,b), (c,e2), (e4,d), (e2, e3), (e1, e3), (e1, e4), (e2, e4).
(e1,e4) and (e2,e3) can have a positive weight to penalize turning.
So I am implementing A* algorithm in C. Here's the procedure.
I am using Priority Queue [using array] for all the open nodes. Since I'll have duplicate distances, that is more than one node with same distance/Priority, hence while inserting a node in PQ, if the parent of the inserted node has the same priority, I still swap them both, so that my newest entered member remains on the top( or as high as possible),so that I keep following a particular direction. Also, on removing, when I swap the topmost element with the last one, then again, if the swapped last element has the same as one of its children, then it gets swapped to the bottom.(I am not sure if this will affect in any way).
Now the problem is say I have a 100*100 matrix, and I have obstacles from (0,20) to (15,20) of the 2D array , in which I am moving. Now for a starting position (2,2) and ending position (16,20) I get a straight path, i.e. firstly go all the way to right, then go down till 15 then move one right and I am done.
But, if I have starting as (2,2) and last as (12,78) i.e. the points are separated by the obstacles and the path has to go around it, I still go via (16,20) and my path after (16,20) is still straight, but my path upto (16,20) is zig zag, i.e. I go some distance straight down, then some right, then down then right and so on, ultimately reaching (16,20) and going straight after that.
Why this zig zag path for the first half of the distance, what can I do to make sure that my path is straight, as it is, when my destination is (16,20) and not (12,78).
Thanks.
void findPath(array[ROW][COLUMN],sourceX,sourceY,destX,destY) {
PQ pq[SIZE];
int x,y;
insert(pq,sourceX,sourceY);
while(!empty(pq)) {
remove(pq);
if(removedIsDestination)
break; //Path Found
insertAdjacent(pq,x,y,destX,destY);
}
}
void insert(PQ pq[SIZE],element){
++sizeOfPQ;
PQ[sizeOfPQ]==element
int i=sizeOfPQ;
while(i>0){
if(pq[i].priority <= pq[(i-1)/2].priority){
swapWithParent
i=(i-1)/2;
}
else
break;
}
}
You should change your scoring part. Right now you calculate absolute distance. Instead calculate min move distance. If you count each move as one then if you were at (x,y) and going to (dX,dY) that would be
distance moved + (max(x,dX) - min(x,dx) + max(y,dY) - min(y,dY))
A lower value is considered a higher score.
This heuristic is a guess at how many moves it would take if there was nothing in the way.
The nice thing about the heuristic is you can change it to get the results you want, for example if you prefer to move in a straight line as you suggest, then you can make this change:
= distance moved + (max(x,dX) - min(x,dx) + max(y,dY) - min(y,dY))
+ (1 if this is a turn from the last move)
This will cause you to "find" solutions which tend to go in the same direction.
If you want to FORCE as few turns as possible:
= distance moved + (max(x,dX) - min(x,dx) + max(y,dY) - min(y,dY))
+ (1 times the number of turns made)
This is what is nice about A* -- the heuristic will inform the search -- you will still always find a solution, but if there is more than one you can influence where you look first -- this makes it good for simulating AI behavior.
Doubt : How is the first one and second calculating way different from
each other?
The first one puts a lower priority on a move that is a turn. The second one puts a lower priority on a path with more turns. In some cases (eg, the first turn) the value will be the same, but over all the 2nd one will pick paths that have as few turns as possible, where the first one might not.
Also, 1 if this is a turn from the last move , for this,
say i have source at top left and destination at bottom right, now my
path normally would be, left,left,left...down,down,down.... Now, 1 if
this is a turn from the last move, according to this, when I change
from left to down, will I add 1?
Yes
Wont it make the total value more and the priority for down will decrease.
Yes, exactly. You want to not look at choices that have a turn in them first. This will make them lower priority and your algorithm will investigate other options with a higher priority -- exactly what you want.
Or 1 if this is a turn from the last move is when I move to a cell, that is not abutting the cell previously worked upon? Thnks –
No, I don't understand this question -- I don't think it makes sense in this context -- all moves have to abut the previous cell, diagonal moves are not allowed.
Though, I'd really appreciate if you could tell me one instance where the first and second methods will give different answers. If you could. Thanks alot. :)
Not so easy without seeing the details of your algorithm but the following might work:
The red are blocks. The green is what I would expect the first one to do, it locally tries to find the least turn. The blue is the least turn solution. Note, how far the red areas are from each other and the details of how your algorithm influence if this will work. As I have it above -- having an extra turn only costs 1 in the heuristic. SO, if you want to be sure this will work change the heuristic like this:
= distance moved + (max(x,dX) - min(x,dx) + max(y,dY) - min(y,dY))
+ (25 times the number of turns made)
Where 25 is bigger than the distance to get past the 2nd turn in the green path. (Thus after the 2nd turn the blue path will be searched.)
This is a homework question. I do not want the solution - I'm offering the solution I've been thinking of and wish to know whether is it good or why is it flawed.
My motivation is to find what edges of an unweighted, undirected graph are not a part of any MST. This problem only makes sense when several edges have the same values, otherwise the MST is unique.
My idea comes from Prim's Algorithm with a slight change - instead of adding the minimum edge from S to T on every step (where S and T being the two sets of vertex) - instead look for the minimum edge and more edges of the same value going from S to the vertex the minimum edge goes to. By doing that, (so I suppose) we will receive a graph containing all the edges which appear in any MST. If this is right, I can simply XOR the edges list with the original graph edges list to find what edges are not in any MST.
Thanks in advance.
Do you add all the edges you find (=those with equal weight)? If so, you will lose some edges:
Consider a pentagon with equal edge costs. You start with 1 node and add the 2 edges to the 2 adjacent nodes. In you next step you would add the 2 edges going from those 2 adjacent nodes to the 2 disconnected nodes and you would be done. However, all edges are of equal cost and they are all valid to be in the MST. The edge between the last 2 nodes is not included by your algorithm but could be part of the MST.
It's even worse. Suppose that last edge is of lower cost. Your algorithm still doesn't include it, yet it's present in every MST. You're adding several edges per step to account for all the possibilities but adding those edges changes the next steps.
I'm working on a school project that involves taking a lat/long point and finding the top five closest points in a known list of places. The list is to be stored in memory, with the caveat that we must choose an "appropriate data structure" -- that is, we cannot simply store all the places in an array and compare distances one-by-one in a linear fashion. The teacher suggested grouping the place data by US State to prevent calculating the distance for places that are obviously too far away. I think I can do better.
From my research online it seems like an R-Tree or one of its variants might be a neat solution. Unfortunately, that sentence is as far as I've gotten with understanding the actual technique, as the literature is simply too dense for my non-academic head.
Can somebody give me a really high overview of what the process is for populating an R-Tree with lat/long data, and then traversing the tree to find those 5 nearest neighbors of a given point?
Additionally the project is in C, and I don't have to reinvent the wheel on this, so if you've used an existing open source C implementation of an R Tree I'd be interested in your experiences.
UPDATE: This blog post describes a straightforward search algorithm for a regionally partitioned space (like a PR quadtree). Hope that helps a future reader.
Have you considered alternative data structures?
I believe, instead of R-tree a Point Quadtree would be more effective for your need.Spatial Index Demos provides some demos for a list of possible data structures including R-tree and Point Quadtree. Hope it gives an insight.
Quad Trees
A quad tree takes a square of space and divides it into four children with half the dimensions along the X and Y axis.
+---+---+
| | | Each square is a child
| | | of the parent; when you
+---+---+ get to leaves a node has
| | | a single point or a list
| | | of points.
+---+---+
This data structure is recursive and you search for points by checking which child holds the point until you get to the leaf. A leaf either has a single member (point with X,Y coords) or a list of members, depending on the implementation. If you fill up a node you split it into 4 and distribute the children. Essentially, the data structure is a generalisation of a binary tree, so it is not necessarily balanced.
Balancing a quad tree may not be necessary for your purposes and is left as an exercise for the reader - try searching on the web for 'balanced quad tree'
Note that this data structure cannot index items that can overlap, but if you're only storing points this won't be a problem.
Finding nearest neighbours in a quad tree
Off the top of my head, here's a quick and dirty algorithm for finding the 'n' nearest neighbours to your point. It's not necessarily optimially efficient, but it will be fairly simple to implement. If someone has a link to a better one, feel free to post it in a comment or answer.
Locate the quad tree node containing
your point, keeping a list of its
parents.
Push all of the points in the
node into a priority queue based on
their distance from your base point
(i.e. by the length of the hypotenuse
per Pythagoras' theorem). Depending
on the implementation there may be
one or more per node. For a simple
implementation of a priority queue
data structure, look up 'binary
heap'.
If any of the 'n' points are further away then the edges of the bounding box, add the contents of its neighbours. i.e. If your base point is close to the edge of the bounding box, it is possible that neighbouring tree nodes might contain points that are closer than the points found within your bounding box. You will need to back up the tree to do this, which is why you need to keep track of your parent nodes.
When all of the 'n' closest points are closer than the edges of your bounding box you know that there could not possibly be neighbours that you have missed. Therefore, the 'n' closest points within this box must be your 'n' closest neighbours.
I do work in theoretical chemistry on a high performance cluster, often involving molecular dynamics simulations. One of the problems my work addresses involves a static field of N-dimensional (typically N = 2-5) hyper-spheres, that a test particle may collide with. I'm looking to optimize (read: overhaul) the the data structure I use for representing the field of spheres so I can do rapid collision detection. Currently I use a dead simple array of pointers to an N-membered struct (doubles for each coordinate of the center) and a nearest-neighbor list. I've heard of oct- and quad- trees but haven't found a clear explanation of how they work, how to efficiently implement one, or how to then do fast collision detection with one. Given the size of my simulations, memory is (almost) no object, but cycles are.
How best to approach this for your problem depends on several factors that you have not described:
- Will the same hypersphere arrangement be used for many particle collision calculations?
- Are the hyperspheres uniform size?
- What is the movement of the particle (e.g. straight line/curve) and is that movement affected by the spheres?
- Do you consider the particle to have zero volume?
I assume that the particle does not have simple straight line movement as that would be the relatively fast calculation of finding the closest point between a line and a point, which is likely going to be about the same speed as finding which of the boxes the line intersects with (to determine where in the n-tree to examine).
If your hypersphere positions are fixed for a lot of particle collisions then computing a voronoi decomposition/Dirichlet tessellation would give you a fast way of later finding exactly which sphere is closest to your particle for any given point in the space.
However to answer your original question about octrees/quadtrees/2^n-trees, in n dimensions you start with a (hyper)-cube that contains the area of space that you are interested in. This will be subdivided into 2^n hypercubes if you deem the contents to be too complicated. This continues recursively until you have only simple elements (e.g. one hypersphere centroid) in the leaf nodes.
Now that the n-tree is built you use it for collision detection by taking the path of your particle and intersecting it with the outer hypercube. The intersection position will tell you which hypercube in the next level down of the tree to visit next, and you determine the position of intersection with all 2^n hypercubes at that level, following downwards until you reach a leaf node. Once you reach the leaf you can examine interactions between your particle path and the hypersphere stored at that leaf. If you have collision you have finished, otherwise you have to find the exit point of the particle path from the current hypercube leaf and determine which hypercube it moves to next. Continue until you find a collision or entirely leave the overall bounding hypercube.
Efficiently finding the neighbouring hypercube when exiting a hypercube is one of the most challenging parts of this approach. For 2^n trees Samet's approaches {1, 2} can be adapted. For kd-trees (binary trees) an approach is suggested in {3} section 4.3.3.
Efficient implementation can be as simple as storing a list of 8 pointers from each hypercube to its children hypercubes, and marking the hypercube in a special way if it is a leaf (e.g. make all pointers NULL).
A description of dividing space to create a quadtree (which you can generalise to n-tree) can be found in Klinger & Dyer {4}
As others have mentioned kd-trees may be more suited than 2^n-trees as extension to an arbitrary number of dimensions is more straightforward, however they will result in a deeper tree. It is also easier to adapt the split positions to match the geometry of your
hyperspheres with a kd-tree. The description above of collision detection in a 2^n tree is equally applicable to a kd-tree.
{1} Connected Component Labeling, Hanan Samet, Using Quadtrees Journal of the ACM Volume 28 , Issue 3 (July 1981)
{2} Neighbor finding in images represented by octrees, Hanan Samet, Computer Vision, Graphics, and Image Processing Volume 46 , Issue 3 (June 1989)
{3} Convex hull generation, connected component labelling, and minimum distance
calculation for set-theoretically defined models, Dan Pidcock, 2000
{4} Experiments in picture representation using regular decomposition, Klinger, A., and Dyer, C.R. E, Comptr. Graphics and Image Processing 5 (1976), 68-105.
It sounds like you'd want to implement a kd-tree, which would allow you to more quickly search the N-dimensional space. There's some more information and links to implementations at the Stony Brook Algorithm Repository.
Since your field is static (by which I'm assuming you mean that the hyper spheres don't move), then the fastest solution I know of is a Kdtree.
You can either make your own, or use someone else's, like this one:
http://libkdtree.alioth.debian.org/
A Quad tree is a 2 dimensional tree, in which at each level a node has 4 children, each of which covers 1/4 of the area of the parent node.
An Oct tree is a 3 dimensional tree, in which at each level a node has 8 children, each of which contains 1/8th of the volume of the parent node. Here is picture to help you visualize it: http://en.wikipedia.org/wiki/Octree
If you're doing N dimensional intersection tests, you could generalize this to an N tree.
Intersection algorithms work by starting at the top of the tree and recursively traversing into any child nodes that intersect the object being tested, at some point you get to leaf nodes, which contain the actual objects.
An octree will work as long as you can specify the spheres by their centres - it hierarchically bins points into cubic regions with eight children. Working out neighbours in an octree data structure will require you to do sphere-intersecting-cube calculations (to some extent easier than they look) to work out which cubic regions in an octree are within the sphere.
Finding the nearest neighbours means walking back up the tree until you get a node with more than one populated child and all surrounding nodes included (this ensures the query gets all sides).
From memory, this is the (somewhat naive) basic algorithm for sphere-cube intersection:
i. Is the centre within the cube (this gets the eponymous situation)
ii. Are any of the corners of the cube within radius r of the centre (corners within the sphere)
iii. For each surface of the cube (you can eliminate some of the surfaces by working out which side of the surface the centre lies on) work out (this is all first-year vector arithmetic):
a. A normal of the surface that goes to the centre of the sphere
b. The distance from the centre of the sphere to the intersection of the normal with the plane of the surface (chord intersets plane the surface of the cube)
c. Intersection of the plane lies within the side of the cube (one condition of chord intersection to the cube)
iv. Calculate the size of the chord (Sin of Cos^-1 of ratio of normal length to radius of sphere)
v. If the nearest point on the line is less than the distance of the chord and the point lies between the ends of the line the chord intersects one of the edges of the cube (chord intersects cube surface somewhere along one of the edges).
Slightly dimly remembered but this is something I did for a situation involving spherical regions using an octee data structure (many years ago). You may also wish to check out KD-trees as some of the other posters suggest but your initial question sounds very similar to what I did.