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• Visualizing Undirected Graph That's Too Large for GraphViz?

  - by Gabe

  Hi Everyone, I was wondering if anyone has any advice for rendering an undirected graph with 178,000 nodes and 500,000 edges. I've tried Neato, Tulip, and Cytoscape. Neato doesn't even come remotely close, and Tulip and Cytoscape claim they can handle it but don't seem to be able to. (Tulip does nothing and Cytoscape claims to be working, and then just stops.) Does anyone have any ideas? I'd just like a vector format file (ps or pdf) with a remotely reasonable layout of the nodes. Thanks!

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• Small 3D Scene Graph

  - by Alon

  I'm looking for a 3D graphics library (not a complete game engine). Preferred a scene graph. Something small (unlike jME, XNA or Unity), that I can easily expand and change. Preferred features: Cross Platform Wrriten in Java/Scala (JOGL or LWJGL), C# (preferred OpenTK), Python or JavaScript/WebGL. Support for OpenGL is a must. Direct3D is optional. Some material system Full support for some model format with full animation support (preferred COLLADA) Level of Detail (LOD) support Lighting support Shaders, GUI, Input and Terrain/Water support are also preferred, but not required Thanks!

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• Finding an A* heuristic for a directed graph

  - by Janis Peisenieks

  In a previous question, I asked about finding a route (or path if you will) in a city. That is all dandy. The solution I chose was with the A* algorithm, which really seems to suit my needs. What I find puzzling is heuristic. How do I find one in an environment without constant distance between 2 nodes? Meaning, not every 2 nodes have the same distance between them. What I have is nodes (junctures), streets with weight (which may also be one-way), a start/finish node (since the start and end is always in the same place) and a goal node. In an ordinary case, I would just use the same way I got to goal to go back, but since one of the streets could have been a one-way, that may not be possible. The main question How do I find a heuristic in a directed graph?

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• Custom graph comparison?

  - by user57828

  I'm trying to compare two graphs using hash value ( i.e, at the time of comparison, try to avoid traversing the graph ) Is there a way to make a function such that the hash values compared can also lead to determining at which height the graphs differ? The comparisons between two graphs are to be made by comparing children at a certain level. One way to compare the graphs is have a final hash value for the root node and compare them, but that wouldn't directly reflect at which level the graphs differ, since their immediate children might be the same ( or any other case ).

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• Javascript Graph Layout Engine

  - by GJK

  I'm looking for a Javascript library/engine that can do graph layouts. (And when I say layouts, I mean logically position vertices nicely.) The graphs I'm working with are all m-ary trees. M is usually no more than 5 or 6, but it can be greater in some cases. I do have something that I use now, Graphviz's node program, and it works perfectly. The problem is, when running a web app, I have to send a request to the server every time I want a layout. Preferably, I would like something written in Javascript that can be quickly run on the client side. All it needs to do is provide layout information (relative positioning and whatnot). I don't need it to draw to a canvas or use SVG or anything, all I'm interested in is the layout. Library use like jQuery or RaphaelJS is fine by me. I'll work with it. I'm just looking for something to speed things along a little. Also, I'd consider writing my own if I could find a nice description of an algorithm to do the layouts. But I really don't want to spend too much time. I have something that works now, so getting it on the client side is just a bonus, not a necessity.

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• Problem with DirectX scene-graph

  - by Alex

  I'm trying to implement a basic scene graph in DirectX using C++. I am using a left child-right sibling binary tree to do this. I'm having trouble updating each node's world transformation relative to its parent (and its parent's parent etc.). I'm struggling to get it to work recursively, though I can get it to work like this: for(int i = 0; i < NUM_OBJECTS; i++) { // Initialize to identity matrix. D3DXMatrixIdentity(&mObject[i].toWorldXForm); int k = i; while( k != -1 ) { mObject[i].toWorldXForm *= mObject[k].toParentXForm; k = mObject[k].parent; } } toWorldXForm is the object's world transform and toParentXForm is the object's transform relative to the parent. I want to do this using a method within my object class (the code above is in my main class). This is what I've tried but it doesn't work (only works with nodes 1 generation away from the root) if (this->sibling != NULL) this->sibling->update(toParentXForm); D3DXMatrixIdentity(&toWorldXForm); this->toWorldXForm *= this->toParentXForm; this->toWorldXForm *= toParentXForm; toParentXForm *= this->toParentXForm; if (this->child != NULL) this->child->update(toParentXForm); Sorry if I've not been clear, please tell me if there's anything else you need to know. I've no doubt it's merely a silly mistake on my part, hopefully an outside view will be able to spot the problem.

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• Looking for a small, light scene graph style abstraction lib for shader based OpenGL

  - by Pris

  I'm looking for a 'lean and mean' c/c++ scene graph library for OpenGL that doesn't use any deprecated functionality. It should be cross platform (strictly speaking I just dev on Linux so no love lost if it doesn't work on Windows), and it should be possible to deploy to mobile targets (ie OpenGLES2, and no crazy mandatory dependencies that wouldn't port well to modern mobile frameworks like iOS, Android, etc), with a license that's compatible with closed source software (LGPL or more liberal). Specific nice-to-haves would be: Cameras and Viewers (trackball, fly-by, etc) Object transform hierarchies (if B is a child of A, and you move A, B has the same transform applied to it) Simple animation Scene optimization (frustum culling, use VBOs, minimize state changes, etc) Text I've played around with OpenSceneGraph a lot and it's pretty amazing for fixed function pipeline stuff, but I've had a few of problems using it with the programmable pipeline and after going through their mailing list, it seems several people have had similar issues (going back years). Kitware's VES looks neat (http://www.vtk.org/Wiki/VES), but VES + VTK is pretty heavy. VTK is also typically for analyzing scientific data and I've read that it's not that appropriate for a general use case (not that great at rendering a lot of objects on scene,etc) I'm currently looking at VisualizationLibrary (http://www.visualizationlibrary.org/documentation/pag_gallery.html) which looks like it offers some of the functionality I'd like, but it doesn't explicitly support mobile targets. Other solutions like Ogre, Horde3D, Irrlicht, etc tend to be full on game engines and that's not really what I'm looking for. I'd like some suggestions for other libraries that I may have missed... please note I'm not willing to roll my own solution from scratch.

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• 2D scene graph not transforming relative to parent

  - by Dr.Denis McCracleJizz

  I am currently in the process of coding my own 2D Scene graph, which is basically a port of flash's render engine. The problem I have right now is my rendering doesn't seem to be working properly. This code creates the localTransform property for each DisplayObject. Matrix m_transform = Matrix.CreateRotationZ(rotation) * Matrix.CreateScale(scaleX, scaleY, 1) * Matrix.CreateTranslation(new Vector3(x, y, z)); This is my render code. float dRotation; Vector2 dPosition, dScale; Matrix transform; transform = this.localTransform; if (parent != null) transform = localTransform * parent.localTransform; DecomposeMatrix(ref transform, out dPosition, out dRotation, out dScale); spriteBatch.Draw(this.texture, dPosition, null, Color.White, dRotation, new Vector2(originX, originY), dScale, SpriteEffects.None, 0.0f); Here is the result when I try to add the Stage then to the stage a First DisplayObjectContainer and then a second one. It may look fine but the problem lies in the fact that I add a first DisplayObjectContainer at (400,400) and the second one within it (that's the smallest one) at position (0,0). So he should be right over its parent but he gets render within the parent at the same position the parent has (400, 400) for some reason. It's just as if I double the parent's localMatrix and then render the second cat there. This is the code i use to loop through every childs. base.Draw(spriteBatch); foreach (DisplayObject childs in _childs) { childs.Draw(spriteBatch); }

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• What is the relaxation condition in graph theory

  - by windopal

  Hi, I'm trying to understand the main concepts of graph theory and the algorithms within it. Most algorithms seem to contain a "Relaxation Condition" I'm unsure about what this is. Could some one explain it to me please. An example of this is dijkstras algorithm, here is the pseudo-code. 1 function Dijkstra(Graph, source): 2 for each vertex v in Graph: // Initializations 3 dist[v] := infinity // Unknown distance function from source to v 4 previous[v] := undefined // Previous node in optimal path from source 5 dist[source] := 0 // Distance from source to source 6 Q := the set of all nodes in Graph // All nodes in the graph are unoptimized - thus are in Q 7 while Q is not empty: // The main loop 8 u := vertex in Q with smallest dist[] 9 if dist[u] = infinity: 10 break // all remaining vertices are inaccessible from source 11 remove u from Q 12 for each neighbor v of u: // where v has not yet been removed from Q. 13 alt := dist[u] + dist_between(u, v) 14 if alt < dist[v]: // Relax (u,v,a) 15 dist[v] := alt 16 previous[v] := u 17 return dist[] Thanks

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• What types of programming require practical category theory?

  - by Alexander Gruber

  Category theory has applications in theoretical computer science and obviously is central to abstract mathematics. I have heard that it also has direct practical applications in programming and software development. What type of programming is practical category theory necessary for? What do programmers use category theory to accomplish? Please note my use of "necessary" and "require" in this post. I realize that in some sense most programmers will benefit from having experience in different types of theories, but I am looking for direct applications where the usage of category theory is essential, i.e. if you didn't know category theory, you probably couldn't do it. Also, I'd like to clarify that by "what type of programming," I am hoping less for a broad answer like "functional programming," and more for specific applications like "writing bank software" or "making operating systems."

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• What should be contained in a game scene graph?

  - by Bunkai.Satori

  Would you help me to clarify, please, what what exactly should be contained within a game scene graph? See the following list, please: Game Actors? (obviously yes, all the objects changing state should be the major prart of the Scene Graph) Simple static game ojbects? (I mean ojects places in the background that do not get animated, neither do they collide) Game Triggers? Game Lights? Game Cameras? Weapon Bullets? Game Explosions and Special Effects? The above considered object types. Now to the coverage of the scene graph: Should a scene graph contain the whole game level map since the level start, or should it contain only the visible portion of the map? If the second is true, it would mean that scene graph would be continuously updated, by adding/removing game objects, as the player moves. However, containing only the visible are of the map obviously would be much faster to traverse and update.

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• Moving sprites on a graph in libGDX

  - by nosferat

  In my game I'd like to move sprites on a fixed path. Until this point I was trying to stick with the tools already provided by libGDX, like the Tiled map renderer classes so I'm looking for a solution nearly as convenient as that, e.g. I'd like to avoid creating the adjacency matrix by hand. Tiled has the functionality to add objects to the map but I'm not sure if I can use it for this purpose. Any idea?

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• When can I be sure a directed graph is acyclic?

  - by Daniel Scocco

  The definition for directed acyclic graph is this: "there is no way to start at some vertex v and follow a sequence of edges that eventually loops back to v again." So far so good, but I am trying to find some premises that will be simpler to test and that will also guarantee the graph is acyclic. I came up with those premises, but they are pretty basic so I am sure other people figured it out in the past (or they are incorrect). The problem is I couldn't find anything related on books/online, hence why I decided to post this question. Premise 1: If all vertices of the graph have an incoming edge, then the graph can't be acyclic. Is this correct? Premise 2: Assume the graph in question does have one vertex with no incoming edges. In this case, in order to have a cycle, at least one of the other vertices would need to have two or more incoming edges. Is this correct?

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• Merging similar graphs based solely on the graph structure?

  - by Buttons840

  I am looking for (or attempting to design) a technique for matching nodes from very similar graphs based on the structure of the graph*. In the examples below, the top graph has 5 nodes, and the bottom graph has 6 nodes. I would like to match the nodes from the top graph to the nodes in the bottom graph, such that the "0" nodes match, and the "1" nodes match, etc. This seems logically possible, because I can do it in my head for these simple examples. Now I just need to express my intuition in code. Are there any established algorithms or patterns I might consider? (* When I say based on the structure of the graph, I mean the solution shouldn't depend on the node labels; the numeric labels on the nodes are only for demonstration.) I'm also interested in the performance of any potential solutions. How well will they scale? Could I merge graphs with millions of nodes? In more complex cases, I recognize that the best solution may be subject to interpretation. Still, I'm hoping for a "good" way to merge complex graphs. (These are directed graphs; the thicker portion of an edge represents the head.)

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• Facebook Graph API - likes returns me an empty set...

  - by Vinch

  When I try to get all my "likes" (formerly fan pages) on Facebook Graph API, sometimes it returns me an empty set: { "data": [ ] } I tried with https://graph.facebook.com/me/likes?access_token=MY_ACCESS_TOKEN and with graph.facebook.com/vinch/likes?access_token=MY_ACCESS_TOKEN but the result is exactly the same (empty). Any idea of what it can be? I need it to know if a user likes (is fan of) a specific page.

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• Suggestions of the easiest algorithms for some Graph operations

  - by Nazgulled

  Hi, The deadline for this project is closing in very quickly and I don't have much time to deal with what it's left. So, instead of looking for the best (and probably more complicated/time consuming) algorithms, I'm looking for the easiest algorithms to implement a few operations on a Graph structure. The operations I'll need to do is as follows: List all users in the graph network given a distance X List all users in the graph network given a distance X and the type of relation Calculate the shortest path between 2 users on the graph network given a type of relation Calculate the maximum distance between 2 users on the graph network Calculate the most distant connected users on the graph network A few notes about my Graph implementation: The edge node has 2 properties, one is of type char and another int. They represent the type of relation and weight, respectively. The Graph is implemented with linked lists, for both the vertices and edges. I mean, each vertex points to the next one and each vertex also points to the head of a different linked list, the edges for that specific vertex. What I know about what I need to do: I don't know if this is the easiest as I said above, but for the shortest path between 2 users, I believe the Dijkstra algorithm is what people seem to recommend pretty often so I think I'm going with that. I've been searching and searching and I'm finding it hard to implement this algorithm, does anyone know of any tutorial or something easy to understand so I can implement this algorithm myself? If possible, with C source code examples, it would help a lot. I see many examples with math notations but that just confuses me even more. Do you think it would help if I "converted" the graph to an adjacency matrix to represent the links weight and relation type? Would it be easier to perform the algorithm on that instead of the linked lists? I could easily implement a function to do that conversion when needed. I'm saying this because I got the feeling it would be easier after reading a couple of pages about the subject, but I could be wrong. I don't have any ideas about the other 4 operations, suggestions?

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• algorithm to use to return a specific range of nodes in a directed graph

  - by GatesReign

  I have a class Graph with two lists types namely nodes and edges I have a function List<int> GetNodesInRange(Graph graph, int Range) when I get these parameters I need an algorithm that will go through the graph and return the list of nodes only as deep (the level) as the range. The algorithm should be able to accommodate large number of nodes and large ranges. Atop this, should I use a similar function List<int> GetNodesInRange(Graph graph, int Range, int selected) I want to be able to search outwards from it, to the number of nodes outwards (range) specified. So in the first function, I expect it to return the nodes placed in the blue box. The other function, if I pass the nodes as in the graph with a range of 1 and it starts at node 5, I want it to return the list of nodes that satisfy this criteria (placed in the orange box)

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• Graph theory in python

  - by Dan

  I was wondering how people deal with graph theory in python? How is a graph stored? Are there libraries for this? For example how would I input a graph and then find its Chromatic polynomial? Or its girth? Or the number of unique spanning trees? How about problems that involve edge weight like salesman problems? I don't need all of these answered, I'm just looking for a method or tool set that will be able to help me approach solve problems like this. Thanks, Dan

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• Generic Adjacency List Graph implementation

  - by DmainEvent

  I am trying to come up with a decent Adjacency List graph implementation so I can start tooling around with all kinds of graph problems and algorithms like traveling salesman and other problems... But I can't seem to come up with a decent implementation. This is probably because I am trying to dust the cobwebs off my data structures class. But what I have so far... and this is implemented in Java... is basically an edgeNode class that has a generic type and a weight-in the event the graph is indeed weighted. public class edgeNode<E> { private E y; private int weight; //... getters and setters as well as constructors... } I have a graph class that has a list of edges a value for the number of Vertices and and an int value for edges as well as a boolean value for whether or not it is directed. The brings up my first question, if the graph is indeed directed, shouldn't I have a value in my edgeNode class? Or would I just need to add another vertices to my LinkedList? That would imply that a directed graph is 2X as big as an undirected graph wouldn't it? public class graph { private List<edgeNode<?>> edges; private int nVertices; private int nEdges; private boolean directed; //... getters and setters as well as constructors... } Finally does anybody have a standard way of initializing there graph? I was thinking of reading in a pipe-delimited file but that is so 1997. public graph GenereateGraph(boolean directed, String file){ List<edgeNode<?>> edges; graph g; try{ int count = 0; String line; FileReader input = new FileReader("C:\\Users\\derekww\\Documents\\JavaEE Projects\\graphFile"); BufferedReader bufRead = new BufferedReader(input); line = bufRead.readLine(); count++; edges = new ArrayList<edgeNode<?>>(); while(line != null){ line = bufRead.readLine(); Object edgeInfo = line.split("|")[0]; int weight = Integer.parseInt(line.split("|")[1]); edgeNode<String> e = new edgeNode<String>((String) edges.add(e); } return g; } catch(Exception e){ return null; } } I guess when I am adding edges if boolean is true I would be adding a second edge. So far, this all depends on the file I write. So if I wrote a file with the following Vertices and weights... Buffalo | 18 br Pittsburgh | 20 br New York | 15 br D.C | 45 br I would obviously load them into my list of edges, but how can I represent one vertices connected to the other... so on... I would need the opposite vertices? Say I was representing Highways connected to each city weighted and un-directed (each edge is bi-directional with weights in some fictional distance unit)... Would my implementation be the best way to do that? I found this tutorial online Graph Tutorial that has a connector object. This appears to me be a collection of vertices pointing to each other. So you would have A and B each with there weights and so on, and you would add this to a list and this list of connectors to your graph... That strikes me as somewhat cumbersome and a little dismissive of the adjacency list concept? Am I wrong and that is a novel solution? This is all inspired by steve skiena's Algorithm Design Manual. Which I have to say is pretty good so far. Thanks for any help you can provide.

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• .NET implementation of planarity testing

  - by DixonD

  Is there any .NET implementation of any planarity testing algorithm like Boyer-Myrvold's or anyone else? I looked through the web but I didn't manage to find

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• How to represent a graph with multiple edges allowed between nodes and edges that can selectively disappear

  - by Pops

  I'm trying to figure out what sort of data structure to use for modeling some hypothetical, idealized network usage. In my scenario, a number of users who are hostile to each other are all trying to form networks of computers where all potential connections are known. The computers that one user needs to connect may not be the same as the ones another user needs to connect, though; user 1 might need to connect computers A, B and D while user 2 might need to connect computers B, C and E. Image generated with the help of NCTM Graph Creator I think the core of this is going to be an undirected cyclic graph, with nodes representing computers and edges representing Ethernet cables. However, due to the nature of the scenario, there are a few uncommon features that rule out adjacency lists and adjacency matrices (at least, without non-trivial modifications): edges can become restricted-use; that is, if one user acquires a given network connection, no other user may use that connection in the example, the green user cannot possibly connect to computer A, but the red user has connected B to E despite not having a direct link between them in some cases, a given pair of nodes will be connected by more than one edge in the example, there are two independent cables running from D to E, so the green and blue users were both able to connect those machines directly; however, red can no longer make such a connection if two computers are connected by more than one cable, each user may own no more than one of those cables I'll need to do several operations on this graph, such as: determining whether any particular pair of computers is connected for a given user identifying the optimal path for a given user to connect target computers identifying the highest-latency computer connection for a given user (i.e. longest path without branching) My first thought was to simply create a collection of all of the edges, but that's terrible for searching. The best thing I can think to do now is to modify an adjacency list so that each item in the list contains not only the edge length but also its cost and current owner. Is this a sensible approach? Assuming space is not a concern, would it be reasonable to create multiple copies of the graph (one for each user) rather than a single graph?

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• Graphviz or Dynagraph for Graph-manipulation Program?

  - by noahlavine

  I'm looking into writing a program that will show a graph to the user. The graph will change over time (the user should be able to right-click on a graph item and ask for more detail, which will pop out new bits of the graph), and the user might be able to drag parts of the graph around. I would ideally also like to be able to specify the relative layout of certain parts of the graph myself while leaving the overall layout up to a library, but that's not essential. I'm trying to decide on a graph layout library to use. As far as I can tell, the two leading candidates are Graphviz and Dynagraph. The Dynagraph website suggests that Graphviz is for drawing static graphs, and that Dynagraph was forked from Graphviz and contains algorithms for graphs that will be updated. It has a sample program called Dynasty that does exactly what I want. However, the Graphviz site contains an example program called Lefty which seems to do exactly what I want. Graphviz also seems to be much more widely used, judging by Google (and SO) results. Finally, I'd like to code the GUI part in a language like Python or Scheme, which makes me a bit hesitant to use C++ because I understand it's harder to interface that to interpreters. So my question is, which library is better for what I'm trying to do? Do they both have strong and weak points? Has one of them actually ceased development and is just leaving its website up to confuse me? (I've seen http://stackoverflow.com/questions/464000/simple-dynamic-graph-display-for-c and http://stackoverflow.com/questions/2376987/open-source-libraries-to-design-directed-graphs, but I can't tell whether they're right about the Graphviz or Dynagraph choice because of Lefty and also the language issue.)

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• Scalable / Parallel Large Graph Analysis Library?

  - by Joel Hoff

  I am looking for good recommendations for scalable and/or parallel large graph analysis libraries in various languages. The problems I am working on involve significant computational analysis of graphs/networks with 1-100 million nodes and 10 million to 1+ billion edges. The largest SMP computer I am using has 256 GB memory, but I also have access to an HPC cluster with 1000 cores, 2 TB aggregate memory, and MPI for communication. I am primarily looking for scalable, high-performance graph libraries that could be used in either single or multi-threaded scenarios, but parallel analysis libraries based on MPI or a similar protocol for communication and/or distributed memory are also of interest for high-end problems. Target programming languages include C++, C, Java, and Python. My research to-date has come up with the following possible solutions for these languages: C++ -- The most viable solutions appear to be the Boost Graph Library and Parallel Boost Graph Library. I have looked briefly at MTGL, but it is currently slanted more toward massively multithreaded hardware architectures like the Cray XMT. C - igraph and SNAP (Small-world Network Analysis and Partitioning); latter uses OpenMP for parallelism on SMP systems. Java - I have found no parallel libraries here yet, but JGraphT and perhaps JUNG are leading contenders in the non-parallel space. Python - igraph and NetworkX look like the most solid options, though neither is parallel. There used to be Python bindings for BGL, but these are now unsupported; last release in 2005 looks stale now. Other topics here on SO that I've looked at have discussed graph libraries in C++, Java, Python, and other languages. However, none of these topics focused significantly on scalability. Does anyone have recommendations they can offer based on experience with any of the above or other library packages when applied to large graph analysis problems? Performance, scalability, and code stability/maturity are my primary concerns. Most of the specialized algorithms will be developed by my team with the exception of any graph-oriented parallel communication or distributed memory frameworks (where the graph state is distributed across a cluster).

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• Why does NUnit ignore datapoints when using generics in a theory

  - by The Chairman

  I'm trying to make use of the TheoryAttribute, introduced in NUnit 2.5. Everything works fine as long as the arguments are of a defined type: [Datapoint] public double[,] Array2X2 = new double[,] { { 1, 0 }, { 0, 1 } }; [Theory] public void TestForArbitraryArray(double[,] array) { // ... } It does not work, when I use generics: [Datapoint] public double[,] Array2X2 = new double[,] { { 1, 0 }, { 0, 1 } }; [Theory] public void TestForArbitraryArray<T>(T[,] array) { // ... } NUnit gives a warning saying No arguments were provided. Why is that?

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• Excel Graph: How can I turn data below in to a 'time based' graph

  - by Mike

  In my spreadsheet I am collecting time periods when certain values have been changed. The user is restricted to 4 time periods. I would like to show the data based on thos time periods. I've included a mock up' of the data and the type of graph I would like to create. I've tried to create it for the last hour but am obviously missing something so thought I'd ask around. http://i48.tinypic.com/55lezr.jpg Many thanks for any help Mike P.S How do I make this image appear in the message and not as a link?

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