Gephi forums

Re: Using RadialAxisLayout in toolkit?

2012-04-16T01:10:51+01:00

kinjal wrote:I have a quick question: I have a network I want to visualise using radial axis; when I group nodes according to degree I get axes but if I sort according to modularity I only get a circular layout and the axes disappear. I want my modules to be sorted as axes. Any idea how I can fix this?
Thanks

Hi Kinjal,
Any time I have seen this it is the result of each node being ranked separately. I would recommend you check the modularity in the data laboratory to see if this is the case.

Also, it probably makes more sense to create a new thread rather than post at the end of multuple old threads.

Thanks,
Matt

Statistics:Posted by mgroeninger — 16 Apr 2012 01:10

Re: Using RadialAxisLayout in toolkit?

2012-04-11T18:34:36+01:00

I have a quick question: I have a network I want to visualise using radial axis; when I group nodes according to degree I get axes but if I sort according to modularity I only get a circular layout and the axes disappear. I want my modules to be sorted as axes. Any idea how I can fix this?
Thanks

Statistics:Posted by kinjal — 11 Apr 2012 18:34

Re: Using RadialAxisLayout in toolkit?

2011-10-09T13:19:10+01:00

I guess there is no problem using it with the GUI because properties are reset.
But maybe do a reset in the constructor just to avoid null intial values.

Eduardo

Statistics:Posted by eduramiba — 09 Oct 2011 13:19

Re: Using RadialAxisLayout in toolkit?

2011-10-06T06:09:02+01:00

Sorry to post on a topic that is so old but I haven't been paying attention.

Mark, did you get this working? And is there any way I can see a peek at what you are doing? (I'm curious about the uses people find for the Radial Axis layout.)

Eduardo, is there anything my plugin should be doing to check for unset/null properties? (I've done a bit, but I have not been thorough.)

Statistics:Posted by mgroeninger — 06 Oct 2011 06:09

Re: Using RadialAxisLayout in toolkit?

2011-08-11T13:21:07+01:00

Hi,
The NPE is probably because some properties are null.
Call it always in the exact same order as here http://wiki.gephi.org/index.php/Toolkit_-_Layout_graph:
initAlgo right after setModel
Reset properties (or set every property with a desired value)
Run the algorithm

Eduardo

Statistics:Posted by eduramiba — 11 Aug 2011 13:21

Re: Using RadialAxisLayout in toolkit?

2011-08-11T00:30:10+01:00

eduramiba wrote:Looking at RadialAxisLayout code, you have to call initAlgo() first so it gets the current graph from the graphModel. Indeed, initAlgo() should always be called with any layout so I edited the example http://wiki.gephi.org/index.php/Toolkit_-_Layout_graph
You downloaded CircularLayout code to use it with gephi toolkit, I guess?

Eduardo, I've tried it with initAlgo() as well and get the same results (NPE).

Here's a simple test case:

CODE:

    //Init a project - and therefore a workspace    ProjectController pc = Lookup.getDefault().lookup(ProjectController.class);    pc.newProject();    Workspace workspace = pc.getCurrentWorkspace();    //Get a graph model - it exists because we have a workspace    GraphModel graphModel = Lookup.getDefault().lookup(GraphController.class).getModel();    //Create three nodes    Node n0 = graphModel.factory().newNode("n0");    n0.getNodeData().setLabel("Node 0");    Node n1 = graphModel.factory().newNode("n1");    n1.getNodeData().setLabel("Node 1");    Node n2 = graphModel.factory().newNode("n2");    n2.getNodeData().setLabel("Node 2");    //Create three edges    Edge e1 = graphModel.factory().newEdge(n1, n2, 1f, true);    e1.getEdgeData().setLabel("Edge 1");    Edge e2 = graphModel.factory().newEdge(n0, n2, 2f, true);    e2.getEdgeData().setLabel("Edge 2");    Edge e3 = graphModel.factory().newEdge(n2, n0, 2f, true);   //This is e2's mutual edge    e3.getEdgeData().setLabel("Edge 3");    //Append as a Directed Graph    DirectedGraph directedGraph = graphModel.getDirectedGraph();    directedGraph.addNode(n0);    directedGraph.addNode(n1);    directedGraph.addNode(n2);    directedGraph.addEdge(e1);    directedGraph.addEdge(e2);    directedGraph.addEdge(e3);    RadialAxisLayout layout = new RadialAxisLayout(new RadialAxisLayoutBuilder(), 10, false);    layout.setGraphModel(graphModel);    if (layout.canAlgo()) {      layout.initAlgo();      for (int i = 0; i < 100 && layout.canAlgo(); i++) {        layout.goAlgo();      }      layout.endAlgo();    }

Yes, I'm using the latest version of the Circular Layout plugin, downloaded yesterday.

Statistics:Posted by markwoon — 11 Aug 2011 00:30

Re: Using RadialAxisLayout in toolkit?

2011-08-10T15:41:46+01:00

Hi,

The RadialAxisLayout is a plugin so not directly available in Gephi. See this page to use a plugin in the toolkit.

Statistics:Posted by admin — 10 Aug 2011 15:41

Re: Using RadialAxisLayout in toolkit?

2011-08-10T14:48:48+01:00

Hi,
Looking at RadialAxisLayout code, you have to call initAlgo() first so it gets the current graph from the graphModel. Indeed, initAlgo() should always be called with any layout so I edited the example http://wiki.gephi.org/index.php/Toolkit_-_Layout_graph
You downloaded CircularLayout code to use it with gephi toolkit, I guess?

Eduardo

Statistics:Posted by eduramiba — 10 Aug 2011 14:48

Using RadialAxisLayout in toolkit?

2011-08-10T10:15:18+01:00

Does anyone know if it's possible to use the RadialAxisLayout (from the Circular Layout plugin) from the toolkit?

I'm getting:

CODE:

java.lang.NullPointerExceptionat org.gephi.layout.plugin.circularlayout.radialaxislayout.RadialAxisLayout.goAlgo(RadialAxisLayout.java:121)

When I try to run:

CODE:

        RadialAxisLayout layout = new RadialAxisLayout(new RadialAxisLayoutBuilder(), 10, false);        layout.setGraphModel(graphModel);        if (layout.canAlgo()) {          for (int i = 0; i < 100 && layout.canAlgo(); i++) {            layout.goAlgo();          }        }

I'm new to Gephi, so it's entirely possible I'm just not calling the layout properly. I'm just basing this of the example for running the YifanHuLayout. If this is wrong, how should I be invoking the layout to run on a graph?

Thanks.

Statistics:Posted by markwoon — 10 Aug 2011 10:15