Home Wiki Blog Forum GEXF.net

Gephi forums

Community support

3D Graph - Functional brain network

Algorithms and parameters to put data in space

3D Graph - Functional brain network

Postby HamPlanet » 04 May 2013 19:07

Hi,

I need to make a 3D graph layout, which is different from existing 3D layouts (at least layouts i have seen) because it is just 3D grid - I dont need to compute edge lengths and change them, I know x,y,z coordinate of every node in the graph.

Graph will be Functional brain network - http://www.sharpbrains.com/wp-content/u ... in-Web.jpg , http://www.sciguru.com/news/science/sci ... etwork.jpg

I am working on the plugin which will take fmri data and make a Functional brain network, this is my first plugin but I have ben programming for 10 years, I just need to know the best way to do this.

THANKS

p.s.: Sorry for bad english :(
HamPlanet
 
Posts: 10
Joined: 04 May 2013 18:51

Re: 3D Graph - Functional brain network

Postby francis_flavin » 05 May 2013 21:20

Hi HamPlanet,

Wow, so you're working on a 3-space graph layout plugin? I'm thrilled to hear that--it will be a great addition to the Gephi platform.

I'm not sure if you're asking how to build a plug-in in general or what sort of design for a plugin might work well.

If you're looking for some general info on how to design and share plugins with the Gephi community, you can check this out:

https://marketplace.gephi.org/faq/

If you're looking for what sort of functionality might work well for a 3-space layout algorithm, I can offer a few suggestions.

First, there used to be a very nice 3-space graph layout plugin, but I think it has since disappeared from the Gephi plugin marketplace. If you can find it, that might be a helpful place to start. I think it was called "Transformation" or something like that.

That plugin could do the following:

PLACE NODES IN 3-SPACE: Set the x, y, and z values for a graph based on any numeric column in the Data Lab's nodes table. Of course, a user didn't have to populate all three coordinates; the user could choose to populate whichever of the 3 coordinates that he or she wanted.

ROTATE A GRAPH AROUND ANY AXIS: The user could put a value (in degrees) in the layout dialog for rotating around the x, y, and z axes. When the user clicked "run" the plugin would rotate the graph accordingly. This can produce a really cool effect. For example, a user could enter "5" for the Rotate(Y) value and "0.2" for the Rotate(X) value and then keep hitting the "run" button and the graph would rotate in 3-space. This can produce results that are visually stunning.

SKEW A GRAPH IN 3-SPACE: The user could enter a number that would serve as a coefficient for skewing the graph in the x, y, and z axes. This, too, can produce some cool effects.


Oh, I just did a Google search on the plugin and I think this the old plugin that I mentioned above:

https://gephi.org/plugins/geometrictransformation/

Maybe there's a way to find it and use it as guidance.

Thanks, HamPlanet. Best of luck in your project. It's a great idea and I hope you share your plugin with the Gephi community.


Francis

P.S. Your English is quite good!
francis_flavin
 
Posts: 55
Joined: 21 Jan 2012 19:34
Location: Washington, DC, USA

Re: 3D Graph - Functional brain network

Postby HamPlanet » 06 May 2013 21:52

Thanks, that is exactly what i was looking for.

Main purpose of my plugin will be construction of functional brain network (which is a graph) from fMRI data, but because in fMRI data (http://mialab.mrn.org/software/fit/imag ... fusion.jpg) each voxel have sepcific x,y,z position - nodes in my graph must preserve them (so graph will look more like brain).

Here is good example - http://blog.senc.es/wp-content/uploads/ ... etwork.jpg

Google image serach of functional brain network - https://www.google.sk/search?q=function ... sgbq_IHYBg

And i already started programming plugin and its pretty easy, I know java well so in the meantime I don't need help with that.

Thanks again :)
HamPlanet
 
Posts: 10
Joined: 04 May 2013 18:51

Re: 3D Graph - Functional brain network

Postby seinecle » 06 May 2013 22:51

Hi,

Great project!!

Can you please post an announcement here (on this thread), so that we can make some buzz when you're finished?

Best,

Clement
http://www.clementlevallois.net
Gephi tutorials and personalized trainings: http://www.clementlevallois.net/training.html
Join the Gephi Facebook group for help and support: https://www.facebook.com/groups/gephi/
User avatar
seinecle
Gephi Community Support
 
Posts: 527
Joined: 08 Feb 2010 17:55
Location: Lyon, France

Re: 3D Graph - Functional brain network

Postby HamPlanet » 06 May 2013 23:43

Sure, i can even post here my progress but it will be pretty slow because it is my master thesis and I have a whole year to finish it.
HamPlanet
 
Posts: 10
Joined: 04 May 2013 18:51

Re: 3D Graph - Functional brain network

Postby francis_flavin » 06 May 2013 23:54

Good things are worth the wait....

And, best of luck on your thesis!
francis_flavin
 
Posts: 55
Joined: 21 Jan 2012 19:34
Location: Washington, DC, USA

Re: 3D Graph - Functional brain network

Postby HamPlanet » 29 Sep 2013 22:19

I started working on my project again, and i realized that i need API not the plugin, because when I am creating nodes i need to set their X, Y, Z... and call all the methodes from my code...
HamPlanet
 
Posts: 10
Joined: 04 May 2013 18:51

Re: 3D Graph - Functional brain network

Postby seinecle » 30 Sep 2013 20:47

Hi,

You can now visualize a graph in 3D: https://marketplace.gephi.org/plugin/force-atlas-3d/

And you can use the library from your preferred programming language to create a network with x, y z coordinates in the gexf format:

http://gexf.net/format/ (check "tools" in the right column).

Best,

Clement
http://www.clementlevallois.net
Gephi tutorials and personalized trainings: http://www.clementlevallois.net/training.html
Join the Gephi Facebook group for help and support: https://www.facebook.com/groups/gephi/
User avatar
seinecle
Gephi Community Support
 
Posts: 527
Joined: 08 Feb 2010 17:55
Location: Lyon, France

Re: 3D Graph - Functional brain network

Postby HamPlanet » 07 Dec 2013 22:07

Hi,

i have some problems with understanding tables and filters. I want to iterate over all rows in node table and create edges based on some attributes located in node table. I used this method Attributes[] getTableAttributeRows(AttributeTable table) ( http://gephi.org/docs/api/org/gephi/dat ... teTable%29 ) to obtain values stored in node table, but then i found out that it returns all rows of table, but i only want rows that are displayed in data laboratory - i am using filters before this step.

Thanks.
HamPlanet
 
Posts: 10
Joined: 04 May 2013 18:51

Re: 3D Graph - Functional brain network

Postby seinecle » 08 Dec 2013 00:40

Hi,
Can you please resend this post as a new thread?
Thanks
Clement
http://www.clementlevallois.net
Gephi tutorials and personalized trainings: http://www.clementlevallois.net/training.html
Join the Gephi Facebook group for help and support: https://www.facebook.com/groups/gephi/
User avatar
seinecle
Gephi Community Support
 
Posts: 527
Joined: 08 Feb 2010 17:55
Location: Lyon, France

Next

Return to Layouts

Who is online

Users browsing this forum: No registered users and 0 guests

cron