3D Graph - Functional brain network
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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
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
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Re: 3D Graph - Functional brain network
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!
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!
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Re: 3D Graph - Functional brain network
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
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
Re: 3D Graph - Functional brain network
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
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
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Re: 3D Graph - Functional brain network
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.
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Re: 3D Graph - Functional brain network
Good things are worth the wait....
And, best of luck on your thesis!
And, best of luck on your thesis!
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Re: 3D Graph - Functional brain network
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...
Re: 3D Graph - Functional brain network
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
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
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Re: 3D Graph - Functional brain network
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.
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.
Re: 3D Graph - Functional brain network
Hi,
Can you please resend this post as a new thread?
Thanks
Clement
Can you please resend this post as a new thread?
Thanks
Clement