Networkx export graph to graphml or gexf

[Semanti Basu]

My networkx graph has python objects as nodes. Is there a way to write the graph to any standard form? I tried to use the write_gexf, read_graphml, generate_graphml and other functions. However these do not seem to correctly load the graph.

[Dan Schult]

Actually, ;) all networkx graphs have python objects as nodes. :) (everything in python is an object)

So, you need to find a format that supports the features of YOUR python objects. 

If you create anything python-dependent in your node objects, it is unlikely that these formats can write that information.

You might consider relabeling your nodes to integers (https://networkx.github.io/documentation/stable/reference/relabel.html)

and then storing that graph in a standard format. The node object information would need to be stored another way. 

On Sat, Jun 29, 2019 at 9:27 AM Semanti Basu <renia...@gmail.com> wrote:

My networkx graph has python objects as nodes. Is there a way to write the graph to any standard form? I tried to use the write_gexf, read_graphml, generate_graphml and other functions. However these do not seem to correctly load the graph.

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[Semanti Basu]

Thanks Dan! If I could relabel my nodes to integers and store the node object information in a different way. But then I would not be able load a networkx graph directly using read_gexf , right? I would need a custom reader?

On Friday, June 28, 2019 at 8:39:03 PM UTC-4, Dan Schult wrote:

Actually, ;) all networkx graphs have python objects as nodes. :) (everything in python is an object)

So, you need to find a format that supports the features of YOUR python objects. 

If you create anything python-dependent in your node objects, it is unlikely that these formats can write that information.

You might consider relabeling your nodes to integers (https://networkx.github.io/documentation/stable/reference/relabel.html)

and then storing that graph in a standard format. The node object information would need to be stored another way. 

On Sat, Jun 29, 2019 at 9:27 AM Semanti Basu <renia...@gmail.com> wrote:

My networkx graph has python objects as nodes. Is there a way to write the graph to any standard form? I tried to use the write_gexf, read_graphml, generate_graphml and other functions. However these do not seem to correctly load the graph.

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[Dan Schult]

If you just want to write the graph to a file and reload it into NetworkX, then you probably want to use Python's "pickle" library.

If you want to read it into other non-python programs, then look to markup languages like gml, graphml, etc.

Using pickle will store your python object nodes without any issues.

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