GraphView and subclasses of Graph

graph-tool
1

Hi! Thanks for graph-tools, it looks like a fab project!

I am toying around with a particular class of graphs for which I wrote a
subclass of `graph_tools.Graph`. It should be great to be able to use
`GraphView` for filtering (I'm implementing a divide-and-conquer
algorithm and want to recur on subgraphs), but it seems that those will
always behave as `Graph`, even if I instantiate them with an object of
my subclass.

Is there a better way to filter my graphs than writing a custom
`GraphView` subclass for it?

Cheers,
Patrick

2

I am toying around with a particular class of graphs for which I wrote a
subclass of `graph_tools.Graph`. It should be great to be able to use
`GraphView` for filtering (I'm implementing a divide-and-conquer
algorithm and want to recur on subgraphs), but it seems that those will
always behave as `Graph`, even if I instantiate them with an object of
my subclass.

Of course, GraphView is a subclass of Graph, not of your subclass.

Is there a better way to filter my graphs than writing a custom
`GraphView` subclass for it?

You can just use the set_edge/vertex_filter() methods of Graph.

Best,
Tiago

3

Hi Tiago, thanks for your prompt reply.

Quoting Tiago de Paula Peixoto (2016-09-21 10:35:39)

> I am toying around with a particular class of graphs for which I wrote a
> subclass of `graph_tools.Graph`. It should be great to be able to use
> `GraphView` for filtering (I'm implementing a divide-and-conquer
> algorithm and want to recur on subgraphs), but it seems that those will
> always behave as `Graph`, even if I instantiate them with an object of
> my subclass.

Of course, GraphView is a subclass of Graph, not of your subclass.

Sure I understand. I was hoping for some magic via mixins or the like
to make this work anyway..

> Is there a better way to filter my graphs than writing a custom
> `GraphView` subclass for it?

You can just use the set_edge/vertex_filter() methods of Graph.

Yes, but as far as I understand one cannot add multiple vertex-filters
right? I mean in order to solve my problem recursively on subgraphs,
I can of course set a filter and then recur. But then "setting a
filter" would amount to amending an already existing one...

Another related question: my algorithm could potentially parallelize the
recursive calls dealing with subgraphs.
If I use filters as you suggest to identify subgraphs, does the fact
that concurrent recursive calls handle the same graph object with
different filters cause any problems?

Could you point me towards example (python) code that utilizes parallel
threads? Or is this done only on a libboost level?

Thanks again for your help and apologies for my rather vague noob questions.
Best,
Patrick

BTW: I believe there is a typo in the docstring for `Graph.set_filters`:
  "Only the vertices and edges with value different than True are kept in
   the filtered graph"
Shouldn't it say values different from `False`, as in `set_vertex_filter`?

4

Is there a better way to filter my graphs than writing a custom
`GraphView` subclass for it?

You can just use the set_edge/vertex_filter() methods of Graph.et

Yes, but as far as I understand one cannot add multiple vertex-filters
right? I mean in order to solve my problem recursively on subgraphs,
I can of course set a filter and then recur. But then "setting a
filter" would amount to amending an already existing one...

You can just keep several copies of the mask, and compose them by hand:

    old_mask = g.get_vertex_filter()[0]
    mask = old_mask.copy()
    for v in sub_graph_vertices:
        mask[v] = False
    g.set_vertex_filter(mask)
    # now g does no longer contains those vertices

It is easy to do this recursively, and it amounts to what is actually done
with GraphView, although it is less elegant.

Another related question: my algorithm could potentially parallelize the
recursive calls dealing with subgraphs.
If I use filters as you suggest to identify subgraphs, does the fact
that concurrent recursive calls handle the same graph object with
different filters cause any problems?

Yes, it would cause problems, since you would have only one graph instance,
whereas with GraphView it would not.

However, this is an entirely moot point, since you cannot truly parallelize
things in (pure) Python. You would get nothing for it.

Could you point me towards example (python) code that utilizes parallel
threads? Or is this done only on a libboost level?

It can't be done in Pure python, only if you drop to C/C++. You can read
more here: GlobalInterpreterLock - Python Wiki

BTW: I believe there is a typo in the docstring for `Graph.set_filters`:
  "Only the vertices and edges with value different than True are kept in
   the filtered graph"
Shouldn't it say values different from `False`, as in `set_vertex_filter`?

Yes, it is a typo. Thanks for catching it.

Best,
Tiago

5

Quoting Tiago de Paula Peixoto (2016-09-21 17:45:32)