- 14 Apr, 2008 1 commit
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Tiago Peixoto authored
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- 10 Apr, 2008 1 commit
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Tiago Peixoto authored
The whole histogram code has been redone, and the code has been simplified. The three-point vertex-edge-vertex correlation has been scrapped, since it's not frequently used, and would make compilation even more expensive. This also adds some missing files to the generation routine.
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- 06 Apr, 2008 1 commit
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Tiago Peixoto authored
It is now much simpler, and works better.
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- 04 Apr, 2008 1 commit
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Tiago Peixoto authored
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- 27 Mar, 2008 3 commits
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Tiago Peixoto authored
This adds the graph_tool.test module, which can be run with graph_tool.test.run()
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Tiago Peixoto authored
Put the run_action function in a separate submodule, and make it work properly with the new code.
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Tiago Peixoto authored
Now graphml files properly contain all the supported value types, which are all perfectly preserved when read (floating point data is now saved in hexadecimal format). Several other improvements were made, such as the ability to read and write to python file-like objects. It is also now possible to have arbitrary python object properties, and store them persistently (which is done internally with the pickling interface). vector<bool> was totally abolished, since its implementation is quite broken. See: http://www.gotw.ca/publications/N1211.pdf and http://www.gotw.ca/publications/N1185.pdf Now a uint8_t (aka. char) is used in graph properties instead of a bool. Graph types can now be fully pickled (this may not be feasible memory-wise if the graph is too large, since the whole XML representation is dumped to a string before it is saved on disc).
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- 17 Feb, 2008 1 commit
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Tiago Peixoto authored
This commit splits libraph_tool into different libraries: - libgraph_tool_core - libgraph_tool_clustering (*) - libgraph_tool_community (*) - libgraph_tool_correlations (*) - libgraph_tool_distance (*) - libgraph_tool_generation (*) - libgraph_tool_layout (*) - libgraph_tool_misc (*) - libgraph_tool_stats (*) It also adds the python sub-module 'test', which provides extensive unit testing of the core functionality. The core library is fully functional and all test pass successfully. (*) -> module needs to be ported to new refactoring, and does not yet build
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- 10 Feb, 2008 1 commit
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Tiago Peixoto authored
This is a huge commit which completely refactors the metaprogramming engine which generates and selects (at run time) the graph view type and the desired algorithm implementation (template instantiation) that runs on it. Things are laid out now as following. There exists a main underlying graph type (GraphInterface::multigraph_t) and several other template classes that mask it some way or another, in a hierarchic fashion: multigraph_t -> filtered_graph (edges only, vertices only, both) | | | | | | | | |-------(reversed_graph)--------|-----------|-----------| | | | | \------(UndirectedAdaptor)------------------------------/ The filtered_graph filters out edges and/or vertices from the graph based on some scalar boolean property. The reversed_graph reversed the direction of the edges and, finally, the UndirectedAdaptor treats the original directed graphs as undirected, transversing the in- and out-edges of each vertex indifferently. Thus, the total number of graph view types is 12. (The option --disable-graph-filtering can be passed to the configure script, which will disable graph filtering altogether and bring the total number down to 3, to reduce compile time and memory usage) In general, some specific algorithm, implemented as a template function object, needs to be instantiated for each of those types. Furthermore, the algorithm may also depend on other types, such as specific property_maps. Thus, the following scheme is used: struct my_algorithm // algorithm to be implemented { template <class Graph, class PropertyMap> void operator()(Graph *g, PropertyMap p, double& result) const { // ... } }; // in order for the above code to be instantiated at compile time // and selected at run time, the run_action template function object // is used from a member function of the GraphInterface class: double GraphInterface::MyAlgorithm(string prop_name) { double result; boost::any vprop = prop(property, _vertex_index, _properties); run_action<>()(*this, bind<void>(my_algorithm(), _1, _2, var(result)), vertex_scalar_properties())(vprop); return result; } The whole code was changed to reflect this scheme, but now things are more centralized and less ad-hoc code needed to be written. Unfortunately, due to GCC's high memory usage during template instantiations, some of the code (namely all the degree correlation things) had to be split in multiple compilation units... Maybe this will change in the future if GCC gets optimized. This commit also touches other parts of code. More specifically, the way filtering gets done is very different. Now we only filter on boolean properties, and with the above scheme, the desired implementation runs with the correct chosen type, and no implicit type conversions should ever happen, which would have a bad impact on performance.
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- 21 Dec, 2007 2 commits
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Tiago Peixoto authored
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Tiago Peixoto authored
Everything was moved into the graph_tool directory, which should have, after installation, the following structure: graph_tool/ Top-level package __init__.py Initialize the graph_tool package libgraph_tool.so libgraph_tool submodule libgraph_tool.la libtool file for libgraph_tool include/ C++ include files for dynamically compiled code
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- 17 Dec, 2007 1 commit
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Tiago Peixoto authored
Some visibility voodoo is necessary to ensure that RTTI work properly across DSO boundaries, which is necessary to properly handle dynamic property maps and such. Additionally, the action template must have a different name each time the action code changes, to avoid additional weirdness. This also adds some other utility functions/typedefs to make writing "inline" c++ code easier.
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- 14 Dec, 2007 2 commits
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Tiago Peixoto authored
add_edge_property() should return a edge property not a vertex_property
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Tiago Peixoto authored
It is now possible to run arbitrary "inline" C++ code from python, using scipy.weave, as such: g = graph_tool.Graph() g.load("foo.xml") value = 2.0 g.run_action('cout << num_vertices(g) << " " << value << endl;', ["value"]); The code gets compiled the first time, and is reused after that. Python local and global variables can be passed to C++, as shown above, by specifying a list of passed variables as the second argument.
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- 13 Dec, 2007 1 commit
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Tiago Peixoto authored
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- 06 Dec, 2007 2 commits
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Tiago Peixoto authored
The graph object passed to the edit function is now a instance of the Graph class which wraps GraphInterface, not a GraphInterface instance.
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Tiago Peixoto authored
Graphs can now be loaded "lazily" with the lazy_load() function, which works just like load(), but doesn't actually load the graph, which is delayed until the graph is accessed for the first time, e.g. import graph_tool g = graph_tool.Graph() g.lazy_load("example.xml") g.number_of_vertices() # <- the graph is only loaded here
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- 03 Dec, 2007 6 commits
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Tiago Peixoto authored
Move remaining parallelism check out of the outer/inner loops and into the parallel_check() function.
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Ale Abdo authored
3) missing parallel edge check in uncorrelated strategy 2) "_in()" for target and source of "target swap edge" 1) order of arguments of swap_edge_triad::parallel_check melodrama time... "premature optimization is the root of all evil" "careless abstraction are the fruits of its tree"
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Tiago Peixoto authored
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Tiago Peixoto authored
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Tiago Peixoto authored
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Tiago Peixoto authored
The check for parallel edges was cleaned up and abstracted into a function, and other minor things were changed. Code comments were added to places where it might have been hard to understand.
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- 30 Nov, 2007 2 commits
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Tiago Peixoto authored
Improve formatting of src/graph/graph_rewiring.cc (line breaks at column 80, typedefs, trailing whitespace removal, etc) Conflicts: src/graph-tool src/graph/graph_bind.cc
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Tiago Peixoto authored
Property maps can now be obtained as such: weight = g.edge_properties['weight'] print weight[v] # v is a Vertex object weight[v] = 2.0 # and so on... The list of properties is obtained from g.vertex_properties, g.edge_properties and g.graph_properties, which can be read as dictionaries. The last can be set also, as such: g.graph_properties = {foo:"bar", baz:42} Functions to add and remove vertices or adges were also added (add_{vertex|edge}, remove_{vertex|edgge}). Vertex and Edge types can also now be printed for convenience, as such: for v in g.vertices(): print v for e in g.edges(): print e which results, for example, in: 0 1 2 3 4 5 6 (0,1) (1,2) (2,6) (3,4) (4,5) (4,2) (5,6) (6,1) (this also adds the forgotten graph_tool.py file, which was previously on .gitignore)
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- 28 Nov, 2007 1 commit
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Ale Abdo authored
Major changes to both correlated and uncorrelated rewiring code. Both cases are now functional and use iterative shuffling. Uncorrelated picks edges to rewire directly, correlated picks vertices in order to choose edges.
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- 26 Nov, 2007 3 commits
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Tiago Peixoto authored
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Tiago Peixoto authored
Vertices and edges can be accessed from the graph class, as such: import graph_tool g = graph_tool.Graph() for v in g.vertices(): for e in v.out_edges(): # do something... Additionally, the --edit-{vertex|edge|graph}-property was ported to the new interface, and is working again, as it used to. The Vertex and Edge class no longer have the 'get_property' and 'set_property' method. They'll be replaced by a new method of accessing property maps.
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- 20 Nov, 2007 1 commit
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Tiago Peixoto authored
The program was split in two parts: 1. A python module, graph_tool.py, which encapsulates the graph manipulation under a Graph class. Now the following can be done: import graph_tool g1 = graph_tool.Graph() g2 = graph_tool.Graph() g1.load("foo.xml") g2.load("bar.xml") print g1.number_of_vertices(), g2.number_of_vertices() 2. A standalone command line tool, graph-tool, which imports graph_tool.py, and exposes the Graph methods as command line options. The whole command line engine was thus (once again) entirely rewritten. It is now Crack-Free™, and simply mirrors the methods of the Graph class as command line options, using, for this, the beauty of function decorators. It classifies now, I believe, as Pythonic™.
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- 11 Nov, 2007 1 commit
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Tiago Peixoto authored
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- 10 Nov, 2007 2 commits
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Tiago Peixoto authored
This fixes a bug where properties with 'long long' types were not handled properly through the python interface.
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Tiago Peixoto authored
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- 05 Nov, 2007 1 commit
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Ale Abdo authored
Several changes in the random rewiring code, making it fully functional for the correlated case. The reshuffling operations lag in efficiency, even though already the algorithm runs in little time.
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- 04 Nov, 2007 4 commits
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Ale Abdo authored
Merge branch 'master' of git://finn.forked.de/~count0/stuff/workspace/graph-tool into rewiring-merge
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Tiago Peixoto authored
Line breaks at column 80 were added, and all trailing whitespace was deleted. Code comments were modified and some more were added.
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Tiago Peixoto authored
It should be 'size_t' instead of 'long'.
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- 27 Oct, 2007 1 commit
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Ale Abdo authored
bool entries in option random-rewire were stated as string, causing graph-tool to crash before loading.
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- 24 Oct, 2007 1 commit
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Ale Abdo authored
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