graph_bind.cc 14.5 KB
Newer Older
Tiago Peixoto's avatar
Tiago Peixoto committed
1
2
// graph-tool -- a general graph modification and manipulation thingy
//
Tiago Peixoto's avatar
Tiago Peixoto committed
3
// Copyright (C) 2006-2013 Tiago de Paula Peixoto <tiago@skewed.de>
Tiago Peixoto's avatar
Tiago Peixoto committed
4
5
6
//
// This program is free software; you can redistribute it and/or
// modify it under the terms of the GNU General Public License
Tiago Peixoto's avatar
Tiago Peixoto committed
7
// as published by the Free Software Foundation; either version 3
Tiago Peixoto's avatar
Tiago Peixoto committed
8
9
10
11
12
13
14
15
// of the License, or (at your option) any later version.
//
// This program is distributed in the hope that it will be useful,
// but WITHOUT ANY WARRANTY; without even the implied warranty of
// MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
// GNU General Public License for more details.
//
// You should have received a copy of the GNU General Public License
16
17
// along with this program. If not, see <http://www.gnu.org/licenses/>.

18
19
#include <boost/python.hpp>
#include <boost/python/suite/indexing/vector_indexing_suite.hpp>
20
#include "bytesobject.h"
21

22
#define NUMPY_EXPORT
23
24
25
#include "numpy_bind.hh"

#include "graph.hh"
26
#include "graph_python_interface.hh"
27
#include "graph_util.hh"
Tiago Peixoto's avatar
Tiago Peixoto committed
28

29
30
#include "random.hh"

Tiago Peixoto's avatar
Tiago Peixoto committed
31
32
#ifdef HAVE_SCIPY // integration with scipy weave
#include "weave/scxx/object.h"
33
34
35
36
#include "weave/scxx/list.h"
#include "weave/scxx/tuple.h"
#include "weave/scxx/dict.h"
#include "weave/scxx/str.h"
Tiago Peixoto's avatar
Tiago Peixoto committed
37
38
#endif

Tiago Peixoto's avatar
Tiago Peixoto committed
39
40
41
42
43
using namespace std;
using namespace graph_tool;
using namespace boost;
using namespace boost::python;

44
struct LibInfo
Tiago Peixoto's avatar
Tiago Peixoto committed
45
{
46
47
48
49
50
51
    string GetName()      const {return PACKAGE_NAME;}
    string GetAuthor()    const {return AUTHOR;}
    string GetCopyright() const {return COPYRIGHT;}
    string GetVersion()   const {return VERSION " (commit " GIT_COMMIT
                                        ", " GIT_COMMIT_DATE ")";}
    string GetLicense()   const {return "GPL version 3 or above";}
Tiago Peixoto's avatar
Tiago Peixoto committed
52
    string GetCXXFLAGS()  const {return CPPFLAGS " " CXXFLAGS " " LDFLAGS;}
53
54
    string GetInstallPrefix() const {return INSTALL_PREFIX;}
    string GetPythonDir() const {return PYTHON_DIR;}
Tiago Peixoto's avatar
Tiago Peixoto committed
55
56
57
58
59
60
    string GetGCCVersion() const
    {
        stringstream s;
        s << __GNUC__ << "." << __GNUC_MINOR__ << "." <<  __GNUC_PATCHLEVEL__;
        return s.str();
    }
Tiago Peixoto's avatar
Tiago Peixoto committed
61
62
};

63
64
template <class ValueType>
struct vector_from_list
Tiago Peixoto's avatar
Tiago Peixoto committed
65
{
66
    vector_from_list()
Tiago Peixoto's avatar
Tiago Peixoto committed
67
    {
68
        converter::registry::push_back
69
            (&convertible, &construct,
70
             boost::python::type_id<vector<ValueType> >());
Tiago Peixoto's avatar
Tiago Peixoto committed
71
72
73
74
    }

    static void* convertible(PyObject* obj_ptr)
    {
75
76
        handle<> x(borrowed(obj_ptr));
        object o(x);
77
78
79
80
81
82
83
        size_t N = len(o);
        for (size_t i = 0; i < N; ++i)
        {
            extract<ValueType> elem(o[i]);
            if (!elem.check())
                return 0;
        }
84
        return obj_ptr;
Tiago Peixoto's avatar
Tiago Peixoto committed
85
86
    }

87
    static void construct(PyObject* obj_ptr,
88
                          converter::rvalue_from_python_stage1_data* data)
89
    {
90
91
        handle<> x(borrowed(obj_ptr));
        object o(x);
92
93
94
95
        vector<ValueType> value;
        size_t N = len(o);
        for (size_t i = 0; i < N; ++i)
            value.push_back(extract<ValueType>(o[i]));
96
        void* storage =
97
            ( (boost::python::converter::rvalue_from_python_storage
98
99
               <vector<ValueType> >*) data)->storage.bytes;
        new (storage) vector<ValueType>(value);
100
        data->convertible = storage;
Tiago Peixoto's avatar
Tiago Peixoto committed
101
102
103
    }
};

104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
template <class ValueType>
bool vector_equal_compare(const vector<ValueType>& v1,
                          const vector<ValueType>& v2)
{
    if (v1.size() != v2.size())
        return false;
    for (size_t i = 0; i < v1.size(); ++i)
    {
        if (v1[i] != v2[i])
            return false;
    }
    return true;
}

template <class ValueType>
bool vector_nequal_compare(const vector<ValueType>& v1,
                           const vector<ValueType>& v2)
{
    return !vector_equal_compare(v1,v2);
}

125
struct export_vector_types
Tiago Peixoto's avatar
Tiago Peixoto committed
126
{
127
128
    template <class ValueType>
    void operator()(ValueType) const
Tiago Peixoto's avatar
Tiago Peixoto committed
129
    {
130
131
132
133
        string type_name = get_type_name<>()(typeid(ValueType));
        if (type_name == "long double")
            type_name = "long_double";
        string name = "Vector_" + type_name;
134
135
        class_<vector<ValueType> > vc(name.c_str());
        vc.def(vector_indexing_suite<vector<ValueType> >())
136
137
            .def("__eq__", &vector_equal_compare<ValueType>)
            .def("__ne__", &vector_nequal_compare<ValueType>);
138
        wrap_array(vc, typename mpl::has_key<numpy_types,ValueType>::type());
139
        vector_from_list<ValueType>();
Tiago Peixoto's avatar
Tiago Peixoto committed
140
    }
141
142
143
144
145
146
147
148
149
150
151

    template <class ValueType>
    void wrap_array(class_<vector<ValueType> >& vc, mpl::true_) const
    {
        vc.def("get_array", &wrap_vector_not_owned<ValueType>);
    }

    template <class ValueType>
    void wrap_array(class_<vector<ValueType> >& vc, mpl::false_) const
    {
    }
152
};
Tiago Peixoto's avatar
Tiago Peixoto committed
153

154
155
// exception translation
template <class Exception>
Tiago Peixoto's avatar
Tiago Peixoto committed
156
void graph_exception_translator(const Exception& e)
157
{
Tiago Peixoto's avatar
Tiago Peixoto committed
158
159
160
161
162
163
164
165
    PyObject* error;
    if (is_same<Exception, GraphException>::value)
        error = PyExc_RuntimeError;
    if (is_same<Exception, IOException>::value)
        error = PyExc_IOError;
    if (is_same<Exception, ValueException>::value)
        error = PyExc_ValueError;

166
    PyObject* message = PyUnicode_FromString(e.what());
Tiago Peixoto's avatar
Tiago Peixoto committed
167
168
    PyObject_SetAttrString(error, "message", message);
    PyErr_SetString(error, e.what());
169
}
Tiago Peixoto's avatar
Tiago Peixoto committed
170

171
172
173
174
void raise_error(const string& msg)
{
    throw GraphException(msg);
}
Tiago Peixoto's avatar
Tiago Peixoto committed
175

176
177
template <class T1, class T2>
struct pair_to_tuple
Tiago Peixoto's avatar
Tiago Peixoto committed
178
{
179
    static PyObject* convert(const pair<T1,T2>& p)
Tiago Peixoto's avatar
Tiago Peixoto committed
180
    {
181
182
        boost::python::tuple t = boost::python::make_tuple(p.first,p.second);
        return incref(t.ptr());
Tiago Peixoto's avatar
Tiago Peixoto committed
183
184
185
    }
};

186
187
188
189
190
191
192
193
194
195
196
197
198
template <class T1, class T2>
struct pair_from_tuple
{
    pair_from_tuple()
    {
        converter::registry::push_back(&convertible, &construct,
                                       boost::python::type_id<pair<T1,T2> >());
    }

    static void* convertible(PyObject* obj_ptr)
    {
        handle<> x(borrowed(obj_ptr));
        object o(x);
199
200
        if (python::len(o) < 2)
            return 0;
201
202
203
204
205
206
207
208
209
210
211
212
213
        extract<T1> first(o[0]);
        extract<T2> second(o[1]);
        if (!first.check() || !second.check())
            return 0;
        return obj_ptr;
    }

    static void construct(PyObject* obj_ptr,
                          converter::rvalue_from_python_stage1_data* data)
    {
        handle<> x(borrowed(obj_ptr));
        object o(x);
        pair<T1,T2> value;
214
215
        if (python::len(o) < 2)
            throw ValueException("Invalid conversion to pair... Sequence is too short.");
216
217
218
219
220
221
222
223
224
225
226
227
228
229
230
231
232
233
234
235
236
237
238
239
240
241
242
243
244
245
246
247
248
249
250
251
252
253
254
255
256
257
258
259
260
        value.first = extract<T1>(o[0]);
        value.second = extract<T2>(o[1]);
        void* storage =
            ( (boost::python::converter::rvalue_from_python_storage
               <pair<T1,T2> >*) data)->storage.bytes;
        new (storage) pair<T1,T2>(value);
        data->convertible = storage;
    }
};

template <class ValueType>
struct variant_from_python
{
    variant_from_python()
    {
        converter::registry::push_back
            (&convertible, &construct,
             boost::python::type_id<GraphInterface::deg_t>());
    }

    static void* convertible(PyObject* obj_ptr)
    {
        handle<> x(borrowed(obj_ptr));
        object o(x);
        extract<ValueType> str(o);
        if (!str.check())
            return 0;
        return obj_ptr;
    }

    static void construct(PyObject* obj_ptr,
                          converter::rvalue_from_python_stage1_data* data)
    {
        handle<> x(borrowed(obj_ptr));
        object o(x);
        ValueType value = extract<ValueType>(o);
        GraphInterface::deg_t deg = value;
        void* storage =
            ( (boost::python::converter::rvalue_from_python_storage
               <GraphInterface::deg_t>*) data)->storage.bytes;
        new (storage) GraphInterface::deg_t(deg);
        data->convertible = storage;
    }
};

Tiago Peixoto's avatar
Tiago Peixoto committed
261
262
// scipy weave integration
#ifdef HAVE_SCIPY
263
template <class ScxxType>
Tiago Peixoto's avatar
Tiago Peixoto committed
264
265
struct scxx_to_python
{
266
    static PyObject* convert(const ScxxType& o)
Tiago Peixoto's avatar
Tiago Peixoto committed
267
268
269
270
271
272
    {
        return incref((PyObject*)(o));
    }
};
#endif

273
274
275
276
277
278
279
280
281
282
283
284
285
286
287
288
289
// persistent python object IO
namespace graph_tool
{
extern python::object object_pickler;
extern python::object object_unpickler;
}

void set_pickler(python::object o)
{
    graph_tool::object_pickler = o;
}

void set_unpickler(python::object o)
{
    graph_tool::object_unpickler = o;
}

Tiago Peixoto's avatar
Tiago Peixoto committed
290
291
292
293
294
295
296
297
python::list get_property_types()
{
    python::list plist;
    for (int i = 0; i < mpl::size<value_types>::value; ++i)
        plist.append(string(type_names[i]));
    return plist;
}

Tiago Peixoto's avatar
Tiago Peixoto committed
298
299
300
struct graph_type_name
{
    template <class Graph>
301
    void operator()(const Graph& g, string& name) const
Tiago Peixoto's avatar
Tiago Peixoto committed
302
303
304
305
306
307
308
309
310
    {
        using python::detail::gcc_demangle;
        name = string(gcc_demangle(typeid(Graph).name()));
    }
};

string get_graph_type(GraphInterface& g)
{
    string name;
311
    run_action<>()(g, bind<void>(graph_type_name(), _1, ref(name)))();
Tiago Peixoto's avatar
Tiago Peixoto committed
312
313
314
    return name;
}

Tiago Peixoto's avatar
Tiago Peixoto committed
315
316
bool openmp_enabled()
{
Tiago Peixoto's avatar
Tiago Peixoto committed
317
#ifdef USING_OPENMP
Tiago Peixoto's avatar
Tiago Peixoto committed
318
    return true;
Tiago Peixoto's avatar
Tiago Peixoto committed
319
#else
Tiago Peixoto's avatar
Tiago Peixoto committed
320
    return false;
Tiago Peixoto's avatar
Tiago Peixoto committed
321
#endif
Tiago Peixoto's avatar
Tiago Peixoto committed
322
323
}

324
325
326
327
328
329
330
// numpy array interface weirdness
void* do_import_array()
{
    import_array1(NULL);
    return NULL;
}

331
332
333
334
void ungroup_vector_property(GraphInterface& g, boost::any vector_prop,
                             boost::any prop, size_t pos, bool edge);
void group_vector_property(GraphInterface& g, boost::any vector_prop,
                           boost::any prop, size_t pos, bool edge);
335
336
void infect_vertex_property(GraphInterface& gi, boost::any prop,
                            python::object val);
Tiago Peixoto's avatar
Tiago Peixoto committed
337
338
void edge_difference(GraphInterface& gi, boost::any prop,
                     boost::any eprop);
339
340
void mark_edges(GraphInterface& gi, boost::any prop);

341
void export_python_interface();
342

343
BOOST_PYTHON_MODULE(libgraph_tool_core)
Tiago Peixoto's avatar
Tiago Peixoto committed
344
{
345
    // numpy
346
    do_import_array();
347
    export_python_interface();
Tiago Peixoto's avatar
Tiago Peixoto committed
348

349
350
351
352
    // random numbers
    class_<rng_t>("rng_t");
    def("get_rng", get_rng);

Tiago Peixoto's avatar
Tiago Peixoto committed
353
354
355
356
357
358
    register_exception_translator<GraphException>
        (graph_exception_translator<GraphException>);
    register_exception_translator<IOException>
        (graph_exception_translator<IOException>);
    register_exception_translator<ValueException>
        (graph_exception_translator<ValueException>);
Tiago Peixoto's avatar
Tiago Peixoto committed
359

360
    def("raise_error", &raise_error);
Tiago Peixoto's avatar
Tiago Peixoto committed
361
    def("get_property_types", &get_property_types);
362
363
    class_<boost::any>("any")
        .def("empty", &boost::any::empty);
364

365
    def("graph_filtering_enabled", &graph_filtering_enabled);
Tiago Peixoto's avatar
Tiago Peixoto committed
366
    def("openmp_enabled", &openmp_enabled);
367

368
369
370
    mpl::for_each<mpl::push_back<scalar_types,string>::type>(export_vector_types());

    class_<GraphInterface>("GraphInterface", init<>())
371
        .def(init<GraphInterface,bool,python::object,python::object,python::object>())
372
373
374
375
376
377
        .def("GetNumberOfVertices", &GraphInterface::GetNumberOfVertices)
        .def("GetNumberOfEdges", &GraphInterface::GetNumberOfEdges)
        .def("SetDirected", &GraphInterface::SetDirected)
        .def("GetDirected", &GraphInterface::GetDirected)
        .def("SetReversed", &GraphInterface::SetReversed)
        .def("GetReversed", &GraphInterface::GetReversed)
378
379
        .def("SetKeepEpos", &GraphInterface::SetKeepEpos)
        .def("GetKeepEpos", &GraphInterface::GetKeepEpos)
380
381
382
        .def("SetVertexFilterProperty",
             &GraphInterface::SetVertexFilterProperty)
        .def("IsVertexFilterActive", &GraphInterface::IsVertexFilterActive)
383
        .def("SetEdgeFilterProperty",
384
385
386
387
             &GraphInterface::SetEdgeFilterProperty)
        .def("IsEdgeFilterActive", &GraphInterface::IsEdgeFilterActive)
        .def("PurgeVertices",  &GraphInterface::PurgeVertices)
        .def("PurgeEdges",  &GraphInterface::PurgeEdges)
388
        .def("ShiftVertexProperty",  &GraphInterface::ShiftVertexProperty)
389
        .def("MoveVertexProperty",  &GraphInterface::MoveVertexProperty)
390
        .def("ReIndexVertexProperty",  &GraphInterface::ReIndexVertexProperty)
391
392
        .def("WriteToFile", &GraphInterface::WriteToFile)
        .def("ReadFromFile",&GraphInterface::ReadFromFile)
393
        .def("DegreeMap", &GraphInterface::DegreeMap)
394
        .def("Clear", &GraphInterface::Clear)
395
396
397
        .def("ClearEdges", &GraphInterface::ClearEdges)
        .def("GetVertexIndex", &GraphInterface::GetVertexIndex)
        .def("GetEdgeIndex", &GraphInterface::GetEdgeIndex)
398
        .def("GetMaxEdgeIndex", &GraphInterface::GetMaxEdgeIndex)
399
        .def("ReIndexEdges", &GraphInterface::ReIndexEdges)
400
401
402
        .def("GetGraphIndex", &GraphInterface::GetGraphIndex)
        .def("CopyVertexProperty", &GraphInterface::CopyVertexProperty)
        .def("CopyEdgeProperty", &GraphInterface::CopyEdgeProperty);
403

404
405
406
407
    class_<GraphInterface::vertex_index_map_t>("vertex_index_map", no_init);
    class_<GraphInterface::edge_index_map_t>("edge_index_map", no_init);
    class_<GraphInterface::graph_index_map_t>("graph_index_map", no_init);

408
409
410
411
412
    enum_<GraphInterface::degree_t>("Degree")
        .value("In", GraphInterface::IN_DEGREE)
        .value("Out", GraphInterface::OUT_DEGREE)
        .value("Total", GraphInterface::TOTAL_DEGREE);

413
    variant_from_python<boost::any>();
414
    variant_from_python<GraphInterface::degree_t>();
415
    to_python_converter<pair<string,bool>, pair_to_tuple<string,bool> >();
416
    to_python_converter<pair<size_t,size_t>, pair_to_tuple<size_t,size_t> >();
417
    to_python_converter<pair<double,double>, pair_to_tuple<double,double> >();
418
419
    pair_from_tuple<double,double>();
    pair_from_tuple<size_t,size_t>();
Tiago Peixoto's avatar
Tiago Peixoto committed
420
#ifdef HAVE_SCIPY
421
422
423
424
425
    to_python_converter<py::object, scxx_to_python<py::object> >();
    to_python_converter<py::tuple, scxx_to_python<py::tuple> >();
    to_python_converter<py::list, scxx_to_python<py::list> >();
    to_python_converter<py::dict, scxx_to_python<py::dict> >();
    to_python_converter<py::str, scxx_to_python<py::str> >();
Tiago Peixoto's avatar
Tiago Peixoto committed
426
#endif
Tiago Peixoto's avatar
Tiago Peixoto committed
427

428
429
430
431
432
433
    class_<IStream>("IStream", no_init).def("Read", &IStream::Read);
    class_<OStream>("OStream", no_init).def("Write", &OStream::Write).
        def("Flush", &OStream::Flush);
    def("set_pickler", &set_pickler);
    def("set_unpickler", &set_unpickler);

434
435
    def("group_vector_property", &group_vector_property);
    def("ungroup_vector_property", &ungroup_vector_property);
436
    def("infect_vertex_property", &infect_vertex_property);
Tiago Peixoto's avatar
Tiago Peixoto committed
437
    def("edge_difference", &edge_difference);
438
    def("mark_edges", &mark_edges);
439

Tiago Peixoto's avatar
Tiago Peixoto committed
440
    class_<LibInfo>("mod_info")
441
442
443
        .add_property("name", &LibInfo::GetName)
        .add_property("author", &LibInfo::GetAuthor)
        .add_property("copyright", &LibInfo::GetCopyright)
444
        .add_property("version", &LibInfo::GetVersion)
445
446
447
        .add_property("license", &LibInfo::GetLicense)
        .add_property("cxxflags", &LibInfo::GetCXXFLAGS)
        .add_property("install_prefix", &LibInfo::GetInstallPrefix)
Tiago Peixoto's avatar
Tiago Peixoto committed
448
449
        .add_property("python_dir", &LibInfo::GetPythonDir)
        .add_property("gcc_version", &LibInfo::GetGCCVersion);
Tiago Peixoto's avatar
Tiago Peixoto committed
450
451

    def("get_graph_type", &get_graph_type);
Tiago Peixoto's avatar
Tiago Peixoto committed
452
}