graph_bind.cc 14 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) 2007-2012 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

Tiago Peixoto's avatar
Tiago Peixoto committed
29
30
#ifdef HAVE_SCIPY // integration with scipy weave
#include "weave/scxx/object.h"
31
32
33
34
#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
35
36
#endif

Tiago Peixoto's avatar
Tiago Peixoto committed
37
38
39
40
41
using namespace std;
using namespace graph_tool;
using namespace boost;
using namespace boost::python;

42
struct LibInfo
Tiago Peixoto's avatar
Tiago Peixoto committed
43
{
44
45
46
47
48
49
    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
50
    string GetCXXFLAGS()  const {return CPPFLAGS " " CXXFLAGS " " LDFLAGS;}
51
52
    string GetInstallPrefix() const {return INSTALL_PREFIX;}
    string GetPythonDir() const {return PYTHON_DIR;}
Tiago Peixoto's avatar
Tiago Peixoto committed
53
54
55
56
57
58
    string GetGCCVersion() const
    {
        stringstream s;
        s << __GNUC__ << "." << __GNUC_MINOR__ << "." <<  __GNUC_PATCHLEVEL__;
        return s.str();
    }
Tiago Peixoto's avatar
Tiago Peixoto committed
59
60
};

61
62
template <class ValueType>
struct vector_from_list
Tiago Peixoto's avatar
Tiago Peixoto committed
63
{
64
    vector_from_list()
Tiago Peixoto's avatar
Tiago Peixoto committed
65
    {
66
        converter::registry::push_back
67
            (&convertible, &construct,
68
             boost::python::type_id<vector<ValueType> >());
Tiago Peixoto's avatar
Tiago Peixoto committed
69
70
71
72
    }

    static void* convertible(PyObject* obj_ptr)
    {
73
74
        handle<> x(borrowed(obj_ptr));
        object o(x);
75
76
77
78
79
80
81
        size_t N = len(o);
        for (size_t i = 0; i < N; ++i)
        {
            extract<ValueType> elem(o[i]);
            if (!elem.check())
                return 0;
        }
82
        return obj_ptr;
Tiago Peixoto's avatar
Tiago Peixoto committed
83
84
    }

85
    static void construct(PyObject* obj_ptr,
86
                          converter::rvalue_from_python_stage1_data* data)
87
    {
88
89
        handle<> x(borrowed(obj_ptr));
        object o(x);
90
91
92
93
        vector<ValueType> value;
        size_t N = len(o);
        for (size_t i = 0; i < N; ++i)
            value.push_back(extract<ValueType>(o[i]));
94
        void* storage =
95
            ( (boost::python::converter::rvalue_from_python_storage
96
97
               <vector<ValueType> >*) data)->storage.bytes;
        new (storage) vector<ValueType>(value);
98
        data->convertible = storage;
Tiago Peixoto's avatar
Tiago Peixoto committed
99
100
101
    }
};

102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
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);
}

123
struct export_vector_types
Tiago Peixoto's avatar
Tiago Peixoto committed
124
{
125
126
    template <class ValueType>
    void operator()(ValueType) const
Tiago Peixoto's avatar
Tiago Peixoto committed
127
    {
128
129
130
131
        string type_name = get_type_name<>()(typeid(ValueType));
        if (type_name == "long double")
            type_name = "long_double";
        string name = "Vector_" + type_name;
132
133
        class_<vector<ValueType> > vc(name.c_str());
        vc.def(vector_indexing_suite<vector<ValueType> >())
134
135
            .def("__eq__", &vector_equal_compare<ValueType>)
            .def("__ne__", &vector_nequal_compare<ValueType>);
136
        wrap_array(vc, typename mpl::has_key<numpy_types,ValueType>::type());
137
        vector_from_list<ValueType>();
Tiago Peixoto's avatar
Tiago Peixoto committed
138
    }
139
140
141
142
143
144
145
146
147
148
149

    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
    {
    }
150
};
Tiago Peixoto's avatar
Tiago Peixoto committed
151

152
153
// exception translation
template <class Exception>
Tiago Peixoto's avatar
Tiago Peixoto committed
154
void graph_exception_translator(const Exception& e)
155
{
Tiago Peixoto's avatar
Tiago Peixoto committed
156
157
158
159
160
161
162
163
    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;

164
    PyObject* message = PyUnicode_FromString(e.what());
Tiago Peixoto's avatar
Tiago Peixoto committed
165
166
    PyObject_SetAttrString(error, "message", message);
    PyErr_SetString(error, e.what());
167
}
Tiago Peixoto's avatar
Tiago Peixoto committed
168

169
170
171
172
void raise_error(const string& msg)
{
    throw GraphException(msg);
}
Tiago Peixoto's avatar
Tiago Peixoto committed
173

174
175
template <class T1, class T2>
struct pair_to_tuple
Tiago Peixoto's avatar
Tiago Peixoto committed
176
{
177
    static PyObject* convert(const pair<T1,T2>& p)
Tiago Peixoto's avatar
Tiago Peixoto committed
178
    {
179
180
        boost::python::tuple t = boost::python::make_tuple(p.first,p.second);
        return incref(t.ptr());
Tiago Peixoto's avatar
Tiago Peixoto committed
181
182
183
    }
};

184
185
186
187
188
189
190
191
192
193
194
195
196
197
198
199
200
201
202
203
204
205
206
207
208
209
210
211
212
213
214
215
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
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);
        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;
        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
255
256
// scipy weave integration
#ifdef HAVE_SCIPY
257
template <class ScxxType>
Tiago Peixoto's avatar
Tiago Peixoto committed
258
259
struct scxx_to_python
{
260
    static PyObject* convert(const ScxxType& o)
Tiago Peixoto's avatar
Tiago Peixoto committed
261
262
263
264
265
266
    {
        return incref((PyObject*)(o));
    }
};
#endif

267
268
269
270
271
272
273
274
275
276
277
278
279
280
281
282
283
// 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
284
285
286
287
288
289
290
291
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
292
293
294
struct graph_type_name
{
    template <class Graph>
295
    void operator()(const Graph& g, string& name) const
Tiago Peixoto's avatar
Tiago Peixoto committed
296
297
298
299
300
301
302
303
304
    {
        using python::detail::gcc_demangle;
        name = string(gcc_demangle(typeid(Graph).name()));
    }
};

string get_graph_type(GraphInterface& g)
{
    string name;
305
    run_action<>()(g, bind<void>(graph_type_name(), _1, ref(name)))();
Tiago Peixoto's avatar
Tiago Peixoto committed
306
307
308
    return name;
}

Tiago Peixoto's avatar
Tiago Peixoto committed
309
310
bool openmp_enabled()
{
Tiago Peixoto's avatar
Tiago Peixoto committed
311
#ifdef USING_OPENMP
Tiago Peixoto's avatar
Tiago Peixoto committed
312
    return true;
Tiago Peixoto's avatar
Tiago Peixoto committed
313
#else
Tiago Peixoto's avatar
Tiago Peixoto committed
314
    return false;
Tiago Peixoto's avatar
Tiago Peixoto committed
315
#endif
Tiago Peixoto's avatar
Tiago Peixoto committed
316
317
}

318
319
320
321
322
323
324
// numpy array interface weirdness
void* do_import_array()
{
    import_array1(NULL);
    return NULL;
}

325
326
327
328
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);
329
330
void infect_vertex_property(GraphInterface& gi, boost::any prop,
                            python::object val);
Tiago Peixoto's avatar
Tiago Peixoto committed
331
332
void edge_difference(GraphInterface& gi, boost::any prop,
                     boost::any eprop);
333
void export_python_interface();
334

335
BOOST_PYTHON_MODULE(libgraph_tool_core)
Tiago Peixoto's avatar
Tiago Peixoto committed
336
{
337
    // numpy
338
    do_import_array();
339
    export_python_interface();
Tiago Peixoto's avatar
Tiago Peixoto committed
340

341
342
343
344
    // random numbers
    class_<rng_t>("rng_t");
    def("get_rng", get_rng);

Tiago Peixoto's avatar
Tiago Peixoto committed
345
346
347
348
349
350
    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
351

352
    def("raise_error", &raise_error);
Tiago Peixoto's avatar
Tiago Peixoto committed
353
    def("get_property_types", &get_property_types);
354
355
    class_<boost::any>("any")
        .def("empty", &boost::any::empty);
356

357
    def("graph_filtering_enabled", &graph_filtering_enabled);
Tiago Peixoto's avatar
Tiago Peixoto committed
358
    def("openmp_enabled", &openmp_enabled);
359

360
361
362
    mpl::for_each<mpl::push_back<scalar_types,string>::type>(export_vector_types());

    class_<GraphInterface>("GraphInterface", init<>())
363
        .def(init<GraphInterface,bool,python::object,python::object>())
364
365
366
367
368
369
370
371
372
        .def("GetNumberOfVertices", &GraphInterface::GetNumberOfVertices)
        .def("GetNumberOfEdges", &GraphInterface::GetNumberOfEdges)
        .def("SetDirected", &GraphInterface::SetDirected)
        .def("GetDirected", &GraphInterface::GetDirected)
        .def("SetReversed", &GraphInterface::SetReversed)
        .def("GetReversed", &GraphInterface::GetReversed)
        .def("SetVertexFilterProperty",
             &GraphInterface::SetVertexFilterProperty)
        .def("IsVertexFilterActive", &GraphInterface::IsVertexFilterActive)
373
        .def("SetEdgeFilterProperty",
374
375
376
377
             &GraphInterface::SetEdgeFilterProperty)
        .def("IsEdgeFilterActive", &GraphInterface::IsEdgeFilterActive)
        .def("PurgeVertices",  &GraphInterface::PurgeVertices)
        .def("PurgeEdges",  &GraphInterface::PurgeEdges)
378
        .def("ShiftVertexProperty",  &GraphInterface::ShiftVertexProperty)
379
        .def("ReIndexVertexProperty",  &GraphInterface::ReIndexVertexProperty)
380
381
        .def("WriteToFile", &GraphInterface::WriteToFile)
        .def("ReadFromFile",&GraphInterface::ReadFromFile)
382
        .def("DegreeMap", &GraphInterface::DegreeMap)
383
        .def("Clear", &GraphInterface::Clear)
384
385
386
        .def("ClearEdges", &GraphInterface::ClearEdges)
        .def("GetVertexIndex", &GraphInterface::GetVertexIndex)
        .def("GetEdgeIndex", &GraphInterface::GetEdgeIndex)
387
        .def("GetMaxEdgeIndex", &GraphInterface::GetMaxEdgeIndex)
388
        .def("ReIndexEdges", &GraphInterface::ReIndexEdges)
389
390
391
        .def("GetGraphIndex", &GraphInterface::GetGraphIndex)
        .def("CopyVertexProperty", &GraphInterface::CopyVertexProperty)
        .def("CopyEdgeProperty", &GraphInterface::CopyEdgeProperty);
392

393
394
395
396
    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);

397
398
399
400
401
    enum_<GraphInterface::degree_t>("Degree")
        .value("In", GraphInterface::IN_DEGREE)
        .value("Out", GraphInterface::OUT_DEGREE)
        .value("Total", GraphInterface::TOTAL_DEGREE);

402
    variant_from_python<boost::any>();
403
    variant_from_python<GraphInterface::degree_t>();
404
    to_python_converter<pair<string,bool>, pair_to_tuple<string,bool> >();
405
    to_python_converter<pair<size_t,size_t>, pair_to_tuple<size_t,size_t> >();
406
    to_python_converter<pair<double,double>, pair_to_tuple<double,double> >();
407
408
    pair_from_tuple<double,double>();
    pair_from_tuple<size_t,size_t>();
Tiago Peixoto's avatar
Tiago Peixoto committed
409
#ifdef HAVE_SCIPY
410
411
412
413
414
    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
415
#endif
Tiago Peixoto's avatar
Tiago Peixoto committed
416

417
418
419
420
421
422
    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);

423
424
    def("group_vector_property", &group_vector_property);
    def("ungroup_vector_property", &ungroup_vector_property);
425
    def("infect_vertex_property", &infect_vertex_property);
Tiago Peixoto's avatar
Tiago Peixoto committed
426
    def("edge_difference", &edge_difference);
427

Tiago Peixoto's avatar
Tiago Peixoto committed
428
    class_<LibInfo>("mod_info")
429
430
431
        .add_property("name", &LibInfo::GetName)
        .add_property("author", &LibInfo::GetAuthor)
        .add_property("copyright", &LibInfo::GetCopyright)
432
        .add_property("version", &LibInfo::GetVersion)
433
434
435
        .add_property("license", &LibInfo::GetLicense)
        .add_property("cxxflags", &LibInfo::GetCXXFLAGS)
        .add_property("install_prefix", &LibInfo::GetInstallPrefix)
Tiago Peixoto's avatar
Tiago Peixoto committed
436
437
        .add_property("python_dir", &LibInfo::GetPythonDir)
        .add_property("gcc_version", &LibInfo::GetGCCVersion);
Tiago Peixoto's avatar
Tiago Peixoto committed
438
439

    def("get_graph_type", &get_graph_type);
Tiago Peixoto's avatar
Tiago Peixoto committed
440
}
Tiago Peixoto's avatar
Tiago Peixoto committed
441