Merge pull request #35 from KrishnaswamyLab/feature/to_pkl

adding to_pickle and read_pickle

Author: scottgigante

graphtools/__init__.py

@@ -1,2 +1,2 @@
-from .api import Graph, from_igraph
+from .api import Graph, from_igraph, read_pickle
 from .version import __version__

graphtools/api.py

@@ -2,6 +2,8 @@
 import warnings
 import tasklogger
 from scipy import sparse
+import pickle
+import pygsp
 
 from . import base
 from . import graphs
@@ -283,3 +285,22 @@ def from_igraph(G, attribute="weight", **kwargs):
         K = G.get_adjacency(attribute=None).data
     return Graph(sparse.coo_matrix(K),
                  precomputed='adjacency', **kwargs)
+
+
+def read_pickle(path):
+    """Load pickled Graphtools object (or any object) from file.
+
+    Parameters
+    ----------
+    path : str
+        File path where the pickled object will be loaded.
+    """
+    with open(path, 'rb') as f:
+        G = pickle.load(f)
+
+    if not isinstance(G, base.BaseGraph):
+        warnings.warn(
+            'Returning object that is not a graphtools.base.BaseGraph')
+    elif isinstance(G, base.PyGSPGraph) and isinstance(G.logger, str):
+        G.logger = pygsp.utils.build_logger(G.logger)
+    return G

graphtools/base.py

@@ -10,6 +10,8 @@
 import warnings
 import numbers
 import tasklogger
+import pickle
+import sys
 
 try:
     import pandas as pd
@@ -635,6 +637,23 @@ def to_igraph(self, attribute="weight", **kwargs):
         return ig.Graph.Weighted_Adjacency(utils.to_dense(W).tolist(),
                                            attr=attribute, **kwargs)
 
+    def to_pickle(self, path):
+        """Save the current Graph to a pickle.
+
+        Parameters
+        ----------
+        path : str
+            File path where the pickled object will be stored.
+        """
+        if int(sys.version.split(".")[1]) < 7 and isinstance(self, pygsp.graphs.Graph):
+            # python 3.5, 3.6
+            logger = self.logger
+            self.logger = logger.name
+        with open(path, 'wb') as f:
+            pickle.dump(self, f)
+        if int(sys.version.split(".")[1]) < 7 and isinstance(self, pygsp.graphs.Graph):
+            self.logger = logger
+
 
 class PyGSPGraph(with_metaclass(abc.ABCMeta, pygsp.graphs.Graph, Base)):
     """Interface between BaseGraph and PyGSP.

graphtools/graphs.py

@@ -14,8 +14,6 @@
 import tasklogger
 
 from .utils import (set_diagonal,
-                    elementwise_minimum,
-                    elementwise_maximum,
                     set_submatrix)
 from .base import DataGraph, PyGSPGraph
 

test/test_api.py

@@ -9,6 +9,8 @@
 import igraph
 import numpy as np
 import graphtools
+import tempfile
+import os
 
 
 def test_from_igraph():
@@ -81,6 +83,56 @@ def test_to_igraph():
         attribute="weight").data) == G.W)
 
 
+def test_pickle_io_knngraph():
+    G = build_graph(data, knn=5, decay=None)
+    with tempfile.TemporaryDirectory() as tempdir:
+        path = os.path.join(tempdir, 'tmp.pkl')
+        G.to_pickle(path)
+        G_prime = graphtools.read_pickle(path)
+    assert isinstance(G_prime, type(G))
+
+
+def test_pickle_io_traditionalgraph():
+    G = build_graph(data, knn=5, decay=10, thresh=0)
+    with tempfile.TemporaryDirectory() as tempdir:
+        path = os.path.join(tempdir, 'tmp.pkl')
+        G.to_pickle(path)
+        G_prime = graphtools.read_pickle(path)
+    assert isinstance(G_prime, type(G))
+
+
+def test_pickle_io_landmarkgraph():
+    G = build_graph(data, knn=5, decay=None,
+                    n_landmark=data.shape[0] // 2)
+    L = G.landmark_op
+    with tempfile.TemporaryDirectory() as tempdir:
+        path = os.path.join(tempdir, 'tmp.pkl')
+        G.to_pickle(path)
+        G_prime = graphtools.read_pickle(path)
+    assert isinstance(G_prime, type(G))
+    np.testing.assert_array_equal(L, G_prime._landmark_op)
+
+
+def test_pickle_io_pygspgraph():
+    G = build_graph(data, knn=5, decay=None, use_pygsp=True)
+    with tempfile.TemporaryDirectory() as tempdir:
+        path = os.path.join(tempdir, 'tmp.pkl')
+        G.to_pickle(path)
+        G_prime = graphtools.read_pickle(path)
+    assert isinstance(G_prime, type(G))
+    assert G_prime.logger.name == G.logger.name
+
+
+@warns(UserWarning)
+def test_pickle_bad_pickle():
+    import pickle
+    with tempfile.TemporaryDirectory() as tempdir:
+        path = os.path.join(tempdir, 'tmp.pkl')
+        with open(path, 'wb') as f:
+            pickle.dump('hello world', f)
+        G = graphtools.read_pickle(path)
+
+
 @warns(UserWarning)
 def test_to_pygsp_invalid_precomputed():
     G = build_graph(data)