handle scipy change to ndarray

KrishnaswamyLab · May 31, 2019 · 4803a0b · 4803a0b
1 parent 438bbf3
commit 4803a0b
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Showing 2 changed files with 5 additions and 3 deletions.
diff --git a/graphtools/base.py b/graphtools/base.py
@@ -527,7 +527,7 @@ def diff_aff(self):
             symmetric diffusion affinity matrix defined as a
             doubly-stochastic form of the kernel matrix
         """
-        row_degrees = self.kernel.sum(axis=1).A
+        row_degrees = utils.to_array(self.kernel.sum(axis=1))
         if sparse.issparse(self.kernel):
             # diagonal matrix
             degrees = sparse.csr_matrix((1 / np.sqrt(row_degrees.flatten()),
@@ -638,7 +638,7 @@ def to_igraph(self, attribute="weight", **kwargs):
             # not a pygsp graph
             W = self.K.copy()
             W = utils.set_diagonal(W, 0)
-        return ig.Graph.Weighted_Adjacency(utils.to_dense(W).tolist(),
+        return ig.Graph.Weighted_Adjacency(utils.to_array(W).tolist(),
                                            attr=attribute, **kwargs)
 
     def to_pickle(self, path):

diff --git a/graphtools/utils.py b/graphtools/utils.py
@@ -49,7 +49,9 @@ def set_submatrix(X, i, j, values):
     return X
 
 
-def to_dense(X):
+def to_array(X):
     if sparse.issparse(X):
         X = X.toarray()
+    elif isinstance(X, np.matrix):
+        X = X.A
     return X