2_basics.py

"""
.. currentmodule:: dgl

DGLGraph and Node/edge Features
===============================

**Author**: `Minjie Wang <https://jermainewang.github.io/>`_, Quan Gan, Yu Gai,
Zheng Zhang

In this tutorial, you learn how to create a graph and how to read and write node and edge representations.
"""

###############################################################################
# Creating a graph
# ----------------
# The design of :class:`DGLGraph` was influenced by other graph libraries. You 
# can create a graph from networkx and convert it into a :class:`DGLGraph` and 
# vice versa.

import networkx as nx
import dgl

g_nx = nx.petersen_graph()
g_dgl = dgl.DGLGraph(g_nx)

import matplotlib.pyplot as plt
plt.subplot(121)
nx.draw(g_nx, with_labels=True)
plt.subplot(122)
nx.draw(g_dgl.to_networkx(), with_labels=True)

plt.show()


###############################################################################
# There are many ways to construct a :class:`DGLGraph`. Below are the allowed
# data types ordered by our recommendataion.
#
# * A pair of arrays ``(u, v)`` storing the source and destination nodes respectively.
#   They can be numpy arrays or tensor objects from the backend framework.
# * ``scipy`` sparse matrix representing the adjacency matrix of the graph to be
#   constructed.
# * ``networkx`` graph object.
# * A list of edges in the form of integer pairs.
#
# The examples below construct the same star graph via different methods.
#
# :class:`DGLGraph` nodes are a consecutive range of integers between 0 and
# :func:`number_of_nodes() <DGLGraph.number_of_nodes>`. 
# :class:`DGLGraph` edges are in order of their additions. Note that
# edges are accessed in much the same way as nodes, with one extra feature:
# *edge broadcasting*.

import torch as th
import numpy as np
import scipy.sparse as spp

# Create a star graph from a pair of arrays (using ``numpy.array`` works too).
u = th.tensor([0, 0, 0, 0, 0])
v = th.tensor([1, 2, 3, 4, 5])
star1 = dgl.DGLGraph((u, v))

# Create the same graph in one go! Essentially, if one of the arrays is a scalar,
# the value is automatically broadcasted to match the length of the other array
# -- a feature called *edge broadcasting*.
start2 = dgl.DGLGraph((0, v))

# Create the same graph from a scipy sparse matrix (using ``scipy.sparse.csr_matrix`` works too).
adj = spp.coo_matrix((np.ones(len(u)), (u.numpy(), v.numpy())))
star3 = dgl.DGLGraph(adj)

# Create the same graph from a list of integer pairs.
elist = [(0, 1), (0, 2), (0, 3), (0, 4), (0, 5)]
star4 = dgl.DGLGraph(elist)

###############################################################################
# You can also create a graph by progressively adding more nodes and edges.
# Although it is not as efficient as the above constructors, it is suitable
# for applications where the graph cannot be constructed in one shot.

g = dgl.DGLGraph()
g.add_nodes(10)
# A couple edges one-by-one
for i in range(1, 4):
    g.add_edge(i, 0)
# A few more with a paired list
src = list(range(5, 8)); dst = [0]*3
g.add_edges(src, dst)
# finish with a pair of tensors
src = th.tensor([8, 9]); dst = th.tensor([0, 0])
g.add_edges(src, dst)

# Edge broadcasting will do star graph in one go!
g.clear(); g.add_nodes(10)
src = th.tensor(list(range(1, 10)));
g.add_edges(src, 0)

# Visualize the graph.
nx.draw(g.to_networkx(), with_labels=True)
plt.show()

###############################################################################
# Assigning a feature
# -------------------
# You can also assign features to nodes and edges of a :class:`DGLGraph`.  The
# features are represented as dictionary of names (strings) and tensors,
# called **fields**.
#
# The following code snippet assigns each node a vector (len=3).
#
# .. note::
#
#    DGL aims to be framework-agnostic, and currently it supports PyTorch and
#    MXNet tensors. The following examples use PyTorch only.

import dgl
import torch as th

x = th.randn(10, 3)
g.ndata['x'] = x

###############################################################################
# :func:`ndata <DGLGraph.ndata>` is a syntax sugar to access the feature
# data of all nodes. To get the features of some particular nodes, slice out
# the corresponding rows.

g.ndata['x'][0] = th.zeros(1, 3)
g.ndata['x'][[0, 1, 2]] = th.zeros(3, 3)
g.ndata['x'][th.tensor([0, 1, 2])] = th.randn((3, 3))

###############################################################################
# Assigning edge features is similar to that of node features,
# except that you can also do it by specifying endpoints of the edges.

g.edata['w'] = th.randn(9, 2)

# Access edge set with IDs in integer, list, or integer tensor
g.edata['w'][1] = th.randn(1, 2)
g.edata['w'][[0, 1, 2]] = th.zeros(3, 2)
g.edata['w'][th.tensor([0, 1, 2])] = th.zeros(3, 2)

# You can get the edge ids by giving endpoints, which are useful for accessing the features.
g.edata['w'][g.edge_id(1, 0)] = th.ones(1, 2)                   # edge 1 -> 0
g.edata['w'][g.edge_ids([1, 2, 3], [0, 0, 0])] = th.ones(3, 2)  # edges [1, 2, 3] -> 0
# Use edge broadcasting whenever applicable.
g.edata['w'][g.edge_ids([1, 2, 3], 0)] = th.ones(3, 2)          # edges [1, 2, 3] -> 0

###############################################################################
# After assignments, each node or edge field will be associated with a scheme
# containing the shape and data type (dtype) of its field value.

print(g.node_attr_schemes())
g.ndata['x'] = th.zeros((10, 4))
print(g.node_attr_schemes())


###############################################################################
# You can also remove node or edge states from the graph. This is particularly
# useful to save memory during inference.

g.ndata.pop('x')
g.edata.pop('w')


###############################################################################
# Working with multigraphs
# ~~~~~~~~~~~~~~~~~~~~~~~~
# Many graph applications need parallel edges,
# which class:DGLGraph supports by default.

g_multi = dgl.DGLGraph()
g_multi.add_nodes(10)
g_multi.ndata['x'] = th.randn(10, 2)

g_multi.add_edges(list(range(1, 10)), 0)
g_multi.add_edge(1, 0) # two edges on 1->0

g_multi.edata['w'] = th.randn(10, 2)
g_multi.edges[1].data['w'] = th.zeros(1, 2)
print(g_multi.edges())


###############################################################################
# An edge in multigraph cannot be uniquely identified by using its incident nodes
# :math:`u` and :math:`v`; query their edge IDs use ``edge_id`` interface.

eid_10 = g_multi.edge_id(1, 0, return_array=True)
g_multi.edges[eid_10].data['w'] = th.ones(len(eid_10), 2)
print(g_multi.edata['w'])


###############################################################################
# .. note::
#
#    * Updating a feature of different schemes raises the risk of error on individual nodes (or
#      node subset).

###############################################################################
# Next steps
# ----------
# In the :doc:`next tutorial <3_pagerank>` you learn the
# DGL message passing interface by implementing PageRank.