In [1]:

    

import sys
sys.path.append('/Users/erickpeirson/tethne')


    

In [2]:

    

from tethne.persistence.hdf5.graphcollection import HDF5Graph


    

In [3]:

    

from networkx import Graph


    

In [4]:

    

import tables


    

In [5]:

    

from tethne.persistence.hdf5.util import get_h5file, get_or_create_group


    

In [6]:

    

h5file,a,b = get_h5file('test')


    

In [7]:

    

group = get_or_create_group(h5file, 'testgroup')


    

In [8]:

    

g = Graph()


    

In [9]:

    

g.add_edge(0,1)
g.add_edge(1,2, weight=5)
g.add_edge(5,0, {'weight':3, 'girth':'wtf'})
g.add_node(0, {'size':0.5, 'label':'bob'})


    

In [10]:

    

g.node[0]


    

    
Out[10]:





{'label': 'bob', 'size': 0.5}

In [11]:

    

hg = HDF5Graph(h5file, group, 'test', g)


    

In [12]:

    

g.nodes(data=True)


    

    
Out[12]:





[(0, {'label': 'bob', 'size': 0.5}), (1, {}), (2, {}), (5, {})]

In [13]:

    

hg.nodes(data=True)


    

    
Out[13]:





[(0, {'label': 'bob', 'size': 0.5}), (1, {}), (2, {}), (5, {})]

In [14]:

    

g.edges(data=True)


    

    
Out[14]:





[(0, 1, {}), (0, 5, {'girth': 'wtf', 'weight': 3}), (1, 2, {'weight': 5})]

In [15]:

    

hg.edges(data=True)


    

    
Out[15]:





[(0, 1, {}), (0, 5, {'girth': 'wtf', 'weight': 3}), (1, 2, {'weight': 5})]

In [16]:

    

hg.node[0]['asdf'] = 'wtf'


    

In [17]:

    

hg.node[0]


    

    
Out[17]:





{'label': 'bob', 'size': 0.5}

In [18]:

    

len(hg.edge)


    

    
Out[18]:





3

In [19]:

    




    

    
Out[19]:





4

In [29]:

    

g.edges(data=True)


    

    
Out[29]:





[(0, 1, {}), (0, 3, {'weight': 3}), (1, 2, {'weight': 5})]

In [15]:

    

from scipy.sparse import coo_matrix


    

In [20]:

    

array(hg.edge.neighbors.I), array(hg.edge.neighbors.J), array(hg.edge.neighbors.K)


    

    
Out[20]:





(array([0, 0, 1, 1, 2, 3]),
 array([1, 3, 0, 2, 1, 0]),
 array([1, 2, 3, 4, 5, 6]))

In [16]:

    

A = coo_matrix(hg.edge.neighbors.K, (hg.edge.neighbors.I, hg.edge.neighbors.J))


    

In [25]:

    

A.data


    

    
Out[25]:





array([1, 2, 3, 4, 5, 6])

In [23]:

    

for i, n in g.edge.iteritems():
    for j, attr in n.iteritems():
        print i, j


    

    




0 1
0 3
1 0
1 2
2 1
3 0

In [23]:

    

zip(array(hg.edge.neighbors.I), array(hg.edge.neighbors.J))


    

    
Out[23]:





[(0, 1), (0, 3), (1, 0), (1, 2), (2, 1), (3, 0)]

In [26]:

    

B = A.tocsr()


    

In [27]:

    

B.nonzero()


    

    
Out[27]:





(array([0, 0, 0, 0, 0, 0], dtype=int32),
 array([0, 1, 2, 3, 4, 5], dtype=int32))

In [39]:

    

r = hg.edges()
r_ = []
while len(r) > 0:
    t = r.pop()
    t_ = (min(t), max(t))
    if t_ not in r_:
        r_.append(t_)


    

    




223 [0 0 1 1 2 3] [1 3 0 2 1 0]
229 [(0, 1), (0, 3), (1, 0), (1, 2), (2, 1), (3, 0)]
[(0, 1), (0, 3), (1, 0), (1, 2), (2, 1), (3, 0)]
[(0, 1), (0, 3), (1, 0), (1, 2), (2, 1), (3, 0)]

In [40]:

    

g.edges()


    

    
Out[40]:





[(0, 1), (0, 3), (1, 2)]

In [41]:

    

r_


    

    
Out[41]:





[(0, 3), (1, 2), (0, 1)]

In [17]:

    

list(numpy.array([2,3])).index(3)


    

    
Out[17]:





1

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