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h5sparse
Scipy sparse matrix in HDF5.
Installation
pip install h5sparseTesting
for single environment:
python setup.py testfor all environments:
tox
Examples
Create dataset
In [1]: import scipy.sparse as ss
...: import h5sparse
...: import numpy as np
...:
In [2]: sparse_matrix = ss.csr_matrix([[0, 1, 0],
...: [0, 0, 1],
...: [0, 0, 0],
...: [1, 1, 0]],
...: dtype=np.float64)
In [3]: # create dataset from scipy sparse matrix
...: with h5sparse.File("test.h5") as h5f:
...: h5f.create_dataset('sparse/matrix', data=sparse_matrix)
In [4]: # you can also create dataset from another dataset
...: with h5sparse.File("test.h5") as h5f:
...: h5f.create_dataset('sparse/matrix2', data=h5f['sparse/matrix'])
In [5]: # you can also create dataset using the formats that original h5py accepts
...: with h5sparse.File("test.h5") as h5f:
...: h5f.create_dataset('sparse/matrix3', data=[1,2,3])Read dataset
In [6]: h5f = h5sparse.File("test.h5")
In [7]: h5f['sparse/matrix'][1:3]
Out[7]:
<2x3 sparse matrix of type '<class 'numpy.float64'>'
with 1 stored elements in Compressed Sparse Row format>
In [8]: h5f['sparse/matrix'][1:3].toarray()
Out[8]:
array([[ 0., 0., 1.],
[ 0., 0., 0.]])
In [9]: h5f['sparse']['matrix'][1:3].toarray()
Out[9]:
array([[ 0., 0., 1.],
[ 0., 0., 0.]])
In [10]: h5f['sparse']['matrix'][2:].toarray()
Out[10]:
array([[ 0., 0., 0.],
[ 1., 1., 0.]])
In [11]: h5f['sparse']['matrix'][:2].toarray()
Out[11]:
array([[ 0., 1., 0.],
[ 0., 0., 1.]])
In [12]: h5f['sparse']['matrix'][-2:].toarray()
Out[12]:
array([[ 0., 0., 0.],
[ 1., 1., 0.]])
In [13]: h5f['sparse']['matrix'][:-2].toarray()
Out[13]:
array([[ 0., 1., 0.],
[ 0., 0., 1.]])
In [14]: h5f['sparse']['matrix'][()].toarray()
Out[14]:
array([[ 0., 1., 0.],
[ 0., 0., 1.],
[ 0., 0., 0.],
[ 1., 1., 0.]])
In [15]: import h5py
In [16]: h5py_h5f = h5py.File("test.h5")
In [17]: h5sparse.Group(h5py_h5f.id)['sparse/matrix'][()]
Out[17]:
<4x3 sparse matrix of type '<class 'numpy.float64'>'
with 4 stored elements in Compressed Sparse Row format>
In [18]: h5sparse.Group(h5py_h5f['sparse'].id)['matrix'][()]
Out[18]:
<4x3 sparse matrix of type '<class 'numpy.float64'>'
with 4 stored elements in Compressed Sparse Row format>
In [19]: h5sparse.Dataset(h5py_h5f['sparse/matrix'])[()]
Out[19]:
<4x3 sparse matrix of type '<class 'numpy.float64'>'
with 4 stored elements in Compressed Sparse Row format>Append dataset
In [20]: to_append = ss.csr_matrix([[0, 1, 1],
...: [1, 0, 0]],
...: dtype=np.float64)
In [21]: h5f.create_dataset('matrix', data=sparse_matrix, chunks=(100000,),
...: maxshape=(None,))
In [22]: h5f['matrix'].append(to_append)
In [23]: h5f['matrix'][()]
Out[23]:
<6x3 sparse matrix of type '<class 'numpy.float64'>'
with 7 stored elements in Compressed Sparse Row format>
In [24]: h5f['matrix'][()].toarray()
Out[24]:
array([[ 0., 1., 0.],
[ 0., 0., 1.],
[ 0., 0., 0.],
[ 1., 1., 0.],
[ 0., 1., 1.],
[ 1., 0., 0.]])
Release files for h5sparse 0.1.0
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Total release size: 11.4 kB
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