PyTables read random subset

Question

Is it possible to read a random subset of rows from HDF5 (via pyTables or, preferably pandas)? I have a very large dataset with million of rows, but only need a sample of few th

Answer 1

Using HDFStore docs are here, compression docs are here

Random access via a constructed index is supported in 0.13

In [26]: df = DataFrame(np.random.randn(100,2),columns=['A','B'])

In [27]: df.to_hdf('test.h5','df',mode='w',format='table')

In [28]: store = pd.HDFStore('test.h5')

In [29]: nrows = store.get_storer('df').nrows

In [30]: nrows
Out[30]: 100

In [32]: r = np.random.randint(0,nrows,size=10)

In [33]: r
Out[33]: array([69, 28,  8,  2, 14, 51, 92, 25, 82, 64])

In [34]: pd.read_hdf('test.h5','df',where=pd.Index(r))
Out[34]: 
           A         B
69 -0.370739 -0.325433
28  0.155775  0.961421
8   0.101041 -0.047499
2   0.204417  0.470805
14  0.599348  1.174012
51  0.634044 -0.769770
92  0.240077 -0.154110
25  0.367211 -1.027087
82 -0.698825 -0.084713
64 -1.029897 -0.796999

[10 rows x 2 columns]

To include an additional condition you would do like this:

# make sure that we have indexable columns
df.to_hdf('test.h5','df',mode='w',format='table',data_columns=True)

# select where the index (an integer index) matches r and A > 0
In [14]: r
Out[14]: array([33, 51, 33, 95, 69, 21, 43, 58, 58, 58])

In [13]: pd.read_hdf('test.h5','df',where='index=r & A>0')
Out[13]: 
           A         B
21  1.456244  0.173443
43  0.174464 -0.444029

[2 rows x 2 columns]