python - h5py:如何读取 hdf5 文件的选定行？

Question

是否可以在不加载整个文件的情况下从 hdf5 文件中读取一组给定的行？我有相当大的 hdf5 文件，其中包含大量数据集，这是我想减少时间和内存使用的示例:

#! /usr/bin/env python

import numpy as np
import h5py

infile = 'field1.87.hdf5'
f = h5py.File(infile,'r')
group = f['Data']

mdisk = group['mdisk'].value

val = 2.*pow(10.,10.)
ind = np.where(mdisk>val)[0]

m = group['mcold'][ind]
print m

ind 给出的不是连续的行，而是分散的行。

上面的代码失败了，但它遵循了切片 hdf5 数据集的标准方法。我收到的错误消息是:

Traceback (most recent call last):
  File "./read_rows.py", line 17, in <module>
    m = group['mcold'][ind]
  File "/cosma/local/Python/2.7.3/lib/python2.7/site-packages/h5py-2.3.1-py2.7-linux-x86_64.egg/h5py/_hl/dataset.py", line 425, in __getitem__
    selection = sel.select(self.shape, args, dsid=self.id)
  File "/cosma/local/Python/2.7.3/lib/python2.7/site-packages/h5py-2.3.1-py2.7-linux-x86_64.egg/h5py/_hl/selections.py", line 71, in select
    sel[arg]
  File "/cosma/local/Python/2.7.3/lib/python2.7/site-packages/h5py-2.3.1-py2.7-linux-x86_64.egg/h5py/_hl/selections.py", line 209, in __getitem__
    raise TypeError("PointSelection __getitem__ only works with bool arrays")
TypeError: PointSelection __getitem__ only works with bool arrays

Answer 1

我有一个示例 h5py 文件:

data = f['data']
#  <HDF5 dataset "data": shape (3, 6), type "<i4">
# is arange(18).reshape(3,6)
ind=np.where(data[:]%2)[0]
# array([0, 0, 0, 1, 1, 1, 2, 2, 2], dtype=int32)
data[ind]  # getitem only works with boolean arrays error
data[ind.tolist()] # can't read data (Dataset: Read failed) error

最后一个错误是由列表中的重复值引起的。

但是使用具有唯一值的列表进行索引工作正常

In [150]: data[[0,2]]
Out[150]: 
array([[ 0,  1,  2,  3,  4,  5],
       [12, 13, 14, 15, 16, 17]])

In [151]: data[:,[0,3,5]]
Out[151]: 
array([[ 0,  3,  5],
       [ 6,  9, 11],
       [12, 15, 17]])

具有适当维度切片的数组也是如此:

In [157]: data[ind[[0,3,6]],:]
Out[157]: 
array([[ 0,  1,  2,  3,  4,  5],
       [ 6,  7,  8,  9, 10, 11],
       [12, 13, 14, 15, 16, 17]])
In [165]: f['data'][:2,np.array([0,3,5])]
Out[165]: 
array([[ 0,  3,  5],
       [ 6,  9, 11]])
In [166]: f['data'][[0,1],np.array([0,3,5])]  
# errror about only one indexing array allowed

因此，如果索引是正确的 - 唯一值，并且匹配数组维度，它应该可以工作。

我的简单示例并未测试加载了多少数组。文档听起来好像是从文件中选择元素，而不是将整个数组加载到内存中。