我以前从未使用过HDF5文件，为了开始我收到了一些示例文件。我一直在查看h5py的所有基础知识，查看这些文件中的不同组，它们的名称，键，值等等。一切正常，直到我想查看组中保存的数据集。我得到他们的.shape和.dtype，但当我尝试通过索引（例如grp["dset"][0]）访问随机值时，我收到以下错误：
IOError Traceback (most recent call last)
<ipython-input-45-509cebb66565> in <module>()
1 print geno["matrix"].shape
2 print geno["matrix"].dtype
----> 3 geno["matrix"][0]
/home/sarah/anaconda/lib/python2.7/site-packages/h5py/_hl/dataset.pyc in __getitem__(self, args)
443 mspace = h5s.create_simple(mshape)
444 fspace = selection._id
--> 445 self.id.read(mspace, fspace, arr, mtype)
446
447 # Patch up the output for NumPy
/home/sarah/anaconda/lib/python2.7/site-packages/h5py/h5d.so in h5py.h5d.DatasetID.read (h5py/h5d.c:2782)()
/home/sarah/anaconda/lib/python2.7/site-packages/h5py/_proxy.so in h5py._proxy.dset_rw (h5py/_proxy.c:1709)()
/home/sarah/anaconda/lib/python2.7/site-packages/h5py/_proxy.so in h5py._proxy.H5PY_H5Dread (h5py/_proxy.c:1379)()
IOError: Can't read data (Can't open directory)
我在h5py Google group中发布了这个问题，建议在我没有安装的数据集上有一个过滤器。但据我所知，HDF5文件仅使用gzip压缩创建，应该是便携式标准。 有人知道我在这里可能会缺少什么吗？我甚至无法在任何地方找到此错误或类似问题的描述，并且可以使用HDFView软件轻松打开文件，包括有问题的数据集。
编辑 显然，出现此错误是因为由于某种原因，我的系统上没有gzip压缩过滤器。如果我尝试使用gzip压缩创建示例文件，则会发生以下情况：
---------------------------------------------------------------------------
ValueError Traceback (most recent call last)
<ipython-input-33-dd7b9e3b6314> in <module>()
1 grp = f.create_group("subgroup")
----> 2 grp_dset = grp.create_dataset("dataset", (50,), dtype="uint8", chunks=True, compression="gzip")
/home/sarah/anaconda/lib/python2.7/site-packages/h5py/_hl/group.pyc in create_dataset(self, name, shape, dtype, data, **kwds)
92 """
93
---> 94 dsid = dataset.make_new_dset(self, shape, dtype, data, **kwds)
95 dset = dataset.Dataset(dsid)
96 if name is not None:
/home/sarah/anaconda/lib/python2.7/site-packages/h5py/_hl/dataset.pyc in make_new_dset(parent, shape, dtype, data, chunks, compression, shuffle, fletcher32, maxshape, compression_opts, fillvalue, scaleoffset, track_times)
97
98 dcpl = filters.generate_dcpl(shape, dtype, chunks, compression, compression_opts,
---> 99 shuffle, fletcher32, maxshape, scaleoffset)
100
101 if fillvalue is not None:
/home/sarah/anaconda/lib/python2.7/site-packages/h5py/_hl/filters.pyc in generate_dcpl(shape, dtype, chunks, compression, compression_opts, shuffle, fletcher32, maxshape, scaleoffset)
101
102 if compression not in encode:
--> 103 raise ValueError('Compression filter "%s" is unavailable' % compression)
104
105 if compression == 'gzip':
ValueError: Compression filter "gzip" is unavailable
有人有经验吗？ HDF5库以及h5py软件包的安装似乎没有出错......
不能只评论 - 声誉太低。
我有同样的问题，只需运行“conda update anaconda”，问题就消失了。
我有一个类似的问题，
$ python3 -c 'import h5py; f=h5py.File("file.h5"); d=f["FVC"][:,:]'
Traceback (most recent call last):
File "<string>", line 1, in <module>
File "h5py/_objects.pyx", line 54, in h5py._objects.with_phil.wrapper (/home/ilan/minonda/conda-bld/work/h5py/_objects.c:2696)
File "h5py/_objects.pyx", line 55, in h5py._objects.with_phil.wrapper (/home/ilan/minonda/conda-bld/work/h5py/_objects.c:2654)
File "/home/pinaultf/system/anaconda2/envs/deveg-dev/lib/python3.5/site-packages/h5py/_hl/dataset.py", line 482, in __getitem__
self.id.read(mspace, fspace, arr, mtype, dxpl=self._dxpl)
File "h5py/_objects.pyx", line 54, in h5py._objects.with_phil.wrapper (/home/ilan/minonda/conda-bld/work/h5py/_objects.c:2696)
File "h5py/_objects.pyx", line 55, in h5py._objects.with_phil.wrapper (/home/ilan/minonda/conda-bld/work/h5py/_objects.c:2654)
File "h5py/h5d.pyx", line 181, in h5py.h5d.DatasetID.read (/home/ilan/minonda/conda-bld/work/h5py/h5d.c:3240)
File "h5py/_proxy.pyx", line 130, in h5py._proxy.dset_rw (/home/ilan/minonda/conda-bld/work/h5py/_proxy.c:1869)
File "h5py/_proxy.pyx", line 84, in h5py._proxy.H5PY_H5Dread (/home/ilan/minonda/conda-bld/work/h5py/_proxy.c:1517)
OSError: Can't read data (Can't open directory)
我在一个虚拟环境中遇到此问题而在另一个虚拟环境中没有，即使显然h5py版本相同（2.6.0）。
我解决了这个问题：
$ pip uninstall h5py
$ pip install h5py
我有同样的问题。我用它解决了
import tables
它现在工作正常