IOError:无法读取数据(无法打开目录) - 缺少 gzip 压缩过滤器 [英] IOError: Can't read data (Can't open directory) - Missing gzip compression filter

问题描述

我以前从未使用过 HDF5 文件，开始时我收到了一些示例文件.我一直在使用 h5py 查看所有基础知识，查看这些文件中的不同组、它们的名称、键、值等等.一切正常，直到我想查看保存在组中的数据集.我得到了他们的 .shape 和 .dtype，但是当我尝试通过索引访问随机值时(例如 grp["dset"][0])，我收到以下错误:

I have never worked with HDF5 files before, and to get started I received some example files. I've been checking out all the basics with h5py, looking at the different groups in these files, their names, keys, values and so on. Everything works fine, until I want to look at the datasets that are saved in the groups. I get their .shape and .dtype, but when I try accessing a random value by indexing (e.g. grp["dset"][0]), I get the following error:

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)

我已在 h5py Google 组中发布了这个问题，有人建议我没有安装的数据集上可能有一个过滤器.但是 HDF5 文件是仅使用 gzip 压缩创建的，据我了解，这应该是一种可移植的标准.
有人知道我在这里可能会错过什么吗?我什至在任何地方都找不到这个错误或类似问题的描述，而且文件，包括有问题的数据集，都可以用 HDFView 软件轻松打开.

I've posted this problem in the h5py Google group, where it was suggested that there might be a filter on the dataset I don't have installed. But the HDF5 file was created using only gzip compression, which should be a portable standard, as far as I understood.
Does someone know what I might be missing here? I can't even find a description of this error or similar problems anywhere, and the file, including the problematic dataset, can be easily opened with the HDFView software.

编辑
显然，发生此错误是因为出于某种原因，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，则会发生这种情况:

Edit
Apparently, this error occurs because, for some reason, the gzip compression filter is not available on my system. If I try to create an example file with gzip compression, this happens:

---------------------------------------------------------------------------
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

有人有这方面的经验吗?HDF5库以及h5py包的安装好像没有出错...

Does anyone have experience with that? The installation of the HDF5 library as well as the h5py package didn't seem to go wrong...

推荐答案

不能只评论 - 声誉太低.

Can't just comment - reputation too low.

我遇到了同样的问题，只需运行conda update anaconda"，问题就消失了.

I had the same issue, simply ran "conda update anaconda" and the problem is gone.

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