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Python:h5py给出了一个错误:无法读取数据(inflate()失败),即使之前已经打开了它

h5py numpy python-3.x python

ojunk · 技术社区 · 8 年前

Python 3.5。我有几百个。目录中的mat文件(版本7.3)。我正在遍历所有这些数据以提取数据的两个不同部分。我循环得到第一批数据,没有任何问题,但当我再次做完全相同的事情时,只提取了数据的不同部分,我得到了以下错误:

Traceback (most recent call last):
  File "v73_test.py", line 43, in <module>
    mrfs_data = extract.convert1simProteinComCountsIntoDataFrame(path2mats)
  File "/home/oli/Downloads/PhD/wc/mg/version_73_stuff/functions_for_joshuas_matFiles/extract_matFile_data_v73.py", line 586, in convert1simProteinComCountsIntoDataFrame
    raw_data = getMatureProteinComplexs(path2mats, state_no)
  File "/home/oli/Downloads/PhD/wc/mg/version_73_stuff/functions_for_joshuas_matFiles/extract_matFile_data_v73.py", line 53, in getMatureProteinComplexs
    if len(np.array(state_file['ProteinComplex']['counts']).shape) == 3:
  File "h5py/_objects.pyx", line 54, in h5py._objects.with_phil.wrapper
  File "h5py/_objects.pyx", line 55, in h5py._objects.with_phil.wrapper
  File "/home/oli/virtualenvs/standard_python3.5/lib/python3.5/site-packages/h5py/_hl/dataset.py", line 696, in __array__
    self.read_direct(arr)
  File "/home/oli/virtualenvs/standard_python3.5/lib/python3.5/site-packages/h5py/_hl/dataset.py", line 657, in read_direct
    self.id.read(mspace, fspace, dest, dxpl=self._dxpl)
  File "h5py/_objects.pyx", line 54, in h5py._objects.with_phil.wrapper
  File "h5py/_objects.pyx", line 55, in h5py._objects.with_phil.wrapper
  File "h5py/h5d.pyx", line 181, in h5py.h5d.DatasetID.read
  File "h5py/_proxy.pyx", line 130, in h5py._proxy.dset_rw
  File "h5py/_proxy.pyx", line 84, in h5py._proxy.H5PY_H5Dread
OSError: Can't read data (inflate() failed)

所以文件肯定在那里并且可以访问,所以我唯一能想到的是数据被破坏了,但如果是这样的话,我肯定无法从中提取任何数据?

2 回复 | 直到 8 年前

ojunk 7 年前

我在这里回答了我自己的问题,因为网上没有太多关于这个错误的信息,我学到了一些东西,所以也许它会帮助其他人。

因此,我意识到数据实际上已经损坏。我认为如果一个文件被破坏了,那么你将无法从中提取任何东西,但事实证明,在这种情况下,这不是真的,你唯一不能访问的是被破坏的特定位。基于对其他版本的的经验,这不是我所期望的。但是现在我想这个版本实际上是什么,看起来有点明显。

DarylVanDam 6 年前

Python 3.6。我遇到了类似的问题,我可以读取输出数据(2D SHETRAN水文模型中给定网格单元的数据),例如,直到第24个时间步长:

 f['VARIABLES']['  6 srf_dep']['value'][0,0,24]

 Out[272]: -1.0

但到了第240个时间点,我得到了同样的错误:

['VARIABLES']['  6 srf_dep']['value'][0,0,240]


 Traceback (most recent call last):

  File "<ipython-input-273-1f12011309c3>", line 1, in <module>
    f['VARIABLES']['  6 srf_dep']['value'][0,0,240]

  File "h5py\_objects.pyx", line 54, in h5py._objects.with_phil.wrapper

  File "h5py\_objects.pyx", line 55, in h5py._objects.with_phil.wrapper

  File "C:\Anaconda3\lib\site-packages\h5py\_hl\dataset.py", line 496, in __getitem__
    self.id.read(mspace, fspace, arr, mtype, dxpl=self._dxpl)

  File "h5py\_objects.pyx", line 54, in h5py._objects.with_phil.wrapper

  File "h5py\_objects.pyx", line 55, in h5py._objects.with_phil.wrapper

  File "h5py\h5d.pyx", line 181, in h5py.h5d.DatasetID.read

  File "h5py\_proxy.pyx", line 130, in h5py._proxy.dset_rw

  File "h5py\_proxy.pyx", line 84, in h5py._proxy.H5PY_H5Dread

 OSError: Can't read data (inflate() failed)

我通过删除有问题的H5文件,重新打开IDE并再次运行来解决这个问题。谢谢你的解决方案。