How to read HDF5 files in Python

Question

I am trying to read data from hdf5 file in Python  I can read the hdf5 file using h5py  but I cannot figure out how to access data within the file   My code  import h5py     import numpy as np     f1   h5py File file name  r          This works and the file is read  But how can I access data inside the file object f1

User · Answer

from keras models import load model   h  load model  FILE NAME h5

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you can use Pandas   import pandas as pd pd read hdf filename key

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Using bits of answers from this question and the latest doc  I was able to extract my numerical arrays using  import h5py with h5py File filename   r   as h5f      h5x   h5f list h5f keys    0    x         Where  x  is simply the X coordinate in my case

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Read HDF5  import h5py filename    file hdf5   with h5py File filename   r   as f        List all groups     print  Keys   s    f keys        a group key   list f keys    0         Get the data     data   list f a group key     Write HDF5  import h5py    Create random data import numpy as np data matrix   np random uniform -1  1  size  10  3      Write data to HDF5 with h5py File  file hdf5    w   as data file      data file create dataset  group name   data data matrix    See h5py docs for more information   Alternatives   JSON  Nice for writing human-readable data  VERY commonly used  read  amp  write  CSV  Super simple format  read  amp  write  pickle  A Python serialization format  read  amp  write  MessagePack  Python package   More compact representation  read  amp  write  HDF5  Python package   Nice for matrices  read  amp  write  XML  exists too  sigh   read  amp  write    For your application  the following might be important    Support by other programming languages Reading   writing performance Compactness  file size    See also  Comparison of data serialization formats  In case you are rather looking for a way to make configuration files  you might want to read my short article Configuration files in Python

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To read the content of  hdf5 file as an array  you can do something as follow   gt  import numpy as np   gt  myarray   np fromfile  file hdf5   dtype float   gt  print myarray

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Use below code to data read and convert into numpy array  import h5py f1   h5py File  data 1 h5    r   list f1 keys    X1   f1  x   y1 f1  y   df1  np array X1 value  dfy1  np array y1 value  print  df1 shape  print  dfy1 shape

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Reading the file   import h5py  f   h5py File file name  mode    Studying the structure of the file by printing what HDF5 groups are present  for key in f keys        print key   Names of the groups in HDF5 file    Extracting the data   Get the HDF5 group group   f key    Checkout what keys are inside that group  for key in group keys        print key   data   group some key inside the group  value  Do whatever you want with data   After you are done f close

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If you have named datasets in the hdf file then you can use the following code to read and convert these datasets in numpy arrays  import h5py file   h5py File  filename h5    r    xdata   file get  xdata   xdata  np array xdata   If your file is in a different directory you can add the path in front of filename h5

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What you need to do is create a dataset  If you take a look at the quickstart guide  it shows you that you need to use the file object in order to create a dataset  So  f create dataset and then you can read the data  This is explained in the docs

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Here s a simple function I just wrote which reads a  hdf5 file generated by the save weights function in keras and returns a dict with layer names and weights   def read hdf5 path        weights           keys          with h5py File path   r   as f    open file         f visit keys append    append all keys to list         for key in keys              if     in key    contains data if     in key                 print f key  name                  weights f key  name    f key  value     return weights   https   gist github com Attila94 fb917e03b04035f3737cc8860d9e9f9b   Haven t tested it thoroughly but does the job for me

[python] How to read HDF5 files in Python

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