Reading a binary file with python

Question

I find particularly difficult reading binary file with Python  Can you give me a hand  I need to read this file  which in Fortran 90 is easily read by  int 4 n particles  n groups real 4 group id n particles  read     n particles  n groups read      group id j  j 1 n particles    In detail  the file format is   Bytes 1-4 -- The integer 8  Bytes 5-8 -- The number of particles  N  Bytes 9-12 -- The number of groups  Bytes 13-16 -- The integer 8  Bytes 17-20 -- The integer 4 N  Next many bytes -- The group ID numbers for all the particles  Last 4 bytes -- The integer 4 N     How can I read this with Python  I tried everything but it never worked  Is there any chance I might use a f90 program in python  reading this binary file and then save the data that I need to use

User · Answer

You could use numpy fromfile  which can read data from both text and binary files  You would first construct a data type  which represents your file format  using numpy dtype  and then read this type from file using numpy fromfile

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I too found Python lacking when it comes to reading and writing binary files  so I wrote a small module  for Python 3 6    With binaryfile you d do something like this  I m guessing  since I don t know Fortran   import binaryfile  def particle file f       f array  group ids      Declare group ids to be an array  so we can use it in a loop      f skip 4     Bytes 1-4     num particles   f count  num particles    group ids   4     Bytes 5-8     f int  num groups   4     Bytes 9-12     f skip 8     Bytes 13-20     for i in range num particles           f struct  group ids     gt f      4 bytes x num particles     f skip 4   with open  myfile bin    rb   as fh      result   binaryfile read fh  particle file  print result   Which produces an output like this         group ids     1 0     0 0     2 0     0 0     1 0            skipped    b  x00 x00 x00 x08   b  x00 x00 x00 x08 x00 x00 x00 x14   b  x00 x00 x00 x14         num particles   5       num groups   3    I used skip   to skip the additional data Fortran adds  but you may want to add a utility to handle Fortran records properly instead  If you do  a pull request would be welcome

User · Answer

Read the binary file content like this   with open fileName  mode  rb   as file    b is important - gt  binary     fileContent   file read     then  unpack  binary data using struct unpack   The start bytes  struct unpack  iiiii   fileContent  20    The body  ignore the heading bytes and the trailing byte    24   The remaining part forms the body  to know the number of bytes in the body do an integer division by 4  The obtained quotient is multiplied by the string  i  to create the correct format for the unpack method   struct unpack  i      len fileContent  -24     4   fileContent 20 -4     The end byte  struct unpack  i   fileContent -4

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To read a binary file to a bytes object   from pathlib import Path data   Path   path to file   read bytes      Python 3 5    To create an int from bytes 0-3 of the data   i   int from bytes data  4   byteorder  little   signed False    To unpack multiple ints from the data   import struct ints   struct unpack  iiii   data  16      pathlib int from bytes   struct

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import pickle f open  filename dat   rb   try      while True          x pickle load f          print x except EOFError      pass f close

User · Answer

In general  I would recommend that you look into using Python s struct module for this  It s standard with Python  and it should be easy to translate your question s specification into a formatting string suitable for struct unpack     Do note that if there s  invisible  padding between around the fields  you will need to figure that out and include it in the unpack   call  or you will read the wrong bits   Reading the contents of the file in order to have something to unpack is pretty trivial   import struct  data   open  from fortran bin    rb   read     eight  N    struct unpack   II   data    This unpacks the first two fields  assuming they start at the very beginning of the file  no padding or extraneous data   and also assuming native byte-order  the   symbol   The Is in the formatting string mean  unsigned integer  32 bits

[python] Reading a binary file with python

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