[python] Reading a binary file with python

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?

import pickle
f=open("filename.dat","rb")
try:
    while True:
        x=pickle.load(f)
        print x
except EOFError:
    pass
f.close()

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".

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.

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

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', '>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.