CODEWITHSUNDEEP
pythonarrayspython-2.7numpybinaryfiles
Pakox.Wang
Pakox.Wang

Reputation: 61

Python - Reading and Writing Structured Binary Files

Currently I'm trying to manipulate a kind of binary file, which structure is like this:

FileHeader + [SectionHeader + Binary(1D-array)] * NumSetions

After searching on the internet, I came up with the following code to read it:

import numpy as np

# Always BIG Endian
#file_header bytes: 12
file_header_dtype = np.dtype([
    ('nsection', '>i4'), # number of sections
    ('nsample', '>i4'), # number of samples for each section
    ('dt', '>f4'), # sampling rate
    ])

#section_header bytes: 28
section_header_dtype = np.dtype([
    ('rec', '>i4'), # record number
    ('x', '>f8'), # x, in meter
    ('y', '>f8'), # y, in meter
    ('z', '>f8'), # z, in meter
    ])

def dtype_section(nt):
    return np.dtype(section_header_dtype.descr + [('binary', ('>f4',nt))])

def read_file_header(_file):
    with open(_file, 'rb') as f:
        file_header = np.fromstring(f.read(12), dtype=file_header_dtype)
    return file_header

def readFile(filename):
    raw = open(filename, 'rb')
    file_header = np.fromstring(raw.read(12), dtype=file_header_dtype)
    nt = file_header['nsample'][0]
    dtype_file_sections = dtype_section(nt)
    data = np.fromstring(raw.read(), dtype=dtype_file_sections)
    return (file_header, data)

With this way, I can easily call the header-striped binary part and perform plt.imshow or anything else.

data = readFile('site1.bin')
data_arr = data[1]['binary']
#plt.imshow(data_arr)

The problem is, I cannot find a way to output the data while maintaining same data structure

ndarray.tofile() only works for one array per time

And np.array((data[0],data[1])).tofile('test') would cause IOError

IOError: cannot write object arrays to a file in binary mode

I'm pretty new to Python and I'm not sure if I made any mistake. Or should I consider another way to read this kind of file, rather than using numpy.dtype? Please help me.

Upvotes: 3

Views: 686

Answers (1)

juanpa.arrivillaga
juanpa.arrivillaga

Reputation: 95948

The straightforward way would be to simply write to a binary file:

with open('test','wb') as f:
    f.write(data[0].tobytes())
    f.write(data[1].tobytes())

Upvotes: 2

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