Writing Fortran unformatted files with Python

Question

I have some single-precision little-endian unformatted data files written by Fortran77. I am reading these files using Python using the following commands:

import numpy as np
original_data = np.dtype('float32')
f = open(file_name,'rb')                                                                                                 
original_data = np.fromfile(f,dtype='float32',count=-1)                                                                            
f.close()

After some data manipulation in Python, I (am trying to) write them back in the original format using Python using the following commands:

out_file = open(output_file,"wb")                                                                                             
s = struct.pack('f'*len(manipulated_data), *manipulated_data)                                                                     
out_file.write(s)
out_file.close()

But it doesn't seem to be working. Any ideas what is the right way of writing the data using Python back in the original fortran unformatted format?

Details of the problem:

I am able to read the final file with manipulated data from Fortran. However, I want to visualize these data using a software (Paraview). For this I convert the unformatted data files in the *h5 format. I am able to convert both the original and manipulated data in h5 format using h5 utilities. But while Paraview is able to read the *h5 files created from original data, Paraview is not able to read the *h5 files created from the manipulated data. I am guessing something is being lost in translation.

This is how I am opening the file written by Python in Fortran (single precision data):

open (in_file_id,FILE=in_file,form='unformatted',access='direct',recl=4*n*n*n)

And this is I am writing the original unformatted data by Fortran:

open(out_file_id,FILE=out_file,form="unformatted")

Is this information sufficient?

Answer 1

this is creating an unformatted sequential access file:

open(out_file_id,FILE=out_file,form="unformatted")

Assuming you are writing a single array real a(n,n,n) using simply write(out_file_id)a you should see a file size 4*n^3+8 bytes. The extra 8 bytes being a 4 byte integer (=4n^3) repeated at the start and end of the record.

the second form:

open (in_file_id,FILE=in_file,form='unformatted',access='direct',recl=4*n*n*n)

opens direct acess, which does not have those headers. For writing now you'd have write(unit,rec=1)a. If you read your sequential access file using direct acess it will read without error but you'll get that integer header read as a float (garbage) as the (1,1,1) array value, then everything else is shifted. You say you can read with fortran ,but are you looking to see that you are really reading what you expect?

The best fix to this is to fix your original fortran code to use unformatted,direct access for both reading and writing. This gives you an 'ordinary' raw binary file, no headers.

Alternately in your python you need to first read that 4 byte integer, then your data. On output you could put the integer headers back or not depending on what your paraview filter is expecting.

---------- here is python to read/modify/write an unformatted sequential fortran file containing a single record:

import struct
import numpy as np
f=open('infile','rb')
recl=struct.unpack('i',f.read(4))[0]
numval=recl/np.dtype('float32').itemsize
data=np.fromfile(f,dtype='float32',count=numval)
endrec=struct.unpack('i',f.read(4))[0]
if endrec is not recl: print "error unexpected end rec"
f.close()
f=open('outfile') 
f.write(struct.pack('i',recl))
for i in range(0,len(data)):data[i] = data[i]**2  #example data modification
data.tofile(f)
f.write(struct.pack('i',recl)

just loop for multiple records.. note that the data here is read as a vector and assumed to be all floats. Of course you need to know the actuall data type to make use if it.. Also be aware you may need to deal with byte order issues depending on platform.

Answer 2

Have you tried using the .tofile method of the manipulated data array? It will write the array in C order but is capable of writing plain binary.

The documentation for .tofile also suggests this is the same as:

with open(outfile, 'wb') as fout:
    fout.write(manipulated_data.tostring())