The FortranFile class
This subclass of file is designed to simplify reading of Fortran unformatted binary files which are typically saved in a record-based format.
# Copyright 2008, 2009 Neil Martinsen-Burrell
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"""Defines a file-derived class to read/write Fortran unformatted files.
The assumption is that a Fortran unformatted file is being written by
the Fortran runtime as a sequence of records. Each record consists of
an integer (of the default size [usually 32 or 64 bits]) giving the
length of the following data in bytes, then the data itself, then the
same integer as before.
Examples
--------
To use the default endian and size settings, one can just do::
>>> f = FortranFile('filename')
>>> x = f.readReals()
One can read arrays with varying precisions::
>>> f = FortranFile('filename')
>>> x = f.readInts('h')
>>> y = f.readInts('q')
>>> z = f.readReals('f')
Where the format codes are those used by Python's struct module.
One can change the default endian-ness and header precision::
>>> f = FortranFile('filename', endian='>', header_prec='l')
for a file with little-endian data whose record headers are long
integers.
"""
__docformat__ = "restructuredtext en"
import struct
import numpy
class FortranFile(file):
"""File with methods for dealing with fortran unformatted data files"""
def _get_header_length(self):
return struct.calcsize(self._header_prec)
_header_length = property(fget=_get_header_length)
def _set_endian(self,c):
"""Set endian to big (c='>') or little (c='<') or native (c='@')
:Parameters:
`c` : string
The endian-ness to use when reading from this file.
"""
if c in '<>@=':
self._endian = c
else:
raise ValueError('Cannot set endian-ness')
def _get_endian(self):
return self._endian
ENDIAN = property(fset=_set_endian,
fget=_get_endian,
doc="Possible endian values are '<', '>', '@', '='"
)
def _set_header_prec(self, prec):
if prec in 'hilq':
self._header_prec = prec
else:
raise ValueError('Cannot set header precision')
def _get_header_prec(self):
return self._header_prec
HEADER_PREC = property(fset=_set_header_prec,
fget=_get_header_prec,
doc="Possible header precisions are 'h', 'i', 'l', 'q'"
)
def __init__(self, fname, endian='@', header_prec='i', *args, **kwargs):
"""Open a Fortran unformatted file for writing.
Parameters
----------
endian : character, optional
Specify the endian-ness of the file. Possible values are
'>', '<', '@' and '='. See the documentation of Python's
struct module for their meanings. The deafult is '>' (native
byte order)
header_prec : character, optional
Specify the precision used for the record headers. Possible
values are 'h', 'i', 'l' and 'q' with their meanings from
Python's struct module. The default is 'i' (the system's
default integer).
"""
file.__init__(self, fname, *args, **kwargs)
self.ENDIAN = endian
self.HEADER_PREC = header_prec
def _read_exactly(self, num_bytes):
"""Read in exactly num_bytes, raising an error if it can't be done."""
data = ''
while True:
l = len(data)
if l == num_bytes:
return data
else:
read_data = self.read(num_bytes - l)
if read_data == '':
raise IOError('Could not read enough data.'
' Wanted %d bytes, got %d.' % (num_bytes, l))
data += read_data
def _read_check(self):
return struct.unpack(self.ENDIAN+self.HEADER_PREC,
self._read_exactly(self._header_length)
)[0]
def _write_check(self, number_of_bytes):
"""Write the header for the given number of bytes"""
self.write(struct.pack(self.ENDIAN+self.HEADER_PREC,
number_of_bytes))
def readRecord(self):
"""Read a single fortran record"""
l = self._read_check()
data_str = self._read_exactly(l)
check_size = self._read_check()
if check_size != l:
raise IOError('Error reading record from data file')
return data_str
def writeRecord(self,s):
"""Write a record with the given bytes.
Parameters
----------
s : the string to write
"""
length_bytes = len(s)
self._write_check(length_bytes)
self.write(s)
self._write_check(length_bytes)
def readString(self):
"""Read a string."""
return self.readRecord()
def writeString(self,s):
"""Write a string
Parameters
----------
s : the string to write
"""
self.writeRecord(s)
_real_precisions = 'df'
def readReals(self, prec='f'):
"""Read in an array of real numbers.
Parameters
----------
prec : character, optional
Specify the precision of the array using character codes from
Python's struct module. Possible values are 'd' and 'f'.
"""
_numpy_precisions = {'d': numpy.float64,
'f': numpy.float32
}
if prec not in self._real_precisions:
raise ValueError('Not an appropriate precision')
data_str = self.readRecord()
num = len(data_str)/struct.calcsize(prec)
numbers =struct.unpack(self.ENDIAN+str(num)+prec,data_str)
return numpy.array(numbers, dtype=_numpy_precisions[prec])
def writeReals(self, reals, prec='f'):
"""Write an array of floats in given precision
Parameters
----------
reals : array
Data to write
prec` : string
Character code for the precision to use in writing
"""
if prec not in self._real_precisions:
raise ValueError('Not an appropriate precision')
# Don't use writeRecord to avoid having to form a
# string as large as the array of numbers
length_bytes = len(reals)*struct.calcsize(prec)
self._write_check(length_bytes)
_fmt = self.ENDIAN + prec
for r in reals:
self.write(struct.pack(_fmt,r))
self._write_check(length_bytes)
_int_precisions = 'hilq'
def readInts(self, prec='i'):
"""Read an array of integers.
Parameters
----------
prec : character, optional
Specify the precision of the data to be read using
character codes from Python's struct module. Possible
values are 'h', 'i', 'l' and 'q'
"""
if prec not in self._int_precisions:
raise ValueError('Not an appropriate precision')
data_str = self.readRecord()
num = len(data_str)/struct.calcsize(prec)
return numpy.array(struct.unpack(self.ENDIAN+str(num)+prec,data_str))
def writeInts(self, ints, prec='i'):
"""Write an array of integers in given precision
Parameters
----------
reals : array
Data to write
prec : string
Character code for the precision to use in writing
"""
if prec not in self._int_precisions:
raise ValueError('Not an appropriate precision')
# Don't use writeRecord to avoid having to form a
# string as large as the array of numbers
length_bytes = len(ints)*struct.calcsize(prec)
self._write_check(length_bytes)
_fmt = self.ENDIAN + prec
for item in ints:
self.write(struct.pack(_fmt,item))
self._write_check(length_bytes)