"""
Module to read / write Fortran unformatted sequential files.
This is in the spirit of code written by Neil Martinsen-Burrell and Joe Zuntz.
"""
import warnings
import numpy as np
__all__ = ['FortranFile', 'FortranEOFError', 'FortranFormattingError']
class FortranEOFError(TypeError, OSError):
"""Indicates that the file ended properly.
This error descends from TypeError because the code used to raise
TypeError (and this was the only way to know that the file had
ended) so users might have ``except TypeError:``.
"""
pass
class FortranFormattingError(TypeError, OSError):
"""Indicates that the file ended mid-record.
Descends from TypeError for backward compatibility.
"""
pass
class FortranFile:
"""
A file object for unformatted sequential files from Fortran code.
Parameters
----------
filename : file or str
Open file object or filename.
mode : {'r', 'w'}, optional
Read-write mode, default is 'r'.
header_dtype : dtype, optional
Data type of the header. Size and endianness must match the input/output file.
Notes
-----
These files are broken up into records of unspecified types. The size of
each record is given at the start (although the size of this header is not
standard) and the data is written onto disk without any formatting. Fortran
compilers supporting the BACKSPACE statement will write a second copy of
the size to facilitate backwards seeking.
This class only supports files written with both sizes for the record.
It also does not support the subrecords used in Intel and gfortran compilers
for records which are greater than 2GB with a 4-byte header.
An example of an unformatted sequential file in Fortran would be written as::
OPEN(1, FILE=myfilename, FORM='unformatted')
WRITE(1) myvariable
Since this is a non-standard file format, whose contents depend on the
compiler and the endianness of the machine, caution is advised. Files from
gfortran 4.8.0 and gfortran 4.1.2 on x86_64 are known to work.
Consider using Fortran direct-access files or files from the newer Stream
I/O, which can be easily read by `numpy.fromfile`.
Examples
--------
To create an unformatted sequential Fortran file:
>>> from scipy.io import FortranFile
>>> import numpy as np
>>> f = FortranFile('test.unf', 'w')
>>> f.write_record(np.array([1,2,3,4,5], dtype=np.int32))
>>> f.write_record(np.linspace(0,1,20).reshape((5,4)).T)
>>> f.close()
To read this file:
>>> f = FortranFile('test.unf', 'r')
>>> print(f.read_ints(np.int32))
[1 2 3 4 5]
>>> print(f.read_reals(float).reshape((5,4), order="F"))
[[0. 0.05263158 0.10526316 0.15789474]
[0.21052632 0.26315789 0.31578947 0.36842105]
[0.42105263 0.47368421 0.52631579 0.57894737]
[0.63157895 0.68421053 0.73684211 0.78947368]
[0.84210526 0.89473684 0.94736842 1. ]]
>>> f.close()
Or, in Fortran::
integer :: a(5), i
double precision :: b(5,4)
open(1, file='test.unf', form='unformatted')
read(1) a
read(1) b
close(1)
write(*,*) a
do i = 1, 5
write(*,*) b(i,:)
end do
"""
def __init__(self, filename, mode='r', header_dtype=np.uint32):
if header_dtype is None:
raise ValueError('Must specify dtype')
header_dtype = np.dtype(header_dtype)
if header_dtype.kind != 'u':
warnings.warn("Given a dtype which is not unsigned.", stacklevel=2)
if mode not in 'rw' or len(mode) != 1:
raise ValueError('mode must be either r or w')
if hasattr(filename, 'seek'):
self._fp = filename
else:
self._fp = open(filename, f'{mode}b')
self._header_dtype = header_dtype
def _read_size(self, eof_ok=False):
n = self._header_dtype.itemsize
b = self._fp.read(n)
if (not b) and eof_ok:
raise FortranEOFError("End of file occurred at end of record")
elif len(b) < n:
raise FortranFormattingError(
"End of file in the middle of the record size")
return int(np.frombuffer(b, dtype=self._header_dtype, count=1)[0])
def write_record(self, *items):
"""
Write a record (including sizes) to the file.
Parameters
----------
*items : array_like
The data arrays to write.
Notes
-----
Writes data items to a file::
write_record(a.T, b.T, c.T, ...)
write(1) a, b, c, ...
Note that data in multidimensional arrays is written in
row-major order --- to make them read correctly by Fortran
programs, you need to transpose the arrays yourself when
writing them.
"""
items = tuple(np.asarray(item) for item in items)
total_size = sum(item.nbytes for item in items)
nb = np.array([total_size], dtype=self._header_dtype)
nb.tofile(self._fp)
for item in items:
item.tofile(self._fp)
nb.tofile(self._fp)
def read_record(self, *dtypes, **kwargs):
"""
Reads a record of a given type from the file.
Parameters
----------
*dtypes : dtypes, optional
Data type(s) specifying the size and endianness of the data.
Returns
-------
data : ndarray
A 1-D array object.
Raises
------
FortranEOFError
To signal that no further records are available
FortranFormattingError
To signal that the end of the file was encountered
part-way through a record
Notes
-----
If the record contains a multidimensional array, you can specify
the size in the dtype. For example::
INTEGER var(5,4)
can be read with::
read_record('(4,5)i4').T
Note that this function does **not** assume the file data is in Fortran
column major order, so you need to (i) swap the order of dimensions
when reading and (ii) transpose the resulting array.
Alternatively, you can read the data as a 1-D array and handle the
ordering yourself. For example::
read_record('i4').reshape(5, 4, order='F')
For records that contain several variables or mixed types (as opposed
to single scalar or array types), give them as separate arguments::
double precision :: a
integer :: b
write(1) a, b
record = f.read_record('