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fortranfile.py
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fortranfile.py
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# Copyright 2008-2010 Neil Martinsen-Burrell
#
# Permission is hereby granted, free of charge, to any person obtaining a copy
# of this software and associated documentation files (the "Software"), to deal
# in the Software without restriction, including without limitation the rights
# to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
# copies of the Software, and to permit persons to whom the Software is
# furnished to do so, subject to the following conditions:
# The above copyright notice and this permission notice shall be included in
# all copies or substantial portions of the Software.
# THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
# IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
# FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
# AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
# LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
# OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
# THE SOFTWARE.
"""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 precision 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
numpy
class
FortranFile
(
file
):
"""File with methods for dealing with fortran unformatted data files"""
def
_get_header_length
(
self
):
return
numpy
.
dtype
(
self
.
_header_prec
)
.
itemsize
_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
'<>@='
:
if
c
==
'@'
:
c
=
'='
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
numpy
.
fromstring
(
self
.
_read_exactly
(
self
.
_header_length
),
dtype
=
self
.
ENDIAN
+
self
.
HEADER_PREC
)[
0
]
def
_write_check
(
self
,
number_of_bytes
):
"""Write the header for the given number of bytes"""
self
.
write
(
numpy
.
array
(
number_of_bytes
,
dtype
=
self
.
ENDIAN
+
self
.
HEADER_PREC
,)
.
tostring
()
)
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
()
return
numpy
.
fromstring
(
data_str
,
dtype
=
self
.
ENDIAN
+
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'
)
nums
=
numpy
.
array
(
reals
,
dtype
=
self
.
ENDIAN
+
prec
)
self
.
writeRecord
(
nums
.
tostring
())
_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
()
return
numpy
.
fromstring
(
data_str
,
dtype
=
self
.
ENDIAN
+
prec
)
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'
)
nums
=
numpy
.
array
(
ints
,
dtype
=
self
.
ENDIAN
+
prec
)
self
.
writeRecord
(
nums
.
tostring
())
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