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"""
Module for reading and writing matlab (TM) .mat files
"""
# Authors: Travis Oliphant, Matthew Brett
from __future__ import division, print_function, absolute_import
import os
import sys
import warnings
from scipy.lib.six import string_types
from .miobase import get_matfile_version, docfiller
from .mio4 import MatFile4Reader, MatFile4Writer
from .mio5 import MatFile5Reader, MatFile5Writer
__all__ = ['find_mat_file', 'mat_reader_factory', 'loadmat', 'savemat',
'whosmat']
@docfiller
def find_mat_file(file_name, appendmat=True):
''' Try to find .mat file on system path
Parameters
----------
file_name : str
file name for mat file
%(append_arg)s
Returns
-------
full_name : string
possibly modified name after path search
'''
warnings.warn('Searching for mat files on python system path will be ' +
'removed in next version of scipy',
DeprecationWarning, stacklevel=2)
if appendmat and file_name.endswith(".mat"):
file_name = file_name[:-4]
if os.sep in file_name:
full_name = file_name
if appendmat:
full_name = file_name + ".mat"
else:
full_name = None
junk, file_name = os.path.split(file_name)
for path in [os.curdir] + list(sys.path):
test_name = os.path.join(path, file_name)
if appendmat:
test_name += ".mat"
try:
fid = open(test_name,'rb')
fid.close()
full_name = test_name
break
except IOError:
pass
return full_name
def _open_file(file_like, appendmat):
''' Open `file_like` and return as file-like object '''
if isinstance(file_like, string_types):
try:
return open(file_like, 'rb')
except IOError:
pass
if appendmat and not file_like.endswith('.mat'):
try:
return open(file_like + '.mat', 'rb')
except IOError:
pass
# search the python path - we'll remove this soon
full_name = find_mat_file(file_like, appendmat)
if full_name is None:
raise IOError("%s not found on the path."
% file_like)
return open(full_name, 'rb')
# not a string - maybe file-like object
try:
file_like.read(0)
except AttributeError:
raise IOError('Reader needs file name or open file-like object')
return file_like
@docfiller
def mat_reader_factory(file_name, appendmat=True, **kwargs):
"""Create reader for matlab .mat format files
Parameters
----------
%(file_arg)s
%(append_arg)s
%(load_args)s
%(struct_arg)s
Returns
-------
matreader : MatFileReader object
Initialized instance of MatFileReader class matching the mat file
type detected in `filename`.
"""
byte_stream = _open_file(file_name, appendmat)
mjv, mnv = get_matfile_version(byte_stream)
if mjv == 0:
return MatFile4Reader(byte_stream, **kwargs)
elif mjv == 1:
return MatFile5Reader(byte_stream, **kwargs)
elif mjv == 2:
raise NotImplementedError('Please use HDF reader for matlab v7.3 files')
else:
raise TypeError('Did not recognize version %s' % mjv)
@docfiller
def loadmat(file_name, mdict=None, appendmat=True, **kwargs):
"""
Load MATLAB file
Parameters
----------
file_name : str
Name of the mat file (do not need .mat extension if
appendmat==True) Can also pass open file-like object.
m_dict : dict, optional
Dictionary in which to insert matfile variables.
appendmat : bool, optional
True to append the .mat extension to the end of the given
filename, if not already present.
byte_order : str or None, optional
None by default, implying byte order guessed from mat
file. Otherwise can be one of ('native', '=', 'little', '<',
'BIG', '>').
mat_dtype : bool, optional
If True, return arrays in same dtype as would be loaded into
MATLAB (instead of the dtype with which they are saved).
squeeze_me : bool, optional
Whether to squeeze unit matrix dimensions or not.
chars_as_strings : bool, optional
Whether to convert char arrays to string arrays.
matlab_compatible : bool, optional
Returns matrices as would be loaded by MATLAB (implies
squeeze_me=False, chars_as_strings=False, mat_dtype=True,
struct_as_record=True).
struct_as_record : bool, optional
Whether to load MATLAB structs as numpy record arrays, or as
old-style numpy arrays with dtype=object. Setting this flag to
False replicates the behavior of scipy version 0.7.x (returning
numpy object arrays). The default setting is True, because it
allows easier round-trip load and save of MATLAB files.
variable_names : None or sequence
If None (the default) - read all variables in file. Otherwise
`variable_names` should be a sequence of strings, giving names of the
matlab variables to read from the file. The reader will skip any
variable with a name not in this sequence, possibly saving some read
processing.
Returns
-------
mat_dict : dict
dictionary with variable names as keys, and loaded matrices as
values
Notes
-----
v4 (Level 1.0), v6 and v7 to 7.2 matfiles are supported.
You will need an HDF5 python library to read matlab 7.3 format mat
files. Because scipy does not supply one, we do not implement the
HDF5 / 7.3 interface here.
"""
variable_names = kwargs.pop('variable_names', None)
MR = mat_reader_factory(file_name, appendmat, **kwargs)
matfile_dict = MR.get_variables(variable_names)
if mdict is not None:
mdict.update(matfile_dict)
else:
mdict = matfile_dict
if isinstance(file_name, string_types):
MR.mat_stream.close()
return mdict
@docfiller
def savemat(file_name, mdict,
appendmat=True,
format='5',
long_field_names=False,
do_compression=False,
oned_as=None):
"""
Save a dictionary of names and arrays into a MATLAB-style .mat file.
This saves the array objects in the given dictionary to a MATLAB-
style .mat file.
Parameters
----------
file_name : str or file-like object
Name of the .mat file (.mat extension not needed if ``appendmat ==
True``).
Can also pass open file_like object.
mdict : dict
Dictionary from which to save matfile variables.
appendmat : bool, optional
True (the default) to append the .mat extension to the end of the
given filename, if not already present.
format : {'5', '4'}, string, optional
'5' (the default) for MATLAB 5 and up (to 7.2),
'4' for MATLAB 4 .mat files
long_field_names : bool, optional
False (the default) - maximum field name length in a structure is
31 characters which is the documented maximum length.
True - maximum field name length in a structure is 63 characters
which works for MATLAB 7.6+
do_compression : bool, optional
Whether or not to compress matrices on write. Default is False.
oned_as : {'column', 'row', None}, optional
If 'column', write 1-D numpy arrays as column vectors.
If 'row', write 1-D numpy arrays as row vectors.
If None (the default), the behavior depends on the value of `format`
(see Notes below).
See also
--------
mio4.MatFile4Writer
mio5.MatFile5Writer
Notes
-----
If ``format == '4'``, `mio4.MatFile4Writer` is called, which sets
`oned_as` to 'row' if it had been None. If ``format == '5'``,
`mio5.MatFile5Writer` is called, which sets `oned_as` to 'column' if
it had been None, but first it executes:
``warnings.warn("Using oned_as default value ('column')" +``
``" This will change to 'row' in future versions",``
``FutureWarning, stacklevel=2)``
without being more specific as to precisely when the change will take
place.
"""
file_is_string = isinstance(file_name, string_types)
if file_is_string:
if appendmat and file_name[-4:] != ".mat":
file_name = file_name + ".mat"
file_stream = open(file_name, 'wb')
else:
try:
file_name.write(b'')
except AttributeError:
raise IOError('Writer needs file name or writeable '
'file-like object')
file_stream = file_name
if format == '4':
if long_field_names:
raise ValueError("Long field names are not available for version 4 files")
MW = MatFile4Writer(file_stream, oned_as)
elif format == '5':
MW = MatFile5Writer(file_stream,
do_compression=do_compression,
unicode_strings=True,
long_field_names=long_field_names,
oned_as=oned_as)
else:
raise ValueError("Format should be '4' or '5'")
MW.put_variables(mdict)
if file_is_string:
file_stream.close()
@docfiller
def whosmat(file_name, appendmat=True, **kwargs):
"""
List variables inside a MATLAB file
.. versionadded:: 0.12.0
Parameters
----------
%(file_arg)s
%(append_arg)s
%(load_args)s
%(struct_arg)s
Returns
-------
variables : list of tuples
A list of tuples, where each tuple holds the matrix name (a string),
its shape (tuple of ints), and its data class (a string).
Possible data classes are: int8, uint8, int16, uint16, int32, uint32,
int64, uint64, single, double, cell, struct, object, char, sparse,
function, opaque, unknown.
Notes
-----
v4 (Level 1.0), v6 and v7 to 7.2 matfiles are supported.
You will need an HDF5 python library to read matlab 7.3 format mat
files. Because scipy does not supply one, we do not implement the
HDF5 / 7.3 interface here.
"""
ML = mat_reader_factory(file_name, **kwargs)
variables = ML.list_variables()
if isinstance(file_name, string_types):
ML.mat_stream.close()
return variables
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