1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
|
# -*- coding: UTF-8 -*-
# Copyright (c) 2018, Dirk Gütlin & Thomas Hartmann
# All rights reserved.
#
# This file is part of the pymatreader Project, see:
# https://gitlab.com/obob/pymatreader
#
# Redistribution and use in source and binary forms, with or without
# modification, are permitted provided that the following conditions are met:
#
# * Redistributions of source code must retain the above copyright notice, this
# list of conditions and the following disclaimer.
#
# * Redistributions in binary form must reproduce the above copyright notice,
# this list of conditions and the following disclaimer in the documentation
# and/or other materials provided with the distribution.
#
# THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
# AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
# IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
# ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE
# LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR
# CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF
# SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS
# INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN
# CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE)
# ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE
# POSSIBILITY OF SUCH DAMAGE.
import scipy.io
import os
from .utils import _import_h5py, _hdf5todict, _check_for_scipy_mat_struct
__all__ = 'read_mat'
"""
This is a small module intended to facilitate reading .mat files containing
large data structures into python, disregarding of the underlying .mat
file version.
"""
def read_mat(filename, variable_names=None, ignore_fields=None,
uint16_codec=None):
"""This function reads .mat files of version <7.3 or 7.3 and returns the
contained data structure as a dictionary of nested substructure similar
to scipy.io.loadmat style.
Parameters
----------
filename: str
Path and filename of the .mat file containing the data.
variable_names: list of strings, optional
Reads only the data contained in the specified dict key or
variable name. Default is None.
ignore_fields: list of strings, optional
Ignores every dict key/variable name specified in the list within the
entire structure. Only works for .mat files v 7.3. Default is [].
uint16_codec : str | None
If your file contains non-ascii characters, sometimes reading
it may fail and give rise to error message stating that "buffer is
too small". ``uint16_codec`` allows to specify what codec (for example:
'latin1' or 'utf-8') should be used when reading character arrays and
can therefore help you solve this problem.
Returns
-------
dict
A structure of nested dictionaries, with variable names as keys and
variable data as values.
"""
if not os.path.exists(filename):
raise IOError('The file %s does not exist.' % (filename,))
if ignore_fields is None:
ignore_fields = []
try:
with open(filename, 'rb') as fid: # avoid open file warnings on error
raw_data = scipy.io.loadmat(fid, struct_as_record=True,
squeeze_me=True, mat_dtype=True,
variable_names=variable_names,
uint16_codec=uint16_codec)
data = _check_for_scipy_mat_struct(raw_data)
except NotImplementedError:
ignore_fields.append('#refs#')
h5py = _import_h5py()
with h5py.File(filename, 'r') as hdf5_file:
data = _hdf5todict(hdf5_file, variable_names=variable_names,
ignore_fields=ignore_fields)
return data
|
