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
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190
191
192
193
194
195
196
197
198
199
200
201
202
203
204
205
206
207
208
209
210
211
212
213
214
215
216
217
218
219
220
221
222
223
224
225
226
227
228
229
230
231
232
233
234
235
236
237
238
239
240
241
242
243
244
245
246
247
248
249
250
251
252
253
254
255
256
257
258
259
260
261
262
263
264
265
266
267
268
269
270
271
272
273
274
275
276
277
278
279
280
281
282
283
284
285
|
# -*- coding: utf-8 -*-
# Authors: Alexandre Gramfort <alexandre.gramfort@telecom-paristech.fr>
# Matti Hamalainen <msh@nmr.mgh.harvard.edu>
#
# License: BSD (3-clause)
import os.path as op
from io import BytesIO
from gzip import GzipFile
import numpy as np
from scipy import sparse
from .tag import read_tag_info, read_tag, read_big, Tag, _call_dict_names
from .tree import make_dir_tree, dir_tree_find
from .constants import FIFF
from ..utils import logger, verbose
from ..externals.six import string_types, iteritems, text_type
def _fiff_get_fid(fname):
"""Open a FIF file with no additional parsing."""
if isinstance(fname, string_types):
if op.splitext(fname)[1].lower() == '.gz':
logger.debug('Using gzip')
fid = GzipFile(fname, "rb") # Open in binary mode
else:
logger.debug('Using normal I/O')
fid = open(fname, "rb") # Open in binary mode
else:
fid = fname
fid.seek(0)
return fid
def _get_next_fname(fid, fname, tree):
"""Get the next filename in split files."""
nodes_list = dir_tree_find(tree, FIFF.FIFFB_REF)
next_fname = None
for nodes in nodes_list:
next_fname = None
for ent in nodes['directory']:
if ent.kind == FIFF.FIFF_REF_ROLE:
tag = read_tag(fid, ent.pos)
role = int(tag.data)
if role != FIFF.FIFFV_ROLE_NEXT_FILE:
next_fname = None
break
if ent.kind == FIFF.FIFF_REF_FILE_NAME:
tag = read_tag(fid, ent.pos)
next_fname = op.join(op.dirname(fname), tag.data)
if ent.kind == FIFF.FIFF_REF_FILE_NUM:
# Some files don't have the name, just the number. So
# we construct the name from the current name.
if next_fname is not None:
continue
next_num = read_tag(fid, ent.pos).data
path, base = op.split(fname)
idx = base.find('.')
idx2 = base.rfind('-')
if idx2 < 0 and next_num == 1:
# this is the first file, which may not be numbered
next_fname = op.join(
path, '%s-%d.%s' % (base[:idx], next_num,
base[idx + 1:]))
continue
num_str = base[idx2 + 1:idx]
if not num_str.isdigit():
continue
next_fname = op.join(path, '%s-%d.%s'
% (base[:idx2], next_num, base[idx + 1:]))
if next_fname is not None:
break
return next_fname
@verbose
def fiff_open(fname, preload=False, verbose=None):
"""Open a FIF file.
Parameters
----------
fname : string | fid
Name of the fif file, or an opened file (will seek back to 0).
preload : bool
If True, all data from the file is read into a memory buffer. This
requires more memory, but can be faster for I/O operations that require
frequent seeks.
verbose : bool, str, int, or None
If not None, override default verbose level (see :func:`mne.verbose`
and :ref:`Logging documentation <tut_logging>` for more).
Returns
-------
fid : file
The file descriptor of the open file
tree : fif tree
The tree is a complex structure filled with dictionaries,
lists and tags.
directory : list
A list of tags.
"""
fid = _fiff_get_fid(fname)
# do preloading of entire file
if preload:
# note that StringIO objects instantiated this way are read-only,
# but that's okay here since we are using mode "rb" anyway
fid_old = fid
fid = BytesIO(read_big(fid_old))
fid_old.close()
tag = read_tag_info(fid)
# Check that this looks like a fif file
if tag.kind != FIFF.FIFF_FILE_ID:
raise ValueError('file does not start with a file id tag')
if tag.type != FIFF.FIFFT_ID_STRUCT:
raise ValueError('file does not start with a file id tag')
if tag.size != 20:
raise ValueError('file does not start with a file id tag')
tag = read_tag(fid)
if tag.kind != FIFF.FIFF_DIR_POINTER:
raise ValueError('file does not have a directory pointer')
# Read or create the directory tree
logger.debug(' Creating tag directory for %s...' % fname)
dirpos = int(tag.data)
if dirpos > 0:
tag = read_tag(fid, dirpos)
directory = tag.data
else:
fid.seek(0, 0)
directory = list()
while tag.next >= 0:
pos = fid.tell()
tag = read_tag_info(fid)
if tag is None:
break # HACK : to fix file ending with empty tag...
else:
tag.pos = pos
directory.append(tag)
tree, _ = make_dir_tree(fid, directory)
logger.debug('[done]')
# Back to the beginning
fid.seek(0)
return fid, tree, directory
def show_fiff(fname, indent=' ', read_limit=np.inf, max_str=30,
output=str, tag=None, verbose=None):
"""Show FIFF information.
This function is similar to mne_show_fiff.
Parameters
----------
fname : str
Filename to evaluate.
indent : str
How to indent the lines.
read_limit : int
Max number of bytes of data to read from a tag. Can be np.inf
to always read all data (helps test read completion).
max_str : int
Max number of characters of string representation to print for
each tag's data.
output : type
Either str or list. str is a convenience output for printing.
tag : int | None
Provide information about this tag. If None (default), all information
is shown.
verbose : bool, str, int, or None
If not None, override default verbose level (see :func:`mne.verbose`
and :ref:`Logging documentation <tut_logging>` for more).
"""
if output not in [list, str]:
raise ValueError('output must be list or str')
if isinstance(tag, string_types): # command mne show_fiff passes string
tag = int(tag)
f, tree, directory = fiff_open(fname)
# This gets set to 0 (unknown) by fiff_open, but FIFFB_ROOT probably
# makes more sense for display
tree['block'] = FIFF.FIFFB_ROOT
with f as fid:
out = _show_tree(fid, tree, indent=indent, level=0,
read_limit=read_limit, max_str=max_str, tag_id=tag)
if output == str:
out = '\n'.join(out)
return out
def _find_type(value, fmts=['FIFF_'], exclude=['FIFF_UNIT']):
"""Find matching values."""
value = int(value)
vals = [k for k, v in iteritems(FIFF)
if v == value and any(fmt in k for fmt in fmts) and
not any(exc in k for exc in exclude)]
if len(vals) == 0:
vals = ['???']
return vals
def _show_tree(fid, tree, indent, level, read_limit, max_str, tag_id):
"""Show FIFF tree."""
this_idt = indent * level
next_idt = indent * (level + 1)
# print block-level information
out = [this_idt + str(int(tree['block'])) + ' = ' +
'/'.join(_find_type(tree['block'], fmts=['FIFFB_']))]
tag_found = False
if tag_id is None or out[0].strip().startswith(str(tag_id)):
tag_found = True
if tree['directory'] is not None:
kinds = [ent.kind for ent in tree['directory']] + [-1]
types = [ent.type for ent in tree['directory']]
sizes = [ent.size for ent in tree['directory']]
poss = [ent.pos for ent in tree['directory']]
counter = 0
good = True
for k, kn, size, pos, type_ in zip(kinds[:-1], kinds[1:], sizes, poss,
types):
if not tag_found and k != tag_id:
continue
tag = Tag(k, size, 0, pos)
if read_limit is None or size <= read_limit:
try:
tag = read_tag(fid, pos)
except Exception:
good = False
if kn == k:
# don't print if the next item is the same type (count 'em)
counter += 1
else:
# find the tag type
this_type = _find_type(k, fmts=['FIFF_'])
# prepend a count if necessary
prepend = 'x' + str(counter + 1) + ': ' if counter > 0 else ''
postpend = ''
# print tag data nicely
if tag.data is not None:
postpend = ' = ' + text_type(tag.data)[:max_str]
if isinstance(tag.data, np.ndarray):
if tag.data.size > 1:
postpend += ' ... array size=' + str(tag.data.size)
elif isinstance(tag.data, dict):
postpend += ' ... dict len=' + str(len(tag.data))
elif isinstance(tag.data, string_types):
postpend += ' ... str len=' + str(len(tag.data))
elif isinstance(tag.data, (list, tuple)):
postpend += ' ... list len=' + str(len(tag.data))
elif sparse.issparse(tag.data):
postpend += (' ... sparse (%s) shape=%s'
% (tag.data.getformat(), tag.data.shape))
else:
postpend += ' ... type=' + str(type(tag.data))
postpend = '>' * 20 + 'BAD' if not good else postpend
type_ = _call_dict_names.get(type_, '?%s?' % (type_,))
out += [next_idt + prepend + str(k) + ' = ' +
'/'.join(this_type) +
' (' + str(size) + 'b %s)' % type_ +
postpend]
out[-1] = out[-1].replace('\n', u'ΒΆ')
counter = 0
good = True
if tag_id in kinds:
tag_found = True
if not tag_found:
out = ['']
level = -1 # removes extra indent
# deal with children
for branch in tree['children']:
out += _show_tree(fid, branch, indent, level + 1, read_limit, max_str,
tag_id)
return out
|
