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# Authors: Alexandre Gramfort <alexandre.gramfort@telecom-paristech.fr>
# Matti Hamalainen <msh@nmr.mgh.harvard.edu>
#
# License: BSD (3-clause)
from ..externals.six import string_types
import numpy as np
import os.path as op
from io import BytesIO
from .tag import read_tag_info, read_tag, read_big, Tag
from .tree import make_dir_tree
from .constants import FIFF
from ..utils import logger, verbose
from ..externals import six
from ..fixes import gzip_open
def _fiff_get_fid(fname):
"""Helper to 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 = gzip_open(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
@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 mne.verbose).
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, 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 equivalent to ``"\n".join(list)``,
which is more convenient for using ``print show_fiff(...)``.
verbose : bool, str, int, or None
If not None, override default verbose level (see mne.verbose).
"""
if not output in [list, str]:
raise ValueError('output must be list or str')
f, tree, directory = fiff_open(fname)
with f as fid:
out = _show_tree(fid, tree['children'][0], indent=indent, level=0,
read_limit=read_limit, max_str=max_str)
if output == str:
out = '\n'.join(out)
return out
def _find_type(value, fmts=['FIFF_'], exclude=['FIFF_UNIT']):
"""Helper to find matching values"""
vals = [k for k, v in six.iteritems(FIFF)
if v == value and any([fmt in k for fmt in fmts])
and not any(exc in k for exc in exclude)]
return vals
def _show_tree(fid, tree, indent, level, read_limit, max_str):
"""Helper for showing FIFF"""
this_idt = indent * level
next_idt = indent * (level + 1)
# print block-level information
out = [this_idt + str(tree['block'][0]) + ' = '
+ '/'.join(_find_type(tree['block'], fmts=['FIFFB_']))]
if tree['directory'] is not None:
kinds = [ent.kind for ent in tree['directory']] + [-1]
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 in zip(kinds[:-1], kinds[1:], sizes, poss):
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 = ' = ' + str(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))
else:
postpend += ' ... (unknown type)'
postpend = '>' * 20 + 'BAD' if not good else postpend
out += [next_idt + prepend + str(k) + ' = '
+ '/'.join(this_type) + ' (' + str(size) + ')'
+ postpend]
counter = 0
good = True
# deal with children
for branch in tree['children']:
out += _show_tree(fid, branch, indent, level + 1, read_limit, max_str)
return out
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