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# Authors: Alexandre Gramfort <alexandre.gramfort@telecom-paristech.fr>
# Matti Hamalainen <msh@nmr.mgh.harvard.edu>
#
# License: BSD (3-clause)
from gzip import GzipFile
import os.path as op
import re
import time
import uuid
import numpy as np
from scipy import linalg, sparse
from .constants import FIFF
from ..utils import logger
from ..externals.jdcal import jcal2jd
from ..externals.six import string_types, b
# We choose a "magic" date to store (because meas_date is obligatory)
# to treat as meas_date=None. This one should be impossible for systems
# to write -- the second field is microseconds, so anything >= 1e6
# should be moved into the first field (seconds).
DATE_NONE = (0, 2 ** 31 - 1)
def _write(fid, data, kind, data_size, FIFFT_TYPE, dtype):
"""Write data."""
if isinstance(data, np.ndarray):
data_size *= data.size
# XXX for string types the data size is used as
# computed in ``write_string``.
fid.write(np.array(kind, dtype='>i4').tostring())
fid.write(np.array(FIFFT_TYPE, dtype='>i4').tostring())
fid.write(np.array(data_size, dtype='>i4').tostring())
fid.write(np.array(FIFF.FIFFV_NEXT_SEQ, dtype='>i4').tostring())
fid.write(np.array(data, dtype=dtype).tostring())
def _get_split_size(split_size):
"""Convert human-readable bytes to machine-readable bytes."""
if isinstance(split_size, string_types):
exp = dict(MB=20, GB=30).get(split_size[-2:], None)
if exp is None:
raise ValueError('split_size has to end with either'
'"MB" or "GB"')
split_size = int(float(split_size[:-2]) * 2 ** exp)
if split_size > 2147483648:
raise ValueError('split_size cannot be larger than 2GB')
return split_size
def write_nop(fid, last=False):
"""Write a FIFF_NOP."""
fid.write(np.array(FIFF.FIFF_NOP, dtype='>i4').tostring())
fid.write(np.array(FIFF.FIFFT_VOID, dtype='>i4').tostring())
fid.write(np.array(0, dtype='>i4').tostring())
next_ = FIFF.FIFFV_NEXT_NONE if last else FIFF.FIFFV_NEXT_SEQ
fid.write(np.array(next_, dtype='>i4').tostring())
def write_int(fid, kind, data):
"""Write a 32-bit integer tag to a fif file."""
data_size = 4
data = np.array(data, dtype='>i4').T
_write(fid, data, kind, data_size, FIFF.FIFFT_INT, '>i4')
def write_double(fid, kind, data):
"""Write a double-precision floating point tag to a fif file."""
data_size = 8
data = np.array(data, dtype='>f8').T
_write(fid, data, kind, data_size, FIFF.FIFFT_DOUBLE, '>f8')
def write_float(fid, kind, data):
"""Write a single-precision floating point tag to a fif file."""
data_size = 4
data = np.array(data, dtype='>f4').T
_write(fid, data, kind, data_size, FIFF.FIFFT_FLOAT, '>f4')
def write_dau_pack16(fid, kind, data):
"""Write a dau_pack16 tag to a fif file."""
data_size = 2
data = np.array(data, dtype='>i2').T
_write(fid, data, kind, data_size, FIFF.FIFFT_DAU_PACK16, '>i2')
def write_complex64(fid, kind, data):
"""Write a 64 bit complex floating point tag to a fif file."""
data_size = 8
data = np.array(data, dtype='>c8').T
_write(fid, data, kind, data_size, FIFF.FIFFT_COMPLEX_FLOAT, '>c8')
def write_complex128(fid, kind, data):
"""Write a 128 bit complex floating point tag to a fif file."""
data_size = 16
data = np.array(data, dtype='>c16').T
_write(fid, data, kind, data_size, FIFF.FIFFT_COMPLEX_FLOAT, '>c16')
def write_julian(fid, kind, data):
"""Write a Julian-formatted date to a FIF file."""
assert len(data) == 3
data_size = 4
jd = np.sum(jcal2jd(*data))
data = np.array(jd, dtype='>i4')
_write(fid, data, kind, data_size, FIFF.FIFFT_JULIAN, '>i4')
def write_string(fid, kind, data):
"""Write a string tag."""
str_data = data.encode('latin1')
data_size = len(str_data) # therefore compute size here
my_dtype = '>a' # py2/3 compatible on writing -- don't ask me why
if data_size > 0:
_write(fid, str_data, kind, data_size, FIFF.FIFFT_STRING, my_dtype)
def write_name_list(fid, kind, data):
"""Write a colon-separated list of names.
Parameters
----------
data : list of strings
"""
write_string(fid, kind, ':'.join(data))
def write_float_matrix(fid, kind, mat):
"""Write a single-precision floating-point matrix tag."""
FIFFT_MATRIX = 1 << 30
FIFFT_MATRIX_FLOAT = FIFF.FIFFT_FLOAT | FIFFT_MATRIX
data_size = 4 * mat.size + 4 * (mat.ndim + 1)
fid.write(np.array(kind, dtype='>i4').tostring())
fid.write(np.array(FIFFT_MATRIX_FLOAT, dtype='>i4').tostring())
fid.write(np.array(data_size, dtype='>i4').tostring())
fid.write(np.array(FIFF.FIFFV_NEXT_SEQ, dtype='>i4').tostring())
fid.write(np.array(mat, dtype='>f4').tostring())
dims = np.empty(mat.ndim + 1, dtype=np.int32)
dims[:mat.ndim] = mat.shape[::-1]
dims[-1] = mat.ndim
fid.write(np.array(dims, dtype='>i4').tostring())
check_fiff_length(fid)
def write_double_matrix(fid, kind, mat):
"""Write a double-precision floating-point matrix tag."""
FIFFT_MATRIX = 1 << 30
FIFFT_MATRIX_DOUBLE = FIFF.FIFFT_DOUBLE | FIFFT_MATRIX
data_size = 8 * mat.size + 4 * (mat.ndim + 1)
fid.write(np.array(kind, dtype='>i4').tostring())
fid.write(np.array(FIFFT_MATRIX_DOUBLE, dtype='>i4').tostring())
fid.write(np.array(data_size, dtype='>i4').tostring())
fid.write(np.array(FIFF.FIFFV_NEXT_SEQ, dtype='>i4').tostring())
fid.write(np.array(mat, dtype='>f8').tostring())
dims = np.empty(mat.ndim + 1, dtype=np.int32)
dims[:mat.ndim] = mat.shape[::-1]
dims[-1] = mat.ndim
fid.write(np.array(dims, dtype='>i4').tostring())
check_fiff_length(fid)
def write_int_matrix(fid, kind, mat):
"""Write integer 32 matrix tag."""
FIFFT_MATRIX = 1 << 30
FIFFT_MATRIX_INT = FIFF.FIFFT_INT | FIFFT_MATRIX
data_size = 4 * mat.size + 4 * 3
fid.write(np.array(kind, dtype='>i4').tostring())
fid.write(np.array(FIFFT_MATRIX_INT, dtype='>i4').tostring())
fid.write(np.array(data_size, dtype='>i4').tostring())
fid.write(np.array(FIFF.FIFFV_NEXT_SEQ, dtype='>i4').tostring())
fid.write(np.array(mat, dtype='>i4').tostring())
dims = np.empty(3, dtype=np.int32)
dims[0] = mat.shape[1]
dims[1] = mat.shape[0]
dims[2] = 2
fid.write(np.array(dims, dtype='>i4').tostring())
check_fiff_length(fid)
def write_complex_float_matrix(fid, kind, mat):
"""Write complex 64 matrix tag."""
FIFFT_MATRIX = 1 << 30
FIFFT_MATRIX_COMPLEX_FLOAT = FIFF.FIFFT_COMPLEX_FLOAT | FIFFT_MATRIX
data_size = 4 * 2 * mat.size + 4 * (mat.ndim + 1)
fid.write(np.array(kind, dtype='>i4').tostring())
fid.write(np.array(FIFFT_MATRIX_COMPLEX_FLOAT, dtype='>i4').tostring())
fid.write(np.array(data_size, dtype='>i4').tostring())
fid.write(np.array(FIFF.FIFFV_NEXT_SEQ, dtype='>i4').tostring())
fid.write(np.array(mat, dtype='>c8').tostring())
dims = np.empty(mat.ndim + 1, dtype=np.int32)
dims[:mat.ndim] = mat.shape[::-1]
dims[-1] = mat.ndim
fid.write(np.array(dims, dtype='>i4').tostring())
check_fiff_length(fid)
def write_complex_double_matrix(fid, kind, mat):
"""Write complex 128 matrix tag."""
FIFFT_MATRIX = 1 << 30
FIFFT_MATRIX_COMPLEX_DOUBLE = FIFF.FIFFT_COMPLEX_DOUBLE | FIFFT_MATRIX
data_size = 8 * 2 * mat.size + 4 * (mat.ndim + 1)
fid.write(np.array(kind, dtype='>i4').tostring())
fid.write(np.array(FIFFT_MATRIX_COMPLEX_DOUBLE, dtype='>i4').tostring())
fid.write(np.array(data_size, dtype='>i4').tostring())
fid.write(np.array(FIFF.FIFFV_NEXT_SEQ, dtype='>i4').tostring())
fid.write(np.array(mat, dtype='>c16').tostring())
dims = np.empty(mat.ndim + 1, dtype=np.int32)
dims[:mat.ndim] = mat.shape[::-1]
dims[-1] = mat.ndim
fid.write(np.array(dims, dtype='>i4').tostring())
check_fiff_length(fid)
def get_machid():
"""Get (mostly) unique machine ID.
Returns
-------
ids : array (length 2, int32)
The machine identifier used in MNE.
"""
mac = b('%012x' % uuid.getnode()) # byte conversion for Py3
mac = re.findall(b'..', mac) # split string
mac += [b'00', b'00'] # add two more fields
# Convert to integer in reverse-order (for some reason)
from codecs import encode
mac = b''.join([encode(h, 'hex_codec') for h in mac[::-1]])
ids = np.flipud(np.frombuffer(mac, np.int32, count=2))
return ids
def get_new_file_id():
"""Create a new file ID tag."""
secs, usecs = divmod(time.time(), 1.)
secs, usecs = int(secs), int(usecs * 1e6)
return {'machid': get_machid(), 'version': FIFF.FIFFC_VERSION,
'secs': secs, 'usecs': usecs}
def write_id(fid, kind, id_=None):
"""Write fiff id."""
id_ = _generate_meas_id() if id_ is None else id_
data_size = 5 * 4 # The id comprises five integers
fid.write(np.array(kind, dtype='>i4').tostring())
fid.write(np.array(FIFF.FIFFT_ID_STRUCT, dtype='>i4').tostring())
fid.write(np.array(data_size, dtype='>i4').tostring())
fid.write(np.array(FIFF.FIFFV_NEXT_SEQ, dtype='>i4').tostring())
# Collect the bits together for one write
arr = np.array([id_['version'],
id_['machid'][0], id_['machid'][1],
id_['secs'], id_['usecs']], dtype='>i4')
fid.write(arr.tostring())
def start_block(fid, kind):
"""Write a FIFF_BLOCK_START tag."""
write_int(fid, FIFF.FIFF_BLOCK_START, kind)
def end_block(fid, kind):
"""Write a FIFF_BLOCK_END tag."""
write_int(fid, FIFF.FIFF_BLOCK_END, kind)
def start_file(fname, id_=None):
"""Open a fif file for writing and writes the compulsory header tags.
Parameters
----------
fname : string | fid
The name of the file to open. It is recommended
that the name ends with .fif or .fif.gz. Can also be an
already opened file.
id_ : dict | None
ID to use for the FIFF_FILE_ID.
"""
if isinstance(fname, string_types):
if op.splitext(fname)[1].lower() == '.gz':
logger.debug('Writing using gzip')
# defaults to compression level 9, which is barely smaller but much
# slower. 2 offers a good compromise.
fid = GzipFile(fname, "wb", compresslevel=2)
else:
logger.debug('Writing using normal I/O')
fid = open(fname, "wb")
else:
logger.debug('Writing using %s I/O' % type(fname))
fid = fname
fid.seek(0)
# Write the compulsory items
write_id(fid, FIFF.FIFF_FILE_ID, id_)
write_int(fid, FIFF.FIFF_DIR_POINTER, -1)
write_int(fid, FIFF.FIFF_FREE_LIST, -1)
return fid
def check_fiff_length(fid, close=True):
"""Ensure our file hasn't grown too large to work properly."""
if fid.tell() > 2147483648: # 2 ** 31, FIFF uses signed 32-bit locations
if close:
fid.close()
raise IOError('FIFF file exceeded 2GB limit, please split file or '
'save to a different format')
def end_file(fid):
"""Write the closing tags to a fif file and closes the file."""
write_nop(fid, last=True)
check_fiff_length(fid)
fid.close()
def write_coord_trans(fid, trans):
"""Write a coordinate transformation structure."""
data_size = 4 * 2 * 12 + 4 * 2
fid.write(np.array(FIFF.FIFF_COORD_TRANS, dtype='>i4').tostring())
fid.write(np.array(FIFF.FIFFT_COORD_TRANS_STRUCT, dtype='>i4').tostring())
fid.write(np.array(data_size, dtype='>i4').tostring())
fid.write(np.array(FIFF.FIFFV_NEXT_SEQ, dtype='>i4').tostring())
fid.write(np.array(trans['from'], dtype='>i4').tostring())
fid.write(np.array(trans['to'], dtype='>i4').tostring())
# The transform...
rot = trans['trans'][:3, :3]
move = trans['trans'][:3, 3]
fid.write(np.array(rot, dtype='>f4').tostring())
fid.write(np.array(move, dtype='>f4').tostring())
# ...and its inverse
trans_inv = linalg.inv(trans['trans'])
rot = trans_inv[:3, :3]
move = trans_inv[:3, 3]
fid.write(np.array(rot, dtype='>f4').tostring())
fid.write(np.array(move, dtype='>f4').tostring())
def write_ch_info(fid, ch):
"""Write a channel information record to a fif file."""
data_size = 4 * 13 + 4 * 7 + 16
fid.write(np.array(FIFF.FIFF_CH_INFO, dtype='>i4').tostring())
fid.write(np.array(FIFF.FIFFT_CH_INFO_STRUCT, dtype='>i4').tostring())
fid.write(np.array(data_size, dtype='>i4').tostring())
fid.write(np.array(FIFF.FIFFV_NEXT_SEQ, dtype='>i4').tostring())
# Start writing fiffChInfoRec
fid.write(np.array(ch['scanno'], dtype='>i4').tostring())
fid.write(np.array(ch['logno'], dtype='>i4').tostring())
fid.write(np.array(ch['kind'], dtype='>i4').tostring())
fid.write(np.array(ch['range'], dtype='>f4').tostring())
fid.write(np.array(ch['cal'], dtype='>f4').tostring())
fid.write(np.array(ch['coil_type'], dtype='>i4').tostring())
fid.write(np.array(ch['loc'], dtype='>f4').tostring()) # writing 12 values
# unit and unit multiplier
fid.write(np.array(ch['unit'], dtype='>i4').tostring())
fid.write(np.array(ch['unit_mul'], dtype='>i4').tostring())
# Finally channel name
ch_name = ch['ch_name'][:15]
fid.write(np.array(ch_name, dtype='>c').tostring())
fid.write(b('\0') * (16 - len(ch_name)))
def write_dig_points(fid, dig, block=False, coord_frame=None):
"""Write a set of digitizer data points into a fif file."""
if dig is not None:
data_size = 5 * 4
if block:
start_block(fid, FIFF.FIFFB_ISOTRAK)
if coord_frame is not None:
write_int(fid, FIFF.FIFF_MNE_COORD_FRAME, coord_frame)
for d in dig:
fid.write(np.array(FIFF.FIFF_DIG_POINT, '>i4').tostring())
fid.write(np.array(FIFF.FIFFT_DIG_POINT_STRUCT, '>i4').tostring())
fid.write(np.array(data_size, dtype='>i4').tostring())
fid.write(np.array(FIFF.FIFFV_NEXT_SEQ, '>i4').tostring())
# Start writing fiffDigPointRec
fid.write(np.array(d['kind'], '>i4').tostring())
fid.write(np.array(d['ident'], '>i4').tostring())
fid.write(np.array(d['r'][:3], '>f4').tostring())
if block:
end_block(fid, FIFF.FIFFB_ISOTRAK)
def write_float_sparse_rcs(fid, kind, mat):
"""Write a single-precision sparse compressed row matrix tag."""
return write_float_sparse(fid, kind, mat, fmt='csr')
def write_float_sparse_ccs(fid, kind, mat):
"""Write a single-precision sparse compressed column matrix tag."""
return write_float_sparse(fid, kind, mat, fmt='csc')
def write_float_sparse(fid, kind, mat, fmt='auto'):
"""Write a single-precision floating-point sparse matrix tag."""
from .tag import _matrix_coding_CCS, _matrix_coding_RCS
if fmt == 'auto':
fmt = 'csr' if isinstance(mat, sparse.csr_matrix) else 'csc'
if fmt == 'csr':
need = sparse.csr_matrix
bits = _matrix_coding_RCS
else:
need = sparse.csc_matrix
bits = _matrix_coding_CCS
if not isinstance(mat, need):
raise TypeError('Must write %s, got %s' % (fmt.upper(), type(mat),))
FIFFT_MATRIX = bits << 16
FIFFT_MATRIX_FLOAT_RCS = FIFF.FIFFT_FLOAT | FIFFT_MATRIX
nnzm = mat.nnz
nrow = mat.shape[0]
data_size = 4 * nnzm + 4 * nnzm + 4 * (nrow + 1) + 4 * 4
fid.write(np.array(kind, dtype='>i4').tostring())
fid.write(np.array(FIFFT_MATRIX_FLOAT_RCS, dtype='>i4').tostring())
fid.write(np.array(data_size, dtype='>i4').tostring())
fid.write(np.array(FIFF.FIFFV_NEXT_SEQ, dtype='>i4').tostring())
fid.write(np.array(mat.data, dtype='>f4').tostring())
fid.write(np.array(mat.indices, dtype='>i4').tostring())
fid.write(np.array(mat.indptr, dtype='>i4').tostring())
dims = [nnzm, mat.shape[0], mat.shape[1], 2]
fid.write(np.array(dims, dtype='>i4').tostring())
check_fiff_length(fid)
def _generate_meas_id():
"""Generate a new meas_id dict."""
id_ = dict()
id_['version'] = FIFF.FIFFC_VERSION
id_['machid'] = get_machid()
id_['secs'], id_['usecs'] = DATE_NONE
return id_
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