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# -*- coding: utf-8 -*-
# Authors: Denis A. Engemann <denis.engemann@gmail.com>
# Eric Larson <larson.eric.d@gmail.com>
# License: Simplified BSD
from os import path as op
import numpy as np
from scipy.sparse import csc_matrix
from .open import read_tag, fiff_open
from .tree import dir_tree_find
from .write import (start_block, end_block, write_int, write_float,
write_string, write_float_matrix, write_int_matrix,
write_float_sparse, write_id)
from .tag import find_tag
from .constants import FIFF
from ..externals.six import text_type, string_types
from ..utils import warn, logger
_proc_keys = ['parent_file_id', 'block_id', 'parent_block_id',
'date', 'experimenter', 'creator']
_proc_ids = [FIFF.FIFF_PARENT_FILE_ID,
FIFF.FIFF_BLOCK_ID,
FIFF.FIFF_PARENT_BLOCK_ID,
FIFF.FIFF_MEAS_DATE,
FIFF.FIFF_EXPERIMENTER,
FIFF.FIFF_CREATOR]
_proc_writers = [write_id, write_id, write_id,
write_int, write_string, write_string]
_proc_casters = [dict, dict, dict,
np.array, text_type, text_type]
def _read_proc_history(fid, tree):
"""Read processing history from fiff file.
This function reads the SSS info, the CTC correction and the
calibaraions from the SSS processing logs inside af a raw file
(C.f. Maxfilter v2.2 manual (October 2010), page 21)::
104 = { 900 = proc. history
104 = { 901 = proc. record
103 = block ID
204 = date
212 = scientist
113 = creator program
104 = { 502 = SSS info
264 = SSS task
263 = SSS coord frame
265 = SSS origin
266 = SSS ins.order
267 = SSS outs.order
268 = SSS nr chnls
269 = SSS components
278 = SSS nfree
243 = HPI g limit 0.98
244 = HPI dist limit 0.005
105 = } 502 = SSS info
104 = { 504 = MaxST info
264 = SSS task
272 = SSST subspace correlation
279 = SSST buffer length
105 = }
104 = { 501 = CTC correction
103 = block ID
204 = date
113 = creator program
800 = CTC matrix
3417 = proj item chs
105 = } 501 = CTC correction
104 = { 503 = SSS finecalib.
270 = SSS cal chnls
271 = SSS cal coeff
105 = } 503 = SSS finecalib.
105 = } 901 = proc. record
105 = } 900 = proc. history
"""
proc_history = dir_tree_find(tree, FIFF.FIFFB_PROCESSING_HISTORY)
out = list()
if len(proc_history) > 0:
proc_history = proc_history[0]
proc_records = dir_tree_find(proc_history,
FIFF.FIFFB_PROCESSING_RECORD)
for proc_record in proc_records:
record = dict()
for i_ent in range(proc_record['nent']):
kind = proc_record['directory'][i_ent].kind
pos = proc_record['directory'][i_ent].pos
for key, id_, cast in zip(_proc_keys, _proc_ids,
_proc_casters):
if kind == id_:
tag = read_tag(fid, pos)
record[key] = cast(tag.data)
break
else:
warn('Unknown processing history item %s' % kind)
record['max_info'] = _read_maxfilter_record(fid, proc_record)
smartshields = dir_tree_find(proc_record,
FIFF.FIFFB_SMARTSHIELD)
if len(smartshields) > 0:
# XXX should eventually populate this
ss = [dict() for _ in range(len(smartshields))]
record['smartshield'] = ss
if len(record['max_info']) > 0:
out.append(record)
return out
def _write_proc_history(fid, info):
"""Write processing history to file."""
if len(info['proc_history']) > 0:
start_block(fid, FIFF.FIFFB_PROCESSING_HISTORY)
for record in info['proc_history']:
start_block(fid, FIFF.FIFFB_PROCESSING_RECORD)
for key, id_, writer in zip(_proc_keys, _proc_ids, _proc_writers):
if key in record:
writer(fid, id_, record[key])
_write_maxfilter_record(fid, record['max_info'])
if 'smartshield' in record:
for ss in record['smartshield']:
start_block(fid, FIFF.FIFFB_SMARTSHIELD)
# XXX should eventually populate this
end_block(fid, FIFF.FIFFB_SMARTSHIELD)
end_block(fid, FIFF.FIFFB_PROCESSING_RECORD)
end_block(fid, FIFF.FIFFB_PROCESSING_HISTORY)
_sss_info_keys = ('job', 'frame', 'origin', 'in_order',
'out_order', 'nchan', 'components', 'nfree',
'hpi_g_limit', 'hpi_dist_limit')
_sss_info_ids = (FIFF.FIFF_SSS_JOB,
FIFF.FIFF_SSS_FRAME,
FIFF.FIFF_SSS_ORIGIN,
FIFF.FIFF_SSS_ORD_IN,
FIFF.FIFF_SSS_ORD_OUT,
FIFF.FIFF_SSS_NMAG,
FIFF.FIFF_SSS_COMPONENTS,
FIFF.FIFF_SSS_NFREE,
FIFF.FIFF_HPI_FIT_GOOD_LIMIT,
FIFF.FIFF_HPI_FIT_DIST_LIMIT)
_sss_info_writers = (write_int, write_int, write_float, write_int,
write_int, write_int, write_int, write_int,
write_float, write_float)
_sss_info_casters = (int, int, np.array, int,
int, int, np.array, int,
float, float)
_max_st_keys = ('job', 'subspcorr', 'buflen')
_max_st_ids = (FIFF.FIFF_SSS_JOB, FIFF.FIFF_SSS_ST_CORR,
FIFF.FIFF_SSS_ST_LENGTH)
_max_st_writers = (write_int, write_float, write_float)
_max_st_casters = (int, float, float)
_sss_ctc_keys = ('block_id', 'date', 'creator', 'decoupler')
_sss_ctc_ids = (FIFF.FIFF_BLOCK_ID,
FIFF.FIFF_MEAS_DATE,
FIFF.FIFF_CREATOR,
FIFF.FIFF_DECOUPLER_MATRIX)
_sss_ctc_writers = (write_id, write_int, write_string, write_float_sparse)
_sss_ctc_casters = (dict, np.array, text_type, csc_matrix)
_sss_cal_keys = ('cal_chans', 'cal_corrs')
_sss_cal_ids = (FIFF.FIFF_SSS_CAL_CHANS, FIFF.FIFF_SSS_CAL_CORRS)
_sss_cal_writers = (write_int_matrix, write_float_matrix)
_sss_cal_casters = (np.array, np.array)
def _read_ctc(fname):
"""Read cross-talk correction matrix."""
if not isinstance(fname, string_types) or not op.isfile(fname):
raise ValueError('fname must be a file that exists, not %s' % fname)
f, tree, _ = fiff_open(fname)
with f as fid:
sss_ctc = _read_maxfilter_record(fid, tree)['sss_ctc']
bad_str = 'Invalid cross-talk FIF: %s' % fname
if len(sss_ctc) == 0:
raise ValueError(bad_str)
node = dir_tree_find(tree, FIFF.FIFFB_DATA_CORRECTION)[0]
comment = find_tag(fid, node, FIFF.FIFF_COMMENT).data
if comment != 'cross-talk compensation matrix':
raise ValueError(bad_str)
sss_ctc['creator'] = find_tag(fid, node, FIFF.FIFF_CREATOR).data
sss_ctc['date'] = find_tag(fid, node, FIFF.FIFF_MEAS_DATE).data
return sss_ctc
def _read_maxfilter_record(fid, tree):
"""Read maxfilter processing record from file."""
sss_info_block = dir_tree_find(tree, FIFF.FIFFB_SSS_INFO) # 502
sss_info = dict()
if len(sss_info_block) > 0:
sss_info_block = sss_info_block[0]
for i_ent in range(sss_info_block['nent']):
kind = sss_info_block['directory'][i_ent].kind
pos = sss_info_block['directory'][i_ent].pos
for key, id_, cast in zip(_sss_info_keys, _sss_info_ids,
_sss_info_casters):
if kind == id_:
tag = read_tag(fid, pos)
sss_info[key] = cast(tag.data)
break
max_st_block = dir_tree_find(tree, FIFF.FIFFB_SSS_ST_INFO) # 504
max_st = dict()
if len(max_st_block) > 0:
max_st_block = max_st_block[0]
for i_ent in range(max_st_block['nent']):
kind = max_st_block['directory'][i_ent].kind
pos = max_st_block['directory'][i_ent].pos
for key, id_, cast in zip(_max_st_keys, _max_st_ids,
_max_st_casters):
if kind == id_:
tag = read_tag(fid, pos)
max_st[key] = cast(tag.data)
break
sss_ctc_block = dir_tree_find(tree, FIFF.FIFFB_CHANNEL_DECOUPLER) # 501
sss_ctc = dict()
if len(sss_ctc_block) > 0:
sss_ctc_block = sss_ctc_block[0]
for i_ent in range(sss_ctc_block['nent']):
kind = sss_ctc_block['directory'][i_ent].kind
pos = sss_ctc_block['directory'][i_ent].pos
for key, id_, cast in zip(_sss_ctc_keys, _sss_ctc_ids,
_sss_ctc_casters):
if kind == id_:
tag = read_tag(fid, pos)
sss_ctc[key] = cast(tag.data)
break
else:
if kind == FIFF.FIFF_PROJ_ITEM_CH_NAME_LIST:
tag = read_tag(fid, pos)
chs = tag.data.split(':')
# XXX for some reason this list can have a bunch of junk
# in the last entry, e.g.:
# [..., u'MEG2642', u'MEG2643', u'MEG2641\x00 ... \x00']
chs[-1] = chs[-1].split('\x00')[0]
sss_ctc['proj_items_chs'] = chs
sss_cal_block = dir_tree_find(tree, FIFF.FIFFB_SSS_CAL) # 503
sss_cal = dict()
if len(sss_cal_block) > 0:
sss_cal_block = sss_cal_block[0]
for i_ent in range(sss_cal_block['nent']):
kind = sss_cal_block['directory'][i_ent].kind
pos = sss_cal_block['directory'][i_ent].pos
for key, id_, cast in zip(_sss_cal_keys, _sss_cal_ids,
_sss_cal_casters):
if kind == id_:
tag = read_tag(fid, pos)
sss_cal[key] = cast(tag.data)
break
max_info = dict(sss_info=sss_info, sss_ctc=sss_ctc,
sss_cal=sss_cal, max_st=max_st)
return max_info
def _write_maxfilter_record(fid, record):
"""Write maxfilter processing record to file."""
sss_info = record['sss_info']
if len(sss_info) > 0:
start_block(fid, FIFF.FIFFB_SSS_INFO)
for key, id_, writer in zip(_sss_info_keys, _sss_info_ids,
_sss_info_writers):
if key in sss_info:
writer(fid, id_, sss_info[key])
end_block(fid, FIFF.FIFFB_SSS_INFO)
max_st = record['max_st']
if len(max_st) > 0:
start_block(fid, FIFF.FIFFB_SSS_ST_INFO)
for key, id_, writer in zip(_max_st_keys, _max_st_ids,
_max_st_writers):
if key in max_st:
writer(fid, id_, max_st[key])
end_block(fid, FIFF.FIFFB_SSS_ST_INFO)
sss_ctc = record['sss_ctc']
if len(sss_ctc) > 0: # dict has entries
start_block(fid, FIFF.FIFFB_CHANNEL_DECOUPLER)
for key, id_, writer in zip(_sss_ctc_keys, _sss_ctc_ids,
_sss_ctc_writers):
if key in sss_ctc:
writer(fid, id_, sss_ctc[key])
if 'proj_items_chs' in sss_ctc:
write_string(fid, FIFF.FIFF_PROJ_ITEM_CH_NAME_LIST,
':'.join(sss_ctc['proj_items_chs']))
end_block(fid, FIFF.FIFFB_CHANNEL_DECOUPLER)
sss_cal = record['sss_cal']
if len(sss_cal) > 0:
start_block(fid, FIFF.FIFFB_SSS_CAL)
for key, id_, writer in zip(_sss_cal_keys, _sss_cal_ids,
_sss_cal_writers):
if key in sss_cal:
writer(fid, id_, sss_cal[key])
end_block(fid, FIFF.FIFFB_SSS_CAL)
def _get_sss_rank(sss):
"""Get SSS rank."""
inside = sss['sss_info']['in_order']
nfree = (inside + 1) ** 2 - 1
nfree -= (len(sss['sss_info']['components'][:nfree]) -
sss['sss_info']['components'][:nfree].sum())
return nfree
def _get_rank_sss(inst):
"""Look up rank from SSS data.
.. note::
Throws an error if SSS has not been applied.
Parameters
----------
inst : instance of Raw, Epochs or Evoked, or Info
Any MNE object with an .info attribute
Returns
-------
rank : int
The numerical rank as predicted by the number of SSS
components.
"""
from .meas_info import Info
info = inst if isinstance(inst, Info) else inst.info
del inst
max_infos = list()
for proc_info in info.get('proc_history', list()):
max_info = proc_info.get('max_info')
if max_info is not None:
if len(max_info) > 0:
max_infos.append(max_info)
elif len(max_info) > 1:
logger.info('found multiple SSS records. Using the first.')
elif len(max_info) == 0:
raise ValueError(
'Did not find any SSS record. You should use data-based '
'rank estimate instead')
if len(max_infos) > 0:
max_info = max_infos[0]
else:
raise ValueError('There is no `max_info` here. Sorry.')
return _get_sss_rank(max_info)
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