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"""Read .res4 files."""
# Author: Eric Larson <larson.eric.d<gmail.com>
#
# License: BSD (3-clause)
import os.path as op
import numpy as np
from ...utils import logger
from .constants import CTF
def _make_ctf_name(directory, extra, raise_error=True):
"""Make a CTF name."""
fname = op.join(directory, op.basename(directory)[:-3] + '.' + extra)
if not op.isfile(fname):
if raise_error:
raise IOError('Standard file %s not found' % fname)
else:
return None
return fname
def _read_double(fid, n=1):
"""Read a double."""
return np.fromfile(fid, '>f8', n)
def _read_string(fid, n_bytes, decode=True):
"""Read string."""
s0 = fid.read(n_bytes)
s = s0.split(b'\x00')[0]
return s.decode('utf-8') if decode else s
def _read_ustring(fid, n_bytes):
"""Read unsigned character string."""
return np.fromfile(fid, '>B', n_bytes)
def _read_int2(fid):
"""Read int from short."""
return np.fromfile(fid, '>i2', 1)[0]
def _read_int(fid):
"""Read a 32-bit integer."""
return np.fromfile(fid, '>i4', 1)[0]
def _move_to_next(fid, byte=8):
"""Move to next byte boundary."""
now = fid.tell()
if now % byte != 0:
now = now - (now % byte) + byte
fid.seek(now, 0)
def _read_filter(fid):
"""Read filter information."""
f = dict()
f['freq'] = _read_double(fid)[0]
f['class'] = _read_int(fid)
f['type'] = _read_int(fid)
f['npar'] = _read_int2(fid)
f['pars'] = _read_double(fid, f['npar'])
return f
def _read_comp_coeff(fid, d):
"""Read compensation coefficients."""
# Read the coefficients and initialize
d['ncomp'] = _read_int2(fid)
d['comp'] = list()
# Read each record
dt = np.dtype([
('sensor_name', 'S32'),
('coeff_type', '>i4'), ('d0', '>i4'),
('ncoeff', '>i2'),
('sensors', 'S%s' % CTF.CTFV_SENSOR_LABEL, CTF.CTFV_MAX_BALANCING),
('coeffs', '>f8', CTF.CTFV_MAX_BALANCING)])
comps = np.fromfile(fid, dt, d['ncomp'])
for k in range(d['ncomp']):
comp = dict()
d['comp'].append(comp)
comp['sensor_name'] = \
comps['sensor_name'][k].split(b'\x00')[0].decode('utf-8')
comp['coeff_type'] = comps['coeff_type'][k]
comp['ncoeff'] = comps['ncoeff'][k]
comp['sensors'] = [s.split(b'\x00')[0].decode('utf-8')
for s in comps['sensors'][k][:comp['ncoeff']]]
comp['coeffs'] = comps['coeffs'][k][:comp['ncoeff']]
comp['scanno'] = d['ch_names'].index(comp['sensor_name'])
def _read_res4(dsdir):
"""Read the magical res4 file."""
# adapted from read_res4.c
name = _make_ctf_name(dsdir, 'res4')
res = dict()
with open(name, 'rb') as fid:
# Read the fields
res['head'] = _read_string(fid, 8)
res['appname'] = _read_string(fid, 256)
res['origin'] = _read_string(fid, 256)
res['desc'] = _read_string(fid, 256)
res['nave'] = _read_int2(fid)
res['data_time'] = _read_string(fid, 255)
res['data_date'] = _read_string(fid, 255)
# Seems that date and time can be swapped
# (are they entered manually?!)
if '/' in res['data_time'] and ':' in res['data_date']:
data_date = res['data_date']
res['data_date'] = res['data_time']
res['data_time'] = data_date
res['nsamp'] = _read_int(fid)
res['nchan'] = _read_int2(fid)
_move_to_next(fid, 8)
res['sfreq'] = _read_double(fid)[0]
res['epoch_time'] = _read_double(fid)[0]
res['no_trials'] = _read_int2(fid)
_move_to_next(fid, 4)
res['pre_trig_pts'] = _read_int(fid)
res['no_trials_done'] = _read_int2(fid)
res['no_trials_bst_message_windowlay'] = _read_int2(fid)
_move_to_next(fid, 4)
res['save_trials'] = _read_int(fid)
res['primary_trigger'] = fid.read(1)
res['secondary_trigger'] = [fid.read(1)
for k in range(CTF.CTFV_MAX_AVERAGE_BINS)]
res['trigger_polarity_mask'] = fid.read(1)
res['trigger_mode'] = _read_int2(fid)
_move_to_next(fid, 4)
res['accept_reject'] = _read_int(fid)
res['run_time_bst_message_windowlay'] = _read_int2(fid)
_move_to_next(fid, 4)
res['zero_head'] = _read_int(fid)
_move_to_next(fid, 4)
res['artifact_mode'] = _read_int(fid)
_read_int(fid) # padding
res['nf_run_name'] = _read_string(fid, 32)
res['nf_run_title'] = _read_string(fid, 256)
res['nf_instruments'] = _read_string(fid, 32)
res['nf_collect_descriptor'] = _read_string(fid, 32)
res['nf_subject_id'] = _read_string(fid, 32)
res['nf_operator'] = _read_string(fid, 32)
if len(res['nf_operator']) == 0:
res['nf_operator'] = None
res['nf_sensor_file_name'] = _read_ustring(fid, 60)
_move_to_next(fid, 4)
res['rdlen'] = _read_int(fid)
fid.seek(CTF.FUNNY_POS, 0)
if res['rdlen'] > 0:
res['run_desc'] = _read_string(fid, res['rdlen'])
# Filters
res['nfilt'] = _read_int2(fid)
res['filters'] = list()
for k in range(res['nfilt']):
res['filters'].append(_read_filter(fid))
# Channel information (names, then data)
res['ch_names'] = list()
for k in range(res['nchan']):
ch_name = _read_string(fid, 32)
res['ch_names'].append(ch_name)
_coil_dt = np.dtype([
('pos', '>f8', 3), ('d0', '>f8'),
('norm', '>f8', 3), ('d1', '>f8'),
('turns', '>i2'), ('d2', '>i4'), ('d3', '>i2'),
('area', '>f8')])
_ch_dt = np.dtype([
('sensor_type_index', '>i2'),
('original_run_no', '>i2'),
('coil_type', '>i4'),
('proper_gain', '>f8'),
('qgain', '>f8'),
('io_gain', '>f8'),
('io_offset', '>f8'),
('num_coils', '>i2'),
('grad_order_no', '>i2'), ('d0', '>i4'),
('coil', _coil_dt, CTF.CTFV_MAX_COILS),
('head_coil', _coil_dt, CTF.CTFV_MAX_COILS)])
chs = np.fromfile(fid, _ch_dt, res['nchan'])
for coil in (chs['coil'], chs['head_coil']):
coil['pos'] /= 100.
coil['area'] *= 1e-4
# convert to dict
chs = [dict(zip(chs.dtype.names, x)) for x in chs]
res['chs'] = chs
for k in range(res['nchan']):
res['chs'][k]['ch_name'] = res['ch_names'][k]
# The compensation coefficients
_read_comp_coeff(fid, res)
logger.info(' res4 data read.')
return res
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