"""Read .res4 files.""" # Author: Eric Larson # # 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