def _fast_map_meg_channels(inst, pick_from, pick_to, mode='fast'):
from mne.io.pick import pick_info
from mne.forward._field_interpolation import _setup_dots
from mne.forward._field_interpolation import _compute_mapping_matrix
from mne.forward._make_forward import _create_meg_coils, _read_coil_defs
from mne.forward._lead_dots import _do_self_dots, _do_cross_dots
from mne.bem import _check_origin
miss = 1e-4 # Smoothing criterion for MEG
def _compute_dots(info, mode='fast'):
"""Compute all-to-all dots.
"""
templates = _read_coil_defs()
coils = _create_meg_coils(info['chs'], 'normal', info['dev_head_t'],
templates)
my_origin = _check_origin((0., 0., 0.04), info_from)
int_rad, noise, lut_fun, n_fact = _setup_dots(mode, coils, 'meg')
self_dots = _do_self_dots(int_rad,
False,
coils,
my_origin,
'meg',
lut_fun,
n_fact,
n_jobs=1)
cross_dots = _do_cross_dots(int_rad, False, coils, coils, my_origin,
'meg', lut_fun, n_fact).T
return self_dots, cross_dots
_compute_fast_dots = mem.cache(_compute_dots)
info = inst.info.copy()
info['bads'] = [] # if bads is different, hash will be different
info_from = pick_info(info, pick_from, copy=True)
templates = _read_coil_defs()
coils_from = _create_meg_coils(info_from['chs'], 'normal',
info_from['dev_head_t'], templates)
my_origin = _check_origin((0., 0., 0.04), info_from)
int_rad, noise, lut_fun, n_fact = _setup_dots(mode, coils_from, 'meg')
self_dots, cross_dots = _compute_fast_dots(info, mode=mode)
cross_dots = cross_dots[pick_to, :][:, pick_from]
self_dots = self_dots[pick_from, :][:, pick_from]
ch_names = [c['ch_name'] for c in info_from['chs']]
fmd = dict(kind='meg',
ch_names=ch_names,
origin=my_origin,
noise=noise,
self_dots=self_dots,
surface_dots=cross_dots,
int_rad=int_rad,
miss=miss)
fmd['data'] = _compute_mapping_matrix(fmd, info_from)
return fmd['data']
def _fast_map_meg_channels(info, pick_from, pick_to,
mode='fast'):
from mne.io.pick import pick_info
from mne.forward._field_interpolation import _setup_dots
from mne.forward._field_interpolation import _compute_mapping_matrix
from mne.forward._make_forward import _create_meg_coils, _read_coil_defs
from mne.forward._lead_dots import _do_self_dots, _do_cross_dots
from mne.bem import _check_origin
miss = 1e-4 # Smoothing criterion for MEG
# XXX: hack to silence _compute_mapping_matrix
verbose = mne.get_config('MNE_LOGGING_LEVEL', 'INFO')
mne.set_log_level('WARNING')
def _compute_dots(info, mode='fast'):
"""Compute all-to-all dots."""
templates = _read_coil_defs()
coils = _create_meg_coils(info['chs'], 'normal', info['dev_head_t'],
templates)
my_origin = _check_origin((0., 0., 0.04), info_from)
int_rad, noise, lut_fun, n_fact = _setup_dots(mode, coils, 'meg')
self_dots = _do_self_dots(int_rad, False, coils, my_origin, 'meg',
lut_fun, n_fact, n_jobs=1)
cross_dots = _do_cross_dots(int_rad, False, coils, coils,
my_origin, 'meg', lut_fun, n_fact).T
return self_dots, cross_dots
_compute_fast_dots = mem.cache(_compute_dots, verbose=0)
info['bads'] = [] # if bads is different, hash will be different
info_from = pick_info(info, pick_from, copy=True)
templates = _read_coil_defs()
coils_from = _create_meg_coils(info_from['chs'], 'normal',
info_from['dev_head_t'], templates)
my_origin = _check_origin((0., 0., 0.04), info_from)
int_rad, noise, lut_fun, n_fact = _setup_dots(mode, coils_from, 'meg')
# This function needs a clean input. It hates the presence of other
# channels than MEG channels. Make sure all is picked.
self_dots, cross_dots = _compute_fast_dots(
info, mode=mode)
cross_dots = cross_dots[pick_to, :][:, pick_from]
self_dots = self_dots[pick_from, :][:, pick_from]
ch_names = [c['ch_name'] for c in info_from['chs']]
fmd = dict(kind='meg', ch_names=ch_names,
origin=my_origin, noise=noise, self_dots=self_dots,
surface_dots=cross_dots, int_rad=int_rad, miss=miss)
fmd['data'] = _compute_mapping_matrix(fmd, info_from)
mne.set_log_level(verbose)
return fmd['data']
def map_meg_loocv_channels(inst,
pick_from,
pick_to,
self_dots=None,
cross_dots=None,
mode='fast'):
from mne.io.pick import pick_info
from mne.forward._lead_dots import _do_self_dots, _do_cross_dots
from mne.forward._make_forward import _create_meg_coils, _read_coil_defs
from mne.forward._field_interpolation import _setup_dots
from mne.forward._field_interpolation import _compute_mapping_matrix
from mne.bem import _check_origin
info_from = pick_info(inst.info, pick_from, copy=True)
info_to = pick_info(inst.info, pick_to, copy=True)
# no need to apply trans because both from and to coils are in device
# coordinates
templates = _read_coil_defs(verbose=False)
coils_from = _create_meg_coils(info_from['chs'], 'normal',
info_from['dev_head_t'], templates)
coils_to = _create_meg_coils(info_to['chs'], 'normal',
info_to['dev_head_t'], templates)
miss = 1e-4 # Smoothing criterion for MEG
int_rad, noise, lut_fun, n_fact = _setup_dots(mode, coils_from, 'meg')
my_origin = _check_origin((0., 0., 0.04), info_from)
if self_dots is None:
self_dots = _do_self_dots(int_rad,
False,
coils_from,
my_origin,
'meg',
lut_fun,
n_fact,
n_jobs=1)
if cross_dots is None:
cross_dots = _do_cross_dots(int_rad, False, coils_from, coils_to,
my_origin, 'meg', lut_fun, n_fact).T
ch_names = [c['ch_name'] for c in info_from['chs']]
fmd = dict(kind='meg',
ch_names=ch_names,
origin=my_origin,
noise=noise,
self_dots=self_dots,
surface_dots=cross_dots,
int_rad=int_rad,
miss=miss)
fmd['data'] = _compute_mapping_matrix(fmd, info_from)
return fmd['data'], self_dots, cross_dots
def _compute_dots(info, mode='fast'):
"""Compute all-to-all dots."""
templates = _read_coil_defs()
coils = _create_meg_coils(info['chs'], 'normal', info['dev_head_t'],
templates)
my_origin = _check_origin((0., 0., 0.04), info_from)
int_rad, noise, lut_fun, n_fact = _setup_dots(mode, coils, 'meg')
self_dots = _do_self_dots(int_rad, False, coils, my_origin, 'meg',
lut_fun, n_fact, n_jobs=1)
cross_dots = _do_cross_dots(int_rad, False, coils, coils,
my_origin, 'meg', lut_fun, n_fact).T
return self_dots, cross_dots
def _compute_dots(info, mode='fast'):
"""Compute all-to-all dots.
"""
templates = _read_coil_defs()
coils = _create_meg_coils(info['chs'], 'normal', info['dev_head_t'],
templates)
my_origin = _check_origin((0., 0., 0.04), info_from)
int_rad, noise, lut_fun, n_fact = _setup_dots(mode, coils, 'meg')
self_dots = _do_self_dots(int_rad, False, coils, my_origin, 'meg',
lut_fun, n_fact, n_jobs=1)
cross_dots = _do_cross_dots(int_rad, False, coils, coils,
my_origin, 'meg', lut_fun, n_fact).T
return self_dots, cross_dots
def _fast_map_meg_channels(inst, pick_from, pick_to, mode='fast'):
from mne.io.pick import pick_info
from mne.forward._field_interpolation import _setup_dots
from mne.forward._field_interpolation import _compute_mapping_matrix
from mne.forward._make_forward import _create_meg_coils, _read_coil_defs
from mne.forward._lead_dots import _do_self_dots, _do_cross_dots
from mne.bem import _check_origin
miss = 1e-4 # Smoothing criterion for MEG
def _compute_dots(info, mode='fast'):
"""Compute all-to-all dots.
"""
templates = _read_coil_defs()
coils = _create_meg_coils(info['chs'], 'normal', info['dev_head_t'],
templates)
my_origin = _check_origin((0., 0., 0.04), info_from)
int_rad, noise, lut_fun, n_fact = _setup_dots(mode, coils, 'meg')
self_dots = _do_self_dots(int_rad, False, coils, my_origin, 'meg',
lut_fun, n_fact, n_jobs=1)
cross_dots = _do_cross_dots(int_rad, False, coils, coils,
my_origin, 'meg', lut_fun, n_fact).T
return self_dots, cross_dots
_compute_fast_dots = mem.cache(_compute_dots)
info = inst.info.copy()
info['bads'] = [] # if bads is different, hash will be different
info_from = pick_info(info, pick_from, copy=True)
templates = _read_coil_defs()
coils_from = _create_meg_coils(info_from['chs'], 'normal',
info_from['dev_head_t'], templates)
my_origin = _check_origin((0., 0., 0.04), info_from)
int_rad, noise, lut_fun, n_fact = _setup_dots(mode, coils_from, 'meg')
self_dots, cross_dots = _compute_fast_dots(info, mode=mode)
cross_dots = cross_dots[pick_to, :][:, pick_from]
self_dots = self_dots[pick_from, :][:, pick_from]
ch_names = [c['ch_name'] for c in info_from['chs']]
fmd = dict(kind='meg', ch_names=ch_names,
origin=my_origin, noise=noise, self_dots=self_dots,
surface_dots=cross_dots, int_rad=int_rad, miss=miss)
fmd['data'] = _compute_mapping_matrix(fmd, info_from)
return fmd['data']
def _compute_dots(info, mode='fast'):
"""Compute all-to-all dots."""
from mne.forward._field_interpolation import _setup_dots
from mne.forward._lead_dots import _do_self_dots, _do_cross_dots
from mne.forward._make_forward import _create_meg_coils, _read_coil_defs
from mne.bem import _check_origin
templates = _read_coil_defs()
coils = _create_meg_coils(info['chs'], 'normal', info['dev_head_t'],
templates)
my_origin = _check_origin((0., 0., 0.04), info)
int_rad, noise, lut_fun, n_fact = _setup_dots(mode, coils, 'meg')
self_dots = _do_self_dots(int_rad, False, coils, my_origin, 'meg',
lut_fun, n_fact, n_jobs=1)
cross_dots = _do_cross_dots(int_rad, False, coils, coils,
my_origin, 'meg', lut_fun, n_fact).T
return self_dots, cross_dots
def _compute_dots(info, mode='fast'):
"""Compute all-to-all dots."""
from mne.forward._field_interpolation import _setup_dots
from mne.forward._lead_dots import _do_self_dots, _do_cross_dots
from mne.forward._make_forward import _create_meg_coils, _read_coil_defs
from mne.bem import _check_origin
templates = _read_coil_defs()
coils = _create_meg_coils(info['chs'], 'normal', info['dev_head_t'],
templates)
my_origin = _check_origin((0., 0., 0.04), info)
int_rad, noise, lut_fun, n_fact = _setup_dots(mode, coils, 'meg')
self_dots = _do_self_dots(int_rad, False, coils, my_origin, 'meg',
lut_fun, n_fact, n_jobs=1)
cross_dots = _do_cross_dots(int_rad, False, coils, coils,
my_origin, 'meg', lut_fun, n_fact).T
return self_dots, cross_dots
def _fast_map_meg_channels(info, pick_from, pick_to, dots=None, mode='fast'):
from mne.io.pick import pick_info
from mne.forward._field_interpolation import _compute_mapping_matrix
from mne.forward._make_forward import _create_meg_coils, _read_coil_defs
from mne.bem import _check_origin
miss = 1e-4 # Smoothing criterion for MEG
# XXX: hack to silence _compute_mapping_matrix
verbose = mne.get_config('MNE_LOGGING_LEVEL', 'INFO')
mne.set_log_level('WARNING')
info_from = pick_info(info, pick_from, copy=True)
templates = _read_coil_defs()
coils_from = _create_meg_coils(info_from['chs'], 'normal',
info_from['dev_head_t'], templates)
my_origin = _check_origin((0., 0., 0.04), info_from)
int_rad, noise, lut_fun, n_fact = _patch_setup_dots(
mode, info_from, coils_from, 'meg')
# This function needs a clean input. It hates the presence of other
# channels than MEG channels. Make sure all is picked.
if dots is None:
dots = self_dots, cross_dots = _compute_dots(info, mode=mode)
else:
self_dots, cross_dots = dots
self_dots, cross_dots = _pick_dots(dots, pick_from, pick_to)
ch_names = [c['ch_name'] for c in info_from['chs']]
fmd = dict(kind='meg',
ch_names=ch_names,
origin=my_origin,
noise=noise,
self_dots=self_dots,
surface_dots=cross_dots,
int_rad=int_rad,
miss=miss)
fmd['data'] = _compute_mapping_matrix(fmd, info_from)
mne.set_log_level(verbose)
return fmd['data']
def map_meg_loocv_channels(inst, pick_from, pick_to, self_dots=None,
cross_dots=None, mode='fast'):
from mne.io.pick import pick_info
from mne.forward._lead_dots import _do_self_dots, _do_cross_dots
from mne.forward._make_forward import _create_meg_coils, _read_coil_defs
from mne.forward._field_interpolation import _setup_dots
from mne.forward._field_interpolation import _compute_mapping_matrix
from mne.bem import _check_origin
info_from = pick_info(inst.info, pick_from, copy=True)
info_to = pick_info(inst.info, pick_to, copy=True)
# no need to apply trans because both from and to coils are in device
# coordinates
templates = _read_coil_defs(verbose=False)
coils_from = _create_meg_coils(info_from['chs'], 'normal',
info_from['dev_head_t'], templates)
coils_to = _create_meg_coils(info_to['chs'], 'normal',
info_to['dev_head_t'], templates)
miss = 1e-4 # Smoothing criterion for MEG
int_rad, noise, lut_fun, n_fact = _setup_dots(mode, coils_from, 'meg')
my_origin = _check_origin((0., 0., 0.04), info_from)
if self_dots is None:
self_dots = _do_self_dots(int_rad, False, coils_from, my_origin, 'meg',
lut_fun, n_fact, n_jobs=1)
if cross_dots is None:
cross_dots = _do_cross_dots(int_rad, False, coils_from, coils_to,
my_origin, 'meg', lut_fun, n_fact).T
ch_names = [c['ch_name'] for c in info_from['chs']]
fmd = dict(kind='meg', ch_names=ch_names,
origin=my_origin, noise=noise, self_dots=self_dots,
surface_dots=cross_dots, int_rad=int_rad, miss=miss)
fmd['data'] = _compute_mapping_matrix(fmd, info_from)
return fmd['data'], self_dots, cross_dots
def _fast_map_meg_channels(info, pick_from, pick_to,
dots=None, mode='fast'):
from mne.io.pick import pick_info
from mne.forward._field_interpolation import _setup_dots
from mne.forward._field_interpolation import _compute_mapping_matrix
from mne.forward._make_forward import _create_meg_coils, _read_coil_defs
from mne.bem import _check_origin
miss = 1e-4 # Smoothing criterion for MEG
# XXX: hack to silence _compute_mapping_matrix
verbose = mne.get_config('MNE_LOGGING_LEVEL', 'INFO')
mne.set_log_level('WARNING')
info_from = pick_info(info, pick_from, copy=True)
templates = _read_coil_defs()
coils_from = _create_meg_coils(info_from['chs'], 'normal',
info_from['dev_head_t'], templates)
my_origin = _check_origin((0., 0., 0.04), info_from)
int_rad, noise, lut_fun, n_fact = _setup_dots(mode, coils_from, 'meg')
# This function needs a clean input. It hates the presence of other
# channels than MEG channels. Make sure all is picked.
if dots is None:
dots = self_dots, cross_dots = _compute_dots(info, mode=mode)
else:
self_dots, cross_dots = dots
self_dots, cross_dots = _pick_dots(dots, pick_from, pick_to)
ch_names = [c['ch_name'] for c in info_from['chs']]
fmd = dict(kind='meg', ch_names=ch_names,
origin=my_origin, noise=noise, self_dots=self_dots,
surface_dots=cross_dots, int_rad=int_rad, miss=miss)
fmd['data'] = _compute_mapping_matrix(fmd, info_from)
mne.set_log_level(verbose)
return fmd['data']
def test_constants(tmpdir):
"""Test compensation."""
tmpdir = str(tmpdir) # old pytest...
dest = op.join(tmpdir, 'fiff.zip')
_fetch_file(
'https://codeload.github.com/'
f'{REPO}/fiff-constants/zip/{COMMIT}', dest)
names = list()
with zipfile.ZipFile(dest, 'r') as ff:
for name in ff.namelist():
if 'Dictionary' in name:
ff.extract(name, tmpdir)
names.append(op.basename(name))
shutil.move(op.join(tmpdir, name), op.join(tmpdir, names[-1]))
names = sorted(names)
assert names == [
'DictionaryIOD.txt', 'DictionaryIOD_MNE.txt',
'DictionaryStructures.txt', 'DictionaryTags.txt',
'DictionaryTags_MNE.txt', 'DictionaryTypes.txt',
'DictionaryTypes_MNE.txt'
]
# IOD (MEGIN and MNE)
fif = dict(iod=dict(), tags=dict(), types=dict(), defines=dict())
con = dict(iod=dict(), tags=dict(), types=dict(), defines=dict())
fiff_version = None
for name in ['DictionaryIOD.txt', 'DictionaryIOD_MNE.txt']:
with open(op.join(tmpdir, name), 'rb') as fid:
for line in fid:
line = line.decode('latin1').strip()
if line.startswith('# Packing revision'):
assert fiff_version is None
fiff_version = line.split()[-1]
if (line.startswith('#') or line.startswith('alias')
or len(line) == 0):
continue
line = line.split('"')
assert len(line) in (1, 2, 3)
desc = '' if len(line) == 1 else line[1]
line = line[0].split()
assert len(line) in (2, 3)
if len(line) == 2:
kind, id_ = line
else:
kind, id_, tagged = line
assert tagged in ('tagged', )
id_ = int(id_)
if id_ not in iod_dups:
assert id_ not in fif['iod']
fif['iod'][id_] = [kind, desc]
# Tags (MEGIN)
with open(op.join(tmpdir, 'DictionaryTags.txt'), 'rb') as fid:
for line in fid:
line = line.decode('ISO-8859-1').strip()
if (line.startswith('#') or line.startswith('alias')
or line.startswith(':') or len(line) == 0):
continue
line = line.split('"')
assert len(line) in (1, 2, 3), line
desc = '' if len(line) == 1 else line[1]
line = line[0].split()
assert len(line) == 4, line
kind, id_, dtype, unit = line
id_ = int(id_)
val = [kind, dtype, unit]
assert id_ not in fif['tags'], (fif['tags'].get(id_), val)
fif['tags'][id_] = val
# Tags (MNE)
with open(op.join(tmpdir, 'DictionaryTags_MNE.txt'), 'rb') as fid:
for li, line in enumerate(fid):
line = line.decode('ISO-8859-1').strip()
# ignore continuation lines (*)
if (line.startswith('#') or line.startswith('alias')
or line.startswith(':') or line.startswith('*')
or len(line) == 0):
continue
# weird syntax around line 80:
if line in ('/*', '"'):
continue
line = line.split('"')
assert len(line) in (1, 2, 3), line
if len(line) == 3 and len(line[2]) > 0:
l2 = line[2].strip()
assert l2.startswith('/*') and l2.endswith('*/'), l2
desc = '' if len(line) == 1 else line[1]
line = line[0].split()
assert len(line) == 3, (li + 1, line)
kind, id_, dtype = line
unit = '-'
id_ = int(id_)
val = [kind, dtype, unit]
if id_ not in tag_dups:
assert id_ not in fif['tags'], (fif['tags'].get(id_), val)
fif['tags'][id_] = val
# Types and enums
in_ = None
re_prim = re.compile(r'^primitive\((.*)\)\s*(\S*)\s*"(.*)"$')
re_enum = re.compile(r'^enum\((\S*)\)\s*".*"$')
re_enum_entry = re.compile(r'\s*(\S*)\s*(\S*)\s*"(.*)"$')
re_defi = re.compile(r'#define\s*(\S*)\s*(\S*)\s*"(.*)"$')
used_enums = list()
for extra in ('', '_MNE'):
with open(op.join(tmpdir, 'DictionaryTypes%s.txt' % (extra, )),
'rb') as fid:
for li, line in enumerate(fid):
line = line.decode('ISO-8859-1').strip()
if in_ is None:
p = re_prim.match(line)
e = re_enum.match(line)
d = re_defi.match(line)
if p is not None:
t, s, d = p.groups()
s = int(s)
assert s not in fif['types']
fif['types'][s] = [t, d]
elif e is not None:
# entering an enum
this_enum = e.group(1)
if this_enum not in fif:
used_enums.append(this_enum)
fif[this_enum] = dict()
con[this_enum] = dict()
in_ = fif[this_enum]
elif d is not None:
t, s, d = d.groups()
s = int(s)
fif['defines'][t] = [s, d]
else:
assert not line.startswith('enum(')
else: # in an enum
if line == '{':
continue
elif line == '}':
in_ = None
continue
t, s, d = re_enum_entry.match(line).groups()
s = int(s)
if t != 'ecg' and s != 3: # ecg defined the same way
assert s not in in_
in_[s] = [t, d]
#
# Assertions
#
# Version
mne_version = '%d.%d' % (FIFF.FIFFC_MAJOR_VERSION,
FIFF.FIFFC_MINOR_VERSION)
assert fiff_version == mne_version
unknowns = list()
# Assert that all our constants are in the FIF def
assert 'FIFFV_SSS_JOB_NOTHING' in dir(FIFF)
for name in sorted(dir(FIFF)):
if name.startswith('_') or name in _dir_ignore_names:
continue
check = None
val = getattr(FIFF, name)
if name in fif['defines']:
assert fif['defines'][name][0] == val
elif name.startswith('FIFFC_'):
# Checked above
assert name in ('FIFFC_MAJOR_VERSION', 'FIFFC_MINOR_VERSION',
'FIFFC_VERSION')
elif name.startswith('FIFFB_'):
check = 'iod'
elif name.startswith('FIFFT_'):
check = 'types'
elif name.startswith('FIFFV_'):
if name.startswith('FIFFV_MNE_') and name.endswith('_ORI'):
check = 'mne_ori'
elif name.startswith('FIFFV_MNE_') and name.endswith('_COV'):
check = 'covariance_type'
elif name.startswith('FIFFV_MNE_COORD'):
check = 'coord' # weird wrapper
elif name.endswith('_CH') or '_QUAT_' in name or name in \
('FIFFV_DIPOLE_WAVE', 'FIFFV_GOODNESS_FIT',
'FIFFV_HPI_ERR', 'FIFFV_HPI_G', 'FIFFV_HPI_MOV'):
check = 'ch_type'
elif name.startswith('FIFFV_SUBJ_'):
check = name.split('_')[2].lower()
elif name in ('FIFFV_POINT_LPA', 'FIFFV_POINT_NASION',
'FIFFV_POINT_RPA', 'FIFFV_POINT_INION'):
check = 'cardinal_point'
else:
for check in used_enums:
if name.startswith('FIFFV_' + check.upper()):
break
else:
if name not in _tag_ignore_names:
raise RuntimeError('Could not find %s' % (name, ))
assert check in used_enums, name
if 'SSS' in check:
raise RuntimeError
elif name.startswith('FIFF_UNIT'): # units and multipliers
check = name.split('_')[1].lower()
elif name.startswith('FIFF_'):
check = 'tags'
else:
unknowns.append((name, val))
if check is not None and name not in _tag_ignore_names:
assert val in fif[check], '%s: %s, %s' % (check, val, name)
if val in con[check]:
msg = "%s='%s' ?" % (name, con[check][val])
assert _aliases.get(name) == con[check][val], msg
else:
con[check][val] = name
unknowns = '\n\t'.join('%s (%s)' % u for u in unknowns)
assert len(unknowns) == 0, 'Unknown types\n\t%s' % unknowns
# Assert that all the FIF defs are in our constants
assert set(fif.keys()) == set(con.keys())
for key in sorted(set(fif.keys()) - {'defines'}):
this_fif, this_con = fif[key], con[key]
assert len(set(this_fif.keys())) == len(this_fif)
assert len(set(this_con.keys())) == len(this_con)
missing_from_con = sorted(set(this_con.keys()) - set(this_fif.keys()))
assert missing_from_con == [], key
if key not in _ignore_incomplete_enums:
missing_from_fif = sorted(
set(this_fif.keys()) - set(this_con.keys()))
assert missing_from_fif == [], key
# Assert that `coil_def.dat` has accurate descriptions of all enum(coil)
coil_def = _read_coil_defs()
coil_desc = np.array([c['desc'] for c in coil_def])
coil_def = np.array([(c['coil_type'], c['accuracy']) for c in coil_def],
int)
mask = (coil_def[:, 1] == FWD.COIL_ACCURACY_ACCURATE)
coil_def = coil_def[mask, 0]
coil_desc = coil_desc[mask]
bad_list = []
for key in fif['coil']:
if key not in _missing_coil_def and key not in coil_def:
bad_list.append((' %s,' % key).ljust(10) + ' # ' +
fif['coil'][key][1])
assert len(bad_list) == 0, \
'\nIn fiff-constants, missing from coil_def:\n' + '\n'.join(bad_list)
# Assert that enum(coil) has all `coil_def.dat` entries
for key, desc in zip(coil_def, coil_desc):
if key not in fif['coil']:
bad_list.append((' %s,' % key).ljust(10) + ' # ' + desc)
assert len(bad_list) == 0, \
'In coil_def, missing from fiff-constants:\n' + '\n'.join(bad_list)
def test_constants(tmpdir):
"""Test compensation."""
tmpdir = str(tmpdir) # old pytest...
dest = op.join(tmpdir, 'fiff.zip')
_fetch_file('https://codeload.github.com/mne-tools/fiff-constants/zip/' +
commit, dest)
names = list()
with zipfile.ZipFile(dest, 'r') as ff:
for name in ff.namelist():
if 'Dictionary' in name:
ff.extract(name, tmpdir)
names.append(op.basename(name))
shutil.move(op.join(tmpdir, name), op.join(tmpdir, names[-1]))
names = sorted(names)
assert names == ['DictionaryIOD.txt', 'DictionaryIOD_MNE.txt',
'DictionaryStructures.txt',
'DictionaryTags.txt', 'DictionaryTags_MNE.txt',
'DictionaryTypes.txt', 'DictionaryTypes_MNE.txt']
# IOD (MEGIN and MNE)
fif = dict(iod=dict(), tags=dict(), types=dict(), defines=dict())
con = dict(iod=dict(), tags=dict(), types=dict(), defines=dict())
fiff_version = None
for name in ['DictionaryIOD.txt', 'DictionaryIOD_MNE.txt']:
with open(op.join(tmpdir, name), 'rb') as fid:
for line in fid:
line = line.decode('latin1').strip()
if line.startswith('# Packing revision'):
assert fiff_version is None
fiff_version = line.split()[-1]
if (line.startswith('#') or line.startswith('alias') or
len(line) == 0):
continue
line = line.split('"')
assert len(line) in (1, 2, 3)
desc = '' if len(line) == 1 else line[1]
line = line[0].split()
assert len(line) in (2, 3)
if len(line) == 2:
kind, id_ = line
else:
kind, id_, tagged = line
assert tagged in ('tagged',)
id_ = int(id_)
if id_ not in iod_dups:
assert id_ not in fif['iod']
fif['iod'][id_] = [kind, desc]
# Tags (MEGIN)
with open(op.join(tmpdir, 'DictionaryTags.txt'), 'rb') as fid:
for line in fid:
line = line.decode('ISO-8859-1').strip()
if (line.startswith('#') or line.startswith('alias') or
line.startswith(':') or len(line) == 0):
continue
line = line.split('"')
assert len(line) in (1, 2, 3), line
desc = '' if len(line) == 1 else line[1]
line = line[0].split()
assert len(line) == 4, line
kind, id_, dtype, unit = line
id_ = int(id_)
val = [kind, dtype, unit]
assert id_ not in fif['tags'], (fif['tags'].get(id_), val)
fif['tags'][id_] = val
# Tags (MNE)
with open(op.join(tmpdir, 'DictionaryTags_MNE.txt'), 'rb') as fid:
for li, line in enumerate(fid):
line = line.decode('ISO-8859-1').strip()
# ignore continuation lines (*)
if (line.startswith('#') or line.startswith('alias') or
line.startswith(':') or line.startswith('*') or
len(line) == 0):
continue
# weird syntax around line 80:
if line in ('/*', '"'):
continue
line = line.split('"')
assert len(line) in (1, 2, 3), line
if len(line) == 3 and len(line[2]) > 0:
l2 = line[2].strip()
assert l2.startswith('/*') and l2.endswith('*/'), l2
desc = '' if len(line) == 1 else line[1]
line = line[0].split()
assert len(line) == 3, (li + 1, line)
kind, id_, dtype = line
unit = '-'
id_ = int(id_)
val = [kind, dtype, unit]
if id_ not in tag_dups:
assert id_ not in fif['tags'], (fif['tags'].get(id_), val)
fif['tags'][id_] = val
# Types and enums
in_ = None
re_prim = re.compile(r'^primitive\((.*)\)\s*(\S*)\s*"(.*)"$')
re_enum = re.compile(r'^enum\((\S*)\)\s*".*"$')
re_enum_entry = re.compile(r'\s*(\S*)\s*(\S*)\s*"(.*)"$')
re_defi = re.compile(r'#define\s*(\S*)\s*(\S*)\s*"(.*)"$')
used_enums = list()
for extra in ('', '_MNE'):
with open(op.join(tmpdir, 'DictionaryTypes%s.txt'
% (extra,)), 'rb') as fid:
for li, line in enumerate(fid):
line = line.decode('ISO-8859-1').strip()
if in_ is None:
p = re_prim.match(line)
e = re_enum.match(line)
d = re_defi.match(line)
if p is not None:
t, s, d = p.groups()
s = int(s)
assert s not in fif['types']
fif['types'][s] = [t, d]
elif e is not None:
# entering an enum
this_enum = e.group(1)
if this_enum not in fif:
used_enums.append(this_enum)
fif[this_enum] = dict()
con[this_enum] = dict()
in_ = fif[this_enum]
elif d is not None:
t, s, d = d.groups()
s = int(s)
fif['defines'][t] = [s, d]
else:
assert not line.startswith('enum(')
else: # in an enum
if line == '{':
continue
elif line == '}':
in_ = None
continue
t, s, d = re_enum_entry.match(line).groups()
s = int(s)
if t != 'ecg' and s != 3: # ecg defined the same way
assert s not in in_
in_[s] = [t, d]
#
# Assertions
#
# Version
mne_version = '%d.%d' % (FIFF.FIFFC_MAJOR_VERSION,
FIFF.FIFFC_MINOR_VERSION)
assert fiff_version == mne_version
unknowns = list()
# Assert that all our constants are in the FIF def
assert 'FIFFV_SSS_JOB_NOTHING' in dir(FIFF)
for name in sorted(dir(FIFF)):
if name.startswith('_') or name in _dir_ignore_names:
continue
check = None
val = getattr(FIFF, name)
if name in fif['defines']:
assert fif['defines'][name][0] == val
elif name.startswith('FIFFC_'):
# Checked above
assert name in ('FIFFC_MAJOR_VERSION', 'FIFFC_MINOR_VERSION',
'FIFFC_VERSION')
elif name.startswith('FIFFB_'):
check = 'iod'
elif name.startswith('FIFFT_'):
check = 'types'
elif name.startswith('FIFFV_'):
if name.startswith('FIFFV_MNE_') and name.endswith('_ORI'):
check = 'mne_ori'
elif name.startswith('FIFFV_MNE_') and name.endswith('_COV'):
check = 'covariance_type'
elif name.startswith('FIFFV_MNE_COORD'):
check = 'coord' # weird wrapper
elif name.endswith('_CH') or '_QUAT_' in name or name in \
('FIFFV_DIPOLE_WAVE', 'FIFFV_GOODNESS_FIT',
'FIFFV_HPI_ERR', 'FIFFV_HPI_G', 'FIFFV_HPI_MOV'):
check = 'ch_type'
elif name.startswith('FIFFV_SUBJ_'):
check = name.split('_')[2].lower()
elif name in ('FIFFV_POINT_LPA', 'FIFFV_POINT_NASION',
'FIFFV_POINT_RPA'):
check = 'cardinal_point'
else:
for check in used_enums:
if name.startswith('FIFFV_' + check.upper()):
break
else:
raise RuntimeError('Could not find %s' % (name,))
assert check in used_enums, name
if 'SSS' in check:
raise RuntimeError
elif name.startswith('FIFF_UNIT'): # units and multipliers
check = name.split('_')[1].lower()
elif name.startswith('FIFF_'):
check = 'tags'
else:
unknowns.append((name, val))
if check is not None and name not in _tag_ignore_names:
assert val in fif[check], '%s: %s, %s' % (check, val, name)
if val in con[check]:
msg = "%s='%s' ?" % (name, con[check][val])
assert _aliases.get(name) == con[check][val], msg
else:
con[check][val] = name
unknowns = '\n\t'.join('%s (%s)' % u for u in unknowns)
assert len(unknowns) == 0, 'Unknown types\n\t%s' % unknowns
# Assert that all the FIF defs are in our constants
assert set(fif.keys()) == set(con.keys())
for key in sorted(set(fif.keys()) - {'defines'}):
this_fif, this_con = fif[key], con[key]
assert len(set(this_fif.keys())) == len(this_fif)
assert len(set(this_con.keys())) == len(this_con)
missing_from_con = sorted(set(this_con.keys()) - set(this_fif.keys()))
assert missing_from_con == [], key
if key not in _ignore_incomplete_enums:
missing_from_fif = sorted(set(this_fif.keys()) -
set(this_con.keys()))
assert missing_from_fif == [], key
# Assert that `coil_def.dat` has accurate descriptions of all enum(coil)
coil_def = _read_coil_defs()
coil_desc = np.array([c['desc'] for c in coil_def])
coil_def = np.array([(c['coil_type'], c['accuracy'])
for c in coil_def], int)
mask = (coil_def[:, 1] == FWD.COIL_ACCURACY_ACCURATE)
coil_def = coil_def[mask, 0]
coil_desc = coil_desc[mask]
bad_list = []
for key in fif['coil']:
if key not in _missing_coil_def and key not in coil_def:
bad_list.append((' %s,' % key).ljust(10) +
' # ' + fif['coil'][key][1])
assert len(bad_list) == 0, '\n' + '\n'.join(bad_list)
# Assert that enum(coil) has all `coil_def.dat` entries
for key, desc in zip(coil_def, coil_desc):
if key not in fif['coil']:
bad_list.append((' %s,' % key).ljust(10) + ' # ' + desc)
assert len(bad_list) == 0, '\n' + '\n'.join(bad_list)
