def test_samples_sesssions():
set_log_level('warning', 'mne')
SampleExperiment = import_attr(sample_path / 'sample_experiment_sessions.py', 'SampleExperiment')
tempdir = TempDir()
datasets.setup_samples_experiment(tempdir, 2, 1, 2)
root = join(tempdir, 'SampleExperiment')
e = SampleExperiment(root)
# bad channels
e.make_bad_channels('0111')
eq_(e.load_bad_channels(), ['MEG 0111'])
eq_(e.load_bad_channels(session='sample2'), [])
e.show_bad_channels()
e.merge_bad_channels()
eq_(e.load_bad_channels(session='sample2'), ['MEG 0111'])
e.show_bad_channels()
# rejection
for _ in e:
for epoch in ('target1', 'target2'):
e.set(epoch=epoch)
e.make_rej(auto=2e-12)
ds = e.load_evoked('R0000', epoch='target2')
e.set(session='sample1')
ds2 = e.load_evoked('R0000')
assert_dataobj_equal(ds2, ds)
# super-epoch
ds1 = e.load_epochs(epoch='target1')
ds2 = e.load_epochs(epoch='target2')
ds_super = e.load_epochs(epoch='super')
assert_dataobj_equal(ds_super['meg'], combine((ds1['meg'], ds2['meg'])))
def test_table():
table = fmtxt.Table('ll')
table.cells('A', 'B')
table.midrule()
table.cells('a1', 'b1', 'a2', 'b2')
eq_(str(table), 'A B \n-------\na1 b1\na2 b2')
eq_(table.get_html(), u'<figure><table rules="none" cellpadding="2" '
u'frame="hsides" border="1"><tr>\n'
u' <td>A</td>\n <td>B</td>\n</tr>\n<tr>\n'
u' <td>a1</td>\n <td>b1</td>\n</tr>\n<tr>\n'
u' <td>a2</td>\n <td>b2</td>\n</tr></table></figure>')
eq_(table.get_rtf(), '\\trowd\n\\cellx0000\n\\cellx1000\n\\row\n'
'A\\intbl\\cell\nB\\intbl\\cell\n\\row\n'
'a1\\intbl\\cell\nb1\\intbl\\cell\n\\row\n'
'a2\\intbl\\cell\nb2\\intbl\\cell\n\\row')
eq_(table.get_tex(), '\\begin{center}\n\\begin{tabular}{ll}\n\\toprule\n'
'A & B \\\\\n\\midrule\n'
'a1 & b1 \\\\\na2 & b2 \\\\\n'
'\\bottomrule\n\\end{tabular}\n\\end{center}')
# empty table
str(fmtxt.Table(''))
# saving
tempdir = TempDir()
# HTML
path = os.path.join(tempdir, 'test.html')
table.save_html(path)
eq_(open(path).read(), '<!DOCTYPE html>\n<html>\n<head>\n'
' <title>Untitled</title>\n'
'<style>\n\n.float {\n float:left\n}\n\n'
'</style>\n</head>\n\n'
'<body>\n\n<figure>'
'<table rules="none" cellpadding="2" frame="hsides" '
'border="1"><tr>\n'
' <td>A</td>\n <td>B</td>\n</tr>\n<tr>\n'
' <td>a1</td>\n <td>b1</td>\n</tr>\n<tr>\n'
' <td>a2</td>\n <td>b2</td>\n</tr>'
'</table></figure>\n\n</body>\n</html>\n')
# rtf
path = os.path.join(tempdir, 'test.rtf')
table.save_rtf(path)
eq_(open(path).read(), '{\\rtf1\\ansi\\deff0\n\n'
'\\trowd\n\\cellx0000\n\\cellx1000\n\\row\n'
'A\\intbl\\cell\nB\\intbl\\cell\n\\row\n'
'a1\\intbl\\cell\nb1\\intbl\\cell\n\\row\n'
'a2\\intbl\\cell\nb2\\intbl\\cell\n\\row\n}')
# TeX
path = os.path.join(tempdir, 'test.tex')
table.save_tex(path)
eq_(open(path).read(), '\\begin{center}\n\\begin{tabular}{ll}\n\\toprule\n'
'A & B \\\\\n\\midrule\n'
'a1 & b1 \\\\\na2 & b2 \\\\\n'
'\\bottomrule\n\\end{tabular}\n\\end{center}')
# txt
path = os.path.join(tempdir, 'test.txt')
table.save_txt(path)
eq_(open(path).read(), 'A B \n-------\na1 b1\na2 b2')
def test_image():
"Test FMText Image"
tempdir = TempDir()
filename = os.path.join(tempdir, 'rgb.png')
rgba = np.random.uniform(0, 1, (100, 100, 4))
rgb = rgba[:, :, :3]
for array in (rgb, rgba):
im = fmtxt.Image.from_array(array, alt='array')
im.save_image(filename)
ok_(im.get_html().startswith('<img src='))
im2 = fmtxt.Image.from_file(filename, alt='array')
eq_(im.get_html(), im2.get_html())
def test_file_handling():
"Test MneExperiment with actual files"
tempdir = TempDir()
for subject in SUBJECTS:
sdir = os.path.join(tempdir, 'meg', subject)
os.makedirs(sdir)
e = FileExperiment(tempdir)
eq_(e.get('subject'), SUBJECTS[0])
eq_([s for s in e.iter(group='all')], SUBJECTS)
eq_([s for s in e.iter(group='gsub')], SUBJECTS[1:])
eq_([s for s in e.iter(group='gexc')], SUBJECTS[1:])
eq_([s for s in e.iter(group='gexc2')], SUBJECTS[1:-1])
eq_(e.get('subject'), SUBJECTS[1])
eq_(e.get('subject', group='all'), SUBJECTS[1])
e.set(SUBJECTS[0])
eq_(e.get('subject'), SUBJECTS[0])
eq_(e.get('subject', group='gsub'), SUBJECTS[1])
e = FileExperimentDefaults(tempdir)
eq_(e.get('group'), 'gsub')
eq_(e.get('subject'), SUBJECTS[1])
def test_select_components():
"Test Select-Epochs GUI Document"
tempdir = TempDir()
PATH = join(tempdir, 'test-ica.fif')
ds = datasets.get_mne_sample()
ds['epochs'] = ds['epochs'].pick_types('mag')
ica = mne.preprocessing.ICA(0.95)
ica.fit(ds['epochs'])
ica.save(PATH)
frame = gui.select_components(PATH, ds)
frame.model.toggle(1)
frame.OnSave(None)
ica = mne.preprocessing.read_ica(PATH)
assert ica.exclude == [1]
frame.OnUndo(None)
frame.OnSave(None)
ica = mne.preprocessing.read_ica(PATH)
assert ica.exclude == []
frame.Close()
def test_mne_experiment_templates():
"Test MneExperiment template formatting"
tempdir = TempDir()
e = BaseExperiment(tempdir, False)
# Don't create dirs without root
ok_(e.get('raw-file', mkdir=True).endswith('-raw.fif'))
# model
eq_(e.get('model', model='a % b'), 'a%b')
eq_(e.get('model', model='b % a'), 'a%b')
assert_raises(ValueError, e.set, model='a*b')
assert_raises(ValueError, e.set, model='log(a)')
# compounds
eq_(e.get('src_kind'), '0-40 bestreg free-3-dSPM')
e.set_inv('fixed')
eq_(e.get('src_kind'), '0-40 bestreg fixed-3-dSPM')
e.set(cov='noreg')
eq_(e.get('src_kind'), '0-40 noreg fixed-3-dSPM')
e.set(raw='1-40')
eq_(e.get('src_kind'), '1-40 noreg fixed-3-dSPM')
e.set(src='ico-5')
eq_(e.get('src_kind'), '1-40 noreg ico-5 fixed-3-dSPM')
e.set(src='ico-4')
eq_(e.get('src_kind'), '1-40 noreg fixed-3-dSPM')
# find terminal field names
eq_(e.find_keys('raw-file'), {'root', 'subject', 'session'})
eq_(
e.find_keys('evoked-file', False), {
'subject',
'session',
'modality',
'raw',
'epoch',
'rej',
'equalize_evoked_count',
'model',
})
# inv
SNR1 = 1.
SNR2 = 1. / 2**2
SNR3 = 1. / 3**2
def set_inv(inv, make_kw, apply_kw, *args):
e.reset()
e.set(inv=inv)
eq_(e._params['make_inv_kw'], make_kw)
eq_(e._params['apply_inv_kw'], apply_kw)
e.reset()
e.set_inv(*args)
eq_(e.get('inv'), inv)
eq_(e._params['make_inv_kw'], make_kw)
eq_(e._params['apply_inv_kw'], apply_kw)
yield (set_inv, 'free-3-MNE', {
'loose': 1,
'depth': 0.8
}, {
'method': 'MNE',
'lambda2': SNR3
}, 'free', 3, 'MNE')
yield (set_inv, 'free-3-dSPM-0.2-pick_normal', {
'loose': 1,
'depth': 0.2
}, {
'method': 'dSPM',
'lambda2': SNR3,
'pick_ori': 'normal'
}, 'free', 3, 'dSPM', .2, True)
yield (set_inv, 'fixed-2-MNE-0.2', {
'fixed': True,
'depth': 0.2
}, {
'method': 'MNE',
'lambda2': SNR2
}, 'fixed', 2, 'MNE', .2)
yield (set_inv, 'fixed-2-MNE-pick_normal', {
'fixed': True,
'depth': 0.8
}, {
'method': 'MNE',
'lambda2': SNR2,
'pick_ori': 'normal'
}, 'fixed', 2, 'MNE', None, True)
yield (set_inv, 'loose.5-3-sLORETA', {
'loose': 0.5,
'depth': 0.8
}, {
'method': 'sLORETA',
'lambda2': SNR3
}, 0.5, 3, 'sLORETA')
yield (set_inv, 'fixed-1-MNE-0', {
'fixed': True,
'depth': None
}, {
'method': 'MNE',
'lambda2': SNR1
}, 'fixed', 1, 'MNE', 0)
# should remove this
yield (set_inv, 'fixed-1-MNE-0.8', {
'fixed': True,
'depth': 0.8
}, {
'method': 'MNE',
'lambda2': SNR1
}, 'fixed', 1, 'MNE', 0.8)
assert_raises(ValueError, e.set_inv, 'free', -3, 'dSPM')
assert_raises(ValueError, e.set, inv='free-3-mne')
assert_raises(ValueError, e.set, inv='free-3-MNE-2')
def test_select_epochs():
"Test Select-Epochs GUI Document"
set_log_level('warning', 'mne')
ds = datasets.get_mne_sample(sns=True)
tempdir = TempDir()
path = os.path.join(tempdir, 'rej.pickled')
# Test Document
# =============
# create a file
doc = Document(ds, 'meg')
doc.set_path(path)
doc.set_case(1, False, 'tag', None)
doc.set_case(2, None, None, ['2'])
doc.set_bad_channels([1])
# check modifications
eq_(doc.accept[1], False)
eq_(doc.tag[1], 'tag')
eq_(doc.interpolate[1], [])
eq_(doc.interpolate[2], ['2'])
eq_(doc.bad_channels, [1])
assert_array_equal(doc.accept[2:], True)
# save
doc.save()
# check the file
ds_ = load.unpickle(path)
eq_(doc.epochs.sensor._array_index(ds_.info['bad_channels']), [1])
# load the file
ds = datasets.get_mne_sample(sns=True)
doc = Document(ds, 'meg', path=path)
# modification checks
eq_(doc.accept[1], False)
eq_(doc.tag[1], 'tag')
eq_(doc.interpolate[1], [])
eq_(doc.interpolate[2], ['2'])
eq_(doc.bad_channels, [1])
assert_array_equal(doc.accept[2:], True)
# Test Model
# ==========
ds = datasets.get_mne_sample(sns=True)
doc = Document(ds, 'meg')
model = Model(doc)
# accept
model.set_case(0, False, None, None)
eq_(doc.accept[0], False)
model.history.undo()
eq_(doc.accept[0], True)
model.history.redo()
eq_(doc.accept[0], False)
# interpolate
model.toggle_interpolation(2, '3')
eq_(doc.interpolate[2], ['3'])
model.toggle_interpolation(2, '4')
eq_(doc.interpolate[2], ['3', '4'])
model.toggle_interpolation(2, '3')
eq_(doc.interpolate[2], ['4'])
model.toggle_interpolation(3, '3')
eq_(doc.interpolate[2], ['4'])
eq_(doc.interpolate[3], ['3'])
model.history.undo()
model.history.undo()
eq_(doc.interpolate[2], ['3', '4'])
eq_(doc.interpolate[3], [])
model.history.redo()
eq_(doc.interpolate[2], ['4'])
# bad channels
model.set_bad_channels([1])
model.set_bad_channels([1, 10])
eq_(doc.bad_channels, [1, 10])
model.history.undo()
eq_(doc.bad_channels, [1])
model.history.redo()
eq_(doc.bad_channels, [1, 10])
# reload to reset
model.load(path)
# tests
eq_(doc.accept[1], False)
eq_(doc.tag[1], 'tag')
eq_(doc.interpolate[1], [])
eq_(doc.interpolate[2], ['2'])
eq_(doc.bad_channels, [1])
assert_array_equal(doc.accept[2:], True)
# Test GUI
# ========
frame = gui.select_epochs(ds)
assert_false(frame.CanBackward())
ok_(frame.CanForward())
frame.OnForward(None)
def test_sample():
set_log_level('warning', 'mne')
# import from file: http://stackoverflow.com/a/67692/166700
SampleExperiment = import_attr(sample_path / 'sample_experiment.py', 'SampleExperiment')
tempdir = TempDir()
datasets.setup_samples_experiment(tempdir, 3, 2)
root = join(tempdir, 'SampleExperiment')
e = SampleExperiment(root)
eq_(e.get('subject'), 'R0000')
eq_(e.get('subject', subject='R0002'), 'R0002')
# events
e.set('R0001', rej='')
ds = e.load_selected_events(epoch='target')
assert ds.n_cases == 39
ds = e.load_selected_events(epoch='auditory')
assert ds.n_cases == 20
ds = e.load_selected_events(epoch='av')
assert ds.n_cases == 39
# evoked cache invalidated by change in bads
e.set('R0001', rej='', epoch='target')
ds = e.load_evoked()
eq_(ds[0, 'evoked'].info['bads'], [])
e.make_bad_channels(['MEG 0331'])
ds = e.load_evoked()
eq_(ds[0, 'evoked'].info['bads'], ['MEG 0331'])
e.set(rej='man', model='modality')
sds = []
for _ in e:
e.make_rej(auto=2.5e-12)
sds.append(e.load_evoked())
ds = e.load_evoked('all')
assert_dataobj_equal(combine(sds), ds)
# test with data parameter
megs = [e.load_evoked(cat='auditory')['meg'] for _ in e]
res = e.load_test('a>v', 0.05, 0.2, 0.05, samples=100, data='sensor.rms',
sns_baseline=False, make=True)
meg_rms = combine(meg.rms('sensor') for meg in megs).mean('case', name='auditory')
assert_dataobj_equal(res.c1_mean, meg_rms, decimal=21)
res = e.load_test('a>v', 0.05, 0.2, 0.05, samples=100, data='sensor.mean',
sns_baseline=False, make=True)
meg_mean = combine(meg.mean('sensor') for meg in megs).mean('case', name='auditory')
assert_dataobj_equal(res.c1_mean, meg_mean, decimal=21)
# e._report_subject_info() broke with non-alphabetic subject order
subjects = e.get_field_values('subject')
ds = Dataset()
ds['subject'] = Factor(reversed(subjects))
ds['n'] = Var(range(3))
s_table = e._report_subject_info(ds, '')
# test multiple epochs with same time stamp
class Experiment(SampleExperiment):
epochs = SampleExperiment.epochs.copy()
Experiment.epochs['v1'] = {'base': 'visual', 'vars': {'shift': 'Var([0.0], repeat=len(side))'}}
Experiment.epochs['v2'] = {'base': 'visual', 'vars': {'shift': 'Var([0.1], repeat=len(side))'}}
Experiment.epochs['vc'] = {'sub_epochs': ('v1', 'v2'), 'post_baseline_trigger_shift': 'shift', 'post_baseline_trigger_shift_max': 0.1, 'post_baseline_trigger_shift_min': 0.0}
e = Experiment(root)
ds = e.load_epochs(baseline=True, epoch='vc')
v1 = ds.sub("epoch=='v1'", 'meg').sub(time=(0, 0.199))
v2 = ds.sub("epoch=='v2'", 'meg').sub(time=(-0.1, 0.099))
assert_dataobj_equal(v1, v2, decimal=20)
# duplicate subject
class BadExperiment(SampleExperiment):
groups = {'group': ('R0001', 'R0002', 'R0002')}
assert_raises(DefinitionError, BadExperiment, root)
# non-existing subject
class BadExperiment(SampleExperiment):
groups = {'group': ('R0001', 'R0003', 'R0002')}
assert_raises(DefinitionError, BadExperiment, root)
# unsorted subjects
class Experiment(SampleExperiment):
groups = {'group': ('R0002', 'R0000', 'R0001')}
e = Experiment(root)
eq_([s for s in e], ['R0000', 'R0001', 'R0002'])
# changes
class Changed(SampleExperiment):
variables = {
'event': {(1, 2, 3, 4): 'target', 5: 'smiley', 32: 'button'},
'side': {(1, 3): 'left', (2, 4): 'right_changed'},
'modality': {(1, 2): 'auditory', (3, 4): 'visual'}
}
tests = {
'twostage': {
'kind': 'two-stage',
'stage 1': 'side_left + modality_a',
'vars': {
'side_left': "side == 'left'",
'modality_a': "modality == 'auditory'",
}
},
'novars': {
'kind': 'two-stage',
'stage 1': 'side + modality'
},
}
e = Changed(root)
# changed variable, while a test with model=None is not changed
class Changed(Changed):
variables = {
'side': {(1, 3): 'left', (2, 4): 'right_changed'},
'modality': {(1, 2): 'auditory', (3, 4): 'visual_changed'}
}
e = Changed(root)
# changed variable, unchanged test with vardef=None
class Changed(Changed):
variables = {
'side': {(1, 3): 'left', (2, 4): 'right_changed'},
'modality': {(1, 2): 'auditory', (3, 4): 'visual_changed'}
}
e = Changed(root)
# ICA
# ---
e = SampleExperiment(root)
ica_path = e.make_ica(raw='ica')
e.set(raw='ica1-40', model='')
e.make_rej(auto=2e-12, overwrite=True)
ds1 = e.load_evoked(raw='ica1-40')
ica = e.load_ica(raw='ica')
ica.exclude = [0, 1, 2]
ica.save(ica_path)
ds2 = e.load_evoked(raw='ica1-40')
assert not np.allclose(ds1['meg'].x, ds2['meg'].x, atol=1e-20), "ICA change ignored"