def test_apply_function_verbose():
"""Test apply function verbosity
"""
n_chan = 2
n_times = 3
ch_names = [str(ii) for ii in range(n_chan)]
raw = RawArray(np.zeros((n_chan, n_times)),
create_info(ch_names, 1., 'mag'))
# test return types in both code paths (parallel / 1 job)
assert_raises(TypeError, raw.apply_function, bad_1, None, None, 1)
assert_raises(ValueError, raw.apply_function, bad_2, None, None, 1)
assert_raises(TypeError, raw.apply_function, bad_1, None, None, 2)
assert_raises(ValueError, raw.apply_function, bad_2, None, None, 2)
# check our arguments
tempdir = _TempDir()
test_name = op.join(tempdir, 'test.log')
set_log_file(test_name)
try:
raw.apply_function(printer, None, None, 1, verbose=False)
with open(test_name) as fid:
assert_equal(len(fid.readlines()), 0)
raw.apply_function(printer, None, None, 1, verbose=True)
with open(test_name) as fid:
assert_equal(len(fid.readlines()), n_chan)
finally:
set_log_file(None)
def test_calculate_chpi_positions():
"""Test calculation of cHPI positions
"""
trans, rot, t = get_chpi_positions(pos_fname)
with warnings.catch_warnings(record=True):
raw = Raw(raw_fif_fname, allow_maxshield=True, preload=True)
t -= raw.first_samp / raw.info['sfreq']
trans_est, rot_est, t_est = _calculate_chpi_positions(raw, verbose='debug')
_compare_positions((trans, rot, t), (trans_est, rot_est, t_est))
# degenerate conditions
raw_no_chpi = Raw(test_fif_fname)
assert_raises(RuntimeError, _calculate_chpi_positions, raw_no_chpi)
raw_bad = raw.copy()
for d in raw_bad.info['dig']:
if d['kind'] == FIFF.FIFFV_POINT_HPI:
d['coord_frame'] = 999
break
assert_raises(RuntimeError, _calculate_chpi_positions, raw_bad)
raw_bad = raw.copy()
for d in raw_bad.info['dig']:
if d['kind'] == FIFF.FIFFV_POINT_HPI:
d['r'] = np.ones(3)
raw_bad.crop(0, 1., copy=False)
tempdir = _TempDir()
log_file = op.join(tempdir, 'temp_log.txt')
set_log_file(log_file, overwrite=True)
try:
_calculate_chpi_positions(raw_bad)
finally:
set_log_file()
with open(log_file, 'r') as fid:
for line in fid:
assert_true('0/5 acceptable' in line)
def test_ica_reject_buffer():
"""Test ICA data raw buffer rejection"""
tempdir = _TempDir()
raw = io.Raw(raw_fname, preload=True).crop(0, stop, False).crop(1.5)
picks = pick_types(raw.info,
meg=True,
stim=False,
ecg=False,
eog=False,
exclude='bads')
ica = ICA(n_components=3, max_pca_components=4, n_pca_components=4)
raw._data[2, 1000:1005] = 5e-12
drop_log = op.join(op.dirname(tempdir), 'ica_drop.log')
set_log_file(drop_log, overwrite=True)
with warnings.catch_warnings(record=True):
ica.fit(raw,
picks[:5],
reject=dict(mag=2.5e-12),
decim=2,
tstep=0.01,
verbose=True)
assert_true(raw._data[:5, ::2].shape[1] - 4 == ica.n_samples_)
with open(drop_log) as fid:
log = [l for l in fid if 'detected' in l]
assert_equal(len(log), 1)
def test_calculate_chpi_positions():
"""Test calculation of cHPI positions
"""
trans, rot, t = get_chpi_positions(pos_fname)
with warnings.catch_warnings(record=True):
raw = Raw(raw_fif_fname, allow_maxshield=True, preload=True)
t -= raw.first_samp / raw.info['sfreq']
trans_est, rot_est, t_est = _calculate_chpi_positions(raw, verbose='debug')
_compare_positions((trans, rot, t), (trans_est, rot_est, t_est))
# degenerate conditions
raw_no_chpi = Raw(test_fif_fname)
assert_raises(RuntimeError, _calculate_chpi_positions, raw_no_chpi)
raw_bad = raw.copy()
for d in raw_bad.info['dig']:
if d['kind'] == FIFF.FIFFV_POINT_HPI:
d['coord_frame'] = 999
break
assert_raises(RuntimeError, _calculate_chpi_positions, raw_bad)
raw_bad = raw.copy()
for d in raw_bad.info['dig']:
if d['kind'] == FIFF.FIFFV_POINT_HPI:
d['r'] = np.ones(3)
raw_bad.crop(0, 1., copy=False)
tempdir = _TempDir()
log_file = op.join(tempdir, 'temp_log.txt')
set_log_file(log_file, overwrite=True)
try:
_calculate_chpi_positions(raw_bad)
finally:
set_log_file()
with open(log_file, 'r') as fid:
for line in fid:
assert_true('0/5 acceptable' in line)
def test_apply_function_verbose():
"""Test apply function verbosity
"""
n_chan = 2
n_times = 3
ch_names = [str(ii) for ii in range(n_chan)]
raw = RawArray(np.zeros((n_chan, n_times)),
create_info(ch_names, 1., 'mag'))
# test return types in both code paths (parallel / 1 job)
assert_raises(TypeError, raw.apply_function, bad_1,
None, None, 1)
assert_raises(ValueError, raw.apply_function, bad_2,
None, None, 1)
assert_raises(TypeError, raw.apply_function, bad_1,
None, None, 2)
assert_raises(ValueError, raw.apply_function, bad_2,
None, None, 2)
# check our arguments
tempdir = _TempDir()
test_name = op.join(tempdir, 'test.log')
set_log_file(test_name)
try:
raw.apply_function(printer, None, None, 1, verbose=False)
with open(test_name) as fid:
assert_equal(len(fid.readlines()), 0)
raw.apply_function(printer, None, None, 1, verbose=True)
with open(test_name) as fid:
assert_equal(len(fid.readlines()), n_chan)
finally:
set_log_file(None)
def test_cache_dir():
"""Test use of cache dir
"""
tempdir = _TempDir()
orig_dir = os.getenv("MNE_CACHE_DIR", None)
orig_size = os.getenv("MNE_MEMMAP_MIN_SIZE", None)
rng = np.random.RandomState(0)
X = rng.randn(9, 2, 10)
log_file = op.join(tempdir, "log.txt")
try:
os.environ["MNE_MEMMAP_MIN_SIZE"] = "1K"
os.environ["MNE_CACHE_DIR"] = tempdir
# Fix error for #1507: in-place when memmapping
permutation_cluster_1samp_test(
X, buffer_size=None, n_jobs=2, n_permutations=1, seed=0, stat_fun=ttest_1samp_no_p, verbose=False
)
# ensure that non-independence yields warning
stat_fun = partial(ttest_1samp_no_p, sigma=1e-3)
set_log_file(log_file)
permutation_cluster_1samp_test(
X, buffer_size=10, n_jobs=2, n_permutations=1, seed=0, stat_fun=stat_fun, verbose=False
)
with open(log_file, "r") as fid:
assert_true("independently" in "".join(fid.readlines()))
finally:
if orig_dir is not None:
os.environ["MNE_CACHE_DIR"] = orig_dir
else:
del os.environ["MNE_CACHE_DIR"]
if orig_size is not None:
os.environ["MNE_MEMMAP_MIN_SIZE"] = orig_size
else:
del os.environ["MNE_MEMMAP_MIN_SIZE"]
set_log_file(None)
def test_ica_reject_buffer():
"""Test ICA data raw buffer rejection"""
raw = io.Raw(raw_fname, preload=True).crop(0, stop, False).crop(1.5)
picks = pick_types(raw.info, meg=True, stim=False, ecg=False,
eog=False, exclude='bads')
ica = ICA(n_components=3, max_pca_components=4, n_pca_components=4)
raw._data[2, 1000:1005] = 5e-12
drop_log = op.join(op.dirname(tempdir), 'ica_drop.log')
set_log_file(drop_log, overwrite=True)
ica.decompose_raw(raw, picks[:5], reject=dict(mag=2.5e-12), decim=2,
tstep=0.01, verbose=True)
assert_true(raw._data[:5, ::2].shape[1] - 4 == ica.n_samples_)
log = [l for l in open(drop_log) if 'detected' in l]
assert_equal(len(log), 1)
def test_ica_reject_buffer():
"""Test ICA data raw buffer rejection"""
tempdir = _TempDir()
raw = io.Raw(raw_fname).crop(1.5, stop, False)
raw.load_data()
picks = pick_types(raw.info, meg=True, stim=False, ecg=False, eog=False, exclude="bads")
ica = ICA(n_components=3, max_pca_components=4, n_pca_components=4)
raw._data[2, 1000:1005] = 5e-12
drop_log = op.join(op.dirname(tempdir), "ica_drop.log")
set_log_file(drop_log, overwrite=True)
with warnings.catch_warnings(record=True):
ica.fit(raw, picks[:5], reject=dict(mag=2.5e-12), decim=2, tstep=0.01, verbose=True)
assert_true(raw._data[:5, ::2].shape[1] - 4 == ica.n_samples_)
with open(drop_log) as fid:
log = [l for l in fid if "detected" in l]
assert_equal(len(log), 1)
def test_cache_dir():
"""Test use of cache dir
"""
tempdir = _TempDir()
orig_dir = os.getenv('MNE_CACHE_DIR', None)
orig_size = os.getenv('MNE_MEMMAP_MIN_SIZE', None)
rng = np.random.RandomState(0)
X = rng.randn(9, 2, 10)
log_file = op.join(tempdir, 'log.txt')
try:
os.environ['MNE_MEMMAP_MIN_SIZE'] = '1K'
os.environ['MNE_CACHE_DIR'] = tempdir
# Fix error for #1507: in-place when memmapping
permutation_cluster_1samp_test(X,
buffer_size=None,
n_jobs=2,
n_permutations=1,
seed=0,
stat_fun=ttest_1samp_no_p,
verbose=False)
# ensure that non-independence yields warning
stat_fun = partial(ttest_1samp_no_p, sigma=1e-3)
set_log_file(log_file)
permutation_cluster_1samp_test(X,
buffer_size=10,
n_jobs=2,
n_permutations=1,
seed=0,
stat_fun=stat_fun,
verbose=False)
with open(log_file, 'r') as fid:
assert_true('independently' in ''.join(fid.readlines()))
finally:
if orig_dir is not None:
os.environ['MNE_CACHE_DIR'] = orig_dir
else:
del os.environ['MNE_CACHE_DIR']
if orig_size is not None:
os.environ['MNE_MEMMAP_MIN_SIZE'] = orig_size
else:
del os.environ['MNE_MEMMAP_MIN_SIZE']
set_log_file(None)
def configure_logging(path):
"""Set format to file logging and add stdout logging
Log file messages will be: DATE - LEVEL - MESSAGE
"""
fname = op.join(op.dirname(path), 'eeg_cleaner.log')
set_log_file(fname, overwrite=False)
handlers = logger.handlers
file_output_format = '%(asctime)s %(levelname)s %(message)s'
date_format = '%d/%m/%Y %H:%M:%S'
output_format = '%(message)s'
for h in handlers:
if not isinstance(h, logging.FileHandler):
logger.removeHandler(h)
print('Removing handler {}'.format(h))
else:
h.setFormatter(
logging.Formatter(file_output_format, datefmt=date_format))
lh = logging.StreamHandler(WrapStdOut())
lh.setFormatter(logging.Formatter(output_format))
logger.addHandler(lh)
def setup_provenance(script,
results_dir,
config=None,
use_agg=True,
run_id=None):
"""Setup provenance tracking
Parameters
----------
script : str
The script that was executed.
results_dir : str
The results directory.
config : None | str
The name of the config file. By default, the function expects the
config to be under `__script__/' named `config.py`. It can also
be another kind of textfile, e.g. .json.
use_agg : bool
Whether to use the 'Agg' backend for matplotlib or not.
Returns
-------
report : mne.report.Report
The mne report.
Side-effects
------------
- make results dir if it does not exists
- sets log file for sterr output
- writes log file with runtime information
"""
if use_agg is True:
import matplotlib
matplotlib.use('Agg')
if not op.isfile(script):
raise ValueError('sorry, this is not a script!')
if not op.isdir(results_dir):
results_dir = op.join(op.dirname(op.dirname(script)), results_dir)
step = op.splitext(op.split(script)[1])[0]
if not op.isabs(results_dir):
results_dir = op.abspath(results_dir)
start_path = op.dirname(results_dir)
results_dir = op.join(results_dir, step)
if not op.exists(results_dir):
logger.info('generating results dir')
_forec_create_dir(results_dir, start=start_path)
if run_id is None:
run_id = create_run_id()
logger.info('generated run id: %s' % run_id)
else:
logger.info('using existing run id: %s' % run_id)
logger.info('preparing logging:')
logging_dir = op.join(results_dir, run_id)
if not op.exists(logging_dir):
logger.info('... making logging directory: %s' % logging_dir)
os.mkdir(logging_dir)
else:
logger.info('... using logging directory: %s' % logging_dir)
modules = get_versions(sys)
runtime_log = op.join(logging_dir, 'run_time.json')
with open(runtime_log, 'w') as fid:
json.dump(modules, fid)
logger.info('... writing runtime info to: %s' % runtime_log)
script_code = op.join(logging_dir, 'script.py')
if not op.isfile(script_code):
with open(script_code, 'w') as fid:
with open(script) as script_fid:
source_code = script_fid.read()
fid.write(source_code)
logger.info('... logging source code of calling script')
if config is None:
config = 'config.py'
if op.isabs(config):
config_fname = config
else:
config_fname = op.join(op.dirname(script), config)
config_code = op.join( # weird behavior of join if last arg is path
results_dir, run_id,
op.split(config_fname)[-1])
if not op.isfile(config_fname):
logger.info('... No config found. Logging nothing.')
elif op.isfile(config_code):
logger.info('... Config already written. I assume that you are using'
' the same run_id for different runs of your script.')
else:
with open(config_code, 'w') as fid:
with open(config_fname) as config_fid:
source_code = config_fid.read()
fid.write(source_code)
logger.info('... logging source code of "%s".' % config_fname)
logger.info('... preparing Report')
report = Report(title=step)
report.data_path = logging_dir
std_logfile = op.join(logging_dir, 'run_output.log')
logger.info('... setting logfile: %s' % std_logfile)
set_log_file(std_logfile)
return report, run_id, results_dir, logger
def test_logging():
"""Test logging (to file)
"""
with open(fname_log, 'r') as old_log_file:
old_lines = clean_lines(old_log_file.readlines())
with open(fname_log_2, 'r') as old_log_file_2:
old_lines_2 = clean_lines(old_log_file_2.readlines())
if op.isfile(test_name):
os.remove(test_name)
# test it one way (printing default off)
set_log_file(test_name)
set_log_level('WARNING')
# should NOT print
evoked = Evoked(fname_evoked, condition=1)
with open(test_name) as fid:
assert_true(fid.readlines() == [])
# should NOT print
evoked = Evoked(fname_evoked, condition=1, verbose=False)
with open(test_name) as fid:
assert_true(fid.readlines() == [])
# should NOT print
evoked = Evoked(fname_evoked, condition=1, verbose='WARNING')
with open(test_name) as fid:
assert_true(fid.readlines() == [])
# SHOULD print
evoked = Evoked(fname_evoked, condition=1, verbose=True)
with open(test_name, 'r') as new_log_file:
new_lines = clean_lines(new_log_file.readlines())
assert_equal(new_lines, old_lines)
set_log_file(None) # Need to do this to close the old file
os.remove(test_name)
# now go the other way (printing default on)
set_log_file(test_name)
set_log_level('INFO')
# should NOT print
evoked = Evoked(fname_evoked, condition=1, verbose='WARNING')
with open(test_name) as fid:
assert_true(fid.readlines() == [])
# should NOT print
evoked = Evoked(fname_evoked, condition=1, verbose=False)
with open(test_name) as fid:
assert_true(fid.readlines() == [])
# SHOULD print
evoked = Evoked(fname_evoked, condition=1)
with open(test_name, 'r') as new_log_file:
new_lines = clean_lines(new_log_file.readlines())
with open(fname_log, 'r') as old_log_file:
assert_equal(new_lines, old_lines)
# check to make sure appending works (and as default, raises a warning)
with warnings.catch_warnings(record=True) as w:
warnings.simplefilter('always')
set_log_file(test_name, overwrite=False)
assert len(w) == 0
set_log_file(test_name)
assert len(w) == 1
evoked = Evoked(fname_evoked, condition=1)
with open(test_name, 'r') as new_log_file:
new_lines = clean_lines(new_log_file.readlines())
assert_equal(new_lines, old_lines_2)
# make sure overwriting works
set_log_file(test_name, overwrite=True)
# this line needs to be called to actually do some logging
evoked = Evoked(fname_evoked, condition=1)
del evoked
with open(test_name, 'r') as new_log_file:
new_lines = clean_lines(new_log_file.readlines())
assert_equal(new_lines, old_lines)
#!/usr/bin/env python2.7 from mne import utils utils.set_log_file(fname = '/home/kjs/logs/mne.log', overwrite=False) utils.set_log_level(verbose = True) utils.logger.propagate = True LOGGER = utils.logger import numpy as np from scipy.stats import skew, kurtosis import pyeeg import file_handler import csv import time from mne.filter import high_pass_filter, band_stop_filter import random from decs import coroutine from mpi4py import MPI ''' The feature extractor creates a features.csv file The file is organized row by column, sample by features Names of features must be know before writing the file For electrode specific features, we use the max_e If a sample uses less electrodes that max_e, then it will have NA values for these electrodes In cases where a calculation is recycled in 2+ features, ex first order differential the calc is stroed in a by electrode dictionary
def test_logging():
"""Test logging (to file)."""
pytest.raises(ValueError, set_log_level, 'foo')
tempdir = _TempDir()
test_name = op.join(tempdir, 'test.log')
with open(fname_log, 'r') as old_log_file:
# [:-1] used to strip an extra "No baseline correction applied"
old_lines = clean_lines(old_log_file.readlines())
old_lines.pop(-1)
with open(fname_log_2, 'r') as old_log_file_2:
old_lines_2 = clean_lines(old_log_file_2.readlines())
old_lines_2.pop(14)
old_lines_2.pop(-1)
if op.isfile(test_name):
os.remove(test_name)
# test it one way (printing default off)
set_log_file(test_name)
set_log_level('WARNING')
# should NOT print
evoked = read_evokeds(fname_evoked, condition=1)
with open(test_name) as fid:
assert (fid.readlines() == [])
# should NOT print
evoked = read_evokeds(fname_evoked, condition=1, verbose=False)
with open(test_name) as fid:
assert (fid.readlines() == [])
# should NOT print
evoked = read_evokeds(fname_evoked, condition=1, verbose='WARNING')
with open(test_name) as fid:
assert (fid.readlines() == [])
# SHOULD print
evoked = read_evokeds(fname_evoked, condition=1, verbose=True)
with open(test_name, 'r') as new_log_file:
new_lines = clean_lines(new_log_file.readlines())
assert_equal(new_lines, old_lines)
set_log_file(None) # Need to do this to close the old file
os.remove(test_name)
# now go the other way (printing default on)
set_log_file(test_name)
set_log_level('INFO')
# should NOT print
evoked = read_evokeds(fname_evoked, condition=1, verbose='WARNING')
with open(test_name) as fid:
assert (fid.readlines() == [])
# should NOT print
evoked = read_evokeds(fname_evoked, condition=1, verbose=False)
with open(test_name) as fid:
assert (fid.readlines() == [])
# SHOULD print
evoked = read_evokeds(fname_evoked, condition=1)
with open(test_name, 'r') as new_log_file:
new_lines = clean_lines(new_log_file.readlines())
assert_equal(new_lines, old_lines)
# check to make sure appending works (and as default, raises a warning)
set_log_file(test_name, overwrite=False)
with pytest.warns(RuntimeWarning, match='appended to the file'):
set_log_file(test_name)
evoked = read_evokeds(fname_evoked, condition=1)
with open(test_name, 'r') as new_log_file:
new_lines = clean_lines(new_log_file.readlines())
assert_equal(new_lines, old_lines_2)
# make sure overwriting works
set_log_file(test_name, overwrite=True)
# this line needs to be called to actually do some logging
evoked = read_evokeds(fname_evoked, condition=1)
del evoked
with open(test_name, 'r') as new_log_file:
new_lines = clean_lines(new_log_file.readlines())
assert_equal(new_lines, old_lines)
def setup_provenance(script, results_dir, config=None, use_agg=True,
run_id=None):
"""Setup provenance tracking
Parameters
----------
script : str
The script that was executed.
results_dir : str
The results directory.
config : None | str
The name of the config file. By default, the function expects the
config to be under `__script__/' named `config.py`. It can also
be another kind of textfile, e.g. .json.
use_agg : bool
Whether to use the 'Agg' backend for matplotlib or not.
Returns
-------
report : mne.report.Report
The mne report.
Side-effects
------------
- make results dir if it does not exists
- sets log file for sterr output
- writes log file with runtime information
"""
if use_agg is True:
import matplotlib
matplotlib.use('Agg')
if not callable(script):
if not op.isfile(script):
raise ValueError('sorry, this is not a script!')
if not op.isdir(results_dir) and not callable(script):
results_dir = op.join(op.dirname(op.dirname(script)), results_dir)
else:
results_dir = op.join(op.curdir, results_dir)
if not callable(script):
step = op.splitext(op.split(script)[1])[0]
else:
step = script.__name__
if not op.isabs(results_dir):
results_dir = op.abspath(results_dir)
start_path = op.dirname(results_dir)
results_dir = op.join(results_dir, step)
if not op.exists(results_dir):
logger.info('generating results dir')
_forec_create_dir(results_dir, start=start_path)
if run_id is None:
run_id = create_run_id()
logger.info('generated run id: %s' % run_id)
else:
logger.info('using existing run id: %s' % run_id)
logger.info('preparing logging:')
logging_dir = op.join(results_dir, run_id)
if not op.exists(logging_dir):
logger.info('... making logging directory: %s' % logging_dir)
os.mkdir(logging_dir)
else:
logger.info('... using logging directory: %s' % logging_dir)
modules = get_versions(sys)
runtime_log = op.join(logging_dir, 'run_time.json')
with open(runtime_log, 'w') as fid:
json.dump(modules, fid)
logger.info('... writing runtime info to: %s' % runtime_log)
script_code_out = op.join(logging_dir, 'script.py')
if callable(script):
script_code_in = inspect.getsourcefile(script)
else:
script_code_in = script
if not op.isfile(script_code_out):
with open(script_code_out, 'w') as fid:
with open(script_code_in) as script_fid:
source_code = script_fid.read()
fid.write(source_code)
logger.info('... logging source code of calling script')
if config is None:
config = 'config.py'
if op.isabs(config):
config_fname = config
else:
config_fname = ''
config_code = op.join( # weird behavior of join if last arg is path
results_dir, run_id, op.split(config_fname)[-1])
if not op.isfile(config_fname):
logger.info('... No config found. Logging nothing.')
elif op.isfile(config_code):
logger.info('... Config already written. I assume that you are using'
' the same run_id for different runs of your script.')
else:
with open(config_code, 'w') as fid:
with open(config_fname) as config_fid:
source_code = config_fid.read()
fid.write(source_code)
logger.info('... logging source code of "%s".' % config_fname)
logger.info('... preparing Report')
report = Report(title=step)
report.data_path = logging_dir
std_logfile = op.join(logging_dir, 'run_output.log')
logger.info('... setting logfile: %s' % std_logfile)
set_log_file(std_logfile)
return report, run_id, results_dir, logger
def test_logging():
"""Test logging (to file)."""
assert_raises(ValueError, set_log_level, 'foo')
tempdir = _TempDir()
test_name = op.join(tempdir, 'test.log')
with open(fname_log, 'r') as old_log_file:
# [:-1] used to strip an extra "No baseline correction applied"
old_lines = clean_lines(old_log_file.readlines())
old_lines.pop(-1)
with open(fname_log_2, 'r') as old_log_file_2:
old_lines_2 = clean_lines(old_log_file_2.readlines())
old_lines_2.pop(14)
old_lines_2.pop(-1)
if op.isfile(test_name):
os.remove(test_name)
# test it one way (printing default off)
set_log_file(test_name)
set_log_level('WARNING')
# should NOT print
evoked = read_evokeds(fname_evoked, condition=1)
with open(test_name) as fid:
assert_true(fid.readlines() == [])
# should NOT print
evoked = read_evokeds(fname_evoked, condition=1, verbose=False)
with open(test_name) as fid:
assert_true(fid.readlines() == [])
# should NOT print
evoked = read_evokeds(fname_evoked, condition=1, verbose='WARNING')
with open(test_name) as fid:
assert_true(fid.readlines() == [])
# SHOULD print
evoked = read_evokeds(fname_evoked, condition=1, verbose=True)
with open(test_name, 'r') as new_log_file:
new_lines = clean_lines(new_log_file.readlines())
assert_equal(new_lines, old_lines)
set_log_file(None) # Need to do this to close the old file
os.remove(test_name)
# now go the other way (printing default on)
set_log_file(test_name)
set_log_level('INFO')
# should NOT print
evoked = read_evokeds(fname_evoked, condition=1, verbose='WARNING')
with open(test_name) as fid:
assert_true(fid.readlines() == [])
# should NOT print
evoked = read_evokeds(fname_evoked, condition=1, verbose=False)
with open(test_name) as fid:
assert_true(fid.readlines() == [])
# SHOULD print
evoked = read_evokeds(fname_evoked, condition=1)
with open(test_name, 'r') as new_log_file:
new_lines = clean_lines(new_log_file.readlines())
assert_equal(new_lines, old_lines)
# check to make sure appending works (and as default, raises a warning)
with warnings.catch_warnings(record=True) as w:
warnings.simplefilter('always')
set_log_file(test_name, overwrite=False)
assert_equal(len(w), 0)
set_log_file(test_name)
assert_equal(len(w), 1)
assert_true('test_utils.py' in w[0].filename)
evoked = read_evokeds(fname_evoked, condition=1)
with open(test_name, 'r') as new_log_file:
new_lines = clean_lines(new_log_file.readlines())
assert_equal(new_lines, old_lines_2)
# make sure overwriting works
set_log_file(test_name, overwrite=True)
# this line needs to be called to actually do some logging
evoked = read_evokeds(fname_evoked, condition=1)
del evoked
with open(test_name, 'r') as new_log_file:
new_lines = clean_lines(new_log_file.readlines())
assert_equal(new_lines, old_lines)
def test_logging():
"""Test logging (to file)
"""
assert_raises(ValueError, set_log_level, 'foo')
tempdir = _TempDir()
test_name = op.join(tempdir, 'test.log')
with open(fname_log, 'r') as old_log_file:
old_lines = clean_lines(old_log_file.readlines())
with open(fname_log_2, 'r') as old_log_file_2:
old_lines_2 = clean_lines(old_log_file_2.readlines())
# we changed our logging a little bit
old_lines = [o.replace('No baseline correction applied...',
'No baseline correction applied')
for o in old_lines]
old_lines_2 = [o.replace('No baseline correction applied...',
'No baseline correction applied')
for o in old_lines_2]
if op.isfile(test_name):
os.remove(test_name)
# test it one way (printing default off)
set_log_file(test_name)
set_log_level('WARNING')
# should NOT print
evoked = read_evokeds(fname_evoked, condition=1)
with open(test_name) as fid:
assert_true(fid.readlines() == [])
# should NOT print
evoked = read_evokeds(fname_evoked, condition=1, verbose=False)
with open(test_name) as fid:
assert_true(fid.readlines() == [])
# should NOT print
evoked = read_evokeds(fname_evoked, condition=1, verbose='WARNING')
with open(test_name) as fid:
assert_true(fid.readlines() == [])
# SHOULD print
evoked = read_evokeds(fname_evoked, condition=1, verbose=True)
with open(test_name, 'r') as new_log_file:
new_lines = clean_lines(new_log_file.readlines())
assert_equal(new_lines, old_lines)
set_log_file(None) # Need to do this to close the old file
os.remove(test_name)
# now go the other way (printing default on)
set_log_file(test_name)
set_log_level('INFO')
# should NOT print
evoked = read_evokeds(fname_evoked, condition=1, verbose='WARNING')
with open(test_name) as fid:
assert_true(fid.readlines() == [])
# should NOT print
evoked = read_evokeds(fname_evoked, condition=1, verbose=False)
with open(test_name) as fid:
assert_true(fid.readlines() == [])
# SHOULD print
evoked = read_evokeds(fname_evoked, condition=1)
with open(test_name, 'r') as new_log_file:
new_lines = clean_lines(new_log_file.readlines())
with open(fname_log, 'r') as old_log_file:
assert_equal(new_lines, old_lines)
# check to make sure appending works (and as default, raises a warning)
with warnings.catch_warnings(record=True) as w:
warnings.simplefilter('always')
set_log_file(test_name, overwrite=False)
assert_equal(len(w), 0)
set_log_file(test_name)
assert_equal(len(w), 1)
assert_true('test_utils.py' in w[0].filename)
evoked = read_evokeds(fname_evoked, condition=1)
with open(test_name, 'r') as new_log_file:
new_lines = clean_lines(new_log_file.readlines())
assert_equal(new_lines, old_lines_2)
# make sure overwriting works
set_log_file(test_name, overwrite=True)
# this line needs to be called to actually do some logging
evoked = read_evokeds(fname_evoked, condition=1)
del evoked
with open(test_name, 'r') as new_log_file:
new_lines = clean_lines(new_log_file.readlines())
assert_equal(new_lines, old_lines)
def test_logging():
"""Test logging (to file)
"""
with open(fname_log, 'r') as old_log_file:
old_lines = clean_lines(old_log_file.readlines())
with open(fname_log_2, 'r') as old_log_file_2:
old_lines_2 = clean_lines(old_log_file_2.readlines())
if op.isfile(test_name):
os.remove(test_name)
# test it one way (printing default off)
set_log_file(test_name)
set_log_level('WARNING')
# should NOT print
evoked = Evoked(fname_evoked, condition=1)
with open(test_name) as fid:
assert_true(fid.readlines() == [])
# should NOT print
evoked = Evoked(fname_evoked, condition=1, verbose=False)
with open(test_name) as fid:
assert_true(fid.readlines() == [])
# should NOT print
evoked = Evoked(fname_evoked, condition=1, verbose='WARNING')
with open(test_name) as fid:
assert_true(fid.readlines() == [])
# SHOULD print
evoked = Evoked(fname_evoked, condition=1, verbose=True)
with open(test_name, 'r') as new_log_file:
new_lines = clean_lines(new_log_file.readlines())
assert_equal(new_lines, old_lines)
set_log_file(None) # Need to do this to close the old file
os.remove(test_name)
# now go the other way (printing default on)
set_log_file(test_name)
set_log_level('INFO')
# should NOT print
evoked = Evoked(fname_evoked, condition=1, verbose='WARNING')
with open(test_name) as fid:
assert_true(fid.readlines() == [])
# should NOT print
evoked = Evoked(fname_evoked, condition=1, verbose=False)
with open(test_name) as fid:
assert_true(fid.readlines() == [])
# SHOULD print
evoked = Evoked(fname_evoked, condition=1)
with open(test_name, 'r') as new_log_file:
new_lines = clean_lines(new_log_file.readlines())
with open(fname_log, 'r') as old_log_file:
assert_equal(new_lines, old_lines)
# check to make sure appending works (and as default, raises a warning)
with warnings.catch_warnings(record=True) as w:
warnings.simplefilter('always')
set_log_file(test_name, overwrite=False)
assert len(w) == 0
set_log_file(test_name)
assert len(w) == 1
evoked = Evoked(fname_evoked, condition=1)
with open(test_name, 'r') as new_log_file:
new_lines = clean_lines(new_log_file.readlines())
assert_equal(new_lines, old_lines_2)
# make sure overwriting works
set_log_file(test_name, overwrite=True)
# this line needs to be called to actually do some logging
evoked = Evoked(fname_evoked, condition=1)
del evoked
with open(test_name, 'r') as new_log_file:
new_lines = clean_lines(new_log_file.readlines())
assert_equal(new_lines, old_lines)
def setup_provenance(script, results_dir, use_agg=True):
"""Setup provenance tracking
Parameters
----------
script : str
The script that was executed.
results_dir : str
The results directory.
use_agg : bool
Whether to use the 'Agg' backend for matplotlib or not.
Returns
-------
report : mne.report.Report
The mne report.
Side-effects
------------
- make results dir if it does not exists
- sets log file for sterr output
- writes log file with runtime information
"""
if use_agg is True:
import matplotlib
matplotlib.use('Agg')
if not op.isfile(script):
raise ValueError('sorry, this is not a script!')
step = op.splitext(op.split(script)[1])[0]
results_dir = op.join(results_dir, step)
if not op.exists(results_dir):
logger.info('generating results dir')
os.mkdir(results_dir)
run_id = create_run_id()
logger.info('generated run id: %s' % run_id)
logger.info('preparing logging:')
logging_dir = op.join(results_dir, run_id)
logger.info('... making logging directory: %s' % logging_dir)
os.mkdir(logging_dir)
modules = get_versions(sys)
runtime_log = op.join(logging_dir, 'run_time.json')
with open(runtime_log, 'w') as fid:
json.dump(modules, fid)
logger.info('... writing runtime info to: %s' % runtime_log)
std_logfile = op.join(logging_dir, 'run_output.log')
script_code = op.join(logging_dir, 'script.py')
with open(script_code, 'w') as fid:
with open(script) as script_fid:
source_code = script_fid.read()
fid.write(source_code)
logger.info('... logging source code')
logger.info('... preparing Report')
report = Report(title=step)
report.data_path = logging_dir
logger.info('... setting logfile: %s' % std_logfile)
set_log_file(std_logfile)
return report, run_id, results_dir, logger
def test_logging(tmpdir):
"""Test logging (to file)."""
pytest.raises(ValueError, set_log_level, 'foo')
tempdir = str(tmpdir)
test_name = op.join(tempdir, 'test.log')
with open(fname_log, 'r') as old_log_file:
# [:-1] used to strip an extra "No baseline correction applied"
old_lines = clean_lines(old_log_file.readlines())
old_lines.pop(-1)
with open(fname_log_2, 'r') as old_log_file_2:
old_lines_2 = clean_lines(old_log_file_2.readlines())
old_lines_2.pop(14)
old_lines_2.pop(-1)
if op.isfile(test_name):
os.remove(test_name)
# test it one way (printing default off)
set_log_file(test_name)
set_log_level('WARNING')
# should NOT print
evoked = read_evokeds(fname_evoked, condition=1)
with open(test_name) as fid:
assert (fid.readlines() == [])
# should NOT print
evoked = read_evokeds(fname_evoked, condition=1, verbose=False)
with open(test_name) as fid:
assert (fid.readlines() == [])
# should NOT print
evoked = read_evokeds(fname_evoked, condition=1, verbose='WARNING')
with open(test_name) as fid:
assert (fid.readlines() == [])
# SHOULD print
evoked = read_evokeds(fname_evoked, condition=1, verbose=True)
with open(test_name, 'r') as new_log_file:
new_lines = clean_lines(new_log_file.readlines())
assert new_lines == old_lines
set_log_file(None) # Need to do this to close the old file
os.remove(test_name)
# now go the other way (printing default on)
set_log_file(test_name)
set_log_level('INFO')
# should NOT print
evoked = read_evokeds(fname_evoked, condition=1, verbose='WARNING')
with open(test_name) as fid:
assert (fid.readlines() == [])
# should NOT print
evoked = read_evokeds(fname_evoked, condition=1, verbose=False)
with open(test_name) as fid:
assert (fid.readlines() == [])
# SHOULD print
evoked = read_evokeds(fname_evoked, condition=1)
with open(test_name, 'r') as new_log_file:
new_lines = clean_lines(new_log_file.readlines())
assert new_lines == old_lines
# check to make sure appending works (and as default, raises a warning)
set_log_file(test_name, overwrite=False)
with pytest.warns(RuntimeWarning, match='appended to the file'):
set_log_file(test_name)
evoked = read_evokeds(fname_evoked, condition=1)
with open(test_name, 'r') as new_log_file:
new_lines = clean_lines(new_log_file.readlines())
assert new_lines == old_lines_2
# make sure overwriting works
set_log_file(test_name, overwrite=True)
# this line needs to be called to actually do some logging
evoked = read_evokeds(fname_evoked, condition=1)
del evoked
with open(test_name, 'r') as new_log_file:
new_lines = clean_lines(new_log_file.readlines())
assert new_lines == old_lines
