def test_setup_provenance():
"""Test provenance tracking"""
tmp_dir = _TempDir()
report, run_id, results_dir, logger = setup_provenance(script=__file__,
results_dir=tmp_dir)
logging_dir = op.join(results_dir, run_id)
assert_true(op.isdir(logging_dir))
assert_true(op.isfile(op.join(logging_dir, 'run_time.json')))
assert_true(op.isfile(op.join(logging_dir, 'run_output.log')))
assert_true(op.isfile(op.join(logging_dir, 'script.py')))
with open(__file__) as fid:
this_file_code = fid.read()
with open(op.join(results_dir, run_id, 'script.py')) as fid:
other_file_code = fid.read()
assert_equals(this_file_code, other_file_code)
with open(op.join(results_dir, run_id, 'run_time.json')) as fid:
modules = json.load(fid)
assert_true('meeg_preprocessing' in modules)
assert_equals(report.title, op.splitext(op.split(__file__)[1])[0])
assert_equals(report.data_path, logging_dir)
def test_setup_provenance():
"""Test provenance tracking"""
for config_opt in ['abs_py', 'default', 'other']:
tmp_dir = _TempDir()
if config_opt == 'default':
config_fname = op.join(op.dirname(__file__), 'config.py')
config_content = 'import this'
config_param = None
elif config_opt == 'abs_py':
config_fname = op.join(tmp_dir, 'config.py')
config_content = 'import antigravity'
config_param = config_fname
elif config_opt == 'other':
config_fname = op.join(tmp_dir, 'config.txt')
config_content = 'my_config :: 42'
config_param = config_fname
with open(config_fname, 'w') as fid_config:
fid_config.write(config_content)
report, run_id, results_dir, logger = setup_provenance(
script=__file__, results_dir=tmp_dir, config=config_param)
logging_dir = op.join(results_dir, run_id)
assert_true(op.isdir(logging_dir))
assert_true(op.isfile(op.join(logging_dir, 'run_time.json')))
assert_true(op.isfile(op.join(logging_dir, 'run_output.log')))
assert_true(op.isfile(op.join(logging_dir, 'script.py')))
config_basename = op.split(config_fname)[-1]
with open(op.join(results_dir, run_id, config_basename)) as config_fid:
config_code = config_fid.read()
assert_equal(config_code, config_content)
with open(__file__) as fid:
this_file_code = fid.read()
with open(op.join(results_dir, run_id, 'script.py')) as fid:
other_file_code = fid.read()
assert_equals(this_file_code, other_file_code)
with open(op.join(results_dir, run_id, 'run_time.json')) as fid:
modules = json.load(fid)
assert_true('meeg_preprocessing' in modules)
assert_equals(report.title, op.splitext(op.split(__file__)[1])[0])
assert_equals(report.data_path, logging_dir)
if config_opt == 'default':
os.remove(config_fname)
def test_setup_provenance():
"""Test provenance tracking"""
for config_opt in ['abs_py', 'default', 'other']:
tmp_dir = _TempDir()
if config_opt == 'default':
config_fname = op.join(op.dirname(__file__), 'config.py')
config_content = 'import this'
config_param = None
elif config_opt == 'abs_py':
config_fname = op.join(tmp_dir, 'config.py')
config_content = 'import antigravity'
config_param = config_fname
elif config_opt == 'other':
config_fname = op.join(tmp_dir, 'config.txt')
config_content = 'my_config :: 42'
config_param = config_fname
with open(config_fname, 'w') as fid_config:
fid_config.write(config_content)
report, run_id, results_dir, logger = setup_provenance(
script=__file__, results_dir=tmp_dir, config=config_param)
logging_dir = op.join(results_dir, run_id)
assert_true(op.isdir(logging_dir))
assert_true(op.isfile(op.join(logging_dir, 'run_time.json')))
assert_true(op.isfile(op.join(logging_dir, 'run_output.log')))
assert_true(op.isfile(op.join(logging_dir, 'script.py')))
config_basename = op.split(config_fname)[-1]
with open(op.join(results_dir, run_id, config_basename)) as config_fid:
config_code = config_fid.read()
assert_equal(config_code, config_content)
with open(__file__) as fid:
this_file_code = fid.read()
with open(op.join(results_dir, run_id, 'script.py')) as fid:
other_file_code = fid.read()
assert_equals(this_file_code, other_file_code)
with open(op.join(results_dir, run_id, 'run_time.json')) as fid:
modules = json.load(fid)
assert_true('meeg_preprocessing' in modules)
assert_equals(report.title, op.splitext(op.split(__file__)[1])[0])
assert_equals(report.data_path, logging_dir)
if config_opt == 'default':
os.remove(config_fname)
def _setup_provenance(self):
import os
from meeg_preprocessing.utils import setup_provenance
if not os.path.isdir(self.results_dir):
os.mkdir(self.results_dir)
# Read script
with open(self.script, 'rb') as f:
self.pyscript = f.read()
# Setup display environment
if self.use_agg is None:
self.use_agg = os.getenv('use_agg')
if self.use_agg:
self.use_agg = True
# Create report
self.report, self.run_id, self.results_dir, self.logger = \
setup_provenance(self.script, self.results_dir,
use_agg=self.use_agg)
def _setup_provenance(self):
import os
from meeg_preprocessing.utils import setup_provenance
if not os.path.isdir(self.results_dir):
os.mkdir(self.results_dir)
# Read script
with open(self.script, 'rb') as f:
self.pyscript = f.read()
# Setup display environment
if self.use_agg is None:
self.use_agg = os.getenv('use_agg')
if self.use_agg:
self.use_agg = True
# Create report
self.report, self.run_id, self.results_dir, self.logger = \
setup_provenance(self.script, self.results_dir,
use_agg=self.use_agg)
from toolbox.utils import find_in_df, build_contrast, save_to_dict
from utils import get_data
from config import (
data_path,
pyoutput_path,
subjects,
paths('report'),
contrasts,
open_browser,
chan_types,
)
report, run_id, _, logger = setup_provenance(script=__file__,
results_dir=paths('report'))
mne.set_log_level('INFO')
# force separation of magnetometers and gradiometers
if 'meg' in [i['name'] for i in chan_types]:
chan_types = [dict(name='mag'), dict(name='grad')] + \
[dict(name=i['name']) for i in chan_types
if i['name'] != 'meg']
for subject in subjects:
# Extract events from mat file
meg_fname = op.join(data_path, subject, 'preprocessed', subject + '_preprocessed')
bhv_fname = op.join(data_path, subject, 'behavior', subject + '_fixed.mat')
epochs, events = get_data(meg_fname, bhv_fname)
# Author: Denis A. Engemann <*****@*****.**>
# License: BSD (3-clause)
import os.path as op
from meeg_preprocessing import check_apply_filter
from meeg_preprocessing.utils import setup_provenance
from mne import io
from config import (
subject,
fname,
filter_params,
notch_filter_params,
plot_fmin,
plot_fmax,
n_jobs,
)
report, run_id, results_dir, logger = setup_provenance(
script=__file__, results_dir='results')
raw = io.Raw(fname, preload=True)
fig, report = check_apply_filter(
raw, subject=subject, filter_params=filter_params,
notch_filter_params=notch_filter_params,
plot_fmin=plot_fmin, plot_fmax=plot_fmax,
n_jobs=n_jobs)
report.save(op.join(results_dir, run_id, 'report.html'))