def main():
# Generate a json.product to display messages on Brainlife UI
dict_json_product = {'brainlife': []}
# Load inputs from config.json
with open('config.json') as config_json:
config = json.load(config_json)
# Read all raw files and store them in a list
list_raw = []
for data_file in config["fif_runs"]:
raw = mne.io.read_raw_fif(data_file, allow_maxshield=True)
list_raw.append(raw)
# Test if at least two runs are given
if len(list_raw) < 2:
value_error_message = f'Only one run was given. This App needs at least two runs to compute ' \
f'the mean transformation matrix.'
raise ValueError(value_error_message)
# Read and save optional files
helper.read_optional_files(config, 'out_dir')
# Compute mean transformation matrix
mean_transformation_matrix(list_raw)
# Success message in product.json
dict_json_product['brainlife'].append({
'type':
'success',
'msg':
'Mean transformation matrix was computed successfully.'
})
# Save the dict_json_product in a json file
with open('product.json', 'w') as outfile:
json.dump(dict_json_product, outfile)
def main():
# Generate a json.product to display messages on Brainlife UI
dict_json_product = {'brainlife': []}
# Load inputs from config.json
with open('config.json') as config_json:
config = json.load(config_json)
# Read the files
data_file = config.pop('fif')
raw = mne.io.read_raw_fif(data_file, allow_maxshield=True)
# Convert empty strings values to None
config = helper.convert_parameters_to_None(config)
# Check if param_extended_proj parameter is empty
if config['param_extended_proj'] == '[]':
config['param_extended_proj'] = []
# Read and save optional files
config, cross_talk_file, calibration_file, events_file, head_pos_file, channels_file, destination = helper.read_optional_files(
config, 'out_dir_maxwell_filter')
# Raise a value error if the user provides both the destination file and the destination parameter
if config['param_destination'] is not None and destination is not None:
value_error_message = f"You can't provide both a destination file and a " \
f"destination parameter. One of them must be None."
raise ValueError(value_error_message)
# Channels.tsv must be BIDS compliant
if channels_file is not None:
user_warning_message_channels = f'The channels file provided must be ' \
f'BIDS compliant and the column "status" must be present. '
warnings.warn(user_warning_message_channels)
dict_json_product['brainlife'].append({
'type':
'warning',
'msg':
user_warning_message_channels
})
# Update raw.info['bads'] with info contained in channels.tsv
raw, user_warning_message_channels = helper.update_data_info_bads(
raw, channels_file)
if user_warning_message_channels is not None:
warnings.warn(user_warning_message_channels)
dict_json_product['brainlife'].append({
'type':
'warning',
'msg':
user_warning_message_channels
})
## Convert parameters ##
# Deal with param_origin parameter #
# Convert origin parameter into array when the app is run locally
if isinstance(config['param_origin'], list):
config['param_origin'] = np.array(config['param_origin'])
# Convert origin parameter into array when the app is run on BL
if isinstance(config['param_origin'],
str) and config['param_origin'] != "auto":
param_origin = list(map(float, config['param_origin'].split(', ')))
config['param_origin'] = np.array(param_origin)
# Raise an error if param origin is not an array of shape 3
if config['param_origin'] != "auto" and config['param_origin'].shape[
0] != 3:
value_error_message = f"Origin parameter must contain three elements."
raise ValueError(value_error_message)
# Deal with param_destination parameter #
if config['param_destination'] is not None:
destination = config['param_destination']
report_param_destination = destination
# Convert destination parameter into array when the app is run locally
if isinstance(destination, list):
destination = np.array(destination)
# Convert destination parameter into array when the app is run on BL
if isinstance(destination, str):
report_param_destination = destination
destination = list(map(float, destination.split(', ')))
destination = np.array(destination)
# Raise an error if param destination is not an array of shape 3
if isinstance(destination, np.ndarray) and destination.shape[0] != 3:
value_error_message = f"Destination parameter must contain three elements."
raise ValueError(value_error_message)
else:
report_param_destination = None
# Deal with param_mag_scale parameter #
# Convert param_mag_scale parameter into float when the app is run on BL
if isinstance(config['param_mag_scale'],
str) and config['param_mag_scale'] != "auto":
config['param_mag_scale'] = float(config['param_mag_scale'])
# Deal with skip_by_annotation parameter #
# Convert param_mag_scale into a list of strings when the app runs on BL
skip_by_an = config['param_skip_by_annotation']
if skip_by_an == "[]":
skip_by_an = []
elif isinstance(skip_by_an,
str) and skip_by_an.find("[") != -1 and skip_by_an != "[]":
skip_by_an = skip_by_an.replace('[', '')
skip_by_an = skip_by_an.replace(']', '')
skip_by_an = list(map(str, skip_by_an.split(', ')))
config['param_skip_by_annotation'] = skip_by_an
# Display a warning if bad channels are empty
if not raw.info['bads']:
user_warning_message = f'No channels are marked as bad. ' \
f'Make sure to check (automatically or visually) for bad channels before ' \
f'applying Maxwell Filtering.'
warnings.warn(user_warning_message)
dict_json_product['brainlife'].append({
'type': 'warning',
'msg': user_warning_message
})
## Define kwargs ##
# Delete keys values in config.json when this app is executed on Brainlife
config = helper.define_kwargs(config)
# Delete the param_destination key
del config['param_destination']
# Define kwargs
kwargs = config
# Keep bad channels in memory
bad_channels = raw.info['bads']
# Apply Maxwell Filter
raw_maxwell_filter = apply_maxwell_filter(raw, calibration_file,
cross_talk_file, head_pos_file,
destination, **kwargs)
# Update channels.tsv if it exists because bad channels were interpolated
if channels_file is not None:
df_channels = pd.read_csv(channels_file, sep='\t')
for bad in bad_channels:
index_bad_channel = df_channels[df_channels['name'] == bad].index
df_channels.loc[index_bad_channel, 'status'] = 'good'
# Save channels.tsv
df_channels.to_csv('out_dir_maxwell_filter/channels.tsv',
sep='\t',
index=False)
# Write a success message in product.json
dict_json_product['brainlife'].append({
'type':
'success',
'msg':
'Maxwell Filter was applied successfully.'
})
# Compute SNR on magnetometers
# snr_before_mag = _compute_snr(raw, meg_channels_type='mag')
# snr_after_mag = _compute_snr(raw_maxfilter, meg_channels_type='mag')
# Compute SNR on gradiometers
# snr_before_mag = _compute_snr(raw, meg_channels_type='grad')
# snr_after_mag = _compute_snr(raw_maxfilter, meg_channels_type='grad')
## Generate html report ##
# Get messages to add to the html report
report_calibration_file, report_cross_talk_file, report_head_pos_file, report_destination_file = helper.message_optional_files_in_reports(
calibration_file, cross_talk_file, head_pos_file, destination)
# Generate report
_generate_report(data_file, raw, raw_maxwell_filter, bad_channels,
report_cross_talk_file, report_calibration_file,
report_head_pos_file, report_destination_file,
report_param_destination, **kwargs)
# Save the dict_json_product in a json file
with open('product.json', 'w') as outfile:
json.dump(dict_json_product, outfile)
def main():
# Generate a json.product to display messages on Brainlife UI
dict_json_product = {'brainlife': []}
# Load inputs from config.json
with open('config.json') as config_json:
config = json.load(config_json)
# Read the raw file
data_file = config.pop('fif')
raw = mne.io.read_raw_fif(data_file, allow_maxshield=True)
# Read and save optional files
config, cross_talk_file, calibration_file, events_file, head_pos_file, channels_file, destination = helper.read_optional_files(config, 'out_dir_bad_channels')
# Convert empty strings values to None
config = helper.convert_parameters_to_None(config)
# Channels.tsv must be BIDS compliant
if channels_file is not None:
user_warning_message_channels = f'The channels file provided must be ' \
f'BIDS compliant and the column "status" must be present. '
warnings.warn(user_warning_message_channels)
dict_json_product['brainlife'].append({'type': 'warning', 'msg': user_warning_message_channels})
# Udpate raw.info['bads'] with info contained in channels.tsv
raw, user_warning_message_channels = helper.update_data_info_bads(raw, channels_file)
if user_warning_message_channels is not None:
warnings.warn(user_warning_message_channels)
dict_json_product['brainlife'].append({'type': 'warning', 'msg': user_warning_message_channels})
else:
# Create a BIDSPath
bids_path = BIDSPath(subject='subject',
session=None,
task='task',
run='01',
acquisition=None,
processing=None,
recording=None,
space=None,
suffix=None,
datatype='meg',
root='bids')
# Write BIDS to create channels.tsv BIDS compliant
write_raw_bids(raw, bids_path, overwrite=True)
# Extract channels.tsv from bids path
channels_file = 'bids/sub-subject/meg/sub-subject_task-task_run-01_channels.tsv'
# Check if param_extended_proj parameter is an empty list string
if config['param_extended_proj'] == '[]':
config['param_extended_proj'] = [] # required to run a pipeline on BL
# Display a warning if h_freq is None
if config['param_h_freq'] is None:
user_warning_message = f'No low-pass filter will be applied to the data. ' \
f'Make sure line noise and cHPI artifacts were removed before finding ' \
f'bad channels.'
warnings.warn(user_warning_message)
dict_json_product['brainlife'].append({'type': 'warning', 'msg': user_warning_message})
# Check if config['param_return_scores'] is True
if config['param_return_scores'] is not True:
value_error_message = f'param_return_scores must be True.'
raise ValueError(value_error_message)
## Convert parameters ##
# Deal with param_origin parameter #
# Convert origin parameter into array when the app is run locally
if isinstance(config['param_origin'], list):
config['param_origin'] = np.array(config['param_origin'])
# Convert origin parameter into array when the app is run on BL
if isinstance(config['param_origin'], str) and config['param_origin'] != "auto":
param_origin = list(map(float, config['param_origin'].split(', ')))
config['param_origin'] = np.array(param_origin)
# Raise an error if param origin is not an array of shape 3
if config['param_origin'] != "auto" and config['param_origin'].shape[0] != 3:
value_error_message = f"Origin parameter must contain three elements."
raise ValueError(value_error_message)
# Deal with param_mag_scale parameter #
# Convert param_mag_scale into a float when not "auto" when the app runs on BL
if isinstance(config['param_mag_scale'], str) and config['param_mag_scale'] != "auto":
config['param_mag_scale'] = float(config['param_mag_scale'])
# Deal with skip_by_annotation parameter #
# Convert param_mag_scale into a list of strings when the app runs on BL
skip_by_an = config['param_skip_by_annotation']
if skip_by_an == "[]":
skip_by_an = []
elif isinstance(skip_by_an, str) and skip_by_an.find("[") != -1 and skip_by_an != "[]":
skip_by_an = skip_by_an.replace('[', '')
skip_by_an = skip_by_an.replace(']', '')
skip_by_an = list(map(str, skip_by_an.split(', ')))
config['param_skip_by_annotation'] = skip_by_an
# Delete keys values in config.json when this app is executed on Brainlife
kwargs = helper.define_kwargs(config)
# Apply find bad channels
raw_copy = raw.copy()
raw_bad_channels, auto_noisy_chs, auto_flat_chs, auto_scores = find_bad_channels(raw_copy, cross_talk_file,
calibration_file,
head_pos_file,
**kwargs)
# Delete the copy
del raw_copy
## Update channels.tsv with bad channels ##
# Read it as a dataframe
df_channels = pd.read_csv(channels_file, sep='\t')
# Update df_channels with bad channels
bads = raw_bad_channels.info['bads']
for bad in bads:
index_bad_channel = df_channels[df_channels['name'] == bad].index
df_channels.loc[index_bad_channel, 'status'] = 'bad'
# Save channels.tsv
df_channels.to_csv('out_dir_bad_channels/channels.tsv', sep = '\t', index=False)
# Write a success message in product.json
dict_json_product['brainlife'].append({'type': 'success', 'msg': 'Bad channels were successfully detected and written in channels.tsv.'})
# Write an info message in product.json
dict_json_product['brainlife'].append({'type': 'info', 'msg': f'This algorithm is not fully reliable. '
f"Don't hesitate to check all of the "
f"signals visually "
f"before performing an another preprocessing step."})
## Generate html report ##
# Get messages to add to the html report
report_calibration_file, report_cross_talk_file, report_head_pos_file, report_destination = helper.message_optional_files_in_reports(calibration_file, cross_talk_file, head_pos_file, destination)
# Generate html report
_generate_report(raw, raw_bad_channels, auto_scores, auto_noisy_chs, auto_flat_chs, data_file,
report_cross_talk_file, report_calibration_file, report_head_pos_file, **kwargs)
# Save the dict_json_product in a json file
with open('product.json', 'w') as outfile:
json.dump(dict_json_product, outfile)
def main():
# Generate a json.product to display messages on Brainlife UI
dict_json_product = {'brainlife': []}
# Load inputs from config.json
with open('config.json') as config_json:
config = json.load(config_json)
# Read the MEG file
data_file = config.pop('fif')
raw = mne.io.read_raw_fif(data_file, allow_maxshield=True)
# Read and save optional files
config, cross_talk_file, calibration_file, events_file, head_pos_file, channels_file, destination = helper.read_optional_files(config, 'out_dir_make_epochs')
# Convert empty strings values to None
config = helper.convert_parameters_to_None(config)
# Channels.tsv must be BIDS compliant
if channels_file is not None:
user_warning_message_channels = f'The channels file provided must be ' \
f'BIDS compliant and the column "status" must be present. '
warnings.warn(user_warning_message_channels)
dict_json_product['brainlife'].append({'type': 'warning', 'msg': user_warning_message_channels})
raw, user_warning_message_channels = helper.update_data_info_bads(raw, channels_file)
if user_warning_message_channels is not None:
warnings.warn(user_warning_message_channels)
dict_json_product['brainlife'].append({'type': 'warning', 'msg': user_warning_message_channels})
## Extract the matrix of events ##
# Test if an events file is given
if events_file is None:
value_error_message = f'You need to provide events.tsv to make epochs. ' \
f'Please use the app-get-events to create such file.'
# Raise exception
raise ValueError(value_error_message)
# Get the matrix of events
elif events_file is not None:
# Warning: events file must be BIDS compliant
user_warning_message_events = f'The events file provided must be ' \
f'BIDS compliant.'
warnings.warn(user_warning_message_events)
dict_json_product['brainlife'].append({'type': 'warning', 'msg': user_warning_message_events})
############### TO BE TESTED ON NO RESTING STATE DATA
# Compute the events matrix #
df_events = pd.read_csv(events_file, sep='\t')
# Extract relevant info from df_events
samples = df_events['sample'].values
event_id = df_events['value'].values
# Compute the values for events matrix
events_time_in_sample = [raw.first_samp + sample for sample in samples]
values_of_trigger_channels = [0]*len(events_time_in_sample)
# Create a dataframe
df_events_matrix = pd.DataFrame([events_time_in_sample, values_of_trigger_channels, event_id])
df_events_matrix = df_events_matrix.transpose()
# Convert dataframe to numpy array
events_matrix = df_events_matrix.to_numpy()
## Convert parameters ##
# Deal with param_baseline parameter #
# Convert baseline parameter into tuple when the app runs locally
if isinstance(config['param_baseline'], list):
config['param_baseline'] = tuple(config['param_baseline'])
# Convert baseline parameter into tuple when the App runs on BL
if isinstance(config['param_baseline'], str):
param_baseline = list(map(str, config['param_baseline'].split(', ')))
param_baseline = [None if i=='None' else i for i in param_baseline]
param_baseline = [float(i) if isinstance(i, str) else i for i in param_baseline]
config['param_baseline'] = tuple(param_baseline)
# Deal with param_proj parameter #
# Convert string into boolean when app runs on BL
if config['param_proj'] == "True":
config['param_proj'] = True
elif config['param_proj'] == "False":
config['param_proj'] = False
# Deal with param_picks_by_channel_indices parameter #
# Convert it into a slice When the App is run locally and on BL
picks = config['param_picks_by_channel_indices']
if isinstance(picks, str) and picks.find(",") != -1 and picks.find("[") == -1 and picks is not None:
picks = list(map(int, picks.split(', ')))
if len(picks) == 2:
config['param_picks_by_channel_indices'] = slice(picks[0], picks[1])
elif len(picks) == 3:
config['param_picks_by_channel_indices'] = slice(picks[0], picks[1], picks[2])
else:
value_error_message = f"If you want to select channels using a slice, you must give two or three elements."
raise ValueError(value_error_message)
# Convert it into a list of integers when the App is run on BL
if isinstance(picks, str) and picks.find(",") != -1 and picks.find("[") != -1 and picks is not None:
picks = picks.replace('[', '')
picks = picks.replace(']', '')
config['param_picks_by_channel_indices'] = list(map(int, picks.split(', ')))
# Deal with param_picks_by_channel_types_or_name parameter #
# Convert it into a list of str when the App is run on BL
picks = config['param_picks_by_channel_types_or_names']
if isinstance(picks, str) and picks.find("[") != -1 and picks is not None:
picks = picks.replace('[', '')
picks = picks.replace(']', '')
config['param_picks_by_channel_types_or_names'] = list(map(str, picks.split(', ')))
# Deal with event id #
# Convert it into a list of int or an int When it is run on BL
if config['param_event_id'] is not None:
if config['param_event_id'].find("[") != -1:
config['param_event_id'] = config['param_event_id'].replace('[', '')
config['param_event_id'] = config['param_event_id'].replace(']', '')
config['param_event_id'] = list(map(int, config['param_event_id'].split(', ')))
else:
config['param_event_id'] = int(config['param_event_id'])
# Deal with param metadata #
# Convert it into a pd.Dataframe when the App runs locally
if isinstance(config['param_metadata'], str):
config['param_metadata'] = pd.read_csv(config['param_metadata'])
elif isinstance(config['param_metadata'], dict):
config['param_metadata'] = pd.DataFrame(list(config['param_metadata'].items()))
# Deal with param detrend #
# Convert it into an int if not None
if isinstance(config['param_detrend'], str):
config['param_detrend'] = int(config['param_detrend'])
# Delete keys values in config.json when this app is executed on Brainlife
kwargs = helper.define_kwargs(config)
# Epoch data
epoched_data = make_epochs(raw, events_matrix, **kwargs)
# Success message in product.json
dict_json_product['brainlife'].append({'type': 'success', 'msg': 'Data was successfully epoched.'})
# Save the dict_json_product in a json file
with open('product.json', 'w') as outfile:
json.dump(dict_json_product, outfile)
def main():
# Generate a json.product to display messages on Brainlife UI
dict_json_product = {'brainlife': []}
# Load inputs from config.json
with open('config.json') as config_json:
config = json.load(config_json)
# Read the files
data_file = config.pop('fif')
if config['param_epoched_data'] is False:
data = mne.io.read_raw_fif(data_file, allow_maxshield=True)
else:
data = mne.read_epochs(data_file)
# Read and save optional files
config, cross_talk_file, calibration_file, events_file, head_pos_file, channels_file, destination = helper.read_optional_files(
config, 'out_dir_resampling')
# Convert empty strings values to None
config = helper.convert_parameters_to_None(config)
# Channels.tsv must be BIDS compliant
if channels_file is not None:
user_warning_message_channels = f'The channels file provided must be ' \
f'BIDS compliant and the column "status" must be present. '
warnings.warn(user_warning_message_channels)
dict_json_product['brainlife'].append({
'type':
'warning',
'msg':
user_warning_message_channels
})
# Udpate data.info['bads'] with info contained in channels.tsv
data, user_warning_message_channels = helper.update_data_info_bads(
data, channels_file)
if user_warning_message_channels is not None:
warnings.warn(user_warning_message_channels)
dict_json_product['brainlife'].append({
'type':
'warning',
'msg':
user_warning_message_channels
})
# Extract the matrix of events #
if config['param_epoched_data'] is False:
if events_file is not None:
# Warning: events file must be BIDS compliant
user_warning_message_events = f'The events file provided must be ' \
f'BIDS compliant.'
warnings.warn(user_warning_message_events)
dict_json_product['brainlife'].append({
'type':
'warning',
'msg':
user_warning_message_events
})
############### TO BE TESTED ON NO RESTING STATE DATA
# Compute the events matrix #
df_events = pd.read_csv(events_file, sep='\t')
# Extract relevant info from df_events
samples = df_events['sample'].values
event_id = df_events['value'].values
# Compute the values for events matrix
events_time_in_sample = [
data.first_samp + sample for sample in samples
]
values_of_trigger_channels = [0] * len(events_time_in_sample)
# Create a dataframe
df_events_matrix = pd.DataFrame(
[events_time_in_sample, values_of_trigger_channels, event_id])
df_events_matrix = df_events_matrix.transpose()
# Convert dataframe to numpy array
events_matrix = df_events_matrix.to_numpy()
else:
events_matrix = None
else:
events_matrix = None
# Info message about resampling if applied
if config['param_epoched_data'] is False:
dict_json_product['brainlife'].append({
'type':
'info',
'msg':
f'Data was resampled at '
f'{config["param_sfreq"]}. '
f'Please bear in mind that it is generally '
f'recommended not to epoch '
f'downsampled data, but instead epoch '
f'and then downsample.'
})
# Comment about resampling
comments_resample_freq = f'{config["param_sfreq"]}Hz'
# Check if the user will save an empty events file
if events_file is None and config[
'param_save_jointly_resampled_events'] is True:
value_error_message = f'You cannot save en empty events file. ' \
f"If you haven't an events file, please set " \
f"'param_save_jointly_resampled_event' to False."
# Raise exception
raise ValueError(value_error_message)
## Convert parameters ##
# Deal with param_npad parameter #
# Convert param_npad into int if not "auto" when the App is run on BL
if config['param_npad'] != "auto":
config['param_npad'] = int(config['param_npad'])
# Deal with param_n_jobs parameter #
# Convert n jobs into int when the App is run on BL
if config['param_n_jobs'] != 'cuda':
config['param_n_jobs'] = int(config['param_n_jobs'])
# Deal with stim picks parameter #
# Convert stim picks into a list of int when the App is run on BL
if isinstance(config['param_stim_picks'],
str) and config['param_stim_picks'] is not None:
config['param_stim_picks'] = config['param_stim_picks'].replace(
'[', '')
config['param_stim_picks'] = config['param_stim_picks'].replace(
']', '')
config['param_stim_picks'] = list(
map(int, config['param_stim_picks'].split(', ')))
# Keep bad channels in memory
bad_channels = data.info['bads']
# Define the type of data
data = data.pick(picks=config['param_pick_type'])
# Delete keys values in config.json when this app is executed on Brainlife
del config['param_pick_type']
kwargs = helper.define_kwargs(config)
# Apply resampling
data_copy = data.copy()
data_resampled, events_resampled = resampling(data_copy, events_matrix,
**kwargs)
del data_copy
## Create BIDS compliant events file if existed ##
if events_resampled is not None and config['param_epoched_data'] is False:
# Create a BIDSPath
bids_path = BIDSPath(subject='subject',
session=None,
task='task',
run='01',
acquisition=None,
processing=None,
recording=None,
space=None,
suffix=None,
datatype='meg',
root='bids')
# Extract event_id value #
# to be tested when events are extracted from data
event_id_value = list(
events_resampled[:, 2]
) # the third column of events corresponds to the value column of BIDS events.tsv
id_values_occurrences = Counter(
event_id_value) # number of different events
id_values_occurrences = list(id_values_occurrences.keys())
trials_type = [
f"events_{i}" for i in range(1,
len(id_values_occurrences) + 1)
] # for trial type column of BIDS events.tsv
dict_event_id = dict(
(k, v) for k, v in zip(trials_type, id_values_occurrences))
# Write BIDS to create events.tsv BIDS compliant
write_raw_bids(data,
bids_path,
events_data=events_resampled,
event_id=dict_event_id,
overwrite=True)
# Extract events.tsv from bids path
events_file = 'bids/sub-subject/meg/sub-subject_task-task_run-01_events.tsv'
# Copy events.tsv in outdir
shutil.copy2(events_file, 'out_dir_resampling/events.tsv')
# Info message in product.json
dict_json_product['brainlife'].append({
'type':
'info',
'msg':
'Jointly resampled events are saved in events.tsv.'
})
# Success message in product.json
dict_json_product['brainlife'].append({
'type':
'success',
'msg':
'Data was successfully resampled.'
})
# Save the dict_json_product in a json file
with open('product.json', 'w') as outfile:
json.dump(dict_json_product, outfile)
def main():
# Generate a json.product to display messages on Brainlife UI
dict_json_product = {'brainlife': []}
# Load inputs from config.json
with open('config.json') as config_json:
config = json.load(config_json)
# Read the files
data_file = config.pop('fif')
raw = mne.io.read_raw_fif(data_file, allow_maxshield=True)
# Read and save optional files
config, cross_talk_file, calibration_file, events_file, head_pos_file, channels_file, destination = helper.read_optional_files(
config, 'out_dir_notch_filter')
# Convert empty strings values to None
config = helper.convert_parameters_to_None(config)
# Raise error if no start parameter and method is wrong
if config['param_freqs_specific_or_start'] is None and config[
'param_method'] != 'spectrum_fit':
value_error_message = f'This frequency can only be None when method is spectrum_fit.'
# Raise exception
raise ValueError(value_error_message)
## Convert parameters ##
# Deal with param_picks_by_channel_indices parameter #
# Convert it into a slice When the App is run locally and on BL
picks = config['param_picks_by_channel_indices']
if isinstance(picks, str) and picks.find(",") != -1 and picks.find(
"[") == -1 and picks is not None:
picks = list(map(int, picks.split(', ')))
if len(picks) == 2:
config['param_picks_by_channel_indices'] = slice(
picks[0], picks[1])
elif len(picks) == 3:
config['param_picks_by_channel_indices'] = slice(
picks[0], picks[1], picks[2])
else:
value_error_message = f"If you want to select channels using a slice, you must give two or three elements."
raise ValueError(value_error_message)
# Convert it into a list of int when the app is run on BL
if isinstance(picks, str) and picks.find(",") != -1 and picks.find(
"[") != -1 and picks is not None:
picks = picks.replace('[', '')
picks = picks.replace(']', '')
config['param_picks_by_channel_indices'] = list(
map(int, picks.split(', ')))
# Deal with param_picks_by_channel_types_or_name parameter #
# Convert it into a list of str when the App is run on BL
picks = config['param_picks_by_channel_types_or_names']
if isinstance(picks, str) and picks.find("[") != -1 and picks is not None:
picks = picks.replace('[', '')
picks = picks.replace(']', '')
config['param_picks_by_channel_types_or_names'] = list(
map(str, picks.split(', ')))
# Deal with filter_length parameter #
# Convert it into int if not "auto" when the App runs on BL
if config['param_filter_length'] != "auto" and config[
'param_filter_length'].find("s") == -1:
config['param_filter_length'] = int(config['param_filter_length'])
# Deal with param_notch_widths parameter #
# Convert notch widths parameter into array when the app is run locally
if isinstance(config['param_notch_widths'], list):
config['param_notch_widths'] = np.array(config['param_notch_widths'])
# Convert notch widths parameter into array when the app is run on BL
if isinstance(config['param_notch_widths'], str):
config['param_notch_widths'] = list(
map(float, config['param_notch_widths'].split(', ')))
if len(config['param_notch_widths']) == 1:
config['param_notch_widths'] = float(
config['param_notch_widths'][0])
else:
config['param_notch_widths'] = np.array(
config['param_notch_widths'])
# Deal with param_n_jobs parameter #
# Convert it into into if not "cuda" When the App is run on BL
if config['param_n_jobs'] != 'cuda':
config['param_n_jobs'] = int(config['param_n_jobs'])
# Comments messages about filtering #
if config['param_freqs_specific_or_start'] is not None and config[
'param_freqs_end'] is None:
comments_notch = f"{config['param_freqs_specific_or_start']}Hz"
elif config['param_freqs_specific_or_start'] is not None and config[
'param_freqs_end'] is not None:
comments_notch = f"Between {config['param_freqs_specific_or_start']} and {config['param_freqs_end']}Hz"
if config['param_freqs_step'] is not None:
comments_notch = f"Between {config['param_freqs_specific_or_start']} and " \
f"{config['param_freqs_end']}Hz every {config['param_freqs_step']}Hz"
# Channels.tsv must be BIDS compliant
if channels_file is not None:
user_warning_message_channels = f'The channels file provided must be ' \
f'BIDS compliant and the column "status" must be present. '
warnings.warn(user_warning_message_channels)
dict_json_product['brainlife'].append({
'type':
'warning',
'msg':
user_warning_message_channels
})
# Udpate raw.info['bads'] with info contained in channels.tsv
raw, user_warning_message_channels = helper.update_data_info_bads(
raw, channels_file)
if user_warning_message_channels is not None:
warnings.warn(user_warning_message_channels)
dict_json_product['brainlife'].append({
'type':
'warning',
'msg':
user_warning_message_channels
})
# Keep bad channels in memory #
bad_channels = raw.info['bads']
# Delete keys values in config.json when this app is executed on Brainlife
kwargs = helper.define_kwargs(config)
# Apply temporal filtering
raw_copy = raw.copy()
raw_notch_filtered = notch_filter(raw_copy, **kwargs)
del raw_copy
# Success message in product.json
dict_json_product['brainlife'].append({
'type':
'success',
'msg':
'Notch filter was applied successfully.'
})
# Compute SNR
# snr_before = _compute_snr(raw)
# snr_after = _compute_snr(raw_filtered)
# Generate a report
_generate_report(data_file, raw, raw_notch_filtered, bad_channels,
comments_notch, **kwargs)
# Save the dict_json_product in a json file
with open('product.json', 'w') as outfile:
json.dump(dict_json_product, outfile)
def main():
# Generate a json.product to display messages on Brainlife UI
dict_json_product = {'brainlife': []}
# Load inputs from config.json
with open('config.json') as config_json:
config = json.load(config_json)
# Read the MEG file
data_file = config.pop('fif')
raw = mne.io.read_raw_fif(data_file, allow_maxshield=True)
# Read and save optional files
config, cross_talk_file, calibration_file, events_file, head_pos_file, channels_file, destination = helper.read_optional_files(
config, 'out_dir_get_events')
# Convert empty strings values to None
config = helper.convert_parameters_to_None(config)
# Channels.tsv must be BIDS compliant
if channels_file is not None:
user_warning_message_channels = f'The channels file provided must be ' \
f'BIDS compliant and the column "status" must be present. '
warnings.warn(user_warning_message_channels)
dict_json_product['brainlife'].append({
'type':
'warning',
'msg':
user_warning_message_channels
})
# Udpate raw.info['bads'] with info contained in channels.tsv
raw, user_warning_message_channels = helper.update_data_info_bads(
raw, channels_file)
if user_warning_message_channels is not None:
warnings.warn(user_warning_message_channels)
dict_json_product['brainlife'].append({
'type':
'warning',
'msg':
user_warning_message_channels
})
# Events file
if events_file is not None:
user_warning_message_events = f'The events.tsv file provided will be ' \
f'overwritten with the new events obtained by this App.'
warnings.warn(user_warning_message_events)
dict_json_product['brainlife'].append({
'type':
'warning',
'msg':
user_warning_message_events
})
## Convert parameters ##
# Deal with stim channels #
# Convert it into a list of strings it is run on BL
stim_channels = config['param_find_events_stim_channels']
if isinstance(stim_channels, str) and stim_channels.find(
"[") != -1 and stim_channels is not None:
stim_channels = stim_channels.replace('[', '')
stim_channels = stim_channels.replace(']', '')
config['param_find_events_stim_channels'] = list(
map(str, stim_channels.split(', ')))
# Deal with param consecutive #
# Convert it into a bool if necessary
if config['param_find_events_consecutive'] == "True":
config['param_find_events_consecutive'] = True
elif config['param_find_events_consecutive'] == "False":
config['param_find_events_consecutive'] = False
# Test if the data contains events
if raw.info['events'] and config['param_make_events'] is True:
user_warning_message = f'Events already exist in this raw file. ' \
f'You are going to create an events.tsv file with events ' \
f'different from those contained in the raw file.'
warnings.warn(user_warning_message)
dict_json_product['brainlife'].append({
'type': 'warning',
'msg': user_warning_message
})
elif not raw.info['events'] and config['param_make_events'] is False:
error_value_message = f"You can't extract events from this raw file because it doesn't contain " \
f"any events. Please set param_make_events to 'True' so that fixed " \
f"length events will be created."
raise ValueError(error_value_message)
# Delete keys values in config.json when this app is executed on Brainlife
kwargs = helper.define_kwargs(config)
# Create or extract events
events = get_events(raw, **kwargs)
## Create BIDS compliant events file ##
# Create a BIDSPath
bids_path = BIDSPath(subject='subject',
session=None,
task='task',
run='01',
acquisition=None,
processing=None,
recording=None,
space=None,
suffix=None,
datatype='meg',
root='bids')
# Extract event_id value #
# When fixed length events were created
if config['param_make_events'] is True:
dict_event_id = {'event': config['param_make_events_id']}
# When existing events were extracted
else: # to be tested
event_id_value = list(
events[:, 2]
) # the third column of events corresponds to the value column of BIDS events.tsv
id_values_occurrences = Counter(
event_id_value) # number of different events
id_values_occurrences = list(id_values_occurrences.keys())
trials_type = [
f"events_{i}" for i in range(1,
len(id_values_occurrences) + 1)
] # for trial type column of BIDS events.tsv
dict_event_id = dict(
(k, v) for k, v in zip(trials_type, id_values_occurrences))
# Write BIDS to create events.tsv BIDS compliant
write_raw_bids(raw,
bids_path,
events_data=events,
event_id=dict_event_id,
overwrite=True)
# Extract events.tsv from bids path
events_file = 'bids/sub-subject/meg/sub-subject_task-task_run-01_events.tsv'
# Copy events.tsv in outdir
shutil.copy2(events_file, 'out_dir_get_events/events.tsv')
# Success message in product.json
if config['param_make_events'] is True:
dict_json_product['brainlife'].append({
'type':
'success',
'msg':
'Events were successfully created.'
})
else:
dict_json_product['brainlife'].append({
'type':
'success',
'msg':
'Events were successfully extracted.'
})
# Save the dict_json_product in a json file
with open('product.json', 'w') as outfile:
json.dump(dict_json_product, outfile)
def main():
# Generate a json.product to display messages on Brainlife UI
dict_json_product = {'brainlife': []}
# Load inputs from config.json
with open('config.json') as config_json:
config = json.load(config_json)
# Read the files
data_file = config.pop('fif')
if config['param_epoched_data'] is False:
data = mne.io.read_raw_fif(data_file, allow_maxshield=True)
else:
data = mne.read_epochs(data_file)
# Read and save optional files
config, cross_talk_file, calibration_file, events_file, head_pos_file, channels_file, destination = helper.read_optional_files(
config, 'out_dir_temporal_filtering')
# Convert empty strings values to None
config = helper.convert_parameters_to_None(config)
## Convert parameters ##
# Deal with param_picks_by_channel_indices parameter #
# Convert param_picks_by_channel_indices into slice when the App is run locally and on BL
picks = config['param_picks_by_channel_indices']
if isinstance(picks, str) and picks.find(",") != -1 and picks.find(
"[") == -1 and picks is not None:
picks = list(map(int, picks.split(', ')))
if len(picks) == 2:
config['param_picks_by_channel_indices'] = slice(
picks[0], picks[1])
elif len(picks) == 3:
config['param_picks_by_channel_indices'] = slice(
picks[0], picks[1], picks[2])
else:
value_error_message = f"If you want to select channels using a slice, you must give two or three elements."
raise ValueError(value_error_message)
# Convert param_picks_by_channel_indices into a list of integers when the App is run on BL
if isinstance(picks, str) and picks.find(",") != -1 and picks.find(
"[") != -1 and picks is not None:
picks = picks.replace('[', '')
picks = picks.replace(']', '')
config['param_picks_by_channel_indices'] = list(
map(int, picks.split(', ')))
# Deal with param_picks_by_channel_types_or_name parameter #
# Convert param_picks_by_channel_types_or_names into a list of string when the App is run on BL
picks = config['param_picks_by_channel_types_or_names']
if isinstance(picks, str) and picks.find("[") != -1 and picks is not None:
picks = picks.replace('[', '')
picks = picks.replace(']', '')
config['param_picks_by_channel_types_or_names'] = list(
map(str, picks.split(', ')))
# Deal with filter_length parameter on BL #
# Convert param_filter_length into int if not auto and not a length in time when the App is run on BL
if config['param_filter_length'] != "auto" and config[
'param_filter_length'].find("s") == -1:
config['param_filter_length'] = int(config['param_filter_length'])
# Deal with param_l_trans_bandwidth parameter on BL #
# Convert param_l_trans_bandwidth into a float if not auto when the App is run on BL
if isinstance(config['param_l_trans_bandwidth'],
str) and config['param_l_trans_bandwidth'] != "auto":
config['param_l_trans_bandwidth'] = float(
config['param_l_trans_bandwidth'])
# Deal with param_h_trans_bandwidth parameter on BL #
# Convert param_h_trans_bandwidth into a float if not auto when the App is run on BL
if isinstance(config['param_h_trans_bandwidth'],
str) and config['param_h_trans_bandwidth'] != "auto":
config['param_h_trans_bandwidth'] = float(
config['param_h_trans_bandwidth'])
# Deal with param_n_jobs parameter on BL #
# Convert param n jobs into an int if not cuda
if config['param_n_jobs'] != 'cuda':
config['param_n_jobs'] = int(config['param_n_jobs'])
# Deal with skip_by_annotation parameter #
# Convert param_mag_scale into a list of strings when the app runs on BL
skip_by_an = config['param_skip_by_annotation']
if skip_by_an == "[]":
skip_by_an = []
elif isinstance(skip_by_an,
str) and skip_by_an.find("[") != -1 and skip_by_an != "[]":
skip_by_an = skip_by_an.replace('[', '')
skip_by_an = skip_by_an.replace(']', '')
skip_by_an = list(map(str, skip_by_an.split(', ')))
config['param_skip_by_annotation'] = skip_by_an
## Info message about filtering ##
# Band pass filter
if config['param_l_freq'] is not None and config[
'param_h_freq'] is not None:
comments_about_filtering = f'Data was filtered between ' \
f'{config["param_l_freq"]} ' \
f'and {config["param_h_freq"]}Hz.'
dict_json_product['brainlife'].append({
'type': 'info',
'msg': comments_about_filtering
})
filter_type = "band-pass"
# Lowpass filter
elif config['param_l_freq'] is None and config['param_h_freq'] is not None:
comments_about_filtering = f'Lowpass filter was applied at {config["param_h_freq"]}Hz.'
dict_json_product['brainlife'].append({
'type': 'info',
'msg': comments_about_filtering
})
filter_type = "low-pass"
# Highpass filter
elif config['param_l_freq'] is not None and config['param_h_freq'] is None:
comments_about_filtering = f'Highpass filter was applied at {config["param_l_freq"]}Hz.'
dict_json_product['brainlife'].append({
'type': 'info',
'msg': comments_about_filtering
})
filter_type = "high-pass"
# Raise an exception if both param_filter_l_freq and param_filter_h_freq are None
elif config['param_l_freq'] is None and config["param_h_freq"] is None:
value_error_message = f'You must specify a value for param_l_freq or param_h_freq, ' \
f"they can't both be set to None."
# Raise exception
raise ValueError(value_error_message)
# Channels.tsv must be BIDS compliant
if channels_file is not None:
user_warning_message_channels = f'The channels file provided must be ' \
f'BIDS compliant and the column "status" must be present. '
warnings.warn(user_warning_message_channels)
dict_json_product['brainlife'].append({
'type':
'warning',
'msg':
user_warning_message_channels
})
# Udpate data.info['bads'] with info contained in channels.tsv
data, user_warning_message_channels = helper.update_data_info_bads(
data, channels_file)
if user_warning_message_channels is not None:
warnings.warn(user_warning_message_channels)
dict_json_product['brainlife'].append({
'type':
'warning',
'msg':
user_warning_message_channels
})
# Keep bad channels in memory
bad_channels = data.info['bads']
# Delete keys values in config.json when this app is executed on Brainlife
kwargs = helper.define_kwargs(config)
# Apply temporal filtering
data_copy = data.copy()
data_filtered = temporal_filtering(data_copy, **kwargs)
del data_copy
# Success message in product.json
dict_json_product['brainlife'].append({
'type':
'success',
'msg':
'Filtering was applied successfully.'
})
# Compute SNR
#snr_before = _compute_snr(data)
#snr_after = _compute_snr(data_filtered)
# Generate a report
_generate_report(data_file, data, data_filtered, bad_channels,
comments_about_filtering, **kwargs)
# Save the dict_json_product in a json file
with open('product.json', 'w') as outfile:
json.dump(dict_json_product, outfile)