def get_config(subject: Optional[str] = None,
session: Optional[str] = None) -> BunchConst:
cfg = BunchConst(task=config.get_task(),
datatype=config.get_datatype(),
runs=config.get_runs(subject=subject),
acq=config.acq,
rec=config.rec,
space=config.space,
deriv_root=config.get_deriv_root(),
interactive=config.interactive,
ica_l_freq=config.ica_l_freq,
ica_algorithm=config.ica_algorithm,
ica_n_components=config.ica_n_components,
ica_max_iterations=config.ica_max_iterations,
ica_decim=config.ica_decim,
ica_reject=config.get_ica_reject(),
ica_eog_threshold=config.ica_eog_threshold,
ica_ctps_ecg_threshold=config.ica_ctps_ecg_threshold,
random_state=config.random_state,
ch_types=config.ch_types,
l_freq=config.l_freq,
decim=config.decim,
resample_sfreq=config.resample_sfreq,
event_repeated=config.event_repeated,
epochs_tmin=config.epochs_tmin,
epochs_tmax=config.epochs_tmax,
eeg_reference=config.get_eeg_reference(),
eog_channels=config.eog_channels)
return cfg
def get_config(
subject: Optional[str] = None,
session: Optional[str] = None
) -> BunchConst:
cfg = BunchConst(
subjects=config.get_subjects(),
task=config.get_task(),
datatype=config.get_datatype(),
acq=config.acq,
rec=config.rec,
space=config.space,
proc=config.proc,
deriv_root=config.get_deriv_root(),
conditions=config.conditions,
contrasts=config.contrasts,
decode=config.decode,
decoding_metric=config.decoding_metric,
decoding_n_splits=config.decoding_n_splits,
random_state=config.random_state,
n_boot=config.n_boot,
analyze_channels=config.analyze_channels,
interpolate_bads_grand_average=config.interpolate_bads_grand_average,
ch_types=config.ch_types,
eeg_reference=config.get_eeg_reference(),
interactive=config.interactive
)
return cfg
def get_config(
subject: Optional[str] = None,
session: Optional[str] = None
) -> BunchConst:
cfg = BunchConst(
process_er=config.process_er,
runs=config.get_runs(subject=subject),
use_maxwell_filter=config.use_maxwell_filter,
proc=config.proc,
task=config.get_task(),
datatype=config.get_datatype(),
session=session,
acq=config.acq,
rec=config.rec,
space=config.space,
bids_root=config.get_bids_root(),
deriv_root=config.get_deriv_root(),
interactive=config.interactive,
epochs_tmin=config.epochs_tmin,
epochs_tmax=config.epochs_tmax,
epochs_metadata_tmin=config.epochs_metadata_tmin,
epochs_metadata_tmax=config.epochs_metadata_tmax,
epochs_metadata_keep_first=config.epochs_metadata_keep_first,
epochs_metadata_keep_last=config.epochs_metadata_keep_last,
event_repeated=config.event_repeated,
decim=config.decim,
ch_types=config.ch_types,
eeg_reference=config.get_eeg_reference()
)
return cfg
def get_config(subject: Optional[str] = None,
session: Optional[str] = None) -> BunchConst:
cfg = BunchConst(datatype=config.get_datatype(),
deriv_root=config.get_deriv_root(),
PIPELINE_NAME=config.PIPELINE_NAME,
VERSION=config.VERSION,
CODE_URL=config.CODE_URL)
return cfg
def get_config(subject: Optional[str] = None,
session: Optional[str] = None) -> SimpleNamespace:
cfg = SimpleNamespace(datatype=config.get_datatype(),
deriv_root=config.get_deriv_root(),
PIPELINE_NAME=config.PIPELINE_NAME,
VERSION=config.VERSION,
CODE_URL=config.CODE_URL)
return cfg
def get_config(subject: Optional[str] = None,
session: Optional[str] = None) -> BunchConst:
cfg = BunchConst(
task=config.get_task(),
datatype=config.get_datatype(),
acq=config.acq,
rec=config.rec,
space=config.space,
deriv_root=config.get_deriv_root(),
)
return cfg
def get_config(subject: Optional[str] = None,
session: Optional[str] = None) -> SimpleNamespace:
cfg = SimpleNamespace(task=config.get_task(),
datatype=config.get_datatype(),
acq=config.acq,
rec=config.rec,
space=config.space,
deriv_root=config.get_deriv_root(),
interactive=config.interactive,
baseline=config.baseline,
ica_reject=config.get_ica_reject())
return cfg
def get_config(
subject: Optional[str] = None,
session: Optional[str] = None
) -> SimpleNamespace:
cfg = SimpleNamespace(
task=config.get_task(),
datatype=config.get_datatype(),
acq=config.acq,
rec=config.rec,
space=config.space,
deriv_root=config.get_deriv_root(),
)
return cfg
def get_config(subject: Optional[str] = None,
session: Optional[str] = None) -> SimpleNamespace:
# Deal with configurations where `deriv_root` was specified, but not
# `fs_subjects_dir`. We normally raise an exception in this case in
# `get_fs_subjects_dir()`. However, in situations where users only run the
# sensor-space scripts, we never call this function, so everything works
# totally fine at first (which is expected). Yet, when creating the
# reports, the pipeline would fail with an exception – which is
# unjustified, as it would not make sense to force users to provide an
# `fs_subjects_dir` if they don't care about source analysis anyway! So
# simply assign a dummy value in such cases.
# `get_fs_subject()` calls `get_fs_subjects_dir()`, so take care of this
# too.
try:
fs_subjects_dir = config.get_fs_subjects_dir()
except ValueError:
fs_subjects_dir = None
fs_subject = None
else:
fs_subject = config.get_fs_subject(subject=subject)
cfg = SimpleNamespace(
task=config.get_task(),
runs=config.get_runs(subject=subject),
datatype=config.get_datatype(),
acq=config.acq,
rec=config.rec,
space=config.space,
proc=config.proc,
analyze_channels=config.analyze_channels,
process_er=config.process_er,
find_noisy_channels_meg=config.find_noisy_channels_meg,
h_freq=config.h_freq,
spatial_filter=config.spatial_filter,
ica_reject=config.ica_reject,
conditions=config.conditions,
contrasts=config.contrasts,
time_frequency_conditions=config.time_frequency_conditions,
decode=config.decode,
decoding_metric=config.decoding_metric,
n_boot=config.n_boot,
inverse_method=config.inverse_method,
fs_subject=fs_subject,
fs_subjects_dir=fs_subjects_dir,
deriv_root=config.get_deriv_root(),
bids_root=config.get_bids_root(),
use_template_mri=config.use_template_mri,
interactive=config.interactive,
plot_psd_for_runs=config.plot_psd_for_runs,
)
return cfg
def get_config() -> BunchConst:
cfg = BunchConst(
task=config.get_task(),
datatype=config.get_datatype(),
acq=config.acq,
rec=config.rec,
space=config.space,
proc=config.proc,
conditions=config.conditions,
inverse_method=config.inverse_method,
fs_subjects_dir=config.get_fs_subjects_dir(),
deriv_root=config.get_deriv_root(),
)
return cfg
def get_config(subject: Optional[str] = None,
session: Optional[str] = None) -> BunchConst:
cfg = BunchConst(
task=config.get_task(),
datatype=config.get_datatype(),
acq=config.acq,
rec=config.rec,
space=config.space,
ch_types=config.ch_types,
conditions=config.conditions,
inverse_method=config.inverse_method,
deriv_root=config.get_deriv_root(),
)
return cfg
def get_config(subject: Optional[str] = None,
session: Optional[str] = None) -> BunchConst:
cfg = BunchConst(task=config.get_task(),
datatype=config.get_datatype(),
acq=config.acq,
rec=config.rec,
space=config.space,
baseline=config.baseline,
reject_tmin=config.reject_tmin,
reject_tmax=config.reject_tmax,
spatial_filter=config.spatial_filter,
ica_reject=config.get_ica_reject(),
deriv_root=config.get_deriv_root(),
decim=config.decim)
return cfg
def get_config(subject: Optional[str] = None,
session: Optional[str] = None) -> BunchConst:
cfg = BunchConst(
task=config.get_task(),
datatype=config.get_datatype(),
acq=config.acq,
rec=config.rec,
space=config.space,
proc=config.proc,
noise_cov=config.noise_cov,
spatial_filter=config.spatial_filter,
ch_types=config.ch_types,
deriv_root=config.get_deriv_root(),
)
return cfg
def get_config(subject: Optional[str] = None,
session: Optional[str] = None) -> SimpleNamespace:
cfg = SimpleNamespace(
task=config.get_task(),
datatype=config.get_datatype(),
acq=config.acq,
rec=config.rec,
space=config.space,
deriv_root=config.get_deriv_root(),
time_frequency_conditions=config.time_frequency_conditions,
analyze_channels=config.analyze_channels,
spatial_filter=config.spatial_filter,
ch_types=config.ch_types,
eeg_reference=config.get_eeg_reference(),
time_frequency_freq_min=config.time_frequency_freq_min,
time_frequency_freq_max=config.time_frequency_freq_max)
return cfg
def get_config(subject: Optional[str] = None,
session: Optional[str] = None) -> BunchConst:
cfg = BunchConst(task=config.get_task(),
datatype=config.get_datatype(),
acq=config.acq,
rec=config.rec,
space=config.space,
deriv_root=config.get_deriv_root(),
conditions=config.conditions,
contrasts=config.contrasts,
decode=config.decode,
decoding_metric=config.decoding_metric,
decoding_n_splits=config.decoding_n_splits,
random_state=config.random_state,
analyze_channels=config.analyze_channels,
ch_types=config.ch_types,
eeg_reference=config.get_eeg_reference(),
n_jobs=config.get_n_jobs())
return cfg
def get_config(
subject: Optional[str] = None,
session: Optional[str] = None
) -> SimpleNamespace:
cfg = SimpleNamespace(
task=config.get_task(),
datatype=config.get_datatype(),
acq=config.acq,
rec=config.rec,
space=config.space,
source_info_path_update=config.source_info_path_update,
inverse_targets=config.inverse_targets,
noise_cov=config.noise_cov,
ch_types=config.ch_types,
conditions=config.conditions,
inverse_method=config.inverse_method,
deriv_root=config.get_deriv_root(),
)
return cfg
def get_config(subject: Optional[str] = None,
session: Optional[str] = None) -> SimpleNamespace:
cfg = SimpleNamespace(
runs=config.get_runs(subject=subject),
task=config.get_task(),
datatype=config.get_datatype(),
acq=config.acq,
rec=config.rec,
space=config.space,
eog_channels=config.eog_channels,
deriv_root=config.get_deriv_root(),
ssp_reject_ecg=config.ssp_reject_ecg,
ecg_proj_from_average=config.ecg_proj_from_average,
ssp_reject_eog=config.ssp_reject_eog,
eog_proj_from_average=config.eog_proj_from_average,
n_proj_eog=config.n_proj_eog,
n_proj_ecg=config.n_proj_ecg,
)
return cfg
def get_config(subject: Optional[str] = None,
session: Optional[str] = None) -> SimpleNamespace:
cfg = SimpleNamespace(
task=config.get_task(),
runs=config.get_runs(subject=subject),
datatype=config.get_datatype(),
acq=config.acq,
rec=config.rec,
space=config.space,
mindist=config.mindist,
spacing=config.spacing,
use_template_mri=config.use_template_mri,
source_info_path_update=config.source_info_path_update,
ch_types=config.ch_types,
fs_subject=config.get_fs_subject(subject=subject),
fs_subjects_dir=config.get_fs_subjects_dir(),
deriv_root=config.get_deriv_root(),
bids_root=config.get_bids_root(),
n_jobs=config.get_n_jobs())
return cfg
def get_config(subject: Optional[str] = None,
session: Optional[str] = None) -> BunchConst:
cfg = BunchConst(
process_er=config.process_er,
runs=config.get_runs(subject=subject),
use_maxwell_filter=config.use_maxwell_filter,
proc=config.proc,
task=config.get_task(),
datatype=config.get_datatype(),
acq=config.acq,
rec=config.rec,
space=config.space,
bids_root=config.get_bids_root(),
deriv_root=config.get_deriv_root(),
l_freq=config.l_freq,
h_freq=config.h_freq,
l_trans_bandwidth=config.l_trans_bandwidth,
h_trans_bandwidth=config.h_trans_bandwidth,
resample_sfreq=config.resample_sfreq,
crop_runs=config.crop_runs,
interactive=config.interactive,
rename_events=config.rename_events,
eeg_bipolar_channels=config.eeg_bipolar_channels,
eeg_template_montage=config.eeg_template_montage,
fix_stim_artifact=config.fix_stim_artifact,
stim_artifact_tmin=config.stim_artifact_tmin,
stim_artifact_tmax=config.stim_artifact_tmax,
find_flat_channels_meg=config.find_flat_channels_meg,
find_noisy_channels_meg=config.find_noisy_channels_meg,
reference_run=config.get_mf_reference_run(),
drop_channels=config.drop_channels,
find_breaks=config.find_breaks,
min_break_duration=config.min_break_duration,
t_break_annot_start_after_previous_event=config.
t_break_annot_start_after_previous_event, # noqa:E501
t_break_annot_stop_before_next_event=config.
t_break_annot_stop_before_next_event, # noqa:E501
)
return cfg
def get_config(
subject: Optional[str] = None,
session: Optional[str] = None
) -> BunchConst:
cfg = BunchConst(
task=config.get_task(),
runs=config.get_runs(subject=subject),
datatype=config.get_datatype(),
acq=config.acq,
rec=config.rec,
space=config.space,
mindist=config.mindist,
spacing=config.spacing,
use_template_mri=config.use_template_mri,
ch_types=config.ch_types,
fs_subject=config.get_fs_subject(subject=subject),
fs_subjects_dir=config.get_fs_subjects_dir(),
deriv_root=config.get_deriv_root(),
bids_root=config.get_bids_root(),
n_jobs=config.get_n_jobs()
)
return cfg
def get_config(
subject: Optional[str] = None,
session: Optional[str] = None
) -> BunchConst:
cfg = BunchConst(
mf_cal_fname=config.get_mf_cal_fname(subject, session),
mf_ctc_fname=config.get_mf_ctc_fname(subject, session),
mf_st_duration=config.mf_st_duration,
mf_head_origin=config.mf_head_origin,
process_er=config.process_er,
runs=config.get_runs(subject=subject), # XXX needs to accept session!
use_maxwell_filter=config.use_maxwell_filter,
proc=config.proc,
task=config.get_task(),
datatype=config.get_datatype(),
acq=config.acq,
rec=config.rec,
space=config.space,
bids_root=config.get_bids_root(),
deriv_root=config.get_deriv_root(),
crop_runs=config.crop_runs,
interactive=config.interactive,
rename_events=config.rename_events,
eeg_template_montage=config.eeg_template_montage,
fix_stim_artifact=config.fix_stim_artifact,
stim_artifact_tmin=config.stim_artifact_tmin,
stim_artifact_tmax=config.stim_artifact_tmax,
find_flat_channels_meg=config.find_flat_channels_meg,
find_noisy_channels_meg=config.find_noisy_channels_meg,
mf_reference_run=config.get_mf_reference_run(),
drop_channels=config.drop_channels,
find_breaks=config.find_breaks,
min_break_duration=config.min_break_duration,
t_break_annot_start_after_previous_event=config.t_break_annot_start_after_previous_event, # noqa:E501
t_break_annot_stop_before_next_event=config.t_break_annot_stop_before_next_event, # noqa:E501
)
return cfg
