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Make it work for "inconsistent runs" (using ds001971) #41

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Make it work for "inconsistent runs" (using ds001971) #41

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49c5a1b
TST for ds001971
jasmainak Aug 7, 2019
892efd8
FIX uniqify events
jasmainak Aug 7, 2019
b499082
FIX: more fixes
jasmainak Aug 7, 2019
2893b8e
FIX for rebase
jasmainak Aug 7, 2019
d98d149
apparently i dont know how to rebase
sappelhoff Aug 8, 2019
4685209
make ds001917 work
sappelhoff Aug 8, 2019
a4fde6a
address review by @jasmainak
sappelhoff Aug 8, 2019
dc3e184
try unequal runs
sappelhoff Aug 21, 2019
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9 changes: 9 additions & 0 deletions .circleci/config.yml
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Expand Up @@ -100,6 +100,15 @@ jobs:
export MNE_BIDS_STUDY_CONFIG=config_matchingpennies
make sensor

- run:
name: test ds001971
command: |
export DATASET=ds001971
make fetch
export BIDS_ROOT=$DATA_DIR/ds001971
export MNE_BIDS_STUDY_CONFIG=config_ds001971
make sensor

- run:
name: test somato data
command: |
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8 changes: 8 additions & 0 deletions 04-make_epochs.py
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Expand Up @@ -10,8 +10,10 @@
To save space, the epoch data can be decimated.
"""

import numpy as np
import os.path as op
import itertools
import warnings

import mne
from mne.parallel import parallel_func
Expand Down Expand Up @@ -70,6 +72,12 @@ def run_epochs(subject, session=None):
raw = mne.concatenate_raws(raw_list)

events, event_id = mne.events_from_annotations(raw)

if len(np.unique(events[:, 0])) != len(events):
warnings.warn('Events are not unique. Uniqifying them')
_, idx = np.unique(events[:, 0], return_index=True)
events = events[idx]
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if "eeg" in config.ch_types:
raw.set_eeg_reference(projection=True)

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8 changes: 8 additions & 0 deletions 05a-run_ica.py
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Expand Up @@ -11,6 +11,9 @@

import os.path as op
import itertools
import warnings

import numpy as np

import mne
from mne.report import Report
Expand Down Expand Up @@ -74,6 +77,11 @@ def run_ica(subject, session=None):

events, event_id = mne.events_from_annotations(raw)

if len(np.unique(events[:, 0])) != len(events):
warnings.warn('Events are not unique. Uniqifying them')
_, idx = np.unique(events[:, 0], return_index=True)
events = events[idx]

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with mne-tools/mne-python#6688 being merged, we can outsource handling of non-unique events to MNE-Python and remove this code in the study template

if "eeg" in config.ch_types or config.kind == 'eeg':
raw.set_eeg_reference(projection=True)
del raw_list
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1 change: 0 additions & 1 deletion config.py
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Expand Up @@ -36,7 +36,6 @@
# If running the scripts from a notebook or spyder
# run %matplotlib qt in the command line to get the plots in extra windows

plot = True
plot = False

# ``crop``: tuple or None
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16 changes: 6 additions & 10 deletions tests/configs/config_ds001971.py
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Expand Up @@ -14,15 +14,11 @@

study_name = 'ds001971'
task = 'AudioCueWalkingStudy'
kind = 'eeg'
plot = False
reject = {'eeg': 150e-6}
conditions = ['left', 'right']
decoding_conditions = [('left', 'right')]
reject = {'eeg': 350e-6}
conditions = ['UncuedWalking', 'PreferredCadence', 'AdvanceTempo',
'DelayTempo']
decoding_conditions = [['AdvanceTempo', 'DelayTempo']]
use_ssp = False
use_ica = False


subjects_list = ['001']

runs = ['01']
subjects_list = ['001', '002']
runs = ['01', '02']
16 changes: 16 additions & 0 deletions tests/download_test_data.py
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Expand Up @@ -52,6 +52,22 @@ def _provide_get_dict(dataset=None):
'sub-001/eeg/sub-001_task-AudioCueWalkingStudy_run-01_electrodes.tsv', # noqa: E501
'sub-001/eeg/sub-001_task-AudioCueWalkingStudy_run-01_coordsystem.json', # noqa: E501
'sub-001/eeg/sub-001_task-AudioCueWalkingStudy_run-01_channels.tsv', # noqa: E501

'sub-002/eeg/sub-002_task-AudioCueWalkingStudy_run-01_events.tsv', # noqa: E501
'sub-002/eeg/sub-002_task-AudioCueWalkingStudy_run-01_eeg.set', # noqa: E501
'sub-002/eeg/sub-002_task-AudioCueWalkingStudy_run-01_eeg.fdt', # noqa: E501
'sub-002/eeg/sub-002_task-AudioCueWalkingStudy_run-01_eeg.json', # noqa: E501
'sub-002/eeg/sub-002_task-AudioCueWalkingStudy_run-01_electrodes.tsv', # noqa: E501
'sub-002/eeg/sub-002_task-AudioCueWalkingStudy_run-01_coordsystem.json', # noqa: E501
'sub-002/eeg/sub-002_task-AudioCueWalkingStudy_run-01_channels.tsv', # noqa: E501

'sub-002/eeg/sub-002_task-AudioCueWalkingStudy_run-02_events.tsv', # noqa: E501
'sub-002/eeg/sub-002_task-AudioCueWalkingStudy_run-02_eeg.set', # noqa: E501
'sub-002/eeg/sub-002_task-AudioCueWalkingStudy_run-02_eeg.fdt', # noqa: E501
'sub-002/eeg/sub-002_task-AudioCueWalkingStudy_run-02_eeg.json', # noqa: E501
'sub-002/eeg/sub-002_task-AudioCueWalkingStudy_run-02_electrodes.tsv', # noqa: E501
'sub-002/eeg/sub-002_task-AudioCueWalkingStudy_run-02_coordsystem.json', # noqa: E501
'sub-002/eeg/sub-002_task-AudioCueWalkingStudy_run-02_channels.tsv', # noqa: E501 ],
],
}
if dataset is None:
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