allow missing sessions

mne_bids_pipeline/_config.py

@@ -79,6 +79,12 @@
 BIDS dataset.
 """
 
+allow_missing_sessions: bool = False
+"""
+Whether to continue processing the dataset if some combinations of `subjects` and
+`sessions` are missing.
+"""
+
 task: str = ""
 """
 The task to process.

mne_bids_pipeline/_config_utils.py

@@ -132,6 +132,31 @@ def get_sessions(config: SimpleNamespace) -> list[None] | list[str]:
         return sessions
 
 
+def get_subjects_sessions(config: SimpleNamespace) -> dict[str, list[str]]:
+    subj_sessions = dict()
+    all_sessions = _get_entity_vals_cached(
+        config.bids_root,
+        entity_key="session",
+        ignore_datatypes=_get_ignore_datatypes(config),
+    )
+    for subject in get_subjects(config):
+        # Only traverse through the current subject's directory
+        valid_sessions_subj = _get_entity_vals_cached(
+            config.bids_root / f"sub-{subject}",
+            entity_key="session",
+            ignore_datatypes=_get_ignore_datatypes(config),
+        )
+        missing_sessions = set(all_sessions) - set(valid_sessions_subj)
+        if missing_sessions and not config.allow_missing_sessions:
+            raise RuntimeError(
+                f"Subject {subject} is missing session{_pl(missing_sessions)} "
+                f"{tuple(sorted(missing_sessions))}, and "
+                "`config.allow_missing_sessions` is False"
+            )
+        subj_sessions[subject] = valid_sessions_subj
+    return subj_sessions
+
+
 def get_runs_all_subjects(
     config: SimpleNamespace,
 ) -> dict[str, list[None] | list[str]]:

mne_bids_pipeline/steps/init/_01_init_derivatives_dir.py

@@ -9,7 +9,7 @@
 from mne_bids.config import BIDS_VERSION
 from mne_bids.utils import _write_json
 
-from mne_bids_pipeline._config_utils import _bids_kwargs, get_sessions, get_subjects
+from mne_bids_pipeline._config_utils import _bids_kwargs, get_subjects_sessions
 from mne_bids_pipeline._logging import gen_log_kwargs, logger
 from mne_bids_pipeline._run import _prep_out_files, failsafe_run
 
@@ -76,8 +76,8 @@ def main(*, config):
     init_dataset(cfg=get_config(config=config), exec_params=config.exec_params)
     # Don't bother with parallelization here as I/O operations are generally
     # not well parallelized (and this should be very fast anyway)
-    for subject in get_subjects(config):
-        for session in get_sessions(config):
+    for subject, sessions in get_subjects_sessions(config).items():
+        for session in sessions:
             init_subject_dirs(
                 cfg=get_config(
                     config=config,

mne_bids_pipeline/steps/init/_02_find_empty_room.py

@@ -9,8 +9,7 @@
     _pl,
     get_datatype,
     get_mf_reference_run,
-    get_sessions,
-    get_subjects,
+    get_subjects_sessions,
 )
 from mne_bids_pipeline._import_data import _empty_room_match_path
 from mne_bids_pipeline._io import _write_json
@@ -127,8 +126,8 @@ def main(*, config) -> None:
     # This will be I/O bound if the sidecar is not complete, so let's not run
     # in parallel.
     logs = list()
-    for subject in get_subjects(config):
-        for session in get_sessions(config):
+    for subject, sessions in get_subjects_sessions(config).items():
+        for session in sessions:
             run = get_mf_reference_run(config=config)
             logs.append(
                 find_empty_room(

mne_bids_pipeline/steps/preprocessing/_01_data_quality.py

@@ -11,8 +11,7 @@
     get_mf_cal_fname,
     get_mf_ctc_fname,
     get_runs_tasks,
-    get_sessions,
-    get_subjects,
+    get_subjects_sessions,
 )
 from mne_bids_pipeline._import_data import (
     _bads_path,
@@ -349,8 +348,8 @@ def main(*, config: SimpleNamespace) -> None:
                 run=run,
                 task=task,
             )
-            for subject in get_subjects(config)
-            for session in get_sessions(config)
+            for subject, sessions in get_subjects_sessions(config).items()
+            for session in sessions
             for run, task in get_runs_tasks(
                 config=config,
                 subject=subject,

mne_bids_pipeline/steps/preprocessing/_02_head_pos.py

@@ -4,7 +4,7 @@
 
 import mne
 
-from mne_bids_pipeline._config_utils import get_runs_tasks, get_sessions, get_subjects
+from mne_bids_pipeline._config_utils import get_runs_tasks, get_subjects_sessions
 from mne_bids_pipeline._import_data import (
     _get_run_rest_noise_path,
     _import_data_kwargs,
@@ -173,8 +173,8 @@ def main(*, config: SimpleNamespace) -> None:
                 run=run,
                 task=task,
             )
-            for subject in get_subjects(config)
-            for session in get_sessions(config)
+            for subject, sessions in get_subjects_sessions(config).items()
+            for session in sessions
             for run, task in get_runs_tasks(
                 config=config,
                 subject=subject,

mne_bids_pipeline/steps/preprocessing/_03_maxfilter.py

@@ -27,8 +27,7 @@
     get_mf_cal_fname,
     get_mf_ctc_fname,
     get_runs_tasks,
-    get_sessions,
-    get_subjects,
+    get_subjects_sessions,
 )
 from mne_bids_pipeline._import_data import (
     _get_mf_reference_run_path,
@@ -613,8 +612,8 @@ def main(*, config: SimpleNamespace) -> None:
                     subject=subject,
                     session=session,
                 )
-                for subject in get_subjects(config)
-                for session in get_sessions(config)
+                for subject, sessions in get_subjects_sessions(config).items()
+                for session in sessions
             )
 
         # Second: maxwell_filter
@@ -637,8 +636,8 @@ def main(*, config: SimpleNamespace) -> None:
                     run=run,
                     task=task,
                 )
-                for subject in get_subjects(config)
-                for session in get_sessions(config)
+                for subject, sessions in get_subjects_sessions(config).items()
+                for session in sessions
                 for run, task in get_runs_tasks(
                     config=config,
                     subject=subject,

mne_bids_pipeline/steps/preprocessing/_04_frequency_filter.py

@@ -23,7 +23,7 @@
 from mne.io.pick import _picks_to_idx
 from mne.preprocessing import EOGRegression
 
-from mne_bids_pipeline._config_utils import get_runs_tasks, get_sessions, get_subjects
+from mne_bids_pipeline._config_utils import get_runs_tasks, get_subjects_sessions
 from mne_bids_pipeline._import_data import (
     _get_run_rest_noise_path,
     _import_data_kwargs,
@@ -328,8 +328,8 @@ def main(*, config: SimpleNamespace) -> None:
                 run=run,
                 task=task,
             )
-            for subject in get_subjects(config)
-            for session in get_sessions(config)
+            for subject, sessions in get_subjects_sessions(config).items()
+            for session in sessions
             for run, task in get_runs_tasks(
                 config=config,
                 subject=subject,

mne_bids_pipeline/steps/preprocessing/_05_regress_artifact.py

@@ -6,7 +6,7 @@
 from mne.io.pick import _picks_to_idx
 from mne.preprocessing import EOGRegression
 
-from mne_bids_pipeline._config_utils import get_runs_tasks, get_sessions, get_subjects
+from mne_bids_pipeline._config_utils import get_runs_tasks, get_subjects_sessions
 from mne_bids_pipeline._import_data import (
     _get_run_rest_noise_path,
     _import_data_kwargs,
@@ -159,8 +159,8 @@ def main(*, config: SimpleNamespace) -> None:
                 run=run,
                 task=task,
             )
-            for subject in get_subjects(config)
-            for session in get_sessions(config)
+            for subject, sessions in get_subjects_sessions(config).items()
+            for session in sessions
             for run, task in get_runs_tasks(
                 config=config,
                 subject=subject,

mne_bids_pipeline/steps/preprocessing/_06a1_fit_ica.py

@@ -21,8 +21,7 @@
     _bids_kwargs,
     get_eeg_reference,
     get_runs,
-    get_sessions,
-    get_subjects,
+    get_subjects_sessions,
 )
 from mne_bids_pipeline._import_data import annotations_to_events, make_epochs
 from mne_bids_pipeline._logging import gen_log_kwargs, logger
@@ -377,7 +376,7 @@ def main(*, config: SimpleNamespace) -> None:
                 subject=subject,
                 session=session,
             )
-            for subject in get_subjects(config)
-            for session in get_sessions(config)
+            for subject, sessions in get_subjects_sessions(config).items()
+            for session in sessions
         )
     save_logs(config=config, logs=logs)

mne_bids_pipeline/steps/preprocessing/_06a2_find_ica_artifacts.py

@@ -20,8 +20,7 @@
     _bids_kwargs,
     get_eeg_reference,
     get_runs,
-    get_sessions,
-    get_subjects,
+    get_subjects_sessions,
 )
 from mne_bids_pipeline._logging import gen_log_kwargs, logger
 from mne_bids_pipeline._parallel import get_parallel_backend, parallel_func
@@ -394,7 +393,7 @@ def main(*, config: SimpleNamespace) -> None:
                 subject=subject,
                 session=session,
             )
-            for subject in get_subjects(config)
-            for session in get_sessions(config)
+            for subject, sessions in get_subjects_sessions(config).items()
+            for session in sessions
         )
     save_logs(config=config, logs=logs)

mne_bids_pipeline/steps/preprocessing/_06b_run_ssp.py

@@ -17,8 +17,7 @@
     _pl,
     _proj_path,
     get_runs,
-    get_sessions,
-    get_subjects,
+    get_subjects_sessions,
 )
 from mne_bids_pipeline._logging import gen_log_kwargs, logger
 from mne_bids_pipeline._parallel import get_parallel_backend, parallel_func
@@ -279,7 +278,7 @@ def main(*, config: SimpleNamespace) -> None:
                 subject=subject,
                 session=session,
             )
-            for subject in get_subjects(config)
-            for session in get_sessions(config)
+            for subject, sessions in get_subjects_sessions(config).items()
+            for session in sessions
         )
     save_logs(config=config, logs=logs)

mne_bids_pipeline/steps/preprocessing/_07_make_epochs.py

@@ -17,8 +17,7 @@
     _bids_kwargs,
     get_eeg_reference,
     get_runs,
-    get_sessions,
-    get_subjects,
+    get_subjects_sessions,
 )
 from mne_bids_pipeline._import_data import annotations_to_events, make_epochs
 from mne_bids_pipeline._logging import gen_log_kwargs, logger
@@ -355,7 +354,7 @@ def main(*, config) -> None:
                 subject=subject,
                 session=session,
             )
-            for subject in get_subjects(config)
-            for session in get_sessions(config)
+            for subject, sessions in get_subjects_sessions(config).items()
+            for session in sessions
         )
     save_logs(config=config, logs=logs)

mne_bids_pipeline/steps/preprocessing/_08a_apply_ica.py

@@ -12,7 +12,7 @@
 from mne.preprocessing import read_ica
 from mne_bids import BIDSPath
 
-from mne_bids_pipeline._config_utils import get_runs_tasks, get_sessions, get_subjects
+from mne_bids_pipeline._config_utils import get_runs_tasks, get_subjects_sessions
 from mne_bids_pipeline._import_data import _get_run_rest_noise_path, _import_data_kwargs
 from mne_bids_pipeline._logging import gen_log_kwargs, logger
 from mne_bids_pipeline._parallel import get_parallel_backend, parallel_func
@@ -273,8 +273,8 @@ def main(*, config: SimpleNamespace) -> None:
                 subject=subject,
                 session=session,
             )
-            for subject in get_subjects(config)
-            for session in get_sessions(config)
+            for subject, sessions in get_subjects_sessions(config).items()
+            for session in sessions
         )
         # Raw
         parallel, run_func = parallel_func(
@@ -292,8 +292,8 @@ def main(*, config: SimpleNamespace) -> None:
                 run=run,
                 task=task,
             )
-            for subject in get_subjects(config)
-            for session in get_sessions(config)
+            for subject, sessions in get_subjects_sessions(config).items()
+            for session in sessions
             for run, task in get_runs_tasks(
                 config=config,
                 subject=subject,

mne_bids_pipeline/steps/preprocessing/_08b_apply_ssp.py

@@ -11,8 +11,7 @@
 from mne_bids_pipeline._config_utils import (
     _proj_path,
     get_runs_tasks,
-    get_sessions,
-    get_subjects,
+    get_subjects_sessions,
 )
 from mne_bids_pipeline._import_data import _get_run_rest_noise_path, _import_data_kwargs
 from mne_bids_pipeline._logging import gen_log_kwargs, logger
@@ -183,8 +182,8 @@ def main(*, config: SimpleNamespace) -> None:
                 subject=subject,
                 session=session,
             )
-            for subject in get_subjects(config)
-            for session in get_sessions(config)
+            for subject, sessions in get_subjects_sessions(config).items()
+            for session in sessions
         )
         # Raw
         parallel, run_func = parallel_func(
@@ -202,8 +201,8 @@ def main(*, config: SimpleNamespace) -> None:
                 run=run,
                 task=task,
             )
-            for subject in get_subjects(config)
-            for session in get_sessions(config)
+            for subject, sessions in get_subjects_sessions(config).items()
+            for session in sessions
             for run, task in get_runs_tasks(
                 config=config,
                 subject=subject,

mne_bids_pipeline/steps/preprocessing/_09_ptp_reject.py

@@ -15,7 +15,7 @@
 import numpy as np
 from mne_bids import BIDSPath
 
-from mne_bids_pipeline._config_utils import _bids_kwargs, get_sessions, get_subjects
+from mne_bids_pipeline._config_utils import _bids_kwargs, get_subjects_sessions
 from mne_bids_pipeline._logging import gen_log_kwargs, logger
 from mne_bids_pipeline._parallel import get_parallel_backend, parallel_func
 from mne_bids_pipeline._reject import _get_reject
@@ -275,7 +275,7 @@ def main(*, config: SimpleNamespace) -> None:
                 subject=subject,
                 session=session,
             )
-            for subject in get_subjects(config)
-            for session in get_sessions(config)
+            for subject, sessions in get_subjects_sessions(config).items()
+            for session in sessions
         )
     save_logs(config=config, logs=logs)

mne_bids_pipeline/steps/sensor/_01_make_evoked.py

@@ -11,8 +11,7 @@
     _restrict_analyze_channels,
     get_all_contrasts,
     get_eeg_reference,
-    get_sessions,
-    get_subjects,
+    get_subjects_sessions,
 )
 from mne_bids_pipeline._logging import gen_log_kwargs, logger
 from mne_bids_pipeline._parallel import get_parallel_backend, parallel_func
@@ -198,7 +197,7 @@ def main(*, config: SimpleNamespace) -> None:
                 subject=subject,
                 session=session,
             )
-            for subject in get_subjects(config)
-            for session in get_sessions(config)
+            for subject, sessions in get_subjects_sessions(config).items()
+            for session in sessions
         )
     save_logs(config=config, logs=logs)