Merge pull request #115 from Remi-Gau/group

[ENH] add group level QA plot and table

Author: Remi-Gau

bidsmreye/bids_utils.py

@@ -218,10 +218,10 @@ def list_subjects(cfg: Config, layout: BIDSLayout) -> list[str]:
     :return: _description_
     :rtype: list
     """
-    subjects = layout.get(return_type="id", target="subject", subject=cfg.participant)
+    subjects = layout.get(return_type="id", target="subject", subject=cfg.subjects)
 
     if subjects == [] or subjects is None:
-        raise RuntimeError("No subject found")
+        raise RuntimeError(f"No subject found in layout:\n\t{layout.root}")
 
     if cfg.debug:
         subjects = [subjects[0]]

bidsmreye/bidsmreye.py

@@ -13,6 +13,7 @@
 
 from . import _version
 from bidsmreye.configuration import Config
+from bidsmreye.defaults import allowed_actions
 from bidsmreye.defaults import available_models
 from bidsmreye.defaults import default_log_level
 from bidsmreye.defaults import default_model
@@ -22,6 +23,7 @@
 from bidsmreye.logging import bidsmreye_log
 from bidsmreye.prepare_data import prepare_data
 from bidsmreye.quality_control import quality_control_input
+from bidsmreye.visualize import group_report
 
 __version__ = _version.get_versions()["version"]
 
@@ -92,7 +94,7 @@ def bidsmreye(
     cfg = Config(
         bids_dir,
         output_dir,
-        participant=participant_label or None,
+        subjects=participant_label or None,
         space=space or None,
         task=task or None,
         run=run or None,
@@ -121,23 +123,29 @@ def bidsmreye(
     if action in {"all", "generalize"} and isinstance(cfg.model_weights_file, str):
         cfg.model_weights_file = download(cfg.model_weights_file)
 
-    if analysis_level == "participant":
+    dispatch(analysis_level=analysis_level, action=action, cfg=cfg)
 
+
+def dispatch(analysis_level: str, action: str, cfg: Config) -> None:
+    if analysis_level == "group":
+        if action == "qc":
+            group_report(cfg=cfg)
+        else:
+            log.error("Unknown group level action")
+            sys.exit(1)
+
+    elif analysis_level == "participant":
         if action == "all":
             prepare_data(cfg)
             generalize(cfg)
-
         elif action == "prepare":
             prepare_data(cfg)
-
         elif action == "generalize":
             generalize(cfg)
-
         elif action == "qc":
             quality_control_input(cfg)
-
         else:
-            log.error("Unknown action")
+            log.error("Unknown participant level action")
             sys.exit(1)
 
 
@@ -175,15 +183,15 @@ def common_parser() -> MuhParser:
         Multiple participant level analyses can be run independently (in parallel)
         using the same output_dir.
         """,
-        choices=["participant"],
+        choices=["participant", "group"],
         default="participant",
     )
     parser.add_argument(
         "--action",
         help="""
         What action to perform.
         """,
-        choices=["all", "prepare", "generalize", "qc"],
+        choices=allowed_actions(),
         default="all",
     )
     parser.add_argument(

bidsmreye/config/default_filter_file.json

@@ -16,5 +16,9 @@
     "eyetrack": {
         "suffix": "^eyetrack$$",
         "extension": "tsv"
+    },
+    "eyetrack_qc": {
+        "suffix": "^eyetrack$$",
+        "extension": "json"
     }
 }

bidsmreye/configuration.py

@@ -46,7 +46,7 @@ def _check_input_dir(self, attribute: str, value: Path) -> None:
 
     output_dir: Path = field(default=None, converter=Path)
 
-    participant: Any | None = field(kw_only=True, default=None)
+    subjects: Any | None = field(kw_only=True, default=None)
 
     space: Any | None = field(kw_only=True, default=None)
     task: Any | None = field(kw_only=True, default=None)
@@ -101,7 +101,7 @@ def __attrs_post_init__(self) -> None:
         if not database_path.is_dir():
             layout_in.save(database_path)
 
-        self.check_argument(attribute="participant", layout_in=layout_in)
+        self.check_argument(attribute="subjects", layout_in=layout_in)
         self.check_argument(attribute="task", layout_in=layout_in)
         self.check_argument(attribute="run", layout_in=layout_in)
         self.check_argument(attribute="space", layout_in=layout_in)
@@ -120,7 +120,7 @@ def check_argument(self, attribute: str, layout_in: BIDSLayout) -> Config:
         :return:
         :rtype: Config
         """
-        if attribute == "participant":
+        if attribute == "subjects":
             value = layout_in.get_subjects()
         elif attribute == "task":
             value = layout_in.get_tasks()

bidsmreye/defaults.py

@@ -2,6 +2,11 @@
 from __future__ import annotations
 
 
+def allowed_actions() -> list[str]:
+    """Return a list of allowed actions."""
+    return ["all", "prepare", "generalize", "qc"]
+
+
 def default_log_level() -> str:
     """Return default log level."""
     return "WARNING"

bidsmreye/generalize.py

@@ -24,6 +24,7 @@
 from bidsmreye.logging import bidsmreye_log
 from bidsmreye.quality_control import quality_control_output
 from bidsmreye.utils import add_sidecar_in_root
+from bidsmreye.utils import check_if_file_found
 from bidsmreye.utils import create_dir_for_file
 from bidsmreye.utils import move_file
 from bidsmreye.utils import set_this_filter
@@ -160,11 +161,7 @@ def process_subject(cfg: Config, layout_out: BIDSLayout, subject_label: str) ->
         **this_filter,
     )
 
-    if len(bf) == 0:
-        log.warning(f"No file found for subject {subject_label}")
-    else:
-        to_print = [str(Path(x).relative_to(layout_out.root)) for x in bf]
-        log.debug(f"Found files\n{to_print}")
+    check_if_file_found(bf, this_filter, layout_out)
 
     for file in bf:
 

bidsmreye/prepare_data.py

@@ -18,6 +18,7 @@
 from bidsmreye.bids_utils import list_subjects
 from bidsmreye.configuration import Config
 from bidsmreye.logging import bidsmreye_log
+from bidsmreye.utils import check_if_file_found
 from bidsmreye.utils import get_deepmreye_filename
 from bidsmreye.utils import move_file
 from bidsmreye.utils import set_this_filter
@@ -133,11 +134,7 @@ def process_subject(
         **this_filter,
     )
 
-    if len(bf) == 0:
-        log.warning(f"No file found for subject {subject_label}")
-    else:
-        to_print = [str(Path(x).relative_to(layout_in.root)) for x in bf]
-        log.debug(f"Found files\n{to_print}")
+    check_if_file_found(bf, this_filter, layout_in)
 
     for img in bf:
 

bidsmreye/quality_control.py

@@ -18,6 +18,7 @@
 from bidsmreye.bids_utils import list_subjects
 from bidsmreye.configuration import Config
 from bidsmreye.logging import bidsmreye_log
+from bidsmreye.utils import check_if_file_found
 from bidsmreye.utils import create_dir_for_file
 from bidsmreye.utils import set_this_filter
 from bidsmreye.visualize import visualize_eye_gaze_data
@@ -204,11 +205,7 @@ def qc_subject(
         **this_filter,
     )
 
-    if len(bf) == 0:
-        log.warning(f"No file found for subject {subject_label}")
-    else:
-        to_print = [str(Path(x).relative_to(layout_in.root)) for x in bf]
-        log.debug(f"Found files\n{to_print}")
+    check_if_file_found(bf, this_filter, layout_in)
 
     for file in bf:
 

bidsmreye/utils.py

@@ -45,12 +45,22 @@ def add_sidecar_in_root(layout_out: BIDSLayout) -> None:
     json.dump(content, open(sidecar_name, "w"), indent=4)
 
 
-def set_this_filter(cfg: Config, subject_label: str, filter_type: str) -> dict[str, Any]:
+def check_if_file_found(bf: Any, this_filter: dict[str, Any], layout: BIDSLayout) -> None:
+    if len(bf) == 0:
+        log.warning(f"No file found for filter {this_filter}")
+    else:
+        to_print = [str(Path(x).relative_to(layout.root)) for x in bf]
+        log.debug(f"Found files\n{to_print}")
+
+
+def set_this_filter(
+    cfg: Config, subject_label: str | list[str], filter_type: str
+) -> dict[str, Any]:
 
     this_filter = cfg.bids_filter[filter_type]
     this_filter["suffix"] = return_regex(this_filter["suffix"])
     this_filter["task"] = return_regex(cfg.task)
-    if filter_type not in ("eyetrack"):
+    if filter_type not in ("eyetrack", "eyetrack_qc"):
         this_filter["space"] = return_regex(cfg.space)
     this_filter["subject"] = subject_label
     if cfg.run: