refactor: make parcellation accept str or list of str across codebase

synchon · synchon · commit 58312708ce95 · 2025-11-27T11:06:13.000+01:00
diff --git a/docs/extending/masks.rst b/docs/extending/masks.rst
@@ -86,7 +86,7 @@ mask as an argument. For example:
   markers:
     - name: CustomMaskParcelAggregation_mean
       kind: ParcelAggregation
-      parcellation: [Schaefer200x17]
+      parcellation: Schaefer200x17
       method: mean
       masks: "my_custom_mask"
 
diff --git a/docs/extending/parcellations.rst b/docs/extending/parcellations.rst
@@ -124,7 +124,7 @@ parcellation when registering it. For example, we can add a
   markers:
     - name: CustomParcellation_mean
       kind: ParcelAggregation
-      parcellation: [<my_custom_parcellation>]
+      parcellation: <my_custom_parcellation>
       method: mean
 
 Now, you can simply use this YAML file to run your pipeline.
diff --git a/docs/using/codeless.rst b/docs/using/codeless.rst
@@ -171,11 +171,11 @@ For the ``Oasis VBM Testing dataset`` example, we want to compute the mean
   markers:
     - name: Schaefer100x7_mean
       kind: ParcelAggregation
-      parcellation: [Schaefer100x7]
+      parcellation: Schaefer100x7
       method: mean
     - name: Schaefer200x7_mean
       kind: ParcelAggregation
-      parcellation: [Schaefer200x7]
+      parcellation: Schaefer200x7
       method: mean
     - name: DMNBuckner_5mm_mean
       kind: SphereAggregation
@@ -219,11 +219,11 @@ looks like:
   markers:
     - name: Schaefer100x7_mean
       kind: ParcelAggregation
-      parcellation: [Schaefer100x7]
+      parcellation: Schaefer100x7
       method: mean
     - name: Schaefer200x7_mean
       kind: ParcelAggregation
-      parcellation: [Schaefer200x7]
+      parcellation: Schaefer200x7
       method: mean
     - name: DMNBuckner_5mm_mean
       kind: SphereAggregation
diff --git a/examples/run_compute_parcel_mean.py b/examples/run_compute_parcel_mean.py
@@ -35,7 +35,7 @@
     element_data = DefaultDataReader().fit_transform(dg[element])
     # Initialize marker
     marker = ParcelAggregation(
-        parcellation=["Schaefer100x7"],
+        parcellation="Schaefer100x7",
         method=AggFunc.Mean,
     )
     # Compute feature
@@ -53,7 +53,7 @@
     element_data = DefaultDataReader().fit_transform(dg[element])
     # Initialize marker
     marker = ParcelAggregation(
-        parcellation=["Schaefer100x7"],
+        parcellation="Schaefer100x7",
         method=AggFunc.Mean,
         on=[DataType.BOLD],
     )
diff --git a/examples/run_ets_rss_marker.py b/examples/run_ets_rss_marker.py
@@ -36,12 +36,12 @@
     {
         "name": "Schaefer100x17_RSSETS",
         "kind": "RSSETSMarker",
-        "parcellation": ["Schaefer100x17"],
+        "parcellation": "Schaefer100x17",
     },
     {
         "name": "Schaefer200x17_RSSETS",
         "kind": "RSSETSMarker",
-        "parcellation": ["Schaefer200x17"],
+        "parcellation": "Schaefer200x17",
     },
 ]
 
diff --git a/examples/run_junifer_julearn.py b/examples/run_junifer_julearn.py
@@ -36,14 +36,14 @@
     {
         "name": "Schaefer100x17_TrimMean80",
         "kind": "ParcelAggregation",
-        "parcellation": ["Schaefer100x17"],
+        "parcellation": "Schaefer100x17",
         "method": "trim_mean",
         "method_params": {"proportiontocut": 0.2},
     },
     {
         "name": "Schaefer200x17_Mean",
         "kind": "ParcelAggregation",
-        "parcellation": ["Schaefer200x17"],
+        "parcellation": "Schaefer200x17",
         "method": "mean",
     },
 ]
diff --git a/examples/run_run_gmd_mean.py b/examples/run_run_gmd_mean.py
@@ -20,20 +20,20 @@
     {
         "name": "Schaefer1000x7_TrimMean80",
         "kind": "ParcelAggregation",
-        "parcellation": ["Schaefer1000x7"],
+        "parcellation": "Schaefer1000x7",
         "method": "trim_mean",
         "method_params": {"proportiontocut": 0.2},
     },
     {
         "name": "Schaefer1000x7_Mean",
         "kind": "ParcelAggregation",
-        "parcellation": ["Schaefer1000x7"],
+        "parcellation": "Schaefer1000x7",
         "method": "mean",
     },
     {
         "name": "Schaefer1000x7_Std",
         "kind": "ParcelAggregation",
-        "parcellation": ["Schaefer1000x7"],
+        "parcellation": "Schaefer1000x7",
         "method": "std",
     },
 ]
diff --git a/examples/yamls/gmd_mean.yaml b/examples/yamls/gmd_mean.yaml
@@ -7,17 +7,17 @@ elements:
 markers:
   - name: Schaefer1000x7_TrimMean80
     kind: ParcelAggregation
-    parcellation: [Schaefer1000x7]
+    parcellation: Schaefer1000x7
     method: trim_mean
     method_params:
       proportiontocut: 0.2
   - name: Schaefer1000x7_Mean
     kind: ParcelAggregation
-    parcellation: [Schaefer1000x7]
+    parcellation: Schaefer1000x7
     method: mean
   - name: Schaefer1000x7_Std
     kind: ParcelAggregation
-    parcellation: [Schaefer1000x7]
+    parcellation: Schaefer1000x7
     method: std
 storage:
   kind: SQLiteFeatureStorage
diff --git a/examples/yamls/gmd_mean_htcondor.yaml b/examples/yamls/gmd_mean_htcondor.yaml
@@ -6,7 +6,7 @@ datagrabber:
 markers:
   - name: Schaefer1000x7_Mean
     kind: ParcelAggregation
-    parcellation: [Schaefer1000x7]
+    parcellation: Schaefer1000x7
     method: mean
 storage:
   kind: SQLiteFeatureStorage
diff --git a/examples/yamls/partly_cloudy_agg_mean_tian.yml b/examples/yamls/partly_cloudy_agg_mean_tian.yml
@@ -7,7 +7,7 @@ datagrabber:
 
 markers:
   - kind: ParcelAggregation
-    parcellation: [TianxS1x3TxMNInonlinear2009cAsym]
+    parcellation: TianxS1x3TxMNInonlinear2009cAsym
     method: mean
     name: tian-s1-3T_mean
 
diff --git a/examples/yamls/ukb_gmd_mean.yaml b/examples/yamls/ukb_gmd_mean.yaml
@@ -7,17 +7,17 @@ elements:
 markers:
   - name: Schaefer1000x7_TrimMean80
     kind: ParcelAggregation
-    parcellation: [Schaefer1000x7]
+    parcellation: Schaefer1000x7
     method: trim_mean
     method_params:
       proportiontocut: 0.2
   - name: Schaefer1000x7_Mean
     kind: ParcelAggregation
-    parcellation: [Schaefer1000x7]
+    parcellation: Schaefer1000x7
     method: mean
   - name: Schaefer1000x7_Std
     kind: ParcelAggregation
-    parcellation: [Schaefer1000x7]
+    parcellation: Schaefer1000x7
     method: std
 storage:
   kind: SQLiteFeatureStorage
diff --git a/junifer/api/tests/test_functions.py b/junifer/api/tests/test_functions.py
@@ -68,13 +68,13 @@ def markers() -> list[dict[str, Union[list[str], str]]]:
         {
             "name": "tian-s1-3T_mean",
             "kind": "ParcelAggregation",
-            "parcellation": ["TianxS1x3TxMNInonlinear2009cAsym"],
+            "parcellation": "TianxS1x3TxMNInonlinear2009cAsym",
             "method": "mean",
         },
         {
             "name": "tian-s1-3T_std",
             "kind": "ParcelAggregation",
-            "parcellation": ["TianxS1x3TxMNInonlinear2009cAsym"],
+            "parcellation": "TianxS1x3TxMNInonlinear2009cAsym",
             "method": "std",
         },
     ]
diff --git a/junifer/cli/tests/data/gmd_mean.yaml b/junifer/cli/tests/data/gmd_mean.yaml
@@ -7,7 +7,7 @@ elements: [1, 2]
 markers:
   - name: Schaefer1000x7_Mean
     kind: ParcelAggregation
-    parcellation: [Schaefer1000x7]
+    parcellation: Schaefer1000x7
     method: mean
 storage:
   kind: SQLiteFeatureStorage
diff --git a/junifer/cli/tests/data/gmd_mean_htcondor.yaml b/junifer/cli/tests/data/gmd_mean_htcondor.yaml
@@ -6,7 +6,7 @@ datagrabber:
 markers:
   - name: Schaefer1000x7_Mean
     kind: ParcelAggregation
-    parcellation: [Schaefer1000x7]
+    parcellation: Schaefer1000x7
     method: mean
 storage:
   kind: SQLiteFeatureStorage
diff --git a/junifer/cli/tests/data/partly_cloudy_agg_mean_tian.yml b/junifer/cli/tests/data/partly_cloudy_agg_mean_tian.yml
@@ -7,7 +7,7 @@ datagrabber:
 
 markers:
   - kind: ParcelAggregation
-    parcellation: [TianxS1x3TxMNInonlinear2009cAsym]
+    parcellation: TianxS1x3TxMNInonlinear2009cAsym
     method: mean
     name: tian-s1-3T_mean
 
diff --git a/junifer/markers/complexity/complexity_base.py b/junifer/markers/complexity/complexity_base.py
@@ -7,19 +7,23 @@
 from abc import abstractmethod
 from typing import (
     TYPE_CHECKING,
+    Annotated,
     Any,
     ClassVar,
     Literal,
     Optional,
     Union,
 )
 
+from pydantic import BeforeValidator
+
 from ...datagrabber import DataType
 from ...storage import StorageType
 from ...typing import Dependencies, MarkerInOutMappings
 from ...utils import raise_error
 from ..base import BaseMarker
 from ..parcel_aggregation import ParcelAggregation
+from ..utils import _ensure_list
 
 
 if TYPE_CHECKING:
@@ -34,7 +38,7 @@ class ComplexityBase(BaseMarker):
 
     Parameters
     ----------
-    parcellation : list of str
+    parcellation : str or list of str
         The name(s) of the parcellation(s) to use.
         See :func:`.list_data` for options.
     agg_method : str, optional
@@ -62,7 +66,9 @@ class ComplexityBase(BaseMarker):
         },
     }
 
-    parcellation: list[str]
+    parcellation: Annotated[
+        Union[str, list[str]], BeforeValidator(_ensure_list)
+    ]
     agg_method: str = "mean"
     agg_method_params: Optional[dict] = None
     masks: Optional[list[Union[dict, str]]] = None
diff --git a/junifer/markers/complexity/hurst_exponent.py b/junifer/markers/complexity/hurst_exponent.py
@@ -25,7 +25,7 @@ class HurstExponent(ComplexityBase):
 
     Parameters
     ----------
-    parcellation : list of str
+    parcellation : str or list of str
         The name(s) of the parcellation(s) to use.
         See :func:`.list_data` for options.
     agg_method : str, optional
diff --git a/junifer/markers/complexity/multiscale_entropy_auc.py b/junifer/markers/complexity/multiscale_entropy_auc.py
@@ -25,7 +25,7 @@ class MultiscaleEntropyAUC(ComplexityBase):
 
     Parameters
     ----------
-    parcellation : list of str
+    parcellation : str or list of str
         The name(s) of the parcellation(s) to use.
         See :func:`.list_data` for options.
     agg_method : str, optional
diff --git a/junifer/markers/complexity/perm_entropy.py b/junifer/markers/complexity/perm_entropy.py
@@ -25,7 +25,7 @@ class PermEntropy(ComplexityBase):
 
     Parameters
     ----------
-    parcellation : list of str
+    parcellation : str or list of str
         The name(s) of the parcellation(s) to use.
         See :func:`.list_data` for options.
     agg_method : str, optional
diff --git a/junifer/markers/complexity/range_entropy.py b/junifer/markers/complexity/range_entropy.py
@@ -25,7 +25,7 @@ class RangeEntropy(ComplexityBase):
 
     Parameters
     ----------
-    parcellation : list of str
+    parcellation : str or list of str
         The name(s) of the parcellation(s) to use.
         See :func:`.list_data` for options.
     agg_method : str, optional
diff --git a/junifer/markers/complexity/range_entropy_auc.py b/junifer/markers/complexity/range_entropy_auc.py
@@ -25,7 +25,7 @@ class RangeEntropyAUC(ComplexityBase):
 
     Parameters
     ----------
-    parcellation : list of str
+    parcellation : str or list of str
         The name(s) of the parcellation(s) to use.
         See :func:`.list_data` for options.
     agg_method : str, optional
diff --git a/junifer/markers/complexity/sample_entropy.py b/junifer/markers/complexity/sample_entropy.py
@@ -25,7 +25,7 @@ class SampleEntropy(ComplexityBase):
 
     Parameters
     ----------
-    parcellation : list of str
+    parcellation : str or list of str
         The name(s) of the parcellation(s) to use.
         See :func:`.list_data` for options.
     agg_method : str, optional
diff --git a/junifer/markers/complexity/tests/test_hurst_exponent.py b/junifer/markers/complexity/tests/test_hurst_exponent.py
@@ -23,7 +23,7 @@
 
 
 # Set parcellation
-PARCELLATION = ["Schaefer100x17"]
+PARCELLATION = "Schaefer100x17"
 
 
 @pytest.mark.skipif(
diff --git a/junifer/markers/complexity/tests/test_multiscale_entropy_auc.py b/junifer/markers/complexity/tests/test_multiscale_entropy_auc.py
@@ -22,7 +22,7 @@
 
 
 # Set parcellation
-PARCELLATION = ["Schaefer100x17"]
+PARCELLATION = "Schaefer100x17"
 
 
 @pytest.mark.skipif(
diff --git a/junifer/markers/complexity/tests/test_perm_entropy.py b/junifer/markers/complexity/tests/test_perm_entropy.py
@@ -22,7 +22,7 @@
 
 
 # Set parcellation
-PARCELLATION = ["Schaefer100x17"]
+PARCELLATION = "Schaefer100x17"
 
 
 @pytest.mark.skipif(
diff --git a/junifer/markers/complexity/tests/test_range_entropy.py b/junifer/markers/complexity/tests/test_range_entropy.py
@@ -23,7 +23,7 @@
 
 
 # Set parcellation
-PARCELLATION = ["Schaefer100x17"]
+PARCELLATION = "Schaefer100x17"
 
 
 @pytest.mark.skipif(
diff --git a/junifer/markers/complexity/tests/test_range_entropy_auc.py b/junifer/markers/complexity/tests/test_range_entropy_auc.py
@@ -23,7 +23,7 @@
 
 
 # Set parcellation
-PARCELLATION = ["Schaefer100x17"]
+PARCELLATION = "Schaefer100x17"
 
 
 @pytest.mark.skipif(
diff --git a/junifer/markers/complexity/tests/test_sample_entropy.py b/junifer/markers/complexity/tests/test_sample_entropy.py
@@ -22,7 +22,7 @@
 
 
 # Set parcellation
-PARCELLATION = ["Schaefer100x17"]
+PARCELLATION = "Schaefer100x17"
 
 
 @pytest.mark.skipif(
diff --git a/junifer/markers/complexity/tests/test_weighted_perm_entropy.py b/junifer/markers/complexity/tests/test_weighted_perm_entropy.py
@@ -22,7 +22,7 @@
 
 
 # Set parcellation
-PARCELLATION = ["Schaefer100x17"]
+PARCELLATION = "Schaefer100x17"
 
 
 @pytest.mark.skipif(
diff --git a/junifer/markers/complexity/weighted_perm_entropy.py b/junifer/markers/complexity/weighted_perm_entropy.py
@@ -25,7 +25,7 @@ class WeightedPermEntropy(ComplexityBase):
 
     Parameters
     ----------
-    parcellation : list of str
+    parcellation : str or list of str
         The name(s) of the parcellation(s) to use.
         See :func:`.list_data` for options.
     agg_method : str, optional
diff --git a/junifer/markers/ets_rss.py b/junifer/markers/ets_rss.py
diff --git a/junifer/markers/falff/falff_parcels.py b/junifer/markers/falff/falff_parcels.py
diff --git a/junifer/markers/falff/tests/test_falff_parcels.py b/junifer/markers/falff/tests/test_falff_parcels.py
diff --git a/junifer/markers/functional_connectivity/edge_functional_connectivity_parcels.py b/junifer/markers/functional_connectivity/edge_functional_connectivity_parcels.py
diff --git a/junifer/markers/functional_connectivity/functional_connectivity_parcels.py b/junifer/markers/functional_connectivity/functional_connectivity_parcels.py
diff --git a/junifer/markers/functional_connectivity/tests/test_edge_functional_connectivity_parcels.py b/junifer/markers/functional_connectivity/tests/test_edge_functional_connectivity_parcels.py
diff --git a/junifer/markers/functional_connectivity/tests/test_functional_connectivity_parcels.py b/junifer/markers/functional_connectivity/tests/test_functional_connectivity_parcels.py
diff --git a/junifer/markers/parcel_aggregation.py b/junifer/markers/parcel_aggregation.py
diff --git a/junifer/markers/reho/reho_parcels.py b/junifer/markers/reho/reho_parcels.py
diff --git a/junifer/markers/reho/tests/test_reho_parcels.py b/junifer/markers/reho/tests/test_reho_parcels.py
diff --git a/junifer/markers/temporal_snr/temporal_snr_parcels.py b/junifer/markers/temporal_snr/temporal_snr_parcels.py
diff --git a/junifer/markers/temporal_snr/tests/test_temporal_snr_parcels.py b/junifer/markers/temporal_snr/tests/test_temporal_snr_parcels.py
diff --git a/junifer/markers/tests/test_ets_rss.py b/junifer/markers/tests/test_ets_rss.py
diff --git a/junifer/markers/tests/test_parcel_aggregation.py b/junifer/markers/tests/test_parcel_aggregation.py
diff --git a/junifer/pipeline/tests/test_marker_collection.py b/junifer/pipeline/tests/test_marker_collection.py

Original file line number	Diff line number	Diff line change
`@@ -36,12 +36,12 @@`
`36`	`36`	`{`
`37`	`37`	`"name": "Schaefer100x17_RSSETS",`
`38`	`38`	`"kind": "RSSETSMarker",`
`39`		`- "parcellation": ["Schaefer100x17"],`
	`39`	`+ "parcellation": "Schaefer100x17",`
`40`	`40`	`},`
`41`	`41`	`{`
`42`	`42`	`"name": "Schaefer200x17_RSSETS",`
`43`	`43`	`"kind": "RSSETSMarker",`
`44`		`- "parcellation": ["Schaefer200x17"],`
	`44`	`+ "parcellation": "Schaefer200x17",`
`45`	`45`	`},`
`46`	`46`	`]`
`47`	`47`
Original file line number	Diff line number	Diff line change
`@@ -36,14 +36,14 @@`
`36`	`36`	`{`
`37`	`37`	`"name": "Schaefer100x17_TrimMean80",`
`38`	`38`	`"kind": "ParcelAggregation",`
`39`		`- "parcellation": ["Schaefer100x17"],`
	`39`	`+ "parcellation": "Schaefer100x17",`
`40`	`40`	`"method": "trim_mean",`
`41`	`41`	`"method_params": {"proportiontocut": 0.2},`
`42`	`42`	`},`
`43`	`43`	`{`
`44`	`44`	`"name": "Schaefer200x17_Mean",`
`45`	`45`	`"kind": "ParcelAggregation",`
`46`		`- "parcellation": ["Schaefer200x17"],`
	`46`	`+ "parcellation": "Schaefer200x17",`
`47`	`47`	`"method": "mean",`
`48`	`48`	`},`
`49`	`49`	`]`
Original file line number	Diff line number	Diff line change
`@@ -20,20 +20,20 @@`
`20`	`20`	`{`
`21`	`21`	`"name": "Schaefer1000x7_TrimMean80",`
`22`	`22`	`"kind": "ParcelAggregation",`
`23`		`- "parcellation": ["Schaefer1000x7"],`
	`23`	`+ "parcellation": "Schaefer1000x7",`
`24`	`24`	`"method": "trim_mean",`
`25`	`25`	`"method_params": {"proportiontocut": 0.2},`
`26`	`26`	`},`
`27`	`27`	`{`
`28`	`28`	`"name": "Schaefer1000x7_Mean",`
`29`	`29`	`"kind": "ParcelAggregation",`
`30`		`- "parcellation": ["Schaefer1000x7"],`
	`30`	`+ "parcellation": "Schaefer1000x7",`
`31`	`31`	`"method": "mean",`
`32`	`32`	`},`
`33`	`33`	`{`
`34`	`34`	`"name": "Schaefer1000x7_Std",`
`35`	`35`	`"kind": "ParcelAggregation",`
`36`		`- "parcellation": ["Schaefer1000x7"],`
	`36`	`+ "parcellation": "Schaefer1000x7",`
`37`	`37`	`"method": "std",`
`38`	`38`	`},`
`39`	`39`	`]`