docs/changes/newsfragments/477.enh

@@ -0,0 +1 @@
+Improve ``Marker`` interface and implementations by `Synchon Mandal`_

junifer/markers/base.py

@@ -6,10 +6,10 @@
 
 from abc import ABC, abstractmethod
 from copy import deepcopy
-from typing import Any, Optional, Union
+from typing import Any, ClassVar, Optional, Union
 
 from ..pipeline import PipelineStepMixin, UpdateMetaMixin
-from ..typing import StorageLike
+from ..typing import MarkerInOutMappings, StorageLike
 from ..utils import logger, raise_error
 
 
@@ -17,9 +17,9 @@ __all__ = ["BaseMarker"]
 
 
 class BaseMarker(ABC, PipelineStepMixin, UpdateMetaMixin):
-    """Abstract base class for all markers.
+    """Abstract base class for marker.
 
-    For every interface that is required, one needs to provide a concrete
+    For every marker, one needs to provide a concrete
     implementation of this abstract class.
 
     Parameters
@@ -34,12 +34,14 @@ class BaseMarker(ABC, PipelineStepMixin, UpdateMetaMixin):
     Raises
     ------
     AttributeError
-        If the marker does not have `_MARKER_INOUT_MAPPINGS` attribute.
+        If the marker does not have ``_MARKER_INOUT_MAPPINGS`` attribute.
     ValueError
         If required input data type(s) is(are) not found.
 
     """
 
+    _MARKER_INOUT_MAPPINGS: ClassVar[MarkerInOutMappings]
+
     def __init__(
         self,
         on: Optional[Union[list[str], str]] = None,
@@ -105,8 +107,8 @@ class BaseMarker(ABC, PipelineStepMixin, UpdateMetaMixin):
         """
         return list(self._MARKER_INOUT_MAPPINGS.keys())
 
-    def get_output_type(self, input_type: str, output_feature: str) -> str:
+    def storage_type(self, input_type: str, output_feature: str) -> str:
-        """Get output type.
+        """Get storage type for a feature.
 
         Parameters
         ----------
@@ -172,7 +174,7 @@ class BaseMarker(ABC, PipelineStepMixin, UpdateMetaMixin):
             The storage class, for example, SQLiteFeatureStorage.
 
         """
-        output_type_ = self.get_output_type(type_, feature)
+        output_type_ = self.storage_type(type_, feature)
         logger.debug(f"Storing {output_type_} in {storage}")
         storage.store(kind=output_type_, **out)
 

junifer/markers/complexity/tests/test_hurst_exponent.py

@@ -43,11 +43,11 @@ def test_compute() -> None:
         assert feature_map["BOLD"]["complexity"]["data"].ndim == 2
 
 
-def test_get_output_type() -> None:
+def test_storage_type() -> None:
-    """Test HurstExponent get_output_type()."""
+    """Test HurstExponent storage_type."""
-    assert "vector" == HurstExponent(
+    assert "vector" == HurstExponent(parcellation=PARCELLATION).storage_type(
-        parcellation=PARCELLATION
+        input_type="BOLD", output_feature="complexity"
-    ).get_output_type(input_type="BOLD", output_feature="complexity")
+    )
 
 
 @pytest.mark.skipif(

junifer/markers/complexity/tests/test_multiscale_entropy_auc.py

@@ -42,11 +42,11 @@ def test_compute() -> None:
         assert feature_map["BOLD"]["complexity"]["data"].ndim == 2
 
 
-def test_get_output_type() -> None:
+def test_storage_type() -> None:
-    """Test MultiscaleEntropyAUC get_output_type()."""
+    """Test MultiscaleEntropyAUC storage_type."""
     assert "vector" == MultiscaleEntropyAUC(
         parcellation=PARCELLATION
-    ).get_output_type(input_type="BOLD", output_feature="complexity")
+    ).storage_type(input_type="BOLD", output_feature="complexity")
 
 
 @pytest.mark.skipif(

junifer/markers/complexity/tests/test_perm_entropy.py

@@ -42,9 +42,9 @@ def test_compute() -> None:
         assert feature_map["BOLD"]["complexity"]["data"].ndim == 2
 
 
-def test_get_output_type() -> None:
+def test_storage_type() -> None:
-    """Test PermEntropy get_output_type()."""
+    """Test PermEntropy storage_type."""
-    assert "vector" == PermEntropy(parcellation=PARCELLATION).get_output_type(
+    assert "vector" == PermEntropy(parcellation=PARCELLATION).storage_type(
         input_type="BOLD", output_feature="complexity"
     )
 

junifer/markers/complexity/tests/test_range_entropy.py

@@ -43,9 +43,9 @@ def test_compute() -> None:
         assert feature_map["BOLD"]["complexity"]["data"].ndim == 2
 
 
-def test_get_output_type() -> None:
+def test_storage_type() -> None:
-    """Test RangeEntropy get_output_type()."""
+    """Test RangeEntropy storage_type."""
-    assert "vector" == RangeEntropy(parcellation=PARCELLATION).get_output_type(
+    assert "vector" == RangeEntropy(parcellation=PARCELLATION).storage_type(
         input_type="BOLD", output_feature="complexity"
     )
 

junifer/markers/complexity/tests/test_range_entropy_auc.py

@@ -43,11 +43,11 @@ def test_compute() -> None:
         assert feature_map["BOLD"]["complexity"]["data"].ndim == 2
 
 
-def test_get_output_type() -> None:
+def test_storage_type() -> None:
-    """Test RangeEntropyAUC get_output_type()."""
+    """Test RangeEntropyAUC storage_type."""
-    assert "vector" == RangeEntropyAUC(
+    assert "vector" == RangeEntropyAUC(parcellation=PARCELLATION).storage_type(
-        parcellation=PARCELLATION
+        input_type="BOLD", output_feature="complexity"
-    ).get_output_type(input_type="BOLD", output_feature="complexity")
+    )
 
 
 @pytest.mark.skipif(

junifer/markers/complexity/tests/test_sample_entropy.py

@@ -42,11 +42,11 @@ def test_compute() -> None:
         assert feature_map["BOLD"]["complexity"]["data"].ndim == 2
 
 
-def test_get_output_type() -> None:
+def test_storage_type() -> None:
-    """Test SampleEntropy get_output_type()."""
+    """Test SampleEntropy storage_type."""
-    assert "vector" == SampleEntropy(
+    assert "vector" == SampleEntropy(parcellation=PARCELLATION).storage_type(
-        parcellation=PARCELLATION
+        input_type="BOLD", output_feature="complexity"
-    ).get_output_type(input_type="BOLD", output_feature="complexity")
+    )
 
 
 @pytest.mark.skipif(

junifer/markers/complexity/tests/test_weighted_perm_entropy.py

@@ -42,11 +42,11 @@ def test_compute() -> None:
         assert feature_map["BOLD"]["complexity"]["data"].ndim == 2
 
 
-def test_get_output_type() -> None:
+def test_storage_type() -> None:
-    """Test WeightedPermEntropy get_output_type()."""
+    """Test WeightedPermEntropy storage_type."""
     assert "vector" == WeightedPermEntropy(
         parcellation=PARCELLATION
-    ).get_output_type(input_type="BOLD", output_feature="complexity")
+    ).storage_type(input_type="BOLD", output_feature="complexity")
 
 
 @pytest.mark.skipif(

junifer/markers/falff/tests/test_falff_maps.py

@@ -27,8 +27,8 @@ MAPS = "Smith_rsn_10"
         "falff",
     ],
 )
-def test_ALFFMaps_get_output_type(feature: str) -> None:
+def test_ALFFMaps_storage_type(feature: str) -> None:
-    """Test ALFFMaps get_output_type().
+    """Test ALFFMaps storage_type.
 
     Parameters
     ----------
@@ -39,7 +39,7 @@ def test_ALFFMaps_get_output_type(feature: str) -> None:
     assert "vector" == ALFFMaps(
         maps=MAPS,
         using="junifer",
-    ).get_output_type(input_type="BOLD", output_feature=feature)
+    ).storage_type(input_type="BOLD", output_feature=feature)
 
 
 def test_ALFFMaps(
@@ -74,7 +74,7 @@ def test_ALFFMaps(
             )
             # Check correct output
             for name in ["alff", "falff"]:
-                assert "vector" == marker.get_output_type(
+                assert "vector" == marker.storage_type(
                     input_type="BOLD", output_feature=name
                 )
 

junifer/markers/falff/tests/test_falff_parcels.py

@@ -28,8 +28,8 @@ PARCELLATION = "TianxS1x3TxMNInonlinear2009cAsym"
         "falff",
     ],
 )
-def test_ALFFParcels_get_output_type(feature: str) -> None:
+def test_ALFFParcels_storage_type(feature: str) -> None:
-    """Test ALFFParcels get_output_type().
+    """Test ALFFParcels storage_type.
 
     Parameters
     ----------
@@ -40,7 +40,7 @@ def test_ALFFParcels_get_output_type(feature: str) -> None:
     assert "vector" == ALFFParcels(
         parcellation=PARCELLATION,
         using="junifer",
-    ).get_output_type(input_type="BOLD", output_feature=feature)
+    ).storage_type(input_type="BOLD", output_feature=feature)
 
 
 def test_ALFFParcels(caplog: pytest.LogCaptureFixture, tmp_path: Path) -> None:

junifer/markers/falff/tests/test_falff_spheres.py

@@ -28,8 +28,8 @@ COORDINATES = "DMNBuckner"
         "falff",
     ],
 )
-def test_ALFFSpheres_get_output_type(feature: str) -> None:
+def test_ALFFSpheres_storage_type(feature: str) -> None:
-    """Test ALFFSpheres get_output_type().
+    """Test ALFFSpheres storage_type.
 
     Parameters
     ----------
@@ -40,7 +40,7 @@ def test_ALFFSpheres_get_output_type(feature: str) -> None:
     assert "vector" == ALFFSpheres(
         coords=COORDINATES,
         using="junifer",
-    ).get_output_type(input_type="BOLD", output_feature=feature)
+    ).storage_type(input_type="BOLD", output_feature=feature)
 
 
 def test_ALFFSpheres(caplog: pytest.LogCaptureFixture, tmp_path: Path) -> None:

junifer/markers/functional_connectivity/tests/test_crossparcellation_functional_connectivity.py

@@ -31,13 +31,11 @@ def test_init() -> None:
         )
 
 
-def test_get_output_type() -> None:
+def test_storage_type() -> None:
-    """Test CrossParcellationFC get_output_type()."""
+    """Test CrossParcellationFC storage_type."""
     assert "matrix" == CrossParcellationFC(
         parcellation_one=parcellation_one, parcellation_two=parcellation_two
-    ).get_output_type(
+    ).storage_type(input_type="BOLD", output_feature="functional_connectivity")
-        input_type="BOLD", output_feature="functional_connectivity"
-    )
 
 
 @pytest.mark.skipif(

junifer/markers/functional_connectivity/tests/test_edge_functional_connectivity_maps.py

@@ -47,7 +47,7 @@ def test_EdgeCentricFCMaps(
             conn_method_params=conn_method_params,
         )
         # Check correct output
-        assert "matrix" == marker.get_output_type(
+        assert "matrix" == marker.storage_type(
             input_type="BOLD", output_feature="functional_connectivity"
         )
 

junifer/markers/functional_connectivity/tests/test_edge_functional_connectivity_parcels.py

@@ -45,7 +45,7 @@ def test_EdgeCentricFCParcels(
             conn_method_params=conn_method_params,
         )
         # Check correct output
-        assert "matrix" == marker.get_output_type(
+        assert "matrix" == marker.storage_type(
             input_type="BOLD", output_feature="functional_connectivity"
         )
 

junifer/markers/functional_connectivity/tests/test_edge_functional_connectivity_spheres.py

@@ -46,7 +46,7 @@ def test_EdgeCentricFCSpheres(
             conn_method_params=conn_method_params,
         )
         # Check correct output
-        assert "matrix" == marker.get_output_type(
+        assert "matrix" == marker.storage_type(
             input_type="BOLD", output_feature="functional_connectivity"
         )
 

junifer/markers/functional_connectivity/tests/test_functional_connectivity_maps.py

@@ -60,7 +60,7 @@ def test_FunctionalConnectivityMaps(
             conn_method_params=conn_method_params,
         )
         # Check correct output
-        assert "matrix" == marker.get_output_type(
+        assert "matrix" == marker.storage_type(
             input_type="BOLD", output_feature="functional_connectivity"
         )
 

junifer/markers/functional_connectivity/tests/test_functional_connectivity_parcels.py

@@ -61,7 +61,7 @@ def test_FunctionalConnectivityParcels(
             conn_method_params=conn_method_params,
         )
         # Check correct output
-        assert "matrix" == marker.get_output_type(
+        assert "matrix" == marker.storage_type(
             input_type="BOLD", output_feature="functional_connectivity"
         )
 

junifer/markers/functional_connectivity/tests/test_functional_connectivity_spheres.py

@@ -63,7 +63,7 @@ def test_FunctionalConnectivitySpheres(
             conn_method_params=conn_method_params,
         )
         # Check correct output
-        assert "matrix" == marker.get_output_type(
+        assert "matrix" == marker.storage_type(
             input_type="BOLD", output_feature="functional_connectivity"
         )
 

junifer/markers/reho/tests/test_reho_maps.py

@@ -48,7 +48,7 @@ def test_ReHoMaps(
                 using="junifer",
             )
             # Check correct output
-            assert "vector" == marker.get_output_type(
+            assert "vector" == marker.storage_type(
                 input_type="BOLD", output_feature="reho"
             )
 

junifer/markers/reho/tests/test_reho_parcels.py

@@ -43,7 +43,7 @@ def test_ReHoParcels(caplog: pytest.LogCaptureFixture, tmp_path: Path) -> None:
                 using="junifer",
             )
             # Check correct output
-            assert "vector" == marker.get_output_type(
+            assert "vector" == marker.storage_type(
                 input_type="BOLD", output_feature="reho"
             )
 

junifer/markers/reho/tests/test_reho_spheres.py

@@ -41,7 +41,7 @@ def test_ReHoSpheres(caplog: pytest.LogCaptureFixture, tmp_path: Path) -> None:
                 coords=COORDINATES, using="junifer", radius=10.0
             )
             # Check correct output
-            assert "vector" == marker.get_output_type(
+            assert "vector" == marker.storage_type(
                 input_type="BOLD", output_feature="reho"
             )
 

junifer/markers/temporal_snr/tests/test_temporal_snr_maps.py

@@ -27,7 +27,7 @@ def test_TemporalSNRMaps_computation(
         element_data = DefaultDataReader().fit_transform(element)
         marker = TemporalSNRMaps(maps="Smith_rsn_10")
         # Check correct output
-        assert "vector" == marker.get_output_type(
+        assert "vector" == marker.storage_type(
             input_type="BOLD", output_feature="tsnr"
         )
 

junifer/markers/temporal_snr/tests/test_temporal_snr_parcels.py

@@ -20,7 +20,7 @@ def test_TemporalSNRParcels_computation() -> None:
             parcellation="TianxS1x3TxMNInonlinear2009cAsym"
         )
         # Check correct output
-        assert "vector" == marker.get_output_type(
+        assert "vector" == marker.storage_type(
             input_type="BOLD", output_feature="tsnr"
         )
 

junifer/markers/temporal_snr/tests/test_temporal_snr_spheres.py

@@ -20,7 +20,7 @@ def test_TemporalSNRSpheres_computation() -> None:
         element_data = DefaultDataReader().fit_transform(dg["sub001"])
         marker = TemporalSNRSpheres(coords="DMNBuckner", radius=5.0)
         # Check correct output
-        assert "vector" == marker.get_output_type(
+        assert "vector" == marker.storage_type(
             input_type="BOLD", output_feature="tsnr"
         )
 

junifer/markers/tests/test_brainprint.py

@@ -22,8 +22,8 @@ from junifer.pipeline.utils import _check_freesurfer
         ("distances", "vector"),
     ],
 )
-def test_get_output_type(feature: str, storage_type: str) -> None:
+def test_storage_type(feature: str, storage_type: str) -> None:
-    """Test BrainPrint get_output_type().
+    """Test BrainPrint storage_type.
 
     Parameters
     ----------
@@ -33,7 +33,7 @@ def test_get_output_type(feature: str, storage_type: str) -> None:
         The parametrized storage type.
 
     """
-    assert storage_type == BrainPrint().get_output_type(
+    assert storage_type == BrainPrint().storage_type(
         input_type="FreeSurfer", output_feature=feature
     )
 

junifer/markers/tests/test_ets_rss.py

@@ -45,11 +45,11 @@ def test_compute() -> None:
         assert extacted_timeseries.shape[0] == len(rss_ets["rss_ets"]["data"])
 
 
-def test_get_output_type() -> None:
+def test_storage_type() -> None:
-    """Test RSS ETS get_output_type()."""
+    """Test RSS ETS storage_type."""
     assert "timeseries" == RSSETSMarker(
         parcellation=PARCELLATION
-    ).get_output_type(input_type="BOLD", output_feature="rss_ets")
+    ).storage_type(input_type="BOLD", output_feature="rss_ets")
 
 
 def test_store(tmp_path: Path) -> None:

junifer/markers/tests/test_maps_aggregation.py

@@ -74,7 +74,7 @@ def test_MapsAggregation_input_output(
     """
     assert storage_type == MapsAggregation(
         maps="Smith_rsn_10", on=input_type
-    ).get_output_type(input_type=input_type, output_feature="aggregation")
+    ).storage_type(input_type=input_type, output_feature="aggregation")
 
 
 def test_MapsAggregation_3D(

junifer/markers/tests/test_parcel_aggregation.py

@@ -79,7 +79,7 @@ def test_ParcelAggregation_input_output(
     """
     assert storage_type == ParcelAggregation(
         parcellation="Schaefer100x7", method="mean", on=input_type
-    ).get_output_type(input_type=input_type, output_feature="aggregation")
+    ).storage_type(input_type=input_type, output_feature="aggregation")
 
 
 def test_ParcelAggregation_3D() -> None:

junifer/markers/tests/test_sphere_aggregation.py

@@ -83,7 +83,7 @@ def test_SphereAggregation_input_output(
         coords="DMNBuckner",
         method="mean",
         on=input_type,
-    ).get_output_type(input_type=input_type, output_feature="aggregation")
+    ).storage_type(input_type=input_type, output_feature="aggregation")
 
 
 def test_SphereAggregation_3D() -> None: