junifer 0.0.7.dev332__py3-none-any.whl → 0.0.8__py3-none-any.whl

junifer/markers/functional_connectivity/functional_connectivity_parcels.py

@@ -5,9 +5,13 @@
 #          Synchon Mandal <s.mandal@fz-juelich.de>
 # License: AGPL
 
-from typing import Any, Optional, Union
+from typing import Annotated, Any
+
+from pydantic import BeforeValidator
 
 from ...api.decorators import register_marker
+from ...datagrabber import DataType
+from ...utils import ensure_list
 from ..parcel_aggregation import ParcelAggregation
 from .functional_connectivity_base import FunctionalConnectivityBase
 
@@ -25,56 +29,37 @@ class FunctionalConnectivityParcels(FunctionalConnectivityBase):
         The name(s) of the parcellation(s) to use.
         See :func:`.list_data` for options.
     agg_method : str, optional
-        The method to perform aggregation using.
+        The aggregation function to use.
         See :func:`.get_aggfunc_by_name` for options
         (default "mean").
-    agg_method_params : dict, optional
-        Parameters to pass to the aggregation function.
-        See :func:`.get_aggfunc_by_name` for options
-        (default None).
+    agg_method_params : dict or None, optional
+        The parameters to pass to the aggregation function.
+        See :func:`.get_aggfunc_by_name` for options (default None).
     conn_method : str, optional
-        The method to perform connectivity measure using.
+        The connectivity measure to use.
         See :class:`.JuniferConnectivityMeasure` for options
         (default "correlation").
-    conn_method_params : dict, optional
-        Parameters to pass to :class:`.JuniferConnectivityMeasure`.
+    conn_method_params : dict or None, optional
+        The parameters to pass to :class:`.JuniferConnectivityMeasure`.
         If None, ``{"empirical": True}`` will be used, which would mean
         :class:`sklearn.covariance.EmpiricalCovariance` is used to compute
         covariance. If usage of :class:`sklearn.covariance.LedoitWolf` is
         desired, ``{"empirical": False}`` should be passed
         (default None).
-    masks : str, dict or list of dict or str, optional
+    masks : str, dict, list of them or None, optional
         The specification of the masks to apply to regions before extracting
         signals. Check :ref:`Using Masks <using_masks>` for more details.
         If None, will not apply any mask (default None).
-    name : str, optional
-        The name of the marker. If None, will use
-        ``BOLD_FunctionalConnectivityParcels`` (default None).
+    name : str or None, optional
+        The name of the marker.
+        If None, will use the class name (default None).
 
     """
 
-    def __init__(
-        self,
-        parcellation: Union[str, list[str]],
-        agg_method: str = "mean",
-        agg_method_params: Optional[dict] = None,
-        conn_method: str = "correlation",
-        conn_method_params: Optional[dict] = None,
-        masks: Union[str, dict, list[Union[dict, str]], None] = None,
-        name: Optional[str] = None,
-    ) -> None:
-        self.parcellation = parcellation
-        super().__init__(
-            agg_method=agg_method,
-            agg_method_params=agg_method_params,
-            conn_method=conn_method,
-            conn_method_params=conn_method_params,
-            masks=masks,
-            name=name,
-        )
+    parcellation: Annotated[str | list[str], BeforeValidator(ensure_list)]
 
     def aggregate(
-        self, input: dict[str, Any], extra_input: Optional[dict] = None
+        self, input: dict[str, Any], extra_input: dict | None = None
     ) -> dict:
         """Perform parcel aggregation.
 
@@ -107,5 +92,5 @@ class FunctionalConnectivityParcels(FunctionalConnectivityBase):
             method=self.agg_method,
             method_params=self.agg_method_params,
             masks=self.masks,
-            on="BOLD",
+            on=DataType.BOLD,
         ).compute(input=input, extra_input=extra_input)

junifer/markers/functional_connectivity/functional_connectivity_spheres.py

@@ -5,11 +5,13 @@
 #          Synchon Mandal <s.mandal@fz-juelich.de>
 # License: AGPL
 
-from typing import Any, Optional, Union
+from typing import Any, Literal
+
+from pydantic import PositiveFloat
 
 from ...api.decorators import register_marker
+from ...datagrabber import DataType
 from ..sphere_aggregation import SphereAggregation
-from ..utils import raise_error
 from .functional_connectivity_base import FunctionalConnectivityBase
 
 
@@ -25,71 +27,48 @@ class FunctionalConnectivitySpheres(FunctionalConnectivityBase):
     coords : str
         The name of the coordinates list to use.
         See :func:`.list_data` for options.
-    radius : positive float, optional
-        The radius of the sphere around each coordinates in millimetres.
+    radius : ``zero`` or positive float or None, optional
+        The radius of the sphere in millimetres.
         If None, the signal will be extracted from a single voxel.
         See :class:`.JuniferNiftiSpheresMasker` for more information
         (default None).
     allow_overlap : bool, optional
-        Whether to allow overlapping spheres. If False, an error is raised if
-        the spheres overlap (default False).
+        Whether to allow overlapping spheres.
+        If False, an error is raised if the spheres overlap (default False).
     agg_method : str, optional
-        The method to perform aggregation using.
+        The aggregation function to use.
         See :func:`.get_aggfunc_by_name` for options
         (default "mean").
-    agg_method_params : dict, optional
-        Parameters to pass to the aggregation function.
-        See :func:`.get_aggfunc_by_name` for options
-        (default None).
+    agg_method_params : dict or None, optional
+        The parameters to pass to the aggregation function.
+        See :func:`.get_aggfunc_by_name` for options (default None).
     conn_method : str, optional
-        The method to perform connectivity measure using.
+        The connectivity measure to use.
         See :class:`.JuniferConnectivityMeasure` for options
         (default "correlation").
-    conn_method_params : dict, optional
-        Parameters to pass to :class:`.JuniferConnectivityMeasure`.
+    conn_method_params : dict or None, optional
+        The parameters to pass to :class:`.JuniferConnectivityMeasure`.
         If None, ``{"empirical": True}`` will be used, which would mean
         :class:`sklearn.covariance.EmpiricalCovariance` is used to compute
         covariance. If usage of :class:`sklearn.covariance.LedoitWolf` is
         desired, ``{"empirical": False}`` should be passed
         (default None).
-    masks : str, dict or list of dict or str, optional
+    masks : str, dict, list of them or None, optional
         The specification of the masks to apply to regions before extracting
         signals. Check :ref:`Using Masks <using_masks>` for more details.
         If None, will not apply any mask (default None).
-    name : str, optional
-        The name of the marker. If None, will use
-        ``BOLD_FunctionalConnectivitySpheres`` (default None).
+    name : str or None, optional
+        The name of the marker.
+        If None, will use the class name (default None).
 
     """
 
-    def __init__(
-        self,
-        coords: str,
-        radius: Optional[float] = None,
-        allow_overlap: bool = False,
-        agg_method: str = "mean",
-        agg_method_params: Optional[dict] = None,
-        conn_method: str = "correlation",
-        conn_method_params: Optional[dict] = None,
-        masks: Union[str, dict, list[Union[dict, str]], None] = None,
-        name: Optional[str] = None,
-    ) -> None:
-        self.coords = coords
-        self.radius = radius
-        self.allow_overlap = allow_overlap
-        if radius is None or radius <= 0:
-            raise_error(f"radius should be > 0: provided {radius}")
-        super().__init__(
-            agg_method=agg_method,
-            agg_method_params=agg_method_params,
-            conn_method=conn_method,
-            conn_method_params=conn_method_params,
-            masks=masks,
-            name=name,
-        )
+    coords: str
+    radius: Literal[0] | PositiveFloat | None = None
+    allow_overlap: bool = False
 
     def aggregate(
-        self, input: dict[str, Any], extra_input: Optional[dict] = None
+        self, input: dict[str, Any], extra_input: dict | None = None
     ) -> dict:
         """Perform sphere aggregation.
 
@@ -124,5 +103,5 @@ class FunctionalConnectivitySpheres(FunctionalConnectivityBase):
             method=self.agg_method,
             method_params=self.agg_method_params,
             masks=self.masks,
-            on="BOLD",
+            on=DataType.BOLD,
         ).compute(input=input, extra_input=extra_input)

junifer/markers/functional_connectivity/tests/test_crossparcellation_functional_connectivity.py

@@ -9,16 +9,19 @@ from pathlib import Path
 
 import pytest
 
+from junifer.datagrabber import DataType
 from junifer.datareader import DefaultDataReader
-from junifer.markers.functional_connectivity import CrossParcellationFC
+from junifer.markers import CrossParcellationFC
 from junifer.pipeline import WorkDirManager
-from junifer.pipeline.utils import _check_ants
-from junifer.storage import SQLiteFeatureStorage
-from junifer.testing.datagrabbers import SPMAuditoryTestingDataGrabber
+from junifer.storage import HDF5FeatureStorage
+from junifer.testing.datagrabbers import PartlyCloudyTestingDataGrabber
 
 
-parcellation_one = "Schaefer100x17"
-parcellation_two = "Schaefer200x17"
+pytestmark = pytest.mark.external
+
+
+parcellation_one = "Shen_2013_50"
+parcellation_two = "Shen_2013_100"
 
 
 def test_init() -> None:
@@ -35,12 +38,11 @@ def test_storage_type() -> None:
     """Test CrossParcellationFC storage_type."""
     assert "matrix" == CrossParcellationFC(
         parcellation_one=parcellation_one, parcellation_two=parcellation_two
-    ).storage_type(input_type="BOLD", output_feature="functional_connectivity")
+    ).storage_type(
+        input_type=DataType.BOLD, output_feature="functional_connectivity"
+    )
 
 
-@pytest.mark.skipif(
-    _check_ants() is False, reason="requires ANTs to be in PATH"
-)
 def test_compute(tmp_path: Path) -> None:
     """Test CrossParcellationFC compute().
 
@@ -50,8 +52,8 @@ def test_compute(tmp_path: Path) -> None:
         The path to the test directory.
 
     """
-    with SPMAuditoryTestingDataGrabber() as dg:
-        element_data = DefaultDataReader().fit_transform(dg["sub001"])
+    with PartlyCloudyTestingDataGrabber() as dg:
+        element_data = DefaultDataReader().fit_transform(dg["sub-01"])
         WorkDirManager().workdir = tmp_path
         crossparcellation = CrossParcellationFC(
             parcellation_one=parcellation_one,
@@ -61,14 +63,11 @@ def test_compute(tmp_path: Path) -> None:
         out = crossparcellation.compute(element_data["BOLD"])[
             "functional_connectivity"
         ]
-        assert out["data"].shape == (200, 100)
-        assert len(out["col_names"]) == 100
-        assert len(out["row_names"]) == 200
+        assert out["data"].shape == (184, 93)
+        assert len(out["col_names"]) == 93
+        assert len(out["row_names"]) == 184
 
 
-@pytest.mark.skipif(
-    _check_ants() is False, reason="requires ANTs to be in PATH"
-)
 def test_store(tmp_path: Path) -> None:
     """Test CrossParcellationFC store().
 
@@ -78,16 +77,16 @@ def test_store(tmp_path: Path) -> None:
         The path to the test directory.
 
     """
-    with SPMAuditoryTestingDataGrabber() as dg:
-        element_data = DefaultDataReader().fit_transform(dg["sub001"])
+    with PartlyCloudyTestingDataGrabber() as dg:
+        element_data = DefaultDataReader().fit_transform(dg["sub-01"])
         WorkDirManager().workdir = tmp_path
         crossparcellation = CrossParcellationFC(
             parcellation_one=parcellation_one,
             parcellation_two=parcellation_two,
             corr_method="spearman",
         )
-        storage = SQLiteFeatureStorage(
-            uri=tmp_path / "test_crossparcellation.sqlite", upsert="ignore"
+        storage = HDF5FeatureStorage(
+            uri=tmp_path / "test_crossparcellation.hdf5",
         )
         # Fit transform marker on data with storage
         crossparcellation.fit_transform(input=element_data, storage=storage)

junifer/markers/functional_connectivity/tests/test_edge_functional_connectivity_maps.py

@@ -7,10 +7,14 @@ from pathlib import Path
 
 import pytest
 
-from junifer.datagrabber import PatternDataladDataGrabber
+from junifer.datagrabber import DataType
 from junifer.datareader import DefaultDataReader
 from junifer.markers import EdgeCentricFCMaps
 from junifer.storage import HDF5FeatureStorage
+from junifer.testing.datagrabbers import ADHDTestingDataGrabber
+
+
+pytestmark = pytest.mark.external
 
 
 @pytest.mark.parametrize(
@@ -22,7 +26,6 @@ from junifer.storage import HDF5FeatureStorage
 )
 def test_EdgeCentricFCMaps(
     tmp_path: Path,
-    maps_datagrabber: PatternDataladDataGrabber,
     conn_method_params: dict[str, bool],
 ) -> None:
     """Test EdgeCentricFCMaps.
@@ -31,14 +34,12 @@ def test_EdgeCentricFCMaps(
     ----------
     tmp_path : pathlib.Path
         The path to the test directory.
-    maps_datagrabber : PatternDataladDataGrabber
-        The testing PatternDataladDataGrabber, as fixture.
     conn_method_params : dict
         The parametrized parameters to connectivity measure method.
 
     """
-    with maps_datagrabber as dg:
-        element = dg[("sub-01", "sub-001", "rest", "1")]
+    with ADHDTestingDataGrabber() as dg:
+        element = dg["sub-01"]
         element_data = DefaultDataReader().fit_transform(element)
         # Setup marker
         marker = EdgeCentricFCMaps(
@@ -48,7 +49,7 @@ def test_EdgeCentricFCMaps(
         )
         # Check correct output
         assert "matrix" == marker.storage_type(
-            input_type="BOLD", output_feature="functional_connectivity"
+            input_type=DataType.BOLD, output_feature="functional_connectivity"
         )
 
         # Fit-transform the data

junifer/markers/functional_connectivity/tests/test_edge_functional_connectivity_parcels.py

@@ -8,12 +8,16 @@ from pathlib import Path
 
 import pytest
 
+from junifer.datagrabber import DataType
 from junifer.datareader import DefaultDataReader
 from junifer.markers.functional_connectivity import EdgeCentricFCParcels
-from junifer.storage import SQLiteFeatureStorage
+from junifer.storage import HDF5FeatureStorage
 from junifer.testing.datagrabbers import PartlyCloudyTestingDataGrabber
 
 
+pytestmark = pytest.mark.external
+
+
 @pytest.mark.parametrize(
     "conn_method_params",
     [
@@ -46,7 +50,7 @@ def test_EdgeCentricFCParcels(
         )
         # Check correct output
         assert "matrix" == marker.storage_type(
-            input_type="BOLD", output_feature="functional_connectivity"
+            input_type=DataType.BOLD, output_feature="functional_connectivity"
         )
 
         # Fit-transform the data
@@ -63,8 +67,8 @@ def test_EdgeCentricFCParcels(
         assert len(set(edge_fc_bold["col_names"])) == n_edges
 
         # Store
-        storage = SQLiteFeatureStorage(
-            uri=tmp_path / "test_edge_fc_parcels.sqlite", upsert="ignore"
+        storage = HDF5FeatureStorage(
+            uri=tmp_path / "test_edge_fc_parcels.hdf5",
         )
         marker.fit_transform(input=element_data, storage=storage)
         features = storage.list_features()

junifer/markers/functional_connectivity/tests/test_edge_functional_connectivity_spheres.py

@@ -8,12 +8,16 @@ from pathlib import Path
 
 import pytest
 
+from junifer.datagrabber import DataType
 from junifer.datareader import DefaultDataReader
 from junifer.markers.functional_connectivity import EdgeCentricFCSpheres
-from junifer.storage import SQLiteFeatureStorage
+from junifer.storage import HDF5FeatureStorage
 from junifer.testing.datagrabbers import SPMAuditoryTestingDataGrabber
 
 
+pytestmark = pytest.mark.external
+
+
 @pytest.mark.parametrize(
     "conn_method_params",
     [
@@ -47,7 +51,7 @@ def test_EdgeCentricFCSpheres(
         )
         # Check correct output
         assert "matrix" == marker.storage_type(
-            input_type="BOLD", output_feature="functional_connectivity"
+            input_type=DataType.BOLD, output_feature="functional_connectivity"
         )
 
         # Fit-transform the data
@@ -65,8 +69,8 @@ def test_EdgeCentricFCSpheres(
         assert len(set(edge_fc_bold["col_names"])) == n_edges
 
         # Store
-        storage = SQLiteFeatureStorage(
-            uri=tmp_path / "test_edge_fc_spheres.sqlite", upsert="ignore"
+        storage = HDF5FeatureStorage(
+            uri=tmp_path / "test_edge_fc_spheres.hdf5",
         )
         marker.fit_transform(input=element_data, storage=storage)
         features = storage.list_features()

junifer/markers/functional_connectivity/tests/test_functional_connectivity_maps.py

@@ -13,10 +13,14 @@ from numpy.testing import assert_array_almost_equal
 from sklearn.covariance import EmpiricalCovariance, LedoitWolf
 
 from junifer.data import MapsRegistry
-from junifer.datagrabber import PatternDataladDataGrabber
+from junifer.datagrabber import DataType
 from junifer.datareader import DefaultDataReader
 from junifer.markers import FunctionalConnectivityMaps
 from junifer.storage import HDF5FeatureStorage
+from junifer.testing.datagrabbers import ADHDTestingDataGrabber
+
+
+pytestmark = pytest.mark.external
 
 
 if TYPE_CHECKING:
@@ -32,7 +36,6 @@ if TYPE_CHECKING:
 )
 def test_FunctionalConnectivityMaps(
     tmp_path: Path,
-    maps_datagrabber: PatternDataladDataGrabber,
     conn_method_params: dict[str, bool],
     cov_estimator: type["BaseEstimator"],
 ) -> None:
@@ -42,16 +45,14 @@ def test_FunctionalConnectivityMaps(
     ----------
     tmp_path : pathlib.Path
         The path to the test directory.
-    maps_datagrabber : PatternDataladDataGrabber
-        The testing PatternDataladDataGrabber, as fixture.
     conn_method_params : dict
         The parametrized parameters to connectivity measure method.
     cov_estimator : estimator object
         The parametrized covariance estimator.
 
     """
-    with maps_datagrabber as dg:
-        element = dg[("sub-01", "sub-001", "rest", "1")]
+    with ADHDTestingDataGrabber() as dg:
+        element = dg["sub-01"]
         element_data = DefaultDataReader().fit_transform(element)
         # Setup marker
         marker = FunctionalConnectivityMaps(
@@ -61,7 +62,7 @@ def test_FunctionalConnectivityMaps(
         )
         # Check correct output
         assert "matrix" == marker.storage_type(
-            input_type="BOLD", output_feature="functional_connectivity"
+            input_type=DataType.BOLD, output_feature="functional_connectivity"
         )
 
         # Fit-transform the data

junifer/markers/functional_connectivity/tests/test_functional_connectivity_parcels.py

@@ -15,14 +15,18 @@ from numpy.testing import assert_array_almost_equal
 from sklearn.covariance import EmpiricalCovariance, LedoitWolf
 
 from junifer.data import ParcellationRegistry
+from junifer.datagrabber import DataType
 from junifer.datareader import DefaultDataReader
-from junifer.markers.functional_connectivity import (
+from junifer.markers import (
     FunctionalConnectivityParcels,
 )
-from junifer.storage import SQLiteFeatureStorage
+from junifer.storage import HDF5FeatureStorage
 from junifer.testing.datagrabbers import PartlyCloudyTestingDataGrabber
 
 
+pytestmark = pytest.mark.external
+
+
 if TYPE_CHECKING:
     from sklearn.base import BaseEstimator
 
@@ -62,7 +66,7 @@ def test_FunctionalConnectivityParcels(
         )
         # Check correct output
         assert "matrix" == marker.storage_type(
-            input_type="BOLD", output_feature="functional_connectivity"
+            input_type=DataType.BOLD, output_feature="functional_connectivity"
         )
 
         # Fit-transform the data
@@ -101,8 +105,8 @@ def test_FunctionalConnectivityParcels(
         )
 
         # Store
-        storage = SQLiteFeatureStorage(
-            uri=tmp_path / "test_fc_parcels.sqlite", upsert="ignore"
+        storage = HDF5FeatureStorage(
+            uri=tmp_path / "test_fc_parcels.hdf5",
         )
         marker.fit_transform(input=element_data, storage=storage)
         features = storage.list_features()

junifer/markers/functional_connectivity/tests/test_functional_connectivity_spheres.py

@@ -16,14 +16,18 @@ from numpy.testing import assert_array_almost_equal
 from sklearn.covariance import EmpiricalCovariance, LedoitWolf
 
 from junifer.data import CoordinatesRegistry
+from junifer.datagrabber import DataType
 from junifer.datareader import DefaultDataReader
 from junifer.markers.functional_connectivity import (
     FunctionalConnectivitySpheres,
 )
-from junifer.storage import SQLiteFeatureStorage
+from junifer.storage import HDF5FeatureStorage
 from junifer.testing.datagrabbers import SPMAuditoryTestingDataGrabber
 
 
+pytestmark = pytest.mark.external
+
+
 if TYPE_CHECKING:
     from sklearn.base import BaseEstimator
 
@@ -64,7 +68,7 @@ def test_FunctionalConnectivitySpheres(
         )
         # Check correct output
         assert "matrix" == marker.storage_type(
-            input_type="BOLD", output_feature="functional_connectivity"
+            input_type=DataType.BOLD, output_feature="functional_connectivity"
         )
 
         # Fit-transform the data
@@ -102,8 +106,8 @@ def test_FunctionalConnectivitySpheres(
         )
 
         # Store
-        storage = SQLiteFeatureStorage(
-            uri=tmp_path / "test_fc_spheres.sqlite", upsert="ignore"
+        storage = HDF5FeatureStorage(
+            uri=tmp_path / "test_fc_spheres.hdf5",
         )
         marker.fit_transform(input=element_data, storage=storage)
         features = storage.list_features()
@@ -112,11 +116,3 @@ def test_FunctionalConnectivitySpheres(
             == "BOLD_FunctionalConnectivitySpheres_functional_connectivity"
             for x in features.values()
         )
-
-
-def test_FunctionalConnectivitySpheres_error() -> None:
-    """Test FunctionalConnectivitySpheres errors."""
-    with pytest.raises(ValueError, match="radius should be > 0"):
-        FunctionalConnectivitySpheres(
-            coords="DMNBuckner", radius=-0.1, conn_method="correlation"
-        )