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

junifer/markers/temporal_snr/temporal_snr_parcels.py

@@ -1,11 +1,16 @@
 """Provide class for temporal SNR using parcels."""
 
 # Authors: Leonard Sasse <l.sasse@fz-juelich.de>
+#          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 .temporal_snr_base import TemporalSNRBase
 
@@ -23,39 +28,26 @@ class TemporalSNRParcels(TemporalSNRBase):
         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. Check valid options in
-        :func:`.get_aggfunc_by_name` (default "mean").
-    agg_method_params : dict, optional
-        Parameters to pass to the aggregation function. Check valid options in
-        :func:`.get_aggfunc_by_name` (default None).
-    masks : str, dict or list of dict or str, optional
+        The aggregation function to use.
+        See :func:`.get_aggfunc_by_name` for options
+        (default "mean").
+    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).
+    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 the class name (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,
-        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,
-            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.
 
@@ -88,5 +80,5 @@ class TemporalSNRParcels(TemporalSNRBase):
             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/temporal_snr/temporal_snr_spheres.py

@@ -1,13 +1,16 @@
 """Provide class for temporal SNR using spheres."""
 
 # Authors: Leonard Sasse <l.sasse@fz-juelich.de>
+#          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 .temporal_snr_base import TemporalSNRBase
 
 
@@ -23,54 +26,37 @@ class TemporalSNRSpheres(TemporalSNRBase):
     coords : str
         The name of the coordinates list to use.
         See :func:`.list_data` for options.
-    radius : float, optional
-        The radius of the sphere in mm. If None, the signal will be extracted
-        from a single voxel. See :class:`nilearn.maskers.NiftiSpheresMasker`
-        for more information (default None).
+    radius : ``zero`` or positive float or None, optional
+        The radius of the sphere in millimeters.
+        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 is False).
+        Whether to allow overlapping spheres.
+        If False, an error is raised if the spheres overlap (default is False).
     agg_method : str, optional
-        The aggregation method to use.
-        See :func:`.get_aggfunc_by_name` for more information
-        (default None).
-    agg_method_params : dict, optional
-        The parameters to pass to the aggregation method (default None).
-    masks : str, dict or list of dict or str, optional
+        The aggregation function to use.
+        See :func:`.get_aggfunc_by_name` for options
+        (default "mean").
+    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).
+    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. By default, it will use
-        KIND_FunctionalConnectivitySpheres where KIND is the kind of data it
-        was applied to (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,
-        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,
-            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.
 
@@ -105,5 +91,5 @@ class TemporalSNRSpheres(TemporalSNRBase):
             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/temporal_snr/tests/test_temporal_snr_base.py

@@ -6,10 +6,10 @@
 import pytest
 
 # done to keep line length 79
-import junifer.markers.temporal_snr as tsnr
+from junifer.markers.temporal_snr import temporal_snr_base as tsb
 
 
 def test_base_temporal_snr_marker_abstractness() -> None:
     """Test TemporalSNRBase is an abstract base class."""
     with pytest.raises(TypeError, match="abstract"):
-        tsnr.temporal_snr_base.TemporalSNRBase()
+        tsb.TemporalSNRBase()

junifer/markers/temporal_snr/tests/test_temporal_snr_maps.py

@@ -5,34 +5,33 @@
 
 from pathlib import Path
 
-from junifer.datagrabber import PatternDataladDataGrabber
+import pytest
+
+from junifer.datagrabber import DataType
 from junifer.datareader import DefaultDataReader
 from junifer.markers import TemporalSNRMaps
 from junifer.storage import HDF5FeatureStorage
+from junifer.testing.datagrabbers import ADHDTestingDataGrabber
 
 
-def test_TemporalSNRMaps_computation(
-    maps_datagrabber: PatternDataladDataGrabber,
-) -> None:
-    """Test TemporalSNRMaps fit-transform.
+pytestmark = pytest.mark.external
 
-    Parameters
-    ----------
-    maps_datagrabber : PatternDataladDataGrabber
-        The testing PatternDataladDataGrabber, as fixture.
 
-    """
-    with maps_datagrabber as dg:
-        element = dg[("sub-01", "sub-001", "rest", "1")]
+def test_TemporalSNRMaps_computation() -> None:
+    """Test TemporalSNRMaps fit-transform."""
+    with ADHDTestingDataGrabber() as dg:
+        element = dg["sub-01"]
         element_data = DefaultDataReader().fit_transform(element)
         marker = TemporalSNRMaps(maps="Smith_rsn_10")
         # Check correct output
         assert "vector" == marker.storage_type(
-            input_type="BOLD", output_feature="tsnr"
+            input_type=DataType.BOLD, output_feature="tsnr"
         )
-
         # Fit-transform the data
+        bold_img = element_data["BOLD"]["data"]
         tsnr_parcels = marker.fit_transform(element_data)
+        # The input is not changed
+        assert element_data["BOLD"]["data"] is bold_img
         tsnr_parcels_bold = tsnr_parcels["BOLD"]["tsnr"]
 
         assert "data" in tsnr_parcels_bold
@@ -41,25 +40,21 @@ def test_TemporalSNRMaps_computation(
         assert len(set(tsnr_parcels_bold["col_names"])) == 10
 
 
-def test_TemporalSNRMaps_storage(
-    tmp_path: Path, maps_datagrabber: PatternDataladDataGrabber
-) -> None:
+def test_TemporalSNRMaps_storage(tmp_path: Path) -> None:
     """Test TemporalSNRMaps store.
 
     Parameters
     ----------
     tmp_path : pathlib.Path
         The path to the test directory.
-    maps_datagrabber : PatternDataladDataGrabber
-        The testing PatternDataladDataGrabber, as fixture.
 
     """
-    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)
         marker = TemporalSNRMaps(maps="Smith_rsn_10")
         # Store
-        storage = HDF5FeatureStorage(tmp_path / "test_tsnr_maps.hdf5")
+        storage = HDF5FeatureStorage(uri=tmp_path / "test_tsnr_maps.hdf5")
         marker.fit_transform(input=element_data, storage=storage)
         features = storage.list_features()
         assert any(

junifer/markers/temporal_snr/tests/test_temporal_snr_parcels.py

@@ -6,12 +6,18 @@
 
 from pathlib import Path
 
+import pytest
+
+from junifer.datagrabber import DataType
 from junifer.datareader import DefaultDataReader
 from junifer.markers.temporal_snr import TemporalSNRParcels
 from junifer.storage import HDF5FeatureStorage
 from junifer.testing.datagrabbers import PartlyCloudyTestingDataGrabber
 
 
+pytestmark = pytest.mark.external
+
+
 def test_TemporalSNRParcels_computation() -> None:
     """Test TemporalSNRParcels fit-transform."""
     with PartlyCloudyTestingDataGrabber() as dg:
@@ -21,11 +27,13 @@ def test_TemporalSNRParcels_computation() -> None:
         )
         # Check correct output
         assert "vector" == marker.storage_type(
-            input_type="BOLD", output_feature="tsnr"
+            input_type=DataType.BOLD, output_feature="tsnr"
         )
-
         # Fit-transform the data
+        bold_img = element_data["BOLD"]["data"]
         tsnr_parcels = marker.fit_transform(element_data)
+        # The input is not changed
+        assert element_data["BOLD"]["data"] is bold_img
         tsnr_parcels_bold = tsnr_parcels["BOLD"]["tsnr"]
 
         assert "data" in tsnr_parcels_bold
@@ -49,7 +57,7 @@ def test_TemporalSNRParcels_storage(tmp_path: Path) -> None:
             parcellation="TianxS1x3TxMNInonlinear2009cAsym"
         )
         # Store
-        storage = HDF5FeatureStorage(tmp_path / "test_tsnr_parcels.hdf5")
+        storage = HDF5FeatureStorage(uri=tmp_path / "test_tsnr_parcels.hdf5")
         marker.fit_transform(input=element_data, storage=storage)
         features = storage.list_features()
         assert any(

junifer/markers/temporal_snr/tests/test_temporal_snr_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.temporal_snr import TemporalSNRSpheres
 from junifer.storage import HDF5FeatureStorage
 from junifer.testing.datagrabbers import SPMAuditoryTestingDataGrabber
 
 
+pytestmark = pytest.mark.external
+
+
 def test_TemporalSNRSpheres_computation() -> None:
     """Test TemporalSNRSpheres fit-transform."""
     with SPMAuditoryTestingDataGrabber() as dg:
@@ -21,11 +25,13 @@ def test_TemporalSNRSpheres_computation() -> None:
         marker = TemporalSNRSpheres(coords="DMNBuckner", radius=5.0)
         # Check correct output
         assert "vector" == marker.storage_type(
-            input_type="BOLD", output_feature="tsnr"
+            input_type=DataType.BOLD, output_feature="tsnr"
         )
-
         # Fit-transform the data
+        bold_img = element_data["BOLD"]["data"]
         tsnr_spheres = marker.fit_transform(element_data)
+        # The input is not changed
+        assert element_data["BOLD"]["data"] is bold_img
         tsnr_spheres_bold = tsnr_spheres["BOLD"]["tsnr"]
 
         assert "data" in tsnr_spheres_bold
@@ -47,16 +53,10 @@ def test_TemporalSNRSpheres_storage(tmp_path: Path) -> None:
         element_data = DefaultDataReader().fit_transform(dg["sub001"])
         marker = TemporalSNRSpheres(coords="DMNBuckner", radius=5.0)
         # Store
-        storage = HDF5FeatureStorage(tmp_path / "test_tsnr_spheres.hdf5")
+        storage = HDF5FeatureStorage(uri=tmp_path / "test_tsnr_spheres.hdf5")
         marker.fit_transform(input=element_data, storage=storage)
         features = storage.list_features()
         assert any(
             x["name"] == "BOLD_TemporalSNRSpheres_tsnr"
             for x in features.values()
         )
-
-
-def test_TemporalSNRSpheres_error() -> None:
-    """Test TemporalSNRSpheres errors."""
-    with pytest.raises(ValueError, match="radius should be > 0"):
-        TemporalSNRSpheres(coords="DMNBuckner", radius=-0.1)

junifer/markers/tests/test_brainprint.py

@@ -7,34 +7,35 @@ import socket
 
 import pytest
 
-from junifer.datagrabber import DataladAOMICID1000
+from junifer.datagrabber import DataladAOMICID1000, DataType
 from junifer.datareader import DefaultDataReader
 from junifer.markers import BrainPrint
 from junifer.pipeline.utils import _check_freesurfer
+from junifer.storage import StorageType
 
 
 @pytest.mark.parametrize(
     "feature, storage_type",
     [
-        ("eigenvalues", "scalar_table"),
-        ("areas", "vector"),
-        ("volumes", "vector"),
-        ("distances", "vector"),
+        ("eigenvalues", StorageType.ScalarTable),
+        ("areas", StorageType.Vector),
+        ("volumes", StorageType.Vector),
+        ("distances", StorageType.Vector),
     ],
 )
-def test_storage_type(feature: str, storage_type: str) -> None:
+def test_storage_type(feature: str, storage_type: StorageType) -> None:
     """Test BrainPrint storage_type.
 
     Parameters
     ----------
     feature : str
         The parametrized feature name.
-    storage_type : str
+    storage_type : StorageType
         The parametrized storage type.
 
     """
     assert storage_type == BrainPrint().storage_type(
-        input_type="FreeSurfer", output_feature=feature
+        input_type=DataType.FreeSurfer, output_feature=feature
     )
 
 
@@ -47,7 +48,7 @@ def test_storage_type(feature: str, storage_type: str) -> None:
 )
 def test_compute() -> None:
     """Test BrainPrint compute()."""
-    with DataladAOMICID1000(types="FreeSurfer") as dg:
+    with DataladAOMICID1000(types=[DataType.FreeSurfer]) as dg:
         # Fetch element
         element = dg["sub-0001"]
         # Fetch element data

junifer/markers/tests/test_ets_rss.py

@@ -8,15 +8,19 @@
 
 from pathlib import Path
 
+import pytest
 from nilearn.maskers import NiftiLabelsMasker
 
 from junifer.data import ParcellationRegistry
 from junifer.datareader import DefaultDataReader
 from junifer.markers.ets_rss import RSSETSMarker
-from junifer.storage import SQLiteFeatureStorage
+from junifer.storage import HDF5FeatureStorage
 from junifer.testing.datagrabbers import PartlyCloudyTestingDataGrabber
 
 
+pytestmark = pytest.mark.external
+
+
 # Set parcellation
 PARCELLATION = "TianxS1x3TxMNInonlinear2009cAsym"
 
@@ -33,7 +37,7 @@ def test_compute() -> None:
         # Compare with nilearn
         # Load testing parcellation
         test_parcellation, _ = ParcellationRegistry().get(
-            parcellations=[PARCELLATION],
+            parcellations=PARCELLATION,
             target_data=element_data["BOLD"],
         )
         # Extract timeseries
@@ -65,7 +69,7 @@ def test_store(tmp_path: Path) -> None:
         # Get element data
         element_data = DefaultDataReader().fit_transform(dg["sub-01"])
         # Create storage
-        storage = SQLiteFeatureStorage(tmp_path / "test_rss_ets.sqlite")
+        storage = HDF5FeatureStorage(uri=tmp_path / "test_rss_ets.hdf5")
         # Compute the RSSETSMarker and store
         _ = RSSETSMarker(parcellation=PARCELLATION).fit_transform(
             input=element_data, storage=storage