junifer 0.0.4.dev831__py3-none-any.whl → 0.0.5__py3-none-any.whl

junifer/markers/complexity/tests/test_hurst_exponent.py

@@ -14,6 +14,7 @@ pytest.importorskip("neurokit2")
 
 from junifer.datareader import DefaultDataReader  # noqa: E402
 from junifer.markers.complexity import HurstExponent  # noqa: E402
+from junifer.pipeline.utils import _check_ants  # noqa: E402
 from junifer.storage import SQLiteFeatureStorage  # noqa: E402
 from junifer.testing.datagrabbers import (  # noqa: E402
     SPMAuditoryTestingDataGrabber,
@@ -24,6 +25,9 @@ from junifer.testing.datagrabbers import (  # noqa: E402
 PARCELLATION = "Schaefer100x17"
 
 
+@pytest.mark.skipif(
+    _check_ants() is False, reason="requires ANTs to be in PATH"
+)
 def test_compute() -> None:
     """Test HurstExponent compute()."""
     with SPMAuditoryTestingDataGrabber() as dg:
@@ -36,15 +40,19 @@ def test_compute() -> None:
         # Compute the marker
         feature_map = marker.fit_transform(element_data)
         # Assert the dimension of timeseries
-        assert feature_map["BOLD"]["data"].ndim == 2
+        assert feature_map["BOLD"]["complexity"]["data"].ndim == 2
 
 
 def test_get_output_type() -> None:
     """Test HurstExponent get_output_type()."""
-    marker = HurstExponent(parcellation=PARCELLATION)
-    assert marker.get_output_type("BOLD") == "vector"
+    assert "vector" == HurstExponent(
+        parcellation=PARCELLATION
+    ).get_output_type(input_type="BOLD", output_feature="complexity")
 
 
+@pytest.mark.skipif(
+    _check_ants() is False, reason="requires ANTs to be in PATH"
+)
 def test_store(tmp_path: Path) -> None:
     """Test HurstExponent store().
 

junifer/markers/complexity/tests/test_multiscale_entropy_auc.py

@@ -13,6 +13,7 @@ pytest.importorskip("neurokit2")
 
 from junifer.datareader import DefaultDataReader  # noqa: E402
 from junifer.markers.complexity import MultiscaleEntropyAUC  # noqa: E402
+from junifer.pipeline.utils import _check_ants  # noqa: E402
 from junifer.storage import SQLiteFeatureStorage  # noqa: E402
 from junifer.testing.datagrabbers import (  # noqa: E402
     SPMAuditoryTestingDataGrabber,
@@ -23,6 +24,9 @@ from junifer.testing.datagrabbers import (  # noqa: E402
 PARCELLATION = "Schaefer100x17"
 
 
+@pytest.mark.skipif(
+    _check_ants() is False, reason="requires ANTs to be in PATH"
+)
 def test_compute() -> None:
     """Test MultiscaleEntropyAUC compute()."""
     with SPMAuditoryTestingDataGrabber() as dg:
@@ -35,15 +39,19 @@ def test_compute() -> None:
         # Compute the marker
         feature_map = marker.fit_transform(element_data)
         # Assert the dimension of timeseries
-        assert feature_map["BOLD"]["data"].ndim == 2
+        assert feature_map["BOLD"]["complexity"]["data"].ndim == 2
 
 
 def test_get_output_type() -> None:
     """Test MultiscaleEntropyAUC get_output_type()."""
-    marker = MultiscaleEntropyAUC(parcellation=PARCELLATION)
-    assert marker.get_output_type("BOLD") == "vector"
+    assert "vector" == MultiscaleEntropyAUC(
+        parcellation=PARCELLATION
+    ).get_output_type(input_type="BOLD", output_feature="complexity")
 
 
+@pytest.mark.skipif(
+    _check_ants() is False, reason="requires ANTs to be in PATH"
+)
 def test_store(tmp_path: Path) -> None:
     """Test MultiscaleEntropyAUC store().
 

junifer/markers/complexity/tests/test_perm_entropy.py

@@ -13,6 +13,7 @@ pytest.importorskip("neurokit2")
 
 from junifer.datareader import DefaultDataReader  # noqa: E402
 from junifer.markers.complexity import PermEntropy  # noqa: E402
+from junifer.pipeline.utils import _check_ants  # noqa: E402
 from junifer.storage import SQLiteFeatureStorage  # noqa: E402
 from junifer.testing.datagrabbers import (  # noqa: E402
     SPMAuditoryTestingDataGrabber,
@@ -23,6 +24,9 @@ from junifer.testing.datagrabbers import (  # noqa: E402
 PARCELLATION = "Schaefer100x17"
 
 
+@pytest.mark.skipif(
+    _check_ants() is False, reason="requires ANTs to be in PATH"
+)
 def test_compute() -> None:
     """Test PermEntropy compute()."""
     with SPMAuditoryTestingDataGrabber() as dg:
@@ -35,15 +39,19 @@ def test_compute() -> None:
         # Compute the marker
         feature_map = marker.fit_transform(element_data)
         # Assert the dimension of timeseries
-        assert feature_map["BOLD"]["data"].ndim == 2
+        assert feature_map["BOLD"]["complexity"]["data"].ndim == 2
 
 
 def test_get_output_type() -> None:
     """Test PermEntropy get_output_type()."""
-    marker = PermEntropy(parcellation=PARCELLATION)
-    assert marker.get_output_type("BOLD") == "vector"
+    assert "vector" == PermEntropy(parcellation=PARCELLATION).get_output_type(
+        input_type="BOLD", output_feature="complexity"
+    )
 
 
+@pytest.mark.skipif(
+    _check_ants() is False, reason="requires ANTs to be in PATH"
+)
 def test_store(tmp_path: Path) -> None:
     """Test PermEntropy store().
 

junifer/markers/complexity/tests/test_range_entropy.py

@@ -14,6 +14,7 @@ pytest.importorskip("neurokit2")
 
 from junifer.datareader import DefaultDataReader  # noqa: E402
 from junifer.markers.complexity import RangeEntropy  # noqa: E402
+from junifer.pipeline.utils import _check_ants  # noqa: E402
 from junifer.storage import SQLiteFeatureStorage  # noqa: E402
 from junifer.testing.datagrabbers import (  # noqa: E402
     SPMAuditoryTestingDataGrabber,
@@ -24,6 +25,9 @@ from junifer.testing.datagrabbers import (  # noqa: E402
 PARCELLATION = "Schaefer100x17"
 
 
+@pytest.mark.skipif(
+    _check_ants() is False, reason="requires ANTs to be in PATH"
+)
 def test_compute() -> None:
     """Test RangeEntropy compute()."""
     with SPMAuditoryTestingDataGrabber() as dg:
@@ -36,15 +40,19 @@ def test_compute() -> None:
         # Compute the marker
         feature_map = marker.fit_transform(element_data)
         # Assert the dimension of timeseries
-        assert feature_map["BOLD"]["data"].ndim == 2
+        assert feature_map["BOLD"]["complexity"]["data"].ndim == 2
 
 
 def test_get_output_type() -> None:
     """Test RangeEntropy get_output_type()."""
-    marker = RangeEntropy(parcellation=PARCELLATION)
-    assert marker.get_output_type("BOLD") == "vector"
+    assert "vector" == RangeEntropy(parcellation=PARCELLATION).get_output_type(
+        input_type="BOLD", output_feature="complexity"
+    )
 
 
+@pytest.mark.skipif(
+    _check_ants() is False, reason="requires ANTs to be in PATH"
+)
 def test_store(tmp_path: Path) -> None:
     """Test RangeEntropy store().
 

junifer/markers/complexity/tests/test_range_entropy_auc.py

@@ -14,6 +14,7 @@ pytest.importorskip("neurokit2")
 
 from junifer.datareader import DefaultDataReader  # noqa: E402
 from junifer.markers.complexity import RangeEntropyAUC  # noqa: E402
+from junifer.pipeline.utils import _check_ants  # noqa: E402
 from junifer.storage import SQLiteFeatureStorage  # noqa: E402
 from junifer.testing.datagrabbers import (  # noqa: E402
     SPMAuditoryTestingDataGrabber,
@@ -24,6 +25,9 @@ from junifer.testing.datagrabbers import (  # noqa: E402
 PARCELLATION = "Schaefer100x17"
 
 
+@pytest.mark.skipif(
+    _check_ants() is False, reason="requires ANTs to be in PATH"
+)
 def test_compute() -> None:
     """Test RangeEntropyAUC compute()."""
     with SPMAuditoryTestingDataGrabber() as dg:
@@ -36,15 +40,19 @@ def test_compute() -> None:
         # Compute the marker
         feature_map = marker.fit_transform(element_data)
         # Assert the dimension of timeseries
-        assert feature_map["BOLD"]["data"].ndim == 2
+        assert feature_map["BOLD"]["complexity"]["data"].ndim == 2
 
 
 def test_get_output_type() -> None:
     """Test RangeEntropyAUC get_output_type()."""
-    marker = RangeEntropyAUC(parcellation=PARCELLATION)
-    assert marker.get_output_type("BOLD") == "vector"
+    assert "vector" == RangeEntropyAUC(
+        parcellation=PARCELLATION
+    ).get_output_type(input_type="BOLD", output_feature="complexity")
 
 
+@pytest.mark.skipif(
+    _check_ants() is False, reason="requires ANTs to be in PATH"
+)
 def test_store(tmp_path: Path) -> None:
     """Test RangeEntropyAUC store().
 

junifer/markers/complexity/tests/test_sample_entropy.py

@@ -13,6 +13,7 @@ pytest.importorskip("neurokit2")
 
 from junifer.datareader import DefaultDataReader  # noqa: E402
 from junifer.markers.complexity import SampleEntropy  # noqa: E402
+from junifer.pipeline.utils import _check_ants  # noqa: E402
 from junifer.storage import SQLiteFeatureStorage  # noqa: E402
 from junifer.testing.datagrabbers import (  # noqa: E402
     SPMAuditoryTestingDataGrabber,
@@ -23,6 +24,9 @@ from junifer.testing.datagrabbers import (  # noqa: E402
 PARCELLATION = "Schaefer100x17"
 
 
+@pytest.mark.skipif(
+    _check_ants() is False, reason="requires ANTs to be in PATH"
+)
 def test_compute() -> None:
     """Test SampleEntropy compute()."""
     with SPMAuditoryTestingDataGrabber() as dg:
@@ -35,15 +39,19 @@ def test_compute() -> None:
         # Compute the marker
         feature_map = marker.fit_transform(element_data)
         # Assert the dimension of timeseries
-        assert feature_map["BOLD"]["data"].ndim == 2
+        assert feature_map["BOLD"]["complexity"]["data"].ndim == 2
 
 
 def test_get_output_type() -> None:
     """Test SampleEntropy get_output_type()."""
-    marker = SampleEntropy(parcellation=PARCELLATION)
-    assert marker.get_output_type("BOLD") == "vector"
+    assert "vector" == SampleEntropy(
+        parcellation=PARCELLATION
+    ).get_output_type(input_type="BOLD", output_feature="complexity")
 
 
+@pytest.mark.skipif(
+    _check_ants() is False, reason="requires ANTs to be in PATH"
+)
 def test_store(tmp_path: Path) -> None:
     """Test SampleEntropy store().
 

junifer/markers/complexity/tests/test_weighted_perm_entropy.py

@@ -13,6 +13,7 @@ pytest.importorskip("neurokit2")
 
 from junifer.datareader import DefaultDataReader  # noqa: E402
 from junifer.markers.complexity import WeightedPermEntropy  # noqa: E402
+from junifer.pipeline.utils import _check_ants  # noqa: E402
 from junifer.storage import SQLiteFeatureStorage  # noqa: E402
 from junifer.testing.datagrabbers import (  # noqa: E402
     SPMAuditoryTestingDataGrabber,
@@ -23,6 +24,9 @@ from junifer.testing.datagrabbers import (  # noqa: E402
 PARCELLATION = "Schaefer100x17"
 
 
+@pytest.mark.skipif(
+    _check_ants() is False, reason="requires ANTs to be in PATH"
+)
 def test_compute() -> None:
     """Test WeightedPermEntropy compute()."""
     with SPMAuditoryTestingDataGrabber() as dg:
@@ -35,15 +39,19 @@ def test_compute() -> None:
         # Compute the marker
         feature_map = marker.fit_transform(element_data)
         # Assert the dimension of timeseries
-        assert feature_map["BOLD"]["data"].ndim == 2
+        assert feature_map["BOLD"]["complexity"]["data"].ndim == 2
 
 
 def test_get_output_type() -> None:
     """Test WeightedPermEntropy get_output_type()."""
-    marker = WeightedPermEntropy(parcellation=PARCELLATION)
-    assert marker.get_output_type("BOLD") == "vector"
+    assert "vector" == WeightedPermEntropy(
+        parcellation=PARCELLATION
+    ).get_output_type(input_type="BOLD", output_feature="complexity")
 
 
+@pytest.mark.skipif(
+    _check_ants() is False, reason="requires ANTs to be in PATH"
+)
 def test_store(tmp_path: Path) -> None:
     """Test WeightedPermEntropy store().
 

junifer/markers/complexity/weighted_perm_entropy.py

@@ -14,6 +14,9 @@ from ...utils import logger, warn_with_log
 from .complexity_base import ComplexityBase
 
 
+__all__ = ["WeightedPermEntropy"]
+
+
 @register_marker
 class WeightedPermEntropy(ComplexityBase):
     """Class for weighted permutation entropy of a time series.

junifer/markers/ets_rss.py

@@ -17,6 +17,9 @@ from .parcel_aggregation import ParcelAggregation
 from .utils import _ets
 
 
+__all__ = ["RSSETSMarker"]
+
+
 @register_marker
 class RSSETSMarker(BaseMarker):
     """Class for root sum of squares of edgewise timeseries.
@@ -44,6 +47,12 @@ class RSSETSMarker(BaseMarker):
 
     _DEPENDENCIES: ClassVar[Set[str]] = {"nilearn"}
 
+    _MARKER_INOUT_MAPPINGS: ClassVar[Dict[str, Dict[str, str]]] = {
+        "BOLD": {
+            "rss_ets": "timeseries",
+        },
+    }
+
     def __init__(
         self,
         parcellation: Union[str, List[str]],
@@ -58,33 +67,6 @@ class RSSETSMarker(BaseMarker):
         self.masks = masks
         super().__init__(name=name)
 
-    def get_valid_inputs(self) -> List[str]:
-        """Get valid data types for input.
-
-        Returns
-        -------
-        list of str
-            The list of data types that can be used as input for this marker.
-
-        """
-        return ["BOLD"]
-
-    def get_output_type(self, input_type: str) -> str:
-        """Get output type.
-
-        Parameters
-        ----------
-        input_type : str
-            The data type input to the marker.
-
-        Returns
-        -------
-        str
-            The storage type output by the marker.
-
-        """
-        return "timeseries"
-
     def compute(
         self,
         input: Dict[str, Any],
@@ -106,8 +88,9 @@ class RSSETSMarker(BaseMarker):
         Returns
         -------
         dict
-            The computed result as dictionary. The dictionary has the following
-            keys:
+            The computed result as dictionary. This will be either returned
+            to the user or stored in the storage by calling the store method
+            with this as a parameter. The dictionary has the following keys:
 
             * ``data`` : the actual computed values as a numpy.ndarray
             * ``col_names`` : the column labels for the computed values as list
@@ -121,20 +104,22 @@ class RSSETSMarker(BaseMarker):
 
         """
         logger.debug("Calculating root sum of squares of edgewise timeseries.")
-        # Initialize a ParcelAggregation
-        parcel_aggregation = ParcelAggregation(
+        # Perform aggregation
+        aggregation = ParcelAggregation(
             parcellation=self.parcellation,
             method=self.agg_method,
             method_params=self.agg_method_params,
             masks=self.masks,
-        )
-        # Compute the parcel aggregation
-        out = parcel_aggregation.compute(input=input, extra_input=extra_input)
-        edge_ts, _ = _ets(out["data"])
-        # Compute the RSS
-        out["data"] = np.sum(edge_ts**2, 1) ** 0.5
-        # Make it 2D
-        out["data"] = out["data"][:, np.newaxis]
-        # Set correct column label
-        out["col_names"] = ["root_sum_of_squares_ets"]
-        return out
+        ).compute(input=input, extra_input=extra_input)
+        # Compute edgewise timeseries
+        edge_ts, _ = _ets(aggregation["aggregation"]["data"])
+        # Compute the RSS of edgewise timeseries
+        rss = np.sum(edge_ts**2, 1) ** 0.5
+
+        return {
+            "rss_ets": {
+                # Make it 2D
+                "data": rss[:, np.newaxis],
+                "col_names": ["root_sum_of_squares_ets"],
+            }
+        }

junifer/markers/falff/__init__.py

@@ -5,3 +5,6 @@
 
 from .falff_parcels import ALFFParcels
 from .falff_spheres import ALFFSpheres
+
+
+__all__ = ["ALFFParcels", "ALFFSpheres"]

junifer/markers/falff/_afni_falff.py

@@ -26,6 +26,9 @@ if TYPE_CHECKING:
     from nibabel import Nifti1Image
 
 
+__all__ = ["AFNIALFF"]
+
+
 @singleton
 class AFNIALFF:
     """Class for computing ALFF using AFNI.
@@ -121,7 +124,7 @@ class AFNIALFF:
         convert_alff_cmd = [
             "3dAFNItoNIFTI",
             f"-prefix {alff_afni_to_nifti_out_path.resolve()}",
-            f"{alff_falff_out_path_prefix}_ALFF+tlrc.BRIK",
+            f"{alff_falff_out_path_prefix}_ALFF+orig.BRIK",
         ]
         # Call 3dAFNItoNIFTI
         run_ext_cmd(name="3dAFNItoNIFTI", cmd=convert_alff_cmd)
@@ -133,7 +136,7 @@ class AFNIALFF:
         convert_falff_cmd = [
             "3dAFNItoNIFTI",
             f"-prefix {falff_afni_to_nifti_out_path.resolve()}",
-            f"{alff_falff_out_path_prefix}_fALFF+tlrc.BRIK",
+            f"{alff_falff_out_path_prefix}_fALFF+orig.BRIK",
         ]
         # Call 3dAFNItoNIFTI
         run_ext_cmd(name="3dAFNItoNIFTI", cmd=convert_falff_cmd)

junifer/markers/falff/_junifer_falff.py

@@ -27,6 +27,9 @@ if TYPE_CHECKING:
     from nibabel import Nifti1Image
 
 
+__all__ = ["JuniferALFF"]
+
+
 @singleton
 class JuniferALFF:
     """Class for computing ALFF using junifer.

junifer/markers/falff/falff_base.py

@@ -29,13 +29,14 @@ if TYPE_CHECKING:
     from nibabel import Nifti1Image
 
 
+__all__ = ["ALFFBase"]
+
+
 class ALFFBase(BaseMarker):
     """Base class for (fractional) Amplitude Low Frequency Fluctuation.
 
     Parameters
     ----------
-    fractional : bool
-        Whether to compute fractional ALFF.
     highpass : positive float
         Highpass cutoff frequency.
     lowpass : positive float
@@ -82,9 +83,15 @@ class ALFFBase(BaseMarker):
         },
     ]
 
+    _MARKER_INOUT_MAPPINGS: ClassVar[Dict[str, Dict[str, str]]] = {
+        "BOLD": {
+            "alff": "vector",
+            "falff": "vector",
+        },
+    }
+
     def __init__(
         self,
-        fractional: bool,
         highpass: float,
         lowpass: float,
         using: str,
@@ -107,45 +114,12 @@ class ALFFBase(BaseMarker):
             )
         self.using = using
         self.tr = tr
-        self.fractional = fractional
-
-        # Create a name based on the class name if none is provided
-        if name is None:
-            suffix = "_fractional" if fractional else ""
-            name = f"{self.__class__.__name__}{suffix}"
         super().__init__(on="BOLD", name=name)
 
-    def get_valid_inputs(self) -> List[str]:
-        """Get valid data types for input.
-
-        Returns
-        -------
-        list of str
-            The list of data types that can be used as input for this marker.
-
-        """
-        return ["BOLD"]
-
-    def get_output_type(self, input_type: str) -> str:
-        """Get output type.
-
-        Parameters
-        ----------
-        input_type : str
-            The data type input to the marker.
-
-        Returns
-        -------
-        str
-            The storage type output by the marker.
-
-        """
-        return "vector"
-
     def _compute(
         self,
         input_data: Dict[str, Any],
-    ) -> Tuple["Nifti1Image", Path]:
+    ) -> Tuple["Nifti1Image", "Nifti1Image", Path, Path]:
         """Compute ALFF and fALFF.
 
         Parameters
@@ -158,9 +132,13 @@ class ALFFBase(BaseMarker):
         Returns
         -------
         Niimg-like object
-            The ALFF / fALFF as NIfTI.
+            The ALFF as NIfTI.
+        Niimg-like object
+            The fALFF as NIfTI.
+        pathlib.Path
+            The path to the ALFF as NIfTI.
         pathlib.Path
-            The path to the ALFF / fALFF as NIfTI.
+            The path to the fALFF as NIfTI.
 
         """
         logger.debug("Calculating ALFF and fALFF")
@@ -183,11 +161,7 @@ class ALFFBase(BaseMarker):
         # parcellation / coordinates to native space, else the
         # path should be passed for use later if required.
         # TODO(synchon): will be taken care in #292
-        if input_data["space"] == "native" and self.fractional:
-            return falff, input_data["path"]
-        elif input_data["space"] == "native" and not self.fractional:
-            return alff, input_data["path"]
-        elif input_data["space"] != "native" and self.fractional:
-            return falff, falff_path
+        if input_data["space"] == "native":
+            return alff, falff, input_data["path"], input_data["path"]
         else:
-            return alff, alff_path
+            return alff, falff, alff_path, falff_path