junifer 0.0.6.dev538__py3-none-any.whl → 0.0.7.dev43__py3-none-any.whl

junifer/datagrabber/tests/test_dmcc13_benchmark.py

@@ -264,7 +264,7 @@ def test_DMCC13Benchmark_invalid_sessions():
     """Test DMCC13Benchmark DataGrabber invalid sessions."""
     with pytest.raises(
         ValueError,
-        match=("phonyses is not a valid session in " "the DMCC dataset"),
+        match=("phonyses is not a valid session in the DMCC dataset"),
     ):
         DMCC13Benchmark(sessions="phonyses")
 
@@ -273,9 +273,7 @@ def test_DMCC13Benchmark_invalid_tasks():
     """Test DMCC13Benchmark DataGrabber invalid tasks."""
     with pytest.raises(
         ValueError,
-        match=(
-            "thisisnotarealtask is not a valid task in " "the DMCC dataset"
-        ),
+        match=("thisisnotarealtask is not a valid task in the DMCC dataset"),
     ):
         DMCC13Benchmark(tasks="thisisnotarealtask")
 
@@ -284,9 +282,7 @@ def test_DMCC13Benchmark_phase_encodings():
     """Test DMCC13Benchmark DataGrabber invalid phase encodings."""
     with pytest.raises(
         ValueError,
-        match=(
-            "moonphase is not a valid phase encoding in " "the DMCC dataset"
-        ),
+        match=("moonphase is not a valid phase encoding in the DMCC dataset"),
     ):
         DMCC13Benchmark(phase_encodings="moonphase")
 
@@ -295,6 +291,6 @@ def test_DMCC13Benchmark_runs():
     """Test DMCC13Benchmark DataGrabber invalid runs."""
     with pytest.raises(
         ValueError,
-        match=("cerebralrun is not a valid run in " "the DMCC dataset"),
+        match=("cerebralrun is not a valid run in the DMCC dataset"),
     ):
         DMCC13Benchmark(runs="cerebralrun")

junifer/external/nilearn/junifer_connectivity_measure.py

@@ -3,6 +3,8 @@
 # Authors: Synchon Mandal <s.mandal@fz-juelich.de>
 # License: AGPL
 
+import sys
+from itertools import product
 from typing import Callable, Optional
 
 import numpy as np
@@ -322,11 +324,13 @@ class JuniferConnectivityMeasure(ConnectivityMeasure):
         The covariance estimator
         (default ``EmpiricalCovariance(store_precision=False)``).
     kind : {"covariance", "correlation", "spearman correlation", \
-            "partial correlation", "tangent", "precision"}, optional
+            "partial correlation", "xi correlation", "tangent", \
+            "precision"}, optional
         The matrix kind. The default value uses Pearson's correlation.
         If ``"spearman correlation"`` is used, the data will be ranked before
-        estimating the covariance. For the use of ``"tangent"`` see [1]_
-        (default "correlation").
+        estimating the covariance. For ``"xi correlation"``, the coefficient
+        is not symmetric and should be interpreted as a measure of dependence
+        [2]_ . For the use of ``"tangent"`` see [1]_ (default "correlation").
     vectorize : bool, optional
         If True, connectivity matrices are reshaped into 1D arrays and only
         their flattened lower triangular parts are returned (default False).
@@ -372,6 +376,12 @@ class JuniferConnectivityMeasure(ConnectivityMeasure):
            Springer.
            doi:10/cn2h9c.
 
+    .. [2] Chatterjee, S.
+           A new coefficient of correlation.
+           Journal of the American Statistical Association 116.536 (2021):
+           2009-2022.
+           doi:10.1080/01621459.2020.1758115.
+
     """
 
     def __init__(
@@ -420,6 +430,25 @@ class JuniferConnectivityMeasure(ConnectivityMeasure):
                 covariances_std.append(self.cov_estimator_.fit(x).covariance_)
 
             connectivities = [cov_to_corr(cov) for cov in covariances_std]
+        elif self.kind == "xi correlation":
+            if sys.version_info < (3, 10):  # pragma: no cover
+                raise_error(
+                    klass=RuntimeError,
+                    msg=(
+                        "scipy.stats.chatterjeexi is available from "
+                        "scipy 1.15.0 and that requires Python 3.10 and above."
+                    ),
+                )
+            connectivities = []
+            for x in X:
+                n_rois = x.shape[1]
+                connectivity = np.ones((n_rois, n_rois))
+                for i, j in product(range(n_rois), range(n_rois)):
+                    if i != j:
+                        connectivity[i, j] = stats.chatterjeexi(
+                            x[:, i], x[:, j], y_continuous=True
+                        ).statistic
+                connectivities.append(connectivity)
         else:
             covariances = [self.cov_estimator_.fit(x).covariance_ for x in X]
             if self.kind in ("covariance", "tangent"):

junifer/external/nilearn/tests/test_junifer_connectivity_measure.py

@@ -4,6 +4,7 @@
 # License: AGPL
 
 import copy
+import sys
 import warnings
 from math import cosh, exp, log, sinh, sqrt
 from typing import TYPE_CHECKING, Optional, Union
@@ -12,7 +13,11 @@ import numpy as np
 import pytest
 from nilearn.connectome.connectivity_matrices import sym_matrix_to_vec
 from nilearn.tests.test_signal import generate_signals
-from numpy.testing import assert_array_almost_equal, assert_array_equal
+from numpy.testing import (
+    assert_allclose,
+    assert_array_almost_equal,
+    assert_array_equal,
+)
 from pandas import DataFrame
 from scipy import linalg
 from sklearn.covariance import EmpiricalCovariance, LedoitWolf
@@ -1088,3 +1093,42 @@ def test_connectivity_measure_standardize(
         ).fit_transform(signals)
         for m in record:
             assert match not in m.message
+
+
+@pytest.mark.skipif(
+    sys.version_info > (3, 9),
+    reason="will have correct scipy version so no error",
+)
+def test_xi_correlation_error() -> None:
+    """Check xi correlation according to paper."""
+    with pytest.raises(RuntimeError, match="scipy.stats.chatterjeexi"):
+        JuniferConnectivityMeasure(kind="xi correlation").fit_transform(
+            np.zeros((2, 2))
+        )
+
+
+@pytest.mark.skipif(
+    sys.version_info < (3, 10),
+    reason=(
+        "needs scipy 1.15.0 and above which in turn requires "
+        "python 3.10 and above"
+    ),
+)
+def test_xi_correlation() -> None:
+    """Check xi correlation according to paper."""
+    rng = np.random.default_rng(25982435982346983)
+    x = rng.random(size=10)
+    y = rng.random(size=10)
+    arr = np.column_stack((x, y))
+    expected = np.array(
+        [
+            [
+                [1.0, -0.3030303],
+                [-0.18181818, 1.0],
+            ]
+        ]
+    )
+    got = JuniferConnectivityMeasure(kind="xi correlation").fit_transform(
+        [arr]
+    )
+    assert_allclose(expected, got)

junifer/markers/base.py

@@ -229,9 +229,9 @@ class BaseMarker(ABC, PipelineStepMixin, UpdateMetaMixin):
                     # feature data is not manipulated, only meta
                     self.update_meta(feature_data_copy, "marker")
                     # Update marker feature's metadata name
-                    feature_data_copy["meta"]["marker"][
-                        "name"
-                    ] += f"_{feature_name}"
+                    feature_data_copy["meta"]["marker"]["name"] += (
+                        f"_{feature_name}"
+                    )
 
                     if storage is not None:
                         logger.info(f"Storing in {storage}")

junifer/markers/brainprint.py

@@ -116,7 +116,7 @@ class BrainPrint(BaseMarker):
         aseg_path: Path,
         norm_path: Path,
         indices: list,
-    ) -> Path:
+    ) -> Path:  # pragma: no cover
         """Generate a surface from the aseg and label files.
 
         Parameters
@@ -191,7 +191,7 @@ class BrainPrint(BaseMarker):
         self,
         aseg_path: Path,
         norm_path: Path,
-    ) -> dict[str, Path]:
+    ) -> dict[str, Path]:  # pragma: no cover
         """Create surfaces from FreeSurfer aseg labels.
 
         Parameters
@@ -266,7 +266,7 @@ class BrainPrint(BaseMarker):
         rh_white_path: Path,
         lh_pial_path: Path,
         rh_pial_path: Path,
-    ) -> dict[str, Path]:
+    ) -> dict[str, Path]:  # pragma: no cover
         """Create cortical surfaces from FreeSurfer labels.
 
         Parameters
@@ -308,7 +308,7 @@ class BrainPrint(BaseMarker):
     def _fix_nan(
         self,
         input_data: list[Union[float, str, npt.ArrayLike]],
-    ) -> np.ndarray:
+    ) -> np.ndarray:  # pragma: no cover
         """Convert BrainPrint output with string NaN to ``numpy.nan``.
 
         Parameters
@@ -330,7 +330,7 @@ class BrainPrint(BaseMarker):
         self,
         input: dict[str, Any],
         extra_input: Optional[dict] = None,
-    ) -> dict:
+    ) -> dict:  # pragma: no cover
         """Compute.
 
         Parameters

junifer/markers/complexity/multiscale_entropy_auc.py

@@ -114,9 +114,9 @@ class MultiscaleEntropyAUC(ComplexityBase):
 
         assert isinstance(emb_dim, int), "Embedding dimension must be integer."
         assert isinstance(scale, int), "Scale must be integer."
-        assert isinstance(
-            tol, float
-        ), "Tolerance must be a positive float number."
+        assert isinstance(tol, float), (
+            "Tolerance must be a positive float number."
+        )
 
         _, n_roi = extracted_bold_values.shape
         MSEn_auc_roi = np.zeros((n_roi, 1))

junifer/markers/complexity/range_entropy.py

@@ -114,9 +114,9 @@ class RangeEntropy(ComplexityBase):
 
         assert isinstance(emb_dim, int), "Embedding dimension must be integer."
         assert isinstance(delay, int), "Delay must be integer."
-        assert isinstance(
-            tolerance, float
-        ), "Tolerance must be a float number between 0 and 1."
+        assert isinstance(tolerance, float), (
+            "Tolerance must be a float number between 0 and 1."
+        )
 
         _, n_roi = extracted_bold_values.shape
         range_en_roi = np.zeros((n_roi, 1))

junifer/markers/complexity/sample_entropy.py

@@ -115,9 +115,9 @@ class SampleEntropy(ComplexityBase):
 
         assert isinstance(emb_dim, int), "Embedding dimension must be integer."
         assert isinstance(delay, int), "Delay must be integer."
-        assert isinstance(
-            tol, float
-        ), "Tolerance must be a positive float number."
+        assert isinstance(tol, float), (
+            "Tolerance must be a positive float number."
+        )
 
         _, n_roi = extracted_bold_values.shape
         samp_en_roi = np.zeros((n_roi, 1))

junifer/markers/falff/falff_parcels.py

@@ -151,9 +151,7 @@ class ALFFParcels(ALFFBase):
                 ).compute(
                     input=aggregation_alff_input,
                     extra_input=extra_input,
-                )[
-                    "aggregation"
-                ],
+                )["aggregation"],
             },
             "falff": {
                 **ParcelAggregation(
@@ -165,8 +163,6 @@ class ALFFParcels(ALFFBase):
                 ).compute(
                     input=aggregation_falff_input,
                     extra_input=extra_input,
-                )[
-                    "aggregation"
-                ],
+                )["aggregation"],
             },
         }

junifer/markers/falff/falff_spheres.py

@@ -164,9 +164,7 @@ class ALFFSpheres(ALFFBase):
                 ).compute(
                     input=aggregation_alff_input,
                     extra_input=extra_input,
-                )[
-                    "aggregation"
-                ],
+                )["aggregation"],
             },
             "falff": {
                 **SphereAggregation(
@@ -180,8 +178,6 @@ class ALFFSpheres(ALFFBase):
                 ).compute(
                     input=aggregation_falff_input,
                     extra_input=extra_input,
-                )[
-                    "aggregation"
-                ],
+                )["aggregation"],
             },
         }

junifer/markers/functional_connectivity/functional_connectivity_base.py

@@ -3,7 +3,6 @@
 # Authors: Synchon Mandal <s.mandal@fz-juelich.de>
 # License: AGPL
 
-
 from abc import abstractmethod
 from typing import Any, ClassVar, Optional, Union
 
@@ -143,14 +142,17 @@ class FunctionalConnectivityBase(BaseMarker):
             },
         )
         # Create dictionary for output
+        labels = aggregation["aggregation"]["col_names"]
         return {
             "functional_connectivity": {
                 "data": connectivity.fit_transform(
                     [aggregation["aggregation"]["data"]]
                 )[0],
-                # Create column names
-                "row_names": aggregation["aggregation"]["col_names"],
-                "col_names": aggregation["aggregation"]["col_names"],
-                "matrix_kind": "tril",
+                "row_names": labels,
+                "col_names": labels,
+                # xi correlation coefficient is not symmetric
+                "matrix_kind": (
+                    "full" if self.conn_method == "xi correlation" else "tril"
+                ),
             },
         }

junifer/markers/functional_connectivity/tests/test_functional_connectivity_parcels.py

@@ -91,7 +91,8 @@ def test_FunctionalConnectivityParcels(
         )
         # Compute the connectivity measure
         connectivity_measure = ConnectivityMeasure(
-            cov_estimator=cov_estimator, kind="correlation"  # type: ignore
+            cov_estimator=cov_estimator,
+            kind="correlation",  # type: ignore
         ).fit_transform([extracted_timeseries])[0]
 
         # Check that FC are almost equal

junifer/markers/functional_connectivity/tests/test_functional_connectivity_spheres.py

@@ -92,7 +92,8 @@ def test_FunctionalConnectivitySpheres(
         )
         # Compute the connectivity measure
         connectivity_measure = ConnectivityMeasure(
-            cov_estimator=cov_estimator, kind="correlation"  # type: ignore
+            cov_estimator=cov_estimator,
+            kind="correlation",  # type: ignore
         ).fit_transform([extracted_timeseries])[0]
 
         # Check that FC are almost equal

junifer/markers/reho/_afni_reho.py

@@ -41,7 +41,7 @@ class AFNIReHo(metaclass=Singleton):
         },
     ]
 
-    def __del__(self) -> None:
+    def __del__(self) -> None:  # pragma: no cover
         """Terminate the class."""
         # Clear the computation cache
         logger.debug("Clearing cache for ReHo computation via AFNI")

junifer/markers/reho/reho_base.py

@@ -3,7 +3,6 @@
 # Authors: Synchon Mandal <s.mandal@fz-juelich.de>
 # License: AGPL
 
-
 from pathlib import Path
 from typing import (
     TYPE_CHECKING,

junifer/markers/reho/reho_parcels.py

@@ -3,7 +3,6 @@
 # Authors: Synchon Mandal <s.mandal@fz-juelich.de>
 # License: AGPL
 
-
 from typing import Any, Optional, Union
 
 import numpy as np

junifer/markers/reho/reho_spheres.py

@@ -3,7 +3,6 @@
 # Authors: Synchon Mandal <s.mandal@fz-juelich.de>
 # License: AGPL
 
-
 from typing import Any, Optional, Union
 
 import numpy as np

junifer/markers/temporal_snr/temporal_snr_base.py

@@ -3,7 +3,6 @@
 # Authors: Leonard Sasse <l.sasse@fz-juelich.de>
 # License: AGPL
 
-
 from abc import abstractmethod
 from typing import Any, ClassVar, Optional, Union
 

junifer/markers/tests/test_markers_base.py

@@ -20,7 +20,6 @@ def test_base_marker_subclassing() -> None:
 
     # Create concrete class
     class MyBaseMarker(BaseMarker):
-
         _MARKER_INOUT_MAPPINGS = {  # noqa: RUF012
             "BOLD": {
                 "feat_1": "timeseries",

junifer/onthefly/_brainprint.py

@@ -19,7 +19,7 @@ def normalize(
     storage: StorageLike,
     features: dict[str, dict[str, Optional[str]]],
     kind: str,
-) -> pd.DataFrame:
+) -> pd.DataFrame:  # pragma: no cover
     """Read stored brainprint data and normalize either surfaces or volumes.
 
     Parameters
@@ -79,7 +79,7 @@ def normalize(
         )
     else:
         raise_error(
-            "Invalid value for `kind`, should be one of: " f"{valid_kind}"
+            f"Invalid value for `kind`, should be one of: {valid_kind}"
         )
 
     return normalized_df
@@ -89,7 +89,7 @@ def reweight(
     storage: StorageLike,
     feature_name: Optional[str] = None,
     feature_md5: Optional[str] = None,
-) -> pd.DataFrame:
+) -> pd.DataFrame:  # pragma: no cover
     """Read stored brainprint data and reweight eigenvalues.
 
     Parameters

junifer/onthefly/read_transform.py

@@ -3,7 +3,6 @@
 # Authors: Synchon Mandal <s.mandal@fz-juelich.de>
 # License: AGPL
 
-
 from typing import Optional
 
 import pandas as pd
@@ -85,7 +84,7 @@ def read_transform(
         # Check bctpy import
         try:
             import bct
-        except ImportError as err:
+        except ImportError as err:  # pragma: no cover
             raise_error(msg=str(err), klass=ImportError)
 
         # Warning about function usage

junifer/onthefly/tests/test_read_transform.py

@@ -3,7 +3,6 @@
 # Authors: Synchon Mandal <s.mandal@fz-juelich.de>
 # License: AGPL
 
-
 import logging
 from pathlib import Path
 

junifer/pipeline/tests/test_marker_collection.py

@@ -186,7 +186,8 @@ def test_marker_collection_storage(tmp_path: Path) -> None:
         assert out is None
 
     mc2 = MarkerCollection(
-        markers=markers, datareader=DefaultDataReader()  # type: ignore
+        markers=markers,
+        datareader=DefaultDataReader(),  # type: ignore
     )
     mc2.validate(dg)
     assert mc2._storage is None

junifer/pipeline/workdir_manager.py

@@ -197,8 +197,7 @@ class WorkDirManager(metaclass=Singleton):
             return
         if self._elementdir is not None:
             logger.debug(
-                "Deleting element directory at "
-                f"{self._elementdir.resolve()!s}"
+                f"Deleting element directory at {self._elementdir.resolve()!s}"
             )
             shutil.rmtree(self._elementdir, ignore_errors=True)
             self._elementdir = None

junifer/preprocess/confounds/fmriprep_confound_remover.py

@@ -572,7 +572,7 @@ class fMRIPrepConfoundRemover(BasePreprocessor):
         if bold_img.get_fdata().shape[3] != len(confound_df):
             raise_error(
                 "Image time series and confounds have different length!\n"
-                f"\tImage time series: { bold_img.get_fdata().shape[3]}\n"
+                f"\tImage time series: {bold_img.get_fdata().shape[3]}\n"
                 f"\tConfounds: {len(confound_df)}"
             )
 

junifer/preprocess/confounds/tests/test_fmriprep_confound_remover.py

@@ -5,7 +5,6 @@
 #          Synchon Mandal <s.mandal@fz-juelich.de>
 # License: AGPL
 
-
 import numpy as np
 import pandas as pd
 import pytest

junifer/preprocess/smoothing/tests/test_smoothing.py

@@ -3,7 +3,6 @@
 # Authors: Synchon Mandal <s.mandal@fz-juelich.de>
 # License: AGPL
 
-
 import pytest
 
 from junifer.datareader import DefaultDataReader

junifer/preprocess/warping/_ants_warper.py

@@ -72,7 +72,7 @@ class ANTsWarper:
         )
 
         # Native space warping
-        if reference == "T1w":
+        if reference == "T1w":  # pragma: no cover
             logger.debug("Using ANTs for space warping")
 
             # Get the min of the voxel sizes from input and use it as the
@@ -237,8 +237,7 @@ class ANTsWarper:
             if input.get("mask") is not None:
                 # Create a tempfile for warped mask output
                 apply_transforms_mask_out_path = element_tempdir / (
-                    f"warped_mask_from_{input['space']}_to_"
-                    f"{reference}.nii.gz"
+                    f"warped_mask_from_{input['space']}_to_{reference}.nii.gz"
                 )
                 # Set antsApplyTransforms command
                 apply_transforms_mask_cmd = [

junifer/preprocess/warping/_fsl_warper.py

@@ -40,7 +40,7 @@ class FSLWarper:
         self,
         input: dict[str, Any],
         extra_input: dict[str, Any],
-    ) -> dict[str, Any]:
+    ) -> dict[str, Any]:  # pragma: no cover
         """Preprocess using FSL.
 
         Parameters

junifer/preprocess/warping/space_warper.py

@@ -77,7 +77,7 @@ class SpaceWarper(BasePreprocessor):
         self.reference = reference
         # Set required data types based on reference and
         # initialize superclass
-        if self.reference == "T1w":
+        if self.reference == "T1w":  # pragma: no cover
             required_data_types = [self.reference, "Warp"]
             # Listify on
             if not isinstance(on, list):
@@ -170,7 +170,9 @@ class SpaceWarper(BasePreprocessor):
         """
         logger.info(f"Warping to {self.reference} space using SpaceWarper")
         # Transform to native space
-        if self.using in ["fsl", "ants", "auto"] and self.reference == "T1w":
+        if (
+            self.using in ["fsl", "ants", "auto"] and self.reference == "T1w"
+        ):  # pragma: no cover
             # Check for extra inputs
             if extra_input is None:
                 raise_error(

junifer/storage/pandas_base.py

@@ -187,7 +187,9 @@ class PandasBaseFeatureStorage(BaseFeatureStorage):
         )
         # Prepare new dataframe
         df = pd.DataFrame(
-            data=data, columns=col_names, index=idx  # type: ignore
+            data=data,
+            columns=col_names,
+            index=idx,  # type: ignore
         )
         # Store dataframe
         self.store_df(meta_md5=meta_md5, element=element, df=df)

junifer/storage/sqlite.py

@@ -229,9 +229,7 @@ class SQLiteFeatureStorage(PandasBaseFeatureStorage):
         # Format index names for retrieved data
         meta_df.index = meta_df.index.str.replace(r"meta_", "")
         # Convert dataframe to dictionary
-        out: dict[str, dict[str, str]] = meta_df.to_dict(
-            orient="index"
-        )  # type: ignore
+        out: dict[str, dict[str, str]] = meta_df.to_dict(orient="index")  # type: ignore
         # Format output
         for md5, t_meta in out.items():
             for k, v in t_meta.items():
@@ -536,8 +534,7 @@ class SQLiteFeatureStorage(PandasBaseFeatureStorage):
                 klass=IOError,
             )
         logger.info(
-            "Collecting data from "
-            f"{self.uri.parent}/*{self.uri.name}"  # type: ignore
+            f"Collecting data from {self.uri.parent}/*{self.uri.name}"  # type: ignore
         )
         # Create new instance
         out_storage = SQLiteFeatureStorage(uri=self.uri, upsert="ignore")
@@ -596,9 +593,7 @@ def _generate_update_statements(table, index_col, rows_to_update):
     for i, (_, keys) in enumerate(pk_indb.iterrows()):
         stmt = (
             table.update()
-            .where(
-                and_(col == keys[j] for j, col in enumerate(pk_cols))
-            )  # type: ignore
+            .where(and_(col == keys[j] for j, col in enumerate(pk_cols)))  # type: ignore
             .values(new_records[i])
         )
         stmts.append(stmt)

junifer/storage/tests/test_pandas_base.py

@@ -37,7 +37,8 @@ def test_element_to_index() -> None:
     assert index.levels[1].name == "idx"  # type: ignore
     # Check second index level values
     assert all(
-        x == i for i, x in enumerate(index.levels[1].values)  # type: ignore
+        x == i
+        for i, x in enumerate(index.levels[1].values)  # type: ignore
     )
     # Check second index level values shape
     assert index.levels[1].values.shape == (10,)  # type: ignore
@@ -69,7 +70,8 @@ def test_element_to_index() -> None:
     assert index.levels[1].name == "scan"  # type: ignore
     # Check second index level values
     assert all(
-        x == i for i, x in enumerate(index.levels[1].values)  # type: ignore
+        x == i
+        for i, x in enumerate(index.levels[1].values)  # type: ignore
     )
     # Check second index level values shape
     assert index.levels[1].values.shape == (7,)  # type: ignore
@@ -97,7 +99,8 @@ def test_element_to_index() -> None:
     assert index.levels[2].name == "idx"  # type: ignore
     # Check third index level values
     assert all(
-        x == i for i, x in enumerate(index.levels[2].values)  # type: ignore
+        x == i
+        for i, x in enumerate(index.levels[2].values)  # type: ignore
     )
     # Check third index level values shape
     assert index.levels[2].values.shape == (10,)  # type: ignore