junifer 0.0.3.dev188__py3-none-any.whl → 0.0.4__py3-none-any.whl

junifer/markers/falff/tests/test_falff_parcels.py

@@ -1,158 +1,126 @@
-"""Provide test for parcel-aggregated (f)ALFF."""
+"""Provide tests for ALFFParcels."""
 
 # Authors: Federico Raimondo <f.raimondo@fz-juelich.de>
 #          Synchon Mandal <s.mandal@fz-juelich.de>
 # License: AGPL
 
+import logging
 from pathlib import Path
 
 import pytest
-from numpy.testing import assert_array_equal
-from scipy.stats import pearsonr
+import scipy as sp
 
 from junifer.datareader import DefaultDataReader
 from junifer.markers.falff import ALFFParcels
+from junifer.pipeline import WorkDirManager
 from junifer.pipeline.utils import _check_afni
 from junifer.storage import SQLiteFeatureStorage
 from junifer.testing.datagrabbers import PartlyCloudyTestingDataGrabber
-from junifer.utils import logger
 
 
-_PARCELLATION = "Schaefer100x7"
+PARCELLATION = "TianxS1x3TxMNInonlinear2009cAsym"
 
 
-def test_ALFFParcels_python() -> None:
-    """Test ALFFParcels using python."""
-    # Get the SPM auditory data:
-
-    with PartlyCloudyTestingDataGrabber() as dg:
-        input = dg["sub-01"]
-
-    input = DefaultDataReader().fit_transform(input)
-    # Create ParcelAggregation object
-    marker = ALFFParcels(
-        parcellation=_PARCELLATION,
-        method="mean",
-        use_afni=False,
-        fractional=False,
-    )
-    python_values = marker.fit_transform(input)["BOLD"]["data"]
-
-    assert marker.use_afni is False
-    assert python_values.ndim == 2
-    assert python_values.shape == (1, 100)
+def test_ALFFParcels(caplog: pytest.LogCaptureFixture, tmp_path: Path) -> None:
+    """Test ALFFParcels.
 
+    Parameters
+    ----------
+    caplog : pytest.LogCaptureFixture
+        The pytest.LogCaptureFixture object.
+    tmp_path : pathlib.Path
+        The path to the test directory.
 
-@pytest.mark.skipif(
-    _check_afni() is False, reason="requires afni to be in PATH"
-)
-def test_ALFFParcels_afni() -> None:
-    """Test ALFFParcels using afni."""
-    # Get the SPM auditory data:
-    with PartlyCloudyTestingDataGrabber() as dg:
-        input = dg["sub-01"]
-
-    input = DefaultDataReader().fit_transform(input)
-    # Create ParcelAggregation object
-    marker = ALFFParcels(
-        parcellation=_PARCELLATION,
-        method="mean",
-        use_afni=True,
-        fractional=False,
-    )
-    assert marker.use_afni is True
-    afni_values = marker.fit_transform(input)["BOLD"]["data"]
-
-    assert afni_values.ndim == 2
-    assert afni_values.shape == (1, 100)
-
-    # Again, should be blazing fast
-    marker = ALFFParcels(
-        parcellation=_PARCELLATION, method="mean", fractional=False
-    )
-    assert marker.use_afni is None
-    afni_values2 = marker.fit_transform(input)["BOLD"]["data"]
-    assert marker.use_afni is True
-    assert_array_equal(afni_values, afni_values2)
+    """
+    with caplog.at_level(logging.DEBUG):
+        with PartlyCloudyTestingDataGrabber() as dg:
+            element_data = DefaultDataReader().fit_transform(dg["sub-01"])
+            # Update workdir to current test's tmp_path
+            WorkDirManager().workdir = tmp_path
+
+            # Initialize marker
+            marker = ALFFParcels(
+                parcellation=PARCELLATION,
+                fractional=False,
+                using="junifer",
+            )
+            # Fit transform marker on data
+            output = marker.fit_transform(element_data)
+
+            assert "Creating cache" in caplog.text
+
+            # Get BOLD output
+            assert "BOLD" in output
+            output_bold = output["BOLD"]
+            # Assert BOLD output keys
+            assert "data" in output_bold
+            assert "col_names" in output_bold
+
+            output_bold_data = output_bold["data"]
+            # Assert BOLD output data dimension
+            assert output_bold_data.ndim == 2
+            assert output_bold_data.shape == (1, 16)
+
+            # Reset log capture
+            caplog.clear()
+            # Initialize storage
+            storage = SQLiteFeatureStorage(tmp_path / "falff_parcels.sqlite")
+            # Fit transform marker on data with storage
+            marker.fit_transform(
+                input=element_data,
+                storage=storage,
+            )
+            # Cache working correctly
+            assert "Creating cache" not in caplog.text
 
 
 @pytest.mark.skipif(
-    _check_afni() is False, reason="requires afni to be in PATH"
+    _check_afni() is False, reason="requires AFNI to be in PATH"
 )
 @pytest.mark.parametrize(
     "fractional", [True, False], ids=["fractional", "non-fractional"]
 )
-def test_ALFFParcels_python_vs_afni(
-    fractional: bool,
-) -> None:
-    """Test ALFFParcels using python.
+def test_ALFFParcels_comparison(tmp_path: Path, fractional: bool) -> None:
+    """Test ALFFParcels implementation comparison.
 
     Parameters
     ----------
+    tmp_path : pathlib.Path
+        The path to the test directory.
     fractional : bool
         Whether to compute fractional ALFF or not.
 
     """
-
-    with PartlyCloudyTestingDataGrabber() as dg:
-        input = dg["sub-01"]
-
-    input = DefaultDataReader().fit_transform(input)
-    # Create ParcelAggregation object
-    marker_python = ALFFParcels(
-        parcellation=_PARCELLATION,
-        method="mean",
-        use_afni=False,
-        fractional=fractional,
-    )
-    python_values = marker_python.fit_transform(input)["BOLD"]["data"]
-
-    assert marker_python.use_afni is False
-    assert python_values.ndim == 2
-    assert python_values.shape == (1, 100)
-
-    marker_afni = ALFFParcels(
-        parcellation=_PARCELLATION,
-        method="mean",
-        use_afni=True,
-        fractional=fractional,
-    )
-    afni_values = marker_afni.fit_transform(input)["BOLD"]["data"]
-
-    assert marker_afni.use_afni is True
-    assert afni_values.ndim == 2
-    assert afni_values.shape == (1, 100)
-
-    r, p = pearsonr(python_values[0], afni_values[0])
-    logger.info(f"Correlation between python and afni: {r} (p={p})")
-    assert r > 0.99
-
-
-def test_ALFFParcels_storage(
-    tmp_path: Path,
-) -> None:
-    """Test ALFFParcels storage.
-
-    Parameters
-    ----------
-    tmp_path : pathlib.Path
-        The path to the test directory.
-    """
     with PartlyCloudyTestingDataGrabber() as dg:
-        # Use first subject
-        input = dg["sub-01"]
-        input = DefaultDataReader().fit_transform(input)
-        # Create ParcelAggregation object
-        marker = ALFFParcels(
-            parcellation=_PARCELLATION,
-            method="mean",
-            use_afni=False,
-            fractional=True,
+        element_data = DefaultDataReader().fit_transform(dg["sub-01"])
+        # Update workdir to current test's tmp_path
+        WorkDirManager().workdir = tmp_path
+
+        # Initialize marker
+        junifer_marker = ALFFParcels(
+            parcellation=PARCELLATION,
+            fractional=fractional,
+            using="junifer",
         )
-        storage = SQLiteFeatureStorage(tmp_path / "alff_parcels.sqlite")
-
-        # Fit transform marker on data with storage
-        marker.fit_transform(
-            input=input,
-            storage=storage,
+        # Fit transform marker on data
+        junifer_output = junifer_marker.fit_transform(element_data)
+        # Get BOLD output
+        junifer_output_bold = junifer_output["BOLD"]
+
+        # Initialize marker
+        afni_marker = ALFFParcels(
+            parcellation=PARCELLATION,
+            fractional=fractional,
+            using="afni",
+        )
+        # Fit transform marker on data
+        afni_output = afni_marker.fit_transform(element_data)
+        # Get BOLD output
+        afni_output_bold = afni_output["BOLD"]
+
+        # Check for Pearson correlation coefficient
+        r, _ = sp.stats.pearsonr(
+            junifer_output_bold["data"][0],
+            afni_output_bold["data"][0],
         )
+        assert r > 0.97

junifer/markers/falff/tests/test_falff_spheres.py

@@ -1,164 +1,129 @@
-"""Provide test for sphere-aggregated (f)ALFF."""
+"""Provide tests for ALFFSpheres."""
 
 # Authors: Federico Raimondo <f.raimondo@fz-juelich.de>
 #          Synchon Mandal <s.mandal@fz-juelich.de>
 # License: AGPL
 
+import logging
 from pathlib import Path
 
 import pytest
-from numpy.testing import assert_array_equal
-from scipy.stats import pearsonr
+import scipy as sp
 
 from junifer.datareader import DefaultDataReader
 from junifer.markers.falff import ALFFSpheres
+from junifer.pipeline import WorkDirManager
 from junifer.pipeline.utils import _check_afni
 from junifer.storage import SQLiteFeatureStorage
 from junifer.testing.datagrabbers import PartlyCloudyTestingDataGrabber
-from junifer.utils import logger
 
 
-_COORDINATES = "DMNBuckner"
+COORDINATES = "DMNBuckner"
 
 
-def test_ALFFSpheres_python() -> None:
-    """Test ALFFSpheres using python."""
-    # Get the SPM auditory data:
-
-    with PartlyCloudyTestingDataGrabber() as dg:
-        input = dg["sub-01"]
-
-    input = DefaultDataReader().fit_transform(input)
-    # Create ParcelAggregation object
-    marker = ALFFSpheres(
-        coords=_COORDINATES,
-        radius=5,
-        method="mean",
-        use_afni=False,
-        fractional=False,
-    )
-    python_values = marker.fit_transform(input)["BOLD"]["data"]
-
-    assert marker.use_afni is False
-    assert python_values.ndim == 2
-    assert python_values.shape == (1, 6)
+def test_ALFFSpheres(caplog: pytest.LogCaptureFixture, tmp_path: Path) -> None:
+    """Test ALFFSpheres.
 
+    Parameters
+    ----------
+    caplog : pytest.LogCaptureFixture
+        The pytest.LogCaptureFixture object.
+    tmp_path : pathlib.Path
+        The path to the test directory.
 
-@pytest.mark.skipif(
-    _check_afni() is False, reason="requires afni to be in PATH"
-)
-def test_ALFFSpheres_afni() -> None:
-    """Test ALFFSpheres using afni."""
-    # Get the SPM auditory data:
-    with PartlyCloudyTestingDataGrabber() as dg:
-        input = dg["sub-01"]
-
-    input = DefaultDataReader().fit_transform(input)
-    # Create ParcelAggregation object
-    marker = ALFFSpheres(
-        coords=_COORDINATES,
-        radius=5,
-        method="mean",
-        use_afni=True,
-        fractional=False,
-    )
-    assert marker.use_afni is True
-    afni_values = marker.fit_transform(input)["BOLD"]["data"]
-
-    assert afni_values.ndim == 2
-    assert afni_values.shape == (1, 6)
-
-    # Again, should be blazing fast
-    marker = ALFFSpheres(
-        coords=_COORDINATES,
-        radius=5,
-        method="mean",
-        fractional=False,
-    )
-    assert marker.use_afni is None
-    afni_values2 = marker.fit_transform(input)["BOLD"]["data"]
-    assert marker.use_afni is True
-    assert_array_equal(afni_values, afni_values2)
+    """
+    with caplog.at_level(logging.DEBUG):
+        with PartlyCloudyTestingDataGrabber() as dg:
+            element_data = DefaultDataReader().fit_transform(dg["sub-01"])
+            # Update workdir to current test's tmp_path
+            WorkDirManager().workdir = tmp_path
+
+            # Initialize marker
+            marker = ALFFSpheres(
+                coords=COORDINATES,
+                fractional=False,
+                using="junifer",
+                radius=5.0,
+            )
+            # Fit transform marker on data
+            output = marker.fit_transform(element_data)
+
+            assert "Creating cache" in caplog.text
+
+            # Get BOLD output
+            assert "BOLD" in output
+            output_bold = output["BOLD"]
+            # Assert BOLD output keys
+            assert "data" in output_bold
+            assert "col_names" in output_bold
+
+            output_bold_data = output_bold["data"]
+            # Assert BOLD output data dimension
+            assert output_bold_data.ndim == 2
+            assert output_bold_data.shape == (1, 6)
+
+            # Reset log capture
+            caplog.clear()
+            # Initialize storage
+            storage = SQLiteFeatureStorage(tmp_path / "falff_spheres.sqlite")
+            # Fit transform marker on data with storage
+            marker.fit_transform(
+                input=element_data,
+                storage=storage,
+            )
+            # Cache working correctly
+            assert "Creating cache" not in caplog.text
 
 
 @pytest.mark.skipif(
-    _check_afni() is False, reason="requires afni to be in PATH"
+    _check_afni() is False, reason="requires AFNI to be in PATH"
 )
 @pytest.mark.parametrize(
     "fractional", [True, False], ids=["fractional", "non-fractional"]
 )
-def test_ALFFSpheres_python_vs_afni(
-    fractional: bool,
-) -> None:
-    """Test ALFFSpheres python vs afni results.
+def test_ALFFSpheres_comparison(tmp_path: Path, fractional: bool) -> None:
+    """Test ALFFSpheres implementation comparison.
 
     Parameters
     ----------
+    tmp_path : pathlib.Path
+        The path to the test directory.
     fractional : bool
         Whether to compute fractional ALFF or not.
-    """
-    with PartlyCloudyTestingDataGrabber() as dg:
-        input = dg["sub-01"]
-
-    input = DefaultDataReader().fit_transform(input)
-    # Create ParcelAggregation object
-    marker_python = ALFFSpheres(
-        coords=_COORDINATES,
-        radius=5,
-        method="mean",
-        use_afni=False,
-        fractional=fractional,
-    )
-    python_values = marker_python.fit_transform(input)["BOLD"]["data"]
-
-    assert marker_python.use_afni is False
-    assert python_values.ndim == 2
-    assert python_values.shape == (1, 6)
-
-    marker_afni = ALFFSpheres(
-        coords=_COORDINATES,
-        radius=5,
-        method="mean",
-        use_afni=True,
-        fractional=fractional,
-    )
-    afni_values = marker_afni.fit_transform(input)["BOLD"]["data"]
-
-    assert marker_afni.use_afni is True
-    assert afni_values.ndim == 2
-    assert afni_values.shape == (1, 6)
-
-    r, p = pearsonr(python_values[0], afni_values[0])
-    logger.info(f"Correlation between python and afni: {r} (p={p})")
-    assert r > 0.99
-
-
-def test_ALFFSpheres_storage(
-    tmp_path: Path,
-) -> None:
-    """Test ALFFSpheres storage.
 
-    Parameters
-    ----------
-    tmp_path : pathlib.Path
-        The path to the test directory.
     """
     with PartlyCloudyTestingDataGrabber() as dg:
-        # Use first subject
-        input = dg["sub-01"]
-        input = DefaultDataReader().fit_transform(input)
-        # Create ParcelAggregation object
-        marker = ALFFSpheres(
-            coords=_COORDINATES,
-            radius=5,
-            method="mean",
-            use_afni=False,
-            fractional=True,
+        element_data = DefaultDataReader().fit_transform(dg["sub-01"])
+        # Update workdir to current test's tmp_path
+        WorkDirManager().workdir = tmp_path
+
+        # Initialize marker
+        junifer_marker = ALFFSpheres(
+            coords=COORDINATES,
+            fractional=fractional,
+            using="junifer",
+            radius=5.0,
         )
-        storage = SQLiteFeatureStorage(tmp_path / "alff_parcels.sqlite")
-
-        # Fit transform marker on data with storage
-        marker.fit_transform(
-            input=input,
-            storage=storage,
+        # Fit transform marker on data
+        junifer_output = junifer_marker.fit_transform(element_data)
+        # Get BOLD output
+        junifer_output_bold = junifer_output["BOLD"]
+
+        # Initialize marker
+        afni_marker = ALFFSpheres(
+            coords=COORDINATES,
+            fractional=fractional,
+            using="afni",
+            radius=5.0,
+        )
+        # Fit transform marker on data
+        afni_output = afni_marker.fit_transform(element_data)
+        # Get BOLD output
+        afni_output_bold = afni_output["BOLD"]
+
+        # Check for Pearson correlation coefficient
+        r, _ = sp.stats.pearsonr(
+            junifer_output_bold["data"][0],
+            afni_output_bold["data"][0],
         )
+        assert r > 0.99

junifer/markers/functional_connectivity/crossparcellation_functional_connectivity.py

@@ -37,6 +37,7 @@ class CrossParcellationFC(BaseMarker):
     name : str, optional
         The name of the marker. If None, will use the class name
         (default None).
+
     """
 
     _DEPENDENCIES: ClassVar[Set[str]] = {"nilearn"}

junifer/markers/functional_connectivity/edge_functional_connectivity_parcels.py

@@ -97,6 +97,7 @@ class EdgeCentricFCParcels(FunctionalConnectivityBase):
 
             * ``data`` : the actual computed values as a numpy.ndarray
             * ``col_names`` : the column labels for the computed values as list
+
         """
         parcel_aggregation = ParcelAggregation(
             parcellation=self.parcellation,

junifer/markers/functional_connectivity/functional_connectivity_base.py

@@ -84,6 +84,7 @@ class FunctionalConnectivityBase(BaseMarker):
         -------
         list of str
             The list of data types that can be used as input for this marker.
+
         """
         return ["BOLD"]
 

junifer/markers/functional_connectivity/tests/test_crossparcellation_functional_connectivity.py

@@ -2,14 +2,17 @@
 
 # Authors: Leonard Sasse <l.sasse@fz-juelich.de>
 #          Kaustubh R. Patil <k.patil@fz-juelich.de>
+#          Synchon Mandal <s.mandal@fz-juelich.de>
 # License: AGPL
 
 from pathlib import Path
 
 import pytest
-from nilearn import image
 
+from junifer.datareader import DefaultDataReader
 from junifer.markers.functional_connectivity 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
 
@@ -18,31 +21,53 @@ parcellation_one = "Schaefer100x17"
 parcellation_two = "Schaefer200x17"
 
 
-def test_compute() -> None:
-    """Test CrossParcellationFC compute()."""
+def test_init() -> None:
+    """Test CrossParcellationFC init()."""
+    with pytest.raises(ValueError, match="must be different"):
+        CrossParcellationFC(
+            parcellation_one="a",
+            parcellation_two="a",
+            correlation_method="pearson",
+        )
 
-    with SPMAuditoryTestingDataGrabber() as dg:
-        out = dg["sub001"]
-        niimg = image.load_img(str(out["BOLD"]["path"].absolute()))
-        input_dict = {
-            "BOLD": {
-                "data": niimg,
-                "path": out["BOLD"]["path"],
-                "meta": {"element": "sub001"},
-            }
-        }
 
+def test_get_output_type() -> None:
+    """Test CrossParcellationFC get_output_type()."""
+    crossparcellation = CrossParcellationFC(
+        parcellation_one=parcellation_one, parcellation_two=parcellation_two
+    )
+    assert "matrix" == crossparcellation.get_output_type("BOLD")
+
+
+@pytest.mark.skipif(
+    _check_ants() is False, reason="requires ANTs to be in PATH"
+)
+def test_compute(tmp_path: Path) -> None:
+    """Test CrossParcellationFC compute().
+
+    Parameters
+    ----------
+    tmp_path : pathlib.Path
+        The path to the test directory.
+
+    """
+    with SPMAuditoryTestingDataGrabber() as dg:
+        element_data = DefaultDataReader().fit_transform(dg["sub001"])
+        WorkDirManager().workdir = tmp_path
         crossparcellation = CrossParcellationFC(
             parcellation_one=parcellation_one,
             parcellation_two=parcellation_two,
             correlation_method="spearman",
         )
-        out = crossparcellation.compute(input_dict["BOLD"])
+        out = crossparcellation.compute(element_data["BOLD"])
         assert out["data"].shape == (200, 100)
         assert len(out["col_names"]) == 100
         assert len(out["row_names"]) == 200
 
 
+@pytest.mark.skipif(
+    _check_ants() is False, reason="requires ANTs to be in PATH"
+)
 def test_store(tmp_path: Path) -> None:
     """Test CrossParcellationFC store().
 
@@ -52,43 +77,20 @@ def test_store(tmp_path: Path) -> None:
         The path to the test directory.
 
     """
-
     with SPMAuditoryTestingDataGrabber() as dg:
-        input_dict = dg["sub001"]
-        niimg = image.load_img(str(input_dict["BOLD"]["path"].absolute()))
-
-        input_dict["BOLD"]["data"] = niimg
-
+        element_data = DefaultDataReader().fit_transform(dg["sub001"])
+        WorkDirManager().workdir = tmp_path
         crossparcellation = CrossParcellationFC(
             parcellation_one=parcellation_one,
             parcellation_two=parcellation_two,
             correlation_method="spearman",
         )
-        uri = tmp_path / "test_crossparcellation.sqlite"
-        storage = SQLiteFeatureStorage(uri=uri, upsert="ignore")
-        crossparcellation.fit_transform(input_dict, storage=storage)
+        storage = SQLiteFeatureStorage(
+            uri=tmp_path / "test_crossparcellation.sqlite", upsert="ignore"
+        )
+        # Fit transform marker on data with storage
+        crossparcellation.fit_transform(input=element_data, storage=storage)
         features = storage.list_features()
         assert any(
             x["name"] == "BOLD_CrossParcellationFC" for x in features.values()
         )
-
-
-def test_get_output_type() -> None:
-    """Test CrossParcellationFC get_output_type()."""
-
-    crossparcellation = CrossParcellationFC(
-        parcellation_one=parcellation_one, parcellation_two=parcellation_two
-    )
-    input_ = "BOLD"
-    output = crossparcellation.get_output_type(input_)
-    assert output == "matrix"
-
-
-def test_init_() -> None:
-    """Test CrossParcellationFC init()."""
-    with pytest.raises(ValueError, match="must be different"):
-        CrossParcellationFC(
-            parcellation_one="a",
-            parcellation_two="a",
-            correlation_method="pearson",
-        )