junifer 0.0.5__py3-none-any.whl → 0.0.5.dev11__py3-none-any.whl

junifer/markers/tests/test_parcel_aggregation.py

@@ -23,63 +23,16 @@ from junifer.storage import SQLiteFeatureStorage
 from junifer.testing.datagrabbers import PartlyCloudyTestingDataGrabber
 
 
-@pytest.mark.parametrize(
-    "input_type, storage_type",
-    [
-        (
-            "T1w",
-            "vector",
-        ),
-        (
-            "T2w",
-            "vector",
-        ),
-        (
-            "BOLD",
-            "timeseries",
-        ),
-        (
-            "VBM_GM",
-            "vector",
-        ),
-        (
-            "VBM_WM",
-            "vector",
-        ),
-        (
-            "VBM_CSF",
-            "vector",
-        ),
-        (
-            "fALFF",
-            "vector",
-        ),
-        (
-            "GCOR",
-            "vector",
-        ),
-        (
-            "LCOR",
-            "vector",
-        ),
-    ],
-)
-def test_ParcelAggregation_input_output(
-    input_type: str, storage_type: str
-) -> None:
-    """Test ParcelAggregation input and output types.
+def test_ParcelAggregation_input_output() -> None:
+    """Test ParcelAggregation input and output types."""
+    marker = ParcelAggregation(
+        parcellation="Schaefer100x7", method="mean", on="VBM_GM"
+    )
+    for in_, out_ in [("VBM_GM", "vector"), ("BOLD", "timeseries")]:
+        assert marker.get_output_type(in_) == out_
 
-    Parameters
-    ----------
-    input_type : str
-        The parametrized input type.
-    storage_type : str
-        The parametrized storage type.
-
-    """
-    assert storage_type == ParcelAggregation(
-        parcellation="Schaefer100x7", method="mean", on=input_type
-    ).get_output_type(input_type=input_type, output_feature="aggregation")
+    with pytest.raises(ValueError, match="Unknown input"):
+        marker.get_output_type("unknown")
 
 
 def test_ParcelAggregation_3D() -> None:
@@ -132,8 +85,8 @@ def test_ParcelAggregation_3D() -> None:
         )
 
         parcel_agg_mean_bold_data = marker.fit_transform(element_data)["BOLD"][
-            "aggregation"
-        ]["data"]
+            "data"
+        ]
         # Check that arrays are almost equal
         assert_array_equal(parcel_agg_mean_bold_data, manual)
         assert_array_almost_equal(nifti_labels_masked_bold, manual)
@@ -160,8 +113,8 @@ def test_ParcelAggregation_3D() -> None:
             on="BOLD",
         )
         parcel_agg_std_bold_data = marker.fit_transform(element_data)["BOLD"][
-            "aggregation"
-        ]["data"]
+            "data"
+        ]
         assert parcel_agg_std_bold_data.ndim == 2
         assert parcel_agg_std_bold_data.shape[0] == 1
         assert_array_equal(parcel_agg_std_bold_data, manual)
@@ -186,7 +139,7 @@ def test_ParcelAggregation_3D() -> None:
         )
         parcel_agg_trim_mean_bold_data = marker.fit_transform(element_data)[
             "BOLD"
-        ]["aggregation"]["data"]
+        ]["data"]
         assert parcel_agg_trim_mean_bold_data.ndim == 2
         assert parcel_agg_trim_mean_bold_data.shape[0] == 1
         assert_array_equal(parcel_agg_trim_mean_bold_data, manual)
@@ -201,8 +154,8 @@ def test_ParcelAggregation_4D():
             parcellation="TianxS1x3TxMNInonlinear2009cAsym", method="mean"
         )
         parcel_agg_bold_data = marker.fit_transform(element_data)["BOLD"][
-            "aggregation"
-        ]["data"]
+            "data"
+        ]
 
         # Compare with nilearn
         # Load testing parcellation
@@ -251,8 +204,7 @@ def test_ParcelAggregation_storage(tmp_path: Path) -> None:
         marker.fit_transform(input=element_data, storage=storage)
         features = storage.list_features()
         assert any(
-            x["name"] == "BOLD_ParcelAggregation_aggregation"
-            for x in features.values()
+            x["name"] == "BOLD_ParcelAggregation" for x in features.values()
         )
 
     # Store 4D
@@ -269,8 +221,7 @@ def test_ParcelAggregation_storage(tmp_path: Path) -> None:
         marker.fit_transform(input=element_data, storage=storage)
         features = storage.list_features()
         assert any(
-            x["name"] == "BOLD_ParcelAggregation_aggregation"
-            for x in features.values()
+            x["name"] == "BOLD_ParcelAggregation" for x in features.values()
         )
 
 
@@ -290,8 +241,8 @@ def test_ParcelAggregation_3D_mask() -> None:
             ..., 0:1
         ]
         parcel_agg_bold_data = marker.fit_transform(element_data)["BOLD"][
-            "aggregation"
-        ]["data"]
+            "data"
+        ]
 
         # Compare with nilearn
         # Load testing parcellation
@@ -365,8 +316,8 @@ def test_ParcelAggregation_3D_mask_computed() -> None:
             on="BOLD",
         )
         parcel_agg_mean_bold_data = marker.fit_transform(element_data)["BOLD"][
-            "aggregation"
-        ]["data"]
+            "data"
+        ]
 
         assert parcel_agg_mean_bold_data.ndim == 2
         assert parcel_agg_mean_bold_data.shape[0] == 1
@@ -446,9 +397,7 @@ def test_ParcelAggregation_3D_multiple_non_overlapping(tmp_path: Path) -> None:
             name="tian_mean",
             on="BOLD",
         )
-        orig_mean = marker_original.fit_transform(element_data)["BOLD"][
-            "aggregation"
-        ]
+        orig_mean = marker_original.fit_transform(element_data)["BOLD"]
 
         orig_mean_data = orig_mean["data"]
         assert orig_mean_data.ndim == 2
@@ -468,9 +417,7 @@ def test_ParcelAggregation_3D_multiple_non_overlapping(tmp_path: Path) -> None:
         # No warnings should be raised
         with warnings.catch_warnings():
             warnings.simplefilter("error", category=UserWarning)
-            split_mean = marker_split.fit_transform(element_data)["BOLD"][
-                "aggregation"
-            ]
+            split_mean = marker_split.fit_transform(element_data)["BOLD"]
 
         split_mean_data = split_mean["data"]
 
@@ -550,9 +497,7 @@ def test_ParcelAggregation_3D_multiple_overlapping(tmp_path: Path) -> None:
             name="tian_mean",
             on="BOLD",
         )
-        orig_mean = marker_original.fit_transform(element_data)["BOLD"][
-            "aggregation"
-        ]
+        orig_mean = marker_original.fit_transform(element_data)["BOLD"]
 
         orig_mean_data = orig_mean["data"]
         assert orig_mean_data.ndim == 2
@@ -570,9 +515,7 @@ def test_ParcelAggregation_3D_multiple_overlapping(tmp_path: Path) -> None:
         )
         # Warning should be raised
         with pytest.warns(RuntimeWarning, match="overlapping voxels"):
-            split_mean = marker_split.fit_transform(element_data)["BOLD"][
-                "aggregation"
-            ]
+            split_mean = marker_split.fit_transform(element_data)["BOLD"]
 
         split_mean_data = split_mean["data"]
 
@@ -659,9 +602,7 @@ def test_ParcelAggregation_3D_multiple_duplicated_labels(
             name="tian_mean",
             on="BOLD",
         )
-        orig_mean = marker_original.fit_transform(element_data)["BOLD"][
-            "aggregation"
-        ]
+        orig_mean = marker_original.fit_transform(element_data)["BOLD"]
 
         orig_mean_data = orig_mean["data"]
         assert orig_mean_data.ndim == 2
@@ -680,9 +621,7 @@ def test_ParcelAggregation_3D_multiple_duplicated_labels(
 
         # Warning should be raised
         with pytest.warns(RuntimeWarning, match="duplicated labels."):
-            split_mean = marker_split.fit_transform(element_data)["BOLD"][
-                "aggregation"
-            ]
+            split_mean = marker_split.fit_transform(element_data)["BOLD"]
 
         split_mean_data = split_mean["data"]
 
@@ -714,8 +653,8 @@ def test_ParcelAggregation_4D_agg_time():
             on="BOLD",
         )
         parcel_agg_bold_data = marker.fit_transform(element_data)["BOLD"][
-            "aggregation"
-        ]["data"]
+            "data"
+        ]
 
         # Compare with nilearn
         # Loading testing parcellation
@@ -750,8 +689,8 @@ def test_ParcelAggregation_4D_agg_time():
             on="BOLD",
         )
         parcel_agg_bold_data = marker.fit_transform(element_data)["BOLD"][
-            "aggregation"
-        ]["data"]
+            "data"
+        ]
 
         assert parcel_agg_bold_data.ndim == 2
         assert_array_equal(

junifer/markers/tests/test_sphere_aggregation.py

@@ -25,65 +25,14 @@ COORDS = "DMNBuckner"
 RADIUS = 8
 
 
-@pytest.mark.parametrize(
-    "input_type, storage_type",
-    [
-        (
-            "T1w",
-            "vector",
-        ),
-        (
-            "T2w",
-            "vector",
-        ),
-        (
-            "BOLD",
-            "timeseries",
-        ),
-        (
-            "VBM_GM",
-            "vector",
-        ),
-        (
-            "VBM_WM",
-            "vector",
-        ),
-        (
-            "VBM_CSF",
-            "vector",
-        ),
-        (
-            "fALFF",
-            "vector",
-        ),
-        (
-            "GCOR",
-            "vector",
-        ),
-        (
-            "LCOR",
-            "vector",
-        ),
-    ],
-)
-def test_SphereAggregation_input_output(
-    input_type: str, storage_type: str
-) -> None:
-    """Test SphereAggregation input and output types.
+def test_SphereAggregation_input_output() -> None:
+    """Test SphereAggregation input and output types."""
+    marker = SphereAggregation(coords="DMNBuckner", method="mean", on="VBM_GM")
+    for in_, out_ in [("VBM_GM", "vector"), ("BOLD", "timeseries")]:
+        assert marker.get_output_type(in_) == out_
 
-    Parameters
-    ----------
-    input_type : str
-        The parametrized input type.
-    storage_type : str
-        The parametrized storage type.
-
-    """
-    assert storage_type == SphereAggregation(
-        coords="DMNBuckner",
-        method="mean",
-        on=input_type,
-    ).get_output_type(input_type=input_type, output_feature="aggregation")
+    with pytest.raises(ValueError, match="Unknown input"):
+        marker.get_output_type("unknown")
 
 
 def test_SphereAggregation_3D() -> None:
@@ -95,8 +44,8 @@ def test_SphereAggregation_3D() -> None:
             coords=COORDS, method="mean", radius=RADIUS, on="VBM_GM"
         )
         sphere_agg_vbm_gm_data = marker.fit_transform(element_data)["VBM_GM"][
-            "aggregation"
-        ]["data"]
+            "data"
+        ]
 
         # Compare with nilearn
         # Load testing coordinates
@@ -127,8 +76,8 @@ def test_SphereAggregation_4D() -> None:
             coords=COORDS, method="mean", radius=RADIUS, on="BOLD"
         )
         sphere_agg_bold_data = marker.fit_transform(element_data)["BOLD"][
-            "aggregation"
-        ]["data"]
+            "data"
+        ]
 
         # Compare with nilearn
         # Load testing coordinates
@@ -171,8 +120,7 @@ def test_SphereAggregation_storage(tmp_path: Path) -> None:
         marker.fit_transform(input=element_data, storage=storage)
         features = storage.list_features()
         assert any(
-            x["name"] == "VBM_GM_SphereAggregation_aggregation"
-            for x in features.values()
+            x["name"] == "VBM_GM_SphereAggregation" for x in features.values()
         )
 
     # Store 4D
@@ -187,8 +135,7 @@ def test_SphereAggregation_storage(tmp_path: Path) -> None:
         marker.fit_transform(input=element_data, storage=storage)
         features = storage.list_features()
         assert any(
-            x["name"] == "BOLD_SphereAggregation_aggregation"
-            for x in features.values()
+            x["name"] == "BOLD_SphereAggregation" for x in features.values()
         )
 
 
@@ -205,8 +152,8 @@ def test_SphereAggregation_3D_mask() -> None:
             masks="compute_brain_mask",
         )
         sphere_agg_vbm_gm_data = marker.fit_transform(element_data)["VBM_GM"][
-            "aggregation"
-        ]["data"]
+            "data"
+        ]
 
         # Compare with nilearn
         # Load testing coordinates
@@ -248,8 +195,8 @@ def test_SphereAggregation_4D_agg_time() -> None:
             on="BOLD",
         )
         sphere_agg_bold_data = marker.fit_transform(element_data)["BOLD"][
-            "aggregation"
-        ]["data"]
+            "data"
+        ]
 
         # Compare with nilearn
         # Load testing coordinates
@@ -284,8 +231,8 @@ def test_SphereAggregation_4D_agg_time() -> None:
             on="BOLD",
         )
         sphere_agg_bold_data = marker.fit_transform(element_data)["BOLD"][
-            "aggregation"
-        ]["data"]
+            "data"
+        ]
 
         assert sphere_agg_bold_data.ndim == 2
         assert_array_equal(

junifer/onthefly/__init__.py

@@ -1,9 +1,6 @@
-"""Utilities for on-the-fly analyses."""
+"""Provide imports for onthefly sub-package."""
 
 # Authors: Synchon Mandal <s.mandal@fz-juelich.de>
 # License: AGPL
 
 from .read_transform import read_transform
-
-
-__all__ = ["read_transform"]

junifer/onthefly/read_transform.py

@@ -15,9 +15,6 @@ if TYPE_CHECKING:
     from junifer.storage import BaseFeatureStorage
 
 
-__all__ = ["read_transform"]
-
-
 def read_transform(
     storage: Type["BaseFeatureStorage"],
     transform: str,

junifer/pipeline/__init__.py

@@ -1,4 +1,4 @@
-"""Pipeline components."""
+"""Provide imports for pipeline sub-package."""
 
 # Authors: Synchon Mandal <s.mandal@fz-juelich.de>
 # License: AGPL
@@ -7,11 +7,3 @@ from . import registry
 from .pipeline_step_mixin import PipelineStepMixin
 from .update_meta_mixin import UpdateMetaMixin
 from .workdir_manager import WorkDirManager
-
-
-__all__ = [
-    "registry",
-    "PipelineStepMixin",
-    "UpdateMetaMixin",
-    "WorkDirManager",
-]

junifer/pipeline/pipeline_step_mixin.py

@@ -4,14 +4,10 @@
 #          Synchon Mandal <s.mandal@fz-juelich.de>
 # License: AGPL
 
-import sys
-
-
-if sys.version_info < (3, 11):  # pragma: no cover
-    from importlib_metadata import packages_distributions
-else:
+try:
     from importlib.metadata import packages_distributions
-
+except ImportError:  # pragma: no cover
+    from importlib_metadata import packages_distributions
 
 from importlib.util import find_spec
 from itertools import chain
@@ -21,9 +17,6 @@ from ..utils import raise_error
 from .utils import check_ext_dependencies
 
 
-__all__ = ["PipelineStepMixin"]
-
-
 class PipelineStepMixin:
     """Mixin class for a pipeline step."""
 
@@ -210,17 +203,7 @@ class PipelineStepMixin:
         # Validate input
         fit_input = self.validate_input(input=input)
         # Validate output type
-        # Nested output type for marker
-        if hasattr(self, "_MARKER_INOUT_MAPPINGS"):
-            outputs = list(
-                {
-                    val
-                    for t_input in fit_input
-                    for val in self._MARKER_INOUT_MAPPINGS[t_input].values()
-                }
-            )
-        else:
-            outputs = [self.get_output_type(t_input) for t_input in fit_input]
+        outputs = [self.get_output_type(t_input) for t_input in fit_input]
         return outputs
 
     def fit_transform(

junifer/pipeline/registry.py

@@ -16,9 +16,6 @@ if TYPE_CHECKING:
     from .pipeline_step_mixin import PipelineStepMixin
 
 
-__all__ = ["register", "get_step_names", "get_class", "build"]
-
-
 # Define valid steps for operation
 _VALID_STEPS: List[str] = [
     "datagrabber",

junifer/pipeline/singleton.py

@@ -6,9 +6,6 @@
 from typing import Any, Dict, Type
 
 
-__all__ = ["singleton"]
-
-
 def singleton(cls: Type) -> Type:
     """Make a class singleton.
 

junifer/pipeline/tests/test_registry.py

@@ -101,7 +101,7 @@ def test_get_class():
     register(step="datagrabber", name="bar", klass=str)
     # Get class
     obj = get_class(step="datagrabber", name="bar")
-    assert isinstance(obj, type(str))
+    assert obj == str
 
 
 # TODO: possible parametrization?

junifer/pipeline/update_meta_mixin.py

@@ -7,9 +7,6 @@
 from typing import Dict
 
 
-__all__ = ["UpdateMetaMixin"]
-
-
 class UpdateMetaMixin:
     """Mixin class for updating meta."""
 

junifer/pipeline/utils.py

@@ -10,9 +10,6 @@ from typing import Any, List, Optional
 from junifer.utils.logging import raise_error, warn_with_log
 
 
-__all__ = ["check_ext_dependencies"]
-
-
 def check_ext_dependencies(
     name: str, optional: bool = False, **kwargs: Any
 ) -> bool:
@@ -40,7 +37,7 @@ def check_ext_dependencies(
         If ``name`` is mandatory and is not found.
 
     """
-    valid_ext_dependencies = ("afni", "fsl", "ants", "freesurfer")
+    valid_ext_dependencies = ("afni", "fsl", "ants")
     if name not in valid_ext_dependencies:
         raise_error(
             "Invalid value for `name`, should be one of: "
@@ -55,9 +52,6 @@ def check_ext_dependencies(
     # Check for ants
     elif name == "ants":
         found = _check_ants(**kwargs)
-    # Check for freesurfer
-    elif name == "freesurfer":
-        found = _check_freesurfer(**kwargs)
 
     # Check if the dependency is mandatory in case it's not found
     if not found and not optional:
@@ -251,63 +245,3 @@ def _check_ants(commands: Optional[List[str]] = None) -> bool:
                 f"{commands_found_results}"
             )
     return ants_found
-
-
-def _check_freesurfer(commands: Optional[List[str]] = None) -> bool:
-    """Check if FreeSurfer is present in the system.
-
-    Parameters
-    ----------
-    commands : list of str, optional
-        The commands to specifically check for from FreeSurfer. If None, only
-        the basic FreeSurfer help would be looked up, else, would also
-        check for specific commands (default None).
-
-    Returns
-    -------
-    bool
-        Whether FreeSurfer is found or not.
-
-    """
-    completed_process = subprocess.run(
-        "recon-all -help",
-        stdin=subprocess.DEVNULL,
-        stdout=subprocess.DEVNULL,
-        stderr=subprocess.STDOUT,
-        shell=True,  # is unsafe but kept for resolution via PATH
-        check=False,
-    )
-    fs_found = completed_process.returncode == 0
-
-    # Check for specific commands
-    if fs_found and commands is not None:
-        if not isinstance(commands, list):
-            commands = [commands]
-        # Store command found results
-        commands_found_results = {}
-        # Set all commands found flag to True
-        all_commands_found = True
-        # Check commands' existence
-        for command in commands:
-            command_process = subprocess.run(
-                [command],
-                stdin=subprocess.DEVNULL,
-                stdout=subprocess.DEVNULL,
-                stderr=subprocess.STDOUT,
-                shell=True,  # is unsafe but kept for resolution via PATH
-                check=False,
-            )
-            command_found = command_process.returncode == 0
-            commands_found_results[command] = (
-                "found" if command_found else "not found"
-            )
-            # Set flag to trigger warning
-            all_commands_found = all_commands_found and command_found
-        # One or more commands were missing
-        if not all_commands_found:
-            warn_with_log(
-                "FreeSurfer is installed but some of the required commands "
-                "were not found. These are the results: "
-                f"{commands_found_results}"
-            )
-    return fs_found

junifer/pipeline/workdir_manager.py

@@ -13,9 +13,6 @@ from ..utils import logger
 from .singleton import singleton
 
 
-__all__ = ["WorkDirManager"]
-
-
 @singleton
 class WorkDirManager:
     """Class for working directory manager.

junifer/preprocess/__init__.py

@@ -1,4 +1,4 @@
-"""Preprocessors for preprocessing data before feature extraction."""
+"""Provide imports for preprocess sub-package."""
 
 # Authors: Federico Raimondo <f.raimondo@fz-juelich.de>
 #          Leonard Sasse <l.sasse@fz-juelich.de>
@@ -7,13 +7,5 @@
 
 from .base import BasePreprocessor
 from .confounds import fMRIPrepConfoundRemover
+from .bold_warper import BOLDWarper
 from .warping import SpaceWarper
-from .smoothing import Smoothing
-
-
-__all__ = [
-    "BasePreprocessor",
-    "fMRIPrepConfoundRemover",
-    "SpaceWarper",
-    "Smoothing",
-]

junifer/preprocess/ants/__init__.py

@@ -0,0 +1,4 @@
+"""Provide imports for ants sub-package."""
+
+# Authors: Synchon Mandal <s.mandal@fz-juelich.de>
+# License: AGPL