junifer 0.0.5.dev240__py3-none-any.whl → 0.0.6__py3-none-any.whl

junifer/data/{tests → parcellations/tests}/test_parcellations.py

@@ -6,7 +6,6 @@
 # License: AGPL
 
 from pathlib import Path
-from typing import List
 
 import nibabel as nib
 import numpy as np
@@ -14,20 +13,16 @@ import pytest
 from nilearn.image import new_img_like, resample_to_img
 from numpy.testing import assert_array_almost_equal, assert_array_equal
 
-from junifer.data.parcellations import (
+from junifer.data import ParcellationRegistry
+from junifer.data.parcellations import merge_parcellations
+from junifer.data.parcellations._parcellations import (
     _retrieve_aicha,
     _retrieve_brainnetome,
-    _retrieve_parcellation,
     _retrieve_schaefer,
     _retrieve_shen,
     _retrieve_suit,
     _retrieve_tian,
     _retrieve_yan,
-    get_parcellation,
-    list_parcellations,
-    load_parcellation,
-    merge_parcellations,
-    register_parcellation,
 )
 from junifer.datareader import DefaultDataReader
 from junifer.pipeline.utils import _check_ants
@@ -37,10 +32,10 @@ from junifer.testing.datagrabbers import (
 )
 
 
-def test_register_parcellation_built_in_check() -> None:
+def test_register_built_in_check() -> None:
     """Test parcellation registration check for built-in parcellations."""
     with pytest.raises(ValueError, match=r"built-in parcellation"):
-        register_parcellation(
+        ParcellationRegistry().register(
             name="SUITxSUIT",
             parcellation_path="testparc.nii.gz",
             parcels_labels=["1", "2", "3"],
@@ -49,35 +44,36 @@ def test_register_parcellation_built_in_check() -> None:
         )
 
 
-def test_list_parcellations_incorrect() -> None:
+def test_list_incorrect() -> None:
     """Test incorrect information check for list parcellations."""
-    parcellations = list_parcellations()
-    assert "testparc" not in parcellations
+    assert "testparc" not in ParcellationRegistry().list
 
 
-def test_register_parcellation_already_registered() -> None:
+def test_register_already_registered() -> None:
     """Test parcellation registration check for already registered."""
     # Register custom parcellation
-    register_parcellation(
+    ParcellationRegistry().register(
         name="testparc",
         parcellation_path="testparc.nii.gz",
         parcels_labels=["1", "2", "3"],
         space="MNI152Lin",
     )
     assert (
-        load_parcellation("testparc", path_only=True)[2].name
+        ParcellationRegistry()
+        .load("testparc", target_space="MNI152Lin", path_only=True)[2]
+        .name
         == "testparc.nii.gz"
     )
 
     # Try registering again
     with pytest.raises(ValueError, match=r"already registered."):
-        register_parcellation(
+        ParcellationRegistry().register(
             name="testparc",
             parcellation_path="testparc.nii.gz",
             parcels_labels=["1", "2", "3"],
             space="MNI152Lin",
         )
-    register_parcellation(
+    ParcellationRegistry().register(
         name="testparc",
         parcellation_path="testparc2.nii.gz",
         parcels_labels=["1", "2", "3"],
@@ -86,7 +82,9 @@ def test_register_parcellation_already_registered() -> None:
     )
 
     assert (
-        load_parcellation("testparc", path_only=True)[2].name
+        ParcellationRegistry()
+        .load("testparc", target_space="MNI152Lin", path_only=True)[2]
+        .name
         == "testparc2.nii.gz"
     )
 
@@ -100,24 +98,27 @@ def test_parcellation_wrong_labels_values(tmp_path: Path) -> None:
         The path to the test directory.
 
     """
-    schaefer, labels, schaefer_path, _ = load_parcellation("Schaefer100x7")
+    schaefer, labels, schaefer_path, _ = ParcellationRegistry().load(
+        "Schaefer100x7",
+        "MNI152NLin6Asym",
+    )
     assert schaefer is not None
 
     # Test wrong number of labels
-    register_parcellation(
+    ParcellationRegistry().register(
         "WrongLabels", schaefer_path, labels[:10], "MNI152Lin"
     )
 
     with pytest.raises(ValueError, match=r"has 100 parcels but 10"):
-        load_parcellation("WrongLabels")
+        ParcellationRegistry().load("WrongLabels", "MNI152NLin6Asym")
 
     # Test wrong number of labels
-    register_parcellation(
+    ParcellationRegistry().register(
         "WrongLabels2", schaefer_path, [*labels, "wrong"], "MNI152Lin"
     )
 
     with pytest.raises(ValueError, match=r"has 100 parcels but 101"):
-        load_parcellation("WrongLabels2")
+        ParcellationRegistry().load("WrongLabels2", "MNI152NLin6Asym")
 
     schaefer_data = schaefer.get_fdata().copy()
     schaefer_data[schaefer_data == 50] = 0
@@ -125,11 +126,11 @@ def test_parcellation_wrong_labels_values(tmp_path: Path) -> None:
     new_schaefer_img = new_img_like(schaefer, schaefer_data)
     nib.save(new_schaefer_img, new_schaefer_path)
 
-    register_parcellation(
+    ParcellationRegistry().register(
         "WrongValues", new_schaefer_path, labels[:-1], "MNI152Lin"
     )
-    with pytest.raises(ValueError, match=r"the range [0, 99]"):
-        load_parcellation("WrongValues")
+    with pytest.raises(ValueError, match=r"must have all the values in the"):
+        ParcellationRegistry().load("WrongValues", "MNI152NLin6Asym")
 
     schaefer_data = schaefer.get_fdata().copy()
     schaefer_data[schaefer_data == 50] = 200
@@ -137,11 +138,11 @@ def test_parcellation_wrong_labels_values(tmp_path: Path) -> None:
     new_schaefer_img = new_img_like(schaefer, schaefer_data)
     nib.save(new_schaefer_img, new_schaefer_path)
 
-    register_parcellation(
+    ParcellationRegistry().register(
         "WrongValues2", new_schaefer_path, labels, "MNI152Lin"
     )
-    with pytest.raises(ValueError, match=r"the range [0, 100]"):
-        load_parcellation("WrongValues2")
+    with pytest.raises(ValueError, match=r"must have all the values in the"):
+        ParcellationRegistry().load("WrongValues2", "MNI152NLin6Asym")
 
 
 @pytest.mark.parametrize(
@@ -170,10 +171,10 @@ def test_parcellation_wrong_labels_values(tmp_path: Path) -> None:
         ),
     ],
 )
-def test_register_parcellation(
+def test_register(
     name: str,
     parcellation_path: str,
-    parcels_labels: List[str],
+    parcels_labels: list[str],
     space: str,
     overwrite: bool,
 ) -> None:
@@ -194,7 +195,7 @@ def test_register_parcellation(
 
     """
     # Register custom parcellation
-    register_parcellation(
+    ParcellationRegistry().register(
         name=name,
         parcellation_path=parcellation_path,
         parcels_labels=parcels_labels,
@@ -202,11 +203,10 @@ def test_register_parcellation(
         overwrite=overwrite,
     )
     # List available parcellation and check registration
-    parcellations = list_parcellations()
-    assert name in parcellations
+    assert name in ParcellationRegistry().list
     # Load registered parcellation
-    _, lbl, fname, parcellation_space = load_parcellation(
-        name=name, path_only=True
+    _, lbl, fname, parcellation_space = ParcellationRegistry().load(
+        name=name, target_space=space, path_only=True
     )
     # Check values for registered parcellation
     assert lbl == parcels_labels
@@ -228,7 +228,7 @@ def test_register_parcellation(
         "TianxS4x3TxMNInonlinear2009cAsym",
     ],
 )
-def test_list_parcellations_correct(parcellation_name: str) -> None:
+def test_list_correct(parcellation_name: str) -> None:
     """Test correct information check for list parcellations.
 
     Parameters
@@ -237,20 +237,13 @@ def test_list_parcellations_correct(parcellation_name: str) -> None:
         The parametrized parcellation name.
 
     """
-    parcellations = list_parcellations()
-    assert parcellation_name in parcellations
+    assert parcellation_name in ParcellationRegistry().list
 
 
-def test_load_parcellation_incorrect() -> None:
+def test_load_incorrect() -> None:
     """Test loading of invalid parcellations."""
     with pytest.raises(ValueError, match=r"not found"):
-        load_parcellation("wrongparcellation")
-
-
-def test_retrieve_parcellation_incorrect() -> None:
-    """Test retrieval of invalid parcellations."""
-    with pytest.raises(ValueError, match=r"provided parcellation name"):
-        _retrieve_parcellation("wrongparcellation")
+        ParcellationRegistry().load("wrongparcellation", "MNI152NLin6Asym")
 
 
 @pytest.mark.parametrize(
@@ -299,7 +292,6 @@ def test_retrieve_parcellation_incorrect() -> None:
     ],
 )
 def test_schaefer(
-    tmp_path: Path,
     resolution: float,
     n_rois: int,
     yeo_networks: int,
@@ -308,8 +300,6 @@ def test_schaefer(
 
     Parameters
     ----------
-    tmp_path : pathlib.Path
-        The path to the test directory.
     resolution : float
         The parametrized resolution values.
     n_rois : int
@@ -318,18 +308,17 @@ def test_schaefer(
         The parametrized Yeo networks values.
 
     """
-    parcellations = list_parcellations()
     parcellation_name = f"Schaefer{n_rois}x{yeo_networks}"
-    assert parcellation_name in parcellations
+    assert parcellation_name in ParcellationRegistry().list
 
     parcellation_file = (
         f"Schaefer2018_{n_rois}Parcels_{yeo_networks}Networks_order_FSLMNI152_"
         f"{int(resolution)}mm.nii.gz"
     )
     # Load parcellation
-    img, label, img_path, space = load_parcellation(
+    img, label, img_path, space = ParcellationRegistry().load(
         name=parcellation_name,
-        parcellations_dir=tmp_path,
+        target_space="MNI152NLin6Asym",
         resolution=resolution,
     )
     assert img is not None
@@ -341,36 +330,20 @@ def test_schaefer(
     )
 
 
-def test_retrieve_schaefer_incorrect_n_rois(tmp_path: Path) -> None:
-    """Test retrieve Schaefer with incorrect ROIs.
-
-    Parameters
-    ----------
-    tmp_path : pathlib.Path
-        The path to the test directory.
-
-    """
+def test_retrieve_schaefer_incorrect_n_rois() -> None:
+    """Test retrieve Schaefer with incorrect ROIs."""
     with pytest.raises(ValueError, match=r"The parameter `n_rois`"):
         _retrieve_schaefer(
-            parcellations_dir=tmp_path,
             resolution=1,
             n_rois=101,
             yeo_networks=7,
         )
 
 
-def test_retrieve_schaefer_incorrect_yeo_networks(tmp_path: Path) -> None:
-    """Test retrieve Schaefer with incorrect Yeo networks.
-
-    Parameters
-    ----------
-    tmp_path : pathlib.Path
-        The path to the test directory.
-
-    """
+def test_retrieve_schaefer_incorrect_yeo_networks() -> None:
+    """Test retrieve Schaefer with incorrect Yeo networks."""
     with pytest.raises(ValueError, match=r"The parameter `yeo_networks`"):
         _retrieve_schaefer(
-            parcellations_dir=tmp_path,
             resolution=1,
             n_rois=100,
             yeo_networks=8,
@@ -381,25 +354,22 @@ def test_retrieve_schaefer_incorrect_yeo_networks(tmp_path: Path) -> None:
     "space_key, space",
     [("SUIT", "SUIT"), ("MNI", "MNI152NLin6Asym")],
 )
-def test_suit(tmp_path: Path, space_key: str, space: str) -> None:
+def test_suit(space_key: str, space: str) -> None:
     """Test SUIT parcellation.
 
     Parameters
     ----------
-    tmp_path : pathlib.Path
-        The path to the test directory.
     space_key : str
         The parametrized space values for the key.
     space : str
         The parametrized space values.
 
     """
-    parcellations = list_parcellations()
-    assert f"SUITx{space_key}" in parcellations
+    assert f"SUITx{space_key}" in ParcellationRegistry().list
     # Load parcellation
-    img, label, img_path, parcellation_space = load_parcellation(
+    img, label, img_path, parcellation_space = ParcellationRegistry().load(
         name=f"SUITx{space_key}",
-        parcellations_dir=tmp_path,
+        target_space=space,
     )
     assert img is not None
     assert img_path.name == f"SUIT_{space_key}Space_1mm.nii"
@@ -408,130 +378,123 @@ def test_suit(tmp_path: Path, space_key: str, space: str) -> None:
     assert_array_equal(img.header["pixdim"][1:4], [1, 1, 1])  # type: ignore
 
 
-def test_retrieve_suit_incorrect_space(tmp_path: Path) -> None:
-    """Test retrieve SUIT with incorrect space.
-
-    Parameters
-    ----------
-    tmp_path : pathlib.Path
-        The path to the test directory.
-
-    """
+def test_retrieve_suit_incorrect_space() -> None:
+    """Test retrieve SUIT with incorrect space."""
     with pytest.raises(ValueError, match=r"The parameter `space`"):
-        _retrieve_suit(
-            parcellations_dir=tmp_path, resolution=1.0, space="wrong"
-        )
+        _retrieve_suit(resolution=1.0, space="wrong")
 
 
 @pytest.mark.parametrize(
     "scale, n_label", [(1, 16), (2, 32), (3, 50), (4, 54)]
 )
-def test_tian_3T_6thgeneration(
-    tmp_path: Path, scale: int, n_label: int
-) -> None:
+def test_tian_3T_6thgeneration(scale: int, n_label: int) -> None:
     """Test Tian parcellation.
 
     Parameters
     ----------
-    tmp_path : pathlib.Path
-        The path to the test directory.
     scale : int
         The parametrized scale values.
     n_label : int
         The parametrized n_label values.
 
     """
-    parcellations = list_parcellations()
+    parcellations = ParcellationRegistry().list
     assert "TianxS1x3TxMNI6thgeneration" in parcellations
     assert "TianxS2x3TxMNI6thgeneration" in parcellations
     assert "TianxS3x3TxMNI6thgeneration" in parcellations
     assert "TianxS4x3TxMNI6thgeneration" in parcellations
     # Load parcellation
-    img, lbl, fname, parcellation_space_1 = load_parcellation(
-        name=f"TianxS{scale}x3TxMNI6thgeneration", parcellations_dir=tmp_path
+    img, lbl, fname, space = ParcellationRegistry().load(
+        name=f"TianxS{scale}x3TxMNI6thgeneration",
+        target_space="MNI152NLin2009cAsym",  # force highest resolution
     )
-    fname1 = f"Tian_Subcortex_S{scale}_3T_1mm.nii.gz"
+    expected_fname = f"Tian_Subcortex_S{scale}_3T_1mm.nii.gz"
     assert img is not None
-    assert fname.name == fname1
-    assert parcellation_space_1 == "MNI152NLin6Asym"
+    assert fname.name == expected_fname
+    assert space == "MNI152NLin6Asym"
     assert len(lbl) == n_label
-    assert_array_equal(img.header["pixdim"][1:4], [1, 1, 1])  # type: ignore
+    assert_array_equal(img.header["pixdim"][1:4], [1, 1, 1])
     # Load parcellation
-    img, lbl, fname, parcellation_space_2 = load_parcellation(
+    img, lbl, fname, space = ParcellationRegistry().load(
         name=f"TianxS{scale}x3TxMNI6thgeneration",
-        parcellations_dir=tmp_path,
+        target_space="MNI152NLin6Asym",
         resolution=2,
     )
-    fname1 = f"Tian_Subcortex_S{scale}_3T.nii.gz"
+    expected_fname = f"Tian_Subcortex_S{scale}_3T.nii.gz"
     assert img is not None
-    assert fname.name == fname1
-    assert parcellation_space_2 == "MNI152NLin6Asym"
+    assert fname.name == expected_fname
+    assert space == "MNI152NLin6Asym"
     assert len(lbl) == n_label
-    assert_array_equal(img.header["pixdim"][1:4], [2, 2, 2])  # type: ignore
+    assert_array_equal(img.header["pixdim"][1:4], [2, 2, 2])
 
 
 @pytest.mark.parametrize(
     "scale, n_label", [(1, 16), (2, 32), (3, 50), (4, 54)]
 )
-def test_tian_3T_nonlinear2009cAsym(
-    tmp_path: Path, scale: int, n_label: int
-) -> None:
+def test_tian_3T_nonlinear2009cAsym(scale: int, n_label: int) -> None:
     """Test Tian parcellation.
 
     Parameters
     ----------
-    tmp_path : pathlib.Path
-        The path to the test directory.
     scale : int
         The parametrized scale values.
     n_label : int
         The parametrized n_label values.
 
     """
-    parcellations = list_parcellations()
+    parcellations = ParcellationRegistry().list
     assert "TianxS1x3TxMNInonlinear2009cAsym" in parcellations
     assert "TianxS2x3TxMNInonlinear2009cAsym" in parcellations
     assert "TianxS3x3TxMNInonlinear2009cAsym" in parcellations
     assert "TianxS4x3TxMNInonlinear2009cAsym" in parcellations
     # Load parcellation
-    img, lbl, fname, space = load_parcellation(
+    img, lbl, fname, space = ParcellationRegistry().load(
         name=f"TianxS{scale}x3TxMNInonlinear2009cAsym",
-        parcellations_dir=tmp_path,
+        target_space="MNI152NLin6Asym",  # force highest resolution
     )
-    fname1 = f"Tian_Subcortex_S{scale}_3T_2009cAsym.nii.gz"
+    expected_fname = f"Tian_Subcortex_S{scale}_3T_2009cAsym_1mm.nii.gz"
     assert img is not None
-    assert fname.name == fname1
+    assert fname.name == expected_fname
     assert space == "MNI152NLin2009cAsym"
     assert len(lbl) == n_label
-    assert_array_equal(img.header["pixdim"][1:4], [2, 2, 2])  # type: ignore
+    assert_array_equal(img.header["pixdim"][1:4], [1, 1, 1])
+    # Load parcellation
+    img, lbl, fname, space = ParcellationRegistry().load(
+        name=f"TianxS{scale}x3TxMNInonlinear2009cAsym",
+        target_space="MNI152NLin2009cAsym",
+        resolution=2,
+    )
+    expected_fname = f"Tian_Subcortex_S{scale}_3T_2009cAsym.nii.gz"
+    assert img is not None
+    assert fname.name == expected_fname
+    assert space == "MNI152NLin2009cAsym"
+    assert len(lbl) == n_label
+    assert_array_equal(img.header["pixdim"][1:4], [2, 2, 2])
 
 
 @pytest.mark.parametrize(
     "scale, n_label", [(1, 16), (2, 34), (3, 54), (4, 62)]
 )
-def test_tian_7T_6thgeneration(
-    tmp_path: Path, scale: int, n_label: int
-) -> None:
+def test_tian_7T_6thgeneration(scale: int, n_label: int) -> None:
     """Test Tian parcellation.
 
     Parameters
     ----------
-    tmp_path : pathlib.Path
-        The path to the test directory.
     scale : int
         The parametrized scale values.
     n_label : int
         The parametrized n_label values.
 
     """
-    parcellations = list_parcellations()
+    parcellations = ParcellationRegistry().list
     assert "TianxS1x7TxMNI6thgeneration" in parcellations
     assert "TianxS2x7TxMNI6thgeneration" in parcellations
     assert "TianxS3x7TxMNI6thgeneration" in parcellations
     assert "TianxS4x7TxMNI6thgeneration" in parcellations
     # Load parcellation
-    img, lbl, fname, space = load_parcellation(
-        name=f"TianxS{scale}x7TxMNI6thgeneration", parcellations_dir=tmp_path
+    img, lbl, fname, space = ParcellationRegistry().load(
+        name=f"TianxS{scale}x7TxMNI6thgeneration",
+        target_space="MNI152NLin6Asym",
     )
     fname1 = f"Tian_Subcortex_S{scale}_7T.nii.gz"
     assert img is not None
@@ -543,23 +506,13 @@ def test_tian_7T_6thgeneration(
     )
 
 
-def test_retrieve_tian_incorrect_space(tmp_path: Path) -> None:
-    """Test retrieve tian with incorrect space.
-
-    Parameters
-    ----------
-    tmp_path : pathlib.Path
-        The path to the test directory.
-
-    """
+def test_retrieve_tian_incorrect_space() -> None:
+    """Test retrieve tian with incorrect space."""
     with pytest.raises(ValueError, match=r"The parameter `space`"):
-        _retrieve_tian(
-            parcellations_dir=tmp_path, resolution=1, scale=1, space="wrong"
-        )
+        _retrieve_tian(resolution=1, scale=1, space="wrong")
 
     with pytest.raises(ValueError, match=r"MNI152NLin6Asym"):
         _retrieve_tian(
-            parcellations_dir=tmp_path,
             resolution=1,
             scale=1,
             magneticfield="7T",
@@ -567,18 +520,10 @@ def test_retrieve_tian_incorrect_space(tmp_path: Path) -> None:
         )
 
 
-def test_retrieve_tian_incorrect_magneticfield(tmp_path: Path) -> None:
-    """Test retrieve tian with incorrect magneticfield.
-
-    Parameters
-    ----------
-    tmp_path : pathlib.Path
-        The path to the test directory.
-
-    """
+def test_retrieve_tian_incorrect_magneticfield() -> None:
+    """Test retrieve tian with incorrect magneticfield."""
     with pytest.raises(ValueError, match=r"The parameter `magneticfield`"):
         _retrieve_tian(
-            parcellations_dir=tmp_path,
             resolution=1,
             scale=1,
             magneticfield="wrong",
@@ -586,17 +531,9 @@ def test_retrieve_tian_incorrect_magneticfield(tmp_path: Path) -> None:
 
 
 def test_retrieve_tian_incorrect_scale(tmp_path: Path) -> None:
-    """Test retrieve tian with incorrect scale.
-
-    Parameters
-    ----------
-    tmp_path : pathlib.Path
-        The path to the test directory.
-
-    """
+    """Test retrieve tian with incorrect scale."""
     with pytest.raises(ValueError, match=r"The parameter `scale`"):
         _retrieve_tian(
-            parcellations_dir=tmp_path,
             resolution=1,
             scale=5,
             space="MNI152NLin6Asym",
@@ -604,7 +541,7 @@ def test_retrieve_tian_incorrect_scale(tmp_path: Path) -> None:
 
 
 @pytest.mark.parametrize("version", [1, 2])
-def test_aicha(tmp_path: Path, version: int) -> None:
+def test_aicha(version: int) -> None:
     """Test AICHA parcellation.
 
     Parameters
@@ -615,11 +552,11 @@ def test_aicha(tmp_path: Path, version: int) -> None:
         The parametrized version values.
 
     """
-    parcellations = list_parcellations()
-    assert f"AICHA_v{version}" in parcellations
+    assert f"AICHA_v{version}" in ParcellationRegistry().list
     # Load parcellation
-    img, label, img_path, space = load_parcellation(
-        name=f"AICHA_v{version}", parcellations_dir=tmp_path
+    img, label, img_path, space = ParcellationRegistry().load(
+        name=f"AICHA_v{version}",
+        target_space="IXI549Space",
     )
     assert img is not None
     assert img_path.name == "AICHA.nii"
@@ -628,18 +565,10 @@ def test_aicha(tmp_path: Path, version: int) -> None:
     assert_array_equal(img.header["pixdim"][1:4], [2, 2, 2])  # type: ignore
 
 
-def test_retrieve_aicha_incorrect_version(tmp_path: Path) -> None:
-    """Test retrieve AICHA with incorrect version.
-
-    Parameters
-    ----------
-    tmp_path : pathlib.Path
-        The path to the test directory.
-
-    """
+def test_retrieve_aicha_incorrect_version() -> None:
+    """Test retrieve AICHA with incorrect version."""
     with pytest.raises(ValueError, match="The parameter `version`"):
         _retrieve_aicha(
-            parcellations_dir=tmp_path,
             version=100,
         )
 
@@ -659,7 +588,6 @@ def test_retrieve_aicha_incorrect_version(tmp_path: Path) -> None:
     ],
 )
 def test_shen(
-    tmp_path: Path,
     resolution: float,
     year: int,
     n_rois: int,
@@ -670,8 +598,6 @@ def test_shen(
 
     Parameters
     ----------
-    tmp_path : pathlib.Path
-        The path to the test directory.
     resolution : float
         The parametrized resolution values.
     year : int
@@ -684,12 +610,11 @@ def test_shen(
         The parametrized partial file names.
 
     """
-    parcellations = list_parcellations()
-    assert f"Shen_{year}_{n_rois}" in parcellations
+    assert f"Shen_{year}_{n_rois}" in ParcellationRegistry().list
     # Load parcellation
-    img, label, img_path, space = load_parcellation(
+    img, label, img_path, space = ParcellationRegistry().load(
         name=f"Shen_{year}_{n_rois}",
-        parcellations_dir=tmp_path,
+        target_space="MNI152NLin2009cAsym",
         resolution=resolution,
     )
     assert img is not None
@@ -701,34 +626,18 @@ def test_shen(
     )
 
 
-def test_retrieve_shen_incorrect_year(tmp_path: Path) -> None:
-    """Test retrieve Shen with incorrect year.
-
-    Parameters
-    ----------
-    tmp_path : pathlib.Path
-        The path to the test directory.
-
-    """
+def test_retrieve_shen_incorrect_year() -> None:
+    """Test retrieve Shen with incorrect year."""
     with pytest.raises(ValueError, match="The parameter `year`"):
         _retrieve_shen(
-            parcellations_dir=tmp_path,
             year=1969,
         )
 
 
-def test_retrieve_shen_incorrect_n_rois(tmp_path: Path) -> None:
-    """Test retrieve Shen with incorrect ROIs.
-
-    Parameters
-    ----------
-    tmp_path : pathlib.Path
-        The path to the test directory.
-
-    """
+def test_retrieve_shen_incorrect_n_rois() -> None:
+    """Test retrieve Shen with incorrect ROIs."""
     with pytest.raises(ValueError, match="The parameter `n_rois`"):
         _retrieve_shen(
-            parcellations_dir=tmp_path,
             year=2015,
             n_rois=10,
         )
@@ -751,7 +660,6 @@ def test_retrieve_shen_incorrect_n_rois(tmp_path: Path) -> None:
     ],
 )
 def test_retrieve_shen_incorrect_param_combo(
-    tmp_path: Path,
     resolution: float,
     year: int,
     n_rois: int,
@@ -772,7 +680,6 @@ def test_retrieve_shen_incorrect_param_combo(
     """
     with pytest.raises(ValueError, match="The parameter combination"):
         _retrieve_shen(
-            parcellations_dir=tmp_path,
             resolution=resolution,
             year=year,
             n_rois=n_rois,
@@ -845,7 +752,6 @@ def test_retrieve_shen_incorrect_param_combo(
     ],
 )
 def test_yan(
-    tmp_path: Path,
     resolution: float,
     n_rois: int,
     yeo_networks: int,
@@ -855,8 +761,6 @@ def test_yan(
 
     Parameters
     ----------
-    tmp_path : pathlib.Path
-        The path to the test directory.
     resolution : float
         The parametrized resolution values.
     n_rois : int
@@ -867,7 +771,7 @@ def test_yan(
         The parametrized Kong networks values.
 
     """
-    parcellations = list_parcellations()
+    parcellations = ParcellationRegistry().list
     if yeo_networks:
         parcellation_name = f"Yan{n_rois}xYeo{yeo_networks}"
         assert parcellation_name in parcellations
@@ -883,9 +787,9 @@ def test_yan(
             f"{int(resolution)}mm.nii.gz"
         )
     # Load parcellation
-    img, label, img_path, space = load_parcellation(
-        name=parcellation_name,  # type: ignore
-        parcellations_dir=tmp_path,
+    img, label, img_path, space = ParcellationRegistry().load(
+        name=parcellation_name,
+        target_space="MNI152NLin6Asym",
         resolution=resolution,
     )
     assert img is not None
@@ -897,20 +801,12 @@ def test_yan(
     )
 
 
-def test_retrieve_yan_incorrect_networks(tmp_path: Path) -> None:
-    """Test retrieve Yan with incorrect networks.
-
-    Parameters
-    ----------
-    tmp_path : pathlib.Path
-        The path to the test directory.
-
-    """
+def test_retrieve_yan_incorrect_networks() -> None:
+    """Test retrieve Yan with incorrect networks."""
     with pytest.raises(
         ValueError, match="Either one of `yeo_networks` or `kong_networks`"
     ):
         _retrieve_yan(
-            parcellations_dir=tmp_path,
             n_rois=31418,
             yeo_networks=100,
             kong_networks=100,
@@ -920,59 +816,34 @@ def test_retrieve_yan_incorrect_networks(tmp_path: Path) -> None:
         ValueError, match="Either one of `yeo_networks` or `kong_networks`"
     ):
         _retrieve_yan(
-            parcellations_dir=tmp_path,
             n_rois=31418,
             yeo_networks=None,
             kong_networks=None,
         )
 
 
-def test_retrieve_yan_incorrect_n_rois(tmp_path: Path) -> None:
-    """Test retrieve Yan with incorrect ROIs.
-
-    Parameters
-    ----------
-    tmp_path : pathlib.Path
-        The path to the test directory.
-
-    """
+def test_retrieve_yan_incorrect_n_rois() -> None:
+    """Test retrieve Yan with incorrect ROIs."""
     with pytest.raises(ValueError, match="The parameter `n_rois`"):
         _retrieve_yan(
-            parcellations_dir=tmp_path,
             n_rois=31418,
             yeo_networks=7,
         )
 
 
-def test_retrieve_yan_incorrect_yeo_networks(tmp_path: Path) -> None:
-    """Test retrieve Yan with incorrect Yeo networks.
-
-    Parameters
-    ----------
-    tmp_path : pathlib.Path
-        The path to the test directory.
-
-    """
+def test_retrieve_yan_incorrect_yeo_networks() -> None:
+    """Test retrieve Yan with incorrect Yeo networks."""
     with pytest.raises(ValueError, match="The parameter `yeo_networks`"):
         _retrieve_yan(
-            parcellations_dir=tmp_path,
             n_rois=100,
             yeo_networks=27,
         )
 
 
-def test_retrieve_yan_incorrect_kong_networks(tmp_path: Path) -> None:
-    """Test retrieve Yan with incorrect Kong networks.
-
-    Parameters
-    ----------
-    tmp_path : pathlib.Path
-        The path to the test directory.
-
-    """
+def test_retrieve_yan_incorrect_kong_networks() -> None:
+    """Test retrieve Yan with incorrect Kong networks."""
     with pytest.raises(ValueError, match="The parameter `kong_networks`"):
         _retrieve_yan(
-            parcellations_dir=tmp_path,
             n_rois=100,
             kong_networks=27,
         )
@@ -993,7 +864,6 @@ def test_retrieve_yan_incorrect_kong_networks(tmp_path: Path) -> None:
     ],
 )
 def test_brainnetome(
-    tmp_path: Path,
     resolution: float,
     threshold: int,
 ) -> None:
@@ -1001,15 +871,13 @@ def test_brainnetome(
 
     Parameters
     ----------
-    tmp_path : pathlib.Path
-        The path to the test directory.
     resolution : float
         The parametrized resolution values.
     threshold : int
         The parametrized threshold values.
 
     """
-    parcellations = list_parcellations()
+    parcellations = ParcellationRegistry().list
     parcellation_name = f"Brainnetome_thr{threshold}"
     assert parcellation_name in parcellations
 
@@ -1019,9 +887,9 @@ def test_brainnetome(
 
     parcellation_file = f"BNA-maxprob-thr{threshold}-{resolution}mm.nii.gz"
     # Load parcellation
-    img, label, img_path, space = load_parcellation(
+    img, label, img_path, space = ParcellationRegistry().load(
         name=parcellation_name,
-        parcellations_dir=tmp_path,
+        target_space="MNI152NLin6Asym",
         resolution=resolution,
     )
     assert img is not None
@@ -1033,18 +901,10 @@ def test_brainnetome(
     )
 
 
-def test_retrieve_brainnetome_incorrect_threshold(tmp_path: Path) -> None:
-    """Test retrieve Brainnetome with incorrect threshold.
-
-    Parameters
-    ----------
-    tmp_path : pathlib.Path
-        The path to the test directory.
-
-    """
+def test_retrieve_brainnetome_incorrect_threshold() -> None:
+    """Test retrieve Brainnetome with incorrect threshold."""
     with pytest.raises(ValueError, match="The parameter `threshold`"):
         _retrieve_brainnetome(
-            parcellations_dir=tmp_path,
             threshold=100,
         )
 
@@ -1052,11 +912,12 @@ def test_retrieve_brainnetome_incorrect_threshold(tmp_path: Path) -> None:
 def test_merge_parcellations() -> None:
     """Test merging parcellations."""
     # load some parcellations for testing
-    schaefer_parcellation, schaefer_labels, _, _ = load_parcellation(
-        "Schaefer100x17"
+    schaefer_parcellation, schaefer_labels, _, _ = ParcellationRegistry().load(
+        "Schaefer100x17", target_space="MNI152NLin2009cAsym"
     )
-    tian_parcellation, tian_labels, _, _ = load_parcellation(
-        "TianxS2x3TxMNInonlinear2009cAsym"
+    tian_parcellation, tian_labels, _, _ = ParcellationRegistry().load(
+        "TianxS2x3TxMNInonlinear2009cAsym",
+        target_space="MNI152NLin2009cAsym",
     )
     # prepare the list of the actual parcellations
     parcellation_list = [schaefer_parcellation, tian_parcellation]
@@ -1088,7 +949,9 @@ def test_merge_parcellations_3D_multiple_non_overlapping(
 
     """
     # Get the testing parcellation
-    parcellation, labels, _, _ = load_parcellation("Schaefer100x7")
+    parcellation, labels, _, _ = ParcellationRegistry().load(
+        "Schaefer100x7", target_space="MNI152NLin2009cAsym"
+    )
 
     assert parcellation is not None
 
@@ -1123,7 +986,9 @@ def test_merge_parcellations_3D_multiple_overlapping() -> None:
     """Test merge_parcellations with multiple overlapping parcellations."""
 
     # Get the testing parcellation
-    parcellation, labels, _, _ = load_parcellation("Schaefer100x7")
+    parcellation, labels, _, _ = ParcellationRegistry().load(
+        "Schaefer100x7", target_space="MNI152NLin2009cAsym"
+    )
 
     assert parcellation is not None
 
@@ -1147,9 +1012,7 @@ def test_merge_parcellations_3D_multiple_overlapping() -> None:
     labels_lists = [labels1, labels2]
 
     with pytest.warns(RuntimeWarning, match="overlapping voxels"):
-        merged_parc, merged_labels = merge_parcellations(
-            parcellation_list, names, labels_lists
-        )
+        merge_parcellations(parcellation_list, names, labels_lists)
 
     parc_data = parcellation.get_fdata()
     assert len(labels) == 100
@@ -1160,7 +1023,9 @@ def test_merge_parcellations_3D_multiple_duplicated_labels() -> None:
     """Test merge_parcellations with duplicated labels."""
 
     # Get the testing parcellation
-    parcellation, labels, _, _ = load_parcellation("Schaefer100x7")
+    parcellation, labels, _, _ = ParcellationRegistry().load(
+        "Schaefer100x7", target_space="MNI152NLin2009cAsym"
+    )
 
     assert parcellation is not None
 
@@ -1182,7 +1047,7 @@ def test_merge_parcellations_3D_multiple_duplicated_labels() -> None:
     labels_lists = [labels1, labels2]
 
     with pytest.warns(RuntimeWarning, match="duplicated labels."):
-        merged_parc, merged_labels = merge_parcellations(
+        merged_parc, _ = merge_parcellations(
             parcellation_list, names, labels_lists
         )
 
@@ -1192,24 +1057,25 @@ def test_merge_parcellations_3D_multiple_duplicated_labels() -> None:
     assert len(np.unique(parc_data)) == 101  # 100 + 1 because background 0
 
 
-def test_get_parcellation_single() -> None:
+def test_get_single() -> None:
     """Test tailored single parcellation fetch."""
     with PartlyCloudyTestingDataGrabber() as dg:
         element_data = DefaultDataReader().fit_transform(dg["sub-01"])
         bold = element_data["BOLD"]
         bold_img = bold["data"]
         # Get tailored parcellation
-        tailored_parcellation, tailored_labels = get_parcellation(
-            parcellation=["TianxS1x3TxMNInonlinear2009cAsym"],
+        tailored_parcellation, tailored_labels = ParcellationRegistry().get(
+            parcellations=["Shen_2015_268"],
             target_data=bold,
         )
         # Check shape and affine with original element data
         assert tailored_parcellation.shape == bold_img.shape[:3]
         assert_array_equal(tailored_parcellation.affine, bold_img.affine)
         # Get raw parcellation
-        raw_parcellation, raw_labels, _, _ = load_parcellation(
-            "TianxS1x3TxMNInonlinear2009cAsym",
-            resolution=1.5,
+        raw_parcellation, raw_labels, _, _ = ParcellationRegistry().load(
+            name="Shen_2015_268",
+            target_space="MNI152NLin2009cAsym",
+            resolution=4,
         )
         resampled_raw_parcellation = resample_to_img(
             source_img=raw_parcellation,
@@ -1225,15 +1091,15 @@ def test_get_parcellation_single() -> None:
         assert tailored_labels == raw_labels
 
 
-def test_get_parcellation_multi_same_space() -> None:
+def test_get_multi_same_space() -> None:
     """Test tailored multi parcellation fetch in same space."""
     with PartlyCloudyTestingDataGrabber() as dg:
         element_data = DefaultDataReader().fit_transform(dg["sub-01"])
         bold = element_data["BOLD"]
         bold_img = bold["data"]
         # Get tailored parcellation
-        tailored_parcellation, tailored_labels = get_parcellation(
-            parcellation=[
+        tailored_parcellation, tailored_labels = ParcellationRegistry().get(
+            parcellations=[
                 "Shen_2015_268",
                 "TianxS1x3TxMNInonlinear2009cAsym",
             ],
@@ -1250,7 +1116,11 @@ def test_get_parcellation_multi_same_space() -> None:
             "TianxS1x3TxMNInonlinear2009cAsym",
         ]
         for name in parcellations_names:
-            img, labels, _, _ = load_parcellation(name=name, resolution=1.5)
+            img, labels, _, _ = ParcellationRegistry().load(
+                name=name,
+                target_space="MNI152NLin2009cAsym",
+                resolution=4,
+            )
             # Resample raw parcellations
             resampled_img = resample_to_img(
                 source_img=img,
@@ -1277,13 +1147,13 @@ def test_get_parcellation_multi_same_space() -> None:
 @pytest.mark.skipif(
     _check_ants() is False, reason="requires ANTs to be in PATH"
 )
-def test_get_parcellation_multi_different_space() -> None:
+def test_get_multi_different_space() -> None:
     """Test tailored multi parcellation fetch in different space."""
     with OasisVBMTestingDataGrabber() as dg:
         element_data = DefaultDataReader().fit_transform(dg["sub-01"])
         # Get tailored parcellation
-        get_parcellation(
-            parcellation=[
+        ParcellationRegistry().get(
+            parcellations=[
                 "Schaefer100x7",
                 "TianxS1x3TxMNInonlinear2009cAsym",
             ],