junifer 0.0.3.dev186__py3-none-any.whl → 0.0.4__py3-none-any.whl

junifer/data/tests/test_parcellations.py

@@ -11,22 +11,30 @@ from typing import List
 import nibabel as nib
 import numpy as np
 import pytest
-from nilearn.image import new_img_like
+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 (
     _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
+from junifer.testing.datagrabbers import (
+    OasisVBMTestingDataGrabber,
+    PartlyCloudyTestingDataGrabber,
+)
 
 
 def test_register_parcellation_built_in_check() -> None:
@@ -36,6 +44,7 @@ def test_register_parcellation_built_in_check() -> None:
             name="SUITxSUIT",
             parcellation_path="testparc.nii.gz",
             parcels_labels=["1", "2", "3"],
+            space="SUIT",
             overwrite=True,
         )
 
@@ -53,6 +62,7 @@ def test_register_parcellation_already_registered() -> None:
         name="testparc",
         parcellation_path="testparc.nii.gz",
         parcels_labels=["1", "2", "3"],
+        space="MNI152Lin",
     )
     assert (
         load_parcellation("testparc", path_only=True)[2].name
@@ -65,11 +75,13 @@ def test_register_parcellation_already_registered() -> None:
             name="testparc",
             parcellation_path="testparc.nii.gz",
             parcels_labels=["1", "2", "3"],
+            space="MNI152Lin",
         )
     register_parcellation(
         name="testparc",
         parcellation_path="testparc2.nii.gz",
         parcels_labels=["1", "2", "3"],
+        space="MNI152Lin",
         overwrite=True,
     )
 
@@ -86,18 +98,23 @@ def test_parcellation_wrong_labels_values(tmp_path: Path) -> None:
     ----------
     tmp_path : pathlib.Path
         The path to the test directory.
+
     """
-    schaefer, labels, schaefer_path = load_parcellation("Schaefer100x7")
+    schaefer, labels, schaefer_path, _ = load_parcellation("Schaefer100x7")
     assert schaefer is not None
 
     # Test wrong number of labels
-    register_parcellation("WrongLabels", schaefer_path, labels[:10])
+    register_parcellation(
+        "WrongLabels", schaefer_path, labels[:10], "MNI152Lin"
+    )
 
     with pytest.raises(ValueError, match=r"has 100 parcels but 10"):
         load_parcellation("WrongLabels")
 
     # Test wrong number of labels
-    register_parcellation("WrongLabels2", schaefer_path, [*labels, "wrong"])
+    register_parcellation(
+        "WrongLabels2", schaefer_path, [*labels, "wrong"], "MNI152Lin"
+    )
 
     with pytest.raises(ValueError, match=r"has 100 parcels but 101"):
         load_parcellation("WrongLabels2")
@@ -108,7 +125,9 @@ 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("WrongValues", new_schaefer_path, labels[:-1])
+    register_parcellation(
+        "WrongValues", new_schaefer_path, labels[:-1], "MNI152Lin"
+    )
     with pytest.raises(ValueError, match=r"the range [0, 99]"):
         load_parcellation("WrongValues")
 
@@ -118,23 +137,44 @@ 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("WrongValues2", new_schaefer_path, labels)
+    register_parcellation(
+        "WrongValues2", new_schaefer_path, labels, "MNI152Lin"
+    )
     with pytest.raises(ValueError, match=r"the range [0, 100]"):
         load_parcellation("WrongValues2")
 
 
 @pytest.mark.parametrize(
-    "name, parcellation_path, parcels_labels, overwrite",
+    "name, parcellation_path, parcels_labels, space, overwrite",
     [
-        ("testparc_1", "testparc_1.nii.gz", ["1", "2", "3"], True),
-        ("testparc_2", "testparc_2.nii.gz", ["1", "2", "6"], True),
-        ("testparc_3", Path("testparc_3.nii.gz"), ["1", "2", "6"], True),
+        (
+            "testparc_1",
+            "testparc_1.nii.gz",
+            ["1", "2", "3"],
+            "MNI152Lin",
+            True,
+        ),
+        (
+            "testparc_2",
+            "testparc_2.nii.gz",
+            ["1", "2", "6"],
+            "MNI152Lin",
+            True,
+        ),
+        (
+            "testparc_3",
+            Path("testparc_3.nii.gz"),
+            ["1", "2", "6"],
+            "MNI152Lin",
+            True,
+        ),
     ],
 )
 def test_register_parcellation(
     name: str,
     parcellation_path: str,
     parcels_labels: List[str],
+    space: str,
     overwrite: bool,
 ) -> None:
     """Test parcellation registration.
@@ -147,6 +187,8 @@ def test_register_parcellation(
         The parametrized parcellation path.
     parcels_labels : list of str
         The parametrized parcellation labels.
+    space : str
+        The parametrized parcellation space.
     overwrite : bool
         The parametrized parcellation overwrite value.
 
@@ -156,16 +198,20 @@ def test_register_parcellation(
         name=name,
         parcellation_path=parcellation_path,
         parcels_labels=parcels_labels,
+        space=space,
         overwrite=overwrite,
     )
     # List available parcellation and check registration
     parcellations = list_parcellations()
     assert name in parcellations
     # Load registered parcellation
-    _, lbl, fname = load_parcellation(name=name, path_only=True)
+    _, lbl, fname, parcellation_space = load_parcellation(
+        name=name, path_only=True
+    )
     # Check values for registered parcellation
     assert lbl == parcels_labels
     assert fname.name == f"{name}.nii.gz"
+    assert parcellation_space == space
 
 
 @pytest.mark.parametrize(
@@ -281,7 +327,7 @@ def test_schaefer(
         f"{int(resolution)}mm.nii.gz"
     )
     # Load parcellation
-    img, label, img_path = load_parcellation(
+    img, label, img_path, space = load_parcellation(
         name=parcellation_name,
         parcellations_dir=tmp_path,
         resolution=resolution,
@@ -289,6 +335,7 @@ def test_schaefer(
     assert img is not None
     assert img_path.name == parcellation_file
     assert len(label) == n_rois
+    assert space == "MNI152NLin6Asym"
     assert_array_equal(
         img.header["pixdim"][1:4], 3 * [resolution]  # type: ignore
     )
@@ -331,29 +378,32 @@ def test_retrieve_schaefer_incorrect_yeo_networks(tmp_path: Path) -> None:
 
 
 @pytest.mark.parametrize(
-    "space",
-    ["SUIT", "MNI"],
+    "space_key, space",
+    [("SUIT", "SUIT"), ("MNI", "MNI152NLin6Asym")],
 )
-def test_suit(tmp_path: Path, space: str) -> None:
+def test_suit(tmp_path: Path, 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}" in parcellations
+    assert f"SUITx{space_key}" in parcellations
     # Load parcellation
-    img, label, img_path = load_parcellation(
-        name=f"SUITx{space}",
+    img, label, img_path, parcellation_space = load_parcellation(
+        name=f"SUITx{space_key}",
         parcellations_dir=tmp_path,
     )
     assert img is not None
-    assert img_path.name == f"SUIT_{space}Space_1mm.nii"
+    assert img_path.name == f"SUIT_{space_key}Space_1mm.nii"
+    assert parcellation_space == space
     assert len(label) == 34
     assert_array_equal(img.header["pixdim"][1:4], [1, 1, 1])  # type: ignore
 
@@ -397,16 +447,17 @@ def test_tian_3T_6thgeneration(
     assert "TianxS3x3TxMNI6thgeneration" in parcellations
     assert "TianxS4x3TxMNI6thgeneration" in parcellations
     # Load parcellation
-    img, lbl, fname = load_parcellation(
+    img, lbl, fname, parcellation_space_1 = load_parcellation(
         name=f"TianxS{scale}x3TxMNI6thgeneration", parcellations_dir=tmp_path
     )
     fname1 = f"Tian_Subcortex_S{scale}_3T_1mm.nii.gz"
     assert img is not None
     assert fname.name == fname1
+    assert parcellation_space_1 == "MNI152NLin6Asym"
     assert len(lbl) == n_label
     assert_array_equal(img.header["pixdim"][1:4], [1, 1, 1])  # type: ignore
     # Load parcellation
-    img, lbl, fname = load_parcellation(
+    img, lbl, fname, parcellation_space_2 = load_parcellation(
         name=f"TianxS{scale}x3TxMNI6thgeneration",
         parcellations_dir=tmp_path,
         resolution=2,
@@ -414,6 +465,7 @@ def test_tian_3T_6thgeneration(
     fname1 = f"Tian_Subcortex_S{scale}_3T.nii.gz"
     assert img is not None
     assert fname.name == fname1
+    assert parcellation_space_2 == "MNI152NLin6Asym"
     assert len(lbl) == n_label
     assert_array_equal(img.header["pixdim"][1:4], [2, 2, 2])  # type: ignore
 
@@ -442,13 +494,14 @@ def test_tian_3T_nonlinear2009cAsym(
     assert "TianxS3x3TxMNInonlinear2009cAsym" in parcellations
     assert "TianxS4x3TxMNInonlinear2009cAsym" in parcellations
     # Load parcellation
-    img, lbl, fname = load_parcellation(
+    img, lbl, fname, space = load_parcellation(
         name=f"TianxS{scale}x3TxMNInonlinear2009cAsym",
         parcellations_dir=tmp_path,
     )
     fname1 = f"Tian_Subcortex_S{scale}_3T_2009cAsym.nii.gz"
     assert img is not None
     assert fname.name == fname1
+    assert space == "MNI152NLin2009cAsym"
     assert len(lbl) == n_label
     assert_array_equal(img.header["pixdim"][1:4], [2, 2, 2])  # type: ignore
 
@@ -477,12 +530,13 @@ def test_tian_7T_6thgeneration(
     assert "TianxS3x7TxMNI6thgeneration" in parcellations
     assert "TianxS4x7TxMNI6thgeneration" in parcellations
     # Load parcellation
-    img, lbl, fname = load_parcellation(
+    img, lbl, fname, space = load_parcellation(
         name=f"TianxS{scale}x7TxMNI6thgeneration", parcellations_dir=tmp_path
     )
     fname1 = f"Tian_Subcortex_S{scale}_7T.nii.gz"
     assert img is not None
     assert fname.name == fname1
+    assert space == "MNI152NLin6Asym"
     assert len(lbl) == n_label
     assert_array_almost_equal(
         img.header["pixdim"][1:4], [1.6, 1.6, 1.6]  # type: ignore
@@ -503,13 +557,13 @@ def test_retrieve_tian_incorrect_space(tmp_path: Path) -> None:
             parcellations_dir=tmp_path, resolution=1, scale=1, space="wrong"
         )
 
-    with pytest.raises(ValueError, match=r"MNI6thgeneration"):
+    with pytest.raises(ValueError, match=r"MNI152NLin6Asym"):
         _retrieve_tian(
             parcellations_dir=tmp_path,
             resolution=1,
             scale=1,
             magneticfield="7T",
-            space="MNInonlinear2009cAsym",
+            space="MNI152NLin2009cAsym",
         )
 
 
@@ -545,7 +599,7 @@ def test_retrieve_tian_incorrect_scale(tmp_path: Path) -> None:
             parcellations_dir=tmp_path,
             resolution=1,
             scale=5,
-            space="MNI6thgeneration",
+            space="MNI152NLin6Asym",
         )
 
 
@@ -564,11 +618,12 @@ def test_aicha(tmp_path: Path, version: int) -> None:
     parcellations = list_parcellations()
     assert f"AICHA_v{version}" in parcellations
     # Load parcellation
-    img, label, img_path = load_parcellation(
+    img, label, img_path, space = load_parcellation(
         name=f"AICHA_v{version}", parcellations_dir=tmp_path
     )
     assert img is not None
     assert img_path.name == "AICHA.nii"
+    assert space == "IXI549Space"
     assert len(label) == 384
     assert_array_equal(img.header["pixdim"][1:4], [2, 2, 2])  # type: ignore
 
@@ -632,13 +687,14 @@ def test_shen(
     parcellations = list_parcellations()
     assert f"Shen_{year}_{n_rois}" in parcellations
     # Load parcellation
-    img, label, img_path = load_parcellation(
+    img, label, img_path, space = load_parcellation(
         name=f"Shen_{year}_{n_rois}",
         parcellations_dir=tmp_path,
         resolution=resolution,
     )
     assert img is not None
     assert img_name in img_path.name
+    assert space == "MNI152NLin2009cAsym"
     assert len(label) == n_labels
     assert_array_equal(
         img.header["pixdim"][1:4], 3 * [resolution]  # type: ignore
@@ -827,13 +883,14 @@ def test_yan(
             f"{int(resolution)}mm.nii.gz"
         )
     # Load parcellation
-    img, label, img_path = load_parcellation(
+    img, label, img_path, space = load_parcellation(
         name=parcellation_name,  # type: ignore
         parcellations_dir=tmp_path,
         resolution=resolution,
     )
     assert img is not None
     assert img_path.name == parcellation_file  # type: ignore
+    assert space == "MNI152NLin6Asym"
     assert len(label) == n_rois
     assert_array_equal(
         img.header["pixdim"][1:4], 3 * [resolution]  # type: ignore
@@ -921,13 +978,84 @@ def test_retrieve_yan_incorrect_kong_networks(tmp_path: Path) -> None:
         )
 
 
+@pytest.mark.parametrize(
+    "resolution, threshold",
+    [
+        (1.0, 0),
+        (1.0, 25),
+        (1.0, 50),
+        (1.25, 0),
+        (1.25, 25),
+        (1.25, 50),
+        (2, 0),
+        (2, 25),
+        (2, 50),
+    ],
+)
+def test_brainnetome(
+    tmp_path: Path,
+    resolution: float,
+    threshold: int,
+) -> None:
+    """Test Brainnetome parcellation.
+
+    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()
+    parcellation_name = f"Brainnetome_thr{threshold}"
+    assert parcellation_name in parcellations
+
+    # Fix resolution
+    if resolution in [1.0, 2.0]:
+        resolution = int(resolution)
+
+    parcellation_file = f"BNA-maxprob-thr{threshold}-{resolution}mm.nii.gz"
+    # Load parcellation
+    img, label, img_path, space = load_parcellation(
+        name=parcellation_name,
+        parcellations_dir=tmp_path,
+        resolution=resolution,
+    )
+    assert img is not None
+    assert img_path.name == parcellation_file
+    assert space == "MNI152NLin6Asym"
+    assert len(label) == 246
+    assert_array_equal(
+        img.header["pixdim"][1:4], 3 * [resolution]  # type: ignore
+    )
+
+
+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.
+
+    """
+    with pytest.raises(ValueError, match="The parameter `threshold`"):
+        _retrieve_brainnetome(
+            parcellations_dir=tmp_path,
+            threshold=100,
+        )
+
+
 def test_merge_parcellations() -> None:
     """Test merging parcellations."""
     # load some parcellations for testing
-    schaefer_parcellation, schaefer_labels, _ = load_parcellation(
+    schaefer_parcellation, schaefer_labels, _, _ = load_parcellation(
         "Schaefer100x17"
     )
-    tian_parcellation, tian_labels, _ = load_parcellation(
+    tian_parcellation, tian_labels, _, _ = load_parcellation(
         "TianxS2x3TxMNInonlinear2009cAsym"
     )
     # prepare the list of the actual parcellations
@@ -960,7 +1088,7 @@ def test_merge_parcellations_3D_multiple_non_overlapping(
 
     """
     # Get the testing parcellation
-    parcellation, labels, _ = load_parcellation("Schaefer100x7")
+    parcellation, labels, _, _ = load_parcellation("Schaefer100x7")
 
     assert parcellation is not None
 
@@ -981,7 +1109,7 @@ def test_merge_parcellations_3D_multiple_non_overlapping(
     names = ["high", "low"]
     labels_lists = [labels1, labels2]
 
-    merged_parc, merged_labels = merge_parcellations(
+    merged_parc, _ = merge_parcellations(
         parcellation_list, names, labels_lists
     )
 
@@ -991,18 +1119,11 @@ def test_merge_parcellations_3D_multiple_non_overlapping(
     assert len(np.unique(parc_data)) == 101  # 100 + 1 because background 0
 
 
-def test_merge_parcellations_3D_multiple_overlapping(tmp_path: Path) -> None:
-    """Test merge_parcellations with multiple overlapping parcellations.
-
-    Parameters
-    ----------
-    tmp_path : pathlib.Path
-        The path to the test directory.
-
-    """
+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, _, _ = load_parcellation("Schaefer100x7")
 
     assert parcellation is not None
 
@@ -1035,20 +1156,11 @@ def test_merge_parcellations_3D_multiple_overlapping(tmp_path: Path) -> None:
     assert len(np.unique(parc_data)) == 101  # 100 + 1 because background 0
 
 
-def test_merge_parcellations_3D_multiple_duplicated_labels(
-    tmp_path: Path,
-) -> None:
-    """Test merge_parcellations with two parcellations with duplicated labels.
-
-    Parameters
-    ----------
-    tmp_path : pathlib.Path
-        The path to the test directory.
-
-    """
+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, _, _ = load_parcellation("Schaefer100x7")
 
     assert parcellation is not None
 
@@ -1078,3 +1190,102 @@ def test_merge_parcellations_3D_multiple_duplicated_labels(
     assert_array_equal(parc_data, merged_parc.get_fdata())
     assert len(labels) == 100
     assert len(np.unique(parc_data)) == 101  # 100 + 1 because background 0
+
+
+def test_get_parcellation_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"],
+            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,
+        )
+        resampled_raw_parcellation = resample_to_img(
+            source_img=raw_parcellation,
+            target_img=bold_img,
+            interpolation="nearest",
+            copy=True,
+        )
+        # Check resampled data with tailored data
+        assert_array_equal(
+            tailored_parcellation.get_fdata(),
+            resampled_raw_parcellation.get_fdata(),
+        )
+        assert tailored_labels == raw_labels
+
+
+def test_get_parcellation_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=[
+                "Shen_2015_268",
+                "TianxS1x3TxMNInonlinear2009cAsym",
+            ],
+            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 parcellations
+        raw_parcellations = []
+        raw_labels = []
+        parcellations_names = [
+            "Shen_2015_268",
+            "TianxS1x3TxMNInonlinear2009cAsym",
+        ]
+        for name in parcellations_names:
+            img, labels, _, _ = load_parcellation(name=name, resolution=1.5)
+            # Resample raw parcellations
+            resampled_img = resample_to_img(
+                source_img=img,
+                target_img=bold_img,
+                interpolation="nearest",
+                copy=True,
+            )
+            raw_parcellations.append(resampled_img)
+            raw_labels.append(labels)
+        # Merge resampled parcellations
+        merged_resampled_parcellations, merged_labels = merge_parcellations(
+            parcellations_list=raw_parcellations,
+            parcellations_names=parcellations_names,
+            labels_lists=raw_labels,
+        )
+        # Check resampled data with tailored data
+        assert_array_equal(
+            tailored_parcellation.get_fdata(),
+            merged_resampled_parcellations.get_fdata(),
+        )
+        assert tailored_labels == merged_labels
+
+
+@pytest.mark.skipif(
+    _check_ants() is False, reason="requires ANTs to be in PATH"
+)
+def test_get_parcellation_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=[
+                "Schaefer100x7",
+                "TianxS1x3TxMNInonlinear2009cAsym",
+            ],
+            target_data=element_data["VBM_GM"],
+        )