junifer 0.0.7.dev332__py3-none-any.whl → 0.0.8__py3-none-any.whl

junifer/data/coordinates/tests/test_coordinates_names.py

@@ -0,0 +1,37 @@
+"""Provide tests for coordinates VOI names sanitizing."""
+
+# Authors: Federico Raimondo <f.raimondo@fz-juelich.de>
+# License: AGPL
+
+import pytest
+
+from junifer.data.coordinates._coordinates import _sanitize_names
+
+
+@pytest.mark.parametrize(
+    "names, expected",
+    [
+        (["a", "b", "c"], ["a", "b", "c"]),
+        (["inf cerebellum", "vmPFC"], ["inf_cerebellum", "vmPFC"]),
+        (["a", "b", "a", "c", "a"], ["a-1", "b", "a-2", "c", "a-3"]),
+        (
+            ["mid insula", "mid insula", "x"],
+            ["mid_insula-1", "mid_insula-2", "x"],
+        ),
+        ([1, 2, 3], [1, 2, 3]),
+        (["a", "a", "a-1"], ["a-2", "a-3", "a-1"]),
+        (["a-1", "a", "a"], ["a-1", "a-2", "a-3"]),
+    ],
+)
+def test_sanitize_names(names: list, expected: list) -> None:
+    """Test _sanitize_names.
+
+    Parameters
+    ----------
+    names : list
+        The parametrized VOI names.
+    expected : list
+        The parametrized expected sanitized names.
+
+    """
+    assert _sanitize_names(names) == expected

junifer/data/maps/_ants_maps_warper.py

@@ -4,12 +4,13 @@
 # License: AGPL
 
 import uuid
-from typing import TYPE_CHECKING, Any, Optional
+from typing import TYPE_CHECKING, Any
 
 import nibabel as nib
 
 from ...pipeline import WorkDirManager
-from ...utils import logger, raise_error, run_ext_cmd
+from ...typing import SpaceLike
+from ...utils import raise_error, run_ext_cmd
 from ..template_spaces import get_template, get_xfm
 
 
@@ -31,10 +32,10 @@ class ANTsMapsWarper:
         self,
         maps_name: str,
         maps_img: "Nifti1Image",
-        src: str,
-        dst: str,
+        src: SpaceLike,
+        dst: SpaceLike,
         target_data: dict[str, Any],
-        warp_data: Optional[dict[str, Any]],
+        warp_data: dict[str, Any] | None,
     ) -> "Nifti1Image":
         """Warp ``maps_img`` to correct space.
 
@@ -44,10 +45,10 @@ class ANTsMapsWarper:
             The name of the maps.
         maps_img : nibabel.nifti1.Nifti1Image
             The maps image to transform.
-        src : str
+        src : str or Enum
             The data type or template space to warp from.
             It should be empty string if ``dst="T1w"``.
-        dst : str
+        dst : str or Enum
             The data type or template space to warp to.
             `"T1w"` is the only allowed data type and it uses the resampled T1w
             found in ``target_data.reference``. The ``"reference"``
@@ -71,6 +72,9 @@ class ANTsMapsWarper:
             If ``warp_data`` is None when ``dst="T1w"``.
 
         """
+        # Imported here to avoid circular import
+        from ._maps import logger
+
         # Create element-scoped tempdir so that warped maps is
         # available later as nibabel stores file path reference for
         # loading on computation
@@ -96,16 +100,17 @@ class ANTsMapsWarper:
             logger.debug("Using ANTs for maps transformation")
 
             # Save existing maps image to a tempfile
-            prewarp_maps_path = element_tempdir / "prewarp_maps.nii.gz"
+            prewarp_maps_path = element_tempdir / "prewarp_maps.nii"
             nib.save(maps_img, prewarp_maps_path)
 
             # Create a tempfile for warped output
-            warped_maps_path = element_tempdir / "maps_warped.nii.gz"
+            warped_maps_path = element_tempdir / "maps_warped.nii"
             # Set antsApplyTransforms command
             apply_transforms_cmd = [
                 "antsApplyTransforms",
                 "-d 3",
                 "-e 3",
+                "--float 1",
                 "-n LanczosWindowedSinc",
                 f"-i {prewarp_maps_path.resolve()}",
                 # use resampled reference
@@ -129,20 +134,21 @@ class ANTsMapsWarper:
                 extra_input=None,
             )
             # Save template to a tempfile
-            template_space_img_path = element_tempdir / f"{dst}_T1w.nii.gz"
+            template_space_img_path = element_tempdir / f"{dst}_T1w.nii"
             nib.save(template_space_img, template_space_img_path)
 
             # Save existing maps image to a tempfile
-            prewarp_maps_path = element_tempdir / "prewarp_maps.nii.gz"
+            prewarp_maps_path = element_tempdir / "prewarp_maps.nii"
             nib.save(maps_img, prewarp_maps_path)
 
             # Create a tempfile for warped output
-            warped_maps_path = element_tempdir / "maps_warped.nii.gz"
+            warped_maps_path = element_tempdir / "maps_warped.nii"
             # Set antsApplyTransforms command
             apply_transforms_cmd = [
                 "antsApplyTransforms",
                 "-d 3",
                 "-e 3",
+                "--float 1",
                 "-n LanczosWindowedSinc",
                 f"-i {prewarp_maps_path.resolve()}",
                 f"-r {template_space_img_path.resolve()}",

junifer/data/maps/_fsl_maps_warper.py

@@ -9,7 +9,7 @@ from typing import TYPE_CHECKING, Any
 import nibabel as nib
 
 from ...pipeline import WorkDirManager
-from ...utils import logger, run_ext_cmd
+from ...utils import run_ext_cmd
 
 
 if TYPE_CHECKING:
@@ -53,6 +53,9 @@ class FSLMapsWarper:
             The transformed maps image.
 
         """
+        # Imported here to avoid circular import
+        from ._maps import logger
+
         logger.debug("Using FSL for maps transformation")
 
         # Create element-scoped tempdir so that warped maps is
@@ -63,13 +66,14 @@ class FSLMapsWarper:
         )
 
         # Save existing maps image to a tempfile
-        prewarp_maps_path = element_tempdir / "prewarp_maps.nii.gz"
+        prewarp_maps_path = element_tempdir / "prewarp_maps.nii"
         nib.save(maps_img, prewarp_maps_path)
 
         # Create a tempfile for warped output
-        warped_maps_path = element_tempdir / "maps_warped.nii.gz"
+        warped_maps_path = element_tempdir / "maps_warped.nii"
         # Set applywarp command
         applywarp_cmd = [
+            "FSLOUTPUTTYPE=NIFTI",
             "applywarp",
             "--interp=spline",
             f"-i {prewarp_maps_path.resolve()}",

junifer/data/maps/_maps.py

@@ -4,14 +4,15 @@
 # License: AGPL
 
 from pathlib import Path
-from typing import TYPE_CHECKING, Any, Optional, Union
+from typing import TYPE_CHECKING, Any, Optional
 
 import nibabel as nib
 import nilearn.image as nimg
 import numpy as np
+import structlog
 from junifer_data import get
 
-from ...utils import logger, raise_error
+from ...utils import raise_error
 from ..pipeline_data_registry_base import BasePipelineDataRegistry
 from ..utils import (
     JUNIFER_DATA_PARAMS,
@@ -29,6 +30,9 @@ if TYPE_CHECKING:
 
 __all__ = ["MapsRegistry"]
 
+_log = structlog.get_logger("junifer")
+logger = _log.bind(pkg="data")
+
 
 class MapsRegistry(BasePipelineDataRegistry):
     """Class for maps data registry.
@@ -74,7 +78,7 @@ class MapsRegistry(BasePipelineDataRegistry):
     def register(
         self,
         name: str,
-        maps_path: Union[str, Path],
+        maps_path: str | Path,
         maps_labels: list[str],
         space: str,
         overwrite: bool = False,
@@ -156,7 +160,7 @@ class MapsRegistry(BasePipelineDataRegistry):
         self,
         name: str,
         target_space: str,
-        resolution: Optional[float] = None,
+        resolution: float | None = None,
         path_only: bool = False,
     ) -> tuple[Optional["Nifti1Image"], list[str], Path, str]:
         """Load map(s) and labels.
@@ -251,7 +255,7 @@ class MapsRegistry(BasePipelineDataRegistry):
         self,
         maps: str,
         target_data: dict[str, Any],
-        extra_input: Optional[dict[str, Any]] = None,
+        extra_input: dict[str, Any] | None = None,
     ) -> tuple["Nifti1Image", list[str]]:
         """Get map(s), tailored for the target image.
 
@@ -376,9 +380,9 @@ class MapsRegistry(BasePipelineDataRegistry):
 
 
 def _retrieve_smith(
-    resolution: Optional[float] = None,
-    components: Optional[str] = None,
-    dimension: Optional[int] = None,
+    resolution: float | None = None,
+    components: str | None = None,
+    dimension: int | None = None,
 ) -> tuple[Path, list[str]]:
     """Retrieve Smith maps.
 

junifer/data/maps/tests/test_maps.py

@@ -4,7 +4,7 @@
 # License: AGPL
 
 import pytest
-from numpy.testing import assert_array_equal
+from numpy.testing import assert_array_almost_equal, assert_array_equal
 
 from junifer.data import (
     deregister_data,
@@ -14,10 +14,15 @@ from junifer.data import (
     register_data,
 )
 from junifer.data.maps._maps import _retrieve_smith
-from junifer.datagrabber import PatternDataladDataGrabber
 from junifer.datareader import DefaultDataReader
 from junifer.pipeline.utils import _check_ants
-from junifer.testing.datagrabbers import PartlyCloudyTestingDataGrabber
+from junifer.testing.datagrabbers import (
+    ADHDTestingDataGrabber,
+    PartlyCloudyTestingDataGrabber,
+)
+
+
+pytestmark = pytest.mark.external
 
 
 def test_register_built_in_check() -> None:
@@ -116,22 +121,8 @@ def test_load_nonexisting() -> None:
 
 def test_get() -> None:
     """Test tailored maps fetch."""
-    with PatternDataladDataGrabber(
-        uri="https://github.com/OpenNeuroDatasets/ds005226.git",
-        types=["BOLD"],
-        patterns={
-            "BOLD": {
-                "pattern": (
-                    "derivatives/pre-processed_data/space-MNI/{subject}/"
-                    "{subject-padded}_task-{task}_run-{run}_space-MNI152NLin6Asym"
-                    "_res-2_desc-preproc_bold.nii.gz"
-                ),
-                "space": "MNI152NLin6Asym",
-            },
-        },
-        replacements=["subject", "subject-padded", "task", "run"],
-    ) as dg:
-        element = dg[("sub-01", "sub-001", "rest", "1")]
+    with ADHDTestingDataGrabber() as dg:
+        element = dg["sub-01"]
         element_data = DefaultDataReader().fit_transform(element)
         bold = element_data["BOLD"]
         bold_img = bold["data"]
@@ -147,8 +138,9 @@ def test_get() -> None:
         raw_maps, raw_labels, _, _ = load_data(
             kind="maps", name="Smith_rsn_10", target_space="MNI152NLin6Asym"
         )
-        # Tailored and raw shape should be same
-        assert tailored_maps.shape[:3] == raw_maps.shape[:3]
+        # Tailored maps are on the BOLD grid and keep all the raw maps
+        assert_array_almost_equal(tailored_maps.affine, bold_img.affine)
+        assert tailored_maps.shape[3] == raw_maps.shape[3]
         assert tailored_labels == raw_labels
 
 

junifer/data/masks/_ants_mask_warper.py

@@ -4,13 +4,14 @@
 # License: AGPL
 
 import uuid
-from typing import TYPE_CHECKING, Any, Optional
+from typing import TYPE_CHECKING, Any
 
 import nibabel as nib
 import numpy as np
 
 from ...pipeline import WorkDirManager
-from ...utils import logger, raise_error, run_ext_cmd
+from ...typing import SpaceLike
+from ...utils import raise_error, run_ext_cmd
 from ..template_spaces import get_template, get_xfm
 
 
@@ -52,10 +53,10 @@ class ANTsMaskWarper:
         self,
         mask_name: str,
         mask_img: "Nifti1Image",
-        src: str,
-        dst: str,
+        src: SpaceLike,
+        dst: SpaceLike,
         target_data: dict[str, Any],
-        warp_data: Optional[dict[str, Any]],
+        warp_data: dict[str, Any] | None,
     ) -> "Nifti1Image":  # pragma: no cover
         """Warp ``mask_img`` to correct space.
 
@@ -65,10 +66,10 @@ class ANTsMaskWarper:
             The name of the mask.
         mask_img : nibabel.nifti1.Nifti1Image
             The mask image to transform.
-        src : str
+        src : str or Enum
             The data type or template space to warp from.
             It should be empty string if ``dst="native"``.
-        dst : str
+        dst : str or Enum
             The data type or template space to warp to.
             `"native"` is the only allowed data type and it uses the resampled
             T1w found in ``target_data.reference``. The
@@ -92,6 +93,9 @@ class ANTsMaskWarper:
             If ``warp_data`` is None when ``dst="T1w"``.
 
         """
+        # Imported here to avoid circular import
+        from ._masks import logger
+
         # Create element-scoped tempdir so that warped mask is
         # available later as nibabel stores file path reference for
         # loading on computation
@@ -117,16 +121,17 @@ class ANTsMaskWarper:
             logger.debug("Using ANTs for mask transformation")
 
             # Save existing mask image to a tempfile
-            prewarp_mask_path = element_tempdir / "prewarp_mask.nii.gz"
+            prewarp_mask_path = element_tempdir / "prewarp_mask.nii"
             nib.save(mask_img, prewarp_mask_path)
 
             # Create a tempfile for warped output
-            warped_mask_path = element_tempdir / "mask_warped.nii.gz"
+            warped_mask_path = element_tempdir / "mask_warped.nii"
             # Set antsApplyTransforms command
             apply_transforms_cmd = [
                 "antsApplyTransforms",
                 "-d 3",
                 "-e 3",
+                "--float 1",
                 "-n 'GenericLabel[NearestNeighbor]'",
                 f"-i {prewarp_mask_path.resolve()}",
                 # use resampled reference
@@ -150,20 +155,21 @@ class ANTsMaskWarper:
                 extra_input=None,
             )
             # Save template to a tempfile
-            template_space_img_path = element_tempdir / f"{dst}_T1w.nii.gz"
+            template_space_img_path = element_tempdir / f"{dst}_T1w.nii"
             nib.save(template_space_img, template_space_img_path)
 
             # Save existing mask image to a tempfile
-            prewarp_mask_path = element_tempdir / "prewarp_mask.nii.gz"
+            prewarp_mask_path = element_tempdir / "prewarp_mask.nii"
             nib.save(mask_img, prewarp_mask_path)
 
             # Create a tempfile for warped output
-            warped_mask_path = element_tempdir / "mask_warped.nii.gz"
+            warped_mask_path = element_tempdir / "mask_warped.nii"
             # Set antsApplyTransforms command
             apply_transforms_cmd = [
                 "antsApplyTransforms",
                 "-d 3",
                 "-e 3",
+                "--float 1",
                 f"-n {_get_interpolation_method(mask_img)}",
                 f"-i {prewarp_mask_path.resolve()}",
                 f"-r {template_space_img_path.resolve()}",

junifer/data/masks/_fsl_mask_warper.py

@@ -10,7 +10,7 @@ import nibabel as nib
 import numpy as np
 
 from ...pipeline import WorkDirManager
-from ...utils import logger, run_ext_cmd
+from ...utils import run_ext_cmd
 
 
 if TYPE_CHECKING:
@@ -74,6 +74,9 @@ class FSLMaskWarper:
             The transformed mask image.
 
         """
+        # Imported here to avoid circular import
+        from ._masks import logger
+
         logger.debug("Using FSL for mask transformation")
 
         # Create element-scoped tempdir so that warped mask is
@@ -84,13 +87,14 @@ class FSLMaskWarper:
         )
 
         # Save existing mask image to a tempfile
-        prewarp_mask_path = element_tempdir / "prewarp_mask.nii.gz"
+        prewarp_mask_path = element_tempdir / "prewarp_mask.nii"
         nib.save(mask_img, prewarp_mask_path)
 
         # Create a tempfile for warped output
-        warped_mask_path = element_tempdir / "mask_warped.nii.gz"
+        warped_mask_path = element_tempdir / "mask_warped.nii"
         # Set applywarp command
         applywarp_cmd = [
+            "FSLOUTPUTTYPE=NIFTI",
             "applywarp",
             f"--interp={_get_interpolation_method(mask_img)}",
             f"-i {prewarp_mask_path.resolve()}",

junifer/data/masks/_masks.py

@@ -4,18 +4,18 @@
 #          Synchon Mandal <s.mandal@fz-juelich.de>
 # License: AGPL
 
+from collections.abc import Callable
 from pathlib import Path
 from typing import (
     TYPE_CHECKING,
     Any,
-    Callable,
-    Optional,
     Union,
 )
 
 import nibabel as nib
 import nilearn.image as nimg
 import numpy as np
+import structlog
 from junifer_data import get
 from nilearn.masking import (
     compute_background_mask,
@@ -23,7 +23,7 @@ from nilearn.masking import (
     intersect_masks,
 )
 
-from ...utils import logger, raise_error
+from ...utils import raise_error
 from ..pipeline_data_registry_base import BasePipelineDataRegistry
 from ..template_spaces import get_template
 from ..utils import (
@@ -42,15 +42,18 @@ if TYPE_CHECKING:
 
 __all__ = ["MaskRegistry", "compute_brain_mask"]
 
+_log = structlog.get_logger("junifer")
+logger = _log.bind(pkg="data")
+
 
 def compute_brain_mask(
     target_data: dict[str, Any],
-    warp_data: Optional[dict[str, Any]] = None,
+    warp_data: dict[str, Any] | None = None,
     mask_type: str = "brain",
     threshold: float = 0.5,
     source: str = "template",
-    template_space: Optional[str] = None,
-    extra_input: Optional[dict[str, Any]] = None,
+    template_space: str | None = None,
+    extra_input: dict[str, Any] | None = None,
 ) -> "Nifti1Image":
     """Compute the whole-brain, grey-matter or white-matter mask.
 
@@ -281,7 +284,7 @@ class MaskRegistry(BasePipelineDataRegistry):
     def register(
         self,
         name: str,
-        mask_path: Union[str, Path],
+        mask_path: str | Path,
         space: str,
         overwrite: bool = False,
     ) -> None:
@@ -355,9 +358,9 @@ class MaskRegistry(BasePipelineDataRegistry):
     def load(
         self,
         name: str,
-        resolution: Optional[float] = None,
+        resolution: float | None = None,
         path_only: bool = False,
-    ) -> tuple[Optional[Union["Nifti1Image", Callable]], Optional[Path], str]:
+    ) -> tuple[Union["Nifti1Image", Callable] | None, Path | None, str]:
         """Load mask.
 
         Parameters
@@ -428,9 +431,9 @@ class MaskRegistry(BasePipelineDataRegistry):
 
     def get(  # noqa: C901
         self,
-        masks: Union[str, dict, list[Union[dict, str]]],
+        masks: str | dict | list[dict | str],
         target_data: dict[str, Any],
-        extra_input: Optional[dict[str, Any]] = None,
+        extra_input: dict[str, Any] | None = None,
     ) -> "Nifti1Image":
         """Get mask, tailored for the target image.
 
@@ -718,7 +721,7 @@ class MaskRegistry(BasePipelineDataRegistry):
 
 def _load_vickery_patil_mask(
     name: str,
-    resolution: Optional[float] = None,
+    resolution: float | None = None,
 ) -> Path:
     """Load Vickery-Patil mask.
 

junifer/data/masks/tests/test_masks.py

@@ -6,8 +6,8 @@
 # License: AGPL
 
 import socket
+from collections.abc import Callable
 from pathlib import Path
-from typing import Callable, Optional, Union
 
 import nibabel as nib
 import numpy as np
@@ -36,12 +36,15 @@ from junifer.data.masks._masks import (
 from junifer.datagrabber import DMCC13Benchmark
 from junifer.datareader import DefaultDataReader
 from junifer.testing.datagrabbers import (
-    OasisVBMTestingDataGrabber,
     PartlyCloudyTestingDataGrabber,
     SPMAuditoryTestingDataGrabber,
+    UCLACNPVBMTestingDataGrabber,
 )
 
 
+pytestmark = pytest.mark.external
+
+
 @pytest.mark.parametrize(
     "mask_type, threshold",
     [
@@ -98,11 +101,11 @@ def test_compute_brain_mask_for_native(mask_type: str) -> None:
 
     """
     with DMCC13Benchmark(
-        types=["BOLD"],
-        sessions=["ses-wave1bas"],
-        tasks=["Rest"],
-        phase_encodings=["AP"],
-        runs=["1"],
+        types="BOLD",
+        sessions="ses-wave1bas",
+        tasks="Rest",
+        phase_encodings="AP",
+        runs="1",
         native_t1w=True,
     ) as dg:
         element_data = DefaultDataReader().fit_transform(
@@ -177,7 +180,7 @@ def test_register_already_registered() -> None:
 )
 def test_register(
     name: str,
-    mask_path: str,
+    mask_path: str | Path,
     space: str,
     overwrite: bool,
 ) -> None:
@@ -264,7 +267,7 @@ def test_load_incorrect() -> None:
 )
 def test_vickery_patil(
     name: str,
-    resolution: Optional[float],
+    resolution: float | None,
     pixdim: list[float],
     fname: str,
 ) -> None:
@@ -319,8 +322,8 @@ def test_ukb_error() -> None:
 
 def test_get() -> None:
     """Test tailored mask fetch."""
-    with OasisVBMTestingDataGrabber() as dg:
-        element_data = DefaultDataReader().fit_transform(dg["sub-01"])
+    with UCLACNPVBMTestingDataGrabber() as dg:
+        element_data = DefaultDataReader().fit_transform(dg["sub-10206"])
         vbm_gm = element_data["VBM_GM"]
         vbm_gm_img = vbm_gm["data"]
         mask = get_data(
@@ -354,8 +357,8 @@ def test_mask_callable() -> None:
         "func": ident,
         "space": "MNI152Lin",
     }
-    with OasisVBMTestingDataGrabber() as dg:
-        element_data = DefaultDataReader().fit_transform(dg["sub-01"])
+    with UCLACNPVBMTestingDataGrabber() as dg:
+        element_data = DefaultDataReader().fit_transform(dg["sub-10206"])
         vbm_gm = element_data["VBM_GM"]
         vbm_gm_img = vbm_gm["data"]
         mask = MaskRegistry().get(masks="identity", target_data=vbm_gm)
@@ -367,8 +370,8 @@ def test_mask_callable() -> None:
 
 def test_get_errors() -> None:
     """Test passing wrong parameters to fetch mask."""
-    with OasisVBMTestingDataGrabber() as dg:
-        element_data = DefaultDataReader().fit_transform(dg["sub-01"])
+    with UCLACNPVBMTestingDataGrabber() as dg:
+        element_data = DefaultDataReader().fit_transform(dg["sub-10206"])
         vbm_gm = element_data["VBM_GM"]
         # Test wrong masks definitions (more than one key per dict)
         with pytest.raises(ValueError, match=r"only one key"):
@@ -417,7 +420,7 @@ def test_get_errors() -> None:
 def test_nilearn_compute_masks(
     mask_name: str,
     function: Callable,
-    params: Union[dict, None],
+    params: dict | None,
     resample: bool,
 ) -> None:
     """Test using nilearn compute mask functions.
@@ -502,7 +505,7 @@ def test_get_inherit() -> None:
     ],
 )
 def test_get_multiple(
-    masks: Union[str, dict, list[Union[dict, str]]], params: dict
+    masks: str | dict | list[dict | str], params: dict
 ) -> None:
     """Test getting multiple masks.