junifer 0.0.7.dev132__py3-none-any.whl → 0.0.7.dev169__py3-none-any.whl

junifer/_version.py

@@ -28,7 +28,7 @@ version_tuple: VERSION_TUPLE
 commit_id: COMMIT_ID
 __commit_id__: COMMIT_ID
 
-__version__ = version = '0.0.7.dev132'
-__version_tuple__ = version_tuple = (0, 0, 7, 'dev132')
+__version__ = version = '0.0.7.dev169'
+__version_tuple__ = version_tuple = (0, 0, 7, 'dev169')
 
 __commit_id__ = commit_id = None

junifer/conftest.py

@@ -1,10 +1,14 @@
 """Provide conftest for pytest."""
 
 # Authors: Federico Raimondo <f.raimondo@fz-juelich.de>
+#          Synchon Mandal <s.mandal@fz-juelich.de>
 # License: AGPL
 
+from pathlib import Path
+
 import pytest
 
+from junifer.datagrabber import PatternDataladDataGrabber
 from junifer.utils.singleton import Singleton
 
 
@@ -23,3 +27,31 @@ def reset_singletons() -> None:
     # Force deleting the singletons
     for elem in to_remove:
         del elem
+
+
+@pytest.fixture
+def maps_datagrabber(tmp_path: Path) -> PatternDataladDataGrabber:
+    """Return a PatternDataladDataGrabber for maps testing.
+
+    Parameters
+    ----------
+    tmp_path : pathlib.Path
+        The path to the test directory.
+
+    """
+    dg = 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"],
+    )
+    return dg

junifer/data/__init__.pyi

@@ -3,6 +3,7 @@ __all__ = [
     "CoordinatesRegistry",
     "DataDispatcher",
     "ParcellationRegistry",
+    "MapsRegistry",
     "MaskRegistry",
     "get_data",
     "list_data",
@@ -17,6 +18,7 @@ __all__ = [
 from .pipeline_data_registry_base import BasePipelineDataRegistry
 from .coordinates import CoordinatesRegistry
 from .parcellations import ParcellationRegistry
+from .maps import MapsRegistry
 from .masks import MaskRegistry
 
 from ._dispatch import (

junifer/data/_dispatch.py

@@ -17,6 +17,7 @@ from numpy.typing import ArrayLike
 
 from ..utils import raise_error
 from .coordinates import CoordinatesRegistry
+from .maps import MapsRegistry
 from .masks import MaskRegistry
 from .parcellations import ParcellationRegistry
 from .pipeline_data_registry_base import BasePipelineDataRegistry
@@ -52,6 +53,7 @@ class DataDispatcher(MutableMapping):
                 {
                     "coordinates": CoordinatesRegistry,
                     "parcellation": ParcellationRegistry,
+                    "maps": MapsRegistry,
                     "mask": MaskRegistry,
                 }
             )
@@ -118,14 +120,14 @@ def get_data(
     extra_input: Optional[dict[str, Any]] = None,
 ) -> Union[
     tuple[ArrayLike, list[str]],  # coordinates
-    tuple["Nifti1Image", list[str]],  # parcellation
+    tuple["Nifti1Image", list[str]],  # parcellation / maps
     "Nifti1Image",  # mask
 ]:
     """Get tailored ``kind`` for ``target_data``.
 
     Parameters
     ----------
-    kind : {"coordinates", "parcellation", "mask"}
+    kind : {"coordinates", "parcellation", "mask", "maps"}
         Kind of data to fetch and apply.
     names : str or dict or list of str / dict
         The registered name(s) of the data.
@@ -166,7 +168,7 @@ def list_data(kind: str) -> list[str]:
 
     Parameters
     ----------
-    kind : {"coordinates", "parcellation", "mask"}
+    kind : {"coordinates", "parcellation", "mask", "maps"}
         Kind of data registry to list.
 
     Returns
@@ -195,7 +197,9 @@ def load_data(
     **kwargs,
 ) -> Union[
     tuple[ArrayLike, list[str], str],  # coordinates
-    tuple[Optional["Nifti1Image"], list[str], Path, str],  # parcellation
+    tuple[
+        Optional["Nifti1Image"], list[str], Path, str
+    ],  # parcellation / maps
     tuple[
         Optional[Union["Nifti1Image", Callable]], Optional[Path], str
     ],  # mask
@@ -204,7 +208,7 @@ def load_data(
 
     Parameters
     ----------
-    kind : {"coordinates", "parcellation", "mask"}
+    kind : {"coordinates", "parcellation", "mask", "maps"}
         Kind of data to load.
     name : str
         The registered name of the data.
@@ -244,7 +248,7 @@ def register_data(
 
     Parameters
     ----------
-    kind : {"coordinates", "parcellation", "mask"}
+    kind : {"coordinates", "parcellation", "mask", "maps"}
         Kind of data to register.
     name : str
         The name to register.
@@ -277,7 +281,7 @@ def deregister_data(kind: str, name: str) -> None:
 
     Parameters
     ----------
-    kind : {"coordinates", "parcellation", "mask"}
+    kind : {"coordinates", "parcellation", "mask", "maps"}
         Kind of data to register.
     name : str
         The name to de-register.

junifer/data/maps/__init__.py

@@ -0,0 +1,9 @@
+"""Maps."""
+
+# Authors: Synchon Mandal <s.mandal@fz-juelich.de>
+# License: AGPL
+
+import lazy_loader as lazy
+
+
+__getattr__, __dir__, __all__ = lazy.attach_stub(__name__, __file__)

junifer/data/maps/__init__.pyi

@@ -0,0 +1,5 @@
+__all__ = [
+    "MapsRegistry",
+]
+
+from ._maps import MapsRegistry

junifer/data/maps/_ants_maps_warper.py

@@ -0,0 +1,156 @@
+"""Provide class for maps space warping via ANTs."""
+
+# Authors: Synchon Mandal <s.mandal@fz-juelich.de>
+# License: AGPL
+
+import uuid
+from typing import TYPE_CHECKING, Any, Optional
+
+import nibabel as nib
+
+from ...pipeline import WorkDirManager
+from ...utils import logger, raise_error, run_ext_cmd
+from ..template_spaces import get_template, get_xfm
+
+
+if TYPE_CHECKING:
+    from nibabel.nifti1 import Nifti1Image
+
+
+__all__ = ["ANTsMapsWarper"]
+
+
+class ANTsMapsWarper:
+    """Class for maps space warping via ANTs.
+
+    This class uses ANTs ``antsApplyTransforms`` for transformation.
+
+    """
+
+    def warp(
+        self,
+        maps_name: str,
+        maps_img: "Nifti1Image",
+        src: str,
+        dst: str,
+        target_data: dict[str, Any],
+        warp_data: Optional[dict[str, Any]],
+    ) -> "Nifti1Image":
+        """Warp ``maps_img`` to correct space.
+
+        Parameters
+        ----------
+        maps_name : str
+            The name of the maps.
+        maps_img : nibabel.nifti1.Nifti1Image
+            The maps image to transform.
+        src : str
+            The data type or template space to warp from.
+            It should be empty string if ``dst="T1w"``.
+        dst : str
+            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"``
+            key is added if the :class:`.SpaceWarper` is used or if the
+            data is provided in native space.
+        target_data : dict
+            The corresponding item of the data object to which the maps
+            will be applied.
+        warp_data : dict or None
+            The warp data item of the data object. The value is unused if
+            ``dst!="T1w"``.
+
+        Returns
+        -------
+        nibabel.nifti1.Nifti1Image
+            The transformed maps image.
+
+        Raises
+        ------
+        ValueError
+            If ``warp_data`` is None when ``dst="T1w"``.
+
+        """
+        # Create element-scoped tempdir so that warped maps is
+        # available later as nibabel stores file path reference for
+        # loading on computation
+        prefix = (
+            f"ants_maps_warper_{maps_name}"
+            f"{'' if not src else f'_from_{src}'}_to_{dst}_"
+            f"{uuid.uuid1()}"
+        )
+        element_tempdir = WorkDirManager().get_element_tempdir(
+            prefix=prefix,
+        )
+
+        # Native space warping
+        if dst == "native":  # pragma: no cover
+            # Warp data check
+            if warp_data is None:
+                raise_error("No `warp_data` provided")
+            if "reference" not in target_data:
+                raise_error("No `reference` provided")
+            if "path" not in target_data["reference"]:
+                raise_error("No `path` provided in `reference`")
+
+            logger.debug("Using ANTs for maps transformation")
+
+            # Save existing maps image to a tempfile
+            prewarp_maps_path = element_tempdir / "prewarp_maps.nii.gz"
+            nib.save(maps_img, prewarp_maps_path)
+
+            # Create a tempfile for warped output
+            warped_maps_path = element_tempdir / "maps_warped.nii.gz"
+            # Set antsApplyTransforms command
+            apply_transforms_cmd = [
+                "antsApplyTransforms",
+                "-d 3",
+                "-e 3",
+                "-n LanczosWindowedSinc",
+                f"-i {prewarp_maps_path.resolve()}",
+                # use resampled reference
+                f"-r {target_data['reference']['path'].resolve()}",
+                f"-t {warp_data['path'].resolve()}",
+                f"-o {warped_maps_path.resolve()}",
+            ]
+            # Call antsApplyTransforms
+            run_ext_cmd(name="antsApplyTransforms", cmd=apply_transforms_cmd)
+
+        # Template space warping
+        else:
+            logger.debug(f"Using ANTs to warp maps from {src} to {dst}")
+
+            # Get xfm file
+            xfm_file_path = get_xfm(src=src, dst=dst)
+            # Get template space image
+            template_space_img = get_template(
+                space=dst,
+                target_img=maps_img,
+                extra_input=None,
+            )
+            # Save template to a tempfile
+            template_space_img_path = element_tempdir / f"{dst}_T1w.nii.gz"
+            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"
+            nib.save(maps_img, prewarp_maps_path)
+
+            # Create a tempfile for warped output
+            warped_maps_path = element_tempdir / "maps_warped.nii.gz"
+            # Set antsApplyTransforms command
+            apply_transforms_cmd = [
+                "antsApplyTransforms",
+                "-d 3",
+                "-e 3",
+                "-n LanczosWindowedSinc",
+                f"-i {prewarp_maps_path.resolve()}",
+                f"-r {template_space_img_path.resolve()}",
+                f"-t {xfm_file_path.resolve()}",
+                f"-o {warped_maps_path.resolve()}",
+            ]
+            # Call antsApplyTransforms
+            run_ext_cmd(name="antsApplyTransforms", cmd=apply_transforms_cmd)
+
+        # Load nifti
+        return nib.load(warped_maps_path)

junifer/data/maps/_fsl_maps_warper.py

@@ -0,0 +1,85 @@
+"""Provide class for maps space warping via FSL FLIRT."""
+
+# Authors: Synchon Mandal <s.mandal@fz-juelich.de>
+# License: AGPL
+
+import uuid
+from typing import TYPE_CHECKING, Any
+
+import nibabel as nib
+
+from ...pipeline import WorkDirManager
+from ...utils import logger, run_ext_cmd
+
+
+if TYPE_CHECKING:
+    from nibabel.nifti1 import Nifti1Image
+
+
+__all__ = ["FSLMapsWarper"]
+
+
+class FSLMapsWarper:
+    """Class for maps space warping via FSL FLIRT.
+
+    This class uses FSL FLIRT's ``applywarp`` for transformation.
+
+    """
+
+    def warp(
+        self,
+        maps_name: str,
+        maps_img: "Nifti1Image",
+        target_data: dict[str, Any],
+        warp_data: dict[str, Any],
+    ) -> "Nifti1Image":  # pragma: no cover
+        """Warp ``maps_img`` to correct space.
+
+        Parameters
+        ----------
+        maps_name : str
+            The name of the maps.
+        maps_img : nibabel.nifti1.Nifti1Image
+            The maps image to transform.
+        target_data : dict
+            The corresponding item of the data object to which the maps
+            will be applied.
+        warp_data : dict
+            The warp data item of the data object.
+
+        Returns
+        -------
+        nibabel.nifti1.Nifti1Image
+            The transformed maps image.
+
+        """
+        logger.debug("Using FSL for maps transformation")
+
+        # Create element-scoped tempdir so that warped maps is
+        # available later as nibabel stores file path reference for
+        # loading on computation
+        element_tempdir = WorkDirManager().get_element_tempdir(
+            prefix=f"fsl_maps_warper_{maps_name}_{uuid.uuid1()}"
+        )
+
+        # Save existing maps image to a tempfile
+        prewarp_maps_path = element_tempdir / "prewarp_maps.nii.gz"
+        nib.save(maps_img, prewarp_maps_path)
+
+        # Create a tempfile for warped output
+        warped_maps_path = element_tempdir / "maps_warped.nii.gz"
+        # Set applywarp command
+        applywarp_cmd = [
+            "applywarp",
+            "--interp=spline",
+            f"-i {prewarp_maps_path.resolve()}",
+            # use resampled reference
+            f"-r {target_data['reference']['path'].resolve()}",
+            f"-w {warp_data['path'].resolve()}",
+            f"-o {warped_maps_path.resolve()}",
+        ]
+        # Call applywarp
+        run_ext_cmd(name="applywarp", cmd=applywarp_cmd)
+
+        # Load nifti
+        return nib.load(warped_maps_path)