junifer 0.0.6.dev154__py3-none-any.whl → 0.0.6.dev194__py3-none-any.whl

junifer/data/masks/__init__.py

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+"""Masks."""
+
+# 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/masks/__init__.pyi

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+__all__ = [
+    "MaskRegistry",
+    "compute_brain_mask",
+]
+
+from ._masks import MaskRegistry, compute_brain_mask

junifer/data/masks/_ants_mask_warper.py

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+"""Provide class for mask space warping via ANTs."""
+
+# Authors: Synchon Mandal <s.mandal@fz-juelich.de>
+# License: AGPL
+
+import uuid
+from typing import TYPE_CHECKING, Any, Dict, Optional
+
+import nibabel as nib
+
+from ...pipeline import WorkDirManager
+from ...utils import logger, run_ext_cmd
+from ..template_spaces import get_template, get_xfm
+
+
+if TYPE_CHECKING:
+    from nibabel.nifti1 import Nifti1Image
+
+
+__all__ = ["ANTsMaskWarper"]
+
+
+class ANTsMaskWarper:
+    """Class for mask space warping via ANTs.
+
+    This class uses ANTs ``antsApplyTransforms`` for transformation.
+
+    """
+
+    def warp(
+        self,
+        mask_name: str,
+        mask_img: "Nifti1Image",
+        src: str,
+        dst: str,
+        target_data: Dict[str, Any],
+        extra_input: Optional[Dict[str, Any]] = None,
+    ) -> "Nifti1Image":
+        """Warp ``mask_img`` to correct space.
+
+        Parameters
+        ----------
+        mask_name : str
+            The name of the mask.
+        mask_img : nibabel.nifti1.Nifti1Image
+            The mask 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_path``. The ``"reference_path"``
+            key is added when :class:`.SpaceWarper` is used.
+        target_data : dict
+            The corresponding item of the data object to which the mask
+            will be applied.
+        extra_input : dict, optional
+            The other fields in the data object. Useful for accessing other
+            data kinds that needs to be used in the computation of mask
+            (default None).
+
+
+        Returns
+        -------
+        nibabel.nifti1.Nifti1Image
+            The transformed mask image.
+
+        """
+        # Create element-scoped tempdir so that warped mask is
+        # available later as nibabel stores file path reference for
+        # loading on computation
+        prefix = (
+            f"ants_mask_warper_{mask_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 == "T1w":
+            logger.debug("Using ANTs for mask transformation")
+
+            # Save existing mask image to a tempfile
+            prewarp_mask_path = element_tempdir / "prewarp_mask.nii.gz"
+            nib.save(mask_img, prewarp_mask_path)
+
+            # Create a tempfile for warped output
+            warped_mask_path = element_tempdir / "mask_warped.nii.gz"
+            # Set antsApplyTransforms command
+            apply_transforms_cmd = [
+                "antsApplyTransforms",
+                "-d 3",
+                "-e 3",
+                "-n 'GenericLabel[NearestNeighbor]'",
+                f"-i {prewarp_mask_path.resolve()}",
+                # use resampled reference
+                f"-r {target_data['reference_path'].resolve()}",
+                f"-t {extra_input['Warp']['path'].resolve()}",
+                f"-o {warped_mask_path.resolve()}",
+            ]
+            # Call antsApplyTransforms
+            run_ext_cmd(name="antsApplyTransforms", cmd=apply_transforms_cmd)
+
+        # Template space warping
+        else:
+            logger.debug(f"Using ANTs to warp mask 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_data=target_data,
+                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 mask image to a tempfile
+            prewarp_mask_path = element_tempdir / "prewarp_mask.nii.gz"
+            nib.save(mask_img, prewarp_mask_path)
+
+            # Create a tempfile for warped output
+            warped_mask_path = element_tempdir / "mask_warped.nii.gz"
+            # Set antsApplyTransforms command
+            apply_transforms_cmd = [
+                "antsApplyTransforms",
+                "-d 3",
+                "-e 3",
+                "-n 'GenericLabel[NearestNeighbor]'",
+                f"-i {prewarp_mask_path.resolve()}",
+                f"-r {template_space_img_path.resolve()}",
+                f"-t {xfm_file_path.resolve()}",
+                f"-o {warped_mask_path.resolve()}",
+            ]
+            # Call antsApplyTransforms
+            run_ext_cmd(name="antsApplyTransforms", cmd=apply_transforms_cmd)
+
+        # Load nifti
+        return nib.load(warped_mask_path)

junifer/data/masks/_fsl_mask_warper.py

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+"""Provide class for mask space warping via FSL FLIRT."""
+
+# Authors: Synchon Mandal <s.mandal@fz-juelich.de>
+# License: AGPL
+
+import uuid
+from typing import TYPE_CHECKING, Any, Dict
+
+import nibabel as nib
+
+from ...pipeline import WorkDirManager
+from ...utils import logger, run_ext_cmd
+
+
+if TYPE_CHECKING:
+    from nibabel.nifti1 import Nifti1Image
+
+
+__all__ = ["FSLMaskWarper"]
+
+
+class FSLMaskWarper:
+    """Class for mask space warping via FSL FLIRT.
+
+    This class uses FSL FLIRT's ``applywarp`` for transformation.
+
+    """
+
+    def warp(
+        self,
+        mask_name: str,
+        mask_img: "Nifti1Image",
+        target_data: Dict[str, Any],
+        extra_input: Dict[str, Any],
+    ) -> "Nifti1Image":
+        """Warp ``mask_img`` to correct space.
+
+        Parameters
+        ----------
+        mask_name : str
+            The name of the mask.
+        mask_img : nibabel.nifti1.Nifti1Image
+            The mask image to transform.
+        target_data : dict
+            The corresponding item of the data object to which the mask
+            will be applied.
+        extra_input : dict, optional
+            The other fields in the data object. Useful for accessing other
+            data kinds that needs to be used in the computation of mask
+            (default None).
+
+        Returns
+        -------
+        nibabel.nifti1.Nifti1Image
+            The transformed mask image.
+
+        """
+        logger.debug("Using FSL for mask transformation")
+
+        # Create element-scoped tempdir so that warped mask is
+        # available later as nibabel stores file path reference for
+        # loading on computation
+        element_tempdir = WorkDirManager().get_element_tempdir(
+            prefix=f"fsl_mask_warper_{mask_name}_{uuid.uuid1()}"
+        )
+
+        # Save existing mask image to a tempfile
+        prewarp_mask_path = element_tempdir / "prewarp_mask.nii.gz"
+        nib.save(mask_img, prewarp_mask_path)
+
+        # Create a tempfile for warped output
+        warped_mask_path = element_tempdir / "mask_warped.nii.gz"
+        # Set applywarp command
+        applywarp_cmd = [
+            "applywarp",
+            "--interp=nn",
+            f"-i {prewarp_mask_path.resolve()}",
+            # use resampled reference
+            f"-r {target_data['reference_path'].resolve()}",
+            f"-w {extra_input['Warp']['path'].resolve()}",
+            f"-o {warped_mask_path.resolve()}",
+        ]
+        # Call applywarp
+        run_ext_cmd(name="applywarp", cmd=applywarp_cmd)
+
+        # Load nifti
+        return nib.load(warped_mask_path)