junifer 0.0.6.dev227__py3-none-any.whl → 0.0.6.dev248__py3-none-any.whl

junifer/_version.py

@@ -12,5 +12,5 @@ __version__: str
 __version_tuple__: VERSION_TUPLE
 version_tuple: VERSION_TUPLE
 
-__version__ = version = '0.0.6.dev227'
-__version_tuple__ = version_tuple = (0, 0, 6, 'dev227')
+__version__ = version = '0.0.6.dev248'
+__version_tuple__ = version_tuple = (0, 0, 6, 'dev248')

junifer/data/coordinates/_ants_coordinates_warper.py

@@ -26,7 +26,7 @@ class ANTsCoordinatesWarper:
         self,
         seeds: ArrayLike,
         target_data: Dict[str, Any],
-        extra_input: Dict[str, Any],
+        warp_data: Dict[str, Any],
     ) -> ArrayLike:
         """Warp ``seeds`` to correct space.
 
@@ -37,10 +37,8 @@ class ANTsCoordinatesWarper:
         target_data : dict
             The corresponding item of the data object to which the coordinates
             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 coordinates
-            (default None).
+        warp_data : dict or None
+            The warp data item of the data object.
 
         Returns
         -------
@@ -79,7 +77,7 @@ class ANTsCoordinatesWarper:
             "-f 0",
             f"-i {pretransform_coordinates_path.resolve()}",
             f"-o {transformed_coords_path.resolve()}",
-            f"-t {extra_input['Warp']['path'].resolve()};",
+            f"-t {warp_data['path'].resolve()}",
         ]
         # Call antsApplyTransformsToPoints
         run_ext_cmd(

junifer/data/coordinates/_coordinates.py

@@ -14,6 +14,7 @@ from numpy.typing import ArrayLike
 from ...utils import logger, raise_error
 from ...utils.singleton import Singleton
 from ..pipeline_data_registry_base import BasePipelineDataRegistry
+from ..utils import get_native_warper
 from ._ants_coordinates_warper import ANTsCoordinatesWarper
 from ._fsl_coordinates_warper import FSLCoordinatesWarper
 
@@ -311,7 +312,8 @@ class CoordinatesRegistry(BasePipelineDataRegistry, metaclass=Singleton):
         Raises
         ------
         RuntimeError
-            If warp / transformation file extension is not ".mat" or ".h5".
+            If warping specification required for warping using ANTs, is not
+            found.
         ValueError
             If ``extra_input`` is None when ``target_data``'s space is native.
 
@@ -329,27 +331,38 @@ class CoordinatesRegistry(BasePipelineDataRegistry, metaclass=Singleton):
                     f"{target_data['space']} space for further computation."
                 )
 
-            # Check for warp file type to use correct tool
-            warp_file_ext = extra_input["Warp"]["path"].suffix
-            if warp_file_ext == ".mat":
+            # Get native space warper spec
+            warper_spec = get_native_warper(
+                target_data=target_data,
+                other_data=extra_input,
+            )
+            # Conditional for warping tool implementation
+            if warper_spec["warper"] == "fsl":
                 seeds = FSLCoordinatesWarper().warp(
                     seeds=seeds,
                     target_data=target_data,
-                    extra_input=extra_input,
+                    warp_data=warper_spec,
+                )
+            elif warper_spec["warper"] == "ants":
+                # Requires the inverse warp
+                inverse_warper_spec = get_native_warper(
+                    target_data=target_data,
+                    other_data=extra_input,
+                    inverse=True,
                 )
-            elif warp_file_ext == ".h5":
+                # Check warper
+                if inverse_warper_spec["warper"] != "ants":
+                    raise_error(
+                        klass=RuntimeError,
+                        msg=(
+                            "Warping specification mismatch for native space "
+                            "warping of coordinates using ANTs."
+                        ),
+                    )
                 seeds = ANTsCoordinatesWarper().warp(
                     seeds=seeds,
                     target_data=target_data,
-                    extra_input=extra_input,
-                )
-            else:
-                raise_error(
-                    msg=(
-                        "Unknown warp / transformation file extension: "
-                        f"{warp_file_ext}"
-                    ),
-                    klass=RuntimeError,
+                    warp_data=warper_spec,
                 )
 
         return seeds, labels

junifer/data/coordinates/_fsl_coordinates_warper.py

@@ -26,7 +26,7 @@ class FSLCoordinatesWarper:
         self,
         seeds: ArrayLike,
         target_data: Dict[str, Any],
-        extra_input: Dict[str, Any],
+        warp_data: Dict[str, Any],
     ) -> ArrayLike:
         """Warp ``seeds`` to correct space.
 
@@ -37,10 +37,8 @@ class FSLCoordinatesWarper:
         target_data : dict
             The corresponding item of the data object to which the coordinates
             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 coordinates
-            (default None).
+        warp_data : dict
+            The warp data item of the data object.
 
         Returns
         -------
@@ -72,7 +70,7 @@ class FSLCoordinatesWarper:
             "| img2imgcoord -mm",
             f"-src {target_data['path'].resolve()}",
             f"-dest {target_data['reference_path'].resolve()}",
-            f"-warp {extra_input['Warp']['path'].resolve()}",
+            f"-warp {warp_data['path'].resolve()}",
             f"> {transformed_coords_path.resolve()};",
             f"sed -i 1d {transformed_coords_path.resolve()}",
         ]

junifer/data/masks/_ants_mask_warper.py

@@ -9,7 +9,7 @@ from typing import TYPE_CHECKING, Any, Dict, Optional
 import nibabel as nib
 
 from ...pipeline import WorkDirManager
-from ...utils import logger, run_ext_cmd
+from ...utils import logger, raise_error, run_ext_cmd
 from ..template_spaces import get_template, get_xfm
 
 
@@ -34,7 +34,7 @@ class ANTsMaskWarper:
         src: str,
         dst: str,
         target_data: Dict[str, Any],
-        extra_input: Optional[Dict[str, Any]] = None,
+        warp_data: Optional[Dict[str, Any]],
     ) -> "Nifti1Image":
         """Warp ``mask_img`` to correct space.
 
@@ -55,17 +55,20 @@ class ANTsMaskWarper:
         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).
-
+        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 mask image.
 
+        Raises
+        ------
+        RuntimeError
+            If ``warp_data`` is None when ``dst="T1w"``.
+
         """
         # Create element-scoped tempdir so that warped mask is
         # available later as nibabel stores file path reference for
@@ -80,7 +83,11 @@ class ANTsMaskWarper:
         )
 
         # Native space warping
-        if dst == "T1w":
+        if dst == "native":
+            # Warp data check
+            if warp_data is None:
+                raise_error("No `warp_data` provided")
+
             logger.debug("Using ANTs for mask transformation")
 
             # Save existing mask image to a tempfile
@@ -98,7 +105,7 @@ class ANTsMaskWarper:
                 f"-i {prewarp_mask_path.resolve()}",
                 # use resampled reference
                 f"-r {target_data['reference_path'].resolve()}",
-                f"-t {extra_input['Warp']['path'].resolve()}",
+                f"-t {warp_data['path'].resolve()}",
                 f"-o {warped_mask_path.resolve()}",
             ]
             # Call antsApplyTransforms

junifer/data/masks/_fsl_mask_warper.py

@@ -31,7 +31,7 @@ class FSLMaskWarper:
         mask_name: str,
         mask_img: "Nifti1Image",
         target_data: Dict[str, Any],
-        extra_input: Dict[str, Any],
+        warp_data: Dict[str, Any],
     ) -> "Nifti1Image":
         """Warp ``mask_img`` to correct space.
 
@@ -44,10 +44,8 @@ class FSLMaskWarper:
         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).
+        warp_data : dict
+            The warp data item of the data object.
 
         Returns
         -------
@@ -77,7 +75,7 @@ class FSLMaskWarper:
             f"-i {prewarp_mask_path.resolve()}",
             # use resampled reference
             f"-r {target_data['reference_path'].resolve()}",
-            f"-w {extra_input['Warp']['path'].resolve()}",
+            f"-w {warp_data['path'].resolve()}",
             f"-o {warped_mask_path.resolve()}",
         ]
         # Call applywarp

junifer/data/masks/_masks.py

@@ -29,7 +29,7 @@ from ...utils import logger, raise_error
 from ...utils.singleton import Singleton
 from ..pipeline_data_registry_base import BasePipelineDataRegistry
 from ..template_spaces import get_template
-from ..utils import closest_resolution
+from ..utils import closest_resolution, get_native_warper
 from ._ants_mask_warper import ANTsMaskWarper
 from ._fsl_mask_warper import FSLMaskWarper
 
@@ -105,14 +105,16 @@ def compute_brain_mask(
                 "data type to infer target template space."
             )
         # Set target standard space to warp file space source
-        target_std_space = extra_input["Warp"]["src"]
+        for entry in extra_input["Warp"]:
+            if entry["dst"] == "native":
+                target_std_space = entry["src"]
 
     # Fetch template in closest resolution
     template = get_template(
         space=target_std_space,
         target_data=target_data,
         extra_input=extra_input,
-        template_type=mask_type if mask_type in ["gm", "wm"] else "T1w",
+        template_type=mask_type,
     )
     # Resample template to target image
     target_img = target_data["data"]
@@ -357,8 +359,6 @@ class MaskRegistry(BasePipelineDataRegistry, metaclass=Singleton):
 
         Raises
         ------
-        RuntimeError
-            If warp / transformation file extension is not ".mat" or ".h5".
         ValueError
             If extra key is provided in addition to mask name in ``masks`` or
             if no mask is provided or
@@ -372,8 +372,6 @@ class MaskRegistry(BasePipelineDataRegistry, metaclass=Singleton):
         """
         # Check pre-requirements for space manipulation
         target_space = target_data["space"]
-        # Set target standard space to target space
-        target_std_space = target_space
         # Extra data type requirement check if target space is native
         if target_space == "native":
             # Check for extra inputs
@@ -383,8 +381,16 @@ class MaskRegistry(BasePipelineDataRegistry, metaclass=Singleton):
                     "data types in particular for transformation to "
                     f"{target_data['space']} space for further computation."
                 )
+            # Get native space warper spec
+            warper_spec = get_native_warper(
+                target_data=target_data,
+                other_data=extra_input,
+            )
             # Set target standard space to warp file space source
-            target_std_space = extra_input["Warp"]["src"]
+            target_std_space = warper_spec["src"]
+        else:
+            # Set target standard space to target space
+            target_std_space = target_space
 
         # Get the min of the voxels sizes and use it as the resolution
         target_img = target_data["data"]
@@ -489,7 +495,7 @@ class MaskRegistry(BasePipelineDataRegistry, metaclass=Singleton):
                         src=mask_space,
                         dst=target_std_space,
                         target_data=target_data,
-                        extra_input=None,
+                        warp_data=None,
                     )
 
             all_masks.append(mask_img)
@@ -510,32 +516,22 @@ class MaskRegistry(BasePipelineDataRegistry, metaclass=Singleton):
 
         # Warp mask if target data is native
         if target_space == "native":
-            # extra_input check done earlier
-            # Check for warp file type to use correct tool
-            warp_file_ext = extra_input["Warp"]["path"].suffix
-            if warp_file_ext == ".mat":
+            # extra_input check done earlier and warper_spec exists
+            if warper_spec["warper"] == "fsl":
                 mask_img = FSLMaskWarper().warp(
                     mask_name="native",
                     mask_img=mask_img,
                     target_data=target_data,
-                    extra_input=extra_input,
+                    warp_data=warper_spec,
                 )
-            elif warp_file_ext == ".h5":
+            elif warper_spec["warper"] == "ants":
                 mask_img = ANTsMaskWarper().warp(
                     mask_name="native",
                     mask_img=mask_img,
                     src="",
-                    dst="T1w",
+                    dst="native",
                     target_data=target_data,
-                    extra_input=extra_input,
-                )
-            else:
-                raise_error(
-                    msg=(
-                        "Unknown warp / transformation file extension: "
-                        f"{warp_file_ext}"
-                    ),
-                    klass=RuntimeError,
+                    warp_data=warper_spec,
                 )
 
         return mask_img

junifer/data/parcellations/_ants_parcellation_warper.py

@@ -9,7 +9,7 @@ from typing import TYPE_CHECKING, Any, Dict, Optional
 import nibabel as nib
 
 from ...pipeline import WorkDirManager
-from ...utils import logger, run_ext_cmd
+from ...utils import logger, raise_error, run_ext_cmd
 from ..template_spaces import get_template, get_xfm
 
 
@@ -34,7 +34,7 @@ class ANTsParcellationWarper:
         src: str,
         dst: str,
         target_data: Dict[str, Any],
-        extra_input: Optional[Dict[str, Any]] = None,
+        warp_data: Optional[Dict[str, Any]],
     ) -> "Nifti1Image":
         """Warp ``parcellation_img`` to correct space.
 
@@ -55,17 +55,20 @@ class ANTsParcellationWarper:
         target_data : dict
             The corresponding item of the data object to which the parcellation
             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 parcellation
-            (default None).
-
+        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 parcellation image.
 
+        Raises
+        ------
+        ValueError
+            If ``warp_data`` is None when ``dst="T1w"``.
+
         """
         # Create element-scoped tempdir so that warped parcellation is
         # available later as nibabel stores file path reference for
@@ -80,7 +83,11 @@ class ANTsParcellationWarper:
         )
 
         # Native space warping
-        if dst == "T1w":
+        if dst == "native":
+            # Warp data check
+            if warp_data is None:
+                raise_error("No `warp_data` provided")
+
             logger.debug("Using ANTs for parcellation transformation")
 
             # Save existing parcellation image to a tempfile
@@ -102,7 +109,7 @@ class ANTsParcellationWarper:
                 f"-i {prewarp_parcellation_path.resolve()}",
                 # use resampled reference
                 f"-r {target_data['reference_path'].resolve()}",
-                f"-t {extra_input['Warp']['path'].resolve()}",
+                f"-t {warp_data['path'].resolve()}",
                 f"-o {warped_parcellation_path.resolve()}",
             ]
             # Call antsApplyTransforms

junifer/data/parcellations/_fsl_parcellation_warper.py

@@ -31,7 +31,7 @@ class FSLParcellationWarper:
         parcellation_name: str,
         parcellation_img: "Nifti1Image",
         target_data: Dict[str, Any],
-        extra_input: Dict[str, Any],
+        warp_data: Dict[str, Any],
     ) -> "Nifti1Image":
         """Warp ``parcellation_img`` to correct space.
 
@@ -44,10 +44,8 @@ class FSLParcellationWarper:
         target_data : dict
             The corresponding item of the data object to which the parcellation
             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 parcellation
-            (default None).
+        warp_data : dict
+            The warp data item of the data object.
 
         Returns
         -------
@@ -81,7 +79,7 @@ class FSLParcellationWarper:
             f"-i {prewarp_parcellation_path.resolve()}",
             # use resampled reference
             f"-r {target_data['reference_path'].resolve()}",
-            f"-w {extra_input['Warp']['path'].resolve()}",
+            f"-w {warp_data['path'].resolve()}",
             f"-o {warped_parcellation_path.resolve()}",
         ]
         # Call applywarp

junifer/data/parcellations/_parcellations.py

@@ -23,7 +23,7 @@ from nilearn import datasets, image
 from ...utils import logger, raise_error, warn_with_log
 from ...utils.singleton import Singleton
 from ..pipeline_data_registry_base import BasePipelineDataRegistry
-from ..utils import closest_resolution
+from ..utils import closest_resolution, get_native_warper
 from ._ants_parcellation_warper import ANTsParcellationWarper
 from ._fsl_parcellation_warper import FSLParcellationWarper
 
@@ -394,16 +394,12 @@ class ParcellationRegistry(BasePipelineDataRegistry, metaclass=Singleton):
 
         Raises
         ------
-        RuntimeError
-            If warp / transformation file extension is not ".mat" or ".h5".
         ValueError
             If ``extra_input`` is None when ``target_data``'s space is native.
 
         """
         # Check pre-requirements for space manipulation
         target_space = target_data["space"]
-        # Set target standard space to target space
-        target_std_space = target_space
         # Extra data type requirement check if target space is native
         if target_space == "native":
             # Check for extra inputs
@@ -413,8 +409,16 @@ class ParcellationRegistry(BasePipelineDataRegistry, metaclass=Singleton):
                     "data types in particular for transformation to "
                     f"{target_data['space']} space for further computation."
                 )
+            # Get native space warper spec
+            warper_spec = get_native_warper(
+                target_data=target_data,
+                other_data=extra_input,
+            )
             # Set target standard space to warp file space source
-            target_std_space = extra_input["Warp"]["src"]
+            target_std_space = warper_spec["src"]
+        else:
+            # Set target standard space to target space
+            target_std_space = target_space
 
         # Get the min of the voxels sizes and use it as the resolution
         target_img = target_data["data"]
@@ -428,12 +432,14 @@ class ParcellationRegistry(BasePipelineDataRegistry, metaclass=Singleton):
         all_parcellations = []
         all_labels = []
         for name in parcellations:
+            # Load parcellation
             img, labels, _, space = self.load(
                 name=name,
                 resolution=resolution,
             )
 
-            # Convert parcellation spaces if required
+            # Convert parcellation spaces if required;
+            # cannot be "native" due to earlier check
             if space != target_std_space:
                 raw_img = ANTsParcellationWarper().warp(
                     parcellation_name=name,
@@ -441,7 +447,7 @@ class ParcellationRegistry(BasePipelineDataRegistry, metaclass=Singleton):
                     src=space,
                     dst=target_std_space,
                     target_data=target_data,
-                    extra_input=None,
+                    warp_data=None,
                 )
                 # Remove extra dimension added by ANTs
                 img = image.math_img("np.squeeze(img)", img=raw_img)
@@ -471,32 +477,22 @@ class ParcellationRegistry(BasePipelineDataRegistry, metaclass=Singleton):
 
         # Warp parcellation if target space is native
         if target_space == "native":
-            # extra_input check done earlier
-            # Check for warp file type to use correct tool
-            warp_file_ext = extra_input["Warp"]["path"].suffix
-            if warp_file_ext == ".mat":
+            # extra_input check done earlier and warper_spec exists
+            if warper_spec["warper"] == "fsl":
                 resampled_parcellation_img = FSLParcellationWarper().warp(
                     parcellation_name="native",
                     parcellation_img=resampled_parcellation_img,
                     target_data=target_data,
-                    extra_input=extra_input,
+                    warp_data=warper_spec,
                 )
-            elif warp_file_ext == ".h5":
+            elif warper_spec["warper"] == "ants":
                 resampled_parcellation_img = ANTsParcellationWarper().warp(
                     parcellation_name="native",
                     parcellation_img=resampled_parcellation_img,
                     src="",
-                    dst="T1w",
+                    dst="native",
                     target_data=target_data,
-                    extra_input=extra_input,
-                )
-            else:
-                raise_error(
-                    msg=(
-                        "Unknown warp / transformation file extension: "
-                        f"{warp_file_ext}"
-                    ),
-                    klass=RuntimeError,
+                    warp_data=warper_spec,
                 )
 
         return resampled_parcellation_img, labels

junifer/data/utils.py

@@ -4,14 +4,14 @@
 #          Synchon Mandal <s.mandal@fz-juelich.de>
 # License: AGPL
 
-from typing import List, Optional, Union
+from typing import Dict, List, MutableMapping, Optional, Union
 
 import numpy as np
 
-from ..utils.logging import logger
+from ..utils import logger, raise_error
 
 
-__all__ = ["closest_resolution"]
+__all__ = ["closest_resolution", "get_native_warper"]
 
 
 def closest_resolution(
@@ -49,3 +49,67 @@ def closest_resolution(
         closest = np.min(valid_resolution)
 
     return closest
+
+
+def get_native_warper(
+    target_data: MutableMapping,
+    other_data: MutableMapping,
+    inverse: bool = False,
+) -> Dict:
+    """Get correct warping specification for native space.
+
+    Parameters
+    ----------
+    target_data : dict
+        The target data from the pipeline data object.
+    other_data : dict
+        The other data in the pipeline data object.
+    inverse : bool, optional
+        Whether to get the inverse warping specification (default False).
+
+    Returns
+    -------
+    dict
+        The correct warping specification.
+
+    Raises
+    ------
+    RuntimeError
+        If no warper or multiple possible warpers are found.
+
+    """
+    # Get possible warpers
+    possible_warpers = []
+    for entry in other_data["Warp"]:
+        if not inverse:
+            if (
+                entry["src"] == target_data["prewarp_space"]
+                and entry["dst"] == "native"
+            ):
+                possible_warpers.append(entry)
+        else:
+            if (
+                entry["dst"] == target_data["prewarp_space"]
+                and entry["src"] == "native"
+            ):
+                possible_warpers.append(entry)
+
+    # Check for no warper
+    if not possible_warpers:
+        raise_error(
+            klass=RuntimeError,
+            msg="Could not find correct warping specification",
+        )
+
+    # Check for multiple possible warpers
+    if len(possible_warpers) > 1:
+        raise_error(
+            klass=RuntimeError,
+            msg=(
+                "Cannot proceed as multiple warping specification found, "
+                "adjust either the DataGrabber or the working space: "
+                f"{possible_warpers}"
+            ),
+        )
+
+    return possible_warpers[0]