junifer 0.0.6.dev219__py3-none-any.whl → 0.0.6.dev248__py3-none-any.whl

junifer/preprocess/smoothing/_fsl_smoothing.py

@@ -6,20 +6,17 @@
 from typing import (
     TYPE_CHECKING,
     ClassVar,
-    Dict,
-    List,
-    Set,
-    Union,
 )
 
 import nibabel as nib
 
 from ...pipeline import WorkDirManager
+from ...typing import Dependencies, ExternalDependencies
 from ...utils import logger, run_ext_cmd
 
 
 if TYPE_CHECKING:
-    from nibabel import Nifti1Image
+    from nibabel.nifti1 import Nifti1Image
 
 
 __all__ = ["FSLSmoothing"]
@@ -32,14 +29,14 @@ class FSLSmoothing:
 
     """
 
-    _EXT_DEPENDENCIES: ClassVar[List[Dict[str, Union[str, List[str]]]]] = [
+    _EXT_DEPENDENCIES: ClassVar[ExternalDependencies] = [
         {
             "name": "fsl",
             "commands": ["susan"],
         },
     ]
 
-    _DEPENDENCIES: ClassVar[Set[str]] = {"nibabel"}
+    _DEPENDENCIES: ClassVar[Dependencies] = {"nibabel"}
 
     def preprocess(
         self,

junifer/preprocess/smoothing/_nilearn_smoothing.py

@@ -7,18 +7,18 @@ from typing import (
     TYPE_CHECKING,
     ClassVar,
     Literal,
-    Set,
     Union,
 )
 
 from nilearn import image as nimg
 from numpy.typing import ArrayLike
 
+from ...typing import Dependencies
 from ...utils import logger
 
 
 if TYPE_CHECKING:
-    from nibabel import Nifti1Image
+    from nibabel.nifti1 import Nifti1Image
 
 
 __all__ = ["NilearnSmoothing"]
@@ -31,7 +31,7 @@ class NilearnSmoothing:
 
     """
 
-    _DEPENDENCIES: ClassVar[Set[str]] = {"nilearn"}
+    _DEPENDENCIES: ClassVar[Dependencies] = {"nilearn"}
 
     def preprocess(
         self,

junifer/preprocess/smoothing/smoothing.py

@@ -3,9 +3,10 @@
 # Authors: Synchon Mandal <s.mandal@fz-juelich.de>
 # License: AGPL
 
-from typing import Any, ClassVar, Dict, List, Optional, Tuple, Type, Union
+from typing import Any, ClassVar, Dict, List, Optional, Tuple, Union
 
 from ...api.decorators import register_preprocessor
+from ...typing import ConditionalDependencies
 from ...utils import logger, raise_error
 from ..base import BasePreprocessor
 from ._afni_smoothing import AFNISmoothing
@@ -67,7 +68,7 @@ class Smoothing(BasePreprocessor):
 
     """
 
-    _CONDITIONAL_DEPENDENCIES: ClassVar[List[Dict[str, Union[str, Type]]]] = [
+    _CONDITIONAL_DEPENDENCIES: ClassVar[ConditionalDependencies] = [
         {
             "using": "nilearn",
             "depends_on": NilearnSmoothing,

junifer/preprocess/warping/_ants_warper.py

@@ -7,9 +7,6 @@ from typing import (
     Any,
     ClassVar,
     Dict,
-    List,
-    Set,
-    Union,
 )
 
 import nibabel as nib
@@ -17,7 +14,8 @@ import numpy as np
 
 from ...data import get_template, get_xfm
 from ...pipeline import WorkDirManager
-from ...utils import logger, run_ext_cmd
+from ...typing import Dependencies, ExternalDependencies
+from ...utils import logger, raise_error, run_ext_cmd
 
 
 __all__ = ["ANTsWarper"]
@@ -31,14 +29,14 @@ class ANTsWarper:
 
     """
 
-    _EXT_DEPENDENCIES: ClassVar[List[Dict[str, Union[str, List[str]]]]] = [
+    _EXT_DEPENDENCIES: ClassVar[ExternalDependencies] = [
         {
             "name": "ants",
             "commands": ["ResampleImage", "antsApplyTransforms"],
         },
     ]
 
-    _DEPENDENCIES: ClassVar[Set[str]] = {"numpy", "nibabel"}
+    _DEPENDENCIES: ClassVar[Dependencies] = {"numpy", "nibabel"}
 
     def preprocess(
         self,
@@ -65,6 +63,11 @@ class ANTsWarper:
             values and new ``reference_path`` key whose value points to the
             reference file used for warping.
 
+        Raises
+        ------
+        RuntimeError
+            If warp file path could not be found in ``extra_input``.
+
         """
         # Create element-specific tempdir for storing post-warping assets
         element_tempdir = WorkDirManager().get_element_tempdir(
@@ -79,6 +82,17 @@ class ANTsWarper:
             # resolution
             resolution = np.min(input["data"].header.get_zooms()[:3])
 
+            # Get warp file path
+            warp_file_path = None
+            for entry in extra_input["Warp"]:
+                if entry["dst"] == "native":
+                    warp_file_path = entry["path"]
+            if warp_file_path is None:
+                raise_error(
+                    klass=RuntimeError,
+                    msg="Could not find correct warp file path",
+                )
+
             # Create a tempfile for resampled reference output
             resample_image_out_path = (
                 element_tempdir / "resampled_reference.nii.gz"
@@ -107,7 +121,7 @@ class ANTsWarper:
                 f"-i {input['path'].resolve()}",
                 # use resampled reference
                 f"-r {resample_image_out_path.resolve()}",
-                f"-t {extra_input['Warp']['path'].resolve()}",
+                f"-t {warp_file_path.resolve()}",
                 f"-o {apply_transforms_out_path.resolve()}",
             ]
             # Call antsApplyTransforms
@@ -117,6 +131,8 @@ class ANTsWarper:
             input["data"] = nib.load(apply_transforms_out_path)
             # Save resampled reference path
             input["reference_path"] = resample_image_out_path
+            # Keep pre-warp space for further operations
+            input["prewarp_space"] = input["space"]
             # Use reference input's space as warped input's space
             input["space"] = extra_input["T1w"]["space"]
 
@@ -165,6 +181,9 @@ class ANTsWarper:
 
             # Modify target data
             input["data"] = nib.load(warped_output_path)
+            # Keep pre-warp space for further operations
+            input["prewarp_space"] = input["space"]
+            # Update warped input's space
             input["space"] = reference
 
         return input

junifer/preprocess/warping/_fsl_warper.py

@@ -7,16 +7,14 @@ from typing import (
     Any,
     ClassVar,
     Dict,
-    List,
-    Set,
-    Union,
 )
 
 import nibabel as nib
 import numpy as np
 
 from ...pipeline import WorkDirManager
-from ...utils import logger, run_ext_cmd
+from ...typing import Dependencies, ExternalDependencies
+from ...utils import logger, raise_error, run_ext_cmd
 
 
 __all__ = ["FSLWarper"]
@@ -30,14 +28,14 @@ class FSLWarper:
 
     """
 
-    _EXT_DEPENDENCIES: ClassVar[List[Dict[str, Union[str, List[str]]]]] = [
+    _EXT_DEPENDENCIES: ClassVar[ExternalDependencies] = [
         {
             "name": "fsl",
             "commands": ["flirt", "applywarp"],
         },
     ]
 
-    _DEPENDENCIES: ClassVar[Set[str]] = {"numpy", "nibabel"}
+    _DEPENDENCIES: ClassVar[Dependencies] = {"numpy", "nibabel"}
 
     def preprocess(
         self,
@@ -61,6 +59,11 @@ class FSLWarper:
             values and new ``reference_path`` key whose value points to the
             reference file used for warping.
 
+        Raises
+        ------
+        RuntimeError
+            If warp file path could not be found in ``extra_input``.
+
         """
         logger.debug("Using FSL for space warping")
 
@@ -68,6 +71,16 @@ class FSLWarper:
         # resolution
         resolution = np.min(input["data"].header.get_zooms()[:3])
 
+        # Get warp file path
+        warp_file_path = None
+        for entry in extra_input["Warp"]:
+            if entry["dst"] == "native":
+                warp_file_path = entry["path"]
+        if warp_file_path is None:
+            raise_error(
+                klass=RuntimeError, msg="Could not find correct warp file path"
+            )
+
         # Create element-specific tempdir for storing post-warping assets
         element_tempdir = WorkDirManager().get_element_tempdir(
             prefix="fsl_warper"
@@ -95,7 +108,7 @@ class FSLWarper:
             "--interp=spline",
             f"-i {input['path'].resolve()}",
             f"-r {flirt_out_path.resolve()}",  # use resampled reference
-            f"-w {extra_input['Warp']['path'].resolve()}",
+            f"-w {warp_file_path.resolve()}",
             f"-o {applywarp_out_path.resolve()}",
         ]
         # Call applywarp
@@ -105,7 +118,8 @@ class FSLWarper:
         input["data"] = nib.load(applywarp_out_path)
         # Save resampled reference path
         input["reference_path"] = flirt_out_path
-
+        # Keep pre-warp space for further operations
+        input["prewarp_space"] = input["space"]
         # Use reference input's space as warped input's space
         input["space"] = extra_input["T1w"]["space"]
 

junifer/preprocess/warping/space_warper.py

@@ -3,11 +3,12 @@
 # Authors: Synchon Mandal <s.mandal@fz-juelich.de>
 # License: AGPL
 
-from typing import Any, ClassVar, Dict, List, Optional, Tuple, Type, Union
+from typing import Any, ClassVar, Dict, List, Optional, Tuple, Union
 
 from templateflow import api as tflow
 
 from ...api.decorators import register_preprocessor
+from ...typing import ConditionalDependencies
 from ...utils import logger, raise_error
 from ..base import BasePreprocessor
 from ._ants_warper import ANTsWarper
@@ -23,11 +24,12 @@ class SpaceWarper(BasePreprocessor):
 
     Parameters
     ----------
-    using : {"fsl", "ants"}
+    using : {"fsl", "ants", "auto"}
         Implementation to use for warping:
 
         * "fsl" : Use FSL's ``applywarp``
         * "ants" : Use ANTs' ``antsApplyTransforms``
+        * "auto" : Auto-select tool when ``reference="T1w"``
 
     reference : str
         The data type to use as reference for warping, can be either a data
@@ -46,7 +48,7 @@ class SpaceWarper(BasePreprocessor):
 
     """
 
-    _CONDITIONAL_DEPENDENCIES: ClassVar[List[Dict[str, Union[str, Type]]]] = [
+    _CONDITIONAL_DEPENDENCIES: ClassVar[ConditionalDependencies] = [
         {
             "using": "fsl",
             "depends_on": FSLWarper,
@@ -55,6 +57,10 @@ class SpaceWarper(BasePreprocessor):
             "using": "ants",
             "depends_on": ANTsWarper,
         },
+        {
+            "using": "auto",
+            "depends_on": [FSLWarper, ANTsWarper],
+        },
     ]
 
     def __init__(
@@ -155,14 +161,16 @@ class SpaceWarper(BasePreprocessor):
             If ``extra_input`` is None when transforming to native space
             i.e., using ``"T1w"`` as reference.
         RuntimeError
-            If the data is in the correct space and does not require
+            If warper could not be found in ``extra_input`` when
+            ``using="auto"`` or
+            if the data is in the correct space and does not require
             warping or
-            if FSL is used for template space warping.
+            if FSL is used when ``reference="T1w"``.
 
         """
         logger.info(f"Warping to {self.reference} space using SpaceWarper")
         # Transform to native space
-        if self.using in ["fsl", "ants"] and self.reference == "T1w":
+        if self.using in ["fsl", "ants", "auto"] and self.reference == "T1w":
             # Check for extra inputs
             if extra_input is None:
                 raise_error(
@@ -181,6 +189,26 @@ class SpaceWarper(BasePreprocessor):
                     extra_input=extra_input,
                     reference=self.reference,
                 )
+            elif self.using == "auto":
+                warper = None
+                for entry in extra_input["Warp"]:
+                    if entry["dst"] == "native":
+                        warper = entry["warper"]
+                if warper is None:
+                    raise_error(
+                        klass=RuntimeError, msg="Could not find correct warper"
+                    )
+                if warper == "fsl":
+                    input = FSLWarper().preprocess(
+                        input=input,
+                        extra_input=extra_input,
+                    )
+                elif warper == "ants":
+                    input = ANTsWarper().preprocess(
+                        input=input,
+                        extra_input=extra_input,
+                        reference=self.reference,
+                    )
         # Transform to template space with ANTs possible
         elif self.using == "ants" and self.reference != "T1w":
             # Check pre-requirements for space manipulation

junifer/preprocess/warping/tests/test_space_warper.py

@@ -4,7 +4,7 @@
 # License: AGPL
 
 import socket
-from typing import TYPE_CHECKING, Tuple, Type
+from typing import Tuple, Type
 
 import pytest
 from numpy.testing import assert_array_equal, assert_raises
@@ -14,10 +14,7 @@ from junifer.datareader import DefaultDataReader
 from junifer.pipeline.utils import _check_ants, _check_fsl
 from junifer.preprocess import SpaceWarper
 from junifer.testing.datagrabbers import PartlyCloudyTestingDataGrabber
-
-
-if TYPE_CHECKING:
-    from junifer.datagrabber import BaseDataGrabber
+from junifer.typing import DataGrabberLike
 
 
 @pytest.mark.parametrize(
@@ -99,7 +96,7 @@ def test_SpaceWarper_errors(
     reason="only for juseless",
 )
 def test_SpaceWarper_native(
-    datagrabber: "BaseDataGrabber", element: Tuple[str, ...], using: str
+    datagrabber: DataGrabberLike, element: Tuple[str, ...], using: str
 ) -> None:
     """Test SpaceWarper for native space warping.
 
@@ -162,7 +159,7 @@ def test_SpaceWarper_native(
     _check_ants() is False, reason="requires ANTs to be in PATH"
 )
 def test_SpaceWarper_multi_mni(
-    datagrabber: "BaseDataGrabber",
+    datagrabber: DataGrabberLike,
     element: Tuple[str, ...],
     space: str,
 ) -> None:

junifer/typing/__init__.py

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

junifer/typing/__init__.pyi

@@ -0,0 +1,23 @@
+__all__ = [
+    "DataGrabberLike",
+    "PreprocessorLike",
+    "MarkerLike",
+    "StorageLike",
+    "PipelineComponent",
+    "Dependencies",
+    "ConditionalDependencies",
+    "ExternalDependencies",
+    "MarkerInOutMappings",
+]
+
+from ._typing import (
+    DataGrabberLike,
+    PreprocessorLike,
+    MarkerLike,
+    StorageLike,
+    PipelineComponent,
+    Dependencies,
+    ConditionalDependencies,
+    ExternalDependencies,
+    MarkerInOutMappings,
+)

junifer/typing/_typing.py

@@ -0,0 +1,61 @@
+"""Provide type hints for internal and external use."""
+
+# Authors: Synchon Mandal <s.mandal@fz-juelich.de>
+# License: AGPL
+
+from typing import (
+    TYPE_CHECKING,
+    AbstractSet,
+    MutableMapping,
+    Sequence,
+    Type,
+    Union,
+)
+
+
+if TYPE_CHECKING:
+    from ..datagrabber import BaseDataGrabber
+    from ..datareader import DefaultDataReader
+    from ..markers import BaseMarker
+    from ..preprocess import BasePreprocessor
+    from ..storage import BaseFeatureStorage
+
+
+__all__ = [
+    "DataGrabberLike",
+    "PreprocessorLike",
+    "MarkerLike",
+    "StorageLike",
+    "PipelineComponent",
+    "Dependencies",
+    "ConditionalDependencies",
+    "ExternalDependencies",
+    "MarkerInOutMappings",
+]
+
+
+DataGrabberLike = Type["BaseDataGrabber"]
+PreprocessorLike = Type["BasePreprocessor"]
+MarkerLike = Type["BaseMarker"]
+StorageLike = Type["BaseFeatureStorage"]
+PipelineComponent = Union[
+    "DataGrabberLike",
+    "DefaultDataReader",
+    "PreprocessorLike",
+    "MarkerLike",
+    "StorageLike",
+]
+Dependencies = AbstractSet[str]
+ConditionalDependencies = Sequence[
+    MutableMapping[
+        str,
+        Union[
+            str,
+            PipelineComponent,
+            Sequence[str],
+            Sequence[PipelineComponent],
+        ],
+    ]
+]
+ExternalDependencies = Sequence[MutableMapping[str, Union[str, Sequence[str]]]]
+MarkerInOutMappings = MutableMapping[str, MutableMapping[str, str]]

{junifer-0.0.6.dev219.dist-info → junifer-0.0.6.dev248.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: junifer
-Version: 0.0.6.dev219
+Version: 0.0.6.dev248
 Summary: JUelich NeuroImaging FEature extractoR
 Author-email: Fede Raimondo <f.raimondo@fz-juelich.de>, Synchon Mandal <s.mandal@fz-juelich.de>
 Maintainer-email: Fede Raimondo <f.raimondo@fz-juelich.de>, Synchon Mandal <s.mandal@fz-juelich.de>
@@ -111,6 +111,7 @@ The documentation is available at [https://juaml.github.io/junifer](https://juam
   * `preprocess`: Preprocessing module.
   * `storage`: Storage module.
   * `testing`: Testing components module.
+  * `typing`: Type hints module.
   * `utils`: Utilities module (e.g. logging).
 
 ## Installation