junifer 0.0.5__py3-none-any.whl → 0.0.5.dev24__py3-none-any.whl

junifer/preprocess/ants/ants_apply_transforms_warper.py

@@ -0,0 +1,185 @@
+"""Provide class for warping via ANTs antsApplyTransforms."""
+
+# Authors: Synchon Mandal <s.mandal@fz-juelich.de>
+# License: AGPL
+
+from pathlib import Path
+from typing import (
+    TYPE_CHECKING,
+    Any,
+    ClassVar,
+    Dict,
+    List,
+    Optional,
+    Tuple,
+    Union,
+)
+
+import nibabel as nib
+import numpy as np
+
+from ...pipeline import WorkDirManager
+from ...utils import logger, raise_error, run_ext_cmd
+
+
+if TYPE_CHECKING:
+    from nibabel import Nifti1Image
+
+
+class _AntsApplyTransformsWarper:
+    """Class for warping NIfTI images via ANTs antsApplyTransforms.
+
+    Warps ANTs ``antsApplyTransforms``.
+
+    Parameters
+    ----------
+    reference : str
+        The data type to use as reference for warping.
+    on : str
+        The data type to use for warping.
+
+    Raises
+    ------
+    ValueError
+        If a list was passed for ``on``.
+
+    """
+
+    _EXT_DEPENDENCIES: ClassVar[List[Dict[str, Union[str, List[str]]]]] = [
+        {
+            "name": "ants",
+            "commands": ["ResampleImage", "antsApplyTransforms"],
+        },
+    ]
+
+    def __init__(self, reference: str, on: str) -> None:
+        """Initialize the class."""
+        self.ref = reference
+        # Check only single data type is passed
+        if isinstance(on, list):
+            raise_error("Can only work on single data type, list was passed.")
+        self.on = on
+
+    def _run_apply_transforms(
+        self,
+        input_data: Dict,
+        ref_path: Path,
+        warp_path: Path,
+    ) -> Tuple["Nifti1Image", Path]:
+        """Run ``antsApplyTransforms``.
+
+        Parameters
+        ----------
+        input_data : dict
+            The input data.
+        ref_path : pathlib.Path
+            The path to the reference file.
+        warp_path : pathlib.Path
+            The path to the warp file.
+
+        Returns
+        -------
+        Niimg-like object
+            The warped input image.
+        pathlib.Path
+            The path to the resampled reference image.
+
+        """
+        # Get the min of the voxel sizes from input and use it as the
+        # resolution
+        resolution = np.min(input_data["data"].header.get_zooms()[:3])
+
+        # Create element-specific tempdir for storing post-warping assets
+        tempdir = WorkDirManager().get_element_tempdir(
+            prefix="applytransforms"
+        )
+
+        # Create a tempfile for resampled reference output
+        resample_image_out_path = tempdir / "reference_resampled.nii.gz"
+        # Set ResampleImage command
+        resample_image_cmd = [
+            "ResampleImage",
+            "3",  # image dimension
+            f"{ref_path.resolve()}",
+            f"{resample_image_out_path.resolve()}",
+            f"{resolution}x{resolution}x{resolution}",
+            "0",  # option for spacing and not size
+            "3 3",  # Lanczos windowed sinc
+        ]
+        # Call ResampleImage
+        run_ext_cmd(name="ResampleImage", cmd=resample_image_cmd)
+
+        # Create a tempfile for warped output
+        apply_transforms_out_path = tempdir / "input_warped.nii.gz"
+        # Set antsApplyTransforms command
+        apply_transforms_cmd = [
+            "antsApplyTransforms",
+            "-d 3",
+            "-e 3",
+            "-n LanczosWindowedSinc",
+            f"-i {input_data['path'].resolve()}",
+            # use resampled reference
+            f"-r {resample_image_out_path.resolve()}",
+            f"-t {warp_path.resolve()}",
+            f"-o {apply_transforms_out_path.resolve()}",
+        ]
+        # Call antsApplyTransforms
+        run_ext_cmd(name="antsApplyTransforms", cmd=apply_transforms_cmd)
+
+        # Load nifti
+        output_img = nib.load(apply_transforms_out_path)
+
+        return output_img, resample_image_out_path  # type: ignore
+
+    def preprocess(
+        self,
+        input: Dict[str, Any],
+        extra_input: Optional[Dict[str, Any]] = None,
+    ) -> Tuple[str, Dict[str, Any]]:
+        """Preprocess.
+
+        Parameters
+        ----------
+        input : dict
+            A single input from the Junifer Data object in which to preprocess.
+        extra_input : dict, optional
+            The other fields in the Junifer Data object. Must include the
+            ``Warp`` and ``ref`` value's keys.
+
+        Returns
+        -------
+        str
+            The key to store the output in the Junifer Data object.
+        dict
+            The computed result as dictionary. This will be stored in the
+            Junifer Data object under the key ``data`` of the data type.
+
+        Raises
+        ------
+        ValueError
+            If ``extra_input`` is None.
+
+        """
+        logger.debug("Warping via ANTs using antsApplyTransforms")
+        # Check for extra inputs
+        if extra_input is None:
+            raise_error(
+                f"No extra input provided, requires `Warp` and `{self.ref}` "
+                "data types in particular."
+            )
+        # Retrieve data type info to warp
+        to_warp_input = input
+        # Retrieve data type info to use as reference
+        ref_input = extra_input[self.ref]
+        # Retrieve Warp data
+        warp = extra_input["Warp"]
+        # Replace original data with warped data and add resampled reference
+        # path
+        input["data"], input["reference_path"] = self._run_apply_transforms(
+            input_data=to_warp_input,
+            ref_path=ref_input["path"],
+            warp_path=warp["path"],
+        )
+        # Use reference input's space as warped input's space
+        input["space"] = ref_input["space"]
+        return self.on, input

junifer/preprocess/ants/tests/test_ants_apply_transforms_warper.py

@@ -0,0 +1,56 @@
+"""Provide tests for AntsApplyTransformsWarper."""
+
+# Authors: Synchon Mandal <s.mandal@fz-juelich.de>
+# License: AGPL
+
+import socket
+
+import pytest
+
+from junifer.datagrabber import DMCC13Benchmark
+from junifer.datareader import DefaultDataReader
+from junifer.pipeline.utils import _check_ants
+from junifer.preprocess.ants.ants_apply_transforms_warper import (
+    _AntsApplyTransformsWarper,
+)
+
+
+def test_AntsApplyTransformsWarper_init() -> None:
+    """Test AntsApplyTransformsWarper init."""
+    ants_apply_transforms_warper = _AntsApplyTransformsWarper(
+        reference="T1w", on="BOLD"
+    )
+    assert ants_apply_transforms_warper.ref == "T1w"
+    assert ants_apply_transforms_warper.on == "BOLD"
+
+
+@pytest.mark.skipif(
+    _check_ants() is False, reason="requires ANTs to be in PATH"
+)
+@pytest.mark.skipif(
+    socket.gethostname() != "juseless",
+    reason="only for juseless",
+)
+def test_AntsApplyTransformsWarper_preprocess() -> None:
+    """Test AntsApplyTransformsWarper preprocess."""
+    with DMCC13Benchmark(
+        types=["BOLD", "T1w", "Warp"],
+        sessions=["ses-wave1bas"],
+        tasks=["Rest"],
+        phase_encodings=["AP"],
+        runs=["1"],
+        native_t1w=True,
+    ) as dg:
+        # Read data
+        element_data = DefaultDataReader().fit_transform(
+            dg[("sub-f9057kp", "ses-wave1bas", "Rest", "AP", "1")]
+        )
+        # Preprocess data
+        data_type, data = _AntsApplyTransformsWarper(
+            reference="T1w", on="BOLD"
+        ).preprocess(
+            input=element_data["BOLD"],
+            extra_input=element_data,
+        )
+        assert isinstance(data_type, str)
+        assert isinstance(data, dict)

junifer/preprocess/base.py

@@ -11,9 +11,6 @@ from ..pipeline import PipelineStepMixin, UpdateMetaMixin
 from ..utils import logger, raise_error
 
 
-__all__ = ["BasePreprocessor"]
-
-
 class BasePreprocessor(ABC, PipelineStepMixin, UpdateMetaMixin):
     """Abstract base class for all preprocessors.
 
@@ -139,7 +136,7 @@ class BasePreprocessor(ABC, PipelineStepMixin, UpdateMetaMixin):
             A single input from the Junifer Data object to preprocess.
         extra_input : dict, optional
             The other fields in the Junifer Data object. Useful for accessing
-            other data type that needs to be used in the computation. For
+            other data kind that needs to be used in the computation. For
             example, the confound removers can make use of the
             confounds if available (default None).
 
@@ -149,8 +146,8 @@ class BasePreprocessor(ABC, PipelineStepMixin, UpdateMetaMixin):
             The computed result as dictionary.
         dict or None
             Extra "helper" data types as dictionary to add to the Junifer Data
-            object. If no new "helper" data type(s) is(are) created, None is to
-            be passed.
+            object. For example, computed BOLD mask can be passed via this.
+            If no new "helper" data types is created, None is to be passed.
 
         """
         raise_error(

junifer/preprocess/bold_warper.py

@@ -0,0 +1,265 @@
+"""Provide class for warping BOLD to other template spaces."""
+
+# Authors: Synchon Mandal <s.mandal@fz-juelich.de>
+# License: AGPL
+
+from typing import (
+    Any,
+    ClassVar,
+    Dict,
+    List,
+    Optional,
+    Tuple,
+    Type,
+    Union,
+)
+
+import nibabel as nib
+from templateflow import api as tflow
+
+from ..api.decorators import register_preprocessor
+from ..data import get_template, get_xfm
+from ..pipeline import WorkDirManager
+from ..utils import logger, raise_error, run_ext_cmd
+from .ants.ants_apply_transforms_warper import _AntsApplyTransformsWarper
+from .base import BasePreprocessor
+from .fsl.apply_warper import _ApplyWarper
+
+
+@register_preprocessor
+class BOLDWarper(BasePreprocessor):
+    """Class for warping BOLD NIfTI images.
+
+    .. deprecated:: 0.0.3
+              `BOLDWarper` will be removed in v0.0.4, it is replaced by
+              `SpaceWarper` because the latter works also with T1w data.
+
+    Parameters
+    ----------
+    using : {"fsl", "ants"}
+        Implementation to use for warping:
+
+        * "fsl" : Use FSL's ``applywarp``
+        * "afni" : Use ANTs' ``antsApplyTransforms``
+
+    reference : str
+        The data type to use as reference for warping, can be either a data
+        type like "T1w" or a template space like "MNI152NLin2009cAsym".
+
+    Raises
+    ------
+    ValueError
+        If ``using`` is invalid or
+        if ``reference`` is invalid.
+
+    Notes
+    -----
+    If you are setting ``reference`` to a template space like
+    "MNI152NLin2009cAsym", make sure ANTs is available for the
+    transformation else it will fail during runtime. It is tricky to validate
+    this beforehand and difficult to enforce this as a requirement, hence the
+    heads-up.
+
+    """
+
+    _CONDITIONAL_DEPENDENCIES: ClassVar[List[Dict[str, Union[str, Type]]]] = [
+        {
+            "using": "fsl",
+            "depends_on": _ApplyWarper,
+        },
+        {
+            "using": "ants",
+            "depends_on": _AntsApplyTransformsWarper,
+        },
+    ]
+
+    def __init__(self, using: str, reference: str) -> None:
+        """Initialize the class."""
+        # Validate `using` parameter
+        valid_using = [dep["using"] for dep in self._CONDITIONAL_DEPENDENCIES]
+        if using not in valid_using:
+            raise_error(
+                f"Invalid value for `using`, should be one of: {valid_using}"
+            )
+        self.using = using
+        self.ref = reference
+        # Initialize superclass based on reference
+        if self.ref == "T1w":
+            super().__init__(
+                on="BOLD", required_data_types=["BOLD", self.ref, "Warp"]
+            )
+        elif self.ref in tflow.templates():
+            super().__init__(on="BOLD", required_data_types=["BOLD"])
+        else:
+            raise_error(f"Unknown reference: {self.ref}")
+
+    def get_valid_inputs(self) -> List[str]:
+        """Get valid data types for input.
+
+        Returns
+        -------
+        list of str
+            The list of data types that can be used as input for this
+            preprocessor.
+
+        """
+        return ["BOLD"]
+
+    def get_output_type(self, input_type: str) -> str:
+        """Get output type.
+
+        Parameters
+        ----------
+        input_type : str
+            The data type input to the preprocessor.
+
+        Returns
+        -------
+        str
+            The data type output by the preprocessor.
+
+        """
+        # Does not add any new keys
+        return input_type
+
+    def preprocess(
+        self,
+        input: Dict[str, Any],
+        extra_input: Optional[Dict[str, Any]] = None,
+    ) -> Tuple[Dict[str, Any], Optional[Dict[str, Dict[str, Any]]]]:
+        """Preprocess.
+
+        Parameters
+        ----------
+        input : dict
+            The BOLD input from the Junifer Data object.
+        extra_input : dict, optional
+            The other fields in the Junifer Data object. Must include the
+            ``Warp`` and ``ref`` value's keys if native space transformation is
+            needed.
+
+        Returns
+        -------
+        dict
+            The computed result as dictionary.
+        None
+            Extra "helper" data types as dictionary to add to the Junifer Data
+            object.
+
+        Raises
+        ------
+        ValueError
+            If ``extra_input`` is None when transforming to native space
+            i.e., using "T1w" as reference.
+        RuntimeError
+            If warp / transformation file extension is not ".mat" or ".h5"
+            when transforming to native space or
+            if the BOLD data is in the correct space and does not require
+            warping.
+
+        """
+        logger.info(f"Warping BOLD to {self.ref} space using BOLDWarper")
+        # Transform to native space
+        if self.ref == "T1w":
+            # Check for extra inputs
+            if extra_input is None:
+                raise_error(
+                    "No extra input provided, requires `Warp` and "
+                    f"`{self.ref}` data types in particular."
+                )
+            # Check for warp file type to use correct tool
+            warp_file_ext = extra_input["Warp"]["path"].suffix
+            if warp_file_ext == ".mat":
+                logger.debug("Using FSL with BOLDWarper")
+                # Initialize ApplyWarper for computation
+                apply_warper = _ApplyWarper(reference=self.ref, on="BOLD")
+                # Replace original BOLD data with warped BOLD data
+                _, input = apply_warper.preprocess(
+                    input=input,
+                    extra_input=extra_input,
+                )
+            elif warp_file_ext == ".h5":
+                logger.debug("Using ANTs with BOLDWarper")
+                # Initialize AntsApplyTransformsWarper for computation
+                ants_apply_transforms_warper = _AntsApplyTransformsWarper(
+                    reference=self.ref, on="BOLD"
+                )
+                # Replace original BOLD data with warped BOLD data
+                _, input = ants_apply_transforms_warper.preprocess(
+                    input=input,
+                    extra_input=extra_input,
+                )
+            else:
+                raise_error(
+                    msg=(
+                        "Unknown warp / transformation file extension: "
+                        f"{warp_file_ext}"
+                    ),
+                    klass=RuntimeError,
+                )
+        # Transform to template space
+        else:
+            # Check pre-requirements for space manipulation
+            if self.ref == input["space"]:
+                raise_error(
+                    (
+                        f"Skipped warping as the BOLD data is in {self.ref} "
+                        "space which would mean that you can remove the "
+                        "BOLDWarper from the preprocess step."
+                    ),
+                    klass=RuntimeError,
+                )
+            else:
+                # Get xfm file
+                xfm_file_path = get_xfm(src=input["space"], dst=self.ref)
+                # Get template space image
+                template_space_img = get_template(
+                    space=self.ref,
+                    target_data=input,
+                    extra_input=None,
+                )
+
+                # Create component-scoped tempdir
+                tempdir = WorkDirManager().get_tempdir(prefix="boldwarper")
+                # Create element-scoped tempdir so that warped BOLD is
+                # available later as nibabel stores file path reference for
+                # loading on computation
+                element_tempdir = WorkDirManager().get_element_tempdir(
+                    prefix="boldwarper"
+                )
+
+                # Save template
+                template_space_img_path = tempdir / f"{self.ref}_T1w.nii.gz"
+                nib.save(template_space_img, template_space_img_path)
+
+                # Create a tempfile for warped output
+                warped_bold_path = (
+                    element_tempdir
+                    / f"bold_warped_from_{input['space']}_to_{self.ref}.nii.gz"
+                )
+
+                logger.debug(
+                    f"Using ANTs to warp BOLD "
+                    f"from {input['space']} to {self.ref}"
+                )
+                # Set antsApplyTransforms command
+                apply_transforms_cmd = [
+                    "antsApplyTransforms",
+                    "-d 3",
+                    "-e 3",
+                    "-n LanczosWindowedSinc",
+                    f"-i {input['path'].resolve()}",
+                    f"-r {template_space_img_path.resolve()}",
+                    f"-t {xfm_file_path.resolve()}",
+                    f"-o {warped_bold_path.resolve()}",
+                ]
+                # Call antsApplyTransforms
+                run_ext_cmd(
+                    name="antsApplyTransforms", cmd=apply_transforms_cmd
+                )
+
+                # Modify target data
+                input["data"] = nib.load(warped_bold_path)
+                input["space"] = self.ref
+
+        return input, None

junifer/preprocess/confounds/__init__.py

@@ -5,6 +5,3 @@
 # License: AGPL
 
 from .fmriprep_confound_remover import fMRIPrepConfoundRemover
-
-
-__all__ = ["fMRIPrepConfoundRemover"]