junifer 0.0.4.dev663__tar.gz → 0.0.4.dev691__tar.gz

{junifer-0.0.4.dev663 → junifer-0.0.4.dev691}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: junifer
-Version: 0.0.4.dev663
+Version: 0.0.4.dev691
 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>

junifer-0.0.4.dev691/docs/changes/newsfragments/301.feature

@@ -0,0 +1 @@
+Introduce :class:`.SpaceWarper` for warping ``T1w``, ``BOLD``, ``VBM_GM``, ``VBM_WM``, ``fALFF``, ``GCOR`` and ``LCOR`` data to other spaces by `Synchon Mandal`_

junifer-0.0.4.dev691/docs/changes/newsfragments/301.removal

@@ -0,0 +1 @@
+Deprecate :class:`.BOLDWarper` and mark for removal in v0.0.4 by `Synchon Mandal`_

junifer-0.0.4.dev691/docs/changes/newsfragments/312.bugfix

@@ -0,0 +1 @@
+Fix :class:`.HTCondorAdapter`'s script generation to use double quotes instead of single quotes for HTCondor's ``VARS`` by `Synchon Mandal`_

{junifer-0.0.4.dev663 → junifer-0.0.4.dev691}/junifer/_version.py

@@ -12,5 +12,5 @@ __version__: str
 __version_tuple__: VERSION_TUPLE
 version_tuple: VERSION_TUPLE
 
-__version__ = version = '0.0.4.dev663'
-__version_tuple__ = version_tuple = (0, 0, 4, 'dev663')
+__version__ = version = '0.0.4.dev691'
+__version_tuple__ = version_tuple = (0, 0, 4, 'dev691')

{junifer-0.0.4.dev663 → junifer-0.0.4.dev691}/junifer/api/queue_context/htcondor_adapter.py

@@ -274,8 +274,8 @@ class HTCondorAdapter(QueueContextAdapter):
             )
             fixed += (
                 f"JOB run{idx} {self._submit_run_path}\n"
-                f"VARS run{idx} element='{str_element}' "
-                f"log_element='{log_element}'\n\n"
+                f'VARS run{idx} element="{str_element}" '  # needs to be
+                f'log_element="{log_element}"\n\n'  # double quoted
             )
         var = ""
         if self._collect == "yes":

{junifer-0.0.4.dev663 → junifer-0.0.4.dev691}/junifer/api/queue_context/tests/test_htcondor_adapter.py

@@ -139,13 +139,13 @@ def test_HTCondorAdapter_run_collect(
         (
             [("sub01", "ses01")],
             "yes",
-            "element='sub01,ses01' log_element='sub01-ses01'",
+            'element="sub01,ses01" log_element="sub01-ses01"',
         ),
         (["sub01"], "on_success_only", "JOB collect"),
         (
             [("sub01", "ses01")],
             "on_success_only",
-            "element='sub01,ses01' log_element='sub01-ses01'",
+            'element="sub01,ses01" log_element="sub01-ses01"',
         ),
     ],
 )

{junifer-0.0.4.dev663 → junifer-0.0.4.dev691}/junifer/preprocess/__init__.py

@@ -8,3 +8,4 @@
 from .base import BasePreprocessor
 from .confounds import fMRIPrepConfoundRemover
 from .bold_warper import BOLDWarper
+from .warping import SpaceWarper

{junifer-0.0.4.dev663 → junifer-0.0.4.dev691}/junifer/preprocess/bold_warper.py

@@ -30,6 +30,10 @@ from .fsl.apply_warper import _ApplyWarper
 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"}

junifer-0.0.4.dev691/junifer/preprocess/warping/__init__.py

@@ -0,0 +1,6 @@
+"""Provide imports for warping sub-package."""
+
+# Authors: Synchon Mandal <s.mandal@fz-juelich.de>
+# License: AGPL
+
+from .space_warper import SpaceWarper

junifer-0.0.4.dev691/junifer/preprocess/warping/_ants_warper.py

@@ -0,0 +1,167 @@
+"""Provide class for space warping via ANTs antsApplyTransforms."""
+
+# Authors: Synchon Mandal <s.mandal@fz-juelich.de>
+# License: AGPL
+
+from typing import (
+    Any,
+    ClassVar,
+    Dict,
+    List,
+    Set,
+    Union,
+)
+
+import nibabel as nib
+import numpy as np
+
+from ...data import get_template, get_xfm
+from ...pipeline import WorkDirManager
+from ...utils import logger, run_ext_cmd
+
+
+class ANTsWarper:
+    """Class for space warping via ANTs antsApplyTransforms.
+
+    This class uses ANTs' ``ResampleImage`` for resampling (if required) and
+    ``antsApplyTransforms`` for transformation.
+
+    """
+
+    _EXT_DEPENDENCIES: ClassVar[List[Dict[str, Union[str, List[str]]]]] = [
+        {
+            "name": "ants",
+            "commands": ["ResampleImage", "antsApplyTransforms"],
+        },
+    ]
+
+    _DEPENDENCIES: ClassVar[Set[str]] = {"numpy", "nibabel"}
+
+    def preprocess(
+        self,
+        input: Dict[str, Any],
+        extra_input: Dict[str, Any],
+        reference: str,
+    ) -> Dict[str, Any]:
+        """Preprocess using ANTs.
+
+        Parameters
+        ----------
+        input : dict
+            A single input from the Junifer Data object in which to preprocess.
+        extra_input : dict
+            The other fields in the Junifer Data object. Should have ``T1w``
+            and ``Warp`` data types.
+        reference : str
+            The data type or template space to use as reference for warping.
+
+        Returns
+        -------
+        dict
+            The ``input`` dictionary with modified ``data`` and ``space`` key
+            values and new ``reference_path`` key whose value points to the
+            reference file used for warping.
+
+        """
+        # Create element-specific tempdir for storing post-warping assets
+        element_tempdir = WorkDirManager().get_element_tempdir(
+            prefix="ants_warper"
+        )
+
+        # Native space warping
+        if reference == "T1w":
+            logger.debug("Using ANTs for space warping")
+
+            # Get the min of the voxel sizes from input and use it as the
+            # resolution
+            resolution = np.min(input["data"].header.get_zooms()[:3])
+
+            # Create a tempfile for resampled reference output
+            resample_image_out_path = (
+                element_tempdir / "resampled_reference.nii.gz"
+            )
+            # Set ResampleImage command
+            resample_image_cmd = [
+                "ResampleImage",
+                "3",  # image dimension
+                f"{extra_input['T1w']['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 = element_tempdir / "output.nii.gz"
+            # Set antsApplyTransforms command
+            apply_transforms_cmd = [
+                "antsApplyTransforms",
+                "-d 3",
+                "-e 3",
+                "-n LanczosWindowedSinc",
+                f"-i {input['path'].resolve()}",
+                # use resampled reference
+                f"-r {resample_image_out_path.resolve()}",
+                f"-t {extra_input['Warp']['path'].resolve()}",
+                f"-o {apply_transforms_out_path.resolve()}",
+            ]
+            # Call antsApplyTransforms
+            run_ext_cmd(name="antsApplyTransforms", cmd=apply_transforms_cmd)
+
+            # Load nifti
+            input["data"] = nib.load(apply_transforms_out_path)
+            # Save resampled reference path
+            input["reference_path"] = resample_image_out_path
+            # Use reference input's space as warped input's space
+            input["space"] = extra_input["T1w"]["space"]
+
+        # Template space warping
+        else:
+            logger.debug(
+                f"Using ANTs to warp data from {input['space']} to {reference}"
+            )
+
+            # Get xfm file
+            xfm_file_path = get_xfm(src=input["space"], dst=reference)
+            # Get template space image
+            template_space_img = get_template(
+                space=reference,
+                target_data=input,
+                extra_input=None,
+            )
+
+            # Create component-scoped tempdir
+            tempdir = WorkDirManager().get_tempdir(prefix="ants_warper")
+            # Save template
+            template_space_img_path = tempdir / f"{reference}_T1w.nii.gz"
+            nib.save(template_space_img, template_space_img_path)
+
+            # Create a tempfile for warped output
+            warped_output_path = element_tempdir / (
+                f"data_warped_from_{input['space']}_to_" f"{reference}.nii.gz"
+            )
+
+            # 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_output_path.resolve()}",
+            ]
+            # Call antsApplyTransforms
+            run_ext_cmd(name="antsApplyTransforms", cmd=apply_transforms_cmd)
+
+            # Delete tempdir
+            WorkDirManager().delete_tempdir(tempdir)
+
+            # Modify target data
+            input["data"] = nib.load(warped_output_path)
+            input["space"] = reference
+
+        return input

junifer-0.0.4.dev691/junifer/preprocess/warping/_fsl_warper.py

@@ -0,0 +1,109 @@
+"""Provide class for space warping via FSL FLIRT."""
+
+# Authors: Synchon Mandal <s.mandal@fz-juelich.de>
+# License: AGPL
+
+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
+
+
+class FSLWarper:
+    """Class for space warping via FSL FLIRT.
+
+    This class uses FSL FLIRT's ``flirt`` for resampling and ``applywarp`` for
+    transformation.
+
+    """
+
+    _EXT_DEPENDENCIES: ClassVar[List[Dict[str, Union[str, List[str]]]]] = [
+        {
+            "name": "fsl",
+            "commands": ["flirt", "applywarp"],
+        },
+    ]
+
+    _DEPENDENCIES: ClassVar[Set[str]] = {"numpy", "nibabel"}
+
+    def preprocess(
+        self,
+        input: Dict[str, Any],
+        extra_input: Dict[str, Any],
+    ) -> Dict[str, Any]:
+        """Preprocess using FSL.
+
+        Parameters
+        ----------
+        input : dict
+            A single input from the Junifer Data object in which to preprocess.
+        extra_input : dict
+            The other fields in the Junifer Data object. Should have ``T1w``
+            and ``Warp`` data types.
+
+        Returns
+        -------
+        dict
+            The ``input`` dictionary with modified ``data`` and ``space`` key
+            values and new ``reference_path`` key whose value points to the
+            reference file used for warping.
+
+        """
+        logger.debug("Using FSL for space warping")
+
+        # Get the min of the voxel sizes from input and use it as the
+        # resolution
+        resolution = np.min(input["data"].header.get_zooms()[:3])
+
+        # Create element-specific tempdir for storing post-warping assets
+        element_tempdir = WorkDirManager().get_element_tempdir(
+            prefix="fsl_warper"
+        )
+
+        # Create a tempfile for resampled reference output
+        flirt_out_path = element_tempdir / "resampled_reference.nii.gz"
+        # Set flirt command
+        flirt_cmd = [
+            "flirt",
+            "-interp spline",
+            f"-in {extra_input['T1w']['path'].resolve()}",
+            f"-ref {extra_input['T1w']['path'].resolve()}",
+            f"-applyisoxfm {resolution}",
+            f"-out {flirt_out_path.resolve()}",
+        ]
+        # Call flirt
+        run_ext_cmd(name="flirt", cmd=flirt_cmd)
+
+        # Create a tempfile for warped output
+        applywarp_out_path = element_tempdir / "output.nii.gz"
+        # Set applywarp command
+        applywarp_cmd = [
+            "applywarp",
+            "--interp=spline",
+            f"-i {input['path'].resolve()}",
+            f"-r {flirt_out_path.resolve()}",  # use resampled reference
+            f"-w {extra_input['Warp']['path'].resolve()}",
+            f"-o {applywarp_out_path.resolve()}",
+        ]
+        # Call applywarp
+        run_ext_cmd(name="applywarp", cmd=applywarp_cmd)
+
+        # Load nifti
+        input["data"] = nib.load(applywarp_out_path)
+        # Save resampled reference path
+        input["reference_path"] = flirt_out_path
+
+        # Use reference input's space as warped input's space
+        input["space"] = extra_input["T1w"]["space"]
+
+        return input

junifer-0.0.4.dev691/junifer/preprocess/warping/space_warper.py

@@ -0,0 +1,203 @@
+"""Provide class for warping data 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
+
+from templateflow import api as tflow
+
+from ...api.decorators import register_preprocessor
+from ...utils import logger, raise_error
+from ..base import BasePreprocessor
+from ._ants_warper import ANTsWarper
+from ._fsl_warper import FSLWarper
+
+
+__all__ = ["SpaceWarper"]
+
+
+@register_preprocessor
+class SpaceWarper(BasePreprocessor):
+    """Class for warping data to other template spaces.
+
+    Parameters
+    ----------
+    using : {"fsl", "ants"}
+        Implementation to use for warping:
+
+        * "fsl" : Use FSL's ``applywarp``
+        * "ants" : 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"``.
+        Use ``"T1w"`` for native space warping and named templates for
+        template space warping.
+    on : {"T1w", "BOLD", "VBM_GM", "VBM_WM", "fALFF", "GCOR", "LCOR"} or list \
+         of the options
+        The data type to warp.
+
+    Raises
+    ------
+    ValueError
+        If ``using`` is invalid or
+        if ``reference`` is invalid.
+
+    """
+
+    _CONDITIONAL_DEPENDENCIES: ClassVar[List[Dict[str, Union[str, Type]]]] = [
+        {
+            "using": "fsl",
+            "depends_on": FSLWarper,
+        },
+        {
+            "using": "ants",
+            "depends_on": ANTsWarper,
+        },
+    ]
+
+    def __init__(
+        self, using: str, reference: str, on: Union[List[str], 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.reference = reference
+        # Set required data types based on reference and
+        # initialize superclass
+        if self.reference == "T1w":
+            required_data_types = [self.reference, "Warp"]
+            # Listify on
+            if not isinstance(on, list):
+                on = [on]
+            # Extend required data types
+            required_data_types.extend(on)
+
+            super().__init__(
+                on=on,
+                required_data_types=required_data_types,
+            )
+        elif self.reference in tflow.templates():
+            super().__init__(on=on)
+        else:
+            raise_error(f"Unknown reference: {self.reference}")
+
+    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 ["T1w", "BOLD", "VBM_GM", "VBM_WM", "fALFF", "GCOR", "LCOR"]
+
+    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 input from the Junifer Data object.
+        extra_input : dict, optional
+            The other fields in the Junifer Data object.
+
+        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 the data is in the correct space and does not require
+            warping or
+            if FSL is used for template space warping.
+
+        """
+        logger.info(f"Warping to {self.reference} space using SpaceWarper")
+        # Transform to native space
+        if self.using in ["fsl", "ants"] and self.reference == "T1w":
+            # Check for extra inputs
+            if extra_input is None:
+                raise_error(
+                    "No extra input provided, requires `Warp` and "
+                    f"`{self.reference}` data types in particular."
+                )
+            # Conditional preprocessor
+            if self.using == "fsl":
+                input = FSLWarper().preprocess(
+                    input=input,
+                    extra_input=extra_input,
+                )
+            elif self.using == "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
+            if self.reference == input["space"]:
+                raise_error(
+                    (
+                        f"The target data is in {self.reference} space "
+                        "and thus warping will not be performed, hence you "
+                        "should remove the SpaceWarper from the preprocess "
+                        "step."
+                    ),
+                    klass=RuntimeError,
+                )
+
+            input = ANTsWarper().preprocess(
+                input=input,
+                extra_input={},
+                reference=self.reference,
+            )
+        # Transform to template space with FSL not possible
+        elif self.using == "fsl" and self.reference != "T1w":
+            raise_error(
+                (
+                    f"Warping to {self.reference} space not possible with "
+                    "FSL, use ANTs instead."
+                ),
+                klass=RuntimeError,
+            )
+
+        return input, None