junifer 0.0.4.dev517__tar.gz → 0.0.4.dev530__tar.gz

{junifer-0.0.4.dev517 → junifer-0.0.4.dev530}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: junifer
-Version: 0.0.4.dev517
+Version: 0.0.4.dev530
 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.dev530/docs/changes/newsfragments/295.feature

@@ -0,0 +1 @@
+Introduce :func:`.run_ext_cmd` to take care of the boilerplate code for running external commands from FSL, ANTs and others by `Synchon Mandal`_

{junifer-0.0.4.dev517 → junifer-0.0.4.dev530}/junifer/_version.py

@@ -12,5 +12,5 @@ __version__: str
 __version_tuple__: VERSION_TUPLE
 version_tuple: VERSION_TUPLE
 
-__version__ = version = '0.0.4.dev517'
-__version_tuple__ = version_tuple = (0, 0, 4, 'dev517')
+__version__ = version = '0.0.4.dev530'
+__version_tuple__ = version_tuple = (0, 0, 4, 'dev530')

{junifer-0.0.4.dev517 → junifer-0.0.4.dev530}/junifer/data/coordinates.py

@@ -4,7 +4,6 @@
 #          Synchon Mandal <s.mandal@fz-juelich.de>
 # License: AGPL
 
-import subprocess
 import typing
 from pathlib import Path
 from typing import Any, Dict, List, Optional, Tuple, Union
@@ -14,7 +13,7 @@ import pandas as pd
 from numpy.typing import ArrayLike
 
 from ..pipeline import WorkDirManager
-from ..utils.logging import logger, raise_error, warn_with_log
+from ..utils import logger, raise_error, run_ext_cmd, warn_with_log
 
 
 # Path to the VOIs
@@ -231,6 +230,8 @@ def get_coordinates(
 
     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.
 
@@ -286,30 +287,7 @@ def get_coordinates(
                 f"sed -i 1d {transformed_coords_path.resolve()}",
             ]
             # Call img2imgcoord
-            img2imgcoord_cmd_str = " ".join(img2imgcoord_cmd)
-            logger.info(
-                f"img2imgcoord command to be executed: {img2imgcoord_cmd_str}"
-            )
-            img2imgcoord_process = subprocess.run(
-                img2imgcoord_cmd_str,  # string needed with shell=True
-                stdin=subprocess.DEVNULL,
-                stdout=subprocess.PIPE,
-                stderr=subprocess.STDOUT,
-                shell=True,  # needed for respecting $PATH
-                check=False,
-            )
-            # Check for success or failure
-            if img2imgcoord_process.returncode == 0:
-                logger.info(
-                    "img2imgcoord succeeded with the following output: "
-                    f"{img2imgcoord_process.stdout}"
-                )
-            else:
-                raise_error(
-                    msg="img2imgcoord failed with the following error: "
-                    f"{img2imgcoord_process.stdout}",
-                    klass=RuntimeError,
-                )
+            run_ext_cmd(name="img2imgcoord", cmd=img2imgcoord_cmd)
 
             # Load coordinates
             seeds = np.loadtxt(transformed_coords_path)
@@ -345,36 +323,10 @@ def get_coordinates(
                 f"-t {extra_input['Warp']['path'].resolve()};",
             ]
             # Call antsApplyTransformsToPoints
-            apply_transforms_to_points_cmd_str = " ".join(
-                apply_transforms_to_points_cmd
-            )
-            logger.info(
-                "antsApplyTransformsToPoints command to be executed: "
-                f"{apply_transforms_to_points_cmd_str}"
-            )
-            apply_transforms_to_points_process = subprocess.run(
-                # string needed with shell=True
-                apply_transforms_to_points_cmd_str,
-                stdin=subprocess.DEVNULL,
-                stdout=subprocess.PIPE,
-                stderr=subprocess.STDOUT,
-                shell=True,  # needed for respecting $PATH
-                check=False,
+            run_ext_cmd(
+                name="antsApplyTransformsToPoints",
+                cmd=apply_transforms_to_points_cmd,
             )
-            if apply_transforms_to_points_process.returncode == 0:
-                logger.info(
-                    "antsApplyTransformsToPoints succeeded with the following "
-                    f"output: {apply_transforms_to_points_process.stdout}"
-                )
-            else:
-                raise_error(
-                    msg=(
-                        "antsApplyTransformsToPoints failed with the "
-                        "following error: "
-                        f"{apply_transforms_to_points_process.stdout}"
-                    ),
-                    klass=RuntimeError,
-                )
 
             # Load coordinates
             seeds = np.loadtxt(

{junifer-0.0.4.dev517 → junifer-0.0.4.dev530}/junifer/data/masks.py

@@ -4,7 +4,6 @@
 #          Synchon Mandal <s.mandal@fz-juelich.de>
 # License: AGPL
 
-import subprocess
 import typing
 from pathlib import Path
 from typing import (
@@ -30,7 +29,7 @@ from nilearn.masking import (
 )
 
 from ..pipeline import WorkDirManager
-from ..utils.logging import logger, raise_error
+from ..utils import logger, raise_error, run_ext_cmd
 from .utils import closest_resolution
 
 
@@ -201,8 +200,7 @@ def get_mask(  # noqa: C901
     RuntimeError
         If masks are in different spaces and they need to be intersected /
         unionized or
-        if warp / transformation file extension is not ".mat" or ".h5" or
-        if external tool execution failed.
+        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
@@ -384,30 +382,8 @@ def get_mask(  # noqa: C901
                 f"-o {warped_mask_path.resolve()}",
             ]
             # Call applywarp
-            applywarp_cmd_str = " ".join(applywarp_cmd)
-            logger.info(
-                f"applywarp command to be executed: {applywarp_cmd_str}"
-            )
-            applywarp_process = subprocess.run(
-                applywarp_cmd_str,  # string needed with shell=True
-                stdin=subprocess.DEVNULL,
-                stdout=subprocess.PIPE,
-                stderr=subprocess.STDOUT,
-                shell=True,  # needed for respecting $PATH
-                check=False,
-            )
-            # Check for success or failure
-            if applywarp_process.returncode == 0:
-                logger.info(
-                    "applywarp succeeded with the following output: "
-                    f"{applywarp_process.stdout}"
-                )
-            else:
-                raise_error(
-                    msg="applywarp failed with the following error: "
-                    f"{applywarp_process.stdout}",
-                    klass=RuntimeError,
-                )
+            run_ext_cmd(name="applywarp", cmd=applywarp_cmd)
+
         elif warp_file_ext == ".h5":
             logger.debug("Using ANTs for mask warping")
             # Set antsApplyTransforms command
@@ -423,32 +399,8 @@ def get_mask(  # noqa: C901
                 f"-o {warped_mask_path.resolve()}",
             ]
             # Call antsApplyTransforms
-            apply_transforms_cmd_str = " ".join(apply_transforms_cmd)
-            logger.info(
-                "antsApplyTransforms command to be executed: "
-                f"{apply_transforms_cmd_str}"
-            )
-            apply_transforms_process = subprocess.run(
-                apply_transforms_cmd_str,  # string needed with shell=True
-                stdin=subprocess.DEVNULL,
-                stdout=subprocess.PIPE,
-                stderr=subprocess.STDOUT,
-                shell=True,  # needed for respecting $PATH
-                check=False,
-            )
-            if apply_transforms_process.returncode == 0:
-                logger.info(
-                    "antsApplyTransforms succeeded with the following output: "
-                    f"{apply_transforms_process.stdout}"
-                )
-            else:
-                raise_error(
-                    msg=(
-                        "antsApplyTransforms failed with the following error: "
-                        f"{apply_transforms_process.stdout}"
-                    ),
-                    klass=RuntimeError,
-                )
+            run_ext_cmd(name="antsApplyTransforms", cmd=apply_transforms_cmd)
+
         else:
             raise_error(
                 msg=(

{junifer-0.0.4.dev517 → junifer-0.0.4.dev530}/junifer/data/parcellations.py

@@ -7,7 +7,6 @@
 
 import io
 import shutil
-import subprocess
 import tarfile
 import tempfile
 import typing
@@ -23,7 +22,7 @@ from nilearn import datasets, image
 from requests.exceptions import ConnectionError, HTTPError, ReadTimeout
 
 from ..pipeline import WorkDirManager
-from ..utils.logging import logger, raise_error, warn_with_log
+from ..utils import logger, raise_error, run_ext_cmd, warn_with_log
 from .utils import closest_resolution
 
 
@@ -232,8 +231,7 @@ def get_parcellation(
     ------
     RuntimeError
         If parcellations are in different spaces and they need to be merged or
-        if warp / transformation file extension is not ".mat" or ".h5" or
-        if external tool execution failed.
+        if warp / transformation file extension is not ".mat" or ".h5".
     ValueError
         If ``extra_input`` is None when ``target_data``'s space is native.
 
@@ -324,30 +322,8 @@ def get_parcellation(
                 f"-o {warped_parcellation_path.resolve()}",
             ]
             # Call applywarp
-            applywarp_cmd_str = " ".join(applywarp_cmd)
-            logger.info(
-                f"applywarp command to be executed: {applywarp_cmd_str}"
-            )
-            applywarp_process = subprocess.run(
-                applywarp_cmd_str,  # string needed with shell=True
-                stdin=subprocess.DEVNULL,
-                stdout=subprocess.PIPE,
-                stderr=subprocess.STDOUT,
-                shell=True,  # needed for respecting $PATH
-                check=False,
-            )
-            # Check for success or failure
-            if applywarp_process.returncode == 0:
-                logger.info(
-                    "applywarp succeeded with the following output: "
-                    f"{applywarp_process.stdout}"
-                )
-            else:
-                raise_error(
-                    msg="applywarp failed with the following error: "
-                    f"{applywarp_process.stdout}",
-                    klass=RuntimeError,
-                )
+            run_ext_cmd(name="applywarp", cmd=applywarp_cmd)
+
         elif warp_file_ext == ".h5":
             logger.debug("Using ANTs for parcellation warping")
             # Set antsApplyTransforms command
@@ -363,32 +339,8 @@ def get_parcellation(
                 f"-o {warped_parcellation_path.resolve()}",
             ]
             # Call antsApplyTransforms
-            apply_transforms_cmd_str = " ".join(apply_transforms_cmd)
-            logger.info(
-                "antsApplyTransforms command to be executed: "
-                f"{apply_transforms_cmd_str}"
-            )
-            apply_transforms_process = subprocess.run(
-                apply_transforms_cmd_str,  # string needed with shell=True
-                stdin=subprocess.DEVNULL,
-                stdout=subprocess.PIPE,
-                stderr=subprocess.STDOUT,
-                shell=True,  # needed for respecting $PATH
-                check=False,
-            )
-            if apply_transforms_process.returncode == 0:
-                logger.info(
-                    "antsApplyTransforms succeeded with the following output: "
-                    f"{apply_transforms_process.stdout}"
-                )
-            else:
-                raise_error(
-                    msg=(
-                        "antsApplyTransforms failed with the following error: "
-                        f"{apply_transforms_process.stdout}"
-                    ),
-                    klass=RuntimeError,
-                )
+            run_ext_cmd(name="antsApplyTransforms", cmd=apply_transforms_cmd)
+
         else:
             raise_error(
                 msg=(

{junifer-0.0.4.dev517 → junifer-0.0.4.dev530}/junifer/markers/falff/falff_estimator.py

@@ -4,11 +4,10 @@
 #          Federico Raimondo <f.raimondo@fz-juelich.de>
 # License: AGPL
 
-import subprocess
 import typing
 from functools import lru_cache
 from pathlib import Path
-from typing import TYPE_CHECKING, Any, Dict, Optional, Tuple, Union, cast
+from typing import TYPE_CHECKING, Any, Dict, Optional, Tuple, Union
 
 import nibabel as nib
 import numpy as np
@@ -17,7 +16,7 @@ from scipy.fft import fft, fftfreq
 
 from ...pipeline import WorkDirManager
 from ...pipeline.singleton import singleton
-from ...utils import logger, raise_error
+from ...utils import logger, run_ext_cmd
 
 
 if TYPE_CHECKING:
@@ -54,42 +53,6 @@ class ALFFEstimator:
         if self.temp_dir_path is not None:
             WorkDirManager().delete_tempdir(self.temp_dir_path)
 
-    @staticmethod
-    def _run_afni_cmd(cmd: str) -> None:
-        """Run AFNI command.
-
-        Parameters
-        ----------
-        cmd : str
-            AFNI command to be executed.
-
-        Raises
-        ------
-        RuntimeError
-            If AFNI command fails.
-
-        """
-        logger.info(f"AFNI command to be executed: {cmd}")
-        process = subprocess.run(
-            cmd,
-            stdin=subprocess.DEVNULL,
-            stdout=subprocess.PIPE,
-            stderr=subprocess.STDOUT,
-            shell=True,
-            check=False,
-        )
-        if process.returncode == 0:
-            logger.info(
-                "AFNI command succeeded with the following output: "
-                f"{process.stdout}"
-            )
-        else:
-            raise_error(
-                msg="AFNI command failed with the following error: "
-                f"{process.stdout}",
-                klass=RuntimeError,
-            )
-
     def _compute_alff_afni(
         self,
         data: Union["Nifti1Image", "Nifti2Image"],
@@ -121,11 +84,6 @@ class ALFFEstimator:
         pathlib.Path
             The path to the fALFF map as NIfTI.
 
-        Raises
-        ------
-        RuntimeError
-            If the AFNI commands fails due to some issues.
-
         """
         # Note: self.temp_dir_path is sure to exist before proceeding, so
         #       types checks are ignored further on.
@@ -150,31 +108,36 @@ class ALFFEstimator:
             self.temp_dir_path / "temp_falff"  # type: ignore
         )
 
-        bp_cmd = (
-            "3dRSFC "
-            f"-prefix {falff_afni_out_path_prefix.resolve()} "
-            f"-input {nifti_in_file_path.resolve()} "
-            f"-band {highpass} {lowpass} "
-            "-no_rsfa -nosat -nodetrend "
-        )
+        # Set 3dRSFC command
+        bp_cmd = [
+            "3dRSFC",
+            f"-prefix {falff_afni_out_path_prefix.resolve()}",
+            f"-input {nifti_in_file_path.resolve()}",
+            f"-band {highpass} {lowpass}",
+            "-no_rsfa -nosat -nodetrend",
+        ]
         if tr is not None:
-            bp_cmd += f"-dt {tr} "
-        self._run_afni_cmd(bp_cmd)
-
-        # Convert afni's output to nifti
-        convert_cmd = (
-            "3dAFNItoNIFTI "
-            f"-prefix {alff_fname.resolve()} "
-            f"{falff_afni_out_path_prefix}_ALFF+tlrc.BRIK "
-        )
-        self._run_afni_cmd(convert_cmd)
-
-        convert_cmd = (
-            "3dAFNItoNIFTI "
-            f"-prefix {falff_fname.resolve()} "
-            f"{falff_afni_out_path_prefix}_fALFF+tlrc.BRIK "
-        )
-        self._run_afni_cmd(convert_cmd)
+            bp_cmd.append(f"-dt {tr}")
+        # Call 3dRSFC
+        run_ext_cmd(name="3dRSFC", cmd=bp_cmd)
+
+        # Convert alff output to nifti
+        convert_alff_cmd = [
+            "3dAFNItoNIFTI",
+            f"-prefix {alff_fname.resolve()}",
+            f"{falff_afni_out_path_prefix}_ALFF+tlrc.BRIK",
+        ]
+        # Call 3dAFNItoNIFTI
+        run_ext_cmd(name="3dAFNItoNIFTI", cmd=convert_alff_cmd)
+
+        # Convert falff output to nifti
+        convert_falff_cmd = [
+            "3dAFNItoNIFTI",
+            f"-prefix {falff_fname.resolve()}",
+            f"{falff_afni_out_path_prefix}_fALFF+tlrc.BRIK",
+        ]
+        # Call 3dAFNItoNIFTI
+        run_ext_cmd(name="3dAFNItoNIFTI", cmd=convert_falff_cmd)
 
         # Cleanup intermediate files
         for fname in self.temp_dir_path.glob("temp_*"):  # type: ignore
@@ -183,10 +146,8 @@ class ALFFEstimator:
         # Load niftis
         alff_img = nib.load(alff_fname)
         falff_img = nib.load(falff_fname)
-        # Cast image type
-        alff_img = cast("Nifti1Image", alff_img)
-        falff_img = cast("Nifti1Image", falff_img)
-        return alff_img, falff_img, alff_fname, falff_fname
+
+        return alff_img, falff_img, alff_fname, falff_fname  # type: ignore
 
     def _compute_alff_python(
         self,

{junifer-0.0.4.dev517 → junifer-0.0.4.dev530}/junifer/markers/reho/reho_estimator.py

@@ -6,11 +6,10 @@
 
 
 import hashlib
-import subprocess
 from functools import lru_cache
 from itertools import product
 from pathlib import Path
-from typing import TYPE_CHECKING, Any, Dict, List, Optional, Tuple, cast
+from typing import TYPE_CHECKING, Any, Dict, List, Optional, Tuple
 
 import nibabel as nib
 import numpy as np
@@ -20,7 +19,7 @@ from scipy.stats import rankdata
 
 from ...pipeline import WorkDirManager
 from ...pipeline.singleton import singleton
-from ...utils import logger, raise_error
+from ...utils import logger, raise_error, run_ext_cmd
 
 
 if TYPE_CHECKING:
@@ -112,11 +111,6 @@ class ReHoEstimator:
         pathlib.Path
             The path to the ReHo map as NIfTI.
 
-        Raises
-        ------
-        RuntimeError
-            If the 3dReHo command fails due to some issue.
-
         Notes
         -----
         For more information on the publication, please check [1]_ , and for
@@ -174,30 +168,10 @@ class ReHoEstimator:
         else:
             reho_cmd.append(f"-nneigh {nneigh}")
         # Call 3dReHo
-        reho_cmd_str = " ".join(reho_cmd)
-        logger.info(f"3dReHo command to be executed: {reho_cmd_str}")
-        reho_process = subprocess.run(
-            reho_cmd_str,  # string needed with shell=True
-            stdin=subprocess.DEVNULL,
-            stdout=subprocess.PIPE,
-            stderr=subprocess.STDOUT,
-            shell=True,  # needed for respecting $PATH
-            check=False,
-        )
-        if reho_process.returncode == 0:
-            logger.info(
-                "3dReHo succeeded with the following output: "
-                f"{reho_process.stdout}"
-            )
-        else:
-            raise_error(
-                msg="3dReHo failed with the following error: "
-                f"{reho_process.stdout}",
-                klass=RuntimeError,
-            )
+        run_ext_cmd(name="3dReHo", cmd=reho_cmd)
 
         # SHA256 for bypassing memmap
-        sha256_params = hashlib.sha256(bytes(reho_cmd_str, "utf-8"))
+        sha256_params = hashlib.sha256(bytes(" ".join(reho_cmd), "utf-8"))
         # Create element-scoped tempdir so that the ReHo map is
         # available later as get_coordinates and the like need it
         # in ReHoSpheres and the like to transform to other template
@@ -216,27 +190,7 @@ class ReHoEstimator:
             f"{reho_afni_out_path_prefix}+tlrc.BRIK",
         ]
         # Call 3dAFNItoNIFTI
-        convert_cmd_str = " ".join(convert_cmd)
-        logger.info(f"3dAFNItoNIFTI command to be executed: {convert_cmd_str}")
-        convert_process = subprocess.run(
-            convert_cmd_str,  # string needed with shell=True
-            stdin=subprocess.DEVNULL,
-            stdout=subprocess.PIPE,
-            stderr=subprocess.STDOUT,
-            shell=True,  # needed for respecting $PATH
-            check=False,
-        )
-        if convert_process.returncode == 0:
-            logger.info(
-                "3dAFNItoNIFTI succeeded with the following output: "
-                f"{convert_process.stdout}"
-            )
-        else:
-            raise_error(
-                msg="3dAFNItoNIFTI failed with the following error: "
-                f"{convert_process.stdout}",
-                klass=RuntimeError,
-            )
+        run_ext_cmd(name="3dAFNItoNIFTI", cmd=convert_cmd)
 
         # Cleanup intermediate files
         for fname in self.temp_dir_path.glob("reho*"):  # type: ignore
@@ -244,9 +198,8 @@ class ReHoEstimator:
 
         # Load nifti
         output_data = nib.load(reho_afni_to_nifti_out_path)
-        # Stupid casting
-        output_data = cast("Nifti1Image", output_data)
-        return output_data, reho_afni_to_nifti_out_path
+
+        return output_data, reho_afni_to_nifti_out_path  # type: ignore
 
     def _compute_reho_python(
         self,

{junifer-0.0.4.dev517 → junifer-0.0.4.dev530}/junifer/preprocess/ants/ants_apply_transforms_warper.py

@@ -3,7 +3,6 @@
 # Authors: Synchon Mandal <s.mandal@fz-juelich.de>
 # License: AGPL
 
-import subprocess
 from pathlib import Path
 from typing import (
     TYPE_CHECKING,
@@ -14,14 +13,13 @@ from typing import (
     Optional,
     Tuple,
     Union,
-    cast,
 )
 
 import nibabel as nib
 import numpy as np
 
 from ...pipeline import WorkDirManager
-from ...utils import logger, raise_error
+from ...utils import logger, raise_error, run_ext_cmd
 from ..base import BasePreprocessor
 
 
@@ -125,11 +123,6 @@ class _AntsApplyTransformsWarper(BasePreprocessor):
         pathlib.Path
             The path to the resampled reference image.
 
-        Raises
-        ------
-        RuntimeError
-            If ANTs command fails.
-
         """
         # Get the min of the voxel sizes from input and use it as the
         # resolution
@@ -153,29 +146,7 @@ class _AntsApplyTransformsWarper(BasePreprocessor):
             "3 3",  # Lanczos windowed sinc
         ]
         # Call ResampleImage
-        resample_image_cmd_str = " ".join(resample_image_cmd)
-        logger.info(
-            f"ResampleImage command to be executed: {resample_image_cmd_str}"
-        )
-        resample_image_process = subprocess.run(
-            resample_image_cmd_str,
-            stdin=subprocess.DEVNULL,
-            stdout=subprocess.PIPE,
-            stderr=subprocess.STDOUT,
-            shell=True,  # needed for respecting $PATH
-            check=False,
-        )
-        if resample_image_process.returncode == 0:
-            logger.info(
-                "ResampleImage succeeded with the following output: "
-                f"{resample_image_process.stdout}"
-            )
-        else:
-            raise_error(
-                msg="ResampleImage failed with the following error: "
-                f"{resample_image_process.stdout}",
-                klass=RuntimeError,
-            )
+        run_ext_cmd(name="ResampleImage", cmd=resample_image_cmd)
 
         # Create a tempfile for warped output
         apply_transforms_out_path = tempdir / "input_warped.nii.gz"
@@ -192,39 +163,12 @@ class _AntsApplyTransformsWarper(BasePreprocessor):
             f"-o {apply_transforms_out_path.resolve()}",
         ]
         # Call antsApplyTransforms
-        apply_transforms_cmd_str = " ".join(apply_transforms_cmd)
-        logger.info(
-            "antsApplyTransforms command to be executed: "
-            f"{apply_transforms_cmd_str}"
-        )
-        apply_transforms_process = subprocess.run(
-            apply_transforms_cmd_str,  # string needed with shell=True
-            stdin=subprocess.DEVNULL,
-            stdout=subprocess.PIPE,
-            stderr=subprocess.STDOUT,
-            shell=True,  # needed for respecting $PATH
-            check=False,
-        )
-        if apply_transforms_process.returncode == 0:
-            logger.info(
-                "antsApplyTransforms succeeded with the following output: "
-                f"{apply_transforms_process.stdout}"
-            )
-        else:
-            raise_error(
-                msg=(
-                    "antsApplyTransforms failed with the following error: "
-                    f"{apply_transforms_process.stdout}"
-                ),
-                klass=RuntimeError,
-            )
+        run_ext_cmd(name="antsApplyTransforms", cmd=apply_transforms_cmd)
 
         # Load nifti
         output_img = nib.load(apply_transforms_out_path)
 
-        # Stupid casting
-        output_img = cast("Nifti1Image", output_img)
-        return output_img, resample_image_out_path
+        return output_img, resample_image_out_path  # type: ignore
 
     def preprocess(
         self,