junifer 0.0.4.dev517__py3-none-any.whl → 0.0.4.dev530__py3-none-any.whl

junifer/_version.py

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

junifer/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/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/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/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/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/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,

junifer/preprocess/fsl/apply_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 _ApplyWarper(BasePreprocessor):
         pathlib.Path
             The path to the resampled reference image.
 
-        Raises
-        ------
-        RuntimeError
-            If FSL commands fail.
-
         """
         # Get the min of the voxel sizes from input and use it as the
         # resolution
@@ -150,29 +143,7 @@ class _ApplyWarper(BasePreprocessor):
             f"-out {flirt_out_path.resolve()}",
         ]
         # Call flirt
-        flirt_cmd_str = " ".join(flirt_cmd)
-        logger.info(f"flirt command to be executed: {flirt_cmd_str}")
-        flirt_process = subprocess.run(
-            flirt_cmd_str,
-            stdin=subprocess.DEVNULL,
-            stdout=subprocess.PIPE,
-            stderr=subprocess.STDOUT,
-            shell=True,  # needed for respecting $PATH
-            check=False,
-        )
-        if flirt_process.returncode == 0:
-            logger.info(
-                "flirt succeeded with the following output: "
-                f"{flirt_process.stdout}"
-            )
-        else:
-            raise_error(
-                msg="flirt failed with the following error: "
-                f"{flirt_process.stdout}",
-                klass=RuntimeError,
-            )
-
-        # TODO(synchon): Modify reference or not?
+        run_ext_cmd(name="flirt", cmd=flirt_cmd)
 
         # Create a tempfile for warped output
         applywarp_out_path = tempdir / "input_warped.nii.gz"
@@ -186,34 +157,12 @@ class _ApplyWarper(BasePreprocessor):
             f"-o {applywarp_out_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,
-        )
-        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)
 
         # Load nifti
         output_img = nib.load(applywarp_out_path)
 
-        # Stupid casting
-        output_img = cast("Nifti1Image", output_img)
-        return output_img, flirt_out_path
+        return output_img, flirt_out_path  # type: ignore
 
     def preprocess(
         self,

junifer/utils/__init__.py

@@ -6,3 +6,4 @@
 
 from .fs import make_executable
 from .logging import configure_logging, logger, raise_error, warn_with_log
+from .helpers import run_ext_cmd

junifer/utils/helpers.py

@@ -0,0 +1,53 @@
+"""Provide helper functions for the package."""
+
+# Authors: Synchon Mandal <s.mandal@fz-juelich.de>
+# License: AGPL
+
+import subprocess
+from typing import List
+
+from .logging import logger, raise_error
+
+
+def run_ext_cmd(name: str, cmd: List[str]) -> None:
+    """Run external command via subprocess.
+
+    Parameters
+    ----------
+    name : str
+        The name of the command.
+    cmd : list of str
+        The command to run as list of string.
+
+    Raises
+    ------
+    RuntimeError
+        If command fails.
+
+    """
+    # Convert list to str
+    cmd_str = " ".join(cmd)
+    logger.info(f"{name} command to be executed:\n{cmd_str}")
+    # Run command via subprocess
+    process = subprocess.run(
+        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 process.returncode == 0:
+        logger.info(
+            f"{name} command succeeded with the following output:\n"
+            f"{process.stdout}"
+        )
+    else:
+        raise_error(
+            msg=(
+                f"{name} command failed with the following error:\n"
+                f"{process.stdout}"
+            ),
+            klass=RuntimeError,
+        )

junifer/utils/tests/test_helpers.py

@@ -0,0 +1,35 @@
+"""Provide tests for helper functions."""
+
+# Authors: Synchon Mandal <s.mandal@fz-juelich.de>
+# License: AGPL
+
+import logging
+
+import pytest
+
+from junifer.utils.helpers import run_ext_cmd
+
+
+def test_run_ext_cmd_success(caplog: pytest.LogCaptureFixture) -> None:
+    """Test external command run success.
+
+    Parameters
+    ----------
+    caplog : pytest.LogCaptureFixture
+        The pytest.LogCaptureFixture object.
+
+    """
+    # Set log capturing at INFO
+    with caplog.at_level(logging.INFO):
+        # Run external command
+        run_ext_cmd(name="pwd", cmd=["pwd"])
+        # Check logging message
+        assert "executed" in caplog.text
+        assert "succeeded" in caplog.text
+
+
+def test_run_ext_cmd_failure() -> None:
+    """Test external command run failure."""
+    with pytest.raises(RuntimeError, match="failed"):
+        # Run external command
+        run_ext_cmd(name="flymetothemoon", cmd=["flymetothemoon"])

{junifer-0.0.4.dev517.dist-info → junifer-0.0.4.dev530.dist-info}/METADATA

@@ -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.dev517.dist-info → junifer-0.0.4.dev530.dist-info}/RECORD

@@ -1,5 +1,5 @@
 junifer/__init__.py,sha256=x1UR2jUcrUdm2HNl-3Qvyi4UUrU6ms5qm2qcmNY7zZk,391
-junifer/_version.py,sha256=QBJ7nIQfuU9e2GfHlCvw-1zMTxlX-anU-jj0fbWnfiA,428
+junifer/_version.py,sha256=UAZSywn04AiXQwVQkUu_X6dPMnW5TVCTZAN98gzqfqU,428
 junifer/stats.py,sha256=sU5IZ2qFZWbzgSutQS_z42miIVItpSGmQYBn6KkD5fA,6162
 junifer/api/__init__.py,sha256=YILu9M7SC0Ri4CVd90fELH2OnK_gvCYAXCoqBNCFE8E,257
 junifer/api/cli.py,sha256=xScav2mF-Jr8JjVFt8kaHuLpX5l_jVTaQGPgQL3VNvA,12881
@@ -42,9 +42,9 @@ junifer/configs/juseless/datagrabbers/tests/test_ixi_vbm.py,sha256=8jxpNZelXwpJG
 junifer/configs/juseless/datagrabbers/tests/test_ucla.py,sha256=e-jdvcZ9B0mka6_573JJU_cGwSaUV54U8X_n0UadtJY,3351
 junifer/configs/juseless/datagrabbers/tests/test_ukb_vbm.py,sha256=b9hjc1mgO--PSRC3id2EzzfE2yWNsuZ2UI47a6sfGZU,1025
 junifer/data/__init__.py,sha256=oUjOs8_M6fitNb44izxpXf3su1e4pG_vCdjwVYkjZjQ,550
-junifer/data/coordinates.py,sha256=tEZmtrlior0RhM07JyE9Mg2-gWOesnreMcDC51ahBf8,14730
-junifer/data/masks.py,sha256=MINm4u_g6kQPUWtkWfPAPmZTSfgbY1mVkxtzkapkOFc,19767
-junifer/data/parcellations.py,sha256=fAB9Rlcb_NCM-n2lC4CYYD4uUiIfadJ949LL_QNqMV4,58234
+junifer/data/coordinates.py,sha256=GcL95_wzW5t4iNNmRbgD6IwwH-ERMChJK3kWfZ3ORDc,12701
+junifer/data/masks.py,sha256=81v3GhAf9lc_CobV9f6n_vMK1jWZCbeANmopa02XZOQ,17744
+junifer/data/parcellations.py,sha256=72Gv7Rn5Ppyi2z7m9t9cuwS62yocXEL_bG2uoFUyWww,56211
 junifer/data/utils.py,sha256=K9quLIoWRmm2QFM8Rdy_5bYsWb_XhL0l5Uq_1Sie0kA,1274
 junifer/data/VOIs/meta/CogAC_VOIs.txt,sha256=Sr5_E712OLdeQRyUcDNM0wLBvZIyO6gc9Q7KkyJHX1A,398
 junifer/data/VOIs/meta/CogAR_VOIs.txt,sha256=t3NLwEVUZTPP34p15SaB3UInLrQyK-7Qc4iLBuQlZu8,189
@@ -135,7 +135,7 @@ junifer/markers/complexity/tests/test_sample_entropy.py,sha256=3IeDnDgSeFNmUoPxQ
 junifer/markers/complexity/tests/test_weighted_perm_entropy.py,sha256=M7Qt_SFZSmptMi0cBGh5Merd1_3hPieIddl_pz7MWbs,2088
 junifer/markers/falff/__init__.py,sha256=QAUIVtaOFWDL7B8xFrDgsmRum7Q0DCENyDYD1cPMJmM,197
 junifer/markers/falff/falff_base.py,sha256=isHD643TvDFg7YJxpopHSrpJlgUwx2fW0tzJeSio6c8,6323
-junifer/markers/falff/falff_estimator.py,sha256=ayXdQWHUyYyeR7NulOPZpYXkjQ2V8HlbHhy-jDKtZI0,12869
+junifer/markers/falff/falff_estimator.py,sha256=U56sp9wfo5T-MOQN79XSiwj3113x-z8wFIMIwrP5KME,11905
 junifer/markers/falff/falff_parcels.py,sha256=UTADrIl96eO_xZ90LtOIt7tuN2eLDPnfIJghr9HAO88,4550
 junifer/markers/falff/falff_spheres.py,sha256=XR2pcBRxjyTZ-J7j_HOjL20_2IHgYO0dI9x4LlQFoVE,5086
 junifer/markers/falff/tests/test_falff_estimator.py,sha256=aVnkFvPqA5mTb9dXegwAJPku8Tf-1jWtDkfXhdcjDj8,8259
@@ -156,7 +156,7 @@ junifer/markers/functional_connectivity/tests/test_functional_connectivity_parce
 junifer/markers/functional_connectivity/tests/test_functional_connectivity_spheres.py,sha256=KOaMkLf7CEd1H8A92WpZAy6X6VNf6TADzYqsqXqvV4Q,4278
 junifer/markers/reho/__init__.py,sha256=9IfeAxKEVgMWbhud-8T54Le07I4pR6A29sMKeFtvEPg,189
 junifer/markers/reho/reho_base.py,sha256=d6oxynZ41EGd7f3zorRww6vMtFYF0PjD6RdAVlLq9BA,3932
-junifer/markers/reho/reho_estimator.py,sha256=88Ki-Ysq7MfmODynA_wk-7tvYdggmB_Z5HDa3gaZeoM,19692
+junifer/markers/reho/reho_estimator.py,sha256=vLGQDBs9QMT7E7Oc9e8Jz70CScQ9JmlrDdxbEMAz8WA,17996
 junifer/markers/reho/reho_parcels.py,sha256=Q-gkB9aO0ncxgEQ68XEQKekpLLu_kXiYC6Xqkv8cdvY,6048
 junifer/markers/reho/reho_spheres.py,sha256=ng5JzYorEnYmFVlxRMOMwkLNFsq2FlMN4o95B_BBVo0,6565
 junifer/markers/reho/tests/test_reho_estimator.py,sha256=V_584X3I5a-XXAIs8YtR4TMuSqhMvGd5E1vcoDj8gQA,10168
@@ -193,13 +193,13 @@ junifer/preprocess/__init__.py,sha256=-3exohZnw-gJ-MjVM63WcXzBW1mbSetEVozcDfs5et
 junifer/preprocess/base.py,sha256=syiNqI8pUjoGyShZSjs_RTsd5VHhwoqzIfPfFstr4f4,6230
 junifer/preprocess/bold_warper.py,sha256=KOYCPCTJE92yI1juXK-3yl7VUxUhbzqqQxJrCYgk-0E,4572
 junifer/preprocess/ants/__init__.py,sha256=Uobmbhh6_gOowkF2hQNSQOh3AYeaXzarBXEcLJzhERE,112
-junifer/preprocess/ants/ants_apply_transforms_warper.py,sha256=BWXurnmQeeRjfrHUjtVqgofKe9migd6yQsyXC643Yxk,8537
+junifer/preprocess/ants/ants_apply_transforms_warper.py,sha256=V3y9EIGdIeJhJpnEVi123fHTK3R0sv_-OmWY7R_DC1M,6627
 junifer/preprocess/ants/tests/test_ants_apply_transforms_warper.py,sha256=ibLLISss0o0wg3lqpLhL1oO7MfU_bZF5PBqY3OOd9sg,3737
 junifer/preprocess/confounds/__init__.py,sha256=EDlcD9jy8O9xluJr6XOnFXtjGCDVqwg6sDIRDMbM8ZU,235
 junifer/preprocess/confounds/fmriprep_confound_remover.py,sha256=23UJ6miqX0iE3dUMsZ1hzWoJDnMLl6WMlT-k9GFmAAU,21904
 junifer/preprocess/confounds/tests/test_fmriprep_confound_remover.py,sha256=OKACXAHytNrOAFZ5I2UcyfcYz5s2qeu31MZ9K71rWGc,22167
 junifer/preprocess/fsl/__init__.py,sha256=DerGFQ-dIuX5PT9a_BH6QkIXkJZVymjYy-woXF7tYGc,111
-junifer/preprocess/fsl/apply_warper.py,sha256=sUCH06fSIFHp9cOMdlzICOGqo7p0ABjjoPmLbTtZO54,7924
+junifer/preprocess/fsl/apply_warper.py,sha256=_HU1-63A32cSQw9eNdgpKN52BFivn6cZaDa0_at-4UY,6215
 junifer/preprocess/fsl/tests/test_apply_warper.py,sha256=b--MMPlaJw284gJWw-QV8rz6Rb2zmcBjYaY-cb6-uNU,3024
 junifer/preprocess/tests/test_bold_warper.py,sha256=X4rs-IBu_Oe9wF81Xlh6ih9BCu8SUyDm64lXKk-l9Q8,2831
 junifer/preprocess/tests/test_preprocess_base.py,sha256=UHuH_YOK7AU3AfApWqgB6YLG-J669BgztuxNSWCtmtI,2560
@@ -225,15 +225,17 @@ junifer/testing/tests/test_spmauditory_datagrabber.py,sha256=1G1emk-Ze59HiNLaYsy
 junifer/testing/tests/test_testing_registry.py,sha256=oerticBaPRaRZm3yANzInLac0Mqph3Y0aZPQFayu7xA,827
 junifer/tests/test_main.py,sha256=GMff7jlisGM9_FsiUwWDte43j-KQJGFRYZpwRRqTkd8,373
 junifer/tests/test_stats.py,sha256=3vPMgYYpWxk8ECDFOMm3-dFBlh4XxjL83SwRBSBAHok,4155
-junifer/utils/__init__.py,sha256=ZDPU9ezSKawAJhb-3T67jDf-16QEyF6e7ONyu-lnBtQ,277
+junifer/utils/__init__.py,sha256=sFpsDKbPPtoU3Db3OSO9Vo45u4yE7UfocNaBtD-qvdk,310
 junifer/utils/fs.py,sha256=Jd9AoV2fIF7pT7KhXsn8T1O1fJ1_SFZgaFuOBAM7DG8,460
+junifer/utils/helpers.py,sha256=Hp3yGZa9x659BCqFTd4keEU1gbHXNAbJ1_lHG1M6lwI,1338
 junifer/utils/logging.py,sha256=4kH8j9X_J2bMdnBJMldVF95C5sURa5UAsLmSgRaD9Ig,9117
 junifer/utils/tests/test_fs.py,sha256=WQS7cKlKEZ742CIuiOYYpueeAhY9PqlastfDVpVVtvE,923
+junifer/utils/tests/test_helpers.py,sha256=k5qqfxK8dFyuewTJyR1Qn6-nFaYNuVr0ysc18bfPjyU,929
 junifer/utils/tests/test_logging.py,sha256=l8oo-AiBV7H6_IzlsNcj__cLeZBUvgIGoaMszD9VaJg,7754
-junifer-0.0.4.dev517.dist-info/AUTHORS.rst,sha256=rmULKpchpSol4ExWFdm-qu4fkpSZPYqIESVJBZtGb6E,163
-junifer-0.0.4.dev517.dist-info/LICENSE.md,sha256=MqCnOBu8uXsEOzRZWh9EBVfVz-kE9NkXcLCrtGXo2yU,34354
-junifer-0.0.4.dev517.dist-info/METADATA,sha256=RzDBLpqCrGN-QuGdRMQThJ37K9uGxPXJa2H8TZXGufw,7745
-junifer-0.0.4.dev517.dist-info/WHEEL,sha256=oiQVh_5PnQM0E3gPdiz09WCNmwiHDMaGer_elqB3coM,92
-junifer-0.0.4.dev517.dist-info/entry_points.txt,sha256=DxFvKq0pOqRunAK0FxwJcoDfV1-dZvsFDpD5HRqSDhw,48
-junifer-0.0.4.dev517.dist-info/top_level.txt,sha256=4bAq1R2QFQ4b3hohjys2JBvxrl0GKk5LNFzYvz9VGcA,8
-junifer-0.0.4.dev517.dist-info/RECORD,,
+junifer-0.0.4.dev530.dist-info/AUTHORS.rst,sha256=rmULKpchpSol4ExWFdm-qu4fkpSZPYqIESVJBZtGb6E,163
+junifer-0.0.4.dev530.dist-info/LICENSE.md,sha256=MqCnOBu8uXsEOzRZWh9EBVfVz-kE9NkXcLCrtGXo2yU,34354
+junifer-0.0.4.dev530.dist-info/METADATA,sha256=7NtLR9A6bZqYUGw4dYhUS1oA3Bj-r1dEKbz85m560Y4,7745
+junifer-0.0.4.dev530.dist-info/WHEEL,sha256=oiQVh_5PnQM0E3gPdiz09WCNmwiHDMaGer_elqB3coM,92
+junifer-0.0.4.dev530.dist-info/entry_points.txt,sha256=DxFvKq0pOqRunAK0FxwJcoDfV1-dZvsFDpD5HRqSDhw,48
+junifer-0.0.4.dev530.dist-info/top_level.txt,sha256=4bAq1R2QFQ4b3hohjys2JBvxrl0GKk5LNFzYvz9VGcA,8
+junifer-0.0.4.dev530.dist-info/RECORD,,