junifer 0.0.5.dev39__py3-none-any.whl → 0.0.5.dev48__py3-none-any.whl

junifer/_version.py

@@ -12,5 +12,5 @@ __version__: str
 __version_tuple__: VERSION_TUPLE
 version_tuple: VERSION_TUPLE
 
-__version__ = version = '0.0.5.dev39'
-__version_tuple__ = version_tuple = (0, 0, 5, 'dev39')
+__version__ = version = '0.0.5.dev48'
+__version_tuple__ = version_tuple = (0, 0, 5, 'dev48')

junifer/api/functions.py

@@ -5,6 +5,7 @@
 #          Synchon Mandal <s.mandal@fz-juelich.de>
 # License: AGPL
 
+import os
 import shutil
 import typing
 from pathlib import Path
@@ -339,12 +340,12 @@ def reset(config: Dict) -> None:
     storage = config["storage"]
     storage_uri = Path(storage["uri"])
     logger.info(f"Deleting {storage_uri.resolve()!s}")
-    # Delete storage; will be str
+    # Delete storage
     if storage_uri.exists():
-        # Delete files in the directory
-        for file in storage_uri.iterdir():
+        # Delete files in the job storage directory
+        for file in storage_uri.parent.iterdir():
             file.unlink(missing_ok=True)
-        # Remove directory
+        # Remove job storage directory
         storage_uri.parent.rmdir()
 
     # Fetch job name (if present)
@@ -359,8 +360,9 @@ def reset(config: Dict) -> None:
         if job_dir.exists():
             # Remove files and directories
             shutil.rmtree(job_dir)
-            # Remove directory
-            job_dir.parent.rmdir()
+            # Remove parent directory (if empty)
+            if not next(os.scandir(job_dir.parent), None):
+                job_dir.parent.rmdir()        
 
 
 def list_elements(

junifer/data/coordinates.py

@@ -13,7 +13,7 @@ import pandas as pd
 from numpy.typing import ArrayLike
 
 from ..pipeline import WorkDirManager
-from ..utils import logger, raise_error, run_ext_cmd, warn_with_log
+from ..utils import logger, raise_error, run_ext_cmd
 
 
 # Path to the VOIs
@@ -377,11 +377,6 @@ def load_coordinates(name: str) -> Tuple[ArrayLike, List[str], str]:
     ValueError
         If ``name`` is invalid.
 
-    Warns
-    -----
-    DeprecationWarning
-        If ``Power`` is provided as the ``name``.
-
     """
     # Check for valid coordinates name
     if name not in _available_coordinates:
@@ -389,18 +384,6 @@ def load_coordinates(name: str) -> Tuple[ArrayLike, List[str], str]:
             f"Coordinates {name} not found. "
             f"Valid options are: {list_coordinates()}"
         )
-
-    # Put up deprecation notice
-    if name == "Power":
-        warn_with_log(
-            msg=(
-                "`Power` has been replaced with `Power2011` and will be "
-                "removed in the next release. For now, it's available for "
-                "backward compatibility."
-            ),
-            category=DeprecationWarning,
-        )
-
     # Load coordinates
     t_coord = _available_coordinates[name]
     if isinstance(t_coord.get("path"), Path):

junifer/data/masks.py

@@ -19,7 +19,6 @@ from typing import (
 
 import nibabel as nib
 import numpy as np
-from nilearn.datasets import fetch_icbm152_brain_gm_mask
 from nilearn.image import get_data, new_img_like, resample_to_img
 from nilearn.masking import (
     compute_background_mask,
@@ -28,7 +27,7 @@ from nilearn.masking import (
 )
 
 from ..pipeline import WorkDirManager
-from ..utils import logger, raise_error, run_ext_cmd, warn_with_log
+from ..utils import logger, raise_error, run_ext_cmd
 from .template_spaces import get_template, get_xfm
 from .utils import closest_resolution
 
@@ -121,46 +120,6 @@ def compute_brain_mask(
     return new_img_like(target_img, mask)  # type: ignore
 
 
-def _fetch_icbm152_brain_gm_mask(
-    target_img: "Nifti1Image",
-    **kwargs,
-) -> "Nifti1Image":
-    """Fetch ICBM152 brain mask and resample.
-
-    Parameters
-    ----------
-    target_img : nibabel.Nifti1Image
-        The image to which the mask will be resampled.
-    **kwargs : dict
-        Keyword arguments to be passed to
-        :func:`nilearn.datasets.fetch_icbm152_brain_gm_mask`.
-
-    Returns
-    -------
-    nibabel.Nifti1Image
-        The resampled mask.
-
-    Warns
-    -----
-    DeprecationWarning
-        If this function is used.
-
-    """
-    warn_with_log(
-        msg=(
-            "It is recommended to use ``compute_brain_mask`` with "
-            "``mask_type='gm'``. This function will be removed in the next "
-            "release. For now, it's available for backward compatibility."
-        ),
-        category=DeprecationWarning,
-    )
-    mask = fetch_icbm152_brain_gm_mask(**kwargs)
-    mask = resample_to_img(
-        mask, target_img, interpolation="nearest", copy=True
-    )
-    return mask
-
-
 # A dictionary containing all supported masks and their respective file or
 # data.
 
@@ -194,11 +153,6 @@ _available_masks: Dict[str, Dict[str, Any]] = {
         "func": compute_epi_mask,
         "space": "inherit",
     },
-    "fetch_icbm152_brain_gm_mask": {
-        "family": "Callable",
-        "func": _fetch_icbm152_brain_gm_mask,
-        "space": "MNI152NLin2009aAsym",
-    },
 }
 
 
@@ -292,9 +246,7 @@ def get_mask(  # noqa: C901
     Raises
     ------
     RuntimeError
-        If warp / transformation file extension is not ".mat" or ".h5" or
-        if fetch_icbm152_brain_gm_mask is used and requires warping to
-        other template space.
+        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
@@ -402,21 +354,6 @@ def get_mask(  # noqa: C901
             mask_img = extra_input[inherited_mask_item]["data"]
         # Starting with new mask
         else:
-            # Restrict fetch_icbm152_brain_gm_mask if target std space doesn't
-            # match
-            if (
-                mask_name == "fetch_icbm152_brain_gm_mask"
-                and target_std_space != "MNI152NLin2009aAsym"
-            ):
-                raise_error(
-                    (
-                        "``fetch_icbm152_brain_gm_mask`` is deprecated and "
-                        "space transformation to any other template space is "
-                        "prohibited as it will lead to unforeseen errors. "
-                        "``compute_brain_mask`` is a better alternative."
-                    ),
-                    klass=RuntimeError,
-                )
             # Load mask
             mask_object, _, mask_space = load_mask(
                 mask_name, path_only=False, resolution=resolution

junifer/data/tests/test_masks.py

@@ -386,14 +386,6 @@ def test_get_mask_errors() -> None:
                 masks="inherit", target_data=vbm_gm, extra_input=extra_input
             )
 
-        # Block fetch_icbm152_brain_gm_mask space transformation
-        with pytest.raises(RuntimeError, match="prohibited"):
-            get_mask(
-                masks="fetch_icbm152_brain_gm_mask",
-                target_data=vbm_gm,
-                extra_input=extra_input,
-            )
-
 
 @pytest.mark.parametrize(
     "mask_name,function,params,resample",

junifer/preprocess/__init__.py

@@ -7,6 +7,5 @@
 
 from .base import BasePreprocessor
 from .confounds import fMRIPrepConfoundRemover
-from .bold_warper import BOLDWarper
 from .warping import SpaceWarper
 from .smoothing import Smoothing

{junifer-0.0.5.dev39.dist-info → junifer-0.0.5.dev48.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: junifer
-Version: 0.0.5.dev39
+Version: 0.0.5.dev48
 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-0.0.5.dev39.dist-info → junifer-0.0.5.dev48.dist-info}/RECORD

@@ -1,10 +1,10 @@
 junifer/__init__.py,sha256=x1UR2jUcrUdm2HNl-3Qvyi4UUrU6ms5qm2qcmNY7zZk,391
-junifer/_version.py,sha256=l1LfA0OgiHtlGqU1WbRoivsWTb_BlPL87yDQLjByFJY,426
+junifer/_version.py,sha256=EyYigB7-PzZ_TCv16ateewbga35csyccbEi_liFHPpY,426
 junifer/stats.py,sha256=jN22_qFvWYBU9ZIMnCSzN4iOscWnWrcrUPIdLeDkV64,6163
 junifer/api/__init__.py,sha256=pSj8V8tmwOAQ3sshWJfRfB-n3z5bcJj3pHOBX4-8ONc,251
 junifer/api/cli.py,sha256=wtU7Rv9tDIT-4KQAkG6WxiE6mop3cuz6XxGDewceHPs,15329
 junifer/api/decorators.py,sha256=8bnwHPAe7VgzKxl--M_e0umdAlTVSzaJQHEJZ5kof5k,2580
-junifer/api/functions.py,sha256=29bGcpFueL3mjOcoNWU0xaHpM5aIrRQod-U2o-5_TSs,12938
+junifer/api/functions.py,sha256=zCWLXDZ_cAqRZ5bFeky0KeqBztuoa6L3-djI65tqtpY,13055
 junifer/api/parser.py,sha256=a3SSC2xO-PF1pqXZXFq8Sh9aVd-dmHolJbCkGyOUTAM,4416
 junifer/api/utils.py,sha256=dyjTdPMwX9qeCrn8SQT2Pjshfnu-y1FEyujV7lCzvm0,3333
 junifer/api/queue_context/__init__.py,sha256=_yXJ8woTxLNLoSR3yLxAW7MtC5sa-oCRxewsZ9D3j98,271
@@ -52,8 +52,8 @@ junifer/configs/juseless/datagrabbers/tests/test_ixi_vbm.py,sha256=8jxpNZelXwpJG
 junifer/configs/juseless/datagrabbers/tests/test_ucla.py,sha256=fFxllR0yvt7hiQYdSXJkl9_05UwemKfcp1vC6xf0X-U,3315
 junifer/configs/juseless/datagrabbers/tests/test_ukb_vbm.py,sha256=b9hjc1mgO--PSRC3id2EzzfE2yWNsuZ2UI47a6sfGZU,1025
 junifer/data/__init__.py,sha256=Z3CdIXpXK3Avxm2Qj7MsuNNZSM8Pc5KBa9D51DYd1v0,602
-junifer/data/coordinates.py,sha256=YzFUTeV9H8feWDlexz1v0E6UXERFeoP8ia1j5qYg8JU,12847
-junifer/data/masks.py,sha256=onSBFxar8l6TwNg3aUotSodv0-yabsWK8oF6qomcMxc,23477
+junifer/data/coordinates.py,sha256=AovvAdPhl9oQoH4T24jhzW0UuNL8wRYtkYrYHhvtRC8,12381
+junifer/data/masks.py,sha256=x2vjMLRRGWt0fRGJ67_TjAdrrHZLE0VVnr3KizSbMnI,21427
 junifer/data/parcellations.py,sha256=reNi0YdxP0sQYnB_tnxabP73FkvkdXXGsDLn68-hnfM,65225
 junifer/data/template_spaces.py,sha256=2dD9GIBgsd764ol3ZvmHL11VrsaBC78CwrMaMh4TCGQ,5756
 junifer/data/utils.py,sha256=Jmbc7SLzy4nLP_zkWv_aJzb1MZ27tutJ98ifsECCamM,1295
@@ -81,7 +81,7 @@ junifer/data/masks/vickery-patil/CAT12_IXI555_MNI152_TMP_GS_GMprob0.2_clean_3mm.
 junifer/data/masks/vickery-patil/GMprob0.2_cortex_3mm_NA_rm.nii.gz,sha256=jfMe_4H9XEnArYms5bSQbqS2V1_HbLHTfI5amQa_Pes,8700
 junifer/data/tests/test_coordinates.py,sha256=BNkz9qFbnwAI0oVlIm_XrT-z4Vsia_rMtMVaoFXT6mU,4328
 junifer/data/tests/test_data_utils.py,sha256=_DaiC8K79gs9HFHxr-udNeE2YTM6JA0-1i-K2cqK9qA,1087
-junifer/data/tests/test_masks.py,sha256=hJAvwPElhzvHYN15-6n98ABgCD-3lBY5WwHFuhImRe0,16172
+junifer/data/tests/test_masks.py,sha256=JVg-9ZNkOGaATihLVxg0LAW4DJnvnhln7EJtB3glqLo,15878
 junifer/data/tests/test_parcellations.py,sha256=ZEU1VHIK0AyxpclcJhG_0rQU0phaBU_dHP7Erfi3mN8,38222
 junifer/data/tests/test_template_spaces.py,sha256=PJulN7xHpAcSOTY-UzTG_WPywZEBSlAZGiNG4gzk1_8,3144
 junifer/datagrabber/__init__.py,sha256=fhHKsZyBeqCFJJMr53VF6EUkNrFuUZkNR8QZbaoHTNg,680
@@ -202,25 +202,17 @@ junifer/pipeline/tests/test_pipeline_step_mixin.py,sha256=_ykZzyNzREXy-r_yv1gY_j
 junifer/pipeline/tests/test_registry.py,sha256=rYN0pO3gSueQ6XsasEM9VU5BkLyaNl8WaCZiaO8Rno0,4105
 junifer/pipeline/tests/test_update_meta_mixin.py,sha256=UeWwpUi-Q5WVd36Fgfn_utXplSVXMSjLcdO2mR2xLTk,1355
 junifer/pipeline/tests/test_workdir_manager.py,sha256=E1WY4C-GDsx2c49sePqr1WR_Y3nZ1kiRn4Veu506uTs,2801
-junifer/preprocess/__init__.py,sha256=lWxDgXD_Ms7FPz70JUcUJT5AbEs-v65K2xrdh3d-a80,428
+junifer/preprocess/__init__.py,sha256=lpkT_mhsRjkmk676u-jWDMlPTp1Kdls-KLsXHrhiDyw,392
 junifer/preprocess/base.py,sha256=Bn1VdonQ1f_DDPwFMpdaeyfLfNSnROulr-U8HuGQ81A,6697
-junifer/preprocess/bold_warper.py,sha256=pEQ1GaWTV2Ili9WyqJgtq0PGHm4hNztXyY9ixoLNZnw,9060
-junifer/preprocess/ants/__init__.py,sha256=Uobmbhh6_gOowkF2hQNSQOh3AYeaXzarBXEcLJzhERE,112
-junifer/preprocess/ants/ants_apply_transforms_warper.py,sha256=1qkTq4NoW-c8CDEvh8j4uuN_HtneXSpG0mqRc6_qrNk,5556
-junifer/preprocess/ants/tests/test_ants_apply_transforms_warper.py,sha256=IIwzo7iTFR2xy00S59ubXb0JSPukdPiRv6mdd25oeBA,1678
 junifer/preprocess/confounds/__init__.py,sha256=EDlcD9jy8O9xluJr6XOnFXtjGCDVqwg6sDIRDMbM8ZU,235
 junifer/preprocess/confounds/fmriprep_confound_remover.py,sha256=UN9B5P-Lqa5mA9jWi3gFJ7iBx1HSyfFrGuTZt4u4h1M,20841
 junifer/preprocess/confounds/tests/test_fmriprep_confound_remover.py,sha256=noKP4YvghNzVvIRjDHnANCBFmbZiAKcDQG22dwqLvss,20757
-junifer/preprocess/fsl/__init__.py,sha256=DerGFQ-dIuX5PT9a_BH6QkIXkJZVymjYy-woXF7tYGc,111
-junifer/preprocess/fsl/apply_warper.py,sha256=k6ZzoDhXgsqcJZYYdx45Y3rN9xJERc02953_qhTqMtE,5144
-junifer/preprocess/fsl/tests/test_apply_warper.py,sha256=eCrSPYIGTKFDiBtseZFkghjhU7j7np59TZeGdKHkhMs,1324
 junifer/preprocess/smoothing/__init__.py,sha256=3l8nay8Zm_BIZLEj4CwmIye5-q7lQ_niGO_Cv4Hd21c,151
 junifer/preprocess/smoothing/_afni_smoothing.py,sha256=FLJIrlYGxMT8rJdhV3LjALFIC9EPp902OuXt0FqAA_s,3266
 junifer/preprocess/smoothing/_fsl_smoothing.py,sha256=ZBdP4VsaQEYD9JYUitAXSccwvP3GZ0FyqhriV8gJxyk,3035
 junifer/preprocess/smoothing/_nilearn_smoothing.py,sha256=bshMj2DKEFkNiUbpaBoBfFFI6O80FIN49Oa3nc6FgaA,1928
 junifer/preprocess/smoothing/smoothing.py,sha256=Bb9_0wvt1CfwzpxN_svPiQ2euOZkAT9S--4qr8omhyQ,5355
 junifer/preprocess/smoothing/tests/test_smoothing.py,sha256=t1j3zEvJk5XLO4fzcb-wQyBMH-xuvR1k6WYm8zriwik,2390
-junifer/preprocess/tests/test_bold_warper.py,sha256=U_r7DwPWoO_it1LIkhuQWBe20a-6X5c8o0AvTOnWKEc,4636
 junifer/preprocess/tests/test_preprocess_base.py,sha256=-0rpe8QjqYES36H6MHuDs3cv_6upHBdVHnFMgQsmEX4,2571
 junifer/preprocess/warping/__init__.py,sha256=zW4DVt_RPJWT0-AsylGmh9wgFBDPkU-hx4VzV_qPayU,154
 junifer/preprocess/warping/_ants_warper.py,sha256=Y1UzZ5jy1TvlLEkaQKW7jCNvEHufZMdQFbg2JpY3UaM,5690
@@ -256,10 +248,10 @@ junifer/utils/logging.py,sha256=furcU3XIUpUvnpe4PEwzWWIWgmH4j2ZA4MQdvSGWjj0,9216
 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-0.0.5.dev39.dist-info/AUTHORS.rst,sha256=rmULKpchpSol4ExWFdm-qu4fkpSZPYqIESVJBZtGb6E,163
-junifer-0.0.5.dev39.dist-info/LICENSE.md,sha256=MqCnOBu8uXsEOzRZWh9EBVfVz-kE9NkXcLCrtGXo2yU,34354
-junifer-0.0.5.dev39.dist-info/METADATA,sha256=TtMlS1WQvAo-VPc3ntTj7-SSkK4bbFB2MKivxcTPKok,8234
-junifer-0.0.5.dev39.dist-info/WHEEL,sha256=GJ7t_kWBFywbagK5eo9IoUwLW6oyOeTKmQ-9iHFVNxQ,92
-junifer-0.0.5.dev39.dist-info/entry_points.txt,sha256=DxFvKq0pOqRunAK0FxwJcoDfV1-dZvsFDpD5HRqSDhw,48
-junifer-0.0.5.dev39.dist-info/top_level.txt,sha256=4bAq1R2QFQ4b3hohjys2JBvxrl0GKk5LNFzYvz9VGcA,8
-junifer-0.0.5.dev39.dist-info/RECORD,,
+junifer-0.0.5.dev48.dist-info/AUTHORS.rst,sha256=rmULKpchpSol4ExWFdm-qu4fkpSZPYqIESVJBZtGb6E,163
+junifer-0.0.5.dev48.dist-info/LICENSE.md,sha256=MqCnOBu8uXsEOzRZWh9EBVfVz-kE9NkXcLCrtGXo2yU,34354
+junifer-0.0.5.dev48.dist-info/METADATA,sha256=HcvOlaAOoZhs_ipslMx8_9IRDL4aDzQSLgIp4d0zx6o,8234
+junifer-0.0.5.dev48.dist-info/WHEEL,sha256=GJ7t_kWBFywbagK5eo9IoUwLW6oyOeTKmQ-9iHFVNxQ,92
+junifer-0.0.5.dev48.dist-info/entry_points.txt,sha256=DxFvKq0pOqRunAK0FxwJcoDfV1-dZvsFDpD5HRqSDhw,48
+junifer-0.0.5.dev48.dist-info/top_level.txt,sha256=4bAq1R2QFQ4b3hohjys2JBvxrl0GKk5LNFzYvz9VGcA,8
+junifer-0.0.5.dev48.dist-info/RECORD,,

junifer/preprocess/ants/__init__.py

@@ -1,4 +0,0 @@
-"""Provide imports for ants sub-package."""
-
-# Authors: Synchon Mandal <s.mandal@fz-juelich.de>
-# License: AGPL

junifer/preprocess/ants/ants_apply_transforms_warper.py

@@ -1,185 +0,0 @@
-"""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

@@ -1,56 +0,0 @@
-"""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/bold_warper.py

@@ -1,265 +0,0 @@
-"""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/fsl/__init__.py

@@ -1,4 +0,0 @@
-"""Provide imports for fsl sub-package."""
-
-# Authors: Synchon Mandal <s.mandal@fz-juelich.de>
-# License: AGPL

junifer/preprocess/fsl/apply_warper.py

@@ -1,179 +0,0 @@
-"""Provide class for warping via FSL FLIRT."""
-
-# 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 _ApplyWarper:
-    """Class for warping NIfTI images via FSL FLIRT.
-
-    Wraps FSL FLIRT ``applywarp``.
-
-    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": "fsl",
-            "commands": ["flirt", "applywarp"],
-        },
-    ]
-
-    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_applywarp(
-        self,
-        input_data: Dict,
-        ref_path: Path,
-        warp_path: Path,
-    ) -> Tuple["Nifti1Image", Path]:
-        """Run ``applywarp``.
-
-        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="applywarp")
-
-        # Create a tempfile for resampled reference output
-        flirt_out_path = tempdir / "reference_resampled.nii.gz"
-        # Set flirt command
-        flirt_cmd = [
-            "flirt",
-            "-interp spline",
-            f"-in {ref_path.resolve()}",
-            f"-ref {ref_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 = tempdir / "input_warped.nii.gz"
-        # Set applywarp command
-        applywarp_cmd = [
-            "applywarp",
-            "--interp=spline",
-            f"-i {input_data['path'].resolve()}",
-            f"-r {flirt_out_path.resolve()}",  # use resampled reference
-            f"-w {warp_path.resolve()}",
-            f"-o {applywarp_out_path.resolve()}",
-        ]
-        # Call applywarp
-        run_ext_cmd(name="applywarp", cmd=applywarp_cmd)
-
-        # Load nifti
-        output_img = nib.load(applywarp_out_path)
-
-        return output_img, flirt_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 FSL using ApplyWarper")
-        # 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_applywarp(
-            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/fsl/tests/test_apply_warper.py

@@ -1,45 +0,0 @@
-"""Provide tests for ApplyWarper."""
-
-# Authors: Synchon Mandal <s.mandal@fz-juelich.de>
-# License: AGPL
-
-import socket
-
-import pytest
-
-from junifer.datagrabber import DataladHCP1200
-from junifer.datareader import DefaultDataReader
-from junifer.pipeline.utils import _check_fsl
-from junifer.preprocess.fsl.apply_warper import _ApplyWarper
-
-
-def test_ApplyWarper_init() -> None:
-    """Test ApplyWarper init."""
-    apply_warper = _ApplyWarper(reference="T1w", on="BOLD")
-    assert apply_warper.ref == "T1w"
-    assert apply_warper.on == "BOLD"
-
-
-@pytest.mark.skipif(_check_fsl() is False, reason="requires FSL to be in PATH")
-@pytest.mark.skipif(
-    socket.gethostname() != "juseless",
-    reason="only for juseless",
-)
-def test_ApplyWarper_preprocess() -> None:
-    """Test ApplyWarper preprocess."""
-    with DataladHCP1200(
-        tasks=["REST1"],
-        phase_encodings=["LR"],
-        ica_fix=True,
-    ) as dg:
-        # Read data
-        element_data = DefaultDataReader().fit_transform(
-            dg[("100206", "REST1", "LR")]
-        )
-        # Preprocess data
-        data_type, data = _ApplyWarper(reference="T1w", on="BOLD").preprocess(
-            input=element_data["BOLD"],
-            extra_input=element_data,
-        )
-        assert isinstance(data_type, str)
-        assert isinstance(data, dict)

junifer/preprocess/tests/test_bold_warper.py

@@ -1,159 +0,0 @@
-"""Provide tests for BOLDWarper."""
-
-# Authors: Synchon Mandal <s.mandal@fz-juelich.de>
-# License: AGPL
-
-import socket
-from typing import TYPE_CHECKING, Tuple
-
-import pytest
-from numpy.testing import assert_array_equal, assert_raises
-
-from junifer.datagrabber import DataladHCP1200, DMCC13Benchmark
-from junifer.datareader import DefaultDataReader
-from junifer.pipeline.utils import _check_ants, _check_fsl
-from junifer.preprocess import BOLDWarper
-
-
-if TYPE_CHECKING:
-    from junifer.datagrabber import BaseDataGrabber
-
-
-def test_BOLDWarper_init() -> None:
-    """Test BOLDWarper init."""
-    bold_warper = BOLDWarper(using="ants", reference="T1w")
-    assert bold_warper._on == ["BOLD"]
-
-
-def test_BOLDWarper_get_valid_inputs() -> None:
-    """Test BOLDWarper get_valid_inputs."""
-    bold_warper = BOLDWarper(using="ants", reference="T1w")
-    assert bold_warper.get_valid_inputs() == ["BOLD"]
-
-
-def test_BOLDWarper_get_output_type() -> None:
-    """Test BOLDWarper get_output_type."""
-    bold_warper = BOLDWarper(using="ants", reference="T1w")
-    assert bold_warper.get_output_type("BOLD") == "BOLD"
-
-
-@pytest.mark.parametrize(
-    "datagrabber, element",
-    [
-        [
-            DMCC13Benchmark(
-                types=["BOLD", "T1w", "Warp"],
-                sessions=["ses-wave1bas"],
-                tasks=["Rest"],
-                phase_encodings=["AP"],
-                runs=["1"],
-                native_t1w=True,
-            ),
-            ("sub-f9057kp", "ses-wave1bas", "Rest", "AP", "1"),
-        ],
-        [
-            DataladHCP1200(
-                tasks=["REST1"],
-                phase_encodings=["LR"],
-                ica_fix=True,
-            ),
-            ("100206", "REST1", "LR"),
-        ],
-    ],
-)
-@pytest.mark.skipif(_check_fsl() is False, reason="requires FSL to be in PATH")
-@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_BOLDWarper_preprocess_to_native(
-    datagrabber: "BaseDataGrabber", element: Tuple[str, ...]
-) -> None:
-    """Test BOLDWarper preprocess.
-
-    Parameters
-    ----------
-    datagrabber : DataGrabber-like object
-        The parametrized DataGrabber objects.
-    element : tuple of str
-        The parametrized elements.
-
-    """
-    with datagrabber as dg:
-        # Read data
-        element_data = DefaultDataReader().fit_transform(dg[element])
-        # Preprocess data
-        data, _ = BOLDWarper(reference="T1w").preprocess(
-            input=element_data["BOLD"],
-            extra_input=element_data,
-        )
-        assert isinstance(data, dict)
-
-
-@pytest.mark.parametrize(
-    "datagrabber, element, space",
-    [
-        [
-            DMCC13Benchmark(
-                types=["BOLD"],
-                sessions=["ses-wave1bas"],
-                tasks=["Rest"],
-                phase_encodings=["AP"],
-                runs=["1"],
-                native_t1w=False,
-            ),
-            ("sub-f9057kp", "ses-wave1bas", "Rest", "AP", "1"),
-            "MNI152NLin2009aAsym",
-        ],
-        [
-            DMCC13Benchmark(
-                types=["BOLD"],
-                sessions=["ses-wave1bas"],
-                tasks=["Rest"],
-                phase_encodings=["AP"],
-                runs=["1"],
-                native_t1w=False,
-            ),
-            ("sub-f9057kp", "ses-wave1bas", "Rest", "AP", "1"),
-            "MNI152NLin6Asym",
-        ],
-    ],
-)
-@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_BOLDWarper_preprocess_to_multi_mni(
-    datagrabber: "BaseDataGrabber", element: Tuple[str, ...], space: str
-) -> None:
-    """Test BOLDWarper preprocess.
-
-    Parameters
-    ----------
-    datagrabber : DataGrabber-like object
-        The parametrized DataGrabber objects.
-    element : tuple of str
-        The parametrized elements.
-    space : str
-        The parametrized template space to transform to.
-
-    """
-    with datagrabber as dg:
-        # Read data
-        element_data = DefaultDataReader().fit_transform(dg[element])
-        pre_xfm_data = element_data["BOLD"]["data"].get_fdata().copy()
-        # Preprocess data
-        data, _ = BOLDWarper(reference=space).preprocess(
-            input=element_data["BOLD"],
-            extra_input=element_data,
-        )
-        assert isinstance(data, dict)
-        assert data["space"] == space
-        with assert_raises(AssertionError):
-            assert_array_equal(pre_xfm_data, data["data"])