junifer 0.0.6.dev285__py3-none-any.whl → 0.0.6.dev302__py3-none-any.whl

junifer/_version.py

@@ -12,5 +12,5 @@ __version__: str
 __version_tuple__: VERSION_TUPLE
 version_tuple: VERSION_TUPLE
 
-__version__ = version = '0.0.6.dev285'
-__version_tuple__ = version_tuple = (0, 0, 6, 'dev285')
+__version__ = version = '0.0.6.dev302'
+__version_tuple__ = version_tuple = (0, 0, 6, 'dev302')

junifer/api/functions.py

@@ -21,7 +21,7 @@ from ..pipeline import (
 from ..preprocess import BasePreprocessor
 from ..storage import BaseFeatureStorage
 from ..typing import DataGrabberLike, MarkerLike, PreprocessorLike, StorageLike
-from ..utils import logger, raise_error, yaml
+from ..utils import logger, raise_error, warn_with_log, yaml
 
 
 __all__ = ["collect", "list_elements", "queue", "reset", "run"]
@@ -116,18 +116,18 @@ def _get_storage(storage_config: dict) -> StorageLike:
 
 
 def run(
-    workdir: Union[str, Path],
+    workdir: Union[str, Path, dict],
     datagrabber: dict,
     markers: list[dict],
     storage: dict,
     preprocessors: Optional[list[dict]] = None,
-    elements: Union[str, list[Union[str, tuple]], tuple, None] = None,
+    elements: Optional[list[tuple[str, ...]]] = None,
 ) -> None:
     """Run the pipeline on the selected element.
 
     Parameters
     ----------
-    workdir : str or pathlib.Path
+    workdir : str or pathlib.Path or dict
         Directory where the pipeline will be executed.
     datagrabber : dict
         DataGrabber to use. Must have a key ``kind`` with the kind of
@@ -143,23 +143,38 @@ def run(
         Storage to use. Must have a key ``kind`` with the kind of
         storage to use. All other keys are passed to the storage
         constructor.
-    preprocessors : list of dict, optional
+    preprocessors : list of dict or None, optional
         List of preprocessors to use. Each preprocessor is a dict with at
         least a key ``kind`` specifying the preprocessor to use. All other keys
         are passed to the preprocessor constructor (default None).
-    elements : str or tuple or list of str or tuple, optional
+    elements : list of tuple or None, optional
         Element(s) to process. Will be used to index the DataGrabber
         (default None).
 
+    Raises
+    ------
+    ValueError
+        If ``workdir.cleanup=False`` when ``len(elements) > 1``.
+
     """
-    # Convert str to Path
-    if isinstance(workdir, str):
-        workdir = Path(workdir)
-    # Initiate working directory manager
-    WorkDirManager(workdir)
+    # Conditional to handle workdir config
+    if isinstance(workdir, (str, Path)):
+        if isinstance(workdir, str):
+            workdir = {"workdir": Path(workdir), "cleanup": True}
+        else:
+            workdir = {"workdir": workdir, "cleanup": True}
+    elif isinstance(workdir, dict):
+        workdir["workdir"] = workdir.pop("path")
 
-    if not isinstance(elements, list) and elements is not None:
-        elements = [elements]
+    # Initiate working directory manager with correct variation
+    if not workdir["cleanup"]:
+        if elements is None or len(elements) > 1:
+            raise_error(
+                "Cannot disable `workdir.cleanup` as "
+                f"{len(elements) if elements is not None else 'all'} "
+                "elements will be processed"
+            )
+    WorkDirManager(**workdir)
 
     # Get datagrabber to use
     datagrabber_object = _get_datagrabber(datagrabber.copy())
@@ -228,7 +243,7 @@ def queue(
     kind: str,
     jobname: str = "junifer_job",
     overwrite: bool = False,
-    elements: Union[str, list[Union[str, tuple]], tuple, None] = None,
+    elements: Optional[list[tuple[str, ...]]] = None,
     **kwargs: Union[str, int, bool, dict, tuple, list],
 ) -> None:
     """Queue a job to be executed later.
@@ -243,7 +258,7 @@ def queue(
         The name of the job (default "junifer_job").
     overwrite : bool, optional
         Whether to overwrite if job directory already exists (default False).
-    elements : str or tuple or list of str or tuple, optional
+    elements : list of tuple or None, optional
         Element(s) to process. Will be used to index the DataGrabber
         (default None).
     **kwargs : dict
@@ -282,6 +297,16 @@ def queue(
             shutil.rmtree(jobdir)
     jobdir.mkdir(exist_ok=True, parents=True)
 
+    # Check workdir config
+    if "workdir" in config:
+        if isinstance(config["workdir"], dict):
+            if not config["workdir"]["cleanup"]:
+                warn_with_log(
+                    "`workdir.cleanup` will be set to True when queueing"
+                )
+            # Set cleanup
+            config["workdir"]["cleanup"] = True
+
     # Load modules
     if "with" in config:
         to_load = config["with"]
@@ -381,7 +406,7 @@ def reset(config: dict) -> None:
 
 def list_elements(
     datagrabber: dict,
-    elements: Union[str, list[Union[str, tuple]], tuple, None] = None,
+    elements: Optional[list[tuple[str, ...]]] = None,
 ) -> str:
     """List elements of the datagrabber filtered using `elements`.
 
@@ -391,7 +416,7 @@ def list_elements(
         DataGrabber to index. Must have a key ``kind`` with the kind of
         DataGrabber to use. All other keys are passed to the DataGrabber
         constructor.
-    elements : str or tuple or list of str or tuple, optional
+    elements : list of tuple or None, optional
         Element(s) to filter using. Will be used to index the DataGrabber
         (default None).
 

junifer/api/tests/test_functions.py

@@ -88,7 +88,7 @@ def test_run_single_element(
         datagrabber=datagrabber,
         markers=markers,
         storage=storage,
-        elements=["sub-01"],
+        elements=[("sub-01",)],
     )
     # Check files
     files = list(tmp_path.glob("*.sqlite"))
@@ -116,7 +116,7 @@ def test_run_single_element_with_preprocessing(
     storage["uri"] = str((tmp_path / "out.sqlite").resolve())
     # Run operations
     run(
-        workdir=tmp_path,
+        workdir={"path": tmp_path, "cleanup": False},
         datagrabber={
             "kind": "PartlyCloudyTestingDataGrabber",
             "reduce_confounds": False,
@@ -128,7 +128,7 @@ def test_run_single_element_with_preprocessing(
                 "kind": "fMRIPrepConfoundRemover",
             }
         ],
-        elements=["sub-01"],
+        elements=[("sub-01",)],
     )
     # Check files
     files = list(tmp_path.glob("*.sqlite"))
@@ -164,7 +164,7 @@ def test_run_multi_element_multi_output(
         datagrabber=datagrabber,
         markers=markers,
         storage=storage,
-        elements=["sub-01", "sub-03"],
+        elements=[("sub-01",), ("sub-03",)],
     )
     # Check files
     files = list(tmp_path.glob("*.sqlite"))
@@ -200,7 +200,7 @@ def test_run_multi_element_single_output(
         datagrabber=datagrabber,
         markers=markers,
         storage=storage,
-        elements=["sub-01", "sub-03"],
+        elements=[("sub-01",), ("sub-03",)],
     )
     # Check files
     files = list(tmp_path.glob("*.sqlite"))
@@ -287,7 +287,10 @@ def test_queue_correct_yaml_config(
             queue(
                 config={
                     "with": "junifer.testing.registry",
-                    "workdir": str(tmp_path.resolve()),
+                    "workdir": {
+                        "path": str(tmp_path.resolve()),
+                        "cleanup": True,
+                    },
                     "datagrabber": datagrabber,
                     "markers": markers,
                     "storage": storage,
@@ -342,7 +345,7 @@ def test_queue_invalid_job_queue(
         with monkeypatch.context() as m:
             m.chdir(tmp_path)
             queue(
-                config={"elements": ["sub-001"]},
+                config={"elements": [("sub-001",)]},
                 kind="ABC",
             )
 
@@ -366,13 +369,13 @@ def test_queue_assets_disallow_overwrite(
             m.chdir(tmp_path)
             # First generate assets
             queue(
-                config={"elements": ["sub-001"]},
+                config={"elements": [("sub-001",)]},
                 kind="HTCondor",
                 jobname="prevent_overwrite",
             )
             # Re-run to trigger error
             queue(
-                config={"elements": ["sub-001"]},
+                config={"elements": [("sub-001",)]},
                 kind="HTCondor",
                 jobname="prevent_overwrite",
             )
@@ -399,14 +402,14 @@ def test_queue_assets_allow_overwrite(
         m.chdir(tmp_path)
         # First generate assets
         queue(
-            config={"elements": ["sub-001"]},
+            config={"elements": [("sub-001",)]},
             kind="HTCondor",
             jobname="allow_overwrite",
         )
         with caplog.at_level(logging.INFO):
             # Re-run to overwrite
             queue(
-                config={"elements": ["sub-001"]},
+                config={"elements": [("sub-001",)]},
                 kind="HTCondor",
                 jobname="allow_overwrite",
                 overwrite=True,
@@ -448,10 +451,16 @@ def test_queue_with_imports(
         (tmp_path / "a.py").touch()
         with caplog.at_level(logging.DEBUG):
             queue(
-                config={"with": with_},
+                config={
+                    "with": with_,
+                    "workdir": {
+                        "path": str(tmp_path.resolve()),
+                        "cleanup": False,
+                    },
+                },
                 kind="HTCondor",
                 jobname="with_import_check",
-                elements="sub-001",
+                elements=[("sub-001",)],
             )
             assert "Copying" in caplog.text
             assert "Queue done" in caplog.text
@@ -465,10 +474,8 @@ def test_queue_with_imports(
 @pytest.mark.parametrize(
     "elements",
     [
-        "sub-001",
-        ["sub-001"],
-        ["sub-001", "sub-002"],
-        ("sub-001", "ses-001"),
+        [("sub-001",)],
+        [("sub-001",), ("sub-002",)],
         [("sub-001", "ses-001")],
         [("sub-001", "ses-001"), ("sub-001", "ses-002")],
     ],
@@ -477,7 +484,7 @@ def test_queue_with_elements(
     tmp_path: Path,
     monkeypatch: pytest.MonkeyPatch,
     caplog: pytest.LogCaptureFixture,
-    elements: Union[str, list[Union[str, tuple[str]]], tuple[str]],
+    elements: list[tuple[str, ...]],
 ) -> None:
     """Test queue with elements.
 
@@ -489,7 +496,7 @@ def test_queue_with_elements(
         The pytest.MonkeyPatch object.
     caplog : pytest.LogCaptureFixture
         The pytest.LogCaptureFixture object.
-    elements : str of list of str
+    elements : list of tuple
         The parametrized elements for the queue.
 
     """
@@ -562,7 +569,7 @@ def test_reset_run(
         datagrabber=datagrabber,
         markers=markers,
         storage=storage,
-        elements=["sub-01"],
+        elements=[("sub-01",)],
     )
     # Reset operation
     reset(config={"storage": storage})
@@ -642,13 +649,13 @@ def test_reset_queue(
 @pytest.mark.parametrize(
     "elements",
     [
-        ["sub-01"],
+        [("sub-01",)],
         None,
     ],
 )
 def test_list_elements(
     datagrabber: dict[str, str],
-    elements: Optional[list[str]],
+    elements: Optional[list[tuple[str, ...]]],
 ) -> None:
     """Test elements listing.
 

junifer/cli/cli.py

@@ -117,15 +117,16 @@ def run(
     filepath : click.Path
         The filepath to the configuration file.
     element : tuple of str
-        The element to operate on.
+        The element(s) to operate on.
     verbose : click.Choice
         The verbosity level: warning, info or debug (default "info").
 
     """
+    # Setup logging
     configure_logging(level=verbose)
     # TODO(synchon): add validation
     # Parse YAML
-    config = parse_yaml(filepath)  # type: ignore
+    config = parse_yaml(filepath)
     # Retrieve working directory
     workdir = config["workdir"]
     # Fetch datagrabber
@@ -179,9 +180,12 @@ def collect(filepath: click.Path, verbose: Union[str, int]) -> None:
         The verbosity level: warning, info or debug (default "info").
 
     """
+    # Setup logging
     configure_logging(level=verbose)
     # TODO: add validation
-    config = parse_yaml(filepath)  # type: ignore
+    # Parse YAML
+    config = parse_yaml(filepath)
+    # Fetch storage
     storage = config["storage"]
     # Perform operation
     cli_func.collect(storage=storage)
@@ -206,7 +210,7 @@ def collect(filepath: click.Path, verbose: Union[str, int]) -> None:
 )
 def queue(
     filepath: click.Path,
-    element: str,
+    element: tuple[str],
     overwrite: bool,
     submit: bool,
     verbose: Union[str, int],
@@ -219,8 +223,8 @@ def queue(
     ----------
     filepath : click.Path
         The filepath to the configuration file.
-    element : str
-        The element to operate using.
+    element : tuple of str
+        The element(s) to operate on.
     overwrite : bool
         Whether to overwrite existing directory.
     submit : bool
@@ -228,15 +232,26 @@ def queue(
     verbose : click.Choice
         The verbosity level: warning, info or debug (default "info").
 
+    Raises
+    ------
+    ValueError
+        If no ``queue`` section is found in the YAML.
+
     """
+    # Setup logging
     configure_logging(level=verbose)
     # TODO: add validation
+    # Parse YAML
     config = parse_yaml(filepath)  # type: ignore
-    elements = parse_elements(element, config)
+    # Check queue section
     if "queue" not in config:
         raise_error(f"No queue configuration found in {filepath}.")
+    # Parse elements
+    elements = parse_elements(element, config)
+    # Separate out queue section
     queue_config = config.pop("queue")
     kind = queue_config.pop("kind")
+    # Perform operation
     cli_func.queue(
         config=config,
         kind=kind,
@@ -366,6 +381,7 @@ def reset(
         The verbosity level: warning, info or debug (default "info").
 
     """
+    # Setup logging
     configure_logging(level=verbose)
     # Parse YAML
     config = parse_yaml(filepath)
@@ -408,7 +424,7 @@ def list_elements(
     filepath : click.Path
         The filepath to the configuration file.
     element : tuple of str
-        The element to operate on.
+        The element(s) to operate on.
     output_file : click.Path or None
         The path to write the output to. If not None, writing to
         stdout is not performed.
@@ -416,9 +432,10 @@ def list_elements(
         The verbosity level: warning, info or debug (default "info").
 
     """
+    # Setup logging
     configure_logging(level=verbose)
     # Parse YAML
-    config = parse_yaml(filepath)  # type: ignore
+    config = parse_yaml(filepath)
     # Fetch datagrabber
     datagrabber = config["datagrabber"]
     # Parse elements

junifer/cli/parser.py

@@ -140,7 +140,9 @@ def parse_yaml(filepath: Union[str, Path]) -> dict:  # noqa: C901
     return contents
 
 
-def parse_elements(element: tuple[str], config: dict) -> Union[list, None]:
+def parse_elements(
+    element: tuple[str, ...], config: dict
+) -> Union[list[tuple[str, ...]], None]:
     """Parse elements from cli.
 
     Parameters
@@ -170,7 +172,7 @@ def parse_elements(element: tuple[str], config: dict) -> Union[list, None]:
     """
     logger.debug(f"Parsing elements: {element}")
     # Early return None to continue with all elements
-    if len(element) == 0:
+    if not element:
         return None
     # Check if the element is a file for single element;
     # if yes, then parse elements from it

junifer/data/coordinates/_fsl_coordinates_warper.py

@@ -69,7 +69,7 @@ class FSLCoordinatesWarper:
             f"{pretransform_coordinates_path.resolve()}",
             "| img2imgcoord -mm",
             f"-src {target_data['path'].resolve()}",
-            f"-dest {target_data['reference_path'].resolve()}",
+            f"-dest {target_data['reference']['path'].resolve()}",
             f"-warp {warp_data['path'].resolve()}",
             f"> {transformed_coords_path.resolve()};",
             f"sed -i 1d {transformed_coords_path.resolve()}",

junifer/data/masks/_ants_mask_warper.py

@@ -49,9 +49,10 @@ class ANTsMaskWarper:
             It should be empty string if ``dst="T1w"``.
         dst : str
             The data type or template space to warp to.
-            `"T1w"` is the only allowed data type and it uses the resampled T1w
-            found in ``target_data.reference_path``. The ``"reference_path"``
-            key is added when :class:`.SpaceWarper` is used.
+            `"native"` is the only allowed data type and it uses the resampled
+            T1w found in ``target_data.reference``. The
+            ``"reference"`` key is added when :class:`.SpaceWarper` is
+            used or if the data is provided native space.
         target_data : dict
             The corresponding item of the data object to which the mask
             will be applied.
@@ -87,6 +88,10 @@ class ANTsMaskWarper:
             # Warp data check
             if warp_data is None:
                 raise_error("No `warp_data` provided")
+            if "reference" not in target_data:
+                raise_error("No `reference` provided")
+            if "path" not in target_data["reference"]:
+                raise_error("No `path` provided in `reference`")
 
             logger.debug("Using ANTs for mask transformation")
 
@@ -104,7 +109,7 @@ class ANTsMaskWarper:
                 "-n 'GenericLabel[NearestNeighbor]'",
                 f"-i {prewarp_mask_path.resolve()}",
                 # use resampled reference
-                f"-r {target_data['reference_path'].resolve()}",
+                f"-r {target_data['reference']['path'].resolve()}",
                 f"-t {warp_data['path'].resolve()}",
                 f"-o {warped_mask_path.resolve()}",
             ]

junifer/data/masks/_fsl_mask_warper.py

@@ -74,7 +74,7 @@ class FSLMaskWarper:
             "--interp=nn",
             f"-i {prewarp_mask_path.resolve()}",
             # use resampled reference
-            f"-r {target_data['reference_path'].resolve()}",
+            f"-r {target_data['reference']['path'].resolve()}",
             f"-w {warp_data['path'].resolve()}",
             f"-o {warped_mask_path.resolve()}",
         ]

junifer/data/parcellations/_ants_parcellation_warper.py

@@ -50,8 +50,9 @@ class ANTsParcellationWarper:
         dst : str
             The data type or template space to warp to.
             `"T1w"` is the only allowed data type and it uses the resampled T1w
-            found in ``target_data.reference_path``. The ``"reference_path"``
-            key is added when :class:`.SpaceWarper` is used.
+            found in ``target_data.reference``. The ``"reference"``
+            key is added if the :class:`.SpaceWarper` is used or if the
+            data is provided in native space.
         target_data : dict
             The corresponding item of the data object to which the parcellation
             will be applied.
@@ -87,6 +88,10 @@ class ANTsParcellationWarper:
             # Warp data check
             if warp_data is None:
                 raise_error("No `warp_data` provided")
+            if "reference" not in target_data:
+                raise_error("No `reference` provided")
+            if "path" not in target_data["reference"]:
+                raise_error("No `path` provided in `reference`")
 
             logger.debug("Using ANTs for parcellation transformation")
 
@@ -108,7 +113,7 @@ class ANTsParcellationWarper:
                 "-n 'GenericLabel[NearestNeighbor]'",
                 f"-i {prewarp_parcellation_path.resolve()}",
                 # use resampled reference
-                f"-r {target_data['reference_path'].resolve()}",
+                f"-r {target_data['reference']['path'].resolve()}",
                 f"-t {warp_data['path'].resolve()}",
                 f"-o {warped_parcellation_path.resolve()}",
             ]

junifer/data/parcellations/_fsl_parcellation_warper.py

@@ -78,7 +78,7 @@ class FSLParcellationWarper:
             "--interp=nn",
             f"-i {prewarp_parcellation_path.resolve()}",
             # use resampled reference
-            f"-r {target_data['reference_path'].resolve()}",
+            f"-r {target_data['reference']['path'].resolve()}",
             f"-w {warp_data['path'].resolve()}",
             f"-o {warped_parcellation_path.resolve()}",
         ]

junifer/datagrabber/pattern_validation_mixin.py

@@ -33,6 +33,8 @@ PATTERNS_SCHEMA = {
                 "mandatory": ["pattern", "format"],
                 "optional": ["mappings"],
             },
+            "reference": {"mandatory": ["pattern"], "optional": []},
+            "prewarp_space": {"mandatory": [], "optional": []},
         },
     },
     "Warp": {

junifer/pipeline/workdir_manager.py

@@ -30,6 +30,9 @@ class WorkDirManager(metaclass=Singleton):
     workdir : str or pathlib.Path, optional
         The path to the super-directory. If None, "TMPDIR/junifer" is used
         where TMPDIR is the platform-dependent temporary directory.
+    cleanup : bool, optional
+        If False, the directories are not cleaned up after the object is
+        destroyed. This is useful for debugging purposes (default True).
 
     Attributes
     ----------
@@ -39,14 +42,11 @@ class WorkDirManager(metaclass=Singleton):
         The path to the element directory.
     root_tempdir : pathlib.Path or None
         The path to the root temporary directory.
-    cleanup : bool, optional
-        If False, the directories are not cleaned up after the object is
-        destroyed. This is useful for debugging purposes (default True).
 
     """
 
     def __init__(
-        self, workdir: Optional[Union[str, Path]] = None, cleanup=True
+        self, workdir: Optional[Union[str, Path]] = None, cleanup: bool = True
     ) -> None:
         """Initialize the class."""
         self._workdir = Path(workdir) if isinstance(workdir, str) else workdir

junifer/preprocess/warping/_ants_warper.py

@@ -59,7 +59,7 @@ class ANTsWarper:
         -------
         dict
             The ``input`` dictionary with modified ``data`` and ``space`` key
-            values and new ``reference_path`` key whose value points to the
+            values and new ``reference`` key whose value points to the
             reference file used for warping.
 
         Raises
@@ -129,7 +129,7 @@ class ANTsWarper:
             # Load nifti
             input["data"] = nib.load(apply_transforms_out_path)
             # Save resampled reference path
-            input["reference_path"] = resample_image_out_path
+            input["reference"] = {"path": resample_image_out_path}
             # Keep pre-warp space for further operations
             input["prewarp_space"] = input["space"]
             # Use reference input's space as warped input's space

junifer/preprocess/warping/_fsl_warper.py

@@ -55,7 +55,7 @@ class FSLWarper:
         -------
         dict
             The ``input`` dictionary with modified ``data`` and ``space`` key
-            values and new ``reference_path`` key whose value points to the
+            values and new ``reference`` key whose value points to the
             reference file used for warping.
 
         Raises
@@ -116,7 +116,7 @@ class FSLWarper:
         # Load nifti
         input["data"] = nib.load(applywarp_out_path)
         # Save resampled reference path
-        input["reference_path"] = flirt_out_path
+        input["reference"] = {"path": flirt_out_path}
         # Keep pre-warp space for further operations
         input["prewarp_space"] = input["space"]
         # Use reference input's space as warped input's space

{junifer-0.0.6.dev285.dist-info → junifer-0.0.6.dev302.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: junifer
-Version: 0.0.6.dev285
+Version: 0.0.6.dev302
 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-0.0.6.dev285.dist-info → junifer-0.0.6.dev302.dist-info}/RECORD

@@ -1,13 +1,13 @@
 junifer/__init__.py,sha256=2McgH1yNue6Z1V26-uN_mfMjbTcx4CLhym-DMBl5xA4,266
 junifer/__init__.pyi,sha256=SsTvgq2Dod6UqJN96GH1lCphH6hJQQurEJHGNhHjGUI,508
-junifer/_version.py,sha256=VOqNBo1Uj5NzgtOfO88V2py3fLW1gPgO44Cm-fu8TeY,428
+junifer/_version.py,sha256=6ivRaEJnq1nwi7sNAqQwwarVpyzKReHtuarvntATZ2E,428
 junifer/conftest.py,sha256=PWYkkRDU8ly2lYwv7VBKMHje4et6HX7Yey3Md_I2KbA,613
 junifer/py.typed,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 junifer/stats.py,sha256=e9aaagMGtgpRfW3Wdpz9ocpnYld1IWylCDcjFUgX9Mk,6225
 junifer/api/__init__.py,sha256=aAXW_KAEGQ8aAP5Eni2G1R4MWBF7UgjKOgM6akLuJco,252
 junifer/api/__init__.pyi,sha256=UJu55ApMFd43N0xlQyNKrYpCdzqhAxA3Jjaj0ETwCXU,169
 junifer/api/decorators.py,sha256=xphy55NJHnMZnJ-aNA70UzHUJ3SIgh5Xc8ekcozvj3U,2854
-junifer/api/functions.py,sha256=ebKz9WVdDcVWX32p2MHiYEEN-FEcsGcRWEN6u4pFnro,12826
+junifer/api/functions.py,sha256=Tq1LKoxJuHHylcCFJ6SrPoPriIsnTLdbQ5K6w8gdTE8,13697
 junifer/api/py.typed,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 junifer/api/queue_context/__init__.py,sha256=glr8x4aMm4EvVrHywDIlugdNlwD1RzqV2FTDNPqYQZ4,204
 junifer/api/queue_context/__init__.pyi,sha256=LoDQFGZ9wCDmgx5a1_nhKo4zOSvqViXZ8V882DksF7U,246
@@ -40,11 +40,11 @@ junifer/api/res/fsl/flirt,sha256=tSjiUco8ui8AbHD7mTzChEwbR0Rf_4iJTgzYTPF_WuQ,42
 junifer/api/res/fsl/img2imgcoord,sha256=Zmaw3oJYrEltcXiPyEubXry9ppAq3SND52tdDWGgeZk,49
 junifer/api/res/fsl/run_fsl_docker.sh,sha256=pq-fcNdLuvHzVIQePN4GebZGlcE2UF-xj5rBIqAMz4g,1122
 junifer/api/res/fsl/std2imgcoord,sha256=-X5wRH6XMl0yqnTACJX6MFhO8DFOEWg42MHRxGvimXg,49
-junifer/api/tests/test_functions.py,sha256=aBAZ2EveiBHbAM5w6j2QxMHBze-XiVD3Td1kAE946ps,17786
+junifer/api/tests/test_functions.py,sha256=PPkjs_FqjZZgsEa3a81ulzPxLskVh5HmnaG8TaNCwR0,18084
 junifer/cli/__init__.py,sha256=DS3kZKHeVDxt6d1MLBerZ2fcAwrEBHee5JOBhOLajUI,197
 junifer/cli/__init__.pyi,sha256=PiV4znUnzSeuSSJGz-RT8N21PiMqoSMwYcypi7nt2Js,40
-junifer/cli/cli.py,sha256=kzSM-5nZWgQ4iaGbcjDkU2JgdYcUF-zsYskuq9_ewM0,13195
-junifer/cli/parser.py,sha256=Ok_ADyoDfjlAxl9NP36dtzFHp9QTL87V_cRxCa44UKs,8336
+junifer/cli/cli.py,sha256=Q0l7dBclLrM0P5MU2G0MA7W8u23VtqIQdwaeoOy-_ws,13519
+junifer/cli/parser.py,sha256=ouVnk4NrOmVMNnQDMsqAjt2BaOT05bNJq0LVRsIakXI,8358
 junifer/cli/py.typed,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 junifer/cli/utils.py,sha256=AbPQC0Kl-tHMNKiPxp_01gLAGD3IGoLbsq3rXyPMM-c,3116
 junifer/cli/tests/test_cli.py,sha256=AYL4my12GmFRCbI3JV7-rju32heYxAqbXNwnV8PwqVY,10982
@@ -81,7 +81,7 @@ junifer/data/coordinates/__init__.py,sha256=ffM8rwcHLgHAWixJbKrATrbUKzX940V1UF6R
 junifer/data/coordinates/__init__.pyi,sha256=Z-Ti5XD3HigkZ8uYN6oYsLqw40-F1GvTVQ5QAy08Wng,88
 junifer/data/coordinates/_ants_coordinates_warper.py,sha256=5RWDC-nI3VG9lkSJ-_y_hlDtjPctKSJokQOp3v8ozwY,2956
 junifer/data/coordinates/_coordinates.py,sha256=fBXVvuTxYLTNBSrQiTCiQsxpT0SdbQze3DYuGGgz_mY,12501
-junifer/data/coordinates/_fsl_coordinates_warper.py,sha256=GI0SrkNyAuRsoRSxI5WNvQmtPXQ3MlXvPx9lrd3NYB4,2406
+junifer/data/coordinates/_fsl_coordinates_warper.py,sha256=5h7rwiPMYBQlA3sMZUImcpnNLLWvIp2-bAEaaHtzX9c,2409
 junifer/data/coordinates/VOIs/meta/AutobiographicalMemory_VOIs.txt,sha256=9af38naeL18Tlt_gy_ep6vyTAxOB336JYjbo5FvP8PQ,686
 junifer/data/coordinates/VOIs/meta/CogAC_VOIs.txt,sha256=Sr5_E712OLdeQRyUcDNM0wLBvZIyO6gc9Q7KkyJHX1A,398
 junifer/data/coordinates/VOIs/meta/CogAR_VOIs.txt,sha256=t3NLwEVUZTPP34p15SaB3UInLrQyK-7Qc4iLBuQlZu8,189
@@ -104,8 +104,8 @@ junifer/data/coordinates/VOIs/meta/extDMN_VOIs.txt,sha256=Ogx1QvqZcnXDM3ncF2ha78
 junifer/data/coordinates/tests/test_coordinates.py,sha256=_c2P4oaDGpsmui5gJBe_jN6HLGiKxONkYPR69sRBUlU,4219
 junifer/data/masks/__init__.py,sha256=eEEhHglyVEx1LrqwXjq3cOmjf4sTsgBstRx5-k7zIQU,180
 junifer/data/masks/__init__.pyi,sha256=lcgr8gmWDPibC4RxnWBXb8DDpIkO73Aax09u6VXiJJI,114
-junifer/data/masks/_ants_mask_warper.py,sha256=yGjC-b6Ui-MpPG3FpRnI8pEAxjMUfSSuUGVIeazjN7I,5078
-junifer/data/masks/_fsl_mask_warper.py,sha256=_7UkX3-wFXQs4KwxopO-QjMyB6aeq1GAkiGSGpG-OzM,2412
+junifer/data/masks/_ants_mask_warper.py,sha256=6ex2jxxKI5yA4G1rebSpcAYGGisflVK-DwhtUtWY964,5348
+junifer/data/masks/_fsl_mask_warper.py,sha256=VApp-ofGBKePNmCdgTg1HoEA66lMQiAPT0ihkhB2ezY,2415
 junifer/data/masks/_masks.py,sha256=96NKsSSosD6r03Jb2N1xQoyOc2Vl5miokcQdSeuM6SY,20729
 junifer/data/masks/tests/test_masks.py,sha256=1Zm09ZSdUlR278DTCZeVuxuQntryefsnYYPP02MttVE,16120
 junifer/data/masks/ukb/UKB_15K_GM_template.nii.gz,sha256=jcX1pDOrDsoph8cPMNFVKH5gZYio5G4rJNpOFXm9wJI,946636
@@ -114,8 +114,8 @@ 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/parcellations/__init__.py,sha256=6-Ysil3NyZ69V6rWx4RO15_d-iDKizfbHuxSjsHNt24,188
 junifer/data/parcellations/__init__.pyi,sha256=lhBHTbMDizzqUqVHrx2eyfPFodrTBgMFeTgxfESSkQ8,140
-junifer/data/parcellations/_ants_parcellation_warper.py,sha256=UBjO9W8jWcM8GK80pbIzORir60ZFAhLTttGtaaDNT2g,5530
-junifer/data/parcellations/_fsl_parcellation_warper.py,sha256=pUsLbR34Ry3e_0_5KxngI-jU06YmXTU795k-SjJHmig,2676
+junifer/data/parcellations/_ants_parcellation_warper.py,sha256=4CYieBer6ow4i8o4NjKsfufc96XdtsMGwfBbMF-Kw78,5802
+junifer/data/parcellations/_fsl_parcellation_warper.py,sha256=JfJ022flg5OR48P4OAALVHHQgTVxdMBXT-fAqBl3nUM,2679
 junifer/data/parcellations/_parcellations.py,sha256=uOqoucoynv--iEftrhdnOd3jBcqq9PSDgs9DYhbeN24,65611
 junifer/data/parcellations/tests/test_parcellations.py,sha256=crluGgUjocVZ0ZIkMpUVol27A-Px6oc2eflY5g0C4BY,38315
 junifer/data/tests/test_data_utils.py,sha256=136iGPjGecCxyqgUwU8VZMHoE6imcYJ0WNC32PDGK4g,1063
@@ -128,7 +128,7 @@ junifer/datagrabber/dmcc13_benchmark.py,sha256=VMyiwvkr4qSvzBICSksPPKOI2w_WVo06H
 junifer/datagrabber/multiple.py,sha256=4tCOzojs3hoG7daHJJ7HUsx15atWR5nTmyP0S0__aig,6666
 junifer/datagrabber/pattern.py,sha256=UwJQ0MObBIS6eHH9FfoM_sBYuNM9n5NAX7DA0HdtL1A,18709
 junifer/datagrabber/pattern_datalad.py,sha256=QPWXIToYHDU4mvm9lz_hy8BjdqqoCXiGiJKCcATrT-w,4568
-junifer/datagrabber/pattern_validation_mixin.py,sha256=MlcQIDyPHtqPcq1eHkwvrp-m5MhZaxTG1l2j3JM6FOc,19236
+junifer/datagrabber/pattern_validation_mixin.py,sha256=6IlL5EMbr-XEtiiXs_buD3DJkujjs335BmAgAiWGZ3M,19369
 junifer/datagrabber/py.typed,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 junifer/datagrabber/aomic/__init__.py,sha256=ATxzXq9NBPmWowTMuL77zqrmIbbnk0Wd1iXtXCP3XDg,266
 junifer/datagrabber/aomic/__init__.pyi,sha256=Rp6C075fZDdKY8VIq508_g4NhVj8bWzR6zb9yln761Q,189
@@ -268,7 +268,7 @@ junifer/pipeline/pipeline_step_mixin.py,sha256=oXfJh27yifHs1V3V_tMPCanRiHX1ggOVI
 junifer/pipeline/py.typed,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 junifer/pipeline/update_meta_mixin.py,sha256=yzGCx8AUbc9mMnWKRu4qaIXTBBSIxtNlGH5zIQIUvzM,1812
 junifer/pipeline/utils.py,sha256=27KYbUS6t1kb3vP_C5BoRBFfKPzfUKQK8Ut-aBERshk,10285
-junifer/pipeline/workdir_manager.py,sha256=T7-sZY_Gj0SM7p9N1ATjUFK2T-6CYIMQeYwHpBz96Gs,8616
+junifer/pipeline/workdir_manager.py,sha256=r5hhizktLat2bN_A-ZGeeBVWmpRUkUCiZeIDxG-9umM,8624
 junifer/pipeline/tests/test_marker_collection.py,sha256=edBHfmwMTXG_q0ZagApbAbkFNoegi3hVEQiNcBtZOKc,6959
 junifer/pipeline/tests/test_pipeline_component_registry.py,sha256=mrbz285K_TzSILRn9X-AyzcNXuPRHGBZY6dQiq5_9So,5776
 junifer/pipeline/tests/test_pipeline_step_mixin.py,sha256=KCdhFdThm9TGkUvhGzQF3zR9SoZ9ont1z8yZELB2TtQ,7752
@@ -294,8 +294,8 @@ junifer/preprocess/smoothing/tests/test_smoothing.py,sha256=t1j3zEvJk5XLO4fzcb-w
 junifer/preprocess/tests/test_preprocess_base.py,sha256=-0rpe8QjqYES36H6MHuDs3cv_6upHBdVHnFMgQsmEX4,2571
 junifer/preprocess/warping/__init__.py,sha256=rzUUP7-6H_nygQ7a7TBZ4_RY7p0ELacosYsWQbSdVZk,214
 junifer/preprocess/warping/__init__.pyi,sha256=Drbqp8N3uprvXcKSxqdfj90fesz9XYVLgivhPnKAYcc,65
-junifer/preprocess/warping/_ants_warper.py,sha256=oJrTW_YG-VJ-piq_L1CX5fEoERyRtsMpFEQQ-0fUFMg,6502
-junifer/preprocess/warping/_fsl_warper.py,sha256=IV_vkn3TGDPWM_N-hEQv1YC4LYMTfZfDmuYu5MW_TQ8,3798
+junifer/preprocess/warping/_ants_warper.py,sha256=BHfweLDtq3J8NmgUFvA7bfWIN4kDvo0RiB1fNDJ71qw,6502
+junifer/preprocess/warping/_fsl_warper.py,sha256=yilHysV9t9bkBDK_eQzjROzlwhXStVzflCaEkxkwjlY,3798
 junifer/preprocess/warping/py.typed,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 junifer/preprocess/warping/space_warper.py,sha256=mf7SDu574R3TXNt82fqGl_hcEYx7SjXwz2TcmWObHQA,7706
 junifer/preprocess/warping/tests/test_space_warper.py,sha256=amFHtt-q7L7v9uL4cOvrmHEbUOGDhmoMHkLnKJ0dF7A,5543
@@ -341,10 +341,10 @@ junifer/utils/tests/test_config.py,sha256=7ltIXuwb_W4Mv_1dxQWyiyM10XgUAfsWKV6D_i
 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=duO4ou365hxwa_kwihFtKPLaL6LC5XHiyhOijrrngbA,8009
-junifer-0.0.6.dev285.dist-info/AUTHORS.rst,sha256=rmULKpchpSol4ExWFdm-qu4fkpSZPYqIESVJBZtGb6E,163
-junifer-0.0.6.dev285.dist-info/LICENSE.md,sha256=MqCnOBu8uXsEOzRZWh9EBVfVz-kE9NkXcLCrtGXo2yU,34354
-junifer-0.0.6.dev285.dist-info/METADATA,sha256=fplMcovyUZPFi6ONcaA66A1mhJkxK4a3948mXRfW328,8429
-junifer-0.0.6.dev285.dist-info/WHEEL,sha256=PZUExdf71Ui_so67QXpySuHtCi3-J3wvF4ORK6k_S8U,91
-junifer-0.0.6.dev285.dist-info/entry_points.txt,sha256=6O8ru0BP-SP7YMUZiizFNoaZ2HvJpadO2G7nKk4PwjI,48
-junifer-0.0.6.dev285.dist-info/top_level.txt,sha256=4bAq1R2QFQ4b3hohjys2JBvxrl0GKk5LNFzYvz9VGcA,8
-junifer-0.0.6.dev285.dist-info/RECORD,,
+junifer-0.0.6.dev302.dist-info/AUTHORS.rst,sha256=rmULKpchpSol4ExWFdm-qu4fkpSZPYqIESVJBZtGb6E,163
+junifer-0.0.6.dev302.dist-info/LICENSE.md,sha256=MqCnOBu8uXsEOzRZWh9EBVfVz-kE9NkXcLCrtGXo2yU,34354
+junifer-0.0.6.dev302.dist-info/METADATA,sha256=-xzY1LfIMeHg8ism1hOUBXsfcyjaW58Mu1VuATPtKXY,8429
+junifer-0.0.6.dev302.dist-info/WHEEL,sha256=PZUExdf71Ui_so67QXpySuHtCi3-J3wvF4ORK6k_S8U,91
+junifer-0.0.6.dev302.dist-info/entry_points.txt,sha256=6O8ru0BP-SP7YMUZiizFNoaZ2HvJpadO2G7nKk4PwjI,48
+junifer-0.0.6.dev302.dist-info/top_level.txt,sha256=4bAq1R2QFQ4b3hohjys2JBvxrl0GKk5LNFzYvz9VGcA,8
+junifer-0.0.6.dev302.dist-info/RECORD,,