junifer 0.0.6.dev445__tar.gz → 0.0.6.dev474__tar.gz

{junifer-0.0.6.dev445 → junifer-0.0.6.dev474}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.2
 Name: junifer
-Version: 0.0.6.dev445
+Version: 0.0.6.dev474
 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>
@@ -44,6 +44,7 @@ Requires-Dist: lapy<2.0.0,>=1.0.0
 Requires-Dist: lazy_loader==0.4
 Requires-Dist: importlib_metadata; python_version < "3.9"
 Requires-Dist: looseversion==1.3.0; python_version >= "3.12"
+Requires-Dist: junifer_data==1.1.0
 Provides-Extra: all
 Requires-Dist: bctpy==0.6.0; extra == "all"
 Requires-Dist: neurokit2>=0.1.7; extra == "all"

junifer-0.0.6.dev474/docs/changes/newsfragments/421.change

@@ -0,0 +1 @@
+Add ``scrub``, ``fd_threshold`` and ``std_vars_threshold`` parameters to :class:`.fMRIPrepConfoundRemover` and allow ``"scrubbing"`` key of type bool for ``strategy`` by `Synchon Mandal`_

junifer-0.0.6.dev474/docs/changes/newsfragments/421.enh

@@ -0,0 +1 @@
+Add scrubbing support to :class:`.fMRIPrepConfoundRemover` by `Synchon Mandal`_

{junifer-0.0.6.dev445 → junifer-0.0.6.dev474}/junifer/_version.py

@@ -12,5 +12,5 @@ __version__: str
 __version_tuple__: VERSION_TUPLE
 version_tuple: VERSION_TUPLE
 
-__version__ = version = '0.0.6.dev445'
-__version_tuple__ = version_tuple = (0, 0, 6, 'dev445')
+__version__ = version = '0.0.6.dev474'
+__version_tuple__ = version_tuple = (0, 0, 6, 'dev474')

{junifer-0.0.6.dev445 → junifer-0.0.6.dev474}/junifer/cli/tests/test_cli_utils.py

@@ -48,6 +48,7 @@ def test_get_dependency_information_short() -> None:
         "lapy",
         "lazy_loader",
         "looseversion",
+        "junifer_data",
     ]
 
     if sys.version_info < (3, 11):

{junifer-0.0.6.dev445 → junifer-0.0.6.dev474}/junifer/data/coordinates/_coordinates.py

@@ -4,16 +4,18 @@
 #          Synchon Mandal <s.mandal@fz-juelich.de>
 # License: AGPL
 
+from pathlib import Path
 from typing import Any, Optional
 
 import numpy as np
 import pandas as pd
+from junifer_data import get
 from numpy.typing import ArrayLike
 
 from ...utils import logger, raise_error
 from ...utils.singleton import Singleton
 from ..pipeline_data_registry_base import BasePipelineDataRegistry
-from ..utils import check_dataset, fetch_file_via_datalad, get_native_warper
+from ..utils import JUNIFER_DATA_VERSION, get_dataset_path, get_native_warper
 from ._ants_coordinates_warper import ANTsCoordinatesWarper
 from ._fsl_coordinates_warper import FSLCoordinatesWarper
 
@@ -273,23 +275,17 @@ class CoordinatesRegistry(BasePipelineDataRegistry, metaclass=Singleton):
 
         # Load data for in-built ones
         if t_coord.get("file_path_suffix") is not None:
-            # Get dataset
-            dataset = check_dataset()
             # Set file path to retrieve
-            coords_file_path = (
-                dataset.pathobj
-                / "coordinates"
-                / name
-                / t_coord["file_path_suffix"]
-            )
-            logger.debug(
-                f"Loading coordinates `{name}` from: "
-                f"{coords_file_path.absolute()!s}"
+            coords_file_path = Path(
+                f"coordinates/{name}/{t_coord['file_path_suffix']}"
             )
+            logger.debug(f"Loading coordinates: `{name}`")
             # Load via pandas
             df_coords = pd.read_csv(
-                fetch_file_via_datalad(
-                    dataset=dataset, file_path=coords_file_path
+                get(
+                    file_path=coords_file_path,
+                    dataset_path=get_dataset_path(),
+                    tag=JUNIFER_DATA_VERSION,
                 ),
                 sep="\t",
                 header=None,

{junifer-0.0.6.dev445 → junifer-0.0.6.dev474}/junifer/data/masks/_masks.py

@@ -16,6 +16,7 @@ from typing import (
 import nibabel as nib
 import nilearn.image as nimg
 import numpy as np
+from junifer_data import get
 from nilearn.masking import (
     compute_background_mask,
     compute_epi_mask,
@@ -27,9 +28,9 @@ from ...utils.singleton import Singleton
 from ..pipeline_data_registry_base import BasePipelineDataRegistry
 from ..template_spaces import get_template
 from ..utils import (
-    check_dataset,
+    JUNIFER_DATA_VERSION,
     closest_resolution,
-    fetch_file_via_datalad,
+    get_dataset_path,
     get_native_warper,
 )
 from ._ants_mask_warper import ANTsMaskWarper
@@ -37,7 +38,6 @@ from ._fsl_mask_warper import FSLMaskWarper
 
 
 if TYPE_CHECKING:
-    from datalad.api import Dataset
     from nibabel.nifti1 import Nifti1Image
 
 
@@ -406,17 +406,14 @@ class MaskRegistry(BasePipelineDataRegistry, metaclass=Singleton):
             mask_img = mask_definition["func"]
             mask_fname = None
         elif t_family in ["Vickery-Patil", "UKB"]:
-            # Get dataset
-            dataset = check_dataset()
             # Load mask
             if t_family == "Vickery-Patil":
                 mask_fname = _load_vickery_patil_mask(
-                    dataset=dataset,
                     name=name,
                     resolution=resolution,
                 )
             elif t_family == "UKB":
-                mask_fname = _load_ukb_mask(dataset=dataset, name=name)
+                mask_fname = _load_ukb_mask(name=name)
         else:
             raise_error(f"Unknown mask family: {t_family}")
 
@@ -698,7 +695,6 @@ class MaskRegistry(BasePipelineDataRegistry, metaclass=Singleton):
 
 
 def _load_vickery_patil_mask(
-    dataset: "Dataset",
     name: str,
     resolution: Optional[float] = None,
 ) -> Path:
@@ -706,8 +702,6 @@ def _load_vickery_patil_mask(
 
     Parameters
     ----------
-    dataset : datalad.api.Dataset
-        The datalad dataset to fetch mask from.
     name : {"GM_prob0.2", "GM_prob0.2_cortex"}
         The name of the mask.
     resolution : float, optional
@@ -748,19 +742,18 @@ def _load_vickery_patil_mask(
         raise_error(f"Cannot find a Vickery-Patil mask called {name}")
 
     # Fetch file
-    return fetch_file_via_datalad(
-        dataset=dataset,
-        file_path=dataset.pathobj / "masks" / "Vickery-Patil" / mask_fname,
+    return get(
+        file_path=Path(f"masks/Vickery-Patil/{mask_fname}"),
+        dataset_path=get_dataset_path(),
+        tag=JUNIFER_DATA_VERSION,
     )
 
 
-def _load_ukb_mask(dataset: "Dataset", name: str) -> Path:
+def _load_ukb_mask(name: str) -> Path:
     """Load UKB mask.
 
     Parameters
     ----------
-    dataset : datalad.api.Dataset
-        The datalad dataset to fetch mask from.
     name : {"UKB_15K_GM"}
         The name of the mask.
 
@@ -782,9 +775,10 @@ def _load_ukb_mask(dataset: "Dataset", name: str) -> Path:
         raise_error(f"Cannot find a UKB mask called {name}")
 
     # Fetch file
-    return fetch_file_via_datalad(
-        dataset=dataset,
-        file_path=dataset.pathobj / "masks" / "UKB" / mask_fname,
+    return get(
+        file_path=Path(f"masks/UKB/{mask_fname}"),
+        dataset_path=get_dataset_path(),
+        tag=JUNIFER_DATA_VERSION,
     )
 
 

{junifer-0.0.6.dev445 → junifer-0.0.6.dev474}/junifer/data/masks/tests/test_masks.py

@@ -26,7 +26,6 @@ from junifer.data.masks._masks import (
     _load_ukb_mask,
     _load_vickery_patil_mask,
 )
-from junifer.data.utils import check_dataset
 from junifer.datagrabber import DMCC13Benchmark
 from junifer.datareader import DefaultDataReader
 from junifer.testing.datagrabbers import (
@@ -283,9 +282,7 @@ def test_vickery_patil(
 def test_vickery_patil_error() -> None:
     """Test error for Vickery-Patil mask."""
     with pytest.raises(ValueError, match=r"find a Vickery-Patil mask "):
-        _load_vickery_patil_mask(
-            dataset=check_dataset(), name="wrong", resolution=2.0
-        )
+        _load_vickery_patil_mask(name="wrong", resolution=2.0)
 
 
 def test_ukb() -> None:
@@ -300,7 +297,7 @@ def test_ukb() -> None:
 def test_ukb_error() -> None:
     """Test error for UKB mask."""
     with pytest.raises(ValueError, match=r"find a UKB mask "):
-        _load_ukb_mask(dataset=check_dataset(), name="wrong")
+        _load_ukb_mask(name="wrong")
 
 
 def test_get() -> None: