junifer 0.0.5.dev180__tar.gz → 0.0.5.dev183__tar.gz

{junifer-0.0.5.dev180 → junifer-0.0.5.dev183}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: junifer
-Version: 0.0.5.dev180
+Version: 0.0.5.dev183
 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.dev183/docs/changes/newsfragments/350.enh

@@ -0,0 +1 @@
+Add support for ``UKB_15K_GM`` mask by `Synchon Mandal`_

{junifer-0.0.5.dev180 → junifer-0.0.5.dev183}/junifer/_version.py

@@ -12,5 +12,5 @@ __version__: str
 __version_tuple__: VERSION_TUPLE
 version_tuple: VERSION_TUPLE
 
-__version__ = version = '0.0.5.dev180'
-__version_tuple__ = version_tuple = (0, 0, 5, 'dev180')
+__version__ = version = '0.0.5.dev183'
+__version_tuple__ = version_tuple = (0, 0, 5, 'dev183')

{junifer-0.0.5.dev180 → junifer-0.0.5.dev183}/junifer/data/masks.py

@@ -163,6 +163,10 @@ _available_masks: Dict[str, Dict[str, Any]] = {
         "func": compute_epi_mask,
         "space": "inherit",
     },
+    "UKB_15K_GM": {
+        "family": "UKB",
+        "space": "MNI152NLin6Asym",
+    },
 }
 
 
@@ -567,6 +571,8 @@ def load_mask(
     elif t_family == "Callable":
         mask_img = mask_definition["func"]
         mask_fname = None
+    elif t_family == "UKB":
+        mask_fname = _load_ukb_mask(name)
     else:
         raise_error(f"I don't know about the {t_family} mask family.")
 
@@ -632,3 +638,33 @@ def _load_vickery_patil_mask(
     mask_fname = _masks_path / "vickery-patil" / mask_fname
 
     return mask_fname
+
+
+def _load_ukb_mask(name: str) -> Path:
+    """Load UKB mask.
+
+    Parameters
+    ----------
+    name : {"UKB_15K_GM"}
+        The name of the mask.
+
+    Returns
+    -------
+    pathlib.Path
+        File path to the mask image.
+
+    Raises
+    ------
+    ValueError
+        If ``name`` is invalid.
+
+    """
+    if name == "UKB_15K_GM":
+        mask_fname = "UKB_15K_GM_template.nii.gz"
+    else:
+        raise_error(f"Cannot find a UKB mask called {name}")
+
+    # Set path for masks
+    mask_fname = _masks_path / "ukb" / mask_fname
+
+    return mask_fname

{junifer-0.0.5.dev180 → junifer-0.0.5.dev183}/junifer/data/tests/test_masks.py

@@ -22,6 +22,7 @@ from numpy.testing import assert_array_almost_equal, assert_array_equal
 
 from junifer.data.masks import (
     _available_masks,
+    _load_ukb_mask,
     _load_vickery_patil_mask,
     compute_brain_mask,
     get_mask,
@@ -212,6 +213,7 @@ def test_register_mask(
     [
         "GM_prob0.2",
         "GM_prob0.2_cortex",
+        "UKB_15K_GM",
     ],
 )
 def test_list_masks_correct(mask_name: str) -> None:
@@ -291,6 +293,21 @@ def test_vickery_patil_error() -> None:
         _load_vickery_patil_mask(name="wrong", resolution=2.0)
 
 
+def test_ukb() -> None:
+    """Test UKB mask."""
+    mask, mask_fname, space = load_mask("UKB_15K_GM", resolution=2.0)
+    assert_array_almost_equal(mask.header["pixdim"][1:4], 2.0)  # type: ignore
+    assert space == "MNI152NLin6Asym"
+    assert mask_fname is not None
+    assert mask_fname.name == "UKB_15K_GM_template.nii.gz"
+
+
+def test_ukb_error() -> None:
+    """Test error for UKB mask."""
+    with pytest.raises(ValueError, match=r"find a UKB mask "):
+        _load_ukb_mask(name="wrong")
+
+
 def test_get_mask() -> None:
     """Test the get_mask function."""
     with OasisVBMTestingDataGrabber() as dg:

{junifer-0.0.5.dev180 → junifer-0.0.5.dev183}/junifer.egg-info/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: junifer
-Version: 0.0.5.dev180
+Version: 0.0.5.dev183
 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.dev180 → junifer-0.0.5.dev183}/junifer.egg-info/SOURCES.txt

@@ -80,6 +80,7 @@ docs/changes/newsfragments/345.feature
 docs/changes/newsfragments/346.enh
 docs/changes/newsfragments/346.feature
 docs/changes/newsfragments/347.misc
+docs/changes/newsfragments/350.enh
 docs/extending/coordinates.rst
 docs/extending/datagrabber.rst
 docs/extending/dependencies.rst
@@ -205,6 +206,7 @@ junifer/data/VOIs/meta/WM_VOIs.txt
 junifer/data/VOIs/meta/eMDN_VOIs.txt
 junifer/data/VOIs/meta/eSAD_VOIs.txt
 junifer/data/VOIs/meta/extDMN_VOIs.txt
+junifer/data/masks/ukb/UKB_15K_GM_template.nii.gz
 junifer/data/masks/vickery-patil/CAT12_IXI555_MNI152_TMP_GS_GMprob0.2_clean.nii.gz
 junifer/data/masks/vickery-patil/CAT12_IXI555_MNI152_TMP_GS_GMprob0.2_clean_3mm.nii.gz
 junifer/data/masks/vickery-patil/GMprob0.2_cortex_3mm_NA_rm.nii.gz