junifer 0.0.4.dev477__tar.gz → 0.0.4.dev493__tar.gz

{junifer-0.0.4.dev477 → junifer-0.0.4.dev493}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: junifer
-Version: 0.0.4.dev477
+Version: 0.0.4.dev493
 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>
@@ -28,6 +28,7 @@ License-File: LICENSE.md
 License-File: AUTHORS.rst
 Requires-Dist: click<8.2,>=8.1.3
 Requires-Dist: numpy<1.27,>=1.24
+Requires-Dist: scipy<=1.11.4,>=1.9.0
 Requires-Dist: datalad<0.20,>=0.15.4
 Requires-Dist: pandas<2.2,>=1.4.0
 Requires-Dist: nibabel<5.11,>=3.2.0

junifer-0.0.4.dev493/docs/changes/newsfragments/284.bugfix

@@ -0,0 +1 @@
+Avoid warping mask preprocessed with :class:`.fMRIPrepConfoundRemover` and used by markers with ``mask="inherit"`` in subject-native template space by `Fede Raimondo`_ and `Synchon Mandal`_

junifer-0.0.4.dev493/docs/changes/newsfragments/287.enh

@@ -0,0 +1 @@
+Add ``mode`` as an aggregation function option in :func:`.get_aggfunc_by_name` by `Synchon Mandal`_

{junifer-0.0.4.dev477 → junifer-0.0.4.dev493}/junifer/_version.py

@@ -12,5 +12,5 @@ __version__: str
 __version_tuple__: VERSION_TUPLE
 version_tuple: VERSION_TUPLE
 
-__version__ = version = '0.0.4.dev477'
-__version_tuple__ = version_tuple = (0, 0, 4, 'dev477')
+__version__ = version = '0.0.4.dev493'
+__version_tuple__ = version_tuple = (0, 0, 4, 'dev493')

{junifer-0.0.4.dev477 → junifer-0.0.4.dev493}/junifer/api/tests/test_api_utils.py

@@ -35,6 +35,7 @@ def test_get_dependency_information_short() -> None:
     assert list(dependency_information.keys()) == [
         "click",
         "numpy",
+        "scipy",
         "datalad",
         "pandas",
         "nibabel",
@@ -51,6 +52,7 @@ def test_get_dependency_information_long() -> None:
     for key in [
         "click",
         "numpy",
+        "scipy",
         "datalad",
         "pandas",
         "nibabel",

{junifer-0.0.4.dev477 → junifer-0.0.4.dev493}/junifer/data/masks.py

@@ -280,12 +280,16 @@ def get_mask(  # noqa: C901
                     f"because the item ({inherited_mask_item}) does not exist."
                 )
             mask_img = extra_input[inherited_mask_item]["data"]
+            mask_space = target_data["space"]
         # Starting with new mask
         else:
             # Load mask
             mask_object, _, mask_space = load_mask(
                 mask_name, path_only=False, resolution=resolution
             )
+            # Replace mask space with target space if mask's space is inherit
+            if mask_space == "inherit":
+                mask_space = target_data["space"]
             # If mask is callable like from nilearn
             if callable(mask_object):
                 if mask_params is None:
@@ -306,20 +310,22 @@ def get_mask(  # noqa: C901
                     interpolation="nearest",
                     copy=True,
                 )
-            all_spaces.append(mask_space)
+        all_spaces.append(mask_space)
         all_masks.append(mask_img)
 
     # Multiple masks, need intersection / union
     if len(all_masks) > 1:
-        # Filter out "inherit" and make a set for spaces
-        filtered_spaces = set(filter(lambda x: x != "inherit", all_spaces))
+        # Make a set of unique spaces
+        unique_spaces = set(all_spaces)
         # Intersect / union of masks only if all masks are in the same space
-        if len(filtered_spaces) == 1:
+        if len(unique_spaces) == 1:
             mask_img = intersect_masks(all_masks, **intersect_params)
+            # Store the mask space for further checks
+            mask_space = next(iter(unique_spaces))
         else:
             raise_error(
                 msg=(
-                    f"Masks are in different spaces: {filtered_spaces}, "
+                    f"Masks are in different spaces: {unique_spaces}, "
                     "unable to merge."
                 ),
                 klass=RuntimeError,
@@ -333,9 +339,10 @@ def get_mask(  # noqa: C901
                 "when there is only one mask."
             )
         mask_img = all_masks[0]
+        mask_space = all_spaces[0]
 
-    # Warp mask if target data is native
-    if target_data["space"] == "native":
+    # Warp mask if target data is native and mask space is not native
+    if target_data["space"] == "native" and target_data["space"] != mask_space:
         # Check for extra inputs
         if extra_input is None:
             raise_error(

{junifer-0.0.4.dev477 → junifer-0.0.4.dev493}/junifer/data/tests/test_masks.py

@@ -392,7 +392,9 @@ def test_get_mask_inherit() -> None:
 
         # Now get the mask using the inherit functionality, passing the
         # computed mask as extra data
-        extra_input = {"BOLD_MASK": {"data": gm_mask}}
+        extra_input = {
+            "BOLD_MASK": {"data": gm_mask, "space": input["BOLD"]["space"]}
+        }
         input["BOLD"]["mask_item"] = "BOLD_MASK"
         mask2 = get_mask(
             masks="inherit", target_data=input["BOLD"], extra_input=extra_input
@@ -405,11 +407,9 @@ def test_get_mask_inherit() -> None:
 @pytest.mark.parametrize(
     "masks,params",
     [
-        (["GM_prob0.2", "compute_brain_mask"], {}),
-        (
-            ["GM_prob0.2", "compute_brain_mask"],
-            {"threshold": 0.2},
-        ),
+        (["GM_prob0.2", "GM_prob0.2_cortex"], {}),
+        (["compute_brain_mask", "compute_background_mask"], {}),
+        (["compute_brain_mask", "compute_epi_mask"], {}),
     ],
 )
 def test_get_mask_multiple(

{junifer-0.0.4.dev477 → junifer-0.0.4.dev493}/junifer/preprocess/confounds/fmriprep_confound_remover.py

@@ -574,7 +574,10 @@ class fMRIPrepConfoundRemover(BasePreprocessor):
             # this allows to use "inherit" down the pipeline
             if extra_input is not None:
                 logger.debug("Setting mask_item")
-                extra_input["BOLD_mask"] = {"data": mask_img}
+                extra_input["BOLD_mask"] = {
+                    "data": mask_img,
+                    "space": input["space"],
+                }
                 input["mask_item"] = "BOLD_mask"
 
         logger.info("Cleaning image")

{junifer-0.0.4.dev477 → junifer-0.0.4.dev493}/junifer/stats.py

@@ -7,7 +7,7 @@
 from typing import Any, Callable, Dict, List, Optional
 
 import numpy as np
-from scipy.stats import trim_mean
+from scipy.stats import mode, trim_mean
 from scipy.stats.mstats import winsorize
 
 from .utils import logger, raise_error
@@ -24,10 +24,11 @@ def get_aggfunc_by_name(
         Name to identify the function. Currently supported names and
         corresponding functions are:
 
-        * ``winsorized_mean`` -> :func:`scipy.stats.mstats.winsorize`
         * ``mean`` -> :func:`numpy.mean`
-        * ``std`` -> :func:`numpy.std`
+        * ``winsorized_mean`` -> :func:`scipy.stats.mstats.winsorize`
         * ``trim_mean`` -> :func:`scipy.stats.trim_mean`
+        * ``mode`` -> :func:`scipy.stats.mode`
+        * ``std`` -> :func:`numpy.std`
         * ``count`` -> :func:`.count`
         * ``select`` -> :func:`.select`
 
@@ -40,6 +41,7 @@ def get_aggfunc_by_name(
     -------
     function
         Respective function with ``func_params`` parameter set.
+
     """
     from functools import partial  # local import to avoid sphinx error
 
@@ -51,6 +53,7 @@ def get_aggfunc_by_name(
         "trim_mean",
         "count",
         "select",
+        "mode",
     }
     if func_params is None:
         func_params = {}
@@ -93,6 +96,8 @@ def get_aggfunc_by_name(
         elif pick is not None and drop is not None:
             raise_error("Either pick or drop must be specified, not both.")
         func = partial(select, **func_params)
+    elif name == "mode":
+        func = partial(mode, **func_params)
     else:
         raise_error(
             f"Function {name} unknown. Please provide any of "
@@ -115,6 +120,7 @@ def count(data: np.ndarray, axis: int = 0) -> np.ndarray:
     -------
     numpy.ndarray
         Number of elements along the given axis.
+
     """
     ax_size = data.shape[axis]
     if axis < 0:
@@ -137,7 +143,7 @@ def winsorized_mean(
         The axis to calculate winsorized mean on (default None).
     **win_params : dict
         Dictionary containing the keyword arguments for the winsorize function.
-        E.g. ``{'limits': [0.1, 0.1]}``.
+        E.g., ``{'limits': [0.1, 0.1]}``.
 
     Returns
     -------
@@ -149,6 +155,7 @@ def winsorized_mean(
     --------
     scipy.stats.mstats.winsorize :
         The winsorize function used in this function.
+
     """
     win_dat = winsorize(data, axis=axis, **win_params)
     win_mean = win_dat.mean(axis=axis)
@@ -180,6 +187,13 @@ def select(
     numpy.ndarray
         Subset of the inputted data with the select settings
         applied as specified in ``select_params``.
+
+    Raises
+    ------
+    ValueError
+        If both ``pick`` and ``drop`` are None or
+        if both ``pick`` and ``drop`` are not None.
+
     """
 
     if pick is None and drop is None:

{junifer-0.0.4.dev477 → junifer-0.0.4.dev493}/junifer/tests/test_stats.py

@@ -21,6 +21,8 @@ from junifer.stats import count, get_aggfunc_by_name, select, winsorized_mean
         ("count", None),
         ("trim_mean", None),
         ("trim_mean", {"proportiontocut": 0.1}),
+        ("mode", None),
+        ("mode", {"keepdims": True}),
     ],
 )
 def test_get_aggfunc_by_name(name: str, params: Optional[Dict]) -> None:

{junifer-0.0.4.dev477 → junifer-0.0.4.dev493}/junifer.egg-info/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: junifer
-Version: 0.0.4.dev477
+Version: 0.0.4.dev493
 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>
@@ -28,6 +28,7 @@ License-File: LICENSE.md
 License-File: AUTHORS.rst
 Requires-Dist: click<8.2,>=8.1.3
 Requires-Dist: numpy<1.27,>=1.24
+Requires-Dist: scipy<=1.11.4,>=1.9.0
 Requires-Dist: datalad<0.20,>=0.15.4
 Requires-Dist: pandas<2.2,>=1.4.0
 Requires-Dist: nibabel<5.11,>=3.2.0

{junifer-0.0.4.dev477 → junifer-0.0.4.dev493}/junifer.egg-info/SOURCES.txt

@@ -94,7 +94,9 @@ docs/changes/newsfragments/281.bugfix
 docs/changes/newsfragments/281.misc
 docs/changes/newsfragments/282.bugfix
 docs/changes/newsfragments/283.bugfix
+docs/changes/newsfragments/284.bugfix
 docs/changes/newsfragments/286.bugfix
+docs/changes/newsfragments/287.enh
 docs/changes/newsfragments/288.misc
 docs/changes/newsfragments/291.doc
 docs/changes/newsfragments/294.misc

{junifer-0.0.4.dev477 → junifer-0.0.4.dev493}/junifer.egg-info/requires.txt

@@ -1,5 +1,6 @@
 click<8.2,>=8.1.3
 numpy<1.27,>=1.24
+scipy<=1.11.4,>=1.9.0
 datalad<0.20,>=0.15.4
 pandas<2.2,>=1.4.0
 nibabel<5.11,>=3.2.0

{junifer-0.0.4.dev477 → junifer-0.0.4.dev493}/pyproject.toml

@@ -37,6 +37,7 @@ classifiers = [
 dependencies = [
     "click>=8.1.3,<8.2",
     "numpy>=1.24,<1.27",
+    "scipy>=1.9.0,<=1.11.4",
     "datalad>=0.15.4,<0.20",
     "pandas>=1.4.0,<2.2",
     "nibabel>=3.2.0,<5.11",
@@ -177,6 +178,7 @@ known-first-party = ["junifer"]
 known-third-party =[
     "click",
     "numpy",
+    "scipy",
     "datalad",
     "pandas",
     "nibabel",