junifer 0.0.4.dev477__py3-none-any.whl → 0.0.4.dev493__py3-none-any.whl

junifer/_version.py

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

junifer/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/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/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/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/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/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.dist-info → junifer-0.0.4.dev493.dist-info}/METADATA

@@ -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.dist-info → junifer-0.0.4.dev493.dist-info}/RECORD

@@ -1,6 +1,6 @@
 junifer/__init__.py,sha256=x1UR2jUcrUdm2HNl-3Qvyi4UUrU6ms5qm2qcmNY7zZk,391
-junifer/_version.py,sha256=M4X3STs52HWvFyMwLZ_m-ldav_VVRF4lDp3N_LiwSn8,428
-junifer/stats.py,sha256=KUX4jJcLWnlE34coet8EkdFypFd-td4Vtpx5LvlomVs,5879
+junifer/_version.py,sha256=s3b4obIT6-Dm0gw7Hf_6VelPhsN39hihLhhrnI_A6sU,428
+junifer/stats.py,sha256=sU5IZ2qFZWbzgSutQS_z42miIVItpSGmQYBn6KkD5fA,6162
 junifer/api/__init__.py,sha256=YILu9M7SC0Ri4CVd90fELH2OnK_gvCYAXCoqBNCFE8E,257
 junifer/api/cli.py,sha256=xScav2mF-Jr8JjVFt8kaHuLpX5l_jVTaQGPgQL3VNvA,12881
 junifer/api/decorators.py,sha256=8bnwHPAe7VgzKxl--M_e0umdAlTVSzaJQHEJZ5kof5k,2580
@@ -21,7 +21,7 @@ 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=mRLtZo0OgDwleoee2MG6rYI37HVuGNk9zOADwcl97RA,1122
 junifer/api/res/fsl/std2imgcoord,sha256=-X5wRH6XMl0yqnTACJX6MFhO8DFOEWg42MHRxGvimXg,49
-junifer/api/tests/test_api_utils.py,sha256=_ykEECJN0qTEBcJ2YSvOAQrRN-xmEilRLPyirC5cO_o,2285
+junifer/api/tests/test_api_utils.py,sha256=dexkg5U8JSo3wEU6EUIWnPNuVzHxRMXH1o2sBchMEu0,2319
 junifer/api/tests/test_cli.py,sha256=qKWkAf-A1DeDwCtrOaCrQ5bmuUYcLWeRbGk2K95OMHQ,5717
 junifer/api/tests/test_functions.py,sha256=0XHxCC7-jfVqV7m-R-eGiEwZPjEoBzdS0zperVIyNow,24659
 junifer/api/tests/test_parser.py,sha256=eUz2JPVb0_cxvoeI1O_C5PMNs5v_lDzGsN6fV1VW5Eg,6109
@@ -42,7 +42,7 @@ junifer/configs/juseless/datagrabbers/tests/test_ucla.py,sha256=e-jdvcZ9B0mka6_5
 junifer/configs/juseless/datagrabbers/tests/test_ukb_vbm.py,sha256=b9hjc1mgO--PSRC3id2EzzfE2yWNsuZ2UI47a6sfGZU,1025
 junifer/data/__init__.py,sha256=oUjOs8_M6fitNb44izxpXf3su1e4pG_vCdjwVYkjZjQ,550
 junifer/data/coordinates.py,sha256=rwjPb6hYlCpxqM73UNatl7bLtXEF9o8nIEwXz1iwERE,11317
-junifer/data/masks.py,sha256=chWSl-vyv5Nsd9GuQzydXPOY3AdhApOJq_42NSKpykQ,16952
+junifer/data/masks.py,sha256=gsA8_1l011uq2E0hRZvQvfk3_ER8HFsmWd3h6o5qPxE,17311
 junifer/data/parcellations.py,sha256=wL8lkAYYvg7NDt160EA8N_xFjK8ZtDwoXYJQHNHwbDU,55805
 junifer/data/utils.py,sha256=K9quLIoWRmm2QFM8Rdy_5bYsWb_XhL0l5Uq_1Sie0kA,1274
 junifer/data/VOIs/meta/CogAC_VOIs.txt,sha256=Sr5_E712OLdeQRyUcDNM0wLBvZIyO6gc9Q7KkyJHX1A,398
@@ -68,7 +68,7 @@ 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=Vy7x8zaHws5hmn92PKSv3H38hU2kamOpyaH6nG_NNpw,1086
-junifer/data/tests/test_masks.py,sha256=njo6yEzrBYDsojm6_7xGV3B8FvjmjK3zX3WBBYAs7aA,14496
+junifer/data/tests/test_masks.py,sha256=Q_iMNktcxweRzoe5esFTpYgjt1pwPqIJk1Gqk0pb5GE,14570
 junifer/data/tests/test_parcellations.py,sha256=3Tk0bU4xT9TJfdrDWcUMq6ns-IPJUpZzkiR-PEbmM6M,36212
 junifer/datagrabber/__init__.py,sha256=pZHJIY8nAlbVngsyRScE6a6GKbytiwjJB7SdJNqIbl4,680
 junifer/datagrabber/base.py,sha256=clErdDX5jz8LTjwPTQPCv3jfELCJ2vObg7ks8imAx8Y,6224
@@ -192,7 +192,7 @@ junifer/preprocess/__init__.py,sha256=-3exohZnw-gJ-MjVM63WcXzBW1mbSetEVozcDfs5et
 junifer/preprocess/base.py,sha256=syiNqI8pUjoGyShZSjs_RTsd5VHhwoqzIfPfFstr4f4,6230
 junifer/preprocess/bold_warper.py,sha256=Sia8mCdluYNrFkYsRx0vP-z_RNF7x-dwHcEDkmpvnHo,3277
 junifer/preprocess/confounds/__init__.py,sha256=EDlcD9jy8O9xluJr6XOnFXtjGCDVqwg6sDIRDMbM8ZU,235
-junifer/preprocess/confounds/fmriprep_confound_remover.py,sha256=C6P00Ge5j5vxu7HSz4OXFML2aQAQseGXM45fXl-vTbs,21820
+junifer/preprocess/confounds/fmriprep_confound_remover.py,sha256=23UJ6miqX0iE3dUMsZ1hzWoJDnMLl6WMlT-k9GFmAAU,21904
 junifer/preprocess/confounds/tests/test_fmriprep_confound_remover.py,sha256=OKACXAHytNrOAFZ5I2UcyfcYz5s2qeu31MZ9K71rWGc,22167
 junifer/preprocess/fsl/__init__.py,sha256=DerGFQ-dIuX5PT9a_BH6QkIXkJZVymjYy-woXF7tYGc,111
 junifer/preprocess/fsl/apply_warper.py,sha256=QTls4z2oF0qVqZ_S1yc-uYNUE9MeJZR4Lesv98SnJrc,7915
@@ -220,16 +220,16 @@ junifer/testing/tests/test_partlycloudytesting_datagrabber.py,sha256=1VY71RhGtLD
 junifer/testing/tests/test_spmauditory_datagrabber.py,sha256=1G1emk-Ze59HiNLaYsyIz5O1YGW9darcqlzvhE-J_Mc,919
 junifer/testing/tests/test_testing_registry.py,sha256=oerticBaPRaRZm3yANzInLac0Mqph3Y0aZPQFayu7xA,827
 junifer/tests/test_main.py,sha256=GMff7jlisGM9_FsiUwWDte43j-KQJGFRYZpwRRqTkd8,373
-junifer/tests/test_stats.py,sha256=u3bLjbshzc5fV207tLM79rR5vHDvNhdN7ZoYI1UTI04,4093
+junifer/tests/test_stats.py,sha256=3vPMgYYpWxk8ECDFOMm3-dFBlh4XxjL83SwRBSBAHok,4155
 junifer/utils/__init__.py,sha256=ZDPU9ezSKawAJhb-3T67jDf-16QEyF6e7ONyu-lnBtQ,277
 junifer/utils/fs.py,sha256=Jd9AoV2fIF7pT7KhXsn8T1O1fJ1_SFZgaFuOBAM7DG8,460
 junifer/utils/logging.py,sha256=4kH8j9X_J2bMdnBJMldVF95C5sURa5UAsLmSgRaD9Ig,9117
 junifer/utils/tests/test_fs.py,sha256=WQS7cKlKEZ742CIuiOYYpueeAhY9PqlastfDVpVVtvE,923
 junifer/utils/tests/test_logging.py,sha256=l8oo-AiBV7H6_IzlsNcj__cLeZBUvgIGoaMszD9VaJg,7754
-junifer-0.0.4.dev477.dist-info/AUTHORS.rst,sha256=rmULKpchpSol4ExWFdm-qu4fkpSZPYqIESVJBZtGb6E,163
-junifer-0.0.4.dev477.dist-info/LICENSE.md,sha256=MqCnOBu8uXsEOzRZWh9EBVfVz-kE9NkXcLCrtGXo2yU,34354
-junifer-0.0.4.dev477.dist-info/METADATA,sha256=rRpLolV-SBGOl-4ktutkDrIhIpWnB9fjsFS55rS66QM,7707
-junifer-0.0.4.dev477.dist-info/WHEEL,sha256=oiQVh_5PnQM0E3gPdiz09WCNmwiHDMaGer_elqB3coM,92
-junifer-0.0.4.dev477.dist-info/entry_points.txt,sha256=DxFvKq0pOqRunAK0FxwJcoDfV1-dZvsFDpD5HRqSDhw,48
-junifer-0.0.4.dev477.dist-info/top_level.txt,sha256=4bAq1R2QFQ4b3hohjys2JBvxrl0GKk5LNFzYvz9VGcA,8
-junifer-0.0.4.dev477.dist-info/RECORD,,
+junifer-0.0.4.dev493.dist-info/AUTHORS.rst,sha256=rmULKpchpSol4ExWFdm-qu4fkpSZPYqIESVJBZtGb6E,163
+junifer-0.0.4.dev493.dist-info/LICENSE.md,sha256=MqCnOBu8uXsEOzRZWh9EBVfVz-kE9NkXcLCrtGXo2yU,34354
+junifer-0.0.4.dev493.dist-info/METADATA,sha256=_3K04VVuQxUyuIslgoc7stjFrg9UP2yAychS_LN6gtY,7745
+junifer-0.0.4.dev493.dist-info/WHEEL,sha256=oiQVh_5PnQM0E3gPdiz09WCNmwiHDMaGer_elqB3coM,92
+junifer-0.0.4.dev493.dist-info/entry_points.txt,sha256=DxFvKq0pOqRunAK0FxwJcoDfV1-dZvsFDpD5HRqSDhw,48
+junifer-0.0.4.dev493.dist-info/top_level.txt,sha256=4bAq1R2QFQ4b3hohjys2JBvxrl0GKk5LNFzYvz9VGcA,8
+junifer-0.0.4.dev493.dist-info/RECORD,,