junifer 0.0.6.dev358__py3-none-any.whl → 0.0.6.dev371__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.dev358'
-__version_tuple__ = version_tuple = (0, 0, 6, 'dev358')
+__version__ = version = '0.0.6.dev371'
+__version_tuple__ = version_tuple = (0, 0, 6, 'dev371')

junifer/data/masks/_masks.py

@@ -14,8 +14,8 @@ from typing import (
 )
 
 import nibabel as nib
+import nilearn.image as nimg
 import numpy as np
-from nilearn.image import get_data, new_img_like, resample_to_img
 from nilearn.masking import (
     compute_background_mask,
     compute_epi_mask,
@@ -48,6 +48,7 @@ def compute_brain_mask(
     mask_type: str = "brain",
     threshold: float = 0.5,
     source: str = "template",
+    template_space: Optional[str] = None,
     extra_input: Optional[dict[str, Any]] = None,
 ) -> "Nifti1Image":
     """Compute the whole-brain, grey-matter or white-matter mask.
@@ -78,6 +79,9 @@ def compute_brain_mask(
         The source of the mask. If "subject", the mask is computed from the
         subject's data (``VBM_GM`` or ``VBM_WM``). If "template", the mask is
         computed from the template data (default "template").
+    template_space : str, optional
+        The space of the template. If not provided, the space is inferred from
+        the ``target_data`` (default None).
     extra_input : dict, optional
          The other fields in the data object. Useful for accessing other data
          types (default None).
@@ -93,6 +97,7 @@ def compute_brain_mask(
         If ``mask_type`` is invalid or
         if ``source`` is invalid or
         if ``source="subject"`` and ``mask_type`` is invalid or
+        if ``template_space`` is provided when ``source="subject"`` or
         if ``warp_data`` is None when ``target_data``'s space is native or
         if ``extra_input`` is None when ``source="subject"`` or
         if ``VBM_GM`` or ``VBM_WM`` data types are not in ``extra_input``
@@ -111,6 +116,9 @@ def compute_brain_mask(
     if source == "subject" and mask_type not in ["gm", "wm"]:
         raise_error(f"Unknown mask type: {mask_type} for subject space")
 
+    if source == "subject" and template_space is not None:
+        raise_error("Cannot provide `template_space` when source is `subject`")
+
     # Check pre-requirements for space manipulation
     if target_data["space"] == "native":
         # Warp data check
@@ -138,15 +146,40 @@ def compute_brain_mask(
             )
         template = extra_input[key]["data"]
         template_space = extra_input[key]["space"]
+        logger.debug(f"Using {key} in {template_space} for mask computation.")
     else:
+        template_resolution = None
+        if template_space is None:
+            template_space = target_std_space
+        elif template_space != target_std_space:
+            # We re going to warp, so get the highest resolution
+            template_resolution = "highest"
+
         # Fetch template in closest resolution
         template = get_template(
-            space=target_std_space,
+            space=template_space,
             target_img=target_data["data"],
             extra_input=None,
             template_type=mask_type,
+            resolution=template_resolution,
         )
-        template_space = target_std_space
+
+    mask_name = f"template_{target_std_space}_for_compute_brain_mask"
+
+    # Warp template to correct space (MNI to MNI)
+    if template_space != "native" and template_space != target_std_space:
+        logger.debug(
+            f"Warping template to {target_std_space} space using ANTs."
+        )
+        template = ANTsMaskWarper().warp(
+            mask_name=mask_name,
+            mask_img=template,
+            src=template_space,
+            dst=target_std_space,
+            target_data=target_data,
+            warp_data=None,
+        )
+
     # Resample and warp template if target space is native
     if target_data["space"] == "native" and template_space != "native":
         if warp_data["warper"] == "fsl":
@@ -168,14 +201,16 @@ def compute_brain_mask(
             )
     # Resample template to target image
     else:
-        resampled_template = resample_to_img(
+        # Resample template to target image
+        resampled_template = nimg.resample_to_img(
             source_img=template, target_img=target_data["data"]
         )
 
     # Threshold resampled template and get mask
-    mask = (get_data(resampled_template) >= threshold).astype("int8")
-
-    return new_img_like(target_data["data"], mask)  # type: ignore
+    logger.debug("Thresholding template to get mask.")
+    mask = (nimg.get_data(resampled_template) >= threshold).astype("int8")
+    logger.debug("Mask computation from brain template complete.")
+    return nimg.new_img_like(target_data["data"], mask)  # type: ignore
 
 
 class MaskRegistry(BasePipelineDataRegistry, metaclass=Singleton):
@@ -523,7 +558,7 @@ class MaskRegistry(BasePipelineDataRegistry, metaclass=Singleton):
                     )
                 logger.debug("Resampling inherited mask to target image.")
                 # Resample inherited mask to target image
-                mask_img = resample_to_img(
+                mask_img = nimg.resample_to_img(
                     source_img=mask_img,
                     target_img=target_data["data"],
                 )
@@ -568,34 +603,41 @@ class MaskRegistry(BasePipelineDataRegistry, metaclass=Singleton):
                             "mask."
                         )
 
+                    # Set here to simplify things later
+                    mask_img: nib.nifti1.Nifti1Image = mask_object
+
                     # Resample and warp mask to standard space
                     if mask_space != target_std_space:
                         logger.debug(
                             f"Warping {t_mask} to {target_std_space} space "
-                            "using ants."
+                            "using ANTs."
                         )
                         mask_img = ANTsMaskWarper().warp(
                             mask_name=mask_name,
-                            mask_img=mask_object,
+                            mask_img=mask_img,
                             src=mask_space,
                             dst=target_std_space,
                             target_data=target_data,
                             warp_data=warper_spec,
                         )
+                        # Remove extra dimension added by ANTs
+                        mask_img = nimg.math_img(
+                            "np.squeeze(img)", img=mask_img
+                        )
 
-                    else:
-                        # Resample mask to target image; no further warping
+                    if target_space != "native":
+                        # No warping is going to happen, just resampling,
+                        # because we are in the correct space
                         logger.debug(f"Resampling {t_mask} to target image.")
-                        if target_space != "native":
-                            mask_img = resample_to_img(
-                                source_img=mask_object,
-                                target_img=target_data["data"],
-                            )
-                        # Set mask_img in case no warping happens before this
-                        else:
-                            mask_img = mask_object
-                    # Resample and warp mask if target data is native
-                    if target_space == "native":
+                        mask_img = nimg.resample_to_img(
+                            source_img=mask_img,
+                            target_img=target_img,
+                        )
+                    else:
+                        # Warp mask if target space is native as
+                        # either the image is in the right non-native space or
+                        # it's warped from one non-native space to another
+                        # non-native space
                         logger.debug(
                             "Warping mask to native space using "
                             f"{warper_spec['warper']}."

junifer/data/parcellations/_parcellations.py

@@ -16,9 +16,10 @@ from typing import TYPE_CHECKING, Any, Optional, Union
 
 import httpx
 import nibabel as nib
+import nilearn.image as nimg
 import numpy as np
 import pandas as pd
-from nilearn import datasets, image
+from nilearn import datasets
 
 from ...utils import logger, raise_error, warn_with_log
 from ...utils.singleton import Singleton
@@ -470,28 +471,23 @@ class ParcellationRegistry(BasePipelineDataRegistry, metaclass=Singleton):
                     warp_data=None,
                 )
                 # Remove extra dimension added by ANTs
-                img = image.math_img("np.squeeze(img)", img=raw_img)
-                # Set correct affine as resolution won't be correct
-                img = image.resample_img(
-                    img=img,
-                    target_affine=target_img.affine,
+                img = nimg.math_img("np.squeeze(img)", img=raw_img)
+
+            if target_space != "native":
+                # No warping is going to happen, just resampling, because
+                # we are in the correct space
+                logger.debug(f"Resampling {name} to target image.")
+                # Resample parcellation to target image
+                img = nimg.resample_to_img(
+                    source_img=img,
+                    target_img=target_img,
                     interpolation="nearest",
+                    copy=True,
                 )
             else:
-                if target_space != "native":
-                    # No warping is going to happen, just resampling, because
-                    # we are in the correct space
-                    logger.debug(f"Resampling {name} to target image.")
-                    # Resample parcellation to target image
-                    img = image.resample_to_img(
-                        source_img=img,
-                        target_img=target_img,
-                        interpolation="nearest",
-                        copy=True,
-                    )
-
-            # Warp parcellation if target space is native
-            if target_space == "native":
+                # Warp parcellation if target space is native as either
+                # the image is in the right non-native space or it's
+                # warped from one non-native space to another non-native space
                 logger.debug(
                     "Warping parcellation to native space using "
                     f"{warper_spec['warper']}."
@@ -1807,7 +1803,7 @@ def merge_parcellations(
                 "The parcellations have different resolutions!"
                 "Resampling all parcellations to the first one in the list."
             )
-            t_parc = image.resample_to_img(
+            t_parc = nimg.resample_to_img(
                 t_parc, ref_parc, interpolation="nearest", copy=True
             )
 
@@ -1833,6 +1829,6 @@ def merge_parcellations(
             "parcellation that was first in the list."
         )
 
-    parcellation_img_res = image.new_img_like(parcellations_list[0], parc_data)
+    parcellation_img_res = nimg.new_img_like(parcellations_list[0], parc_data)
 
     return parcellation_img_res, labels

junifer/data/template_spaces.py

@@ -125,6 +125,7 @@ def get_template(
     target_img: nib.Nifti1Image,
     extra_input: Optional[dict[str, Any]] = None,
     template_type: str = "T1w",
+    resolution: Optional[Union[int, "str"]] = None,
 ) -> nib.Nifti1Image:
     """Get template for the space, tailored for the target image.
 
@@ -140,6 +141,10 @@ def get_template(
         types (default None).
     template_type : {"T1w", "brain", "gm", "wm", "csf"}, optional
         The template type to retrieve (default "T1w").
+    resolution : int or "highest", optional
+        The resolution of the template to fetch. If None, the closest
+        resolution to the target image is used (default None). If "highest",
+        the highest resolution is used.
 
     Returns
     -------
@@ -149,7 +154,8 @@ def get_template(
     Raises
     ------
     ValueError
-        If ``space`` or ``template_type`` is invalid.
+        If ``space`` or ``template_type`` is invalid or
+        if ``resolution`` is not at int or "highest".
     RuntimeError
         If required template is not found.
 
@@ -162,18 +168,30 @@ def get_template(
     if template_type not in ["T1w", "brain", "gm", "wm", "csf"]:
         raise_error(f"Unknown template type: {template_type}")
 
-    # Get the min of the voxels sizes and use it as the resolution
-    resolution = np.min(target_img.header.get_zooms()[:3]).astype(int)
+    if isinstance(resolution, str) and resolution != "highest":
+        raise_error(
+            "Invalid resolution value. Must be an integer or 'highest'"
+        )
 
     # Fetch available resolutions for the template
     available_resolutions = [
         int(min(val["zooms"]))
         for val in tflow.get_metadata(space)["res"].values()
     ]
+
+    # Get the min of the voxels sizes and use it as the resolution
+    if resolution is None:
+        resolution = np.min(target_img.header.get_zooms()[:3]).astype(int)
+    elif resolution == "highest":
+        resolution = 0
+
     # Use the closest resolution if desired resolution is not found
     resolution = closest_resolution(resolution, available_resolutions)
 
-    logger.info(f"Downloading template {space} in resolution {resolution}")
+    logger.info(
+        f"Downloading template {space} ({template_type} in "
+        f"resolution {resolution}"
+    )
     # Retrieve template
     try:
         suffix = None

junifer/markers/reho/tests/test_reho_parcels.py

@@ -86,10 +86,6 @@ def test_ReHoParcels(caplog: pytest.LogCaptureFixture, tmp_path: Path) -> None:
 @pytest.mark.skipif(
     _check_afni() is False, reason="requires AFNI to be in PATH"
 )
-@pytest.mark.xfail(
-    reason="junifer ReHo needs to use the correct mask",
-    raises=AssertionError,
-)
 def test_ReHoParcels_comparison(tmp_path: Path) -> None:
     """Test ReHoParcels implementation comparison.
 

{junifer-0.0.6.dev358.dist-info → junifer-0.0.6.dev371.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: junifer
-Version: 0.0.6.dev358
+Version: 0.0.6.dev371
 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.dev358.dist-info → junifer-0.0.6.dev371.dist-info}/RECORD

@@ -1,6 +1,6 @@
 junifer/__init__.py,sha256=2McgH1yNue6Z1V26-uN_mfMjbTcx4CLhym-DMBl5xA4,266
 junifer/__init__.pyi,sha256=SsTvgq2Dod6UqJN96GH1lCphH6hJQQurEJHGNhHjGUI,508
-junifer/_version.py,sha256=FgjmOt5uZU0g8aIkualgel30oxeUJfjpBfbQcVNHwH8,428
+junifer/_version.py,sha256=onk4xlkzaS1Ll-ut-FU2OO_R2pb-yHUL5TWaWF6Lxt0,428
 junifer/conftest.py,sha256=PWYkkRDU8ly2lYwv7VBKMHje4et6HX7Yey3Md_I2KbA,613
 junifer/py.typed,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 junifer/stats.py,sha256=e9aaagMGtgpRfW3Wdpz9ocpnYld1IWylCDcjFUgX9Mk,6225
@@ -75,7 +75,7 @@ junifer/data/__init__.pyi,sha256=qYszjUYcbFi_2zO23MnbA2HhTW-Ad2oh1pqPQYd6yt0,542
 junifer/data/_dispatch.py,sha256=O524U1R4MtbGhGJsL0HSh9EqisapBFJWK7uupXrJuMg,6158
 junifer/data/pipeline_data_registry_base.py,sha256=G8bE3WTj4D_rKC4ZKZe6E48Sd96CGea1PS3SxmTgGK4,2010
 junifer/data/py.typed,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
-junifer/data/template_spaces.py,sha256=JPsrGyfbaVgZ75uB3ci2CUuVxUg3NDi6HhO_VTIHeOE,6508
+junifer/data/template_spaces.py,sha256=wkxaDA_I_W5FB42GPxOKrl_A_fp0Crdrh6wFux27_NA,7147
 junifer/data/utils.py,sha256=5r-0QGQCNZvDM1tVcl9xyrIdgAO85mww0plpM1RUaGA,3247
 junifer/data/coordinates/__init__.py,sha256=ffM8rwcHLgHAWixJbKrATrbUKzX940V1UF6RAxZdUMg,186
 junifer/data/coordinates/__init__.pyi,sha256=Z-Ti5XD3HigkZ8uYN6oYsLqw40-F1GvTVQ5QAy08Wng,88
@@ -106,7 +106,7 @@ junifer/data/masks/__init__.py,sha256=eEEhHglyVEx1LrqwXjq3cOmjf4sTsgBstRx5-k7zIQ
 junifer/data/masks/__init__.pyi,sha256=lcgr8gmWDPibC4RxnWBXb8DDpIkO73Aax09u6VXiJJI,114
 junifer/data/masks/_ants_mask_warper.py,sha256=Mwgc2_ZMf28vS_-fviRvZnHyT7JoQ1cQLozo7nUZSyM,5350
 junifer/data/masks/_fsl_mask_warper.py,sha256=VApp-ofGBKePNmCdgTg1HoEA66lMQiAPT0ihkhB2ezY,2415
-junifer/data/masks/_masks.py,sha256=8w-J-ZBKuik99gk9tYHntbmanpx_Mbu9oUujzxO7y1w,25874
+junifer/data/masks/_masks.py,sha256=NBkcIhjiSPoBE8J2BGkSfoun9Kpc2k_b2AhSf-E5cjU,27672
 junifer/data/masks/tests/test_masks.py,sha256=W0bzRB5Bp-iGO44VtEmaf7BuT-joe_2tQI0lma5NQHA,16090
 junifer/data/masks/ukb/UKB_15K_GM_template.nii.gz,sha256=jcX1pDOrDsoph8cPMNFVKH5gZYio5G4rJNpOFXm9wJI,946636
 junifer/data/masks/vickery-patil/CAT12_IXI555_MNI152_TMP_GS_GMprob0.2_clean.nii.gz,sha256=j6EY8EtRnUuRxeKgD65Q6B0GPEPIALKDJEIje1TfnAU,88270
@@ -116,7 +116,7 @@ junifer/data/parcellations/__init__.py,sha256=6-Ysil3NyZ69V6rWx4RO15_d-iDKizfbHu
 junifer/data/parcellations/__init__.pyi,sha256=lhBHTbMDizzqUqVHrx2eyfPFodrTBgMFeTgxfESSkQ8,140
 junifer/data/parcellations/_ants_parcellation_warper.py,sha256=YUCJC0_wutGw7j_n9JRU3LCwm9Ttg5PIlJUgqejfRhs,5806
 junifer/data/parcellations/_fsl_parcellation_warper.py,sha256=JfJ022flg5OR48P4OAALVHHQgTVxdMBXT-fAqBl3nUM,2679
-junifer/data/parcellations/_parcellations.py,sha256=9azcYRBjwGuwZvKdFJj34BWPcCblxe2Ps8obbyl58k8,67179
+junifer/data/parcellations/_parcellations.py,sha256=JUUglL0ZM_UKL5jTG1q-3x6Fd3CUO6Hl4YAGAUsGtmI,67019
 junifer/data/parcellations/tests/test_parcellations.py,sha256=ESQI-KWsepmgKB2BWWWUxjkpjOWeIZhhlKxNuTsRPJg,39268
 junifer/data/tests/test_data_utils.py,sha256=136iGPjGecCxyqgUwU8VZMHoE6imcYJ0WNC32PDGK4g,1063
 junifer/data/tests/test_template_spaces.py,sha256=ZEicEcLqOJ-NpuBZ5SYh4yZ0xZRkhYHnYXiC_YSxjrY,3219
@@ -239,7 +239,7 @@ junifer/markers/reho/py.typed,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU
 junifer/markers/reho/reho_base.py,sha256=Q88TbhIM4rQWdeQPLwwxwZ9DrR8l09orD1rdTkSYDtc,4077
 junifer/markers/reho/reho_parcels.py,sha256=UE1ia3uqbmTcZMc_FI625xVPLxBYvwpfrcvhekopbkI,6392
 junifer/markers/reho/reho_spheres.py,sha256=FCC2qncC85Kd82hg-MOu4T7NAKEkXHUaCcwC9taau9Y,6996
-junifer/markers/reho/tests/test_reho_parcels.py,sha256=dek2TMxMZ04o5s_06ZudZihDer55dAIFUhFexWQAH18,4181
+junifer/markers/reho/tests/test_reho_parcels.py,sha256=bRtDi91qRcRYaRqqQjuSU6NuNz-KwLVCoTYo-e5VmsI,4075
 junifer/markers/reho/tests/test_reho_spheres.py,sha256=VyyQ3hhD6ArFc1BmigmAdePACB1EMQlo1mDr2QKvT2I,3989
 junifer/markers/temporal_snr/__init__.py,sha256=86hNMyaSfWlWOXZ6m9reSDtMIgUaByOXjcxCvo7LmDw,235
 junifer/markers/temporal_snr/__init__.pyi,sha256=20FhG9ZkAHQfmJ0r5p6fRMxhK8xrFQeFr0cgTrqu3ik,162
@@ -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.dev358.dist-info/AUTHORS.rst,sha256=rmULKpchpSol4ExWFdm-qu4fkpSZPYqIESVJBZtGb6E,163
-junifer-0.0.6.dev358.dist-info/LICENSE.md,sha256=MqCnOBu8uXsEOzRZWh9EBVfVz-kE9NkXcLCrtGXo2yU,34354
-junifer-0.0.6.dev358.dist-info/METADATA,sha256=aw963eFey-7fsO__-qenMulbVlYGZ6vnMJl7sDRhjDY,8429
-junifer-0.0.6.dev358.dist-info/WHEEL,sha256=PZUExdf71Ui_so67QXpySuHtCi3-J3wvF4ORK6k_S8U,91
-junifer-0.0.6.dev358.dist-info/entry_points.txt,sha256=6O8ru0BP-SP7YMUZiizFNoaZ2HvJpadO2G7nKk4PwjI,48
-junifer-0.0.6.dev358.dist-info/top_level.txt,sha256=4bAq1R2QFQ4b3hohjys2JBvxrl0GKk5LNFzYvz9VGcA,8
-junifer-0.0.6.dev358.dist-info/RECORD,,
+junifer-0.0.6.dev371.dist-info/AUTHORS.rst,sha256=rmULKpchpSol4ExWFdm-qu4fkpSZPYqIESVJBZtGb6E,163
+junifer-0.0.6.dev371.dist-info/LICENSE.md,sha256=MqCnOBu8uXsEOzRZWh9EBVfVz-kE9NkXcLCrtGXo2yU,34354
+junifer-0.0.6.dev371.dist-info/METADATA,sha256=UHywu8RLD9o6oUt1r5pQlfxWb9AG3nogaV_kfRJe778,8429
+junifer-0.0.6.dev371.dist-info/WHEEL,sha256=PZUExdf71Ui_so67QXpySuHtCi3-J3wvF4ORK6k_S8U,91
+junifer-0.0.6.dev371.dist-info/entry_points.txt,sha256=6O8ru0BP-SP7YMUZiizFNoaZ2HvJpadO2G7nKk4PwjI,48
+junifer-0.0.6.dev371.dist-info/top_level.txt,sha256=4bAq1R2QFQ4b3hohjys2JBvxrl0GKk5LNFzYvz9VGcA,8
+junifer-0.0.6.dev371.dist-info/RECORD,,