junifer 0.0.6.dev371__py3-none-any.whl → 0.0.6.dev378__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.dev371'
-__version_tuple__ = version_tuple = (0, 0, 6, 'dev371')
+__version__ = version = '0.0.6.dev378'
+__version_tuple__ = version_tuple = (0, 0, 6, 'dev378')

junifer/data/masks/_ants_mask_warper.py

@@ -7,6 +7,7 @@ import uuid
 from typing import TYPE_CHECKING, Any, Optional
 
 import nibabel as nib
+import numpy as np
 
 from ...pipeline import WorkDirManager
 from ...utils import logger, raise_error, run_ext_cmd
@@ -20,6 +21,26 @@ if TYPE_CHECKING:
 __all__ = ["ANTsMaskWarper"]
 
 
+def _get_interpolation_method(img: "Nifti1Image") -> str:
+    """Get correct interpolation method for `img`.
+
+    Parameters
+    ----------
+    img : nibabel.nifti1.Nifti1Image
+        The image.
+
+    Returns
+    -------
+    str
+        The interpolation method.
+
+    """
+    if np.array_equal(np.unique(img.get_fdata()), [0, 1]):
+        return "'GenericLabel[NearestNeighbor]'"
+    else:
+        return "LanczosWindowedSinc"
+
+
 class ANTsMaskWarper:
     """Class for mask space warping via ANTs.
 
@@ -143,7 +164,7 @@ class ANTsMaskWarper:
                 "antsApplyTransforms",
                 "-d 3",
                 "-e 3",
-                "-n 'GenericLabel[NearestNeighbor]'",
+                f"-n {_get_interpolation_method(mask_img)}",
                 f"-i {prewarp_mask_path.resolve()}",
                 f"-r {template_space_img_path.resolve()}",
                 f"-t {xfm_file_path.resolve()}",

junifer/data/masks/_fsl_mask_warper.py

@@ -7,6 +7,7 @@ import uuid
 from typing import TYPE_CHECKING, Any
 
 import nibabel as nib
+import numpy as np
 
 from ...pipeline import WorkDirManager
 from ...utils import logger, run_ext_cmd
@@ -19,6 +20,26 @@ if TYPE_CHECKING:
 __all__ = ["FSLMaskWarper"]
 
 
+def _get_interpolation_method(img: "Nifti1Image") -> str:
+    """Get correct interpolation method for `img`.
+
+    Parameters
+    ----------
+    img : nibabel.nifti1.Nifti1Image
+        The image.
+
+    Returns
+    -------
+    str
+        The interpolation method.
+
+    """
+    if np.array_equal(np.unique(img.get_fdata()), [0, 1]):
+        return "nn"
+    else:
+        return "spline"
+
+
 class FSLMaskWarper:
     """Class for mask space warping via FSL FLIRT.
 
@@ -71,7 +92,7 @@ class FSLMaskWarper:
         # Set applywarp command
         applywarp_cmd = [
             "applywarp",
-            "--interp=nn",
+            f"--interp={_get_interpolation_method(mask_img)}",
             f"-i {prewarp_mask_path.resolve()}",
             # use resampled reference
             f"-r {target_data['reference']['path'].resolve()}",

junifer/data/masks/_masks.py

@@ -165,33 +165,18 @@ def compute_brain_mask(
         )
 
     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":
             resampled_template = FSLMaskWarper().warp(
-                mask_name=f"template_{target_std_space}_for_compute_brain_mask",
+                mask_name=mask_name,
                 mask_img=template,
                 target_data=target_data,
                 warp_data=warp_data,
             )
         elif warp_data["warper"] == "ants":
             resampled_template = ANTsMaskWarper().warp(
-                mask_name=f"template_{target_std_space}_for_compute_brain_mask",
+                mask_name=mask_name,
                 # use template here
                 mask_img=template,
                 src=target_std_space,
@@ -199,11 +184,25 @@ def compute_brain_mask(
                 target_data=target_data,
                 warp_data=warp_data,
             )
-    # Resample template to target image
     else:
+        # Warp template to correct space
+        if 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 template to target image
         resampled_template = nimg.resample_to_img(
-            source_img=template, target_img=target_data["data"]
+            source_img=template,
+            target_img=target_data["data"],
+            interpolation=_get_interpolation_method(template),
         )
 
     # Threshold resampled template and get mask
@@ -561,6 +560,7 @@ class MaskRegistry(BasePipelineDataRegistry, metaclass=Singleton):
                 mask_img = nimg.resample_to_img(
                     source_img=mask_img,
                     target_img=target_data["data"],
+                    interpolation=_get_interpolation_method(mask_img),
                 )
             # Starting with new mask
             else:
@@ -632,6 +632,7 @@ class MaskRegistry(BasePipelineDataRegistry, metaclass=Singleton):
                         mask_img = nimg.resample_to_img(
                             source_img=mask_img,
                             target_img=target_img,
+                            interpolation=_get_interpolation_method(mask_img),
                         )
                     else:
                         # Warp mask if target space is native as
@@ -761,3 +762,23 @@ def _load_ukb_mask(name: str) -> Path:
     mask_fname = _masks_path / "ukb" / mask_fname
 
     return mask_fname
+
+
+def _get_interpolation_method(img: "Nifti1Image") -> str:
+    """Get correct interpolation method for `img`.
+
+    Parameters
+    ----------
+    img : nibabel.nifti1.Nifti1Image
+        The image.
+
+    Returns
+    -------
+    str
+        The interpolation method.
+
+    """
+    if np.array_equal(np.unique(img.get_fdata()), [0, 1]):
+        return "nearest"
+    else:
+        return "continuous"

{junifer-0.0.6.dev371.dist-info → junifer-0.0.6.dev378.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: junifer
-Version: 0.0.6.dev371
+Version: 0.0.6.dev378
 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.dev371.dist-info → junifer-0.0.6.dev378.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=onk4xlkzaS1Ll-ut-FU2OO_R2pb-yHUL5TWaWF6Lxt0,428
+junifer/_version.py,sha256=oYfebrtAvhll95HaoOLZCO0IYYGaqQpsY-CgDqPH8w4,428
 junifer/conftest.py,sha256=PWYkkRDU8ly2lYwv7VBKMHje4et6HX7Yey3Md_I2KbA,613
 junifer/py.typed,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 junifer/stats.py,sha256=e9aaagMGtgpRfW3Wdpz9ocpnYld1IWylCDcjFUgX9Mk,6225
@@ -104,9 +104,9 @@ junifer/data/coordinates/VOIs/meta/extDMN_VOIs.txt,sha256=Ogx1QvqZcnXDM3ncF2ha78
 junifer/data/coordinates/tests/test_coordinates.py,sha256=_c2P4oaDGpsmui5gJBe_jN6HLGiKxONkYPR69sRBUlU,4219
 junifer/data/masks/__init__.py,sha256=eEEhHglyVEx1LrqwXjq3cOmjf4sTsgBstRx5-k7zIQU,180
 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=NBkcIhjiSPoBE8J2BGkSfoun9Kpc2k_b2AhSf-E5cjU,27672
+junifer/data/masks/_ants_mask_warper.py,sha256=JLK2Jh2AOAiv_NoUGhRoTBEhRFXPRXTDPmQGH9vBSok,5805
+junifer/data/masks/_fsl_mask_warper.py,sha256=YZOMlRgQ7_4shnXNc_05tmwDk5xHI-1wqle-RdNsJ34,2857
+junifer/data/masks/_masks.py,sha256=ZR0pfwIBiyJ3tGKo0mHW5Pu5asaZHeTvYbgJrUwZh24,28172
 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
@@ -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.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,,
+junifer-0.0.6.dev378.dist-info/AUTHORS.rst,sha256=rmULKpchpSol4ExWFdm-qu4fkpSZPYqIESVJBZtGb6E,163
+junifer-0.0.6.dev378.dist-info/LICENSE.md,sha256=MqCnOBu8uXsEOzRZWh9EBVfVz-kE9NkXcLCrtGXo2yU,34354
+junifer-0.0.6.dev378.dist-info/METADATA,sha256=1i1ttfHKfKnLZhJQxPgbjBGDS5rw3l7O1R0OtIldFO4,8429
+junifer-0.0.6.dev378.dist-info/WHEEL,sha256=PZUExdf71Ui_so67QXpySuHtCi3-J3wvF4ORK6k_S8U,91
+junifer-0.0.6.dev378.dist-info/entry_points.txt,sha256=6O8ru0BP-SP7YMUZiizFNoaZ2HvJpadO2G7nKk4PwjI,48
+junifer-0.0.6.dev378.dist-info/top_level.txt,sha256=4bAq1R2QFQ4b3hohjys2JBvxrl0GKk5LNFzYvz9VGcA,8
+junifer-0.0.6.dev378.dist-info/RECORD,,