junifer 0.0.6.dev366__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.dev366'
-__version_tuple__ = version_tuple = (0, 0, 6, 'dev366')
+__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

@@ -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
@@ -138,27 +146,37 @@ 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"
     # 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,
@@ -166,15 +184,31 @@ 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
+    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
 
 
@@ -526,6 +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:
@@ -597,6 +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
@@ -726,3 +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/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-0.0.6.dev366.dist-info → junifer-0.0.6.dev378.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: junifer
-Version: 0.0.6.dev366
+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.dev366.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=t-3cRoRiLKJo00UFpf7tn_vToC9PLS2rVeH50rEhEGs,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
@@ -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
@@ -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=ZJ5kmZQCL854k0gwXQhsWnWVI2hzdDnz2O6kIe2Ih2A,26194
+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.dev366.dist-info/AUTHORS.rst,sha256=rmULKpchpSol4ExWFdm-qu4fkpSZPYqIESVJBZtGb6E,163
-junifer-0.0.6.dev366.dist-info/LICENSE.md,sha256=MqCnOBu8uXsEOzRZWh9EBVfVz-kE9NkXcLCrtGXo2yU,34354
-junifer-0.0.6.dev366.dist-info/METADATA,sha256=1bnN5jpKnbFsIC94NMUL1xwIOpl-LhdAYQmDFrKNa3g,8429
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-junifer-0.0.6.dev366.dist-info/entry_points.txt,sha256=6O8ru0BP-SP7YMUZiizFNoaZ2HvJpadO2G7nKk4PwjI,48
-junifer-0.0.6.dev366.dist-info/top_level.txt,sha256=4bAq1R2QFQ4b3hohjys2JBvxrl0GKk5LNFzYvz9VGcA,8
-junifer-0.0.6.dev366.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
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+junifer-0.0.6.dev378.dist-info/top_level.txt,sha256=4bAq1R2QFQ4b3hohjys2JBvxrl0GKk5LNFzYvz9VGcA,8
+junifer-0.0.6.dev378.dist-info/RECORD,,