junifer 0.0.6.dev422__tar.gz → 0.0.6.dev445__tar.gz

{junifer-0.0.6.dev422 → junifer-0.0.6.dev445}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.2
 Name: junifer
-Version: 0.0.6.dev422
+Version: 0.0.6.dev445
 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>
@@ -38,7 +38,6 @@ Requires-Dist: nilearn<=0.10.4,>=0.10.3
 Requires-Dist: sqlalchemy<=2.1.0,>=2.0.25
 Requires-Dist: ruamel.yaml<0.19,>=0.17
 Requires-Dist: h5py>=3.10
-Requires-Dist: httpx[http2]<0.28.0,>=0.26.0
 Requires-Dist: tqdm<4.67.0,>=4.66.1
 Requires-Dist: templateflow>=23.0.0
 Requires-Dist: lapy<2.0.0,>=1.0.0

junifer-0.0.6.dev445/docs/changes/newsfragments/418.enh

@@ -0,0 +1 @@
+Adapt usage of ``junifer-data`` DataLad dataset to fetch parcellations, masks, coordinates and xfms by `Synchon Mandal`_

junifer-0.0.6.dev445/docs/changes/newsfragments/418.misc

@@ -0,0 +1 @@
+Remove ``httpx`` as a dependency by `Synchon Mandal`_

{junifer-0.0.6.dev422 → junifer-0.0.6.dev445}/junifer/_version.py

@@ -12,5 +12,5 @@ __version__: str
 __version_tuple__: VERSION_TUPLE
 version_tuple: VERSION_TUPLE
 
-__version__ = version = '0.0.6.dev422'
-__version_tuple__ = version_tuple = (0, 0, 6, 'dev422')
+__version__ = version = '0.0.6.dev445'
+__version_tuple__ = version_tuple = (0, 0, 6, 'dev445')

{junifer-0.0.6.dev422 → junifer-0.0.6.dev445}/junifer/cli/tests/test_cli_utils.py

@@ -43,7 +43,6 @@ def test_get_dependency_information_short() -> None:
         "nilearn",
         "sqlalchemy",
         "ruamel.yaml",
-        "httpx",
         "tqdm",
         "templateflow",
         "lapy",
@@ -73,7 +72,6 @@ def test_get_dependency_information_long() -> None:
         "nilearn",
         "sqlalchemy",
         "ruamel.yaml",
-        "httpx",
         "tqdm",
         "templateflow",
         "lapy",

{junifer-0.0.6.dev422 → junifer-0.0.6.dev445}/junifer/data/coordinates/_coordinates.py

@@ -4,7 +4,6 @@
 #          Synchon Mandal <s.mandal@fz-juelich.de>
 # License: AGPL
 
-from pathlib import Path
 from typing import Any, Optional
 
 import numpy as np
@@ -14,7 +13,7 @@ from numpy.typing import ArrayLike
 from ...utils import logger, raise_error
 from ...utils.singleton import Singleton
 from ..pipeline_data_registry_base import BasePipelineDataRegistry
-from ..utils import get_native_warper
+from ..utils import check_dataset, fetch_file_via_datalad, get_native_warper
 from ._ants_coordinates_warper import ANTsCoordinatesWarper
 from ._fsl_coordinates_warper import FSLCoordinatesWarper
 
@@ -32,104 +31,104 @@ class CoordinatesRegistry(BasePipelineDataRegistry, metaclass=Singleton):
 
     def __init__(self) -> None:
         """Initialize the class."""
+        super().__init__()
         # Each entry in registry is a dictionary that must contain at least
         # the following keys:
         # * 'space': the coordinates' space (e.g., 'MNI')
-        # The built-in coordinates are files that are shipped with the package
-        # in the data/VOIs directory. The user can also register their own
+        # The built-in coordinates are files that are shipped with the
+        # junifer-data dataset. The user can also register their own
         # coordinates, which will be stored as numpy arrays in the dictionary.
         # Make built-in and external dictionaries for validation later
         self._builtin = {}
         self._external = {}
 
-        # Path to the metadata of the VOIs
-        _vois_meta_path = Path(__file__).parent / "VOIs" / "meta"
-
-        self._builtin = {
-            "CogAC": {
-                "path": _vois_meta_path / "CogAC_VOIs.txt",
-                "space": "MNI",
-            },
-            "CogAR": {
-                "path": _vois_meta_path / "CogAR_VOIs.txt",
-                "space": "MNI",
-            },
-            "DMNBuckner": {
-                "path": _vois_meta_path / "DMNBuckner_VOIs.txt",
-                "space": "MNI",
-            },
-            "eMDN": {
-                "path": _vois_meta_path / "eMDN_VOIs.txt",
-                "space": "MNI",
-            },
-            "Empathy": {
-                "path": _vois_meta_path / "Empathy_VOIs.txt",
-                "space": "MNI",
-            },
-            "eSAD": {
-                "path": _vois_meta_path / "eSAD_VOIs.txt",
-                "space": "MNI",
-            },
-            "extDMN": {
-                "path": _vois_meta_path / "extDMN_VOIs.txt",
-                "space": "MNI",
-            },
-            "Motor": {
-                "path": _vois_meta_path / "Motor_VOIs.txt",
-                "space": "MNI",
-            },
-            "MultiTask": {
-                "path": _vois_meta_path / "MultiTask_VOIs.txt",
-                "space": "MNI",
-            },
-            "PhysioStress": {
-                "path": _vois_meta_path / "PhysioStress_VOIs.txt",
-                "space": "MNI",
-            },
-            "Rew": {
-                "path": _vois_meta_path / "Rew_VOIs.txt",
-                "space": "MNI",
-            },
-            "Somatosensory": {
-                "path": _vois_meta_path / "Somatosensory_VOIs.txt",
-                "space": "MNI",
-            },
-            "ToM": {
-                "path": _vois_meta_path / "ToM_VOIs.txt",
-                "space": "MNI",
-            },
-            "VigAtt": {
-                "path": _vois_meta_path / "VigAtt_VOIs.txt",
-                "space": "MNI",
-            },
-            "WM": {
-                "path": _vois_meta_path / "WM_VOIs.txt",
-                "space": "MNI",
-            },
-            "Power": {
-                "path": _vois_meta_path / "Power2011_MNI_VOIs.txt",
-                "space": "MNI",
-            },
-            "Power2011": {
-                "path": _vois_meta_path / "Power2011_MNI_VOIs.txt",
-                "space": "MNI",
-            },
-            "Dosenbach": {
-                "path": _vois_meta_path / "Dosenbach2010_MNI_VOIs.txt",
-                "space": "MNI",
-            },
-            "Power2013": {
-                "path": _vois_meta_path / "Power2013_MNI_VOIs.tsv",
-                "space": "MNI",
-            },
-            "AutobiographicalMemory": {
-                "path": _vois_meta_path / "AutobiographicalMemory_VOIs.txt",
-                "space": "MNI",
-            },
-        }
-
-        # Set built-in to registry
-        self._registry = self._builtin
+        self._builtin.update(
+            {
+                "CogAC": {
+                    "file_path_suffix": "CogAC_VOIs.txt",
+                    "space": "MNI",
+                },
+                "CogAR": {
+                    "file_path_suffix": "CogAR_VOIs.txt",
+                    "space": "MNI",
+                },
+                "DMNBuckner": {
+                    "file_path_suffix": "DMNBuckner_VOIs.txt",
+                    "space": "MNI",
+                },
+                "eMDN": {
+                    "file_path_suffix": "eMDN_VOIs.txt",
+                    "space": "MNI",
+                },
+                "Empathy": {
+                    "file_path_suffix": "Empathy_VOIs.txt",
+                    "space": "MNI",
+                },
+                "eSAD": {
+                    "file_path_suffix": "eSAD_VOIs.txt",
+                    "space": "MNI",
+                },
+                "extDMN": {
+                    "file_path_suffix": "extDMN_VOIs.txt",
+                    "space": "MNI",
+                },
+                "Motor": {
+                    "file_path_suffix": "Motor_VOIs.txt",
+                    "space": "MNI",
+                },
+                "MultiTask": {
+                    "file_path_suffix": "MultiTask_VOIs.txt",
+                    "space": "MNI",
+                },
+                "PhysioStress": {
+                    "file_path_suffix": "PhysioStress_VOIs.txt",
+                    "space": "MNI",
+                },
+                "Rew": {
+                    "file_path_suffix": "Rew_VOIs.txt",
+                    "space": "MNI",
+                },
+                "Somatosensory": {
+                    "file_path_suffix": "Somatosensory_VOIs.txt",
+                    "space": "MNI",
+                },
+                "ToM": {
+                    "file_path_suffix": "ToM_VOIs.txt",
+                    "space": "MNI",
+                },
+                "VigAtt": {
+                    "file_path_suffix": "VigAtt_VOIs.txt",
+                    "space": "MNI",
+                },
+                "WM": {
+                    "file_path_suffix": "WM_VOIs.txt",
+                    "space": "MNI",
+                },
+                "Power": {
+                    "file_path_suffix": "Power2011_MNI_VOIs.txt",
+                    "space": "MNI",
+                },
+                "Power2011": {
+                    "file_path_suffix": "Power2011_MNI_VOIs.txt",
+                    "space": "MNI",
+                },
+                "Dosenbach": {
+                    "file_path_suffix": "Dosenbach2010_MNI_VOIs.txt",
+                    "space": "MNI",
+                },
+                "Power2013": {
+                    "file_path_suffix": "Power2013_MNI_VOIs.tsv",
+                    "space": "MNI",
+                },
+                "AutobiographicalMemory": {
+                    "file_path_suffix": "AutobiographicalMemory_VOIs.txt",
+                    "space": "MNI",
+                },
+            }
+        )
+
+        # Update registry with built-in ones
+        self._registry.update(self._builtin)
 
     def register(
         self,
@@ -161,9 +160,9 @@ class CoordinatesRegistry(BasePipelineDataRegistry, metaclass=Singleton):
         Raises
         ------
         ValueError
-            If the coordinates ``name`` is already registered and
+            If the coordinates ``name`` is a built-in coordinates or
+            if the coordinates ``name`` is already registered and
             ``overwrite=False`` or
-            if the coordinates ``name`` is a built-in coordinates or
             if the ``coordinates`` is not a 2D array or
             if coordinate value does not have 3 components or
             if the ``voi_names`` shape does not match the
@@ -174,11 +173,12 @@ class CoordinatesRegistry(BasePipelineDataRegistry, metaclass=Singleton):
         """
         # Check for attempt of overwriting built-in coordinates
         if name in self._builtin:
-            if isinstance(self._registry[name].get("path"), Path):
-                raise_error(
-                    f"Coordinates: {name} already registered as built-in "
-                    "coordinates."
-                )
+            raise_error(
+                f"Coordinates: {name} already registered as built-in "
+                "coordinates."
+            )
+        # Check for attempt of overwriting external coordinates
+        if name in self._external:
             if overwrite:
                 logger.info(f"Overwriting coordinates: {name}")
             else:
@@ -186,7 +186,7 @@ class CoordinatesRegistry(BasePipelineDataRegistry, metaclass=Singleton):
                     f"Coordinates: {name} already registered. "
                     "Set `overwrite=True` to update its value."
                 )
-
+        # Further checks
         if not isinstance(coordinates, np.ndarray):
             raise_error(
                 "Coordinates must be a `numpy.ndarray`, "
@@ -207,6 +207,7 @@ class CoordinatesRegistry(BasePipelineDataRegistry, metaclass=Singleton):
                 f"Length of `voi_names` ({len(voi_names)}) does not match the "
                 f"number of `coordinates` ({coordinates.shape[0]})."
             )
+        # Registration
         logger.info(f"Registering coordinates: {name}")
         # Add coordinates info
         self._external[name] = {
@@ -257,6 +258,8 @@ class CoordinatesRegistry(BasePipelineDataRegistry, metaclass=Singleton):
         ------
         ValueError
             If ``name`` is invalid.
+        RuntimeError
+            If there is a problem fetching the coordinates file.
 
         """
         # Check for valid coordinates name
@@ -265,17 +268,37 @@ class CoordinatesRegistry(BasePipelineDataRegistry, metaclass=Singleton):
                 f"Coordinates: {name} not found. "
                 f"Valid options are: {self.list}"
             )
-        # Load coordinates
+        # Load coordinates info
         t_coord = self._registry[name]
-        # Load data
-        if isinstance(t_coord.get("path"), Path):
-            logger.debug(f"Loading coordinates {t_coord['path'].absolute()!s}")
+
+        # Load data for in-built ones
+        if t_coord.get("file_path_suffix") is not None:
+            # Get dataset
+            dataset = check_dataset()
+            # Set file path to retrieve
+            coords_file_path = (
+                dataset.pathobj
+                / "coordinates"
+                / name
+                / t_coord["file_path_suffix"]
+            )
+            logger.debug(
+                f"Loading coordinates `{name}` from: "
+                f"{coords_file_path.absolute()!s}"
+            )
             # Load via pandas
-            df_coords = pd.read_csv(t_coord["path"], sep="\t", header=None)
+            df_coords = pd.read_csv(
+                fetch_file_via_datalad(
+                    dataset=dataset, file_path=coords_file_path
+                ),
+                sep="\t",
+                header=None,
+            )
             # Convert dataframe to numpy ndarray
             coords = df_coords.iloc[:, [0, 1, 2]].to_numpy()
             # Get label names
             names = list(df_coords.iloc[:, [3]].values[:, 0])
+        # Load data for external ones
         else:
             coords = t_coord["coords"]
             names = t_coord["voi_names"]

{junifer-0.0.6.dev422 → junifer-0.0.6.dev445}/junifer/data/coordinates/tests/test_coordinates.py

@@ -21,7 +21,6 @@ def test_register_built_in_check() -> None:
             coordinates=np.zeros(2),
             voi_names=["1", "2"],
             space="MNI",
-            overwrite=True,
         )
 
 
@@ -32,7 +31,6 @@ def test_register_overwrite() -> None:
         coordinates=np.zeros((2, 3)),
         voi_names=["roi1", "roi2"],
         space="MNI",
-        overwrite=True,
     )
     with pytest.raises(ValueError, match=r"already registered"):
         CoordinatesRegistry().register(
@@ -40,6 +38,7 @@ def test_register_overwrite() -> None:
             coordinates=np.ones((2, 3)),
             voi_names=["roi2", "roi3"],
             space="MNI",
+            overwrite=False,
         )
 
     CoordinatesRegistry().register(

{junifer-0.0.6.dev422 → junifer-0.0.6.dev445}/junifer/data/masks/_masks.py

@@ -26,22 +26,24 @@ from ...utils import logger, raise_error
 from ...utils.singleton import Singleton
 from ..pipeline_data_registry_base import BasePipelineDataRegistry
 from ..template_spaces import get_template
-from ..utils import closest_resolution, get_native_warper
+from ..utils import (
+    check_dataset,
+    closest_resolution,
+    fetch_file_via_datalad,
+    get_native_warper,
+)
 from ._ants_mask_warper import ANTsMaskWarper
 from ._fsl_mask_warper import FSLMaskWarper
 
 
 if TYPE_CHECKING:
+    from datalad.api import Dataset
     from nibabel.nifti1 import Nifti1Image
 
 
 __all__ = ["MaskRegistry", "compute_brain_mask"]
 
 
-# Path to the masks
-_masks_path = Path(__file__).parent
-
-
 def compute_brain_mask(
     target_data: dict[str, Any],
     warp_data: Optional[dict[str, Any]] = None,
@@ -224,6 +226,7 @@ class MaskRegistry(BasePipelineDataRegistry, metaclass=Singleton):
 
     def __init__(self) -> None:
         """Initialize the class."""
+        super().__init__()
         # Each entry in registry is a dictionary that must contain at least
         # the following keys:
         # * 'family': the mask's family name
@@ -240,38 +243,40 @@ class MaskRegistry(BasePipelineDataRegistry, metaclass=Singleton):
         self._builtin = {}
         self._external = {}
 
-        self._builtin = {
-            "GM_prob0.2": {
-                "family": "Vickery-Patil",
-                "space": "IXI549Space",
-            },
-            "GM_prob0.2_cortex": {
-                "family": "Vickery-Patil",
-                "space": "IXI549Space",
-            },
-            "compute_brain_mask": {
-                "family": "Callable",
-                "func": compute_brain_mask,
-                "space": "inherit",
-            },
-            "compute_background_mask": {
-                "family": "Callable",
-                "func": compute_background_mask,
-                "space": "inherit",
-            },
-            "compute_epi_mask": {
-                "family": "Callable",
-                "func": compute_epi_mask,
-                "space": "inherit",
-            },
-            "UKB_15K_GM": {
-                "family": "UKB",
-                "space": "MNI152NLin6Asym",
-            },
-        }
+        self._builtin.update(
+            {
+                "GM_prob0.2": {
+                    "family": "Vickery-Patil",
+                    "space": "IXI549Space",
+                },
+                "GM_prob0.2_cortex": {
+                    "family": "Vickery-Patil",
+                    "space": "IXI549Space",
+                },
+                "compute_brain_mask": {
+                    "family": "Callable",
+                    "func": compute_brain_mask,
+                    "space": "inherit",
+                },
+                "compute_background_mask": {
+                    "family": "Callable",
+                    "func": compute_background_mask,
+                    "space": "inherit",
+                },
+                "compute_epi_mask": {
+                    "family": "Callable",
+                    "func": compute_epi_mask,
+                    "space": "inherit",
+                },
+                "UKB_15K_GM": {
+                    "family": "UKB",
+                    "space": "MNI152NLin6Asym",
+                },
+            }
+        )
 
-        # Set built-in to registry
-        self._registry = self._builtin
+        # Update registry with built-in ones
+        self._registry.update(self._builtin)
 
     def register(
         self,
@@ -297,19 +302,18 @@ class MaskRegistry(BasePipelineDataRegistry, metaclass=Singleton):
         Raises
         ------
         ValueError
-            If the mask ``name`` is already registered and
-            ``overwrite=False`` or
-            if the mask ``name`` is a built-in mask.
+            If the mask ``name`` is a built-in mask or
+            if the mask ``name`` is already registered and
+            ``overwrite=False``.
 
         """
         # Check for attempt of overwriting built-in mask
         if name in self._builtin:
+            raise_error(f"Mask: {name} already registered as built-in mask.")
+        # Check for attempt of overwriting external masks
+        if name in self._external:
             if overwrite:
                 logger.info(f"Overwriting mask: {name}")
-                if self._registry[name]["family"] != "CustomUserMask":
-                    raise_error(
-                        f"Mask: {name} already registered as built-in mask."
-                    )
             else:
                 raise_error(
                     f"Mask: {name} already registered. Set `overwrite=True` "
@@ -318,16 +322,17 @@ class MaskRegistry(BasePipelineDataRegistry, metaclass=Singleton):
         # Convert str to Path
         if not isinstance(mask_path, Path):
             mask_path = Path(mask_path)
+        # Registration
         logger.info(f"Registering mask: {name}")
         # Add mask info
         self._external[name] = {
-            "path": str(mask_path.absolute()),
+            "path": mask_path,
             "family": "CustomUserMask",
             "space": space,
         }
         # Update registry
         self._registry[name] = {
-            "path": str(mask_path.absolute()),
+            "path": mask_path,
             "family": "CustomUserMask",
             "space": space,
         }
@@ -396,14 +401,22 @@ class MaskRegistry(BasePipelineDataRegistry, metaclass=Singleton):
         # Check if the mask family is custom or built-in
         mask_img = None
         if t_family == "CustomUserMask":
-            mask_fname = Path(mask_definition["path"])
-        elif t_family == "Vickery-Patil":
-            mask_fname = _load_vickery_patil_mask(name, resolution)
+            mask_fname = mask_definition["path"]
         elif t_family == "Callable":
             mask_img = mask_definition["func"]
             mask_fname = None
-        elif t_family == "UKB":
-            mask_fname = _load_ukb_mask(name)
+        elif t_family in ["Vickery-Patil", "UKB"]:
+            # Get dataset
+            dataset = check_dataset()
+            # Load mask
+            if t_family == "Vickery-Patil":
+                mask_fname = _load_vickery_patil_mask(
+                    dataset=dataset,
+                    name=name,
+                    resolution=resolution,
+                )
+            elif t_family == "UKB":
+                mask_fname = _load_ukb_mask(dataset=dataset, name=name)
         else:
             raise_error(f"Unknown mask family: {t_family}")
 
@@ -685,6 +698,7 @@ class MaskRegistry(BasePipelineDataRegistry, metaclass=Singleton):
 
 
 def _load_vickery_patil_mask(
+    dataset: "Dataset",
     name: str,
     resolution: Optional[float] = None,
 ) -> Path:
@@ -692,6 +706,8 @@ def _load_vickery_patil_mask(
 
     Parameters
     ----------
+    dataset : datalad.api.Dataset
+        The datalad dataset to fetch mask from.
     name : {"GM_prob0.2", "GM_prob0.2_cortex"}
         The name of the mask.
     resolution : float, optional
@@ -712,6 +728,7 @@ def _load_vickery_patil_mask(
         ``name = "GM_prob0.2"``.
 
     """
+    # Check name
     if name == "GM_prob0.2":
         available_resolutions = [1.5, 3.0]
         to_load = closest_resolution(resolution, available_resolutions)
@@ -730,17 +747,20 @@ def _load_vickery_patil_mask(
     else:
         raise_error(f"Cannot find a Vickery-Patil mask called {name}")
 
-    # Set path for masks
-    mask_fname = _masks_path / "vickery-patil" / mask_fname
+    # Fetch file
+    return fetch_file_via_datalad(
+        dataset=dataset,
+        file_path=dataset.pathobj / "masks" / "Vickery-Patil" / mask_fname,
+    )
 
-    return mask_fname
 
-
-def _load_ukb_mask(name: str) -> Path:
+def _load_ukb_mask(dataset: "Dataset", name: str) -> Path:
     """Load UKB mask.
 
     Parameters
     ----------
+    dataset : datalad.api.Dataset
+        The datalad dataset to fetch mask from.
     name : {"UKB_15K_GM"}
         The name of the mask.
 
@@ -755,15 +775,17 @@ def _load_ukb_mask(name: str) -> Path:
         If ``name`` is invalid.
 
     """
+    # Check name
     if name == "UKB_15K_GM":
         mask_fname = "UKB_15K_GM_template.nii.gz"
     else:
         raise_error(f"Cannot find a UKB mask called {name}")
 
-    # Set path for masks
-    mask_fname = _masks_path / "ukb" / mask_fname
-
-    return mask_fname
+    # Fetch file
+    return fetch_file_via_datalad(
+        dataset=dataset,
+        file_path=dataset.pathobj / "masks" / "UKB" / mask_fname,
+    )
 
 
 def _get_interpolation_method(img: "Nifti1Image") -> str: