siibra 1.0.1a0__py3-none-any.whl → 1.0.1a2__py3-none-any.whl

siibra/VERSION

@@ -1 +1 @@
-1.0.1-alpha.0
+1.0.1-alpha.2

siibra/__init__.py

@@ -1,4 +1,4 @@
-# Copyright 2018-2024
+# Copyright 2018-2025
 # Institute of Neuroscience and Medicine (INM-1), Forschungszentrum Jülich GmbH
 
 # Licensed under the Apache License, Version 2.0 (the "License");
@@ -13,35 +13,29 @@
 # See the License for the specific language governing permissions and
 # limitations under the License.
 
+import os as _os
+
 from .commons import (
     logger,
     QUIET,
     VERBOSE,
     MapType,
-    MapIndex,
     set_log_level,
     __version__
 )
-
+from . import configuration, features, livequeries
+from .configuration import factory
 from .core import (
     atlas as _atlas,
     parcellation as _parcellation,
     space as _space
 )
 from .volumes import parcellationmap as _parcellationmap
-from .retrieval.requests import (
-    EbrainsRequest as _EbrainsRequest,
-    CACHE as cache
-)
+from .retrieval.requests import CACHE as cache
 from .retrieval.cache import Warmup, WarmupLevel
+from .locations import Point, PointCloud, Plane, BoundingBox
 
-from . import configuration
-from . import experimental
-from .configuration import factory
-from . import features, livequeries
-from siibra.locations import Point, PointCloud
 
-import os as _os
 logger.info(f"Version: {__version__}")
 logger.warning("This is a development release. Use at your own risk.")
 logger.info(
@@ -49,8 +43,6 @@ logger.info(
 )
 
 # forward access to some functions
-set_ebrains_token = _EbrainsRequest.set_token
-fetch_ebrains_token = _EbrainsRequest.fetch_token
 find_regions = _parcellation.find_regions
 from_json = factory.Factory.from_json
 
@@ -108,7 +100,7 @@ def set_feasible_download_size(maxsize_gbyte):
 
 def set_cache_size(maxsize_gbyte: int):
     """
-    siibra runs maintainance on its local cache to keep it under a predetermined
+    siibra runs maintenance on its local cache to keep it under a predetermined
     size of 2 gigabytes. This method changes the cache size.
 
     Parameters
@@ -129,9 +121,9 @@ def warm_cache(level=WarmupLevel.INSTANCE):
     Preload preconfigured siibra concepts.
 
     Siibra relies on preconfigurations that simplify integrating various
-    concepts such as parcellations, refernce spaces, and multimodal data
+    concepts such as parcellations, reference spaces, and multimodal data
     features. By preloading the instances, siibra commits all preconfigurations
-    to the memory at once instead of commiting them when required.
+    to the memory at once instead of committing them when required.
     """
     Warmup.warmup(level)
 
@@ -151,10 +143,9 @@ def __dir__():
         "MapType",
         "Point",
         "PointCloud",
+        "BoundingBox",
         "QUIET",
         "VERBOSE",
-        "fetch_ebrains_token",
-        "set_ebrains_token",
         "vocabularies",
         "__version__",
         "cache",

siibra/commons.py

@@ -1,4 +1,4 @@
-# Copyright 2018-2024
+# Copyright 2018-2025
 # Institute of Neuroscience and Medicine (INM-1), Forschungszentrum Jülich GmbH
 
 # Licensed under the Apache License, Version 2.0 (the "License");
@@ -17,24 +17,26 @@
 import os
 import re
 from enum import Enum
-from nibabel import Nifti1Image
-from nilearn.image import resample_to_img
 import logging
-from tqdm import tqdm
-import numpy as np
-import pandas as pd
-from typing import Generic, Iterable, Iterator, List, TypeVar, Union, Dict, Generator, Tuple
-from skimage.filters import gaussian
 from dataclasses import dataclass
 from hashlib import md5
 from uuid import UUID
 import math
+from typing import Generic, Iterable, Iterator, List, TypeVar, Union, Dict, Generator, Tuple
 try:
     from typing import TypedDict
 except ImportError:
     # support python 3.7
     from typing_extensions import TypedDict
 
+from tqdm import tqdm
+import numpy as np
+import pandas as pd
+from nibabel import Nifti1Image
+from nilearn.image import resample_to_img
+from skimage.filters import gaussian
+
+
 logging.addLevelName(21, "INFO_WO_PROGRESS_BARS")
 logger = logging.getLogger(__name__.split(os.path.extsep)[0])
 ch = logging.StreamHandler()
@@ -139,7 +141,7 @@ class InstanceTable(Generic[T], Iterable):
         return (w for w in self._elements.values())
 
     def __contains__(self, key: Union[str, T]) -> bool:
-        """Test wether the given key or element is defined by the registry."""
+        """Test whether the given key or element is defined by the registry."""
         if isinstance(key, str):
             return key in self._elements
         return key in [item for _, item in self._elements.values()]
@@ -536,7 +538,8 @@ def resample_img_to_img(
     resampled_img = resample_to_img(
         source_img=source_img,
         target_img=target_img,
-        interpolation=interpolation
+        interpolation=interpolation,
+        force_resample=True,  # False is intended for testing. see nilearn docs
     )
     return resampled_img
 
@@ -554,7 +557,7 @@ def connected_components(
 
     Note
     ----
-    `Uses skimage.measure.label()` to determine foreground compenents.
+    `Uses skimage.measure.label()` to determine foreground components.
 
     Parameters
     ----------
@@ -568,7 +571,7 @@ def connected_components(
     Yields
     ------
     Generator[Tuple[int, np.ndarray], None, None]
-        tuple of integer label of the component and component as an nd.array in
+        tuple of integer label of the component and component as an ndarray in
         the shape of the original image.
     """
     from skimage import measure
@@ -644,11 +647,11 @@ def MI(arr1, arr2, nbins=100, normalized=True):
     assert (all(arr.size > 0) for arr in [arr1, arr2])
 
     # compute the normalized joint 2D histogram as an
-    # empirical measure of the joint probabily of arr1 and arr2
+    # empirical measure of the joint probability of arr1 and arr2
     pxy, _, _ = np.histogram2d(arr1.ravel(), arr2.ravel(), bins=nbins)
     pxy /= pxy.sum()
 
-    # extract the empirical propabilities of intensities
+    # extract the empirical probabilities of intensities
     # from the joint histogram
     px = np.sum(pxy, axis=1)  # marginal for x over y
     py = np.sum(pxy, axis=0)  # marginal for y over x

siibra/configuration/__init__.py

@@ -1,4 +1,4 @@
-# Copyright 2018-2024
+# Copyright 2018-2025
 # Institute of Neuroscience and Medicine (INM-1), Forschungszentrum Jülich GmbH
 
 # Licensed under the Apache License, Version 2.0 (the "License");

siibra/configuration/configuration.py

@@ -1,4 +1,4 @@
-# Copyright 2018-2024
+# Copyright 2018-2025
 # Institute of Neuroscience and Medicine (INM-1), Forschungszentrum Jülich GmbH
 
 # Licensed under the Apache License, Version 2.0 (the "License");
@@ -13,16 +13,16 @@
 # See the License for the specific language governing permissions and
 # limitations under the License.
 
-from ..commons import logger, __version__, SIIBRA_USE_CONFIGURATION, siibra_tqdm
-from ..retrieval.repositories import GitlabConnector, RepositoryConnector, GithubConnector
-from ..retrieval.exceptions import NoSiibraConfigMirrorsAvailableException
-from ..retrieval.requests import SiibraHttpRequestError
-
 from typing import Union, List
 from collections import defaultdict
 from requests.exceptions import ConnectionError
 from os import path
 
+from ..commons import logger, __version__, SIIBRA_USE_CONFIGURATION, siibra_tqdm
+from ..retrieval.repositories import GitlabConnector, RepositoryConnector, GithubConnector
+from ..retrieval.exceptions import NoSiibraConfigMirrorsAvailableException
+from ..retrieval.requests import SiibraHttpRequestError
+
 
 class Configuration:
     """

siibra/configuration/factory.py

@@ -1,4 +1,4 @@
-# Copyright 2018-2024
+# Copyright 2018-2025
 # Institute of Neuroscience and Medicine (INM-1), Forschungszentrum Jülich GmbH
 
 # Licensed under the Apache License, Version 2.0 (the "License");
@@ -13,6 +13,15 @@
 # See the License for the specific language governing permissions and
 # limitations under the License.
 
+from os import path
+import json
+from typing import List, Dict, Callable
+from io import BytesIO
+from functools import wraps
+
+import numpy as np
+import pandas as pd
+
 from ..commons import logger, Species
 from ..features import anchor, connectivity
 from ..features.tabular import (
@@ -29,14 +38,6 @@ from ..retrieval import datasets, repositories
 from ..volumes import volume, sparsemap, parcellationmap
 from ..volumes.providers.provider import VolumeProvider
 
-from os import path
-import json
-import numpy as np
-from typing import List, Dict, Callable
-import pandas as pd
-from io import BytesIO
-from functools import wraps
-
 
 _registered_build_fns: Dict[str, Callable] = {}
 

siibra/core/__init__.py

@@ -1,4 +1,4 @@
-# Copyright 2018-2024
+# Copyright 2018-2025
 # Institute of Neuroscience and Medicine (INM-1), Forschungszentrum Jülich GmbH
 
 # Licensed under the Apache License, Version 2.0 (the "License");
@@ -12,5 +12,5 @@
 # WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
 # See the License for the specific language governing permissions and
 # limitations under the License.
-""":ref:`Main siibra concepts<mainconcepts>`"""
+"""Core concepts behind siibra, :ref:`see glossary <glossary>` for details."""
 from . import atlas, parcellation, space

siibra/core/assignment.py

@@ -1,4 +1,4 @@
-# Copyright 2018-2024
+# Copyright 2018-2025
 # Institute of Neuroscience and Medicine (INM-1), Forschungszentrum Jülich GmbH
 
 # Licensed under the Apache License, Version 2.0 (the "License");
@@ -17,6 +17,7 @@
 from enum import Enum
 from dataclasses import dataclass
 from typing import Dict, Generic, TypeVar, TYPE_CHECKING
+
 if TYPE_CHECKING:
     from .structure import BrainStructure
 

siibra/core/atlas.py

@@ -1,4 +1,4 @@
-# Copyright 2018-2024
+# Copyright 2018-2025
 # Institute of Neuroscience and Medicine (INM-1), Forschungszentrum Jülich GmbH
 
 # Licensed under the Apache License, Version 2.0 (the "License");
@@ -13,12 +13,12 @@
 # See the License for the specific language governing permissions and
 # limitations under the License.
 """Provides reference systems for brains."""
-from . import concept, space as _space, parcellation as _parcellation
-
-from ..commons import MapType, logger, InstanceTable, Species
 
 from typing import List
 
+from . import concept, space as _space, parcellation as _parcellation
+from ..commons import MapType, logger, InstanceTable, Species
+
 
 VERSION_BLACKLIST_WORDS = ["beta", "rc", "alpha"]
 

siibra/core/concept.py

@@ -1,4 +1,4 @@
-# Copyright 2018-2024
+# Copyright 2018-2025
 # Institute of Neuroscience and Medicine (INM-1), Forschungszentrum Jülich GmbH
 
 # Licensed under the Apache License, Version 2.0 (the "License");
@@ -13,6 +13,10 @@
 # See the License for the specific language governing permissions and
 # limitations under the License.
 """Parent class to siibra main concepts."""
+
+import re
+from typing import TypeVar, Type, Union, List, TYPE_CHECKING, Dict
+
 from ..commons import (
     create_key,
     clear_name,
@@ -23,8 +27,6 @@ from ..commons import (
 )
 from ..retrieval import cache
 
-import re
-from typing import TypeVar, Type, Union, List, TYPE_CHECKING, Dict
 
 T = TypeVar("T", bound="AtlasConcept")
 _REGISTRIES: Dict[Type[T], InstanceTable[T]] = {}
@@ -145,9 +147,9 @@ class AtlasConcept:
     @property
     def authors(self):
         return [
-            contributer['name']
+            contributor['name']
             for ds in self.datasets
-            for contributer in ds.contributors
+            for contributor in ds.contributors
         ]
 
     @property

siibra/core/parcellation.py

@@ -1,4 +1,4 @@
-# Copyright 2018-2024
+# Copyright 2018-2025
 # Institute of Neuroscience and Medicine (INM-1), Forschungszentrum Jülich GmbH
 
 # Licensed under the Apache License, Version 2.0 (the "License");
@@ -13,11 +13,6 @@
 # See the License for the specific language governing permissions and
 # limitations under the License.
 """Hierarchal brain regions and metadata."""
-from . import region
-
-from ..commons import logger, MapType, Species
-from ..volumes import parcellationmap
-from ..exceptions import NoMapMatchingValues
 
 from functools import lru_cache
 import re
@@ -28,6 +23,11 @@ except ImportError:
     # support python 3.7
     from typing_extensions import Literal
 
+from . import region
+from ..commons import logger, MapType, Species
+from ..volumes import parcellationmap
+from ..exceptions import MapNotFound
+
 
 if TYPE_CHECKING:
     from .space import Space
@@ -193,13 +193,13 @@ class Parcellation(region.Region, configuration_folder="parcellations"):
             and m.parcellation.matches(self)
         ]
         if len(candidates) == 0:
-            raise NoMapMatchingValues(f"No '{maptype}' map in '{space}' available for {str(self)}")
+            raise MapNotFound(f"No '{maptype}' map in '{space}' available for {str(self)}")
         if len(candidates) > 1:
             spec_candidates = [
                 c for c in candidates if all(w.lower() in c.id.lower() for w in spec.split())
             ]
             if len(spec_candidates) == 0:
-                raise NoMapMatchingValues(f"'{spec}' does not match any options from {[c.name for c in candidates]}.")
+                raise MapNotFound(f"'{spec}' does not match any options from {[c.name for c in candidates]}.")
             if len(spec_candidates) > 1:
                 logger.warning(
                     f"Multiple maps are available in this specification of space, parcellation, and map type.\n"
@@ -221,7 +221,7 @@ class Parcellation(region.Region, configuration_folder="parcellations"):
         """
         spec = re.sub(r'Group: *', '', spec)
         for substr in re.findall(r'\(.*?\)', spec):
-            # temporarilty replace commas inside brackets with a placeholder
+            # temporarily replace commas inside brackets with a placeholder
             # because these are not region spec delimiters
             spec = spec.replace(substr, re.sub(r', *', '##', substr))
         # process the comma separated substrings
@@ -354,7 +354,7 @@ def find_regions(
 ):
     """
     Find regions matching the given region specification across all parcellation
-    instances in the registery.
+    instances in the registry.
 
     Parameters
     ----------