siibra 1.0.1a0__tar.gz → 1.0.1a2__tar.gz

{siibra-1.0.1a0/siibra.egg-info → siibra-1.0.1a2}/PKG-INFO

@@ -1,6 +1,6 @@
-Metadata-Version: 2.1
+Metadata-Version: 2.2
 Name: siibra
-Version: 1.0.1a0
+Version: 1.0.1a2
 Summary: siibra - Software interfaces for interacting with brain atlases
 Home-page: https://github.com/FZJ-INM1-BDA/siibra-python
 Author: Big Data Analytics Group, Forschungszentrum Juelich, Institute of Neuroscience and Medicine (INM-1)
@@ -27,6 +27,15 @@ Requires-Dist: nilearn
 Requires-Dist: typing-extensions; python_version < "3.8"
 Requires-Dist: filelock
 Requires-Dist: ebrains-drive>=0.6.0
+Dynamic: author
+Dynamic: author-email
+Dynamic: classifier
+Dynamic: description
+Dynamic: description-content-type
+Dynamic: home-page
+Dynamic: requires-dist
+Dynamic: requires-python
+Dynamic: summary
 
 |License| |PyPI version| |doi| |Python versions| |Documentation Status|
 
@@ -34,7 +43,7 @@ Requires-Dist: ebrains-drive>=0.6.0
 siibra - Software interface for interacting with brain atlases
 ==============================================================
 
-Copyright 2020-2024, Forschungszentrum Jülich GmbH
+Copyright 2018-2024, Forschungszentrum Jülich GmbH
 
 *Authors: Big Data Analytics Group, Institute of Neuroscience and
 Medicine (INM-1), Forschungszentrum Jülich GmbH*
@@ -50,6 +59,14 @@ It aims to facilitate programmatic and reproducible incorporation of brain parce
 It supports both discretely labelled and statistical (probabilistic) parcellation maps, which can be used to assign brain regions to spatial locations and image signals, to retrieve region-specific neuroscience datasets from multiple online repositories, and to sample information from high-resolution image data. 
 The datasets anchored to brain regions address features of molecular, cellular and architecture as well as connectivity, and are complemented with live queries to external repositories as well as dynamic extraction from "big" image volumes such as the 20 micrometer BigBrain model.
 
+``siibra`` hides much of the complexity that would be required to collect and interact with the individual parcellations, templates and data repositories.
+By encapsulating many aspects of interacting with different maps and reference templates spaces, it also minimizes common errors like misinterpretation of coordinates from different reference spaces, confusing label indices of brain regions, or using inconsistent versions of parcellation maps. 
+It aims to provide a safe way of using maps defined across multiple spatial scales for reproducible analysis.
+
+.. intro-end
+
+.. about-start
+
 ``siibra`` was developed in the frame of the `Human Brain Project <https://humanbrainproject.eu>`__ for accessing the `EBRAINS
 human brain atlas <https://ebrains.eu/service/human-brain-atlas>`__. 
 It stores most of its contents as sustainable and open datasets in the `EBRAINS Knowledge Graph <https://kg.ebrains.eu>`__, and is designed to support the `OpenMINDS metadata standards <https://github.com/HumanBrainProject/openMINDS_SANDS>`__. 
@@ -58,11 +75,7 @@ In fact, the viewer is a good resource for exploring ``siibra``\ ’s core funct
 Feature queries in ``siibra`` are parameterized by data modality and anatomical location, while the latter could be a brain region, brain parcellation, or location in reference space. 
 Beyond the explorative focus of ``siibra-explorer``, the Python library supports a range of data analysis functions suitable for typical neuroscience workflows.
 
-``siibra`` hides much of the complexity that would be required to collect and interact with the individual parcellations, templates and data repositories.
-By encapsulating many aspects of interacting with different maps and reference templates spaces, it also minimizes common errors like misinterpretation of coordinates from different reference spaces, confusing label indices of brain regions, or using inconsistent versions of parcellation maps. 
-It aims to provide a safe way of using maps defined across multiple spatial scales for reproducible analysis.
-
-.. intro-end
+.. about-end
 
 .. getting-started-start
 

{siibra-1.0.1a0 → siibra-1.0.1a2}/README.rst

@@ -4,7 +4,7 @@
 siibra - Software interface for interacting with brain atlases
 ==============================================================
 
-Copyright 2020-2024, Forschungszentrum Jülich GmbH
+Copyright 2018-2024, Forschungszentrum Jülich GmbH
 
 *Authors: Big Data Analytics Group, Institute of Neuroscience and
 Medicine (INM-1), Forschungszentrum Jülich GmbH*
@@ -20,6 +20,14 @@ It aims to facilitate programmatic and reproducible incorporation of brain parce
 It supports both discretely labelled and statistical (probabilistic) parcellation maps, which can be used to assign brain regions to spatial locations and image signals, to retrieve region-specific neuroscience datasets from multiple online repositories, and to sample information from high-resolution image data. 
 The datasets anchored to brain regions address features of molecular, cellular and architecture as well as connectivity, and are complemented with live queries to external repositories as well as dynamic extraction from "big" image volumes such as the 20 micrometer BigBrain model.
 
+``siibra`` hides much of the complexity that would be required to collect and interact with the individual parcellations, templates and data repositories.
+By encapsulating many aspects of interacting with different maps and reference templates spaces, it also minimizes common errors like misinterpretation of coordinates from different reference spaces, confusing label indices of brain regions, or using inconsistent versions of parcellation maps. 
+It aims to provide a safe way of using maps defined across multiple spatial scales for reproducible analysis.
+
+.. intro-end
+
+.. about-start
+
 ``siibra`` was developed in the frame of the `Human Brain Project <https://humanbrainproject.eu>`__ for accessing the `EBRAINS
 human brain atlas <https://ebrains.eu/service/human-brain-atlas>`__. 
 It stores most of its contents as sustainable and open datasets in the `EBRAINS Knowledge Graph <https://kg.ebrains.eu>`__, and is designed to support the `OpenMINDS metadata standards <https://github.com/HumanBrainProject/openMINDS_SANDS>`__. 
@@ -28,11 +36,7 @@ In fact, the viewer is a good resource for exploring ``siibra``\ ’s core funct
 Feature queries in ``siibra`` are parameterized by data modality and anatomical location, while the latter could be a brain region, brain parcellation, or location in reference space. 
 Beyond the explorative focus of ``siibra-explorer``, the Python library supports a range of data analysis functions suitable for typical neuroscience workflows.
 
-``siibra`` hides much of the complexity that would be required to collect and interact with the individual parcellations, templates and data repositories.
-By encapsulating many aspects of interacting with different maps and reference templates spaces, it also minimizes common errors like misinterpretation of coordinates from different reference spaces, confusing label indices of brain regions, or using inconsistent versions of parcellation maps. 
-It aims to provide a safe way of using maps defined across multiple spatial scales for reproducible analysis.
-
-.. intro-end
+.. about-end
 
 .. getting-started-start
 

siibra-1.0.1a2/siibra/VERSION

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

{siibra-1.0.1a0 → siibra-1.0.1a2}/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-1.0.1a0 → siibra-1.0.1a2}/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-1.0.1a0 → siibra-1.0.1a2}/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-1.0.1a0 → siibra-1.0.1a2}/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-1.0.1a0 → siibra-1.0.1a2}/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-1.0.1a0 → siibra-1.0.1a2}/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-1.0.1a0 → siibra-1.0.1a2}/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-1.0.1a0 → siibra-1.0.1a2}/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-1.0.1a0 → siibra-1.0.1a2}/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-1.0.1a0 → siibra-1.0.1a2}/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
     ----------