siibra 1.0.1a1__tar.gz → 1.0.1a5__tar.gz

{siibra-1.0.1a1/siibra.egg-info → siibra-1.0.1a5}/PKG-INFO

@@ -1,6 +1,6 @@
-Metadata-Version: 2.2
+Metadata-Version: 2.4
 Name: siibra
-Version: 1.0.1a1
+Version: 1.0.1a5
 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)
@@ -33,6 +33,7 @@ Dynamic: classifier
 Dynamic: description
 Dynamic: description-content-type
 Dynamic: home-page
+Dynamic: license-file
 Dynamic: requires-dist
 Dynamic: requires-python
 Dynamic: summary
@@ -43,22 +44,28 @@ Dynamic: summary
 siibra - Software interface for interacting with brain atlases
 ==============================================================
 
-Copyright 2018-2024, Forschungszentrum Jülich GmbH
+Copyright 2018-2025, Forschungszentrum Jülich GmbH
 
 *Authors: Big Data Analytics Group, Institute of Neuroscience and
 Medicine (INM-1), Forschungszentrum Jülich GmbH*
 
 .. intro-start
 
-``siibra`` is a Python client to a brain atlas framework that integrates brain parcellations and reference spaces at different spatial scales, and connects them with a broad range of multimodal regional data features. 
+``siibra-python`` is a Python client to a brain atlas framework that integrates brain parcellations and reference spaces at different spatial scales, and connects them with a broad range of multimodal regional data features. 
 It aims to facilitate programmatic and reproducible incorporation of brain parcellations and brain region features from different sources into neuroscience workflows.
 
-    **Note:** ``siibra-python`` *is still in development. While care is taken that it works reliably, its API is not yet stable and you may still encounter bugs when using it.*
-
 ``siibra`` provides structured access to parcellation schemes in different brain reference spaces, including volumetric reference templates at  macroscopic and microscopic resolutions as well as surface representations. 
 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>`__. 
@@ -67,11 +74,7 @@ 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
 
@@ -80,10 +83,26 @@ Installation
 
 ``siibra`` is available on pypi. 
 To install the latest released version, simply run ``pip install siibra``. 
+The installation typically takes about 2 minutes on a standard computer where Python is already installed.
 In order to work with the latest version from github, use ``pip install git+https://github.com/FZJ-INM1-BDA/siibra-python.git@main``.
 
-There is also an image based on jupyter:scipy-notebook, which already includes ``siibra``.
-
+``siibra-python`` should be installable on recent versions of Windows, Linux and Mac OS in a recent Python 3 environment.
+We run continuous integration tests for versions 3.7 - 3.12 on recent Ubuntu images. 
+
+The library requires a couple of open source packages, namely:
+```
+anytree >= 2.12.1
+nibabel >= 5.3.2
+appdirs >= 1.4.4
+scikit-image >= 0.25.0
+requests >= 2.32.3
+neuroglancer-scripts >= 1.2.0
+nilearn >= 0.11.0
+filelock >= 3.16.1
+ebrains-drive >= 0.6.0
+```
+
+You can also install a docker image with all dependencies included:
 .. code-block:: sh
 
   docker run -dit \
@@ -93,19 +112,20 @@ There is also an image based on jupyter:scipy-notebook, which already includes `
         docker-registry.ebrains.eu/siibra/siibra-python:latest
 
 
+
 Documentation & Help
 ====================
 
 ``siibra-python``\ ’s documentation is hosted on https://siibra-python.readthedocs.io.
 The documentation includes a catalogue of documented code examples that walk you through the different concepts and functionalities.
+These examples use real data and include both the code and the produced expected outputs.
+They can be accessed at https://siibra-python.readthedocs.io/en/latest/examples.html, and are
+automatically tested and updated whenever a new version of ``siibra-python`` is published.
 As a new user, it is recommended to go through these examples - they are easy and will quickly provide you with the right code snippets that get you started.
-Furthermore, a set of jupyter notebooks demonstrating more extensive example use cases are maintained in the `siibra-tutorials <https://github.com/FZJ-INM1-BDA/siibra-tutorials>`__ repository.
-We are working on a full API documentation of the library. You find the current status on readthedocs, but be aware that it is not yet complete and as up-to-date as the code examples.
+The documentation on readthedocs further includes introductory explanations and an API reference.
 
 If you run into issues, please open a ticket on `EBRAINS support <https://ebrains.eu/support/>`__ or file bugs and
 feature requests on `github <https://github.com/FZJ-INM1-BDA/siibra-python/issues>`__.
-Please keep in mind that ``siibra-python`` is still in development.
-While care is taken to make everything work reliably, the API of the library is not yet stable, and the software is not yet fully tested.
 
 .. getting-started-end
 

{siibra-1.0.1a1 → siibra-1.0.1a5}/README.rst

@@ -4,22 +4,28 @@
 siibra - Software interface for interacting with brain atlases
 ==============================================================
 
-Copyright 2018-2024, Forschungszentrum Jülich GmbH
+Copyright 2018-2025, Forschungszentrum Jülich GmbH
 
 *Authors: Big Data Analytics Group, Institute of Neuroscience and
 Medicine (INM-1), Forschungszentrum Jülich GmbH*
 
 .. intro-start
 
-``siibra`` is a Python client to a brain atlas framework that integrates brain parcellations and reference spaces at different spatial scales, and connects them with a broad range of multimodal regional data features. 
+``siibra-python`` is a Python client to a brain atlas framework that integrates brain parcellations and reference spaces at different spatial scales, and connects them with a broad range of multimodal regional data features. 
 It aims to facilitate programmatic and reproducible incorporation of brain parcellations and brain region features from different sources into neuroscience workflows.
 
-    **Note:** ``siibra-python`` *is still in development. While care is taken that it works reliably, its API is not yet stable and you may still encounter bugs when using it.*
-
 ``siibra`` provides structured access to parcellation schemes in different brain reference spaces, including volumetric reference templates at  macroscopic and microscopic resolutions as well as surface representations. 
 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 +34,7 @@ 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
 
@@ -41,10 +43,26 @@ Installation
 
 ``siibra`` is available on pypi. 
 To install the latest released version, simply run ``pip install siibra``. 
+The installation typically takes about 2 minutes on a standard computer where Python is already installed.
 In order to work with the latest version from github, use ``pip install git+https://github.com/FZJ-INM1-BDA/siibra-python.git@main``.
 
-There is also an image based on jupyter:scipy-notebook, which already includes ``siibra``.
-
+``siibra-python`` should be installable on recent versions of Windows, Linux and Mac OS in a recent Python 3 environment.
+We run continuous integration tests for versions 3.7 - 3.12 on recent Ubuntu images. 
+
+The library requires a couple of open source packages, namely:
+```
+anytree >= 2.12.1
+nibabel >= 5.3.2
+appdirs >= 1.4.4
+scikit-image >= 0.25.0
+requests >= 2.32.3
+neuroglancer-scripts >= 1.2.0
+nilearn >= 0.11.0
+filelock >= 3.16.1
+ebrains-drive >= 0.6.0
+```
+
+You can also install a docker image with all dependencies included:
 .. code-block:: sh
 
   docker run -dit \
@@ -54,19 +72,20 @@ There is also an image based on jupyter:scipy-notebook, which already includes `
         docker-registry.ebrains.eu/siibra/siibra-python:latest
 
 
+
 Documentation & Help
 ====================
 
 ``siibra-python``\ ’s documentation is hosted on https://siibra-python.readthedocs.io.
 The documentation includes a catalogue of documented code examples that walk you through the different concepts and functionalities.
+These examples use real data and include both the code and the produced expected outputs.
+They can be accessed at https://siibra-python.readthedocs.io/en/latest/examples.html, and are
+automatically tested and updated whenever a new version of ``siibra-python`` is published.
 As a new user, it is recommended to go through these examples - they are easy and will quickly provide you with the right code snippets that get you started.
-Furthermore, a set of jupyter notebooks demonstrating more extensive example use cases are maintained in the `siibra-tutorials <https://github.com/FZJ-INM1-BDA/siibra-tutorials>`__ repository.
-We are working on a full API documentation of the library. You find the current status on readthedocs, but be aware that it is not yet complete and as up-to-date as the code examples.
+The documentation on readthedocs further includes introductory explanations and an API reference.
 
 If you run into issues, please open a ticket on `EBRAINS support <https://ebrains.eu/support/>`__ or file bugs and
 feature requests on `github <https://github.com/FZJ-INM1-BDA/siibra-python/issues>`__.
-Please keep in mind that ``siibra-python`` is still in development.
-While care is taken to make everything work reliably, the API of the library is not yet stable, and the software is not yet fully tested.
 
 .. getting-started-end
 

siibra-1.0.1a5/siibra/VERSION

@@ -0,0 +1 @@
+1.0.1-alpha.5

{siibra-1.0.1a1 → siibra-1.0.1a5}/siibra/__init__.py

@@ -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
 
@@ -151,10 +143,9 @@ def __dir__():
         "MapType",
         "Point",
         "PointCloud",
+        "BoundingBox",
         "QUIET",
         "VERBOSE",
-        "fetch_ebrains_token",
-        "set_ebrains_token",
         "vocabularies",
         "__version__",
         "cache",

{siibra-1.0.1a1 → siibra-1.0.1a5}/siibra/commons.py

@@ -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()
@@ -532,13 +534,21 @@ def resample_img_to_img(
     -------
     Nifti1Image
     """
+    from nilearn._version import version as nilearn_version
+    from packaging.version import Version
+
     interpolation = "nearest" if np.array_equal(np.unique(source_img.dataobj), [0, 1]) else "linear"
-    resampled_img = resample_to_img(
+    kwargs = dict(
         source_img=source_img,
         target_img=target_img,
         interpolation=interpolation,
         force_resample=True,  # False is intended for testing. see nilearn docs
     )
+    if Version(nilearn_version) >= Version("0.11.0"):
+        # because nilearn>=0.11.0 don't support "copy_header" and python <= 3.8
+        kwargs["copy_header"] = True  # use new default in nilearn >= 0.11.0
+
+    resampled_img = resample_to_img(**kwargs)
     return resampled_img
 
 
@@ -723,6 +733,7 @@ class Species(Enum):
     MACACA_MULATTA = 5
     MACACA_FUSCATA = 6
     CHLOROCEBUS_AETHIOPS_SABAEUS = 7
+    CALLITHRIX_JACCHUS = 8
 
     UNSPECIFIED_SPECIES = 999
 

{siibra-1.0.1a1 → siibra-1.0.1a5}/siibra/configuration/configuration.py

@@ -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:
     """
@@ -185,5 +185,4 @@ class Configuration:
 
 
 if SIIBRA_USE_CONFIGURATION:
-    logger.warning(f"config.SIIBRA_USE_CONFIGURATION defined, use configuration at {SIIBRA_USE_CONFIGURATION}")
     Configuration.use_configuration(SIIBRA_USE_CONFIGURATION)

{siibra-1.0.1a1 → siibra-1.0.1a5}/siibra/configuration/factory.py

@@ -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] = {}
 
@@ -486,6 +487,10 @@ class Factory:
             return volume_of_interest.LSFMVolumeOfInterest(
                 modality="Light Sheet Fluorescence Microscopy", **kwargs
             )
+        elif modality == "morphometry":
+            return volume_of_interest.MorphometryVolumeOfInterest(
+                modality="Morphometry", **kwargs
+            )
         else:
             raise ValueError(
                 f"No method for building image section feature type {modality}."

{siibra-1.0.1a1 → siibra-1.0.1a5}/siibra/core/__init__.py

@@ -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-1.0.1a1 → siibra-1.0.1a5}/siibra/core/assignment.py

@@ -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
 
@@ -25,12 +26,12 @@ T = TypeVar("T")
 
 class Qualification(Enum):
     EXACT = 1
-    OVERLAPS = 2
-    CONTAINED = 3
-    CONTAINS = 4
-    APPROXIMATE = 5
-    HOMOLOGOUS = 6
-    OTHER_VERSION = 7
+    APPROXIMATE = 2
+    OTHER_VERSION = 3
+    CONTAINED = 4
+    CONTAINS = 5
+    OVERLAPS = 6
+    HOMOLOGOUS = 7
 
     @property
     def verb(self):
@@ -66,6 +67,17 @@ class Qualification(Enum):
         assert self in inverses, f"{str(self)} inverses cannot be found."
         return inverses[self]
 
+    def __lt__(self, other: "Qualification"):
+        """
+        This is used to sort feature query results. Since it is very difficult
+        to determine a well-ordering principle and it is difficult to sort
+        without one, the enum values are used for sorting. This means
+        not all comparisons have logical basis but they are well-defined,
+        making it reproducible but also clearly distinguishes important
+        comparisons.
+        """
+        return self.value < other.value
+
     def __str__(self):
         return f"{self.__class__.__name__}={self.name.lower()}"
 
@@ -107,4 +119,4 @@ class AnatomicalAssignment(Generic[T]):
     def __lt__(self, other: 'AnatomicalAssignment'):
         if not isinstance(other, AnatomicalAssignment):
             raise ValueError(f"Cannot compare AnatomicalAssignment with instances of '{type(other)}'")
-        return self.qualification.value < other.qualification.value
+        return self.qualification < other.qualification

{siibra-1.0.1a1 → siibra-1.0.1a5}/siibra/core/concept.py

@@ -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]] = {}

{siibra-1.0.1a1 → siibra-1.0.1a5}/siibra/core/region.py

@@ -14,9 +14,18 @@
 # limitations under the License.
 """Representation of a brain region."""
 
-from . import concept, structure, space as _space, parcellation as _parcellation
-from .assignment import Qualification, AnatomicalAssignment
+import re
+from typing import List, Union, Iterable, Dict, Callable, Tuple, Set
+from difflib import SequenceMatcher
+import json
+from functools import wraps, reduce
+from concurrent.futures import ThreadPoolExecutor
+from functools import lru_cache
+
+import anytree
+from ebrains_drive import BucketApiClient
 
+from . import concept, structure, space as _space, parcellation as _parcellation, assignment
 from ..retrieval.cache import cache_user_fn
 from ..locations import location, pointcloud, boundingbox as _boundingbox
 from ..volumes import parcellationmap, volume
@@ -29,16 +38,6 @@ from ..commons import (
 )
 from ..exceptions import NoMapAvailableError, SpaceWarpingFailedError
 
-import re
-import anytree
-from typing import List, Union, Iterable, Dict, Callable, Tuple, Set
-from difflib import SequenceMatcher
-from ebrains_drive import BucketApiClient
-import json
-from functools import wraps, reduce
-from concurrent.futures import ThreadPoolExecutor
-from functools import lru_cache
-
 
 REGEX_TYPE = type(re.compile("test"))
 
@@ -128,7 +127,7 @@ class Region(anytree.NodeMixin, concept.AtlasConcept, structure.BrainStructure):
 
         Yields
         ------
-        Qualification
+        assignment.Qualification
 
         Example
         -------
@@ -595,7 +594,7 @@ class Region(anytree.NodeMixin, concept.AtlasConcept, structure.BrainStructure):
             except NoMapAvailableError:
                 return False
 
-    def assign(self, other: structure.BrainStructure) -> AnatomicalAssignment:
+    def assign(self, other: structure.BrainStructure) -> assignment.AnatomicalAssignment:
         """
         Compute assignment of a location to this region.
 
@@ -609,8 +608,8 @@ class Region(anytree.NodeMixin, concept.AtlasConcept, structure.BrainStructure):
 
         Returns
         -------
-        AnatomicalAssignment or None
-            None if there is no Qualification found.
+        assignment.AnatomicalAssignment or None
+            None if there is no assignment.Qualification found.
         """
         if (self, other) in self._ASSIGNMENT_CACHE:
             return self._ASSIGNMENT_CACHE[self, other]
@@ -659,17 +658,17 @@ class Region(anytree.NodeMixin, concept.AtlasConcept, structure.BrainStructure):
         else:  # other is a Region
             assert isinstance(other, Region)
             if self == other:
-                qualification = Qualification.EXACT
+                qualification = assignment.Qualification.EXACT
             elif self.__contains__(other):
-                qualification = Qualification.CONTAINS
+                qualification = assignment.Qualification.CONTAINS
             elif other.__contains__(self):
-                qualification = Qualification.CONTAINED
+                qualification = assignment.Qualification.CONTAINED
             else:
                 qualification = None
             if qualification is None:
                 self._ASSIGNMENT_CACHE[self, other] = None
             else:
-                self._ASSIGNMENT_CACHE[self, other] = AnatomicalAssignment(self, other, qualification)
+                self._ASSIGNMENT_CACHE[self, other] = assignment.AnatomicalAssignment(self, other, qualification)
         return self._ASSIGNMENT_CACHE[self, other]
 
     def tree2str(self):
@@ -926,7 +925,7 @@ def get_related_regions(region: Region) -> Iterable["RegionRelationAssessments"]
 
     Yields
     ------
-    Qualification
+    assignment.Qualification
 
     Example
     -------
@@ -968,7 +967,7 @@ def _register_region_reference_type(ebrain_type: str):
     return outer
 
 
-class RegionRelationAssessments(AnatomicalAssignment[Region]):
+class RegionRelationAssessments(assignment.AnatomicalAssignment[Region]):
     """
     A collection of methods on finding related regions and the quantification
     of the relationship.
@@ -1110,7 +1109,7 @@ class RegionRelationAssessments(AnatomicalAssignment[Region]):
                 yield cls(
                     query_structure=src,
                     assigned_structure=found_target,
-                    qualification=Qualification.parse_relation_assessment(overlap)
+                    qualification=assignment.Qualification.parse_relation_assessment(overlap)
                 )
 
             if "https://openminds.ebrains.eu/sands/ParcellationEntity" in target.get("type"):
@@ -1124,7 +1123,7 @@ class RegionRelationAssessments(AnatomicalAssignment[Region]):
                         yield cls(
                             query_structure=src,
                             assigned_structure=reg,
-                            qualification=Qualification.parse_relation_assessment(overlap)
+                            qualification=assignment.Qualification.parse_relation_assessment(overlap)
                         )
 
     @classmethod
@@ -1178,7 +1177,7 @@ class RegionRelationAssessments(AnatomicalAssignment[Region]):
                     yield cls(
                         query_structure=src,
                         assigned_structure=region,
-                        qualification=Qualification.OTHER_VERSION
+                        qualification=assignment.Qualification.OTHER_VERSION
                     )
 
             # homologuous

{siibra-1.0.1a1 → siibra-1.0.1a5}/siibra/core/space.py

@@ -14,18 +14,16 @@
 # limitations under the License.
 """A particular brain reference space."""
 
+from typing import List, TYPE_CHECKING, Union
 
-from .concept import AtlasConcept
-
+from . import concept
 from ..commons import logger, Species
 
-from typing import List, TYPE_CHECKING, Union
-
 if TYPE_CHECKING:
     from ..volumes import volume
 
 
-class Space(AtlasConcept, configuration_folder="spaces"):
+class Space(concept.AtlasConcept, configuration_folder="spaces"):
 
     def __init__(
         self,
@@ -66,7 +64,7 @@ class Space(AtlasConcept, configuration_folder="spaces"):
                 Key: EBRAINS KG schema, value: EBRAINS KG @id
         """
 
-        AtlasConcept.__init__(
+        concept.AtlasConcept.__init__(
             self,
             identifier=identifier,
             name=name,