siibra 1.0.1a1__py3-none-any.whl → 1.0.1a2__py3-none-any.whl

siibra/VERSION

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

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/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()

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:
     """

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] = {}
 

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/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
 

siibra/core/atlas.py

@@ -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

@@ -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/core/parcellation.py

@@ -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 MapNotFound
 
 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

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/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,

siibra/core/structure.py

@@ -21,11 +21,11 @@ a brain region is a structure which is at the same time an AtlasConcept. A
 bounding box in MNI space is a structure, but not an AtlasConcept.
 """
 
-from . import assignment, region as _region
-
 from abc import ABC, abstractmethod
 from typing import Tuple, Dict
 
+from . import assignment, region as _region
+
 
 class BrainStructure(ABC):
     """Abstract base class for types who can act as a location filter."""

siibra/features/anchor.py

@@ -14,8 +14,9 @@
 # limitations under the License.
 """Handles the relation between study targets and BrainStructures."""
 
-from ..commons import Species, logger
+from typing import Union, List, Dict, Iterable
 
+from ..commons import Species, logger
 from ..core.structure import BrainStructure
 from ..core.assignment import AnatomicalAssignment, Qualification
 from ..locations.location import Location
@@ -23,11 +24,8 @@ from ..core.parcellation import Parcellation, find_regions
 from ..core.region import Region
 from ..core.space import Space
 from ..exceptions import SpaceWarpingFailedError
-
 from ..vocabularies import REGION_ALIASES
 
-from typing import Union, List, Dict, Iterable
-
 
 class AnatomicalAnchor:
     """

siibra/features/connectivity/regional_connectivity.py

@@ -14,11 +14,18 @@
 # limitations under the License.
 
 from zipfile import ZipFile
-from ..feature import Feature, Compoundable
-from ..tabular.tabular import Tabular
+from typing import Callable, Union, List, Tuple, Iterator
+try:
+    from typing import Literal
+except ImportError:  # support python 3.7
+    from typing_extensions import Literal
 
-from .. import anchor as _anchor
+import numpy as np
+import pandas as pd
 
+from .. import anchor as _anchor
+from ..feature import Feature, Compoundable
+from ..tabular.tabular import Tabular
 from ...commons import logger, QUIET, siibra_tqdm
 from ...core import region as _region
 from ...locations import pointcloud
@@ -26,16 +33,6 @@ from ...retrieval.repositories import RepositoryConnector
 from ...retrieval.requests import HttpRequest
 
 
-import pandas as pd
-import numpy as np
-from typing import Callable, Union, List, Tuple, Iterator
-
-try:
-    from typing import Literal
-except ImportError:  # support python 3.7
-    from typing_extensions import Literal
-
-
 class RegionalConnectivity(Feature, Compoundable):
     """
     Parcellation-averaged connectivity, providing one or more matrices of a

siibra/features/dataset/ebrains.py

@@ -15,9 +15,9 @@
 """Non-preconfigured data features hosted at EBRAINS."""
 
 from zipfile import ZipFile
+
 from .. import anchor as _anchor
 from .. import feature
-
 from ...retrieval import datasets
 
 

siibra/features/feature.py

@@ -14,12 +14,6 @@
 # limitations under the License.
 """Handles multimodal data features and related queries."""
 
-from . import anchor as _anchor
-
-from ..commons import logger, InstanceTable, siibra_tqdm, __version__
-from ..core import concept, space, region, parcellation, structure
-from ..volumes import volume
-
 from typing import Union, TYPE_CHECKING, List, Dict, Type, Tuple, BinaryIO, Any, Iterator
 from hashlib import md5
 from collections import defaultdict
@@ -28,6 +22,11 @@ from abc import ABC, abstractmethod
 from re import sub
 from textwrap import wrap
 
+from . import anchor as _anchor
+from ..commons import logger, InstanceTable, siibra_tqdm, __version__
+from ..core import concept, space, region, parcellation, structure
+from ..volumes import volume
+
 if TYPE_CHECKING:
     from ..retrieval.datasets import EbrainsDataset
     TypeDataset = EbrainsDataset
@@ -130,23 +129,22 @@ class Feature:
         # allows subclasses to implement lazy loading of an anchor
         return self._anchor_cached
 
-    def __init_subclass__(cls, configuration_folder=None, category=None, do_not_index=False, **kwargs):
+    def __init_subclass__(cls, configuration_folder=None, category=None, **kwargs):
 
         # Feature.SUBCLASSES serves as an index where feature class inheritance is cached. When users
         # queries a branch on the hierarchy, all children will also be queried. There are usecases where
         # such behavior is not desired (e.g. ProxyFeature, which wraps livequery features id to capture the
         # query context).
-        # do_not_index flag allow the default index behavior to be toggled off.
-
-        if do_not_index is False:
+        if "ProxyFeature" in cls.__name__:
+            return
 
-            # extend the subclass lists
-            # Iterate over all mro, not just immediate base classes
-            for BaseCls in cls.__mro__:
-                # some base classes may not be sub class of feature, ignore these
-                if not issubclass(BaseCls, Feature):
-                    continue
-                cls._SUBCLASSES[BaseCls].append(cls)
+        # extend the subclass lists
+        # Iterate over all mro, not just immediate base classes
+        for BaseCls in cls.__mro__:
+            # some base classes may not be sub class of feature, ignore these
+            if not issubclass(BaseCls, Feature):
+                continue
+            cls._SUBCLASSES[BaseCls].append(cls)
 
         cls._live_queries = []
         cls._preconfigured_instances = None
@@ -156,6 +154,9 @@ class Feature:
             cls._CATEGORIZED[category].add(cls.__name__, cls)
         return super().__init_subclass__(**kwargs)
 
+    def __repr__(self) -> str:
+        return f"<{self.__class__.__name__}(id='{self.id}', name='{self.name}')>"
+
     @classmethod
     def _get_subclasses(cls):
         return {Cls.__name__: Cls for Cls in cls._SUBCLASSES}
@@ -625,7 +626,9 @@ class Feature:
 
         See docstring of serialize_query_context for further context.
         """
-        class ProxyFeature(feature.__class__, do_not_index=True):
+
+        # if you change the name of this class, change the string in Feature.__init_subclass__
+        class ProxyFeature(feature.__class__):
 
             # override __class__ property
             # some instances of features accesses inst.__class__

siibra/features/image/__init__.py

@@ -22,6 +22,8 @@ from .volume_of_interest import (
     XPCTVolumeOfInterest,
     LSFMVolumeOfInterest,
     DTIVolumeOfInterest
-    # SegmentedVolumeOfInterest
 )
-from .sections import CellbodyStainedSection
+from .sections import (
+    CellbodyStainedSection,
+    BigBrain1MicronPatch
+)

siibra/features/image/image.py

@@ -14,15 +14,13 @@
 # limitations under the License.
 """Base type of features in volume format and related anatomical anchor."""
 
+from typing import List, TYPE_CHECKING
 from zipfile import ZipFile
-from .. import feature
 
+from .. import feature
 from .. import anchor as _anchor
-
 from ...volumes import volume as _volume
 
-from typing import List, TYPE_CHECKING
-
 if TYPE_CHECKING:
     from ...locations.boundingbox import BoundingBox
     from ...volumes.providers import provider