siibra 1.0.1a1__py3-none-any.whl → 1.0.1a5__py3-none-any.whl

siibra/VERSION

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

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()
@@ -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/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/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/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
 
@@ -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/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/explorer/url.py

@@ -136,7 +136,7 @@ def encode_url(
 
     try:
         result_props = region.spatial_props(space, maptype="labelled")
-        if len(result_props.components) == 0:
+        if len(result_props) == 0:
             return return_url + nav_string.format(encoded_nav=encoded_position or "0.0.0", **zoom_kwargs)
     except Exception as e:
         print(f"Cannot get_spatial_props {str(e)}")
@@ -144,7 +144,7 @@ def encode_url(
             raise e
         return return_url + nav_string.format(encoded_nav=encoded_position or "0.0.0", **zoom_kwargs)
 
-    centroid = result_props.components[0].centroid
+    centroid = result_props[0].centroid
 
     encoded_centroid = separator.join(
         [encode_number(math.floor(val * 1e6)) for val in centroid]

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:
     """
@@ -178,9 +176,7 @@ class AnatomicalAnchor:
                 assignments.append(region.assign(concept))
             self._assignments[concept] = sorted(a for a in assignments if a is not None)
 
-        self._last_matched_concept = concept \
-            if len(self._assignments[concept]) > 0 \
-            else None
+        self._last_matched_concept = concept if len(self._assignments[concept]) > 0 else None
         return self._assignments[concept]
 
     def matches(self, concept: Union[BrainStructure, Space]) -> bool: