Merge pull request #646 from FZJ-INM1-BDA/maint_imports_and_packages

Maint imports and packages

Author: AhmetNSimsek

siibra/core/region.py

@@ -14,9 +14,7 @@
 # limitations under the License.
 """Representation of a brain region."""
 
-from . import concept, structure, space as _space, parcellation as _parcellation
-from .assignment import Qualification, AnatomicalAssignment
-
+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
@@ -128,7 +126,7 @@ def get_related_regions(self) -> Iterable["RegionRelationAssessments"]:
 
         Yields
         ------
-        Qualification
+        assignment.Qualification
 
         Example
         -------
@@ -595,7 +593,7 @@ def __contains__(self, other: Union[location.Location, 'Region']) -> bool:
             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 +607,8 @@ def assign(self, other: structure.BrainStructure) -> AnatomicalAssignment:
 
         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 +657,17 @@ def assign(self, other: structure.BrainStructure) -> AnatomicalAssignment:
         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 +924,7 @@ def get_related_regions(region: Region) -> Iterable["RegionRelationAssessments"]
 
     Yields
     ------
-    Qualification
+    assignment.Qualification
 
     Example
     -------
@@ -968,7 +966,7 @@ def inner(*args, **kwargs):
     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 +1108,7 @@ def parse_relationship_assessment(cls, src: "Region", assessment):
                 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 +1122,7 @@ def parse_relationship_assessment(cls, src: "Region", assessment):
                         yield cls(
                             query_structure=src,
                             assigned_structure=reg,
-                            qualification=Qualification.parse_relation_assessment(overlap)
+                            qualification=assignment.Qualification.parse_relation_assessment(overlap)
                         )
 
     @classmethod
@@ -1178,7 +1176,7 @@ def translate_pes(cls, src: "Region", _id: Union[str, List[str]]):
                     yield cls(
                         query_structure=src,
                         assigned_structure=region,
-                        qualification=Qualification.OTHER_VERSION
+                        qualification=assignment.Qualification.OTHER_VERSION
                     )
 
             # homologuous

siibra/core/space.py

@@ -15,8 +15,7 @@
 """A particular brain reference space."""
 
 
-from .concept import AtlasConcept
-
+from . import concept
 from ..commons import logger, Species
 
 from typing import List, TYPE_CHECKING, Union
@@ -25,7 +24,7 @@
     from ..volumes import volume
 
 
-class Space(AtlasConcept, configuration_folder="spaces"):
+class Space(concept.AtlasConcept, configuration_folder="spaces"):
 
     def __init__(
         self,
@@ -66,7 +65,7 @@ def __init__(
                 Key: EBRAINS KG schema, value: EBRAINS KG @id
         """
 
-        AtlasConcept.__init__(
+        concept.AtlasConcept.__init__(
             self,
             identifier=identifier,
             name=name,

siibra/features/tabular/__init__.py

@@ -15,7 +15,7 @@
 """Multimodal data features in tabular formats."""
 
 from .bigbrain_intensity_profile import BigBrainIntensityProfile
-from .cell_density_profile import CellDensityProfile
+from .cell_density_profile import CellDensityProfile, cell_reader, layer_reader
 from .gene_expression import GeneExpressions
 from .layerwise_bigbrain_intensities import LayerwiseBigBrainIntensities
 from .layerwise_cell_density import LayerwiseCellDensity

siibra/features/tabular/layerwise_cell_density.py

@@ -14,10 +14,8 @@
 # limitations under the License.
 
 from . import cortical_profile
+from . import tabular, cell_reader, layer_reader
 from .. import anchor as _anchor
-from . import tabular
-from ..tabular.cell_density_profile import cell_reader, layer_reader
-
 from ... import commons
 from ...retrieval import requests
 

siibra/livequeries/allen.py

@@ -14,7 +14,7 @@
 # limitations under the License.
 """Query Allen Human Brain Atlas microarray data in specified volume."""
 
-from .query import LiveQuery
+from . import query as _query
 
 from ..core import space as _space, structure
 from ..features import anchor as _anchor
@@ -51,7 +51,7 @@ class InvalidAllenAPIResponseException(Exception):
     pass
 
 
-class AllenBrainAtlasQuery(LiveQuery, args=['gene'], FeatureType=GeneExpressions):
+class AllenBrainAtlasQuery(_query.LiveQuery, args=['gene'], FeatureType=GeneExpressions):
     """
     Interface to Allen Human Brain Atlas microarray data.
 
@@ -117,7 +117,7 @@ def __init__(self, **kwargs):
         will be tested against the region mask in ICBM space
         to produce a table of outputs.
         """
-        LiveQuery.__init__(self, **kwargs)
+        _query.LiveQuery.__init__(self, **kwargs)
         gene = kwargs.get('gene')
 
         def parse_gene(spec):

siibra/locations/boundingbox.py

@@ -14,7 +14,7 @@
 # limitations under the License.
 """A box defined by two farthest corner coordinates on a specific space."""
 
-from . import point, pointcloud, location
+from . import location, point, pointcloud
 
 from ..commons import logger
 from ..exceptions import SpaceWarpingFailedError

siibra/locations/location.py

@@ -17,13 +17,12 @@
 from __future__ import annotations
 
 from ..core.structure import BrainStructure
+from ..core import space as _space
 
 import numpy as np
 from abc import abstractmethod
 
-from typing import TYPE_CHECKING, Union, Dict
-if TYPE_CHECKING:
-    from siibra.core.space import Space
+from typing import Union, Dict
 
 
 class Location(BrainStructure):
@@ -46,29 +45,28 @@ class Location(BrainStructure):
     _MASK_MEMO = {}  # cache region masks for Location._assign_region()
     _ASSIGNMENT_CACHE = {}  # caches assignment results, see Region.assign()
 
-    def __init__(self, spacespec: Union[str, Dict[str, str], "Space"]):
+    def __init__(self, spacespec: Union[str, Dict[str, str], "_space.Space"]):
         self._space_spec = spacespec
         self._space_cached = None
 
     @property
-    def space(self):
+    def space(self) -> "_space.Space":
         if self._space_cached is None:
-            from ..core.space import Space
             if isinstance(self._space_spec, dict):
                 spec = self._space_spec.get("@id") or self._space_spec.get("name")
-                self._space_cached = Space.get_instance(spec)
+                self._space_cached = _space.Space.get_instance(spec)
             else:
-                self._space_cached = Space.get_instance(self._space_spec)
+                self._space_cached = _space.Space.get_instance(self._space_spec)
         return self._space_cached
 
     @abstractmethod
-    def warp(self, space):
+    def warp(self, space: Union[str, "_space.Space"]):
         """Generates a new location by warping the
         current one into another reference space."""
         pass
 
     @abstractmethod
-    def transform(self, affine: np.ndarray, space=None):
+    def transform(self, affine: np.ndarray, space: Union[str, "_space.Space", None] = None):
         """Returns a new location obtained by transforming the
         reference coordinates of this one with the given affine matrix.
 

siibra/retrieval/datasets.py

@@ -18,7 +18,7 @@
 
 import re
 from typing import Union, List
-from abc import ABC, abstractproperty
+from abc import ABC, abstractmethod
 from hashlib import md5
 
 try:
@@ -48,31 +48,38 @@ class EbrainsDatasetUrl(TypedDict):
 
 
 class EbrainsBaseDataset(ABC):
-    @abstractproperty
+    @property
+    @abstractmethod
     def id(self) -> str:
         raise NotImplementedError
 
-    @abstractproperty
+    @property
+    @abstractmethod
     def name(self) -> str:
         raise NotImplementedError
 
-    @abstractproperty
+    @property
+    @abstractmethod
     def urls(self) -> List[EbrainsDatasetUrl]:
         raise NotImplementedError
 
-    @abstractproperty
+    @property
+    @abstractmethod
     def description(self) -> str:
         raise NotImplementedError
 
-    @abstractproperty
+    @property
+    @abstractmethod
     def contributors(self) -> List[EbrainsDatasetPerson]:
         raise NotImplementedError
 
-    @abstractproperty
+    @property
+    @abstractmethod
     def ebrains_page(self) -> str:
         raise NotImplementedError
 
-    @abstractproperty
+    @property
+    @abstractmethod
     def custodians(self) -> List[EbrainsDatasetPerson]:
         raise NotImplementedError
 
@@ -342,7 +349,7 @@ def version_ids(self) -> List['str']:
         return [version.get("id") for version in self._detail.get("versions", [])]
 
 
-class GenericDataset():
+class GenericDataset:
 
     def __init__(
         self,

siibra/retrieval/requests.py

@@ -15,7 +15,7 @@
 """Request files with decoders, lazy loading, and caching."""
 
 from .cache import CACHE, cache_user_fn
-from .exceptions import EbrainsAuthenticationError
+from . import exceptions as _exceptions
 from ..commons import (
     logger,
     HBP_AUTH_TOKEN,
@@ -388,7 +388,7 @@ def device_flow(cls, **kwargs):
                 ),  # if explicitly enabled by env var, do not raise
             ]
         ):
-            raise EbrainsAuthenticationError(
+            raise _exceptions.EbrainsAuthenticationError(
                 "sys.stdout is not tty, SIIBRA_ENABLE_DEVICE_FLOW is not set,"
                 "and not running in a notebook. Are you running in batch mode?"
             )
@@ -444,7 +444,7 @@ def get_scope() -> str:
                     f"exceeded max attempts: {cls._IAM_DEVICE_MAXTRIES}, aborting..."
                 )
                 logger.error(message)
-                raise EbrainsAuthenticationError(message)
+                raise _exceptions.EbrainsAuthenticationError(message)
             attempt_number += 1
             resp = requests.post(
                 url=cls._IAM_TOKEN_ENDPOINT,
@@ -470,7 +470,7 @@ def get_scope() -> str:
                 logger.debug(f"400 error: {resp.content}")
                 continue
 
-            raise EbrainsAuthenticationError(resp.content)
+            raise _exceptions.EbrainsAuthenticationError(resp.content)
 
     @classmethod
     def set_token(cls, token):