siibra 1.0a14__py3-none-any.whl → 1.0a19__py3-none-any.whl

siibra/core/assignment.py

@@ -1,4 +1,4 @@
-# Copyright 2018-2023
+# Copyright 2018-2024
 # Institute of Neuroscience and Medicine (INM-1), Forschungszentrum Jülich GmbH
 
 # Licensed under the Apache License, Version 2.0 (the "License");

siibra/core/atlas.py

@@ -1,4 +1,4 @@
-# Copyright 2018-2021
+# Copyright 2018-2024
 # Institute of Neuroscience and Medicine (INM-1), Forschungszentrum Jülich GmbH
 
 # Licensed under the Apache License, Version 2.0 (the "License");
@@ -30,14 +30,15 @@ class Atlas(concept.AtlasConcept, configuration_folder="atlases"):
     spaces, as well as common functionalities of those.
     """
 
-    def __init__(self, identifier: str, name: str, species: Species):
+    def __init__(self, identifier: str, name: str, species: Species, **kwargs):
         """Construct an empty atlas object with a name and identifier."""
 
         concept.AtlasConcept.__init__(
             self,
             identifier=identifier,
             name=name,
-            species=species
+            species=species,
+            **kwargs
         )
         self._parcellation_ids: List[str] = []
         self._space_ids: List[str] = []

siibra/core/concept.py

@@ -1,4 +1,4 @@
-# Copyright 2018-2021
+# Copyright 2018-2024
 # Institute of Neuroscience and Medicine (INM-1), Forschungszentrum Jülich GmbH
 
 # Licensed under the Apache License, Version 2.0 (the "License");
@@ -67,7 +67,8 @@ class AtlasConcept:
         modality: str = "",
         publications: List[TypePublication] = [],
         datasets: List['TypeDataset'] = [],
-        spec=None
+        spec=None,
+        prerelease: bool = False,
     ):
         """
         Construct a new atlas concept base object.
@@ -94,7 +95,7 @@ class AtlasConcept:
             The preconfigured specification.
         """
         self._id = identifier
-        self.name = name
+        self.name = name if not prerelease else f"[PRERELEASE] {name}"
         self._species_cached = None if species is None \
             else Species.decode(species)  # overwritable property implementation below
         self.shortname = shortname
@@ -104,6 +105,7 @@ class AtlasConcept:
         self.datasets = datasets
         self._spec = spec
         self._CACHED_MATCHES = {}  # we cache match() function results
+        self._prerelease = prerelease
 
     @property
     def description(self):
@@ -116,12 +118,19 @@ class AtlasConcept:
 
     @property
     def LICENSE(self) -> str:
-        licenses = {ds.LICENSE for ds in self.datasets if ds.LICENSE}
-        if not licenses:
-            return "No license information is found."
-        if len(licenses) == 1:
-            return next(iter(licenses))
-        logger.info("Found multiple licenses corresponding to datasets.")
+        licenses = []
+        for ds in self.datasets:
+            if ds.LICENSE is None or ds.LICENSE == "No license information is found.":
+                continue
+            if isinstance(ds.LICENSE, str):
+                licenses.append(ds.LICENSE)
+            if isinstance(ds.LICENSE, list):
+                licenses.extend(ds.LICENSE)
+        if len(licenses) == 0:
+            logger.warning("No license information is found.")
+            return ""
+        if len(licenses) > 1:
+            logger.info("Found multiple licenses corresponding to datasets.")
         return '\n'.join(licenses)
 
     @property

siibra/core/parcellation.py

@@ -1,4 +1,4 @@
-# Copyright 2018-2023
+# Copyright 2018-2024
 # Institute of Neuroscience and Medicine (INM-1), Forschungszentrum Jülich GmbH
 
 # Licensed under the Apache License, Version 2.0 (the "License");
@@ -82,6 +82,7 @@ class Parcellation(region.Region, configuration_folder="parcellations"):
         modality: str = None,
         publications: list = [],
         datasets: list = [],
+        prerelease: bool = False,
     ):
         """
         Constructs a new parcellation object.
@@ -118,7 +119,8 @@ class Parcellation(region.Region, configuration_folder="parcellations"):
             description=description,
             publications=publications,
             datasets=datasets,
-            modality=modality
+            modality=modality,
+            prerelease=prerelease,
         )
         self._species_cached = Species.decode(species)
         self._id = identifier
@@ -309,7 +311,11 @@ class Parcellation(region.Region, configuration_folder="parcellations"):
 
         # if there exist an exact match of region spec to region name, return
         if isinstance(regionspec, str):
-            exact_match = [region for region in self if hasattr(region, "name") and region.name == regionspec]
+            exact_match = [
+                region
+                for region in self
+                if region.name == regionspec or region.key == regionspec
+            ]
             if len(exact_match) == 1:
                 return exact_match[0]
             if len(exact_match) > 1:

siibra/core/region.py

@@ -1,4 +1,4 @@
-# Copyright 2018-2023
+# Copyright 2018-2024
 # Institute of Neuroscience and Medicine (INM-1), Forschungszentrum Jülich GmbH
 
 # Licensed under the Apache License, Version 2.0 (the "License");
@@ -18,12 +18,11 @@ from . import concept, structure, space as _space, parcellation as _parcellation
 from .assignment import Qualification, AnatomicalAssignment
 
 from ..retrieval.cache import cache_user_fn
-from ..locations import location, point, pointset
+from ..locations import location, pointset, boundingbox as _boundingbox
 from ..volumes import parcellationmap, volume
 from ..commons import (
     logger,
     MapType,
-    affine_scaling,
     create_key,
     clear_name,
     InstanceTable,
@@ -37,7 +36,6 @@ import re
 import anytree
 from typing import List, Union, Iterable, Dict, Callable, Tuple
 from difflib import SequenceMatcher
-from dataclasses import dataclass, field
 from ebrains_drive import BucketApiClient
 import json
 from functools import wraps, reduce
@@ -49,19 +47,6 @@ REGEX_TYPE = type(re.compile("test"))
 THRESHOLD_STATISTICAL_MAPS = None
 
 
-@dataclass
-class SpatialPropCmpt:
-    centroid: point.Point
-    volume: int
-
-
-@dataclass
-class SpatialProp:
-    cog: SpatialPropCmpt = None
-    components: List[SpatialPropCmpt] = field(default_factory=list)
-    space: _space.Space = None
-
-
 class Region(anytree.NodeMixin, concept.AtlasConcept, structure.BrainStructure):
     """
     Representation of a region with name and more optional attributes
@@ -85,6 +70,7 @@ class Region(anytree.NodeMixin, concept.AtlasConcept, structure.BrainStructure):
         datasets: list = [],
         rgb: str = None,
         spec=None,
+        prerelease: bool = False,
     ):
         """
         Constructs a new Region object.
@@ -122,7 +108,8 @@ class Region(anytree.NodeMixin, concept.AtlasConcept, structure.BrainStructure):
             modality=modality,
             publications=publications,
             datasets=datasets,
-            spec=spec
+            spec=spec,
+            prerelease=prerelease,
         )
 
         # anytree node will take care to use this appropriately
@@ -646,17 +633,29 @@ class Region(anytree.NodeMixin, concept.AtlasConcept, structure.BrainStructure):
                 self._ASSIGNMENT_CACHE[self, other] = regionmap.assign(other)
                 return self._ASSIGNMENT_CACHE[self, other]
 
+            if isinstance(other, _boundingbox.BoundingBox):  # volume.intersection(bbox) gets boundingbox anyway
+                try:
+                    regionbbox_otherspace = self.get_boundingbox(other.space, restrict_space=False)
+                    if regionbbox_otherspace is not None:
+                        self._ASSIGNMENT_CACHE[self, other] = regionbbox_otherspace.assign(other)
+                        return self._ASSIGNMENT_CACHE[self, other]
+                except Exception as e:
+                    logger.debug(e)
+
             assignment_result = None
-            for space in self.supported_spaces:
+            for targetspace in self.supported_spaces:
                 try:
-                    other_warped = other.warp(space)
-                    regionmap = self.get_regional_map(space)
+                    other_warped = other.warp(targetspace)
+                    regionmap = self.get_regional_map(targetspace)
                     assignment_result = regionmap.assign(other_warped)
                 except SpaceWarpingFailedError:
                     try:
-                        regionbbox_warped = self.get_boundingbox(
-                            space, restrict_space=True
-                        ).warp(other.space)
+                        regionbbox_targetspace = self.get_boundingbox(
+                            targetspace, restrict_space=True
+                        )
+                        if regionbbox_targetspace is None:
+                            continue
+                        regionbbox_warped = regionbbox_targetspace.warp(other.space)
                     except SpaceWarpingFailedError:
                         continue
                     assignment_result = regionbbox_warped.assign(other)
@@ -698,7 +697,7 @@ class Region(anytree.NodeMixin, concept.AtlasConcept, structure.BrainStructure):
         space: _space.Space,
         maptype: MapType = MapType.LABELLED,
         threshold_statistical=None,
-        restrict_space=False,
+        restrict_space=True,
         **fetch_kwargs
     ):
         """
@@ -745,7 +744,7 @@ class Region(anytree.NodeMixin, concept.AtlasConcept, structure.BrainStructure):
                             bbox_warped = bbox.warp(spaceobj)
                         except SpaceWarpingFailedError:
                             continue
-                        logger.warning(
+                        logger.debug(
                             f"No bounding box for {self.name} defined in {spaceobj.name}, "
                             f"warped the bounding box from {other_space.name} instead."
                         )
@@ -776,7 +775,7 @@ class Region(anytree.NodeMixin, concept.AtlasConcept, structure.BrainStructure):
         """
         props = self.spatial_props(space)
         return pointset.PointSet(
-            [c.centroid for c in props.components],
+            [c.centroid for c in props],
             space=space
         )
 
@@ -785,12 +784,10 @@ class Region(anytree.NodeMixin, concept.AtlasConcept, structure.BrainStructure):
         space: _space.Space,
         maptype: MapType = MapType.LABELLED,
         threshold_statistical=None,
-    ) -> SpatialProp:
+    ):
         """
         Compute spatial properties for connected components of this region in the given space.
 
-        TODO: this should go to the Volume class and just be called from here.
-
         Parameters
         ----------
         space: Space
@@ -808,49 +805,22 @@ class Region(anytree.NodeMixin, concept.AtlasConcept, structure.BrainStructure):
         Dict
             Dictionary of region's spatial properties
         """
-        from skimage import measure
-
         if not isinstance(space, _space.Space):
             space = _space.Space.get_instance(space)
 
-        result = SpatialProp(space=space)
-
-        if not self.mapped_in_space(space):
-            logger.warning(
+        # build binary mask of the image
+        try:
+            region_vol = self.get_regional_map(
+                space, maptype=maptype, threshold=threshold_statistical
+            )
+        except NoMapAvailableError:
+            raise ValueError(
                 f"Spatial properties of {self.name} cannot be computed in {space.name}. "
                 "This region is only mapped in these spaces: "
                 f"{', '.join(s.name for s in self.supported_spaces)}"
             )
-            return result
 
-        # build binary mask of the image
-        pimg = self.get_regional_map(
-            space, maptype=maptype, threshold=threshold_statistical
-        ).fetch()
-
-        # determine scaling factor from voxels to cube mm
-        scale = affine_scaling(pimg.affine)
-
-        # compute properties of labelled volume
-        A = np.asarray(pimg.get_fdata(), dtype=np.int32).squeeze()
-        C = measure.label(A)
-
-        # compute spatial properties of each connected component
-        for label in range(1, C.max() + 1):
-            nonzero = np.c_[np.nonzero(C == label)]
-            result.components.append(
-                SpatialPropCmpt(
-                    centroid=point.Point(
-                        np.dot(pimg.affine, np.r_[nonzero.mean(0), 1])[:3], space=space
-                    ),
-                    volume=nonzero.shape[0] * scale,
-                )
-            )
-
-        # sort by volume
-        result.components.sort(key=lambda cmp: cmp.volume, reverse=True)
-
-        return result
+        return region_vol.compute_spatial_props()
 
     def __iter__(self):
         """

siibra/core/space.py

@@ -1,4 +1,4 @@
-# Copyright 2018-2021
+# Copyright 2018-2024
 # Institute of Neuroscience and Medicine (INM-1), Forschungszentrum Jülich GmbH
 
 # Licensed under the Apache License, Version 2.0 (the "License");
@@ -38,6 +38,7 @@ class Space(AtlasConcept, configuration_folder="spaces"):
         modality: str = "",
         publications: list = [],
         datasets: list = [],
+        prerelease: bool = False,
     ):
         """
         Constructs a new parcellation object.
@@ -75,6 +76,7 @@ class Space(AtlasConcept, configuration_folder="spaces"):
             modality=modality,
             publications=publications,
             datasets=datasets,
+            prerelease=prerelease,
         )
         self.volumes = volumes
         for v in self.volumes:

siibra/core/structure.py

@@ -1,5 +1,4 @@
-
-# Copyright 2018-2023
+# Copyright 2018-2024
 # Institute of Neuroscience and Medicine (INM-1), Forschungszentrum Jülich GmbH
 
 # Licensed under the Apache License, Version 2.0 (the "License");

siibra/exceptions.py

@@ -1,4 +1,4 @@
-# Copyright 2018-2021
+# Copyright 2018-2024
 # Institute of Neuroscience and Medicine (INM-1), Forschungszentrum Jülich GmbH
 
 # Licensed under the Apache License, Version 2.0 (the "License");
@@ -45,3 +45,11 @@ class NoVolumeFound(RuntimeError):
 
 class WarmupRegException(Exception):
     pass
+
+
+class ZeroVolumeBoundingBox(Exception):
+    pass
+
+
+class NoneCoordinateSuppliedError(ValueError):
+    pass

siibra/explorer/__init__.py

@@ -1,4 +1,4 @@
-# Copyright 2018-2023
+# Copyright 2018-2024
 # Institute of Neuroscience and Medicine (INM-1), Forschungszentrum Jülich GmbH
 
 # Licensed under the Apache License, Version 2.0 (the "License");

siibra/explorer/url.py

@@ -1,3 +1,18 @@
+# Copyright 2018-2024
+# Institute of Neuroscience and Medicine (INM-1), Forschungszentrum Jülich GmbH
+
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+
+#     http://www.apache.org/licenses/LICENSE-2.0
+
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# 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.
+
 from typing import Optional, TYPE_CHECKING
 from urllib.parse import quote_plus
 from numpy import int32

siibra/explorer/util.py

@@ -1,4 +1,4 @@
-# Copyright 2018-2023
+# Copyright 2018-2024
 # Institute of Neuroscience and Medicine (INM-1), Forschungszentrum Jülich GmbH
 
 # Licensed under the Apache License, Version 2.0 (the "License");

siibra/features/__init__.py

@@ -1,4 +1,4 @@
-# Copyright 2018-2021
+# Copyright 2018-2024
 # Institute of Neuroscience and Medicine (INM-1), Forschungszentrum Jülich GmbH
 
 # Licensed under the Apache License, Version 2.0 (the "License");

siibra/features/anchor.py

@@ -1,4 +1,4 @@
-# Copyright 2018-2023
+# Copyright 2018-2024
 # Institute of Neuroscience and Medicine (INM-1), Forschungszentrum Jülich GmbH
 
 # Licensed under the Apache License, Version 2.0 (the "License");

siibra/features/connectivity/__init__.py

@@ -1,4 +1,4 @@
-# Copyright 2018-2021
+# Copyright 2018-2024
 # Institute of Neuroscience and Medicine (INM-1), Forschungszentrum Jülich GmbH
 
 # Licensed under the Apache License, Version 2.0 (the "License");

siibra/features/connectivity/functional_connectivity.py

@@ -1,4 +1,4 @@
-# Copyright 2018-2021
+# Copyright 2018-2024
 # Institute of Neuroscience and Medicine (INM-1), Forschungszentrum Jülich GmbH
 
 # Licensed under the Apache License, Version 2.0 (the "License");

siibra/features/connectivity/regional_connectivity.py

@@ -1,4 +1,4 @@
-# Copyright 2018-2021
+# Copyright 2018-2024
 # Institute of Neuroscience and Medicine (INM-1), Forschungszentrum Jülich GmbH
 
 # Licensed under the Apache License, Version 2.0 (the "License");
@@ -58,7 +58,8 @@ class RegionalConnectivity(Feature, Compoundable):
         datasets: list = [],
         subject: str = "average",
         feature: str = None,
-        id: str = None
+        id: str = None,
+        prerelease: bool = False,
     ):
         """
         Construct a parcellation-averaged connectivity matrix.
@@ -92,7 +93,8 @@ class RegionalConnectivity(Feature, Compoundable):
             description=description,
             anchor=anchor,
             datasets=datasets,
-            id=id
+            id=id,
+            prerelease=prerelease
         )
         self.cohort = cohort.upper()
         if isinstance(connector, str) and connector:

siibra/features/connectivity/streamline_counts.py

@@ -1,4 +1,4 @@
-# Copyright 2018-2021
+# Copyright 2018-2024
 # Institute of Neuroscience and Medicine (INM-1), Forschungszentrum Jülich GmbH
 
 # Licensed under the Apache License, Version 2.0 (the "License");

siibra/features/connectivity/streamline_lengths.py

@@ -1,4 +1,4 @@
-# Copyright 2018-2021
+# Copyright 2018-2024
 # Institute of Neuroscience and Medicine (INM-1), Forschungszentrum Jülich GmbH
 
 # Licensed under the Apache License, Version 2.0 (the "License");

siibra/features/connectivity/tracing_connectivity.py

@@ -1,4 +1,4 @@
-# Copyright 2018-2021
+# Copyright 2018-2024
 # Institute of Neuroscience and Medicine (INM-1), Forschungszentrum Jülich GmbH
 
 # Licensed under the Apache License, Version 2.0 (the "License");

siibra/features/dataset/__init__.py

@@ -1,4 +1,4 @@
-# Copyright 2018-2021
+# Copyright 2018-2024
 # Institute of Neuroscience and Medicine (INM-1), Forschungszentrum Jülich GmbH
 
 # Licensed under the Apache License, Version 2.0 (the "License");

siibra/features/dataset/ebrains.py

@@ -1,4 +1,4 @@
-# Copyright 2018-2021
+# Copyright 2018-2024
 # Institute of Neuroscience and Medicine (INM-1), Forschungszentrum Jülich GmbH
 
 # Licensed under the Apache License, Version 2.0 (the "License");

siibra/features/feature.py

@@ -1,4 +1,4 @@
-# Copyright 2018-2023
+# Copyright 2018-2024
 # Institute of Neuroscience and Medicine (INM-1), Forschungszentrum Jülich GmbH
 
 # Licensed under the Apache License, Version 2.0 (the "License");
@@ -99,7 +99,8 @@ class Feature:
         description: str,
         anchor: _anchor.AnatomicalAnchor,
         datasets: List['TypeDataset'] = [],
-        id: str = None
+        id: str = None,
+        prerelease: bool = False,
     ):
         """
         Parameters
@@ -117,6 +118,7 @@ class Feature:
         self._anchor_cached = anchor
         self.datasets = datasets
         self._id = id
+        self._prerelease = prerelease
 
     @property
     def modality(self):
@@ -170,12 +172,19 @@ class Feature:
 
     @property
     def LICENSE(self) -> str:
-        licenses = {ds.LICENSE for ds in self.datasets if ds.LICENSE}
-        if not licenses:
-            return "No license information is found."
-        if len(licenses) == 1:
-            return next(iter(licenses))
-        logger.info("Found multiple licenses corresponding to datasets.")
+        licenses = []
+        for ds in self.datasets:
+            if ds.LICENSE is None or ds.LICENSE == "No license information is found.":
+                continue
+            if isinstance(ds.LICENSE, str):
+                licenses.append(ds.LICENSE)
+            if isinstance(ds.LICENSE, list):
+                licenses.extend(ds.LICENSE)
+        if len(licenses) == 0:
+            logger.warning("No license information is found.")
+            return ""
+        if len(licenses) > 1:
+            logger.info("Found multiple licenses corresponding to datasets.")
         return '\n'.join(licenses)
 
     @property
@@ -199,7 +208,8 @@ class Feature:
     def name(self):
         """Returns a short human-readable name of this feature."""
         readable_class_name = sub("([a-z])([A-Z])", r"\g<1> \g<2>", self.__class__.__name__)
-        return sub("([b,B]ig [b,B]rain)", "BigBrain", readable_class_name)
+        name_ = sub("([b,B]ig [b,B]rain)", "BigBrain", readable_class_name)
+        return name_ if not self._prerelease else f"[PRERELEASE] {name_}"
 
     @classmethod
     def _get_instances(cls, **kwargs) -> List['Feature']:
@@ -268,13 +278,18 @@ class Feature:
         if self._id:
             return self._id
 
+        if self._prerelease:
+            name_ = self.name.replace("[PRERELEASE] ", "")
+        else:
+            name_ = self.name
+
         prefix = ''
         for ds in self.datasets:
             if hasattr(ds, "id"):
                 prefix = ds.id + '--'
                 break
         return prefix + md5(
-            f"{self.name} - {self.anchor}".encode("utf-8")
+            f"{name_} - {self.anchor}".encode("utf-8")
         ).hexdigest()
 
     def _to_zip(self, fh: ZipFile):
@@ -468,7 +483,10 @@ class Feature:
                 f"objects linked to {str(concept)}{argstr}"
             )
             q = QueryType(**kwargs)
-            features = q.query(concept)
+            try:
+                features = q.query(concept)
+            except StopIteration:
+                continue
             live_instances.extend(
                 Feature._wrap_livequery_feature(f, Feature._serialize_query_context(f, concept))
                 for f in features
@@ -721,7 +739,7 @@ class CompoundFeature(Feature):
     def __init__(
         self,
         elements: List['Feature'],
-        queryconcept: Union[region.Region, parcellation.Parcellation, space.Space]
+        queryconcept: Union[region.Region, parcellation.Parcellation, space.Space],
     ):
         """
         A compound of several features of the same type with an anchor created
@@ -754,7 +772,8 @@ class CompoundFeature(Feature):
             modality=modality,
             description="\n".join({f.description for f in elements}),
             anchor=self._feature_type._merge_anchors([f.anchor for f in elements]),
-            datasets=list(dict.fromkeys([ds for f in elements for ds in f.datasets]))
+            datasets=list(dict.fromkeys([ds for f in elements for ds in f.datasets])),
+            prerelease=all(f._prerelease for f in elements),
         )
         self._queryconcept = queryconcept
         self._merged_feature_cached = None
@@ -830,16 +849,21 @@ class CompoundFeature(Feature):
             for k, v in self._compounding_attributes.items()
             if k != 'modality'
         ])
-        return f"{len(self)} {readable_feature_type} features{f' {groupby}' if groupby else ''}"
+        cf_name = f"{len(self)} {readable_feature_type} features{f' {groupby}' if groupby else ''}"
+        return cf_name if not self._prerelease else f"[PRERELEASE] {cf_name}"
 
     @property
     def id(self) -> str:
+        if self._prerelease:
+            name_ = self.name.replace("[PRERELEASE] ", "")
+        else:
+            name_ = self.name
         return "::".join((
             "cf0",
             f"{self._feature_type.__name__}",
             self._encode_concept(self._queryconcept),
             self.datasets[0].id if self.datasets else "nodsid",
-            md5(self.name.encode("utf-8")).hexdigest()
+            md5(name_.encode("utf-8")).hexdigest()
         ))
 
     def __iter__(self) -> Iterator['Feature']:

siibra/features/image/__init__.py

@@ -1,4 +1,4 @@
-# Copyright 2018-2021
+# Copyright 2018-2024
 # Institute of Neuroscience and Medicine (INM-1), Forschungszentrum Jülich GmbH
 
 # Licensed under the Apache License, Version 2.0 (the "License");