siibra 1.0a19__py3-none-any.whl → 1.0.1a1__py3-none-any.whl

siibra/experimental/contour.py

@@ -1,4 +1,4 @@
-# Copyright 2018-2024
+# Copyright 2018-2025
 # Institute of Neuroscience and Medicine (INM-1), Forschungszentrum Jülich GmbH
 
 # Licensed under the Apache License, Version 2.0 (the "License");
@@ -13,22 +13,22 @@
 # See the License for the specific language governing permissions and
 # limitations under the License.
 
-from ..locations import point, pointset, boundingbox
+from ..locations import point, pointcloud, boundingbox
 
 import numpy as np
 
 
-class Contour(pointset.PointSet):
+class Contour(pointcloud.PointCloud):
     """
-    A PointSet that represents a contour line.
+    A PointCloud that represents a contour line.
     The only difference is that the point order is relevant,
     and consecutive points are thought as being connected by an edge.
 
-    In fact, PointSet assumes order as well, but no connections between points.
+    In fact, PointCloud assumes order as well, but no connections between points.
     """
 
     def __init__(self, coordinates, space=None, sigma_mm=0, labels: list = None):
-        pointset.PointSet.__init__(self, coordinates, space, sigma_mm, labels)
+        pointcloud.PointCloud.__init__(self, coordinates, space, sigma_mm, labels)
 
     def crop(self, voi: boundingbox.BoundingBox):
         """
@@ -45,8 +45,8 @@ class Contour(pointset.PointSet):
         cropped = self.intersection(voi)
 
         if cropped is not None and not isinstance(cropped, point.Point):
-            assert isinstance(cropped, pointset.PointSet)
-            # Identifiy contour splits are by discontinuouities ("jumps")
+            assert isinstance(cropped, pointcloud.PointCloud)
+            # Identify contour splits are by discontinuouities ("jumps")
             # of their labels, which denote positions in the original contour
             jumps = np.diff([self.labels.index(lb) for lb in cropped.labels])
             splits = [0] + list(np.where(jumps > 1)[0] + 1) + [len(cropped)]

siibra/experimental/cortical_profile_sampler.py

@@ -1,4 +1,4 @@
-# Copyright 2018-2024
+# Copyright 2018-2025
 # Institute of Neuroscience and Medicine (INM-1), Forschungszentrum Jülich GmbH
 
 # Licensed under the Apache License, Version 2.0 (the "License");

siibra/experimental/patch.py

@@ -1,4 +1,4 @@
-# Copyright 2018-2024
+# Copyright 2018-2025
 # Institute of Neuroscience and Medicine (INM-1), Forschungszentrum Jülich GmbH
 
 # Licensed under the Apache License, Version 2.0 (the "License");
@@ -14,7 +14,7 @@
 # limitations under the License.
 
 from ..volumes import volume
-from ..locations import pointset, boundingbox
+from ..locations import pointcloud, boundingbox
 from ..commons import translation_matrix, y_rotation_matrix
 
 import numpy as np
@@ -24,7 +24,7 @@ from nilearn import image
 
 class Patch:
 
-    def __init__(self, corners: pointset.PointSet):
+    def __init__(self, corners: pointcloud.PointCloud):
         """Construct a patch in physical coordinates.
         As of now, only patches aligned in the y plane of the physical space
         are supported."""

siibra/experimental/plane3d.py

@@ -1,4 +1,4 @@
-# Copyright 2018-2024
+# Copyright 2018-2025
 # Institute of Neuroscience and Medicine (INM-1), Forschungszentrum Jülich GmbH
 
 # Licensed under the Apache License, Version 2.0 (the "License");
@@ -15,7 +15,7 @@
 
 from . import contour
 from . import patch
-from ..locations import point, pointset
+from ..locations import point, pointcloud
 from ..volumes import volume
 
 import numpy as np
@@ -33,7 +33,7 @@ class Plane3D:
         The plane's reference space is defined by the first point.
         """
         self.space = point1.space
-        # normal is the cross product of two arbitray in-plane vectors
+        # normal is the cross product of two arbitrary in-plane vectors
         n = np.cross(
             (point2.warp(self.space) - point1).coordinate,
             (point3.warp(self.space) - point1).coordinate,
@@ -93,9 +93,9 @@ class Plane3D:
         and an Mx3 array "faces" of face definitions.
         Each row in the face array corresponds to the three indices of vertices making up the
         triangle.
-        The result is a list of contour segments, each represented as a PointSet
+        The result is a list of contour segments, each represented as a PointCloud
         holding the ordered list of contour points.
-        The point labels in each "contour" PointSet hold the index of the face in the
+        The point labels in each "contour" PointCloud hold the index of the face in the
         mesh which made up each contour point.
         """
 
@@ -107,7 +107,7 @@ class Plane3D:
         )[0]
         faces = mesh["faces"][face_indices]
 
-        # for each of N selected faces, indicate wether we cross the plane
+        # for each of N selected faces, indicate whether we cross the plane
         # as we go from vertex 2->0, 0->1, 1->2, respectively.
         # This gives us an Nx3 array, where forward crossings are identified by 1,
         # and backward crossings by -1.
@@ -160,7 +160,7 @@ class Plane3D:
         face_id = 0  # index of the mesh face to consider
         while len(face_indices) > 0:
 
-            # continue the contour with the next foward edge intersection
+            # continue the contour with the next forward edge intersection
             p = fwd_intersections[face_id]
             points.append(p)
             # Remember the ids of the face and start-/end vertices for the point
@@ -185,17 +185,17 @@ class Plane3D:
 
         return result
 
-    def project_points(self, points: pointset.PointSet):
+    def project_points(self, points: pointcloud.PointCloud):
         """projects the given points onto the plane."""
         assert self.space == points.space
         XYZ = points.coordinates
         N = XYZ.shape[0]
         dists = np.dot(self._n, XYZ.T) - self._d
-        return pointset.PointSet(
+        return pointcloud.PointCloud(
             XYZ - np.tile(self._n, (N, 1)) * dists[:, np.newaxis], space=self.space
         )
 
-    def get_enclosing_patch(self, points: pointset.PointSet, margin=[0.5, 0.5]):
+    def get_enclosing_patch(self, points: pointcloud.PointCloud, margin=[0.5, 0.5]):
         """
         Computes the enclosing patch in the given plane
         which contains the projections of the given points.
@@ -225,7 +225,7 @@ class Plane3D:
 
         m0, m1 = margin
         w = np.linalg.norm(p3 - p2)
-        corners = pointset.PointSet(
+        corners = pointcloud.PointCloud(
             [
                 p1 + (w / 2 + m1) * v2 + m0 * v1,
                 p0 + (w / 2 + m1) * v2 - m0 * v1,
@@ -249,7 +249,7 @@ class Plane3D:
         assert isinstance(image, volume.Volume)
         im_lowres = image.fetch(resolution_mm=1)
         plane_dims = np.where(np.argsort(im_lowres.shape) < 2)[0]
-        voxels = pointset.PointSet(
+        voxels = pointcloud.PointCloud(
             np.vstack(([0, 0, 0], np.identity(3)[plane_dims])), space=None
         )
         points = voxels.transform(im_lowres.affine, space=image.space)

siibra/explorer/__init__.py

@@ -1,4 +1,4 @@
-# Copyright 2018-2024
+# Copyright 2018-2025
 # Institute of Neuroscience and Medicine (INM-1), Forschungszentrum Jülich GmbH
 
 # Licensed under the Apache License, Version 2.0 (the "License");

siibra/explorer/url.py

@@ -1,4 +1,4 @@
-# Copyright 2018-2024
+# Copyright 2018-2025
 # Institute of Neuroscience and Medicine (INM-1), Forschungszentrum Jülich GmbH
 
 # Licensed under the Apache License, Version 2.0 (the "License");
@@ -211,7 +211,7 @@ def get_hash(full_string: str):
         for char in full_string:
             # overflowing is expected and in fact the whole reason why convert number to int32
 
-            # in windows, int32((0 - min_int32) << 5), rather than overflow to wraper around, raises OverflowError
+            # in windows, int32((0 - min_int32) << 5), rather than overflow to wrapper around, raises OverflowError
             shifted_5 = int32(
                 (return_val - min_int32) if return_val > max_int32 else return_val << 5
             )

siibra/explorer/util.py

@@ -1,4 +1,4 @@
-# Copyright 2018-2024
+# Copyright 2018-2025
 # 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 2018-2024
+# Copyright 2018-2025
 # 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 2018-2024
+# Copyright 2018-2025
 # Institute of Neuroscience and Medicine (INM-1), Forschungszentrum Jülich GmbH
 
 # Licensed under the Apache License, Version 2.0 (the "License");
@@ -19,7 +19,7 @@ from ..commons import Species, logger
 from ..core.structure import BrainStructure
 from ..core.assignment import AnatomicalAssignment, Qualification
 from ..locations.location import Location
-from ..core.parcellation import Parcellation
+from ..core.parcellation import Parcellation, find_regions
 from ..core.region import Region
 from ..core.space import Space
 from ..exceptions import SpaceWarpingFailedError
@@ -88,7 +88,7 @@ class AnatomicalAnchor:
 
     @property
     def space(self) -> Space:
-        # may be overriden by derived classes, e.g. in features.VolumeOfInterest
+        # may be overridden by derived classes, e.g. in features.VolumeOfInterest
         return None if self.location is None else self.location.space
 
     @property
@@ -126,13 +126,13 @@ class AnatomicalAnchor:
             # decode the region specification into a dict of region objects and assignment qualifications
             regions = {
                 region: Qualification.EXACT
-                for region in Parcellation.find_regions(self._regionspec)
+                for region in find_regions(self._regionspec, filter_children=True, find_topmost=False)
                 if region.species in self.species
             }
             # add more regions from possible aliases of the region spec
             for alt_species, aliases in self.region_aliases.items():
                 for alias_regionspec, qualificationspec in aliases.items():
-                    for r in Parcellation.find_regions(alias_regionspec):
+                    for r in find_regions(alias_regionspec, filter_children=True, find_topmost=False):
                         if r.species != alt_species:
                             continue
                         if r not in regions:
@@ -156,18 +156,17 @@ class AnatomicalAnchor:
         else:
             return region + separator + location
 
-    def assign(self, concept: BrainStructure, restrict_space: bool = False) -> AnatomicalAssignment:
+    def assign(self, concept: Union[BrainStructure, Space]) -> AnatomicalAssignment:
         """
         Match this anchor to a query concept. Assignments are cached at runtime,
         so repeated assignment with the same concept will be cheap.
         """
-        if (
-            restrict_space
-            and self.location is not None
-            and isinstance(concept, Location)
-            and not self.location.space.matches(concept.space)
-        ):
-            return []
+        if isinstance(concept, Space):
+            if self.location is not None and self.location.space.matches(concept):
+                return [AnatomicalAssignment(concept, self.location, Qualification.CONTAINED)]
+            else:
+                return []
+
         if concept not in self._assignments:
             assignments: List[AnatomicalAssignment] = []
             if self.location is not None:
@@ -184,8 +183,8 @@ class AnatomicalAnchor:
             else None
         return self._assignments[concept]
 
-    def matches(self, concept: BrainStructure, restrict_space: bool = False) -> bool:
-        return len(self.assign(concept, restrict_space)) > 0
+    def matches(self, concept: Union[BrainStructure, Space]) -> bool:
+        return len(self.assign(concept)) > 0
 
     def represented_parcellations(self) -> List[Parcellation]:
         """

siibra/features/connectivity/__init__.py

@@ -1,4 +1,4 @@
-# Copyright 2018-2024
+# Copyright 2018-2025
 # 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 2018-2024
+# Copyright 2018-2025
 # 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 2018-2024
+# Copyright 2018-2025
 # Institute of Neuroscience and Medicine (INM-1), Forschungszentrum Jülich GmbH
 
 # Licensed under the Apache License, Version 2.0 (the "License");
@@ -21,7 +21,7 @@ from .. import anchor as _anchor
 
 from ...commons import logger, QUIET, siibra_tqdm
 from ...core import region as _region
-from ...locations import pointset
+from ...locations import pointcloud
 from ...retrieval.repositories import RepositoryConnector
 from ...retrieval.requests import HttpRequest
 
@@ -275,7 +275,7 @@ class RegionalConnectivity(Feature, Compoundable):
 
         regions = [r for r in matrix.index if matches(r, region)]
         if len(regions) == 0:
-            raise ValueError(f"Invalid region specificiation: {region}")
+            raise ValueError(f"Invalid region specification: {region}")
         elif len(regions) > 1:
             raise ValueError(f"Region specification {region} matched more than one profile: {regions}")
         else:
@@ -440,7 +440,7 @@ class RegionalConnectivity(Feature, Compoundable):
                 found = [r for r in region if r.name in all_centroids]
             assert len(found) > 0
             result.append(
-                tuple(pointset.PointSet(
+                tuple(pointcloud.PointCloud(
                     [all_centroids[r.name] for r in found], space=space
                 ).centroid)
             )

siibra/features/connectivity/streamline_counts.py

@@ -1,4 +1,4 @@
-# Copyright 2018-2024
+# Copyright 2018-2025
 # 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 2018-2024
+# Copyright 2018-2025
 # 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 2018-2024
+# Copyright 2018-2025
 # 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 2018-2024
+# Copyright 2018-2025
 # 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 2018-2024
+# Copyright 2018-2025
 # 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 2018-2024
+# Copyright 2018-2025
 # Institute of Neuroscience and Medicine (INM-1), Forschungszentrum Jülich GmbH
 
 # Licensed under the Apache License, Version 2.0 (the "License");
@@ -53,7 +53,7 @@ _README_TMPL = """
 Downloaded from siibra toolsuite.
 siibra-python version: {version}
 
-All releated resources (e.g. doi, web resources) are categorized under publications.
+All related resources (e.g. doi, web resources) are categorized under publications.
 
 Name
 ----
@@ -199,9 +199,9 @@ class Feature:
     @property
     def authors(self):
         return [
-            contributer['name']
+            contributor['name']
             for ds in self.datasets
-            for contributer in ds.contributors
+            for contributor in ds.contributors
         ]
 
     @property
@@ -251,13 +251,16 @@ class Feature:
         """ Removes all instantiated object instances"""
         cls._preconfigured_instances = None
 
-    def matches(self, concept: structure.BrainStructure, restrict_space: bool = False) -> bool:
+    def matches(
+        self,
+        concept: Union[structure.BrainStructure, space.Space],
+    ) -> bool:
         """
-        Match the features anatomical anchor agains the given query concept.
+        Match the features anatomical anchor against the given query concept.
         Record the most recently matched concept for inspection by the caller.
         """
         # TODO: storing the last matched concept. It is not ideal, might cause problems in multithreading
-        if self.anchor and self.anchor.matches(concept, restrict_space):
+        if self.anchor and self.anchor.matches(concept):
             self.anchor._last_matched_concept = concept
             return True
         self.anchor._last_matched_concept = None
@@ -483,10 +486,10 @@ class Feature:
                 f"objects linked to {str(concept)}{argstr}"
             )
             q = QueryType(**kwargs)
-            try:
+            if isinstance(concept, space.Space):
+                features = q.query(concept.get_template())
+            else:
                 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
@@ -497,9 +500,8 @@ class Feature:
     @classmethod
     def _match(
         cls,
-        concept: structure.BrainStructure,
+        concept: Union[structure.BrainStructure, space.Space],
         feature_type: Union[str, Type['Feature'], list],
-        restrict_space: bool = False,
         **kwargs
     ) -> List['Feature']:
         """
@@ -507,7 +509,7 @@ class Feature:
         This will
         - call Feature.match(concept) for any registered preconfigured features
         - run any registered live queries
-        The preconfigured and live query instances are merged and returend as a list.
+        The preconfigured and live query instances are merged and returned as a list.
 
         If multiple feature types are given, recurse for each of them.
 
@@ -517,11 +519,7 @@ class Feature:
         concept: AtlasConcept
             An anatomical concept, typically a brain region or parcellation.
         feature_type: subclass of Feature, str
-            specififies the type of features ("modality")
-        restrict_space: bool: default: False
-            If true, will skip features anchored at spatial locations of
-            different spaces than the concept. Requires concept to be a
-            Location.
+            specifies the type of features ("modality")
         """
         if isinstance(feature_type, list):
             # a list of feature types is given, collect match results on those
@@ -531,7 +529,7 @@ class Feature:
             )
             return list(dict.fromkeys(
                 sum((
-                    cls._match(concept, t, restrict_space, **kwargs) for t in feature_type
+                    cls._match(concept, t, **kwargs) for t in feature_type
                 ), [])
             ))
 
@@ -548,15 +546,15 @@ class Feature:
                 f"'{feature_type}' decoded as feature type/s: "
                 f"{[c.__name__ for c in ftype_candidates]}."
             )
-            return cls._match(concept, ftype_candidates, restrict_space, **kwargs)
+            return cls._match(concept, ftype_candidates, **kwargs)
 
         assert issubclass(feature_type, Feature)
 
         # At this stage, no recursion is needed.
         # We expect a specific supported feature type is to be matched now.
-        if not isinstance(concept, structure.BrainStructure):
+        if not isinstance(concept, (structure.BrainStructure, space.Space)):
             raise ValueError(
-                f"{concept.__class__.__name__} cannot be used for feature queries as it is not a BrainStructure type."
+                f"{concept.__class__.__name__} cannot be used for feature queries as it is not a `BrainStructure` or a `Space` type."
             )
 
         # Collect any preconfigured instances of the requested feature type
@@ -574,7 +572,7 @@ class Feature:
                 total=len(instances),
                 disable=(not instances)
             )
-            if f.matches(concept, restrict_space)
+            if f.matches(concept)
         ]
 
         # Then run any registered live queries for the requested feature type
@@ -606,7 +604,7 @@ class Feature:
                 if inst.id == feature_id
             ]
             if len(candidates) == 0:
-                raise NotFoundException(f"No feature instance wth {feature_id} found.")
+                raise NotFoundException(f"No feature instance with {feature_id} found.")
             if len(candidates) == 1:
                 return candidates[0]
             else:
@@ -721,7 +719,7 @@ class Compoundable(ABC):
         """
         Compute the merge data and create a merged instance from a set of
         elements of this class. This will be used by CompoundFeature to
-        create the aggegated data and plot it. For example, to compute an
+        create the aggregated data and plot it. For example, to compute an
         average connectivity matrix from a set of subfeatures, we create a
         RegionalConnectivty feature.
         """
@@ -730,7 +728,7 @@ class Compoundable(ABC):
 
 class CompoundFeature(Feature):
     """
-    A compound aggregating mutliple features of the same type, forming its
+    A compound aggregating multiple features of the same type, forming its
     elements. The anatomical anchors and data of the features is merged.
     Features need to subclass "Compoundable" to allow aggregation
     into a compound feature.

siibra/features/image/__init__.py

@@ -1,4 +1,4 @@
-# Copyright 2018-2024
+# Copyright 2018-2025
 # Institute of Neuroscience and Medicine (INM-1), Forschungszentrum Jülich GmbH
 
 # Licensed under the Apache License, Version 2.0 (the "License");

siibra/features/image/image.py

@@ -1,4 +1,4 @@
-# Copyright 2018-2024
+# Copyright 2018-2025
 # Institute of Neuroscience and Medicine (INM-1), Forschungszentrum Jülich GmbH
 
 # Licensed under the Apache License, Version 2.0 (the "License");
@@ -44,7 +44,7 @@ class ImageAnchor(_anchor.AnatomicalAnchor):
         if self._location_cached is None:
             self._location_cached = self.volume.get_boundingbox(
                 clip=False
-            )  # use unclipped to preseve exisiting behaviour
+            )  # use unclipped to preserve existing behaviour
         return self._location_cached
 
     @property

siibra/features/image/sections.py

@@ -1,4 +1,4 @@
-# Copyright 2018-2024
+# Copyright 2018-2025
 # Institute of Neuroscience and Medicine (INM-1), Forschungszentrum Jülich GmbH
 
 # Licensed under the Apache License, Version 2.0 (the "License");

siibra/features/image/volume_of_interest.py

@@ -1,4 +1,4 @@
-# Copyright 2018-2024
+# Copyright 2018-2025
 # Institute of Neuroscience and Medicine (INM-1), Forschungszentrum Jülich GmbH
 
 # Licensed under the Apache License, Version 2.0 (the "License");

siibra/features/tabular/__init__.py

@@ -1,4 +1,4 @@
-# Copyright 2018-2024
+# Copyright 2018-2025
 # Institute of Neuroscience and Medicine (INM-1), Forschungszentrum Jülich GmbH
 
 # Licensed under the Apache License, Version 2.0 (the "License");

siibra/features/tabular/bigbrain_intensity_profile.py

@@ -1,4 +1,4 @@
-# Copyright 2018-2024
+# Copyright 2018-2025
 # Institute of Neuroscience and Medicine (INM-1), Forschungszentrum Jülich GmbH
 
 # Licensed under the Apache License, Version 2.0 (the "License");
@@ -65,7 +65,7 @@ class BigBrainIntensityProfile(
 
     @classmethod
     def _merge_anchors(cls, anchors: List['AnatomicalAnchor']):
-        from ...locations.pointset import from_points
+        from ...locations.pointcloud import from_points
         from ...features.anchor import AnatomicalAnchor
 
         location = from_points([anchor.location for anchor in anchors])