siibra 1.0a11__py3-none-any.whl → 1.0a19__py3-none-any.whl

siibra/locations/pointset.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");
@@ -18,6 +18,7 @@ from . import location, point, boundingbox as _boundingbox
 
 from ..retrieval.requests import HttpRequest
 from ..commons import logger
+from ..exceptions import SpaceWarpingFailedError
 
 from typing import List, Union, Tuple
 import numbers
@@ -149,7 +150,7 @@ class PointSet(location.Location):
         if spaceobj == self.space:
             return self
         if any(_ not in location.Location.SPACEWARP_IDS for _ in [self.space.id, spaceobj.id]):
-            raise ValueError(
+            raise SpaceWarpingFailedError(
                 f"Cannot convert coordinates between {self.space.id} and {spaceobj.id}"
             )
 
@@ -178,6 +179,10 @@ class PointSet(location.Location):
             ).data
             tgt_points.extend(list(response["target_points"]))
 
+        # TODO: consider using np.isnan(np.dot(arr, arr)). see https://stackoverflow.com/a/45011547
+        if np.any(np.isnan(response['target_points'])):
+            raise SpaceWarpingFailedError(f'Warping {str(self)} to {spaceobj.name} resulted in NaN')
+
         return self.__class__(coordinates=tuple(tgt_points), space=spaceobj, labels=self.labels)
 
     def transform(self, affine: np.ndarray, space=None):
@@ -243,15 +248,15 @@ class PointSet(location.Location):
 
     @property
     def boundingbox(self):
-        """Return the bounding box of these points.
-        TODO revisit the numerical margin of 1e-6, should not be necessary.
         """
-        XYZ = self.coordinates
-        sigma_min = max(self.sigma[i] for i in XYZ.argmin(0))
-        sigma_max = max(self.sigma[i] for i in XYZ.argmax(0))
+        Return the bounding box of these points.
+        """
+        coords = self.coordinates
+        sigma_min = max(self.sigma[i] for i in coords.argmin(0))
+        sigma_max = max(self.sigma[i] for i in coords.argmax(0))
         return _boundingbox.BoundingBox(
-            point1=XYZ.min(0) - max(sigma_min, 1e-6),
-            point2=XYZ.max(0) + max(sigma_max, 1e-6),
+            point1=coords.min(0),
+            point2=coords.max(0),
             space=self.space,
             sigma_mm=[sigma_min, sigma_max]
         )
@@ -276,7 +281,34 @@ class PointSet(location.Location):
         """Access the list of 3D point as an Nx4 array of homogeneous coordinates."""
         return np.c_[self.coordinates, np.ones(len(self))]
 
-    def find_clusters(self, min_fraction=1 / 200, max_fraction=1 / 8):
+    def find_clusters(
+        self,
+        min_fraction: float = 1 / 200,
+        max_fraction: float = 1 / 8
+    ) -> List[int]:
+        """
+        Find clusters using HDBSCAN (https://dl.acm.org/doi/10.1145/2733381)
+        implementation of scikit-learn (https://dl.acm.org/doi/10.5555/1953048.2078195).
+
+        Parameters
+        ----------
+        min_fraction: min cluster size as a fraction of total points in the PointSet
+        max_fraction: max cluster size as a fraction of total points in the PointSet
+
+        Returns
+        -------
+        List[int]
+            Returns the cluster labels found by skilearn.cluster.HDBSCAN.
+
+            Note
+            ----
+            Replaces the labels of the PointSet instance with these labels.
+
+        Raises
+        ------
+        RuntimeError
+            If a sklearn version without HDBSCAN is installed.
+        """
         if not _HAS_HDBSCAN:
             raise RuntimeError(
                 f"HDBSCAN is not available with your version {sklearn.__version__} "
@@ -289,7 +321,9 @@ class PointSet(location.Location):
             max_cluster_size=int(N * max_fraction),
         )
         if self.labels is not None:
-            logger.warn("Existing labels of PointSet will be overwritten with cluster labels.")
+            logger.warning(
+                "Existing labels of PointSet will be overwritten with cluster labels."
+            )
         self.labels = clustering.fit_predict(points)
         return self.labels
 

siibra/retrieval/__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/retrieval/cache.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/retrieval/datasets.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/retrieval/exceptions/__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/retrieval/repositories.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/retrieval/requests.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/vocabularies/__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/volumes/__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/volumes/parcellationmap.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");
@@ -76,6 +76,7 @@ class Map(concept.AtlasConcept, configuration_folder="maps"):
         modality: str = None,
         publications: list = [],
         datasets: list = [],
+        prerelease: bool = False,
     ):
         """
         Constructs a new parcellation object.
@@ -120,12 +121,11 @@ class Map(concept.AtlasConcept, configuration_folder="maps"):
             description=description,
             publications=publications,
             datasets=datasets,
-            modality=modality
+            modality=modality,
+            prerelease=prerelease,
         )
         self._space_spec = space_spec
         self._parcellation_spec = parcellation_spec
-        if 'prerelease' in self.parcellation.name.lower():
-            self.name = f"[PRERELEASE] {self.name}"
 
         # Since the volumes might include 4D arrays, where the actual
         # volume index points to a z coordinate, we create subvolume
@@ -572,32 +572,52 @@ class Map(concept.AtlasConcept, configuration_folder="maps"):
             )]
         )
 
-    def compute_centroids(self) -> Dict[str, point.Point]:
+    def compute_centroids(self, split_components: bool = True) -> Dict[str, pointset.PointSet]:
         """
-        Compute a dictionary of the centroids of all regions in this map.
+        Compute a dictionary of all regions in this map to their centroids.
+        By default, the regional masks will be split to connected components
+        and each point in the PointSet corresponds to a region component.
+
+        Parameters
+        ----------
+        split_components: bool, default: True
+            If True, finds the spatial properties for each connected component
+            found by skimage.measure.label.
 
         Returns
         -------
         Dict[str, point.Point]
             Region names as keys and computed centroids as items.
         """
-        centroids = {}
-        maparr = None
+        centroids = dict()
         for regionname, indexlist in siibra_tqdm(
             self._indices.items(), unit="regions", desc="Computing centroids"
         ):
-            assert len(indexlist) == 1
-            index = indexlist[0]
-            if index.label == 0:
-                continue
-            with QUIET:
-                mapimg = self.fetch(index=index)  # returns a mask of the region
-            maparr = np.asanyarray(mapimg.dataobj)
-            centroid_vox = np.mean(np.where(maparr == 1), axis=1)
             assert regionname not in centroids
-            centroids[regionname] = point.Point(
-                np.dot(mapimg.affine, np.r_[centroid_vox, 1])[:3], space=self.space
+            # get the mask of the region in this map
+            with QUIET:
+                if len(indexlist) >= 1:
+                    merged_volume = _volume.merge(
+                        [
+                            _volume.from_nifti(
+                                self.fetch(index=index),
+                                self.space,
+                                f"{self.name} - {index}"
+                            )
+                            for index in indexlist
+                        ],
+                        labels=[1] * len(indexlist)
+                    )
+                    mapimg = merged_volume.fetch()
+                elif len(indexlist) == 1:
+                    index = indexlist[0]
+                    mapimg = self.fetch(index=index)  # returns a mask of the region
+            props = _volume.ComponentSpatialProperties.compute_from_image(
+                img=mapimg,
+                space=self.space,
+                split_components=split_components,
             )
+            centroids[regionname] = pointset.from_points([c.centroid for c in props])
         return centroids
 
     def get_resampled_template(self, **fetch_kwargs) -> _volume.Volume:

siibra/volumes/providers/__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/volumes/providers/freesurfer.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/volumes/providers/gifti.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/volumes/providers/neuroglancer.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");
@@ -26,7 +26,7 @@ from ...commons import (
 from ...retrieval import requests, cache
 from ...locations import boundingbox as _boundingbox
 
-from neuroglancer_scripts.precomputed_io import get_IO_for_existing_dataset
+from neuroglancer_scripts.precomputed_io import get_IO_for_existing_dataset, PrecomputedIO
 from neuroglancer_scripts.http_accessor import HttpAccessor
 from neuroglancer_scripts.mesh import read_precomputed_mesh, affine_transform_mesh
 from io import BytesIO
@@ -243,7 +243,7 @@ class NeuroglancerVolume:
         self._scales_cached = None
         self._info = None
         self._transform_nm = None
-        self._io = None
+        self._io: PrecomputedIO = None
 
     @property
     def transform_nm(self):
@@ -266,7 +266,7 @@ class NeuroglancerVolume:
         self._transform_nm = val
 
     @property
-    def io(self):
+    def io(self) -> PrecomputedIO:
         if self._io is None:
             accessor = HttpAccessor(self.url)
             self._io = get_IO_for_existing_dataset(accessor)
@@ -385,7 +385,7 @@ class NeuroglancerScale:
 
     color_warning_issued = False
 
-    def __init__(self, volume: NeuroglancerProvider, scaleinfo: dict):
+    def __init__(self, volume: NeuroglancerVolume, scaleinfo: dict):
         self.volume = volume
         self.chunk_sizes = np.array(scaleinfo["chunk_sizes"]).squeeze()
         self.encoding = scaleinfo["encoding"]
@@ -532,8 +532,8 @@ class NeuroglancerScale:
         # determine the remaining offset from the "chunk mosaic" to the
         # exact bounding box requested, to cut off undesired borders
         data_min = np.array([gx0, gy0, gz0]) * self.chunk_sizes
-        x0, y0, z0 = (np.array(tuple(bbox_.minpoint)) - data_min).astype("int")
-        xd, yd, zd = np.array(bbox_.shape).astype("int")
+        x0, y0, z0 = (np.array(bbox_.minpoint) - data_min).astype("int")
+        xd, yd, zd = np.ceil((np.array(bbox_.maxpoint))).astype(int) - np.floor((np.array(bbox_.minpoint))).astype(int)  # TODO: consider 0.5 voxel shift
         offset = tuple(bbox_.minpoint)
 
         # build the nifti image

siibra/volumes/providers/nifti.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");
@@ -65,7 +65,7 @@ class NiftiProvider(_provider.VolumeProvider, srctype="nii"):
     def fragments(self):
         return [k for k in self._img_loaders if k is not None]
 
-    def get_boundingbox(self, clip=True, background=0, **fetch_kwargs) -> "_boundingbox.BoundingBox":
+    def get_boundingbox(self, clip=True, background=0., **fetch_kwargs) -> "_boundingbox.BoundingBox":
         """
         Return the bounding box in physical coordinates of the union of
         fragments in this nifti volume.
@@ -188,19 +188,23 @@ class NiftiProvider(_provider.VolumeProvider, srctype="nii"):
             result = loader()
 
         if voi is not None:
+            zoom_xyz = np.array(result.header.get_zooms())  # voxel dimensions in xyzt_units
             bb_vox = voi.transform(np.linalg.inv(result.affine))
-            (x0, y0, z0), (x1, y1, z1) = bb_vox.minpoint, bb_vox.maxpoint
+            x0, y0, z0 = np.floor(np.array(bb_vox.minpoint.coordinate) / zoom_xyz).astype(int)
+            x1, y1, z1 = np.ceil(np.array(bb_vox.maxpoint.coordinate) / zoom_xyz).astype(int)
             shift = np.identity(4)
             shift[:3, -1] = bb_vox.minpoint
             result = nib.Nifti1Image(
                 dataobj=result.dataobj[x0:x1, y0:y1, z0:z1],
                 affine=np.dot(result.affine, shift),
+                dtype=result.header.get_data_dtype(),
             )
 
         if label is not None:
             result = nib.Nifti1Image(
                 (result.get_fdata() == label).astype('uint8'),
-                result.affine
+                result.affine,
+                dtype='uint8'
             )
 
         return result

siibra/volumes/providers/provider.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");
@@ -28,7 +28,7 @@ VolumeData = Union[Nifti1Image, Dict]
 
 class VolumeProvider(ABC):
 
-    _SUBCLASSES = []
+    _SUBCLASSES: List[VolumeProvider] = []
 
     def __init_subclass__(cls, srctype: str) -> None:
         cls.srctype = srctype

siibra/volumes/sparsemap.py

@@ -1,4 +1,4 @@
-# Copyright 2018-2022
+# Copyright 2018-2024
 # Institute of Neuroscience and Medicine (INM-1), Forschungszentrum Jülich GmbH
 
 # Licensed under the Apache License, Version 2.0 (the "License");
@@ -20,6 +20,7 @@ from ..commons import MapIndex, logger, connected_components, siibra_tqdm
 from ..locations import boundingbox
 from ..retrieval import cache
 from ..retrieval.repositories import ZipfileConnector, GitlabConnector
+from ..exceptions import InsufficientArgumentException, ExcessiveArgumentException
 
 from os import path, rename, makedirs
 from zipfile import ZipFile, ZIP_DEFLATED
@@ -226,7 +227,8 @@ class SparseMap(parcellationmap.Map):
         description: str = "",
         modality: str = None,
         publications: list = [],
-        datasets: list = []
+        datasets: list = [],
+        prerelease: bool = False,
     ):
         parcellationmap.Map.__init__(
             self,
@@ -241,6 +243,7 @@ class SparseMap(parcellationmap.Map):
             publications=publications,
             datasets=datasets,
             volumes=volumes,
+            prerelease=prerelease,
         )
         self._sparse_index_cached = None
 
@@ -390,7 +393,7 @@ class SparseMap(parcellationmap.Map):
             assert length == 1
         except AssertionError:
             if length > 1:
-                raise parcellationmap.ExcessiveArgumentException(
+                raise ExcessiveArgumentException(
                     "One and only one of region_or_index, region, index can be defined for fetch"
                 )
             # user can provide no arguments, which assumes one and only one volume present
@@ -416,7 +419,7 @@ class SparseMap(parcellationmap.Map):
                 assert len(self) == 1
                 volidx = 0
             except AssertionError:
-                raise parcellationmap.InsufficientArgumentException(
+                raise InsufficientArgumentException(
                     f"{self.__class__.__name__} provides {len(self)} volumes. "
                     "Specify 'region' or 'index' for fetch() to identify one."
                 )

siibra/volumes/volume.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");
@@ -20,9 +20,10 @@ from .. import logger
 from ..retrieval import requests
 from ..core import space as _space, structure
 from ..locations import location, point, pointset, boundingbox
-from ..commons import resample_img_to_img, siibra_tqdm
+from ..commons import resample_img_to_img, siibra_tqdm, affine_scaling, connected_components
 from ..exceptions import NoMapAvailableError, SpaceWarpingFailedError
 
+from dataclasses import dataclass
 from nibabel import Nifti1Image
 import numpy as np
 from typing import List, Dict, Union, Set, TYPE_CHECKING
@@ -36,6 +37,61 @@ if TYPE_CHECKING:
     TypeDataset = EbrainsDataset
 
 
+@dataclass
+class ComponentSpatialProperties:
+    """
+    Centroid and nonzero volume of an image.
+    """
+    centroid: point.Point
+    volume: int
+
+    @staticmethod
+    def compute_from_image(
+        img: Nifti1Image,
+        space: Union[str, "_space.Space"],
+        split_components: bool = True
+
+    ) -> List["ComponentSpatialProperties"]:
+        """
+        Find the center of an image in its (non-zero) voxel space and and its
+        volume.
+
+        Parameters
+        ----------
+        img: Nifti1Image
+        space: str, Space
+        split_components: bool, default: True
+            If True, finds the spatial properties for each connected component
+            found by skimage.measure.label.
+        """
+        scale = affine_scaling(img.affine)
+        if split_components:
+            iter_components = lambda img: connected_components(
+                np.asanyarray(img.dataobj),
+                connectivity=None
+            )
+        else:
+            iter_components = lambda img: [(0, np.asanyarray(img.dataobj))]
+
+        spatial_props: List[ComponentSpatialProperties] = []
+        for _, component in iter_components(img):
+            nonzero: np.ndarray = np.c_[np.nonzero(component)]
+            spatial_props.append(
+                ComponentSpatialProperties(
+                    centroid=point.Point(
+                        np.dot(img.affine, np.r_[nonzero.mean(0), 1])[:3],
+                        space=space
+                    ),
+                    volume=nonzero.shape[0] * scale,
+                )
+            )
+
+        # sort by volume
+        spatial_props.sort(key=lambda cmp: cmp.volume, reverse=True)
+
+        return spatial_props
+
+
 class Volume(location.Location):
     """
     A volume is a specific mesh or 3D array,
@@ -77,12 +133,14 @@ class Volume(location.Location):
         name: str = "",
         variant: str = None,
         datasets: List['TypeDataset'] = [],
+        bbox: "boundingbox.BoundingBox" = None
     ):
         self._name = name
         self._space_spec = space_spec
         self.variant = variant
         self._providers: Dict[str, _provider.VolumeProvider] = {}
         self.datasets = datasets
+        self._boundingbox = bbox
         for provider in providers:
             srctype = provider.srctype
             assert srctype not in self._providers
@@ -142,6 +200,9 @@ class Volume(location.Location):
         RuntimeError
             If the volume provider does not have a bounding box calculator.
         """
+        if self._boundingbox is not None and len(fetch_kwargs) == 0:
+            return self._boundingbox
+
         fmt = fetch_kwargs.get("format")
         if (fmt is not None) and (fmt not in self.formats):
             raise ValueError(
@@ -253,9 +314,8 @@ class Volume(location.Location):
             raise NotImplementedError("Filtering of points by pure mesh volumes not yet implemented.")
 
         # make sure the points are in the same physical space as this volume
-        warped = (
-            pointset.from_points([points]) if isinstance(points, point.Point) else points
-        ).warp(self.space)
+        as_pointset = pointset.from_points([points]) if isinstance(points, point.Point) else points
+        warped = as_pointset.warp(self.space)
         assert warped is not None, SpaceWarpingFailedError
 
         # get the voxel array of this volume
@@ -340,6 +400,8 @@ class Volume(location.Location):
         elif isinstance(other, boundingbox.BoundingBox):
             return self.get_boundingbox(clip=True, background=0.0, **fetch_kwargs).intersection(other)
         elif isinstance(other, Volume):
+            if self.space != other.space:
+                raise NotImplementedError("Cannot intersect volumes from different spaces. Try comparing their boudning boxes.")
             format = fetch_kwargs.pop('format', 'image')
             v1 = self.fetch(format=format, **fetch_kwargs)
             v2 = other.fetch(format=format, **fetch_kwargs)
@@ -416,6 +478,20 @@ class Volume(location.Location):
                 f"volume are: {self.formats}"
             )
 
+        # ensure the voi is inside the template
+        voi = kwargs.get("voi", None)
+        if voi is not None and voi.space is not None:
+            assert isinstance(voi, boundingbox.BoundingBox)
+            tmplt_bbox = voi.space.get_template().get_boundingbox(clip=False)
+            intersection_bbox = voi.intersection(tmplt_bbox)
+            if intersection_bbox is None:
+                raise RuntimeError(f"voi provided ({voi}) lies out side the voxel space of the {voi.space.name} template.")
+            if intersection_bbox != voi:
+                logger.info(
+                    f"Since provided voi lies outside the template ({voi.space}) it is clipped as: {intersection_bbox}"
+                )
+                kwargs["voi"] = intersection_bbox
+
         result = None
         # try each possible format
         for fmt in possible_formats:
@@ -460,19 +536,37 @@ class Volume(location.Location):
 
         return self._FETCH_CACHE[fetch_hash]
 
-    def fetch_connected_components(self, **kwargs):
+    def fetch_connected_components(self, **fetch_kwargs):
         """
-        Provide an iterator over masks of connected components in the volume
+        Provide an generator over masks of connected components in the volume
         """
-        img = self.fetch(**kwargs)
-        from skimage import measure
-        imgdata = np.asanyarray(img.dataobj).squeeze()
-        components = measure.label(imgdata > 0)
-        component_labels = np.unique(components)
-        assert component_labels[0] == 0
-        return (
-            (label, Nifti1Image((components == label).astype('uint8'), img.affine))
-            for label in component_labels[1:]
+        img = self.fetch(**fetch_kwargs)
+        assert isinstance(img, Nifti1Image), NotImplementedError(
+            f"Connected components for type {type(img)} is not yet implemeneted."
+        )
+        for label, component in connected_components(np.asanyarray(img.dataobj)):
+            yield (
+                label,
+                Nifti1Image(component, img.affine)
+            )
+
+    def compute_spatial_props(self, split_components: bool = True, **fetch_kwargs) -> List[ComponentSpatialProperties]:
+        """
+        Find the center of this volume in its (non-zero) voxel space and and its
+        volume.
+
+        Parameters
+        ----------
+        split_components: bool, default: True
+            If True, finds the spatial properties for each connected component
+            found by skimage.measure.label.
+        """
+        assert self.provides_image, NotImplementedError("Spatial properties can currently on be calculated for images.")
+        img = self.fetch(format="image", **fetch_kwargs)
+        return ComponentSpatialProperties.compute_from_image(
+            img=img,
+            space=self.space,
+            split_components=split_components
         )
 
     def draw_samples(self, N: int, sample_size: int = 100, e: float = 1, sigma_mm=None, invert=False, **kwargs):
@@ -670,6 +764,10 @@ def merge(volumes: List[Volume], labels: List[int] = [], **fetch_kwargs) -> Volu
     -------
     Volume
     """
+    if len(volumes) == 1:
+        logger.debug("Only one volume supplied returning as is (kwargs are ignored).")
+        return volumes[0]
+
     assert len(volumes) > 1, "Need to supply at least two volumes to merge."
     if labels:
         assert len(volumes) == len(labels), "Need to supply as many labels as volumes."

{siibra-1.0a11.dist-info → siibra-1.0a19.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: siibra
-Version: 1.0a11
+Version: 1.0a19
 Summary: siibra - Software interfaces for interacting with brain atlases
 Home-page: https://github.com/FZJ-INM1-BDA/siibra-python
 Author: Big Data Analytics Group, Forschungszentrum Juelich, Institute of Neuroscience and Medicine (INM-1)
@@ -25,8 +25,8 @@ Requires-Dist: requests
 Requires-Dist: neuroglancer-scripts
 Requires-Dist: nilearn
 Requires-Dist: filelock
-Requires-Dist: ebrains-drive >=0.6.0
-Requires-Dist: typing-extensions ; python_version < "3.8"
+Requires-Dist: ebrains-drive>=0.6.0
+Requires-Dist: typing-extensions; python_version < "3.8"
 
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