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Volume subclass BrainStructure #630

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merged 2 commits into from
Dec 12, 2024
Merged

Volume subclass BrainStructure #630

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e669b8e
`Volume` subclasses `BrainStructure` not `Location`
AhmetNSimsek Dec 12, 2024
4d21343
Merge branch 'main' into maint_volume_as_brainstructure
AhmetNSimsek Dec 12, 2024
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2 changes: 1 addition & 1 deletion siibra/core/region.py
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Original file line number Diff line number Diff line change
Expand Up @@ -615,7 +615,7 @@ def assign(self, other: structure.BrainStructure) -> AnatomicalAssignment:
return None
return self._ASSIGNMENT_CACHE[other, self].invert()

if isinstance(other, location.Location):
if isinstance(other, (location.Location, volume.Volume)):
if self.mapped_in_space(other.space):
regionmap = self.get_regional_mask(other.space)
self._ASSIGNMENT_CACHE[self, other] = regionmap.assign(other)
Expand Down
21 changes: 2 additions & 19 deletions siibra/volumes/volume.py
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Original file line number Diff line number Diff line change
Expand Up @@ -19,7 +19,7 @@
from .. import logger
from ..retrieval import requests
from ..core import space as _space, structure
from ..locations import location, point, pointset, boundingbox
from ..locations import point, pointset, boundingbox
from ..commons import resample_img_to_img, siibra_tqdm, affine_scaling, connected_components
from ..exceptions import NoMapAvailableError, SpaceWarpingFailedError

Expand Down Expand Up @@ -92,7 +92,7 @@ def compute_from_image(
return spatial_props


class Volume(location.Location):
class Volume(structure.BrainStructure):
"""
A volume is a specific mesh or 3D array,
which can be accessible via multiple providers in different formats.
Expand Down Expand Up @@ -390,14 +390,6 @@ def _points_inside(
newlabels=None if keep_labels else inside
)

def union(self, other: location.Location):
if isinstance(other, Volume):
return merge([self, other])
else:
raise NotImplementedError(
f"There are no union method for {(self.__class__.__name__, other.__class__.__name__)}"
)

def intersection(self, other: structure.BrainStructure, **fetch_kwargs) -> structure.BrainStructure:
"""
Compute the intersection of a location with this volume. This will
Expand Down Expand Up @@ -436,15 +428,6 @@ def intersection(self, other: structure.BrainStructure, **fetch_kwargs) -> struc
except NoMapAvailableError:
return None

def transform(self, affine: np.ndarray, space=None):
raise NotImplementedError("Volume transformation is not yet implemented.")

def warp(self, space):
if self.space.matches(space):
return self
else:
raise SpaceWarpingFailedError('Warping of full volumes is not yet supported.')

def fetch(
self,
format: str = None,
Expand Down
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