siibra 0.4a76__py3-none-any.whl → 0.5a1__py3-none-any.whl
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- siibra/VERSION +1 -1
- siibra/commons.py +3 -2
- siibra/configuration/configuration.py +6 -2
- siibra/configuration/factory.py +48 -27
- siibra/explorer/__init__.py +1 -0
- siibra/explorer/url.py +162 -0
- siibra/explorer/util.py +65 -0
- siibra/features/anchor.py +36 -9
- siibra/features/connectivity/__init__.py +6 -2
- siibra/features/connectivity/functional_connectivity.py +21 -0
- siibra/features/connectivity/regional_connectivity.py +91 -86
- siibra/features/dataset/ebrains.py +1 -1
- siibra/features/feature.py +331 -35
- siibra/features/tabular/bigbrain_intensity_profile.py +5 -2
- siibra/features/tabular/cell_density_profile.py +3 -1
- siibra/features/tabular/cortical_profile.py +14 -10
- siibra/features/tabular/gene_expression.py +0 -2
- siibra/features/tabular/layerwise_bigbrain_intensities.py +3 -2
- siibra/features/tabular/receptor_density_profile.py +7 -1
- siibra/features/tabular/regional_timeseries_activity.py +81 -102
- siibra/features/tabular/tabular.py +21 -9
- siibra/livequeries/bigbrain.py +11 -22
- siibra/locations/__init__.py +65 -1
- siibra/locations/boundingbox.py +0 -16
- siibra/locations/location.py +13 -0
- siibra/locations/pointset.py +1 -3
- siibra/retrieval/cache.py +5 -3
- siibra/retrieval/datasets.py +27 -27
- siibra/volumes/neuroglancer.py +6 -9
- {siibra-0.4a76.dist-info → siibra-0.5a1.dist-info}/METADATA +1 -1
- {siibra-0.4a76.dist-info → siibra-0.5a1.dist-info}/RECORD +34 -31
- {siibra-0.4a76.dist-info → siibra-0.5a1.dist-info}/WHEEL +1 -1
- {siibra-0.4a76.dist-info → siibra-0.5a1.dist-info}/LICENSE +0 -0
- {siibra-0.4a76.dist-info → siibra-0.5a1.dist-info}/top_level.txt +0 -0
siibra/retrieval/datasets.py
CHANGED
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@@ -128,7 +128,7 @@ class EbrainsDataset(EbrainsBaseDataset):
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return self._id
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@property
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def
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def _detail(self):
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if not self._cached_data:
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match = re.search(r"([a-f0-9-]+)$", self.id)
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instance_id = match.group(1)
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@@ -145,7 +145,7 @@ class EbrainsDataset(EbrainsBaseDataset):
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@property
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def name(self) -> str:
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if self._name is None:
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self._name = self.
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self._name = self._detail.get("name")
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return self._name
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@property
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@@ -154,16 +154,16 @@ class EbrainsDataset(EbrainsBaseDataset):
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{
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"url": f if f.startswith("http") else f"https://doi.org/{f}",
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}
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for f in self.
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for f in self._detail.get("kgReference", [])
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]
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@property
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def description(self) -> str:
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return self.
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return self._detail.get("description")
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@property
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def contributors(self) -> List[EbrainsDatasetPerson]:
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return self.
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return self._detail.get("contributors")
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@property
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def ebrains_page(self):
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@@ -171,16 +171,16 @@ class EbrainsDataset(EbrainsBaseDataset):
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@property
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def custodians(self) -> EbrainsDatasetPerson:
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return self.
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return self._detail.get("custodians")
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@property
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def LICENSE(self) -> str:
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return self.
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return self._detail.get("license", "No license information is found.")
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class EbrainsV3DatasetVersion(EbrainsBaseDataset):
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@staticmethod
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def
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def _parse_person(d: dict) -> EbrainsDatasetPerson:
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assert "https://openminds.ebrains.eu/core/Person" in d.get("type"), "Cannot convert a non person to a person dict!"
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_id = d.get("id")
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name = f"{d.get('givenName')} {d.get('familyName')}"
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@@ -199,7 +199,7 @@ class EbrainsV3DatasetVersion(EbrainsBaseDataset):
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self._cached_data = cached_data
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@property
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def
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def _detail(self):
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if not self._cached_data:
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match = re.search(r"([a-f0-9-]+)$", self._id)
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instance_id = match.group(1)
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@@ -219,30 +219,30 @@ class EbrainsV3DatasetVersion(EbrainsBaseDataset):
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@property
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def name(self) -> str:
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fullname = self.
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fullname = self._detail.get("fullName")
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if not fullname:
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for dataset in self.is_version_of:
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if fullname:
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break
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fullname = dataset.name
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version_id = self.
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version_id = self._detail.get("versionIdentifier")
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return f"{fullname} ({version_id})"
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@property
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def is_version_of(self):
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if not hasattr(self, "_is_version_of"):
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self._is_version_of = [EbrainsV3Dataset(id=id.get("id")) for id in self.
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self._is_version_of = [EbrainsV3Dataset(id=id.get("id")) for id in self._detail.get("isVersionOf", [])]
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return self._is_version_of
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@property
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def urls(self) -> List[EbrainsDatasetUrl]:
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return [{
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"url": doi.get("identifier", None)
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} for doi in self.
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} for doi in self._detail.get("doi", [])]
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@property
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def description(self) -> str:
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description = self.
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description = self._detail.get("description")
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for ds in self.is_version_of:
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if description:
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break
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@@ -251,7 +251,7 @@ class EbrainsV3DatasetVersion(EbrainsBaseDataset):
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@property
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def contributors(self) -> List[EbrainsDatasetPerson]:
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return [EbrainsV3DatasetVersion.
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return [EbrainsV3DatasetVersion._parse_person(d) for d in self._detail.get("author", [])]
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@property
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def ebrains_page(self) -> str:
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@@ -261,19 +261,19 @@ class EbrainsV3DatasetVersion(EbrainsBaseDataset):
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@property
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def custodians(self) -> EbrainsDatasetPerson:
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return [EbrainsV3DatasetVersion.
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return [EbrainsV3DatasetVersion._parse_person(d) for d in self._detail.get("custodian", [])]
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@property
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def
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return self.
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def version_changelog(self):
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return self._detail.get("versionInnovation", "")
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@property
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def version_identifier(self):
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return self.
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return self._detail.get("versionIdentifier", "")
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@property
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def LICENSE(self) -> str:
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return self.
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return self._detail.get("license", "No license information is found.")
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class EbrainsV3Dataset(EbrainsBaseDataset):
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@property
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def name(self) -> str:
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return self.
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return self._detail.get("fullName")
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@property
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def urls(self) -> List[EbrainsDatasetUrl]:
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return [{
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"url": doi.get("identifier", None)
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} for doi in self.
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} for doi in self._detail.get("doi", [])]
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@property
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def
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def _detail(self):
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if not self._cached_data:
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match = re.search(r"([a-f0-9-]+)$", self._id)
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instance_id = match.group(1)
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@property
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def description(self) -> str:
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return self.
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return self._detail.get("description", "")
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@property
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def contributors(self):
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@property
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def custodians(self) -> EbrainsDatasetPerson:
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return [EbrainsV3DatasetVersion.
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return [EbrainsV3DatasetVersion._parse_person(d) for d in self._detail.get("custodian", [])]
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@property
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def version_ids(self) -> List['str']:
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return [version.get("id") for version in self.
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return [version.get("id") for version in self._detail.get("versions", [])]
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@property
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def LICENSE(self) -> str:
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return self.
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return self._detail.get("license", "No license information is found.")
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class GenericDataset():
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siibra/volumes/neuroglancer.py
CHANGED
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from . import volume
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from ..commons import logger, MapType, merge_meshes
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from ..commons import logger, MapType, merge_meshes, NEUROGLANCER_MAX_GIB
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from ..retrieval import requests, cache
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from ..locations import boundingbox as _boundingbox
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class NeuroglancerVolume:
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# Number of bytes at which an image array is considered to large to fetch
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MAX_GiB = 0.2
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# Wether to keep fetched data in local cache
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USE_CACHE = False
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@property
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def MAX_BYTES(self):
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"Number of bytes at which an image array is considered to large to fetch"
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return NEUROGLANCER_MAX_GIB * 1024 ** 3
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def __init__(self, url: str):
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# TODO do we still need VolumeProvider.__init__ ? given it's not a subclass of VolumeProvider?
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else:
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scale = self.scales[0]
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logger.warning(
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f"Requested resolution {resolution_mm} is not available
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f"Falling back to the highest possible resolution of "
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f"{', '.join(map('{:.
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f"Requested resolution {resolution_mm}mm is not available for "
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f"all axes. Falling back to the highest possible resolution of "
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f"({', '.join(map('{:.4f}mm'.format, scale.res_mm))})."
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)
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scale_changed = False
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Metadata-Version: 2.1
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Name: siibra
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Version: 0.
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Version: 0.5a1
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Summary: siibra - Software interfaces for interacting with brain atlases
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Home-page: https://github.com/FZJ-INM1-BDA/siibra-python
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Author: Big Data Analytics Group, Forschungszentrum Juelich, Institute of Neuroscience and Medicine (INM-1)
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siibra/VERSION,sha256=
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siibra/VERSION,sha256=_pBYKH2kRUgC4bB0SlnS6S10C1La6Jboq2dyXNVCOPA,7
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siibra/__init__.py,sha256=qBxxMRyl9RojNt0twQr2LDk1Nyk5eNsPHFxxoIwnpx4,4540
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siibra/commons.py,sha256=
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siibra/commons.py,sha256=EbFb3q7k2R6NY4pGFk89ApRjky_PeoE-UV6vdtUJa4s,25875
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siibra/configuration/__init__.py,sha256=-_Kuf0TfMEdFXiSCTAdcHUL_krA8-cxhJypSNNay53Q,752
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siibra/configuration/configuration.py,sha256=
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siibra/configuration/factory.py,sha256=
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siibra/configuration/configuration.py,sha256=ZZgQX_5PtOuDYFqFY9Zo84XLZAu-GKwpvPJFKmvld_c,7070
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siibra/configuration/factory.py,sha256=EGOQGxJxWIku8sP7PvZUhRE-Pv-jnFkjKkNx_ygfHKk,20547
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siibra/core/__init__.py,sha256=z22elfoi5_TscUb17-pBoGyfT_q9PQpvgOgSLEJe2WE,916
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siibra/core/atlas.py,sha256=dZkvQZRHeAPdt8MGh3oi9QyYf_QL8L8PY9PZ7WwPIiE,7807
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siibra/core/concept.py,sha256=dT8uyG_l3jnD9gmXg54G2kvbvwxVjmr-Qi2LetakqCI,9160
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@@ -11,45 +11,48 @@ siibra/core/parcellation.py,sha256=Eob_rMtxQTOcFFbWuE0dbRXfHM8ALaeDsNpoyD7tVOc,1
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siibra/core/region.py,sha256=P_WIC_TWAZmzrr1i4ZrKlj4y9IwHbXkdSSsRKF4W3Bw,32817
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siibra/core/relation_qualification.py,sha256=EUU9EPkV0mdCjGUU2hki1rQ5R5U4X2YoFmvwOirO2_E,3641
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siibra/core/space.py,sha256=dC225jhRFt0KlPtjKEEVre6X8HoDupsymEOrc7AdmmI,5774
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siibra/explorer/__init__.py,sha256=_9gCCp7P8AniGlztulrRyleIOEKcNZlBFVurtnI8GBM,40
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siibra/explorer/url.py,sha256=mUAFN7OHfLELfdqqJmSdAkmXJjKCv6Qh5RHtyxNQjfo,5868
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siibra/explorer/util.py,sha256=Z2ruicDL3S_qcxhHHW0GF1q5-r963tJpzgtQmAn8YSM,1424
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siibra/features/__init__.py,sha256=Y5q2M7HoToTcfAdO50jmnPGZybJOi5GyEcbxQRscJjo,1518
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siibra/features/anchor.py,sha256=
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siibra/features/feature.py,sha256=
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siibra/features/connectivity/__init__.py,sha256=
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siibra/features/connectivity/functional_connectivity.py,sha256=
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siibra/features/connectivity/regional_connectivity.py,sha256=
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siibra/features/anchor.py,sha256=lv_F_Ld3ovwd0krB1mxGDKs2ZyniN6tqsGjtk0Nx7IM,15289
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siibra/features/feature.py,sha256=pNxNtFJiOelp6DRQ-QO-cjSRUkKjLzxBb2Q_Xng6NjQ,30442
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siibra/retrieval/exceptions/__init__.py,sha256=_w996kp5rxuvi-_iLhrByrH2OtApxm_TykthkaQvKpo,874
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siibra-0.5a1.dist-info/METADATA,sha256=-0iiAEE8P8cFDhM6jjqAGGCf8VQ4vpBmd7cpapozqaI,9803
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siibra-0.5a1.dist-info/WHEEL,sha256=Xo9-1PvkuimrydujYJAjF7pCkriuXBpUPEjma1nZyJ0,92
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siibra-0.5a1.dist-info/top_level.txt,sha256=NF0OSGLL0li2qyC7MaU0iBB5Y9S09_euPpvisD0-8Hg,7
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