siibra 1.0a9__py3-none-any.whl → 1.0a14__py3-none-any.whl
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- siibra/VERSION +1 -1
- siibra/commons.py +44 -27
- siibra/configuration/factory.py +15 -16
- siibra/core/atlas.py +40 -16
- siibra/core/region.py +241 -38
- siibra/features/__init__.py +19 -8
- siibra/features/connectivity/functional_connectivity.py +1 -1
- siibra/features/connectivity/regional_connectivity.py +45 -3
- siibra/features/feature.py +65 -12
- siibra/features/image/image.py +3 -1
- siibra/features/tabular/bigbrain_intensity_profile.py +1 -1
- siibra/features/tabular/cell_density_profile.py +5 -3
- siibra/features/tabular/cortical_profile.py +79 -15
- siibra/features/tabular/gene_expression.py +111 -2
- siibra/features/tabular/layerwise_bigbrain_intensities.py +1 -1
- siibra/features/tabular/layerwise_cell_density.py +3 -1
- siibra/features/tabular/receptor_density_fingerprint.py +3 -1
- siibra/features/tabular/receptor_density_profile.py +3 -5
- siibra/features/tabular/regional_timeseries_activity.py +59 -10
- siibra/features/tabular/tabular.py +4 -2
- siibra/livequeries/bigbrain.py +34 -0
- siibra/retrieval/cache.py +14 -9
- siibra/retrieval/requests.py +30 -1
- siibra/volumes/parcellationmap.py +17 -21
- siibra/volumes/providers/__init__.py +1 -0
- siibra/volumes/providers/freesurfer.py +113 -0
- siibra/volumes/providers/neuroglancer.py +55 -25
- siibra/volumes/providers/nifti.py +14 -16
- siibra/volumes/sparsemap.py +4 -3
- siibra/volumes/volume.py +13 -15
- {siibra-1.0a9.dist-info → siibra-1.0a14.dist-info}/METADATA +1 -1
- {siibra-1.0a9.dist-info → siibra-1.0a14.dist-info}/RECORD +35 -34
- {siibra-1.0a9.dist-info → siibra-1.0a14.dist-info}/WHEEL +1 -1
- {siibra-1.0a9.dist-info → siibra-1.0a14.dist-info}/LICENSE +0 -0
- {siibra-1.0a9.dist-info → siibra-1.0a14.dist-info}/top_level.txt +0 -0
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@@ -15,7 +15,7 @@
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from . import provider as _provider
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from ...commons import logger
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from ...commons import logger, resample_img_to_img
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from ...retrieval import requests
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from ...locations import pointset, boundingbox as _boundingbox
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@@ -108,11 +108,9 @@ class NiftiProvider(_provider.VolumeProvider, srctype="nii"):
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return bbox
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def _merge_fragments(self) -> nib.Nifti1Image:
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# TODO this only performs nearest neighbor interpolation, optimized for float types.
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bbox = self.get_boundingbox(clip=False, background=0.0)
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num_conflicts = 0
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result = None
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for loader in self._img_loaders.values():
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img = loader()
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if result is None:
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@@ -120,25 +118,25 @@ class NiftiProvider(_provider.VolumeProvider, srctype="nii"):
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s0 = np.identity(4)
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s0[:3, -1] = list(bbox.minpoint.transform(np.linalg.inv(img.affine)))
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result_affine = np.dot(img.affine, s0) # adjust global bounding box offset to get global affine
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voxdims = np.asanyarray(
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voxdims = np.asanyarray(np.ceil(
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bbox.transform(np.linalg.inv(result_affine)).shape
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), dtype="int")
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result_arr = np.zeros(voxdims, dtype=img.dataobj.dtype)
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result = nib.Nifti1Image(dataobj=result_arr, affine=result_affine)
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) + .5).astype('int'),
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4, axis=0
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)
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num_conflicts += np.count_nonzero(result_arr[Xt, Yt, Zt])
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result_arr[Xt, Yt, Zt] = arr[Xs, Ys, Zs]
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# resample to merge template and update it
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resampled_img = resample_img_to_img(source_img=img, target_img=result)
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arr = np.asanyarray(resampled_img.dataobj)
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nonzero_voxels = arr != 0
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num_conflicts += np.count_nonzero(result_arr[nonzero_voxels])
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result_arr[nonzero_voxels] = arr[nonzero_voxels]
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if num_conflicts > 0:
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num_voxels = np.count_nonzero(result_arr)
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logger.warning(
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logger.warning(
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f"Merging fragments required to overwrite {num_conflicts} "
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f"conflicting voxels ({num_conflicts / num_voxels * 100.:2.1f}%)."
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)
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return result
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siibra/volumes/sparsemap.py
CHANGED
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@@ -20,6 +20,7 @@ from ..commons import MapIndex, logger, connected_components, siibra_tqdm
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from ..locations import boundingbox
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from ..retrieval import cache
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from ..retrieval.repositories import ZipfileConnector, GitlabConnector
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from ..exceptions import InsufficientArgumentException, ExcessiveArgumentException
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from os import path, rename, makedirs
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from zipfile import ZipFile, ZIP_DEFLATED
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@@ -390,7 +391,7 @@ class SparseMap(parcellationmap.Map):
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assert length == 1
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except AssertionError:
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if length > 1:
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raise
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raise ExcessiveArgumentException(
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"One and only one of region_or_index, region, index can be defined for fetch"
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)
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# user can provide no arguments, which assumes one and only one volume present
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assert len(self) == 1
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volidx = 0
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except AssertionError:
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raise
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raise InsufficientArgumentException(
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f"{self.__class__.__name__} provides {len(self)} volumes. "
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"Specify 'region' or 'index' for fetch() to identify one."
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)
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"""
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Assign an image volume to this sparse map.
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Parameters
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Parameters
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-----------
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queryvolume: Volume
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the volume to be compared with maps
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siibra/volumes/volume.py
CHANGED
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from ..retrieval import requests
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from ..core import space as _space, structure
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from ..locations import location, point, pointset, boundingbox
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from ..commons import
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from ..commons import resample_img_to_img, siibra_tqdm
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from ..exceptions import NoMapAvailableError, SpaceWarpingFailedError
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from nibabel import Nifti1Image
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@@ -52,7 +52,9 @@ class Volume(location.Location):
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"neuroglancer/precompmesh",
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"neuroglancer/precompmesh/surface",
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"gii-mesh",
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"gii-label"
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"gii-label",
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"freesurfer-annot",
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"zip/freesurfer-annot",
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]
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SUPPORTED_FORMATS = IMAGE_FORMATS + MESH_FORMATS
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assert srctype not in self._providers
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self._providers[srctype] = provider
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if len(self._providers) == 0:
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logger.debug(f"No provider for volume {
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logger.debug(f"No provider for volume {name}")
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def __hash__(self):
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If the volume provider does not have a bounding box calculator.
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"""
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fmt = fetch_kwargs.get("format")
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if fmt in self.
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if (fmt is not None) and (fmt not in self.formats):
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raise ValueError(
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f"Requested format {fmt} is not available as provider of "
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"this volume. See `volume.formats` for possible options."
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bbox.minpoint._space_cached = self.space
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bbox.maxpoint._space_cached = self.space
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except NotImplementedError as e:
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logger.info(e)
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continue
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return bbox
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raise RuntimeError(f"No bounding box specified by any volume provider of {str(self)}")
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v1 = self.fetch(format=format, **fetch_kwargs)
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v2 = other.fetch(format=format, **fetch_kwargs)
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arr1 = np.asanyarray(v1.dataobj)
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arr2 =
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arr2 = np.asanyarray(resample_img_to_img(v2, v1).dataobj)
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pointwise_min = np.minimum(arr1, arr2)
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fwd_args = {k: v for k, v in kwargs.items() if k != "format"}
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try:
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if fmt
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if fmt in ["gii-label", "freesurfer-annot", "zip/freesurfer-annot"]:
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labels = self._providers[fmt].fetch(**fwd_args)
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assert all(v.space == space for v in volumes), "Cannot merge volumes from different spaces."
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template_img = space.get_template().fetch(**fetch_kwargs)
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merged_array = np.zeros(template_img.shape, dtype='uint8')
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for i, vol in siibra_tqdm(
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return from_array(
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Metadata-Version: 2.1
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Name: siibra
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Version: 1.
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Version: 1.0a14
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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=WbSXoTCdjXhUGy1ETxp0o0n2LBufojSia_MjjoGVmVI,7
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siibra/__init__.py,sha256=01VIBU4L5NLBTNFoAUskc7brJ-8TanNwl1Ejtl47YGI,4463
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siibra/commons.py,sha256=
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siibra/commons.py,sha256=saHGFqOe2fYPhQJE6u0Ivo11F1jI9Irg8uL3_sliwN8,28820
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siibra/exceptions.py,sha256=bs79_vEK9Dz4TntJnD66L_bJ5Tt4Z0mO9GXQ4f9kNQE,1109
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siibra/configuration/__init__.py,sha256=-_Kuf0TfMEdFXiSCTAdcHUL_krA8-cxhJypSNNay53Q,752
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siibra/configuration/configuration.py,sha256=p2R0dxD8HdvrwHokXuTCrVgz9DvXmEmHkxRL_oT0VRI,7263
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siibra/configuration/factory.py,sha256=
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siibra/configuration/factory.py,sha256=4IGayJJ47PXa9jdwnmcrPLeYa0Pmu1EJehG4LR-smbw,21110
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siibra/core/__init__.py,sha256=YQkeqGqpOT3aH-PPHeGb1kxSyMbgR3ZHqDCy2I0Zlsk,735
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siibra/core/assignment.py,sha256=pWkivLA54NrX3j21E_YxSX9_S70MrGuGq_6aQQ5IBB4,3819
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siibra/core/atlas.py,sha256=
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siibra/core/atlas.py,sha256=XZ0vy6_l-kuiNF6KYs1PpTk2XwBK-aMY6cUKUnLYb3A,8299
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siibra/core/concept.py,sha256=zL220pIYmqWhEZNMo01p2o0IC37rjApdNd1_dPmbNvU,10496
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siibra/core/parcellation.py,sha256=iIESwMVg-YQLkCn7KSj8LZl1QDttMxJOVGoRv7DL2kU,13873
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siibra/core/region.py,sha256=
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siibra/core/region.py,sha256=2tDlrjoVKTz2dO4Y3Q2GAVPIWbZuDnGc04iEOPLPveM,44049
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siibra/core/space.py,sha256=TvOvcBKextuRrptdFKU-je6w5g5lqK0I_Wga73jd0zk,4517
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siibra/core/structure.py,sha256=cZFR_eyXt6j2KT6ohiOQFnjmntFVcvA4k2FpSinPzWI,4498
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siibra/experimental/__init__.py,sha256=s4bEYpMO4Ox-Xlx3FdnRUNKYs0mTHz5Hu4VnfNXpgxU,791
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siibra/explorer/__init__.py,sha256=9TYF4i5o3guwqDtsQ7mV6MLVmKQIFG0AwxN8PA_6ctw,781
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siibra/explorer/url.py,sha256=kxfrfz8v6gl_Z2Vu4jJkb54WYk8reFJxf3TXhJGu2VQ,6421
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siibra/explorer/util.py,sha256=8Ap0tnVFk1LOzD70o-EUbHk6HPLAG4SLaDrvrEzaJGk,2083
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siibra/features/__init__.py,sha256=
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siibra/features/__init__.py,sha256=Jd19RXFBuVemhF6AtrhOG4luocYGauA0FjnaEZdyaa8,3970
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siibra/features/anchor.py,sha256=cp5cu-tJceenbJESXLe3DXhmjtdhdyTN0KYOIXDkhmU,9068
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siibra/features/feature.py,sha256=
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siibra/features/feature.py,sha256=bA3ME8Anc_rAa6g8cdagDFG5nfAOUud2t3YPinMPbwE,34492
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siibra/features/connectivity/__init__.py,sha256=XU6w7kX6lN_fZLt0TFGqg39Z9FCfbcotSR79p-JhLV4,1161
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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/connectivity/functional_connectivity.py,sha256=USnlse_qmThBxqINnv9EmecQewxuOvK3Mzy3DqbQBzc,2122
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siibra/locations/__init__.py,sha256=rp-a39N3mVTMMuQOP4j6C_R_uziMOaPkIKzTJZuLVUM,3316
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siibra-1.0a14.dist-info/METADATA,sha256=18r8gJfzqz4ujV6IqivYuVBERmmYb4cRKiriDg1Z96A,8432
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siibra-1.0a14.dist-info/WHEEL,sha256=y4mX-SOX4fYIkonsAGA5N0Oy-8_gI4FXw5HNI1xqvWg,91
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siibra-1.0a14.dist-info/top_level.txt,sha256=NF0OSGLL0li2qyC7MaU0iBB5Y9S09_euPpvisD0-8Hg,7
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