siibra 0.5a2__py3-none-any.whl → 1.0.0a1__py3-none-any.whl
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- siibra/VERSION +1 -1
- siibra/__init__.py +20 -12
- siibra/commons.py +145 -90
- siibra/configuration/__init__.py +1 -1
- siibra/configuration/configuration.py +22 -17
- siibra/configuration/factory.py +177 -128
- siibra/core/__init__.py +1 -8
- siibra/core/{relation_qualification.py → assignment.py} +17 -14
- siibra/core/atlas.py +66 -35
- siibra/core/concept.py +81 -39
- siibra/core/parcellation.py +83 -67
- siibra/core/region.py +569 -263
- siibra/core/space.py +7 -39
- siibra/core/structure.py +111 -0
- siibra/exceptions.py +63 -0
- siibra/experimental/__init__.py +19 -0
- siibra/experimental/contour.py +61 -0
- siibra/experimental/cortical_profile_sampler.py +57 -0
- siibra/experimental/patch.py +98 -0
- siibra/experimental/plane3d.py +256 -0
- siibra/explorer/__init__.py +16 -0
- siibra/explorer/url.py +112 -52
- siibra/explorer/util.py +31 -9
- siibra/features/__init__.py +73 -8
- siibra/features/anchor.py +75 -196
- siibra/features/connectivity/__init__.py +1 -1
- siibra/features/connectivity/functional_connectivity.py +2 -2
- siibra/features/connectivity/regional_connectivity.py +99 -10
- siibra/features/connectivity/streamline_counts.py +1 -1
- siibra/features/connectivity/streamline_lengths.py +1 -1
- siibra/features/connectivity/tracing_connectivity.py +1 -1
- siibra/features/dataset/__init__.py +1 -1
- siibra/features/dataset/ebrains.py +3 -3
- siibra/features/feature.py +219 -110
- siibra/features/image/__init__.py +1 -1
- siibra/features/image/image.py +21 -13
- siibra/features/image/sections.py +1 -1
- siibra/features/image/volume_of_interest.py +1 -1
- siibra/features/tabular/__init__.py +1 -1
- siibra/features/tabular/bigbrain_intensity_profile.py +24 -13
- siibra/features/tabular/cell_density_profile.py +111 -69
- siibra/features/tabular/cortical_profile.py +82 -16
- siibra/features/tabular/gene_expression.py +117 -6
- siibra/features/tabular/layerwise_bigbrain_intensities.py +7 -9
- siibra/features/tabular/layerwise_cell_density.py +9 -24
- siibra/features/tabular/receptor_density_fingerprint.py +11 -6
- siibra/features/tabular/receptor_density_profile.py +12 -15
- siibra/features/tabular/regional_timeseries_activity.py +74 -18
- siibra/features/tabular/tabular.py +17 -8
- siibra/livequeries/__init__.py +1 -7
- siibra/livequeries/allen.py +139 -77
- siibra/livequeries/bigbrain.py +104 -128
- siibra/livequeries/ebrains.py +7 -4
- siibra/livequeries/query.py +1 -2
- siibra/locations/__init__.py +32 -25
- siibra/locations/boundingbox.py +153 -127
- siibra/locations/location.py +45 -80
- siibra/locations/point.py +97 -83
- siibra/locations/pointcloud.py +349 -0
- siibra/retrieval/__init__.py +1 -1
- siibra/retrieval/cache.py +107 -13
- siibra/retrieval/datasets.py +9 -14
- siibra/retrieval/exceptions/__init__.py +2 -1
- siibra/retrieval/repositories.py +147 -53
- siibra/retrieval/requests.py +64 -29
- siibra/vocabularies/__init__.py +2 -2
- siibra/volumes/__init__.py +7 -9
- siibra/volumes/parcellationmap.py +396 -253
- siibra/volumes/providers/__init__.py +20 -0
- siibra/volumes/providers/freesurfer.py +113 -0
- siibra/volumes/{gifti.py → providers/gifti.py} +29 -18
- siibra/volumes/{neuroglancer.py → providers/neuroglancer.py} +204 -92
- siibra/volumes/{nifti.py → providers/nifti.py} +64 -44
- siibra/volumes/providers/provider.py +107 -0
- siibra/volumes/sparsemap.py +159 -260
- siibra/volumes/volume.py +720 -152
- {siibra-0.5a2.dist-info → siibra-1.0.0a1.dist-info}/METADATA +25 -28
- siibra-1.0.0a1.dist-info/RECORD +84 -0
- {siibra-0.5a2.dist-info → siibra-1.0.0a1.dist-info}/WHEEL +1 -1
- siibra/locations/pointset.py +0 -198
- siibra-0.5a2.dist-info/RECORD +0 -74
- {siibra-0.5a2.dist-info → siibra-1.0.0a1.dist-info}/LICENSE +0 -0
- {siibra-0.5a2.dist-info → siibra-1.0.0a1.dist-info}/top_level.txt +0 -0
siibra/vocabularies/__init__.py
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# Copyright 2018-
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# Copyright 2018-2024
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# Institute of Neuroscience and Medicine (INM-1), Forschungszentrum Jülich GmbH
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# Licensed under the Apache License, Version 2.0 (the "License");
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with open(runtime_path('gene_names.json'), 'r') as f:
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_gene_names = json.load(f)
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GENE_NAMES = InstanceTable
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GENE_NAMES = InstanceTable(
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elements={
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k: {'symbol': k, 'description': v}
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for k, v in _gene_names.items()
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siibra/volumes/__init__.py
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# Copyright 2018-
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# Copyright 2018-2024
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# Institute of Neuroscience and Medicine (INM-1), Forschungszentrum Jülich GmbH
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# Licensed under the Apache License, Version 2.0 (the "License");
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# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
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# See the License for the specific language governing permissions and
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# limitations under the License.
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"""Package handling variety of volumes"""
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"""Package handling variety of volumes and volume operations"""
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from .parcellationmap import Map
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from .
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from .
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from .gifti import GiftiSurfaceLabeling, GiftiMesh
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from .providers import provider
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from .volume import from_array, from_file, from_pointcloud, from_nifti, Volume
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_ = Map.registry()
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from ..commons import logger
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from typing import List, Union
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import numpy as np
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