.coveragerc
.gitignore
.readthedocs.yml
AUTHORS.txt
CHANGELOG.rst
CONTRIBUTING.md
LICENSE.txt
MANIFEST.in
Makefile
README.md
pyproject.toml
tox.ini
.github/workflows/sdist.yml
.github/workflows/tox.yml
ArchNGV.egg-info/PKG-INFO
ArchNGV.egg-info/SOURCES.txt
ArchNGV.egg-info/dependency_links.txt
ArchNGV.egg-info/entry_points.txt
ArchNGV.egg-info/requires.txt
ArchNGV.egg-info/top_level.txt
archngv/__init__.py
archngv/exceptions.py
archngv/testing.py
archngv/app/__init__.py
archngv/app/__main__.py
archngv/app/logger.py
archngv/app/ngv.py
archngv/app/utils.py
archngv/app/exemplar/launch.sbatch
archngv/app/exemplar/run.sh
archngv/app/exemplar/bioname/MANIFEST.yaml
archngv/app/exemplar/bioname/astrocyte_gap_junction_recipe.xml
archngv/app/exemplar/bioname/cluster.yaml
archngv/app/exemplar/bioname/er_data.json
archngv/app/exemplar/bioname/tns_context.json
archngv/app/exemplar/bioname/tns_distributions.json
archngv/app/exemplar/bioname/tns_parameters.json
archngv/app/snakemake/Snakefile
archngv/building/__init__.py
archngv/building/checks.py
archngv/building/config.py
archngv/building/exporters.py
archngv/building/legacy.py
archngv/building/microdomains.py
archngv/building/types.py
archngv/building/cell_placement/__init__.py
archngv/building/cell_placement/atlas.py
archngv/building/cell_placement/energy.py
archngv/building/cell_placement/export.py
archngv/building/cell_placement/generation.py
archngv/building/cell_placement/pattern.py
archngv/building/cell_placement/positions.py
archngv/building/cell_placement/potentials.py
archngv/building/cell_placement/soma_generation.py
archngv/building/connectivity/__init__.py
archngv/building/connectivity/glialglial.py
archngv/building/connectivity/gliovascular.py
archngv/building/connectivity/neuroglial_generation.py
archngv/building/connectivity/detail/__init__.py
archngv/building/connectivity/detail/gliovascular_generation/__init__.py
archngv/building/connectivity/detail/gliovascular_generation/check.py
archngv/building/connectivity/detail/gliovascular_generation/graph_connect.py
archngv/building/connectivity/detail/gliovascular_generation/graph_reachout.py
archngv/building/connectivity/detail/gliovascular_generation/graph_targeting.py
archngv/building/connectivity/detail/gliovascular_generation/surface_intersection.py
archngv/building/endfeet_reconstruction/__init__.py
archngv/building/endfeet_reconstruction/area_generation.py
archngv/building/endfeet_reconstruction/area_mapping.py
archngv/building/endfeet_reconstruction/area_shrinking.py
archngv/building/endfeet_reconstruction/fast_marching_method.py
archngv/building/endfeet_reconstruction/gliovascular_properties.py
archngv/building/endfeet_reconstruction/groups.py
archngv/building/morphology_synthesis/__init__.py
archngv/building/morphology_synthesis/annotation.py
archngv/building/morphology_synthesis/data_extraction.py
archngv/building/morphology_synthesis/data_structures.py
archngv/building/morphology_synthesis/domain_boundary.py
archngv/building/morphology_synthesis/domain_orientation.py
archngv/building/morphology_synthesis/endfoot_compartment.py
archngv/building/morphology_synthesis/endoplasmic_reticulum.py
archngv/building/morphology_synthesis/full_astrocyte.py
archngv/building/morphology_synthesis/neuroglial_properties.py
archngv/building/morphology_synthesis/perimeters.py
archngv/building/morphology_synthesis/properties.py
archngv/building/morphology_synthesis/tns_wrapper.py
archngv/core/__init__.py
archngv/core/circuit.py
archngv/core/constants.py
archngv/core/cut_points.py
archngv/core/datasets.py
archngv/core/sonata_readers.py
archngv/core/structures.py
archngv/core/pytouchreader/__init__.py
archngv/core/pytouchreader/_touches.py
archngv/core/pytouchreader/caching.py
archngv/core/pytouchreader/utils.py
archngv/spatial/__init__.py
archngv/spatial/bounding_box.py
archngv/spatial/collision.py
archngv/spatial/gjk_algorithm.py
archngv/spatial/hashmap.py
archngv/spatial/inclusion.py
archngv/spatial/shapes.py
archngv/spatial/support_functions.py
archngv/spatial/uniform_grid.py
archngv/spatial/utils.py
archngv/utils/__init__.py
archngv/utils/binning.py
archngv/utils/combinatronics.py
archngv/utils/decorators.py
archngv/utils/functional.py
archngv/utils/generics.py
archngv/utils/geometry.py
archngv/utils/linear_algebra.py
archngv/utils/natural_breaks.py
archngv/utils/ndimage.py
archngv/utils/ngons.py
archngv/utils/projections.py
archngv/utils/statistics.py
doc/source/bioname.rst
doc/source/conf.py
doc/source/index.rst
doc/source/tutorial.rst
notebooks/microdomain_orientations_testing.ipynb
notebooks/microdomains.h5
notebooks/analysis/analytics.py
notebooks/analysis/circuit_interface.py
notebooks/analysis/circuit_properties.py
notebooks/analysis/common.py
notebooks/analysis/data_prediction.ipynb
notebooks/analysis/data_prediction.py
notebooks/analysis/data_validation.ipynb
notebooks/analysis/data_validation.json
notebooks/analysis/data_validation.py
notebooks/analysis/organizational_prefiction.py
notebooks/analysis/organizational_validation.py
notebooks/analysis/plots_globals.py
notebooks/analysis/segment_index.py
scripts/astrocyte_data_interface.py
scripts/launch.sbatch
scripts/test_run.sh
scripts/mock_datasets/create_test_datasets.py
specifications/output.yaml
tests/functional/input_data_builder.py
tests/functional/run.sh
tests/functional/test_build.py
tests/functional/test_circuit_integrity.py
tests/functional/test_specifications.py
tests/functional/bioname/MANIFEST.yaml
tests/functional/bioname/astrocyte_gap_junction_recipe.xml
tests/functional/bioname/cluster.yaml
tests/functional/bioname/er_data.json
tests/functional/bioname/tns_context.json
tests/functional/bioname/tns_distributions.json
tests/functional/bioname/tns_parameters.json
tests/functional/data/atlas/[density]astrocytes.nrrd
tests/functional/data/atlas/brain_regions.nrrd
tests/functional/data/atlas/hierarchy.json
tests/functional/data/atlas/vasculature.h5
tests/functional/data/atlas/vasculature.mtl
tests/functional/data/atlas/vasculature.obj
tests/functional/data/circuit/circuit_config.json
tests/functional/data/circuit/edges.h5
tests/functional/data/circuit/nodes.h5
tests/functional/data/circuit/spatial_index_synapses/index.spi
tests/functional/data/circuit/spatial_index_synapses/meta_data.json
tests/functional/expected/endfeet_meshes.h5
tests/functional/expected/microdomains.h5
tests/functional/expected/ngv_prepared_tetrahedral_mesh.geo
tests/functional/expected/ngv_refined_tetrahedral_mesh.msh
tests/functional/expected/morphologies/GLIA_0000000000000.h5
tests/functional/expected/morphologies/GLIA_0000000000001.h5
tests/functional/expected/morphologies/GLIA_0000000000002.h5
tests/functional/expected/morphologies/GLIA_0000000000003.h5
tests/functional/expected/morphologies/GLIA_0000000000004.h5
tests/functional/expected/morphologies/_DONE
tests/functional/expected/sonata.tmp/edges/gliovascular.connectivity.h5
tests/functional/expected/sonata.tmp/edges/neuroglial.connectivity.h5
tests/functional/expected/sonata.tmp/nodes/glia.emodels.h5
tests/functional/expected/sonata.tmp/nodes/glia.somata.h5
tests/functional/expected/sonata/networks/edges/glialglial/edges.h5
tests/functional/expected/sonata/networks/edges/gliovascular/edges.h5
tests/functional/expected/sonata/networks/edges/neuroglial/edges.h5
tests/functional/expected/sonata/networks/nodes/astrocytes/nodes.h5
tests/functional/expected/sonata/networks/nodes/vasculature/nodes.h5
tests/unit/__init__.py
tests/unit/app/__init__.py
tests/unit/app/test_ngv.py
tests/unit/app/test_utils.py
tests/unit/app/data/bioname/MANIFEST.yaml
tests/unit/app/data/bioname/astrocyte_gap_junction_recipe.xml
tests/unit/app/data/bioname/cluster.yaml
tests/unit/app/data/bioname/er_data.json
tests/unit/app/data/bioname/tns_context.json
tests/unit/app/data/bioname/tns_distributions.json
tests/unit/app/data/bioname/tns_parameters.json
tests/unit/app/data/external/atlas/[density]astrocytes.nrrd
tests/unit/app/data/external/atlas/[mask]H.nrrd
tests/unit/app/data/external/atlas/brain_regions.nrrd
tests/unit/app/data/external/atlas/hierarchy.json
tests/unit/app/data/external/atlas/vasculature.h5
tests/unit/app/data/external/atlas/vasculature.mtl
tests/unit/app/data/external/atlas/vasculature.obj
tests/unit/app/data/external/circuit/circuit_config.json
tests/unit/app/data/external/circuit/edges.h5
tests/unit/app/data/external/circuit/nodes.h5
tests/unit/app/data/external/circuit/spatial_index_synapses/index.spi
tests/unit/app/data/external/circuit/spatial_index_synapses/meta_data.json
tests/unit/app/data/frozen-build/endfeet_meshes.h5
tests/unit/app/data/frozen-build/microdomains.h5
tests/unit/app/data/frozen-build/ngv_config.json
tests/unit/app/data/frozen-build/connectome/touches/SaveState.bin
tests/unit/app/data/frozen-build/connectome/touches/Slices.5.txt
tests/unit/app/data/frozen-build/connectome/touches/_SUCCESS
tests/unit/app/data/frozen-build/connectome/touches/touches.0
tests/unit/app/data/frozen-build/connectome/touches/touchesData.0
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tests/unit/app/data/frozen-build/morphologies/GLIA_0000000000001.h5
tests/unit/app/data/frozen-build/morphologies/GLIA_0000000000002.h5
tests/unit/app/data/frozen-build/morphologies/GLIA_0000000000003.h5
tests/unit/app/data/frozen-build/morphologies/GLIA_0000000000004.h5
tests/unit/app/data/frozen-build/sonata.tmp/edges/gliovascular.connectivity.h5
tests/unit/app/data/frozen-build/sonata.tmp/edges/neuroglial.connectivity.h5
tests/unit/app/data/frozen-build/sonata.tmp/nodes/glia.emodels.h5
tests/unit/app/data/frozen-build/sonata.tmp/nodes/glia.somata.h5
tests/unit/app/data/frozen-build/sonata/edges/glialglial.h5
tests/unit/app/data/frozen-build/sonata/edges/gliovascular.h5
tests/unit/app/data/frozen-build/sonata/edges/neuroglial.h5
tests/unit/app/data/frozen-build/sonata/nodes/glia.h5
tests/unit/app/data/frozen-build/sonata/nodes/vasculature.h5
tests/unit/app/data/frozen-build/spatial_index_synapses/index.spi
tests/unit/app/data/frozen-build/spatial_index_synapses/meta_data.json
tests/unit/building/__init__.py
tests/unit/building/test_checks.py
tests/unit/building/test_legacy.py
tests/unit/building/test_microdomains.py
tests/unit/building/cell_placement/__init__.py
tests/unit/building/cell_placement/test_export.py
tests/unit/building/cell_placement/test_generation.py
tests/unit/building/cell_placement/test_pattern.py
tests/unit/building/cell_placement/test_potentials.py
tests/unit/building/connectivity/__init__.py
tests/unit/building/connectivity/test_glialglial.py
tests/unit/building/connectivity/test_graph_targeting.py
tests/unit/building/connectivity/test_maximum_reachout.py
tests/unit/building/data/legacy/add_astrocyte_segment_center_property/expected_astrocyte_centers.npy
tests/unit/building/data/legacy/add_astrocyte_segment_center_property/glia.h5
tests/unit/building/data/legacy/add_astrocyte_segment_center_property/neuroglial.h5
tests/unit/building/data/legacy/add_astrocyte_segment_center_property/morphologies/GLIA_0000000000000.h5
tests/unit/building/data/legacy/add_astrocyte_segment_center_property/morphologies/GLIA_0000000000001.h5
tests/unit/building/data/legacy/add_astrocyte_segment_center_property/morphologies/GLIA_0000000000002.h5
tests/unit/building/data/legacy/add_astrocyte_segment_center_property/morphologies/GLIA_0000000000003.h5
tests/unit/building/data/legacy/add_astrocyte_segment_center_property/morphologies/GLIA_0000000000004.h5
tests/unit/building/data/legacy/convert_endfeet_to_generic_format/endfeet_areas.h5
tests/unit/building/data/legacy/convert_microdomains_to_generic_format/microdomains.h5
tests/unit/building/data/legacy/merge_configuration_files/old_bioname/MANIFEST.yaml
tests/unit/building/data/legacy/merge_configuration_files/old_bioname/cell_placement.yaml
tests/unit/building/data/legacy/merge_configuration_files/old_bioname/endfeet_area.yaml
tests/unit/building/data/legacy/merge_configuration_files/old_bioname/gliovascular_connectivity.yaml
tests/unit/building/data/legacy/merge_configuration_files/old_bioname/microdomains.yaml
tests/unit/building/data/legacy/merge_configuration_files/old_bioname/synthesis.yaml
tests/unit/building/data/legacy/merge_microdomain_files/microdomains.h5
tests/unit/building/data/legacy/merge_microdomain_files/overlapping_microdomains.h5
tests/unit/building/endfeet_reconstruction/__init__.py
tests/unit/building/endfeet_reconstruction/test_area_generation.py
tests/unit/building/endfeet_reconstruction/test_area_mapping.py
tests/unit/building/endfeet_reconstruction/test_area_shrinking.py
tests/unit/building/endfeet_reconstruction/test_endfeet_reconstruction_integration.py
tests/unit/building/endfeet_reconstruction/test_fmm_growing.py
tests/unit/building/endfeet_reconstruction/test_groups.py
tests/unit/building/endfeet_reconstruction/utils.py
tests/unit/building/endfeet_reconstruction/data/cube-minimal.obj
tests/unit/building/endfeet_reconstruction/data/plane_10x10.obj
tests/unit/building/exporters/__init__.py
tests/unit/building/exporters/test_edge_population.py
tests/unit/building/exporters/test_grouped_properties.py
tests/unit/building/exporters/data/gliovascular.h5
tests/unit/building/morphology_synthesis/__init__.py
tests/unit/building/morphology_synthesis/test_annotation.py
tests/unit/building/morphology_synthesis/test_domain_boundary.py
tests/unit/building/morphology_synthesis/test_domain_orientation.py
tests/unit/building/morphology_synthesis/test_endfoot_compartment.py
tests/unit/building/morphology_synthesis/test_full_astrocyte.py
tests/unit/building/morphology_synthesis/test_perimeters.py
tests/unit/core/test_data_endfeetome.py
tests/unit/core/test_datasets.py
tests/unit/core/test_microdomain_tessellation.py
tests/unit/core/test_ngvcircuit.py
tests/unit/core/test_sonata_reader.py
tests/unit/core/test_vasculature.py
tests/unit/core/utils.py
tests/unit/core/data/circuit_config.json
tests/unit/core/data/create_datasets.py
tests/unit/core/data/edges.h5
tests/unit/core/data/edges_fail.h5
tests/unit/core/data/endfeet_meshes.h5
tests/unit/core/data/glia.h5
tests/unit/core/data/glialglial.h5
tests/unit/core/data/gliovascular.h5
tests/unit/core/data/microdomains.h5
tests/unit/core/data/my_atlas.nrrd
tests/unit/core/data/neuroglial.h5
tests/unit/core/data/nodes.h5
tests/unit/core/data/overlapping_microdomains.h5
tests/unit/core/data/synaptic_data.h5
tests/unit/core/data/vasculature.h5
tests/unit/core/data/vasculature_mesh.obj
tests/unit/core/data/vasculature_new_spec.h5
tests/unit/core/data/vasculature_old_spec.h5
tests/unit/core/data/vasculature_sonata.h5
tests/unit/core/data/help/unittest_graph.dia
tests/unit/core/data/help/unittest_graph.png
tests/unit/core/data/morphologies/morph-A.swc
tests/unit/core/data/morphologies/morph-B.swc
tests/unit/core/data/morphologies/morph-C.swc
tests/unit/core/data/morphologies-astro/morph-A.h5
tests/unit/core/data/morphologies-astro/morph-B.h5
tests/unit/core/data/morphologies-astro/morph-C.h5
tests/unit/spatial/test_bounding_box.py
tests/unit/spatial/test_collision.py
tests/unit/spatial/test_hashmap.py
tests/unit/spatial/test_inclusion.py
tests/unit/spatial/test_shapes.py
tests/unit/spatial/test_utils.py
tests/unit/utils/__init__.py
tests/unit/utils/test_combinatronics.py
tests/unit/utils/test_functional.py
tests/unit/utils/test_generics.py
tests/unit/utils/test_geometry.py
tests/unit/utils/test_math.py
tests/unit/utils/test_natural_breaks.py
tests/unit/utils/test_ndimage.py
tests/unit/utils/test_ngons.py
tests/unit/utils/test_ngons_2.py
tests/unit/utils/test_projections.py
tests/unit/utils/test_statistics.py