Metadata-Version: 2.1
Name: voxcell
Version: 3.1.9
Summary: Voxcell is a small library to handle probability distributions that have a spatial component and to use them to build collection of cells in space.
Home-page: https://github.com/BlueBrain/voxcell
Author: Blue Brain Project, EPFL
License: Apache-2
Download-URL: https://github.com/BlueBrain/voxcell
Description: Overview
        ========
        
        This is a library to build circuits and atlases. It contains tools to handle
        
        * "traits fields" and collections and the logic to assign them.
        * volumetric data within NRRD files
        * Cell collection access / writer.
        * to build, transform and handle fields of vectors and orientations.
        * querying `Region hierarchy tree`, such as the one available from the `Allen Institute for Brain Science (AIBS)`_: `Mouse Brain Atlas Ontology's StructureGraph`_ (aka 1.json).
        
        Installation
        ============
        
        Install from PyPI:
        
        .. code-block:: bash
        
            pip install voxcell
        
        Or an editable install:
        
        .. code-block:: bash
        
            git clone https://github.com/BlueBrain/voxcell
            cd voxcell
            pip install -e .
        
        Examples
        ========
        
        To use the following examples, one must download an NRRD file and the Ontology Structure:
        
        .. code-block:: bash
        
            curl -o brain_regions.nrrd http://download.alleninstitute.org/informatics-archive/current-release/mouse_ccf/annotation/ccf_2017/annotation_100.nrrd
            curl -o hierarchy.json http://api.brain-map.org/api/v2/structure_graph_download/1.json
        
        One can open NRRD files, and perform operations on them:
        
        .. code-block:: python
        
            import voxcell
            voxels = voxcell.VoxelData.load_nrrd('brain_regions.nrrd')
            print(voxels.voxel_dimensions)  # prints array([100., 100., 100.], dtype=float32)
        
        One can also use the `Atlas` object to load at both the atlas and the hierarchy:
        
        .. code-block:: python
        
            import numpy as np
            from voxcell.nexus.voxelbrain import Atlas
            atlas = Atlas.open('.')
            brain_regions = atlas.load_data('brain_regions')
            rm = atlas.load_region_map()
            # count the number of voxels in the VIS region, and all its descendents
            ids = rm.find('VIS', 'acronym', with_descendants=True)
            np.count_nonzero(np.isin(brain_regions.raw, list(ids)))
        
        Citation
        ========
        
        When you use this software, we kindly ask you to cite the following DOI:
        
        .. image:: https://zenodo.org/badge/451807050.svg
           :target: https://zenodo.org/badge/latestdoi/451807050
           
        
        Acknowledgements
        ================
        
        The development of this software was supported by funding to the Blue Brain Project, a research center of the École polytechnique fédérale de Lausanne (EPFL), from the Swiss government’s ETH Board of the Swiss Federal Institutes of Technology.
        
        For license and authors, see LICENSE.txt and AUTHORS.txt respectively.
        
        Copyright (c) 2022-2024 Blue Brain Project/EPFL
        
        .. _`Allen Institute for Brain Science (AIBS)`: https://alleninstitute.org/what-we-do/brain-science/
        .. _`Mouse Brain Atlas Ontology's StructureGraph`: http://api.brain-map.org/api/v2/structure_graph_download/1.json
        
Platform: UNKNOWN
Classifier: Development Status :: 2 - Pre-Alpha
Classifier: Programming Language :: Python
Classifier: Programming Language :: Python :: 3
Classifier: Programming Language :: Python :: 3.8
Classifier: Programming Language :: Python :: 3.9
Classifier: Programming Language :: Python :: 3.10
Classifier: Programming Language :: Python :: 3.11
Requires-Python: >=3.8
Description-Content-Type: text/x-rst
Provides-Extra: docs
