Metadata-Version: 2.1
Name: atlas-direction-vectors
Version: 0.1.3
Summary: Commands to compute direction vectors in volumetric brain regions. Direction vectors are 3D unit vectors associated to voxels of a brain region. They represent the directions of the fiber tracts.
Home-page: https://github.com/BlueBrain/atlas-direction-vectors
Author: Blue Brain Project, EPFL
License: Apache-2
Download-URL: https://github.com/BlueBrain/atlas-direction-vectors
Description: .. image:: atlas-direction-vectors.jpg
        
        Overview
        =========
        
        This project contains the commands which create direction vectors for several brain regions including the cerebellum, the isocortex, and the thalamus of the AIBS P56 mouse brain.
        
        Direction vectors are 3D unit vectors associated to voxels of a brain region.
        They represent the directions of the fiber tracts and their streamlines are assumed to cross transversely layers in laminar brain regions.
        
        Direction vectors are used in placement-algorithm to set cells orientations.
        
        Direction vectors are also used to compute placement hints and split layer 2/3 of the AIBS mouse isocortex.
        
        After installation, you can display the available command lines with the following ``bash`` command:
        
        .. code-block:: bash
        
            atlas-direction-vectors --help
        
        Installation
        ============
        
        .. code-block:: bash
        
            pip install atlas-direction-vectors
        
        Examples
        ========
        
        Direction Vectors
        -----------------
        
        Get the required input files:
        
        .. code-block:: bash
        
           mkdir -p data/ccfv3
        
           # hierarchy file:
           curl -o data/1.json http://api.brain-map.org/api/v2/structure_graph_download/1.json
        
           # CCFv3 annotation volume:
           curl -o data/ccfv3/annotation_25.nrrd http://download.alleninstitute.org/informatics-archive/current-release/mouse_ccf/annotation/ccf_2017/annotation_25.nrrd
        
        Run the code (note, depending on the resolution of the volume, this may require significant amounts of available RAM):
        
        .. code-block:: bash
        
            atlas-direction-vectors direction-vectors isocortex \
                --hierarchy-path data/1.json                    \
                --annotation-path data/ccfv3/annotation_25.nrrd \
                --algorithm shading-blur-gradient               \
                --output-path data/ccfv3/direction_vectors.nrrd
        
        Instructions for developers
        ===========================
        
        Run the following commands before submitting your code for review:
        
        .. code-block:: bash
        
            cd atlas-direction-vectors
            isort -l 100 --profile black atlas_direction_vectors tests setup.py
            black -l 100 atlas_direction_vectors tests setup.py
        
        These formatting operations will help you pass the linting check `testenv:lint` defined in `tox.ini`.
        
        Citation
        ========
        
        When you use this software, we kindly ask you to cite the following DOI:
        
        .. image:: https://zenodo.org/badge/451806460.svg
           :target: https://zenodo.org/badge/latestdoi/451806460
        
        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 © 2022 Blue Brain Project/EPFL
        
Platform: UNKNOWN
Classifier: Development Status :: 2 - Pre-Alpha
Classifier: Programming Language :: Python
Classifier: Programming Language :: Python :: 3
Classifier: Programming Language :: Python :: 3.7
Classifier: Programming Language :: Python :: 3.8
Classifier: Programming Language :: Python :: 3.9
Classifier: Programming Language :: Python :: 3.10
Requires-Python: >=3.7.0
Description-Content-Type: text/x-rst
Provides-Extra: tests
