{"name":"napari-hdf5-labels-io","display_name":"napari-hdf5-labels-io","visibility":"public","icon":"","categories":[],"schema_version":"0.2.0","on_activate":null,"on_deactivate":null,"contributions":{"commands":[{"id":"napari-hdf5-labels-io.napari_write_image","title":"napari_write_image","python_name":"napari_hdf5_labels_io._writer:napari_write_image","short_title":null,"category":null,"icon":null,"enablement":null},{"id":"napari-hdf5-labels-io.napari_write_labels","title":"napari_write_labels","python_name":"napari_hdf5_labels_io._writer:napari_write_labels","short_title":null,"category":null,"icon":null,"enablement":null},{"id":"napari-hdf5-labels-io.napari_write_points","title":"napari_write_points","python_name":"napari_hdf5_labels_io._writer:napari_write_points","short_title":null,"category":null,"icon":null,"enablement":null}],"readers":[{"command":"napari-hdf5-labels-io.h5_to_napari","filename_patterns":["*"],"accepts_directories":true}],"writers":[{"command":"napari-hdf5-labels-io.napari_write_image","layer_types":["image"],"filename_extensions":[],"display_name":"image"},{"command":"napari-hdf5-labels-io.napari_write_labels","layer_types":["labels"],"filename_extensions":[],"display_name":"labels"},{"command":"napari-hdf5-labels-io.napari_write_points","layer_types":["points"],"filename_extensions":[],"display_name":"points"}],"widgets":null,"sample_data":null,"themes":null,"menus":{},"submenus":null,"keybindings":null,"configuration":[]},"package_metadata":{"metadata_version":"2.1","name":"napari-hdf5-labels-io","version":"0.3.dev16","dynamic":null,"platform":["UNKNOWN"],"supported_platform":null,"summary":"Napari plugin to store set of layers in a .h5 file. Label layer are stored in a sparse representation.","description":"# napari-hdf5-labels-io\n\n[![License](https://img.shields.io/pypi/l/napari-hdf5-labels-io.svg?color=green)](https://github.com/yapic/napari-hdf5-labels-io/raw/master/LICENSE)\n[![PyPI](https://img.shields.io/pypi/v/napari-hdf5-labels-io.svg?color=green)](https://pypi.org/project/napari-hdf5-labels-io)\n[![Python Version](https://img.shields.io/pypi/pyversions/napari-hdf5-labels-io.svg?color=green)](https://python.org)\n[![tests](https://github.com/yapic/napari-hdf5-labels-io/workflows/tests/badge.svg)](https://github.com/yapic/napari-hdf5-labels-io/actions)\n[![codecov](https://codecov.io/gh/yapic/napari-hdf5-labels-io/branch/master/graph/badge.svg)](https://codecov.io/gh/yapic/napari-hdf5-labels-io)\n\nnapari plugin to store napari projects in a .h5 file. Label layer are stored in a sparse representation (COO list).\n\n----------------------------------\n\nThis [napari] plugin was generated with [Cookiecutter] using with [@napari]'s [cookiecutter-napari-plugin] template.\n\n\n\n## Description\n\nThis napari plugin provides a writer and reader to store existing layers in the current napari window, all the metadata is stored as well in a HDF5 file. All the stored preferences are included when a project file is opened.\n\nLabel layers are stored in a coordinate list sparse representation with the [Sparse module](https://sparse.pydata.org/) to keep the project file size minimum when possible (aiming to implement this in other layers in the future).\n\n## HDF5 file architecture\n\nThe project file is a HDF5 generated with the [h5py module](https://docs.h5py.org). The file groups correspond to the different napari layer types and the layer metadata is stored as attributes of each layer.\n\nIn the case of the meta dictionary which is nested in the LayerData meta dictionary (napari IO), new keys are generated in the outer dictionary to use them as h5 dataset attributes. This nested dictionary architecture is reconstructed by the reader to ensure format compatibility.\n\n## Installation\n\nYou can install `napari-hdf5-labels-io` via [pip]:\n\n pip install napari-hdf5-labels-io\n\n## Contributing\n\nContributions are very welcome. Tests can be run with [tox], please ensure\nthe coverage at least stays the same before you submit a pull request.\n\n## License\n\nDistributed under the terms of the [GNU GPL v3.0] license,\n\"napari-hdf5-labels-io\" is free and open source software.\n\n## Issues\n\nIf you encounter any problems, please [file an issue] along with a detailed description.\n\n[napari]: https://github.com/napari/napari\n[Cookiecutter]: https://github.com/audreyr/cookiecutter\n[@napari]: https://github.com/napari\n[MIT]: http://opensource.org/licenses/MIT\n[BSD-3]: http://opensource.org/licenses/BSD-3-Clause\n[GNU GPL v3.0]: http://www.gnu.org/licenses/gpl-3.0.txt\n[GNU LGPL v3.0]: http://www.gnu.org/licenses/lgpl-3.0.txt\n[Apache Software License 2.0]: http://www.apache.org/licenses/LICENSE-2.0\n[Mozilla Public License 2.0]: https://www.mozilla.org/media/MPL/2.0/index.txt\n[cookiecutter-napari-plugin]: https://github.com/napari/cookiecutter-napari-plugin\n[file an issue]: https://github.com/yapic/napari-hdf5-labels-io/issues\n[napari]: https://github.com/napari/napari\n[tox]: https://tox.readthedocs.io/en/latest/\n[pip]: https://pypi.org/project/pip/\n[PyPI]: https://pypi.org/\n\n\n","description_content_type":"text/markdown","keywords":null,"home_page":"https://github.com/yapic/napari-hdf5-labels-io","download_url":null,"author":"Duway Nicolas Lesmes Leon, Pranjal Dhole","author_email":"dlesmesleon@hotmail.com, dhole.pranjal@gmail.com","maintainer":null,"maintainer_email":null,"license":"GNU GPL v3.0","classifier":["Development Status :: 4 - Beta","Intended Audience :: Developers","Framework :: napari","Topic :: Software Development :: Testing","Programming Language :: Python","Programming Language :: Python :: 3","Programming Language :: Python :: 3.7","Programming Language :: Python :: 3.8","Operating System :: OS Independent","License :: OSI Approved :: GNU General Public License v3 (GPLv3)"],"requires_dist":["napari-plugin-engine (>=0.1.4)","typing","numpy","sparse","h5py (==2.10.0)","zarr"],"requires_python":"<3.9","requires_external":null,"project_url":null,"provides_extra":null,"provides_dist":null,"obsoletes_dist":null},"npe1_shim":true}