{"name":"napari-caphid","display_name":"CAphid","visibility":"public","icon":"","categories":[],"schema_version":"0.2.0","on_activate":null,"on_deactivate":null,"contributions":{"commands":[{"id":"napari-caphid.get_reader","title":"Open data with CAphid","python_name":"napari_caphid._reader:napari_get_reader","short_title":null,"category":null,"icon":null,"enablement":null},{"id":"napari-caphid.write_multiple","title":"Save multi-layer data with CAphid","python_name":"napari_caphid._writer:write_multiple","short_title":null,"category":null,"icon":null,"enablement":null},{"id":"napari-caphid.write_single_image","title":"Save image data with CAphid","python_name":"napari_caphid._writer:write_single_image","short_title":null,"category":null,"icon":null,"enablement":null},{"id":"napari-caphid.make_process_func","title":"Update table","python_name":"napari_caphid._widget:process_func","short_title":null,"category":null,"icon":null,"enablement":null}],"readers":[{"command":"napari-caphid.get_reader","filename_patterns":["*.npy"],"accepts_directories":false}],"writers":[{"command":"napari-caphid.write_multiple","layer_types":["image*","labels*"],"filename_extensions":[],"display_name":""},{"command":"napari-caphid.write_single_image","layer_types":["image"],"filename_extensions":[".npy"],"display_name":""}],"widgets":[{"command":"napari-caphid.make_process_func","display_name":"Update table","autogenerate":false}],"sample_data":null,"themes":null,"menus":{},"submenus":null,"keybindings":null,"configuration":[]},"package_metadata":{"metadata_version":"2.1","name":"napari-caphid","version":"0.0.1","dynamic":null,"platform":null,"supported_platform":null,"summary":"Annotation of aphid and update table","description":"# napari-caphid\n\n[![License BSD-3](https://img.shields.io/pypi/l/napari-caphid.svg?color=green)](https://github.com/hereariim/napari-caphid/raw/main/LICENSE)\n[![PyPI](https://img.shields.io/pypi/v/napari-caphid.svg?color=green)](https://pypi.org/project/napari-caphid)\n[![Python Version](https://img.shields.io/pypi/pyversions/napari-caphid.svg?color=green)](https://python.org)\n[![tests](https://github.com/hereariim/napari-caphid/workflows/tests/badge.svg)](https://github.com/hereariim/napari-caphid/actions)\n[![codecov](https://codecov.io/gh/hereariim/napari-caphid/branch/main/graph/badge.svg)](https://codecov.io/gh/hereariim/napari-caphid)\n[![napari hub](https://img.shields.io/endpoint?url=https://api.napari-hub.org/shields/napari-caphid)](https://napari-hub.org/plugins/napari-caphid)\n\nAnnotation of aphid and update table\n\n----------------------------------\n\nNapari-caphid was developed for updating table of quantitative data from images. Napari-caphid was developed by Imhorphen Team (french team of University of Angers and INRAe Angers) for ECLECTIC Team (french team of University of Paris-Saclay and CNRS).\n\n<!--\nDon't miss the full getting started guide to set up your new package:\nhttps://github.com/napari/cookiecutter-napari-plugin#getting-started\n\nand review the napari docs for plugin developers:\nhttps://napari.org/stable/plugins/index.html\n-->\n\n## Installation\n\nYou can install `napari-caphid` via [pip]:\n\n    pip install napari-caphid\n\n\n\nTo install latest development version :\n\n    pip install git+https://github.com/hereariim/napari-caphid.git\n\n## Getting started\n\n### Foreword\n\nBefore using the plugin, the directory must be structured as follows:\n\n```\n└── Directory\n    ├── France\n    │   ├── image\n    │   │   ├── img_1.tif\n    │   │   ├── img_2.tif\n    │   │   ...\n    │   │   └── img_n.tif\n    │   ├── mask\n    │   │   ├── msk_1.tif\n    │   │   ├── msk_2.tif\n    │   │   ...\n    │   │   └── msk_n.tif\n    │   ├── img_1.tif\n    │   ├── msk_1.tif\n    │   ├── img_2.tif\n    │   ├── msk_2.tif\n    │   ...\n    │   ├── img_n.tif\n    │   └── msk_n.tif\n    │ \n    ├── Belgium\n    │   ├── image\n    │   │   └── ...\n    │   ├── mask\n    │   │   └── ...\n    │   └── ...\n    ├── Spain\n    │   ├── image\n    │   │   └── ...\n    │   ├── mask\n    │   │   └── ...\n    │   └── ...\n    └── Aphid.csv\n```\n\nSome explanation about structure. The directory contained three folders (France, Spain, Belgium) and one file (Aphid.csv).\n- Each folders (France, Spain, Belgium) contains a set of images and masks and two folders (image, mask). The folder image contains images from the set of images. The folder mask contains masks from the set of masks.\n- The file Aphid.csv is a table with quantitative data of aphids from inital process of aphid image processing.\n\nImportant:\n- The structure of directory is very important because it will be useful to get image name.\n\n### Getting started\n\nThe widget get three input:\n- Mask : Mask stack\n- Pick a table : Path/to/Directory/Aphid.csv\n- Country : The country where images were taken\n\nThe widget gives one output:\n- A new table .csv which is the Aphid.csv updated.\n\n### What's it for ?\n\nThis widget gives quantitative data from Mask stack. These quantitative data will be contained into dataframe. Quantitative data linked to current masks contained in the Aphid.csv file will be deleted. Then, the new quantitative data contained in the dataframe will be integrated into the Aphid.csv file. In this way, the Aphid.csv file is updated.\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 [BSD-3] license,\n\"napari-caphid\" 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\n[file an issue]: https://github.com/hereariim/napari-caphid/issues\n\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","description_content_type":"text/markdown","keywords":null,"home_page":"https://github.com/hereariim/napari-caphid","download_url":null,"author":"Herearii Metuarea","author_email":"herearii.metuarea@gmail.com","maintainer":null,"maintainer_email":null,"license":"BSD-3-Clause","classifier":["Development Status :: 2 - Pre-Alpha","Framework :: napari","Intended Audience :: Developers","License :: OSI Approved :: BSD License","Operating System :: OS Independent","Programming Language :: Python","Programming Language :: Python :: 3","Programming Language :: Python :: 3 :: Only","Programming Language :: Python :: 3.8","Programming Language :: Python :: 3.9","Programming Language :: Python :: 3.10","Topic :: Scientific/Engineering :: Image Processing"],"requires_dist":["numpy","magicgui","qtpy","opencv-python","tqdm","pandas","Pillow","tox ; extra == 'testing'","pytest ; extra == 'testing'","pytest-cov ; extra == 'testing'","pytest-qt ; extra == 'testing'","napari ; extra == 'testing'","pyqt5 ; extra == 'testing'"],"requires_python":">=3.8","requires_external":null,"project_url":["Bug Tracker, https://github.com/hereariim/napari-caphid/issues","Documentation, https://github.com/hereariim/napari-caphid#README.md","Source Code, https://github.com/hereariim/napari-caphid","User Support, https://github.com/hereariim/napari-caphid/issues"],"provides_extra":["testing"],"provides_dist":null,"obsoletes_dist":null},"npe1_shim":false}