{"name":"napari-indices","display_name":"indices","visibility":"public","icon":"","categories":[],"schema_version":"0.2.0","on_activate":null,"on_deactivate":null,"contributions":{"commands":[{"id":"napari-indices.get_reader","title":"Open data with indices","python_name":"napari_indices._reader:napari_get_reader","short_title":null,"category":null,"icon":null,"enablement":null},{"id":"napari-indices.write_multiple","title":"Save multi-layer data with indices","python_name":"napari_indices._writer:write_multiple","short_title":null,"category":null,"icon":null,"enablement":null},{"id":"napari-indices.write_single_image","title":"Save image data with indices","python_name":"napari_indices._writer:write_single_image","short_title":null,"category":null,"icon":null,"enablement":null},{"id":"napari-indices.make_sample_data","title":"Load sample data from indices","python_name":"napari_indices._sample_data:make_sample_data","short_title":null,"category":null,"icon":null,"enablement":null},{"id":"napari-indices.make_qwidget","title":"Make example QWidget","python_name":"napari_indices._widget:ExampleQWidget","short_title":null,"category":null,"icon":null,"enablement":null},{"id":"napari-indices.make_magic_widget","title":"Calculate indice","python_name":"napari_indices._widget:calculate_indice","short_title":null,"category":null,"icon":null,"enablement":null}],"readers":[{"command":"napari-indices.get_reader","filename_patterns":["*.npy"],"accepts_directories":false}],"writers":[{"command":"napari-indices.write_multiple","layer_types":["image*","labels*"],"filename_extensions":[],"display_name":""},{"command":"napari-indices.write_single_image","layer_types":["image"],"filename_extensions":[".npy"],"display_name":""}],"widgets":[{"command":"napari-indices.make_qwidget","display_name":"Example QWidget","autogenerate":false},{"command":"napari-indices.make_magic_widget","display_name":"Vegetation indices","autogenerate":false}],"sample_data":[{"command":"napari-indices.make_sample_data","key":"unique_id.1","display_name":"indices"}],"themes":null,"menus":{},"submenus":null,"keybindings":null,"configuration":[]},"package_metadata":{"metadata_version":"2.1","name":"napari-indices","version":"0.0.2","dynamic":null,"platform":null,"supported_platform":null,"summary":"Calculer les indices de végétation","description":"# napari-indices\n\n[![License BSD-3](https://img.shields.io/pypi/l/napari-indices.svg?color=green)](https://github.com/Emmanulla0/napari-indices/raw/main/LICENSE)\n[![PyPI](https://img.shields.io/pypi/v/napari-indices.svg?color=green)](https://pypi.org/project/napari-indices)\n[![Python Version](https://img.shields.io/pypi/pyversions/napari-indices.svg?color=green)](https://python.org)\n[![tests](https://github.com/Emmanulla0/napari-indices/workflows/tests/badge.svg)](https://github.com/Emmanulla0/napari-indices/actions)\n[![codecov](https://codecov.io/gh/Emmanulla0/napari-indices/branch/main/graph/badge.svg)](https://codecov.io/gh/Emmanulla0/napari-indices)\n[![napari hub](https://img.shields.io/endpoint?url=https://api.napari-hub.org/shields/napari-indices)](https://napari-hub.org/plugins/napari-indices)\n\nCalculer les indices de végétation\n\n----------------------------------\n\nThis [napari] plugin was generated with [Cookiecutter] using [@napari]'s [cookiecutter-napari-plugin] template.\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-->\nEmmanuella OKAFOR (L3 PA CMI-PSI_Université d'Angers) developed this plugin during her internship with a french team called ImHorPHen (lead by David ROUSSEAU). This plugin realises vegetation indexes computation with hyperspectral images. For the momment, there are five vegetation indexes : NDVI, TCARI, NPCI, SGI, NDGI.\n## Installation\n\nYou can install `napari-indices` via [pip]:\n\n    pip install napari-indices\n\n\n\nTo install latest development version :\n\n    pip install git+https://github.com/Emmanulla0/napari-indices.git\n\n## Plugin description\n\n\nUsing this plugin requires importing the bands of a hyperspectral image into a **tif file**, in our case, 160 bands. You must launch it by accessing the **Plugins > napari-indices> Vegetation indices** menu.\n\n![Capture d'écran 2023-05-29 124720](https://github.com/Emmanuella0/napari-indices/assets/132358490/3b3895df-d0a7-466e-8ada-92bd4b642852)\n\nThen select the vegetation index to be calculated and the different bands to be used, then click the **Run** button to start the calculation. This results in the images corresponding to the calculated indices.\n\n![etape_2](https://github.com/Emmanuella0/napari-indices/assets/132358490/4875f0fc-3435-4875-ba4e-8881cb179b96)\n\n\nThe areas of interest to be analysed must then be defined. To do this, click the **Shapes** button on the Napari interface and choose the **add rectangle** shape from the menu that appears. Using the mouse, it is then possible to draw a rectangle on each of the two areas to be analyzed, for example a tree sheet and a green sheet of paper. \n\n![etape_3](https://github.com/Emmanuella0/napari-indices/assets/132358490/fc8612fe-5deb-4290-b4c3-9cac20acf1ce)\n\n\nTo perform the Fisher ratio calculation and display the histogram, it is necessary to go back to the **Plugins > napari-indices > ExempleQWidget** menu and click the **Click me! **. This action opens a new window displaying the best vegetation index to use, its corresponding Fisher ratio and the histogram of the two selected regions on the image of the vegetation index concerned. A video explaining the plugin is available at: https://uabox.univ-angers.fr/index.php/s/LqB0qs11n3jxZVJ.\n\n![Histogram](https://github.com/Emmanuella0/napari-indices/assets/132358490/be176176-1972-402c-9a01-8e367347d9d8)\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-indices\" 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/Emmanulla0/napari-indices/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/Emmanulla0/napari-indices","download_url":null,"author":"Emmanuella OKAFOR","author_email":"eokafor010@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","spectral","matplotlib","tifffile","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/Emmanulla0/napari-indices/issues","Documentation, https://github.com/Emmanulla0/napari-indices#README.md","Source Code, https://github.com/Emmanulla0/napari-indices","User Support, https://github.com/Emmanulla0/napari-indices/issues"],"provides_extra":["testing"],"provides_dist":null,"obsoletes_dist":null},"npe1_shim":false}