{"name":"napari-sediment","display_name":"napari Sediment","visibility":"public","icon":"","categories":[],"schema_version":"0.2.1","on_activate":null,"on_deactivate":null,"contributions":{"commands":[{"id":"napari-sediment.get_reader","title":"Open data with napari Sediment","python_name":"napari_sediment.utilities._reader:napari_get_reader","short_title":null,"category":null,"icon":null,"enablement":null},{"id":"napari-sediment.make_qwidget","title":"Make Sediment QWidget","python_name":"napari_sediment.widgets.sediment_widget:SedimentWidget","short_title":null,"category":null,"icon":null,"enablement":null},{"id":"napari-sediment.make_hyperwidget","title":"Make Hyperanalysis QWidget","python_name":"napari_sediment.widgets.hyperanalysis_widget:HyperAnalysisWidget","short_title":null,"category":null,"icon":null,"enablement":null},{"id":"napari-sediment.make_spectralindexwidget","title":"Make Spectral Indices QWidget","python_name":"napari_sediment.widgets.spectral_indices_widget:SpectralIndexWidget","short_title":null,"category":null,"icon":null,"enablement":null},{"id":"napari-sediment.make_batchwidget","title":"Make Batch Index QWidget","python_name":"napari_sediment.widgets.batch_indices:BatchIndexWidget","short_title":null,"category":null,"icon":null,"enablement":null},{"id":"napari-sediment.make_preproc_batchwidget","title":"Make Batch Preprocess QWidget","python_name":"napari_sediment.widgets.batch_preproc_widget:BatchPreprocWidget","short_title":null,"category":null,"icon":null,"enablement":null},{"id":"napari-sediment.make_concatwidget","title":"Make Concatenation QWidget","python_name":"napari_sediment.widgets.concatenation_widget:ConcatenationWidget","short_title":null,"category":null,"icon":null,"enablement":null},{"id":"napari-sediment.make_convertwidget","title":"Make Convert QWidget","python_name":"napari_sediment.widgets.convert_widget:ConvertWidget","short_title":null,"category":null,"icon":null,"enablement":null},{"id":"napari-sediment.create_demo_data","title":"Create demo data","python_name":"napari_sediment.data.data_contribution:demo_data","short_title":null,"category":null,"icon":null,"enablement":null}],"readers":[{"command":"napari-sediment.get_reader","filename_patterns":["*.hdr","*.zarr"],"accepts_directories":true}],"writers":null,"widgets":[{"command":"napari-sediment.make_qwidget","display_name":"Sediment","autogenerate":false},{"command":"napari-sediment.make_hyperwidget","display_name":"HyperAnalysis","autogenerate":false},{"command":"napari-sediment.make_spectralindexwidget","display_name":"SpectralIndices","autogenerate":false},{"command":"napari-sediment.make_batchwidget","display_name":"BatchIndex","autogenerate":false},{"command":"napari-sediment.make_preproc_batchwidget","display_name":"BatchPreproc","autogenerate":false},{"command":"napari-sediment.make_concatwidget","display_name":"Concatenation","autogenerate":false},{"command":"napari-sediment.make_convertwidget","display_name":"Convert","autogenerate":false},{"command":"napari-sediment.create_demo_data","display_name":"Demo Data","autogenerate":false}],"sample_data":null,"themes":null,"menus":{},"submenus":null,"keybindings":null,"configuration":[]},"package_metadata":{"metadata_version":"2.4","name":"napari-sediment","version":"0.5.3","dynamic":["license-file"],"platform":null,"supported_platform":null,"summary":"A plugin to process hyperspectral images of sediments","description":"# napari-sediment\n\n[![License BSD-3](https://img.shields.io/pypi/l/napari-sediment.svg?color=green)](https://github.com/guiwitz/napari-sediment/raw/main/LICENSE)\n[![PyPI](https://img.shields.io/pypi/v/napari-sediment.svg?color=green)](https://pypi.org/project/napari-sediment)\n[![Python Version](https://img.shields.io/pypi/pyversions/napari-sediment.svg?color=green)](https://python.org)\n[![tests](https://github.com/guiwitz/napari-sediment/workflows/tests/badge.svg)](https://github.com/guiwitz/napari-sediment/actions)\n[![codecov](https://codecov.io/gh/guiwitz/napari-sediment/branch/main/graph/badge.svg)](https://codecov.io/gh/guiwitz/napari-sediment)\n[![napari hub](https://img.shields.io/endpoint?url=https://api.napari-hub.org/shields/napari-sediment)](https://napari-hub.org/plugins/napari-sediment)\n\nThis napari plugin is designed to hyper-spectral images of sediment cores. It is composed of three interfaces allowing the user to:\n\n- import HDR images\n- normalize the images using white and dark references\n- mask unwanted regions\n- perform spectral dimensionality reduction via minimum noise fraction analysis\n- perform spatial dimensionality reduction based on pixel purity indices\n- identify representative end-members by clustering pure pixels\n- select relevant regions in spectra to compute absorption indices and create absorption maps \n\n### Pre-processing: Sediment widget\n\nThe sediment widget allows the user to import an HDR image and to normalize it using white and dark references. The widget also allows the user to mask unwanted regions of the images.\n\n## Documentation\n\nYou can find a detailed documentation [here](https://guiwitz.github.io/napari-sediment).\n## Installation\n\nCreate a conda environment and activate it. If you don't have conda installed you can for example install [miniforge](https://github.com/conda-forge/miniforge?tab=readme-ov-file#install).\n\n    conda create -n sediment python=3.12 napari pyqt -c conda-forge\n    conda activate sediment\n\nThen you can install `napari-sediment` use:\n\n    pip install napari-sediment\n\nOr you can install the latest development version directly from the GitHub repository:\n\n    pip install git+https://github.com/guiwitz/napari-sediment.git\n\nOn Windows, there is sometimes an issue installing PyTorch (needed for pixel classification) leading to an error about loading a dependency (typically fbgemm.dll). In that case we recommend the following:\n\n    conda create -n sediment python=3.12 napari pyqt -c conda-forge\n    conda activate sediment\n    pip install napari-sediment\n    pip uninstall torch\n    conda install -c conda-forge pytorch llvm-openmp\n\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-sediment\" is free and open source software\n\n## Authors\n\nThis plugin has been developed by Guillaume Witz at the Data Science Lab of the University of Bern in collaboration with Petra Zahajská, Institue of Geography of the University of Bern. Funding for development was provided by Prof. Martin Grosjean, Institute of Geography of the University of Bern.\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/guiwitz/napari-sediment/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":null,"download_url":null,"author":"Guillaume Witz","author_email":"guillaume.witz@unibe.ch","maintainer":null,"maintainer_email":null,"license":"Copyright (c) 2023, University of Bern, Data Science Lab, Guillaume Witz\nAll rights reserved.\n\nRedistribution and use in source and binary forms, with or without\nmodification, are permitted provided that the following conditions are met:\n\n* Redistributions of source code must retain the above copyright notice, this\n  list of conditions and the following disclaimer.\n\n* Redistributions in binary form must reproduce the above copyright notice,\n  this list of conditions and the following disclaimer in the documentation\n  and/or other materials provided with the distribution.\n\n* Neither the name of copyright holder nor the names of its\n  contributors may be used to endorse or promote products derived from\n  this software without specific prior written permission.\n\nTHIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS \"AS IS\"\nAND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE\nIMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE\nDISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE\nFOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL\nDAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR\nSERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER\nCAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY,\nOR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE\nOF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.\n","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 :: 3.11","Programming Language :: Python :: 3.12","Programming Language :: Python :: 3.13","Topic :: Scientific/Engineering :: Image Processing"],"requires_dist":["numpy<2.4.0","zarr==3.*","magicgui","qtpy","napari-guitils>0.1.0","napari-convpaint==0.6.0","torch<2.9.0","superqt","natsort","spectral","matplotlib","scikit-image","scikit-learn","PyYAML","microfilm","dask","distributed","tqdm","cmap","colour-science","tox; extra == \"testing\"","pytest; extra == \"testing\"","pytest-cov; extra == \"testing\"","pytest-qt; extra == \"testing\"","napari; extra == \"testing\"","pyqt5; extra == \"testing\"","torch; extra == \"classifier\"","torchvision; extra == \"classifier\""],"requires_python":">=3.11","requires_external":null,"project_url":["Bug Tracker, https://github.com/guiwitz/napari-sediment/issues","Documentation, https://github.com/guiwitz/napari-sediment#README.md","Source Code, https://github.com/guiwitz/napari-sediment","User Support, https://github.com/guiwitz/napari-sediment/issues"],"provides_extra":["testing","classifier"],"provides_dist":null,"obsoletes_dist":null},"npe1_shim":false}