{"name":"napari-reco-plugin","display_name":"Reconstruction Plugin","visibility":"public","icon":"","categories":[],"schema_version":"0.2.0","on_activate":null,"on_deactivate":null,"contributions":{"commands":[{"id":"napari-reco-plugin.reconstruction","title":"Reconstruction","python_name":"reco_plugin._widget:ReconstructionWidget","short_title":null,"category":null,"icon":null,"enablement":null},{"id":"napari-reco-plugin.multi_paganin","title":"Multi Paganin","python_name":"reco_plugin._widget:MultiPaganinWidget","short_title":null,"category":null,"icon":null,"enablement":null},{"id":"napari-reco-plugin.get_reader","title":"Read NXS Files","python_name":"reco_plugin._reader:napari_get_reader","short_title":null,"category":null,"icon":null,"enablement":null},{"id":"napari-reco-plugin.tif_writer","title":"Write TIF Files","python_name":"reco_plugin._writer:write_tiff","short_title":null,"category":null,"icon":null,"enablement":null},{"id":"napari-reco-plugin.raw_writer","title":"Write Raw Files","python_name":"reco_plugin._writer:write_raw","short_title":null,"category":null,"icon":null,"enablement":null}],"readers":[{"command":"napari-reco-plugin.get_reader","filename_patterns":["*.nxs","*.tdf"],"accepts_directories":false}],"writers":[{"command":"napari-reco-plugin.tif_writer","layer_types":["image"],"filename_extensions":[".tif"],"display_name":""},{"command":"napari-reco-plugin.raw_writer","layer_types":["image"],"filename_extensions":[".raw"],"display_name":""}],"widgets":[{"command":"napari-reco-plugin.reconstruction","display_name":"Reconstruction","autogenerate":false},{"command":"napari-reco-plugin.multi_paganin","display_name":"Multi Paganin","autogenerate":false}],"sample_data":null,"themes":null,"menus":{},"submenus":null,"keybindings":null,"configuration":[]},"package_metadata":{"metadata_version":"2.4","name":"napari-reco-plugin","version":"0.1.5","dynamic":["license-file"],"platform":null,"supported_platform":null,"summary":"A Napari plugin for tomographic reconstruction using the ASTRA Toolbox, with optional Paganin phase retrieval filter for phase-contrast data.","description":"# Reconstruction Napari Plugin\n\nA Napari plugin for tomographic reconstruction using the [ASTRA Toolbox](https://www.astra-toolbox.com/), with optional Paganin phase retrieval filter for phase-contrast data.\n\nSupported reconstruction algorithms: **FBP**, **BP**, **SIRT**, **SART**, **CGLS** — all available in CPU or GPU (CUDA) mode.\n\n## Installation\n\n### Option 1 — Install from Napari Hub (recommended)\n\nOnce published, the plugin can be installed directly from the Napari plugin manager:\n\n1. Open **Napari**\n2. Go to **Plugins > Install/Uninstall Plugins**\n3. Search for **\"napari-reco-plugin\"**\n4. Click **Install**\n\nAlternatively, install via pip:\n\n```bash\npip install napari-reco-plugin\n```\n\n---\n\n### Option 2 — Manual installation (development)\n\n#### 1. Create and activate a conda environment\n\n```bash\nconda create -n napari-env python=3.12\nconda activate napari-env\n```\n\n#### 2. Install main dependencies\n\n```bash\nconda install -c conda-forge napari pyqt\nconda install -c astra-toolbox -c nvidia astra-toolbox\n\n# Ensure compatibility with ASTRA\npip install numpy==1.26.4\n\n# Install CuPy depending on your CUDA version\npip install cupy-cuda12x  # or cupy-cuda11x\n```\n\n#### 3. Clone the repository\n\n```bash\ngit clone https://github.com/Clementcmoi/Reconstruction-napari-plugin.git\ncd Reconstruction-napari-plugin\n```\n\n#### 4. Install the plugin\n\n```bash\npip install -e .\n```\n\n---\n\n## Requirements\n\n### Core\n\n* Python ≥ 3.9\n* Napari\n* ASTRA Toolbox\n\n### Optional (for GPU acceleration)\n\n* CUDA Toolkit\n* CuPy\n\n\n> ⚠️ GPU dependencies are not installed automatically. You must install them manually according to your system configuration.\n\n---\n\n## Usage\n\nStart Napari:\n\n```bash\nnapari\n```\n\nThen open the plugin via:\n\n```\nPlugins > Reconstruction Plugin\n```\n\nAvailable tools:\n\n* **Reconstruction**\n* **Multi Paganin**\n\n---\n\n## Launchers Templates\n\nTemplate scripts for launching Napari with the correct environment are available in the `launchers/` folder.\n\n### Usage\n\n1. Copy a `.bat` file from `launchers/`\n2. Edit:\n\n   * `<path_to_conda>` → your Anaconda/Miniconda path\n   * `<your_napari_env>` → your environment name\n3. Double-click to launch\n\n### Desktop shortcut (optional)\n\n* Right-click `.bat` → **Send to Desktop**\n* (Optional) Change icon via shortcut properties\n\n---\n\n## Project Structure\n\n* Plugin source code: `src/reco_plugin/`\n* Plugin manifest: `src/reco_plugin/napari.yaml`\n\n---\n\n## License\n\nThis project is licensed under the GNU General Public License v3.0 (GPL-3.0), in compliance with the [ASTRA Toolbox license](https://www.astra-toolbox.com/).\n","description_content_type":"text/markdown","keywords":null,"home_page":null,"download_url":null,"author":null,"author_email":"Clément Capdeville <clement.capdeville@univ-lyon1.fr>","maintainer":null,"maintainer_email":null,"license":"MIT License\n\nCopyright (c) 2024 Clément Capdeville\n\nPermission is hereby granted, free of charge, to any person obtaining a copy\nof this software and associated documentation files (the \"Software\"), to deal\nin the Software without restriction, including without limitation the rights\nto use, copy, modify, merge, publish, distribute, sublicense, and/or sell\ncopies of the Software, and to permit persons to whom the Software is\nfurnished to do so, subject to the following conditions:\n\nThe above copyright notice and this permission notice shall be included in all\ncopies or substantial portions of the Software.\n\nTHE SOFTWARE IS PROVIDED \"AS IS\", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR\nIMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,\nFITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE\nAUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER\nLIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,\nOUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE\nSOFTWARE.\n","classifier":["Development Status :: 3 - Alpha","Framework :: napari","Intended Audience :: Science/Research","License :: OSI Approved :: GNU General Public License v3 or later (GPLv3+)","Operating System :: OS Independent","Programming Language :: Python :: 3","Programming Language :: Python :: 3.9","Programming Language :: Python :: 3.10","Programming Language :: Python :: 3.11","Programming Language :: Python :: 3.12","Topic :: Scientific/Engineering :: Image Processing","Topic :: Scientific/Engineering :: Medical Science Apps."],"requires_dist":["h5py","numpy","scipy","tqdm","scikit-image","matplotlib>=3.5","dask[array]","qtpy","napari>=0.4.18","pytest; extra == \"testing\"","pytest-qt; extra == \"testing\"","napari[pyqt5]; extra == \"testing\""],"requires_python":">=3.9","requires_external":null,"project_url":["Bug Tracker, https://github.com/Clementcmoi/Reconstruction-napari-plugin/issues","Source Code, https://github.com/Clementcmoi/Reconstruction-napari-plugin"],"provides_extra":["testing"],"provides_dist":null,"obsoletes_dist":null},"npe1_shim":false}