{"name":"napari-macrokit","display_name":"napari macro-kit","visibility":"public","icon":"","categories":[],"schema_version":"0.2.0","on_activate":null,"on_deactivate":null,"contributions":{"commands":[{"id":"napari-macrokit.make_qwidget","title":"View macro scripts","python_name":"napari_macrokit:QMacroView","short_title":null,"category":null,"icon":null,"enablement":null}],"readers":null,"writers":null,"widgets":[{"command":"napari-macrokit.make_qwidget","display_name":"napari-macrokit","autogenerate":false}],"sample_data":null,"themes":null,"menus":{},"submenus":null,"keybindings":null,"configuration":[]},"package_metadata":{"metadata_version":"2.1","name":"napari-macrokit","version":"0.0.1","dynamic":null,"platform":null,"supported_platform":null,"summary":"Executable script generation for napari plugins","description":"# napari-macrokit\n\n[![License BSD-3](https://img.shields.io/pypi/l/napari-macrokit.svg?color=green)](https://github.com/hanjinliu/napari-macrokit/raw/main/LICENSE)\n[![PyPI](https://img.shields.io/pypi/v/napari-macrokit.svg?color=green)](https://pypi.org/project/napari-macrokit)\n[![Python Version](https://img.shields.io/pypi/pyversions/napari-macrokit.svg?color=green)](https://python.org)\n[![tests](https://github.com/hanjinliu/napari-macrokit/workflows/tests/badge.svg)](https://github.com/hanjinliu/napari-macrokit/actions)\n[![codecov](https://codecov.io/gh/hanjinliu/napari-macrokit/branch/main/graph/badge.svg)](https://codecov.io/gh/hanjinliu/napari-macrokit)\n[![napari hub](https://img.shields.io/endpoint?url=https://api.napari-hub.org/shields/napari-macrokit)](https://napari-hub.org/plugins/napari-macrokit)\n\nExecutable script generation for napari plugins.\n\n![](https://github.com/hanjinliu/napari-macrokit/blob/main/images/example.gif)\n↑ [Example](https://github.com/hanjinliu/napari-macrokit/blob/main/examples/regionprops.py) showing the real-time recording of GUI operation.\n\nThis napari plugin aims at making image analysis reproducible with arbitrary input/output types.\n\n## Usage\n\nCreate a macro object, decorate functions with `record` method and run!\n\n```python\nfrom napari_macrokit import get_macro\n\nmacro = get_macro(\"my-plugin-specifier\")  # get macro object\n\n# define a function\n@macro.record\ndef add(a: float, b: float) -> float:\n    return a + b\n\n# run\nresult = add(3.2, 5.4)\nadd(result, 1.0)\n\nmacro\n\n# Out:\n# >>> float0 = add(3.2, 5.4)\n# >>> float1 = add(float0, 1.0)\n```\n\n## Record GUI Operations\n\nYou can use recordable functions in your widgets to keep tracks of GUI operations.\nMore simply, you can double-decorate functions with `record` and `magicgui`.\n\n```python\nimport numpy as np\nfrom magicgui import magicgui\nimport napari\nfrom napari.types import ImageData\nfrom napari_macrokit import get_macro\n\nmacro = get_macro(\"my-plugin-specifier\")  # get macro object\n\n# define recordable magicgui\n@magicgui\n@macro.record\ndef add(image: ImageData, b: float) -> ImageData:\n    return image + b\n\nviewer = napari.Viewer()  # launch a viewer\nviewer.add_image(np.random.random((100, 100)))  # image data\nviewer.window.add_dock_widget(add)  # add magicgui to the viewer\n```\n\nRunning add twice in GUI and you'll find macro updated like below.\n\n```python\nmacro\n# Out\n# >>> image0 = add(viewer.layers['Image'].data, 0.06)\n# >>> image1 = add(image0, 0.12)\n```\n\n## Combining Plugins\n\nSuppose you have two modules that use `napari-macrokit`.\n\n```python\n# napari_module_0.py\n\nfrom napari.types import ImageData\nfrom scipy import ndimage as ndi\nfrom napari_macrokit import get_macro\n\nmacro = get_macro(\"napari-module-0\")\n\n@macro.record\ndef gaussian_filter(image: ImageData, sigma: float) -> ImageData:\n    return ndi.gaussian_filter(image, sigma=sigma)\n\n@macro.record\ndef threshold(image: ImageData, value: float) -> ImageData:\n    return image > value\n```\n\n```python\n# napari_module_1.py\n\nfrom napari.types import ImageData\nimport numpy as np\nfrom napari_macrokit import get_macro\nmacro = get_macro(\"napari-module-1\")\n\n@macro.record\ndef estimate_background(image: ImageData) -> float:\n    return np.percentile(image, 10.0)\n\n```\n\nYou can use functions from both modules to build an analysis workflow by collecting existing macro objects with `collect_macro` function. All the recordable actions in the modules will also be recorded to the returned macro object.\n\n```python\nimport numpy as np\nfrom napari_macrokit import collect_macro\nfrom napari_module_0 import gaussian_filter, threshold\nfrom napari_module_1 import estimate_background\n\n# global_macro will record all the macro available at this point\nglobal_macro = collect_macro()\n\n# start image analysis!\nimage = np.random.random((100, 100))\n\nout = gaussian_filter(image, 2.0)\nthresh = estimate_background(out)\nbinary = threshold(out, thresh)\n\nmacro\n# Out\n# >>> image0 = gaussian_filter(arr0, 2.0)\n# >>> float0 = estimate_background(image0)\n# >>> image1 = threshold(image1, float0)\n```\n\n---------------------------------\n\nThis [napari] plugin was generated with [Cookiecutter] using [@napari]'s [cookiecutter-napari-plugin] template.\n\n## Installation\n\nYou can install `napari-macrokit` via [pip]:\n\n    pip install napari-macrokit\n\n\n\nTo install latest development version :\n\n    pip install git+https://github.com/hanjinliu/napari-macrokit.git\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-macrokit\" 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/hanjinliu/napari-macrokit/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/hanjinliu/napari-macrokit","download_url":null,"author":"Hanjin Liu","author_email":"liuhanjin-sc@g.ecc.u-tokyo.ac.jp","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","macro-kit (>=0.4.0)","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/hanjinliu/napari-macrokit/issues","Documentation, https://github.com/hanjinliu/napari-macrokit#README.md","Source Code, https://github.com/hanjinliu/napari-macrokit","User Support, https://github.com/hanjinliu/napari-macrokit/issues"],"provides_extra":["testing"],"provides_dist":null,"obsoletes_dist":null},"npe1_shim":false}