Metadata-Version: 2.1
Name: napari-ndtiffs
Version: 0.1.0
Summary: napari plugin for nd tiff folders with OpenCl deskew
Home-page: https://github.com/tlambert03/napari-ndtiffs
Author: Talley Lambert
Author-email: talley.lambert@gmail.com
License: BSD-3
Description: # napari-ndtiffs
        
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        napari plugin for nd tiff folders with optional OpenCl-based deskewing.
        
        Built-in support for folders of (skewed) lattice light sheet tiffs. file.
        
        ![napari-ndtiffs demo](demo.gif)
        
        ----------------------------------
        
        *This [napari] plugin was generated with [Cookiecutter] using with [@napari]'s [cookiecutter-napari-plugin] template.*
        
        ## Features
        
        - Drag and drop a folder of tiffs onto napari window to view easily 
          - (currently designed to detect  lattice light sheet tiffs, but easily
            adjustable)
        - If lattice `Settings.txt` file is found, will deskew automatically (only if
          necessary)
        - Lazily loads dataset on demand.  quickly load preview your data.
        - Handles `.zip` archives as well!  Just directly compress your tiff folder,
          then drop it into napari.
        - All-openCL deskewing, works on GPU as well as CPU, falls back to scipy if
          pyopencl is unavailable.
        
        It would not be hard to support arbitrary filenaming patterns!  If you have a
        folder of tiffs with a consistent naming scheme and would like to take advantage
        of this plugin, feel free to open an issue!*
        
        ## Usage
        
        In most cases, just drop your folder onto napari, or use `viewer.open("path")`
        
        ### Overriding parameters
        
        You can control things like voxel size and deskewing angle as follows:
        
        ```python
        from napari_ndtiffs import parameter_override
        import napari
        
        viewer = napari.Viewer()
        with parameter_override(angle=45, name="my image"):
            viewer.open("path/to/folder", plugin="ndtiffs")
        ```
        
        Valid keys for `parameter_override` include:
        
        - **dx**: (`float`) the pixel size, in microns
        - **dz**: (`float`)the z step size, in microns
        - **deskew**: (`bool`) whether or not to deskew, (by default, will deskew if angle > 0, or if a lattice metadata file is detected that requires deskewing) 
        - **angle**: (`float`) the angle of the light sheet relative to the coverslip
        - **padval**: (`float`) the value with which to pad the image edges when deskewing (default is 0)
        - **contrast_limits**: (`2-tuple of int`) (min, max) contrast_limits to use when viewing the image
        - **name**: (`str`) an optional name for the image
        
        ### Sample data
        
        Try it out with test data: [download sample data](https://www.dropbox.com/s/up4ywrn2sckjunc/lls_mitosis.zip?dl=1)
        
        You can unzip if you like, or just drag the zip file onto the napari window.
        
        Or, from command line, use:
        
        ```bash
        napari path/to/lls_mitosis.zip
        ```
        
        ## Installation
        
        You can install `napari-ndtiffs` via [pip]:
        
            pip install napari-ndtiffs
        
        ## Debugging
        
        To monitor file io and deskew activity, enter the following in the napari console:
        
        ```python
        import logging
        logging.getLogger('napari_llsfolder').setLevel('DEBUG')
        ```
        
        
        ## Contributing
        
        Contributions are very welcome. Tests can be run with [tox], please ensure
        the coverage at least stays the same before you submit a pull request.
        
        ## License
        
        Distributed under the terms of the [BSD-3] license,
        "napari-ndtiffs" is free and open source software
        
        ## Issues
        
        If you encounter any problems, please [file an issue] along with a detailed description.
        
        [napari]: https://github.com/napari/napari
        [Cookiecutter]: https://github.com/audreyr/cookiecutter
        [@napari]: https://github.com/napari
        [BSD-3]: http://opensource.org/licenses/BSD-3-Clause
        [cookiecutter-napari-plugin]: https://github.com/napari/cookiecutter-napari-plugin
        [file an issue]: https://github.com/tlambert03/napari-ndtiffs/issues
        [napari]: https://github.com/napari/napari
        [tox]: https://tox.readthedocs.io/en/latest/
        [pip]: https://pypi.org/project/pip/
        [PyPI]: https://pypi.org/
Platform: UNKNOWN
Classifier: Development Status :: 4 - Beta
Classifier: Intended Audience :: Developers
Classifier: Topic :: Software Development :: Testing
Classifier: Programming Language :: Python
Classifier: Programming Language :: Python :: 3
Classifier: Programming Language :: Python :: 3.6
Classifier: Programming Language :: Python :: 3.7
Classifier: Programming Language :: Python :: 3.8
Classifier: Programming Language :: Python :: Implementation :: CPython
Classifier: Programming Language :: Python :: Implementation :: PyPy
Classifier: Operating System :: OS Independent
Classifier: License :: OSI Approved :: BSD License
Requires-Python: >=3.6
Description-Content-Type: text/markdown
