Metadata-Version: 2.1
Name: ome-zarr
Version: 0.0.19
Summary: Implementation of images in Zarr files.
Home-page: https://github.com/ome/ome-zarr-py
Author: The Open Microscopy Team
License: UNKNOWN
Description: ===========
        ome-zarr-py
        ===========
        
        Experimental support for multi-resolution images stored in Zarr filesets, according to the `OME zarr spec`_.
        
        
        Features
        --------
        
        - Use as a image reader plugin for `napari`_. The `napari`_ plugin was generated with `Cookiecutter`_ along with `@napari`_'s `cookiecutter-napari-plugin`_ template.
        - Simple command-line to read and download conforming Zarr filesets.
        - Helper methods for parsing related metadata.
        
        
        Installation
        ------------
        
        Install the latest release of `ome-zarr`_ from PyPI::
        
            pip install ome-zarr
        
        
        Install developer mode to run from your current branch::
        
            git clone git@github.com:ome/ome-zarr-py.git
            cd ome-zarr-py
            pip install -e .
        
        
        Usage
        -----
        
        Open Zarr filesets containing images with associated OME metadata.
        The examples below use the image at http://idr.openmicroscopy.org/webclient/?show=image-6001240.
        
        All examples can be made more or less verbose by passing `-v` or `-q` one or more times::
        
            # ome_zarr -vvv ...
        
        
        info
        ====
        
        Use the `ome_zarr` command to interrogate Zarr datasets::
        
            # Remote data
            $ ome_zarr info https://s3.embassy.ebi.ac.uk/idr/zarr/v0.1/6001240.zarr/
        
            # Local data (after downloading as below)
            $ ome_zarr info 6001240.zarr/
        
        download
        ========
        
        To download all the resolutions and metadata for an image::
        
            # creates local 6001240.zarr/
            $ ome_zarr download https://s3.embassy.ebi.ac.uk/idr/zarr/v0.1/6001240.zarr/
        
            # Specify output directory
            $ ome_zarr download https://s3.embassy.ebi.ac.uk/idr/zarr/v0.1/6001240.zarr/ --output image_dir
        
        napari plugin
        =============
        
        Napari will use `ome-zarr` to open images that the plugin recognises as ome-zarr.
        The image metadata from OMERO will be used to set channel names and rendering settings
        in napari::
        
            $ napari 'https://s3.embassy.ebi.ac.uk/idr/zarr/v0.1/6001240.zarr/'
        
            # Also works with local files
            $ napari 6001240.zarr
        
        OR in python::
        
            import napari
            with napari.gui_qt():
                viewer = napari.Viewer()
                viewer.open('https://s3.embassy.ebi.ac.uk/idr/zarr/v0.1/6001240.zarr/')
        
        If single zarray is passed to the plugin, it will be opened without the use of
        the metadata::
        
            $ napari '/tmp/6001240.zarr/0'
        
        csv to labels
        =============
        
        The `csv_to_labels` command uses a CSV file to add key:value properties to labels
        under an OME-Zarr Image or Plate.
        
        The OME-Zarr labels metadata must already contain a `properties`
        list of `{key:value}` objects, each with a unique key:ID. This key is `omero:shapeId`
        in the example below.
        
        This ID can be used to identify a single row of the CSV table by specifying the name of
        a column with unique values, e.g. `shape_id` below.
        This row is used to add additional column_name:value data to the label properties.
        
        You also need to specify which columns from the CSV to use, e.g. `"area,X,Y,Width,Height"`.
        You can also specify the column types (as in https://github.com/ome/omero-metadata/)
        to specify the data-type for each column (string by default).
        
         - `d`: `DoubleColumn`, for floating point numbers
         - `l`: `LongColumn`, for integer numbers
         - `s`: `StringColumn`, for text
         - `b`: `BoolColumn`, for true/false
        
        Use e.g. `#d` as a suffix in the column name to denote a `float` column, no spaces etc:
        ```
        "area#d,label_text#s,Width#l,Height#l"
        ```
        
        For example, to take values from columns named `area`, `label_text`, `Width` and `Height`
        within a CSV file named `labels_data.csv` with an ID column named `shape_id` and add these
        values to label properties with an ID key of `omero:shapeId` in an Image or Plate named `123.zarr`::
        
            ome_zarr csv_to_labels labels_data.csv shape_id "area#d,label_text#s,Width#l,Height#l" 123.zarr omero:shapeId```
        
        
        Release process
        ---------------
        
        This repository uses `bump2version <https://pypi.org/project/bump2version/>`_ to manage version numbers.
        To tag a release run::
        
            $ bumpversion release
        
        This will remove the ``.dev0`` suffix from the current version, commit, and tag the release.
        
        To switch back to a development version run::
        
            $ bumpversion --no-tag [major|minor|patch]
        
        specifying ``major``, ``minor`` or ``patch`` depending on whether the development branch will be a `major, minor or patch release <https://semver.org/>`_. This will also add the ``.dev0`` suffix.
        
        Remember to ``git push`` all commits and tags.
        
        
        License
        -------
        
        Distributed under the terms of the `BSD`_ license,
        "ome-zarr-py" is free and open source software
        
        .. _`OME zarr spec`: https://github.com/ome/omero-ms-zarr/blob/master/spec.md
        .. _`Cookiecutter`: https://github.com/audreyr/cookiecutter
        .. _`@napari`: https://github.com/napari
        .. _`BSD`: https://opensource.org/licenses/BSD-2-Clause
        .. _`Apache Software License 2.0`: http://www.apache.org/licenses/LICENSE-2.0
        .. _`Mozilla Public License 2.0`: https://www.mozilla.org/media/MPL/2.0/index.txt
        .. _`cookiecutter-napari-plugin`: https://github.com/napari/cookiecutter-napari-plugin
        .. _`napari`: https://github.com/napari/napari
        .. _`ome-zarr`: https://pypi.org/project/ome-zarr/
        
Platform: UNKNOWN
Classifier: Development Status :: 4 - Beta
Classifier: Intended Audience :: Developers
Classifier: Intended Audience :: Science/Research
Classifier: Topic :: Software Development :: Libraries :: Python Modules
Classifier: Programming Language :: Python
Classifier: Programming Language :: Python :: 3
Classifier: Operating System :: OS Independent
Classifier: License :: OSI Approved :: BSD License
Classifier: Framework :: napari
Requires-Python: >=3.6
Provides-Extra: napari
