Metadata-Version: 2.1
Name: imglyb
Version: 2.0.0
Summary: A python module to bring together the worlds of numpy (Python) and ImgLib2 (Java).
Home-page: https://github.com/imglib/imglyb
Author: Philipp Hanslovsky, Curtis Rueden, Edward Evans, Mark Hiner
Author-email: ctrueden@wisc.edu
License: Simplified BSD License
Description: # imglyb
        
        `imglyb` aims at connecting two worlds that have been seperated for too long:
         * Python with [numpy](https://github.com/numpy/numpy)
         * Java with [ImgLib2](https://github.com/imglib/imglib2)
        
        `imglyb` uses [jpype](http://jpype.org) to access `numpy` arrays and expose
        them to `ImgLib2` through
        [`imglib2-imglyb`](https://github.com/imglib/imglib2-imglyb).
        This means **shared memory** between `numpy` and `ImgLib2`, i.e. any `ImgLib2`
        algorithm can run on `numpy` arrays without creating copies of the data!
        For example, Python users can now make use of the
        [BigDataViewer extension](https://github.com/imglib/imglyb-bdv) to visualize dense volumetric
        data.
        
        If you are interested in using `imglyb`, have a look at the `examples` folder
        and extend the examples as needed!
        
        **Note**:
        [`NEP 18`](https://numpy.org/neps/nep-0018-array-function-protocol.html) has
        the potential to improve `numpy` - `imglib` interoperability, especially when
        converting `imglib2` data structures to `numpy`.
        
        ## Installation
        
        ### Prerequisites
        
        `imglyb` has been tested on Linux, macOS, and Windows.
        
        The following tools are required:
        
         * Python 3
         * Java 8 or 11 JDK (JRE is not enough)
         * [Apache Maven](https://maven.apache.org/)
        
        If you use [conda](https://conda.io/), these will be installed for you.
        
        ### Installing with conda
        
        ```shell
        conda install -c conda-forge imglyb
        ```
        
        ### Installing with pip
        
        First, install the prerequisites above. Then run:
        
        ```shell
        pip install imglyb
        ```
        
        It is recommended to do this from inside a virtualenv or conda environment,
        rather than system-wide.
        
        ### Installing from source
        
        First, install the prerequisites above. Then run:
        
        ```shell
        git clone git://github.com/imglib/imglyb
        cd imglyb
        pip install -e .
        ```
        
        It is recommended to do this from inside a virtualenv or conda environment,
        rather than system-wide.
        
        ## Usage
        
        It is suggested to follow and extend the examples in the `examples` folder
        according to your needs.
        
        Or, for a higher-level way to use `imglyb`, check out
        [pyimagej](https://github.com/imagej/pyimagej).
        
        ## Known Issues
        
        ### AWT on macOS
        
        AWT and Cocoa do not get along perfectly. In general, the Cocoa event loop
        needs to be started before the JVM is loaded. (Thanks to @tpietzsch for
        figuring this out!) This requires some macOS specific code, written using
        `PyObjC`, to properly start up and shut down the Cocoa application and start
        the Java/Python code within it.
        
        The `OSXAWTwrapper.py` script included in the `imglyb` library provides an
        example of Cocoa code and can be used to run the `imglyb` examples. Two
        packages from `PyObjC` are required for this wrapper (`pyobjc-core` and
        `pyobjc-framework-cocoa`), and they should be installed with `imglyb`
        on macOS.
        
        When running the wrapper, one can either provide the name of the target module
        (as if using `python -m`) or the full path to the target script. So using the
        module name, the command to run the "butterfly" script in `imglyb-examples`
        looks like this:
        ```shell
        python imglyb/OSXAWTwrapper.py imglyb-examples.butterfly
        ```
        Running `OSXAWTwrapper.py` via `python -m` does not work at this time.
        
Platform: UNKNOWN
Requires-Python: >=3
Description-Content-Type: text/markdown
