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imglyb

imglyb aims at connecting two worlds that have been seperated for too long:

imglyb uses jpype to access numpy arrays and expose them to ImgLib2 through 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 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 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

If you use conda, these will be installed for you.

Installing with conda

conda install -c conda-forge imglyb

Installing with pip

First, install the prerequisites above. Then run:

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:

git clone https://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.

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:

python imglyb/OSXAWTwrapper.py imglyb-examples.butterfly

Running OSXAWTwrapper.py via python -m does not work at this time.