Awesome
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.