Hi all, In mid-November, the ImageJ2 team at LOCI was visited by Christian Dietz of the University of Konstanz, lead developer of the KNIME Image Processing project [1]. We spent a week of intensely programming to improve the integration of KNIME with ImgLib2 and ImageJ2.
Christian wrote up a summary of the topics covered and work performed: IJ2 <-> KNIME bi-directional integration (goal: have something end of 2013) * KNIME automatically generates Nodes from Plugins (DONE) * IJ2 will be able to record KNIME Workflows (WIP) * IJ2 runs KNIME Workflows Headless (WIP) * IJ2 provides an update-site for OSGi wrapped bundles (WIP) * KNIME can be updated using the IJ2 Update-Sites/FIJI-Personal Update-Sites (WIP) Come up with a plan for Algorithms/Experimental and make these suggestions * Common code repository for plugins (scijava-ops) * Started to define interfaces * We need to reimplement / unify a lot of stuff * General convolution/wrapping methods are needed * Define coding conventions for imglib2-algorithms * Define coding (social and technical) conventions for scijava-ops Get a grip on descriptor sets * Unified interfaces * Now part of scijava-ops, using scijava-common Discuss/Merge all open pull-requests ImgLib2 (Done) * Projectors merged! * WrappedImg merged! * FlatIterableInterval merged! * Mail sent to clean-up branches SCIFIOCellImg with Memory Service * Development branch: https://github.com/scifio/scifio/tree/cache-imps * Refactored SCIFIOCells to cache via phantom reference instead of finalization (done) * Created MemoryService to manage a new RefHandler class of plugins and provide configurable memory safeguards (done) * Taking a test case of re-writing each pixel in a dataset, improved cache performance from 59.6s write, 57.1s read to 35.2s write, 1.6s read (done) * Two tests still failing unpredictably due to garbage collection reliance (I think). As soon as these are fixed, the update SCIFIOCell/MemoryService functionality will be released in SCIFIO 0.7.4. * Integration to KNIME started but not finished (easy task, thanks Mark!) Have a running real-life example at LOCI (or start setting one up) (Done) * Working Examples running at LOCI (Tracking/Segmentation/Measurement) * Two more potential projects for integration * Anytime: Just ask Martin/Christian for any assistance or even send them the images as they are happy to help with workflows * Guide how to install KNIME Image Processing (DONE) Overall, it was an immensely productive hackathon. For most of the "WIP" items above, we have working code which just needs a little polish. I will send out a separate email soon with more details on the scijava-ops project. Any other questions, feel free to ask! Regards, Curtis [1] http://knime.imagej.net/
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