batch execution



while fiddeling around with batch execution of KNIME, I got stuck executing an ImageJ Macro. In GUI mode, the workflow runs fine. In batch mode I recieve an error reading

WARN      KNIME-Worker-2 ValueToCellNodeModel     Problem occured in rowRow 0 : The specified macro has thrown an error while execution. Make sure that the used plugins are available in the selected IJ1 plugin folder! See KNIME Log for details! Missing cell has been inserted
Unrecognized command: "Subtract Background..."

The commandline call was

/home/bq_mgunkel/KNIME/knime_3.3.1/knime -noSplash -application org.knime.product.KNIME_BATCH_APPLICATION -workflowDir="/home/bq_mgunkel/KNIME/workflows/deNBI/01-ImageProcessing-FIRST_Imperial"  -reset -workflow.variable=data_path,"/home/bq_mgunkel/Data/BatchTestData/data",String -workflow.variable=csv_path,"/home/bq_mgunkel/Data/BatchTestData/out1.csv",String

Am I missing something here?


EDIT: BTW, it seems nothing gets written to the log file in .metadata/knime/knime.log during batch execution.





Hi Manuel,

the problem is, that IJ1 isn't supported in batch mode :-( This is due to a limitation of IJ1 itself. Sorry, that I don't have better news.


Hi Christian,


OK, I think I can handle that. Many thanks for clarifying!





@christian.dietz: Are there any plans to support ImageJ1 plugins in a batch mode?

When I run any local operation, e.g. median filter or local thresholding, with radius larger then 3 pixels, native KNIME nodes work very slow, whether ImageJ1 macro node does the job much faster. Would be great if the same can be done in the batch mode.

Or is there any other way to make naighbourhood operations faster?