Import Ilastik HDF5 \ h5 files with jython

Hi All,

I’m trying to import h5 image stack (…-data_Probabilities.h5) files with jython. using:

IJ.run(“Import HDF5”, “select=[”+pathtfile+"] datasetname=[/exported_data_batch: (1, 1, 1040, 1392, 1) uint8] axisorder=tzyxc")

my problem is that it opens the image, while I need to work in hidden mode.
Is there a way to work without opening the image ?

Best Regards

Hi @Ebi,

I have really no clue about that, maybe @wolny, or @Christian_Tischer can say something about this?

Cheers

Try this:

Note: I have not tried it myself, but sounds promising…

Otherwise you have to find the actual Java (i.e. jython) calls for what you need. I think you should be able to find them here: https://github.com/fiji/HDF5_Vibez/

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