HDF5 import issue in headless mode - no image opened

[Alxcho]

Hi,

I have a IJ macro that opens HDF5 images from Ilastik for processing and runs fine when started from IJ in batch mode with the standard run("Import HDF5", "select=[" + inputFilePath + "] datasetname=" + datasetpath + "axisorder=" + yxc). Images are processed, everything is fine.

But this doesn't seem to work when the macro is ran in headless mode / from cmd line. The import seems to complete (message reads [INFO] Import dataset finished in xxx seconds), but the image is nowhere to be found, getTitle(), or any similar command fails with the same message: Macro Error: There are no images open.

Any workaround / anything I am missing (any macro extension to call for Ilastik plugin?) or run("Import HDF5) doesn't work in headless mode /from cmd line (yet?)

[k-dominik]

Hello @Alxcho,

first of all sorry for the delayed reply. I don't know how this slipped through the cracks of our attention. And second, thank you for reporting this issue.

I vaguely remember running into this, too. It seems that the macro does not properly wait until the image is open when run in headless. I didn't find a solution back then. On the image.sc forum there are some discussions, but I think those did not help me (this for example).