I’m trying to batch process images using ilastik-1.4.0b1 in headless mode from Windows (server 2012). I can analyze (pixel classification) multiple images at the same time if I individually list them like this:
"C:\Program Files\ilastik-1.4.0b1\run-ilastik.bat" --headless --readonly --project="20191220_stingscreen_dapi_pixel_Miner.ilp" foo1.tif foo2.tif
However, for actual production use, I’ll be doing multiple directories of multiple files per directory. I’ve tried wildcarding “foo1.tif foo2.tif” into variations of “foo*.tif”, with and without single or double quotes, etc, but ilastik always errors out:
ilastik.applets.dataSelection.opDataSelection.UnsuitedAxistagsException: Axistags ['y', 'x'] don't fit data shape (2, 1024, 1024)
When I try to go headless on my Mac laptop, I can wildcard with no problems:
(ilastik_dapi_batch.sh is a small sh script I wrote to simplify testing and takes the first parameter in quotes " " above as $1). The actual ilastik command is otherwise identical (except run_ilastik.sh vs run-ilastik.bat).
But unfortunately, the mac is not good enough to run all the images I must do production analysis on Windows.
How can I pass wildcards on my image list on Windows?