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Multicut headless expects all inputs #1954

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constantinpape opened this Issue Feb 10, 2019 · 3 comments

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constantinpape commented Feb 10, 2019

Multicut in headless mode expects to get all 4 inputs from the data-selection applet:
raw data, probabilities, superpixels and groundtruth.
However, this does not make sense, because we want to use the headless mode to
process new data without groundtruth and potentially also without superpixels to
use the built-in wsdt superpixels.

For reference, if not all inputs are provided, ilastik will fail with:

  File "/home/cpape/Work/software/src/ilastik-1.3.2rc2-Linux/ilastik-meta/ilastik/ilastik/applets/batchProcessing/batchProcessingApplet.py", line 56, in parse_known_cmdline_args
    cmdline_args, role_names)
  File "/home/cpape/Work/software/src/ilastik-1.3.2rc2-Linux/ilastik-meta/ilastik/ilastik/applets/dataSelection/dataSelectionApplet.py", line 143, in parse_known_cmdline_args
    "" + role_args_str)
Exception: Invalid command line arguments: All roles must be configured explicitly.
Use the following flags to specify which files are matched with which inputs:
--raw_data, --probabilities, --superpixels, --groundtruth
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k-dominik commented Feb 10, 2019

Could you please post the actual command line you were using? I'm pretty sure the help message is misleading here.

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constantinpape commented Feb 10, 2019

@k-dominik you are right:
This was caused because I misnamed the argument output_filename_format to output_file_format. If I change this everything seems to work.

Nevertheless, the error message is very confusing, because it implies something is wrong
with the input data. Would be nice to fix this.

For reference, this is the command that produced the error.
I inserted line-breaks to make this more readable:

./run_ilastik.sh --project /home/cpape/Work/data/mc_ilastik/mc_test.ilp\
                        --headless --readonly 1\
                        --output_format tif\
                        --output_file_format im_0_seg.tif\ 
                        --raw_data /home/cpape/Work/data/mc_ilastik/im_0.tif\
                        --probabilities /home/cpape/Work/data/mc_ilastik/im_25_pmap.tif
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k-dominik commented Feb 10, 2019

I agree

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