I am doing a bunch of Manual Tracking using probability files that I am generating in batch in Ilastik. To speed up the tracking a bit, I automatically create the Manual Tracking projects using the headless mode of Ilastik. What would really help would be if I could not only create the Manual Tracking projects, but also pre-load the raw data and probability files in each of the manual tracking ilp files. Also, if I could automatically load in some settings for each of these files (e.g. set smoothing and thresholding parameters), that would speed things up for me and make this all much less tedious. Is there any way of doing this using the headless mode? I use the following bit of python to create the projects in batch.
for filename in os.listdir(data_dir): if '.tif' in filename: str = '/Applications/ilastik-1.3.2post1-OSX.app/Contents/ilastik-release/run_ilastik.sh --headless --new_project %s --workflow "Manual Tracking Workflow"'%(os.path.join(data_dir,filename.replace('.tif','.ilp'))) os.system(str)
I’ve tried to also use the --raw_data and --prediction_maps flags from the documentation, but the raw data and prediction data are not saved into the new Manual Tracking Workflow project. I guess these flags are more for outputting data in batch? Any advice on how to batch load in the images/settings for each project would be very appreciated! Thanks!