Our FIBICS NPVE pattern generator that we use with our HIM or Ga-FIB creates tiff images during the mill process. From time to time it is useful to have those together with the other metadata that is recorded in txt files for the mill process. The images are nicely stored in a directory tree
project - sample - mill shape - tiff and data files
The sample directory might contain additional not automatically recorded images.
I’d like to import these files into omero mapping sample to project and mill shape to dataset. I tried to do this in python from a jupyter notebook but failed to get the code working for filesets. I can use the CLI from my python script but these seems to be clumsy and surprisingly slow. I’ve got the image upload working and now I am trying to get the txt files from each shape uploaded and linked to the datasets.
My question essentially boils down to
How can I do
omero import /path/to/my-dir -T Project:name:MyProjectName/Dataset:name:MyDatasetName --parallel-upload=8
from python so I can easily traverse sub-directories and construct the Dataset and Project names from other input available in those directories.
I can provide data and also the code that I already have but what I think I need is a good example on how to upload filesets from python.