Segmenter workflow engine - Batch processing

[Aerendel]

Story As a scientist, I want to execute segmentation workflows on a batch of many files so that I can do real science

A/C

• I can use the Segmenter workflow engine to run a previously loaded workflow on a batch of files within a single directory
• File batches undergo a rudimentary set of validation checks before being processed and I am notified if the validation fails
• Beyond initial validation, individual file processing failures do not fail the whole batch
• When processing is complete, I can see a simple text report of successes and failures

Details

• Implement core batch processing functionality for the worklow engine in classic Segmenter
• Necessary inputs for batch processing should be:
  • input directory
  • output directory
  • structure channel index
• Supported image formats:
  • TIFF (including OME TIFF), CZI
    • look for the following extensions: .tif, .tiff, .czi, .ome.tif, .ome.tiff
• Implement basic validation of batch before processing anything. Check the following basic things:
  • input directory exists
  • output directory exists or can be created
• Implement validation on each file individually before running said file:
  • is the the image 3D
  • does the specified channel exist in image
• Generate output log with successes and failures
  • show "100 images out of 150 were successfully segmented"
  • show which files failed, with associated error message / exception
  • format can be a simple txt file / log