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merge-fallback

The merge-fallback command merges a WEBKNOSSOS volume annotation layer with its fallback layer. It uses multi-processing or SLURM for parallel execution and accepts customization via options.

Usage

webknossos merge-fallback [OPTIONS] TARGET SOURCE_ANNOTATION DATASET_DIRECTORY

Arguments

  • TARGET
    Path to your WEBKNOSSOS output dataset.
    Example: /path/to/output/dataset or s3://bucket-name/output-dataset.

  • SOURCE_ANNOTATION
    Path to the WEBKNOSSOS zip annotation file containing the fallback layer. A link for working with Annotations with webknossos and how to export them can be found here. Example: /path/to/source/annotation.zip.

  • DATASET_DIRECTORY
    Path to your WEBKNOSSOS dataset folder.
    Example: /path/to/dataset/folder.

Options

  • --volume-layer-name
    Name of the volume layer to merge with the fallback layer.
    Optional; if not provided, the default volume annotation layer is used.

  • --jobs
    Number of processes to be spawned for parallel execution.
    Default: Number of CPU cores.

  • --distribution-strategy
    Strategy to distribute the task across CPUs or nodes.
    Options: multiprocessing, slurm, kubernetes, sequential. Default: multiprocessing.

  • --job-resources
    Specify resources for jobs when using the SLURM distribution strategy.
    Example: --job-resources '{"mem": "10M"}'.

Example Commands

Merge fallback layer using default settings:

webknossos merge-fallback /path/to/output/dataset /path/to/source/annotation.zip /path/to/dataset/folder
Merges the fallback annotation into the volume layer using the default multiprocessing strategy.

Merge fallback layer with a specific volume layer:

webknossos merge-fallback --volume-layer-name my_volume /path/to/output/dataset /path/to/source/annotation.zip /path/to/dataset/folder

Merge fallback layer with parallel execution and custom job settings:

webknossos merge-fallback --jobs 4 --distribution-strategy slurm --job-resources '{"mem": "10M"}' /path/to/output/dataset /path/to/source/annotation.zip /path/to/dataset/folder
Uses 4 parallel processes with SLURM to merge the fallback layer, allocating custom memory to each job.

Notes

  • Ensure that the target dataset, source annotation, and dataset directory are correctly accessible.
  • Set any necessary environment variables or credentials for remote paths.
  • The SLURM distribution strategy requires specifying job resources via the --job-resources option.
  • This command facilitates efficient merging of volume annotations with fallback layers by leveraging configurable parallel execution strategies.