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upsample

The upsample command allows you to upsample a WEBKNOSSOS dataset. It supports upsampling either a specific layer or all layers in the dataset. The command provides options to customize the sampling mode, starting magnification, parallel execution, and distribution strategy.

Usage

webknossos upsample [OPTIONS] SOURCE

Arguments

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

Options

  • --sampling-mode
    The sampling mode to use for upsampling.
    Options: anisotropic, isotropic, constant_z.
    Default: anisotropic.

  • --from-mag
    Magnification level to start upsampling from.
    Accepts a single number or a minus separated string (e.g., 2 or 2-2-2).
    Example: --from-mag 2.

  • --layer-name
    Name of the layer that should be upsampled. If not provided, all layers will be processed.
    Example: --layer-name gray_matter.

  • --jobs
    Number of processes to be spawned for parallel execution.
    Default: Number of CPU cores.
    Example: --jobs 4.

  • --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.
    Should be a JSON string.
    Example: --job-resources '{"mem": "10M"}'.

Example Commands

Upsample all layers:

webknossos upsample --from-mag 2 /path/to/dataset
This command upsamples all layers in the dataset starting from magnification 2 using the default sampling mode.

Upsample a specific layer:

webknossos upsample --from-mag 2-2-1 --layer-name gray_matter /path/to/dataset
This command upsamples only the layer named "gray_matter" in the dataset.

Upsample with parallel execution using SLURM:

webknossos upsample --from-mag 2 --distribution-strategy slurm --job-resources '{"mem": "10M"}' /path/to/dataset
This command uses the SLURM distribution strategy with custom job resources for the upsampling process.

Notes

  • Ensure that the dataset path is accessible and properly configured.
  • If --layer-name is omitted, the command will upsample all layers in the dataset.
  • Adjust the --jobs option to optimize performance based on your system's resources.
  • When using the SLURM strategy, make sure that the provided --job-resources JSON string correctly specifies the required resources.