Command Line Interface

Phenotastic provides a command line interface for running pipelines, managing configurations, and visualizing meshes.

Global Options

phenotastic --version  # Show version
phenotastic --help     # Show help

Commands

run

Run the phenotyping pipeline on an input file.

phenotastic run INPUT_FILE [OPTIONS]

Arguments:

  • INPUT_FILE: 3D image (TIFF) or mesh file (VTK, PLY, STL)

Options:

  • -c, --config PATH: YAML pipeline configuration file

  • -p, --preset [default]: Use a preset pipeline (default: ‘default’)

  • -o, --output PATH: Output directory for results

  • --save-mesh / --no-save-mesh: Save output mesh (default: yes)

  • --save-domains / --no-save-domains: Save domain data CSV (default: yes)

  • --verbose / --quiet: Print progress information (default: verbose)

Examples:

# Run with default pipeline
phenotastic run image.tif --output results/

# Run with custom config
phenotastic run mesh.vtk --config my_pipeline.yaml -o output/

# Quiet mode, mesh only
phenotastic run image.tif --quiet --no-save-domains -o out/

init-config

Generate a pipeline configuration file from the default preset.

phenotastic init-config OUTPUT_FILE

Arguments:

  • OUTPUT_FILE: Path for the generated YAML file

Example:

phenotastic init-config my_pipeline.yaml

list-operations

List all available pipeline operations.

phenotastic list-operations [OPTIONS]

Options:

  • -c, --category [all|contour|mesh|domain]: Filter by category (default: all)

Examples:

# List all operations
phenotastic list-operations

# List only mesh operations
phenotastic list-operations --category mesh

list-presets

List available preset pipeline configurations.

phenotastic list-presets

validate

Validate a pipeline configuration file.

phenotastic validate CONFIG_FILE

Arguments:

  • CONFIG_FILE: Path to the YAML configuration file

Example:

phenotastic validate my_pipeline.yaml

view

Visualize a mesh file interactively.

phenotastic view MESH_FILE [OPTIONS]

Arguments:

  • MESH_FILE: Path to the mesh file (VTK, PLY, STL, OBJ)

Options:

  • -s, --scalars NAME: Scalar array to color by (e.g., ‘curvature’, ‘domains’)

  • --cmap NAME: Colormap for visualization (default: ‘viridis’)

Examples:

# Basic view
phenotastic view mesh.vtk

# View with curvature coloring
phenotastic view mesh.vtk --scalars curvature

# View domains with custom colormap
phenotastic view mesh.vtk --scalars domains --cmap tab20