API Reference

This section provides detailed API documentation for all public classes, functions, and modules in Phenotastic.

• PhenoMesh
  • PhenoMesh Class
  • Usage Examples
• Pipeline
  • Pipeline Class
  • PipelineContext Class
  • StepConfig Class
  • OperationRegistry Class
  • Preset Functions
• mesh Module
  • Contour Generation
  • Mesh Creation
  • Mesh Smoothing
  • Mesh Remeshing
  • Mesh Repair
  • Mesh Filtering
  • Mesh Processing
  • Mesh Analysis
  • Vertex Operations
  • Edge Operations
  • Labeling
• domains Module
  • Domain Segmentation
  • Domain Merging
  • Domain Analysis
  • Scalar Filtering
• Exceptions
  • Exception Hierarchy
  • Base Exception
  • Pipeline Exceptions
  • Data Validation Exceptions
  • Usage Example

Public API Overview

Classes

• PhenoMesh - Extension of PyVista PolyData for phenotyping

• Pipeline - Pipeline executor

• PipelineContext - State container for pipeline execution

• StepConfig - Configuration for a pipeline step

• OperationRegistry - Registry of available operations

Functions

• load_preset() - Load a preset pipeline

• list_presets() - List available presets

• get_preset_yaml() - Get preset configuration as YAML

• save_pipeline_yaml() - Save pipeline to YAML file

Exceptions

• PhenotasticError - Base exception

• PipelineError - Pipeline execution errors

• ConfigurationError - Configuration errors

• InvalidImageError - Invalid image data

• InvalidMeshError - Invalid mesh data