API Reference

Complete API documentation for PhysioTwin4D modules.

This section provides detailed documentation for all PhysioTwin4D classes, functions, and modules organized by functionality.

Core Modules

• Base Class
  • Class Reference
  • Logging
  • Extension Notes
  • See Also
• Workflow Classes
  • Available Workflows
  • Convert Image to USD
  • Image to VTK
  • VTK to USD
  • Statistical Shape Modeling
  • High-Resolution 4D CT Reconstruction
  • Finetune ICON Registration
  • See Also
• Segmentation Modules
  • Overview
  • Quick Links
  • Choosing a Method
  • Quick Start
  • Module Documentation
  • Common Operations
  • See Also
• Image Registration Modules
  • Registration Base Class
  • ANTs Registration
  • Greedy Registration
  • ICON Image Registration
  • Chained Image Registration
  • Time-Series Registration
  • Common Result Shape
  • Basic Example
  • See Also
• Model Registration Modules
  • ICP (Iterative Closest Point)
  • ICP with ITK Backend
  • Distance Map Registration
  • PCA-Based Registration
  • Available Classes
  • Workflow-Level Use
  • See Also
• PhysicsNeMo AI Surrogates
  • The Per-Subject Manifest
  • Training a Mesh-Stage Model
  • Predicting With a Mesh-Stage Model
  • Scoring a Mesh-Stage Model Against Images
• USD Generation Modules
  • Overview
  • Quick Links
  • Module Documentation
  • Quick Start
  • See Also
• Utility Modules
  • Overview
  • Quick Links
  • Module Documentation
  • See Also
• CLI Entry-Point API
  • convert_image_4d_to_3d (CLI)
  • convert_image_to_usd (CLI)
  • convert_image_to_vtk (CLI)
  • convert_vtk_to_usd (CLI)
  • create_statistical_model (CLI)
  • download_data (CLI)
  • fit_statistical_model_to_patient (CLI)
  • infer_physicsnemo (CLI)
  • reconstruct_highres_4d_ct (CLI)
  • train_physicsnemo (CLI)
  • visualize_pca_modes (CLI)
  • See Also

Quick Navigation

By Category

Core Classes

• PhysioTwin4DBase - Base class for all components

Workflows

• WorkflowConvertImageToUSD - CT time series to animated USD

• WorkflowConvertImageToVTK - Segmentation to VTK surfaces

• WorkflowConvertVTKToUSD - Meshes to USD

• WorkflowReconstructHighres4DCT - High-resolution 4D reconstruction

• WorkflowFinetuneICONRegistration - Finetune ICON on your cohort

• WorkflowCreateMeanSurface - Unbiased mean surface / atlas

• WorkflowCreateStatisticalModel - Create PCA statistical shape model

• WorkflowFitStatisticalModelToPatient - Fit the model to a patient

AI Surrogates (PhysicsNeMo)

• WorkflowTrainPhysicsNeMo - Train a mesh-stage model

• WorkflowInferPhysicsNeMo - Predict per-point targets

• WorkflowInferMovement - Turn predictions back into geometry

• WorkflowEvaluateMovement - Score predictions against the acquired frames

Segmentation

• SegmentAnatomyBase - Base segmentation class

• SegmentChestTotalSegmentator - TotalSegmentator

• SegmentChestTotalSegmentatorWithContrast - TotalSegmentator for contrast-enhanced CT

• SegmentHeartSimpleware - Simpleware cardiac segmentation

• SegmentHeartSimplewareTrimmedBranches - Simpleware with trimmed great vessels

• SegmentNVSegmentCTMRI - NV-Segment-CTMR, CT and MRI

Image Registration

• RegisterImagesBase - Base registration class

• RegisterImagesANTS - ANTs registration

• RegisterImagesGreedy - Greedy classical deformable registration

• RegisterImagesICON - Icon deep learning registration

• RegisterImagesChain - Run registrations back to back

• RegisterImagesGreedyICON - Greedy then ICON, as a preset chain

• RegisterTimeSeriesImages - 4D time series registration

Model Registration

• RegisterModelsICP - Iterative Closest Point

• RegisterModelsICPITK - ICP with ITK

• RegisterModelsDistanceMaps - Distance map-based

• RegisterModelsPCA - PCA-based registration

USD Tools

• usd_tools - USD file utilities

• usd_anatomy_tools - Anatomical structure tools

• ConvertVTKToUSD - VTK to USD conversion

Module Index

• Index

• Module Index

• Search Page