Architecture Overview

PhysioMotion4D is an early-beta scientific Python package built from workflow classes plus reusable segmentation, registration, geometry, image, and USD components. Runtime classes inherit from PhysioMotion4DBase for logging and consistent configuration.

Architecture Diagram

CLI scripts / tutorials
       |
       v
Workflow classes
   |       |       |       |
   v       v       v       v
ITK images  Segmentation  Registration  PyVista meshes
   |              |             |             |
   +--------------+-------------+-------------+
                      |
                      v
            ContourTools / TransformTools
                      |
                      v
           ConvertVTKToUSD / vtk_to_usd
                      |
                      v
              OpenUSD / Omniverse

Workflow Classes

WorkflowConvertHeartGatedCTToUSD: Orchestrates 4D CT loading, segmentation, image registration, contour transformation, and animated USD generation.
WorkflowConvertCTToVTK: Converts one CT image into labeled VTK surface and voxel-mesh outputs.
WorkflowCreateStatisticalModel: Builds a PCA statistical shape model from aligned population meshes.
WorkflowFitStatisticalModelToPatient: Applies a template or PCA model to patient surfaces with model-registration stages.
WorkflowReconstructHighres4DCT: Reconstructs high-resolution 4D CT frames using time-series registration to a fixed high-resolution reference.
WorkflowConvertVTKToUSD: Wraps VTK-to-USD conversion for repository workflows and CLI use.

Key Boundaries

Image processing uses ITK images. Surface and volume meshes use PyVista/VTK. USD export converts those meshes to OpenUSD and applies the repository’s RAS-to-Y-up transform at the VTK-to-USD boundary.

The installed CLI commands are thin wrappers around these workflow classes. They are the best executable references for supported API usage.