Welcome to the Open Simulation Pipeline for Deforming Organs!

Setting up many simulations to train machine learning algorithms is a lot of work. This project aims to aid researchers by providing commonly used functionality, example pipelines and the building blocks to set up their own pipelines.

Contents:

• Introduction
  • The DataSample
  • The PipelineBlock
  • The Pipeline
• Data Sample
  • Scene Objects
• Building your own PipelineBlocks
  • Determinism
  • Adding PipelineBlocks to a Pipeline
  • Raising issues
• Building your Pipeline
• Errors, partial runs and re-running on the same folder
  • Logging and locating errors:
  • Recovering from partial runs:
  • Intentional partial runs:
  • When to delete data:
• Troubleshooting
  • Debugging a single sample:
  • Analyze (Deprecated)
  • Log files
  • Bash output log files
  • Running sequentially
  • Common issues
• Using real patient data in your pipeline
  • Step 1: Prepare your input meshes
  • Step 2: Let the pipeline use your meshes:
• Hints and Remarks
  • Units
  • Random values and determinism
  • Print Dataset Results
• API
  • core
  • blocks
  • utils