PDM-cli: Point Distribution Model Building and Fitting Tool

A command-line tool for building, fitting, and visualizing Point Distribution Models (PDMs) using the Scalismo library.

Overview

PDM-cli provides a streamlined workflow for statistical shape modeling:

1. Build PDMs from training datasets
2. Fit PDMs to new data using posterior or ICP approaches
3. Visualize models and fitting results

Usage

Build PDM

scala-cli run build.scala -- /path/to/your/training/data

The tool will:

• Load point clouds from the specified directory
• Compute the mean shape
• Build a statistical model using PCA
• Save the model to the models directory

Fit PDM

# Posterior-based fitting (for indexed point clouds that are algined and have correspondences)
scala-cli run fit.scala -- posterior --pdm models/your_pdm.h5.json --input /path/to/target/data

# ICP-based fitting (for point clouds that are aligned but do not have correspondences)
scala-cli run fit.scala -- icp --pdm models/your_pdm.h5.json --input /path/to/target/data

The tool will:

• Load the PDM from the specified file
• Load the from target point cloud folder
• Fit the PDM to the target data using the specified method (posterior or ICP)
• Save the fitted model to the output directory

Additional options:

• --output <dir> - Custom output directory
• --iterations <number> - Number of ICP iterations (default: 20)
• --visualize - Enable UI visualization during fitting

Note: The posterior-based fitting requires indexed point clouds, while the ICP-based fitting can be used with any point cloud.

Visualize PDM

scala-cli run visualize.scala -- /path/to/your/pdm.h5.json

The tool will:

• Load the PDM from the specified file
• Visualize the mean shape and modes of variation

Dependencies

This project uses Scalismo, a library for statistical shape modeling.

Dependencies are managed through Scala CLI directives at the top of each file:

//> using scala "3.3"
//> using dep "ch.unibas.cs.gravis::scalismo-ui:0.92.0"

Compiling to Java Bytecode

You may wish to compile the Scala fitting code to so you can run it without the need for scala and its dependencies. This is useful for deployment or distribution. To compile the Scala code to a JAR file, you can use the following command:

scala-cli package --power --assembly fit.scala   --main-class PDMFittingTool   --output scalismo_fit.jar

This all. An example of how to call the JAR file is as follows:

java -jar scalismo_fit.jar icp --pdm models/your_pdm.h5.json --input /path/to/target/data