Ellipsoid: Shape Evaluation in Python
What is the Use Case?
The ellipsoid_evaluate use case demonstrates the functionality of shape evaluation tools of ShapeWorks python API. These API's include calculation of quantitative evaluation metrics such as specificity, generalization, and compactness.For detailed explaination of the evaluation metrics, refer to Shape Model Evaluation.
This use case reads the correspondence model of the ellipsoid segmentation images use case.
Relevant Arguments
Analyzing Shape Model Using Python APIs
The ShapeEvaluation() module of ShapeWorks python API, calcutates the three evaluation metrics given the correspondence model. The correspondence model can be read using the ParticleSystem() module.
```python
Read the particle files from a pre-trained shape model
particle_data = sw.ParticleSystem()
```
The ShapeEvaluation() module has two types of commands which can query either a particular metric at the specified mode of variation or get the metric values for all the modes of variation.
To access the metrics at a specified mode of variation:
```python
Get the compactness of a specific mode
nCompactness = sw.ShapeEvaluation.ComputeCompactness(particleSystem=particle_data,Modes=3)
Get the generalization of a specific mode and saves the reconstructions
nGeneralization = sw.ShapeEvaluation.compute_generalization(particleSystem=particle_data, nModes=3,saveTo=save_dir)
Calculate specificity of a given mode and saves the reconstructions
nSpecificity = sw.ShapeEvaluation.ComputeSpecificity(particleSystem=particle_data, nModes=3,saveTo=save_dir) ```
To access the metrics for all the modes of variations:
```python
Get compactness of all the modes
allCompactness = sw.ShapeEvaluation.ComputeFullCompactness(particleSystem=particle_data)
Get generalization values for all modes
allGeneralization = sw.ShapeEvaluation.ComputeFullGeneralization(particleSystem=particle_data)
Get specificity values for all modes
allSpecificity = sw.ShapeEvaluation.ComputeFullSpecificity(particleSystem=particle_data) ```
Details about the evaluation functions can be found in the API Reference
Generalization value of the 3rd mode - 0.09600121582319728
Generalization Best Reconstruction
Generalization Worst Reconstruction
Specificity value of the 3rd mode - 0.21431799055403217
Specificity Best Reconstruction
Specificity Worst Reconstruction