Python PCA API

[akenmorris]

• Python API for PCA Analysis #2425

This PR adds additional functionality to support using ShapeWorks PCA from Python.

Example script:

import shapeworks as sw
import glob
import os
import sys
import numpy as np


def read_data():
    # create ParticleSystem
    script_dir = os.path.dirname(os.path.abspath(__file__))
    particleFilesDir = script_dir + "/data/la_particles/"
    particleFilesList = glob.glob(particleFilesDir + "*world.particles")
    print(particleFilesList)
    ps = sw.ParticleSystem(particleFilesList)
    return ps


# now load data/la_particles/CARMA0046_groomed_world.particles using numpy
new_sample = np.loadtxt(os.path.dirname(os.path.abspath(__file__)) +
                        "/data/la_particles/CARMA0046_groomed_world.particles")
# flatten new_sample to 1D array
new_sample = new_sample.flatten()

# To use raw particle files
# ps = read_data()
# pca = sw.ParticleShapeStatistics()
# pca.PCA(ps)

# To use ShapeWorks Projects
project = sw.Project()
os.chdir("data")
project.load("la.xlsx")
pca = sw.ParticleShapeStatistics()
pca.PCA(project)

# print the mean shape particles
mean_shape = pca.getMean()
print("Mean shape: ", mean_shape)

eigenvalues = pca.eigenValues()
print("Eigenvalues: ", eigenvalues)

eigenvectors = pca.eigenVectors()
print("Eigenvectors: ", eigenvectors)

scores = pca.projectNewSample(new_sample)
print("Scores: ", scores)