rpotter6298
69 lines
2.4 KiB
Python
69 lines
2.4 KiB
Python
#!/usr/bin/env python3
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"""figure5.py — PCA and t-SNE of VGG16 features, colored by class.
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Usage:
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python scripts/visualizations/figure5.py
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python scripts/visualizations/figure5.py --tag v2
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"""
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import os, sys, argparse
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import numpy as np
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import matplotlib
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matplotlib.use("Agg")
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import matplotlib.pyplot as plt
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from sklearn.decomposition import PCA
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from sklearn.manifold import TSNE
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sys.path.insert(0, os.path.dirname(os.path.dirname(os.path.dirname(
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os.path.abspath(__file__)))))
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ROOT = os.path.dirname(os.path.dirname(os.path.dirname(
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os.path.abspath(__file__))))
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FEATURES_DIR = os.path.join(ROOT, "features")
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PLOTS_DIR = os.path.join(ROOT, "plots")
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SEED = 42
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CLASS_COLORS = {"Bengin cases": "#2CA02C", "Malignant cases": "#D62728",
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"Normal cases": "#1F77B4"}
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def main():
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ap = argparse.ArgumentParser()
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ap.add_argument("--tag", default="", help="Append tag to filename")
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args = ap.parse_args()
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tag = f"_{args.tag}" if args.tag else ""
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data = np.load(os.path.join(FEATURES_DIR, "VGG16_features.npz"),
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allow_pickle=True)
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X, Y = data["X"], data["Y"]
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pca50 = PCA(n_components=50, random_state=SEED).fit_transform(X)
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pca2 = PCA(n_components=2, random_state=SEED).fit_transform(pca50)
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tsne = TSNE(n_components=2, random_state=SEED, perplexity=30,
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max_iter=1000).fit_transform(pca50)
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fig, axes = plt.subplots(1, 2, figsize=(12, 5))
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for ax, coords, title in [(axes[0], pca2, "(a) PCA"),
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(axes[1], tsne, "(b) t-SNE")]:
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for cls in sorted(np.unique(Y)):
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mask = Y == cls
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label = cls.replace("Bengin cases", "Benign")
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ax.scatter(coords[mask, 0], coords[mask, 1],
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c=CLASS_COLORS[cls], label=label,
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alpha=0.6, s=15, edgecolors="none")
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ax.set_title(title, fontsize=12)
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ax.set_xlabel("Component 1")
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ax.set_ylabel("Component 2")
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ax.legend(markerscale=2, fontsize=9)
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ax.grid(alpha=0.2)
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fig.suptitle("Figure 5 — PCA and t-SNE of VGG16 Features (by class)",
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fontsize=13)
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plt.tight_layout()
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out = os.path.join(PLOTS_DIR, "figure5", f"figure5{tag}.png")
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os.makedirs(os.path.dirname(out), exist_ok=True)
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plt.savefig(out, dpi=150)
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plt.close()
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print(f"Saved → {out}")
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if __name__ == "__main__":
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main()
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