2026001
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rpotter6298
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#!/usr/bin/env python3
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"""
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compare_clustering_methods.py
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Compare two patient-clustering approaches against the v8 "reference":
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1. Thumbnail-based (64×64 grayscale K-means — the manuscript's method)
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2. Feature-based (PCA-50d of VGG16 features → K-means — our method)
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Metrics (all label-invariant):
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- Adjusted Rand Index (ARI)
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- Normalized Mutual Information (NMI)
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- V-measure (homogeneity + completeness)
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Usage:
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conda activate fundus_imaging
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python scripts/compare_clustering_methods.py
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"""
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import os, sys, csv, re
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import numpy as np
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sys.path.insert(0, os.path.dirname(os.path.dirname(os.path.abspath(__file__))))
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from sklearn.metrics import (
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adjusted_rand_score,
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normalized_mutual_info_score,
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homogeneity_completeness_v_measure,
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)
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from sklearn.decomposition import PCA
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from sklearn.cluster import KMeans
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from PIL import Image
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# ---------------------------------------------------------------------------
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# Config
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# ---------------------------------------------------------------------------
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ROOT = os.path.dirname(os.path.dirname(os.path.abspath(__file__)))
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DATASET_PATH = os.path.expanduser("~/Documents/data_leakage/The IQ-OTHNCCD lung cancer dataset")
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MANIFEST_V8 = os.path.join(ROOT, ".archive", "results", "patient_manifest_v8.csv")
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MANIFEST_SIMPLE = os.path.join(ROOT, "results", "simple_patient_manifest.csv")
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FEATURES_PATH = os.path.join(ROOT, "features", "VGG16_features.npz")
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PATIENT_COUNTS = {
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"Bengin cases": 15,
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"Malignant cases": 40,
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"Normal cases": 55,
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}
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CLASS_ORDER = ["Bengin cases", "Malignant cases", "Normal cases"]
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SEED = 42
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THUMBNAIL_SIZE = (64, 64)
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# ---------------------------------------------------------------------------
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# Helpers
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# ---------------------------------------------------------------------------
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def f2n(fname):
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m = re.search(r"\((\d+)\)", fname)
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num = int(m.group(1)) if m else None
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for cls_key, prefix in [
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("Bengin cases", "B"),
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("Malignant cases", "M"),
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("Normal cases", "N"),
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]:
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if fname.startswith(cls_key.rstrip("s")):
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return f"{prefix}_{num:03d}" if num else fname
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return fname
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def load_v8_assignments(path):
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"""Load v8 manifest, return {image_name: patient_id}."""
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mapping = {}
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with open(path, newline="") as f:
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reader = csv.DictReader(f)
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for row in reader:
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for img in row["confirmed_images"].split(";"):
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if img:
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mapping[img] = row["patient_id"]
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return mapping
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def load_simple_assignments(path):
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"""Load simple feature-based manifest, return {image_name: patient_id}."""
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mapping = {}
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with open(path, newline="") as f:
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reader = csv.DictReader(f)
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for row in reader:
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for img in row["images"].split(";"):
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if img:
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mapping[img] = row["patient_id"]
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return mapping
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def run_thumbnail_clustering(dataset_path, filenames, labels):
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"""Run 64×64 grayscale thumbnail K-means (manuscript method)."""
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groups = np.array([None] * len(labels), dtype=object)
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for class_name, n_clusters in PATIENT_COUNTS.items():
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idx_class = np.where(labels == class_name)[0]
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# Load thumbnails
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X = []
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for i in idx_class:
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fname = filenames[i]
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img_path = os.path.join(dataset_path, class_name, fname)
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try:
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img = Image.open(img_path).convert("L")
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img = img.resize(THUMBNAIL_SIZE)
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img_arr = np.array(img, dtype=np.float32) / 255.0
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X.append(img_arr.flatten())
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except Exception:
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X.append(np.zeros(64 * 64, dtype=np.float32))
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X = np.array(X, dtype=np.float32)
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# PCA → 50d
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n_pca = min(50, X.shape[0] - 1, X.shape[1])
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pca = PCA(n_components=n_pca, random_state=SEED)
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X_pca = pca.fit_transform(X)
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# K-means
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kmeans = KMeans(n_clusters=n_clusters, random_state=SEED, n_init=20)
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clusters = kmeans.fit_predict(X_pca)
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for i, cluster_id in zip(idx_class, clusters):
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groups[i] = f"{class_name}_cluster_{cluster_id}"
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sizes = np.bincount(clusters)
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print(f" {class_name}: k={n_clusters}, sizes min={sizes.min()} max={sizes.max()} mean={sizes.mean():.1f}")
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return groups
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# ---------------------------------------------------------------------------
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# Main
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# ---------------------------------------------------------------------------
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print("Loading VGG16 features for filename/label reference...")
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data = np.load(FEATURES_PATH, allow_pickle=True)
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all_filenames = data["filenames"]
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all_labels = data["Y"]
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X_vgg16 = data["X"]
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print(f" {len(all_filenames)} images across {len(np.unique(all_labels))} classes")
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# Load reference (v8) and our feature-based assignments
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v8_map = load_v8_assignments(MANIFEST_V8)
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simple_map = load_simple_assignments(MANIFEST_SIMPLE)
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# Build per-image label arrays for all three methods, aligned by filename
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# We need all images that exist in ALL three
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v8_labels_list = []
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simple_labels_list = []
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thumb_labels_list = [] # filled after clustering
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common_filenames = []
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common_labels = []
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# First, run thumbnail clustering
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print("\nRunning thumbnail-based K-means (manuscript method)...")
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thumb_groups = run_thumbnail_clustering(DATASET_PATH, all_filenames, all_labels)
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# Build thumbnail mapping (using short names like B_001)
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thumb_map = {}
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for fname, group in zip(all_filenames, thumb_groups):
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short = f2n(fname)
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for cls in CLASS_ORDER:
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if group.startswith(cls):
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cluster_id = int(group.split("_cluster_")[-1])
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prefix = {"Bengin cases": "Benign", "Malignant cases": "Malignant", "Normal cases": "Normal"}[cls]
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thumb_map[short] = f"thumb_{prefix}_{cluster_id:02d}"
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break
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# Filter to images present in all three
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# Feature filenames are like "Bengin case (1).jpg", manifests use "B_001"
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for fname, label in zip(all_filenames, all_labels):
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short_name = f2n(fname)
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v8_id = v8_map.get(short_name)
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simple_id = simple_map.get(short_name)
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thumb_id = thumb_map.get(short_name)
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if v8_id and simple_id and thumb_id:
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common_filenames.append(short_name)
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common_labels.append(label)
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v8_labels_list.append(v8_id)
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simple_labels_list.append(simple_id)
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thumb_labels_list.append(thumb_id)
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print(f"\nImages common to all three methods: {len(common_filenames)}")
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# Convert to numpy arrays
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v8_labels_arr = np.array(v8_labels_list)
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simple_labels_arr = np.array(simple_labels_list)
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thumb_labels_arr = np.array(thumb_labels_list)
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common_labels_arr = np.array(common_labels)
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# ---------------------------------------------------------------------------
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# Compute agreement metrics — per-class and overall
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# ---------------------------------------------------------------------------
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def compute_metrics(ref, pred, name):
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"""Compute clustering agreement metrics against reference."""
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ari = adjusted_rand_score(ref, pred)
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nmi = normalized_mutual_info_score(ref, pred)
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h, c, v = homogeneity_completeness_v_measure(ref, pred)
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return {"name": name, "ARI": ari, "NMI": nmi, "Homogeneity": h, "Completeness": c, "V_measure": v}
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print("\n" + "=" * 80)
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print("OVERALL AGREEMENT WITH v8 REFERENCE")
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print("=" * 80)
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results = []
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for name, pred in [("Thumbnail (manuscript)", thumb_labels_arr), ("Feature-based (ours)", simple_labels_arr)]:
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r = compute_metrics(v8_labels_arr, pred, name)
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results.append(r)
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print(f"\n{'Method':<30s} {'ARI':>8s} {'NMI':>8s} {'Homog':>8s} {'Compl':>8s} {'V_meas':>8s}")
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print("-" * 72)
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for r in results:
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print(f"{r['name']:<30s} {r['ARI']:>8.4f} {r['NMI']:>8.4f} {r['Homogeneity']:>8.4f} {r['Completeness']:>8.4f} {r['V_measure']:>8.4f}")
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# Per-class breakdown
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print("\n" + "=" * 80)
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print("PER-CLASS ARI WITH v8 REFERENCE")
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print("=" * 80)
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print(f"\n{'Class':<20s} {'Thumbnail':>10s} {'Feature-based':>15s}")
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print("-" * 47)
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for cls in CLASS_ORDER:
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mask = common_labels_arr == cls
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if mask.sum() < 2:
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continue
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thumb_ari = adjusted_rand_score(v8_labels_arr[mask], thumb_labels_arr[mask])
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feat_ari = adjusted_rand_score(v8_labels_arr[mask], simple_labels_arr[mask])
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better = " ←" if feat_ari > thumb_ari else ""
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print(f"{cls:<20s} {thumb_ari:>10.4f} {feat_ari:>15.4f}{better}")
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# Also: direct agreement between thumbnail and feature-based
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print("\n" + "=" * 80)
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print("THUMBNAIL vs FEATURE-BASED (direct agreement)")
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print("=" * 80)
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direct = compute_metrics(thumb_labels_arr, simple_labels_arr, "Thumb vs Feature")
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print(f" ARI={direct['ARI']:.4f} NMI={direct['NMI']:.4f} V_measure={direct['V_measure']:.4f}")
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print("\nDONE")
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