2026001
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rpotter6298
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#!/usr/bin/env python3
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"""
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manifest_html.py — Generate HTML pages for visually inspecting patient manifests.
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One HTML file per class, each patient's assigned images shown in a row.
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Usage:
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python scripts/visualizations/manifest_html.py
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python scripts/visualizations/manifest_html.py --method siamese
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python scripts/visualizations/manifest_html.py --manifest results/simple_patient_manifest.csv --method pca50
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"""
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import os, sys, csv, argparse, base64
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from io import BytesIO
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from PIL import Image
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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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DATASET = os.path.join(os.path.dirname(ROOT), "The IQ-OTHNCCD lung cancer dataset")
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RESULTS_DIR = os.path.join(ROOT, "results")
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HTML_DIR = os.path.join(ROOT, "plots", "html")
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MANIFESTS = {
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"pca50": os.path.join(RESULTS_DIR, "simple_patient_manifest.csv"),
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"thumbnail": os.path.join(RESULTS_DIR, "thumbnail_patient_manifest.csv"),
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"siamese": os.path.join(RESULTS_DIR, "siamese_manifest.csv"),
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}
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THUMB_SIZE = 150 # px, display width
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def f2n_back(short_name):
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"""B_009 → ('Bengin cases', 'Bengin case (9).jpg')"""
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prefix = short_name[0]
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num = int(short_name.split("_")[1])
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cls_map = {"B": ("Bengin cases", "Bengin"),
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"M": ("Malignant cases", "Malignant"),
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"N": ("Normal cases", "Normal")}
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dir_name, file_prefix = cls_map[prefix]
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return dir_name, f"{file_prefix} case ({num}).jpg"
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def img_to_b64(path, size=THUMB_SIZE):
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"""Load an image and return a base64 data URI."""
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try:
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img = Image.open(path).convert("L")
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img.thumbnail((size, size), Image.LANCZOS)
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buf = BytesIO()
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img.save(buf, format="PNG")
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return f"data:image/png;base64,{base64.b64encode(buf.getvalue()).decode()}"
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except Exception:
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return ""
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def build_html(manifest_path, method, class_name, class_dir, patients):
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"""Generate an HTML string for one class."""
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rows = []
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for pid, short_names in patients.items():
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# Build image cards
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cards = []
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for sn in short_names:
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dir_name, fname = f2n_back(sn)
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img_path = os.path.join(DATASET, dir_name, fname)
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b64 = img_to_b64(img_path)
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if b64:
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cards.append(
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f'<div class="card">'
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f'<img src="{b64}" alt="{sn}">'
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f'<div class="label">{sn}</div>'
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f'</div>')
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if cards:
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rows.append(
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f'<div class="patient">'
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f'<h3>{pid} <span class="count">({len(cards)} images)</span></h3>'
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f'<div class="images">{"".join(cards)}</div>'
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f'</div>')
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return f"""<!DOCTYPE html>
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<html lang="en">
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<head>
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<meta charset="UTF-8">
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<title>{method} — {class_name}</title>
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<style>
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body {{ font-family: -apple-system, sans-serif; background: #1a1a2e; color: #eee; margin: 20px; }}
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h1 {{ color: #e94560; }}
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.patient {{ margin-bottom: 30px; border-bottom: 1px solid #333; padding-bottom: 15px; }}
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.patient h3 {{ margin: 0 0 8px 0; color: #0f3460; background: #16213e; padding: 6px 12px; border-radius: 4px; display: inline-block; }}
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.count {{ font-weight: normal; color: #888; font-size: 0.85em; }}
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.images {{ display: flex; flex-wrap: wrap; gap: 8px; }}
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.card {{ background: #16213e; border-radius: 4px; overflow: hidden; width: {THUMB_SIZE + 20}px; }}
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.card img {{ display: block; width: {THUMB_SIZE}px; height: {THUMB_SIZE}px; object-fit: contain; margin: 0 auto; background: #000; }}
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.label {{ font-size: 9px; color: #aaa; text-align: center; padding: 4px; word-break: break-all; }}
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a.nav {{ color: #e94560; margin-right: 15px; }}
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</style>
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</head>
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<body>
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<h1>{method} — {class_name} <small>({len(patients)} patients, {sum(len(v) for v in patients.values())} images)</small></h1>
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<p>
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<a class="nav" href="{method}_Benign.html">Benign</a>
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<a class="nav" href="{method}_Malignant.html">Malignant</a>
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<a class="nav" href="{method}_Normal.html">Normal</a>
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</p>
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{"".join(rows)}
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</body>
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</html>"""
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def main():
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ap = argparse.ArgumentParser()
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ap.add_argument("--method", default=None,
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help="Which manifest method (pca50, thumbnail, siamese). "
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"Default: all.")
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ap.add_argument("--manifest", default=None,
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help="Path to manifest CSV (overrides --method).")
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args = ap.parse_args()
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os.makedirs(HTML_DIR, exist_ok=True)
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methods_to_run = [args.method] if args.method else list(MANIFESTS.keys())
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for method in methods_to_run:
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manifest_path = args.manifest or MANIFESTS.get(method)
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if not manifest_path or not os.path.exists(manifest_path):
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print(f" {method}: manifest not found ({manifest_path})")
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continue
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# Load manifest, group by class
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patients_by_class = {"Benign": {}, "Malignant": {}, "Normal": {}}
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with open(manifest_path, newline="") as f:
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reader = csv.DictReader(f)
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img_col = ("images" if "images" in reader.fieldnames
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else "confirmed_images")
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for row in reader:
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cls = row.get("class", "").strip()
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# Normalize class names
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cls_lower = cls.lower()
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if cls_lower in ("benign", "bengin"):
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cls = "Benign"
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elif cls_lower in ("malignant", "malig"):
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cls = "Malignant"
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elif cls_lower == "normal":
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cls = "Normal"
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elif cls_lower == "unknown":
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# Infer from patient_id prefix
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pid = row.get("patient_id", "")
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if pid.lower().startswith("benign") or pid.lower().startswith("bengin"):
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cls = "Benign"
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elif pid.lower().startswith("malignant") or pid.lower().startswith("malig"):
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cls = "Malignant"
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elif pid.lower().startswith("normal"):
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cls = "Normal"
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if cls not in patients_by_class:
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continue
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pid = row["patient_id"]
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imgs = row[img_col].split(";") if row[img_col] else []
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if imgs:
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patients_by_class[cls][pid] = imgs
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for cls_name in ["Benign", "Malignant", "Normal"]:
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patients = patients_by_class[cls_name]
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if not patients:
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print(f" {method}/{cls_name}: no patients, skipping")
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continue
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html = build_html(manifest_path, method, cls_name,
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"", patients)
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out_path = os.path.join(HTML_DIR, f"{method}_{cls_name}.html")
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with open(out_path, "w") as f:
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f.write(html)
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print(f" Saved → plots/html/{method}_{cls_name}.html "
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f"({len(patients)} patients)")
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print("DONE")
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if __name__ == "__main__":
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main()
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