rpotter6298
60 lines
2.6 KiB
Python
60 lines
2.6 KiB
Python
#!/usr/bin/env python3
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"""figure_s3.py — Example CT images from estimated patient clusters.
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Usage: python scripts/visualizations/figure_s3.py [--tag TAG]"""
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import os, sys, csv, argparse
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import numpy as np
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import matplotlib; matplotlib.use("Agg")
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import matplotlib.pyplot as plt
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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(os.path.abspath(__file__)))))
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ROOT = os.path.dirname(os.path.dirname(os.path.dirname(os.path.abspath(__file__))))
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MANIFEST = os.path.join(ROOT, "results", "simple_patient_manifest.csv")
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DATASET = os.path.join(os.path.dirname(ROOT), "The IQ-OTHNCCD lung cancer dataset")
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PLOTS_DIR = os.path.join(ROOT, "plots")
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N_EXAMPLES = 5
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CLASS_MAP = {"Benign": ("Bengin cases", "B"), "Malignant": ("Malignant cases", "M"), "Normal": ("Normal cases", "N")}
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def f2n_back(fname):
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prefix = fname[0]; num = int(fname.split("_")[1])
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cls = {"B": ("Bengin cases", "Bengin"), "M": ("Malignant cases", "Malignant"), "N": ("Normal cases", "Normal")}[prefix]
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return cls[0], f"{cls[1]} case ({num}).jpg"
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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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patients = {}
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with open(MANIFEST, newline="") as f:
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reader = csv.DictReader(f)
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img_col = "confirmed_images" if "confirmed_images" in reader.fieldnames else "images"
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for row in reader:
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imgs = row[img_col].split(";")
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if imgs: patients[row["patient_id"]] = imgs
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fig, axes = plt.subplots(3, N_EXAMPLES, figsize=(12, 8))
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for row, (cls_label, (cls_dir, _)) in enumerate(CLASS_MAP.items()):
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cls_patients = [(p, imgs) for p, imgs in patients.items() if p.lower().startswith(cls_label.lower()) and len(imgs) >= N_EXAMPLES]
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if not cls_patients: continue
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pid, imgs = cls_patients[0]
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for col in range(N_EXAMPLES):
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ax = axes[row, col]
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try:
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cls_dir_name, orig_fname = f2n_back(imgs[col])
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img = Image.open(os.path.join(DATASET, cls_dir_name, orig_fname)).convert("L")
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ax.imshow(img, cmap="gray")
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except Exception as e:
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ax.text(0.5, 0.5, f"error: {e}", ha="center", va="center", fontsize=7)
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ax.set_xticks([]); ax.set_yticks([])
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if col == 0: ax.set_ylabel(f"{cls_label}\nPatient {pid}", fontsize=9, rotation=0, labelpad=40, va="center")
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fig.suptitle("Figure S3 — Example CT images from estimated patient clusters", fontsize=12, y=1.01)
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plt.tight_layout()
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out = os.path.join(PLOTS_DIR, "figure_s3", f"figure_s3{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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