extract_polygons.py

"""
Gleason_CNN masklerinden polygon CSV'si üretir → polygons.csv

Maske değer sözlüğü (palette PNG, tam sayı indeks):
  0 = Benign
  1 = Gleason_3  → G3
  2 = Gleason_4  → G4
  3 = Gleason_5  → G5
  4 = unlabelled → atlanır

Üç kaynak klasör ve karşılık gelen creator:
  Gleason_masks_train             → "train"
  Gleason_masks_test_pathologist1 → "test_pathologist1"
  Gleason_masks_test_pathologist2 → "test_pathologist2"

Her polygon seyreltilir (approxPolyDP, epsilon_start=2.0, max_points=50).
"""

import csv
import json
import os
import re
from pathlib import Path

import cv2
import numpy as np
from PIL import Image

# ---------------------------------------------------------------------------
# Konfigürasyon
# ---------------------------------------------------------------------------

ORIGIN_DIR = Path("origin")
OUT_CSV    = Path("polygons.csv")

LABEL_MAP = {0: "Benign", 1: "G3", 2: "G4", 3: "G5"}  # 4 = unlabelled, atlanır

MIN_AREA      = 150   # piksel cinsinden minimum alan (küçük artefaktları at)
EPSILON_START = 2.0   # approxPolyDP başlangıç epsilonu
MAX_POINTS    = 50    # polygon başına maksimum köşe noktası

SOURCES = [
    ("Gleason_masks_train",             "train",             re.compile(r"^mask_(.+)\.png$")),
    ("Gleason_masks_test_pathologist1", "test_pathologist1", re.compile(r"^mask1_(.+)\.png$")),
    ("Gleason_masks_test_pathologist2", "test_pathologist2", re.compile(r"^mask2_(.+)\.png$")),
]


# ---------------------------------------------------------------------------
# Yardımcı fonksiyonlar
# ---------------------------------------------------------------------------

def simplify_contour(contour) -> list[list[int]] | None:
    """Kontur → basitleştirilmiş kapalı polygon noktaları [[x, y], ...]."""
    approx = cv2.approxPolyDP(contour, EPSILON_START, closed=True)
    eps = EPSILON_START
    while len(approx) > MAX_POINTS and eps <= 20.0:
        eps *= 1.5
        approx = cv2.approxPolyDP(approx.astype(np.float32), eps, closed=True)
    if len(approx) < 3:
        return None
    pts = [[int(p[0][0]), int(p[0][1])] for p in approx]
    pts.append(pts[0])   # kapanış noktası
    return pts


def remove_small_components(binary: np.ndarray) -> np.ndarray:
    n, labels, stats, _ = cv2.connectedComponentsWithStats(binary, connectivity=8)
    clean = np.zeros_like(binary)
    for lid in range(1, n):
        if stats[lid, cv2.CC_STAT_AREA] >= MIN_AREA:
            clean[labels == lid] = 1
    return clean


def process_mask(mask_path: Path, creator: str, image_name: str) -> list[dict]:
    """Maskten polygon satırlarını üretir."""
    try:
        arr = np.array(Image.open(mask_path))
    except Exception as e:
        print(f"  UYARI okuma hatası ({mask_path.name}): {e}")
        return []

    rows = []
    for class_idx, label in LABEL_MAP.items():
        binary = (arr == class_idx).astype(np.uint8)
        if binary.sum() == 0:
            continue

        binary = remove_small_components(binary)
        if binary.sum() == 0:
            continue

        contours, _ = cv2.findContours(binary, cv2.RETR_EXTERNAL, cv2.CHAIN_APPROX_SIMPLE)
        for cnt in contours:
            if cv2.contourArea(cnt) < MIN_AREA:
                continue
            pts = simplify_contour(cnt)
            if pts is None:
                continue
            rows.append({
                "image_name": image_name,
                "label":      label,
                "polygon":    json.dumps(pts),
                "creator":    creator,
            })
    return rows


# ---------------------------------------------------------------------------
# Ana akış
# ---------------------------------------------------------------------------

def main():
    all_rows: list[dict] = []

    for folder_name, creator, name_re in SOURCES:
        folder = ORIGIN_DIR / folder_name
        if not folder.exists():
            print(f"UYARI: klasör bulunamadı → {folder}")
            continue

        mask_files = sorted(
            p for p in folder.glob("*.png")
            if not p.name.startswith("._")
        )
        print(f"\n{folder_name}  ({len(mask_files)} maske)  creator='{creator}'")

        skipped = 0
        for mf in mask_files:
            m = name_re.match(mf.name)
            if not m:
                skipped += 1
                continue
            image_name = m.group(1)
            rows = process_mask(mf, creator, image_name)
            all_rows.extend(rows)

        if skipped:
            print(f"  {skipped} dosya isim kalıbına uymadı, atlandı.")

    print(f"\nToplam {len(all_rows)} polygon satırı → {OUT_CSV}")
    with open(OUT_CSV, "w", newline="") as f:
        writer = csv.DictWriter(
            f, fieldnames=["image_name", "label", "polygon", "creator"]
        )
        writer.writeheader()
        writer.writerows(all_rows)

    print("Tamamlandı.")


if __name__ == "__main__":
    os.chdir(Path(__file__).parent)
    main()