reworked iop_corr, added explainability tools and plotting tools, cleanup codebase

2026-03-12 16:12:59 +01:00
parent 13ad32683f
commit 6d0698d0fb
35 changed files with 7765 additions and 5723 deletions
@@ -0,0 +1,87 @@
+"""Shared helpers for deriving disc/cup geometry features."""
+
+from __future__ import annotations
+
+from collections import Counter
+from typing import Tuple
+
+import numpy as np
+from PIL import Image
+
+EPS = 1e-6
+FEATURE_DIM = 5
+
+
+def disc_cup_from_mask_image(mask_img: Image.Image) -> Tuple[np.ndarray, np.ndarray]:
+    """Return binary disc/cup masks from a REFUGE-style annotation image."""
+    arr = np.asarray(mask_img)
+    if arr.ndim == 3:
+        h, w, c = arr.shape
+        border = np.concatenate(
+            [arr[0, :, :], arr[-1, :, :], arr[:, 0, :], arr[:, -1, :]],
+            axis=0,
+        )
+        border_counts = Counter(map(tuple, border))
+        bg_color = border_counts.most_common(1)[0][0]
+        flat = arr.reshape(-1, c)
+        colors = Counter(map(tuple, flat))
+        colors.pop(bg_color, None)
+        disc = (~np.all(arr == bg_color, axis=-1)).astype(np.uint8)
+        if colors:
+            cup_color = min(colors.keys(), key=lambda col: sum(col))
+            cup = np.all(arr == cup_color, axis=-1).astype(np.uint8)
+        else:
+            cup = np.zeros((h, w), dtype=np.uint8)
+    else:
+        border = np.concatenate([arr[0, :], arr[-1, :], arr[:, 0], arr[:, -1]])
+        counts = Counter(border.tolist())
+        bg_value = counts.most_common(1)[0][0]
+        disc = (arr != bg_value).astype(np.uint8)
+        fg = arr[arr != bg_value]
+        if fg.size > 0:
+            cup_value = int(np.min(fg))
+            cup = (arr == cup_value).astype(np.uint8)
+        else:
+            cup = np.zeros_like(arr, dtype=np.uint8)
+    cup = (cup > 0) & (disc > 0)
+    return disc.astype(np.uint8), cup.astype(np.uint8)
+
+
+def compute_geometry_features(disc_mask: np.ndarray, cup_mask: np.ndarray) -> np.ndarray:
+    """Compute cup/disc geometry descriptors (area, rim, diameter ratios, centre shift)."""
+    disc = (disc_mask > 0).astype(np.float32)
+    cup = (cup_mask > 0).astype(np.float32)
+
+    disc_area = disc.sum()
+    cup_area = cup.sum()
+    area_ratio = cup_area / (disc_area + EPS)
+    rim_ratio = (disc_area - cup_area) / (disc_area + EPS)
+
+    disc_rows = np.any(disc > 0, axis=1)
+    cup_rows = np.any(cup > 0, axis=1)
+    disc_cols = np.any(disc > 0, axis=0)
+    cup_cols = np.any(cup > 0, axis=0)
+
+    disc_height = float(disc_rows.sum())
+    cup_height = float(cup_rows.sum())
+    disc_width = float(disc_cols.sum())
+    cup_width = float(cup_cols.sum())
+
+    vertical_ratio = cup_height / (disc_height + EPS)
+    horizontal_ratio = cup_width / (disc_width + EPS)
+
+    def _centre(mask: np.ndarray) -> Tuple[float, float]:
+        coords = np.argwhere(mask > 0)
+        if coords.size == 0:
+            return 0.5, 0.5
+        ys, xs = coords[:, 0], coords[:, 1]
+        return float(xs.mean()) / mask.shape[1], float(ys.mean()) / mask.shape[0]
+
+    disc_cx, disc_cy = _centre(disc)
+    cup_cx, cup_cy = _centre(cup)
+    centre_shift = float(np.hypot(cup_cx - disc_cx, cup_cy - disc_cy))
+
+    return np.array(
+        [area_ratio, rim_ratio, vertical_ratio, horizontal_ratio, centre_shift],
+        dtype=np.float32,
+    )