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

scripts/main/refuge/run_unet_segmenter.py

@@ -13,7 +13,7 @@ REPO_ROOT = Path(__file__).resolve().parents[3]
 if str(REPO_ROOT) not in sys.path:
     sys.path.insert(0, str(REPO_ROOT))
 
-from classes.unet_segmenter import UNetSegmenter
+from classes.v2.unet_segmenter import UNetSegmenter
 
 
 def parse_args() -> argparse.Namespace:

scripts/main/v2/run_imgonly_v2.21.sh

@@ -0,0 +1,68 @@
+#!/usr/bin/env bash
+set -euo pipefail
+
+# Image-only runs v2.21 (6 total):
+#   No crop:    binary | multiclass
+#   GT crop:    binary | multiclass
+#   UNet crop:  binary | multiclass
+#
+# Purpose: isolate the effect of ROI cropping at the single-CNN level,
+# without any MD tower contribution (bridge-mode=image_only).
+
+ROOT_DIR="$(cd "$(dirname "${BASH_SOURCE[0]}")/../../.." && pwd)"
+cd "$ROOT_DIR"
+
+MANIFEST="manifest.csv"
+UNET_WEIGHTS="models/v2/refuge/segmentation/per_image/best.pt"
+
+COMMON=(
+  --epochs 40
+  --n-splits 5
+  --batch-size 8
+  --backbone refugelike
+  --tower-mode single
+  --bridge-mode image_only
+  --single-warmup-tower-epochs 4
+  --single-warmup-fused-epochs 0
+  --img-crop-manifest "$MANIFEST"
+)
+
+# ── No crop ──────────────────────────────────────────────────────────────────
+
+echo "[1/6] No crop — binary, image-only..."
+python3 scripts/main/v2/run_multifold_v2.py \
+  "${COMMON[@]}" --eval-mode binary \
+  --run-name v2.21_imgonly_binary_nocrop_40ep_5fold
+
+echo "[2/6] No crop — multiclass, image-only..."
+python3 scripts/main/v2/run_multifold_v2.py \
+  "${COMMON[@]}" --eval-mode multiclass \
+  --run-name v2.21_imgonly_multiclass_nocrop_40ep_5fold
+
+# ── GT crop ──────────────────────────────────────────────────────────────────
+
+echo "[3/6] GT crop — binary, image-only..."
+python3 scripts/main/v2/run_multifold_v2.py \
+  "${COMMON[@]}" --eval-mode binary --img-crop-gt \
+  --run-name v2.21_imgonly_binary_gt_40ep_5fold
+
+echo "[4/6] GT crop — multiclass, image-only..."
+python3 scripts/main/v2/run_multifold_v2.py \
+  "${COMMON[@]}" --eval-mode multiclass --img-crop-gt \
+  --run-name v2.21_imgonly_multiclass_gt_40ep_5fold
+
+# ── UNet crop ────────────────────────────────────────────────────────────────
+
+echo "[5/6] UNet crop — binary, image-only..."
+python3 scripts/main/v2/run_multifold_v2.py \
+  "${COMMON[@]}" --eval-mode binary \
+  --img-crop-weights "$UNET_WEIGHTS" \
+  --run-name v2.21_imgonly_binary_unet_40ep_5fold
+
+echo "[6/6] UNet crop — multiclass, image-only..."
+python3 scripts/main/v2/run_multifold_v2.py \
+  "${COMMON[@]}" --eval-mode multiclass \
+  --img-crop-weights "$UNET_WEIGHTS" \
+  --run-name v2.21_imgonly_multiclass_unet_40ep_5fold
+
+echo "Image-only v2.21 runs complete."

scripts/main/v2/run_v2.3_ensemble_nocrop.sh

@@ -0,0 +1,20 @@
+#!/usr/bin/env bash
+set -e
+
+echo "=== v2.3 ensemble binary nocrop ==="
+python scripts/basic_analysis/compare_hypertower_modes.py \
+  --tower-modes ensemble --eval-modes binary \
+  --epochs 40 --n-splits 5 \
+  --backbone refugelike \
+  --img-crop-manifest analysis_data/unet_manifest.csv \
+  --run-name v2.3_ensemble_binary_nocrop
+
+echo "=== v2.3 ensemble multiclass nocrop ==="
+python scripts/basic_analysis/compare_hypertower_modes.py \
+  --tower-modes ensemble --eval-modes multiclass \
+  --epochs 40 --n-splits 5 \
+  --backbone refugelike \
+  --img-crop-manifest analysis_data/unet_manifest.csv \
+  --run-name v2.3_ensemble_multiclass_nocrop
+
+echo "=== done ==="

scripts/main/v2/run_v2.3_fused_nocrop.sh

@@ -0,0 +1,24 @@
+#!/usr/bin/env bash
+set -e
+
+echo "=== v2.3 fused binary nocrop ==="
+python scripts/basic_analysis/compare_hypertower_modes.py \
+  --tower-modes ensemble --eval-modes binary \
+  --epochs 40 --n-splits 5 \
+  --backbone refugelike \
+  --img-crop-manifest analysis_data/unet_manifest.csv \
+  --warmup-md-epochs 50 \
+  --fused-head \
+  --run-name v2.3_fused_binary_nocrop
+
+echo "=== v2.3 fused multiclass nocrop ==="
+python scripts/basic_analysis/compare_hypertower_modes.py \
+  --tower-modes ensemble --eval-modes multiclass \
+  --epochs 40 --n-splits 5 \
+  --backbone refugelike \
+  --img-crop-manifest analysis_data/unet_manifest.csv \
+  --warmup-md-epochs 50 \
+  --fused-head \
+  --run-name v2.3_fused_multiclass_nocrop
+
+echo "=== done ==="