added fused classifier head

scripts/main/v2/run_fused_head_overnight.sh

@@ -0,0 +1,41 @@
+#!/usr/bin/env bash
+set -euo pipefail
+
+# Fused-head ensemble runs (2 total) — UNet ROI crop:
+#   binary     × ensemble + fused head
+#   multiclass × ensemble + fused head
+
+ROOT_DIR="$(cd "$(dirname "${BASH_SOURCE[0]}")/../../.." && pwd)"
+cd "$ROOT_DIR"
+
+CROP_ARGS=(
+  --img-crop-manifest manifest.csv
+  --img-crop-weights models/v2/refuge/segmentation/per_image_refuge_build/best.pt
+  --img-crop-normalize per_image
+)
+
+COMMON_ARGS=(
+  --epochs 40
+  --n-splits 5
+  --batch-size 8
+  --backbone refugelike
+  --tower-mode ensemble
+  --fused-head
+  --fusion-epochs 10
+)
+
+echo "[1/2] UNet ROI — binary, ensemble + fused head..."
+python3 scripts/main/v2/run_multifold_v2.py \
+  "${COMMON_ARGS[@]}" \
+  "${CROP_ARGS[@]}" \
+  --eval-mode binary \
+  --run-name v2_ensemble_fused_binary_unet_40ep_5fold_v1
+
+echo "[2/2] UNet ROI — multiclass, ensemble + fused head..."
+python3 scripts/main/v2/run_multifold_v2.py \
+  "${COMMON_ARGS[@]}" \
+  "${CROP_ARGS[@]}" \
+  --eval-mode multiclass \
+  --run-name v2_ensemble_fused_multiclass_unet_40ep_5fold_v1
+
+echo "Fused-head runs complete."

scripts/main/v2/run_modes_roi_overnight.sh

@@ -1,34 +1,45 @@
 #!/usr/bin/env bash
 set -euo pipefail
 
-# Runs two back-to-back Hypertower mode comparisons with ROI cropping:
-#   1) GT masks
-#   2) UNet masks
+# Six V2HyperTower runs using GT ROI crop:
+#   binary  × {ensemble, bilateral}               (runs 1-2)
+#   multiclass × {ensemble, bilateral}             (runs 3-4)
+#   multiclass × {ensemble, bilateral} + balanced  (runs 5-6)
 
 ROOT_DIR="$(cd "$(dirname "${BASH_SOURCE[0]}")/../../.." && pwd)"
 cd "$ROOT_DIR"
 
+CROP_ARGS=(
+  --img-crop-manifest manifest.csv
+  --img-crop-gt
+)
+
 COMMON_ARGS=(
-  --eval-modes binary multiclass
-  --tower-modes single ensemble bilateral
   --epochs 40
   --n-splits 5
   --batch-size 8
   --backbone refugelike
-  --img-crop-manifest manifest.csv
 )
 
-echo "[1/2] Starting GT ROI run..."
+# Runs 1-4: binary + multiclass, ensemble + bilateral, no balanced sampling
+echo "[1/2] GT ROI — binary + multiclass, ensemble + bilateral..."
 python3 scripts/basic_analysis/compare_hypertower_modes.py \
   "${COMMON_ARGS[@]}" \
-  --img-crop-gt \
-  --run-name v2_modes_full_40ep_5fold_roi_gt_holdout
+  "${CROP_ARGS[@]}" \
+  --eval-modes binary multiclass \
+  --tower-modes ensemble bilateral \
+  --run-name v2_modes_gt_40ep_5fold_no_single_v2
 
-echo "[2/2] Starting UNet ROI run..."
+# Runs 5-6: multiclass only, ensemble + bilateral, balanced sampling
+# (reuse the crop cache built during runs 1-4)
+echo "[2/2] GT ROI — multiclass, ensemble + bilateral, balanced sampling..."
 python3 scripts/basic_analysis/compare_hypertower_modes.py \
   "${COMMON_ARGS[@]}" \
-  --img-crop-weights models/v2/refuge/segmentation/per_image_refuge_build/best.pt \
-  --img-crop-normalize per_image \
-  --run-name v2_modes_full_40ep_5fold_roi_unet_perimage_refugebuild_holdout
+  "${CROP_ARGS[@]}" \
+  --eval-modes multiclass \
+  --tower-modes ensemble bilateral \
+  --balanced-sampling \
+  --persist-img-crop-cache \
+  --run-name v2_modes_gt_40ep_5fold_multiclass_balanced_v2
 
 echo "All runs complete."

scripts/main/v2/run_modes_roi_overnight_bilateral.sh

@@ -0,0 +1,44 @@
+#!/usr/bin/env bash
+set -euo pipefail
+
+# Bilateral tower runs (3 total):
+#   binary     × bilateral
+#   multiclass × bilateral
+#   multiclass × bilateral + balanced sampling
+
+ROOT_DIR="$(cd "$(dirname "${BASH_SOURCE[0]}")/../../.." && pwd)"
+cd "$ROOT_DIR"
+
+CROP_ARGS=(
+  --img-crop-manifest manifest.csv
+  --img-crop-gt
+)
+
+COMMON_ARGS=(
+  --epochs 40
+  --n-splits 5
+  --batch-size 8
+  --backbone refugelike
+  --tower-modes bilateral
+)
+
+# Runs 1-2: binary + multiclass bilateral (no balanced sampling)
+echo "[1/2] GT ROI — binary + multiclass, bilateral..."
+python3 scripts/basic_analysis/compare_hypertower_modes.py \
+  "${COMMON_ARGS[@]}" \
+  "${CROP_ARGS[@]}" \
+  --eval-modes binary multiclass \
+  --run-name v2_modes_gt_40ep_5fold_bilateral_v2
+
+# Run 3: multiclass bilateral + balanced sampling
+# (reuse the crop cache built above)
+echo "[2/2] GT ROI — multiclass, bilateral, balanced sampling..."
+python3 scripts/basic_analysis/compare_hypertower_modes.py \
+  "${COMMON_ARGS[@]}" \
+  "${CROP_ARGS[@]}" \
+  --eval-modes multiclass \
+  --balanced-sampling \
+  --persist-img-crop-cache \
+  --run-name v2_modes_gt_40ep_5fold_bilateral_balanced_v2
+
+echo "Bilateral runs complete."

scripts/main/v2/run_modes_roi_overnight_bilateral_unet.sh

@@ -0,0 +1,45 @@
+#!/usr/bin/env bash
+set -euo pipefail
+
+# Bilateral tower runs (3 total) — UNet ROI crop:
+#   binary     × bilateral
+#   multiclass × bilateral
+#   multiclass × bilateral + balanced sampling
+
+ROOT_DIR="$(cd "$(dirname "${BASH_SOURCE[0]}")/../../.." && pwd)"
+cd "$ROOT_DIR"
+
+CROP_ARGS=(
+  --img-crop-manifest manifest.csv
+  --img-crop-weights models/v2/refuge/segmentation/per_image_refuge_build/best.pt
+  --img-crop-normalize per_image
+)
+
+COMMON_ARGS=(
+  --epochs 40
+  --n-splits 5
+  --batch-size 8
+  --backbone refugelike
+  --tower-modes bilateral
+)
+
+# Runs 1-2: binary + multiclass bilateral (no balanced sampling)
+echo "[1/2] UNet ROI — binary + multiclass, bilateral..."
+python3 scripts/basic_analysis/compare_hypertower_modes.py \
+  "${COMMON_ARGS[@]}" \
+  "${CROP_ARGS[@]}" \
+  --eval-modes binary multiclass \
+  --run-name v2_modes_unet_40ep_5fold_bilateral_v2
+
+# Run 3: multiclass bilateral + balanced sampling
+# (reuse the crop cache built above)
+echo "[2/2] UNet ROI — multiclass, bilateral, balanced sampling..."
+python3 scripts/basic_analysis/compare_hypertower_modes.py \
+  "${COMMON_ARGS[@]}" \
+  "${CROP_ARGS[@]}" \
+  --eval-modes multiclass \
+  --balanced-sampling \
+  --persist-img-crop-cache \
+  --run-name v2_modes_unet_40ep_5fold_bilateral_balanced_v2
+
+echo "Bilateral UNet runs complete."

scripts/main/v2/run_modes_roi_overnight_ensemble.sh

@@ -0,0 +1,44 @@
+#!/usr/bin/env bash
+set -euo pipefail
+
+# Ensemble tower runs (3 total):
+#   binary     × ensemble
+#   multiclass × ensemble
+#   multiclass × ensemble + balanced sampling
+
+ROOT_DIR="$(cd "$(dirname "${BASH_SOURCE[0]}")/../../.." && pwd)"
+cd "$ROOT_DIR"
+
+CROP_ARGS=(
+  --img-crop-manifest manifest.csv
+  --img-crop-gt
+)
+
+COMMON_ARGS=(
+  --epochs 40
+  --n-splits 5
+  --batch-size 8
+  --backbone refugelike
+  --tower-modes ensemble
+)
+
+# Runs 1-2: binary + multiclass ensemble (no balanced sampling)
+echo "[1/2] GT ROI — binary + multiclass, ensemble..."
+python3 scripts/basic_analysis/compare_hypertower_modes.py \
+  "${COMMON_ARGS[@]}" \
+  "${CROP_ARGS[@]}" \
+  --eval-modes binary multiclass \
+  --run-name v2_modes_gt_40ep_5fold_ensemble_v2
+
+# Run 3: multiclass ensemble + balanced sampling
+# (reuse the crop cache built above)
+echo "[2/2] GT ROI — multiclass, ensemble, balanced sampling..."
+python3 scripts/basic_analysis/compare_hypertower_modes.py \
+  "${COMMON_ARGS[@]}" \
+  "${CROP_ARGS[@]}" \
+  --eval-modes multiclass \
+  --balanced-sampling \
+  --persist-img-crop-cache \
+  --run-name v2_modes_gt_40ep_5fold_ensemble_balanced_v2
+
+echo "Ensemble runs complete."

scripts/main/v2/run_modes_roi_overnight_ensemble_unet.sh

@@ -0,0 +1,45 @@
+#!/usr/bin/env bash
+set -euo pipefail
+
+# Ensemble tower runs (3 total) — UNet ROI crop:
+#   binary     × ensemble
+#   multiclass × ensemble
+#   multiclass × ensemble + balanced sampling
+
+ROOT_DIR="$(cd "$(dirname "${BASH_SOURCE[0]}")/../../.." && pwd)"
+cd "$ROOT_DIR"
+
+CROP_ARGS=(
+  --img-crop-manifest manifest.csv
+  --img-crop-weights models/v2/refuge/segmentation/per_image_refuge_build/best.pt
+  --img-crop-normalize per_image
+)
+
+COMMON_ARGS=(
+  --epochs 40
+  --n-splits 5
+  --batch-size 8
+  --backbone refugelike
+  --tower-modes ensemble
+)
+
+# Runs 1-2: binary + multiclass ensemble (no balanced sampling)
+echo "[1/2] UNet ROI — binary + multiclass, ensemble..."
+python3 scripts/basic_analysis/compare_hypertower_modes.py \
+  "${COMMON_ARGS[@]}" \
+  "${CROP_ARGS[@]}" \
+  --eval-modes binary multiclass \
+  --run-name v2_modes_unet_40ep_5fold_ensemble_v2
+
+# Run 3: multiclass ensemble + balanced sampling
+# (reuse the crop cache built above)
+echo "[2/2] UNet ROI — multiclass, ensemble, balanced sampling..."
+python3 scripts/basic_analysis/compare_hypertower_modes.py \
+  "${COMMON_ARGS[@]}" \
+  "${CROP_ARGS[@]}" \
+  --eval-modes multiclass \
+  --balanced-sampling \
+  --persist-img-crop-cache \
+  --run-name v2_modes_unet_40ep_5fold_ensemble_balanced_v2
+
+echo "Ensemble UNet runs complete."

scripts/utility/backup_mirror_with_archive.sh

@@ -0,0 +1,63 @@
+#!/usr/bin/env bash
+set -euo pipefail
+
+# Mirror SOURCE -> DEST while archiving files that would be deleted/overwritten.
+# Archived files are moved under DEST/.archive/<timestamp>/ preserving hierarchy.
+#
+# Usage:
+#   bash scripts/utility/backup_mirror_with_archive.sh
+#   bash scripts/utility/backup_mirror_with_archive.sh --dry-run
+#   bash scripts/utility/backup_mirror_with_archive.sh --source /src --dest /dst
+
+SOURCE="/home/rpotter/hypertower/"
+DEST="/Muspelheim/PhD/00.3_hypertower/"
+DRY_RUN=0
+
+while [[ $# -gt 0 ]]; do
+  case "$1" in
+    --source)
+      SOURCE="$2"
+      shift 2
+      ;;
+    --dest)
+      DEST="$2"
+      shift 2
+      ;;
+    --dry-run)
+      DRY_RUN=1
+      shift
+      ;;
+    *)
+      echo "Unknown argument: $1" >&2
+      exit 2
+      ;;
+  esac
+done
+
+ts="$(date +%Y%m%d_%H%M%S)"
+archive_dir="${DEST%/}/.archive/${ts}"
+
+mkdir -p "$archive_dir"
+
+cmd=(
+  rsync -avh --progress
+  --delete
+  --backup
+  --backup-dir="$archive_dir"
+  --exclude=".archive/"
+  "${SOURCE%/}/"
+  "${DEST%/}/"
+)
+
+if [[ "$DRY_RUN" -eq 1 ]]; then
+  cmd+=(--dry-run)
+fi
+
+echo "Source:  ${SOURCE%/}/"
+echo "Dest:    ${DEST%/}/"
+echo "Archive: $archive_dir"
+[[ "$DRY_RUN" -eq 1 ]] && echo "Mode:    dry-run"
+echo
+
+"${cmd[@]}"
+