Initial commit: grid-based multi-photon reconstruction

Code, configs, charge LUTs, best.pth and evaluation records for each
training run, the knife-edge / Siemens-star / XRF notebooks with
outputs, and the overnight run reports. Epoch checkpoints, inference
results and HTML exports stay local (see .gitignore).

Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>

scripts/rerun_star_column_masked.sh

@@ -0,0 +1,83 @@
+#!/usr/bin/env bash
+# Siemens star again with the masked column common mode (2026-09-28).
+# The 09-27 run used the plain column median, which the ~5 % occupancy of the
+# star pulls up: the 15 keV line came out at 14.47 keV.  Outputs carry the tag
+# _poly2to20_cmmasked, next to the old _poly2to20 ones.
+#
+#   setsid nohup bash scripts/rerun_star_column_masked.sh \
+#       >> Results/overnight_poly2to20keV_Moench040/driver.log 2>&1 < /dev/null &
+#
+# After parts 0-1 (half of the 20 M frames) the notebook is executed on them and
+# kept as SiemensStar_poly2to20keV_15keV_50pct.ipynb (+ HTML, summary json), so
+# a result exists even if the rest does not finish; after all four parts the
+# main notebook is executed in place.
+
+set -u
+cd /home/xie_x1/MLXID/GridBased
+ENV_BIN=/home/xie_x1/software/miniforge3/envs/pytorch_nightly/bin
+PY=$ENV_BIN/python
+BASE=Results/overnight_poly2to20keV_Moench040
+LOG=$BASE/logs
+STATE=$BASE/state
+STATUS=$BASE/status.md
+REPORT=$BASE/report
+STAR=Configs/infer_measurement_poly_Moench040_star.yaml
+TAG=poly2to20_cmmasked
+experiment=$(cat "$STATE/experiment")
+checkpoint=$experiment/Models/best.pth
+export OMP_NUM_THREADS=4 MKL_NUM_THREADS=4
+export PATH=$ENV_BIN:$PATH GRID_POLY_TAG=$TAG
+NOTEBOOK=Notebooks/SiemensStar_poly2to20keV_15keV
+
+note() {
+    echo "- $(date '+%m-%d %H:%M:%S') $*" >> "$STATUS"
+    echo "$(date '+%m-%d %H:%M:%S') $*"
+}
+
+run() {
+    local name=$1; shift
+    if [ -f "$STATE/$name.done" ]; then
+        note "$name: already done, skipped"; return 0
+    fi
+    note "$name: started"
+    local started=$(date +%s)
+    "$@" > "$LOG/$name.log" 2>&1
+    local status=$?
+    local minutes=$(( ($(date +%s) - started) / 60 ))
+    if [ $status -eq 0 ]; then
+        touch "$STATE/$name.done"
+        note "$name: done (${minutes} min) $(grep -o '([0-9]* frame/s)' "$LOG/$name.log" | tail -1)"
+    else
+        note "$name: **FAILED** (exit $status after ${minutes} min), see logs/$name.log"
+    fi
+    return $status
+}
+
+snapshot() {    # executed copy of the notebook on the first two parts
+    GRID_STAR_RUNS=SiemensStar_15keV_part0,SiemensStar_15keV_part1 \
+    GRID_STAR_SUMMARY=siemens_star_poly2to20keV_summary_50pct.json \
+    jupyter nbconvert --to notebook --execute --ExecutePreprocessor.timeout=3600 \
+        --ExecutePreprocessor.kernel_name=python3 \
+        --output SiemensStar_poly2to20keV_15keV_50pct.ipynb "$NOTEBOOK.ipynb" && \
+    jupyter nbconvert --to html --output-dir "$REPORT" "${NOTEBOOK}_50pct.ipynb"
+}
+
+full() {
+    jupyter nbconvert --to notebook --execute --inplace --ExecutePreprocessor.timeout=3600 \
+        --ExecutePreprocessor.kernel_name=python3 "$NOTEBOOK.ipynb" && \
+    jupyter nbconvert --to html --output-dir "$REPORT" "$NOTEBOOK.ipynb"
+}
+
+note "=== Siemens star rerun, column_masked (pid $$), tag $TAG ==="
+for part in 0 1; do
+    run infer_star_cmmasked_part$part $PY scripts/05_infer_measurement.py --config $STAR \
+        --run SiemensStar_15keV_part$part --checkpoint "$checkpoint" --tag $TAG
+done
+run notebook_star_cmmasked_50pct snapshot
+for part in 2 3; do
+    run infer_star_cmmasked_part$part $PY scripts/05_infer_measurement.py --config $STAR \
+        --run SiemensStar_15keV_part$part --checkpoint "$checkpoint" --tag $TAG
+done
+rm -f "$STATE/notebook_star_cmmasked.done"
+run notebook_star_cmmasked full
+note "=== Siemens star rerun finished ==="