#!/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 ==="