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#!/bin/bash # Exostrata — LiCSBAS processing for Bucks + Beds + Herts # Clips from all-England data on E:, then runs steps 11-13 # With validation between each step set -euo pipefail export PATH="/c/msys64/mingw64/bin:$PATH" export PYTHONPATH="C:\\Users\\Administrator\\LiCSBAS\\LiCSBAS_lib" PYTHON="C:\\Users\\Administrator\\Documents\\AllStrata\\.venv-licsbas\\Scripts\\python.exe" # Source data (all-England clipped interferograms) SRC_DIR="E:\\AllStrata\\GEOCml10clip_desc" # Output directories CLIP_DIR="E:\\AllStrata\\GEOCml10clip_3counties" TS_DIR="E:\\AllStrata\\TS_3counties" # Bounding box: Bucks + Beds + Herts with 5km buffer (verified from postcodes) CLIP_BOX="-1.04/0.04/51.52/52.3" LOG="C:\\Users\\Administrator\\Documents\\AllStrata\\three_counties.log" log() { echo "[$(date '+%Y-%m-%d %H:%M:%S')] $1" | tee -a "$LOG" } log "==========================================" log "Three Counties Processing Pipeline" log "Clip box: $CLIP_BOX" log "==========================================" # ============================================================ # STEP 05: Clip to three counties # ============================================================ log "" log "[STEP 05] Clipping to Bucks + Beds + Herts" # Clean any previous attempt rm -rf "$CLIP_DIR" "$TS_DIR" $PYTHON "C:\\Users\\Administrator\\LiCSBAS\\bin\\LiCSBAS05op_clip_unw.py" \ -i "$SRC_DIR" \ -o "$CLIP_DIR" \ -g "$CLIP_BOX" \ --n_para 1 2>&1 | tee -a "$LOG" # --- VALIDATE STEP 05 --- log "" log "[VALIDATE 05] Checking clip output..." # Check EQA.dem_par exists and has correct dimensions if [ ! -f "$CLIP_DIR/EQA.dem_par" ]; then log "[FAIL] No EQA.dem_par — clip failed" exit 1 fi # Verify grid dimensions match expected EXPECTED_W=1080 EXPECTED_H=779 ACTUAL_W=$(grep "^width:" "$CLIP_DIR/EQA.dem_par" | awk '{print $2}') ACTUAL_H=$(grep "^nlines:" "$CLIP_DIR/EQA.dem_par" | awk '{print $2}') log " Grid size: ${ACTUAL_W} x ${ACTUAL_H} (expected ~${EXPECTED_W} x ${EXPECTED_H})" if [ "$ACTUAL_W" -lt 500 ] || [ "$ACTUAL_H" -lt 500 ]; then log "[FAIL] Grid too small — clip bounds wrong?" exit 1 fi # Count clipped IFG directories N_IFGS=$(ls -d "$CLIP_DIR"/20*/ 2>/dev/null | wc -l) log " IFG directories: $N_IFGS" if [ "$N_IFGS" -lt 1000 ]; then log "[FAIL] Too few IFGs ($N_IFGS). Expected ~1900+" exit 1 fi # Check a sample IFG has the right file size SAMPLE_DIR=$(ls -d "$CLIP_DIR"/20*/ 2>/dev/null | head -1) SAMPLE_UNW=$(ls "$SAMPLE_DIR"/*.unw 2>/dev/null | head -1) if [ -z "$SAMPLE_UNW" ]; then log "[FAIL] No .unw file in sample IFG directory" exit 1 fi SAMPLE_SIZE=$(stat -c %s "$SAMPLE_UNW" 2>/dev/null || wc -c < "$SAMPLE_UNW") EXPECTED_SIZE=$((ACTUAL_W * ACTUAL_H * 4)) # float32 = 4 bytes log " Sample unw size: $SAMPLE_SIZE bytes (expected: $EXPECTED_SIZE)" if [ "$SAMPLE_SIZE" -ne "$EXPECTED_SIZE" ]; then log "[WARN] Sample unw size doesn't match expected grid dimensions" fi log "[VALIDATE 05] PASSED" log " Clipped data: $(du -sh "$CLIP_DIR" | awk '{print $1}')" # ============================================================ # STEP 11: Check interferogram quality # ============================================================ log "" log "[STEP 11] Check interferogram quality" $PYTHON "C:\\Users\\Administrator\\LiCSBAS\\bin\\LiCSBAS11_check_unw.py" \ -d "$CLIP_DIR" \ -t "$TS_DIR" \ -c 0.05 2>&1 | tee -a "$LOG" # --- VALIDATE STEP 11 --- log "" log "[VALIDATE 11] Checking step 11 output..." if [ ! -d "$TS_DIR/info" ]; then log "[FAIL] No info directory created" exit 1 fi if [ ! -f "$TS_DIR/info/11ifg_stats.txt" ]; then log "[FAIL] No 11ifg_stats.txt" exit 1 fi N_BAD_11=$(wc -l < "$TS_DIR/info/11bad_ifg.txt" 2>/dev/null || echo 0) N_REMOVED_11=$(wc -l < "$TS_DIR/info/11removed_image.txt" 2>/dev/null || echo 0) N_VALID=$(head -1 "$TS_DIR/info/11ifg_stats.txt" | grep -oP 'n_valid: \K\d+') log " Bad IFGs: $N_BAD_11" log " Removed images: $N_REMOVED_11" log " Valid pixels: $N_VALID" if [ -z "$N_VALID" ] || [ "$N_VALID" -lt 10000 ]; then log "[FAIL] Too few valid pixels ($N_VALID). Data may be corrupted." exit 1 fi log "[VALIDATE 11] PASSED" # ============================================================ # STEP 12: Loop closure # ============================================================ log "" log "[STEP 12] Loop closure check" $PYTHON "C:\\Users\\Administrator\\LiCSBAS\\bin\\LiCSBAS12_loop_closure.py" \ -d "$CLIP_DIR" \ -t "$TS_DIR" 2>&1 | tee -a "$LOG" # --- VALIDATE STEP 12 --- log "" log "[VALIDATE 12] Checking step 12 output..." N_BAD_12=$(wc -l < "$TS_DIR/info/12bad_ifg.txt" 2>/dev/null || echo 0) N_REMOVED_12=$(wc -l < "$TS_DIR/info/12removed_image.txt" 2>/dev/null || echo 0) log " Bad IFGs (loop closure): $N_BAD_12" log " Removed images: $N_REMOVED_12" # Check network plots were generated if ls "$TS_DIR/network/network12"* 1>/dev/null 2>&1; then log " Network plots: generated" else log " [WARN] No network12 plots (may be OK if no removals)" fi log "[VALIDATE 12] PASSED" # ============================================================ # STEP 13: NSBAS inversion # ============================================================ log "" log "[STEP 13] NSBAS time series inversion" log " This is the heavy step — estimated 2-4 hours" $PYTHON "C:\\Users\\Administrator\\LiCSBAS\\bin\\LiCSBAS13_sb_inv.py" \ -d "$CLIP_DIR" \ -t "$TS_DIR" 2>&1 | tee -a "$LOG" # --- VALIDATE STEP 13 --- log "" log "[VALIDATE 13] Checking step 13 output..." if [ ! -f "$TS_DIR/cum.h5" ]; then log "[FAIL] No cum.h5 — inversion failed" exit 1 fi CUM_SIZE=$(du -sh "$TS_DIR/cum.h5" | awk '{print $1}') log " cum.h5: $CUM_SIZE" # Verify cum.h5 is a valid HDF5 with expected datasets $PYTHON -c " import h5py import numpy as np with h5py.File(r'$TS_DIR/cum.h5', 'r') as f: print(' HDF5 datasets:', list(f.keys())) if 'cum' in f: shape = f['cum'].shape print(f' cum shape: {shape}') print(f' Epochs: {shape[0]}') print(f' Grid: {shape[1]} x {shape[2]}') # Check it's not all NaN sample = f['cum'][-1, :, :] valid = np.count_nonzero(~np.isnan(sample)) total = sample.size print(f' Valid pixels (last epoch): {valid}/{total} ({valid/total*100:.1f}%)') if 'imdates' in f: dates = f['imdates'][:] print(f' Date range: {dates[0]} to {dates[-1]}') " 2>&1 | tee -a "$LOG" # Check velocity file if [ -f "$TS_DIR/results/vel" ] || [ -f "$TS_DIR/vel" ]; then log " Velocity file: exists" else log " [WARN] No velocity file found" fi log "[VALIDATE 13] PASSED" # ============================================================ # SUMMARY # ============================================================ log "" log "==========================================" log "THREE COUNTIES PROCESSING COMPLETE" log "Finished: $(date)" log "==========================================" log "Output: $TS_DIR" log "Size: $(du -sh "$TS_DIR" | awk '{print $1}')" log "" log "Disk:" df -h / /e | grep -v Filesystem | tee -a "$LOG"