#!/bin/bash
# runPostProcess-Ncases.sh - Run post-processing pipeline on multiple VE simulation cases
# Author: Vatsal Sanjay
# [email protected]
# CoMPhy Lab - Durham University
# Last updated: Jan 2026
set -euo pipefail # Exit on error, unset variables, pipeline failures
# ============================================================
# Configuration
# ============================================================
SCRIPT_DIR="\$(cd "\$(dirname "\${BASH_SOURCE[0]}")" && pwd)"
# Source parameter parsing library
if [ -f "\${SCRIPT_DIR}/src-local/parse_params.sh" ]; then
source "\${SCRIPT_DIR}/src-local/parse_params.sh"
else
echo "ERROR: src-local/parse_params.sh not found" >&2
exit 1
fi
# Post-processing script paths
VIDEO_SCRIPT="\${SCRIPT_DIR}/postProcess/Video.py"
# C helper executables
HELPER_GETFACET="\${SCRIPT_DIR}/postProcess/getFacet"
HELPER_GETDATA="\${SCRIPT_DIR}/postProcess/getData"
# Case directory root
CASES_DIR="\${SCRIPT_DIR}/simulationCases"
# ============================================================
# Usage Information
# ============================================================
usage() {
cat <<EOF
Usage: \$0 [OPTIONS] CASE_NO [CASE_NO ...]
Run post-processing pipeline on multiple viscoelastic bubble bursting simulation cases.
For each case, generates video frames with strain-rate and velocity fields,
and interface facets.
Options:
--CPUs N Number of parallel workers (default: 4)
--nGFS N Number of snapshots to process (default: 500)
--tsnap F Time interval between snapshots (default: 0.01)
--GridsPerR N Radial grid resolution for video (default: 256)
--ZMIN F Minimum Z coordinate (default: -4.0)
--ZMAX F Maximum Z coordinate (default: 4.0)
--RMAX F Maximum R coordinate (default: 2.0)
Colorbar bounds:
--d2-vmin F Min value for strain-rate colorbar (default: -3.0)
--d2-vmax F Max value for strain-rate colorbar (default: 2.0)
--vel-vmin F Min value for velocity colorbar (default: 0.0)
--vel-vmax F Max value for velocity colorbar (default: 1.0)
--skip-video-encode Skip ffmpeg video encoding after frame generation
-n, --dry-run Show what would run without executing
-v, --verbose Verbose output
-h, --help Show this help message
Arguments:
CASE_NO 4-digit case numbers (1000-9999)
Examples:
# Process multiple cases with default settings
\$0 1000 1001 1002
# Process with 8 CPUs
\$0 --CPUs 8 1000 1001
# Process first 100 snapshots only (for testing)
\$0 --nGFS 100 1000
# Skip video encoding (only generate frames)
\$0 --skip-video-encode 1000 1001
# Dry run to preview commands
\$0 --dry-run 1000
Output locations:
simulationCases/<CaseNo>/Video/ # PNG frames
simulationCases/<CaseNo>/<CaseNo>.mp4 # Encoded video
For more information, see CLAUDE.md
EOF
}
# ============================================================
# Parse Command Line Options
# ============================================================
CPUS=4
NGFS=500
TSNAP=0.01
GRIDS_PER_R=256
ZMIN="-4.0"
ZMAX="4.0"
RMAX="2.0"
D2_VMIN="-3.0"
D2_VMAX="2.0"
VEL_VMIN="0.0"
VEL_VMAX="1.0"
SKIP_VIDEO_ENCODE=0
DRY_RUN=0
VERBOSE=0
CASE_NUMBERS=()
while [[ \$# -gt 0 ]]; do
case \$1 in
--CPUs)
CPUS="\$2"
if ! [[ "\$CPUS" =~ ^[0-9]+\$ ]] || [ "\$CPUS" -lt 1 ]; then
echo "ERROR: --CPUs requires a positive integer, got: \$CPUS" >&2
exit 1
fi
shift 2
;;
--nGFS)
NGFS="\$2"
if ! [[ "\$NGFS" =~ ^[0-9]+\$ ]] || [ "\$NGFS" -lt 1 ]; then
echo "ERROR: --nGFS requires a positive integer, got: \$NGFS" >&2
exit 1
fi
shift 2
;;
--tsnap)
TSNAP="\$2"
shift 2
;;
--GridsPerR)
GRIDS_PER_R="\$2"
if ! [[ "\$GRIDS_PER_R" =~ ^[0-9]+\$ ]] || [ "\$GRIDS_PER_R" -lt 1 ]; then
echo "ERROR: --GridsPerR requires a positive integer, got: \$GRIDS_PER_R" >&2
exit 1
fi
shift 2
;;
--ZMIN)
ZMIN="\$2"
shift 2
;;
--ZMAX)
ZMAX="\$2"
shift 2
;;
--RMAX)
RMAX="\$2"
shift 2
;;
--d2-vmin)
D2_VMIN="\$2"
shift 2
;;
--d2-vmax)
D2_VMAX="\$2"
shift 2
;;
--vel-vmin)
VEL_VMIN="\$2"
shift 2
;;
--vel-vmax)
VEL_VMAX="\$2"
shift 2
;;
--skip-video-encode)
SKIP_VIDEO_ENCODE=1
shift
;;
-n|--dry-run)
DRY_RUN=1
shift
;;
-v|--verbose)
VERBOSE=1
shift
;;
-h|--help)
usage
exit 0
;;
-*)
echo "ERROR: Unknown option: \$1" >&2
usage
exit 1
;;
*)
# Collect case numbers
CASE_NUMBERS+=("\$1")
shift
;;
esac
done
# ============================================================
# Validation
# ============================================================
# Check at least one case number provided
if [ \${#CASE_NUMBERS[@]} -eq 0 ]; then
echo "ERROR: No case numbers provided" >&2
usage
exit 1
fi
# Validate case numbers are 4-digit
for case_no in "\${CASE_NUMBERS[@]}"; do
if ! [[ "\$case_no" =~ ^[0-9]{4}\$ ]]; then
echo "ERROR: Case number must be 4 digits (1000-9999), got: \$case_no" >&2
exit 1
fi
if [ "\$case_no" -lt 1000 ] || [ "\$case_no" -gt 9999 ]; then
echo "ERROR: Case number out of range (1000-9999), got: \$case_no" >&2
exit 1
fi
done
# Check Python availability
if ! command -v python &> /dev/null; then
echo "ERROR: python not found in PATH" >&2
exit 1
fi
# Check Python script exists
if [ ! -f "\$VIDEO_SCRIPT" ]; then
echo "ERROR: Python script not found: \$VIDEO_SCRIPT" >&2
exit 1
fi
# Check C helpers exist
for helper in "\$HELPER_GETFACET" "\$HELPER_GETDATA"; do
if [ ! -x "\$helper" ]; then
helper_name=\$(basename "\$helper")
echo "ERROR: Compiled helper not found or not executable: \$helper" >&2
echo " Compile with: qcc -O2 -Wall postProcess/\${helper_name}.c -o postProcess/\${helper_name} -lm" >&2
exit 1
fi
done
# ============================================================
# Display Configuration
# ============================================================
echo "========================================="
echo "Viscoelastic Bubble Bursting - Post-Processing Pipeline"
echo "========================================="
echo "Cases to process: \${CASE_NUMBERS[*]}"
echo "Total cases: \${#CASE_NUMBERS[@]}"
echo ""
echo "Settings:"
echo " CPUs: \$CPUS"
echo " nGFS: \$NGFS"
echo " tsnap: \$TSNAP"
echo " GridsPerR: \$GRIDS_PER_R"
echo " Domain: Z=[\$ZMIN, \$ZMAX], R=[0, \$RMAX]"
echo " Colorbars: D2=[\$D2_VMIN, \$D2_VMAX], vel=[\$VEL_VMIN, \$VEL_VMAX]"
echo ""
echo "Pipeline:"
[ \$SKIP_VIDEO_ENCODE -eq 0 ] && echo " [1] Video.py (frames + video)" || echo " [1] Video.py (frames only, video SKIPPED)"
echo ""
[ \$DRY_RUN -eq 1 ] && echo "Mode: DRY RUN (no execution)"
echo ""
# ============================================================
# Processing Functions
# ============================================================
run_video() {
local case_no="\$1"
local case_dir="\${CASES_DIR}/\${case_no}"
local video_dir="\${case_dir}/Video"
# Build command
local cmd_args=(
"--caseToProcess" "\${case_dir}"
"--folderToSave" "\${video_dir}"
"--CPUs" "\${CPUS}"
"--nGFS" "\${NGFS}"
"--tsnap" "\${TSNAP}"
"--GridsPerR" "\${GRIDS_PER_R}"
"--ZMIN" "\${ZMIN}"
"--ZMAX" "\${ZMAX}"
"--RMAX" "\${RMAX}"
"--d2-vmin" "\${D2_VMIN}"
"--d2-vmax" "\${D2_VMAX}"
"--vel-vmin" "\${VEL_VMIN}"
"--vel-vmax" "\${VEL_VMAX}"
)
# Add skip flag if needed
[ \$SKIP_VIDEO_ENCODE -eq 1 ] && cmd_args+=("--skip-video-encode")
if [ \$VERBOSE -eq 1 ] || [ \$DRY_RUN -eq 1 ]; then
echo " CMD: python \${VIDEO_SCRIPT} \${cmd_args[*]}"
fi
if [ \$DRY_RUN -eq 0 ]; then
python "\${VIDEO_SCRIPT}" "\${cmd_args[@]}"
fi
}
# ============================================================
# Main Processing Loop
# ============================================================
echo "========================================="
echo "Processing Cases"
echo "========================================="
SUCCESSFUL_CASES=()
FAILED_CASES=()
FAILURE_REASONS=()
for case_no in "\${CASE_NUMBERS[@]}"; do
echo ""
echo "-----------------------------------------"
echo "Case \$case_no"
echo "-----------------------------------------"
case_dir="\${CASES_DIR}/\${case_no}"
intermediate_dir="\${case_dir}/intermediate"
# Validate case directory exists
if [ ! -d "\$case_dir" ]; then
echo " ERROR: Case directory not found: \$case_dir"
FAILED_CASES+=("\$case_no")
FAILURE_REASONS+=("Case directory not found")
continue
fi
if [ ! -d "\$intermediate_dir" ]; then
echo " ERROR: Intermediate directory not found: \$intermediate_dir"
FAILED_CASES+=("\$case_no")
FAILURE_REASONS+=("No intermediate/ snapshots")
continue
fi
# Count snapshots
snapshot_count=\$(find "\$intermediate_dir" -name "snapshot-*" 2>/dev/null | wc -l | tr -d ' ')
echo " Found \$snapshot_count snapshots in intermediate/"
if [ "\$snapshot_count" -eq 0 ]; then
echo " ERROR: No snapshots found"
FAILED_CASES+=("\$case_no")
FAILURE_REASONS+=("No snapshots in intermediate/")
continue
fi
# Display case parameters if case.params exists
case_params="\${case_dir}/case.params"
if [ -f "\$case_params" ] && [ \$VERBOSE -eq 1 ]; then
parse_param_file "\$case_params"
echo " Parameters: De=\$(get_param "De" "?"), Ec=\$(get_param "Ec" "?"), Oh=\$(get_param "Oh" "?")"
fi
# Track step failures
step_failed=0
# Run video generation
echo ""
echo " [1/1] Running Video.py..."
if ! run_video "\$case_no"; then
echo " ERROR: Video generation failed"
step_failed=1
else
[ \$DRY_RUN -eq 0 ] && echo " [1/1] Video generation complete"
fi
# Record result
if [ \$step_failed -eq 0 ]; then
SUCCESSFUL_CASES+=("\$case_no")
echo ""
echo " Case \$case_no: SUCCESS"
else
FAILED_CASES+=("\$case_no")
FAILURE_REASONS+=("Processing step failed")
echo ""
echo " Case \$case_no: FAILED"
fi
done
# ============================================================
# Summary
# ============================================================
echo ""
echo "========================================="
echo "Post-Processing Complete"
echo "========================================="
echo "Total cases: \${#CASE_NUMBERS[@]}"
echo "Successful: \${#SUCCESSFUL_CASES[@]}"
echo "Failed: \${#FAILED_CASES[@]}"
if [ \${#FAILED_CASES[@]} -gt 0 ]; then
echo ""
echo "Failed cases:"
for i in "\${!FAILED_CASES[@]}"; do
echo " - Case \${FAILED_CASES[\$i]}: \${FAILURE_REASONS[\$i]}"
done
fi
if [ \${#SUCCESSFUL_CASES[@]} -gt 0 ]; then
echo ""
echo "Output locations:"
for case_no in "\${SUCCESSFUL_CASES[@]}"; do
echo " \${CASES_DIR}/\${case_no}/"
done
fi
echo ""
# Exit with error if any cases failed
if [ \${#FAILED_CASES[@]} -gt 0 ]; then
exit 1
fi
exit 0
