#!/bin/bash
# runPostProcess-Ncases.sh - Run post-processing pipeline on multiple 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-generic.py"
# Python interpreter (prefer python3 when python is absent)
PYTHON_BIN=""
# C helper executables
HELPER_GETFACET="\${SCRIPT_DIR}/postProcess/getFacet"
HELPER_GETDATA="\${SCRIPT_DIR}/postProcess/getData-generic"
HELPER_GETCOM="\${SCRIPT_DIR}/postProcess/getCOM"
# 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 bubble coalescence simulation cases.
For each case, generates video frames with strain-rate/velocity fields,
interface facets, and center of mass tracking.
Options:
--CPUs N Number of parallel workers (default: 4)
--nGFS N Number of snapshots to process (default: 4000)
--tsnap F Time interval between snapshots (default: 0.01)
--GridsPerR N Radial grid resolution for video (default: 256)
--ZMIN F Override minimum Z (auto: max(-2-zWall, -3.0))
--ZMAX F Override maximum Z (auto: 5*Rr-2.0)
--RMAX F Override maximum R (auto: 2.5*Rr)
Note: Rr and zWall are auto-extracted from each case's case.params file.
Domain bounds are calculated per-case unless overridden above.
--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) or ranges (e.g., 3000-3010)
Examples:
# Process multiple cases with default settings
\$0 3000 3001 3002
# Process a range of cases
\$0 3000-3010
# Mix individual cases and ranges
\$0 3000 3005-3007 3010
# Process with 8 CPUs
\$0 --CPUs 8 3000 3001
# Process first 100 snapshots only (for testing)
\$0 --nGFS 100 3000
# Skip video encoding (only generate frames)
\$0 --skip-video-encode 3000 3001
# Dry run to preview commands
\$0 --dry-run 3000
Output locations:
simulationCases/<CaseNo>/Video/ # PNG frames
simulationCases/<CaseNo>/<CaseNo>_COMData.csv # COM time series
simulationCases/<CaseNo>/<CaseNo>.mp4 # Encoded video
For more information, see README.md
EOF
}
# ============================================================
# Helper: Expand Case Argument (single number or range)
# ============================================================
expand_case_arg() {
local arg="\$1"
# Check if it's a range (contains hyphen between two 4-digit numbers)
if [[ "\$arg" =~ ^([0-9]{4})-([0-9]{4})\$ ]]; then
local start="\${BASH_REMATCH[1]}"
local end="\${BASH_REMATCH[2]}"
if [ "\$start" -gt "\$end" ]; then
echo "ERROR: Invalid range \$arg (start > end)" >&2
return 1
fi
seq "\$start" "\$end"
return 0
fi
# Single case number
echo "\$arg"
return 0
}
# ============================================================
# Parse Command Line Options
# ============================================================
CPUS=4
NGFS=4000
TSNAP=0.01
GRIDS_PER_R=256
ZMIN=""
ZMAX=""
RMAX=""
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
;;
--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
;;
*)
# Expand ranges and collect case numbers
# Capture output and check exit status before appending
if ! expanded_cases=\$(expand_case_arg "\$1"); then
# expand_case_arg already printed error to stderr
exit 1
fi
while IFS= read -r case_no; do
CASE_NUMBERS+=("\$case_no")
done <<< "\$expanded_cases"
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
# Check Python availability
if command -v python3 &> /dev/null; then
PYTHON_BIN="\$(command -v python3)"
elif command -v python &> /dev/null; then
PYTHON_BIN="\$(command -v python)"
else
echo "ERROR: Neither python3 nor python was found in PATH" >&2
exit 1
fi
# Check qcc availability (needed to compile helpers)
if ! command -v qcc &> /dev/null; then
echo "ERROR: qcc 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
# Compile C helpers (always recompile to ensure consistency)
echo "Compiling C helpers..."
pushd "\${SCRIPT_DIR}/postProcess" > /dev/null
if ! qcc -O2 -Wall -disable-dimensions getFacet.c -o getFacet -lm; then
echo "ERROR: Failed to compile getFacet.c" >&2
popd > /dev/null
exit 1
fi
if ! qcc -O2 -Wall -disable-dimensions getData-generic.c -o getData-generic -lm; then
echo "ERROR: Failed to compile getData-generic.c" >&2
popd > /dev/null
exit 1
fi
if ! qcc -O2 -Wall -disable-dimensions getCOM.c -o getCOM -lm; then
echo "ERROR: Failed to compile getCOM.c" >&2
popd > /dev/null
exit 1
fi
popd > /dev/null
echo "C helpers compiled successfully"
# Validate helpers are executable (sanity check after compilation)
for helper in "\$HELPER_GETFACET" "\$HELPER_GETDATA" "\$HELPER_GETCOM"; do
if [ ! -x "\$helper" ]; then
echo "ERROR: Compiled helper not executable: \$helper" >&2
exit 1
fi
done
# ============================================================
# Display Configuration
# ============================================================
echo "========================================="
echo "Bubble Coalescence - 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 bounds: auto-calculated from case.params (Rr, zWall)"
if [ -n "\$ZMIN" ]; then echo " ZMIN: \$ZMIN (override)"; fi
if [ -n "\$ZMAX" ]; then echo " ZMAX: \$ZMAX (override)"; fi
if [ -n "\$RMAX" ]; then echo " RMAX: \$RMAX (override)"; fi
echo ""
echo "Pipeline:"
[ \$SKIP_VIDEO_ENCODE -eq 0 ] && echo " [1] Video-generic.py (frames + video)" || echo " [1] Video-generic.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"
# Read Rr and zWall from case.params
local case_params="\${case_dir}/case.params"
local case_rr="1.0"
local case_zwall="4.0" # default from default.params
if [ -f "\$case_params" ]; then
parse_param_file "\$case_params"
case_rr=\$(get_param "Rr" "1.0")
case_zwall=\$(get_param "zWall" "4.0")
else
echo " WARNING: case.params not found, using defaults (Rr=1.0, zWall=4.0)"
fi
# Calculate domain bounds
local calc_zmin=\$(echo "-2 - \$case_zwall" | bc -l)
local calc_zmax=\$(echo "5 * \$case_rr - 2.0" | bc -l)
local calc_rmax=\$(echo "2.5 * \$case_rr" | bc -l)
# Apply ZMIN clamp: max(-2-zWall, -3.0)
if (( \$(echo "\$calc_zmin < -3.0" | bc -l) )); then
calc_zmin="-3.0"
fi
# Use command-line overrides if provided, otherwise use calculated values
local use_zmin="\${ZMIN:-\$calc_zmin}"
local use_zmax="\${ZMAX:-\$calc_zmax}"
local use_rmax="\${RMAX:-\$calc_rmax}"
if [ \$VERBOSE -eq 1 ]; then
echo " Extracted: Rr=\$case_rr, zWall=\$case_zwall"
echo " Calculated: ZMIN=\$use_zmin, ZMAX=\$use_zmax, RMAX=\$use_rmax"
fi
# Build command with calculated/override values
local cmd_args=(
"--caseToProcess" "\${case_dir}"
"--folderToSave" "\${video_dir}"
"--CPUs" "\${CPUS}"
"--nGFS" "\${NGFS}"
"--tsnap" "\${TSNAP}"
"--GridsPerR" "\${GRIDS_PER_R}"
"--Rr" "\${case_rr}"
"--ZMIN" "\${use_zmin}"
"--ZMAX" "\${use_zmax}"
"--RMAX" "\${use_rmax}"
)
# 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_BIN} \${VIDEO_SCRIPT} \${cmd_args[*]}"
fi
if [ \$DRY_RUN -eq 0 ]; then
"\${PYTHON_BIN}" "\${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/"
# 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: OhOut=\$(get_param "OhOut" "?"), Rr=\$(get_param "Rr" "?"), MAXlevel=\$(get_param "MAXlevel" "?")"
fi
if [ "\$snapshot_count" -eq 0 ]; then
echo " ERROR: No snapshots found"
FAILED_CASES+=("\$case_no")
FAILURE_REASONS+=("No snapshots in intermediate/")
continue
fi
# Track step failures
step_failed=0
# Run video generation
echo ""
echo " [1/1] Running Video-generic.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
