main.sh

#!/usr/bin/env bash

# This is the main script that will call the other scripts

#!/bin/bash

# Default values
REALTIME=false
SKIP_COMPILE=false
LAYOUT=""
ARCHITECTURE=""

# Function to display usage
usage() {
    echo "usage: $0 [-l LAYOUT] [-r] [-a ARCHITECTURE] input output"
    echo ""
    echo "Compile and animate neutral atom instruction. This script depends on the following scripts:"
    echo "  - compile.py: Compiles the input file into a format that can be used by the animation script."
    echo "  - animate.R: Animates the compiled file and produces a movie file [.mp4]."
    echo ""
    echo "positional arguments:"
    echo "  input                 .na file to animate or .csv if already compiled."
    echo "  output                File name of the movie [.mp4]."
    echo ""
    echo "options:"
    echo "  -x, --skipCompile     Skip the compilation step if the input file is already compiled."
    echo "                        This is useful if the input file is already compiled and you only want to animate it."
    echo "                        Provide the compiled csv file as the input file."
    echo "  -r, --realtime        Use real time specification for operations."
    echo "                        Necessitates the specification of an architecture file."
    echo "                        Otherwise every operation will take 1 time unit."
    echo "  -s, --speed SPEED     Speed of the animation. Default is 1."
    echo "  -a ARCHITECTURE, --architecture ARCHITECTURE"
    echo "                        The architecture file to use for realtime mode [.json]."
    echo "                        In particular, this has to specify the durations of the different operations."
    echo "                        For an example of such a file see config/wide.json."
    echo "                        This is necessary for the real time mode."
    echo "  -l LAYOUT, --layout LAYOUT"
    echo "                        Layout file [.csv]. This specifies the location of traps and their color based on"
    echo "                        their type. See config/wide.csv for an example."
}

# Parse options
while [[ $# -gt 0 ]]; do
    case "$1" in
        -x|--skipCompile)
            SKIP_COMPILE=true
            shift
            ;;
        -r|--realtime)
            REALTIME=true
            shift
            ;;
        -s|--speed)
            SPEED="$2"
            shift 2
            ;;
        -a|--architecture)
            ARCHITECTURE="$(realpath "$2")"
            shift 2
            ;;
        -l|--layout)
            LAYOUT="$(realpath "$2")"
            shift 2
            ;;
        *)
            break
            ;;
    esac
done

# Validate that input file is csv if skip compile is specified
if [[ "$SKIP_COMPILE" = true && ! "$1" =~ \.csv$ ]]; then
    usage
    echo "Error: Input file must be a .csv file if skip compile is specified."
    exit 1
fi

# Validate if realtime is specified without architecture
if [[ "$REALTIME" = true && -z "$ARCHITECTURE" ]]; then
    usage
    echo "Error: Realtime option specified without an architecture."
    exit 1
fi

# Set default speed if not specified
if [[ -z "$SPEED" ]]; then
    SPEED=1
fi
# set speed to its inverse times 50
SPEED=$(echo "scale=2; 1/$SPEED*50" | bc)

# Validate if realtime is specified without architecture
if [[ -z "$LAYOUT" ]]; then
    usage
    echo "Error: Layout must be specified."
    exit 1
fi

# Check if input and output file names are provided
if [[ $# -ne 2 ]]; then
    usage
    echo "Error: Input and output file names are required."
    exit 1
fi

# Assign positional arguments
INPUT="$(realpath "$1")"
COMPILED="$(dirname "$INPUT")/$(basename "$INPUT" .na).csv"
if [[ "$SKIP_COMPILE" = true ]]; then
    COMPILED="$INPUT"
fi
touch "$2"
OUTPUT="$(realpath "$2")"
# set working directory to the directory of the source file
# This step is important for the python and R script to be availale
cd "$(dirname "$0")"
if [[ "$SKIP_COMPILE" = false ]]; then
    echo "Compiling the input file..."
    echo ""
if [[ "$REALTIME" = true ]]; then
    python3 compile.py --realtime --architecture $ARCHITECTURE $INPUT $COMPILED
else
    python3 compile.py $INPUT $COMPILED
fi
result=$?
if [[ $result -ne 0 ]]; then
    echo "Error: Compilation failed with exit code: $result."
    exit 1
fi
fi
echo ""
Rscript animate.R --layout $LAYOUT --ratio $SPEED $COMPILED $OUTPUT
result=$?
if [[ $result -ne 0 ]]; then
    echo "Error: Animation failed with exit code: $result."
    exit 1
fi
# rm -f $COMPILED
echo ""
echo "Successfully compiled the input file and created the neutral atom animation."
echo "Input file: $INPUT"
echo "Output file: $OUTPUT"