foamSequenceVTKFilesForFFarm

#!/bin/sh

#---------------------------------------------------------------------------- #
# foamSequenceVTKFilesForFFarm
#
#     This script is based on OpenFOAM's original foamSequenceVTKFiles
#     If not additional paramters are passed, this function acts exactly
#     like the original from OpenFOAM 6.
#
#     Function modified by Regis Thedin on Aug 2022 to handle FAST.Farm
#     ambient wind files. The modifications include the option to copy,
#     rather than link, the output files; as well as the renaming structure.
#     Note that the renaming can still be changed through some input variables
#     Creates symbolic links to all VTK files in a post-processing directory
#
#     Original description:
#     Links form a sequence like name.0000.vtk, name.0001.vtk, etc.
#     Paraview recognises link names as a sequence which can be animated.
#     The sequence of links can be used to create a video from the images.
#     - Default directory name for VTK files is postProcessing
#
#---------------------------------------------------------------------------- #
error() {
    exec 1>&2
    while [ "$#" -ge 1 ]; do echo "$1"; shift; done
    usage
    exit 1
}

usage() {
        cat <<USAGE

Usage: ${0##*/} [OPTIONS] ...
options:
  -case    | -c <dir>      specify case directory (default = local dir)
  -dir     | -d <dir>      post-processing directory <dir> (default = postProcessing)
  -help    | -h            print the usage
  -out     | -o <dir>      output links directory <dir> (default = sequencedVTK)
  -format  | -f <str>      format option of output files
  -mode    | -m <str>      mode of operation, ln or cp (default=ln)
  -lzero   | -lz <bool>    numbered output files contain leading zeros (default=true)
  -zeroind | -zind <bool>  start numbering at zero (default=false)
  -apath   | -ap <bool>    if `-mode ln`, use absolute path or not (default=false)
  -fsuffix | -fs <str>     suffix of the vtk files if there are multiple (default=vtk)

Creates symbolic links to selected VTK files in a post-processing directory
Links form a sequence like name.0000.vtk, name.0001.vtk, etc.

The format can be changed to Amb.t0000.vtk, for example, by using the -f flag.

Selected VTK output with certain preffix can be changed using the -fsuffix
flag, e.g., if you have Low_U.vtk, Low_U_adj.vtk, and Low_U_adj_coords.vtk in 
all time directories, you can call this function giving -fs _adj.vtk

Paraview recognises the link names as a sequence which can be opened and played.
The sequence of links to images can be used to create a video from the images.

- Default directory name for VTK files is postProcessing

- Example call for processing of FAST.Farm results
  foamSequenceVTKFilesForFFarm -dir postProcessing/Low -out Low -format Amb.t 
                               -mode cp -lzero false
  foamSequenceVTKFilesForFFarm -dir postProcessing/Low -out Low -format Amb.t 
                               -mode ln -lzero false -apath true -fs _adj.vtk
USAGE
}

dir=postProcessing
out=sequencedVTK
format=none
mode=ln
lzero=true
zeroind=false
apath=false
fsuffix=vtk

while [ "$#" -gt 0 ]
do
   case "$1" in
   -c | -case)
      [ "$#" -ge 2 ] || error "'$1' option requires an argument"
      cd "$2" 2>/dev/null || error "directory does not exist:  '$2'"
      shift 2
      ;;
   -d | -dir)
      [ "$#" -ge 2 ] || error "'$1' option requires an argument"
      dir=$2
      shift 2
      ;;
   -h | -help)
      usage && exit 0
      ;;
   -o | -out)
      [ "$#" -ge 2 ] || error "'$1' option requires an argument"
      out=$2
      shift 2
      ;;
   -f | -format)
      [ "$#" -ge 2 ] || error "'$1' option requires an argument"
      format=$2
      shift 2
      ;;
   -m | -mode)
      [ "$#" -ge 2 ] || error "'$1' option requires an argument"
      mode=$2
      shift 2
      ;;
   -lz| -lzero)
      [ "$#" -ge 2 ] || error "'$1' option requires an argument"
      lzero=$2
      shift 2
      ;;
   -zind| -zeroind)
      [ "$#" -ge 2 ] || error "'$1' option requires an argument"
      zeroind=$2
      shift 2
      ;;
   -ap| -apath)
      [ "$#" -ge 2 ] || error "'$1' option requires an argument"
      apath=$2
      shift 2
      ;;
   -fs| -fsuffix)
      [ "$#" -ge 2 ] || error "'$1' option requires an argument"
      fsuffix=$2
      shift 2
      ;;
   -*)
      error "invalid option '$1'"
      ;;
   *)
      break
      ;;
    esac
done

[ ! -d "$dir" ] && error "Cannot find postProcessing directory, exiting."

files=$(find "$dir" -type f -name "*$fsuffix")
names=$(for f in $files; do basename "$f" .vtk; done | sort -u)

if [ -d "$out" ]; then
    echo "$out directory already exists.  Deleting links within it..."
    rm "${out:?}"/* 2>/dev/null
else
    echo "Creating $out directory..."
    mkdir "$out"
fi

for n in $names
do
    echo "Sequencing all VTK files named $n.vtk"

    # Create list of VTK files, ordered by time step
    file_list=$(echo "$files" | \
        tr " " "\n" | \
        grep -w "$n\.vtk" | \
        awk -F'/' '{print($(NF-1)" "$0)}' | \
        LC_ALL=C  sort -k 1 -g | \
        cut -d' ' -f2)

    if $zeroind; then
        # Starting at -1 since the first thing in the loop is to add 1
        # so it brings to zero.
        i=-1
    else
        i=0
    fi

    for f in $file_list
    do
        i=$(( i + 1 )) # Relies on ordered list of files

        if $lzero; then
            if [[ $format == "none" ]]; then
                link=$(printf "${n}.%04d.vtk" $i)
            else
                link=$(printf "${format}%04d.vtk" $i)
            fi

        else
            if [[ $format == "none" ]]; then
                link=$(printf "${n}.%d.vtk" $i)
            else
                link=$(printf "${format}%d.vtk" $i)
            fi

        fi

        if [[ $mode == "cp" ]]; then
            cp    "$f" "$out/$link"
        else
            if $apath; then
                ln -s "$(pwd -P)/$f" "$out/$link"
            else
                ln -s "../$f" "$out/$link"
            fi
        fi
    done
done