Setup and prepare for running the OpenSimRoot demo.

run_opensimroot_demo

#!/usr/bin/env bash

#
# Setup and prepare for visualizing the OpenSimRoot demo.
#
#   Stages:
#     * Get OpenSimRoot and its dependencies,
#     * Get the demo data,
#     * Execute the data crunching,
#     * Explain how to run the visualization.
#
#   This script tries to automate most of the steps to see the results.
#
#   Tested on Linux (Ubuntu 16_04).
#
# Usage:
#   * [If necessary] Make executable: `chmod +x run_opensimroot_demo`
#   * Run with: `./run_opensimroot_demo`
#

set -e

# Check a directory exit, and make it as necessary.
function check_dir() {
  if [ ! -d "$1" ]; then
    mkdir -p "$1"
  fi
}

# Check file is present and ready for use.
#
# Params:
#   $1 Piece name, for reporting only.
#   $2 File name to check.
#   $3 Command to get the file, if necessary.
#   $4 Post-processing command, if necessary.
function check_file() {
  if [ ! -f "$2" ]; then
    echo -n "Getting $1..."
    $($3 > /dev/null)
    $($4 > /dev/null)
    echo "ok"
  fi
}


DEMO_DIR=$(pwd)/osr_demo
TOOLS_DIR=$DEMO_DIR/tools
RUNFILES_DIR=$DEMO_DIR/runfiles
check_dir $DEMO_DIR
check_dir $TOOLS_DIR
check_dir $RUNFILES_DIR


PARAVIEW_FILE_NAME='ParaView-5.4.0-Qt5-OpenGL2-MPI-Linux-64bit.tar.gz'
pushd $TOOLS_DIR
check_file "OpenSimRoot" "OpenSimRoot_Linux_x64" \
  "wget http://rootmodels.gitlab.io/OpenSimRoot/executables/OpenSimRoot_Linux_x64" \
  "chmod +x OpenSimRoot_Linux_x64"
check_file "OSR Demo Data" "inputfiles_osr.zip" \
  "wget http://rootmodels.gitlab.io/OpenSimRoot/inputfiles/inputfiles_osr.zip" \
  "unzip inputfiles_osr.zip"
check_file "ParaView" "$PARAVIEW_FILE_NAME" \
  "wget -O $PARAVIEW_FILE_NAME https://www.paraview.org/paraview-downloads/download.php?submit=Download&version=v5.4&type=binary&os=linux64&downloadFile=$PARAVIEW_FILE_NAME" \
  "tar xvfz $PARAVIEW_FILE_NAME"
popd


pushd $RUNFILES_DIR
$TOOLS_DIR/OpenSimRoot_Linux_x64 -f $TOOLS_DIR/InputFiles/runBean.xml
popd


echo "Vizualize demo results with: $TOOLS_DIR/ParaView-5.4.0-Qt5-OpenGL2-MPI-Linux-64bit/bin/paraview --mesa"
echo "  * In the paraview console, open:"
echo "        $RUNFILES_DIR/visualisationroots.pvd"
echo "      or"
echo "        $RUNFILES_DIR/visualisation_phosphorus_DepletionZone.pvd"
echo "      data file."
echo "  * After opening a file, press the Apply button on the left-hand side panel, then the play button on the top panel."
echo "  * Playing the file should show daily root growth. You can try the different colour settings to see interesting representations."