runscript.sh

#!/bin/bash


export LD_LIBRARY_PATH=/usr/local/MATLAB/MATLAB_Compiler_Runtime/v81/runtime/glnxa64:/usr/local/MATLAB/MATLAB_Compiler_Runtime/v81/bin/glnxa64:/usr/local/MATLAB/MATLAB_Compiler_Runtime/v81/sys/os/glnxa64:/usr/local/MATLAB/MATLAB_Compiler_Runtime/v81/sys/java/jre/glnxa64/jre/lib/amd64/native_threads:/usr/local/MATLAB/MATLAB_Compiler_Runtime/v81/sys/java/jre/glnxa64/jre/lib/amd64/server:/usr/local/MATLAB/MATLAB_Compiler_Runtime/v81/sys/java/jre/glnxa64/jre/lib/amd64:$LD_LIBRARY_PATH

export PATH=/usr/local/MATLAB/MATLAB_Compiler_Runtime/v81/bin/:$PATH

declare chm="chm-compiled-r2013a-2.1.367"

declare version="@@VERSION@@"

if [ $# -eq 0 ] ; then
  echo "$0 <train|test|verify|licenses> <images> <labels> (options)"
  echo ""
  echo "This singularity image runs CHM train or test ($chm)"
  echo ""
  echo "NOTE: This image bundles Matlab Compiled Runtime 2013a."
  echo "      Using this image implies consent of its license found by"
  echo "      running this command again with license as first argument."
  echo "      Other licenses can be found by visiting: "
  echo "      https://github.com/CRBS/chm_singularity"
  echo ""
  echo "  The mode is determined by the first argument <train|test|verify>"
  echo "  If first argument is:"
  echo ""
  echo "    train -- Runs CHM Train"
  echo "    test -- Runs CHM Test"
  echo "    verify -- Runs a quick test to verify CHM Train & Test work"
  echo "    version -- Outputs version of CHM singularity image"
  echo "    <file> -- If first argument is a file then probability map"
  echo "              viewer external script mode is used which assumes 3 args"
  echo "              <input tile> <output tile> <model directory>"
  echo ""
  echo "  To see more help run one of the following commands"
  echo "    $0 <file>"
  echo "    $0 train"
  echo "    $0 test"
  echo "    $0 license"
  echo "    $0 verify"
  echo "    $0 version"
  echo ""
  echo "  For information on how this image was created please visit:"
  echo "  https://github.com/CRBS/chm_singularity"
  echo ""
  exit 1
fi

declare mode=$1

# remove the first argument
shift
matlab=" -M /usr/local/MATLAB/MATLAB_Compiler_Runtime/v81"

if [ "$mode" == "license" ] ; then
  echo "MATLAB LICENSE:"
  cat /usr/local/MATLAB/MATLAB_Compiler_Runtime/v81/license.txt
  echo "Visit https://github.com/CRBS/chm_singularity"
  echo "for licenses for CHM and the code to generate this image"
  echo ""
  exit 0
fi

if [ "$mode" == "version" ] ; then
  echo "$version"
  exit 0
fi

if [ "$mode" == "train" ] ; then
  exec /$chm/CHM_train.sh "$@" $matlab
fi


if [ "$mode" == "test" ] ; then
  exec /$chm/CHM_test.sh "$@" $matlab
fi
 
if [ "$mode" == "verify" ] ; then
  if [ $# -ne 1 ] ; then
    echo "$0 verify <tmp directory>"
    echo ""
    echo "Runs CHM train and test on some internal test data"
    echo "to verify image is configured correctly."
    echo ""
    echo "To run please pass path to tmp directory with write access"
    echo "code will exit 0 upon success otherwise failure"
    exit 2
  fi
  declare my_tmp=$1
  echo "Removing $my_tmp/testimage.png before running test"
  rm -f "$my_tmp/testimage.png"
  /$chm/CHM_train.sh /chm_singularity_test_data/images /chm_singularity_test_data/labels -S 2 -L 1 $matlab -m $my_tmp/model
  if [ $? != 0 ] ; then
    echo "Error chm train failed to run /$chm/CHM_train.sh /chm_singularity_test_data/images /chm_singularity_test_data/labels -S 2 -L 1 $matlab -m $my_tmp/model"
    exit 3
  fi
  echo "Training completed. Running CHM test..."
  /$chm/CHM_test.sh /chm_singularity_test_data $my_tmp -m $my_tmp/model -b 100x95 -t 1,1 -o 0x0 -h $matlab
  if [ $? != 0 ] ; then
    echo "Error chm test failed to run /$chm/CHM_test.sh $my_tmp /chm_singularity_test_data -m $my_tmp/model -b 100x95 -t 1,1 -o 0x0 -h $matlab"
    exit 4
  fi
  echo "Verifying probability map exists with size greater then 0"
  if [ -s "$my_tmp/testimage.png" ] ; then
    echo "Test passed..."
    exit 0
  fi
  echo "Test failed... No resulting probability map found"
  exit 5
fi

# Probability map viewer mode check
if [ -f "$mode" ] ; then
  if [ $# -ne 2 ] ; then
    echo ""
    echo "$0 <input tile> <output tile> <model directory>"
    echo ""
    echo "CHM test in Probability Map Viewer mode."
    
    echo "In this mode CHM test is run on <input tile> image file using the model"
    echo "specified by <model directory>. The overlap is "
    echo "set to 0x0 and block/tile size is set to size of <input tile> image."
    echo "After CHM is run, the Image Magick convert command is used to threshold the"
    echo "image using the flag -threshold 30% to zero out intensities below this" 
    echo "threshold. The resulting image is stored in <output tile> image file as a png"
    echo ""
    exit 7
  fi
  if [ $# -eq 2 ] ; then
    input="$mode"
    output="$1"
    outputdir=`dirname $output`
    model="$2"
    tilesize=`identify -format "%[fx:w]x%[fx:h]" $input`
    /$chm/CHM_test.sh "$input" "$outputdir" -h -m "$model" -b $tilesize -o 0x0 -t 1,1 $matlab
    exitcode=$?
    outimage=`find $output -name "*.png" -type f`
    outimagetmp="${outimage}.tmp.png"
    echo "Running convert: $outimage -threshold 30% $outimagetmp"
    convert "$outimage" -threshold 30% "$outimagetmp"
    echo "Running mv $outimagetmp $outimage"
    mv "$outimagetmp" "$outimage"
    exit $?
  fi
fi

echo "Invalid mode: $mode. Run $0 with no arguments for help"
exit 6