Convert CIOS DICOM to Video

convert_fluoro_file_to_video.sh

#!/bin/bash
xray_dir=$1
output_dir=$2

cwd=$(pwd)

convert_fluoro_file_to_video () {
    filename=$(echo $1 | sed 's/[.].*$//')  # strip anything after period (e.g. file extension)
    frame_rate=$(medcon -f $1 | grep CineRate | sed -n 's/.*\[\([^]]*\)\].*/\1/p') # check to see if this is a set of fluoro images (from the dicom header)
    if [ -z ${frame_rate} ]
        then
            echo $filename "does not appear to be a series of fluoro images"
        else
            echo "Processing: " $filename "with framerate: " $frame_rate
            mkdir -p $2/$filename/
            medcon -f $1 -c png -o $2/$filename/slice.png # make a dir of pngs
            ffmpeg -r $frame_rate -pattern_type glob -i $2/$filename/"*.png" -c:v libx264 -crf 0 $2/$filename.avi  # make pngs into mp4 at specified framerate
    fi  
}

cd $xray_dir
for FILE in * 
do 
    convert_fluoro_file_to_video $FILE $output_dir & # run all in parallel
done
wait

cd $cwd