run_invitro.sh

#!/bin/sh -l

classifier="$1"
video="$2"
prefix=${video%.*}
echo "Video prefix: \"$prefix\""
segmentation="$prefix.seg"
registration="$prefix.reg"
masterframe="$prefix.masterframe"
mask="$prefix.mask.png"

mpiexec chromas-classify-video \
    --classifier "$classifier" \
    --video "$video" "$segmentation" \
    --video-start 0

./registration/register_segmentation.py \
    --segmentation "$segmentation" \
    --background background \
    --det-min-points 10 \
    --det-max-points 60 \
    --det-circularity-thresh .1 \
     "$registration"

mpiexec ./master_frame/generate_master_frame.py \
    --registration "$registration" \
    --background background \
    "$masterframe"

./master_frame/background_mask.py \
    "$masterframe" \
    "$mask"