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Update simset conversion files to read out multiple energy bin sinograms #1608

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Update simset conversion files to read out multiple energy bin sinograms #1608

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68 changes: 51 additions & 17 deletions src/SimSET/scripts/conv_SimSET_projdata_to_STIR.sh
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Original file line number Diff line number Diff line change
Expand Up @@ -61,8 +61,26 @@ fi

# find min and max scatter bins in the SimSET file
min_scatter_bin_num=`${PRINTHEADER} ${simset_file} |grep "Binning: min number of scatters" |awk '{ print $6 }'`

echo "Min scatter bin number: $min_scatter_bin_num"

max_scatter_bin_num=`${PRINTHEADER} ${simset_file} |grep "Binning: max number of scatters" |awk '{ print $6 }'`

echo "Max scatter bin number: $max_scatter_bin_num"

en1_bin_num=`${PRINTHEADER} ${simset_file} |grep "Binning: number of Eenergy(1) bins" |awk '{ print $6 }'`

echo "Energy(1) bin number: $en1_bin_num"

en2_bin_num=`${PRINTHEADER} ${simset_file} |grep "Binning: number of Energy(2) bins" |awk '{ print $6 }'`

echo "Energy(2) bin number: $en2_bin_num"


echo "DEBUG: All energy-related lines:"
${PRINTHEADER} ${simset_file} | grep -i "energy"


# find scatter_parameter (maybe called scatter_randoms_parameter in the future)
scatter_parameter=`${PRINTHEADER} ${simset_file} |grep "Binning: scatter.*parameter" |awk '{ print $4 }'`

Expand All @@ -83,23 +101,34 @@ all_scatter_bin_nums=`count $min_scatter_bin_num $max_scatter_bin_num`

echo Executing ${conv_cmdline}

for en1 in `count 0 $(($en1_bin_num - 1))` ;
do for en2 in `count 0 $(($en2_bin_num - 1))` ; do
en_bin_num=$(( ${en2_bin_num} * $en1 + $en2 ))
en_dataset=$(( ${en_bin_num} * ${num_scatter_bins}))
en_name=__${en1}_${en2}
echo "extracting energy bin $en_bin_num, dataset ${en_dataset}, corresponding to $en1, $en2"

case $scatter_parameter in

0)
eval ${conv_cmdline} 0 total
eval ${conv_cmdline} 0 total${en_name}
;;

1|6)
if [ $min_scatter_bin_num == 0 ]; then
eval ${conv_cmdline} 0 noscatter
dataset=$(( ${en_dataset} + 0))
eval ${conv_cmdline} ${dataset} noscatter${en_name}
if [ $max_scatter_bin_num -ge 1 ]; then
eval ${conv_cmdline} 1 scatter
dataset=$(( ${en_dataset} + 1))
eval ${conv_cmdline} ${dataset} scatter${en_name}
if [ $scatter_parameter == 6 ]; then
eval ${conv_cmdline} 2 randoms
dataset=$(( ${en_dataset} + 2))
eval ${conv_cmdline} ${dataset} randoms${en_name}
fi
else
if [ $scatter_parameter == 6 ]; then
eval ${conv_cmdline} 1 randoms
dataset=$(( ${en_dataset} + 1))
eval ${conv_cmdline} ${dataset} randoms${en_name}
fi
fi
fi
Expand All @@ -113,8 +142,9 @@ case $scatter_parameter in
do
scatter_bin_num=$(( ${num_scatter_bins} * $i + $j ))
echo extracting scatter bin $scatter_bin_num
echo ${conv_cmdline} ${scatter_bin_num} blue${i}_pink${j};
eval ${conv_cmdline} ${scatter_bin_num} blue${i}_pink${j};
dataset=$(( ${en_dataset} + ${scatter_bin_num} ))
echo ${conv_cmdline} ${dataset} blue${i}_pink${j}${en_name};
eval ${conv_cmdline} ${dataset} blue${i}_pink${j}${en_name};
done
done

Expand All @@ -131,7 +161,7 @@ case $scatter_parameter in
do for j in $all_scatter_bin_nums
do
k=$(( $i + $j ))
current=blue${i}_pink${j}.hs
current=blue${i}_pink${j}${en_name}.hs
if [ $k -eq 0 ]; then all_trues="$all_trues $current"; fi
if [ $k -eq 1 ]; then all_singles="$all_singles $current"; fi
if [ $k -eq 2 ]; then if [ $i -eq 1 ]; then all_singles12="$all_singles12 $current";fi; fi;
Expand All @@ -142,15 +172,15 @@ case $scatter_parameter in
done

# TODO we currently pipe all output to /dev/null because there's a lot of stuff because blocksizes do not work
stir_math -s --add trues $all_trues >& /dev/null
stir_math -s --add singles $all_singles >& /dev/null
stir_math -s --add trues${en_name} $all_trues >& /dev/null
stir_math -s --add singles${en_name} $all_singles >& /dev/null
if [ ! -z "$all_singles12" ]; then
stir_math -s --add doubles11 $all_singles12 >& /dev/null
stir_math -s --add doubles11${en_name} $all_singles12 >& /dev/null
fi
if [ ! -z "$all_doubles1" ]; then
stir_math -s --add doubles20 $all_doubles1 $all_doubles2 >& /dev/null
stir_math -s --add doubles20${en_name} $all_doubles1 $all_doubles2 >& /dev/null
fi
stir_math -s --add multiples $all_multiples >& /dev/null
stir_math -s --add multiples${en_name} $all_multiples >& /dev/null

rm -f blue*s

Expand All @@ -169,12 +199,13 @@ case $scatter_parameter in
do
echo extracting scatter bin $scatter_bin_num
idx=$((scatter_bin_num - min_scatter_bin_num))
echo ${conv_cmdline} ${idx} scatter${scatter_bin_num};
eval ${conv_cmdline} ${idx} scatter${scatter_bin_num};
dataset=$(( ${en_dataset} + ${idx} ))
echo ${conv_cmdline} ${dataset} scatter${scatter_bin_num}${en_name};
eval ${conv_cmdline} ${dataset} scatter${scatter_bin_num}${en_name};
done
if [ $scatter_parameter == 10 -o $scatter_parameter == 9 ]; then
echo ${conv_cmdline} $((max_scatter_bin_num - min_scatter_bin_num + 1)) randoms
eval ${conv_cmdline} $((max_scatter_bin_num - min_scatter_bin_num + 1)) randoms
dataset=$(( ${en_dataset} + max_scatter_bin_num - min_scatter_bin_num + 1 ))
echo ${conv_cmdline} ${dataset} randoms${en_name}
fi
;;

Expand All @@ -184,3 +215,6 @@ case $scatter_parameter in
;;

esac

done
done
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