add in legacy calibration routine

#!/bin/bash

local_cc_file=$1

working_dir="/SNS/NOM/shared/CALIBRATION/"

cd $working_dir

dia_file=$(python utils_legacy/load.py $local_cc_file)

run_num=$(python utils_legacy/rn_config.py $dia_file)

run_date=$(python utils_legacy/rd_config.py $local_cc_file)

sam_env=$(python utils_legacy/se_config.py $local_cc_file)

gen_mask_file=$(python utils_legacy/mg_config.py $local_cc_file)

running_dir="/SNS/NOM/shared/CALIBRATION/.cache/"

group_method=$(python utils_legacy/gm_config.py $local_cc_file)

out_dir=$(python utils_legacy/od_config.py $local_cc_file)

out_dir_alt="/SNS/NOM/shared/autoreduce/calibration"

# Create the output directory if not existing

if [ ! -d $out_dir ] ; then

    mkdir -p $out_dir

fi

# echo settings

echo "+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+"

echo "Working directory: $working_dir"

echo "Calibrant file: $dia_file"

echo "Diamond run number: $run_num"

echo "Diamond run date: $run_date"

echo "Sample environment: $sam_env"

echo "Generate shadow mask file: $gen_mask_file"

echo "Running directory: $running_dir"

echo "Grouping method: $group_method"

echo "Output directory: $out_dir"

echo "+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+"

# Generate mask

if [ ! $gen_mask_file = "no" ]; then

    echo "Generating mask..."

    mantidpython $working_dir/inputs/mask_gen/nom_shadow_mask_gen.py $dia_file

    rm -rf $running_dir/manual_mask_cache/gen_mask/$gen_mask_file

    Rscript $working_dir/inputs/mask_gen/find_dip.R $gen_mask_file

    cat $working_dir/inputs/mask.in \

        $running_dir/manual_mask_cache/gen_mask/$gen_mask_file \

        > $running_dir/mask_combined_cache.in

else

	cat $working_dir/inputs/mask.in > $running_dir/mask_combined_cache.in

fi

cd $running_dir

sed -i -r '/^\s*$/d' mask_combined_cache.in

if [ -d "tmp" ]; then

	rm -rf tmp

fi

cp autogrouping_config_template.json autogrouping_config.json

sed -i "s%TO_REPLACE_CALIBRANT%${dia_file}%" autogrouping_config.json

sed -i "s%TO_REPLACE_GM%${group_method}%" autogrouping_config.json

sed -i "s%TO_REPLACE_MF%mask_combined_cache.in%" autogrouping_config.json

# Grouping

. /opt/anaconda/etc/profile.d/conda.sh

# In case the `dev` environment is not working properly,

# one can roll back to the `prod` version by switching

# the commented line below.

conda activate mantidtotalscattering-dev

# conda activate mantidtotalscattering

python autogrouping.py

conda deactivate

if [ "$group_method" = "KMEANS_ED" ]; then

	sed -i '3d' outputgrouping.xml

	sed -i '4d' outputgrouping.xml

	ex -s -c 3m4 -c w -c q outputgrouping.xml

fi

# External call to translate the mask file in plain text form to

# its XML form.

conda activate ~y8z/miniconda/envs/nom_calib

python group_calib_prep.py

conda deactivate

cd $working_dir

# Calibration

mantidpython $working_dir/utils_legacy/nom_cal.py $working_dir $local_cc_file

if [ ! -d $out_dir/input_configs ] ; then

    mkdir $out_dir/input_configs

fi

if [ ! -d $out_dir_alt/input_configs ] ; then

    mkdir $out_dir_alt/input_configs

fi

file_name=NOMAD_${run_num}_${run_date}_${sam_env}.json

cp $local_cc_file $out_dir/input_configs/$file_name

cp $local_cc_file $out_dir_alt/input_configs/$file_name

echo ""

echo "+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+"

echo "Info> Calibration job done!"

echo "Info> h5 file written to $out_dir"

echo "+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+"

echo ""