howto_run_SimSET_multi_tomos.sh

#! /bin/bash

# This is an example run with the templates distributed with STIR (appropriate for the HR+).
# The code below works in bash, sh, ksh etc, but needs to be modified for csh.
# Authors: Kris Thielemans
#
#
#  Copyright (C) 2005 - 2006, Hammersmith Imanet Ltd
#  Copyright (C) 2011-07-01 - 2012, Kris Thielemans
#  This file is part of STIR.
#
#  SPDX-License-Identifier: Apache-2.0
#
#  See STIR/LICENSE.txt for details

# adjust location of SimSET to where you have it installed.
# set SIMSET_DIR if it isnt set by the user
: ${SIMSET_DIR:=/home/treeves/2.9.2}
export SIMSET_DIR

PATH=/home/treeves/devel/build/sources/STIR/src/SimSET/scripts:$PATH


#All STIR utilities/scripts have to be in your path, e.g. if your 
#INSTALL_PREFIX was ~/STIR-bin, you could do
#   PATH=$PATH:~/STIR-bin/bin

# generate emission image
# generate_image generate_uniform_cylinder.par 
# use the same size for the attenuation in this example
# above par file sets image values to 1, so line below will use water for attenuation

# give the simulation a name. All output files will go into a new subdirectory of this name
SIM_NAME=/home/treeves/devel/build/sources/STIR/src/SimSET/examples/TOF_Scatter_Simulation
# number of decays to simulate
PHOTONS=300000000
# specify names/locations of input files
EMISS_DATA=Initial_phantom_activity_path
ATTEN_DATA=Atten_image_path
templ_dir=SimSET_examples_directory
DIR_INPUT=SimSET_examples_directory
TEMPLATE_PHG=${templ_dir}/phg_with_tomos.rec
#TEMPLATE_BIN=${templ_dir}/template_bin.rec
#TEMPLATE_BIN_2=${templ_dir}/template_bin_energy_params_2.rec
TEMPLATE_DET=${templ_dir}/template_det.rec
# specify scanner
SCANNER="GE Discovery 690" # this doesn't matter much
# maximum ring difference to store in conversion from SimSET to Interfile projdata
NUM_SEG=0
# export all variables
export SIM_NAME EMISS_DATA ATTEN_DATA TEMPLATE_PHG  
export PHOTONS NUM_SEG SCANNER
export DIR_INPUT
DIR_OUTPUT=${SIM_NAME}
export DIR_OUTPUT


# set the simulation going
run_SimSET_multi_parameter.sh

echo "Current working directory: $(pwd)"

# Start phg in background
#$SIMSET_DIR/bin/phg "${DIR_OUTPUT}/phg.rec" > "${DIR_OUTPUT}/phg.log" 2>&1 &

PHG_PID=$!

# Wait for phg to finish
wait $PHG_PID