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Toni REEVES
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Adding files for different scenarios for running SimSET
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‎src/SimSET/examples/howto_run_SimSET_multi_tomos.sh‎

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#! /bin/bash
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# This is an example run with the templates distributed with STIR (appropriate for the HR+).
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# The code below works in bash, sh, ksh etc, but needs to be modified for csh.
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# Authors: Kris Thielemans
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#
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#
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# Copyright (C) 2005 - 2006, Hammersmith Imanet Ltd
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# Copyright (C) 2011-07-01 - 2012, Kris Thielemans
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# This file is part of STIR.
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#
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# SPDX-License-Identifier: Apache-2.0
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#
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# See STIR/LICENSE.txt for details
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# adjust location of SimSET to where you have it installed.
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# set SIMSET_DIR if it isnt set by the user
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: ${SIMSET_DIR:=/home/treeves/2.9.2}
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export SIMSET_DIR
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PATH=/home/treeves/devel/build/sources/STIR/src/SimSET/scripts:$PATH
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#All STIR utilities/scripts have to be in your path, e.g. if your
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#INSTALL_PREFIX was ~/STIR-bin, you could do
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# PATH=$PATH:~/STIR-bin/bin
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# generate emission image
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# generate_image generate_uniform_cylinder.par
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# use the same size for the attenuation in this example
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# above par file sets image values to 1, so line below will use water for attenuation
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# give the simulation a name. All output files will go into a new subdirectory of this name
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SIM_NAME=/home/treeves/devel/build/sources/STIR/src/SimSET/examples/TOF_Scatter_Simulation
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# number of decays to simulate
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PHOTONS=300000000
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# specify names/locations of input files
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EMISS_DATA=/SAN/medic/Energy_PET_STIR_Sims/Image_Data/XCAT_data/XCAT_act_resample_171_2nd_downsample_TOF_scatter.hv
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ATTEN_DATA=/SAN/medic/Energy_PET_STIR_Sims/Image_Data/XCAT_data/XCAT_atn_correct_resample_171_2nd_downsample_TOF_scatter.hv
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templ_dir=/home/treeves/devel/build/sources/STIR/src/SimSET/examples
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DIR_INPUT=/home/treeves/devel/build/sources/STIR/src/SimSET/examples
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TEMPLATE_PHG=${templ_dir}/phg_with_tomos.rec
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#TEMPLATE_BIN=${templ_dir}/template_bin.rec
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#TEMPLATE_BIN_2=${templ_dir}/template_bin_energy_params_2.rec
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TEMPLATE_DET=${templ_dir}/template_det.rec
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# specify scanner
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SCANNER="GE Discovery 690"
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# maximum ring difference to store in conversion from SimSET to Interfile projdata
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NUM_SEG=0
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# export all variables
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export SIM_NAME EMISS_DATA ATTEN_DATA TEMPLATE_PHG
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export PHOTONS NUM_SEG SCANNER
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export DIR_INPUT
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DIR_OUTPUT=${SIM_NAME}
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export DIR_OUTPUT
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# set the simulation going
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run_SimSET_multi_parameter.sh
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echo "Current working directory: $(pwd)"
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# Start phg in background
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#$SIMSET_DIR/bin/phg "${DIR_OUTPUT}/phg.rec" > "${DIR_OUTPUT}/phg.log" 2>&1 &
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PHG_PID=$!
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# Wait for phg to finish
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wait $PHG_PID
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‎src/SimSET/examples/howto_run_SimSET_multi_tomos_omni.sh‎

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#! /bin/bash
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# This is an example run with the templates distributed with STIR (appropriate for the HR+).
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# The code below works in bash, sh, ksh etc, but needs to be modified for csh.
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# Authors: Kris Thielemans
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#
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#
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# Copyright (C) 2005 - 2006, Hammersmith Imanet Ltd
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# Copyright (C) 2011-07-01 - 2012, Kris Thielemans
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# This file is part of STIR.
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#
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# SPDX-License-Identifier: Apache-2.0
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#
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# See STIR/LICENSE.txt for details
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# adjust location of SimSET to where you have it installed.
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# set SIMSET_DIR if it isnt set by the user
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: ${SIMSET_DIR:=/home/treeves/2.9.2}
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export SIMSET_DIR
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PATH=/home/treeves/devel/build/sources/STIR/src/SimSET/scripts:$PATH
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#All STIR utilities/scripts have to be in your path, e.g. if your
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#INSTALL_PREFIX was ~/STIR-bin, you could do
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# PATH=$PATH:~/STIR-bin/bin
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# generate emission image
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# generate_image generate_uniform_cylinder.par
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# use the same size for the attenuation in this example
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# above par file sets image values to 1, so line below will use water for attenuation
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# give the simulation a name. All output files will go into a new subdirectory of this name
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SIM_NAME=/SAN/medic/Energy_PET_STIR_Sims/SimSET_Data_output/XCAT_brain_test_omni_downsampled
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# number of decays to simulate
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PHOTONS=70000000
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# specify names/locations of input files
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EMISS_DATA=/SAN/medic/Energy_PET_STIR_Sims/Image_Data/XCAT_data/XCAT_act_resample_171_2nd_downsample.hv
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ATTEN_DATA=/SAN/medic/Energy_PET_STIR_Sims/Image_Data/XCAT_data/XCAT_resample_171_2nd_downsample_empty_atten.hv
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templ_dir=/home/treeves/devel/build/sources/STIR/src/SimSET/examples
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DIR_INPUT=/home/treeves/devel/build/sources/STIR/src/SimSET/examples
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TEMPLATE_PHG=${templ_dir}/template_phg_omni.rec
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#TEMPLATE_BIN=${templ_dir}/template_bin.rec
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#TEMPLATE_BIN_2=${templ_dir}/template_bin_energy_params_2.rec
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TEMPLATE_DET=${templ_dir}/Omni_files/detConfig/omni70cm_6R_31_May_2020_new.detcfg
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# specify scanner
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SCANNER="GE Discovery 690"
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# maximum ring difference to store in conversion from SimSET to Interfile projdata
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NUM_SEG=0
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# export all variables
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export SIM_NAME EMISS_DATA ATTEN_DATA TEMPLATE_PHG TEMPLATE_DET
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export PHOTONS NUM_SEG SCANNER
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export DIR_INPUT
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DIR_OUTPUT=${SIM_NAME}
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export DIR_OUTPUT
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# set the simulation going
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run_SimSET_omni.sh
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echo "Current working directory: $(pwd)"
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# Start phg in background
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#$SIMSET_DIR/bin/phg "${DIR_OUTPUT}/phg.rec" > "${DIR_OUTPUT}/phg.log" 2>&1 &
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PHG_PID=$!
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# Wait for phg to finish
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wait $PHG_PID
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‎src/SimSET/examples/howto_run_SimSET_normalisation_multi_tomos.sh‎

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#! /bin/bash
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# This is an example run with the templates distributed with STIR (appropriate for the HR+).
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# The code below works in bash, sh, ksh etc, but needs to be modified for csh.
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# Authors: Kris Thielemans
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#
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#
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# Copyright (C) 2005 - 2006, Hammersmith Imanet Ltd
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# Copyright (C) 2011-07-01 - 2012, Kris Thielemans
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# This file is part of STIR.
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#
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# SPDX-License-Identifier: Apache-2.0
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#
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# See STIR/LICENSE.txt for details
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# adjust location of SimSET to where you have it installed.
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# set SIMSET_DIR if it isnt set by the user
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: ${SIMSET_DIR:=/home/treeves/Software/2.9.2}
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export SIMSET_DIR
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PATH=/home/treeves/devel/build/sources/STIR/src/SimSET/scripts:$PATH
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#All STIR utilities/scripts have to be in your path, e.g. if your
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#INSTALL_PREFIX was ~/STIR-bin, you could do
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# PATH=$PATH:~/STIR-bin/bin
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# generate emission image
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# generate_image generate_uniform_cylinder.par
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# use the same size for the attenuation in this example
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# above par file sets image values to 1, so line below will use water for attenuation
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# generate emission image
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generate_image generate_uniform_cylinder.par
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# use the same size for the attenuation in this example
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# above par file sets image values to 1, so line below will use water for attenuation
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stir_math --including-first --times-scalar 0 uniform_cylinder_atten.hv my_uniform_cylinder.hv
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# give the simulation a name. All output files will go into a new subdirectory of this name
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SIM_NAME=multi_tomos_bladder_0_act_sim_bladder_normalisation
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# number of decays to simulate
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PHOTONS=40000000
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# specify names/locations of input files
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#EMISS_DATA=/SAN/medic/Energy_PET_STIR_Sims/XCAT/bladder_only_region_select_XCAT_act.hv
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#ATTEN_DATA=/SAN/medic/Energy_PET_STIR_Sims/XCAT/bladder_only_region_select_XCAT_atn.hv
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templ_dir=/home/treeves/devel/build/sources/STIR/src/SimSET/examples
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DIR_INPUT=/home/treeves/devel/build/sources/STIR/src/SimSET/examples
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TEMPLATE_PHG=${templ_dir}/phg_with_tomos.rec
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#TEMPLATE_BIN=${templ_dir}/template_bin.rec
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#TEMPLATE_BIN_2=${templ_dir}/template_bin_energy_params_2.rec
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TEMPLATE_DET=${templ_dir}/template_det.rec
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# specify scanner
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SCANNER="GE Discovery 690"
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# maximum ring difference to store in conversion from SimSET to Interfile projdata
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NUM_SEG=0
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# export all variables
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export SIM_NAME EMISS_DATA ATTEN_DATA TEMPLATE_PHG
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export PHOTONS NUM_SEG SCANNER
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export DIR_INPUT
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DIR_OUTPUT=${DIR_INPUT}/${SIM_NAME}
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export DIR_OUTPUT
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# set the simulation going
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run_SimSET_multi_parameter_modified.sh
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echo "Current working directory: $(pwd)"
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# Start phg in background
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$SIMSET_DIR/bin/phg "${DIR_OUTPUT}/phg.rec" > "${DIR_OUTPUT}/phg.log" 2>&1 &
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PHG_PID=$!
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# Wait for phg to finish
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wait $PHG_PID
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