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batch_LiCSBAS.sh
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batch_LiCSBAS.sh
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#!/bin/bash -eu
# LiCSBAS steps:
# 01: LiCSBAS01_get_geotiff.py
# 02: LiCSBAS02_ml_prep.py
# 03: LiCSBAS03op_GACOS.py (optional)
# 04: LiCSBAS04op_mask_unw.py (optional)
# 05: LiCSBAS05op_clip_unw.py (optional)
# 11: LiCSBAS11_check_unw.py
# 12: LiCSBAS12_loop_closure.py
# 13: LiCSBAS13_sb_inv.py
# 14: LiCSBAS14_vel_std.py
# 15: LiCSBAS15_mask_ts.py
# 16: LiCSBAS16_filt_ts.py
#################
### Settings ####
#################
start_step="01" # 01-05, 11-16
end_step="16" # 01-05, 11-16
nlook="1" # multilook factor, used in step02
GEOCmldir="GEOCml${nlook}" # If start from 11 or later after doing 03-05, use e.g., GEOCml${nlook}GACOSmaskclip
n_para="" # Number of paralell processing in step 02-05,12,13,16. default: number of usable CPU
check_only="n" # y/n. If y, not run scripts and just show commands to be done
logdir="log"
log="$logdir/$(date +%Y%m%d%H%M)$(basename $0 .sh)_${start_step}_${end_step}.log"
### Optional steps (03-05) ###
do03op_GACOS="n" # y/n
do04op_mask="n" # y/n
do05op_clip="n" # y/n
p04_mask_coh_thre="" # e.g. 0.2
p04_mask_range="" # e.g. 10:100/20:200 (ix start from 0)
p04_mask_range_file="" # Name of file containing range list
p05_clip_range="" # e.g. 10:100/20:200 (ix start from 0)
p05_clip_range_geo="" # e.g. 130.11/131.12/34.34/34.6 (in deg)
### Frequently used options. If blank, use default. ###
p11_unw_thre="" # default: 0.3
p11_coh_thre="" # default: 0.05
p12_loop_thre="" # default: 1.5 rad
p15_coh_thre="" # default: 0.05
p15_n_unw_r_thre="" # default: 1.5
p15_vstd_thre="" # default: 100 mm/yr
p15_maxTlen_thre="" # default: 1 yr
p15_n_gap_thre="" # default: 10
p15_stc_thre="" # default: 5 mm
p15_n_ifg_noloop_thre="" # default: 50
p15_n_loop_err_thre="" # default: 5
p15_resid_rms_thre="" # default: 2 mm
p16_filtwidth_km="" # default: 2 km
p16_filtwidth_yr="" # default: avg_interval*3 yr
p16_deg_deramp="" # 1, bl, or 2. default: no deramp
p16_hgt_linear="n" # y/n. default: n
p16_range="" # e.g. 10:100/20:200 (ix start from 0)
p16_range_geo="" # e.g. 130.11/131.12/34.34/34.6 (in deg)
p16_ex_range="" # e.g. 10:100/20:200 (ix start from 0)
p16_ex_range_geo="" # e.g. 130.11/131.12/34.34/34.6 (in deg)
### Less frequently used options. If blank, use default. ###
p01_frame="" # e.g. 021D_04972_131213
p01_start_date="" # default: 20141001
p01_end_date="" # default: today
p01_get_gacos="n" # y/n
p01_n_para="" # default: 4
p02_GEOCdir="" # default: GEOC
p02_GEOCmldir="" # default: GEOCml$nlook
p02_freq="" # default: 5.405e9 Hz
p02_n_para="" # default: # of usable CPU
order_op03_05="03 04 05" # can change order e.g., 05 03 04
p03_inGEOCmldir="" # default: $GEOCmldir
p03_outGEOCmldir_suffix="" # default: GACOS
p03_fillhole="y" # y/n. default: n
p03_gacosdir="" # default: GACOS
p03_n_para="" # default: # of usable CPU
p04_inGEOCmldir="" # default: $GEOCmldir
p04_outGEOCmldir_suffix="" # default: mask
p04_n_para="" # default: # of usable CPU
p05_inGEOCmldir="" # default: $GEOCmldir
p05_outGEOCmldir_suffix="" # default: clip
p05_n_para="" # default: # of usable CPU
p11_GEOCmldir="" # default: $GEOCmldir
p11_TSdir="" # default: TS_$GEOCmldir
p12_GEOCmldir="" # default: $GEOCmldir
p12_TSdir="" # default: TS_$GEOCmldir
p12_n_para="" # default: # of usable CPU
p12_multi_prime="n" # y/n. default: n
p13_GEOCmldir="" # default: $GEOCmldir
p13_TSdir="" # default: TS_$GEOCmldir
p13_inv_alg="" # LS (default) or WLS
p13_mem_size="" # default: 4000 (MB)
p13_gamma="" # default: 0.0001
p13_n_para="" # default: # of usable CPU
p13_n_unw_r_thre="" # defualt: 1
p13_keep_incfile="n" # y/n. default: n
p14_TSdir="" # default: TS_$GEOCmldir
p14_mem_size="" # default: 4000 (MB)
p15_TSdir="" # default: TS_$GEOCmldir
p15_vmin="" # default: auto (mm/yr)
p15_vmax="" # default: auto (mm/yr)
p15_keep_isolated="n" # y/n. default: n
p15_noautoadjust="n" # y/n. default: n
p16_TSdir="" # default: TS_$GEOCmldir
p16_hgt_min="" # default: 200 (m)
p16_hgt_max="" # default: 10000 (m)
p16_nomask="n" # y/n. default: n
p16_n_para="" # default: # of usable CPU
#############################
### Run (No need to edit) ###
#############################
echo ""
echo "Start step: $start_step"
echo "End step: $end_step"
echo "Log file: $log"
echo ""
mkdir -p $logdir
if [ $start_step -le 01 -a $end_step -ge 01 ];then
p01_op=""
if [ ! -z $p01_frame ];then p01_op="$p01_op -f $p01_frame"; fi
if [ ! -z $p01_start_date ];then p01_op="$p01_op -s $p01_start_date"; fi
if [ ! -z $p01_end_date ];then p01_op="$p01_op -e $p01_end_date"; fi
if [ $p01_get_gacos == "y" ];then p01_op="$p01_op --get_gacos"; fi
if [ ! -z $p01_n_para ];then p01_op="$p01_op --n_para $p01_n_para"; fi
if [ $check_only == "y" ];then
echo "LiCSBAS01_get_geotiff.py $p01_op"
else
LiCSBAS01_get_geotiff.py $p01_op 2>&1 | tee -a $log
if [ ${PIPESTATUS[0]} -ne 0 ];then exit 1; fi
fi
fi
if [ $start_step -le 02 -a $end_step -ge 02 ];then
p02_op=""
if [ ! -z $p02_GEOCdir ];then p02_op="$p02_op -i $p02_GEOCdir";
else p02_op="$p02_op -i GEOC"; fi
if [ ! -z $p02_GEOCmldir ];then p02_op="$p02_op -o $p02_GEOCmldir"; fi
if [ ! -z $nlook ];then p02_op="$p02_op -n $nlook"; fi
if [ ! -z $p02_freq ];then p02_op="$p02_op --freq $p02_freq"; fi
if [ ! -z $p02_n_para ];then p02_op="$p02_op --n_para $p02_n_para";
elif [ ! -z $n_para ];then p02_op="$p02_op --n_para $n_para";fi
if [ $check_only == "y" ];then
echo "LiCSBAS02_ml_prep.py $p02_op"
else
LiCSBAS02_ml_prep.py $p02_op 2>&1 | tee -a $log
if [ ${PIPESTATUS[0]} -ne 0 ];then exit 1; fi
fi
fi
## Optional steps
for step in $order_op03_05; do ##1
if [ $step -eq 03 -a $start_step -le 03 -a $end_step -ge 03 ];then
if [ $do03op_GACOS == "y" ]; then
p03_op=""
if [ ! -z $p03_inGEOCmldir ];then inGEOCmldir="$p03_inGEOCmldir";
else inGEOCmldir="$GEOCmldir"; fi
p03_op="$p03_op -i $inGEOCmldir"
if [ ! -z $p03_outGEOCmldir_suffix ];then outGEOCmldir="$inGEOCmldir$p03_outGEOCmldir_suffix";
else outGEOCmldir="${inGEOCmldir}GACOS"; fi
p03_op="$p03_op -o $outGEOCmldir"
if [ ! -z $p03_gacosdir ];then p03_op="$p03_op -g $p03_gacosdir"; fi
if [ $p03_fillhole == "y" ];then p03_op="$p03_op --fillhole"; fi
if [ ! -z $p03_n_para ];then p03_op="$p03_op --n_para $p03_n_para";
elif [ ! -z $n_para ];then p03_op="$p03_op --n_para $n_para";fi
if [ $check_only == "y" ];then
echo "LiCSBAS03op_GACOS.py $p03_op"
else
LiCSBAS03op_GACOS.py $p03_op 2>&1 | tee -a $log
if [ ${PIPESTATUS[0]} -ne 0 ];then exit 1; fi
fi
### Update GEOCmldir to be used for following steps
GEOCmldir="$outGEOCmldir"
fi
fi
if [ $step -eq 04 -a $start_step -le 04 -a $end_step -ge 04 ];then
if [ $do04op_mask == "y" ]; then
p04_op=""
if [ ! -z $p04_inGEOCmldir ];then inGEOCmldir="$p04_inGEOCmldir";
else inGEOCmldir="$GEOCmldir"; fi
p04_op="$p04_op -i $inGEOCmldir"
if [ ! -z $p04_outGEOCmldir_suffix ];then outGEOCmldir="$inGEOCmldir$p04_outGEOCmldir_suffix";
else outGEOCmldir="${inGEOCmldir}mask"; fi
p04_op="$p04_op -o $outGEOCmldir"
if [ ! -z $p04_mask_coh_thre ];then p04_op="$p04_op -c $p04_mask_coh_thre"; fi
if [ ! -z $p04_mask_range ];then p04_op="$p04_op -r $p04_mask_range"; fi
if [ ! -z $p04_mask_range_file ];then p04_op="$p04_op -f $p04_mask_range_file"; fi
if [ ! -z $p04_n_para ];then p04_op="$p04_op --n_para $p04_n_para";
elif [ ! -z $n_para ];then p04_op="$p04_op --n_para $n_para";fi
if [ $check_only == "y" ];then
echo "LiCSBAS04op_mask_unw.py $p04_op"
else
LiCSBAS04op_mask_unw.py $p04_op 2>&1 | tee -a $log
if [ ${PIPESTATUS[0]} -ne 0 ];then exit 1; fi
fi
### Update GEOCmldir to be used for following steps
GEOCmldir="$outGEOCmldir"
fi
fi
if [ $step -eq 05 -a $start_step -le 05 -a $end_step -ge 05 ];then
if [ $do05op_clip == "y" ]; then
p05_op=""
if [ ! -z $p05_inGEOCmldir ];then inGEOCmldir="$p05_inGEOCmldir";
else inGEOCmldir="$GEOCmldir"; fi
p05_op="$p05_op -i $inGEOCmldir"
if [ ! -z $p05_outGEOCmldir_suffix ];then outGEOCmldir="$inGEOCmldir$p05_outGEOCmldir_suffix";
else outGEOCmldir="${GEOCmldir}clip"; fi
p05_op="$p05_op -o $outGEOCmldir"
if [ ! -z $p05_clip_range ];then p05_op="$p05_op -r $p05_clip_range"; fi
if [ ! -z $p05_clip_range_geo ];then p05_op="$p05_op -g $p05_clip_range_geo"; fi
if [ ! -z $p05_n_para ];then p05_op="$p05_op --n_para $p05_n_para";
elif [ ! -z $n_para ];then p05_op="$p05_op --n_para $n_para";fi
if [ $check_only == "y" ];then
echo "LiCSBAS05op_clip_unw.py $p05_op"
else
LiCSBAS05op_clip_unw.py $p05_op 2>&1 | tee -a $log
if [ ${PIPESTATUS[0]} -ne 0 ];then exit 1; fi
fi
### Update GEOCmldir to be used for following steps
GEOCmldir="$outGEOCmldir"
fi
fi
done ##1
### Determine name of TSdir
TSdir="TS_$GEOCmldir"
if [ $start_step -le 11 -a $end_step -ge 11 ];then
p11_op=""
if [ ! -z $p11_GEOCmldir ];then p11_op="$p11_op -d $p11_GEOCmldir";
else p11_op="$p11_op -d $GEOCmldir"; fi
if [ ! -z $p11_TSdir ];then p11_op="$p11_op -t $p11_TSdir"; fi
if [ ! -z $p11_unw_thre ];then p11_op="$p11_op -u $p11_unw_thre"; fi
if [ ! -z $p11_coh_thre ];then p11_op="$p11_op -c $p11_coh_thre"; fi
if [ $check_only == "y" ];then
echo "LiCSBAS11_check_unw.py $p11_op"
else
LiCSBAS11_check_unw.py $p11_op 2>&1 | tee -a $log
if [ ${PIPESTATUS[0]} -ne 0 ];then exit 1; fi
fi
fi
if [ $start_step -le 12 -a $end_step -ge 12 ];then
p12_op=""
if [ ! -z $p12_GEOCmldir ];then p12_op="$p12_op -d $p12_GEOCmldir";
else p12_op="$p12_op -d $GEOCmldir"; fi
if [ ! -z $p12_TSdir ];then p12_op="$p12_op -t $p12_TSdir"; fi
if [ ! -z $p12_loop_thre ];then p12_op="$p12_op -l $p12_loop_thre"; fi
if [ $p12_multi_prime == "y" ];then p12_op="$p12_op --multi_prime"; fi
if [ ! -z $p12_n_para ];then p12_op="$p12_op --n_para $p12_n_para";
elif [ ! -z $n_para ];then p12_op="$p12_op --n_para $n_para";fi
if [ $check_only == "y" ];then
echo "LiCSBAS12_loop_closure.py $p12_op"
else
LiCSBAS12_loop_closure.py $p12_op 2>&1 | tee -a $log
if [ ${PIPESTATUS[0]} -ne 0 ];then exit 1; fi
fi
fi
if [ $start_step -le 13 -a $end_step -ge 13 ];then
p13_op=""
if [ ! -z $p13_GEOCmldir ];then p13_op="$p13_op -d $p13_GEOCmldir";
else p13_op="$p13_op -d $GEOCmldir"; fi
if [ ! -z $p13_TSdir ];then p13_op="$p13_op -t $p13_TSdir"; fi
if [ ! -z $p13_inv_alg ];then p13_op="$p13_op --inv_alg $p13_inv_alg"; fi
if [ ! -z $p13_mem_size ];then p13_op="$p13_op --mem_size $p13_mem_size"; fi
if [ ! -z $p13_gamma ];then p13_op="$p13_op --gamma $p13_gamma"; fi
if [ ! -z $p13_n_para ];then p13_op="$p13_op --n_para $p13_n_para";
elif [ ! -z $n_para ];then p13_op="$p13_op --n_para $n_para";fi
if [ ! -z $p13_n_para ];then p13_op="$p13_op --n_para $p13_n_para"; fi
if [ ! -z $p13_n_unw_r_thre ];then p13_op="$p13_op --n_unw_r_thre $p13_n_unw_r_thre"; fi
if [ $p13_keep_incfile == "y" ];then p13_op="$p13_op --keep_incfile"; fi
if [ $check_only == "y" ];then
echo "LiCSBAS13_sb_inv.py $p13_op"
else
LiCSBAS13_sb_inv.py $p13_op 2>&1 | tee -a $log
if [ ${PIPESTATUS[0]} -ne 0 ];then exit 1; fi
fi
fi
if [ $start_step -le 14 -a $end_step -ge 14 ];then
p14_op=""
if [ ! -z $p14_TSdir ];then p14_op="$p14_op -t $p14_TSdir";
else p14_op="$p14_op -t $TSdir"; fi
if [ ! -z $p14_mem_size ];then p14_op="$p14_op --mem_size $p14_mem_size"; fi
if [ $check_only == "y" ];then
echo "LiCSBAS14_vel_std.py $p14_op"
else
LiCSBAS14_vel_std.py $p14_op 2>&1 | tee -a $log
if [ ${PIPESTATUS[0]} -ne 0 ];then exit 1; fi
fi
fi
if [ $start_step -le 15 -a $end_step -ge 15 ];then
p15_op=""
if [ ! -z $p15_TSdir ];then p15_op="$p15_op -t $p15_TSdir";
else p15_op="$p15_op -t $TSdir"; fi
if [ ! -z $p15_coh_thre ];then p15_op="$p15_op -c $p15_coh_thre"; fi
if [ ! -z $p15_n_unw_r_thre ];then p15_op="$p15_op -u $p15_n_unw_r_thre"; fi
if [ ! -z $p15_vstd_thre ];then p15_op="$p15_op -v $p15_vstd_thre"; fi
if [ ! -z $p15_maxTlen_thre ];then p15_op="$p15_op -T $p15_maxTlen_thre"; fi
if [ ! -z $p15_n_gap_thre ];then p15_op="$p15_op -g $p15_n_gap_thre"; fi
if [ ! -z $p15_stc_thre ];then p15_op="$p15_op -s $p15_stc_thre"; fi
if [ ! -z $p15_n_ifg_noloop_thre ];then p15_op="$p15_op -i $p15_n_ifg_noloop_thre"; fi
if [ ! -z $p15_n_loop_err_thre ];then p15_op="$p15_op -l $p15_n_loop_err_thre"; fi
if [ ! -z $p15_resid_rms_thre ];then p15_op="$p15_op -r $p15_resid_rms_thre"; fi
if [ ! -z $p15_vmin ];then p15_op="$p15_op --vmin $p15_vmin"; fi
if [ ! -z $p15_vmax ];then p15_op="$p15_op --vmax $p15_vmax"; fi
if [ $p15_keep_isolated == "y" ];then p15_op="$p15_op --keep_isolated"; fi
if [ $p15_noautoadjust == "y" ];then p15_op="$p15_op --noautoadjust"; fi
if [ $check_only == "y" ];then
echo "LiCSBAS15_mask_ts.py $p15_op"
else
LiCSBAS15_mask_ts.py $p15_op 2>&1 | tee -a $log
if [ ${PIPESTATUS[0]} -ne 0 ];then exit 1; fi
fi
fi
if [ $start_step -le 16 -a $end_step -ge 16 ];then
p16_op=""
if [ ! -z $p16_TSdir ];then p16_op="$p16_op -t $p16_TSdir";
else p16_op="$p16_op -t $TSdir"; fi
if [ ! -z $p16_filtwidth_km ];then p16_op="$p16_op -s $p16_filtwidth_km"; fi
if [ ! -z $p16_filtwidth_yr ];then p16_op="$p16_op -y $p16_filtwidth_yr"; fi
if [ ! -z $p16_deg_deramp ];then p16_op="$p16_op -r $p16_deg_deramp"; fi
if [ $p16_hgt_linear == "y" ];then p16_op="$p16_op --hgt_linear"; fi
if [ ! -z $p16_hgt_min ];then p16_op="$p16_op --hgt_min $p16_hgt_min"; fi
if [ ! -z $p16_hgt_max ];then p16_op="$p16_op --hgt_max $p16_hgt_max"; fi
if [ $p16_nomask == "y" ];then p16_op="$p16_op --nomask"; fi
if [ ! -z $p16_n_para ];then p16_op="$p16_op --n_para $p16_n_para";
elif [ ! -z $n_para ];then p16_op="$p16_op --n_para $n_para";fi
if [ ! -z $p16_range ];then p16_op="$p16_op --range $p16_range"; fi
if [ ! -z $p16_range_geo ];then p16_op="$p16_op --range_geo $p16_range_geo"; fi
if [ ! -z $p16_ex_range ];then p16_op="$p16_op --ex_range $p16_ex_range"; fi
if [ ! -z $p16_ex_range_geo ];then p16_op="$p16_op --ex_range_geo $p16_ex_range_geo"; fi
if [ $check_only == "y" ];then
echo "LiCSBAS16_filt_ts.py $p16_op"
else
LiCSBAS16_filt_ts.py $p16_op 2>&1 | tee -a $log
if [ ${PIPESTATUS[0]} -ne 0 ];then exit 1; fi
fi
fi
if [ $check_only == "y" ];then
echo ""
echo "Above commands will run when you change check_only to \"n\""
echo ""
fi