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#!/bin/bash -eu # LiCSBAS steps: # 01: LiCSBAS01_get_geotiff.py # 02to05: LiCSBAS02to05_unwrap.py or 02: LiCSBAS02_ml_prep.py # 03: LiCSBAS03op_GACOS.py (optional) # 04: LiCSBAS04op_mask_unw.py (optional) # 05: LiCSBAS05op_clip_unw.py (optional) # 06: LiCSBAS03op_ERA5.py (optional) # 11: LiCSBAS11_check_unw.py # (optional) 120: LiCSBAS120_choose_reference.py - RECOMMENDED, especially if nullification is used, thus added to cometdev # 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 # # Status of COMET dev version - the experimental functions are turned on with # ################# ### Settings #### ################# start_step="01" # 01-05, 11-16 end_step="16" # 01-05, 11-16 cometdev='0' # shortcut to use COMET's experimental/dev functions. At this moment, '1' will turn on the nullification. Recommended: 0 eqoffs="n" # if 'y', it will do: get_eq_offsets, then invert. if singular_gauss, then set use of model (not recommended now, experimental/need some work). 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 parallel processing in step 02-05,12,13,16. default: number of usable CPU gpu="n" # y/n check_only="n" # y/n. If y, not run scripts and just show commands to be done sbovl_abs="n" #if y, will close the referencing in step 12,13,16 and add ICC+ESD offset and apply absolute SET and Iono correction to sbovl time series #MN logdir="log" log="$logdir/$(date +%Y%m%d%H%M)$(basename $0 .sh)_${start_step}_${end_step}.log" freq="" # default: 5.405e9 Hz ### Running the updated pipelines: run_reunwrapping='n' # y/n. default: 'n'. Reunwrapping would use 02to05 script instead of the original 02[,03,04,05] ### Optional steps (03-06) ### order_op03_05="03 04 05 06" # can change order e.g., 05 03 04 do03op_GACOS="n" # y/n do04op_mask="n" # y/n do05op_clip="n" # y/n do06op_ERA5="n" #"y" # ERA5 apply if icams files in LiCSAR p04_mask_coh_thre_avg="" # e.g. 0.2 p04_mask_coh_thre_ifg="" # e.g. 0.2 p04_mask_range="" # e.g. 10:100/20:200 (ix start from 0) p04_mask_range_file="" # Name of file containing range list p05_clip_range="" # e.g. 10:100/20:200 (ix start from 0) p05_clip_range_geo="" # e.g. 130.11/131.12/34.34/34.6 (in deg) # Optional reunwrapping: p02to05_freq=$freq # default: 5.405e9 Hz p02to05_gacos="" # y/n. default: 'y'. Use gacos data if available (for majority of epochs, data without GACOS corr would be dropped) p02to05_hgtcorr="" # y/n. default: 'n'. Recommended for regions with high and varying topography p02to05_cascade="" # y/n. default: 'n'. Cascade from higher multilook factor would propagate to higher resolution (lower ML factor) data. Useful but not universal p02to05_filter="" # gold, gauss or adf. Default: 'gold' p02to05_thres="" # default: 0.35. Spatial consistence of the interferogram. Recommended to keep this value. If too much is masked, may try getting close to 0 (although, this would introduce some unw errors) p02to05_cliparea_geo=$p05_clip_range_geo # setting the clip range, e.g. 130.11/131.12/34.34/34.6 (in deg) p02to05_n_para=$n_para p02to05_op_GEOCdir="" # by default, if none, it will use GEOC directory ### Frequently used options. If blank, use default. ### p01_start_date="" # default: 20141001 p01_end_date="" # default: today p01_get_gacos="n" # y/n p01_get_pha="n" # y/n p01_get_mli="n" # y/n p01_sbovl="n" p02_sbovl="n" p04_sbovl="n" p11_unw_thre="" # default: 0.3 p11_coh_thre="" # default: 0.05 p11_s_param="n" # y/n p11_sbovl="n" p120_use="n" # y/n p120_sbovl="n" p12_loop_thre="" # default: 1.5 rad. With --nullify, recommended higher value (as this is an average over the whole scene) p12_multi_prime="y" # y/n. y recommended p12_nullify="" # y/n. y recommended p12_rm_ifg_list="" # List file containing ifgs to be manually removed p12_skippngs="" # y/n. n by default p13_nullify_noloops="" # y/n. n by default (but it is recommended to use this option with p12_nullify) p13_ignore_nullification="" # y/n. n by default p13_singular="" # y/n. n by default p13_singular_gauss="" # y/n. n by default p13_skippngs="" # y/n. n by default p13_sbovl="n" # p131_sbovl_abs="n" ## adding ICC+ESD offfset and apply SET and Iono correction to sbovl time series p131_sbovl_model="n" ## adding RANSAC model guide for daz values to handle the outliers especially between 2018-2021 p131_sbovl_tide="n" p131_sbovl_iono="n" p14_sbovl="n" p15_coh_thre="" # default: 0.05 p15_n_unw_r_thre="" # default: 1.5 p15_vstd_thre="" # default: 100 mm/yr p15_maxTlen_thre="1" # default: 1 yr p15_n_gap_thre="" # default: 10 p15_stc_thre="" # default: 10 mm p15_n_ifg_noloop_thre="" # default: 500 - setting this much higher than orig since we nullify them (p13_nullify_noloops) p15_n_loop_err_thre="" # default: 5 p15_n_loop_err_ratio_thre="" # default: 0.7 - in future we will switch to this ratio term, instead of n_loop_err p15_resid_rms_thre="" # default: 15 mm p15_avg_phasebias="" # default: not used. Setting 1 or 1.2 rad is good option p15_n_gap_use_merged="y" # default: 'y' p15_sbovl="n" # p15_sbovl_tide="n" ##these already depend on p131_sbovl_tide and p131_sbovl_iono, so I will use them to call # p15_sbovl_iono="n" 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_demerr="n" # y/n. default: n p16_hgt_linear="n" # y/n. default: n p16_hgt_min="" # default: 200 (m) p16_hgt_max="" # default: 10000 (m) 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) p16_interpolate_nans="y" # will interpolate nans in unmasked pixels p16_skippngs="" # y/n. n by default p16_sbovl="n" # p16_sbovl_tide="n" ##these already depend on p131_sbovl_tide and p131_sbovl_iono, so I will use them to call # p16_sbovl_iono="n" ### Less frequently used options. If blank, use default. ### p01_frame="" # e.g. 021D_04972_131213 p01_n_para=$n_para # default: 4 p01_rngoff="n" p02_rngoff="n" p02_GEOCdir="" # default: GEOC p02_GEOCmldir="" # default: GEOCml$nlook p02_freq=$freq # default: 5.405e9 Hz p02_n_para=$n_para # default: # of usable CPU p03_inGEOCmldir="" # default: $GEOCmldir p03_outGEOCmldir_suffix="" # default: GACOS p03_fillhole="y" # y/n. default: n p03_gacosdir="" # default: GACOS p03_n_para=$n_para # default: # of usable CPU p04_inGEOCmldir="" # default: $GEOCmldir p04_outGEOCmldir_suffix="" # default: mask p04_n_para=$n_para # default: # of usable CPU p05_inGEOCmldir="" # default: $GEOCmldir p05_outGEOCmldir_suffix="" # default: clip p05_n_para=$n_para # default: # of usable CPU p06_fillhole="y" # y/n. default: n p06_era5dir="ERA5" # default: ERA5 p06_n_para="" # default: # of usable CPU p06_inGEOCmldir="" # default: $GEOCmldir p06_outGEOCmldir_suffix="ERA5" # default: ERA5 p11_GEOCmldir="" # default: $GEOCmldir p11_TSdir="" # default: TS_$GEOCmldir p11_minbtemp="" # default: 0 (not use) p11_maxbtemp="" # default: 0 (not use) p120_ignoreconncomp="n" # y/n p12_GEOCmldir="" # default: $GEOCmldir p12_TSdir="" # default: TS_$GEOCmldir p12_n_para=$n_para # default: # of usable CPU p12_nullify_fix_ref='' # y/n p13_GEOCmldir="" # default: $GEOCmldir p13_TSdir="" # default: TS_$GEOCmldir p13_inv_alg="" # LS (default) or WLS p13_mem_size="" # default: 8000 (MB) p13_gamma="" # default: 0.0001 p13_inputunit="" # rad by default p13_n_para=$n_para # default: # of usable CPU p13_n_unw_r_thre="" # default: 1 for shorter-than-L-band-wavelength (if cometdev, will set to 0.1) p13_keep_incfile="n" # y/n. default: n p14_TSdir="" # default: TS_$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_nomask="n" # y/n. default: n p16_n_para=$n_para # default: # of usable CPU ##just for sbovl high residual detection p13resid_rerun="n" # y/n. default: n # eqoffs eqoffs_minmag="0" # min magnitude of earthquakes to auto-find. 0 means skipping the estimation. eqoffs_txtfile="eqoffsets.txt" # path to txt file containing custom-set earthquake dates (if eqoffs_minmag is disabled/0) or that will use results of auto-find eqoffs_buffer="0.1" # buffer (in degrees, assuming work with WGS-84 geocoded data) to search for earthquakes (if eqoffs_minmag is set) ############################# ### 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 [ $run_reunwrapping == "y" ]; then # do some additional settings for the reunwrapping: p01_get_pha="y" p01_get_mli="y" # not really needed but useful for weighting in multilooking order_op03_05='' #skipping the optional 03-05 steps, contained here skipstep02=1 else skipstep02=0 fi 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 [ ! -z $p01_n_para ];then p01_op="$p01_op --n_para $p01_n_para"; fi # Add --sbovl option if p01_sbovl is "y" if [ "$p01_sbovl" == "y" ]; then p01_op="$p01_op --sbovl"; fi if [ "$p01_rngoff" == "y" ]; then p01_op="$p01_op --rngoff"; fi if [ "$p01_get_gacos" == "y" ]; then p01_op="$p01_op --get_gacos"; fi if [ "$p01_get_pha" == "y" ]; then p01_op="$p01_op --get_pha"; fi if [ "$p01_get_mli" == "y" ]; then p01_op="$p01_op --get_mli"; 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 [ ${PIPESTATUS[0]} -ne 0 ];then exit 1; fi fi fi if [ "$skipstep02" -eq 1 ]; then p02to05_op="" # Setting the GEOC directory if [ ! -z "$p02to05_op_GEOCdir" ]; then p02to05_op="$p02to05_op -i $p02to05_op_GEOCdir" else p02to05_op="$p02to05_op -i GEOC" fi # Additional parameters if [ ! -z "$nlook" ]; then p02to05_op="$p02to05_op -M $nlook"; fi if [ ! -z "$p02to05_freq" ]; then p02to05_op="$p02to05_op --freq $p02to05_freq"; fi if [ ! -z "$p02to05_n_para" ]; then p02to05_op="$p02to05_op --n_para $p02to05_n_para"; fi if [ ! -z "$p02to05_thres" ]; then p02to05_op="$p02to05_op --thres $p02to05_thres"; fi if [ ! -z "$p02to05_filter" ]; then p02to05_op="$p02to05_op --filter $p02to05_filter"; fi if [ ! -z "$p02to05_cliparea_geo" ]; then p02to05_op="$p02to05_op -g $p02to05_cliparea_geo"; fi if [ "$p02to05_cascade" == "y" ]; then p02to05_op="$p02to05_op --cascade"; fi if [ "$p02to05_hgtcorr" == "y" ]; then p02to05_op="$p02to05_op --hgtcorr"; fi if [ "$p02to05_gacos" == "y" ]; then p02to05_op="$p02to05_op --gacos"; fi # Execute or check-only mode if [ "$check_only" == "y" ]; then echo "LiCSBAS02to05_unwrap.py $p02to05_op" else LiCSBAS02to05_unwrap.py $p02to05_op 2>&1 | tee -a "$log" if [ "${PIPESTATUS[0]}" -ne 0 ]; then exit 1; fi fi else # Run step 02 if not skipped if [ "$start_step" -le 02 -a "$end_step" -ge 02 -a "$skipstep02" -eq 0 ]; then p02_op="" # Set the GEOC directories 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 $p02_freq"; fi # Parallel processing if [ ! -z "$p02_n_para" ]; then p02_op="$p02_op --n_para $p02_n_para" elif [ ! -z "$n_para" ]; then p02_op="$p02_op --n_para $n_para" fi if [ "$p02_sbovl" == "y" ]; then p02_op="$p02_op --sbovl"; fi if [ "$p02_rngoff" == "y" ]; then p02_op="$p02_op --rngoff"; 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 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 $p04_mask_coh_thre_avg ];then p04_op="$p04_op -c $p04_mask_coh_thre_avg"; fi if [ ! -z $p04_mask_coh_thre_ifg ];then p04_op="$p04_op -s $p04_mask_coh_thre_ifg"; 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 $p04_mask_range_file"; fi if [ "$p04_sbovl" == "y" ]; then p04_op="$p04_op --sbovl"; 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 if [ $step -eq 06 -a $start_step -le 06 -a $end_step -ge 06 ];then if [ $do06op_ERA5 == "y" ]; then p06_op="" if [ ! -z $p06_inGEOCmldir ];then inGEOCmldir="$p06_inGEOCmldir"; else inGEOCmldir="$GEOCmldir"; fi p06_op="$p06_op -i $inGEOCmldir" if [ ! -z $p06_outGEOCmldir_suffix ];then outGEOCmldir="$inGEOCmldir$p06_outGEOCmldir_suffix"; else outGEOCmldir="${inGEOCmldir}ERA5"; fi p06_op="$p06_op -o $outGEOCmldir" if [ ! -z $p06_era5dir ];then p06_op="$p06_op -g $p06_era5dir"; fi if [ $p06_fillhole == "y" ];then p06_op="$p06_op --fillhole"; fi if [ ! -z $p06_n_para ];then p06_op="$p06_op --n_para $p06_n_para"; elif [ ! -z $n_para ];then p06_op="$p06_op --n_para $n_para";fi if [ $check_only == "y" ];then echo "LiCSBAS03op_ERA5.py $p06_op" else LiCSBAS03op_ERA5.py $p06_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 if [ $start_step -gt 10 -a $do04op_mask == "y" ]; then # If mask step was done, use the masked GEOCmldir GEOCmldir="${GEOCmldir}mask" elif [ $start_step -gt 10 -a $do05op_clip == "y" ]; then # If clip step was done, use the clipped GEOCmldir GEOCmldir="${GEOCmldir}clip" fi 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 [ ! -z $p11_minbtemp ];then p11_op="$p11_op --minbtemp $p11_minbtemp"; fi if [ ! -z $p11_maxbtemp ];then p11_op="$p11_op --maxbtemp $p11_maxbtemp"; fi if [ $p11_sbovl == "y" ];then p11_op="$p11_op --sbovl"; fi if [ $p11_s_param == "y" ];then p11_op="$p11_op -s"; 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 $end_step -ge 12 ];then if [ "$cometdev" -eq 1 ] || [ "$p120_sbovl" == "y" ]; then p120_use='y' fi if [ $p120_use == "y" ]; then dirset="-c $GEOCmldir -d $GEOCmldir -t $TSdir " extra="" if [ $p120_ignoreconncomp == "y" ]; then extra="--ignore_comp" fi if [ $p120_sbovl == "y" ]; then extra="--sbovl" fi if [ $check_only == "y" ];then echo "LiCSBAS120_choose_reference.py $dirset "$extra else LiCSBAS120_choose_reference.py $dirset $extra 2>&1 | tee -a $log if [ ${PIPESTATUS[0]} -ne 0 ];then echo "WARNING, LiCSBAS120 failed. Reverting to original LiCSBAS ref selection"; fi; #exit 1; fi # this often fails, so only warning message fi fi if [ $p120_sbovl != "y" ]; then p12_op="" # if [ $cometdev -eq 1 ]; then # p12_nullify="y" # fi 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 [ $p12_nullify == "y" ];then p12_op="$p12_op --nullify"; fi if [ $p12_nullify_fix_ref == "y" ]; then p12_op="$p12_op --nullify_fix_ref"; fi if [ $p12_skippngs == "y" ];then p12_op="$p12_op --nopngs"; fi if [ ! -z $p12_rm_ifg_list ];then p12_op="$p12_op --rm_ifg_list $p12_rm_ifg_list"; 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 # 2024/11/13: updated nullification may cause extra all-nans-in-ref area. Rerunning step 120 if set to be used if [ $p12_nullify == "y" ];then if [ $p120_use == "y" ]; then dirset="-c $GEOCmldir -d $GEOCmldir -t $TSdir " extra="" if [ $p120_ignoreconncomp == "y" ]; then extra="--ignore_comp" fi if [ $check_only == "y" ];then echo "LiCSBAS120_choose_reference.py $dirset "$extra else LiCSBAS120_choose_reference.py $dirset $extra 2>&1 | tee -a $log if [ ${PIPESTATUS[0]} -ne 0 ];then echo "WARNING, LiCSBAS120 failed. Reverting to original LiCSBAS ref selection"; fi; # # if [ ${PIPESTATUS[0]} -ne 0 ];then exit 1; fi fi fi fi fi fi # This section is for step 13 rerun if the user sets p13resid_rerun to "y". # This is necessary for the SBOI rerun to identify problematic interferogram pairs # to remove in the first iterative step, and then rerun step 13 after removing # high-RMS interferograms. if [ $start_step -le 13 -a $end_step -ge 13 ];then if [ $p13resid_rerun == "y" ];then extra2='-t '$TSdir p13_skippngs="n" # rerunning step 13, so no need to create pngs # getting eq offsets here: if [ "$eqoffs" == "y" -a $eqoffs_minmag -gt 0 ]; then extra='-M '$eqoffs_minmag extra=$extra' -t '$TSdir extra=$extra' -o '$eqoffs_txtfile extra=$extra' --buffer '$eqoffs_buffer if [ "$check_only" == "y" ];then echo "LiCSBAS_get_eqoffsets.py $extra" else LiCSBAS_get_eqoffsets.py $extra fi fi p13_op="" if [ ! -z "$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_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="$p13_op --keep_incfile"; fi if [ "$p13_nullify_noloops" == "y" ];then p13_op="$p13_op --nullify_noloops"; fi if [ "$p13_singular" == "y" ];then p13_op="$p13_op --singular"; fi if [ "$sbovl_abs" == "y" ];then p13_op="$p13_op --sbovl_abs"; elif [ "$p13_sbovl" == "y" ];then p13_op="$p13_op --sbovl"; fi if [ "$p13_singular_gauss" == "y" ];then p13_op="$p13_op --singular_gauss"; fi if [ "$p13_skippngs" == "y" ];then p13_op="$p13_op --nopngs"; fi if [ "$gpu" == "y" ];then p13_op="$p13_op --gpu"; fi if [ "$cometdev" -eq 1 ];then extra='--nopngs' if [ -z "$p13_n_unw_r_thre" ];then extra="$extra --n_unw_r_thre 0.4"; fi extra="$extra --singular_gauss" else extra='' fi if [ "$eqoffs" == "y" ]; then touch $eqoffs_txtfile # just in case it would fail earlier extra='--offsets '$eqoffs_txtfile fi if [ "$check_only" == "y" ];then echo "LiCSBAS13_sb_inv.py $extra $p13_op" echo "LiCSBASresid_check.py $extra2" else LiCSBAS13_sb_inv.py $extra $p13_op 2>&1 | tee -a $log pstat=(${PIPESTATUS[0]}) LiCSBASresid_check.py $extra2 2>&1 | tee -a $log pstat2=(${PIPESTATUS[0]}) if [ "$p12_nullify" == "y" ];then if [ $pstat -ne 0 ];then echo "Fixing the unresolved-yet issue with NaNs in ref area by just rerunning step 13" LiCSBAS13_sb_inv.py $extra $p13_op 2>&1 | tee -a $log pstat=(${PIPESTATUS[0]}) fi fi if [ $pstat -ne 0 ];then exit 1; fi fi fi fi ##################### if [ $start_step -le 13 -a $end_step -ge 13 ];then # getting eq offsets here: if [ "$eqoffs" == "y" -a $eqoffs_minmag -gt 0 ]; then extra='-M '$eqoffs_minmag extra=$extra' -t '$TSdir extra=$extra' -o '$eqoffs_txtfile extra=$extra' --buffer '$eqoffs_buffer if [ "$check_only" == "y" ];then echo "LiCSBAS_get_eqoffsets.py $extra" else LiCSBAS_get_eqoffsets.py $extra fi fi p13_op="" if [ ! -z "$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_inputunit" ];then p13_op="$p13_op --input_units $p13_inputunit"; fi if [ ! -z "$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_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="$p13_op --keep_incfile"; fi if [ "$p13_ignore_nullification" == "y" ]; then p13_op="$p13_op --ignore_nullification"; fi if [ "$p13_nullify_noloops" == "y" ];then p13_op="$p13_op --nullify_noloops"; fi if [ "$p13_singular" == "y" ];then p13_op="$p13_op --singular"; fi if [ "$sbovl_abs" == "y" ];then p13_op="$p13_op --sbovl_abs"; elif [ "$p13_sbovl" == "y" ];then p13_op="$p13_op --sbovl"; fi if [ "$p13_singular_gauss" == "y" ];then p13_op="$p13_op --singular_gauss"; fi if [ "$p13_skippngs" == "y" ];then p13_op="$p13_op --nopngs"; fi if [ "$gpu" == "y" ];then p13_op="$p13_op --gpu"; fi if [ "$cometdev" -eq 1 ];then extra='--nopngs' if [ -z "$p13_n_unw_r_thre" ];then extra="$extra --n_unw_r_thre 0.4"; fi extra="$extra --singular_gauss" else extra='' fi if [ "$eqoffs" == "y" ]; then touch $eqoffs_txtfile # just in case it would fail earlier extra='--offsets '$eqoffs_txtfile fi if [ "$check_only" == "y" ];then echo "LiCSBAS13_sb_inv.py $extra $p13_op" else LiCSBAS13_sb_inv.py $extra $p13_op 2>&1 | tee -a $log pstat=(${PIPESTATUS[0]}) if [ "$p12_nullify" == "y" ];then if [ $pstat -ne 0 ];then echo "Fixing the unresolved-yet issue with NaNs in ref area by just rerunning step 13" LiCSBAS13_sb_inv.py $extra $p13_op 2>&1 | tee -a $log pstat=(${PIPESTATUS[0]}) fi fi if [ $pstat -ne 0 ];then exit 1; fi fi fi ###TODO I know it is not tidy but I need to call them before step 14 for sbovl processing, MN if [ $start_step -le 13 -a $end_step -ge 13 ];then if [ "$p13_sbovl" == "y" ]; then if [ "$sbovl_abs" == "y" ]; then # p131_sbovl_abs='y' #no need anymore, MN extra="-t $TSdir" if [ "$p131_sbovl_model" == "y" ]; then extra="$extra --model" fi # if [ "$p131_sbovl_tide" == "y" ]; then # extra="$extra --tide" # fi # if [ "$p131_sbovl_iono" == "y" ]; then # extra="$extra --iono" # fi if [ "$check_only" == "y" ];then echo 'python3 -c "from lics_tstools import *; correct_cum_from_tifs('$TSdir/cum.h5', 'GEOC.EPOCHS', 'tide.geo.azi.tif', 1000, directcorrect = False, sbovl=True)"' echo 'python3 -c "from lics_tstools import *; correct_cum_from_tifs('$TSdir/cum.h5', 'GEOC.EPOCHS', 'geo.iono.code.sTECA.tif', 14000, directcorrect = False, sbovl=True)"' echo "LiCSBAS131_boi_absolute.py $extra" else python3 -c "from lics_tstools import *; correct_cum_from_tifs('$TSdir/cum.h5', 'GEOC.EPOCHS', 'tide.geo.azi.tif', 1000, directcorrect = False, sbovl=True)" python3 -c "from lics_tstools import *; correct_cum_from_tifs('$TSdir/cum.h5', 'GEOC.EPOCHS', 'geo.iono.code.sTECA.tif', 14000, directcorrect = False, sbovl=True)" LiCSBAS131_boi_absolute.py $extra fi else if [ "$check_only" == "y" ];then if [ "$p131_sbovl_tide" == "y" ]; then echo 'python3 -c "from lics_tstools import *; correct_cum_from_tifs('$TSdir/cum.h5', 'GEOC.EPOCHS', 'tide.geo.azi.tif', 1000, directcorrect = False, sbovl=True)"' fi if [ "$p131_sbovl_iono" == "y" ]; then echo 'python3 -c "from lics_tstools import *; correct_cum_from_tifs('$TSdir/cum.h5', 'GEOC.EPOCHS', 'geo.iono.code.sTECA.tif', 14000, directcorrect = False, sbovl=True)"' fi else if [ "$p131_sbovl_tide" == "y" ]; then python3 -c "from lics_tstools import *; correct_cum_from_tifs('$TSdir/cum.h5', 'GEOC.EPOCHS', 'tide.geo.azi.tif', 1000, directcorrect = False, sbovl=True)" fi if [ "$p131_sbovl_iono" == "y" ]; then python3 -c "from lics_tstools import *; correct_cum_from_tifs('$TSdir/cum.h5', 'GEOC.EPOCHS', 'geo.iono.code.sTECA.tif', 14000, directcorrect = False, sbovl=True)" fi fi 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 $p14_mem_size"; fi if [ "$sbovl_abs" == "y" ];then p14_op="$p14_op --sbovl_abs"; #--ransac elif [ "$p14_sbovl" == "y" ];then p14_op="$p14_op --sbovl"; fi if [ $gpu == "y" ];then p14_op="$p14_op --gpu"; fi if [ "$eqoffs" == "y" ] && [ "$p14_sbovl" != "y" ]; then # we then do not want to regenerate vstd extra='--skipexisting' else extra='' fi if [ $check_only == "y" ];then echo "LiCSBAS14_vel_std.py $extra $p14_op" else LiCSBAS14_vel_std.py $extra $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_n_loop_err_ratio_thre" ];then p15_op="$p15_op -L $p15_n_loop_err_ratio_thre"; fi if [ ! -z "$p15_avg_phasebias" ] && [ "$p15_sbovl" != "y" ];then p15_op="$p15_op --avg_phase_bias $p15_avg_phasebias"; fi if [ ! -z "$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="$p15_op --noautoadjust"; fi if [ "$sbovl_abs" == "y" ];then p15_op="$p15_op --sbovl_abs"; # if [ "$p131_sbovl_tide" == "y" ];then # p15_op="$p15_op --tide" # fi # if [ "$p131_sbovl_iono" == "y" ];then # p15_op="$p15_op --iono" # fi elif [ "$p15_sbovl" == "y" ];then p15_op="$p15_op --sbovl"; fi if [ "$p15_n_gap_use_merged" == "y" ];then p15_op="$p15_op --n_gap_use_merged"; fi if [ "$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_demerr" == "y" ];then p16_op="$p16_op --demerr"; fi if [ "$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 $p16_ex_range_geo"; fi if [ "$p16_interpolate_nans" == "y" ];then p16_op="$p16_op --interpolate_nans"; fi if [ "$p16_sbovl" == "y" ];then p16_op="$p16_op --sbovl "; if [ "$sbovl_abs" == "y" ];then p16_op="$p16_op --sbovl_abs "; fi if [ "$p131_sbovl_tide" == "y" ];then p16_op="$p16_op --tide" fi if [ "$p131_sbovl_iono" == "y" ];then p16_op="$p16_op --iono" fi fi if [ "$p16_skippngs" == "y" ];then p16_op="$p16_op --nopngs"; fi if [ "$eqoffs" == "y" ]; then extra='--from_model '$TSdir/model.h5 else extra='' fi if [ "$check_only" == "y" ];then echo "LiCSBAS16_filt_ts.py $extra $p16_op" else LiCSBAS16_filt_ts.py $extra $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