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#!/usr/bin/env python3 """ ======== Overview ======== This script checks quality of unw data and identifies bad interferograms based on average coherence and coverage of the unw data. This also prepares a time series working directory (overwrite if already exists). This script also identifies coregistration error, which looks like a ramp in azimuth, based on the absolute slope and R-squares obtained from a linear fit to the pixels in the middle column o the ifg =============== Input & output files =============== Inputs in GEOCml*/ : - yyyymmdd_yyyymmdd/ - yyyymmdd_yyyymmdd.unw[.png] - yyyymmdd_yyyymmdd.cc - yyyymmdd_yyyymmdd.sbovldiff.adf.mm[.png] (if --sbovl is used) - slc.mli[.par|.png] - baselines (can be dummy) - EQA.dem_par Outputs in TS_GEOCml*/ : - info/ - 11bad_ifg.txt : List of bad ifgs discarded from further processing - 11ifg_stats.txt : Statistics of interferograms - EQA.dem_par (copy) - slc.mli.par (copy) - results/ - slc.mli[.png] (copy, if exist) - hgt[.png, U] (copy, if exist) - 11bad_ifg_ras/yyyymmdd_yyyymmdd.unw.png : png of bad ifgs - 11ifg_ras/yyyymmdd_yyyymmdd.unw.png : png of good ifgs - network/network11*.png : Figures of baseline configuration ===== Usage ===== LiCSBAS11_check_unw.py -d ifgdir [-t tsadir] [-c coh_thre] [-u unw_thre] [--maxbtemp maxbtemp] [--minbtemp minbtemp] [-s] [--sbovl] [--skip_dates eqoffsets.txt] -d Path to the GEOCml* dir containing stack of unw data. -t Path to the output TS_GEOCml* dir. (Default: TS_GEOCml*) -c Threshold of average coherence (Default: 0.05) -u Threshold of coverage of unw data (Default: 0.3) --minbtemp Minimal Btemp in days (Default: 0 = not use) --maxbtemp Maximal Btemp in days (Default: 0 = not use) -s Check for coregistration error in the form of a significant azimuthal ramp --sbovl only applying step 11 for sbovl --skip_dates dates.txt Will skip interferograms covering given dates (in the form of either yyyymmdd or yyyy-mm-dd inside the txt file) """ #%% Change log ''' 20250109 ML - add option to ignore ifgs covering given epoch 20241030 M Nergizci - add sbovl flag 20241028 ML - add also max btemp 20240115 ML - add min btemp parameter (to avoid fading bias in agri areas, we recommend setting minbtemp=12 for S1. Or nullify with smaller threshold in step 1-2) v1.4 20221011 Qi Ou, Uni of Leeds - Detect coregistration error as big azimuthal ramp in the middle (arbitrary) column - Shortlist by slope > 30, R2 > 0.95, then expand based on repeated epochs in the shortlist, threshold with slopd > 20 v1.3.4 20211129 Milan Lazecky, Uni of Leeds - Extra check on file dimensions - happens if LiCSAR data is inconsistent - should be moved to previous step v1.3.3 20210402 Yu Morishita, GSI - Treat all nan as bad ifg - Raise error if all ifgs are bad v1.3.2 20201116 Yu Morishita, GSI - Exit if suffix is not set v1.3.1 20200911 Yu Morishita, GSI - Change default to -c 0.05 -u 0.3 v1.3 20200703 Yu Morishita, GSI - Replace problematic terms v1.2 20200225 Yu Morishita, Uni of Leeds and GSI - Not output network pdf - Deal with cc file in uint8 format v1.1 20191115 Yu Morishita, Uni of Leeds and GSI - Add hgt v1.0 20190729 Yu Morishita, Uni of Leeds and GSI - Original implementation ''' #%% Import from LiCSBAS_meta import * import getopt import os import sys import time import shutil import numpy as np import datetime as dt import LiCSBAS_io_lib as io_lib import LiCSBAS_tools_lib as tools_lib import LiCSBAS_plot_lib as plot_lib from scipy import stats class Usage(Exception): """Usage context manager""" def __init__(self, msg): self.msg = msg #%% Main def main(argv=None): #%% Check argv if argv == None: argv = sys.argv start = time.time() print("\n{} ver{} {} {}".format(os.path.basename(argv[0]), ver, date, author), flush=True) print("{} {}".format(os.path.basename(argv[0]), ' '.join(argv[1:])), flush=True) #%% Set default ifgdir = [] tsadir = [] coh_thre = 0.05 unw_cov_thre = 0.3 check_coreg_slope = False minbtemp = 0 maxbtemp = 0 # 0 means not use sbovl = False skipdatesfile = [] #%% Read options try: try: opts, args = getopt.getopt(argv[1:], "hd:t:c:u:s", ["help", "minbtemp=", "skip_dates=", "maxbtemp=","sbovl"]) except getopt.error as msg: raise Usage(msg) for o, a in opts: if o == '-h' or o == '--help': print(__doc__) return 0 elif o == '-d': ifgdir = a elif o == '-t': tsadir = a elif o == '-c': coh_thre = float(a) elif o == '-u': unw_cov_thre = float(a) elif o == '--minbtemp': minbtemp = float(a) elif o == '--maxbtemp': maxbtemp = float(a) elif o == '-s': check_coreg_slope = True elif o == '--sbovl': sbovl = True elif o == '--skip_dates': skipdatesfile = a if not ifgdir: raise Usage('No data directory given, -d is not optional!') elif not os.path.isdir(ifgdir): raise Usage('No {} dir exists!'.format(ifgdir)) elif not os.path.exists(os.path.join(ifgdir, 'slc.mli.par')): raise Usage('No slc.mli.par file exists in {}!'.format(ifgdir)) if skipdatesfile: if not os.path.exists(skipdatesfile): raise Usage('skipdatesfile does not exist') except Usage as err: print("\nERROR:", file=sys.stderr, end='') print(" "+str(err.msg), file=sys.stderr) print("\nFor help, use -h or --help.\n", file=sys.stderr) return 2 print("\ncoh_thre : {}".format(coh_thre), flush=True) print("unw_cov_thre : {}".format(unw_cov_thre), flush=True) #%% Directory setting ifgdir = os.path.abspath(ifgdir) if not tsadir: tsadir = os.path.join(os.path.dirname(ifgdir), 'TS_'+os.path.basename(ifgdir)) if not os.path.exists(tsadir): os.mkdir(tsadir) ifg_rasdir = os.path.join(tsadir, '11ifg_ras') bad_ifg_rasdir = os.path.join(tsadir, '11bad_ifg_ras') if os.path.exists(ifg_rasdir): shutil.rmtree(ifg_rasdir) if os.path.exists(bad_ifg_rasdir): shutil.rmtree(bad_ifg_rasdir) os.mkdir(ifg_rasdir) os.mkdir(bad_ifg_rasdir) netdir = os.path.join(tsadir, 'network') if not os.path.exists(netdir): os.mkdir(netdir) infodir = os.path.join(tsadir, 'info') if not os.path.exists(infodir): os.mkdir(infodir) resultsdir = os.path.join(tsadir, 'results') if not os.path.exists(resultsdir): os.mkdir(resultsdir) # txt file might be corrupted, so loading it here: skipdates = [] if skipdatesfile: with open(skipdatesfile, 'r') as f: for l in f: try: ep = l.split()[0] ep = ep.replace('-','') skipdates.append(int(ep)) except: print('a line from skipdatesfile file not loaded, continuing') skipdates = list(set(skipdates)) print('Loaded ' + str(len(skipdates)) + ' epochs to skip:') print(skipdates) ### Get size mlipar = os.path.join(ifgdir, 'slc.mli.par') width = int(io_lib.get_param_par(mlipar, 'range_samples')) length = int(io_lib.get_param_par(mlipar, 'azimuth_lines')) print("\nSize : {} x {}".format(width, length), flush=True) ### Get resolution dempar = os.path.join(ifgdir, 'EQA.dem_par') lattitude_resolution = float(io_lib.get_param_par(dempar, 'post_lat')) ### Check for corrupted or wrong size unws - remove from ifgdir ifgdates = tools_lib.get_ifgdates(ifgdir) n_ifg = len(ifgdates) for ifgix, ifgd in enumerate(ifgdates): if np.mod(ifgix,100) == 0: print(" {0:3}/{1:3}th unw checked for dimension and readability".format(ifgix, n_ifg), flush=True) if sbovl: unwfile = os.path.join(ifgdir, ifgd, ifgd+'.sbovldiff.adf.mm') else: unwfile = os.path.join(ifgdir, ifgd, ifgd+'.unw') try: unw = io_lib.read_img(unwfile, length, width) except: print('probably dimension ERROR in '+ifgd+' unw file - source file inconsistent in LiCSAR frame. Moving to a backup folder (will not use)') #we can directly delete it here, as we work with ml* data #shutil.rmtree(os.path.dirname(unwfile)) backupsfolder = os.path.dirname(unwfile)[:-18]+'.backup' if not os.path.exists(backupsfolder): os.mkdir(backupsfolder) if os.path.exists(os.path.join(backupsfolder, ifgd)): shutil.rmtree(os.path.join(ifgdir, ifgd)) else: shutil.move(os.path.join(ifgdir, ifgd), os.path.join(backupsfolder, ifgd)) #%% Read date and network information ### Get dates ifgdates = tools_lib.get_ifgdates(ifgdir) imdates = tools_lib.ifgdates2imdates(ifgdates) n_ifg = len(ifgdates) n_im = len(imdates) ### Copy dempar and mli[png|par] for file in ['slc.mli.par', 'EQA.dem_par']: if os.path.exists(os.path.join(ifgdir, file)): shutil.copy(os.path.join(ifgdir, file), infodir) for file in ['slc.mli', 'slc.mli.png', 'hgt', 'hgt.png', 'U']: if os.path.exists(os.path.join(ifgdir, file)): shutil.copy(os.path.join(ifgdir, file), resultsdir) #%% Read data ### Allocate memory n_unw = np.zeros((length, width), dtype=np.float32) coh_avg_ifg = [] n_unw_ifg = [] slope_ifg = [] r_square_ifg = [] ### Read data and calculate print('\nReading unw and cc data...', flush=True) ## First, identify valid area (n_unw>im) for ifgix, ifgd in enumerate(ifgdates): if np.mod(ifgix,100) == 0: print(" {0:3}/{1:3}th unw to identify valid area...".format(ifgix, n_ifg), flush=True) if sbovl: unwfile = os.path.join(ifgdir, ifgd, ifgd+'.sbovldiff.adf.mm') else: unwfile = os.path.join(ifgdir, ifgd, ifgd+'.unw') unw = io_lib.read_img(unwfile, length, width) unw[unw == 0] = np.nan # Fill 0 with nan n_unw += ~np.isnan(unw) # Summing number of unnan unw ## Identify valid area and calc rate_cov bool_valid = (n_unw>=n_im) n_unw_valid = bool_valid.sum() ## coregistration error shortlist coreg_error_ifg = [] ## Read cc and unw data for ifgix, ifgd in enumerate(ifgdates): if np.mod(ifgix,100) == 0: print(" {0:3}/{1:3}th cc and unw...".format(ifgix, n_ifg), flush=True) ## unw if sbovl: unwfile = os.path.join(ifgdir, ifgd, ifgd+'.sbovldiff.adf.mm') else: unwfile = os.path.join(ifgdir, ifgd, ifgd+'.unw') unw = io_lib.read_img(unwfile, length, width) unw[unw == 0] = np.nan # Fill 0 with nan unw[~bool_valid] = np.nan # Fill sea area with nan n_unw_ifg.append((~np.isnan(unw)).sum()) ## cc ccfile = os.path.join(ifgdir, ifgd, ifgd+'.cc') if os.path.getsize(ccfile) == length*width: coh = io_lib.read_img(ccfile, length, width, np.uint8) coh = coh.astype(np.float32)/255 coh[coh==0] = np.nan else: coh = io_lib.read_img(ccfile, length, width) coh_avg_ifg.append(np.nanmean(coh[bool_valid])) # Use valid area only if check_coreg_slope: ## middle column slope middle_column = unw[:, width // 2] middle_column_latitudes = np.arange(length) * lattitude_resolution non_nan_mask = ~np.isnan(middle_column) if np.sum(non_nan_mask) > 1: slope, intercept, r_value, p_value, std_err = stats.linregress(middle_column_latitudes[non_nan_mask], middle_column[non_nan_mask]) slope_ifg.append(abs(slope)) r_square_ifg.append(r_value**2) if abs(slope) > 30 and r_value**2 > 0.95: coreg_error_ifg.append(ifgd) else: slope_ifg.append(0) r_square_ifg.append(0) if check_coreg_slope: ## identify epochs with more than 1 coreg_errors captured by threshold: primarylist = [] secondarylist = [] for pairs in coreg_error_ifg: primarylist.append(pairs[:8]) secondarylist.append(pairs[-8:]) all_epochs = primarylist + secondarylist all_epochs.sort() coreg_error_epochs, counts = np.unique(all_epochs, return_counts=True) coreg_error_epochs = coreg_error_epochs[counts>1] ## grow the shortlist with repeated epochs in the shortlist ifg_containing_coreg_error_epochs = np.zeros(len(ifgdates)) all_ifg_epoch1 = [] all_ifg_epoch2 = [] for pairs in ifgdates: all_ifg_epoch1.append(pairs[:8]) all_ifg_epoch2.append(pairs[-8:]) for epoch in coreg_error_epochs: ifg_containing_coreg_error_epochs += np.array(all_ifg_epoch1) == epoch ifg_containing_coreg_error_epochs += np.array(all_ifg_epoch2) == epoch ## threshold the expanded list with criteria slope_ifg => 20 ifg_containing_coreg_error_epochs[np.array(slope_ifg) < 20] = 0 else: ifg_containing_coreg_error_epochs = np.zeros(len(ifgdates)) # dummy ## convert unw pixels into percentage unw coverage rate_cov = np.array(n_unw_ifg)/n_unw_valid ## Read bperp data or dummy bperp_file = os.path.join(ifgdir, 'baselines') if os.path.exists(bperp_file): with open(bperp_file, 'r') as f: lines = [line.strip() for line in f if line.strip()] # Remove empty lines if len(lines) >= len(imdates): # Ensure enough entries bperp = io_lib.read_bperp_file(bperp_file, imdates) else: ##baselines file contain fewer entries than the number of ifgs, so dummy values will be used bperp = np.random.random(len(imdates)).tolist() else: # Generate dummy baselines if file doesn't exist print(f"WARNING: Baselines file not found. Using dummy values.") bperp = np.random.random(len(imdates)).tolist() ## Check if bperp values are valid if all(v == 0 for v in bperp): bperp = np.random.random(len(imdates)).tolist() #%% Identify bad ifgs, link ras and output stats information bad_ifgdates = [] ixs_bad_ifgdates = [] ### Header of stats file ifg_statsfile = os.path.join(infodir, '11ifg_stats.txt') fstats = open(ifg_statsfile, 'w') print('# Size: {0}({1}x{2}), n_valid: {3}'.format(width*length, width, length, n_unw_valid), file=fstats) if check_coreg_slope: print('# unw_cov_thre: {0}, coh_thre: {1}, |slope|:30 & r^2: 0.95 => repeated epochs => |slope|:20'.format(unw_cov_thre, coh_thre), file=fstats) print('# ifg dates bperp dt unw_cov coh_av |slope| r^2', file=fstats) else: print('# unw_cov_thre: {0}, coh_thre: {1}'.format(unw_cov_thre, coh_thre), file=fstats) print('# ifg dates bperp dt unw_cov coh_av', file=fstats) ### Identify suffix of raster image (png, ras or bmp?) if sbovl: unwfile = os.path.join(ifgdir, ifgdates[0], ifgdates[0]+'.sbovldiff.adf.mm') else: unwfile = os.path.join(ifgdir, ifgdates[0], ifgdates[0]+'.unw') if os.path.exists(unwfile+'.ras'): suffix = '.ras' elif os.path.exists(unwfile+'.bmp'): suffix = '.bmp' elif os.path.exists(unwfile+'.png'): suffix = '.png' else: suffix = '' print('\nWARNING: No browse image available for {}\n' .format(unwfile), file=sys.stderr) #return 2 for i, ifgd in enumerate(ifgdates): if skipdates: toskip = False ep1 = int(ifgd[:8]) ep2 = int(ifgd[-8:]) for skep in skipdates: if (ep1 < skep) and (ep2 > skep): print('skipping coseismic ifg '+ifgd) bad_ifgdates.append(ifgd) toskip = True continue if toskip: continue if suffix: if sbovl: rasname = ifgdates[i]+'.sbovldiff.adf.mm'+suffix else: rasname = ifgdates[i]+'.unw'+suffix rasorg = os.path.join(ifgdir, ifgdates[i], rasname) if not os.path.exists(rasorg): print('WARNING: No browse image {} available!\n'.format(rasorg)) print('assuming there is an error and skipping this ifg') bad_ifgdates.append(ifgd) continue ### Identify bad ifgs and link ras if rate_cov[i] < unw_cov_thre or coh_avg_ifg[i] < coh_thre or \ np.isnan(rate_cov[i]) or np.isnan(coh_avg_ifg[i]) or ifg_containing_coreg_error_epochs[i] > 0: bad_ifgdates.append(ifgd) rm_flag = '*' if suffix: os.symlink(os.path.abspath(rasorg), os.path.join(bad_ifg_rasdir, rasname)) else: if suffix: os.symlink(os.path.abspath(rasorg), os.path.join(ifg_rasdir, rasname)) rm_flag = '' ### For stats file ix_primary = imdates.index(ifgd[:8]) ix_secondary = imdates.index(ifgd[-8:]) bperp_ifg = bperp[ix_secondary]-bperp[ix_primary] mday = dt.datetime.strptime(ifgd[:8], '%Y%m%d').toordinal() sday = dt.datetime.strptime(ifgd[-8:], '%Y%m%d').toordinal() dt_ifg = sday-mday if check_coreg_slope: print('{0} {1:6.1f} {2:3} {3:5.3f} {4:5.3f} {5:5.3f} {6:5.3f} {7}'.format(ifgd, bperp_ifg, dt_ifg, rate_cov[i], coh_avg_ifg[i], slope_ifg[i], r_square_ifg[i], rm_flag), file=fstats) else: print('{0} {1:6.1f} {2:3} {3:5.3f} {4:5.3f} {5}'.format(ifgd, bperp_ifg, dt_ifg, rate_cov[i], coh_avg_ifg[i], rm_flag), file=fstats) fstats.close() ### Raise error if all ifgs are bad if len(bad_ifgdates) == n_ifg: raise ValueError('All ifgs are regarded as bad!\nChange the parameters or check the input ifgs.\n') # Not use ifgs below given btemp if minbtemp > 0: btemps = tools_lib.calc_temporal_baseline(ifgdates) remsel = list(np.array(ifgdates)[np.array(btemps) <= minbtemp]) bad_ifgdates += remsel print('Disabling ' + str(len(remsel)) + ' interferograms below min Btemp = ' + str(minbtemp) + ' days.') # Not use ifgs above given btemp if maxbtemp > 0: btemps = tools_lib.calc_temporal_baseline(ifgdates) remsel = list(np.array(ifgdates)[np.array(btemps) >= maxbtemp]) bad_ifgdates += remsel print('Disabling ' + str(len(remsel)) + ' interferograms above max Btemp = ' + str(maxbtemp) + ' days.') # regenerating full ixs: bad_ifgdates = list(set(bad_ifgdates)) ixs_ifgdates = np.array(range(len(ifgdates))) ixs_bad_ifgdates = ixs_ifgdates[np.isin(ifgdates, bad_ifgdates)] ### Output list of bad ifg bad_ifgfile = os.path.join(infodir, '11bad_ifg.txt') print('\n{0}/{1} ifgs are discarded from further processing.'.format(len(bad_ifgdates), n_ifg)) with open(bad_ifgfile, 'w') as f: if check_coreg_slope: print('ifg dates unw_cov coh_av |slope| R^2') for i, ifgd in enumerate(bad_ifgdates): print('{}'.format(ifgd), file=f) print('{} {:5.3f} {:5.3f} {:5.3f} {:5.3f}'.format(ifgd, rate_cov[ixs_bad_ifgdates[i]], coh_avg_ifg[ixs_bad_ifgdates[i]], slope_ifg[ixs_bad_ifgdates[i]], r_square_ifg[ixs_bad_ifgdates[i]]), flush=True) else: print('ifg dates unw_cov coh_av') for i, ifgd in enumerate(bad_ifgdates): print('{}'.format(ifgd), file=f) print('{} {:5.3f} {:5.3f}'.format(ifgd, rate_cov[ixs_bad_ifgdates[i]], coh_avg_ifg[ixs_bad_ifgdates[i]]), flush=True) #%% Identify removed image and output file good_ifgdates = list(set(ifgdates)-set(bad_ifgdates)) good_ifgdates.sort() good_imdates = tools_lib.ifgdates2imdates(good_ifgdates) bad_imdates = list(set(imdates)-set(good_imdates)) bad_imdates.sort() ### Output list of removed image bad_imfile = os.path.join(infodir, '11removed_image.txt') with open(bad_imfile, 'w') as f: for i in bad_imdates: print('{}'.format(i), file=f) #%% Plot network pngfile = os.path.join(netdir, 'network11_all.png') plot_lib.plot_network(ifgdates, bperp, [], pngfile) pngfile = os.path.join(netdir, 'network11.png') plot_lib.plot_network(ifgdates, bperp, bad_ifgdates, pngfile) pngfile = os.path.join(netdir, 'network11_nobad.png') plot_lib.plot_network(ifgdates, bperp, bad_ifgdates, pngfile, plot_bad=False) #%% Finish print('\nCheck network/*, 11bad_ifg_ras/* and 11ifg_ras/* in TS dir.') print('If you want to change the bad ifgs to be discarded, re-run with different thresholds or make a ifg list and indicate it by --rm_ifg_list option in the next step.') elapsed_time = time.time()-start hour = int(elapsed_time/3600) minite = int(np.mod((elapsed_time/60),60)) sec = int(np.mod(elapsed_time,60)) print("\nElapsed time: {0:02}h {1:02}m {2:02}s".format(hour,minite,sec)) print('\n{} Successfully finished!!\n'.format(os.path.basename(argv[0]))) print('Output directory: {}\n'.format(os.path.abspath(tsadir))) #%% main if __name__ == "__main__": sys.exit(main())