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#!/usr/bin/env python3 """ v1.5.5 20201119 Yu Morishita, GSI This script applies a tropospheric correction to unw data using GACOS data. GACOS data may be automatically downloaded from COMET-LiCS web at step01 (if available), or could be externally obtained by requesting on a GACOS web (http://www.gacos.net/). If you request the GACOS data through the GACOS web, the dates and time of interest can be found in baselines and slc.mli.par, respectively. These are also available on the COMET-LiCS web portal. Once the GACOS data are ready, download the tar.gz, uncompress it, and put into GACOS dir. Existing files are not re-created to save time, i.e., only the newly available data will be processed. The impact of the correction can be visually checked by showing GACOS_info.png and */*.gacos.png. This step is optional. =============== Input & output files =============== Inputs in GEOCml*/ : - yyyymmdd_yyyymmdd/ - yyyymmdd_yyyymmdd.unw - yyyymmdd_yyyymmdd.cc - U.geo - EQA.dem_par - slc.mli.par Inputs in GACOS/ : - yyyymmdd.sltd.geo.tif and/or - yyyymmdd.ztd[.rsc] and/or - yyyymmdd.ztd.tif Outputs in GEOCml*GACOS/ - yyyymmdd_yyyymmdd/ - yyyymmdd_yyyymmdd.unw[.png] : Corrected unw - yyyymmdd_yyyymmdd.gacos.png : Comparison image - yyyymmdd_yyyymmdd.cc : Coherence (symbolic link) - GACOS_info.txt : List of noise reduction rates - GACOS_info.png : Correlation diagram of STD between before and after - no_gacos_ifg.txt : List of removed ifg because no GACOS data available - no_gacos_im.txt : List of images with no available GACOS data - sltd/ - yyyymmdd.sltd.geo : Slantrange tropospheric delay in rad - other files needed for following time series analysis ===== Usage ===== LiCSBAS03op_GACOS.py -i in_dir -o out_dir [-g gacosdir] [--fillhole] [--n_para int] -i Path to the GEOCml* dir containing stack of unw data -o Path to the output dir -g Path to the dir containing GACOS data (Default: GACOS) --fillhole Fill holes of GACOS data at hgt=0 in SRTM3 by averaging surrounding pixels --n_para Number of parallel processing (Default: # of usable CPU) """ #%% Change log ''' v1.5.5 20201119 Yu Morishita, GSI - Change default cmap for wrapped phase from insar to SCM.romaO v1.5.4 20201119 Yu Morishita, GSI - New GACOS format (ztd.tif) available v1.5.3 20201118 Yu Morishita, GSI - Again Bug fix of multiprocessing v1.5.2 20201116 Yu Morishita, GSI - Bug fix of multiprocessing in Mac python>=3.8 v1.5.1 20201028 Yu Morishita, GSI - Update how to get n_para v1.5 20200909 Yu Morishita, GSI - Parallel processing v1.4 20200703 Yu Morioshita, GSI - Replace problematic terms v1.3 20200609 Yu Morishita, GSI - Avoid reading error of ztd (unkown cause) by addding subtle value v1.2 20200228 Yu Morishita, Uni of Leeds and GSI - Compatible with GACOS data provided from LiCSAR-portal - Output correlation plot - Output no_gacos_im.txt - Change option from -z (still available) to -g and set GACOS as default v1.1 20190812 Yu Morishita, Uni of Leeds and GSI - Add fillhole option 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 glob import numpy as np from osgeo import gdal import multiprocessing as multi import cmcrameri.cm as cmc #SCM import LiCSBAS_io_lib as io_lib import LiCSBAS_tools_lib as tools_lib import LiCSBAS_plot_lib as plot_lib class Usage(Exception): """Usage context manager""" def __init__(self, msg): self.msg = msg #%% fill hole function def fillhole(ztd): """ Fill holes (no data) surrounded by valid data by averaging surrounding pixels. 0 in ztd means no data. """ length, width = ztd.shape ### Add 1 pixel margin to ztd data filled with 0 ztd1 = np.zeros((length+2, width+2), dtype=np.float32) ztd1[1:length+1, 1:width+1] = ztd n_ztd1 = np.int16(ztd1!=0) # 1 if exist, 0 if no data ### Average 8 srrounding pixels. [1, 1] is center pixels = [[0, 0], [0, 1], [0, 2], [1, 0], [1, 2], [2, 0], [2, 1], [2, 2]] _ztd = np.zeros_like(ztd) _n_ztd = np.zeros_like(ztd) for pixel in pixels: ### Adding data and number of data _ztd = _ztd + ztd1[pixel[0]:length+pixel[0],pixel[1]:width+pixel[1]] _n_ztd = _n_ztd + n_ztd1[pixel[0]:length+pixel[0],pixel[1]:width+pixel[1]] _n_ztd[_n_ztd==0] = 1 # avoid 0 division _ztd = _ztd/_n_ztd ### Fill hole ztd[ztd==0] = _ztd[ztd==0] return ztd #%% make_hdr def make_hdr(ztdpar, hdrfile): ### Get ztd info. Grid registration width_ztd = int(io_lib.get_param_par(ztdpar, 'WIDTH')) length_ztd = int(io_lib.get_param_par(ztdpar, 'FILE_LENGTH')) dlat_ztd = float(io_lib.get_param_par(ztdpar, 'Y_STEP')) #minus dlon_ztd = float(io_lib.get_param_par(ztdpar, 'X_STEP')) latn_ztd = float(io_lib.get_param_par(ztdpar, 'Y_FIRST')) lonw_ztd = float(io_lib.get_param_par(ztdpar, 'X_FIRST')) ### Make hdr file of ztd strings = ["NROWS {}".format(length_ztd), "NCOLS {}".format(width_ztd), "NBITS 32", "PIXELTYPE FLOAT", "BYTEORDER I", "LAYOUT BIL", "ULXMAP {}".format(lonw_ztd), "ULYMAP {}".format(latn_ztd), "XDIM {}".format(dlon_ztd), "YDIM {}".format(np.abs(dlat_ztd))] with open(hdrfile, "w") as f: f.write("\n".join(strings)) #%% Main def main(argv=None): #%% Check argv if argv == None: argv = sys.argv start = time.time() ver="1.5.5"; date=20201119; author="Y. Morishita" 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) ### For parallel processing global imdates2, gacosdir, outputBounds, width_geo, length_geo, resampleAlg,\ sltddir, LOSu, m2r_coef, fillholeflag, ifgdates2,\ in_dir, out_dir, length_unw, width_unw, cycle, cmap_wrap #%% Set default in_dir = [] out_dir = [] gacosdir = 'GACOS' resampleAlg = 'cubicspline'# None # 'cubic' fillholeflag = False try: n_para = len(os.sched_getaffinity(0)) except: n_para = multi.cpu_count() import win_compat; q = win_compat.get_compatible_context() cmap_wrap = cmc.romaO #SCM.romaO #%% Read options try: try: opts, args = getopt.getopt(argv[1:], "hi:o:g:z:", ["fillhole", "help", "n_para="]) 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 == '-i': in_dir = a elif o == '-o': out_dir = a elif o == '-z': ## for backward-compatible gacosdir = a elif o == '-g': gacosdir = a elif o == "--fillhole": fillholeflag = True elif o == '--n_para': n_para = int(a) if not in_dir: raise Usage('No input directory given, -i is not optional!') elif not os.path.isdir(in_dir): raise Usage('No {} dir exists!'.format(in_dir)) elif len(os.listdir(in_dir)) == 0: raise Usage('Dir {} is empty, cancelling'.format(in_dir)) elif not os.path.exists(os.path.join(in_dir, 'slc.mli.par')): raise Usage('No slc.mli.par file exists in {}!'.format(in_dir)) if not out_dir: raise Usage('No output directory given, -o is not optional!') if not os.path.isdir(gacosdir): raise Usage('No {} dir exists!'.format(gacosdir)) 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 #%% Read data information ### Directory in_dir = os.path.abspath(in_dir) gacosdir = os.path.abspath(gacosdir) out_dir = os.path.abspath(out_dir) if not os.path.exists(out_dir): os.mkdir(out_dir) sltddir = os.path.join(os.path.join(out_dir),'sltd') if not os.path.exists(sltddir): os.mkdir(sltddir) ### Get general info mlipar = os.path.join(in_dir, 'slc.mli.par') width_unw = int(io_lib.get_param_par(mlipar, 'range_samples')) length_unw = int(io_lib.get_param_par(mlipar, 'azimuth_lines')) speed_of_light = 299792458 #m/s radar_frequency = float(io_lib.get_param_par(mlipar, 'radar_frequency')) #Hz wavelength = speed_of_light/radar_frequency #meter m2r_coef = 4*np.pi/wavelength if wavelength > 0.2: ## L-band cycle = 1.5 # 2pi/cycle for png else: ## C-band cycle = 3 # 2pi*3/cycle for png ### Get geo info. Grid registration dempar = os.path.join(in_dir, 'EQA.dem_par') width_geo = int(io_lib.get_param_par(dempar, 'width')) length_geo = int(io_lib.get_param_par(dempar, 'nlines')) dlat_geo = float(io_lib.get_param_par(dempar, 'post_lat')) #minus dlon_geo = float(io_lib.get_param_par(dempar, 'post_lon')) latn_geo = float(io_lib.get_param_par(dempar, 'corner_lat')) lonw_geo = float(io_lib.get_param_par(dempar, 'corner_lon')) lats_geo = latn_geo+dlat_geo*(length_geo-1) lone_geo = lonw_geo+dlon_geo*(width_geo-1) outputBounds = (lonw_geo, lats_geo, lone_geo, latn_geo) ### Check coordinate if width_unw!=width_geo or length_unw!=length_geo: print('\n{} seems to contain files in radar coordinate!!\n'.format(in_dir), file=sys.stderr) print('Not supported.\n', file=sys.stderr) return 1 ### Calc incidence angle from U.geo ufile = os.path.join(in_dir, 'U.geo') LOSu = io_lib.read_img(ufile, length_geo, width_geo) LOSu[LOSu==0] = np.nan ### Get ifgdates and imdates ifgdates = tools_lib.get_ifgdates(in_dir) imdates = tools_lib.ifgdates2imdates(ifgdates) n_ifg = len(ifgdates) n_im = len(imdates) #%% Process ztd files print('\nConvert ztd/sltd.geo.tif files to sltd.geo files...', flush=True) no_gacos_imfile = os.path.join(out_dir, 'no_gacos_im.txt') if os.path.exists(no_gacos_imfile): os.remove(no_gacos_imfile) ### First check if sltd already exist imdates2 = [] for imd in imdates: sltd_geofile = os.path.join(sltddir, imd+'.sltd.geo') if not os.path.exists(sltd_geofile): imdates2.append(imd) n_im2 = len(imdates2) if n_im-n_im2 > 0: print(" {0:3}/{1:3} sltd already exist. Skip".format(n_im-n_im2, n_im), flush=True) if n_im2 > 0: ### Convert with parallel processing if n_para > n_im2: _n_para = n_im2 else: _n_para = n_para print(' {} parallel processing...'.format(_n_para), flush=True) p = q.Pool(_n_para) no_gacos_imds = p.map(convert_wrapper, range(n_im2)) p.close() for imd in no_gacos_imds: if imd is not None: with open(no_gacos_imfile, mode='a') as fnogacos: print('{}'.format(imd), file=fnogacos) #%% Correct unw files print('\nCorrect unw data...', flush=True) ### Information files gacinfofile = os.path.join(out_dir, 'GACOS_info.txt') if not os.path.exists(gacinfofile): ### Add header with open(gacinfofile, "w") as f: print(' Phase STD (rad) Before After ReductionRate', file=f) no_gacos_ifgfile = os.path.join(out_dir, 'no_gacos_ifg.txt') if os.path.exists(no_gacos_ifgfile): os.remove(no_gacos_ifgfile) ### First check if already corrected unw exist ifgdates2 = [] for i, ifgd in enumerate(ifgdates): out_dir1 = os.path.join(out_dir, ifgd) unw_corfile = os.path.join(out_dir1, ifgd+'.unw') if not os.path.exists(unw_corfile): ifgdates2.append(ifgd) n_ifg2 = len(ifgdates2) if n_ifg-n_ifg2 > 0: print(" {0:3}/{1:3} corrected unw already exist. Skip".format(n_ifg-n_ifg2, n_ifg), flush=True) if n_ifg2 > 0: ### Correct with parallel processing if n_para > n_ifg2: _n_para = n_ifg2 else: _n_para = n_para print(' {} parallel processing...'.format(_n_para), flush=True) p = q.Pool(_n_para) _return = p.map(correct_wrapper, range(n_ifg2)) p.close() for i in range(n_ifg2): if _return[i][0] == 1: with open(no_gacos_ifgfile, mode='a') as fnogacos: print('{}'.format(_return[i][1]), file=fnogacos) elif _return[i][0] == 2: with open(gacinfofile, "a") as f: print('{0} {1:4.1f} {2:4.1f} {3:5.1f}%'.format(*_return[i][1]), file=f) print("", flush=True) #%% Create correlation png pngfile = os.path.join(out_dir, 'GACOS_info.png') plot_lib.plot_gacos_info(gacinfofile, pngfile) #%% Copy other files files = glob.glob(os.path.join(in_dir, '*')) for file in files: if not os.path.isdir(file): #not copy directory, only file print('Copy {}'.format(os.path.basename(file)), flush=True) shutil.copy(file, out_dir) #%% Finish 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(out_dir))) if os.path.exists(no_gacos_ifgfile): print('Caution: Some ifgs below are excluded due to GACOS unavailable') with open(no_gacos_ifgfile) as f: for line in f: print(line, end='') print('') if os.path.exists(no_gacos_imfile): print('GACOS data for the following dates are missing:') with open(no_gacos_imfile) as f: for line in f: print(line, end='') print('') #%% def convert_wrapper(ix_im): imd = imdates2[ix_im] if np.mod(ix_im, 10)==0: print(' Finished {0:4}/{1:4}th sltd...'.format(ix_im, len(imdates2)), flush=True) ztdfile = os.path.join(gacosdir, imd+'.ztd') ztdtiffile = os.path.join(gacosdir, imd+'.ztd.tif') sltdtiffile = os.path.join(gacosdir, imd+'.sltd.geo.tif') if os.path.exists(sltdtiffile): print(' Use {}.sltd.geo.tif'.format(imd), flush=True) infile = os.path.basename(sltdtiffile) try: ### Cut and resapmle. Already in rad. sltd_geo = gdal.Warp("", sltdtiffile, format='MEM', outputBounds=outputBounds, width=width_geo, height=length_geo, resampleAlg=resampleAlg, srcNodata=0).ReadAsArray() except: ## if broken print (' {} cannot open. Skip'.format(infile), flush=True) return imd elif os.path.exists(ztdtiffile): print(' Use {}.ztd.tif'.format(imd), flush=True) infile = os.path.basename(ztdtiffile) try: ### Cut and resapmle ztd to geo ztd_geo = gdal.Warp("", ztdtiffile, format='MEM', outputBounds=outputBounds, width=width_geo, height=length_geo, resampleAlg=resampleAlg, srcNodata=0).ReadAsArray() except: ## if broken print (' {} cannot open. Skip'.format(infile), flush=True) return imd ### Meter to rad, slantrange sltd_geo = ztd_geo/LOSu*m2r_coef ## LOSu=cos(inc) elif os.path.exists(ztdfile): print(' Use {}.ztd[.rsc]'.format(imd), flush=True) infile = os.path.basename(ztdfile) hdrfile = os.path.join(sltddir, imd+'.hdr') bilfile = os.path.join(sltddir, imd+'.bil') if os.path.exists(hdrfile): os.remove(hdrfile) if os.path.exists(bilfile): os.remove(bilfile) make_hdr(ztdfile+'.rsc', hdrfile) os.symlink(os.path.abspath(ztdfile, sltddir), bilfile) ## Check read error with unkown cause if gdal.Info(bilfile) is None: ### Create new ztd by adding 0.0001m print('{} cannot open, but trying minor update. You can ignore this error unless this script stops.'.format(ztdfile)) shutil.copy2(ztdfile, ztdfile+'.org') ## Backup _ztd = np.fromfile(ztdfile, dtype=np.float32) _ztd[_ztd!=0] = _ztd[_ztd!=0]+0.001 _ztd.tofile(ztdfile) ### Cut and resapmle ztd to geo ztd_geo = gdal.Warp("", bilfile, format='MEM', outputBounds=outputBounds, width=width_geo, height=length_geo, resampleAlg=resampleAlg, srcNodata=0).ReadAsArray() os.remove(hdrfile) os.remove(bilfile) ### Meter to rad, slantrange sltd_geo = ztd_geo/LOSu*m2r_coef ## LOSu=cos(inc) else: print(' No {}.ztd|ztd.tif|sltd.geo.tif! Skip.'.format(imd), flush=True) return imd ## Next imd ### Skip if no data in the area if np.all((sltd_geo==0)|np.isnan(sltd_geo)): print(' No valid data in {}! Skip.'.format(infile), flush=True) return imd ## Next imd ### Fill hole is specified if fillholeflag: sltd_geo = fillhole(sltd_geo) ### Output as sltd.geo sltd_geofile = os.path.join(sltddir, imd+'.sltd.geo') sltd_geo.tofile(sltd_geofile) return #%% def correct_wrapper(i): ifgd = ifgdates2[i] if np.mod(i, 10)==0: print(' Finished {0:4}/{1:4}th unw...'.format(i, len(ifgdates2)), flush=True) md = ifgd[:8] sd = ifgd[-8:] msltdfile = os.path.join(sltddir, md+'.sltd.geo') ssltdfile = os.path.join(sltddir, sd+'.sltd.geo') in_dir1 = os.path.join(in_dir, ifgd) out_dir1 = os.path.join(out_dir, ifgd) ### Check if sltd available for both primary and secondary. If not continue ## Not use in tsa because loop cannot be closed if not (os.path.exists(msltdfile) and os.path.exists(ssltdfile)): print(' ztd file not available for {}'.format(ifgd), flush=True) return 1, ifgd ### Prepare directory and file if not os.path.exists(out_dir1): os.mkdir(out_dir1) unwfile = os.path.join(in_dir1, ifgd+'.unw') unw_corfile = os.path.join(out_dir1, ifgd+'.unw') ### Calculate dsltd msltd = io_lib.read_img(msltdfile, length_unw, width_unw) ssltd = io_lib.read_img(ssltdfile, length_unw, width_unw) msltd[msltd==0] = np.nan ssltd[ssltd==0] = np.nan dsltd = ssltd-msltd ### Correct unw unw = io_lib.read_img(unwfile, length_unw, width_unw) unw[unw==0] = np.nan unw_cor = unw-dsltd unw_cor.tofile(unw_corfile) ### Calc std std_unw = np.nanstd(unw) std_unwcor = np.nanstd(unw_cor) rate = (std_unw-std_unwcor)/std_unw*100 ### Link cc if not os.path.exists(os.path.join(out_dir1, ifgd+'.cc')): os.symlink(os.path.abspath(os.path.join(in_dir1, ifgd+'.cc'), out_dir1), os.path.join(out_dir1, ifgd+'.cc')) ### Output png for comparison data3 = [np.angle(np.exp(1j*(data/cycle))*cycle) for data in [unw, unw_cor, dsltd]] title3 = ['unw_org (STD: {:.1f} rad)'.format(std_unw), 'unw_cor (STD: {:.1f} rad)'.format(std_unwcor), 'dsltd ({:.1f}% reduced)'.format(rate)] pngfile = os.path.join(out_dir1, ifgd+'.gacos.png') plot_lib.make_3im_png(data3, pngfile, cmap_wrap, title3, vmin=-np.pi, vmax=np.pi, cbar=False) ## Output png for corrected unw pngfile = os.path.join(out_dir1, ifgd+'.unw.png') title = '{} ({}pi/cycle)'.format(ifgd, cycle*2) plot_lib.make_im_png(np.angle(np.exp(1j*unw_cor/cycle)*cycle), pngfile, cmap_wrap, title, -np.pi, np.pi, cbar=False) return 2, [ifgd, std_unw, std_unwcor, rate] #%% main if __name__ == "__main__": sys.exit(main())