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#!/usr/bin/env python3 """ v1.3.5 20210105 Yu Morishita, GSI This script masks specified areas or low coherence areas in the unw data. The masking is effective when the unw data include areas which have many unwrapping errors and are not of interest, and can improve the result of Step 1-2 (loop closure). Existing files are not re-created to save time, i.e., only the newly available data will be processed. This step is optional. =============== Input & output files =============== Inputs in GEOCml*/: - yyyymmdd_yyyymmdd/ - yyyymmdd_yyyymmdd.unw - yyyymmdd_yyyymmdd.cc - slc.mli.par Outputs in GEOCml*mask/ - yyyymmdd_yyyymmdd/ - yyyymmdd_yyyymmdd.unw[.png] - yyyymmdd_yyyymmdd.cc (symbolic link) - mask[.png] [- coh_avg[.png]] (if -c is used) - Other files in input directory ===== Usage ===== LiCSBAS04op_mask_unw.py -i in_dir -o out_dir [-c coh_thre] [-s cc_ifg_thre] [-r x1:x2/y1:y2] [-f txtfile] [--n_para int] -i Path to the GEOCml* dir containing stack of unw data. -o Path to the output dir. -c Threshold for average coherence (e.g., 0.2) -s Threshold to individual coherence (e.g., 0.1) -r Range to be masked. Index starts from 0. 0 for x2/y2 means all. (i.e., 0:0/0:0 means whole area). -f Text file of a list of ranges to be masked (format is x1:x2/y1:y2) -p Text file containing polygon coords to be masked --n_para Number of parallel processing (Default: # of usable CPU) Note: either -c, -r, -f, or -p must be specified. """ #%% Change log ''' 20241220 Muhammet Nergizci - skipping the non exist .unw .cc files in the mask_wrapper function 20230803 Jack McGrath - add option to individually mask IFGs based on coh 20220121 Andrew Watson - added option to mask polygons v1.3.5 20210105 Yu Morishita, GSI - Fill 0 by nan in unw v1.3.4 20201119 Yu Morishita, GSI - Change default cmap for wrapped phase from insar to SCM.romaO v1.3.3 20201118 Yu Morishita, GSI - Again Bug fix of multiprocessing v1.3.2 20201116 Yu Morishita, GSI - Bug fix of multiprocessing in Mac python>=3.8 v1.3.1 20201028 Yu Morishita, GSI - Update how to get n_para v1.3 20200909 Yu Morishita, GSI - Parallel processing v1.2 20200614 Yu Morishita, GSI - Wrong png name printing fixed v1.1 20200409 Yu Morishita, GSI - Add -c (coherence based mask) option v1.0 20190730 Yu Morishita, Uni of Leeds and GSI - Original implementation ''' #%% Import from LiCSBAS_meta import * import getopt import os import sys import glob import shutil import time import numpy as np 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 #%% def main(argv=None): #%% Check argv if argv == None: argv = sys.argv start = time.time() ver="1.3.5"; date=20210105; 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 ifgdates2, in_dir, out_dir, length, width, bool_mask, cycle, cmap_wrap, cc_ifg_thre #%% Set default in_dir = [] out_dir = [] coh_thre = [] cc_ifg_thre = [] ex_range_str = [] ex_range_file = [] poly_file = [] sbovl = False try: n_para = len(os.sched_getaffinity(0)) except: n_para = multi.cpu_count() cmap_noise = 'viridis' cmap_wrap = cmc.romaO import win_compat; q = win_compat.get_compatible_context() # breakpoint() #%% Read options try: try: opts, args = getopt.getopt(argv[1:], "hi:o:c:r:f:p:s:", ["help", "n_para=", "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 == '-i': in_dir = a elif o == '-o': out_dir = a elif o == '-c': coh_thre = float(a) elif o == '-s': cc_ifg_thre = float(a) elif o == '-r': ex_range_str = a elif o == '-f': ex_range_file = a elif o == '-p': poly_file = a elif o == '--sbovl': sbovl = True elif o == '--n_para': n_para = int(a) if not in_dir: raise Usage('No input directory given, -i is not optional!') if not out_dir: raise Usage('No output directory given, -o is not optional!') if not coh_thre and not ex_range_str and not ex_range_file and not poly_file and not cc_ifg_thre: raise Usage('Neither -r, -f, -p nor -s option is given!') elif not os.path.isdir(in_dir): raise Usage('No {} dir exists!'.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 coh_thre and cc_ifg_thre: print('Masking based of average then individual coherence. May be better to run seperately...') 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 # breakpoint() #%% Read info and make dir in_dir = os.path.abspath(in_dir) out_dir = os.path.abspath(out_dir) ifgdates = tools_lib.get_ifgdates(in_dir) n_ifg = len(ifgdates) mlipar = os.path.join(in_dir, 'slc.mli.par') width = int(io_lib.get_param_par(mlipar, 'range_samples')) length = 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 if wavelength > 0.2: ## L-band cycle = 1.5 # 2pi/cycle for png else: ## C-band cycle = 3 # 2pi*3/cycle for png if sbovl: cycle = 75 if not os.path.exists(out_dir): os.mkdir(out_dir) bool_mask = np.zeros((length, width), dtype=bool) #%% Check and set pixels to be masked based on coherence if coh_thre: ### Calc coh_avg print("\nCalculate coh_avg and define mask (<={})".format(coh_thre), flush=True) coh_avg = np.zeros((length, width), dtype=np.float32) n_coh = np.zeros((length, width), dtype=np.int16) for ifgix, ifgd in enumerate(ifgdates): ccfile = os.path.join(in_dir, 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 else: coh = io_lib.read_img(ccfile, length, width) coh[np.isnan(coh)] = 0 # Fill nan with 0 coh_avg += coh n_coh += (coh!=0) n_coh = n_coh.astype(np.int32) #OverflowError: Python integer 99999 out of bounds for int16 # thanks PEB for fixing this n_coh[n_coh==0] = 99999 #to avoid zero division coh_avg = coh_avg/n_coh ### Set mask bool_mask[coh_avg <= coh_thre] = True ### Save image coh_avgfile = os.path.join(out_dir, 'coh_avg') coh_avg.tofile(coh_avgfile) title = 'Average coherence' plot_lib.make_im_png(coh_avg, coh_avgfile+'.png', cmap_noise, title) #%% Check and set range to be masked based on specified area ### Read -r option if ex_range_str: if not tools_lib.read_range(ex_range_str, width, length): print('ERROR in {}\n'.format(ex_range_str)) return 1 else: x1, x2, y1, y2 = tools_lib.read_range(ex_range_str, width, length) bool_mask[y1:y2, x1:x2] = True ### Read -f option if ex_range_file: with open(ex_range_file) as f: ex_range_str_all = f.readlines() for ex_range_str1 in ex_range_str_all: if not tools_lib.read_range(ex_range_str1, width, length): print('ERROR in {}\n'.format(ex_range_str1)) return 1 else: x1, x2, y1, y2 = tools_lib.read_range(ex_range_str1, width, length) bool_mask[y1:y2, x1:x2] = True ### Read -p option if poly_file: print('Masking using polygon file') with open(poly_file) as f: poly_strings_all = f.readlines() dempar = os.path.join(in_dir, 'EQA.dem_par') lat1 = float(io_lib.get_param_par(dempar, 'corner_lat')) # north lon1 = float(io_lib.get_param_par(dempar, 'corner_lon')) # west postlat = float(io_lib.get_param_par(dempar, 'post_lat')) # negative postlon = float(io_lib.get_param_par(dempar, 'post_lon')) # positive lat2 = lat1+postlat*(length-1) # south lon2 = lon1+postlon*(width-1) # east #lon, lat = np.arange(lon1, lon2+postlon, postlon), np.arange(lat1, lat2+postlat, postlat) lon, lat = np.linspace(lon1, lon2, width), np.linspace(lat1, lat2, length) for poly_str in poly_strings_all: bool_mask = bool_mask + tools_lib.poly_mask(poly_str, lon, lat) ### Save image of mask mask = np.float32(~bool_mask) maskfile = os.path.join(out_dir, 'mask') mask.tofile(maskfile) pngfile = maskfile+'.png' title = 'Mask' plot_lib.make_im_png(mask, pngfile, cmap_noise, title, 0, 1) print('\nMask defined.') #%% Mask unw print('\nMask unw and link cc', flush=True) ### First, check if already exist ifgdates2 = [] for ifgix, ifgd in enumerate(ifgdates): out_dir1 = os.path.join(out_dir, ifgd) if sbovl: unwfile_m = os.path.join(out_dir1, ifgd+'.sbovldiff.adf.mm') else: unwfile_m = os.path.join(out_dir1, ifgd+'.unw') ccfile_m = os.path.join(out_dir1, ifgd+'.cc') if not (os.path.exists(unwfile_m) and os.path.exists(ccfile_m)): ifgdates2.append(ifgd) n_ifg2 = len(ifgdates2) if n_ifg-n_ifg2 > 0: print(" {0:3}/{1:3} masked unw and cc already exist. Skip".format(n_ifg-n_ifg2, n_ifg), flush=True) if n_ifg2 > 0: ### Mask with parallel processing if n_para > n_ifg2: n_para = n_ifg2 print(' {} parallel processing...'.format(n_para), flush=True) p = q.Pool(n_para) args_list = [(ifgix, sbovl) for ifgix in range(n_ifg2)] # p.starmap(mask_wrapper, range(n_ifg2)) p.starmap(mask_wrapper, args_list) p.close() print("", flush=True) #%% 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) print('\nMasked area can be check in:') print('{}'.format(os.path.abspath(maskfile+'.png')), flush=True) #%% 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))) #%% def mask_wrapper(ifgix, sbovl=False): ifgd = ifgdates2[ifgix] if np.mod(ifgix, 100) == 0: print(" {0:3}/{1:3}th unw...".format(ifgix, len(ifgdates2)), flush=True) # Construct file paths if sbovl: unwfile = os.path.join(in_dir, ifgd, ifgd + '.sbovldiff.adf.mm') else: unwfile = os.path.join(in_dir, ifgd, ifgd + '.unw') ccfile = os.path.join(in_dir, ifgd, ifgd + '.cc') # Check if the unw file exists if not os.path.exists(unwfile): print(f" WARNING: File not found: {unwfile}. Skipping...", flush=True) return # Read unw file unw = io_lib.read_img(unwfile, length, width) unw[unw == 0] = np.nan # Apply mask unw[bool_mask] = np.nan # Check if cc file exists and apply coherence threshold if cc_ifg_thre: if not os.path.exists(ccfile): print(f" WARNING: File not found: {ccfile}. Skipping coherence masking...", flush=True) else: if os.path.getsize(ccfile) == length * width: coh = io_lib.read_img(ccfile, length, width, np.uint8) coh = coh.astype(np.float32) / 255 else: coh = io_lib.read_img(ccfile, length, width) coh[np.isnan(coh)] = 0 # Fill NaNs with 0 unw[np.where(coh < cc_ifg_thre)] = np.nan # Create output directory out_dir1 = os.path.join(out_dir, ifgd) if not os.path.exists(out_dir1): os.mkdir(out_dir1) # Save masked unw file if sbovl: unw.tofile(os.path.join(out_dir1, ifgd + '.sbovldiff.adf.mm')) else: unw.tofile(os.path.join(out_dir1, ifgd + '.unw')) # Create symbolic link for cc file if not os.path.exists(os.path.join(out_dir1, ifgd + '.cc')): os.symlink(os.path.abspath(ccfile, out_dir1), os.path.join(out_dir1, ifgd + '.cc')) # Generate PNG for masked unw if sbovl: pngfile = os.path.join(out_dir1, ifgd + '.sbovldiff.adf.mm.png') else: 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 / cycle) * cycle), pngfile, cmap_wrap, title, -np.pi, np.pi, cbar=False) #%% main if __name__ == "__main__": sys.exit(main())