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#!/usr/bin/env python3 """ ======== Overview ======== This script calculates velocity and its standard deviation from cum*.h5 and outputs them as a float32 file. Amplitude and time offset of the annual displacement can also be calculated by --sin option. It can estimate offsets based on earthquake event datetime or external offsets.txt file. This will not work with --sin. However --vstd would in such case be calculated from residuals. ===== Usage ===== LiCSBAS_cum2vel.py [-s yyyymmdd] [-e yyyymmdd] [-i infile] [-o outfilenamestr] [-r x1:x2/y1:y2] [--ref_geo lon1/lon2/lat1/lat2] [--vstd] [--sin] [--mask maskfile] [--png] [--eqoffsets minmag] [--offsets offsets.txt] [--export_model outmodelfile.h5] -s Start date of period to calculate velocity (Default: first date) -e End date of period to calculate velocity (Default: last date) -i Path to input cum file (Default: cum_filt.h5) -o Output filename root string - will use to name modeled variables (Default: yyyymmdd_yyyymmdd -> yyyymmdd_yyyymmdd.vel[.mskd]) -r Reference area (Default: same as info/*ref.txt) Note: x1/y1 range 0 to width-1, while x2/y2 range 1 to width 0 for x2/y2 means all. (i.e., 0:0/0:0 means whole area). --ref_geo Reference area in geographical coordinates. --vstd Calculate vstd (+ stc and RMSE) (Default: No) --sin Add sin (annual) funcsion to linear model (Default: No) *.amp and *.dt (time difference wrt Jan 1) are output --mask Path to mask file for ref phase calculation (Default: No mask) --png Make png file (Default: Not make png) --eqoffsets minmag Estimate also offsets for earthquakes above minmag (float) in the region (defaults to M6.5+) --offsets offsets.txt Estimate offsets read from external txt file - both yyyymmdd and yyyy-mm-dd form is supported --export_model modelfile.h5 Export the model time series to H5 file. Can be used for step 16 (Default: not export) --store_to_results Setting this parameter, outputs will be stored to the results directory (overwriting existing files) --datavar cum Option to change the input data variable name (standard is 'cum' - will work for any with the expected shape) """ #%% Change log ''' 2024-12 ML, ULeeds: - added calc of RMSE 2024-11 ML, ULeeds: - added also offsets 2024-10-22 Milan Lazecky, ULeeds - added eqoffsets - recalc vstd and stc based on residuals from the model with offsets v1.3.3 20210910 Yu Morishita, GSI - Avoid error for refarea in bytes v1.3.2 20210125 Yu Morishita, GSI - Change cmap for vstd, amp, dt v1.3.1 20210107 Yu Morishita, GSI - Replace jet with SCM.roma_r v1.3 20200703 Yu Morishita, GSI - Add --ref_geo option v1.2 20190807 Yu Morishita, Uni of Leeds and GSI - Add sin option v1.1 20190802 Yu Morishita, Uni of Leeds and GSI - Make vstd optional v1.0 20190730 Yu Morishita, Uni of Leeds and GSI - Original implementationf ''' #%% Import import getopt import os import sys import re import time import numpy as np import datetime as dt import h5py as h5 import cmcrameri.cm as cmc import LiCSBAS_io_lib as io_lib import LiCSBAS_inv_lib as inv_lib import LiCSBAS_tools_lib as tools_lib import LiCSBAS_plot_lib as plot_lib from LiCSBAS_meta import * 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() #ver="1.3.3"; date=20210910; author="Y. Morishita" # this is from LiCSBAS_meta now 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 imd_s = [] imd_e = [] cumfile = 'cum_filt.h5' datavar = 'cum' outfile = [] refarea = [] refarea_geo = [] maskfile = [] vstdflag = False stcflag = False sinflag = False pngflag = False eqoffsetsflag = False offsetsflag = False offsetsfile = [] exportmodelfile = [] modelflag = False minmag = 6.5 cmap = cmc.romaO.reversed() cmap_vstd = 'viridis_r' cmap_stc = 'viridis_r' cmap_amp = 'viridis_r' cmap_dt = cmc.romaO.reversed() compress = 'gzip' store_to_results = False #%% Read options try: try: opts, args = getopt.getopt(argv[1:], "hs:e:i:o:r:", ["help", "datavar=", "store_to_results", "vstd", "sin", "eqoffsets=", "offsets=","export_model=","png", "ref_geo=", "mask="]) 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 == '-s': imd_s = a elif o == '-e': imd_e = a elif o == '-i': cumfile = a elif o == '-o': outfile = a elif o == '-r': refarea = a elif o == '--ref_geo': refarea_geo = a elif o == '--vstd': vstdflag = True stcflag = True modelflag = True elif o == '--sin': sinflag = True elif o == '--mask': maskfile = a elif o == '--png': pngflag = True elif o == '--datavar': datavar = a elif o == '--eqoffsets': minmag = float(a) eqoffsetsflag = True elif o == '--offsets': offsetsfile = a offsetsflag = True elif o == '--export_model': exportmodelfile = a modelflag = True elif o == '--store_to_results': store_to_results = True if not os.path.exists(cumfile): raise Usage('No {} exists! Use -i option.'.format(cumfile)) if sinflag and (eqoffsetsflag or offsetsflag): raise Usage('--sin does not (yet) work together with offsets estimation - cancelling') if offsetsflag: if not os.path.exists(offsetsfile): raise Usage('Offsets file not provided') #raise Usage('Sorry, this functionality is not implemented yet - please raise Issue on github') if store_to_results: tsdir = os.path.dirname(cumfile) resultsdir = os.path.join(tsdir, 'results') if not os.path.exists(resultsdir): raise Usage('ERROR: The results directory is not provided with the input file') 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 if eqoffsetsflag: print('getting earthquakes over the region') offsets = tools_lib.get_earthquake_dates(cumfile, minmag=minmag, maxdepth=60) print('identified '+str(len(offsets))+' earthquake candidates to solve') print('') try: outxt = os.path.join(os.path.dirname(cumfile), 'info', 'eqoffsets.txt') with open(outxt, 'w') as f: for i in offsets: print('{}'.format(i), file=f) print('stored to file:') print(outxt) except: print('some error storing earthquake offsets to '+outxt+'. Continuing') if offsetsflag: if not eqoffsetsflag: offsets = io_lib.read_epochlist(offsetsfile, outasdt=True) print('Loaded '+str(len(offsets))+' offsets:') print(offsets) print('') #%% Read info ### Read cumfile cumh5 = h5.File(cumfile,'r') imdates = cumh5['imdates'][()].astype(str).tolist() # cumh5 = xr.open_dataset(cumfile) # future: xr # imdates = list(a.time.dt.strftime('%Y%m%d').values) cum = cumh5[datavar] n_im_all, length, width = cum.shape if refarea: if not tools_lib.read_range(refarea, width, length): print('\nERROR in {}\n'.format(refarea), file=sys.stderr) return 2 else: refx1, refx2, refy1, refy2 = tools_lib.read_range(refarea, width, length) elif refarea_geo: lat1 = float(cumh5['corner_lat'][()]) lon1 = float(cumh5['corner_lon'][()]) dlat = float(cumh5['post_lat'][()]) dlon = float(cumh5['post_lon'][()]) if not tools_lib.read_range_geo(refarea_geo, width, length, lat1, dlat, lon1, dlon): print('\nERROR in {}\n'.format(refarea_geo), file=sys.stderr) return 2 else: refx1, refx2, refy1, refy2 = tools_lib.read_range_geo(refarea_geo, width, length, lat1, dlat, lon1, dlon) else: refarea = cumh5['refarea'][()] if type(refarea) is bytes: refarea = refarea.decode('utf-8') refx1, refx2, refy1, refy2 = [int(s) for s in re.split('[:/]', refarea)] #%% Setting ### Dates if not imd_s: imd_s = imdates[0] if not imd_e: imd_e = imdates[-1] ### mask if maskfile: mask = io_lib.read_img(maskfile, length, width) mask[mask==0] = np.nan suffix_mask = '.mskd' else: mask = np.ones((length, width), dtype=np.float32) suffix_mask = '' ### Find date index if not exist in imdates if not imd_s in imdates: for imd in imdates: if int(imd) >= int(imd_s): ## First larger one than imd_s imd_s = imd break if not imd_e in imdates: for imd in imdates[::-1]: if int(imd) <= int(imd_e): ## Last smaller one than imd_e imd_e = imd break ix_s = imdates.index(imd_s) ix_e = imdates.index(imd_e)+1 #+1 for python custom n_im = ix_e-ix_s ### Calc dt in year imdates_dt = ([dt.datetime.strptime(imd, '%Y%m%d').toordinal() for imd in imdates[ix_s:ix_e]]) dt_cum = np.float32((np.array(imdates_dt)-imdates_dt[0])/365.25) ### Outfile if not outfile: outfile = '{}_{}'.format(imd_s, imd_e) if store_to_results: velfile = os.path.join(resultsdir, 'vel'+suffix_mask) vconstfile = os.path.join(resultsdir, 'vconst'+suffix_mask) else: velfile = outfile + '.vel' + suffix_mask vconstfile = outfile + '.vconst' + suffix_mask #%% Display info print('') print('Start date : {}'.format(imdates[ix_s])) print('End date : {}'.format(imdates[ix_e-1])) print('# of images : {}'.format(n_im)) print('Ref area : {}:{}/{}:{}'.format(refx1, refx2, refy1, refy2)) print('') #%% Calc velocity and vstd vconst = np.zeros((length, width), dtype=np.float32)*np.nan vel = np.zeros((length, width), dtype=np.float32)*np.nan ### Read cum data cum_tmp = cum[ix_s:ix_e, :, :]*mask cum_ref = np.nanmean(cum[ix_s:ix_e, refy1:refy2, refx1:refx2]*mask[refy1:refy2, refx1:refx2], axis=(1, 2)) if np.all(np.isnan(cum_ref)): print('\nERROR: Ref area has only NaN value!\n', file=sys.stderr) return 2 cum_tmp = cum_tmp-cum_ref[:, np.newaxis, np.newaxis] ### Extract not nan points bool_allnan = np.all(np.isnan(cum_tmp), axis=0) cum_tmp_resh = cum_tmp.reshape(n_im, length*width)[:, ~bool_allnan.ravel()].transpose() # if exportmodelfile: # get the output model h5 file ready: modh5file = os.path.join(os.path.dirname(cumfile), 'model.h5') modh5 = h5.File(modh5file, 'w') if eqoffsetsflag or offsetsflag: print('Calc vel and earthquake offsets') result, datavarnames, G = inv_lib.calc_vel_offsets(cum_tmp_resh, imdates_dt, offsets, return_G = True) params_sorted = [] print('') for i in range(len(datavarnames)): dvarname = datavarnames[i] print('storing '+dvarname) dvar = np.zeros((length, width), dtype=np.float32)*np.nan dvar[~bool_allnan] = result[i,:] if store_to_results: outvarfile = os.path.join(resultsdir, dvarname + suffix_mask) else: outvarfile = outfile+'.'+dvarname+suffix_mask dvar.tofile(outvarfile) # also use vel (and vconst?) as usual: if dvarname == 'vel': vel = dvar if exportmodelfile: # also export to the h5 (why not) modh5.create_dataset(dvarname, data=dvar, compression=compress) if modelflag: # add as inputs for the model params_sorted.append(dvar) if pngflag: pngfile = outvarfile + '.png' # title = 'n_im: {}, Ref X/Y {}:{}/{}:{}'.format(n_im, refx1, refx2, refy1, refy2) cmin = np.nanpercentile(dvar, 1) cmax = np.nanpercentile(dvar, 99) plot_lib.make_im_png(dvar, pngfile, cmap, dvarname, cmin, cmax) if modelflag: model = inv_lib.get_model_cum(G, params_sorted) degfree=len(params_sorted) # del G else: if not sinflag: ## Linear function print('Calc velocity...') vconst[~bool_allnan], vel[~bool_allnan], G = inv_lib.calc_vel(cum_tmp_resh, dt_cum, return_G = True) if modelflag: model = inv_lib.get_model_cum(G, [vconst, vel]) degfree = 2 vel.tofile(velfile) vconst.tofile(vconstfile) else: ## Linear+sin function print('Calc velocity and annual components...') amp = np.zeros((length, width), dtype=np.float32)*np.nan delta_t = np.zeros((length, width), dtype=np.float32)*np.nan if store_to_results: ampfile = os.path.join(resultsdir, 'amp' + suffix_mask) dtfile = os.path.join(resultsdir, 'dt' + suffix_mask) else: ampfile = outfile+'.amp'+suffix_mask dtfile = outfile+'.dt'+suffix_mask if modelflag: coef_s = np.zeros((length, width), dtype=np.float32)*np.nan coef_c = np.zeros((length, width), dtype=np.float32) * np.nan vconst[~bool_allnan], vel[~bool_allnan], coef_s[~bool_allnan], coef_c[~bool_allnan], amp[~bool_allnan], delta_t[~bool_allnan], G = inv_lib.calc_velsin( cum_tmp_resh, dt_cum, imdates[0], return_G = True) model = inv_lib.get_model_cum(G, [vconst, vel, coef_s, coef_c]) degfree = 4 else: vel[~bool_allnan], vconst[~bool_allnan], amp[~bool_allnan], delta_t[~bool_allnan] = inv_lib.calc_velsin(cum_tmp_resh, dt_cum, imdates[0]) vel.tofile(velfile) amp.tofile(ampfile) delta_t.tofile(dtfile) if exportmodelfile: print('Exporting model time series to '+modh5file) modh5.create_dataset('cum_model', data=model, compression=compress) modh5.close() if modelflag: try: # let's also calculate RMSE using the model values: resid = cum_tmp - model rmse = np.zeros((length, width), dtype=np.float32) * np.nan #rmse = np.sqrt(np.nanmean(resid**2, axis=0)) # simple without degs of freedom count = np.sum(~np.isnan(resid), axis=0, dtype=np.float32) count[count == 0] = np.nan rmse = np.sqrt(np.nansum(resid ** 2, axis=0) / (count - degfree)) if store_to_results: rmsefile = os.path.join(resultsdir, 'rmse' + suffix_mask) else: rmsefile = outfile+'.rmse'+suffix_mask rmse.tofile(rmsefile) del resid except: print('Some error creating RMSE') ### vstd if vstdflag: if store_to_results: vstdfile = os.path.join(resultsdir, 'vstd' + suffix_mask) bootvelfile = os.path.join(resultsdir, 'bootvel' + suffix_mask) else: vstdfile = outfile+'.vstd'+suffix_mask bootvelfile = outfile+'.bootvel'+suffix_mask vstd = np.zeros((length, width), dtype=np.float32)*np.nan bootvel = np.zeros((length, width), dtype=np.float32) * np.nan print('Calc vstd...') if offsetsflag or eqoffsetsflag: cum_tmp_resh = cum_tmp_resh - model.reshape(n_im, length*width)[:, ~bool_allnan.ravel()].transpose() vstd[~bool_allnan], bootvel[~bool_allnan] = inv_lib.calc_velstd_withnan(cum_tmp_resh, dt_cum) vstd.tofile(vstdfile) bootvel.tofile(bootvelfile) # #_cum = cum[:, rows[0]-row_ex1:rows[1]+row_ex2, :].reshape(n_im, lengththis+row_ex1+row_ex2, width) ### Calc STC #stc = inv_lib.calc_stc(_cum, gpu=gpu)[row_ex1:lengththis+row_ex1, :] ## original length # if stcflag: print('Calc stc...') # here, stc calc accepts nans and need 3D cube - so getting the original cum_tmp then if store_to_results: stcfile = os.path.join(resultsdir, 'stc' + suffix_mask) else: stcfile = outfile + '.stc' + suffix_mask # cum_tmp = cum_tmp.reshape(n_im, length, width) # this will not work! if offsetsflag or eqoffsetsflag: cum_tmp = cum_tmp - model # or should this be transposed? stc = inv_lib.calc_stc(cum_tmp) openmode = 'w' with open(stcfile, openmode) as f: stc.tofile(f) #%% Make png if specified if pngflag: pngfile = velfile+'.png' title = 'Velocity (n_im: {}, Ref X/Y {}:{}/{}:{})'.format(n_im, refx1, refx2, refy1, refy2) cmin = np.nanpercentile(vel, 1) cmax = np.nanpercentile(vel, 99) plot_lib.make_im_png(vel, pngfile, cmap, title, cmin, cmax) # plot_lib.make_im_png(dvar, pngfile, cmap, dvarname, cmin, cmax) if sinflag: amp_max = np.nanpercentile(amp, 99) plot_lib.make_im_png(amp, ampfile+'.png', cmap_amp, title, vmax=amp_max) plot_lib.make_im_png(delta_t, dtfile+'.png', cmap_dt, title) if vstdflag: title = 'STD of velocity (mm/yr)' cmin = np.nanpercentile(vstd, 1) cmax = np.nanpercentile(vstd, 99) plot_lib.make_im_png(vstd, vstdfile+'.png', cmap_vstd, title, cmin, cmax) title = 'Bootstrapped velocity (mm/yr)' cmin = np.nanpercentile(bootvel, 1) cmax = np.nanpercentile(bootvel, 99) plot_lib.make_im_png(bootvel, bootvelfile + '.png', cmap, title, cmin, cmax) if stcflag: title = 'Spatio-temporal consistency (mm)' cmin = np.nanpercentile(stc, 1) cmax = np.nanpercentile(stc, 99) plot_lib.make_im_png(stc, stcfile + '.png', cmap_stc, title, cmin, cmax) if modelflag: title = 'RMSE of applied model (mm)' cmin = np.nanpercentile(rmse, 1) cmax = np.nanpercentile(rmse, 99) try: plot_lib.make_im_png(rmse, rmsefile + '.png', cmap_stc, title, cmin, cmax) except: print('error generating rmse preview') #%% 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: {}'.format(velfile), flush=True) if vstdflag: print(' {}'.format(vstdfile), flush=True) if stcflag: print(' {}'.format(stcfile), flush=True) if sinflag: print(' {}'.format(ampfile), flush=True) print(' {}'.format(dtfile), flush=True) print('') #%% main if __name__ == "__main__": sys.exit(main())