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#!/usr/bin/env python3 """ ======== Overview ======== This script loads epoch-wide tif files into an h5 cube referenced to the first epoch, and copy over other metadata from an existing cum.h5 """ import numpy as np import matplotlib.pyplot as plt import os import argparse import time import sys from matplotlib import cm import cmcrameri.cm as cmc import glob from osgeo import gdal import h5py as h5 global ver, date, author ver = "1.0"; date = 20230605; author = "Qi Ou, ULeeds" # generalise to any epoch class OpenTif: """ a Class that stores the band array and metadata of a Gtiff file.""" def __init__(self, filename, sigfile=None, incidence=None, heading=None, N=None, E=None, U=None): self.ds = gdal.Open(filename) self.basename = os.path.splitext(os.path.basename(filename))[0] self.band = self.ds.GetRasterBand(1) self.data = self.band.ReadAsArray() self.xsize = self.ds.RasterXSize self.ysize = self.ds.RasterYSize self.left = self.ds.GetGeoTransform()[0] self.top = self.ds.GetGeoTransform()[3] self.xres = self.ds.GetGeoTransform()[1] self.yres = self.ds.GetGeoTransform()[5] self.right = self.left + self.xsize * self.xres self.bottom = self.top + self.ysize * self.yres self.projection = self.ds.GetProjection() pix_lin, pix_col = np.indices((self.ds.RasterYSize, self.ds.RasterXSize)) self.lat, self.lon = self.top + self.yres*pix_lin, self.left+self.xres*pix_col # convert 0 and 255 to NaN self.data[self.data==0.] = np.nan class CustomFormatter(argparse.ArgumentDefaultsHelpFormatter, argparse.RawDescriptionHelpFormatter): ''' Use a multiple inheritance approach to use features of both classes. The ArgumentDefaultsHelpFormatter class adds argument default values to the usage help message The RawDescriptionHelpFormatter class keeps the indentation and line breaks in the ___doc___ ''' pass def init_args(): global args parser = argparse.ArgumentParser(description=__doc__, formatter_class=CustomFormatter) parser.add_argument('-i', dest='input_dir', default="./GACOSml10/", type=str, help="input directory containing gacos epochs") parser.add_argument('-s', dest='input_suffix', default=".sltd.geo.tif", type=str, help="suffix of gacos epochs") parser.add_argument('-o', dest='outfile', default="gacos_cum.h5", type=str, help="output cumulative displacement from gacos epochs") parser.add_argument('-c', dest='existing_cumh5file', default='TS_GEOCml10GACOS/cum.h5', type=str, help="cumulative displacement from LiCSBAS inversion to copy over meta data only") parser.add_argument('-e', dest='same_epochs_as_existing_h5', default=False, action='store_true', help="only add the same epochs as in the existing h5") parser.add_argument('--radian2mm', default=False, action='store_true', help="convert from radian to mm") args = parser.parse_args() def start(): global start_time # intialise and print info on screen start_time = time.time() print("\n{} ver{} {} {}".format(os.path.basename(sys.argv[0]), ver, date, author), flush=True) print("{} {}".format(os.path.basename(sys.argv[0]), ' '.join(sys.argv[1:])), flush=True) def finish(): #%% Finish elapsed_time = time.time() - start_time 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{} {}".format(os.path.basename(sys.argv[0]), ' '.join(sys.argv[1:])), flush=True) print('Output: {}\n'.format(os.path.abspath(args.outfile))) if __name__ == "__main__": init_args() start() # Open existing cum.h5 for reading metadata cumh5 = h5.File(args.existing_cumh5file, 'a') # if adding all available epochs into cube if not args.same_epochs_as_existing_h5: # add epochs into cube referenced to the first epoch tifList = sorted(glob.glob(os.path.join(args.input_dir, '*'+args.input_suffix))) ref_tif = OpenTif(tifList[0]) cube = np.ones([len(tifList), ref_tif.ysize, ref_tif.xsize]) for i, tif in enumerate(tifList): print(tif) slice = OpenTif(tif) cube[i, :, :] = slice.data - ref_tif.data else: # keep the epochs the same as in existing h5 ref_tif = OpenTif(glob.glob(os.path.join(args.input_dir, str(cumh5['imdates'][0])+"*"+args.input_suffix))[0]) cube = np.ones([len(cumh5['imdates']), ref_tif.ysize, ref_tif.xsize]) for i, tif in enumerate(cumh5['imdates']): print(tif) slice = OpenTif(glob.glob(os.path.join(args.input_dir, str(cumh5['imdates'][i])+"*"+args.input_suffix))[0]) cube[i, :, :] = slice.data - ref_tif.data ### Get scaling factor if args.radian2mm: speed_of_light = 299792458 #m/s radar_frequency = 5405000000.0 #Hz wavelength = speed_of_light/radar_frequency #meter coef_r2m = -wavelength/4/np.pi*1000 #rad -> mm, positive is -LOS else: coef_r2m = 1 # write into new cum.h5 gacosh5 = h5.File(args.outfile, 'w') compress = 'gzip' gacosh5.create_dataset('cum', data=cube*coef_r2m, compression=compress) gacosh5.create_dataset('refarea', data=cumh5['refarea'] ) gacosh5.create_dataset('imdates', data=cumh5['imdates'] ) gacosh5.create_dataset('corner_lat', data=cumh5['refarea']) gacosh5.create_dataset('corner_lon', data=cumh5['corner_lon']) gacosh5.create_dataset('post_lat', data=cumh5['post_lat']) gacosh5.create_dataset('post_lon', data=cumh5['post_lon']) # close new cum.h5 gacosh5.close() # close existing cum.h5 cumh5.close() finish()