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#!/usr/bin/env python3 """ v1.5.1 20210209 Yu Morishita, GSI ======== Overview ======== This script makes a GeoTIFF file from an image file (only in float32 format). The geotiff file can be read by a GIS software (e.g., QGIS) and used to make a figure. Nan will be regarded as NoDataValue as default. 0 can be replaced with nan. ===== Usage ===== LiCSBAS_flt2geotiff.py -i infile -p dempar [-o outfile] [--zero2nan] [--nan2zero] [--a_nodata num] [--bigendian] -i Path to input file (float, little endian) -p Path to dem parameter file (EQA.dem_par) -o Output geotiff file (Default: infile[.geo].tif) --a_nodata Assign a specified nodata value in output (Default: nan) "None" assigns no value as nodata --zero2nan Replace 0 with nan (Default: NOT replace 0 with nan) --nan2zero Replace nan with 0 (Default: NOT replace nan with 0) --bigendian If input file is in big endian """ ## Hidden option: --gamma #%% Change log ''' v1.5.1 20210209 Yu Morishita, GSI - Move make_geotiff to library v1.5 20200902 Yu Morishita, GSI - Do not add .geo when already added v1.4 20200214 Yu Morishita, Uni of Leeds and GSI - Change Default nodata to nan - Remove --keep_nan and add --nan2zero v1.3 20200211 Yu Morishita, Uni of Leeds and GSI - Add --keep_nan, --zero2nan, and --nodata options - Change default to replace nan with 0. v1.2 20200130 Yu Morishita, Uni of Leeds and GSI - Add compress option with DEFLATE for gdal v1.0 20190729 Yu Morishita, Uni of Leeds and GSI - Original implementationf ''' #%% Import import getopt import shutil import os import sys import time import subprocess as subp import numpy as np import LiCSBAS_io_lib as io_lib 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="1.5.1"; date=20210209; 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) #%% Set default infile = [] dempar = [] outfile = [] nodata = np.nan endian = 'little' nan2zero_flag = False zero2nan_flag = False gamma_flag = False compress_option = ['COMPRESS=DEFLATE', 'PREDICTOR=3'] ## ['COMPRESS=LZW', 'PREDICTOR=3'], ['COMPRESS=PACKBITS'] #%% Read options try: try: opts, args = getopt.getopt(argv[1:], "hi:p:o:", ["help", "a_nodata=", "nan2zero", "zero2nan", "bigendian", "gamma"]) 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': infile = a elif o == '-p': dempar = a elif o == '-o': outfile = a elif o == '--a_nodata': if a.isdecimal(): nodata = int(a) elif a == 'None': nodata = None else: nodata = float(a) elif o == '--nan2zero': nan2zero_flag = True elif o == '--zero2nan': zero2nan_flag = True elif o == '--bigendian': endian = 'big' elif o == '--gamma': ## hidden option gamma_flag = True if not infile: raise Usage('No input file given, -i is not optional!') elif not os.path.exists(infile): raise Usage('No {} exists!'.format(infile)) elif not dempar: raise Usage('No dempar file given, -p is not optional!') elif not os.path.exists(dempar): raise Usage('No {} exists!'.format(dempar)) if nan2zero_flag and zero2nan_flag: raise Usage("Don't use both --zero2nan and --nan2zero!") 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 info if not outfile: outfile = infile.replace('.geo', '')+'.geo.tif' width = int(io_lib.get_param_par(dempar, 'width')) length = int(io_lib.get_param_par(dempar, 'nlines')) #%% If data2geotiff (GAMMA) is available and --gamma is used gamma_comm = 'data2geotiff' if shutil.which(gamma_comm) and gamma_flag: dtype = '2' # float print('Use data2geotiff in GAMMA') ### No replacement of nan and 0 is done ### Nodata is set to 0 if endian == 'little': ### Make temporary big endian file data = io_lib.read_img(infile, length, width, endian=endian) data.byteswap().tofile(infile+'.bigendian') infile = infile+'.bigendian' print('{} {} {} {} {}'.format(gamma_comm, dempar, infile, dtype, outfile)) call=[gamma_comm, dempar, infile, dtype, outfile] subp.run(call) if endian == 'little': ### Remove temporary file os.remove(infile) #%% if gdal and osr available else: print('Use gdal module') try: from osgeo import gdal, osr except: print("\nERROR: gdal must be installed.", file=sys.stderr) return 1 width = int(io_lib.get_param_par(dempar, 'width')) length = int(io_lib.get_param_par(dempar, 'nlines')) dlat = float(io_lib.get_param_par(dempar, 'post_lat')) dlon = float(io_lib.get_param_par(dempar, 'post_lon')) lat_n_g = float(io_lib.get_param_par(dempar, 'corner_lat')) #grid reg lon_w_g = float(io_lib.get_param_par(dempar, 'corner_lon')) #grid reg ## Grid registration to pixel registration by shifing half pixel lat_n_p = lat_n_g - dlat/2 lon_w_p = lon_w_g - dlon/2 data = io_lib.read_img(infile, length, width, endian=endian) if zero2nan_flag: ### Replace 0 with nan data[data==0] = np.nan if nan2zero_flag: ### Replace nan with 0 data[np.isnan(data)] = 0 io_lib.make_geotiff(data, lat_n_p, lon_w_p, dlat, dlon, outfile, compress_option, nodata) #%% 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: {}\n'.format(outfile), flush=True) #%% main if __name__ == "__main__": sys.exit(main())