270 lines
10 KiB
Python
270 lines
10 KiB
Python
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#!/usr/bin/env python3
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# Script that computes the baselines for a given master based on a stack of baselines
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#
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#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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# Copyright 2017 California Institute of Technology. ALL RIGHTS RESERVED.
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#
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# Licensed under the Apache License, Version 2.0 (the "License");
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# you may not use this file except in compliance with the License.
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# You may obtain a copy of the License at
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#
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# http://www.apache.org/licenses/LICENSE-2.0
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#
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# Unless required by applicable law or agreed to in writing, software
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# distributed under the License is distributed on an "AS IS" BASIS,
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# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
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# See the License for the specific language governing permissions and
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# limitations under the License.
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#
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# United States Government Sponsorship acknowledged. This software is subject to
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# U.S. export control laws and regulations and has been classified as 'EAR99 NLR'
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# (No [Export] License Required except when exporting to an embargoed country,
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# end user, or in support of a prohibited end use). By downloading this software,
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# the user agrees to comply with all applicable U.S. export laws and regulations.
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# The user has the responsibility to obtain export licenses, or other export
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# authority as may be required before exporting this software to any 'EAR99'
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# embargoed foreign country or citizen of those countries.
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#
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# Author: David Bekaert
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#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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import argparse
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from glob import glob
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import numpy as np
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import scipy
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import os
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# command line parsing of input file
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def cmdLineParse():
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'''
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Command line parser.
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'''
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parser = argparse.ArgumentParser(description='baseline re-estimation for a master date')
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parser.add_argument('-i','--input', dest='baseline_dir', type=str,required=True, help='Path to the baseline directory')
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parser.add_argument('-m', '--master_date' ,dest='new_master', type=str, required=True , help='New master date for stack')
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return parser.parse_args()
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def baselinegrid(inps):
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"""
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Basline files are given as grids
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"""
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import gdal
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# parsing the command line inputs
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baseline_dir = inps.baseline_dir
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new_master = int(inps.new_master)
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# check if the baseline grids are all in the same folder or if they are date YYYYMMDD_YYYYMMDD folders.
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baseline_files = glob(os.path.join(baseline_dir,"2*","2*[0-9].vrt"))
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if not baseline_files:
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# try to see if they are all local
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baseline_files = glob(os.path.join(baseline_dir,"2*[0-9].vrt"))
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if not baseline_files:
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# need to raize error as no baseline files where found
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raise ValueError('No Baseline files were found')
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# finding the master baseline grid file
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master_file = False
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for baseline_file in baseline_files:
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date = os.path.basename(baseline_file)
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date = date.split('.vrt')
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date = int(date[0])
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if date == new_master:
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master_file = os.path.join(os.path.dirname(baseline_file),str(date))
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if not master_file:
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raise Exception('Could not find the master baseline grid')
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# generate new baseline grid for each slave and also store the average for overview
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baselines_new = [float(0)]
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dates_new = [new_master]
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for baseline_file in baseline_files:
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date = os.path.basename(baseline_file)
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date = date.split('.vrt')
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date = int(date[0])
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# check if this is a slave date
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if not date == new_master:
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slave_file = os.path.join(os.path.dirname(baseline_file),str(date))
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local_baseline_file = "baselineGRID_" + str(date)
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cmd = "imageMath.py -e='a-b' --a=" + slave_file + " --b=" + master_file + " -o " + local_baseline_file + " -t FLOAT -s BIP"
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os.system(cmd)
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# generating a vrt file as well
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cmd = "isce2gis.py vrt -i " + local_baseline_file
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os.system(cmd)
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# compute the average as well for baseline overview
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if os.path.isfile(local_baseline_file):
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dataset_avg = gdal.Open(local_baseline_file + '.vrt',gdal.GA_ReadOnly)
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stats = dataset_avg.GetRasterBand(1).GetStatistics(0,1)
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average = stats[2]
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baselines_new.append(average)
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dates_new.append(date)
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# convert to numpy arrays
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baselines_new = np.reshape(np.array(baselines_new),(-1,1))
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dates_new = np.reshape(np.array(dates_new),(-1,1))
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temp =np.hstack([dates_new,baselines_new])
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temp = temp[temp[:, 0].argsort()]
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np.savetxt('baseline_overview_new', temp, fmt='%.f %.2f ', delimiter='\t', newline='\n')
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# generate a baseline file for each acquisition
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for counter in range(temp.shape[0]):
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if temp[counter,0] == new_master:
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dir_name = 'master'
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else:
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dir_name = str(int(temp[counter,0]))
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# generate the directory if it does not exist yet
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try:
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os.stat(dir_name)
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except:
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os.mkdir(dir_name)
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np.savetxt(os.path.join(dir_name,'baseline'), [temp[counter,:]], fmt='%.f %.2f ', delimiter='\t', newline='\n')
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def baselinefile(inps):
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"""
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Baseline files are txt files with a single value in them
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"""
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# parsing the command line inputs
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baseline_dir = inps.baseline_dir
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new_master = int(inps.new_master)
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# check if the baseline files are all in the same folder or if they are date YYYYMMDD_YYYYMMDD folders.
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baseline_files = glob(os.path.join(baseline_dir,"2*","2*.txt"))
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if not baseline_files:
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# try to see if they are all local
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baseline_files = glob(os.path.join(baseline_dir,"2*.txt"))
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if not baseline_files:
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# need to raize error as no baseline files where found
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raise ValueError('No Baseline files were found')
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# generate an array of dates
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master = []
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slave = []
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baseline = []
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for baseline_file in baseline_files:
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dates = os.path.basename(baseline_file)
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dates = dates.split('.')[0]
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master.append(int(dates.split('_')[0]))
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slave.append(int(dates.split('_')[1]))
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# read file and either catch a single value or read for specific -perp (average):- string
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file = open(baseline_file,'r')
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file_lines = file.readlines()
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# there is only one line for the baseline
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if len(file_lines)==1:
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baseline.append(float(file_lines[0]))
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# there are multiple lines, only extract the specific string
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else:
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baseline_temp=[]
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for file_line in file_lines:
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if file_line.find("perp (average):") != -1:
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# getting the string with the value
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temp = file_line.split("perp (average):")[1]
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# removing the newline character
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temp = temp.split("\n")[0]
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baseline_temp.append(float(temp))
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# take the mean
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baseline.append(np.mean(np.array(baseline_temp)))
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# converting to an numpy array
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baseline = np.reshape(np.array(baseline),(-1,1))
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master = np.reshape(np.array(master),(-1,1))
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slave = np.reshape(np.array(slave),(-1,1))
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# count the number of nan in the baseline
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ix_count = np.count_nonzero(np.isnan(baseline))
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if ix_count>0:
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for ix in range(baseline.shape[0]):
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if np.isnan(baseline[ix])==1:
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print(str(master[ix,0]) + "_" + str(slave[ix,0]))
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# now raize error
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raise ValueError('NaN found for baseline...')
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# generating an array of acquisitions
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dates= np.reshape(np.unique(np.concatenate((master,slave), axis=0)),(-1,1))
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# getting number of baseline combinations and the number of acquisitions
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n_acquistions = dates.shape[0]
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n_combinations = baseline.shape[0]
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#### mapping the baselines to a new master
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# generate the design matrix that maps the baselines to dates
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A = np.zeros((n_combinations,n_acquistions))
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for counter in range(n_combinations):
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pos_master, temp = np.where(dates == master[counter])
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pos_slave, temp = np.where(dates == slave[counter])
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A[counter,pos_master]=-1
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A[counter,pos_slave]=1
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del pos_slave
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del pos_master
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# location of the requested master
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pos_master, temp = np.where(dates == new_master)
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# remove the new master from the design matrix and acquisitions
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A[:,pos_master[0]]=0
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# compute the new baselines
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baselines_new = np.linalg.lstsq(A, baseline)[0]
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# # add the new master back in and write out the file
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# baselines_new = np.concatenate((baselines_new, np.zeros((1,1))))
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# dates = np.concatenate((dates, [[new_master]]))
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# concatenate together to write single matrix
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temp= np.concatenate((dates, baselines_new), axis=1)
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np.savetxt('baseline_overview', temp, fmt='%.f %.2f ', delimiter='\t', newline='\n')
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# generate a baseline file for each acquisition
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for counter in range(n_acquistions):
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if temp[counter,0] == new_master:
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dir_name = 'master'
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else:
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dir_name = str(int(temp[counter,0]))
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# generate the directory if it does not exist yet
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try:
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os.stat(dir_name)
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except:
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os.mkdir(dir_name)
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np.savetxt(os.path.join(dir_name,'baseline'), [temp[counter,:]], fmt='%.f %.2f ', delimiter='\t', newline='\n')
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# main script
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if __name__ == '__main__':
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'''
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Main driver.
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'''
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# parsing the command line inputs
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inps = cmdLineParse()
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### check if the baselines are as single txt file or as a grid
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# baseline files
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baseline_files = glob(os.path.join(inps.baseline_dir,"2*","2*.txt"))
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if not baseline_files:
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# try to see if they are all local
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baseline_files = glob(os.path.join(inps.baseline_dir,"2*.txt"))
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# baseline grid
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baseline_grids = glob(os.path.join(inps.baseline_dir,"2*","2*[0-9].vrt"))
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if not baseline_grids:
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# try to see if they are all local
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baseline_grids = glob(os.path.join(inps.baseline_dir,"2*[0-9].vrt"))
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### let the grid take priority
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if baseline_grids:
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baselinegrid(inps)
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elif baseline_files:
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baselinefile(inps)
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