mainALE.py

#!/usr/bin/env python3
# -*- coding: utf-8 -*-
"""
Main function to perform radar reflector analysis using GRTx

R. Czikhardt 
29.7.2020
"""

print('\n')
print('Caroline Radar-Coding Toolbox (based on GECORIS v.1.0)')
print('Copyright (c) 2021 Richard Czikhardt, czikhardt.richard@gmail.com')
print('Dept. of Geosciences and Remote Sensing, Delft University of Technology')
print('-----------------------------------------------------------------------')
print('License: GNU GPL v3+')
print('-----------------------------------------------------------------------')

import sys
import os
import glob
from gecoris import ioUtils, plotUtils, atmoUtils



def main(parms):    
    # unpack:
    stationLog = parms['stationLog']
    stacksLog = parms['stackLog']
    outDir = parms['outDir']
    posFlag = parms['precisePosFlag']
    ovsFactor = parms['ovsFactor']
    atmoFlag = parms['atmoFlag']
    plotFlag = parms['plotFlag']
    #
    print('Initializing reflectors...')
    if stationLog.lower().endswith('.json'):
        stations = ioUtils.load_station_log(stationLog)
    elif stationLog.endswith('.csv'):
        stations = ioUtils.fromCSV(stationLog)
    else:
        print('Unknown station log file format. Use .json or .csv.')
        raise
    STATIONS = stations
    print(f'{len(stations)} stations to process...')
    # prepare atmo. data dir:
    if atmoFlag:
        atmoDir = outDir + os.sep + 'atmo/'
        if not os.path.exists(atmoDir):
            os.makedirs(atmoDir)
    # iterate over every single station
    for i in range(len(STATIONS)):
        stations = STATIONS[i:i+1]
        print(f'***Current station: {stations[0].id}\n')
        print('Loading SAR data stacks...')
        if stacksLog.lower().endswith('.json'):
            stacks = ioUtils.load_stacks(stacksLog)
        elif stacksLog.lower().endswith('.csv'):
            stacks = ioUtils.stacks_fromCSV(stacksLog)
        else:
            print('Unknown stacks log file format. Use .json or .csv.')
        # load data:
        for stack in stacks: 
            stack.readData(stations)
            ioUtils.toJSON(stack, parms['outDir']) # save to JSON
            if atmoFlag:
                print('Preparing atmo. models for stack '+stack.id)
                atmoUtils.prepareAtmo(stack, atmoDir)        
        # check if output directory exists and load already processed:
        if not os.path.exists(outDir):
            os.makedirs(outDir)
            logs = []
        else:
            logs = glob.glob(outDir + os.sep +"*.json")
        #
        print(str(len(stations))+ ' reflectors on ' +str(len(stacks))
                + ' stacks to process.')
        # iterate over list indices to modify objects:
        i=0
        try:
            # check if analysis already performed:
            inJSON = [q for q in logs 
                        if stations[i].id+'.json' in q.split(os.sep)[-1]]
            if inJSON:
                print('Station '+stations[i].id+ ' already analyzed, updating.')
                stations[i] = ioUtils.fromJSON(inJSON[0])
                for stack in stacks:
                    if atmoFlag:
                        stations[i].updateStack(stack, ovsFactor=ovsFactor, 
                                                posFlag=posFlag, atmoDir=atmoDir)
                    else:
                        stations[i].updateStack(stack, ovsFactor=ovsFactor,
                                                posFlag=posFlag)
            else:
                for stack in stacks:
                    if atmoFlag:
                        stations[i].addStack(stack, ovsFactor=ovsFactor, 
                                                posFlag=posFlag, plotFlag=plotFlag,
                                                outDir=outDir+stations[i].id,
                                                atmoDir=atmoDir)
                    else:
                        stations[i].addStack(stack, ovsFactor=ovsFactor, 
                                                posFlag=posFlag, plotFlag=plotFlag,
                                                outDir=outDir+stations[i].id)
            stations[i].print_all_timeseries(outDir)
            print('Removing outliers.')
            stations[i].detectOutliers()
            print('Performing RCS and SCR analysis.')
            stations[i].RCSanalysis()
            if posFlag and plotFlag > 0:
                print('Plotting ALE.')
                for stack in stacks:
                    if atmoFlag:
                        stations[i].plotALE(stack.id,outDir,atmoDir)
                    else:
                        stations[i].plotALE(stack.id,outDir)
                stations[i].plotALE_TS(outDir)
            if plotFlag > 0:
                print('Plotting RCS time series.')
                stations[i].plotRCS(outDir)
            #
            print('Exporting to JSON dumps.')
            stations[i].toJSON(outDir)
            stations[i].statsToJSON(outDir)
        except IndexError as e:
            print(f'skipping station {stations[i].id}... \nThe footprint of the burst selected doesn\'t agree with the real coverage of the SAR data. \nThe burst corresponding needs to be selected manually (possible to hard code it in the function swathburst, in dorisUtils.py)\n')
    stations = STATIONS
    if len(stations) > 2 and plotFlag > 0:
        print('Generating network plots.')
        plotUtils.plotNetworkALE(stations, outDir+os.sep+'network_ALE.png')
        plotUtils.plotNetworkRCS(stations, outDir+os.sep+'network_RCS.png')
        plotUtils.plotNetworkSCR_hz(stations, outDir+os.sep+'network_SCR.png')
    #
    print('Done. Thank you for using GECORIS. Do not forget to reference.')
    print('In case of any inquries, please contact czikhardt.richard@gmail.com')


def parse_parms(parms_file):
    try:
        with open(parms_file,'r') as inp:
            try:
                parms = eval(inp.read())
            except:
                print("Something wrong with parameters file.")
                raise
        return parms
    except:
        print("Specified parameters file not found.")
        raise


if __name__ == "__main__":
    # load parameters:
    if len(sys.argv) > 1:
        parms = parse_parms(sys.argv[1])
        main(parms)
    else:
        print('Not enough input arguments!')