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ISCE_INSAR/contrib/stack/alosStack/ion_filt.py

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new alosStack application
2020-10-20 02:42:07 +00:00
#!/usr/bin/env python3
#
# Author: Cunren Liang
# Copyright 2015-present, NASA-JPL/Caltech
#
import os
import glob
import shutil
import datetime
import numpy as np
import xml.etree.ElementTree as ET
import isce, isceobj
from isceobj.Alos2Proc.runIonFilt import computeIonosphere
from isceobj.Alos2Proc.runIonFilt import gaussian
#from isceobj.Alos2Proc.runIonFilt import least_sqares
from isceobj.Alos2Proc.runIonFilt import polyfit_2d
from isceobj.Alos2Proc.runIonFilt import adaptive_gaussian
from isceobj.Alos2Proc.runIonFilt import reformatMaskedAreas
from StackPulic import loadTrack
from StackPulic import createObject
from StackPulic import stackDateStatistics
from StackPulic import acquisitionModesAlos2
from StackPulic import subbandParameters
from compute_burst_sync import computeBurstSynchronization
def ionFilt(self, referenceTrack, catalog=None):
from isceobj.Alos2Proc.runIonSubband import defineIonDir
ionDir = defineIonDir()
subbandPrefix = ['lower', 'upper']
ionCalDir = os.path.join(ionDir['ion'], ionDir['ionCal'])
os.makedirs(ionCalDir, exist_ok=True)
os.chdir(ionCalDir)
log = ''
############################################################
# STEP 1. compute ionospheric phase
############################################################
from isceobj.Constants import SPEED_OF_LIGHT
from isceobj.Alos2Proc.Alos2ProcPublic import create_xml
###################################
#SET PARAMETERS HERE
#THESE SHOULD BE GOOD ENOUGH, NO NEED TO SET IN setup(self)
corThresholdAdj = 0.97
corOrderAdj = 20
###################################
print('\ncomputing ionosphere')
#get files
ml2 = '_{}rlks_{}alks'.format(self._insar.numberRangeLooks1*self._insar.numberRangeLooksIon,
self._insar.numberAzimuthLooks1*self._insar.numberAzimuthLooksIon)
lowerUnwfile = subbandPrefix[0]+ml2+'.unw'
upperUnwfile = subbandPrefix[1]+ml2+'.unw'
corfile = 'diff'+ml2+'.cor'
#use image size from lower unwrapped interferogram
img = isceobj.createImage()
img.load(lowerUnwfile + '.xml')
width = img.width
length = img.length
lowerUnw = (np.fromfile(lowerUnwfile, dtype=np.float32).reshape(length*2, width))[1:length*2:2, :]
upperUnw = (np.fromfile(upperUnwfile, dtype=np.float32).reshape(length*2, width))[1:length*2:2, :]
cor = (np.fromfile(corfile, dtype=np.float32).reshape(length*2, width))[1:length*2:2, :]
#amp = (np.fromfile(corfile, dtype=np.float32).reshape(length*2, width))[0:length*2:2, :]
#masked out user-specified areas
if self.maskedAreasIon != None:
maskedAreas = reformatMaskedAreas(self.maskedAreasIon, length, width)
for area in maskedAreas:
lowerUnw[area[0]:area[1], area[2]:area[3]] = 0
upperUnw[area[0]:area[1], area[2]:area[3]] = 0
cor[area[0]:area[1], area[2]:area[3]] = 0
#remove possible wired values in coherence
cor[np.nonzero(cor<0)] = 0.0
cor[np.nonzero(cor>1)] = 0.0
#remove water body
wbd = np.fromfile('wbd'+ml2+'.wbd', dtype=np.int8).reshape(length, width)
cor[np.nonzero(wbd==-1)] = 0.0
#remove small values
cor[np.nonzero(cor<corThresholdAdj)] = 0.0
#compute ionosphere
fl = SPEED_OF_LIGHT / self._insar.subbandRadarWavelength[0]
fu = SPEED_OF_LIGHT / self._insar.subbandRadarWavelength[1]
adjFlag = 1
ionos = computeIonosphere(lowerUnw, upperUnw, cor**corOrderAdj, fl, fu, adjFlag, 0)
#dump ionosphere
ionfile = 'ion'+ml2+'.ion'
# ion = np.zeros((length*2, width), dtype=np.float32)
# ion[0:length*2:2, :] = amp
# ion[1:length*2:2, :] = ionos
# ion.astype(np.float32).tofile(ionfile)
# img.filename = ionfile
# img.extraFilename = ionfile + '.vrt'
# img.renderHdr()
ionos.astype(np.float32).tofile(ionfile)
create_xml(ionfile, width, length, 'float')
############################################################
# STEP 2. filter ionospheric phase
############################################################
import scipy.signal as ss
#################################################
#SET PARAMETERS HERE
#fit and filter ionosphere
fit = self.fitIon
filt = self.filtIon
fitAdaptive = self.fitAdaptiveIon
filtSecondary = self.filtSecondaryIon
if (fit == False) and (filt == False):
raise Exception('either fit ionosphere or filt ionosphere should be True when doing ionospheric correction\n')
#filtering window size
size_max = self.filteringWinsizeMaxIon
size_min = self.filteringWinsizeMinIon
size_secondary = self.filteringWinsizeSecondaryIon
if size_min > size_max:
print('\n\nWARNING: minimum window size for filtering ionosphere phase {} > maximum window size {}'.format(size_min, size_max))
print(' re-setting maximum window size to {}\n\n'.format(size_min))
size_max = size_min
if size_secondary % 2 != 1:
size_secondary += 1
print('window size of secondary filtering of ionosphere phase should be odd, window size changed to {}'.format(size_secondary))
#coherence threshold for fitting a polynomial
corThresholdFit = 0.25
#ionospheric phase standard deviation after filtering
std_out0 = self.filterStdIon
#std_out0 = 0.1
#################################################
print('\nfiltering ionosphere')
#input files
ionfile = 'ion'+ml2+'.ion'
#corfile = 'diff'+ml2+'.cor'
corLowerfile = subbandPrefix[0]+ml2+'.cor'
corUpperfile = subbandPrefix[1]+ml2+'.cor'
#output files
ionfiltfile = 'filt_ion'+ml2+'.ion'
stdfiltfile = 'filt_ion'+ml2+'.std'
windowsizefiltfile = 'filt_ion'+ml2+'.win'
#read data
img = isceobj.createImage()
img.load(ionfile + '.xml')
width = img.width
length = img.length
ion = np.fromfile(ionfile, dtype=np.float32).reshape(length, width)
corLower = (np.fromfile(corLowerfile, dtype=np.float32).reshape(length*2, width))[1:length*2:2, :]
corUpper = (np.fromfile(corUpperfile, dtype=np.float32).reshape(length*2, width))[1:length*2:2, :]
cor = (corLower + corUpper) / 2.0
index = np.nonzero(np.logical_or(corLower==0, corUpper==0))
cor[index] = 0
del corLower, corUpper
#masked out user-specified areas
if self.maskedAreasIon != None:
maskedAreas = reformatMaskedAreas(self.maskedAreasIon, length, width)
for area in maskedAreas:
ion[area[0]:area[1], area[2]:area[3]] = 0
cor[area[0]:area[1], area[2]:area[3]] = 0
#remove possible wired values in coherence
cor[np.nonzero(cor<0)] = 0.0
cor[np.nonzero(cor>1)] = 0.0
#remove water body. Not helpful, just leave it here
wbd = np.fromfile('wbd'+ml2+'.wbd', dtype=np.int8).reshape(length, width)
cor[np.nonzero(wbd==-1)] = 0.0
# #applying water body mask here
# waterBodyFile = 'wbd'+ml2+'.wbd'
# if os.path.isfile(waterBodyFile):
# print('applying water body mask to coherence used to compute ionospheric phase')
# wbd = np.fromfile(waterBodyFile, dtype=np.int8).reshape(length, width)
# cor[np.nonzero(wbd!=0)] = 0.00001
#minimize the effect of low coherence pixels
#cor[np.nonzero( (cor<0.85)*(cor!=0) )] = 0.00001
#filt = adaptive_gaussian(ion, cor, size_max, size_min)
#cor**14 should be a good weight to use. 22-APR-2018
#filt = adaptive_gaussian_v0(ion, cor**corOrderFilt, size_max, size_min)
#1. compute number of looks
azimuthBandwidth = 0
for i, frameNumber in enumerate(self._insar.referenceFrames):
for j, swathNumber in enumerate(range(self._insar.startingSwath, self._insar.endingSwath + 1)):
#azimuthBandwidth += 2270.575 * 0.85
azimuthBandwidth += referenceTrack.frames[i].swaths[j].azimuthBandwidth
azimuthBandwidth = azimuthBandwidth / (len(self._insar.referenceFrames)*(self._insar.endingSwath-self._insar.startingSwath+1))
#azimuth number of looks should also apply to burst mode
#assume range bandwidth of subband image is 1/3 of orginal range bandwidth, as in runIonSubband.py!!!
numberOfLooks = referenceTrack.azimuthLineInterval * self._insar.numberAzimuthLooks1*self._insar.numberAzimuthLooksIon / (1.0/azimuthBandwidth) *\
referenceTrack.frames[0].swaths[0].rangeBandwidth / 3.0 / referenceTrack.rangeSamplingRate * self._insar.numberRangeLooks1*self._insar.numberRangeLooksIon
#consider also burst characteristics. In ScanSAR-stripmap interferometry, azimuthBandwidth is from referenceTrack (ScanSAR)
if self._insar.modeCombination in [21, 31]:
numberOfLooks /= 5.0
if self._insar.modeCombination in [22, 32]:
numberOfLooks /= 7.0
if self._insar.modeCombination in [21]:
numberOfLooks *= (self._insar.burstSynchronization/100.0)
#numberOfLooks checked
print('number of looks to be used for computing subband interferogram standard deviation: {}'.format(numberOfLooks))
if catalog is not None:
catalog.addItem('number of looks of subband interferograms', numberOfLooks, 'runIonFilt')
log += 'number of looks of subband interferograms: {}\n'.format(numberOfLooks)
#2. compute standard deviation of the raw ionospheric phase
#f0 same as in runIonSubband.py!!!
def ion_std(fl, fu, numberOfLooks, cor):
'''
compute standard deviation of ionospheric phase
fl: lower band center frequency
fu: upper band center frequency
cor: coherence, must be numpy array
'''
f0 = (fl + fu) / 2.0
interferogramVar = (1.0 - cor**2) / (2.0 * numberOfLooks * cor**2 + (cor==0))
std = fl*fu/f0/(fu**2-fl**2)*np.sqrt(fu**2*interferogramVar+fl**2*interferogramVar)
std[np.nonzero(cor==0)] = 0
return std
std = ion_std(fl, fu, numberOfLooks, cor)
#3. compute minimum filter window size for given coherence and standard deviation of filtered ionospheric phase
cor2 = np.linspace(0.1, 0.9, num=9, endpoint=True)
std2 = ion_std(fl, fu, numberOfLooks, cor2)
std_out2 = np.zeros(cor2.size)
win2 = np.zeros(cor2.size, dtype=np.int32)
for i in range(cor2.size):
for size in range(9, 10001, 2):
#this window must be the same as those used in adaptive_gaussian!!!
gw = gaussian(size, size/2.0, scale=1.0)
scale = 1.0 / np.sum(gw / std2[i]**2)
std_out2[i] = scale * np.sqrt(np.sum(gw**2 / std2[i]**2))
win2[i] = size
if std_out2[i] <= std_out0:
break
print('if ionospheric phase standard deviation <= {} rad, minimum filtering window size required:'.format(std_out0))
print('coherence window size')
print('************************')
for x, y in zip(cor2, win2):
print(' %5.2f %5d'%(x, y))
print()
if catalog is not None:
catalog.addItem('coherence value', cor2, 'runIonFilt')
catalog.addItem('minimum filter window size', win2, 'runIonFilt')
log += 'coherence value: {}\n'.format(cor2)
log += 'minimum filter window size: {}\n'.format(win2)
#4. filter interferogram
#fit ionosphere
if fit:
#prepare weight
wgt = std**2
wgt[np.nonzero(cor<corThresholdFit)] = 0
index = np.nonzero(wgt!=0)
wgt[index] = 1.0/(wgt[index])
#fit
ion_fit, coeff = polyfit_2d(ion, wgt, 2)
ion -= ion_fit * (ion!=0)
#filter the rest of the ionosphere
if filt:
(ion_filt, std_out, window_size_out) = adaptive_gaussian(ion, std, size_min, size_max, std_out0, fit=fitAdaptive)
if filtSecondary:
g2d = gaussian(size_secondary, size_secondary/2.0, scale=1.0)
scale = ss.fftconvolve((ion_filt!=0), g2d, mode='same')
ion_filt = (ion_filt!=0) * ss.fftconvolve(ion_filt, g2d, mode='same') / (scale + (scale==0))
if catalog is not None:
catalog.addItem('standard deviation of filtered ionospheric phase', std_out0, 'runIonFilt')
log += 'standard deviation of filtered ionospheric phase: {}\n'.format(std_out0)
#get final results
if (fit == True) and (filt == True):
ion_final = ion_filt + ion_fit * (ion_filt!=0)
elif (fit == True) and (filt == False):
ion_final = ion_fit
elif (fit == False) and (filt == True):
ion_final = ion_filt
else:
ion_final = ion
#output results
ion_final.astype(np.float32).tofile(ionfiltfile)
create_xml(ionfiltfile, width, length, 'float')
if filt == True:
std_out.astype(np.float32).tofile(stdfiltfile)
create_xml(stdfiltfile, width, length, 'float')
window_size_out.astype(np.float32).tofile(windowsizefiltfile)
create_xml(windowsizefiltfile, width, length, 'float')
os.chdir('../../')
return log
def cmdLineParse():
'''
command line parser.
'''
import sys
import argparse
parser = argparse.ArgumentParser(description='unwrap subband interferograms for ionospheric correction')
parser.add_argument('-idir', dest='idir', type=str, required=True,
help = 'input directory where resampled data of each date (YYMMDD) is located. only folders are recognized')
parser.add_argument('-idir2', dest='idir2', type=str, required=True,
help = 'input directory where original data of each date (YYMMDD) is located. only folders are recognized')
parser.add_argument('-ref_date_stack', dest='ref_date_stack', type=str, required=True,
help = 'reference date of stack. format: YYMMDD')
parser.add_argument('-ref_date', dest='ref_date', type=str, required=True,
help = 'reference date of this pair. format: YYMMDD')
parser.add_argument('-sec_date', dest='sec_date', type=str, required=True,
help = 'reference date of this pair. format: YYMMDD')
parser.add_argument('-nrlks1', dest='nrlks1', type=int, default=1,
help = 'number of range looks 1. default: 1')
parser.add_argument('-nalks1', dest='nalks1', type=int, default=1,
help = 'number of azimuth looks 1. default: 1')
parser.add_argument('-nrlks2', dest='nrlks2', type=int, default=1,
help = 'number of range looks 2. default: 1')
parser.add_argument('-nalks2', dest='nalks2', type=int, default=1,
help = 'number of azimuth looks 2. default: 1')
parser.add_argument('-nrlks_ion', dest='nrlks_ion', type=int, default=1,
help = 'number of range looks ion. default: 1')
parser.add_argument('-nalks_ion', dest='nalks_ion', type=int, default=1,
help = 'number of azimuth looks ion. default: 1')
parser.add_argument('-fit', dest='fit', action='store_true', default=False,
help='apply polynomial fit before filtering ionosphere phase')
parser.add_argument('-filt', dest='filt', action='store_true', default=False,
help='filtering ionosphere phase')
parser.add_argument('-fit_adaptive', dest='fit_adaptive', action='store_true', default=False,
help='apply polynomial fit in adaptive filtering window')
parser.add_argument('-filt_secondary', dest='filt_secondary', action='store_true', default=False,
help='secondary filtering of ionosphere phase')
parser.add_argument('-win_min', dest='win_min', type=int, default=11,
help = 'minimum filtering window size. default: 11')
parser.add_argument('-win_max', dest='win_max', type=int, default=301,
help = 'maximum filtering window size. default: 301')
parser.add_argument('-win_secondary', dest='win_secondary', type=int, default=5,
help = 'secondary filtering window size. default: 5')
parser.add_argument('-filter_std_ion', dest='filter_std_ion', type=float, default=None,
help = 'standard deviation after ionosphere filtering. default: None, automatically set by the program')
Update ion_filt.py minor update
2020-11-15 09:00:27 +00:00
parser.add_argument('-masked_areas', dest='masked_areas', type=int, nargs='+', action='append', default=None,
new alosStack application
2020-10-20 02:42:07 +00:00
help='This is a 2-d list. Each element in the 2-D list is a four-element list: [firstLine, lastLine, firstColumn, lastColumn], with line/column numbers starting with 1. If one of the four elements is specified with -1, the program will use firstLine/lastLine/firstColumn/lastColumn instead. e.g. two areas masked out: -masked_areas 10 20 10 20 -masked_areas 110 120 110 120')
if len(sys.argv) <= 1:
print('')
parser.print_help()
sys.exit(1)
else:
return parser.parse_args()
if __name__ == '__main__':
inps = cmdLineParse()
#get user parameters from input
idir = inps.idir
idir2 = inps.idir2
dateReferenceStack = inps.ref_date_stack
dateReference = inps.ref_date
dateSecondary = inps.sec_date
numberRangeLooks1 = inps.nrlks1
numberAzimuthLooks1 = inps.nalks1
numberRangeLooks2 = inps.nrlks2
numberAzimuthLooks2 = inps.nalks2
numberRangeLooksIon = inps.nrlks_ion
numberAzimuthLooksIon = inps.nalks_ion
fitIon = inps.fit
filtIon = inps.filt
fitAdaptiveIon = inps.fit_adaptive
filtSecondaryIon = inps.filt_secondary
filteringWinsizeMinIon = inps.win_min
filteringWinsizeMaxIon = inps.win_max
filteringWinsizeSecondaryIon = inps.win_secondary
filterStdIon = inps.filter_std_ion
maskedAreasIon = inps.masked_areas
#######################################################
pair = '{}-{}'.format(dateReference, dateSecondary)
ms = pair
ml1 = '_{}rlks_{}alks'.format(numberRangeLooks1, numberAzimuthLooks1)
ml2 = '_{}rlks_{}alks'.format(numberRangeLooks1*numberRangeLooks2, numberAzimuthLooks1*numberAzimuthLooks2)
dateDirs, dates, frames, swaths, dateIndexReference = stackDateStatistics(idir, dateReferenceStack)
dateDirs2, dates2, frames2, swaths2, dateIndexReference2 = stackDateStatistics(idir2, dateReferenceStack)
spotlightModes, stripmapModes, scansarNominalModes, scansarWideModes, scansarModes = acquisitionModesAlos2()
trackReferenceStack = loadTrack(os.path.join(idir, dateReferenceStack), dateReferenceStack)
trackReference = loadTrack(os.path.join(idir2, dateReference), dateReference)
trackSecondary = loadTrack(os.path.join(idir2, dateSecondary), dateSecondary)
subbandRadarWavelength, subbandBandWidth, subbandFrequencyCenter, subbandPrefix = subbandParameters(trackReferenceStack)
self = createObject()
self._insar = createObject()
self._insar.numberRangeLooks1 = numberRangeLooks1
self._insar.numberAzimuthLooks1 = numberAzimuthLooks1
self._insar.numberRangeLooks2 = numberRangeLooks2
self._insar.numberAzimuthLooks2 = numberAzimuthLooks2
self._insar.numberRangeLooksIon = numberRangeLooksIon
self._insar.numberAzimuthLooksIon = numberAzimuthLooksIon
self.fitIon = fitIon
self.filtIon = filtIon
self.fitAdaptiveIon = fitAdaptiveIon
self.filtSecondaryIon = filtSecondaryIon
self.filteringWinsizeMaxIon = filteringWinsizeMaxIon
self.filteringWinsizeMinIon = filteringWinsizeMinIon
self.filteringWinsizeSecondaryIon = filteringWinsizeSecondaryIon
self.maskedAreasIon = maskedAreasIon
self.applyIon = False
#ionospheric phase standard deviation after filtering
if filterStdIon is not None:
self.filterStdIon = filterStdIon
else:
if trackReference.operationMode == trackSecondary.operationMode:
from isceobj.Alos2Proc.Alos2ProcPublic import modeProcParDict
self.filterStdIon = modeProcParDict['ALOS-2'][trackReference.operationMode]['filterStdIon']
else:
from isceobj.Alos2Proc.Alos2ProcPublic import filterStdPolyIon
self.filterStdIon = np.polyval(filterStdPolyIon, trackReference.frames[0].swaths[0].rangeBandwidth/(1e6))
self._insar.referenceFrames = frames
self._insar.startingSwath = swaths[0]
self._insar.endingSwath = swaths[-1]
self._insar.subbandRadarWavelength = subbandRadarWavelength
self._insar.multilookIon = ms + ml2 + '.ion'
self._insar.multilookDifferentialInterferogram = 'diff_' + ms + ml2 + '.int'
self._insar.multilookDifferentialInterferogramOriginal = 'diff_' + ms + ml2 + '_ori.int'
#usable combinations
referenceMode = trackReference.operationMode
secondaryMode = trackSecondary.operationMode
if (referenceMode in spotlightModes) and (secondaryMode in spotlightModes):
self._insar.modeCombination = 0
elif (referenceMode in stripmapModes) and (secondaryMode in stripmapModes):
self._insar.modeCombination = 1
elif (referenceMode in scansarNominalModes) and (secondaryMode in scansarNominalModes):
self._insar.modeCombination = 21
elif (referenceMode in scansarWideModes) and (secondaryMode in scansarWideModes):
self._insar.modeCombination = 22
elif (referenceMode in scansarNominalModes) and (secondaryMode in stripmapModes):
self._insar.modeCombination = 31
elif (referenceMode in scansarWideModes) and (secondaryMode in stripmapModes):
self._insar.modeCombination = 32
else:
print('\n\nthis mode combination is not possible')
print('note that for ScanSAR-stripmap, ScanSAR must be reference\n\n')
raise Exception('mode combination not supported')
if self._insar.modeCombination in [21]:
unsynTimeAll, synPercentageAll = computeBurstSynchronization(trackReference, trackSecondary)
self._insar.burstSynchronization = np.mean(np.array(synPercentageAll), dtype=np.float64)
else:
self._insar.burstSynchronization = 100.0
#log output info
log = '{} at {}\n'.format(os.path.basename(__file__), datetime.datetime.now())
log += '================================================================================================\n'
log += ionFilt(self, trackReferenceStack)
log += '\n'
logFile = 'process.log'
with open(logFile, 'a') as f:
f.write(log)