def runFilt(self):
'''filter interferogram
'''
catalog = isceobj.Catalog.createCatalog(self._insar.procDoc.name)
self.updateParamemetersFromUser()
#masterTrack = self._insar.loadTrack(master=True)
#slaveTrack = self._insar.loadTrack(master=False)
insarDir = 'insar'
os.makedirs(insarDir, exist_ok=True)
os.chdir(insarDir)
############################################################
# STEP 1. filter interferogram
############################################################
print('\nfilter interferogram: {}'.format(
self._insar.multilookDifferentialInterferogram))
toBeFiltered = self._insar.multilookDifferentialInterferogram
if self.removeMagnitudeBeforeFiltering:
toBeFiltered = 'tmp.int'
cmd = "imageMath.py -e='a/(abs(a)+(a==0))' --a={} -o {} -t cfloat -s BSQ".format(
self._insar.multilookDifferentialInterferogram, toBeFiltered)
runCmd(cmd)
#if shutil.which('psfilt1') != None:
if True:
intImage = isceobj.createIntImage()
intImage.load(toBeFiltered + '.xml')
width = intImage.width
length = intImage.length
# cmd = "psfilt1 {int} {filtint} {width} {filterstrength} 64 16".format(
# int = toBeFiltered,
# filtint = self._insar.filteredInterferogram,
# width = width,
# filterstrength = self.filterStrength
# )
# runCmd(cmd)
windowSize = self.filterWinsize
stepSize = self.filterStepsize
psfilt1(toBeFiltered, self._insar.filteredInterferogram, width,
self.filterStrength, windowSize, stepSize)
create_xml(self._insar.filteredInterferogram, width, length, 'int')
else:
#original
intImage = isceobj.createIntImage()
intImage.load(toBeFiltered + '.xml')
intImage.setAccessMode('read')
intImage.createImage()
width = intImage.width
length = intImage.length
#filtered
filtImage = isceobj.createIntImage()
filtImage.setFilename(self._insar.filteredInterferogram)
filtImage.setWidth(width)
filtImage.setAccessMode('write')
filtImage.createImage()
#looks like the ps filtering program keep the original interferogram magnitude, which is bad for phase unwrapping?
filters = Filter()
filters.wireInputPort(name='interferogram', object=intImage)
filters.wireOutputPort(name='filtered interferogram', object=filtImage)
filters.goldsteinWerner(alpha=self.filterStrength)
intImage.finalizeImage()
filtImage.finalizeImage()
del intImage, filtImage, filters
if self.removeMagnitudeBeforeFiltering:
os.remove(toBeFiltered)
os.remove(toBeFiltered + '.vrt')
os.remove(toBeFiltered + '.xml')
#restore original magnitude
tmpFile = 'tmp.int'
renameFile(self._insar.filteredInterferogram, tmpFile)
cmd = "imageMath.py -e='a*abs(b)' --a={} --b={} -o {} -t cfloat -s BSQ".format(
tmpFile, self._insar.multilookDifferentialInterferogram,
self._insar.filteredInterferogram)
runCmd(cmd)
os.remove(tmpFile)
os.remove(tmpFile + '.vrt')
os.remove(tmpFile + '.xml')
############################################################
# STEP 2. create phase sigma using filtered interferogram
############################################################
print('\ncreate phase sigma using: {}'.format(
self._insar.filteredInterferogram))
#recreate filtered image
filtImage = isceobj.createIntImage()
filtImage.load(self._insar.filteredInterferogram + '.xml')
filtImage.setAccessMode('read')
filtImage.createImage()
#amplitude image
ampImage = isceobj.createAmpImage()
ampImage.load(self._insar.multilookAmplitude + '.xml')
ampImage.setAccessMode('read')
ampImage.createImage()
#phase sigma correlation image
phsigImage = isceobj.createImage()
phsigImage.setFilename(self._insar.multilookPhsig)
phsigImage.setWidth(width)
phsigImage.dataType = 'FLOAT'
phsigImage.bands = 1
phsigImage.setImageType('cor')
phsigImage.setAccessMode('write')
phsigImage.createImage()
icu = Icu(name='insarapp_filter_icu')
icu.configure()
icu.unwrappingFlag = False
icu.icu(intImage=filtImage, ampImage=ampImage, phsigImage=phsigImage)
phsigImage.renderHdr()
filtImage.finalizeImage()
ampImage.finalizeImage()
phsigImage.finalizeImage()
del filtImage
del ampImage
del phsigImage
del icu
############################################################
# STEP 3. mask filtered interferogram using water body
############################################################
print('\nmask filtered interferogram using: {}'.format(
self._insar.multilookWbdOut))
if self.waterBodyMaskStartingStep == 'filt':
if not os.path.exists(self._insar.multilookWbdOut):
catalog.addItem(
'warning message',
'requested masking interferogram with water body, but water body does not exist',
'runFilt')
else:
wbd = np.fromfile(self._insar.multilookWbdOut,
dtype=np.int8).reshape(length, width)
phsig = np.memmap(self._insar.multilookPhsig,
dtype='float32',
mode='r+',
shape=(length, width))
phsig[np.nonzero(wbd == -1)] = 0
del phsig
filt = np.memmap(self._insar.filteredInterferogram,
dtype='complex64',
mode='r+',
shape=(length, width))
filt[np.nonzero(wbd == -1)] = 0
del filt
del wbd
os.chdir('../')
catalog.printToLog(logger, "runFilt")
self._insar.procDoc.addAllFromCatalog(catalog)
#os.makedirs(insarDir, exist_ok=True)
os.chdir(insarDir)
if not os.path.isfile(ionosphereReference):
raise Exception(
'ionospheric phase file: {} of reference date does not exist in {}.\n'
.format(os.path.basename(ionosphereReference), ion_dir))
if not os.path.isfile(ionosphereSecondary):
raise Exception(
'ionospheric phase file: {} of secondary date does not exist in {}.\n'
.format(os.path.basename(ionosphereSecondary), ion_dir))
#correct interferogram
if os.path.isfile(multilookDifferentialInterferogramOriginal):
print('original interferogram: {} is already here, do not rename: {}'.
format(multilookDifferentialInterferogramOriginal,
multilookDifferentialInterferogram))
else:
print('renaming {} to {}'.format(
multilookDifferentialInterferogram,
multilookDifferentialInterferogramOriginal))
renameFile(multilookDifferentialInterferogram,
multilookDifferentialInterferogramOriginal)
cmd = "imageMath.py -e='a*exp(-1.0*J*(b-c))' --a={} --b={} --c={} -s BIP -t cfloat -o {}".format(
multilookDifferentialInterferogramOriginal, ionosphereReference,
ionosphereSecondary, multilookDifferentialInterferogram)
runCmd(cmd)
os.chdir('../')
def runIonFilt(self):
'''compute and filter ionospheric phase
'''
catalog = isceobj.Catalog.createCatalog(self._insar.procDoc.name)
self.updateParamemetersFromUser()
if not self.doIon:
catalog.printToLog(logger, "runIonFilt")
self._insar.procDoc.addAllFromCatalog(catalog)
return
masterTrack = self._insar.loadTrack(master=True)
slaveTrack = self._insar.loadTrack(master=False)
from isceobj.Alos2Proc.runIonSubband import defineIonDir
ionDir = defineIonDir()
subbandPrefix = ['lower', 'upper']
ionCalDir = os.path.join(ionDir['ion'], ionDir['ionCal'])
if not os.path.exists(ionCalDir):
os.makedirs(ionCalDir)
os.chdir(ionCalDir)
############################################################
# 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 = 0.85
###################################
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
#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, fl, fu, adjFlag, corThresholdAdj, 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
############################################################
#################################################
#SET PARAMETERS HERE
#if applying polynomial fitting
#False: no fitting, True: with fitting
fit = self.fitIon
#gaussian filtering window size
size_max = self.filteringWinsizeMaxIon
size_min = self.filteringWinsizeMinIon
#THESE SHOULD BE GOOD ENOUGH, NO NEED TO SET IN setup(self)
corThresholdIon = 0.85
#################################################
print('\nfiltering ionosphere')
ionfile = 'ion'+ml2+'.ion'
corfile = 'diff'+ml2+'.cor'
ionfiltfile = 'filt_ion'+ml2+'.ion'
img = isceobj.createImage()
img.load(ionfile + '.xml')
width = img.width
length = img.length
#ion = (np.fromfile(ionfile, dtype=np.float32).reshape(length*2, width))[1:length*2:2, :]
ion = np.fromfile(ionfile, dtype=np.float32).reshape(length, width)
cor = (np.fromfile(corfile, dtype=np.float32).reshape(length*2, width))[1:length*2:2, :]
#amp = (np.fromfile(ionfile, 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:
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
# #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
if fit:
ion_fit = weight_fitting(ion, cor, width, length, 1, 1, 1, 1, 2, corThresholdIon)
ion -= ion_fit * (ion!=0)
#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(ion, cor**14, size_max, size_min)
if fit:
filt += ion_fit * (filt!=0)
# ion = np.zeros((length*2, width), dtype=np.float32)
# ion[0:length*2:2, :] = amp
# ion[1:length*2:2, :] = filt
# ion.astype(np.float32).tofile(ionfiltfile)
# img.filename = ionfiltfile
# img.extraFilename = ionfiltfile + '.vrt'
# img.renderHdr()
filt.astype(np.float32).tofile(ionfiltfile)
create_xml(ionfiltfile, width, length, 'float')
############################################################
# STEP 3. resample ionospheric phase
############################################################
from contrib.alos2proc_f.alos2proc_f import rect
from isceobj.Alos2Proc.Alos2ProcPublic import create_xml
from scipy.interpolate import interp1d
import shutil
#################################################
#SET PARAMETERS HERE
#interpolation method
interpolationMethod = 1
#################################################
print('\ninterpolate ionosphere')
ml3 = '_{}rlks_{}alks'.format(self._insar.numberRangeLooks1*self._insar.numberRangeLooks2,
self._insar.numberAzimuthLooks1*self._insar.numberAzimuthLooks2)
ionfiltfile = 'filt_ion'+ml2+'.ion'
#ionrectfile = 'filt_ion'+ml3+'.ion'
ionrectfile = self._insar.multilookIon
img = isceobj.createImage()
img.load(ionfiltfile + '.xml')
width2 = img.width
length2 = img.length
img = isceobj.createImage()
img.load(os.path.join('../../', ionDir['insar'], self._insar.multilookDifferentialInterferogram) + '.xml')
width3 = img.width
length3 = img.length
#number of range looks output
nrlo = self._insar.numberRangeLooks1*self._insar.numberRangeLooks2
#number of range looks input
nrli = self._insar.numberRangeLooks1*self._insar.numberRangeLooksIon
#number of azimuth looks output
nalo = self._insar.numberAzimuthLooks1*self._insar.numberAzimuthLooks2
#number of azimuth looks input
nali = self._insar.numberAzimuthLooks1*self._insar.numberAzimuthLooksIon
if (self._insar.numberRangeLooks2 != self._insar.numberRangeLooksIon) or \
(self._insar.numberAzimuthLooks2 != self._insar.numberAzimuthLooksIon):
#this should be faster using fortran
if interpolationMethod == 0:
rect(ionfiltfile, ionrectfile,
width2,length2,
width3,length3,
nrlo/nrli, 0.0,
0.0, nalo/nali,
(nrlo-nrli)/(2.0*nrli),
(nalo-nali)/(2.0*nali),
'REAL','Bilinear')
#finer, but slower method
else:
ionfilt = np.fromfile(ionfiltfile, dtype=np.float32).reshape(length2, width2)
index2 = np.linspace(0, width2-1, num=width2, endpoint=True)
index3 = np.linspace(0, width3-1, num=width3, endpoint=True) * nrlo/nrli + (nrlo-nrli)/(2.0*nrli)
ionrect = np.zeros((length3, width3), dtype=np.float32)
for i in range(length2):
f = interp1d(index2, ionfilt[i,:], kind='cubic', fill_value="extrapolate")
ionrect[i, :] = f(index3)
index2 = np.linspace(0, length2-1, num=length2, endpoint=True)
index3 = np.linspace(0, length3-1, num=length3, endpoint=True) * nalo/nali + (nalo-nali)/(2.0*nali)
for j in range(width3):
f = interp1d(index2, ionrect[0:length2, j], kind='cubic', fill_value="extrapolate")
ionrect[:, j] = f(index3)
ionrect.astype(np.float32).tofile(ionrectfile)
del ionrect
create_xml(ionrectfile, width3, length3, 'float')
os.rename(ionrectfile, os.path.join('../../insar', ionrectfile))
os.rename(ionrectfile+'.vrt', os.path.join('../../insar', ionrectfile)+'.vrt')
os.rename(ionrectfile+'.xml', os.path.join('../../insar', ionrectfile)+'.xml')
os.chdir('../../insar')
else:
shutil.copyfile(ionfiltfile, os.path.join('../../insar', ionrectfile))
os.chdir('../../insar')
create_xml(ionrectfile, width3, length3, 'float')
#now we are in 'insar'
############################################################
# STEP 4. correct interferogram
############################################################
from isceobj.Alos2Proc.Alos2ProcPublic import renameFile
from isceobj.Alos2Proc.Alos2ProcPublic import runCmd
if self.applyIon:
print('\ncorrect interferogram')
if os.path.isfile(self._insar.multilookDifferentialInterferogramOriginal):
print('original interferogram: {} is already here, do not rename: {}'.format(self._insar.multilookDifferentialInterferogramOriginal, self._insar.multilookDifferentialInterferogram))
else:
print('renaming {} to {}'.format(self._insar.multilookDifferentialInterferogram, self._insar.multilookDifferentialInterferogramOriginal))
renameFile(self._insar.multilookDifferentialInterferogram, self._insar.multilookDifferentialInterferogramOriginal)
cmd = "imageMath.py -e='a*exp(-1.0*J*b)' --a={} --b={} -s BIP -t cfloat -o {}".format(
self._insar.multilookDifferentialInterferogramOriginal,
self._insar.multilookIon,
self._insar.multilookDifferentialInterferogram)
runCmd(cmd)
else:
print('\nionospheric phase estimation finished, but correction of interfeorgram not requested')
os.chdir('../')
catalog.printToLog(logger, "runIonFilt")
self._insar.procDoc.addAllFromCatalog(catalog)
def runIonCorrect(self):
'''resample original ionosphere and ionospheric correction
'''
if hasattr(self, 'doInSAR'):
if not self.doInSAR:
return
catalog = isceobj.Catalog.createCatalog(self._insar.procDoc.name)
self.updateParamemetersFromUser()
if not self.doIon:
catalog.printToLog(logger, "runIonCorrect")
self._insar.procDoc.addAllFromCatalog(catalog)
return
referenceTrack = self._insar.loadTrack(reference=True)
secondaryTrack = self._insar.loadTrack(reference=False)
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)
############################################################
# STEP 3. resample ionospheric phase
############################################################
from contrib.alos2proc_f.alos2proc_f import rect
from isceobj.Alos2Proc.Alos2ProcPublic import create_xml
from scipy.interpolate import interp1d
import shutil
#################################################
#SET PARAMETERS HERE
#interpolation method
interpolationMethod = 1
#################################################
print('\ninterpolate ionosphere')
ml2 = '_{}rlks_{}alks'.format(
self._insar.numberRangeLooks1 * self._insar.numberRangeLooksIon,
self._insar.numberAzimuthLooks1 * self._insar.numberAzimuthLooksIon)
ml3 = '_{}rlks_{}alks'.format(
self._insar.numberRangeLooks1 * self._insar.numberRangeLooks2,
self._insar.numberAzimuthLooks1 * self._insar.numberAzimuthLooks2)
ionfiltfile = 'filt_ion' + ml2 + '.ion'
#ionrectfile = 'filt_ion'+ml3+'.ion'
ionrectfile = self._insar.multilookIon
img = isceobj.createImage()
img.load(ionfiltfile + '.xml')
width2 = img.width
length2 = img.length
img = isceobj.createImage()
img.load(
os.path.join('../../', ionDir['insar'],
self._insar.multilookDifferentialInterferogram) + '.xml')
width3 = img.width
length3 = img.length
#number of range looks output
nrlo = self._insar.numberRangeLooks1 * self._insar.numberRangeLooks2
#number of range looks input
nrli = self._insar.numberRangeLooks1 * self._insar.numberRangeLooksIon
#number of azimuth looks output
nalo = self._insar.numberAzimuthLooks1 * self._insar.numberAzimuthLooks2
#number of azimuth looks input
nali = self._insar.numberAzimuthLooks1 * self._insar.numberAzimuthLooksIon
if (self._insar.numberRangeLooks2 != self._insar.numberRangeLooksIon) or \
(self._insar.numberAzimuthLooks2 != self._insar.numberAzimuthLooksIon):
#this should be faster using fortran
if interpolationMethod == 0:
rect(ionfiltfile, ionrectfile, width2, length2, width3, length3,
nrlo / nrli, 0.0, 0.0, nalo / nali,
(nrlo - nrli) / (2.0 * nrli), (nalo - nali) / (2.0 * nali),
'REAL', 'Bilinear')
#finer, but slower method
else:
ionfilt = np.fromfile(ionfiltfile,
dtype=np.float32).reshape(length2, width2)
index2 = np.linspace(0, width2 - 1, num=width2, endpoint=True)
index3 = np.linspace(0, width3 - 1, num=width3, endpoint=True
) * nrlo / nrli + (nrlo - nrli) / (2.0 * nrli)
ionrect = np.zeros((length3, width3), dtype=np.float32)
for i in range(length2):
f = interp1d(index2,
ionfilt[i, :],
kind='cubic',
fill_value="extrapolate")
ionrect[i, :] = f(index3)
index2 = np.linspace(0, length2 - 1, num=length2, endpoint=True)
index3 = np.linspace(0, length3 - 1, num=length3, endpoint=True
) * nalo / nali + (nalo - nali) / (2.0 * nali)
for j in range(width3):
f = interp1d(index2,
ionrect[0:length2, j],
kind='cubic',
fill_value="extrapolate")
ionrect[:, j] = f(index3)
ionrect.astype(np.float32).tofile(ionrectfile)
del ionrect
create_xml(ionrectfile, width3, length3, 'float')
os.rename(ionrectfile, os.path.join('../../insar', ionrectfile))
os.rename(ionrectfile + '.vrt',
os.path.join('../../insar', ionrectfile) + '.vrt')
os.rename(ionrectfile + '.xml',
os.path.join('../../insar', ionrectfile) + '.xml')
os.chdir('../../insar')
else:
shutil.copyfile(ionfiltfile, os.path.join('../../insar', ionrectfile))
os.chdir('../../insar')
create_xml(ionrectfile, width3, length3, 'float')
#now we are in 'insar'
############################################################
# STEP 4. correct interferogram
############################################################
from isceobj.Alos2Proc.Alos2ProcPublic import renameFile
from isceobj.Alos2Proc.Alos2ProcPublic import runCmd
if self.applyIon:
print('\ncorrect interferogram')
if os.path.isfile(
self._insar.multilookDifferentialInterferogramOriginal):
print(
'original interferogram: {} is already here, do not rename: {}'
.format(self._insar.multilookDifferentialInterferogramOriginal,
self._insar.multilookDifferentialInterferogram))
else:
print('renaming {} to {}'.format(
self._insar.multilookDifferentialInterferogram,
self._insar.multilookDifferentialInterferogramOriginal))
renameFile(self._insar.multilookDifferentialInterferogram,
self._insar.multilookDifferentialInterferogramOriginal)
cmd = "imageMath.py -e='a*exp(-1.0*J*b)' --a={} --b={} -s BIP -t cfloat -o {}".format(
self._insar.multilookDifferentialInterferogramOriginal,
self._insar.multilookIon,
self._insar.multilookDifferentialInterferogram)
runCmd(cmd)
else:
print(
'\nionospheric phase estimation finished, but correction of interfeorgram not requested'
)
os.chdir('../')
catalog.printToLog(logger, "runIonCorrect")
self._insar.procDoc.addAllFromCatalog(catalog)