def runUnwrapSnaphu(self):
'''unwrap filtered 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. unwrap interferogram
############################################################
if shutil.which('snaphu') != None:
print('\noriginal snaphu program found')
print(
'unwrap {} using original snaphu, rather than that in ISCE'.format(
self._insar.filteredInterferogram))
snaphuUnwrapOriginal(self._insar.filteredInterferogram,
self._insar.multilookPhsig,
self._insar.multilookAmplitude,
self._insar.unwrappedInterferogram,
costMode='s',
initMethod='mcf')
else:
tmid = masterTrack.sensingStart + datetime.timedelta(
seconds=(self._insar.numberAzimuthLooks1 - 1.0) / 2.0 *
masterTrack.azimuthLineInterval + masterTrack.numberOfLines / 2.0 *
self._insar.numberAzimuthLooks1 * masterTrack.azimuthLineInterval)
snaphuUnwrap(
masterTrack,
tmid,
self._insar.filteredInterferogram,
self._insar.multilookPhsig,
self._insar.unwrappedInterferogram,
self._insar.numberRangeLooks1 * self._insar.numberRangeLooks2,
self._insar.numberAzimuthLooks1 * self._insar.numberAzimuthLooks2,
costMode='SMOOTH',
initMethod='MCF',
defomax=2,
initOnly=True)
############################################################
# STEP 2. mask using connected components
############################################################
cmd = "imageMath.py -e='a_0*(b>0);a_1*(b>0)' --a={} --b={} -s BIL -t float -o={}".format(
self._insar.unwrappedInterferogram,
self._insar.unwrappedInterferogram + '.conncomp',
self._insar.unwrappedMaskedInterferogram)
runCmd(cmd)
############################################################
# STEP 3. mask using water body
############################################################
if self.waterBodyMaskStartingStep == 'unwrap':
wbdImage = isceobj.createImage()
wbdImage.load(self._insar.multilookWbdOut + '.xml')
width = wbdImage.width
length = wbdImage.length
if not os.path.exists(self._insar.multilookWbdOut):
catalog.addItem(
'warning message',
'requested masking interferogram with water body, but water body does not exist',
'runUnwrapSnaphu')
else:
wbd = np.fromfile(self._insar.multilookWbdOut,
dtype=np.int8).reshape(length, width)
unw = np.memmap(self._insar.unwrappedInterferogram,
dtype='float32',
mode='r+',
shape=(length * 2, width))
(unw[0:length * 2:2, :])[np.nonzero(wbd == -1)] = 0
(unw[1:length * 2:2, :])[np.nonzero(wbd == -1)] = 0
del unw
unw = np.memmap(self._insar.unwrappedMaskedInterferogram,
dtype='float32',
mode='r+',
shape=(length * 2, width))
(unw[0:length * 2:2, :])[np.nonzero(wbd == -1)] = 0
(unw[1:length * 2:2, :])[np.nonzero(wbd == -1)] = 0
del unw, wbd
os.chdir('../')
catalog.printToLog(logger, "runUnwrapSnaphu")
self._insar.procDoc.addAllFromCatalog(catalog)
def runIonUwrap(self):
'''unwrap subband interferograms
'''
catalog = isceobj.Catalog.createCatalog(self._insar.procDoc.name)
self.updateParamemetersFromUser()
if not self.doIon:
catalog.printToLog(logger, "runIonUwrap")
self._insar.procDoc.addAllFromCatalog(catalog)
return
referenceTrack = self._insar.loadTrack(reference=True)
secondaryTrack = self._insar.loadTrack(reference=False)
wbdFile = os.path.abspath(self._insar.wbd)
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 1. take looks
############################################################
from isceobj.Alos2Proc.Alos2ProcPublic import create_xml
from contrib.alos2proc.alos2proc import look
from isceobj.Alos2Proc.Alos2ProcPublic import waterBodyRadar
ml2 = '_{}rlks_{}alks'.format(self._insar.numberRangeLooks1*self._insar.numberRangeLooksIon,
self._insar.numberAzimuthLooks1*self._insar.numberAzimuthLooksIon)
for k in range(2):
fullbandDir = os.path.join('../../', ionDir['insar'])
subbandDir = os.path.join('../', ionDir['subband'][k], ionDir['insar'])
prefix = subbandPrefix[k]
amp = isceobj.createImage()
amp.load(os.path.join(subbandDir, self._insar.amplitude)+'.xml')
width = amp.width
length = amp.length
width2 = int(width / self._insar.numberRangeLooksIon)
length2 = int(length / self._insar.numberAzimuthLooksIon)
#take looks
look(os.path.join(subbandDir, self._insar.differentialInterferogram), prefix+ml2+'.int', width, self._insar.numberRangeLooksIon, self._insar.numberAzimuthLooksIon, 4, 0, 1)
create_xml(prefix+ml2+'.int', width2, length2, 'int')
look(os.path.join(subbandDir, self._insar.amplitude), prefix+ml2+'.amp', width, self._insar.numberRangeLooksIon, self._insar.numberAzimuthLooksIon, 4, 1, 1)
create_xml(prefix+ml2+'.amp', width2, length2, 'amp')
# #water body
# if k == 0:
# wbdOutFile = os.path.join(fullbandDir, self._insar.wbdOut)
# if os.path.isfile(wbdOutFile):
# look(wbdOutFile, 'wbd'+ml2+'.wbd', width, self._insar.numberRangeLooksIon, self._insar.numberAzimuthLooksIon, 0, 0, 1)
# create_xml('wbd'+ml2+'.wbd', width2, length2, 'byte')
#water body
if k == 0:
look(os.path.join(fullbandDir, self._insar.latitude), 'lat'+ml2+'.lat', width, self._insar.numberRangeLooksIon, self._insar.numberAzimuthLooksIon, 3, 0, 1)
look(os.path.join(fullbandDir, self._insar.longitude), 'lon'+ml2+'.lon', width, self._insar.numberRangeLooksIon, self._insar.numberAzimuthLooksIon, 3, 0, 1)
create_xml('lat'+ml2+'.lat', width2, length2, 'double')
create_xml('lon'+ml2+'.lon', width2, length2, 'double')
waterBodyRadar('lat'+ml2+'.lat', 'lon'+ml2+'.lon', wbdFile, 'wbd'+ml2+'.wbd')
############################################################
# STEP 2. compute coherence
############################################################
from isceobj.Alos2Proc.Alos2ProcPublic import cal_coherence
lowerbandInterferogramFile = subbandPrefix[0]+ml2+'.int'
upperbandInterferogramFile = subbandPrefix[1]+ml2+'.int'
lowerbandAmplitudeFile = subbandPrefix[0]+ml2+'.amp'
upperbandAmplitudeFile = subbandPrefix[1]+ml2+'.amp'
lowerbandCoherenceFile = subbandPrefix[0]+ml2+'.cor'
upperbandCoherenceFile = subbandPrefix[1]+ml2+'.cor'
coherenceFile = 'diff'+ml2+'.cor'
lowerint = np.fromfile(lowerbandInterferogramFile, dtype=np.complex64).reshape(length2, width2)
upperint = np.fromfile(upperbandInterferogramFile, dtype=np.complex64).reshape(length2, width2)
loweramp = np.fromfile(lowerbandAmplitudeFile, dtype=np.float32).reshape(length2, width2*2)
upperamp = np.fromfile(upperbandAmplitudeFile, dtype=np.float32).reshape(length2, width2*2)
#compute coherence only using interferogram
#here I use differential interferogram of lower and upper band interferograms
#so that coherence is not affected by fringes
cord = cal_coherence(lowerint*np.conjugate(upperint), win=3, edge=4)
cor = np.zeros((length2*2, width2), dtype=np.float32)
cor[0:length2*2:2, :] = np.sqrt( (np.absolute(lowerint)+np.absolute(upperint))/2.0 )
cor[1:length2*2:2, :] = cord
cor.astype(np.float32).tofile(coherenceFile)
create_xml(coherenceFile, width2, length2, 'cor')
#create lower and upper band coherence files
#lower
amp1 = loweramp[:, 0:width2*2:2]
amp2 = loweramp[:, 1:width2*2:2]
cor[1:length2*2:2, :] = np.absolute(lowerint)/(amp1+(amp1==0))/(amp2+(amp2==0))*(amp1!=0)*(amp2!=0)
cor.astype(np.float32).tofile(lowerbandCoherenceFile)
create_xml(lowerbandCoherenceFile, width2, length2, 'cor')
#upper
amp1 = upperamp[:, 0:width2*2:2]
amp2 = upperamp[:, 1:width2*2:2]
cor[1:length2*2:2, :] = np.absolute(upperint)/(amp1+(amp1==0))/(amp2+(amp2==0))*(amp1!=0)*(amp2!=0)
cor.astype(np.float32).tofile(upperbandCoherenceFile)
create_xml(upperbandCoherenceFile, width2, length2, 'cor')
############################################################
# STEP 3. filtering subband interferograms
############################################################
from contrib.alos2filter.alos2filter import psfilt1
from isceobj.Alos2Proc.Alos2ProcPublic import runCmd
from isceobj.Alos2Proc.Alos2ProcPublic import create_xml
from mroipac.icu.Icu import Icu
if self.filterSubbandInt:
for k in range(2):
toBeFiltered = 'tmp.int'
if self.removeMagnitudeBeforeFilteringSubbandInt:
cmd = "imageMath.py -e='a/(abs(a)+(a==0))' --a={} -o {} -t cfloat -s BSQ".format(subbandPrefix[k]+ml2+'.int', toBeFiltered)
else:
#scale the inteferogram, otherwise its magnitude is too large for filtering
cmd = "imageMath.py -e='a/100000.0' --a={} -o {} -t cfloat -s BSQ".format(subbandPrefix[k]+ml2+'.int', toBeFiltered)
runCmd(cmd)
intImage = isceobj.createIntImage()
intImage.load(toBeFiltered + '.xml')
width = intImage.width
length = intImage.length
windowSize = self.filterWinsizeSubbandInt
stepSize = self.filterStepsizeSubbandInt
psfilt1(toBeFiltered, 'filt_'+subbandPrefix[k]+ml2+'.int', width, self.filterStrengthSubbandInt, windowSize, stepSize)
create_xml('filt_'+subbandPrefix[k]+ml2+'.int', width, length, 'int')
os.remove(toBeFiltered)
os.remove(toBeFiltered + '.vrt')
os.remove(toBeFiltered + '.xml')
#create phase sigma for phase unwrapping
#recreate filtered image
filtImage = isceobj.createIntImage()
filtImage.load('filt_'+subbandPrefix[k]+ml2+'.int' + '.xml')
filtImage.setAccessMode('read')
filtImage.createImage()
#amplitude image
ampImage = isceobj.createAmpImage()
ampImage.load(subbandPrefix[k]+ml2+'.amp' + '.xml')
ampImage.setAccessMode('read')
ampImage.createImage()
#phase sigma correlation image
phsigImage = isceobj.createImage()
phsigImage.setFilename(subbandPrefix[k]+ml2+'.phsig')
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()
############################################################
# STEP 4. phase unwrapping
############################################################
from isceobj.Alos2Proc.Alos2ProcPublic import snaphuUnwrap
for k in range(2):
tmid = referenceTrack.sensingStart + datetime.timedelta(seconds=(self._insar.numberAzimuthLooks1-1.0)/2.0*referenceTrack.azimuthLineInterval+
referenceTrack.numberOfLines/2.0*self._insar.numberAzimuthLooks1*referenceTrack.azimuthLineInterval)
if self.filterSubbandInt:
toBeUnwrapped = 'filt_'+subbandPrefix[k]+ml2+'.int'
coherenceFile = subbandPrefix[k]+ml2+'.phsig'
else:
toBeUnwrapped = subbandPrefix[k]+ml2+'.int'
coherenceFile = 'diff'+ml2+'.cor'
snaphuUnwrap(referenceTrack, tmid,
toBeUnwrapped,
coherenceFile,
subbandPrefix[k]+ml2+'.unw',
self._insar.numberRangeLooks1*self._insar.numberRangeLooksIon,
self._insar.numberAzimuthLooks1*self._insar.numberAzimuthLooksIon,
costMode = 'SMOOTH',initMethod = 'MCF', defomax = 2, initOnly = True)
os.chdir('../../')
catalog.printToLog(logger, "runIonUwrap")
self._insar.procDoc.addAllFromCatalog(catalog)
def runUnwrapSnaphuSd(self):
'''unwrap filtered interferogram
'''
catalog = isceobj.Catalog.createCatalog(self._insar.procDoc.name)
self.updateParamemetersFromUser()
masterTrack = self._insar.loadTrack(master=True)
#slaveTrack = self._insar.loadTrack(master=False)
sdDir = 'sd'
if not os.path.exists(sdDir):
os.makedirs(sdDir)
os.chdir(sdDir)
############################################################
# STEP 1. unwrap interferogram
############################################################
nsd = len(self._insar.filteredInterferogramSd)
img = isceobj.createImage()
img.load(self._insar.filteredInterferogramSd[0] + '.xml')
width = img.width
length = img.length
if shutil.which('snaphu') != None:
print(
'\noriginal snaphu program found, use it for unwrapping interferograms'
)
useOriginalSnaphu = True
#create an amplitude for use
# amplitude = os.path.join('../insar', self._insar.amplitude)
# amplitudeMultilook = 'tmp.amp'
# img = isceobj.createImage()
# img.load(amplitude+'.xml')
# look(amplitude, amplitudeMultilook, img.width, self._insar.numberRangeLooksSd, self._insar.numberAzimuthLooksSd, 4, 1, 1)
else:
useOriginalSnaphu = False
for sdCoherence, sdInterferogramFilt, sdInterferogramUnwrap in zip(
self._insar.multilookCoherenceSd,
self._insar.filteredInterferogramSd,
self._insar.unwrappedInterferogramSd):
if useOriginalSnaphu:
amplitudeMultilook = 'tmp.amp'
cmd = "imageMath.py -e='sqrt(abs(a));sqrt(abs(a))' --a={} -o {} -t float -s BSQ".format(
sdInterferogramFilt, amplitudeMultilook)
runCmd(cmd)
snaphuUnwrapOriginal(sdInterferogramFilt,
sdCoherence,
amplitudeMultilook,
sdInterferogramUnwrap,
costMode='s',
initMethod='mcf')
os.remove(amplitudeMultilook)
os.remove(amplitudeMultilook + '.vrt')
os.remove(amplitudeMultilook + '.xml')
else:
tmid = masterTrack.sensingStart + datetime.timedelta(
seconds=(self._insar.numberAzimuthLooks1 - 1.0) / 2.0 *
masterTrack.azimuthLineInterval + masterTrack.numberOfLines /
2.0 * self._insar.numberAzimuthLooks1 *
masterTrack.azimuthLineInterval)
snaphuUnwrap(masterTrack,
tmid,
sdInterferogramFilt,
sdCoherence,
sdInterferogramUnwrap,
self._insar.numberRangeLooks1 *
self._insar.numberRangeLooksSd,
self._insar.numberAzimuthLooks1 *
self._insar.numberAzimuthLooksSd,
costMode='SMOOTH',
initMethod='MCF',
defomax=2,
initOnly=True)
#if useOriginalSnaphu:
# os.remove(amplitudeMultilook)
############################################################
# STEP 2. mask using connected components
############################################################
for sdInterferogramUnwrap, sdInterferogramUnwrapMasked in zip(
self._insar.unwrappedInterferogramSd,
self._insar.unwrappedMaskedInterferogramSd):
cmd = "imageMath.py -e='a_0*(b>0);a_1*(b>0)' --a={} --b={} -s BIL -t float -o={}".format(
sdInterferogramUnwrap, sdInterferogramUnwrap + '.conncomp',
sdInterferogramUnwrapMasked)
runCmd(cmd)
############################################################
# STEP 3. mask using water body
############################################################
if self.waterBodyMaskStartingStepSd == 'unwrap':
wbd = np.fromfile(self._insar.multilookWbdOutSd,
dtype=np.int8).reshape(length, width)
for sdInterferogramUnwrap, sdInterferogramUnwrapMasked in zip(
self._insar.unwrappedInterferogramSd,
self._insar.unwrappedMaskedInterferogramSd):
unw = np.memmap(sdInterferogramUnwrap,
dtype='float32',
mode='r+',
shape=(length * 2, width))
(unw[0:length * 2:2, :])[np.nonzero(wbd == -1)] = 0
(unw[1:length * 2:2, :])[np.nonzero(wbd == -1)] = 0
unw = np.memmap(sdInterferogramUnwrapMasked,
dtype='float32',
mode='r+',
shape=(length * 2, width))
(unw[0:length * 2:2, :])[np.nonzero(wbd == -1)] = 0
(unw[1:length * 2:2, :])[np.nonzero(wbd == -1)] = 0
############################################################
# STEP 4. convert to azimuth deformation
############################################################
#burst cycle in s
burstCycleLength = masterTrack.frames[0].swaths[
0].burstCycleLength / masterTrack.frames[0].swaths[0].prf
#compute azimuth fmrate
#stack all azimuth fmrates
index = np.array([], dtype=np.float64)
ka = np.array([], dtype=np.float64)
for frame in masterTrack.frames:
for swath in frame.swaths:
startingRangeMultilook = masterTrack.frames[0].swaths[0].startingRange + \
(self._insar.numberRangeLooks1*self._insar.numberRangeLooksSd-1.0)/2.0*masterTrack.frames[0].swaths[0].rangePixelSize
rangePixelSizeMultilook = self._insar.numberRangeLooks1 * self._insar.numberRangeLooksSd * masterTrack.frames[
0].swaths[0].rangePixelSize
index0 = (swath.startingRange +
np.arange(swath.numberOfSamples) * swath.rangePixelSize -
startingRangeMultilook) / rangePixelSizeMultilook
ka0 = np.polyval(swath.azimuthFmrateVsPixel[::-1],
np.arange(swath.numberOfSamples))
index = np.concatenate((index, index0))
ka = np.concatenate((ka, ka0))
p = np.polyfit(index, ka, 3)
#new ka
ka = np.polyval(p, np.arange(width))
#compute radar beam footprint velocity at middle track
tmid = masterTrack.sensingStart + datetime.timedelta(
seconds=(self._insar.numberAzimuthLooks1 - 1.0) / 2.0 *
masterTrack.azimuthLineInterval + masterTrack.numberOfLines / 2.0 *
self._insar.numberAzimuthLooks1 * masterTrack.azimuthLineInterval)
svmid = masterTrack.orbit.interpolateOrbit(tmid, method='hermite')
#earth radius in meters
r = 6371 * 1000.0
#radar footprint velocity
veln = np.linalg.norm(svmid.getVelocity()) * r / np.linalg.norm(
svmid.getPosition())
print('radar beam footprint velocity at middle track: %8.2f m/s' % veln)
#phase to defo factor
factor = -1.0 * veln / (2.0 * np.pi * ka * burstCycleLength)
#process unwrapped without mask
sdunw_out = np.zeros((length * 2, width))
flag = np.zeros((length, width))
wgt = np.zeros((length, width))
for i in range(nsd):
sdunw = np.fromfile(self._insar.unwrappedInterferogramSd[i],
dtype=np.float32).reshape(length * 2, width)
sdunw[1:length * 2:2, :] *= factor[None, :] / (i + 1.0)
sdunw.astype(np.float32).tofile(self._insar.azimuthDeformationSd[i])
create_xml(self._insar.azimuthDeformationSd[i], width, length, 'rmg')
flag += (sdunw[1:length * 2:2, :] != 0)
#since the interferogram is filtered, we only use this light weight
wgt0 = (i + 1)**2
wgt += wgt0 * (sdunw[1:length * 2:2, :] != 0)
sdunw_out[0:length * 2:2, :] += (sdunw[0:length * 2:2, :])**2
sdunw_out[1:length * 2:2, :] += wgt0 * sdunw[1:length * 2:2, :]
#output weighting average
index = np.nonzero(flag != 0)
(sdunw_out[0:length * 2:2, :])[index] = np.sqrt(
(sdunw_out[0:length * 2:2, :])[index] / flag[index])
(sdunw_out[1:length * 2:2, :]
)[index] = (sdunw_out[1:length * 2:2, :])[index] / wgt[index]
if not self.unionSd:
(sdunw_out[0:length * 2:2, :])[np.nonzero(flag < nsd)] = 0
(sdunw_out[1:length * 2:2, :])[np.nonzero(flag < nsd)] = 0
sdunw_out.astype(np.float32).tofile(self._insar.azimuthDeformationSd[-1])
create_xml(self._insar.azimuthDeformationSd[-1], width, length, 'rmg')
#process unwrapped with mask
sdunw_out = np.zeros((length * 2, width))
flag = np.zeros((length, width))
wgt = np.zeros((length, width))
for i in range(nsd):
sdunw = np.fromfile(self._insar.unwrappedMaskedInterferogramSd[i],
dtype=np.float32).reshape(length * 2, width)
sdunw[1:length * 2:2, :] *= factor[None, :] / (i + 1.0)
sdunw.astype(np.float32).tofile(
self._insar.maskedAzimuthDeformationSd[i])
create_xml(self._insar.maskedAzimuthDeformationSd[i], width, length,
'rmg')
flag += (sdunw[1:length * 2:2, :] != 0)
#since the interferogram is filtered, we only use this light weight
wgt0 = (i + 1)**2
wgt += wgt0 * (sdunw[1:length * 2:2, :] != 0)
sdunw_out[0:length * 2:2, :] += (sdunw[0:length * 2:2, :])**2
sdunw_out[1:length * 2:2, :] += wgt0 * sdunw[1:length * 2:2, :]
#output weighting average
index = np.nonzero(flag != 0)
(sdunw_out[0:length * 2:2, :])[index] = np.sqrt(
(sdunw_out[0:length * 2:2, :])[index] / flag[index])
(sdunw_out[1:length * 2:2, :]
)[index] = (sdunw_out[1:length * 2:2, :])[index] / wgt[index]
if not self.unionSd:
(sdunw_out[0:length * 2:2, :])[np.nonzero(flag < nsd)] = 0
(sdunw_out[1:length * 2:2, :])[np.nonzero(flag < nsd)] = 0
sdunw_out.astype(np.float32).tofile(
self._insar.maskedAzimuthDeformationSd[-1])
create_xml(self._insar.maskedAzimuthDeformationSd[-1], width, length,
'rmg')
os.chdir('../')
catalog.printToLog(logger, "runUnwrapSnaphuSd")
self._insar.procDoc.addAllFromCatalog(catalog)