def formInterferogram(slcReference, slcSecondary, interferogram, amplitude,
numberRangeLooks, numberAzimuthLooks):
import numpy as np
import isce, isceobj
from isceobj.Alos2Proc.Alos2ProcPublic import multilook
from isceobj.Alos2Proc.Alos2ProcPublic import create_xml
img = isceobj.createImage()
img.load(slcReference + '.xml')
width = img.width
length = img.length
width2 = int(width / numberRangeLooks)
length2 = int(length / numberAzimuthLooks)
fpRef = open(slcReference, 'rb')
fpSec = open(slcSecondary, 'rb')
fpInf = open(interferogram, 'wb')
fpAmp = open(amplitude, 'wb')
for k in range(length2):
if (((k + 1) % 200) == 0):
print("processing line %6d of %6d" % (k + 1, length2),
end='\r',
flush=True)
ref = np.fromfile(fpRef,
dtype=np.complex64,
count=numberAzimuthLooks * width).reshape(
numberAzimuthLooks, width)
sec = np.fromfile(fpSec,
dtype=np.complex64,
count=numberAzimuthLooks * width).reshape(
numberAzimuthLooks, width)
inf = multilook(ref * np.conjugate(sec),
numberAzimuthLooks,
numberRangeLooks,
mean=False)
amp = np.sqrt(multilook(ref.real*ref.real+ref.imag*ref.imag, numberAzimuthLooks, numberRangeLooks, mean=False)) + 1j * \
np.sqrt(multilook(sec.real*sec.real+sec.imag*sec.imag, numberAzimuthLooks, numberRangeLooks, mean=False))
index = np.nonzero((np.real(amp) == 0) + (np.imag(amp) == 0))
amp[index] = 0
inf.tofile(fpInf)
amp.tofile(fpAmp)
print("processing line %6d of %6d" % (length2, length2))
fpRef.close()
fpSec.close()
fpInf.close()
fpAmp.close()
create_xml(interferogram, width2, length2, 'int')
create_xml(amplitude, width2, length2, 'amp')
def swathMosaic(frame,
inputFiles,
outputfile,
rangeOffsets,
azimuthOffsets,
numberOfRangeLooks,
numberOfAzimuthLooks,
updateFrame=False,
phaseCompensation=False,
pcRangeLooks=1,
pcAzimuthLooks=4,
filt=False,
resamplingMethod=0):
'''
mosaic swaths
frame: frame
inputFiles: input file list
output file: output mosaic file
rangeOffsets: range offsets
azimuthOffsets: azimuth offsets
numberOfRangeLooks: number of range looks of the input files
numberOfAzimuthLooks: number of azimuth looks of the input files
phaseCompensation: whether do phase compensation for each swath
pcRangeLooks: number of range looks to take when compute swath phase difference
pcAzimuthLooks: number of azimuth looks to take when compute swath phase difference
filt: whether do filtering when compute swath phase difference
resamplingMethod: 0: amp resampling. 1: int resampling.
'''
from contrib.alos2proc_f.alos2proc_f import rect_with_looks
from contrib.alos2proc.alos2proc import mosaicsubswath
from isceobj.Alos2Proc.Alos2ProcPublic import multilook
from isceobj.Alos2Proc.Alos2ProcPublic import cal_coherence_1
from isceobj.Alos2Proc.Alos2ProcPublic import filterInterferogram
numberOfSwaths = len(frame.swaths)
swaths = frame.swaths
rangeScale = []
azimuthScale = []
rectWidth = []
rectLength = []
for i in range(numberOfSwaths):
rangeScale.append(swaths[0].rangePixelSize / swaths[i].rangePixelSize)
azimuthScale.append(swaths[0].azimuthLineInterval /
swaths[i].azimuthLineInterval)
if i == 0:
rectWidth.append(
int(swaths[i].numberOfSamples / numberOfRangeLooks))
rectLength.append(
int(swaths[i].numberOfLines / numberOfAzimuthLooks))
else:
rectWidth.append(
int(1.0 / rangeScale[i] *
int(swaths[i].numberOfSamples / numberOfRangeLooks)))
rectLength.append(
int(1.0 / azimuthScale[i] *
int(swaths[i].numberOfLines / numberOfAzimuthLooks)))
#convert original offset to offset for images with looks
#use list instead of np.array to make it consistent with the rest of the code
rangeOffsets1 = [i / numberOfRangeLooks for i in rangeOffsets]
azimuthOffsets1 = [i / numberOfAzimuthLooks for i in azimuthOffsets]
#get offset relative to the first frame
rangeOffsets2 = [0.0]
azimuthOffsets2 = [0.0]
for i in range(1, numberOfSwaths):
rangeOffsets2.append(0.0)
azimuthOffsets2.append(0.0)
for j in range(1, i + 1):
rangeOffsets2[i] += rangeOffsets1[j]
azimuthOffsets2[i] += azimuthOffsets1[j]
#resample each swath
rinfs = []
for i, inf in enumerate(inputFiles):
rinfs.append("{}_{}{}".format(
os.path.splitext(os.path.basename(inf))[0], i,
os.path.splitext(os.path.basename(inf))[1]))
#do not resample first swath
if i == 0:
if os.path.isfile(rinfs[i]):
os.remove(rinfs[i])
os.symlink(inf, rinfs[i])
else:
infImg = isceobj.createImage()
infImg.load(inf + '.xml')
rangeOffsets2Frac = rangeOffsets2[i] - int(rangeOffsets2[i])
azimuthOffsets2Frac = azimuthOffsets2[i] - int(azimuthOffsets2[i])
if resamplingMethod == 0:
rect_with_looks(inf, rinfs[i], infImg.width, infImg.length,
rectWidth[i], rectLength[i], rangeScale[i],
0.0, 0.0, azimuthScale[i],
rangeOffsets2Frac * rangeScale[i],
azimuthOffsets2Frac * azimuthScale[i], 1, 1, 1,
1, 'COMPLEX', 'Bilinear')
elif resamplingMethod == 1:
#decompose amplitude and phase
phaseFile = 'phase'
amplitudeFile = 'amplitude'
data = np.fromfile(inf, dtype=np.complex64).reshape(
infImg.length, infImg.width)
phase = np.exp(np.complex64(1j) * np.angle(data))
phase[np.nonzero(data == 0)] = 0
phase.astype(np.complex64).tofile(phaseFile)
amplitude = np.absolute(data)
amplitude.astype(np.float32).tofile(amplitudeFile)
#resampling
phaseRectFile = 'phaseRect'
amplitudeRectFile = 'amplitudeRect'
rect_with_looks(phaseFile, phaseRectFile, infImg.width,
infImg.length, rectWidth[i], rectLength[i],
rangeScale[i], 0.0, 0.0, azimuthScale[i],
rangeOffsets2Frac * rangeScale[i],
azimuthOffsets2Frac * azimuthScale[i], 1, 1, 1,
1, 'COMPLEX', 'Sinc')
rect_with_looks(amplitudeFile, amplitudeRectFile, infImg.width,
infImg.length, rectWidth[i], rectLength[i],
rangeScale[i], 0.0, 0.0, azimuthScale[i],
rangeOffsets2Frac * rangeScale[i],
azimuthOffsets2Frac * azimuthScale[i], 1, 1, 1,
1, 'REAL', 'Bilinear')
#recombine amplitude and phase
phase = np.fromfile(phaseRectFile, dtype=np.complex64).reshape(
rectLength[i], rectWidth[i])
amplitude = np.fromfile(amplitudeRectFile,
dtype=np.float32).reshape(
rectLength[i], rectWidth[i])
(phase * amplitude).astype(np.complex64).tofile(rinfs[i])
#tidy up
os.remove(phaseFile)
os.remove(amplitudeFile)
os.remove(phaseRectFile)
os.remove(amplitudeRectFile)
#determine output width and length
#actually no need to calculate in range direction
xs = []
xe = []
ys = []
ye = []
for i in range(numberOfSwaths):
if i == 0:
xs.append(0)
xe.append(rectWidth[i] - 1)
ys.append(0)
ye.append(rectLength[i] - 1)
else:
xs.append(0 - int(rangeOffsets2[i]))
xe.append(rectWidth[i] - 1 - int(rangeOffsets2[i]))
ys.append(0 - int(azimuthOffsets2[i]))
ye.append(rectLength[i] - 1 - int(azimuthOffsets2[i]))
(xmin, xminIndex) = min((v, i) for i, v in enumerate(xs))
(xmax, xmaxIndex) = max((v, i) for i, v in enumerate(xe))
(ymin, yminIndex) = min((v, i) for i, v in enumerate(ys))
(ymax, ymaxIndex) = max((v, i) for i, v in enumerate(ye))
outWidth = xmax - xmin + 1
outLength = ymax - ymin + 1
#prepare offset for mosaicing
rangeOffsets3 = []
azimuthOffsets3 = []
for i in range(numberOfSwaths):
azimuthOffsets3.append(
int(azimuthOffsets2[i]) - int(azimuthOffsets2[yminIndex]))
if i != 0:
rangeOffsets3.append(
int(rangeOffsets2[i]) - int(rangeOffsets2[i - 1]))
else:
rangeOffsets3.append(0)
delta = int(30 / numberOfRangeLooks)
#compute compensation phase for each swath
diffMean2 = [0.0 for i in range(numberOfSwaths)]
if phaseCompensation:
#compute swath phase offset
diffMean = [0.0]
for i in range(1, numberOfSwaths):
#all indexes start with zero, all the computed start/end sample/line indexes are included.
#no need to add edge here, as we are going to find first/last nonzero sample/lines later
#edge = delta
edge = 0
#image i-1
startSample1 = edge + 0 - int(rangeOffsets2[i]) + int(
rangeOffsets2[i - 1])
endSample1 = -edge + rectWidth[i - 1] - 1
startLine1 = edge + max(
0 - int(azimuthOffsets2[i]) + int(azimuthOffsets2[i - 1]), 0)
endLine1 = -edge + min(
rectLength[i] - 1 - int(azimuthOffsets2[i]) +
int(azimuthOffsets2[i - 1]), rectLength[i - 1] - 1)
data1 = readImage(rinfs[i - 1], rectWidth[i - 1],
rectLength[i - 1], startSample1, endSample1,
startLine1, endLine1)
#image i
startSample2 = edge + 0
endSample2 = -edge + rectWidth[i - 1] - 1 - int(
rangeOffsets2[i - 1]) + int(rangeOffsets2[i])
startLine2 = edge + max(
0 - int(azimuthOffsets2[i - 1]) + int(azimuthOffsets2[i]), 0)
endLine2 = -edge + min(
rectLength[i - 1] - 1 - int(azimuthOffsets2[i - 1]) +
int(azimuthOffsets2[i]), rectLength[i] - 1)
data2 = readImage(rinfs[i], rectWidth[i], rectLength[i],
startSample2, endSample2, startLine2, endLine2)
#remove edge due to incomplete covolution in resampling
edge = 9
(startLine0, endLine0, startSample0, endSample0) = findNonzero(
np.logical_and((data1 != 0), (data2 != 0)))
data1 = data1[startLine0 + edge:endLine0 + 1 - edge,
startSample0 + edge:endSample0 + 1 - edge]
data2 = data2[startLine0 + edge:endLine0 + 1 - edge,
startSample0 + edge:endSample0 + 1 - edge]
#take looks
data1 = multilook(data1, pcAzimuthLooks, pcRangeLooks)
data2 = multilook(data2, pcAzimuthLooks, pcRangeLooks)
#filter
if filt:
data1 /= (np.absolute(data1) + (data1 == 0))
data2 /= (np.absolute(data2) + (data2 == 0))
data1 = filterInterferogram(data1, 3.0, 64, 1)
data2 = filterInterferogram(data2, 3.0, 64, 1)
#get difference
corth = 0.87
if filt:
corth = 0.90
diffMean0 = 0.0
for k in range(5):
dataDiff = data1 * np.conj(data2)
cor = cal_coherence_1(dataDiff, win=3)
index = np.nonzero(np.logical_and(cor > corth, dataDiff != 0))
if index[0].size < 100:
diffMean0 = 0.0
print(
'\n\nWARNING: too few high coherence pixels for swath phase difference estimation between swath {} and {}'
.format(i - 1, i))
print(' : first swath swath number: 0\n\n')
break
angle = np.mean(np.angle(dataDiff[index]), dtype=np.float64)
diffMean0 += angle
data2 *= np.exp(np.complex64(1j) * angle)
print('phase offset: %15.12f rad after loop: %3d' %
(diffMean0, k))
DEBUG = False
if DEBUG and (k == 0):
from isceobj.Alos2Proc.Alos2ProcPublic import create_xml
(lengthxx, widthxx) = dataDiff.shape
filtnamePrefix = 'subswath{}_subswath{}_loop{}'.format(
frame.swaths[i - 1].swathNumber,
frame.swaths[i].swathNumber, k)
cor.astype(np.float32).tofile(filtnamePrefix + '.cor')
create_xml(filtnamePrefix + '.cor', widthxx, lengthxx,
'float')
dataDiff.astype(np.complex64).tofile(filtnamePrefix +
'.int')
create_xml(filtnamePrefix + '.int', widthxx, lengthxx,
'int')
diffMean.append(diffMean0)
print('phase offset: subswath{} - subswath{}: {}'.format(
frame.swaths[i - 1].swathNumber, frame.swaths[i].swathNumber,
diffMean0))
for i in range(1, numberOfSwaths):
for j in range(1, i + 1):
diffMean2[i] += diffMean[j]
#mosaic swaths
diffflag = 1
oflag = [0 for i in range(numberOfSwaths)]
mosaicsubswath(outputfile, outWidth, outLength, delta, diffflag,
numberOfSwaths, rinfs, rectWidth, rangeOffsets3,
azimuthOffsets3, diffMean2, oflag)
#remove tmp files
for x in rinfs:
os.remove(x)
#update frame parameters
if updateFrame:
#mosaic size
frame.numberOfSamples = outWidth
frame.numberOfLines = outLength
#NOTE THAT WE ARE STILL USING SINGLE LOOK PARAMETERS HERE
#range parameters
frame.startingRange = frame.swaths[0].startingRange
frame.rangeSamplingRate = frame.swaths[0].rangeSamplingRate
frame.rangePixelSize = frame.swaths[0].rangePixelSize
#azimuth parameters
azimuthTimeOffset = -max([
int(x) for x in azimuthOffsets2
]) * numberOfAzimuthLooks * frame.swaths[0].azimuthLineInterval
frame.sensingStart = frame.swaths[0].sensingStart + datetime.timedelta(
seconds=azimuthTimeOffset)
frame.prf = frame.swaths[0].prf
frame.azimuthPixelSize = frame.swaths[0].azimuthPixelSize
frame.azimuthLineInterval = frame.swaths[0].azimuthLineInterval
def swathMosaic(frame,
inputFiles,
outputfile,
rangeOffsets,
azimuthOffsets,
numberOfRangeLooks,
numberOfAzimuthLooks,
updateFrame=False,
phaseCompensation=False,
phaseDiff=None,
phaseDiffFixed=None,
snapThreshold=None,
snapSwath=None,
pcRangeLooks=1,
pcAzimuthLooks=4,
filt=False,
resamplingMethod=0):
'''
mosaic swaths
#PART 1. REGULAR INPUT PARAMTERS
frame: frame
inputFiles: input file list
outputfile: output mosaic file
rangeOffsets: range offsets
azimuthOffsets: azimuth offsets
numberOfRangeLooks: number of range looks of the input files
numberOfAzimuthLooks: number of azimuth looks of the input files
updateFrame: whether update frame parameters
#PART 2. PARAMETERS FOR COMPUTING PHASE DIFFERENCE BETWEEN SUBSWATHS
phaseCompensation: whether do phase compensation for each swath
phaseDiff: pre-computed compensation phase for each swath
phaseDiffFixed: if provided, the estimated value will snap to one of these values, which is nearest to the estimated one.
snapThreshold: this is used with phaseDiffFixed
snapSwath: indicate whether snap to fixed values for each swath phase diff, must be specified if phaseDiffFixed!=None
pcRangeLooks: number of range looks to take when compute swath phase difference
pcAzimuthLooks: number of azimuth looks to take when compute swath phase difference
filt: whether do filtering when compute swath phase difference
#PART 3. RESAMPLING METHOD
resamplingMethod: 0: amp resampling. 1: int resampling.
'''
from contrib.alos2proc_f.alos2proc_f import rect_with_looks
from contrib.alos2proc.alos2proc import mosaicsubswath
from isceobj.Alos2Proc.Alos2ProcPublic import multilook
from isceobj.Alos2Proc.Alos2ProcPublic import cal_coherence_1
from isceobj.Alos2Proc.Alos2ProcPublic import filterInterferogram
from isceobj.Alos2Proc.Alos2ProcPublic import computePhaseDiff
from isceobj.Alos2Proc.Alos2ProcPublic import snap
numberOfSwaths = len(frame.swaths)
swaths = frame.swaths
rangeScale = []
azimuthScale = []
rectWidth = []
rectLength = []
for i in range(numberOfSwaths):
rangeScale.append(swaths[0].rangePixelSize / swaths[i].rangePixelSize)
azimuthScale.append(swaths[0].azimuthLineInterval /
swaths[i].azimuthLineInterval)
if i == 0:
rectWidth.append(
int(swaths[i].numberOfSamples / numberOfRangeLooks))
rectLength.append(
int(swaths[i].numberOfLines / numberOfAzimuthLooks))
else:
rectWidth.append(
round(1.0 / rangeScale[i] *
int(swaths[i].numberOfSamples / numberOfRangeLooks)))
rectLength.append(
round(1.0 / azimuthScale[i] *
int(swaths[i].numberOfLines / numberOfAzimuthLooks)))
#rectWidth.append( int(1.0 / rangeScale[i] * int(swaths[i].numberOfSamples / numberOfRangeLooks)) )
#rectLength.append( int(1.0 / azimuthScale[i] * int(swaths[i].numberOfLines / numberOfAzimuthLooks)) )
#convert original offset to offset for images with looks
#use list instead of np.array to make it consistent with the rest of the code
rangeOffsets1 = [i / numberOfRangeLooks for i in rangeOffsets]
azimuthOffsets1 = [i / numberOfAzimuthLooks for i in azimuthOffsets]
#get offset relative to the first frame
rangeOffsets2 = [0.0]
azimuthOffsets2 = [0.0]
for i in range(1, numberOfSwaths):
rangeOffsets2.append(0.0)
azimuthOffsets2.append(0.0)
for j in range(1, i + 1):
rangeOffsets2[i] += rangeOffsets1[j]
azimuthOffsets2[i] += azimuthOffsets1[j]
#resample each swath
rinfs = []
for i, inf in enumerate(inputFiles):
rinfs.append("{}_{}{}".format(
os.path.splitext(os.path.basename(inf))[0], i,
os.path.splitext(os.path.basename(inf))[1]))
#do not resample first swath
if i == 0:
if os.path.isfile(rinfs[i]):
os.remove(rinfs[i])
os.symlink(inf, rinfs[i])
else:
#no need to resample
if (abs(rangeOffsets2[i] - round(rangeOffsets2[i])) < 0.0001) and (
abs(azimuthOffsets2[i] - round(azimuthOffsets2[i])) <
0.0001):
if os.path.isfile(rinfs[i]):
os.remove(rinfs[i])
os.symlink(inf, rinfs[i])
#all of the following use of rangeOffsets2/azimuthOffsets2 is inside int(), we do the following in case it is like
#4.99999999999...
rangeOffsets2[i] = round(rangeOffsets2[i])
azimuthOffsets2[i] = round(azimuthOffsets2[i])
else:
infImg = isceobj.createImage()
infImg.load(inf + '.xml')
rangeOffsets2Frac = rangeOffsets2[i] - int(rangeOffsets2[i])
azimuthOffsets2Frac = azimuthOffsets2[i] - int(
azimuthOffsets2[i])
if resamplingMethod == 0:
rect_with_looks(inf, rinfs[i], infImg.width, infImg.length,
rectWidth[i], rectLength[i], rangeScale[i],
0.0, 0.0, azimuthScale[i],
rangeOffsets2Frac * rangeScale[i],
azimuthOffsets2Frac * azimuthScale[i], 1,
1, 1, 1, 'COMPLEX', 'Bilinear')
elif resamplingMethod == 1:
#decompose amplitude and phase
phaseFile = 'phase'
amplitudeFile = 'amplitude'
data = np.fromfile(inf, dtype=np.complex64).reshape(
infImg.length, infImg.width)
phase = np.exp(np.complex64(1j) * np.angle(data))
phase[np.nonzero(data == 0)] = 0
phase.astype(np.complex64).tofile(phaseFile)
amplitude = np.absolute(data)
amplitude.astype(np.float32).tofile(amplitudeFile)
#resampling
phaseRectFile = 'phaseRect'
amplitudeRectFile = 'amplitudeRect'
rect_with_looks(phaseFile, phaseRectFile, infImg.width,
infImg.length, rectWidth[i], rectLength[i],
rangeScale[i], 0.0, 0.0, azimuthScale[i],
rangeOffsets2Frac * rangeScale[i],
azimuthOffsets2Frac * azimuthScale[i], 1,
1, 1, 1, 'COMPLEX', 'Sinc')
rect_with_looks(amplitudeFile, amplitudeRectFile,
infImg.width, infImg.length, rectWidth[i],
rectLength[i], rangeScale[i], 0.0, 0.0,
azimuthScale[i],
rangeOffsets2Frac * rangeScale[i],
azimuthOffsets2Frac * azimuthScale[i], 1,
1, 1, 1, 'REAL', 'Bilinear')
#recombine amplitude and phase
phase = np.fromfile(phaseRectFile,
dtype=np.complex64).reshape(
rectLength[i], rectWidth[i])
amplitude = np.fromfile(amplitudeRectFile,
dtype=np.float32).reshape(
rectLength[i], rectWidth[i])
(phase * amplitude).astype(np.complex64).tofile(rinfs[i])
#tidy up
os.remove(phaseFile)
os.remove(amplitudeFile)
os.remove(phaseRectFile)
os.remove(amplitudeRectFile)
#determine output width and length
#actually no need to calculate in range direction
xs = []
xe = []
ys = []
ye = []
for i in range(numberOfSwaths):
if i == 0:
xs.append(0)
xe.append(rectWidth[i] - 1)
ys.append(0)
ye.append(rectLength[i] - 1)
else:
xs.append(0 - int(rangeOffsets2[i]))
xe.append(rectWidth[i] - 1 - int(rangeOffsets2[i]))
ys.append(0 - int(azimuthOffsets2[i]))
ye.append(rectLength[i] - 1 - int(azimuthOffsets2[i]))
(xmin, xminIndex) = min((v, i) for i, v in enumerate(xs))
(xmax, xmaxIndex) = max((v, i) for i, v in enumerate(xe))
(ymin, yminIndex) = min((v, i) for i, v in enumerate(ys))
(ymax, ymaxIndex) = max((v, i) for i, v in enumerate(ye))
outWidth = xmax - xmin + 1
outLength = ymax - ymin + 1
#prepare offset for mosaicing
rangeOffsets3 = []
azimuthOffsets3 = []
for i in range(numberOfSwaths):
azimuthOffsets3.append(
int(azimuthOffsets2[i]) - int(azimuthOffsets2[yminIndex]))
if i != 0:
rangeOffsets3.append(
int(rangeOffsets2[i]) - int(rangeOffsets2[i - 1]))
else:
rangeOffsets3.append(0)
delta = int(30 / numberOfRangeLooks)
#compute compensation phase for each swath
diffMean2 = [0.0 for i in range(numberOfSwaths)]
phaseDiffEst = [None for i in range(numberOfSwaths)]
#True if:
# (1) used diff phase from input
# (2) used estimated diff phase after snapping to a fixed diff phase provided
#False if:
# (1) used purely estimated diff phase
phaseDiffSource = ['estimated' for i in range(numberOfSwaths)]
# 1. 'estimated': estimated from subswath overlap
# 2. 'estimated+snap': estimated from subswath overlap and snap to a fixed value
# 3. 'input': pre-computed
# confidence level: 3 > 2 > 1
numberOfValidSamples = [None for i in range(numberOfSwaths)]
# only record when (filt == False) and (index[0].size >= 4000)
if phaseCompensation:
#compute swath phase offset
diffMean = [0.0]
for i in range(1, numberOfSwaths):
#no need to estimate diff phase if provided from input
#####################################################################
if phaseDiff != None:
if phaseDiff[i] != None:
diffMean.append(phaseDiff[i])
phaseDiffSource[i] = 'input'
print('using pre-computed phase offset given from input')
print('phase offset: subswath{} - subswath{}: {}'.format(
frame.swaths[i - 1].swathNumber,
frame.swaths[i].swathNumber, phaseDiff[i]))
continue
#####################################################################
#all indexes start with zero, all the computed start/end sample/line indexes are included.
#no need to add edge here, as we are going to find first/last nonzero sample/lines later
#edge = delta
edge = 0
#image i-1
startSample1 = edge + 0 - int(rangeOffsets2[i]) + int(
rangeOffsets2[i - 1])
endSample1 = -edge + rectWidth[i - 1] - 1
startLine1 = edge + max(
0 - int(azimuthOffsets2[i]) + int(azimuthOffsets2[i - 1]), 0)
endLine1 = -edge + min(
rectLength[i] - 1 - int(azimuthOffsets2[i]) +
int(azimuthOffsets2[i - 1]), rectLength[i - 1] - 1)
data1 = readImage(rinfs[i - 1], rectWidth[i - 1],
rectLength[i - 1], startSample1, endSample1,
startLine1, endLine1)
#image i
startSample2 = edge + 0
endSample2 = -edge + rectWidth[i - 1] - 1 - int(
rangeOffsets2[i - 1]) + int(rangeOffsets2[i])
startLine2 = edge + max(
0 - int(azimuthOffsets2[i - 1]) + int(azimuthOffsets2[i]), 0)
endLine2 = -edge + min(
rectLength[i - 1] - 1 - int(azimuthOffsets2[i - 1]) +
int(azimuthOffsets2[i]), rectLength[i] - 1)
data2 = readImage(rinfs[i], rectWidth[i], rectLength[i],
startSample2, endSample2, startLine2, endLine2)
#remove edge due to incomplete covolution in resampling
edge = 9
(startLine0, endLine0, startSample0, endSample0) = findNonzero(
np.logical_and((data1 != 0), (data2 != 0)))
data1 = data1[startLine0 + edge:endLine0 + 1 - edge,
startSample0 + edge:endSample0 + 1 - edge]
data2 = data2[startLine0 + edge:endLine0 + 1 - edge,
startSample0 + edge:endSample0 + 1 - edge]
#take looks
data1 = multilook(data1, pcAzimuthLooks, pcRangeLooks)
data2 = multilook(data2, pcAzimuthLooks, pcRangeLooks)
#filter
if filt:
data1 /= (np.absolute(data1) + (data1 == 0))
data2 /= (np.absolute(data2) + (data2 == 0))
data1 = filterInterferogram(data1, 3.0, 64, 1)
data2 = filterInterferogram(data2, 3.0, 64, 1)
#get difference
dataDiff = data1 * np.conj(data2)
cor = cal_coherence_1(dataDiff, win=5)
index = np.nonzero(np.logical_and(cor > 0.85, dataDiff != 0))
DEBUG = False
if DEBUG:
from isceobj.Alos2Proc.Alos2ProcPublic import create_xml
(length7, width7) = dataDiff.shape
filename = 'diff_ori_s{}-s{}.int'.format(
frame.swaths[i - 1].swathNumber,
frame.swaths[i].swathNumber)
dataDiff.astype(np.complex64).tofile(filename)
create_xml(filename, width7, length7, 'int')
filename = 'cor_ori_s{}-s{}.cor'.format(
frame.swaths[i - 1].swathNumber,
frame.swaths[i].swathNumber)
cor.astype(np.float32).tofile(filename)
create_xml(filename, width7, length7, 'float')
print('\ncompute phase difference between subswaths {} and {}'.
format(frame.swaths[i - 1].swathNumber,
frame.swaths[i].swathNumber))
print('number of pixels with coherence > 0.85: {}'.format(
index[0].size))
#if already filtered the subswath overlap interferograms (MAI), do not filtered differential interferograms
if (filt == False) and (index[0].size < 4000):
#coherence too low, filter subswath overlap differential interferogram
diffMean0 = 0.0
breakFlag = False
for (filterStrength, filterWinSize) in zip([3.0, 9.0],
[64, 128]):
dataDiff = data1 * np.conj(data2)
dataDiff /= (np.absolute(dataDiff) + (dataDiff == 0))
dataDiff = filterInterferogram(dataDiff, filterStrength,
filterWinSize, 1)
cor = cal_coherence_1(dataDiff, win=7)
DEBUG = False
if DEBUG:
from isceobj.Alos2Proc.Alos2ProcPublic import create_xml
(length7, width7) = dataDiff.shape
filename = 'diff_filt_s{}-s{}_strength_{}_winsize_{}.int'.format(
frame.swaths[i - 1].swathNumber,
frame.swaths[i].swathNumber, filterStrength,
filterWinSize)
dataDiff.astype(np.complex64).tofile(filename)
create_xml(filename, width7, length7, 'int')
filename = 'cor_filt_s{}-s{}_strength_{}_winsize_{}.cor'.format(
frame.swaths[i - 1].swathNumber,
frame.swaths[i].swathNumber, filterStrength,
filterWinSize)
cor.astype(np.float32).tofile(filename)
create_xml(filename, width7, length7, 'float')
for corth in [0.99999, 0.9999]:
index = np.nonzero(
np.logical_and(cor > corth, dataDiff != 0))
if index[0].size > 30000:
breakFlag = True
break
if breakFlag:
break
if index[0].size < 100:
diffMean0 = 0.0
print(
'\n\nWARNING: too few high coherence pixels for swath phase difference estimation'
)
print(' number of high coherence pixels: {}\n\n'.
format(index[0].size))
else:
print(
'filtered coherence threshold used: {}, number of pixels used: {}'
.format(corth, index[0].size))
angle = np.mean(np.angle(dataDiff[index]),
dtype=np.float64)
diffMean0 += angle
data2 *= np.exp(np.complex64(1j) * angle)
print(
'phase offset: %15.12f rad with filter strength: %f, window size: %3d'
% (diffMean0, filterStrength, filterWinSize))
else:
if filt:
(diffMean0, numberOfValidSamples[i]) = computePhaseDiff(
data1,
data2,
coherenceWindowSize=5,
coherenceThreshold=0.95)
else:
(diffMean0, numberOfValidSamples[i]) = computePhaseDiff(
data1,
data2,
coherenceWindowSize=5,
coherenceThreshold=0.85)
if numberOfValidSamples[i] < 100:
diffMean0 = 0.0
print(
'\n\nWARNING: too few high coherence pixels for swath phase difference estimation'
)
print(' number of high coherence pixels: {}\n\n'.
format(numberOfValidSamples[i]))
#do not record when filt
if filt:
numberOfValidSamples[i] = None
#save purely estimated diff phase
phaseDiffEst[i] = diffMean0
#if fixed diff phase provided and the estimated diff phase is close enough to a fixed value, snap to it
if phaseDiffFixed != None:
if snapSwath[i - 1] == True:
(outputValue, snapped) = snap(diffMean0, phaseDiffFixed,
snapThreshold)
if snapped == True:
diffMean0 = outputValue
phaseDiffSource[i] = 'estimated+snap'
diffMean.append(diffMean0)
print('phase offset: subswath{} - subswath{}: {}'.format(
frame.swaths[i - 1].swathNumber, frame.swaths[i].swathNumber,
diffMean0))
for i in range(1, numberOfSwaths):
for j in range(1, i + 1):
diffMean2[i] += diffMean[j]
#mosaic swaths
diffflag = 1
oflag = [0 for i in range(numberOfSwaths)]
mosaicsubswath(outputfile, outWidth, outLength, delta, diffflag,
numberOfSwaths, rinfs, rectWidth, rangeOffsets3,
azimuthOffsets3, diffMean2, oflag)
#remove tmp files
for x in rinfs:
os.remove(x)
#update frame parameters
if updateFrame:
#mosaic size
frame.numberOfSamples = outWidth
frame.numberOfLines = outLength
#NOTE THAT WE ARE STILL USING SINGLE LOOK PARAMETERS HERE
#range parameters
frame.startingRange = frame.swaths[0].startingRange
frame.rangeSamplingRate = frame.swaths[0].rangeSamplingRate
frame.rangePixelSize = frame.swaths[0].rangePixelSize
#azimuth parameters
azimuthTimeOffset = -max([
int(x) for x in azimuthOffsets2
]) * numberOfAzimuthLooks * frame.swaths[0].azimuthLineInterval
frame.sensingStart = frame.swaths[0].sensingStart + datetime.timedelta(
seconds=azimuthTimeOffset)
frame.prf = frame.swaths[0].prf
frame.azimuthPixelSize = frame.swaths[0].azimuthPixelSize
frame.azimuthLineInterval = frame.swaths[0].azimuthLineInterval
if phaseCompensation:
# estimated phase diff, used phase diff, used phase diff source
return (phaseDiffEst, diffMean, phaseDiffSource, numberOfValidSamples)
def estimateSwathOffset(swath1,
swath2,
image1,
image2,
rangeScale1=1,
azimuthScale1=1,
rangeScale2=1,
azimuthScale2=1,
numberOfAzimuthLooks=10):
'''
estimate offset of two adjacent swaths using matching
'''
from osgeo import gdal
import isceobj
from contrib.alos2proc_f.alos2proc_f import rect_with_looks
from isceobj.Alos2Proc.Alos2ProcPublic import create_xml
from isceobj.Alos2Proc.Alos2ProcPublic import cullOffsets
from isceobj.Alos2Proc.Alos2ProcPublic import meanOffset
from mroipac.ampcor.Ampcor import Ampcor
#processing image 1
rangeOff1 = int(
(swath2.startingRange - swath1.startingRange) / swath1.rangePixelSize)
if rangeOff1 < 0:
rangeOff1 = 0
numberOfSamples1 = swath1.numberOfSamples - rangeOff1
numberOfSamplesRect1 = int(numberOfSamples1 / rangeScale1)
numberOfLinesRect1 = int(swath1.numberOfLines / azimuthScale1)
numberOfSamplesLook1 = int(numberOfSamplesRect1 / 1)
numberOfLinesLook1 = int(numberOfLinesRect1 / numberOfAzimuthLooks)
#get magnitude image whether complex or not
#ReadAsArray: https://pcjericks.github.io/py-gdalogr-cookbook/raster_layers.html
ds = gdal.Open(image1 + '.vrt', gdal.GA_ReadOnly)
data = ds.ReadAsArray(rangeOff1, 0, numberOfSamples1, swath1.numberOfLines)
ds = None
(np.absolute(data)).astype(np.float32).tofile('image1.float')
#rectify
if rangeScale1 == 1 and azimuthScale1 == 1:
os.rename('image1.float', 'image1_rect.float')
else:
rect_with_looks('image1.float', 'image1_rect.float', numberOfSamples1,
swath1.numberOfLines, numberOfSamplesRect1,
numberOfLinesRect1, rangeScale1, 0.0, 0.0,
azimuthScale1, 0.0, 0.0, 1, 1, 1, 1, 'REAL',
'Bilinear')
os.remove('image1.float')
#take looks
if numberOfAzimuthLooks == 1:
os.rename('image1_rect.float', 'image1_look.float')
else:
data1 = np.fromfile('image1_rect.float',
dtype=np.float32).reshape(numberOfLinesRect1,
numberOfSamplesRect1)
data1 = np.sqrt(multilook(data1**2, numberOfAzimuthLooks, 1))
data1.astype(np.float32).tofile('image1_look.float')
os.remove('image1_rect.float')
create_xml('image1_look.float', numberOfSamplesLook1, numberOfLinesLook1,
'float')
#processing image 2
rangeOff2 = 0
numberOfSamples2 = int(
(swath1.startingRange + swath1.rangePixelSize *
(swath1.numberOfSamples - 1) - swath2.startingRange) /
swath2.rangePixelSize) + 1
if numberOfSamples2 > swath2.numberOfSamples:
numberOfSamples2 = swath2.numberOfSamples
numberOfSamplesRect2 = int(numberOfSamples2 / rangeScale2)
numberOfLinesRect2 = int(swath2.numberOfLines / azimuthScale2)
numberOfSamplesLook2 = int(numberOfSamplesRect2 / 1)
numberOfLinesLook2 = int(numberOfLinesRect2 / numberOfAzimuthLooks)
#get magnitude image whether complex or not
ds = gdal.Open(image2 + '.vrt', gdal.GA_ReadOnly)
data = ds.ReadAsArray(rangeOff2, 0, numberOfSamples2, swath2.numberOfLines)
ds = None
(np.absolute(data)).astype(np.float32).tofile('image2.float')
#rectify
if rangeScale2 == 1 and azimuthScale2 == 1:
os.rename('image2.float', 'image2_rect.float')
else:
rect_with_looks('image2.float', 'image2_rect.float', numberOfSamples2,
swath2.numberOfLines, numberOfSamplesRect2,
numberOfLinesRect2, rangeScale2, 0.0, 0.0,
azimuthScale2, 0.0, 0.0, 1, 1, 1, 1, 'REAL',
'Bilinear')
os.remove('image2.float')
#take looks
if numberOfAzimuthLooks == 1:
os.rename('image2_rect.float', 'image2_look.float')
else:
data2 = np.fromfile('image2_rect.float',
dtype=np.float32).reshape(numberOfLinesRect2,
numberOfSamplesRect2)
data2 = np.sqrt(multilook(data2**2, numberOfAzimuthLooks, 1))
data2.astype(np.float32).tofile('image2_look.float')
os.remove('image2_rect.float')
create_xml('image2_look.float', numberOfSamplesLook2, numberOfLinesLook2,
'float')
#matching
ampcor = Ampcor(name='insarapp_slcs_ampcor')
ampcor.configure()
mMag = isceobj.createImage()
mMag.load('image1_look.float.xml')
mMag.setAccessMode('read')
mMag.createImage()
sMag = isceobj.createImage()
sMag.load('image2_look.float.xml')
sMag.setAccessMode('read')
sMag.createImage()
ampcor.setImageDataType1('real')
ampcor.setImageDataType2('real')
ampcor.setReferenceSlcImage(mMag)
ampcor.setSecondarySlcImage(sMag)
#MATCH REGION
rgoff = 0
azoff = int(
(swath1.sensingStart - swath2.sensingStart).total_seconds() /
swath1.azimuthLineInterval / azimuthScale1 / numberOfAzimuthLooks)
#it seems that we cannot use 0, haven't look into the problem
if rgoff == 0:
rgoff = 1
if azoff == 0:
azoff = 1
firstSample = 1
if rgoff < 0:
firstSample = int(35 - rgoff)
firstLine = 1
if azoff < 0:
firstLine = int(35 - azoff)
ampcor.setAcrossGrossOffset(rgoff)
ampcor.setDownGrossOffset(azoff)
ampcor.setFirstSampleAcross(firstSample)
ampcor.setLastSampleAcross(numberOfSamplesLook1)
ampcor.setNumberLocationAcross(20)
ampcor.setFirstSampleDown(firstLine)
ampcor.setLastSampleDown(numberOfLinesLook1)
ampcor.setNumberLocationDown(100)
#MATCH PARAMETERS
ampcor.setWindowSizeWidth(32)
ampcor.setWindowSizeHeight(32)
#note this is the half width/length of search area, so number of resulting correlation samples: 8*2+1
ampcor.setSearchWindowSizeWidth(8)
ampcor.setSearchWindowSizeHeight(8)
#REST OF THE STUFF
ampcor.setAcrossLooks(1)
ampcor.setDownLooks(1)
ampcor.setOversamplingFactor(64)
ampcor.setZoomWindowSize(16)
#1. The following not set
#Matching Scale for Sample/Line Directions (-) = 1. 1.
#should add the following in Ampcor.py?
#if not set, in this case, Ampcor.py'value is also 1. 1.
#ampcor.setScaleFactorX(1.)
#ampcor.setScaleFactorY(1.)
#MATCH THRESHOLDS AND DEBUG DATA
#2. The following not set
#in roi_pac the value is set to 0 1
#in isce the value is set to 0.001 1000.0
#SNR and Covariance Thresholds (-) = {s1} {s2}
#should add the following in Ampcor?
#THIS SHOULD BE THE ONLY THING THAT IS DIFFERENT FROM THAT OF ROI_PAC
#ampcor.setThresholdSNR(0)
#ampcor.setThresholdCov(1)
ampcor.setDebugFlag(False)
ampcor.setDisplayFlag(False)
#in summary, only two things not set which are indicated by 'The following not set' above.
#run ampcor
ampcor.ampcor()
offsets = ampcor.getOffsetField()
refinedOffsets = cullOffsets(offsets)
#finalize image, and re-create it
#otherwise the file pointer is still at the end of the image
mMag.finalizeImage()
sMag.finalizeImage()
os.remove('image1_look.float')
os.remove('image1_look.float.vrt')
os.remove('image1_look.float.xml')
os.remove('image2_look.float')
os.remove('image2_look.float.vrt')
os.remove('image2_look.float.xml')
if refinedOffsets != None:
rangeOffset, azimuthOffset = meanOffset(refinedOffsets)
rangeOffset -= rangeOff1 / rangeScale1
azimuthOffset *= numberOfAzimuthLooks
return (rangeOffset, azimuthOffset)
else:
return None
def spectralDiversity(referenceSwath,
interferogramDir,
interferogramPrefix,
outputList,
numberLooksScanSAR=None,
numberRangeLooks=20,
numberAzimuthLooks=10,
coherenceThreshold=0.85,
keep=False,
filt=False,
filtWinSizeRange=5,
filtWinSizeAzimuth=5):
'''
numberLooksScanSAR: number of looks of the ScanSAR system
numberRangeLooks: number of range looks to take
numberAzimuthLooks: number of azimuth looks to take
keep: whether keep intermediate files
'''
import os
import numpy as np
from isceobj.Alos2Proc.Alos2ProcPublic import create_multi_index
from isceobj.Alos2Proc.Alos2ProcPublic import create_xml
from isceobj.Alos2Proc.Alos2ProcPublic import multilook
from isceobj.Alos2Proc.Alos2ProcPublic import cal_coherence_1
width = referenceSwath.numberOfSamples
length = referenceSwath.numberOfLines
lengthBurst = referenceSwath.burstSlcNumberOfLines
nBurst = referenceSwath.numberOfBursts
azsi = referenceSwath.azimuthLineInterval
tc = referenceSwath.burstCycleLength / referenceSwath.prf
bursts = [
os.path.join(interferogramDir,
interferogramPrefix + '_%02d.int' % (i + 1))
for i in range(referenceSwath.numberOfBursts)
]
####################################################
#input parameters
rgl = numberRangeLooks
azl = numberAzimuthLooks
cor_th = coherenceThreshold
nls0 = lengthBurst / (referenceSwath.burstSlcFirstLineOffsets[nBurst - 1] /
(nBurst - 1.0))
print('number of looks of the ScanSAR system: {}'.format(nls0))
if numberLooksScanSAR != None:
nls = numberLooksScanSAR
else:
nls = int(nls0)
print('number of looks to be used: {}'.format(nls))
####################################################
#read burst interferograms
inf = np.zeros((length, width, nls), dtype=np.complex64)
cnt = np.zeros((length, width), dtype=np.int8)
for i in range(nBurst):
if (i + 1) % 5 == 0 or (i + 1) == nBurst:
print('reading burst %02d' % (i + 1))
burst = np.fromfile(bursts[i],
dtype=np.complex64).reshape(lengthBurst, width)
#subset for the burst
cntBurst = cnt[0 +
referenceSwath.burstSlcFirstLineOffsets[i]:lengthBurst +
referenceSwath.burstSlcFirstLineOffsets[i], :]
infBurst = inf[0 +
referenceSwath.burstSlcFirstLineOffsets[i]:lengthBurst +
referenceSwath.burstSlcFirstLineOffsets[i], :, :]
#set number of non-zero pixels
cntBurst[np.nonzero(burst)] += 1
#get index
index1 = np.nonzero(np.logical_and(burst != 0, cntBurst <= nls))
index2 = index1 + (cntBurst[index1] - 1, )
#set values
infBurst[index2] = burst[index1]
#number of looks for each sample
if keep:
nlFile = 'number_of_looks.nl'
cnt.astype(np.int8).tofile(nlFile)
create_xml(nlFile, width, length, 'byte')
if filt:
import scipy.signal as ss
filterKernel = np.ones((filtWinSizeAzimuth, filtWinSizeRange),
dtype=np.float64)
for i in range(nls):
print('filtering look {}'.format(i + 1))
flag = (inf[:, :, i] != 0)
#scale = ss.fftconvolve(flag, filterKernel, mode='same')
#inf[:,:,i] = flag*ss.fftconvolve(inf[:,:,i], filterKernel, mode='same') / (scale + (scale==0))
#this should be faster?
scale = ss.convolve2d(flag, filterKernel, mode='same')
inf[:, :, i] = flag * ss.convolve2d(
inf[:, :, i], filterKernel, mode='same') / (scale +
(scale == 0))
#width and length after multilooking
widthm = int(width / rgl)
lengthm = int(length / azl)
#use the convention that ka > 0
ka = -np.polyval(referenceSwath.azimuthFmrateVsPixel[::-1],
create_multi_index(width, rgl))
#get spectral diversity inteferogram
offset_sd = []
for i in range(1, nls):
print('ouput spectral diversity inteferogram %d' % i)
#original spectral diversity inteferogram
sd = inf[:, :, 0] * np.conj(inf[:, :, i])
#replace original amplitude with its square root
index = np.nonzero(sd != 0)
sd[index] /= np.sqrt(np.absolute(sd[index]))
sdFile = outputList[i - 1]
sd.astype(np.complex64).tofile(sdFile)
create_xml(sdFile, width, length, 'int')
#multi look
sdm = multilook(sd, azl, rgl)
cor = cal_coherence_1(sdm)
#convert phase to offset
offset = np.angle(sdm) / (2.0 * np.pi * ka * tc * i)[None, :] / azsi
#compute offset using good samples
point_index = np.nonzero(
np.logical_and(cor >= cor_th,
np.angle(sdm) != 0))
npoint = round(np.size(point_index) / 2)
if npoint < 20:
print(
'WARNING: too few good samples for spectral diversity at look {}: {}'
.format(i, npoint))
offset_sd.append(0)
else:
offset_sd.append(
np.sum(offset[point_index] * cor[point_index]) /
np.sum(cor[point_index]))
if keep:
sdmFile = 'sd_%d_%drlks_%dalks.int' % (i, rgl, azl)
sdm.astype(np.complex64).tofile(sdmFile)
create_xml(sdmFile, widthm, lengthm, 'int')
corFile = 'sd_%d_%drlks_%dalks.cor' % (i, rgl, azl)
cor.astype(np.float32).tofile(corFile)
create_xml(corFile, widthm, lengthm, 'float')
offsetFile = 'sd_%d_%drlks_%dalks.off' % (i, rgl, azl)
offset.astype(np.float32).tofile(offsetFile)
create_xml(offsetFile, widthm, lengthm, 'float')
offset_mean = np.sum(np.array(offset_sd) * np.arange(1, nls)) / np.sum(
np.arange(1, nls))
return offset_mean