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ISCE_INSAR/components/isceobj/Sensor/GRD/Radarsat2.py

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#!/usr/bin/env python3
#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
# Copyright 2014 California Institute of Technology. ALL RIGHTS RESERVED.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or agreed to in writing, software
# distributed under the License is distributed on an "AS IS" BASIS,
# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
# See the License for the specific language governing permissions and
# limitations under the License.
#
# United States Government Sponsorship acknowledged. This software is subject to
# U.S. export control laws and regulations and has been classified as 'EAR99 NLR'
# (No [Export] License Required except when exporting to an embargoed country,
# end user, or in support of a prohibited end use). By downloading this software,
# the user agrees to comply with all applicable U.S. export laws and regulations.
# The user has the responsibility to obtain export licenses, or other export
# authority as may be required before exporting this software to any 'EAR99'
# embargoed foreign country or citizen of those countries.
#
# Author: Piyush Agram
#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
import isce
import xml.etree.ElementTree as ElementTree
import datetime
import isceobj
from isceobj.Util import Poly1D, Poly2D
from isceobj.Scene.Frame import Frame
from isceobj.Sensor.Sensor import Sensor
from isceobj.Planet.Planet import Planet
from isceobj.Orbit.Orbit import StateVector, Orbit
from isceobj.Orbit.OrbitExtender import OrbitExtender
from isceobj.Planet.AstronomicalHandbook import Const
from iscesys.Component.Component import Component
from iscesys.DateTimeUtil.DateTimeUtil import DateTimeUtil as DTUtil
from GRDProduct import GRDProduct
import os
import glob
import json
import numpy as np
import shelve
import re
import matplotlib.pyplot as plt
sep = "\n"
tab = " "
lookMap = { 'RIGHT' : -1,
'LEFT' : 1}
class Radarsat2_GRD(Component):
"""
A Class representing RadarSAT 2 data
"""
def __init__(self):
Component.__init__(self)
self.xml = None
self.tiff = None
self.orbitFile = None
self.auxFile = None
self.orbitDir = None
self.auxDir = None
self.lutSigmaXml = None
self.productXml = None
self.noiseXml = None
self.noiseCorrectionApplied = False
self.noiseLUT = None
#self.manifest = None
#self.IPFversion = None
self.slantRangeFile = None
self._xml_root=None
self.output= None
self.lutSigma = None
self.product = GRDProduct()
self.product.configure()
def parse(self):
try:
with open(self.xml, 'r') as fid:
xmlstring = fid.read()
xmlstr = re.sub('\\sxmlns="[^"]+"', '', xmlstring, count=1)
except:
raise Exception('Could not read xml file {0}'.format(self.xml))
self._xml_root = ElementTree.fromstring(xmlstr)
self.populateMetadata()
self.populateBbox()
####Tru and locate an orbit file
if self.orbitFile is None:
if self.orbitDir is not None:
self.orbitFile = self.findOrbitFile()
####Read in the orbits
if self.orbitFile:
orb = self.extractPreciseOrbit()
else:
orb = self.getOrbitFromXML()
self.product.orbit.setOrbitSource('Header')
for sv in orb:
self.product.orbit.addStateVector(sv)
####Read in the gcps
if self.readGCPsFromXML:
gcps = self.readGCPsFromXML()
########
self.extractlutSigma()
#self.extractNoiseLUT()
self.extractgr2sr()
def getxmlattr(self, path, key):
try:
res = self._xml_root.find(path).attrib[key]
except:
raise Exception('Cannot find attribute %s at %s'%(key, path))
return res
def getxmlvalue(self, path):
try:
res = self._xml_root.find(path).text
except:
raise Exception('Tag= %s not found'%(path))
if res is None:
raise Exception('Tag = %s not found'%(path))
return res
def getxmlelement(self, path):
try:
res = self._xml_root.find(path)
except:
raise Exception('Cannot find path %s'%(path))
if res is None:
raise Exception('Cannot find path %s'%(path))
return res
def convertToDateTime(self, string):
dt = datetime.datetime.strptime(string,"%Y-%m-%dT%H:%M:%S.%fZ")
return dt
def getFrame(self):
return self.frame
def populateMetadata(self):
"""
Create metadata objects from the metadata files
"""
####Set each parameter one - by - one
mission = self.getxmlvalue('sourceAttributes/satellite')
swath = self.getxmlvalue('sourceAttributes/radarParameters/beams')
polarization = self.getxmlvalue('sourceAttributes/radarParameters/polarizations')
orig_prf = float(self.getxmlvalue('sourceAttributes/radarParameters/pulseRepetitionFrequency'))
#orbitnumber = int(self.getxmlvalue('adsHeader/absoluteOrbitNumber'))
frequency = float(self.getxmlvalue('sourceAttributes/radarParameters/radarCenterFrequency'))
#passDirection = self.getxmlvalue('sourceAttributes/orbitAndAttitude/orbitInformation/passDirection')
groundRangePixelSize = float(self.getxmlvalue('imageAttributes/rasterAttributes/sampledPixelSpacing'))
azimuthPixelSize = float(self.getxmlvalue('imageAttributes/rasterAttributes/sampledLineSpacing'))
rank = self.getxmlvalue('sourceAttributes/radarParameters/rank')
##################################
orb = self.getOrbitFromXML()
self.product.orbit.setOrbitSource('Header')
gcps = self.readGCPsFromXML()
#print('gcps=',gcps)
azt = np.zeros((len(gcps),3), dtype=np.float)
nvalid = 0
for ind,gcp in enumerate(gcps):
try:
tt,rr = orb.geo2rdr(gcp[2:])
aztime = tt.hour * 3600 + tt.minute * 60 + tt.second + 1e-6 * tt.microsecond
azt[nvalid,:] = [gcp[0], gcp[1], aztime] #line, pixel, time
nvalid += 1
#print('nvalid=',nvalid)
#print('aztime=',aztime)
#print('azt=',azt)
except:
pass
###Fit linear polynomial
pp = np.polyfit(azt[:nvalid,0], azt[::-1,2],1)
azimuthTimeInterval = abs(pp[0])
print('azimuthTimeInterval=',azimuthTimeInterval)
#print("Offset should be close to sensing start: ", datetime.timedelta(seconds=pp[0]))
#gcp = [line, pixel, lat, lon, hgt]
####################################
lines = int(self.getxmlvalue('imageAttributes/rasterAttributes/numberOfLines'))
print('startlines=',lines)
samples = int(self.getxmlvalue('imageAttributes/rasterAttributes/numberOfSamplesPerLine'))
totalProcessedAzimuthBandwidth = self.getxmlvalue('imageGenerationParameters/sarProcessingInformation/totalProcessedAzimuthBandwidth')
prf = totalProcessedAzimuthBandwidth # effective PRF can be double original, suggested by Piyush
#slantRangeTime = float(self.getxmlvalue('imageAnnotation/imageInformation/slantRangeTime'))
startingSlantRange = float(self.getxmlvalue('imageGenerationParameters/slantRangeToGroundRange/slantRangeTimeToFirstRangeSample')) * (Const.c/2)
incidenceAngle = (float(self.getxmlvalue('imageGenerationParameters/sarProcessingInformation/incidenceAngleNearRange')) + float(self.getxmlvalue('imageGenerationParameters/sarProcessingInformation/incidenceAngleFarRange')))/2.0
lineFlip = self.getxmlvalue('imageAttributes/rasterAttributes/lineTimeOrdering').upper() == 'DECREASING'
print('lineFlip',lineFlip)
if lineFlip:
sensingStop = self.convertToDateTime(self.getxmlvalue('imageGenerationParameters/sarProcessingInformation/zeroDopplerTimeFirstLine'))
sensingStart = self.convertToDateTime(self.getxmlvalue('imageGenerationParameters/sarProcessingInformation/zeroDopplerTimeLastLine'))
else:
sensingStart = self.convertToDateTime(self.getxmlvalue('imageGenerationParameters/sarProcessingInformation/zeroDopplerTimeFirstLine'))
sensingStop = self.convertToDateTime(self.getxmlvalue('imageGenerationParameters/sarProcessingInformation/zeroDopplerTimeLastLine'))
####Radarsat 2 me be right looking or left looking
#lookSide = -1
lookSide = lookMap[self.getxmlvalue('sourceAttributes/radarParameters/antennaPointing').upper()]
print('lookSide=',lookSide)
###Read ascending node for phase calibration
###Noise correction
#correctionApplied = self.getxmlvalue('imageGenerationParameters/sarProcessingInformation/radiometricSmoothingPerformed').upper() == 'TRUE'
correctionApplied = False
print('correctionApplied=',correctionApplied)
#Populate Frame
self.product.numberOfSamples = samples
self.product.numberOfLines = lines
self.product.startingGroundRange = 0.0
self.product.startingSlantRange = startingSlantRange
#self.product.trackNumber = ((orbitnumber-73)%175) + 1
#self.product.orbitNumber = orbitnumber
self.product.frameNumber = 1
self.product.polarization = polarization
self.product.prf = prf
self.product.azimuthTimeInterval = azimuthTimeInterval
#self.product.passDirection = passDirection
self.product.radarWavelength = Const.c / frequency
self.product.groundRangePixelSize = groundRangePixelSize
#self.product.ascendingNodeTime = ascTime
#self.product.slantRangeTime = slantRangeTime
self.product.sensingStart = sensingStart
self.product.sensingStop = sensingStop
self.noiseCorrectionApplied = correctionApplied
def populateBbox(self, margin=0.1):
'''
Populate the bounding box from metadata.
'''
glist = (self.getxmlelement('imageAttributes/geographicInformation/geolocationGrid'))
lat = []
lon = []
for child in glist.getchildren():
for grandchild in child.getchildren():
string = ElementTree.tostring(grandchild, encoding = 'unicode', method = 'xml')
string = string.split("<")[1]
string = string.split(">")[0]
if string == 'geodeticCoordinate':
lat.append( float(grandchild.find('latitude').text))
lon.append( float(grandchild.find('longitude').text))
self.product.bbox = [min(lat) - margin, max(lat) + margin, min(lon) - margin, max(lon) + margin]
print('coordinate=',self.product.bbox)
return
#################################
def getOrbitFromXML(self):
'''
Populate orbit.
'''
orb = Orbit()
orb.configure()
for node in self._xml_root.find('sourceAttributes/orbitAndAttitude/orbitInformation'):
if node.tag == 'stateVector':
sv = StateVector()
sv.configure()
for z in node.getchildren():
if z.tag == 'timeStamp':
timeStamp = self.convertToDateTime(z.text)
elif z.tag == 'xPosition':
xPosition = float(z.text)
elif z.tag == 'yPosition':
yPosition = float(z.text)
elif z.tag == 'zPosition':
zPosition = float(z.text)
elif z.tag == 'xVelocity':
xVelocity = float(z.text)
elif z.tag == 'yVelocity':
yVelocity = float(z.text)
elif z.tag == 'zVelocity':
zVelocity = float(z.text)
sv.setTime(timeStamp)
sv.setPosition([xPosition, yPosition, zPosition])
sv.setVelocity([xVelocity, yVelocity, zVelocity])
orb.addStateVector(sv)
orbExt = OrbitExtender(planet=Planet(pname='Earth'))
orbExt.configure()
newOrb = orbExt.extendOrbit(orb)
return newOrb
self.product.orbit.setOrbitSource('Header')
for sv in newOrb:
self.product.orbit.addStateVector(sv)
def readGCPsFromXML(self):
'''
Populate GCPS
'''
gcps = []
for node in self._xml_root.find('imageAttributes/geographicInformation/geolocationGrid'):
if not node.tag == 'imageTiePoint':
continue
for z in node.getchildren():
if z.tag == 'imageCoordinate':
for zz in z.getchildren():
if zz.tag == 'line':
line = float(zz.text)
elif zz.tag == 'pixel':
pixel = float(zz.text)
if z.tag == 'geodeticCoordinate':
for zz in z.getchildren():
if zz.tag == 'latitude':
lat = float(zz.text)
elif zz.tag == 'longitude':
lon = float(zz.text)
elif zz.tag == 'height':
hgt = float(zz.text)
pt = [line, pixel, lat, lon, hgt]
gcps.append(pt)
return gcps
#######################################
def extractlutSigma(self, iargs=None):
'''
Extract Sigma nought look up table from calibration file.
'''
from scipy.interpolate import RectBivariateSpline
from scipy.interpolate import interp1d
from scipy.interpolate import Rbf, InterpolatedUnivariateSpline
if self.lutSigmaXml is None:
raise Exception('No calibration file provided')
try:
with open(self.lutSigmaXml, 'r') as fid:
xmlstr = fid.read()
except:
raise Exception('Could not read calibration file: {0}'.format(self.lutSigmaXml))
_xml_root = ElementTree.fromstring(xmlstr)
#print(_xml_root)
node = _xml_root.find('gains').text
node = node.split(' ')
node = [float(x) for x in node]
#data = None
#nump = len(node) #this is the length of gains
#numps = list(range(nump))
sigmadata = np.asarray(node)
self.lutSigma = sigmadata
#self.lutSigma = interp1d(numps, sigmadata, kind='cubic')
#self.lutSigma = InterpolatedUnivariateSpline(numps, sigmadata)
if False:
import matplotlib.pyplot as plt
plt.figure()
plt.imshow(data)
plt.colorbar()
plt.show()
return
#====================================
def extractgr2sr(self):
'''
Extract Slant Range to Ground Range polynomial
'''
from scipy.interpolate import interp1d
node = self._xml_root.find('imageGenerationParameters')
#num = int(node.attrib['count'])
lines = []
data = []
for child in node.getchildren():
for child in node.getchildren():
string = ElementTree.tostring(child, encoding = 'unicode', method = 'xml')
string = string.split("<")[1]
string = string.split(">")[0]
if string == 'slantRangeToGroundRange':
t0 = self.convertToDateTime(child.find('zeroDopplerAzimuthTime').text)
lines.append( (t0-self.product.sensingStart).total_seconds()/self.product.azimuthTimeInterval)
pp = [float(x) for x in child.find('groundToSlantRangeCoefficients').text.split()]
meangr = float( child.find('groundRangeOrigin').text)
if meangr !=0 :
raise Exception('Ground range image does not start at zero coordinate')
data.append(pp[::-1])
#print('lines123=',lines)
#print('data0=',data)
###If polynomial starts beyond first line
if lines[0] > 0:
lines.insert(0, 0.)
pp = data[0]
data.insert(0,pp)
#print('data1=',data)
####If polynomial ends before last line
if lines[-1] < (self.product.numberOfLines-1):
lines.append(self.product.numberOfLines-1.0)
pp = data[-1]
data.append(pp)
#print('data2=',data)
lines = np.array(lines)
data = np.array(data)
#print('lines=',lines)
#print('data=',data)
LUT = []
for ii in range(data.shape[1]):
col = data[:,ii]
#print('col=',col)
LUT.append(interp1d(lines, col, bounds_error=False, assume_sorted=True))
self.gr2srLUT = LUT
#print('lines=',len(self.gr2srLUT))
#print('data=',data)
if False:
import matplotlib.pyplot as plt
plt.figure()
plt.imshow(data)
plt.colorbar()
plt.show()
return
def extractImage(self, parse=False, removeNoise=False, verbose=True):
"""
Use gdal python bindings to extract image
"""
try:
from osgeo import gdal
except ImportError:
raise Exception('GDAL python bindings not found. Need this for RSAT2/ TandemX / Sentinel1A.')
from scipy.interpolate import interp2d
if parse:
self.parse()
print('Extracting normalized image ....')
src = gdal.Open(self.tiff.strip(), gdal.GA_ReadOnly)
band = src.GetRasterBand(1)
if self.product.numberOfSamples != src.RasterXSize:
raise Exception('Width in metadata and image dont match')
if self.product.numberOfLines != src.RasterYSize:
raise Exception('Length in metadata and image dont match')
noiseFactor = 0.0
if (not removeNoise) and self.noiseCorrectionApplied:
print('User asked for data without noise corrections, but product appears to be corrected. Adding back noise from LUT ....')
noiseFactor = 1.0
elif removeNoise and (not self.noiseCorrectionApplied):
print('User asked for data with noise corrections, but the products appears to not be corrected. Applying noise corrections from LUT ....')
noiseFactor = -1.0
elif (not removeNoise) and (not self.noiseCorrectionApplied):
print('User asked for data without noise corrections. The product contains uncorrected data ... unpacking ....')
else:
print('User asked for noise corrected data and the product appears to be noise corrected .... unpacking ....')
###Write original GRD to file
fid = open(self.output, 'wb')
lineFlip = self.getxmlvalue('imageAttributes/rasterAttributes/lineTimeOrdering').upper() == 'DECREASING'
pixFlip = self.getxmlvalue('imageAttributes/rasterAttributes/pixelTimeOrdering').upper() == 'DECREASING'
lines = int(self.getxmlvalue('imageAttributes/rasterAttributes/numberOfLines'))
pix = np.arange(self.product.numberOfSamples)
lin =np.arange(self.product.numberOfLines)
for ii in range(self.product.numberOfLines//lines + 1):
ymin = int(ii*lines)
ymax = int(np.clip(ymin+lines,0, self.product.numberOfLines))
print('ymin=',ymin)
print('ymax=',ymax)
if ymax == ymin:
break
lin = np.arange(ymin,ymax)
####Read in one line of data
data = 1.0 * band.ReadAsArray(0, ymin, self.product.numberOfSamples, ymax-ymin)
#lut = self.lutSigma(lin,pix,grid=True)
lut = self.lutSigma
if noiseFactor != 0.0:
noise = self.noiseLUT(lin,pix)
#noise = self.noiseLUT(lin,pix,grid=True)
else:
noise = 0.0
#outdata = data
outdata = data*data/(lut*lut) + noiseFactor * noise/(lut*lut)
#outdata = 10 * np.log10(outdata)
if lineFlip:
if verbose:
print('Vertically Flipping data')
outdata = np.flipud(outdata)
if pixFlip:
if verbose:
print('Horizontally Flipping data')
outdata = np.fliplr(outdata)
outdata.astype(np.float32).tofile(fid)
fid.close()
####Render ISCE XML
L1cImage = isceobj.createImage()
L1cImage.setByteOrder('l')
L1cImage.dataType = 'FLOAT'
L1cImage.setFilename(self.output)
L1cImage.setAccessMode('read')
L1cImage.setWidth(self.product.numberOfSamples)
L1cImage.setLength(self.product.numberOfLines)
L1cImage.renderHdr()
L1cImage.renderVRT()
band = None
src = None
self.extractSlantRange()
return
def extractSlantRange(self):
'''
Extract pixel-by-pixel slant range file for GRD files.
'''
if self.slantRangeFile is None:
return
print('Extracing slant range ....')
###Write original L1c to file
fid = open(self.slantRangeFile, 'wb')
pix = np.arange(self.product.numberOfSamples) * self.product.groundRangePixelSize
lin = np.arange(self.product.numberOfLines)
polys = np.zeros((self.product.numberOfLines, len(self.gr2srLUT)))
for ii, intp in enumerate(self.gr2srLUT):
polys[:,ii] = intp(lin)
for ii in range(self.product.numberOfLines):
pp = polys[ii,:]
outdata = np.polyval(pp, pix)
outdata.tofile(fid)
fid.close()
####Render ISCE XML
L1cImage = isceobj.createImage()
L1cImage.setByteOrder('l')
L1cImage.dataType = 'DOUBLE'
L1cImage.setFilename(self.slantRangeFile)
L1cImage.setAccessMode('read')
L1cImage.setWidth(self.product.numberOfSamples)
L1cImage.setLength(self.product.numberOfLines)
L1cImage.renderHdr()
L1cImage.renderVRT()
self.product.slantRangeimage = L1cImage
def createParser():
import argparse
parser = argparse.ArgumentParser( description = 'Radarsar parser' )
parser.add_argument('-d', '--dirname', dest='dirname', type=str,
default=None, help='SAFE format directory. (Recommended)')
parser.add_argument('-o', '--outdir', dest='outdir', type=str,
required=True, help='Output L1c prefix.')
parser.add_argument('--orbitdir', dest='orbitdir', type=str,
default=None, help = 'Directory with all the orbits')
parser.add_argument('--auxdir', dest='auxdir', type=str,
default=None, help = 'Directory with all the aux products')
parser.add_argument('--denoise', dest='denoise', action='store_true',
default=False, help = 'Add noise back if removed')
return parser
def cmdLineParse(iargs=None):
'''
Command Line Parser.
'''
import fnmatch
import glob
parser = createParser()
inps = parser.parse_args(args=iargs)
print('inpssss=',inps.dirname)
if inps.dirname is None:
raise Exception('File is not provided')
####First find HH Product path
swathid = 'product.xml'
swathid1 = 'imagery_HH.'
swathid2 = 'lutSigma.xml'
inps.data = {}
#Find XML file
patt = os.path.join('RS2_*', swathid)
match = glob.glob(patt)
if len(match) == 0:
raise Exception('Target file {0} not found'.format(patt))
inps.data['xml'] = match[0]
#Find TIFF file
patt = os.path.join('RS2_*', swathid1+'*')
match = glob.glob(patt)
if len(match) == 0 :
raise Exception('Target file {0} not found'.format(patt))
inps.data['tiff'] = match[0]
#Find Calibration file
patt = os.path.join('RS2_*', swathid2)
match = glob.glob(patt)
if len(match) == 0 :
raise Exception('Target file {0} not found'.format(patt))
inps.data['calibration'] = match[0]
return inps
def main(iargs=None):
inps = cmdLineParse(iargs)
rangeDone = False
obj = Radarsat2_GRD()
obj.configure()
obj.xml = inps.data['xml']
obj.tiff = inps.data['tiff']
obj.lutSigmaXml = inps.data['calibration']
if not os.path.isdir(inps.outdir):
os.mkdir(inps.outdir)
else:
print('Output directory {0} already exists.'.format(inps.outdir))
obj.output = os.path.join(inps.outdir, 'Sigma0_' + 'HH' + '.img')
if not rangeDone:
obj.slantRangeFile = os.path.join(inps.outdir, 'slantRange.img')
rangeDone = True
obj.parse()
obj.extractImage(removeNoise=inps.denoise)
dbname = os.path.join(inps.outdir, 'metadata')
with shelve.open(dbname) as db:
db['HH'] = obj.product
if __name__ == '__main__':
'''
Main driver.
'''
main()
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