#!/usr/bin/env python3
# Author: Piyush Agram
# Copyright 2016
#
# Heresh Fattahi, updated for stack processing
import os
import glob
import datetime
import logging
import argparse
import numpy as np
from osgeo import gdal
import isce
import isceobj
from isceobj.Util.ImageUtil import ImageLib as IML
from isceobj.Util.decorators import use_api
import s1a_isce_utils as ut
from isce.applications.gdal2isce_xml import gdal2isce_xml
def createParser():
'''
Create command line parser.
'''
parser = argparse.ArgumentParser( description='Generate offset field between two Sentinel swaths')
parser.add_argument('-i', '--inp_reference', type=str, dest='reference', required=True,
help='Directory with the reference image')
parser.add_argument('-s', '--stack', type=str, dest='stack', default = None,
help='Directory with the stack xml files which includes the common valid region of the stack')
parser.add_argument('-d', '--dirname', type=str, dest='dirname', required=True,
help='directory with products to merge')
parser.add_argument('-o', '--outfile', type=str, dest='outfile', required=True,
help='Output merged file')
parser.add_argument('-m', '--method', type=str, dest='method', default='avg',
help='Method: top / bot/ avg')
parser.add_argument('-a', '--aligned', action='store_true', dest='isaligned', default=False,
help='Use reference information instead of coreg for merged grid.')
parser.add_argument('-l', '--multilook', action='store_true', dest='multilook', default=False,
help='Multilook the merged products. True or False')
parser.add_argument('-A', '--azimuth_looks', type=str, dest='numberAzimuthLooks', default=3, help='azimuth looks')
parser.add_argument('-R', '--range_looks', type=str, dest='numberRangeLooks', default=9, help='range looks')
parser.add_argument('-n', '--name_pattern', type=str, dest='namePattern', default='fine*int',
help='a name pattern of burst products that will be merged. '
'default: fine. it can be lat, lon, los, burst, hgt, shadowMask, incLocal')
parser.add_argument('-v', '--valid_only', action='store_true', dest='validOnly', default=False,
help='True for SLC, int and coherence. False for geometry files (lat, lon, los, hgt, shadowMask, incLocal).')
parser.add_argument('-u', '--use_virtual_files', action='store_true', dest='useVirtualFiles', default=False,
help='writing only a vrt of merged file. Default: True.')
parser.add_argument('-M', '--multilook_tool', type=str, dest='multilookTool', default='isce',
help='The tool used for multi-looking')
parser.add_argument('-N', '--no_data_value', type=float, dest='noData', default=None,
help='no data value when gdal is used for multi-looking')
return parser
def cmdLineParse(iargs = None):
'''
Command line parser.
'''
parser = createParser()
inps = parser.parse_args(args=iargs)
if inps.method not in ['top', 'bot', 'avg']:
raise Exception('Merge method should be in top / bot / avg')
return inps
def mergeBurstsVirtual(frame, referenceFrame, fileList, outfile, validOnly=True):
'''
Merging using VRTs.
'''
from VRTManager import Swath, VRTConstructor
swaths = [Swath(x) for x in frame]
refSwaths = [Swath(x) for x in referenceFrame]
###Identify the 4 corners and dimensions
#topSwath = min(swaths, key = lambda x: x.sensingStart)
#botSwath = max(swaths, key = lambda x: x.sensingStop)
#leftSwath = min(swaths, key = lambda x: x.nearRange)
#rightSwath = max(swaths, key = lambda x: x.farRange)
topSwath = min(refSwaths, key = lambda x: x.sensingStart)
botSwath = max(refSwaths, key = lambda x: x.sensingStop)
leftSwath = min(refSwaths, key = lambda x: x.nearRange)
rightSwath = max(refSwaths, key = lambda x: x.farRange)
totalWidth = int(np.round((rightSwath.farRange - leftSwath.nearRange)/leftSwath.dr + 1))
totalLength = int(np.round((botSwath.sensingStop - topSwath.sensingStart).total_seconds()/topSwath.dt + 1 ))
###Determine number of bands and type
img = isceobj.createImage()
img.load( fileList[0][0] + '.xml')
bands = img.bands
dtype = img.dataType
img.filename = outfile
#####Start the builder
###Now start building the VRT and then render it
builder = VRTConstructor(totalLength, totalWidth)
builder.setReferenceTime( topSwath.sensingStart)
builder.setReferenceRange( leftSwath.nearRange)
builder.setTimeSpacing( topSwath.dt )
builder.setRangeSpacing( leftSwath.dr)
builder.setDataType( dtype.upper())
builder.initVRT()
####Render XML and default VRT. VRT will be overwritten.
img.width = totalWidth
img.length =totalLength
img.renderHdr()
for bnd in range(1,bands+1):
builder.initBand(band = bnd)
for ind, swath in enumerate(swaths):
####Relative path
relfilelist = [os.path.relpath(x,
os.path.dirname(outfile)) for x in fileList[ind]]
builder.addSwath(swath, relfilelist, band=bnd, validOnly=validOnly)
builder.finishBand()
builder.finishVRT()
with open(outfile + '.vrt', 'w') as fid:
fid.write(builder.vrt)
def mergeBursts(frame, fileList, outfile,
method='top'):
'''
Merge burst products into single file.
Simple numpy based stitching
'''
###Check against metadata
if frame.numberOfBursts != len(fileList):
print('Warning : Number of burst products does not appear to match number of bursts in metadata')
t0 = frame.bursts[0].sensingStart
dt = frame.bursts[0].azimuthTimeInterval
width = frame.bursts[0].numberOfSamples
#######
tstart = frame.bursts[0].sensingStart
tend = frame.bursts[-1].sensingStop
nLines = int( np.round((tend - tstart).total_seconds() / dt)) + 1
print('Expected total nLines: ', nLines)
img = isceobj.createImage()
img.load( fileList[0] + '.xml')
bands = img.bands
scheme = img.scheme
npType = IML.NUMPY_type(img.dataType)
azReferenceOff = []
for index in range(frame.numberOfBursts):
burst = frame.bursts[index]
soff = burst.sensingStart + datetime.timedelta(seconds = (burst.firstValidLine*dt))
start = int(np.round((soff - tstart).total_seconds() / dt))
end = start + burst.numValidLines
azReferenceOff.append([start,end])
print('Burst: ', index, [start,end])
if index == 0:
linecount = start
outMap = IML.memmap(outfile, mode='write', nchannels=bands,
nxx=width, nyy=nLines, scheme=scheme, dataType=npType)
for index in range(frame.numberOfBursts):
curBurst = frame.bursts[index]
curLimit = azReferenceOff[index]
curMap = IML.mmapFromISCE(fileList[index], logging)
#####If middle burst
if index > 0:
topBurst = frame.bursts[index-1]
topLimit = azReferenceOff[index-1]
topMap = IML.mmapFromISCE(fileList[index-1], logging)
olap = topLimit[1] - curLimit[0]
print("olap: ", olap)
if olap <= 0:
raise Exception('No Burst Overlap')
for bb in range(bands):
topData = topMap.bands[bb][topBurst.firstValidLine: topBurst.firstValidLine + topBurst.numValidLines,:]
curData = curMap.bands[bb][curBurst.firstValidLine: curBurst.firstValidLine + curBurst.numValidLines,:]
im1 = topData[-olap:,:]
im2 = curData[:olap,:]
if method=='avg':
data = 0.5*(im1 + im2)
elif method == 'top':
data = im1
elif method == 'bot':
data = im2
else:
raise Exception('Method should be top/bot/avg')
outMap.bands[bb][linecount:linecount+olap,:] = data
tlim = olap
else:
tlim = 0
linecount += tlim
if index != (frame.numberOfBursts-1):
botBurst = frame.bursts[index+1]
botLimit = azReferenceOff[index+1]
olap = curLimit[1] - botLimit[0]
if olap < 0:
raise Exception('No Burst Overlap')
blim = botLimit[0] - curLimit[0]
else:
blim = curBurst.numValidLines
lineout = blim - tlim
for bb in range(bands):
curData = curMap.bands[bb][curBurst.firstValidLine: curBurst.firstValidLine + curBurst.numValidLines,:]
outMap.bands[bb][linecount:linecount+lineout,:] = curData[tlim:blim,:]
linecount += lineout
curMap = None
topMap = None
IML.renderISCEXML(outfile, bands,
nLines, width,
img.dataType, scheme)
oimg = isceobj.createImage()
oimg.load(outfile + '.xml')
oimg.imageType = img.imageType
oimg.renderHdr()
try:
outMap.bands[0].base.base.flush()
except:
pass
def multilook(infile, outname=None, alks=5, rlks=15, multilook_tool="isce", no_data=None):
'''
Take looks.
'''
# default output filename
if outname is None:
spl = os.path.splitext(infile)
ext = '.{0}alks_{1}rlks'.format(alks, rlks)
outname = spl[0] + ext + spl[1]
if multilook_tool=="gdal":
# remove existing *.hdr files, to avoid the following gdal error:
# ERROR 1: Input and output dataset sizes or band counts do not match in GDALDatasetCopyWholeRaster()
fbase = os.path.splitext(outname)[0]
print(f'remove {fbase}*.hdr')
for fname in glob.glob(f'{fbase}*.hdr'):
os.remove(fname)
print(f"multilooking {rlks} x {alks} using gdal for {infile} ...")
ds = gdal.Open(infile+'.vrt', gdal.GA_ReadOnly)
xSize = ds.RasterXSize
ySize = ds.RasterYSize
outXSize = int(xSize / int(rlks))
outYSize = int(ySize / int(alks))
srcXSize = outXSize * int(rlks)
srcYSize = outYSize * int(alks)
options_str = f'-of ENVI -outsize {outXSize} {outYSize} -srcwin 0 0 {srcXSize} {srcYSize} '
options_str += f'-a_nodata {no_data}' if no_data else ''
gdal.Translate(outname, ds, options=options_str)
# generate VRT file
gdal.Translate(outname+".vrt", outname, options='-of VRT')
gdal2isce_xml(outname)
else:
from mroipac.looks.Looks import Looks
print(f'multilooking {rlks} x {alks} using isce2 for {infile} ...')
inimg = isceobj.createImage()
inimg.load(infile + '.xml')
lkObj = Looks()
lkObj.setDownLooks(alks)
lkObj.setAcrossLooks(rlks)
lkObj.setInputImage(inimg)
lkObj.setOutputFilename(outname)
lkObj.looks()
return outname
def progress_cb(complete, message, cb_data):
'''Emit progress report in numbers for 10% intervals and dots for 3%
Link: https://stackoverflow.com/questions/68025043/adding-a-progress-bar-to-gdal-translate
'''
if int(complete*100) % 10 == 0:
msg = f'{complete*100:.0f}'
print(msg, end='', flush=True)
if msg == '100':
print(' ')
elif int(complete*100) % 3 == 0:
print(f'{cb_data}', end='', flush=True)
return
def main(iargs=None):
'''
Merge burst products to make it look like stripmap.
Currently will merge interferogram, lat, lon, z and los.
'''
inps=cmdLineParse(iargs)
virtual = inps.useVirtualFiles
swathList = ut.getSwathList(inps.reference)
referenceFrames = []
frames=[]
fileList = []
namePattern = inps.namePattern.split('*')
for swath in swathList:
ifg = ut.loadProduct(os.path.join(inps.reference , 'IW{0}.xml'.format(swath)))
if inps.stack:
stack = ut.loadProduct(os.path.join(inps.stack , 'IW{0}.xml'.format(swath)))
if inps.isaligned:
reference = ifg.reference
#this does not make sense, number of burst in reference is not necessarily number of bursts in interferogram.
#so comment it out.
# # checking inconsistent number of bursts in the secondary acquisitions
# if reference.numberOfBursts != ifg.numberOfBursts:
# raise ValueError('{} has different number of bursts ({}) than the reference ({})'.format(
# inps.reference, ifg.numberOfBursts, reference.numberOfBursts))
else:
reference = ifg
minBurst = ifg.bursts[0].burstNumber
maxBurst = ifg.bursts[-1].burstNumber
if minBurst==maxBurst:
print('Skipping processing of swath {0}'.format(swath))
continue
if inps.stack:
minStack = stack.bursts[0].burstNumber
print('Updating the valid region of each burst to the common valid region of the stack')
for ii in range(minBurst, maxBurst + 1):
ifg.bursts[ii-minBurst].firstValidLine = stack.bursts[ii-minStack].firstValidLine
ifg.bursts[ii-minBurst].firstValidSample = stack.bursts[ii-minStack].firstValidSample
ifg.bursts[ii-minBurst].numValidLines = stack.bursts[ii-minStack].numValidLines
ifg.bursts[ii-minBurst].numValidSamples = stack.bursts[ii-minStack].numValidSamples
frames.append(ifg)
referenceFrames.append(reference)
print('bursts: ', minBurst, maxBurst)
fileList.append([os.path.join(inps.dirname, 'IW{0}'.format(swath), namePattern[0] + '_%02d.%s'%(x,namePattern[1]))
for x in range(minBurst, maxBurst+1)])
mergedir = os.path.dirname(inps.outfile)
os.makedirs(mergedir, exist_ok=True)
suffix = '.full'
if (inps.numberRangeLooks == 1) and (inps.numberAzimuthLooks==1):
suffix=''
####Virtual flag is ignored for multi-swath data
if (not virtual):
print('User requested for multi-swath stitching.')
print('Virtual files are the only option for this.')
print('Proceeding with virtual files.')
mergeBurstsVirtual(frames, referenceFrames, fileList, inps.outfile+suffix, validOnly=inps.validOnly)
if (not virtual):
print('writing merged file to disk via gdal.Translate ...')
gdal.Translate(inps.outfile+suffix, inps.outfile+suffix+'.vrt',
options='-of ENVI -co INTERLEAVE=BIL',
callback=progress_cb,
callback_data='.')
if inps.multilook:
multilook(inps.outfile+suffix,
outname=inps.outfile,
alks=inps.numberAzimuthLooks,
rlks=inps.numberRangeLooks,
multilook_tool=inps.multilookTool,
no_data=inps.noData)
else:
print('Skipping multi-looking ....')
if __name__ == '__main__' :
'''
Merge products burst-by-burst.
'''
main()