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FilterAndCoh: use fine.cor(.full) for multilooked (full-reso) cpx cor file 

topsStack/FilterAndCoherence.py:
+ add .full suffix to the complex coherence filename only if the multilook number is 1
+ for multilook number as 1, do not run looks sub-module

topsStack/Stack.filter_coherence(): add .full suffix only when azLooks * rgLooks == 1

topsStack/mergeBursts.py: add python3 at the top of script
LT1AB
yunjunz 2020-05-14 15:23:17 -07:00 committed by piyushrpt
parent 89839bc453
commit 6a02f79277
3 changed files with 55 additions and 50 deletions
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32
contrib/stack/topsStack/FilterAndCoherence.py
View File

@ -128,25 +128,31 @@ def estCpxCoherence(slc1_file, slc2_file, cpx_coh_file, alks=3, rlks=9):
from isceobj.TopsProc.runBurstIfg import computeCoherence from isceobj.TopsProc.runBurstIfg import computeCoherence
from mroipac.looks.Looks import Looks from mroipac.looks.Looks import Looks
# get the full resolution file name
if alks * rlks == 1:
cpx_coh_file_full = cpx_coh_file
else:
cpx_coh_file_full = cpx_coh_file+'.full'
# calculate complex coherence in full resolution # calculate complex coherence in full resolution
computeCoherence(slc1_file, slc2_file, cpx_coh_file) computeCoherence(slc1_file, slc2_file, cpx_coh_file_full)
# multilook # multilook
print('Multilooking {0} ...'.format(cpx_coh_file)) if alks * rlks > 1:
print('Multilooking {0} ...'.format(cpx_coh_file_full))
inimg = isceobj.createImage() inimg = isceobj.createImage()
inimg.load(cpx_coh_file + '.xml') inimg.load(cpx_coh_file_full + '.xml')
outname = os.path.splitext(inimg.filename)[0] lkObj = Looks()
lkObj = Looks() lkObj.setDownLooks(alks)
lkObj.setDownLooks(alks) lkObj.setAcrossLooks(rlks)
lkObj.setAcrossLooks(rlks) lkObj.setInputImage(inimg)
lkObj.setInputImage(inimg) lkObj.setOutputFilename(cpx_coh_file)
lkObj.setOutputFilename(outname) lkObj.looks()
lkObj.looks()
# remove full resolution coherence file # remove full resolution coherence file
ret=os.system('rm '+cpx_coh_file) os.remove(cpx_coh_file_full)
return return

71
contrib/stack/topsStack/Stack.py
View File

@ -76,7 +76,7 @@ class config(object):
self.f.write('dem : ' + self.dem + '\n') self.f.write('dem : ' + self.dem + '\n')
self.f.write('geom_referenceDir : ' + self.geom_referenceDir + '\n') self.f.write('geom_referenceDir : ' + self.geom_referenceDir + '\n')
self.f.write('##########################' + '\n') self.f.write('##########################' + '\n')
def geo2rdr(self,function): def geo2rdr(self,function):
self.f.write('##########################' + '\n') self.f.write('##########################' + '\n')
self.f.write(function + '\n') self.f.write(function + '\n')
@ -207,10 +207,10 @@ class config(object):
self.f.write('strength : ' + self.filtStrength + '\n') self.f.write('strength : ' + self.filtStrength + '\n')
self.f.write('slc1 : ' + self.slc1 + '\n') self.f.write('slc1 : ' + self.slc1 + '\n')
self.f.write('slc2 : ' + self.slc2 + '\n') self.f.write('slc2 : ' + self.slc2 + '\n')
self.f.write('complex_coh : '+ self.cpxcor + '\n') self.f.write('complex_coh : '+ self.cpxCohName + '\n')
self.f.write('range_looks : ' + self.rangeLooks + '\n') self.f.write('range_looks : ' + self.rangeLooks + '\n')
self.f.write('azimuth_looks : ' + self.azimuthLooks + '\n') self.f.write('azimuth_looks : ' + self.azimuthLooks + '\n')
def unwrap(self, function): def unwrap(self, function):
self.f.write('###################################'+'\n') self.f.write('###################################'+'\n')
self.f.write(function + '\n') self.f.write(function + '\n')
@ -248,18 +248,18 @@ class config(object):
# CPU or GPU # CPU or GPU
self.f.write('denseOffsets : ' + '\n') self.f.write('denseOffsets : ' + '\n')
#self.f.write('DenseOffsets : ' + '\n') #self.f.write('DenseOffsets : ' + '\n')
#self.f.write('cuDenseOffsets : ' + '\n') #self.f.write('cuDenseOffsets : ' + '\n')
self.f.write('reference : ' + self.reference + '\n') self.f.write('reference : ' + self.reference + '\n')
self.f.write('secondary : ' + self.secondary + '\n') self.f.write('secondary : ' + self.secondary + '\n')
self.f.write('outprefix : ' + self.output + '\n') self.f.write('outprefix : ' + self.output + '\n')
#self.f.write('ww : 256\n') #self.f.write('ww : 256\n')
#self.f.write('wh : 128\n') #self.f.write('wh : 128\n')
def finalize(self): def finalize(self):
self.f.close() self.f.close()
class run(object): class run(object):
""" """
@ -360,7 +360,7 @@ class run(object):
configObj.reference = os.path.join(self.work_dir,'reference/') configObj.reference = os.path.join(self.work_dir,'reference/')
configObj.secondary = os.path.join(self.work_dir,'secondarys/'+secondary) configObj.secondary = os.path.join(self.work_dir,'secondarys/'+secondary)
configObj.baselineFile = os.path.join(self.work_dir, 'merged/baselines/' + secondary + '/' + secondary ) configObj.baselineFile = os.path.join(self.work_dir, 'merged/baselines/' + secondary + '/' + secondary )
configObj.computeGridBaseline('[Function-1]') configObj.computeGridBaseline('[Function-1]')
configObj.finalize() configObj.finalize()
del configObj del configObj
self.runf.write(self.text_cmd + 'SentinelWrapper.py -c ' + configName+'\n') self.runf.write(self.text_cmd + 'SentinelWrapper.py -c ' + configName+'\n')
@ -370,8 +370,8 @@ class run(object):
configObj.configure(self) configObj.configure(self)
configObj.reference = os.path.join(self.work_dir,'reference/') configObj.reference = os.path.join(self.work_dir,'reference/')
configObj.secondary = os.path.join(self.work_dir,'reference/') configObj.secondary = os.path.join(self.work_dir,'reference/')
configObj.baselineFile = os.path.join(self.work_dir, 'merged/baselines/' + stackReferenceDate + '/' + stackReferenceDate) configObj.baselineFile = os.path.join(self.work_dir, 'merged/baselines/' + stackReferenceDate + '/' + stackReferenceDate)
configObj.computeGridBaseline('[Function-1]') configObj.computeGridBaseline('[Function-1]')
configObj.finalize() configObj.finalize()
del configObj del configObj
self.runf.write(self.text_cmd + 'SentinelWrapper.py -c ' + configName+'\n') self.runf.write(self.text_cmd + 'SentinelWrapper.py -c ' + configName+'\n')
@ -476,11 +476,11 @@ class run(object):
configObj.misregFile = os.path.join(self.work_dir , 'misreg/range/pairs/' + reference+'_'+secondary + '/' + reference+'_'+secondary + '.txt') configObj.misregFile = os.path.join(self.work_dir , 'misreg/range/pairs/' + reference+'_'+secondary + '/' + reference+'_'+secondary + '.txt')
configObj.rangeMisreg('[Function-4]') configObj.rangeMisreg('[Function-4]')
configObj.finalize() configObj.finalize()
self.runf.write(self.text_cmd + 'SentinelWrapper.py -c ' + configName + '\n') self.runf.write(self.text_cmd + 'SentinelWrapper.py -c ' + configName + '\n')
######################## ########################
def timeseries_misregistration(self): def timeseries_misregistration(self):
#inverting the misregistration offsets of the overlap pairs to estimate the offsets of each date #inverting the misregistration offsets of the overlap pairs to estimate the offsets of each date
@ -588,7 +588,7 @@ class run(object):
geometryList = ['lat*rdr', 'lon*rdr', 'los*rdr', 'hgt*rdr', 'shadowMask*rdr','incLocal*rdr'] geometryList = ['lat*rdr', 'lon*rdr', 'los*rdr', 'hgt*rdr', 'shadowMask*rdr','incLocal*rdr']
multiookToolDict = {'lat*rdr': 'gdal', 'lon*rdr': 'gdal', 'los*rdr': 'gdal' , 'hgt*rdr':"gdal", 'shadowMask*rdr':"isce",'incLocal*rdr':"gdal"} multiookToolDict = {'lat*rdr': 'gdal', 'lon*rdr': 'gdal', 'los*rdr': 'gdal' , 'hgt*rdr':"gdal", 'shadowMask*rdr':"isce",'incLocal*rdr':"gdal"}
noDataDict = {'lat*rdr': '0', 'lon*rdr': '0', 'los*rdr': '0' , 'hgt*rdr':None, 'shadowMask*rdr':None,'incLocal*rdr':"0"} noDataDict = {'lat*rdr': '0', 'lon*rdr': '0', 'los*rdr': '0' , 'hgt*rdr':None, 'shadowMask*rdr':None,'incLocal*rdr':"0"}
for i in range(len(geometryList)): for i in range(len(geometryList)):
pattern = geometryList[i] pattern = geometryList[i]
configName = os.path.join(self.config_path,'config_merge_' + pattern.split('*')[0]) configName = os.path.join(self.config_path,'config_merge_' + pattern.split('*')[0])
@ -629,7 +629,7 @@ class run(object):
configObj.mergeBurst('[Function-1]') configObj.mergeBurst('[Function-1]')
configObj.finalize() configObj.finalize()
self.runf.write(self.text_cmd + 'SentinelWrapper.py -c ' + configName + '\n') self.runf.write(self.text_cmd + 'SentinelWrapper.py -c ' + configName + '\n')
geometryList = ['lat*rdr', 'lon*rdr', 'los*rdr', 'hgt*rdr', 'shadowMask*rdr','incLocal*rdr'] geometryList = ['lat*rdr', 'lon*rdr', 'los*rdr', 'hgt*rdr', 'shadowMask*rdr','incLocal*rdr']
for i in range(len(geometryList)): for i in range(len(geometryList)):
pattern = geometryList[i] pattern = geometryList[i]
@ -656,16 +656,18 @@ class run(object):
reference = pair[0] reference = pair[0]
secondary = pair[1] secondary = pair[1]
mergedDir = os.path.join(self.work_dir, 'merged/interferograms/' + reference + '_' + secondary) mergedDir = os.path.join(self.work_dir, 'merged/interferograms/' + reference + '_' + secondary)
mergedSLCDir = os.path.join(self.work_dir, 'merged/SLC') mergedSLCDir = os.path.join(self.work_dir, 'merged/SLC')
configName = os.path.join(self.config_path ,'config_igram_filt_coh_' + reference + '_' + secondary) configName = os.path.join(self.config_path, 'config_igram_filt_coh_' + reference + '_' + secondary)
configObj = config(configName) configObj = config(configName)
configObj.configure(self) configObj.configure(self)
configObj.input = os.path.join(mergedDir,'fine.int') configObj.input = os.path.join(mergedDir, 'fine.int')
configObj.filtName = os.path.join(mergedDir,'filt_fine.int') configObj.filtName = os.path.join(mergedDir, 'filt_fine.int')
configObj.cohName = os.path.join(mergedDir,'filt_fine.cor') configObj.cohName = os.path.join(mergedDir, 'filt_fine.cor')
configObj.slc1=os.path.join(mergedSLCDir, '{}/{}.slc.full'.format(reference, reference)) configObj.slc1 = os.path.join(mergedSLCDir, '{}/{}.slc.full'.format(reference, reference))
configObj.slc2=os.path.join(mergedSLCDir, '{}/{}.slc.full'.format(secondary, secondary)) configObj.slc2 = os.path.join(mergedSLCDir, '{}/{}.slc.full'.format(secondary, secondary))
configObj.cpxcor=os.path.join(mergedDir,'fine.cor.full') configObj.cpxCohName = os.path.join(mergedDir, 'fine.cor')
if int(self.rangeLooks) * int(self.azimuthLooks) == 1:
configObj.cpxCohName += '.full'
#configObj.filtStrength = str(self.filtStrength) #configObj.filtStrength = str(self.filtStrength)
configObj.FilterAndCoherence('[Function-1]') configObj.FilterAndCoherence('[Function-1]')
configObj.finalize() configObj.finalize()
@ -769,7 +771,7 @@ class sentinelSLC(object):
start = '<coordinates>' start = '<coordinates>'
end = '</coordinates>' end = '</coordinates>'
pnts = xmlstr[xmlstr.find(start)+len(start):xmlstr.find(end)].split() pnts = xmlstr[xmlstr.find(start)+len(start):xmlstr.find(end)].split()
else: else:
file=os.path.join(safe,'preview/map-overlay.kml') file=os.path.join(safe,'preview/map-overlay.kml')
kmlFile = open( file, 'r' ).read(-1) kmlFile = open( file, 'r' ).read(-1)
@ -777,7 +779,7 @@ class sentinelSLC(object):
kmlData = ET.fromstring( kmlFile ) kmlData = ET.fromstring( kmlFile )
document = kmlData.find('Document/Folder/GroundOverlay/gxLatLonQuad') document = kmlData.find('Document/Folder/GroundOverlay/gxLatLonQuad')
pnts = document.find('coordinates').text.split() pnts = document.find('coordinates').text.split()
# convert the pnts to a list # convert the pnts to a list
from scipy.spatial import distance as dist from scipy.spatial import distance as dist
import numpy as np import numpy as np
@ -816,7 +818,7 @@ class sentinelSLC(object):
# our bottom-right point # our bottom-right point
D = dist.cdist(tl[np.newaxis], rightMost, "euclidean")[0] D = dist.cdist(tl[np.newaxis], rightMost, "euclidean")[0]
(br, tr) = rightMost[np.argsort(D)[::-1], :] (br, tr) = rightMost[np.argsort(D)[::-1], :]
# return the coordinates in top-left, top-right, # return the coordinates in top-left, top-right,
# bottom-right, and bottom-left order # bottom-right, and bottom-left order
temp = np.array([tl, tr, br, bl], dtype="float32") temp = np.array([tl, tr, br, bl], dtype="float32")
@ -839,7 +841,7 @@ class sentinelSLC(object):
for safe in self.safe_file.split(): for safe in self.safe_file.split():
safeObj=sentinelSLC(safe) safeObj=sentinelSLC(safe)
pnts = safeObj.getkmlQUAD(safe) pnts = safeObj.getkmlQUAD(safe)
# The coordinates must be specified in counter-clockwise order with the first coordinate corresponding # The coordinates must be specified in counter-clockwise order with the first coordinate corresponding
# to the lower-left corner of the overlayed image # to the lower-left corner of the overlayed image
counter=0 counter=0
for pnt in pnts: for pnt in pnts:
@ -852,7 +854,7 @@ class sentinelSLC(object):
elif counter==3: elif counter==3:
lat_frame_max.append(float(pnt.split(',')[1])) lat_frame_max.append(float(pnt.split(',')[1]))
counter+=1 counter+=1
self.SNWE=[min(lats),max(lats),min(lons),max(lons)] self.SNWE=[min(lats),max(lats),min(lons),max(lons)]
# checking for missing gaps, by doing a difference between end and start of frames # checking for missing gaps, by doing a difference between end and start of frames
@ -864,7 +866,7 @@ class sentinelSLC(object):
lat_frame_min.sort() lat_frame_min.sort()
lat_frame_max.append(temp2) lat_frame_max.append(temp2)
lat_frame_max.sort() lat_frame_max.sort()
# combining the frame north and south left edge # combining the frame north and south left edge
lat_frame_min = np.transpose(np.array(lat_frame_min)) lat_frame_min = np.transpose(np.array(lat_frame_min))
lat_frame_max = np.transpose(np.array(lat_frame_max)) lat_frame_max = np.transpose(np.array(lat_frame_max))
@ -882,7 +884,7 @@ class sentinelSLC(object):
print(lat_frame_max) print(lat_frame_max)
print(lat_frame_min-lat_frame_max) print(lat_frame_min-lat_frame_max)
print("gap")""" print("gap")"""
#raise Exception("STOP") #raise Exception("STOP")
self.frame_nogap=overlap_check self.frame_nogap=overlap_check
@ -899,7 +901,7 @@ class sentinelSLC(object):
print(obj.polarization) print(obj.polarization)
# add by Minyan # add by Minyan
obj.polarization='vv' obj.polarization='vv'
#obj.output = '{0}-SW{1}'.format(safe,swathnum) #obj.output = '{0}-SW{1}'.format(safe,swathnum)
obj.parse() obj.parse()
s,n,w,e = obj.product.bursts[0].getBbox() s,n,w,e = obj.product.bursts[0].getBbox()
@ -1001,7 +1003,7 @@ echo This jobs runs on the following processors:
echo `cat $PBS_NODEFILE` echo `cat $PBS_NODEFILE`
echo " " echo " "
# #
# Run the parallel with the nodelist and command file # Run the parallel with the nodelist and command file
# #
@ -1010,8 +1012,5 @@ echo " "
f.write('parallel --sshloginfile $PBS_NODEFILE -a ' + os.path.basename(runFile) + '\n') f.write('parallel --sshloginfile $PBS_NODEFILE -a ' + os.path.basename(runFile) + '\n')
f.write('') f.write('')
f.close() f.close()
""" """

2
contrib/stack/topsStack/mergeBursts.py
View File

@ -1,4 +1,4 @@
# #!/usr/bin/env python3
# Author: Piyush Agram # Author: Piyush Agram
# Copyright 2016 # Copyright 2016
# #