def main(argv):
inps = cmdLineParse()
if inps.template_file:
inps = read_template2inps(inps.template_file)
if inps.ref_date == 'no':
print 'No reference date input, skip this step.'
return inps.timeseries_file
elif inps.ref_date.lower() in ['auto']:
print '------------------------------------------------------------'
print 'auto choose reference date based on minimum residual RMS'
if not inps.resid_file:
inps.resid_file = os.path.splitext(
inps.timeseries_file)[0] + 'InvResid.h5'
rms_list, date_list = ut.get_residual_rms(inps.resid_file,
inps.mask_file,
inps.ramp_type)
ref_idx = np.argmin(rms_list)
inps.ref_date = date_list[ref_idx]
print 'date with minimum residual RMS: %s - %.4f' % (inps.ref_date,
rms_list[ref_idx])
print '------------------------------------------------------------'
elif os.path.isfile(inps.ref_date):
print 'read reference date from file: ' + inps.ref_date
inps.ref_date = ptime.read_date_list(inps.ref_date)[0]
# Referencing input file
inps.outfile = ref_date_file(inps.timeseries_file, inps.ref_date,
inps.outfile)
return inps.outfile
def main(argv):
try:
timeSeriesFile = argv[0]
refDate = argv[1]
except: Usage() ; sys.exit(1)
if os.path.isfile(refDate):
try: refDate = ptime.read_date_list(refDate)[0]
except: print 'Can not read reference date file: '+refDate
if len(refDate)==6: refDate=yymmdd2yyyymmdd(refDate)
try: outName = argv[2]
except: outName = timeSeriesFile.split('.h5')[0]+'_refDate.h5'
#except: outName = timeSeriesFile.split('.h5')[0]+'_ref'+refDate+'.h5'
h5t=h5py.File(timeSeriesFile)
dateList = h5t['timeseries'].keys()
dateList = sorted(dateList)
if not refDate in dateList:
print '''**********************
Error: Reference date was not found.
Choose a date available in the time-series.
Exit without any action.
'''
sys.exit(1)
print '\n************* Reference Epoch ***************'
refDataSet=h5t['timeseries'].get(refDate)
refData=refDataSet[0:refDataSet.shape[0],0:refDataSet.shape[1]]
print 'referencing all epochs to ' + refDate
h5t2=h5py.File(outName,'w'); print 'writing >>> '+outName
group = h5t2.create_group('timeseries')
for d in dateList:
print d
ds=h5t['timeseries'].get(d)
data=ds[0:ds.shape[0],0:ds.shape[1]]
dset = group.create_dataset(d, data=data-refData, compression='gzip')
## Attributes
for key,value in h5t['timeseries'].attrs.iteritems():
group.attrs[key] = value
#group.attrs['DATE'] = refDate[2:8]
group.attrs['ref_date']=refDate
try:
h5t['mask'].get('mask')
dset1 = h5t['mask'].get('mask')
Mask = dset1[0:dset1.shape[0],0:dset1.shape[1]]
group=h5t2.create_group('mask')
dset = group.create_dataset('mask', data=Mask, compression='gzip')
except:
print 'no mask in the file.'
def main(argv):
try:
timeSeriesFile = argv[0]
refDate = argv[1]
except: usage() ; sys.exit(1)
if os.path.isfile(refDate):
try: refDate = ptime.read_date_list(refDate)[0]
except: print 'Can not read reference date file: '+refDate
if len(refDate)==6: refDate=yymmdd2yyyymmdd(refDate)
try: outName = argv[2]
except: outName = timeSeriesFile.split('.h5')[0]+'_refDate.h5'
#except: outName = timeSeriesFile.split('.h5')[0]+'_ref'+refDate+'.h5'
h5t=h5py.File(timeSeriesFile)
dateList = sorted(h5t['timeseries'].keys())
if not refDate in dateList:
print '''**********************
Error: Reference date was not found.
Choose a date available in the time-series.
Exit without any action.
'''
sys.exit(1)
print '\n************* Reference Epoch ***************'
refDataSet=h5t['timeseries'].get(refDate)
refData=refDataSet[0:refDataSet.shape[0],0:refDataSet.shape[1]]
print 'referencing all epochs to ' + refDate
h5t2=h5py.File(outName,'w'); print 'writing >>> '+outName
group = h5t2.create_group('timeseries')
for d in dateList:
print d
ds=h5t['timeseries'].get(d)
data=ds[0:ds.shape[0],0:ds.shape[1]]
dset = group.create_dataset(d, data=data-refData, compression='gzip')
## Attributes
for key,value in h5t['timeseries'].attrs.iteritems():
group.attrs[key] = value
#group.attrs['DATE'] = refDate[2:8]
group.attrs['ref_date']=refDate
try:
h5t['mask'].get('mask')
dset1 = h5t['mask'].get('mask')
Mask = dset1[0:dset1.shape[0],0:dset1.shape[1]]
group=h5t2.create_group('mask')
dset = group.create_dataset('mask', data=Mask, compression='gzip')
except:
print 'no mask in the file.'
def get_exclude_date(inps, date_list_all):
'''Get inps.ex_date full list
Inputs:
inps - Namespace,
date_list_all - list of string for all available date in YYYYMMDD format
Output:
inps.ex_date - list of string for exclude date in YYYYMMDD format
'''
yy_list_all = ptime.yyyymmdd2years(date_list_all)
# 1. template_file
if inps.template_file:
print 'read option from template file: ' + inps.template_file
inps = read_template2inps(inps.template_file, inps)
# 2. ex_date
input_ex_date = list(inps.ex_date)
inps.ex_date = []
if input_ex_date:
for ex_date in input_ex_date:
if os.path.isfile(ex_date):
ex_date = ptime.read_date_list(ex_date)
else:
ex_date = [ptime.yyyymmdd(ex_date)]
inps.ex_date += list(set(ex_date) - set(inps.ex_date))
# delete dates not existed in input file
inps.ex_date = list(set(inps.ex_date).intersection(date_list_all))
print 'exclude date:' + str(inps.ex_date)
# 3. min_date
if inps.min_date:
print 'start date: ' + inps.min_date
yy_min = ptime.yyyymmdd2years(ptime.yyyymmdd(inps.min_date))
for i in range(len(date_list_all)):
date = date_list_all[i]
if yy_list_all[i] < yy_min and date not in inps.ex_date:
print ' remove date: ' + date
inps.ex_date.append(date)
# 4. max_date
if inps.max_date:
print 'end date: ' + inps.max_date
yy_max = ptime.yyyymmdd2years(ptime.yyyymmdd(inps.max_date))
for i in range(len(date_list_all)):
date = date_list_all[i]
if yy_list_all[i] > yy_max and date not in inps.ex_date:
print ' remove date: ' + date
inps.ex_date.append(date)
return inps.ex_date
def get_exclude_date(inps, date_list_all):
input_ex_date = list(inps.ex_date)
inps.ex_date = []
if input_ex_date:
for ex_date in input_ex_date:
if os.path.isfile(ex_date):
ex_date = ptime.read_date_list(ex_date)
else:
ex_date = [ptime.yyyymmdd(ex_date)]
inps.ex_date += list(set(ex_date) - set(inps.ex_date))
# delete dates not existed in input file
inps.ex_date = sorted(
list(set(inps.ex_date).intersection(date_list_all)))
print 'Exclude date for DEM error estimation:'
print inps.ex_date
return inps
def main(argv):
inps = cmdLineParse()
if inps.template_file:
inps = read_template2inps(inps.template_file)
if inps.ref_date == 'no':
print 'No reference date input, skip this step.'
return inps.timeseries_file
elif inps.ref_date.lower() in ['auto']:
print '------------------------------------------------------------'
print 'auto choose reference date based on minimum Residual Standard Deviation (RSD)'
if not inps.resid_file:
inps.resid_file = os.path.splitext(
inps.timeseries_file)[0] + 'InvResid.h5'
std_list, date_list = ut.get_residual_std(inps.resid_file,
inps.mask_file,
inps.ramp_type)
ref_idx = np.argmin(std_list)
inps.ref_date = date_list[ref_idx]
print 'date with minimum residual std: %s - %.4f' % (inps.ref_date,
std_list[ref_idx])
#txtFile = 'reference_date.txt'
#f = open(txtFile, 'w')
#f.write(inps.ref_date+'\n')
#f.close()
#print 'save date to file: '+txtFile
print '------------------------------------------------------------'
elif os.path.isfile(inps.ref_date):
print 'read reference date from file: ' + inps.ref_date
inps.ref_date = ptime.read_date_list(inps.ref_date)[0]
# Referencing input file
inps.outfile = ref_date_file(inps.timeseries_file, inps.ref_date,
inps.outfile)
return inps.outfile
def check_exclude_date(exDateIn, dateList):
'''Read exclude dates info
Inputs:
exDateIn - list of string, date in YYMMDD or YYYYMMDD format,
or text file with date in it
dateList - list of string, date in YYYYMMDD format
Output:
exDateOut - list of string, date in YYYYMMDD format
'''
if not exDateIn:
return []
exDateOut = []
for exDate in exDateIn:
if os.path.isfile(exDate):
exDate = ptime.read_date_list(exDate)
else:
exDate = [ptime.yyyymmdd(exDate)]
exDateOut += exDate
exDateOut = sorted(list(set(exDateOut).intersection(dateList)))
print 'Exclude date for DEM error estimation:'
print exDateOut
return exDateOut
def main(argv):
if len(sys.argv)>2:
try: opts, args = getopt.getopt(argv,"f:E:m:M:h:o:t:")
except getopt.GetoptError: Usage() ; sys.exit(1)
for opt,arg in opts:
if opt == '-f': timeSeriesFile = arg
elif opt == '-E': datesNot2include = arg.replace(' ','').split(',')
elif opt == '-m': minDate = arg
elif opt == '-M': maxDate = arg
elif opt == '-o': outName = arg
elif opt == '-t': templateFile = arg
elif len(sys.argv)==2:
if argv[0]=='-h': Usage(); sys.exit(1)
elif os.path.isfile(argv[0]): timeSeriesFile = argv[0]
else: Usage(); sys.exit(1)
else: Usage(); sys.exit(1)
##### Read excluded date list Input
try: datesNot2include
except:
try:
templateFile
templateContents = readfile.read_template(templateFile)
datesNot2include = templateContents['pysar.drop.date'].replace(' ','').split(',')
except: pass
##############################################################
print '\n********** Inversion: Time Series to Velocity ***********'
atr = readfile.read_attributes(timeSeriesFile)
k = atr['FILE_TYPE']
print 'input file: '+k
if not k == 'timeseries': print 'Input file is not timeseries!'; sys.exit(1)
print "Loading time series file: " + timeSeriesFile
h5timeseries = h5py.File(timeSeriesFile)
dateList1 = h5timeseries[k].keys()
dateList1 = sorted(dateList1)
##############################################################
print '--------------------------------------------'
print 'Dates from input file: '+str(len(dateList1))
print dateList1
try:
datesNot2include
if os.path.isfile(datesNot2include[0]):
try: datesNot2include = ptime.read_date_list(datesNot2include[0])
except: print 'Can not read date list file: '+datesNot2include[0]
print '--------------------------------------------'
print 'Date excluded: '+str(len(datesNot2include))
print datesNot2include
except:
datesNot2include=[]
try:
minDate
minDateyy=yyyymmdd2years(minDate)
print 'minimum date: '+minDate
for date in dateList1:
yy=yyyymmdd2years(date)
if yy < minDateyy:
print ' remove date: '+date
datesNot2include.append(date)
except: pass
try:
maxDate
maxDateyy=yyyymmdd2years(maxDate)
print 'maximum date: '+maxDate
for date in dateList1:
yy=yyyymmdd2years(date)
if yy > maxDateyy:
print ' remove date: '+date
datesNot2include.append(date)
except: pass
try:
dateList=[]
for date in dateList1:
if date not in datesNot2include:
dateList.append(date)
except: pass
print '--------------------------------------------'
if len(dateList) == len(dateList1):
print 'using all dates to calculate the vlocity'
else:
print 'Dates used to estimate the velocity: '+str(len(dateList))
print dateList
print '--------------------------------------------'
##############################################################
dateIndex={}
for ni in range(len(dateList)):
dateIndex[dateList[ni]]=ni
tbase=[]
d1 = datetime.datetime(*time.strptime(dateList[0],"%Y%m%d")[0:5])
for ni in range(len(dateList)):
d2 = datetime.datetime(*time.strptime(dateList[ni],"%Y%m%d")[0:5])
diff = d2-d1
tbase.append(diff.days)
dates=[]
for ni in range(len(dateList)):
d = datetime.datetime(*time.strptime(dateList[ni],"%Y%m%d")[0:5])
dates.append(d)
###########################################
print 'Calculating Velocity'
datevector=[]
for i in range(len(dates)):
datevector.append(np.float(dates[i].year) + np.float(dates[i].month-1)/12 + np.float(dates[i].day-1)/365)
B=np.ones([len(datevector),2])
B[:,0]=datevector
#B1 = np.linalg.pinv(B)
B1 = np.dot(np.linalg.inv(np.dot(B.T,B)),B.T)
B1 = np.array(B1,np.float32)
#########################################
width = int(atr['WIDTH'])
length = int(atr['FILE_LENGTH'])
lt = len(dateList)
timeseries = np.zeros((lt,length,width),np.float32)
for date in dateList:
timeseries[dateIndex[date]] = h5timeseries[k].get(date)
numpixels=length*width
Data=np.zeros([lt,numpixels])
for i in range(lt):
Data[i,:]=np.reshape(timeseries[i],[1,numpixels])
x=np.dot(B1,Data)
velocity=np.reshape(x[0,:],[length,width])
#####################################################
print 'Calculating rmse'
Data_linear=np.dot(B,x)
rmse=np.reshape(np.sqrt((np.sum((Data_linear-Data)**2,0))/lt),[length,width])
# se=np.reshape((np.sum(np.abs(Data_linear-Data),0)/lt),[length,width])
# rmse=np.reshape((np.sum((Data_linear-Data)**2,0))/lt,[length,width])
######################################################
print 'Calculating the standard deviation of the estimated velocities'
residual=Data_linear-Data
s1=np.sqrt(np.sum(residual**2,0)/(lt-2))
s2=np.sqrt(np.sum((datevector-np.mean(datevector))**2))
se=np.reshape(s1/s2,[length,width])
######################################################
# SSt=np.sum((Data-np.mean(Data,0))**2,0)
# SSres=np.sum(residual**2,0)
# SS_REG=SSt-SSres
# Rsquared=np.reshape(SS_REG/SSt,[length,width])
######################################################
# covariance of the velocities
##### Output File Name
try: outName
except:
if not datesNot2include == []: outName = 'velocity_ex.h5'
else: outName = 'velocity.h5'
outName_rmse='rmse_'+outName
outName_se='std_'+outName
outName_Rsquared='R2_'+outName
#####################################
print '--------------------------------------'
print 'writing to '+outName
h5velocity = h5py.File(outName,'w')
group=h5velocity.create_group('velocity')
dset = group.create_dataset('velocity', data=velocity, compression='gzip')
group.attrs['date1'] = datevector[0]
group.attrs['date2'] = datevector[lt-1]
for key , value in atr.iteritems():
group.attrs[key]=value
h5velocity.close()
#####################################
print 'writing to '+outName_rmse
h5file = outName_rmse
h5rmse = h5py.File(h5file,'w')
group=h5rmse.create_group('rmse')
dset = group.create_dataset(os.path.basename('rmse'), data=rmse, compression='gzip')
group.attrs['date1'] = datevector[0]
group.attrs['date2'] = datevector[lt-1]
for key , value in atr.iteritems():
group.attrs[key]=value
#####################################
print 'writing to '+outName_se
h5se = h5py.File(outName_se,'w')
group=h5se.create_group('rmse')
dset = group.create_dataset('rmse', data=se, compression='gzip')
group.attrs['date1'] = datevector[0]
group.attrs['date2'] = datevector[lt-1]
for key , value in atr.iteritems():
group.attrs[key]=value
# print 'writing to '+outName_Rsquared
# h5rsquared = h5py.File(outName_Rsquared,'w')
# group=h5rsquared.create_group('rmse')
# dset = group.create_dataset('rmse', data=Rsquared, compression='gzip')
# group.attrs['date1'] = datevector[0]
# group.attrs['date2'] = datevector[lt-1]
# h5rsquared.close()
h5se.close()
h5rmse.close()
h5timeseries.close()
print 'Done.'
def main(argv):
## Default settings
contour_step = 200.0
contour_sigma = 3.0
demShade = "yes"
demContour = "yes"
global markerSize, markderSize2, markerColor, markerColor2, rectColor
global lineWidth, lineWidth2, edgeWidth, fontSize
# global markerColor_ref, markerColor_ref2
markerSize = 16
markerSize2 = 16
markerColor = "crimson" # g
markerColor2 = "lightgray"
markerColor_ref = "white"
markerColor_ref2 = "lightgray"
rectColor = "black"
lineWidth = 0
lineWidth2 = 0
edgeWidth = 1.5
fontSize = 16
global unit, radius, saveFig, dispFig, fig_dpi
fig_dpi = 300
radius = 0
saveFig = "no"
dispFig = "yes"
unit = "cm"
dispDisplacement = "no"
dispOpposite = "no"
dispContour = "only"
smoothContour = "no"
contour_step = 200
showRef = "yes"
vel_alpha = 1.0
zero_start = "yes"
global ref_xsub, ref_ysub, ref_date
global h5timeseries_2, dates_2, dateList_2
global lbound, hbound
############### Check Inputs ##################
if len(sys.argv) < 2:
Usage()
sys.exit(1)
elif len(sys.argv) == 2:
if argv[0] == "-h":
Usage()
sys.exit(1)
elif os.path.isfile(argv[0]):
timeSeriesFile = argv[0]
h5timeseries = h5py.File(timeSeriesFile)
k = h5timeseries.keys()
if not "timeseries" in k:
print "ERROR: Input file is " + k[0] + ".\n\tOnly timeseries is supported.\n"
sys.exit(1)
else:
Usage()
sys.exit(1)
elif len(sys.argv) > 2:
try:
opts, args = getopt.getopt(
argv,
"f:F:v:a:b:s:m:c:w:u:l:h:D:V:t:T:d:r:x:y:X:Y:o:E:",
[
"save",
"nodisplay",
"unit=",
"exclude=",
"ref-date=",
"rect-color=",
"zero-start=",
"zoom-x=",
"zoom-y=",
"zoom-lon",
"zoom-lat",
"lalo=",
"opposite",
"dem-nocontour",
"dem-noshade",
"displacement",
"contour-step=",
"contour-smooth=",
"LALO=",
],
)
except getopt.GetoptError:
Usage()
sys.exit(1)
for opt, arg in opts:
if opt == "-f":
timeSeriesFile = arg
elif opt == "-F":
timeSeriesFile_2 = arg
elif opt == "-v":
velocityFile = arg
elif opt == "-a":
vmin = float(arg)
elif opt == "-b":
vmax = float(arg)
elif opt == "-s":
fontSize = int(arg)
elif opt == "-m":
markerSize = int(arg)
markerSize2 = int(arg)
elif opt == "-c":
markerColor = arg
elif opt == "-w":
lineWidth = int(arg)
elif opt == "-u":
unit = arg
elif opt == "-l":
lbound = float(arg)
elif opt == "-h":
hbound = float(arg)
elif opt == "-D":
demFile = arg
elif opt == "-V":
contour_step = float(arg)
elif opt == "-t":
minDate = arg
elif opt == "-T":
maxDate = arg
elif opt == "-r":
radius = abs(int(arg))
elif opt == "-x":
xsub = [int(i) for i in arg.split(":")]
xsub.sort()
# dispVelFig='no'
elif opt == "-y":
ysub = [int(i) for i in arg.split(":")]
ysub.sort()
# dispVelFig='no'
elif opt == "-X":
ref_xsub = [int(i) for i in arg.split(":")]
ref_xsub.sort()
elif opt == "-Y":
ref_ysub = [int(i) for i in arg.split(":")]
ref_ysub.sort()
# dispVelFig='no'
elif opt == "--contour-step":
contour_step = float(arg)
elif opt == "--contour-smooth":
contour_sigma = float(arg)
elif opt == "--dem-nocontour":
demContour = "no"
elif opt == "--dem-noshade":
demShade = "no"
elif opt == "--displacement":
dispDisplacement = "yes"
elif opt in ["-E", "--exclude"]:
datesNot2show = arg.split(",")
elif opt in "--lalo":
lalosub = [float(i) for i in arg.split(",")]
elif opt in "--LALO":
ref_lalosub = [float(i) for i in arg.split(",")]
elif opt in ["--rect-color"]:
rectColor = arg
elif opt in ["--ref-date"]:
ref_date = ptime.yyyymmdd(arg)
elif opt in ["-u", "--unit"]:
unit = arg.lower()
elif opt == "--save":
saveFig = "yes"
elif opt == "--nodisplay":
dispFig = "no"
saveFig = "yes"
elif opt == "--opposite":
dispOpposite = "yes"
elif opt == "--zero-start":
zero_start = arg.lower()
elif opt == "--zoom-x":
win_x = [int(i) for i in arg.split(":")]
win_x.sort()
elif opt == "--zoom-y":
win_y = [int(i) for i in arg.split(":")]
win_y.sort()
elif opt == "--zoom-lon":
win_lon = [float(i) for i in arg.split(":")]
win_lon.sort()
elif opt == "--zoom-lat":
win_lat = [float(i) for i in arg.split(":")]
win_lat.sort()
##############################################################
## Read time series file info
if not os.path.isfile(timeSeriesFile):
print "\nERROR: Input time series file does not exist: " + timeSeriesFile + "\n"
sys.exit(1)
h5timeseries = h5py.File(timeSeriesFile)
k = h5timeseries.keys()
# read h5 file and its group type
if not "timeseries" in k:
print "ERROR: Input file is " + k[0] + ".\n\tOnly timeseries is supported.\n"
sys.exit(1)
atr = readfile.read_attributes(timeSeriesFile)
dateList1 = h5timeseries["timeseries"].keys()
dateList1 = sorted(dateList1)
dates1, datevector1 = ptime.date_list2vector(dateList1)
print "\n************ Time Series Display - Point *************"
##### Select Check
try:
lalosub
xsub = subset.coord_geo2radar([lalosub[1]], atr, "longitude")
ysub = subset.coord_geo2radar([lalosub[0]], atr, "latitude")
xsub = [xsub]
ysub = [ysub]
if radius == 0:
radius = 3
except:
pass
try:
ref_lalosub
ref_xsub = subset.coord_geo2radar([ref_lalosub[1]], atr, "longitude")
ref_ysub = subset.coord_geo2radar([ref_lalosub[0]], atr, "latitude")
ref_xsub = [ref_xsub]
ref_ysub = [ref_ysub]
if radius == 0:
radius = 3
except:
pass
##############################################################
global dates, dateList, datevector_all, dateListMinMax
print "*******************"
print "All dates existed:"
print dateList1
print "*******************"
## Check exclude date input
try:
datesNot2show
if os.path.isfile(datesNot2show[0]):
try:
datesNot2show = ptime.read_date_list(datesNot2show[0])
except:
print "Can not read date list file: " + datesNot2show[0]
print "dates not to show: " + str(datesNot2show)
except:
datesNot2show = []
## Check Min / Max Date
dateListMinMax = []
try:
minDate
minDate = ptime.yyyymmdd(minDate)
dateListMinMax.append(minDate)
minDateyy = ptime.yyyymmdd2years(minDate)
print "minimum date: " + minDate
for date in dateList1:
yy = ptime.yyyymmdd2years(date)
if yy < minDateyy:
datesNot2show.append(date)
except:
pass
try:
maxDate
maxDate = ptime.yyyymmdd(maxDate)
dateListMinMax.append(maxDate)
maxDateyy = ptime.yyyymmdd2years(maxDate)
print "maximum date: " + maxDate
for date in dateList1:
yy = ptime.yyyymmdd2years(date)
if yy > maxDateyy:
datesNot2show.append(date)
except:
pass
dateListMinMax = sorted(dateListMinMax)
if not dateListMinMax:
print "no min/max date input."
else:
datesMinMax, dateVecMinMax = ptime.date_list2vector(dateListMinMax)
## Finalize Date List
try:
dateList = []
for date in dateList1:
if date not in datesNot2show:
dateList.append(date)
print "--------------------------------------------"
print "dates used to show time series displacements:"
print dateList
print "--------------------------------------------"
except:
dateList = dateList1
print "using all dates to show time series displacement"
## Read Date Info (x axis for time series display)
dates, datevector = ptime.date_list2vector(dateList)
datevector_all = list(datevector)
## Check reference date input
try:
ref_date
if not ref_date in dateList:
print "Reference date - " + ref_date + " - is not included in date list to show."
sys.exit(1)
else:
print "reference date: " + ref_date
except:
if zero_start == "yes":
ref_date = dateList[0]
print "set the 1st date as reference for displacement display."
else:
pass
##############################################################
##### Plot Fig 1 - Velocity / last epoch of time series / DEM
fig = plt.figure(1)
ax = fig.add_subplot(111)
##### Check subset range
width = int(atr["WIDTH"])
length = int(atr["FILE_LENGTH"])
print "file size: " + str(length) + ", " + str(width)
try:
win_y = subset.coord_geo2radar(win_lat, atr, "latitude")
except:
try:
win_y
except:
win_y = [0, length]
try:
win_x = subset.coord_geo2radar(win_lon, atr, "longitude")
except:
try:
win_x
except:
win_x = [0, width]
win_y, win_x = subset.check_subset_range(win_y, win_x, atr)
try:
velocityFile
try:
vel, vel_atr = readfile.read(velocityFile)
except:
vel, vel_atr = readfile.read(timeSeriesFile, velocityFile)
ax.set_title(velocityFile)
print "display: " + velocityFile
except:
vel, vel_atr = readfile.read(timeSeriesFile, dateList1[-1])
ax.set_title("epoch: " + dateList1[-1])
print "display last epoch"
##### show displacement instead of phase
if vel_atr["FILE_TYPE"] in ["interferograms", ".unw"] and dispDisplacement == "yes":
print "show displacement"
phase2range = -float(vel_atr["WAVELENGTH"]) / (4 * np.pi)
vel *= phase2range
else:
dispDisplacement = "no"
## Reference Point
if showRef == "yes":
try:
ax.plot(int(atr["ref_x"]), int(atr["ref_y"]), "ks", ms=6)
except:
pass
if dispOpposite == "yes":
print "show opposite value in figure/map 1"
vel *= -1
## Flip
try:
flip_lr
except:
try:
flip_ud
except:
flip_lr, flip_ud = view.auto_flip_check(atr)
## Status bar
## Geo coordinate
try:
ullon = float(atr["X_FIRST"])
ullat = float(atr["Y_FIRST"])
lon_step = float(atr["X_STEP"])
lat_step = float(atr["Y_STEP"])
lon_unit = atr["Y_UNIT"]
lat_unit = atr["X_UNIT"]
geocoord = "yes"
print "Input file is Geocoded"
except:
geocoord = "no"
def format_coord(x, y):
col = int(x + 0.5)
row = int(y + 0.5)
if col >= 0 and col <= width and row >= 0 and row <= length:
z = vel[row, col]
try:
lon = ullon + x * lon_step
lat = ullat + y * lat_step
return "x=%.1f, y=%.1f, value=%.4f, lon=%.4f, lat=%.4f" % (x, y, z, lon, lat)
except:
return "x=%.1f, y=%.1f, value=%.4f" % (x, y, z)
ax.format_coord = format_coord
## DEM
try:
demFile
dem, demRsc = readfile.read(demFile)
ax = view.plot_dem_yx(ax, dem, demShade, demContour, contour_step, contour_sigma)
vel_alpha = 0.8
except:
print "No DEM file"
try:
img = ax.imshow(vel, vmin=vmin, vmax=vmax, alpha=vel_alpha)
except:
img = ax.imshow(vel, alpha=vel_alpha)
plt.colorbar(img)
## Zoom In (subset)
if flip_lr == "yes":
ax.set_xlim(win_x[1], win_x[0])
else:
ax.set_xlim(win_x[0], win_x[1])
if flip_ud == "yes":
ax.set_ylim(win_y[0], win_y[1])
else:
ax.set_ylim(win_y[1], win_y[0])
## Flip
# if flip_lr == 'yes': fig.gca().invert_xaxis()
# if flip_ud == 'yes': fig.gca().invert_yaxis()
##########################################
##### Plot Fig 2 - Time series plot
# fig2 = plt.figure(num=2,figsize=(12,6))
fig2 = plt.figure(2, figsize=(12, 6))
ax2 = fig2.add_subplot(111)
try:
timeSeriesFile_2
h5timeseries_2 = h5py.File(timeSeriesFile_2)
dateList_2 = h5timeseries_2["timeseries"].keys()
dateList_2 = sorted(dateList_2)
dates_2, datevector_2 = ptime.date_list2vector(dateList_2)
datevector_all += list(set(datevector_2) - set(datevector_all))
datevector_all = sorted(datevector_all)
except:
pass
################################ Plot Code Package <start> #################################
def plot_ts(ax, ax2, fig2, xsub, ysub, h5timeseries):
ax2.cla()
print "\n-------------------------------------------------------------------------------"
disp_min = 0
disp_max = 0
############################# Plot Time Series ##############################
global ref_xsub, ref_ysub
##### 1.1 Plot Reference time series
try:
ref_xsub
ref_ysub
ref_xsub, ref_ysub = check_yx(ref_xsub, ref_ysub, radius, ax, rectColor)
print "----------------------------------------------------"
print "Reference Point:"
print "ref_x=" + str(ref_xsub[0]) + ":" + str(ref_xsub[1])
print "ref_y=" + str(ref_ysub[0]) + ":" + str(ref_ysub[1])
print "-----------------------------"
print "Time series with all dates:"
dis1, dis1_mean, dis1_std, dis1_vel = read_dis(ref_xsub, ref_ysub, dateList1, h5timeseries, unit)
(_, caps, _) = ax2.errorbar(
dates1,
dis1_mean,
yerr=dis1_std,
fmt="-ks",
ms=markerSize2,
lw=0,
alpha=1,
mfc=markerColor_ref,
mew=edgeWidth,
elinewidth=edgeWidth,
ecolor="black",
capsize=markerSize * 0.5,
)
for cap in caps:
cap.set_markeredgewidth(edgeWidth)
disp_min, disp_max = update_lim(disp_min, disp_max, dis1_mean, dis1_std)
if not len(dateList) == len(dateList1):
print "-----------------------------"
print "Time series with dates of interest:"
dis12, dis12_mean, dis12_std, dis12_vel = read_dis(ref_xsub, ref_ysub, dateList, h5timeseries, unit)
(_, caps, _) = ax2.errorbar(
dates,
dis12_mean,
yerr=dis12_std,
fmt="-ks",
ms=markerSize2,
lw=0,
alpha=1,
mfc=markerColor_ref2,
mew=edgeWidth,
elinewidth=edgeWidth,
ecolor="black",
capsize=markerSize * 0.5,
)
for cap in caps:
cap.set_markeredgewidth(edgeWidth)
disp_min, disp_max = update_lim(disp_min, disp_max, dis12_mean, dis12_std)
except:
pass
##### 1.2.0 Read y/x
print "\n----------------------------------------------------"
print "Point of Interest:"
xsub, ysub = check_yx(xsub, ysub, radius, ax, rectColor)
print "x=" + str(xsub[0]) + ":" + str(xsub[1])
print "y=" + str(ysub[0]) + ":" + str(ysub[1])
##### 1.2.1 Plot 2nd time series
try:
timeSeriesFile_2
print "-----------------------------"
print "2nd Time Series:"
dis2, dis2_mean, dis2_std, dis2_vel = read_dis(xsub, ysub, dateList_2, h5timeseries_2, unit)
(_, caps, _) = ax2.errorbar(
dates_2,
dis2_mean,
yerr=dis2_std,
fmt="-ko",
ms=markerSize2,
lw=0,
alpha=1,
mfc=markerColor2,
elinewidth=0,
ecolor="black",
capsize=0,
)
for cap in caps:
cap.set_markeredgewidth(edgeWidth)
disp_min, disp_max = update_lim(disp_min, disp_max, dis2_mean, dis2_std)
except:
pass
##### 1.2.2 Plot 1st time series
print "-----------------------------"
print "Time Series:"
dis, dis_mean, dis_std, dis_vel = read_dis(xsub, ysub, dateList, h5timeseries, unit)
(_, caps, _) = ax2.errorbar(
dates,
dis_mean,
yerr=dis_std,
fmt="-ko",
ms=markerSize,
lw=lineWidth,
alpha=1,
mfc=markerColor,
elinewidth=edgeWidth,
ecolor="black",
capsize=markerSize * 0.5,
)
for cap in caps:
cap.set_markeredgewidth(edgeWidth)
disp_min, disp_max = update_lim(disp_min, disp_max, dis_mean, dis_std)
####################### Figure Format #######################
## x axis format
try:
ax2 = ptime.adjust_xaxis_date(ax2, dateVecMinMax, fontSize)
except:
ax2 = ptime.adjust_xaxis_date(ax2, datevector_all, fontSize)
## y axis format
ax2.set_ylabel("Displacement [" + unit + "]", fontsize=fontSize)
try:
lbound
hbound
ax2.set_ylim(lbound, hbound)
except:
disp_buf = 0.2 * (disp_max - disp_min)
ax2.set_ylim(disp_min - disp_buf, disp_max + disp_buf)
for tick in ax2.yaxis.get_major_ticks():
tick.label.set_fontsize(fontSize)
## title
figTitle = "x=" + str(xsub[0]) + ":" + str(xsub[1]) + ", y=" + str(ysub[0]) + ":" + str(ysub[1])
try:
lonc = ullon + (xsub[0] + xsub[1]) / 2.0 * lon_step
latc = ullat + (ysub[0] + ysub[1]) / 2.0 * lat_step
figTitle += ", lalo=" + "%.4f,%.4f" % (latc, lonc)
except:
pass
ax2.set_title(figTitle)
################## Save and Output #####################
if saveFig == "yes":
print "-----------------------------"
Delay = {}
Delay["displacement"] = dis
Delay["unit"] = unit
Delay["time"] = datevector
Delay["velocity"] = dis_vel[0]
Delay["velocity_unit"] = unit + "/yr"
Delay["velocity_std"] = dis_vel[4]
figBase = "x" + str(xsub[0]) + "_" + str(xsub[1] - 1) + "y" + str(ysub[0]) + "_" + str(ysub[1] - 1)
sio.savemat(figBase + "_ts.mat", {"displacement": Delay})
print "saved " + figBase + "_ts.mat"
fig2.savefig(figBase + "_ts.pdf", bbox_inches="tight", transparent=True, dpi=fig_dpi)
print "saved " + figBase + "_ts.pdf"
if dispFig == "no":
fig.savefig(figBase + "_vel.png", bbox_inches="tight", transparent=True, dpi=fig_dpi)
print "saved " + figBase + "_vel.png"
################################ Plot Code Package <end> #################################
########### 1. Plot Time Series with x/y ##########
try:
xsub
ysub
plot_ts(ax, ax2, fig2, xsub, ysub, h5timeseries)
except:
print "No x/y input"
pass
########### 2. Plot Time Series with Click ##########
## similar to 1. Plot Time Series with x/y
def onclick(event):
ax2.cla()
xsub = [int(event.xdata)]
ysub = [int(event.ydata)]
plot_ts(ax, ax2, fig2, xsub, ysub, h5timeseries)
if dispFig == "yes":
plt.show()
try:
cid = fig.canvas.mpl_connect("button_press_event", onclick)
except:
pass
if dispFig == "yes":
plt.show()
def main(argv):
inps = cmdLineParse()
#print '\n********** Inversion: Time Series to Velocity ***********'
atr = readfile.read_attribute(inps.timeseries_file)
k = atr['FILE_TYPE']
print 'input '+k+' file: '+inps.timeseries_file
if not k == 'timeseries':
sys.exit('ERROR: input file is not timeseries!')
h5file = h5py.File(inps.timeseries_file)
#####################################
## Date Info
dateListAll = sorted(h5file[k].keys())
dateListAll = ptime.yyyymmdd(dateListAll)
yyListAll = ptime.yyyymmdd2years(dateListAll)
print '--------------------------------------------'
print 'Dates from input file: '+str(len(dateListAll))
print dateListAll
# Extrac exclude dates from input arguments
inps.datesNot2include = []
# 1. template_file
if inps.template_file:
inps = update_inps_from_template(inps, inps.template_file)
# 2. ex_date
if inps.ex_date:
for ex_date in inps.ex_date:
if os.path.isfile(ex_date):
ex_date = ptime.read_date_list(ex_date)
else:
ex_date = [ptime.yyyymmdd(ex_date)]
inps.datesNot2include += list(set(ex_date) - set(inps.datesNot2include))
# delete dates not existed in input file
inps.datesNot2include = list(set(inps.datesNot2include).intersection(dateListAll))
print 'date excluded:'+str(inps.datesNot2include)
# 3. min_date
if inps.min_date:
inps.min_date = ptime.yyyymmdd(inps.min_date)
print 'minimum date: '+inps.min_date
yy_min = ptime.yyyymmdd2years(inps.min_date)
for i in range(len(dateListAll)):
date = dateListAll[i]
if yyListAll[i] < yy_min and date not in inps.datesNot2include:
print ' remove date: '+date
inps.datesNot2include.append(date)
# 4. max_date
if inps.max_date:
inps.max_date = ptime.yyyymmdd(inps.max_date)
print 'minimum date: '+inps.max_date
yy_max = ptime.yyyymmdd2years(inps.max_date)
for i in range(len(dateListAll)):
date = dateListAll[i]
if yyListAll[i] > yy_max and date not in inps.datesNot2include:
print ' remove date: '+date
inps.datesNot2include.append(date)
# Summary
dateList = sorted(list(set(dateListAll) - set(inps.datesNot2include)))
print '--------------------------------------------'
if len(dateList) == len(dateListAll):
print 'using all dates to calculate the velocity'
else:
print 'Dates used to estimate the velocity: '+str(len(dateList))
print dateList
print '--------------------------------------------'
# Date Aux Info
dates, datevector = ptime.date_list2vector(dateList)
#####################################
## Inversion
# Design matrix
B=np.ones([len(datevector),2])
B[:,0]=datevector
#B1 = np.linalg.pinv(B)
B1 = np.dot(np.linalg.inv(np.dot(B.T,B)),B.T)
B1 = np.array(B1,np.float32)
# Loading timeseries
print "Loading time series file: "+inps.timeseries_file+' ...'
width = int(atr['WIDTH'])
length = int(atr['FILE_LENGTH'])
dateNum = len(dateList)
timeseries = np.zeros([dateNum,length*width],np.float32)
start_time = time.time()
for i in range(dateNum):
date = dateList[i]
ut.print_progress(i+1, dateNum, prefix='loading:', suffix=date, elapsed_time=time.time()-start_time)
timeseries[i,:] = h5file[k].get(date)[:].flatten()
h5file.close()
# Velocity Inversion
print 'Calculating velocity ...'
x = np.dot(B1,timeseries)
velocity = np.reshape(x[0,:],[length,width])
print 'Calculating rmse ...'
timeseries_linear = np.dot(B,x)
rmse = np.reshape(np.sqrt((np.sum((timeseries_linear-timeseries)**2,0))/dateNum),[length,width])
print 'Calculating the standard deviation of the estimated velocity ...'
residual = timeseries_linear - timeseries
s1 = np.sqrt(np.sum(residual**2,0)/(dateNum-2))
s2 = np.sqrt(np.sum((datevector-np.mean(datevector))**2))
std = np.reshape(s1/s2,[length,width])
# SSt=np.sum((timeseries-np.mean(timeseries,0))**2,0)
# SSres=np.sum(residual**2,0)
# SS_REG=SSt-SSres
# Rsquared=np.reshape(SS_REG/SSt,[length,width])
######################################################
# covariance of the velocities
#####################################
# Output file name
if not inps.outfile:
inps.outfile = 'velocity.h5'
if inps.datesNot2include:
inps.outfile = os.path.splitext(inps.outfile)[0]+'_ex'+os.path.splitext(inps.outfile)[1]
inps.outfile_rmse = 'rmse_'+inps.outfile
inps.outfile_std = 'std_'+inps.outfile
inps.outfile_r2 = 'R2_'+inps.outfile
# Attributes
atr['date1'] = datevector[0]
atr['date2'] = datevector[dateNum-1]
# File Writing
print '--------------------------------------'
atr['FILE_TYPE'] = 'velocity'
print 'writing >>> '+inps.outfile
writefile.write(velocity, atr, inps.outfile)
atr['FILE_TYPE'] = 'rmse'
print 'writing >>> '+inps.outfile_rmse
writefile.write(rmse, atr, inps.outfile_rmse)
atr['FILE_TYPE'] = 'rmse'
print 'writing >>> '+inps.outfile_std
writefile.write(std, atr, inps.outfile_std)
print 'Done.'
return inps.outfile
if not k == 'timeseries':
raise ValueError('Only timeseries file is supported!')
h5 = h5py.File(inps.timeseries_file, 'r')
dateList = sorted(h5[k].keys())
date_num = len(dateList)
inps.dates, tims = ptime.date_list2vector(dateList)
# Read exclude dates
if inps.ex_date_list:
input_ex_date = list(inps.ex_date_list)
inps.ex_date_list = []
if input_ex_date:
for ex_date in input_ex_date:
if os.path.isfile(ex_date):
ex_date = ptime.read_date_list(ex_date)
else:
ex_date = [ptime.yyyymmdd(ex_date)]
inps.ex_date_list += list(
set(ex_date) - set(inps.ex_date_list))
# delete dates not existed in input file
inps.ex_date_list = sorted(
list(set(inps.ex_date_list).intersection(dateList)))
inps.ex_dates = ptime.date_list2vector(inps.ex_date_list)[0]
inps.ex_idx_list = sorted(
[dateList.index(i) for i in inps.ex_date_list])
print 'exclude date:' + str(inps.ex_date_list)
## Zero displacement for 1st acquisition
if inps.zero_first:
if inps.ex_date_list:
def main(argv):
## Default settings
contour_step = 200.0
contour_sigma = 3.0
demShade = 'yes'
demContour = 'yes'
global markerSize, markderSize2, markerColor, markerColor2, rectColor
global lineWidth, lineWidth2, edgeWidth, fontSize
#global markerColor_ref, markerColor_ref2
markerSize = 16
markerSize2 = 16
markerColor = 'crimson' # g
markerColor2 = 'lightgray'
markerColor_ref = 'white'
markerColor_ref2 = 'lightgray'
rectColor = 'black'
lineWidth = 0
lineWidth2 = 0
edgeWidth = 1.5
fontSize = 16
global unit, radius, saveFig, dispFig, fig_dpi
fig_dpi = 300
radius = 0
saveFig = 'no'
dispFig = 'yes'
unit = 'cm'
dispDisplacement = 'no'
dispOpposite = 'no'
dispContour = 'only'
smoothContour = 'no'
contour_step = 200
showRef = 'yes'
vel_alpha = 1.0
zero_start = 'yes'
global ref_xsub, ref_ysub, ref_date
global h5timeseries_2, dates_2, dateList_2
global lbound, hbound
############### Check Inputs ##################
if len(sys.argv) < 2:
usage()
sys.exit(1)
elif len(sys.argv) == 2:
if argv[0] == '-h':
usage()
sys.exit(1)
elif os.path.isfile(argv[0]):
timeSeriesFile = argv[0]
h5timeseries = h5py.File(timeSeriesFile)
k = h5timeseries.keys()
if not 'timeseries' in k:
print 'ERROR: Input file is ' + k[
0] + '.\n\tOnly timeseries is supported.\n'
sys.exit(1)
else:
usage()
sys.exit(1)
elif len(sys.argv) > 2:
try: opts, args = getopt.getopt(argv,"f:F:v:a:b:s:m:c:w:u:l:h:D:V:t:T:d:r:x:y:X:Y:o:E:",
['save','nodisplay','unit=','exclude=','ref-date=','rect-color=',\
'zero-start=','zoom-x=','zoom-y=','zoom-lon','zoom-lat','lalo=',\
'opposite','dem-nocontour','dem-noshade','displacement','contour-step=',\
'contour-smooth=','LALO='])
except getopt.GetoptError:
usage()
sys.exit(1)
for opt, arg in opts:
if opt == '-f': timeSeriesFile = arg
elif opt == '-F': timeSeriesFile_2 = arg
elif opt == '-v': velocityFile = arg
elif opt == '-a': vmin = float(arg)
elif opt == '-b': vmax = float(arg)
elif opt == '-s': fontSize = int(arg)
elif opt == '-m':
markerSize = int(arg)
markerSize2 = int(arg)
elif opt == '-c':
markerColor = arg
elif opt == '-w':
lineWidth = int(arg)
elif opt == '-u':
unit = arg
elif opt == '-l':
lbound = float(arg)
elif opt == '-h':
hbound = float(arg)
elif opt == '-D':
demFile = arg
elif opt == '-V':
contour_step = float(arg)
elif opt == '-t':
minDate = arg
elif opt == '-T':
maxDate = arg
elif opt == '-r':
radius = abs(int(arg))
elif opt == '-x':
xsub = sorted([int(i) for i in arg.split(':')])
elif opt == '-y':
ysub = sorted([int(i) for i in arg.split(':')])
elif opt == '-X':
ref_xsub = sorted([int(i) for i in arg.split(':')])
elif opt == '-Y':
ref_ysub = sorted([int(i) for i in arg.split(':')])
elif opt == '--contour-step':
contour_step = float(arg)
elif opt == '--contour-smooth':
contour_sigma = float(arg)
elif opt == '--dem-nocontour':
demContour = 'no'
elif opt == '--dem-noshade':
demShade = 'no'
elif opt == '--displacement':
dispDisplacement = 'yes'
elif opt in ['-E', '--exclude']:
datesNot2show = arg.split(',')
elif opt in '--lalo':
lalosub = [float(i) for i in arg.split(',')]
elif opt in '--LALO':
ref_lalosub = [float(i) for i in arg.split(',')]
elif opt in ['--rect-color']:
rectColor = arg
elif opt in ['--ref-date']:
ref_date = ptime.yyyymmdd(arg)
elif opt in ['-u', '--unit']:
unit = arg.lower()
elif opt == '--save':
saveFig = 'yes'
elif opt == '--nodisplay':
dispFig = 'no'
saveFig = 'yes'
elif opt == '--opposite':
dispOpposite = 'yes'
elif opt == '--zero-start':
zero_start = arg.lower()
elif opt == '--zoom-x':
win_x = sorted([int(i) for i in arg.split(':')])
elif opt == '--zoom-y':
win_y = sorted([int(i) for i in arg.split(':')])
elif opt == '--zoom-lon':
win_lon = sorted([float(i) for i in arg.split(':')])
elif opt == '--zoom-lat':
win_lat = sorted([float(i) for i in arg.split(':')])
##############################################################
## Read time series file info
if not os.path.isfile(timeSeriesFile):
print '\nERROR: Input time series file does not exist: ' + timeSeriesFile + '\n'
sys.exit(1)
h5timeseries = h5py.File(timeSeriesFile, 'r')
k = h5timeseries.keys()
# read h5 file and its group type
if not 'timeseries' in k:
print 'ERROR: Input file is ' + k[
0] + '.\n\tOnly timeseries is supported.\n'
sys.exit(1)
atr = readfile.read_attribute(timeSeriesFile)
dateList1 = sorted(h5timeseries['timeseries'].keys())
dates1, datevector1 = ptime.date_list2vector(dateList1)
print '\n************ Time Series Display - Point *************'
##### Select Check
try:
lalosub
xsub = subset.coord_geo2radar([lalosub[1]], atr, 'longitude')
ysub = subset.coord_geo2radar([lalosub[0]], atr, 'latitude')
xsub = [xsub]
ysub = [ysub]
if radius == 0: radius = 3
except:
pass
try:
ref_lalosub
ref_xsub = subset.coord_geo2radar([ref_lalosub[1]], atr, 'longitude')
ref_ysub = subset.coord_geo2radar([ref_lalosub[0]], atr, 'latitude')
ref_xsub = [ref_xsub]
ref_ysub = [ref_ysub]
if radius == 0: radius = 3
except:
pass
##############################################################
global dates, dateList, datevector_all, dateListMinMax
print '*******************'
print 'All dates existed:'
print dateList1
print '*******************'
## Check exclude date input
try:
datesNot2show
if os.path.isfile(datesNot2show[0]):
try:
datesNot2show = ptime.read_date_list(datesNot2show[0])
except:
print 'Can not read date list file: ' + datesNot2show[0]
print 'dates not to show: ' + str(datesNot2show)
except:
datesNot2show = []
## Check Min / Max Date
dateListMinMax = []
try:
minDate
minDate = ptime.yyyymmdd(minDate)
dateListMinMax.append(minDate)
minDateyy = ptime.yyyymmdd2years(minDate)
print 'minimum date: ' + minDate
for date in dateList1:
yy = ptime.yyyymmdd2years(date)
if yy < minDateyy:
datesNot2show.append(date)
except:
pass
try:
maxDate
maxDate = ptime.yyyymmdd(maxDate)
dateListMinMax.append(maxDate)
maxDateyy = ptime.yyyymmdd2years(maxDate)
print 'maximum date: ' + maxDate
for date in dateList1:
yy = ptime.yyyymmdd2years(date)
if yy > maxDateyy:
datesNot2show.append(date)
except:
pass
dateListMinMax = sorted(dateListMinMax)
if not dateListMinMax: print 'no min/max date input.'
else: datesMinMax, dateVecMinMax = ptime.date_list2vector(dateListMinMax)
## Finalize Date List
try:
dateList = []
for date in dateList1:
if date not in datesNot2show:
dateList.append(date)
print '--------------------------------------------'
print 'dates used to show time series displacements:'
print dateList
print '--------------------------------------------'
except:
dateList = dateList1
print 'using all dates to show time series displacement'
## Read Date Info (x axis for time series display)
dates, datevector = ptime.date_list2vector(dateList)
datevector_all = list(datevector)
## Check reference date input
try:
ref_date
if not ref_date in dateList:
print 'Reference date - ' + ref_date + ' - is not included in date list to show.'
sys.exit(1)
else:
print 'reference date: ' + ref_date
except:
if zero_start == 'yes':
ref_date = dateList[0]
print 'set the 1st date as reference for displacement display.'
else:
pass
##############################################################
##### Plot Fig 1 - Velocity / last epoch of time series / DEM
fig = plt.figure(1)
ax = fig.add_subplot(111)
##### Check subset range
width = int(atr['WIDTH'])
length = int(atr['FILE_LENGTH'])
print 'file size: ' + str(length) + ', ' + str(width)
try:
win_y = subset.coord_geo2radar(win_lat, atr, 'latitude')
except:
try:
win_y
except:
win_y = [0, length]
try:
win_x = subset.coord_geo2radar(win_lon, atr, 'longitude')
except:
try:
win_x
except:
win_x = [0, width]
win_box = (win_x[0], win_y[0], win_x[1], win_y[1])
win_box = subset.check_box_within_data_coverage(win_box, atr)
try:
velocityFile
try:
vel, vel_atr = readfile.read(velocityFile)
except:
vel, vel_atr = readfile.read(timeSeriesFile, velocityFile)
ax.set_title(velocityFile)
print 'display: ' + velocityFile
except:
vel, vel_atr = readfile.read(timeSeriesFile, dateList1[-1])
ax.set_title('epoch: ' + dateList1[-1])
print 'display last epoch'
##### show displacement instead of phase
if vel_atr['FILE_TYPE'] in ['interferograms', '.unw'
] and dispDisplacement == 'yes':
print 'show displacement'
phase2range = -float(vel_atr['WAVELENGTH']) / (4 * np.pi)
vel *= phase2range
else:
dispDisplacement = 'no'
## Reference Point
if showRef == 'yes':
try:
ax.plot(int(atr['ref_x']), int(atr['ref_y']), 'ks', ms=6)
except:
pass
if dispOpposite == 'yes':
print 'show opposite value in figure/map 1'
vel *= -1
## Flip
try:
flip_lr
except:
try:
flip_ud
except:
flip_lr, flip_ud = view.auto_flip_direction(atr)
## Status bar
## Geo coordinate
try:
ullon = float(atr['X_FIRST'])
ullat = float(atr['Y_FIRST'])
lon_step = float(atr['X_STEP'])
lat_step = float(atr['Y_STEP'])
lon_unit = atr['Y_UNIT']
lat_unit = atr['X_UNIT']
geocoord = 'yes'
print 'Input file is Geocoded'
except:
geocoord = 'no'
def format_coord(x, y):
col = int(x + 0.5)
row = int(y + 0.5)
if col >= 0 and col <= width and row >= 0 and row <= length:
z = vel[row, col]
try:
lon = ullon + x * lon_step
lat = ullat + y * lat_step
return 'x=%.1f, y=%.1f, value=%.4f, lon=%.4f, lat=%.4f' % (
x, y, z, lon, lat)
except:
return 'x=%.1f, y=%.1f, value=%.4f' % (x, y, z)
ax.format_coord = format_coord
## DEM
try:
demFile
dem, demRsc = readfile.read(demFile)
ax = view.plot_dem_yx(ax, dem, demShade, demContour, contour_step,
contour_sigma)
vel_alpha = 0.8
except:
print 'No DEM file'
try:
img = ax.imshow(vel, vmin=vmin, vmax=vmax, alpha=vel_alpha)
except:
img = ax.imshow(vel, alpha=vel_alpha)
plt.colorbar(img)
## Zoom In (subset)
if flip_lr == 'yes': ax.set_xlim(win_box[2], win_box[0])
else: ax.set_xlim(win_box[0], win_box[2])
if flip_ud == 'yes': ax.set_ylim(win_box[1], win_box[3])
else: ax.set_ylim(win_box[3], win_box[1])
## Flip
#if flip_lr == 'yes': fig.gca().invert_xaxis()
#if flip_ud == 'yes': fig.gca().invert_yaxis()
##########################################
##### Plot Fig 2 - Time series plot
#fig2 = plt.figure(num=2,figsize=(12,6))
fig2 = plt.figure(2, figsize=(12, 6))
ax2 = fig2.add_subplot(111)
try:
timeSeriesFile_2
h5timeseries_2 = h5py.File(timeSeriesFile_2)
dateList_2 = sorted(h5timeseries_2['timeseries'].keys())
dates_2, datevector_2 = ptime.date_list2vector(dateList_2)
datevector_all += list(set(datevector_2) - set(datevector_all))
datevector_all = sorted(datevector_all)
except:
pass
################################ Plot Code Package <start> #################################
def plot_ts(ax, ax2, fig2, xsub, ysub, h5timeseries):
ax2.cla()
print '\n-------------------------------------------------------------------------------'
disp_min = 0
disp_max = 0
############################# Plot Time Series ##############################
global ref_xsub, ref_ysub
##### 1.1 Plot Reference time series
try:
ref_xsub
ref_ysub
ref_xsub, ref_ysub = check_yx(ref_xsub, ref_ysub, radius, ax,
rectColor)
print '----------------------------------------------------'
print 'Reference Point:'
print 'ref_x=' + str(ref_xsub[0]) + ':' + str(ref_xsub[1])
print 'ref_y=' + str(ref_ysub[0]) + ':' + str(ref_ysub[1])
print '-----------------------------'
print 'Time series with all dates:'
dis1, dis1_mean, dis1_std, dis1_vel = read_dis_xy(
ref_xsub, ref_ysub, dateList1, h5timeseries, unit)
(_, caps, _)=ax2.errorbar(dates1,dis1_mean,yerr=dis1_std,fmt='-ks',\
ms=markerSize2, lw=0, alpha=1,mfc=markerColor_ref,mew=edgeWidth,\
elinewidth=edgeWidth,ecolor='black',capsize=markerSize*0.5)
for cap in caps:
cap.set_markeredgewidth(edgeWidth)
disp_min, disp_max = update_lim(disp_min, disp_max, dis1_mean,
dis1_std)
if not len(dateList) == len(dateList1):
print '-----------------------------'
print 'Time series with dates of interest:'
dis12, dis12_mean, dis12_std, dis12_vel = read_dis_xy(
ref_xsub, ref_ysub, dateList, h5timeseries, unit)
(_, caps, _)=ax2.errorbar(dates,dis12_mean,yerr=dis12_std,fmt='-ks',\
ms=markerSize2, lw=0, alpha=1,mfc=markerColor_ref2,mew=edgeWidth,\
elinewidth=edgeWidth,ecolor='black',capsize=markerSize*0.5)
for cap in caps:
cap.set_markeredgewidth(edgeWidth)
disp_min, disp_max = update_lim(disp_min, disp_max, dis12_mean,
dis12_std)
except:
pass
##### 1.2.0 Read y/x
print '\n----------------------------------------------------'
print 'Point of Interest:'
xsub, ysub = check_yx(xsub, ysub, radius, ax, rectColor)
print 'x=' + str(xsub[0]) + ':' + str(xsub[1])
print 'y=' + str(ysub[0]) + ':' + str(ysub[1])
##### 1.2.1 Plot 2nd time series
try:
timeSeriesFile_2
print '-----------------------------'
print '2nd Time Series:'
dis2, dis2_mean, dis2_std, dis2_vel = read_dis_xy(
xsub, ysub, dateList_2, h5timeseries_2, unit)
(_, caps, _)=ax2.errorbar(dates_2,dis2_mean,yerr=dis2_std,fmt='-ko',\
ms=markerSize2, lw=0, alpha=1, mfc=markerColor2,\
elinewidth=0,ecolor='black',capsize=0)
for cap in caps:
cap.set_markeredgewidth(edgeWidth)
disp_min, disp_max = update_lim(disp_min, disp_max, dis2_mean,
dis2_std)
except:
pass
##### 1.2.2 Plot 1st time series
print '-----------------------------'
print 'Time Series:'
dis, dis_mean, dis_std, dis_vel = read_dis_xy(xsub, ysub, dateList,
h5timeseries, unit)
(_, caps, _)=ax2.errorbar(dates,dis_mean,yerr=dis_std,fmt='-ko',\
ms=markerSize, lw=lineWidth, alpha=1, mfc=markerColor,\
elinewidth=edgeWidth,ecolor='black',capsize=markerSize*0.5)
for cap in caps:
cap.set_markeredgewidth(edgeWidth)
disp_min, disp_max = update_lim(disp_min, disp_max, dis_mean, dis_std)
####################### Figure Format #######################
## x axis format
try:
ax2 = ptime.auto_adjust_xaxis_date(ax2, dateVecMinMax, fontSize)
except:
ax2 = ptime.auto_adjust_xaxis_date(ax2, datevector_all, fontSize)
## y axis format
ax2.set_ylabel('Displacement [' + unit + ']', fontsize=fontSize)
try:
lbound
hbound
ax2.set_ylim(lbound, hbound)
except:
disp_buf = 0.2 * (disp_max - disp_min)
ax2.set_ylim(disp_min - disp_buf, disp_max + disp_buf)
for tick in ax2.yaxis.get_major_ticks():
tick.label.set_fontsize(fontSize)
## title
figTitle = 'x=' + str(xsub[0]) + ':' + str(xsub[1]) + ', y=' + str(
ysub[0]) + ':' + str(ysub[1])
try:
lonc = ullon + (xsub[0] + xsub[1]) / 2.0 * lon_step
latc = ullat + (ysub[0] + ysub[1]) / 2.0 * lat_step
figTitle += ', lalo=' + '%.4f,%.4f' % (latc, lonc)
except:
pass
ax2.set_title(figTitle)
################## Save and Output #####################
if saveFig == 'yes':
print '-----------------------------'
Delay = {}
Delay['displacement'] = dis
Delay['unit'] = unit
Delay['time'] = datevector
Delay['velocity'] = dis_vel[0]
Delay['velocity_unit'] = unit + '/yr'
Delay['velocity_std'] = dis_vel[4]
figBase = 'x' + str(xsub[0]) + '_' + str(xsub[1] - 1) + 'y' + str(
ysub[0]) + '_' + str(ysub[1] - 1)
sio.savemat(figBase + '_ts.mat', {'displacement': Delay})
print 'saved ' + figBase + '_ts.mat'
fig2.savefig(figBase + '_ts.pdf',
bbox_inches='tight',
transparent=True,
dpi=fig_dpi)
print 'saved ' + figBase + '_ts.pdf'
if dispFig == 'no':
fig.savefig(figBase + '_vel.png',
bbox_inches='tight',
transparent=True,
dpi=fig_dpi)
print 'saved ' + figBase + '_vel.png'
################################ Plot Code Package <end> #################################
########### 1. Plot Time Series with x/y ##########
try:
xsub
ysub
plot_ts(ax, ax2, fig2, xsub, ysub, h5timeseries)
except:
print 'No x/y input'
pass
########### 2. Plot Time Series with Click ##########
## similar to 1. Plot Time Series with x/y
def onclick(event):
ax2.cla()
xsub = [int(event.xdata)]
ysub = [int(event.ydata)]
plot_ts(ax, ax2, fig2, xsub, ysub, h5timeseries)
if dispFig == 'yes': plt.show()
try:
cid = fig.canvas.mpl_connect('button_press_event', onclick)
except:
pass
if dispFig == 'yes': plt.show()
