def geocode_data_roipac(data, geomapFile, outname):
print 'writing to roi_pac unw file format'
writefile.write_float32(data, outname)
f = open(outname + '.rsc', 'w')
f.write('FILE_LENGTH ' + str(data.shape[0]) + '\n')
f.write('WIDTH ' + str(data.shape[1]) + '\n')
f.close()
geoCmd = 'geocode.pl ' + geomapFile + ' ' + outname + ' geo_' + outname
print geoCmd
os.system(geoCmd)
print 'reading geocoded file...'
amp, unw, unwrsc = readfile.read_float32('geo_' + outname)
rmCmd = 'rm ' + outname
os.system(rmCmd)
print rmCmd
rmCmd = 'rm ' + outname + '.rsc'
os.system(rmCmd)
print rmCmd
rmCmd = 'rm geo_' + outname
os.system(rmCmd)
print rmCmd
rmCmd = 'rm geo_' + outname + '.rsc'
os.system(rmCmd)
print rmCmd
return amp, unw, unwrsc
def main(argv):
try:
file = argv[0]
except:
usage()
sys.exit(1)
print '\n*************** Save to GRD file for GMT ****************'
print 'Input file: ' + file
ext = os.path.splitext(file)[1]
########## PySAR HDF5 Files ################
if ext == '.h5':
h5 = h5py.File(file, 'r')
k = h5.keys()
if 'interferograms' in k: k[0] = 'interferograms'
elif 'coherence' in k: k[0] = 'coherence'
elif 'timeseries' in k: k[0] = 'timeseries'
if k[0] in ('interferograms', 'coherence', 'wrapped'):
atr = h5[k[0]][h5[k[0]].keys()[0]].attrs
elif k[0] in ('dem', 'velocity', 'mask', 'temporal_coherence', 'rmse',
'timeseries'):
atr = h5[k[0]].attrs
if 'timeseries' in k:
try:
d = sys.argv[2]
except:
print 'No input date... continue to convert the last date of timeseries'
dateList = h5['timeseries'].keys()
d = dateList[-1]
print 'reading ' + d + ' ... '
dset = h5['timeseries'].get(d)
elif k[0] in ['interferograms', 'coherence', 'wrapped']:
print 'interferograms is not supported currently.'
sys.exit(1)
else:
dset = h5[k[0]].get(k[0])
z = dset[0:dset.shape[0], 0:dset.shape[1]]
########## ROI_PAC Files ##################
elif ext in ['.unw', '.cor', '.hgt', '.dem']:
if ext == '.dem': z, atr = readfile.read_real_int16(file)
if ext in ['.unw', '.cor', '.hgt']:
a, z, atr = readfile.read_float32(file)
else:
print 'Unsupported file extension: ' + ext
sys.exit(1)
lats, lons = get_geo_lat_lon(atr)
#fname='velocity.grd'
outName = os.path.basename(file).replace(ext, '') + '.grd'
print 'Output (GMT grd file): ' + outName
_gmt.write_gmt_simple(lons, flipud(lats), flipud(z), outName, title='default', name='velocity',\
scale=1.0, offset=0, units='meters')
def main(argv):
try: file = argv[0]
except: Usage(); sys.exit(1)
print '\n*************** Save to GRD file for GMT ****************'
print 'Input file: '+file
ext = os.path.splitext(file)[1]
########## PySAR HDF5 Files ################
if ext == '.h5':
h5=h5py.File(file,'r')
k=h5.keys()
if 'interferograms' in k: k[0] = 'interferograms'
elif 'coherence' in k: k[0] = 'coherence'
elif 'timeseries' in k: k[0] = 'timeseries'
if k[0] in ('interferograms','coherence','wrapped'):
atr = h5[k[0]][h5[k[0]].keys()[0]].attrs
elif k[0] in ('dem','velocity','mask','temporal_coherence','rmse','timeseries'):
atr = h5[k[0]].attrs
if 'timeseries' in k:
try:
d=sys.argv[2]
except:
print 'No input date... continue to convert the last date of timeseries'
dateList=h5['timeseries'].keys()
d=dateList[-1]
print 'reading '+d + ' ... '
dset=h5['timeseries'].get(d)
elif k[0] in ['interferograms','coherence','wrapped']:
print 'interferograms is not supported currently.'; sys.exit(1)
else: dset=h5[k[0]].get(k[0])
z=dset[0:dset.shape[0],0:dset.shape[1]]
########## ROI_PAC Files ##################
elif ext in ['.unw','.cor','.hgt','.dem']:
import pysar._readfile as readfile
if ext == '.dem' : z,atr = readfile.read_real_int16(file)
if ext in ['.unw','.cor','.hgt']: a,z,atr = readfile.read_float32(file)
else: print 'Unsupported file extension: '+ext; sys.exit(1)
lats,lons=get_geo_lat_lon(atr)
#fname='velocity.grd'
outName=os.path.basename(file).replace(ext,'')+'.grd'; print 'Output (GMT grd file): '+outName
_gmt.write_gmt_simple(lons, flipud(lats), flipud(z), outName, title='default', name='velocity',\
scale=1.0, offset=0, units='meters')
def roipac_nonzero_mask(unwFileList, maskFile='Mask.h5'):
'''Generate mask for non-zero amplitude pixel of ROI_PAC .unw file list.'''
unwFileList, width, length = check_file_size(unwFileList)
if unwFileList:
# Initial mask value
if os.path.isfile(maskFile):
maskZero, atr = readfile.read(maskFile)
print 'update existing mask file: '+maskFile
else:
maskZero = np.ones([int(length), int(width)])
atr = None
print 'create initial mask matrix'
# Update mask from input .unw file list
fileNum = len(unwFileList)
for i in range(fileNum):
file = unwFileList[i]
amp, unw, rsc = readfile.read_float32(file)
maskZero *= amp
ut.print_progress(i+1, fileNum, prefix='loading', suffix=os.path.basename(file))
mask = np.ones([int(length), int(width)])
mask[maskZero==0] = 0
# write mask hdf5 file
print 'writing >>> '+maskFile
h5 = h5py.File(maskFile,'w')
group = h5.create_group('mask')
dset = group.create_dataset('mask', data=mask, compression='gzip')
# Attribute - *.unw.rsc
for key,value in rsc.iteritems():
group.attrs[key] = value
# Attribute - *baseline.rsc
d1, d2 = rsc['DATE12'].split('-')
baseline_file = os.path.dirname(file)+'/'+d1+'_'+d2+'_baseline.rsc'
baseline_rsc = readfile.read_roipac_rsc(baseline_file)
for key,value in baseline_rsc.iteritems():
group.attrs[key] = value
# Attribute - existed file
if atr:
for key, value in atr.iteritems():
group.attrs[key] = value
return maskFile, unwFileList
def geomap4subset_radar_file(radar_atr, geomap_file):
''' Add offset value to geomap file if input radar file has been subsetted.'''
if 'subset_x0' in radar_atr.keys():
x0 = float(radar_atr['subset_x0'])
y0 = float(radar_atr['subset_y0'])
print '\nInput radar coord file has been subsetted.\n creating temporary geomap file for it...'
rg, az, rsc = readfile.read_float32(geomap_file)
rg = rg - x0
az = az - y0
geomap_file = 'temp_' + geomap_file
print ' writing >>> ' + geomap_file + '\n'
writefile.write_float32(rg, az, geomap_file)
f = open(geomap_file + '.rsc', 'w')
for key in rsc.keys():
f.write(key + ' ' + rsc[key] + '\n')
f.close()
return geomap_file
def geocode_one(data,geomapFile,outname):
print 'writing to roi_pac unw file format'
writefile.write_float32(data,outname)
f = open(outname+'.rsc','w')
f.write('FILE_LENGTH '+str(data.shape[0])+'\n')
f.write('WIDTH '+str(data.shape[1])+'\n')
f.close()
geoCmd='geocode.pl '+geomapFile+' '+outname+' geo_'+outname
print geoCmd
os.system(geoCmd)
print 'reading geocoded file...'
amp,unw,unwrsc = readfile.read_float32('geo_'+outname)
rmCmd='rm '+outname; os.system(rmCmd); print rmCmd
rmCmd='rm '+outname+'.rsc'; os.system(rmCmd); print rmCmd
rmCmd='rm geo_'+outname; os.system(rmCmd); print rmCmd
rmCmd='rm geo_'+outname+'.rsc'; os.system(rmCmd); print rmCmd
return amp, unw, unwrsc
def main(argv):
method = 'triangular_consistency' ## or 'bonding_point'
ramp_type = 'plane'
save_rampCor = 'yes'
plot_bonding_points = 'yes'
##### Check Inputs
if len(sys.argv)>2:
try: opts, args = getopt.getopt(argv,'h:f:m:x:y:o:t:',['ramp=','no-ramp-save'])
except getopt.GetoptError: print 'Error while getting args'; Usage(); sys.exit(1)
for opt,arg in opts:
if opt in ['-h','--help']: Usage(); sys.exit()
elif opt in '-f': File = arg
elif opt in '-m': maskFile = arg
elif opt in '-o': outName = arg
elif opt in '-x': x = [int(i) for i in arg.split(',')]; method = 'bonding_point'
elif opt in '-y': y = [int(i) for i in arg.split(',')]; method = 'bonding_point'
elif opt in '-t': templateFile = arg
elif opt in '--ramp' : ramp_type = arg.lower()
elif opt in '--no-ramp-save' : save_rampCor = 'no'
elif len(sys.argv)==2:
if argv[0] in ['-h','--help']: Usage(); sys.exit()
elif os.path.isfile(argv[0]): File = argv[0]; maskFile = argv[1]
else: print 'Input file does not existed: '+argv[0]; sys.exit(1)
else: Usage(); sys.exit(1)
##### Check template file
try:
templateFile
templateContents = readfile.read_template(templateFile)
except: pass
try:
yx = [int(i) for i in templateContents['pysar.unwrapError.yx'].split(',')]
x = yx[1::2]
y = yx[0::2]
method = 'bonding_point'
except: pass
##### Read Mask File
## Priority:
## Input mask file > pysar.mask.file > existed Modified_Mask.h5 > existed Mask.h5
try: maskFile
except:
try: maskFile = templateContents['pysar.mask.file']
except:
if os.path.isfile('Modified_Mask.h5'): maskFile = 'Modified_Mask.h5'
elif os.path.isfile('Mask.h5'): maskFile = 'Mask.h5'
else: print 'No mask found!'; sys.exit(1)
try: Mask,Matr = readfile.read(maskFile); print 'mask: '+maskFile
except: print 'Can not open mask file: '+maskFile; sys.exit(1)
##### Output file name
ext = os.path.splitext(File)[1]
try: outName
except: outName = File.split('.')[0]+'_unwCor'+ext
print '\n**************** Unwrapping Error Correction ******************'
#################### Triangular Consistency (Phase Closure) ####################
if method == 'triangular_consistency':
print 'Phase unwrapping error correction using Triangular Consistency / Phase Closure'
h5file=h5py.File(File)
ifgramList = h5file['interferograms'].keys()
sx = int(h5file['interferograms'][ifgramList[0]].attrs['WIDTH'])
sy = int(h5file['interferograms'][ifgramList[0]].attrs['FILE_LENGTH'])
curls,Triangles,C=ut.get_triangles(h5file)
A,B = ut.design_matrix(h5file)
ligram,lv=np.shape(B)
lcurls=np.shape(curls)[0]
print 'Number of all triangles: '+ str(lcurls)
print 'Number of interferograms: '+ str(ligram)
#print curls
curlfile='curls.h5'
if not os.path.isfile(curlfile):
ut.generate_curls(curlfile,h5file,Triangles,curls)
thr=0.50
curls=np.array(curls); n1=curls[:,0]; n2=curls[:,1]; n3=curls[:,2]
numPixels=sy*sx
print 'reading interferograms...'
data = np.zeros((ligram,numPixels),np.float32)
for ni in range(ligram):
dset=h5file['interferograms'][ifgramList[ni]].get(ifgramList[ni])
d = dset[0:dset.shape[0],0:dset.shape[1]]
data[ni] = d.flatten(1)
print np.shape(data)
print 'reading curls ...'
h5curl=h5py.File(curlfile)
curlList=h5curl['interferograms'].keys()
curlData = np.zeros((lcurls,numPixels),np.float32)
for ni in range(lcurls):
dset=h5curl['interferograms'][curlList[ni]].get(curlList[ni])
d = dset[0:dset.shape[0],0:dset.shape[1]]
curlData[ni] = d.flatten(1)
pi=np.pi
EstUnwrap=np.zeros((ligram,numPixels),np.float32)
#try:
# maskFile=argv[1]
# h5Mask=h5py.File(maskFile)
# dset = h5Mask['mask'].get('mask')
# Mask=dset[0:dset.shape[0],0:dset.shape[1]]
#except:
# dset = h5file['mask'].get('mask')
# Mask=dset[0:dset.shape[0],0:dset.shape[1]]
Mask=Mask.flatten(1)
from scipy.linalg import pinv as pinv
for ni in range(numPixels):
#dU = np.zeros([ligram,1])
#print np.shape(dU)
#print np.shape(data[:,ni])
if Mask[ni]==1:
dU = data[:,ni]
#nan_ndx = dataPoint == 0.
unwCurl = np.array(curlData[:,ni])
#print unwCurl
ind = np.abs(unwCurl)>=thr; N1 =n1[ind]; N2 =n2[ind]; N3 =n3[ind]
indC = np.abs(unwCurl)< thr; Nc1=n1[indC]; Nc2=n2[indC]; Nc3=n3[indC]
N =np.hstack([N1, N2, N3]); UniN =np.unique(N)
Nc=np.hstack([Nc1,Nc2,Nc3]); UniNc=np.unique(Nc)
inter=list(set(UniNc) & set(UniN)) # intersetion
UniNc= list(UniNc)
for x in inter:
UniNc.remove(x)
D=np.zeros([len(UniNc),ligram])
for i in range(len(UniNc)):
D[i,UniNc[i]]=1
AAA=np.vstack([-2*pi*C,D])
#AAA1=np.hstack([AAA,np.zeros([AAA.shape[0],lv])])
#AAA2=np.hstack([-2*pi*np.eye(ligram),B])
#AAAA=np.vstack([AAA1,AAA2])
AAAA=np.vstack([AAA,0.25*np.eye(ligram)])
#print '************************'
#print np.linalg.matrix_rank(C)
#print np.linalg.matrix_rank(AAA)
#print np.linalg.matrix_rank(AAAA)
#print '************************'
#LLL=list(np.dot(C,dU)) + list(np.zeros(np.shape(UniNc)[0]))# + list(dU)
#ind=np.isnan(AAA)
#M1=pinv(AAA)
#M=np.dot(M1,LLL)
#EstUnwrap[:,ni]=np.round(M[0:ligram])*2.0*np.pi
##########
# with Tikhonov regularization:
AAAA=np.vstack([AAA,0.25*np.eye(ligram)])
LLL=list(np.dot(C,dU)) + list(np.zeros(np.shape(UniNc)[0])) + list(np.zeros(ligram))
ind=np.isnan(AAAA)
M1=pinv(AAAA)
M=np.dot(M1,LLL)
EstUnwrap[:,ni]=np.round(M[0:ligram])*2.0*np.pi
#print M[0:ligram]
#print np.round(M[0:ligram])
else:
EstUnwrap[:,ni]=np.zeros([ligram])
if not np.remainder(ni,10000): print 'Processing point: %7d of %7d ' % (ni,numPixels)
##### Output
dataCor = data+EstUnwrap
unwCorFile=File.replace('.h5','')+'_unwCor.h5'; print 'writing >>> '+unwCorFile
h5unwCor=h5py.File(unwCorFile,'w')
gg = h5unwCor.create_group('interferograms')
for i in range(ligram):
group = gg.create_group(ifgramList[i])
dset = group.create_dataset(ifgramList[i], data=np.reshape(dataCor[i,:],[sx,sy]).T, compression='gzip')
for key, value in h5file['interferograms'][ifgramList[i]].attrs.iteritems():
group.attrs[key] = value
try:
MASK=h5file['mask'].get('mask')
gm = h5unwCor.create_group('mask')
dset = gm.create_dataset('mask', data=MASK, compression='gzip')
except: pass
h5unwCor.close()
h5file.close()
h5curl.close()
#################### Bonding Points (Spatial Continuity) ####################
elif method == 'bonding_point':
print 'Phase unwrapping error correction using Bonding Points / Spatial Continuity'
##### Read Bridge Points Info
try:
x
y
if len(x) != len(y) or np.mod(len(x),2) != 0:
print 'Wrong number of bridge points input: '+str(len(x))+' for x, '+str(len(y))+' for y'
Usage(); sys.exit(1)
except: print 'Error in reading bridge points info!'; Usage(); sys.exit(1)
for i in range(0,len(x)):
if Mask[y[i],x[i]] == 0:
print '\nERROR: Connecting point ('+str(y[i])+','+str(x[i])+') is out of masked area! Select them again!\n'
sys.exit(1)
print 'Number of bonding point pairs: '+str(len(x)/2)
print 'Bonding points coordinates:\nx: '+str(x)+'\ny: '+str(y)
## Plot Connecting Pair of Points
if plot_bonding_points == 'yes':
point_yx = ''
line_yx = ''
n_bridge = len(x)/2
for i in range(n_bridge):
pair_yx = str(y[2*i])+','+str(x[2*i])+','+str(y[2*i+1])+','+str(x[2*i+1])
if not i == n_bridge-1:
point_yx += pair_yx+','
line_yx += pair_yx+';'
else:
point_yx += pair_yx
line_yx += pair_yx
try:
plot_cmd = 'view.py --point-yx="'+point_yx+'" --line-yx="'+line_yx+\
'" --nodisplay -o bonding_points.png -f '+maskFile
print plot_cmd
os.system(plot_cmd)
except: pass
##### Ramp Info
ramp_mask = Mask==1
print 'estimate phase ramp during the correction'
print 'ramp type: '+ramp_type
if save_rampCor == 'yes':
outName_ramp = os.path.basename(outName).split(ext)[0]+'_'+ramp_type+ext
########## PySAR ##########
if ext == '.h5':
##### Read
try: h5file=h5py.File(File,'r')
except: print 'ERROR: Cannot open input file: '+File; sys.exit(1)
k=h5file.keys()
if 'interferograms' in k: k[0] = 'interferograms'; print 'Input file is '+k[0]
else: print 'Input file - '+File+' - is not interferograms.'; Usage(); sys.exit(1)
igramList = h5file[k[0]].keys()
igramList = sorted(igramList)
#### Write
h5out = h5py.File(outName,'w')
gg = h5out.create_group(k[0])
print 'writing >>> '+outName
if save_rampCor == 'yes':
h5out_ramp = h5py.File(outName_ramp,'w')
gg_ramp = h5out_ramp.create_group(k[0])
print 'writing >>> '+outName_ramp
##### Loop
print 'Number of interferograms: '+str(len(igramList))
for igram in igramList:
print igram
data = h5file[k[0]][igram].get(igram)[:]
data_ramp,ramp = rm.remove_data_surface(data,ramp_mask,ramp_type)
#ramp = data_ramp - data
data_rampCor = phase_bonding(data_ramp,Mask,x,y)
dataCor = data_rampCor - ramp
group = gg.create_group(igram)
dset = group.create_dataset(igram, data=dataCor, compression='gzip')
for key, value in h5file[k[0]][igram].attrs.iteritems():
group.attrs[key]=value
if save_rampCor == 'yes':
group_ramp = gg_ramp.create_group(igram)
dset = group_ramp.create_dataset(igram, data=data_rampCor, compression='gzip')
for key, value in h5file[k[0]][igram].attrs.iteritems():
group_ramp.attrs[key]=value
try:
mask = h5file['mask'].get('mask');
gm = h5out.create_group('mask')
dset = gm.create_dataset('mask', data=mask[0:mask.shape[0],0:mask.shape[1]], compression='gzip')
except: print 'no mask group found.'
h5file.close()
h5out.close()
if save_rampCor == 'yes':
h5out_ramp.close()
########## ROI_PAC ##########
elif ext == '.unw':
print 'Input file is '+ext
a,data,atr = readfile.read_float32(File);
data_ramp,ramp = rm.remove_data_surface(data,ramp_mask,ramp_type)
#ramp = data_ramp - data
data_rampCor = phase_bonding(data_ramp,Mask,x,y)
dataCor = data_rampCor - ramp
writefile.write(dataCor, atr, outName)
if save_rampCor == 'yes':
writefile.write(data_rampCor,atr,outName_ramp)
else: print 'Un-supported file type: '+ext; Usage(); sys.exit(1)
def main(argv):
cbar_bin_num = 9
cbar_label = 'Mean LOS velocity'
color_map = 'jet'
data_alpha = 0.7
disp_opposite = 'no'
disp_colorbar = 'yes'
rewrapping = 'no'
fig_dpi = 500
#fig_size = [6.0,9.0]
fig_unit = 'mm/yr'
disp_ref = 'yes'
ref_size = 5
dispDisplacement = 'no'
if len(sys.argv)>2:
try: opts, args = getopt.getopt(argv,"f:m:M:d:c:w:i:r:",['noreference','fig-size',\
'ref-size=','cbar-label=','displacement','cbar-bin-num='])
except getopt.GetoptError: Usage() ; sys.exit(1)
for opt,arg in opts:
if opt == '-f': File = arg
elif opt == '-m': Vmin = float(arg)
elif opt == '-M': Vmax = float(arg)
elif opt == '-d': epoch_date = arg
elif opt == '-c': color_map = arg
elif opt == '-i': disp_opposite = arg
elif opt == '-w': rewrapping = arg
elif opt == '-r': fig_dpi = int(arg)
elif opt == '--cbar-bin-num' : cbar_bin_num = int(arg)
elif opt == '--cbar-label' : cbar_label = arg
elif opt == '--displacement' : dispDisplacement = 'yes'
elif opt == '--fig-size' : fig_size = [float(i) for i in arg.split(',')][0:2]
elif opt == '--ref-size' : ref_size = int(arg)
elif opt == '--noreference' : disp_ref = 'no'
elif len(sys.argv)==2:
if argv[0]=='-h': Usage(); sys.exit(1)
elif os.path.isfile(argv[0]): File = argv[0]
else: Usage(); sys.exit(1)
else: Usage(); sys.exit(1)
#######################################################
################### Prepare Data ####################
## prepare: data, North, East, South, West
ext = os.path.splitext(File)[1].lower()
atr = readfile.read_attributes(File)
k = atr['FILE_TYPE']
print '\n*************** Output to KMZ file ****************'
print 'Input file is '+k
if ext == '.h5':
try: h5file=h5py.File(File,'r')
except: Usage() ; sys.exit(1)
outName=File.split('.')[0]
if k in ('interferograms','wrapped','coherence'):
ifgramList=h5file[k].keys()
for i in range(len(ifgramList)):
if epoch_date in ifgramList[i]:
epoch_number = i
print ifgramList[epoch_number]
outName = ifgramList[epoch_number]
#outName=epoch_date
dset = h5file[k][ifgramList[epoch_number]].get(ifgramList[epoch_number])
data = dset[0:dset.shape[0],0:dset.shape[1]]
if k == 'wrapped':
print 'No wrapping for wrapped interferograms. Set rewrapping=no'
rewrapping = 'no'
Vmin = -np.pi
Vmax = np.pi
elif 'timeseries' in k:
epochList=h5file['timeseries'].keys()
for i in range(len(epochList)):
if epoch_date in epochList[i]:
epoch_number = i
#### Out name
try: ref_date = atr['ref_date']
except: ref_date = ut.yyyymmdd(atr['DATE'])[0]
#ref_date=h5file['timeseries'].attrs['ref_date']
if len(epoch_date)==8: outName=ref_date[2:]+'-'+epoch_date[2:]
else: outName=ref_date[2:]+'-'+epoch_date
dset = h5file['timeseries'].get(epochList[epoch_number])
data = dset[0:dset.shape[0],0:dset.shape[1]]
### one dataset format: velocity, mask, temporal_coherence, rmse, std, etc.
else:
dset = h5file[k].get(k)
data=dset[0:dset.shape[0],0:dset.shape[1]]
if disp_opposite in('yes','Yes','Y','y','YES'):
data=-1*data
try:
xref=h5file[k].attrs['ref_x']
yref=h5file[k].attrs['ref_y']
except: pass
elif ext in ['.unw','.cor','.hgt','.trans','.dem']:
if ext in ['.unw','.cor','.hgt','.trans']:
a,data,atr = readfile.read_float32(File)
outName = File
if ext in ['.unw']:
if dispDisplacement == 'yes':
print 'show displacement'
phase2range = -float(atr['WAVELENGTH']) / (4*np.pi)
data *= phase2range
atr['UNIT'] = 'm'
rewrapping == 'no'
fig_unit = 'mm'
if rewrapping == 'yes':
data = rewrap(data,atr)
fig_unit = 'radian'
elif ext == '.dem':
data,atr = readfile.read_real_int16(File)
outName = File
if ext in ['.hgt','.dem']: fig_unit = 'm'
elif ext in ['.cor','.trans']: fig_unit = ' '
else: sys.exit('Do not support '+ext+' file!')
########################################################
if rewrapping=='yes':
data=rewrap(data)
Vmin = -np.pi #[-pi,pi] for wrapped interferograms
Vmax = np.pi
else:
try: Vmin
except: Vmin = np.nanmin(data)
try: Vmax
except: Vmax = np.nanmax(data)
try:
lon_step = float(atr['X_STEP'])
lat_step = float(atr['Y_STEP'])
lon_unit = atr['Y_UNIT']
lat_unit = atr['X_UNIT']
West = float(atr['X_FIRST'])
North = float(atr['Y_FIRST'])
South = North+lat_step*(data.shape[0]-1)
East = West +lon_step*(data.shape[1]-1)
geocoord = 'yes'
print 'Geocoded'
except:
print '%%%%%%%%%%'
print 'Error:\nThe input file is not geocoded\n'
print '%%%%%%%%%%'
Usage();sys.exit(1)
#######################################################
################### Output KMZ ######################
############### Make PNG file
print 'Making png file ...'
length = data.shape[0]
width = data.shape[1]
try:fig_size
except:
fig_size_0 = 6.0 ## min figure dimension: 6.0
ratio = float(length)/float(width)
fig_size = [fig_size_0,fig_size_0*ratio]
print 'figure size: %.1f, %.1f'%(fig_size[0],fig_size[1])
ccmap = plt.get_cmap(color_map)
fig = plt.figure(figsize=fig_size,frameon=False)
ax = fig.add_axes([0., 0., 1., 1.])
ax.set_axis_off()
aspect = width/(length*1.0)
try: ax.imshow(data,aspect='auto',cmap=ccmap,vmax=Vmax,vmin=Vmin)
except: ax.imshow(data,aspect='auto',cmap=ccmap)
if disp_ref == 'yes':
try:
xref = int(atr['ref_x'])
yref = int(atr['ref_y'])
ax.plot(xref,yref,'ks',ms=ref_size)
print 'show reference point'
except: print 'Cannot find reference point info!'
ax.set_xlim([0,width])
ax.set_ylim([length,0])
figName = outName + '.png'
print 'writing '+figName
plt.savefig(figName, pad_inches=0.0, transparent=True, dpi=fig_dpi)
############### Making colorbar
pc = plt.figure(figsize=(1,8))
axc = pc.add_subplot(111)
if fig_unit in ['mm','mm/yr']: v_scale = 1000
elif fig_unit in ['cm','cm/yr']: v_scale = 100
elif fig_unit in ['m', 'm/yr']: v_scale = 1
norm = mpl.colors.Normalize(vmin=Vmin*v_scale, vmax=Vmax*v_scale)
clb = mpl.colorbar.ColorbarBase(axc,cmap=ccmap,norm=norm, orientation='vertical')
#clb.set_label(fig_unit)
clb.set_label(cbar_label+' ['+fig_unit+']')
clb.locator = ticker.MaxNLocator(nbins=cbar_bin_num)
clb.update_ticks()
pc.subplots_adjust(left=0.2,bottom=0.3,right=0.4,top=0.7)
pc.patch.set_facecolor('white')
pc.patch.set_alpha(0.7)
pc.savefig('colorbar.png',bbox_inches='tight',facecolor=pc.get_facecolor(),dpi=300)
############## Generate KMZ file
print 'generating kml file ...'
try: doc = KML.kml(KML.Folder(KML.name(atr['PROJECT_NAME'])))
except: doc = KML.kml(KML.Folder(KML.name('PySAR product')))
slc = KML.GroundOverlay(KML.name(figName),KML.Icon(KML.href(figName)),\
KML.altitudeMode('clampToGround'),\
KML.LatLonBox(KML.north(str(North)),KML.south(str(South)),\
KML.east( str(East)), KML.west( str(West))))
doc.Folder.append(slc)
#############################
print 'adding colorscale ...'
cb_rg = min(North-South, East-West)
cb_N = (North+South)/2.0 + 0.5*0.5*cb_rg
cb_W = East + 0.1*cb_rg
slc1 = KML.GroundOverlay(KML.name('colorbar'),KML.Icon(KML.href('colorbar.png')),\
KML.altitude('2000'),KML.altitudeMode('absolute'),\
KML.LatLonBox(KML.north(str(cb_N)),KML.south(str(cb_N-0.5*cb_rg)),\
KML.west( str(cb_W)),KML.east( str(cb_W+0.14*cb_rg))))
doc.Folder.append(slc1)
#############################
kmlstr = etree.tostring(doc, pretty_print=True)
kmlname = outName + '.kml'
print 'writing '+kmlname
kmlfile = open(kmlname,'w')
kmlfile.write(kmlstr)
kmlfile.close()
kmzName = outName + '.kmz'
print 'writing '+kmzName
cmdKMZ = 'zip ' + kmzName +' '+ kmlname +' ' + figName + ' colorbar.png'
os.system(cmdKMZ)
cmdClean = 'rm '+kmlname; print cmdClean; os.system(cmdClean)
cmdClean = 'rm '+figName; print cmdClean; os.system(cmdClean)
cmdClean = 'rm colorbar.png'; print cmdClean; os.system(cmdClean)
def main(argv):
################# default values ################
flip_lr = 'no'
flip_ud = 'no'
disp_geo = 'yes'
#font_size=8
color_map = 'jet'
figs_rows = 5
figs_cols = 8
rewrapping = 'yes'
allData2display = 'yes'
Wspace = 0.1
Hspace = 0.1
title = 'out'
showRef = 'yes'
ref_color = 'k'
ref_symbol = 's'
ref_size = 10
dip_opposite = 'no'
saveFig = 'no'
dispFig = 'yes'
dispContour = 'only'
contour_step = 200
contour_sigma = 3.0
fig_dpi = 300
################### get input args ###############
if len(sys.argv) > 2:
try:
opts, args = getopt.getopt(
argv,
"h:D:O:G:S:f:m:M:v:u:s:c:e:d:r:p:w:i:j:t:R:a:b:k:x:y:C:V:P:o:g:l:L:"
)
except getopt.GetoptError:
Usage()
sys.exit(1)
if opts == []:
Usage()
sys.exit(1)
for opt, arg in opts:
if opt in ("-h", "--help"):
Usage()
sys.exit()
elif opt == '-f':
File = arg
elif opt == '-D':
demFile = arg
elif opt == '-w':
rewrapping = arg
elif opt == '-m':
min = float(arg)
rewrapping = 'no'
elif opt == '-M':
max = float(arg)
rewrapping = 'no'
elif opt == '-v':
flip_lr = arg
elif opt == '-u':
flip_ud = arg
elif opt == '-s':
font_size = int(arg)
elif opt == '-c':
color_map = arg
elif opt == '-e':
epoch_number = int(arg)
allData2display = 'no'
elif opt == '-d':
epoch_date = arg
allData2display = 'no'
elif opt == '-r':
figs_rows = int(arg)
elif opt == '-p':
figs_cols = int(arg)
elif opt == '-i':
Wspace = float(arg)
elif opt == '-j':
Hspace = float(arg)
elif opt == '-t':
title = arg
elif opt == '-R':
showRef = arg
elif opt == '-a':
ref_color = arg
elif opt == '-b':
ref_symbol = arg
elif opt == '-k':
ref_size = int(arg)
elif opt == '-x':
win_x = [int(i) for i in arg.split(':')]
win_x.sort()
elif opt == '-y':
win_y = [int(i) for i in arg.split(':')]
win_y.sort()
elif opt == '-G':
disp_geo = arg
elif opt == '-O':
dip_opposite = arg
elif opt == '-S':
saveFig = arg
elif opt == '-C':
dispContour = arg
elif opt == '-V':
contour_step = float(arg)
elif opt == '-P':
dispFig = arg
elif opt == '-o':
figName = arg
elif opt == '-g':
contour_sigma = float(arg)
elif opt == '-l':
win_lat = [float(i) for i in arg.split(':')]
win_lat.sort()
elif opt == '-L':
win_lon = [float(i) for i in arg.split(':')]
win_lon.sort()
elif len(sys.argv) == 2:
if argv[0] == '-h':
Usage()
sys.exit(1)
elif os.path.isfile(argv[0]):
File = argv[0]
else:
print 'Input file does not existed: ' + argv[0]
sys.exit(1)
elif len(sys.argv) < 2:
Usage()
sys.exit(1)
if color_map == 'hsv':
################################################
cdict1 = {
'red': ((0.0, 0.0, 0.0), (0.5, 0.0, 0.0), (0.6, 1.0, 1.0),
(0.8, 1.0, 1.0), (1.0, 0.5, 0.5)),
'green': ((0.0, 0.0, 0.0), (0.2, 0.0, 0.0), (0.4, 1.0, 1.0),
(0.6, 1.0, 1.0), (0.8, 0.0, 0.0), (1.0, 0.0, 0.0)),
'blue': (
(0.0, 0.5, .5),
(0.2, 1.0, 1.0),
(0.4, 1.0, 1.0),
(0.5, 0.0, 0.0),
(1.0, 0.0, 0.0),
)
}
from matplotlib.colors import LinearSegmentedColormap
ccmap = LinearSegmentedColormap('BlueRed1', cdict1)
################################################
else:
ccmap = plt.get_cmap(color_map)
##################################################
ext = os.path.splitext(File)[1]
if ext == '.h5':
import h5py
h5file = h5py.File(File, 'r')
k = h5file.keys()
if 'interferograms' in k: k[0] = 'interferograms'
elif 'coherence' in k: k[0] = 'coherence'
elif 'timeseries' in k: k[0] = 'timeseries'
print 'Input: ' + str(k)
if k[0] in ('dem', 'velocity', 'mask', 'temporal_coherence', 'rmse'):
allData2display = 'no'
elif ext in [
'.unw', '.int', '.cor', '.hgt', '.dem', '.trans', '.mli', '.slc'
]:
import pysar._readfile as readfile
allData2display = 'no'
k = [ext]
else:
print 'File extension not recogized: ' + ext
print 'Support file format:\n\
PySAR HDF5 files: velocity.h5, timeseries.h5, LoadedData.h5, ...\n\
ROI_PAC files: .unw .cor .int .hgt .dem .trans .mli'
sys.exit(1)
####################################################################
########################## Plot One ################################
if allData2display == 'no':
try:
font_size
except:
font_size = 12
################# File Reading ##################
##### PySAR HDF5
if k[0] in ('dem', 'velocity', 'mask', 'temporal_coherence', 'rmse'):
atr = h5file[k[0]].attrs
dset = h5file[k[0]].get(k[0])
data = dset[0:dset.shape[0], 0:dset.shape[1]]
# rewrapping
if rewrapping in ('yes', 'Yes', 'Y', 'y', 'YES'):
print 'Rewrapping disabled for ' + k[0]
elif k[0] == 'timeseries':
dateList = h5file[k[0]].keys()
try:
epoch_number
except:
try:
epoch_date
if len(epoch_date) == 6:
epoch_date = yymmdd2yyyymmdd(epoch_date)
epoch_number = dateList.index(epoch_date)
except:
print 'Unrecognized epoch input!'
sys.exit(1)
print 'Displaying date: ' + dateList[epoch_number]
atr = h5file[k[0]].attrs
dset = h5file[k[0]].get(dateList[epoch_number])
data = dset[0:dset.shape[0], 0:dset.shape[1]]
# rewrapping
if rewrapping in ('yes', 'Yes', 'y', 'Y', 'YES'):
print 'Rewrapping. Set min/max to -pi/pi. Showing phase'
range2phase = 4 * np.pi / float(
atr['WAVELENGTH']) #double-way, 2*2*pi/lamda
data = range2phase * data
data = rewrap(data)
min = -np.pi
max = np.pi
figUnit = '(radian)'
elif rewrapping in ('no', 'No', 'N', 'n', 'NO'):
print 'No rewrapping. Showing displacement.'
figUnit = '(m)'
elif k[0] in ('interferograms', 'coherence', 'wrapped'):
ifgramList = h5file[k[0]].keys()
try:
epoch_number
except:
for i in range(len(ifgramList)):
if epoch_date in ifgramList[i]: epoch_number = i
print 'Displaying: ' + ifgramList[epoch_number]
atr = h5file[k[0]][ifgramList[epoch_number]].attrs
dset = h5file[k[0]][ifgramList[epoch_number]].get(
ifgramList[epoch_number])
data = dset[0:dset.shape[0], 0:dset.shape[1]]
# rewrapping
if k[0] in ('coherence',
'wrapped') and rewrapping in ('yes', 'Yes', 'y', 'Y',
'YES'):
print 'No rewrapping for coherence/wrapped files, set to "no"'
rewrapping = 'no'
if rewrapping in ('yes', 'Yes', 'y', 'Y', 'YES'):
print 'Rewrapping. Set min/max to -pi/pi.'
data = np.angle(np.exp(1j * data))
min = -np.pi
max = np.pi
##### ROI_PAC product
elif k[0] in ['.slc', '.mli']:
data, p, atr = readfile.read_complex64(File)
data = np.nanlog10(data)
figUnit = '(dB)'
elif k[0] == '.int':
a, data, atr = readfile.read_complex64(File)
min = -np.pi
max = np.pi
rewrapping = 'no'
figUnit = '(radian)'
elif k[0] in ['.unw', '.cor', '.hgt', '.trans']:
a, data, atr = readfile.read_float32(File)
if k[0] == '.unw': figUnit = '(radian)'
elif k[0] == '.hgt': figUnit = '(m)'
if k[0] in ['.cor', '.hgt', '.trans']: rewrapping = 'no'
if rewrapping in ('yes', 'Yes', 'y', 'Y', 'True', 'true'):
print 'Rewrapping. Set min/max to -pi/pi.'
data = rewrap(data)
min = -np.pi
max = np.pi
elif k[0] == '.dem':
data, atr = readfile.read_dem(File)
figUnit = '(m)'
############## Data Option ##################
# Opposite Sign
if dip_opposite in ('yes', 'Yes', 'Y', 'y', 'YES'):
data = -1 * data
# Subset
try: # y/latitude direction
win_lat
try:
atr['Y_FIRST']
win_y = [0] * 2
win_y[0] = int((win_lat[1] - float(atr['Y_FIRST'])) /
float(atr['Y_STEP']))
win_y[1] = int((win_lat[0] - float(atr['Y_FIRST'])) /
float(atr['Y_STEP']))
if win_y[0] < 0:
win_y[0] = 0
print 'input latitude > max latitude! Set to max'
print 'subset in latitude - ' + str(win_lat[0]) + ':' + str(
win_lat[1])
except:
print 'Non-geocoded file, cannot use LatLon option'
Usage()
sys.exit(1)
except:
try:
win_y
print 'subset in y direction - ' + str(win_y[0]) + ':' + str(
win_y[1])
except:
win_y = [0, int(atr['FILE_LENGTH'])]
try: # x/longitude direction
win_lon
try:
atr['X_FIRST']
win_x = [0] * 2
win_x[0] = int((win_lon[0] - float(atr['X_FIRST'])) /
float(atr['X_STEP']))
win_x[1] = int((win_lon[1] - float(atr['X_FIRST'])) /
float(atr['X_STEP']))
if win_x[0] < 0:
win_x[0] = 0
print 'input longitude > max longitude! Set to max'
print 'subset in longitude - ' + str(win_lon[0]) + ':' + str(
win_lon[1])
except:
print 'Non-geocoded file, cannot use LatLon option'
Usage()
sys.exit(1)
except:
try:
win_x
print 'subset in x direction - ' + str(win_x[0]) + ':' + str(
win_x[1])
except:
win_x = [0, int(atr['WIDTH'])]
data = data[win_y[0]:win_y[1], win_x[0]:win_x[1]]
# Reference Point
try:
xref = atr['ref_x'] - win_x[0]
yref = atr['ref_y'] - win_y[0]
except:
print 'No reference point'
try:
xref = xref - atr['subset_x0']
yref = yref - atr['subset_y0']
except:
print 'No subset'
# Geo coordinate
try:
lon_step = float(atr['X_STEP'])
lat_step = float(atr['Y_STEP'])
lon_unit = atr['Y_UNIT']
lat_unit = atr['X_UNIT']
ullon = float(atr['X_FIRST']) + win_x[0] * lon_step
ullat = float(atr['Y_FIRST']) + win_y[0] * lat_step
llcrnrlon = ullon
llcrnrlat = ullat + lat_step * data.shape[0]
urcrnrlon = ullon + lon_step * data.shape[1]
urcrnrlat = ullat
geocoord = 'yes'
print 'Input file is Geocoded'
except:
geocoord = 'no'
# Flip
if flip_lr in ('yes', 'Yes', 'Y', 'y', 'YES'):
data = np.fliplr(data)
xref = np.shape(data)[1] - xref - 1
if flip_ud in ('yes', 'Yes', 'Y', 'y', 'YES'):
data = np.flipud(data)
yref = np.shape(data)[0] - yref - 1
# Colorbar Extend
data_min = np.nanmin(data)
data_max = np.nanmax(data)
try:
min
except:
min = data_min
try:
max
except:
max = data_max
if min <= data_min and max >= data_max: cb_extend = 'neither'
elif min > data_min and max >= data_max: cb_extend = 'min'
elif min <= data_min and max < data_max: cb_extend = 'max'
else: cb_extend = 'both'
############## DEM Option ##################
try:
demFile
print 'Show topography'
import pysar._readfile as readfile
if os.path.basename(demFile).split('.')[1] == 'hgt':
amp, dem, demRsc = readfile.read_float32(demFile)
elif os.path.basename(demFile).split('.')[1] == 'dem':
dem, demRsc = readfile.read_dem(demFile)
# Subset
dem = dem[win_y[0]:win_y[1], win_x[0]:win_x[1]]
# Flip
if flip_lr in ('yes', 'Yes', 'Y', 'y', 'YES'): dem = np.fliplr(dem)
if flip_ud in ('yes', 'Yes', 'Y', 'y', 'YES'): dem = np.flipud(dem)
# DEM data preparation
if dispContour in ('no', 'No', 'n', 'N', 'NO', 'yes', 'Yes', 'y',
'Y', 'YES'): #DEM basemap
print 'plot DEM as basemap'
cmap_dem = plt.get_cmap('gray')
import pysar._pysar_utilities as ut
if dispContour in ('only', 'Only', 'o', 'O', 'ONLY', 'yes', 'Yes',
'y', 'Y', 'YES'): #contour
print 'plot contour'
#if smoothContour in ('yes','Yes','y','Y','YES'):
import scipy.ndimage as ndimage
dem = ndimage.gaussian_filter(dem,
sigma=contour_sigma,
order=0)
contour_sequence = np.arange(-6000, 9000, contour_step)
except:
print 'No DEM file'
############## Data Plot and Output ################
# Figure Title
if k[0] == 'velocity': figTitle = 'Velocity (m/yr)'
elif k[0] == 'temporal_coherence': figTitle = 'Temporal coherence'
elif k[0] == 'dem': figTitle = 'DEM error'
elif k[0] == 'rmse': figTitle = 'RMSE (m/yr)'
elif k[0] == 'mask': figTitle = 'Pixels with no valid value.'
elif k[0] == 'coherence': figTitle = ifgramList[epoch_number]
elif k[0] in ('interferograms', 'wrapped'):
figTitle = ifgramList[epoch_number] + ' (radian)'
elif k[0] == 'timeseries':
try:
master_date = atr['ref_date']
except:
master_date = atr['DATE']
if len(master_date) == 6:
master_date = yymmdd2yyyymmdd(master_date)
if dip_opposite in ('yes', 'Yes', 'Y', 'y', 'YES'):
figTitle = dateList[
epoch_number] + '_' + master_date + ' ' + figUnit
else:
figTitle = master_date + '_' + dateList[
epoch_number] + ' ' + figUnit
elif k[0] in [
'.unw', '.cor', '.hgt', '.dem', '.trans', '.mli', '.slc'
]:
try:
figTitle = File + ' ' + figUnit
except:
figTitle = File
# Plot in Geo-coordinate: plot in map
if geocoord == 'yes' and disp_geo in ('yes', 'Yes', 'y', 'Y', 'YES'):
print 'display Lat/Lon'
fig = plt.figure()
ax = fig.add_axes([0.1, 0.1, 0.8, 0.8])
try:
plt.title(figTitle, fontsize=font_size)
except:
pass
# Map - DEM - Data
from mpl_toolkits.basemap import Basemap
m = Basemap(llcrnrlon=llcrnrlon,
llcrnrlat=llcrnrlat,
urcrnrlon=urcrnrlon,
urcrnrlat=urcrnrlat,
resolution='l',
area_thresh=1.,
projection='cyl',
suppress_ticks=False,
ax=ax)
try:
demFile
if dispContour in ('no', 'No', 'n', 'N', 'NO', 'yes', 'Yes',
'y', 'Y', 'YES'):
m.imshow(ut.hillshade(np.flipud(dem), 50.0), cmap=cmap_dem)
if dispContour in ('only', 'Only', 'o', 'O', 'ONLY', 'yes',
'Yes', 'y', 'Y', 'YES'):
import numpy.matlib
c_x = np.linspace(llcrnrlon,
urcrnrlon,
num=dem.shape[1],
endpoint='FALSE').reshape(
1, dem.shape[1])
c_xx = np.matlib.repmat(c_x, dem.shape[0], 1)
c_y = np.linspace(llcrnrlat,
urcrnrlat,
num=dem.shape[0],
endpoint='FALSE').reshape(
dem.shape[0], 1)
c_yy = np.matlib.repmat(c_y, 1, dem.shape[1])
m.contour(c_xx,
c_yy,
np.flipud(dem),
contour_sequence,
origin='lower',
colors='black',
alpha=0.5,
latlon='FALSE')
except:
pass
try:
im = m.imshow(np.flipud(data), cmap=ccmap, vmin=min, vmax=max)
except:
im = m.imshow(np.flipud(data), cmap=ccmap)
# Reference Point
if showRef in ('yes', 'Yes', 'Y', 'y', 'YES'):
try:
refPoint = ref_color + ref_symbol
ref_lon = llcrnrlon + xref * lon_step
ref_lat = urcrnrlat + yref * lat_step
plt.plot(ref_lon, ref_lat, refPoint, ms=ref_size)
except:
print 'No reference point'
# Colorbar
from mpl_toolkits.axes_grid1 import make_axes_locatable
divider = make_axes_locatable(ax)
cax = divider.append_axes("right", size="5%", pad=0.30)
plt.colorbar(im, cax=cax, extend=cb_extend)
#plt.colorbar(im,cax=cax)
# Status bar
def format_coord(x, y):
col = int((x - ullon) / lon_step + 0.5)
row = int((y - ullat) / lat_step + 0.5)
if col >= 0 and col <= data.shape[
1] and row >= 0 and row <= data.shape[0]:
z = data[row, col]
return 'lat=%.4f, lon=%.4f, value=%.4f' % (x, y, z)
else:
return 'lat=%.4f, lon=%.4f' % (x, y)
ax.format_coord = format_coord
# Plot in x/y coordinate: row and column
else:
fig = plt.figure()
ax = fig.add_axes([0.1, 0.1, 0.8, 0.8])
try:
plt.title(figTitle, fontsize=font_size)
except:
pass
# Plot
try:
demFile
if dispContour in ('no', 'No', 'n', 'N', 'NO', 'yes', 'Yes',
'y', 'Y', 'YES'):
ax.imshow(ut.hillshade(dem, 50.0), cmap=cmap_dem)
if dispContour in ('only', 'Only', 'o', 'O', 'ONLY', 'yes',
'Yes', 'y', 'Y', 'YES'):
ax.contour(dem,
contour_sequence,
origin='lower',
colors='black',
alpha=0.5)
except:
pass
try:
im = ax.imshow(data, cmap=ccmap, vmin=min, vmax=max)
except:
im = ax.imshow(data, cmap=ccmap)
cbar = plt.colorbar(im, extend=cb_extend)
#cbar.set_label('m/yr')
# Reference Point
if showRef in ('yes', 'Yes', 'Y', 'y', 'YES'):
try:
refPoint = ref_color + ref_symbol
ax.plot(xref, yref, refPoint, ms=ref_size)
except:
print 'No reference point'
plt.xlim(0, np.shape(data)[1])
plt.ylim(np.shape(data)[0], 0)
# Status bar
def format_coord(x, y):
col = int(x + 0.5)
row = int(y + 0.5)
if col >= 0 and col <= data.shape[
1] and row >= 0 and row <= data.shape[0]:
z = data[row, col]
return 'x=%.4f, y=%.4f, value=%.4f' % (x, y, z)
else:
return 'x=%.4f, y=%.4f' % (x, y)
ax.format_coord = format_coord
# Save Figure
if saveFig in ('yes', 'Yes', 'Y', 'y', 'YES'):
try:
figName
except:
if k[0] == 'velocity': figName = 'velocity.pdf'
elif k[0] == 'temporal_coherence':
figName = 'temporal_coherence.pdf'
elif k[0] == 'dem':
figName = 'DEM_error.pdf'
elif k[0] == 'rmse':
figName = 'rmse.pdf'
elif k[0] == 'mask':
figName = 'mask.pdf'
elif k[0] == 'timeseries':
figName = os.path.basename(File).split(
'.')[0] + '_' + dateList[epoch_number] + '.pdf'
elif k[0] in ('interferograms', 'coherence', 'wrapped'):
figName = ifgramList[epoch_number] + '.pdf'
elif k[0] in [
'.unw', '.cor', '.hgt', '.dem', '.trans', '.mli',
'.slc'
]:
figName = File + '.pdf'
plt.savefig(figName, dpi=fig_dpi)
print 'Saved figure to ' + figName
# Show Figure
if dispFig in ('yes', 'Yes', 'Y', 'y', 'YES'):
plt.show()
####################################################################
########################## Plot All ################################
elif allData2display == 'yes':
try:
font_size
except:
font_size = 8
if k[0] == 'timeseries':
atr = h5file[k[0]].attrs
# rewrapping
if rewrapping in ('yes', 'Yes', 'Y', 'y', 'YES'):
print 'Rewrapping. Set min/max to -pi/pi. Showing phase.'
range2phase = 4 * np.pi / float(
h5file['timeseries'].attrs['WAVELENGTH'])
min = -np.pi
max = np.pi
else:
print 'No rewrapping. Showing displacement.'
elif k[0] in ('interferograms', 'coherence', 'wrapped'):
atr = h5file[k[0]][h5file[k[0]].keys()[0]].attrs
# rewrapping
if k[0] in ('coherence',
'wrapped') and rewrapping in ('yes', 'Yes', 'y', 'Y',
'YES'):
print 'No rewrapping for coherence/wrapped files, set to "no"'
rewrapping = 'no'
if rewrapping in ('yes', 'Yes', 'Y', 'y', 'YES'):
print 'Rewrapping. Set min/max to -pi/pi.'
min = -np.pi
max = np.pi
else:
print 'No rewrapping'
### Subset Option ###
try: # y/latitude direction
win_lat
try:
atr['Y_FIRST']
win_y = [0] * 2
win_y[0] = int((win_lat[1] - float(atr['Y_FIRST'])) /
float(atr['Y_STEP']))
win_y[1] = int((win_lat[0] - float(atr['Y_FIRST'])) /
float(atr['Y_STEP']))
if win_y[0] < 0:
win_y[0] = 0
print 'input latitude > max latitude! Set to max'
print 'subset in latitude - ' + str(win_lat[0]) + ':' + str(
win_lat[1])
except:
print 'Non-geocoded file, cannot use LatLon option'
Usage()
sys.exit(1)
except:
try:
win_y
print 'subset in y direction - ' + str(win_y[0]) + ':' + str(
win_y[1])
except:
win_y = [0, int(atr['FILE_LENGTH'])]
try: # x/longitude direction
win_lon
try:
atr['X_FIRST']
win_x = [0] * 2
win_x[0] = int((win_lon[0] - float(atr['X_FIRST'])) /
float(atr['X_STEP']))
win_x[1] = int((win_lon[1] - float(atr['X_FIRST'])) /
float(atr['X_STEP']))
if win_x[0] < 0:
win_x[0] = 0
print 'input longitude > max longitude! Set to max'
print 'subset in longitude - ' + str(win_lon[0]) + ':' + str(
win_lon[1])
except:
print 'Non-geocoded file, cannot use LatLon option'
Usage()
sys.exit(1)
except:
try:
win_x
print 'subset in x direction - ' + str(win_x[0]) + ':' + str(
win_x[1])
except:
win_x = [0, int(atr['WIDTH'])]
# Figure Name
if saveFig in ('yes', 'Yes', 'Y', 'y', 'YES'):
try:
figName
figNameBase = os.path.basename(figName).split('.')[0]
figNameExt = os.path.basename(figName).split('.')[1]
except:
figNameBase = os.path.basename(File).split('.')[0]
figNameExt = '.pdf'
################## DEM Options ####################
try:
demFile
print 'Show topography'
import pysar._readfile as readfile
if os.path.basename(demFile).split('.')[1] == 'hgt':
amp, dem, demRsc = readfile.read_float32(demFile)
elif os.path.basename(demFile).split('.')[1] == 'dem':
dem, demRsc = readfile.read_dem(demFile)
# Subset
dem = dem[win_y[0]:win_y[1], win_x[0]:win_x[1]]
if dispContour in ('no', 'No', 'n', 'N', 'NO', 'yes', 'Yes', 'y',
'Y', 'YES'): #DEM basemap
print 'plot DEM as basemap'
cmap_dem = plt.get_cmap('gray')
import pysar._pysar_utilities as ut
hillshade_dem = ut.hillshade(dem, 50.0)
if dispContour in ('only', 'Only', 'o', 'O', 'ONLY', 'yes', 'Yes',
'y', 'Y', 'YES'): #contour
print 'plot contour'
#if smoothContour in ('yes','Yes','y','Y','YES'):
import scipy.ndimage as ndimage
dem = ndimage.gaussian_filter(dem,
sigma=contour_sigma,
order=0)
contour_sequence = np.arange(-6000, 9000, contour_step)
except:
print 'No DEM file'
################## Plot Loop ####################
ifgramList = h5file[k[0]].keys()
nfigs = figs_rows * figs_cols
lifgram = len(ifgramList)
print 'number of epochs/interferograms to display:' + str(lifgram)
kk = int(lifgram / nfigs) + 1
ii = 0
# plot (1,end-1) figures
for j in range(1, kk):
fig = plt.figure(j)
ii = (j - 1) * nfigs + 1
for i in range(ii, ii + nfigs):
print 'loading ' + ifgramList[i - 1]
ax = fig.add_subplot(figs_rows, figs_cols, i - ii + 1)
# Data option
if k[0] == 'timeseries':
figTitle = ifgramList[i - 1]
dset = h5file[k[0]].get(ifgramList[i - 1])
data = dset[0:dset.shape[0], 0:dset.shape[1]]
if rewrapping in ('yes', 'Yes', 'Y', 'y', 'YES'):
data = range2phase * data
data = rewrap(data)
elif k[0] in ('interferograms', 'coherence', 'wrapped'):
figTitle = str(i) + ' : ' + h5file[k[0]][ifgramList[
i - 1]].attrs['DATE12']
dset = h5file[k[0]][ifgramList[i - 1]].get(ifgramList[i -
1])
data = dset[0:dset.shape[0], 0:dset.shape[1]]
if rewrapping in ('yes', 'Yes', 'Y', 'y', 'YES'):
data = np.angle(np.exp(1j * data))
data = data[win_y[0]:win_y[1], win_x[0]:win_x[1]]
# Plot
try:
demFile
if dispContour in ('no', 'No', 'n', 'N', 'NO', 'yes',
'Yes', 'y', 'Y', 'YES'):
plt.imshow(hillshade_dem, cmap=cmap_dem)
if dispContour in ('only', 'Only', 'o', 'O', 'ONLY', 'yes',
'Yes', 'y', 'Y', 'YES'):
plt.contour(dem,
contour_sequence,
origin='lower',
colors='black',
alpha=0.5)
except:
pass
try:
ax.imshow(data, cmap=ccmap, vmin=min, vmax=max)
except:
ax.imshow(data, cmap=ccmap)
ax.set_yticklabels([])
ax.set_xticklabels([])
ax.set_xticks([])
ax.set_yticks([])
if title == 'out': ax.set_title(figTitle, fontsize=font_size)
elif title == 'in': add_inner_title(ax, figTitle, loc=1)
fig.subplots_adjust(wspace=Wspace, hspace=Hspace)
if saveFig in ('yes', 'Yes', 'Y', 'y', 'YES'):
figName = figNameBase + '_' + str(j) + figNameExt
plt.savefig(figName, dpi=fig_dpi)
# plot the last figure
fig = plt.figure(kk)
ii = (kk - 1) * nfigs + 1
for i in range(ii, lifgram + 1):
print 'loading ' + ifgramList[i - 1]
ax = fig.add_subplot(figs_rows, figs_cols, i - ii + 1)
# Data option
if k[0] == 'timeseries':
figTitle = ifgramList[i - 1]
dset = h5file[k[0]].get(ifgramList[i - 1])
data = dset[0:dset.shape[0], 0:dset.shape[1]]
if rewrapping in ('yes', 'Yes', 'Y', 'y', 'YES'):
data = range2phase * data
data = rewrap(data)
elif k[0] in ('interferograms', 'coherence', 'wrapped'):
figTitle = str(i) + ' : ' + h5file[k[0]][ifgramList[
i - 1]].attrs['DATE12']
dset = h5file[k[0]][ifgramList[i - 1]].get(ifgramList[i - 1])
data = dset[0:dset.shape[0], 0:dset.shape[1]]
if rewrapping in ('yes', 'Yes', 'Y', 'y', 'YES'):
data = np.angle(np.exp(1j * data))
data = data[win_y[0]:win_y[1], win_x[0]:win_x[1]]
# Plot
try:
demFile
if dispContour in ('no', 'No', 'n', 'N', 'NO', 'yes', 'Yes',
'y', 'Y', 'YES'):
plt.imshow(hillshade_dem, cmap=cmap_dem)
if dispContour in ('only', 'Only', 'o', 'O', 'ONLY', 'yes',
'Yes', 'y', 'Y', 'YES'):
plt.contour(dem,
contour_sequence,
origin='lower',
colors='black',
alpha=0.5)
except:
pass
try:
ax.imshow(data, cmap=ccmap, vmin=min, vmax=max)
except:
ax.imshow(data, cmap=ccmap)
ax.xaxis.label.set_fontsize(20)
ax.set_yticklabels([])
ax.set_xticklabels([])
ax.set_xticks([])
ax.set_yticks([])
if title == 'out': ax.set_title(figTitle, fontsize=font_size)
elif title == 'in': add_inner_title(ax, figTitle, loc=1)
fig.subplots_adjust(wspace=Wspace, hspace=Hspace)
if saveFig in ('yes', 'Yes', 'Y', 'y', 'YES'):
figName = figNameBase + '_' + str(kk) + figNameExt
plt.savefig(figName, dpi=fig_dpi)
print 'Saved figure to ' + figNameBase + '_*' + figNameExt
if dispFig in ('yes', 'Yes', 'Y', 'y', 'YES'):
plt.show()
####################################################################
####################################################################
try:
h5file.close()
except:
pass
def main(argv):
try: opts, args = getopt.getopt(argv,"h:f:t:p:")
except getopt.GetoptError:
Usage() ; sys.exit(1)
if opts==[]:
Usage() ; sys.exit(1)
for opt,arg in opts:
if opt in ("-h","--help"): Usage(); sys.exit()
elif opt == '-f': file = arg
elif opt == '-t': filtType = arg
elif opt == '-p': par = arg
ext = os.path.splitext(file)[1]
outName=file.split('.')[0]+'_'+filtType+ext
try: par
except: par=[]
#print '+++++++++++++++++++++++++++'
print 'Filter type : '+filtType
print 'parameters : ' + str(par)
#print '+++++++++++++++++++++++++++'
###############################################
if ext == '.int' or ext == '.slc':
a,p,r = readfile.read_complex_float32(file)
plks=multilook(p,alks,rlks)
alks=multilook(a,alks,rlks)
r['FILE_LENGTH']=str(dlks.shape[0])
r['WIDTH']=str(dlks.shape[1])
r['XMAX']=str(int(r['WIDTH']) - 1)
r['YMAX']=str(int(r['FILE_LENGTH']) - 1)
try:
r['Y_STEP']=str(float(r['Y_STEP'])*alks)
r['X_STEP']=str(float(r['X_STEP'])*rlks)
except:
Geo=0
f = open(outName+'.rsc','w')
for k in r.keys():
f.write(k+' '+r[k]+'\n')
f.close()
elif ext == '.unw' or ext == '.cor' or ext == '.hgt':
a,p,r = readfile.read_float32(file)
plks=multilook(p,alks,rlks)
alks=multilook(a,alks,rlks)
writefile.write_float32(plks,outName)
r['FILE_LENGTH']=str(dlks.shape[0])
r['WIDTH']=str(dlks.shape[1])
r['XMAX']=str(int(r['WIDTH']) - 1)
r['YMAX']=str(int(r['FILE_LENGTH']) - 1)
try:
r['Y_STEP']=str(float(r['Y_STEP'])*alks)
r['X_STEP']=str(float(r['X_STEP'])*rlks)
except:
Geo=0
f = open(outName+'.rsc','w')
for k in r.keys():
f.write(k+' '+r[k]+'\n')
f.close()
elif ext == ('.dem'):
d,r = readfile.read_real_int16(file)
dlks=multilook(d,alks,rlks)
print 'writing '+outName
writefile.write_real_int16(dlks,outName)
r['FILE_LENGTH']=str(dlks.shape[0])
r['WIDTH']=str(dlks.shape[1])
r['XMAX']=str(int(r['WIDTH']) - 1)
r['YMAX']=str(int(r['FILE_LENGTH']) - 1)
try:
r['Y_STEP']=str(float(r['Y_STEP'])*alks)
r['X_STEP']=str(float(r['X_STEP'])*rlks)
except:
Geo=0
f = open(outName+'.rsc','w')
for k in r.keys():
f.write(k+' '+r[k]+'\n')
f.close()
elif ext in ['.jpeg','jpg','png']:
import Image
im = Image.open(file)
width = im.size[0] / int(rlks)
height = im.size[1] / int(alks)
imlks = im.resize((width, height), Image.NEAREST)
print 'writing ' + outName
imlks.save(outName)
try:
r=readfile.read_roipac_rsc(file+'.rsc')
except:
sys.exit(1)
r['FILE_LENGTH']=str(height)
r['WIDTH']=str(width)
r['XMAX']=str(int(r['WIDTH']) - 1)
r['YMAX']=str(int(r['FILE_LENGTH']) - 1)
try:
r['Y_STEP']=str(float(r['Y_STEP'])*alks)
r['X_STEP']=str(float(r['X_STEP'])*rlks)
except:
Geo=0
f = open(outName+'.rsc','w')
for k in r.keys():
f.write(k+' '+r[k]+'\n')
f.close()
elif ext == ('.h5'):
h5file=h5py.File(file,'r')
# outName=file.split('.')[0]+'_a'+str(int(alks))+'lks_r'+str(int(rlks))+'lks.h5'
h5file_lks=h5py.File(outName,'w')
if 'interferograms' in h5file.keys():
print 'Filtering the interferograms in space'
gg = h5file_lks.create_group('interferograms')
igramList=h5file['interferograms'].keys()
for igram in igramList:
print igram
unwSet = h5file['interferograms'][igram].get(igram)
unw=unwSet[0:unwSet.shape[0],0:unwSet.shape[1]]
unw=filter(unw,filtType,par)
group = gg.create_group(igram)
dset = group.create_dataset(igram, data=unw, compression='gzip')
for key, value in h5file['interferograms'][igram].attrs.iteritems():
group.attrs[key] = value
dset1=h5file['mask'].get('mask')
mask=dset1[0:dset1.shape[0],0:dset1.shape[1]]
group=h5file_lks.create_group('mask')
dset = group.create_dataset('mask', data=mask, compression='gzip')
elif 'timeseries' in h5file.keys():
print 'Filtering the time-series'
group = h5file_lks.create_group('timeseries')
dateList=h5file['timeseries'].keys()
for d in dateList:
print d
dset1 = h5file['timeseries'].get(d)
data=dset1[0:dset1.shape[0],0:dset1.shape[1]]
data=filter(data,filtType,par)
dset = group.create_dataset(d, data=data, compression='gzip')
for key,value in h5file['timeseries'].attrs.iteritems():
group.attrs[key] = value
try:
dset1 = h5file['mask'].get('mask')
Mask = dset1[0:dset1.shape[0],0:dset1.shape[1]]
# Masklks=multilook(Mask,alks,rlks)
group=h5file_lks.create_group('mask')
dset = group.create_dataset('mask', data=Mask, compression='gzip')
except:
print 'Filterd file does not include the maske'
elif 'temporal_coherence' in h5file.keys() or 'velocity' in h5file.keys() or 'mask' in h5file.keys():
k=h5file.keys()
print 'filtering the '+ k[0]
group=h5file_lks.create_group(k[0])
dset1 = h5file[k[0]].get(k[0])
data = dset1[0:dset1.shape[0],0:dset1.shape[1]]
data = filter(data,filtType,par)
dset = group.create_dataset(k[0], data=data, compression='gzip')
for key , value in h5file[k[0]].attrs.iteritems():
group.attrs[key]=value
h5file.close()
h5file_lks.close()
print 'writing >>> '+outName
def main(argv):
method = 'triangular_consistency' ## or 'bonding_point'
ramp_type = 'plane'
save_rampCor = 'yes'
plot_bonding_points = 'yes'
##### Check Inputs
if len(sys.argv) > 2:
try:
opts, args = getopt.getopt(argv, 'h:f:m:x:y:o:t:',
['ramp=', 'no-ramp-save'])
except getopt.GetoptError:
print 'Error while getting args'
usage()
sys.exit(1)
for opt, arg in opts:
if opt in ['-h', '--help']:
usage()
sys.exit()
elif opt in '-f':
File = arg
elif opt in '-m':
maskFile = arg
elif opt in '-o':
outName = arg
elif opt in '-x':
x = [int(i) for i in arg.split(',')]
method = 'bonding_point'
elif opt in '-y':
y = [int(i) for i in arg.split(',')]
method = 'bonding_point'
elif opt in '-t':
templateFile = arg
elif opt in '--ramp':
ramp_type = arg.lower()
elif opt in '--no-ramp-save':
save_rampCor = 'no'
elif len(sys.argv) == 2:
if argv[0] in ['-h', '--help']:
usage()
sys.exit()
elif os.path.isfile(argv[0]):
File = argv[0]
maskFile = argv[1]
else:
print 'Input file does not existed: ' + argv[0]
sys.exit(1)
else:
usage()
sys.exit(1)
##### Check template file
try:
templateFile
templateContents = readfile.read_template(templateFile)
except:
pass
try:
yx = [
int(i) for i in templateContents['pysar.unwrapError.yx'].split(',')
]
x = yx[1::2]
y = yx[0::2]
method = 'bonding_point'
except:
pass
##### Read Mask File
## Priority:
## Input mask file > pysar.mask.file > existed Modified_Mask.h5 > existed Mask.h5
try:
maskFile
except:
try:
maskFile = templateContents['pysar.mask.file']
except:
if os.path.isfile('Modified_Mask.h5'):
maskFile = 'Modified_Mask.h5'
elif os.path.isfile('Mask.h5'):
maskFile = 'Mask.h5'
else:
print 'No mask found!'
sys.exit(1)
try:
Mask, Matr = readfile.read(maskFile)
print 'mask: ' + maskFile
except:
print 'Can not open mask file: ' + maskFile
sys.exit(1)
##### Output file name
ext = os.path.splitext(File)[1]
try:
outName
except:
outName = File.split('.')[0] + '_unwCor' + ext
print '\n**************** Unwrapping Error Correction ******************'
#################### Triangular Consistency (Phase Closure) ####################
if method == 'triangular_consistency':
print 'Phase unwrapping error correction using Triangular Consistency / Phase Closure'
h5file = h5py.File(File)
ifgramList = h5file['interferograms'].keys()
sx = int(h5file['interferograms'][ifgramList[0]].attrs['WIDTH'])
sy = int(h5file['interferograms'][ifgramList[0]].attrs['FILE_LENGTH'])
curls, Triangles, C = ut.get_triangles(h5file)
A, B = ut.design_matrix(h5file)
ligram, lv = np.shape(B)
lcurls = np.shape(curls)[0]
print 'Number of all triangles: ' + str(lcurls)
print 'Number of interferograms: ' + str(ligram)
#print curls
curlfile = 'curls.h5'
if not os.path.isfile(curlfile):
ut.generate_curls(curlfile, h5file, Triangles, curls)
thr = 0.50
curls = np.array(curls)
n1 = curls[:, 0]
n2 = curls[:, 1]
n3 = curls[:, 2]
numPixels = sy * sx
print 'reading interferograms...'
data = np.zeros((ligram, numPixels), np.float32)
for ni in range(ligram):
dset = h5file['interferograms'][ifgramList[ni]].get(ifgramList[ni])
d = dset[0:dset.shape[0], 0:dset.shape[1]]
data[ni] = d.flatten(1)
print np.shape(data)
print 'reading curls ...'
h5curl = h5py.File(curlfile)
curlList = h5curl['interferograms'].keys()
curlData = np.zeros((lcurls, numPixels), np.float32)
for ni in range(lcurls):
dset = h5curl['interferograms'][curlList[ni]].get(curlList[ni])
d = dset[0:dset.shape[0], 0:dset.shape[1]]
curlData[ni] = d.flatten(1)
pi = np.pi
EstUnwrap = np.zeros((ligram, numPixels), np.float32)
#try:
# maskFile=argv[1]
# h5Mask=h5py.File(maskFile)
# dset = h5Mask['mask'].get('mask')
# Mask=dset[0:dset.shape[0],0:dset.shape[1]]
#except:
# dset = h5file['mask'].get('mask')
# Mask=dset[0:dset.shape[0],0:dset.shape[1]]
Mask = Mask.flatten(1)
for ni in range(numPixels):
#dU = np.zeros([ligram,1])
#print np.shape(dU)
#print np.shape(data[:,ni])
if Mask[ni] == 1:
dU = data[:, ni]
#nan_ndx = dataPoint == 0.
unwCurl = np.array(curlData[:, ni])
#print unwCurl
ind = np.abs(unwCurl) >= thr
N1 = n1[ind]
N2 = n2[ind]
N3 = n3[ind]
indC = np.abs(unwCurl) < thr
Nc1 = n1[indC]
Nc2 = n2[indC]
Nc3 = n3[indC]
N = np.hstack([N1, N2, N3])
UniN = np.unique(N)
Nc = np.hstack([Nc1, Nc2, Nc3])
UniNc = np.unique(Nc)
inter = list(set(UniNc) & set(UniN)) # intersetion
UniNc = list(UniNc)
for x in inter:
UniNc.remove(x)
D = np.zeros([len(UniNc), ligram])
for i in range(len(UniNc)):
D[i, UniNc[i]] = 1
AAA = np.vstack([-2 * pi * C, D])
#AAA1=np.hstack([AAA,np.zeros([AAA.shape[0],lv])])
#AAA2=np.hstack([-2*pi*np.eye(ligram),B])
#AAAA=np.vstack([AAA1,AAA2])
AAAA = np.vstack([AAA, 0.25 * np.eye(ligram)])
#print '************************'
#print np.linalg.matrix_rank(C)
#print np.linalg.matrix_rank(AAA)
#print np.linalg.matrix_rank(AAAA)
#print '************************'
#LLL=list(np.dot(C,dU)) + list(np.zeros(np.shape(UniNc)[0]))# + list(dU)
#ind=np.isnan(AAA)
#M1=pinv(AAA)
#M=np.dot(M1,LLL)
#EstUnwrap[:,ni]=np.round(M[0:ligram])*2.0*np.pi
##########
# with Tikhonov regularization:
AAAA = np.vstack([AAA, 0.25 * np.eye(ligram)])
LLL = list(np.dot(C, dU)) + list(np.zeros(
np.shape(UniNc)[0])) + list(np.zeros(ligram))
ind = np.isnan(AAAA)
M1 = pinv(AAAA)
M = np.dot(M1, LLL)
EstUnwrap[:, ni] = np.round(M[0:ligram]) * 2.0 * np.pi
#print M[0:ligram]
#print np.round(M[0:ligram])
else:
EstUnwrap[:, ni] = np.zeros([ligram])
if not np.remainder(ni, 10000):
print 'Processing point: %7d of %7d ' % (ni, numPixels)
##### Output
dataCor = data + EstUnwrap
unwCorFile = File.replace('.h5', '') + '_unwCor.h5'
print 'writing >>> ' + unwCorFile
h5unwCor = h5py.File(unwCorFile, 'w')
gg = h5unwCor.create_group('interferograms')
for i in range(ligram):
group = gg.create_group(ifgramList[i])
dset = group.create_dataset(ifgramList[i],
data=np.reshape(
dataCor[i, :], [sx, sy]).T,
compression='gzip')
for key, value in h5file['interferograms'][
ifgramList[i]].attrs.iteritems():
group.attrs[key] = value
try:
MASK = h5file['mask'].get('mask')
gm = h5unwCor.create_group('mask')
dset = gm.create_dataset('mask', data=MASK, compression='gzip')
except:
pass
h5unwCor.close()
h5file.close()
h5curl.close()
#################### Bonding Points (Spatial Continuity) ####################
elif method == 'bonding_point':
print 'Phase unwrapping error correction using Bonding Points / Spatial Continuity'
##### Read Bridge Points Info
try:
x
y
if len(x) != len(y) or np.mod(len(x), 2) != 0:
print 'Wrong number of bridge points input: ' + str(
len(x)) + ' for x, ' + str(len(y)) + ' for y'
usage()
sys.exit(1)
except:
print 'Error in reading bridge points info!'
usage()
sys.exit(1)
for i in range(0, len(x)):
if Mask[y[i], x[i]] == 0:
print '\nERROR: Connecting point (' + str(y[i]) + ',' + str(
x[i]) + ') is out of masked area! Select them again!\n'
sys.exit(1)
print 'Number of bonding point pairs: ' + str(len(x) / 2)
print 'Bonding points coordinates:\nx: ' + str(x) + '\ny: ' + str(y)
## Plot Connecting Pair of Points
if plot_bonding_points == 'yes':
point_yx = ''
line_yx = ''
n_bridge = len(x) / 2
for i in range(n_bridge):
pair_yx = str(y[2 * i]) + ',' + str(x[2 * i]) + ',' + str(
y[2 * i + 1]) + ',' + str(x[2 * i + 1])
if not i == n_bridge - 1:
point_yx += pair_yx + ','
line_yx += pair_yx + ';'
else:
point_yx += pair_yx
line_yx += pair_yx
try:
plot_cmd = 'view.py --point-yx="'+point_yx+'" --line-yx="'+line_yx+\
'" --nodisplay -o bonding_points.png -f '+maskFile
print plot_cmd
os.system(plot_cmd)
except:
pass
##### Ramp Info
ramp_mask = Mask == 1
print 'estimate phase ramp during the correction'
print 'ramp type: ' + ramp_type
if save_rampCor == 'yes':
outName_ramp = os.path.basename(outName).split(
ext)[0] + '_' + ramp_type + ext
########## PySAR ##########
if ext == '.h5':
##### Read
try:
h5file = h5py.File(File, 'r')
except:
print 'ERROR: Cannot open input file: ' + File
sys.exit(1)
k = h5file.keys()
if 'interferograms' in k:
k[0] = 'interferograms'
print 'Input file is ' + k[0]
else:
print 'Input file - ' + File + ' - is not interferograms.'
usage()
sys.exit(1)
igramList = sorted(h5file[k[0]].keys())
#### Write
h5out = h5py.File(outName, 'w')
gg = h5out.create_group(k[0])
print 'writing >>> ' + outName
if save_rampCor == 'yes':
h5out_ramp = h5py.File(outName_ramp, 'w')
gg_ramp = h5out_ramp.create_group(k[0])
print 'writing >>> ' + outName_ramp
##### Loop
print 'Number of interferograms: ' + str(len(igramList))
for igram in igramList:
print igram
data = h5file[k[0]][igram].get(igram)[:]
data_ramp, ramp = rm.remove_data_surface(
data, ramp_mask, ramp_type)
#ramp = data_ramp - data
data_rampCor = phase_bonding(data_ramp, Mask, x, y)
dataCor = data_rampCor - ramp
group = gg.create_group(igram)
dset = group.create_dataset(igram,
data=dataCor,
compression='gzip')
for key, value in h5file[k[0]][igram].attrs.iteritems():
group.attrs[key] = value
if save_rampCor == 'yes':
group_ramp = gg_ramp.create_group(igram)
dset = group_ramp.create_dataset(igram,
data=data_rampCor,
compression='gzip')
for key, value in h5file[k[0]][igram].attrs.iteritems():
group_ramp.attrs[key] = value
try:
mask = h5file['mask'].get('mask')
gm = h5out.create_group('mask')
dset = gm.create_dataset('mask',
data=mask[0:mask.shape[0],
0:mask.shape[1]],
compression='gzip')
except:
print 'no mask group found.'
h5file.close()
h5out.close()
if save_rampCor == 'yes':
h5out_ramp.close()
########## ROI_PAC ##########
elif ext == '.unw':
print 'Input file is ' + ext
a, data, atr = readfile.read_float32(File)
data_ramp, ramp = rm.remove_data_surface(data, ramp_mask,
ramp_type)
#ramp = data_ramp - data
data_rampCor = phase_bonding(data_ramp, Mask, x, y)
dataCor = data_rampCor - ramp
writefile.write(dataCor, atr, outName)
if save_rampCor == 'yes':
writefile.write(data_rampCor, atr, outName_ramp)
else:
print 'Un-supported file type: ' + ext
usage()
sys.exit(1)
correlation_with_dem.py radar_8rlks.hgt velocity_masked.h5
***********************************************************************
***********************************************************************
'''
try:
demFile=sys.argv[1]
File=sys.argv[2]
except:
Usage()
sys.exit(1)
if os.path.basename(demFile).split('.')[1]=='hgt':
amp,dem,demRsc = readfile.read_float32(demFile)
elif os.path.basename(demFile).split('.')[1]=='dem':
dem,demRsc = readfile.read_real_int16(demFile)
#amp,dem,demRsc = readfile.read_float32(demFile)
h5data = h5py.File(File)
dset = h5data['velocity'].get('velocity')
data = dset[0:dset.shape[0],0:dset.shape[1]]
try:
suby=sys.argv[3].split(':')
subx=sys.argv[4].split(':')
data = data[int(suby[0]):int(suby[1]),int(subx[0]):int(subx[1])]
dem = dem[int(suby[0]):int(suby[1]),int(subx[0]):int(subx[1])]
except:
def main(argv):
if len(sys.argv) > 2:
try:
opts, args = getopt.getopt(argv, "h:f:x:y:o:l:L:")
except getopt.GetoptError:
print 'Error while getting args'
Usage()
sys.exit(1)
for opt, arg in opts:
if opt in ("-h", "--help"):
Usage()
sys.exit()
elif opt == '-f':
File = arg
elif opt == '-y':
ysub = [int(i) for i in arg.split(':')]
ysub.sort()
elif opt == '-x':
xsub = [int(i) for i in arg.split(':')]
xsub.sort()
elif opt == '-o':
outName = arg
elif opt == '-l':
Latsub = [float(i) for i in arg.split(':')]
Latsub.sort()
elif opt == '-L':
Lonsub = [float(i) for i in arg.split(':')]
Lonsub.sort()
else:
Usage()
sys.exit(1)
try:
outName
except:
outName = 'subset_' + File
ext = os.path.splitext(File)[1]
############################################################################
################################# PySAR ##################################
if ext == '.h5':
try:
h5file = h5py.File(File, 'r')
except:
Usage()
sys.exit(1)
k = h5file.keys()
if 'interferograms' in k: k[0] = 'interferograms'
elif 'coherence' in k: k[0] = 'coherence'
elif 'timeseries' in k: k[0] = 'timeseries'
if k[0] in ('interferograms', 'coherence', 'wrapped'):
atr = h5file[k[0]][h5file[k[0]].keys()[0]].attrs
elif k[0] in ('dem', 'velocity', 'mask', 'temporal_coherence', 'rmse',
'timeseries'):
atr = h5file[k[0]].attrs
############# Subset Option #############
width = int(atr['WIDTH'])
length = int(atr['FILE_LENGTH'])
try:
Latsub
try:
lat_step = float(atr['Y_STEP'])
lat1 = float(atr['Y_FIRST'])
lat0 = lat1 + length * lat_step
if Latsub[0] < lat0:
Latsub[0] = lat0
print 'WARNING: input latitude < min (' + str(
lat0) + ')! Set it to min.'
if Latsub[1] > lat1:
Latsub[1] = lat1
print 'WARNING: input latitude > max (' + str(
lat1) + ')! Set it to max.'
print 'subset in latitude - ' + str(Latsub[0]) + ':' + str(
Latsub[1])
ysub = [0] * 2
ysub[0] = int((Latsub[1] - lat1) / lat_step)
ysub[1] = int((Latsub[0] - lat1) / lat_step)
except:
print 'Not geocoded file, cannot be subseted with LatLon.'
Usage()
return
except:
try:
ysub
if ysub[0] < 0:
ysub[0] = 0
print 'WARNING: input y < min (0)! Set it to min.'
if ysub[1] > length:
ysub[1] = length
print 'WARNING: input y > max (' + str(
length) + ')! Set it to max.'
print 'subset in y direction - ' + str(ysub[0]) + ':' + str(
ysub[1])
except:
ysub = [0, length]
try:
Lonsub
try:
lon_step = float(atr['X_STEP'])
lon0 = float(atr['X_FIRST'])
lon1 = lon0 + width * lon_step
if Lonsub[0] < lon0:
Lonsub[0] = lon0
print 'WARNING: input longitude < min (' + str(
lon0) + ')! Set it to min.'
if Lonsub[1] > lon1:
Lonsub[1] = lon1
print 'WARNING: input longitude > max (' + str(
lon1) + ')! Set it to max.'
print 'subset in longitude - ' + str(Lonsub[0]) + ':' + str(
Lonsub[1])
xsub = [0] * 2
xsub[0] = int((Lonsub[0] - lon0) / lon_step)
xsub[1] = int((Lonsub[1] - lon0) / lon_step)
except:
print 'Not geocoded file, cannot be subseted with LatLon.'
Usage()
return
except:
try:
xsub
if xsub[0] < 0:
xsub[0] = 0
print 'WARNING: input x < min (0)! Set it to min.'
if xsub[1] > width:
xsub[1] = width
print 'WARNING: input x > max (' + str(
width) + ')! Set it to max x.'
print 'subset in x direction - ' + str(xsub[0]) + ':' + str(
xsub[1])
except:
xsub = [0, width]
if ysub[0] > length or ysub[1] < 0 or xsub[0] > length or xsub[1] < 0:
print 'ERROR: input index is out of data range!'
print 'range in rdr: x - 0:' + str(width) + ' y - 0:' + str(
length)
try:
print 'range in geo: lat - ' + str(lat0) + ':' + str(
lat1) + ' lon - ' + str(lon0) + ':' + str(lon1)
except:
Geo = 0
sys.exit(1)
######## Data Read, Crop and Write #######
##### N dset, N attributes
if k[0] in ('interferograms', 'coherence', 'wrapped'):
print 'writing >>> ' + outName
h5out = h5py.File(outName, 'w')
gg = h5out.create_group(k[0])
igramList = h5file[k[0]].keys()
for igram in igramList:
print igram
dset1 = h5file[k[0]][igram].get(igram)
group = gg.create_group(igram)
dset = group.create_dataset(igram,
data=dset1[ysub[0]:ysub[1],
xsub[0]:xsub[1]],
compression='gzip')
for key, value in h5file[k[0]][igram].attrs.iteritems():
group.attrs[key] = value
group.attrs['FILE_LENGTH'] = ysub[1] - ysub[0]
group.attrs['WIDTH'] = xsub[1] - xsub[0]
try:
sub_x0_ori = int(group.attrs['subset_x0'])
group.attrs['subset_x0'] = xsub[0] + sub_x0_ori
group.attrs['subset_x1'] = xsub[1] + sub_x0_ori
except:
group.attrs['subset_x0'] = xsub[0]
group.attrs['subset_x1'] = xsub[1]
try:
sub_y0_ori = int(group.attrs['subset_y0'])
group.attrs['subset_y0'] = ysub[0] + sub_y0_ori
group.attrs['subset_y1'] = ysub[1] + sub_y0_ori
except:
group.attrs['subset_y0'] = ysub[0]
group.attrs['subset_y1'] = ysub[1]
if 'X_FIRST' in atr.keys():
group.attrs['X_FIRST'] = float(
atr['X_FIRST']) + xsub[0] * float(atr['X_STEP'])
group.attrs['Y_FIRST'] = float(
atr['Y_FIRST']) + ysub[0] * float(atr['Y_STEP'])
## support of old format
try:
Mset = h5file['mask'].get('mask')
gm = h5out.create_group('mask')
dset = gm.create_dataset('mask',
data=Mset[ysub[0]:ysub[1],
xsub[0]:xsub[1]],
compression='gzip')
except:
print 'No group for mask found in the file.'
try:
Cset = h5file['meanCoherence'].get('meanCoherence')
gm = h5out.create_group('meanCoherence')
dset = gm.create_dataset('meanCoherence',
data=Cset[ysub[0]:ysub[1],
xsub[0]:xsub[1]],
compression='gzip')
except:
print 'No group for meanCoherence found in the file'
h5file.close()
h5out.close()
##### N/1 dset, 1 attributes
elif k[0] in [
'timeseries', 'temporal_coherence', 'velocity', 'mask', 'rmse'
]:
print 'writing >>> ' + outName
h5out = h5py.File(outName, 'w')
group = h5out.create_group(k[0])
if k[0] == 'timeseries':
dateList = h5file[k[0]].keys()
for d in dateList:
print d
dset1 = h5file[k[0]].get(d)
dset = group.create_dataset(d,
data=dset1[ysub[0]:ysub[1],
xsub[0]:xsub[1]],
compression='gzip')
elif k[0] in ['temporal_coherence', 'velocity', 'mask', 'rmse']:
dset1 = h5file[k[0]].get(k[0])
dset = group.create_dataset(k[0],
data=dset1[ysub[0]:ysub[1],
xsub[0]:xsub[1]],
compression='gzip')
## Update attributes
for key, value in h5file[k[0]].attrs.iteritems():
group.attrs[key] = value
group.attrs['FILE_LENGTH'] = ysub[1] - ysub[0]
group.attrs['WIDTH'] = xsub[1] - xsub[0]
try:
sub_x0_ori = int(group.attrs['subset_x0'])
group.attrs['subset_x0'] = xsub[0] + sub_x0_ori
group.attrs['subset_x1'] = xsub[1] + sub_x0_ori
except:
group.attrs['subset_x0'] = xsub[0]
group.attrs['subset_x1'] = xsub[1]
try:
sub_y0_ori = int(group.attrs['subset_y0'])
group.attrs['subset_y0'] = ysub[0] + sub_y0_ori
group.attrs['subset_y1'] = ysub[1] + sub_y0_ori
except:
group.attrs['subset_y0'] = ysub[0]
group.attrs['subset_y1'] = ysub[1]
if 'X_FIRST' in atr.keys():
group.attrs['X_FIRST'] = float(
atr['X_FIRST']) + xsub[0] * float(atr['X_STEP'])
group.attrs['Y_FIRST'] = float(
atr['Y_FIRST']) + ysub[0] * float(atr['Y_STEP'])
h5file.close()
h5out.close()
else:
print 'Error: group of HDF5 file not recogized!'
h5file.close()
Usage()
sys.exit(1)
############################################################################
######################### ROI_PAC / Image / GAMMA ########################
elif ext in ['.unw','.cor','.hgt','.dem','.trans'] or\
ext in ['.jpeg','.jpg','.png','.ras','.bmp'] or\
ext in ['.mli','.slc']:
try:
atr = readfile.read_rsc_file(File + '.rsc')
except:
try:
atr = readfile.read_par_file(File + '.par')
except:
atr = readfile.read_par_file(
os.path.splitext(File)[0] + '.par')
############# Subset Option #############
try:
width = int(atr['WIDTH'])
length = int(atr['FILE_LENGTH'])
except:
width = int(atr['range_samples:'])
length = int(atr['azimuth_lines:'])
try:
Latsub
try:
lat_step = float(atr['Y_STEP'])
lat1 = float(atr['Y_FIRST'])
lat0 = lat1 + length * lat_step
if Latsub[0] < lat0:
Latsub[0] = lat0
print 'WARNING: input latitude < min (' + str(
lat0) + ')! Set it to min.'
if Latsub[1] > lat1:
Latsub[1] = lat1
print 'WARNING: input latitude > max (' + str(
lat1) + ')! Set it to max.'
print 'subset in latitude - ' + str(Latsub[0]) + ':' + str(
Latsub[1])
ysub = [0] * 2
ysub[0] = int((Latsub[1] - lat1) / lat_step)
ysub[1] = int((Latsub[0] - lat1) / lat_step)
except:
print 'Not geocoded file, cannot be subseted with LatLon.'
Usage()
return
except:
try:
ysub
if ysub[0] < 0:
ysub[0] = 0
print 'WARNING: input y < min (0)! Set it to min.'
if ysub[1] > length:
ysub[1] = length
print 'WARNING: input y > max (' + str(
length) + ')! Set it to max.'
print 'subset in y direction - ' + str(ysub[0]) + ':' + str(
ysub[1])
except:
ysub = [0, length]
try:
Lonsub
try:
lon_step = float(atr['X_STEP'])
lon0 = float(atr['X_FIRST'])
lon1 = lon0 + width * lon_step
if Lonsub[0] < lon0:
Lonsub[0] = lon0
print 'WARNING: input longitude < min (' + str(
lon0) + ')! Set it to min.'
if Lonsub[1] > lon1:
Lonsub[1] = lon1
print 'WARNING: input longitude > max (' + str(
lon1) + ')! Set it to max.'
print 'subset in longitude - ' + str(Lonsub[0]) + ':' + str(
Lonsub[1])
xsub = [0] * 2
xsub[0] = int((Lonsub[0] - lon0) / lon_step)
xsub[1] = int((Lonsub[1] - lon0) / lon_step)
except:
print 'Not geocoded file, cannot be subseted with LatLon.'
Usage()
return
except:
try:
xsub
if xsub[0] < 0:
xsub[0] = 0
print 'WARNING: input x < min (0)! Set it to min.'
if xsub[1] > width:
xsub[1] = width
print 'WARNING: input x > max (' + str(
width) + ')! Set it to max x.'
print 'subset in x direction - ' + str(xsub[0]) + ':' + str(
xsub[1])
except:
xsub = [0, width]
if ysub[0] > length or ysub[1] < 0 or xsub[0] > length or xsub[1] < 0:
print 'ERROR: input index is out of data range!'
print 'range in rdr: x - 0:' + str(width) + ' y - 0:' + str(
length)
try:
print 'range in geo: lat - ' + str(lat0) + ':' + str(
lat1) + ' lon - ' + str(lon0) + ':' + str(lon1)
except:
Geo = 0
sys.exit(1)
######## Data Read, Crop and Write #######
print 'writing >>> ' + outName
box = (xsub[0], ysub[0], xsub[1], ysub[1])
if ext in ['.unw', '.cor', '.hgt']:
a, p, r = readfile.read_float32(File, box)
#p = p[ysub[0]:ysub[1],xsub[0]:xsub[1]]
writefile.write_float32(p, outName)
elif ext == '.dem':
p, r = readfile.read_dem(File)
p = p[ysub[0]:ysub[1], xsub[0]:xsub[1]]
writefile.write_dem(p, outName)
elif ext == '.trans':
a, p, r = readfile.read_float32(File, box)
#a = a[ysub[0]:ysub[1],xsub[0]:xsub[1]]
#p = p[ysub[0]:ysub[1],xsub[0]:xsub[1]]
writefile.write_float32(a, p, outName)
elif ext in ['.jpeg', '.jpg', '.png', '.ras', '.bmp']:
import Image
im = Image.open(File)
box = (xsub[0], ysub[0], xsub[1], ysub[1])
output_img = im.crop(box)
output_img.save(outName)
elif ext == '.mli':
d, r = readfile.read_gamma_float(File)
d = d[ysub[0]:ysub[1], xsub[0]:xsub[1]]
writefile.write_gamma_float(d, outName)
elif ext == '.slc':
d, r = readfile.read_gamma_scomplex(File, box)
writefile.write_gamma_scomplex(d, outName)
########### Update .rsc file #############
atr['FILE_LENGTH'] = str(ysub[1] - ysub[0])
atr['WIDTH'] = str(xsub[1] - xsub[0])
atr['XMAX'] = str(width - 1)
atr['YMAX'] = str(length - 1)
try:
sub_x0_ori = int(atr['subset_x0'])
atr['subset_x0'] = str(xsub[0] + sub_x0_ori)
atr['subset_x1'] = str(xsub[1] + sub_x0_ori)
except:
atr['subset_x0'] = str(xsub[0])
atr['subset_x1'] = str(xsub[1])
try:
sub_y0_ori = int(atr['subset_y0'])
atr['subset_y0'] = str(ysub[0] + sub_y0_ori)
atr['subset_y1'] = str(ysub[1] + sub_y0_ori)
except:
atr['subset_y0'] = str(ysub[0])
atr['subset_y1'] = str(ysub[1])
if 'X_FIRST' in atr.keys():
atr['Y_FIRST'] = str(
float(atr['Y_FIRST']) + ysub[0] * float(atr['Y_STEP']))
atr['X_FIRST'] = str(
float(atr['X_FIRST']) + xsub[0] * float(atr['X_STEP']))
f = open(outName + '.rsc', 'w')
for k in atr.keys():
f.write(k + ' ' + atr[k] + '\n')
f.close()
###########################################################################
else:
print 'File extension not recogized.'
Usage()
sys.exit(1)
def main(argv):
plt.switch_backend('Agg')
cbar_bin_num = 9
cbar_label = 'Mean LOS velocity'
color_map = 'jet'
data_alpha = 0.7
disp_opposite = 'no'
disp_colorbar = 'yes'
rewrapping = 'no'
fig_dpi = 500
#fig_size = [6.0,9.0]
fig_unit = 'mm/yr'
disp_ref = 'yes'
ref_size = 5
dispDisplacement = 'no'
if len(sys.argv)>2:
try: opts, args = getopt.getopt(argv,"f:m:M:d:c:w:i:r:",['noreference','fig-size',\
'ref-size=','cbar-label=','displacement','cbar-bin-num='])
except getopt.GetoptError: usage() ; sys.exit(1)
for opt,arg in opts:
if opt == '-f': File = arg
elif opt == '-m': Vmin = float(arg)
elif opt == '-M': Vmax = float(arg)
elif opt == '-d': epoch_date = arg
elif opt == '-c': color_map = arg
elif opt == '-i': disp_opposite = arg
elif opt == '-w': rewrapping = arg
elif opt == '-r': fig_dpi = int(arg)
elif opt == '--cbar-bin-num' : cbar_bin_num = int(arg)
elif opt == '--cbar-label' : cbar_label = arg
elif opt == '--displacement' : dispDisplacement = 'yes'
elif opt == '--fig-size' : fig_size = [float(i) for i in arg.split(',')][0:2]
elif opt == '--ref-size' : ref_size = int(arg)
elif opt == '--noreference' : disp_ref = 'no'
elif len(sys.argv)==2:
if argv[0]=='-h': usage(); sys.exit(1)
elif os.path.isfile(argv[0]): File = argv[0]
else: usage(); sys.exit(1)
else: usage(); sys.exit(1)
#######################################################
################### Prepare Data ####################
## prepare: data, North, East, South, West
ext = os.path.splitext(File)[1].lower()
atr = readfile.read_attribute(File)
k = atr['FILE_TYPE']
#print '\n*************** Output to KMZ file ****************'
print 'Input file is '+k
if ext == '.h5':
try: h5file=h5py.File(File,'r')
except: usage() ; sys.exit(1)
outName=File.split('.')[0]
if k in ('interferograms','wrapped','coherence'):
ifgramList=h5file[k].keys()
for i in range(len(ifgramList)):
if epoch_date in ifgramList[i]:
epoch_number = i
print ifgramList[epoch_number]
outName = ifgramList[epoch_number]
#outName=epoch_date
dset = h5file[k][ifgramList[epoch_number]].get(ifgramList[epoch_number])
data = dset[0:dset.shape[0],0:dset.shape[1]]
if k == 'wrapped':
print 'No wrapping for wrapped interferograms. Set rewrapping=no'
rewrapping = 'no'
Vmin = -np.pi
Vmax = np.pi
elif 'timeseries' in k:
epochList=h5file['timeseries'].keys()
for i in range(len(epochList)):
if epoch_date in epochList[i]:
epoch_number = i
#### Out name
try: ref_date = atr['ref_date']
except: ref_date = ut.yyyymmdd(atr['DATE'])[0]
#ref_date=h5file['timeseries'].attrs['ref_date']
if len(epoch_date)==8: outName=ref_date[2:]+'-'+epoch_date[2:]
else: outName=ref_date[2:]+'-'+epoch_date
dset = h5file['timeseries'].get(epochList[epoch_number])
data = dset[0:dset.shape[0],0:dset.shape[1]]
### one dataset format: velocity, mask, temporal_coherence, rmse, std, etc.
else:
dset = h5file[k].get(k)
data=dset[0:dset.shape[0],0:dset.shape[1]]
if disp_opposite in('yes','Yes','Y','y','YES'):
data=-1*data
try:
xref=h5file[k].attrs['ref_x']
yref=h5file[k].attrs['ref_y']
except: pass
elif ext in ['.unw','.cor','.hgt','.trans','.dem']:
if ext in ['.unw','.cor','.hgt','.trans']:
a,data,atr = readfile.read_float32(File)
outName = File
if ext in ['.unw']:
if dispDisplacement == 'yes':
print 'show displacement'
phase2range = -float(atr['WAVELENGTH']) / (4*np.pi)
data *= phase2range
atr['UNIT'] = 'm'
rewrapping == 'no'
fig_unit = 'mm'
if rewrapping == 'yes':
data = rewrap(data,atr)
fig_unit = 'radian'
elif ext == '.dem':
data,atr = readfile.read_real_int16(File)
outName = File
if ext in ['.hgt','.dem']: fig_unit = 'm'
elif ext in ['.cor','.trans']: fig_unit = ' '
else: sys.exit('Do not support '+ext+' file!')
########################################################
if rewrapping=='yes':
data=rewrap(data)
Vmin = -np.pi #[-pi,pi] for wrapped interferograms
Vmax = np.pi
else:
try: Vmin
except: Vmin = np.nanmin(data)
try: Vmax
except: Vmax = np.nanmax(data)
try:
lon_step = float(atr['X_STEP'])
lat_step = float(atr['Y_STEP'])
lon_unit = atr['Y_UNIT']
lat_unit = atr['X_UNIT']
West = float(atr['X_FIRST'])
North = float(atr['Y_FIRST'])
South = North+lat_step*(data.shape[0]-1)
East = West +lon_step*(data.shape[1]-1)
geocoord = 'yes'
print 'Geocoded'
except:
print '%%%%%%%%%%'
print 'Error:\nThe input file is not geocoded\n'
print '%%%%%%%%%%'
usage();sys.exit(1)
#######################################################
################### Output KMZ ######################
############### Make PNG file
print 'Making png file ...'
length = data.shape[0]
width = data.shape[1]
try:fig_size
except:
fig_size_0 = 6.0 ## min figure dimension: 6.0
ratio = float(length)/float(width)
fig_size = [fig_size_0,fig_size_0*ratio]
print 'figure size: %.1f, %.1f'%(fig_size[0],fig_size[1])
ccmap = plt.get_cmap(color_map)
fig = plt.figure(figsize=fig_size,frameon=False)
ax = fig.add_axes([0., 0., 1., 1.])
ax.set_axis_off()
aspect = width/(length*1.0)
try: ax.imshow(data,aspect='auto',cmap=ccmap,vmax=Vmax,vmin=Vmin)
except: ax.imshow(data,aspect='auto',cmap=ccmap)
if disp_ref == 'yes':
try:
xref = int(atr['ref_x'])
yref = int(atr['ref_y'])
ax.plot(xref,yref,'ks',ms=ref_size)
print 'show reference point'
except: print 'Cannot find reference point info!'
ax.set_xlim([0,width])
ax.set_ylim([length,0])
figName = outName + '.png'
print 'writing '+figName
plt.savefig(figName, pad_inches=0.0, transparent=True, dpi=fig_dpi)
############### Making colorbar
pc = plt.figure(figsize=(1,8))
axc = pc.add_subplot(111)
if fig_unit in ['mm','mm/yr']: v_scale = 1000
elif fig_unit in ['cm','cm/yr']: v_scale = 100
elif fig_unit in ['m', 'm/yr']: v_scale = 1
norm = mpl.colors.Normalize(vmin=Vmin*v_scale, vmax=Vmax*v_scale)
clb = mpl.colorbar.ColorbarBase(axc,cmap=ccmap,norm=norm, orientation='vertical')
#clb.set_label(fig_unit)
clb.set_label(cbar_label+' ['+fig_unit+']')
clb.locator = mpl.ticker.MaxNLocator(nbins=cbar_bin_num)
clb.update_ticks()
pc.subplots_adjust(left=0.2,bottom=0.3,right=0.4,top=0.7)
pc.patch.set_facecolor('white')
pc.patch.set_alpha(0.7)
pc.savefig('colorbar.png',bbox_inches='tight',facecolor=pc.get_facecolor(),dpi=300)
############## Generate KMZ file
print 'generating kml file ...'
try: doc = KML.kml(KML.Folder(KML.name(atr['PROJECT_NAME'])))
except: doc = KML.kml(KML.Folder(KML.name('PySAR product')))
slc = KML.GroundOverlay(KML.name(figName),KML.Icon(KML.href(figName)),\
KML.altitudeMode('clampToGround'),\
KML.LatLonBox(KML.north(str(North)),KML.south(str(South)),\
KML.east( str(East)), KML.west( str(West))))
doc.Folder.append(slc)
#############################
print 'adding colorscale ...'
cb_rg = min(North-South, East-West)
cb_N = (North+South)/2.0 + 0.5*0.5*cb_rg
cb_W = East + 0.1*cb_rg
slc1 = KML.GroundOverlay(KML.name('colorbar'),KML.Icon(KML.href('colorbar.png')),\
KML.altitude('2000'),KML.altitudeMode('absolute'),\
KML.LatLonBox(KML.north(str(cb_N)),KML.south(str(cb_N-0.5*cb_rg)),\
KML.west( str(cb_W)),KML.east( str(cb_W+0.14*cb_rg))))
doc.Folder.append(slc1)
#############################
kmlstr = etree.tostring(doc, pretty_print=True)
kmlname = outName + '.kml'
print 'writing '+kmlname
kmlfile = open(kmlname,'w')
kmlfile.write(kmlstr)
kmlfile.close()
kmzName = outName + '.kmz'
print 'writing '+kmzName
cmdKMZ = 'zip ' + kmzName +' '+ kmlname +' ' + figName + ' colorbar.png'
os.system(cmdKMZ)
cmdClean = 'rm '+kmlname; print cmdClean; os.system(cmdClean)
cmdClean = 'rm '+figName; print cmdClean; os.system(cmdClean)
cmdClean = 'rm colorbar.png'; print cmdClean; os.system(cmdClean)
def main(argv):
try:
file=argv[0]
geomap=argv[1]
except:
Usage();sys.exit(1)
######################################################################################
fileName=os.path.basename(file).split('.')[0]
h5file=h5py.File(file,'r')
atr = readfile.read_attributes(file)
k = atr['FILE_TYPE']
print '\n***************** Geocoding *******************'
print 'input file: '+k
#### Subsetted radar coded file
try:
x0 = float(atr['subset_x0'])
y0 = float(atr['subset_y0'])
print '\nSubsetted radar coded file:\n creating temporary geomap file for it...'
rg,az,rsc = readfile.read_float32(geomap)
rg = rg - x0
az = az - y0
geomap = 'temp_'+geomap
print ' writing '+geomap+'\n'
writefile.write_float32(rg,az,geomap)
fg = open(geomap+'.rsc','w')
for kg in rsc.keys(): fg.write(kg+' '+rsc[kg]+'\n')
fg.close()
except: pass
######################################################################################
if k in ['timeseries']:
outname='epoch_temp.unw'
f = h5py.File('geo_'+file,'w')
group = f.create_group('timeseries')
epochList = h5file['timeseries'].keys()
epochList = sorted(epochList)
for epoch in epochList:
print 'geocoding '+epoch
data = h5file['timeseries'].get(epoch)[:]
amp,unw,unwrsc = geocode_one(data,geomap,outname)
dset = group.create_dataset(epoch, data=unw, compression='gzip')
atr = geocode_attributes(atr,unwrsc)
for key,value in atr.iteritems():
group.attrs[key] = value
######################################################################################
elif k in ['interferograms','coherence','wrapped']:
if k == 'interferograms': outname = k[0]+'_temp.unw'
elif k == 'coherence' : outname = k[0]+'_temp.cor'
else: outname = k[0]+'_temp.int'
f = h5py.File('geo_'+file,'w')
gg = f.create_group('interferograms')
igramList = h5file[k].keys()
igramList = sorted(igramList)
for igram in igramList:
print 'geocoding '+igram
data = h5file[k][igram].get(igram)[:]
amp,unw,unwrsc = geocode_one(data,geomap,outname)
group = gg.create_group('geo_'+igram)
dset = group.create_dataset('geo_'+igram, data=unw, compression='gzip')
atr = geocode_attributes(h5file[k][igram].attrs, unwrsc)
for key,value in atr.iteritems():
group.attrs[key] = value
####################### support of old format #######################
### mask
try:
data = h5file['mask'].get('mask')[:]
amp,unw,unwrsc = geocode_one(data,geomap,'mask_'+outname)
gm = f.create_group('mask')
dset = gm.create_dataset('mask', data=unw, compression='gzip')
except: print 'No group for mask found in the file.'
### meanCoherence
try:
data = h5file['meanCoherence'].get('meanCoherence')[:]
amp,unw,unwrsc = geocode_one(data,geomap,'meanCoherence_'+outname)
gm = f.create_group('meanCoherence')
dset = gm.create_dataset('meanCoherence', data=unw, compression='gzip')
except: print 'No group for meanCoherence found in the file'
######################################################################################
else:
data,atr = readfile.read(file)
outname=fileName+'.unw'
amp,unw,unwrsc = geocode_one(data,geomap,outname)
atr = geocode_attributes(atr,unwrsc)
writefile.write(unw,atr,'geo_'+file)
######################################################################################
try:
atr['subset_x0']
rmCmd='rm '+geomap; os.system(rmCmd); print rmCmd
rmCmd='rm '+geomap+'.rsc'; os.system(rmCmd); print rmCmd
except: pass
try:
f.close()
h5file.close()
except: pass
def main(argv):
#lineWidth=4
#fontSize=32
#markerColor='orange'
#markerSize=20
#if len(sys.argv)>2:
try:
opts, args = getopt.getopt(argv, "h:f:m:t:x:y:o:")
except getopt.GetoptError:
Usage()
sys.exit(1)
for opt, arg in opts:
if opt in ("-h", "--help"):
Usage()
sys.exit()
elif opt == '-f':
File = arg
elif opt == '-m':
maskFile = arg
elif opt == '-t':
thr = float(arg)
elif opt == '-y':
ysub = [int(i) for i in arg.split(':')]
ysub.sort()
elif opt == '-x':
xsub = [int(i) for i in arg.split(':')]
xsub.sort()
elif opt == '-o':
MaskedFile = arg
try:
File
maskFile
except:
Usage()
sys.exit(1)
######################################
ext = os.path.splitext(File)[1]
import h5py
import numpy as np
################################ PySAR HDF5 #################################
if ext == '.h5':
h5file = h5py.File(File, 'r')
h5mask = h5py.File(maskFile, 'r')
kf = h5file.keys()
if 'coherence' not in h5mask.keys():
Mset = h5mask[h5mask.keys()[0]].get(h5mask.keys()[0])
M = Mset[0:Mset.shape[0], 0:Mset.shape[1]]
try:
MaskedFile
except:
MaskedFile = File.split('.')[0] + '_masked.h5'
h5file2 = h5py.File(MaskedFile, 'w')
if len(kf) == 1 and kf[0] in ('velocity', 'temporal_coherence', 'rmse',
'mask'):
Vset = h5file[h5file.keys()[0]].get(h5file.keys()[0])
V = Vset[0:Vset.shape[0], 0:Vset.shape[1]]
try:
xsub
ysub
M[ysub[0]:ysub[1], xsub[0]:xsub[1]] = 0
except:
print 'No subset'
try:
V[M < thr] = np.nan
except:
V[M == 0] = np.nan
group = h5file2.create_group(kf[0])
dset = group.create_dataset(os.path.basename(kf[0]),
data=V,
compression='gzip')
for key, value in h5file[kf[0]].attrs.iteritems():
group.attrs[key] = value
elif 'timeseries' in h5file.keys():
print 'Masking the time-series'
group = h5file2.create_group('timeseries')
dateList = h5file['timeseries'].keys()
for d in dateList:
print d
unwset = h5file['timeseries'].get(d)
unw = unwset[0:unwset.shape[0], 0:unwset.shape[1]]
try:
unw[M < thr] = np.nan
except:
unw[M == 0] = np.nan
dset = group.create_dataset(d, data=unw, compression='gzip')
for key, value in h5file['timeseries'].attrs.iteritems():
group.attrs[key] = value
elif kf[0] in ('interferograms',
'wrapped') and 'coherence' in h5mask.keys():
print 'Masking each ' + kf[0] + ' using its coherence file'
igramList = h5file[kf[0]].keys()
cohList = h5mask['coherence'].keys()
gg = h5file2.create_group(kf[0])
for igram in igramList:
print igram
date12 = h5file[kf[0]][igram].attrs['DATE12']
for cohFile in cohList:
if h5mask['coherence'][cohFile].attrs['DATE12'] == date12:
igramCoh = cohFile
print igramCoh
unwset = h5file[kf[0]][igram].get(igram)
unw = unwset[0:unwset.shape[0], 0:unwset.shape[1]]
cohset = h5mask['coherence'][igramCoh].get(igramCoh)
coh = cohset[0:cohset.shape[0], 0:cohset.shape[1]]
unw[coh < thr] = np.nan
group = gg.create_group(igram)
dset = group.create_dataset(igram,
data=unw,
compression='gzip')
for key, value in h5file[kf[0]][igram].attrs.iteritems():
group.attrs[key] = value
try:
#if kf[0] == 'interferograms':
mask = h5file['mask'].get('mask')
gm = h5file2.create_group('mask')
dset = gm.create_dataset('mask', data=mask, compression='gzip')
except:
print 'no mask group found.'
elif kf[0] in ('interferograms',
'wrapped') and 'coherence' not in h5mask.keys():
print 'Masking the ' + kf[0]
igramList = h5file[kf[0]].keys()
gg = h5file2.create_group(kf[0])
for igram in igramList:
print igram
unwset = h5file[kf[0]][igram].get(igram)
unw = unwset[0:unwset.shape[0], 0:unwset.shape[1]]
try:
unw[M < thr] = np.nan
except:
unw[M == 0] = np.nan
group = gg.create_group(igram)
dset = group.create_dataset(igram,
data=unw,
compression='gzip')
for key, value in h5file[kf[0]][igram].attrs.iteritems():
group.attrs[key] = value
try:
#if kf[0] == 'interferograms':
mask = h5file['mask'].get('mask')
gm = h5file2.create_group('mask')
dset = gm.create_dataset('mask', data=mask, compression='gzip')
except:
print 'no mask group found.'
h5file.close()
h5mask.close()
h5file2.close()
################################ ROI_PAC ######################################
elif ext in ['.unw', '.int']:
import pysar._readfile as readfile
import pysar._writefile as writefile
Mext = os.path.splitext(maskFile)[1]
if Mext == '.cor':
a, M, atr = readfile.read_float32(maskFile)
elif Mext == '.h5':
h5mask = h5py.File(maskFile, 'r')
Mset = h5mask[h5mask.keys()[0]].get(h5mask.keys()[0])
M = Mset[0:Mset.shape[0], 0:Mset.shape[1]]
else:
sys.exit(['Un-recoganized mask file extension: ' + Mext])
try:
MaskedFile
except:
MaskedFile = File.split('.')[0] + '_masked' + ext
a, unw, atr = readfile.read_float32(File)
try:
unw[M < thr] = np.nan
except:
unw[M == 0] = np.nan
print 'writting >>> ' + MaskedFile
writefile.write_float32(unw, MaskedFile)
f = open(MaskedFile + '.rsc', 'w')
for k in atr.keys():
f.write(k + ' ' + atr[k] + '\n')
f.close()
try:
h5mask.close()
except:
pass
def main(argv):
################# default values ################
flip_lr='no'
flip_ud='no'
disp_geo = 'yes'
#font_size=8
color_map='jet'
figs_rows=5
figs_cols=8
rewrapping='yes'
allData2display='yes'
Wspace = 0.1
Hspace = 0.1
title = 'out'
showRef = 'yes'
ref_color='k'
ref_symbol='s'
ref_size =10
dip_opposite = 'no'
saveFig='no'
dispFig='yes'
dispContour='only'
contour_step=200
contour_sigma=3.0
fig_dpi=300
################### get input args ###############
if len(sys.argv)>2:
try:
opts, args = getopt.getopt(argv,"h:D:O:G:S:f:m:M:v:u:s:c:e:d:r:p:w:i:j:t:R:a:b:k:x:y:C:V:P:o:g:l:L:")
except getopt.GetoptError:
Usage() ; sys.exit(1)
if opts==[]: Usage() ; sys.exit(1)
for opt,arg in opts:
if opt in ("-h","--help"):
Usage() ; sys.exit()
elif opt == '-f': File = arg
elif opt == '-D': demFile=arg
elif opt == '-w': rewrapping = arg
elif opt == '-m': min = float(arg); rewrapping='no'
elif opt == '-M': max = float(arg); rewrapping='no'
elif opt == '-v': flip_lr = arg
elif opt == '-u': flip_ud = arg
elif opt == '-s': font_size = int(arg)
elif opt == '-c': color_map = arg
elif opt == '-e': epoch_number = int(arg); allData2display='no'
elif opt == '-d': epoch_date = arg; allData2display='no'
elif opt == '-r': figs_rows = int(arg)
elif opt == '-p': figs_cols = int(arg)
elif opt == '-i': Wspace = float(arg)
elif opt == '-j': Hspace = float(arg)
elif opt == '-t': title = arg
elif opt == '-R': showRef = arg
elif opt == '-a': ref_color = arg
elif opt == '-b': ref_symbol = arg
elif opt == '-k': ref_size=int(arg)
elif opt == '-x': win_x = [int(i) for i in arg.split(':')]; win_x.sort()
elif opt == '-y': win_y = [int(i) for i in arg.split(':')]; win_y.sort()
elif opt == '-G': disp_geo = arg
elif opt == '-O': dip_opposite=arg
elif opt == '-S': saveFig=arg
elif opt == '-C': dispContour=arg
elif opt == '-V': contour_step=float(arg)
elif opt == '-P': dispFig=arg
elif opt == '-o': figName=arg
elif opt == '-g': contour_sigma = float(arg)
elif opt == '-l': win_lat = [float(i) for i in arg.split(':')]; win_lat.sort()
elif opt == '-L': win_lon = [float(i) for i in arg.split(':')]; win_lon.sort()
elif len(sys.argv)==2:
if argv[0]=='-h': Usage(); sys.exit(1)
elif os.path.isfile(argv[0]): File = argv[0]
else:
print 'Input file does not existed: '+argv[0]; sys.exit(1)
elif len(sys.argv)<2: Usage(); sys.exit(1)
if color_map == 'hsv':
################################################
cdict1 = {'red': ((0.0, 0.0, 0.0),
(0.5, 0.0, 0.0),
(0.6, 1.0, 1.0),
(0.8, 1.0, 1.0),
(1.0, 0.5, 0.5)),
'green': ((0.0, 0.0, 0.0),
(0.2, 0.0, 0.0),
(0.4, 1.0, 1.0),
(0.6, 1.0, 1.0),
(0.8, 0.0, 0.0),
(1.0, 0.0, 0.0)),
'blue': ((0.0, 0.5, .5),
(0.2, 1.0, 1.0),
(0.4, 1.0, 1.0),
(0.5, 0.0, 0.0),
(1.0, 0.0, 0.0),)
}
from matplotlib.colors import LinearSegmentedColormap
ccmap = LinearSegmentedColormap('BlueRed1', cdict1)
################################################
else: ccmap=plt.get_cmap(color_map)
##################################################
ext = os.path.splitext(File)[1]
if ext == '.h5':
import h5py
h5file=h5py.File(File,'r')
k=h5file.keys()
if 'interferograms' in k: k[0] = 'interferograms'
elif 'coherence' in k: k[0] = 'coherence'
elif 'timeseries' in k: k[0] = 'timeseries'
print 'Input: '+str(k)
if k[0] in ('dem','velocity','mask','temporal_coherence','rmse'):
allData2display = 'no'
elif ext in ['.unw','.int','.cor','.hgt','.dem','.trans','.mli','.slc']:
import pysar._readfile as readfile
allData2display = 'no'
k = [ext]
else:
print 'File extension not recogized: '+ext
print 'Support file format:\n\
PySAR HDF5 files: velocity.h5, timeseries.h5, LoadedData.h5, ...\n\
ROI_PAC files: .unw .cor .int .hgt .dem .trans .mli'
sys.exit(1)
####################################################################
########################## Plot One ################################
if allData2display == 'no':
try: font_size
except: font_size=12
################# File Reading ##################
##### PySAR HDF5
if k[0] in ('dem','velocity','mask','temporal_coherence','rmse'):
atr = h5file[k[0]].attrs
dset = h5file[k[0]].get(k[0])
data = dset[0:dset.shape[0],0:dset.shape[1]]
# rewrapping
if rewrapping in ('yes','Yes','Y','y','YES'):
print 'Rewrapping disabled for '+k[0]
elif k[0] == 'timeseries':
dateList=h5file[k[0]].keys()
try:
epoch_number
except:
try:
epoch_date
if len(epoch_date)==6: epoch_date=yymmdd2yyyymmdd(epoch_date)
epoch_number=dateList.index(epoch_date)
except:
print 'Unrecognized epoch input!'; sys.exit(1)
print 'Displaying date: '+dateList[epoch_number]
atr = h5file[k[0]].attrs
dset = h5file[k[0]].get(dateList[epoch_number])
data = dset[0:dset.shape[0],0:dset.shape[1]]
# rewrapping
if rewrapping in ('yes','Yes','y','Y','YES'):
print 'Rewrapping. Set min/max to -pi/pi. Showing phase'
range2phase=4*np.pi/float(atr['WAVELENGTH']) #double-way, 2*2*pi/lamda
data=range2phase*data
data=rewrap(data)
min = -np.pi
max = np.pi
figUnit='(radian)'
elif rewrapping in ('no','No','N','n','NO'):
print 'No rewrapping. Showing displacement.'
figUnit='(m)'
elif k[0] in ('interferograms','coherence','wrapped'):
ifgramList=h5file[k[0]].keys()
try:
epoch_number
except:
for i in range(len(ifgramList)):
if epoch_date in ifgramList[i]: epoch_number = i
print 'Displaying: '+ifgramList[epoch_number]
atr = h5file[k[0]][ifgramList[epoch_number]].attrs
dset = h5file[k[0]][ifgramList[epoch_number]].get(ifgramList[epoch_number])
data = dset[0:dset.shape[0],0:dset.shape[1]]
# rewrapping
if k[0] in ('coherence','wrapped') and rewrapping in ('yes','Yes','y','Y','YES'):
print 'No rewrapping for coherence/wrapped files, set to "no"'
rewrapping='no'
if rewrapping in ('yes','Yes','y','Y','YES'):
print 'Rewrapping. Set min/max to -pi/pi.'
data = np.angle(np.exp(1j*data))
min = -np.pi
max = np.pi
##### ROI_PAC product
elif k[0] in ['.slc','.mli']:
data,p,atr = readfile.read_complex64(File)
data= np.nanlog10(data)
figUnit = '(dB)'
elif k[0] == '.int':
a,data,atr = readfile.read_complex64(File)
min = -np.pi
max = np.pi
rewrapping = 'no'
figUnit = '(radian)'
elif k[0] in ['.unw', '.cor', '.hgt', '.trans']:
a,data,atr = readfile.read_float32(File)
if k[0] == '.unw': figUnit = '(radian)'
elif k[0] == '.hgt': figUnit = '(m)'
if k[0] in ['.cor','.hgt','.trans']: rewrapping='no'
if rewrapping in ('yes','Yes','y','Y','True','true'):
print 'Rewrapping. Set min/max to -pi/pi.'
data = rewrap(data)
min = -np.pi
max = np.pi
elif k[0] == '.dem':
data,atr = readfile.read_dem(File)
figUnit = '(m)'
############## Data Option ##################
# Opposite Sign
if dip_opposite in ('yes','Yes','Y','y','YES'):
data=-1*data
# Subset
try: # y/latitude direction
win_lat
try:
atr['Y_FIRST']
win_y=[0]*2
win_y[0]=int((win_lat[1]-float(atr['Y_FIRST']))/float(atr['Y_STEP']))
win_y[1]=int((win_lat[0]-float(atr['Y_FIRST']))/float(atr['Y_STEP']))
if win_y[0]<0: win_y[0]=0; print 'input latitude > max latitude! Set to max'
print 'subset in latitude - '+str(win_lat[0])+':'+str(win_lat[1])
except: print 'Non-geocoded file, cannot use LatLon option'; Usage(); sys.exit(1)
except:
try:
win_y
print 'subset in y direction - '+str(win_y[0])+':'+str(win_y[1])
except: win_y = [0,int(atr['FILE_LENGTH'])]
try: # x/longitude direction
win_lon
try:
atr['X_FIRST']
win_x=[0]*2
win_x[0]=int((win_lon[0]-float(atr['X_FIRST']))/float(atr['X_STEP']))
win_x[1]=int((win_lon[1]-float(atr['X_FIRST']))/float(atr['X_STEP']))
if win_x[0]<0: win_x[0]=0; print 'input longitude > max longitude! Set to max'
print 'subset in longitude - '+str(win_lon[0])+':'+str(win_lon[1])
except: print 'Non-geocoded file, cannot use LatLon option'; Usage(); sys.exit(1)
except:
try:
win_x
print 'subset in x direction - '+str(win_x[0])+':'+str(win_x[1])
except: win_x = [0,int(atr['WIDTH'])]
data = data[win_y[0]:win_y[1],win_x[0]:win_x[1]]
# Reference Point
try:
xref=atr['ref_x']-win_x[0]
yref=atr['ref_y']-win_y[0]
except: print 'No reference point'
try:
xref=xref-atr['subset_x0']
yref=yref-atr['subset_y0']
except: print 'No subset'
# Geo coordinate
try:
lon_step = float(atr['X_STEP'])
lat_step = float(atr['Y_STEP'])
lon_unit = atr['Y_UNIT']
lat_unit = atr['X_UNIT']
ullon = float(atr['X_FIRST'])+win_x[0]*lon_step
ullat = float(atr['Y_FIRST'])+win_y[0]*lat_step
llcrnrlon = ullon
llcrnrlat = ullat+lat_step*data.shape[0]
urcrnrlon = ullon+lon_step*data.shape[1]
urcrnrlat = ullat
geocoord='yes'
print 'Input file is Geocoded'
except: geocoord='no'
# Flip
if flip_lr in ('yes','Yes','Y','y','YES'): data=np.fliplr(data); xref=np.shape(data)[1]-xref-1
if flip_ud in ('yes','Yes','Y','y','YES'): data=np.flipud(data); yref=np.shape(data)[0]-yref-1
# Colorbar Extend
data_min = np.nanmin(data)
data_max = np.nanmax(data)
try: min
except: min = data_min
try: max
except: max = data_max
if min <= data_min and max >= data_max: cb_extend='neither'
elif min > data_min and max >= data_max: cb_extend='min'
elif min <= data_min and max < data_max: cb_extend='max'
else: cb_extend='both'
############## DEM Option ##################
try:
demFile
print 'Show topography'
import pysar._readfile as readfile
if os.path.basename(demFile).split('.')[1]=='hgt': amp,dem,demRsc = readfile.read_float32(demFile)
elif os.path.basename(demFile).split('.')[1]=='dem': dem,demRsc = readfile.read_dem(demFile)
# Subset
dem = dem[win_y[0]:win_y[1],win_x[0]:win_x[1]]
# Flip
if flip_lr in ('yes','Yes','Y','y','YES'): dem=np.fliplr(dem)
if flip_ud in ('yes','Yes','Y','y','YES'): dem=np.flipud(dem)
# DEM data preparation
if dispContour in ('no','No','n','N','NO','yes','Yes','y','Y','YES'): #DEM basemap
print 'plot DEM as basemap'
cmap_dem=plt.get_cmap('gray')
import pysar._pysar_utilities as ut
if dispContour in ('only','Only','o','O','ONLY','yes','Yes','y','Y','YES'): #contour
print 'plot contour'
#if smoothContour in ('yes','Yes','y','Y','YES'):
import scipy.ndimage as ndimage
dem=ndimage.gaussian_filter(dem,sigma=contour_sigma,order=0)
contour_sequence=np.arange(-6000,9000,contour_step)
except: print 'No DEM file'
############## Data Plot and Output ################
# Figure Title
if k[0]=='velocity': figTitle = 'Velocity (m/yr)'
elif k[0]=='temporal_coherence': figTitle = 'Temporal coherence'
elif k[0]=='dem': figTitle = 'DEM error'
elif k[0]=='rmse': figTitle = 'RMSE (m/yr)'
elif k[0]=='mask': figTitle = 'Pixels with no valid value.'
elif k[0]=='coherence': figTitle = ifgramList[epoch_number]
elif k[0]in('interferograms','wrapped'): figTitle = ifgramList[epoch_number]+' (radian)'
elif k[0]=='timeseries':
try: master_date=atr['ref_date']
except: master_date=atr['DATE']
if len(master_date)==6: master_date=yymmdd2yyyymmdd(master_date)
if dip_opposite in ('yes','Yes','Y','y','YES'): figTitle = dateList[epoch_number]+'_'+master_date+' '+figUnit
else: figTitle = master_date+'_'+dateList[epoch_number]+' '+figUnit
elif k[0] in ['.unw','.cor','.hgt','.dem','.trans','.mli','.slc']:
try: figTitle = File+' '+figUnit
except: figTitle = File
# Plot in Geo-coordinate: plot in map
if geocoord == 'yes' and disp_geo in ('yes','Yes','y','Y','YES'):
print 'display Lat/Lon'
fig = plt.figure()
ax = fig.add_axes([0.1,0.1,0.8,0.8])
try: plt.title(figTitle,fontsize=font_size)
except: pass
# Map - DEM - Data
from mpl_toolkits.basemap import Basemap
m = Basemap(llcrnrlon=llcrnrlon, llcrnrlat=llcrnrlat, urcrnrlon=urcrnrlon, urcrnrlat=urcrnrlat,
resolution='l', area_thresh=1., projection='cyl',suppress_ticks=False,ax=ax)
try:
demFile
if dispContour in ('no','No','n','N','NO','yes','Yes','y','Y','YES'):
m.imshow(ut.hillshade(np.flipud(dem),50.0),cmap=cmap_dem)
if dispContour in ('only','Only','o','O','ONLY','yes','Yes','y','Y','YES'):
import numpy.matlib
c_x = np.linspace(llcrnrlon,urcrnrlon,num=dem.shape[1],endpoint='FALSE').reshape(1,dem.shape[1])
c_xx= np.matlib.repmat(c_x,dem.shape[0],1)
c_y = np.linspace(llcrnrlat,urcrnrlat,num=dem.shape[0],endpoint='FALSE').reshape(dem.shape[0],1)
c_yy= np.matlib.repmat(c_y,1,dem.shape[1])
m.contour(c_xx,c_yy,np.flipud(dem),contour_sequence,origin='lower',colors='black',alpha=0.5,latlon='FALSE')
except: pass
try: im = m.imshow(np.flipud(data),cmap=ccmap,vmin=min,vmax=max)
except: im = m.imshow(np.flipud(data),cmap=ccmap)
# Reference Point
if showRef in ('yes','Yes','Y','y','YES'):
try:
refPoint=ref_color+ref_symbol
ref_lon = llcrnrlon + xref*lon_step
ref_lat = urcrnrlat + yref*lat_step
plt.plot(ref_lon,ref_lat,refPoint,ms=ref_size)
except: print 'No reference point'
# Colorbar
from mpl_toolkits.axes_grid1 import make_axes_locatable
divider = make_axes_locatable(ax)
cax = divider.append_axes("right",size="5%", pad=0.30)
plt.colorbar(im,cax=cax,extend=cb_extend)
#plt.colorbar(im,cax=cax)
# Status bar
def format_coord(x,y):
col = int((x-ullon)/lon_step+0.5)
row = int((y-ullat)/lat_step+0.5)
if col>=0 and col<=data.shape[1] and row >=0 and row<=data.shape[0]:
z = data[row,col]
return 'lat=%.4f, lon=%.4f, value=%.4f'%(x,y,z)
else:
return 'lat=%.4f, lon=%.4f'%(x,y)
ax.format_coord = format_coord
# Plot in x/y coordinate: row and column
else:
fig = plt.figure()
ax = fig.add_axes([0.1,0.1,0.8,0.8])
try: plt.title(figTitle,fontsize=font_size)
except: pass
# Plot
try:
demFile
if dispContour in ('no','No','n','N','NO','yes','Yes','y','Y','YES'):
ax.imshow(ut.hillshade(dem,50.0),cmap=cmap_dem)
if dispContour in ('only','Only','o','O','ONLY','yes','Yes','y','Y','YES'):
ax.contour(dem,contour_sequence,origin='lower',colors='black',alpha=0.5)
except: pass
try: im = ax.imshow(data,cmap=ccmap, vmin=min, vmax=max)
except: im = ax.imshow(data,cmap=ccmap)
cbar = plt.colorbar(im,extend=cb_extend)
#cbar.set_label('m/yr')
# Reference Point
if showRef in ('yes','Yes','Y','y','YES'):
try:
refPoint=ref_color+ref_symbol
ax.plot(xref,yref,refPoint,ms=ref_size)
except: print 'No reference point'
plt.xlim(0,np.shape(data)[1])
plt.ylim( np.shape(data)[0],0)
# Status bar
def format_coord(x,y):
col = int(x+0.5)
row = int(y+0.5)
if col>=0 and col<=data.shape[1] and row >=0 and row<=data.shape[0]:
z = data[row,col]
return 'x=%.4f, y=%.4f, value=%.4f'%(x,y,z)
else:
return 'x=%.4f, y=%.4f'%(x,y)
ax.format_coord = format_coord
# Save Figure
if saveFig in ('yes','Yes','Y','y','YES'):
try: figName
except:
if k[0]=='velocity': figName='velocity.pdf'
elif k[0]=='temporal_coherence': figName='temporal_coherence.pdf'
elif k[0]=='dem': figName='DEM_error.pdf'
elif k[0]=='rmse': figName='rmse.pdf'
elif k[0]=='mask': figName='mask.pdf'
elif k[0]=='timeseries':
figName=os.path.basename(File).split('.')[0]+'_'+dateList[epoch_number]+'.pdf'
elif k[0] in ('interferograms','coherence','wrapped'):
figName=ifgramList[epoch_number]+'.pdf'
elif k[0] in ['.unw','.cor','.hgt','.dem','.trans','.mli','.slc']:
figName=File+'.pdf'
plt.savefig(figName,dpi=fig_dpi)
print 'Saved figure to '+figName
# Show Figure
if dispFig in ('yes','Yes','Y','y','YES'):
plt.show()
####################################################################
########################## Plot All ################################
elif allData2display == 'yes':
try: font_size
except: font_size=8
if k[0] == 'timeseries':
atr = h5file[k[0]].attrs
# rewrapping
if rewrapping in ('yes','Yes','Y','y','YES'):
print 'Rewrapping. Set min/max to -pi/pi. Showing phase.'
range2phase=4*np.pi/float(h5file['timeseries'].attrs['WAVELENGTH'])
min=-np.pi
max=np.pi
else: print 'No rewrapping. Showing displacement.'
elif k[0] in ('interferograms','coherence','wrapped'):
atr = h5file[k[0]][h5file[k[0]].keys()[0]].attrs
# rewrapping
if k[0] in ('coherence','wrapped') and rewrapping in ('yes','Yes','y','Y','YES'):
print 'No rewrapping for coherence/wrapped files, set to "no"'
rewrapping='no'
if rewrapping in ('yes','Yes','Y','y','YES'):
print 'Rewrapping. Set min/max to -pi/pi.'
min=-np.pi
max=np.pi
else: print 'No rewrapping'
### Subset Option ###
try: # y/latitude direction
win_lat
try:
atr['Y_FIRST']
win_y=[0]*2
win_y[0]=int((win_lat[1]-float(atr['Y_FIRST']))/float(atr['Y_STEP']))
win_y[1]=int((win_lat[0]-float(atr['Y_FIRST']))/float(atr['Y_STEP']))
if win_y[0]<0: win_y[0]=0; print 'input latitude > max latitude! Set to max'
print 'subset in latitude - '+str(win_lat[0])+':'+str(win_lat[1])
except: print 'Non-geocoded file, cannot use LatLon option'; Usage(); sys.exit(1)
except:
try:
win_y
print 'subset in y direction - '+str(win_y[0])+':'+str(win_y[1])
except: win_y = [0,int(atr['FILE_LENGTH'])]
try: # x/longitude direction
win_lon
try:
atr['X_FIRST']
win_x=[0]*2
win_x[0]=int((win_lon[0]-float(atr['X_FIRST']))/float(atr['X_STEP']))
win_x[1]=int((win_lon[1]-float(atr['X_FIRST']))/float(atr['X_STEP']))
if win_x[0]<0: win_x[0]=0; print 'input longitude > max longitude! Set to max'
print 'subset in longitude - '+str(win_lon[0])+':'+str(win_lon[1])
except: print 'Non-geocoded file, cannot use LatLon option'; Usage(); sys.exit(1)
except:
try:
win_x
print 'subset in x direction - '+str(win_x[0])+':'+str(win_x[1])
except: win_x = [0,int(atr['WIDTH'])]
# Figure Name
if saveFig in ('yes','Yes','Y','y','YES'):
try:
figName
figNameBase = os.path.basename(figName).split('.')[0]
figNameExt = os.path.basename(figName).split('.')[1]
except:
figNameBase = os.path.basename(File).split('.')[0]
figNameExt = '.pdf'
################## DEM Options ####################
try:
demFile
print 'Show topography'
import pysar._readfile as readfile
if os.path.basename(demFile).split('.')[1]=='hgt': amp,dem,demRsc = readfile.read_float32(demFile)
elif os.path.basename(demFile).split('.')[1]=='dem': dem,demRsc = readfile.read_dem(demFile)
# Subset
dem = dem[win_y[0]:win_y[1],win_x[0]:win_x[1]]
if dispContour in ('no','No','n','N','NO','yes','Yes','y','Y','YES'): #DEM basemap
print 'plot DEM as basemap'
cmap_dem=plt.get_cmap('gray')
import pysar._pysar_utilities as ut
hillshade_dem=ut.hillshade(dem,50.0)
if dispContour in ('only','Only','o','O','ONLY','yes','Yes','y','Y','YES'): #contour
print 'plot contour'
#if smoothContour in ('yes','Yes','y','Y','YES'):
import scipy.ndimage as ndimage
dem=ndimage.gaussian_filter(dem,sigma=contour_sigma,order=0)
contour_sequence=np.arange(-6000,9000,contour_step)
except: print 'No DEM file'
################## Plot Loop ####################
ifgramList=h5file[k[0]].keys()
nfigs = figs_rows*figs_cols
lifgram = len(ifgramList)
print 'number of epochs/interferograms to display:'+ str(lifgram)
kk=int(lifgram/nfigs)+1
ii=0
# plot (1,end-1) figures
for j in range(1,kk):
fig = plt.figure(j)
ii=(j-1)*nfigs+1
for i in range(ii,ii+nfigs):
print 'loading '+ifgramList[i-1]
ax = fig.add_subplot(figs_rows,figs_cols,i-ii+1)
# Data option
if k[0] == 'timeseries':
figTitle = ifgramList[i-1]
dset = h5file[k[0]].get(ifgramList[i-1])
data = dset[0:dset.shape[0],0:dset.shape[1]]
if rewrapping in ('yes','Yes','Y','y','YES'):
data=range2phase*data
data=rewrap(data)
elif k[0] in ('interferograms','coherence','wrapped'):
figTitle = str(i)+' : '+h5file[k[0]][ifgramList[i-1]].attrs['DATE12']
dset = h5file[k[0]][ifgramList[i-1]].get(ifgramList[i-1])
data = dset[0:dset.shape[0],0:dset.shape[1]]
if rewrapping in ('yes','Yes','Y','y','YES'):
data=np.angle(np.exp(1j*data))
data = data[win_y[0]:win_y[1],win_x[0]:win_x[1]]
# Plot
try:
demFile
if dispContour in ('no','No','n','N','NO','yes','Yes','y','Y','YES'):
plt.imshow(hillshade_dem,cmap=cmap_dem)
if dispContour in ('only','Only','o','O','ONLY','yes','Yes','y','Y','YES'):
plt.contour(dem,contour_sequence,origin='lower',colors='black',alpha=0.5)
except: pass
try: ax.imshow(data,cmap=ccmap,vmin=min,vmax=max)
except: ax.imshow(data,cmap=ccmap)
ax.set_yticklabels([])
ax.set_xticklabels([])
ax.set_xticks([])
ax.set_yticks([])
if title=='out': ax.set_title(figTitle,fontsize=font_size)
elif title=='in': add_inner_title(ax, figTitle, loc=1)
fig.subplots_adjust(wspace=Wspace,hspace=Hspace)
if saveFig in ('yes','Yes','Y','y','YES'):
figName=figNameBase+'_'+str(j)+figNameExt
plt.savefig(figName,dpi=fig_dpi)
# plot the last figure
fig = plt.figure(kk)
ii=(kk-1)*nfigs+1
for i in range(ii,lifgram+1):
print 'loading '+ifgramList[i-1]
ax = fig.add_subplot(figs_rows,figs_cols,i-ii+1)
# Data option
if k[0] == 'timeseries':
figTitle = ifgramList[i-1]
dset = h5file[k[0]].get(ifgramList[i-1])
data = dset[0:dset.shape[0],0:dset.shape[1]]
if rewrapping in ('yes','Yes','Y','y','YES'):
data=range2phase*data
data=rewrap(data)
elif k[0] in ('interferograms','coherence','wrapped'):
figTitle = str(i)+' : '+h5file[k[0]][ifgramList[i-1]].attrs['DATE12']
dset = h5file[k[0]][ifgramList[i-1]].get(ifgramList[i-1])
data = dset[0:dset.shape[0],0:dset.shape[1]]
if rewrapping in ('yes','Yes','Y','y','YES'):
data=np.angle(np.exp(1j*data))
data = data[win_y[0]:win_y[1],win_x[0]:win_x[1]]
# Plot
try:
demFile
if dispContour in ('no','No','n','N','NO','yes','Yes','y','Y','YES'):
plt.imshow(hillshade_dem,cmap=cmap_dem)
if dispContour in ('only','Only','o','O','ONLY','yes','Yes','y','Y','YES'):
plt.contour(dem,contour_sequence,origin='lower',colors='black',alpha=0.5)
except: pass
try: ax.imshow(data,cmap=ccmap,vmin=min,vmax=max)
except: ax.imshow(data,cmap=ccmap)
ax.xaxis.label.set_fontsize(20)
ax.set_yticklabels([])
ax.set_xticklabels([])
ax.set_xticks([])
ax.set_yticks([])
if title=='out': ax.set_title(figTitle,fontsize=font_size)
elif title =='in': add_inner_title(ax, figTitle, loc=1)
fig.subplots_adjust(wspace=Wspace,hspace=Hspace)
if saveFig in ('yes','Yes','Y','y','YES'):
figName=figNameBase+'_'+str(kk)+figNameExt
plt.savefig(figName,dpi=fig_dpi)
print 'Saved figure to '+figNameBase+'_*'+figNameExt
if dispFig in ('yes','Yes','Y','y','YES'):
plt.show()
####################################################################
####################################################################
try: h5file.close()
except: pass
load_dem.py SanAndreas.dem
load_dem.py SanAndreas.dem SanAndreas.h5
load_dem.py radar_8rlks.hgt radar_8rlks.h5
********************************
********************************
'''
sys.exit(1)
ext = os.path.splitext(demFile)[1]
if ext == '.hgt': amp,dem,demRsc = readfile.read_float32(demFile)
elif ext == '.dem': dem,demRsc = readfile.read_real_int16(demFile)
try: outName = sys.argv[2]
except: outName = 'dem.h5'
h5=h5py.File(outName,'w')
group=h5.create_group('dem')
dset = group.create_dataset('dem', data=dem, compression='gzip')
for key , value in demRsc.iteritems():
group.attrs[key]=value
def main(argv):
########### Check Inputs #############
try:
file = sys.argv[1]
operator = sys.argv[2]
operand = float(sys.argv[3])
except:
Usage();sys.exit(1)
if operator in ['+','plus', 'add', 'addition']: operator = 'plus'
elif operator in ['-','minus', 'substract','substraction']: operator = 'minus'
elif operator in ['*','times', 'multiply', 'multiplication']: operator = 'multiply'
elif operator in ['/','obelus','divide', 'division']: operator = 'divide'
elif operator in ['^','exp', 'exponential']: operator = 'exp'
else: print 'ERROR: Unrecognized operator: '+operator; sys.exit(1)
print '\n*************** Image Math ******************'
print 'operation: '+operator+' '+str(operand)
ext = os.path.splitext(file)[1]
try: outName = sys.argv[4]
except: outName = file.split('.')[0]+'_'+operator+str(operand)+ext
########### Read - Calculate - Write ###########
##### PySAR HDF5 files ######
if ext == '.h5':
import h5py
try: h5file=h5py.File(file,'r')
except: print 'ERROR: can not open file: '+file; sys.exit(1)
k=h5file.keys()
if 'interferograms' in k: k[0] = 'interferograms'
elif 'coherence' in k: k[0] = 'coherence'
elif 'timeseries' in k: k[0] = 'timeseries'
print 'Input file is '+k[0]
h5fileOut = h5py.File(outName,'w'); print 'writing >>> '+outName
group = h5fileOut.create_group(k[0])
if k[0] in ('velocity','temporal_coherence','rmse','mask','dem'):
dset = h5file[k[0]].get(k[0])
data = dset[0:dset.shape[0],0:dset.shape[1]]
dataOut = operation(data,operator,operand)
dset = group.create_dataset(k[0], data=dataOut, compression='gzip')
for key , value in h5file[k[0]].attrs.iteritems():
group.attrs[key]=value
elif k[0] == 'timeseries':
dateList = h5file[k[0]].keys(); print 'number of dates: '+str(len(dateList))
for date in dateList:
print date
dset = h5file[k[0]].get(date)
data = dset[0:dset.shape[0],0:dset.shape[1]]
dataOut = operation(data,operator,operand)
dset = group.create_dataset(date, data=dataOut, compression='gzip')
for key,value in h5file[k[0]].attrs.iteritems():
group.attrs[key] = value
elif k[0] in ['interferograms','coherence','wrapped']:
ifgramList = h5file[k[0]].keys(); print 'number of epochs: '+str(len(ifgramList))
for igram in ifgramList:
print igram
dset = h5file[k[0]][igram].get(igram)
data = dset[0:dset.shape[0],0:dset.shape[1]]
dataOut = operation(data,operator,operand)
group2 = group.create_group(igram)
dset = group2.create_dataset(igram, data=dataOut, compression='gzip')
for key, value in h5file[k[0]][igram].attrs.iteritems():
group2.attrs[key] = value
try:
mask = h5file['mask'].get('mask')
gm = h5fileOut.create_group('mask')
dset = gm.create_dataset('mask', data=mask, compression='gzip')
except: print 'No group for mask found in the file.'
try:
Cset = h5file['meanCoherence'].get('meanCoherence')
gm = h5fileOut.create_group('meanCoherence')
dset = gm.create_dataset('meanCoherence', data=Cset, compression='gzip')
except: print 'No group for meanCoherence found in the file'
else: print 'ERROR: Unrecognized HDF5 file type: '+k[0]; sys.exit(1)
h5file.close()
h5fileOut.close()
##### ROI_PAC files #######
elif ext in ['.unw','.cor','.hgt','.dem','.trans']:
import pysar._readfile as readfile
import pysar._writefile as writefile
print 'Input file is '+ext+'\nwriting >>> '+outName
if ext in ['.unw','.cor','.hgt']:
a,p,r = readfile.read_float32(file)
p2 = operation(p,operator,operand)
writefile.write_float32(p2,outName)
elif ext == '.dem':
p,r = readfile.read_real_int16(file)
p2 = operation(p,operator,operand)
writefile.write_real_int16(p2,outName)
elif ext == '.trans':
a,p,r = readfile.read_float32(file)
a2 = operation(a,operator,operand)
p2 = operation(p,operator,operand)
writefile.write_float32(a2,p2,outName)
## Write atrributes file
f = open(outName+'.rsc','w')
for k in r.keys(): f.write(k+' '+r[k]+'\n')
f.close()
else: print 'ERROR: Unrecognized file extension: '+ext; sys.exit(1)
print 'Done.'
def main(argv):
try:
file=argv[0]
geomap=argv[1]
except:
Usage();sys.exit(1)
######################################################################################
fileName=os.path.basename(file).split('.')[0]
h5file=h5py.File(file,'r')
k=h5file.keys()
if 'interferograms' in k: k[0] = 'interferograms'
elif 'coherence' in k: k[0] = 'coherence'
elif 'timeseries' in k: k[0] = 'timeseries'
if k[0] in ('interferograms','coherence','wrapped'):
atr = h5file[k[0]][h5file[k[0]].keys()[0]].attrs
elif k[0] in ('dem','velocity','mask','temporal_coherence','rmse','timeseries'):
atr = h5file[k[0]].attrs
#### Subsetted radar coded file
try:
x0 = float(atr['subset_x0'])
y0 = float(atr['subset_y0'])
print '\nSubsetted radar coded file:\n creating temporary geomap file for it...'
rg,az,rsc = readfile.read_float32(geomap)
rg = rg - x0
az = az - y0
geomap = 'temp_'+geomap
print ' writing '+geomap+'\n'
writefile.write_float32(rg,az,geomap)
fg = open(geomap+'.rsc','w')
for kg in rsc.keys(): fg.write(kg+' '+rsc[kg]+'\n')
fg.close()
except: pass
######################################################################################
if k[0] in ('velocity','temporal_coherence','mask','rmse','dem'):
dset = h5file[k[0]].get(k[0])
data = dset[0:dset.shape[0],0:dset.shape[1]]
outname=fileName+'.unw'
amp,unw,unwrsc = geocode_one(data,geomap,outname)
f = h5py.File('geo_'+file,'w')
group=f.create_group(k[0])
dset = group.create_dataset(k[0], data=unw, compression='gzip')
for key,value in h5file[k[0]].attrs.iteritems(): group.attrs[key]=value
for key,value in unwrsc.iteritems(): group.attrs[key] = value
######################################################################################
elif 'timeseries' in k:
print 'geocoding timeseries:'
outname='epoch_temp.unw'
f = h5py.File('geo_'+file,'w')
group = f.create_group('timeseries')
epochList=h5file['timeseries'].keys()
for epoch in epochList:
print 'geocoding '+epoch
d = h5file['timeseries'].get(epoch)
data = d[0:d.shape[0],0:d.shape[1]]
amp,unw,unwrsc = geocode_one(data,geomap,outname)
dset = group.create_dataset(epoch, data=unw, compression='gzip')
for key,value in unwrsc.iteritems(): group.attrs[key] = value
for key,value in h5file[k[0]].attrs.iteritems(): group.attrs[key] = value
group.attrs['WIDTH'] = unwrsc['WIDTH']
group.attrs['FILE_LENGTH'] = unwrsc['FILE_LENGTH']
######################################################################################
elif k[0] in ['interferograms','coherence','wrapped']:
print 'geocoding '+k[0]+' ...'
if k[0] == 'interferograms': outname = k[0]+'_temp.unw'
elif k[0] == 'coherence': outname = k[0]+'_temp.cor'
else: outname = k[0]+'_temp.int'
f = h5py.File('geo_'+file,'w')
gg = f.create_group('interferograms')
igramList=h5file[k[0]].keys()
for igram in igramList:
print 'geocoding '+igram
d = h5file[k[0]][igram].get(igram)
data = d[0:d.shape[0],0:d.shape[1]]
amp,unw,unwrsc = geocode_one(data,geomap,outname)
group = gg.create_group('geo_'+igram)
dset = group.create_dataset('geo_'+igram, data=unw, compression='gzip')
for key,value in unwrsc.iteritems(): group.attrs[key] = value
for key,value in h5file[k[0]][igram].attrs.iteritems(): group.attrs[key] = value
group.attrs['WIDTH'] = unwrsc['WIDTH']
group.attrs['FILE_LENGTH'] = unwrsc['FILE_LENGTH']
####################### support of old format #######################
### mask
try:
d = h5file['mask'].get('mask')
data = d[0:d.shape[0],0:d.shape[1]]
amp,unw,unwrsc = geocode_one(data,geomap,'mask_'+outname)
gm = f.create_group('mask')
dset = gm.create_dataset('mask', data=unw, compression='gzip')
except: print 'No group for mask found in the file.'
### meanCoherence
try:
d = h5file['meanCoherence'].get('meanCoherence')
data = d[0:d.shape[0],0:d.shape[1]]
amp,unw,unwrsc = geocode_one(data,geomap,'meanCoherence_'+outname)
gm = f.create_group('meanCoherence')
dset = gm.create_dataset('meanCoherence', data=unw, compression='gzip')
except: print 'No group for meanCoherence found in the file'
######################################################################################
try:
atr['subset_x0']
rmCmd='rm '+geomap; os.system(rmCmd); print rmCmd
rmCmd='rm '+geomap+'.rsc'; os.system(rmCmd); print rmCmd
except: pass
f.close()
h5file.close()
Usage:
load_dem.py input [output]
Example:
load_dem.py SanAndreas.dem
load_dem.py SanAndreas.dem SanAndreas.h5
load_dem.py radar_8rlks.hgt radar_8rlks.h5
*****************************************************************
'''
sys.exit(1)
ext = os.path.splitext(demFile)[1]
if ext == '.hgt': amp, dem, demRsc = readfile.read_float32(demFile)
elif ext == '.dem': dem, demRsc = readfile.read_real_int16(demFile)
try:
outName = sys.argv[2]
except:
outName = 'dem.h5'
print 'writing >>> ' + outName
h5 = h5py.File(outName, 'w')
group = h5.create_group('dem')
dset = group.create_dataset('dem', data=dem, compression='gzip')
for key, value in demRsc.iteritems():
group.attrs[key] = value
def main(argv):
#lineWidth=4
#fontSize=32
#markerColor='orange'
#markerSize=20
#if len(sys.argv)>2:
try:
opts, args = getopt.getopt(argv,"h:f:m:t:x:y:o:")
except getopt.GetoptError:
Usage() ; sys.exit(1)
for opt,arg in opts:
if opt in ("-h","--help"):
Usage()
sys.exit()
elif opt == '-f': File = arg
elif opt == '-m': maskFile = arg
elif opt == '-t': thr = float(arg)
elif opt == '-y': ysub = [int(i) for i in arg.split(':')]; ysub.sort()
elif opt == '-x': xsub = [int(i) for i in arg.split(':')]; xsub.sort()
elif opt == '-o': MaskedFile = arg
try:
File
maskFile
except:
Usage() ; sys.exit(1)
######################################
ext = os.path.splitext(File)[1]
import h5py
import numpy as np
################################ PySAR HDF5 #################################
if ext == '.h5':
h5file=h5py.File(File,'r')
h5mask=h5py.File(maskFile,'r')
kf=h5file.keys()
if 'coherence' not in h5mask.keys():
Mset=h5mask[h5mask.keys()[0]].get(h5mask.keys()[0])
M=Mset[0:Mset.shape[0],0:Mset.shape[1]]
try: MaskedFile
except: MaskedFile = File.split('.')[0]+'_masked.h5'
h5file2 = h5py.File(MaskedFile,'w')
if len(kf)==1 and kf[0] in ('velocity','temporal_coherence','rmse','mask'):
Vset=h5file[h5file.keys()[0]].get(h5file.keys()[0])
V=Vset[0:Vset.shape[0],0:Vset.shape[1]]
try:
xsub
ysub
M[ysub[0]:ysub[1],xsub[0]:xsub[1]]=0
except: print 'No subset'
try: V[M<thr] = np.nan
except: V[M==0] = np.nan
group=h5file2.create_group(kf[0])
dset = group.create_dataset(os.path.basename(kf[0]), data=V, compression='gzip')
for key, value in h5file[kf[0]].attrs.iteritems():
group.attrs[key] = value
elif 'timeseries' in h5file.keys():
print 'Masking the time-series'
group = h5file2.create_group('timeseries')
dateList=h5file['timeseries'].keys()
for d in dateList:
print d
unwset = h5file['timeseries'].get(d)
unw=unwset[0:unwset.shape[0],0:unwset.shape[1]]
try: unw[M<thr] = np.nan
except: unw[M==0] = np.nan
dset = group.create_dataset(d, data=unw, compression='gzip')
for key,value in h5file['timeseries'].attrs.iteritems():
group.attrs[key] = value
elif kf[0] in ('interferograms','wrapped') and 'coherence' in h5mask.keys():
print 'Masking each '+kf[0]+' using its coherence file'
igramList=h5file[kf[0]].keys()
cohList=h5mask['coherence'].keys()
gg = h5file2.create_group(kf[0])
for igram in igramList:
print igram
date12 = h5file[kf[0]][igram].attrs['DATE12']
for cohFile in cohList:
if h5mask['coherence'][cohFile].attrs['DATE12']==date12:
igramCoh=cohFile
print igramCoh
unwset = h5file[kf[0]][igram].get(igram)
unw=unwset[0:unwset.shape[0],0:unwset.shape[1]]
cohset=h5mask['coherence'][igramCoh].get(igramCoh)
coh=cohset[0:cohset.shape[0],0:cohset.shape[1]]
unw[coh<thr]=np.nan
group = gg.create_group(igram)
dset = group.create_dataset(igram, data=unw, compression='gzip')
for key, value in h5file[kf[0]][igram].attrs.iteritems():
group.attrs[key] = value
try:
#if kf[0] == 'interferograms':
mask = h5file['mask'].get('mask')
gm = h5file2.create_group('mask')
dset = gm.create_dataset('mask', data=mask, compression='gzip')
except: print 'no mask group found.'
elif kf[0] in ('interferograms','wrapped') and 'coherence' not in h5mask.keys():
print 'Masking the '+kf[0]
igramList=h5file[kf[0]].keys()
gg = h5file2.create_group(kf[0])
for igram in igramList:
print igram
unwset = h5file[kf[0]][igram].get(igram)
unw=unwset[0:unwset.shape[0],0:unwset.shape[1]]
try: unw[M<thr] = np.nan
except: unw[M==0] = np.nan
group = gg.create_group(igram)
dset = group.create_dataset(igram, data=unw, compression='gzip')
for key, value in h5file[kf[0]][igram].attrs.iteritems():
group.attrs[key] = value
try:
#if kf[0] == 'interferograms':
mask = h5file['mask'].get('mask')
gm = h5file2.create_group('mask')
dset = gm.create_dataset('mask', data=mask, compression='gzip')
except: print 'no mask group found.'
h5file.close()
h5mask.close()
h5file2.close()
################################ ROI_PAC ######################################
elif ext in ['.unw','.int']:
import pysar._readfile as readfile
import pysar._writefile as writefile
Mext = os.path.splitext(maskFile)[1]
if Mext == '.cor':
a,M,atr = readfile.read_float32(maskFile)
elif Mext == '.h5':
h5mask=h5py.File(maskFile,'r')
Mset=h5mask[h5mask.keys()[0]].get(h5mask.keys()[0])
M=Mset[0:Mset.shape[0],0:Mset.shape[1]]
else: sys.exit(['Un-recoganized mask file extension: '+Mext])
try: MaskedFile
except: MaskedFile = File.split('.')[0]+'_masked'+ext
a,unw,atr = readfile.read_float32(File)
try: unw[M<thr] = np.nan
except: unw[M==0] = np.nan
print 'writting >>> '+MaskedFile
writefile.write_float32(unw,MaskedFile)
f = open(MaskedFile+'.rsc','w')
for k in atr.keys(): f.write(k+' '+atr[k]+'\n')
f.close()
try: h5mask.close()
except: pass
def main(argv):
try:
file=argv[0]
alks=float(argv[1])
rlks=float(argv[2])
except:
try:
file=argv[0]
alks=float(argv[1])
rlks=float(argv[1])
except: Usage();sys.exit(1)
ext = os.path.splitext(file)[1]
outName=file.split('.')[0]+'_a'+str(int(alks))+'lks_r'+str(int(rlks))+'lks'+ext
################################################################################
if ext == '.h5':
import h5py
h5file_mli=h5py.File(outName,'w')
h5file=h5py.File(file,'r')
k=h5file.keys()
if 'interferograms' in k: k[0] = 'interferograms'
elif 'coherence' in k: k[0] = 'coherence'
elif 'timeseries' in k: k[0] = 'timeseries'
if k[0] in ['interferograms','coherence','wrapped']:
print 'Multilooking the interferograms'
gg = h5file_mli.create_group(k[0])
igramList=h5file[k[0]].keys()
for igram in igramList:
print igram
unw = h5file[k[0]][igram].get(igram)
unwlks=multilook(unw,alks,rlks)
group = gg.create_group(igram)
dset = group.create_dataset(igram, data=unwlks, compression='gzip')
for key, value in h5file[k[0]][igram].attrs.iteritems():
group.attrs[key] = value
group.attrs['WIDTH'] = unwlks.shape[1]
group.attrs['FILE_LENGTH'] = unwlks.shape[0]
try:
group.attrs['Y_STEP']=alks*float(group.attrs['Y_STEP'])
group.attrs['X_STEP']=rlks*float(group.attrs['X_STEP'])
except:
group.attrs['AZIMUTH_PIXEL_SIZE'] = alks*float(group.attrs['AZIMUTH_PIXEL_SIZE'])
group.attrs['RANGE_PIXEL_SIZE'] = rlks*float(group.attrs['RANGE_PIXEL_SIZE'])
try:
dset1=h5file['mask'].get('mask')
mask=dset1[0:dset1.shape[0],0:dset1.shape[1]]
masklks=multilook(mask,alks,rlks)
group=h5file_mli.create_group('mask')
dset = group.create_dataset('mask', data=masklks, compression='gzip')
except: print 'No mask group found.'
elif k[0] in ['timeseries','temporal_coherence', 'velocity', 'mask', 'rmse']:
print 'Multilooking '+k[0]
group = h5file_mli.create_group(k[0])
if k[0] == 'timeseries':
dateList=h5file[k[0]].keys()
for d in dateList:
print d
unw = h5file[k[0]].get(d)
unwlks=multilook(unw,alks,rlks)
dset = group.create_dataset(d, data=unwlks, compression='gzip')
elif k[0] in ['temporal_coherence', 'velocity', 'mask', 'rmse']:
dset1 = h5file[k[0]].get(k[0])
unw = dset1[0:dset1.shape[0],0:dset1.shape[1]]
unwlks=multilook(unw,alks,rlks)
dset = group.create_dataset(k[0], data=unwlks, compression='gzip')
try:
dset1 = h5file['mask'].get('mask')
Mask = dset1[0:dset1.shape[0],0:dset1.shape[1]]
Masklks=multilook(Mask,alks,rlks)
group=h5file_mli.create_group('mask')
dset = group.create_dataset('mask', data=Masklks, compression='gzip')
except: print 'No mask group found.'
## Update attributes
for key,value in h5file[k[0]].attrs.iteritems(): group.attrs[key] = value
group.attrs['WIDTH'] = unwlks.shape[1]
group.attrs['FILE_LENGTH'] = unwlks.shape[0]
try:
group.attrs['Y_STEP']=alks*float(group.attrs['Y_STEP'])
group.attrs['X_STEP']=rlks*float(group.attrs['X_STEP'])
except:
group.attrs['AZIMUTH_PIXEL_SIZE'] = alks*float(group.attrs['AZIMUTH_PIXEL_SIZE'])
group.attrs['RANGE_PIXEL_SIZE'] = rlks*float(group.attrs['RANGE_PIXEL_SIZE'])
h5file.close()
h5file_mli.close()
################################################################################
elif ext in ['.unw','.cor','.hgt','.dem','.trans'] or\
ext in ['.jpeg','.jpg','.png','.ras','.bmp'] or\
ext in ['.mli','.slc']:
import pysar._readfile as readfile
import pysar._writefile as writefile
r = readfile.read_rsc_file(file + '.rsc')
if ext == '.int' or ext == '.slc':
a,p,r = readfile.read_complex64(file)
pmli=multilook(p,alks,rlks)
amli=multilook(a,alks,rlks)
r['FILE_LENGTH']=str(pmli.shape[0])
r['WIDTH'] =str(pmli.shape[1])
elif ext == '.unw' or ext == '.cor' or ext == '.hgt':
a,p,r = readfile.read_float32(file)
pmli=multilook(p,alks,rlks)
amli=multilook(a,alks,rlks)
print 'writing >>>'+outName
writefile.write_float32(pmli,outName)
r['FILE_LENGTH']=str(pmli.shape[0])
r['WIDTH'] =str(pmli.shape[1])
elif ext == ('.dem'):
d,r = readfile.read_dem(file)
dmli=multilook(d,alks,rlks)
print 'writing >>>'+outName
writefile.write_dem(dmli,outName)
r['FILE_LENGTH']=str(dmli.shape[0])
r['WIDTH'] =str(dmli.shape[1])
elif ext in ['.jpeg','.jpg','.png','.bmp']:
import Image
im = Image.open(file)
width = im.size[0] / int(rlks)
height = im.size[1] / int(alks)
imlks = im.resize((width, height), Image.NEAREST)
print 'writing >>>'+outName
imlks.save(outName)
r['FILE_LENGTH']=str(height)
r['WIDTH'] =str(width)
## Update attributes
r['XMAX']=str(int(r['WIDTH']) - 1)
r['YMAX']=str(int(r['FILE_LENGTH']) - 1)
try:
r['Y_STEP']=str(float(r['Y_STEP'])*alks)
r['X_STEP']=str(float(r['X_STEP'])*rlks)
except:
r['AZIMUTH_PIXEL_SIZE'] = alks*float(r['AZIMUTH_PIXEL_SIZE'])
r['RANGE_PIXEL_SIZE'] = rlks*float(r['RANGE_PIXEL_SIZE'])
f = open(outName+'.rsc','w')
for k in r.keys():
f.write(k+' '+r[k]+'\n')
f.close()
def main(argv):
try:
File = argv[0]
demFile=argv[1]
p=int(argv[2])
except:
Usage() ; sys.exit(1)
try: baseline_error=argv[3]
except: baseline_error='range_and_azimuth'
print baseline_error
##################################
h5file = h5py.File(File)
dateList = h5file['timeseries'].keys()
##################################
try: maskFile=argv[4]
except:
if os.path.isfile('Modified_Mask.h5'): maskFile = 'Modified_Mask.h5'
elif os.path.isfile('Mask.h5'): maskFile = 'Mask.h5'
else: print 'No mask found!'; sys.exit(1)
try: Mask,Matr = readfile.read(maskFile); print 'mask: '+maskFile
except: print 'Can not open mask file: '+maskFile; sys.exit(1)
#try:
# maskFile=argv[4]
# h5Mask = h5py.File(maskFile,'r')
# kMask=h5Mask.keys()
# dset1 = h5Mask[kMask[0]].get(kMask[0])
# Mask = dset1[0:dset1.shape[0],0:dset1.shape[1]]
#except:
# dset1 = h5file['mask'].get('mask')
# Mask = dset1[0:dset1.shape[0],0:dset1.shape[1]]
##################################
Mask=Mask.flatten(1)
ndx= Mask !=0
##################################
# h5file = h5py.File(File)
# dateList = h5file['timeseries'].keys()
##################################
nt=float(h5file['timeseries'].attrs['LOOK_REF1'])
ft=float(h5file['timeseries'].attrs['LOOK_REF2'])
sy,sx=np.shape(dset1)
npixel=sx*sy
lookangle=np.tile(np.linspace(nt,ft,sx),[sy,1])
lookangle=lookangle.flatten(1)*np.pi/180.0
Fh=-np.sin(lookangle)
Fv=-np.cos(lookangle)
print 'Looking for azimuth pixel size'
try:
daz=float(h5file['timeseries'].attrs['AZIMUTH_PIXEL_SIZE'])
except:
print'''
ERROR!
The attribute AZIMUTH_PIXEL_SIZE was not found!
Possible cause of error: Geo coordinate.
This function works only in radar coordinate system.
'''
sys.exit(1)
lines=np.tile(np.arange(0,sy,1),[1,sx])
lines=lines.flatten(1)
rs=lines*daz
if baseline_error=='range_and_azimuth':
A = np.zeros([npixel,4])
A[:,0]=Fh
A[:,1]=Fh*rs
A[:,2]=Fv
A[:,3]=Fv*rs
num_base_par=4
elif baseline_error=='range':
A = np.zeros([npixel,2])
A[:,0]=Fh
A[:,1]=Fv
num_base_par=2
###########################################
yref=int(h5file['timeseries'].attrs['ref_y'])
xref=int(h5file['timeseries'].attrs['ref_x'])
###########################################
if os.path.basename(demFile).split('.')[1]=='hgt':
amp,dem,demRsc = readfile.read_float32(demFile)
elif os.path.basename(demFile).split('.')[1]=='dem':
dem,demRsc = readfile.read_real_int16(demFile)
dem=dem-dem[yref][xref]
dem=dem.flatten(1)
###################################################
if p==1:
# A=np.vstack((dem[ndx],np.ones(len(dem[ndx])))).T
B = np.vstack((dem,np.ones(len(dem)))).T
elif p==2:
# A=np.vstack((dem[ndx]**2,dem[ndx],np.ones(len(dem[ndx])))).T
B = np.vstack((dem**2,dem,np.ones(len(dem)))).T
elif p==3:
# A = np.vstack((dem[ndx]**3,dem[ndx]**2,dem[ndx],np.ones(len(dem[ndx])))).T
B = np.vstack((dem**3,dem**2,dem,np.ones(len(dem)))).T
print np.shape(A)
Ainv=np.linalg.pinv(A)
###################################################
Bh=[]
Bv=[]
Bhrate=[]
Bvrate=[]
Be=np.zeros([len(dateList),num_base_par+p+1])
print '%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%'
for i in range(1,len(dateList)):
dset = h5file['timeseries'].get(dateList[i])
data = dset[0:dset.shape[0],0:dset.shape[1]]
L = data.flatten(1)
M=np.hstack((A,B))
Berror=np.dot(np.linalg.pinv(M[ndx]),L[ndx])
Bh.append(Berror[0])
Bhrate.append(Berror[1])
Bv.append(Berror[2])
Bvrate.append(Berror[3])
Be[i,:]=Berror
print Berror
print '%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%'
print 'baseline error mean std'
print ' bh : ' +str(np.mean(Bh)) + ' , '+str(np.std(Bh))
print ' bh rate : ' +str(np.mean(Bhrate)) + ' , '+str(np.std(Bhrate))
print ' bv : ' +str(np.mean(Bv)) + ' , '+str(np.std(Bv))
print ' bv rate : ' +str(np.mean(Bvrate)) + ' , '+str(np.std(Bvrate))
print '%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%'
# plt.hist(Bh,bins=8,normed=True)
# formatter = FuncFormatter(to_percent)
# Set the formatter
# plt.gca().yaxis.set_major_formatter(formatter)
# plt.show()
print '%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%'
# print 'Estimating Baseline error from each differences ...'
orbEffect=np.zeros([len(dateList),sy,sx])
for i in range(1,len(dateList)):
effect=np.dot(M,Be[i,:])
effect=np.reshape(effect,[sx,sy]).T
# orbEffect[i,:,:]=orbEffect[i-1,:,:]+effect
# orbEffect[i,:,:]=orbEffect[i,:,:]-orbEffect[i,yref,xref]
orbEffect[i,:,:]=effect - effect[yref,xref]
del effect
print 'Correctiing the time series '
outName=File.replace('.h5','')+'_BaseTropCor.h5'
h5orbCor=h5py.File(outName,'w')
group = h5orbCor.create_group('timeseries')
for i in range(len(dateList)):
dset1 = h5file['timeseries'].get(dateList[i])
data = dset1[0:dset1.shape[0],0:dset1.shape[1]] - orbEffect[i,:,:]
dset = group.create_dataset(dateList[i], data=data, compression='gzip')
for key,value in h5file['timeseries'].attrs.iteritems():
group.attrs[key] = value
dset1 = h5file['mask'].get('mask')
group=h5orbCor.create_group('mask')
dset = group.create_dataset('mask', data=dset1, compression='gzip')
h5file.close()
h5orbCor.close()
def main(argv):
try:
templateFile = argv[1]
except:
Usage()
sys.exit(1)
from pysar._pysar_utilities import check_variable_name
templateContents = readfile.read_template(templateFile)
projectName = os.path.basename(templateFile).partition(".")[0]
try:
processProjectDir = argv[2]
tssarProjectDir = argv[3]
except:
if os.getenv("PARENTDIR"):
processProjectDir = os.getenv("SCRATCHDIR") + "/" + projectName + "/PROCESS"
tssarProjectDir = os.getenv("SCRATCHDIR") + "/" + projectName + "/TSSAR"
else:
processProjectDir = os.getenv("PROCESSDIR") + "/" + projectName
tssarProjectDir = os.getenv("TSSARDIR") + "/" + projectName
print "\n*************** Loading Data into PySAR ****************"
print "PROCESS directory: " + processProjectDir
print "TSSAR directory: " + tssarProjectDir
if not os.path.isdir(tssarProjectDir):
os.mkdir(tssarProjectDir)
########### Use defaults if paths not given in template file #########
import h5py
import numpy as np
optionName = {}
optionName["interferograms"] = "pysar.inputFiles"
optionName["coherence"] = "pysar.corFiles"
optionName["wrapped"] = "pysar.wrappedFiles"
optionName["geomap"] = "pysar.geomap"
optionName["demGeo"] = "pysar.dem.geoCoord"
optionName["demRdr"] = "pysar.dem.radarCoord"
try:
igramPath = templateContents["pysar.inputFiles"]
igramPath = check_variable_name(igramPath)
except:
igramPath = processProjectDir + "/DONE/IFGRAM*/filt_*.unw"
print "Path pattern for unwrapped interferogram: " + igramPath
# except: igramPath = os.getenv('SCRATCHDIR') + '/' + projectName + '/PROCESS/DONE/IFGRAM*/filt_*.unw'
try:
corPath = templateContents["pysar.corFiles"]
corPath = check_variable_name(corPath)
except:
corPath = processProjectDir + "/DONE/IFGRAM*/filt_*rlks.cor"
print "Path pattern for coherence: " + corPath
try:
wrapPath = templateContents["pysar.wrappedFiles"]
wrapPath = check_variable_name(wrapPath)
except:
wrapPath = processProjectDir + "/DONE/IFGRAM*/filt_*rlks.int"
print "Path pattern for wrapped interferogram: " + wrapPath
# try: demRdrPath = templateContents['pysar.dem.radarCoord']; demRdrPath = check_variable_name(demRdrPath)
# except:
# demRdrList=glob.glob(demRdrPath)
###########################################################################
######################### Unwrapped Interferograms ########################
try:
if os.path.isfile(tssarProjectDir + "/LoadedData.h5"):
print "\nLoadedData.h5" + " already exists."
sys.exit(1)
igramList = glob.glob(igramPath)
igramList = sorted(igramList)
k = "interferograms"
check_number(k, optionName[k], igramList) # number check
print "loading interferograms ..."
igramList, mode_width, mode_length = check_size(k, igramList) # size check
igramList = sorted(igramList)
h5file = tssarProjectDir + "/LoadedData.h5"
f = h5py.File(h5file, "w")
gg = f.create_group("interferograms")
MaskZero = np.ones([int(mode_length), int(mode_width)])
for igram in igramList:
if not os.path.basename(igram) in f:
print "Adding " + igram
group = gg.create_group(os.path.basename(igram))
amp, unw, unwrsc = readfile.read_float32(igram)
MaskZero *= amp
dset = group.create_dataset(os.path.basename(igram), data=unw, compression="gzip")
for key, value in unwrsc.iteritems():
group.attrs[key] = value
d1, d2 = unwrsc["DATE12"].split("-")
baseline_file = os.path.dirname(igram) + "/" + d1 + "_" + d2 + "_baseline.rsc"
baseline = readfile.read_roipac_rsc(baseline_file)
for key, value in baseline.iteritems():
group.attrs[key] = value
group.attrs["PROJECT_NAME"] = projectName
group.attrs["UNIT"] = "radian"
else:
print os.path.basename(h5file) + " already contains " + os.path.basename(igram)
Mask = np.ones([int(mode_length), int(mode_width)])
Mask[MaskZero == 0] = 0
# gm = f.create_group('mask')
# dset = gm.create_dataset('mask', data=Mask, compression='gzip')
f.close()
############## Mask file ###############
print "writing to Mask.h5\n"
# Mask=np.ones([int(mode_length),int(mode_width)])
# Mask[MaskZero==0]=0
h5file = tssarProjectDir + "/Mask.h5"
h5mask = h5py.File(h5file, "w")
group = h5mask.create_group("mask")
dset = group.create_dataset(os.path.basename("mask"), data=Mask, compression="gzip")
for key, value in unwrsc.iteritems():
group.attrs[key] = value
h5mask.close()
except:
print "No unwrapped interferogram is loaded.\n"
########################################################################
############################# Coherence ################################
try:
if os.path.isfile(tssarProjectDir + "/Coherence.h5"):
print "\nCoherence.h5" + " already exists."
sys.exit(1)
corList = glob.glob(corPath)
corList = sorted(corList)
k = "coherence"
check_number(k, optionName[k], corList) # number check
print "loading coherence files ..."
corList, mode_width, mode_length = check_size(k, corList) # size check
corList = sorted(corList)
h5file = tssarProjectDir + "/Coherence.h5"
fcor = h5py.File(h5file, "w")
gg = fcor.create_group("coherence")
meanCoherence = np.zeros([int(mode_length), int(mode_width)])
for cor in corList:
if not os.path.basename(cor) in fcor:
print "Adding " + cor
group = gg.create_group(os.path.basename(cor))
amp, unw, unwrsc = readfile.read_float32(cor)
meanCoherence += unw
dset = group.create_dataset(os.path.basename(cor), data=unw, compression="gzip")
for key, value in unwrsc.iteritems():
group.attrs[key] = value
d1, d2 = unwrsc["DATE12"].split("-")
baseline_file = os.path.dirname(cor) + "/" + d1 + "_" + d2 + "_baseline.rsc"
baseline = readfile.read_roipac_rsc(baseline_file)
for key, value in baseline.iteritems():
group.attrs[key] = value
group.attrs["PROJECT_NAME"] = projectName
group.attrs["UNIT"] = "1"
else:
print os.path.basename(h5file) + " already contains " + os.path.basename(cor)
# fcor.close()
########### mean coherence file ###############
meanCoherence = meanCoherence / (len(corList))
print "writing meanCoherence group to the coherence h5 file"
gc = fcor.create_group("meanCoherence")
dset = gc.create_dataset("meanCoherence", data=meanCoherence, compression="gzip")
print "writing average_spatial_coherence.h5\n"
h5file_CorMean = tssarProjectDir + "/average_spatial_coherence.h5"
fcor_mean = h5py.File(h5file_CorMean, "w")
group = fcor_mean.create_group("mask")
dset = group.create_dataset(os.path.basename("mask"), data=meanCoherence, compression="gzip")
for key, value in unwrsc.iteritems():
group.attrs[key] = value
fcor_mean.close()
fcor.close()
except:
print "No correlation file is loaded.\n"
##############################################################################
########################## Wrapped Interferograms ############################
try:
if os.path.isfile(tssarProjectDir + "/Wrapped.h5"):
print "\nWrapped.h5" + " already exists."
sys.exit(1)
wrapList = glob.glob(wrapPath)
wrapList = sorted(wrapList)
k = "wrapped"
check_number(k, optionName[k], wrapList) # number check
print "loading wrapped phase ..."
wrapList, mode_width, mode_length = check_size(k, wrapList) # size check
wrapList = sorted(wrapList)
h5file = tssarProjectDir + "/Wrapped.h5"
fw = h5py.File(h5file, "w")
gg = fw.create_group("wrapped")
for wrap in wrapList:
if not os.path.basename(wrap) in fw:
print "Adding " + wrap
group = gg.create_group(os.path.basename(wrap))
amp, unw, unwrsc = readfile.read_complex_float32(wrap)
dset = group.create_dataset(os.path.basename(wrap), data=unw, compression="gzip")
for key, value in unwrsc.iteritems():
group.attrs[key] = value
d1, d2 = unwrsc["DATE12"].split("-")
baseline_file = os.path.dirname(wrap) + "/" + d1 + "_" + d2 + "_baseline.rsc"
baseline = readfile.read_roipac_rsc(baseline_file)
for key, value in baseline.iteritems():
group.attrs[key] = value
group.attrs["PROJECT_NAME"] = projectName
group.attrs["UNIT"] = "radian"
else:
print os.path.basename(h5file) + " already contains " + os.path.basename(wrap)
fw.close()
print "Writed " + str(len(wrapList)) + " wrapped interferograms to " + h5file + "\n"
except:
print "No wrapped interferogram is loaded.\n"
##############################################################################
################################# geomap.trans ###############################
try:
geomapPath = tssarProjectDir + "/geomap*.trans"
geomapList = glob.glob(geomapPath)
if len(geomapList) > 0:
print "\ngeomap*.trans" + " already exists."
sys.exit(1)
geomapPath = templateContents["pysar.geomap"]
geomapPath = check_variable_name(geomapPath)
geomapList = glob.glob(geomapPath)
cpCmd = "cp " + geomapList[0] + " " + tssarProjectDir
print cpCmd
os.system(cpCmd)
cpCmd = "cp " + geomapList[0] + ".rsc " + tssarProjectDir
print cpCmd + "\n"
os.system(cpCmd)
except:
# print "*********************************"
print "no geomap file is loaded.\n"
# print "*********************************\n"
##############################################################################
################################## DEM #####################################
try:
demRdrPath = tssarProjectDir + "/radar*.hgt"
demRdrList = glob.glob(demRdrPath)
if len(demRdrList) > 0:
print "\nradar*.hgt" + " already exists."
sys.exit(1)
demRdrPath = templateContents["pysar.dem.radarCoord"]
demRdrPath = check_variable_name(demRdrPath)
demRdrList = glob.glob(demRdrPath)
cpCmd = "cp " + demRdrList[0] + " " + tssarProjectDir
print cpCmd
os.system(cpCmd)
cpCmd = "cp " + demRdrList[0] + ".rsc " + tssarProjectDir
print cpCmd + "\n"
os.system(cpCmd)
except:
# print "*********************************"
print "no DEM (radar coordinate) file is loaded.\n"
# print "*********************************"
try:
demGeoPath = tssarProjectDir + "/*.dem"
demGeoList = glob.glob(demGeoPath)
if len(demGeoList) > 0:
print "\n*.dem" + " already exists."
sys.exit(1)
demGeoPath = templateContents["pysar.dem.geoCoord"]
demGeoPath = check_variable_name(demGeoPath)
demGeoList = glob.glob(demGeoPath)
cpCmd = "cp " + demGeoList[0] + " " + tssarProjectDir
print cpCmd
os.system(cpCmd)
cpCmd = "cp " + demGeoList[0] + ".rsc " + tssarProjectDir
print cpCmd + "\n"
os.system(cpCmd)
except:
# print "*********************************"
print "no DEM (geo coordinate) file is loaded.\n"
def main(argv):
try:
opts, args = getopt.getopt(argv, "h:f:t:p:")
except getopt.GetoptError:
usage()
sys.exit(1)
if opts == []:
usage()
sys.exit(1)
for opt, arg in opts:
if opt in ("-h", "--help"):
usage()
sys.exit()
elif opt == '-f':
file = arg
elif opt == '-t':
filtType = arg
elif opt == '-p':
par = arg
ext = os.path.splitext(file)[1]
outName = file.split('.')[0] + '_' + filtType + ext
try:
par
except:
par = []
#print '+++++++++++++++++++++++++++'
print 'Filter type : ' + filtType
print 'parameters : ' + str(par)
#print '+++++++++++++++++++++++++++'
###############################################
if ext == '.int' or ext == '.slc':
a, p, r = readfile.read_complex_float32(file)
plks = multilook(p, alks, rlks)
alks = multilook(a, alks, rlks)
r['FILE_LENGTH'] = str(dlks.shape[0])
r['WIDTH'] = str(dlks.shape[1])
r['XMAX'] = str(int(r['WIDTH']) - 1)
r['YMAX'] = str(int(r['FILE_LENGTH']) - 1)
try:
r['Y_STEP'] = str(float(r['Y_STEP']) * alks)
r['X_STEP'] = str(float(r['X_STEP']) * rlks)
except:
Geo = 0
f = open(outName + '.rsc', 'w')
for k in r.keys():
f.write(k + ' ' + r[k] + '\n')
f.close()
elif ext == '.unw' or ext == '.cor' or ext == '.hgt':
a, p, r = readfile.read_float32(file)
plks = multilook(p, alks, rlks)
alks = multilook(a, alks, rlks)
writefile.write_float32(plks, outName)
r['FILE_LENGTH'] = str(dlks.shape[0])
r['WIDTH'] = str(dlks.shape[1])
r['XMAX'] = str(int(r['WIDTH']) - 1)
r['YMAX'] = str(int(r['FILE_LENGTH']) - 1)
try:
r['Y_STEP'] = str(float(r['Y_STEP']) * alks)
r['X_STEP'] = str(float(r['X_STEP']) * rlks)
except:
Geo = 0
f = open(outName + '.rsc', 'w')
for k in r.keys():
f.write(k + ' ' + r[k] + '\n')
f.close()
elif ext == ('.dem'):
d, r = readfile.read_real_int16(file)
dlks = multilook(d, alks, rlks)
print 'writing ' + outName
writefile.write_real_int16(dlks, outName)
r['FILE_LENGTH'] = str(dlks.shape[0])
r['WIDTH'] = str(dlks.shape[1])
r['XMAX'] = str(int(r['WIDTH']) - 1)
r['YMAX'] = str(int(r['FILE_LENGTH']) - 1)
try:
r['Y_STEP'] = str(float(r['Y_STEP']) * alks)
r['X_STEP'] = str(float(r['X_STEP']) * rlks)
except:
Geo = 0
f = open(outName + '.rsc', 'w')
for k in r.keys():
f.write(k + ' ' + r[k] + '\n')
f.close()
elif ext in ['.jpeg', 'jpg', 'png']:
im = Image.open(file)
width = im.size[0] / int(rlks)
height = im.size[1] / int(alks)
imlks = im.resize((width, height), Image.NEAREST)
print 'writing ' + outName
imlks.save(outName)
try:
r = readfile.read_roipac_rsc(file + '.rsc')
except:
sys.exit(1)
r['FILE_LENGTH'] = str(height)
r['WIDTH'] = str(width)
r['XMAX'] = str(int(r['WIDTH']) - 1)
r['YMAX'] = str(int(r['FILE_LENGTH']) - 1)
try:
r['Y_STEP'] = str(float(r['Y_STEP']) * alks)
r['X_STEP'] = str(float(r['X_STEP']) * rlks)
except:
Geo = 0
f = open(outName + '.rsc', 'w')
for k in r.keys():
f.write(k + ' ' + r[k] + '\n')
f.close()
elif ext == ('.h5'):
h5file = h5py.File(file, 'r')
# outName=file.split('.')[0]+'_a'+str(int(alks))+'lks_r'+str(int(rlks))+'lks.h5'
h5file_lks = h5py.File(outName, 'w')
if 'interferograms' in h5file.keys():
print 'Filtering the interferograms in space'
gg = h5file_lks.create_group('interferograms')
igramList = h5file['interferograms'].keys()
for igram in igramList:
print igram
unwSet = h5file['interferograms'][igram].get(igram)
unw = unwSet[0:unwSet.shape[0], 0:unwSet.shape[1]]
unw = filter(unw, filtType, par)
group = gg.create_group(igram)
dset = group.create_dataset(igram,
data=unw,
compression='gzip')
for key, value in h5file['interferograms'][
igram].attrs.iteritems():
group.attrs[key] = value
dset1 = h5file['mask'].get('mask')
mask = dset1[0:dset1.shape[0], 0:dset1.shape[1]]
group = h5file_lks.create_group('mask')
dset = group.create_dataset('mask', data=mask, compression='gzip')
elif 'timeseries' in h5file.keys():
print 'Filtering the time-series'
group = h5file_lks.create_group('timeseries')
dateList = h5file['timeseries'].keys()
for d in dateList:
print d
dset1 = h5file['timeseries'].get(d)
data = dset1[0:dset1.shape[0], 0:dset1.shape[1]]
data = filter(data, filtType, par)
dset = group.create_dataset(d, data=data, compression='gzip')
for key, value in h5file['timeseries'].attrs.iteritems():
group.attrs[key] = value
try:
dset1 = h5file['mask'].get('mask')
Mask = dset1[0:dset1.shape[0], 0:dset1.shape[1]]
# Masklks=multilook(Mask,alks,rlks)
group = h5file_lks.create_group('mask')
dset = group.create_dataset('mask',
data=Mask,
compression='gzip')
except:
print 'Filterd file does not include the maske'
elif 'temporal_coherence' in h5file.keys(
) or 'velocity' in h5file.keys() or 'mask' in h5file.keys():
k = h5file.keys()
print 'filtering the ' + k[0]
group = h5file_lks.create_group(k[0])
dset1 = h5file[k[0]].get(k[0])
data = dset1[0:dset1.shape[0], 0:dset1.shape[1]]
data = filter(data, filtType, par)
dset = group.create_dataset(k[0], data=data, compression='gzip')
for key, value in h5file[k[0]].attrs.iteritems():
group.attrs[key] = value
h5file.close()
h5file_lks.close()
print 'writing >>> ' + outName
def main(argv):
if len(sys.argv)>2:
try:
opts, args = getopt.getopt(argv,"h:f:x:y:o:l:L:")
except getopt.GetoptError:
print 'Error while getting args'
Usage() ; sys.exit(1)
for opt,arg in opts:
if opt in ("-h","--help"): Usage() ; sys.exit()
elif opt == '-f': File = arg
elif opt == '-y': ysub = [int(i) for i in arg.split(':')]; ysub.sort()
elif opt == '-x': xsub = [int(i) for i in arg.split(':')]; xsub.sort()
elif opt == '-o': outName=arg
elif opt == '-l': Latsub = [float(i) for i in arg.split(':')]; Latsub.sort()
elif opt == '-L': Lonsub = [float(i) for i in arg.split(':')]; Lonsub.sort()
else: Usage(); sys.exit(1)
try: outName
except: outName='subset_'+File
ext = os.path.splitext(File)[1]
############################################################################
################################# PySAR ##################################
if ext == '.h5':
try: h5file=h5py.File(File,'r')
except: Usage() ; sys.exit(1)
k=h5file.keys()
if 'interferograms' in k: k[0] = 'interferograms'
elif 'coherence' in k: k[0] = 'coherence'
elif 'timeseries' in k: k[0] = 'timeseries'
if k[0] in ('interferograms','coherence','wrapped'):
atr = h5file[k[0]][h5file[k[0]].keys()[0]].attrs
elif k[0] in ('dem','velocity','mask','temporal_coherence','rmse','timeseries'):
atr = h5file[k[0]].attrs
############# Subset Option #############
width=int(atr['WIDTH'])
length=int(atr['FILE_LENGTH'])
try:
Latsub
try:
lat_step = float(atr['Y_STEP'])
lat1 = float(atr['Y_FIRST'])
lat0 = lat1 + length*lat_step
if Latsub[0]<lat0: Latsub[0]=lat0; print 'WARNING: input latitude < min ('+str(lat0)+')! Set it to min.'
if Latsub[1]>lat1: Latsub[1]=lat1; print 'WARNING: input latitude > max ('+str(lat1)+')! Set it to max.'
print 'subset in latitude - '+str(Latsub[0])+':'+str(Latsub[1])
ysub=[0]*2
ysub[0] = int((Latsub[1]-lat1)/lat_step)
ysub[1] = int((Latsub[0]-lat1)/lat_step)
except:
print 'Not geocoded file, cannot be subseted with LatLon.'
Usage() ; return
except:
try:
ysub
if ysub[0]<0: ysub[0]=0; print 'WARNING: input y < min (0)! Set it to min.'
if ysub[1]>length: ysub[1]=length; print 'WARNING: input y > max ('+str(length)+')! Set it to max.'
print 'subset in y direction - '+str(ysub[0])+':'+str(ysub[1])
except: ysub = [0,length]
try:
Lonsub
try:
lon_step = float(atr['X_STEP'])
lon0 = float(atr['X_FIRST'])
lon1 = lon0 + width*lon_step
if Lonsub[0]<lon0: Lonsub[0]=lon0; print 'WARNING: input longitude < min ('+str(lon0)+')! Set it to min.'
if Lonsub[1]>lon1: Lonsub[1]=lon1; print 'WARNING: input longitude > max ('+str(lon1)+')! Set it to max.'
print 'subset in longitude - '+str(Lonsub[0])+':'+str(Lonsub[1])
xsub=[0]*2
xsub[0]=int((Lonsub[0]-lon0)/lon_step)
xsub[1]=int((Lonsub[1]-lon0)/lon_step)
except:
print 'Not geocoded file, cannot be subseted with LatLon.'
Usage() ; return
except:
try:
xsub
if xsub[0]<0: xsub[0]=0; print 'WARNING: input x < min (0)! Set it to min.'
if xsub[1]>width: xsub[1]=width; print 'WARNING: input x > max ('+str(width)+')! Set it to max x.'
print 'subset in x direction - '+str(xsub[0])+':'+str(xsub[1])
except: xsub = [0,width]
if ysub[0]>length or ysub[1]<0 or xsub[0]>length or xsub[1]<0:
print 'ERROR: input index is out of data range!'
print 'range in rdr: x - 0:'+str(width)+' y - 0:'+str(length)
try: print 'range in geo: lat - '+str(lat0)+':'+str(lat1)+' lon - '+str(lon0)+':'+str(lon1)
except: Geo=0
sys.exit(1)
######## Data Read, Crop and Write #######
##### N dset, N attributes
if k[0] in ('interferograms','coherence','wrapped'):
print 'writing >>> ' +outName
h5out=h5py.File(outName,'w')
gg=h5out.create_group(k[0])
igramList=h5file[k[0]].keys()
for igram in igramList:
print igram
dset1=h5file[k[0]][igram].get(igram)
group=gg.create_group(igram)
dset=group.create_dataset(igram, data=dset1[ysub[0]:ysub[1],xsub[0]:xsub[1]], compression='gzip')
for key, value in h5file[k[0]][igram].attrs.iteritems(): group.attrs[key] = value
group.attrs['FILE_LENGTH']=ysub[1]-ysub[0]
group.attrs['WIDTH'] =xsub[1]-xsub[0]
try:
sub_x0_ori = int(group.attrs['subset_x0'])
group.attrs['subset_x0'] = xsub[0]+sub_x0_ori
group.attrs['subset_x1'] = xsub[1]+sub_x0_ori
except:
group.attrs['subset_x0']=xsub[0]
group.attrs['subset_x1']=xsub[1]
try:
sub_y0_ori = int(group.attrs['subset_y0'])
group.attrs['subset_y0'] = ysub[0]+sub_y0_ori
group.attrs['subset_y1'] = ysub[1]+sub_y0_ori
except:
group.attrs['subset_y0']=ysub[0]
group.attrs['subset_y1']=ysub[1]
if 'X_FIRST' in atr.keys():
group.attrs['X_FIRST']=float(atr['X_FIRST']) + xsub[0]*float(atr['X_STEP'])
group.attrs['Y_FIRST']=float(atr['Y_FIRST']) + ysub[0]*float(atr['Y_STEP'])
## support of old format
try:
Mset=h5file['mask'].get('mask')
gm=h5out.create_group('mask')
dset=gm.create_dataset('mask', data=Mset[ysub[0]:ysub[1],xsub[0]:xsub[1]], compression='gzip')
except: print 'No group for mask found in the file.'
try:
Cset=h5file['meanCoherence'].get('meanCoherence')
gm=h5out.create_group('meanCoherence')
dset=gm.create_dataset('meanCoherence', data=Cset[ysub[0]:ysub[1],xsub[0]:xsub[1]], compression='gzip')
except: print 'No group for meanCoherence found in the file'
h5file.close()
h5out.close()
##### N/1 dset, 1 attributes
elif k[0] in ['timeseries', 'temporal_coherence', 'velocity', 'mask', 'rmse']:
print 'writing >>> ' +outName
h5out=h5py.File(outName,'w')
group=h5out.create_group(k[0])
if k[0] == 'timeseries':
dateList=h5file[k[0]].keys()
for d in dateList:
print d
dset1=h5file[k[0]].get(d)
dset=group.create_dataset(d, data=dset1[ysub[0]:ysub[1],xsub[0]:xsub[1]], compression='gzip')
elif k[0] in ['temporal_coherence', 'velocity', 'mask', 'rmse']:
dset1=h5file[k[0]].get(k[0])
dset=group.create_dataset(k[0],data=dset1[ysub[0]:ysub[1],xsub[0]:xsub[1]],compression='gzip')
## Update attributes
for key, value in h5file[k[0]].attrs.iteritems(): group.attrs[key] = value
group.attrs['FILE_LENGTH']=ysub[1]-ysub[0]
group.attrs['WIDTH'] =xsub[1]-xsub[0]
try:
sub_x0_ori = int(group.attrs['subset_x0'])
group.attrs['subset_x0'] = xsub[0]+sub_x0_ori
group.attrs['subset_x1'] = xsub[1]+sub_x0_ori
except:
group.attrs['subset_x0']=xsub[0]
group.attrs['subset_x1']=xsub[1]
try:
sub_y0_ori = int(group.attrs['subset_y0'])
group.attrs['subset_y0'] = ysub[0]+sub_y0_ori
group.attrs['subset_y1'] = ysub[1]+sub_y0_ori
except:
group.attrs['subset_y0']=ysub[0]
group.attrs['subset_y1']=ysub[1]
if 'X_FIRST' in atr.keys():
group.attrs['X_FIRST']=float(atr['X_FIRST']) + xsub[0]*float(atr['X_STEP'])
group.attrs['Y_FIRST']=float(atr['Y_FIRST']) + ysub[0]*float(atr['Y_STEP'])
h5file.close()
h5out.close()
else:
print 'Error: group of HDF5 file not recogized!'
h5file.close()
Usage() ; sys.exit(1)
############################################################################
######################### ROI_PAC / Image / GAMMA ########################
elif ext in ['.unw','.cor','.hgt','.dem','.trans'] or\
ext in ['.jpeg','.jpg','.png','.ras','.bmp'] or\
ext in ['.mli','.slc']:
try: atr = readfile.read_rsc_file(File + '.rsc')
except:
try: atr = readfile.read_par_file(File + '.par')
except: atr = readfile.read_par_file(os.path.splitext(File)[0] + '.par')
############# Subset Option #############
try: width = int(atr['WIDTH']); length = int(atr['FILE_LENGTH'])
except: width = int(atr['range_samples:']); length = int(atr['azimuth_lines:'])
try:
Latsub
try:
lat_step = float(atr['Y_STEP'])
lat1 = float(atr['Y_FIRST'])
lat0 = lat1 + length*lat_step
if Latsub[0]<lat0: Latsub[0]=lat0; print 'WARNING: input latitude < min ('+str(lat0)+')! Set it to min.'
if Latsub[1]>lat1: Latsub[1]=lat1; print 'WARNING: input latitude > max ('+str(lat1)+')! Set it to max.'
print 'subset in latitude - '+str(Latsub[0])+':'+str(Latsub[1])
ysub=[0]*2
ysub[0] = int((Latsub[1]-lat1)/lat_step)
ysub[1] = int((Latsub[0]-lat1)/lat_step)
except:
print 'Not geocoded file, cannot be subseted with LatLon.'
Usage() ; return
except:
try:
ysub
if ysub[0]<0: ysub[0]=0; print 'WARNING: input y < min (0)! Set it to min.'
if ysub[1]>length: ysub[1]=length; print 'WARNING: input y > max ('+str(length)+')! Set it to max.'
print 'subset in y direction - '+str(ysub[0])+':'+str(ysub[1])
except: ysub = [0,length]
try:
Lonsub
try:
lon_step = float(atr['X_STEP'])
lon0 = float(atr['X_FIRST'])
lon1 = lon0 + width*lon_step
if Lonsub[0]<lon0: Lonsub[0]=lon0; print 'WARNING: input longitude < min ('+str(lon0)+')! Set it to min.'
if Lonsub[1]>lon1: Lonsub[1]=lon1; print 'WARNING: input longitude > max ('+str(lon1)+')! Set it to max.'
print 'subset in longitude - '+str(Lonsub[0])+':'+str(Lonsub[1])
xsub=[0]*2
xsub[0]=int((Lonsub[0]-lon0)/lon_step)
xsub[1]=int((Lonsub[1]-lon0)/lon_step)
except:
print 'Not geocoded file, cannot be subseted with LatLon.'
Usage() ; return
except:
try:
xsub
if xsub[0]<0: xsub[0]=0; print 'WARNING: input x < min (0)! Set it to min.'
if xsub[1]>width: xsub[1]=width; print 'WARNING: input x > max ('+str(width)+')! Set it to max x.'
print 'subset in x direction - '+str(xsub[0])+':'+str(xsub[1])
except: xsub = [0,width]
if ysub[0]>length or ysub[1]<0 or xsub[0]>length or xsub[1]<0:
print 'ERROR: input index is out of data range!'
print 'range in rdr: x - 0:'+str(width)+' y - 0:'+str(length)
try: print 'range in geo: lat - '+str(lat0)+':'+str(lat1)+' lon - '+str(lon0)+':'+str(lon1)
except: Geo=0
sys.exit(1)
######## Data Read, Crop and Write #######
print 'writing >>> '+outName
box = (xsub[0],ysub[0],xsub[1],ysub[1])
if ext in ['.unw','.cor','.hgt']:
a,p,r = readfile.read_float32(File,box)
#p = p[ysub[0]:ysub[1],xsub[0]:xsub[1]]
writefile.write_float32(p,outName)
elif ext == '.dem':
p,r = readfile.read_dem(File)
p = p[ysub[0]:ysub[1],xsub[0]:xsub[1]]
writefile.write_dem(p,outName)
elif ext == '.trans':
a,p,r = readfile.read_float32(File,box)
#a = a[ysub[0]:ysub[1],xsub[0]:xsub[1]]
#p = p[ysub[0]:ysub[1],xsub[0]:xsub[1]]
writefile.write_float32(a,p,outName)
elif ext in ['.jpeg','.jpg','.png','.ras','.bmp']:
import Image
im = Image.open(File)
box = (xsub[0],ysub[0],xsub[1],ysub[1])
output_img = im.crop(box)
output_img.save(outName)
elif ext == '.mli':
d,r = readfile.read_gamma_float(File)
d = d[ysub[0]:ysub[1],xsub[0]:xsub[1]]
writefile.write_gamma_float(d,outName)
elif ext == '.slc':
d,r = readfile.read_gamma_scomplex(File,box)
writefile.write_gamma_scomplex(d,outName)
########### Update .rsc file #############
atr['FILE_LENGTH'] = str(ysub[1]-ysub[0])
atr['WIDTH'] = str(xsub[1]-xsub[0])
atr['XMAX'] = str(width - 1)
atr['YMAX'] = str(length - 1)
try:
sub_x0_ori = int(atr['subset_x0'])
atr['subset_x0'] = str(xsub[0] + sub_x0_ori)
atr['subset_x1'] = str(xsub[1] + sub_x0_ori)
except:
atr['subset_x0'] = str(xsub[0])
atr['subset_x1'] = str(xsub[1])
try:
sub_y0_ori = int(atr['subset_y0'])
atr['subset_y0'] = str(ysub[0] + sub_y0_ori)
atr['subset_y1'] = str(ysub[1] + sub_y0_ori)
except:
atr['subset_y0'] = str(ysub[0])
atr['subset_y1'] = str(ysub[1])
if 'X_FIRST' in atr.keys():
atr['Y_FIRST']=str(float(atr['Y_FIRST'])+ysub[0]*float(atr['Y_STEP']))
atr['X_FIRST']=str(float(atr['X_FIRST'])+xsub[0]*float(atr['X_STEP']))
f = open(outName+'.rsc','w')
for k in atr.keys():
f.write(k+' '+atr[k]+'\n')
f.close()
###########################################################################
else:
print 'File extension not recogized.'
Usage() ; sys.exit(1)
def main(argv):
try:
file = argv[0]
alks = float(argv[1])
rlks = float(argv[2])
except:
try:
file = argv[0]
alks = float(argv[1])
rlks = float(argv[1])
except:
Usage()
sys.exit(1)
ext = os.path.splitext(file)[1]
outName = file.split('.')[0] + '_a' + str(int(alks)) + 'lks_r' + str(
int(rlks)) + 'lks' + ext
################################################################################
if ext == '.h5':
import h5py
h5file_mli = h5py.File(outName, 'w')
h5file = h5py.File(file, 'r')
k = h5file.keys()
if 'interferograms' in k: k[0] = 'interferograms'
elif 'coherence' in k: k[0] = 'coherence'
elif 'timeseries' in k: k[0] = 'timeseries'
if k[0] in ['interferograms', 'coherence', 'wrapped']:
print 'Multilooking the interferograms'
gg = h5file_mli.create_group(k[0])
igramList = h5file[k[0]].keys()
for igram in igramList:
print igram
unw = h5file[k[0]][igram].get(igram)
unwlks = multilook(unw, alks, rlks)
group = gg.create_group(igram)
dset = group.create_dataset(igram,
data=unwlks,
compression='gzip')
for key, value in h5file[k[0]][igram].attrs.iteritems():
group.attrs[key] = value
group.attrs['WIDTH'] = unwlks.shape[1]
group.attrs['FILE_LENGTH'] = unwlks.shape[0]
try:
group.attrs['Y_STEP'] = alks * float(group.attrs['Y_STEP'])
group.attrs['X_STEP'] = rlks * float(group.attrs['X_STEP'])
except:
group.attrs['AZIMUTH_PIXEL_SIZE'] = alks * float(
group.attrs['AZIMUTH_PIXEL_SIZE'])
group.attrs['RANGE_PIXEL_SIZE'] = rlks * float(
group.attrs['RANGE_PIXEL_SIZE'])
try:
dset1 = h5file['mask'].get('mask')
mask = dset1[0:dset1.shape[0], 0:dset1.shape[1]]
masklks = multilook(mask, alks, rlks)
group = h5file_mli.create_group('mask')
dset = group.create_dataset('mask',
data=masklks,
compression='gzip')
except:
print 'No mask group found.'
elif k[0] in [
'timeseries', 'temporal_coherence', 'velocity', 'mask', 'rmse'
]:
print 'Multilooking ' + k[0]
group = h5file_mli.create_group(k[0])
if k[0] == 'timeseries':
dateList = h5file[k[0]].keys()
for d in dateList:
print d
unw = h5file[k[0]].get(d)
unwlks = multilook(unw, alks, rlks)
dset = group.create_dataset(d,
data=unwlks,
compression='gzip')
elif k[0] in ['temporal_coherence', 'velocity', 'mask', 'rmse']:
dset1 = h5file[k[0]].get(k[0])
unw = dset1[0:dset1.shape[0], 0:dset1.shape[1]]
unwlks = multilook(unw, alks, rlks)
dset = group.create_dataset(k[0],
data=unwlks,
compression='gzip')
try:
dset1 = h5file['mask'].get('mask')
Mask = dset1[0:dset1.shape[0], 0:dset1.shape[1]]
Masklks = multilook(Mask, alks, rlks)
group = h5file_mli.create_group('mask')
dset = group.create_dataset('mask',
data=Masklks,
compression='gzip')
except:
print 'No mask group found.'
## Update attributes
for key, value in h5file[k[0]].attrs.iteritems():
group.attrs[key] = value
group.attrs['WIDTH'] = unwlks.shape[1]
group.attrs['FILE_LENGTH'] = unwlks.shape[0]
try:
group.attrs['Y_STEP'] = alks * float(group.attrs['Y_STEP'])
group.attrs['X_STEP'] = rlks * float(group.attrs['X_STEP'])
except:
group.attrs['AZIMUTH_PIXEL_SIZE'] = alks * float(
group.attrs['AZIMUTH_PIXEL_SIZE'])
group.attrs['RANGE_PIXEL_SIZE'] = rlks * float(
group.attrs['RANGE_PIXEL_SIZE'])
h5file.close()
h5file_mli.close()
################################################################################
elif ext in ['.unw','.cor','.hgt','.dem','.trans'] or\
ext in ['.jpeg','.jpg','.png','.ras','.bmp'] or\
ext in ['.mli','.slc']:
import pysar._readfile as readfile
import pysar._writefile as writefile
r = readfile.read_rsc_file(file + '.rsc')
if ext == '.int' or ext == '.slc':
a, p, r = readfile.read_complex64(file)
pmli = multilook(p, alks, rlks)
amli = multilook(a, alks, rlks)
r['FILE_LENGTH'] = str(pmli.shape[0])
r['WIDTH'] = str(pmli.shape[1])
elif ext == '.unw' or ext == '.cor' or ext == '.hgt':
a, p, r = readfile.read_float32(file)
pmli = multilook(p, alks, rlks)
amli = multilook(a, alks, rlks)
print 'writing >>>' + outName
writefile.write_float32(pmli, outName)
r['FILE_LENGTH'] = str(pmli.shape[0])
r['WIDTH'] = str(pmli.shape[1])
elif ext == ('.dem'):
d, r = readfile.read_dem(file)
dmli = multilook(d, alks, rlks)
print 'writing >>>' + outName
writefile.write_dem(dmli, outName)
r['FILE_LENGTH'] = str(dmli.shape[0])
r['WIDTH'] = str(dmli.shape[1])
elif ext in ['.jpeg', '.jpg', '.png', '.bmp']:
import Image
im = Image.open(file)
width = im.size[0] / int(rlks)
height = im.size[1] / int(alks)
imlks = im.resize((width, height), Image.NEAREST)
print 'writing >>>' + outName
imlks.save(outName)
r['FILE_LENGTH'] = str(height)
r['WIDTH'] = str(width)
## Update attributes
r['XMAX'] = str(int(r['WIDTH']) - 1)
r['YMAX'] = str(int(r['FILE_LENGTH']) - 1)
try:
r['Y_STEP'] = str(float(r['Y_STEP']) * alks)
r['X_STEP'] = str(float(r['X_STEP']) * rlks)
except:
r['AZIMUTH_PIXEL_SIZE'] = alks * float(r['AZIMUTH_PIXEL_SIZE'])
r['RANGE_PIXEL_SIZE'] = rlks * float(r['RANGE_PIXEL_SIZE'])
f = open(outName + '.rsc', 'w')
for k in r.keys():
f.write(k + ' ' + r[k] + '\n')
f.close()
def main(argv):
color_map = 'jet'
disp_opposite = 'no'
disp_colorbar = 'yes'
rewrapping = 'no'
dpi = 500
if len(sys.argv) > 2:
try:
opts, args = getopt.getopt(argv, "f:m:M:d:c:w:i:r:")
except getopt.GetoptError:
Usage()
sys.exit(1)
for opt, arg in opts:
if opt == '-f': File = arg
elif opt == '-m': Vmin = float(arg)
elif opt == '-M': Vmax = float(arg)
elif opt == '-d': epoch_date = arg
elif opt == '-c': color_map = arg
elif opt == '-i': disp_opposite = arg
elif opt == '-w': rewrapping = arg
elif opt == '-r': dpi = int(arg)
elif len(sys.argv) == 2:
if argv[0] == '-h':
Usage()
sys.exit(1)
elif os.path.isfile(argv[0]):
File = argv[0]
else:
Usage()
sys.exit(1)
else:
Usage()
sys.exit(1)
#######################################################
################### Prepare Data ####################
## prepare: data, North, East, South, West
import matplotlib.pyplot as plt
ext = os.path.splitext(File)[1]
map = plt.get_cmap(color_map)
if ext == '.h5':
import h5py
try:
h5file = h5py.File(File, 'r')
except:
Usage()
sys.exit(1)
outName = File.split('.')[0]
k = h5file.keys()
if 'interferograms' in k: k[0] = 'interferograms'
elif 'coherence' in k: k[0] = 'coherence'
elif 'timeseries' in k: k[0] = 'timeseries'
if k[0] in ('interferograms', 'coherence', 'wrapped'):
atr = h5file[k[0]][h5file[k[0]].keys()[0]].attrs
elif k[0] in ('dem', 'velocity', 'mask', 'temporal_coherence', 'rmse',
'timeseries'):
atr = h5file[k[0]].attrs
print 'Input file is ' + k[0]
if k[0] in ('interferograms', 'wrapped', 'coherence'):
ifgramList = h5file[k[0]].keys()
for i in range(len(ifgramList)):
if epoch_date in ifgramList[i]:
epoch_number = i
print ifgramList[epoch_number]
outName = ifgramList[epoch_number]
#outName=epoch_date
dset = h5file[k[0]][ifgramList[epoch_number]].get(
ifgramList[epoch_number])
data = dset[0:dset.shape[0], 0:dset.shape[1]]
if k[0] == 'wrapped':
print 'No wrapping for wrapped interferograms. Set rewrapping=no'
rewrapping = 'no'
Vmin = -np.pi
Vmax = np.pi
elif 'timeseries' in k:
epochList = h5file['timeseries'].keys()
for i in range(len(epochList)):
if epoch_date in epochList[i]:
epoch_number = i
#### Out name
ref_date = h5file['timeseries'].attrs['ref_date']
if len(epoch_date) == 8:
outName = ref_date[2:] + '-' + epoch_date[2:]
else:
outName = ref_date[2:] + '-' + epoch_date
dset = h5file['timeseries'].get(epochList[epoch_number])
data = dset[0:dset.shape[0], 0:dset.shape[1]]
### one dataset format: velocity, mask, temporal_coherence, rmse, std, etc.
else:
dset = h5file[k[0]].get(k[0])
data = dset[0:dset.shape[0], 0:dset.shape[1]]
if disp_opposite in ('yes', 'Yes', 'Y', 'y', 'YES'):
data = -1 * data
try:
xref = h5file[k[0]].attrs['ref_x']
yref = h5file[k[0]].attrs['ref_y']
except:
pass
elif ext in ['.unw', '.cor', '.hgt', '.trans', '.dem']:
import pysar._readfile as readfile
if ext in ['.unw', '.cor', '.hgt', '.trans']:
a, data, atr = readfile.read_float32(File)
outName = File
elif ext == '.dem':
data, atr = readfile.read_dem(File)
outName = File
else:
sys.exit('Do not support ' + ext + ' file!')
########################################################
if rewrapping == 'yes':
data = rewrap(data)
Vmin = -np.pi #[-pi,pi] for wrapped interferograms
Vmax = np.pi
else:
try:
Vmin
except:
Vmin = np.nanmin(data)
try:
Vmax
except:
Vmax = np.nanmax(data)
try:
lon_step = float(atr['X_STEP'])
lat_step = float(atr['Y_STEP'])
lon_unit = atr['Y_UNIT']
lat_unit = atr['X_UNIT']
West = float(atr['X_FIRST'])
North = float(atr['Y_FIRST'])
South = North + lat_step * (data.shape[0] - 1)
East = West + lon_step * (data.shape[1] - 1)
geocoord = 'yes'
print 'Input file is Geocoded.'
except:
print '%%%%%%%%%%'
print 'Error:\nThe input file is not geocoded\n'
print '%%%%%%%%%%'
Usage()
sys.exit(1)
#######################################################
################### Output KMZ ######################
############### Make PNG file
print 'Making png file ...'
length = data.shape[0]
width = data.shape[1]
fig = plt.figure()
fig = plt.figure(frameon=False)
# fig.set_size_inches(width/1000,length/1000)
ax = plt.Axes(
fig,
[0., 0., 1., 1.],
)
ax.set_axis_off()
fig.add_axes(ax)
aspect = width / (length * 1.0)
# ax.imshow(data,aspect='normal')
try:
ax.imshow(data, aspect='normal', vmax=Vmax, vmin=Vmin)
except:
ax.imshow(data, aspect='normal')
ax.set_xlim([0, width])
ax.set_ylim([length, 0])
# figName = k[0]+'.png'
figName = outName + '.png'
plt.savefig(figName, pad_inches=0.0, dpi=dpi)
# plt.show()
############### Making colorbar
pc = plt.figure(figsize=(1, 4))
axc = pc.add_subplot(111)
cmap = mpl.cm.jet
norm = mpl.colors.Normalize(vmin=Vmin * 1000, vmax=Vmax * 1000)
clb = mpl.colorbar.ColorbarBase(axc,
cmap=cmap,
norm=norm,
orientation='vertical')
clb.set_label('mm/yr')
pc.subplots_adjust(left=0.25, bottom=0.1, right=0.4, top=0.9)
pc.savefig('colorbar.png', transparent=True, dpi=300)
############## Generate KMZ file
print 'generating kml file'
doc = KML.kml(KML.Folder(KML.name('PySAR product')))
slc = KML.GroundOverlay(KML.name(figName),KML.Icon(KML.href(figName)),\
KML.TimeSpan(KML.begin('2003'),KML.end('2010')),\
KML.LatLonBox(KML.north(str(North)),KML.south(str(South)),\
KML.east(str(East)), KML.west(str(West))))
doc.Folder.append(slc)
#############################
print 'adding colorscale'
latdel = North - South
londel = East - West
slc1 = KML.GroundOverlay(KML.name('colorbar'),KML.Icon(KML.href('colorbar.png')),\
KML.altitude('9000'),KML.altitudeMode('absolute'),\
KML.LatLonBox(KML.north(str(North-latdel/2.+0.5)),KML.south(str(South+latdel/2.0-0.5)),\
KML.east(str(West-0.2*londel)), KML.west(str(West-0.4*londel))))
doc.Folder.append(slc1)
#############################
from lxml import etree
kmlstr = etree.tostring(doc, pretty_print=True)
# kmlname=k[0]+'.kml'
kmlname = outName + '.kml'
print 'writing ' + kmlname
kmlfile = open(kmlname, 'w')
kmlfile.write(kmlstr)
kmlfile.close()
# kmzName = k[0]+'.kmz'
kmzName = outName + '.kmz'
print 'writing ' + kmzName
# cmdKMZ = 'zip ' + kmzName +' '+ kmlname +' ' + figName
cmdKMZ = 'zip ' + kmzName + ' ' + kmlname + ' ' + figName + ' colorbar.png'
os.system(cmdKMZ)
cmdClean = 'rm ' + kmlname
os.system(cmdClean)
cmdClean = 'rm ' + figName
os.system(cmdClean)
cmdClean = 'rm colorbar.png'
os.system(cmdClean)
def main(argv):
########### Check Inputs #############
try:
file = sys.argv[1]
operator = sys.argv[2]
operand = float(sys.argv[3])
except:
usage()
sys.exit(1)
if operator in ['+', 'plus', 'add', 'addition']: operator = 'plus'
elif operator in ['-', 'minus', 'substract', 'substraction']:
operator = 'minus'
elif operator in ['*', 'times', 'multiply', 'multiplication']:
operator = 'multiply'
elif operator in ['/', 'obelus', 'divide', 'division']:
operator = 'divide'
elif operator in ['^', 'exp', 'exponential']:
operator = 'exp'
else:
print 'ERROR: Unrecognized operator: ' + operator
sys.exit(1)
print '\n*************** Image Math ******************'
print 'operation: ' + operator + ' ' + str(operand)
ext = os.path.splitext(file)[1]
try:
outName = sys.argv[4]
except:
outName = file.split('.')[0] + '_' + operator + str(operand) + ext
########### Read - Calculate - Write ###########
##### PySAR HDF5 files ######
if ext in ['.h5', '.he5']:
try:
h5file = h5py.File(file, 'r')
except:
print 'ERROR: can not open file: ' + file
sys.exit(1)
k = h5file.keys()
if 'interferograms' in k: k[0] = 'interferograms'
elif 'coherence' in k: k[0] = 'coherence'
elif 'timeseries' in k: k[0] = 'timeseries'
print 'Input file is ' + k[0]
h5fileOut = h5py.File(outName, 'w')
print 'writing >>> ' + outName
group = h5fileOut.create_group(k[0])
if k[0] in ('velocity', 'temporal_coherence', 'rmse', 'mask', 'dem'):
dset = h5file[k[0]].get(k[0])
data = dset[0:dset.shape[0], 0:dset.shape[1]]
dataOut = operation(data, operator, operand)
dset = group.create_dataset(k[0], data=dataOut, compression='gzip')
for key, value in h5file[k[0]].attrs.iteritems():
group.attrs[key] = value
elif k[0] == 'timeseries':
dateList = h5file[k[0]].keys()
print 'number of dates: ' + str(len(dateList))
for date in dateList:
print date
dset = h5file[k[0]].get(date)
data = dset[0:dset.shape[0], 0:dset.shape[1]]
dataOut = operation(data, operator, operand)
dset = group.create_dataset(date,
data=dataOut,
compression='gzip')
for key, value in h5file[k[0]].attrs.iteritems():
group.attrs[key] = value
elif k[0] in ['interferograms', 'coherence', 'wrapped']:
ifgramList = h5file[k[0]].keys()
print 'number of epochs: ' + str(len(ifgramList))
for igram in ifgramList:
print igram
dset = h5file[k[0]][igram].get(igram)
data = dset[0:dset.shape[0], 0:dset.shape[1]]
dataOut = operation(data, operator, operand)
group2 = group.create_group(igram)
dset = group2.create_dataset(igram,
data=dataOut,
compression='gzip')
for key, value in h5file[k[0]][igram].attrs.iteritems():
group2.attrs[key] = value
try:
mask = h5file['mask'].get('mask')
gm = h5fileOut.create_group('mask')
dset = gm.create_dataset('mask', data=mask, compression='gzip')
except:
print 'No group for mask found in the file.'
try:
Cset = h5file['meanCoherence'].get('meanCoherence')
gm = h5fileOut.create_group('meanCoherence')
dset = gm.create_dataset('meanCoherence',
data=Cset,
compression='gzip')
except:
print 'No group for meanCoherence found in the file'
else:
print 'ERROR: Unrecognized HDF5 file type: ' + k[0]
sys.exit(1)
h5file.close()
h5fileOut.close()
##### ROI_PAC files #######
elif ext in ['.unw', '.cor', '.hgt', '.dem', '.trans']:
print 'Input file is ' + ext + '\nwriting >>> ' + outName
if ext in ['.unw', '.cor', '.hgt']:
a, p, r = readfile.read_float32(file)
p2 = operation(p, operator, operand)
writefile.write_float32(p2, outName)
elif ext == '.dem':
p, r = readfile.read_real_int16(file)
p2 = operation(p, operator, operand)
writefile.write_real_int16(p2, outName)
elif ext == '.trans':
a, p, r = readfile.read_float32(file)
a2 = operation(a, operator, operand)
p2 = operation(p, operator, operand)
writefile.write_float32(a2, p2, outName)
## Write atrributes file
f = open(outName + '.rsc', 'w')
for k in r.keys():
f.write(k + ' ' + r[k] + '\n')
f.close()
else:
print 'ERROR: Unrecognized file extension: ' + ext
sys.exit(1)
print 'Done.'
Example:
correlation_with_dem.py radar_8rlks.hgt velocity_masked.h5
***********************************************************************
'''
try:
demFile = sys.argv[1]
File = sys.argv[2]
except:
usage()
sys.exit(1)
if os.path.basename(demFile).split('.')[1] == 'hgt':
amp, dem, demRsc = readfile.read_float32(demFile)
elif os.path.basename(demFile).split('.')[1] == 'dem':
dem, demRsc = readfile.read_real_int16(demFile)
#amp,dem,demRsc = readfile.read_float32(demFile)
h5data = h5py.File(File)
dset = h5data['velocity'].get('velocity')
data = dset[0:dset.shape[0], 0:dset.shape[1]]
try:
suby = sys.argv[3].split(':')
subx = sys.argv[4].split(':')
data = data[int(suby[0]):int(suby[1]), int(subx[0]):int(subx[1])]
dem = dem[int(suby[0]):int(suby[1]), int(subx[0]):int(subx[1])]
except:
def main(argv):
try:
File = argv[0]
demFile = argv[1]
p = int(argv[2])
except:
usage()
sys.exit(1)
try:
baseline_error = argv[3]
except:
baseline_error = 'range_and_azimuth'
print baseline_error
##################################
h5file = h5py.File(File)
dateList = h5file['timeseries'].keys()
##################################
try:
maskFile = argv[4]
except:
if os.path.isfile('Modified_Mask.h5'): maskFile = 'Modified_Mask.h5'
elif os.path.isfile('Mask.h5'): maskFile = 'Mask.h5'
else:
print 'No mask found!'
sys.exit(1)
try:
Mask, Matr = readfile.read(maskFile)
print 'mask: ' + maskFile
except:
print 'Can not open mask file: ' + maskFile
sys.exit(1)
#try:
# maskFile=argv[4]
# h5Mask = h5py.File(maskFile,'r')
# kMask=h5Mask.keys()
# dset1 = h5Mask[kMask[0]].get(kMask[0])
# Mask = dset1[0:dset1.shape[0],0:dset1.shape[1]]
#except:
# dset1 = h5file['mask'].get('mask')
# Mask = dset1[0:dset1.shape[0],0:dset1.shape[1]]
##################################
Mask = Mask.flatten(1)
ndx = Mask != 0
##################################
# h5file = h5py.File(File)
# dateList = h5file['timeseries'].keys()
##################################
nt = float(h5file['timeseries'].attrs['LOOK_REF1'])
ft = float(h5file['timeseries'].attrs['LOOK_REF2'])
sy, sx = np.shape(dset1)
npixel = sx * sy
lookangle = np.tile(np.linspace(nt, ft, sx), [sy, 1])
lookangle = lookangle.flatten(1) * np.pi / 180.0
Fh = -np.sin(lookangle)
Fv = -np.cos(lookangle)
print 'Looking for azimuth pixel size'
try:
daz = float(h5file['timeseries'].attrs['AZIMUTH_PIXEL_SIZE'])
except:
print '''
ERROR!
The attribute AZIMUTH_PIXEL_SIZE was not found!
Possible cause of error: Geo coordinate.
This function works only in radar coordinate system.
'''
sys.exit(1)
lines = np.tile(np.arange(0, sy, 1), [1, sx])
lines = lines.flatten(1)
rs = lines * daz
if baseline_error == 'range_and_azimuth':
A = np.zeros([npixel, 4])
A[:, 0] = Fh
A[:, 1] = Fh * rs
A[:, 2] = Fv
A[:, 3] = Fv * rs
num_base_par = 4
elif baseline_error == 'range':
A = np.zeros([npixel, 2])
A[:, 0] = Fh
A[:, 1] = Fv
num_base_par = 2
###########################################
yref = int(h5file['timeseries'].attrs['ref_y'])
xref = int(h5file['timeseries'].attrs['ref_x'])
###########################################
if os.path.basename(demFile).split('.')[1] == 'hgt':
amp, dem, demRsc = readfile.read_float32(demFile)
elif os.path.basename(demFile).split('.')[1] == 'dem':
dem, demRsc = readfile.read_real_int16(demFile)
dem = dem - dem[yref][xref]
dem = dem.flatten(1)
###################################################
if p == 1:
# A=np.vstack((dem[ndx],np.ones(len(dem[ndx])))).T
B = np.vstack((dem, np.ones(len(dem)))).T
elif p == 2:
# A=np.vstack((dem[ndx]**2,dem[ndx],np.ones(len(dem[ndx])))).T
B = np.vstack((dem**2, dem, np.ones(len(dem)))).T
elif p == 3:
# A = np.vstack((dem[ndx]**3,dem[ndx]**2,dem[ndx],np.ones(len(dem[ndx])))).T
B = np.vstack((dem**3, dem**2, dem, np.ones(len(dem)))).T
print np.shape(A)
Ainv = np.linalg.pinv(A)
###################################################
Bh = []
Bv = []
Bhrate = []
Bvrate = []
Be = np.zeros([len(dateList), num_base_par + p + 1])
print '%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%'
for i in range(1, len(dateList)):
dset = h5file['timeseries'].get(dateList[i])
data = dset[0:dset.shape[0], 0:dset.shape[1]]
L = data.flatten(1)
M = np.hstack((A, B))
Berror = np.dot(np.linalg.pinv(M[ndx]), L[ndx])
Bh.append(Berror[0])
Bhrate.append(Berror[1])
Bv.append(Berror[2])
Bvrate.append(Berror[3])
Be[i, :] = Berror
print Berror
print '%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%'
print 'baseline error mean std'
print ' bh : ' + str(np.mean(Bh)) + ' , ' + str(np.std(Bh))
print ' bh rate : ' + str(np.mean(Bhrate)) + ' , ' + str(
np.std(Bhrate))
print ' bv : ' + str(np.mean(Bv)) + ' , ' + str(np.std(Bv))
print ' bv rate : ' + str(np.mean(Bvrate)) + ' , ' + str(
np.std(Bvrate))
print '%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%'
# plt.hist(Bh,bins=8,normed=True)
# formatter = FuncFormatter(to_percent)
# Set the formatter
# plt.gca().yaxis.set_major_formatter(formatter)
# plt.show()
print '%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%'
# print 'Estimating Baseline error from each differences ...'
orbEffect = np.zeros([len(dateList), sy, sx])
for i in range(1, len(dateList)):
effect = np.dot(M, Be[i, :])
effect = np.reshape(effect, [sx, sy]).T
# orbEffect[i,:,:]=orbEffect[i-1,:,:]+effect
# orbEffect[i,:,:]=orbEffect[i,:,:]-orbEffect[i,yref,xref]
orbEffect[i, :, :] = effect - effect[yref, xref]
del effect
print 'Correctiing the time series '
outName = File.replace('.h5', '') + '_baseTropCor.h5'
h5orbCor = h5py.File(outName, 'w')
group = h5orbCor.create_group('timeseries')
for i in range(len(dateList)):
dset1 = h5file['timeseries'].get(dateList[i])
data = dset1[0:dset1.shape[0], 0:dset1.shape[1]] - orbEffect[i, :, :]
dset = group.create_dataset(dateList[i], data=data, compression='gzip')
for key, value in h5file['timeseries'].attrs.iteritems():
group.attrs[key] = value
dset1 = h5file['mask'].get('mask')
group = h5orbCor.create_group('mask')
dset = group.create_dataset('mask', data=dset1, compression='gzip')
h5file.close()
h5orbCor.close()
def main(argv):
color_map = "jet"
disp_opposite = "no"
disp_colorbar = "yes"
rewrapping = "no"
dpi = 500
if len(sys.argv) > 2:
try:
opts, args = getopt.getopt(argv, "f:m:M:d:c:w:i:r:")
except getopt.GetoptError:
Usage()
sys.exit(1)
for opt, arg in opts:
if opt == "-f":
File = arg
elif opt == "-m":
Vmin = float(arg)
elif opt == "-M":
Vmax = float(arg)
elif opt == "-d":
epoch_date = arg
elif opt == "-c":
color_map = arg
elif opt == "-i":
disp_opposite = arg
elif opt == "-w":
rewrapping = arg
elif opt == "-r":
dpi = int(arg)
elif len(sys.argv) == 2:
if argv[0] == "-h":
Usage()
sys.exit(1)
elif os.path.isfile(argv[0]):
File = argv[0]
else:
Usage()
sys.exit(1)
else:
Usage()
sys.exit(1)
#######################################################
################### Prepare Data ####################
## prepare: data, North, East, South, West
import matplotlib.pyplot as plt
ext = os.path.splitext(File)[1]
map = plt.get_cmap(color_map)
if ext == ".h5":
import h5py
try:
h5file = h5py.File(File, "r")
except:
Usage()
sys.exit(1)
outName = File.split(".")[0]
k = h5file.keys()
if "interferograms" in k:
k[0] = "interferograms"
elif "coherence" in k:
k[0] = "coherence"
elif "timeseries" in k:
k[0] = "timeseries"
if k[0] in ("interferograms", "coherence", "wrapped"):
atr = h5file[k[0]][h5file[k[0]].keys()[0]].attrs
elif k[0] in ("dem", "velocity", "mask", "temporal_coherence", "rmse", "timeseries"):
atr = h5file[k[0]].attrs
print "Input file is " + k[0]
if k[0] in ("interferograms", "wrapped", "coherence"):
ifgramList = h5file[k[0]].keys()
for i in range(len(ifgramList)):
if epoch_date in ifgramList[i]:
epoch_number = i
print ifgramList[epoch_number]
outName = ifgramList[epoch_number]
# outName=epoch_date
dset = h5file[k[0]][ifgramList[epoch_number]].get(ifgramList[epoch_number])
data = dset[0 : dset.shape[0], 0 : dset.shape[1]]
if k[0] == "wrapped":
print "No wrapping for wrapped interferograms. Set rewrapping=no"
rewrapping = "no"
Vmin = -np.pi
Vmax = np.pi
elif "timeseries" in k:
epochList = h5file["timeseries"].keys()
for i in range(len(epochList)):
if epoch_date in epochList[i]:
epoch_number = i
#### Out name
ref_date = h5file["timeseries"].attrs["ref_date"]
if len(epoch_date) == 8:
outName = ref_date[2:] + "-" + epoch_date[2:]
else:
outName = ref_date[2:] + "-" + epoch_date
dset = h5file["timeseries"].get(epochList[epoch_number])
data = dset[0 : dset.shape[0], 0 : dset.shape[1]]
### one dataset format: velocity, mask, temporal_coherence, rmse, std, etc.
else:
dset = h5file[k[0]].get(k[0])
data = dset[0 : dset.shape[0], 0 : dset.shape[1]]
if disp_opposite in ("yes", "Yes", "Y", "y", "YES"):
data = -1 * data
try:
xref = h5file[k[0]].attrs["ref_x"]
yref = h5file[k[0]].attrs["ref_y"]
except:
pass
elif ext in [".unw", ".cor", ".hgt", ".trans", ".dem"]:
import pysar._readfile as readfile
if ext in [".unw", ".cor", ".hgt", ".trans"]:
a, data, atr = readfile.read_float32(File)
outName = File
elif ext == ".dem":
data, atr = readfile.read_dem(File)
outName = File
else:
sys.exit("Do not support " + ext + " file!")
########################################################
if rewrapping == "yes":
data = rewrap(data)
Vmin = -np.pi # [-pi,pi] for wrapped interferograms
Vmax = np.pi
else:
try:
Vmin
except:
Vmin = np.nanmin(data)
try:
Vmax
except:
Vmax = np.nanmax(data)
try:
lon_step = float(atr["X_STEP"])
lat_step = float(atr["Y_STEP"])
lon_unit = atr["Y_UNIT"]
lat_unit = atr["X_UNIT"]
West = float(atr["X_FIRST"])
North = float(atr["Y_FIRST"])
South = North + lat_step * (data.shape[0] - 1)
East = West + lon_step * (data.shape[1] - 1)
geocoord = "yes"
print "Input file is Geocoded."
except:
print "%%%%%%%%%%"
print "Error:\nThe input file is not geocoded\n"
print "%%%%%%%%%%"
Usage()
sys.exit(1)
#######################################################
################### Output KMZ ######################
############### Make PNG file
print "Making png file ..."
length = data.shape[0]
width = data.shape[1]
fig = plt.figure()
fig = plt.figure(frameon=False)
# fig.set_size_inches(width/1000,length/1000)
ax = plt.Axes(fig, [0.0, 0.0, 1.0, 1.0])
ax.set_axis_off()
fig.add_axes(ax)
aspect = width / (length * 1.0)
# ax.imshow(data,aspect='normal')
try:
ax.imshow(data, aspect="normal", vmax=Vmax, vmin=Vmin)
except:
ax.imshow(data, aspect="normal")
ax.set_xlim([0, width])
ax.set_ylim([length, 0])
# figName = k[0]+'.png'
figName = outName + ".png"
plt.savefig(figName, pad_inches=0.0, dpi=dpi)
# plt.show()
############### Making colorbar
pc = plt.figure(figsize=(1, 4))
axc = pc.add_subplot(111)
cmap = mpl.cm.jet
norm = mpl.colors.Normalize(vmin=Vmin * 1000, vmax=Vmax * 1000)
clb = mpl.colorbar.ColorbarBase(axc, cmap=cmap, norm=norm, orientation="vertical")
clb.set_label("mm/yr")
pc.subplots_adjust(left=0.25, bottom=0.1, right=0.4, top=0.9)
pc.savefig("colorbar.png", transparent=True, dpi=300)
############## Generate KMZ file
print "generating kml file"
doc = KML.kml(KML.Folder(KML.name("PySAR product")))
slc = KML.GroundOverlay(
KML.name(figName),
KML.Icon(KML.href(figName)),
KML.TimeSpan(KML.begin("2003"), KML.end("2010")),
KML.LatLonBox(KML.north(str(North)), KML.south(str(South)), KML.east(str(East)), KML.west(str(West))),
)
doc.Folder.append(slc)
#############################
print "adding colorscale"
latdel = North - South
londel = East - West
slc1 = KML.GroundOverlay(
KML.name("colorbar"),
KML.Icon(KML.href("colorbar.png")),
KML.altitude("9000"),
KML.altitudeMode("absolute"),
KML.LatLonBox(
KML.north(str(North - latdel / 2.0 + 0.5)),
KML.south(str(South + latdel / 2.0 - 0.5)),
KML.east(str(West - 0.2 * londel)),
KML.west(str(West - 0.4 * londel)),
),
)
doc.Folder.append(slc1)
#############################
from lxml import etree
kmlstr = etree.tostring(doc, pretty_print=True)
# kmlname=k[0]+'.kml'
kmlname = outName + ".kml"
print "writing " + kmlname
kmlfile = open(kmlname, "w")
kmlfile.write(kmlstr)
kmlfile.close()
# kmzName = k[0]+'.kmz'
kmzName = outName + ".kmz"
print "writing " + kmzName
# cmdKMZ = 'zip ' + kmzName +' '+ kmlname +' ' + figName
cmdKMZ = "zip " + kmzName + " " + kmlname + " " + figName + " colorbar.png"
os.system(cmdKMZ)
cmdClean = "rm " + kmlname
os.system(cmdClean)
cmdClean = "rm " + figName
os.system(cmdClean)
cmdClean = "rm colorbar.png"
os.system(cmdClean)