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:
dem_file = argv[1]
dem_error = argv[2]
except:
usage()
sys.exit(1)
dem, demrsc = _readfile.read_real_int16(dem_file)
g = h5py.File(dem_error, 'r')
dset = g['dem'].get('dem')
dem_error = dset[0:dset.shape[0]]
print 'Correcting the DEM'
sum = dem + dem_error
print 'Creating the new DEM'
_writefile.write_real_int16(sum, 'DEM_w_error.dem')
rsc_file = open('DEM_w_error.dem.rsc', 'w')
for k in demrsc.keys():
rsc_file.write(k + ' ' + demrsc[k] + '\n')
rsc_file.close
date12_file = open('111111-222222_baseline.rsc', 'w')
date12_file.write('P_BASELINE_TOP_ODR' + ' ' + '000')
date12_file.close
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 main(argv):
try:
dem_file = argv[1]
dem_error = argv[2]
except:
print '''
*******************************************
Usage: correct_dem.py demFile geo_demErrorFile
Example:
correct_dem.py $DEMDIR/Socorro-30/Socorro_30.dem geo_DEM_error.h5
correct_dem.py $DEMDIR/Socorro-30/Socorro_30.dem geo_DEM_error.h5
*******************************************
'''
sys.exit(1)
dem, demrsc = _readfile.read_real_int16(dem_file)
g = h5py.File(dem_error,'r')
dset = g['dem'].get('dem')
dem_error = dset[0:dset.shape[0]]
print 'Correcting the DEM'
sum = dem + dem_error
print 'Creating the new DEM'
_writefile.write_real_int16(sum,'DEM_w_error.dem')
rsc_file = open('DEM_w_error.dem.rsc','w')
for k in demrsc.keys():
rsc_file.write(k+' '+demrsc[k]+'\n')
rsc_file.close
date12_file=open('111111-222222_baseline.rsc','w')
date12_file.write('P_BASELINE_TOP_ODR'+' '+ '000')
date12_file.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: 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):
########### 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.'
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
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):
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):
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)
***********************************************************************
'''
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:
print 'no subset'
dem = dem.flatten(1)
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
group.attrs['ref_y']=0
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):
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)
***********************************************************************
'''
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:
print 'no subset'
dem=dem.flatten(1)
