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 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):
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]
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:
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):
#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]
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()
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]
except:
Usage()
sys.exit(1)
from numpy import pi
import h5py
import pysar._writefile as writefile
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 'velocity' in k:
dset = h5file['velocity'].get('velocity')
data = dset[0:dset.shape[0], 0:dset.shape[1]]
print "converting velocity to a 1 year interferogram."
wvl = float(h5file[k[0]].attrs['WAVELENGTH'])
data = (-4 * pi / wvl) * data
outname = File.split('.')[0] + '.unw'
print 'writing >>> ' + outname
writefile.write_float32(data, outname)
f = open(outname + '.rsc', 'w')
for key, value in h5file[k[0]].attrs.iteritems():
f.write(key + ' ' + str(value) + '\n')
f.close()
elif k[0] in ['rmse', 'temporal_coherence', 'mask']:
dset = h5file[k[0]].get(k[0])
data = dset[0:dset.shape[0], 0:dset.shape[1]]
if k[0] == 'temporal_coherence': outname = File.split('.')[0] + '.cor'
else: outname = File.split('.')[0] + '.unw'
print 'writing >>> ' + outname
writefile.write_float32(data, outname)
f = open(outname + '.rsc', 'w')
for key, value in h5file[k[0]].attrs.iteritems():
f.write(key + ' ' + str(value) + '\n')
f.close()
elif 'timeseries' in k:
dateList = h5file['timeseries'].keys()
## Input
if len(sys.argv) == 2:
print 'No input date specified >>> continue with the last date'
dateList = h5file['timeseries'].keys()
d = dateList[-1]
elif len(sys.argv) == 3:
d = sys.argv[2]
elif len(sys.argv) == 4:
ds = sys.argv[2:4]
ds.sort()
d_ref = ds[0]
d = ds[1]
else:
Usage()
sys.exit(1)
## Data Operation
print 'reading ' + d + ' ... '
dset = h5file['timeseries'].get(d)
data = dset[0:dset.shape[0], 0:dset.shape[1]]
try:
dset_ref = h5file['timeseries'].get(d_ref)
print 'reading ' + d_ref + ' ... '
data_ref = dset_ref[0:dset_ref.shape[0], 0:dset_ref.shape[1]]
data = data - data_ref
except:
pass
wvl = float(h5file[k[0]].attrs['WAVELENGTH'])
data = (-4 * pi / wvl) * data
## outName
try:
master_d = d_ref
except:
try:
master_d = h5file[k[0]].attrs['ref_date']
except:
master_d = h5file[k[0]].attrs['DATE']
if len(master_d) == 8: master_d = master_d[2:8]
if len(d) == 8: d = d[2:8]
outname = master_d + '_' + d + '.unw'
print 'writing >>> ' + outname
writefile.write_float32(data, outname)
f = open(outname + '.rsc', 'w')
for key, value in h5file[k[0]].attrs.iteritems():
if key == 'DATE12':
f.write(key + ' ' + master_d + '-' + d + '\n')
else:
f.write(key + ' ' + str(value) + '\n')
f.close()
elif k[0] in ['interferograms', 'coherence', 'wrapped']:
igramList = h5file[k[0]].keys()
try:
d = sys.argv[2]
except:
d = igramList[-1]
print 'No input date specified >>> continue with the last date'
print 'reading ' + d + ' ... '
dset = h5file[k[0]][d].get(d)
data = dset[0:dset.shape[0], 0:dset.shape[1]]
outname = d
print 'writing >>> ' + outname
writefile.write_float32(data, outname)
f = open(outname + '.rsc', 'w')
for key, value in h5file[k[0]][d].attrs.iteritems():
f.write(key + ' ' + str(value) + '\n')
f.close()
h5file.close()
def main(argv):
try: File=argv[0]
except: Usage();sys.exit(1)
atr = readfile.read_attributes(File)
k = atr['FILE_TYPE']
h5file=h5py.File(File,'r')
print '\n************* Output to ROI_PAC format ***************'
if k == 'velocity':
dset = h5file['velocity'].get('velocity')
data = dset[0:dset.shape[0],0:dset.shape[1]]
print "converting velocity to a 1 year interferogram."
wvl=float(h5file[k].attrs['WAVELENGTH'])
data=(-4*pi/wvl)*data
outname=File.split('.')[0]+'.unw'
writefile.write(data,atr,outname)
elif k == 'timeseries':
dateList=h5file['timeseries'].keys()
## Input
if len(sys.argv)==2:
print 'No input date specified >>> continue with the last date'
dateList=h5file['timeseries'].keys()
d=dateList[-1]
elif len(sys.argv)==3:
d=sys.argv[2]
elif len(sys.argv)==4:
ds=sys.argv[2:4]; ds.sort()
d_ref = ds[0]
d = ds[1]
else: Usage(); sys.exit(1)
d = ptime.yyyymmdd(d)
try: d_ref = ptime.yyyymmdd(d_ref)
except: pass
## Data
print 'reading '+d+' ... '
data = h5file['timeseries'].get(d)[:]
try:
print 'reading '+d_ref+' ... '
data_ref = h5file['timeseries'].get(d_ref)[:]
data = data - data_ref
except: pass
wvl=float(atr['WAVELENGTH'])
data *= -4*pi/wvl
## outName
try: master_d = d_ref
except:
try: master_d = atr['ref_date']
except: master_d = atr['DATE']
if len(master_d)==8: master_d=master_d[2:8]
if len(d)==8: d=d[2:8]
outname = master_d+'_'+d+'.unw'
## Attributes
atr['FILE_TYPE'] = '.unw'
atr['P_BASELINE_TIMESERIES'] = '0.0'
atr['UNIT'] = 'radian'
atr['DATE'] = master_d
atr['DATE12'] = master_d+'-'+d
## Writing
writefile.write(data,atr,outname)
elif k in ['interferograms','coherence','wrapped']:
## Check input
igramList=h5file[k].keys()
try:
d = sys.argv[2]
for i in range(len(igramList)):
if d in igramList[i]:
igram = igramList[i]
except:
igram = igramList[-1]; print 'No input date specified >>> continue with the last date'
## Read and Write
print 'reading '+igram+' ... '
dset = h5file[k][igram].get(igram)
data = dset[0:dset.shape[0],0:dset.shape[1]]
outname = igram
print 'writing >>> '+ outname
writefile.write_float32(data,outname)
f = open(outname+'.rsc','w')
for key , value in h5file[k][igram].attrs.iteritems():
f.write(key+' '+str(value)+'\n')
f.close()
else:
dset = h5file[k].get(k)
data = dset[0:dset.shape[0],0:dset.shape[1]]
if k == 'temporal_coherence': outname=File.split('.')[0]+'.cor'
else: outname=File.split('.')[0]+'.unw'
writefile.write(data,atr,outname)
h5file.close()
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):
########### 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):
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: 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):
try: File=argv[0]
except: Usage();sys.exit(1)
from numpy import pi
import h5py
import pysar._writefile as writefile
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 'velocity' in k:
dset = h5file['velocity'].get('velocity')
data = dset[0:dset.shape[0],0:dset.shape[1]]
print "converting velocity to a 1 year interferogram."
wvl=float(h5file[k[0]].attrs['WAVELENGTH'])
data=(-4*pi/wvl)*data
outname=File.split('.')[0]+'.unw'
print 'writing >>> '+ outname
writefile.write_float32(data,outname)
f = open(outname+'.rsc','w')
for key , value in h5file[k[0]].attrs.iteritems():
f.write(key+' '+str(value)+'\n')
f.close()
elif k[0] in ['rmse','temporal_coherence','mask']:
dset = h5file[k[0]].get(k[0])
data = dset[0:dset.shape[0],0:dset.shape[1]]
if k[0] == 'temporal_coherence': outname=File.split('.')[0]+'.cor'
else: outname=File.split('.')[0]+'.unw'
print 'writing >>> '+ outname
writefile.write_float32(data,outname)
f = open(outname+'.rsc','w')
for key , value in h5file[k[0]].attrs.iteritems():
f.write(key+' '+str(value)+'\n')
f.close()
elif 'timeseries' in k:
dateList=h5file['timeseries'].keys()
## Input
if len(sys.argv)==2:
print 'No input date specified >>> continue with the last date'
dateList=h5file['timeseries'].keys()
d=dateList[-1]
elif len(sys.argv)==3:
d=sys.argv[2]
elif len(sys.argv)==4:
ds=sys.argv[2:4]; ds.sort()
d_ref = ds[0]
d = ds[1]
else: Usage(); sys.exit(1)
## Data Operation
print 'reading '+d+' ... '
dset = h5file['timeseries'].get(d)
data = dset[0:dset.shape[0],0:dset.shape[1]]
try:
dset_ref = h5file['timeseries'].get(d_ref)
print 'reading '+d_ref+' ... '
data_ref = dset_ref[0:dset_ref.shape[0],0:dset_ref.shape[1]]
data = data - data_ref
except: pass
wvl=float(h5file[k[0]].attrs['WAVELENGTH'])
data=(-4*pi/wvl)*data
## outName
try: master_d = d_ref
except:
try: master_d = h5file[k[0]].attrs['ref_date']
except: master_d = h5file[k[0]].attrs['DATE']
if len(master_d)==8: master_d=master_d[2:8]
if len(d)==8: d=d[2:8]
outname = master_d+'_'+d+'.unw'
print 'writing >>> '+ outname
writefile.write_float32(data,outname)
f = open(outname+'.rsc','w')
for key , value in h5file[k[0]].attrs.iteritems():
if key=='DATE12':
f.write(key+' '+master_d+'-'+d+'\n')
else:
f.write(key+' '+str(value)+'\n')
f.close()
elif k[0] in ['interferograms','coherence','wrapped']:
igramList=h5file[k[0]].keys()
try: d=sys.argv[2]
except: d=igramList[-1]; print 'No input date specified >>> continue with the last date'
print 'reading '+d + ' ... '
dset=h5file[k[0]][d].get(d)
data = dset[0:dset.shape[0],0:dset.shape[1]]
outname=d
print 'writing >>> '+ outname
writefile.write_float32(data,outname)
f = open(outname+'.rsc','w')
for key , value in h5file[k[0]][d].attrs.iteritems():
f.write(key+' '+str(value)+'\n')
f.close()
h5file.close()
