def main(argv):
##### Check Inputs
if not argv or argv[0] in ['-h','--help']:
usage()
sys.exit(1)
if len(argv) < 2: print('\nAt lease 2 inputs are needed.\n'); sys.exit(1)
##### Read Original Attributes
print '************ Add / Update HDF5 File Attributes *************'
File = argv[0]
atr = readfile.read_attribute(File)
print 'Input file is '+atr['PROCESSOR']+' '+atr['FILE_TYPE']+': '+File
##### Read New Attributes
atr_new = dict()
for i in range(1,len(argv)):
if os.path.isfile(argv[i]):
atr_tmp = readfile.read_template(argv[i])
atr_new.update(atr_tmp)
else:
atr_tmp = argv[i].split('=')
atr_new[atr_tmp[0].strip()] = atr_tmp[1].strip()
print 'The following attributes will be added/updated:'
info.print_attributes(atr_new)
##### Update h5 File
k = atr['FILE_TYPE']
h5 = h5py.File(File,'r+')
for key, value in atr_new.iteritems():
h5[k].attrs[key] = value
h5.close
print 'Done.'
return
def main(argv):
##### Check Inputs
if not argv or argv[0] in ['-h', '--help']:
usage()
sys.exit(1)
if len(argv) < 2 or not argv[1]:
raise Exception('\nAt lease 2 inputs are needed.\n')
##### Read Original Attributes
#print '************ Add / Update HDF5 File Attributes *************'
File = argv[0]
atr = readfile.read_attribute(File)
print 'Input file is ' + atr['PROCESSOR'] + ' ' + atr[
'FILE_TYPE'] + ': ' + File
##### Read New Attributes
atr_new = dict()
for i in range(1, len(argv)):
if os.path.isfile(argv[i]):
atr_tmp = readfile.read_template(argv[i])
atr_new.update(atr_tmp)
else:
atr_tmp = argv[i].split('=')
atr_new[atr_tmp[0].strip()] = atr_tmp[1].strip()
print "The following attributes will be added/updated, or removed if new value is 'None':"
info.print_attributes(atr_new)
ext = os.path.splitext(File)[1]
##### Update h5 File
if ext in ['.h5', '.he5']:
File = ut.add_attribute(File, atr_new)
else:
if not ut.update_attribute_or_not(atr_new, atr):
print 'All updated (removed) attributes already exists (do not exists) and have the same value, skip update.'
else:
for key, value in atr_new.iteritems():
# delete the item is new value is None
if value == 'None':
try:
atr.pop(key)
except:
pass
else:
atr[key] = value
if atr['PROCESSOR'] == 'roipac':
print 'writing >>> ' + File + '.rsc'
writefile.write_roipac_rsc(atr, File + '.rsc')
return File
def prep_metadata(ts_file, print_msg=True):
"""Prepare metadata for HDF-EOS5 file"""
ts_obj = timeseries(ts_file)
ts_obj.open(print_msg=False)
unavco_meta_dict = metadata_pysar2unavco(ts_obj.metadata, ts_obj.dateList)
if print_msg:
print('## UNAVCO Metadata:')
print('-----------------------------------------')
info.print_attributes(unavco_meta_dict)
print('-----------------------------------------')
meta_dict = dict(ts_obj.metadata)
meta_dict.update(unavco_meta_dict)
meta_dict['FILE_TYPE'] = 'HDFEOS'
return meta_dict
def read_input_attribute(argv, print_msg=True):
atr_new = dict()
for i in range(1, len(argv)):
if os.path.isfile(argv[i]):
atr_tmp = readfile.read_template(argv[i])
atr_new.update(atr_tmp)
else:
atr_tmp = argv[i].split('=')
atr_new[atr_tmp[0].strip()] = atr_tmp[1].strip()
if print_msg:
print(
"The following attributes will be added/updated, or removed if new value is 'None':"
)
info.print_attributes(atr_new)
return atr_new
def main(argv):
inps = cmdLineParse()
if inps.template_file:
inps = read_template2inps(inps.template_file, inps)
##### Prepare Metadata
pysar_meta_dict = readfile.read_attribute(inps.timeseries_file)
k = pysar_meta_dict['FILE_TYPE']
length = int(pysar_meta_dict['FILE_LENGTH'])
width = int(pysar_meta_dict['WIDTH'])
h5_timeseries = h5py.File(inps.timeseries_file, 'r')
dateList = sorted(h5_timeseries[k].keys())
dateNum = len(dateList)
dateListStr = str(dateList).translate(None, "[],u'")
pysar_meta_dict['DATE_TIMESERIES'] = dateListStr
unavco_meta_dict = metadata_pysar2unavco(pysar_meta_dict, dateList)
print '## UNAVCO Metadata:'
print '-----------------------------------------'
info.print_attributes(unavco_meta_dict)
meta_dict = pysar_meta_dict.copy()
meta_dict.update(unavco_meta_dict)
print '-----------------------------------------'
##### Open HDF5 File
#####Get output filename
SAT = meta_dict['mission']
SW = meta_dict['beam_mode']
if meta_dict['beam_swath']:
SW += str(meta_dict['beam_swath'])
RELORB = "%03d" % (int(meta_dict['relative_orbit']))
##Frist and/or Last Frame
frame1 = int(meta_dict['frame'])
key = 'first_frame'
if key in meta_dict.keys():
frame1 = int(meta_dict[key])
FRAME = "%04d" % (frame1)
key = 'last_frame'
if key in meta_dict.keys():
frame2 = int(meta_dict[key])
if frame2 != frame1:
FRAME += "_%04d" % (frame2)
TBASE = "%04d" % (0)
BPERP = "%05d" % (0)
DATE1 = dt.datetime.strptime(meta_dict['first_date'],
'%Y-%m-%d').strftime('%Y%m%d')
DATE2 = dt.datetime.strptime(meta_dict['last_date'],
'%Y-%m-%d').strftime('%Y%m%d')
#end_date = dt.datetime.strptime(meta_dict['last_date'], '%Y-%m-%d')
#if inps.update and (dt.datetime.utcnow() - end_date) < dt.timedelta(days=365):
if inps.update:
print 'Update mode is enabled, put endDate as XXXXXXXX.'
DATE2 = 'XXXXXXXX'
#outName = SAT+'_'+SW+'_'+RELORB+'_'+FRAME+'_'+DATE1+'-'+DATE2+'_'+TBASE+'_'+BPERP+'.he5'
outName = SAT + '_' + SW + '_' + RELORB + '_' + FRAME + '_' + DATE1 + '_' + DATE2 + '.he5'
if inps.subset:
print 'Subset mode is enabled, put subset range info in output filename.'
lat1 = float(meta_dict['Y_FIRST'])
lon0 = float(meta_dict['X_FIRST'])
lat0 = lat1 + float(meta_dict['Y_STEP']) * length
lon1 = lon0 + float(meta_dict['X_STEP']) * width
lat0Str = 'N%05d' % (round(lat0 * 1e3))
lat1Str = 'N%05d' % (round(lat1 * 1e3))
lon0Str = 'E%06d' % (round(lon0 * 1e3))
lon1Str = 'E%06d' % (round(lon1 * 1e3))
if lat0 < 0.0: lat0Str = 'S%05d' % (round(abs(lat0) * 1e3))
if lat1 < 0.0: lat1Str = 'S%05d' % (round(abs(lat1) * 1e3))
if lon0 < 0.0: lon0Str = 'W%06d' % (round(abs(lon0) * 1e3))
if lon1 < 0.0: lon1Str = 'W%06d' % (round(abs(lon1) * 1e3))
SUB = '_%s_%s_%s_%s' % (lat0Str, lat1Str, lon0Str, lon1Str)
outName = os.path.splitext(outName)[0] + SUB + os.path.splitext(
outName)[1]
##### Open HDF5 File
print 'writing >>> ' + outName
f = h5py.File(outName, 'w')
hdfeos = f.create_group('HDFEOS')
if 'Y_FIRST' in meta_dict.keys():
gg_coord = hdfeos.create_group('GRIDS')
else:
gg_coord = hdfeos.create_group('SWATHS')
group = gg_coord.create_group('timeseries')
##### Write Attributes to the HDF File
print 'write metadata to ' + str(f)
for key, value in meta_dict.iteritems():
f.attrs[key] = value
##### Write Observation - Displacement
groupObs = group.create_group('observation')
print 'write data to ' + str(groupObs)
disDset = np.zeros((dateNum, length, width), np.float32)
for i in range(dateNum):
sys.stdout.write('\rreading 3D displacement from file %s: %d/%d ...' %
(inps.timeseries_file, i + 1, dateNum))
sys.stdout.flush()
disDset[i] = h5_timeseries[k].get(dateList[i])[:]
print ' '
dset = groupObs.create_dataset('displacement',
data=disDset,
dtype=np.float32)
dset.attrs['DATE_TIMESERIES'] = dateListStr
dset.attrs['Title'] = 'Displacement time-series'
dset.attrs['MissingValue'] = FLOAT_ZERO
dset.attrs['Units'] = 'meters'
dset.attrs['_FillValue'] = FLOAT_ZERO
##### Write Quality
groupQ = group.create_group('quality')
print 'write data to ' + str(groupQ)
## 1 - temporalCoherence
print 'reading coherence from file: ' + inps.coherence_file
data = readfile.read(inps.coherence_file)[0]
dset = groupQ.create_dataset('temporalCoherence',
data=data,
compression='gzip')
dset.attrs['Title'] = 'Temporal Coherence'
dset.attrs['MissingValue'] = FLOAT_ZERO
dset.attrs['Units'] = '1'
dset.attrs['_FillValue'] = FLOAT_ZERO
## 2 - mask
print 'reading mask from file: ' + inps.mask_file
data = readfile.read(inps.mask_file, epoch='mask')[0]
dset = groupQ.create_dataset('mask', data=data, compression='gzip')
dset.attrs['Title'] = 'Mask'
dset.attrs['MissingValue'] = BOOL_ZERO
dset.attrs['Units'] = '1'
dset.attrs['_FillValue'] = BOOL_ZERO
##### Write Geometry
## Required: height, incidenceAngle
## Optional: rangeCoord, azimuthCoord, headingAngle, slantRangeDistance, waterMask, shadowMask
groupGeom = group.create_group('geometry')
print 'write data to ' + str(groupGeom)
## 1 - height
print 'reading height from file: ' + inps.dem_file
data = readfile.read(inps.dem_file, epoch='height')[0]
dset = groupGeom.create_dataset('height', data=data, compression='gzip')
dset.attrs['Title'] = 'Digital elevatino model'
dset.attrs['MissingValue'] = INT_ZERO
dset.attrs['Units'] = 'meters'
dset.attrs['_FillValue'] = INT_ZERO
## 2 - incidenceAngle
print 'reading incidence angle from file: ' + inps.inc_angle_file
data = readfile.read(inps.inc_angle_file, epoch='incidenceAngle')[0]
dset = groupGeom.create_dataset('incidenceAngle',
data=data,
compression='gzip')
dset.attrs['Title'] = 'Incidence angle'
dset.attrs['MissingValue'] = FLOAT_ZERO
dset.attrs['Units'] = 'degrees'
dset.attrs['_FillValue'] = FLOAT_ZERO
## 3 - rangeCoord
try:
data = readfile.read(inps.rg_coord_file,
epoch='rangeCoord',
print_msg=False)[0]
print 'reading range coord from file: ' + inps.rg_coord_file
dset = groupGeom.create_dataset('rangeCoord',
data=data,
compression='gzip')
dset.attrs['Title'] = 'Range Coordinates'
dset.attrs['MissingValue'] = FLOAT_ZERO
dset.attrs['Units'] = '1'
dset.attrs['_FillValue'] = FLOAT_ZERO
except:
print 'No rangeCoord found in file %s' % (inps.rg_coord_file)
## 4 - azimuthCoord
try:
data = readfile.read(inps.az_coord_file,
epoch='azimuthCoord',
print_msg=False)[0]
print 'reading azimuth coord from file: ' + inps.az_coord_file
dset = groupGeom.create_dataset('azimuthCoord',
data=data,
compression='gzip')
dset.attrs['Title'] = 'Azimuth Coordinates'
dset.attrs['MissingValue'] = FLOAT_ZERO
dset.attrs['Units'] = '1'
dset.attrs['_FillValue'] = FLOAT_ZERO
except:
print 'No azimuthCoord found in file %s' % (inps.az_coord_file)
## 5 - headingAngle
try:
data = readfile.read(inps.head_angle_file,
epoch='heandingAngle',
print_msg=False)[0]
print 'reading azimuth coord from file: ' + inps.head_angle_file
dset = groupGeom.create_dataset('heandingAngle',
data=data,
compression='gzip')
dset.attrs['Title'] = 'Heanding Angle'
dset.attrs['MissingValue'] = FLOAT_ZERO
dset.attrs['Units'] = 'degrees'
dset.attrs['_FillValue'] = FLOAT_ZERO
except:
print 'No headingAngle found in file %s' % (inps.head_angle_file)
## 6 - slantRangeDistance
try:
data = readfile.read(inps.slant_range_dist_file,
epoch='slantRangeDistance',
print_msg=False)[0]
print 'reading slant range distance from file: ' + inps.slant_range_dist_file
dset = groupGeom.create_dataset('slantRangeDistance',
data=data,
compression='gzip')
dset.attrs['Title'] = 'Slant Range Distance'
dset.attrs['MissingValue'] = FLOAT_ZERO
dset.attrs['Units'] = 'meters'
dset.attrs['_FillValue'] = FLOAT_ZERO
except:
print 'No slantRangeDistance found in file %s' % (
inps.slant_range_dist_file)
## 7 - waterMask
try:
data = readfile.read(inps.water_mask_file,
epoch='waterMask',
print_msg=False)[0]
print 'reading water mask from file: ' + inps.water_mask_file
dset = groupGeom.create_dataset('waterMask',
data=data,
compression='gzip')
dset.attrs['Title'] = 'Water Mask'
dset.attrs['MissingValue'] = BOOL_ZERO
dset.attrs['Units'] = '1'
dset.attrs['_FillValue'] = BOOL_ZERO
except:
print 'No waterMask found in file %s' % (inps.water_mask_file)
## 8 - shadowMask
try:
data = readfile.read(inps.shadow_mask_file,
epoch='shadowMask',
print_msg=False)[0]
print 'reading shadow mask from file: ' + inps.shadow_mask_file
dset = groupGeom.create_dataset('shadowMask',
data=data,
compression='gzip')
dset.attrs['Title'] = 'Shadow Mask'
dset.attrs['MissingValue'] = BOOL_ZERO
dset.attrs['Units'] = '1'
dset.attrs['_FillValue'] = BOOL_ZERO
except:
print 'No shadowMask found in file %s' % (inps.shadow_mask_file)
f.close()
print 'Done.'
return
def main(argv):
inps = cmdLineParse()
#print '\n**************** Output to UNAVCO **************'
##### Prepare Metadata
pysar_meta_dict = readfile.read_attribute(inps.timeseries)
k = pysar_meta_dict['FILE_TYPE']
h5_timeseries = h5py.File(inps.timeseries, 'r')
dateList = sorted(h5_timeseries[k].keys())
unavco_meta_dict = metadata_pysar2unavco(pysar_meta_dict, dateList)
print '## UNAVCO Metadata:'
print '-----------------------------------------'
info.print_attributes(unavco_meta_dict)
meta_dict = pysar_meta_dict.copy()
meta_dict.update(unavco_meta_dict)
#### Open HDF5 File
SAT = meta_dict['mission']
SW = meta_dict[
'beam_mode'] # should be like FB08 for ALOS, need to find out, Yunjun, 2016-12-26
RELORB = "%03d" % (int(meta_dict['relative_orbit']))
FRAME = "%04d" % (int(meta_dict['frame']))
DATE1 = dt.strptime(meta_dict['first_date'], '%Y-%m-%d').strftime('%Y%m%d')
DATE2 = dt.strptime(meta_dict['last_date'], '%Y-%m-%d').strftime('%Y%m%d')
TBASE = "%04d" % (0)
BPERP = "%05d" % (0)
outName = SAT + '_' + SW + '_' + RELORB + '_' + FRAME + '_' + DATE1 + '-' + DATE2 + '_' + TBASE + '_' + BPERP + '.he5'
print '-----------------------------------------'
print 'writing >>> ' + outName
f = h5py.File(outName, 'w')
hdfeos = f.create_group('HDFEOS')
if 'Y_FIRST' in meta_dict.keys():
gg_coord = hdfeos.create_group('GRIDS')
else:
gg_coord = hdfeos.create_group('SWATHS')
group = gg_coord.create_group('timeseries')
##### Write Attributes to the HDF File
print 'write metadata to ' + str(f)
for key, value in meta_dict.iteritems():
f.attrs[key] = value
print 'write data to ' + str(group)
##### Write Time Series Data
print 'reading file: ' + inps.timeseries
print 'number of acquisitions: %d' % len(dateList)
for date in dateList:
print date
data = h5_timeseries[k].get(date)[:, :]
dset = group.create_dataset(date, data=data, compression='gzip')
dset.attrs['Title'] = 'Time series displacement'
dset.attrs['MissingValue'] = FLOAT_ZERO
dset.attrs['Units'] = 'meters'
dset.attrs['_FillValue'] = FLOAT_ZERO
##### Write Incidence_Angle
if os.path.isfile(inps.incidence_angle):
print 'reading file: ' + inps.incidence_angle
inc_angle, inc_angle_meta = readfile.read(inps.incidence_angle)
dset = group.create_dataset('incidence_angle',
data=inc_angle,
compression='gzip')
dset.attrs['Title'] = 'Incidence angle'
dset.attrs['MissingValue'] = FLOAT_ZERO
dset.attrs['Units'] = 'degrees'
dset.attrs['_FillValue'] = FLOAT_ZERO
##### Write DEM
if os.path.isfile(inps.dem):
print 'reading file: ' + inps.dem
dem, dem_meta = readfile.read(inps.dem)
dset = group.create_dataset('dem', data=dem, compression='gzip')
dset.attrs['Title'] = 'Digital elevatino model'
dset.attrs['MissingValue'] = INT_ZERO
dset.attrs['Units'] = 'meters'
dset.attrs['_FillValue'] = INT_ZERO
##### Write Coherence
if os.path.isfile(inps.coherence):
print 'reading file: ' + inps.coherence
coherence, coherence_meta = readfile.read(inps.coherence)
dset = group.create_dataset('coherence',
data=coherence,
compression='gzip')
dset.attrs['Title'] = 'Temporal Coherence'
dset.attrs['MissingValue'] = FLOAT_ZERO
dset.attrs['Units'] = 'None'
dset.attrs['_FillValue'] = FLOAT_ZERO
##### Write Mask
if os.path.isfile(inps.mask):
print 'reading file: ' + inps.mask
mask, mask_meta = readfile.read(inps.mask)
dset = group.create_dataset('mask', data=mask, compression='gzip')
dset.attrs['Title'] = 'Mask'
dset.attrs['MissingValue'] = INT_ZERO
dset.attrs['Units'] = 'None'
dset.attrs['_FillValue'] = INT_ZERO
f.close()
print 'Done.'
return