def mosaic_timescan(burst_inventory, processing_dir, temp_dir, proc_file,
cut_to_aoi=False, exec_file=None):
# load ard parameters
with open(proc_file, 'r') as ard_file:
ard_params = json.load(ard_file)['processing parameters']
metrics = ard_params['time-scan ARD']['metrics']
if 'harmonics' in metrics:
metrics.remove('harmonics')
metrics.extend(['amplitude', 'phase', 'residuals'])
if 'percentiles' in metrics:
metrics.remove('percentiles')
metrics.extend(['p95', 'p5'])
# a products list
product_list = ['bs.HH', 'bs.VV', 'bs.HV', 'bs.VH',
'coh.VV', 'coh.VH', 'coh.HH', 'coh.HV',
'pol.Entropy', 'pol.Anisotropy', 'pol.Alpha']
tscan_dir = opj(processing_dir, 'Mosaic', 'Timescan')
os.makedirs(tscan_dir, exist_ok=True)
outfiles = []
for product, metric in itertools.product(product_list, metrics): # ****
filelist = glob.glob(
opj(processing_dir, '*', 'Timescan',
'*{}.{}.tif'.format(product, metric))
)
if not len(filelist) >= 2:
continue
filelist = ' '.join(filelist)
outfile = opj(tscan_dir, '{}.{}.tif'.format(product, metric))
check_file = opj(
os.path.dirname(outfile),
'.{}.processed'.format(os.path.basename(outfile)[:-4])
)
if os.path.isfile(check_file):
print(' INFO: Mosaic layer {} already '
' processed.'.format(os.path.basename(outfile)))
continue
print(' INFO: Mosaicking layer {}.'.format(os.path.basename(outfile)))
mosaic.mosaic(filelist, outfile, temp_dir, cut_to_aoi)
outfiles.append(outfile)
if exec_file:
print(' gdalbuildvrt ....command, outfiles')
else:
# create vrt
ras.create_tscan_vrt(tscan_dir, proc_file)
def mosaic_timescan(inventory_df,
processing_dir,
temp_dir,
proc_file,
cut_to_aoi=False,
exec_file=None):
# load ard parameters
with open(proc_file, 'r') as ard_file:
ard_params = json.load(ard_file)['processing parameters']
metrics = ard_params['time-scan ARD']['metrics']
if 'harmonics' in metrics:
metrics.remove('harmonics')
metrics.extend(['amplitude', 'phase', 'residuals'])
if 'percentiles' in metrics:
metrics.remove('percentiles')
metrics.extend(['p95', 'p5'])
# create out directory of not existent
tscan_dir = opj(processing_dir, 'Mosaic', 'Timescan')
os.makedirs(tscan_dir, exist_ok=True)
outfiles = []
# loop through all pontial proucts
for polar, metric in itertools.product(['VV', 'HH', 'VH', 'HV'], metrics):
# create a list of files based on polarisation and metric
filelist = glob.glob(
opj(processing_dir, '*', 'Timescan',
'*bs.{}.{}.tif'.format(polar, metric)))
# break loop if there are no files
if not len(filelist) >= 2:
continue
# get number
filelist = ' '.join(filelist)
outfile = opj(tscan_dir, 'bs.{}.{}.tif'.format(polar, metric))
check_file = opj(
os.path.dirname(outfile),
'.{}.processed'.format(os.path.basename(outfile)[:-4]))
if os.path.isfile(check_file):
print(' INFO: Mosaic layer {} already '
' processed.'.format(os.path.basename(outfile)))
continue
print(' INFO: Mosaicking layer {}.'.format(os.path.basename(outfile)))
mosaic.mosaic(filelist, outfile, temp_dir, cut_to_aoi)
outfiles.append(outfile)
if exec_file:
print(' gdalbuildvrt ....command, outfiles')
else:
ras.create_tscan_vrt(tscan_dir, proc_file)
def mosaic_timescan(
processing_dir,
ard_params,
cut_to_aoi=False,
):
metrics = ard_params['metrics']
if 'harmonics' in metrics:
metrics.remove('harmonics')
metrics.extend(['amplitude', 'phase', 'residuals'])
if 'percentiles' in metrics:
metrics.remove('percentiles')
metrics.extend(['p95', 'p5'])
# create out directory of not existent
tscan_dir = opj(processing_dir, 'Mosaic', 'Timescan')
os.makedirs(tscan_dir, exist_ok=True)
outfiles = []
# loop through all pontial proucts
for polar, metric in itertools.product(['VV', 'HH', 'VH', 'HV'], metrics):
# create a list of files based on polarisation and metric
filelist = glob.glob(
opj(processing_dir, '*', 'Timescan',
'*TC.{}.{}.tif'.format(polar, metric)))
# break loop if there are no files
if not len(filelist) >= 2:
continue
# get number
filelist = ' '.join(filelist)
outfile = opj(tscan_dir, 'BS.{}.{}.tif'.format(polar, metric))
check_file = opj(
os.path.dirname(outfile),
'.{}.processed'.format(os.path.basename(outfile)[:-4]))
if os.path.isfile(check_file):
logger.debug('INFO: Mosaic layer {} already '
' processed.'.format(os.path.basename(outfile)))
continue
logger.debug('INFO: Mosaicking layer {}.'.format(
os.path.basename(outfile)))
mosaic.mosaic(filelist, outfile, cut_to_aoi)
outfiles.append(outfile)
create_tscan_vrt(tscan_dir, ard_params)
def mosaic_timeseries(burst_inventory, processing_dir, temp_dir,
cut_to_aoi=False, exec_file=None):
print(' ------------------------------------')
print(' INFO: Mosaicking Time-series layers.')
print(' ------------------------------------')
# create output folder
ts_dir = opj(processing_dir, 'Mosaic', 'Timeseries')
os.makedirs(ts_dir, exist_ok=True)
# a products list
product_list = ['bs.HH', 'bs.VV', 'bs.HV', 'bs.VH',
'coh.VV', 'coh.VH', 'coh.HH', 'coh.HV',
'pol.Entropy', 'pol.Anisotropy', 'pol.Alpha']
# now we loop through each timestep and product
for product in product_list: # ****
bursts = burst_inventory.bid.unique()
nr_of_ts = len(glob.glob(opj(
processing_dir,
bursts[0],
'Timeseries',
'*.{}.tif'.format(product)))
)
if not nr_of_ts > 1:
continue
outfiles = []
for i in range(1, nr_of_ts + 1):
filelist = glob.glob(opj(
processing_dir, '*', 'Timeseries', '{}.*{}.tif'
.format(i, product)))
filelist = [file for file in filelist if 'Mosaic' not in file]
print(' INFO: Creating timeseries mosaic {} for {}.'.format(
i, product))
# create dates for timseries naming
datelist = []
for file in filelist:
if '.coh.' in file:
datelist.append('{}_{}'.format(
os.path.basename(file).split('.')[2],
os.path.basename(file).split('.')[1]))
else:
datelist.append(os.path.basename(file).split('.')[1])
start, end = sorted(datelist)[0], sorted(datelist)[-1]
filelist = ' '.join(filelist)
if start == end:
outfile = opj(ts_dir, '{}.{}.{}.tif'.format(i, start, product))
else:
outfile = opj(ts_dir, '{}.{}-{}.{}.tif'.format(i, start, end, product))
check_file = opj(
os.path.dirname(outfile),
'.{}.processed'.format(os.path.basename(outfile)[:-4])
)
outfiles.append(outfile)
if os.path.isfile(check_file):
print( 'INFO: Mosaic layer {} already'
' processed.'.format(outfile))
continue
# the command
print(' INFO: Mosaicking layer {}.'.format(os.path.basename(outfile)))
mosaic.mosaic(filelist, outfile, temp_dir, cut_to_aoi)
# create vrt
if exec_file:
continue
# create final vrt
vrt_options = gdal.BuildVRTOptions(srcNodata=0, separate=True)
gdal.BuildVRT(opj(ts_dir, '{}.Timeseries.vrt'.format(product)),
outfiles,
options=vrt_options)
def mosaic_timeseries(inventory_df,
processing_dir,
temp_dir,
cut_to_aoi=False,
exec_file=None):
logger.debug(' -----------------------------------')
logger.debug('INFO: Mosaicking Time-series layers')
logger.debug(' -----------------------------------')
# create output folder
ts_dir = opj(processing_dir, 'Mosaic', 'Timeseries')
os.makedirs(ts_dir, exist_ok=True)
# loop through polarisations
for p in ['VV', 'VH', 'HH', 'HV']:
tracks = inventory_df.relativeorbit.unique()
nr_of_ts = len(
glob.glob(
opj(processing_dir, tracks[0], 'Timeseries',
'*.{}.tif'.format(p))))
if not nr_of_ts >= 1:
continue
outfiles = []
for i in range(1, nr_of_ts + 1):
filelist = glob.glob(
opj(processing_dir, '*', 'Timeseries',
'{}.*.{}.tif'.format(i, p)))
filelist = [file for file in filelist if 'Mosaic' not in file]
# create
datelist = []
for file in filelist:
datelist.append(os.path.basename(file).split('.')[1])
filelist = ' '.join(filelist)
start, end = sorted(datelist)[0], sorted(datelist)[-1]
if start == end:
outfile = opj(ts_dir, '{}.{}.BS.{}.tif'.format(i, start, p))
else:
outfile = opj(ts_dir,
'{}.{}-{}.BS.{}.tif'.format(i, start, end, p))
check_file = opj(
os.path.dirname(outfile),
'.{}.processed'.format(os.path.basename(outfile)[:-4]))
outfiles.append(outfile)
if os.path.isfile(check_file):
logger.debug('INFO: Mosaic layer {} already'
' processed.'.format(os.path.basename(outfile)))
continue
logger.debug('INFO: Mosaicking layer {}.'.format(
os.path.basename(outfile)))
mosaic.mosaic(filelist, outfile, cut_to_aoi)
if exec_file:
logger.debug(' gdalbuildvrt ....command, outfiles')
continue
# create vrt
vrt_options = gdal.BuildVRTOptions(srcNodata=0, separate=True)
gdal.BuildVRT(opj(ts_dir, 'Timeseries.{}.vrt'.format(p)),
outfiles,
options=vrt_options)
def mosaic_timescan(burst_inventory, processing_dir, temp_dir, proc_file,
cut_to_aoi=False, exec_file=None, ncores=os.cpu_count()):
# load ard parameters
with open(proc_file, 'r') as ard_file:
ard_params = json.load(ard_file)['processing parameters']
metrics = ard_params['time-scan ARD']['metrics']
if 'harmonics' in metrics:
metrics.remove('harmonics')
metrics.extend(['amplitude', 'phase', 'residuals'])
if 'percentiles' in metrics:
metrics.remove('percentiles')
metrics.extend(['p95', 'p5'])
# a products list
product_list = ['bs.HH', 'bs.VV', 'bs.HV', 'bs.VH',
'coh.VV', 'coh.VH', 'coh.HH', 'coh.HV',
'pol.Entropy', 'pol.Anisotropy', 'pol.Alpha']
tscan_dir = opj(processing_dir, 'Mosaic', 'Timescan')
os.makedirs(tscan_dir, exist_ok=True)
outfiles = []
for product, metric in itertools.product(product_list, metrics): # ****
filelist = glob.glob(
opj(processing_dir, '*', 'Timescan',
'*{}.{}.tif'.format(product, metric))
)
if not len(filelist) >= 1:
continue
filelist = ' '.join(filelist)
outfile = opj(tscan_dir, '{}.{}.tif'.format(product, metric))
check_file = opj(
os.path.dirname(outfile),
'.{}.processed'.format(os.path.basename(outfile)[:-4])
)
if os.path.isfile(check_file):
print(' INFO: Mosaic layer {} already '
' processed.'.format(os.path.basename(outfile)))
continue
if exec_file:
filelist = filelist.split(" ")
if cut_to_aoi==False:
cut_to_aoi = 'False'
parallel_temp_dir = temp_dir + '/temp_' + product + '_mosaic_tscan'
os.makedirs(parallel_temp_dir, exist_ok=True)
args = ('{};{};{};{};{}').format(
filelist, outfile, parallel_temp_dir, cut_to_aoi, ncores)
# get path to graph
# rootpath = imp.find_module('ost')[1]
# python_exe = opj(rootpath, 'mosaic', 'mosaic.py')
exec_mosaic_timescan = exec_file + '_mosaic_tscan.txt'
with open(exec_mosaic_timescan, 'a') as exe:
exe.write('{}\n'.format(args))
else:
print(' INFO: Mosaicking layer {}.'.format(os.path.basename(outfile)))
mosaic.mosaic(filelist, outfile, temp_dir, cut_to_aoi)
outfiles.append(outfile)
if not exec_file:
# create vrt
ras.create_tscan_vrt(tscan_dir, proc_file)
else:
#create vrt exec file
exec_mosaic_tscan_vrt = exec_file + '_mosaic_tscan_vrt.txt'
with open(exec_mosaic_tscan_vrt, 'a') as exe:
exe.write('{};{}\n'.format(tscan_dir, proc_file))
def mosaic_timeseries(burst_inventory, processing_dir, temp_dir,
cut_to_aoi=False, exec_file=None, ncores=os.cpu_count()):
print(' ------------------------------------')
print(' INFO: Mosaicking Time-series layers.')
print(' ------------------------------------')
# create output folder
ts_dir = opj(processing_dir, 'Mosaic', 'Timeseries')
os.makedirs(ts_dir, exist_ok=True)
# a products list
product_list = ['bs.HH', 'bs.VV', 'bs.HV', 'bs.VH',
'coh.VV', 'coh.VH', 'coh.HH', 'coh.HV',
'pol.Entropy', 'pol.Anisotropy', 'pol.Alpha']
# now we loop through each timestep and product
for product in product_list: # ****
bursts = burst_inventory.bid.unique()
nr_of_ts = len(glob.glob(opj(
processing_dir,
bursts[0],
'Timeseries',
'*.{}.tif'.format(product)))
)
if not nr_of_ts > 1:
continue
outfiles = []
for i in range(1, nr_of_ts + 1):
filelist = glob.glob(opj(
processing_dir, '*', 'Timeseries', '{:02d}.*{}.tif'
.format(i, product)))
filelist = [file for file in filelist if 'Mosaic' not in file]
print(' INFO: Creating timeseries mosaic {:02d} for {}.'.format(
i, product))
# create dates for timseries naming
datelist = []
for file in filelist:
if '.coh.' in file:
datelist.append('{}_{}'.format(
os.path.basename(file).split('.')[2],
os.path.basename(file).split('.')[1]))
else:
datelist.append(os.path.basename(file).split('.')[1])
start, end = sorted(datelist)[0], sorted(datelist)[-1]
filelist = ' '.join(filelist)
if start == end:
outfile = opj(ts_dir, '{:02d}.{}.{}.tif'.format(i, start, product))
else:
outfile = opj(ts_dir, '{:02d}.{}-{}.{}.tif'.format(i, start, end, product))
check_file = opj(
os.path.dirname(outfile),
'.{}.processed'.format(os.path.basename(outfile)[:-4])
)
outfiles.append(outfile)
if os.path.isfile(check_file):
print( 'INFO: Mosaic layer {} already'
' processed.'.format(outfile))
continue
if exec_file:
filelist=filelist.split(" ")
if cut_to_aoi == False:
cut_to_aoi = 'False'
parallel_temp_dir = temp_dir + '/temp_' + product + '_' + str(i) + '_mosaic_timeseries'
os.makedirs(parallel_temp_dir, exist_ok=True)
args = ('{};{};{};{};{}').format(
filelist, outfile, parallel_temp_dir, cut_to_aoi, ncores)
# get path to graph
# rootpath = imp.find_module('ost')[1]
# python_exe = opj(rootpath, 'mosaic', 'mosaic.py')
exec_mosaic_timeseries = exec_file + '_mosaic_timeseries.txt'
with open(exec_mosaic_timeseries, 'a') as exe:
exe.write('{}\n'.format(args))
else:
# the command
print(' INFO: Mosaicking layer {}.'.format(os.path.basename(outfile)))
mosaic.mosaic(filelist, outfile, temp_dir, cut_to_aoi)
# create vrt
if not exec_file:
# create final vrt
vrt_options = gdal.BuildVRTOptions(srcNodata=0, separate=True)
gdal.BuildVRT(opj(ts_dir, '{}.Timeseries.vrt'.format(product)),
outfiles,
options=vrt_options)
else:
# create vrt exec file
exec_mosaic_ts_vrt = exec_file + '_mosaic_ts_vrt.txt'
with open(exec_mosaic_ts_vrt, 'a') as exe:
exe.write('{};{};{}\n'.format(ts_dir, product, outfiles))