def mt_layover(filelist, outfile, extent):
'''
This function is usally used in the time-series workflow of OST. A list
of the filepaths layover/shadow masks
:param filelist - list of files
:param out_dir - directory where the output file will be stored
:return path to the multi-temporal layover/shadow mask file generated
'''
# get the start time for Info on processing time
start = time.time()
with TemporaryDirectory() as temp:
# create path to out file
ls_layer = opj(temp, os.path.basename(outfile))
# create a vrt-stack out of
logger.debug('INFO: Creating common Layover/Shadow Mask')
vrt_options = gdal.BuildVRTOptions(srcNodata=0, separate=True)
gdal.BuildVRT(opj(temp, 'ls.vrt'), filelist, options=vrt_options)
with rasterio.open(opj(temp, 'ls.vrt')) as src:
# get metadata
meta = src.meta
# update driver and reduced band count
meta.update(driver='GTiff', count=1, dtype='uint8')
# create outfiles
with rasterio.open(ls_layer, 'w', **meta) as out_min:
# loop through blocks
for _, window in src.block_windows(1):
# read array with all bands
stack = src.read(range(1, src.count + 1), window=window)
# get stats
arr_max = np.nanmax(stack, axis=0)
arr = arr_max / arr_max
out_min.write(np.uint8(arr), window=window, indexes=1)
ras.mask_by_shape(ls_layer,
outfile,
extent,
to_db=False,
datatype='uint8',
rescale=False,
ndv=0)
# os.remove(ls_layer)
h.timer(start)
return outfile
def mt_layover_old(list_of_files, config_file):
"""
:param list_of_files:
:param config_file:
:return:
"""
# this is a godale thing
with open(config_file) as file:
config_dict = json.load(file)
temp_dir = Path(config_dict['temp_dir'])
update_extent = (
config_dict['processing']['time-series_ARD']['apply_ls_mask'])
target_dir = Path(list_of_files[0]).parent.parent.parent
outfile = target_dir.joinpath(f'{target_dir.name}.ls_mask.tif')
extent = target_dir.joinpath(f'{target_dir.name}.extent.gpkg')
burst_dir = Path(outfile).parent
burst = burst_dir.name
logger.info(
f'Creating common Layover/Shadow mask for track {target_dir.name}.')
with TemporaryDirectory(prefix=f'{temp_dir}/') as temp:
# temp to Path object
temp = Path(temp)
# create path to temp file
ls_layer = temp.joinpath(Path(outfile).name)
# create a vrt-stack out of
vrt_options = gdal.BuildVRTOptions(srcNodata=0, separate=True)
gdal.BuildVRT(str(temp.joinpath('ls.vrt')),
list_of_files,
options=vrt_options)
with rasterio.open(temp.joinpath('ls.vrt')) as src:
# get metadata
meta = src.meta
# update driver and reduced band count
meta.update(driver='GTiff', count=1, dtype='uint8')
# create outfiles
with rasterio.open(ls_layer, 'w', **meta) as out_min:
# loop through blocks
for _, window in src.block_windows(1):
# read array with all bands
stack = src.read(range(1, src.count + 1), window=window)
# get stats
arr_max = np.nanmax(stack, axis=0)
arr = np.divide(arr_max, arr_max)
out_min.write(np.uint8(arr), window=window, indexes=1)
ras.mask_by_shape(ls_layer,
outfile,
extent,
to_db=False,
datatype='uint8',
rescale=False,
ndv=0)
ls_layer.unlink()
extent_ls_masked = None
if update_extent:
logger.info(
'Calculating symmetrical difference of extent and ls_mask')
# polygonize the multi-temporal ls mask
ras.polygonize_raster(outfile, f'{str(outfile)[:-4]}.gpkg')
# create file for masked extent
extent_ls_masked = burst_dir.joinpath(
f'{burst}.extent.masked.gpkg')
# calculate difference between burst extent
# and ls mask, for masked extent
try:
vec.difference(extent, f'{outfile.stem}.gpkg',
extent_ls_masked)
except:
shutil.copy(extent, extent_ls_masked)
return burst_dir, list_of_files, outfile, extent_ls_masked
def mt_layover(filelist, outfile, temp_dir, extent, update_extent=False):
'''
This function is usally used in the time-series workflow of OST. A list
of the filepaths layover/shadow masks
:param filelist - list of files
:param out_dir - directory where the output file will be stored
:return path to the multi-temporal layover/shadow mask file generated
'''
# get some info
burst_dir = os.path.dirname(outfile)
burst = os.path.basename(burst_dir)
extent = opj(burst_dir, '{}.extent.shp'.format(burst))
# get the start time for Info on processing time
start = time.time()
# create path to out file
ls_layer = opj(temp_dir, os.path.basename(outfile))
# create a vrt-stack out of
print(' INFO: Creating common Layover/Shadow Mask')
vrt_options = gdal.BuildVRTOptions(srcNodata=0, separate=True)
gdal.BuildVRT(opj(temp_dir, 'ls.vrt'), filelist, options=vrt_options)
with rasterio.open(opj(temp_dir, 'ls.vrt')) as src:
# get metadata
meta = src.meta
# update driver and reduced band count
meta.update(driver='GTiff', count=1, dtype='uint8')
# create outfiles
with rasterio.open(ls_layer, 'w', **meta) as out_min:
# loop through blocks
for _, window in src.block_windows(1):
# read array with all bands
stack = src.read(range(1, src.count + 1), window=window)
# get stats
arr_max = np.nanmax(stack, axis=0)
arr = arr_max / arr_max
out_min.write(np.uint8(arr), window=window, indexes=1)
ras.mask_by_shape(ls_layer,
outfile,
extent,
to_db=False,
datatype='uint8',
rescale=False,
ndv=0)
os.remove(ls_layer)
h.timer(start)
if update_extent:
print(' INFO: Calculating symetrical difference of extent and ls_mask')
# polygonize the multi-temporal ls mask
ras.polygonize_raster(outfile, '{}.shp'.format(outfile[:-4]))
# create file for masked extent
extent_ls_masked = opj(burst_dir, '{}.extent.masked.shp'.format(burst))
# calculate difference between burst exntetn and ls mask, fr masked extent
vec.difference(extent, '{}.shp'.format(outfile[:-4]), extent_ls_masked)
def ard_to_ts(list_of_files, burst, product, pol, config_file):
# -------------------------------------------
# 1 unpack list of args
# convert list of files readable for snap
list_of_files = f"\'{','.join(str(x) for x in list_of_files)}\'"
# -------------------------------------------
# 2 read config file
with open(config_file, 'r') as file:
config_dict = json.load(file)
processing_dir = Path(config_dict['processing_dir'])
ard = config_dict['processing']['single_ARD']
ard_mt = config_dict['processing']['time-series_ARD']
# -------------------------------------------
# 3 get namespace of directories and check if already processed
# get the burst directory
burst_dir = processing_dir.joinpath(burst)
# get timeseries directory and create if non existent
out_dir = burst_dir.joinpath('Timeseries')
Path.mkdir(out_dir, parents=True, exist_ok=True)
# in case some processing has been done before, check if already processed
check_file = out_dir.joinpath(f'.{product}.{pol}.processed')
if Path.exists(check_file):
logger.info(
f'Timeseries of {burst} for {product} in {pol} '
f'polarisation already processed.'
)
out_files = 'already_processed'
out_vrt = 'already_processed'
return (
burst, list_of_files, out_files, out_vrt, f'{product}.{pol}', None
)
# -------------------------------------------
# 4 adjust processing parameters according to config
# get the db scaling right
to_db = ard['to_db']
if to_db or product != 'bs':
to_db = False
logger.debug(f'Not converting to dB for {product}')
else:
to_db = ard_mt['to_db']
logger.debug(f'Converting to dB for {product}')
if ard_mt['apply_ls_mask']:
extent = burst_dir.joinpath(f'{burst}.valid.json')
else:
extent = burst_dir.joinpath(f'{burst}.min_bounds.json')
# -------------------------------------------
# 5 SNAP processing
with TemporaryDirectory(prefix=f"{config_dict['temp_dir']}/") as temp:
# turn to Path object
temp = Path(temp)
# create namespaces
temp_stack = temp.joinpath(f'{burst}_{product}_{pol}')
out_stack = temp.joinpath(f'{burst}_{product}_{pol}_mt')
stack_log = out_dir.joinpath(f'{burst}_{product}_{pol}_stack.err_log')
# run stacking routine
if pol in ['Alpha', 'Anisotropy', 'Entropy']:
logger.info(
f'Creating multi-temporal stack of images of burst/track '
f'{burst} for the {pol} band of the polarimetric '
f'H-A-Alpha decomposition.'
)
try:
create_stack(
list_of_files, temp_stack, stack_log, config_dict,
pattern=pol
)
except (GPTRuntimeError, NotValidFileError) as error:
logger.info(error)
return None, None, None, None, None, error
else:
logger.info(
f'Creating multi-temporal stack of images of burst/track '
f'{burst} for {product} product in {pol} polarization.'
)
try:
create_stack(
list_of_files, temp_stack, stack_log, config_dict,
polarisation=pol
)
except (GPTRuntimeError, NotValidFileError) as error:
logger.info(error)
return None, None, None, None, None, error
# run mt speckle filter
if ard_mt['remove_mt_speckle'] is True:
speckle_log = out_dir.joinpath(
f'{burst}_{product}_{pol}_mt_speckle.err_log'
)
logger.debug('Applying multi-temporal speckle filter')
try:
mt_speckle_filter(
temp_stack.with_suffix('.dim'), out_stack, speckle_log,
config_dict
)
except (GPTRuntimeError, NotValidFileError) as error:
logger.info(error)
return None, None, None, None, None, error
# remove tmp files
h.delete_dimap(temp_stack)
else:
out_stack = temp_stack
# -----------------------------------------------
# 6 Conversion to GeoTiff
# min max dict for stretching in case of 16 or 8 bit datatype
mm_dict = {'bs': {'min': -30, 'max': 5},
'coh': {'min': 0.000001, 'max': 1},
'Alpha': {'min': 0.000001, 'max': 90},
'Anisotropy': {'min': 0.000001, 'max': 1},
'Entropy': {'min': 0.000001, 'max': 1}
}
stretch = pol if pol in ['Alpha', 'Anisotropy', 'Entropy'] else product
if product == 'coh':
# get slave and master dates from file names and sort them
mst_dates = sorted([
dt.strptime(
file.name.split('_')[3].split('.')[0], SNAP_DATEFORMAT
)
for file in list(out_stack.with_suffix('.data').glob('*.img'))
])
slv_dates = sorted([
dt.strptime(
file.name.split('_')[4].split('.')[0], SNAP_DATEFORMAT
)
for file in list(out_stack.with_suffix('.data').glob('*.img'))
])
# write them back to string for following loop
mst_dates = [dt.strftime(ts, SNAP_DATEFORMAT) for ts in mst_dates]
slv_dates = [dt.strftime(ts, SNAP_DATEFORMAT) for ts in slv_dates]
out_files = []
for i, (mst, slv) in enumerate(zip(mst_dates, slv_dates)):
# re-construct namespace for input file
infile = list(
out_stack.with_suffix('.data').glob(
f'*{pol}*{mst}_{slv}*img'
)
)[0]
# rename dates to YYYYMMDD format
mst = dt.strftime(dt.strptime(mst, SNAP_DATEFORMAT), '%y%m%d')
slv = dt.strftime(dt.strptime(slv, SNAP_DATEFORMAT), '%y%m%d')
# create namespace for output file with renamed dates
outfile = out_dir.joinpath(
f'{i+1:02d}.{mst}.{slv}.{product}.{pol}.tif'
)
# fill internal values if any
#with rasterio.open(str(infile), 'r') as src:
# meta = src.meta.copy()
# filled = ras.fill_internal_nans(src.read())
#with rasterio.open(str(infile), 'w', **meta) as dest:
# dest.write(filled)
#print('filled')
# produce final outputfile,
# including dtype conversion and ls mask
ras.mask_by_shape(
infile, outfile, extent, to_db=to_db,
datatype=ard_mt['dtype_output'],
min_value=mm_dict[stretch]['min'],
max_value=mm_dict[stretch]['max'],
ndv=0.0, description=True)
# add ot a list for subsequent vrt creation
out_files.append(str(outfile))
else:
# get the dates of the files
dates = sorted([dt.strptime(
file.name.split('_')[-1][:-4], SNAP_DATEFORMAT)
for file in list(out_stack.with_suffix('.data').glob('*.img'))
])
# write them back to string for following loop
dates = [dt.strftime(ts, "%d%b%Y") for ts in dates]
out_files = []
for i, date in enumerate(dates):
# re-construct namespace for input file
infile = list(
out_stack.with_suffix('.data').glob(f'*{pol}*{date}*img')
)[0]
# restructure date to YYMMDD
date = dt.strftime(
dt.strptime(date, SNAP_DATEFORMAT), '%y%m%d'
)
# create namespace for output file
outfile = out_dir.joinpath(
f'{i+1:02d}.{date}.{product}.{pol}.tif'
)
# fill internal nodata
#if ard['image_type'] == 'SLC':
#with rasterio.open(str(infile), 'r') as src:
# meta = src.meta.copy()
#filled = ras.fill_internal_nans(src.read())
#with rasterio.open(str(infile), 'w', **meta) as dest:
# dest.write(filled)
#print('filledbs')
# run conversion routine
ras.mask_by_shape(infile, outfile, extent,
to_db=to_db,
datatype=ard_mt['dtype_output'],
min_value=mm_dict[stretch]['min'],
max_value=mm_dict[stretch]['max'],
ndv=0.0)
# add ot a list for subsequent vrt creation
out_files.append(str(outfile))
# -----------------------------------------------
# 7 Filechecks
for file in out_files:
return_code = h.check_out_tiff(file)
if return_code != 0:
for file_ in out_files:
Path(file_).unlink()
if Path(f'{file}.xml').exists():
Path(f'{file}.xml').unlink()
return (
burst, list_of_files, None, None,
f'{product}.{pol}', return_code
)
# write file, so we know this ts has been successfully processed
with open(str(check_file), 'w') as file:
file.write('passed all tests \n')
# -----------------------------------------------
# 8 Create vrts
vrt_options = gdal.BuildVRTOptions(srcNodata=0, separate=True)
out_vrt = str(out_dir.joinpath(f'Timeseries.{product}.{pol}.vrt'))
gdal.BuildVRT(
out_vrt,
out_files,
options=vrt_options
)
return burst, list_of_files, out_files, out_vrt, f'{product}.{pol}', None
def ard_to_ts(list_of_files,
processing_dir,
temp_dir,
burst,
proc_file,
product,
pol,
ncores=os.cpu_count()):
if type(list_of_files) == str:
list_of_files = list_of_files.replace("'", '').strip('][').split(', ')
# get the burst directory
burst_dir = opj(processing_dir, burst)
# check routine if timeseries has already been processed
check_file = opj(burst_dir, 'Timeseries',
'.{}.{}.processed'.format(product, pol))
if os.path.isfile(check_file):
print(' INFO: Timeseries of {} for {} in {} polarisation already'
' processed'.format(burst, product, pol))
return
# load ard parameters
with open(proc_file, 'r') as ard_file:
ard_params = json.load(ard_file)['processing parameters']
ard = ard_params['single ARD']
ard_mt = ard_params['time-series ARD']
if ard_mt['remove mt speckle'] is True:
ard_mt_speck = ard_params['time-series ARD']['mt speckle filter']
# get the db scaling right
to_db = ard['to db']
if to_db or product != 'bs':
to_db = False
print('INFO: Not converting to dB for {}'.format(product))
else:
to_db = ard_mt['to db']
print('INFO: Converting to dB for {}'.format(product))
if ard['apply ls mask']:
extent = opj(burst_dir, '{}.extent.masked.shp'.format(burst))
else:
extent = opj(burst_dir, '{}.extent.shp'.format(burst))
# min max dict for stretching in case of 16 or 8 bit datatype
mm_dict = {
'bs': {
'min': -30,
'max': 5
},
'coh': {
'min': 0.000001,
'max': 1
},
'Alpha': {
'min': 0.000001,
'max': 90
},
'Anisotropy': {
'min': 0.000001,
'max': 1
},
'Entropy': {
'min': 0.000001,
'max': 1
}
}
stretch = pol if pol in ['Alpha', 'Anisotropy', 'Entropy'] else product
# define out_dir for stacking routine
out_dir = opj(processing_dir, '{}'.format(burst), 'Timeseries')
os.makedirs(out_dir, exist_ok=True)
# create namespaces
temp_stack = opj(temp_dir, '{}_{}_{}'.format(burst, product, pol))
out_stack = opj(temp_dir, '{}_{}_{}_mt'.format(burst, product, pol))
stack_log = opj(out_dir,
'{}_{}_{}_stack.err_log'.format(burst, product, pol))
# run stacking routines
# convert list of files readable for snap
list_of_files = '\'{}\''.format(','.join(list_of_files))
if pol in ['Alpha', 'Anisotropy', 'Entropy']:
print(
' INFO: Creating multi-temporal stack of images of burst/track {} for'
' the {} band of the polarimetric H-A-Alpha'
' decomposition.'.format(burst, pol))
create_stack(list_of_files, temp_stack, stack_log, pattern=pol)
else:
print(
' INFO: Creating multi-temporal stack of images of burst/track {} for'
' {} product in {} polarization.'.format(burst, product, pol))
create_stack(list_of_files, temp_stack, stack_log, polarisation=pol)
# run mt speckle filter
if ard_mt['remove mt speckle'] is True:
speckle_log = opj(
out_dir, '{}_{}_{}_mt_speckle.err_log'.format(burst, product, pol))
print(' INFO: Applying multi-temporal speckle filter')
mt_speckle_filter('{}.dim'.format(temp_stack),
out_stack,
speckle_log,
speckle_dict=ard_mt_speck,
ncores=ncores)
# remove tmp files
h.delete_dimap(temp_stack)
else:
out_stack = temp_stack
if product == 'coh':
# get slave and master Date
mstDates = [
datetime.datetime.strptime(
os.path.basename(x).split('_')[3].split('.')[0], '%d%b%Y')
for x in glob.glob(opj('{}.data'.format(out_stack), '*img'))
]
slvDates = [
datetime.datetime.strptime(
os.path.basename(x).split('_')[4].split('.')[0], '%d%b%Y')
for x in glob.glob(opj('{}.data'.format(out_stack), '*img'))
]
# sort them
mstDates.sort()
slvDates.sort()
# write them back to string for following loop
sortedMstDates = [
datetime.datetime.strftime(ts, "%d%b%Y") for ts in mstDates
]
sortedSlvDates = [
datetime.datetime.strftime(ts, "%d%b%Y") for ts in slvDates
]
i, outfiles = 1, []
for mst, slv in zip(sortedMstDates, sortedSlvDates):
inMst = datetime.datetime.strptime(mst, '%d%b%Y')
inSlv = datetime.datetime.strptime(slv, '%d%b%Y')
outMst = datetime.datetime.strftime(inMst, '%y%m%d')
outSlv = datetime.datetime.strftime(inSlv, '%y%m%d')
infile = glob.glob(
opj('{}.data'.format(out_stack),
'*{}*{}_{}*img'.format(pol, mst, slv)))[0]
outfile = opj(
out_dir,
'{:02d}.{}.{}.{}.{}.tif'.format(i, outMst, outSlv, product,
pol))
ras.mask_by_shape(infile,
outfile,
extent,
to_db=to_db,
datatype=ard_mt['dtype output'],
min_value=mm_dict[stretch]['min'],
max_value=mm_dict[stretch]['max'],
ndv=0.0,
description=True)
# add ot a list for subsequent vrt creation
outfiles.append(outfile)
i += 1
else:
# get the dates of the files
dates = [
datetime.datetime.strptime(x.split('_')[-1][:-4], '%d%b%Y')
for x in glob.glob(opj('{}.data'.format(out_stack), '*img'))
]
# sort them
dates.sort()
# write them back to string for following loop
sortedDates = [
datetime.datetime.strftime(ts, "%d%b%Y") for ts in dates
]
i, outfiles = 1, []
for date in sortedDates:
# restructure date to YYMMDD
inDate = datetime.datetime.strptime(date, '%d%b%Y')
outDate = datetime.datetime.strftime(inDate, '%y%m%d')
infile = glob.glob(
opj('{}.data'.format(out_stack),
'*{}*{}*img'.format(pol, date)))[0]
# create outfile
outfile = opj(
out_dir, '{:02d}.{}.{}.{}.tif'.format(i, outDate, product,
pol))
ras.mask_by_shape(infile,
outfile,
extent,
to_db=to_db,
datatype=ard_mt['dtype output'],
min_value=mm_dict[stretch]['min'],
max_value=mm_dict[stretch]['max'],
ndv=0.0)
# add ot a list for subsequent vrt creation
outfiles.append(outfile)
i += 1
for file in outfiles:
return_code = h.check_out_tiff(file)
if return_code != 0:
h.remove_folder_content(temp_dir)
os.remove(file)
return return_code
# write file, so we know this ts has been succesfully processed
if return_code == 0:
with open(str(check_file), 'w') as file:
file.write('passed all tests \n')
# build vrt of timeseries
vrt_options = gdal.BuildVRTOptions(srcNodata=0, separate=True)
gdal.BuildVRT(opj(out_dir, 'Timeseries.{}.{}.vrt'.format(product, pol)),
outfiles,
options=vrt_options)
# remove tmp files
h.delete_dimap(out_stack)
def _ard_to_ts(burst_inventory, processing_dir, temp_dir, burst, to_db,
ls_mask_create, ls_mask_apply, mt_speckle_filter, datatype):
burst_dir = opj(processing_dir, burst)
# get common burst extent
list_of_scenes = glob.glob(opj(burst_dir, '20*', '*data*', '*img'))
list_of_scenes = [x for x in list_of_scenes if 'layover' not in x]
extent = opj(burst_dir, '{}.extent.shp'.format(burst))
ts.mt_extent(list_of_scenes, extent, temp_dir, buffer=-0.0018)
# remove inital extent
for file in glob.glob(opj(burst_dir, 'tmp*')):
os.remove(file)
# layover/shadow mask
if ls_mask_create is True:
list_of_scenes = glob.glob(opj(burst_dir, '20*', '*data*', '*img'))
list_of_layover = [x for x in list_of_scenes if 'layover' in x]
out_ls = opj(burst_dir, '{}.ls_mask.tif'.format(burst))
ts.mt_layover(list_of_layover, out_ls, temp_dir, extent=extent)
print(' INFO: Our common layover mask is located at {}'.format(out_ls))
if ls_mask_apply:
print(' INFO: Calculating symetrical difference of extent and ls_mask')
ras.polygonize_raster(out_ls, '{}.shp'.format(out_ls[:-4]))
extent_ls_masked = opj(burst_dir, '{}.extent.masked.shp'.format(burst))
vec.difference(extent, '{}.shp'.format(out_ls[:-4]), extent_ls_masked)
extent = extent_ls_masked
list_of_product_types = {'BS': 'Gamma0', 'coh': 'coh', 'ha_alpha': 'Alpha'}
# we loop through each possible product
for p, product_name in list_of_product_types.items():
# we loop through each polarisation
for pol in ['VV', 'VH', 'HH', 'HV']:
# see if there is actually any imagery
list_of_ts_bursts = sorted(
glob.glob(
opj(processing_dir, burst, '20*', '*data*',
'{}*{}*img'.format(product_name, pol))))
if len(list_of_ts_bursts) > 1:
# check for all datafiles of this product type
list_of_ts_bursts = sorted(
glob.glob(
opj(processing_dir, burst, '20*/',
'*{}*dim'.format(p))))
list_of_ts_bursts = '\'{}\''.format(
','.join(list_of_ts_bursts))
# define out_dir for stacking routine
out_dir = opj(processing_dir, '{}/Timeseries'.format(burst))
os.makedirs(out_dir, exist_ok=True)
# create namespaces
temp_stack = opj(temp_dir, '{}_{}_{}_mt'.format(burst, p, pol))
out_stack = opj(out_dir, '{}_{}_{}_mt'.format(burst, p, pol))
stack_log = opj(out_dir,
'{}_{}_{}_stack.err_log'.format(burst, p, pol))
# run stacking routines
ts.create_stack(list_of_ts_bursts,
temp_stack,
stack_log,
polarisation=pol)
# run mt speckle filter
if mt_speckle_filter is True:
speckle_log = opj(
out_dir,
'{}_{}_{}_mt_speckle.err_log'.format(burst, p, pol))
ts.mt_speckle_filter('{}.dim'.format(temp_stack),
out_stack, speckle_log)
# remove tmp files
h.delete_dimap(temp_stack)
else:
out_stack = temp_stack
# convert to GeoTiffs
if p == 'BS':
# get the dates of the files
dates = [
datetime.datetime.strptime(
x.split('_')[-1][:-4], '%d%b%Y')
for x in glob.glob(
opj('{}.data'.format(out_stack), '*img'))
]
# sort them
dates.sort()
# write them back to string for following loop
sortedDates = [
datetime.datetime.strftime(ts, "%d%b%Y")
for ts in dates
]
i, outfiles = 1, []
for date in sortedDates:
# restructure date to YYMMDD
inDate = datetime.datetime.strptime(date, '%d%b%Y')
outDate = datetime.datetime.strftime(inDate, '%y%m%d')
infile = glob.glob(
opj('{}.data'.format(out_stack),
'*{}*{}*img'.format(pol, date)))[0]
# create outfile
outfile = opj(
out_dir,
'{}.{}.{}.{}.tif'.format(i, outDate, p, pol))
# mask by extent
ras.mask_by_shape(infile,
outfile,
extent,
to_db=to_db,
datatype=datatype,
min_value=-30,
max_value=5,
ndv=0)
# add ot a list for subsequent vrt creation
outfiles.append(outfile)
i += 1
# build vrt of timeseries
vrt_options = gdal.BuildVRTOptions(srcNodata=0,
separate=True)
gdal.BuildVRT(opj(out_dir,
'Timeseries.{}.{}.vrt'.format(p, pol)),
outfiles,
options=vrt_options)
if p == 'coh':
# get slave and master Date
mstDates = [
datetime.datetime.strptime(
os.path.basename(x).split('_')[3].split('.')[0],
'%d%b%Y') for x in glob.glob(
opj('{}.data'.format(out_stack), '*img'))
]
slvDates = [
datetime.datetime.strptime(
os.path.basename(x).split('_')[4].split('.')[0],
'%d%b%Y') for x in glob.glob(
opj('{}.data'.format(out_stack), '*img'))
]
# sort them
mstDates.sort()
slvDates.sort()
# write them back to string for following loop
sortedMstDates = [
datetime.datetime.strftime(ts, "%d%b%Y")
for ts in mstDates
]
sortedSlvDates = [
datetime.datetime.strftime(ts, "%d%b%Y")
for ts in slvDates
]
i, outfiles = 1, []
for mst, slv in zip(sortedMstDates, sortedSlvDates):
inMst = datetime.datetime.strptime(mst, '%d%b%Y')
inSlv = datetime.datetime.strptime(slv, '%d%b%Y')
outMst = datetime.datetime.strftime(inMst, '%y%m%d')
outSlv = datetime.datetime.strftime(inSlv, '%y%m%d')
infile = glob.glob(
opj('{}.data'.format(out_stack),
'*{}*{}_{}*img'.format(pol, mst, slv)))[0]
outfile = opj(
out_dir, '{}.{}.{}.{}.{}.tif'.format(
i, outMst, outSlv, p, pol))
ras.mask_by_shape(infile,
outfile,
extent,
to_db=False,
datatype=datatype,
min_value=0.000001,
max_value=1,
ndv=0)
# add ot a list for subsequent vrt creation
outfiles.append(outfile)
i += 1
# build vrt of timeseries
vrt_options = gdal.BuildVRTOptions(srcNodata=0,
separate=True)
gdal.BuildVRT(opj(out_dir,
'Timeseries.{}.{}.vrt'.format(p, pol)),
outfiles,
options=vrt_options)
# remove tmp files
h.delete_dimap(out_stack)
for pol in ['Alpha', 'Entropy', 'Anisotropy']:
list_of_ts_bursts = sorted(
glob.glob(
opj(processing_dir, burst, '20*', '*{}*'.format(p),
'*{}.img'.format(pol))))
if len(list_of_ts_bursts) > 1:
list_of_ts_bursts = sorted(
glob.glob(
opj(processing_dir, burst, '20*/', '*{}*dim'.format(p))))
list_of_ts_bursts = '\'{}\''.format(','.join(list_of_ts_bursts))
# print(list_of_ts_bursts)
out_dir = opj(processing_dir, '{}/Timeseries'.format(burst))
os.makedirs(out_dir, exist_ok=True)
temp_stack = opj(temp_dir, '{}_{}_mt'.format(burst, pol))
out_stack = opj(out_dir, '{}_{}_mt'.format(burst, pol))
stack_log = opj(out_dir, '{}_{}_stack.err_log'.format(burst, pol))
# processing routines
ts.create_stack(list_of_ts_bursts,
temp_stack,
stack_log,
pattern=pol)
if mt_speckle_filter is True:
speckle_log = opj(
out_dir, '{}_{}_mt_speckle.err_log'.format(burst, pol))
ts.mt_speckle_filter('{}.dim'.format(temp_stack), out_stack,
speckle_log)
# remove tmp files
h.delete_dimap(temp_stack)
else:
out_stack = temp_stack
# get the dates of the files
dates = [
datetime.datetime.strptime(x.split('_')[-1][:-4], '%d%b%Y')
for x in glob.glob(opj('{}.data'.format(out_stack), '*img'))
]
# sort them
dates.sort()
# write them back to string for following loop
sortedDates = [
datetime.datetime.strftime(ts, "%d%b%Y") for ts in dates
]
i, outfiles = 1, []
for date in sortedDates:
# restructure date to YYMMDD
inDate = datetime.datetime.strptime(date, '%d%b%Y')
outDate = datetime.datetime.strftime(inDate, '%y%m%d')
infile = glob.glob(
opj('{}.data'.format(out_stack),
'*{}*{}*img'.format(pol, date)))[0]
# create outfile
outfile = opj(out_dir,
'{}.{}.{}.{}.tif'.format(i, outDate, p, pol))
# mask by extent
max_value = 90 if pol is 'Alpha' else 1
ras.mask_by_shape(infile,
outfile,
extent,
to_db=False,
datatype=datatype,
min_value=0.000001,
max_value=max_value,
ndv=0)
# add ot a list for subsequent vrt creation
outfiles.append(outfile)
i += 1
# build vrt of timeseries
vrt_options = gdal.BuildVRTOptions(srcNodata=0, separate=True)
gdal.BuildVRT(opj(out_dir, 'Timeseries.{}.vrt'.format(pol)),
outfiles,
options=vrt_options)
# remove tmp files
h.delete_dimap(out_stack)