def main(iargs=None):
""" email mintpy or insarmaps results """
inps = putils.cmd_line_parse(iargs, script='email_results')
email_address = os.getenv('NOTIFICATIONEMAIL')
if not iargs is None:
message_rsmas.log(
inps.work_dir,
os.path.basename(__file__) + ' ' + ' '.join(iargs[:]))
else:
message_rsmas.log(
inps.work_dir,
os.path.basename(__file__) + ' ' + ' '.join(sys.argv[1::]))
if inps.email_insarmaps_flag:
email_insarmaps_results(email_address)
if int(inps.template['cleanopt']) == 4:
cleanlist = pathObj.isce_clean_list
putils.remove_directories(cleanlist[4])
return
if inps.email_mintpy_flag:
email_mintpy_results(email_address)
return
return None
def main(iargs=None):
inps = putils.cmd_line_parse(iargs)
if not iargs is None:
input_arguments = iargs
else:
input_arguments = sys.argv[1::]
message_rsmas.log(
inps.work_dir,
os.path.basename(__file__) + ' ' + ' '.join(input_arguments))
os.chdir(inps.work_dir)
time.sleep(putils.pause_seconds(inps.wait_time))
#########################################
# Submit job
#########################################
if inps.submit_flag:
job_obj = JOB_SUBMIT(inps)
job_name = 'create_runfiles'
job_file_name = job_name
if '--submit' in input_arguments:
input_arguments.remove('--submit')
command = [os.path.abspath(__file__)] + input_arguments
job_obj.submit_script(job_name, job_file_name, command)
sys.exit(0)
try:
dem_file = glob.glob('DEM/*.wgs84')[0]
inps.template['topsStack.demDir'] = dem_file
except:
raise SystemExit('DEM does not exist')
# check for orbits
orbit_dir = os.getenv('SENTINEL_ORBITS')
# make run file
inps.topsStack_template = pathObj.correct_for_isce_naming_convention(inps)
runObj = CreateRun(inps)
runObj.run_stack_workflow()
run_file_list = putils.make_run_list(inps.work_dir)
with open(inps.work_dir + '/run_files_list', 'w') as run_file:
for item in run_file_list:
run_file.writelines(item + '\n')
local_orbit = os.path.join(inps.work_dir, 'orbits')
precise_orbits_in_local = glob.glob(local_orbit + '/*/*POEORB*')
if len(precise_orbits_in_local) > 0:
for orbit_file in precise_orbits_in_local:
os.system('cp {} {}'.format(orbit_file, orbit_dir))
return None
def main(iargs=None):
inps = putils.cmd_line_parse(iargs)
config = putils.get_config_defaults(config_file='job_defaults.cfg')
os.chdir(inps.work_dir)
job_file_name = 'create_runfiles'
job_name = job_file_name
if inps.wall_time == 'None':
inps.wall_time = config[job_file_name]['walltime']
wait_seconds, new_wall_time = putils.add_pause_to_walltime(
inps.wall_time, inps.wait_time)
#########################################
# Submit job
#########################################
if inps.submit_flag:
js.submit_script(job_name, job_file_name, sys.argv[:], inps.work_dir,
new_wall_time)
sys.exit(0)
time.sleep(wait_seconds)
if not iargs is None:
message_rsmas.log(
inps.work_dir,
os.path.basename(__file__) + ' ' + ' '.join(iargs[:]))
else:
message_rsmas.log(
inps.work_dir,
os.path.basename(__file__) + ' ' + ' '.join(sys.argv[1::]))
try:
dem_file = glob.glob('DEM/*.wgs84')[0]
inps.template['topsStack.demDir'] = dem_file
except:
raise SystemExit('DEM does not exist')
inps.topsStack_template = pathObj.correct_for_isce_naming_convention(inps)
runObj = CreateRun(inps)
runObj.run_stack_workflow()
run_file_list = putils.make_run_list(inps.work_dir)
with open(inps.work_dir + '/run_files_list', 'w') as run_file:
for item in run_file_list:
run_file.writelines(item + '\n')
if inps.template['topsStack.workflow'] in ['interferogram', 'slc']:
runObj.run_post_stack()
return None
def main(iargs=None):
inps = putils.cmd_line_parse(iargs, script='download_rsmas')
config = putils.get_config_defaults(config_file='job_defaults.cfg')
if not iargs is None:
message_rsmas.log(
inps.work_dir,
os.path.basename(__file__) + ' ' + ' '.join(iargs[:]))
else:
message_rsmas.log(
inps.work_dir,
os.path.basename(__file__) + ' ' + ' '.join(sys.argv[1::]))
logfile_name = inps.work_dir + '/asfserial_rsmas.log'
logger = RsmasLogger(file_name=logfile_name)
#########################################
# Submit job
#########################################
if inps.submit_flag:
job_file_name = 'download_asfserial_rsmas'
job_name = inps.custom_template_file.split(os.sep)[-1].split('.')[0]
work_dir = inps.work_dir
if inps.wall_time == 'None':
inps.wall_time = config['download_rsmas']['walltime']
js.submit_script(job_name, job_file_name, sys.argv[:], work_dir,
inps.wall_time)
os.chdir(inps.work_dir)
if not inps.template['topsStack.slcDir'] is None:
inps.slc_dir = inps.template['topsStack.slcDir']
else:
inps.slc_dir = os.path.join(inps.work_dir, 'SLC')
project_slc_dir = os.path.join(inps.work_dir, 'SLC')
os.chdir(inps.slc_dir)
try:
os.remove(os.path.expanduser('~') + '/.bulk_download_cookiejar.txt')
except OSError:
pass
generate_files_csv(project_slc_dir, inps.custom_template_file)
succesful = run_download_asf_serial(project_slc_dir, logger)
change_file_permissions()
logger.log(loglevel.INFO, "SUCCESS: %s", str(succesful))
logger.log(loglevel.INFO, "------------------------------------")
return None
def main(iargs=None):
inps = putils.cmd_line_parse(iargs, script='smallbaseline_wrapper')
config = putils.get_config_defaults(config_file='job_defaults.cfg')
job_file_name = 'smallbaseline_wrapper'
job_name = job_file_name
if inps.wall_time == 'None':
inps.wall_time = config[job_file_name]['walltime']
wait_seconds, new_wall_time = putils.add_pause_to_walltime(
inps.wall_time, inps.wait_time)
#########################################
# Submit job
#########################################
if inps.submit_flag:
js.submit_script(job_name, job_file_name, sys.argv[:], inps.work_dir,
new_wall_time)
sys.exit(0)
if not iargs is None:
message_rsmas.log(
inps.work_dir,
os.path.basename(__file__) + ' ' + ' '.join(iargs[:]))
else:
message_rsmas.log(
inps.work_dir,
os.path.basename(__file__) + ' ' + ' '.join(sys.argv[1::]))
os.chdir(inps.work_dir)
time.sleep(wait_seconds)
try:
with open('out_mintpy.o', 'w') as f:
with contextlib.redirect_stdout(f):
smallbaselineApp.main([inps.customTemplateFile])
except:
with open('out_mintpy.e', 'w') as g:
with contextlib.redirect_stderr(g):
smallbaselineApp.main([inps.customTemplateFile])
inps.mintpy_dir = os.path.join(inps.work_dir, pathObj.mintpydir)
putils.set_permission_dask_files(directory=inps.mintpy_dir)
# Email Mintpy results
if inps.email:
email_results.main([inps.customTemplateFile])
return None
def main(iargs=None):
inps = putils.cmd_line_parse(iargs, script='download_rsmas')
config = putils.get_config_defaults(config_file='job_defaults.cfg')
if not iargs is None:
message_rsmas.log(
inps.work_dir,
os.path.basename(__file__) + ' ' + ' '.join(iargs[:]))
else:
message_rsmas.log(
inps.work_dir,
os.path.basename(__file__) + ' ' + ' '.join(sys.argv[1::]))
logfile_name = inps.work_dir + '/ssara_rsmas.log'
logger = RsmasLogger(file_name=logfile_name)
if not inps.template['topsStack.slcDir'] is None:
inps.slc_dir = inps.template['topsStack.slcDir']
else:
inps.slc_dir = os.path.join(inps.work_dir, 'SLC')
project_slc_dir = os.path.join(inps.work_dir, 'SLC')
#########################################
# Submit job
#########################################
if inps.submit_flag:
job_file_name = 'download_ssara_rsmas'
job_name = inps.custom_template_file.split(os.sep)[-1].split('.')[0]
if inps.wall_time == 'None':
inps.wall_time = config['download_rsmas']['walltime']
js.submit_script(job_name, job_file_name, sys.argv[:], inps.work_dir,
inps.wall_time)
sys.exit(0)
if not os.path.isdir(project_slc_dir):
os.makedirs(project_slc_dir)
os.chdir(inps.slc_dir)
logger.log(loglevel.INFO, "DATASET: %s",
str(inps.custom_template_file.split('/')[-1].split(".")[0]))
logger.log(loglevel.INFO, "DATE: %s",
datetime.datetime.now().strftime("%Y-%m-%dT%H:%M:%S.%f"))
succesful = run_ssara(project_slc_dir, inps.custom_template_file,
inps.delta_lat, logger)
logger.log(loglevel.INFO, "SUCCESS: %s", str(succesful))
logger.log(loglevel.INFO, "------------------------------------")
return None
def main(iargs=None):
inps = putils.cmd_line_parse(iargs, script='minopy_wrapper')
if not iargs is None:
input_arguments = iargs
else:
input_arguments = sys.argv[1::]
message_rsmas.log(
inps.work_dir,
os.path.basename(__file__) + ' ' + ' '.join(input_arguments))
time.sleep(putils.pause_seconds(inps.wait_time))
#########################################
# Submit job
#########################################
if inps.submit_flag:
job_obj = JOB_SUBMIT(inps)
job_name = 'minopy_wrapper'
job_file_name = job_name
if '--submit' in input_arguments:
input_arguments.remove('--submit')
command = [os.path.abspath(__file__)] + input_arguments
job_obj.submit_script(job_name, job_file_name, command)
os.chdir(inps.work_dir)
try:
with open('out_minopy.o', 'w') as f:
with contextlib.redirect_stdout(f):
smallbaselineApp.main(
[inps.custom_template_file, '--dir', pathObj.mintpydir])
except:
with open('out_minopy.e', 'w') as g:
with contextlib.redirect_stderr(g):
smallbaselineApp.main(
[inps.custom_template_file, '--dir', pathObj.mintpydir])
inps.mintpy_dir = os.path.join(inps.work_dir, pathObj.mintpydir)
putils.set_permission_dask_files(directory=inps.mintpy_dir)
# Email Minopy results
if inps.email:
email_results.main([inps.custom_template_file, '--minopy'])
return None
def main(iargs=None):
inps = putils.cmd_line_parse(iargs, script='download_rsmas')
if not iargs is None:
input_arguments = iargs
else:
input_arguments = sys.argv[1::]
message_rsmas.log(
inps.work_dir,
os.path.basename(__file__) + ' ' + ' '.join(input_arguments))
logfile_name = inps.work_dir + '/ssara_rsmas.log'
logger = RsmasLogger(file_name=logfile_name)
if not inps.template['topsStack.slcDir'] is None:
inps.slc_dir = inps.template['topsStack.slcDir']
else:
inps.slc_dir = os.path.join(inps.work_dir, 'SLC')
project_slc_dir = os.path.join(inps.work_dir, 'SLC')
#########################################
# Submit job
#########################################
if inps.submit_flag:
job_file_name = 'download_ssara_rsmas'
job_name = inps.custom_template_file.split(os.sep)[-1].split('.')[0]
job_obj = JOB_SUBMIT(inps)
if '--submit' in input_arguments:
input_arguments.remove('--submit')
command = [os.path.abspath(__file__)] + input_arguments
job_obj.submit_script(job_name, job_file_name, command)
sys.exit(0)
if not os.path.isdir(project_slc_dir):
os.makedirs(project_slc_dir)
os.chdir(inps.slc_dir)
logger.log(loglevel.INFO, "DATASET: %s",
str(inps.custom_template_file.split('/')[-1].split(".")[0]))
logger.log(loglevel.INFO, "DATE: %s",
datetime.datetime.now().strftime("%Y-%m-%dT%H:%M:%S.%f"))
succesful = run_ssara(project_slc_dir, inps.custom_template_file,
inps.delta_lat, logger)
logger.log(loglevel.INFO, "SUCCESS: %s", str(succesful))
logger.log(loglevel.INFO, "------------------------------------")
return None
def main(iargs=None):
inps = putils.cmd_line_parse(iargs, script='download_rsmas')
if not iargs is None:
input_arguments = iargs
else:
input_arguments = sys.argv[1::]
message_rsmas.log(
inps.work_dir,
os.path.basename(__file__) + ' ' + ' '.join(input_arguments))
logfile_name = inps.work_dir + '/ssara_rsmas.log'
logger = RsmasLogger(file_name=logfile_name)
#import pdb; pdb.set_trace()
if not inps.template[inps.prefix + 'Stack.slcDir'] is None:
inps.download_dir = inps.template[inps.prefix + 'Stack.slcDir']
if 'COSMO' in inps.template['ssaraopt.platform']:
inps.download_dir = os.path.join(inps.work_dir, 'RAW_data')
else:
inps.download_dir = os.path.join(inps.work_dir, 'SLC')
#########################################
# Submit job
#########################################
if inps.submit_flag:
job_file_name = 'download_ssara_rsmas'
job_name = inps.custom_template_file.split(os.sep)[-1].split('.')[0]
job_obj = JOB_SUBMIT(inps)
if '--submit' in input_arguments:
input_arguments.remove('--submit')
command = [os.path.abspath(__file__)] + input_arguments
job_obj.submit_script(job_name, job_file_name, command)
sys.exit(0)
if not os.path.isdir(inps.download_dir):
os.makedirs(inps.download_dir)
os.chdir(inps.download_dir)
succesful = run_ssara(inps.download_dir, inps.custom_template_file,
inps.delta_lat, logger)
return None
def main(iargs=None):
inps = putils.cmd_line_parse(iargs, script='smallbaseline_wrapper')
time.sleep(putils.pause_seconds(inps.wait_time))
#########################################
# Submit job
#########################################
if inps.submit_flag:
job_name = 'smallbaseline_wrapper'
job_file_name = job_name
js.submit_script(job_name, job_file_name, sys.argv[:], inps.work_dir)
sys.exit(0)
if not iargs is None:
message_rsmas.log(
inps.work_dir,
os.path.basename(__file__) + ' ' + ' '.join(iargs[:]))
else:
message_rsmas.log(
inps.work_dir,
os.path.basename(__file__) + ' ' + ' '.join(sys.argv[1::]))
os.chdir(inps.work_dir)
try:
with open('out_mintpy.o', 'w') as f:
with contextlib.redirect_stdout(f):
smallbaselineApp.main([inps.custom_template_file])
except:
with open('out_mintpy.e', 'w') as g:
with contextlib.redirect_stderr(g):
smallbaselineApp.main([inps.custom_template_file])
inps.mintpy_dir = os.path.join(inps.work_dir, pathObj.mintpydir)
putils.set_permission_dask_files(directory=inps.mintpy_dir)
# Email Mintpy results
if inps.email:
email_results.main([inps.custom_template_file, '--mintpy'])
return None
def main(iargs=None):
""" create template files for chunk processing """
inps = putils.cmd_line_parse(iargs, script='generate_chunk_template_files')
os.chdir(inps.work_dir)
if not iargs is None:
input_arguments = iargs
else:
input_arguments = sys.argv[1::]
message_rsmas.log(
inps.work_dir,
os.path.basename(__file__) + ' ' + ' '.join(input_arguments))
run_generate_chunk_template_files(inps)
return
def main(iargs=None):
inps = putils.cmd_line_parse(iargs, script='execute_runfiles')
os.chdir(inps.work_dir)
config = putils.get_config_defaults(config_file='job_defaults.cfg')
job_file_name = 'execute_runfiles'
job_name = job_file_name
if inps.wall_time == 'None':
inps.wall_time = config[job_file_name]['walltime']
wait_seconds, new_wall_time = putils.add_pause_to_walltime(
inps.wall_time, inps.wait_time)
#########################################
# Submit job
#########################################
if inps.submit_flag:
js.submit_script(job_name, job_file_name, sys.argv[:], inps.work_dir,
new_wall_time)
sys.exit(0)
time.sleep(wait_seconds)
run_file_list = putils.read_run_list(inps.work_dir)
if inps.end_run == 0:
inps.end_run = len(run_file_list)
if not inps.start_run == 0:
inps.start_run = inps.start_run - 1
if not iargs is None:
message_rsmas.log(
inps.work_dir,
os.path.basename(__file__) + ' ' + ' '.join(iargs[:]))
else:
message_rsmas.log(
inps.work_dir,
os.path.basename(__file__) + ' ' + ' '.join(sys.argv[1::]))
run_file_list = run_file_list[inps.start_run:inps.end_run]
supported_schedulers = ['LSF', 'PBS', 'SLURM']
if os.getenv('JOBSCHEDULER') in supported_schedulers:
for item in run_file_list:
step_name = '_'
step_name = step_name.join(item.split('_')[3::])
try:
memorymax = config[step_name]['memory']
except:
memorymax = config['DEFAULT']['memory']
try:
# FA 26 Dec commented out as it seemed wrong
#if config[step_name]['adjust'] == 'True':
# walltimelimit = putils.walltime_adjust(inps, config[step_name]['walltime'])
#else:
# walltimelimit = config[step_name]['walltime']
walltimelimit = config[step_name]['walltime']
except:
walltimelimit = config['DEFAULT']['walltime']
queuename = os.getenv('QUEUENAME')
putils.remove_last_job_running_products(run_file=item)
if os.getenv('JOBSCHEDULER') in ['SLURM', 'sge']:
js.submit_job_with_launcher(batch_file=item,
work_dir=os.path.join(
inps.work_dir, 'run_files'),
memory=memorymax,
walltime=walltimelimit,
queue=queuename)
else:
jobs = js.submit_batch_jobs(batch_file=item,
out_dir=os.path.join(
inps.work_dir, 'run_files'),
work_dir=inps.work_dir,
memory=memorymax,
walltime=walltimelimit,
queue=queuename)
putils.remove_zero_size_or_length_error_files(run_file=item)
putils.rerun_job_if_exit_code_140(run_file=item)
putils.raise_exception_if_job_exited(run_file=item)
putils.concatenate_error_files(run_file=item,
work_dir=inps.work_dir)
putils.move_out_job_files_to_stdout(run_file=item)
date_str = datetime.datetime.strftime(datetime.datetime.now(),
'%Y%m%d:%H%M%S')
print(date_str + ' * Job {} completed'.format(item))
date_str = datetime.datetime.strftime(datetime.datetime.now(),
'%Y%m%d:%H%M%S')
print(date_str +
' * all jobs from {} to {} have been completed'.format(
os.path.basename(run_file_list[0]),
os.path.basename(run_file_list[-1])))
else:
for item in run_file_list:
with open(item, 'r') as f:
command_lines = f.readlines()
for command_line in command_lines:
os.system(command_line)
return None
def main(iargs=None):
inps = putils.cmd_line_parse(iargs, script='ingest_insarmaps')
if not iargs is None:
input_arguments = iargs
else:
input_arguments = sys.argv[1::]
message_rsmas.log(
inps.work_dir,
os.path.basename(__file__) + ' ' + ' '.join(input_arguments))
#time.sleep(putils.pause_seconds(inps.wait_time))
#########################################
# Submit job
#########################################
if inps.submit_flag:
job_obj = JOB_SUBMIT(inps)
job_name = 'ingest_insarmaps'
job_file_name = job_name
if '--submit' in input_arguments:
input_arguments.remove('--submit')
command = [os.path.abspath(__file__)] + input_arguments
job_obj.submit_script(job_name, job_file_name, command)
os.chdir(inps.work_dir)
hdfeos_file = glob.glob(inps.work_dir + '/mintpy/*.he5')
hdfeos_file.append(glob.glob(inps.work_dir + '/mintpy/SUBSET_*/*.he5'))
hdfeos_file = hdfeos_file[0]
json_folder = inps.work_dir + '/mintpy/JSON'
mbtiles_file = json_folder + '/' + os.path.splitext(
os.path.basename(hdfeos_file))[0] + '.mbtiles'
if os.path.isdir(json_folder):
shutil.rmtree(json_folder)
command1 = 'hdfeos5_2json_mbtiles.py ' + hdfeos_file + ' ' + json_folder
command2 = 'json_mbtiles2insarmaps.py -u ' + password.insaruser + ' -p ' + password.insarpass + ' --host ' + \
'insarmaps.miami.edu -P rsmastest -U rsmas\@gmail.com --json_folder ' + \
json_folder + ' --mbtiles_file ' + mbtiles_file
with open(inps.work_dir + '/run_insarmaps', 'w') as f:
f.write(command1 + '\n')
f.write(command2 + '\n')
out_file = 'out_ingest_insarmaps'
message_rsmas.log(inps.work_dir, command1)
#command1 = '('+command1+' | tee '+out_file+'.o) 3>&1 1>&2 2>&3 | tee '+out_file+'.e'
status = subprocess.Popen(command1, shell=True).wait()
if status is not 0:
raise Exception('ERROR in hdfeos5_2json_mbtiles.py')
# TODO: Change subprocess call to get back error code and send error code to logger
message_rsmas.log(inps.work_dir, command2)
#command2 = '('+command2+' | tee -a '+out_file+'.o) 3>&1 1>&2 2>&3 | tee -a '+out_file+'.e'
status = subprocess.Popen(command2, shell=True).wait()
if status is not 0:
raise Exception('ERROR in json_mbtiles2insarmaps.py')
# Email insarmaps results:
if inps.email:
message_rsmas.log(
inps.work_dir,
'email_results.py --insarmaps ' + inps.custom_template_file)
email_results.main([inps.custom_template_file, '--insarmaps'])
return None
def main(iargs=None):
# set defaults: ssara=True is set in dem_parser, use custom_pemp[late field if given
inps = cmd_line_parse(iargs, script='dem_rsmas')
if not iargs is None:
message_rsmas.log(inps.work_dir, os.path.basename(__file__) + ' ' + ' '.join(iargs[:]))
else:
message_rsmas.log(inps.work_dir, os.path.basename(__file__) + ' ' + ' '.join(sys.argv[1::]))
if not inps.flag_boundingBox and not inps.flag_ssara:
if 'demMethod' in list(inps.template.keys()):
if inps.template['demMethod'] == 'ssara':
inps.flag_ssara = True
inps.flag_boundingBox = False
if inps.template['demMethod'] == 'boundingBox':
inps.flag_ssara = False
inps.flag_boundingBox = True
elif inps.flag_boundingBox:
inps.flag_ssara = False
else:
inps.flag_ssara = True
dem_dir = make_dem_dir(inps.work_dir)
if dem_dir:
if inps.flag_ssara:
call_ssara_dem(inps, dem_dir)
print('You have finished SSARA!')
elif inps.flag_boundingBox:
print('DEM generation using ISCE')
bbox = inps.template['topsStack.boundingBox'].strip("'")
bbox = [val for val in bbox.split()]
south = bbox[0]
north = bbox[1]
west = bbox[2]
east = bbox[3].split('\'')[0]
south = math.floor(float(south) - 0.5)
north = math.ceil(float(north) + 0.5)
west = math.floor(float(west) - 0.5)
east = math.ceil(float(east) + 0.5 )
demBbox = str(int(south)) + ' ' + str(int(north)) + ' ' + str(int(west)) + ' ' + str(int(east))
command = 'dem.py -a stitch -b ' + demBbox + ' -c -u https://e4ftl01.cr.usgs.gov/MEASURES/SRTMGL1.003/2000.02.11/'
message_rsmas.log(os.getcwd(), command)
if os.getenv('DOWNLOADHOST') == 'local':
try:
proc = subprocess.Popen(command, stderr=subprocess.PIPE, stdout=subprocess.PIPE, shell=True, universal_newlines=True)
output, error = proc.communicate()
if proc.returncode is not 0:
raise Exception('ERROR starting dem.py subprocess') # FA 8/19: I don't think this happens, errors are is output
except subprocess.CalledProcessError as exc:
print("Command failed. Exit code, StdErr:", exc.returncode, exc.output)
sys.exit('Error produced by dem.py')
else:
if 'Could not create a stitched DEM. Some tiles are missing' in output:
os.chdir('..')
shutil.rmtree('DEM')
sys.exit('Error in dem.py: Tiles are missing. Ocean???')
else:
dem_dir = os.getcwd()
ssh_command_list = ['s.bgood', 'cd {0}'.format(dem_dir), command]
host = os.getenv('DOWNLOADHOST')
try:
status = ssh_with_commands(host, ssh_command_list)
except subprocess.CalledProcessError as exc:
print("Command failed. Exit code, StdErr:", exc.returncode, exc.output)
sys.exit('Error produced by dem.py using ' + host)
#print('Exit status from dem.py: {0}'.format(status))
xmlFile = glob.glob('demLat_*.wgs84.xml')[0]
fin = open(xmlFile, 'r')
fout = open("tmp.txt", "wt")
for line in fin:
fout.write(line.replace('demLat', dem_dir + '/demLat'))
fin.close()
fout.close()
os.rename('tmp.txt', xmlFile)
else:
sys.ext('Error unspported demMethod option: ' + inps.template['topsStack.demMethod'])
print('\n###############################################')
print('End of dem_rsmas.py')
print('################################################\n')
return None
def main(iargs=None):
inps = putils.cmd_line_parse(iargs, script='create_runfiles')
if not iargs is None:
input_arguments = iargs
else:
input_arguments = sys.argv[1::]
message_rsmas.log(
inps.work_dir,
os.path.basename(__file__) + ' ' + ' '.join(input_arguments))
os.chdir(inps.work_dir)
#time.sleep(putils.pause_seconds(inps.wait_time))
inps.out_dir = inps.work_dir
inps.num_data = 1
job_obj = JOB_SUBMIT(inps)
#########################################
# Submit job
#########################################
if inps.submit_flag:
job_name = 'create_runfiles'
job_file_name = job_name
if '--submit' in input_arguments:
input_arguments.remove('--submit')
command = [os.path.abspath(__file__)] + input_arguments
job_obj.submit_script(job_name, job_file_name, command)
sys.exit(0)
try:
dem_dir = inps.template[inps.prefix + 'Stack.demDir']
except:
dem_dir = 'DEM'
try:
dem_file = glob.glob(dem_dir + '/*.wgs84')[0]
inps.template[inps.prefix + 'Stack.demDir'] = dem_file
except:
raise SystemExit('DEM does not exist')
slc_dir = inps.template[inps.prefix + 'Stack.slcDir']
os.makedirs(slc_dir, exist_ok=True)
if int(
get_size(slc_dir) / 1024**2
) < 500: # calculate slc_dir size in MB and see if there are SLCs according to size
# Unpack Raw data:
if not inps.template['raw_image_dir'] in [None, 'None']:
raw_image_dir = inps.template['raw_image_dir']
else:
raw_image_dir = os.path.join(inps.work_dir, 'RAW_data')
if os.path.exists(raw_image_dir):
unpackObj = Sensors(
raw_image_dir,
slc_dir,
remove_file='False',
multiple_raw_frame=inps.template['multiple_raw_frame'])
unpack_run_file = unpackObj.start()
unpackObj.close()
job_obj.write_batch_jobs(batch_file=unpack_run_file)
job_status = job_obj.submit_batch_jobs(batch_file=unpack_run_file)
if not job_status:
raise Exception('ERROR: Unpacking was failed')
else:
raise Exception('ERROR: No data (SLC or Raw) available')
# make run file:
run_files_dirname = "run_files"
config_dirnane = "configs"
if inps.copy_to_tmp:
run_files_dirname += "_tmp"
config_dirnane += "_tmp"
run_dir = os.path.join(inps.work_dir, run_files_dirname)
config_dir = os.path.join(inps.work_dir, config_dirnane)
for directory in [run_dir, config_dir]:
if os.path.exists(directory):
shutil.rmtree(directory)
inps.Stack_template = pathObj.correct_for_isce_naming_convention(inps)
if inps.ignore_stack and os.path.exists(inps.work_dir +
'/coreg_secondarys'):
shutil.rmtree(inps.work_dir + '/tmp_coreg_secondarys',
ignore_errors=True)
shutil.move(inps.work_dir + '/coreg_secondarys',
inps.work_dir + '/tmp_coreg_secondarys')
runObj = CreateRun(inps)
runObj.run_stack_workflow()
if inps.ignore_stack and os.path.exists(inps.work_dir +
'/tmp_coreg_secondarys'):
shutil.move(inps.work_dir + '/tmp_coreg_secondarys',
inps.work_dir + '/coreg_secondarys')
if os.path.isfile(run_dir + '/run_06_extract_stack_valid_region'):
with open(run_dir + '/run_06_extract_stack_valid_region', 'r') as f:
line = f.readlines()
with open(run_dir + '/run_06_extract_stack_valid_region', 'w') as f:
f.writelines(['rm -rf ./stack; '] + line)
run_file_list = putils.make_run_list(inps.work_dir)
with open(inps.work_dir + '/run_files_list', 'w') as run_file:
for item in run_file_list:
run_file.writelines(item + '\n')
if inps.copy_to_tmp:
run_file_list = [
item.replace("/run_files/", "/run_files_tmp/")
for item in run_file_list
]
with open(inps.work_dir + '/run_files_tmp_list', 'w') as run_file:
for item in run_file_list:
run_file.writelines(item + '\n')
shutil.copytree(pathObj.rundir, run_dir)
if inps.prefix == 'tops':
# check for orbits
orbit_dir = os.getenv('SENTINEL_ORBITS')
local_orbit = os.path.join(inps.work_dir, 'orbits')
precise_orbits_in_local = glob.glob(local_orbit + '/*/*POEORB*')
if len(precise_orbits_in_local) > 0:
for orbit_file in precise_orbits_in_local:
os.system('cp {} {}'.format(orbit_file, orbit_dir))
# Writing job files
if inps.write_jobs:
for item in run_file_list:
job_obj.write_batch_jobs(batch_file=item)
if inps.template['processingMethod'] == 'smallbaseline':
job_name = 'smallbaseline_wrapper'
job_file_name = job_name
command = [
'smallbaselineApp.py', inps.custom_template_file, '--dir',
'mintpy'
]
# pre_command = ["""[[ $(ls mintpy/time* | wc -l) -eq 1 ]] && rm mintpy/time*"""]
pre_command = ["clean_mintpy_dir.bash;"]
command = pre_command + command
job_obj.submit_script(job_name,
job_file_name,
command,
writeOnly='True')
else:
job_name = 'minopy_wrapper'
job_file_name = job_name
command = [
'minopyApp.py', inps.custom_template_file, '--dir', 'minopy'
]
job_obj.submit_script(job_name,
job_file_name,
command,
writeOnly='True')
job_name = 'insarmaps'
job_file_name = job_name
command = ['ingest_insarmaps.py', inps.custom_template_file]
job_obj.submit_script(job_name,
job_file_name,
command,
writeOnly='True')
print("copy_to_tmp: {}".format(inps.copy_to_tmp))
if inps.copy_to_tmp:
#run_dir_tmp = os.path.join(inps.work_dir, 'run_files_tmp')
config_dir_tmp = os.path.join(inps.work_dir, 'configs_tmp')
shutil.copytree(os.path.join(inps.work_dir, "configs"), config_dir_tmp)
cmd = "update_configs_for_tmp.bash {}".format(inps.work_dir)
subprocess.Popen(cmd, shell=True)
return None
def main(iargs=None):
inps = putils.cmd_line_parse(iargs, script='upload_data_products')
if inps.image_products_flag:
inps.mintpy_products_flag = False
os.chdir(inps.work_dir)
if not iargs is None:
input_arguments = iargs
else:
input_arguments = sys.argv[1::]
message_rsmas.log(inps.work_dir, os.path.basename(__file__) + ' ' + ' '.join(input_arguments))
# get DATA_SERVER and return if it does not exist
DATA_SERVER = '[email protected]'
#try:
# DATA_SERVER = os.getenv('DATA_SERVER')
#except:
# return
project_name = putils.get_project_name(inps.custom_template_file)
if inps.mintpy_products_flag:
REMOTE_DIR = '/data/HDF5EOS/'
destination = DATA_SERVER + ':' + REMOTE_DIR
scp_list = [
'/mintpy/pic',
'/mintpy/*.he5',
'/mintpy/inputs',
'/remora_*'
]
if inps.mintpy_products_all_flag:
scp_list = [ '/mintpy' ]
command = 'ssh ' + DATA_SERVER + ' mkdir -p ' + REMOTE_DIR + project_name + '/mintpy'
print (command)
status = subprocess.Popen(command, shell=True).wait()
if status is not 0:
raise Exception('ERROR in upload_data_products.py')
for pattern in scp_list:
if ( len(glob.glob(inps.work_dir + '/' + pattern)) >= 1 ):
command = 'scp -r ' + inps.work_dir + pattern + ' ' + destination + project_name + '/'.join(pattern.split('/')[0:-1])
print (command)
status = subprocess.Popen(command, shell=True).wait()
if status is not 0:
raise Exception('ERROR in upload_data_products.py')
print ('\nAdjusting permissions:')
command = 'ssh ' + DATA_SERVER + ' chmod -R u=rwX,go=rX ' + REMOTE_DIR + project_name
print (command)
status = subprocess.Popen(command, shell=True).wait()
if status is not 0:
raise Exception('ERROR in upload_data_products.py')
if inps.image_products_flag:
REMOTE_DIR = '/data/image_products/'
destination = DATA_SERVER + ':' + REMOTE_DIR
rsync_list = [
'/image_products/*',
]
command = 'ssh ' + DATA_SERVER + ' mkdir -p ' + REMOTE_DIR + project_name
print (command)
status = subprocess.Popen(command, shell=True).wait()
if status is not 0:
raise Exception('ERROR in upload_data_products.py')
for pattern in rsync_list:
command = 'rsync -avuz -e ssh --chmod=Du=rwx,Dg=rx,Do=rx,Fu=rw,Fg=r,Fo=r ' + inps.work_dir + pattern + ' ' + destination + project_name + '/'.join(pattern.split('/')[0:-1])
print (command)
status = subprocess.Popen(command, shell=True).wait()
if status is not 0:
raise Exception('ERROR in upload_data_products.py')
return None
return None
def main(iargs=None):
"""Downloads data with ssara and asfserial scripts."""
inps = putils.cmd_line_parse(iargs, script='download_rsmas')
if not iargs is None:
input_arguments = iargs
else:
input_arguments = sys.argv[1::]
message_rsmas.log(inps.work_dir, os.path.basename(__file__) + ' ' + ' '.join(input_arguments))
time.sleep(putils.pause_seconds(inps.wait_time))
#########################################
# Submit job
#########################################
if inps.submit_flag:
job_obj = JOB_SUBMIT(inps)
job_name = 'download_rsmas'
job_file_name = job_name
if '--submit' in input_arguments:
input_arguments.remove('--submit')
command = [os.path.abspath(__file__)] + input_arguments
job_obj.submit_script(job_name, job_file_name, command)
sys.exit(0)
if inps.prefix == 'tops':
if not inps.template[inps.prefix + 'Stack.slcDir'] is None:
download_dir = inps.template[inps.prefix + 'Stack.slcDir']
else:
download_dir = os.path.join(inps.work_dir, 'SLC')
else:
if not inps.template['raw_image_dir'] in [None, 'None']:
download_dir = inps.template['raw_image_dir']
else:
download_dir = os.path.join(inps.work_dir, 'RAW_data')
os.makedirs(inps.work_dir, exist_ok=True)
os.makedirs(download_dir, exist_ok=True)
if 'SenDT' not in inps.project_name and 'SenAT' not in inps.project_name or os.getenv('SSARA_ASF') == 'False':
try:
inps.template['ssaraopt.intersectsWithPoint']
inps.ssaraopt = ' '.join(add_point_to_ssaraopt(inps.template, inps.ssaraopt.split(' ')))
except:
inps.ssaraopt = ' '.join(add_polygon_to_ssaraopt(inps.template, inps.ssaraopt.split(' '), delta_lat=inps.delta_lat))
command = 'ssara_federated_query.py ' + inps.ssaraopt + ' --print' + ' --download'
os.chdir(download_dir)
message_rsmas.log(download_dir, command)
status = subprocess.Popen(command, shell=True).wait()
if status is not 0:
raise Exception('ERROR in ssara_federated_query.py')
os.chdir(inps.work_dir)
return
if os.getenv('SSARA_ASF') == 'False':
return
download('ssara', inps.custom_template_file, download_dir, outnum=1)
#download('asfserial', inps.custom_template_file, download_dir, outnum = 1)
for i_download in [2, 3]:
download_success = run_check_download(download_dir = download_dir)
if not download_success:
print('check_download.py: There were bad files, download again')
message_rsmas.log(inps.work_dir,'check_download.py: there were bad files, download again')
download('ssara', inps.custom_template_file, download_dir, outnum = i_download)
def main(iargs=None):
inps = putils.cmd_line_parse(iargs, script='upload_data_products')
os.chdir(inps.work_dir)
if not iargs is None:
message_rsmas.log(
inps.work_dir,
os.path.basename(__file__) + ' ' + ' '.join(iargs[:]))
else:
message_rsmas.log(
inps.work_dir,
os.path.basename(__file__) + ' ' + ' '.join(sys.argv[1::]))
# get DATA_SERVER and return if it does not exist
DATA_SERVER = '[email protected]'
#try:
# DATA_SERVER = os.getenv('DATA_SERVER')
#except:
# return
project_name = putils.get_project_name(inps.custom_template_file)
if inps.flag_mintpy_products:
REMOTE_DIR = '/data/HDF5EOS/'
destination = DATA_SERVER + ':' + REMOTE_DIR
rsync_list = ['/mintpy/inputs', '/mintpy/pic', '/mintpy/*.he5']
command = 'ssh ' + DATA_SERVER + ' mkdir -p ' + REMOTE_DIR + project_name
print(command)
status = subprocess.Popen(command, shell=True).wait()
if status is not 0:
raise Exception('ERROR in upload_data_products.py')
for pattern in rsync_list:
command = 'rsync -avuz -e ssh --chmod=Du=rwx,Dg=rx,Do=rx,Fu=rw,Fg=r,Fo=r ' + inps.work_dir + pattern + ' ' + destination + project_name + '/'.join(
pattern.split('/')[0:-1])
print(command)
status = subprocess.Popen(command, shell=True).wait()
if status is not 0:
raise Exception('ERROR in upload_data_products.py')
# temporary rsync of full mintpy folder
# text for test PR 2
command = 'rsync -avuz -e ssh --chmod=Du=rwx,Dg=rx,Do=rx,Fu=rw,Fg=r,Fo=r ' + inps.work_dir + '/mintpy ' + destination + project_name + '/full_mintpy'
print(command)
status = subprocess.Popen(command, shell=True).wait()
if status is not 0:
raise Exception('ERROR in upload_data_products.py')
return None
if inps.flag_image_products:
REMOTE_DIR = '/data/image_products/'
destination = DATA_SERVER + ':' + REMOTE_DIR
rsync_list = [
'/image_products/*',
]
command = 'ssh ' + DATA_SERVER + ' mkdir -p ' + REMOTE_DIR + project_name
print(command)
status = subprocess.Popen(command, shell=True).wait()
if status is not 0:
raise Exception('ERROR in upload_data_products.py')
for pattern in rsync_list:
command = 'rsync -avuz -e ssh --chmod=Du=rwx,Dg=rx,Do=rx,Fu=rw,Fg=r,Fo=r ' + inps.work_dir + pattern + ' ' + destination + project_name + '/'.join(
pattern.split('/')[0:-1])
print(command)
status = subprocess.Popen(command, shell=True).wait()
if status is not 0:
raise Exception('ERROR in upload_data_products.py')
return None
return None
def main(iargs=None):
"""
Crops SLC images from Isce merged/SLC directory and creates georectified and orthorectified products.
"""
inps = cmd_line_parse(iargs, script='export_amplitude_tif')
secondary_dir = os.path.join(inps.work_dir, pathObj.mergedslcdir)
pic_dir = os.path.join(inps.work_dir, pathObj.tiffdir)
if not os.path.exists(pic_dir):
os.mkdir(pic_dir)
if not iargs is None:
input_arguments = iargs
else:
input_arguments = sys.argv[1::]
message_rsmas.log(pic_dir, os.path.basename(__file__) + ' ' + ' '.join(input_arguments))
os.chdir(secondary_dir)
try:
os.system('rm '+ inps.input_file + '/geo*')
except:
print('geocoding ...')
slc = inps.input_file
if inps.im_type == 'ortho':
inps.geo_reference_dir = os.path.join(inps.work_dir, pathObj.georeferencedir)
else:
inps.geo_reference_dir = os.path.join(inps.work_dir, pathObj.geomlatlondir)
os.chdir(os.path.join(secondary_dir, inps.input_file))
geocode_file(inps)
gfile = 'geo_' + slc + '.slc.ml'
ds = gdal.Open(gfile + '.vrt', gdal.GA_ReadOnly)
array = np.abs(ds.GetRasterBand(1).ReadAsArray())
del ds
##
array = np.where(array > 0, 10.0 * np.log10(pow(array, 2)) - 83.0, array)
if inps.im_type == 'ortho':
dst_file = 'orthorectified_' + slc + '_backscatter.tif'
else:
dst_file = 'georectified_' + slc + '_backscatter.tif'
data = gdal.Open(gfile, gdal.GA_ReadOnly)
transform = data.GetGeoTransform()
##
xmlfile = glob.glob(os.path.join(inps.work_dir, pathObj.referencedir, '*.xml'))[0]
attributes = xmlread(xmlfile)
Metadata = {'SAT': attributes['missionname'], 'Mode': attributes['passdirection'],
'Image_Type': '{}_BackScatter'.format(inps.im_type), 'Date': slc}
raster2geotiff(dst_file, transform, array, Metadata)
print('Find the output in {}'.format(pic_dir))
os.system('mv *.tif {}'.format(pic_dir))
os.system('rm geo*')
return
def main(iargs=None):
inps = putils.cmd_line_parse(iargs, script='download_rsmas')
if not iargs is None:
input_arguments = iargs
else:
input_arguments = sys.argv[1::]
message_rsmas.log(
inps.work_dir,
os.path.basename(__file__) + ' ' + ' '.join(input_arguments))
logfile_name = inps.work_dir + '/asfserial_rsmas.log'
global logger
logger = RsmasLogger(file_name=logfile_name)
#########################################
# Submit job
#########################################
if inps.submit_flag:
job_file_name = 'download_asfserial_rsmas'
job_name = inps.custom_template_file.split(os.sep)[-1].split('.')[0]
job_obj = JOB_SUBMIT(inps)
if '--submit' in input_arguments:
input_arguments.remove('--submit')
command = [os.path.abspath(__file__)] + input_arguments
job_obj.submit_script(job_name, job_file_name, command)
sys.exit(0)
os.chdir(inps.work_dir)
if not inps.template[inps.prefix + 'Stack.slcDir'] is None:
inps.slc_dir = inps.template[inps.prefix + 'Stack.slcDir']
else:
inps.slc_dir = os.path.join(inps.work_dir, 'SLC')
global project_slc_dir
project_slc_dir = os.path.join(inps.work_dir, 'SLC')
if not os.path.exists(inps.slc_dir):
os.mkdir(inps.slc_dir)
os.chdir(inps.slc_dir)
try:
os.remove(os.path.expanduser('~') + '/.bulk_download_cookiejar.txt')
except OSError:
pass
dataset_template = Template(inps.custom_template_file)
dataset_template.options.update(
PathFind.correct_for_ssara_date_format(dataset_template.options))
subprocess.Popen("rm " + project_slc_dir + "/new_files*.csv",
shell=True).wait()
seasonal_start_date = None
seasonal_end_date = None
try:
if dataset_template.options[
'seasonalStartDate'] is not None and dataset_template.options[
'seasonalEndDate'] is not None:
seasonal_start_date = dataset_template.options['seasonalStartDate']
seasonal_end_date = dataset_template.options['seasonalEndDate']
except:
pass
if inps.seasonalStartDate is not None and inps.seasonalEndDate is not None:
seasonal_start_date = inps.seasonalStartDate
seasonal_end_date = inps.seasonalEndDate
if seasonal_start_date is not None and seasonal_end_date is not None:
generate_seasonal_files_csv(dataset_template, seasonal_start_date,
seasonal_end_date)
else:
generate_files_csv(project_slc_dir, dataset_template)
parallel = False
try:
if dataset_template.options['parallel'] == 'yes':
parallel = True
except:
pass
"""if inps.parallel == 'yes':
parallel = True"""
threads = os.cpu_count()
try:
if dataset_template.options['threads'] is not None:
threads = int(dataset_template.options['threads'])
except:
pass
"""if inps.processes is not None:
processes = inps.processes"""
if parallel:
run_parallel_download_asf_serial(project_slc_dir, threads)
else:
succesful = run_download_asf_serial(project_slc_dir, logger)
logger.log(loglevel.INFO, "SUCCESS: %s", str(succesful))
change_file_permissions()
logger.log(loglevel.INFO, "------------------------------------")
subprocess.Popen("rm " + project_slc_dir + "/new_files*.csv",
shell=True).wait()
return None
def main(iargs=None):
inps = putils.cmd_line_parse(iargs, script='create_runfiles')
if not iargs is None:
input_arguments = iargs
else:
input_arguments = sys.argv[1::]
message_rsmas.log(
inps.work_dir,
os.path.basename(__file__) + ' ' + ' '.join(input_arguments))
os.chdir(inps.work_dir)
time.sleep(putils.pause_seconds(inps.wait_time))
inps.out_dir = inps.work_dir
job_obj = JOB_SUBMIT(inps)
#########################################
# Submit job
#########################################
if inps.submit_flag:
job_name = 'create_runfiles'
job_file_name = job_name
if '--submit' in input_arguments:
input_arguments.remove('--submit')
command = [os.path.abspath(__file__)] + input_arguments
job_obj.submit_script(job_name, job_file_name, command)
sys.exit(0)
try:
dem_file = glob.glob('DEM/*.wgs84')[0]
inps.template[inps.prefix + 'Stack.demDir'] = dem_file
except:
raise SystemExit('DEM does not exist')
slc_dir = inps.template[inps.prefix + 'Stack.slcDir']
os.makedirs(slc_dir, exist_ok=True)
if int(
get_size(slc_dir) / 1024**2
) < 500: # calculate slc_dir size in MB and see if there are SLCs according to size
# Unpack Raw data:
if not inps.template['raw_image_dir'] in [None, 'None']:
raw_image_dir = inps.template['raw_image_dir']
else:
raw_image_dir = os.path.join(inps.work_dir, 'RAW_data')
if os.path.exists(raw_image_dir):
unpackObj = Sensors(
raw_image_dir,
slc_dir,
remove_file='False',
multiple_raw_frame=inps.template['multiple_raw_frame'])
unpack_run_file = unpackObj.start()
unpackObj.close()
job_obj.write_batch_jobs(batch_file=unpack_run_file)
job_status = job_obj.submit_batch_jobs(batch_file=unpack_run_file)
if not job_status:
raise Exception('ERROR: Unpacking was failed')
else:
raise Exception('ERROR: No data (SLC or Raw) available')
# make run file:
run_dir = os.path.join(inps.work_dir, 'run_files')
config_dir = os.path.join(inps.work_dir, 'configs')
for directory in [run_dir, config_dir]:
if os.path.exists(directory):
shutil.rmtree(directory)
inps.Stack_template = pathObj.correct_for_isce_naming_convention(inps)
runObj = CreateRun(inps)
runObj.run_stack_workflow()
run_file_list = putils.make_run_list(inps.work_dir)
with open(inps.work_dir + '/run_files_list', 'w') as run_file:
for item in run_file_list:
run_file.writelines(item + '\n')
if inps.prefix == 'tops':
# check for orbits
orbit_dir = os.getenv('SENTINEL_ORBITS')
local_orbit = os.path.join(inps.work_dir, 'orbits')
precise_orbits_in_local = glob.glob(local_orbit + '/*/*POEORB*')
if len(precise_orbits_in_local) > 0:
for orbit_file in precise_orbits_in_local:
os.system('cp {} {}'.format(orbit_file, orbit_dir))
# Writing job files
if inps.write_jobs:
for item in run_file_list:
job_obj.write_batch_jobs(batch_file=item)
if inps.template['processingMethod'] == 'smallbaseline':
job_name = 'smallbaseline_wrapper'
job_file_name = job_name
command = [
'smallbaselineApp.py', inps.custom_template_file, '--dir',
'mintpy'
]
job_obj.submit_script(job_name,
job_file_name,
command,
writeOnly='True')
else:
job_name = 'minopy_wrapper'
job_file_name = job_name
command = [
'minopyApp.py', inps.custom_template_file, '--dir', 'minopy'
]
job_obj.submit_script(job_name,
job_file_name,
command,
writeOnly='True')
job_name = 'insarmaps'
job_file_name = job_name
command = ['ingest_insarmaps.py', inps.custom_template_file]
job_obj.submit_script(job_name,
job_file_name,
command,
writeOnly='True')
return None
def main(iargs=None):
""" generates interferograms and coherence images in GeoTiff format """
inps = putils.cmd_line_parse(iargs)
if not iargs is None:
input_arguments = iargs
else:
input_arguments = sys.argv[1::]
message_rsmas.log(
inps.work_dir,
os.path.basename(__file__) + ' ' + ' '.join(input_arguments))
time.sleep(putils.pause_seconds(inps.wait_time))
#########################################
# Submit job
#########################################
if inps.submit_flag:
job_obj = JOB_SUBMIT(inps)
job_name = 'ifgramStack_to_ifgram_and_coherence'
job_file_name = job_name
if '--submit' in input_arguments:
input_arguments.remove('--submit')
command = [os.path.abspath(__file__)] + input_arguments
job_obj.submit_script(job_name, job_file_name, command)
sys.exit(0)
out_dir = inps.work_dir + '/' + pathObj.tiffdir
if not os.path.isdir(out_dir):
os.makedirs(out_dir)
try:
file = glob.glob(inps.work_dir + '/mintpy/inputs/ifgramStack.h5')[0]
except:
raise Exception('ERROR in ' + os.path.basename(__file__) +
': file ifgramStack.h5 not found')
# modify network so that only one connection left
arg_string = file + ' --max-conn-num 1'
print('modify_network.py', arg_string)
mintpy.modify_network.main(arg_string.split())
if not os.path.isdir(inps.work_dir + '/mintpy/geo'):
os.makedirs(inps.work_dir + '/mintpy/geo')
# geocode ifgramStack
geo_file = os.path.dirname(
os.path.dirname(file)) + '/geo/geo_' + os.path.basename(file)
lookup_file = os.path.dirname(
os.path.dirname(file)) + '/inputs/geometryRadar.h5'
template_file = os.path.dirname(
os.path.dirname(file)) + '/smallbaselineApp_template.txt'
arg_string = file + ' -t ' + template_file + ' -l ' + lookup_file + ' -o ' + geo_file
print('geocode.py', arg_string)
mintpy.geocode.main(arg_string.split())
# loop over all interferograms
obj = ifgramStack(geo_file)
obj.open()
date12_list = obj.get_date12_list()
# dummy_data, atr = readfile.read(geo_file)
for i in range(len(date12_list)):
date_str = date12_list[i]
print('Working on ... ' + date_str)
data_coh = readfile.read(file, datasetName='coherence-' + date_str)[0]
data_unw = readfile.read(file,
datasetName='unwrapPhase-' + date_str)[0]
fname_coh = out_dir + '/coherence_' + date_str + '.tif'
fname_unw = out_dir + '/interferogram_' + date_str + '.tif'
create_geotiff(obj,
data=data_coh,
outfile=fname_coh,
type='coherence',
work_dir=inps.work_dir)
create_geotiff(obj,
data=data_unw,
outfile=fname_unw,
type='interferogram',
work_dir=inps.work_dir)
return
def main(iargs=None):
""" create orth and geo rectifying run jobs and submit them. """
inps = putils.cmd_line_parse(iargs)
inps.geom_masterDir = os.path.join(inps.work_dir, pathObj.geomlatlondir)
inps.master = os.path.join(inps.work_dir, pathObj.masterdir)
try:
inps.dem = glob.glob('{}/DEM/*.wgs84'.format(inps.work_dir))[0]
except:
print('DEM not exists!')
sys.exit(1)
if not os.path.exists(inps.geom_masterDir):
os.mkdir(inps.geom_masterDir)
config = putils.get_config_defaults(config_file='job_defaults.cfg')
job_file_name = 'export_ortho_geo'
job_name = job_file_name
if inps.wall_time == 'None':
inps.wall_time = config[job_file_name]['walltime']
wait_seconds, new_wall_time = putils.add_pause_to_walltime(inps.wall_time, inps.wait_time)
#########################################
# Submit job
#########################################
if inps.submit_flag:
js.submit_script(job_name, job_file_name, sys.argv[:], inps.work_dir, new_wall_time)
sys.exit(0)
time.sleep(wait_seconds)
if not iargs is None:
message_rsmas.log(inps.work_dir, os.path.basename(__file__) + ' ' + ' '.join(iargs[:]))
else:
message_rsmas.log(inps.work_dir, os.path.basename(__file__) + ' ' + ' '.join(sys.argv[1::]))
demZero = create_demZero(inps.dem, inps.geom_masterDir)
swathList = ut.getSwathList(inps.master)
create_georectified_lat_lon(swathList, inps.master, inps.geom_masterDir, demZero)
merge_burst_lat_lon(inps)
multilook_images(inps)
run_file_list = make_run_list_amplitude(inps)
for item in run_file_list:
step_name = 'amplitude_ortho_geo'
try:
memorymax = config[step_name]['memory']
except:
memorymax = config['DEFAULT']['memory']
try:
if config[step_name]['adjust'] == 'True':
walltimelimit = putils.walltime_adjust(config[step_name]['walltime'])
else:
walltimelimit = config[step_name]['walltime']
except:
walltimelimit = config['DEFAULT']['walltime']
queuename = os.getenv('QUEUENAME')
putils.remove_last_job_running_products(run_file=item)
jobs = js.submit_batch_jobs(batch_file=item,
out_dir=os.path.join(inps.work_dir, 'run_files'),
work_dir=inps.work_dir, memory=memorymax,
walltime=walltimelimit, queue=queuename)
putils.remove_zero_size_or_length_error_files(run_file=item)
putils.raise_exception_if_job_exited(run_file=item)
putils.concatenate_error_files(run_file=item, work_dir=inps.work_dir)
putils.move_out_job_files_to_stdout(run_file=item)
return
def main(iargs=None):
inps = putils.cmd_line_parse(iargs, script='smallbaseline_wrapper')
if not iargs is None:
input_arguments = iargs
else:
input_arguments = sys.argv[1::]
message_rsmas.log(inps.work_dir, os.path.basename(__file__) + ' ' + ' '.join(input_arguments))
time.sleep(putils.pause_seconds(inps.wait_time))
#########################################
# stripmap prep to isce
#########################################
if inps.template['acquisition_mode']=='stripmap':
inps.dsetDir = inps.work_dir +'/Igrams';
inps.slcDir = inps.work_dir +'/merged/SLC';
inps.geometryDir = inps.work_dir +'/geom_master';
inps.baselineDir = inps.work_dir +'/baselines';
masterDate= inps.template['stripmapStack.master']
if masterDate=='None':
command1= 'cp -r '+inps.slcDir+'/'+os.listdir(inps.slcDir)[0]+'/'+'masterShelve '+inps.work_dir+'/.';
else:
command1= 'cp -r '+inps.slcDir+'/' + masterDate+'/'+'masterShelve '+inps.work_dir+'/.';
print(command1);subprocess.Popen(command1, shell=True).wait();
inps.metaFile= inps.work_dir+'/' +'masterShelve/data.dat';
command2= 'prep_isce.py -d '+inps.dsetDir+' -m '+inps.metaFile+' -b '+inps.baselineDir+' -g '+inps.geometryDir;
print(command2)
subprocess.Popen(command2, shell=True).wait();
#########################################
# Submit job
#########################################
if inps.submit_flag:
job_obj = JOB_SUBMIT(inps)
job_name = 'smallbaseline_wrapper'
job_file_name = job_name
if '--submit' in input_arguments:
input_arguments.remove('--submit')
command = [os.path.abspath(__file__)] + input_arguments
job_obj.submit_script(job_name, job_file_name, command)
sys.exit(0)
os.chdir(inps.work_dir)
try:
with open('out_mintpy.o', 'w') as f:
with contextlib.redirect_stdout(f):
smallbaselineApp.main([inps.custom_template_file])
except:
with open('out_mintpy.e', 'w') as g:
with contextlib.redirect_stderr(g):
smallbaselineApp.main([inps.custom_template_file])
inps.mintpy_dir = os.path.join(inps.work_dir, pathObj.mintpydir)
putils.set_permission_dask_files(directory=inps.mintpy_dir)
# Email Mintpy results
if inps.email:
email_results.main([inps.custom_template_file, '--mintpy'])
return None
def main(iargs=None):
"""Downloads data with ssara and asfserial scripts."""
inps = putils.cmd_line_parse(iargs, script='download_rsmas')
config = putils.get_config_defaults(config_file='job_defaults.cfg')
job_file_name = 'download_rsmas'
job_name = job_file_name
if inps.wall_time == 'None':
inps.wall_time = config[job_file_name]['walltime']
wait_seconds, new_wall_time = putils.add_pause_to_walltime(inps.wall_time, inps.wait_time)
#########################################
# Submit job
#########################################
if inps.submit_flag:
js.submit_script(job_name, job_file_name, sys.argv[:], inps.work_dir, new_wall_time)
sys.exit(0)
time.sleep(wait_seconds)
if not iargs is None:
message_rsmas.log(inps.work_dir, os.path.basename(__file__) + ' ' + ' '.join(iargs[:]))
else:
message_rsmas.log(inps.work_dir, os.path.basename(__file__) + ' ' + ' '.join(sys.argv[1::]))
if not inps.template['topsStack.slcDir'] is None:
slc_dir = inps.template['topsStack.slcDir']
else:
slc_dir = os.path.join(inps.work_dir, 'SLC')
if not os.path.isdir(inps.work_dir):
os.makedirs(inps.work_dir)
if not os.path.isdir(slc_dir):
os.makedirs(slc_dir)
# if satellite is not Sentinel (not tried yet)
if 'SenDT' not in inps.project_name and 'SenAT' not in inps.project_name:
ssara_call = ['ssara_federated_query.py'] + inps.ssaraopt + ['--print', '--download']
ssara_process = subprocess.Popen(ssara_call, shell=True).wait()
completion_status = ssara_process.poll()
return
download('ssara', inps.custom_template_file, slc_dir, outnum=1)
download('asfserial', inps.custom_template_file, slc_dir, outnum = 1)
for i_download in [2,3]:
download_success = run_check_download(slc_dir = slc_dir)
if not download_success:
print('check_download.py: There were bad files, download again')
message_rsmas.log(inps.work_dir,'check_download.py: there were bad files, download again')
download('ssara', inps.custom_template_file, slc_dir, outnum = i_download)
download('asfserial', inps.custom_template_file, slc_dir, outnum = i_download)
def main(iargs=None):
# set defaults: ssara=True is set in dem_parser, use custom_pemp[late field if given
inps = cmd_line_parse(iargs, script='dem_rsmas')
if not iargs is None:
input_arguments = iargs
else:
input_arguments = sys.argv[1::]
message_rsmas.log(inps.work_dir, os.path.basename(__file__) + ' ' + ' '.join(input_arguments))
if not inps.flag_boundingBox and not inps.flag_ssara:
if 'demMethod' in list(inps.template.keys()):
if inps.template['demMethod'] == 'ssara':
inps.flag_ssara = True
inps.flag_boundingBox = False
if inps.template['demMethod'] == 'boundingBox':
inps.flag_ssara = False
inps.flag_boundingBox = True
elif inps.flag_boundingBox:
inps.flag_ssara = False
else:
inps.flag_ssara = True
dem_dir = os.path.join(inps.work_dir, 'DEM')
if not exist_valid_dem_dir(dem_dir):
os.mkdir(dem_dir)
try:
inps.slc_dir = inps.template['topsStack.slcDir']
except:
inps.slc_dir = os.path.join(inps.work_dir, 'SLC')
# 10/21: inps.template['topsStack.slcDir'] may contain ./SLC (it would be better to change where topsStack.slcDir is assigned)
if '.' in inps.slc_dir:
inps.slc_dir = inps.slc_dir.replace(".",os.getcwd())
if 'COSMO-SKYMED' in inps.ssaraopt:
inps.slc_dir = inps.slc_dir.replace('SLC','RAW_data')
# FA 10/2021: We probably should check here whether a DEM/*wgs84 file exist and exit if it does.
# That could save time. On the other hand, most steps allow to be run even if data exist
os.chdir(dem_dir)
if inps.flag_ssara:
call_ssara_dem(inps, dem_dir)
print('You have finished SSARA!')
cmd = 'fixImageXml.py -f -i {}'.format(glob.glob(dem_dir + '/dem*.wgs84')[0])
os.system(cmd)
elif inps.flag_boundingBox or inps.flag_ssara_kml:
print('DEM generation using ISCE')
if inps.flag_boundingBox:
bbox = inps.template[inps.prefix + 'Stack.boundingBox'].strip("'")
if inps.flag_ssara_kml:
#ssara_kml_file=sorted( glob.glob(inps.work_dir + '/SLC/ssara_search_*.kml') )[-1]
try:
ssara_kml_file=sorted( glob.glob(inps.slc_dir + '/ssara_search_*.kml') )[-1]
except:
raise FileExistsError('No SLC/ssara_search_*.kml found')
bbox = get_boundingBox_from_kml.main( [ssara_kml_file, '--delta_lon' , '0'] )
bbox = bbox.split('SNWE:')[1]
print('bbox:',bbox)
bbox = [val for val in bbox.split()]
south = bbox[0]
north = bbox[1]
west = bbox[2]
east = bbox[3].split('\'')[0]
south = math.floor(float(south) - 0.5)
north = math.ceil(float(north) + 0.5)
west = math.floor(float(west) - 0.5)
east = math.ceil(float(east) + 0.5)
demBbox = str(int(south)) + ' ' + str(int(north)) + ' ' + str(int(west)) + ' ' + str(int(east))
command = 'dem.py -a stitch --filling --filling_value 0 -b ' + demBbox + ' -c -u https://e4ftl01.cr.usgs.gov/MEASURES/SRTMGL1.003/2000.02.11/'
message_rsmas.log(os.getcwd(), command)
if os.getenv('DOWNLOADHOST') == 'local':
try:
proc = subprocess.Popen(command, stderr=subprocess.PIPE, stdout=subprocess.PIPE, shell=True,
universal_newlines=True)
output, error = proc.communicate()
print(error)
if proc.returncode is not 0:
raise Exception(
'ERROR starting dem.py subprocess') # FA 8/19: I don't think this happens, errors are is output
print(output)
print(error, file=sys.stderr)
except subprocess.CalledProcessError as exc:
print("Command failed. Exit code, StdErr:", exc.returncode, exc.output)
sys.exit('Error produced by dem.py')
else:
if 'Could not create a stitched DEM. Some tiles are missing' in output:
os.chdir('..')
shutil.rmtree('DEM')
sys.exit('Error in dem.py: Tiles are missing. Ocean???')
else:
dem_dir = os.getcwd()
ssh_command_list = ['s.bgood', 'cd {0}'.format(dem_dir), command]
host = os.getenv('DOWNLOADHOST')
try:
status = ssh_with_commands(host, ssh_command_list)
except subprocess.CalledProcessError as exc:
print("Command failed. Exit code, StdErr:", exc.returncode, exc.output)
sys.exit('Error produced by dem.py using ' + host)
cmd = 'fixImageXml.py -f -i {}'.format(glob.glob(dem_dir + '/demLat_*.wgs84')[0])
os.system(cmd)
# print('Exit status from dem.py: {0}'.format(status))
# xmlFile = glob.glob('demLat_*.wgs84.xml')[0]
# fin = open(xmlFile, 'r')
# fout = open("tmp.txt", "wt")
# for line in fin:
# fout.write(line.replace('demLat', dem_dir + '/demLat'))
# fin.close()
# fout.close()
# os.rename('tmp.txt', xmlFile)
else:
sys.exit('Error unspported demMethod option: ' + inps.template['demMethod'])
print('\n###############################################')
print('End of dem_rsmas.py')
print('################################################\n')
return None
def main(iargs=None):
inps = putils.cmd_line_parse(iargs, script='ingest_insarmaps')
config = putils.get_config_defaults(config_file='job_defaults.cfg')
job_file_name = 'ingest_insarmaps'
job_name = job_file_name
if inps.wall_time == 'None':
inps.wall_time = config[job_file_name]['walltime']
wait_seconds, new_wall_time = putils.add_pause_to_walltime(inps.wall_time, inps.wait_time)
#########################################
# Submit job
#########################################
if inps.submit_flag:
js.submit_script(job_name, job_file_name, sys.argv[:], inps.work_dir, new_wall_time)
time.sleep(wait_seconds)
os.chdir(inps.work_dir)
if not iargs is None:
message_rsmas.log(inps.work_dir, os.path.basename(__file__) + ' ' + ' '.join(iargs[:]))
else:
message_rsmas.log(inps.work_dir, os.path.basename(__file__) + ' ' + ' '.join(sys.argv[1::]))
hdfeos_file = glob.glob(inps.work_dir + '/mintpy/S1*.he5')
hdfeos_file.append(glob.glob(inps.work_dir +'/mintpy/SUBSET_*/S1*.he5'))
hdfeos_file = hdfeos_file[0]
json_folder = inps.work_dir + '/mintpy/JSON'
mbtiles_file = json_folder + '/' + os.path.splitext(os.path.basename(hdfeos_file))[0] + '.mbtiles'
if os.path.isdir(json_folder):
shutil.rmtree(json_folder)
command1 = 'hdfeos5_2json_mbtiles.py ' + hdfeos_file + ' ' + json_folder + ' |& tee out_insarmaps.log'
command2 = 'json_mbtiles2insarmaps.py -u ' + password.insaruser + ' -p ' + password.insarpass + ' --host ' + \
'insarmaps.miami.edu -P rsmastest -U rsmas\@gmail.com --json_folder ' + \
json_folder + ' --mbtiles_file ' + mbtiles_file + ' |& tee -a out_insarmaps.log'
with open(inps.work_dir + '/mintpy/run_insarmaps', 'w') as f:
f.write(command1 + '\n')
f.write(command2 + '\n')
out_file = 'out_insarmaps'
message_rsmas.log(inps.work_dir, command1)
command1 = '('+command1+' | tee '+out_file+'.o) 3>&1 1>&2 2>&3 | tee '+out_file+'.e'
status = subprocess.Popen(command1, shell=True).wait()
if status is not 0:
raise Exception('ERROR in hdfeos5_2json_mbtiles.py')
# TODO: Change subprocess call to get back error code and send error code to logger
message_rsmas.log(inps.work_dir, command2)
command2 = '('+command2+' | tee -a '+out_file+'.o) 3>&1 1>&2 2>&3 | tee -a '+out_file+'.e'
status = subprocess.Popen(command2, shell=True).wait()
if status is not 0:
raise Exception('ERROR in json_mbtiles2insarmaps.py')
# Email insarmaps results:
if inps.email:
email_results.main([inps.custom_template_file, '--insarmap'])
return None
def main(iargs=None):
inps = putils.cmd_line_parse(iargs, script='execute_runfiles')
if not iargs is None:
input_arguments = iargs
else:
input_arguments = sys.argv[1::]
message_rsmas.log(
inps.work_dir,
os.path.basename(__file__) + ' ' + ' '.join(input_arguments))
os.chdir(inps.work_dir)
time.sleep(putils.pause_seconds(inps.wait_time))
if inps.prefix == 'stripmap':
inps.num_bursts = 1
inps.out_dir = os.path.join(inps.work_dir, 'run_files')
job_obj = JOB_SUBMIT(inps)
#########################################
# Submit job
#########################################
if inps.submit_flag:
job_name = 'execute_runfiles'
job_file_name = job_name
if '--submit' in input_arguments:
input_arguments.remove('--submit')
command = [os.path.abspath(__file__)] + input_arguments
job_obj.submit_script(job_name, job_file_name, command)
sys.exit(0)
run_file_list = putils.read_run_list(inps.work_dir)
if inps.end_run == 0:
inps.end_run = len(run_file_list)
if not inps.start_run == 0:
inps.start_run = inps.start_run - 1
if inps.step:
inps.start_run = inps.step - 1
inps.end_run = inps.step
run_file_list = run_file_list[inps.start_run:inps.end_run]
for item in run_file_list:
putils.remove_last_job_running_products(run_file=item)
job_status = job_obj.submit_batch_jobs(batch_file=item)
if job_status:
putils.remove_zero_size_or_length_error_files(run_file=item)
putils.rerun_job_if_exit_code_140(run_file=item, inps_dict=inps)
putils.raise_exception_if_job_exited(run_file=item)
putils.concatenate_error_files(run_file=item,
work_dir=inps.work_dir)
putils.move_out_job_files_to_stdout(run_file=item)
date_str = datetime.datetime.strftime(datetime.datetime.now(),
'%Y%m%d:%H%M%S')
print(date_str + ' * Job {} completed'.format(item))
date_str = datetime.datetime.strftime(datetime.datetime.now(),
'%Y%m%d:%H%M%S')
print(date_str + ' * all jobs from {} to {} have been completed'.format(
os.path.basename(run_file_list[0]), os.path.basename(
run_file_list[-1])))
return None
def main(iargs=None):
inps = putils.cmd_line_parse(iargs, script='execute_runfiles')
os.chdir(inps.work_dir)
config = putils.get_config_defaults(config_file='job_defaults.cfg')
job_file_name = 'execute_runfiles'
job_name = job_file_name
if inps.wall_time == 'None':
inps.wall_time = config[job_file_name]['walltime']
wait_seconds, new_wall_time = putils.add_pause_to_walltime(
inps.wall_time, inps.wait_time)
#########################################
# Submit job
#########################################
if inps.submit_flag:
js.submit_script(job_name, job_file_name, sys.argv[:], inps.work_dir,
new_wall_time)
sys.exit(0)
time.sleep(wait_seconds)
command_line = os.path.basename(sys.argv[0]) + ' ' + ' '.join(sys.argv[1:])
message_rsmas.log(inps.work_dir, command_line)
run_file_list = putils.read_run_list(inps.work_dir)
if inps.endrun == 0:
inps.endrun = len(run_file_list)
if not inps.startrun == 0:
inps.startrun = inps.startrun - 1
run_file_list = run_file_list[inps.startrun:inps.endrun]
if os.getenv('JOBSCHEDULER') == 'LSF' or os.getenv(
'JOBSCHEDULER') == 'PBS':
for item in run_file_list:
step_name = '_'
step_name = step_name.join(item.split('_')[3::])
try:
memorymax = config[step_name]['memory']
except:
memorymax = config['DEFAULT']['memory']
try:
if config[step_name]['adjust'] == 'True':
walltimelimit = putils.walltime_adjust(
inps, config[step_name]['walltime'])
else:
walltimelimit = config[step_name]['walltime']
except:
walltimelimit = config['DEFAULT']['walltime']
queuename = os.getenv('QUEUENAME')
putils.remove_last_job_running_products(run_file=item)
jobs = js.submit_batch_jobs(batch_file=item,
out_dir=os.path.join(
inps.work_dir, 'run_files'),
work_dir=inps.work_dir,
memory=memorymax,
walltime=walltimelimit,
queue=queuename)
putils.remove_zero_size_or_length_error_files(run_file=item)
putils.raise_exception_if_job_exited(run_file=item)
putils.concatenate_error_files(run_file=item,
work_dir=inps.work_dir)
putils.move_out_job_files_to_stdout(run_file=item)
else:
for item in run_file_list:
with open(item, 'r') as f:
command_lines = f.readlines()
for command_line in command_lines:
os.system(command_line)
return None
def main(iargs=None):
""" create orth and geo rectifying run jobs and submit them. """
inps = putils.cmd_line_parse(iargs)
import s1a_isce_utils as ut
import mergeBursts as mb
if not iargs is None:
input_arguments = iargs
else:
input_arguments = sys.argv[1::]
message_rsmas.log(
inps.work_dir,
os.path.basename(__file__) + ' ' + ' '.join(input_arguments))
inps.geom_masterDir = os.path.join(inps.work_dir, pathObj.geomlatlondir)
inps.master = os.path.join(inps.work_dir, pathObj.masterdir)
try:
inps.dem = glob.glob('{}/DEM/*.wgs84'.format(inps.work_dir))[0]
except:
print('DEM not exists!')
sys.exit(1)
if not os.path.exists(inps.geom_masterDir):
os.mkdir(inps.geom_masterDir)
time.sleep(putils.pause_seconds(inps.wait_time))
inps.out_dir = os.path.join(inps.work_dir, 'run_files')
job_obj = JOB_SUBMIT(inps)
#########################################
# Submit job
#########################################
if inps.submit_flag:
job_name = 'export_ortho_geo'
job_file_name = job_name
if '--submit' in input_arguments:
input_arguments.remove('--submit')
command = [os.path.abspath(__file__)] + input_arguments
job_obj.submit_script(job_name, job_file_name, command)
sys.exit(0)
pic_dir = os.path.join(inps.work_dir, pathObj.tiffdir)
if not os.path.exists(pic_dir):
os.mkdir(pic_dir)
demZero = create_demZero(inps.dem, inps.geom_masterDir)
swathList = ut.getSwathList(inps.master)
create_georectified_lat_lon(swathList, inps.master, inps.geom_masterDir,
demZero)
merge_burst_lat_lon(inps)
multilook_images(inps)
run_file_list = make_run_list(inps)
for item in run_file_list:
putils.remove_last_job_running_products(run_file=item)
job_status = job_obj.submit_batch_jobs(batch_file=item)
if job_status:
putils.remove_zero_size_or_length_error_files(run_file=item)
putils.rerun_job_if_exit_code_140(run_file=item, inps_dict=inps)
putils.raise_exception_if_job_exited(run_file=item)
putils.concatenate_error_files(run_file=item,
work_dir=inps.work_dir)
putils.move_out_job_files_to_stdout(run_file=item)
#upload_to_s3(pic_dir)
minsar.upload_data_products.main(
[inps.custom_template_file, '--imageProducts'])
return