def get_memory_walltime(self, job_name, job_type='batch'):
"""
get memory, walltime and number of threads for the job from job_defaults.cfg
:param job_name: the job file name
:param job_type: 'batch' or 'script'
"""
config = putils.get_config_defaults(config_file='job_defaults.cfg')
if job_type == 'batch':
step_name = '_'
step_name = step_name.join(job_name.split('/')[-1].split('_')[2::])
else:
step_name = job_name
if self.prefix == 'tops' and job_type == 'batch':
if self.num_bursts is None:
self.num_bursts = putils.get_number_of_bursts(self.inps)
if self.num_bursts:
number_of_bursts = self.num_bursts
else:
number_of_bursts = 1
if self.memory in [None, 'None']:
if step_name in config:
c_memory = config[step_name]['c_memory']
s_memory = config[step_name]['s_memory']
else:
c_memory = config['default']['c_memory']
s_memory = config['default']['s_memory']
self.default_memory = putils.scale_memory(number_of_bursts, c_memory, s_memory)
else:
self.default_memory = self.memory
if self.wall_time in [None, 'None']:
if step_name in config:
c_walltime = config[step_name]['c_walltime']
s_walltime = config[step_name]['s_walltime']
else:
c_walltime = config['default']['c_walltime']
s_walltime = config['default']['s_walltime']
self.default_wall_time = putils.scale_walltime(number_of_bursts, self.wall_time_factor,
c_walltime, s_walltime, self.scheduler)
else:
#self.default_wall_time = self.wall_time
c_walltime = self.wall_time
s_walltime = '0'
self.default_wall_time = putils.scale_walltime(number_of_bursts, self.wall_time_factor,
c_walltime, s_walltime, self.scheduler)
if step_name in config:
self.default_num_threads = config[step_name]['num_threads']
else:
self.default_num_threads = config['default']['num_threads']
return
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='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 + '/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='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):
start_time = time.time()
inps = process_rsmas_cmd_line_parse(iargs)
template_file = pathObj.auto_template
# print default template
if inps.print_template:
raise SystemExit(open(template_file, 'r').read())
inps = check_directories_and_inputs(inps)
command_line = os.path.basename(sys.argv[0]) + ' ' + ' '.join(sys.argv[1:])
message_rsmas.log(inps.work_dir, '##### NEW RUN #####')
message_rsmas.log(inps.work_dir, command_line)
config = putils.get_config_defaults(config_file='job_defaults.cfg')
job_file_name = 'process_rsmas'
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:
job = js.submit_script(inps.project_name, job_file_name, sys.argv[:],
inps.work_dir, new_wall_time)
# run_operations.py needs this print statement for now.
# This is not for debugging purposes.
# DO NOT REMOVE.
print(job)
else:
time.sleep(wait_seconds)
objInsar = RsmasInsar(inps)
objInsar.run(steps=inps.runSteps)
# Timing
m, s = divmod(time.time() - start_time, 60)
print('\nTotal time: {:02.0f} mins {:02.1f} secs'.format(m, s))
return
def get_memory_walltime(job_name,
job_type='batch',
wall_time=None,
memory=None):
"""
get memory and walltime for the job from job_defaults.cfg
:param job_name: the job file name
:param job_type: 'batch' or 'script'
:param wall_time: wall time required for the job
:param memory: memory required for the job
:return: memory, wall_time, number_of_threads
"""
config = putils.get_config_defaults(config_file='job_defaults.cfg')
num_threads = 4
if job_type == 'batch':
step_name = '_'
step_name = step_name.join(job_name.split('/')[-1].split('_')[2::])
if memory is None:
if step_name in config:
memory = config[step_name]['memory']
else:
memory = config['DEFAULT']['memory']
if wall_time is None:
if step_name in config:
wall_time = config[step_name]['walltime']
else:
wall_time = config['DEFAULT']['walltime']
if step_name in config:
num_threads = config[step_name]['num_threads']
else:
num_threads = config[step_name]['num_threads']
elif job_type == 'script':
if wall_time is None:
if job_name in config:
wall_time = config[job_name]['walltime']
else:
wall_time = config['DEFAULT']['walltime']
return memory, wall_time, num_threads
def get_memory_walltime(self, job_name, job_type='batch'):
"""
get memory, walltime and number of threads for the job from job_defaults.cfg
:param job_name: the job file name
:param job_type: 'batch' or 'script'
"""
config = putils.get_config_defaults(config_file='job_defaults.cfg')
if job_type == 'batch':
step_name = '_'
step_name = step_name.join(job_name.split('/')[-1].split('_')[2::])
else:
step_name = job_name
if self.memory in [None, 'None']:
if step_name in config:
self.default_memory = config[step_name]['memory']
else:
self.default_memory = config['DEFAULT']['memory']
else:
self.default_memory = self.memory
if self.wall_time in [None, 'None']:
if step_name in config:
self.default_wall_time = config[step_name]['walltime']
if config[step_name]['adjust'] == 'True':
if self.num_bursts is None:
self.num_bursts = putils.get_number_of_bursts(self)
else:
self.default_wall_time = config['DEFAULT']['walltime']
self.default_wall_time = putils.walltime_adjust(
self.num_bursts,
self.default_wall_time,
self.scheduler,
adjust=config[step_name]['adjust'])
else:
self.default_wall_time = self.wall_time
if step_name in config:
self.default_num_threads = config[step_name]['num_threads']
else:
self.default_num_threads = config['DEFAULT']['num_threads']
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)
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):
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):
"""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):
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):
""" 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):
""" generates interferograms and coherence images in GeoTiff format """
inps = putils.cmd_line_parse(iargs)
config = putils.get_config_defaults(config_file='job_defaults.cfg')
job_file_name = 'ifgramStack_to_ifgram_and_coherence'
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)
message_rsmas.log(inps.work_dir,
os.path.basename(__file__) + ' ' + ' '.join(iargs[:]))
out_dir = inps.work_dir + '/' + inps.out_dir
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):
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'
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]
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')
global project_slc_dir
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
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='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
dataset_template = Template(inps.custom_template_file)
dataset_template.options.update(
PathFind.correct_for_ssara_date_format(dataset_template.options))
subprocess.Popen("rm new_files.csv", shell=True).wait()
standardTuple = (inps, dataset_template)
if inps.seasonalStartDate is not None and inps.seasonalEndDate is not None:
ogStartYearInt = int(
dataset_template.options['ssaraopt.startDate'][:4])
if int(inps.seasonalStartDate) > int(inps.seasonalEndDate):
y = 1
else:
y = 0
YearRange = int(dataset_template.options['ssaraopt.endDate']
[:4]) - ogStartYearInt + 1
if YearRange > 1 and y == 1:
YearRange = YearRange - 1
seasonalStartDateAddOn = '-' + inps.seasonalStartDate[:
2] + '-' + inps.seasonalStartDate[
2:]
seasonalEndDateAddOn = '-' + inps.seasonalEndDate[:
2] + '-' + inps.seasonalEndDate[
2:]
ogEndDate = dataset_template.options['ssaraopt.endDate']
for x in range(YearRange):
seasonalTuple = standardTuple + (x, ogStartYearInt, y, YearRange,
seasonalStartDateAddOn,
seasonalEndDateAddOn, ogEndDate)
generate_files_csv(project_slc_dir, inps.custom_template_file,
seasonalTuple)
y += 1
else:
generate_files_csv(project_slc_dir, inps.custom_template_file,
standardTuple)
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
