def main(iargs=None):
start_time = time.time()
inps = process_rsmas_cmd_line_parse(iargs)
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)
time.sleep(putils.pause_seconds(inps.wait_time))
#########################################
# Submit job
#########################################
if inps.submit_flag:
job_obj = JOB_SUBMIT(inps)
job_file_name = 'process_rsmas'
job = job_obj.submit_script(inps.project_name, job_file_name,
sys.argv[:])
# run_operations.py needs this print statement for now.
# This is not for debugging purposes.
# DO NOT REMOVE.
print(job)
else:
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 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 rerun_job_if_exit_code_140(run_file, inps_dict):
"""Find files that exited because walltime exceeed and run again with twice the walltime"""
from minsar.job_submission import JOB_SUBMIT
inps = inps_dict
search_string = 'Exited with exit code 140.'
files, job_files = find_completed_jobs_matching_search_string(
run_file, search_string)
if len(files) == 0:
return
rerun_file = create_rerun_run_file(job_files)
wall_time = extract_walltime_from_job_file(job_files[0])
memory = extract_memory_from_job_file(job_files[0])
new_wall_time = multiply_walltime(wall_time, factor=2)
print(new_wall_time)
print(memory)
for file in files:
os.remove(file.replace('.o*', '.e*'))
move_out_job_files_to_stdout(run_file)
# renaming of stdout dir as otherwise it will get deleted in later move_out_job_files_to_stdout step
stdout_dir = os.path.dirname(run_file) + '/stdout_' + os.path.basename(
run_file)
os.rename(stdout_dir, stdout_dir + '_pre_rerun')
remove_last_job_running_products(run_file)
#queuename = os.getenv('QUEUENAME')
inps.wall_time = new_wall_time
inps.work_dir = os.path.dirname(os.path.dirname(rerun_file))
inps.out_dir = os.path.dirname(rerun_file)
#inps.queue = queuename
job_obj = JOB_SUBMIT(inps)
job_obj.write_batch_jobs(batch_file=rerun_file)
jobs = job_obj.submit_batch_jobs(batch_file=rerun_file)
remove_zero_size_or_length_error_files(run_file=rerun_file)
raise_exception_if_job_exited(run_file=rerun_file)
concatenate_error_files(run_file=rerun_file,
work_dir=os.path.dirname(
os.path.dirname(run_file)))
move_out_job_files_to_stdout(rerun_file)
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='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)
#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 create_run_files(self):
print('-' * 50)
print('Create run files for all the steps')
os.makedirs(self.run_dir, exist_ok=True)
if self.write_job:
from minsar.job_submission import JOB_SUBMIT
inps = self.inps
inps.custom_template_file = self.org_custom_template
if self.org_custom_template is None:
inps.custom_template_file = self.templateFile
inps.work_dir = os.path.dirname(self.run_dir)
inps.out_dir = self.run_dir
inps.num_data = self.num_images
job_obj = JOB_SUBMIT(inps)
else:
job_obj = None
self.run_load_data('load_data', job_obj)
self.run_phase_linking('phase_linking', job_obj)
self.run_phase_linking('concatenate_patch', job_obj)
self.run_interferogram('generate_ifgram', job_obj)
self.run_unwrap('unwrap_ifgram', job_obj)
self.run_load_ifg('load_ifgram', job_obj)
self.run_ifgram_correction('ifgram_correction', job_obj)
self.run_network_inversion('invert_network', job_obj)
self.run_timeseries_correction('timeseries_correction', job_obj)
del job_obj
run_file_list = []
for key, value in RUN_FILES.items():
run_file_list.append(value)
with open(self.workDir + '/run_files_list', 'w') as run_file:
for item in run_file_list:
run_file.writelines(item + '\n')
return
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):
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='')
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 + '/gep_download.log'
logger = RsmasLogger(file_name=logfile_name)
if not inps.template['raw_image_dir'] is None:
inps.slc_dir = inps.template['raw_image_dir']
else:
inps.slc_dir = os.path.join(inps.work_dir, 'raw')
project_slc_dir = os.path.join(inps.work_dir, 'raw')
#########################################
# Submit job
#########################################
if inps.submit_flag:
job_file_name = 'download_gep_csk'
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"))
start_date = inps.template['ssaraopt.startDate']
start_date = datetime.datetime.strptime(start_date, '%Y%m%d')
end_date = inps.template['ssaraopt.endDate']
end_date = datetime.datetime.strptime(end_date, '%Y%m%d')
if 'stripmapStack.boundingBox' in inps.template:
bbox = inps.template['stripmapStack.boundingBox']
else:
bbox = inps.template['topsStack.boundingBox']
bbox = bbox.split(' ')
bbox = '{},{},{},{}'.format(bbox[2], bbox[0], bbox[3], bbox[1])
user = subprocess.check_output(
"grep gepuser $RSMASINSAR_HOME/3rdparty/SSARA/password_config.py |\
sed 's/\"//g''' | cut -d '=' -f 2",
shell=True).decode('UTF-8').split('\n')[0]
passwd = subprocess.check_output(
"grep geppass $RSMASINSAR_HOME/3rdparty/SSARA/password_config.py |\
sed 's/\"//g''' | cut -d '=' -f 2",
shell=True).decode('UTF-8').split('\n')[0]
command_get_list = 'curl -s "https://catalog.terradue.com/csk/search?format=atom&count=1000&bbox={bbox}" |\
xmllint --format - | grep enclosure | sed "s/.*<link rel="enclosure".*href="\(.*\)"\/>/\1/g"'.format(
bbox=bbox)
print(command_get_list)
data_list = subprocess.check_output(command_get_list, shell=True).decode(
'UTF-8') #os.system(command_get_list)
data_list = data_list.split('/>\n')
data_list = [x.split('"')[-2] for x in data_list[0:-1]]
cmd_all = []
for data in data_list:
date = datetime.datetime.strptime(
data.split('.h5')[0].split('_')[-1][0:8], '%Y%m%d')
if date >= start_date and date <= end_date:
cmd = 'curl -u {username}:{password} -o $(basename ${enclosure}) {enclosure}'.format(
username=user, password=passwd, enclosure=data)
cmd_all.append(cmd)
pool = mp.Pool(6)
pool.map(os.system, cmd_all)
pool.close()
logger.log(loglevel.INFO, "Download Finish")
logger.log(loglevel.INFO, "------------------------------------")
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)
ssaraopt = [ x for x in ssaraopt if not x[0:7]=='--frame']
return ssaraopt
if __name__ == "__main__":
inps = command_line_parse(sys.argv[1:])
inps.project_name = putils.get_project_name(custom_template_file=inps.template)
inps.work_dir = putils.get_work_directory(None, inps.project_name)
inps.slc_dir = inps.work_dir + "/SLC"
#########################################
# Submit job
#########################################
if inps.submit_flag:
job_file_name = 'download_ssara_rsmas'
job_name = inps.template.split(os.sep)[-1].split('.')[0]
inps.wall_time = '24:00'
job_obj = JOB_SUBMIT(inps)
job_obj.submit_script(job_name, job_file_name, sys.argv[:])
sys.exit(0)
os.chdir(inps.work_dir)
message_rsmas.log(inps.work_dir, os.path.basename(__file__) + ' ' + ' '.join(sys.argv[1::]))
if not os.path.isdir(inps.slc_dir):
os.makedirs(inps.slc_dir)
os.chdir(inps.slc_dir)
succesful = run_ssara(inps.work_dir, inps.template, inps.delta_lat)
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
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):
""" create orth and geo rectifying run jobs and submit them. """
inps = putils.cmd_line_parse(iargs)
if 'stripmap' in inps.prefix:
sys.path.append(os.path.join(os.getenv('ISCE_STACK'), 'stripmapStack'))
else:
sys.path.append(os.path.join(os.getenv('ISCE_STACK'), 'topsStack'))
from s1a_isce_utils import loadProduct, getSwathList
import mergeBursts
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_referenceDir = os.path.join(inps.work_dir, pathObj.geomlatlondir)
inps.reference = os.path.join(inps.work_dir, pathObj.referencedir)
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_referenceDir):
os.mkdir(inps.geom_referenceDir)
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)
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_referenceDir)
swathList = getSwathList(inps.reference)
create_georectified_lat_lon(swathList, inps.reference,
inps.geom_referenceDir, demZero, loadProduct)
merge_burst_lat_lon(inps, mergeBursts)
multilook_images(inps, mergeBursts)
run_file_list = make_run_list(inps)
for item in run_file_list:
putils.remove_last_job_running_products(run_file=item)
job_obj.write_batch_jobs(batch_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)
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):
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):
"""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 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)