def read_inps2dict(inps):
"""Read input Namespace object info into inpsDict
It grab the following contents into inpsDict
1. inps & all template files
2. configurations: processor, autoPath, updateMode, compression
3. extra metadata: PLATFORM, PROJECT_NAME,
4. translate autoPath
"""
# Read input info into inpsDict
inpsDict = vars(inps)
inpsDict['PLATFORM'] = None
# Read template file
template = {}
for fname in inps.template_file:
temp = readfile.read_template(fname)
temp = ut.check_template_auto_value(temp)
template.update(temp)
for key, value in template.items():
inpsDict[key] = value
if 'processor' in template.keys():
template['mintpy.load.processor'] = template['processor']
prefix = 'mintpy.load.'
key_list = [i.split(prefix)[1] for i in template.keys() if i.startswith(prefix)]
for key in key_list:
value = template[prefix+key]
if key in ['processor', 'autoPath', 'updateMode', 'compression']:
inpsDict[key] = template[prefix+key]
elif value:
inpsDict[prefix+key] = template[prefix+key]
print('processor : {}'.format(inpsDict['processor']))
if inpsDict['compression'] == False:
inpsDict['compression'] = None
# PROJECT_NAME --> PLATFORM
if not inpsDict['PROJECT_NAME']:
cfile = [i for i in list(inps.template_file) if os.path.basename(i) != 'smallbaselineApp.cfg']
inpsDict['PROJECT_NAME'] = sensor.project_name2sensor_name(cfile)[1]
msg = 'SAR platform/sensor : '
sensor_name = sensor.project_name2sensor_name(str(inpsDict['PROJECT_NAME']))[0]
if sensor_name:
msg += str(sensor_name)
inpsDict['PLATFORM'] = str(sensor_name)
else:
msg += 'unknown from project name "{}"'.format(inpsDict['PROJECT_NAME'])
print(msg)
# update file path with auto
if inpsDict.get('autoPath', False):
print('use auto path defined in mintpy.defaults.auto_path for options in auto')
inpsDict = auto_path.get_auto_path(processor=inpsDict['processor'],
work_dir=os.path.dirname(inpsDict['outdir']),
template=inpsDict)
return inpsDict
def read_inps2dict(inps):
"""Read input Namespace object info into inpsDict"""
# Read input info into inpsDict
inpsDict = vars(inps)
inpsDict['PLATFORM'] = None
# Read template file
template = {}
for fname in inps.template_file:
temp = readfile.read_template(fname)
temp = ut.check_template_auto_value(temp)
template.update(temp)
for key, value in template.items():
inpsDict[key] = value
if 'processor' in template.keys():
template['mintpy.load.processor'] = template['processor']
prefix = 'mintpy.load.'
key_list = [
i.split(prefix)[1] for i in template.keys() if i.startswith(prefix)
]
for key in key_list:
value = template[prefix + key]
if key in ['processor', 'updateMode', 'compression']:
inpsDict[key] = template[prefix + key]
elif value:
inpsDict[prefix + key] = template[prefix + key]
if inpsDict['compression'] == False:
inpsDict['compression'] = None
# PROJECT_NAME --> PLATFORM
if not inpsDict['PROJECT_NAME']:
cfile = [
i for i in list(inps.template_file)
if os.path.basename(i) != 'smallbaselineApp.cfg'
]
inpsDict['PROJECT_NAME'] = sensor.project_name2sensor_name(cfile)[1]
inpsDict['PLATFORM'] = str(
sensor.project_name2sensor_name(str(inpsDict['PROJECT_NAME']))[0])
if inpsDict['PLATFORM']:
print('SAR platform/sensor : {}'.format(inpsDict['PLATFORM']))
print('processor: {}'.format(inpsDict['processor']))
# Here to insert code to check default file path for miami user
if (auto_path.autoPath and 'SCRATCHDIR' in os.environ
and inpsDict['PROJECT_NAME'] is not None
and inpsDict['mintpy.load.unwFile']) == 'auto':
print(('check auto path setting for Univ of Miami users'
' for processor: {}'.format(inpsDict['processor'])))
inpsDict = auto_path.get_auto_path(
processor=inpsDict['processor'],
project_name=inpsDict['PROJECT_NAME'],
template=inpsDict)
return inpsDict
def read_inps2dict(inps):
"""Read input Namespace object info into inpsDict"""
# Read input info into inpsDict
inpsDict = vars(inps)
inpsDict['PLATFORM'] = None
# Read template file
template = {}
for fname in inps.template_file:
temp = readfile.read_template(fname)
temp = ut.check_template_auto_value(temp)
template.update(temp)
for key, value in template.items():
inpsDict[key] = value
if 'processor' in template.keys():
template['mintpy.load.processor'] = template['processor']
prefix = 'mintpy.load.'
key_list = [
i.split(prefix)[1] for i in template.keys() if i.startswith(prefix)
]
for key in key_list:
value = template[prefix + key]
if key in ['processor', 'autoPath', 'updateMode', 'compression']:
inpsDict[key] = template[prefix + key]
elif value:
inpsDict[prefix + key] = template[prefix + key]
if inpsDict['compression'] == False:
inpsDict['compression'] = None
# PROJECT_NAME --> PLATFORM
if not inpsDict['PROJECT_NAME']:
cfile = [
i for i in list(inps.template_file)
if os.path.basename(i) != 'smallbaselineApp.cfg'
]
inpsDict['PROJECT_NAME'] = sensor.project_name2sensor_name(cfile)[1]
inpsDict['PLATFORM'] = str(
sensor.project_name2sensor_name(str(inpsDict['PROJECT_NAME']))[0])
print('SAR platform/sensor : {}'.format(inpsDict['PLATFORM']))
print('processor: {}'.format(inpsDict['processor']))
# update file path with auto
if inpsDict['autoPath']:
print(
'use auto path defined in mintpy.defaults.auto_path for options in auto'
)
inpsDict = auto_path.get_auto_path(processor=inpsDict['processor'],
work_dir=os.path.dirname(
inpsDict['outdir']),
template=inpsDict)
return inpsDict
def read_inps2dict(inps):
"""Read input Namespace object info into inpsDict"""
# Read input info into inpsDict
inpsDict = vars(inps)
inpsDict['PLATFORM'] = None
# Read template file
template = {}
for fname in inps.template_file:
temp = readfile.read_template(fname)
temp = ut.check_template_auto_value(temp)
template.update(temp)
for key, value in template.items():
inpsDict[key] = value
if 'processor' in template.keys():
template['mintpy.load.processor'] = template['processor']
prefix = 'mintpy.load.'
key_list = [i.split(prefix)[1] for i in template.keys() if i.startswith(prefix)]
for key in key_list:
value = template[prefix+key]
if key in ['processor', 'updateMode', 'compression']:
inpsDict[key] = template[prefix+key]
elif value:
inpsDict[prefix+key] = template[prefix+key]
if inpsDict['compression'] == False:
inpsDict['compression'] = None
# PROJECT_NAME --> PLATFORM
if not inpsDict['PROJECT_NAME']:
cfile = [i for i in list(inps.template_file) if os.path.basename(i) != 'smallbaselineApp.cfg']
inpsDict['PROJECT_NAME'] = sensor.project_name2sensor_name(cfile)[1]
inpsDict['PLATFORM'] = str(sensor.project_name2sensor_name(str(inpsDict['PROJECT_NAME']))[0])
if inpsDict['PLATFORM']:
print('platform : {}'.format(inpsDict['PLATFORM']))
print('processor: {}'.format(inpsDict['processor']))
# Here to insert code to check default file path for miami user
if (auto_path.autoPath
and 'SCRATCHDIR' in os.environ
and inpsDict['PROJECT_NAME'] is not None):
print(('check auto path setting for Univ of Miami users'
' for processor: {}'.format(inpsDict['processor'])))
inpsDict = auto_path.get_auto_path(processor=inpsDict['processor'],
project_name=inpsDict['PROJECT_NAME'],
template=inpsDict)
return inpsDict
def write_job_file(iDict):
"""Write job file to submit process_isce_stack.py as a job"""
# command line
cmd = 'process_isce_stack.py -t {}'.format(iDict['templateFile'])
if iDict['startNum']:
cmd += ' --start {} '.format(iDict['startNum'])
if iDict['endNum']:
cmd += ' --end {} '.format(iDict['endNum'])
print('run the following command in bsub mode')
print(cmd)
# write job file
job_dir = os.getcwd()
job_file = os.path.join(job_dir, 'z_input_process_isce_stack.job')
job_name = sensor.project_name2sensor_name(iDict['templateFile'])[1]
with open(job_file, 'w') as f:
f.write('#! /bin/tcsh\n')
f.write('#BSUB -J {}\n'.format(job_name))
f.write('#BSUB -P insarlab\n')
f.write('#BSUB -o z_output_{}.%J.o\n'.format(job_name))
f.write('#BSUB -e z_output_{}.%J.e\n'.format(job_name))
f.write('#BSUB -W {}\n'.format(iDict['walltime']))
f.write('#BSUB -q general\n')
f.write('#BSUB -n 1\n')
f.write('#BSUB -R "rusage[mem={}]"\n'.format(iDict['memory']))
if iDict['email']:
f.write('#BSUB -u {}\n'.format(iDict['email']))
f.write('#BSUB -N\n')
# write cd work directory
f.write('\n')
f.write('cd {}\n'.format(job_dir))
f.write('{}\n'.format(cmd))
print('finished writing job file: {}'.format(job_file))
return job_file
def write_to_one_file(outfile, dH, dV, atr, dLOS, atr_list, ref_file=None):
"""Write all datasets into one HDF5 file"""
from mintpy.objects import sensor
print('write all datasets into {}'.format(outfile))
length, width = dH.shape
dsDict = {}
for i in range(len(atr_list)):
# auto dataset name
atr = atr_list[i]
dsName = sensor.project_name2sensor_name(atr['FILE_PATH'])[0]
if atr['ORBIT_DIRECTION'].lower().startswith('asc'):
dsName += 'A'
else:
dsName += 'D'
if 'trackNumber' in atr.keys():
dsName += 'T{}'.format(atr['trackNumber'])
dsName += '_{}'.format(atr['DATE12'])
dsDict[dsName] = dLOS[i,:].reshape(length, width)
dsDict['vertical'] = dV
dsDict['horizontal'] = dH
writefile.write(dsDict, out_file=outfile, metadata=atr, ref_file=ref_file)
return outfile
def write_to_one_file(outfile,
dH,
dV,
atr,
dLOS_list,
atr_list,
ref_file=None):
"""Write all datasets into one HDF5 file"""
print('write all datasets into {}'.format(outfile))
dsDict = {}
for i in range(len(atr_list)):
# auto dataset name
atr_i = atr_list[i]
dsName = sensor.project_name2sensor_name(atr_i['PROJECT_NAME'])[0]
if atr['ORBIT_DIRECTION'].lower().startswith('asc'):
dsName += 'A'
else:
dsName += 'D'
if 'trackNumber' in atr_i.keys():
dsName += 'T{}'.format(atr_i['trackNumber'])
dsName += '_{}'.format(atr_i['DATE12'])
dsDict[dsName] = dLOS_list[i]
dsDict['vertical'] = dV
dsDict['horizontal'] = dH
writefile.write(dsDict, out_file=outfile, metadata=atr, ref_file=ref_file)
return outfile
def wait4jobs2finish(run_file, num_job):
job_name = os.path.basename(run_file)
file_pattern = 'z_output_{}.*.o'.format(job_name)
proj_name = sensor.project_name2sensor_name(os.getcwd())[1]
print('-'*50)
print('sleeping until {} jobs are done for {}'.format(num_job, job_name))
t_sec = 0
num_file = len(glob.glob(file_pattern))
while num_file < num_job:
time.sleep(1) #wait one second
msg = '# of '
if proj_name:
msg += '{}/'.format(proj_name)
msg += '{} files: {} / {} after {} mins'.format(file_pattern, num_file, num_job, int(t_sec/60))
if t_sec <= 600:
if t_sec % 60 == 0:
print(msg)
else:
if t_sec % 300 == 0:
print(msg)
num_file = len(glob.glob(file_pattern))
t_sec += 1
print('-'*50)
print('ALL {} jobs are done for {}'.format(num_job, job_name))
m, s = divmod(t_sec, 60); h, m = divmod(m, 60)
print('Total used time: {:02d} hours {:02d} mins {:02d} secs'.format(h,m,s))
return
def write_job_file(iDict):
"""Write job file to submit process_isce_stack.py as a job"""
# command line
cmd = 'process_isce_stack.py -t {}'.format(iDict['templateFile'])
if iDict['startNum']:
cmd += ' --start {} '.format(iDict['startNum'])
if iDict['endNum']:
cmd += ' --end {} '.format(iDict['endNum'])
print('run the following command in bsub mode')
print(cmd)
# write job file
job_dir = os.getcwd()
job_file = os.path.join(job_dir, 'z_input_process_isce_stack.job')
job_name = sensor.project_name2sensor_name(iDict['templateFile'])[1]
with open(job_file, 'w') as f:
f.write('#! /bin/tcsh\n')
f.write('#BSUB -J {}\n'.format(job_name))
f.write('#BSUB -P insarlab\n')
f.write('#BSUB -o z_output_{}.%J.o\n'.format(job_name))
f.write('#BSUB -e z_output_{}.%J.e\n'.format(job_name))
f.write('#BSUB -W {}\n'.format(iDict['walltime']))
f.write('#BSUB -q general\n')
f.write('#BSUB -n 1\n')
f.write('#BSUB -R "rusage[mem={}]"\n'.format(iDict['memory']))
if iDict['email']:
f.write('#BSUB -u {}\n'.format(iDict['email']))
f.write('#BSUB -N\n')
# write cd work directory
f.write('\n')
f.write('cd {}\n'.format(job_dir))
f.write('{}\n'.format(cmd))
print('finished writing job file: {}'.format(job_file))
return job_file
def read_inps2dict(inps):
print('read options from template file: '+os.path.basename(inps.templateFile))
template = readfile.read_template(inps.templateFile)
template = ut.check_template_auto_value(template)
iDict = vars(inps)
key_prefix = 'isce.'
key_list = [i.split(key_prefix)[1] for i in template.keys() if i.startswith(key_prefix)]
for key in key_list:
iDict[key] = template[key_prefix+key]
iDict['sensor'], iDict['projectName'] = sensor.project_name2sensor_name(iDict['templateFile'])
return iDict
def prepare_metadata4giant(fname, meta_files=None):
"""Extract metadata from xml files for GIAnT time-series file."""
# check xml files
if not meta_files:
meta_files = auto_xml_file4giant(fname)
if not meta_files:
raise FileNotFoundError("no xml file found.")
# extract metadata from xml files
rsc_files = [i for i in meta_files if i.endswith('.rsc')]
xml_files = [i for i in meta_files if i.endswith('.xml')]
xml_dict = {}
for rsc_file in rsc_files:
print('reading {}'.format(rsc_file))
rsc_dict = readfile.read_roipac_rsc(rsc_file)
for key in ['length', 'LENGTH', 'FILE_LENGTH', 'width', 'WIDTH']:
try:
rsc_dict.pop(key)
except:
pass
xml_dict.update(rsc_dict)
for xml_file in xml_files:
print('reading {}'.format(xml_file))
xml_dict.update(read_giant_xml(xml_file))
if not xml_dict:
raise ValueError('No metadata found in file: ' + xml_file)
# standardize metadata names
xml_dict = readfile.standardize_metadata(xml_dict)
# project name
sensor_name, project_name = sensor.project_name2sensor_name(
os.path.abspath(fname))
if sensor_name:
xml_dict['PLATFORM'] = sensor_name
if project_name:
xml_dict['PROJECT_NAME'] = project_name
if sensor_name in project_name:
tmp = project_name.split(sensor_name)[1][0]
if tmp == 'A':
xml_dict['ORBIT_DIRECTION'] = 'ASCENDING'
else:
xml_dict['ORBIT_DIRECTION'] = 'DESCENDING'
# update GIAnT HDF5 file
fname = ut.add_attribute(fname, xml_dict, print_msg=True)
return fname
def prepare_metadata4giant(fname, meta_files=None):
"""Extract metadata from xml files for GIAnT time-series file."""
# check xml files
if not meta_files:
meta_files = auto_xml_file4giant(fname)
if not meta_files:
raise FileNotFoundError("no xml file found.")
# extract metadata from xml files
rsc_files = [i for i in meta_files if i.endswith('.rsc')]
xml_files = [i for i in meta_files if i.endswith('.xml')]
xml_dict = {}
for rsc_file in rsc_files:
print('reading {}'.format(rsc_file))
rsc_dict = readfile.read_roipac_rsc(rsc_file)
for key in ['length', 'LENGTH', 'FILE_LENGTH', 'width', 'WIDTH']:
try:
rsc_dict.pop(key)
except:
pass
xml_dict.update(rsc_dict)
for xml_file in xml_files:
print('reading {}'.format(xml_file))
xml_dict.update(read_giant_xml(xml_file))
if not xml_dict:
raise ValueError('No metadata found in file: '+xml_file)
# standardize metadata names
xml_dict = readfile.standardize_metadata(xml_dict)
# project name
sensor_name, project_name = sensor.project_name2sensor_name(os.path.abspath(fname))
if sensor_name:
xml_dict['PLATFORM'] = sensor_name
if project_name:
xml_dict['PROJECT_NAME'] = project_name
if sensor_name in project_name:
tmp = project_name.split(sensor_name)[1][0]
if tmp == 'A':
xml_dict['ORBIT_DIRECTION'] = 'ASCENDING'
else:
xml_dict['ORBIT_DIRECTION'] = 'DESCENDING'
# update GIAnT HDF5 file
fname = ut.add_attribute(fname, xml_dict, print_msg=True)
return fname
def read_inps2dict(inps):
print('read options from template file: ' +
os.path.basename(inps.templateFile))
template = readfile.read_template(inps.templateFile)
template = ut.check_template_auto_value(template)
iDict = vars(inps)
key_list = [
i.split(key_prefix)[1] for i in template.keys()
if i.startswith(key_prefix)
]
for key in key_list:
iDict[key] = template[key_prefix + key]
# default values if options are not specified in the template file
for key in AUTO_DICT.keys():
if key not in iDict.keys():
iDict[key] = AUTO_DICT[key]
iDict['sensor'], iDict['projectName'] = sensor.project_name2sensor_name(
iDict['templateFile'])
# check
if iDict['processor'] not in ['topsStack', 'stripmapStack']:
msg = 'un-recognized ISCE-2 stack processor: {}'.format(
iDict['processor'])
msg += 'supported processors: [topsStack, stripmapStack]'
raise ValueError(msg)
# expand all paths to abspath
for key in iDict.keys():
if key.endswith(('File', 'Dir')) and iDict[key]:
iDict[key] = os.path.expanduser(iDict[key])
iDict[key] = os.path.expandvars(iDict[key])
iDict[key] = os.path.abspath(iDict[key])
# --text_cmd
if iDict['processor'] == 'topsStack':
iDict['text_cmd'] = 'export PATH=${PATH}:${ISCE_STACK}/topsStack'
else:
iDict['text_cmd'] = 'export PATH=${PATH}:${ISCE_STACK}/stripmapStack'
return iDict
def run_asc_desc2horz_vert(inps):
"""Decompose asc / desc LOS files into horz / vert file(s).
Parameters: inps - namespace, input parameters
Returns: inps.outfile - str(s) output file(s)
"""
## 1. calculate the overlaping area in lat/lon
atr_list = [
readfile.read_attribute(fname, datasetName=inps.ds_name)
for fname in inps.file
]
S, N, W, E = get_overlap_lalo(atr_list)
lat_step = float(atr_list[0]['Y_STEP'])
lon_step = float(atr_list[0]['X_STEP'])
length = int(round((S - N) / lat_step))
width = int(round((E - W) / lon_step))
print('overlaping area in SNWE: {}'.format((S, N, W, E)))
## 2. read LOS data and geometry
num_file = len(inps.file)
num_pixel = length * width
dlos = np.zeros((num_file, length, width), dtype=np.float32)
if inps.geom_file:
los_inc_angle = np.zeros((num_file, length, width), dtype=np.float32)
los_az_angle = np.zeros((num_file, length, width), dtype=np.float32)
else:
los_inc_angle = np.zeros(num_file, dtype=np.float32)
los_az_angle = np.zeros(num_file, dtype=np.float32)
for i, (atr, fname) in enumerate(zip(atr_list, inps.file)):
# overlap SNWE --> box to read for each specific file
coord = ut.coordinate(atr)
x0 = coord.lalo2yx(W, coord_type='lon')
y0 = coord.lalo2yx(N, coord_type='lat')
box = (x0, y0, x0 + width, y0 + length)
# read data
dlos[i, :] = readfile.read(fname, box=box, datasetName=inps.ds_name)[0]
msg = f'{inps.ds_name} ' if inps.ds_name else ''
print(f'read {msg} from file: {fname}')
# read geometry
if inps.geom_file:
los_inc_angle[i, :] = readfile.read(
inps.geom_file[i], box=box, datasetName='incidenceAngle')[0]
los_az_angle[i, :] = readfile.read(inps.geom_file[i],
box=box,
datasetName='azimuthAngle')[0]
print(
f'read 2D LOS incidence / azimuth angles from file: {inps.geom_file[i]}'
)
else:
los_inc_angle[i] = ut.incidence_angle(atr,
dimension=0,
print_msg=False)
los_az_angle[i] = ut.heading2azimuth_angle(float(atr['HEADING']))
print(
'calculate the constant LOS incidence / azimuth angles from metadata as:'
)
print(f'LOS incidence angle: {los_inc_angle[i]:.1f} deg')
print(f'LOS azimuth angle: {los_az_angle[i]:.1f} deg')
## 3. decompose LOS displacements into horizontal / Vertical displacements
print('---------------------')
dhorz, dvert = asc_desc2horz_vert(dlos, los_inc_angle, los_az_angle,
inps.horz_az_angle)
## 4. write outputs
print('---------------------')
# Update attributes
atr = atr_list[0].copy()
if inps.ds_name and atr['FILE_TYPE'] in [
'ifgramStack', 'timeseries', 'HDFEOS'
]:
atr['FILE_TYPE'] = 'displacement'
atr['WIDTH'] = str(width)
atr['LENGTH'] = str(length)
atr['X_STEP'] = str(lon_step)
atr['Y_STEP'] = str(lat_step)
atr['X_FIRST'] = str(W)
atr['Y_FIRST'] = str(N)
# update REF_X/Y
ref_lat, ref_lon = float(atr['REF_LAT']), float(atr['REF_LON'])
[ref_y, ref_x] = ut.coordinate(atr).geo2radar(ref_lat, ref_lon)[0:2]
atr['REF_Y'] = int(ref_y)
atr['REF_X'] = int(ref_x)
# use ref_file for time-series file writing
ref_file = inps.file[0] if atr_list[0][
'FILE_TYPE'] == 'timeseries' else None
if inps.one_outfile:
print('write asc/desc/horz/vert datasets into {}'.format(
inps.one_outfile))
dsDict = {}
for i, atr in enumerate(atr_list):
# dataset name for LOS data
track_num = atr.get('trackNumber', None)
proj_name = atr.get('PROJECT_NAME', None)
if proj_name in ['none', 'None', None]:
proj_name = atr.get('FILE_PATH', None)
proj_name = sensor.project_name2sensor_name(proj_name)[0]
ds_name = proj_name if proj_name else ''
ds_name += 'A' if atr['ORBIT_DIRECTION'].lower().startswith(
'asc') else 'D'
ds_name += f'T{track_num}' if track_num else ''
ds_name += '_{}'.format(atr['DATE12'])
# assign dataset value
dsDict[ds_name] = dlos[i]
dsDict['horizontal'] = dhorz
dsDict['vertical'] = dvert
writefile.write(dsDict,
out_file=inps.one_outfile,
metadata=atr,
ref_file=ref_file)
else:
print('writing horizontal component to file: ' + inps.outfile[0])
writefile.write(dhorz,
out_file=inps.outfile[0],
metadata=atr,
ref_file=ref_file)
print('writing vertical component to file: ' + inps.outfile[1])
writefile.write(dvert,
out_file=inps.outfile[1],
metadata=atr,
ref_file=ref_file)
return inps.outfile
def read_data(inps):
"""
Returns: defo: 2D np.array with in-valid/masked-out pixel in NaN
"""
# metadata
inps.metadata = readfile.read_attribute(inps.file)
k = inps.metadata['FILE_TYPE']
inps.range2phase = -4. * np.pi / float(inps.metadata['WAVELENGTH'])
# mask
if inps.mask_file:
inps.mask = readfile.read(inps.mask_file)[0]
else:
inps.mask = np.ones((int(inps.metadata['LENGTH']),
int(inps.metadata['WIDTH'])), dtype=np.bool_)
# data
if k in ['.unw','velocity']:
inps.phase = readfile.read(inps.file)[0]
if k == 'velocity':
# velocity to displacement
date1, date2 = inps.metadata['DATE12'].split('_')
dt1, dt2 = ptime.date_list2vector([date1, date2])[0]
inps.phase *= (dt2 - dt1).days / 365.25
# displacement to phase
inps.phase *= inps.range2phase
# update mask to exclude pixel with NaN value
inps.mask *= ~np.isnan(inps.phase)
# set all masked out pixel to NaN
inps.phase[inps.mask==0] = np.nan
else:
raise ValueError("input file not support yet: {}".format(k))
print('number of pixels: {}'.format(np.sum(inps.mask)))
# change reference point
if inps.ref_lalo:
coord = ut.coordinate(inps.metadata)
ref_lat, ref_lon = inps.ref_lalo
ref_y, ref_x = coord.geo2radar(ref_lat, ref_lon)[0:2]
# update data
inps.phase -= inps.phase[ref_y, ref_x]
# update metadata
inps.metadata['REF_LAT'] = ref_lat
inps.metadata['REF_LON'] = ref_lon
inps.metadata['REF_Y'] = ref_y
inps.metadata['REF_X'] = ref_x
# read geometry
inps.lat, inps.lon = ut.get_lat_lon(inps.metadata)
inps.inc_angle = readfile.read(inps.geom_file, datasetName='incidenceAngle')[0]
inps.head_angle = np.ones(inps.inc_angle.shape, dtype=np.float32) * float(inps.metadata['HEADING'])
inps.height = readfile.read(inps.geom_file, datasetName='height')[0]
# convert the height of ellipsoid to geoid (mean sea level)
# ref: https://github.com/vandry/geoidheight
if inps.ellipsoid2geoid:
# import geoid module
try:
import geoid
except:
raise ImportError('Can not import geoidheight!')
# calculate offset and correct height
egm_file = os.path.join(os.path.dirname(geoid.__file__), 'geoids/egm2008-1.pgm')
gh_obj = geoid.GeoidHeight(egm_file)
h_offset = gh_obj.get(lat=np.nanmean(inps.lat), lon=np.nanmean(inps.lon))
inps.height -= h_offset
# print message
msg = 'convert height from ellipsoid to geoid'
msg += '\n\tby subtracting a constant offset of {:.2f} m'.format(h_offset)
print(msg)
inps.lat[inps.mask==0] = np.nan
inps.lon[inps.mask==0] = np.nan
inps.inc_angle[inps.mask==0] = np.nan
inps.head_angle[inps.mask==0] = np.nan
inps.height[inps.mask==0] = np.nan
# output filename
if not inps.outfile:
proj_name = sensor.project_name2sensor_name(inps.file)[1]
if not proj_name:
raise ValueError('No custom/auto output filename found.')
inps.outfile = '{}_{}.mat'.format(proj_name, inps.metadata['DATE12'])
if not inps.outdir:
inps.outdir = os.path.dirname(inps.file)
inps.outfile = os.path.join(inps.outdir, inps.outfile)
inps.outfile = os.path.abspath(inps.outfile)
return
def read_data(inps):
"""
Returns: defo: 2D np.array with in-valid/masked-out pixel in NaN
"""
# metadata
inps.metadata = readfile.read_attribute(inps.file)
k = inps.metadata['FILE_TYPE']
inps.range2phase = -4. * np.pi / float(inps.metadata['WAVELENGTH'])
ext = os.path.splitext(inps.file)[1]
# mask
if inps.mask_file:
inps.mask = readfile.read(inps.mask_file)[0]
else:
inps.mask = np.ones(
(int(inps.metadata['LENGTH']), int(inps.metadata['WIDTH'])),
dtype=np.bool_)
# data
if k in ['.unw', 'velocity']:
inps.phase = readfile.read(inps.file)[0]
if k == 'velocity':
# velocity to displacement
date1, date2 = inps.metadata['DATE12'].split('_')
dt1, dt2 = ptime.date_list2vector([date1, date2])[0]
inps.phase *= (dt2 - dt1).days / 365.25
# displacement to phase
inps.phase *= inps.range2phase
# update mask to exclude pixel with NaN value
inps.mask *= ~np.isnan(inps.phase)
# set all masked out pixel to NaN
inps.phase[inps.mask == 0] = np.nan
else:
raise ValueError("input file not support yet: {}".format(k))
print('number of pixels: {}'.format(np.sum(inps.mask)))
# change reference point
if inps.ref_lalo:
coord = ut.coordinate(inps.metadata)
ref_lat, ref_lon = inps.ref_lalo
ref_y, ref_x = coord.geo2radar(ref_lat, ref_lon)[0:2]
# update data
inps.phase -= inps.phase[ref_y, ref_x]
# update metadata
inps.metadata['REF_LAT'] = ref_lat
inps.metadata['REF_LON'] = ref_lon
inps.metadata['REF_Y'] = ref_y
inps.metadata['REF_X'] = ref_x
# read geometry
inps.lat, inps.lon = ut.get_lat_lon(inps.metadata)
inps.inc_angle = readfile.read(inps.geom_file,
datasetName='incidenceAngle')[0]
inps.head_angle = np.ones(inps.inc_angle.shape, dtype=np.float32) * float(
inps.metadata['HEADING'])
inps.lat[inps.mask == 0] = np.nan
inps.lon[inps.mask == 0] = np.nan
inps.inc_angle[inps.mask == 0] = np.nan
inps.head_angle[inps.mask == 0] = np.nan
# output filename
if not inps.outfile:
out_dir = os.path.dirname(inps.file)
proj_name = sensor.project_name2sensor_name(out_dir)[1]
if not proj_name:
raise ValueError('No custom/auto output filename found.')
inps.outfile = '{}_{}.mat'.format(proj_name, inps.metadata['DATE12'])
inps.outfile = os.path.join(out_dir, inps.outfile)
inps.outfile = os.path.abspath(inps.outfile)
return
#ax.set_xlim(dt.date(2015, 1, 1), dt.date(2019, 12, 31))
ax.set_ylim([-20, 20])
ax.grid(linewidth=0.25, alpha=0.5)
ofile = odir + '/' + sname + '.png'
print(f'{i}: Saving file: {ofile}')
fig.savefig(ofile, dpi=300, transparent=False, bbox_inches='tight')
except:
print(f'No GPS data for well {sname} or something went wrong.\n')
# plt.show()
if plot_temporal_corehence:
work_dir = os.path.expanduser(
'/scratch/hpham/insar/insar_pahrump/P173_F_470/TOPSTACK/mintpy/')
os.chdir(work_dir)
print('Go to directory', work_dir)
proj_name = sensor.project_name2sensor_name(work_dir)[1]
# spatialCoh vs tempCoh
spatial_coh_file = 'avgSpatialCoherence.h5'
# 'temporalCoherence.h5' with unw err cor
temp_coh_file = 'UNW_COR/tempCoh_unwrapPhase.h5'
water_mask_file = 'waterMask.h5'
# lava flow
#ts_file = 'geo/geo_timeseries_ECMWF_ramp_demErr.h5'
#vel_file = 'geo/geo_velocity.h5'
ts_file = 'geo/geo_timeseries_ERA5_ramp_demErr.h5'
vel_file = 'geo/geo_velocity.h5'
dem_file = '/scratch/hpham/insar/insar_pahrump/P173_F_470/ISCE/demLat_N35_N38_Lon_W117_W113.dem.wgs84'
ifgram_file = 'inputs/ifgramStack.h5'
def read_template2inps(templateFile, inps=None):
"""Read network options from template file into Namespace variable inps"""
if not inps:
inps = cmd_line_parse()
inpsDict = vars(inps)
# Read template file
template = readfile.read_template(templateFile)
auto_file = os.path.join(os.path.dirname(mintpy.__file__),
'defaults/selectNetwork.cfg')
template = ut.check_template_auto_value(template, auto_file=auto_file)
if not template:
log('Empty template: ' + templateFile)
return None
prefix = 'selectNetwork.'
# Check obsolete option prefix
for i in ['selectPairs.', 'select.network.']:
if any(i in key for key in template.keys()):
msg = 'obsolete option prefix detected: {}\n'.format(i)
msg += 'Use {} instead'.format(prefix)
raise Exception(msg)
if all(prefix not in key for key in template.keys()):
msg = 'no valid input option deteced in template file!\n'
msg += 'Check the template below for supported options:\n'
msg += TEMPLATE
raise Exception(msg)
# convert template into inpsDict
keyList = [
i for i in list(inpsDict.keys()) if prefix + i in template.keys()
]
for key in keyList:
value = template[prefix + key]
# bool
if key in ['keepSeasonal']:
inpsDict[key] = value
elif value:
# str
if key in ['method', 'referenceFile', 'tempPerpList']:
inpsDict[key] = value
# date in YYYYMMDD
elif key in ['referenceDate', 'startDate', 'endDate']:
inpsDict[key] = ptime.yyyymmdd(value)
# list of dates in YYYYMMDD
elif key in ['excludeDate']:
inps.excludeDate = ptime.yyyymmdd(
[i.strip() for i in value.split(',')])
# float
elif key in [
'perpBaseMax', 'tempBaseMax', 'tempBaseMin',
'dopOverlapMin'
]:
inpsDict[key] = float(value)
# int
elif key in ['connNum']:
inpsDict[key] = int(value)
# read tempPerpList from str
if isinstance(inps.tempPerpList, str):
inps.tempPerpList = [[float(j) for j in i.split(',')]
for i in inps.tempPerpList.split(';')]
# Initial network using input methods
inps.method = inps.method.lower().replace('-', '_')
if inps.method in ['star', 'ps']:
inps.method = 'star'
elif inps.method.startswith('seq'):
inps.method = 'sequential'
elif inps.method.startswith('hierar'):
inps.method = 'hierarchical'
elif inps.method in ['mst', 'min_spanning_tree', 'minimum_spanning_tree']:
inps.method = 'mst'
elif inps.method in ['all', 'sb']:
inps.method = 'all'
# for coherence prediction
key = 'PLATFORM'
if key in template.keys() and not inps.sensor:
inps.sensor = template[key]
key = 'COH_COLOR_JUMP'
if key in template.keys():
inps.coh_thres = float(template[key])
# project name and sensor
project_name = os.path.splitext(os.path.basename(inps.template_file))[0]
log('project name: ' + project_name)
if not inps.sensor:
inps.sensor = sensor.project_name2sensor_name(project_name)[0]
# Output directory/filename
if not inps.outfile:
if 'SCRATCHDIR' in os.environ:
inps.out_dir = os.getenv(
'SCRATCHDIR') + '/' + project_name + '/PROCESS'
else:
try:
inps.out_dir = os.path.dirname(
os.path.abspath(inps.referenceFile))
except:
inps.out_dir = os.path.dirname(
os.path.abspath(inps.baseline_file))
inps.outfile = inps.out_dir + '/ifgram_list.txt'
# Auto path of bl_list.txt file (for Miami user)
if not inps.baseline_file and 'SCRATCHDIR' in os.environ:
bl_file = os.path.join(os.getenv('SCRATCHDIR'),
'{}/SLC/bl_list.txt'.format(project_name))
if os.path.isfile(bl_file):
inps.baseline_file = bl_file
if not inps.referenceFile and not inps.baseline_file:
raise Exception(
'No baseline file or reference file found! At least one is required.'
)
return inps
def read_inps2dict(inps):
"""Read input Namespace object info into inpsDict"""
# Read input info into inpsDict
inpsDict = vars(inps)
inpsDict['PLATFORM'] = None
auto_template = os.path.join(os.path.dirname(__file__),
'defaults/minopyApp_auto.cfg')
# Read template file
template = {}
for fname in list(inps.template_file):
temp = readfile.read_template(fname)
temp = check_template_auto_value(temp, auto_file=auto_template)
template.update(temp)
for key, value in template.items():
inpsDict[key] = value
if 'processor' in template.keys():
template['minopy.load.processor'] = template['processor']
prefix = 'minopy.load.'
key_list = [
i.split(prefix)[1] for i in template.keys() if i.startswith(prefix)
]
for key in key_list:
value = template[prefix + key]
if key in ['processor', 'updateMode', 'compression', 'autoPath']:
inpsDict[key] = template[prefix + key]
elif key in ['xstep', 'ystep']:
inpsDict[key] = int(template[prefix + key])
elif value:
inpsDict[prefix + key] = template[prefix + key]
if not 'compression' in inpsDict or inpsDict['compression'] == False:
inpsDict['compression'] = None
inpsDict['xstep'] = inpsDict.get('xstep', 1)
inpsDict['ystep'] = inpsDict.get('ystep', 1)
# PROJECT_NAME --> PLATFORM
if not 'PROJECT_NAME' in inpsDict:
cfile = [
i for i in list(inps.template_file)
if os.path.basename(i) != 'minopyApp.cfg'
]
inpsDict['PROJECT_NAME'] = sensor.project_name2sensor_name(cfile)[1]
msg = 'SAR platform/sensor : '
sensor_name = sensor.project_name2sensor_name(str(
inpsDict['PROJECT_NAME']))[0]
if sensor_name:
msg += str(sensor_name)
inpsDict['PLATFORM'] = str(sensor_name)
else:
msg += 'unknown from project name "{}"'.format(
inpsDict['PROJECT_NAME'])
print(msg)
# Here to insert code to check default file path for miami user
work_dir = os.path.dirname(
os.path.dirname(os.path.dirname(inpsDict['outfile'][0])))
if inpsDict.get('autoPath', False):
print(('check auto path setting for Univ of Miami users'
' for processor: {}'.format(inpsDict['processor'])))
inpsDict = auto_path.get_auto_path(processor=inpsDict['processor'],
work_dir=work_dir,
template=inpsDict)
return inpsDict
