def get_gps_los_velocity(self, geom_obj, start_date=None, end_date=None, ref_site=None,
gps_comp='enu2los', horz_az_angle=-90.):
dates, dis = self.read_gps_los_displacement(
geom_obj,
start_date=start_date,
end_date=end_date,
ref_site=ref_site,
gps_comp=gps_comp,
horz_az_angle=horz_az_angle)[:2]
# displacement -> velocity
# if:
# 1. num of observations > 2 AND
# 2. time overlap > 1/4
dis2vel = True
if len(dates) <= 2:
dis2vel = False
elif start_date and end_date:
t0 = ptime.date_list2vector([start_date])[0][0]
t1 = ptime.date_list2vector([end_date])[0][0]
if dates[-1] - dates[0] <= (t1 - t0) / 4:
dis2vel = False
if dis2vel:
date_list = [dt.datetime.strftime(i, '%Y%m%d') for i in dates]
A = time_func.get_design_matrix4time_func(date_list)
self.velocity = np.dot(np.linalg.pinv(A), dis)[1]
else:
self.velocity = np.nan
return self.velocity, dis
def search_gps(SNWE,
start_date=None,
end_date=None,
site_list_file=None,
min_num_solution=50,
print_msg=True):
"""Search available GPS sites within the geo bounding box from UNR website
Parameters: SNWE : tuple of 4 float, indicating (South, North, West, East) in degrees
start_date : string in YYYYMMDD format
end_date : string in YYYYMMDD format
site_list_file : string.
min_num_solution : int, minimum number of solutions available
Returns: site_names : 1D np.array of string for GPS station names
site_lats : 1D np.array for lat
site_lons : 1D np.array for lon
"""
# download site list file if it's not found in current directory
if site_list_file is None:
site_list_file = os.path.basename(unr_site_list_file)
if not os.path.isfile(site_list_file):
dload_site_list(print_msg=print_msg)
txt_data = np.loadtxt(site_list_file,
dtype=bytes,
skiprows=1,
usecols=(0, 1, 2, 3, 4, 5, 6, 7, 8, 9,
10)).astype(str)
site_names = txt_data[:, 0]
site_lats, site_lons = txt_data[:, 1:3].astype(np.float32).T
site_lons -= np.round(site_lons / (360.)) * 360.
t_start = np.array([
dt(*time.strptime(i, "%Y-%m-%d")[0:5])
for i in txt_data[:, 7].astype(str)
])
t_end = np.array([
dt(*time.strptime(i, "%Y-%m-%d")[0:5])
for i in txt_data[:, 8].astype(str)
])
num_solution = txt_data[:, 10].astype(np.int16)
# limit on space
idx = ((site_lats >= SNWE[0]) * (site_lats <= SNWE[1]) *
(site_lons >= SNWE[2]) * (site_lons <= SNWE[3]))
# limit on time
if start_date:
t0 = ptime.date_list2vector([start_date])[0][0]
idx *= t_end >= t0
if end_date:
t1 = ptime.date_list2vector([end_date])[0][0]
idx *= t_start <= t1
# limit on number of solutions
if min_num_solution is not None:
idx *= num_solution >= min_num_solution
return site_names[idx], site_lats[idx], site_lons[idx]
def read_displacement(self,
start_date=None,
end_date=None,
print_msg=True,
display=False):
""" Read GPS displacement time-series (defined by start/end_date)
Parameters: start/end_date : str in YYYYMMDD format
Returns: dates : 1D np.ndarray of datetime.datetime object
dis_e/n/u : 1D np.ndarray of displacement in meters in np.float32
std_e/n/u : 1D np.ndarray of displacement STD in meters in np.float32
"""
# download file if it's not exists.
if not os.path.isfile(self.file):
self.dload_site(print_msg=print_msg)
# read dates, dis_e, dis_n, dis_u
if print_msg:
print(
'reading time and displacement in east/north/vertical direction'
)
data = np.loadtxt(self.file, dtype=bytes, skiprows=1).astype(str)
self.dates = np.array(
[dt.datetime.strptime(i, "%y%b%d") for i in data[:, 1]])
#self.dates = np.array([ptime.decimal_year2datetime(i) for i in data[:, 2]])
self.date_list = [x.strftime('%Y%m%d') for x in self.dates]
(self.dis_e, self.dis_n, self.dis_u, self.std_e, self.std_n,
self.std_u) = data[:, (8, 10, 12, 14, 15, 16)].astype(np.float32).T
# cut out the specified time range
t_flag = np.ones(len(self.dates), np.bool_)
if start_date:
t0 = ptime.date_list2vector([start_date])[0][0]
t_flag[self.dates < t0] = 0
if end_date:
t1 = ptime.date_list2vector([end_date])[0][0]
t_flag[self.dates > t1] = 0
self.dates = self.dates[t_flag]
self.dis_e = self.dis_e[t_flag]
self.dis_n = self.dis_n[t_flag]
self.dis_u = self.dis_u[t_flag]
self.std_e = self.std_e[t_flag]
self.std_n = self.std_n[t_flag]
self.std_u = self.std_u[t_flag]
if display:
import matplotlib.pyplot as plt
fig, ax = plt.subplots(nrows=3, ncols=1, sharex=True)
ax[0].scatter(self.dates, self.dis_e, s=2**2, label='East')
ax[1].scatter(self.dates, self.dis_n, s=2**2, label='North')
ax[2].scatter(self.dates, self.dis_u, s=2**2, label='Up')
plt.show()
return (self.dates, self.dis_e, self.dis_n, self.dis_u, self.std_e,
self.std_n, self.std_u)
def velocity2timeseries(date_list, vel=0.03, display=False):
'''Simulate displacement time-series from linear velocity
Inputs:
date_list - list of string in YYYYMMDD or YYMMDD format
vel - float, velocity in meter per year
display - bool, display simulation or not
Output:
ts - 2D np.array in size of (date_num,1), displacement time-series in m
Example:
date_list = pnet.read_baseline_file('bl_list.txt')[0]
ts0 = simulate_timeseries(date_list, vel=0.03, display=True)
'''
tbase_list = ptime.date_list2tbase(date_list)[0]
ts = vel / 365.25 * np.array(tbase_list)
ts = ts.reshape(-1,1)
if display:
dates = ptime.date_list2vector(date_list)[0]
## Display
marker_size = 5
plt.figure()
plt.scatter(dates, ts*100.0, s=marker_size**2)
plt.xlabel('Time (years)')
plt.ylabel('LOS Displacement (cm)')
plt.title('Displacement time-series with velocity = '+str(vel)+' m/yr')
plt.show()
return ts
def read_timeseries_yx(y, x, ts_file, ref_y=None, ref_x=None, win_size=1):
""" Read time-series of one pixel with input y/x
Parameters: y/x : int, row/column number of interest
ts_file : string, filename of time-series HDF5 file
ref_y/x : int, row/column number of reference pixel
Returns: dates : 1D np.array of datetime.datetime objects, i.e. datetime.datetime(2010, 10, 20, 0, 0)
dis : 1D np.array of float in meter
"""
# read date
obj = timeseries(ts_file)
obj.open(print_msg=False)
dates = ptime.date_list2vector(obj.dateList)[0]
dates = np.array(dates)
# read displacement
print('input y / x: {} / {}'.format(y, x))
box = (x, y, x + 1, y + 1)
dis = readfile.read(ts_file, box=box)[0]
if win_size != 1:
buf = int(win_size / 2)
box_win = (x - buf, y - buf, x + buf + 1, y + buf + 1)
dis_win = readfile.read(ts_file, box=box_win)[0]
dis = np.nanmean(dis_win.reshape((obj.numDate, -1)), axis=1)
# reference pixel
if ref_y is not None:
ref_box = (ref_x, ref_y, ref_x + 1, ref_y + 1)
dis -= readfile.read(ts_file, box=ref_box)[0]
#start at zero
dis -= dis[0]
return dates, dis
def exclude_dates():
global inps, dateList
if inps.ex_date_list:
input_ex_date = list(inps.ex_date_list)
inps.ex_date_list = []
if input_ex_date:
for ex_date in input_ex_date:
if os.path.isfile(ex_date):
ex_date = ptime.read_date_list(ex_date)
else:
ex_date = [ptime.yyyymmdd(ex_date)]
inps.ex_date_list += list(
set(ex_date) - set(inps.ex_date_list))
# delete dates not existed in input file
inps.ex_date_list = sorted(
list(set(inps.ex_date_list).intersection(dateList)))
inps.ex_dates = ptime.date_list2vector(inps.ex_date_list)[0]
inps.ex_idx_list = sorted(
[dateList.index(i) for i in inps.ex_date_list])
print(('exclude date:' + str(inps.ex_date_list)))
def velocity2timeseries(date_list, vel=0.03, display=False):
'''Simulate displacement time-series from linear velocity
Inputs:
date_list - list of string in YYYYMMDD or YYMMDD format
vel - float, velocity in meter per year
display - bool, display simulation or not
Output:
ts - 2D np.array in size of (date_num,1), displacement time-series in m
Example:
date_list = pnet.read_baseline_file('bl_list.txt')[0]
ts0 = simulate_timeseries(date_list, vel=0.03, display=True)
'''
tbase_list = ptime.date_list2tbase(date_list)[0]
ts = vel / 365.25 * np.array(tbase_list)
ts = ts.reshape(-1, 1)
if display:
dates = ptime.date_list2vector(date_list)[0]
## Display
marker_size = 5
plt.figure()
plt.scatter(dates, ts * 100.0, s=marker_size**2)
plt.xlabel('time [years]')
plt.ylabel('LOS displacement [cm]')
plt.title('displacement time-series with velocity = ' + str(vel) +
' m/yr')
plt.show()
return ts
def read_displacement(self, start_date=None, end_date=None, print_msg=True, display=False):
# download file if it's not exists.
if not os.path.isfile(self.file):
self.dload_site(print_msg=print_msg)
# read dates, dis_e, dis_n, dis_u
if print_msg:
print('reading time and displacement in east/north/vertical direction')
data = np.loadtxt(self.file, dtype=bytes, skiprows=1).astype(str)
self.dates = np.array([dt(*time.strptime(i, "%y%b%d")[0:5])
for i in data[:, 1]])
#self.dates = np.array([ptime.decimal_year2datetime(i) for i in data[:, 2]])
(self.dis_e,
self.dis_n,
self.dis_u,
self.std_e,
self.std_n,
self.std_u) = data[:, (8,10,12,14,15,16)].astype(np.float32).T
# cut out the specified time range
t_flag = np.ones(len(self.dates), np.bool_)
if start_date:
t0 = ptime.date_list2vector([start_date])[0][0]
t_flag[self.dates < t0] = 0
if end_date:
t1 = ptime.date_list2vector([end_date])[0][0]
t_flag[self.dates > t1] = 0
self.dates = self.dates[t_flag]
self.dis_e = self.dis_e[t_flag]
self.dis_n = self.dis_n[t_flag]
self.dis_u = self.dis_u[t_flag]
self.std_e = self.std_e[t_flag]
self.std_n = self.std_n[t_flag]
self.std_u = self.std_u[t_flag]
if display:
import matplotlib.pyplot as plt
fig, ax = plt.subplots(nrows=3, ncols=1, sharex=True)
ax[0].scatter(self.dates, self.dis_e, s=2**2, label='East')
ax[1].scatter(self.dates, self.dis_n, s=2**2, label='North')
ax[2].scatter(self.dates, self.dis_u, s=2**2, label='Up')
plt.show()
return (self.dates,
self.dis_e, self.dis_n, self.dis_u,
self.std_e, self.std_n, self.std_u)
def manual_select_pairs_to_remove(stackFile):
"""Manually select interferograms to remove"""
print('\n-------------------------------------------------------------')
print('Manually select interferograms to remove')
print('1) click two dates/points to select one pair of interferogram')
print('2) repeat until you select all pairs you would like to remove')
print('3) close the figure to continue the program ...')
print('-------------------------------------------------------------\n')
obj = ifgramStack(stackFile)
obj.open()
date12ListAll = obj.date12List
pbase = obj.get_perp_baseline_timeseries(dropIfgram=False)
dateList = obj.dateList
datesNum = mdates.date2num(np.array(ptime.date_list2vector(dateList)[0]))
date12ListKept = obj.get_date12_list(dropIfgram=True)
date12ListDropped = sorted(list(set(date12ListAll) - set(date12ListKept)))
# Display the network
fig = plt.figure()
ax = fig.add_subplot(111)
ax = pp.plot_network(ax,
date12ListAll,
dateList,
list(pbase),
date12List_drop=date12ListDropped)
print('display the network of interferogram of file: ' + stackFile)
date_click = []
date12_click = []
def onclick(event):
idx = nearest_neighbor(event.xdata, event.ydata, datesNum, pbase)
print('click at ' + dateList[idx])
date_click.append(dateList[idx])
if len(date_click) % 2 == 0 and date_click[-2] != date_click[-1]:
[mDate, sDate] = sorted(date_click[-2:])
mIdx = dateList.index(mDate)
sIdx = dateList.index(sDate)
date12 = mDate + '_' + sDate
if date12 in date12ListAll:
print('select date12: ' + date12)
date12_click.append(date12)
ax.plot([datesNum[mIdx], datesNum[sIdx]],
[pbase[mIdx], pbase[sIdx]],
'r',
lw=4)
else:
print(date12 + ' is not existed in input file')
plt.draw()
cid = fig.canvas.mpl_connect('button_press_event', onclick)
plt.show()
if not ut.yes_or_no('Proceed to drop the ifgrams/date12?'):
date12_click = None
return date12_click
def print_timseries_date_stat(dateList):
datevector = ptime.date_list2vector(dateList)[1]
print('Start Date: {}'.format(dateList[0]))
print('End Date: {}'.format(dateList[-1]))
print('Number of dates : {}'.format(len(dateList)))
print('STD of datetimes : {:.2f} years'.format(np.std(datevector)))
#print('----------------------')
#print('List of dates:\n{}'.format(dateList))
#print('----------------------')
#print('List of dates in years:\n{}'.format(datevector))
return
def estimate_S1AB_bias(mintpy_dir, dates, ts_dis):
"""Estimate the bias between Sentinel-1 A and B.
Parameters: mintpy_dir - str, path of the mintpy working directory
dates - list of datetime.datetime objects
ts_dis - 2D np.ndarray in size of (num_date, num_pixel) in float32
Returns: bias - 1D np.ndarray in size of (num_pixel) in float32
flagA/B - 1D np.ndarray in size of (num_date) in bool
dates_fit - list of datetime.datetime objects
ts_fitA/B - 1D np.ndarray in size of (num_date_fit) in float32
"""
num_date = len(dates)
ts_dis = ts_dis.reshape(num_date, -1)
# dates/flags for S1A/B
date_listA = np.loadtxt(os.path.join(mintpy_dir, 'S1A_date.txt'),
dtype=str).tolist()
date_listB = np.loadtxt(os.path.join(mintpy_dir, 'S1B_date.txt'),
dtype=str).tolist()
date_list = sorted(date_listA + date_listB)
min_date = date_listB[0]
flagA = np.array([x in date_listA and x >= min_date for x in date_list],
dtype=np.bool_)
flagB = np.array([x in date_listB and x >= min_date for x in date_list],
dtype=np.bool_)
# update date_list to the shared time period only
date_listA = np.array(date_list)[flagA].tolist()
date_listB = np.array(date_list)[flagB].tolist()
# fit
model = dict(polynomial=1)
mA = time_func.estimate_time_func(model,
date_listA,
ts_dis[flagA, :],
ref_date=date_listA[0])[1]
mB = time_func.estimate_time_func(model,
date_listB,
ts_dis[flagB, :],
ref_date=date_listB[0])[1]
# grab bias/offset from the fitting time-series
date_list_fit = ptime.get_date_range(min_date, date_list[-1], dstep=1)
dates_fit = ptime.date_list2vector(date_list_fit)[0]
GA_fit = time_func.get_design_matrix4time_func(date_list_fit,
model,
ref_date=date_listA[0])
GB_fit = time_func.get_design_matrix4time_func(date_list_fit,
model,
ref_date=date_listB[0])
ts_fitA = np.matmul(GA_fit, mA)
ts_fitB = np.matmul(GB_fit, mB)
bias = np.median(ts_fitB - ts_fitA, axis=0)
return bias, flagA, flagB, dates_fit, ts_fitA, ts_fitB
def print_timseries_date_stat(dateList):
datevector = ptime.date_list2vector(dateList)[1]
print('Start Date: ' + dateList[0])
print('End Date: ' + dateList[-1])
print('Number of acquisitions : %d' % len(dateList))
print('Std. of acquisition times : %.2f yeras' % std(datevector))
print('----------------------')
print('List of dates:')
print(dateList)
print('----------------------')
print('List of dates in years')
print(datevector)
return
def print_timseries_date_stat(dateList):
datevector = ptime.date_list2vector(dateList)[1]
print('Start Date: '+dateList[0])
print('End Date: '+dateList[-1])
print('Number of acquisitions : %d' % len(dateList))
print('Std. of acquisition times : %.2f yeras' % std(datevector))
print('----------------------')
print('List of dates:')
print(dateList)
print('----------------------')
print('List of dates in years')
print(datevector)
return
def search_gps(SNWE, start_date=None, end_date=None, site_list_file=None, print_msg=True):
"""Search available GPS sites within the geo bounding box from UNR website
Parameters: SNWE : tuple of 4 float, indicating (South, North, West, East) in degrees
start_date : string in YYYYMMDD format
end_date : string in YYYYMMDD format
site_list_file : string.
Returns: site_names : 1D np.array of string for GPS station names
site_lats : 1D np.array for lat
site_lons : 1D np.array for lon
"""
# download site list file if it's not found in current directory
if site_list_file is None:
site_list_file = os.path.basename(unr_site_list_file)
if not os.path.isfile(site_list_file):
dload_site_list(print_msg=print_msg)
txt_data = np.loadtxt(site_list_file,
dtype=bytes,
skiprows=1,
usecols=(0,1,2,3,4,5,6,7,8,9)).astype(str)
site_names = txt_data[:, 0]
site_lats, site_lons = txt_data[:, 1:3].astype(np.float32).T
site_lons -= np.round(site_lons / (360.)) * 360.
t_start = np.array([dt(*time.strptime(i, "%Y-%m-%d")[0:5]) for i in txt_data[:, 7].astype(str)])
t_end = np.array([dt(*time.strptime(i, "%Y-%m-%d")[0:5]) for i in txt_data[:, 8].astype(str)])
# limit on space
idx = ((site_lats >= SNWE[0]) * (site_lats <= SNWE[1]) *
(site_lons >= SNWE[2]) * (site_lons <= SNWE[3]))
# limit on time
if start_date:
t0 = ptime.date_list2vector([start_date])[0][0]
idx *= t_end >= t0
if end_date:
t1 = ptime.date_list2vector([end_date])[0][0]
idx *= t_start <= t1
return site_names[idx], site_lats[idx], site_lons[idx]
def read_exclude_date(input_ex_date, dateListAll):
# default value
ex_date_list = []
ex_dates = []
ex_flag = np.ones((len(dateListAll)), np.bool_)
ex_date_list = ptime.read_date_list(input_ex_date,
date_list_all=dateListAll)
if ex_date_list:
ex_dates = ptime.date_list2vector(ex_date_list)[0]
for i in ex_date_list:
ex_flag[dateListAll.index(i)] = False
vprint('exclude date:' + str(ex_date_list))
return ex_date_list, ex_dates, ex_flag
def manual_select_pairs_to_remove(stackFile):
"""Manually select interferograms to remove"""
print('\n-------------------------------------------------------------')
print('Manually select interferograms to remove')
print('1) click two dates/points to select one pair of interferogram')
print('2) repeat until you select all pairs you would like to remove')
print('3) close the figure to continue the program ...')
print('-------------------------------------------------------------\n')
obj = ifgramStack(stackFile)
obj.open()
date12ListAll = obj.date12List
pbase = obj.get_perp_baseline_timeseries(dropIfgram=False)
dateList = obj.dateList
datesNum = mdates.date2num(np.array(ptime.date_list2vector(dateList)[0]))
date12ListKept = obj.get_date12_list(dropIfgram=True)
date12ListDropped = sorted(list(set(date12ListAll) - set(date12ListKept)))
# Display the network
fig = plt.figure()
ax = fig.add_subplot(111)
ax = pp.plot_network(ax, date12ListAll, dateList, list(pbase), date12List_drop=date12ListDropped)
print('display the network of interferogram of file: '+stackFile)
date_click = []
date12_click = []
def onclick(event):
idx = nearest_neighbor(event.xdata, event.ydata, datesNum, pbase)
print('click at '+dateList[idx])
date_click.append(dateList[idx])
if len(date_click) % 2 == 0 and date_click[-2] != date_click[-1]:
[mDate, sDate] = sorted(date_click[-2:])
mIdx = dateList.index(mDate)
sIdx = dateList.index(sDate)
date12 = mDate+'_'+sDate
if date12 in date12ListAll:
print('select date12: '+date12)
date12_click.append(date12)
ax.plot([datesNum[mIdx], datesNum[sIdx]], [pbase[mIdx], pbase[sIdx]], 'r', lw=4)
else:
print(date12+' is not existed in input file')
plt.draw()
cid = fig.canvas.mpl_connect('button_press_event', onclick)
plt.show()
if not ut.yes_or_no('Proceed to drop the ifgrams/date12?'):
date12_click = None
return date12_click
def velo_disp(inps):
"""calculated displacement during startDate_endDate period based on linear assumption and velocity.h5"""
data, atr = readfile.read('geo_velocity.h5')
# calculate disp
dt1, dt2 = ptime.date_list2vector([inps.startDate, inps.endDate])[0]
data *= (dt2 - dt1).days / 365.25
# displacement to phase
range2phase = -4. * np.pi / float(atr['WAVELENGTH'])
data *= range2phase
# write atr
atr['PROCESSOR'] = 'roipac'
atr['FILE_TYPE'] = '.unw'
atr['UNIT'] = 'radian'
out_file = 'geo_' + '{}_{}.unw'.format(inps.startDate, inps.endDate)
writefile.write(data, out_file=out_file, metadata=atr)
def read_timeseries_info():
global atr, k, h5, dateList, tims, date_num, inps
atr = readfile.read_attribute(inps.timeseries_file)
k = atr['FILE_TYPE']
print(('input file is '+k+': '+inps.timeseries_file))
if not k in ['timeseries','GIANT_TS']:
raise ValueError('Only timeseries file is supported!')
h5 = h5py.File(inps.timeseries_file,'r')
if k in ['GIANT_TS']:
dateList = [dt.fromordinal(int(i)).strftime('%Y%m%d') for i in h5['dates'][:].tolist()]
else:
dateList = timeseries(inps.timeseries_file).get_date_list()
date_num = len(dateList)
inps.dates, tims = ptime.date_list2vector(dateList)
def read_timeseries_info():
"""Reads basic information about timeseries file being viewed"""
global atr, k, h5, dateList, inps.tims, inps.num_date, inps
atr = readfile.read_attribute(inps.timeseries_file)
k = atr['FILE_TYPE']
print(('input file is '+k+': '+inps.timeseries_file))
if not k in ['timeseries','giantTimeseries']:
raise ValueError('Only timeseries file is supported!')
h5 = h5py.File(inps.timeseries_file,'r')
if k in ['giantTimeseries']:
dateList = [dt.fromordinal(int(i)).strftime('%Y%m%d') for i in h5['dates'][:].tolist()]
else:
dateList = timeseries(inps.timeseries_file).get_date_list()
inps.num_date = len(dateList)
inps.dates, inps.tims = ptime.date_list2vector(dateList)
def read_timeseries_info():
global atr, k, h5, dateList, tims, date_num, inps
atr = readfile.read_attribute(inps.timeseries_file)
k = atr['FILE_TYPE']
print(('input file is ' + k + ': ' + inps.timeseries_file))
if not k in ['timeseries', 'GIANT_TS']:
raise ValueError('Only timeseries file is supported!')
h5 = h5py.File(inps.timeseries_file, 'r')
if k in ['GIANT_TS']:
dateList = [
dt.fromordinal(int(i)).strftime('%Y%m%d')
for i in h5['dates'][:].tolist()
]
else:
dateList = timeseries(inps.timeseries_file).get_date_list()
date_num = len(dateList)
inps.dates, tims = ptime.date_list2vector(dateList)
def read_exclude_date(input_ex_date, dateListAll):
"""
Parameters: input_ex_date : list of string in YYYYMMDD or filenames for excluded dates
dateListAll : list of string in YYYYMMDD for all dates
Returns: ex_date_list : list of string in YYYYMMDD for excluded dates
ex_dates : list of datetime.datetime objects for excluded dates
ex_flag : 1D np.ndarray in size of (num_date), 1/True for kept, 0/False for excluded
"""
# default value
ex_date_list = []
ex_dates = []
ex_flag = np.ones((len(dateListAll)), np.bool_)
ex_date_list = ptime.read_date_list(input_ex_date, date_list_all=dateListAll)
if ex_date_list:
ex_dates = ptime.date_list2vector(ex_date_list)[0]
for i in ex_date_list:
ex_flag[dateListAll.index(i)] = False
vprint('exclude date:'+str(ex_date_list))
return ex_date_list, ex_dates, ex_flag
def main(iargs=None):
inps = cmd_line_parse(iargs)
print('\n*************** Spatial Average ******************')
mean_list, date_list = ut.spatial_average(inps.file,
datasetName=inps.datasetName,
maskFile=inps.mask_file,
saveList=True)
atr = readfile.read_attribute(inps.file)
k = atr['FILE_TYPE']
if inps.disp_fig and k == 'timeseries':
dates, datevector = ptime.date_list2vector(date_list)
# plot
fig = plt.figure()
ax = fig.add_subplot(111)
ax.plot(dates, mean_list, '-o')#, lw=2, ms=16, alpha=0.7) #, mfc='crimson')
ax.set_title('Spatial Average', fontsize=12)
ax = pp.auto_adjust_xaxis_date(ax, datevector)[0]
ax.set_xlabel('Time [years]', fontsize=12)
ax.set_ylabel('Mean', fontsize=12)
plt.show()
return
def exclude_dates():
global inps, dateList
if inps.ex_date_list:
input_ex_date = list(inps.ex_date_list)
inps.ex_date_list = []
if input_ex_date:
for ex_date in input_ex_date:
if os.path.isfile(ex_date):
ex_date = ptime.read_date_list(ex_date)
else:
ex_date = [ptime.yyyymmdd(ex_date)]
inps.ex_date_list += list(set(ex_date) - set(inps.ex_date_list))
# delete dates not existed in input file
inps.ex_date_list = sorted(list(set(inps.ex_date_list).intersection(dateList)))
inps.ex_dates = ptime.date_list2vector(inps.ex_date_list)[0]
inps.ex_idx_list = sorted([dateList.index(i) for i in inps.ex_date_list])
print(('exclude date:' + str(inps.ex_date_list)))
def read_timeseries_yx(y,
x,
ts_file,
ref_y=None,
ref_x=None,
zero_first=True,
win_size=1,
unit='m',
method='mean',
print_msg=True):
""" Read time-series of one pixel with input y/x
Parameters: y/x - int, row/column number of interest
ts_file - string, filename of time-series HDF5 file
ref_y/x - int, row/column number of reference pixel
zero_first - bool, shift the time-series so that it starts from zero
win_size - int, windows size centered at point of interest
unit - str, output displacement unit
method - str, method to calculate the output displacement and its dispersity
Returns: dates - 1D np.ndarray of datetime.datetime objects, i.e. datetime.datetime(2010, 10, 20, 0, 0)
dis - 1D np.ndarray of float32, displacement
dis_std - 1D np.ndarray of float32, displacement dispersity
"""
# read date
obj = timeseries(ts_file)
obj.open(print_msg=False)
dates = ptime.date_list2vector(obj.dateList)[0]
dates = np.array(dates)
# read displacement
if print_msg:
print('input y / x: {} / {}'.format(y, x))
box = (x, y, x + 1, y + 1)
dis = readfile.read(ts_file, box=box)[0]
dis_std = None
if win_size != 1:
buf = int(win_size / 2)
box_win = (x - buf, y - buf, x + buf + 1, y + buf + 1)
dis_win = readfile.read(ts_file,
box=box_win)[0].reshape(obj.numDate, -1)
if method == 'mean':
dis = np.nanmean(dis_win, axis=1)
dis_std = np.nanstd(dis_win, axis=1)
elif method == 'median':
dis = np.nanmedian(dis_win, axis=1)
dis_std = median_abs_deviation(dis_win)
else:
raise ValueError('un-recognized method: {}'.format(method))
# reference pixel
if ref_y is not None:
ref_box = (ref_x, ref_y, ref_x + 1, ref_y + 1)
dis -= readfile.read(ts_file, box=ref_box)[0]
#start at zero
if zero_first:
dis -= dis[0]
# custom output unit
if unit == 'm':
pass
elif unit == 'cm':
dis *= 100.
dis_std *= 100.
elif unit == 'mm':
dis *= 1000.
dis_std *= 1000.
else:
raise ValueError('un-supported output unit: {}'.format(unit))
return dates, dis, dis_std
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
def read_init_info(inps):
# Time Series Info
atr = readfile.read_attribute(inps.file[0])
inps.key = atr['FILE_TYPE']
if inps.key == 'timeseries':
obj = timeseries(inps.file[0])
elif inps.key == 'giantTimeseries':
obj = giantTimeseries(inps.file[0])
elif inps.key == 'HDFEOS':
obj = HDFEOS(inps.file[0])
else:
raise ValueError('input file is {}, not timeseries.'.format(inps.key))
obj.open(print_msg=inps.print_msg)
inps.seconds = atr.get('CENTER_LINE_UTC', 0)
if not inps.file_label:
inps.file_label = []
for fname in inps.file:
fbase = os.path.splitext(os.path.basename(fname))[0]
fbase = fbase.replace('timeseries', '')
inps.file_label.append(fbase)
# default mask file
if not inps.mask_file and 'msk' not in inps.file[0]:
dir_name = os.path.dirname(inps.file[0])
if 'Y_FIRST' in atr.keys():
inps.mask_file = os.path.join(dir_name, 'geo_maskTempCoh.h5')
else:
inps.mask_file = os.path.join(dir_name, 'maskTempCoh.h5')
if not os.path.isfile(inps.mask_file):
inps.mask_file = None
## date info
inps.date_list = obj.dateList
inps.num_date = len(inps.date_list)
if inps.start_date:
inps.date_list = [i for i in inps.date_list if int(i) >= int(inps.start_date)]
if inps.end_date:
inps.date_list = [i for i in inps.date_list if int(i) <= int(inps.end_date)]
inps.num_date = len(inps.date_list)
inps.dates, inps.yearList = ptime.date_list2vector(inps.date_list)
(inps.ex_date_list,
inps.ex_dates,
inps.ex_flag) = read_exclude_date(inps.ex_date_list, inps.date_list)
# reference date/index
if not inps.ref_date:
inps.ref_date = atr.get('REF_DATE', None)
if inps.ref_date:
inps.ref_idx = inps.date_list.index(inps.ref_date)
else:
inps.ref_idx = None
# date/index of interest for initial display
if not inps.idx:
if (not inps.ref_idx) or (inps.ref_idx < inps.num_date / 2.):
inps.idx = inps.num_date - 2
else:
inps.idx = 2
# Display Unit
(inps.disp_unit,
inps.unit_fac) = pp.scale_data2disp_unit(metadata=atr, disp_unit=inps.disp_unit)[1:3]
# Map info - coordinate unit
inps.coord_unit = atr.get('Y_UNIT', 'degrees').lower()
# Read Error List
inps.ts_plot_func = plot_ts_scatter
inps.error_ts = None
inps.ex_error_ts = None
if inps.error_file:
# assign plot function
inps.ts_plot_func = plot_ts_errorbar
# read error file
error_fc = np.loadtxt(inps.error_file, dtype=bytes).astype(str)
inps.error_ts = error_fc[:, 1].astype(np.float)*inps.unit_fac
# update error file with exlcude date
if inps.ex_date_list:
e_ts = inps.error_ts[:]
inps.ex_error_ts = e_ts[inps.ex_flag == 0]
inps.error_ts = e_ts[inps.ex_flag == 1]
# Zero displacement for 1st acquisition
if inps.zero_first:
inps.zero_idx = min(0, np.min(np.where(inps.ex_flag)[0]))
# default lookup table file and coordinate object
if not inps.lookup_file:
inps.lookup_file = ut.get_lookup_file('./inputs/geometryRadar.h5')
inps.coord = ut.coordinate(atr, inps.lookup_file)
## size and lalo info
inps.pix_box, inps.geo_box = subset.subset_input_dict2box(vars(inps), atr)
inps.pix_box = inps.coord.check_box_within_data_coverage(inps.pix_box)
inps.geo_box = inps.coord.box_pixel2geo(inps.pix_box)
data_box = (0, 0, int(atr['WIDTH']), int(atr['LENGTH']))
vprint('data coverage in y/x: '+str(data_box))
vprint('subset coverage in y/x: '+str(inps.pix_box))
vprint('data coverage in lat/lon: '+str(inps.coord.box_pixel2geo(data_box)))
vprint('subset coverage in lat/lon: '+str(inps.geo_box))
vprint('------------------------------------------------------------------------')
# calculate multilook_num
# ONLY IF:
# inps.multilook is True (no --nomultilook input) AND
# inps.multilook_num ==1 (no --multilook-num input)
# Note: inps.multilook is used for this check ONLY
# Note: multilooking is only applied to the 3D data cubes and their related operations:
# e.g. spatial indexing, referencing, etc. All the other variables are in the original grid
# so that users get the same result as the non-multilooked version.
if inps.multilook and inps.multilook_num == 1:
inps.multilook_num = pp.auto_multilook_num(inps.pix_box, inps.num_date,
max_memory=inps.maxMemory,
print_msg=inps.print_msg)
## reference pixel
if not inps.ref_lalo and 'REF_LAT' in atr.keys():
inps.ref_lalo = (float(atr['REF_LAT']), float(atr['REF_LON']))
if inps.ref_lalo:
# set longitude to [-180, 180)
if inps.coord_unit.lower().startswith('deg') and inps.ref_lalo[1] >= 180.:
inps.ref_lalo[1] -= 360.
# ref_lalo --> ref_yx if not set in cmd
if not inps.ref_yx:
inps.ref_yx = inps.coord.geo2radar(inps.ref_lalo[0], inps.ref_lalo[1], print_msg=False)[0:2]
# use REF_Y/X if ref_yx not set in cmd
if not inps.ref_yx and 'REF_Y' in atr.keys():
inps.ref_yx = (int(atr['REF_Y']), int(atr['REF_X']))
# ref_yx --> ref_lalo if in geo-coord
# for plotting purpose only
if inps.ref_yx and 'Y_FIRST' in atr.keys():
inps.ref_lalo = inps.coord.radar2geo(inps.ref_yx[0], inps.ref_yx[1], print_msg=False)[0:2]
# do not plot native reference point if it's out of the coverage due to subset
if (inps.ref_yx and 'Y_FIRST' in atr.keys()
and inps.ref_yx == (int(atr.get('REF_Y',-999)), int(atr.get('REF_X',-999)))
and not ( inps.pix_box[0] <= inps.ref_yx[1] < inps.pix_box[2]
and inps.pix_box[1] <= inps.ref_yx[0] < inps.pix_box[3])):
inps.disp_ref_pixel = False
print('the native REF_Y/X is out of subset box, thus do not display')
## initial pixel coord
if inps.lalo:
inps.yx = inps.coord.geo2radar(inps.lalo[0], inps.lalo[1], print_msg=False)[0:2]
try:
inps.lalo = inps.coord.radar2geo(inps.yx[0], inps.yx[1], print_msg=False)[0:2]
except:
inps.lalo = None
## figure settings
# Flip up-down / left-right
if inps.auto_flip:
inps.flip_lr, inps.flip_ud = pp.auto_flip_direction(atr, print_msg=inps.print_msg)
# Transparency - Alpha
if not inps.transparency:
# Auto adjust transparency value when showing shaded relief DEM
if inps.dem_file and inps.disp_dem_shade:
inps.transparency = 0.7
else:
inps.transparency = 1.0
## display unit ans wrap
# if wrap_step == 2*np.pi (default value), set disp_unit_img = radian;
# otherwise set disp_unit_img = disp_unit
inps.disp_unit_img = inps.disp_unit
if inps.wrap:
inps.range2phase = -4. * np.pi / float(atr['WAVELENGTH'])
if 'cm' == inps.disp_unit.split('/')[0]: inps.range2phase /= 100.
elif 'mm' == inps.disp_unit.split('/')[0]: inps.range2phase /= 1000.
elif 'm' == inps.disp_unit.split('/')[0]: inps.range2phase /= 1.
else:
raise ValueError('un-recognized display unit: {}'.format(inps.disp_unit))
if (inps.wrap_range[1] - inps.wrap_range[0]) == 2*np.pi:
inps.disp_unit_img = 'radian'
inps.vlim = inps.wrap_range
inps.cbar_label = 'Displacement [{}]'.format(inps.disp_unit_img)
## fit a suite of time func to the time series
inps.model, inps.num_param = ts2vel.read_inps2model(inps, date_list=inps.date_list)
# dense TS for plotting
inps.date_list_fit = ptime.get_date_range(inps.date_list[0], inps.date_list[-1])
inps.dates_fit = ptime.date_list2vector(inps.date_list_fit)[0]
inps.G_fit = time_func.get_design_matrix4time_func(
date_list=inps.date_list_fit,
model=inps.model,
seconds=inps.seconds)
return inps, atr
def read_init_info(inps):
# Time Series Info
ts_file0 = inps.file[0]
atr = readfile.read_attribute(ts_file0)
inps.key = atr['FILE_TYPE']
if inps.key == 'timeseries':
obj = timeseries(ts_file0)
elif inps.key == 'giantTimeseries':
obj = giantTimeseries(ts_file0)
elif inps.key == 'HDFEOS':
obj = HDFEOS(ts_file0)
else:
raise ValueError('input file is {}, not timeseries.'.format(inps.key))
obj.open(print_msg=inps.print_msg)
if not inps.file_label:
inps.file_label = [str(i) for i in list(range(len(inps.file)))]
# default mask file
if not inps.mask_file and 'masked' not in ts_file0:
dir_name = os.path.dirname(ts_file0)
if 'Y_FIRST' in atr.keys():
inps.mask_file = os.path.join(dir_name, 'geo_maskTempCoh.h5')
else:
inps.mask_file = os.path.join(dir_name, 'maskTempCoh.h5')
if not os.path.isfile(inps.mask_file):
inps.mask_file = None
# date info
inps.date_list = obj.dateList
inps.num_date = len(inps.date_list)
if inps.start_date:
inps.date_list = [
i for i in inps.date_list if int(i) >= int(inps.start_date)
]
if inps.end_date:
inps.date_list = [
i for i in inps.date_list if int(i) <= int(inps.end_date)
]
inps.num_date = len(inps.date_list)
inps.dates, inps.yearList = ptime.date_list2vector(inps.date_list)
(inps.ex_date_list, inps.ex_dates,
inps.ex_flag) = read_exclude_date(inps.ex_date_list, inps.date_list)
# initial display index
#if atr['REF_DATE'] in inps.date_list:
# inps.ref_idx = inps.date_list.index(atr['REF_DATE'])
#else:
# inps.ref_idx = 0
if inps.ref_date:
inps.ref_idx = inps.date_list.index(inps.ref_date)
else:
inps.ref_idx = 3
if not inps.idx:
if inps.ref_idx < inps.num_date / 2.:
inps.idx = inps.num_date - 3
else:
inps.idx = 3
# Display Unit
(inps.disp_unit,
inps.unit_fac) = pp.scale_data2disp_unit(metadata=atr,
disp_unit=inps.disp_unit)[1:3]
# Map info - coordinate unit
inps.coord_unit = atr.get('Y_UNIT', 'degrees').lower()
# Read Error List
inps.ts_plot_func = plot_ts_scatter
inps.error_ts = None
inps.ex_error_ts = None
if inps.error_file:
# assign plot function
inps.ts_plot_func = plot_ts_errorbar
# read error file
error_fc = np.loadtxt(inps.error_file, dtype=bytes).astype(str)
inps.error_ts = error_fc[:, 1].astype(np.float) * inps.unit_fac
# update error file with exlcude date
if inps.ex_date_list:
e_ts = inps.error_ts[:]
inps.ex_error_ts = e_ts[inps.ex_flag == 0]
inps.error_ts = e_ts[inps.ex_flag == 1]
# Zero displacement for 1st acquisition
if inps.zero_first:
inps.zero_idx = min(0, np.min(np.where(inps.ex_flag)[0]))
# default lookup table file
if not inps.lookup_file:
inps.lookup_file = ut.get_lookup_file('./inputs/geometryRadar.h5')
inps.coord = ut.coordinate(atr, inps.lookup_file)
# size and lalo info
inps.pix_box, inps.geo_box = subset.subset_input_dict2box(vars(inps), atr)
inps.pix_box = inps.coord.check_box_within_data_coverage(inps.pix_box)
inps.geo_box = inps.coord.box_pixel2geo(inps.pix_box)
data_box = (0, 0, int(atr['WIDTH']), int(atr['LENGTH']))
vprint('data coverage in y/x: ' + str(data_box))
vprint('subset coverage in y/x: ' + str(inps.pix_box))
vprint('data coverage in lat/lon: ' +
str(inps.coord.box_pixel2geo(data_box)))
vprint('subset coverage in lat/lon: ' + str(inps.geo_box))
vprint(
'------------------------------------------------------------------------'
)
# reference pixel
if not inps.ref_lalo and 'REF_LAT' in atr.keys():
inps.ref_lalo = (float(atr['REF_LAT']), float(atr['REF_LON']))
if inps.ref_lalo:
if inps.ref_lalo[1] > 180.:
inps.ref_lalo[1] -= 360.
inps.ref_yx = inps.coord.geo2radar(inps.ref_lalo[0],
inps.ref_lalo[1],
print_msg=False)[0:2]
if not inps.ref_yx and 'REF_Y' in atr.keys():
inps.ref_yx = [int(atr['REF_Y']), int(atr['REF_X'])]
# Initial Pixel Coord
if inps.lalo:
inps.yx = inps.coord.geo2radar(inps.lalo[0],
inps.lalo[1],
print_msg=False)[0:2]
try:
inps.lalo = inps.coord.radar2geo(inps.yx[0],
inps.yx[1],
print_msg=False)[0:2]
except:
inps.lalo = None
# Flip up-down / left-right
if inps.auto_flip:
inps.flip_lr, inps.flip_ud = pp.auto_flip_direction(
atr, print_msg=inps.print_msg)
# Transparency - Alpha
if not inps.transparency:
# Auto adjust transparency value when showing shaded relief DEM
if inps.dem_file and inps.disp_dem_shade:
inps.transparency = 0.7
else:
inps.transparency = 1.0
# display unit ans wrap
# if wrap_step == 2*np.pi (default value), set disp_unit_img = radian;
# otherwise set disp_unit_img = disp_unit
inps.disp_unit_img = inps.disp_unit
if inps.wrap:
inps.range2phase = -4. * np.pi / float(atr['WAVELENGTH'])
if 'cm' == inps.disp_unit.split('/')[0]: inps.range2phase /= 100.
elif 'mm' == inps.disp_unit.split('/')[0]: inps.range2phase /= 1000.
elif 'm' == inps.disp_unit.split('/')[0]: inps.range2phase /= 1.
else:
raise ValueError('un-recognized display unit: {}'.format(
inps.disp_unit))
if (inps.wrap_range[1] - inps.wrap_range[0]) == 2 * np.pi:
inps.disp_unit_img = 'radian'
inps.vlim = inps.wrap_range
inps.cbar_label = 'Displacement [{}]'.format(inps.disp_unit_img)
return inps, atr
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
transparent=True,
dpi=fig_dpi)
# plt.show()
# Backup - Plot Velocity with POI displacement timeseries
# read ts data
# load coordinates of observed wells
# ll = pd.read_csv('/scratch/hpham/insar/insar_pahrump/GPS_points_PV1.csv') # only gps sta
#ll = pd.read_csv('/scratch/hpham/insar/insar_pahrump/GPS_points_PV1_full.csv') #
print(f'Reading ifile_loc {ifile_loc} \n')
ll = pd.read_csv(ifile_loc)
obj = timeseries(ts_file)
obj.open()
dates = ptime.date_list2vector(obj.dateList)[0]
df = pd.DataFrame({'Date': dates})
for i in range(ll.shape[0]):
cur_point = str(ll['Name'][i])
lat, lon = ll['Latitude'][i], ll['Longitude'][i]
print(f'\nName={cur_point}, lat={lat}, lon={lon}')
y, x = coord.geo2radar(lat, lon)[0:2]
print(f'x={x}, y={y}')
print('y/x: {}/{}'.format(y, x))
d_ts = np.squeeze(readfile.read(ts_file,
box=(x, y, x + 1, y + 1))[0]) * 100.
# d_ts = d_ts/
#(Unw_Phase * wavelength in cm) / (-4 * PI * cos(rad(incident_angle)))
# https://forum.step.esa.int/t/subswath-iw2-sentinel-1a/4322/4
try:
def plot_rms_bar(ax,
date_list,
rms,
cutoff=3.,
font_size=12,
tick_year_num=1,
legend_loc='best',
disp_legend=True,
disp_side_plot=True,
disp_thres_text=False,
ylabel=r'Residual Phase $\hat \phi_{resid}$ RMS [mm]'):
""" Bar plot Phase Residual RMS
Parameters: ax : Axes object
date_list : list of string in YYYYMMDD format
rms : 1D np.array of float for RMS value in mm
cutoff : cutoff value of MAD outlier detection
tick_year_num : int, number of years per major tick
legend_loc : 'upper right' or (0.5, 0.5)
Returns: ax : Axes object
"""
dates, datevector = ptime.date_list2vector(date_list)
dates = np.array(dates)
try:
bar_width = min(ut.most_common(np.diff(dates).tolist(), k=2)) * 3 / 4
except:
bar_width = np.min(np.diff(dates).tolist()) * 3 / 4
rms = np.array(rms)
# Plot all dates
ax.bar(dates, rms, bar_width.days, color=pp.mplColors[0])
# Plot reference date
ref_idx = np.argmin(rms)
ax.bar(dates[ref_idx],
rms[ref_idx],
bar_width.days,
color=pp.mplColors[1],
label='Reference date')
# Plot exclude dates
rms_threshold = ut.median_abs_deviation_threshold(rms,
center=0.,
cutoff=cutoff)
ex_idx = rms > rms_threshold
if not np.all(ex_idx == False):
ax.bar(dates[ex_idx],
rms[ex_idx],
bar_width.days,
color='darkgray',
label='Exclude date')
# Plot rms_threshold line
(ax, xmin, xmax) = pp.auto_adjust_xaxis_date(ax,
datevector,
font_size,
every_year=tick_year_num)
ax.plot(np.array([xmin, xmax]),
np.array([rms_threshold, rms_threshold]),
'--k',
label='Median Abs Dev * {}'.format(cutoff))
# axis format
ax = pp.auto_adjust_yaxis(ax,
np.append(rms, rms_threshold),
font_size,
ymin=0.0)
ax.set_xlabel('Time [years]', fontsize=font_size)
ax.set_ylabel(ylabel, fontsize=font_size)
ax.tick_params(which='both',
direction='in',
labelsize=font_size,
bottom=True,
top=True,
left=True,
right=True)
# 2nd axes for circles
if disp_side_plot:
divider = make_axes_locatable(ax)
ax2 = divider.append_axes("right", "10%", pad="2%")
ax2.plot(np.ones(rms.shape, np.float32) * 0.5,
rms,
'o',
mfc='none',
color=pp.mplColors[0])
ax2.plot(np.ones(rms.shape, np.float32)[ref_idx] * 0.5,
rms[ref_idx],
'o',
mfc='none',
color=pp.mplColors[1])
if not np.all(ex_idx == False):
ax2.plot(np.ones(rms.shape, np.float32)[ex_idx] * 0.5,
rms[ex_idx],
'o',
mfc='none',
color='darkgray')
ax2.plot(np.array([0, 1]), np.array([rms_threshold, rms_threshold]),
'--k')
ax2.set_ylim(ax.get_ylim())
ax2.set_xlim([0, 1])
ax2.tick_params(which='both',
direction='in',
labelsize=font_size,
bottom=True,
top=True,
left=True,
right=True)
ax2.get_xaxis().set_ticks([])
ax2.get_yaxis().set_ticklabels([])
if disp_legend:
ax.legend(loc=legend_loc, frameon=False, fontsize=font_size)
# rms_threshold text
if disp_thres_text:
ymin, ymax = ax.get_ylim()
yoff = (ymax - ymin) * 0.1
if (rms_threshold - ymin) > 0.5 * (ymax - ymin):
yoff *= -1.
ax.annotate('Median Abs Dev * {}'.format(cutoff),
xy=(xmin + (xmax - xmin) * 0.05, rms_threshold + yoff),
color='k',
xycoords='data',
fontsize=font_size)
return ax
def vtec2iono_ramp_timeseries(date_list,
vtec_list,
geom_file,
iono_file,
sub_tec_ratio=None,
ds_dict_ext=None,
update_mode=True):
"""Convert zenith TEC to 2D slant range delay (ramp due to the incidence angle variation)
and write to HDF5 time-series file.
Parameters: date_list - list of str, dates in YYYYMMDD format
vtec_list - list of float32, zenith TEC in TECU
geom_file - str, path of the geometry file including incidenceAngle data
iono_file - str, path of output iono ramp time-series file
update_mode - bool,
ds_dict_ext - dict, extra dictionary of dataset to be saved into the HDF5 file.
Returns: iono_file - str, path of output iono ramp time-series file
"""
top_perc_file = os.path.join(os.path.dirname(mintpy.__file__), 'data',
'top_tec_perc_s1.txt')
# prepare geometry
(iono_inc_angle, iono_lat, iono_lon,
iono_height) = iono.prep_geometry_iono(geom_file, print_msg=True)
# prepare date/time
num_date = len(date_list)
if len(vtec_list) != num_date:
msg = 'Input tec_list and date_list have different size!'
msg += '\nFor acquisitions without TEC data, set it to NaN.'
raise ValueError(msg)
meta = readfile.read_attribute(geom_file)
length = int(meta['LENGTH'])
width = int(meta['WIDTH'])
freq = SPEED_OF_LIGHT / float(meta['WAVELENGTH'])
# Note: Scaling gives slightly better RMSE for SenD but much worse RMSE for SenA and Alos2
# thus this is not used by default.
if sub_tec_ratio is not None:
if ut.is_number(sub_tec_ratio):
print('multiply VTEC by {}'.format(sub_tec_ratio))
vtec_list = (np.array(vtec_list).flatten() *
float(sub_tec_ratio)).tolist()
elif sub_tec_ratio.startswith('adap'):
dates = ptime.date_list2vector(date_list)[0]
ydays = np.array([x.timetuple().tm_yday for x in dates])
fc = np.loadtxt(top_perc_file, dtype=bytes).astype(np.float32)
print(
'multiply VTEC adaptively based on the day of the year from: {}'
.format(top_perc_file))
sub_perc = fc[:, 2][np.array(ydays)]
vtec_list = (np.array(vtec_list).flatten() * sub_perc).tolist()
# loop to calculate the range delay (ramp)
print('calculating ionospheric phase ramp time-series from TEC ...')
ts_ramp = np.zeros((num_date, length, width), dtype=np.float32)
prog_bar = ptime.progressBar(maxValue=num_date)
for i, date_str in enumerate(date_list):
ts_ramp[i, :, :] = iono.vtec2range_delay(
vtec_list[i],
inc_angle=iono_inc_angle,
freq=freq,
)
prog_bar.update(i + 1, suffix=date_str)
prog_bar.close()
## output
# prepare metadata
meta['FILE_TYPE'] = 'timeseries'
meta['UNIT'] = 'm'
meta['IONO_LAT'] = iono_lat
meta['IONO_LON'] = iono_lon
meta['IONO_HEIGHT'] = iono_height
meta['IONO_INCIDENCE_ANGLE'] = np.nanmean(iono_inc_angle)
# absolute delay without double reference
for key in ['REF_X', 'REF_Y', 'REF_LAT', 'REF_LON', 'REF_DATE']:
if key in meta.keys():
meta.pop(key)
# prepare data matrix
ds_dict = {}
ds_dict['date'] = np.array(date_list, dtype=np.string_)
ds_dict['vtec'] = np.array(vtec_list, dtype=np.float32)
ds_dict['timeseries'] = ts_ramp
# add the extra dataset if specified, e.g. vtec_gim, vtec_top, vtec_sub
if ds_dict_ext is not None:
ds_names = ds_dict.keys()
for ds_name, ds_val in ds_dict_ext.items():
if ds_name not in ds_names:
ds_dict[ds_name] = ds_val
# write to disk
writefile.write(ds_dict, iono_file, metadata=meta)
return iono_file
def plot_rms_bar(ax, date_list, rms, cutoff=3., font_size=12,
tick_year_num=1, legend_loc='best',
disp_legend=True, disp_side_plot=True, disp_thres_text=True,
ylabel=r'Residual Phase $\hat \phi_{resid}$ RMS [mm]'):
""" Bar plot Phase Residual RMS
Parameters: ax : Axes object
date_list : list of string in YYYYMMDD format
rms : 1D np.array of float for RMS value in mm
cutoff : cutoff value of MAD outlier detection
tick_year_num : int, number of years per major tick
legend_loc : 'upper right' or (0.5, 0.5)
Returns: ax : Axes object
"""
dates, datevector = ptime.date_list2vector(date_list)
dates = np.array(dates)
try:
bar_width = min(ut.most_common(np.diff(dates).tolist(), k=2))*3/4
except:
bar_width = np.min(np.diff(dates).tolist())*3/4
rms = np.array(rms)
# Plot all dates
ax.bar(dates, rms, bar_width.days, color=pp.mplColors[0])
# Plot reference date
ref_idx = np.argmin(rms)
ax.bar(dates[ref_idx], rms[ref_idx], bar_width.days, color=pp.mplColors[1], label='Reference date')
# Plot exclude dates
rms_threshold = ut.median_abs_deviation_threshold(rms, center=0., cutoff=cutoff)
ex_idx = rms > rms_threshold
if not np.all(ex_idx==False):
ax.bar(dates[ex_idx], rms[ex_idx], bar_width.days, color='darkgray', label='Exclude date')
# Plot rms_threshold line
(ax, xmin, xmax) = pp.auto_adjust_xaxis_date(ax, datevector, font_size, every_year=tick_year_num)
ax.plot(np.array([xmin, xmax]), np.array([rms_threshold, rms_threshold]), '--k', label='RMS threshold')
# axis format
ax = pp.auto_adjust_yaxis(ax, np.append(rms, rms_threshold), font_size, ymin=0.0)
ax.set_xlabel('Time [years]', fontsize=font_size)
ax.set_ylabel(ylabel, fontsize=font_size)
ax.tick_params(which='both', direction='in', labelsize=font_size,
bottom=True, top=True, left=True, right=True)
# 2nd axes for circles
if disp_side_plot:
divider = make_axes_locatable(ax)
ax2 = divider.append_axes("right", "10%", pad="2%")
ax2.plot(np.ones(rms.shape, np.float32) * 0.5, rms, 'o', mfc='none', color=pp.mplColors[0])
ax2.plot(np.ones(rms.shape, np.float32)[ref_idx] * 0.5, rms[ref_idx], 'o', mfc='none', color=pp.mplColors[1])
if not np.all(ex_idx==False):
ax2.plot(np.ones(rms.shape, np.float32)[ex_idx] * 0.5, rms[ex_idx], 'o', mfc='none', color='darkgray')
ax2.plot(np.array([0, 1]), np.array([rms_threshold, rms_threshold]), '--k')
ax2.set_ylim(ax.get_ylim())
ax2.set_xlim([0, 1])
ax2.tick_params(which='both', direction='in', labelsize=font_size,
bottom=True, top=True, left=True, right=True)
ax2.get_xaxis().set_ticks([])
ax2.get_yaxis().set_ticklabels([])
if disp_legend:
ax.legend(loc=legend_loc, frameon=False, fontsize=font_size)
# rms_threshold text
if disp_thres_text:
ymin, ymax = ax.get_ylim()
yoff = (ymax - ymin) * 0.1
if (rms_threshold - ymin) > 0.5 * (ymax - ymin):
yoff *= -1.
ax.annotate('Median Abs Dev * {}'.format(cutoff),
xy=(xmin + (xmax-xmin)*0.05, rms_threshold + yoff ),
color='k', xycoords='data', fontsize=font_size)
return ax
def read_data(inps):
# metadata
atr = readfile.read_attribute(inps.file)
if 'WAVELENGTH' in atr.keys():
range2phase = -4 * np.pi / float(atr['WAVELENGTH'])
# change reference pixel
if inps.ref_lalo:
if 'Y_FIRST' in atr.keys():
coord = ut.coordinate(atr)
ref_y, ref_x = coord.geo2radar(inps.ref_lalo[0],
inps.ref_lalo[1])[0:2]
inps.ref_yx = [ref_y, ref_x]
else:
raise ValueError(
"input file is not geocoded --> reference point in lat/lon is NOT support"
)
if inps.ref_yx:
atr['REF_Y'] = inps.ref_yx[0]
atr['REF_X'] = inps.ref_yx[1]
if 'Y_FIRST' in atr.keys():
coord = ut.coordinate(atr)
ref_lat, ref_lon = coord.radar2geo(inps.ref_yx[0],
inps.ref_yx[1])[0:2]
atr['REF_LAT'] = ref_lat
atr['REF_LON'] = ref_lon
print('change reference point to y/x: {}'.format(inps.ref_yx))
# various file types
print('read {} from file {}'.format(inps.dset, inps.file))
k = atr['FILE_TYPE']
if k == 'velocity':
# read/prepare data
data = readfile.read(inps.file)[0]
# velocity to displacement
print('convert velocity to displacement for {}'.format(atr['DATE12']))
date1, date2 = atr['DATE12'].split('_')
dt1, dt2 = ptime.date_list2vector([date1, date2])[0]
data *= (dt2 - dt1).days / 365.25
# displacement to phase
print('convert displacement to phase in radian')
data *= range2phase
if inps.ref_yx:
data -= data[inps.ref_yx[0], inps.ref_yx[1]]
# metadata
atr['FILE_TYPE'] = '.unw'
atr['UNIT'] = 'radian'
# output filename
if not inps.outfile:
inps.outfile = os.path.join(os.path.dirname(inps.file),
'{}.unw'.format(atr['DATE12']))
elif k == 'timeseries':
# date1 and date2
if '_' in inps.dset:
date1, date2 = ptime.yyyymmdd(inps.dset.split('_'))
else:
date1 = atr['REF_DATE']
date2 = ptime.yyyymmdd(inps.dset)
# read/prepare data
data = readfile.read(inps.file, datasetName=date2)[0]
data -= readfile.read(inps.file, datasetName=date1)[0]
print('converting range to phase')
data *= range2phase
if inps.ref_yx:
data -= data[inps.ref_yx[0], inps.ref_yx[1]]
# metadata
atr['DATE'] = date1[2:8]
atr['DATE12'] = '{}-{}'.format(date1[2:8], date2[2:8])
atr['FILE_TYPE'] = '.unw'
atr['UNIT'] = 'radian'
# output filename
if not inps.outfile:
inps.outfile = '{}_{}.unw'.format(date1, date2)
if inps.file.startswith('geo_'):
inps.outfile = 'geo_' + inps.outfile
elif k == 'HDFEOS':
dname = inps.dset.split('-')[0]
# date1 and date2
if dname == 'displacement':
if '-' in inps.dset:
suffix = inps.dset.split('-')[1]
if '_' in suffix:
date1, date2 = ptime.yyyymmdd(suffix.split('_'))
else:
date1 = atr['REF_DATE']
date2 = ptime.yyyymmdd(suffix)
else:
raise ValueError(
"No '-' in input dataset! It is required for {}".format(
dname))
else:
date_list = HDFEOS(inps.file).get_date_list()
date1 = date_list[0]
date2 = date_list[-1]
date12 = '{}_{}'.format(date1, date2)
# read / prepare data
slice_list = readfile.get_slice_list(inps.file)
if 'displacement' in inps.dset:
# read/prepare data
slice_name1 = view.check_dataset_input(
slice_list, '{}-{}'.format(dname, date1))[0][0]
slice_name2 = view.check_dataset_input(
slice_list, '{}-{}'.format(dname, date2))[0][0]
data = readfile.read(inps.file, datasetName=slice_name1)[0]
data -= readfile.read(inps.file, datasetName=slice_name2)[0]
print('converting range to phase')
data *= range2phase
if inps.ref_yx:
data -= data[inps.ref_yx[0], inps.ref_yx[1]]
else:
slice_name = view.check_dataset_input(slice_list, inps.dset)[0][0]
data = readfile.read(inps.file, datasetName=slice_name)[0]
# metadata
atr['DATE'] = date1[2:8]
atr['DATE12'] = '{}-{}'.format(date1[2:8], date2[2:8])
if dname == 'displacement':
atr['FILE_TYPE'] = '.unw'
atr['UNIT'] = 'radian'
elif 'coherence' in dname.lower():
atr['FILE_TYPE'] = '.cor'
atr['UNIT'] = '1'
elif dname == 'height':
atr['FILE_TYPE'] = '.dem'
atr['DATA_TYPE'] = 'int16'
else:
raise ValueError('unrecognized input dataset type: {}'.format(
inps.dset))
# output filename
if not inps.outfile:
inps.outfile = '{}{}'.format(date12, atr['FILE_TYPE'])
elif k == 'ifgramStack':
dname, date12 = inps.dset.split('-')
date1, date2 = date12.split('_')
# read / prepare data
data = readfile.read(inps.file, datasetName=inps.dset)[0]
if dname.startswith('unwrapPhase'):
if 'REF_X' in atr.keys():
data -= data[int(atr['REF_Y']), int(atr['REF_X'])]
print('consider reference pixel in y/x: ({}, {})'.format(
atr['REF_Y'], atr['REF_X']))
else:
print('No REF_Y/X found.')
# metadata
atr['DATE'] = date1[2:8]
atr['DATE12'] = '{}-{}'.format(date1[2:8], date2[2:8])
if dname.startswith('unwrapPhase'):
atr['FILE_TYPE'] = '.unw'
atr['UNIT'] = 'radian'
elif dname == 'coherence':
atr['FILE_TYPE'] = '.cor'
atr['UNIT'] = '1'
elif dname == 'wrapPhase':
atr['FILE_TYPE'] = '.int'
atr['UNIT'] = 'radian'
elif dname == 'connectComponent':
atr['FILE_TYPE'] = '.conncomp'
atr['UNIT'] = '1'
atr['DATA_TYPE'] = 'byte'
else:
raise ValueError('unrecognized dataset type: {}'.format(inps.dset))
# output filename
if not inps.outfile:
inps.outfile = '{}{}'.format(date12, atr['FILE_TYPE'])
if inps.file.startswith('geo_'):
inps.outfile = 'geo_' + inps.outfile
else:
# read data
data = readfile.read(inps.file, datasetName=inps.dset)[0]
if inps.outfile:
fext = os.path.splitext(inps.outfile)[1]
atr['FILE_TYPE'] = fext
else:
# metadata
if 'coherence' in k.lower():
atr['FILE_TYPE'] = '.cor'
elif k in ['mask']:
atr['FILE_TYPE'] = '.msk'
elif k in ['geometry'] and inps.dset == 'height':
if 'Y_FIRST' in atr.keys():
atr['FILE_TYPE'] = '.dem'
else:
atr['FILE_TYPE'] = '.hgt'
atr['UNIT'] = 'm'
else:
atr['FILE_TYPE'] = '.unw'
inps.outfile = '{}{}'.format(
os.path.splitext(inps.file)[0], atr['FILE_TYPE'])
# mask
if inps.mask_file:
for m_file in inps.mask_file:
print('mask data based on input file: {}'.format(m_file))
mask = readfile.read(m_file)[0]
mask *= ~np.isnan(data)
data[mask == 0] = np.nan
# get rid of starting . if output as hdf5 file
if inps.outfile.endswith('.h5'):
if atr['FILE_TYPE'].startswith('.'):
atr['FILE_TYPE'] = atr['FILE_TYPE'][1:]
atr['PROCESSOR'] = 'roipac'
return data, atr, inps.outfile