def main(argv=None):
#%% Check argv
if argv == None:
argv = sys.argv
start = time.time()
ver = 1.4
date = 20201007
author = "Y. Morishita"
print("\n{} ver{} {} {}".format(os.path.basename(argv[0]), ver, date,
author),
flush=True)
print("{} {}".format(os.path.basename(argv[0]), ' '.join(argv[1:])),
flush=True)
global Aloop, ifgdates, ifgdir, length, width, loop_pngdir, cycle, \
multi_prime, bad_ifg, noref_ifg, bad_ifg_all, refy1, refy2, refx1, refx2 ## for parallel processing
#%% Set default
ifgdir = []
tsadir = []
loop_thre = 1.5
multi_prime = False
n_para = len(os.sched_getaffinity(0))
cycle = 3 # 2pi*3/cycle
cmap_noise = 'viridis'
cmap_noise_r = 'viridis_r'
#%% Read options
try:
try:
opts, args = getopt.getopt(argv[1:], "hd:t:l:",
["help", "multi_prime", "n_para="])
except getopt.error as msg:
raise Usage(msg)
for o, a in opts:
if o == '-h' or o == '--help':
print(__doc__)
return 0
elif o == '-d':
ifgdir = a
elif o == '-t':
tsadir = a
elif o == '-l':
loop_thre = float(a)
elif o == '--multi_prime':
multi_prime = True
elif o == '--n_para':
n_para = int(a)
if not ifgdir:
raise Usage('No data directory given, -d is not optional!')
elif not os.path.isdir(ifgdir):
raise Usage('No {} dir exists!'.format(ifgdir))
elif not os.path.exists(os.path.join(ifgdir, 'slc.mli.par')):
raise Usage('No slc.mli.par file exists in {}!'.format(ifgdir))
except Usage as err:
print("\nERROR:", file=sys.stderr, end='')
print(" " + str(err.msg), file=sys.stderr)
print("\nFor help, use -h or --help.\n", file=sys.stderr)
return 2
print("\nloop_thre : {} rad".format(loop_thre), flush=True)
#%% Directory setting
ifgdir = os.path.abspath(ifgdir)
if not tsadir:
tsadir = os.path.join(os.path.dirname(ifgdir),
'TS_' + os.path.basename(ifgdir))
if not os.path.isdir(tsadir):
print('\nNo {} exists!'.format(tsadir), file=sys.stderr)
return 1
tsadir = os.path.abspath(tsadir)
loopdir = os.path.join(tsadir, '12loop')
if not os.path.exists(loopdir): os.mkdir(loopdir)
loop_pngdir = os.path.join(loopdir, 'good_loop_png')
bad_loop_pngdir = os.path.join(loopdir, 'bad_loop_png')
bad_loop_cand_pngdir = os.path.join(loopdir, 'bad_loop_cand_png')
if os.path.exists(loop_pngdir):
shutil.move(loop_pngdir + '/', loop_pngdir + '_old') #move to old dir
if os.path.exists(bad_loop_pngdir):
for png in glob.glob(bad_loop_pngdir + '/*.png'):
shutil.move(png, loop_pngdir + '_old') #move to old dir
shutil.rmtree(bad_loop_pngdir)
if os.path.exists(bad_loop_cand_pngdir):
for png in glob.glob(bad_loop_cand_pngdir + '/*.png'):
shutil.move(png, loop_pngdir + '_old') #move to old dir
shutil.rmtree(bad_loop_cand_pngdir)
os.mkdir(loop_pngdir)
os.mkdir(bad_loop_pngdir)
os.mkdir(bad_loop_cand_pngdir)
ifg_rasdir = os.path.join(tsadir, '12ifg_ras')
if os.path.isdir(ifg_rasdir): shutil.rmtree(ifg_rasdir)
os.mkdir(ifg_rasdir)
bad_ifgrasdir = os.path.join(tsadir, '12bad_ifg_ras')
if os.path.isdir(bad_ifgrasdir): shutil.rmtree(bad_ifgrasdir)
os.mkdir(bad_ifgrasdir)
bad_ifg_candrasdir = os.path.join(tsadir, '12bad_ifg_cand_ras')
if os.path.isdir(bad_ifg_candrasdir): shutil.rmtree(bad_ifg_candrasdir)
os.mkdir(bad_ifg_candrasdir)
no_loop_ifgrasdir = os.path.join(tsadir, '12no_loop_ifg_ras')
if os.path.isdir(no_loop_ifgrasdir): shutil.rmtree(no_loop_ifgrasdir)
os.mkdir(no_loop_ifgrasdir)
infodir = os.path.join(tsadir, 'info')
if not os.path.exists(infodir): os.mkdir(infodir)
resultsdir = os.path.join(tsadir, 'results')
if not os.path.exists(resultsdir): os.mkdir(resultsdir)
netdir = os.path.join(tsadir, 'network')
#%% Read date, network information and size
### Get dates
ifgdates = tools_lib.get_ifgdates(ifgdir)
### Read bad_ifg11
bad_ifg11file = os.path.join(infodir, '11bad_ifg.txt')
bad_ifg11 = io_lib.read_ifg_list(bad_ifg11file)
### Remove bad ifgs and images from list
ifgdates = list(set(ifgdates) - set(bad_ifg11))
ifgdates.sort()
imdates = tools_lib.ifgdates2imdates(ifgdates)
n_ifg = len(ifgdates)
n_im = len(imdates)
### Get size
mlipar = os.path.join(ifgdir, 'slc.mli.par')
width = int(io_lib.get_param_par(mlipar, 'range_samples'))
length = int(io_lib.get_param_par(mlipar, 'azimuth_lines'))
### Get loop matrix
Aloop = loop_lib.make_loop_matrix(ifgdates)
n_loop = Aloop.shape[0]
### Extract no loop ifgs
ns_loop4ifg = np.abs(Aloop).sum(axis=0)
ixs_ifg_no_loop = np.where(ns_loop4ifg == 0)[0]
no_loop_ifg = [ifgdates[ix] for ix in ixs_ifg_no_loop]
#%% 1st loop closure check. First without reference
_n_para = n_para if n_para < n_loop else n_loop
print('\n1st Loop closure check and make png for all possible {} loops,'.
format(n_loop),
flush=True)
print('with {} parallel processing...'.format(_n_para), flush=True)
bad_ifg_cand = []
good_ifg = []
### Parallel processing
p = multi.Pool(_n_para)
loop_ph_rms_ifg = np.array(p.map(loop_closure_1st_wrapper, range(n_loop)),
dtype=np.float32)
p.close()
for i in range(n_loop):
### Find index of ifg
ix_ifg12, ix_ifg23 = np.where(Aloop[i, :] == 1)[0]
ix_ifg13 = np.where(Aloop[i, :] == -1)[0][0]
ifgd12 = ifgdates[ix_ifg12]
ifgd23 = ifgdates[ix_ifg23]
ifgd13 = ifgdates[ix_ifg13]
### List as good or bad candidate
if loop_ph_rms_ifg[i] >= loop_thre: #Bad loop including bad ifg.
bad_ifg_cand.extend([ifgd12, ifgd23, ifgd13])
else:
good_ifg.extend([ifgd12, ifgd23, ifgd13])
if os.path.exists(loop_pngdir + '_old/'):
shutil.rmtree(loop_pngdir + '_old/')
#%% Identify bad ifgs and output text
bad_ifg = loop_lib.identify_bad_ifg(bad_ifg_cand, good_ifg)
bad_ifgfile = os.path.join(loopdir, 'bad_ifg_loop.txt')
with open(bad_ifgfile, 'w') as f:
for i in bad_ifg:
print('{}'.format(i), file=f)
### Compute n_unw without bad_ifg11 and bad_ifg
n_unw = np.zeros((length, width), dtype=np.int16)
for ifgd in ifgdates:
if ifgd in bad_ifg:
continue
unwfile = os.path.join(ifgdir, ifgd, ifgd + '.unw')
unw = io_lib.read_img(unwfile, length, width)
unw[unw == 0] = np.nan # Fill 0 with nan
n_unw += ~np.isnan(unw) # Summing number of unnan unw
#%% 2nd loop closure check without bad ifgs to define stable ref area
### Devide n_loop for paralell proc
_n_para2, args = tools_lib.get_patchrow(1, n_loop, 2**20 / 4,
int(np.ceil(n_loop / n_para)))
print('\n2nd Loop closure check without bad ifgs to define ref area...',
flush=True)
print('with {} parallel processing...'.format(_n_para2), flush=True)
### Parallel processing
p = multi.Pool(_n_para2)
res = np.array(p.map(loop_closure_2nd_wrapper, args), dtype=np.float32)
p.close()
ns_loop_ph = np.sum(res[:, 0, :, :, ], axis=0)
ns_loop_ph[ns_loop_ph == 0] = np.nan # To avoid 0 division
ns_bad_loop = np.sum(res[:, 1, :, :, ], axis=0)
loop_ph_rms_points = np.sum(res[:, 2, :, :, ], axis=0)
loop_ph_rms_points = np.sqrt(loop_ph_rms_points / ns_loop_ph)
### Find stable ref area which have all n_unw and minimum ns_bad_loop and loop_ph_rms_points
mask1 = (n_unw == np.nanmax(n_unw))
min_ns_bad_loop = np.nanmin(ns_bad_loop)
while True:
mask2 = (ns_bad_loop == min_ns_bad_loop)
if np.all(~(mask1 * mask2)): ## All masked
min_ns_bad_loop = min_ns_bad_loop + 1 ## Make mask2 again
else:
break
loop_ph_rms_points_masked = loop_ph_rms_points * mask1 * mask2
loop_ph_rms_points_masked[loop_ph_rms_points_masked == 0] = np.nan
refyx = np.where(
loop_ph_rms_points_masked == np.nanmin(loop_ph_rms_points_masked))
refy1 = refyx[0][0] # start from 0, not 1
refy2 = refyx[0][
0] + 1 # shift +1 for python custom. start from 1 end with width
refx1 = refyx[1][0]
refx2 = refyx[1][0] + 1
### Save 12ref.txt
reffile = os.path.join(infodir, '12ref.txt')
with open(reffile, 'w') as f:
print('{0}:{1}/{2}:{3}'.format(refx1, refx2, refy1, refy2), file=f)
### Save loop_ph_rms_masked and png
loop_ph_rms_maskedfile = os.path.join(loopdir, 'loop_ph_rms_masked')
loop_ph_rms_points_masked.tofile(loop_ph_rms_maskedfile)
cmax = np.nanpercentile(loop_ph_rms_points_masked, 95)
pngfile = loop_ph_rms_maskedfile + '.png'
title = 'RMS of loop phase (rad)'
plot_lib.make_im_png(loop_ph_rms_points_masked, pngfile, cmap_noise_r,
title, None, cmax)
### Check ref exist in unw. If not, list as noref_ifg
noref_ifg = []
for ifgd in ifgdates:
if ifgd in bad_ifg:
continue
unwfile = os.path.join(ifgdir, ifgd, ifgd + '.unw')
unw_ref = io_lib.read_img(unwfile, length, width)[refy1:refy2,
refx1:refx2]
unw_ref[unw_ref == 0] = np.nan # Fill 0 with nan
if np.all(np.isnan(unw_ref)):
noref_ifg.append(ifgd)
bad_ifgfile = os.path.join(loopdir, 'bad_ifg_noref.txt')
with open(bad_ifgfile, 'w') as f:
for i in noref_ifg:
print('{}'.format(i), file=f)
#%% 3rd loop closure check without bad ifgs wrt ref point
print('\n3rd loop closure check taking into account ref phase...',
flush=True)
print('with {} parallel processing...'.format(_n_para), flush=True)
### Parallel processing
p = multi.Pool(_n_para)
loop_ph_rms_ifg2 = list(
np.array(p.map(loop_closure_3rd_wrapper, range(n_loop)),
dtype=np.float32))
p.close()
bad_ifg_cand2 = []
good_ifg2 = []
### List as good or bad candidate
for i in range(n_loop):
if np.isnan(loop_ph_rms_ifg2[i]): # Skipped
loop_ph_rms_ifg2[i] = '--' ## Replace
elif loop_ph_rms_ifg2[i] >= loop_thre: #Bad loop including bad ifg.
bad_ifg_cand2.extend([ifgd12, ifgd23, ifgd13])
else:
good_ifg2.extend([ifgd12, ifgd23, ifgd13])
#%% Identify additional bad ifgs and output text
bad_ifg2 = loop_lib.identify_bad_ifg(bad_ifg_cand2, good_ifg2)
bad_ifgfile = os.path.join(loopdir, 'bad_ifg_loopref.txt')
with open(bad_ifgfile, 'w') as f:
for i in bad_ifg2:
print('{}'.format(i), file=f)
#%% Output all bad ifg list and identify remaining candidate of bad ifgs
### Merge bad ifg, bad_ifg2, noref_ifg
bad_ifg_all = list(set(bad_ifg + bad_ifg2 + noref_ifg)) # Remove multiple
bad_ifg_all.sort()
ifgdates_good = list(set(ifgdates) - set(bad_ifg_all))
ifgdates_good.sort()
bad_ifgfile = os.path.join(infodir, '12bad_ifg.txt')
with open(bad_ifgfile, 'w') as f:
for i in bad_ifg_all:
print('{}'.format(i), file=f)
### Identify removed image and output file
imdates_good = tools_lib.ifgdates2imdates(ifgdates_good)
imdates_bad = list(set(imdates) - set(imdates_good))
imdates_bad.sort()
bad_imfile = os.path.join(infodir, '12removed_image.txt')
with open(bad_imfile, 'w') as f:
for i in imdates_bad:
print('{}'.format(i), file=f)
### Remaining candidate of bad ifg
bad_ifg_cand_res = list(set(bad_ifg_cand2) - set(bad_ifg_all))
bad_ifg_cand_res.sort()
bad_ifg_candfile = os.path.join(infodir, '12bad_ifg_cand.txt')
with open(bad_ifg_candfile, 'w') as f:
for i in bad_ifg_cand_res:
print('{}'.format(i), file=f)
#%% 4th loop to be used to calc n_loop_err and n_ifg_noloop
print('\n4th loop to compute statistics...', flush=True)
print('with {} parallel processing...'.format(_n_para2), flush=True)
### Parallel processing
p = multi.Pool(_n_para2)
res = np.array(p.map(loop_closure_4th_wrapper, args), dtype=np.int16)
p.close()
ns_loop_err = np.sum(res[:, :, :, ], axis=0)
#%% Output loop info, move bad_loop_png
loop_info_file = os.path.join(loopdir, 'loop_info.txt')
f = open(loop_info_file, 'w')
print('# loop_thre: {} rad. *: Removed w/o ref, **: Removed w/ ref'.format(
loop_thre),
file=f)
print('# /: Candidates of bad loops but causative ifgs unidentified',
file=f)
print('# image1 image2 image3 RMS w/oref w/ref', file=f)
for i in range(n_loop):
### Find index of ifg
ix_ifg12, ix_ifg23 = np.where(Aloop[i, :] == 1)[0]
ix_ifg13 = np.where(Aloop[i, :] == -1)[0][0]
ifgd12 = ifgdates[ix_ifg12]
ifgd23 = ifgdates[ix_ifg23]
ifgd13 = ifgdates[ix_ifg13]
imd1 = ifgd12[:8]
imd2 = ifgd23[:8]
imd3 = ifgd23[-8:]
## Move loop_png if bad ifg or bad ifg_cand is included
looppngfile = os.path.join(
loop_pngdir, '{0}_{1}_{2}_loop.png'.format(imd1, imd2, imd3))
badlooppngfile = os.path.join(
bad_loop_pngdir, '{0}_{1}_{2}_loop.png'.format(imd1, imd2, imd3))
badloopcandpngfile = os.path.join(
bad_loop_cand_pngdir,
'{0}_{1}_{2}_loop.png'.format(imd1, imd2, imd3))
badloopflag1 = ' '
badloopflag2 = ' '
if ifgd12 in bad_ifg or ifgd23 in bad_ifg or ifgd13 in bad_ifg:
badloopflag1 = '*'
shutil.move(looppngfile, badlooppngfile)
elif ifgd12 in bad_ifg2 or ifgd23 in bad_ifg2 or ifgd13 in bad_ifg2:
badloopflag2 = '**'
shutil.move(looppngfile, badlooppngfile)
elif ifgd12 in bad_ifg_cand_res or ifgd23 in bad_ifg_cand_res or ifgd13 in bad_ifg_cand_res:
badloopflag1 = '/'
if os.path.exists(looppngfile):
shutil.move(looppngfile, badloopcandpngfile)
if type(loop_ph_rms_ifg2[i]) == np.float32:
str_loop_ph_rms_ifg2 = "{:.2f}".format(loop_ph_rms_ifg2[i])
else: ## --
str_loop_ph_rms_ifg2 = loop_ph_rms_ifg2[i]
print('{0} {1} {2} {3:5.2f} {4} {5:5s} {6}'.format(
imd1, imd2, imd3, loop_ph_rms_ifg[i], badloopflag1,
str_loop_ph_rms_ifg2, badloopflag2),
file=f)
f.close()
#%% Saving coh_avg, n_unw, and n_loop_err only for good ifgs
print('\nSaving coh_avg, n_unw, and n_loop_err...', flush=True)
### Calc coh avg and n_unw
coh_avg = np.zeros((length, width), dtype=np.float32)
n_coh = np.zeros((length, width), dtype=np.int16)
n_unw = np.zeros((length, width), dtype=np.int16)
for ifgd in ifgdates_good:
ccfile = os.path.join(ifgdir, ifgd, ifgd + '.cc')
if os.path.getsize(ccfile) == length * width:
coh = io_lib.read_img(ccfile, length, width, np.uint8)
coh = coh.astype(np.float32) / 255
else:
coh = io_lib.read_img(ccfile, length, width)
coh[np.isnan(coh)] = 0 # Fill nan with 0
coh_avg += coh
n_coh += (coh != 0)
unwfile = os.path.join(ifgdir, ifgd, ifgd + '.unw')
unw = io_lib.read_img(unwfile, length, width)
unw[unw == 0] = np.nan # Fill 0 with nan
n_unw += ~np.isnan(unw) # Summing number of unnan unw
coh_avg[n_coh == 0] = np.nan
n_coh[n_coh == 0] = 1 #to avoid zero division
coh_avg = coh_avg / n_coh
### Save files
n_unwfile = os.path.join(resultsdir, 'n_unw')
np.float32(n_unw).tofile(n_unwfile)
coh_avgfile = os.path.join(resultsdir, 'coh_avg')
coh_avg.tofile(coh_avgfile)
n_loop_errfile = os.path.join(resultsdir, 'n_loop_err')
np.float32(ns_loop_err).tofile(n_loop_errfile)
### Save png
title = 'Average coherence'
plot_lib.make_im_png(coh_avg, coh_avgfile + '.png', cmap_noise, title)
title = 'Number of used unw data'
plot_lib.make_im_png(n_unw, n_unwfile + '.png', cmap_noise, title, n_im)
title = 'Number of unclosed loops'
plot_lib.make_im_png(ns_loop_err, n_loop_errfile + '.png', cmap_noise_r,
title)
#%% Link ras
### First, identify suffix of raster image (ras, bmp, or png?)
unwfile = os.path.join(ifgdir, ifgdates[0], ifgdates[0] + '.unw')
if os.path.exists(unwfile + '.ras'):
suffix = '.ras'
elif os.path.exists(unwfile + '.bmp'):
suffix = '.bmp'
elif os.path.exists(unwfile + '.png'):
suffix = '.png'
for ifgd in ifgdates:
rasname = ifgd + '.unw' + suffix
rasorg = os.path.join(ifgdir, ifgd, rasname)
### Bad ifgs
if ifgd in bad_ifg_all:
os.symlink(os.path.relpath(rasorg, bad_ifgrasdir),
os.path.join(bad_ifgrasdir, rasname))
### Remaining bad ifg candidates
elif ifgd in bad_ifg_cand_res:
os.symlink(os.path.relpath(rasorg, bad_ifg_candrasdir),
os.path.join(bad_ifg_candrasdir, rasname))
### Good ifgs
else:
os.symlink(os.path.relpath(rasorg, ifg_rasdir),
os.path.join(ifg_rasdir, rasname))
if ifgd in no_loop_ifg:
os.symlink(os.path.relpath(rasorg, no_loop_ifgrasdir),
os.path.join(no_loop_ifgrasdir, rasname))
#%% Plot network
## Read bperp data or dummy
bperp_file = os.path.join(ifgdir, 'baselines')
if os.path.exists(bperp_file):
bperp = io_lib.read_bperp_file(bperp_file, imdates)
else: #dummy
bperp = np.random.random(n_im).tolist()
pngfile = os.path.join(netdir, 'network12_all.png')
plot_lib.plot_network(ifgdates, bperp, [], pngfile)
pngfile = os.path.join(netdir, 'network12.png')
plot_lib.plot_network(ifgdates, bperp, bad_ifg_all, pngfile)
pngfile = os.path.join(netdir, 'network12_nobad.png')
plot_lib.plot_network(ifgdates,
bperp,
bad_ifg_all,
pngfile,
plot_bad=False)
### Network info
## Identify gaps
G = inv_lib.make_sb_matrix(ifgdates_good)
ixs_inc_gap = np.where(G.sum(axis=0) == 0)[0]
## Connected network
ix1 = 0
connected_list = []
for ix2 in np.append(ixs_inc_gap,
len(imdates_good) - 1): #append for last image
imd1 = imdates_good[ix1]
imd2 = imdates_good[ix2]
dyear = (dt.datetime.strptime(imd2, '%Y%m%d').toordinal() -
dt.datetime.strptime(imd1, '%Y%m%d').toordinal()) / 365.25
n_im_connect = ix2 - ix1 + 1
connected_list.append(
[imdates_good[ix1], imdates_good[ix2], dyear, n_im_connect])
ix1 = ix2 + 1 # Next connection
#%% Caution about no_loop ifg, remaining large RMS loop and gap
### no_loop ifg
if len(no_loop_ifg) != 0:
no_loop_ifgfile = os.path.join(infodir, '12no_loop_ifg.txt')
with open(no_loop_ifgfile, 'w') as f:
print(
"\nThere are {} ifgs without loop, recommend to check manually in no_loop_ifg_ras12"
.format(len(no_loop_ifg)),
flush=True)
for ifgd in no_loop_ifg:
print('{}'.format(ifgd), flush=True)
print('{}'.format(ifgd), file=f)
### Remaining candidates of bad ifgs
if len(bad_ifg_cand_res) != 0:
print(
"\nThere are {} remaining candidates of bad ifgs but not identified."
.format(len(bad_ifg_cand_res)),
flush=True)
print("Check 12bad_ifg_cand_ras and loop/bad_loop_cand_png.",
flush=True)
# for ifgd in bad_ifg_cand_res:
# print('{}'.format(ifgd))
print('\n{0}/{1} ifgs are discarded from further processing.'.format(
len(bad_ifg_all), n_ifg),
flush=True)
for ifgd in bad_ifg_all:
print('{}'.format(ifgd), flush=True)
### Gap
gap_infofile = os.path.join(infodir, '12network_gap_info.txt')
with open(gap_infofile, 'w') as f:
if ixs_inc_gap.size != 0:
print("Gaps between:", file=f)
print("\nGaps in network between:", flush=True)
for ix in ixs_inc_gap:
print("{} {}".format(imdates_good[ix], imdates_good[ix + 1]),
file=f)
print("{} {}".format(imdates_good[ix], imdates_good[ix + 1]),
flush=True)
print("\nConnected network (year, n_image):", file=f)
print("\nConnected network (year, n_image):", flush=True)
for list1 in connected_list:
print("{0}-{1} ({2:.2f}, {3})".format(list1[0], list1[1], list1[2],
list1[3]),
file=f)
print("{0}-{1} ({2:.2f}, {3})".format(list1[0], list1[1], list1[2],
list1[3]),
flush=True)
print(
'\nIf you want to change the bad ifgs to be discarded, re-run with different thresholds before next step.',
flush=True)
#%% Finish
elapsed_time = time.time() - start
hour = int(elapsed_time / 3600)
minite = int(np.mod((elapsed_time / 60), 60))
sec = int(np.mod(elapsed_time, 60))
print("\nElapsed time: {0:02}h {1:02}m {2:02}s".format(hour, minite, sec))
print('\n{} Successfully finished!!\n'.format(os.path.basename(argv[0])))
print('Output directory: {}\n'.format(os.path.relpath(tsadir)))
def main(argv=None):
#%% Check argv
if argv == None:
argv = sys.argv
start = time.time()
ver = "1.4.8"
date = 20210127
author = "Y. Morishita"
print("\n{} ver{} {} {}".format(os.path.basename(argv[0]), ver, date,
author),
flush=True)
print("{} {}".format(os.path.basename(argv[0]), ' '.join(argv[1:])),
flush=True)
## For parallel processing
global n_para_gap, G, Aloop, unwpatch, imdates, incdir, ifgdir, length, width,\
coef_r2m, ifgdates, ref_unw, cycle, keep_incfile, resdir, restxtfile, \
cmap_vel, cmap_wrap, wavelength
#%% Set default
ifgdir = []
tsadir = []
inv_alg = 'LS'
try:
n_para = len(os.sched_getaffinity(0))
except:
n_para = multi.cpu_count()
n_para_inv = 1
memory_size = 4000
gamma = 0.0001
n_unw_r_thre = []
keep_incfile = False
cmap_vel = SCM.roma.reversed()
cmap_noise = 'viridis'
cmap_noise_r = 'viridis_r'
cmap_wrap = SCM.romaO
# q = multi.get_context('fork')
q = multi.get_context('spawn')
compress = 'gzip'
#%% Read options
try:
try:
opts, args = getopt.getopt(argv[1:], "hd:t:", [
"help", "mem_size=", "gamma=", "n_unw_r_thre=", "keep_incfile",
"inv_alg=", "n_para="
])
except getopt.error as msg:
raise Usage(msg)
for o, a in opts:
if o == '-h' or o == '--help':
print(__doc__)
return 0
elif o == '-d':
ifgdir = a
elif o == '-t':
tsadir = a
elif o == '--mem_size':
memory_size = float(a)
elif o == '--gamma':
gamma = float(a)
elif o == '--n_unw_r_thre':
n_unw_r_thre = float(a)
elif o == '--keep_incfile':
keep_incfile = True
elif o == '--inv_alg':
inv_alg = a
elif o == '--n_para':
n_para = int(a)
if not ifgdir:
raise Usage('No data directory given, -d is not optional!')
elif not os.path.isdir(ifgdir):
raise Usage('No {} dir exists!'.format(ifgdir))
elif not os.path.exists(os.path.join(ifgdir, 'slc.mli.par')):
raise Usage('No slc.mli.par file exists in {}!'.format(ifgdir))
except Usage as err:
print("\nERROR:", file=sys.stderr, end='')
print(" " + str(err.msg), file=sys.stderr)
print("\nFor help, use -h or --help.\n", file=sys.stderr)
return 2
#%% Directory settings
ifgdir = os.path.abspath(ifgdir)
if not tsadir:
tsadir = os.path.join(os.path.dirname(ifgdir),
'TS_' + os.path.basename(ifgdir))
if not os.path.isdir(tsadir):
print('\nNo {} exists!'.format(tsadir), file=sys.stderr)
return 1
tsadir = os.path.abspath(tsadir)
resultsdir = os.path.join(tsadir, 'results')
infodir = os.path.join(tsadir, 'info')
netdir = os.path.join(tsadir, 'network')
bad_ifg11file = os.path.join(infodir, '11bad_ifg.txt')
bad_ifg12file = os.path.join(infodir, '12bad_ifg.txt')
reffile = os.path.join(infodir, '12ref.txt')
if not os.path.exists(reffile): ## for old LiCSBAS12 < v1.1
reffile = os.path.join(infodir, 'ref.txt')
incdir = os.path.join(tsadir, '13increment')
if not os.path.exists(incdir): os.mkdir(incdir)
resdir = os.path.join(tsadir, '13resid')
if not os.path.exists(resdir): os.mkdir(resdir)
restxtfile = os.path.join(infodir, '13resid.txt')
cumh5file = os.path.join(tsadir, 'cum.h5')
#%% Check files
try:
if not os.path.exists(bad_ifg11file):
raise Usage('No 11bad_ifg.txt file exists in {}!'.format(infodir))
if not os.path.exists(bad_ifg12file):
raise Usage('No 12bad_ifg.txt file exists in {}!'.format(infodir))
if not os.path.exists(reffile):
raise Usage('No 12ref.txt file exists in {}!'.format(infodir))
except Usage as err:
print("\nERROR:", file=sys.stderr, end='')
print(" " + str(err.msg), file=sys.stderr)
print("\nFor help, use -h or --help.\n", file=sys.stderr)
return 2
#%% Set preliminaly reference
with open(reffile, "r") as f:
refarea = f.read().split()[0] #str, x1/x2/y1/y2
refx1, refx2, refy1, refy2 = [int(s) for s in re.split('[:/]', refarea)]
#%% Check RAM
mem_avail = (psutil.virtual_memory().available) / 2**20 #MB
if memory_size > mem_avail / 2:
print('\nNot enough memory available compared to mem_size ({} MB).'.
format(memory_size))
print('Reduce mem_size automatically to {} MB.'.format(
int(mem_avail / 2)))
memory_size = int(mem_avail / 2)
#%% Read data information
### Get size
mlipar = os.path.join(ifgdir, 'slc.mli.par')
width = int(io_lib.get_param_par(mlipar, 'range_samples'))
length = int(io_lib.get_param_par(mlipar, 'azimuth_lines'))
speed_of_light = 299792458 #m/s
radar_frequency = float(io_lib.get_param_par(mlipar,
'radar_frequency')) #Hz
wavelength = speed_of_light / radar_frequency #meter
coef_r2m = -wavelength / 4 / np.pi * 1000 #rad -> mm, positive is -LOS
### Calc pixel spacing depending on IFG or GEOC, used in later spatial filter
dempar = os.path.join(ifgdir, 'EQA.dem_par')
width_geo = int(io_lib.get_param_par(dempar, 'width'))
length_geo = int(io_lib.get_param_par(dempar, 'nlines'))
dlat = float(io_lib.get_param_par(dempar, 'post_lat')) #negative
dlon = float(io_lib.get_param_par(dempar, 'post_lon')) #positive
lat1 = float(io_lib.get_param_par(dempar, 'corner_lat'))
lon1 = float(io_lib.get_param_par(dempar, 'corner_lon'))
if width == width_geo and length == length_geo: ## Geocoded
print('\nIn geographical coordinates', flush=True)
centerlat = lat1 + dlat * (length / 2)
ra = float(io_lib.get_param_par(dempar, 'ellipsoid_ra'))
recip_f = float(
io_lib.get_param_par(dempar, 'ellipsoid_reciprocal_flattening'))
rb = ra * (1 - 1 / recip_f) ## polar radius
pixsp_a = 2 * np.pi * rb / 360 * abs(dlat)
pixsp_r = 2 * np.pi * ra / 360 * dlon * np.cos(np.deg2rad(centerlat))
else:
print('\nIn radar coordinates', flush=True)
pixsp_r_org = float(io_lib.get_param_par(mlipar,
'range_pixel_spacing'))
pixsp_a = float(io_lib.get_param_par(mlipar, 'azimuth_pixel_spacing'))
inc_agl = float(io_lib.get_param_par(mlipar, 'incidence_angle'))
pixsp_r = pixsp_r_org / np.sin(np.deg2rad(inc_agl))
### Set n_unw_r_thre and cycle depending on L- or C-band
if wavelength > 0.2: ## L-band
if not n_unw_r_thre: n_unw_r_thre = 0.5
cycle = 1.5 # 2pi/cycle for comparison png
elif wavelength <= 0.2: ## C-band
if not n_unw_r_thre: n_unw_r_thre = 1.0
cycle = 3 # 3*2pi/cycle for comparison png
#%% Read date and network information
### Get all ifgdates in ifgdir
ifgdates_all = tools_lib.get_ifgdates(ifgdir)
imdates_all = tools_lib.ifgdates2imdates(ifgdates_all)
n_im_all = len(imdates_all)
n_ifg_all = len(ifgdates_all)
### Read bad_ifg11 and 12
bad_ifg11 = io_lib.read_ifg_list(bad_ifg11file)
bad_ifg12 = io_lib.read_ifg_list(bad_ifg12file)
bad_ifg_all = list(set(bad_ifg11 + bad_ifg12))
bad_ifg_all.sort()
### Remove bad ifgs and images from list
ifgdates = list(set(ifgdates_all) - set(bad_ifg_all))
ifgdates.sort()
imdates = tools_lib.ifgdates2imdates(ifgdates)
n_ifg = len(ifgdates)
n_ifg_bad = len(set(bad_ifg11 + bad_ifg12))
n_im = len(imdates)
n_unw_thre = int(n_unw_r_thre * n_im)
### Make 13used_image.txt
imfile = os.path.join(infodir, '13used_image.txt')
with open(imfile, 'w') as f:
for i in imdates:
print('{}'.format(i), file=f)
### Calc dt in year
imdates_dt = ([
dt.datetime.strptime(imd, '%Y%m%d').toordinal() for imd in imdates
])
dt_cum = np.float32((np.array(imdates_dt) - imdates_dt[0]) / 365.25)
### Construct G and Aloop matrix for increment and n_gap
G = inv_lib.make_sb_matrix(ifgdates)
Aloop = loop_lib.make_loop_matrix(ifgdates)
#%% Plot network
## Read bperp data or dummy
bperp_file = os.path.join(ifgdir, 'baselines')
if os.path.exists(bperp_file):
bperp_all = io_lib.read_bperp_file(bperp_file, imdates_all)
bperp = io_lib.read_bperp_file(bperp_file, imdates)
else: #dummy
bperp_all = np.random.random(len(imdates_all)).tolist()
bperp = np.random.random(n_im).tolist()
pngfile = os.path.join(netdir, 'network13_all.png')
plot_lib.plot_network(ifgdates_all, bperp_all, [], pngfile)
pngfile = os.path.join(netdir, 'network13.png')
plot_lib.plot_network(ifgdates_all, bperp_all, bad_ifg_all, pngfile)
pngfile = os.path.join(netdir, 'network13_nobad.png')
plot_lib.plot_network(ifgdates_all,
bperp_all,
bad_ifg_all,
pngfile,
plot_bad=False)
#%% Get patch row number
if inv_alg == 'WLS':
n_store_data = n_ifg * 3 + n_im * 2 + n_im * 0.3 #
else:
n_store_data = n_ifg * 2 + n_im * 2 + n_im * 0.3 #not sure
n_patch, patchrow = tools_lib.get_patchrow(width, length, n_store_data,
memory_size)
#%% Display and output settings & parameters
print('')
print('Size of image (w,l) : {}, {}'.format(width, length))
print('# of all images : {}'.format(n_im_all))
print('# of images to be used : {}'.format(n_im))
print('# of all ifgs : {}'.format(n_ifg_all))
print('# of ifgs to be used : {}'.format(n_ifg))
print('# of removed ifgs : {}'.format(n_ifg_bad))
print('Threshold of used unw : {}'.format(n_unw_thre))
print('')
print('Reference area (X/Y) : {}:{}/{}:{}'.format(
refx1, refx2, refy1, refy2))
print('Allowed memory size : {} MB'.format(memory_size))
print('Number of patches : {}'.format(n_patch))
print('Inversion algorism : {}'.format(inv_alg))
print('Gamma value : {}'.format(gamma), flush=True)
with open(os.path.join(infodir, '13parameters.txt'), "w") as f:
print('range_samples: {}'.format(width), file=f)
print('azimuth_lines: {}'.format(length), file=f)
print('wavelength: {}'.format(wavelength), file=f)
print('n_im_all: {}'.format(n_im_all), file=f)
print('n_im: {}'.format(n_im), file=f)
print('n_ifg_all: {}'.format(n_ifg_all), file=f)
print('n_ifg: {}'.format(n_ifg), file=f)
print('n_ifg_bad: {}'.format(n_ifg_bad), file=f)
print('n_unw_thre: {}'.format(n_unw_thre), file=f)
print('ref_area: {}:{}/{}:{}'.format(refx1, refx2, refy1, refy2),
file=f)
print('memory_size: {} MB'.format(memory_size), file=f)
print('n_patch: {}'.format(n_patch), file=f)
print('inv_alg: {}'.format(inv_alg), file=f)
print('gamma: {}'.format(gamma), file=f)
print('pixel_spacing_r: {:.2f} m'.format(pixsp_r), file=f)
print('pixel_spacing_a: {:.2f} m'.format(pixsp_a), file=f)
#%% Ref phase for inversion
lengththis = refy2 - refy1
countf = width * refy1
countl = width * lengththis # Number to be read
ref_unw = []
for i, ifgd in enumerate(ifgdates):
unwfile = os.path.join(ifgdir, ifgd, ifgd + '.unw')
f = open(unwfile, 'rb')
f.seek(countf * 4, os.SEEK_SET) #Seek for >=2nd path, 4 means byte
### Read unw data (mm) at ref area
unw = np.fromfile(f, dtype=np.float32, count=countl).reshape(
(lengththis, width))[:, refx1:refx2] * coef_r2m
unw[unw == 0] = np.nan
if np.all(np.isnan(unw)):
print('All nan in ref area in {}.'.format(ifgd))
print('Rerun LiCSBAS12.')
return 1
ref_unw.append(np.nanmean(unw))
f.close()
#%% Open cum.h5 for output
if os.path.exists(cumh5file): os.remove(cumh5file)
cumh5 = h5.File(cumh5file, 'w')
cumh5.create_dataset('imdates', data=[np.int32(imd) for imd in imdates])
if not np.all(np.abs(np.array(bperp)) <= 1): # if not dummy
cumh5.create_dataset('bperp', data=bperp)
cum = cumh5.require_dataset('cum', (n_im, length, width),
dtype=np.float32,
compression=compress)
vel = cumh5.require_dataset('vel', (length, width),
dtype=np.float32,
compression=compress)
vconst = cumh5.require_dataset('vintercept', (length, width),
dtype=np.float32,
compression=compress)
gap = cumh5.require_dataset('gap', (n_im - 1, length, width),
dtype=np.int8,
compression=compress)
if width == width_geo and length == length_geo: ## if geocoded
cumh5.create_dataset('corner_lat', data=lat1)
cumh5.create_dataset('corner_lon', data=lon1)
cumh5.create_dataset('post_lat', data=dlat)
cumh5.create_dataset('post_lon', data=dlon)
#%% For each patch
for i_patch, rows in enumerate(patchrow):
print('\nProcess {0}/{1}th line ({2}/{3}th patch)...'.format(
rows[1], patchrow[-1][-1], i_patch + 1, n_patch),
flush=True)
start2 = time.time()
#%% Read data
### Allocate memory
lengththis = rows[1] - rows[0]
n_pt_all = lengththis * width
unwpatch = np.zeros((n_ifg, lengththis, width), dtype=np.float32)
if inv_alg == 'WLS':
cohpatch = np.zeros((n_ifg, lengththis, width), dtype=np.float32)
### For each ifg
print(" Reading {0} ifg's unw data...".format(n_ifg), flush=True)
countf = width * rows[0]
countl = width * lengththis
for i, ifgd in enumerate(ifgdates):
unwfile = os.path.join(ifgdir, ifgd, ifgd + '.unw')
f = open(unwfile, 'rb')
f.seek(countf * 4,
os.SEEK_SET) #Seek for >=2nd patch, 4 means byte
### Read unw data (mm) at patch area
unw = np.fromfile(f, dtype=np.float32, count=countl).reshape(
(lengththis, width)) * coef_r2m
unw[unw == 0] = np.nan # Fill 0 with nan
unw = unw - ref_unw[i]
unwpatch[i] = unw
f.close()
### Read coh file at patch area for WLS
if inv_alg == 'WLS':
cohfile = os.path.join(ifgdir, ifgd, ifgd + '.cc')
f = open(cohfile, 'rb')
if os.path.getsize(cohfile) == length * width: ## uint8 format
f.seek(countf, os.SEEK_SET) #Seek for >=2nd patch
cohpatch[i, :, :] = (np.fromfile(
f, dtype=np.uint8, count=countl).reshape(
(lengththis, width))).astype(np.float32) / 255
else: ## old float32 format
f.seek(countf * 4,
os.SEEK_SET) #Seek for >=2nd patch, 4 means byte
cohpatch[i, :, :] = np.fromfile(f,
dtype=np.float32,
count=countl).reshape(
(lengththis, width))
cohpatch[cohpatch == 0] = np.nan
unwpatch = unwpatch.reshape(
(n_ifg, n_pt_all)).transpose() #(n_pt_all, n_ifg)
### Calc variance from coherence for WLS
if inv_alg == 'WLS':
cohpatch = cohpatch.reshape(
(n_ifg, n_pt_all)).transpose() #(n_pt_all, n_ifg)
cohpatch[
cohpatch <
0.01] = 0.01 ## because negative value possible due to geocode
cohpatch[
cohpatch > 0.99] = 0.99 ## because >1 possible due to geocode
varpatch = (1 - cohpatch**2) / (2 * cohpatch**2)
del cohpatch
#%% Remove points with less valid data than n_unw_thre
ix_unnan_pt = np.where(
np.sum(~np.isnan(unwpatch), axis=1) > n_unw_thre)[0]
n_pt_unnan = len(ix_unnan_pt)
unwpatch = unwpatch[ix_unnan_pt, :] ## keep only unnan data
if inv_alg == 'WLS':
varpatch = varpatch[ix_unnan_pt, :] ## keep only unnan data
print(' {}/{} points removed due to not enough ifg data...'.format(
n_pt_all - n_pt_unnan, n_pt_all),
flush=True)
#%% Compute number of gaps, ifg_noloop, maxTlen point-by-point
if n_pt_unnan != 0:
ns_gap_patch = np.zeros((n_pt_all), dtype=np.float32) * np.nan
gap_patch = np.zeros((n_im - 1, n_pt_all), dtype=np.int8)
ns_ifg_noloop_patch = np.zeros(
(n_pt_all), dtype=np.float32) * np.nan
maxTlen_patch = np.zeros((n_pt_all), dtype=np.float32) * np.nan
### Determine n_para
n_pt_patch_min = 1000
if n_pt_patch_min * n_para > n_pt_unnan:
## Too much n_para
n_para_gap = int(np.floor(n_pt_unnan / n_pt_patch_min))
if n_para_gap == 0: n_para_gap = 1
else:
n_para_gap = n_para
print('\n Identifing gaps, and counting n_gap and n_ifg_noloop,')
print(' with {} parallel processing...'.format(n_para_gap),
flush=True)
### Devide unwpatch by n_para for parallel processing
p = q.Pool(n_para_gap)
# _result = np.array(p.map(count_gaps_wrapper, range(n_para_gap)), dtype=object)
_result = np.array(p.map(count_gaps_wrapper,
[(i, n_para_gap, G, Aloop, unwpatch)
for i in range(n_para_gap)]),
dtype=object)
p.close()
ns_gap_patch[ix_unnan_pt] = np.hstack(_result[:, 0]) #n_pt
gap_patch[:, ix_unnan_pt] = np.hstack(_result[:, 1]) #n_im-1, n_pt
ns_ifg_noloop_patch[ix_unnan_pt] = np.hstack(_result[:, 2])
### maxTlen
_maxTlen = np.zeros((n_pt_unnan), dtype=np.float32) #temporaly
_Tlen = np.zeros((n_pt_unnan), dtype=np.float32) #temporaly
for imx in range(n_im - 1):
_Tlen = _Tlen + (dt_cum[imx + 1] - dt_cum[imx]) ## Adding dt
_Tlen[gap_patch[imx,
ix_unnan_pt] == 1] = 0 ## reset to 0 if gap
_maxTlen[_maxTlen < _Tlen] = _Tlen[
_maxTlen < _Tlen] ## Set Tlen to maxTlen
maxTlen_patch[ix_unnan_pt] = _maxTlen
#%% Time series inversion
print('\n Small Baseline inversion by {}...\n'.format(inv_alg),
flush=True)
if inv_alg == 'WLS':
inc_tmp, vel_tmp, vconst_tmp = inv_lib.invert_nsbas_wls(
unwpatch, varpatch, G, dt_cum, gamma, n_para_inv)
else:
inc_tmp, vel_tmp, vconst_tmp = inv_lib.invert_nsbas(
unwpatch, G, dt_cum, gamma, n_para_inv)
### Set to valuables
inc_patch = np.zeros(
(n_im - 1, n_pt_all), dtype=np.float32) * np.nan
vel_patch = np.zeros((n_pt_all), dtype=np.float32) * np.nan
vconst_patch = np.zeros((n_pt_all), dtype=np.float32) * np.nan
inc_patch[:, ix_unnan_pt] = inc_tmp
vel_patch[ix_unnan_pt] = vel_tmp
vconst_patch[ix_unnan_pt] = vconst_tmp
### Calculate residuals
res_patch = np.zeros((n_ifg, n_pt_all), dtype=np.float32) * np.nan
res_patch[:, ix_unnan_pt] = unwpatch.T - np.dot(G, inc_tmp)
res_sumsq = np.nansum(res_patch**2, axis=0)
res_n = np.float32((~np.isnan(res_patch)).sum(axis=0))
res_n[res_n == 0] = np.nan # To avoid 0 division
res_rms_patch = np.sqrt(res_sumsq / res_n)
### Cumulative displacememt
cum_patch = np.zeros((n_im, n_pt_all), dtype=np.float32) * np.nan
cum_patch[1:, :] = np.cumsum(inc_patch, axis=0)
## Fill 1st image with 0 at unnan points from 2nd images
bool_unnan_pt = ~np.isnan(cum_patch[1, :])
cum_patch[0, bool_unnan_pt] = 0
## Drop (fill with nan) interpolated cum by 2 continuous gaps
for i in range(n_im - 2): ## from 1->n_im-1
gap2 = gap_patch[i, :] + gap_patch[i + 1, :]
bool_gap2 = (gap2 == 2
) ## true if 2 continuous gaps for each point
cum_patch[i + 1, :][bool_gap2] = np.nan
## Last (n_im th) image. 1 gap means interpolated
cum_patch[-1, :][gap_patch[-1, :] == 1] = np.nan
#%% Fill by np.nan if n_pt_unnan == 0
else:
cum_patch = np.zeros((n_im, n_pt_all), dtype=np.float32) * np.nan
vel_patch = np.zeros((n_pt_all), dtype=np.float32) * np.nan
vconst_patch = np.zeros((n_pt_all), dtype=np.float32) * np.nan
gap_patch = np.zeros((n_im - 1, n_pt_all), dtype=np.int8)
inc_patch = np.zeros(
(n_im - 1, n_pt_all), dtype=np.float32) * np.nan
res_patch = np.zeros((n_ifg, n_pt_all), dtype=np.float32) * np.nan
res_rms_patch = np.zeros((n_pt_all), dtype=np.float32) * np.nan
ns_gap_patch = np.zeros((n_pt_all), dtype=np.float32) * np.nan
ns_ifg_noloop_patch = np.zeros(
(n_pt_all), dtype=np.float32) * np.nan
maxTlen_patch = np.zeros((n_pt_all), dtype=np.float32) * np.nan
#%% Output data and image
### cum.h5 file
cum[:, rows[0]:rows[1], :] = cum_patch.reshape(
(n_im, lengththis, width))
vel[rows[0]:rows[1], :] = vel_patch.reshape((lengththis, width))
vconst[rows[0]:rows[1], :] = vconst_patch.reshape((lengththis, width))
gap[:, rows[0]:rows[1], :] = gap_patch.reshape(
(n_im - 1, lengththis, width))
### Others
openmode = 'w' if rows[0] == 0 else 'a' #w only 1st patch
## For each imd. cum and inc
for imx, imd in enumerate(imdates):
## Incremental displacement
if imd == imdates[-1]: continue #skip last
incfile = os.path.join(incdir,
'{0}_{1}.inc'.format(imd, imdates[imx + 1]))
with open(incfile, openmode) as f:
inc_patch[imx, :].tofile(f)
## For each ifgd. resid
for i, ifgd in enumerate(ifgdates):
resfile = os.path.join(resdir, '{0}.res'.format(ifgd))
with open(resfile, openmode) as f:
res_patch[i, :].tofile(f)
## velocity and noise indecies in results dir
names = [
'vel', 'vintercept', 'resid_rms', 'n_gap', 'n_ifg_noloop',
'maxTlen'
]
data = [
vel_patch, vconst_patch, res_rms_patch, ns_gap_patch,
ns_ifg_noloop_patch, maxTlen_patch
]
for i in range(len(names)):
file = os.path.join(resultsdir, names[i])
with open(file, openmode) as f:
data[i].tofile(f)
#%% Finish patch
elapsed_time2 = int(time.time() - start2)
hour2 = int(elapsed_time2 / 3600)
minite2 = int(np.mod((elapsed_time2 / 60), 60))
sec2 = int(np.mod(elapsed_time2, 60))
print(" Elapsed time for {0}th patch: {1:02}h {2:02}m {3:02}s".format(
i_patch + 1, hour2, minite2, sec2),
flush=True)
#%% Find stable ref point
print('\nFind stable reference point...', flush=True)
### Compute RMS of time series with reference to all points
sumsq_cum_wrt_med = np.zeros((length, width), dtype=np.float32)
for i in range(n_im):
sumsq_cum_wrt_med = sumsq_cum_wrt_med + (cum[i, :, :] -
np.nanmedian(cum[i, :, :]))**2
rms_cum_wrt_med = np.sqrt(sumsq_cum_wrt_med / n_im)
### Mask by minimum n_gap
n_gap = io_lib.read_img(os.path.join(resultsdir, 'n_gap'), length, width)
min_n_gap = np.nanmin(n_gap)
mask_n_gap = np.float32(n_gap == min_n_gap)
mask_n_gap[mask_n_gap == 0] = np.nan
rms_cum_wrt_med = rms_cum_wrt_med * mask_n_gap
### Find stable reference
min_rms = np.nanmin(rms_cum_wrt_med)
refy1s, refx1s = np.where(rms_cum_wrt_med == min_rms)
refy1s, refx1s = refy1s[0], refx1s[0] ## Only first index
refy2s, refx2s = refy1s + 1, refx1s + 1
print('Selected ref: {}:{}/{}:{}'.format(refx1s, refx2s, refy1s, refy2s),
flush=True)
### Rerferencing cumulative displacement and vel to new stable ref
for i in range(n_im):
cum[i, :, :] = cum[i, :, :] - cum[i, refy1s, refx1s]
vel = vel - vel[refy1s, refx1s]
vconst = vconst - vconst[refy1s, refx1s]
### Save image
rms_cum_wrt_med_file = os.path.join(infodir, '13rms_cum_wrt_med')
with open(rms_cum_wrt_med_file, 'w') as f:
rms_cum_wrt_med.tofile(f)
pngfile = os.path.join(infodir, '13rms_cum_wrt_med.png')
plot_lib.make_im_png(rms_cum_wrt_med, pngfile, cmap_noise_r,
'RMS of cum wrt median (mm)',
np.nanpercentile(rms_cum_wrt_med, 1),
np.nanpercentile(rms_cum_wrt_med, 99))
### Save ref
cumh5.create_dataset('refarea',
data='{}:{}/{}:{}'.format(refx1s, refx2s, refy1s,
refy2s))
refsfile = os.path.join(infodir, '13ref.txt')
with open(refsfile, 'w') as f:
print('{}:{}/{}:{}'.format(refx1s, refx2s, refy1s, refy2s), file=f)
if width == width_geo and length == length_geo: ## Geocoded
### Make ref_stable.kml
reflat = lat1 + dlat * refy1s
reflon = lon1 + dlon * refx1s
io_lib.make_point_kml(reflat, reflon,
os.path.join(infodir, '13ref.kml'))
#%% Close h5 file
cumh5.close()
#%% Output png images
### Incremental displacement
_n_para = n_im - 1 if n_para > n_im - 1 else n_para
print(
'\nOutput increment png images with {} parallel processing...'.format(
_n_para),
flush=True)
p = q.Pool(_n_para)
# p.map(inc_png_wrapper, range(n_im-1))
p.map(inc_png_wrapper,
[(i, imdates, incdir, ifgdir, length, width, coef_r2m, ifgdates,
ref_unw, cycle, cmap_wrap, keep_incfile) for i in range(n_im - 1)])
p.close()
### Residual for each ifg. png and txt.
with open(restxtfile, "w") as f:
print('# RMS of residual (mm)', file=f)
_n_para = n_ifg if n_para > n_ifg else n_para
print('\nOutput residual png images with {} parallel processing...'.format(
_n_para),
flush=True)
p = q.Pool(_n_para)
# p.map(resid_png_wrapper, range(n_ifg))
p.map(resid_png_wrapper, [(i, ifgdates, resdir, length, width, restxtfile,
cmap_vel, wavelength, keep_incfile)
for i in range(n_ifg)])
p.close()
### Velocity and noise indices
cmins = [None, None, None, None, None, None]
cmaxs = [None, None, None, None, None, None]
cmaps = [
cmap_vel, cmap_vel, cmap_noise_r, cmap_noise_r, cmap_noise_r,
cmap_noise
]
titles = [
'Velocity (mm/yr)', 'Intercept of velocity (mm)',
'RMS of residual (mm)', 'Number of gaps in SB network',
'Number of ifgs with no loops',
'Max length of connected SB network (yr)'
]
print('\nOutput noise png images...', flush=True)
for i in range(len(names)):
file = os.path.join(resultsdir, names[i])
data = io_lib.read_img(file, length, width)
pngfile = file + '.png'
## Get color range if None
if cmins[i] is None:
cmins[i] = np.nanpercentile(data, 1)
if cmaxs[i] is None:
cmaxs[i] = np.nanpercentile(data, 99)
if cmins[i] == cmaxs[i]: cmins[i] = cmaxs[i] - 1
plot_lib.make_im_png(data, pngfile, cmaps[i], titles[i], cmins[i],
cmaxs[i])
#%% Finish
elapsed_time = time.time() - start
hour = int(elapsed_time / 3600)
minite = int(np.mod((elapsed_time / 60), 60))
sec = int(np.mod(elapsed_time, 60))
print("\nElapsed time: {0:02}h {1:02}m {2:02}s".format(hour, minite, sec))
print('\n{} Successfully finished!!\n'.format(os.path.basename(argv[0])))
print('Output directory: {}\n'.format(os.path.relpath(tsadir)))
def main(argv=None):
#%% Check argv
if argv == None:
argv = sys.argv
start = time.time()
ver = 1.2
date = 20210309
author = "Y. Morishita"
print("\n{} ver{} {} {}".format(os.path.basename(argv[0]), ver, date,
author),
flush=True)
print("{} {}".format(os.path.basename(argv[0]), ' '.join(argv[1:])),
flush=True)
#%% Set default
tsadir = []
memory_size = 4000
gpu = False
cmap_noise_r = 'viridis_r'
#%% Read options
try:
try:
opts, args = getopt.getopt(argv[1:], "ht:",
["help", "mem_size=", "gpu"])
except getopt.error as msg:
raise Usage(msg)
for o, a in opts:
if o == '-h' or o == '--help':
print(__doc__)
return 0
elif o == '-t':
tsadir = a
elif o == '--mem_size':
memory_size = float(a)
elif o == '--gpu':
gpu = True
if not tsadir:
raise Usage('No tsa directory given, -d is not optional!')
elif not os.path.isdir(tsadir):
raise Usage('No {} dir exists!'.format(tsadir))
if gpu:
print("\nGPU option is activated. Need cupy module.\n")
import cupy as cp
except Usage as err:
print("\nERROR:", file=sys.stderr, end='')
print(" " + str(err.msg), file=sys.stderr)
print("\nFor help, use -h or --help.\n", file=sys.stderr)
return 2
#%% Directory settings
tsadir = os.path.abspath(tsadir)
resultsdir = os.path.join(tsadir, 'results')
#%% Read data information
cumh5 = h5.File(os.path.join(tsadir, 'cum.h5'), 'r')
imdates = cumh5['imdates'][()].astype(str).tolist()
cum = cumh5['cum']
n_im, length, width = cum.shape
imdates_dt = [
dt.datetime.strptime(imd, '%Y%m%d').toordinal() for imd in imdates
]
dt_cum = np.float32((np.array(imdates_dt) - imdates_dt[0]) / 365.25)
#%% Get patch row number
n_store_data = n_im * 2.25 + 100 #3:cum,data,M(bool); 100:bootnum
n_patch, patchrow = tools_lib.get_patchrow(width, length, n_store_data,
memory_size)
#%% For each patch
for i, rows in enumerate(patchrow):
print('\nProcess {0}/{1}th line ({2}/{3}th patch)...'.format(
rows[1], patchrow[-1][-1], i + 1, n_patch),
flush=True)
start2 = time.time()
lengththis = rows[1] - rows[0]
#%% Calc STC
print(' Calculating STC...', flush=True)
### Read data with extra 1 line for overlapping
row_ex1 = 0 if i == 0 else 1 ## first patch
row_ex2 = 0 if i == len(patchrow) - 1 else 1 ## last patch
_cum = cum[:, rows[0] - row_ex1:rows[1] + row_ex2, :].reshape(
n_im, lengththis + row_ex1 + row_ex2, width)
### Calc STC
stc = inv_lib.calc_stc(_cum, gpu=gpu)[row_ex1:lengththis +
row_ex1, :] ## original length
del _cum
### Output data and image
stcfile = os.path.join(resultsdir, 'stc')
openmode = 'w' if i == 0 else 'a' #w only 1st patch
with open(stcfile, openmode) as f:
stc.tofile(f)
#%% Calc vstd
### Read data for vstd
n_pt_all = lengththis * width
cum_patch = cum[:, rows[0]:rows[1], :].reshape(
(n_im, n_pt_all)).transpose() #(n_pt_all, n_im)
### Remove invalid points
bool_unnan_pt = ~np.isnan(cum_patch[:, 0])
cum_patch = cum_patch[bool_unnan_pt, :] ## remain only unnan data
n_pt_unnan = bool_unnan_pt.sum()
print(' {}/{} points removed due to no data...'.format(
n_pt_all - n_pt_unnan, n_pt_all),
flush=True)
### Calc vstd by bootstrap
vstd = np.zeros((n_pt_all), dtype=np.float32) * np.nan
print(' Calculating std of velocity by bootstrap...', flush=True)
vstd[bool_unnan_pt] = inv_lib.calc_velstd_withnan(cum_patch,
dt_cum,
gpu=gpu)
### Output data and image
vstdfile = os.path.join(resultsdir, 'vstd')
openmode = 'w' if i == 0 else 'a' #w only 1st patch
with open(vstdfile, openmode) as f:
vstd.tofile(f)
#%% Finish patch
elapsed_time2 = int(time.time() - start2)
print(' Elapsed time for {0}th patch: {1} sec'.format(
i + 1, elapsed_time2))
#%% Close h5 file
cumh5.close()
#%% Output png
print('\nOutput png images...')
stc = io_lib.read_img(stcfile, length, width)
pngfile = stcfile + '.png'
title = 'Spatio-temporal consistency (mm)'
cmin = np.nanpercentile(stc, 1)
cmax = np.nanpercentile(stc, 99)
plot_lib.make_im_png(stc, pngfile, cmap_noise_r, title, cmin, cmax)
vstd = io_lib.read_img(vstdfile, length, width)
pngfile = vstdfile + '.png'
title = 'STD of velocity (mm/yr)'
cmin = np.nanpercentile(vstd, 1)
cmax = np.nanpercentile(vstd, 99)
plot_lib.make_im_png(vstd, pngfile, cmap_noise_r, title, cmin, cmax)
#%% Finish
elapsed_time = time.time() - start
hour = int(elapsed_time / 3600)
minite = int(np.mod((elapsed_time / 60), 60))
sec = int(np.mod(elapsed_time, 60))
print("\nElapsed time: {0:02}h {1:02}m {2:02}s".format(hour, minite, sec))
print('\n{} Successfully finished!!\n'.format(os.path.basename(argv[0])))
print('Output directory: {}\n'.format(os.path.relpath(tsadir)))
def main(argv=None):
#%% Check argv
if argv == None:
argv = sys.argv
start = time.time()
print("{} {}".format(os.path.basename(argv[0]), ' '.join(argv[1:])),
flush=True)
#%% Set default
ifgdir = []
tsadir = []
refflag = 'auto' ## not supported
inv_alg = 'LS'
n_core = 1
memory_size = 4000
gamma = 0.0001
n_unw_r_thre = []
keep_incfile = False
#%% Read options
try:
try:
opts, args = getopt.getopt(argv[1:], "hd:t:r:", [
"help", "mem_size=", "gamma=", "n_unw_r_thre=", "keep_incfile",
"inv_alg=", "n_core="
])
except getopt.error as msg:
raise Usage(msg)
for o, a in opts:
if o == '-h' or o == '--help':
print(__doc__)
return 0
elif o == '-d':
ifgdir = a
elif o == '-t':
tsadir = a
elif o == '-r':
refflag = a
elif o == '--mem_size':
memory_size = float(a)
elif o == '--gamma':
gamma = float(a)
elif o == '--n_unw_r_thre':
n_unw_r_thre = float(a)
elif o == '--keep_incfile':
keep_incfile = True
elif o == '--inv_alg':
inv_alg = a
elif o == '--n_core':
n_core = int(a)
if not ifgdir:
raise Usage('No data directory given, -d is not optional!')
elif not os.path.isdir(ifgdir):
raise Usage('No {} dir exists!'.format(ifgdir))
elif not os.path.exists(os.path.join(ifgdir, 'slc.mli.par')):
raise Usage('No slc.mli.par file exists in {}!'.format(ifgdir))
except Usage as err:
print("\nERROR:", file=sys.stderr, end='')
print(" " + str(err.msg), file=sys.stderr)
print("\nFor help, use -h or --help.\n", file=sys.stderr)
return 2
#%% Directory settings
ifgdir = os.path.abspath(ifgdir)
if not tsadir:
tsadir = os.path.join(os.path.dirname(ifgdir),
'TS_' + os.path.basename(ifgdir))
if not os.path.isdir(tsadir):
print('\nNo {} exists!'.format(tsadir), file=sys.stderr)
return 1
tsadir = os.path.abspath(tsadir)
resultsdir = os.path.join(tsadir, 'results')
infodir = os.path.join(tsadir, 'info')
netdir = os.path.join(tsadir, 'network')
bad_ifg11file = os.path.join(infodir, '11bad_ifg.txt')
bad_ifg12file = os.path.join(infodir, '12bad_ifg.txt')
reffile = os.path.join(infodir, 'ref.txt')
incdir = os.path.join(tsadir, '13increment')
if not os.path.exists(incdir): os.mkdir(incdir)
resdir = os.path.join(tsadir, '13resid')
if not os.path.exists(resdir): os.mkdir(resdir)
restxtfile = os.path.join(infodir, '13resid.txt')
cumh5file = os.path.join(tsadir, 'cum.h5')
#%% Check files
try:
if not os.path.exists(bad_ifg11file):
raise Usage('No 11bad_ifg.txt file exists in {}!'.format(tsadir))
if not os.path.exists(bad_ifg12file):
raise Usage('No 12bad_ifg.txt file exists in {}!'.format(tsadir))
if not os.path.exists(reffile):
raise Usage('No ref.txt file exists in {}!'.format(tsadir))
except Usage as err:
print("\nERROR:", file=sys.stderr, end='')
print(" " + str(err.msg), file=sys.stderr)
print("\nFor help, use -h or --help.\n", file=sys.stderr)
return 2
#%% Check and set reference
if refflag == 'auto': # Automatic setting based on ref.txt
with open(reffile, "r") as f:
refarea = f.read().split()[0] #str, x1/x2/y1/y2
refx1, refx2, refy1, refy2 = [
int(s) for s in re.split('[:/]', refarea)
]
#%% Read data information
### Get size
mlipar = os.path.join(ifgdir, 'slc.mli.par')
width = int(io_lib.get_param_par(mlipar, 'range_samples'))
length = int(io_lib.get_param_par(mlipar, 'azimuth_lines'))
speed_of_light = 299792458 #m/s
radar_frequency = float(io_lib.get_param_par(mlipar,
'radar_frequency')) #Hz
wavelength = speed_of_light / radar_frequency #meter
coef_r2m = -wavelength / 4 / np.pi * 1000 #rad -> mm, positive is -LOS
### Calc pixel spacing depending on IFG or GEOC, used in later spatial filter
dempar = os.path.join(ifgdir, 'EQA.dem_par')
width_geo = int(io_lib.get_param_par(dempar, 'width'))
length_geo = int(io_lib.get_param_par(dempar, 'nlines'))
dlat = float(io_lib.get_param_par(dempar, 'post_lat')) #negative
dlon = float(io_lib.get_param_par(dempar, 'post_lon')) #positive
lat1 = float(io_lib.get_param_par(dempar, 'corner_lat'))
lon1 = float(io_lib.get_param_par(dempar, 'corner_lon'))
if width == width_geo and length == length_geo: ## Geocoded
print('In geographical coordinates', flush=True)
centerlat = lat1 + dlat * (length / 2)
ra = float(io_lib.get_param_par(dempar, 'ellipsoid_ra'))
recip_f = float(
io_lib.get_param_par(dempar, 'ellipsoid_reciprocal_flattening'))
rb = ra * (1 - 1 / recip_f) ## polar radius
pixsp_a = 2 * np.pi * rb / 360 * abs(dlat)
pixsp_r = 2 * np.pi * ra / 360 * dlon * np.cos(np.deg2rad(centerlat))
### Make ref.kml
reflat = lat1 + dlat * refy1
reflon = lon1 + dlon * refx1
make_point_kml(reflat, reflon, os.path.join(infodir, 'ref.kml'))
else:
print('In radar coordinates', flush=True)
pixsp_r_org = float(io_lib.get_param_par(mlipar,
'range_pixel_spacing'))
pixsp_a = float(io_lib.get_param_par(mlipar, 'azimuth_pixel_spacing'))
inc_agl = float(io_lib.get_param_par(mlipar, 'incidence_angle'))
pixsp_r = pixsp_r_org / np.sin(np.deg2rad(inc_agl))
### Set n_unw_r_thre and cycle depending on L- or C-band
if wavelength > 0.2: ## L-band
if not n_unw_r_thre: n_unw_r_thre = 0.5
cycle = 1.5 # 2pi/cycle for comparison png
elif wavelength <= 0.2: ## C-band
if not n_unw_r_thre: n_unw_r_thre = 1.0
cycle = 3 # 3*2pi/cycle for comparison png
#%% Read date and network information
### Get all ifgdates in ifgdir
ifgdates_all = tools_lib.get_ifgdates(ifgdir)
imdates_all = tools_lib.ifgdates2imdates(ifgdates_all)
n_im_all = len(imdates_all)
n_ifg_all = len(ifgdates_all)
### Read bad_ifg11 and 12
bad_ifg11 = io_lib.read_ifg_list(bad_ifg11file)
bad_ifg12 = io_lib.read_ifg_list(bad_ifg12file)
bad_ifg_all = list(set(bad_ifg11 + bad_ifg12))
bad_ifg_all.sort()
### Remove bad ifgs and images from list
ifgdates = list(set(ifgdates_all) - set(bad_ifg_all))
ifgdates.sort()
imdates = tools_lib.ifgdates2imdates(ifgdates)
n_ifg = len(ifgdates)
n_ifg_bad = len(set(bad_ifg11 + bad_ifg12))
n_im = len(imdates)
n_unw_thre = int(n_unw_r_thre * n_im)
### Make 13used_image.txt
imfile = os.path.join(infodir, '13used_image.txt')
with open(imfile, 'w') as f:
for i in imdates:
print('{}'.format(i), file=f)
### Calc dt in year
imdates_dt = ([
dt.datetime.strptime(imd, '%Y%m%d').toordinal() for imd in imdates
])
dt_cum = np.float32((np.array(imdates_dt) - imdates_dt[0]) / 365.25)
### Construct G and Aloop matrix for increment and n_gap
G = inv_lib.make_sb_matrix(ifgdates)
Aloop = loop_lib.make_loop_matrix(ifgdates)
n_loop = Aloop.shape[0] # (n_loop,n_ifg)
#%% Plot network
## Read bperp data or dummy
bperp_file = os.path.join(ifgdir, 'baselines')
if os.path.exists(bperp_file):
bperp_all = io_lib.read_bperp_file(bperp_file, imdates_all)
bperp = io_lib.read_bperp_file(bperp_file, imdates)
else: #dummy
bperp_all = np.random.random(len(imdates_all)).tolist()
bperp = np.random.random(n_im).tolist()
pngfile = os.path.join(netdir, 'network13_all.png')
plot_lib.plot_network(ifgdates_all, bperp_all, [], pngfile, pdf=True)
pngfile = os.path.join(netdir, 'network13.png')
plot_lib.plot_network(ifgdates_all,
bperp_all,
bad_ifg_all,
pngfile,
pdf=True)
pngfile = os.path.join(netdir, 'network13_nobad.png')
plot_lib.plot_network(ifgdates_all,
bperp_all,
bad_ifg_all,
pngfile,
plot_bad=False,
pdf=True)
#%% Get patch row number
if inv_alg == 'WLS':
n_store_data = n_ifg * 3 + n_im * 2 + n_im * 0.3 #
else:
n_store_data = n_ifg * 2 + n_im * 2 + n_im * 0.3 #not sure
n_patch, patchrow = tools_lib.get_patchrow(width, length, n_store_data,
memory_size)
#%% Display and output settings & paramters
print('')
print('Size of image (w,l) : {}, {}'.format(width, length))
print('# of all images : {}'.format(n_im_all))
print('# of images to be used : {}'.format(n_im))
print('# of all ifgs : {}'.format(n_ifg_all))
print('# of ifgs to be used : {}'.format(n_ifg))
print('# of removed ifgs : {}'.format(n_ifg_bad))
print('Threshold of used unw : {}'.format(n_unw_thre))
print('')
print('Reference area (X/Y) : {}:{}/{}:{}'.format(
refx1, refx2, refy1, refy2))
print('Allowed memory size : {} MB'.format(memory_size))
print('Number of patches : {}'.format(n_patch))
print('Inversion algorism : {}'.format(inv_alg))
print('Gamma value : {}'.format(gamma), flush=True)
with open(os.path.join(infodir, 'parameters.txt'), "w") as f:
print('range_samples: {}'.format(width), file=f)
print('azimuth_lines: {}'.format(length), file=f)
print('wavelength: {}'.format(wavelength), file=f)
print('n_im_all: {}'.format(n_im_all), file=f)
print('n_im: {}'.format(n_im), file=f)
print('n_ifg_all: {}'.format(n_ifg_all), file=f)
print('n_ifg: {}'.format(n_ifg), file=f)
print('n_ifg_bad: {}'.format(n_ifg_bad), file=f)
print('n_unw_thre: {}'.format(n_unw_thre), file=f)
print('ref_area: {}:{}/{}:{}'.format(refx1, refx2, refy1, refy2),
file=f)
print('memory_size: {} MB'.format(memory_size), file=f)
print('n_patch: {}'.format(n_patch), file=f)
print('inv_alg: {}'.format(inv_alg), file=f)
print('gamma: {}'.format(gamma), file=f)
print('pixel_spacing_r: {:.2f} m'.format(pixsp_r), file=f)
print('pixel_spacing_a: {:.2f} m'.format(pixsp_a), file=f)
#%% Ref phase for inversion
lengththis = refy2 - refy1
countf = width * refy1
countl = width * lengththis # Number to be read
ref_unw = []
for i, ifgd in enumerate(ifgdates):
unwfile = os.path.join(ifgdir, ifgd, ifgd + '.unw')
f = open(unwfile, 'rb')
f.seek(countf * 4, os.SEEK_SET) #Seek for >=2nd path, 4 means byte
### Read unw data (mm) at ref area
unw = np.fromfile(f, dtype=np.float32, count=countl).reshape(
(lengththis, width))[:, refx1:refx2] * coef_r2m
unw[unw == 0] = np.nan
if np.all(np.isnan(unw)):
print('All nan in ref area in {}.'.format(ifgd))
print('Rerun LiCSBAS12.')
return 1
ref_unw.append(np.nanmean(unw))
f.close()
#%% Open cum.h5 for output
if os.path.exists(cumh5file): os.remove(cumh5file)
cumh5 = h5.File(cumh5file, 'w')
cumh5.create_dataset('imdates', data=[np.int32(imd) for imd in imdates])
cumh5.create_dataset('refarea', data=refarea)
if not np.all(np.abs(np.array(bperp)) <= 1): # if not dummy
cumh5.create_dataset('bperp', data=bperp)
cum = cumh5.require_dataset('cum', (n_im, length, width), dtype=np.float32)
vel = cumh5.require_dataset('vel', (length, width), dtype=np.float32)
vconst = cumh5.require_dataset('vintercept', (length, width),
dtype=np.float32)
gap = cumh5.require_dataset('gap', (n_im - 1, length, width),
dtype=np.int8)
if width == width_geo and length == length_geo: ## if geocoded
cumh5.create_dataset('corner_lat', data=lat1)
cumh5.create_dataset('corner_lon', data=lon1)
cumh5.create_dataset('post_lat', data=dlat)
cumh5.create_dataset('post_lon', data=dlon)
#%% For each patch
i_patch = 1
for rows in patchrow:
print('\nProcess {0}/{1}th line ({2}/{3}th patch)...'.format(
rows[1], patchrow[-1][-1], i_patch, n_patch),
flush=True)
start2 = time.time()
#%% Read data
### Allocate memory
lengththis = rows[1] - rows[0]
n_pt_all = lengththis * width
unwpatch = np.zeros((n_ifg, lengththis, width), dtype=np.float32)
if inv_alg == 'WLS':
cohpatch = np.zeros((n_ifg, lengththis, width), dtype=np.float32)
### For each ifg
print(" Reading {0} ifg's unw data...".format(n_ifg), flush=True)
countf = width * rows[0]
countl = width * lengththis
for i, ifgd in enumerate(ifgdates):
unwfile = os.path.join(ifgdir, ifgd, ifgd + '.unw')
f = open(unwfile, 'rb')
f.seek(countf * 4, os.SEEK_SET) #Seek for >=2nd path, 4 means byte
### Read unw data (mm) at patch area
unw = np.fromfile(f, dtype=np.float32, count=countl).reshape(
(lengththis, width)) * coef_r2m
unw[unw == 0] = np.nan # Fill 0 with nan
unw = unw - ref_unw[i]
unwpatch[i] = unw
f.close()
### Read coh file at patch area for WLS
if inv_alg == 'WLS':
cohfile = os.path.join(ifgdir, ifgd, ifgd + '.cc')
f = open(cohfile, 'rb')
f.seek(countf * 4,
os.SEEK_SET) #Seek for >=2nd path, 4 means byte
cohpatch[i, :, :] = np.fromfile(f,
dtype=np.float32,
count=countl).reshape(
(lengththis, width))
unwpatch = unwpatch.reshape(
(n_ifg, n_pt_all)).transpose() #(n_pt_all, n_ifg)
### Calc variance from coherence for WLS
if inv_alg == 'WLS':
cohpatch = cohpatch.reshape(
(n_ifg, n_pt_all)).transpose() #(n_pt_all, n_ifg)
cohpatch[
cohpatch <
0.01] = 0.01 ## because negative value possible due to geocode
cohpatch[
cohpatch > 0.99] = 0.99 ## because >1 possible due to geocode
varpatch = (1 - cohpatch**2) / (2 * cohpatch**2)
del cohpatch
#%% Remove points with less valid data than n_unw_thre
ix_unnan_pt = np.where(
np.sum(~np.isnan(unwpatch), axis=1) > n_unw_thre)[0]
n_pt_unnan = len(ix_unnan_pt)
unwpatch = unwpatch[ix_unnan_pt, :] ## keep only unnan data
if inv_alg == 'WLS':
varpatch = varpatch[ix_unnan_pt, :] ## keep only unnan data
print(' {}/{} points removed due to not enough ifg data...'.format(
n_pt_all - n_pt_unnan, n_pt_all),
flush=True)
#%% Compute number of gaps, ifg_noloop, maxTlen point-by-point
ns_gap_patch = np.zeros((n_pt_all), dtype=np.float32) * np.nan
gap_patch = np.zeros((n_im - 1, n_pt_all), dtype=np.int8)
ns_ifg_noloop_patch = np.zeros((n_pt_all), dtype=np.float32) * np.nan
maxTlen_patch = np.zeros((n_pt_all), dtype=np.float32) * np.nan
### n_gap
print('\n Identifing gaps and counting n_gap...', flush=True)
# ns_unw_unnan4inc = (np.matmul(np.int8(G[:, :, None]), (~np.isnan(unwpatch.T))[:, None, :])).sum(axis=0, dtype=np.int16) #n_ifg, n_im-1, n_pt -> n_im-1, n_pt
ns_unw_unnan4inc = np.array([
(G[:, i] * (~np.isnan(unwpatch))).sum(axis=1, dtype=np.int16)
for i in range(n_im - 1)
]) #n_ifg*(n_pt,n_ifg) -> (n_im-1,n_pt)
ns_gap_patch[ix_unnan_pt] = (ns_unw_unnan4inc == 0).sum(axis=0) #n_pt
gap_patch[:, ix_unnan_pt] = ns_unw_unnan4inc == 0
del ns_unw_unnan4inc
### n_ifg_noloop
print(' Counting n_ifg_noloop...', flush=True)
# n_ifg*(n_pt,n_ifg)->(n_loop,n_pt)
# Number of ifgs for each loop at eath point.
# 3 means complete loop, 1 or 2 means broken loop.
ns_ifg4loop = np.array([
(np.abs(Aloop[i, :]) * (~np.isnan(unwpatch))).sum(axis=1)
for i in range(n_loop)
])
bool_loop = (ns_ifg4loop == 3
) #(n_loop,n_pt) identify complete loop only
# n_loop*(n_loop,n_pt)*n_pt->(n_ifg,n_pt)
# Number of loops for each ifg at eath point.
ns_loop4ifg = np.array([((np.abs(Aloop[:, i]) * bool_loop.T).T *
(~np.isnan(unwpatch[:, i]))).sum(axis=0)
for i in range(n_ifg)]) #
ns_ifg_noloop_tmp = (ns_loop4ifg == 0).sum(axis=0) #n_pt
ns_nan_ifg = np.isnan(unwpatch).sum(axis=1) #n_pt, nan ifg count
ns_ifg_noloop_patch[ix_unnan_pt] = ns_ifg_noloop_tmp - ns_nan_ifg
del bool_loop, ns_ifg4loop, ns_loop4ifg
### maxTlen
_maxTlen = np.zeros((n_pt_unnan), dtype=np.float32) #temporaly
_Tlen = np.zeros((n_pt_unnan), dtype=np.float32) #temporaly
for imx in range(n_im - 1):
_Tlen = _Tlen + (dt_cum[imx + 1] - dt_cum[imx]) ## Adding dt
_Tlen[gap_patch[imx, ix_unnan_pt] == 1] = 0 ## reset to 0 if gap
_maxTlen[_maxTlen < _Tlen] = _Tlen[_maxTlen <
_Tlen] ## Set Tlen to maxTlen
maxTlen_patch[ix_unnan_pt] = _maxTlen
#%% Time series inversion
print('\n Small Baseline inversion by {}...\n'.format(inv_alg),
flush=True)
if inv_alg == 'WLS':
inc_tmp, vel_tmp, vconst_tmp = inv_lib.invert_nsbas_wls(
unwpatch, varpatch, G, dt_cum, gamma, n_core)
else:
inc_tmp, vel_tmp, vconst_tmp = inv_lib.invert_nsbas(
unwpatch, G, dt_cum, gamma, n_core)
### Set to valuables
inc_patch = np.zeros((n_im - 1, n_pt_all), dtype=np.float32) * np.nan
vel_patch = np.zeros((n_pt_all), dtype=np.float32) * np.nan
vconst_patch = np.zeros((n_pt_all), dtype=np.float32) * np.nan
inc_patch[:, ix_unnan_pt] = inc_tmp
vel_patch[ix_unnan_pt] = vel_tmp
vconst_patch[ix_unnan_pt] = vconst_tmp
### Calculate residuals
res_patch = np.zeros((n_ifg, n_pt_all), dtype=np.float32) * np.nan
res_patch[:, ix_unnan_pt] = unwpatch.T - np.dot(G, inc_tmp)
res_sumsq = np.nansum(res_patch**2, axis=0)
res_n = np.float32((~np.isnan(res_patch)).sum(axis=0))
res_n[res_n == 0] = np.nan # To avoid 0 division
res_rms_patch = np.sqrt(res_sumsq / res_n)
### Cumulative displacememt
cum_patch = np.zeros((n_im, n_pt_all), dtype=np.float32) * np.nan
cum_patch[1:, :] = np.cumsum(inc_patch, axis=0)
## Fill 1st image with 0 at unnan points from 2nd images
bool_unnan_pt = ~np.isnan(cum_patch[1, :])
cum_patch[0, bool_unnan_pt] = 0
## Drop (fill with nan) interpolated cum by 2 continuous gaps
for i in range(n_im - 2): ## from 1->n_im-1
gap2 = gap_patch[i, :] + gap_patch[i + 1, :]
bool_gap2 = (gap2 == 2
) ## true if 2 continuous gaps for each point
cum_patch[i + 1, :][bool_gap2] = np.nan
## Last (n_im th) image. 1 gap means interpolated
cum_patch[-1, :][gap_patch[-1, :] == 1] = np.nan
#%% Output data and image
### cum.h5 file
cum[:, rows[0]:rows[1], :] = cum_patch.reshape(
(n_im, lengththis, width))
vel[rows[0]:rows[1], :] = vel_patch.reshape((lengththis, width))
vconst[rows[0]:rows[1], :] = vconst_patch.reshape((lengththis, width))
gap[:, rows[0]:rows[1], :] = gap_patch.reshape(
(n_im - 1, lengththis, width))
### Others
openmode = 'w' if rows[0] == 0 else 'a' #w only 1st patch
## For each imd. cum and inc
for imx, imd in enumerate(imdates):
## Incremental displacement
if imd == imdates[-1]: continue #skip last
incfile = os.path.join(incdir,
'{0}_{1}.inc'.format(imd, imdates[imx + 1]))
with open(incfile, openmode) as f:
inc_patch[imx, :].tofile(f)
## For each ifgd. resid
for i, ifgd in enumerate(ifgdates):
resfile = os.path.join(resdir, '{0}.res'.format(ifgd))
with open(resfile, openmode) as f:
res_patch[i, :].tofile(f)
## velocity and noise indecies in results dir
names = [
'vel', 'vintercept', 'resid_rms', 'n_gap', 'n_ifg_noloop',
'maxTlen'
]
data = [
vel_patch, vconst_patch, res_rms_patch, ns_gap_patch,
ns_ifg_noloop_patch, maxTlen_patch
]
for i in range(len(names)):
file = os.path.join(resultsdir, names[i])
with open(file, openmode) as f:
data[i].tofile(f)
#%% Finish patch
elapsed_time2 = int(time.time() - start2)
hour2 = int(elapsed_time2 / 3600)
minite2 = int(np.mod((elapsed_time2 / 60), 60))
sec2 = int(np.mod(elapsed_time2, 60))
print(" Elapsed time for {0}th patch: {1:02}h {2:02}m {3:02}s".format(
i_patch, hour2, minite2, sec2),
flush=True)
i_patch += 1 #Next patch count
#%% Close h5 file
cumh5.close()
#%% Output png images
print('\nOutput png images...', flush=True)
### Incremental displacement
for imx, imd in enumerate(imdates):
if imd == imdates[-1]: continue #skip last for increment
## Comparison of increment and daisy chain pair
ifgd = '{}_{}'.format(imd, imdates[imx + 1])
incfile = os.path.join(incdir, '{}.inc'.format(ifgd))
unwfile = os.path.join(ifgdir, ifgd, '{}.unw'.format(ifgd))
pngfile = os.path.join(incdir, '{}.inc_comp.png'.format(ifgd))
inc = io_lib.read_img(incfile, length, width)
try:
unw = io_lib.read_img(unwfile, length, width) * coef_r2m
ix_ifg = ifgdates.index(ifgd)
unw = unw - ref_unw[ix_ifg]
except:
unw = np.zeros((length, width), dtype=np.float32) * np.nan
### Output png for comparison
data3 = [
np.angle(np.exp(1j * (data / coef_r2m / cycle)) * cycle)
for data in [unw, inc, inc - unw]
]
title3 = ['Daisy-chain IFG', 'Inverted', 'Difference']
pngfile = os.path.join(incdir, '{}.increment.png'.format(ifgd))
plot_lib.make_3im_png(data3,
pngfile,
'insar',
title3,
vmin=-np.pi,
vmax=np.pi,
cbar=False)
if not keep_incfile:
os.remove(incfile)
### Residual for each ifg. png and txt.
cmap = 'jet'
with open(restxtfile, "w") as f:
print('# RMS of residual (mm)', file=f)
for ifgd in ifgdates:
infile = os.path.join(resdir, '{}.res'.format(ifgd))
resid = io_lib.read_img(infile, length, width)
resid_rms = np.sqrt(np.nanmean(resid**2))
with open(restxtfile, "a") as f:
print('{} {:5.2f}'.format(ifgd, resid_rms), file=f)
pngfile = infile + '.png'
title = 'Residual (mm) of {} (RMS:{:.2f}mm)'.format(ifgd, resid_rms)
plot_lib.make_im_png(resid, pngfile, cmap, title,
-wavelength / 2 * 1000, wavelength / 2 * 1000)
if not keep_incfile:
os.remove(infile)
### Velocity and noise indices
#names = ['vel', 'vconst', 'resid_rms', 'n_gap', 'n_ifg_noloop', 'maxTlen']
cmins = [None, None, None, None, None, None]
cmaxs = [None, None, None, None, None, None]
cmaps = ['jet', 'jet', 'viridis_r', 'viridis_r', 'viridis_r', 'viridis']
titles = [
'Velocity (mm/yr)', 'Intercept of velocity (mm)',
'RMS of residual (mm)', 'Number of gaps in SB network',
'Number of ifgs with no loops',
'Max length of connected SB network (yr)'
]
for i in range(len(names)):
file = os.path.join(resultsdir, names[i])
data = io_lib.read_img(file, length, width)
pngfile = file + '.png'
## Get color range if None
if cmins[i] is None:
cmins[i] = np.nanpercentile(data, 1)
if cmaxs[i] is None:
cmaxs[i] = np.nanpercentile(data, 99)
if cmins[i] == cmaxs[i]: cmins[i] = cmaxs[i] - 1
plot_lib.make_im_png(data, pngfile, cmaps[i], titles[i], cmins[i],
cmaxs[i])
#%% Finish
elapsed_time = time.time() - start
hour = int(elapsed_time / 3600)
minite = int(np.mod((elapsed_time / 60), 60))
sec = int(np.mod(elapsed_time, 60))
print("\nElapsed time: {0:02}h {1:02}m {2:02}s".format(hour, minite, sec))
print('\n{} Successfully finished!!\n'.format(os.path.basename(argv[0])))
print('Output directory: {}\n'.format(os.path.relpath(tsadir)))