def main(argv=None):
#%% Check argv
if argv == None:
argv = sys.argv
start = time.time()
#%% Set default
imd_s = []
imd_e = []
cumfile = 'cum_filt.h5'
outfile = []
refarea = []
maskfile = []
vstdflag = False
sinflag = False
pngflag = False
#%% Read options
try:
try:
opts, args = getopt.getopt(argv[1:], "hs:e:i:o:r:",
["help", "vstd", "sin", "png", "mask="])
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 == '-s':
imd_s = a
elif o == '-e':
imd_e = a
elif o == '-i':
cumfile = a
elif o == '-o':
outfile = a
elif o == '-r':
refarea = a
elif o == '--vstd':
vstdflag = True
elif o == '--sin':
sinflag = True
elif o == '--mask':
maskfile = a
elif o == '--png':
pngflag = True
if not os.path.exists(cumfile):
raise Usage('No {} exists! Use -i option.'.format(cumfile))
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
#%% Read info
### Read cumfile
cumh5 = h5.File(cumfile, 'r')
imdates = cumh5['imdates'][()].astype(str).tolist()
cum = cumh5['cum']
n_im_all, length, width = cum.shape
if not refarea:
refarea = cumh5['refarea'][()]
refx1, refx2, refy1, refy2 = [
int(s) for s in re.split('[:/]', refarea)
]
else:
if not tools_lib.read_range(refarea, width, length):
print('\nERROR in {}\n'.format(refarea), file=sys.stderr)
return 2
else:
refx1, refx2, refy1, refy2 = tools_lib.read_range(
refarea, width, length)
#%% Setting
### Dates
if not imd_s:
imd_s = imdates[0]
if not imd_e:
imd_e = imdates[-1]
### mask
if maskfile:
mask = io_lib.read_img(maskfile, length, width)
mask[mask == 0] = np.nan
suffix_mask = '.mskd'
else:
mask = np.ones((length, width), dtype=np.float32)
suffix_mask = ''
### Find date index if not exist in imdates
if not imd_s in imdates:
for imd in imdates:
if int(imd) >= int(imd_s): ## First larger one than imd_s
imd_s = imd
break
if not imd_e in imdates:
for imd in imdates[::-1]:
if int(imd) <= int(imd_e): ## Last smaller one than imd_e
imd_e = imd
break
ix_s = imdates.index(imd_s)
ix_e = imdates.index(imd_e) + 1 #+1 for python custom
n_im = ix_e - ix_s
### Calc dt in year
imdates_dt = ([
dt.datetime.strptime(imd, '%Y%m%d').toordinal()
for imd in imdates[ix_s:ix_e]
])
dt_cum = np.float32((np.array(imdates_dt) - imdates_dt[0]) / 365.25)
### Outfile
if not outfile:
outfile = '{}_{}.vel{}'.format(imd_s, imd_e, suffix_mask)
#%% Display info
print('')
print('Start date : {}'.format(imdates[ix_s]))
print('End date : {}'.format(imdates[ix_e - 1]))
print('# of images : {}'.format(n_im))
print('Ref area : {}:{}/{}:{}'.format(refx1, refx2, refy1, refy2))
print('')
#%% Calc velocity and vstd
vconst = np.zeros((length, width), dtype=np.float32) * np.nan
vel = np.zeros((length, width), dtype=np.float32) * np.nan
### Read cum data
cum_tmp = cum[ix_s:ix_e, :, :] * mask
cum_ref = np.nanmean(cum[ix_s:ix_e, refy1:refy2, refx1:refx2] *
mask[refy1:refy2, refx1:refx2],
axis=(1, 2))
if np.all(np.isnan(cum_ref)):
print('\nERROR: Ref area has only NaN value!\n', file=sys.stderr)
return 2
cum_tmp = cum_tmp - cum_ref[:, np.newaxis, np.newaxis]
### Extract not nan points
bool_allnan = np.all(np.isnan(cum_tmp), axis=0)
cum_tmp = cum_tmp.reshape(n_im, length *
width)[:, ~bool_allnan.ravel()].transpose()
if not sinflag: ## Linear function
print('Calc velocity...')
vel[~bool_allnan], vconst[~bool_allnan] = inv_lib.calc_vel(
cum_tmp, dt_cum)
vel.tofile(outfile)
else: ## Linear+sin function
print('Calc velocity and annual components...')
amp = np.zeros((length, width), dtype=np.float32) * np.nan
delta_t = np.zeros((length, width), dtype=np.float32) * np.nan
ampfile = outfile.replace('vel', 'amp')
dtfile = outfile.replace('vel', 'dt')
vel[~bool_allnan], vconst[~bool_allnan], amp[~bool_allnan], delta_t[
~bool_allnan] = inv_lib.calc_velsin(cum_tmp, dt_cum, imdates[0])
vel.tofile(outfile)
amp.tofile(ampfile)
delta_t.tofile(dtfile)
### vstd
if vstdflag:
vstdfile = outfile.replace('vel', 'vstd')
vstd = np.zeros((length, width), dtype=np.float32) * np.nan
print('Calc vstd...')
vstd[~bool_allnan] = inv_lib.calc_velstd_withnan(cum_tmp, dt_cum)
vstd.tofile(vstdfile)
#%% Make png if specified
if pngflag:
pngfile = outfile + '.png'
title = 'n_im: {}, Ref X/Y {}:{}/{}:{}'.format(n_im, refx1, refx2,
refy1, refy2)
plot_lib.make_im_png(vel, pngfile, 'jet', title)
if sinflag:
amp_max = np.nanpercentile(amp, 99)
plot_lib.make_im_png(amp,
ampfile + '.png',
'viridis',
title,
vmax=amp_max)
plot_lib.make_im_png(delta_t, dtfile + '.png', 'hsv', title)
if vstdflag:
plot_lib.make_im_png(vstd, vstdfile + '.png', 'jet', title)
#%% 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: {}'.format(outfile), flush=True)
if vstdflag:
print(' {}'.format(vstdfile), flush=True)
print('')
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)))