Skip to content

Commit

Permalink
Remove -f option
Browse files Browse the repository at this point in the history
  • Loading branch information
@yumorishita
yumorishita committed Oct 20, 2020
1 parent a8d143a commit 8c18dd5
Show file tree
Hide file tree
Showing 2 changed files with 31 additions and 67 deletions.
4 changes: 1 addition & 3 deletions batch_LiCSBAS.sh
View file
Original file line number Diff line number Diff line change
Expand Up @@ -63,11 +63,10 @@ p16_ex_range_geo="" # e.g. 130.11/131.12/34.34/34.6 (in deg)
p01_frame="" # e.g. 021D_04972_131213
p01_start_date="" # default: 20141001
p01_end_date="" # default: today
p01_get_gacos="y" # y/n
p01_get_gacos="n" # y/n
p01_n_para="" # default: 4
p02_GEOCdir="" # default: GEOC
p02_GEOCmldir="" # default: GEOCml$nlook
p02_frame="" # e.g. 021D_04972_131213
p02_freq="" # default: 5.405e9 Hz
p02_n_para="" # default: # of usable CPU
order_op03_05="03 04 05" # can change order e.g., 05 03 04
Expand Down Expand Up @@ -142,7 +141,6 @@ if [ $start_step -le 02 -a $end_step -ge 02 ];then
else p02_op="$p02_op -i GEOC"; fi
if [ ! -z $p02_GEOCmldir ];then p02_op="$p02_op -o $p02_GEOCmldir"; fi
if [ ! -z $nlook ];then p02_op="$p02_op -n $nlook"; fi
if [ ! -z $p02_frame ];then p02_op="$p02_op -f $p02_frame"; fi
if [ ! -z $p02_freq ];then p02_op="$p02_op --freq $p02_freq"; fi
if [ ! -z $p02_n_para ];then p02_op="$p02_op --n_para $p02_n_para";
elif [ ! -z $n_para ];then p02_op="$p02_op --n_para $n_para";fi
Expand Down
94 changes: 30 additions & 64 deletions bin/LiCSBAS02_ml_prep.py
View file
Original file line number Diff line number Diff line change
@@ -1,24 +1,24 @@
#!/usr/bin/env python3
"""
v1.6.1 20201016 Yu Morishita, GSI
v1.7 20201020 Yu Morishita, GSI
========
Overview
========
This script converts GeoTIFF files of unw and cc to float32 and uint8 format, respectively, for further time series analysis, and also downsamples (multilooks) data if specified. Existing files are not re-created to save time, i.e., only the newly available data will be processed.
===============
====================
Input & output files
===============
====================
Inputs:
- GEOC/
- yyyymmdd_yyyymmdd/
- yyyymmdd_yyyymmdd.geo.unw.tif
- yyyymmdd_yyyymmdd.geo.cc.tif
[- *.geo.mli.tif]
[- *.geo.hgt.tif]
[- *.geo.[E|N|U].tif] (if not exist, try to download from COMET-LiCS web)
[- baselines] (if not exist, try to download from COMET-LiCS web)
[- *.geo.[E|N|U].tif]
[- baselines]
[- metadata.txt]
Outputs in GEOCml*/ (downsampled if indicated):
Expand All @@ -27,28 +27,29 @@
- yyyymmdd_yyyymmdd.cc (uint8)
- baselines (may be dummy)
- EQA.dem_par
- slc.mli[.par|.png]
- hgt[.png]
- [E|N|U].geo (if exist)
- slc.mli.par
- slc.mli[.png] (if input exists)
- hgt[.png] (if input exists)
- [E|N|U].geo (if input exists)
- no_unw_list.txt (if there are unavailable unw|cc)
=====
Usage
=====
LiCSBAS02_ml_prep.py -i GEOCdir [-o GEOCmldir] [-n nlook] [-f frameID] [--freq float] [--n_para int]
LiCSBAS02_ml_prep.py -i GEOCdir [-o GEOCmldir] [-n nlook] [--freq float] [--n_para int]
-i Path to the input GEOC dir containing stack of geotiff data
-o Path to the output GEOCml dir (Default: GEOCml[nlook])
-n Number of donwsampling factor (Default: 1, no donwsampling)
-f Frame ID (e.g., 021D_04972_131213). Used only for downloading ENU
(Default: Read from directory name)
--freq Radar frequency in Hz (Default: 5.405e9 for Sentinel-1)
(e.g., 1.27e9 for ALOS, 1.2575e9 for ALOS-2/U, 1.2365e9 for ALOS-2/{F,W})
--n_para Number of parallel processing (Default: # of usable CPU)
"""
#%% Change log
'''
v1.7 20201020 Yu Morishita, GSI
- Remove -f option and not download tifs here
v1.6.1 20201016 Yu Morishita, GSI
- Deal with mli and hgt in other dtype
v1.6 20201008 Yu Morishita, GSI
Expand Down Expand Up @@ -102,7 +103,7 @@ def main(argv=None):
argv = sys.argv

start = time.time()
ver="1.6.1"; date=20201016; author="Y. Morishita"
ver="1.7"; date=20201020; 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)

Expand All @@ -114,7 +115,6 @@ def main(argv=None):
geocdir = []
outdir = []
nlook = 1
frameID = []
radar_freq = 5.405e9
n_para = len(os.sched_getaffinity(0))

Expand All @@ -126,7 +126,7 @@ def main(argv=None):
#%% Read options
try:
try:
opts, args = getopt.getopt(argv[1:], "hi:o:n:f:", ["help", "freq=", "n_para="])
opts, args = getopt.getopt(argv[1:], "hi:o:n:", ["help", "freq=", "n_para="])
except getopt.error as msg:
raise Usage(msg)
for o, a in opts:
Expand All @@ -139,8 +139,6 @@ def main(argv=None):
outdir = a
elif o == '-n':
nlook = int(a)
elif o == '-f':
frameID = a
elif o == '--freq':
radar_freq = float(a)
elif o == '--n_para':
Expand Down Expand Up @@ -179,18 +177,6 @@ def main(argv=None):
else:
center_time = None

LiCSARweb = 'http://gws-access.ceda.ac.uk/public/nceo_geohazards/LiCSAR_products/'

### Frame ID even if not used
if not frameID: ## if not specified
_tmp = re.findall(r'\d{3}[AD]_\d{5}_\d{6}', geocdir)
##e.g., 021D_04972_131213
if len(_tmp)!=0: ## if not found, keep []
frameID = _tmp[0]
trackID = str(int(frameID[0:3]))
else:
trackID = str(int(frameID[0:3]))


#%% ENU
for ENU in ['E', 'N', 'U']:
Expand All @@ -200,20 +186,8 @@ def main(argv=None):
### Download if not exist
if len(enutif)==0:
print(' No *.geo.{}.tif found in {}'.format(ENU, os.path.basename(geocdir)), flush=True)
continue

if not frameID: ## if frameID not found above
print(' Frame ID cannot be identified from dir name!', file=sys.stderr)
print(' Use -f option if you need {}.geo'.format(ENU), file=sys.stderr)
continue

### Download tif
url = os.path.join(LiCSARweb, trackID, frameID, 'metadata', '{}.geo.{}.tif'.format(frameID, ENU))
enutif = os.path.join(geocdir, '{}.geo.{}.tif'.format(frameID, ENU))
if not tools_lib.download_data(url, enutif):
print(' Error while downloading from {}'.format(url), file=sys.stderr, flush=True)
continue
else:
print(' {} dowonloaded from LiCSAR-portal'.format(os.path.basename(url)), flush=True)
else:
enutif = enutif[0] ## first one

Expand All @@ -231,9 +205,10 @@ def main(argv=None):


#%% mli
mlitif = os.path.join(geocdir, '{}.geo.mli.tif'.format(frameID))
if os.path.exists(mlitif):
print('\nCreate slc.mli', flush=True)
print('\nCreate slc.mli', flush=True)
mlitif = glob.glob(os.path.join(geocdir, '*.geo.mli.tif'))
if len(mlitif)>0:
mlitif = mlitif[0] ## First one
mli = np.float32(gdal.Open(mlitif).ReadAsArray())
mli[mli==0] = np.nan

Expand All @@ -249,15 +224,18 @@ def main(argv=None):
vmax = np.nanpercentile(mli, 95)
plot_lib.make_im_png(mli, mlipngfile, 'gray', 'MLI (log10)', vmin, vmax, cbar=True)
print(' slc.mli[.png] created', flush=True)
else:
print(' No *.geo.mli.tif found in {}'.format(os.path.basename(geocdir)), flush=True)


#%% hgt
hgttif = os.path.join(geocdir, '{}.geo.hgt.tif'.format(frameID))
if os.path.exists(hgttif):
print('\nCreate hgt', flush=True)
print('\nCreate hgt', flush=True)
hgttif = glob.glob(os.path.join(geocdir, '*.geo.hgt.tif'))
if len(hgttif)>0:
hgttif = hgttif[0] ## First one
hgt = np.float32(gdal.Open(hgttif).ReadAsArray())
hgt[hgt==0] = np.nan

if nlook != 1:
### Multilook
hgt = tools_lib.multilook(hgt, nlook, nlook)
Expand All @@ -269,6 +247,8 @@ def main(argv=None):
vmin = -vmax/3 ## bnecause 1/4 of terrain is blue
plot_lib.make_im_png(hgt, hgtpngfile, 'terrain', 'DEM (m)', vmin, vmax, cbar=True)
print(' hgt[.png] created', flush=True)
else:
print(' No *.geo.hgt.tif found in {}'.format(os.path.basename(geocdir)), flush=True)


#%% tif -> float (with multilook/downsampling)
Expand Down Expand Up @@ -384,22 +364,8 @@ def main(argv=None):
else:
shutil.copyfile(bperp_file_in, bperp_file_out)
else:
print(' No valid baselines exists.', flush=True)
if not frameID: ## if frameID not found above
print(' Frame ID cannot be identified from dir name!')
print(' Make dummy.', flush=True)
io_lib.make_dummy_bperp(bperp_file_out, imdates)
else:
print(' Try download.', flush=True)
url = os.path.join(LiCSARweb, trackID, frameID, 'metadata', 'baselines')
if not tools_lib.download_data(url, bperp_file_out):
print(' Error while downloading from {}.\n Make dummy.'.format(url), file=sys.stderr, flush=True)
io_lib.make_dummy_bperp(bperp_file_out, imdates)
else:
print(' {} dowonloaded from LiCSAR-portal'.format(os.path.basename(url)), flush=True)
if not io_lib.read_bperp_file(bperp_file_out, imdates):
print(' but not complete. Make dummy.', flush=True)
io_lib.make_dummy_bperp(bperp_file_out, imdates)
print(' No valid baselines file exists. Make dummy.', flush=True)
io_lib.make_dummy_bperp(bperp_file_out, imdates)


#%% Finish
Expand Down

0 comments on commit 8c18dd5

Please sign in to comment.