Prepare ISCE topsApp interferograms for processing with MintPy
We often use topsApp.py to process sentinel-1 data. However, MintPy can only read the results of topsStack directly at present. We need some post-processing to make MintPy can produce the result of topsApp.py .
Prepare the structured folders
The folder structure required by Minpy to handle tops is as follows ISCE / topsStack:
$DATA_DIR/GalapagosSenDT128
├── baselines
│ ├── 20141213_20141225
│ │ └── 20141213_20141225.txt
│ └── ...
├── reference
│ ├── data.rsc
│ ├── IW1
│ ├── IW1.xml
│ ├── IW2
│ └── IW2.xml
├── merged
│ ├── geom_reference
│ │ ├── hgt.rdr
│ │ ├── hgt.rdr.full.vrt
│ │ ├── hgt.rdr.full.xml
│ │ ├── hgt.rdr.vrt
│ │ ├── hgt.rdr.xml
│ │ ├── lat.rdr
│ │ ├── lat.rdr.full.vrt
│ │ ├── lat.rdr.full.xml
│ │ ├── lat.rdr.vrt
│ │ ├── lat.rdr.xml
│ │ ├── lon.rdr
│ │ ├── lon.rdr.full.vrt
│ │ ├── lon.rdr.full.xml
│ │ ├── lon.rdr.vrt
│ │ ├── lon.rdr.xml
│ │ ├── los.rdr
│ │ ├── los.rdr.full.vrt
│ │ ├── los.rdr.full.xml
│ │ ├── los.rdr.vrt
│ │ ├── los.rdr.xml
│ │ ├── shadowMask.rdr
│ │ ├── shadowMask.rdr.full.vrt
│ │ ├── shadowMask.rdr.full.xml
│ │ ├── shadowMask.rdr.vrt
│ │ └── shadowMask.rdr.xml
│ └── interferograms
│ ├── 20141213_20141225
│ │ ├── filt_fine.cor
│ │ ├── filt_fine.cor.vrt
│ │ ├── filt_fine.cor.xml
│ │ ├── filt_fine.unw
│ │ ├── filt_fine.unw.conncomp
│ │ ├── filt_fine.unw.conncomp.vrt
│ │ ├── filt_fine.unw.conncomp.xml
│ │ ├── filt_fine.unw.vrt
│ │ ├── filt_fine.unw.xml
│ │ ├── ...
│ ├── 20141213_20150307
│ └── ...
├── secondarys
│ ├── 20141225
│ │ ├── IW1
│ │ ├── IW1.xml
│ │ ├── IW2
│ │ └── IW2.xml
│ ├── 20150307
│ └── ...
└── mintpy
└── GalapagosSenDT128.txt
Suppose you process all interferograms in one folder, which has the folder structure as follows:
.
|-- 20210917_20210929
|-- 20210917_20211011
|-- 20210917_20211023
|-- 20210917_20211210
|-- 20210929_20211011
|-- 20210929_20211023
|-- 20210929_20211104
|-- ...
Firstly, import packages and specify the home directory.
import rasterio
import os
from pathlib import Path
import warnings
from tqdm import tqdm
import numpy as np
ifg_home = Path('/data/sentinel1/result/interferogams')
stack_home = Path('/data/sentinel1/result/stacks')
Now, let’s create the folder structure that MintPy required.
def ensure_folder(folder):
if not folder.is_dir():
folder.mkdir(parents=True)
baseline_dir = stack_home / 'baselines'
reference_dir = stack_home / 'reference'
secondarys_dir = stack_home / 'secondarys'
mintpy_dir = stack_home / 'mintpy'
merged_dir = stack_home / 'merged'
geom_reference_dir = merged_dir / 'geom_reference'
interferograms_dir = merged_dir / 'interferograms'
stack_fld_list = [baseline_dir, reference_dir,
secondarys_dir, mintpy_dir,
merged_dir, geom_reference_dir,
interferograms_dir]
for fld in stack_fld_list:
ensure_folder(fld)
Link files
We have created the folders that MintPy required. But there are no files in those folders. We need to link files from ISCE processed into those folders.
def looks(vrt_file, rdr_file, nlook_a, nlook_r):
os.system(f'looks.py -i {vrt_file} -o {rdr_file} -a {nlook_a} -r {nlook_r}')
ifgs_files = sorted(ifg_home.iterdir())
for file in tqdm(ifgs_files, desc='link files'):
name = file.name
ref_name, sec_name = name.split('_')
merged = file / 'merged'
i = 0
if merged.exists():
os.chdir(file)
if i == 0:
i += 1
ref_dir = file / ref_name
ref_cmd = f'ln -sf {ref_dir}/* {reference_dir}/'
os.system(ref_cmd)
looks(merged.joinpath('z.rdr.full.xml'),
geom_reference_dir.joinpath('hgt.rdr'),
4,20)
looks(merged.joinpath('lat.rdr.full.xml'),
geom_reference_dir.joinpath('lat.rdr'),
4,20)
looks(merged.joinpath('lon.rdr.full.xml'),
geom_reference_dir.joinpath('lon.rdr'),
4,20)
looks(merged.joinpath('los.rdr.full.xml'),
geom_reference_dir.joinpath('los.rdr'),
4,20)
ifg_out = interferograms_dir / name
ensure_folder(ifg_out)
ln_cmd1 = f'ln -sf {merged}/filt_* {ifg_out}/'
os.system(ln_cmd1)
ln_cmd2 = f'ln -sf {merged}/phsig.cor* {ifg_out}/'
os.system(ln_cmd2)
sec_dir = file / sec_name
sec_cmd = f'ln -sf {sec_dir} {secondarys_dir}/'
os.system(sec_cmd)
generate baseline
We can use isce2/contrib/stack/topsStack/computeBaseline.py to generate baselines. This script was not installed by default, for example, installed by conda. You need to find its location from the source code of ISCE.
def get_dates_from_ifgs(ifgs):
dates_all = []
for ifg in ifgs:
dates_all.extend(ifg.split('_'))
dates = sorted(set(dates_all))
return dates
ifgs = [i.name for i in ifgs_files]
dates = get_dates_from_ifgs(ifgs)
ref_name = dates[0]
ref_dir = ifgs_files[0] / ref_name
for sec_name in tqdm(dates[1:], desc='generate baselines'):
sec_dir = secondarys_dir / sec_name
bl_name = f'{ref_name}_{sec_name}'
bl_dir = baseline_dir / bl_name
ensure_folder(bl_dir)
bl_file = bl_dir / f'{bl_name}.txt'
bl_cmd = f'/data/isce2/contrib/stack/topsStack/computeBaseline.py -m {ref_dir}/ -s {sec_dir}/ -b {bl_file}'
os.system(bl_cmd)
prep_isce.py
For the folder reference, we need to use prep_isce.py to generate the data.rsc file.
os.chdir(reference_dir)
prep_cmd = ('/root/miniconda3/bin/prep_isce.py'
f' -f "{interferograms_dir}/*/filt_*.unw"'
f' -m {reference_dir}/IW2.xml'
f' -b {baseline_dir}/'
f' -g {geom_reference_dir}/')
print(prep_cmd)
os.system(prep_cmd)
If everything is ok, no errors will be reported.
write options file for MintPy
cfg_file = mintpy_dir / 'mintpy_data_options.cfg'
cfg_info = f'''mintpy.load.processor = isce
##---------for ISCE only:
mintpy.load.metaFile = {reference_dir}/IW*.xml
mintpy.load.baselineDir = {baseline_dir}
##---------interferogram datasets:
mintpy.load.unwFile = {interferograms_dir}/*/filt_*.unw
mintpy.load.corFile = {interferograms_dir}/*/phsig.cor
mintpy.load.connCompFile = {interferograms_dir}/*/filt_*.unw.conncomp
##---------geometry datasets:
mintpy.load.demFile = {geom_reference_dir}/hgt.rdr
mintpy.load.lookupYFile = {geom_reference_dir}/lat.rdr
mintpy.load.lookupXFile = {geom_reference_dir}/lon.rdr
mintpy.load.incAngleFile = {geom_reference_dir}/los.rdr
mintpy.load.azAngleFile = {geom_reference_dir}/los.rdr
# mintpy.load.shadowMaskFile = {geom_reference_dir}/shadowMask.rdr
'''
with open(cfg_file, 'w') as f:
f.write(cfg_info)
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