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stripmapStack: convert README.txt to README.md 

+ convert README.txt to README.md

+ stackStripMap.py: group iono options in createParser()
   - group all iono options in createParser() for more easily navigation in --help.

   - fix typos in the descriptions for the script and --dem option.
LT1AB
Zhang Yunjun 2019-03-18 19:32:08 -04:00
parent 90310c3211
commit 1b70f52f91
4 changed files with 151 additions and 126 deletions
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85
contrib/stack/stripmapStack/README.md Normal file
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@ -0,0 +1,85 @@
## StripMap stack processor
The detailed algorithms and workflow for stack processing of stripmap SAR data can be found here:
+ Fattahi, H., M. Simons, and P. Agram (2017), InSAR Time-Series Estimation of the Ionospheric Phase Delay: An Extension of the Split Range-Spectrum Technique, IEEE Transactions on Geoscience and Remote Sensing, 55(10), 5984-5996, doi:[10.1109/TGRS.2017.2718566](https://ieeexplore.ieee.org/abstract/document/7987747/).
-----------------------------------
To use the stripmap stack processor, make sure to add the path of your `contrib/stack/stripmapStack` folder to your `$PATH` environment varibale.
Currently supported workflows include a coregistered stack of SLC, interferograms, ionospheric delays.
Here are some notes to get started with processing stacks of stripmap data with ISCE.
#### 1. Create your project folder somewhere
```
mkdir MauleAlosDT111
cd MauleAlosDT111
```
#### 2. Prepare DEM
a) create a folder for DEM;
b) create a DEM using dem.py with SNWE of your study area in integer;
d) Keep only ".dem.wgs84", ".dem.wgs84.vrt" and ".dem.wgs84.xml" and remove unnecessary files;
d) fix the path of the file in the xml file of the DEM by using fixImageXml.py.
```
mkdir DEM; cd DEM
dem.py -a stitch -b -37 -31 -72 -69 -r -s 1 -c
rm demLat*.dem demLat*.dem.xml demLat*.dem.vrt
fixImageXml.py -f -i demLat*.dem.wgs84
cd ..
```
#### 3. Download data
##### 3.1 create a folder to download SAR data (i.e. ALOS-1 data from ASF)
```
mkdir download
cd download
```
##### 3.2 Download the data that that you want to process to the "downlowd" directory
#### 4. Prepare SAR data
Once all data have been downloaded, we need to unzip them and move them to different folders and getting ready for unpacking and then SLC generation. This can be done by running the following command in a directory above "download":
```
prepRawALOS.py -i download/ -o SLC
```
This command generates an empty SLC folder and a run file called: "run_unPackALOS".
You could also run prepRawSensor.py which aims to recognize the sensor data automatically followed by running the sensor specific preparation script. For now we include support for ALOS and CSK raw data, but it is trivial to expand and include other sensors as unpacking routines are already included in the distribution.
```
prepRawSensor.py -i download/ -o SLC
```
#### 5. Execute the commands in "run_unPackALOS" file
If you have a cluster that you can submit jobs, you can submit each line of command to a processor. The commands are independent and can be run in parallel.
After successfully running the previous step, you should see acquisition dates in the SLC folder and the ".raw" files for each acquisition.
Note: For ALOS-1, If there is an acquisition that does not include .raw file, this is most likely due to PRF change between frames and can not be currently handled by ISCE. You have to ignore those.
#### 6. Run "stackStripmap.py"
This will generate many config and run files that need to be executed. Here is an example:
```
stackStripMap.py -s SLC/ -d DEM/demLat*.dem.wgs84 -t 250 -b 1000 -a 14 -r 4 -u snaphu
```
This will produce:
a) baseline folder, which contains baseline information
b) pairs.png which is a baseline-time plot of the network of interferograms
c) configs: which contains the configuration parameter to run different InSAR processing steps
d) run_files: a folder that includes several run and job files that needs to be run in order
#### 7. Execute the commands in run files (run_1*, run_2*, etc) in the "run_files" folder

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contrib/stack/stripmapStack/README.txt
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@ -1,64 +0,0 @@
The detailed algorithms for stack processing of stripmap data can be found here:
H. Fattahi, M. Simons, and P. Agram, "InSAR Time-Series Estimation of the Ionospheric Phase Delay: An Extension of the Split Range-Spectrum Technique", IEEE Trans. Geosci. Remote Sens., vol. 55, no. 10, 5984-5996, 2017. (https://ieeexplore.ieee.org/abstract/document/7987747/)
-----------------------------------
Notes on stripmap stack processor:
Here are some notes to get started with processing stacks of stripmap data with ISCE.
1- create a folder somewhere for your project
mkdir MauleT111
cd MauleT111
2- create a DEM:
dem.py -a stitch -b -37 -31 -72 -69 -r -s 1 -c
3- Keep only ".dem.wgs84", ".dem.wgs84.vrt" and ".dem.wgs84.xml" and remove unnecessary files
4- fix the path of the file in the xml file of the DEM by using this command:
fixImageXml.py -f -i demLat_S37_S31_Lon_W072_W069.dem.wgs84
5- create a folder to download the ALOS-1 data from ASF:
mkdir download
cd download
6- Download the data that that you want to process to the downlowd directory.
7- once all data have been downloaded, we need to unzip them and move them to different folders and getting ready for unpacking and then SLC generation.
This can be done by running the following command in a directory above "download":
prepRawALOS.py -i download/ -o SLC
This command generates an empty SLC folder and a run file called: "run_unPackALOS".
You could also run prepRawSensor.py which aims to recognize the sensor data automatically followed by running the sensor specific preparation script. For now we include support for ALOS and CSK raw data, but it is trivial to expand and include other sensors as unpacking routines are already included in the distribution.
prepRawSensor.py -i download/ -o SLC
8- execute the commands inside run_unPackALOS file. If you have a cluster that you can submit jobs, you can submit each line of command to a processor. The commands are independent and can be run in parallel.
9- After successfully running the previous step, you should see acquisition dates in the SLC folder and the ".raw" files for each acquisition
Note: For ALOS-1, If there is an acquisition that does not include .raw file, this is most likely due to PRF change between frames and can not be currently handled by ISCE. You have to ignore those.
10- run stackStripmap.py which will generate many config and run files that need to be executed. Here is an example:
stackStripMap.py -s SLC/ -d demLat_S37_S31_Lon_W072_W069.dem.wgs84 -t 250 -b 1000 -a 14 -r 4 -u snaphu
This will produce:
a) baseline folder, which contains baseline information
b) pairs.png which is a baseline-time plot of the network of interferograms
c) configs: which contains the configuration parameter to run different InSAR processing steps
d) run_files: a folder that includes several run and job files that needs to be run in order
11- execute the commands in run files (run_1, run_2, etc) in the run_files folder

65
contrib/stack/stripmapStack/stackStripMap.py
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@ -5,7 +5,7 @@
import os, imp, sys, glob import os, imp, sys, glob
import argparse import argparse
import configparser import configparser
import datetime import datetime
import numpy as np import numpy as np
import shelve import shelve
import isce import isce
@ -20,7 +20,7 @@ defoMax = '2'
maxNodes = 72 maxNodes = 72
def createParser(): def createParser():
parser = argparse.ArgumentParser( description='Preparing the directory structure and config files for stack processing of Sentinel data') parser = argparse.ArgumentParser( description='Preparing the directory structure and config files for stack processing of StripMap data')
parser.add_argument('-s', '--slc_directory', dest='slcDir', type=str, required=True, parser.add_argument('-s', '--slc_directory', dest='slcDir', type=str, required=True,
help='Directory with all stripmap SLCs') help='Directory with all stripmap SLCs')
@ -31,7 +31,7 @@ def createParser():
help='Working directory ') help='Working directory ')
parser.add_argument('-d', '--dem', dest='dem', type=str, required=True, parser.add_argument('-d', '--dem', dest='dem', type=str, required=True,
help='Directory with the DEM (.xml and .vrt files)') help='DEM file (with .xml and .vrt files)')
parser.add_argument('-m', '--master_date', dest='masterDate', type=str, default=None, parser.add_argument('-m', '--master_date', dest='masterDate', type=str, default=None,
help='Directory with master acquisition') help='Directory with master acquisition')
@ -43,47 +43,54 @@ def createParser():
help='Baseline threshold (max bperp in meters)') help='Baseline threshold (max bperp in meters)')
parser.add_argument('-a', '--azimuth_looks', dest='alks', type=str, default='10', parser.add_argument('-a', '--azimuth_looks', dest='alks', type=str, default='10',
help='Number of looks in azimuth (automaticly computed as AspectR*looks when "S" or "sensor" is defined to give approximately square multi-look pixels)') help='Number of looks in azimuth (automaticly computed as AspectR*looks when '
'"S" or "sensor" is defined to give approximately square multi-look pixels)')
parser.add_argument('-r', '--range_looks', dest='rlks', type=str, default='10', parser.add_argument('-r', '--range_looks', dest='rlks', type=str, default='10',
help='Number of looks in range') help='Number of looks in range')
parser.add_argument('-S', '--sensor', dest='sensor', type=str, required=False, parser.add_argument('-S', '--sensor', dest='sensor', type=str, required=False,
help='SAR sensor used to define square multi-look pixels') help='SAR sensor used to define square multi-look pixels')
parser.add_argument('-L', '--low_band_frequency', dest='fL', type=str, default=None,
help='low band frequency') parser.add_argument('-u', '--unw_method', dest='unwMethod', type=str, default='snaphu',
parser.add_argument('-H', '--high_band_frequency', dest='fH', type=str, default=None, help='unwrapping method (icu, snaphu, or snaphu2stage)')
help='high band frequency')
parser.add_argument('-B', '--subband_bandwidth ', dest='bandWidth', type=str, default=None,
help='sub-band band width')
parser.add_argument('-u', '--unw_method', dest='unwMethod', type=str, default='snaphu'
, help='unwrapping method (icu, snaphu, or snaphu2stage)')
parser.add_argument('-f','--filter_strength', dest='filtStrength', type=str, default=filtStrength, parser.add_argument('-f','--filter_strength', dest='filtStrength', type=str, default=filtStrength,
help='strength of Goldstein filter applied to the wrapped phase before spatial coherence estimation.' help='strength of Goldstein filter applied to the wrapped phase before spatial coherence estimation.'
' Default: {}'.format(filtStrength)) ' Default: {}'.format(filtStrength))
parser.add_argument('--filter_sigma_x', dest='filterSigmaX', type=str, default='100' iono = parser.add_argument_group('Ionosphere', 'Configurationas for ionospheric correction')
, help='filter sigma for gaussian filtering the dispersive and nonDispersive phase') iono.add_argument('-L', '--low_band_frequency', dest='fL', type=str, default=None,
help='low band frequency')
iono.add_argument('-H', '--high_band_frequency', dest='fH', type=str, default=None,
help='high band frequency')
iono.add_argument('-B', '--subband_bandwidth ', dest='bandWidth', type=str, default=None,
help='sub-band band width')
parser.add_argument('--filter_sigma_y', dest='filterSigmaY', type=str, default='100.0', iono.add_argument('--filter_sigma_x', dest='filterSigmaX', type=str, default='100',
help='sigma of the gaussian filter in Y direction, default=100') help='filter sigma for gaussian filtering the dispersive and nonDispersive phase')
parser.add_argument('--filter_size_x', dest='filterSizeX', type=str, default='800.0', iono.add_argument('--filter_sigma_y', dest='filterSigmaY', type=str, default='100.0',
help='size of the gaussian kernel in X direction, default = 800') help='sigma of the gaussian filter in Y direction, default=100')
parser.add_argument('--filter_size_y', dest='filterSizeY', type=str, default='800.0', iono.add_argument('--filter_size_x', dest='filterSizeX', type=str, default='800.0',
help='size of the gaussian kernel in Y direction, default=800') help='size of the gaussian kernel in X direction, default = 800')
parser.add_argument('--filter_kernel_rotation', dest='filterKernelRotation', type=str, default='0.0', iono.add_argument('--filter_size_y', dest='filterSizeY', type=str, default='800.0',
help='rotation angle of the filter kernel in degrees (default = 0.0)') help='size of the gaussian kernel in Y direction, default=800')
parser.add_argument('-W', '--workflow', dest='workflow', type=str, default='slc' iono.add_argument('--filter_kernel_rotation', dest='filterKernelRotation', type=str, default='0.0',
, help='The InSAR processing workflow : (slc, interferogram, ionosphere)') help='rotation angle of the filter kernel in degrees (default = 0.0)')
parser.add_argument('-z', '--zero', dest='zerodop', action='store_true', default=False, help='Use zero doppler geometry for processing - Default : No') parser.add_argument('-W', '--workflow', dest='workflow', type=str, default='slc',
parser.add_argument('--nofocus', dest='nofocus', action='store_true', default=False, help='If input data is already focused to SLCs - Default : do focus') help='The InSAR processing workflow : (slc, interferogram, ionosphere)')
parser.add_argument('-c', '--text_cmd', dest='text_cmd', type=str, default=''
, help='text command to be added to the beginning of each line of the run files. Example : source ~/.bash_profile;') parser.add_argument('-z', '--zero', dest='zerodop', action='store_true', default=False,
parser.add_argument('-useGPU', '--useGPU', dest='useGPU',action='store_true', default=False, help='Allow App to use GPU when available') help='Use zero doppler geometry for processing - Default : No')
parser.add_argument('--nofocus', dest='nofocus', action='store_true', default=False,
help='If input data is already focused to SLCs - Default : do focus')
parser.add_argument('-c', '--text_cmd', dest='text_cmd', type=str, default='',
help='text command to be added to the beginning of each line of the run files. Example : source ~/.bash_profile;')
parser.add_argument('-useGPU', '--useGPU', dest='useGPU',action='store_true', default=False,
help='Allow App to use GPU when available')
parser.add_argument('--summary', dest='summary', action='store_true', default=False, help='Show summary only') parser.add_argument('--summary', dest='summary', action='store_true', default=False, help='Show summary only')
return parser return parser

17
contrib/stack/stripmapStack/topo.py
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@ -1,17 +1,17 @@
#!/usr/bin/env python3 #!/usr/bin/env python3
import argparse
import isce
import isceobj
import numpy as np
import shelve
import os import os
import argparse
import shelve
import datetime import datetime
import shutil import shutil
import numpy as np
import isce
import isceobj
from isceobj.Constants import SPEED_OF_LIGHT from isceobj.Constants import SPEED_OF_LIGHT
from isceobj.Util.Poly2D import Poly2D from isceobj.Util.Poly2D import Poly2D
from mroipac.looks.Looks import Looks from mroipac.looks.Looks import Looks
def createParser(): def createParser():
''' '''
Command line parser. Command line parser.
@ -331,6 +331,7 @@ def runTopoCPU(info, demImage, dop=None,
topo.topo() topo.topo()
return return
def runSimamp(outdir, hname='z.rdr'): def runSimamp(outdir, hname='z.rdr'):
from iscesys.StdOEL.StdOELPy import create_writer from iscesys.StdOEL.StdOELPy import create_writer
@ -502,11 +503,9 @@ def main(iargs=None):
doppler = db['doppler'] doppler = db['doppler']
except: except:
doppler = frame._dopplerVsPixel doppler = frame._dopplerVsPixel
db.close() db.close()
####Setup dem ####Setup dem
demImage = isceobj.createDemImage() demImage = isceobj.createDemImage()
demImage.load(inps.dem + '.xml') demImage.load(inps.dem + '.xml')
@ -522,7 +521,6 @@ def main(iargs=None):
info.incFilename = os.path.join(info.outdir, 'incLocal.rdr') info.incFilename = os.path.join(info.outdir, 'incLocal.rdr')
info.maskFilename = os.path.join(info.outdir, 'shadowMask.rdr') info.maskFilename = os.path.join(info.outdir, 'shadowMask.rdr')
runTopo(info,demImage,dop=doppler,nativedop=inps.nativedop, legendre=inps.legendre) runTopo(info,demImage,dop=doppler,nativedop=inps.nativedop, legendre=inps.legendre)
runSimamp(os.path.dirname(info.heightFilename),os.path.basename(info.heightFilename)) runSimamp(os.path.dirname(info.heightFilename),os.path.basename(info.heightFilename))
@ -540,4 +538,3 @@ if __name__ == '__main__':
Main driver. Main driver.
''' '''
main() main()