Please test the SBAS_snap2stamps

Linya-Peng · January 13, 2021, 2:11pm

Hi CDE, I’m now using snap8.0 in Ubuntu

CDE · January 14, 2021, 2:48pm

when I execute the command : sbas_topsar_coreg.py

I get this error :

*****IW2 of 1IWs :20161220_20151120 coregistration

b’INFO: org.esa.snap.core.gpf.operators.tooladapter.ToolAdapterIO: Initializing external tool adapters’
b’INFO: org.esa.s2tbx.dataio.gdal.GDALVersion: GDAL 2.4.2 found on system. JNI driver will be used.’
b’INFO: org.esa.s2tbx.dataio.gdal.GDALVersion: Installed GDAL 2.4.2 set to be used by SNAP.’
b’INFO: org.esa.snap.core.util.EngineVersionCheckActivator: Please check regularly for new updates for the best SNAP experience.’
b’INFO: org.esa.s2tbx.dataio.gdal.GDALVersion: Installed GDAL 2.4.2 set to be used by SNAP.’
b’Executing processing graph’
b’INFO: org.hsqldb.persist.Logger: dataFileCache open start’
b"-- org.jblas ERROR Couldn’t load copied link file: java.lang.UnsatisfiedLinkError: /tmp/jblas2130262475707773817/libjblas.so: libgfortran.so.5: Ne peut ouvrir le fichier d’objet partag\xc3\xa9: Aucun fichier ou dossier de ce type."
b’’
b’org.jblas.NativeBlas.dgemm(CCIIID[DII[DIID[DII)V’
b’ done.’
b’’
b’Error: [NodeId: Back-Geocoding] org.jblas.NativeBlas.dgemm(CCIIID[DII[DIID[DII)V’
b’-- org.jblas INFO Deleting /tmp/jblas2130262475707773817/libjblas.so’
b’-- org.jblas INFO Deleting /tmp/jblas2130262475707773817/libgfortran-4.so’
b’-- org.jblas INFO Deleting /tmp/jblas2130262475707773817/libjblas_arch_flavor.so’
b’-- org.jblas INFO Deleting /tmp/jblas2130262475707773817/libquadmath-0.so’
b’-- org.jblas INFO Deleting /tmp/jblas2130262475707773817’
033[1;35m Error in processing … coreg_ifg2run

I don’t fix my probem, I need help

Thanks.

ABraun · January 14, 2021, 3:35pm

As I have not developed or tested this script, I cannot help much.

But there is a wiki article on this type of error: https://senbox.atlassian.net/wiki/spaces/SNAP/pages/321126402/Collection+of+FAQs#On-Linux-I-get-the-error-org.jblas.NativeBlas.dgemm(CCIIID[DII[DIID[DII)V

Linya-Peng · January 15, 2021, 4:13am

I met the same error, and I tried to install libgfortran.so.5, but another error occured and I’m now still stuggling with it.

Linya-Peng · January 17, 2021, 7:55am

Hi @dongyusen
I loaded the ‘sbas_topsar_coreg.xml’ graph and found that there was no operator connected after ‘enhance spectral diversity’

Could you please explain why the graph is designed like that? (I’m a beginner in InSAR, maybe I asked a stupid question )
Thank you in advance

panggea · January 18, 2021, 8:08am

I have processed 56 Sentinel 1 data with sbas_snap2stamps and it worked fine, but there are some things to note:

This is different from snap2stamps which separate slave and master SLC data folders, sbas_snap2stamp combines master and slave file folders.
in the configure file, the AOI clip area must be filled in properly, the size must not be more than AOI BBOX DEFINITION.
The order of work:

splitting_master_free
splitting_slave_free
sbas_topsar_coreg
sbas_topsar_ifg
sbas_export

check the baseline with plotbaseline.py, if something is not connected, you can add it to the sbas_add file, then run sbas_topsar_ifg by taking longer temp_baseline on the configure file.

When setting mt_prep_snap rg_patch and az_ptch, for example:
mt_prep_snap 20150119 / min / g / process / stamps / bandung_basin / 149_615 / SBAS / INSAR_20150119 / SMALL_BASELINES / 20141108_20151103 / 0.6 5 5 50 200

this is because all data can be stored and processed.
This is most important, if the stamps are downloaded from https://github.com/dbekaert/StaMPS/ when the sb_parm_initial command is activated or small_baseline_flag: ‘y’ in stamps (1), stamps step 1 will occur an error.

download and replace the sb_load_initial_gamma.m file from https://github.com/limingjia92/StaMPS/blob/patch-2/matlab/sb_load_initial_gamma.m from the matlab folder.

configure file

sbas_bb_149_613
sbas result

.
.
.
and I already process with ps insar
ps_bb_149_613
ps result

dongyusen · January 18, 2021, 10:40am

I had update the sbas_topsar_coreg.xml file, please download the new file.
thx!

dongyusen · January 18, 2021, 10:41am

Well done! Thanks @panggea.

dongyusen · January 18, 2021, 10:42am

the scripts are working on python3.8 and snap7.0, please test the snap8.0. thx

Martini · January 20, 2021, 3:44pm

Good afternoon,
I am using PSI and now i would like to try this new method SBAS, but i cannot understand what cropSx,CropSy…etc means. if you can give me some examples.

Linya-Peng · January 21, 2021, 2:40am

In my opinion, cropSx means ‘Startx’, cropSy means ‘Starty’, and CropWx(y) means the width and hight of the image after subset. I checked these from gpt Subset -h, I don’t know whether my understanding is correct.

CDE · January 21, 2021, 9:15am

Hi @Linya-Peng , @dongyusen

Please we need more clarification and how to obtain them

CropSx=? , CropSy=? , CropWx=? , CropWy=?

Thanks.

Linya-Peng · January 21, 2021, 9:20am

I used the subset operator in SNAP GUI to obtain them

CDE · January 21, 2021, 9:24am

Dear @dongyusen

In the step sbas_topsar_coreg ,I get the error bellow and I fail to fix it

Processing … 4 of 4 dataset…
Processing …20161220_20170302…

*****IW2 of 1IWs :20161220_20170302 coregistration

b’INFO: org.esa.snap.core.gpf.operators.tooladapter.ToolAdapterIO: Initializing external tool adapters’
b"SEVERE: org.esa.s2tbx.dataio.gdal.activator.GDALDistributionInstaller: The environment variable LD_LIBRARY_PATH is not set. It must contain the current folder ‘.’."
b’INFO: org.esa.snap.core.util.EngineVersionCheckActivator: Please check regularly for new updates for the best SNAP experience.’
b’Executing processing graph’
b’INFO: org.hsqldb.persist.Logger: dataFileCache open start’
b"…10%…20%…Java HotSpot™ 64-Bit Server VM warning: INFO: os::commit_memory(0x00007fc9a4580000, 466092032, 0) failed; error=‘Ne peut allouer de la m\xc3\xa9moire’ (errno=12)"
b’#’
b’# There is insufficient memory for the Java Runtime Environment to continue.’
b’# Native memory allocation (mmap) failed to map 466092032 bytes for committing reserved memory.’
b’# An error report file with more information is saved as:’
b’# study/my_sbas/bin/hs_err_pid6633.log’
033[1;35m Error in processing … coreg_ifg2run

hs_err_pid6633.log (141.9 KB)

ABraun · January 21, 2021, 10:33am

this is quite clear I would say…

Linya-Peng · January 21, 2021, 12:18pm

Hi @dongyusen ! Sorry to disturbe~
I finished the “sbas_topsar_coreg.py”, and got 29 coregistration pairs in the tempcoreg folder:

All of them are not empty, and could be opened in SNAP GUI. However, I got a “the specified region if not null, must intersect with the image’s boounds” error while running “sbas_topsar_ifg.py”. I tried to form ifg in SNAP and still got the same error:

However, some ifgs successfully generated, like this:

I search the problem in the forum but the situation is not same, could you please help me?

CDE · January 21, 2021, 12:34pm

but I have sufficient memory , here why I didn’t understand

ABraun · January 21, 2021, 12:57pm

sorry, I don’t know your computer’s capabilities, so I was just interpreting the error message.

Martini · January 21, 2021, 3:46pm

I have a mistake but I don’t know what it is, someone can bend the why?
Cattura

ABraun · January 21, 2021, 4:04pm

please open the script with a text editor, go to line 175 (third from the bottom) and remove the asian characters, then save the file and run the script again.