Snaphu export fails for areas with NaN values (water, border pixels)

[loreabad6]

When doing the unwrapping, with a single tile, Snaphu fails with the following:

snaphu v1.4.2
27 parameters input from file snaphu.conf (84 lines total)
only one tile--disregarding multiprocessor option
only one tile--disregarding tile overlap values
Logging run-time parameters to file snaphu.log
Reading wrapped phase from file Phase_ifg_IW3_VV_25Aug2019_31Aug2019.snaphu.img
NaN or infinity found in input float data
Abort
done

Working on a subset inlands works good.
cc @bro076

[loreabad6]

After further checking, what seems to be the problem is the export step in the pipeline.

It creates weird artifacts on water areas that then result in errors during unwrapping:

The errors are gone using Snaphu Export in SNAP-6, which I have installed locally.

And then unwrapping works:

I found this thread on the STEP forum that might be related, but I am not sure as if this is the case.

My problem is I cannot really test the Export in SNAP 8 Desktop since I don't have it locally.
@bro076 I think you have SNAP-8 desktop, could you give it a try? I added a subset of the output of pipeline II here.
@ZahraDabiri you have SNAP-7 right? Would you also mind testing?

Thank you both!

[bro076]

good stuff! Yes I have snap 8. I am going to another Oslo meeting for a few days now, but I will try it get it running tonight or tomorrow. Can snap 8 not be installed in the docker?

[loreabad6]

Yes but only command line for now. I am trying to determine if this is a bug from snappy, from SNAP-8 or from any other source... That's why I want to run the process on Snap-8 Desktop

[ZahraDabiri]

Hi Lorena,

I did the export, unwrapping, import in the SNAP v7; the results look good

. I saved it on the R drive:
"...\PFG330001_12_SliDEM\04_Work\WP3\DEM generation and Landslide volume estimaiton\test\Snphu" . "out_pipe_II_subset_Snaphu.dim" is the result of the import .

hope it helps :-)

[loreabad6]

Thanks Ani! Yes looks good so SNAP 6 and 7 work ok... let's see if SNAP-8 Desktop gives issues

[bro076]

Looks great! Sorry I haven't had time today yet to check Get Outlook for Android<https://aka.ms/AAb9ysg>

…

________________________________ From: Lorena Abad Crespo ***@***.***> Sent: Wednesday, November 3, 2021 4:54:27 PM To: SliDEM-project/SliDEM-python ***@***.***> Cc: Benjamin Robson ***@***.***>; Mention ***@***.***> Subject: Re: [SliDEM-project/SliDEM-python] Snaphu export fails for subsets with water in SNAP 8 (Issue #9) Thanks Ani! Yes looks good so SNAP 6 and 7 work ok... let's see if SNAP-8 Desktop gives issues — You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub<#9 (comment)>, or unsubscribe<https://github.com/notifications/unsubscribe-auth/AMTZPBK6LYJ4MICMHV4ZT7TUKFLLHANCNFSM5GOD24CA>. Triage notifications on the go with GitHub Mobile for iOS<https://apps.apple.com/app/apple-store/id1477376905?ct=notification-email&mt=8&pt=524675> or Android<https://play.google.com/store/apps/details?id=com.github.android&referrer=utm_campaign%3Dnotification-email%26utm_medium%3Demail%26utm_source%3Dgithub>.

[loreabad6]

No worries! take your time :)

[bro076]

I ran it in python, and I get the result looks the same as when done in SNAP Desktop

[loreabad6]

Maybe related but there have been several failures also with the message:

Reading wrapped phase from file Phase_ifg_IW1_VV_19Jul2018_13Jul2018.snaphu.img
No weight file specified.  Assuming uniform weights
No brightness file specified.  Using interferogram magnitude as intensity
Reading correlation data from file coh_IW1_VV_19Jul2018_13Jul2018.snaphu.img
Calculating topography-mode cost parameters
Despeckling intensity image
Normalizing intensity
Intensity-normalization averaging box too large for input array size
Abort

Some checks indicate that coherence is 0 everywhere, any thoughts @ZahraDabiri?