PyGMTSAR (Python GMTSAR)

[AlexeyPechnikov]

Submitting Author: Alexey Pechnikov (informally) or Aleksei Pechnikov (by passport) (pechnikov@mobigroup.ru)
All current maintainers: (pechnikov@mobigroup.ru)
Package Name: PyGMTSAR
One-Line Description of Package: PyGMTSAR (Python GMTSAR) is an open source project and Python package that provides easy and fast Sentinel-1 Satellite Interferometry for everyone
Repository Link: https://github.com/mobigroup/gmtsar
Version submitted: 2022.9.14.3 (https://pypi.org/project/pygmtsar/)
Editor: TBD
Reviewer 1: TBD
Reviewer 2: TBD
Archive: TBD
Version accepted: TBD
Date accepted (month/day/year): TBD

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Description

PyGMTSAR (Python GMTSAR) is an open source project and Python package that provides easy and fast Sentinel-1 Satellite Interferometry for everyone! While it's pure Python package under the hood it uses GMTSAR binary tools which should be installed.

Scope

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  • [x ] Data extraction
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  • Data deposition
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  • [x ] Geospatial
  • [x ] Education
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As I know the project used in research community, high school teachers and students (see GitHub followers for more details). And it's really available for everyone in just one click by web link, try the Live Google Colab examples on the GitHub project page.

The goal of the project is easy and fast satellite interferometry (InSAR) interactive and batch processing in Python scripts and Jupyter Notebooks for Sentinel-1 radar scenes everywhere as on localhost as on cloud environments like to Google Cloud VM and AI Notebooks and Amazon EC2 and even on free of charge cloud environment Google Colab.

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[lwasser]

👋 hi @mobigroup thank you for this submission. I will get back to you with next steps. In the meantime can you explain what the GMTSAR binary tools are / entail? does this package wrap around them to perform tasks on sentinel data? or is it an API wrapper to download the data? Many thanks for any clarification.

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EDIT: also for all package maintainers, will you please include github handles for each maintainer rather than an email? Many thanks.

[AlexeyPechnikov]

Hi @lwasser GMTSAR is a well-known satellite interferometry (InSAR) system based on GMT tools for geospatial data processing, see details on the project page: https://topex.ucsd.edu/gmtsar/ You’d use GMTSAR for the complete interferometry processing but it doesn’t have any user interface because it’s a set of linux console binaries and shell scripts. Every processing requires lots of manual work even when you are a linux Jedi. Also, there are some issues in the processing like to outdated interpolation methods. I use GMTSAR tools but exclude all the GMT tools for the new generation of a satellite interferometry system. I’m sorry if it sounds not so easy to understand because satellite interferometry system includes hundreds of different tools and we try to reuse some existing ones when it’s possible and add dozens of new ones (because building it from the scratch requires decades of work).

I’m a single developer of PyGMTSAR and there are no other package maintainers. PyGMTSAR GitHub repository includes some 3rd party open source software like to GMTSAR and SNAPHU (satellite interferometry phase unwrapper) and I work on GMTSAR codes too (and send the patches to it’s GitHub) to adopt the required tools to call them from PyGMTSAR. PyGMTSAR python library is located in the project subdirectory (as GMTSAR and SNAPHU codes) and it’s available as PyPi package: https://pypi.org/project/pygmtsar/ Actually, I work on the two projects at the same time: GMTSAR and PyGMTSAR where GMTSAR has lots of developers and PyGMTSAR is my own project.

[lwasser]

hi @mobigroup thank you for your patience with us as we stand up pyOpenSci. I think you have CI already so we can check that box. I am going to look for someone in the community to have a look at this package. We are just getting our editorial board setup and I am trying to create structure for the organization. I want to make sure that you have a good experience with us. Please know that this process may be a bit slower than usual as we get things together.

One other question - are there any other packages that perform overlapping tasks to this package?

Many thanks

[AlexeyPechnikov]

Hi @lwasser thanks, I understand it’s not so easy to review complex software packages! And yes, I’ve added CI tests recently.

One other question - are there any other packages that perform overlapping tasks to this package?

While there are dozens of satellite interferometry packages I don’t know any other available for everyone (you don’t need to write very complex configurations in many separate files and so on) and everywhere (as on local computer as on cloud servers and even on Google Colab) using Python scripts or Jupyter notebooks. Please follow the link to live Google Colab notebook to compute and plot the results (and edit the code and interactively view the changed results) in your browser without long hassles with software installation and other problems. At the same time, PyGMTSAR works fast using parallelization intensively and allows to process huge datasets on very common hardware like to Apple Air (using lazy computations provided by dask and xarray packages). You’d find the community on LinkedIn where I post the package updates and collect the feedback: https://www.linkedin.com/in/alexey-pechnikov/recent-activity/

[lwasser]

hey @mobigroup i just wanted to check in with you - we are searching for an editor so i'm hopeful that we can get things going soon. i'll stay in touch this week as I continue to search. We are just reestablishing our structures so I truly appreciate your patience here. please ping me with any questions

[AlexeyPechnikov]

Hi @lwasser thanks for the update. FYI, In the recent days I’ve shared PyGMTSAR Docker image which includes the ready to use environment and the live Jupyter notebooks to easy start locally without Google Colab usage. See below how to use it.

Configure your Docker runtime (Preferences -> Resources tab for Docker Desktop) to use 2 CPU cores and 8 GB RAM or 4 CPU cores and 16 GB RAM and so on. Download the Docker image (or build it yourself using the Dockerfile in the repository) and run the container forwarding port 8888 to JupyterLab using this commands inside your command line terminal window:

docker pull mobigroup/pygmtsar​
docker run -dp 8888:8888 --name pygmtsar \
    docker.io/mobigroup/pygmtsar​
docker logs pygmtsar

See the output for the JupyterLab link and copy and past it into your web browser address line. Also, the donwloaded Docker image can be started in Docker Desktop app — press “RUN” button and define the container name and the port in the opened dialog window (see “Optional settings” for the port number input field) and click on the newly created container to launch it and see the output log with the clickable link.

[lwasser]

oh that's cool. have you thought about making that image into a binder image? or would it not have enough resources? @mobigroup

and just an update. i think i've found an editor for this. thank you for being so patient. We are just getting the organization structure in place and it just takes time. I think this editor will be back online next monday and then we can kick things off.

In the meantime I have a few additional questions (in the future this will be in the review up front)

1. Do you intend to continue to maintain this package or support this package for the next ~2 years?
   2. Can you please fill out our survey? We will ask the reviewers for this package to also fill it out. It really helps us improve our organization.

Many thanks in advance for your time and patience here.

[lwasser]

One other note - if you want to work on something while we get organized, you could look into the JOSS side of things. We certaintly don't require this but

1. you should check that you package is in scope for joss
2. if it is, you can work on your paper.md file - instructions here

The way this works is that once our review is done, JOSS accepts our review and only looks at your paper. You are thus fast tracked through the JOSS review process via our review.
More soon.

[AlexeyPechnikov]

Hi @lwasser thanks, I'm glad to listen about the progress!

1. Do you intend to continue to maintain this package or support this package for the next ~2 years?

Yes, sure.

2. Can you please fill out our survey?

Ok, I'll.

... paper.md file

Ah, got it, I completely forgot about it!

[lwasser]

Awesome!! Thanks @mobigroup !!! Much appreciated!!

[AlexeyPechnikov]

Update: NASA operator Alaska Satellite Facility has installed GMTSAR on OpenSarLab (OSL). Now you can run PyGMTSAR out of the box right after starting OSL.
https://www.linkedin.com/feed/update/urn:li:activity:6987024568028708864/

[NickleDave]

Hi @mobigroup thank you for the update. It's clear you are doing a lot to make PyGMTSAR accessible for everyone

@lwasser asked me to check in here, in my role as editor in chief.

Just letting you know that we do have a potential editor and reviewers. We're still doing a little more homework about fit and overlap. You should hear back on this issue within a week.

In the meantime, could I just remind you to take this quick (10-15m) survey when you get a chance?

This helps us understand how well we are serving you and the rest of the Python open science community.
Thanks!

[lwasser]

@mobigroup so sorry i gave david the wrong survey link - this is the correct one. . ive updated David's comment above as well. this is my fault.