Notes of Processing SBAS in Mintpy

This blog is about some notes during Mintpy SBAS-InSAR processing using Sentinel-1 data in AutoDL.

Build the environment

Is it possible to process PSInSAR withour Matlab?

Yes, it is absolutely possible to run StaMPS without MATLAB. The primary alternative, and the one most commonly used by researchers who don’t have a MATLAB license, is GNU Octave.

Here’s why Octave is a viable option and some considerations:

GNU Octave: The Open-Source Alternative

MATLAB Compatibility: GNU Octave is a free and open-source software that aims to be largely compatible with MATLAB. Many MATLAB scripts and functions will run in Octave with little to no modification. StaMPS is designed with this compatibility in mind.
Cost-Effective: Since Octave is free, it eliminates the significant cost associated with a MATLAB license, making StaMPS accessible to a wider range of users and institutions.
Active Development: Octave is actively developed, and newer versions continuously improve MATLAB compatibility and performance.

Considerations when using Octave for StaMPS:

Version Compatibility: While Octave strives for compatibility, there might be minor differences in how certain functions behave or syntax is interpreted between MATLAB and Octave. It’s generally recommended to use a recent version of Octave (e.g., Octave 8.x or later) for the best compatibility with StaMPS.
Performance: In some cases, MATLAB might offer better performance for certain operations due to its optimized libraries. However, for most typical StaMPS processing, Octave’s performance is generally sufficient.
Toolboxes: MATLAB has a vast array of specialized toolboxes. While Octave has its own set of packages (often collectively referred to as octave-forge) that provide similar functionalities, you might occasionally encounter a specific MATLAB function used by StaMPS that doesn’t have an exact Octave equivalent or behaves slightly differently. These instances are becoming rarer as Octave matures.
Debugging and Development Environment: MATLAB’s integrated development environment (IDE) and debugging tools are often considered more robust and user-friendly. Octave’s environment is functional but might require a bit more command-line interaction for some tasks.
Installation and Compilation: As mentioned in the previous detailed guide, when compiling StaMPS, you need to ensure your Makefile is correctly configured to use Octave’s MEX compiler (usually mkoctfile) instead of MATLAB’s mex compiler, and the OCTAVE_HOME variable points to your Octave installation.

In summary:

For running StaMPS, GNU Octave is the recommended and widely used free alternative to MATLAB. While there might be occasional minor compatibility quirks, these are usually manageable, and the benefits of an open-source solution often outweigh these small inconveniences. Many StaMPS users successfully process their InSAR data using Octave.

Matlab VS. GUN Octace

You’re in a great position! It’s absolutely possible to process PSInSAR using StaMPS without a MATLAB license, and GNU Octave is the standard and widely accepted open-source alternative for this purpose.

Here’s a breakdown of the differences between MATLAB and GNU Octave, specifically in the context of running StaMPS, and why Octave is a perfectly viable choice:

MATLAB vs. GNU Octave for StaMPS

MATLAB (Proprietary)

Pros:
- Commercial Support & Polished Environment: MathWorks provides professional support, extensive documentation, and a highly polished Integrated Development Environment (IDE) with powerful debugging tools.
- Performance Optimization: MATLAB’s core numerical routines are highly optimized, often benefiting from just-in-time (JIT) compilation, which can lead to faster execution times for certain operations, especially on large datasets.
- Extensive Toolboxes: MATLAB has a vast ecosystem of specialized toolboxes (e.g., Signal Processing, Image Processing, Statistics, Optimization, etc.) that are often highly optimized and well-integrated.
- Industry Standard: In many engineering and scientific fields, MATLAB remains the industry standard, meaning more existing codebases and more professionals are familiar with it.
Cons:
- Cost: This is the primary hurdle. MATLAB licenses are expensive, especially for commercial use or if you need multiple toolboxes. This is the exact reason you’re looking for an alternative!
- Closed Source: Its proprietary nature means you can’t inspect or modify the source code, which can be a limitation for some research or specific customization needs.

GNU Octave (Free & Open Source)

Pros:
- Free and Open Source: This is its biggest advantage. No license fees, no restrictions on use, and the source code is available for inspection and modification. This makes it ideal for academic research, personal projects, and budget-constrained organizations.
- High MATLAB Compatibility: Octave is designed to be syntactically and largely functionally compatible with MATLAB. Most basic MATLAB scripts, including the core of StaMPS, run in Octave with minimal or no modifications. This means your learning curve from any existing MATLAB knowledge is very low.
- Growing Ecosystem: Octave has its own set of community-contributed packages (often from the octave-forge project) that replicate much of the functionality of MATLAB’s toolboxes.
- Community Support: While not as centralized as MathWorks support, there’s an active community that provides help through forums and documentation.
- Deployability: Its open-source nature makes it easier to deploy on cloud platforms or high-performance computing (HPC) clusters without licensing concerns.
Cons:
- Performance: Generally, Octave can be slower than MATLAB, particularly for very large-scale computations or complex operations that leverage MATLAB’s highly optimized internal functions or JIT compiler. However, for many StaMPS processing steps, this difference might not be prohibitive, especially if you provision a sufficiently powerful cloud VM.
- Less Polished IDE/Tooling: While Octave has a graphical interface (since version 4.0), it’s generally considered less refined and feature-rich than MATLAB’s IDE. Debugging and profiling tools might not be as advanced.
- Toolbox Gaps: While octave-forge provides many packages, some highly specialized or cutting-edge MATLAB toolboxes might not have direct, fully equivalent counterparts in Octave. For StaMPS, the required functionalities are generally well-covered.
- Minor Syntax/Functionality Differences: Although highly compatible, there are subtle differences in syntax or how certain functions behave. StaMPS developers are generally aware of Octave compatibility, but occasionally you might encounter a minor issue that requires a small adjustment.

Can You Process PSInSAR using StaMPS with GNU Octave?

Absolutely, yes! Many researchers and practitioners successfully use StaMPS with GNU Octave for PSInSAR processing. The core StaMPS algorithms are written in a way that is compatible with Octave.

Key Steps for Success with Octave:

Correct Octave Installation: As detailed in the previous response, install Octave and its development headers (liboctave-dev on Debian/Ubuntu, octave-devel on CentOS/RHEL).
Required Octave Packages: Install the necessary octave-forge packages from within the Octave environment (e.g., io, signal, general, mapping, optim).
StaMPS Makefile Configuration: Crucially, when compiling StaMPS, ensure your Makefile explicitly points to your Octave installation (OCTAVE_HOME) and uses mkoctfile for compilation instead of MATLAB’s mex.
Environment Variables: Set STAMPS_HOME and add the StaMPS bin directory to your PATH.
Add StaMPS matlab directory to Octave Path: Once in the Octave environment, you’ll likely need to add the StaMPS matlab directory (where the StaMPS .m scripts reside) to Octave’s search path using addpath('/path/to/StaMPS/matlab').

In conclusion:

Given your situation of not having a MATLAB license, GNU Octave is the logical, effective, and widely used solution for running StaMPS to perform PSInSAR processing. While there might be minor performance differences or occasional quirks compared to MATLAB, these are generally manageable, and the “free and open” nature of Octave makes it an excellent choice for your InSAR workflow.