I don’t recommend cygwin. If you have the chance to use Linux for the next steps, download the StaMPS scripts there and set the variables of the other software (you need matlab, triangle and snaphu, the rest is only used for pre-processing which was done in SNAP)
Once you have these programs installed, you source the config file as described in the StaMPS manual or here:
- Linux Installation using StaMPS and S-1 data
- About the STaMPS category
- Workflow between SNAP and StaMPS
- Problem with StaMPS installation using Linux
mdelgado also explained it well here: How to prepare Sentinel-1 images stack for PSI/SBAS in SNAP 5
If everything is installed, you call the scripts to prepare the data for matlab processing as described in the manual under chapter 6 PS processing.