SNAPHU Configuration


I’m back to proces S1 data and I have the same question as I had before I stopped working with s1 and snaphu.

I’ve tried to find (again) an easier way to export the wrapped phase and then unwrap and import it again in snap. I’m unable to do the all plug-in thing and I run directly through the comand line: That’s when the confusion kicks in:

As I understand, i have to use the command line of the wrapped phase in the same EXACT path as snaphu.exe, but when I am exporting I cant export to that exact folder, it creates a new one:

New folder (IFG_ML_flt) Screenshot - 3461c65eaa47814503d68b2d03930e87 - Gyazo

So I have to copy ALL the files from that folder, go BACK in in EXPORT/bin (where snaphu.exe is located) and then run the command line. The problem i have with this is that i’ts very non intuitive, im basically copying the file and pasting (occupying 2x the memory usage) and the file organization is very hard to do.

Is this what it is supposed to be for everyone?

Thank you

Unfortunately, yes. Unless you can automate this with some programming then using SNAPHU with many images is a very hard process.

Thanks for the information, I will try to figure it out for more.

Alright thanks! I thought it was my problem or something like that, at least I’m glad to know that this is the “proper” way

The location of snaphu.exe should not matter. You can put its folder (e.g. C:\snaphu) into your PATH environment variable to call snaphu from any location via the command line. Or did I misunderstand your question?

Yes thats exactly my problem. I think i should be able to call the command line from anywhere and start snaphu. But i only can call it where the snaphu.exe is located and I dont know why

This is no problem. Place the three snaphu files in a directory you like (avoid spaces in the path) and then add the path to this directory to your PATH environment variable: How to set the path and environment variables in Windows
After restarting the command line you can call snaphu from any location you want.

Worked! I put this Windows Variable: Screenshot - 34294f7346f032315fb83aff592d941a - Gyazo from this folder Screenshot - 8c6e45a2ffc78795ebd21b1abd649b08 - Gyazo (which contains all the files from SNAPHU download).

Amazing! And it was pretty straight forward, thank you a lot! It was a headache doing the procedure i was doing

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glad to hear.