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scholi / pySPM

Python library to handle Scanning Probe Microscopy Images. Can read nanoscan .xml data, Bruker AFM images, Nanonis SXM files as well as iontof images(ITA, ITM and ITS).
Apache License 2.0
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Nonsquare scans Bruker files (.spm) #22

Closed GGGGGuillaume closed 2 years ago

GGGGGuillaume commented 2 years ago

Hello, thank you very much for your work, it is great (and very time efficient) to reopen the Bruker files with python !

I have a little trouble with opening scans that are non square (where the aspect ratio is not 1:1). For example, I have a 2:1 aspect ratio scan, X size is 10 µm and Y size = X size/2 = 5 µm, 256 pixels in X, 128 pixels in Y. When I use pySPM, the scan becomes a 10*10 µm scan...

Thanks in advance,

Guillaume

scholi commented 2 years ago

Can you send me some data to test it?

GGGGGuillaume commented 2 years ago

scan_test.zip

Of course, cf. attached file !

scholi commented 2 years ago

I found that Bruker is using an Aspect Ratio info and could fix it so that it works for the example you have sent me. Unfortunately I don't have access to data anymore. Could you pull the git (not pip) and make some tests to see if the results makes sense?

scholi commented 2 years ago 
from pySPM import Bruker
import os.path

b = Bruker(os.path.expanduser("~/desktop/scan_test.spm"))
c = b.get_channel("Height", debug=True)
c.show()

image

GGGGGuillaume commented 2 years ago

I have tested it with a few scans (different aspect ratios), it works perfectly ! Thanks you very much for your quick assistance (and thanks again for the library, it will be very useful for me). aspectratio10