search

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
58 stars 33 forks source link

reuse file format reader in afmformats #19

Closed paulmueller closed 2 years ago

paulmueller commented 2 years ago

Hi Olivier,

I am the author of afmformats (used by PyJibe) and I was wondering whether it would make sense to incorporate the file-reader functionalities of pySPM in afmformats.

  1. I have previously only worked with force-distance data. Are the file formats you have used here plain image files or do they contain the raw force-distance trace data (i.e. cantilever deflection vs. piezo position)?
  2. What do you think about this? Does it even make sense?
  3. My initial thought was to just make pySPM a dependency of afmformats, but then I saw that pySPM depends on several other packages which I would like to avoid. I see that pySPM is licensed under the Apache 2.0 license which would be compatible with the MIT license (afmformats), as far as I know.

Cross-ref: https://github.com/AFM-analysis/afmformats/issues/18

scholi commented 2 years ago

Hi Paul, The data contained in the file will always depend on the experiment you perform. Usually they are 2D arrays or 1D arrays and not multidimentional array such as a force-distance per pixel. From what I see in your package afmformats you just get 1D force-distance curve. Is that correct?

Which new fileformat do you want to read? It makes no sense to implement new file format just to add more fileformat if you don't use them and cannot debug them properly.

paulmueller commented 2 years ago

Yes, afmformats supports 1D force-distance curves, but can handle quantitative map data (force curves aranged on a grid). I am currently just taking a look around to expand general data file format support.

I see your point. Thanks for your reply.

scholi commented 2 years ago

In anycase pySPM is under Apache license and you are free to use it as a dependency or to reuse any python script. Just keep the list of all contributing authors in the header.