Export raw nanoscope data

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Bede Pittenger replied on Tue, Sep 27 2011 4:32 PM

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When you saved the files, did you use offline planefit = full or offline planefit = offset?  If so, it may be difficult to remove the effect of the planefit (except using Roughness raw mean).  If you saved them with offline planefit = none, all of the data is unfiltered and you can use functions like Depth and Bearing to get histograms and Roughness to get absolute numbers as well. 

What are you trying to do with your lateral force data?

--Bede

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JFP replied on Wed, Sep 28 2011 1:35 AM

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Hi Bede,

thanks for your help.

I'm calculating friction force from lateral signal.

You say its difficult to get raw data, so it's possible?

Best regards

Jonas

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JFP replied on Wed, Sep 28 2011 1:37 AM

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ps: offline planefit = full

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Bede Pittenger replied on Thu, Sep 29 2011 6:44 PM

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Oops.  You really don't want to use offline planefit=full...

The situation is this: the real-time software does the planefit and then saves the result as scaled 16bit integers.  The original data is no longer available.  To recover something like the original data, you would need to apply the "Raw mean" calculation from Roughness on all of the pixels in the image.  It might be possible, but it definitely won't be easy. 

What version of the software did you save your data in?  Can you reacquire it with offline planefit=none?  Are you good with Matlab or something like that?

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JHP replied on Wed, Oct 16 2013 11:50 AM

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Dear JFP & Bede Pittenger,

I am confronted with the same problem described above, offline planefit was full during my measurements and I recognized it too late. Was there any follow-up/any communication after that statement?: "It might be possible, but it definitely won't be easy.  What version of the software did you save your data in? Can you reacquire it with offline planefit=none? Are you good with Matlab or something like that?"

Does someone have clear instructions what to do and how to get back the original raw data?

Thanks in advance, Juliane Hopf

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JFP replied on Wed, Oct 16 2013 12:28 PM

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Hallo Juliane,

sorry but I didn't try to get back the original raw data that was saved with offline planefit full. Just disabled planefit in future measurmenents...

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Bede Pittenger replied on Wed, Oct 16 2013 6:02 PM

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Hi Juliane,

Sorry to be so vague, but I have not tried to recover raw data myself. 

It should be possible, but will probably require some work to get it functioning.  I can get someone in software to explain the header parameters that are used to back calculate raw mean in the roughness analysis if you would like to take it on...

--Bede

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JHP replied on Thu, Oct 17 2013 9:48 AM

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Thanks for the quick replies!

Bruker made me aware of Sri Mannes's homepage (http://www.physics.arizona.edu/~smanne/DI/software/fileformats.html) and on his page he delivers a very technical method on how to deal with the problem. Additionally he explained the header parameters in detail. In his pseudo C code section he describes the equation needed for data recovery. My problem is, that I do not know what program he worked with to transform the data back to their 'raw' status (probably Matlab) and if it is somehow possible to re-implement those back into SPM software (Nanoscope, Gwyddion, etc.). Already send him an email asking for further advice/assistance and I hope he can give me an answer to my questions.

In case there is a solution, I'll let you know.

Regards, Juliane Hopf