Dataset structure conventions for AFM data

[PranavSudersan]

A single AFM measurement data typically contains "Forward" and "Backward" trace data for each channel (Topography, Normal force etc.). Currently, are there any conventions being (or planned to be) followed for organizing this within the sidpy dataset object? I went though the code for some of the readers (e.g. BrukerAFMReader, NanoSurfNIDReader) and it seems right now, each channel and "direction" data are organized either as a list or dictionary of sidpy datasets. This data organization does not seem to be consistent across the different data formats. Going through the documentation provided for creating a new reader, I don't find any specific information related to organizing channel/direction data.

I can help with the organization. I already have written my own "reader functions" for JPK Nanowizard and WSxM data formats and I would be happy to integrate this into SciFiReaders (which lacks support for these formats at the moment). If someone could guide me with this, I can help integrate the new readers as well as assist in organizing the existing reader output to follow a common organization rule.

[ramav87]

Hi Pranav, That's a good question. Initially we had made lists of datasets but more recently began converting everything to to dictionaries of datasets. So our desired convention is to save each channel as a new dataset in the dictionary. We should probably add this to the documentation. El mié, 25 de dic de 2024, 1:23 p. m., Pranav Sudersan < ***@***.***> escribió:

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A single AFM measurement data typically contains "Forward" and "Backward" trace data for each channel (Topography, Normal force etc.). Currently, are there any conventions being (or planned to be) followed for organizing this within the sidpy dataset object? I went though the code for some of the readers (e.g. BrukerAFMReader, NanoSurfNIDReader) and it seems right now, each channel and "direction" data are organized either as a list or dictionary of sidpy datasets. This data organization does not seem to be consistent across the different data formats. Going through the documentation <https://pycroscopy.github.io/SciFiReaders/notebooks/00_developing_a_reader/developing_a_reader.html> provided for creating a new reader, I don't find any specific information related to organizing channel/direction data. I can help with the organization. I already have written my own "reader functions" for JPK Nanowizard and WSxM data formats and I would be happy to integrate this into SciFiReaders (which lacks support for these formats at the moment). If someone could guide me with this, I can help integrate the new readers as well as assist in organizing the existing readers to follow a common organization rule. — Reply to this email directly, view it on GitHub <#140>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/ADNDQFOAXFRYP6CHFIOGKML2HLZZXAVCNFSM6AAAAABUGHHYE6VHI2DSMVQWIX3LMV43ASLTON2WKOZSG42TSMBUHEZTGNI> . You are receiving this because you are subscribed to this thread.Message ID: ***@***.***>

[PranavSudersan]

Hi Ramav,
I see, so dictionaries are the way to go, thanks for the quick reply. Have you established any rules regarding how to name the keys of these dictionaries (e.g. "{channel}_{direction}"). If you can point me to an AFM reader class function that follows the desired conventions, I can go through it.
And of course I'll be happy to add this information to the documentation. I'll send out a pull request soon.

[ramav87]

We don't have any specific conventions. You can just stick to "{channel}_{direction}"...