Hi all! I want to use Gwyddion to try processing force curve map data that we can generate. I'm comfortable opening and working with the curves in Python, so I think the easiest way for me to get started is just to know a simple format that works well for Gwyddion to open. I was hoping to be able to figure this out from the example pinpoint.gwy file, but since it's already .gwy I'm a bit lost.
To reiterate: I have data in the form [x pixel], [y pixel], [z values, deflection values]. I can open it as a numpy array in Python and I'm happy to just process it into a Gwyddion-compatible format for now and re-save it that way. I just need to know what a compatible format looks like. Thank you so much for your help, seems like a really cool community and I hope to hang around here a bit in the future!
Last edit: Will Morrison 2024-06-10
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Gwyddion can currently load curve maps in several manufacturer's formats: Anfatec (.par+.dat), JPK (.jpk-qi-data), Molecular Imaging (.mi), Nanoscope (.spm), Park Systems (.ps-ppt) and Sensolytics (.dat), with varying degree of success and implementation completeness. Some of them are saner than others but even when I have some format specifications, it may not be good enough make sure you write valid files and I cannot publish it (or the status is unclear). As far as I know there is no generic format for force curve maps – we would implement it if there was one.
You can write .gwy files using libgwyfile. Unfortunately, while writing things like images is pretty straightforward, for curve maps you need to understand how the curve data are packed in a .gwy file since the functions are kind of low-level.
Last edit: David Nečas 2024-06-11
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Got it. Our company Molecular Vista is partners with Anfatec, so I'll ask Anne about how their force volume files are formatted and convert my data to match. Thanks for the response!
If you would like to refer to this comment somewhere else in this project, copy and paste the following link:
Hi all! I want to use Gwyddion to try processing force curve map data that we can generate. I'm comfortable opening and working with the curves in Python, so I think the easiest way for me to get started is just to know a simple format that works well for Gwyddion to open. I was hoping to be able to figure this out from the example pinpoint.gwy file, but since it's already .gwy I'm a bit lost.
To reiterate: I have data in the form [x pixel], [y pixel], [z values, deflection values]. I can open it as a numpy array in Python and I'm happy to just process it into a Gwyddion-compatible format for now and re-save it that way. I just need to know what a compatible format looks like. Thank you so much for your help, seems like a really cool community and I hope to hang around here a bit in the future!
Last edit: Will Morrison 2024-06-10
Gwyddion can currently load curve maps in several manufacturer's formats: Anfatec (.par+.dat), JPK (.jpk-qi-data), Molecular Imaging (.mi), Nanoscope (.spm), Park Systems (.ps-ppt) and Sensolytics (.dat), with varying degree of success and implementation completeness. Some of them are saner than others but even when I have some format specifications, it may not be good enough make sure you write valid files and I cannot publish it (or the status is unclear). As far as I know there is no generic format for force curve maps – we would implement it if there was one.
You can write .gwy files using libgwyfile. Unfortunately, while writing things like images is pretty straightforward, for curve maps you need to understand how the curve data are packed in a .gwy file since the functions are kind of low-level.
Last edit: David Nečas 2024-06-11
Got it. Our company Molecular Vista is partners with Anfatec, so I'll ask Anne about how their force volume files are formatted and convert my data to match. Thanks for the response!