I'm having a problem with reading Zygo white light inteferometry HDF files (with datx extension). Namely, some of them are opening just fine, and for another one 2 of 3 channes (surface and quality) are read as B/W images with weird units. Intensity channel is read properly at all times.
The bug affects more than 50% of the files, so quite unpleasant.
All files are opening the native Zygo software without problems.
I'm attaching the two exemplary files in question, hopefully you can find the bug.
Thanks for the report and file examples. It seems the file which does not work contains missing/invalid data.
The import module currently does not handle this correctly as I only have a couple of DATX files which only contain valid data. Detecting missing data might be slightly messy. For some reason they are not stored as actual not-a-number or infinity, just as a huge finite number (hence the strange units in Gwyddion). But still the fix should be easy.
I will look into it.
Last edit: David Nečas 2025-05-30
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I added detection of invalid data to DATX import (r28040). It seem to work for me. Please try some future development snapshot of Gwyddion to check the problem is fixed.
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I tested the night build with the fix, seems to work perfectly. I take it that the masked regions are the ones that had faulty data and have been interpolated?
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Yes. The huge values are replaced with interpolated data upon import. Most Gwyddion functions can exclude masked regions from calculations so the interpolated values can often be excluded.
If you would like to refer to this comment somewhere else in this project, copy and paste the following link:
Hello,
I'm having a problem with reading Zygo white light inteferometry HDF files (with datx extension). Namely, some of them are opening just fine, and for another one 2 of 3 channes (surface and quality) are read as B/W images with weird units. Intensity channel is read properly at all times.
The bug affects more than 50% of the files, so quite unpleasant.
All files are opening the native Zygo software without problems.
I'm attaching the two exemplary files in question, hopefully you can find the bug.
Thanks for the report and file examples. It seems the file which does not work contains missing/invalid data.
The import module currently does not handle this correctly as I only have a couple of DATX files which only contain valid data. Detecting missing data might be slightly messy. For some reason they are not stored as actual not-a-number or infinity, just as a huge finite number (hence the strange units in Gwyddion). But still the fix should be easy.
I will look into it.
Last edit: David Nečas 2025-05-30
Great, thank you for the quick response! Do not hesitate to message me, if you'll need more data for tests.
I added detection of invalid data to DATX import (r28040). It seem to work for me. Please try some future development snapshot of Gwyddion to check the problem is fixed.
I tested the night build with the fix, seems to work perfectly. I take it that the masked regions are the ones that had faulty data and have been interpolated?
Yes. The huge values are replaced with interpolated data upon import. Most Gwyddion functions can exclude masked regions from calculations so the interpolated values can often be excluded.