import filter and debug out

  • Jan Höcker

    Jan Höcker - 2014-02-19

    Hi everybody,
    I have got an annoying issue with some import filters (I tried Nanoprobe, WXsM and ASCII) for AFM data. When I import a file with one of those import filters the import itself is successful but the VRangeZ and VOffsetZ values are pinned to either -500nm or 500nm (the default values after start I think). I have to do a dummy scan or open a .nc-file to get the VRangeZ/VOffset buttons working as they should.
    Second thing I want to mention is the debug output. Even if I start GXSM with "gxsm2 --debug-level=6" I see no further debug output after GXSM-UI shows up.
    I have both issues on Ubuntu 12.10 and an up to date ArchLinux with GXSM version 1.50.0. Perhaps someone knows some easy fixes for these issues?

  • Stefan Schroeder

    Hi Jan, thank you for your observations. I have a few questions:

    • What is your exact need? Which one is the import filter that you are actually concerned about?

    • What did you expect the VRangeZ and VOffsetZ to be after importing? Can you please provide a sample file, with an example?

    • Does the problem persist, when you save and reload the imported file as .nc?

    Regarding the debug output:

    I am not sure about the overall state of the debugging macros. What is it, that you try to debug?

  • Jan Höcker

    Jan Höcker - 2014-02-19

    Hallo Stefan,
    thank you for the fast reply.

    • I'm working on some WSxM files, trying to improve the import filter and would like to set the contrast of the picture. But I can not move the VRange Z controller to values in between -500 nm and 500 nm. So no contrast is visible in the picture :(. Only Autodisp works to get a contrast. The Z values in the line profiles are fine, so the Z values seem to be imported correctly. I thought that might be a problem with a not properly set value in the import filter. But changing that doesn't change anything.

    • When I open an *.nc file measured with our STM in gxsm I could move VRange Z in steps of 1 Angstrom in the range of -500 nm to 500 nm. I would expect similar values for WSxM files. I will look for an example file tomorrow.

    • The problem persists when I save the file as .nc and open it again.

    • One thing I also realized: When I export the .nc I mentioned before as WXsM or ASCII and import it back after leaving and starting GXSM, the VRange Z controller has again only the two values -500 nm and 500 nm. Perhaps you can reproduce that?
      During this experiments with the two files I realized by chance that the VRange Z button is moveable for the WXsM file when I load the working .nc file first, kill it and than import the WXsM file. So I thought perhaps there just one line missing in the import filter to set the VRange Z to the right values. Unfortunately I wasn't able to determine that.

    I don't want to debug something special. I was just curious whether I could get any information about the Z values from the debug code. But there is none. But that is not a real problem.

  • Thorsten Wagner

    Thorsten Wagner - 2014-02-19

    Hello Jan.

    I am a little bit confused about what you want to do. Do you want to import or to export data to/from GXSM?

    About GXSM and WSxM: I have in mind that nanotec has implemented some basic import filter for GXSM’s nc-files. Nevertheless, I recommend to use the nc2top converter provided by GXSM. This external binary is called by the export function of GXSM and the external converter. The converter, which you find in the menu bar does also just cal the export function.

    The nc2top tool should work proper for quite some different data arrangements (double/integer, single files/movies/cits, …), but it works only nc -> top and not vice versa.

    The nc2top is called by the WSxM_io plugin of GXSM. So you can call it also from the command line. You may try some -f or --help Option to get more information on the conversion progress. In principle you can compile nc2top also on a Windows machine.

    The import functions are quite fundamental and - if I remember correctly - are implemented directly in the WSXM_io plugin. I am even not sure if all data formats for a single Image are fully supported. I have in mind that at the time the plugin was written there was just an support for 16 bit integers. So please test different data formats. You can change them in GXSM and save the data in a desired format.

    By the way: The z-scale was always tricky in WSxM. I guess the documentation on the Nanotec homepage. It is just a glance of the whole file format. You may need to do some reverse enginerring.

    Finally: To get debug informations from the plugins you have to call GXSM with the option --pi-debug-level=5. In general debug level above 5 are not supported.

    Thorsten 😊


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