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Faulty axis label upon export

Hello!

I am currently trying to export some of my measurements to tiff-files (I 
do not know if the following error is related to tiff's only). For a 
large scan image of 100x150µm the axis dimension labels get messed up 
during export.
For the smaller axis, which is the x axis, the tics are from "0µm" to 
"80" (in that particular zoom and fontsize). The y-axis reads "0.00" to 
"0.14". Therefore I conclude, that the dimension was changed to "mm" for 
the y-axis, but the label can only be found at the x-axis! An example is 
in the attached file (I deleted the data, because it is not published 
yet, and converted to jpg because of filesize).

How can I force gwyddion to use the correct scale?

Best regards,
Henning

--

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Dipl.-NanoSc. Henning Huckfeldt
Arbeitsgruppe Prof. Dr. A. Ehresmann
Experimentalphysik IV
"Funktionale dünne Schichten und Physik mit Synchrotronstrahlung"
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Heinrich-Plett-Str. 40
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(Continue reading)

David Nečas (Yeti | 2 Apr 15:40 2014
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Gwyddion 2.36 was released


Gwyddion 2.36 is now available for download at

  https://sourceforge.net/projects/gwyddion/files/gwyddion/2.36/
  (all released files)

  http://gwyddion.net/download/2.36/
  (source code)

Released files are signed with PGP/GnuPG key

  "David Nečas (Yeti) <yeti <at> gwyddion.net>", id 62A07732
  fingerprint = 263F 9B1E C1E0 5261 C689  D83B 00FD D1D0 62A0 7732

-----------------------------------------------------------------------------

This is a stable version continuing the 2.x series, backward compatible with
previous 2.x versions.

More information about Gwyddion is available at

  http://gwyddion.net/

Bugs should be reported to

  klapetek <at> gwyddion.net

or the mailing list.

-----------------------------------------------------------------------------
(Continue reading)

Dimitar Iankov | 24 Mar 15:56 2014
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roughness in 2D with waviness separation

Hi all,

I was comparing the output for surface roughness from different analysis tools. Very often they separate waviness from roughness by default and only then calculate the roughness parameter (Rq, for example). Gwyddion also do this in the "Roughness" tool but only for a profile (1D) and uses a ratio of the cut-off frequency as user input. Other programs use the wavelength (lambda_c) of the waviness as input. I think this is because in ISO 4287 one has to choose lambda_c to be approx. 1/5 of the scan length. Of course, both values are connected to each other, however the precision in the cut-off input field in Gwyddion (2 decimal places) seems to me a little bit too low.

My question is, how to do waviness separation in 2D (i.e. Sq after ISO 25178)? The "statistical quantities" tool doesn't have this option. This seems to be a common step in other programs and that's why the results often deviate from Gwyddion.

Thanks!
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David Nečas (Yeti | 2 Mar 14:57 2014
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Gwyddion 2.35 was released


Gwyddion 2.35 is now available for download at

  https://sourceforge.net/projects/gwyddion/files/gwyddion/2.35/
  (all released files)

  http://gwyddion.net/download/2.35/
  (source code)

Released files are signed with PGP/GnuPG key

  "David Nečas (Yeti) <yeti <at> gwyddion.net>", id 62A07732
  fingerprint = 263F 9B1E C1E0 5261 C689  D83B 00FD D1D0 62A0 7732

-----------------------------------------------------------------------------

This is a stable version continuing the 2.x series, backward compatible with
previous 2.x versions.

More information about Gwyddion is available at

  http://gwyddion.net/

Bugs should be reported to

  klapetek <at> gwyddion.net

or the mailing list.

-----------------------------------------------------------------------------

Application:
- A log of data modification operations is recorded for each channel and volume
  data. A viewer of data processing operation log is available in the
  right-click menus.  Logging can be enabled and disabled in the Edit menu.
- A workaround for toolbox menus disapparing in Unity was implemented.

Libraries:
- libgwyapp: Functions for logging of data processing operations were added.
- libgwyapp: Missing brick containers items were added to validation and file
  merging operations.
- libgwyprocess: gwy_data_field_grains_get_distribution() no longer incorrectly
  includes the no-grains value in the resulting distribution.
- libgwyddion: GwyStringList has new functions for clearing and adding a string
  with taking the ownership.
- libgwyprocess: A function for removing grains by number was added.
- libgwydggets: Graph window shows reasonable cursor coordinates with
  logscale axes.

Modules:
- Data processing, file and volume modules: Support for logging was added.
- Rank (new): Rank transform-based local constrast ehnancement presentation.
- OME TIFF (new): Import Opem Microscopy Environment (OME) TIFF files.
- Accurex II TXT (new): Imports Accurex II text data files.
- HDR image: 32bit and 64bit integer samples as well as 32bit and 64bit
  floating point samples are supported.  Plain BigTIFF images can be loaded.
- APE file: Metadata handling for different SPM modes was improved.
- nanoscantech: Problems with loading 4d jumping mode spectroscopy fixed.
- NT-MDT: Hybrid mode is loaded with distance calibration,
  precalculated datafields are loaded from hybrid-mode data.
- Scale: Rouding of scaling ratio to some odd values was fixed.
- Pixmap export: Bad row padding for some BMP image widths was fixed.
- RHK SM4: PRM are imported to metadata.
- IGOR file: Infinities and NaNs in the data are filled with a neutral value
  and masked upon import.
- NanoScan: Files with http://www.nanoscan.ch/SPM namespace are recognised.
- Merge: Bug causing occassional use of data outside of the operand images was
  fixed.

-----------------------------------------------------------------------------

Thanks all who contributed,

Yeti

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niv levy | 20 Feb 16:15 2014
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connect pygwy to existing gwyddion instance

Hi,
I'd like to open files through a minimal pygwy script with some applied filtering and datafield / layer selection, and then continue playing with the files interactively in gwyddion after the script closes. . 
I would have thought gwy.gwy_app_file_load(filename) would open the file in an existing instance, but it seems not to - i get an open window, and can open the data browser, but i can't seem to open the main / toolbox window, and it is not connected to a running instance of gwyddion (and of course closes when i quit python). Am i missing something obvious here? Is there a different way to open the file that would do this?
niv 

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Tobias Mönch | 16 Feb 22:51 2014
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Cant open NanoScan files

Hi,

did anyone encountered any problems with opening NanoScan xml files in Gwyddion? I simply can not open them.

I’am using Gwyddion 2.34 on MacOS 10.9.1.

best 

tobias

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Mathias Müller | 7 Feb 11:12 2014
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FFT and reciprocal space


Yeti,

I recently wanted to extract lattice constants from FFT images. I am using reference values obtained from a
commercial software.
Employing the transformation rule from real space to reciprocal space (and vice versa) I do not succeed in
calculating the correct values. However, when multiplying the fft coordinates with 2*pi it fits pretty well.

This leads to one of my questions. Did you implement the crystallographic notation (a_real * a_rec = 1) or
the 
solid state notation (a_real * a_rec = 2*pi) for reciprocal space? (just to ensure the correct transformation)

The second question concerns the result's quality. Using the same data from the commercial software
results in two pretty equal 
lattice constants of the unit cell. Calculating by hand from the very same FFT coordinates (peaks) results
in two similar but 
different values. Using neighbor pixels slightly varies the result, but never matches.

For example a hexagonal structure:

lattice constant	commercial/nm 	Gwyydion-manually/nm

	|a|		1.25		1.29
	|b|		1.24		1.22

The question is why does it differ? Do I have to correct the coordinates if the angle between two vectors of
neighbor peaks
is != 60 degree (i.e. hexagonal structure)? Should I calculate the center of mass of each FFT peak ? Maybe the
latter improves
the precision. However, am I overcritical about a difference of 3 % ?

Cheers,

/M

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Jens Trollmann | 6 Feb 15:28 2014
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Watershed algorithm - Marked grains are smaller than the size of a single drop?

Dear users,

I am working with the watershed algorithm to mark grains and I am
wondering what exactly is meant by the parameter drop size in
percentage. I interpreted this in that way that a drop with a size of
0.1% has a size of 0.001µm² in a 1µm² picture. Is that right?

If so, in a 1µm² picture with 512x512 pixels this drop would have a size
of approximately 272 px², so that the smallest lake/grain marked in the
end should be bigger or equal to 272px², shouldn't it? But I get a lot
of marked grains smaller than this size in my picture (e.g. I can erase
a lot of drops via a surface threshold of lets say 60px²). Which mistake
did I make in my thoughts?

Or is percentage of a volume meant and if so what scale is taken as the
"height" of the volume?

One more question apart from that came into my mind:
Can a drop go into a minimum that is smaller than the size of the drop?
I.e. is the drop "really" a fluid and can change its shape?

Unfortunately I did not find information about this on the Gwyddion web
pages. I would be very thankful for any help.

Best regards,
Jens Trollmann

-- 
----------------------------------------------------------------------------
Jens Trollmann

Kirchhoff-Institut fuer Physik der Universitaet Heidelberg
Im Neuenheimer Feld 227
D-69120 Heidelberg
Raum: 02.301

Tel: +49 6221 54-9892
Fax: +49 6221 54-9875

E-Mail: jens.trollmann@...
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Joe Smerdon | 3 Feb 13:43 2014
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Problems loading files from old Omicron system

Hi,

I’m trying to use an Omicron SCALA system from 1994.  It saves files in the usual .par and as many tiffs as
channels.  Gwyddion can’t load the images; a usual error might be

Expected data size calculated from file headers is 131072 bytes, but the real size is 133040 bytes.

The real size is always bigger than the expected size.  I have other software that can load the files, so they
don’t seem to be corrupted. Is there a way I can upload one so that it can be examined?

Thanks

Joe
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Salman Manzoor | 27 Jan 12:22 2014
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Slope Distribution (Inclination Graph) ?

Hi Gwyddion User!

I am trying to find a slope distribution (gwyddion also refers to this as Inclination graph) from a height matrix that I obtained with AFM. Could someone explain how does gwyddion exactly calculate the slope at each pixel (without local plane fitting)? And what it does when you select the 'Use Local Plane Fitting'? And when you use Local Plane Fitting, there is an option to change the number of pixels, are these pixels selected as a square neighbourhood or linear row/column pixels?

Thanks,

-Salman
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Mathias Müller | 17 Jan 11:03 2014
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false aspect ratio with 2D-FFT


Hi yeti,

it seems I found an issue regarding the 2D-FFT transformation in the current Gwyddion release (v2.34). 

I have (again) data with a physical dimension of 1 x 1 q-microns with a pixel aspect ratio of 2:1.

Performing standard operations like leveling etc everything works fine. But when continuing with FFT transformation
the output relates to the aspect ratio of the pixel size. Not only in the aspect ratio of the displayed image
is falsified but also
its physical dimension. Here, the xrange goes from [-256:256] invers microns, but the yrange is
[-126:126] invers microns. 
This should be equal.

Fruther, the toggle menu in the left corner (change between physically square and pixelwise square) does
not respond.

Is there a chance to fix this? 

Cheers,

/M

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