Judy Phan | 26 Mar 17:36 2015

Profiles x and y scales

Hello,

I'd like to extract profiles of my grains to a plot. I understand that there is profiles tool but the x and y scales are in disagreement. Is there a way I could change the settings to have them in the same unit?

Thanks,
--

Judy Phan

Master of Science in Chemical Engineering, 2015


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Shahid Ali | 11 Mar 15:19 2015
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Grain size measurement by AFM

Dear all,
I have taken AFM image from asylum MFP-3D . 1*1 um image. now I have to measure it's grain size. I have measured it by threshold method and watershed method. The grain size was 3.9 nm and 11 nm respectively. The sample was InGaN sample. now I am confused how to check which one is correct and how to get accurate grain size from gwyddion. do I have to take another image means bigger or smaller image or 1*1 um is fine.
Best shahid

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Matus Michael | 10 Mar 09:58 2015
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Open profiles?

By chance I discovered the possibility to open profile files (of *.x3p type) directly in gwyddion! In
section 3.5 of the documentation this is explicitly negated.

My question: is it intended to keep this feature (which I would highly appreciate)?

Dr. Michael Matus
-------------------------------------------------------------
BEV - Bundesamt fuer Eich- und Vermessungswesen
Leiter des Referates Dimensionelle Groessen, Frequenz, Zeit
(Head of Section, Dimensional Quantities, Frequency, Time)
Tel. +43 1 21110-6540, Fax +43 1 21110-996000
1160 Wien, Arltgasse 35, Austria
michael.matus@...
www.bev.gv.at
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David Nečas (Yeti | 7 Feb 22:44 2015
Picon

Gwyddion 2.40 was released


Gwyddion 2.40 is now available for download at

  https://sourceforge.net/projects/gwyddion/files/gwyddion/2.40/
  (all released files)

  http://gwyddion.net/download/2.40/
  (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.

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

Summary of changes:

Libraries:
- libgwyprocess: GwySpectra has properties specifying the abscissa and
  ordinate labels for the spectra curves.
- libgwyprocess: Pass a NULL error array to gwy_nlfit_preset_fit() works now.
- libgwyprocess: New fitting presets: Two-Gaussian PSDF and parabolic step.
- libgwydgets: In 3D View masked data points can be made completely
  transparent.
- libgwyddion: Aborting/crashing on deserialisation of invalid-sized arrays
  was fixed.

Modules:
- Flatten base (new): Flattens the base of a surface with positive features.
- K-medians (new): K-medians clustering for volume data.
- SEM image (new): Presentation resembling SEM image corresponding to given
  topography.
- XYZ export (new): Exports channel values to simple XYZ text file.
- Image export: It is possible do disable the frame if there are no rulers.
  False colour rendering for inverted gradients and default non-full mappings
  was corrected.  Title centering for non-square images was corrected.  A mask
  colour sample can be rendered below the image with a label.  Error message
  saying ‘Success’ when exporting BMP files was fixed.
- APE DAX: Can also import APDT files now.
- NetCDF: The new setpoint variable ‘sranger_mk2_hwi_mix0_set_point’ is used
  for metadata, if found.
- NRRD: 3D data with all three resolutions large are loaded a volume data
  instead of sequences of channels.
- Merge: Can mask pixels in the result that were outside of either image.  It
  is also possible to automatically crop the result to only inside pixels.
  A new merge type ‘Interpolation’ produces smoother transitions than the old
  ‘Smooth’ which was renamed to ‘Average’.
- Spectro tool: Uses abscissa and ordinate labels from the spectra object, if
  present.
- Omicron, Nanoeducator: X and Y spectra axis labels are set according to the
  imported spectrum type.
- Euclidean distance transform: Function for mask thinning was added.
- Mark by threshold: Percentage interpretation for inverted height was
  changed to be less confusing.
- Raw XYZ: The square image option is not enforced on regular grid data when
  it is not available in the dialog.
- WITec Project: WIT_PR06 recognized as another variant of magic header.
- APE DAX, NanoObserver, NanoScanTech, OpenGPS, SPMx: Opening of files with
  non-ASCII names should work better on MS Windows.

Other:
- Does not attempt to build the hdrimage module with C++ compiler unavailable.

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

Thanks all who contributed,

Yeti

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Moriceau, Julien | 6 Jan 16:35 2015

NaN value in statistical measurment

Hello,

It is my first message to you guys because I am struggling with gwyddion (I precise I am a new user).

I have AFM files that I want to analyze, but a lot of these files are containing NaN value.

I can open these images without too much trouble but the software cannot calculate any of the advanced statistical data (as HHCF that I am interested in) because, I guess, of the NaN values.

Is there any way to correct this problem? Or not to take in account NaN during calculation? (the calculation is working well with the height distribution for example).

Thanks a lot for your help.

Regards,

--

Julien

 

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Deepak Ramtirthe | 18 Dec 10:26 2014
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Gwyddion User

Dear sir,
   I want to analyse the data which is obtained from profilometry. This data is in the form of ".xlsx".How can I insert this data in Gwyddion??
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Judy Phan | 20 Nov 23:36 2014

extract profile vs grain distributions

Hi,
Which sets of data in the grain distributions tool that are corresponding to the data when you use the extract profile tool? Obviously, the profile you get when using the extract profile tool depends on each grain and where on the grain you draw the line. I guess my question is that is there a way I can export the maximum, minimum or average of those data (x and y)? Does the grain distribution tool have a way to scan each grain for all of its profiles and give you a max/min/average values? I know the distributions give you many types of heights and widths but which one of those corresponding to the profile extract tool x and y?
Thanks,

--

Judy Phan

Master of Science in Chemical Engineering, 2015

Bachelor of Science in Chemical Engineering with Cum Laude, 2013

Bucknell Engineering Network Student Liaison

Chair of the Banquet & Society Activities Committee of Tau Beta Pi
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Mathias Müller | 19 Nov 11:36 2014
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PNG Export-Issue


Hi Yeti,

the current stable version of Gwyddion (Linux, V2.39, R2014-11-14) seems to have problems to maintain the
color scale when exporting
processed data to png. However, while writing this mail it seems this problem is persistent for other
formats, too.
The displayed and the written color scale in the export dialog differs from that of the channel I am working
on. It seems that the 
export dialog sets the full data range for color specification per default.

Can you reproduce this issue on your machine?

Cheers,

/M

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David Nečas (Yeti | 14 Nov 17:17 2014
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Gwyddion 2.39 was released


Gwyddion 2.39 is now available for download at

  https://sourceforge.net/projects/gwyddion/files/gwyddion/2.39/
  (all released files)

  http://gwyddion.net/download/2.39/
  (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.

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

Summary of changes:

Application:
- Pango 1.10 and Cairo 1.2 are now required.
- The program should start with a saner working directory by default.
- Translations updated: Czech, French, Russian.
- New translation: Korean.

Libraries:
- libgwyddion: A function for copying GwySIValueFormat was added; the
  structure is also registered as a boxed type now.
- libgwydgets: gwy_axis_get_magnification_string() returns string for the new
  units after gwy_axis_set_si_unit().
- libgwydraw: Adaptive false colour mapping was improved by making it more
  adaptive.
- libgwydraw: It is possible to map user-given values to gradient positions
  using the same mapping as gwy_pixbuf_draw_data_field_adaptive() uses.
- libgwydgets: GwyColorAxis has a new ‘unlabelled’ ticks mode in which the
  interior ticks are drawn without labels.
- libgwydgets: GwyColorAxis permits specifying a non-linear value to gradient
  mapping function.
- libgwydgets: Crash when changing color maps in Gwy3DView with gtk+ version
  greater 2.29 was fixed.
- libgwyapp: When adaptive false colour mapping is used, the axis is set to
  the new ‘unlabelled’ mode so the mapping non-linearity can be seen.

Modules:
- Image export (new): Replaces image rendering in the pixmap module; can
  export to vector graphics formats: PDF, EPS and SVG.  The corresponding
  file types are called ‘pdfcairo’, ‘pngcairo’, etc.
- NX II (new): Imports EMSYS NX II AFM files.
- FemtoScan (new): Imports FemtoScan SPM files.
- SPMx (new): Imports ACT/FemtoScan SPMxFormat files.
- Fractional Brownian motion (new): Generation of fBm-like artifical
  surfaces.
- Renishaw (new): Imports Renishaw WiRE data files.
- Pixmap: Only used for image import; image rendering functions were removed.
- Statistical quantities: Crash in saving the statistics was fixed (introduced
  in 2.38).
- OpenGPS: Format detection was improved to check not just for the presence
  of main.xml also if it really looks like an ISO 5436-2 XML file.
- MIF: X, Y and Z calibration factors are applied to data upon import and
  a different Z conversion formula is used according to z_linearized.
  Multiplicative factors encoded after the image are applied to the data.
- MetroPro: Z scale in files with PhaseRes value of 2 is correct now.
- Grain distributions: The graph abscissas are bin centres now, as is usual,
  instead of bin left edges.
- Noise and line noise synthesis: Settings are remembered also on Cancel.

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

Thanks all who contributed,

Yeti

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Judy Phan | 17 Oct 04:07 2014

Particles/Grains shape

Hi,
I'm working on a project where particles are collected and imaged using the AFM. I've been getting myself familiar with Gwyddion software. My goal is to be able to quantify the particles using the grain properties tools but since I'm working with multiple particles, I need to normalized their properties in order to compare them. So far, I saw people done 2-D parameters such as elongation, convexity, circularity, etc. Does anyone know what are the 3-D parameters? I think comparing the ratios of the major and minor semiaxis of equivalent ellipse with the mean height will give me some sort of elongation. For convexity (surface roughness), in 2-D it is a ratio between the particle area and the total area. Is projected area the total area? And is the surface area actually the particle area? I'd like to translate this to 3-D ratio.

Thanks,

--

Judy Phan

Master of Science in Chemical Engineering, 2015

Bachelor of Science in Chemical Engineering with Cum Laude, 2013

Bucknell Engineering Network Student Liaison

Chair of the Banquet & Society Activities Committee of Tau Beta Pi
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Maxwell Grady | 15 Oct 17:39 2014
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Gwyddion on OSX Yosemite beta-6 via macports fails to load Omicron Scala files

I am running OS X.10 yosemite beta version 6 on a macbok pro early 2011 model.


When I load gwyddion the opening logo says gwyddion 2.4 but when I go to the 'about gwyddion' menu it says gwyddion 2.3.4 released 2013-12-15


I recently found that gwyddion is no longer loading my STM files.
I collect STM data with an Omicron SCALA system. The files are saved in .par and .tfo 


Gwyddion used to open them with no trouble at all. Now when I try to open the files I get various errors about file size.

Strangely enough the file browser window shows a preview of the files correctly. When I highlight, for instance, m10003.par, it shows me a preview of the data and I can see that the data is correct. Then when I try to open the file it tells em there is an error in the file length. The format would require x number of bytes the file is only y bytes long.

here are links to the sample file(s) I will include a link to the .par and the .tf0




-Maxwell Grady




--
University of New Hampshire
Department of Physics
Pohl Group
DeMeritt Hall 119
---
Síocháin agus Grá
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Gmane