David Nečas (Yeti | 26 May 16:44 2015
Picon

Gwyddion 2.41 was released


Gwyddion 2.41 is now available for download at

  https://sourceforge.net/projects/gwyddion/files/gwyddion/2.41/
  (all released files)

  http://gwyddion.net/download/2.41/
  (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)

David Nečas (Yeti | 12 May 17:16 2015
Picon

Re: 3D module - overlay light bug?

On Tue, May 12, 2015 at 09:59:24AM +0200, Giovanni Perotto wrote:
> I'm trying to use the 3D module and use the light overlay option.
> Unfortunately when I save the picture I don't get the nice 3D with the
> light effects but it saves the low res version that you see when you move
> the image around.

Hello, the 3D view is unfortunately somewhat capricious and any problems
depend on the graphic card, drivers, OpenGL libraries, the rest of
graphical environment and phase of Moon...  It will probably redraw when
you run the image file selection dialogue but that should be done faster
than you can choose the file name and actually save the image.

Do you encounter the problem only in the overlay mode?

If the file dialogue covers the 3D view during the saving, even
partially, please check if it makes a difference when you move it away
and only press Save when the 3D view is not covered by anything and
looks as expected.

I have also enabled some debugging messages that will appear in
gwyddion.log and might shed some light on why the 3D view thinks it
needs to be redrawn.  Please install tomorrow's (or later) development
snapshot, do a 3D view image export and post the log.  Since it will
write quite a lot of messages to gwyddion.log keep the interaction with
the 3D view to minimum to improve the SNR: just display it, export the
image and quit Gwyddion.

Regards,

Yeti
(Continue reading)

Giovanni Perotto | 12 May 09:59 2015
Picon

3D module - overlay light bug?

Hi all, 

I'm trying to use the 3D module and use the light overlay option.
Unfortunately when I save the picture I don't get the nice 3D with the light effects but it saves the low res version that you see when you move the image around.

I included here a super low res file of what is saved and a screenshot of the pic I'd like to save. If you need to see the original file or else let me know!

I'm using gwyddion 2.40 32 bit on win 8.1

thanks a lot!

gio
------------------------------------------------------------------------------
One dashboard for servers and applications across Physical-Virtual-Cloud 
Widest out-of-the-box monitoring support with 50+ applications
Performance metrics, stats and reports that give you Actionable Insights
Deep dive visibility with transaction tracing using APM Insight.
http://ad.doubleclick.net/ddm/clk/290420510;117567292;y
_______________________________________________
Gwyddion-users mailing list
Gwyddion-users@...
https://lists.sourceforge.net/lists/listinfo/gwyddion-users
Andrés Muñiz Piniella | 16 Apr 20:30 2015
Picon

Multi section cuts

Hello all,

Has anybody come up with a script that can do multiple sections in on go?

Example: I have several step features in an image.

I want to do three parallel one pixel wide sections on each step feature. I will then average. This way I avoid nasty features.

Ways that I figure doing it:
A) do a script that will do 2 paralell sections at a certain distance from the already existing section lines.
B) change the average feature so it only takes3 sections to do the average. Middle point of data and edges points of data. Less visual but more automatic.

Any suggestions?

Regards,
Andrés.
--
Sent from my Android device with K-9 Mail. Please excuse my brevity.

------------------------------------------------------------------------------
BPM Camp - Free Virtual Workshop May 6th at 10am PDT/1PM EDT
Develop your own process in accordance with the BPMN 2 standard
Learn Process modeling best practices with Bonita BPM through live exercises
http://www.bonitasoft.com/be-part-of-it/events/bpm-camp-virtual- event?utm_
source=Sourceforge_BPM_Camp_5_6_15&utm_medium=email&utm_campaign=VA_SF
_______________________________________________
Gwyddion-users mailing list
Gwyddion-users@...
https://lists.sourceforge.net/lists/listinfo/gwyddion-users
Christian K | 16 Apr 15:04 2015
Picon

creating graphs

Hi,

I cannot figure how to create graphs. All items in the graph menu are greyed
out. I need to analyse step heights for which I use the 'Extract profiles'
tool. But then I am unable to process the results with the graph tools. Am I
doing something wrong?
I am usgin gwyddion 2.40 on windows 7

Thanks for any hints, Christian

------------------------------------------------------------------------------
BPM Camp - Free Virtual Workshop May 6th at 10am PDT/1PM EDT
Develop your own process in accordance with the BPMN 2 standard
Learn Process modeling best practices with Bonita BPM through live exercises
http://www.bonitasoft.com/be-part-of-it/events/bpm-camp-virtual- event?utm_
source=Sourceforge_BPM_Camp_5_6_15&utm_medium=email&utm_campaign=VA_SF
Andrés Muñiz Piniella | 8 Apr 11:36 2015
Picon

fit graph: step height

Hello Users,

When fitting a step (or any other type I guess)  to a section it gives me a value of "error". Would this be an uncertainty with k=1 or k=2?


If so, could we have it renamed as uncertainty rather than error?

Regards,
Andres

--
Andrés Muñiz-Piniella
------------------------------------------------------------------------------
BPM Camp - Free Virtual Workshop May 6th at 10am PDT/1PM EDT
Develop your own process in accordance with the BPMN 2 standard
Learn Process modeling best practices with Bonita BPM through live exercises
http://www.bonitasoft.com/be-part-of-it/events/bpm-camp-virtual- event?utm_
source=Sourceforge_BPM_Camp_5_6_15&utm_medium=email&utm_campaign=VA_SF
_______________________________________________
Gwyddion-users mailing list
Gwyddion-users@...
https://lists.sourceforge.net/lists/listinfo/gwyddion-users
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


------------------------------------------------------------------------------
Dive into the World of Parallel Programming The Go Parallel Website, sponsored
by Intel and developed in partnership with Slashdot Media, is your hub for all
things parallel software development, from weekly thought leadership blogs to
news, videos, case studies, tutorials and more. Take a look and join the 
conversation now. http://goparallel.sourceforge.net/
_______________________________________________
Gwyddion-users mailing list
Gwyddion-users@...
https://lists.sourceforge.net/lists/listinfo/gwyddion-users
Shahid Ali | 11 Mar 15:19 2015
Picon

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

------------------------------------------------------------------------------
Dive into the World of Parallel Programming The Go Parallel Website, sponsored
by Intel and developed in partnership with Slashdot Media, is your hub for all
things parallel software development, from weekly thought leadership blogs to
news, videos, case studies, tutorials and more. Take a look and join the 
conversation now. http://goparallel.sourceforge.net/
_______________________________________________
Gwyddion-users mailing list
Gwyddion-users@...
https://lists.sourceforge.net/lists/listinfo/gwyddion-users
Matus Michael | 10 Mar 09:58 2015
Picon

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

------------------------------------------------------------------------------
Dive into the World of Parallel Programming The Go Parallel Website, sponsored
by Intel and developed in partnership with Slashdot Media, is your hub for all
things parallel software development, from weekly thought leadership blogs to
news, videos, case studies, tutorials and more. Take a look and join the 
conversation now. http://goparallel.sourceforge.net/
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

------------------------------------------------------------------------------
Dive into the World of Parallel Programming. The Go Parallel Website,
sponsored by Intel and developed in partnership with Slashdot Media, is your
hub for all things parallel software development, from weekly thought
leadership blogs to news, videos, case studies, tutorials and more. Take a
look and join the conversation now. http://goparallel.sourceforge.net/
_______________________________________________
Gwyddion-users mailing list
Gwyddion-users <at> lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/gwyddion-users
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

 

------------------------------------------------------------------------------
Dive into the World of Parallel Programming! The Go Parallel Website,
sponsored by Intel and developed in partnership with Slashdot Media, is your
hub for all things parallel software development, from weekly thought
leadership blogs to news, videos, case studies, tutorials and more. Take a
look and join the conversation now. http://goparallel.sourceforge.net
_______________________________________________
Gwyddion-users mailing list
Gwyddion-users@...
https://lists.sourceforge.net/lists/listinfo/gwyddion-users

Gmane