Andrés Muñiz Piniella | 23 Jun 10:58 2015
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Gwyddio.exe:55824 GLIb-error


Hello,

This might be my computer not having enough resources.

I have a 4096 px image from Park XE-100 AFM I set a mask on one image and as I duplicate it to do another mask the gwyddion stops working when I save it.

Message is:
Gwyddion.exe:55824 GLib-ERROR**:../glib/gmemc:168:failed to allocate 536870912 bytes


The main issue I have  is that it corrupts the saved copy and drops from a 131Mb file to a 0Kb file. Losing very little information but If it happens after a lot of data analyis it could be a problem. At the moment I cautiously save my work with save as...

I am using windows 7 32 bit. 4GB (2.68 GB usable) CPU E5-2630 <at> 2.30 GHz

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Nicolas Delorme | 12 Jun 09:28 2015
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image derivatives or pyramid analysis

Hi,
We are studying surfaces formed by pyramids.
We want to statistically analyse their numbers and height (the shape is the same for all the pyramids).
The masking procedure do not work since some of the pyramids are in contact.
One solution would be to derivate the topographic image (but I don't know if gwyddion can do it) and to count the obtained maxima and look at their relative height...
Is there a way to obtain a derivative of an image with Gwyddion?
If you have another solution for the pyramids analysis it will be great.
Best regards,
Nicolas
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Moriceau, Julien | 10 Jun 21:45 2015

False color map - 3D viewer

Hi all,

I was wondering if it was possible to tune the false color map of the 3D viewer to have it always at the same interval (for example between 0-200 µm).

Indeed I would like to have a visual comparison of several surface with always the same color range.

I know we can tune the label but to my knowledge it is not changing the range of the color map.

Please let me know if I am not clear.

Thanks you for your help and responses.

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Evgeniya Khakhalova | 4 Jun 21:36 2015
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Fwd: Calculating specific surface area

Hi Daniil,
Thank you a lot for your helpful suggestions!

To obtain the intersect of two masks I used Data Process-> Mark with-> Intersect masks.
Is the result would be the same if I'd have used multidata arithmetic as you suggested? 

And also when I use Statistical quantities for marked region it gives me Surface area and Projected area. Do you know what is the difference between those two and why the surface area is N.A. for magnetic images (NapPhaseRetrace)?


Thank you!




Be well,
Evgeniya Khakhalova.

On Tue, Jun 2, 2015 at 2:25 PM, Daniil Bratashov <dn2010-Re5JQEeQqe8AvxtiuMwx3w@public.gmane.org> wrote:
On Tue, 2 Jun 2015 13:38:35 -0500
Evgeniya Khakhalova <ekhakhalova-Re5JQEeQqe8AvxtiuMwx3w@public.gmane.org> wrote:

> Is there any ways that  I can calculate average background noise
> (areas outside the grain) and then use it as a threshold value to
> mask dark/light regions inside the grain and then calculate the
> surface areas of those regions only inside the grain?

The main idea is to select region of interest by mask (by
marking grain by height threshold on height image), than to transfer
mask from height image to magnetic, and than use statistics tool on
region under/not under the mask to measure average background noise.

Than you can use threshold on magnetic image, and than use multidata
arithmetic on both masks to get intersection of two masks.

> 2. If it is actually possible to use crop function for some arbitrary
> shapes like on the example?

Crop is not intended for such applications, better to use masks.

> 3. Can I use for example respective topography image to crop the
> magnetic image along its grain boundaries more precisely?

Yes, by obtaining two masks and then use multidata arithmetic.

I suppose this two links will be helpful:
http://gwyddion.net/documentation/user-guide-ru/presentations-masks.html
http://gwyddion.net/documentation/user-guide-ru/multidata.html

WBR, Daniil Bratashov.

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Evgeniya Khakhalova | 2 Jun 20:38 2015
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Calculating specific surface area

Hi everyone,

I'm a new Gwyddion user and I'm trying to figure out if it is possible to do the following:
1. I've got an MFM image of the magnetic grain and my purpose is to calculate surface area of "light" and "dark" magnetic regions within this magnetic grain. 
"Light" domain area is where  Z-component is greater than background noise, and "dark" - where Z-component is smaller than background noise.
Is there any ways that  I can calculate average background noise (areas outside the grain) and then use it as a threshold value to mask dark/light regions inside the grain and then calculate the surface areas of those regions only inside the grain? 

2. If it is actually possible to use crop function for some arbitrary shapes like on the example?
3. Can I use for example respective topography image to crop the magnetic image along its grain boundaries more precisely?

The left image on the example is Nap Phase Retrace image of the grain, the right one is the height retrace:





Thank you.

Best regards,
Evgeniya Khakhalova.

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

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

Summary of changes:

Application:
- Translations updated: Czech, French, Russian.

Libraries:
- libgwyapp: Undo/redo functions now work with graphs so graph modules can
  save undo information.
- libgwyapp: Data choosers are available for graphs.
- libgwyapp: Data browser has functions for watching graphs.
- libgwyapp: Data choosers respond to the current item disappearing by choosing
  ‘none’ (preferably) or at least something.
- libgwydgets: A function for checking the compatibility of units of two
  graph models was added.
- libgwydgets: A function for copying curves appending curves from another
  graph model to a graph model was added.
- libgwyapp: Data containers corresponding to open files have assigned unique
  numerical ids (within one program invocation) that can be requested from
  the data browser.
- libgwyapp: GwyDataChooser has selection setting and obtaining functions
  that work with numerical ids.
- libgwyapp: New functions for ensuring numerical data identifies identify
  a still existing data object.
- libgwyapp: New helper function for adding graph curves to another graph or
  creaing a new graph if units are incompatibile.
- libgwydgets: Graph key frame size should better correspond to the content.
- libprocess: Functions for various simple distance transforms were added.
- libgwyprocess: New fitting presets: Smooth slanted step and Smooth bent
  step.

Modules:
- Align graph (new): Aligns horizontally graph curves.
- Slice volume (new): Simple extraction of planes and lines from volume data.
- Log-Phi PSDF (new): Calculates 2D PSDF transformed to angle-log(frequency)
  coordinates.
- Ballistic deposition synthesis (new): Simple growth simulation using the
  ballistic deposition model.
- Profiles, Statistical functions, Row/column statistics, Roughness and Spectro
  tools: It is possible to select a target graph for the curves.
- Slope distribution, Grain correlations, Curvature, Fractal dimension, FFT
  profile, Drift correction: It is possible to select a target graph for the
  curves.
- Arithmetic: Data fields 2 to 8 are remembered between invocations.
- Calibrate, Merge, Immerse, Attach Presentation, Cross-correlate, FFT, Mark
  With, Mask by Correlation, Neural network training: Second image is
  remembered between invocations.
- Immerse: Detail positions are remembered.
- Merge: New merge mode ‘Join’ suitable for slowly varying data without
  significant features but well defined absolute Z values was added.
- Pygwy: Python modules have sys.path set up the same way as the console now,
  which namely includes the path to gwyutils.py.
- 2D FFT: It is possible to provide the imaginary part and perform inverse
  transforms.
- 1D FFT filter: Occasional ‘Axis with extreme range!’ error was fixed.
- Image export: Alignment of numbers on false colour map scale was improved.
  Drawing of ‘lattice’ selections was implemented.  The decimal separator
  can be controlled.  A rare insufficient precision of ruler ticks was fixed.
- Filters tool: A simple Gaussian sharpening filter was added.
- Affine distortion: The lattice is remembered and recalled.  ACF image uses
  full colour range, correcting problems when fixed colour range is set.
- Selection manager tool: Lattice selections are shown when chosen in the list.
- Tip blind estimate: A memory freeing error was fixed in the stripes mode.
- Fractal dimension: Graph axis labels are somewhat more descriptive.
- Graph level, Graph filter: They are now undoable.
- Graph fit: A button for copying all fitted parameters to estimates was
  added.
- Graph FD fit: The theoretical curve and difference curve are created also
  from estimates, not just after final fit.
- Zeiss: RGB images are accepted and the channels are averaged upon import.
- Color range tool: Fixed color range controls are immediately sensitive when
  this range type is the default.
- XY denoise: Too many data field dereferencing, causing a crash later, was
  fixed.
- Euclidean distance transform: Renamed to Distance transform.  It can
  perform also various simple distance transforms.
- Renishaw: Support for loading some metadata was added.
- Nanonis: Files with unknown multiline header blocks are loaded correctly.
- Nanonics: It should be possible to open incomplete scans.

Other:
- Standalone Python module gwy is now in the gwyddion-devel package instead
  of the main package (it required the devel package to work anyway).

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Thanks all who contributed,

Yeti

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David Nečas (Yeti | 12 May 17:16 2015
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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

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Giovanni Perotto | 12 May 09:59 2015
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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
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Andrés Muñiz Piniella | 16 Apr 20:30 2015
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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.
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Christian K | 16 Apr 15:04 2015
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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

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Andrés Muñiz Piniella | 8 Apr 11:36 2015
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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

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