David Nečas (Yeti | 26 Apr 19:08 2016
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Gwyddion 2.45 was released


Gwyddion 2.45 is now available for download at

  https://sourceforge.net/projects/gwyddion/files/gwyddion/2.45/
  (all released files)

  http://gwyddion.net/download/2.45/
  (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

the mailing list, or the project's web forum at SourceForge.

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

Michele Della Ciana | 24 Apr 19:02 2016
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Installing a module on Gwyddion (using Mac)

Hi! 

My name is Michele and I’m an Italian physics student.

I’m trying to install the minimal module in the totorial's section but when I start gwyddion it says:


(gwyddion:6946): GLib-GObject-WARNING **: cannot register existing type 'gchar'

**

GLib-GObject:ERROR:gvaluetypes.c:455:_g_value_types_init: assertion failed: (type == G_TYPE_CHAR)

Abort trap: 6

logout


and it closes.


To copile the module as a shared library I used: 

gcc -fPIC -shared -o module.so main.cpp `pkg-config --cflags --libs gwyddion`

where main.cpp is the source code of the minimal module.


It compiles fine… the problem occurs when I put the “module.so” file in the module’s directory.

By now I’m using gwyddion just as a library, but I hope to solve the problem!

I think is useful to know that I’m using a mac with OS X Yosemite and I have installed  gwyddion using homebrew!


Sorry for my English, I hope the problem is clear!

Thanks in advance

Michele



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Václav Šmilauer | 27 Mar 20:29 2016
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grain photo segmentation

Hi everybody,

I am new to Gwyddion and would like to try using it for grain size 
analysis from industrial camera images. A typical image is like this: 
http://i.imgur.com/lwuOBeh.jpg (the diagonal separates two types of 
material which has different reflectivity), and I would like to run (at 
some point) unattended analysis of grain size distribution under 
constant conditions (same lighting, similar material).

I was able to use some of the tools provided to improve the picture 
(like Polynomial Background to make the lighting artefacts less visible) 
but I am at loss with segmentation. The simple techniques (e.g. 
watershed) are not suitable, since grains have different luminosity 
(especially the glossy ones).

I will be grateful for hints, pointers or solutions. At this moment, the 
analysis does not have to be unattended, setting parameters or light 
hand-tuning is fine.

Cheers, Václav

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vidyasagar | 18 Mar 01:15 2016
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Hi

Dear sir/madam,

I have downloaded Gwyddion software, but it could not working well in my laptop.
When I opening the file, it says, opening of ....mdt failed. file contrains no (importable) data
Could you plase help me?

Sincerely,
Sagar
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John Dodji Amouzou | 2 Mar 16:32 2016
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Scales conversion (from log scale to linear scale)

Hello,
I recorded AFM images in current sensing mode using Resiscope and PicoView and the Z scale of the recorded images is in log scale. I would like to convert Z scales of current and resistance images into linear scale.
How could I do that?
Thanks for your help.
With regards,
Dodji.
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Andrés Muñiz Piniella | 25 Feb 18:22 2016
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3DPrinting your AFM data

I am sorry as I do not recall who was working on this as well, finally got some time to invest time in it.

I have worked on a little script and procedure that should make it possible to take AFM data (or any data represented in a surface) scale it and transform it into an STL that can be 3D printed.


Happy to walk you through to what I have done. Written explanation attached in comments of python code to get you started.

this can be further streamlined and improved. so that it is a saving module in Gwyddion.


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

Attachment (PrintGWY.py): application/octet-stream, 4568 bytes
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Andrés Muñiz Piniella | 28 Jan 14:52 2016
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windows 32 bit graph and download issues

I am using 2.44 32 bit on windows xp (yes I know it is old).

I noticed that measure distance in graph gives me a value in length but not height.

I was looking to reinstall again but I get sec_error_unknown_issuer
and the address is 139.143.6.160:9091 when following the link from gwiddion.net download page.

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

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David Nečas (Yeti | 11 Jan 15:13 2016
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Gwyddion 2.44 was released


Gwyddion 2.44 is now available for download at

  https://sourceforge.net/projects/gwyddion/files/gwyddion/2.44/
  (all released files)

  http://gwyddion.net/download/2.44/
  (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: Potential corruption of recent file list by Save As introduced in
  2.43 was fixed.
- libgwydgets: Gwy3DView no longer downsamples data during changes, all
  operations are done with full-resolution surfaces.  Its "reduced-size"
  property was deprecated and it has no effect.
- libgwydgets: Gwy3DView light source distance from the surface no longer
  scales with Value scale, improving views with small Value scale a lot.
- libgwyddion: gwy_debug() adds timestamp to the messages (where available).
- libprocess: Rare incorrect memory reallocation in Delaunay triangulation was
  fixed.
- libgwyapp: gwy_app_channel_remove_bad_data() now ensures the mask field has
  the same lateral dimensions and units as the data field.
- libgwyprocess: Bogus value returned by gwy_data_field_area_get_entropy() with
  mask exclusion mode was fixed.
- libgwyprocess: Functions for estimation of the entropy of two-dimensional
  point cloud, and for entropy-from-histogram-at-scale curves were added.
- libgwydgets: Graph labels respond to "label-property" changes.  The property
  is also meaningfully updated when user moves the label around.
- libgwyprocess: An iterative cancellable version of function
  gwy_triangulation_triangulate() was added.
- libgwyprocess: Functions for filling area under mask with a value and
  simple data-average correction using unmasked data were added.
- libgwydgets: GwyGraphModel and GwyGraphCurveModel clone() methods were
  implemented.
- libgwyprocess: Euclidean distance transform with from_border=FALSE actually
  work for all cases, previously the border-influenced ares had to be limited.
- libgwyprocess: New function for simple regularisation of XYZ data to a data
  field was added.
- libgwyapp: Data windows hidden and re-shown from the data browser no longer
  lose the window icon showing a data thumbnail.

Modules:
- Entropy (new): Visualises entropy calculation for distributions of values
  and slopes.
- Leica (new): Imports Leica LIF CLSM images.
- Nano Measuring Machine (new): Imports NMM profile sets and regularises them
  to raster data.
- DM3: Support for Digital Micrograph DM4 files was added.
- Image export: The number of digits in false colour axis ticks can be
  controlled explicitly.  Very small negative values are displayed as ‘0.0’,
  never the odd ‘-0.0’.
- Magellan: RGB images are accepted and the channels are averaged upon import.
- APE file: Crash when loading files with fewer actual data than reported by
  the channels bit mask was fixed.
- Limit Range: Setting range from fixed colour mapping range was fixed.
- NanoScanTech: Loading from raw binary data blocks was implemented.
- Keyence: File loading no longer fails when assembly information seems
  missing or too short as the module does not actually need it.
- All tools: Sensitivity of Apply buttons and auxiliary controls was corrected
  so that can be activated only when there is actually an active image.
- Processing modules with selections in the dialogue: Critical messages when
  the dialogues were displayed were fixed.
- Spectral synthesis: Possible critical message when re-running the function
  after deleting a channel was fixed.
- Rawfile: Replacement value for missing data can be given as text for text
  formats, e.g. ‘BAD’ or ‘NODATA’.
- Raw XYZ: A bug in point merging was fixed that sometimes caused infinities to
  appear in the data.  Triangulation is remembered and not recomputed when
  not necessary.  A progress bar is shown for the trianguation process and it
  is possible to cancel it.  New interpolation type ‘Average’ was added, which
  is always fast and produces a result similar to a bit fuzzier ‘Round’
  interpolation.  Button ‘Reset Ranges’ permits resetting the data ranges to
  the initial values obtained from the file data ranges.  Point density can be
  plotted as another field.
- GWYXYZF: The regularisation method was improved to ‘Average’ from Raw XYZ.
- Nanoscope: Support for 32bit raw data format used since 9.2 was added.
- JEOL: Support for Phase channels was added.
- Statistical quantities: Deficit of entropy to Gaussian distribution with the
  same dispersion was added as a new quantity.  Unavailable quantities are no
  longer printed to reports.
- MI file: Loading of graphs in ASCII format was implemented.
- RHK SM4: Loading of graph data with small Y size works now.
- Raw graph: Curve data are sorted upon import.
- Grain filter: Options for unused quantities (B or C) are now hidden instead
  of insensitivised to reduce visual clutter.
- Graph function fit, FD curve fit, critical dimension: Function names are
  translated also in reports.
- Ballistic deposition synthesis: Progressive preview works now.
- Align graph: Crash with curves not sorted by abscissa was fixed.
- Renishaw: Timestamps in metadata were corrected.

Other:
- MS Windows packages include OpenEXR support now.
- Broken configure detection of libpython on Fedora 23 (and possibly elsewhere)
  was fixed.
- A script generating MS Visual Studio solution files (and other files) was
  added as utils/gen-gwyddion-vs-sln.py.

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

Thanks all who contributed,

Yeti

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Hwansoo Suh | 17 Dec 19:41 2015

FYI, Installing Gwyddion on Mac with homebew

Hi, all.

In the official download page of Gwyddion, for Mac, only MacPorts and Fink packages are presented.

But if you prefer Homebrew as your main package manager in Mac OS X, there is an alternative installation method. See http://brewformulas.org/Gwyddion for more information.

Hope this helps mac users who use Gwyddion.

Best,
Hwansoo

--
Hwansoo Suh, Ph.D.
Visiting Scholar at Stanford University and 
R&D Staff Member
Device Lab.
Samsung Advanced Institute of Technology
Suwon, Korea
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Haeberle, Tobias | 17 Dec 10:32 2015
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Processing Phase Data

Hello,

I want to process some phase data from an AFM scan and correlate it with the topography data. Unfortunately,
gwyddion can’t open the phase image (.tif format). I get the error: 

`````
The type of data is unknown.  Please report it to the developers.

Full file path: .../Img2015_1217_08404721_2INPUT_B.tif.

Loaded using: joel.
`````

The AFM is a JOEL system. I have no problem reading the topography data images. Or is there a
misunderstanding on my part and gwyddion is not designed to look at phase data? 

Thank you!

Best regards
Tobias
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David Nečas (Yeti | 14 Dec 17:14 2015
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User influence survey


Hello all,

we are currently trying to investigate the influence of humans on
quantitative AFM results, in particular on the data processing part.

We would be therefore grateful if you helped us by spending several
minutes of your time by participating in a short survey at

    http://gwyddion.net/survey2/

The survey consists of processing of a couple images (well, three in
fact) and reporting one parameter for each.  No forms with hundreds of
odd questions are involved.  So it should be fun – and if we get enough
responses for statistics it will be also useful as the statistical
results will be used in a paper focusing on the user influence in SPM
data processing.

Please distribute this request to your colleagues who use AFM.

Thank you in advance.

Best regards,

Yeti & Petr

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