Eric Blair | 31 Jul 17:43 2014

Obtaining 2D slope statistics

Hi all,

I am interested in obtaining the 2D equivalent of the Δa and Δq values given by the 1D roughness tools.  In MetroPro, I am able to create a slope map and then take the Ra and Rq of this slope map to get the values I need.

Is there a way to get this information in Gwyddion?

Thanks,

Eric
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Witchukorn Phuthong | 25 Jul 10:12 2014
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Contrast level corresponding with height in Gwydddion exported RGB tiff file

Hi everyone, 

Using Gwyddion, I do the basic leveling, scar removal and fourier noise filtration, adjust the contrast and export my AFM image to RGB tiff file and the contrast level has the height difference about 5 nm. Then, I would like to associate the height and the brightness for further analysis in imageJ. I also convert my RGB tiff file to 8-bit grayscale for this analysis in ImageJ. So, I am wondering if it is valid to use the following relationship: B = (255/5)*H; B = brightness (0-255 in grayscale) and H is the height (nm) shown at a particular pixel of the original image after contrast adjustment, when considering height threshold in ImageJ with brightness? 

For example, if I want to make the threshold height in imageJ to be 2.5 nm, is it valid to set the threshold level for the brightness in imageJ to be B = (255/5)*2.5 = 127.5 ~ 128.

Thanks, 
Champ
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Collin Becker | 20 Jul 18:51 2014
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force curve analysis-Oliver Pharr Method

I searched through the modules and did not see anything, but I thought I would ask anyway:  does Gwyddion offer any force curve analysis, in particular I would like analyze my data using the Oliver Pharr method.

Thanks,

Collin


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Mathias Müller | 18 Jul 10:42 2014
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how to use gwy_app_data_window_change_square or similar


Hi,

I just wanted to write kind of module for gwyddion. However, I got stuck at the point where data is displayed
which is physically squared but not pixel size.
Looking into the API it says one can get the pixel and physical size of a GwyDataView. How is it possible to
reshape the view to make it squared (setting pixel size?)? 
I did not find any reference to this. Do I need to find a way on my own by e.g. interpolating the data or is there
kind of built-in function to apply?

I found some hints in the gwyddion source, but really don't wanna copy paste foreign code. This simply
bloats up the code for this module.

Many thanks in advance!

Cheers,

Mathias

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Mark S. Bentley | 2 Jul 13:04 2014

Populating a DataField object from the gwy module

Dear all,

I have a (hopefully) straightforward question. I have all of my AFM 
image and meta data in python (numpy array and dictionary) and want to 
simply write to a Gwyddion native file. I have imported the gwy module, 
created a new container and DataField object (initialise to the correct 
size/number of pixels), set the meta data and channel title etc. 
However, I can't find an easy way to populate the contents of the data 
itself...

DataField.get_data() works fine, and returns the initialised zero 
values. There is a function DataField.set_data() on inspecting the 
object, but this is not listed in the API and I can't get it to work.

There was a similar question on the list a while back, which was solved 
by using gwyutils. But I guess this only works inside of Gwyddion, and I 
need something that will run standalone...

Calling DataField.set_val() in a loop works fine - is this the preferred 
python option? The docs talk about using get_data() and referencing the 
returned buffer, but I guess this comes directly from the underlying C 
docs and is not relevant here..

Thanks for your help!

Mark

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David Nečas (Yeti | 27 Jun 11:03 2014
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Gwyddion 2.37 was released


Gwyddion 2.37 is now available for download at

  https://sourceforge.net/projects/gwyddion/files/gwyddion/2.37/
  (all released files)

  http://gwyddion.net/download/2.37/
  (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, Italian, Russian.

Libraries:
- libgwyprocess: A function for filling grain voids was added.
- libgwyprocess: A simple x and y derivative filter function was added.
- libgwyprocess: A regional extrema marking function was added.
- libgwyprocess: A classic Vincent watershed algorithm function was added.
- libgwydgets: Several new stock icons were added.
- libgwyprocess: Pixel count was added as a new grain quantity.
- libgwyprocess: Crash in gwy_grain_values_calculate() when a quantity was
  requested multiple times was fixed.
- libgwyprocess: New function for performing one step of facet levelling.
- libgwyddion: New data type GwyRandGenSet providing a convenient set of random
  number generators and functions for sampling from different distributions.
- libgwyprocess: DataField z-value format is now based on autorange instead of
  the full data range.
- libgwyddion: Environment variables such as GWYDDION_LIBDIR override the
  system-default paths on all systems, including OS X now.
- libgwyddion: Module and data paths on OS X are taken from the bundle
  "net.gwyddion" instead of the main bundle, fixing broken paths in the
  standalone Python gwy module.

Modules:
- WinSTM (new): Import WinSTM data files.
- Mark by Segmentation (new): Another segmentation/grain marking module, based
  on the classic Vincent algorithm.
- Grain filter (new): Filtering of grains by range criteria and logical
  expressions.
- Slope statistics (new): Statistics were split off Slope distributions, the
  GUI and functionality is the same as before.
- Lattice synthesis (new): Construction of surfaces based on Voronoi
  tesselation of randomized lattices.
- Grain removal by threshold: Removed.  Threshold-based removal is replaced
  by Grain filter (also replacing it the default toolbox).  Removal of grains
  touching image edges is a standalone menu function now.
- Mask operations: Function for removal of grains touching image edges was
  added.
- Mask editor tool: Fill voids handles correctly different connectivity of
  grain exterior, noticeable for grains separated only by thin lines.  It is
  also possible to fill only simple-connected grains.
- Pixmap: Vertical and horizontal rulers always use the same number format.
  The gap between image and false colour map can be adjusted, as well as the
  gap beteween the inset scale bar and image border.  Missing lower left corner
  of the false colour map scale border was fixed.  Text antialising can be
  disabled.
- Affine distortion: The ACF image can be zoomed.
- NT-MDT: Double inversion of new spectroscopy data properly checked and fixed.
- Slope distribution: Masking is supported.  Plot of total gradient was added.
- NanoScan: A couple of memory-hadling bugs was fixed.
- Grain distributions: Displays a preview graph of the selected quantity.
- Grain correlations: If run interactively and the same-units condition of
  selected quantities is not satisfied, default quantities are selected
  instead of aborting with an error box.
- Slope distributions: Preview of the result was added.
- Dimensions and Units: False colour axis actually starts showing the new
  value units also when you change only the units (not the Z range).
- 2D FFT Filter: FFT output centre of lateral coordinates is at the zero
  frequency now.
- 2D FFT and FFT profile: Slight offset of lateral coordinates for odd-sized
  images was corrected.
- Spectral synthesis: Critical message/crash, occuring when some files were
  loaded but no channel was active while invoking the function, was fixed.
- Cross-correlation: now allowing use of multiple channesl and output of
  all the results together.

Other:
- The standalone Python gwy module uses the correct extension for dlopening,
  fixing the failure to load Gwyddion libraries on OS X.

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

Thanks all who contributed,

Yeti

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Andrés | 22 Jun 21:31 2014
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EU reasearch funding H2020: free software

In case it is of interest https://fosdem.org/2014/schedule/event/eu_research_funding/

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Aaron Katz | 18 Jun 04:18 2014

Distance Measurements on image

Hello all;
Forgive me if there is an obvious answer to this question. I am using
gwiddion to analyze SEM images and in particular to measure distances.
Is there a way to have gwiddion label a measurement bar with the
actual distance? This is the kind of effect I am looking for versus
just a line with '1' that I currently get: http://imgur.com/IsPxkmD

Regards;
Aaron Katz

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YTC | 18 Jun 01:53 2014
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cannot load/save file with pygwy in python console outside gwyddion

I wrote some scripts to batch process files in a python console outside gwyddion on OSX. But it failed to load files.

c=gwy.gwy_file_load(fp, gwy.RUN_NONINTERACTIVE)
Error Output:
/opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/wx-3.0-osx_cocoa/wx/py/PyCrust.py:1: Warning: g_object_unref: assertion 'G_IS_OBJECT (object)' failed
  #!/usr/bin/env python

And it cannot save as well. I have a separate module to load a custom data file.

c=file_load() # returns a gwy container
......
data processing
......
gwy.gwy_file_save(c, 'test.gwy', gwy.RUN_NONINTERACTIVE)

Traceback (most recent call last):
  File "<input>", line 1, in <module>
GError: No module can save to this file type.
executing the last line will crash the python console.

Both scripts work fine in windows, and in the built-in pygwy console on Mac. I suspect it might be problems with loading the gwyddion libraries on OSX, but have no ideas on how to track down the problem. Any help is much appreciated.



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Andrés | 9 Jun 22:44 2014
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Bringing researchers and developers together: a call for proposals | Mozilla Science Lab

http://mozillascience.org/bringing-researchers-and-developers-together-a-call-for-proposals/

Hi all, I thought this might be useful to highlight. 
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Clark, Gregory W. | 6 Jun 18:00 2014

"Statistical Quantities" in Gwyddion 2.36

Hello Gwyddion Users,

 

I am using the "Statistical Quantities" in button in Gwyddion 2.36 to measure various quantities of masked regions for files that I open as “raw data” files.  These are former Bruker (Veeco) .FLT files that I have processed and stored as txt (ASCII) files.  Everything works fine EXCEPT that when I use the “Statistical Quantities” and look at the data in the window under “Parameters” the precision of  the quantities is often too small.  Sometimes I get four decimal places on all the Parameters, but sometimes I only get only two decimal places.  The quantities I’m working with are small (mV) surface potentials.  Is there any way to force Gwyddion to report four or even five decimal places in the Parameters list in the Statistical Quantities window?

 

Thanks for any help,

GWClark

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