Milano, Stefania | 17 Sep 17:30 2014
Picon
Picon

Re: Grain Analysis Measurements


Hi there!
I have a couple of questions about grain analysis (I’m a new Gwyddion user so I apologize for these really basic questions):

1. Regarding the orientation of the major ellipse, when exported the output data are expressed in  φ angles. Is it possible to covert these values in degrees and how?

2. I need to get information about grains shape factors. Which one do you reckon is the best with the data available in the grain distributions?
 I am trying to calculate the circularity through this ratio:

C= 4πA/P^2 (A= area, P=perimeter) .

In this case I am using the projected area (A_0) and the projected boundary length (Lb_0) but I am not sure if this approach is right or there is a better way to do it.
 
Thanks

------------------------------------------------------------------------------
Want excitement?
Manually upgrade your production database.
When you want reliability, choose Perforce
Perforce version control. Predictably reliable.
http://pubads.g.doubleclick.net/gampad/clk?id=157508191&iu=/4140/ostg.clktrk
_______________________________________________
Gwyddion-users mailing list
Gwyddion-users@...
https://lists.sourceforge.net/lists/listinfo/gwyddion-users
Mathias Müller | 12 Sep 15:32 2014
Picon

2D-FFT conversion


Hi,

in my C-code I want to apply the gwyddion fft-transformation to SPM data. 

the code sniplet is:

data_field_fft_r = gwy_data_field_new_alike(data_field, TRUE);
data_field_fft_i = gwy_data_field_new_alike(data_field,
TRUE);
gwy_data_field_2dfft(data_field,NULL,data_field_fft_r,data_field_fft_i,GWY_WINDOWING_NONE,GWY_TRANSFORM_DIRECTION_FORWARD,GWY_INTERPOLATION_ROUND,TRUE,1) ;
gwy_data_field_2dfft_humanize(data_field_fft_r) ;

where data_field is obtained from real space data.

When displaying the artifical data, it looks pretty good, e.g. like a hexagonal structure. Comparing the
coordinates within the differently obtained FFT images, it looks 
like all the x and y values are way larger in the c-code 2d-FFT (no window) then the one from the gwyddion
module. I.e. the very center of the gwyddion-performed fft-image
is nearly at (0.002,0.004) nm^-1. But the data reasulting from
gwy_data_field_2dfft_humanize(data_field_fft_r) show a center at approx.
(3.43886e-08,5.05459e-08)...I guess m^-1. 

There seems to be a juge difference. Does gwyddion itself calculate the 2d-fft in another way?

Thanks for helping.

Cheers,

/M

------------------------------------------------------------------------------
Want excitement?
Manually upgrade your production database.
When you want reliability, choose Perforce
Perforce version control. Predictably reliable.
http://pubads.g.doubleclick.net/gampad/clk?id=157508191&iu=/4140/ostg.clktrk
Mathias Müller | 11 Sep 15:53 2014
Picon

user-set display range in container ignored

Hi,

I wanted to adjust the displayed data in my C code with the following approach:

(...)
data[1] = gwy_container_new();
gwy_container_set_object_by_name(data[1], "/0/data", data_field);
data_view[1] = GWY_DATA_VIEW(gwy_data_view_new(data[1]));
gwy_data_view_set_data_prefix(data_view[1], "/0/data");
gwy_container_set_boolean_by_name(data[1], "/0/data/realsquare", TRUE);	 
gwy_container_set_int32_by_name(data[1], "/0/base/range-type", GWY_LAYER_BASIC_RANGE_FIXED);
gdouble max = gwy_data_field_get_max (data_field);
gdouble avg = gwy_data_field_get_avg(data_field) ;
gwy_container_set_double_by_name(data[1], "/0/base/min", 0); // or max*0.5
gwy_container_set_double_by_name(data[1], "/0/base/max", 1); // or max
(...)

The data from <data_field> are displayed correctly. But what ever I set as min or max value for 
display ranges is being ignored. I would have thought the GWY_LAYER_BASIC_RANGE_FIXED enables the
readout of the min/max values.

Changing the /0/data/range-type to e.g. GWY_LAYER_BASIC_RANGE_AUTO results in a different
display of the data.

Did I do something wrong when adjusting the color scale manually?

Thanks for any help,

/M

------------------------------------------------------------------------------
Want excitement?
Manually upgrade your production database.
When you want reliability, choose Perforce
Perforce version control. Predictably reliable.
http://pubads.g.doubleclick.net/gampad/clk?id=157508191&iu=/4140/ostg.clktrk
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
------------------------------------------------------------------------------
Infragistics Professional
Build stunning WinForms apps today!
Reboot your WinForms applications with our WinForms controls. 
Build a bridge from your legacy apps to the future.
http://pubads.g.doubleclick.net/gampad/clk?id=153845071&iu=/4140/ostg.clktrk
_______________________________________________
Gwyddion-users mailing list
Gwyddion-users@...
https://lists.sourceforge.net/lists/listinfo/gwyddion-users
Witchukorn Phuthong | 25 Jul 10:12 2014
Picon

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
------------------------------------------------------------------------------
Want fast and easy access to all the code in your enterprise? Index and
search up to 200,000 lines of code with a free copy of Black Duck
Code Sight - the same software that powers the world's largest code
search on Ohloh, the Black Duck Open Hub! Try it now.
http://p.sf.net/sfu/bds
_______________________________________________
Gwyddion-users mailing list
Gwyddion-users@...
https://lists.sourceforge.net/lists/listinfo/gwyddion-users
Collin Becker | 20 Jul 18:51 2014
Picon

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


------------------------------------------------------------------------------
Want fast and easy access to all the code in your enterprise? Index and
search up to 200,000 lines of code with a free copy of Black Duck
Code Sight - the same software that powers the world's largest code
search on Ohloh, the Black Duck Open Hub! Try it now.
http://p.sf.net/sfu/bds
_______________________________________________
Gwyddion-users mailing list
Gwyddion-users@...
https://lists.sourceforge.net/lists/listinfo/gwyddion-users
Mathias Müller | 18 Jul 10:42 2014
Picon

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

------------------------------------------------------------------------------
Want fast and easy access to all the code in your enterprise? Index and
search up to 200,000 lines of code with a free copy of Black Duck
Code Sight - the same software that powers the world's largest code
search on Ohloh, the Black Duck Open Hub! Try it now.
http://p.sf.net/sfu/bds
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

------------------------------------------------------------------------------
Open source business process management suite built on Java and Eclipse
Turn processes into business applications with Bonita BPM Community Edition
Quickly connect people, data, and systems into organized workflows
Winner of BOSSIE, CODIE, OW2 and Gartner awards
http://p.sf.net/sfu/Bonitasoft
David Nečas (Yeti | 27 Jun 11:03 2014
Picon

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

------------------------------------------------------------------------------
Open source business process management suite built on Java and Eclipse
Turn processes into business applications with Bonita BPM Community Edition
Quickly connect people, data, and systems into organized workflows
Winner of BOSSIE, CODIE, OW2 and Gartner awards
http://p.sf.net/sfu/Bonitasoft
_______________________________________________
Gwyddion-users mailing list
Gwyddion-users <at> lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/gwyddion-users
Andrés | 22 Jun 21:31 2014
Picon

EU reasearch funding H2020: free software

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

--

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

------------------------------------------------------------------------------
HPCC Systems Open Source Big Data Platform from LexisNexis Risk Solutions
Find What Matters Most in Your Big Data with HPCC Systems
Open Source. Fast. Scalable. Simple. Ideal for Dirty Data.
Leverages Graph Analysis for Fast Processing & Easy Data Exploration
http://p.sf.net/sfu/hpccsystems
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

------------------------------------------------------------------------------
HPCC Systems Open Source Big Data Platform from LexisNexis Risk Solutions
Find What Matters Most in Your Big Data with HPCC Systems
Open Source. Fast. Scalable. Simple. Ideal for Dirty Data.
Leverages Graph Analysis for Fast Processing & Easy Data Exploration
http://p.sf.net/sfu/hpccsystems

Gmane