Judy Phan | 17 Oct 04:07 2014

Particles/Grains shape

Hi,
I'm working on a project where particles are collected and imaged using the AFM. I've been getting myself familiar with Gwyddion software. My goal is to be able to quantify the particles using the grain properties tools but since I'm working with multiple particles, I need to normalized their properties in order to compare them. So far, I saw people done 2-D parameters such as elongation, convexity, circularity, etc. Does anyone know what are the 3-D parameters? I think comparing the ratios of the major and minor semiaxis of equivalent ellipse with the mean height will give me some sort of elongation. For convexity (surface roughness), in 2-D it is a ratio between the particle area and the total area. Is projected area the total area? And is the surface area actually the particle area? I'd like to translate this to 3-D ratio.

Thanks,

--

Judy Phan

Master of Science in Chemical Engineering, 2015

Bachelor of Science in Chemical Engineering with Cum Laude, 2013

Bucknell Engineering Network Student Liaison

Chair of the Banquet & Society Activities Committee of Tau Beta Pi
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Maxwell Grady | 15 Oct 17:39 2014
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Gwyddion on OSX Yosemite beta-6 via macports fails to load Omicron Scala files

I am running OS X.10 yosemite beta version 6 on a macbok pro early 2011 model.


When I load gwyddion the opening logo says gwyddion 2.4 but when I go to the 'about gwyddion' menu it says gwyddion 2.3.4 released 2013-12-15


I recently found that gwyddion is no longer loading my STM files.
I collect STM data with an Omicron SCALA system. The files are saved in .par and .tfo 


Gwyddion used to open them with no trouble at all. Now when I try to open the files I get various errors about file size.

Strangely enough the file browser window shows a preview of the files correctly. When I highlight, for instance, m10003.par, it shows me a preview of the data and I can see that the data is correct. Then when I try to open the file it tells em there is an error in the file length. The format would require x number of bytes the file is only y bytes long.

here are links to the sample file(s) I will include a link to the .par and the .tf0




-Maxwell Grady




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Pohl Group
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Mathias Müller | 26 Sep 09:00 2014
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Gwyddion 2.38 segmentation fault


Hi Yeti,

I recently installed the current stable version of gwyddion (2.38). Unfortunatelly, I experience a
reproducible segmentation fault in the 
statistics dialog. After having determined the rms roughness etc gwyddion crashes when saving the statistics.

I've already cleaned my gwyddion installation and rebuild it. The segfault persists.

Terminal output:

(gwyddion:18814): Gwyddion-CRITICAL **: gwy_si_unit_get_format_with_digits: assertion
'GWY_IS_SI_UNIT(siunit)' failed
zsh: segmentation fault (core dumped)  gwyddion

The core file says :

Core was generated by `gwyddion'.
Program terminated with signal SIGSEGV, Segmentation fault.
#0  0x00007f415c59cf37 in ?? () from /usr/lib/gwyddion/modules/tool/stats.so
(gdb) bt
#0  0x00007f415c59cf37 in ?? () from /usr/lib/gwyddion/modules/tool/stats.so
#1  0x00007f418764d554 in gwy_save_auxiliary_with_callback () from /usr/lib/libgwyapp2.so.0
#2  0x00007f415c59b98f in ?? () from /usr/lib/gwyddion/modules/tool/stats.so
#3  0x00007f418566b664 in ?? () from /usr/lib/libgobject-2.0.so.0
#4  0x00007f4185685b27 in g_signal_emit_valist () from /usr/lib/libgobject-2.0.so.0
#5  0x00007f418568648f in g_signal_emit () from /usr/lib/libgobject-2.0.so.0
#6  0x00007f41865c8185 in ?? () from /usr/lib/libgtk-x11-2.0.so.0
#7  0x00007f418566b664 in ?? () from /usr/lib/libgobject-2.0.so.0
#8  0x00007f4185685b27 in g_signal_emit_valist () from /usr/lib/libgobject-2.0.so.0
#9  0x00007f418568648f in g_signal_emit () from /usr/lib/libgobject-2.0.so.0
#10 0x00007f41865c70b9 in ?? () from /usr/lib/libgtk-x11-2.0.so.0
#11 0x00007f418666d8bf in ?? () from /usr/lib/libgtk-x11-2.0.so.0
#12 0x00007f418566b435 in g_closure_invoke () from /usr/lib/libgobject-2.0.so.0
#13 0x00007f418567d8f2 in ?? () from /usr/lib/libgobject-2.0.so.0
#14 0x00007f4185685d36 in g_signal_emit_valist () from /usr/lib/libgobject-2.0.so.0
#15 0x00007f418568648f in g_signal_emit () from /usr/lib/libgobject-2.0.so.0
#16 0x00007f4186784aac in ?? () from /usr/lib/libgtk-x11-2.0.so.0
#17 0x00007f418666c004 in gtk_propagate_event () from /usr/lib/libgtk-x11-2.0.so.0
#18 0x00007f418666c49b in gtk_main_do_event () from /usr/lib/libgtk-x11-2.0.so.0
#19 0x00007f41862e1e4c in ?? () from /usr/lib/libgdk-x11-2.0.so.0
#20 0x00007f418539ac7d in g_main_context_dispatch () from /usr/lib/libglib-2.0.so.0
#21 0x00007f418539af68 in ?? () from /usr/lib/libglib-2.0.so.0
#22 0x00007f418539b292 in g_main_loop_run () from /usr/lib/libglib-2.0.so.0
#23 0x00007f418666b417 in gtk_main () from /usr/lib/libgtk-x11-2.0.so.0
#24 0x0000000000408a32 in main ()

I tried this on several data files. There is no exception.

Cheers,

/M

P.S.: This mail might be a copy of a mail from the day before yesterday which was kept by the mail server due to
its too large attachement (corefile).

-- 
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Jacob Sebastian Mealy | 22 Sep 12:51 2014
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Average wavelength of surface

Dear list,

I am just wondering how Gwyddion defines and caluclates the average wavelength of a line profile. I am using wavelength to differentiate several surfaces and just need a basic idea of how Gwyddion separates peaks from noise etc and comes up with the number. I have looked in the online documentation but can't find any info on it.

Any help would be greatly appreciated.

Kind regards,

Jake Mealy

Trinity Centre for Bioengineering
Trinity College Dublin
Ireland
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Mathias Müller | 21 Sep 08:47 2014
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mingw update


Yeti,

do you already plan to update the mingw libraries for cross-building gwyddion on e.g. fedora 20 ?
Or will this be suspended for a larger gwyddion release?

Cheers and have a nice weekend,

/M

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David Nečas (Yeti | 18 Sep 10:58 2014
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Gwyddion 2.38 was released


Gwyddion 2.38 is now available for download at

  https://sourceforge.net/projects/gwyddion/files/gwyddion/2.38/
  (all released files)

  http://gwyddion.net/download/2.38/
  (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:
- Pressing F1 shows help, i.e. it points a web browser to the relevant part
  of the user guide (in most program windows).  Most dialogs also have a Help
  button now.
- Translations updated: Czech, French, German, Russian, Spanish.

Libraries:
- libgwyprocess: New function to find a height threshold by the Otsu method.
- libgwyprocess: New functions to calculate data field total variation.
- libgwyprocess: Macro gwy_data_field_invalidate() is also provided as
  a function so it is available in pygwy now.
- libgwymodule: New functions to obtain the name of the currently running
  file, proc, volume and graph module functions.
- libgwyprocess: New functions to count regional minima and maxima.
- libgwyapp: New simplified logging functions that do not require passing the
  function name.
- libgwyprocess: New function for numbering grains assuming the mask is
  periodic and grains can touch across the opposite edges.
- libgwyapp: New functions for help handling.
- libgwydgets: Real scale in 3D view can be set arbitrarily, not just 1:1.
- libgwyprocess: New function to update units and dimensions of 2D FFT output.
- libgwyapp: New file module utility function for masking NaNs and infs.

Modules:
- OpenGPS (new): Imports OpenGPS surface data format (ISO 5436-2).
- JEOL JSPM (new): Imports JEOL JSPM data files.
- Diffusion synthesis (new): Artificial surface generation by a diffussion
  limited aggregation simulation.
- K-means (new): K-means clustering for volume data.
- FITS (new): Imports Flexible Image Transport System images.
- FemtoScan TXT (new): Imports FemtoScan exported TXT data files.
- Filters tool: Gaussian smoothing is no longer limited to integer FWHM.
- Columnar synthesis: Can plot the evolution of some statistics during the
  growth.
- APE DAX: Warning about invalid logging function name was fixed.
- NT-MDT: Fixed loading of old spectroscopy from Nanoeducator2 data.
  Search of external data in another possible location is implemented.
- Pygwy: It is possible to write volume data processing modules in Python.
  Brick has a duplicate() method, gwy_app_data_browser_get_current() supports
  brick-related items.  Python error messages are no longer silenced after
  Python modules are run.
- Color range tool: The range can be set to the range of masked/unmasked
  values.
- HDR image: NaNs and infinites in floating point images are removed and
  masked upon import.
- Slope distribution: A bad typecast causing Gtk+ warning was fixed.

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

Thanks all who contributed,

Yeti

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Milano, Stefania | 17 Sep 17:30 2014
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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

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Mathias Müller | 12 Sep 15:32 2014
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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

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Mathias Müller | 11 Sep 15:53 2014
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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

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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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