Judy Phan | 20 Nov 23:36 2014

extract profile vs grain distributions

Hi,
Which sets of data in the grain distributions tool that are corresponding to the data when you use the extract profile tool? Obviously, the profile you get when using the extract profile tool depends on each grain and where on the grain you draw the line. I guess my question is that is there a way I can export the maximum, minimum or average of those data (x and y)? Does the grain distribution tool have a way to scan each grain for all of its profiles and give you a max/min/average values? I know the distributions give you many types of heights and widths but which one of those corresponding to the profile extract tool x and y?
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
------------------------------------------------------------------------------
Download BIRT iHub F-Type - The Free Enterprise-Grade BIRT Server
from Actuate! Instantly Supercharge Your Business Reports and Dashboards
with Interactivity, Sharing, Native Excel Exports, App Integration & more
Get technology previously reserved for billion-dollar corporations, FREE
http://pubads.g.doubleclick.net/gampad/clk?id=157005751&iu=/4140/ostg.clktrk
_______________________________________________
Gwyddion-users mailing list
Gwyddion-users@...
https://lists.sourceforge.net/lists/listinfo/gwyddion-users
Mathias Müller | 19 Nov 11:36 2014
Picon

PNG Export-Issue


Hi Yeti,

the current stable version of Gwyddion (Linux, V2.39, R2014-11-14) seems to have problems to maintain the
color scale when exporting
processed data to png. However, while writing this mail it seems this problem is persistent for other
formats, too.
The displayed and the written color scale in the export dialog differs from that of the channel I am working
on. It seems that the 
export dialog sets the full data range for color specification per default.

Can you reproduce this issue on your machine?

Cheers,

/M

------------------------------------------------------------------------------
Download BIRT iHub F-Type - The Free Enterprise-Grade BIRT Server
from Actuate! Instantly Supercharge Your Business Reports and Dashboards
with Interactivity, Sharing, Native Excel Exports, App Integration & more
Get technology previously reserved for billion-dollar corporations, FREE
http://pubads.g.doubleclick.net/gampad/clk?id=157005751&iu=/4140/ostg.clktrk
David Nečas (Yeti | 14 Nov 17:17 2014
Picon

Gwyddion 2.39 was released


Gwyddion 2.39 is now available for download at

  https://sourceforge.net/projects/gwyddion/files/gwyddion/2.39/
  (all released files)

  http://gwyddion.net/download/2.39/
  (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:
- Pango 1.10 and Cairo 1.2 are now required.
- The program should start with a saner working directory by default.
- Translations updated: Czech, French, Russian.
- New translation: Korean.

Libraries:
- libgwyddion: A function for copying GwySIValueFormat was added; the
  structure is also registered as a boxed type now.
- libgwydgets: gwy_axis_get_magnification_string() returns string for the new
  units after gwy_axis_set_si_unit().
- libgwydraw: Adaptive false colour mapping was improved by making it more
  adaptive.
- libgwydraw: It is possible to map user-given values to gradient positions
  using the same mapping as gwy_pixbuf_draw_data_field_adaptive() uses.
- libgwydgets: GwyColorAxis has a new ‘unlabelled’ ticks mode in which the
  interior ticks are drawn without labels.
- libgwydgets: GwyColorAxis permits specifying a non-linear value to gradient
  mapping function.
- libgwydgets: Crash when changing color maps in Gwy3DView with gtk+ version
  greater 2.29 was fixed.
- libgwyapp: When adaptive false colour mapping is used, the axis is set to
  the new ‘unlabelled’ mode so the mapping non-linearity can be seen.

Modules:
- Image export (new): Replaces image rendering in the pixmap module; can
  export to vector graphics formats: PDF, EPS and SVG.  The corresponding
  file types are called ‘pdfcairo’, ‘pngcairo’, etc.
- NX II (new): Imports EMSYS NX II AFM files.
- FemtoScan (new): Imports FemtoScan SPM files.
- SPMx (new): Imports ACT/FemtoScan SPMxFormat files.
- Fractional Brownian motion (new): Generation of fBm-like artifical
  surfaces.
- Renishaw (new): Imports Renishaw WiRE data files.
- Pixmap: Only used for image import; image rendering functions were removed.
- Statistical quantities: Crash in saving the statistics was fixed (introduced
  in 2.38).
- OpenGPS: Format detection was improved to check not just for the presence
  of main.xml also if it really looks like an ISO 5436-2 XML file.
- MIF: X, Y and Z calibration factors are applied to data upon import and
  a different Z conversion formula is used according to z_linearized.
  Multiplicative factors encoded after the image are applied to the data.
- MetroPro: Z scale in files with PhaseRes value of 2 is correct now.
- Grain distributions: The graph abscissas are bin centres now, as is usual,
  instead of bin left edges.
- Noise and line noise synthesis: Settings are remembered also on Cancel.

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

Thanks all who contributed,

Yeti

------------------------------------------------------------------------------
Comprehensive Server Monitoring with Site24x7.
Monitor 10 servers for $9/Month.
Get alerted through email, SMS, voice calls or mobile push notifications.
Take corrective actions from your mobile device.
http://pubads.g.doubleclick.net/gampad/clk?id=154624111&iu=/4140/ostg.clktrk
_______________________________________________
Gwyddion-users mailing list
Gwyddion-users <at> lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/gwyddion-users
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
------------------------------------------------------------------------------
Comprehensive Server Monitoring with Site24x7.
Monitor 10 servers for $9/Month.
Get alerted through email, SMS, voice calls or mobile push notifications.
Take corrective actions from your mobile device.
http://p.sf.net/sfu/Zoho
_______________________________________________
Gwyddion-users mailing list
Gwyddion-users@...
https://lists.sourceforge.net/lists/listinfo/gwyddion-users
Maxwell Grady | 15 Oct 17:39 2014
Picon

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




--
University of New Hampshire
Department of Physics
Pohl Group
DeMeritt Hall 119
---
Síocháin agus Grá
------------------------------------------------------------------------------
Comprehensive Server Monitoring with Site24x7.
Monitor 10 servers for $9/Month.
Get alerted through email, SMS, voice calls or mobile push notifications.
Take corrective actions from your mobile device.
http://p.sf.net/sfu/Zoho
_______________________________________________
Gwyddion-users mailing list
Gwyddion-users@...
https://lists.sourceforge.net/lists/listinfo/gwyddion-users
Mathias Müller | 26 Sep 09:00 2014
Picon

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).

-- 
Dipl.-Phys. Mathias Mueller
Christian-Albrechts-Universitaet zu Kiel
Institut fuer Experimentelle und Angewandte Physik
Abteilung: Festkoerperphysik - Grenzflaechen
Leibnizstr. 17-19
24118 Kiel
Germany

Mail: mueller@...
Tel.: +49(0)431 880 3842
Fax : +49(0)431 880 1685

Web:
http://www.ieap.uni-kiel.de
http://www.ieap.uni-kiel.de/solid/ag-magnussen
http://www.sfb677.uni-kiel.de 

------------------------------------------------------------------------------
Meet PCI DSS 3.0 Compliance Requirements with EventLog Analyzer
Achieve PCI DSS 3.0 Compliant Status with Out-of-the-box PCI DSS Reports
Are you Audit-Ready for PCI DSS 3.0 Compliance? Download White paper
Comply to PCI DSS 3.0 Requirement 10 and 11.5 with EventLog Analyzer
http://pubads.g.doubleclick.net/gampad/clk?id=154622311&iu=/4140/ostg.clktrk
Jacob Sebastian Mealy | 22 Sep 12:51 2014
Picon
Picon

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
------------------------------------------------------------------------------
Meet PCI DSS 3.0 Compliance Requirements with EventLog Analyzer
Achieve PCI DSS 3.0 Compliant Status with Out-of-the-box PCI DSS Reports
Are you Audit-Ready for PCI DSS 3.0 Compliance? Download White paper
Comply to PCI DSS 3.0 Requirement 10 and 11.5 with EventLog Analyzer
http://pubads.g.doubleclick.net/gampad/clk?id=154622311&iu=/4140/ostg.clktrk
_______________________________________________
Gwyddion-users mailing list
Gwyddion-users@...
https://lists.sourceforge.net/lists/listinfo/gwyddion-users
Mathias Müller | 21 Sep 08:47 2014
Picon

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

------------------------------------------------------------------------------
Slashdot TV.  Video for Nerds.  Stuff that Matters.
http://pubads.g.doubleclick.net/gampad/clk?id=160591471&iu=/4140/ostg.clktrk
David Nečas (Yeti | 18 Sep 10:58 2014
Picon

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

------------------------------------------------------------------------------
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 <at> lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/gwyddion-users
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

Gmane