On Wed, Mar 30, 2011 at 12:26:46PM +0200, Mark S. Bentley wrote:
I am also working a lot with my data in python, and in the end chose to
write to the BCR format used by SPIP and also opened by Gwyddion. Mainly
because the format specification is fairly simple and well described:
As someone
On Sun, Mar 27, 2011 at 04:47:31PM +0200, Jérôme Borme wrote:
Say I open data files with the raw data filter. The file is then added
to the list of recent files. But trying to open a file from that list
triggers the error No module can load this file type. Did I miss
something ?
If you work
On Fri, Mar 25, 2011 at 09:06:19PM +0100, VAZQUEZ BURGOS, LUIS FERNANDO wrote:
Sorry for my
misunderstanding than comes from the fact that for the adding option
there is no need apparently to previously fill the FFT image, it
works directly.
Well, it does not work any more or less
On Fri, Mar 25, 2011 at 01:53:03PM +0100, luis vazquez wrote:
it seems that the option subtract in 2D FFT filtering does not
work. In previous versions of Gwyddion I had also problems (the
filtered image was totally black when the subtract option was
applied) and in 2.23 it even does not
On Fri, Mar 25, 2011 at 09:07:51PM +0300, Daniil Bratashov wrote:
On Fri, 25 Mar 2011 18:44:30 +0100
David Necas (Yeti) y...@gwyddion.net wrote:
Would starting from a full mask make it better?
It will work, but possibly switch Filter out/keep freqs under mask
will be more suitable
On Fri, Mar 25, 2011 at 09:23:32PM +0200, Amit Finkler wrote:
Maybe you can solve the ambivalence by replacing the string
it is looking for to just # Daisy.
I did exactly this.
Regards,
Yeti
--
Enable your software
On Tue, Mar 22, 2011 at 12:00:55AM +0100, David Necas (Yeti) wrote:
On Mon, Mar 21, 2011 at 10:20:29PM +0100, Jérôme Borme wrote:
Would it be possible to get the Graph menu by a right click on a graph
window ?
Yes, I don't see any problem doing this.
I implemented it. Not sure if putting
On Wed, Mar 23, 2011 at 02:57:16PM +0100, Jérôme Borme wrote:
However, when the Minimum field is actually bigger than the
Maximum, the numerical scale displayed on the image window does not
match this inversion, and therefore the scale does not reflect the
data height of the displayed image.
On Wed, Mar 16, 2011 at 10:05:24AM +0100, David Necas (Yeti) wrote:
On Tue, Mar 15, 2011 at 03:53:30PM +, Farris, Leslie wrote:
I am unable to drag data into a single graph in the 2.23 version. Is
there a fix for this or should I go back to 2.22? Thank you.
It works for me
On Tue, Mar 15, 2011 at 03:53:30PM +, Farris, Leslie wrote:
I am unable to drag data into a single graph in the 2.23 version. Is
there a fix for this or should I go back to 2.22? Thank you.
It works for me but apparently Drag and drop is broken on MS Windows (it
would be nice to mention the
On Wed, Feb 16, 2011 at 10:07:55AM +0100, Palma D'Antonio - Unifg wrote:
Hello, I'm using the 'ISO' button to compute the roughness. It give the
possibility of filtering the data with a variable cut-off, but I'd like
to know (I don't find it in the manual) what kind of transfer function is
On Fri, Feb 04, 2011 at 03:20:46PM -0800, James Mack wrote:
Is it possible to change the folder which initially comes up in the
File-Open dialogue box? I am interested in changing it in both Windows and
Mac installations.
In Windows the default initial folder is C:\system32, but I would like
On Thu, Feb 03, 2011 at 11:14:30AM +0100, Bernd Spangenberg wrote:
I have a problem loading .map files form a realy old version of OptiCode,
It eems in my type of .map files the structure differs form what is in the
MApVue module.
I can use the raw import filter, but it is realy tendious. I
On Thu, Feb 03, 2011 at 02:54:35PM -0800, Nicola Ferralis wrote:
I am sure you followed directions here:
https://lists.sourceforge.net/lists/listinfo/gwyddion-users
Funny he's not among the list members (I checked now). So either he has
already unsubsribed or is getting the list e-mails
On Wed, Feb 02, 2011 at 10:27:36AM -0500, Daniel Casimir wrote:
I downloaded using the GladeWin 32 from the suggested link on the
gwyddion website, however in the folder under the start menu the only
options for Gtk+ I have are Gtk+ demo, theme selector, and uninstall.
Am I missing any
On Thu, Jan 20, 2011 at 04:22:43PM +0100, Ettore Bernardi wrote:
I'm tryng to do the surface reconstruction. I do Data Process → Tip →
Model Tip to model the tip and then Data Process → Tip → Surface
Reconstruction to start surface reconstruction, but at this point I'm not
able to
On Tue, Jan 18, 2011 at 03:40:09PM +0100, Adam Wykrota wrote:
Mac OS leopard 10.5.8
Software crash when I tried to open CITS data
log from X11
Xlib: extension RANDR missing on display :0.0.
(gwyddion:3280): Gtk-WARNING **: Could not find the icon 'application-xml'.
The 'hicolor' theme
On Wed, Jan 19, 2011 at 12:30:21PM -0800, Scott Webster wrote:
Probably this is somehow related to my configuration, but I just
started getting the following error when I try to start gwyddion:
The program 'gwyddion' received an X Window System error.
This probably reflects a bug in the
On Wed, Jan 19, 2011 at 02:02:50PM -0800, Scott Webster wrote:
Interesting... I wonder what would have changed here. I did just
change my physical location, but someone sitting next to me does not
have this problem.
I'm afraid I cannot help you with making OpenGL work; it may be caused
by
On Wed, Jan 19, 2011 at 03:04:36PM -0800, Scott Webster wrote:
Well, I found the cause of my problem... if I have an external monitor
plugged into my mac laptop, running in extended desktop mode, where
you essentially have one big screen spanning the internal and external
monitors, it does not
On Mon, Jan 10, 2011 at 06:08:01PM -0300, Francisco Balzarotti wrote:
I'm working with a homemade afm, I'd like to export files from the
acquisition software (that I wrote) to Gwyddion.
I'd like to export topography and error images. No additional data.
I'm not quite sure which is the most
On Tue, Dec 07, 2010 at 03:15:16PM +0100, VAZQUEZ BURGOS, LUIS FERNANDO wrote:
thank you very much for adding the Radial ACF.
I should probably note (also in the guide) that the row-wise functions
level each row before calculating the correlation function or PSD.
However, the 2D ACF is
On Wed, Nov 17, 2010 at 10:50:13AM -0800, John Futhey wrote:
I want to use the module graph_export_ascii, which I believe is
called Export Text in the Graph Menu. My problem is that when I
select Graph on the Menu, all the selections are grayed-out, i.e.,
inoperative. I am running Windows
On Tue, Nov 09, 2010 at 02:08:15PM +0100, Johannes Römer wrote:
I just tried out the latest nightly snapshot (2.21.20101108). The mask
drawing/erasing tool that you have implemented is exactly what I was
looking for. Thank you very much! I'm sure that a lot of other Gwyddion
users will also
On Mon, Nov 01, 2010 at 09:17:13AM -0700, Scott Webster wrote:
Could one draw a mask in a different program, and then import it
somehow? You could imagine loading the image (or a bitmap export) in
a drawing program and then drawing the mask as a separate layer.
This is possible even though
On Thu, Oct 28, 2010 at 04:06:45PM +0200, Johannes Römer wrote:
I just installed Gwyddion, and I really like the program.
Unfortunately it lacks one function I would need to use it in my
everyday work. The edit mask tool is great, but it only offers
rectangular shapes, elliptic shapes and thin
On Sun, Oct 24, 2010 at 02:51:16PM +0200, Jérôme Borme wrote:
I would like to use the pygwy interface to batch-process containers by
calling
modules with specific parameters. I tried something like this:
cons = gwy_app_data_browser_get_containers()
for c in cons:
--
On Mon, Oct 25, 2010 at 10:16:40AM +0100, Neil Bishop wrote:
We have come across a paper where the authors calculate the
permeability of a rock sample from a 2D backscattered SEM image. In
order to do this they calculate Specific Surface Area using a binary
image (rock is black, pores are
On Thu, Sep 30, 2010 at 03:55:29PM -0700, James Mack wrote:
Is it possible to use pygwy in Windows? I have Gwyddion 2.20 installed on a
32-bit XP system. If it is possible, could you explain the procedure to
me? I am a novice Python user.
Hello, unfortunately, pygwy does not really work on
On Fri, Sep 17, 2010 at 10:31:45AM +0200, Johanna Generosi wrote:
I´d like to open jpk files in gwyddion. These jpk files contain the measured
height, the lock-in phase and other images. When I click on open file in
gwyddion, I can visualize all the images but when I click on open, only
the
On Wed, Aug 04, 2010 at 09:34:09AM -0400, Yaping Dan wrote:
How to open Asylum AFM files? They have a weird extension
.ibw which Gwyddioin cannot recognize.
.ibw is the extenstion of Wavemetrics' Igor Pro files and Gwyddion can
import them normally -- at least those I have. So if it
On Mon, Jul 26, 2010 at 11:01:24AM -0400, Ryan Speller wrote:
If possible I'd like to keep the application as just one that uses the
gwyddion library to avoid the additional overhead that you describe
below. Are there any functions with which I can access the channels in a
given image
On Fri, Jul 23, 2010 at 09:44:00PM +0200, Massimo Vassalli wrote:
The question was related to GUI because I was using a windows PC but I
switched to Linux and using pygwy I attained the task in few lines, even
going further into my image processing steps.
OK, maybe I'll add a simple module for
On Fri, Jul 23, 2010 at 01:08:27PM -0400, Ryan Speller wrote:
I want to modify the code to export 2 different channels to jpeg format.
I notice the function find_some_data is used to find data in the
thumbnailer example. I think I'll probably have to make use of the
On Mon, Jul 26, 2010 at 11:27:15AM +0200, Frimmel Jiří wrote:
I usually use Gwy in my office on Win (at present Gwy 2.13), with
submenus pulled out of main menu to stand-alone windows. Now I did
some work at home on Ubuntu 10.04 and although it is possible to pull
out the submenu, it is
On Mon, Jul 26, 2010 at 11:07:06AM +0200, Frimmel Jiří wrote:
Hello, it will be useful to have possibility to set default channel
for opening MetroPro .dat file, or set as default the phase channel
(opening both channels as default would be confusing).
No problem, I put the phase channel first
On Mon, Jul 26, 2010 at 12:15:00PM +0200, David Necas (Yeti) wrote:
On Mon, Jul 26, 2010 at 11:27:15AM +0200, Frimmel Jiří wrote:
I usually use Gwy in my office on Win (at present Gwy 2.13), with
submenus pulled out of main menu to stand-alone windows. Now I did
some work at home on Ubuntu
On Tue, Jul 20, 2010 at 08:20:05AM +0200, Massimo Vassalli wrote:
The question was: is there a simple way to set the value for all the masked
pixels to a value, e.g. to zero ? I'm actually extracting the mask and
multiplying it by the original image but because I'm working with a large
number
On Mon, Jul 19, 2010 at 02:53:18PM +0200, Jakub Grochowski wrote:
Is it possible in Gwydion 2.20 to export file into TIFF but with 300dpi?
I am exporting (exactly saving-as) files into TIFFs but they are
always only 96dpi...
The pixmap export module does not write any XRresolution and
On Mon, Jul 05, 2010 at 05:29:25PM +0200, Nirav Parekh wrote:
I was using Gwyddion 2.16 without any problems till today. But today when I
wanted to open .txt file, it kept on saying no module can detect your file.
I am surprised as few weeks before it was working perfectly alright. To
check if
On Thu, Jul 01, 2010 at 08:56:54AM -0700, Joey Wallace wrote:
Interesting, and promising. I have tried to open on 3 different
computers, running 3 different versions (2.19 being the most recent I
have, but all are running on some version of Windows). The error is
the same on all versions. I
On Wed, Jun 30, 2010 at 07:47:23AM -0700, Joey Wallace wrote:
Thanks for looking into this. Here is the link to the file:
http://www.filedropper.com/01-loc150um
Thanks, I can open this file normally, all 7 channels are imported and
they look good and I cannot see anything unexpected in the
On Wed, Jun 30, 2010 at 04:41:48PM -0700, Scott Webster wrote:
2010/6/30 marjan zakerin zakerin...@yahoo.com:
Well it is a force volume measurement which you define a grid and in every
point a force distance curve is recorded. so in principle I have a 2D map of
force, adhesion and zero
Gwyddion 2.20 is now available for download at
https://sourceforge.net/projects/gwyddion/files/gwyddion/2.20/
(all released files)
http://gwyddion.net/download/2.20/
(source code)
Released files are signed with PGP/GnuPG key
David Nečas (Yeti) y...@gwyddion.net, id 62A07732
On Wed, Jun 23, 2010 at 06:03:23PM -0400, Justin Silverman wrote:
I have read a number of articles that used SIMAGIS Nanotube Module to
get statistically accurate measurements a large number of carbon
nanotubes. That is the software can identify what is a Single walled
nanotube from what is
On Thu, Jun 24, 2010 at 11:34:26AM +0200, Timmel, Tobias wrote:
For example, how do I explicitly set the color range to an upper and
lower limit?
By setting /0/base/max and/or /0/base/min in the container to the
corresponding values (as floats) where 0 is the channel number.
Generally, all
On Tue, Jun 22, 2010 at 03:16:48PM +0200, tobias.tim...@charite.de wrote:
Hi, as I do time series of AFM images I usually do the same
post-processing steps with all the images of one series. In order to
automate this procedure I started to use the pygwy console.
But I can find only little
On Wed, Jun 16, 2010 at 12:04:19PM +0200, Martin Willenbockel wrote:
is there a certain way how I should cite Gwyddion?
At present, no. There should be one relatively soon (a paper), but now
you essentially have two options:
(a) Name Gwyddion in Methods/Data Processing/... section, with URL in
On Wed, May 19, 2010 at 11:56:13AM +0200, paai wrote:
I am trying to run Gwyddion on a Kubuntu 9.10 X68_64 box, but it keeps
crashing with:
The program 'gwyddion' received an X Window System error.
This probably reflects a bug in the program.
The error was 'BadRequest (invalid request code
On Wed, May 19, 2010 at 12:08:16PM +0200, paai wrote:
GIMP and gtk-demo run just fine...
What remote control backend ./configure shows when you compile it
manually?
Do you run it from menu/command line?
Could you try --no-splash?
Yeti
On Tue, May 04, 2010 at 10:38:18AM -0700, Bibiana Onoa wrote:
What would it be the
best way to post the file on the web? I made a zip file and attached to a
previous post but it is too big.
If you don't have any web space where you can put the file for public
(people in academia usually
On Fri, Apr 30, 2010 at 02:02:27PM -0700, Bibiana Onoa wrote:
I did try to open
the files as raw data, I get something incompressible, lines with different
shades , not very useful.
You have to specify the data offset (can be found in the file), data
format (16bits, little endian) and scales
On Thu, Apr 08, 2010 at 10:34:38AM +0200, Rolf Wuerdemann wrote:
I'm currently working with STM spectra measured with the Omicron
Scala software. As I found out, Gwyddion is only able to deal with
single points, but not grid spectra. It would be nice to have this
feature -- and it is
On Thu, Apr 01, 2010 at 01:33:32AM +0100, Owen Pearse wrote:
As far as I am aware a true radial PSDF should be invariant under rotation
of the original image data.
However the rPSDF in Gwyddion doesn't seem to be invariant under
rotation.
I fixed it, thanks for the report.
which I tested
On Thu, Apr 01, 2010 at 01:33:32AM +0100, Owen Pearse wrote:
As far as I am aware a true radial PSDF should be invariant under rotation
of the original image data.
However the rPSDF in Gwyddion doesn't seem to be invariant under rotation,
which I tested using Gwyddion's rotate by arbitrary
On Tue, Mar 30, 2010 at 04:45:43AM +0100, Owen Pearse wrote:
How do I know if FFTW3 has been compiled and therefore is being used as
rather than gwy_fft_simple, for instance for rPSDF?
You can find about optional features using Meta → About → Features.
Using Gwyddion v2.19 on WinXP.
MS
On Sat, Mar 27, 2010 at 01:29:31PM -0500, Eric Inazaki wrote:
I'm presently using Gwyddion 2.13 on Ubuntu 9.04 and I'm having a problem
opening _some_ .mi files (the header says something about PicoView 0x10600).
I hex dumped two files, one that I can open and one that I can't. In the
file
On Mon, Mar 22, 2010 at 05:44:39PM +0100, Massimo Vassalli wrote:
I read the post you suggested and I agree that leveling is a critical point
in step height determination. Reasonably, using a profile is simpler and
clearer but in my case I need much more statistics than that I can obtaining
by
On Tue, Mar 16, 2010 at 08:20:38PM +, Owen Pearse wrote:
I would like to check whether the radial PSDF is averaging over the angle or
summing over the angle of the 2D PSDF.
Referring to the radial PSDF as defined at:
http://gwyddion.net/documentation/user-guide/statistical-analysis.html
On Wed, Feb 24, 2010 at 09:29:29AM +0100, Elizabeth Goiri wrote:
I'm using Gwyddion to analyze images taken with an Omicron STM, of type .par
I have not yet found a way to make Gwyddion display the parameters (area,
voltage, current, and so on) associated with the image.
How is this done??
Hello, Gwyddion user guide 2009-11-11 was released. It can be browsed
on-line or downloaded from the usual places, see
http://gwyddion.net/documentation/#user
The most important news is that the guide goes international. The
ready-to-read formats were still published only for English
Gwyddion 2.18 is now available for download at
https://sourceforge.net/projects/gwyddion/files/gwyddion/2.18/
(all released files)
http://gwyddion.net/download/2.18/
(source code)
Released files are signed with PGP/GnuPG key
David Nečas (Yeti) y...@gwyddion.net, id 62A07732
On Mon, Oct 26, 2009 at 12:36:17PM -0400, Luke Somers wrote:
Which exact version you use?
I am using 2.16
Then please try 2.18 once it's released; I think it has been corrected
meanwhile.
yes, I'm talking here about the tool Data Process - Mask - Mark
With...
This one really did not
On Thu, Aug 27, 2009 at 06:21:48AM -0700, Angelo Ulivieri wrote:
PLEASE DELETE MY NAME FROM THIS FUCKED MAILING LIST
I SEND THIS MESSAGE SO MUCH MONTHS AGO!!!
So, here are the instructions again. The footer of every e-mail
contains the following link:
On Thu, Aug 13, 2009 at 04:40:23PM +0800, wang.ke...@gmail.com wrote:
I have some AFM images of quantum dots. Now I want to change their height
axes (Z axes) to be -abs(sqrt(dz/dx^2 + dz/dy^2)), where z(x,y) is the
topograph and dz/dx, dz/dy are numerical derivatives along the two image
axes.
On Thu, Jul 23, 2009 at 09:28:31AM +, Ceco Meco wrote:
just got my new Asylum Research MFP-3D delivered, using it and enjoying
it for one week now. Any idea whether Gwyddion can open these IGOR binary
waves? I got so much used to Gwyddion when processing data from our Veeco
machines, it'll
On Thu, Jul 09, 2009 at 10:37:20AM -0400, Luke Somers wrote:
We're taking data off of a Dimension 3000 and a Dimension 3100, using
Nanoscope version 5.31r1 on the 3000 and some variant of version 6 on
the 3100. Both are windows boxes.
I have some files from similar set-ups that load fine
On Thu, Jul 09, 2009 at 10:30:28AM -0500, Husein Rokadia wrote:
1. Re: Opening '.mi' files in Gwyddion
Ans: We have an Agilent AFM here, and use Gwyddion to process '.mi' files.
The key is to save them as 16 bit rather than 32 bit.
If you find out something like this then, please, ask to add
On Tue, Jun 02, 2009 at 04:30:40PM -0700, tim.str...@hitachigst.com wrote:
Just to clarify my previous note, the problem with psia tiff files is when
I drag and drop the file on Gwyddion. It can open those files when I
preselect the psia tiff file type.
This again indicates a problem in
On Thu, May 21, 2009 at 04:51:43PM -0700, tim.str...@hitachigst.com wrote:
I was running 2.14 on MS winxp, service pack 3 without problems. After
installing 2.15, Gwyddion dies without giving an error message whenever I
try to load a .tiff file from the Park Scientific Afm. The same files
On Fri, Mar 27, 2009 at 08:52:25AM +0100, Bernard Watts wrote:
Is it possible to plot the facet analysis plot on a polar projection
net rather than purple on black when the facet analysis is done?
Unfortunately, this is not possible. And since it requires a completely
new type of plot I am
On Sat, Jan 10, 2009 at 11:34:43PM +0100, Jan Beyer wrote:
To Yeti: Is it technically possible to build with pygwy and then just move
the relevant files into a separate package
Yes, this is very common, and according to
Hello,
Gwyddion creates TMS[1]-conforming thumbnails of loaded files so
that other applications can display these thumbnails too.
Some time ago people asked for thumbnails of files that have never been
opened in Gwyddion.
Gwyddion 2.12 comes with gwyddion-thumbnailer which does exactly that.
On Fri, Dec 05, 2008 at 10:57:17AM +0100, Denny Köhler wrote:
If you try to calculate the mean value linewise the it seems to that the
programm assumes a square image or a selected area wich has a square
shape. Because if you change the width or hight to values that are not
in a ratio of 1:1
On Fri, Nov 28, 2008 at 06:13:55PM -0800, Scott Webster wrote:
As you can see, the histogram is maximally sharp at 0 tilt and the
histogram plot looks like you would expect.
Here is some real AFM data (R-plane sapphire atomic steps) and the
resultant histogram:
On Wed, Nov 26, 2008 at 11:39:50PM -0800, Scott Webster wrote:
But I too often use Gwyddion to determine step heights in my images.
I have been using the three-point level tool on one terrace in order
to try to make that (and the other) steps flat. Then I use the 1-D
statistical height
On Fri, Aug 01, 2008 at 09:14:22AM +0200, David Necas (Yeti) wrote:
On Fri, Jul 18, 2008 at 03:49:29PM -0400, Dr. Georg E. Fantner wrote:
I'm having problems opening a Nanoscope IV (v6.12) file with Gwyddion
2.9 or 2.10. The error I get is Header field `Samps/line' is missing.
I looked
On Wed, Nov 12, 2008 at 04:48:10PM +0100, Rolf Würdemann wrote:
The Omicron Scala has it origin for the measurements in the lower left
edge. (Gwyddion uses the upper left). Therefor the topographic data
was flipped while reading some time ago.
This still has to be done for the positions of
On Wed, Nov 12, 2008 at 03:17:29AM +1100, Tom Sobey wrote:
I am trying to run Gwyddion on my Macbook with Leopard. I have successfully
installed it through Macports.
However when I run it from terminal I get the following:
Toms-MacBook:bin tsobey$ export DISPLAY=:0
Toms-MacBook:bin
On Wed, Sep 17, 2008 at 05:33:29PM +0200, Franz J. Schmied wrote:
I want to analyze a line section if there is a recurrent signal or
feature in it. Is this possible in Gwyddion? Otherwise it would be nice,
to have such a tool to analyze a profile.
I am afraid FFT of single lines/profiles is
On Wed, Aug 20, 2008 at 04:31:04PM +0900, Martin SETVIN wrote:
When the lines does not match each other, I usually convolve
the picture by 1-D Gaussian in direction perpendicular to scanning area.
It is quite effective against non-matching lines and it does not hurt
the picture too much.
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