gmane.science.analysis.gwyddion.user

Re: Gwyddion on Win7 64bit

David Nečas (Yeti — 2013-05-22T12:37:14

I cannot test the 64bit Windows nightly build easily but the 32bit seems
to be logging the startup progress fine so I assume the 64bit is also
all right.  Please try it.

Regards,

Yeti


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Re: Gwyddion on Win7 64bit

David Nečas (Yeti — 2013-05-21T21:07:56

Tommorow's night build (2.31.20130522) should log the startup progress
to gwyddion.log; the file will now contain this (for normal startup):

gwyddion.c:102 setup_logging()
gwyddion.c:106 g_setenv()
gwyddion.c:108 g_timer_new()
gwyddion.c:110 gwy_app_check_version()
gwyddion.c:114 gwy_osx_set_locale()
gwyddion.c:117 process_preinit_options()
gwyddion.c:121 gwy_debug_objects_enable()
gwyddion.c:124 gwy_app_settings_create_config_dir()
gwyddion.c:126 debug_time()
gwyddion.c:128 setup_locale_from_win32_registry()
gwyddion.c:130 gtk_init()
gwyddion.c:133 gwy_remote_do()
gwyddion.c:135 gwy_app_init()
gwyddion.c:142 g_file_test()
gwyddion.c:145 gwy_app_splash_start()
gwyddion.c:149 g_build_filename()
gwyddion.c:151 gtk_accel_map_load()
gwyddion.c:155 gwy_app_splash_set_message()
gwyddion.c:157 gwy_app_settings_get_recent_file_list_filename()
gwyddion.c:159 gwy_app_recent_file_list_load()
gwyddion.c:165 gwy_stock_register_stock_items()
gwyddion.c:170 gwy_resource_class_load()
gwyddion.c:173 gwy_resource_class_load

Re: Gwyddion on Win7 64bit

David Nečas (Yeti — 2013-05-21T18:54:33

Looking at how the Gwyddion startup is logged, this doesn't mean much,
unfortunately (the output just goes to stdout which is buffered, for
those who know what I'm talking about).  If the file contained something
we would know how far the startup progressed but empty file just means
we don't know anything.

The puzzling part is the failure is completely silent – quite untypical
for MS Windows.  I'm afraid we can't get anywhere without building
Gwyddion executables with some more robust startup logging specifically
targeted at this.

Regards,

Yeti


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Re: Gwyddion on Win7 64bit

Ekaterina Chernysheva — 2013-05-21T15:59:08

Hi,

Unfortunately, various compatibility modes did not work, nor the
administrator one.

Concerning the *output.log*, the file has been created, but it is empty...

Kind regards,
Ekaterina

ekaterina.chernysheva-o/5/jSaJEHn7CU9A358lRodd74u8MsAO< at >public.gmane.org
M2 NanoSciences Saclay, Ecole Polytechnique, Paris






On 19 May 2013 12:17, Miroslav Valtr <miraval-9Vj9tDbzfuSlVyrhU4qvOw< at >public.gmane.org> wrote:

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Re: Gwyddion on Win7 64bit

Miroslav Valtr — 2013-05-19T10:17:25

Dear Ekaterina,

 

Yeti suggested to run Gwyddion with --startup-time command line option, so 
we could at least guess where the problem could be. I suggest therefore to 
run it from command line and redirect the output to some file (needed in 
order to see the output). So run the console first by clicking Start -> 
search for cmd -> run cmd. A console window should appear. Then fillout the 
path to gwyddion.exe, append it by the option and redirect the output, so it
should be something like

 

"c:\Program Files (x86)\Gwyddion\bin\gwyddion.exe" --startup-time > output.
log

 

Normaly, Gwyddion should start and output.log file should contain something 
like this (I also closed Gwyddion, so it contains also times related to its 
shutdown):

 

                    init:  27.0 ms
              gtk_init(): 130,0 ms
          gwy_app_init(): 698,0 ms
           create splash: 156,0 ms
          load accel map:   9,0 ms
   load document histor

Re: Gwyddion on Win7 64bit

Kostyantyn Nikiforov — 2013-05-16T16:37:24

You may also want to try "run as admin" via rightclick menu and/or "run in
compatibility mode" in properties of the exe. Try "xp sp3" as compatibility
settings.

Regards,
Kostya

On Thu, May 16, 2013 at 3:49 PM, Ekaterina Chernysheva <
kate.chernysheva-Re5JQEeQqe8AvxtiuMwx3w< at >public.gmane.org> wrote:

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Re: Gwyddion on Win7 64bit

Ekaterina Chernysheva — 2013-05-16T13:49:27

Dear Miroslav,

I tried both versions, and tried to put them into different "Program Files"
folders. Also, I tried different languages. It keeps doing the same...
I suppose, there might be some system package or library missing on my
laptop. But I do not know how to detect it.

Still hoping to resolve this issue,
Kind regards,
Ekaterina

ekaterina.chernysheva-o/5/jSaJEHn7CU9A358lRodd74u8MsAO< at >public.gmane.org
M2 NanoSciences Saclay, Ecole Polytechnique, Paris





On 16 May 2013 11:36, Miroslav Valtr <miraval-9Vj9tDbzfuSlVyrhU4qvOw< at >public.gmane.org> wrote:

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Gwyddion-

Re: Gwyddion on Win7 64bit

Miroslav Valtr — 2013-05-16T09:36:59

I saw in the path "Program Files (x86)". Did you installed the 64 bit or 32 
bit version? Gwyddion is compiled for both targets. You can try both. Also 
during the installation did you choose russian or english? I'm not sure 
whether the language selection would alter something, but anyway...

Regards,

Mira

Dne čtvrtek 16 Květen 2013 11:07:12 Ekaterina Chernysheva napsal(a):


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Re: Gwyddion on Win7 64bit

Ekaterina Chernysheva — 2013-05-16T09:07:12

Dear Miroslav and Daniil,

Thanks for your fast answers.

I have just downloaded and re-installed one, but the same thing happens. I
have also tried to launch Gwyddion directly from *C:\Program Files
(x86)\Gwyddion\bin\*. File *gwyddion.log* is empty.

When I launch the program, a process *gwyddion.exe* appears in the Windows
Task Manager for a while and then goes away. No window or error message. It
just goes out from of the list by itself...

Sincerely,
Ekaterina

ekaterina.chernysheva-o/5/jSaJEHn7CU9A358lRodd74u8MsAO< at >public.gmane.org
M2 NanoSciences Saclay, Ecole Polytechnique, Paris




On 16 May 2013 10:57, Daniil Bratashov <dn2010-Re5JQEeQqe8AvxtiuMwx3w< at >public.gmane.org> wrote:



On 16 May 2013 10:33, Miroslav Valtr <miraval-9Vj9tDbzfuSlVyrhU4qvOw< at >public.gmane.org> wrote:

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Re: Gwyddion on Win7 64bit

Miroslav Valtr — 2013-05-16T08:33:10

Dear Ekaterina,

From your description it is hard to tell whats actually going on. I believe 
that if Gwyddion would crash some window with error would appear. I have 
tested Gwyddion on Win7 64 bit and it works fine.

I would recommend first to uninstall and after that to install the latest 
version of Gwyddion. If you have ever installed the 2.22 or earlier version, 
then also Gtk toolkit should be uninstalled first.

Mira

Dne čtvrtek 16 Květen 2013 10:06:23 Ekaterina Chernysheva napsal(a):


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htt

Re: Gwyddion on Win7 64bit

Daniil Bratashov — 2013-05-16T08:57:22

There can be some debug info in log file that placed somewhere like
c:\Users\%username%\gwyddion\gwydddion.log, where %username% is your login
in windows

Also I've got similar problem on win vista. When gwyddion is installed by
one user and then run by another, the program failed to start, but can be
run manually from c:\program files\gwyddion\bin, not from c:\program
files\gwyddion\gwyddion.exe where link points.


WBR, Daniil Bratashov.


On Thu, May 16, 2013 at 12:06 PM, Ekaterina Chernysheva <
kate.chernysheva-Re5JQEeQqe8AvxtiuMwx3w< at >public.gmane.org> wrote:

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Gw

Gwyddion on Win7 64bit

Ekaterina Chernysheva — 2013-05-16T08:06:23

Dear colleagues,

I am facing a problem that I could not overcome for a long time. On my
Windows 7, 64 bit I am not able to launch Gwyddion. No error or something
pops up, but I am not to launch the program...
If anyone has faced the same situation or has an idea what can be done for
that, I sincerely appreciate.

Thank you and have a nice day!

Kind regards,
Ekaterina Chernysheva

ekaterina.chernysheva-o/5/jSaJEHn7CU9A358lRodd74u8MsAO< at >public.gmane.org
M2 NanoSciences Saclay, Ecole Polytechnique, Paris
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efficiently configure, manage, and operate all of your security controls
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Re: Watershed options

Thomas Ganner — 2013-05-15T07:10:48

Morgen Manuel,
Kurze Frage, was ist die kleinste Filtergröße die ihr habt ( für einen Spritzenaufsatz-Filter). 

Danke
Lg Thomas

-----Original Message-----
From: Daniil Bratashov [mailto:dn2010-Re5JQEeQqe8AvxtiuMwx3w< at >public.gmane.org] 
Sent: Tuesday, May 14, 2013 5:35 PM
To: gwyddion-users-5NWGOfrQmneRv+LV9MX5uipxlwaOVQ5f< at >public.gmane.org
Subject: Re: [Gwyddion-users] Watershed options

On Mon, 13 May 2013 23:50:36 +0400
D.Yu.Khanukaeva <khanuk-o+MxOtu4lMCHXe+LvDLADg< at >public.gmane.org> wrote:

It seems that it is maximum value in datafield minus minimum one divided by 5000, it is not actually a percents.

OK, I'm not completely understand current algorithm implemented, but it seems to me that at each step for each point in datafield it is finding local minimum starting from that point and then adding
dropsize*(max-min)/5000 to the value in the minimum and marking this pixel as grain. if the next time it is no longer minimum, grain will grow up.

WBR, Daniil Bratashov.

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

Re: Watershed options

D.Yu.Khanukaeva — 2013-05-14T20:26:33

Thank you, Daniil, for your comments.

Your explanation of Number of steps option in Grain location sections seems very natural and I thought about it in analogous manner. According to this logic, the amount of lakes and their sizes should be directly proportional to the Number of steps. But I have quite opposite situation: the more the Number of steps the less the amount of lakes. And this seems strange...

Thank you anyway :)
Daria.

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Re: Watershed options

Petr Klapetek — 2013-05-14T20:10:05

Dear all,

tomorrow I will try to explain the algorithm parameters more in detail 
in the user guide,
sorry that I hadn't time for that up to now.

Best regards,
Petr



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Re: Watershed options

Daniil Bratashov — 2013-05-14T15:34:41

On Mon, 13 May 2013 23:50:36 +0400
D.Yu.Khanukaeva <khanuk-o+MxOtu4lMCHXe+LvDLADg< at >public.gmane.org> wrote:


It seems that it is maximum value in datafield minus minimum one
divided by 5000, it is not actually a percents.


OK, I'm not completely understand current algorithm implemented, but it
seems to me that at each step for each point in datafield it is finding
local minimum starting from that point and then adding
dropsize*(max-min)/5000 to the value in the minimum and marking this
pixel as grain. if the next time it is no longer minimum, grain will
grow up.


WBR, Daniil Bratashov.

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Watershed options

D.Yu.Khanukaeva — 2013-05-13T19:50:36

Dear colleagues,

my questions are rather simple and I hope, someone will answer. I looked through the forum archive and found analogous post about the meaning of the watershed options. There David recommended reading manual in reply. I've read manual several times, but misunderstanding remains.
The only option which is clear for me is the Threshold - it cuts the noise on the chosen level.
More or less Drop size parameter understandable - the higher its value, the larger lakes on the image. But it is measured in percents. What are these percents of?
Variations of Number of steps in Segmentation section also result in the sizes of the lakes. So I've concluded, that it is the amount of drops put in each chosen grain.
At last, Number of steps in Grain location section gives the most unexpected results for me, that indicates my absolute misunderstanding of its meaning. If the initial drops are located at every point of the image, why do large unmasked regions appear, when this parameter is high? If this is the l

Re: Section across different images on same graph

David Nečas (Yeti — 2013-05-11T16:47:19

You can drag'n'drop compatible curves from the Curves tab of a graph to
another graph.  But don't jump for joy yet... The key word is
compatible.  Primarily it means that abscissa and ordinate of both
graphs match (since it's the graph, not the individual curves, what has
physical units associated, there would be no way to sort them out again
once they are in one graph) – which is not your case so it is not
possible in the GUI.  And it seems pygwy does not go into sufficiently
low-level functions either here.

Yeti


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Section across different images on same graph

andres.muniz-piniella — 2013-05-10T20:14:35

Hello,
This might not be possible or maybe there is a clever workaround by scripting. I tried looking through documentation and email list with no luck.

As an example I have a topography image and a current image recorded at the same time. I draw section lines over areas of interest (1) and (2) on the topography and I use the distribute lines to all images. This gets me (1') and (2') in the current image. 

How do i get Gwyddion to plot all thes sections on the same graph or at least pair up (1) with (1')? All I can do is pair up (1) with (2).

Anything short from plotting it with gnuplot or similar. 






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Re: Gwyddion-users Digest, Vol 74, Issue 1

Peter Eaton — 2013-05-09T08:52:02

Hi Ben,
2: I think, that option probably cannot do much harm.
3: I do not think repeatedly clicking anything until a threshold is met is a
good idea. Each time you remove a scar , it averages part s of the image,
directly reducing roughness. I do not know if clicking this more than once
in Gwyddion actually has any effect, however.

Measured Roughness depends on many factors including:
1.The size of the (physical) area measured
2.The number of pixels sampled
3. Post processing
4. The actual shape of the sample
5. Various artifacts of the AFM.

So, you are trying to isolate only point 4, which is tricky, without
accounting for the other factors!

What I normally do when I want the roughness of some areas in a n image is:
Extract (Crop) a number of ROIs, from the main image (all the same size)
Perform necessary post processing, normally some flattening, to take account
of changes along the slow axis, and curvature on the fast axis, i.e. a 2nd
order horizontal level.
Record the rms/Ra of each area.

You can do

Re: Lost or corrupted settings file?

David Nečas (Yeti — 2013-05-09T05:57:08

To tell whether the file was indeed saved incorrectly or it is not
corrupted but Gwyddion, for whatever reason, cannot parse it, it is best
to look at the file.  You can send it directly to me.  Also, when this
happens there should be a record in gwyddion.log (in the same directory)
saying where exactly it failed.

Regards,

Yeti


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