Gwyddion

On Mon, Aug 13, 2007 at 09:07:22AM +0200, Jan Beyer wrote:
> when looking at graphs of point spectroscopy data (I(V)), I am not able
> to switch the y-axis display to logarithmic. Is this because of the
> negative values for I (for negative U) or is it somehow disabled for
> point spectroscopy data?

It is disabled because of the negative values.

> Would it be possible to implement logarithmic y-axis display anyway (by
> taking the absolute value of all I-values)? That is useful when trying
> to estimate e.g. bandgaps of semiconductors.

This is a good idea -- for the ordinate at least, for the
abscissa limiting to positive values might work.

Yeti

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http://gwyddion.net/

On Mon, Aug 13, 2007 at 12:07:52PM +0200, David Necas (Yeti) wrote:
> 
> > Would it be possible to implement logarithmic y-axis display anyway (by
> > taking the absolute value of all I-values)? That is useful when trying
> > to estimate e.g. bandgaps of semiconductors.
> 
> This is a good idea -- for the ordinate at least, for the
> abscissa limiting to positive values might work.

FYI, I implemented this (unsure whether using the absolute
value for the ordinate is useful or confusing though).

Yeti

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http://gwyddion.net/

On 08/25/2007 02:43 PM, David Necas (Yeti) wrote :
> On Mon, Aug 13, 2007 at 12:07:52PM +0200, David Necas (Yeti) wrote:
>>> Would it be possible to implement logarithmic y-axis display anyway (by
>>> taking the absolute value of all I-values)? That is useful when trying
>>> to estimate e.g. bandgaps of semiconductors.
>> This is a good idea -- for the ordinate at least, for the
>> abscissa limiting to positive values might work.
>
> FYI, I implemented this (unsure whether using the absolute
> value for the ordinate is useful or confusing though).

Great! Many thanks for the fast implementation!
It works nicely!

I don't see any use for the logarithmic ordinate right now - but one never
knows, maybe somewhen somebody will find one... And I don't think it's
disturbing to have the feature...

Thanks again!

Jan

On Wed, Aug 15, 2007 at 12:35:03PM -0700, Samuel Pottish wrote:
> We are scanning on the 
> micron scale and getting plots from small areas, (mm^2). 
> Our signal generates the 3d plot in Gwyddion and I want to 
> find the total volume of the 3d plot, and possibly the 
> volumes above and below the xy plane. Is this type of 
> numerical data gathering possible with Gwyddion

Possible, yes, but straightforward, not quite, at least at
this moment.

Total volume (i.e. integral) is

  Average_value x Projected_area

from Statistical Quantities tool -- if zero level is set
where it should be.

There's no one-click method to separate it into the integral
of positive and negative values.  It can be done for
instance by using Arithmetic, expressions

  min d1,0
  max d1,0

extract positive and negative values into new data fields
you can use Statistical Quantities tool on again.

A slightly better result can be obtained by marking the
complete data field (Mask Editor tool -> Fill) and using
Grain Measure tool to calculate the volume of this `grain'
(use the zero-based volume value).

> I am 
> also interested in fiding the area of positive and 
> negative plots on the xy plane?

You can also use Mark Grains by Threshold to mark the
above/below zero parts, it is not possible to enter the
height threshold as an absolute number, only percentage, but
with the visual feedback it can be probably set relatively
precisely.  Then Grains -> Statistics displays the total
areas and volumes of marked parts.

I hope you will find at least one of the suggested methods
suitable for your needs.

Yeti

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http://gwyddion.net/

On Thu, Aug 02, 2007 at 03:18:43PM -0400, jeremy.beebe@... wrote:
> My hard drive died yesterday, so today after replacing the drive, I
> reinstalled Gwyddion v. 2.7.  As far as I can tell, every feature works
> except the tool used to measure distances between points.  Every time I
> try to use this feature, the program crashes.

Please specify the action that leads to the crash.

Does it crash after switching to Distance tool?
Or only when you try to select something on the data?
Does Profile and Path Level tools work normally then?
Does it crash also when no data is loaded? (You have to
click on the icon second time to bring the tool window in
this case.)

> I have tried installing
> both Gwyddion and the gtk runtime environment several times, and each
> time, I have the same problem.  I had never encountered this problem
> prior to the hard drive crash (I was using v. 2.7 then as well).

Hm, hopefully it is a `random' Gwyddion bug (memory
corruption) that just has never manifested itself on the old
machine.  Problems in system/3rd party libs/Gtk+
combinations are much harder to find and fix.

Please try tomorrow's or later night build and if it crashes
too, send me gwyddion.log.

> Has
> there been an unannounced version update, or patch made to the stable
> version in the past month or so?

No, there hasn't been any -- unless it was unannounced to me
too...

> Has anyone else encountered similar
> problems?  In case it helps, I'm loading Nanoscope III files in a
> Windows environment.

I don't have any working MS Windows at this moment, I'll try
to reproduce it next week, however I expect it to be hard to
hit.  If it was a common problem more people would complain.

Yeti

--
http://gwyddion.net/

> On Thu, Aug 02, 2007 at 03:18:43PM -0400, jeremy.beebe@... 
> wrote:
>> My hard drive died yesterday, so today after replacing the drive, I
>> reinstalled Gwyddion v. 2.7.  As far as I can tell, every feature works
>> except the tool used to measure distances between points.  Every time I
>> try to use this feature, the program crashes.

Hi,
My combination of software works fine... I use Gwyddion 2.7, Gtk+/Win32 
Development Environment (runtime, devel, docs, glade, etc.) Installer 
2.10.6-1 (.exe, 11.41M) on WinXP with SP2 and latest updates.

Mira

On Thu, Aug 02, 2007 at 03:18:43PM -0400, jeremy.beebe@... wrote:
> As far as I can tell, every feature works
> except the tool used to measure distances between points.  Every time I
> try to use this feature, the program crashes.

I'm sorry, I cannot reproduce it.  Have you tried something I
suggested?

Yeti

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http://gwyddion.net/

Jeremy, it seems you are not receiving not just the mailing
list e-mails, but also e-mails I send personally.

Posting to this list and hoping you will read the archives
again is the only way I can reach you.  Please use
a different mail service.

Yeti

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http://gwyddion.net/