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Karthik Vijayraghavan | 12 Jun 2012 02:22
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3D Image overlay question

Hi Everyone,


I saw from the changelog for version 2.26 that libgwydgets supports overlaying a false color map from secondary data in 3D view. I can see the overlay option in the 3D mode but was unsure of how to go about using a secondary data for doing the false coloring. Any pointers to that would be greatly helpful. 

Regards,
Karthik
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David Nečas (Yeti | 12 Jun 2012 10:09
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Re: 3D Image overlay question

On Mon, Jun 11, 2012 at 05:22:08PM -0700, Karthik Vijayraghavan wrote:
> I saw from the changelog for version 2.26 that libgwydgets supports
> overlaying a false color map from secondary data in 3D view. I can see the
> overlay option in the 3D mode but was unsure of how to go about using a
> secondary data for doing the false coloring.

You can choose the second data in Light&Material tab in the expanded 3D
view controls.

Yeti

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Karthik Vijayraghavan | 12 Jun 2012 16:49
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Re: 3D Image overlay question



On Tue, Jun 12, 2012 at 1:09 AM, David Nečas (Yeti) <yeti-OaLk+CuQmGTk1uMJSBkQmQ@public.gmane.org> wrote:
On Mon, Jun 11, 2012 at 05:22:08PM -0700, Karthik Vijayraghavan wrote:
> I saw from the changelog for version 2.26 that libgwydgets supports
> overlaying a false color map from secondary data in 3D view. I can see the
> overlay option in the 3D mode but was unsure of how to go about using a
> secondary data for doing the false coloring.

You can choose the second data in Light&Material tab in the expanded 3D
view controls.

Yeti

 
Thanks! I hadn't noticed the expanded view panel before.

Karthik 
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Karthik Vijayraghavan | 12 Jun 2012 17:18
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Re: 3D Image overlay question



On Tue, Jun 12, 2012 at 7:49 AM, Karthik Vijayraghavan <karthik1024-Re5JQEeQqe8AvxtiuMwx3w@public.gmane.org> wrote:


On Tue, Jun 12, 2012 at 1:09 AM, David Nečas (Yeti) <yeti-OaLk+CuQmGTk1uMJSBkQmQ@public.gmane.org> wrote:
On Mon, Jun 11, 2012 at 05:22:08PM -0700, Karthik Vijayraghavan wrote:
> I saw from the changelog for version 2.26 that libgwydgets supports
> overlaying a false color map from secondary data in 3D view. I can see the
> overlay option in the 3D mode but was unsure of how to go about using a
> secondary data for doing the false coloring.

You can choose the second data in Light&Material tab in the expanded 3D
view controls.

Yeti

 
Thanks! I hadn't noticed the expanded view panel before.

Karthik 

I tried to follow this method and it works for files that have been generated by my Veeco Dimension 3100. However, I want to do this on my own data that I obtained using the raw import function. The overlay panel only allows overlaying additional channels in the same file. Is there a way to add a channel to existing data that have been imported using "raw import"?

Thanks!

Karthik 

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Karthik Vijayraghavan | 12 Jun 2012 19:40
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Re: 3D Image overlay question



On Tue, Jun 12, 2012 at 8:18 AM, Karthik Vijayraghavan <karthik1024-Re5JQEeQqe8AvxtiuMwx3w@public.gmane.org> wrote:


On Tue, Jun 12, 2012 at 7:49 AM, Karthik Vijayraghavan <karthik1024-Re5JQEeQqe8AvxtiuMwx3w@public.gmane.org> wrote:


On Tue, Jun 12, 2012 at 1:09 AM, David Nečas (Yeti) <yeti-OaLk+CuQmGTk1uMJSBkQmQ@public.gmane.org> wrote:
On Mon, Jun 11, 2012 at 05:22:08PM -0700, Karthik Vijayraghavan wrote:
> I saw from the changelog for version 2.26 that libgwydgets supports
> overlaying a false color map from secondary data in 3D view. I can see the
> overlay option in the 3D mode but was unsure of how to go about using a
> secondary data for doing the false coloring.

You can choose the second data in Light&Material tab in the expanded 3D
view controls.

Yeti

 
Thanks! I hadn't noticed the expanded view panel before.

Karthik 

I tried to follow this method and it works for files that have been generated by my Veeco Dimension 3100. However, I want to do this on my own data that I obtained using the raw import function. The overlay panel only allows overlaying additional channels in the same file. Is there a way to add a channel to existing data that have been imported using "raw import"?

Thanks!

Karthik 


I found one way to do this. I open the two raw data files first. With the first image selected I go to  Data Process -> Multidata ->Arithmetic . I then set the arithmetic expression as d2 and select the second image in d2. 

Karthik

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David Nečas (Yeti | 12 Jun 2012 19:56
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Re: 3D Image overlay question

On Tue, Jun 12, 2012 at 8:18 AM, Karthik Vijayraghavan
<karthik1024@...> wrote:
> I tried to follow this method and it works for files that have been
> generated by my Veeco Dimension 3100. However, I want to do this on my own
> data that I obtained using the raw import function. The overlay panel only
> allows overlaying additional channels in the same file. Is there a way to
> add a channel to existing data that have been imported using "raw import"?

You can copy the second data to the first file using Drag'n'Drop from
Data Browser.

Yeti

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Mandl, Magdalena | 18 Jun 2012 15:53
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Filtering in roughness and waviness profile

Hi,

i´m calculating the roughness and waviness in Gwyddion with the ISO button. 
I guess as low-pass filter an Gaussian filter is  used, is this right? What kind of filter is used for the
high-pass filter?

Furthermore, i´m wondering that I just chose one cut-off frequency "fc", which cuts the roughness off
from the waviness and the other way round for the roughness. In ISO 4287 they talk about three cutoff
frequencies (see picture).
What about the Cut-off frequency "fs" in gwyddion, which cuts off the noise and makes the primary profile?
Also what about the Cut-off frequency "ff" in gwyddion, which cuts off the coarse shape and makes together
with the cut off fc the waviness Profile.

Would be great if someone could help me.

Best regards Lena


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Petr Klapetek | 18 Jun 2012 16:34
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Re: Filtering in roughness and waviness profile


Dear Lena,

the module was written by a student in order to comply the ISO standard,
so I am not very sure about all the implementation details.
But as far as I remember, the only frequency is used to separate the
waviness and roughness, assuming that the range of spatial frequencies
that SPM can cover anyway cancels the low and high frequency components
(i.e. acting as two more filters).

If necessary, also Gwyddion 1D or 2D FFT filtering modules could be use 
to create a subset
of spatial frequencies before analysis.

Best regards,

Petr

On 06/18/2012 03:53 PM, Mandl, Magdalena wrote:
> Hi,
>
> i´m calculating the roughness and waviness in Gwyddion with the ISO button.
> I guess as low-pass filter an Gaussian filter is  used, is this right? What kind of filter is used for the
high-pass filter?
>
> Furthermore, i´m wondering that I just chose one cut-off frequency "fc", which cuts the roughness off
from the waviness and the other way round for the roughness. In ISO 4287 they talk about three cutoff
frequencies (see picture).
> What about the Cut-off frequency "fs" in gwyddion, which cuts off the noise and makes the primary profile?
> Also what about the Cut-off frequency "ff" in gwyddion, which cuts off the coarse shape and makes together
with the cut off fc the waviness Profile.
>
> Would be great if someone could help me.
>
> Best regards Lena
>
>
>    
>
>
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> threat landscape has changed and how IT managers can respond. Discussions
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>
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David Nečas (Yeti | 18 Jun 2012 16:39
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Re: Filtering in roughness and waviness profile

On Mon, Jun 18, 2012 at 03:53:08PM +0200, Mandl, Magdalena wrote:
> i´m calculating the roughness and waviness in Gwyddion with the ISO
> button.  I guess as low-pass filter an Gaussian filter is  used, is
> this right?

No, the high/low separation is done directly in the Fourier domain (i.e.
FFT, filtering, and inverse FFT).  I am not an expert at norms I recall
there are several possible separation methods.

> Furthermore, i´m wondering that I just chose one cut-off frequency
> "fc", which cuts the roughness off from the waviness and the other way
> round for the roughness. In ISO 4287 they talk about three cutoff
> frequencies (see picture).  What about the Cut-off frequency "fs" in
> gwyddion, which cuts off the noise and makes the primary profile?
> Also what about the Cut-off frequency "ff" in gwyddion, which cuts off
> the coarse shape and makes together with the cut off fc the waviness
> Profile.

"fs" always infinity and "ff" is always zero.  I.e. anything above "fc"
goes to roughness, anything below goes to waviness.

Regards,

Yeti

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Mandl, Magdalena | 19 Jun 2012 09:23
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Re: Filtering in roughness and waviness profile

Thank you Yeti,

in the Fourier domain (FFT, filtering, inverse FFT) what kind of filtering is used? There should be two
different filters used, one highpass filter for the roughness and a lowpass filter for the waviness,
which seperates the profiles. There are several possible filters for this and I need to know which one is
used in Gwyddion, to be able to compare the waviness and roughness parameters with parameters calculated
with another program for Laser Scanning Microscope Measurements.

Regards,
Lena

-----Ursprüngliche Nachricht-----
Von: David Nečas (Yeti) [mailto:yeti <at> gwyddion.net] 
Gesendet: Montag, 18. Juni 2012 16:40
An: Gwyddion use discussion
Betreff: Re: [Gwyddion-users] Filtering in roughness and waviness profile

On Mon, Jun 18, 2012 at 03:53:08PM +0200, Mandl, Magdalena wrote:
> i´m calculating the roughness and waviness in Gwyddion with the ISO 
> button.  I guess as low-pass filter an Gaussian filter is  used, is 
> this right?

No, the high/low separation is done directly in the Fourier domain (i.e.
FFT, filtering, and inverse FFT).  I am not an expert at norms I recall there are several possible separation methods.

> Furthermore, i´m wondering that I just chose one cut-off frequency 
> "fc", which cuts the roughness off from the waviness and the other way 
> round for the roughness. In ISO 4287 they talk about three cutoff 
> frequencies (see picture).  What about the Cut-off frequency "fs" in 
> gwyddion, which cuts off the noise and makes the primary profile?
> Also what about the Cut-off frequency "ff" in gwyddion, which cuts off 
> the coarse shape and makes together with the cut off fc the waviness 
> Profile.

"fs" always infinity and "ff" is always zero.  I.e. anything above "fc"
goes to roughness, anything below goes to waviness.

Regards,

Yeti


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David Nečas (Yeti | 19 Jun 2012 09:53
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Re: Filtering in roughness and waviness profile

On Tue, Jun 19, 2012 at 09:23:14AM +0200, Mandl, Magdalena wrote:
> in the Fourier domain (FFT, filtering, inverse FFT) what kind of
> filtering is used? There should be two different filters used, one
> highpass filter for the roughness and a lowpass filter for the
> waviness, which seperates the profiles.

As I wrote, a simple splitting by frequency is used: anything above "fc"
goes to roughness, anything below goes to waviness.  So the filters are
Heaviside functions at "fc" in frequency domain, if you wish.

Regards,

Yeti

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Mandl, Magdalena | 19 Jun 2012 09:58
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Re: Filtering in roughness and waviness profile

Hi Yeti,

thank you, hope i got it now :-).

Regards
Lena

-----Ursprüngliche Nachricht-----
Von: David Nečas (Yeti) [mailto:yeti@...] 
Gesendet: Dienstag, 19. Juni 2012 09:53
An: Gwyddion use discussion
Betreff: Re: [Gwyddion-users] Filtering in roughness and waviness profile

On Tue, Jun 19, 2012 at 09:23:14AM +0200, Mandl, Magdalena wrote:
> in the Fourier domain (FFT, filtering, inverse FFT) what kind of 
> filtering is used? There should be two different filters used, one 
> highpass filter for the roughness and a lowpass filter for the 
> waviness, which seperates the profiles.

As I wrote, a simple splitting by frequency is used: anything above "fc"
goes to roughness, anything below goes to waviness.  So the filters are Heaviside functions at "fc" in
frequency domain, if you wish.

Regards,

Yeti

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