[Nexus] pixel_mask documentation

Tue Jul 9 16:56:26 BST 2013

Hi Michael,

Yes, you are right that's what the text says, but I didn't read carefully enough.

As most options are mutually exclusive, I wasn't expecting bits.

Is 6 or 7 targeted for corner pixels on Eiger/Pilatus?
To make it easy for consuming software I would not want any bits to be set for a usable pixel value. 95% would not care about a reason for not using the pixel. Flagging up these special pixels somewhere is useful but maybe not in a "mask". Maybe I am wrong anyway.

What's "5 non uniform" exactly?  Just that I can make the documentation most meaningful.

Bits do come in handy though. It allows us to add:

8 user specified

For pixels that are masked out by the user although they have a physically "correct" reading but for example represent artefacts in the measurement like beamstops. Agreed?

Kind regards,

Tobias

________________________________
From: Michael Rissi [michael.rissi at dectris.com]
Sent: 09 July 2013 15:42
To: Richter, Tobias (DLSLtd,RAL,DIA)
Cc: Herbert J. Bernstein; nexus at nexusformat.org
Subject: Re: [Nexus] pixel_mask documentation

Hi Tobias,
Ok, then our documentation is not clear enough... Sorry for that!

The idea was that pixel_mask is a bit mask with each bit corresponding to a special condition:
0 gap
1 dead
2 under responding
3 over responding
4 noisy
5 non uniform
6 cluster
7 virtual pixel

So e.g. when a pixel is noisy, you will set bit number 4. When the pixel is working properly, all bits are unset, and the pixel mask has the value 0 for the pixel.

Best regards,
Michael

On Tue, Jul 9, 2013 at 4:36 PM, <Tobias.Richter at diamond.ac.uk<mailto:Tobias.Richter at diamond.ac.uk>> wrote:
I like that, but that is not what your documentation says. At least not according to Herbert.

Tobias

________________________________
From: Michael Rissi [michael.rissi at dectris.com<mailto:michael.rissi at dectris.com>]
Sent: 09 July 2013 15:30
To: Richter, Tobias (DLSLtd,RAL,DIA)
Cc: Herbert J. Bernstein; nexus at nexusformat.org<mailto:nexus at nexusformat.org>
Subject: Re: [Nexus] pixel_mask documentation

Hi Tobias and Herbert,
A good pixel has the pixel mask value 0x00 00 00 00 , e.g. 0
Best regards,
Michael

On Tue, Jul 9, 2013 at 4:26 PM, <Tobias.Richter at diamond.ac.uk<mailto:Tobias.Richter at diamond.ac.uk><mailto:Tobias.Richter at diamond.ac.uk<mailto:Tobias.Richter at diamond.ac.uk>>> wrote:
That looks like a nice comprehensive list, only I have no idea what value to put for a good pixel.
And as zero is the single special value I'd prefer that for "good".

Tobias

________________________________________
From: yayahjb [yayahjb at gmail.com<mailto:yayahjb at gmail.com><mailto:yayahjb at gmail.com<mailto:yayahjb at gmail.com>>]
Sent: 09 July 2013 15:08
To: Discussion forum for the NeXus data format
Cc: Richter, Tobias (DLSLtd,RAL,DIA); michael.rissi at dectris.com<mailto:michael.rissi at dectris.com><mailto:michael.rissi at dectris.com<mailto:michael.rissi at dectris.com>>
Subject: Re: [Nexus] pixel_mask documentation

The DECTRIS NeXus header specification includes under the detector
specific information:

pixel_mask      NX_UINT32       Pixel mask with the following bits corresponding
to special pixels:
0 gap
1 dead
2 under responding
3 over responding
4 noisy
5 non uniform
6 cluster
7 virtual pixel

I would suggest conforming the two lists.

Regards,
   Herbert

On 7/9/13 9:28 AM, Tobias.Richter at diamond.ac.uk<mailto:Tobias.Richter at diamond.ac.uk><mailto:Tobias.Richter at diamond.ac.uk<mailto:Tobias.Richter at diamond.ac.uk>> wrote:
> Hi all,
>
> NXdetector has a pixel_mask field that says:
>
>    <field name="pixel_mask" type="NX_FLOAT">
>      <doc>The pixel mask for the detector. Contains information about dead, blind or high pixels.</doc>
>      <dimensions rank="2">
>         <dim index="1" value="i"/>
>         <dim index="2" value="j"/>
>      </dimensions>
>    </field>
>
> First I am surprised it is a NX_FLOAT. And second there is no indication what values are used for what type of pixel.
>
> I'd assume anything non-zero means 'do not use pixel'.
>
> Just to have a start I'd suggest changing this to INT and useing:
>
> 0: pixel okay
> 1: dead
> 2: blind (non-existent virtual pixel)
> 3: high
>
> If I don't hear otherwise I'd update the definition with that clarification in two weeks.
>
> Kind regards,
>
> Tobias
>

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5400 Baden
Switzerland

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+41 56 500 2101 fax
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