JiscMail Logo
Email discussion lists for the UK Education and Research communities

Help for CCP4BB Archives


CCP4BB Archives

CCP4BB Archives


CCP4BB@JISCMAIL.AC.UK


View:

Message:

[

First

|

Previous

|

Next

|

Last

]

By Topic:

[

First

|

Previous

|

Next

|

Last

]

By Author:

[

First

|

Previous

|

Next

|

Last

]

Font:

Proportional Font

LISTSERV Archives

LISTSERV Archives

CCP4BB Home

CCP4BB Home

CCP4BB  March 2009

CCP4BB March 2009

Options

Subscribe or Unsubscribe

Subscribe or Unsubscribe

Log In

Log In

Get Password

Get Password

Subject:

Re: physical meaning of SDB

From:

Phil Evans <[log in to unmask]>

Reply-To:

Phil Evans <[log in to unmask]>

Date:

Mon, 30 Mar 2009 23:46:16 +0100

Content-Type:

text/plain

Parts/Attachments:

Parts/Attachments

text/plain (95 lines)

On 30 Mar 2009, at 18:18, James Holton wrote:

> Phil Evans wrote:
>> The “corrected” sd(Ihl) is calculated in Scala for each observation  
>> as
>>       sd(Ihl)corrected =  SdFac * sqrt{sd(I)**2 + SdB*Ihl*LP +  
>> (SdAdd*Ihl)**2}
>> with the parameters SdFac, SdB & SdAdd determined by trying to make  
>> the RMS normalised deviation Delta(hl) = (Ihl - Ih(avg))/ 
>> sd(Ihl)corrected = 1.0 for all intensity ranges (different  
>> parameters for each run). If the sd estimates are correct, then the  
>> distribution of Delta(hl) should have SD = 1.0, and this  
>> “correction” tries to enforce this.  This is more or less  
>> equivalent to making the RMS scatter == average SD. However the  
>> uncertainties in how best to estimate the real error do then  
>> influence the reliability of the Mn(I/sd) statistic (see (ii) above)
> Uhh... What is "LP"?
>
> I had to look into the latest SCALA manual for that. ;)
>

Actually I need to correct this expression: I did have an LP (lLorentz- 
Polarisation) factor in there for a while, but on further  
consideration I decided to take it out again, so the current  
expression is

sd(Ihl)corrected =  SdFac * sqrt{sd(I)**2 + SdB*Ihl + (SdAdd*Ihl)**2}



> Interesting that the manual says that SDB has "no obvious physical  
> meaning".  I think it does!
>
> What I have learned from simulation is that SDADD is basically the  
> quadrature sum of all the fractional errors in the experiment.   
> These are things like shutter jitter and beam flicker that change an  
> intensity by an amount that is proportional to the intensity.  I. E.  
> things that introduce a "% error".  One of these is the "ripple  
> noise" induced by the detector calibration errors.  In fact, ripple  
> noise seems to be the dominant source of fractional error in PX (~3%).
>

yes I agree

> A non-unity value of SDFAC actually implies an error in detector  
> gain.  Took me a while to figure this out, but it turns out that if  
> you use the right value of GAIN in MOSFLM, then SDFAC will refine to  
> 1.0.  The problem is that MOSFLM encourages you to use the wrong  
> value of GAIN because the calculation of BGRATIO assumes that  
> adjacent pixels are statistically independent.  That is, the point- 
> spread function (PSF) is not infinitely sharp.  The PSF has the  
> effect of "averaging" the background and giving the pixels the  
> appearance of being less noisy than they actually are.  For example,  
> consider a flood-field of 10,000 photons/pixel.  On an ideal  
> detector, the rms deviation from average pixel value (rmsd) will be  
> 100 photons, but if you apply a smoothing function to the image (a  
> PSF), you will get an rmsd of less than 100, giving the illusion  
> that the GAIN setting is too high.  Unfortunately, this illusion  
> does not extent to sharp features such as spots, which will contain  
> the "real" amount of noise.
>

Yes

> Now we come to SDB, which would represent noise that is proportional  
> to the square root of intensity.  Photon-counting noise is one of  
> these!  MOSFLM was supposed to estimate this for us, but Woops!  We  
> used the wrong GAIN!  What does that do?  It makes you have to back- 
> calculate what the intensity on the detector was in photons, and  
> then update the error that way.  I think this is exactly what you  
> are doing with SDB.
>

back calculating to the photon count was the reason I put in the LP  
correction, to get back to the raw intensity, but then I realised that  
the major effect of the Lorentz factor was to spread the spot over  
more images, rather than increasing the counts on each image (for  
reflections close to the rotation axis), so I took it out again.

Empirically, I put  in SdB because you can't get a good fit with just  
SdFac & SdAdd

You may be right

Phil


> Let me know if I am guessing wrong about any of this.
>
> -James
>
>
>
>

Top of Message | Previous Page | Permalink

JiscMail Tools


RSS Feeds and Sharing


Advanced Options


Archives

March 2024
February 2024
January 2024
December 2023
November 2023
October 2023
September 2023
August 2023
July 2023
June 2023
May 2023
April 2023
March 2023
February 2023
January 2023
December 2022
November 2022
October 2022
September 2022
August 2022
July 2022
June 2022
May 2022
April 2022
March 2022
February 2022
January 2022
December 2021
November 2021
October 2021
September 2021
August 2021
July 2021
June 2021
May 2021
April 2021
March 2021
February 2021
January 2021
December 2020
November 2020
October 2020
September 2020
August 2020
July 2020
June 2020
May 2020
April 2020
March 2020
February 2020
January 2020
December 2019
November 2019
October 2019
September 2019
August 2019
July 2019
June 2019
May 2019
April 2019
March 2019
February 2019
January 2019
December 2018
November 2018
October 2018
September 2018
August 2018
July 2018
June 2018
May 2018
April 2018
March 2018
February 2018
January 2018
December 2017
November 2017
October 2017
September 2017
August 2017
July 2017
June 2017
May 2017
April 2017
March 2017
February 2017
January 2017
December 2016
November 2016
October 2016
September 2016
August 2016
July 2016
June 2016
May 2016
April 2016
March 2016
February 2016
January 2016
December 2015
November 2015
October 2015
September 2015
August 2015
July 2015
June 2015
May 2015
April 2015
March 2015
February 2015
January 2015
December 2014
November 2014
October 2014
September 2014
August 2014
July 2014
June 2014
May 2014
April 2014
March 2014
February 2014
January 2014
December 2013
November 2013
October 2013
September 2013
August 2013
July 2013
June 2013
May 2013
April 2013
March 2013
February 2013
January 2013
December 2012
November 2012
October 2012
September 2012
August 2012
July 2012
June 2012
May 2012
April 2012
March 2012
February 2012
January 2012
December 2011
November 2011
October 2011
September 2011
August 2011
July 2011
June 2011
May 2011
April 2011
March 2011
February 2011
January 2011
December 2010
November 2010
October 2010
September 2010
August 2010
July 2010
June 2010
May 2010
April 2010
March 2010
February 2010
January 2010
December 2009
November 2009
October 2009
September 2009
August 2009
July 2009
June 2009
May 2009
April 2009
March 2009
February 2009
January 2009
December 2008
November 2008
October 2008
September 2008
August 2008
July 2008
June 2008
May 2008
April 2008
March 2008
February 2008
January 2008
December 2007
November 2007
October 2007
September 2007
August 2007
July 2007
June 2007
May 2007
April 2007
March 2007
February 2007
January 2007


JiscMail is a Jisc service.

View our service policies at https://www.jiscmail.ac.uk/policyandsecurity/ and Jisc's privacy policy at https://www.jisc.ac.uk/website/privacy-notice

For help and support help@jisc.ac.uk

Secured by F-Secure Anti-Virus CataList Email List Search Powered by the LISTSERV Email List Manager