Author Topic: Questions about MAN background use  (Read 41125 times)

John Donovan

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Re: Questions about MAN background use
« Reply #60 on: April 10, 2017, 09:07:09 AM »
I've just noticed something. When you have elements on multiple spectrometers - and your viewing the MAN curves individually (not something you would normally do - only for testing, comparing spectrometers.. etc). The MAN is wrong for those standards which contain a high abundance of the element on multiple spectrometers.

e.g. If I view Al individually  for Al2O3 and have it on 3 spectrometers.
Total is 189.46 (3*47.5 plus oxygen 47.075) and z-bar is 11.761

Whereas if I aggregate the spectrometers - Total is 100% and Z-BAR is correct 10.666

This is not a problem for analysis - for you'd never use something with 190% total, BUT something to be aware of when doing such tests

Hi Ben,
Yes, when one has a 190% total, how should one calculate the matrix correction (or average Z) for such a non-physical situation?  Answer: any way you feel like!  ;D

The reason the average Z calculation is off when the spectrometers are not aggregated in your example is (I think) because you have several times the Al (from three spectrometers) relative to the specified oxygen (from the standard database), so the average Z is biased towards Al (Z = 13), rather than oxygen (Z = 8 ). 

Try analyzing it in Analyze! using the stoichiometric oxygen option (in Calculation Options dialog).
john
« Last Edit: April 10, 2017, 09:09:06 AM by John Donovan »
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Ben Buse

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Re: Questions about MAN background use
« Reply #61 on: April 10, 2017, 09:19:58 AM »
Hi John,

The difference is that the raw MAN intensities output to a file are *not* corrected for continuum absorption, but the intensities in the MAN plot are corrected for continuum absorption.

Thanks  - that makes sense - and was it!


Try analyzing it in Analyze! using the stoichiometric oxygen option (in Calculation Options dialog).
john

Thanks - that worked - keeping Al and O in proportion - great suggestion

Ben

Ben Buse

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Re: Questions about MAN background use
« Reply #62 on: April 20, 2017, 09:33:53 AM »
Hi,

I just found what I was looking for - on the MAN output to excel you have both

rawcnt: data uncorrected for absorption.
corcnt: data corrected for absorption

Thanks

Ben

John Donovan

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Re: Questions about MAN background use
« Reply #63 on: April 20, 2017, 04:10:22 PM »
I just found what I was looking for - on the MAN output to excel you have both

rawcnt: data uncorrected for absorption.
corcnt: data corrected for absorption

Yes, that's right.  In fact it also outputs all the matrix corrections for those MAN standards so you could also work backwards from the corrected counts...

Note that years ago I originally tried a continuum specific correction from NIST (because the continuum correction should be different from the bulk correction due to the anisotropy of the continuum emission), but it gave worse results than the bulk correction, so the bulk matrix correction term is what we currently use for the MAN continuum absorption correction.
john
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Heather Lowers

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Re: Questions about MAN background use
« Reply #64 on: August 01, 2017, 08:17:57 AM »
Is there an option to output the intercept, slope, curvature, Rel % Deviation for the MAN fits for all the elements in a run, and maybe even which standards are being used?  Playing around with different standards, off peak positions, forcing straight line versus not, etc.  Be nice to have these values easily tabulated.

Probeman

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Re: Questions about MAN background use
« Reply #65 on: August 01, 2017, 10:31:21 AM »
Is there an option to output the intercept, slope, curvature, Rel % Deviation for the MAN fits for all the elements in a run, and maybe even which standards are being used?  Playing around with different standards, off peak positions, forcing straight line versus not, etc.  Be nice to have these values easily tabulated.

Currently these parameters are output from the Output | Save Custom Analysis Output | Save Custom Analysis Format #8 (MAN):

LINE        Data file line number
SNUM        Sample number (standard number)
SNAM        Sample name (standard name)
ZBAR        Sample average atomic number
RAWCNT      Raw count intensity
CORCNT      Corrected count intensity (absorption corrected)
ZEDCOR      Atomic number correction factor
ABSCOR      Absorption correction factor
FLUCOR      Fluorescence correction factor
ZAFCOR      Total ZAF correction factor
ONTIM       On-peak (MAN) counting time
BEAM        Beam current in nA
BEAMCUR     Beam current (combined condition samples)


And if you put the software in DebugMode from the Output menu, you will see this output in the log window:

Elements:
      si      fe      mg      ca       p      al      na      ba       k      ti

MAN Assignments:
     835     835     336     374     336      12     835     336     358     336
      12      12     374     835     374      14      12     358     835     358
      22      14     835      14     835      27      14      12      12     374
      27      22      14      22      12      28      22      14      14     835
      28      28      22      28      14     285      27      27      22      12
     285     285      27       0      22       0      28      28      27      14
       0       0      28       0      27       0     285     160      28      27
       0       0       0       0      28       0       0     285     160      28
       0       0       0       0       0       0       0       0     285     160
       0       0       0       0       0       0       0       0       0     285
BackgroundTypes:
     MAN     MAN     MAN     MAN     MAN     MAN     MAN     MAN     MAN     MAN
MAN Fit Orders:
       2       2       2       2       2       2       2       2       2       2
MAN Absorption Correction Flags:
      -1      -1      -1      -1      -1      -1      -1      -1      -1      -1
MAN Counts:
    74.1    21.7    13.9    29.4     3.5    16.7    22.1    44.1    30.3     1.3
    26.1     6.2    16.2    92.0     3.6    27.2     9.4    47.4    81.6     1.6
    51.7     6.1    22.4    26.3     9.3    32.1     6.8    42.3    25.5     1.9
    55.3     9.5    13.9    43.0     3.3    30.3     8.1    44.1    24.0     8.8
    58.4    15.3    15.7    59.7     3.0    29.4     8.3    93.4    39.2     1.2
    50.0     8.4    17.6      .0     5.5      .0     7.8    94.5    53.7     1.2
      .0      .0    14.5      .0     6.9      .0     9.2    49.2    54.8     3.4
      .0      .0      .0      .0     6.3      .0      .0    55.5    32.0     3.5
      .0      .0      .0      .0      .0      .0      .0      .0    34.4     1.4
      .0      .0      .0      .0      .0      .0      .0      .0      .0     2.0

MAN Fit Coefficients:
 -14.766 -3.2199 -6.5750 -8.5227 -.40542 30.2930 .112198 -.54570 -5.1947 .052925
 5.84314 .946438 2.68385 3.62923 .482494 -.80475 1.00449 3.86722 3.24887 .100007
 -.05119 -.00766 -.02100 -.02692 -.00311 .097303 .019536 -.00100 -.02401 .002169
« Last Edit: August 01, 2017, 10:36:44 AM by Probeman »
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Probeman

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Re: Questions about MAN background use
« Reply #66 on: August 01, 2017, 10:38:11 AM »
And this output as well:

MAN fit data and coefficients for si
Order 2, npts 6
StdAss:      835      12      22      27      28     285
Z-bars:  45.8151 10.4267 16.3920 22.9433 23.7170 14.4794
Counts:  74.1008 26.1434 51.6858 55.3129 58.4085 50.0244
AbsCor:  1.96292 1.57869 1.28689 1.61488 1.68766 1.17433
Counts:  145.454 41.2723 66.5140 89.3238 98.5737 58.7449
Coeffs:  -14.745 5.84054 -.05111

MAN fit data and coefficients for fe
Order 2, npts 6
StdAss:      835      12      14      22      28     285
Z-bars:  45.8151 10.4267 10.8047 16.3920 23.7170 14.4794
Counts:  21.6734 6.21936 6.07033 9.48054 15.2525 8.44972
AbsCor:  1.10816 .996548 .998913 1.03724 1.00089 1.02129
Counts:  24.0175 6.19789 6.06373 9.83355 15.2662 8.62964
Coeffs:  -3.2217 .946670 -.00767

MAN fit data and coefficients for mg
Order 2, npts 7
StdAss:      336     374     835      14      22      27      28
Z-bars:  11.0372 11.9907 45.8151 10.8047 16.3920 22.9433 23.7170
Counts:  13.8886 16.2342 22.3551 13.8539 15.7346 17.5643 14.4872
AbsCor:  1.54794 1.44002 3.23244 1.38991 1.87119 2.72537 2.94422
Counts:  21.4987 23.3775 72.2615 19.2557 29.4423 47.8691 42.6536
Coeffs:  -6.5667 2.68299 -.02098

MAN fit data and coefficients for ca
Order 2, npts 5
StdAss:      374     835      14      22      28
Z-bars:  11.9907 45.8151 10.8047 16.3920 23.7170
Counts:  29.4093 91.9869 26.2621 42.9830 59.6713
AbsCor:  1.07150 1.10091 1.04570 1.00488 1.05021
Counts:  31.5120 101.269 27.4624 43.1929 62.6674
Coeffs:  -8.5125 3.62767 -.02687

MAN fit data and coefficients for p
Order 2, npts 8
StdAss:      336     374     835      12      14      22      27      28
Z-bars:  11.0372 11.9907 45.8151 10.4267 10.8047 16.3920 22.9433 23.7170
Counts:  3.49284 3.59269 9.28106 3.25934 3.04344 5.48866 6.90243 6.28710
AbsCor:  1.36107 1.34961 1.63430 1.35544 1.40684 1.16702 1.38028 1.42656
Counts:  4.75401 4.84874 15.1680 4.41783 4.28163 6.40539 9.52732 8.96890
Coeffs:  -.40611 .482553 -.00311

MAN fit data and coefficients for al
Order 2, npts 5
StdAss:       12      14      27      28     285
Z-bars:  10.4267 10.8047 22.9433 23.7170 14.4794
Counts:  16.7464 27.2437 32.0534 30.2572 29.4431
AbsCor:  1.95626 1.20535 2.01195 2.13817 1.31384
Counts:  32.7604 32.8382 64.4899 64.6951 38.6836
Coeffs:  30.2930 -.80475 .097303

MAN fit data and coefficients for na
Order 2, npts 7
StdAss:      835      12      14      22      27      28     285
Z-bars:  45.8151 10.4267 10.8047 16.3920 22.9433 23.7170 14.4794
Counts:  22.0557 9.42896 6.80209 8.13324 8.26629 7.81730 9.16492
AbsCor:  3.95005 1.49808 1.75421 2.60603 4.07311 4.48371 2.06884
Counts:  87.1213 14.1254 11.9323 21.1955 33.6695 35.0505 18.9608
Coeffs:  .115846 1.00402 .019550

MAN fit data and coefficients for ba
Order 2, npts 8
StdAss:      336     358      12      14      27      28     160     285
Z-bars:  11.0372 12.2316 10.4267 10.8047 22.9433 23.7170 12.6937 14.4794
Counts:  44.0832 47.4109 42.3110 44.0621 93.3551 94.4881 49.2239 55.5154
AbsCor:  .951038 .972255 .942275 .948707 .946385 .952120 .960851 1.00869
Counts:  41.9249 46.0955 39.8686 41.8020 88.3499 89.9640 47.2968 55.9981
Coeffs:  -.54606 3.86727 -.00100

MAN fit data and coefficients for k
Order 2, npts 9
StdAss:      358     835      12      14      22      27      28     160     285
Z-bars:  12.2316 45.8151 10.4267 10.8047 16.3920 22.9433 23.7170 12.6937 14.4794
Counts:  30.2908 81.6375 25.5278 23.9502 39.1737 53.7147 54.8469 31.9706 34.4008
AbsCor:  1.04931 1.14161 1.05343 1.06993 1.01340 1.06181 1.07488 1.05296 1.05273
Counts:  31.7845 93.1984 26.8917 25.6251 39.6985 57.0348 58.9537 33.6638 36.2146
Coeffs:  -5.1908 3.24845 -.02400

MAN fit data and coefficients for ti
Order 2, npts 10
StdAss:      336     358     374     835      12      14      27      28     160     285
Z-bars:  11.0372 12.2316 11.9907 45.8151 10.4267 10.8047 22.9433 23.7170 12.6937 14.4794
Counts:  1.28070 1.59672 1.94603 8.76543 1.19729 1.19741 3.37633 3.52606 1.44701 1.97932
AbsCor:  1.01933 1.04191 1.03182 1.04960 1.01001 1.01684 1.01439 1.02050 1.02978 1.08067
Counts:  1.30545 1.66364 2.00795 9.20017 1.20928 1.21758 3.42492 3.59834 1.49010 2.13899
Coeffs:  .053961 .099936 .002170
The only stupid question is the one not asked!

Heather Lowers

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Re: Questions about MAN background use
« Reply #67 on: August 01, 2017, 02:16:59 PM »
The forum...it does work  ;)

Ben Buse

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Re: Questions about MAN background use
« Reply #68 on: September 05, 2017, 06:34:34 AM »
Hi,

I was just doing MAN for fluorine, clearly a tricky element, it seems to work better without correction for continuum absorption

With absorption correction TiO2, SrTiO3, Cr2O3 plot much higher compared to Barite and HfO2





In the second image, only those standards containing Fe lie significantly above the curve - due to Fe La interference (see wavescan below). giving following.



Removed Fe standards - TiO2 disappointingly low

« Last Edit: April 12, 2020, 07:33:27 PM by John Donovan »

Probeman

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Re: Questions about MAN background use
« Reply #69 on: September 05, 2017, 09:06:22 AM »
Hi Ben,
Yes, I've seen this too.

Because there are so many elements (e.g., L lines) that interfere with fluorine, it is difficult to find a decent set of MAN standards that will work. I generally use the off-peak method for minor/trace fluorine.

An unrelated issue for oxygen is that almost any standard one could utilize for the oxygen MAN curve is oxidized. I have tried MAN calibrations for oxygen using Ge and Au, but haven't found an MAN standard useful at low Z.
john
The only stupid question is the one not asked!

Probeman

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Re: Questions about MAN background use
« Reply #70 on: September 05, 2017, 10:39:04 AM »
Hi Ben,
Also, on the issue of the low intensity for F Ka in TiO2, note that the MAC for F ka in Ti is quite large, around 14500 (actually that is for F Ka in pure Ti. In TiO2 the MAC is more like 13700).

So by not utilizing the continuum correction in the MAN curve you are significantly undercorrecting the F Ka intensity in TiO2.

Here is your F Ka MAN calibration curve at 20 keV (F Ka at 20 keV?), with the continuum absorption correction and with  the Fe bearing standards removed. As you point out there are some on-peak interferences from Fe L lines on the F Ka peak position.  So removing those gives us this:



The high outlier is Cr2O3 and I would suspect a small interference from Cr L also (as I tell my students, if you have a high outlier in the MAN curve it is usually an interference or contamination- so just remove it from the fit- after all background is by definition the lowest thing we can measure).  So now we get this curve:



It's not a terrible fit, but it is worth noting (as you did) that without the absorption correction the fit is better, but the TiO2 is way low as one would expect from the MAC.  It might be worth looking at a wavescan of F ka on your barite standard and see if there is anything unusual in the background shape.

This is worth further study I think.  It reminds me of something that Paul Carpenter once said: using the MAN background method is a good way to check for undeclared elements in one's standards.  See here for that discussion:

http://probesoftware.com/smf/index.php?topic=4.msg499#msg499

john
« Last Edit: April 12, 2020, 07:33:45 PM by John Donovan »
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BenjaminWade

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Re: Questions about MAN background use
« Reply #71 on: September 05, 2017, 07:00:10 PM »
Hi all
I saw this post with interest. F is something that our Geo's always want to measure, and I have resigned myself to never using the MAN fit for it due to the many L line interferences on it when constructing MAN fits. More recently however we have started to quant map fluorine in micas (which needs correction for Fe and a small Mg II order correction for high Mg micas), so I went on a quest to find a set of standards that would work OK for creating a MAN fit for F. I have attached a couple of the latest with/without some higher Z stds. Its seems to work OK, but bear in mind this is not quanting super low level F. It seems to have reasonable accuracy when compared to spot analysis of the same mineral down to ~0.5 wt%.

Haven't had a chance to refine it any further yet though, although I am sure there are some better standards I can use on my other standard blocks to fit it a bit better now that I know what to expect.

If you are interested this is the list of standards populating that MAN fit:
Astimex albite
Astimex Barite
Astimex Sanidine
In-house kyanite standard
Astimex BN
P&H Orthoclase
P&H Corundum
P&H Periclase
Astimex Gold
Astimex Hafnium metal
Astimex Zinc metal
Astimex Germanium metal
Astimex Cuprite

Cheers

P.S. forgot to mention, is anyone else getting that weird display bug as seen in the first image in the MAN fits when they display errors..?
« Last Edit: September 05, 2017, 07:01:56 PM by BenjaminWade »

John Donovan

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Re: Questions about MAN background use
« Reply #72 on: September 05, 2017, 08:55:55 PM »
Hi Ben,
This is all good stuff.

I haven't looked into F by MAN myself, so the fact that you and Ben are investigating this is quite interesting to me.

I see the display bug, and it looks like it's related to the display of error bars.  I've seen this kind of thing before in other plots, so I will try to reproduce it myself so I can fix it, but if you don't mind could you send me your MDB file to my email?  It's not very reproducible because I just looked at 15 or so MAN plots and none of them show that issue so far...

Thanks!
john
« Last Edit: September 05, 2017, 09:00:37 PM by John Donovan »
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BenjaminWade

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Re: Questions about MAN background use
« Reply #73 on: September 05, 2017, 09:13:08 PM »
Hi John
Yes its definitely related to displaying the error bars. You are right its a little random when it will happen or not. Sometimes after excluding a standard and updating the fit it will appear, sometimes not. Sometimes after zooming in and out on the MAN fit it will appear, sometimes not...
I will email you the dropbox link for the displayed MDB file

Cheers

Ben Buse

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Re: Questions about MAN background use
« Reply #74 on: September 06, 2017, 02:30:09 AM »
Thank you John and Ben, that's very helpful; Ben I think I'll try some of the metal standards you suggest; and John good point about TiO2 MAC.
« Last Edit: September 06, 2017, 04:48:06 AM by Ben Buse »