Author Topic: Wish List for PFE Features  (Read 37459 times)

John Donovan

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Re: Wish List for PFE Features
« Reply #345 on: June 16, 2017, 05:49:58 pm »
John, here is my suggestion as an additional capability regarding standards:

Add fields in the standard database for number of oxygens on a per standard basis. So for example each pyroxene standard would have a user-assigned number of oxygens of either 3 or 6, feldspars 8 oxygens, olivines 4 oxygens, etc. If this value is then read by the PFE program during standard acquisition and analysis, the user will not have to enter this oxygen basis each time the standard is analyzed.

Further, adding a field for cation basis would be very helpful too. The calculation of a mineral formula can be done using (for a pyroxene) both a 6 oxygen and a 4 cation basis for a nominal XYSi2O6 pyroxene formula. Inspection of the cation sum when using a 6 oxygen basis, or an anion sum when using a 4 cation basis, reveals issues with the analysis not indicated from the analytical total alone. For example, the presence of Fe3+ can be deduced from these formula calculations, then the Fe cations and oxygens could be adjusted in Elements/Cations to accommodate this.

So what I suggest is having a specific per-standard entry for number of oxygens and number of cations which is then read in by PFE and used for that specific standard. In the log window output and excel output you will also want to have the cation and oxygen summation.

These capabilities really make the analysis output complete. There are analyses that have a slightly low analytical total but excellent stoichiometry, which indicates a global issue with the calibration; alternatively, a problem with a specific element in the calibration can be identified by analysis of a true secondary standard and inspection of the formula basis.

Thanks again for the great software!

Hi Paul,
Interesting idea!

I had to add three new record fields to the standard database for a formula flag (boolean), formula ratio (float) and formula element (string for element symbol or blank for total cation basis), but this then allows one to specify any formula basis for any standard. Here is a shot of the new modify composition dialog in Standard:



The note in the graphic above should actually say "select 'sum' for sum of cations". Then when you double-click that standard in Standard, you now get an additional line of output as seen here:

St  474 Olivine USNM 2566 (Fo 83) Springwater
TakeOff = 40.0  KiloVolt = 15.0  Density =  3.300  Type = olivine

Analysis (wet chemistry) by Gene Jarosewich
Oxide and Elemental Composition

Average Total Oxygen:       41.817     Average Total Weight%:   99.470
Average Calculated Oxygen:  41.820     Average Atomic Number:   12.535
Average Excess Oxygen:       -.003     Average Atomic Weight:   21.723

ELEM:     SiO2     FeO     MgO     MnO   Cr2O3       O
XRAY:      ka      ka      ka      ka      ka      ka
OXWT:   38.951  16.620  43.582    .300    .020   -.003
ELWT:   18.207  12.919  26.281    .232    .014  41.817
KFAC:    .1310   .1099   .1758   .0020   .0001   .2365
ZCOR:   1.3901  1.1758  1.4952  1.1884  1.1083  1.7678
AT% :   14.157   5.052  23.615    .092    .006  57.078
24 O:    5.953   2.124   9.929    .039    .002  24.000
FORM:     .992    .354   1.655    .006    .000   4.000

I think I have implemented this as you asked. 

Next in the latest Probe for EPMA (v. 11.9.2), one simply acquires standards as usual from the Automate! window and if the standard has a formula basis specified in the standard database, that formula basis will be automatically loaded from the standard database, and displayed when the standard is analyzed from the Analyze! window (or when output to Excel). 

Note that if the Calculate Formula checkbox in the Modify Standard dialog is unchecked, then the formula basis will not be loaded by Probe for EPMA, but if another formula basis is specified in a previous standard or unknown then that formula basis will be loaded as usual by Probe for EPMA.
john
« Last Edit: June 16, 2017, 05:51:47 pm by John Donovan »
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Paul Carpenter

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Re: Wish List for PFE Features
« Reply #346 on: June 18, 2017, 11:43:25 am »
Hi John,
First of all, happy father's day!

Thanks for making these changes. To clarify what I think is needed is the capability to define the number of oxygens and the number of cations for formula output on a per standard basis in Standard. So that would involve entering both of these values.

While the predominant output that a user will select is the number of oxygens, it is important to also have the formula on a cation basis rather than an oxygen basis. Especially for minerals with water, OH, Fe3+, or vacancy, these two outputs will be different and can be used to immediately deduce aspects of their importance in the analysis. As it is one has to get the final output from the run and work offline (the output for biotite and amphibole is very helpful but is not a formal part of the user output with all the other data).

This is not an attempt to complicate things, but I suggest that both cation and oxygen can be separately entered in the standard entry so that it does not have to be done again. In the calculation options it would be very helpful if one can select oxygen, cation, or both, for formula output. Is that a hassle to set up?

This is a major step forward as it is to avoid having to enter all these settings each time one analyzes a standard, so again, thanks very much!

Cheers,

Paul
Paul Carpenter
Washington University St. Louis

John Donovan

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Re: Wish List for PFE Features
« Reply #347 on: June 18, 2017, 12:01:25 pm »
Hi John,
First of all, happy father's day!

Thanks for making these changes. To clarify what I think is needed is the capability to define the number of oxygens and the number of cations for formula output on a per standard basis in Standard. So that would involve entering both of these values.

While the predominant output that a user will select is the number of oxygens, it is important to also have the formula on a cation basis rather than an oxygen basis. Especially for minerals with water, OH, Fe3+, or vacancy, these two outputs will be different and can be used to immediately deduce aspects of their importance in the analysis. As it is one has to get the final output from the run and work offline (the output for biotite and amphibole is very helpful but is not a formal part of the user output with all the other data).

This is not an attempt to complicate things, but I suggest that both cation and oxygen can be separately entered in the standard entry so that it does not have to be done again. In the calculation options it would be very helpful if one can select oxygen, cation, or both, for formula output. Is that a hassle to set up?

This is a major step forward as it is to avoid having to enter all these settings each time one analyzes a standard, so again, thanks very much!

Hi Paul,
Thanks.  Our daughters are cooking for us tonight- looking forward to it!

I'm not quite sure I understand as I think I implemented it as requested. That is, the implementation in Standard is now exactly the same as in Probe for EPMA. Specifically, one can specify the number of atoms (or the number of total cations) *and also* specify the element basis (or sum of cations). 

If you are saying you would like to display *both* the formula basis and the sum of cation basis at the same time, that is possible but would require significant changes to Probe for EPMA as well as to Standard. I'm not a geologist but it seems to me that either method provides the requested check of standard compositional stoichiometry... you just need to decide which formula basis is the desired default in Standard (on a standard by standard basis of course), and of course subsequently one can change their minds in PFE, and specify a different formula basis for a particular standard if necessary at run time.  Does that work for you?
john
« Last Edit: June 18, 2017, 03:00:45 pm by John Donovan »
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Ben Buse

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Re: Wish List for PFE Features
« Reply #348 on: July 03, 2017, 07:00:58 am »
Hi,

I wondered if in "Analysis Calculation Options" the check box "use beam drift correction" could be changed to "use beam current drift correction" - in both probe for epma and calcimage.

I was running calcimage - and I wasn't sure whether it mean correct for spatial drift and had to click on the help button!

What do other people think?

Thanks

Ben

John Donovan

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Re: Wish List for PFE Features
« Reply #349 on: July 03, 2017, 01:22:01 pm »
Hi,

I wondered if in "Analysis Calculation Options" the check box "use beam drift correction" could be changed to "use beam current drift correction" - in both probe for epma and calcimage.

I was running calcimage - and I wasn't sure whether it mean correct for spatial drift and had to click on the help button!

What do other people think?

Thanks

Ben

Hi Ben,
It's certainly easy enough to edit the checkbox caption.

The only beam (spatial) drift correction that PFE does is from the Automate! window during acquisition when using beam deflection acquisitions (for very high spatial resolution).  This is the Stage Reproducibility Correction feature.

I call it a Stage Reproducibility Correction, but because it's based on the beam scan image one digitized analysis positions on, it doesn't matter if it was the stage or beam that drifted.
john
« Last Edit: July 03, 2017, 02:59:34 pm by John Donovan »
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John Donovan

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Re: Wish List for PFE Features
« Reply #350 on: August 10, 2017, 09:04:59 pm »
Now that we have error bars for TDI and Multi-point, can we have them for the MAN fits too :D? I always wonder if I am overly critical when fitting and excluding standards.

Thanks!

Hi Anette,
Finally got around to implementing errors bars for the MAN fit dialog in PFE (as usual please use the Help menu to update):



This plot is interesting because it shows that all the MAN standards have zero Na within variance, except for the K-411 glass (#162), which I've determined using off peaks is around a couple hundred PPM... so technically, it should be removed from the fit.

Sorry this feature took so long.  I've been busy!   :)

Hope M&M is going well.  Have you presented the TDI Scanning poster yet?
john
« Last Edit: August 10, 2017, 09:09:46 pm by John Donovan »
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Ben Buse

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Re: Wish List for PFE Features
« Reply #351 on: August 16, 2017, 06:04:24 am »

Hi Anette,
Finally got around to implementing errors bars for the MAN fit dialog in PFE (as usual please use the Help menu to update):



This plot is interesting because it shows that all the MAN standards have zero Na within variance, except for the K-411 glass (#162), which I've determined using off peaks is around a couple hundred PPM... so technically, it should be removed from the fit.

Sorry this feature took so long.  I've been busy!   :)

Hope M&M is going well.  Have you presented the TDI Scanning poster yet?
john

Hi John,

The MAN errors are very nice.

At the moment these are count stats (approximately square root of counts) right? I wonder if it is better to use count stat error or the standard deviation. If people collect multiple points per standard for the MAN backgrounds then the standard deviation of the points is more representative - or maybe a choice?

Ben

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Re: Wish List for PFE Features
« Reply #352 on: August 16, 2017, 10:15:43 am »
Hi John,

The MAN errors are very nice.

At the moment these are count stats (approximately square root of counts) right? I wonder if it is better to use count stat error or the standard deviation. If people collect multiple points per standard for the MAN backgrounds then the standard deviation of the points is more representative - or maybe a choice?

Ben

Hi Ben,
Yes, they are the square root of the raw intensities, so a 1 sigma variance.

Yes, the standard error would be more appropriate since these are usually the average of several points, but well, no one seems to utilize standard errors even when they should!

I once asked a statistics person why don't people use the standard error rather than the standard deviation for the variance of the average and he said: "I don't know, maybe because it's a more conservative number?"

I normally acquire at least 3 data points on each standard (including MAN standards), but others may not, so the variance is a safe bet to display.
john
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