Author Topic: Wish List for PFE Features  (Read 39385 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
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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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Ben Buse

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Re: Wish List for PFE Features
« Reply #353 on: September 05, 2017, 02:57:33 am »
Hi John,

What would be nice when you have spare time! is on export wavescan to either

have options like export unknowns - so you can select which columns you want.

or a export option that just exports mm position (SPC) and intensity (cps/1nA)

Thanks

Ben
« Last Edit: September 05, 2017, 03:07:01 am by Ben Buse »

John Donovan

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Re: Wish List for PFE Features
« Reply #354 on: September 05, 2017, 09:08:55 am »
Hi Ben,
Try the Output | Save Wavescan Output | Save Wavescan Samples (Output based on spectro/element) menu.

This only outputs the spectro position and intensities.
john
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Paul Carpenter

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Re: Wish List for PFE Features
« Reply #355 on: September 07, 2017, 10:43:10 am »
John,
My wish request is as follows, regarding management of the reflected light during automated runs:

Use the "Use Confirm During Acquisitions" flag to set reflected light on/off behavior during automated run. If this is checked, then turn on reflected light so user can check xyz position as run proceeds. If not checked, do not change reflected light on/off state; if light is off, leave it off.

The other request is to add a checkbox to have the reflected light turned off at the end of an automation run. This coupled with turning the filament down (Jeol 8x00, value of 90) would put the instrument in a standby state so that users do not have to somehow turn these two items down either by physically going to the lab or using VNC/Teamview etc. to connect remotely.

The motivation for this is that Jeol 8x00 systems use an Olympus microscope bulb which is no longer manufactured, they have become expensive and difficult to locate. LED substitutes are not available and the power supply is computer controlled on the Jeol.

Cheers,

Paul
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Re: Wish List for PFE Features
« Reply #356 on: September 09, 2017, 09:41:55 pm »
John,
My wish request is as follows, regarding management of the reflected light during automated runs:

Use the "Use Confirm During Acquisitions" flag to set reflected light on/off behavior during automated run. If this is checked, then turn on reflected light so user can check xyz position as run proceeds. If not checked, do not change reflected light on/off state; if light is off, leave it off.

The other request is to add a checkbox to have the reflected light turned off at the end of an automation run. This coupled with turning the filament down (Jeol 8x00, value of 90) would put the instrument in a standby state so that users do not have to somehow turn these two items down either by physically going to the lab or using VNC/Teamview etc. to connect remotely.

The motivation for this is that Jeol 8x00 systems use an Olympus microscope bulb which is no longer manufactured, they have become expensive and difficult to locate. LED substitutes are not available and the power supply is computer controlled on the Jeol.

Cheers,

Paul

Hi Paul,
I think I've implemented your request the way you describe.

1. The light is not turned back on after an automated acquisition, if the Use Confirm During Acquisition checkbox is *not* checked in the Automate! window.

2. The light is turned off after the automation is completed if it is on.

Please download v. 11.9.9. and try it out.
john
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BenjaminWade

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Re: Wish List for PFE Features
« Reply #357 on: September 14, 2017, 07:01:30 pm »
Hi John
I have another wish, which I don't think would be simple or quick to integrate...

It would be great if we could have more control over the fit data through our MPB points. An example below is a F measurement on my albite standard, with my albite wavescan overlain behind. When all 4 points are included either side you can see that the Lo side isn't fit quite right to the measured MBP. There is a potential outlier on the Hi side, so when I exclude that (second attached image), the Lo side fits better but obviously the turning point of the quadratic is now drawn down so I am probably overestimating my F peak measurement.

Granted you could argue that all those points should probably be kept in anyway, but I still think it would be great if we could have more options (up to cubic polynomials, exponential functions?, changing coefficents, turning points etc) so we could further refine the MBP fits when you are dealing with low peak intensities.

I have attached a screenshot of some software we use to process laser ablation data to illustrate the type of thing I am talking about. Its showing an exponential function and the ability to change parameters manually to fit your data. It has other things that wouldn't really be of use in the screenshot, but I was more thinking of just some slider bars to change coefficients, dropdown to change fit types etc.

Anyway definitely a far future dream, but I think it would be a good addition...

Cheers

Karsten Goemann

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Re: Wish List for PFE Features
« Reply #358 on: September 24, 2017, 11:14:18 pm »
I really like the feature with images of the standards popping up when digitizing. (That is, if they have been saved in the default position files folder with the standard number at the beginning of the file name.)

Makes it very easy to tell straightaway if I'm on the right standard or not.

Would it be possible to
(a) make it display the images in the correct aspect ratio by default? My images are all 4:3 and it always starts out with square window, although it can be resized manually.
(b) make it remember the window position, similar to the other PFE windows (and maybe size)?

Many thanks!

John Donovan

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Re: Wish List for PFE Features
« Reply #359 on: September 25, 2017, 07:25:13 pm »
I really like the feature with images of the standards popping up when digitizing. (That is, if they have been saved in the default position files folder with the standard number at the beginning of the file name.)

Makes it very easy to tell straightaway if I'm on the right standard or not.

Would it be possible to
(a) make it display the images in the correct aspect ratio by default? My images are all 4:3 and it always starts out with square window, although it can be resized manually.
(b) make it remember the window position, similar to the other PFE windows (and maybe size)?

Many thanks!

Hi Karsten,
I had forgotten about this feature.  Though it turns out that it's not easy to have both options implemented as you describe above.  But now you can simply resize the standard image and PFE will remember the window position and size from then on.

You can update PFE when you are ready.

Thanks for the suggestion.
john
« Last Edit: September 25, 2017, 10:19:41 pm by John Donovan »
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