Wish List for PFE Features

[John Donovan]

This may fall more in the category of fantasy than wish, but would it be possible to implement TDI corrections for EDS elements?

Dude!  I can't do *everything*.  I mean I've got to leave some things for the "next generation" to do!     

Seriously, that's a tough one because then you'd have to have an array of EDS spectra (for each TDI interval) for each data point...  I'd have to think about that...
john

[John Donovan]

Dude!  I can't do *everything*.  I mean I've got to leave some things for the "next generation" to do!     

Seriously, that's a tough one because then you'd have to have an array of EDS spectra (for each TDI interval) for each data point...  I'd have to think about that...
john

That's what I figured - I could see a lot of problems with just transferring multiple spectra during acquisition, for starters. Just an idea, not a pressing need.

Thanks,
OKN

It sort of sounds like something the EDS vendors should implement, in that they should maybe have a "interval counting" method that extrapolates the spectra to what it looked like at zero time before the sample was damaged.

You saw my new TDI scanning method here for mapping beam sensitive samples?

http://probesoftware.com/smf/index.php?topic=912.0

Anette was telling me that she just tried this replicate TDI method on a super beam sensitive sample as it extrapolated her Na contents from 2 wt% to 13 wt% oxide. She said she'd post it as soon as she gets a chance.

I'm going to try one of the NIST K-375 glasses that are 23 wt% Na!   This sucker gets damaged if one even thinks about analyzing it!   
john

[John Donovan]

Here's an idea - could this be done with the "Assigned" TDI correction? You'd still have to collect a point with a whole bunch of spectra, but you'd only have to do it for a couple of representative TDI calibration samples, rather than at every point. I've never been wild about the "Assigned" TDI method, but it might be better than nothing.

Unfortunately you'd still have to acquire "interval" EDS spectra for the assigned TDI calibration sample.

[BenjaminWade]

Hi John
I understand that it may well have been excluded for space reasons, but it would be really nice if I could plot errors on measurements in the Multipoint Background review window, like we can do when looking at TDI. Would be handy for reviewing and deciding which background points to exclude when dealing with lower level measurements.

Cheers

[John Donovan]

I understand that it may well have been excluded for space reasons, but it would be really nice if I could plot errors on measurements in the Multipoint Background review window, like we can do when looking at TDI. Would be handy for reviewing and deciding which background points to exclude when dealing with lower level measurements.

It's a great idea.  Let me see what I can do.
john

[John Donovan]

Unfortunately you'd still have to acquire "interval" EDS spectra for the assigned TDI calibration sample.

True, but you'd only have to do it once, rather than at every point, and you could do it without acquiring WDS data, which would limit your comms load. I agree it's sub-ideal, but it might be a workable band-aid until the EDS vendors implement their own TDI's.

Hi Owen,
An EDS TDI (time dependent intensity) correction is a cool idea (why didn't I think of it?), and I don't think the spectrum transfer overhead would be too onerous, assuming the TDI intervals aren't too short.  To me the main difficulty is writing all that code!  It's a lot of work to save each EDS spectrum sub interval and fit each energy channel back to zero time.  It's basically a 1 dimensional version of what I recently got working with the TDI Scanning feature here for x-ray maps:

http://probesoftware.com/smf/index.php?topic=912.0

If we assume 5 or 10 sub intervals, that would mean storing 5 or 10 additional spectra.  The good news is that the TDI correction to the raw spectrum intensities could be applied simply to the energy channels without messing with a background correction.   If I ever get a couple of weeks to work on it, I might look into it.  Maybe after EMAS.
john

[John Donovan]

Hi Owen,
An EDS TDI (time dependent intensity) correction is a cool idea (why didn't I think of it?), and I don't think the spectrum transfer overhead would be too onerous, assuming the TDI intervals aren't too short.  To me the main difficulty is writing all that code!  It's a lot of work to save each EDS spectrum sub interval and fit each energy channel back to zero time.  It's basically a 1 dimensional version of what I recently got working with the TDI Scanning feature here for x-ray maps:

http://probesoftware.com/smf/index.php?topic=912.0

If we assume 5 or 10 sub intervals, that would mean storing 5 or 10 additional spectra.  The good news is that the TDI correction to the raw spectrum intensities could be applied simply to the energy channels without messing with a background correction.   If I ever get a couple of weeks to work on it, I might look into it.  Maybe after EMAS.
john

The reason my mind went to the "assigned" TDI is that all of that would have to be done only once, rather than at every point, but it sounds like it's the same amount of labor to implement either way. Would the database files get too unwieldy storing 5 spectra per point instead of one?

Zero rush on this, more of a wish than a need. And I agree with your first assertion that having this done by the EDS software is really the best option.

Thanks,
OKN

Yeah, the "assigned" TDI might be slightly less work than just the "self" TDI, but really both "assigned" and "self" TDI methods should be implemented for EDS if we decide to do it.   

So let's say if I can find 3 weeks or so of free time, I will look into it.   It would indeed be cool.  Please remind me in May if you haven't heard back from me by then...
john

PS Another idea I have for integrated EDS and WDS in Probe for EPMA is to allow simultaneous EDS and WDS acquisition even on combined condition samples.  Right now if one needs to switch beam conditions part way through an acquisition, I don't allow simultaneous EDS spectrum acquisition because the cup needs to go in at some point to set beam current, etc. So as long as the combined condition sample doesn't have a change in keV, I'm going to utilize the pause/unpause feature in the EDS systems to pause the EDS acquisition when the conditions are being changed, and then once the conditions are set, unpause the EDS acquisition again.  The only problem with this idea so far, is that while Thermo has a "pause/unpause" function in their API, Bruker does not.  I might be able to utilize the low level RCL commands to pause/unpause the Bruker acquisition, but I've never tried this direct API yet.  Has anyone here tried talking to the Bruker system using the RCL low level commands directly to the hardware?

[John Donovan]

Hi John
I understand that it may well have been excluded for space reasons, but it would be really nice if I could plot errors on measurements in the Multipoint Background review window, like we can do when looking at TDI. Would be handy for reviewing and deciding which background points to exclude when dealing with lower level measurements.

Hi Ben,
I managed to implement it:



Update from the Help menu as usual.
john

[BenjaminWade]

Legend. Thanks John
Cheers

[Paul Carpenter]

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!

Cheers,

Paul Carpenter

[Anette von der Handt]

Now that we have error bars for TDI and Multi-point, can we have them for the MAN fits too ? I always wonder if I am overly critical when fitting and excluding standards.

Thanks!

[John Donovan]

Now that we have error bars for TDI and Multi-point, can we have them for the MAN fits too ? I always wonder if I am overly critical when fitting and excluding standards.

Hi Anette,
Software is *never* done!   

I'll add this to the list- good idea.
john

[John Donovan]

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

[Paul Carpenter]

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

[John Donovan]

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