Wish List for PFE Features

[dawncruth]

Can we get a string selection box in the Plot window?

[dawncruth]

Can you code in different window colors for PfE if we are opening multiple instances? It can get confusing knowing which windows belong together.

[John Donovan]

Can we get export filter for totals >102 (or whatever we chose)?

If you have high totals they need to be corrected for whatever the issue is (spectral interferences, standard intensity drift, secondary boundary fluorescence, etc.). One cannot simply filter to obtain the results one desires.

[dawncruth]

Can we get export filter for totals >102 (or whatever we chose)?

If you have high totals they need to be corrected for whatever the issue is (spectral interferences, standard intensity drift, secondary boundary fluorescence, etc.). One cannot simply filter to obtain the results one desires.

Of course. However, you do let us filter in the Plot Standard and Unknown Sample Data in the Output dropdown.  And sometimes there are random bad points that just need removing.

[dawncruth]

We are interested in showing the position of all multipoint bkgds in a plot from the Plot! window. Is that possible?

[John Donovan]

Can we add a default value to the wavescan limits?

Because WDS spectral resolution varies with both Bragg crystal 2D and sin theta, it is not possible to assign specific default wavescan limits. Of course once you do assign the specific wavescan limits you want, they can be re-used by simply loading the File Setup from that run into a new run.

The off-peak/peakscan/wavescan calculation is described in the User's Reference manual in the Installation | Configuration Files | SCALERS.DAT section:



So if you want to change the default off-peak/peakscan/wavescan calculation you can "tune it" for each spectrometer by editing these Ofactor values in your SCALERS.DAT file.  But this change will affect all emission lines based on the calculation above for new runs.

[John Donovan]

Can we get a string selection box in the Plot window?

For wavescans with more than 500 points the samples are named "continued" and therefore string selection would not work.

But let me think about it.

[John Donovan]

Can we get export filter for totals >102 (or whatever we chose)?

If you have high totals they need to be corrected for whatever the issue is (spectral interferences, standard intensity drift, secondary boundary fluorescence, etc.). One cannot simply filter to obtain the results one desires.

Of course. However, you do let us filter in the Plot Standard and Unknown Sample Data in the Output dropdown.  And sometimes there are random bad points that just need removing.

Oh, I thought you meant for file export.  For plotting, sure, we could add that. There is already a minimum total filter in that dialog.

[John Donovan]

Can you code in different window colors for PfE if we are opening multiple instances? It can get confusing knowing which windows belong together.

That is non quite trivial, but let us think about it.

[John Donovan]

We are interested in showing the position of all multipoint bkgds in a plot from the Plot! window. Is that possible?

See Julien's tutorial here:

https://probesoftware.com/smf/index.php?topic=131.0

and the following discussion.

But yes, you can view the MPB positions from the Plot! window (and adjust them for subsequent sample acquisitions):



(sorry for the old plot graphics, but I couldn't find a new example)!

But usually people check already acquired MPB data from the Run | Display Multi-Point Background Intensities menu dialog.

[John Donovan]

Can we get export filter for totals >102 (or whatever we chose)?

If you have high totals they need to be corrected for whatever the issue is (spectral interferences, standard intensity drift, secondary boundary fluorescence, etc.). One cannot simply filter to obtain the results one desires.

Of course. However, you do let us filter in the Plot Standard and Unknown Sample Data in the Output dropdown.  And sometimes there are random bad points that just need removing.

Your wish is granted:

[Radek_MM]

PHA Scan peak fit

After peaking an element we often acquire the PHA bias scan. However, in the output (Display PHA, Peaking and Peak Scan Data) we get a peak fit only for the ROM Scan for the peak position, which is automatically updated for the element in the run.

How difficult would it be to implement a peak fit for the Bias Scan, where the peak is not always as smooth as a spectrometer position peak scan?

Or would it be at least possible to implement some feature where, similar to the peak scan position update, upon clicking in the graph, the new value for the bias is automatically updated for the element (would need to be an integer without decimals) ?



Until now we need to determine the new bias by hand from the graph and note the value on a piece of paper (or the more advanced of us use excel or other digital media  ), then go to the PHA dialogue and type it in for every element. Now this might be not such a big deal for the daily routine analysis, but when the routine becomes a set of 20 and more elements it is quite time consuming to do this manually. Sorry for being spoiled...

Rgds,
Radek

[JonF]

Or would it be at least possible to implement some feature where, similar to the peak scan position update, upon clicking in the graph, the new value for the bias is automatically updated for the element (would need to be an integer without decimals) ?

Can I second the above 

I have another request too, assuming that I've not just been using PfE wrong! I imagine it's probably come up before and there's a reason why it's not done this way..
 
When I create a new setup, I add all the elements that I want to acquire in my unknown samples, add all the standards that I want to use and then set the standards I want to use for each element.
After the usual peak and PHA check, the probe will then happily go about acquiring the standards as requested. I usually use either full standards (all elements on all standards) or quick standards with >5wt% majors for the first run.   

When I go back through the acquired standard data, I can see that PfE will quantify the concentration of the elements in the standard relative to whatever standard was chosen for that element in the unknown setup.     

For example, let's say I decide to standardise both wollastonite (CaSiO3) and anorthite (CaAl2Si2O8), measuring both Ca and Si in both phases (I prefer to use silicate standards for silicates and aluminosilicate standards for aluminosilicates, and I typically encounter both during a session). For my unknowns, I decide to default to using wollastonite for the Ca and Si standard. When I click analyze for the anorthite, it will quantify the Ca and Si in anorthite relative to their intensities as measured in wollastonite.

This will then cascade through the rest of the standard dataset. Let's say I measure Fe using my fayalite standard, Fe2SiO4. When I press analyze in this standard, it will report concentrations of Fe relative to the fayalite standard, but Si relative to the Si intensity in wollastonite. For my orthoclase standard, it will quantify K relative to the orthoclase, Al relative to anorthite and Si relative to wollastonite. In my augite standard, Na would be relative to jadeite, Ca relative to wollastonite, Mg relative to periclase, Ti to rutile, Al to anorthite, Fe to fayalite and Si to wollastonite: but I know the concentration of all of those elements in my augite!

To me, this seems to be putting a lot of faith in my e.g. wollastonite standard Si concentration (as it's then used for all silicates, standards and unknowns), and means that all the standards have to have a more significant matrix correction applied.

I then go through each standard and swap all the major elements to be quantified relative to that standard (isn't that the point of having these standards, that we know what the concentrations are in this material?)

Is there a way to set PfE to automatically standardise the elements in the standards relative to the known concentration of those elements in that standard (i.e. from standard.mdb), rather than following the standards as set up for the unknown samples? Obviously for a full standardisation, you will likely measure elements that aren't actually present in that standard, so that would need to fall back on to the standard defined in the unknown setup.     

[John Donovan]

Or would it be at least possible to implement some feature where, similar to the peak scan position update, upon clicking in the graph, the new value for the bias is automatically updated for the element (would need to be an integer without decimals) ?

Can I second the above 

Absolutely.

We just haven't had a chance to get to that item.  But after the Athens EPMA workshop next week we will start on it:

https://sites.google.com/view/epmaathens2024

I have another request too, assuming that I've not just been using PfE wrong! I imagine it's probably come up before and there's a reason why it's not done this way..
 
When I create a new setup, I add all the elements that I want to acquire in my unknown samples, add all the standards that I want to use and then set the standards I want to use for each element...

OK, I'm not sure I understand exactly what you mean, but let me describe how I would handle this situation and then you can tell me if this solution would work for your situation.

Basically if I have a complicated run, where I have different types of samples, different standard assignments, different interference corrections, maybe even different elements, different formula basis, etc., etc. I would start by creating a "mother of all samples" with all the elements I will be running for this run.

This "mother of all" sample would be the unknown sample that I peak all the elements on the assigned standards (which by default are the standards with the highest concentrations of the elements and therefore best for peaking on generally), check all the PHAs, and check all the backgrounds (if not using MAN bgds).  And of course this sample could be loaded from a previous run using the Acquire! window New Sample/Setups | Load File Setup feature in PFE...

Once that "mother of all" sample has been peaked and optimized, I might even acquire all the standards and check that all the secondary standards are giving accurate results, especially standards without the element present to check for spectral interferences and our MAN assignments (and because we want to stress our matrix corrections to make sure everything is extrapolating OK as far as the physics is concerned!).

But then... if I really want to optimize things I would then take that tuned up "mother of all samples" and create several new sample setups (for each material/mineral I expect to analyze), using that "mother of all" sample as a basis and then delete the unneeded elements and perhaps modifying the standard assignments for situations where a more matrix matched standard could provide better accuracy (though with these new matrix corrections/MAC values I find this step is not needed as often these days, as it used to be in the past).

So, for example I might tune up a "mother" sample of Si, Fe, Ca, Al, Na, K, Mn, Mg, Ti, Ba.  Then I select that sample in the Analyze! window and click the "Add To Sample Setups" button. That adds that sample to the Sample Setups list so it can get re-used... and note that sample can be modified subsequently (standard assignments, off-peak bgd models, interference assignments, etc.) because it is just a pointer to that sample and any changes to that sample will get passed on to any subsequent acquisitions using it.

Then I go to Acquire! window New Sample/Setups button and use the Load Sample Setup button to select that "mother" sample and make a new sample called, say, "olivines" and then delete all the elements except Si, Fe, Mg, Ni and Ca.

Again, I go to Acquire! New Sample/Setups and use the Load Sample Setup button to select that "mother" sample (again) and make a new sample called, say "feldspars" and then delete all the elements except Si, Fe, Na, K, Al, Ba and Ca.

And so on and so on.  But now I can go to each of these sample setups from the Analyze! window and select each sample "setup" and change any and all assignments, primary standards, interferences, background models, formula basis, etc., etc.

And then from Analyze! window I click the "Add To Sample Setups" button for each (or all) of these modified sample setups (olivines, feldspars, etc.). That then adds these samples to the Sample Setups list so they can be utilized from the Automate! window for digitizing positions or from the Acquire! window for manual acquisitions.

Then when I am all ready I can go to the Automate! window and digitize each of my materials/minerals as position samples and either before or afterwards select the specific sample setup basis (olivines, feldspars, etc.) using the Sample Setups button in the Automate! window.

Would that work for you?

[Anette von der Handt]

Thanks for adding the import function to PictureSnapApp!

What would be handy is if there would be now a complementary export function in PFE for stage locations of unknowns (but really any kind of locations: standard/wavescans) that would allow me to export them into the PictureSnapApp compliant format with the option of either short-line labels or long-line labels as the comment.

This could either be from the Analyze! window in the right-click context menu (so that I can select subsets of positions) or similarly in the Locate menu.

I would have two main applications: one is that I could easily show locations for a single mineral type or sample without having to disable/enable the individual analyses each time in the mdb. Secondly, at times I run into problems with available memory with large images within PictureSnap but usually not within PictureSnapApp. That problem is on my side of course but it would be a super useful option.