Wish List for PFE Features

[orlandin]

Hi all! I will second Dawn's post above about adding a little more secondary standard functionality in PFE. It would be cool to be able to designate certain unknown samples as secondary standards so that PFE would calculate the deviation from published just it does for standards, plot that deviation by element over the course of the run, maybe send you an email/text message if that deviation exceeds a certain threshold... hey, this is a wish list right? Although maybe I should consider that I'm requesting a future where I'm being texted all night by an 8200...

Also, this is probably way, way less work and I care way, way more: is it possible to disable the warning window that pops up when you have different background methods used between standards and unknowns? Or maybe just a timer that proceeds after 30s if there is no user input? This stupid window has kneecapped several overnight runs because I forget to sit and wait patiently after finally pressing 'run' on Automate, only to find that this window has stopped all data collection and left my beam on all night. Yeah, little window, I know that I'm using different background methods! The ability to use different background methods is one of PFE's most useful features! Stop punishing me for using it!

Usually this window pops up just as the first standard is being run, but last night it seemed to pop up after the standardization and at the first unknown point... at 2:30 am. I did just recently update PFE by quite a few versions so maybe this is going to be my new existence.

[John Donovan]

Hi all! I will second Dawn's post above about adding a little more secondary standard functionality in PFE. It would be cool to be able to designate certain unknown samples as secondary standards so that PFE would calculate the deviation from published just it does for standards, plot that deviation by element over the course of the run, maybe send you an email/text message if that deviation exceeds a certain threshold... hey, this is a wish list right? Although maybe I should consider that I'm requesting a future where I'm being texted all night by an 8200...

Yeah, I can't think of a clever way to do this and I really don't get why you and Dawn just don't run this secondary standard as a standard.

Remember, when a standard isn't assigned as a primary standard it is treated exactly as an unknown in the Analyze! window. You can even specify in Calculation Options that oxygen is calculated by stoichiometry just as it would for an unknown sample.

If it's the acquisition conditions you want to be the same as your unknowns just use the Use Sample Setups feature in the Acquire! or Automate! windows to specify using an unknown sample setup for acquisition that has those conditions.

Also, this is probably way, way less work and I care way, way more: is it possible to disable the warning window that pops up when you have different background methods used between standards and unknowns? Or maybe just a timer that proceeds after 30s if there is no user input? This stupid window has kneecapped several overnight runs because I forget to sit and wait patiently after finally pressing 'run' on Automate, only to find that this window has stopped all data collection and left my beam on all night. Yeah, little window, I know that I'm using different background methods! The ability to use different background methods is one of PFE's most useful features! Stop punishing me for using it!

Usually this window pops up just as the first standard is being run, but last night it seemed to pop up after the standardization and at the first unknown point... at 2:30 am. I did just recently update PFE by quite a few versions so maybe this is going to be my new existence.

Your wish is granted!     

The latest update of Probe for EPMA now modifies this warning dialog to use a 30 second timeout, after which it unloads the warning and assumes one clicked "Yes To All".

[orlandin]

Hello, John! Thank you! I will update immediately!

I really like the idea of running sstds as stds, and your answer is actually what a few others told me as well. This works very well, except that you cannot re-analyze the sstds in a run without using the 're-analyze all standards every X hours' option. Unknowns are allowed to share a name because they all get unique numeric ID even if the sample name text is the same. PFE does not seem to allow you to have multiple Sample lines of the same standard, because each standard has a fixed numeric ID? I usually bookend with the full suite of standards, and then have repeated analyses of sstds distributed throughout the automated run - a smaller time commitment that way, but re-analyzing all stds and sstds at the same time is hardly a waste of time.

Best,

Phil

[John Donovan]

PFE does not seem to allow you to have multiple Sample lines of the same standard, because each standard has a fixed numeric ID? I usually bookend with the full suite of standards, and then have repeated analyses of sstds distributed throughout the automated run - a smaller time commitment that way, but re-analyzing all stds and sstds at the same time is hardly a waste of time.

Yes, the standard number is unique to that standard composition.

Of course one can always digitize any standards as unknowns and have them appear anywhere in the Automate! position list.  See the Digitize! Position button window.

[orlandin]

Yes! Creating unknown samples of standards is very helpful, but it would be even more helpful if you could designate an unknown sample as having a published composition so that PFE would calculate deviation from published the way it does for standards, plot deviation over the run, etc. Sorry, this is where I was coming from in my first post!

[John Donovan]

Yes, I understand. 

Still trying to think of a clever way to do this because how does it know which standard this "unknown" sample is?  Same exact name of course is obvious, but then there's a possibility of a "false positive" if one just happened to enter an unknown name that also happened to  be a standard name, e.g., "Hematite".

[JonF]

Still trying to think of a clever way to do this because how does it know which standard this "unknown" sample is?  Same exact name of course is obvious, but then there's a possibility of a "false positive" if one just happened to enter an unknown name that also happened to  be a standard name, e.g., "Hematite".

Couldn't you manually multi-select (either via ctrl-clicking or the string selection) the secondary standards in the unknown sample list in Analyze! window and have a "Compare Selected Samples against standard composition" button, which would pop up a "select which standard you want to compare with" window?

[John Donovan]

Sure, one can always add more buttons and pop-ups, but I was hoping for a more "elegant" solution!   

[John Donovan]

Still trying to think of a clever way to do this because how does it know which standard this "unknown" sample is?  Same exact name of course is obvious, but then there's a possibility of a "false positive" if one just happened to enter an unknown name that also happened to  be a standard name, e.g., "Hematite".

Couldn't you manually multi-select (either via ctrl-clicking or the string selection) the secondary standards in the unknown sample list in Analyze! window and have a "Compare Selected Samples against standard composition" button, which would pop up a "select which standard you want to compare with" window?

One thing I do sometimes is look at the results in the Analyze! window, and then click on the Run | List Standard Compositions menu in the log window which outputs the standard compositions, and sorts the elements to match your Analyze! window output.

Doesn't provide the relative percent difference, but it might be helpful until I think of a better solution along the lines you've suggested...

[dawncruth]

Yeah, I can't think of a clever way to do this and I really don't get why you and Dawn just don't run this secondary standard as a standard.

Remember, when a standard isn't assigned as a primary standard it is treated exactly as an unknown in the Analyze! window. You can even specify in Calculation Options that oxygen is calculated by stoichiometry just as it would for an unknown sample.

If it's the acquisition conditions you want to be the same as your unknowns just use the Use Sample Setups feature in the Acquire! or Automate! windows to specify using an unknown sample setup for acquisition that has those conditions.

I think it is more of a user experience thing. I think some people want to run standards, and then run unknowns and not mix their runs. But then it just takes getting used to.

On another question/request. Is there a way to output raw x-ray counts? I've been having issues with a spectrometer and found issue was with the detector by looking at x-ray counts with my JEOL side.  If there is, could you point the way?

[Probeman]

There are two ways to get the raw intensity data out of PFE:

1. Turn off all the intensity corrections in the Analytical | Analysis Options dialog:

https://probesoftware.com/smf/index.php?topic=33.msg2155#msg2155

2. Use the Output | Save Custom Analysis Output | Save Custom Analysis Output #7 (NIST) menu.

[JonF]

Sure, one can always add more buttons and pop-ups, but I was hoping for a more "elegant" solution!   

How about multi-selecting the secondary standards and sending them to the Evaluate program?
You could then have them plot up as either intensity (cps/nA) or wt% over time (e.g. all elements vs time), or as a selected element calculated wt% vs published wt% (as it currently does for standards). You could even have them plot up as relative difference vs the average of that element or as the relative difference vs a standard (you'd need your secondary standard compositions in the standard.mdb).

[John Donovan]

I thought we were talking about acquiring standards as unknowns and figuring a way to have the program decide what standard they actually are? 

If they are secondary standards (acquired as standards), the Evaluate program will handle them fine. That is what it is for:



Here, 12 is MgO, 358 is my Chesterman diopside and 160 and 162 are the NIST K-412 and K-411 mineral glasses.

As for intensity vs. time that is what the Drift program is for, and it will handle standards or unknowns:



Getting back to the original request to have standards run as unknowns, but then have PFE know that they are standards, so that it can display the calculated differences to the published values, I am still thinking about how that might be accomplished.

[John Donovan]

Dawn, Jon and Phil,
OK, I think we've got something that will work for you all. Update PFE to version 12.9.9 using the Help menu and let us know what you think.  Here's how it works:

So let's say that you acquired an unknown sample that is actually a standard sample, for example this:



In this case the unknown sample name is exactly the same as the actual standard name, but it doesn't have to be (more on that later). This is exactly what one would normally see when acquiring a standard as an unknown sample. Next you would go into the Calculation Options dialog and select from the drop down list the standard that it is as seen here:



The default selection is "Unknown" in which case the feature is off and the unknown is treated just as a normal unknown.  Next we analyze the sample again and please note that the program now outputs the published composition and the %VAR and DIFF values as it would for a standard:



But the analyses seems off and of course it is because the matrix corrections are completely wrong, as this is a silicate standard and we are not measuring oxygen, so no oxygen is being added into the matrix corrections as it would be normally if the sample was acquired as a standard sample.  So we go back into the Calculations Option dialog and select the Calculate With Stoichiometric Oxygen option:



One could also add a specified amount of oxygen using the Specified Concentrations dialog if desired. Now we analyze again and obtain a better looking result:



So the sequence of events for using this feature might be something like this:

1. From the Digitize! window create an unknown position sample with the name of the standard you want to use as this "secondary standard as an unknown" sample. You can also use the Duplicate As Unknown button accessed from the Digitize! window Position button.  Make as many of these unknown (standard) position samples as you want either during your actual unknown digitizing or afterwards and then move them to your desired acquisition order using the up/down spin button in the top left of the Automate! window.

2. Acquire your standards and unknown samples as usual using the Automate! window. The selected standards will be acquired as specified by you before, after or at specified intervals and the unknowns will be acquired in the order displayed in the Automate window.

3. Once your samples have been acquired you can select the unknown samples that are actually a standard, either manually from the Analyze! window list or use the "string selection" feature to select all unknown samples with that standard name.

4. Then from the Calculation Options dialog select the standard that these unknown samples actually are using this new feature, and click OK.  Note that if the unknown sample is not the same (not case sensitive) as the standard you reference, the program will print this warning message:



But it will still treat the sample as a "Unknown Sample Is A Standard".  Hope this all makes sense and does what you all need.

[Rom]

Hi everyone,
Could you explain how I can decrease time of picture (BSE) collecting. Now I use 5%, 1800*1800. As result collecting time is 1.5 min. I want to decrease collecting time and, of course, quality of picture.

Thank you.
Roman