Author Topic: Wish List for PFE Features  (Read 107354 times)

Ben Buse

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Re: Wish List for PFE Features
« Reply #420 on: September 17, 2018, 06:37:20 am »
Related to Ben's request above we've modified the code to automatically select the proper sample output type (standard vs. unknown) when the user right clicks the selected sample list in the Analyze! window for the "User Specified Output Format" as seen here:



This enables the output of "published" concentration (and variance and difference) values for standards if standard samples were selected.

Thanks for doing that

Ben
« Last Edit: September 17, 2018, 08:51:47 am by John Donovan »

Probeman

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Re: Wish List for PFE Features
« Reply #421 on: September 24, 2018, 10:58:29 am »
The "Email notification" box is also greyed out. I guess I have to put in the accurate SMTP etc notes in the probewin.ini file first which I haven't done yet because I thought it only reports errors  ;). The F1 Help file here also gives no additional information FYI.

All,
I am bringing this post "back from the dead" because Paul Carpenter recently asked me if this email report feature still works and I thought, well I haven't tested it in a while, so I'll do that.  And lo and behold it does still work- at least on our Univ of Oregon email server. 

For those who are not yet familiar with this feature, it is accessed from the Acquisition Options from the Acquire! window as seen here:



The Probe for EPMA help file has this to say:
Quote
SMTPServerAddress="smtp.probesoftware.com"
SMTPAddressFrom="donovan@probesoftware.com"
SMTPAddressTo="donovan@probesoftware.com"
SMTPUserName="donovan"

These keywords are to be used for e-mail notification of real-time automation errors. If these SMTP fields are valid and the option "E-mail Notification of Errors" is checked in the Automation Options dialog, then any real-time errors (for example, a blown filament message) will be trapped and forwarded to the address indicated. This option is only available for automation procedures initiated from the Automate! window.

          SMTPServerAddress: must be a secure email server
          SMTPAddressFrom:   only used for documentation purposes

In addition, a "progress report" message will be sent every 8 hours to the e-mail address specified in order to give positive notification of the normal functioning of the instrument during especially long runs.

Note that the first time the automated acquisition is started and the E-mail Notification of Errors option is checked then the program will prompt the user for the password for the specified user email account. This password will be retained only for the duration of the currently open probe run.

The idea being that when this box is checked the software will send email reports every 8 hours or so on the progress of any automation running in Probe for EPMA. It will also send any errors it detects such as the filament burning out or a vacuum problem.

To test this email reporting feature I entered the relevant information in the [general] section of the Probewin.ini file as seen here:

[general]
SMTPServerAddress="smtp.uoregon.edu"                    ; email server address for error messages
SMTPAddressFrom="epmalab@uoregon.edu"
SMTPAddressTo="epmalab@uoregon.edu"
SMTPUsername="epmalab"

Of course you'll need to use your own email server and addresses!

When you start an automation in Probe for EPMA (in this test I simply confirmed some unknown positions), the software prompts you once for the email password and sends a "Automation initiated" email, and when the automation finishes it sends an "Automation completed" email message.

And as previously mentioned, if the automation runs longer than 8 hours it will send "progress" reports as to which sample it is working on.  Here are the two email messages I received in the probe lab email account for the test I performed:

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Paul Carpenter

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Re: Wish List for PFE Features
« Reply #422 on: September 24, 2018, 12:21:51 pm »
John,
Thanks for posting on this. The capability is good. Keeping the password only for the current session is not convenient. We use an email account for the microprobe at WUSTL and I would favor having some way to store the password but I can see the general IT-freakout of such a policy. Is it possible to securely push an email to an address like you have set up in the ini file?

The status report would be great. It seems to me that PFE is so bullet-proof that actual error messages for an automated run are hard to envisage (since the points are scanned before starting the run). Excessive drift in automated re-standardizations would be good to trap.

I would like to know when the run is finished because we don't use the wav file for this purpose; email is infinitely better for this purpose.

Cheers,

Paul
Paul Carpenter
Washington University St. Louis

Probeman

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Re: Wish List for PFE Features
« Reply #423 on: September 24, 2018, 12:43:51 pm »
Thanks for posting on this. The capability is good. Keeping the password only for the current session is not convenient. We use an email account for the microprobe at WUSTL and I would favor having some way to store the password but I can see the general IT-freakout of such a policy. Is it possible to securely push an email to an address like you have set up in the ini file?

Hi Paul,
I understand what you are saying, but there is no way I can think of to make this secure.  That is why the password is only stored for the current session in the application memory.  This is done so each user can enter their own email address and have status reports sent to their own email account.  Again for security reasons.  I guess you could give your lab email password to your main probe users if you aren't concerned about security...

The status report would be great. It seems to me that PFE is so bullet-proof that actual error messages for an automated run are hard to envisage (since the points are scanned before starting the run). Excessive drift in automated re-standardizations would be good to trap.

Thank-you for saying that!  Yes, the only errors I ever see are instrument errors and those do occur once in a while (right now I'm fighting with my ion pump as it "flashes over" roughly once a week or so, thereby killing the vacuum system), but PFE will report any error whether software or hardware just to be on the safe side. 

I would like to know when the run is finished because we don't use the wav file for this purpose; email is infinitely better for this purpose.

Yup. It will send an email when the automation has completed.
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Ben Buse

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Re: Wish List for PFE Features
« Reply #424 on: November 28, 2018, 05:55:36 am »
Hi John,

I really like the Nth point feature, we regularly use it for standards and turn it off for unknowns. What I find is many users forget to turn it off for unknowns. Could we have a warning when analysing unknowns - stating that Nth point is turned on - e.g. like the other warnings in the PFE window in the bright colors

Thanks

Ben

John Donovan

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Re: Wish List for PFE Features
« Reply #425 on: November 30, 2018, 10:17:20 pm »
Hi John,

I really like the Nth point feature, we regularly use it for standards and turn it off for unknowns. What I find is many users forget to turn it off for unknowns. Could we have a warning when analysing unknowns - stating that Nth point is turned on - e.g. like the other warnings in the PFE window in the bright colors

Thanks

Ben

Hi Ben,
I thought about your request about adding a warning message but I think I came up with a more elegant method. I thought of a way to treat the acquisition code as an "object", and simply utilize another parameter to specify whether standard and/or unknown samples are acquired using the Nth point background method as seen here:



For those of you not aware of this off-peak background method, the help file has this to say:

Quote
Nth Point Off-Peak Acquisition
Another acquisition option method utilized to save time, is the Nth Point background method which simply acquires an off-peak background measurement every “N” points. That is, one performs an off-peak background measurement on the first point of a set of data and then re-uses that off-peak measurement for subsequent data points, instead of explicitly measuring the off-peak background for all points in the data set.

Typically this would be utilized on major and minor elements, with the trace elements continuing to be measured using normal off-peak background measurements.

The downside to this method is that if the composition changes, the average Z of the material will change and according to Kramer's Law, the continuum intensity will change as well. Although the change will be proportional to the degree to which the average Z changes and therefore will be small for a small difference in composition. However if the change in background intensity is greater than the precision of the measurement, it will affect the accuracy of the analysis.

A new option for the Nth Point off-peak background acquisition to handle samples with variable composition is the “smart” monitor element feature. Based on a user specified monitor element the software will automatically re-measure the off-peak backgrounds if the on-peak intensity of the monitor element changes by more than the user specified percentage.

Note that the monitor element should normally be a major element (with a statistical significance that is appropriate for the specified monitor element intensity change percent specified and also an element that finishes its on-peak count integration BEFORE the Nth Point off-peak ground elements in order to function properly.

Anyway, it seems to work quite well, so give it a try and let me know what you think.  Version 12.5.3 is ready to download now.
john
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Ben Buse

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Re: Wish List for PFE Features
« Reply #426 on: December 03, 2018, 07:24:53 am »
Hi John,

That sounds really good, I want to try it, but machine is now down for maintenance.

Ben

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Re: Wish List for PFE Features
« Reply #427 on: January 31, 2019, 09:24:01 am »
This is probably the wrong spot to post, but here it goes anyway. 

Acquire Analytical Conditions inserts the probe current detector on the JEOL 8530F+, before it reads the conditions beam current and mode and magnifications.  Automate "conditions" function does not close the PCD when reading conditions, beam current and mode and magnifications.  This results in a change in beam current as the Automate conditions is sample absorbed current.

My wish is that the conditions function work the same. 

John Donovan

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Re: Wish List for PFE Features
« Reply #428 on: January 31, 2019, 03:23:58 pm »
This is probably the wrong spot to post, but here it goes anyway. 

Acquire Analytical Conditions inserts the probe current detector on the JEOL 8530F+, before it reads the conditions beam current and mode and magnifications.  Automate "conditions" function does not close the PCD when reading conditions, beam current and mode and magnifications.  This results in a change in beam current as the Automate conditions is sample absorbed current.

My wish is that the conditions function work the same.

Ooops.  That got overlooked somehow... we'll fix it tonight.
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John Donovan

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Re: Wish List for PFE Features
« Reply #429 on: January 31, 2019, 09:31:34 pm »
This is probably the wrong spot to post, but here it goes anyway. 

Acquire Analytical Conditions inserts the probe current detector on the JEOL 8530F+, before it reads the conditions beam current and mode and magnifications.  Automate "conditions" function does not close the PCD when reading conditions, beam current and mode and magnifications.  This results in a change in beam current as the Automate conditions is sample absorbed current.

My wish is that the conditions function work the same.

Ooops.  That got overlooked somehow... we'll fix it tonight.

Hi Keith,
OK, we added a call to insert the Faraday cup there.

Update Probe for EPMA from the Update menu and you should be good to go.
john
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dawncruth

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Re: Wish List for PFE Features
« Reply #430 on: March 15, 2019, 07:55:23 am »
Is there a feature that provides optimized scheduling suggestions for the spectrometer setup for a run with given conditions?
For example, a user could input the phases of interest, elements of interest and if they are major minor or trace. PfE already knows the spectrometer setup and could spit out a suggested schedule for the elements (count times and all) on that instrument?

Just a thought.

Probeman

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Re: Wish List for PFE Features
« Reply #431 on: March 15, 2019, 08:31:02 am »
Is there a feature that provides optimized scheduling suggestions for the spectrometer setup for a run with given conditions?
For example, a user could input the phases of interest, elements of interest and if they are major minor or trace. PfE already knows the spectrometer setup and could spit out a suggested schedule for the elements (count times and all) on that instrument?

Just a thought.

It's a good thought. Your idea reminds me of work done by Nicholas Ritchie at NIST on optimizing analytical setups:

https://www.cambridge.org/core/journals/microscopy-and-microanalysis/article/optimizing-the-dose-for-energy-dispersive-electron-probe-xray-microanalysis-measurements/F325C6AEB2241110F2F75E7A005C0725

He was looking at EDS spectrum acquisition, which is easier to model than WDS, due the the large variation in intensity and resolution over the WDS spectrometer range.

The good news is that experienced microprobe (WDS) analysts are less likely to be replaced by an algorithm!  :D
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BenjaminWade

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Re: Wish List for PFE Features
« Reply #432 on: March 20, 2019, 10:00:18 pm »
My wish is for the U-Th-Pb chemical age output to also give individual spot errors.

cheers

Anette von der Handt

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Re: Wish List for PFE Features
« Reply #433 on: March 21, 2019, 09:29:22 am »
My wish would be that PictureSnap can display ProbeImage map files also in rainbow colors.

Thanks
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John Donovan

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Re: Wish List for PFE Features
« Reply #434 on: March 21, 2019, 09:39:56 am »
My wish is for the U-Th-Pb chemical age output to also give individual spot errors.

cheers

What is an "individual spot error"?  Are you saying you want the counting statistics propagated for the calculated age for each data line in the output?

Un    7 Moacyr, Results in Elemental Weight Percents
 
ELEM:        U      Th      Pb       Y      La      Ce       P       O
TYPE:     ANAL    ANAL    ANAL    ANAL    ANAL    DIFF    STOI    CALC
BGDS:      LIN     EXP     LIN     LIN     LIN
TIME:   200.00  200.00  200.00  120.00  120.00     ---     ---     ---
BEAM:    49.82   49.82   49.82   49.82   49.82     ---     ---     ---

ELEM:        U      Th      Pb       Y      La      Ce       P       O   SUM 
   213    .054   6.294    .108   1.148   9.991  42.240  13.097  27.068 100.000
   214    .074   6.247    .132   1.147   9.687  42.552  13.095  27.065 100.000
   215    .059   6.336    .124   1.148   9.703  42.473  13.094  27.063 100.000
   216    .065   6.248    .124   1.133   9.632  42.639  13.095  27.064 100.000
   217    .053   6.267    .111   1.149   9.772  42.481  13.097  27.069 100.000
   218    .047   6.236    .129   1.158   9.767  42.496  13.098  27.070 100.000

AVER:     .059   6.271    .121   1.147   9.759  42.480  13.096  27.066 100.000
SDEV:     .010    .038    .010    .008    .125    .133    .001    .003    .000
SERR:     .004    .015    .004    .003    .051    .054    .001    .001
%RSD:    16.28     .60    8.18     .72    1.28     .31     .01     .01
STDS:       15      18     386    1016     836     ---     ---     ---

STKF:    .8725   .8707   .6861   .4480   .6591     ---     ---     ---
STCT:   137.33   44.30  140.31   38.76   33.08     ---     ---     ---

UNKF:    .0005   .0527   .0009   .0083   .0847     ---     ---     ---
UNCT:      .08    2.68     .19     .72    4.25     ---     ---     ---
UNBG:      .79     .27     .56     .13     .19     ---     ---     ---

ZCOR:   1.1730  1.1895  1.3002  1.3785  1.1521     ---     ---     ---
KRAW:    .0006   .0606   .0014   .0186   .1285     ---     ---     ---
PKBG:     1.10   10.94    1.34    6.49   23.70     ---     ---     ---
INT%:   -63.95    ----  -10.06    ----    ----     ---     ---     ---

Un    7 Moacyr, Results in Millions of Years Ago, EPMA Age (from U, Th, Pb)

         U WT%  Th WT%  Pb WT%   U PPM  Th PPM  Pb PPM Age[My] Calc Pb %Pb(Th)  %Pb(U)
   213 .054288 6.29400 .107605 542.881 62940.0 1076.05 371.500 1076.22 97.2623 2.71051
   214 .074258 6.24715 .132359 742.582 62471.5 1323.59 454.700 1323.82 96.2572 3.72055
   215 .059052 6.33590 .124209 590.521 63359.0 1242.09 424.500 1242.38 97.0420 2.93415
   216 .064551 6.24769 .123637 645.509 62476.9 1236.37 427.100 1236.60 96.7334 3.24296
   217 .053382 6.26723 .110778 533.816 62672.3 1107.78 384.100 1107.97 97.2936 2.68008
   218 .047139 6.23599 .128886 471.395 62359.9 1288.86 449.800 1288.76 97.6238 2.39873

AVER:  .058778 6.27133 .121246 587.784 62713.3 1212.46 418.617 1212.63 97.0354 2.94783
SDEV:  .009568 .037662 .009920 95.6843 376.622 99.1996 34.0364 99.1770 .481923 .471998

That is a very non-trivial exercise. In fact it would be a research project in itself.  Maybe Mike Jercinovic and/or Julien Allaz have some code for this?  If they do, and they are willing to share it, I could implement that in Probe for EPMA.
« Last Edit: March 21, 2019, 09:53:33 am by John Donovan »
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