Probe Software Users Forum
Software => Probe for EPMA => Topic started by: jeb on October 07, 2013, 11:35:16 AM
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Getting the ball rolling on a list of features I, and others, would like to see for PFE (got to keep John busy!):
In the "Display Time Dependent (TDI) and Alternating (on/off) Intensities" window, make it remember the element you have selected from sample to sample and/or eliminate the pop-up every time about there being no TDI data when the element selected doesn't have TDI data (or maybe just have it tell the user once that TDI data is only available for elements X, Y, and Z?)
More suggestions to come I'm sure ;D
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Good idea!
That "behavior" has been bugging me for a while so I'm really glad you brought it up!
Anyway, all fixed now- enjoy!
(https://probesoftware.com/smf/oldpics/i43.tinypic.com/14xml1g.jpg)
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Hi John
I would like to be able to change the order in which standards are analysed.
Please correct me if I’m wrong.
At the moment the standards are analysed in the order of their “sample number”. If you program 10 standards, it will analyse the one with the lowest number first and the one with the highest number last.
We are in the process of replacing all of our standards. Before we feel confident in using the new ones, we would like to measure them against the old standards. However, if I program a run over night that contains 10 old and 10 new standards, it will first analyse all the old standards since they have lower “sample numbers” before it starts analysing the new ones. Any drift of the instrument will results in different number and would make us believe that the standards are not identical in composition.
Ideally, I would like to analyse the standards in pairs, but for that I have to change the order.
Cheers
Sandrin
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Hi Sandrin,
Why don't you just run them as "unknowns" and then you can order them in any order you want?
Hint: use this button in the Position window:
(https://probesoftware.com/smf/oldpics/i43.tinypic.com/s32b8i.jpg)
Then order them using this spin button:
(https://probesoftware.com/smf/oldpics/i44.tinypic.com/auwkm9.jpg)
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Hi John.
I frequently report data in mole% oxide form rather than weight percent. It is a simple calculation in Excel, but it would be nice to be able to have the option to have PFE report oxide wt % in the export and, if possible on the screen. Would anyone else like that option?
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I frequently report data in mole% oxide form rather than weight percent. It is a simple calculation in Excel, but it would be nice to be able to have the option to have PFE report oxide wt % in the export and, if possible on the screen. Would anyone else like that option?
Hi Ben,
I added an option for Oxide Mole Percents in the User Specified Output dialog available from the Output | User Specified Format menu as shown here:
(https://probesoftware.com/smf/oldpics/i41.tinypic.com/2whl9g2.jpg)
When you use the export to Excel option, you'll get this output which I think is what you want...
(https://probesoftware.com/smf/oldpics/i42.tinypic.com/mhdp4o.jpg)
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Hi Sandrin,
Why don't you just run them as "unknowns" and then you can order them in any order you want?
Hint: use this button in the Position window:
(https://probesoftware.com/smf/oldpics/i43.tinypic.com/s32b8i.jpg)
Then order them using this spin button:
(https://probesoftware.com/smf/oldpics/i44.tinypic.com/auwkm9.jpg)
Hi John
Thank you for the quick reply! And sorry that it took me so long to answer. I have been snowed under with work and just today managed to have a look at the forum again.
Following your suggestions would allow me to analysed the standards as unknowns. I could analyse them in the right order. However, if I turn the standards into unknowns I cannot use them as calibration standards any more.
Ideally, I could use the same spin buttons that work nicely for sorting the unknowns also for manipulating the order of the standard acquisition. That would allow me to analyse the standards in my preferred order and I can still use them to calibrate.
Cheers
Sandrin
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Ideally, I could use the same spin buttons that work nicely for sorting the unknowns also for manipulating the order of the standard acquisition. That would allow me to analyse the standards in my preferred order and I can still use them to calibrate.
Hi Sandrin,
If you are only trying to compare the old standards with the new standards, it doesn't really matter that they are unknowns. You're just going to do it once or twice right?
I could allow the user to change the standard acquisition order in the Automate! list, but it's not a trivial change. Do you need it for any other purposes? Note that if there is standard intensity drift, the standard drift correction if PFE works *really* well as long as you run the primary standard both *before* and *after* the secondary standard. So just select all your standards and just run them twice using the "After" checkbox in Automate!
Also you should try out the Evaluate standard program. It allows one to compare all standards in a run for one element at a time as seen here:
(https://probesoftware.com/smf/oldpics/i39.tinypic.com/2dlr778.jpg)
Good for evaluating ones standards for self consistency. Standard #14 is my SiO2 standard. The program automatically uses the standard with the highest concentration as the primary standard. John Fournelle and Paul Carpenter came up with this idea.
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Hi John,
I am jumping in here and ask for something similar to what Sandrin is asking for, namely the option to have a user-defined order of tasks.
What I have in mind is an option that opens a pop-up window/second window where I could define a task list either by drag and drop or similar to the "add standards to run" option and where I can mix and match unknowns and calibration standards. The current function to recalibrate standards after x hours does not completely fulfill my needs because:
1) I would prefer to have control on when the new calibration will happen (between two physical samples) rather after a certain time interval.
2) More importantly, depending on the analytical problem i am investigating, sometimes I would like to recalibrate some elements at different intervals than others. Currently it is either all or none in my understanding. But let's say I want to do calcium in olivine, I may want to run the calcium calibration more often (let's say every 30 analysis) while I only want to re-calibrate the Mg, Fe, Si standards at the beginning and at the end the entire run. With the current setting, depending on what mineral I am looking at, running all standards in short intervals would otherwise add significant time to the run.
Such a function would really put the capability of PFE to correct for drift to a whole other level.
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Hi John,
this one would be a "nice to have" for efficiency and being lazy.
Problem: When I am peaking the spectrometers on the assigned standards, I do not always agree with the results (because some peaking methods seem to work better for some elements but I want to run them as a batch). However, the post-scan confirmation option is not my optimal solution because a) it runs the scan twice which takes time and b) the program wants to handle them one after another which requires me to be present at the machine (and c) sometimes I have problems with overlapping windows that I cannot close for some reason and require me to kill the program).
My dream solution: The peaking runs are all stored and can be looked at under the "Run" option (which is great). I would love to have a button here that saves the new peak position automatically to the set-up if I want to switch from gaussian to maximum intensity or even user-defined (right now I am writing them down and have to type them in one by one).
Thanks.
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And a third one (hey, that is fun):
I really like the option that I can define background positions in a wavescan and the software automatically applies them to the next unknown acquisition.
It would be great to have the additional option to define the positions by straight typing them in as well. When I try to pick them graphically, I always end up with values like 5.03 instead of 5.00. Then I have to go into the set-up, change it there and have to plot it again (because I often print them out for user reference or class) which ends up really time consuming when I have a large number of elements and scans (I have a very varied user base here).
However, I understand that I may be alone with this "problem".
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1) I would prefer to have control on when the new calibration will happen (between two physical samples) rather after a certain time interval.
2) More importantly, depending on the analytical problem i am investigating, sometimes I would like to recalibrate some elements at different intervals than others. Currently it is either all or none in my understanding. But let's say I want to do calcium in olivine, I may want to run the calcium calibration more often (let's say every 30 analysis) while I only want to re-calibrate the Mg, Fe, Si standards at the beginning and at the end the entire run. With the current setting, depending on what mineral I am looking at, running all standards in short intervals would otherwise add significant time to the run.
Hi Anette,
As we discussed off line I will need to think how I can best implement this idea in the current software paradigm. Everything is possible, but some things are easier than others! ;)
In the meantime it's good to hear you have the HVAC in your lab working better. I feel so spoiled in my lab where the temperature is always 72.0 +/- 0.2 F!
Also hopefully a combination of the automatic "before" and "after" standardizations with the interval standardization will get you through this.
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Problem: When I am peaking the spectrometers on the assigned standards, I do not always agree with the results (because some peaking methods seem to work better for some elements but I want to run them as a batch). However, the post-scan confirmation option is not my optimal solution because a) it runs the scan twice which takes time and b) the program wants to handle them one after another which requires me to be present at the machine (and c) sometimes I have problems with overlapping windows that I cannot close for some reason and require me to kill the program).
My dream solution: The peaking runs are all stored and can be looked at under the "Run" option (which is great). I would love to have a button here that saves the new peak position automatically to the set-up if I want to switch from gaussian to maximum intensity or even user-defined (right now I am writing them down and have to type them in one by one).
Hi Anette,
The idea of a way to save the selected peak position with the mouse from the Run | Display, Export PHA, Peak Scans menu dialog is easy and I will implement that ASAP.
Frankly, it's been bugging me too!
john
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I really like the option that I can define background positions in a wavescan and the software automatically applies them to the next unknown acquisition.
It would be great to have the additional option to define the positions by straight typing them in as well. When I try to pick them graphically, I always end up with values like 5.03 instead of 5.00. Then I have to go into the set-up, change it there and have to plot it again (because I often print them out for user reference or class) which ends up really time consuming when I have a large number of elements and scans (I have a very varied user base here).
However, I understand that I may be alone with this "problem".
I guess you must really like "round numbers"!
Note the new feature here that allows you to see exactly what the background offset is that you are selecting:
https://probesoftware.com/smf/index.php?topic=42.msg253#msg253
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Problem: When I am peaking the spectrometers on the assigned standards, I do not always agree with the results (because some peaking methods seem to work better for some elements but I want to run them as a batch). However, the post-scan confirmation option is not my optimal solution because a) it runs the scan twice which takes time and b) the program wants to handle them one after another which requires me to be present at the machine (and c) sometimes I have problems with overlapping windows that I cannot close for some reason and require me to kill the program).
My dream solution: The peaking runs are all stored and can be looked at under the "Run" option (which is great). I would love to have a button here that saves the new peak position automatically to the set-up if I want to switch from gaussian to maximum intensity or even user-defined (right now I am writing them down and have to type them in one by one).
Your wish is granted... 8)
https://probesoftware.com/smf/index.php?topic=42.msg473#msg473
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John,
I have been using the 'Image Shift' mode on my SX100 to shift the beam position when in spot mode. This is a useful function to re-centre the e-beam with the optical crosshair when I am digitising positions using the optical image. I know for the SX there is a text reminder on the 'Analytical Conditions' window
"Image shift not available below 1095x"
but perhaps you could pop-up a message if a shift has been set but the mag is too low for the shift to be applied? Thanks!
Gareth
Hi Gareth,
Good idea!
I've implemented a warning along the lines you suggest for Cameca instruments like your SX100 because the Cameca image shift units are in microns, so the calculation is easy.
But for the JEOL I'll have to wait until Philippe Pinard gets back on his instrument so we can work out what units JEOL is using for image shift.
john
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I'd like to take a moment to start off the new year by thanking all my EPMA colleagues for all their help and support! Most of the features you see in our software are a direct result of scientific collaboration with these talented and dedicated individuals. The following About dialog acknowledges just a few of these amazing people (I can't fit them all in here, but I try- please let me know if I've left someone out that should be included!).
Thank-you again.
(https://probesoftware.com/smf/oldpics/i39.tinypic.com/rhk329.jpg)
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Would it be possible to devise a way where individual analyses can be under slightly different conditions, (i.e., beam current, counting time, TDI on/off, spot size) without having to set up a new sample under analyze? Maybe have the system record the conditions?
Thanks!
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Hi Ben,
You know, this is a good idea...
We already have a keyword called "UseCurrentConditionsAlways" in the software that Paul Carpenter asked for a long time ago, but I realized that we could modify its action slightly by having the software auto-detect a change in the instrument column conditions made by the operator, and automatically create a new sample if necessary, or simply append data to the current sample if there were no changes in conditions.
How's "self documenting" for you? 8)
I also pulled the keyword into the GUI, so you can change the Use Current Conditions Always flag "on the fly" as seen here:
(https://probesoftware.com/smf/oldpics/i41.tinypic.com/2yopwde.jpg)
If you want the software to not automatically set your beam size to zero when an acquisition is finished, you might want to uncheck the "Default Focus" checkbox in the Analytical Conditions dialog as seen here:
(https://probesoftware.com/smf/oldpics/i44.tinypic.com/2vd0e88.jpg)
Ready to download v. 10.2.3 now.
Edit 02/04/2014: By the way, right now the program checks for these parameters being different if the UseCurrentConditionsAlways flag is set, in order to decide if a new sample should be automatically started.
' Check conditions are different
If sample1(1).takeoff! <> sample2(1).takeoff! Then different = True
If sample1(1).kilovolts! <> sample2(1).kilovolts! Then different = True
If sample1(1).beamcurrent! <> sample2(1).beamcurrent! Then different = True
If sample1(1).beamsize! <> sample2(1).beamsize! Then different = True
If sample1(1).ColumnConditionMethod% <> sample2(1).ColumnConditionMethod% Then different = True
If sample1(1).ColumnConditionString$ <> sample2(1).ColumnConditionString$ Then different = True
If sample1(1).ImageShiftX! <> sample2(1).ImageShiftX! Then different = True
If sample1(1).ImageShiftY! <> sample2(1).ImageShiftY! Then different = True
If sample1(1).beammode% <> sample2(1).beammode% Then different = True
If sample1(1).magnificationanalytical! <> sample2(1).magnificationanalytical! Then different = True
More could be added...
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Hi there,
I would like to have proxy support with username password authentication integrated into PfE to use the update feature from within the software.
Cheers
Philipp
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Hi Philipp,
Yes, I have thought about this nice feature, but it's been a question of juggling *assigned* priorities. ;D
I already have this on my own "to do" list, so it will get implemented eventually. In the meantime perhaps you'd be interested in our DVD subscription service which provides you not only with a complete set of the latest PFE and PI updates, but also an up to date copy of the user forum, which allows the user to browse the user forum locally from their DVD drive.
Obviously this is only for those labs that cannot have Internet access- like yours. Here is the email Barb sent out a few weeks ago- perhaps you saw it?
Dear Probe Software Customer,
In this world of Internet connectivity we know that with freedom, come risks for your laboratory security and productivity.
At Probe Software we well aware of these important security issues and have considered options to allow timely updates of our software and access to our on-line user forum, for those customers that are concerned about Internet security and/or have limited access to the Internet.
At this time we are pleased to offer, through DVD based media, our latest software updates, containing bug fixes and new features, and the most current Probe Software user forum content, at a very reasonable subscription cost to your organization.
With your subscription you will receive a DVD containing our current software release and the complete content of our Probe Software user forum, which is locally linked to our software for context sensitive help and advice, at intervals you specify, at $200 per update DVD.
Typical subscriptions models are listed here for your consideration:
1/year $200/year
2/year $400/year
4/year $800/year
1/month $2400/year
Please contact Probe Software for more details.
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Hi John,
yes, I saw the email about the DVD. Good idea.
However, my lab does have internet access, just through a proxy server. I can browse the web fine. It would just be nice if PfE could also use this proxy server, so I could use the online features within PfE, llike the update button.
Cheers
Philipp
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Until I implement a proxy server client in PFE for your updates, I wonder if a VPN "tunnel" would work? Have you asked your IT guys about this possibility? They would only need to allow a "tunnel" to one of our download sites...
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I have been using the 'Image Shift' mode on my SX100 to shift the beam position when in spot mode. This is a useful function to re-centre the e-beam with the optical crosshair when I am digitising positions using the optical image. I know for the SX there is a text reminder on the 'Analytical Conditions' window
"Image shift not available below 1095x"
but perhaps you could pop-up a message if a shift has been set but the mag is too low for the shift to be applied? Thanks!
Gareth
A "too large image shift" error trap is now implemented for both Cameca and JEOL instruments starting in PFE v. 10.2.5.
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Hi John,
I have some new suggestions for what would be improvements for me. I pack them all in one post, so here it goes:
1. An option that a sound (*ding*) occurs when the automation is finished. My office is next doors and having a sound to alert me would be great.
2. The option that an email is send when automation is finished. I have a couple of people sitting in a different building across campus and with the winter as it is here, I am sure they would appreciate this option. Ideally this option would be checked/unchecked in the analysis options rather than acquisition options (or elsewhere), so that I don't need to create a new acquisition sample just for triggering this option.
3. An option in the analysis window that only acquired samples are shown (similar to the plot window). I often have to create new acquisition samples to change the conditions for different sample set-ups and it gets messy quickly.
4. This one may already exist and then I would be grateful to know how to do it - namely the option to update the sample set-ups. I am very often using the sample set-up option and usually have 3-4 different set-ups for a run that differ in their element setup but also the acquisition conditions. I quite often have to change some minor detail in the probe conditions like the beam diameter or the image shift and right now I am re-creating new acquisition samples for each set-up, read in the new conditions each time, re-save them as a new sample set-up and have to re-apply them to the position. (Or could I forgo all that by force current column conditions? Would that then be applied to digitized sample set-ups?).
Thank you!
Anette
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Ups, forgot one.
5. Love the re-standardization feature but I am missing one option. Usually, I standardize first, acquire a few unknowns to check that everything is ok (trust issues here with both machines and humans) and then send off the whole batch. I would like a re-standardization at the end and also after x hours. When choosing "Acquire standard samples (again)" and "Re-standard interval" it gives me an error message and wants me to add "Acquire standards" but I don't want to re-standardize at the beginning of the batch again, so I ask for either the error message to go away or adding that option. The biggest improvement would be IMO to have a re-standardize automation with the options "every x-hours" and "at the end". This would also improve the usability because I used to find the re-standardize option a bit ambiguous in wording.
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1. An option that a sound (*ding*) occurs when the automation is finished. My office is next doors and having a sound to alert me would be great.
Already done!
That is there are already numerous "dings" during acquisition, so it's when the "dings" stop, that you can listen for (might need to turn up your computer speaker volume).
But an even better solution for your request (and requested by John Fournelle many years ago), Probe for EPMA will also play a .wav file of any type when the automation is completed, simply by specifying the .wav file in the Probewin.ini file as follows:
[general]
UseWavFileAfterAutomationString="feelgood.wav" ; WAV file for automation completion
I've attached a few .wav file examples. For instance, I play James Brown "I Feel Good", while I think John Fournelle uses "Shave and a Haircut".
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2. The option that an email is send when automation is finished. I have a couple of people sitting in a different building across campus and with the winter as it is here, I am sure they would appreciate this option. Ideally this option would be checked/unchecked in the analysis options rather than acquisition options (or elsewhere), so that I don't need to create a new acquisition sample just for triggering this option.
Also already done!
Simply enter an email address and check this box here in the Acquisition Options dialog from the Acquire! window:
(https://probesoftware.com/smf/oldpics/i62.tinypic.com/2wlwrpg.jpg)
The cool thing about this feature is that it not only informs you if an error has occurred during the automation (e.g., blown filament), but it also sends you a progress report every 8 hours and also sends a final notice email when the automation is complete! 8)
Note that you can optionally set the default address in the Probewin.ini file, but the smtp server and other essentials must be specified in the probewin.ini file as follows:
[general]
SMTPServerAddress="smtp.uoregon.edu" ; email server address for error messages
SMTPAddressFrom="epmalab@uoregon.edu"
SMTPAddressTo="epmalab@uoregon.edu"
SMTPUsername="epmalab"
The application will prompt you for the password when required. Obviously you will need to enter your own smtp server information in your own Probewin.ini...
How's that sound?
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3. An option in the analysis window that only acquired samples are shown (similar to the plot window). I often have to create new acquisition samples to change the conditions for different sample set-ups and it gets messy quickly.
I'm not exactly sure what you mean. Do you mean an option so you only see samples with data (no asterisk)?
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4. This one may already exist and then I would be grateful to know how to do it - namely the option to update the sample set-ups. I am very often using the sample set-up option and usually have 3-4 different set-ups for a run that differ in their element setup but also the acquisition conditions. I quite often have to change some minor detail in the probe conditions like the beam diameter or the image shift and right now I am re-creating new acquisition samples for each set-up, read in the new conditions each time, re-save them as a new sample set-up and have to re-apply them to the position. (Or could I forgo all that by force current column conditions? Would that then be applied to digitized sample set-ups?).
Hi Anette,
There is an easier way! Just create an empty sample for each sample setup you want to use (do not acquire data to it).
So if the sample (setup) has no data, simply make the additional changes to that sample (setup) from the Analyze! window (Count Times, Analytical Conditions, Calculation Options, whatever) by selecting that sample (setup) and click the appropriate button for the sample changed desired and the Automate! window will automatically include those changes in the next automated acquisition.
Essentially it is best to think of a sample setup as simply a "pointer" to an empty sample which contains certain specific elements and acquisition and analysis options. If you make changes to the sample being "pointed to", the next acquisition using that "sample setup", automatically utilizes those changes in the next acquisition.
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5. Love the re-standardization feature but I am missing one option. Usually, I standardize first, acquire a few unknowns to check that everything is ok (trust issues here with both machines and humans) and then send off the whole batch. I would like a re-standardization at the end and also after x hours. When choosing "Acquire standard samples (again)" and "Re-standard interval" it gives me an error message and wants me to add "Acquire standards" but I don't want to re-standardize at the beginning of the batch again, so I ask for either the error message to go away or adding that option. The biggest improvement would be IMO to have a re-standardize automation with the options "every x-hours" and "at the end". This would also improve the usability because I used to find the re-standardize option a bit ambiguous in wording.
Yeah, I think I understand.
It sounds that you want to be able to acquire interval standardizations, but without having to acquire an initial set of standards also, correct?
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Hi John,
exactly. I often have already acquired the initial set of standards and would like to use the re-standardize function in the following run as well. Having the option to choose Re-standardize after x hours and at the end independent of the first standardization would be extremely helpful.
Edit by John: Ok, that shouldn't be too hard... I can probably do that this weekend. Did my responses to your other wishes (above) work?
That is, starting here:
http://probesoftware.com/smf/index.php?topic=71.msg1015#msg1015
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2. The option that an email is send when automation is finished. I have a couple of people sitting in a different building across campus and with the winter as it is here, I am sure they would appreciate this option. Ideally this option would be checked/unchecked in the analysis options rather than acquisition options (or elsewhere), so that I don't need to create a new acquisition sample just for triggering this option.
Also already done!
Simply enter an email address and check this box here in the Acquisition Options dialog from the Acquire! window:
(https://probesoftware.com/smf/oldpics/i62.tinypic.com/2wlwrpg.jpg)
The cool thing about this feature is that it not only informs you if an error has occurred during the automation (e.g., blown filament), but it also sends you a progress report every 8 hours and also sends a final notice email when the automation is complete! 8)
Note that you can optionally set the default address in the Probewin.ini file, but the smtp server and other essentials must be specified in the probewin.ini file as follows:
[general]
SMTPServerAddress="smtp.uoregon.edu" ; email server address for error messages
SMTPAddressFrom="epmalab@uoregon.edu"
SMTPAddressTo="epmalab@uoregon.edu"
SMTPUsername="epmalab"
The application will prompt you for the password when required. Obviously you will need to enter your own smtp server information in your own Probewin.ini...
How's that sound?
Excellent. I will definitely use that. However I would suggest then to modify the description to remove the word "error" as it is clearly so much more.
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Excellent. I will definitely use that. However I would suggest then to modify the description to remove the word "error" as it is clearly so much more.
Yes you are correct, I will fix that this weekend also. But just FYI you can get additional information on each control by "hovering" the mouse cursor over the control in question, for example see this:
(https://probesoftware.com/smf/oldpics/i57.tinypic.com/168h4dj.jpg)
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Yes, I use and like the mouse-hover- tips but in my version there is no additional mouse-hover information. Actually, the function is blanked out - 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.
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Yes, I use and like the mouse-hover- tips but in my version there is no additional mouse-hover information. Actually, the function is blanked out - 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.
Yes, I noticed that there was no info in the help file under Acquisition Options, but the info for specifying the SMTP settings are there in the configuration file pages.
http://probesoftware.com/download/PROBEWIN.pdf#page=41
Thanks for the "heads up", I will add some additional info this weekend.
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4. This one may already exist and then I would be grateful to know how to do it - namely the option to update the sample set-ups. I am very often using the sample set-up option and usually have 3-4 different set-ups for a run that differ in their element setup but also the acquisition conditions. I quite often have to change some minor detail in the probe conditions like the beam diameter or the image shift and right now I am re-creating new acquisition samples for each set-up, read in the new conditions each time, re-save them as a new sample set-up and have to re-apply them to the position. (Or could I forgo all that by force current column conditions? Would that then be applied to digitized sample set-ups?).
Hi Anette,
There is an easier way! Just create an empty sample for each sample setup you want to use (do not acquire data to it).
So if the sample (setup) has no data, simply make the additional changes to that sample (setup) from the Analyze! window (Count Times, Analytical Conditions, Calculation Options, whatever) by selecting that sample (setup) and click the appropriate button for the sample changed desired and the Automate! window will automatically include those changes in the next automated acquisition.
Essentially it is best to think of a sample setup as simply a "pointer" to an empty sample which contains certain specific elements and acquisition and analysis options. If you make changes to the sample being "pointed to", the next acquisition using that "sample setup", automatically utilizes those changes in the next acquisition.
I think this is a really important feature!!!! This deserves a paragraph in the Users Reference Guide.
So, what about Anette's wish number 3?
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3. An option in the analysis window that only acquired samples are shown (similar to the plot window). I often have to create new acquisition samples to change the conditions for different sample set-ups and it gets messy quickly.
I'm not exactly sure what you mean. Do you mean an option so you only see samples with data (no asterisk)?
I'm waiting for her to answer my question above... did I miss a response somewhere?
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I think this is a really important feature!!!! This deserves a paragraph in the Users Reference Guide.
It is documented! Here is how I found it:
1. I hit the F1 key in the main PFE window.
2. I clicked the Search tab in the Help file.
3. I entered "sample setup" and <enter>
4. The 4th item (Load Sample Setup) listed had this (I didn't look at the others):
(https://probesoftware.com/smf/oldpics/i59.tinypic.com/15p49bs.jpg)
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3. An option in the analysis window that only acquired samples are shown (similar to the plot window). I often have to create new acquisition samples to change the conditions for different sample set-ups and it gets messy quickly.
I'm not exactly sure what you mean. Do you mean an option so you only see samples with data (no asterisk)?
I'm waiting for her to answer my question above... did I miss a response somewhere?
No, I missed your answer, sorry. Yes, that is exactly what I meant: only samples without asterisk.
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John-
I would like to see a way of setting up maps in probe image using chain acquisition in the automate window. Is this in the works?
Dan
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I would like to see a way of setting up maps in probe image using chain acquisition in the automate window. Is this in the works?
Hi Dan,
It is a good idea and it is "in the works" as you said. In fact here's the checkbox that you will use to browse to a specific .PrbAcq Probe Image acquisition file and this will get run after the point analyses and standards have finished.
(https://probesoftware.com/smf/oldpics/i60.tinypic.com/33ju7fd.jpg)
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I think this is a really important feature!!!! This deserves a paragraph in the Users Reference Guide.
It is documented! Here is how I found it:
1. I hit the F1 key in the main PFE window.
2. I clicked the Search tab in the Help file.
3. I entered "sample setup" and <enter>
4. The 4th item (Load Sample Setup) listed had this (I didn't look at the others):
Ok, agreed. It is there. Is it also in the PDF? Anyway, I did not know about it and I find it a really useful thing to know.
Thanks
Philipp
Edit by John: no worries, it is not always easy to find everything but it is usually documented.
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Basically, I have now run into a couple of situations where, after acquiring a bunch of data with off-peak backgrounds, there have a been a few elements where an MAN background would likely have been more suitable, but for several other elements, the off-peak backgrounds were fine. Possibly showing my ignorance of how the MAN backgrounds actually work, but it would be hugely helpful to be able to apply the MAN correction to just a few select off-peak elements in post-processing rather than the whole set.
Hi Owen,
Sorry, but not at this time. Other than first specifying which elements are off-peak and which are MAN (or just making all off-peaks corrected using MAN as you described above), your choices for post processing are limited to one of the many off-peak options as seen here:
(https://probesoftware.com/smf/oldpics/i58.tinypic.com/119nwp0.jpg)
I assume by "a few elements where an MAN background would likely have been more suitable" that you mean that there was an unexpected off-peak interference?
Of course one may find an unexpected off-peak background interference occasionally, but generally an initial spectrometer wavescan (after all elements have been peaked properly), run on a suitable sample, will reveal most off-peak interferences as discussed in this post:
http://probesoftware.com/smf/index.php?topic=30.msg271#msg271
It is nice that PFE allows one to automatically acquire a wavescan for all element "regions of interest" with a single acquisition even if one has 15 or 20 or more elements in the run.
If you still get an off-peak interference you can try using the "Low Only" or "High Only" off-peak backgrounds, which essentially ignores the offending off-peak intensity. If the slope is large and a single off-peak won't suffice, then try either the "Slope Low" or "Slope High" off peak background options.
Ideally perform these background fit evaluations using the wavescan sample as described here:
http://probesoftware.com/smf/index.php?topic=68.msg246#msg246
Another possibility that you might find very powerful is the "multi-point" background which allows the application to acquire multiple background mesurements on each side of the peak as described here:
http://probesoftware.com/smf/index.php?topic=56.0
Note that the multi-point off-peaks can also be treated as normal off-peaks in post processing...
2) A very quick one - could ZAF factors be added to the output options in Plot?
Easier would be to use the Output | User Specified Custom Format Output menu as seen here:
(https://probesoftware.com/smf/oldpics/i58.tinypic.com/dtnbk.jpg)
The nice thing about this "user specified format output" is that the output options you select are remembered the next time the run is re-opened, so you don't have to remember yourself! 8)
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...the reason I asked about having them in plot is that having it would be a nice teaching function, i.e. I can have students acquire some test data, and then can quickly (and graphically) show them how the ZAF factors change for a given element in samples with different matrices. But if this is a pain to code, no problem. Thanks!
Everything is "a pain" when you're the one doing the programming! ;) But seriously, if you are looking for teaching resources for matrix corrections, you might start with this post:
http://probesoftware.com/smf/index.php?topic=126.msg1124#msg1124
I will also try to post how I use CalcZAF to teach about matrix corrections as soon as I get a chance... ok, here's the link:
http://probesoftware.com/smf/index.php?topic=239.msg1126#msg1126
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The Penepma derived matrix correction factors stored in the MATRIX.MDB file have had their access time significantly improved by implementing a new index in the matrix database.
These Monte-Carlo derived k-ratios may be utilized for high speed on-line matrix corrections or model testing and are accessed from the Analytical | ZAF, Phi-Rho-Z, Alpha Factor and Calibration Curve Selections menu as seen here:
(https://probesoftware.com/smf/oldpics/i59.tinypic.com/34so12o.jpg)
and described in more detail here:
http://probesoftware.com/smf/index.php?topic=47.0
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Hi John,
small things. Could you maybe add the "relative line numbers" option to the "save user specified format output", please. It is the only thing I am missing there but it would be very useful.
I also wondered if the "report" output in the Analysis window is customizable? Ideally, I would like to have our Department name in there and maybe a grant number? Maybe also an auto acknowledgement? So I wondered if there is a text file that is read out or if there could be something like that.
Thanks.
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Could you maybe add the "relative line numbers" option to the "save user specified format output", please. It is the only thing I am missing there but it would be very useful.
Excellent idea. I will add that. In the meantime you can utilize the "Stage Relative Distance in Microns" output as shown here:
(https://probesoftware.com/smf/oldpics/i60.tinypic.com/mj5s85.jpg)
or even the Relative Line Numbers output from the Plot! window:
(https://probesoftware.com/smf/oldpics/i57.tinypic.com/1585fev.jpg)
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I also wondered if the "report" output in the Analysis window is customizable? Ideally, I would like to have our Department name in there and maybe a grant number? Maybe also an auto acknowledgement? So I wondered if there is a text file that is read out or if there could be something like that.
Your wish is granted!
Simply edit (or add if the keyword is missing) this keyword to the [general] section of the Probewin.ini file:
InstrumentAcknowledgementString="insert your acknowledgement string here"
This string will appear in your Report text at the end as seen here:
St 396 Set 1 chromite (UC # 523-9)
TakeOff = 40.0 KiloVolt = 15.0 Beam Current = 20.0 Beam Size = 5
(Magnification (analytical) = 40000), Beam Mode = Analog Spot
(Magnification (default) = 0, Magnification (imaging) = 800)
Image Shift (X,Y): .00, .00
Compositional analyses were acquired on an electron microprobe equipped with 5 tunable wavelength dispersive spectrometers. Operating conditions were 40 degrees takeoff angle, and a beam energy of 15 keV.
The beam current was 20 nA, and the beam diameter was 5 microns.
Elements were acquired using analyzing crystals LIF for Fe ka, Cr ka, Ti ka, Mn ka, PET for Ca ka, and TAP for Si ka, Mg ka, Al ka.
The standards were MgO synthetic for Mg ka, Al2O3 synthetic for Al ka, SiO2 synthetic for Si ka, TiO2 synthetic for Ti ka, MnO synthetic for Mn ka, Diopside (Chesterman) for Ca ka, Magnetite U.C. #3380 for Fe ka, and Chromite (UC # 523-9) for Cr ka.
The counting time was 20 seconds for all elements. Unknown and standard intensities were corrected for deadtime. Interference corrections were applied to Fe for interference by Mn, and to Mn for interference by Cr.
See J.J. Donovan, D.A. Snyder and M.L. Rivers, An Improved Interference Correction for Trace Element Analysis in Microbeam Analyis, 2: 23-28, 1993
Results are the average of 5 points and detection limits ranged from .012 weight percent for Mg ka to .013 weight percent for Al ka to .018 weight percent for Ca ka to .049 weight percent for Mn ka to .060 weight percent for Cr ka.
Analytical sensitivity (at the 99% confidence level) ranged from .518 percent relative for Al ka to .594 percent relative for Mg ka to .836 percent relative for Fe ka to 17.602 percent relative for Mn ka to 74.196 percent relative for Ca ka.
The matrix correction method was ZAF or Phi-Rho-Z Calculations and the mass absorption coefficients dataset was LINEMU Henke (LBL, 1985) < 10KeV / CITZMU > 10KeV. The ZAF or Phi-Rho-Z algorithm utilized was Armstrong/Love Scott (default).
See J. T. Armstrong, Quantitative analysis of silicates and oxide minerals: Comparison of Monte-Carlo, ZAF and Phi-Rho-Z procedures, Microbeam Analysis--1988, p 239-246
This instrument was generously funded by NSF EAR-0345908 and the Murdoch Foundation.
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Could you maybe add the "relative line numbers" option to the "save user specified format output", please. It is the only thing I am missing there but it would be very useful.
Your wish is granted!
(https://probesoftware.com/smf/oldpics/i59.tinypic.com/2m5ezc9.jpg)
I also reformatted the dialog and tried to make it more readable...
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:-* Thank you!
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Request:
Add an option to acquire the EDS spectrum as long as the WDS acquisition is running.
Rationale:
It is always better to have as many counts as possible in the EDS spectrum. If the EDS acquisition ends before the one of WDS we are losing counts.
Implementation:
One way to implement would be to acquire a series of 1-sec EDS spectra and sum them at the end.
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Add an option to acquire the EDS spectrum as long as the WDS acquisition is running.
This is a good idea, but I'll have to think about how one might do this. Currently these are asynchronous processes and I just wait for them to complete individually.
The other thing one might do is to set the EDS acquisition time to the estimated acquisition time of the WDS acquisition. Yes, the estimated WDS acquisition time is only accurate to 5% or so, but the real culprit in my mind is the deadtime. Currently I specify "live time" (or as Bruker calls it, "life time" [sic])- that is, the actual integration time (without deadtime) for the EDS acquisition. So depending on the observed deadtime for the sample in question, the acquisition time could take 30 to 60% or more longer than the live time.
You also mentioned in an email that you'd like to control:
- get/set maximum energy (effectively changes the channel energy width)
- get/set maximum pulse throughput (changes the processing time)
from Probe for EPMA. Question: currently the EDS acquisition options are "global", That is, they can be changed manually by the user, but they affect all subsequent acquisitions until they are again changed. Would it be OK to have the max energy and pulse processing time also be globals or did you need to have them specified for each automated sample differently?
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Two more requests:
(1) the ability to change the order that positions are in (just like you can change the order that samples are analyzed in, I would like to be able to change the order of the individual analysis positions).
(2) when a collected unknown sample has been "deleted" from the run, I don't want the analysis spots to still show on the image collected... I think they do...
Thanks John!
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(1) the ability to change the order that positions are in (just like you can change the order that samples are analyzed in, I would like to be able to change the order of the individual analysis positions).
Ok, it is possible. I just have to think of a nice and intuitive way to do it. In the meantime, for the purposes of running every other point in a traverse, simply make a copy of the position sample (see the Duplicate As... buttons in the Position window), and delete all the odd numbered lines from one position sample and all the even numbered lines from the other (using a right mouse click on the position grid from the Automate! window), and that will do what you want for the quartz traverses.
(2) when a collected unknown sample has been "deleted" from the run, I don't want the analysis spots to still show on the image collected... I think they do...
That is easy- see this control in the Image Display dialog:
(https://probesoftware.com/smf/oldpics/i57.tinypic.com/iliwjp.jpg)
Now, without the deleted points:
(https://probesoftware.com/smf/oldpics/i58.tinypic.com/350kmtf.jpg)
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More of a question than a request, but in Automate, is there a way to have PFE not blank the beam when moving from one position to the next?
May I ask why you want to not blank the beam between position samples?
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One reason I can think of is to do polygon mapping using point analysis. If you set the count time to a low time, around 1 second per point, and aquire lots of points then you could have a reasonable map avoiding specific areas. However, the major overhead in this analysis is the beam blank between points, it takes about 3 seconds. This makes it a little impractical for high speed but fine if you use a longer dwell time.
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One reason I can think of is to do polygon mapping using point analysis. If you set the count time to a low time, around 1 second per point, and aquire lots of points then you could have a reasonable map avoiding specific areas. However, the major overhead in this analysis is the beam blank between points, it takes about 3 seconds. This makes it a little impractical for high speed but fine if you use a longer dwell time.
Something isn't right. The software is already designed to not insert the cup when moving between points in a single position sample... oh, maybe you are just seeing the beam current measurement at the end of each analysis? You will need this beam current measurement for the beam drift correction.
In fact, there is an option in the Digitize window to *force* the faraday cup to be inserted for moving between points in a single sample, by incrementing the "grain number" as seen here:
(https://probesoftware.com/smf/oldpics/i57.tinypic.com/2cofz3l.jpg)
So because the "settling time" for the JEOL picoammeter is quite long (and seems to be getting longer with each new probe model!), we have some additional overhead if we want to have our analyses beam drift corrected.
Of course, if the probe is very stable or beam drift isn't a problem then you could disable the beam measurement during sample acquisition by unchecking this box in the Acquire! | Acquisition Options dialog:
(https://probesoftware.com/smf/oldpics/i60.tinypic.com/23s6x02.jpg)
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Actually hadn't thought about that one, but it's a very neat idea. I was more thinking about doing a Confirm a long list of samples, or using Automate for imaging. For example, we do a fair amount of zircon CL imaging, where we import the coordinates into Automate from the ICP laser stage. Automate/Fiducials makes loading the positions and moving around very easy, but 3-4 seconds of PCD insertion/removal for every motion adds up when imaging 1000 zircons (not to mention the extra 1000 mouse clicks, if you're taking the pictures manually).
Again, was more just wondering if this was possible - if it isn't, then it isn't.
Considering that the image acquisition takes a lot more than 3-4 seconds, I don't see your point.
As I said, the cup insertion is for measuring the beam during analyses. I'm pretty sure I modified the code so that the faraday wait in time is *not* applied when just moving the stage, only when measuring the beam current.
Also you might check the acquire images option in Acquisition Options, that way your images are acquired automatically during the unknown acquisition as seen here:
(https://probesoftware.com/smf/oldpics/i58.tinypic.com/4smrty.jpg)
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Hi,
Got already plans for the weekend? I've got something new. I wish that I could apply sample set-ups to analyzed samples. The idea is being able to assign a package set of standard assignments, calculation options, maybe TDI correction on/off - all the various off-line processing options - with one click to multiple samples. That would be a big time saver and then I also don't need to worry that I missed/mixed up any change.
Thanks.
Anette
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Got already plans for the weekend? I've got something new. I wish that I could apply sample set-ups to analyzed samples. The idea is being able to assign a package set of standard assignments, calculation options, maybe TDI correction on/off - all the various off-line processing options - with one click to multiple samples. That would be a big time saver and then I also don't need to worry that I missed/mixed up any change.
Ok, I'll bite! What do you mean? Maybe give an example of what you are trying to do.
If you want to assign standard assignments, TDI, etc. or whatever to a bunch of samples, just select the bunch of samples in the Analyze! window sample list and click the appropriate button (Standard Assignments, Elements/cations, etc.) and the program will assign the specified parameters to all selected samples. Is that what you mean?
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Ok, I'll bite! What do you mean? Maybe give an example of what you are trying to do.
If you want to assign standard assignments, TDI, etc. or whatever to a bunch of samples, just select the bunch of samples in the Analyze! window sample list and click the appropriate button (Standard Assignments, Elements/cations, etc.) and the program will assign the specified parameters to all selected samples. Is that what you mean?
So far I have done it this way (with selecting multiple samples etc) and then changing each property one by one. But right now I am processing a massive amount of samples (big project / + testing new standard block) and would like to get this more efficient and stream lined.
My complaints for a big throughput: it gets tedious to change the standards individually (and loading the available standards gets slow if you have many, many standards calibrated) and can get up to many, many clicks.
My ideal solution: all the information that I want to assign is stored in a sample set-up anyway. I just would like to put together a "master" sample(s) with specific standard assignments, calculation options, save it as a set-up and then be able to assign it to samples in the analysis window just like for the positions.
Let's say for example, I ran various silicates (ol, plag, cpx etc) with the same set-up but then want to have albite as Si-standard for plag, forsterite for olivine etc, TDI correction for the albite but not for the olivine, formula on the basis of 8 O for plag but 4 for olivine and so on. Of course I could just specify that ahead of time with different set-ups before I run it but 1) I am not always that organized, 2) sometimes one mineral turns out to be another. If you have many analyses the clicking around gets old real fast.
Further benefit would be that by assigning a set-up I would minimize the possibility that I forgot to change one of the variables for some of the samples.
Does this make it more clear?
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Yes, but it seems like a lot of work to essentially remove 1 mouse click (using both the Standard Assignments *and* Elements/Cations dialogs instead of a single dialog!)! I think you can do everything you want still with the existing code.
Simply make a sample and do not add data to it (that way you can always go back and make further changes to the sample setup since it has no data). Name it olivine setup or something, then:
1. Once you have the std assignments, TDI assignments, blank assignments, etc. specified, just use the Standard Assignments button to assign those settings to all samples.
2. Once you have the backgrounds, etc specified, just use the Elements/Cations button to assign those settings to all selected samples.
Here's a useful hint however. The last selected sample is the one used as a temple when multiple samples are selected. So when you want to assign everything, just make a new sample using that previously specified sample. Then select all the samples you want to assign that to and those settings will be visible in the dialog and applied to all selected samples.
Or you could also just acquire all your samples, then make a new sample with all the options specified as above, then select all samples you want to assign these to and again use the Standard Assignments and/or Calculation Options dialogs as before (no need to bring the sample setup forward since it is already the last sample).
How does that sound?
john
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John,
That sounds excellent and I never consciously noticed that it is just the last sample set-up. This is a very, very useful hint and will achieve exactly what I need and will save me much time.
Dankesch
Edit by John: Maybe this hint is a good candidate for this topic:
http://probesoftware.com/smf/index.php?topic=8.0
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Hopefully a quick one here - previously, when doing an output (either as a User Specified output or one of the custom output formats), a dialog box would come up giving us the option to sort the elements in traditional geologic order in the output file. This option seems to have disappeared from recent versions (10.3.9, I think) - you can sort them in Analyze, but the dialog no longer comes up when doing an output.
Is there any way this option could come back?
I think you just have to have Display As Oxides (from Analyze! Calculation Options dialog) turned on for this.
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I think you just have to have Display As Oxides (from Analyze! Calculation Options dialog) turned on for this.
OK, I see - if the last sample in the file doesn't have it turned on, it kills it for all the others. Good to know. Thanks!
Yes. The last selected sample has priority for updating all calculation options (when more than one sample is selected), as discussed here:
http://probesoftware.com/smf/index.php?topic=71.msg1418#msg1418
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Hi,
I would wish that the report-function would include more of the vital data, more specifically the data table. Currently it gives Element/Line, Crystal, OnPeak Time, OffPeak Time, Standard, Analytical Error(rel%), Detection Limit(99%).
In addition, I would wish for:
- Spectrometer channel
- Peak position
- Background positions
- Background correction type
- Baseline
- Window
- Gain
- Bias
- Diff/Int
Also the
- accelerating voltage
- beam current
- beam diameter
- spot/scan
- Image shift values
Overall, simply what was set under "Elements/Cations", "Count times" and "Analytical conditions"
Both the JEOL and the Cameca software have a one click option that gives me the set-up. Having such an extended report option in PFE would be incredibly useful. If this already exists and I have again missed it, I am eager to learn where it can be found.
Thank you!
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Both the JEOL and the Cameca software have a one click option that gives me the set-up...
Oh, those are "fighting words"! ;)
Seriously, it would be easy to add, but you know you do get the complete sample setup displayed to the log window when you click the Data button as seen here:
St 336 Set 2 Nepheline (partial anal.)
(Magnification (analytical) = 20000), Beam Mode = Analog Spot
(Magnification (default) = 2524, Magnification (imaging) = 736)
Image Shift (X,Y): -2.00, 3.00
Analysis by ISE Carmichael (Na, K)
Ca = 750 PPM (EPMA by JJD)
Number of Data Lines: 5 Number of 'Good' Data Lines: 5
First/Last Date-Time: 11/26/2013 03:05:16 PM to 11/26/2013 03:15:14 PM
Stage (or Beam Deflection) Coordinate Positions:
X Y Z X Y Z
121G -4470.016 -3138.017 -208.9990 122G -4466.029 -3138.014 -208.9996
123G -4462.015 -3138.019 -208.9998 124G -4458.029 -3138.006 -208.9998
125G -4454.005 -3138.017 -208.9995
Sample Coordinates Referenced to Fiducial Set 2 C:\UserData\StandardPOSData\alkali-glass_pos3.pos
On and Off Peak Positions:
ELEM: na ka si ka k ka al ka mg ka fe ka ca ka s ka cl ka ti ka p ka f ka
ONPEAK 46267.0 81466.0 42614.0 32507.0 38401.0 48102.0 38423.0 61432.0 53911.0 68290.0 24051.0 71137.0
OFFSET 95.8477 -11.523 162.785 -41.074 98.1523 13.3867 -23.414 -16.410 139.859 1.39844 -79.539 177.828
HIPEAK ---- ---- 43422.5 ---- ---- ---- ---- 61934.1 54623.5 68781.5 25462.6 72529.0
LOPEAK ---- ---- 41935.1 ---- ---- ---- ---- 60684.5 53300.2 67865.3 23294.2 69800.0
HI-OFF ---- ---- 808.500 ---- ---- ---- ---- 502.102 712.500 491.500 1411.60 1392.00
LO-OFF ---- ---- -678.90 ---- ---- ---- ---- -747.50 -610.80 -424.70 -756.80 -1337.0
PHA Parameters:
ELEM: na ka si ka k ka al ka mg ka fe ka ca ka s ka cl ka ti ka p ka f ka
DEAD: 3.00 3.25 3.31 2.90 3.00 2.97 3.25 3.25 3.31 2.97 2.90 3.00
BASE: .56 .50 .56 .56 .56 .56 .56 .50 .56 .56 .56 .56
WINDOW 4.00 4.00 4.00 4.00 4.00 4.00 4.00 4.00 4.00 4.00 4.00 4.00
MODE: -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1
GAIN: 2321. 960. 1181. 2241. 2321. 600. 700. 960. 992. 700. 1471. 2321.
BIAS: 1300. 1330. 1850. 1293. 1300. 1840. 1330. 1330. 1850. 1840. 1293. 1320.
Last (Current) On and Off Peak Count Times:
ELEM: na ka si ka k ka al ka mg ka fe ka ca ka s ka cl ka ti ka p ka f ka
BGD: MAN MAN OFF MAN MAN MAN MAN OFF OFF OFF OFF OFF
BGDS: MAN MAN LIN MAN MAN MAN MAN LIN LIN LIN EXP LIN
SPEC: 1 2 3 4 1 5 2 2 3 5 4 1
CRYST: TAP LPET LPET TAP TAP LIF LPET LPET LPET LIF TAP TAP
ORDER: 1 1 1 1 2 1 2 3 2 2 2 3
ONTIM: 30.00 30.00 20.00 40.00 30.00 40.00 20.00 20.00 20.00 20.00 20.00 20.00
HITIM: ---- ---- 10.00 ---- ---- ---- ---- 5.00 5.00 5.00 5.00 10.00
LOTIM: ---- ---- 10.00 ---- ---- ---- ---- 5.00 5.00 5.00 5.00 10.00
Miscellaneous Sample Acquisition/Calculation Parameters:
KILO: 15.00 15.00 15.00 15.00 15.00 15.00 15.00 15.00 15.00 15.00 15.00 15.00
ENERGY 1.041 1.740 3.313 1.487 1.254 6.400 3.691 2.308 2.622 4.509 2.013 .677
EDGE: 1.073 1.839 3.608 1.560 1.305 7.112 4.039 2.472 2.823 4.967 2.146 .687
Eo/Ec: 13.98 8.16 4.16 9.62 11.49 2.11 3.71 6.07 5.31 3.02 6.99 21.83
STDS: 336 162 374 160 162 162 162 730 285 22 285 284
Combined Analytical Condition Arrays:
ELEM: na ka si ka k ka al ka mg ka fe ka ca ka s ka cl ka ti ka p ka f ka
TAKE: 40.0 40.0 40.0 40.0 40.0 40.0 40.0 40.0 40.0 40.0 40.0 40.0
KILO: 15.0 15.0 15.0 15.0 15.0 15.0 15.0 15.0 15.0 15.0 15.0 15.0
CURR: 10.0 10.0 10.0 10.0 10.0 10.0 10.0 50.0 50.0 50.0 50.0 50.0
SIZE: 10.0 10.0 10.0 10.0 10.0 10.0 10.0 10.0 10.0 10.0 10.0 10.0
But, note that you need to have this box checked to get this output as seen here from the Analysis Options from the Analytical menu:
(https://probesoftware.com/smf/oldpics/i58.tinypic.com/254yazs.jpg)
But I will add your requested items to the Analyze! Report output so that it will be tab delimited for import into Excel or Word...
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In addition, I would wish for:
- Spectrometer channel
- Peak position
- Background positions
- Background correction type
- Baseline
- Window
- Gain
- Bias
- Diff/Int
Also the
- accelerating voltage
- beam current
- beam diameter
- spot/scan
- Image shift values
Thank you!
Hi Anette,
Your wish is granted...
New Report Excel output includes all of the above and a little more- with one mouse click!
See attached screenshot.
john
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In addition, I would wish for:
- Spectrometer channel
- Peak position
- Background positions
- Background correction type
- Baseline
- Window
- Gain
- Bias
- Diff/Int
Also the
- accelerating voltage
- beam current
- beam diameter
- spot/scan
- Image shift values
Thank you!
Hi Anette,
Your wish is granted...
New Report Excel output includes all of the above and a little more- with one mouse click!
See attached screenshot.
john
Awesome! That is a fantastic addition. Thanks.
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Hi John,
It's me again ;)
I just did a lot of glass analyses with a PhD student where the TDI function has been a god send.
I also really, really appreciate the option under "run" to assess all the TDI data visually in a quick and efficient way. The only thing missing is to be able to select and display multiple lines(rows) and their TDI-best fit in this dialogue. Is this possible?
Thanks,
Anette
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I also really, really appreciate the option under "run" to assess all the TDI data visually in a quick and efficient way. The only thing missing is to be able to select and display multiple lines(rows) and their TDI-best fit in this dialogue. Is this possible?
Of course!
Go to the Standard Assignments button in Analyze! and then click on the element row, then click the Display TDI Fit button to see all the lines in your sample. It should look something like this:
http://probesoftware.com/smf/index.php?topic=11.msg1345#msg1345
Don't forget the TDI output format from the Output menu!
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Of course! Thanks for reminding me.
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First, I don't typically use Gaussian peaking, but I noticed that the brown line that displays the fit and the light blue line that displays FWHM (I think?) are in different places when in the Peak/ROM/PHA Scan Acquisition window and plots displayed via Run --> Display Peak Scans. They seem to show the same peak positions/fit parameters/etc., so the procedure appears to be working, it just seemed odd that the displayed fits were different. Screenshots attached - does this actually mean something, or am I just being paranoid?
Actually you are being very observant!
The difference is due to the fact that the actual peak center is based on smoothed intensity data, but the dialog displays the unsmoothed data by default (probably should change that!), so if you want to see the smoothed data click the Smooth checkbox and then the peak positions should line up .
Second, this is a really nit-picky one, but in the corresponding dialog window under for loading a different file setup (Acquire --> New Sample --> Load File Setup), there is a box in the lower right corner with the list of elements/crystals/channels/peak positions in that selected file setup, with a slider bar that scrolls up and down so you can see the whole list. However, when trying to load previously-saved sample setup (i.e. Acquire --> New Sample --> Load Sample Setup), the corresponding slider bar is inactive/greyed out (circled in red on attached screenshot). Is there any way this could scroll up and down so I could see the full list? It's a life-saver if you have my sieve-like brain and can't remember which sample setup had what in it.
Yeah I agree, it is pretty nit-picky!
The reason it is disabled is to prevent one from editing another file accidentally. I might be able to find a work around for you...
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Hi John
I have a small wish that I don't think has been mentioned yet, and it is regarding adding an element to a run that has a multi-point background via the "Load Element Setups" button. If you add it to your run and decide to change the spectrometer that it is going to be run on, it wipes all the MP background positions and defaults to analysing it via 2pt linear. Now I understand the reasoning behind this, but for example sometimes I am moving it from a LPET to another LPET and I know that any slight difference in potential interfering peak positions from one crystal to another is going to be inconsequential on the background positions. At the moment I am manually writing the MP background positions down, changing the crystal number, then manually readding the background positions. Not sure if its possible but it would be great if it kept them when switching crystals...
Cheers
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Hi John
I have a small wish that I don't think has been mentioned yet, and it is regarding adding an element to a run that has a multi-point background via the "Load Element Setups" button. If you add it to your run and decide to change the spectrometer that it is going to be run on, it wipes all the MP background positions and defaults to analysing it via 2pt linear. Now I understand the reasoning behind this, but for example sometimes I am moving it from a LPET to another LPET and I know that any slight difference in potential interfering peak positions from one crystal to another is going to be inconsequential on the background positions. At the moment I am manually writing the MP background positions down, changing the crystal number, then manually readding the background positions. Not sure if its possible but it would be great if it kept them when switching crystals...
Well, I have to agree you have a point here, unless the peak positions differ by too much (as do a couple of my crystals), it makes sense to allow this.
But I need to think of a clever way to do it.
By the way, they are not visible, but the multi-point background positions and other parameters are stored in the element setup database (SETUP.MDB) so once they are stored, they can be easily recalled into a new run one element at a time...
(https://probesoftware.com/smf/oldpics/i57.tinypic.com/2u5yn15.jpg)
But also, the easiest way to automatically store all your element setups and standard intensities for general re-use (you can always load a complete file setup obviously too), is by using this handy Save Setups button as seen here:
(https://probesoftware.com/smf/oldpics/i62.tinypic.com/dyr43a.jpg)
If you click this button, the program will search the standard assignments for each element and save the element setup and standard intensities, including all MAN and interference standard intensities with one click! 8)
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Hi John
Many thanks, it would be great if its possible to pull them across. With regards to the Save Setups button, yes I am definitely already using that, a very hand tool.
Cheers
Edit by John: Nice word, "across", isn't it? You almost make it sound easy! ;)
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New request: add a light on/off switch for the verify fiducial marks, thanks!
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New request: add a light on/off switch for the verify fiducial marks, thanks!
Your wish is granted!
(https://probesoftware.com/smf/oldpics/i61.tinypic.com/9johnd.jpg)
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Would it be possible to display standard names, rather than numbers? Can this be implemented for the stage view and for data plot labels?
Technical note: I have tried modifying the standard database.mdb , and exporting and importing a modified database.dat. No success. I noticed the POS data [StandardPOSFileDirectory="C:\UserData\StandardPOSData"] which has name information, but there are very few objects in this folder. Does the documentation suggest that this folder is vestigal for newer operating systems?
Thanks for your consideration,
Jared
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Would it be possible to display standard names, rather than numbers? Can this be implemented for the stage view and for data plot labels?
Yes, of course. So you mean the StageMap window? And the Plot! graph data labels? If so the graph data labels is easy, but the StageMap window will get very crowded. Note that if you resize the StageMap window smaller, eventually even the standard numbers will disappear, so I guess I could make it so if the StageMap is resized large enough I could add the standard names too... or maybe just a mouse hover that causes the label to popup?
Note that in some places (e.g., standard assignments) just hover the mouse over the form and the standard names will pop up.
Technical note: I have tried modifying the standard database.mdb , and exporting and importing a modified database.dat. No success. I noticed the POS data [StandardPOSFileDirectory="C:\UserData\StandardPOSData"] which has name information, but there are very few objects in this folder. Does the documentation suggest that this folder is vestigal for newer operating systems?
Hi Jared,
These are essentially unrelated items.
The standard database can be modified from the Standard | Modify menu. And yes, you can export, edit the standard.dat file and import it back in, but you'll want to clear out the old standards first. A little dangerous. But you can import just one (or more) standard composition(s) to the existing standard.mdb file using this menu if it is in the proper format.
The POS data are for the *.POS standard position files. PFE is different in that the standard compositions are stored in the standard.mdb file (or other .MDB file), but the standard position data can be stored in the .POS files in text. These can be imported into the position database (position.mdb), but I think what you really need is just a couple of days of training from one of our most excellent instrument specialists!
I'm sure I didn't answer your questions so please let us know what specifically you are asking for.
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Thanks for the info, John.
It is the first suggestion that I wish: Plot! graph data labels and StageMap data labels based on standard names rather than standard numbers.
To solve the crowding issue, I would use abbreviated names like "hbl kaka" and keep the full name (e.g. Hornblende (Kakanui) USNM 143965) in the description field. This would really help us facilitate the translation from CAMECA's Peaksight where we have been using these abbreviated names for a long time.
Best,
Jared
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It is the first suggestion that I wish: Plot! graph data labels and StageMap data labels based on standard names rather than standard numbers.
To solve the crowding issue, I would use abbreviated names like "hbl kaka" and keep the full name (e.g. Hornblende (Kakanui) USNM 143965) in the description field. This would really help us facilitate the translation from CAMECA's Peaksight where we have been using these abbreviated names for a long time.
Ok, I added the standard names to the StageMap but only when it is at 150% original size. Note that as it is resized smaller, first the standard names disappear and then the standard numbers.
(https://probesoftware.com/smf/oldpics/i62.tinypic.com/fy022w.jpg)
Here is the large size showing standard names:
(https://probesoftware.com/smf/oldpics/i58.tinypic.com/25r13lz.jpg)
I did not add an option for standard names in the Plot! window as that only displays line numbers, so not sure what you mean... did you mean the Plot button in the Automate! window?
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Hi John,
We're using a petrographical light microscope with a motorised stage to pre-program analysis points for our SX100, mainly polished thin sections (on 3x1" glass slides) of rock samples. The control software is called Digimax and made by Microbeam Services, an Australian company. It uses 2 reference positions for X and Y and calculates the Z plane from 3 points from the sample list. We use TEM grids which we stick on the samples as reference markers.
We have an conversion utility for PeakSight, but it is quite convoluted to import the coordinates in there and then add the points in PFE again point by point. As PFE already has a powerful fiducial coordinate import capability it would be great if we could import the Digimax coordinate files (ASCII text files with .DCD extension) directly into PFE. Other facilities have the Digimax system as well so it might be useful for other people as well.
Below are the first 10 lines from an example .DCD file:
0,0,0,none,No name-1,P1,1,1,1,
20894,33523,0,none,No name-2,P2,1,1,2,
21005,23559,0,none,M-18_Trem1-1,S1,2,1,1,
18497,24085,0,none,M-18_Trem2-2,S2,2,1,2,
13393,25852,0,none,M-18_Trem3-3,S3,2,1,3,
11649,27444,0,none,M-18_Trem4-4,S4,2,1,4,
19634,23847,0,none,M-18_Trem5-5,S5,2,1,5,
14721,27640,0,none,M-18_Trem6-6,S6,2,1,6,
19392,26963,0,none,M-18_Carb1-7,S7,2,1,7,
5413,26693,0,none,M-18_Carb2-8,S8,2,1,8,
The first two rows are the two reference points P1. The following S1.... are sample points.
Columns 1,2,3 are XYZ
Column 4 is the analysis setup, which can be pre-programmed.
Column 5 is the sample description
Column 6 is the sample number (P for reference, S for single point...)
Columns 7-9 are used as number within dataset etc and not critical.
The coordinates would need to be mirrored on import when coming from the light microscope (X becomes -X).
Would it be possible to create an import routine for these coordinate files?
Many thanks, Karsten
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The coordinates would need to be mirrored on import when coming from the light microscope (X becomes -X).
Would it be possible to create an import routine for these coordinate files?
I'd like to say "your wish is granted", but when I implemented this I choose to mirror Y instead of X because I assumed a "petrographic microscope"!
So I'll tweak that tomorrow, but in the meantime v. 10.4.8 should work otherwise. Please see:
http://probesoftware.com/smf/index.php?topic=42.msg1852#msg1852
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I'd like to say "your wish is granted", but when I implemented this I choose to mirror Y instead of X because I assumed a "petrographic microscope"!
Thanks John, yes the Digimax coordinate system is a bit of a funny one. The image viewed through the light microscope is upside down as usual, but they've decided to have the origin of their coordinate system in the top right corner, with +X and +Y going to the left and down, respectively. So as Y is upside down anyway that doesn't have to be mirrored, but X does... I've attached a screenshot.
Many thanks again, I'll try it on Monday!
Karsten
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More discussion on this topic here:
http://probesoftware.com/smf/index.php?topic=46.msg1857#msg1857
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Hi John,
this wish concerns the standard.exe. I am currently having a lot of fun with using MAN backgrounds for PFE and PI applications. In order to pick the best standards for the MAN correction I have standard.exe list my standards with their mean Z (useful function!) and then go and pick from there. Works fine but in order to speed up the process, specifically for lab users that do not necessarily have the most intimate knowledge of all the lab standards I would love to have the following functions added (if they don't already exist and I just haven't found them yet).
1) Would it be possible to have another function where I can first include/exclude elements and then get a list of the filtered standards with their Z? Seems to me just like a combination of what is already available in the program..
2) In standard.exe, I can check for nominal interferences in a given standard composition. However, I cannot choose to specify an element which is not in the element list of the standard. It would be great if I could just choose random elements to quickly verify that I do not have a peak interference in my MAN standard.
I hope it is somewhat clear what I am asking for...
Thanks!
Anette
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1) Would it be possible to have another function where I can first include/exclude elements and then get a list of the filtered standards with their Z? Seems to me just like a combination of what is already available in the program..
2) In standard.exe, I can check for nominal interferences in a given standard composition. However, I cannot choose to specify an element which is not in the element list of the standard. It would be great if I could just choose random elements to quickly verify that I do not have a peak interference in my MAN standard.
I understand #2 well enough. Remember though, the nominal interference calculation assumes Gaussian overlaps and so is not very accurate.
The best practice in my mind is to simply acquire all analyzed elements in all standards (the default non quick standards), and then analyze them (as if they are unknowns from the Analyze! window) and see if anything shows up that shouldn't be there.
Actually even easier is to simply unselect any standard intensities that plot above the general MAN curve trend. After all, background is *by definition* the lowest intensity one can measure, so if the std intensity point is above the trend, it's either a contamination or an interference and you really don't care which it is- just deselect it from the fit.
As for #1, maybe you should provide an example of what you mean.
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Hi John,
Why not display spectro units here (screenshot)? You do that for the off peak interferences. Nice would be also spectro units relative and absolute... Also in calczaf.exe where I do these calculations from time to time.
Thanks!
(https://probesoftware.com/smf/oldpics/i61.tinypic.com/oh96ar.jpg)
Edit by John: Your request has been implemented in v. 10.5.4
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Hi John,
it seems that one cannot use "quick standards" with "digitized sample setups".
To use the combination would be super useful. Could you implement that?
Thanks
Philipp
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Hi John,
It seems that one cannot use "quick standards" with "digitized sample setups".
To use the combination would be super useful. Could you implement that?
I assume you are getting this message?
(https://probesoftware.com/smf/oldpics/i62.tinypic.com/2utt4xs.jpg)
Actually it gets very complicated... can you tell me what exactly you are trying to change in the standards by using sample setups? If it's just the analytical conditions, as the message says, you can use "quick standards" with the Automate! Digitized Conditions acquisition option.
Also be aware that "quick standards" have some nice options themselves in the Acquire! | Acquisition Options dialog as seen here:
http://probesoftware.com/smf/index.php?topic=8.msg1095#msg1095
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1) Would it be possible to have another function where I can first include/exclude elements and then get a list of the filtered standards with their Z? Seems to me just like a combination of what is already available in the program..
2) In standard.exe, I can check for nominal interferences in a given standard composition. However, I cannot choose to specify an element which is not in the element list of the standard. It would be great if I could just choose random elements to quickly verify that I do not have a peak interference in my MAN standard.
I understand #2 well enough. Remember though, the nominal interference calculation assumes Gaussian overlaps and so is not very accurate.
The best practice in my mind is to simply acquire all analyzed elements in all standards (the default non quick standards), and then analyze them (as if they are unknowns from the Analyze! window) and see if anything shows up that shouldn't be there.
Actually even easier is to simply unselect any standard intensities that plot above the general MAN curve trend. After all, background is *by definition* the lowest intensity one can measure, so if the std intensity point is above the trend, it's either a contamination or an interference and you really don't care which it is- just deselect it from the fit.
This certainly works well but in terms of efficiency (time=money) I rather would like to not spend time acquiring data I ultimately will not use. Just having access in this dialogue to the list of nominal interferences would serve as a nice guideline to weed out the obvious non-candidates.
As for #1, maybe you should provide an example of what you mean.
Let's say some user wants to map some multi-phase material with a wider spread of mean Z for various major and minor elements, in total 10 elements. And our metal standard block is in a somewhat rough shape ;), the user does not know our various standards by heart and I, microprobe mastress, am not around. And time is money again (see above).
Right now standard.exe allows me (1) to look up standards that contain a certain element (Find..) or (2) to list all standard names and average Z and. I just thought having the option to combine (1) and (2) in one output or - for the purpose of MAN backgrounds - exclude (rather than find) standards containing a certain element(s) and then list their name and Z.
However, I am aware that I could probably create an excel spreadsheet that would contain this kind of information, so overall this function would be a "nice to have".
Thanks!
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2) In standard.exe, I can check for nominal interferences in a given standard composition. However, I cannot choose to specify an element which is not in the element list of the standard. It would be great if I could just choose random elements to quickly verify that I do not have a peak interference in my MAN standard.
I understand #2 well enough. Remember though, the nominal interference calculation assumes Gaussian overlaps and so is not very accurate.
The best practice in my mind is to simply acquire all analyzed elements in all standards (the default non quick standards), and then analyze them (as if they are unknowns from the Analyze! window) and see if anything shows up that shouldn't be there.
Actually even easier is to simply unselect any standard intensities that plot above the general MAN curve trend. After all, background is *by definition* the lowest intensity one can measure, so if the std intensity point is above the trend, it's either a contamination or an interference and you really don't care which it is- just deselect it from the fit.
This certainly works well but in terms of efficiency (time=money) I rather would like to not spend time acquiring data I ultimately will not use. Just having access in this dialogue to the list of nominal interferences would serve as a nice guideline to weed out the obvious non-candidates.
I just use in standard.exe the "enter unknown" window for this purpose. It allows me to type in any composition I want and to do a thorough intereference check on it for peak and background postitions.
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Hi John,
It seems that one cannot use "quick standards" with "digitized sample setups".
To use the combination would be super useful. Could you implement that?
I assume you are getting this message?
Actually it gets very complicated... can you tell me what exactly you are trying to change in the standards by using sample setups? If it's just the analytical conditions, as the message says, you can use "quick standards" with the Automate! Digitized Conditions acquisition option.
Also be aware that "quick standards" have some nice options themselves in the Acquire! | Acquisition Options dialog as seen here:
http://probesoftware.com/smf/index.php?topic=8.msg1095#msg1095
Yes, that is the message I get. I am trying to measure standards and unknowns in one run and also remeasure the standards after a certain time. For this I need to:
*change the beam current
* change the counting times of some elements
* change the beam size
* set some elements to "acquisition-disabled" (and later re-enable them)
I figured the best way to do this is using "digitized sample setups".
Now, without quick standards, I waste A LOT of time for analyzing all elements over and over again...
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Hi John,
Why not display spectro units here (screenshot)? You do that for the off peak interferences. Nice would be also spectro units relative and absolute... Also in calczaf.exe where I do these calculations from time to time.
Thanks!
(https://probesoftware.com/smf/oldpics/i61.tinypic.com/oh96ar.jpg)
Edit by John: Your request has been implemented in v. 10.5.4
Great, John, thanks a lot. Now, the next wish:
A little tick box: "Tick this box to see the interefence lines in realtive spectro position offsets from the peak".
Would be SUPER handy!
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Yes, that is the message I get. I am trying to measure standards and unknowns in one run and also remeasure the standards after a certain time. For this I need to:
*change the beam current
* change the counting times of some elements
* change the beam size
* set some elements to "acquisition-disabled" (and later re-enable them)
I figured the best way to do this is using "digitized sample setups".
Now, without quick standards, I waste A LOT of time for analyzing all elements over and over again...
Here's what I would do:
1. Set up the counting times on the standards and unknowns differently using the unknown count factors in the Count Times dialog, see here:
http://probesoftware.com/smf/index.php?topic=29.msg397#msg397
2. Using the Digitized Conditions dialog in the Automate! window, specify one set of beam currents and beam sizes for your standard positions and different conditions for your unknown positions.
3. Select "Use Quick Standards" in Automate!
4. As for "Acquisition disabled" flags- go ahead and set them, and then unset them later!
That is all you have to do for your list above!
john
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Yes, that is the message I get. I am trying to measure standards and unknowns in one run and also remeasure the standards after a certain time. For this I need to:
*change the beam current
* change the counting times of some elements
* change the beam size
* set some elements to "acquisition-disabled" (and later re-enable them)
I figured the best way to do this is using "digitized sample setups".
Now, without quick standards, I waste A LOT of time for analyzing all elements over and over again...
Here's what I would do:
1. Set up the counting times on the standards and unknowns differently using the unknown count factors in the Count Times dialog, see here:
http://probesoftware.com/smf/index.php?topic=29.msg397#msg397
2. Using the Digitized Conditions dialog in the Automate! window, specify one set of beam currents and beam sizes for your standard positions and different conditions for your unknown positions.
3. Select "Use Quick Standards" in Automate!
4. As for "Acquisition disabled" flags- go ahead and set them, and then unset them later!
That is all you have to do for your list above!
john
Hi John,
this unknown count time factor is a really cool thing I did not know about. I will check it out. Thanks.
However, I don't see how I can enable/disable elements using your proposal. I am measuring some standards for some virtual standards, and I don't want to waste time measuring these standards of elements that are not present in my sample on the unknown.
I really would like to use the sample setups with "Quick Standards"!! Would solve a lot of problems.
Edit by John: I can understand, but the code is very complicated in this regard and I'm just one guy! Let me think about it and maybe I'll come up with something cool and easy!
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Great, John, thanks a lot. Now, the next wish:
A little tick box: "Tick this box to see the interefence lines in realtive spectro position offsets from the peak".
Would be SUPER handy!
Your wish is granted (no need for a checkbox)!
(https://probesoftware.com/smf/oldpics/i57.tinypic.com/d86k7.jpg)
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Nth background in acquistion options. I regularly use it for standards just measuring the background on the first point. I wish the default when selecting for individual elements was to Yes for Nth Background so that you don't need to turn it on for each element. In which case it would be just controlled by the Nth background on/off overide check box. Maybe an idea for the furture would be to have an option to use Nth backgrounds for standards but not unknowns - so that you can't forgot to turn it off when you go to your unknown samples.
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Nth background in acquistion options. I regularly use it for standards just measuring the background on the first point. I wish the default when selecting for individual elements was to Yes for Nth Background so that you don't need to turn it on for each element. In which case it would be just controlled by the Nth background on/off overide check box. Maybe an idea for the furture would be to have an option to use Nth backgrounds for standards but not unknowns - so that you can't forgot to turn it off when you go to your unknown samples.
Hi Ben,
I have to be careful here because some people depend on the current paradigm.
However, maybe I could implement a method whereby if you click the Use Nth Point For Off-Peaks checkbox and if all the channels are not using Nth point backgrounds already, I could set them all as Nth point backgrounds.
Likewise, if you uncheck the Use Nth Point For Off-Peaks checkbox, I could set all channels to not use Nth point backgrounds, if they are all already set to use Nth point backgrounds.
Would that work for you?
john
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Hi John,
Yes I'm not sure what the best way is. Or what most people do. For as you point out you could imagine a situation where you want to toggle on or off using the check box the 5 of 10 elements which your using nth background for.
I suppose would it be possible to configure the window so you can select multiple elements at once and change the nth yes/no for the multiple selected elements. Like the really nice feature in setting count times where you can select multiple elements by hold and drag and change the count times for all selected elements
Thanks
Ben
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Yes I'm not sure what the best way is. Or what most people do. For as you point out you could imagine a situation where you want to toggle on or off using the check box the 5 of 10 elements which your using nth background for.
I suppose would it be possible to configure the window so you can select multiple elements at once and change the nth yes/no for the multiple selected elements. Like the really nice feature in setting count times where you can select multiple elements by hold and drag and change the count times for all selected elements
Hi Ben,
I modified the Nth point select code in the Acquisition Options. This will be in v. 10.7.4 of PFE. See if this behavior is more to your liking.
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Hi John,
This new behaviour is great. If all the elements are the same it toggles them all off or on. Whereas it elements are doing different things (only some using Nth background) it just disables or enables.
I didn't get originally meant
Thanks
Ben
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Hi John,
Another nit-picky thing to bug you about...
I have been trying to change the off-peak correction type (linear, polynomial, exponential, etc.) from Analyze! --> Elements. Usually this is easy, but I have sporadically been encountering an error related to the Multi-Point Background positions being outside the spectrometer range. Screenshot is attached - the L-values and positions #'s change, but the overall message is the same.
I can't check what the MPB positions are directly, as these samples were not acquired with MPB's and those options are inactive through Analyze --> Elements. But I did "clone" the sample setup through Acquire, and several of the MPB positions are indeed outside the spectro limit. These must be the defaults, as I did not change, click on or use any of the MPB options during setup and acquisition.
Assuming the out-of-range MPB positions is something I've unwittingly screwed up, is there any way the Elements window could ignore the MPB conditions when if you're trying to switch from, say, linear to polynomial backgrounds? Or ignore checking the MPB parameters when post-processing non-MPB samples?
Thanks!
Hi Owen,
The zero in the error message indicates that this is a zero spectro position, so that is why it's flagging it as out of bounds. Note sure why there is a zero position there but I can add code to trap for that and load a default.
john
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Hi Owen,
Is that all? ;)
I just don't understand why you are seeing these errors, and Julie and I never do...
I'll take a look, thanks for the detailed report- that always helps.
john
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I sent Owen a modified PFE executable and we can confirm that the problems he was having with re-processing data from an old run is due to the fact that I was checking background positions for "out of bounds" even for samples with data, which is unnecessary since the background positions cannot be changed once the sample contains data.
I will roll this fix out tonight. Just for a sanity check I also loaded a *very* old data file (v. 3.5) and tried to modify the sample element parameters also, and found a couple of minor checks that weren't necessary (from an old run on an ARL SEMQ containing fixed spectrometers!) and that is also fixed! I think v. 3.x was the first Windows version of my software that utilized Microsoft Access database file?
Anyway, there is another way to avoid the problem that Owen found when re-processing data off-line (on a computer with different instrument configuration files), and the procedure described below is especially useful when attempting to create or run probe data files on another computer in "demo" mode. That is, without an EPMA instrument connected to the computer.
1. Create or open a probe database on your on-line computer (the one connected to the instrument), and using the File | Import Probe Configuration Files menu, load the current instrument configuration files into the opened probe database as seen in this post:
http://probesoftware.com/smf/index.php?topic=42.msg659#msg659
2. Then close the probe database and copy the MDB file to your off-line computer and this time using the File | Export Probe Configuration Files menu, click the Export All button to export the selected instrument configuration files to the off-line computer PFE app folder.
It will ask if you want to overwrite the existing configuration files (and automatically back them up) and also offer to set the instrument InterfaceType parameter to zero for "demo" mode operation.
Pretty cool!
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So it seems like we have a few competing issues here:
1) Default MPB positions are outside spectro range (we'll assume this is operator error on my part, though I can't figure out where).
2) MPB parameters causing errors for samples not acquired using MPB.
3) The values for the MPB positions changing.
Sorry to bring you aggravation so close to quittin' time, but I hope this helps.
Hi Owen,
Ok, what I did was modify the save elements/cations code so that the peak and background positions don't get checked for out of bounds since they can't be updated anyway once the sample contains data. The fact that you were reprocessing data on an off-line computer with different spectro ranges defined in the config files is what was causing the errors.
But all is well now, so update from the Help | Update menu and all will be good.
john
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Two things I've wondered about:
(1) Wavescans with the option of multiple accumulations to allow slow acquistion wavescans of trace elements without having to turn ROM off which is really slow. Also if you can do multiple accumulations over a grid of points you can spread the damage.
(2) Calibration curve for a single element. Let me explain this a bit. What I do when analysing carbon in steels is run a calibration curve for carbon whilst running phi-rho-z for the other elements. Currently PFE only allows you to use a calibration curve if you apply it for all the elements - is there any intrinsic reason for this? I did think alternatively I could analyse carbon using phi-rho-z and using the blank correction to subtract the amount of contamination - has anyone tried this?
Thanks
Ben
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And a third thing:
A way of flaging up duff standards - let me explain the other day - on the rare occasion that the peaking failed to locate the peak and it used the previously stored value. This was good in that it let the rest of the elements finish peaking and calibrating. But it also meant the element without a peak was calibrated and then used in quantification of secondary standards. Amittedly it should have been noticed on checking the standard data that for this element the %SD was high as it was calibrated on background. I wondered if there was a was without bailing out of a automated standardization to notify the user at the end when everythings completed that a particulary element used a previously stored peak value and needs checking. This might be a bit complicated as i think most of the time users would prefer it to continue as it did and run the other elements rather than coming back an hour later and finding it hasn't done anything as it did not find the peak for one element.
Thanks
Ben
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(1) Wavescans with the option of multiple accumulations to allow slow acquisition wavescans of trace elements without having to turn ROM off which is really slow. Also if you can do multiple accumulations over a grid of points you can spread the damage.
For qualitative analysis? I think you mean the ROM scans are fast and count/step scans are slow to very slow depending on the sensitivity you want.
See here:
http://probesoftware.com/smf/index.php?topic=464.msg2537#msg2537
Also, have you tried Multi-Point Backgrounds for traces?
(2) Calibration curve for a single element. Let me explain this a bit. What I do when analysing carbon in steels is run a calibration curve for carbon whilst running phi-rho-z for the other elements. Currently PFE only allows you to use a calibration curve if you apply it for all the elements - is there any intrinsic reason for this? I did think alternatively I could analyse carbon using phi-rho-z and using the blank correction to subtract the amount of contamination - has anyone tried this?
I should have known that once I offered multiple matrix corrections, some people would want to "mix and match" matrix corrections, but I worry about data self consistency, not to mention it would be a coding nightmare!
Here's my suggestion: just make another copy of your probe data file and run it each way in each file. Then output to Excel and "mix and match" there all you want!
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And a third thing:
A way of flaging up duff standards - let me explain the other day - on the rare occasion that the peaking failed to locate the peak and it used the previously stored value. This was good in that it let the rest of the elements finish peaking and calibrating. But it also meant the element without a peak was calibrated and then used in quantification of secondary standards. Amittedly it should have been noticed on checking the standard data that for this element the %SD was high as it was calibrated on background. I wondered if there was a was without bailing out of a automated standardization to notify the user at the end when everythings completed that a particulary element used a previously stored peak value and needs checking. This might be a bit complicated as i think most of the time users would prefer it to continue as it did and run the other elements rather than coming back an hour later and finding it hasn't done anything as it did not find the peak for one element.
Thanks
Ben
I don't think I understand.
If you select peaking and also acquisition from Automate!, then it won't proceed with the acquisition if there any problems with the peaking.
Note the output here from the log window during automated peaking:
Starting spectrometer peaking procedure for na ka on spectro 1 (TAP)...
Na ka Spectro 1, StartPk: 46227.3, StartI: 292.0, HiPeak: 13.7, LoPeak: 13.7, StartP/B: 21.29
ROM Scan completed on spectro 1 with 30 total points
Na ka Spectro 1, StopPk: 46221.6, StopI: 292.4, HiPeak: 13.7, LoPeak: 13.7, StopP/B: 21.32
ROM Brent's Maxima Peak Center Results (cps):
Element Spectr Peaked StartPk StopPk Std Offset StartI StopI StartPB StopPB
na ka 1 TAP Yes 46227.3 46221.6 336 141. 292.0 292.4 21.29 21.32
si ka 2 LPET *No .000000 .000000 162 18.4 .0 .0 .00 .00
k ka 3 LPET *No .000000 .000000 374 151. .0 .0 .00 .00
al ka 4 TAP *No .000000 .000000 160 49.9 .0 .0 .00 .00
mg ka 1 TAP *No .000000 .000000 162 141. .0 .0 .00 .00
ca ka 2 LPET *No .000000 .000000 162 32.7 .0 .0 .00 .00
s ka 2 LPET No .000000 .000000 730 38.8 .0 .0 .00 .00
fe ka 5 LIF No .000000 .000000 162 7.47 .0 .0 .00 .00
cl ka 3 LPET No .000000 .000000 285 118. .0 .0 .00 .00
ti ka 5 LIF No .000000 .000000 22 -127. .0 .0 .00 .00
p ka 4 TAP No .000000 .000000 285 6.00 .0 .0 .00 .00
f ka 1 TAP No .000000 .000000 284 95.0 .0 .0 .00 .00
The No, means the element was *not* selected for peaking. The *No, mean the element was selected for peaking but has not been acquired yet, or it failed. The Yes, means the element selected for peaking did peak properly. In this case Na.
Here is after the K spectrometer was peaked on the assigned standard:
Starting spectrometer peaking procedure for k ka on spectro 3 (LPET)...
K ka Spectro 3, StartPk: 42625.8, StartI: 1367.1, HiPeak: 43.7, LoPeak: 45.6, StartP/B: 30.62
ROM Scan completed on spectro 3 with 30 total points
K ka Spectro 3, StopPk: 42539.5, StopI: 1368.7, HiPeak: 43.7, LoPeak: 45.6, StopP/B: 30.66
ROM Brent's Maxima Peak Center Results (cps):
Element Spectr Peaked StartPk StopPk Std Offset StartI StopI StartPB StopPB
na ka 1 TAP Yes 46227.3 46221.6 336 141. 292.0 292.4 21.29 21.32
si ka 2 LPET *No .000000 .000000 162 18.4 .0 .0 .00 .00
k ka 3 LPET Yes 42625.8 42539.5 374 237. 1367.1 1368.7 30.62 30.66
al ka 4 TAP *No .000000 .000000 160 49.9 .0 .0 .00 .00
mg ka 1 TAP *No .000000 .000000 162 141. .0 .0 .00 .00
ca ka 2 LPET *No .000000 .000000 162 32.7 .0 .0 .00 .00
s ka 2 LPET No .000000 .000000 730 38.8 .0 .0 .00 .00
fe ka 5 LIF No .000000 .000000 162 7.47 .0 .0 .00 .00
cl ka 3 LPET No .000000 .000000 285 118. .0 .0 .00 .00
ti ka 5 LIF No .000000 .000000 22 -127. .0 .0 .00 .00
p ka 4 TAP No .000000 .000000 285 6.00 .0 .0 .00 .00
f ka 1 TAP No .000000 .000000 284 95.0 .0 .0 .00 .00
Calibrate Peak Positions Automation Action is Completed
Warning: si ka on spectrometer 2 LPET could not be peak centered
Warning: al ka on spectrometer 4 TAP could not be peak centered
Warning: mg ka on spectrometer 1 TAP could not be peak centered
Warning: ca ka on spectrometer 2 LPET could not be peak centered
Since elements selected for peaking (Si, Al, Mg, Ca), were not able to be peaked (in this instance because the assigned standard for those elements were not selected in the Automate position list), the run did not proceed to the acquisition step.
Am I missing your question?
-
Yes I thought it would say no and abort. But in this case it did the fine peak scan with the centre of the peak just outside the window, then it did the course peak scan with the centre of the peak just outside the window. Then it said peak failed (can't remember wording), but that it would use previous peak position and changed peaked to yes. It may well be because the coarse scan was set up wrong looking at it now the range had been set to small - I will change this
Thanks
Ben
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Yes I thought it would say no and abort. But in this case it did the fine peak scan with the centre of the peak just outside the window, then it did the course peak scan with the centre of the peak just outside the window. Then it said peak failed (can't remember wording), but that it would use previous peak position and changed peaked to yes. It may well be because the coarse scan was set up wrong looking at it now the range had been set to small - I will change this
Thanks
Ben
Hmmm, still it should not proceed with the standard acquisition if there was an error with the peaking. I'll look into this as well.
john
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Yes I thought it would say no and abort. But in this case it did the fine peak scan with the centre of the peak just outside the window, then it did the course peak scan with the centre of the peak just outside the window. Then it said peak failed (can't remember wording), but that it would use previous peak position and changed peaked to yes. It may well be because the coarse scan was set up wrong looking at it now the range had been set to small - I will change this
Thanks
Ben
Hmmm, still it should not proceed with the standard acquisition if there was an error with the peaking. I'll look into this as well.
john
Hi Ben,
The automation "trap" for unpeaked elements seems to be working. Here is what I get when one or more WDS elements fails to peak:
(https://probesoftware.com/smf/oldpics/i57.tinypic.com/21m4t2b.jpg)
In the log window you should see something such as this:
ROM Brent's Maxima Peak Center Results (cps):
Element Spectr Peaked StartPk StopPk Std Offset StartI StopI StartPB StopPB
rb la 2 LPET *No 83850.4 .000000 1023 -201. 445.8 .0 3.56 .00
sr la 1 PET Yes 78575.2 78508.5 251 -65. 4975.2 5033.8 178.76 180.86
This may be a subtle issue, so let me know if you are still seeing a problem.
john
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Hey John
How's about a drag and job capability for opening an analysis file?
Cheers,
malc.
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Hey John
How's about a drag and job capability for opening an analysis file?
Cheers,
malc.
Did you try? :)
john
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Of course....... It didn't......
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Of course....... It didn't......
Hmmm, it works just fine for me.
So you have a shortcut for PFE on your desktop, and you found a probe MDB file in Windows Explorer and using the mouse you dragged the MDB file to the PFE shortcut and dropped the MDB file on the PFE shortcut and it didn't open PFE and load the file?
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Hey, why drag and drop when you can associate .mdb files with the Probewin.exe and then just double click on any .mdb you like? OK, so if you also use MS Access/.mdb files for other stuff this might not work so well!, but if you double click on a non-PROBE database .mdb, John is smart enough to know about it and warn you accordingly :) Try dragging and dropping xray.mdb or standard.mdb or position.mdb onto your probewin.exe shortcut and see what happens.
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I actually followed the more logical route and dragged and dropped the mdb onto open PfEPMA. That doesn't work.......... it would not have dawned on me to try it any other way. I treated as I would surfer......... or word........
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I actually followed the more logical route and dragged and dropped the mdb onto open PfEPMA. That doesn't work.......... it would not have dawned on me to try it any other way. I treated as I would surfer......... or word........
Actually I think Gareth is correct- the most logical action is to double click the file to open it.
You can set that from the right click menu as seen here:
(https://probesoftware.com/smf/oldpics/i61.tinypic.com/rau6ae.jpg)
Then click the Choose Default Program... option and then Browse button as seen here:
(https://probesoftware.com/smf/oldpics/i62.tinypic.com/v9g7a.jpg)
and browse to the Probewin.exe file and click Open and OK as seen here:
(https://probesoftware.com/smf/oldpics/i58.tinypic.com/2cggfmr.jpg)
You only need to do this once. Note the MDB file icon now shows the PFE icon instead of Microsoft Access icon in Windows Explorer.
At one time I was thinking of allowing the user to merge probe runs by dragging and dropping an MDB file on the open PFE app, as you tried... that is why PFE embeds the MDB file instead of opening it.
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Wish: Right now the "Custom" output window has three different check boxes which give us the option to export measured concentrations elemental wt%, oxide wt% and/or at%. Would it be possible to add two additional check boxes to export calculated detection limits in oxide wt% and/or at%, in addition to the existing option to export them in elemental wt%?
Hi Owen,
It's a good idea!
Question: I updated PFE to 10.9.7 this morning on various lab and personal computers, and when I opened the updated PFE on 32-bit machines, I got the message "C:\Probe Software\Probe For EPMA\STANDARD.MDB was automatically updated for new database fields". I didn't see this message on the 64-bit machines. Everything still seems to work fine, I was just wondering what was going on here - didn't see anything obviously new in STANDARD. Again, functionality not affected, just curious.
Good idea to check the version.txt file where you will see this:
06/27/15 Finish EDS and CL import to Standard.exe.
v. 10.9.4
http://probesoftware.com/smf/index.php?topic=40.msg138#msg138
Basically I added tables for EDS and CL spectra to the Standard.mdb file.
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Good idea to check the version.txt file where you will see this:
06/27/15 Finish EDS and CL import to Standard.exe.
v. 10.9.4
http://probesoftware.com/smf/index.php?topic=40.msg138#msg138
Basically I added tables for EDS and CL spectra to the Standard.mdb file.
Wondered if that was it - I'll be interested to see where this goes. Thanks!
Try it out and tell me!
It accepts EMSA format files and you can have multiple spectra per standard stored as shown here:
http://probesoftware.com/smf/index.php?topic=534.msg2963#msg2963
EDS files must have a single column of data (at this time) and CL files must have two columns of data, one for the CL spectrum (faraday out) and one for the dark spectrum (faraday in).
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It would be nice if the standards in the "Assigned (Primary) Standard" and "Interference Standard" drop down menus in the standard "Assigment Properties" dialog were sorted in some way, probably best by the standard number, or alphabetically.
At the moment they seem to appear in the order in which they were added to the run, which can make standards hard to find if there in those drop down menus are a lot in the run.
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Hi,
can I please have a default keyword in the probewin.ini for the "Use confirm during acquisition" in the Automate! window (I never use it, have the automate confirm delay up at 60s so that I don't have to hit pause and always have to remember to uncheck the box).
Thank you!
-
Hi,
when I set up MAN backgrounds in the "Element/Cations" window, this background type is only applied to the unknowns but the standards are set to off-peak still.
To change them for all elements at once (being lazy) can I please have a button or tick mark box in the "Acquisition properties" window when I highlight the entire row in the "Acquisition Options" window.
Thanks!
-
Hi,
I wish there would be a tick box option in the Analysis window to show "only acquired data".
Thank you!
-
Hi,
I wish that the "Automate Probe Image" option in PFE - Automate! will be implemented soon so that I can do a serial acquisition of spot analysis in PFE and then maps in ProbeImage overnight.
Thank you!
-
Hi,
I've just started using PFE for carbon analysis instead of the Jeol software. It looks good, both the calibration curve option and using phi-rho-z option with a blank assignment to remove contamination. Plus the acquire standards again at end of run.
Just a couple of suggestions, with calibration curve would it be possible to add other curve fitting routines, or more particularly force a straight line?
Using blank assignment, what do you think of the idea of being able to add standards as blank correction sample assigments, for example in this case I've acquired a series of 0-1wt.% C in Steel standards and it be nice to use the 0 wt.% C as the blank correction when using phi-rho-z option. But mainly for testing - allowing comparison of the two methods for the data. I surpose once you found which worked best your'd only need to do one or the other
Ben
-
Hi,
I've just started using PFE for carbon analysis instead of the Jeol software. It looks good, both the calibration curve option and using phi-rho-z option with a blank assignment to remove contamination. Plus the acquire standards again at end of run.
Just a couple of suggestions, with calibration curve would it be possible to add other curve fitting routines, or more particularly force a straight line?
Using blank assignment, what do you think of the idea of being able to add standards as blank correction sample assigments, for example in this case I've acquired a series of 0-1wt.% C in Steel standards and it be nice to use the 0 wt.% C as the blank correction when using phi-rho-z option. But mainly for testing - allowing comparison of the two methods for the data. I surpose once you found which worked best your'd only need to do one or the other
Ben
Hi Ben,
Yes, several steel companies use our calibration curve method (in PFE) and it does work, but one does have to be careful. And one needs several standards with a good matrix match and covering a range of concentrations for the element of interest. And one needs "fresh" carbon in steel standards as well, since carbon-steel standards slowly degrade over about 3 to 5 years.
As for the zero point option, that is already in PFE in the Analytical | Analysis Options as seen here:
(https://probesoftware.com/smf/oldpics/i58.tinypic.com/izrdif.jpg)
I'm sure you are aware that due to the native hydrocarbon and contamination effects, a zero concentration might not correspond to a zero intensity (and of course it goes without saying that this zero point option can only be applied to off-peak elements).
Also see this topic:
http://probesoftware.com/smf/index.php?topic=461.msg2539#msg2539
As for the force a straight line fit option, that is a good idea, but I'd have to implement that option separately for each element- don't you think? And that will require a bit more work.
john
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Hi,
I wish there would be a tick box option in the Analysis window to show "only acquired data".
Thank you!
Your wish is granted! Download v. 10.9.9.
-
Hi,
can I please have a default keyword in the probewin.ini for the "Use confirm during acquisition" in the Automate! window (I never use it, have the automate confirm delay up at 60s so that I don't have to hit pause and always have to remember to uncheck the box).
Thank you!
Your wish is granted! Download v. 10.9.9.
See new keyword in the [software] section.
-
Hi,
I've just started using PFE for carbon analysis instead of the Jeol software. It looks good, both the calibration curve option and using phi-rho-z option with a blank assignment to remove contamination. Plus the acquire standards again at end of run.
Just a couple of suggestions, with calibration curve would it be possible to add other curve fitting routines, or more particularly force a straight line?
Using blank assignment, what do you think of the idea of being able to add standards as blank correction sample assigments, for example in this case I've acquired a series of 0-1wt.% C in Steel standards and it be nice to use the 0 wt.% C as the blank correction when using phi-rho-z option. But mainly for testing - allowing comparison of the two methods for the data. I surpose once you found which worked best your'd only need to do one or the other
Ben
Hi Ben,
Yes, several steel companies use our calibration curve method (in PFE) and it does work, but one does have to be careful. And one needs several standards with a good matrix match and covering a range of concentrations for the element of interest. And one needs "fresh" carbon in steel standards as well, since carbon-steel standards slowly degrade over about 3 to 5 years.
As for the zero point option, that is already in PFE in the Analytical | Analysis Options as seen here:
(https://probesoftware.com/smf/oldpics/i58.tinypic.com/izrdif.jpg)
I'm sure you are aware that due to the native hydrocarbon and contamination effects, a zero concentration might not correspond to a zero intensity (and of course it goes without saying that this zero point option can only be applied to off-peak elements).
Also see this topic:
http://probesoftware.com/smf/index.php?topic=461.msg2539#msg2539
As for the force a straight line fit option, that is a good idea, but I'd have to implement that option separately for each element- don't you think? And that will require a bit more work.
john
Hi John,
Thanks yes I just processed my data and calibration curve looks good. (Regarding force straight line, yes you would need it for each element although you could initially do it just for carbon, -but it would take time - maybe add to the list for the future - when you have a bit of spare time!)
But I realized my error - I can't use phi-rho-z and blank correction to remove contamination. For this is not the point of blank correction - it just subtracts intensity from the unknown. Whereas I need it to subtract the intensity from the unknown and the standard.
Have you any plans to implement an option of subtracting intensity from unknown and standard. This would then allow carbon analysis through phi-rho-z - which would be good when the concentrations don't correspond well with calibration curve standards. I've previously done it using calczaf - and modifying the intensities for standards and unknowns
Thanks
Ben
-
Have you any plans to implement an option of subtracting intensity from unknown and standard. This would then allow carbon analysis through phi-rho-z - which would be good when the concentrations don't correspond well with calibration curve standards. I've previously done it using calczaf - and modifying the intensities for standards and unknowns
Hi Ben,
This sounds a bit like the correlated pixel quantification method that Philippe Pinard had me implement in CalcImage for their carbon analyses. They wanted to acquire the same pixels on their unknown and standard in order to to normalize out the effects from overlapping carbon contamination rings from their analyses. See here:
http://probesoftware.com/smf/index.php?topic=114.msg3258#msg3258
You might also check this discussion:
http://probesoftware.com/smf/index.php?topic=48.0
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Hi John,
I like your attempt to use MAN - collect MAN for various metals - which includes the contamination on those metals - and then subtract it, thus eliminating the need for a calibration curve and allowing phi-rho-z. I will have to give it a go!!
This method subtracts both the background and the contamination from each point. What do you think - do you think its as good as a calibration curve? Also do you think its as good as subtracting a set value for contamination and meansuring the background value to subtract?
Thanks
Ben
-
Hi John,
I like your attempt to use MAN - collect MAN for various metals - which includes the contamination on those metals - and then subtract it, thus eliminating the need for a calibration curve and allowing phi-rho-z. I will have to give it a go!!
This method subtracts both the background and the contamination from each point. What do you think - do you think its as good as a calibration curve? Also do you think its as good as subtracting a set value for contamination and meansuring the background value to subtract?
Thanks
Ben
Hi Ben,
Let me make sure I understand your point. You are saying that if one uses a MAN background calibration curve for carbon measurements, then the natural carbon contamination rate would get normalized out in the background correction? Yes, this is essentially what happens when one uses the multi-standard calibration curve method for carbon analyses, but your idea would allow us to still utilize phi-rho-z, etc.
If this is what you mean, I have to say it might be possible. The only issue I can see is that the carbon contamination rate is somewhat dependent on the thermal conductivity of the surface. That is, the higher the thermal conductivity, the slower the cracking of hydrocarbons and subsequent deposition on the surface... therefore one might want to try and make sure that standards used for the MAN calibration are similar in thermal conductivity to the unknown material. For example, for carbon in steel, one might want to utilize pure metals rather than pure oxides for the MAN calibration...
It's worth a try. Please post your results here, or maybe even better, start a carbon measurement topic and put it there. I'd be very interested to see what you find.
john
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Hi John,
Yes you've got it. With pure metals we assume the contamination rate is the same as on the unknowns. It might be a while before I get a chance, then I'll post it
Thanks
Ben
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2) Would it be possible to make a slight change to the sort order output options? Currently, the option to export in geologic (or atomic number) order is only offered when calculating with stoichiometric oxygen. The current options in "Analysis Options" for sort order during output are:
- Use Traditional Geological Sort Order
- Use Low to High Atomic Number Order
- Use High to Low Atomic Number Order
Could this be modified to have four options:
- Use Traditional Geological Sort Order
- Use Low to High Atomic Number Order
- Use High to Low Atomic Number Order
- Do not re-sort elements (i.e. if this box is checked, don't sort anything)
And have the sort order on output depend on which of those four options is selected, regardless of whether stoichiometric oxygen is used, with the default option able to be specified in the INI file?
Your wish is granted! There is already an option for the default sort order in the INI file. Note that I had to re-index these sort methods, so zero used to be traditional geological order, but now it means no sort.
3) This one may be a bug, or a misunderstanding on my part. In the "Elements/Cations" dialog (accessible from Acquire and Analyze), we have the option to change the cation/oxygen proportions, and the elemental charge, an especially useful feature for things like Fe. I have noticed that when I try to change these parameters, the Cations and Oxygens fields update, but the Charge field does not.
As an example, if Fe is calcualted as FeO (Fe2+) in my initial setup, and I want to change it to Fe2O3 (Fe3+) in post-production, I will:
- Open the Fe element dialog (Analyze --> Elements/Cations --> Fe)
- Change the Cations field from 1 to 2
- Change the Oxygens field from 1 to 3
- Change the Charge field from 2 to 3.
- Hit OK on the Fe dialog and then the Elements/Cations dialog.
If I do this, it will calculate Fe as Fe2O3 without problem. However, if I re-open the the Fe dialog window (Analyze --> Elements/Cations --> Fe) after performing the sequence above, I find that:
- The Cations field still shows 2 (as it should)
- The Oxygens field still shows 3 (as it should)
- But the Charge field will show 2 (when I had put in 3).
I don't know if this actually affects anything (again, the cation/oxygen proportions change as they should), so I may be nit-picking, or completely misusing the feature. That said, is there any reason that updates to the Charge field don't persist? And does this affect any of the charge balance-based calculations?
This was a bug, but is now fixed. The only thing that the elemental atomic charge values are used for is to calculate the charge balance of the composition (see Analytical | Analysis Options menu) and for deciding which elements are cations and which are anions for sum of cation calculations.
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The new sort order options (geo, atomic number...) are working great!
I wished it was possible to send the Save User Specified Format Output directly to Excel, without generating .DAT files first and asking for confirmation.
It would also be great if the column headers didn't have leading spaces. At the moment the first thing I always do in a newly exported Excel file is search for the spaces in the headings and replace them with nothing.
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The new sort order options (geo, atomic number...) are working great!
Thank-you.
I wished it was possible to send the Save User Specified Format Output directly to Excel, without generating .DAT files first and asking for confirmation.
You can. Just select the data type you want to output to Excel in Analytical | Analysis Options menu, use the Output menu to open a link to Excel, then select all samples in the Analyze Window and click Analyze.
It would also be great if the column headers didn't have leading spaces. At the moment the first thing I always do in a newly exported Excel file is search for the spaces in the headings and replace them with nothing.
Why does this matter?
I did it so the DAT file when opened in a text editor looks pretty. Not a great reason, but why do spaces matter? Also, it's always 8 characters, so consistent at least.
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I wished it was possible to send the Save User Specified Format Output directly to Excel, without generating .DAT files first and asking for confirmation.
You can. Just select the data type you want to output to Excel in Analytical | Analysis Options menu, use the Output menu to open a link to Excel, then select all samples in the Analyze Window and click Analyze.
If I do that it will quantify all the data but it does not appear in the Excel file. If I push the ">>Excel" button in the Analyze window it will export the last displayed dataset. Also, it will only export the wt% (or whatever is selected) but not all of the data types I selected in the user specified output options.
It would also be great if the column headers didn't have leading spaces. At the moment the first thing I always do in a newly exported Excel file is search for the spaces in the headings and replace them with nothing.
Why does this matter?
I did it so the DAT file when opened in a text editor looks pretty. Not a great reason, but why do spaces matter? Also, it's always 8 characters, so consistent at least.
I never use the DAT files so the columns don't have to line up in a monospace font for me. The leading spaces make the columns wider than they need to be so there's lots of scrolling involved (as I always export wt%, ox%, CDL, %err, intensities, correction factors... together). The leading spaces also can cause trouble when sorting columns. Some column headers (e.g. intensities, k-raws) and some of the data (DATETIME) have more than 8 characters, don't they?
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I wished it was possible to send the Save User Specified Format Output directly to Excel, without generating .DAT files first and asking for confirmation.
You can. Just select the data type you want to output to Excel in Analytical | Analysis Options menu, use the Output menu to open a link to Excel, then select all samples in the Analyze Window and click Analyze.
If I do that it will quantify all the data but it does not appear in the Excel file. If I push the ">>Excel" button in the Analyze window it will export the last displayed dataset. Also, it will only export the wt% (or whatever is selected) but not all of the data types I selected in the user specified output options.
It would also be great if the column headers didn't have leading spaces. At the moment the first thing I always do in a newly exported Excel file is search for the spaces in the headings and replace them with nothing.
Why does this matter?
I did it so the DAT file when opened in a text editor looks pretty. Not a great reason, but why do spaces matter? Also, it's always 8 characters, so consistent at least.
I never use the DAT files so the columns don't have to line up in a monospace font for me. The leading spaces make the columns wider than they need to be so there's lots of scrolling involved (as I always export wt%, ox%, CDL, %err, intensities, correction factors... together). The leading spaces also can cause trouble when sorting columns. Some column headers (e.g. intensities, k-raws) and some of the data (DATETIME) have more than 8 characters, don't they?
Ok, yes you are correct. I think I had an option there at one time, but it's missing now it seems. I could add it back in if that would be helpful. But it sounds that an output to Excel wouldn't be useful to you unless it's exactly the user specified output options? I wonder if I could add an option to use that format, but on the other hand, this seems merely an effort to save one or two mouse clicks at the end of the run. Are we spoiling you just a wee little bit? :P
On the leading spaces in Excel, yes, they aren't all 8 spaces, but they are consistent on a per column basis.
Are you sure extra spaces in the header row causes sorting problems? Maybe just don't select the first header row when sorting?
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Yes, I admit this is a trivial work flow thing, but after doing the same 10-20 clicks over years it gets a bit annoying and maybe it's not just me and it might be helpful for other people as well? Are many people still using the DAT files and work with their data in a text editor? The procedure involves other steps like always having to delete the .DAT files afterwards. I'm exclusively using the User Specified Output export to Excel and always selecting ranges of datasets to export in Analyze.
I've been using the first row in Excel for sorting (custom lists...) so I can't really exclude it. :-) But now with the better geo and atomic number output sorting I might not have to do that so much anymore.
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Yes, I admit this is a trivial work flow thing, but after doing the same 10-20 clicks over years it gets a bit annoying and maybe it's not just me and it might be helpful for other people as well? Are many people still using the DAT files and work with their data in a text editor? The procedure involves other steps like always having to delete the .DAT files afterwards. I'm exclusively using the User Specified Output export to Excel and always selecting ranges of datasets to export in Analyze.
I've been using the first row in Excel for sorting (custom lists...) so I can't really exclude it. :-) But now with the better geo and atomic number output sorting I might not have to do that so much anymore.
Hi Karsten,
Right now, PFE uses the .DAT file to import into Excel. Otherwise the import would be much, much slower and then I'll hear complaints about that! But seriously, why bother deleting the .DAT file at all? Don't be so "tidy" and just think of it as a "backup"! Besides, the .DAT file has many uses, for example it can be read directly by Surfer, Grapher and many other apps.
I'll have to see if I can think of a clever way to write some code to export quickly to Excel without the .DAT file... maybe it will only take me a few thousand keystrokes and mouse clicks! :(
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Hi John, if it's not easy to do and complicates things don't worry about it! As I don't know the internal machinations that's usually not clear to me before asking. If the .DAT export route is fastest it sounds like a good way of doing it.
Regarding Grapher import I think what works very nicely is linking Excel spreadsheets as data source, basically using Grapher as a plotting backend for Excel.
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Hi John, if it's not easy to do and complicates things don't worry about it! As I don't know the internal machinations that's usually not clear to me before asking. If the .DAT export route is fastest it sounds like a good way of doing it.
Regarding Grapher import I think what works very nicely is linking Excel spreadsheets as data source, basically using Grapher as a plotting backend for Excel.
Yup. Or reading with other scripts.
I just have to see if I can think of a clever method to do the user specified output directly to Excel without the DAT file, but I promised Phil Gopon that I'd work on adding non-traditional lines to the program, so I'll be focusing on that for the time being...
john
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John
TDI. Currently increments XY values during acquisition. Have you thought about allowing these points to be manually automated? My reason is that I am analysing some vesicular glasses with a broad beam. Sometimes there just ain't the space.
Cheers,
Malc.
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John
TDI. Currently increments XY values during acquisition. Have you thought about allowing these points to be manually automated? My reason is that I am analysing some vesicular glasses with a broad beam. Sometimes there just ain't the space.
Cheers,
Malc.
Hi Malcolm,
As I suggested previously, you should not be using the assigned TDI. Please use the self TDI and all will be well. See here:
http://probesoftware.com/smf/index.php?topic=11.msg252#msg252
john
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Hi John
Irrespective of how I go about skinning my cat, how's about thinking about my idea? I'm sure that when doing the acquired TDI, the standards would be in good condition (maybe), but the docs also state that this can be done for an unknown sample similar or more or less the same in composition (matrix) as the actual unknowns. I thought it might be handy in this case to have an addition option for locality selection.
Cheers,
Malc.
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Hi John
Irrespective of how I go about skinning my cat, how's about thinking about my idea? I'm sure that when doing the acquired TDI, the standards would be in good condition (maybe), but the docs also state that this can be done for an unknown sample similar or more or less the same in composition (matrix) as the actual unknowns. I thought it might be handy in this case to have an addition option for locality selection.
Cheers,
Malc.
Hi Malcolm,
It's not a bad idea. It's similar to the increment x/y during wavelength scanning feature in PFE.
But this (assigned) TDI option is used by no one that I know of (except you) because it is only applicable to rare situations where the samples are completely homogeneous. And I've got about a dozen other very cool new ideas I'm implementing at the moment.
So just please, please, please use the self TDI and it will work fine for you.
john
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I wish that in standard.exe and there under interference calculations I could choose not only the element and the line, but also the crystal.
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I wish that in standard.exe and there under interference calculations I could choose not only the element and the line, but also the crystal.
You can change the "default" crystal (and x-ray line) for an element in the ELEMENTS.DAT file.
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Yes, I figured that out, but it is not very convenient, as it is necessary to restart standard.exe. We have several overlapping crystals, PET-QTZ and LiF-QTZ so I usually move elements around and evaluate the theoretical overlaps. The "default crystal" thing is fine, but for us there is usually no such thing as default crystal.
No way to get it implemented?
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Yes, I figured that out, but it is not very convenient, as it is necessary to restart standard.exe. We have several overlapping crystals, PET-QTZ and LiF-QTZ so I usually move elements around and evaluate the theoretical overlaps. The "default crystal" thing is fine, but for us there is usually no such thing as default crystal.
No way to get it implemented?
Of course anything can be implemented. It's just a question of taking time to do it and in such a way that it does what it needs to properly. I'll make a note of it, but let me think a bit about what might be the coolest way to implement it.
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Yes, I figured that out, but it is not very convenient, as it is necessary to restart standard.exe. We have several overlapping crystals, PET-QTZ and LiF-QTZ so I usually move elements around and evaluate the theoretical overlaps. The "default crystal" thing is fine, but for us there is usually no such thing as default crystal.
No way to get it implemented?
And of course you can also model spectral interferences in the Standard Assignments window as discussed in this post (see embedded pictures near the bottom of the post):
http://probesoftware.com/smf/index.php?topic=69.msg257#msg257
This calculation automatically utilizes whatever crystal you are currently using for acquisition/analysis.
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The advantahe of doing it in standard.exe is, that I can enter the composition of my unknown. Like U85 Pu4 O11. Then it takes into account that there is LOTS of U and only LITTLE Pu. This is important for me. However, then I need to fiddle around with my current setup in the Elements/Cations window. I'd prefer not to do that.
By the way the interference calculations in the element properties window do
1) not work for beta lines,
2) and do not show the offset in spectrometer units.
See image below.
(https://probesoftware.com/smf/oldpics/i59.tinypic.com/jha8uv.jpg)
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The advantahe of doing it in standard.exe is, that I can enter the composition of my unknown. Like U85 Pu4 O11. Then it takes into account that there is LOTS of U and only LITTLE Pu. This is important for me. However, then I need to fiddle around with my current setup in the Elements/Cations window. I'd prefer not to do that.
By the way the interference calculations in the element properties window do
1) not work for beta lines,
2) and do not show the offset in spectrometer units.
See image below.
(https://probesoftware.com/smf/oldpics/i59.tinypic.com/jha8uv.jpg)
Hi Philippe,
It looks like it works for beta lines, as you have one displayed in your image!
Unlike Standard, the spectrometer reading in PFE is in absolute value, not offset. I could change that to display in relative spectrometer offset values if you prefer.
john
Edit by John: Ok, I see why the Elements/Cations dialog nominal spectral interferences are not displayed in relative offsets... they *are* displayed in relative offsets in the Standard Assignments dialog because the interference calculation there is for on-peak interferences.
But because the Element/Cations dialog is for *off-peak* interferences, there is a problem with what to reference the relative calculation to if the off-peaks are "same side" off-peaks! So for now they will stay in absolute spectro units... and the topic is open for discussion.
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As you might have noticed it says:
"For Cs Lb LiF at 2.66747 angstroms (66248) ..."
That IS the La peak position. It even calculates the interference with the Cs Lb line, see below. Where it also gives the correct value for the Lb line. The list value for Cs Lb is 66665.9 (2.6843 A) or on my spec it is "On-Peak" 66651.0.
Elighten me, if I am wrong.
As from my point of view, everything is quite ok, but being able to choose the crystal in standard.exe would be very helpful.
(https://probesoftware.com/smf/oldpics/i58.tinypic.com/153briw.jpg)
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As you might have noticed it says:
"For Cs Lb LiF at 2.66747 angstroms (66248) ..."
That IS the La peak position. It even calculates the interference with the Cs Lb line, see below. Where it also gives the correct value for the Lb line. The list value for Cs Lb is 66665.9 (2.6843 A) or on my spec it is "On-Peak" 66651.0.
Elighten me, if I am wrong.
As from my point of view, everything is quite ok, but being able to choose the crystal in standard.exe would be very helpful.
(https://probesoftware.com/smf/oldpics/i58.tinypic.com/153briw.jpg)
Hi Philipp,
Ok, I see the source of your confusion. First of all it appears you are using an edited file of x-ray line energies, which confused me a bit...
But more importantly, when it says "For Cs Lb LiF at 2.66747 angstroms (66248) ..."
The phrase "Cs Lb" doesn't mean the on-peak position of the Cs Lb, it means the off-peak position of Cs Lb. In the screen shot below, because I clicked the "Low Off-Peak Interferences" button, it lists the interferences in the vicinity of the Cs Lb low off-peak position. Which is exactly what one would like to see, correct? If I had clicked the "Hi Off-Peak Interferences" button it would display the interferences around the Cs Lb high off peak position.
(https://probesoftware.com/smf/oldpics/i62.tinypic.com/mrd01l.jpg)
Does that make more sense?
I can fix the output so it states that more clearly. Remember, in the Standard Assignments dialog is where you can see the on-peak interferences...
By the way, I just checked and one can change the default crystal for an element in Standard.exe. The default crystal for that element will then "stick" for that Standard.exe session until the program is closed and will work for the nominal interference calculation in Standard as you asked for.
Do you not see this...?
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Ok, I will check for these low-/high off peak things and report back if that is what I see too.
Can you show me where you change that crystal? I might be blind -- I have not found it yet.
Thanks
Philipp
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Ok, I will check for these low-/high off peak things and report back if that is what I see too.
Can you show me where you change that crystal? I might be blind -- I have not found it yet.
Thanks
Philipp
1. Open your standard database.
2. Select a standard.
3. Click the Standard | Modify menu
4. Click the element you want to change the default crystal for.
5. Click the crystal combo and select the new crystal.
6. Click OK, OK again and Yes.
7. Go to the Options | Interferences menu and perform your nominal interference calculations using the new crystal.
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I wish I could hit my JEOL stor button and it would add a single point to the run table!
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Can you show me where you change that crystal? I might be blind -- I have not found it yet.
1. Open your standard database.
2. Select a standard.
3. Click the Standard | Modify menu
4. Click the element you want to change the default crystal for.
5. Click the crystal combo and select the new crystal.
6. Click OK, OK again and Yes.
7. Go to the Options | Interferences menu and perform your nominal interference calculations using the new crystal.
Great, this does indeed work. Not convenient, but it does work. Well, if one day you are looking for a nice thing to program, a little crystal button would still be appreciated.
Thanks
Ph
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Ok, I see the source of your confusion. First of all it appears you are using an edited file of x-ray line energies, which confused me a bit...
But more importantly, when it says "For Cs Lb LiF at 2.66747 angstroms (66248) ..."
The phrase "Cs Lb" doesn't mean the on-peak position of the Cs Lb, it means the off-peak position of Cs Lb. In the screen shot below, because I clicked the "Low Off-Peak Interferences" button, it lists the interferences in the vicinity of the Cs Lb low off-peak position. Which is exactly what one would like to see, correct? If I had clicked the "Hi Off-Peak Interferences" button it would display the interferences around the Cs Lb high off peak position.
(https://probesoftware.com/smf/oldpics/i62.tinypic.com/mrd01l.jpg)
Does that make more sense?
I can fix the output so it states that more clearly. Remember, in the Standard Assignments dialog is where you can see the on-peak interferences...
Hi John,
yes, this does make more sense. I think a slight rewording of the text might be helpful, because I got confused by the peak position, which was in fact one of the background positions... Maybe this can be made more clear.
Cheers
Philipp
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Ok, I see the source of your confusion. First of all it appears you are using an edited file of x-ray line energies, which confused me a bit...
But more importantly, when it says "For Cs Lb LiF at 2.66747 angstroms (66248) ..."
The phrase "Cs Lb" doesn't mean the on-peak position of the Cs Lb, it means the off-peak position of Cs Lb. In the screen shot below, because I clicked the "Low Off-Peak Interferences" button, it lists the interferences in the vicinity of the Cs Lb low off-peak position. Which is exactly what one would like to see, correct? If I had clicked the "Hi Off-Peak Interferences" button it would display the interferences around the Cs Lb high off peak position.
(https://probesoftware.com/smf/oldpics/i62.tinypic.com/mrd01l.jpg)
Does that make more sense?
I can fix the output so it states that more clearly. Remember, in the Standard Assignments dialog is where you can see the on-peak interferences...
Hi John,
yes, this does make more sense. I think a slight rewording of the text might be helpful, because I got confused by the peak position, which was in fact one of the background positions... Maybe this can be made more clear.
Cheers
Philipp
Yes, the text is now improved as seen here:
For Pr la (hi-off), LIF at 2.48099 angstroms( 61865.7), at an assumed concentration of 1 wt.%
Interference by La LB4 at 2.44970 ( 61088.7) = 2.5%
Interference by Pb LG6 III at 2.45060 ( 61111.1) = .3%
Interference by Pb SLG2` III at 2.45750 ( 61282.4) = 1.8%
Interference by La LB1 at 2.45950 ( 61332.1) = 269.5%
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Hi John,
in PfE, when I output data in user specified format, and I select the sample name column, the sample name is correctly outputted. However, in the average and Stddev rows the sample name is "0". Could we have the sample name also here? It would help sorting samples in excel.
Cheers
Philipp
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Hi John,
in PfE, when I output data in user specified format, and I select the sample name column, the sample name is correctly outputted. However, in the average and Stddev rows the sample name is "0". Could we have the sample name also here? It would help sorting samples in excel.
Cheers
Philipp
Hi Philipp,
How's this for "turn around": your wish is granted- download now!
Also see this please:
http://probesoftware.com/smf/index.php?topic=47.msg3500#msg3500
john
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Sounds great! Thanks a lot!
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Is three a way to automate a varying number of standard analyses? If not this might be a nice feature to have.
For example I was trying to automate standards overnight, and some of our standards are know to be less homogenous than others, which isn't a problem as long as we average a large number of standard analyses (~30-50). However I don't want to run that many standard analyses points on the rest of my standards that are homogenous as that would be a waste of time. My solution was to run the homogenous standards first (with 10 points per standard), and then log in remotely in the evening to run the heterogenous standards (with 30 points per standard).
Couldn't there be an option to run the number of points that are automated (like we do in the unknown automation)?
phil
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Is three a way to automate a varying number of standard analyses? If not this might be a nice feature to have.
For example I was trying to automate standards overnight, and some of our standards are know to be less homogenous than others, which isn't a problem as long as we average a large number of standard analyses (~30-50). However I don't want to run that many standard analyses points on the rest of my standards that are homogenous as that would be a waste of time. My solution was to run the homogenous standards first (with 10 points per standard), and then log in remotely in the evening to run the heterogenous standards (with 30 points per standard).
Couldn't there be an option to run the number of points that are automated (like we do in the unknown automation)?
phil
The only thing I can think of is to create a number of identical MDB files (with slightly different names obviously, for example, 4stdpoints.mdb, 8stdpoints.mdb, etc), where the *only* difference is the number of standard points to acquire in the Automate! window, and then simply use the File Setup as the automation basis for your standards in another MDB file.
john
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Hi John,
I think in PFE you can control the OM light on/off. What we often do on the JEol is use the autofocus which is really good but requires the light on - then if we take automatic pictures the BSE contrast/brightness never works as the reflectivity of the sample keeps changing. What would be really neat would be if during an automated run of points with light on using autofocus, we could check box somewhere that for each automatic image it would turn the light off - acquire the bse image - then turn the light on. What do think? Would it add a large overhead?
Ben
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Hi John,
I think in PFE you can control the OM light on/off. What we often do on the JEol is use the autofocus which is really good but requires the light on - then if we take automatic pictures the BSE contrast/brightness never works as the reflectivity of the sample keeps changing. What would be really neat would be if during an automated run of points with light on using autofocus, we could check box somewhere that for each automatic image it would turn the light off - acquire the bse image - then turn the light on. What do think? Would it add a large overhead?
Ben
So the software doesn't already automatically turn off the light after the auto-focus is run?
It's not a bad idea at all I think. It could be implemented...
john
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Hi John,
Hopefully a pretty quick one for you. When I close DigitizeImage without having saved the acquired image, I receive a very helpful prompt asking whether I want to save the image before exiting. Currently the prompt offers options "Yes" (save the image to the database, then exit DigitizeImage) and "No" (don't save the image, then exit DigitizeImage).
Would it be possible to add a third "Cancel" option to the exit dialog (in addtion to "Yes" and "No"), meaning "return to DigitizeImage without doing anything, do not exit or save/not save the image, Owen clicked the wrong button like an idiot and didn't really want to exit DigitizeImage in the first place." Sometimes, if you hit the Enter key at the wrong time, DigitizeImage closes when you don't mean it to.
Thanks!
Everything is possible, but not always easy!
Why not just re-open the Digitize Image window again if you closed it accidentally?
How's the Boeing installation going?
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Why not just re-open the Digitize Image window again if you closed it accidentally?
If I re-open, the image needs to be re-acquired, and the previously-picked points are not shown on the new image.
Well then, don't close the damn window unless you really want to! ::)
Seriously, I'm sure I could add a Cancel button... this weekend.
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Why not just re-open the Digitize Image window again if you closed it accidentally?
If I re-open, the image needs to be re-acquired, and the previously-picked points are not shown on the new image.
Well then, don't close the damn window unless you really want to! ::)
Seriously, I'm sure I could add a Cancel button... this weekend.
No rush - low priority item. Thanks!
Your wish is granted!
Cancel button added!
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A possibly crazy EDS idea and perhaps a less crazy one...
I'm not sure how well the Thermo software fits EDS backgrounds, but on Bruker some materials don't result in great fits and therefore the background subtraction for net intensities can be off a bit. As an example, I have seen >0.5 wt% Al2O3 reported in a material with no Al because the background model was too low. Other than better EDS background fits, I wonder if MAN for EDS might work. To do this, one would need total counts within a ROI, not just the net counts. Yes, this appears crazy since EDS records the (sometimes cluttered) adjacent backgrounds, but as with the example above, there can be problems with these.
The perhaps more sane idea relates to the overhead of processing runs with lots of EDS data, an overhead that would be multiplied many times over if TDI using EDS intensities is implemented. Perhaps once they are first extracted, the EDS intensities could be cached in the MDB. Then, reprocessing would go much faster. Of course, there would have to be a way to repopulate the cache as needed, either on demand, or if one changes the EDS elements.
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A possibly crazy EDS idea and perhaps a less crazy one...
I'm not sure how well the Thermo software fits EDS backgrounds, but on Bruker some materials don't result in great fits and therefore the background subtraction for net intensities can be off a bit. As an example, I have seen >0.5 wt% Al2O3 reported in a material with no Al because the background model was too low. Other than better EDS background fits, I wonder if MAN for EDS might work. To do this, one would need total counts within a ROI, not just the net counts. Yes, this appears crazy since EDS records the (sometimes cluttered) adjacent backgrounds, but as with the example above, there can be problems with these.
The perhaps more sane idea relates to the overhead of processing runs with lots of EDS data, an overhead that would be multiplied many times over if TDI using EDS intensities is implemented. Perhaps once they are first extracted, the EDS intensities could be cached in the MDB. Then, reprocessing would go much faster. Of course, there would have to be a way to repopulate the cache as needed, either on demand, or if one changes the EDS elements.
Hi Steve,
I seem to have overlooked this post of yours.
In the latest versions of Probe for EPMA one can now specify the quant method (including background fit models) for both Bruker and Thermo integrated EDS-WDS quantification.
For Thermo, the specify quant method is currently global (though Thermo has said they could add an API call that would allow it to be specified on a per sample basis), while with Bruker one can specify the quant method on a per sample basis and PFE automatically saves that info for subsequent processing.
I realize you are still using an ancient version of PFE for data acquisition, but have you tried opening one of your old PFE database files with a new version of PFE for data reprocessing?
As for MAN on EDS ROIs, I'd have to think about that... one issue is that the vendors would have to provide a new get intensity call because they control the ROI widths.
As for EDS TDI, that would be a major task to implement, but maybe someday when I get my head above water... ;)
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John,
I haven't installed the new version yet, but I probably should. I have an offline computer with the Bruker software already on it. So, I would need to download, install (assume I will need a password for a fresh install), and configure.
A couple of years ago, I spent a little time trying to get the Bruker interface working on an offline computer, but I didn't get it working. It wasn't terribly important, and I never got back to it. If I recall correctly, demo mode wouldn't talk to Bruker, and telling it to interface to the probe didn't work since there was no probe.
What is the right way to set up an offline computer (no hardware access) so that it still has an active connection to the EDS software for data reprocessing?
- Steve
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I haven't installed the new version yet, but I probably should. I have an offline computer with the Bruker software already on it. So, I would need to download, install (assume I will need a password for a fresh install), and configure.
A couple of years ago, I spent a little time trying to get the Bruker interface working on an offline computer, but I didn't get it working. It wasn't terribly important, and I never got back to it. If I recall correctly, demo mode wouldn't talk to Bruker, and telling it to interface to the probe didn't work since there was no probe.
What is the right way to set up an offline computer (no hardware access) so that it still has an active connection to the EDS software for data reprocessing?
Hi Steve,
Email me for the PFE download password and I'll also send you a document for installing the Bruker software for off-line EDS-WDS data processing.
Note that you need the API and LAN licenses from Bruker for off-line processing. That's another nice thing about Thermo- no separate license is required for data reprocessing! Just like Probe for EPMA!
john
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Hi John,
I would like to be able to better line up the Automate! Position List numbering scheme, and the quantitative analytical results.
Our student is taking BSE images with Automate! Digitize, Digitize Image.
The student then sets quantitative-analysis points using Automate! Digitize, Single Point.
After the points are run, the student exports all of the BSE images as bitmaps.
The student then goes to Automate! Digitize, Picture Snap and plots the unknowns with long labels, saving the annotated image as a BMP with graphic objects.
Unfortunately, the numbering scheme in the Analyze! Sample List is not the same as in the Automate! Position List.
This means that the annotated image does not match the analytical results, and the labels in the analytical results have to be updated manually.
As per your off-forum email "...thought about adding an additional field that could be saved during automated acquisition that contains the Automate row number for plotting or other purposes." Could you please add this new field? In that way, the annotated BMPs would be a better reflection of the data.
Thanks,
Andrew
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Hi John,
I would like to be able to better line up the Automate! Position List numbering scheme, and the quantitative analytical results.
Our student is taking BSE images with Automate! Digitize, Digitize Image.
The student then sets quantitative-analysis points using Automate! Digitize, Single Point.
After the points are run, the student exports all of the BSE images as bitmaps.
The student then goes to Automate! Digitize, Picture Snap and plots the unknowns with long labels, saving the annotated image as a BMP with graphic objects.
Unfortunately, the numbering scheme in the Analyze! Sample List is not the same as in the Automate! Position List.
This means that the annotated image does not match the analytical results, and the labels in the analytical results have to be updated manually.
As per your off-forum email "...thought about adding an additional field that could be saved during automated acquisition that contains the Automate row number for plotting or other purposes." Could you please add this new field? In that way, the annotated BMPs would be a better reflection of the data.
Thanks,
Andrew
Andrew,
Ok, I see what you mean now.
There is already a solution for displaying the analysis positions in PictureSnap using the Analyze! line numbers as opposed to the Automate! row numbers. Instead of using the menus from PictureSnap, simply open PictureSnap from this menu:
(https://probesoftware.com/smf/oldpics/i68.tinypic.com/2wnttf9.jpg)
and then select the display unknown position and long labels menu as shown to see this:
(https://probesoftware.com/smf/oldpics/i68.tinypic.com/4s1gfk.jpg)
I think that is what you want?
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Just a minor thing, but for me it would be great if in the PHA window there was a "Get all" button or something to read in the PHA values for all elements at once instead of individually clicking on each element, get PHA, click OK. I guess I could just modify the SCALERS.DAT file every time I change the PHA settings...but was just a thought.
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Just a minor thing, but for me it would be great if in the PHA window there was a "Get all" button or something to read in the PHA values for all elements at once instead of individually clicking on each element, get PHA, click OK. I guess I could just modify the SCALERS.DAT file every time I change the PHA settings...but was just a thought.
I could certainly add a "get all" button but if you change the ini file in the [software] section as seen below, it will occur automatically when you start the app.
[software]
UseCurrentConditionsOnStartUp=1 ; non-zero = read current instrument condition on software start
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Hi John,
I have a request for the wish list. I do a lot of MAN and it would be nice if in the "Aquisition Options" it was possible to highlight all of the elements and change them to MAN in one go. It must be possible as you can change all of the on-peak times in the "Count Times" window. ;D
Best wishes
Gareth
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Hi John,
I have a request for the wish list. I do a lot of MAN and it would be nice if in the "Aquisition Options" it was possible to highlight all of the elements and change them to MAN in one go. It must be possible as you can change all of the on-peak times in the "Count Times" window. ;D
Best wishes
Gareth
Hi Gareth,
I can absolutely add a "Change All To MAN" button and also a "Change All To Off-Peak" button. Easy.
You probably know this but since it's related I should mention that one can acquire off-peak data and subsequently process it both using off-peak background corrections and also using MAN background corrections as described here:
http://probesoftware.com/smf/index.php?topic=4.msg189#msg189
If I'm going to be looking at the data repeatedly, I will often make a copy of the MDB data file and leave one file as off-peak (the default), but then use the menus described in the above link for the copied file to calculate everything using MAN backgrounds.
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First, thanks to you and Gareth for all your efforts with the new graphics, the look very nice. A few minor tweaks to consider.
1) On TDI plots, would it be possible to remove (or at least make toggle-able) the thin lines connecting individual data points? They extra lines become distracting, especially if you are displaying multiple TDI's for multiple datapoints. I know you can have the software display a subset of the acquired data from a sample when displaying TDI fits, but sometimes you want to see all the data. See attached screenshot TDI_Lines.jpg.
I agree. Without the connecting lines it looks cleaner as seen here:
(https://probesoftware.com/smf/gallery/1_12_02_16_5_44_00.png)
And if someone still wants connecting lines, I added an option for it:
(https://probesoftware.com/smf/gallery/1_12_02_16_5_44_59.png)
Here's with a zoom:
(https://probesoftware.com/smf/gallery/1_12_02_16_6_03_01.png)
2) For the CalcZAF error histograms, sometimes the histogram data overlaps the displayed metadata about which matrix correction options were selected. Maybe make the font for the metadata could be made smaller, or the metadata could be moved to a separate sub-plot, either off to the side or below the window? See attached screenshot CalcZAF_Histogram.jpg.
Yes, the graphics can be improved in several ways. For example, I also added a 1.0 line as seen here:
(https://probesoftware.com/smf/gallery/1_12_02_16_5_47_43.png)
3) This one may pre-date the graphics conversion, but when using the Evaluate.exe application, when the "Use Average of Sample" option is checked, the standard with the highest concentration does not get displayed on the chart. See attached screenshots Evaluate_Average.jpg and Evaluate_NoAverage.jpg. This does not appear to be a scaling issue - expanding the X and Y does not reveal the missing points, and the data for the highest concentration sample is also omitted in the .DAT file produced by clicking "Save Data to File" when the average is used. Also, this behavior seems to only occur when plotting relative differences - when plotting calculated vs. database concentration (i.e. unchecking "Plot Relative Difference"), the highest concentration sample is displayed regardless of whether Use Average of Sample is checked or not.
I checked and the latest version of Evaluate seems to work:
(https://probesoftware.com/smf/gallery/1_12_02_16_5_49_23.png)
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I have a request for the wish list. I do a lot of MAN and it would be nice if in the "Aquisition Options" it was possible to highlight all of the elements and change them to MAN in one go. It must be possible as you can change all of the on-peak times in the "Count Times" window. ;D
Hi Gareth,
Nice to hear from you. I did it slightly differently as seen here:
(https://probesoftware.com/smf/gallery/1_12_02_16_5_58_52.png)
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I LOVE the new graphics. I'm creating some very pretty multi-background plots at the moment with overlaid wavescan and KLM markers.
I wish that in the Display MultiPoint Backgrounds window it would stay on the same element when switching between datasets and rows (like in the TDI window) and not jump back to the first element in the list when switching datasets or rows.
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I LOVE the new graphics. I'm creating some very pretty multi-background plots at the moment with overlaid wavescan and KLM markers.
I wish that in the Display MultiPoint Backgrounds window it would stay on the same element when switching between datasets and rows (like in the TDI window) and not jump back to the first element in the list when switching datasets or rows.
Very cool. We'd love to see some of your plots- feel free to utilize the new forum gallery.
As requested I'm uploading a new version of PFE now, that has the element selection preserved for different lines/samples in the MPB and also for the calibration curve dialogs.
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Thanks for the new "Change all to MAN" button John, it will certainly reduce the number of clicks I have have to do :)
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John - thanks for the graphics tweaks, they look excellent. Thanks also to you and Gareth H. for the "Change all to MAN" button - very useful feature.
Re: Evaluate, I'm using v11.3.4, updated from the main PFE Help menu at ~10am today. Still seeing the same behavior - the highest-concentration standard does not get displayed when using the "Use Average of Sample" option. Have tried a variety of different MDB files and standard databases, doesn't seem to matter. Also does not seem to be element-specific or standard-specific, and does not change whether there are a "lot" (>20) values to plot or only a "few" (~3-4). However, it's a minor point, so feel free to backburner it - if it's working on your end, it's probably the result of me being stupid rather than a bug. That said, the "Set 2" data points do not seem to get text labels in Evaluate (see screenshots). Not sure if this is intentional or not, but also nitpicky, so feel free to ignore.
Thanks again!
Hi Owen,
I deliberately do not show labels for subsequent sets. I could do that but I thought it would get crowded. That said, something doesn't appear to be quite right in your plots.
For example, standard 1110 is displayed (single square symbol), but there is no label as it's only plotted as a 2nd set for some reason. Perhaps send me the MDB file off-line and let me look closer at it.
I'm pleased that people seem to like the new graphics. These still some tweaking to do, e.g., symbols sizes, etc., but that's easy.
john
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Just a minor thing, but for me it would be great if in the PHA window there was a "Get all" button or something to read in the PHA values for all elements at once instead of individually clicking on each element, get PHA, click OK. I guess I could just modify the SCALERS.DAT file every time I change the PHA settings...but was just a thought.
I could certainly add a "get all" button but if you change the ini file in the [software] section as seen below, it will occur automatically when you start the app.
[software]
UseCurrentConditionsOnStartUp=1 ; non-zero = read current instrument condition on software start
Great, thanks for that tip
I second Karsten's suggestion as well, but am late to the party so looks like that is now implemented as well!
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I LOVE the new graphics. I'm creating some very pretty multi-background plots at the moment with overlaid wavescan and KLM markers.
I wish that in the Display MultiPoint Backgrounds window it would stay on the same element when switching between datasets and rows (like in the TDI window) and not jump back to the first element in the list when switching datasets or rows.
Very cool. We'd love to see some of your plots- feel free to utilize the new forum gallery.
As requested I'm uploading a new version of PFE now, that has the element selection preserved for different lines/samples in the MPB and also for the calibration curve dialogs.
Many thanks, I saw you also removed the connecting lines when displaying all data lines in a sample which looks much cleaner this way.
This is an example for Y in scheelite:
(https://probesoftware.com/smf/gallery/7_23_02_16_4_59_02.png)
Or for S in scheelite:
(https://probesoftware.com/smf/gallery/7_23_02_16_4_59_35.png)
Cheers, Karsten
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Hi John,
Enjoying the discussion about trace elements. It reminded me about one wish I have for the multipoint background display. Being colourblind, the actual spectrum overlay in the displays is just about invisible to me. Is it possible to allow the user to change colour or alt least have a switch that can change the colour to something a bit less pastel. Otherwise I'm finding the colours appropriate, this is about the only place where I've having visibility issues.
Cheers
Glenn
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Hi John,
Enjoying the discussion about trace elements. It reminded me about one wish I have for the multipoint background display. Being colourblind, the actual spectrum overlay in the displays is just about invisible to me. Is it possible to allow the user to change colour or alt least have a switch that can change the colour to something a bit less pastel. Otherwise I'm finding the colours appropriate, this is about the only place where I've having visibility issues.
Cheers
Glenn
Hi Glenn,
Thanks, I'll be posting much more once my stage is fixed!
In the meantime, is this better for you (and everyone else)?
(https://probesoftware.com/smf/gallery/1_22_03_16_11_49_05.png)
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Don't know what colour it is ;D, but its a lot more visible.
Thanks a lot appreciate the quick response.
Glenn
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Don't know what colour it is ;D, but its a lot more visible.
Thanks a lot appreciate the quick response.
Glenn
I made it a little more blue and it can be downloaded now. I too have no idea of the color name.
I can tweak it more if necessary.
john
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Here's what the new MPB wavescan overlay plot color looks like:
(https://probesoftware.com/smf/gallery/395_23_03_16_10_37_24.png)
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Hi,
I wish for an output option for pha scan/peak scan data including the meta data. Currently, when I go into the pha scan dialog I can output only one scan at a time and the ascii file does not include the metadata (spectrometer, bias, gain, count time, etc). Is there another output option where I can select multiple scans or just have all exported at a time?
Thank you!
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Hi,
I wish for an output option for pha scan/peak scan data including the meta data. Currently, when I go into the pha scan dialog I can output only one scan at a time and the ascii file does not include the metadata (spectrometer, bias, gain, count time, etc). Is there another output option where I can select multiple scans or just have all exported at a time?
Thank you!
Hi Anette,
Right now it is as you describe, but it's easy to add an output with the meta data.
We're currently in Provo, UT but will be back in Eugene late Saturday.
john
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Hi,
I wish for an output option for pha scan/peak scan data including the meta data. Currently, when I go into the pha scan dialog I can output only one scan at a time and the ascii file does not include the metadata (spectrometer, bias, gain, count time, etc). Is there another output option where I can select multiple scans or just have all exported at a time?
Thank you!
Hi Anette,
Right now it is as you describe, but it's easy to add an output with the meta data.
We're currently in Provo, UT but will be back in Eugene late Saturday.
john
Hi Anette,
I have a first effort at a peaking or PHA scan output feature in PFE v. 11.5.1.
It's under the Output menu. Please try it and let me know what you think.
john
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Hi,
I wish for an output option for pha scan/peak scan data including the meta data. Currently, when I go into the pha scan dialog I can output only one scan at a time and the ascii file does not include the metadata (spectrometer, bias, gain, count time, etc). Is there another output option where I can select multiple scans or just have all exported at a time?
Thank you!
Hi Anette,
Right now it is as you describe, but it's easy to add an output with the meta data.
We're currently in Provo, UT but will be back in Eugene late Saturday.
john
Hi Anette,
I have a first effort at a peaking or PHA scan output feature in PFE v. 11.5.1.
It's under the Output menu. Please try it and let me know what you think.
john
Here is a screen shot of the PHA data output to Excel:
(https://probesoftware.com/smf/gallery/1_21_06_16_9_52_19.png)
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Hi John,
currently, when I graph a wavescan with a background model and then go to the Export or Customization dialog (right mouse-click on graph), the background model disappears. Could you (or Gareth) make it that the background model stays?
Sometimes I would like to import my graphs including the background model into another program (Illustrator) for publications, presentations etc and therefore export them as wmf from PFE.
Thanks!
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Hi John,
currently, when I graph a wavescan with a background model and then go to the Export or Customization dialog (right mouse-click on graph), the background model disappears. Could you (or Gareth) make it that the background model stays?
Sometimes I would like to import my graphs including the background model into another program (Illustrator) for publications, presentations etc and therefore export them as wmf from PFE.
Thanks!
It works when using the Clipboard button:
(https://probesoftware.com/smf/gallery/1_30_06_16_4_28_17.png)
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The latest version of Probe for EPMA (v. 11.5.5) now displays the specified background fit to the measured off-peak intensities as seen in this exponential (two point) fit to an integrated intensity acquisition:
(https://probesoftware.com/smf/gallery/1_23_07_16_2_23_48.png)
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How about displaying the PHA window on the PHA scan data? Low priority, but could be useful.
e.g.
(https://probesoftware.com/smf/gallery/22_24_02_20_12_56_04.jpeg)
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How about displaying the PHA window on the PHA scan data? Low priority, but could be useful.
How about this?
(https://probesoftware.com/smf/gallery/1_10_09_16_9_40_09.png)
Please use the Help menu to update.
john
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Hi John
First of all, the way you have improved the processing of the integrated intensity scans is awesome! I like the option to be able to delete points and that it uses multiple points at the beginning and end for the background. At the moment the limit is set to 20 points at the beginning and end. Is it possible to increase the number to maybe 50? With trace elements we like to do 50% peak and 50% background. Also could you show somewhere of how many points the scan consists?
Thanks
Sandrin
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First of all, the way you have improved the processing of the integrated intensity scans is awesome! I like the option to be able to delete points and that it uses multiple points at the beginning and end for the background. At the moment the limit is set to 20 points at the beginning and end. Is it possible to increase the number to maybe 50? With trace elements we like to do 50% peak and 50% background. Also could you show somewhere of how many points the scan consists?
Hi Sandrin,
Ok, I made the requested changes. Go ahead and update Probe for EPMA and you will have them.
john
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First of all, the way you have improved the processing of the integrated intensity scans is awesome! I like the option to be able to delete points and that it uses multiple points at the beginning and end for the background. At the moment the limit is set to 20 points at the beginning and end. Is it possible to increase the number to maybe 50? With trace elements we like to do 50% peak and 50% background. Also could you show somewhere of how many points the scan consists?
Hi Sandrin,
Ok, I made the requested changes. Go ahead and update Probe for EPMA and you will have them.
john
Hi Sandrin,
I was thinking about how I might implement a "status" field for the integrated intensity points so they could be disabled/enabled just like normal data, but I wasn't sure how to handle the display and fitting.
Obviously if one needs to re-enable the disabled point(s) one has to see them. But then I thought I might be able to utilize the "missing data" option in the display so they are present, but just not displayed... so I'm still thinking about this.
I hate to permanently delete any data (it goes against my core values!), but I wonder how important it would be to you and Karsten to be able to "undelete" the "deleted" integrated intensity scan points?
john
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After a couple months of testing PfE on my new instrument (8230), I have been wondering about a couple missing (or removed?) options:
(1) A while ago (2010-2011), when we started the Multipoint Background Crusade for the [Holy] Grail of Trace Analysis, the option to "output multipoint background intensities" would actual export the individual measurements on each single background point set. Now, this feature returns only the background intensity under the peak calculated using the currently selected MPB fitting. It would be desirable to have in the multipoint background output the complete list of counting time, intensity, position... on EACH multipoint background.
(2) An option to export the data from a MAN would be welcome (i.e. an output of the average Z and intensity value of each standard for a selected element - ideally this would run as a batch and export all MAN data for all elements). This would allow for instance to compare MAN data overtime. Currently this cannot be done with Probe for EPMA, unless all these data are acquired in the same MDB file.
(3) It appears that the MAN assignment tool only allow for a maximum of 16 standards. I have been running a 31-elements run with 32 standards, and for some, I could well include over 20 standards in the regression! Not that I want to do this all the time, but for these first testing, I would like to see what "best" standard is suitable for the MAN background correction. Being able to plot all standards without limitation (or a high number, like at least 50-100...) would be ideal.
(4) Any chance we can increase the number of interferences per element (currently limited to 5). With my nasty and weird REE mineral analyses, some element would require at least 6 or 7 interferences corrections to be super accurate.
(5) And a long term project... That we could call hyperMAN, or maybe WoMAN? The idea: combining all MAN fit on one spectrometer to obtain a surface fitting
on ANY spectrometer position.
That's all... for the moment ;)
Julien
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(1) A while ago (2010-2011), when we started the Multipoint Background Crusade for the [Holy] Grail of Trace Analysis, the option to "output multipoint background intensities" would actual export the individual measurements on each single background point set. Now, this feature returns only the background intensity under the peak calculated using the currently selected MPB fitting. It would be desirable to have in the multipoint background output the complete list of counting time, intensity, position... on EACH multipoint background.
Hi Julien,
I haven't changed this output format- it still outputs the positions and intensities for each MPB:
(https://probesoftware.com/smf/gallery/1_17_09_16_8_57_20.png)
You're using the MPB output under the Output menu, correct?
(2) An option to export the data from a MAN would be welcome (i.e. an output of the average Z and intensity value of each standard for a selected element - ideally this would run as a batch and export all MAN data for all elements). This would allow for instance to compare MAN data overtime. Currently this cannot be done with Probe for EPMA, unless all these data are acquired in the same MDB file.
The Search.exe application will output all std intensities for a given element and x-ray, but not the average Z. One can get the average Z output for each standard from the Standard.exe application.
Or one could write a small code that opens a folder of MDB files and extracts the info you need.
(3) It appears that the MAN assignment tool only allow for a maximum of 16 standards. I have been running a 31-elements run with 32 standards, and for some, I could well include over 20 standards in the regression! Not that I want to do this all the time, but for these first testing, I would like to see what "best" standard is suitable for the MAN background correction. Being able to plot all standards without limitation (or a high number, like at least 50-100...) would be ideal.
I should be able to do this.
(4) Any chance we can increase the number of interferences per element (currently limited to 5). With my nasty and weird REE mineral analyses, some element would require at least 6 or 7 interferences corrections to be super accurate.
Yes, I think this can be done. There is no intrinsic limitation except the space necessary to fit the additional controls in the Elements/Cations dialog. That is a bit of a problem but I will see what can be done.
john
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(5) And a long term project... That we could call hyperMAN, or maybe WoMAN? The idea: combining all MAN fit on one spectrometer to obtain a surface fitting on ANY spectrometer position.
This reminds me of Steve Kuehn's idea for a full spectrometer scan range background fit. I think these ideas would be exceedingly difficult to implement, if not impossible. Absorption edges are an issue for one thing!
The nice thing about the MAN background method is that one is making a direct measurement of the continuum *directly under the emission peak*, albeit in materials that do not contain the element of interest! But still, there is no interpolation or extrapolation, except for the average Z variation!
Trying to extrapolate the background from other spectrometer positions would also be very difficult because WDS spectrometers are so non-linear in their response. This is exactly why there is no such thing as standardless WDS!
john
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(3) It appears that the MAN assignment tool only allow for a maximum of 16 standards. I have been running a 31-elements run with 32 standards, and for some, I could well include over 20 standards in the regression! Not that I want to do this all the time, but for these first testing, I would like to see what "best" standard is suitable for the MAN background correction. Being able to plot all standards without limitation (or a high number, like at least 50-100...) would be ideal.
Hi Julien,
I increased the number of MAN standard assignments per element to 36. Here's an example:
(https://probesoftware.com/smf/gallery/1_17_09_16_4_08_14.png)
Let's see how this works for you. I could increase it more, but it will eventually slow things down more.
When you are ready please update to v. 11.6.4.
john
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(4) Any chance we can increase the number of interferences per element (currently limited to 5). With my nasty and weird REE mineral analyses, some element would require at least 6 or 7 interferences corrections to be super accurate.
Hi Julien,
I increased the number interfering elements per element to 6 as seen here:
(https://probesoftware.com/smf/gallery/1_17_09_16_4_13_15.png)
I could increase it more but I'd have to work harder to fit everything in. By the way, the 6th interfering element will only be available for new MDB files.
When you are ready please update to v.11.6.4.
john
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Hi,
when acquiring wavescans I would love to be able to acquire simultaneously counts on one or more spectrometers at a fixed position (so like TDI simply). That way I could either monitor carbon contamination or beam damage etc directly. Right now I utilize the JEOL chart recorder at times but it would be nifty to have this as part of my PFE acquisition. Is this already possible or would that be possible to implement?
Thanks!
Anette
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when acquiring wavescans I would love to be able to acquire simultaneously counts on one or more spectrometers at a fixed position (so like TDI simply). That way I could either monitor carbon contamination or beam damage etc directly. Right now I utilize the JEOL chart recorder at times but it would be nifty to have this as part of my PFE acquisition. Is this already possible or would that be possible to implement?
Hi Anette,
I must be missing something because why not just measure carbon as an MAN element on one of your spectrometers to monitor carbon? You can disable quant on it so it doesn't affect your analysis...
As for beam damage, you can measure absorbed current during any TDI measurement:
http://probesoftware.com/smf/index.php?topic=40.msg4006#msg4006
john
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Hi John,
sorry, I think I didn't express myself clear enough. For example: I would like to do a (wide-range) wavescan on Spec1 and Spec2 and at the same time keep monitoring peak counts on Spec3 (like a chart recorder). So essentially a mix and match of TDI and wavescan but both being acquired simultaneously in the same wavescan acquisition. And then when plotted Spec1 and Spec2 have spectrometer units as X-axis and Spec2 has time elapsed.
So what I am looking for would be an additional button in the wavescan set-up -> peak/scan options that functions as "Set wavescan to On Peak" and sets the high/low limits to +0/-0 (no spectrometer movement).
Anette
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sorry, I think I didn't express myself clear enough. For example: I would like to do a (wide-range) wavescan on Spec1 and Spec2 and at the same time keep monitoring peak counts on Spec3 (like a chart recorder). So essentially a mix and match of TDI and wavescan but both being acquired simultaneously in the same wavescan acquisition. And then when plotted Spec1 and Spec2 have spectrometer units as X-axis and Spec2 has time elapsed.
So what I am looking for would be an additional button in the wavescan set-up -> peak/scan options that functions as "Set wavescan to On Peak" and sets the high/low limits to +0/-0 (no spectrometer movement).
OK, I see. That could/should be doable I think.
But did you try setting the wavescan range to a very tiny distance? Say +/- 0.001 mm. Maybe that works?
john
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Non-proprietary Hardware Interface?
How about a modern, completely open, fully-documented TCP-IP interface between PFE and the hardware usable by anyone and by any instrument, including both new and old machines and both EPMA and SEM. In this scenario, John et al. could build the PFE side, and any interested vendors/clients would build their respective machine side. Perhaps most of the configuration information could also be read from the machine at initialization time, reducing (eliminating?) the need for PFE config files.
Questions
- Would this be useful?
- Would there be sufficient client demand to justify doing such a project? (Imagine if everyone could run the latest PFE and ProbeImage on almost any hardware.)
- Is there any chance that JEOL/Cameca might someday switch to such an interface so PFE would no longer need to support multiple instrument interfaces? (Are there any potential incentives to encourage this?)
- What additional vendors might want their machines to work with such an interface, thus expanding the market for PFE?
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Non-proprietary Hardware Interface?
How about a modern, completely open, fully-documented TCP-IP interface between PFE and the hardware usable by anyone and by any instrument, including both new and old machines and both EPMA and SEM. In this scenario, John et al. could build the PFE side, and any interested vendors/clients would build their respective machine side. Perhaps most of the configuration information could also be read from the machine at initialization time, reducing (eliminating?) the need for PFE config files.
Hi Steve,
This reminds me of a proposal made by Dale Newbury some 15 or 20 years ago at an industry round table discussion. His proposal was very reasonable and yet was completely ignored by the vendors present.
And besides the near impossibility of getting hardware vendors to agree on a standard instrument interface (look at how hard the UNIX people tried to standardize UNIX and yet failed), this seems to be a solution in search of a problem. PFE already supports all networked instrument interfaces from JEOL (8900/8200/8500/8230/8530) and Cameca (SX100 and SXFive), so what else is there?
Yes, there is a Shimadzu microprobe offered in Japan and China, but no Shimadzu user has ever approached Probe Software about our software, and in fact at the last MAS EPMA TC in Madison in May, the Shimadzu reps were present, so I chatted with them about the possibility of providing an interface for their instrument, and gave them my card, but no one from the company has ever contacted me, so I guess they are not interested?
The closest thing to a standard interface for JEOL and Cameca instruments is our Remote Automation Server interface which will run the same script on both JEOL and Cameca instruments. How is this possible? By abstracting the instrument interface to be completely hardware independent. But "underneath the hood", all the instrument specific differences are automatically handled by knowing the instrument configuration from the Probewin.ini and other configuration files.
Check the instrument functions in the Remote Server interface documentation here:
http://probesoftware.com/smf/index.php?topic=88.0
It is quite complete and utilized by a number of our customers for custom application development.
john
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Hi John
As promised...
1) The ability for alternating on/off data to be used to correct data as per TDI (long term wish)
2) Slightly odd one. On our SXFive (and I assume SX100?) the joystick to control the stage around has two buttons on its base. One for autofocus of Z, the other automatically adds a position at your current XYZ location if storing in locations using PeakSight. Can this button be utilised so that my lazy butt doesnt have to click the "Single Point" button to store in a location?
Cheers
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1) The ability for alternating on/off data to be used to correct data as per TDI (long term wish)
Hi Ben,
I'm very lazy so I will do this as soon as I think of an elegant way to code it! :)
2) Slightly odd one. On our SXFive (and I assume SX100?) the joystick to control the stage around has two buttons on its base. One for autofocus of Z, the other automatically adds a position at your current XYZ location if storing in locations using PeakSight. Can this button be utilised so that my lazy butt doesnt have to click the "Single Point" button to store in a location?
Not odd, but unfortunately the joystick is connected to the Cameca PC, not the instrument, so I cannot access it from the Probe for EPMA computer. Maybe just use the Digitize Image feature to select single points on a BSE or SE or CL image?
john
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Hi John
Ah ok no problems, it keeps me ambidextrous anyway. I usually have one hand on the joystick the other on the mouse clicking single point at the same time. With regards to using the Digitize Image feature, I do also use that and use the PictureSnap window quite a lot to display and save point locations, but find that I have to go and review the points anyway as I seem to have quite an offset from what I think I am clicking on from the image and where it actually is on the sample. This is making sure there is no beam shift enabled as well. Is there some X/Y offset in an ini file somewhere I am missing?
While I am on a roll, another wish...
When calibrating a picture to the stage via 2/3 point calibrations in the PictureSnap window, it would be really good if you could digitally zoom in on the image you are calibrating to make sure the pixel/feature you are clicking on is correct. Mainly an issue when I have whole thin section scans (even at high res) I feel the need to zoom in on the picture to make sure I am clicking on what I think I am.
Cheers
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Ah ok no problems, it keeps me ambidextrous anyway. I usually have one hand on the joystick the other on the mouse clicking single point at the same time. With regards to using the Digitize Image feature, I do also use that and use the PictureSnap window quite a lot to display and save point locations, but find that I have to go and review the points anyway as I seem to have quite an offset from what I think I am clicking on from the image and where it actually is on the sample. This is making sure there is no beam shift enabled as well. Is there some X/Y offset in an ini file somewhere I am missing?
Hi Ben,
Sounds like you need to perform a beam scan calibration. See this topic here on the best method for this:
http://probesoftware.com/smf/index.php?topic=396.0
When calibrating a picture to the stage via 2/3 point calibrations in the PictureSnap window, it would be really good if you could digitally zoom in on the image you are calibrating to make sure the pixel/feature you are clicking on is correct. Mainly an issue when I have whole thin section scans (even at high res) I feel the need to zoom in on the picture to make sure I am clicking on what I think I am.
I understand.
john
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1) The ability for alternating on/off data to be used to correct data as per TDI (long term wish)
Hi Ben,
I had a small idea. Since this is essentially a simple percent change in intensity (as displayed in the display dialog), we can utilize those values in the Elements/Cations dialog as a Specified APF.
For example, say your alternating on/off peak intensity showed a 2.5% decrease in intensity in the display dialog. That means that we'd need to increase the measured intensity by 2.5% (times 0.5 relative to the integrated intensity), and we can do that by changing the Specified APF from 1.000 to 1.0125.
This manually entered percent change in intensity would of course be applied to all lines in the sample, so that is not ideal, but it might be better than nothing. That's just for the moment. When I get a chance I might implement this in PFE so it automatically computes the percent change for both the on and off-peak intensities and applies them "on the fly" for each line separately in the sample.
I think this would work, what do you think?
john
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1) The ability for alternating on/off data to be used to correct data as per TDI (long term wish)
Hi Ben,
I think I have a nice solution for this request.
I figured out a way to utilize the existing TDI code for the alternating on/off intensity acquisition for correction of time dependent intensity changes as seen here (note the magnitude of the x axis):
(https://probesoftware.com/smf/gallery/1_08_10_16_10_32_09.png)
You can assign these alternating on/off intensity corrections using the existing TDI corrections in the Standard Assignments dialog. This graph depicts a 3.1 % decrease in Cl ka intensity over the elapsed time.
Download the latest PFE update now to get this new capability. It will even work with existing MDB files!
john
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Hi John
Awesome! You are a legend. Just one problem, I can't seem to figure out where to turn it on? Do you mean go under the normal Standard Assignments window and assign "Use TDI Self Calibration.." even though its alternating peak? If so I get the error message "No Time Dependent Intensity (TDI) self-calibration or Alternating On/Off Peak acquisition data for sample row 37, datarow 1, channel 1"? This error comes up for all my samples.
I know I have acquired alternating though as I can plot it under the "Display TDI and Alternating Peak Data" window via the "Run" menu?
Cheers
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Awesome! You are a legend. Just one problem, I can't seem to figure out where to turn it on? Do you mean go under the normal Standard Assignments window and assign "Use TDI Self Calibration.." even though its alternating peak? If so I get the error message "No Time Dependent Intensity (TDI) self-calibration or Alternating On/Off Peak acquisition data for sample row 37, datarow 1, channel 1"? This error comes up for all my samples.
I know I have acquired alternating though as I can plot it under the "Display TDI and Alternating Peak Data" window via the "Run" menu?
Interesting.
Can you email me the MDB file?
john
----
Edit by John: Ok, I see it's an alternating on/off acquisition, but it's also a multi-point bgd acquisition!
So when it's a multi-point bgd acquisition, the alternating on-off intensities are stored in a different table in the database! So I'll have to add code to access that table in this situation.
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Edit by John: Ok, I see it's an alternating on/off acquisition, but it's also a multi-point bgd acquisition!
So when it's a multi-point bgd acquisition, the alternating on-off intensities are stored in a different table in the database! So I'll have to add code to access that table in this situation.
Ah sorry, yes its MPB, which you can't do with TDI hence the error.
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Edit by John: Ok, I see it's an alternating on/off acquisition, but it's also a multi-point bgd acquisition!
So when it's a multi-point bgd acquisition, the alternating on-off intensities are stored in a different table in the database! So I'll have to add code to access that table in this situation.
Ah sorry, yes its MPB, which you can't do with TDI hence the error.
Hi Ben,
That's not correct. You can acquire TDI with multi-point bgds! I just double checked and yes, one can do both TDI and MPB at the same time. :o
But I will get the TDI correction working with MPB alternating on/off acquisitions anyway. It won't be more than a few hours work and I agree that it could be useful.
john
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Hi John
Ok, my mistake again. I would have swore I tried that in the past and it wouldn't let me. I must have been getting confused with something else.
Many thanks for implementing the on/off. We have a very small Cameca demonstration workshop here in a couple of weeks where Cameca want to show the system to some potential customers here in Aus. I am showing the Ti in quartz data amongst other talks (Karsten giving his shared backgrounds talk, one of the PhD students here showing her quant maps of Au/Pt nuggets using CalcImage). Might be slightly embarassing for Cameca that 3 out of the 4 people talking will be using Probe Software rather than PeakSight for data acquisition...
Cheers
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Good afternoon, John:
I have two items for a wishlist, and I'm probably not the first to suggest this. After having trained with Gareth, I found myself wishing that the "Cancel" button at the bottom of the main window was a red colour, so that it would stand out more for beginners like me (or an "Abort run/process".
Also, do you have access to the JEOL triggers that would allow for an electronic autofocus of the electron beam for remote usage? Perhaps a virtual autofocus button? Thanks very much for your consideration.
Best regards
Dan MacDonald
Probe Tech
Dalhousie University
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I have two items for a wishlist, and I'm probably not the first to suggest this. After having trained with Gareth, I found myself wishing that the "Cancel" button at the bottom of the main window was a red colour, so that it would stand out more for beginners like me (or an "Abort run/process".
Sounds like you solved the problem as you now know where it is! :)
Also, do you have access to the JEOL triggers that would allow for an electronic autofocus of the electron beam for remote usage? Perhaps a virtual autofocus button? Thanks very much for your consideration.
There's an autofocus button for the stage focus in the Move window, but I don't know of an JEOL auto-focus function for the electron beam. This is an 8200, correct?
On my Cameca I usually just look at the electron image on my Axis video server and adjust the electron focus in the Cameca software. You mentioned getting an Axis video server up and running- did you do that?
I guess you can't remote into your UNIX box? Is that the issue?
john
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Awesome! You are a legend. Just one problem, I can't seem to figure out where to turn it on? Do you mean go under the normal Standard Assignments window and assign "Use TDI Self Calibration.." even though its alternating peak? If so I get the error message "No Time Dependent Intensity (TDI) self-calibration or Alternating On/Off Peak acquisition data for sample row 37, datarow 1, channel 1"? This error comes up for all my samples.
I know I have acquired alternating though as I can plot it under the "Display TDI and Alternating Peak Data" window via the "Run" menu?
Hi Ben,
OK, I got it all working. Here is your last quartz sample:
(https://probesoftware.com/smf/gallery/1_10_10_16_8_38_54.png)
Wow, I'd say you need a correction all right! Note that the plot is pretty busy with all 45 data points, so if you use the Plot Nth Point TDI and select every 4th point you get this:
(https://probesoftware.com/smf/gallery/1_10_10_16_8_39_09.png)
Go ahead and update PFE and all should be well.
john
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Many thanks for implementing the on/off. We have a very small Cameca demonstration workshop here in a couple of weeks where Cameca want to show the system to some potential customers here in Aus. I am showing the Ti in quartz data amongst other talks (Karsten giving his shared backgrounds talk, one of the PhD students here showing her quant maps of Au/Pt nuggets using CalcImage). Might be slightly embarassing for Cameca that 3 out of the 4 people talking will be using Probe Software rather than PeakSight for data acquisition...
Sounds like a lot of fun. I wish I could be there!
Hey, if you and/or any other attendees are willing to share your presentations as PPT or pdf files, please feel free to post them to the forum, maybe in the Events/Workshops topic here:
http://probesoftware.com/smf/index.php?topic=99.0
I know that I would be very interested in what was presented.
john
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Hi John
Sweet! Many thanks for that implementation. As you mention, there is certainly a degradation over time, most noticeably at the start of the measurement. I will play around with the log-log fit and see how it affects the data.
Just one thing a bit weird happening, of which I assume I am not understanding the processing. I have attached a series of images to hopefully explain what I am seeing.
The first image (No TDI.jpeg) is the data for Un19 without aggregation and without TDI on. If I turn on the TDI fit for sp1 (TDI sp1.jpeg) the concentrations on sp1 go crazy and the other spectrometers are normal. Looking at the TDI graph the intensity change is nowhere near enough to add an order of magnitude concentration, even with the log-log fit.
If I turn the TDI on for all spectrometers (TDI all sp.jpeg) they all show crazy concentrations. I assumed it was some strange matrix affect so disabled quant for all but sp1 (TDI sp1 disable quant.jpeg) but sp1 still shows crazy high concentration.
BUT if I aggregate spectrometers with all quanted (TDI all sp aggregate.jpeg) I get normal concentrations with a sensible TDI correction from the uncorrected data. E.g. row 133 goes from 0.01594 to 0.01655 with the TDI turned on, an increase of ~6ppm.
I can use the aggregated data fine, but was wondering if there was any way to see TDI corrected data on the individual spectrometers without aggregation? Hopefully that makes sense.
With regards to the workshop, I will definitely speak to people to see if they are OK with putting the talks online here.
Cheers
EDIT
Ok I noticed that its only with the log-log fit that the numbers go crazy, linear and quadratic they are sensible. However it still doesnt explain why the numbers go normal when you aggregate. For example for Un19, row133, sp1, the y intercept goes from ~3.26 cps/nA with linear fit, to ~3.37 cps/nA with log-log fit. The concentrations though go from 0.0161wt%(linear) to 0.0990wt% (log-log) despite the cps/nA only changing by 0.11 cps/nA?
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Just one thing a bit weird happening, of which I assume I am not understanding the processing. I have attached a series of images to hopefully explain what I am seeing.
Yes. I need to look at this tomorrow. The question being: how should the TDI correction be treated when duplicate elements are aggregated?
This might be worth a paper... interested?
john
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Ok I noticed that its only with the log-log fit that the numbers go crazy, linear and quadratic they are sensible. However it still doesnt explain why the numbers go normal when you aggregate. For example for Un19, row133, sp1, the y intercept goes from ~3.26 cps/nA with linear fit, to ~3.37 cps/nA with log-log fit. The concentrations though go from 0.0161wt%(linear) to 0.0990wt% (log-log) despite the cps/nA only changing by 0.11 cps/nA?
Hi Ben,
OK. I figured out what was going wrong with your TDI plots when the alternating on/off intensities were aggregated (or not). That is fixed.
The reason it was a problem was because I've been thinking about how to implement an idea that Julien Allaz wrote to me a few months ago, but I hadn't been able to think of an elegant way to do it- until today! (give John a "pat on the back")
The idea Julien had over the summer was that just as we "aggregate" the on-peak and off-peak intensities for better precision/sensitivity, we could also do the same for our (self) TDI correction for beam sensitive samples (and now also for alternating on/of-peak intensities). The problem was, I couldn't think of a clever way to code it, but today I did and here is an example...
Here is one of Ben Wade's quartz samples measuring for Ti on all 5 spectrometers and using alternating on/off intensities to track the sample damage over time. As with normal TDI, this allows us to also correct quantitatively for this change in intensity over time. So here are the data points using normal (unaggregated) intensities and fit to a log-log method:
(https://probesoftware.com/smf/gallery/1_11_10_16_6_52_53.png)\
A very busy plot but note the scatter in some of the data. Now the same TDI data but this time plotted with the aggregate mode turned on so all TDI intensities from all 5 spectrometers are combined prior to the actual TDI correction:
(https://probesoftware.com/smf/gallery/1_11_10_16_6_57_25.png)
Obviously the (log) intensities are higher because we increased the geometric efficiency of our instrument by a factor of (roughly) 5 (for a single element!). But also note that the data scatter is reduced due to this improvement in precision.
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We can confirm this numerically but running the quantification. Here is the TDI without aggregation:
(https://probesoftware.com/smf/gallery/1_11_10_16_6_54_30.png)
Note the DEV% number. Now, here with intensity aggregation:
(https://probesoftware.com/smf/gallery/1_11_10_16_6_54_49.png)
Notice that the TDI DEV% went from 0.6% to 0.2%, a decrease of a factor of three. TDII: is the intensity intercept and TDIL: is the log intensity intercept.
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Hi John
Super cool. Many thanks for developing and implementing that over such a short span, I think it will be very useful. I have sort of highjacked the Wishlist thread into a development thread, so feel free if you want to take these Alternating On/off posts from the Wishlist thread and make a separate thread out of them...
Time to play with the new feature~
Cheers
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Super cool. Many thanks for developing and implementing that over such a short span, I think it will be very useful. I have sort of highjacked the Wishlist thread into a development thread, so feel free if you want to take these Alternating On/off posts from the Wishlist thread and make a separate thread out of them...
Time to play with the new feature~
No worries, this is exactly what this topic is for.
But you're right, we should have a separate topic for alternating on/off intensity discussion. Feel free to create one. On the other hand, there's a nice discussion here
http://probesoftware.com/smf/index.php?topic=29.msg387#msg387
on Ti in Quartz, which would also be appropriate.
john
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I would be interesting to have the user be able to define what is possible in terms of a _low_ Faraday cup current. Currently, it seems that if PfE reads any FA measurement below 1.000 nA, it assumes the filament is blown (or some other non-starter). We would like to do some experiments with PfE using EDS with our SDD detector on beam sensitive materials using _low_ current, below 1 nA. Would you consider permitting a user, say in the probewin.ini file, to set, the lower limit on when PfE issues "your filament is shot" type of comment?
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I would be interesting to have the user be able to define what is possible in terms of a _low_ Faraday cup current. Currently, it seems that if PfE reads any FA measurement below 1.000 nA, it assumes the filament is blown (or some other non-starter). We would like to do some experiments with PfE using EDS with our SDD detector on beam sensitive materials using _low_ current, below 1 nA. Would you consider permitting a user, say in the probewin.ini file, to set, the lower limit on when PfE issues "your filament is shot" type of comment?
Hi John,
It's already there in the Probewin.ini file under the [faraday] section:
[faraday]
MinimumFaradayCurrent=0.1
The default is 0.1 nA so maybe you changed it at some point?
john
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Hi,
just curious. Would it be possible to have Picture Snap as a standalone utility? It gets a lot of use in my lab even when we don't use PFE (like for example with the EDS software). I always have to show the users how to open PFE, create a file etc just to get to PictureSnap. This is obviously not a very big problem but I thought I might ask.
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Just curious. Would it be possible to have Picture Snap as a standalone utility? It gets a lot of use in my lab even when we don't use PFE (like for example with the EDS software). I always have to show the users how to open PFE, create a file etc just to get to PictureSnap. This is obviously not a very big problem but I thought I might ask.
Hi Anette,
Your best bet would be to simply run the Stage utility, as it has PictureSnap also.
john
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Smart! Will do.
Thanks?
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Ok, I will hide my question here as I think I am just missing it (I think I may have even asked this before). Are there probewin.ini keywords to turn on/off:
Automate window: Use confirm during acquisition
Peaking options window: Acquire automated pha scan after peaking
Peak/Scan options: Use ROM based spectrometer scanning
Acquisition options: Quick Standard Acquisition modes (Assigned/Assigned or Major Elements)
Thanks!
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Are there probewin.ini keywords to turn on/off:
Automate window: Use confirm during acquisition
Yes.
[Software]
UseConfirmDuringAcquisitionFlag = 0 ; 0 = off, 1 = on
Peaking options window: Acquire automated pha scan after peaking
No. But the flag is saved to your MDB file for each run.
Peak/Scan options: Use ROM based spectrometer scanning
Yes.
[General]
PeakCenterMethod=2 ; 0 = interval halving, 1 = parabolic, 2 = ROM, 3 = manual
Acquisition options: Quick Standard Acquisition modes (Assigned/Assigned or Major Elements)
No.
Could be added though...
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Hi,
Would it be possible for PfE to check to see if the reflected light is on (and turn it on if necessary) before doing an autofocus and the turn it off again after the autofocus?
or is this already implemented somewhere?
This would be useful when automatically acquiring backscatter images after each analysis.
Thanks!
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Hi,
Would it be possible for PfE to check to see if the reflected light is on (and turn it on if necessary) before doing an autofocus and the turn it off again after the autofocus?
or is this already implemented somewhere?
This would be useful when automatically acquiring backscatter images after each analysis.
Thanks!
Easy peasy!
I am doing it for all the other instruments, but forgot to do this for the 8x30 instruments!
john
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Thanks John! Awesome service :D
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Thanks John! Awesome service :D
You are most welcome.
Please try the test Probewin.exe in the PFE Dropbox.
john
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Hi John,
Just trying the new version with the auto light on and off with autofocus. Nice feature, but can you i) add a delay, of at least a second if not 2, to the the autofocus start allow the light to come on (its a bit too quick off the mark at the moment and tries to focus in the dark so sometimes misses finding focus), and ii) add the option to either toggle the light or not - it's great when running samples, but a bit of a niusance when trying to confirm standard positions and just as you're about to adjust the position the light goes out :o.
Mike
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Mike,
You're reading my mind. I second these suggestions. I love the new feature but it needs a few tweaks.
Cheers
Glenn
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Just trying the new version with the auto light on and off with autofocus. Nice feature, but can you i) add a delay, of at least a second if not 2, to the the autofocus start allow the light to come on (its a bit too quick off the mark at the moment and tries to focus in the dark so sometimes misses finding focus), and ii) add the option to either toggle the light or not - it's great when running samples, but a bit of a niusance when trying to confirm standard positions and just as you're about to adjust the position the light goes out :o.
Easy. I'll add the delay tonight
Ben Buse suggests that I don't turn the light off after the auto-focus unless one is going to acquire images or EDS spectra. In fact, I could move the light off call to just before the start BSE or start EDS (I think it already turns off the light before the start EDS).
john
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That would be an elegant solution... but it would mean you'd pass the chance to add another checkbox ;)
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That would be an elegant solution... but it would mean you'd pass the chance to add another checkbox ;)
And that's just what the software needs! :D
john
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The 8x30's may be faster, but the delay between clicking the turning on the OM light and the light reaching full brightness is ~3.5 seconds on the WSU 8500. May I suggest the "light on" delay be 4-5 seconds, rather than 1-2? The delay when turning the OM off is much smaller, but it is non-zero, so maybe include a 1-second "light off" delay when acquiring EDS data or images?
Hi Owen,
Actually Ben Buse reports it is a full 4 seconds for full brightness on his 8530.
I can also add a 1 second delay for light off before EDS, CL or imaging, though there may be that much latency in starting these acquisitions anyway.
Also, not really a request but a related question - when the stage position is updated after the autofocus finishes, does the software just update the Z position, or the X and Y as well?
I had to check the code. Looks like it updates X, Y and Z after an auto-focus.
john
PS This is the code I am considering prior to starting the EDS, CL or image acquisition. How does it look to you all?
' Deal with optical lamp modes
If TransmittedLightPresent Then
Call RealTimeGetLightMode(mode%) ' check if in transmitted light mode
If ierror Then Exit Sub
If mode% = 1 Then
Call RealTimeSetLightMode(Int(0)) ' set to reflected light if in transmitted light
If ierror Then Exit Sub
End If
End If
Call RealTimeGetReflectedLightMode(mode%) ' check if reflected light is on
If ierror Then Exit Sub
If mode% = 1 Then ' if reflected light is on, turn off
Call RealTimeSetReflectedLightMode(Int(0))
If ierror Then Exit Sub
LightTurnedOff = True
Call MiscDelay3(FormMAIN.StatusBarAuto, "reflected light off...", CDbl(1#), Now) ' wait 1 second for light fully off
If ierror Then Exit Sub
End If
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Huh, didn't think the 8530 would be slower. Fair point about the latency - maybe the light off delay is overkill then.
It's not just the optical light which is getting slower (which is probably to avoid blowing the light bulb out?), the picoammeter "settling" time on the 8x30 is longer also:
http://probesoftware.com/smf/index.php?topic=26.msg789#msg789
If the 1 sec delay for turning off the light is onerous, we can tweak it down a bit.
john
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OK. The latest version of PFE can be updated using the Help menu and has the modified light on/off delays as requested.
john
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OK. The latest version of PFE can be updated using the Help menu and has the modified light on/off delays as requested.
john
Hi John,
Its working very well - timings just right here - for light on for autofocus and light off for BSE
The only thing I wondered was why do you turn the light on at the end of each analysis - It doesn't matter - doesn't affect performance.
Thanks
Ben
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OK. The latest version of PFE can be updated using the Help menu and has the modified light on/off delays as requested.
john
Hi John,
Its working very well - timings just right here - for light on for autofocus and light off for BSE
The only thing I wondered was why do you turn the light on at the end of each analysis - It doesn't matter - doesn't affect performance.
Thanks
Ben
Hi Ben,
Thanks for checking.
I turn it on, because some people want to check the focus for the next acquisition. For example, the Confirm Focus During Acquisition flag might be set.
john
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Hi,
I had a suggestion from someone (Kathy) who uses the probe - whether it would be possible to export two sets of pictures one with the points labelled and scale bar on, and one the raw image for processing. Currently I do this by exporting one lot (through the output menu) then copying it to another folder and reexporting the images.
Thinking about what would be the best way to do this - maybe two sets of bmps with one set labelled "raw", or maybe what would be more useful for the raw image to be in native resolution - i.e. 32 bit - perhaps a option in output menu to export all the images as grid or probeimage files which ever is easier.
What do other people think - would this be useful?
Ben
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I had a suggestion from someone (Kathy) who uses the probe - whether it would be possible to export two sets of pictures one with the points labelled and scale bar on, and one the raw image for processing. Currently I do this by exporting one lot (through the output menu) then copying it to another folder and reexporting the images.
Thinking about what would be the best way to do this - maybe two sets of bmps with one set labelled "raw", or maybe what would be more useful for the raw image to be in native resolution - i.e. 32 bit - perhaps a option in output menu to export all the images as grid or probeimage files which ever is easier.
What do other people think - would this be useful?
I think it's a great idea and the update tonight has _raw.bmp files exported from the Output | Output Images to BMP menu.
john
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Just tried it - works great, very easy
Thanks
Ben
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Hi John,
What would be great if you could add a feature to export aggregate elements to calczaf.
I'm doing secondary fluorescence corrections on trace elements - olivine with Ca on two spectrometers.
Currently the export to calczaf is
1, 8, 20, 40,"81_1475-85_ol1__006", 31.7679, 27.7583, 10.53849
1,"","",0.0,"","",0.0
"Si","ka", 1, 2, 803, 0, 474.9889, 493.3912
"Mg","ka", 1, 1, 803, 0, 298.8863, 386.1489
"Ca","ka", 1, 1, 804, 0, 2.884131, 3115.588
"Fe","ka", 1, 1, 1010, 0, 203.8582, 775.0543
"Ni","ka", 1, 1, 831, 0, 2.680419, 1652.423
"Mn","ka", 1, 1, 818, 0, 2.803117, 1543.256
"Ca","ka", 1, 1, 804, 0, 0, 0
"o ","", 1, 0, 0, 0, 0, 0
What I would like is the following, for aggregate elements
1, 7, 20, 40,"81_1475-85_ol1__006", 31.7679, 27.7583, 10.53849
1,"","",0.0,"","",0.0
"Si","ka", 1, 2, 803, 0, 474.9889, 493.3912
"Mg","ka", 1, 1, 803, 0, 298.8863, 386.1489
"Ca","ka", 1, 1, 804, 0, 2.884131, 3115.588
"Fe","ka", 1, 1, 1010, 0, 203.8582, 775.0543
"Ni","ka", 1, 1, 831, 0, 2.680419, 1652.423
"Mn","ka", 1, 1, 818, 0, 2.803117, 1543.256
"o ","", 1, 0, 0, 0, 0, 0
Thanks
Ben
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Hi John,
What would be great if you could add a feature to export aggregate elements to calczaf.
I'm doing secondary fluorescence corrections on trace elements - olivine with Ca on two spectrometers.
Currently the export to calczaf is
1, 8, 20, 40,"81_1475-85_ol1__006", 31.7679, 27.7583, 10.53849
1,"","",0.0,"","",0.0
"Si","ka", 1, 2, 803, 0, 474.9889, 493.3912
"Mg","ka", 1, 1, 803, 0, 298.8863, 386.1489
"Ca","ka", 1, 1, 804, 0, 2.884131, 3115.588
"Fe","ka", 1, 1, 1010, 0, 203.8582, 775.0543
"Ni","ka", 1, 1, 831, 0, 2.680419, 1652.423
"Mn","ka", 1, 1, 818, 0, 2.803117, 1543.256
"Ca","ka", 1, 1, 804, 0, 0, 0
"o ","", 1, 0, 0, 0, 0, 0
What I would like is the following, for aggregate elements
1, 7, 20, 40,"81_1475-85_ol1__006", 31.7679, 27.7583, 10.53849
1,"","",0.0,"","",0.0
"Si","ka", 1, 2, 803, 0, 474.9889, 493.3912
"Mg","ka", 1, 1, 803, 0, 298.8863, 386.1489
"Ca","ka", 1, 1, 804, 0, 2.884131, 3115.588
"Fe","ka", 1, 1, 1010, 0, 203.8582, 775.0543
"Ni","ka", 1, 1, 831, 0, 2.680419, 1652.423
"Mn","ka", 1, 1, 818, 0, 2.803117, 1543.256
"o ","", 1, 0, 0, 0, 0, 0
Thanks
Ben
Hi Ben,
Let me be sure I understand what you are asking.
You want the aggregated elements output from Probe for EPMA to the CalcZAF import format for performing a secondary boundary fluorescence correction in CalcZAF, and you want the correct aggregated intensity for the duplicate element(s) output properly, but you simply don't want so see the empty duplicate Ca listed in the output file? Is that correct?
john
PS Eventually I will implement this secondary boundary fluorescence correction code for multiple elements in PFE, but it's a large amount of work, because even though I've got the basic secondary fluorescence correction code working, for actual use in the "real world", I also need to implement a correction for spectrometer Bragg crystal defocusing effects, because for WDS (unlike EDS), the degree of secondary fluorescence from a boundary phase, depends greatly on the orientation of the boundary to the Bragg crystal.
That is, if the direction to the boundary phase is towards or away from the spectrometer, the Bragg defocusing really "kicks in", but if the direction to the boundary phase is towards one side or the other from the spectrometer there will be almost no Bragg defocusing effects on the fluorescence from the boundary phase. And of course if the boundary is in a direction that is at an angle to the Bragg crystal, the defocusing effect will be somewhere in between those two extremes depending on the angle and the degree of defocusing. This will be a significant amount of work because I'll have to implement a method to allow the lab manager to easily calibrate a bunch of low mag beam scans for each spectrometer/crystal combination on each instrument, and probably at multiple spectrometer positions (low to high sin theta).
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Hi John,
Yes that's correct - because otherwise calczaf gives an error message for the duplicate Ca stating that it has no counts. Thus I found the way around this is to delete this line and correct the element number. I don't know if there is a better way of doing this
Thanks
Ben
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Yes that's correct - because otherwise calczaf gives an error message for the duplicate Ca stating that it has no counts. Thus I found the way around this is to delete this line and correct the element number. I don't know if there is a better way of doing this
Ok, great. I can fix this easily in the PFE output code. Just wanted to make sure I wasn't missing anything else. I'll have this fixed for you tomorrow!
john
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Hi John,
Yes that's correct - because otherwise calczaf gives an error message for the duplicate Ca stating that it has no counts. Thus I found the way around this is to delete this line and correct the element number. I don't know if there is a better way of doing this
Thanks
Ben
Hi Ben,
Ok, I added code to check for aggregate mode and duplicate elements when outputting the CalcZAF format. I'm uploading the update today (no bump in version number so still 11.8.0), but it should be ready for you by the time you wake up tomorrow (or Monday!).
Here is an example of measuring Ti on all 5 spectrometers, first with no aggregate mode:
2, 7, 20, 40,"1920 sec on SiO2",-10205,-546, 42
1,"","",0.0,"","",0.0
"ti","ka", 1, 2, 922, 0,-5.200063E-07, 0
"ti","ka", 1, 2, 922, 0, 5.729499E-06, 0
"ti","ka", 1, 2, 922, 0, 3.795455E-07, 0
"ti","ka", 1, 2, 922, 0,-9.59413E-07, 0
"ti","ka", 1, 2, 922, 0, 7.634579E-06, 0
"si","", 1, 2, 0, 46.743, 0, 0
"o","", 1, 0, 0, 0, 0, 0
and again, with aggregate mode:
2, 3, 20, 40,"1920 sec on SiO2",-10205,-546, 42
1,"","",0.0,"","",0.0
"ti","ka", 1, 2, 922, 0, 2.77707E-06, 0
"si","", 1, 2, 0, 46.743, 0, 0
"o","", 1, 0, 0, 0, 0, 0
This works for both all data lines or just the average.
john
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Thanks John, all working well - that's great saved me a lot of time editing scripts
Ben
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1) We talked about this off-line, but could the "Stop" button in the Digitize Image window be greyed out/inactive for the JEOL 8x00's, at least until that command is working? I try to scare my users enough that they don't click it, but it's also surprisingly easy to click it by accident, and some of them don't scare easily.
The button has been removed in the latest version of PFE- at least until we get the command working.
2) Would it be possible to output detection limits in units other than wt% elemental? Specifically, would it be possible to add an option to the Output - Save User Specified Format Output window to export detection limits in wt% oxide as well as, or instead of, wt% elemental?
Almost everything is possible! :)
Yes, I can add this. Give me a few days...
john
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Much appreciated - no rush for either item.
Thanks much,
OKN
Hi Owen,
OK, I added detection limit output in oxide wt% to the user specified format in PFE.
Update to v. 11.8.2 and you should be good to go.
john
(https://probesoftware.com/smf/gallery/1_16_02_17_4_06_35.png)
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Hi,
this is coming from the training at Carnegie: When doing combined conditions, it would be good if one could define delays (settling time) for changes in accelerating voltage and beam current (+ beam diameter??)
A crude drawing for an example dialog is attached.
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And this one is from me:
Would it be possible to add a "Clear current element setup" button in the element/cations dialog? This would allow to delete all elements in the current setup to start from scratch. I do that quite often for my major element/trace element setup that I combine later in post-processing.
Serving suggestion attached.
Thanks!
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this is coming from the training at Carnegie: When doing combined conditions, it would be good if one could define delays (settling time) for changes in accelerating voltage and beam current (+ beam diameter??)
Hi Anette,
There are already delays defined for changing keV and beam current (and I think beam size ) in the probewin.ini file. Will that work?
john
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Would it be possible to add a "Clear current element setup" button in the element/cations dialog? This would allow to delete all elements in the current setup to start from scratch. I do that quite often for my major element/trace element setup that I combine later in post-processing.
There is already a Remove All Elements From Sample button in the Element Setups dialog. Will that work?
john
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Hi Anette,
There are already delays defined for changing keV and beam current (and I think beam size ) in the probewin.ini file. Will that work?
john
Hi John,
I would say that this is not visible enough for the user. My suggestion would be to add those fields to the combined conditions dialog and populate the fields with the defaults from the probewin.ini field. Is that possible?
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There is already a Remove All Elements From Sample button in the Element Setups dialog. Will that work?
john
Uh, I learned something new here, I was not aware of that option. I would say it would be great if you could bring that button into the "Acquired and Specified Elements" dialog too. If even I ;) was not aware of it I would say it is too well hidden. And yes, that is exactly what I am looking for.
Thanks!
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Hi Anette,
There are already delays defined for changing keV and beam current (and I think beam size ) in the probewin.ini file. Will that work?
john
Hi John,
I would say that this is not visible enough for the user. My suggestion would be to add those fields to the combined conditions dialog and populate the fields with the defaults from the probewin.ini field. Is that possible?
Hi Anette,
You're saying you want the user to be able to edit these delays within the application? It would certainly be possible, though maybe in the Acquisition Options would be a better place? Curious why you don't just want to modify these delays in the probewin.ini file until they work properly and leave it at that. This would be for the delays *after* setting the column parameters? Correct?
May I ask why you want to change these delays in the application? There is already a TDI incubation and/or carbon decontamination delay in Acquisition Options...
john
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There is already a Remove All Elements From Sample button in the Element Setups dialog. Will that work?
john
Uh, I learned something new here, I was not aware of that option. I would say it would be great if you could bring that button into the "Acquired and Specified Elements" dialog too. If even I ;) was not aware of it I would say it is too well hidden. And yes, that is exactly what I am looking for.
Thanks!
Hi Anette,
I can't easily move the Remove All Elements" button to the Analyze and Specified Elements dialog as there is no room (when loaded from the Analyze! window) without a big re-arrangement of the controls.
Let me think about it some more, but in the meantime "now you know!" (where that button is). ;D
john
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Hi Anette,
You're saying you want the user to be able to edit these delays within the application? It would certainly be possible, though maybe in the Acquisition Options would be a better place? Curious why you don't just want to modify these delays in the probewin.ini file until they work properly and leave it at that. This would be for the delays *after* setting the column parameters? Correct?
May I ask why you want to change these delays in the application? There is already a TDI incubation and/or carbon decontamination delay in Acquisition Options...
john
Hi John, I guess it actually does not make much sense to have them changeable on a sample per sample basis. How about having them on display though as in my dialog layout proposal but not editable. This would accomplish both that the user would be aware that there is a delay being applied upon changing conditions and allow that the values can be critically evaluated (whereas otherwise they would be "hidden" in the probewin.ini file).
What do you/everyone think?
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Hi Anette,
I can't easily move the Remove All Elements" button to the Analyze and Specified Elements dialog as there is no room (when loaded from the Analyze! window) without a big re-arrangement of the controls.
Let me think about it some more, but in the meantime "now you know!" (where that button is). ;D
john
Ah yes, I see. Ok, so I guess for now it is a "tips and tricks" entry until some later time potentially.
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Hi Anette,
You're saying you want the user to be able to edit these delays within the application? It would certainly be possible, though maybe in the Acquisition Options would be a better place? Curious why you don't just want to modify these delays in the probewin.ini file until they work properly and leave it at that. This would be for the delays *after* setting the column parameters? Correct?
May I ask why you want to change these delays in the application? There is already a TDI incubation and/or carbon decontamination delay in Acquisition Options...
john
Hi John, I guess it actually does not make much sense to have them changeable on a sample per sample basis. How about having them on display though as in my dialog layout proposal but not editable. This would accomplish both that the user would be aware that there is a delay being applied upon changing conditions and allow that the values can be critically evaluated (whereas otherwise they would be "hidden" in the probewin.ini file).
What do you/everyone think?
If what is desired is seeing these delays then how about I just add some text to the status bar if it's adding a delay after setting these items?
john
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Hi John, I guess it actually does not make much sense to have them changeable on a sample per sample basis. How about having them on display though as in my dialog layout proposal but not editable. This would accomplish both that the user would be aware that there is a delay being applied upon changing conditions and allow that the values can be critically evaluated (whereas otherwise they would be "hidden" in the probewin.ini file).
What do you/everyone think?
Hi Anette,
Please update PFE and open the Combined Conditions dialog. It now displays the set condition delays and also displays a new message in the status bar as it's setting them.
Let me know if this works for you.
john
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Hi John,
This may be already implemented but I haven't found it.
Would it be possible to select samples by text in the Automate and Analyse windows? Say I have a run that has multiple sample setups and I want to select only the CPX to apply a setup. I'd like to be able to select samples based on their labels (i.e. I'd enter "CPX" in the search box ) and all the sample labels containing the string "CPX" would bet selected. A simple text entry would be great, but wildcards would be nice too (not to mention REGEX).
This comes about because I'm in Cambodia reprocessing some data and I don't have a mouse to use with my laptop, so multiple selection is a pain.
Cheers from balmy Banlung! (29 C at 9:30 high of 35! not that I'm complaining, 35 cm of snow at home!)
Glenn
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Hi John,
This may be already implemented but I haven't found it.
Would it be possible to select samples by text in the Automate and Analyse windows? Say I have a run that has multiple sample setups and I want to select only the CPX to apply a setup. I'd like to be able to select samples based on their labels (i.e. I'd enter "CPX" in the search box ) and all the sample labels containing the string "CPX" would bet selected. A simple text entry would be great, but wildcards would be nice too (not to mention REGEX).
This comes about because I'm in Cambodia reprocessing some data and I don't have a mouse to use with my laptop, so multiple selection is a pain.
Cheers from balmy Banlung! (29 C at 9:30 high of 35! not that I'm complaining, 35 cm of snow at home!)
Glenn
Hi Glenn,
Well I'm going to complain! It's been raining in Oregon for the last 3 months- non-stop it seems sometimes. >:(
You can multiple select samples using the up/down cursor keys and the shift key, but for more flexibility than that, I suspect you'll have to break down and buy yourself a mouse. :'(
john
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Hi John,
Two ideas.
(1) Would it be difficult to have an option of converting a standard sample into an unknown - the example is I collected data as a standard and I want to use it for the blank correction (for which I need an unknown).
(2) When exported apfu (atoms per formula unit) I have to check the option in calculation options. It would be nice to be able to export the data to dat.file and excel without having to check the option in calculation options - for when checked in calculation options in Analyze window instead of seeing wt. % you see apfu.
Thanks
Ben
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Driving home I was thinking...
Regarding (2) I think it would be best if instead we had a check box saying "Display as formula units". So if you want to export you check calculate based on formula but don't check display as formula units. - Same as for display as oxides
What do you think, thanks
Ben
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(1) Would it be difficult to have an option of converting a standard sample into an unknown - the example is I collected data as a standard and I want to use it for the blank correction (for which I need an unknown).
Hi Ben,
I understand this idea. I've had it myself. The issue is that generally we should collect our "blank" sample under the same conditions as our unknowns. Small differences in counting/beam current/etc. could lead to systematic biases in the "blank" calibration. So for now I have resisted this request, but I'm willing to discuss it.
(2) When exported apfu (atoms per formula unit) I have to check the option in calculation options. It would be nice to be able to export the data to dat.file and excel without having to check the option in calculation options - for when checked in calculation options in Analyze window instead of seeing wt. % you see apfu.
This is easy. Just right click the sample(s) in the Analyze! sample list and select the output type you want. usually I use the user specified output format...
Did you also know that by double-clicking any analysis line in the lower data grid in the Analyze! window you can can see *all* the data types for a single data point as shown here:
http://probesoftware.com/smf/index.php?topic=110.msg1141#msg1141
john
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Hi John,
Did you also know that by double-clicking any analysis line in the lower data grid in the Analyze! window you can can see *all* the data types for a single data point as shown here:
http://probesoftware.com/smf/index.php?topic=110.msg1141#msg1141
Thanks - thats good to know
This is easy. Just right click the sample(s) in the Analyze! sample list and select the output type you want. usually I use the user specified output format...
Your right! It works! SORRY I thought when I last tried it it didn't work unless "calculate on formula basis is checked" -but I'm glad I'm wrong.
Select user specified output format... by either right click or from the output menu. Tell it to output formulas -
(https://probesoftware.com/smf/gallery/453_21_03_17_1_34_02.png)
It outputs formula even when "calculate on formula basis" is not checked. Default cations =8, no end member when not configured.
As configured here
(https://probesoftware.com/smf/gallery/453_21_03_17_1_32_52.png)
Thanks
Ben
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Your right! It works! SORRY I thought when I last tried it it didn't work unless "calculate on formula basis is checked" -but I'm glad I'm wrong.
Select user specified output format... by either right click or from the output menu. Tell it to output formulas -
(https://probesoftware.com/smf/gallery/453_21_03_17_1_34_02.png)
It outputs formula even when "calculate on formula basis" is not checked. Default cations =8, no end member when not configured.
I do try to be helpful once in a while... ;)
john
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Regarding the using/converting a standard to an unknown to be used as blank, my take would be that it is already possible to change the acquisition conditions between unknowns. So nothing's really stopping me from picking an unknown as a blank that has been acquired with different conditions, right?
So the limitation to only being allowed to use unknowns as blanks isn't really that much "safer", unless there would be some sanity check to ensure the conditions were the same. And with the latter it should then also be possible to use standards as blanks. Having said that I often acquire standards and unknowns with the same conditions anyway.
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Regarding the using/converting a standard to an unknown to be used as blank, my take would be that it is already possible to change the acquisition conditions between unknowns. So nothing's really stopping me from picking an unknown as a blank that has been acquired with different conditions, right?
So the limitation to only being allowed to use unknowns as blanks isn't really that much "safer", unless there would be some sanity check to ensure the conditions were the same. And with the latter it should then also be possible to use standards as blanks. Having said that I often acquire standards and unknowns with the same conditions anyway.
Hi Karsten,
That's a good point. I could add code to check for similar conditions. So check for matching column conditions and element setup including acquisition order and count times?
This brings up the interesting question of shouldn't our standards always be run at similar conditions to our unknowns? My feeling is that we should, at least if the standards are compositionally similar to the unknowns. But for trace elements we can of course use almost any standard and instead just concentrate on the background measurement accuracy. As you have demonstrated in several presentations, this is because the background measurement method(s) of our unknown always dominates the accuracy (and precision) of the trace elements in our samples, as opposed to the accuracy of the matrix corrections. For those new to thinking about these issues, please consider that the accuracy of the matrix correction of Ti Ka in SiO2 is probably better than 2% relative or so, but the background intensity measurement accuracy can be hundreds of percents in error, due to any number of background artifacts at trace levels.
So for example, I usually count say 40 sec on my TiO2 standard when measuring Ti ka in quartz and at 30 nA, but count say 640 sec and 200 nA on my unknown quartz samples *and again* also 640 sec and 200 nA on the blank standard (e.g., synthetic SiO2). So I do need to add a check for similar conditions at least.
john
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Yes, for traces I usually adjust the beam current between standard and unknown.
Would that check for "similar conditions" also have to include the background correction, i.e. off-peak positions, correction type etc? In the case of blanks in trace element analysis even a slight difference in the background correction will have a big effect.
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On the other hand, is it too much to ask the user to measure a few points on their SiO2 standard using the unknown conditions?
I mean, even if one weren't intending to actually utilize the blank correction, for example you'd still want to see if you can measure zero Ti in the blank standard... and SiO2 won't be a standard anyway since you'd probably wouldn't be measuring Si, and instead be specifying an SiO2 matrix by difference...
john
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Sure, that's fine.
I guess the point I'm trying to make is just that while I understand the reasoning behind the limitation that a blank standard has to be an unknown I still question it. I can change conditions anytime between samples. So even when I use an unknown as blank I still need to make sure that the conditions were the same. And it is easy to run an standard at the same conditions as an unknown and vice versa anyway. So why not run a standard as a standard? ;-) But it is perfectly usable the way it is.
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I hear you, but I guess I just don't see the point of providing this additional flexibility if it "encourages" the user to not do the right thing.
I think the "limitation" of not allowing a standard to be used for the blank correction is essentially insignificant under normal circumstances (we just need to run an extra unknown sample which so happens to be one's blank std using the same sample setup as one's other unknowns that we are automating). This ensures that the blank standard tends to be run at the same conditions as the unknowns, which in our example of trace element standards using different conditions as described above, would *not* be ensured...
Yes, one *could* create a different unknown sample setup from the other unknowns, and then use it to run the blank standard differently, but that would require *extra* effort. The way it is now I think is more "natural" for having the blank std and unknowns all run using the same conditions, because they need to be the same sample type...
The only situation I can think of where allowing a std sample to be utilized as a blank sample would be worthwhile, would be a situation in which one forgot to run the blank std as an unknown. But even in that case it's very likely, for example, that either the SiO2 standard was not run at all (when analyzing Ti in quartz, why would one run an SiO2 std?), or that the standards were run at quite different conditions than the unknowns, for example, using 30 nA on the standards and 200 nA on the unknowns...
Sorry to be so pedantic about all this.
john
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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! ;D
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
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Dude! I can't do *everything*. I mean I've got to leave some things for the "next generation" to do! ;D
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
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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.
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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
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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
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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
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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?
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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:
(https://probesoftware.com/smf/gallery/1_07_04_17_5_56_13.png)
Update from the Help menu as usual.
john
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Legend. Thanks John
Cheers
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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
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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!
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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.
Hi Anette,
Software is *never* done! ;D
I'll add this to the list- good idea.
john
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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:
(https://probesoftware.com/smf/gallery/1_16_06_17_5_48_02.png)
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
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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
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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
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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
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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
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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):
(https://probesoftware.com/smf/gallery/1_10_08_17_8_59_47.png)
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
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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):
(https://probesoftware.com/smf/gallery/1_10_08_17_8_59_47.png)
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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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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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
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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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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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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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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
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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!
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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
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Hi,
not so much a request for PFE but for Drift. Would it be possible to add detector baseline, gain and bias to the output variables?
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Hi,
not so much a request for PFE but for Drift. Would it be possible to add detector baseline, gain and bias to the output variables?
Hi Anette,
I didn't add the PHA parameters to the Drift app to begin with, mostly because I think of them more as settings as opposed to measurements, but I can see how (user) changes in the gain or bias settings over time might be interesting.
So the latest version of Drift.exe has a new checkbox as seen here:
(https://probesoftware.com/smf/gallery/1_29_09_17_6_06_48.png)
Ready to download.
john
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Excellent suggestion there with the PHA parameters in Drift.
Would it be possible to sort the standards in the interference standards drop-down menus in a similar way to the primary standards, i.e. by standard number, or alternatively alphabetically? We tend to have quite a few standards in the runs so it can take a while to find them in there at the moment.
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Would it be possible to sort the standards in the interference standards drop-down menus in a similar way to the primary standards, i.e. by standard number, or alternatively alphabetically? We tend to have quite a few standards in the runs so it can take a while to find them in there at the moment.
Hi Karsten,
I didn't realize that they were loaded differently from the primary standards. I will look into it.
OK, I remember now. You (and Dave Adams) wanted me to increase the number of standards to 132 per run. That is a lot of standards to scroll through!
john
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Excellent suggestion there with the PHA parameters in Drift.
Would it be possible to sort the standards in the interference standards drop-down menus in a similar way to the primary standards, i.e. by standard number, or alternatively alphabetically? We tend to have quite a few standards in the runs so it can take a while to find them in there at the moment.
Hi Karsten,
We changed the interference standard combo controls to sorted and re-wrote the indexing code, so now these controls should be sorted just like the primary standard combo control.
Good suggestion for when there are many standards in your run! What's your record standard count now?
john
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Great, thanks John. We've definitely cracked the old maximum limit for some of the method development stuff.
Our split holder with standards that are permanently in the instrument in the JEOL also now has 111 standards installed. So setting up and maintaining the position file for that gets us close to that new limit. And there is some potential to increase the number of standards in that split holder...
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I noticed that the "Plot Digitized Positions" option is active in the Imaging window that is accessible through the Acquire! window but not when I go through the Automate! window. Would it be possible to have it also working in the latter? That would be incredibly helpful for certain applications.
Thanks!
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I noticed that the "Plot Digitized Positions" option is active in the Imaging window that is accessible through the Acquire! window but not when I go through the Automate! window. Would it be possible to have it also working in the latter? That would be incredibly helpful for certain applications.
Thanks!
Excellent idea!
I had to add additional shape controls to handle the currently digitized points separate from the previously digitized points, but it all works now.
You'll be able to download the update in about 6 hours.
john
Edit by John: OK, ready to download now.
(https://probesoftware.com/smf/gallery/1_19_11_17_6_04_29.png)
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We have a long list of elements (could be 8 or 15) and after 2 days find that we need add another element--C -- to the list. So we know that C is not going to interfere with Fe or Ni or Co or Cr....etc,but we know there are possible n>1 overlaps of Fe Ni Co Cr etc upon C Ka...so we want to do wavescans on the metals ONLY for C Ka. But then we have to DA disable acquisition of all 8 or 15 elements....so wouldn't it be nice if there were a button which one could check saying "Disable ALL elements" that would put DA for each element. Then you only have to click ONE box (C) and away you go, rather than have to click 8 or 15 DA boxes. (Of course, you would all supply an "Enable ALL elements" button. ...just saying.... wouldn't it be nice...
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We have a long list of elements (could be 8 or 15) and after 2 days find that we need add another element--C -- to the list. So we know that C is not going to interfere with Fe or Ni or Co or Cr....etc,but we know there are possible n>1 overlaps of Fe Ni Co Cr etc upon C Ka...so we want to do wavescans on the metals ONLY for C Ka. But then we have to DA disable acquisition of all 8 or 15 elements....so wouldn't it be nice if there were a button which one could check saying "Disable ALL elements" that would put DA for each element. Then you only have to click ONE box (C) and away you go, rather than have to click 8 or 15 DA boxes. (Of course, you would all supply an "Enable ALL elements" button. ...just saying.... wouldn't it be nice...
Hi John,
Your wish is my command. :D
No seriously, that's a good idea. I could use this feature myself.
The latest version has these new buttons in the Elements/Cations dialog:
(https://probesoftware.com/smf/gallery/1_25_11_17_4_25_12.png)
Ready to update now.
john
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Periodically we have material scientists who ONLY look at atomic % data (which is always perfect, always 100%). I try to keep them on the straight and narrow by always verifying that the analytical wt% total is "correct", say between 98 and 102 wt%. But I'm not always around. So here is a suggestion. You currently show in the Analysis window, the wt% total, but it is amongst many other smallish windows and doesn't really stand out if you are singlemindedly looking at the perfect data below. Suggestion: have in the ini flle a min and max range for "realitywarning" keyword, say 3 and 3, i.e. between 97 and 103, nothing happens. But if the analytical total is say 93 or 103.5, then change the small window with the analytical total: make the background red, and the numbers white to stand out. That shouldn't be too hard to program?
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We have a long list of elements (could be 8 or 15) and after 2 days find that we need add another element--C -- to the list. So we know that C is not going to interfere with Fe or Ni or Co or Cr....etc,but we know there are possible n>1 overlaps of Fe Ni Co Cr etc upon C Ka...so we want to do wavescans on the metals ONLY for C Ka. But then we have to DA disable acquisition of all 8 or 15 elements....so wouldn't it be nice if there were a button which one could check saying "Disable ALL elements" that would put DA for each element. Then you only have to click ONE box (C) and away you go, rather than have to click 8 or 15 DA boxes. (Of course, you would all supply an "Enable ALL elements" button. ...just saying.... wouldn't it be nice...
Hi John,
I just realized this morning that you wrote above "disable acquisition", not "disable quant"! :-[
OK, so I changed it for both flags in the Elements/Cations form. Even better! :)
PFE update is ready now.
john
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Hi,
could you also add raw intensities as an option for export as slice/polygon/etc to Surfer?
Thanks!
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Hi,
could you also add raw intensities as an option for export as slice/polygon/etc to Surfer?
Thanks!
(Almost) everything is possible, but I have to ask: why would anyone want to look at raw intensity maps anymore? I mean now that we can get full quant x-ray maps with almost no extra effort?
Is there a special application you are thinking of?
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Hi,
could you also add raw intensities as an option for export as slice/polygon/etc to Surfer?
Thanks!
Hi Anette,
I went to look into this and found the reason one can output x-ray maps of raw intensities, but not for the slice, polygon, etc outputs. It's because there are 256 menus and sub menus in CalcImage (there a lot of output types!) and that is the maximum number of menus allowed in one window, so I would have to re-design things a bit before I can add any new menus to CalcImage.
In the meantime I have a practical suggestion: simply output a slice script for one of the quant types for the project you are working on, and copy that script to another file name. For example, let's say you output a quant script named:
Fe-Mo-Cr-Ni_04-20-2012_Fe-Mo-Cr-1_00451__Quant_Slice.bas
So rename it to something like:
Fe-Mo-Cr-Ni_04-20-2012_Fe-Mo-Cr-1_00451__Raw_Int_Slice.bas
Then open the script in Scripter (or any text editor) and edit the section near the top, to utilize the raw intensity GRD files. So edit this section:
Dim Sample As String
Sample$ = "Fe-Mo-Cr-Ni_04-20-2012_Fe-Mo-Cr-1_00451__Quant_Slice"
Dim SampleTitle As String
SampleTitle$ = "Fe-Mo-Cr-Ni_04-20-2012_Fe-Mo-Cr-1_00451_, Elemental Wt.%"
Dim iMax As Integer
iMax% = 6
XInvert% = -1
YInvert% = -1
XLabel$ = "X (mm) [0.381 mm]"
YLabel$ = "Y (mm) [0.381 mm]"
ReDim FileArray(1 To iMax%) As String
FileArray$(1) = "Fe-Mo-Cr-1_00451_SP1_O_PC1__Quant"
FileArray$(2) = "Fe-Mo-Cr-1_00451_SP2_Mo_LPET__Quant"
FileArray$(3) = "Fe-Mo-Cr-1_00451_SP3_Ni_LLIF__Quant"
FileArray$(4) = "Fe-Mo-Cr-1_00451_SP4_Cr_PET__Quant"
FileArray$(5) = "Fe-Mo-Cr-1_00451_SP5_Fe_LIF__Quant"
FileArray$(6) = "Fe-Mo-Cr-Ni_04-20-2012_Fe-Mo-Cr-1_00451__Total_Quant"
ReDim ZLabel(1 To iMax%) As String
ZLabel$(1) = "O Wt%"
ZLabel$(2) = "Mo Wt%"
ZLabel$(3) = "Ni Wt%"
ZLabel$(4) = "Cr Wt%"
ZLabel$(5) = "Fe Wt%"
ZLabel$(6) = "Total Wt%"
to something like this:
Dim Sample As String
Sample$ = "Fe-Mo-Cr-Ni_04-20-2012_Fe-Mo-Cr-1_00451__Raw_Int_Slice"
Dim SampleTitle As String
SampleTitle$ = "Fe-Mo-Cr-Ni_04-20-2012_Fe-Mo-Cr-1_00451_, Raw Intensity (cps)"
Dim iMax As Integer
iMax% = 5
XInvert% = -1
YInvert% = -1
XLabel$ = "X (mm) [0.381 mm]"
YLabel$ = "Y (mm) [0.381 mm]"
ReDim FileArray(1 To iMax%) As String
FileArray$(1) = "Fe-Mo-Cr-1_00451_SP1_O_PC1_"
FileArray$(2) = "Fe-Mo-Cr-1_00451_SP2_Mo_LPET_"
FileArray$(3) = "Fe-Mo-Cr-1_00451_SP3_Ni_LLIF_"
FileArray$(4) = "Fe-Mo-Cr-1_00451_SP4_Cr_PET_"
FileArray$(5) = "Fe-Mo-Cr-1_00451_SP5_Fe_LIF_"
ReDim ZLabel(1 To iMax%) As String
ZLabel$(1) = "O Intensity (cps)"
ZLabel$(2) = "Mo Intensity (cps)"
ZLabel$(3) = "Ni Intensity (cps)"
ZLabel$(4) = "Cr Intensity (cps)"
ZLabel$(5) = "Fe Intensity (cps)"
Note that I edited (highlighted in red), the sample type and the sample title, and the GRD file names and the label for each raw intensity GRD file and most importantly, changed the number of files to 5 since there is no such thing as a "total" raw intensity file!
I hope this helps whatever you are trying to accomplish. The same technique could be used to output raw intensities using the polygon and strip scripts.
The only useful thing I can think of (though I'm sure there are other useful things one could do) with slices of the raw intensities, is to compare the differences between raw x-ray intensities with the quant values to demonstrate the importance of the background correction, matrix correction and interference corrections, etc. for quantitative maps.
Sort of what you did here (but not using slices through the data):
(https://probesoftware.com/smf/gallery/1_30_11_17_9_17_05.png)
Hope this works for you until I can re-design the CalcImage menus.
Note that if you have version 13 or higher of Surfer, the XInvert and YInvert flags tells Surfer to automatically utilize an anti-Cartesian stage orientation so the slice image will appear in the correct orientation for JEOL instruments!
See attached below, my attempt at modifying a quant slice to use raw intensity GRD files.
john
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Periodically we have material scientists who ONLY look at atomic % data (which is always perfect, always 100%). I try to keep them on the straight and narrow by always verifying that the analytical wt% total is "correct", say between 98 and 102 wt%. But I'm not always around. So here is a suggestion. You currently show in the Analysis window, the wt% total, but it is amongst many other smallish windows and doesn't really stand out if you are singlemindedly looking at the perfect data below. Suggestion: have in the ini flle a min and max range for "realitywarning" keyword, say 3 and 3, i.e. between 97 and 103, nothing happens. But if the analytical total is say 93 or 103.5, then change the small window with the analytical total: make the background red, and the numbers white to stand out. That shouldn't be too hard to program?
Hi John,
Version 12.0.9 has this implemented. It's not blinkin' blinking, but should be more noticeable!
I guess I could also add text warning output to the log window...
Please update PFE from the Help menu and let me know what you think.
john
PS The new default keywords for the probewin.ini file are:
[software]
AnalyticalTotalMinimum=95
AnalyticalTotalMaximum=105
(https://probesoftware.com/smf/gallery/1_01_12_17_6_06_01.png)
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Wish Item for Xmas 2017: For the EPMA lab that doesn't always "do it the same way every day".
We maybe are one of the few labs who doesn't always run their samples at the same column conditions (like we used to in the good ol' days). Now we run some samples 'the old fashioned way, 15 kV" but there are an increasing number of samples we run at 7 or 10 kV. In PfE, there is one default column condition. However, it happens more often than not, we will set up the probe for 7 kV, finish a run, and close the file. Then have the next project also at 7 kV, but if the old brain cells aren't firing quickly enough, I forget to immediately reset the operating conditions in the new file before I start peaking, and the PfE does what you've programmed it to do, it changes the column back to 15 kV, and we have to then spend many minutes realigning the instrument.
So a Holiday Wish: Could you install an option, (which a user can turn off easily), say a key word "AskFirstBeforeDoing". If yes, then when in the code at the first instance of where you check the column kV and see that it is NOT the default, you put up a message on the screen "Do you really want to change from (7) kV to your default (15) kV?" Then if no, the user can remember to go reset the column conditions.
Would make our probing more funner....
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So a Holiday Wish: Could you install an option, (which a user can turn off easily), say a key word "AskFirstBeforeDoing". If yes, then when in the code at the first instance of where you check the column kV and see that it is NOT the default, you put up a message on the screen "Do you really want to change from (7) kV to your default (15) kV?" Then if no, the user can remember to go reset the column conditions.
Would make our probing more funner....
Hi John,
Sounds like you are fighting with yourself for no good reason! ;)
Why don't you simply save your column conditions to a .PCC file, once you've got everything tuned up the way you like it (e.g., 7 keV). And then even if a previous user (or yourself) changed everything later on, you just go to the Windows menu in Probe for EPMA and select the Load Column Conditions From File menu, select the previously saved column condition, and let the software re-load your "tuned up" column settings for you?
Wouldn't that work for you?
john
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No. If my memory was good, your suggestion would work. But if I don't remember, then it doesn't. So a check doesn't hurt.
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Hi John,
I must be missing something because I really don't understand the problem. And besides I need to be sure of making changes such as this, because adding "nuisance messages" will raise the ire of more than one user. You say above:
...but if the old brain cells aren't firing quickly enough, I forget to immediately reset the operating conditions in the new file before I start peaking, and the PfE does what you've programmed it to do, it changes the column back to 15 kV, and we have to then spend many minutes realigning the instrument.
But it seems to me that if you load a file setup from the previous run, you will already have the default keV set where you want it. Or just click the Read Conditions button before starting a peaking method.
As for the situation above where you've spent "many minutes aligning the instrument", and you forget to change the default keV for a new run, the easy cure is to just remember to save the column conditions to a .PCC file after performing a column alignment, so that you can recall all that effort with a couple of mouse clicks in the event that you change something accidentally later on. Just learn to save a .PCC file every time you re-align the column. I save a .PCC file after I align the column on my instrument, and also when I re-saturate the filament (at least you don't have to do that on your instrument!). Hey that reminds me, has Cameca fixed the gun problems you were having last year on your FEG?
Alternatively you could set the UseCurrentConditionsAlways keyword in the Probewin.ini file and then it will simply use the current conditions in the instrument.
I'm really not trying to be difficult, but why do we need to burden every user with such nuisance dialogs every time the keV changes? Just one example, this would be a real problem for multi voltage analysis for thin film characterization for example where the keV is constantly changing.
I think a better solution would be to attach a note to the computer screen to remind you to save the column conditions when the "old brain cells aren't firing quickly enough"...
john
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Hi John,
I'm just analysing some Uranium stuffed full with U-carbides (heterogeneous, lots of big ZAF corrections - the perfect sample!). I've analysed the U but want to try specifying the U content instead, so I disable the quant for U in the Analyze! window and try to specify U but the software won't let me, saying I can't specify a content for a measured element. Can you change this? After all, if I've disabled the quant I'm fixing its value as zero so why can't I fix it as some other value?
Mike
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I'm just analysing some Uranium stuffed full with U-carbides (heterogeneous, lots of big ZAF corrections - the perfect sample!). I've analysed the U but want to try specifying the U content instead, so I disable the quant for U in the Analyze! window and try to specify U but the software won't let me, saying I can't specify a content for a measured element. Can you change this? After all, if I've disabled the quant I'm fixing its value as zero so why can't I fix it as some other value?
Hi Mike, I'll take a look at this. Please give me a few days.
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I'm just analysing some Uranium stuffed full with U-carbides (heterogeneous, lots of big ZAF corrections - the perfect sample!). I've analysed the U but want to try specifying the U content instead, so I disable the quant for U in the Analyze! window and try to specify U but the software won't let me, saying I can't specify a content for a measured element. Can you change this? After all, if I've disabled the quant I'm fixing its value as zero so why can't I fix it as some other value?
Hi Mike,
I did a quick test and it works for me. We must be doing something differently.
I did this in demo mode (not using using the Penepma simulation mode which finds all sorts of off-peak issues that I didn't want to spend time dealing with... by the way in case anyone doesn't know, one can revert back to the "simple" simulation mode in PFE by unchecking the Use Penepma For WDS Simulation checkbox in the Acquisition Options dialog in the Acquire! window).
So I added UO2 and graphite standards to the run, ran each standard and then created an unknown which the software then generates a random uranium carbon composition for and the analysis of that unknown is here:
Un 2 unknown sample, Results in Elemental Weight Percents
ELEM: U C
TYPE: ANAL ANAL
BGDS: LIN LIN
TIME: 10.00 10.00
BEAM: 30.00 30.00
ELEM: U C SUM
4 26.741 72.810 99.551
AVER: 26.741 72.810 99.551
SDEV: .000 .000 .000
SERR: .000 .000
%RSD: .00 .00
STDS: 15 506
I then went to the Analyze! window, clicked Elements/Cations and disabled quant for the uranium channel, then clicked an empty row in that sample to add uranium as a specified element. That gets me this analysis:
Un 2 unknown sample, Results in Elemental Weight Percents
ELEM: U C U
TYPE: ANAL ANAL SPEC
BGDS: LIN LIN
TIME: --- 10.00 ---
BEAM: --- 30.00 ---
ELEM: U-D C U SUM
4 --- 62.998 .000 62.998
AVER: --- 62.998 .000 62.998
SDEV: --- .000 .000 .000
SERR: --- .000 .000
%RSD: --- .00 .00
STDS: --- 506 ---
Then I specified uranium by difference as got this:
Un 2 unknown sample, Results in Elemental Weight Percents
ELEM: U C U
TYPE: ANAL ANAL DIFF
BGDS: LIN LIN
TIME: --- 10.00 ---
BEAM: --- 30.00 ---
ELEM: U-D C U SUM
4 --- 72.904 27.096 100.000
AVER: --- 72.904 27.096 100.000
SDEV: --- .000 .000 .000
SERR: --- .000 .000
%RSD: --- .00 .00
STDS: --- 506 ---
Then I removed the element by difference and specified 27% uranium as a specified concentration and got this:
Un 2 unknown sample, Results in Elemental Weight Percents
ELEM: U C U
TYPE: ANAL ANAL SPEC
BGDS: LIN LIN
TIME: --- 10.00 ---
BEAM: --- 30.00 ---
ELEM: U-D C U SUM
4 --- 72.873 27.000 99.873
AVER: --- 72.873 27.000 99.873
SDEV: --- .000 .000 .000
SERR: --- .000 .000
%RSD: --- .00 .00
STDS: --- 506 ---
So I don't see the problem but I'm sure you're seeing something. Let's take this discussion off-line, but first you should update PFE, just to be sure you're not seeing something I've already fixed! :)
john
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Thanks John,
I hadn't added U back in as an extra, specified, element in Elements/Cations, I'd just tried disabling the U quant and going straight to Specified Concentrations :P.
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Hi,
What would be nice is in acquire window, under peak options - allow the PHA scan without running a peak scan.
So you can Peak and Bias scan. Then set the bias. Then run a base scan for all spectrometers without having to rerun the peak scan
What do you think?
Ben
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What would be nice is in acquire window, under peak options - allow the PHA scan without running a peak scan.
So you can Peak and Bias scan. Then set the bias. Then run a base scan for all spectrometers without having to rerun the peak scan
I second that!
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What would be nice is in acquire window, under peak options - allow the PHA scan without running a peak scan.
So you can Peak and Bias scan. Then set the bias. Then run a base scan for all spectrometers without having to rerun the peak scan
I second that!
I can see the value of that. I'll have to look at the code to see how hard that might be...
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What would be nice is in acquire window, under peak options - allow the PHA scan without running a peak scan.
So you can Peak and Bias scan. Then set the bias. Then run a base scan for all spectrometers without having to rerun the peak scan
I second that!
Hi Ben and Karsten,
Ok, so I let this idea (which is a good one), ferment around in the back of my mind for a few days and finally thought of a cool and easy way to do this. To be honest I think Paul Carpenter asked for something like this a few years ago, but that the time I couldn't think of a nice way to implement it.
So the latest version of Probe for EPMA now has a new checkbox in the Peaking Options dialog as seen here:
(https://probesoftware.com/smf/gallery/1_17_03_18_5_58_59.png)
So now one can acquire multiple spectrometer PHA only scans (for up to 72 elements), automatically on a sample from the Acquire! window.
And from the Automate! window one can run multiple spectrometer PHA scans for multiple standards, also automatically. And on the primary standards, if those standards are assigned as primary standards for the current sample (or on any sample that has sufficient intensities for peaking or PHA scans).
And as usual with PFE, all scans (peaking or PHA) are saved to your run automatically...
Please update from the Help menu and let me know how it works for you all.
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Hi John,
That works great,
Thanks
Ben
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Hi,
Would it be possible to have an option in the "Plot!" window to plot all five spectrometer (or whatever was acquired) wavescans plotted simultaneously (but each in its own window), similar to the real-time wavescan acquisition or peaking window?
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Hi,
Would it be possible to have an option in the "Plot!" window to plot all five spectrometer (or whatever was acquired) wavescans plotted simultaneously (but each in its own window), similar to the real-time wavescan acquisition or peaking window?
We could just reload the wavescan acquisition window with the already acquired intensity data, but may I ask where you eventually want to go with this feature? Do you also want to display KLM markers, pick bgd positions, etc., etc.?
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Hi John,
Nothing fancy, more for teaching and training. When I was gazing at my running wavescans I thought it would be nice to get the same window back at a later time (and being able to export it to clipboard). So reloading the wavescan acquisition window is exactly what I am looking for.
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Hi John,
Nothing fancy, more for teaching and training. When I was gazing at my running wavescans I thought it would be nice to get the same window back at a later time (and being able to export it to clipboard). So reloading the wavescan acquisition window is exactly what I am looking for.
Ok, let me look into it.
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Hi John,
A couple of requests/questions: i) In the Plot window it's really useful that you display relative offset of the cursor from the peak position, but would it be possible to also display the cursor's absolute position in spectrometer units, kV and nm? ii) Is there a way to stop my off-line installation of PfE asking if I want to connect to the instrument every time I launch it? It's only a minor niggle, but I'm never going to be in a position to connect my mac at home to a probe. Is there a switch in Probewin.ini for this?
Mike
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Hi John,
A couple of requests/questions: i) In the Plot window it's really useful that you display relative offset of the cursor from the peak position, but would it be possible to also display the cursor's absolute position in spectrometer units, kV and nm? ii) Is there a way to stop my off-line installation of PfE asking if I want to connect to the instrument every time I launch it? It's only a minor niggle, but I'm never going to be in a position to connect my mac at home to a probe. Is there a switch in Probewin.ini for this?
Mike
Hi Mike,
I can help you with the first one and would like to weigh in with the second one.
You already have the possibility to show absolute spectrometer positions. It is a little check box in the plot window (it always is ;)) See attached screen shot.
For the connect to machine at start-up. I like it. If I say no, I can just process data, even if it has been acquired on a different machine (especially important as I am now switching to a new machine). But if I say yes (and have the correct set-up files for my machine), I can set-up my entire run and play with off-line positions etc. without having to be one the machine. Can just walk to the machine and copy the file to the computer and start. I think it is also needed to run the software in simulation mode (as that option is triggered in Acquisition Options in the Acquire! window) which I used quite a bit so far and not only for teaching.
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Hi Mike,
Anette is exactly correct.
The EDS and WDS simulation modes in Probe for EPMA are based on Penepma Monte Carlo simulations with some additional WDS artifacts added in. Therefore they are surprisingly realistic. One can for example set up one's run and pick backgrounds all in simulation mode. Then simply copy the MDB file to the probe computer, re-peak the spectrometers, check the PHAs and you're ready to go!
But like Anette we use the simulation mode mostly for teaching students and visitors.
Here is a comparison between an actual and simulated WDS scan near the Ar absorption edge using the simulation mode in Probe for EPMA:
http://probesoftware.com/smf/index.php?topic=837.msg5579#msg5579
This should work, even on your Mac! :)
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Thanks Annette and John, I wondered what the check box was for, now I know. Is there any reason, though, why the relative and three sets of absolute values couldn't all be displayed at the same time rather than having to switch between? There's plenty of room that side of the plot window. I'd particularly like to have the absolute energy so I can check my EMAS desk mat (every probe lab should have one😉) to see if it might be an unexpected element in the sample.
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Thanks Annette and John, I wondered what the check box was for, now I know. Is there any reason, though, why the relative and three sets of absolute values couldn't all be displayed at the same time rather than having to switch between? There's plenty of room that side of the plot window. I'd particularly like to have the absolute energy so I can check my EMAS desk mat (every probe lab should have one😉) to see if it might be an unexpected element in the sample.
Hi Mike,
Just a quick note that (almost) every control in Probe for EPMA has a "tool tip help" feature which is visible if you hover the mouse over the button, checkbox, etc. GUI control in our software (Anette's screen shot above shows it nicely). And of course there's actual documentation- not that any one would ever want to crack that open! ;) But if one were willing, one can simply hit the F1 key and (usually) the relevant page in the user manual (for the window/dialog box that has the current mouse focus), will open up in Windows, for your reading pleasure!
Of course asking a question on the forum is really the best way to find out! ;D I've learned that when one person has a question, there's half a dozen others that have been wondering the same darn thing!
As for implementing the cursor position in other units, almost anything is possible in software- just a matter of doing it! :) I'll add it to the list!
john
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Hi John,
I finally got around to writing a script to create a POS file that I can use to import 6610LV coordinates into PFE. It works fine, but I wonder if its possible to make a few modifications to the import dialogs in PFE?
1) When PFE wants you to locate the fiduciary points in the input file it drives the stage to the position of the point. Since the coordinates of these points are coming from the SEM, the stage is now nowhere near the current location of the point. It would be nice if we could turn off this behaviour somehow (perhaps an unlabeled checkbox?)
2) When the import dialog is displayed it holds on to mouse focus so I can't use picturesnap to navigate to my reference points. Could we change the focus behaviour of the import dialog so I can click on picturesnap?
Cheers
Glenn
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Hi Glenn,
There's a couple of things you can do already.
Note the Stage button in the fiducial confirm dialog? If you click this button you can use the StageMap to get you close to the fiducial position and when you close the StageMap window you can click the Update button to update the fiducial you are on.
(https://probesoftware.com/smf/gallery/1_01_05_18_11_26_59.png)
Also, as an alternative, since the FEI and JEOL instruments use mm stage units, you can click "No" when it asks if you want to transform the fiducials and simply apply some mm offsets using the import increment dialog:
(https://probesoftware.com/smf/gallery/1_01_05_18_11_29_28.png)
Edit by John: Ooops! just remembered JEOL is anti-cartesian and FEI is cartesian so the import increment feature won't work! Better to use the fiducial transform or PictureSnapApp as described below...
Does that help at all?
Oh, one more option: if you buy PictureSnapApp for your JEOL instrument you'd be able use PictureSnap as a separate application since it runs from it's own folder. I installed PictureSnapApp on the Cameca PC, so I don't have to use any "real estate" on my PFE monitor. :)
Finally if you got PictureSnapApp running on your SEM you'd also be able to transfer images with stage coordinates between the two instruments easily. That's what it's designed for!
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Thanks John,
Both of these things help. I hadn't calibrated the stage image yet; that helps.
The 6610LV is a JEOL SEM but it doesn't use the EIKS interface( I think only the 7xxx SEMs use it) so I can't run PictureSnapApp :-(
I'm going to buy a standalone copy of PictureSnapApp for the probe computer when I have the cash so that will help too.
Cheers
Glenn
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Hi John,
In the Plot window it's really useful that you display relative offset of the cursor from the peak position, but would it be possible to also display the cursor's absolute position in spectrometer units, kV and nm?
Mike
Hi Mike,
I think we implemented what you want. Here is the modified Plot! dialog in spectro unit mode showing the actual keV of the mouse position:
(https://probesoftware.com/smf/gallery/1_02_05_18_12_07_55.png)
The keV cursor position is also displayed when the plot is in angstrom mode. And here is the same plot, but in keV mode, in which case I decided to plot the additional mouse cursor position in angstroms (not nm, but hey, that's easy to convert in your head!):
(https://probesoftware.com/smf/gallery/1_02_05_18_12_08_10.png)
Update from the Help menu and it should all work. Remember to uncheck the little checkbox for absolute x-position display in whatever plot mode units you are already in.
john
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Thanks John, that's awesome!
Wavelength is fine in Angstroms, as you say it's easy to convert, but one of these days you guys will figure out the metric system ;D
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Thanks John, that's awesome!
Wavelength is fine in Angstroms, as you say it's easy to convert, but one of these days you guys will figure out the metric system ;D
Ha! We 'mericans will never go metric! And beer should not come in pints, right? ;)
Seriously, 10^-10 meters isn't metric? OK, maybe angstroms are not SI, but they're metric I think...
They say that knowing more than one language may have some cognitive advantage- since most in the US are pretty disadvantaged in that sense, maybe having to deal with British and metric units has a similar cognitive value also? But based on the current levels of cognitive dissonance in this country, I sort of doubt it.
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Digitize Image is very useful to set positions to be analyzed on the acquired image.
It would be better if the window is resizable or if the image is zoomable. That is, if the window size for 1024 x 1024 is ~4 times larger than that for 512 x 512, it would be much easier to find good points for measurements. (Same suggestion for displaying window.)
Using PictureSnap is another way to make positions on high-resolution image, but this way is more convenient and more accurate, I guess.
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Digitize Image is very useful to set positions to be analyzed on the acquired image.
It would be better if the window is resizable or if the image is zoomable. That is, if the window size for 1024 x 1024 is ~4 times larger than that for 512 x 512, it would be much easier to find good points for measurements. (Same suggestion for displaying window.)
Using PictureSnap is another way to make positions on high-resolution image, but this way is more convenient and more accurate, I guess.
Hi Changkun,
This is an interesting idea. Let me look into it and see how hard it is to do.
john
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Digitize Image is very useful to set positions to be analyzed on the acquired image.
It would be better if the window is resizable or if the image is zoomable. That is, if the window size for 1024 x 1024 is ~4 times larger than that for 512 x 512, it would be much easier to find good points for measurements. (Same suggestion for displaying window.)
Hi Changkun,
I modified the code for the Imaging and Digitize Image windows. You can now make them as large as your monitor allows.
(https://probesoftware.com/smf/gallery/1_16_05_18_9_35_09.png)
I tested the beam deflection and digitizing functions and they all seem to work with the resizable window. But please let me know if you find anything that doesn't seem right. I haven't had a change to look at the Display Images dialog yet, but I will get to that.
john
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Hi John,
I tested both the Imaging at Acquire! and Digitize Image and both work nicely.
Thanks a lot.
Changkun
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I tested both the Imaging at Acquire! and Digitize Image and both work nicely.
Thanks a lot.
Awesome! Thanks for checking.
We must be doing something right, because we only had to add three lines of code in the window "Resize" event, and it all just worked fine! ;D
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Hi John,
Can you remove the minimum peak to background of 1.5. I want to peak up on Fe Lb and Fe La, and I can't achieve 1.5 over the window for peak search. I'm currently doing wavescans first but this is not ideal
Thanks
Ben
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Hi John,
Can you remove the minimum peak to background of 1.5. I want to peak up on Fe Lb and Fe La, and I can't achieve 1.5 over the window for peak search. I'm currently doing wavescans first but this is not ideal
Thanks
Ben
Hi Ben,
I'd prefer to not remove it completely. How low a P/B do you need do you think? 1.4? 1.3? 1.2?
john
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Hi John,
Sorry I've just looked at it and it should be 0.24/0.12 so 2 and greater, I've currently got the minimum background value set to 2, I think I'll change it to 1.5, and make sure the shoulder of the Fe La is not in the peak window when peak searching for Fe Lb, I'll see how this goes
Thanks
Ben
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Hi John, I can change the minimum background to peak to 1.5 or 1.6 in the software for the current run, but the scalers file will not accept it, it states invalid property. In scalers I currently have 2. which works
One separate thing for wish list - when exporting standard compositions - it be nice to export published values
Thanks
Ben
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Hi John,
I'm copying and pasting in excel, and I have several wishes for exporting data
(1) the suggestion above - exporting published quant.
In addition:
(2) allow export only of average composition and std dev.
(3) the most important - suggested by several users - format data from multiple setups - at the moment if the elements change the columns change and its interrupted by headings. Would it be possible to have the same columns for all the data exported - i.e. look through the list of samples to be exported and pick out the total number of elements - and use these as the columns, OR export the different setups to different files?
Sorry this sounds like a lot of work - I don't know how many people would find pts 1 and 2 useful.
Thanks,
Ben
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Hi John, I can change the minimum background to peak to 1.5 or 1.6 in the software for the current run, but the scalers file will not accept it, it states invalid property. In scalers I currently have 2. which works
Hi Ben,
Yes, that is correct. I'm trying to be conservative and in general prevent people from having a dangerously low minimum P/B for peaking in all runs.
However, as you say, having a specific run with a P/B as low as 1.5 can be specified by the user in the app. And if you create a new run with that low P/B minimum value, it will get loaded into the new run automatically when you use the Load File Setup option.
Will this work for you?
john
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Hi John,
I'm copying and pasting in excel, and I have several wishes for exporting data
(1) the suggestion above - exporting published quant.
In addition:
(2) allow export only of average composition and std dev.
(3) the most important - suggested by several users - format data from multiple setups - at the moment if the elements change the columns change and its interrupted by headings. Would it be possible to have the same columns for all the data exported - i.e. look through the list of samples to be exported and pick out the total number of elements - and use these as the columns, OR export the different setups to different files?
Sorry this sounds like a lot of work - I don't know how many people would find pts 1 and 2 useful.
Thanks,
Ben
Hi Ben,
I want to make sure I'm understanding exactly what you are requesting.
This copying and pasting into Excel- you're doing this from the Analyze! window using the little "Copy" buttons?
john
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Hi Ben,
Yes, that is correct. I'm trying to be conservative and in general prevent people from having a dangerously low minimum P/B for peaking in all runs.
However, as you say, having a specific run with a P/B as low as 1.5 can be specified by the user in the app. And if you create a new run with that low P/B minimum value, it will get loaded into the new run automatically when you use the Load File Setup option.
Will this work for you?
john
Yes that's fine thanks
Ben
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Hi Ben,
I want to make sure I'm understanding exactly what you are requesting.
This copying and pasting into Excel- you're doing this from the Analyze! window using the little "Copy" buttons?
john
Sorry I should have made it clear, I'm reformating the data once I've exported it using the user specified output script, and I was wondering if you could refine it?
Thanks
Ben
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(1) the suggestion above - exporting published quant.
Hi Ben,
Thanks for the clarifications. This option already exists in the user specified output:
(https://probesoftware.com/smf/gallery/1_13_09_18_10_09_42.png)
The only caveat is that the software doesn't select automatically select the proper Standard/Unknowns output option when exporting data from the Analyze! window and using the right click option to export only selected samples. The option is selected on the basis of what output you last did from the Output menu.
I just fixed the code to do this automatically and will upload a new version later today. In the meantime just use the Output | Export User Specified Output menu for standard sample output with the published values options.
(2) allow export only of average composition and std dev.
Yeah, not a bad idea, but the problem is that the user has to select as output type so it knows what data to average. I'll have to think if there's a clever way to do this, but for now you'll have to remove the other rows in your spreadsheet.
(3) the most important - suggested by several users - format data from multiple setups - at the moment if the elements change the columns change and its interrupted by headings. Would it be possible to have the same columns for all the data exported - i.e. look through the list of samples to be exported and pick out the total number of elements - and use these as the columns, OR export the different setups to different files?
I can see that this would be useful, but it would be a lot of work. I'll have to think about it how it might be done.
In the meantime you're a super scripter! I'm sure you could easily knock off an Excel macro to do this... :)
Post it to the forum and you'll be a hero! :-*
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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:
(https://probesoftware.com/smf/gallery/1_14_09_18_12_23_13.png)
This enables the output of "published" concentration (and variance and difference) values for standards if standard samples were selected.
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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:
(https://probesoftware.com/smf/gallery/1_14_09_18_12_23_13.png)
This enables the output of "published" concentration (and variance and difference) values for standards if standard samples were selected.
Thanks for doing that
Ben
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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:
(https://probesoftware.com/smf/gallery/395_24_09_18_10_48_41.png)
The Probe for EPMA help file has this to say:
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:
(https://probesoftware.com/smf/gallery/395_24_09_18_10_55_50.png)
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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
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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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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
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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:
(https://probesoftware.com/smf/gallery/1_30_11_18_10_10_24.png)
For those of you not aware of this off-peak background method, the help file has this to say:
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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Hi John,
That sounds really good, I want to try it, but machine is now down for maintenance.
Ben
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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.
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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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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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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.
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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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My wish is for the U-Th-Pb chemical age output to also give individual spot errors.
cheers
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My wish would be that PictureSnap can display ProbeImage map files also in rainbow colors.
Thanks
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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.
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My wish would be that PictureSnap can display ProbeImage map files also in rainbow colors.
Thanks
Hi Anette,
PictureSnap utilizes the color palette of the imported image, but the PrbImg import in PictureSnapApp utilizes the current color palette in PFE (and Startwin). In PFE, the default color palette is the one defined in the Probewin.ini file for the image acquisition, but this can be changed in the Run | Display, Annotate, Export Analog Signal Images menu. So if you really need a rainbow color palette (really?), you could just change the default color palette in the Run menu, then import the PrbImg file into PictureSnapApp.
Or you could import the PrbImg file into CalcImage. Then convert the color palette to whatever palette you want from the Image Processing menu, and then save it as a BMP file from the File menu. When you save it as a BMP file, it will also save the .ACQ file which is the PictureSnap calibration file. Note that when you import the PrbImg file it looks in the UserImages folder, but when you save it as a BMP file, it defaults to the UserData folder. Then just open the converted BMP file in PictureSnap (or PictureSnapApp) and you should be good to go.
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My wish is that when PfEPMA sets the default standards for the MAN calibration curves that it would not assign those standards to an individual curve that have an assigned overlapping element. For example if Br is the analyzed element and Al is an assigned overlap then PfEPMA will not add any standard that has reported Al concentrations.
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My wish is that when PfEPMA sets the default standards for the MAN calibration curves that it would not assign those standards to an individual curve that have an assigned overlapping element. For example if Br is the analyzed element and Al is an assigned overlap then PfEPMA will not add any standard that has reported Al concentrations.
Hi Dave,
It's a good idea but hard to implement because the MAN assignments are global, but the interference assignments are on a sample basis. If we think of a way to do it, we will add it.
At least spectral interferences (and/or contamination) in the standards show up nicely in the MAN plots, so they can be removed from the assignments!
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My wish is that when PfEPMA sets the default standards for the MAN calibration curves that it would not assign those standards to an individual curve that have an assigned overlapping element. For example if Br is the analyzed element and Al is an assigned overlap then PfEPMA will not add any standard that has reported Al concentrations.
Hi Dave,
It's a good idea but hard to implement because the MAN assignments are global, but the interference assignments are on a sample basis. If we think of a way to do it, we will add it.
At least spectral interferences (and/or contamination) in the standards show up nicely in the MAN plots, so they can be removed from the assignments!
They do show up really well! It's interesting to see when there's an interference that one might have missed.
Is there some way to implement a global setup option in a project? For example if I want to a universal setup for a set of different silicate minerals that use the same instrument setup but the analyst would just disable elements for specific mineral setup samples.
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Hi John
Yes you are correct I was thinking of individual spot age errors based on counting statistics. I have attached a spreadsheet which is a cutdown version of a speadsheet we used to use a long time ago. It had other worksheets in it and a macro to perform the iterative age calculation. I am not sure who created the original sheet, it was just handed down from person to person.
Captured in the cut down worksheet I have attached, is how the individual 1 sigma errors were calculated based on Pk/Bg counts, count times, contributions from U/Th isotopes etc. It doesn't contain any of the original macro for age calculation, but I assume you don't need that as you already have that in your software. All you need are Pk/Bg counts, count times, decay constants, and the "proportions" or contribution of Pb from the different isotopes to calculate the 1 sigma.
Unfortunately I am not an expert of chemical dating (or microprobe!) so I cannot say whether this is the correct way to calculate the 1 sigma errors for chemical probe dating...perhaps Mike or Julien could comment, but it appears logical to me. Anyway I understand its potentially a lot of work for little public demand so understand if you are reticent to put it in.
Cheers
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Is there some way to implement a global setup option in a project? For example if I want to a universal setup for a set of different silicate minerals that use the same instrument setup but the analyst would just disable elements for specific mineral setup samples.
Hi Dave,
Not sure exactly what you mean.
If you mean you'd like to have a "mother of all samples" with all the elements tuned up that one might want to acquire for all minerals, and then just disable the acquisition of elements you don't need for a particular mineral then yes, you can do that using the Disable Acq check box for each element in the Elements/Cations dialog for that element. Is that what you mean?
john
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Is there some way to implement a global setup option in a project? For example if I want to a universal setup for a set of different silicate minerals that use the same instrument setup but the analyst would just disable elements for specific mineral setup samples.
Hi Dave,
Not sure exactly what you mean.
If you mean you'd like to have a "mother of all samples" with all the elements tuned up that one might want to acquire for all minerals, and then just disable the acquisition of elements you don't need for a particular mineral then yes, you can do that using the Disable Acq check box for each element in the Elements/Cations dialog for that element. Is that what you mean?
john
Not exactly. I meant more that is there a way to do a "mother of all samples" for a project where what I was suggesting for the MAN curves would work.
Thanks!
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Hi Dave,
Do you mean where different samples would have different standards assigned to the MAN curves?
john
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Hi Dave,
Do you mean where different samples would have different standards assigned to the MAN curves?
john
Hi John,
Well, I was thinking more that there's a universal setup then one could make sub-setups for different analyses with various elements switched on or off and using the same standards assigned to the universal MAN curves for that .mdb. That way someone could setup a with everything they want, have the overlaps taken into account when assigning the MAN curves and not have to sift through the curves as much, then create sample setups with variations on the universal setup.
dave
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Hi Dave,
Do you mean where different samples would have different standards assigned to the MAN curves?
john
Hi John,
Well, I was thinking more that there's a universal setup then one could make sub-setups for different analyses with various elements switched on or off and using the same standards assigned to the universal MAN curves for that .mdb. That way someone could setup a with everything they want, have the overlaps taken into account when assigning the MAN curves and not have to sift through the curves as much, then create sample setups with variations on the universal setup.
dave
Hi Dave,
This feature will be in the Probe for EPMA "artificial intelligence" edition that I'm working on next! ;)
Seriously, this sounds like a bit of work, but if we can think of an easy way to implement it, maybe it is possible. Let's talk about it over a beer or two!
john
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Hi John,
I am trying to use the user specified output from PfE for some data, where I am only interested in the counts. So I did not measure any standards. The program is complaining that it cannot find standard counts...
Is it possible that if I select in user specified output only net counts and things like that PfE does not check for standards?
Cheers
Philipp
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Hi Philipp,
The user specified output format is intended for quant output, but did you try the NIST output format? It outputs raw intensities.
john
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Hi John,
also the NIST format is asking for standards. :'( :'( :'(
Just would like to export my data. But I do not have standard measurements for this project and it is a lot of work to measure fake standards for many elements and different HVs.
No way to use the user output for intensities without standards?
Cheers
Philipp
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Hi Philipp,
Well you can just double-click the sample to see the raw data in the log window and Analyze! windows, and then use the Copy buttons in the Analyze! window to copy the intensities to the system clipboard and paste them into Excel.
https://probesoftware.com/smf/index.php?topic=227.msg1065#msg1065
john
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Hi John,
I am aware of the copy buttons. But this involves many clicks and lots of sources for errors. It is really not advisable.
So I will make myself some fake standards or something, just to get the data out. It would be really nice to have a tick box somewhere that allows to export unquantified data without the need of fake standards.
Thanks
Philipp
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Hi Philipp,
I think I have an output solution that will work for you (I don't know why I didn't think of it before!).
Simply go to the Output | Output Standard and Unknown XY Plots menu and change the "output target" to Output Data to ASCII as seen here:
(https://probesoftware.com/smf/gallery/1_18_06_19_8_31_56.png)
As long as you don't select one of the quantitative output types, it will just write your data to a tab delimited file, and optionally export it to Excel. Please let me know if this works for you.
john
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Hi John,
good idea! I tried it and it worked. But I also have the 42 fake standards now (7 HVs * 6 elements). So not certain if it would throw an error.
But it looks like it does not try to read any standard data and just spits out the counts. Maybe you should mention this in the PfE tricks thread.
Thanks
Philipp
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I think you should post about this output option and also your "fake standards" method also in the PFE Tips and Tricks topic. Sounds like it could be useful. How did you fake standards? Did you use the simulation mode?
john
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Hi John,
Any chance you could remove the popup window 'bad negative zz' and just log the error message. The problem is it opens the window consecutively many times.
When processing the data, do you do anything different with bad negative zz values. Once I've clicked the message box 20-30x the data often seems ok.
Thanks
Ben
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Hi John,
Any chance you could remove the popup window 'bad negative zz' and just log the error message. The problem is it opens the window consecutively many times.
When processing the data, do you do anything different with bad negative zz values. Once I've clicked the message box 20-30x the data often seems ok.
Thanks
Ben
Hi Ben,
I don't do anything with the negative ZZ value, but the matrix correction physics calculations cannot proceed (usually).
Can you send me the MDB file which contains the problem data points?
john
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Hi John,
Thanks for explaining.
I'll email you.
Ben
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Hi John,
Any chance you could remove the popup window 'bad negative zz' and just log the error message. The problem is it opens the window consecutively many times.
When processing the data, do you do anything different with bad negative zz values. Once I've clicked the message box 20-30x the data often seems ok.
Thanks
Ben
Hi Ben,
I modified the matrix correction error messages to just log the error to the log window when it encounters negative values for certain mathematical operations. You can update to Probe for EPMA v. 12.7.1 whenever you are ready.
Let me know if this works better for you.
john
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Hi, when switching through many of the PfE windows using the TAB key the order in which the fields are selected seems totally random. Is it possible to bring this in order to press TAB and really move to the next field?
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Hi Philipp,
It is possible, and you may find some windows are better organized than others. To be honest, it has not been a priority. Which windows specifically are you looking at?
Also, we've tended to only allow tabbing for the text input controls. How do you feel about that?
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Hi John,
it's various windows... For example in the elements/cations, when I edit an element, or when I use the "edit mac table".
I can see that it is not a priority... There is more important stuff to do. But maybe, when changing some window, the tab order could be checked.
I use TAB and ENTER quite a lot... I am not a big fan of clicking around with the mouse. So I use TAB also to move from "cancel" to "ok" and hit enter.
Nice would be also some keyboard shortcuts... In calczaf you can open the X-ray menu using alt-x, but then there are no furhter keys defined for the submenu.
Cheers
Philipp
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Hi John and Philipp,
I especially agree with Philipp's request for some shortcut keys! One I'd really appreciate would be the Single Points menu on the Digitize positions window.
I'd then be able to assign that key combination to a USB foot pedal and store points without taking my eyes off the JEOL SEM screens. It's all about productivity! ;)
Cheers
Glenn
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Hi John and Philipp,
I especially agree with Philipp's request for some shortcut keys! One I'd really appreciate would be the Single Points menu on the Digitize positions window.
I'd then be able to assign that key combination to a USB foot pedal and store points without taking my eyes off the JEOL SEM screens. It's all about productivity! ;)
Cheers
Glenn
Hi Glenn,
I could add an <alt> S key shortcut for the Single Points button.
john
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That would be perfect!
Thanks
Glenn
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That would be perfect!
Thanks
Glenn
Or maybe I'll make the Single Points button an <alt> P and the Shotgun button an <alt> S?
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Even better!
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Hi John
My wish would be to have the list of standards in the MAN fit window sorted by standard number. I am not too sure what is governing the order they appear at the moment, it doesnt appear to be mean Z.
Cheers
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I second the suggestions for keyboard shortcuts and tab key sequencing. Like Philipp working with the keyboard is much quicker for me than constantly having to put one hand back on the mouse and point that to the next field.
One of my favourite candidates to have the tab key progress through the fields in order (left->right, top->bottom) would be the Element/Cation Properties window, especially the WDS Spectrometer Parameters section.
Cheers, Karsten
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I second the suggestions for keyboard shortcuts and tab key sequencing. Like Philipp working with the keyboard is much quicker for me than constantly having to put one hand back on the mouse and point that to the next field.
One of my favourite candidates to have the tab key progress through the fields in order (left->right, top->bottom) would be the Element/Cation Properties window, especially the WDS Spectrometer Parameters section.
Cheers, Karsten
We'll start working on that. Also we'll take a look at the MAN standards list order as Ben Wade mentions.
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Hi John
My wish would be to have the list of standards in the MAN fit window sorted by standard number. I am not too sure what is governing the order they appear at the moment, it doesnt appear to be mean Z.
Cheers
Hi Ben,
If you update PFE now you should see the standards in the MAN dialog sorted by number.
Good idea!
john
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Awesome, thanks John
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Hi John and Philipp,
I especially agree with Philipp's request for some shortcut keys! One I'd really appreciate would be the Single Points menu on the Digitize positions window.
I'd then be able to assign that key combination to a USB foot pedal and store points without taking my eyes off the JEOL SEM screens. It's all about productivity! ;)
Cheers
Glenn
Hi Glenn, Philipp, and Karsten,
The latest Probe for EPMA v. 12.7.5 now has improved tab order for the standard assignments and Elements/Cations dialogs. It also has shortcut keys for the Single Points and Shotgun buttons in the Digitize dialog.
The Single Points hot key seems to work just fine, but in testing we noticed that on some computers, the shortcut key for the Shotgun button does not work as expected. For some reason on these computers the pressing of the <alt> and s keys changes the s key code to the "application menu" key code. This is apparently due to some other application or the operating system function taking control over this key combination. We are investigating.
Please let us know if there's other places that need improvement in tab order or shortcut keys.
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Hi John,
great, thanks a lot. In calczaf I would like to open the edit mac table dialogue using alt-x and then something. And the tab order in that dialogue would be nice to be fixed.
Cheers
Philipp
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Hi John,
great, thanks a lot. In calczaf I would like to open the edit mac table dialogue using alt-x and then something. And the tab order in that dialogue would be nice to be fixed.
Cheers
Philipp
Hi Philipp,
We did fix the tab order in the Edit MAC Value dialog, but we didn't bump the version number only the revision number, so if you want to have CalcZAF.exe updated you'll have to run the CalcZAF.msi installer file. Or you can run the ProbeforEPMA.msi installer *again* and the 2nd time when it gives you the "Repair" option, choose that.
We'll add the menu shortcuts next.
john
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Hi John,
great, thanks a lot. In calczaf I would like to open the edit mac table dialogue using alt-x and then something. And the tab order in that dialogue would be nice to be fixed.
Cheers
Philipp
Hi Philipp,
We've had a bit of a "hodge-podge" of keyboard shortcuts in PFE and CalcZAF and decided to make them more consistent and uniform for all the apps. First of all we removed all the <ctrl> shortcut keys and replaced most of them with <alt> key shortcut combinations. We also added some new <alt> key shortcuts for some menus, such as the Edit MAC Table as you requested.
As an example, here is what the main main log window in the CalcZAF app looks like when started up:
(https://probesoftware.com/smf/gallery/1_22_09_19_12_10_43.png)
Now when one holds down the <alt> key things change. Can you see that? Yes, each main menu item now has the first letter of each menu *underlined* as seen here:
(https://probesoftware.com/smf/gallery/1_22_09_19_12_11_49.png)
This underlining will now be the new "hint" for the <alt> shortcut keys. Now if the user say, hits the "x" key for the X-Ray menu, the X-Ray menu will be displayed as seen here:
(https://probesoftware.com/smf/gallery/1_22_09_19_12_11_59.png)
Then the user simply hits the "e" key and the Edit MAC Table dialog will appear for custom editing of the current (default) MAC table. So <alt> "x" and then "e" now opens the Edit MAC Table dialog. The tab order should be OK now too.
We've done something similar to most of the Probe software apps, though there is one caveat. Although in principle we could make any character in each menu the "underline" shortcut key, right now we are limiting the <alt> shortcut keys to the first letter of each menu. This means that if more than one menu (within a single menu level) utilizes the same letter, we can only make one of them be the <alt> shortcut key.
But with that caveat in mind, if you or anyone else, sees additional opportunities for further <alt> shortcut keys, please let us know. Thanks!
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I am not sure if this was already discussed but would it be possible to have an "assign to unknown" option in the "Display...TDI dialog? Similar to the background models dialog where I can directly assign the chosen model parameters to the individual unknown.
Thanks!
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I am not sure if this was already discussed but would it be possible to have an "assign to unknown" option in the "Display...TDI dialog? Similar to the background models dialog where I can directly assign the chosen model parameters to the individual unknown.
Thanks!
Anette,
This is a really good idea. Thanks!
So what we did was add a button to assign the currently selected and displayed TDI fit method (linear, quadratic, and logarithmic) to the selected element in them selected sample.
Note that unlike the TDI fit display in the Standard Assignments dialog in the Analyze! window, this TDI dialog only displays one data point (line) at a time, but the TDI fit assignment is applied to all data points (lines) in the sample. So one should be sure that the selected fit is appropriate for all lines in the sample, not just the one displayed.
That said, once we added an assign TDI fit button we then saw a problem, and that was that there is no display for what the current TDI fit assignment actually is! So we added a label that displays the current TDI fit for the selected element and selected sample as seen here:
(https://probesoftware.com/smf/gallery/1_13_12_19_2_39_55.png)
Then when the user selects a different TDI fit, that is displayed in the TDI graph and so if one then clicks the Assign TDI Fit To Sample button the TDI fit is assigned to the selected element and sample as seen here:
(https://probesoftware.com/smf/gallery/1_13_12_19_2_40_12.png)
And the label is updated to reflect the change in the TDI fit type.
Thanks for the cool idea. 8)
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Woohoo!!!!! Instant wish fulfillment. Thank you!
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My wish is to have an "Acquire Images" tick box in Automate | Automation Actions, which would then acquire an image for every sample in the Automate position list (e.g. using the "last unknown" beam settings and Acquire | Imaging image settings) without running an actual x-ray acquisition.
Or is this already possible somehow?
We often acquire automated BSE images during Automate! runs using the functions in the Acquisition Options dialog, as they are very useful for providing textural context to the analysis data, but sometimes something goes wrong - e.g. we've picked the wrong beam current, magnification, brightness/contrast, detector signal for the image acquisition without noticing... and all images (sometimes hundreds...) are useless. So it'd be great if I could just fix the settings and quickly acquire all images again without repeating the actual analyses.
There may be other situations where we may just want to acquire a series of images where this could be useful.
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Hi Karsten,
You can do this already from the Stage application.
Just be sure to use the Imaging button in the Mosaic dialog to adjust the proper imaging parameters first. You don't need to actually digitize mosaic positions, the automation will use whatever position samples you select for the image acquisitions.
https://probesoftware.com/smf/index.php?topic=324.0
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Thanks John, I've just tried that and it works great.
Is there a way how I can set where/how they are saved, e.g. so I don't have to dig them individually out of those sub folders, or for example include a scale bar? I assume there is no way of re-integrating them in the .MDB/.BIM for the run so it can display the analysis location?
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Hi Karsten,
The acquisition also saves the images as GRD files, so they are calibrated, e.g, load them into CalcImage or PictureSnapApp to see the scale bar. The ACQ file also contains the imaging and column conditions.
There is a load PrbImg option in the PFE Imaging window that might work for importing them, but we would need to add support for importing GRD files.
Let me think about it a bit and see what we can come up with.
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Great, many thanks John.
What we love about this automated imaging feature in PFE (and why we basically have it always on by default) is that it is so easy and quick to use - just tick a box and it automatically acquires an image for every dataset, and then we can just export all of them with a single click after the run and have all the image files (with and without scale bar, point location...) in a single folder ready to use.
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Thanks John, I've just tried that and it works great.
Is there a way how I can set where/how they are saved, e.g. so I don't have to dig them individually out of those sub folders, or for example include a scale bar? I assume there is no way of re-integrating them in the .MDB/.BIM for the run so it can display the analysis location?
Hi Karsten,
Your wish is granted! :)
It took a bit of thinking and some code re-arrangement, but we found a way to allow automated acquisition of calibrated images in PFE from the Automate! window when simply confirming stage positions. These images will be automatically saved to your currently open probe database.
(https://probesoftware.com/smf/gallery/1_28_02_20_2_01_01.png)
Download v. 12.8.5 from the PFE Help menu when you are ready to try it out.
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Thanks John, that's awesome. I've just tried it and it works great. After the separate image acquisition I can just use the handy "Match Image Names" feature in the Run | Display/Export Images window to assign the images to the correct measurements (they have the same names as they were both run through Automate) and then do my single click export of all images (with and without analysis locations) as usual!
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Thanks John, that's awesome. I've just tried it and it works great. After the separate image acquisition I can just use the handy "Match Image Names" feature in the Run | Display/Export Images window to assign the images to the correct measurements (they have the same names as they were both run through Automate) and then do my single click export of all images (with and without analysis locations) as usual!
Hi Karsten,
Glad that worked for you.
If anyone else doesn't know about the Match Image Names button that Karsten mentions above, it can be seen here in this post by Andrew Locock:
https://probesoftware.com/smf/index.php?topic=898.msg8581#msg8581
This button is near the bottom of the Display Probe Image Data dialog, which is accessed from the Run | Display, Annotate and Export Analog Signal Images menu in Probe for EPMA.
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Here comes the ultimate request to be lazy. So, Andrew Locock has this nifty spreadsheet to recalculate garnet analyses into a gazillion endmembers and other useful things. I also like it because it gives an assessment on the data quality and I always get good grades ;)
The spreadsheet is set-up slightly different from the available PFE output options and also contains various elements (Sc, Zr, Sn etc) that are not always part of routine analyses. I always spend time rearranging or adding columns to the PFE output to make it fit and usually have to do it multiple times over when data processing.
It would be great if there could be another custom output (like the H.W. and J.J.D. options) that would just create an output with similar element order (and with empty columns if the element was not analyzed) so that I can copy the output straight into his spreadsheet.
The spreadsheet is attached and the paper can be found here: https://www.sciencedirect.com/science/article/pii/S0098300408001064
In case this is not too much work, this would be a great addition to the list of output options.
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I agree this would be really useful. Maybe we could do another custom output for Andrew's excellent amphibole spreadsheet too?
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Here comes the ultimate request to be lazy. So, Andrew Locock has this nifty spreadsheet to recalculate garnet analyses into a gazillion endmembers and other useful things. I also like it because it gives an assessment on the data quality and I always get good grades ;)
The spreadsheet is set-up slightly different from the available PFE output options and also contains various elements (Sc, Zr, Sn etc) that are not always part of routine analyses. I always spend time rearranging or adding columns to the PFE output to make it fit and usually have to do it multiple times over when data processing.
It would be great if there could be another custom output (like the H.W. and J.J.D. options) that would just create an output with similar element order (and with empty columns if the element was not analyzed) so that I can copy the output straight into his spreadsheet.
The spreadsheet is attached and the paper can be found here: https://www.sciencedirect.com/science/article/pii/S0098300408001064
In case this is not too much work, this would be a great addition to the list of output options.
Hi Anette,
It's a bit of work, but doable.
Can you send me an example of the .DAT file that is what you need for output from PFE?
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I agree this would be really useful. Maybe we could do another custom output for Andrew's excellent amphibole spreadsheet too?
Hi Glenn,
I assume the amphibole spreadsheet requires a different element order than the garnet spreadsheet? Can you attach Locock's Excel spreadsheet for amphiboles?
Can you also send me an example .DAT file with the correct formatting for the amphibole spreadsheet?
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I agree this would be really useful. Maybe we could do another custom output for Andrew's excellent amphibole spreadsheet too?
Hi Glenn,
I assume the amphibole spreadsheet requires a different element order than the garnet spreadsheet? Can you attach Locock's Excel spreadsheet for amphiboles?
Can you also send me an example .DAT file with the correct formatting for the amphibole spreadsheet?
Keep in mind that many people do not accept the new amphibole classification of Hawthorne et al. (2012, Am Min 97:2031-2048) and continue to use the older Leake et al. classification. Further, in order to classify an amphibole, it's necessary to recalculate for Fe2O3, and the recalculated value is strongly dependent on the normalization scheme used. For instance, one may obtain radically different wt% Fe2O3 depending on whether Na+ is assumed to reside on M4 or A -- and this is assuming that no O2- substitutes for OH-. I would proceed with extreme caution.
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Hi John
Only a minor thing, but it would be great if there was an increase (or removal?) of the character limit to the "Description" box in the Standard program? I find myself using it to document progressive changes/updates to concentrations, or addition of important notes, but at the moment it seems to be character amount limited and I have reached that limit for some standards. If its not simple to increase thats fine, I will have to start some other database record locally to record when I make changes.
cheers
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Hi Ben,
Yeah the maximum limit for a "text" database field in MS Access is 255 characters. I could change it to a "memo" field but then it would break everyone's current standard databases. It used to be 64 characters, so when I changed it to 255 years ago I thought that would be good enough... :(
Sorry.
john
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Hi John
No worries. When I modify the Standard.mdb I make a dated archive copy so will just wipe the box clean of edits in the new copy each so I have enough room, and just refer back to the older archived mdb files if I want to see historical changes I have made.
Cheers
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Could you add a memo field? If it doesn’t break the database it could be a useful place to keep a version log etc...
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Hi Mike,
Do you mean a single memo field for a single standard database? Or do you mean a single memo field for each PFE MDB database?
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Hi John,
I was just wondering if that would be an option to address Ben’s request.
Mike
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Hi John,
I was just wondering if that would be an option to address Ben’s request.
Mike
Hi Mike,
It's a reasonable idea, so that's why I asked if he needs a single memo field for the standard (or PFE) database, or a memo field for each standard composition.
john
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Hi John
Only a minor thing, but it would be great if there was an increase (or removal?) of the character limit to the "Description" box in the Standard program? I find myself using it to document progressive changes/updates to concentrations, or addition of important notes, but at the moment it seems to be character amount limited and I have reached that limit for some standards. If its not simple to increase thats fine, I will have to start some other database record locally to record when I make changes.
cheers
Hi Ben,
Along the lines that Mike Matthews suggested I think we've implemented something you can use. Update using the Help menu to PFE v. 12.8.9 and open your standard database. There's now a new button in the Standard | Modify menu dialog called Memo Text as seen here:
(https://probesoftware.com/smf/gallery/1_16_08_20_1_52_27.png)
This gives you a 64K character memo field for additional documentation (in addition to the existing 255 character description field).
Let me know if this works for you.
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Hi John and Mike
That is absolutely fantastic and exactly what I was after. Many thanks again
cheers
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Hello,
is it possible to add the multi-point background positions to the analysis setup report output?
Also, I wonder if we could report which standards were used for the MAN calibrations. Currently, it lists all standards in the run and which ones were used for the peak calibrations but it would be nice to also get the ones that were used for the MAN curves either as part of the text output or as another spreadsheet (as their standard database numbers probably).
Thanks!
Anette
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Hello,
is it possible to add the multi-point background positions to the analysis setup report output?
Also, I wonder if we could report which standards were used for the MAN calibrations. Currently, it lists all standards in the run and which ones were used for the peak calibrations but it would be nice to also get the ones that were used for the MAN curves either as part of the text output or as another spreadsheet (as their standard database numbers Thanks!
Anette
OK, we added some code for output of MAN (mean atomic number) background fit assignments and MPB (multi-point background) parameters. Here is the output to Excel for MAN assignments:
(https://probesoftware.com/smf/gallery/1_24_09_20_1_58_40.png)
Add here is the output to Excel for the MPB parameters:
(https://probesoftware.com/smf/gallery/1_24_09_20_1_59_00.png)
Let us know if you need it formatted differently. Update PFE from the Help menu as usual...
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We decided to modify the MPB fit type output to show the "Linear", "Polynomial" and "Exponential" strings instead of just the integer index as shown here:
(https://probesoftware.com/smf/gallery/1_24_09_20_9_13_49.png)
Again, update from the Help menu to obtain this latest version.
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Hi John,
We often use the wavescan function to identify the peak position for S on vg2, with ca. 1000ppm,
Would it be difficult to have a peak fitting function - to read the peak position within the plot window?
Thanks
Ben
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Hi Ben,
Well, you can either uncheck the "Relative Position" checkbox in the Plot! window and use the mouse cursor to display in spectrometer units, as shown here:
(https://probesoftware.com/smf/gallery/1_23_11_20_9_37_28.png)
Or you can use one of the peak fitting methods in the Model Backgrounds dialog as seen here:
(https://probesoftware.com/smf/gallery/1_23_11_20_9_34_08.png)
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Hi John,
Thanks, you learn something new everyday.
So it fits a function to the whole wavescan range is that right?
So Parabolic and Gaussian only work if wavescan range is restricted to the width of the peak, whereas Brent Maxima always works, as its using a parabolic interpolation to find the maxima -
Thanks
Ben
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So it fits a function to the whole wavescan range is that right?
So Parabolic and Gaussian only work if wavescan range is restricted to the width of the peak, whereas Brent Maxima always works, as its using a parabolic interpolation to find the maxima -
Hi Ben,
Yes I noticed that also.
We will try to modify the fitting code to only utilize the current "zoom" range. Give us a few days.
john
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Hi John,
Thanks, you learn something new everyday.
So it fits a function to the whole wavescan range is that right?
So Parabolic and Gaussian only work if wavescan range is restricted to the width of the peak, whereas Brent Maxima always works, as its using a parabolic interpolation to find the maxima -
Thanks
Ben
Hi Ben,
OK, we modified the code to utilize the x-axis "zoomed" range if the plot is "zoomed", and if not, just use the full wavescan range (as before), for the centroid fitting:
(https://probesoftware.com/smf/gallery/1_25_11_20_8_51_37.png)
This version is v. 12.9.0 and just update as usual from the Help menu in PFE to get it.
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Hi,
when doing PHA Bias scans through the peaking dialog, the pop-up monitor window X-axis starts at "0" during the acquisition. Could that be adjusted to start at the individual Bias scan range? Thanks!
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Hi Anette,
I'm not seeing it in my JEOL simulation mode. Can you please send me a screenshot by email?
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When doing PHA Bias scans through the peaking dialog, the pop-up monitor window X-axis starts at "0" during the acquisition. Could that be adjusted to start at the individual Bias scan range? Thanks!
Hi Anette,
OK, we were able to reproduce the issue.
Basically the displayed x-axis range depends on the value of the configuration keyword DisplayFullScanRangeForAcquisitionFlag in the Probewin.ini file. If it is set to zero (the default), the x-axis range is automatically updated as the data is acquired and displayed. In this case the bias scan x-axis range (in bias volts), displayes fine. But if the DisplayFullScanRangeForAcquisitionFlag keyword is set to non-zero, the full x-axis range is displayed from the beginning, and the plot is "filled in" as the bias scan is acquired. This is true also for PHA scans and gain scans (Cameca instruments only).
But for PHA scans, the minimum x-axis data value is often a fraction of a volt, so we have always forced it to zero for the tick marks to display nicely. This didn't affect the bias and gain scans when DisplayFullScanRangeForAcquisitionFlag=0, but it was forcing the x-axis minimum to zero for bias and gain scans as you pointed out, but only when DisplayFullScanRangeForAcquisitionFlag=1 in the Probewin.ini file!
So previously the following code was utilized for all scans:
Call ScanInitGraph(sample(1).MotorNumbers%(chan%), nPoints%(chan%), CSng(0#), stopvolts!(chan%), title$)
If ierror Then Exit Sub
But this is now changed to:
If mode% = 0 Then
Call ScanInitGraph(sample(1).MotorNumbers%(chan%), nPoints%(chan%), CSng(0#), stopvolts!(chan%), title$)
If ierror Then Exit Sub
Else
Call ScanInitGraph(sample(1).MotorNumbers%(chan%), nPoints%(chan%), startvolts!(chan%), stopvolts!(chan%), title$)
If ierror Then Exit Sub
End If
In other words, the x-axis range is now the bias (or gain) scan ranges specified by the user. Basically to make a long story short, it now works as requested!
Simply update Probe for EPMA from the Help menu and you should be good to go.
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Hi John,
Thanks, you learn something new everyday.
So it fits a function to the whole wavescan range is that right?
So Parabolic and Gaussian only work if wavescan range is restricted to the width of the peak, whereas Brent Maxima always works, as its using a parabolic interpolation to find the maxima -
Thanks
Ben
Hi Ben,
OK, we modified the code to utilize the x-axis "zoomed" range if the plot is "zoomed", and if not, just use the full wavescan range (as before), for the centroid fitting:
(https://probesoftware.com/smf/gallery/1_25_11_20_8_51_37.png)
This version is v. 12.9.0 and just update as usual from the Help menu in PFE to get it.
Thanks John,
This is great
I've included an example below - I zoomed in, applied gaussian fit, then zoomed out
(https://probesoftware.com/smf/gallery/453_03_12_20_7_53_56.png)
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I am not sure if I requested this before and there was a practical problem in implementing it or I never voiced it before.
I wish that I could keep a spectrometer stationary during wavescan acquisition. Essentially, that there is a check box in the peak/scan options dialog that would have the spectrometer move to the peak position and then just acquire the intensities in the time interval steps without moving the spectrometer itself. I then just use the line number as X-axis to visualize any change in the plot window.
Idea behind it would be that while I run a wavescan on 4 spectrometers I could monitor carbon contamination or Na loss on the 5th spectrometer. What do you think?
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There's a StripChart.exe app in the TestProbe.msi installer.
(https://probesoftware.com/smf/gallery/1_09_04_21_4_08_54.png)
Maybe that will work for you?
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Hi everyone,
could you suggest me how I can change font and text colour for notes on Probe images.
Thank you.
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Hi everyone,
could you suggest me how I can change font and text colour for notes on Probe images.
Thank you.
If you are asking about the text overlaid on the analog signal images displayed in Probe for EPMA, those cannot be modified at the current time. Of course one can export the images (both annotated and "raw" images are exported), and annotate the images in any image editing software.
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Hi John,
Yes, you are right, I meant the text overlaid the SE and BSE images with markers of the points, where compositions were analysed. The markers, currently used in the Probe for EPMA software are too small and hardly readable when exported to the side applications or software.
If would be great, it the possibility of changing the fonts and colours of these markers and texts will appear.
Thank you so much.
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Hi John,
Yes, you are right, I meant the text overlaid the SE and BSE images with markers of the points, where compositions were analysed. The markers, currently used in the Probe for EPMA software are too small and hardly readable when exported to the side applications or software.
If would be great, it the possibility of changing the fonts and colours of these markers and texts will appear.
Thank you so much.
I will take a look at it as soon as I get a chance.
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Hi John,
Yes, you are right, I meant the text overlaid the SE and BSE images with markers of the points, where compositions were analysed. The markers, currently used in the Probe for EPMA software are too small and hardly readable when exported to the side applications or software.
If would be great, it the possibility of changing the fonts and colours of these markers and texts will appear.
Thank you so much.
I will take a look at it as soon as I get a chance.
Hi John and Rom,
In preparation for M&M 2021 I have just released the newest version of Probelab ReImager which can handle MBD files.
From version 1.7.5 (released today, actually) you can load PFE MDB projects, just select the directory containing both the MDB and BIM files.
https://reimager.probelab.net (https://reimager.probelab.net)
As a side note, Probelab ReImager can open the PFE files on any OS it runs on, this includes Mac. I have had issues with Mac versions older than Catalina (10.15) not always opening MDBs though.
I hope this can help!
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Hi Mia,
I think we are both too responsive to these "feature wishes"! :)
I just finished adding a control for specifying font size for the point labels, but the fact that ReImager can now read images from Probe for EPMA files is wonderful! Does ReImager read the image scales and plot analysis points and labels for PFE MDB files also?
I'll be uploading this new version in a few hours after everything is re-compiled!
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Hi Mia,
I think we are both too responsive to these "feature wishes"! :)
I just finished adding a control for specifying font size for the point labels, but the fact that ReImager can now read images from Probe for EPMA files is wonderful! Does ReImager read the image scales and plot analysis points and labels for PFE MDB files also?
I'll be uploading this new version in a few hours after everything is re-compiled!
This is actually a feature Anette and I have been finishing over the last couple months, the timing is just right.
All the normal features of ReImager are now supporting PFE, so yes, it reads the scale, points, etc. It can also export any image (Thermo, JEOL) as an ACQ file for PictureSnap App integration.
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Hi John,
Yes, you are right, I meant the text overlaid the SE and BSE images with markers of the points, where compositions were analysed. The markers, currently used in the Probe for EPMA software are too small and hardly readable when exported to the side applications or software.
If would be great, it the possibility of changing the fonts and colours of these markers and texts will appear.
Thank you so much.
OK, the latest version of Probe for EPMA (v. 12.9.7) now contains a control for selecting the font size in the saved images dialog for point annotations:
(https://probesoftware.com/smf/gallery/1_21_07_21_9_25_31.png)
If you want to do more fancy annotations I suggest using Mia Kraft's ProbeLab ReImager software which now supports exporting of Probe for EPMA images for additional editing and annotations:
https://probesoftware.com/smf/index.php?board=38.0
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Hi John,
Could we add a "display standard image" (maybe not with this many words) button to the confirm standards countdown dialog? I know there is not much space, maybe as an icon?
We can currently display standard images through the digitize dialog but where this function would be really useful is to be able to access them when doing the confirms. Especially as I could annotate the images if certain grains or phases should be avoided.
I would prefer to not have it automatically launch the images as that I would think it would add time to the confirmation process and sometimes I or experienced users just want to spot check whereas new users might want to see the function for all.
Thanks!
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Hi Anette,
That is a good idea...
For those not familiar with this existing "digitize" feature, it is described here:
https://probesoftware.com/smf/index.php?topic=8.msg1107#msg1107
Interestingly when I started looking closer at the existing code for automatically displaying standard images when digitizing standards, I realized that it wasn't working quite right as intended.
Originally we tried to code this feature so that if one had multiple images (starting with the 4 digit standard number of the standard, e.g., 0012_MgO.bmp, 0358_diopside.bmp, etc., it should display *all* the images starting with that standard number. However, in fact it only displayed the first matching image that it found in the StandardPOSDirectory as defined in the Probewin.ini file.
The idea being that one might have the same standard in several different mounts, any or all of which could be loaded in the instrument at the same time. Also one might want to have several different images for each standard, e.g., a low mag image, a high mag image and maybe even some other documentation saved as a BMP image file.
Anyway, that multiple image feature is now fixed and so now when one clicks on the standard in the Digitize window, it loads and displays all the images starting with that standard number. Unless of course the Do Not Display Standard Images checkbox is checked in the Acquisition Options dialog.
Now to your "wish". We added a Load Standard Images button to the Confirm dialog as requested and it behaves the same way as from the Digitize window, *but* because the Digitize window is "modeless" and the Confirm window is "modal", the Digitize windows displays all the standard images at once, while the Confirm dialog displays multiple images (if they exist) one at a time and then each image has to be closed before one can proceed with the position confirmation.
Of course if one only has a single image image for each standard, then it's not a big deal. Here is what it looks like when confirming standard positions from the Confirm dialog:
(https://probesoftware.com/smf/gallery/1_13_08_21_2_47_04.png)
Hope this is what you wanted. Update from the Help | Update Probe for EPMA as usual.
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Hi John,
Yes, you are right, I meant the text overlaid the SE and BSE images with markers of the points, where compositions were analysed. The markers, currently used in the Probe for EPMA software are too small and hardly readable when exported to the side applications or software.
If would be great, it the possibility of changing the fonts and colours of these markers and texts will appear.
Thank you so much.
OK, the latest version of Probe for EPMA (v. 12.9.7) now contains a control for selecting the font size in the saved images dialog for point annotations:
(https://probesoftware.com/smf/gallery/1_21_07_21_9_25_31.png)
Hi John, it is a good function. Thank you.
How I can change Image name after I create and save it?
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Easy.
Just double-click the image you want to edit the name of. Just to remind everyone, if you "hover" your mouse over a control in Probe for EPMA, there usually pops up some further explanation about that control as shown here:
(https://probesoftware.com/smf/gallery/1_22_08_21_10_09_40.png)
Once you double-click you will see this dialog for editing the image name:
(https://probesoftware.com/smf/gallery/1_22_08_21_10_09_53.png)
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Hi John,
Is there a way to label/characterize our monitor samples? Many folks run standards as unknowns as monitors and it would be nice if we could somehow note 1) that they are monitors, and 2) have the software link it back to the reported compositions. It would be useful because right now, we highlight those monitors of interest (e.g. VG-2, or whatever), analyze, and look at the average and do a visual comparison. The feature I envision would load the reported value and then give the summary stats. I can also see it being useful because then we'd be able to sort by true unknowns and monitors, and then folks who want to look into longer term changes could do that more rapidly. Maybe there is such a feature. If it is present, then please point the way!
Thanks,
Dawn
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Is there a way to label/characterize our monitor samples? Many folks run standards as unknowns as monitors and it would be nice if we could somehow note 1) that they are monitors, and 2) have the software link it back to the reported compositions. It would be useful because right now, we highlight those monitors of interest (e.g. VG-2, or whatever), analyze, and look at the average and do a visual comparison. The feature I envision would load the reported value and then give the summary stats. I can also see it being useful because then we'd be able to sort by true unknowns and monitors, and then folks who want to look into longer term changes could do that more rapidly. Maybe there is such a feature. If it is present, then please point the way!
If you have a sample that you want to utilize as a "monitor" sample, I would simply enter it into the standard composition database and then treat it as a secondary standard. That is, don't assign it as a primary standard, but instead simply acquire it along with your other standards.
Then when you go to analyze it quantitatively, it will be treated as though it were an unknown.
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Hi Anette,
That is a good idea...
For those not familiar with this existing "digitize" feature, it is described here:
https://probesoftware.com/smf/index.php?topic=8.msg1107#msg1107
Interestingly when I started looking closer at the existing code for automatically displaying standard images when digitizing standards, I realized that it wasn't working quite right as intended.
Originally we tried to code this feature so that if one had multiple images (starting with the 4 digit standard number of the standard, e.g., 0012_MgO.bmp, 0358_diopside.bmp, etc., it should display *all* the images starting with that standard number. However, in fact it only displayed the first matching image that it found in the StandardPOSDirectory as defined in the Probewin.ini file.
The idea being that one might have the same standard in several different mounts, any or all of which could be loaded in the instrument at the same time. Also one might want to have several different images for each standard, e.g., a low mag image, a high mag image and maybe even some other documentation saved as a BMP image file.
Anyway, that multiple image feature is now fixed and so now when one clicks on the standard in the Digitize window, it loads and displays all the images starting with that standard number. Unless of course the Do Not Display Standard Images checkbox is checked in the Acquisition Options dialog.
Now to your "wish". We added a Load Standard Images button to the Confirm dialog as requested and it behaves the same way as from the Digitize window, *but* because the Digitize window is "modeless" and the Confirm window is "modal", the Digitize windows displays all the standard images at once, while the Confirm dialog displays multiple images (if they exist) one at a time and then each image has to be closed before one can proceed with the position confirmation.
Of course if one only has a single image image for each standard, then it's not a big deal. Here is what it looks like when confirming standard positions from the Confirm dialog:
(https://probesoftware.com/smf/gallery/1_13_08_21_2_47_04.png)
Hope this is what you wanted. Update from the Help | Update Probe for EPMA as usual.
In the latest version of Probe for EPMA we improved this feature to automatically unload any previously loaded standard images when the next standard is clicked on in the Digitize! window.
In this way, you will know that the last standard image you see loaded is for the last standard clicked on. That is, if no standard image is available for that standard, no image will be visible.
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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.
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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! ;D
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".
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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
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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.
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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!
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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".
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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?
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Sure, one can always add more buttons and pop-ups, but I was hoping for a more "elegant" solution! ;D
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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...
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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?
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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.
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Sure, one can always add more buttons and pop-ups, but I was hoping for a more "elegant" solution! ;D
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).
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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:
(https://probesoftware.com/smf/gallery/1_08_10_21_9_24_36.png)
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:
(https://probesoftware.com/smf/gallery/1_08_10_21_9_29_56.png)
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.
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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:
(https://probesoftware.com/smf/gallery/1_09_10_21_9_05_06.png)
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:
(https://probesoftware.com/smf/gallery/1_09_10_21_9_05_22.png)
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:
(https://probesoftware.com/smf/gallery/1_09_10_21_9_05_36.png)
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:
(https://probesoftware.com/smf/gallery/1_09_10_21_9_05_51.png)
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:
(https://probesoftware.com/smf/gallery/1_09_10_21_9_06_03.png)
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:
(https://probesoftware.com/smf/gallery/1_09_10_21_9_40_00.png)
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.
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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
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Hi colleagues,
Is it possible to work with digitized images of object (choose points for measure for instance) simultaneously with worked spectrometers: during peaking, wave scan or measure processes?
Thank you.
Roman
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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.
Are you asking about analog signal imaging in Probe for EPMA? What do you mean by 5%? You have an 8200 JEOL correct? The valid range of pixel dwell values is 1 to 1000 A/D averages. A value of 1 would be the fastest the imaging hardware can acquire. That will decrease the image quality for sure.
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Is it possible to work with digitized images of object (choose points for measure for instance) simultaneously with worked spectrometers: during peaking, wave scan or measure processes?
Do you mean this?
https://probesoftware.com/smf/index.php?topic=70.msg263#msg263
or perhaps this?
https://probesoftware.com/smf/index.php?topic=14.0
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Is it possible to work with digitized images of object (choose points for measure for instance) simultaneously with worked spectrometers: during peaking, wave scan or measure processes?
Do you mean this?
https://probesoftware.com/smf/index.php?topic=70.msg263#msg263
No, but I don't understand cases for which convenient to deflect the beam, not move the scene - if distance between points of measure very small. What range (in mm) of this possibility?
or perhaps this?
https://probesoftware.com/smf/index.php?topic=14.0
No
I mean I want to choose my points for subsequent measure on digitized pictures during the wave scan process (spectrometers in work, Automate window is busy).
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Is it possible to work with digitized images of object (choose points for measure for instance) simultaneously with worked spectrometers: during peaking, wave scan or measure processes?
Do you mean this?
https://probesoftware.com/smf/index.php?topic=70.msg263#msg263
No, but I don't understand cases for which convenient to deflect the beam, not move the scene - if distance between points of measure very small. What range (in mm) of this possibility?
or perhaps this?
https://probesoftware.com/smf/index.php?topic=14.0
No
I mean I want to choose my points for subsequent measure on digitized pictures during the wave scan process (spectrometers in work, Automate window is busy).
You can't add digitized points to Automate position samples at the same time you are running samples from the Automate! window. But you can if you are acquiring the wavescan sample from the Acquire! window.
You can also run the Stage program to digitize points while Probe for EPMA is running the wavescan. Just use the PictureSnap button from the Digitize! window to load an image in the PictureSnap window, and use the Misc menu and select the Use Right Mouse Click to Digitize Points menu. Assuming the PictureSnap image is already calibrated to your stage of course.
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Thank you!
"You can't add digitized points to Automate position samples at the same time you are running samples from the Automate! window. But you can if you are acquiring the wavescan sample from the Acquire! window."
I didn't do it earlier. I should push the button "Start Wavescan" in Acquire! window when stage is in the right position?
"You can also run the Stage program to digitize points while Probe for EPMA is running the wavescan. Just use the PictureSnap button from the Digitize! window to load an image in the PictureSnap window, and use the Misc menu and select the Use Right Mouse Click to Digitize Points menu. Assuming the PictureSnap image is already calibrated to your stage of course."
I guess the Stage program will ask me to choose *.mdb file which PFE program already uses. Isn't it?
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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).
Turns out, this feature (mostly) already exists! It's under Output > Output Standard and Unknown XY Plots.
It does pretty much what I was after, plotting "DateTime" vs the intensity (BG corrected or not) or the calculated wt%. You can multi-select both the standards/unknowns and the Y axis components.
Only thing I'd ask is whether its possible to have the DateTime formatted as a proper date and time vs the "excel time" value? e.g. 31/10/21 00:00 rather than 44500.
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Thank you!
"You can't add digitized points to Automate position samples at the same time you are running samples from the Automate! window. But you can if you are acquiring the wavescan sample from the Acquire! window."
I didn't do it earlier. I should push the button "Start Wavescan" in Acquire! window when stage is in the right position?
Yes.
"You can also run the Stage program to digitize points while Probe for EPMA is running the wavescan. Just use the PictureSnap button from the Digitize! window to load an image in the PictureSnap window, and use the Misc menu and select the Use Right Mouse Click to Digitize Points menu. Assuming the PictureSnap image is already calibrated to your stage of course."
I guess the Stage program will ask me to choose *.mdb file which PFE program already uses. Isn't it?
There is no probe database in Stage, just the position database (the same one that Probe for EPMA uses).
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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).
Turns out, this feature (mostly) already exists! It's under Output > Output Standard and Unknown XY Plots.
It does pretty much what I was after, plotting "DateTime" vs the intensity (BG corrected or not) or the calculated wt%. You can multi-select both the standards/unknowns and the Y axis components.
Only thing I'd ask is whether its possible to have the DateTime formatted as a proper date and time vs the "excel time" value? e.g. 31/10/21 00:00 rather than 44500.
It's possible, just complicated. Because everyone uses a different date time format convention...
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"You can also run the Stage program to digitize points while Probe for EPMA is running the wavescan. Just use the PictureSnap button from the Digitize! window to load an image in the PictureSnap window, and use the Misc menu and select the Use Right Mouse Click to Digitize Points menu. Assuming the PictureSnap image is already calibrated to your stage of course."
I guess the Stage program will ask me to choose *.mdb file which PFE program already uses. Isn't it?
There is no probe database in Stage, just the position database (the same one that Probe for EPMA uses).
This is a good solution, thank you. But it is necessary to start Stage program before start to run PFE measurements. It is important because in other way if PFE measurements already running, there are possible some glitches at the moment of Stage program starts.
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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.
"Are you asking about analog signal imaging in Probe for EPMA? What do you mean by 5%? You have an 8200 JEOL correct? The valid range of pixel dwell values is 1 to 1000 A/D averages. A value of 1 would be the fastest the imaging hardware can acquire. That will decrease the image quality for sure."
Yes, I asking about analog signal imaging in Probe for EPMA.
5% is 5 in valid range of pixel dwell values - you are right.
Yesterday I checked picture collecting time (image size 1024x1024, mag 300).
If I choose "1", collecting time is 1min 5 sec, as result - black square;
"2" - 1min 12 sec, as result - picture;
"5" - 1min 16 sec;
"7" - 1min 20 sec;
"10" - 1min 28 sec.
At the same time, if I collect the same picture (size close to) in JEOL software, collecting time is approximately 30 sec.
How I can decrease picture collecting time in PFE. Of course, I can take a picture by JEOL and open it in PFE, but it is a strange lame way.
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This is a JEOL 8200?
The A/D value of "1" should work. Ask your service engineer.
This is using the JEOL mapping call which has some overhead. The JEOL video imaging system is faster but we do not have access to it on the 8200. We can access the JEOL video system on the newer (8230/8530/iSP100/iHP200F) JEOL instruments. We can also access the Bruker and Thermo video scan systems if you have a modern EDS system.
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Yes, we use JEOL 8200 and we haven't a modern EDS System.
Thank you for explanation. I will glad if you find a tricky solution for this small task.
With regards.
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One "trick" would be to acquire 512 x 512 images. They will only take 1/4 the time or ~20 sec! :D
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Could we add "Acquisition options" to the Basic EPMA menu (under "Adjust counting times")? I hate to ask for this because I and others might have already created tutorials with screenshots but I am missing "Acquisition options" almost every time and Basic EPMA is otherwise so incredibly useful.
Thanks!
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Could we add "Acquisition options" to the Basic EPMA menu (under "Adjust counting times")? I hate to ask for this because I and others might have already created tutorials with screenshots but I am missing "Acquisition options" almost every time and Basic EPMA is otherwise so incredibly useful.
Thanks!
Your wish is granted! :D
For those not aware of this feature it is a simple checklist of the essential functions in Probe for EPMA for new and/or infrequent users to enable them to easily find the features they need. It is described in more detail here:
https://probesoftware.com/smf/index.php?topic=1267.0
(https://probesoftware.com/smf/gallery/1_08_11_21_11_18_36.png)
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Hi Dawn,
There are already two solutions to your requests:
1. When peak searching, can you add a button link that takes the user right to the display menu?
If you open "Basic EPMA" in the "File" menu, it gets you to what is essentially a link collection. On this is a link to both the Peaking dialog (for manual peaking), Automated Acquisition (for automated peaking on multiple materials) as well as the "Display Peaking ....". Just have that open and it gets you can essentially toggle between your different windows.
2. I usually calibrate with 5 points per standard. However, for Na and K, I calibrate with 7 points (or more). With the Standard Points to Acquire button, we have to designate the highest number. Could you add something that allows me to tell the software to just acquire the number of set points per standard?
My current solution for this is that 1) I have 7 points set on Na and K standards and 5 points on all the other ones, (2) set "7" in "Standard Points to Acquire" in the Automated window but 3) have "Use only digitized standard positions" set in Acquisition Options (under Miscellaneous options).
That way you get PFE to run your custom number of standard positions.
Added by Anette: Maybe I should not have administrator rights here. I accidentally modified the original request by Dawn instead of replying to it. Sorry about that. Not sure how to restore the original version.
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1. When peak searching, can you add a button link that takes the user right to the display menu?
Please explain in more detail, we do not understand.
2. I usually calibrate with 5 points per standard. However, for Na and K, I calibrate with 7 points (or more). With the Standard Points to Acquire button, we have to designate the highest number. Could you add something that allows me to tell the software to just acquire the number of set points per standard?
You can always acquire two different sets of standards and edit the number of points to acquire in between...
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Hi John,
Thanks for adding the "Acquisition options" to Basic EPMA. Much appreciated.
Best,
Anette
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1. When peak searching, can you add a button link that takes the user right to the display menu?
Please explain in more detail, we do not understand.
After peaking we have to go to the Run menu and then display the peak fit box. It would be nice if there was a link from the box that opens during the peak search routine.
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1. When peak searching, can you add a button link that takes the user right to the display menu?
Please explain in more detail, we do not understand.
After peaking we have to go to the Run menu and then display the peak fit box. It would be nice if there was a link from the box that opens during the peak search routine.
Ah.
We used to joke that in PFE one only needed one mouse click, not two... you're taking us seriously! :D
I'll try to squeeze it in...
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1. When peak searching, can you add a button link that takes the user right to the display menu?
Please explain in more detail, we do not understand.
After peaking we have to go to the Run menu and then display the peak fit box. It would be nice if there was a link from the box that opens during the peak search routine.
Ah.
We used to joke that in PFE one only needed one mouse click, not two... you're taking us seriously! :D
I'll try to squeeze it in...
Your wish is granted!
OK, that was a bit more of a pain than one would think because the scan window is a low level form that is also utilized by many smaller apps (e.g., Startwin, Stage, etc) and those other apps cannot access a PFE database.
But it's implemented now, so update from the help menu:
(https://probesoftware.com/smf/gallery/1_11_11_21_11_17_57.png)
The main caveat is that because the scan data dialog is a "modal" form, it will halt any ongoing peaking or PHA acquisition as long as it is open.
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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).
Turns out, this feature (mostly) already exists! It's under Output > Output Standard and Unknown XY Plots.
It does pretty much what I was after, plotting "DateTime" vs the intensity (BG corrected or not) or the calculated wt%. You can multi-select both the standards/unknowns and the Y axis components.
Only thing I'd ask is whether its possible to have the DateTime formatted as a proper date and time vs the "excel time" value? e.g. 31/10/21 00:00 rather than 44500.
It's possible, just complicated. Because everyone uses a different date time format convention...
I think it's also possible, once you open the input file in Excel, to "format" the column into the local time format.
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I wish that when I use the "report" function in "Analyze!" and PFE asks me for a file name for the report table that it also would use this name for the ...report.txt file.
Reason is that I often use different sample setups and want to have a "report" for each of them. While I can modify the table file name and add "...Report_garnet.dat" and "...Report_sulfide.dat", I have to remember to manually change the report.txt file name as it otherwise gets overwritten the next time.
Is that possible and doable?
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I wish that when I use the "report" function in "Analyze!" and PFE asks me for a file name for the report table that it also would use this name for the ...report.txt file.
Reason is that I often use different sample setups and want to have a "report" for each of them. While I can modify the table file name and add "...Report_garnet.dat" and "...Report_sulfide.dat", I have to remember to manually change the report.txt file name as it otherwise gets overwritten the next time.
Is that possible and doable?
That's actually a very good idea! Probeman was just telling me the other day that he often needs to edit the report file name when outputting reports for samples with different conditions within a single run.
Therefore your wish is granted!
Please update your Probe for EPMA from the Help menu and you should be good to go.
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That's actually a very good idea! Probeman was just telling me the other day that he often needs to edit the report file name when outputting reports for samples with different conditions within a single run.
Therefore your wish is granted!
Please update your Probe for EPMA from the Help menu and you should be good to go.
Probegrrrl and I talked and we both agree that you rock. Thanks!
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Hello,
I wish that the Report function in Analyze! was available or customized for Wavescans.
I have run a bunch of long wavescans at high current (to help explain some unusual spectral interferences).
It would be useful for the purposes of documentation to have the conditions, and length of time etc. available for output.
Or am I missing something (again)?
Thanks,
Adnrew
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You are correct that the Report button only applies to standard or unknown samples.
But what is it exactly that you are looking for that isn't already displayed when one simply lists the raw data for a wavescan sample? I would think that all the parameters that one would want are already displayed for a wavescan as seen here for example:
Wa 1 unknown sample
TakeOff = 40.0 KiloVolt = 15.0 Beam Current = 30.0 Beam Size = 2
(Magnification (analytical) = 4000), Beam Mode = Analog Spot
(Magnification (default) = 0, Magnification (imaging) = 100)
Image Shift (X,Y): .00, .00
Normal Wavescan: Step/Count Scan
Number of Data Lines: 50 Number of 'Good' Data Lines: 50
First/Last Date-Time: 10/01/2003 03:57:26 PM to 10/01/2003 04:03:28 PM
Stage position of first data point:
1G 16.0000 26.5000 11.2000
ELEM: Angstro si ka Angstro fe ka Angstro si ka Angstro si ka BEAM1
SPEC: 1 2 3 4
CRYST: TAP LiF TAP TAP
CRY2D: 25.7450 4.0267 25.7450 25.7450
CRYK : .002180 .000058 .002180 .002180
ORDER: 1 1 1 1
WVTIM: 6.00 6.00 6.00 6.00
ONPEAK 77.6740 134.724 77.6740 77.6740
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Hello,
I guess that I am asking that these parameters be exported to a file for later reference (so that I don't have to copy and paste them all individually).
When a wavescan is 500 or 1000 lines long, these parameters flash by pretty quickly ;)
Perhaps the Output | Save Wavescan Output options could be modified to export these parameters for each wavescan?
Cheers, Andrew
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OK, I see. You just don't want to have to cut and paste.
We can work on this. Give us a few days.
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Yes.
I have been spoiled by the utility of the Report function, and the considerable detail in the output of quantitative analyses.
Thanks!
Andrew
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I was trying to be a good lab manager and set my PHAs. I *thought* I could save them to a .mdb file. Turns out, no, I cannot save them. Now I have to re-run them :P
Anyway, is there a feature that allows us to save those non-analytical datasets? Maybe there is and I just don't know where to find it?
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I was trying to be a good lab manager and set my PHAs. I *thought* I could save them to a .mdb file. Turns out, no, I cannot save them. Now I have to re-run them :P
Anyway, is there a feature that allows us to save those non-analytical datasets? Maybe there is and I just don't know where to find it?
Ummm, yes you can. You just have to have a sample in the run with some elements in it (one for each spectrometer if you want to save PHA settings for all spectrometers).
You can also save individual element setups to the element setup database.
Maybe describe in more detail what you are trying to do?
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Hello,
I guess that I am asking that these parameters be exported to a file for later reference (so that I don't have to copy and paste them all individually).
When a wavescan is 500 or 1000 lines long, these parameters flash by pretty quickly ;)
Perhaps the Output | Save Wavescan Output options could be modified to export these parameters for each wavescan?
Cheers, Andrew
Hi Andrew,
OK, it took a bit longer than we thought but we think we have something that will work for you. We couldn't modify the std/unk report output because it was too specific to quantification, but instead we added a right click menu item to the Analyze! window as shown here:
(https://probesoftware.com/smf/gallery/1_15_01_22_12_02_52.png)
The basic output goes to the log window as usual and also to a .TXT file, and the table goes to a .DAT file and optionally an Excel spreadsheet as seen here:
(https://probesoftware.com/smf/gallery/1_15_01_22_12_03_07.png)
One other thing we did was to modify the report filename to include the sample name so now for the wavescan report (and also the std/unk reports) the file name is specified as:
<probe run>_<sample name>_Report.<ext>
Though it can still be edited by the user. This is nice when one selects multiple samples to output reports on and so now the filenames all are unique.
This wavescan report format is yours for now, so let us know if there's anything else you'd like to see added. We don't know what your intended purpose is with these report outputs.
Update as usual from the Help menu to update Probe for EPMA v. 13.0.7.
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(https://probesoftware.com/smf/gallery/1_15_01_22_12_03_07.png)
I feel the need to point out that it is not possible to analyze for Pb and As in the same mineral using Pb Lα and As Kα, as both X-ray lines have essentially the same wavelength. If there is a chance that detectable As and Pb could both be present, then one must use As Lα and Pb Mα. Unfortunately, when Pb is present in low concentration in sulfides, S Kα, S Kβ, and satellites of each interfere severely with measurement of Pb Mα as well as X-ray lines of a variety of other (minor) elements of potential interest:
(https://probesoftware.com/smf/gallery/381_17_01_22_1_46_35.png)
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I feel the need to point out that it is not possible to analyze for Pb and As in the same mineral using Pb Lα and As Kα, as both X-ray lines have essentially the same wavelength.
You might be right, I have not looked at this situation recently. It may depend on the relative ratios of the intensities.
I do recall trying this interference pair in the past, though I have not looked into it in many years (decades!). It took about 50 iterations if I remember correctly on data from my ARL SEMQ with a 127 mm Rowland circle. I should give this a try again on my SX100 (160 mm) when I get a chance again and see if it works better on a higher resolution instrument. Maybe you should try the Probe for EPMA spectral interference correction on your JEOL 140 mm spectrometers. Should be better spectral resolution than the ARL SEMQ spectrometers...
OK, I dug through my ancient files and found this:
(https://probesoftware.com/smf/gallery/1_17_01_22_2_41_47.png)
Not an ideal results, but considering everything...
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I feel the need to point out that it is not possible to analyze for Pb and As in the same mineral using Pb Lα and As Kα, as both X-ray lines have essentially the same wavelength.
You might be right, I have not looked at this situation recently. It may depend on the relative ratios of the intensities.
I do recall trying this interference pair in the past, though I have not looked into it in many years (decades!). It took about 50 iterations if I remember correctly on data from my ARL SEMQ with a 127 mm Rowland circle. I should give this a try again on my SX100 (160 mm) when I get a chance again and see if it works on a lower resolution instrument. Maybe you should try the Probe for EPMA spectral interference correction also since your JEOL spectrometers are 140 mm Rowland. Anyone have a 100mm JEOL spectrometer?
OK, I dug through my ancient files and found this:
(https://probesoftware.com/smf/gallery/1_17_01_22_2_41_47.png)
Not an ideal results, but considering everything...
Considering everything, it makes more sense to use As Lα and Pb Mα (especially in this case, with no interferences at Pb Mα). There is no way to distinguish between As Kα and Pb Lα even with R = 160 mm; the respective sine(θ) values are 0.29203 and 0.29181.
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Considering everything, it makes more sense to use As Lα and Pb Mα (especially in this case, with no interferences at Pb Mα).
Again, you may be right for normal work. But hey, I like a good algorithm challenge! ;D
There is no way to distinguish between As Kα and Pb Lα even with R = 160 mm; the respective sine(θ) values are 0.29203 and 0.29181.
You say there is "no way", yet even a low spectral resolution 127mm instrument was able to iterate fairly well. I'm going to collect some data on this and see. Maybe we'll learn something...
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Hi, could you explain some thing I want to do in "Analog Signal Image Data" window:
(https://probesoftware.com/smf/gallery/1_22_08_21_10_09_40.png)
1. How I can range Analog signal images in this window by image names, not for image numbers which have been given according image collecting time.
Sometimes it is important.
2. How I can plot sample position labels with using current point number in my Unknown, not in all session. For instance, I would like to see a label like this: #un - #pos where #un - number of Unknown , #pos - number of position in this Unknown.
It is possible in PictureSnap window and I hope in this window as well.
3. How I can change plot scale bar. For instance, I would like to see 50 mkm scale bar on all my images independent of picture resolution.
Thank you
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Hi, could you explain some thing I want to do in "Analog Signal Image Data" window:
(https://probesoftware.com/smf/gallery/1_22_08_21_10_09_40.png)
1. How I can range Analog signal images in this window by image names, not for image numbers which have been given according image collecting time. Sometimes it is important.
When you say "range" I assume you mean "sort"? The images are only displayed in the acquisition order. Of course one can export them from the Output menu and then they can be sorted anyway you prefer.
2. How I can plot sample position labels with using current point number in my Unknown, not in all session. For instance, I would like to see a label like this: #un - #pos where #un - number of Unknown , #pos - number of position in this Unknown.
It is possible in PictureSnap window and I hope in this window as well.
Simple uncheck the "Plot Short Labels" checkbox.
3. How I can change plot scale bar. For instance, I would like to see 50 mkm scale bar on all my images independent of picture resolution.
This is not possible. But once the images are exported, you can add any scale bars you prefer.
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1. yes, the range means sorting - ok
2. in this case, I will have the label format #Unknown - #point in the entire session (not #point in this Unknown)
3. What is the best application for receiving exported images? For example, Probelab Reimager is not a stable application and has some drawbacks.
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2. in this case, I will have the label format #Unknown - #point in the entire session (not #point in this Unknown)
Yes, PictureSnap will display the unknown number and the line number in the run. But you will need to use the Run | Display... menu options to display the unk and line numbers if you want to plot already acquired points.
3. What is the best application for receiving exported images? For example, Probelab Reimager is not a stable application and has some drawbacks.
You should report ReImager problems to Mia Kraft.
What imaging app to use if hard to say. It depends on what you want to do. I like Paint.net but there are so many imaging programs to choose from. There is also NIH Image which I hear can handle image calibrations but I have not used it myself.
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Yes, PictureSnap will display the unknown number and the line number in the run. But you will need to use the Run | Display... menu options to display the unk and line numbers if you want to plot already acquired points.
-I know it, thank you but I want to have the same result in "Analog signal images" window because I see here different sizes of "beam" - it is great!
You should report ReImager problems to Mia Kraft.
-We reported several times in a half of year. But the answer is silence ((.
What imaging app to use if hard to say. It depends on what you want to do. I like Paint.net but there are so many imaging programs to choose from. There is also NIH Image which I hear can handle image calibrations but I have not used it myself.
-Thank you.
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Yes, PictureSnap will display the unknown number and the line number in the run. But you will need to use the Run | Display... menu options to display the unk and line numbers if you want to plot already acquired points.
-I know it, thank you but I want to have the same result in "Analog signal images" window because I see here different sizes of "beam" - it is great!
Yes, the Display Analog Signal Images dialog behaves the same as PictureSnap. Just uncheck the Plot Short Labels checkbox.
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I am sorry but unfortunately I see different picture. Could you look at addition file (PictureSnap image vs image in Analog Signal Image Data window)
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I am sorry but unfortunately I see different picture. Could you look at addition file (PictureSnap image vs image in Analog Signal Image Data window)
1. If you load PictureSnap from the Automate window it displays the digitized points from the Automate window (whether they have been acquired or not). These will have the digitized sample number and digitized point number displayed (starting with 1 for each digitized sample).
2. If you load PictureSnap from the Run menu, then it will display points already acquired in the run. These labels are using the acquired sample number and the (consecutive) line number from the run.
3. The Display Analog Signal Image dialog only displays points already acquired in the run. These labels are using the acquired sample number and the (consecutive) line number from the run.
#2 and #3 will display acquired point labels the same way.
If you are asking to have the beam size displayed for acquired points in the PictureSnap window, that is not available because the point labels in PictureSnap needs to be consistent for both digitized points and acquired points, but digitized points do not yet have a beam size defined.
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It would be really helpful to have PfE automatically find the PHA distribution scan and bias voltage scan peak centres similar to how PfE automatically centres the peak for spectrometer scans :D
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Probe for EPMA supports the Adjust PHA feature (see PHA window) for Cameca instruments, but JEOL does not support this method.
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Probe for EPMA supports the Adjust PHA feature (see PHA window) for Cameca instruments, but JEOL does not support this method.
That may be true of older JEOL instruments but the newer (windows software based) instruments automatically choose and set the PHA peak centres when performing bias voltage scans using the JEOL PC-EPMA software.
Even if PfE cannot set the peaks for PHA scans it would still be nice if it could mathematically calculate the peak for testing and purposes (e.g. checking the change in PHA as a function of barometric pressure)
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I did not know that. I have no information regarding this and it does not appear to be supported in the new JEOL MEC interface. Note the Adjust PHA button in the PFE PHA dialog which is disabled for JEOL instruments.
Also for working externally with PHA data you can easily export the data from PFE and do whatever you want.
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I did not know that. I have no information regarding this and it does not appear to be supported in the new JEOL MEC interface.
I can take a video of a PHA scan using the JEOL software if you would like to see it in action
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I did not know that. I have no information regarding this and it does not appear to be supported in the new JEOL MEC interface.
I can take a video of a PHA scan using the JEOL software if you would like to see it in action
No need. If JEOL Japan can provide an API call, I will implement it.
In the meantime just use the JEOL button and then read the PHA settings from PFE using the Get PHA button...
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I am sorry but unfortunately I see different picture. Could you look at addition file (PictureSnap image vs image in Analog Signal Image Data window)
1. If you load PictureSnap from the Automate window it displays the digitized points from the Automate window (whether they have been acquired or not). These will have the digitized sample number and digitized point number displayed (starting with 1 for each digitized sample).
2. If you load PictureSnap from the Run menu, then it will display points already acquired in the run. These labels are using the acquired sample number and the (consecutive) line number from the run.
3. The Display Analog Signal Image dialog only displays points already acquired in the run. These labels are using the acquired sample number and the (consecutive) line number from the run.
#2 and #3 will display acquired point labels the same way.
If you are asking to have the beam size displayed for acquired points in the PictureSnap window, that is not available because the point labels in PictureSnap needs to be consistent for both digitized points and acquired points, but digitized points do not yet have a beam size defined.
Now it is clear, thank you.
Is it hard for you to add to the Display Analog Signal Image dialog the possibility of using point labels in format #Unknown session- #Point in this Unknown? During the session we can use many different conditions. Therefore if we would use continuous numeration of the points it will make identification of the targeted points difficult. For instance, we can measure phases with different probe diameter at the same image, and the numeration will be (1-1. 1-2. 1-3 etc. (for 0PD), then 2-1, 2-2, 2-3, etc. (for 20PD)).
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Hi John,
Do you think it would be possible to have the option to assign fiducial sets to images? Especially I am thinking of having the option to transform image locations (so the information in the ACQ files) using either sample fiducials or constant stage shifts.
The JEOL probes (at least mine) like to have their electronics restarted usually in the most inopportune moments. I loose all the stage positions by powering the stage motors down and on again (no linear encoders). I can use your awesome (!) stage positions import/export option to get everything back in place but have no such ability for the images. Often I just reacquire them.
Related to it, it would generally be quite awesome to be able to import existing images into a new mdb. I think the "load image" option in the digitize image window does not look for existing ACQ files but only wants to import based on the current magnification/stage position. Could it be modified to look for acq files and if present have a popup asking if you want to import based on the acq file or based on current instrument conditions?
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Hi John,
Do you think it would be possible to have the option to assign fiducial sets to images? Especially I am thinking of having the option to transform image locations (so the information in the ACQ files) using either sample fiducials or constant stage shifts.
The JEOL probes (at least mine) like to have their electronics restarted usually in the most inopportune moments. I loose all the stage positions by powering the stage motors down and on again (no linear encoders). I can use your awesome (!) stage positions import/export option to get everything back in place but have no such ability for the images. Often I just reacquire them.
Related to it, it would generally be quite awesome to be able to import existing images into a new mdb. I think the "load image" option in the digitize image window does not look for existing ACQ files but only wants to import based on the current magnification/stage position. Could it be modified to look for acq files and if present have a popup asking if you want to import based on the acq file or based on current instrument conditions?
The regular images in Probe for EPMA only utilize a 2 point calibrations, recently written up in a tutorial by Karsten here:
https://probesoftware.com/smf/index.php?topic=592.msg11195#msg11195
But the calibrated images in the PictureSnap window can utilize 2 or 3 calibration (or fiducial) points and can therefore also handle sample rotation:
https://probesoftware.com/smf/index.php?topic=14.msg7283#msg7283
And of course there's always the PictureSnapApp software in which one can embed any number of calibrated images in a (two or three) fiducial referenced image as shown here:
https://probesoftware.com/smf/index.php?topic=1082.msg7245#msg7245
Does any of that help?
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Hi John,
I am aware of all these options and they are great. However, the problem I am trying to solve is when I am sitting on 10+ images that I have to re-reference one-by-one after I had to cycle the power on the instrument. They would all have to have a consistent shift to be applied so I was looking for a batch transformation option similar to what I can do with unknown positions in this case.
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Hi John,
I am aware of all these options and they are great. However, the problem I am trying to solve is when I am sitting on 10+ images that I have to re-reference one-by-one after I had to cycle the power on the instrument. They would all have to have a consistent shift to be applied so I was looking for a batch transformation option similar to what I can do with unknown positions in this case.
Ah, OK, I think I see now. You want to be able to apply an XY shift correction to the already acquired images.
Let me think about that. What exactly are you doing to "re-reference" them now?
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If I am lucky, I know exactly the position of one of the digitized spots and then just calculate the shift between where it should be and where it is now. I then export the digitized positions to a POS file and then re-import then. PFE allows me to define a X-Y increment factor (THANK YOU!) and that usually shifts them all back. Then I just use the confirm dialog to fix the Z-values. Relatively painless all things considered.
Having something similar where I can re-import images and increment the stage reference point1 and point2 could be really powerful.
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If I am lucky, I know exactly the position of one of the digitized spots and then just calculate the shift between where it should be and where it is now. I then export the digitized positions to a POS file and then re-import then. PFE allows me to define a X-Y increment factor (THANK YOU!) and that usually shifts them all back. Then I just use the confirm dialog to fix the Z-values. Relatively painless all things considered.
Having something similar where I can re-import images and increment the stage reference point1 and point2 could be really powerful.
But shouldn't both image reference points utilize the same XY shift? I can imagine some sort of select a pixel on the image and enter the new XY-coordinates of that point? Then it's simple to update the image coordinates.
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Hi John,
Not a feature for PfE itself, but for the forum. Is it possible to have an error database and possible things to check? For example, a user got an error for a zero current and potentially blown filament. We have a FEG-EPMA, so clearly it isn't the filament. I think there was a power issue, but if there was a place to check how others fixed the error, that would be super helpful.
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Hi John,
Not a feature for PfE itself, but for the forum. Is it possible to have an error database and possible things to check? For example, a user got an error for a zero current and potentially blown filament. We have a FEG-EPMA, so clearly it isn't the filament. I think there was a power issue, but if there was a place to check how others fixed the error, that would be super helpful.
Yes it would be helpful, but would take an enormous amount of effort to try and document all the error trapping in PFE. I suggest you type some keywords in the Search window in the forum and see if something pops up. Or write a few of our consultants. They're always happy to help as am I. :)
There's also this topic:
https://probesoftware.com/smf/index.php?topic=1288.0
As for the zero faraday cup current that could be caused by a "sticky" faraday cup, which I think someone mentioned happened to them. There's also this topic:
https://probesoftware.com/smf/index.php?topic=1260.msg8823#msg8823
to set the delay time for waiting after inserting the faraday cup.
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Greetings,
Wondering if there’s a flag or option somewhere to have PFE always default to acquiring TDI data when creating a new PFE file and/or new sample setup?
I've been burned a couple of times when making a "from scratch" setup, and forgetting to toggle on TDI acquisition in the Special Options dialogue, then running a bunch of analyses without TDI data being collected.
Seems to me, the “conservative” approach would be to have a new PFE MDB or sample setup default to collect the TDI data, as you can always turn it off if not needed, but you can’t “turn it on” if you never collected the TDI in the first place.
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On a tangentially related note:
Would it be possible, when using the Mean Atomic Number Approach, to default that both(!) the unknowns and the standards are set to MAN automatically?
At present in my version of PFE, I have to toggle MAN on for each standard individually....
Thanks,
Andrew
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On a tangentially related note:
Would it be possible, when using the Mean Atomic Number Approach, to default that both(!) the unknowns and the standards are set to MAN automatically?
At present in my version of PFE, I have to toggle MAN on for each standard individually....
Thanks,
Andrew
Hi Andrew,
You can click one button to do this from the Acquisition Options dialog as described here:
(https://probesoftware.com/smf/gallery/1_06_01_23_11_43_47.png)
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Fantastic, thanks!
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Fantastic, thanks!
This Change All To MAN button was actually a feature request by Ben Buse at Bristol a while back. We decided to add Change All To Off-Peak and Change All To MPB buttons at the same time.
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Here is a PHA plot of the Sr La peak (in SrTiO3) showing the new plot title which displays the current bias and gain settings utilized in the scan.
(https://probesoftware.com/smf/gallery/1_07_01_23_10_18_22.png)
Probeman kept complaining to us that we should do this, so the latest version of Probe for EPMA now includes this information in the plot (not just in the "Conditions" text box). :D
Similar also for bias and gain scans, see here:
https://probesoftware.com/smf/index.php?topic=1475.msg11527#msg11527
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Greetings,
Wondering if there’s a flag or option somewhere to have PFE always default to acquiring TDI data when creating a new PFE file and/or new sample setup?
I've been burned a couple of times when making a "from scratch" setup, and forgetting to toggle on TDI acquisition in the Special Options dialogue, then running a bunch of analyses without TDI data being collected.
Seems to me, the “conservative” approach would be to have a new PFE MDB or sample setup default to collect the TDI data, as you can always turn it off if not needed, but you can’t “turn it on” if you never collected the TDI in the first place.
The latest version of Probe for EPMA now adds three new keywords to the probewin.ini file [software] section as shown here:
VolatileSelfCalibrationAcquisitionFlag=0
AcquireVolatileSelfStandardIntensitiesFlag=0
VolatileCountIntervals=5
These should be self explanatory, but the latest User Reference Manual explains them in more detail.
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Hi John,
Would it be possible to add a batch export option for the OEM EDS spectra? It is an option in the "Display and Export EDS Spectra Dialog" but I can only export them one-by-one there.
Thanks!
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Would it be possible to add a batch export option for the OEM EDS spectra? It is an option in the "Display and Export EDS Spectra Dialog" but I can only export them one-by-one there.
Everything is possible but some things are easier than others! :)
This shouldn't be too difficult to do. Give us a few days.
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Would it be possible to add a batch export option for the OEM EDS spectra? It is an option in the "Display and Export EDS Spectra Dialog" but I can only export them one-by-one there.
Everything is possible but some things are easier than others! :)
This shouldn't be too difficult to do. Give us a few days.
Well that was easier than I thought!
I only had to invent a time machine, go back to 2015 and add a Save All EDS Spectra To EMSA menu to the Output menu as shown here:
(https://probesoftware.com/smf/gallery/1_29_01_23_11_16_19.png)
:D
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;D I know and it is great to have that option but when I import the PFE-generated EMSA file into ESPRIT I get an error message ("Problems found in spectrum import. No FWHM calibration"). I will send you example files from both Bruker Esprit and the PFE files and more details by email. There are subtle differences and Bruker probably changed something?
The OEM spectrum file generated by PFE in the "Display and Export EDS spectra" works like a charm but does not support batch export.
I seem to remember that the EMSA import works for Thermo. So I am not sure what it easier to implement. Messing with the EMSA output or adding the OEM version batch output. Let me know what you think.
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;D I know and it is great to have that option but when I import the PFE-generated EMSA file into ESPRIT I get an error message ("Problems found in spectrum import. No FWHM calibration"). I will send you example files from both Bruker Esprit and the PFE files and more details by email. There are subtle differences and Bruker probably changed something?
The OEM spectrum file generated by PFE in the "Display and Export EDS spectra" works like a charm but does not support batch export.
I seem to remember that the EMSA import works for Thermo. So I am not sure what it easier to implement. Messing with the EMSA output or adding the OEM version batch output. Let me know what you think.
Sorry I didn't note that you said OEM format. I can do that and it won't require a time machine! :)
But please do send me a Bruker EMSA file so I can look at what they want for EMSA. I think they are the only ones that require FWHM meta data because they fit the spectra for deconvolution.
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;D I know and it is great to have that option but when I import the PFE-generated EMSA file into ESPRIT I get an error message ("Problems found in spectrum import. No FWHM calibration"). I will send you example files from both Bruker Esprit and the PFE files and more details by email. There are subtle differences and Bruker probably changed something?
The OEM spectrum file generated by PFE in the "Display and Export EDS spectra" works like a charm but does not support batch export.
I seem to remember that the EMSA import works for Thermo. So I am not sure what it easier to implement. Messing with the EMSA output or adding the OEM version batch output. Let me know what you think.
Your wish is granted! :)
We added an export all EDS spectra to OEM format button to the Run | Display and Export EDS Spectra menu dialog as seen here:
(https://probesoftware.com/smf/gallery/1_02_02_23_9_56_54.png)
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Is it possible to include the beam 2 values in the Analyze window? Right now, you can only see them in the working window. See attached files for reference.
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Is it possible to include the beam 2 values in the Analyze window? Right now, you can only see them in the working window. See attached files for reference.
Almost everything is possible. But some things are more work than others!.
Let us take a look at this.
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Is it possible to include the beam 2 values in the Analyze window? Right now, you can only see them in the working window. See attached files for reference.
Your wish is granted:
(https://probesoftware.com/smf/gallery/1_25_02_23_1_37_25.png)
(https://probesoftware.com/smf/gallery/1_25_02_23_1_37_38.png)
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Is it possible to change the frequency of beam current measurements during an analysis run? I poked around, and all I found was “on/off” in the Acquisition Options dialogue, and didn’t see anything relevant in the Probewin.ini file.
I currently have an incredibly stable gun, with typical drift of 0.05% per hour, and as you know, due to the Faraday delays on JEOL probes, the current measurement protocol actually eats up 5-10 seconds per analysis. Would be super cool if I could set it to read the current every X number of analyses, or every X number of minutes.
I can see how that might be tricky to code into the current normalization calculations in Analyze!, but thought I’d mention it and see what you thought.
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Is it possible to change the frequency of beam current measurements during an analysis run? I poked around, and all I found was “on/off” in the Acquisition Options dialogue, and didn’t see anything relevant in the Probewin.ini file.
I currently have an incredibly stable gun, with typical drift of 0.05% per hour, and as you know, due to the Faraday delays on JEOL probes, the current measurement protocol actually eats up 5-10 seconds per analysis. Would be super cool if I could set it to read the current every X number of analyses, or every X number of minutes.
Your wish is granted! :)
We modified the code to add a new checkbox in the Acquisition Options (v. 13.2.9) that now allows the user to only acquire the beam (and absorbed) current once per sample as shown here:
(https://probesoftware.com/smf/gallery/1_03_04_23_8_54_10.png)
When this option is selected then the program only acquires a single beam (and absorbed) beam current measurement per standard or unknown sample and just re-load that first measurement for subsequent data points in that sample, as seen here:
Off-Peak Corrected or MAN On-Peak X-ray Counts (cps/1nA) (and Faraday/Absorbed Currents):
ELEM: c ka si ka BEAM1 BEAM2 ABSD1 ABSD2
194G -.04 96.52 140.059 140.059 110.412 110.412
195G -.03 96.85 140.059 140.059 110.412 110.412
196G -.05 96.85 140.059 140.059 110.412 110.412
AVER: -.04 96.74 140.059 140.059 110.412 110.412
SDEV: .01 .19 .000 .000 .000 .000
1SIG: .00 .26
SERR: .00 .11
%RSD: -16.08 .20
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I like the Sort Stat and Data Grids by Geologic/Atomic Number in the Analyze window (see attached screenshot). Is there a way to turn that on all the time?
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I like the Sort Stat and Data Grids by Geologic/Atomic Number in the Analyze window (see attached screenshot). Is there a way to turn that on all the time?
The only way you can have it "on all the time" is to simply enter (or change the order of) the elements in a sample. For example either when entering the analyzed elements manually from the Elements/Cations dialog or using the up/down arrows in the Combined Conditions dialog from the Acquire! window.
However, you can specify the default sort order by editing the Probewin.ini file as seen here:
[software]
GeologicalSortOrder=1 ; 0 = no sorting, 1 = traditional, 2 = low to high Z, 3 = high to low Z
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Hi John,
I know there's been a lot of work in all the new deadtime corrections, and they look great, but would it be possible to decrease the available deadtimes to below 0.1us? I've tried changing the deadtime in both PfE and directly via the scalars.dat file, but I come up against an error both ways so I'm guessing there's a sanity check in the software.
0.0001us or something would be great :)
Thanks
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Hi John,
I know there's been a lot of work in all the new deadtime corrections, and they look great, but would it be possible to decrease the available deadtimes to below 0.1us? I've tried changing the deadtime in both PfE and directly via the scalars.dat file, but I come up against an error both ways so I'm guessing there's a sanity check in the software.
0.0001us or something would be great :)
Thanks
"Sanity check" is a good way to describe the 0.1 us minimum dead time allowed in the SCALERS.DAT file... :)
Seriously, why would you need this? No WDS hardware I know of can go that low! If you only want to turn off the dead time correction, just turn it off in the Analytical | Analysis Options dialog!
But actually there is a way... just use the Analytical | Update Dead Time Constants menu dialog to edit the values to any value between zero and 20 us. It only updates values for the samples you select in the current run, but it's good enough for "what if" types of questions. You will get a warning to the log window if the value is zero though.
I'm just curious why you'd want to do this.... if you just want to try some modeling just use the TestEDS application and use the Output | Output Dead Time Calculations menu as described here:
https://probesoftware.com/smf/index.php?topic=1466.msg11025#msg11025
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But actually there is a way... just use the Analytical | Update Dead Time Constants menu dialog to edit the values to any value between zero and 20 us. It only updates values for the samples you select in the current run, but it's good enough for "what if" types of questions. You will get a warning to the log window if the value is zero though.
Works like a charm, thanks!
Seriously, why would you need this? No WDS hardware I know of can go that low!
The SXES can!
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Seriously, why would you need this? No WDS hardware I know of can go that low!
The SXES can!
Really!? I didn't know that. Too bad JEOL can't utilize the same pulse processing electronics for our WDS spectrometers!
I'm assuming that PFE is not reading a SXES spectrometer, correct? But if you are somehow able to read the SXES spectrometer in PFE I will edit the "sanity check" for reading the values in the SCALERS.DAT file. How low can the dead time values get on the SXES?
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Really!? I didn't know that. Too bad JEOL can't utilize the same pulse processing electronics for our WDS spectrometers!
I'm assuming that PFE is not reading a SXES spectrometer, correct? But if you are somehow able to read the SXES spectrometer in PFE I will edit the "sanity check" for reading the values in the SCALERS.DAT file. How low can the dead time values get on the SXES?
The SXES is using a CCD rather than proportional counters, so they can work incredibly quickly. The "deadtime" they experience is probably more akin to that of EDS, with the deadtime being proportional to the frequency of the channel reads/resets. I haven't actually run in to a deadtime issue yet, and I know Nick Wilson from CSIRO gave a talk back in M&M 21 that showed a straight line when plotting peak count rate vs beam current up in to the hundreds of nanoamps (as opposed to the curves that we see with GFPCs), and I've seen similar with mine plot cps/na vs cps.
One big advantage of the SXES over GFPCs is the ability to simultaneously acquire backgrounds and integrate peaks for the light elements (I'm currently doing boron and nitrogen), but this leads to large count rate values (100ks of counts) and hence I'm running in to issues with the deadtime correction, not just in PfE but CalcImage too. It'd be great if you could alter that sanity check for the SCALERS.DAT file for both PfE and CalcImage!
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The SXES is using a CCD rather than proportional counters, so they can work incredibly quickly. The "deadtime" they experience is probably more akin to that of EDS, with the deadtime being proportional to the frequency of the channel reads/resets. I haven't actually run in to a deadtime issue yet, and I know Nick Wilson from CSIRO gave a talk back in M&M 21 that showed a straight line when plotting peak count rate vs beam current up in to the hundreds of nanoamps (as opposed to the curves that we see with GFPCs), and I've seen similar with mine plot cps/na vs cps.
Nice to hear that the SXES spectrometer can handle such high count rates and still have a linear response. However, the non-linear response of our GFPC electronics (for count rates over 50 kcps) can be dealt with using the new logarithmic dead time expression that we just published a couple of weeks ago in M&M:
https://probesoftware.com/smf/index.php?topic=1466.msg11858#msg11858
This non-linear expression (and the constant k-ratio procedure outlined in the paper) using Probe for EPMA, is outlined in a pdf available from the Help menu in PFE.
One big advantage of the SXES over GFPCs is the ability to simultaneously acquire backgrounds and integrate peaks for the light elements (I'm currently doing boron and nitrogen), but this leads to large count rate values (100ks of counts) and hence I'm running in to issues with the deadtime correction, not just in PfE but CalcImage too. It'd be great if you could alter that sanity check for the SCALERS.DAT file for both PfE and CalcImage!
I'm still not following: why do you need to read in dead time values less than 0.1 us from the SCALERS.DAT file (the sanity check code is the same for both PFE and CalcImage)? Are you able to read data from the SXES into PFE somehow?
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Yeah, I've got the SXES data going in to PfE and CalcImage.
It'd be great if I could put a dead time value as low as 0.0001us or something ridiculously small in to scalers.dat. My worry is that the very large CPS/nA values I get from integrating the SXES peaks is getting inappropriately dead time corrected.
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Yeah, I've got the SXES data going into PfE and CalcImage.
It'd be great if I could put a dead time value as low as 0.0001us or something ridiculously small in the scalers.dat. My worry is that the very large CPS/nA values I get from integrating the SXES peaks is getting inappropriately dead time corrected.
Very, very interesting. Let me see what we can do. So is the SXES spectrometer sp5 or something in the SCALERS.DAT file?
In the meantime you can certainly just use the Analytical | Update Dead Time Constants menu dialog to select samples and update the dead time values.
Of course dividing the SXES intensities (standard and maps) by a factor of 10x or 100x works too since there's no dead time to speak of.
You should post some results to the CalcImage board. I'd be very interested to see this data.
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SP3 at the minute, I hadn't thought of trying to add SP5 to our instrument. I might have a think about that!
Our SXES-LR on the 8530F takes up the SP5 position, hence our instrument only having 4 "traditional" WDS.
For the Analytical | Update Dead Time Constants - is there an equivalent way of doing this for CalcImage?
At the minute I'm doing exactly as you suggest - dividing the measured intensities across the board by an order of magnitude or two, which wouldn't make a difference in the grand scheme of things, but it would be nice if I didn't have to!
I'll see what I can do about creating some demo data for quant mapping with the combined WDS and SXES: the work I've been doing has all been on client data. I work quite a lot with light elements, and the SXES is a game changer for this.
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SP3 at the minute, I hadn't thought of trying to add SP5 to our instrument. I might have a think about that!
Our SXES-LR on the 8530F takes up the SP5 position, hence our instrument only having 4 "traditional" WDS.
I was just thinking then you could just have a fifth spectrometer used only for this SXES purpose... but to make it work I think you'd have to set the DisableSpectrometerNumber keyword to 5 in the Probewin.ini so the program essentially ignores it for automation as shown here:
[hardware]
DisableSpectrometerNumber=5 ; disable spectrometer flag allows a single spectrometer to be ignored by the program
And of course you'd have to enter dummy values for a 5th spectrometer in the SCALERS.DAT and MOTORS.DAT configuration files.
For the Analytical | Update Dead Time Constants - is there an equivalent way of doing this for CalcImage?
At the minute I'm doing exactly as you suggest - dividing the measured intensities across the board by an order of magnitude or two, which wouldn't make a difference in the grand scheme of things, but it would be nice if I didn't have to!
The updated dead time constants from the PFE dialog will be applied to the CalcImage maps automatically as long as you update the dead time constants in the sample used for the "Sample Setup" in CalcImage, from Probe for EPMA using the Analytical | Update Dead Time Constants menu. I will try to modify the "sanity check" in the SCALERS.DAT file...
I'll see what I can do about creating some demo data for quant mapping with the combined WDS and SXES: the work I've been doing has all been on client data. I work quite a lot with light elements, and the SXES is a game changer for this.
No rush, but that's very interesting to hear. It's too bad JEOL doesn't provide us with a way to read that spectrometer directly in Probe for EPMA. You should bug them about this. I know that Anette and Mia Kraft were working on this before Anette left for UBC.
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Yeah, I've got the SXES data going in to PfE and CalcImage.
It'd be great if I could put a dead time value as low as 0.0001us or something ridiculously small in to scalers.dat. My worry is that the very large CPS/nA values I get from integrating the SXES peaks is getting inappropriately dead time corrected.
We have modified the SCALERS.DAT "sanity check" to allow dead time values as low as 0.0001 us.
Update using the Probe for EPMA Help | Update Probe for EPMA menu as usual.
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Thanks very much!
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Hello everyone,
I just noted that "Display results as oxides" and "calculate atomic percents" in "calculate options" of Analyse do not work together.
It will be good if we can look at our results in at% and in stoichiometric form (on the picture I would like to see ZnO 100% ).
If it possible, off course.
Thank you!
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Hello everyone,
I just noted that "Display results as oxides" and "calculate atomic percents" in "calculate options" of Analyse do not work together.
It will be good if we can look at our results in at% and in stoichiometric form (on the picture I would like to see ZnO 100% ).
If it possible, off course.
Thank you!
I think you are asking for mole percent output.
This option is available when using the User Specified Output from the Analyze! window for selected samples or from the Output menu for standard or unknown samples:
https://probesoftware.com/smf/index.php?topic=71.msg350#msg350
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Thank you, John.
I know that the possibility exists, we can also easily recalculate our results in excel etc.
The benefit of using the options through "Analyse" is speed - we can very quick transform our data to convenient form - just for quick estimation without data saving.
Another point - it logically should work if we choose "Display results as oxides" and "calculate atomic percents" in "calculate options".
But if it is difficult to correct the code - let's forget the question, it is not a big point which deserves lots of discussions))
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Another point - it logically should work if we choose "Display results as oxides" and "calculate atomic percents" in "calculate options".
But if it is difficult to correct the code - let's forget the question, it is not a big point which deserves lots of discussions))
Yes, it is possible to add this output to the Analyze! window output. The problem is that some users expect to see oxide weight percent output *and* elemental atomic percent output. I know that I do. Changing the current behavior might upset some users. That is why we only added mole oxide output in the user specified output where it doesn't disrupt the current behavior of the software.
I will start a poll and if there is overwhelming support for changing the behavior of these options I will consider implementing it.
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Another point - it logically should work if we choose "Display results as oxides" and "calculate atomic percents" in "calculate options".
But if it is difficult to correct the code - let's forget the question, it is not a big point which deserves lots of discussions))
Yes, it is possible to add this output to the Analyze! window output. The problem is that some users expect to see oxide weight percent output *and* elemental atomic percent output. I know that I do. Changing the current behavior might upset some users. That is why we only added mole oxide output in the user specified output where it doesn't disrupt the current behavior of the software.
I will start a poll and if there is overwhelming support for changing the behavior of these options I will consider implementing it.
I sometimes think I'm too helpful! (I blame my mother who always told me: "Be useful"!)
I thought of a way to preserve the current default of elemental atomic output, but allow for the choice of mole oxide output when desired. Here is what the new calculation Options dialog looks like now in v. 13.7.8:
(https://probesoftware.com/smf/gallery/1_17_02_24_12_47_08.png)
The default will always be atomic percent, but one can now select mole oxide output instead. Here the default atomic percent output:
(https://probesoftware.com/smf/gallery/1_17_02_24_12_47_25.png)
And here is the optional mole oxide percent output:
(https://probesoftware.com/smf/gallery/1_17_02_24_12_47_38.png)
Hope that makes *everyone* happy... ;D
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It is great, thank you and your mom.
Could you guess why the option doesn't active for me? Off course, I updated the software version.
Thank you!
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It is great, thank you and your mom.
Could you guess why the option doesn't active for me? Off course, I updated the software version.
Thank you!
You'll have to make a new probe file, since this flag is not available in old databases.
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Hi,
Do you think there is a way to add the blank correction choices to the report and data output options? It could be just the unknown number used as the blank to have listed in either format.
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It is great, thank you and your mom.
Could you guess why the option doesn't active for me? Off course, I updated the software version.
Thank you!
You'll have to make a new probe file, since this flag is not available in old databases.
It is working!
Thank you.
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Hi,
Do you think there is a way to add the blank correction choices to the report and data output options? It could be just the unknown number used as the blank to have listed in either format.
Your wish is my command! ;D
Now in v. 13.7.9 check the user specified output format from the Analyze! window (for output of selected samples) or from the Output menu (for all unknowns or standards) and note the new output option shown here:
(https://probesoftware.com/smf/gallery/1_23_02_24_8_37_45.png)
This output includes the unknown sample number utilized as the assigned blank sample, the blank level (the "true" concentration of trace element in the blank sample) and the blank value (the difference between the blank level and the measured concentration in the blank sample for that spectrometer/crystal).
During quantification, the blank value is converted into a k-ratio intensity based on the composition of the actual unknown sample in question (relative to the blank sample itself), and then subtracted during the matrix iteration. This allows any matrix differences between the blank sample and the unknown sample to be accounted for quantitatively.
(https://probesoftware.com/smf/gallery/1_23_02_24_8_38_02.png)
Note that these blank parameters are the same for all data points within a sample as they are calculated from the blank sample level and the blank sample measurement average. Though of course in the case of duplicate elements (e.g., measuring Ti on all 5 spectrometers), they will likely be slightly different for each duplicate element (different spectrometer).
Finally we also added output of these blank parameters to the Report button output table as seen here:
(https://probesoftware.com/smf/gallery/1_23_02_24_8_38_24.png)
The blank correction itself is described in these topics:
https://probesoftware.com/smf/index.php?topic=29.0
https://probesoftware.com/smf/index.php?topic=454.0
https://probesoftware.com/smf/index.php?topic=1397.0
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Can we get export filter for totals >102 (or whatever we chose)?
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Can we add a default value to the wavescan limits?
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Can we get a string selection box in the Plot window?
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Can you code in different window colors for PfE if we are opening multiple instances? It can get confusing knowing which windows belong together.
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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.
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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.
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We are interested in showing the position of all multipoint bkgds in a plot from the Plot! window. Is that possible?
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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:
(https://probesoftware.com/smf/gallery/1_28_02_24_2_33_56.png)
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.
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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.
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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.
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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.
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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):
(https://probesoftware.com/smf/gallery/1_28_02_24_3_21_12.png)
(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.
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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:
(https://probesoftware.com/smf/gallery/1_05_03_24_8_07_06.png)
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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) ?
(https://probesoftware.com/smf/gallery/2045_14_03_24_7_03_32.jpeg)
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 :P ), 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... ;D
Rgds,
Radek
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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 :D
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.
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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 :D
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?
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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.
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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.
We could do this... but after the EPMA workshop! :)
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Absolutely. Not urgent but thanks for being open as always to add it.
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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) ?
(https://probesoftware.com/smf/gallery/2045_14_03_24_7_03_32.jpeg)
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 :P ), 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... ;D
Rgds,
Radek
Now that the Athens EPMA 2024 workshop has finished:
https://probesoftware.com/smf/index.php?topic=99.msg12500#msg12500
We were able to get back to work! I think we've implemented the right click for bias scans as you wanted:
(https://probesoftware.com/smf/gallery/1_30_03_24_3_25_29.png)
And this right click update now also works on Cameca instruments for gain scans:
(https://probesoftware.com/smf/gallery/1_30_03_24_3_31_49.png)
By the way, just a small aside, I've modified the simulation mode in Probe for EPMA to better simulate a gain or bias scan:
(https://probesoftware.com/smf/gallery/1_30_03_24_3_25_50.png)
Better for teaching in the classroom using Probe for EPMA in simulation mode:
https://probesoftware.com/smf/index.php?topic=837.0
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Hi!
AWESOME! Thank you all for your effort! This is certainly making work with many elements and complicated runs a lot easier (and faster to set up the instrument)!
I checked it with our JEOL and it works just fine. Very much appreciated!
Thanks again!
And sorry I could not join the Athens workshop this time, I was just on holiday skiing in Lapland... :)
Rgds,
Radek
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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.
Your wish is granted! :D
Download PFE v. 13.8.3 using the Help menu and you will find it in the Analyze! window right click menu as seen here:
(https://probesoftware.com/smf/gallery/1_04_04_24_12_18_58.png)
The file format is seen here:
(https://probesoftware.com/smf/gallery/1_04_04_24_12_19_20.png)
And when imported into PictureSnapApp:
(https://probesoftware.com/smf/gallery/1_04_04_24_12_19_40.png)
I hope you find this helpful and I'm glad you are finding PictureSnapApp useful. For those interested in learning more about PictureSnapApp see here:
https://probesoftware.com/PictureSnapApp.html
and here:
https://probesoftware.com/smf/index.php?board=34.0
It's a sample navigation app that is more flexible than one might suspect...
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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) ?
(https://probesoftware.com/smf/gallery/2045_14_03_24_7_03_32.jpeg)
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 :P ), 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... ;D
Rgds,
Radek
This was a fantastic suggestion Radek.
Thanks for implementing this John. Just used it for the first time in version 13.8.3, and it turned one of my least favorite method setup chores into a 90 second breeze!