Author Topic: Latest version changes for Probe for EPMA (and CalcImage) v. 12.9.7  (Read 70949 times)

John Donovan

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Re: Latest version changes for Probe for EPMA (and CalcImage) v. 12.8.9
« Reply #150 on: August 23, 2020, 09:50:35 AM »
This is a small change for the multi-point backgrounds (MPB) in Probe for EPMA but I thought it worth mentioning.

As you know, when using the MPB method in PFE, one can select the number of background positions to acquire background intensities on each side of the emission peak:

https://probesoftware.com/smf/index.php?topic=131.msg540#msg540

The neat thing about the MPB method is that it *automatically* handles background "curvature" and also interfering emission lines on your background measurements.

Previously this list of backgrounds always displayed the maximum number of MPB backgrounds for each side of the peak, that is 12 positions.  But in working with Andrew Locock recently he mentioned that it would be nice to only display the actually number of background positions to be acquired:



So we worked on this and now in the Model Backgrounds dialog the number of MPB positions displayed in the list are only those actually being utilized:



We also implemented the same method for the Elements/Cations dialog as seen here:



Of course, if the sample has no data, then these MPB "acquire" parameters can be modified, and then the MPB position list is updated accordingly.

Update from the Help menu when you are ready.
John J. Donovan, Pres. 
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John Donovan

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Re: Latest version changes for Probe for EPMA (and CalcImage) v. 12.8.9
« Reply #151 on: October 20, 2020, 09:57:06 AM »
Over the last month or two there's been a number of bug fixes and improvements in Probe for EPMA and CalcImage.  See here for details:

https://probesoftware.com/smf/index.php?topic=40.0

Use the Help menu in Probe for EPMA to get the latest update.
John J. Donovan, Pres. 
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John Donovan

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Re: Latest version changes for Probe for EPMA (and CalcImage) v. 12.8.9
« Reply #152 on: October 23, 2020, 01:35:43 PM »
Working with Philipp Poeml we have identified and fixed a number of small bugs using the "align and crop" feature in CalcImage:

https://probesoftware.com/smf/index.php?topic=1152.msg9177#msg9177

These issues were identified when utilizing multiple spectrometer passes when analyzing 20 or more elements on different spectrometers.

If you utilize the "align and crop" method to deal with stage and/or beam drift in your quantitative X-ray maps, you should update CalcImage using the Help menu in Probe for EPMA.

Thank-you Philipp!
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John Donovan

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Re: Latest version changes for Probe for EPMA (and CalcImage) v. 12.9.3
« Reply #153 on: December 29, 2020, 02:33:17 PM »
As noted here:

https://probesoftware.com/smf/index.php?topic=40.msg138#msg138

a number of small changes over the last few weeks in v. 12.9.3 of CalcZAF and Probe for EPMA.
« Last Edit: December 29, 2020, 04:24:29 PM by John Donovan »
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Re: Latest version changes for Probe for EPMA (and CalcImage) v. 12.9.3
« Reply #154 on: January 26, 2021, 02:30:33 PM »
 Recently Julien Allaz at ETH Zurich discovered (and we fixed) a subtle bug in Probe for EPMA that occurred when several specific features were utilized together.

In software development it is one thing to implement a software feature and get it working accurately and reliably. And, it is fairly easy to test these new features with appropriate methods and data. However, it is an entirely different affair to test for all possible interactions *between* software features. The following is an example of this "feature interaction" testing difficulty.

Many of you already utilize the Time Dependent Intensity (TDI) correction in Probe for EPMA to correct for changes in x-ray intensity over time, usually due to ion migration (e.g., alkali glasses) or volatilization (from specimen beam damage). The TDI correction utilizes replicate intensity measurements that are time stamped to characterize these changes in intensity as described here:

https://probesoftware.com/smf/index.php?topic=11.msg234#msg234

So whereas we normally simply record the total integrated intensity, with TDI we not only record the total intensity using sub time increments that are summed together to get our time integrated intensity, we also record the individual sub interval intensities, each with their own time stamp.  This is so that the slope of the sub interval intensities over time can be applied to the total summed intensity to correct for an increase or decrease in the intensities over time. So far so good.

Next we have the Nth point off-peak acquisition method.  With this acquisition method we acquire the on-peak and off-peak intensities as usual on our first acquisition point (and every Nth point from there on), but for subsequent points we only acquire the on-peak intensity and simply utilize the previously acquired off-peak intensities as described here:

https://probesoftware.com/smf/index.php?topic=71.msg7875#msg7875

If anyone interested in seeing how the Nth point off-peak compares to normal off-peak and also to the MAN background correction, see this white paper from a few years ago:

https://epmalab.uoregon.edu/reports/Comparison%20of%20Off-peak,%20MAN%20and%20Nth%20Point%20Backgrounds.pdf

The bottom line on Nth point acquisition is that statistically it compares well to the MAN method, but it does not handle situations when the sample composition changes (due to changes in average Z and hence continuum production). However this is a situation the MAN background method handles easily. Again so far so good, the TDI method and the Nth point method are often utilized at the same time and they work well with each other.

Then we have the "On Peak Time Fraction" parameter option in the Nth point method which is where we can reduce the count time on the Nth point measurement so as to spend a proportionally larger amount of time characterizing the off-peak intensities before the specimen has been beam damaged as described here:

https://probesoftware.com/smf/index.php?topic=806.msg8036#msg8036

Originally the allowable range of values for this On Peak Time Fraction was from 1.0 (the default) to 0.1 (10%). For those of you who happened to make use of the TDI and Nth Point methods with this range of On Peak Time Fraction values everything worked just fine and dandy.

But then, the guys at U Mass Amherst (Mike Jercinovic and Mike Williams), wanted a modification that allowed a *zero* On Peak Time Fraction value, so that the entire on-peak intensity measurement would be skipped altogether, thereby only measuring the off-peak intensities for each Nth point. The idea being to measure the background intensities before any sample damage had begun to occur. Also, they wanted the software to automatically specify each Nth point as being "disabled", so that these Nth points would not be included in any quantitative calculations, since there were no on-peak intensity measurements performed for them this makes sense.

Now we need to take a moment and discuss how the intensity data in Probe for EPMA is saved to the MDB database file. For intensities such as on and off-peak intensities, these values are always stored (even if they are not measured). For example the off-peak intensities when performing MAN background acquisitions are not measured but are stored as zero values. In such cases these zero intensities will be accessible in the database for queries, but not be very useful.

On the other hand, some intensities are only stored if they are acquired. For example, the TDI sub interval intensities are only acquired if they are actually acquired. These TDI database fields are simply not present if no on-peak measurement was acquired.

So the bug that Julien found (you were wondering when I would get around to that!) is related to all of the above. Because when the On Peak Time Fraction for the Nth Point method is greater than zero, every data line will have these TDI intensities stored, and we have no problems. But if the On Peak Time Fraction is zero, then the on peak acquisition is skipped and therefore no TDI intensities are acquired or stored for every Nth noint.

So if you utilize both TDI and Nth point acquisitions *and* you specify a *zero* ON Peak Time, this latest bug fix will take care of it.  As always, please update from the Help menu in Probe for EPMA.

Please let me know if you have any questions at all.
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John Donovan

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Re: Latest version changes for Probe for EPMA (and CalcImage) v. 12.9.5
« Reply #155 on: March 26, 2021, 04:55:37 PM »
Karsten Goemann (Univ. of Tasmania) and Scott Boroughs (Wash. State Univ) both recently reported a problem getting proper image FOV calibrations in PFE when using the Thermo imaging interface.

This now fixed in v. 12.9.5 and can be downloaded using the Help menu in Probe for EPMA. This bug did not affect the JEOL or Cameca mapping or video imaging interfaces, but only the Thermo (and Bruker) imaging interfaces in PFE.
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Re: Latest version changes for Probe for EPMA (and CalcImage) v. 12.9.5
« Reply #156 on: April 24, 2021, 10:13:22 AM »
For JEOL 8230/8530/iSP100/iHP200F EPMA users:

We recently added a new flag in the [hardware] section of the probewin.ini file that will cause the software to issue an "unfreeze" command to the JEOL software after both point and image acquisitions.  This prevents the user from having to constantly click the "Unfreeze" button in the JEOL software.

To obtain this new feature and turn it on, simply update Probe for EPMA using the Help menu, and then edit this flag in the probewin.ini file [hardware] section as shown here:

[hardware]
JEOLUnfreezeAfterFlag=1

The new flag will appear at the end of the section after the updated software has run.
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Re: Latest version changes for Probe for EPMA (and CalcImage) v. 12.9.6
« Reply #157 on: June 30, 2021, 09:12:27 AM »
We made a slight tweak to the STRATAGem Output menu so it now includes BadgerFilm for k-ratio output for thin film reprocessing:



The BadgerFilm board is found here:

https://probesoftware.com/smf/index.php?board=37.0
« Last Edit: July 06, 2021, 09:37:37 PM by John Donovan »
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Re: Latest version changes for Probe for EPMA (and CalcImage) v. 12.9.6
« Reply #158 on: July 06, 2021, 09:39:48 PM »
The latest version of Probe for EPMA (still v. 12.9.6) has a small tweak to the display of EDS parameters during EDS spectrum acquisition.

Update from the Help | Update Probe for EPMA menu.

Also we updated the reference manual and help file for some probewin.ini keywords.
« Last Edit: July 07, 2021, 09:21:54 AM by John Donovan »
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Re: Latest version changes for Probe for EPMA (and CalcImage) v. 12.9.7
« Reply #159 on: July 21, 2021, 01:52:18 PM »
The latest version of Probe for EPMA (v. 12.9.7) now supports fractional beam sizes for JEOL 8230/8530/iSP100/iHP200F instruments when saving or loading .PCC (Probe Column Condition) files.  Thanks to Ben Buse and Anette von der Handt for these suggestions.

We also added a rounding function to the save beam current code in the save PCC code so it rounds the beam current to the nearest nanoamp.
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Re: Latest version changes for Probe for EPMA (and CalcImage) v. 12.9.7
« Reply #160 on: July 26, 2021, 12:02:49 PM »
The latest version of Probe for EPMA (v. 12.9.7) now supports fractional beam sizes for JEOL 8230/8530/iSP100/iHP200F instruments when saving or loading .PCC (Probe Column Condition) files.  Thanks to Ben Buse and Anette von der Handt for these suggestions.

We also added a rounding function to the save beam current code in the save PCC code so it rounds the beam current to the nearest nanoamp.

I should add that we also fixed a small issue with saving/loading of the JEOL sampling/scan modes (spot vs. scan) in the Probe Column Condition (PCC) files for the 8230/8530/iSP100/iHP200F.
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John Donovan

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Re: Latest version changes for Probe for EPMA (and CalcImage) v. 12.9.7
« Reply #161 on: August 14, 2021, 08:04:21 AM »
Small change here, which some might find useful:

We added a new keyword to Probewin.ini to specify which WMF image file to load as default when StageMap form loads. Update PFE, run PFE and find the new keyword in the [standards] section:

StageBitMapIndex=1

Specify the default WMF image file to load as default in StageMap dialog. The default is 1 and the allowed range is 1 to StageBitMapCount as defined in the Probewin.ini file.

Basically this allows one to define the default StageMap image if it is *not* the first image file listed in the Probewin.ini stage bit map arrays.
John J. Donovan, Pres. 
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