Latest version changes for Probe for EPMA (and CalcImage) v. 13.8.6

[John Donovan]

We recently released v. 12.0.1 of Probe for EPMA.   

The main features of this new release are integrated support for JEOL EDS systems (8230/8530) for quant integration of EDS and WDS using full k-ratios and standards for optimum accuracy, and also GUI improvements which will allow better scaling when running on high resolution monitors (e.g., 4K) and also for non-default DPI settings (e.g., for teaching and demonstration).

[John Donovan]

I recently modified the scripting output code to set the "Project Folder" for Surfer, to the folder of the currently open CalcImage project, when a Surfer script is being output.  This is done by editing the registry settings for the Surfer application "Project Folder".

The practical  benefit is merely that when running a "slice" or "polygon" feature extraction script, when the user clicks the Save As menu for the digitized slice or polygon outline, as seen here:



Surfer will now open the current CalcImage project folder by default.  As opposed to having to browse to the correct project folder manually.  Please update to 12.0.1 and you will obtain this small improvement to the CalcImage script processing in Surfer.
john

[John Donovan]

Some of you (Buse, Seward and Moy), have reported to me at one time or another that something wasn't being calculated correctly when a sample contained duplicate elements where the duplicate elements consisted of different x-rays.  For example, Fe Ka and Fe Ll in the same sample. 

Normal samples and even samples with duplicate elements work fine when those duplicate elements have the same x-ray, for example 3 spectrometers tuned to Ti Ka. But when the duplicate elements have different x-rays (or keVs), I found myself tweaking this and that in order to get the std k-factor loading code to work properly.  The problem is due to the fact that when one has duplicate elements in the sample, you don't want to the matrix correction using std k-factors where the element concentration was duplicated in the standard.

This weekend I decided to "grab the bull by the horns", are re-write the std k-factors loading code to clean things up and deal with this properly. I first cleaned up the normal sample code by loading the sample parameters and then applying any missing elements from the standard database. I then added each element concentration in, but only once for a proper std k-factor calculation.  Duplicate elements with the same x-ray are automatically handled because they've already been calculated!

For samples with duplicate elements with different x-rays (or keVs), I wrote entirely new code that loads the sample, then converts all elements to non-analyzed elements, then loops through each analyzed element in the sample one at a time, and loads first the standard concentrations that are not the current element, then loads just the concentration for that specific element, and the actual x-ray (and keV) for that element.

That way we can calculate std k-factors for any combination of elements, x-rays and keVs, but at the cost of calling the physics routines several times.  Because this method is a little slower, I kept the code for normal samples in there.

https://github.com/openmicroanalysis/calczaf

I'm going to try some tests, for example Au La and Au Ma in the NIST Au-Cu standards, next week myself, but please contact me if you have any questions.
john

[John Donovan]

The latest version of Probe for EPMA now displays the EDS sample count time in the Acquire! | Acquisition Options dialog as shown here:



This is the amount of time the program calculates for the WDS (only) acquisition, with an adjustment for the EDS deadtime, so that both the WDS and EDS acquisitions will complete at the same time.  This is a dynamic calculation based on the specific sample configuration for each sample being acquired and is updated for each point acquisition.

[John Donovan]

Paul Carpenter and I worked on the feature described here:

https://probesoftware.com/smf/index.php?topic=40.msg6358#msg6358

where PFE will automatically load a formula basis from the standard composition database if one has been specified.

This formula basis is now loaded for each standard every time a new standard sample is created from either the Acquire! or Automate! windows. Of course one can change the formula basis subsequently in the Analyze! window.  This standard formula basis is specified from the Standard.exe app from the Standard | Modify Standard menu as seen here:



john

[John Donovan]

Because I removed the Zeiss Axioscope interface in v. 12.1.0 of Probe for EPMA I decided to save a copy of the last version of Stage.exe that does support that digitizing stage interface.

The attached zip file below contains a renamed copy of Stage.exe and an example ini and motors.dat file in case anyone still needs this ancient serial interface. It should just be unzipped and copied to an existing (off-line) Probe for EPMA folder if you want to interface to your Zeiss Axioscope optical microscope.

[John Donovan]

We've recently added a new keyword to the Probewin.ini file for specifying that one has a LaB6 emitter electron gun.

Previously if the instrument had a LaB6 emitter, one would simply indicate that the electron gun should not be adjusted for heat or emission by specifying a thermal field emitter in the [hardware] section as seen here:

ThermalFieldEmissionPresent=1      ; non-zero = FEG electron source interface present

The downside was that none of the "filament standby" modes are available for a thermal field emitter. Instead the software merely closes the gun valve for FEG filament standby.  But now we've added this new keyword for LaB6 emitters as seen here:

LAB6FieldEmissionPresent=1      ; non-zero = LaB6 electron source interface present

When this new LaB6 emitter type is specified, the normal "filament standby" modes are now available as seen here:

FilamentStandbyPresent=1   ; non-zero = enable filament standby feature
FilamentStandbyType=2      ; 0 = reduce heat only, 1 = reduce heat and keV, 2 = reduce keV only, 3 = external script
FilamentStandbyExternalScript=""

Generally with a LaB6 emitter one will want to specify reduce keV only, or specify an external script or app for filament standby.

[John Donovan]

In version 12.1.6 of Probe for EPMA we now store the EDS net intensity interface type for off-line processing of EDS spectra.

This means that when you take your probe run file to another computer for reprocessing WDS and EDS intensities for quant, the software will automatically know which EDS interface (Thermo, Bruker, etc.) will be utilized for the EDS net intensity calculations.

For older versions of the MDB file, PFE will now check the EDS acquisition interface and warn you if the currently installed PFE software is correctly configured for re-processing of EDS spectra for quantification.

Please note that at this time, only Probe Software and Thermo Scientific allow for unlimited copying of their software for off-line re-processing and quantification of WDS and EDS data. Our understanding is that one has to purchase a license from Bruker for each computer the software is installed on, even for off-line data re-processing.  Hopefully this will change in the future.

[John Donovan]

This is a very minor feature in Probe for EPMA, Standard, CalcImage, and some other apps that I had forgotten about, but someone might find it useful someday. 

Basically it allows the use of the keyboard cursor (and Enter) keys to select menus. For example, if you hold the <alt> key down on your keyboard, the main menu in PFE shows that the menus have some letters underlined. The desired menu can then be selected by hitting that letter key while the <alt> key is held down. Once the selected menu is visible, simply use the cursor keys to navigate the menus and then hit Enter to select that menu.

Here is the CalcImage menu shown with the <alt> key pressed:



Here is the PFE menus with the <alt> key pressed:



In this example, the user typed <alt> h and the Help menu is now visible:



This keyboard-menu feature used to be called "shortcut keys", but maybe no one uses such keyboard shortcuts nowadays.  But they are there if you want them...

I should also mention that one can do some operations using the <ctrl> key "shortcut".  For example, you can open the Add/Remove Standards dialog by hitting the <ctrl> and s keys at the same time as seen here:



Look in the menus for other <ctrl> shortcuts.

[John Donovan]

Paul Carpenter recently did some Probe for EPMA training at NASA JSC and he suggested we change the aspect ratio of the Display PHA and Peaking dialog for better visibility on small monitors and laptops, so we did:



He also suggested and we also made the default size of the peaking and wavescan "real time" displays larger...  grab v. 12.2.4 by updating from the Help menu as usual.

[John Donovan]

We've introduced several new parameters to the Probewin.ini file.

The first two parameters are in the [standards] section:
LoadFormulasFromStandardDatabaseFlag=0
LoadCalculateOxygenFromStandardDatabaseFlag=0

If these flags (as requested by Paul Carpenter) are changed to non-zero values then PFE will, from the New Sample Setup dialog from the Acquire! window (and even from the Automate! window), automatically load the specified formula basis from the standard composition database and/or the calculate oxygen by stoichiometry flag, based on the Display As Oxide" flag in the standard database (there is no use stoichiometric oxygen flag in the standard database, so we're using the display as oxide flag instead).

The formula basis in the standard database is described here:

https://probesoftware.com/smf/index.php?topic=71.msg6040#msg6040

The last INI parameter is in the [general] section:
SetBeamModeAfterAcquisition=0

This allows the user to specify how to set the beam mode after a *manual* acquisition (from the Acquire window). If 0 it will set the beam to spot mode after acquisition (the default), if 1, then it will set the beam to scan mode after a manual acquisition.

[Paul Carpenter]

John,
Thanks very much for making these changes and improvements to the software. I have seen how much work some very basic requests translate into, and I really appreciate the effort you make.
Cheers,
Paul

[John Donovan]

Those of you with sharp eyes might notice something a little different about the latest version of Probe for EPMA (v. 12.2.9).

We've removed all (we hope) references to the so-called W-motor, so although the changes to the GUI are subtle, the changes to the underlying code were tedious as lots of places had to be edited carefully.

The new software has been tested and we don't currently see any issues, but please let us know if you see any errors or anything else that should be dealt with.  A screen shot is often helpful in these cases.

The w-motor (for those who don't know) were present on some early JEOL 733 EPMA instruments. Yes, ancient history!  The stage consisted of four 25mm sample holes on a rotating turret that rotated each sample hole into the very limited X/Y range of the stage. Yes, very strange indeed.

Anyway, since we have dropped support for these non-networked instruments some time ago, it was finally time to do a little housekeeping and remove this strange rotation motor from our code. 

We also improved some warning messages in v. 12.2.9 for the interference standard assignments in the Standard Assignments dialog.

[John Donovan]

The latest version of PFE (v. 12.3.7) now calculates the stage calibration tilt in PictureSnap  (and also PictureSnapApp) when performing a three point image calibration, and now warns if the stage tilt is greater than 0.5 degrees (similar to what the position sample fiducial calibration does already):

[John Donovan]

The latest version of PFE now supports acquisition of the CL signal on JEOL 8230/8530 instruments.

For these instruments, you'll want to be sure these entries in the probewin.ini file are as follows in the [imaging] section:

ImageInterfaceNameChan1="SE"
ImageInterfaceNameChan2="BSE"
ImageInterfaceNameChan3="CL"

The simply select the third analog signal (CL) and you should be able to acquire stage calibrated CL images from the Imaging window.