Probe Software Users Forum
Software => Probe for EPMA => Topic started by: John Donovan on August 17, 2013, 12:58:53 PM
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PROBE for EPMA XP/Vista/Win7/Win8/Win10/Win11 Xtreme Edition Version Software Changes
User names (in parentheses) indicate grateful attribution for the preceding bug report or suggestion. Users "rule"!
05/01/24 Fix check for std sets > 0 when aggregate mode for interference elements sets (Adams).
04/24/24 Fix user specified format bug where standard number/name didn't have average columns
added (von der Handt).
04/20/24 Fix MPB bug when plotting errors bars and aggregate mode is on.
04/19/24 Fix ferric/ferrous control enables in CalcImage (uses CalcZAF form) (von der Handt).
04/17/24 Add time weighting factor to report format output (Locock). Add iHP200F image
calibration default to CalcImage Clear button (Yu).
04/16/24 Fix bug caused by checking for zero std intensities in UpdateGetStandards and
UpdateCalculateStdDrift procedures caused by new error trapping code for Julien's
combine samples with EDS elements bug (Locock).
04/15/24 Modify CalcImage beam calibration code to utilize more realistic default values for
JEOL and Cameca instruments (Boroughs).
04/10/24 Fix minor bug when adding new elements where beamsize was getting re-set to zero (Boroughs).
04/05/24 Fix subtle bug when combining data lines in Analyze! window with EDS (Allaz).
04/04/24 Modify labels in CalcZAF from K-Value to K-Ratio and for "Use All Matrix Corrections".
v. 13.8.3
04/02/24 Add export of positions for selected samples in Analyze! window right click menu (von der Handt).
03/30/24 Add "KiloVolts" array to plot std/unk output and also to Analyze! window right click.
03/29/24 Modify ScanData code to allow user to modify bias and gain values using right mouse
click (Michallik).
03/21/24 Fix JEOL MEC EDS interface to handle stage position updating (unfreeze JEOL imaging), and add point
v. 13.8.2 reservations (freeze JEOL imaging). Thanks to Scott Boroughs, Ying Yu, Chi Ma and Radek Michallik.
03/20/24 Fix output of specified APFs in AnalyzeTypeResults and when aggregate mode is on for both compound
and specified.
03/19/24 Work more on JEOL MEC EDS interface.
Modify JEOLSetProbeScan (not called by PFE, only by Monitor.exe and TestType.exe) to use
direct TCP/IP calls to 8x30/iHP200F instrument instead of EIKS. Modify JEOLGetMagnification to
use direct TCP/IP call.
03/17/24 Temporarily modify JEOL MEC EDS code to handle new stage move behavior in v. 1.0.7 of JEOL
SEMCenter software (Boroughs).
Add check for mixed bgds for aggregate in AcquireAutomateStart. Allow EDS and WDS aggregate elements.
03/15/24 Fix atomic weight bugs in Import From ASCII codes in Standard.exe.
v. 13.8.1
Modify set mag and beam deflect code to make direct TCP/IP calls to 8x30/iHP200F instruments (Boroughs).
03/14/24 Modify Plot std/unk code to handle samples with different kilovolts (for overvoltage plotting)
03/09/24 Add DoEvents statement in Acquire! MakeNewSample code to prevent file errors in ElementCheckXray.
03/04/24 Fix bugs in plot wavescan when displaying angstroms or keV wavescan plots with EDS spectrum. Also
fix issues with Load Xray Database and User Selected Lines when not plotting in spectrometer units.
Minor tweak to Automate confirm dialog. Trap "File table not found" error because SX.MDB.
03/02/24 Comment out Moy BSC code as it doesn't work as well as original code (need to
v. 13.8.0 modify r correction coefficients).
02/29/24 Add Maximum Total checkbox and text field to Plot stds/unkns dialog (Ruth/Lowers).
Fix MPB shared bgd bug when using combined conditions and not measuring beam currents (Ruth/Lowers).
Add extra warning for not measuring beam currents when using combined conditions with different
beam currents and also in FormGETOPT
Fix sensitivity calculations in CalcImage to load the raw data arrays (forgot to do this
last year!) (von der Handt).
02/23/24 Fix normalize bug when plotting difference wavescans. Modify batch files to compile/sign only
Probewin.exe/ProbeForEPMA.msi when no version change.
02/22/24 Fix bugs when opening total and stoich. oxygen formula GRD files (CalcImageLoadQuantImages).
02/21/24 Add difference wavescan plot option to Plot! window for "Flank" method.
v. 13.7.9 Add blank parameters output to user specified and report table output (von der Handt).
02/16/24 Modify atomic percent output to output atomic or mole oxide percents using new AtomicOrMoleOxideFlag
v. 13.7.8 parameter (Starykh).
Fix dead time de-normalization for six term dead time expression when bgd counts are negative (Nachlas).
02/09/24 Add additional fit statistics to MAN plot window (Locock).
02/08/24 Adjust demo mode time estimation code (fix code for TDI overhead).
02/06/24 Tweak TDI simulation code for better accuracy.
02/02/24 Fix bug when closing database preventing loading of same setup in new database (Williams).
01/30/24 Add Zbar calculations to MAN custom output (Locock).
01/28/24 Minor tweaks to TDI output to handle disable quant flags (Qi).
Minor tweaks to wavescan output to handle "continued" samples.
01/27/24 Fix array dimensioning in TDI output (Qi).
Fixed KLM output for wavescans (Boroughs).
01/26/24 Fix bug when using quick stds where correct count time for unknowns does not get loaded (Buse and vonder Handt).
Temporarily comment out error trap in AcquireStartAutomate to check for using quick stds with digitized sample
setups (it seems to work?).
Add right click menu to Analyze! to export wavescan data for selected samples (Boroughs).
01/24/24 Fix bug when using All Matrix Corrections because DAM was still using XPP parameters (von der Handt).
v. 13.7.7
Fix bug when using Output | TDI Intensities menu when samples have different numbers of elements (Qi).
Modify output TDI code to improve performance for absorbed current data output with TDI.
Mention linear equation fit form in MAN tooltip help (Locock). Add count time for peaking scans to
Run menu display.
01/23/24 Fix plot display issues for stds/unkns (Boroughs).
01/18/24 Fix bug in Standard that prevented H and He from being saved to the standard composition (von der Handt).
v. 13.7.6
Add Brian Joy as contributor to excess oxygen from ferrous/ferric calculations.
01/12/24 Add option to load project flags from an existing project when creating a new project
using the CalcImage project wizard (Boroughs).
Better handle output if Surfer app is not installed.
01/11/24 Fix bug where pre-peaking option was not getting the correct starting peak position if the
element was not the first element in the spectrometer (Williams).
01/08/24 Add tooltip help to CalcImage for analytical total min/max (Boroughs).
Modify MAN get sample elements code in DataLoadAllMAN to prevent elements from being loaded
out of order which can cause a problem if aggregate mode is utilized (Locock).
Modify empirical APF re-normalization code when using different primary standard to multiply
rather than divide (see file Oxygen measured and stoichiometric_11-20-2202.MDB).
Save FormCalcImage form position and size before performing quant (Boroughs).
12/29/23 Finish copyright changes.
v. 13.7.5
12/28/23 Update copyright to 2024.
12/20/23 Use "IdealArraySize" in line profile extraction in case filtering removes some pixels (Neill).
12/19/23 Fix a number of minor bugs when importing JEOL compositions from JEOL folder (Neill).
v. 13.7.4
12/16/23 Make element list in Sample Setup dialog taller so more elements are visible (Boroughs). Also modify
Automate! summary to include number of standard and unknown points (Boroughs). Add position increment
for Z positions when importing .POS files (Boroughs).
12/15/23 Warn user that not all fields are exported in standard database ASCII export.
12/14/23 Add default atomic charges and atomic weights when importing from JEOL and Cameca standard composition
v. 13.7.3 files (Neill).
Add sample and line numbers in PictureSnapApp for Display Selected Samples (in Analyze!) (Chouinard).
12/14/23 Fix bug in loading VolatileSelfCalibrationAcquisitionFlag from probewin.ini file (Boroughs).
Fix bug in combining analysis lines and combining data lines into a new sample if MAN
elements are present (Neill).
Add check for missing atomic weight in standard compositions in standard.mdb file (Neill). This
error should not occur, so please let us know if you see it.
12/12/23 Fix detection limit overflow bug (Chouinard, Moy).
12/11/23 Fix subtle bug when checking for duplicate elements and disable flags (Buse).
12/10/23 Tweak Effective.frm.
11/29/23 Modify Load File Setup code to save standard numbers/names/parameters more
systematically (Buse, von der Handt, Goemann).
11/28/23 Improve error handling in ElementGetData. Rename Effective.frm,frx.
11/27/23 Fix bug in ElementGetData when loading new standards in Standard app (von der Handt).
v. 13.7.1
11/27/23 Add usermac.dat and usermac2.dat (actinide) MAC files to CalcZAF distribution.
v. 13.7.0
11/22/23 Modify GetElmSetElmSave to include code to check for JEOL spectro jog for saving low multi-point
positions (Boroughs). Also fix bug where defaulted multi-point positions were not getting saved!
Also fix MPB index label controls.
11/21/23 Modify JEOL spectro backlash code to check backlash defined in the MOTORS.DAT (Boroughs).
v. 13.6.9
11/21/23 Minor tweak to text explanation in multiple setups dialog (Matthews).
11/19/23 Minor change in effective takeoff angle output in CalcZAF.
v. 13.6.8
11/17/23 Tweak STRATAGem/BadgerFilm GUI. Add set scan rotation controls in Imaging "@" button dialog (Boroughs).
11/16/23 Tweak STRATAGem/BadgerFilm output GUI to skip duplicate aggregated elements and also display x-ray
lines in case of multiple emission lines for an elements (Matthews).
11/13/23 Fix PHA MCA display output bug to FormSCAN. Fix output of duplicate elements in
STRATAGem output (Matthews).
11/12/23 Modify FormSetupRun to make filename label control longer for long folder strings.
Work on code to update FormSCAN if it is visible when running manual PHA scans.
11/10/23 Minor tweaks to standard compositions import from JEOL/Cameca.
11/09/23 Modify GetName code to not update standard name. Comment out code for
checking Surfer startup folder in registry.
11/07/23 Improve JEOL composition and position importing (Standard and Stage).
v. 13.6.7
Improve CalcZAF use All Matrix Corrections output.
11/06/23 Fix code for EDS interface turned off for net intensity calls.
11/04/23 Add link to new Probe Software YouTube channel from Help menu.
11/03/23 Remove temp total flag code from CalcImageLoadQuantImages (only use in output routines).
Add Run | Display Acquired Selected Positions on PictureSnap menu (Chouinard).
Add keV to CalcZAF Use All Matrix Corrections output.
11/02/23 Tweak CalcZAF Use All Matrix Corrections output.
v. 13.6.6
11/01/23 Modify CalcZAF to calculate intensities from concentrations for all matrix corrections.
Fix PictureSnap bug when loading positions for selected sample and no samples are displayed
in the Automate! window and fix DataCorrectDeadTime2 overflow. (Chouinard).
10/31/23 Modify RealTimeROMStartScan code to adjust start scan position if JEOL instrument
v. 13.6.5 to account for JEOL backlash size.
Make copy of standard.mdb for distribution (standard_UofO.mdb)
10/29/23 Disable Effective angle calculations for older MDB files.
Modify effective angle code to rotate spectrometer orientations if JEOL instrument (for anti
Cartesian stage coordinates) (Moy).
Comment out JEOL specific code for ETOA spectrometer orientation rotation (not needed?).
10/28/23 Add scaler effective takeoffs to MDB file. Fix FormGETELM update if user removes all TDI
v. 13.6.4 parameters (von der Handt). Add debug output for secondary boundary correction.
10/27/23 Add spectrometer orientations to MDB file. Work on effective TO code with Moy. More work on effective
v. 13.6.3 take off angle code for sample tilt calculations.
10/26/23 Add "doevents" line in NewMakeNewSample code to ensure sample setups get loaded properly (timing issue).
v. 13.6.2 Modify JEOL standard import to skip standards without element data (Neill).
Enable sample tilt and optional effective angle recalculation button in FormGetElm (Moy).
Add code to check for no EDS elements (Chouinard).
10/25/23 Changes to analytical sensitivity calculations (Buse). Add new plane fit code from Moy to calculate
sample tilt and modify effective takeoff angles.
10/22/23 Modify aggregate code check for different bgds to allow mixing off-peak channels with MPB channels
that have switched MPB channels to use off-peak bgds (Buse).
10/21/23 Fix code for separating or combining samples for TDI and CL data.
10/20/23 Fix problems with saving EDS net intensities when combining, or separating samples from Analyze! window.
v. 13.6.1
10/19/23 Fix a number of small bugs (Allaz, Rom, Nachlas, von der Handt and Seward). See GitHub history for details.
10/16/23 Fix minor bug in CalcZAF (remove unnecessary call to ZAFSetZAF) when calculating intensities
v. 13.6.0 from concentrations (Carpenter).
Start work on new code to calculate effective takeoff angles based on sample tilt.
10/14/23 Fix FormPERIODIC load event issue (Boroughs). Tweak MAN parameters output.
10/13/23 Add output of MAN STD DEV% fit to log window output and also to Report format (Locock). Call calculate
Z bar procedure in MAN dialog more to assure that displayed zbars are up to date.
10/12/23 Fix bug where Zfraction calculation flags were not being utilized in MAN sample calculations.
v. 13.5.9
10/09/23 Add (existing) UseEffectiveTakeOffAnglesFlag and (new) EDSEffectiveTakeoff parameters to
probewin.ini file.
v. 13.5.8
10/05/23 Modify FormGetElm to add extra column to element grid to display more information (Boroughs).
If running multiple sample setups and using "Run Multiple Setups One at a Time", warn user if
selected sample setups are not using the same number of sample setups (Boroughs).
10/03/23 Add spectro # and Bragg crystals to legend when duplicate elements are present to
standard and unknown plot output.
Add code to check for temporarily disabled EDS interface for image interfaces using EDS interface,
e.g., JEOL EDS, JEOL MEC, Bruker or Thermo (von der Handt).
10/02/23 Tweak secondary boundary fluorescence correction labels and captions in forms. Fix bug when
loading element from setup database because effective takeoff angles are not stored in setup
databases.
Add new wavescan report output from Analyze! Report button (von der Handt).
09/29/23 Fix bugs in effective takeoff angle code. Make text control visible.
v. 13.5.7
09/23/23 Tweak Donovan and Moy "BEXP:" output.
v. 13.5.6
09/22/23 Add best fit from Moy for Z fraction exponent as a function of electron beam energy.
09/21/23 Fix output bug in Output12 (TDI) if TDI element is disabled for acquisition or quant (Domanik).
09/19/23 Tweak code for DAM BSE model output.
v. 13.5.5
09/18/23 Modify User Specified code (CONVERT3.BAS) to handle when oxygen is an isotope for
oxide and mol% calculations.
09/17/23 Modify XYSCAN2.BAS to utilize new XInvert/YInvert flags and turn off "hill shading" for
color flood plots.
09/16/23 Modify tooltip help for ZAF GUI.
09/15/23 Modify Donovan and Moy defaults to use Armstrong/Love-Scott absorption options. Tweak MAN code
v. 13.5.4 to handle click events better and add new Confirm All button.
09/14/23 Fix MAN bug when updating element selected or saving assignments (use direct call to
MANSelectStandardList) (Allaz). Fix bug when entering specified element in Elements/Cations (Allaz)
09/12/23 Fix bug in secondary boundary fluorescence correction in PFE for elements with no SF correction.
Add interactive Help button for SF dialog in PFE.
09/09/23 Small tweak to secondary boundary fluorescence GUI. Small tweak to effective k-ratio output (CalcZAF).
v. 13.5.3
09/06/23 Fix bug if no standards loaded in run and closing file.
09/04/23 Update Nachlas cell # in About dialog. Fix problem when oxygen is analyzed, then disabled, then
v. 13.5.2 specified oxygen is added for formula calculations (Nachlas).
Modify Calculation Options dialog to fit on screen better (Nachlas).
08/29/23 Moved source code to NewSource computer (Win 11).
Modify MoveSpin code (Move.bas) to call MoveUpdatePositions instead of MoveUpdateForm.
08/25/23 Add code to just log motion timeout errors in JEOL instruments (just write warning to log window).
Modify FormMOVE code to not call PeriodicLoad if FormMOVE is not visible (to prevent possible out of
memory issues during automation) (Boro).
08/22/23 Add call to DataStandards(2) to save standard compositions before starting automation.
08/21/23 Tweak save element setup to database code to display new record number).
Update literature references (APA format) in report output (von der Handt)
08/19/23 Work more on ConvertToPrbImg code for converting JEOL linescans (von der Handt).
08/18/23 Fix minor display issue in MAN dialog (Neill).
08/17/23 Lost of changes for new continuum and BSE Z fraction code (Moy).
v. 13.5.0
08/16/23 Add JEOLCrystalFlipMillisecDelayAfter keyword to [hardware] for possible
crystal flip hardware issues (Jiang).
Various modifications to MAN and About dialogs (Neill).
08/09/23 Modify Analyze! button Combine Selected Samples into a New Sample button to
v. 13.4.9 allow user to combine sample elements or combine sample data lines into a new
sample (Lowers).
08/05/23 Tweak CalcZAF effective takeoff angle estimation code.
v. 13.4.8
08/03/23 Finish CalcZAF effective takeoff angle estimation code.
v. 13.4.7
08/02/23 Work on effective takeoff angle estimation code.
v. 13.4.6
07/31/23 Add output of variable Z fraction exponent for MAN parameters. Add two more references to AnalyzeTypeReport.
v. 13.4.5 Add variable exponent to Z fraction backscatter exponent code. Add new
Z fraction backscatter parameter to GetZAF form and code.
07/30/23 Modify MAN Z fraction zbar calculation to accept a zero for dynamically calculated
v. 13.4.4 Zbar exponents based on emission line energy.
07/29/23 Add new matrix correction code for Donovan and Moy BSC/BKS corrections (modified from PAP).
07/17/23 Enable secondary fluorescence from boundary code in PFE. Needs testing.
v. 13.4.3
07/14/23 Add code to read "effective takeoff angles" from SCALERS.DAT file and save to MDB database based on
v. 13.4.2 spectrometer/crystal combination.
07/13/23 Fix problem with loading standard parameters on first standard in run.
07/10/23 Small modifications to check for acquisition in progress, rather then RealTimeMode for combining
v. 13.4.1 or separating samples. Also load net intensities after combining or separating samples (Boroughs).
06/21/23 Modify Standard and Probe for EPMA to handle different atomic weights for standards
v. 13.3.2 and unknowns. Lots of code changes- needs to be tested. Note: Isotopes of the same
element should always produce the same x-ray intensities, but the concentrations and
stoichiometries will be different if the atomic weights are different.
E.g. Si28 vs. Si29.
06/05/23 Fix Cameca integer dead time issue (Fellowes).
05/31/23 Modify InitScalers to allows dead time values as low as 0.0001 us for SXES spectrometer intensities (Fellowes).
05/25/23 Add calls to save standard parameters whenever a standard is acquired. This is because if a standard is added
from the DIGITIZE form (Add Standards button) the parameters are not saved to the current probe run because
the DIGITIZE form is also called from the Stage app which cannot have these calls. This was only a problem
if a user copied a probe run database to another computer for re-processing without first closing it.
05/20/23 Add display of faraday cup wait in and out times in FormGETTIM.
05/19/23 Add INI flag DoNotMeasure2ndFaradayAbsorbedCurrentsFlag for JEOL instruments with failing faraday cup
to avoid bad second faraday cup measures (Ruth).
05/17/23 Fix minor bug in separate samples into lines code (Lowers). Update matrix.mdb binary k-ratio database to 860K binaries.
v. 13.3.1
05/11/23 Small tweak to Analyze! create new sample from selected lines.
05/08/23 Add new button for separating samples into single line samples and button for extracting selected
points to a new sample (Lowers).
05/04/23 Add export code to support XMapTools import format in CalcImage (Allaz and Radek).
05/03/23 Finish implementing Cameca SXFive tactis USB image reading.
v. 13.3.0
Add units for Output XY Plots window (Seward).
04/19/23 Modify CalcImage manual image load to warn user to enter beam currents and pixel dwell times
manually (Boroughs).
04/12/23 Add extra error info to automation code to try and track down modal dialog display issue.
04/04/23 Add code to handle histogram display when image has no image Z range (Boroughs).
Modify ConvertToPrbImg.exe to handle JEOL maps up to 5120 pixels (was 4096) (von der Handt).
04/01/23 Add new feature to only measure faraday and absorbed currents on first point of sample (Boroughs).
v. 13.2.9
03/31/23 Modify JEOL MEC EDS interface to close/re-open interface if closed because user switched to the
JEOL Imaging window.
03/29/23 Fix sulfur-oxygen bug for Fanal code.
v. 13.2.8
03/28/23 Modify JEOL EDS MEC interface to close then re-start EDS interface if error in starting spectrum.
Thanks to Chi Ma for help with testing.
03/15/23 Fix minor display issue in Automate window when deleting selected points (Neill).
03/12/23 Add check for combining subsequent samples if TDI data is present (Boroughs).
03/01/23 Add oxygen equivalent of sulfur (negative valences) calculations and output (Allaz).
v. 13.2.7
02/25/23 Modify JEOL MEC EDS code to warn user about closing EDS center window when acquiring EDS data
in Probe for EPMA (Hatton and Ma).
Add output of 2nd beam currents and stats in Analyze! windows for raw data output (Ruth).
02/17/23 Modify Thermo code to add 2nd attempt for socket time out errors (Boroughs).
02/11/23 Fix bug in Locock amphibole and garnet output if using duplicate elements in aggregate mode (Locock).
v. 13.2.6
Modify Alternative Zbar output in Standard.
02/09/23 Minor tweaks to EDS and imaging code (Boroughs).
02/03/23 Bump version to force update to CalcZAF for changes in ZAFSetZAF code.
v. 13.2.5
01/30/23 Minor improvements to EDS OEM export features (von der Handt).
01/23/23 Modify update dead time code (again!). Disable Integrate button in Model Backgrounds if more than one wavescan
is loaded.
Fix coating thickness bug in ZAFSetZAF if passed sample is a standard (Starykh).
01/22/23 Modify Model Background form and code to allow user to select different wavescans
for background fit, if more than one wavescan loaded.
Modify GetDead code to update Current parameters and database table
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The ProbeForEPMA.msi installer now updates the Standard.exe app properly!
john
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Added Thermo support files for spectrum image (SI) file access to ProbeForEPMA.msi installer (v.10.1.6).
Everyone who wants to use the new Hyper-Imaging feature in CalcImage, as described here:
https://probesoftware.com/smf/index.php?topic=83.0
will need to run the ProbeForEPMA.msi installer again (no need to un-install PFE first).
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New versions (and updated documentation) are now available for the Matrix and Remote COM servers (v. 10.1.7)
https://probesoftware.com/Update.htm
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The ProbeforEPMA.msi installer now automatically installs the Thermo spectrum Image (SI) DLLs for the CalcImage "Hyper-Imaging" feature, which automatically integrates WDS quantitative x-ray maps with EDS (hyper-cube) spectrum images.
Apologies for attaching a brochure from the EMAS 2013 meeting to this post, but it does already provide a nice overview of these new CalcImage features- and I'm just too lazy to re-format it! :D
I should add, though current users of Probe for EPMA already know, all users may obtain new features for free, by simply clicking the Help | Update Probe for EPMA menu! 8)
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The current version of Probe for EPMA, with all the latest software and features updates and a current copy of the Probe Software user forum (i.e., this user forum), are now available from Probe Software through our DVD subscription service.
If your laboratory computer running Probe for EPMA is not connected to the Internet for security or other reasons, please contact Probe Software to find out about our automatic DVD subscription service. With this service you will be able to update your Probe for EPMA software and browse our user forum from your probe computer even if it is not connected to the Internet!
Please contact Barbara at Probe Software for more information:
barbara@probesoftware.com
541-343-3400
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Check out this new "self documenting" feature for manual acquisition now available in v. 10.2.3 of Probe for EPMA:
https://probesoftware.com/smf/index.php?topic=71.msg649#msg649
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I should have done this a long time ago, but the latest v. 10.2.4 now automatically loads all EDS spectra that are associated with standard samples if you select to have standard intensities loaded when performing a Load File Setup in Probe for EPMA.
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All PFE apps and installers beginning with v. 10.2.5 are now digitally "signed":
https://probesoftware.com/smf/index.php?topic=42.msg744#msg744
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Add ImageShiftPresent and ImageShiftType keywords to INI file.
For JEOL 8900/8200/8500 and Cameca SX100/SXFive this keyword will default to true, but for the 8230/8530 the keyword has to be added and edited manually in the [hardware] section of the Probewin.ini file.
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Add ImageShiftPresent and ImageShiftType keywords to INI file.
For JEOL 8900/8200/8500 and Cameca SX100/SXFive this keyword will default to true, but for the 8230/8530 the keyword has to be added and edited manually in the [hardware] section of the Probewin.ini file.
Just wondering if any 8230/8530 operators have edited their Probewin.ini file and tested this set image shift code for the new JEOL instruments that Philippe Pinard sent us.
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No bump in the version number, but the latest v. 10.3.3 now has modified the TDI acquisition code for combined condition samples. This should significantly reduce the delay between the Faraday cup out and the TDI counting start.
Try a TDI acquisition with a combined condition sample and let me know what you think!
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A nice simple question for you:
will PFE run on windows 8?
Richard
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A nice simple question for you: will PFE run on windows 8?
Gareth Seward can answer this best. See this thread also:
https://probesoftware.com/smf/index.php?topic=105.0
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The latest list of pre-calculated binaries for fast Monte-Carlo matrix corrections is found here:
https://www.probesoftware.com/download/Calculated%20Alpha%20Binaries.txt
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Just FYI, I added Mo to the geological sorted output as requested by Paul Carpenter.
Note that the "sort" order for analysis output can be "geological" (DHZ) order or ascending or descending atomic number order as selected in the Analytical |Analysis Options dialog as seen here:
(https://probesoftware.com/smf/oldpics/i60.tinypic.com/2przr4z.jpg)
The geological sort order is currently as follows (missing elements are added after the last one specified):
GeologicalOrder$(1) = "nb"
GeologicalOrder$(2) = "ta"
GeologicalOrder$(3) = "mo"
GeologicalOrder$(4) = "w"
GeologicalOrder$(5) = "si"
GeologicalOrder$(6) = "ge"
GeologicalOrder$(7) = "zr"
GeologicalOrder$(8) = "hf"
GeologicalOrder$(9) = "ti"
GeologicalOrder$(10) = "sn"
GeologicalOrder$(11) = "zn"
GeologicalOrder$(12) = "cd"
GeologicalOrder$(13) = "hg"
GeologicalOrder$(14) = "tl"
GeologicalOrder$(15) = "pb"
GeologicalOrder$(16) = "th"
GeologicalOrder$(17) = "u"
GeologicalOrder$(18) = "b"
GeologicalOrder$(19) = "al"
GeologicalOrder$(20) = "ga"
GeologicalOrder$(21) = "in"
GeologicalOrder$(22) = "v"
GeologicalOrder$(23) = "cr"
GeologicalOrder$(24) = "sc"
GeologicalOrder$(25) = "y"
GeologicalOrder$(26) = "la"
GeologicalOrder$(27) = "ce"
GeologicalOrder$(28) = "pr"
GeologicalOrder$(29) = "nd"
GeologicalOrder$(30) = "pm"
GeologicalOrder$(31) = "sm"
GeologicalOrder$(32) = "eu"
GeologicalOrder$(33) = "gd"
GeologicalOrder$(34) = "tb"
GeologicalOrder$(35) = "dy"
GeologicalOrder$(36) = "ho"
GeologicalOrder$(37) = "er"
GeologicalOrder$(38) = "tm"
GeologicalOrder$(39) = "yb"
GeologicalOrder$(40) = "lu"
GeologicalOrder$(41) = "ac"
GeologicalOrder$(42) = "fe"
GeologicalOrder$(43) = "co"
GeologicalOrder$(44) = "ni"
GeologicalOrder$(45) = "cu"
GeologicalOrder$(46) = "mn"
GeologicalOrder$(47) = "be"
GeologicalOrder$(48) = "mg"
GeologicalOrder$(49) = "ca"
GeologicalOrder$(50) = "sr"
GeologicalOrder$(51) = "ba"
GeologicalOrder$(52) = "ra"
GeologicalOrder$(53) = "li"
GeologicalOrder$(54) = "na"
GeologicalOrder$(55) = "k"
GeologicalOrder$(56) = "rb"
GeologicalOrder$(57) = "cs"
GeologicalOrder$(58) = "fr"
GeologicalOrder$(59) = "p"
GeologicalOrder$(60) = "s"
GeologicalOrder$(61) = "as"
GeologicalOrder$(62) = "se"
GeologicalOrder$(63) = "sb"
GeologicalOrder$(64) = "te"
GeologicalOrder$(65) = "he"
GeologicalOrder$(66) = "ne"
GeologicalOrder$(67) = "ar"
GeologicalOrder$(68) = "kr"
GeologicalOrder$(69) = "xe"
GeologicalOrder$(70) = "rn"
GeologicalOrder$(71) = "i"
GeologicalOrder$(72) = "br"
GeologicalOrder$(73) = "cl"
GeologicalOrder$(74) = "f"
GeologicalOrder$(75) = "c"
GeologicalOrder$(76) = "n"
GeologicalOrder$(77) = "o"
GeologicalOrder$(78) = "h"
-
One nice new change is a modified "Calibration Curve" dialog under the Run menu so even when not in Calibration Curve mode, the application will temporarily select Calibration Curve mode:
Warning in CalibrationLoad: Calibration curve mode not selected in the Analytical | Select ZAF, Phi-Rho-Z, Alpha Factor or Calibration Curve menu dialog.
and re-calculate the data for each sample and plotting it up in the calibration curve graph.
Note that the software distinguishes between off-peak and MAN (on-peak) measurements and creates a different calibration curve for each intensity type. Here one can see the Fayalite standard plotted up as an unknown in the Calibration curve dialog:
(https://probesoftware.com/smf/oldpics/i60.tinypic.com/30ktvnm.jpg)
Although, this "Calibration Curve" quant method was developed specifically for carbon in steel measurements, the results on "normal" analyses is often surprisingly good, though not "robust" as they say. The quant results for the above Fayalite sample are shown here:
St 263 Set 1 Fe2SiO4 (synthetic fayalite), Results in Elemental Weight Percents
ELEM: Si Al Fe Mg Cr Ti Mn Ca O
TYPE: ANAL ANAL ANAL ANAL ANAL ANAL ANAL ANAL SPEC
BGDS: LIN LIN LIN LIN LIN LIN LIN LIN
TIME: 20.00 20.00 20.00 20.00 20.00 20.00 20.00 20.00
BEAM: 20.09 20.09 20.09 20.09 20.09 20.09 20.09 20.09
ELEM: Si Al Fe Mg Cr Ti Mn Ca O SUM
131 13.759 -.050 53.957 .549 -.016 -.016 -.008 .014 31.407 99.596
132 13.840 -.061 53.898 .551 .007 -.012 .042 .046 31.407 99.717
133 13.784 -.053 54.145 .550 .023 .009 -.034 .035 31.407 99.866
134 13.811 -.053 53.973 .556 -.009 .043 -.031 .042 31.407 99.740
135 13.815 -.062 54.092 .553 -.019 .033 -.002 .050 31.407 99.866
AVER: 13.802 -.056 54.013 .552 -.003 .011 -.007 .038 31.407 99.757
SDEV: .031 .005 .102 .003 .017 .026 .030 .014 .000 .114
SERR: .014 .002 .046 .001 .008 .012 .014 .006 .000
%RSD: .22 -9.62 .19 .51 -594.05 230.03 -462.80 38.15 .00
PUBL: 13.785 n.a. 54.809 n.a. n.a. n.a. n.a. n.a. 31.407 100.001
%VAR: .12 --- -1.45 --- --- --- --- --- .00
DIFF: .017 --- -.796 --- --- --- --- --- .000
STDS: 14 13 395 12 24 22 25 358 0
Note that the standard for Si was SiO2 (std #14) and the standard for Fe was magnetite (#395) for the above analysis.
-
Recently I discovered that the particle (and thin film) geometry correction method had been broken, but it is now fixed. Here is an example of a CaF2 1 um particle run first without the particle geometry correction as seen here:
CaF2 1 um particle- use Tetragonal Prism model
STANDARD PARAMETERS:
ELEMENT STDNUM STDCONC STDKFAC Z-BAR ABSCOR FLUCOR ZEDCOR ZAFCOR
Ca Ka 831 51.200 .5068 14.6320 1.0043 1.0000 1.0059 1.0102
F Ka 831 48.800 .1080 14.6320 4.6000 .9998 .9822 4.5173
ELEMENT STP-POW BKS-COR F(x)e F(x)s Eo Ec Eo/Ec
Ca Ka 1.0468 .9609 .9383 .9343 20.00 4.0390 4.9517
F Ka .9498 1.0341 .6357 .1382 20.00 .6870 29.1121
SAMPLE: 5, ITERATIONS: 12, Z-BAR: 12.61798
ELEMENT ABSCOR FLUCOR ZEDCOR ZAFCOR STP-POW BKS-COR F(x)u Ec Eo/Ec MACs
Ca ka 1.0060 1.0000 1.0096 1.0157 1.0644 .9485 .9326 4.0390 4.9517 148.028
F ka 3.1457 .9999 .9882 3.1082 .9678 1.0211 .2021 .6870 29.1121 4483.58
ELEMENT K-RAW K-VALUE ELEMWT% OXIDWT% ATOMIC% FORMULA KILOVOL
Ca ka .60920 .30876 31.361 ----- 18.852 8.000 20.00
F ka 1.90570 .20587 63.988 ----- 81.148 34.436 20.00
TOTAL: 95.349 ----- 100.000 42.436
Note that although the total is fairly good (~95%), the atomic ratio (19:81) for Ca and F is very far off from what we should expect, namely 33:66.
Here is the same data now calculated with the particle geometry correction:
CaF2 1 um particle- use Tetragonal Prism model
STANDARD PARAMETERS:
ELEMENT STDNUM STDCONC STDKFAC Z-BAR ABSCOR FLUCOR ZEDCOR ZAFCOR
Ca Ka 831 51.200 .5069 14.6320 1.0043 1.0000 1.0059 1.0102
F Ka 831 48.800 .1082 14.6320 4.5945 .9998 .9822 4.5119
ELEMENT STP-POW BKS-COR F(x)e F(x)s Eo Ec Eo/Ec
Ca Ka 1.0468 .9609 .9384 .9344 20.00 4.0390 4.9517
F Ka .9498 1.0341 .6374 .1387 20.00 .6870 29.1121
SAMPLE: 5, ITERATIONS: 5, Z-BAR: 14.64359
E-RANGE: 11.1913, INTE-STEP: 113
Particle or thin film corrections utilized were Tetragonal Prism (flat top and curved sides)
Particle parameters were a particle diameter of 1 microns, a particle density of 3.1 gm/cm^3, a thickness factor of 1, and a numerical integration step size of 0.00001 microns.
ELEMENT ABSCOR FLUCOR ZEDCOR ZAFCOR STP-POW BKS-COR F(x)u Ec Eo/Ec MACs
Ca ka 1.5595 1.0000 1.0059 1.5687 1.0467 .9610 .6017 4.0390 4.9517 145.163
F ka 2.2710 .9999 .9822 2.2303 .9497 1.0342 .2807 .6870 29.1121 6437.34
ELEMENT K-RAW K-VALUE ELEMWT% OXIDWT% ATOMIC% FORMULA KILOVOL NORMEL% NORMOX%
Ca ka .60920 .30877 48.436 ----- 33.307 8.000 20.00 51.3053 -----
F ka 1.90570 .20612 45.971 ----- 66.693 16.019 20.00 48.6947 -----
TOTAL: 94.408 ----- 100.000 24.019 100.000 -----
Note that now the Ca:F atomic ratio is now as it should be (33:66) even though the total is actually slightly worse!
See this topic for more information on particle corrections:
https://probesoftware.com/smf/index.php?topic=281.0
-
One can now edit the sample name or title for CalcImage output as seen here:
(https://probesoftware.com/smf/oldpics/i59.tinypic.com/15eer90.jpg)
Idea from Paul Carpenter! Thanks, Paul!
john
-
New "interactive Help" buttons:
(https://probesoftware.com/smf/oldpics/i58.tinypic.com/14t223o.jpg)
-
The latest version (10.4.2) has a new feature that allows one to search the standard database for compositions with large matrix corrections.
From the Options | Find menu this dialog is available:
(https://probesoftware.com/smf/oldpics/i58.tinypic.com/s1oi7k.jpg)
Based on the standards found based on the element and wt.% range, this standard list can be further filtered for elements with large matrix effects using these new controls as seen here:
(https://probesoftware.com/smf/oldpics/i62.tinypic.com/242eu75.jpg)
Of course one can change the conditions and or analytical x-ray lines as necessary. The output is as seen here for standards in the Find list, containing elements with a large fluorescence matrix correction under the current conditions:
FindStandardsFilter: Starting standard filter operation...
FindStandardsFilter: large fluorescence correction for NIST SRM C2402 (Hastelloy C) (651), fe ka (7.3 wt.%), = 0.9176308
FindStandardsFilter: large fluorescence correction for Chromite USNM 117075 (455), ti ka (0.072 wt.%), = 0.9484967
FindStandardsFilter: large fluorescence correction for Chromite USNM 117075 (#455) (856), ti ka (0.072 wt.%), = 0.9485086
FindStandardsFilter: large fluorescence correction for Bornite U.C. #827 (709), fe ka (11.15 wt.%), = 0.9287004
FindStandardsFilter: Standard filter operation complete!
-
New wavescan output format (Goemann-Carpenter), is now available from the Output menu and will load each element/spectrometer to a separate Excel sheet for easy comparison of multiple samples as seen here:
(https://probesoftware.com/smf/oldpics/i57.tinypic.com/33p4jsh.jpg)
-
John,
In Picturesnap the .img file filtering in the Open file dialog does not show all the .jpg images when you navigate to a new directory. It seems to require that you go to the all files *.* filtering to work. It may be that it works when you are in the default run directory but not when you go to retrieve an image from another directory. It also seems to show .bmp image but not .jpg images when in the .img filter mode.
Cheers,
Paul
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In Picturesnap the .img file filtering in the Open file dialog does not show all the .jpg images when you navigate to a new directory. It seems to require that you go to the all files *.* filtering to work. It may be that it works when you are in the default run directory but not when you go to retrieve an image from another directory. It also seems to show .bmp image but not .jpg images when in the .img filter mode.
Hmmm, I'm not seeing this issue. I see all the jpg files in my folders as seen here:
(https://probesoftware.com/smf/oldpics/i58.tinypic.com/soqrgi.jpg)
So I guess I'm saying I need more information...
Wait, are they .jpeg files that are missing?
john
Edit by John: I should add that although today the .jpg and .jpeg extensions are used somewhat interchangeably, originally the .jpeg indicated Macintosh format. The difference being that the byte order is different on Mac versus Windows, i.e., big-endian versus little-endian.
To be on the safe side I didn't add .jpeg and .tiff extensions because I'm not sure the VB6 control will always handle these byte flipped images properly, but as you say, you can simply switch to the All Files filter.
-
Hi Paul,
OK, I do see this effect, but only in some folders it seems! I do not understand why, but it might be if the default file is displayed. I will investigate.
One can always type *.jpg to see just the jpg files for example.
Edit by John: OK, I see the problem. If I specify a default file with an extension in the code it only displays files of that type. So I think I can fix that...
-
Hi Paul,
OK, I do see this effect, but only in some folders it seems! I do not understand why, but it might be if the default file is displayed. I will investigate.
One can always type *.jpg to see just the jpg files for example.
Edit by John: OK, I see the problem. If I specify a default file with an extension in the code it only displays files of that type. So I think I can fix that...
The problem was a subtle aspect of the way Microsoft handles the file filter string for multiple extensions. Latest PFE update will fix the issue. Thanks for reporting this!
-
John,
Thanks man! You made the change, it had downstream implications and apparently made Kim Jong disappear from public view, who would have known that. And also a problem with image filtering.
Cheers,
Paul
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On certain Win7 computers (but only on some of them!), when you perform an update from the Help menu, you follow the msi installer prompts to update Probe For EPMA and you will sometimes get this error after clicking the Install button:
(https://probesoftware.com/smf/oldpics/i57.tinypic.com/bitmkh.jpg)
After much investigation we have to admit we do not understand this error (we tried all the suggestions we found after googling this error and nothing seems to fix the issue).
However, if you simply browse to the Probe for EPMA application folder (usually C:\Probe Software\Probe for EPMA) and just double-click the ProbeForEPMA.msi or CalcZAF.msi installer that you downloaded, the msi installer will run fine the 2nd time.
This might be related to recent reports of other Windows installer errors for Skype and Adobe. If you figure out what Microsoft did and know how to fix it, please tell us!
-
For reasons that are not clear to me, the latest update works perfectly on some computers, but on others (with no commonality that I can think of), the update needs to be run twice by clicking the Delete Update button as seen here:
(https://probesoftware.com/smf/oldpics/i58.tinypic.com/2hmkjg4.jpg)
Then just click the Download Update button again.
To make sure that you have the proper update, the version.txt file (accessible from the Help menu also) will have entries dated 12/07/14 or later.
Edit by John: I'm "bumping" the version number from 10.5.4 to 10.5.5 just to insure that the update goes well. The only feature added is an obscure function that is documented here:
https://probesoftware.com/smf/index.php?topic=40.msg138#msg138
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The latest version of Probe for EPMA and CalcImage now include new keywords for the ACQ calibration files. These ACQ calibration files contain stage coordinate calibration information for BMP, JPG and GIF image files. Now these .ACQ files will also contain keV and magnification information as well (if they are beam scan images).
The features affected by this change are the PictureSnap | Save As menu, the Run | Display, Annotate and Export Analog Signal Images menu dialog and the Output | Save Images As BMP Files menu.
This change is implemented to facilitate the loading of beam scan images from the CalcImage | Processing | Calibrate Beam Scan window for beam scan calibration. That is, this information will automatically be loaded to the beam scan image keV and mag text fields when the beam scan image is loaded.
The format of the .ACQ file is now as seen in this example:
[stage]
PictureSnap mode= 0
Number of calibration points= 2
Number of Z calibration points= 0
Screen reference point1 (twips)=7680,5760
Screen reference point2 (twips)=0,0
Stage reference point1=16999.29,-21013.83
Stage reference point2=16756.71,-20830.17
X_Polarity= 0
Y_Polarity= 0
Stage_Units=um
[ColumnConditions]
kilovolts= 15
magnification= 1555
For more information on this cool new way to automatically calibrate your instrument magnification for arbitrary kilovolt settings, see this description here:
https://probesoftware.com/smf/index.php?topic=41.msg2074#msg2074
Edit by John: I also added a scan rotation keyword to the .ACQ files (v. 10.5.7):
[stage]
PictureSnap mode= 0
Number of calibration points= 2
Number of Z calibration points= 0
Screen reference point1 (twips)=7680,7680
Screen reference point2 (twips)=0,0
Stage reference point1=49.9475,50.9015
Stage reference point2=50.7525,50.0985
X_Polarity=-1
Y_Polarity=-1
Stage_Units=mm
[ColumnConditions]
kilovolts= 15
magnification= 400
scanrotation= 9.2
This may be useful as a check when loading beam scan images in the new CalcImage Processing | Calibrate Beam Scan menu described here:
https://probesoftware.com/smf/index.php?topic=396.msg2074#msg2074
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A small change that I think some will appreciate is that I changed the behavior of the "pre-peaking" flags as seen here:
(https://probesoftware.com/smf/oldpics/i58.tinypic.com/k4cdgy.jpg)
so that instead of doing the peaking prior for all elements before the actual sample acquisition (this is for for unknowns only), the program now does the spectrometer peaking for each element "in-line", that is one at a time just before each element is acquired.
The main difference is that only a (fine) ROM spectrometer scan is run instead of all the peaking options. I think this is an improvement.
Of course the pre-peaking is executed only before the first point for each sample is acquired.
-
The latest version of PFE (10.8.5) now has implemented new code for fluorescence by beta lines. This is a significant improvement to the Reed fluorescence method.
To utilize the new fluorescence by beta lines code just check this box as seen here:
(https://probesoftware.com/smf/oldpics/i58.tinypic.com/10yfhid.jpg)
To utilize the new fluorescence by beta lines code as your default, edit this parameters in your Probewin.ini file [software] section:
UseFluorescenceByBetaLinesFlag=-1
-
Hi John,
I just downloaded 10.8.7 yesterday and now I can't change my standards from the default standard with highest intensity. When I change it in standard assignments click ok fine - then I open standard assignments again and it hasn't changed
Thanks
Ben
-
Hi John,
I just downloaded 10.8.7 yesterday and now I can't change my standards from the default standard with highest intensity. When I change it in standard assignments click ok fine - then I open standard assignments again and it hasn't changed
Thanks
Ben
Hi Ben,
Yes, I confirm. Apparently I broke this last weekend as I was prepping for integrating the EDS elements into the Elements/Cations window- a mere slip of the finger! ;) Turns out the standard assignments dialog uses some of the same code as Elements/Cations...
Anyway, I fixed it and it is ready to download now. Sorry for the trouble! :'(
john
-
I recently implemented a new non-linear regression for alpha factor matrix corrections as seen here:
(https://probesoftware.com/smf/oldpics/i60.tinypic.com/c80mx.jpg)
Please note: PFE runs that were previously assigned the calibration curve correction method will now automatically be changed to these new non-linear alpha factors. This is a less than ideal consequence of adding another alpha factor method (in addition to the previous one, two and three regression coefficients) since this new non-linear method utilizes four (yes four!) regression coefficients!
So any existing runs using the calibration curve correction method will have to be switched manually to the calibration curve method using the Analytical | ZAF, Phi-Rho-Z, Alpha Factor and Calibration Curve menu. I am truly sorry about that but there was no other way to do it in the code...
Details regrading this new regression and a short history of these attempts by Ogilvie, Bence, Albee, Rivers, Armstrong are described here:
https://probesoftware.com/smf/index.php?topic=239.msg2763#msg2763
-
Hi John,
did you remove the specified APF factors from the Element/Cations window or move them to another place? I cannot find them anymore and I found them very useful (although the integrated intensity option surely is more rigorous but can't I have both options).
Thanks!
Anette
Edited to add: Ups, found it. You moved it to the top right of the window. All is good. Thanks!
-
Hi John,
did you remove the specified APF factors from the Element/Cations window or move them to another place? I cannot find them anymore and I found them very useful (although the integrated intensity option surely is more rigorous but can't I have both options).
Thanks!
Anette
Edited to add: Ups, found it. You moved it to the top right of the window. All is good. Thanks!
Hi Anette,
Sorry about that but I had to rearrange things a bit for the new WDS/EDX options. I think the new arrangement is better once we all get used to it!
jojn
-
Hi John,
that is fine, I was just blind for a moment. For a second, I worried that you removed a functionality but this is not the PFE way, so not sure why I thought that.
Thanks,
Anette
-
Apparently some people are having trouble updating Probe for EPMA. Here are some explicit instructions:
Open Probe for EPMA by double-clicking the Probe for EPMA icon on your desktop or from the Windows Start button. Once the software launches you will be asked if you want to connect to the instrument. You can click No for connecting to the instrument. Now go to the Help menu and click the Update Probe for EPMA menu as seen here:
(https://probesoftware.com/smf/oldpics/i62.tinypic.com/zlt9g3.jpg)
Note that there is no need to remove your previous version of Probe for EPMA before updating PFE. In fact, we suggest that you *do not* remove PFE prior to updating.
Then click the Download Update button as seen here:
(https://probesoftware.com/smf/oldpics/i62.tinypic.com/2hft578.jpg)
Now wait for several minutes while the latest PFE update downloads. Once the download is complete you will see this:
(https://probesoftware.com/smf/oldpics/i61.tinypic.com/zugr3a.jpg)
If you had a data file open, PFE will prompt you to close it first, but if you didn't open a data file in PFE, the installer will prompt you with this window:
(https://probesoftware.com/smf/oldpics/i59.tinypic.com/25z1mww.jpg)
Just follow the remaining directions in the installer and you will be updated to the latest version of Probe for EPMA! 8)
Please note: unless you are running Windows XP or older, you will have to click Yes on the User Access Control (UAC) dialog to complete the install. It's the law- according to Microsoft.
If you click away from the installer you might have to select the UAC from the task bar as seen here:
(https://probesoftware.com/smf/oldpics/i59.tinypic.com/15ft349.jpg)
-
I found that the easiest installation for version (this goes to!) 11 of Probe for EPMA, is before running the CalcZAF.msi and ProbeForEPMA.msi installers, first delete all desktop and menu shortcuts for all Probe Software apps.
Once you run the new CalcZAF.msi and ProbeForEPMA.msi installers, new menu shortcuts will be created automatically. You'll have to re-create your desktop shortcuts manually if desired.
For some reason, the installers don't remove or replace the old shortcuts... :'(
-
Hi John,
Struggling today. I downloaded the latest PFE 10.9.9 yesterday. But I am now having problems in CalcImage with the quant oxide maps. The totals are less than the individual element oxide totals. So for Calcium hydroxide, I get 70% CaO but a total of 50%. I've recalculated the project on my laptop with PFE 10.9.7. and I get sensible totals. Do you know if you've changed anything that might upset this - or am I doing something stupid.
Thanks
Ben
-
Hi John,
Struggling today. I downloaded the latest PFE 10.9.9 yesterday. But I am now having problems in CalcImage with the quant oxide maps. The totals are less than the individual element oxide totals. So for Calcium hydroxide, I get 70% CaO but a total of 50%. I've recalculated the project on my laptop with PFE 10.9.7. and I get sensible totals. Do you know if you've changed anything that might upset this - or am I doing something stupid.
Thanks
Ben
Hi Ben,
Not that I know of. Ok, I just tried an oxide run and it works fine (open the log window to see the calculations results as the quantification proceeds):
Na Si K Al Mg Fe Ca Mn Ti P O H Total
Weight %: 979 (211,4) 3.29845 31.3922 .720780 11.7624 .032647 .401468 2.69897 .203678 .139854 -.00883 48.8799 .000000 99.5215
Weight %: 980 (212,4) 2.76934 32.3835 .852581 9.66902 .073934 .555545 1.88152 .204453 -.06545 -.00887 47.5982 .000000 95.9138
Weight %: 981 (213,4) 2.02033 37.0464 .704980 6.86879 .144128 .400955 1.20648 .220130 .003332 -.00871 49.9126 .000000 98.5194
Weight %: 982 (214,4) 1.44122 39.3231 .701933 5.09602 .110409 .709962 1.23678 .141067 .071163 -.02037 50.8132 .000000 99.6244
Weight %: 983 (215,4) 1.66466 38.9776 .819676 5.75766 .111931 .308118 1.15845 .162928 -.06485 -.03147 50.8657 .000000 99.7305
Weight %: 984 (216,4) 1.51017 43.6617 1.02181 5.40948 .053808 .400695 .866961 .131934 .071618 -.02015 55.8491 .000000 108.957
Weight %: 985 (217,4) 1.39239 40.9404 .885933 5.58676 .040087 .153872 .867789 .152300 .071972 .008528 52.8013 .000000 102.901
Weight %: 986 (218,4) 2.05945 37.1954 .928486 7.19801 .023321 .431721 1.35110 .137120 .003206 .002638 50.4119 .000000 99.7424
Weight %: 987 (219,4) 1.42849 39.6702 .530955 5.52616 .093580 .401601 .851703 .142047 .071872 -.02572 51.2926 .000000 99.9834
Weight %: 988 (220,4) .876764 41.6110 .322043 3.57161 .197415 .803055 .510864 .243759 .003258 -.03162 51.5540 .000000 99.6622
Weight %: 989 (221,4) .636250 42.8591 .266356 2.66512 .185101 .834001 .429628 .212668 .003286 .008223 52.0854 .000000 100.185
Weight %: 990 (222,4) .437104 41.4851 .127329 1.86113 .117814 .525722 .430092 .069530 .071945 -.00289 49.5644 .000000 94.6873
Weight %: 991 (223,4) .508465 40.9945 .089027 1.93815 .282766 .185396 .640997 .192784 .140511 -.03697 49.2239 .000000 94.1595
Weight %: 992 (224,4) .574218 40.1800 .130278 2.43155 1.05348 1.11075 .669699 .276700 .138733 .002094 49.6237 .000000 96.1912
Weight %: 993 (225,4) .844328 34.8066 .300331 3.76554 2.06298 2.77459 1.71382 .527145 .135120 .022984 46.4724 .000000 93.4258
Weight %: 994 (226,4) 1.87487 30.7206 .767081 6.73338 2.02259 4.28853 2.72552 .490986 .199771 .015888 45.7455 .000000 95.5847
Weight %: 995 (227,4) 2.79331 29.4660 1.06674 9.15421 2.13123 3.60713 2.73010 .253703 .335996 -.01746 46.7072 .000000 98.2281
Weight %: 996 (228,4) 2.80719 29.6150 1.21443 9.58739 1.42697 4.23025 2.74340 .212910 .469921 -.00095 47.1164 .000000 99.4229
Weight %: 997 (229,4) 3.05087 29.0188 1.19110 10.4206 .904456 2.59477 1.98229 .293929 .812400 .005765 46.4031 .000000 96.6781
Weight %: 998 (230,4) 2.50091 27.7767 1.31771 10.0498 1.07634 5.34668 1.48855 .209897 4.01300 .012846 47.3198 .000000 101.112
Weight %: 999 (231,4) 2.00536 25.1349 1.24976 8.27710 2.05486 8.35139 1.30266 .310083 5.94330 -.00774 45.2697 .000000 99.8913
I've seen a situation where CalcImage gets confused and produces low totals- that may be what you are seeing. I don't know what causes it yet, but re-starting CalcImage and re-running the image quant fixes it.
You could also try updating to 11.0.2 and see what that gives you. If you update/try again and are still stuck you'll have to zip the project all up and send it to me.
john
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Hi John,
Struggling today. I downloaded the latest PFE 10.9.9 yesterday. But I am now having problems in CalcImage with the quant oxide maps. The totals are less than the individual element oxide totals. So for Calcium hydroxide, I get 70% CaO but a total of 50%. I've recalculated the project on my laptop with PFE 10.9.7. and I get sensible totals. Do you know if you've changed anything that might upset this - or am I doing something stupid.
Thanks
Ben
Hi Ben,
Ok, I found and fixed the problem with stoichiometric oxygen calculation in both the v. 10.9.9 and v. 11.0.3. It was caused by some code which I had inserted to handle element channels that were disabled for quant in CalcImage (the bug only affected Calcimage). However, the disable quant flag is respected now in any case.
So feel free to update v. 10.9.9 (no version change), or go ahead and manually download v. 11.0.3 and that should fix it also. Note that once you have manually downloaded v. (this goes to) 11 of PFE, you can use the Help | Update Probe for EPMA menu from then on.
john
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The latest version of Probe for EPMA now includes "look and feel" changes to the Output menu, Acquisition Options and Elements/Cations dialogs courtesy of design work by Anette von der Handt.
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Version 11.0.4 is now available for general download from all FTP sites and the Probe Software Update page here:
https://probesoftware.com/Update.html
Details here:
https://probesoftware.com/smf/index.php?topic=40.0
For PFE, you will need to download and install *both* msi files before running the new software!
This new version is in general use at several labs and no one is reporting any issues, but do let us know if you see anything "interesting". Thanks!
john
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Phil Gopon at Madison is testing the new (unreleased as yet) Probe for EPMA, which now includes acquisition and quantification support for six more x-ray lines, specifically, Ln, Lg, Lv, Ll, Mg and Mz.
If you'd like a private copy of this alpha release for Probe for EPMA (and CalcZAF), please contact me directly and I will send you a Dropbox link to download it.
john
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An important note for those updating v. 11.x of PFE.
If you already have version 11.04 (or an earlier 11.x version)of PFE installed on your computer, in addition to updating Probe for EPMA, you *must also* update CalcZAF either using the Help menu in CalcZAF or download the CalcZAF.msi installer from one of our web links or ftp sites.
The reason is that PFE will look for the new x-ray line and fluorescent yield data files and if it doesn't find them, it will create zero size files with those names and then subsequent PFE or CalcZAF updates will not over write these data files (this is in case you decided to edit them for some reason, e.g., missing values).
So just to be sure, it won't hurt to check the ProgramData\Probe Software\Probe for EPMA folder (note that it is a hidden Microsoft folder!) and check for the xline2.dat and xflur2.dat files and see if they are zero bytes. If they are, you must delete them and then re-run the CalcZAF.msi installer. You only need to do this once and only if you see these files listed as zero bytes in size.
Sorry for the trouble, it was an unintended consequence of adding the new L and M x-ray lines for quantification.
Thank-you to Phil Gopon for finding this issue.
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And how would I upgrade my existing xline.dat with all the modifications I did to the new xline2.dat?
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And how would I upgrade my existing xline.dat with all the modifications I did to the new xline2.dat?
The xline.dat is still used for the ka,kb,la,lb,ma,mb lines. No need to "upgrade" anything. The new xline2.dat is used only for the new ln,lg.lv.ll.mg.mz lines.
I should also mention that the current version of PFE now checks for missing/zero size x-ray line files and warns the user if necessary.
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Ok, I see, that is good news. Will you realease a xline2.dat and xflur2.dat file from time to time as it grows?
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Ok, I see, that is good news. Will you realease a xline2.dat and xflur2.dat file from time to time as it grows?
They could "grow" I guess, but they are pretty complete at this time. I don't anticipate needing to update them, so feel free to edit them as you see fit. Here the areas you are interested in:
Table of Emission Energies (KeV)
Element Ln Lg Lv Ll Mg Mz
Po 12.08700 15.74400 16.05500 9.65680 2.82110 1.95360
At 12.47200 16.25100 16.57200 9.89550 2.90850 2.01615
Rn 12.86200 16.77000 17.10200 10.13500 2.99770 2.07955
Fr 13.25800 17.30500 17.64400 10.37600 3.08870 2.14395
Ra 13.66000 17.84900 18.20000 10.62000 3.18120 2.20930
Ac 14.08100 18.40800 18.77000 10.86700 3.27500 2.27550
Th 14.50700 18.98300 19.35400 11.11500 3.36990 2.34275
Pa 14.94500 19.56200 19.95100 11.36400 3.46600 2.41115
U 15.39700 20.16800 20.55700 11.61600 3.56370 2.48090
Np 15.85100 20.76000 21.16300 11.86800 3.66260 2.55080
Pu 16.30500 21.40700 21.76900 12.12200 3.76500 2.62115
Am 16.77800 22.05500 22.37500 12.38100 3.86790 2.69160
Cm
Bk
Cf
Es
Fm
and
Table of Fluorescent Yields
Element Ln Lg Lv Ll Mg Mz
Po .4010 .4010 .4010 .3860 .0060 .0386
At .4150 .4150 .4150 .3990 .0063 .0408
Rn .4290 .4290 .4290 .4110 .0066 .0432
Fr .4430 .4430 .4430 .4240 .0070 .0456
Ra .4560 .4560 .4560 .4370 .0073 .0481
Ac .4680 .4680 .4680 .4500 .0077 .0506
Th .4790 .4790 .4790 .4630 .0080 .0533
Pa .4720 .4720 .4720 .4760
U .4670 .4670 .4670 .4890
Np .4660 .4660 .4660 .5020
Pu .4640 .4640 .4640 .5140
Am .4710 .4710 .4710 .5260
Cm
Bk
Cf
Es
Fm
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OK, I've released v11.06 with support for Ln, Lg, Lv, Ll, Mg and Mz x-ray lines for acquisition and analysis.
Phil Gopon (at Madison) has been running with this new version all week and he says it looks solid with his Fe-Si particle analyses... so update CalcZAF *and* Probe for EPMA and "be the first on your block" to analyze small volumes utilizing the Ln or Ll x-ray lines for 1st row transition metals...
https://probesoftware.com/smf/index.php?topic=40.msg138#msg138
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Can confirm runs great on our SX5. Just a quick note for anyone trying to analyse small volumes, there are three check boxes that you need need need to make sure are checked in PfEPMA. Run in synchronous spectrometer mode (as spectrometer motion causes vibrations), make sure you are running everything as a TDI (as carbon buildup can have a large effect on your emitted X-rays, you can always turn it off if you notice that it isn't a problem for that particular sample), and make sure that PfEPMA does not change the beam or stage conditions prior to an analysis (as any small changes can affect your beam position).
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Gareth Seward noticed that I wasn't saving the carbon calculated by stoichiometry to calculated oxygen (for example, in carbonates), to the classify .DAT files, so I fixed that and also for elements relative to another element. This applies to quant (elemental), atomic, oxide and formula output.
(https://probesoftware.com/smf/oldpics/i59.tinypic.com/2vmsg1h.jpg)
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Please note that the most recent PFE v. 11.07 has an updated "Quick Start" manual (~30 pages), and also an updated "Getting Started" manual (~192 pages), the latter thanks to Karsten (geoman) Goemann.
Both may be accessed from the PFE Help menu after updating Probe for EPMA.
john
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Hi John,
I running v11 and this morning I run update - and on loading the program I get two error windows "InitWindow" and "MoveUpdateFaraday". Within both windows is the same message "Compoenent 'MSCOMCT2.OCX' or one of its dependencies not correctly registered: a file is missing or invalid"
Any suggestions?
Thanks
Ben
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Hi John,
I running v11 and this morning I run update - and on loading the program I get two error windows "InitWindow" and "MoveUpdateFaraday". Within both windows is the same message "Compoenent 'MSCOMCT2.OCX' or one of its dependencies not correctly registered: a file is missing or invalid"
Any suggestions?
Thanks
Ben
Hi Ben,
Yeah sorry, please go back to the previous version of PFE. Just curious... what OS are you running this on?
Find the backup msi file (in C:\ProgramData\Probe Software\Probe for EPMA):
ProbeForEPMA_Backup.MSI
and run that to restore your previous version of Probe for EPMA.
I am replacing some of the legacy controls in the PFE apps and I thought we wouldn't need to do anything special with regard to the installer but apparently we do!
You could also just try this quick fix :
1. Open the command prompt in administrator mode by typing "cmd" in the Start button "Search Programs and Files field, then once the Cmd.exe app appears in the file list, right click the Cmd.exe app and select "Run As Administrator" from the menu.
2. Navigate to “C:\Windows\SysWow64” folder and type this command line:
regsvr32 MSCOMCT2.OCX
That should fix it also.
john
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Thanks John,
Yes, I've already returned to previous version. We've running Windows 7
Ben
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Thanks John,
Yes, I've already returned to previous version. We've running Windows 7
Ben
Hi Ben,
So you didn't try the
regsvr32 MSCOMCT2.OCX
command line?
Interestingly enough, I just installed that same 11.07 version on my SX100 (Win7) computer and I didn't have any problem with the MSCOMCT2.OCX file. I wonder if it's because I also have MS Office on that computer also. Do you?
If you get a chance would you try the latest 11.07 again and this time try the above command line? It would be helpful to know if that helps.
john
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Yeh, I'm afraid I'd downgraded before I saw your message.
That's strange - We have MS office
I don't think i'll be able to try it till end of week/beginning of next.
Just to note you don't see the message unless you tell it to connect to the instrument, I tried it on another computer - running offline no message
Ben
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Yeh, I'm afraid I'd downgraded before I saw your message.
That's strange - We have MS office
I don't think i'll be able to try it till end of week/beginning of next.
Just to note you don't see the message unless you tell it to connect to the instrument, I tried it on another computer - running offline no message
Ben
Hi Ben,
We will fix the installer ASAP, but if anyone wants to manually install the missing file, simply copy the MSCOMCT2.OCX file attached below to your Windows\SysWOW64 folder.
If using Win7 or later, next open a command prompt window in "elevated" mode by typing cmd in the Start button "Search programs and files" field, then when the Cmd.exe file is displayed, right click it and select the Run As Administrator menu. If using WinXP just open a normal command prompt while logged in with an administrative account.
This will usually open a command prompt in the Windows\system32 folder, so then just type cd.. <enter> to change to the Windows folder, and then type cd syswow64 <enter> to change to the SysWOW64 folder and then type:
regsvr32 mscomct2.ocx <enter>
and all should be fine.
Or just wait for Brian and I to add it to the next installer version!
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I encountered the same issue. W8.1
I manually registered the service. PFE now works.
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I encountered the same issue. W8.1
I manually registered the service. PFE now works.
The new components have been added to the latest v. 11.0.8 CalcZAF and PFE installers so now they are registered automatically.
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Gareth Seward had a good idea, and that is that I should also include moving the JEOL EIKS files when updating from v. 10.x to 11.x of PFE.
This is now in the latest version of PFE- 11.1.2
Thank-you Gareth.
Edit by John: I changed my tiny little mind! It makes more sense to simply install the JEOL EIKS files using the PFE and PI (and Thermo NSS and Bruker Esprit) installers, since each app needs their own copy of these JEOL EIKS files in their own application folder anyway (because the JEOL EIKS driver is *not* multi-threaded). And besides only a "trusted" installer can copy files to the Program Files (x86) folder.
The latest version of the ProbeforEPMA.msi installer already has these JEOL EIKS files added and the other installers will follow soon. This change will make JEOL 8230/8530 installations and updates even easier.
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John,
My C: drive crashed so installed a new drive and restored with a disk image. Figuring it would be a good time to upgrade, I downloaded v 11.1.2 (both PfEPMA and CalcZaf) and installed them but nothing would run. When I started probewin, the "Extreme version" splash screen came up both nothing else. I had installed it in the old location C:Probe Software/Probe for EPMA. Since that didn't work, I uninstalled and tried it again, allowing the installer to use the default location of C:Program Files (X86)/Probe Software/Probe for EPMA. Still nothing!! Probewin, CalcZAF, nothing will run past the splash screen. Now I have program files in Program Files(X86) but all the other files, like my std files and dat files, are in C:Program Data/Probe Software/Probe for EPMA. Where should the program be installed?
Following this thread, it looks like there were some problems with registration in Win7 but that is now fixed. Or do I still need to do the command line:
regsvr32 msi.dll ??
Thanks
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John,
My C: drive crashed so installed a new drive and restored with a disk image. Figuring it would be a good time to upgrade, I downloaded v 11.1.2 (both PfEPMA and CalcZaf) and installed them but nothing would run. When I started probewin, the "Extreme version" splash screen came up both nothing else. I had installed it in the old location C:Probe Software/Probe for EPMA. Since that didn't work, I uninstalled and tried it again, allowing the installer to use the default location of C:Program Files (X86)/Probe Software/Probe for EPMA. Still nothing!! Probewin, CalcZAF, nothing will run past the splash screen. Now I have program files in Program Files(X86) but all the other files, like my std files and dat files, are in C:Program Data/Probe Software/Probe for EPMA. Where should the program be installed?
Following this thread, it looks like there were some problems with registration in Win7 but that is now fixed. Or do I still need to do the command line:
regsvr32 msi.dll ??
Thanks
Hi Mike,
First don't panic, we'll get you back up! :)
It's hard to say what exactly is wrong since you've done so many things to the hard drive. You should not have installed v. 11.x to the old folder, but it should not have caused a problem.
I suspect that your basic problem is that you need a new registration because the new hard drive will not be keyed to the existing registration number.
But maybe you should start from scratch, uninstall everything and re-install and follow the directions here for a complete new installation:
https://probesoftware.com/smf/index.php?topic=65.0
But be sure to make copies of your lab specific config files and databases that are listed in the topic.
Attached is an outline of the steps to completely install the software. Can the microprobe specialist that did your installation log in remotely and help you? Who did your installation?
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For those of you with JEOL 8230/8530 instruments, please note that although I've added the JEOL EIKS interface files to the ProbeForEPMA.msi installer (and soon the PI, NSS and Esprit installers), this is really only intended for new installations.
When you update PFE from 10.x to 11.x you will have to manually copy the existing JEOL EIKS files from the old PFE folder
C:\Probe Software\Probe for EPMA
to the new PFE application folder
C:\Program Files (x86)\Probe Software\Probe for EPMA
Why? Because I cannot copy these files from within the PFE app to the Program Files (x86) folder, as I currently do for the config files which are automatically copied to the ProgramData folder. Moving files to the Program Files (x86) requires a "trusted installer" such as ProbeForEPMA.msi or ProbeImage.msi.
So, when you update PFE from 10.x to 11.x you will need to manually move the following files to the new PFE application folder:
eiksJSample.exe
jeoleiks.dll
JeolEIKs.ini
mfc100.dll
msvcr100.dll
It's the law according to JEOL and Microsoft! ::)
Technically you actually only need to move the JeolEIKS.ini file over to the new application folder because the other files will already be installed there, and these other files are not editable.
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This has been mentioned before, but before you install v11 of PFE (when manually updating from v10), it is very helpful to delete all the old PFE icons and Start button PFE menus.
Then once you run the new v11 ProbeForEPMA and CalcZAF msi installers, these new menus will be created automatically.
If you also want desktop icons, just browse to the new PFE application folder (C:\Program Files (x86)\Probe Software\Probe for EPMA) and right click on the exe files you want shortcuts to, select the Create Shortcut menu and the OS will make new icons on the desktop for you.
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The latest version of PFE now saves and restores a number of EDS, CL and imaging parameters when loading a file setup from an old MDB file.
This is important if you switch to a new EDS or CL interface or modify your imaging parameters (for example, the beam scan calibration parameters), and want to use an old MDB file setup but still want to use the new EDS, CL or imaging parameters currently configured on your instrument.
Thanks to Gareth Seward for pointing this out. :-*
Here is the list of parameters I am currently saving and sorry it took so long for me to get around to implementing it! More could be added:
' Load values
tnominalbeam! = NominalBeam!
tNumberOfTunableSpecs% = NumberOfTunableSpecs%
tAutomateNewSampleBasisFlag% = AutomateNewSampleBasisFlag%
tImageDisplaySizeInCentimeters! = ImageDisplaySizeInCentimeters!
tImageInterfaceBeamXPolarity% = ImageInterfaceBeamXPolarity%
tImageInterfaceBeamYPolarity% = ImageInterfaceBeamYPolarity%
tImageInterfaceStageXPolarity% = ImageInterfaceStageXPolarity%
tImageInterfaceStageYPolarity% = ImageInterfaceStageYPolarity%
tImageInterfaceDisplayXPolarity% = ImageInterfaceDisplayXPolarity%
tImageInterfaceDisplayYPolarity% = ImageInterfaceDisplayYPolarity%
tImageInterfaceImageIxIy! = ImageInterfaceImageIxIy!
tEDSSpectraInterfacePresent% = EDSSpectraInterfacePresent%
tEDSSpectraInterfaceType% = EDSSpectraInterfaceType%
tEDSSpectraNetIntensityInterfaceType% = EDSSpectraNetIntensityInterfaceType% ' not stored in MDB file
tEDS_IPAddress$ = EDS_IPAddress$
tEDS_ServicePort$ = EDS_ServicePort$
tNumberOfStageMotors% = NumberOfStageMotors%
tDefaultImageAnalogUnits$ = DefaultImageAnalogUnits$
tImageInterfaceCalNumberOfBeamCalibrations% = ImageInterfaceCalNumberOfBeamCalibrations%
For i% = 1 To MAXBEAMCALIBRATIONS%
tImageInterfaceCalKeVArray!(i%) = ImageInterfaceCalKeVArray!(i%)
tImageInterfaceCalMagArray!(i%) = ImageInterfaceCalMagArray!(i%)
tImageInterfaceCalXMicronsArray!(i%) = ImageInterfaceCalXMicronsArray!(i%)
tImageInterfaceCalYMicronsArray!(i%) = ImageInterfaceCalYMicronsArray!(i%)
tImageInterfaceCalScanRotationArray!(i%) = ImageInterfaceCalScanRotationArray!(i%)
Next i%
tCLSpectraInterfacePresent = CLSpectraInterfacePresent ' not stored in MDB
tCLSpectraInterfaceType% = CLSpectraInterfaceType%
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Thanks John!
I think this has the potential to help people out when doing installs or mods to installations. It also makes it easier to move between EDS+PFE on the same PC and on different PCs and also makes it feasible to easily switch between imaging interfaces e.g. 8x30 people can use the eds imaging hardware to collect faster images for mosaic.
Gareth
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Hi John
Successful upgrade to vers 11. Would it be possible to set up the installer to copy over the required machine specific .dat files during upgrade (scalers, motors and etc)?
Cheers,
Malc.
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Hi John
Successful upgrade to vers 11. Would it be possible to set up the installer to copy over the required machine specific .dat files during upgrade (scalers, motors and etc)?
Cheers,
Malc.
Cool.
Copying these files from the installer is possible, but it was easier to do it automatically from the app the first time it runs.
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For some reason. That didn't happen.
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For some reason. That didn't happen.
The PFE app moves all config files (scalers.dat, probewin.ini, etc), except for the JEOL EIKS files, which have to be moved manually to the Program Files (x86) folder because Microsoft will not allow that from the app level.
In other words, when updating from PFE v. 10.x to v. 11.x, the JEOL 8x30 EIKS files have to be moved manually as stated here:
https://probesoftware.com/smf/index.php?topic=40.msg3677#msg3677
One time only.
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Interestingly enough John.... It happened the other way around. All the EIKS files WERE copied across and none of the others were........... I had to move the .dat ones manually.
Odd...very odd.......
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Interestingly enough John.... It happened the other way around. All the EIKS files WERE copied across and none of the others were........... I had to move the .dat ones manually.
Odd...very odd.......
Odd is an understatement!
Note that the ProbeForEPMA.msi installer will install *default* EIKS files to the new PIE app folder, but one is still required to overwrite the default JeolEIKS.ini file with your site specific file from the old PIE app folder.
John
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The latest version of Probe for EPMA (11.1.7) now has the image shift get/set functions in micron units:
(https://probesoftware.com/smf/oldpics/i65.tinypic.com/ay20d0.jpg)
This has already been the case for Cameca and JEOL 8230/8530 instruments and this change for 8900/8200/8500 instruments has an important implication which I hope to reveal before the end of the year... 8)
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The multi point background (MPB) dialog graphics have been updated:
(https://probesoftware.com/smf/oldpics/i64.tinypic.com/xctcmv.jpg)
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New (multi-standard) Calibration Curve dialog graphics:
(https://probesoftware.com/smf/oldpics/i64.tinypic.com/1z1nc.jpg)
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Nice! It's great that the standard numbers aren't on top of each other anymore.
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Hi John,
I've noticed that since you've upgraded the wavescans and PHA scans to the new graphics (which do look nice) - that when I run through automate - peak and PHA voltage scan after peak - that the PHA scan running for several spectrometers simultaneously is now much slower - its taking 5 minutes to run - with each voltage point taking a long time to acquire. Previously it was just as quick as running them through the PHA menu.
Thanks
Ben
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I've noticed that since you've upgraded the wavescans and PHA scans to the new graphics (which do look nice) - that when I run through automate - peak and PHA voltage scan after peak - that the PHA scan running for several spectrometers simultaneously is now much slower - its taking 5 minutes to run - with each voltage point taking a long time to acquire. Previously it was just as quick as running them through the PHA menu.
Hi Ben,
Actually I think you might be correct! But for the wrong reason- It's got nothing to do with the new graphics and a lot to do with a counting bug that was introduced about 3 months ago in the acquire PHA code.
I found a bug in the count wait code that was returning immediately after the first call even if the specified time hadn't been completed.
The new code fixes that bug and makes sure that you get the full acquisition time specified. If you want to speed things up, just reduce your PHA count time per interval- or reduce the number of PHA intervals.
john
Edit by John: But on thinking a bit more about it, I think I see a better way to parallelize this PHA acquisition. I'm working at Probe Software today, so please give me a few hours to look into it...
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New TDI and Alternating bgd data display dialog graphics:
(https://probesoftware.com/smf/oldpics/i66.tinypic.com/zv4do3.jpg)
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I've noticed that since you've upgraded the wavescans and PHA scans to the new graphics (which do look nice) - that when I run through automate - peak and PHA voltage scan after peak - that the PHA scan running for several spectrometers simultaneously is now much slower - its taking 5 minutes to run - with each voltage point taking a long time to acquire. Previously it was just as quick as running them through the PHA menu.
Hi Ben,
Ok, I modified the PHA acquisition code so all the spectrometers work in parallel now, which greatly speeds up the PHA acquisition.
I didn't notice the problem because on the Cameca we always use the MCA PHA acquisition mode which is super fast compared to the traditional method- though the MCA method is slightly less spectral resolution than the traditional PHA acquisition method by scanning the baseline and window values.
Thanks for catching this! You can download the latest PFE now.
john
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New PHA graphics in the PHA acquire dialog:
(https://probesoftware.com/smf/oldpics/i64.tinypic.com/oktymx.jpg)
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Here's an example of TDI data plotted with the absorbed current option (from Mike Jercinovic, U Mass):
(https://probesoftware.com/smf/oldpics/i67.tinypic.com/2rm155t.jpg)
By the way, I have always been intrigued by the sinusoidal variation in the x-ray intensities in some materials. Also, remember this?
https://probesoftware.com/smf/index.php?topic=144.msg605#msg605
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Some examples of the new Pro Essentials graphics in Standard and Evaluate (see attached images below- remember you need to be logged in to see attachments!).
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I am very pleased to announce that Gareth Seward and I have completed the conversion of all the old graphics calls to the new Pro Essentials graphics calls in CalcZAF, Probe for EPMA and all associated apps. And it only took three months of blood, sweat and tears! ;)
Anyway, here are some links and a few examples of the latest graphics conversions attached below...
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Please note the improved graphics for overlaying wavescan data over the MultiPoint Background intensities as seen here:
(https://probesoftware.com/smf/gallery/395_11_02_16_11_11_09.png)
Let me know what you all think.
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Hi John
Really like the new graphics, they look snazzy. I also like that the sample numbers don't sit on each other in the MAN box. Is there a reason I can't zoom in on areas with the mouse click/drag box on the MAN review window now? I can still do this on the Plot window fine, just don't seem to be able to do it in the MAN box...
cheers
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Hi John
Really like the new graphics, they look snazzy. I also like that the sample numbers don't sit on each other in the MAN box. Is there a reason I can't zoom in on areas with the mouse click/drag box on the MAN review window now? I can still do this on the Plot window fine, just don't seem to be able to do it in the MAN box...
cheers
Hi Ben,
Thank-you!
Indeed. I never thought anyone would want to zoom there, but sure- why not add zoom to the MAN plot? It's a few lines of code and a button for "zoom full".
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Hi John
Really like the new graphics, they look snazzy. I also like that the sample numbers don't sit on each other in the MAN box. Is there a reason I can't zoom in on areas with the mouse click/drag box on the MAN review window now? I can still do this on the Plot window fine, just don't seem to be able to do it in the MAN box...
Hi Ben,
The latest version of Probe for EPMA (v. 11.3.3) has zoom capability in the MAN fit plot dialog as seen here:
https://probesoftware.com/smf/index.php?topic=71.msg4069#msg4069
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I added an Output All button as seen here for the thin film output:
(https://probesoftware.com/smf/gallery/1_12_02_16_6_06_58.png)
This feature then automatically selects each multi-voltage acquisitions with the same name and exports the k-ratios and film geometry for thin film quantification.
This will greatly speed up thin film reprocessing I suspect.
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Hi John
Really like the new graphics, they look snazzy. I also like that the sample numbers don't sit on each other in the MAN box. Is there a reason I can't zoom in on areas with the mouse click/drag box on the MAN review window now? I can still do this on the Plot window fine, just don't seem to be able to do it in the MAN box...
Hi Ben,
The latest version of Probe for EPMA (v. 11.3.3) has zoom capability in the MAN fit plot dialog as seen here:
http://probesoftware.com/smf/index.php?topic=71.msg4069#msg4069
Awesome, thanks. I find it handy if I can zoom in to the lower Z end of the spectrum to see how good the fit is when you are dealing with low level elements and using MAN.
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Hi John
Really like the new graphics, they look snazzy. I also like that the sample numbers don't sit on each other in the MAN box. Is there a reason I can't zoom in on areas with the mouse click/drag box on the MAN review window now? I can still do this on the Plot window fine, just don't seem to be able to do it in the MAN box...
Hi Ben,
The latest version of Probe for EPMA (v. 11.3.3) has zoom capability in the MAN fit plot dialog as seen here:
http://probesoftware.com/smf/index.php?topic=71.msg4069#msg4069
Awesome, thanks. I find it handy if I can zoom in to the lower Z end of the spectrum to see how good the fit is when you are dealing with low level elements and using MAN.
I understand.
Or what I do is to analyze a low Z pure oxide that is not used in the MAN fit to check for zero. In others words, a blank standard. If the blank matrix is similar to one's unknown, then it is a robust check.
What is your matrix?
john
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In version 11.4.0 of Probe for EPMA I modified the MAN dialog to automatically load all MAN elements for all keVs in the run. This way, combined condition samples using MAN backgrounds now get handled automatically. Thank-you Anette!
Here you can see that I've removed the "Re-Load" button and associated takeoff and keV controls and added a column for KeV:
(https://probesoftware.com/smf/gallery/1_27_02_16_10_26_40.png)
Note that both the element takeoff and keV are now stored in the MAN table so one can have different curves for the same element setup at different keVs.
I also added a new keyword to the Probewin.ini which defines the Thermo NSS version number. The program will assume v. 3 of NSS but warns you the first time in case someone out there is still using NSS v. 2.x. Thank-you Ken.
I also (again thanks to Ken) now check if a point deleted in an unknown sample is being used for any blank corrections, and if so it forces a re-calculation of the blank sample on the next analysis.
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Anette made a comment about the Plot button in the Automate! window and I took a look and decided I could plot up position samples up much better with the new library.
Attached below (be sure to login to see attachments) are some screen shots of the new position plot graphics.
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I just made a slight change in the nominal interference calculation code to add the effect of lower resolution at lower sin thetas in the Gaussian peak width calculation.
Please check the on-peak and the off-peak nominal interference calculations in the Standard Assignments and Elements/Cations dialogs (respectively). So update PFE and let me know if you think the nominal interference calculations are more accurate now.
Basically the code wasn't catching the Ti Ka interference on Cs La at low sin thetas on a PET crystal and so this new code should handle these situations better.
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All,
I have been forced to make a change to the code that I did not want to do. It only affects Windows XP (or older) computers running the software when connecting to the instrument (it will not affect running PFE off-line for reprocessing data), but still a hassle and I apologize in advance for your trouble.
The bottom line is that if you are running XP or older and update PFE (to v. 11.8.7) and try to connect to your instrument, PFE will prompt you for a new registration code and you will have to send that to me (or your probe software support person), and I (or they) will generate a new unlock code for you. For general ease of use please utilize the copy button in the Registration dialog to send me the code so typos are kept to a minimum. You should probably wait to update PFE until you think I (or your probe software support person) are awake and able to respond to email. If necessary of course you can call probe software directly by phone and we can get you up and running immediately.
For reasons that I am sure are reasonable to Microsoft but a mystery to me, when a 32 bit app asks what operating system it is running on, Windows 8 and Windows 10 report that the operating system is Win NT and Win XP, respectively. This causes a problem for where to store the copy protection file as the system folders in new operating are now generally off limits to apps.
So I've had to "bit the bullet" and change the code to always store the copy protection file in a place where all operating systems can write it. This means the common app data folder and unfortunately this means that Win XP or older systems will require a new registration number to connect to the instrument.
Again I apologize and hope this doesn't cause too much trouble for those still running Windows XP (or older) operating systems.
john
Remember, if you have Probe Image, you'll need to copy the new xline.dll file to the Probe Image common app data folder:
Windows XP (and older):
C:\Document and Settings\All Users\Application Data\Probe Software\Probe for EPMA
C:\Document and Settings\All Users\Application Data\Probe Software\Probe Image
Please note that these folders may be "hidden" and will need to be made visible using the folder options...
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The latest versions of PFE, CalcImage, etc. have improved performance- up to 10x faster for many operations. Please update using the Help menu and let me know what you find on your computer(s).
john
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The latest version of PFE now loads the Bruker and Thermo maximum high energy cutoff and throughput defaults from the Probewin.ini file.
For a Thermo EDS the keywords in the [hardware] section would look like this:
MaxEnergyArraySize=6
MaxEnergyArrayValue1="5"
MaxEnergyArrayValue2="10"
MaxEnergyArrayValue3="20"
MaxEnergyArrayValue4="40"
MaxEnergyArrayValue5="80"
MaxEnergyArrayValue6="0"
MaxThroughputArraySize=11
MaxThroughputArrayValue1="200"
MaxThroughputArrayValue2="400"
MaxThroughputArrayValue3="600"
MaxThroughputArrayValue4="800"
MaxThroughputArrayValue5="1000"
MaxThroughputArrayValue6="1600"
MaxThroughputArrayValue7="2000"
MaxThroughputArrayValue8="3200"
MaxThroughputArrayValue9="4000"
MaxThroughputArrayValue10="6400"
MaxThroughputArrayValue11="0"
Note that a value of "0" (zero) means auto mode. For quantification of EDS spectra I would suggest keeping a fixed throughput for both the standards and unknowns. I talked with Keith Thompson on this and he said yes, one should use the same time constant for both standards and unknowns, but he mentioned that they have found that quantification works surprisingly well, even when the throughput is set to auto. Just not quite as well.
For Bruker use this setup:
MaxEnergyArraySize=4
MaxEnergyArrayValue1="10"
MaxEnergyArrayValue2="20"
MaxEnergyArrayValue3="40"
MaxEnergyArrayValue4="80"
MaxThroughputArraySize=4
MaxThroughputArrayValue1="275"
MaxThroughputArrayValue2="130"
MaxThroughputArrayValue3="90"
MaxThroughputArrayValue4="60"
If these keywords are missing from the Probewin.ini file, the above values will get loaded automatically. The only reason for having these keywords explicitly in your Probewin.ini is perhaps just in case you wanted to customize the list by leaving some values out to force some user behavior.
john
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All,
Probe for EPMA version 11.9.5 has additional performance improvements.
Ready to download now from Help menu.
john
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The latest version of Probe for EPMA now includes a new text control in the Acquisition Options dialog, for the user to specify the "nominal" dead time of the EDS system as seen here:
(https://probesoftware.com/smf/gallery/1_06_08_17_4_23_37.png)
By "nominal" we mean the approximate EDS dead time in percent. The default is 50% and please note that this text control cannot be edited in demo (simulation) mode as the Penepma based Monte Carlo EDS "acquisition" has no dead time!
This nominal dead time value is stored in your current probe run MDB file, but is only utilized to estimate the acquisition time for the EDS system.
john
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The latest version of Probe for EPMA (v. 11.9.9) now includes updated CalcImage presentation output scripts, which are compatible with Surfer v. 14.
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Thanks to a suggestion from Paul Carpenter, the latest version of Probe for EPMA now reads the specified formula parameters from the standard database and loads them automatically, if this is the first time that standard number has been loaded into the current run. This applies to both the New Sample Setup dialog and also the Automate! window.
If the standard has already been loaded, the program utilizes the formula parameters of that previous standard sample number in the current run.
The idea being that, for example, some may want to have the number of cations set to 3 or the number of oxygens set to 4 for olivine standards. Then when the standard is subsequently "analyzed" from the Analyze! window, one can more easily ascertain the quality of the standard acquisition.
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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).
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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:
(https://probesoftware.com/smf/gallery/1_14_10_17_4_41_06.png)
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
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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
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The latest version of Probe for EPMA now displays the EDS sample count time in the Acquire! | Acquisition Options dialog as shown here:
(https://probesoftware.com/smf/gallery/1_05_11_17_8_07_16.png)
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.
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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:
(https://probesoftware.com/smf/gallery/1_05_11_17_3_01_48.png)
john
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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.
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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.
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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.
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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:
(https://probesoftware.com/smf/gallery/1_08_03_18_5_00_10.png)
Here is the PFE menus with the <alt> key pressed:
(https://probesoftware.com/smf/gallery/1_08_03_18_5_00_26.png)
In this example, the user typed <alt> h and the Help menu is now visible:
(https://probesoftware.com/smf/gallery/1_08_03_18_5_00_47.png)
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:
(https://probesoftware.com/smf/gallery/1_08_03_18_5_06_46.png)
Look in the menus for other <ctrl> shortcuts.
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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:
(https://probesoftware.com/smf/gallery/1_03_04_18_1_27_43.png)
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.
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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.
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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
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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.
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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):
(https://probesoftware.com/smf/gallery/1_04_06_18_2_35_05.png)
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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.
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And it works!
(https://probesoftware.com/smf/gallery/17_26_06_18_6_18_54.jpeg)
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We've been negligent and not documented (in this topic), changes to the software for more than a month. :o
So that is now remedied:
https://probesoftware.com/smf/index.php?topic=40.0
We've just been so much fun improving Probe for EPMA and PictureSnapApp that it slipped our minds...
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This is a tiny tweak, but it bothered me so we fixed it.
Basically when one plots a set of X/Y coordinates in the Digitize Grid or Digitize Polygon dialogs., the software used to just fix the min/max of the X/Y data.
But that could distort the layout if the X/Y points were not equant in extents. So in the previous version you'd get this plot where the shape is made to look square by utilizing the actual X/Y data ranges:
(https://probesoftware.com/smf/gallery/1_21_07_18_2_11_33.png)
But in reality (since most X/Y stages in the world are equal units in X and Y!), it now plots like this:
(https://probesoftware.com/smf/gallery/1_21_07_18_2_11_54.png)
Of course one can still zoom in using a click-drag on the mouse, but it least the plot starts with equal distance in X and Y so as not to distort the initial plot.
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Lots of changes over the last month that we wanted to test carefully before releasing a new version, but our beta testers report that all seems to be working well, so Probe for EPMA v. 12.5.1 is now available for download/updating. The easiest method is to simply use the Help | Update Probe for EPMA menu in Probe for EPMA.
If you have any trouble updating PFE it's probably because of the switch to secure downloads in August this last summer. To fix this update issue, see this post here and follow the instructions:
https://probesoftware.com/smf/index.php?topic=233.msg7513#msg7513
OK, so first of all, we found and fixed a bug in the multi-point background (MPB) when utilizing the shared background method on samples with hundreds of data points. This bug was causing the software write duplicate MPB intensity data to the database, causing the software to slow down when reading sample data. That has now been fixed. See this post for more details:
https://probesoftware.com/smf/index.php?topic=9.msg7764#msg7764
Next we modified the way the Use EDS Element Data flag is utilized in the Analyze! | Calculation Options dialog as shown here:
(https://probesoftware.com/smf/gallery/1_03_11_18_5_27_52.png)
Basically this flag now turns EDS elements on or off for quantification. You will also note that we replaced the two EDS option buttons with a single checkbox for a cleaner look.
In addition to skipping the loading of the EDS net intensities for quant analysis, this flag now enables or disabled any elements that are specified as EDS quant elements if the user changes the status of this flag. So for example, here is an acquisition of WDS and EDS quant on a NIST mineral glass where some elements were acquired using WDS, and some elements using EDS with new flag checked:
ELEM: Si Ca Fe Mg Al Mn O
TYPE: ANAL ANAL ANAL ANAL ANAL SPEC SPEC
BGDS: LIN LIN EDS EDS EDS
TIME: 20.00 20.00 24.00 24.00 24.00 --- ---
BEAM: 30.02 30.02 30.02 30.02 30.02 --- ---
ELEM: Si Ca Fe Mg Al Mn O SUM
5 21.419 11.064 6.588 11.569 4.874 .077 43.597 99.189
AVER: 21.419 11.064 6.588 11.569 4.874 .077 43.597 99.189
SDEV: .000 .000 .000 .000 .000 .000 .000 .000
SERR: .000 .000 .000 .000 .000 .000 .000
%RSD: .00 .00 .00 .00 .00 .00 .00
PUBL: 21.199 10.899 7.742 11.657 4.906 .077 43.597 100.077
%VAR: 1.04 1.52 -14.91 (-.75) (-.64) .00 .00
DIFF: .220 .165 -1.154 (-.09) (-.03) .000 .000
STDS: 162 162 162 160 160 --- ---
Edit: in case anyone is wondering why the above Fe quant by EDS looks so crappy, it's because the WDS counting time was only 24 sec, so the EDS live time was half that (with a 50% deadtime in this simulation). And so running the Penepma Monte Carlo code for the simulated EDS spectrum only ran for 12 seconds! And for an element such as Fe with a relatively high energy edge, the counting statistics are really poor. I'll post an example later today with a longer counting and more than a single "measurement" to show this better.
And here with the flag unchecked:
ELEM: Si Ca Fe Mg Al Mn O
TYPE: ANAL ANAL ANAL ANAL ANAL SPEC SPEC
BGDS: LIN LIN EDS EDS EDS
TIME: 20.00 20.00 --- --- --- --- ---
BEAM: 30.02 30.02 --- --- --- --- ---
ELEM: Si Ca Fe-D Mg-D Al-D Mn O SUM
5 19.430 11.173 --- --- --- .077 43.597 74.277
AVER: 19.430 11.173 --- --- --- .077 43.597 74.277
SDEV: .000 .000 --- --- --- .000 .000 .000
SERR: .000 .000 --- --- --- .000 .000
%RSD: .00 .00 --- --- --- .00 .00
PUBL: 21.199 10.899 n.a. n.a. n.a. .077 43.597 100.077
%VAR: -8.34 2.52 --- --- --- .00 .00
DIFF: -1.769 .274 --- --- --- .000 .000
STDS: 162 162 --- --- --- --- ---
Note that the elements by EDS have been "disabled". However, even though this flag for using EDS elements for quant is unchecked, one can still obtain the EDS net intensities using the Raw Data button as seen here:
On-Peak (off-peak corrected) or EDS (bgd corrected) or MAN On-Peak X-ray Counts (cps/1nA) (and Faraday/Absorbed Currents):
ELEM: si ka ca ka fe ka mg ka al ka BEAM1 BEAM2
BGD: OFF OFF EDS EDS EDS
SPEC: 1 2 0 0 0
CRYST: PET LPET EDS EDS EDS
ORDER: 1 1 1 1 1
5G 56.93 33.28 2.82 22.62 9.75 30.016 29.974
AVER: 56.93 33.28 2.82 22.62 9.75 30.016 29.974
In addition, the software now automatically turns on this flag when EDS elements are added to the sample. Also, it sets another flag to automatically force re-loading of the standard intensity arrays for quantitative analysis the next time a quant is performed. These changes should not only make it much easier to perform WDS and EDS quant, but also allows the user to "turn off" any EDS elements without having to go into the Elements/Cations dialog and set the enable/disable flag for each EDS element. Of course one can still do that, but this new change makes it much easier. And we like easy!
Oh, and I almost forgot, the software now automatically disables the TDI option for elements acquired using EDS spectra. This was a bug where the software would turn on TDI for all elements that were acquired first on each spectrometer, which included elements by EDS, and then one had to go in and turn off the TDI correction for the EDS elements manually. So now this is handled automatically!
Furthermore there is now a new global flag that completely turns off the EDS get net intensity interface, as seen here:
(https://probesoftware.com/smf/gallery/1_03_11_18_5_28_16.png)
This new flag could be useful if you have some samples with some elements (minor elements?) quantified using EDS, but where you need to process the data away from the lab and don't have access to EDS software or server. Fortunately one can install the Thermo or Bruker software for off-line processing on any computer, so this shouldn't really be a problem.
But it may be helpful for the upcoming JEOL EDS API, because the JEOL EDS API only accesses the JEOL server on the JEOL EPMA computer, where the original EDS spectrum file is stored, in order to obtain the EDS net intensities. We are hopeful that eventually we can persuade JEOL to provide an off-line version of their peak stripping program and have it utilize the already stored EDS spectrum in our database for the reprocessing of JEOL EDS spectra on off-line computers that are not on the JEOL instrument network.
We also replaced the Acquire EDS (and CL) spectra option controls with checkbox controls , again, for a cleaner look as seen here in the Acquisition Options dialog:
(https://probesoftware.com/smf/gallery/1_03_11_18_5_28_05.png)
I think that is all for now. So please update Probe for EPMA to v. 12.5.1 when you are ready to, and feel free let us know how everything works. We love hearing from our users! :)
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This is a small thing, but we noticed recently that when plotting up multiple position samples from the Automate! window, the display could be better.
So the latest version of Probe for EPMA (12.5.6) now has improved code to plot multiple samples positions using the Plot button from the Automate! window as seen here:
(https://probesoftware.com/smf/gallery/1_27_12_18_9_06_51.png)
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We recently improved the display of the stage limits in PictureSnapApp when the sample is rotated with respect to the image, as described here:
https://probesoftware.com/smf/index.php?topic=1177.0
And in the latest version of Probe for EPMA we also added support for display of rotated stage limits in the PictureSnap feature in Probe for EPMA:
(https://probesoftware.com/smf/gallery/1_20_02_19_12_45_22.png)
If you look really close you can see that the stage limits (in yellow) are rotated very slightly in the image (about 0.6 degrees).
Also FYI, we fixed a minor bug in the MPB background method (in the Elements/Cations dialog), and improved a warning message for the spectral interference correction as suggested by Owen Neill and Probeman, and described in the latest of the version.txt file available in the current update and also here:
https://probesoftware.com/smf/index.php?topic=40.0
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Late last year we modified the TDI acquisition code to *not* automatically turn on TDI corrections for EDS elements. Eventually we may add TDI corrections for EDS elements to Probe for EPMA, but currently this capability is not available.
Recently Owen Neill reported that one of his users was getting an error message for an unknown sample that there was no TDI data for an EDS element, and that turning off the Use TDI Intensities option for the EDS element did not prevent the error message.
The problem turned out to be that one of the primary standards assigned to this unknown sample also had the Use TDI Intensities option turned on, and that was the actual culprit causing the error message. The difficulty was that the error message reported the sample row number, along with the data row and channel number, which isn't as user friendly as it could be.
To alleviate this misunderstanding for users (especially those processing old probe runs with both TDI and EDS spectrum acquisitions), we added additional information with regards to the actual sample name, etc. which is causing the error message as seen here:
(https://probesoftware.com/smf/gallery/1_02_03_19_10_18_53.png)
This should help in the future. Download now using the Help | Update Probe for EPMA menu for this latest version of Probe for EPMA.
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The latest version of Probe for EPMA (12.6.9) now requires the v. 2.46 of the Ocean Optics OMNI driver for integration of CL spectrum acquisition.
This is because previous versions of the Ocean Optics OMNI driver were not properly signed for Windows 10. The v. 2.46 Ocean Optics OMNI driver is properly signed for Windows 10 (and Windows 8.x if anyone is still using that!).
Please contact support@probesoftware if you have any questions about our integration of EDS and/or CL spectrum acquisition. Or post them here if you prefer.
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As suggested by Dave Adams at the USGS Denver, we added an option to the user specified output that converts all the column headings to be "machine readable". Apparently this means no "special" characters such as spaces, commas, colons, percent signs, etc.:
(https://probesoftware.com/smf/gallery/1_05_09_19_4_06_51.png)\
Download v. 12.7.3 of PFE to get this mod. Also see first post in this topic for additional changes to the program.
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As many of you know Probe for EPMA can acquire EDS spectra from Bruker and Thermo SDD EDS detectors and store the spectra in the user's probe data (MDB) file for subsequent quantitative processing of WDS and EDS (or EDS only) elements for unknown and standard samples. We are currently beta testing the EDS spectra interface to JEOL SDD EDS detectors and it is looking good.
Also, as you all know, Probe for EPMA can be freely installed on any computer or laptop, for performing WDS data analysis and output simply by copying your probe data file over to the off-line computer.
In addition, Probe for EPMA can also reprocess EDS spectra for quantitative analysis of elements by EDS for off-line analysis on other computers, but until now this has required that the Thermo or Bruker software also be installed (in addition to the Probe for EPMA software), on the off-line computer or laptop for obtaining the EDS net intensities for quantification of unknowns and standards.
We feel this it is good to get the net intensities from the EDS software because the peak stripping procedures are best performed by the OEM routines. And because Thermo, and more recently Bruker, now also allow their software to be installed on any computer for off-line processing, this provides fantastic portability for your EPMA WDS and EDS data.
Unfortunately reprocessing of JEOL EDS spectra requires access to the original EDS file saved on the JEOL EPMA computer connected to the instrument, which is generally not available to off-line computers in your office or home.
To avoid getting an error when performing elements quantified by EDS on an off-line computer when the Bruker, Thermo or JEOL software is unavailable, the user would have to either disable those elements for quantification in the Analyze! window from the Elements/Cations dialog, or use this checkbox in the Analytical | Analysis Options menu dialog, which then tells PFE to skip accessing the EDS interface, and then all elements by EDS would return a zero intensity/concentration:
(https://probesoftware.com/smf/gallery/1_18_09_19_1_03_00.png)
Not an altogether satisfactory solution actually.
Meanwhile, Gareth Seward and several others had a bright idea. Why not somehow store these returned EDS net intensities so that they can be accessed locally from Probe for EPMA even if the Thermo, Bruker or JEOL software is not available, and after a bit of thought, we think we have found a solution.
The trick was to utilize the same database tables already used in simulation mode for acquisition of EDS spectra from the Penepma Monte Carlo simulations. If you haven't tried the simulated EDS acquisition and quantification in Probe for EPMA, see here for more details:
https://probesoftware.com/smf/index.php?topic=837.msg7796;topicseen#msg7796
Basically when Penepma calculates a spectrum, it automatically generates a file called pe-intens-01.dat, which contains the photon intensities for any inner shell emissions that occur during the simulation. These are in fact the emission line net intensities. So there is no need to "peak strip" the Penepma spectrum, because Penepma already knows where each photon came from! We did have to deal with a calculation of the continuum intensities for each emission line to provide realistic statistics however.
Anyway, starting in PFE v. 12.7.5 whenever we obtain the net intensities for an element quantified by EDS from the Bruker, Thermo or JEOL software, we automatically store those net intensities in the same database table used by Penepma. It's so *simple*! ;D
So as long as the elements by EDS were specified when Probe for EPMA was connected to the Bruker, Thermo or JEOL software, those EDS net intensities will be available for off-line use on any computer, even without the Bruker, Thermo or JEOL software. All one needs to do is to check this new box in the Analytical | Analysis Option menu dialog as seen here:
(https://probesoftware.com/smf/gallery/1_18_09_19_1_03_17.png)
Now there is one caveat when using this feature. And that is, if one adds a *new* element to be quantified by EDS on the off-line computer, and that computer is not running the Bruker or Thermo software, or is not connected to the JEOL probe computer, those net intensities will always return zero net intensities and hence concentrations.
That is, until that probe data MDB file is re-opened on a computer running or connected to the Bruker, Thermo or JEOL computer and the Use Stored EDS Net Intensities checkbox is unchecked. Then the stored net intensity table will be updated again.
But there is one other major benefit of this checkbox. Once these net intensities are obtained and stored, one simply checks the Use Stored EDS Net Intensities checkbox, and now the calculations will proceed lightning fast because the net intensities are already extracted and locally available.
Oh, and by the way, this table is available for *all* Probe for EPMA MDB data files since version 11.78! It's actually backward compatible! Who would have thunk it?
Try this new feature out on an older PFE data file (v. 11.78 or newer) containing EDS spectra and elemnts to be quantified by EDS, using the latest v. 12.75 of PFE. To update the stored net intensity tables, simply open the old MDB file on your probe computer or any computer running the Bruker, or Thermo software or connected to the JEOL probe computer, go to the Analyze! window, select all samples, and click the Raw Data button. The software will output all WDS and EDS sample data to the log window, but in the background it will be saving all net intensities automatically.
Then go to the Analytical | Analysis Options menu dialog and check the Stored EDS Net Intensities checkbox. Now analyze some samples and see how fast it performs the quant calculation.
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We need to apologize to everyone who has utilized any of the 10 different matrix corrections in Probe for EPMA other than the default "Phi(pz) Absorption of Armstrong/Packwood-Brown 1981 MAS" in any complex probe runs.
Philipp Poeml wrote to us recently saying that the analysis calculations were running very slowly, so we asked him to send the an example data file with the issue. When we loaded it up and clicked the Analyze button on a sample, we saw that he had around 25 elements and as many standards, so the std k-factor calculation indeed took some time (particularly because he had duplicate elements and in this situation PFE has to calculate each emission line separately for the standard k-factors to be accurate).
But then we said, well, once these std k-factors are calculated it will go much faster, so after the std k-factors were calculated we again clicked the Analyze button and to our amazement we saw the program *again* calculate all the std k-factors!
Now if you're running say 10 or 12 elements and 8 or 10 standards you're probably not even going to notice as the calculation normally goes pretty fast, but with this 25 elements and this many standards (and because there were duplicate elements), it takes a bit of time. But why was it re-calculating the standard k-factors again? It should only have to do re-calculate the standard k-factors if one selects a different matrix correction method!
But in looking at the code we immediately saw the problem and it has to do with the option to "Calculate All Matrix Corrections" in the Analyze! window. Even though we weren't calculating all matrix corrections! Basically, if the current matrix correction is the default "Phi(pz) Absorption of Armstrong/Packwood-Brown 1981 MAS", the flag works just fine, and the code skips re-calculating the matrix corrections (unless of course the analyzed elements are different for example). But if you are using another matrix correction for the default matrix correction, such as PAP or XPP, it was resetting a flag to force a re-calculation of the std k-factors!
Again, we're very sorry about this, but if you update to PFE v. 12.7.6 you should see a significant improvement in analysis speed particularly for large runs with lots of elements and standards. That is if you're not using the default Armstrong pr(z) matrix correction.
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Hi John,
"we" is you and Probeman? :P
Why would duplicate elements make the calculation especially slow? You mention that several times in your post.
Cheers
Philipp
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Hi John,
Why would duplicate elements make the calculation especially slow? You mention that several times in your post.
Cheers
Philipp
The calculation of standard k-factors with duplicate elements isn't "especially slow", maybe a little slower. What you and I were seeing in your run is mostly an effect from having lots of elements and lots of standards. And of course the calculate std k-factors flag getting reset each time... which is now fixed.
The reason one has to calculate the standard k-factors differently when duplicate elements are present is that if one includes concentrations from duplicate elements, the composition will be non-physical and the wrong std k-factors will get calculated. The same thing occurs of course for the unknown sample, but it doesn't affect things much if the duplicate elements are present in trace concentrations.
In the case of (primary) standards however, our trace element is usually present in high concentrations, therefore instead of calculating the emission physics for all elements in the standard at once, the program calculates the std k-factors for each standard in an element loop where only one element at a time is specified as an emitter, and the other elements are set to "specified" concentrations.
The latest code always is on Github but I paste it here also. Here is the code when no duplicate elements are present:
Sub UpdateCalculate(row As Integer, num As Integer, analysis As TypeAnalysis, sample() As TypeSample, stdsample() As TypeSample)
' Loads a single standard stdsample array and calculates k-ratios
' "row" is the standard position in the standard list
' "num" is the standard number
ierror = False
On Error GoTo UpdateCalculateError
' New std k-factor calculation code for samples with duplicate elements (with different x-ray lines or different kilovolts!)
If MiscIsElementDuplicatedAndXrayOrKilovoltsDifferent(sample()) Then
Call UpdateCalculate2(row%, num%, analysis, sample(), stdsample)
If ierror Then Exit Sub
Exit Sub
End If
' Update the standard for current sample conditions
Call UpdateCalculateUpdateStandard2(num%, sample(), stdsample())
If ierror Then Exit Sub
' Reload the element arrays for the current sample
If sample(1).LastElm% > 0 Then
Call ElementGetData(sample())
If ierror Then Exit Sub
' Calculate the standard k factors for this standard (also calculate ZAF for calibration curve for demo mode)
If CorrectionFlag% = 0 Or CorrectionFlag% = 5 Then
Call ZAFStd2(row%, analysis, sample(), stdsample())
If ierror Then Exit Sub
ElseIf CorrectionFlag% = MAXCORRECTION% Then
'Call ZAFStd3(row%, analysis, sample(), stdsample())
'If ierror Then Exit Sub
End If
' Calculate the standard beta factors for this standard (0 = phi/rho/z, 1,2,3,4 = alpha fits, 5 = calilbration curve, 6 = fundamental parameters)
If CorrectionFlag% > 0 And CorrectionFlag% < 5 Then
Call AFactorStd(row%, analysis, sample(), stdsample())
If ierror Then Exit Sub
End If
End If
Exit Sub
' Errors
UpdateCalculateError:
MsgBox Error$, vbOKOnly + vbCritical, "UpdateCalculate"
ierror = True
Exit Sub
End Sub
Here is the version for when duplicate elements are present:
Sub UpdateCalculate2(row As Integer, num As Integer, analysis As TypeAnalysis, sample() As TypeSample, stdsample() As TypeSample)
' Loads a single standard stdsample array and calculates k-ratios (version to handle duplicate elements)
' "row" is the standard position in the standard list
' "num" is the standard number
ierror = False
On Error GoTo UpdateCalculate2Error
Dim chan As Integer, i As Integer, j As Integer, ip As Integer
' Get standard composition and cations from the standard database and load in stdsample arrays
If num% > 0 Then
Call StandardGetMDBStandard(num%, stdsample())
If ierror Then Exit Sub
' Load standard as unknown composition if stdnum is zero (random composition)
Else
Call StandardGetMDBStandard(num%, sample())
If ierror Then Exit Sub
stdsample(1) = sample(1)
End If
' Loop on each analyzed element in original sample and load standard composition
For chan% = 1 To sample(1).LastElm%
' Skip disable quant element
If sample(1).DisableQuantFlag%(chan%) = 0 Then
' Skip duplicate element
ip% = IPOS8A(chan%, sample(1).Elsyms$(chan%), sample(1).Xrsyms$(chan%), sample(1).KilovoltsArray!(chan%), sample()) ' find if element is duplicated
If Not UseAggregateIntensitiesFlag Or (UseAggregateIntensitiesFlag And ip% = 0) Then
' Loop on each analyzed element in original sample and calculate standard k-factors *one element at a time*
If VerboseMode% Then
msg$ = vbCrLf & vbCrLf & "Calculating standard k-factors for " & Str$(chan%) & " " & sample(1).Elsyms$(chan%) & " " & sample(1).Xrsyms$(chan%) & ", " & Str$(sample(1).MotorNumbers%(chan%)) & " " & sample(1).CrystalNames$(chan%) & ", " & Format$(sample(1).TakeoffArray!(chan%)) & " " & Format$(sample(1).KilovoltsArray!(chan%))
Call IOWriteLog(msg$)
End If
' Load passed sample into temp std sample
UpdateStdSample(1) = sample(1)
' Now zero out concentrations (in case any are loaded) and specifiy as fixed concentrations
For i% = 1 To UpdateStdSample(1).LastChan%
UpdateStdSample(1).ElmPercents!(i%) = NOT_ANALYZED_VALUE_SINGLE! ' use a non-zero value
Next i%
If VerboseMode% Then
msg$ = vbCrLf & "Standard " & Format$(num%) & ", (original sample):"
Call IOWriteLog(msg$)
For i% = 1 To UpdateStdSample(1).LastChan%
msg$ = Str$(i%) & " " & UpdateStdSample(1).Elsyms$(i%) & " " & UpdateStdSample(1).Xrsyms$(i%) & Str$(UpdateStdSample(1).MotorNumbers%(i%)) & " " & UpdateStdSample(1).CrystalNames$(i%) & ", " & Format$(UpdateStdSample(1).TakeoffArray!(i%)) & " " & Format$(UpdateStdSample(1).KilovoltsArray!(i%))
Call IOWriteLog(msg$)
Next i%
End If
' Now check for elements in the standard that are not in the sample, and add them if necesssary as specified elements
For j% = 1 To stdsample(1).LastChan%
'ip% = IPOS1(UpdateStdSample(1).LastChan%, stdsample(1).Elsyms$(j%), UpdateStdSample(1).Elsyms$()) ' only check element
ip% = IPOS9(stdsample(1).Elsyms$(j%), UpdateStdSample()) ' only check first not disabled occurance of element to load concentration
If ip% = 0 Then
If UpdateStdSample(1).LastChan% + 1 > MAXCHAN% Then GoTo UpdateCalculate2TooManyElements
' Add the standard element to the sample element arrays as a specified element
UpdateStdSample(1).LastChan% = UpdateStdSample(1).LastChan% + 1
UpdateStdSample(1).Elsyms$(UpdateStdSample(1).LastChan%) = stdsample(1).Elsyms$(j%)
UpdateStdSample(1).Xrsyms$(UpdateStdSample(1).LastChan%) = vbNullString
UpdateStdSample(1).MotorNumbers%(UpdateStdSample(1).LastChan%) = 0
UpdateStdSample(1).CrystalNames$(UpdateStdSample(1).LastChan%) = vbNullString
UpdateStdSample(1).numcat%(UpdateStdSample(1).LastChan%) = stdsample(1).numcat%(j%)
UpdateStdSample(1).numoxd%(UpdateStdSample(1).LastChan%) = stdsample(1).numoxd%(j%)
UpdateStdSample(1).AtomicCharges!(UpdateStdSample(1).LastChan%) = stdsample(1).AtomicCharges!(j%)
UpdateStdSample(1).TakeoffArray!(UpdateStdSample(1).LastChan%) = 0#
UpdateStdSample(1).KilovoltsArray!(UpdateStdSample(1).LastChan%) = 0#
End If
Next j%
' Now make all elements specified
For i% = 1 To UpdateStdSample(1).LastChan%
UpdateStdSample(1).Xrsyms$(i%) = vbNullString
UpdateStdSample(1).MotorNumbers%(i%) = 0
UpdateStdSample(1).CrystalNames$(i%) = vbNullString
UpdateStdSample(1).TakeoffArray!(i%) = 0#
UpdateStdSample(1).KilovoltsArray!(i%) = 0#
Next i%
If VerboseMode% Then
msg$ = vbCrLf & "Standard " & Format$(num%) & ", (before update for standard composition):"
Call IOWriteLog(msg$)
For i% = 1 To UpdateStdSample(1).LastChan%
msg$ = Str$(i%) & " " & UpdateStdSample(1).Elsyms$(i%) & " " & UpdateStdSample(1).Xrsyms$(i%) & Str$(UpdateStdSample(1).MotorNumbers%(i%)) & " " & UpdateStdSample(1).CrystalNames$(i%) & ", " & Format$(UpdateStdSample(1).TakeoffArray!(i%)) & " " & Format$(UpdateStdSample(1).KilovoltsArray!(i%))
Call IOWriteLog(msg$)
Next i%
End If
' Now load standard concentrations for all elements other than the current element
For j% = 1 To stdsample(1).LastChan%
If UCase$(stdsample(1).Elsyms$(j%)) <> UCase$(sample(1).Elsyms$(chan%)) Then ' skip loading concentration for current element (it might be duplicated)
ip% = IPOS1(UpdateStdSample(1).LastChan%, stdsample(1).Elsyms$(j%), UpdateStdSample(1).Elsyms$()) ' load first occurrance of all elements in standard
If ip% > 0 Then
UpdateStdSample(1).ElmPercents!(ip%) = stdsample(1).ElmPercents!(j%) ' load concentration from standard database
End If
End If
Next j%
' Now load the concentration for the current element in the current sample for ZAFStd calculations
ip% = IPOS1(stdsample(1).LastChan%, sample(1).Elsyms$(chan%), stdsample(1).Elsyms$())
If ip% > 0 Then
UpdateStdSample(1).ElmPercents!(chan%) = stdsample(1).ElmPercents!(ip%) ' load concentration from standard database if present in standard composition
End If
UpdateStdSample(1).Xrsyms$(chan%) = sample(1).Xrsyms$(chan%) ' load original x-ray line (still in original sample order)
UpdateStdSample(1).MotorNumbers%(chan%) = sample(1).MotorNumbers%(chan%) ' load original sample spectrometer number (still in original sample order)
UpdateStdSample(1).CrystalNames$(chan%) = sample(1).CrystalNames$(chan%) ' load original sample crystal name (still in original sample order)
UpdateStdSample(1).TakeoffArray!(chan%) = sample(1).TakeoffArray!(chan%) ' load original sample takeoff angle (still in original sample order)
UpdateStdSample(1).KilovoltsArray!(chan%) = sample(1).KilovoltsArray!(chan%) ' load original sample kilovolts (still in original sample order)
If VerboseMode% Then
msg$ = vbCrLf & "Standard " & Format$(num%) & ", (after update for standard concentrations):"
Call IOWriteLog(msg$)
For i% = 1 To UpdateStdSample(1).LastChan%
msg$ = Str$(i%) & " " & UpdateStdSample(1).Elsyms$(i%) & " " & UpdateStdSample(1).Xrsyms$(i%) & Str$(UpdateStdSample(1).MotorNumbers%(i%)) & " " & UpdateStdSample(1).CrystalNames$(i%) & ", " & Format$(UpdateStdSample(1).TakeoffArray!(i%)) & " " & Format$(UpdateStdSample(1).KilovoltsArray!(i%)) & ", " & Format$(UpdateStdSample(1).ElmPercents!(i%))
Call IOWriteLog(msg$)
Next i%
End If
' Re-order standard sample because all except one x-ray line was changed to unanalyzed
Call GetElmSaveSampleOnly(Int(1), UpdateStdSample(), Int(0), Int(0))
If ierror Then Exit Sub
If VerboseMode% Then
msg$ = vbCrLf & "Standard " & Str$(num%) & ", (after sort):"
Call IOWriteLog(msg$)
For i% = 1 To UpdateStdSample(1).LastChan%
msg$ = Str$(i%) & " " & UpdateStdSample(1).Elsyms$(i%) & " " & UpdateStdSample(1).Xrsyms$(i%) & Str$(UpdateStdSample(1).MotorNumbers%(i%)) & " " & UpdateStdSample(1).CrystalNames$(i%) & ", " & Format$(UpdateStdSample(1).TakeoffArray!(i%)) & " " & Format$(UpdateStdSample(1).KilovoltsArray!(i%)) & ", " & Format$(UpdateStdSample(1).ElmPercents!(i%))
Call IOWriteLog(msg$)
Next i%
Call IOWriteLog(vbNullString)
End If
' Update some standard sample parameters for ZAFStd calculation
UpdateStdSample(1).number% = num%
UpdateStdSample(1).OxideOrElemental% = 2 ' always calculate standard k-factors as elemental
' Reload the element arrays for the current sample
If UpdateStdSample(1).LastElm% > 0 Then
Call ElementGetData(UpdateStdSample())
If ierror Then Exit Sub
' Calculate the standard k factors for this standard (also calculate ZAF for calibration curve for demo mode)
If CorrectionFlag% = 0 Or CorrectionFlag% = 5 Then
Call ZAFStd2(row%, analysis, sample(), UpdateStdSample())
If ierror Then Exit Sub
ElseIf CorrectionFlag% = MAXCORRECTION% Then
'Call ZAFStd3(row%, analysis, sample(), UpdateStdSample())
'If ierror Then Exit Sub
End If
' Calculate the standard beta factors for this standard (0 = phi/rho/z, 1,2,3,4 = alpha fits, 5 = calilbration curve, 6 = fundamental parameters)
If CorrectionFlag% > 0 And CorrectionFlag% < 5 Then
Call AFactorStd(row%, analysis, sample(), UpdateStdSample())
If ierror Then Exit Sub
End If
End If
' Print out StdZAFCors for MAN dialog (continuum absorption correction)
If DebugMode And VerboseMode Then
Call IOWriteLog("UpdateCalculate2: Standard " & Format$(num%) & " " & StandardNames$(row%) & ", " & sample(1).Elsyms$(chan%) & " " & sample(1).Xrsyms$(chan%) & ", " & Format$(sample(1).TakeoffArray!(chan%)) & " " & Format$(sample(1).KilovoltsArray!(chan%)))
For i% = 1 To sample(1).LastElm%
ip% = IPOS14(i%, sample(), UpdateStdSample()) ' check element, xray, take-off and kilovolts (only one element will qualify at a time)
If ip% > 0 Then
msg$ = UpdateStdSample(1).Elsyms$(ip%) & " " & UpdateStdSample(1).Xrsyms$(ip%) & ", " & Format$(UpdateStdSample(1).TakeoffArray!(ip%)) & " " & Format$(UpdateStdSample(1).KilovoltsArray!(ip%)) & ", " & Format$(UpdateStdSample(1).ElmPercents!(ip%)) & ", " & Format$(analysis.StdZAFCors!(1, row%, ip%)) & ", " & Format$(analysis.StdContinuumCorrections!(row%, ip%))
Call IOWriteLog(msg$)
End If
Next i%
End If
' Re-set current element to specified
UpdateStdSample(1).ElmPercents!(chan%) = NOT_ANALYZED_VALUE_SINGLE!
UpdateStdSample(1).Xrsyms$(chan%) = vbNullString
UpdateStdSample(1).TakeoffArray!(chan%) = 0#
UpdateStdSample(1).KilovoltsArray!(chan%) = 0#
' Calculate std k-factors for next original sample element
End If
End If
Next chan%
Exit Sub
' Errors
UpdateCalculate2Error:
MsgBox Error$, vbOKOnly + vbCritical, "UpdateCalculate2"
ierror = True
Exit Sub
UpdateCalculate2TooManyElements:
msg$ = "Too many elements in standard number " & Str$(stdsample(1).number%)
MsgBox msg$, vbOKOnly + vbExclamation, "UpdateCalculate2"
ierror = True
Exit Sub
End Sub
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Ok, thanks, I see.
What if the second instance of the duplicate element is flagged "disable quant"?Then everything could be handled as if there was each element only once?
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By necessity the Disable Quant flag only applies to the calculation of elements in unknowns, not in standards.
Think of it this way: even if an element is disabled for quantification in an unknown, you'd still want that element utilized in the std k-factor calculation, if it is present in that standard composition.
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By necessity the Disable Quant flag only applies to the calculation of elements in unknowns, not in standards.
Think of it this way: even if an element is disabled for quantification in an unknown, you'd still want that element utilized in the std k-factor calculation, if it is present in that standard composition.
True.
But it wouldn't be duplicate anymore.
But ok, if it does not affect calculation speed or anything, I guess it does not matter.
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By necessity the Disable Quant flag only applies to the calculation of elements in unknowns, not in standards.
Think of it this way: even if an element is disabled for quantification in an unknown, you'd still want that element utilized in the std k-factor calculation, if it is present in that standard composition.
True.
But it wouldn't be duplicate anymore.
But ok, if it does not affect calculation speed or anything, I guess it does not matter.
The std k-factor code knows nothing about disable quant flags. But yes, it doesn't affect the speed much so it really doesn't matter.
john
Edit by John: OK, I now notice that the disable quant flags are checked in the code for the std k-factor calculation, but it still has to calculate std k-factor for each (not quant disabled) emitting line, with all the other elements not duplicated and present as specified concentrations.
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Probeman recently said to us that he wanted to be able to disable/enable individual data points based on their EDS spectra.
It might be because the EDS deadtime was over 90% and the EDS spectra were no longer suitable for quantification, but it also might be that in examining the EDS spectra, it is determined to be necessary to exclude certain data points that are not the phase of interest. For whatever reason.
So we added a disable and an enable button in the Run | Display and Export EDS spectra menu dialog as seen here:
(https://probesoftware.com/smf/gallery/1_09_10_19_5_56_34.png)
Maybe others will find it useful.
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John
I'm having a particular problem that I cannot track easily. I have a win10 machine connected to the new 8530F+ and another for off-line data processing. I am currently having to process the data on line rather than the work station as when I attempt to open the .mdb files acquired on-line with the off line computer I get an error that the database is not is not compatible. It then rolls back and closes. This sounds like some annoying windows type behavior. Anyone seen this already and what should I do about it?? I have 12.7.7 on remote and the previous version on-line. But don't think that this should be an issue after all, I have always opened the .mdb in PfEPMA anyway.
Cheers
Malc
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Hi Malcolm,
Is this the problem you are having?
https://probesoftware.com/smf/index.php?topic=105.msg8095#msg8095
Microsoft broke their Access database support last year, but it seems to have been fixed. Is this computer not able to get Windows updates?
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Hi John
That's the beast. As for updates, it can but I tend not to let it because these are in the hands of UWA IT "Gods" and we cannot foresake control over things things known to be less about our interests.
Cheers
Malc
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Always apply OS updates!
For on-line computers one should select the option to "download updates but let me decide when to install them". So Windows Update doesn't re-boot your computer in the middle of a run!
For off-line computers just let them install automatically. It's important.
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I’ve been getting a similar behaviour (but for a different reason I think). When opening a PfE database file over a network connection I sometimes get a ‘database already open locked for access’ error message. Copying the database file to the desktop solves the problem so I suspect it’s something to do with the slightly slower connection over the network causing a false error. Took me a while to work out that the database files weren’t getting randomly corrupted.
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Hi Mike,
Yeah, that's a different thing.
PFE locks the database when ever it performs a "transaction". That is updating the database. This is to prevent any possibility of data corruption.
https://en.wikipedia.org/wiki/Transaction_processing
You might notice a .LDB file at times in the folder. That is Microsoft's file locking mechanism, but it doesn't work fast enough over a network connection, so yes, copy the database to a local drive and all is well.
john
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Recently we improved the code handling the fact that the JEOL EDS interface can support 3 or 4 pulse processing time constants. Older "white type" JEOL EDS spectrometers usually have 3 time constants, while the newer "black type" spectrometers have 4 time constants.
So when PFE first connects to the JEOL EDS it asks how many time constants do you support. The latest PFE version (update any time), re-configures the dropdown list options to reflect this information as seen in the Acquisition Options dialog:
(https://probesoftware.com/smf/gallery/1_09_11_19_8_39_01.png)
It should also be mentioned that these time constant (throughput) controls shown above may not be active (even you are connected to a Bruker, Thermo or JEOL EDS spectrometer), unless you have the relevant flag set in the Probewin.ini file as shown here in the [hardware] section:
EDSSpectraInterfacePresent=1 ; non-zero EDS spectrum interface feature available (Thermo, Bruker, etc)
EDSSpectraInterfaceType=6 ; 0 = Demo, 1 = Unused, 2 = Bruker, 3 = Oxford, 4 = Unused, 5 = Thermo NSS, 6 = JEOL
EDSMaxEnergyThroughputPresent=1 ; indicate EDS detector get/set max energy and pulse processing
By the way, if you do have a Bruker, Thermo or JEOL EDS detector and would like to integrate WDS and EDS measurements for integrated quantitative analysis please contact us at Probe Software.
For more information on this very cool feature where one can combine acquisition and quantification of elements by WDS and EDS using full spectrum EDS acquisition for maximum flexibility, please see this topic (started in 2013!) and do let us know if you have any questions:
https://probesoftware.com/smf/index.php?topic=79.0
If you would like to jump ahead to a post showing more recent improvements on this integrated WDS and EDS method, specifically demonstrating the ability to perform quantitative spectral interference corrections between WDS and EDS elements, please check this post:
https://probesoftware.com/smf/index.php?topic=79.msg7818#msg7818
Oh, and this latest version fixes a few minor bugs recently reported by Owen Neill and Nick Bulloss. Please update any time using the Help menu in PFE.
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The latest version of Probe for EPMA has a small tweak that some might find useful.
When plotting your wavescans from the Plot! window, one can model their background fits using the Model backgrounds button. This button displays the Model backgrounds dialog which can be utilized to graphically select various background fits, in addition to specifying the multi-point background positions.
In addition one can assign these selections to the current sample (by default), or to a number of selected samples as seen here:
(https://probesoftware.com/smf/gallery/1_11_12_19_4_53_12.png)
In this latest version of PFE, not only are the background fits and multi-point background positions saved to the selected samples, but now also the normal hi and lo off-peak background positions. Previously the hi and lo off-peak background positions were only modified in the current sample.
Of course the software will not modify hi/lo or multi-point background positions for samples which already contain data.
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Theo Ntaflos, via Gareth Seward, reported to us that on one of his new computers, when he tried to display KLM markers in the multi-point-background display window in Probe for EPMA, he got the following error:
(https://probesoftware.com/smf/gallery/1_18_12_19_2_37_34.png)
After a bit of research, we discovered this interesting web page:
http://support.sas.com/kb/48/849.html
Apparently on some Windows computers that only have Microsoft Office 64 bit installed, older versions of Microsoft Access databases (MDB files), are no longer supported. One solution is to load the older Access MDB database file into Microsoft Access and save it as an Access 2000 format database. This may be necessary for Probe for EPMA databases created prior to 2007 or so, as more people install Microsoft Office 64 bit (and Probe for EPMA) on a new computer.
In the case of the XRAY.MDB x-ray database, we have now updated the (NIST) x-ray KLM database for you, to the Access 2000 format in version 12.8.0 of the CalcZAF.msi installer.
So if you see this error from the multi-point background or the Plot! window for displaying wavescans with KLM markers, you will need to update your Probe for EPMA installation by updating your CalcZAF installation. That simply means that you open the CalcZAF application, then click on the Help | Update CalcZAF menu, and download the latest update.
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As requested by Gareth Seward, we made a small modification to the matrix correction (fluorescence) error trapping code in PFE so that the first time you get an error from a bad point, void, etc., the program will ask if you want to skip these pop-up warnings.
If you click Yes, now it will simply log these errors to the log window as it already does for x-ray map quantification in CalcImage.
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A very tiny change in Probe for EPMA regarding the "demo" or "simulation" mode concerning 8230 and 8530 JEOL instruments.
A colleague of ours was recently using Probe for EPMA at home in simulation mode to design experimental setups (due to the recent stay at home situation), and was having trouble setting some high beam currents in demo mode. The issue was that his range of coarse condenser calibration values was too small for setting high beam currents.
Now normally the JEOL simulation (and real time!) mode for 8900/8200/8500/8230/8530 utilizes an iterative method to set the beam current, based on first setting a coarse condenser lens value from a calibration curve (either previously stored or in real time), and then iterating the fine condenser lens value until the desired beam current is reached.
However, starting with version 5 of the EIKS interface, JEOL added a new firmware function to set the beam current internally for 8230 and 8530 instruments using firmware. This is indicated in Probe for EPMA by editing the BeamCurrentType in the Probewin.ini file to be "1". That is:
[hardware]
BeamCurrentType=1
However in simulation mode, PFE was still using the iterative method even when simulating an 8230 or 8530 instrument (and the BeamCurrentType=1). This is now fixed, and so the latest version of Probe for EPMA will now simulate making a firmware call for setting the beam current for 8230/8530 instruments (in demo mode) if the BeamCurrentType=1 in the probewin.ini file.
See here for more details:
https://probesoftware.com/smf/index.php?topic=80.msg7423#msg7423
Hope that is clear.
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Ben Wade reported a small bug that occurs when editing standard assignments in a TDI sample with no TDI data. This is now fixed.
Update to the latest Probe for EPMA from the Help menu and you won't get this spurious warning.
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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:
(https://probesoftware.com/smf/gallery/1_23_08_20_9_41_04.png)
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:
(https://probesoftware.com/smf/gallery/1_23_08_20_9_41_26.png)
We also implemented the same method for the Elements/Cations dialog as seen here:
(https://probesoftware.com/smf/gallery/1_23_08_20_9_41_39.png)
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.
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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.
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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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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.
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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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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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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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We made a slight tweak to the STRATAGem Output menu so it now includes BadgerFilm for k-ratio output for thin film reprocessing:
(https://probesoftware.com/smf/gallery/1_30_06_21_9_09_22.png)
The BadgerFilm board is found here:
https://probesoftware.com/smf/index.php?board=37.0
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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.
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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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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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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.
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Gareth Seward made a suggestion that I think might be useful to many.
What he suggested is to add a new field in the standard databases that allows the user to specify which standard mount(s) that standard can be found in. This field can then be searched to find all standards within a specific mount. Here is the new GUI in the add/modify standard composition dialog:
(https://probesoftware.com/smf/gallery/1_19_09_21_8_44_48.png)
In this case, the text "alkali" has been added to the Standard Mount Name(s) field since this standard is found in our Alkali/Glass standard mount. Note that more than one standard mount names could be added to this field, e.g., "alkali, hydrous" to indicate that a standard is found in both the "alkali" and "hydrous" standard mounts. When the standard composition is output, we see this new field displayed:
St 305 Labradorite (Lake Co.)
TakeOff = 40.0 KiloVolt = 15.0 Density = 2.690 Type = feldspar Mount = alkali, hydrous
Specimen from HR Wenk, UC Berkeley, Geology
See Wenk and Kroll, Bull. Mineral. (1984), 107, 467-487
Oxide and Elemental Composition
Average Total Oxygen: 46.823 Average Total Weight%: 100.060
Average Calculated Oxygen: 46.826 Average Atomic Number: 11.559
Average Excess Oxygen: -.003 Average Atomic Weight: 21.021
ELEM: SiO2 Al2O3 CaO Na2O K2O FeO MgO MnO O
XRAY: ka ka ka ka ka ka ka ka ka
OXWT: 51.253 30.910 13.400 3.830 .120 .410 .139 .000 -.003
ELWT: 23.957 16.359 9.577 2.841 .100 .319 .084 .000 46.823
KFAC: .1840 .1277 .0873 .0155 .0009 .0027 .0006 .0000 .1859
ZCOR: 1.3022 1.2809 1.0968 1.8307 1.1121 1.1948 1.4473 1.2152 2.5193
AT% : 17.920 12.737 5.020 2.596 .054 .120 .073 .000 61.480
24 O: 6.995 4.972 1.960 1.013 .021 .047 .028 .000 24.000
Once these standard mount names have been added this feature is utilized in the Add/Remove Standard dialog as shown here showing all standards in the database because no text has been entered by the user:
(https://probesoftware.com/smf/gallery/1_19_09_21_8_45_16.png)
If the user starts typing the name of one of their standard mounts the dialog re-loads the available standards listing only those standards that match the standard mount name as shown here:
(https://probesoftware.com/smf/gallery/1_19_09_21_8_45_31.png)
Another good idea from Gareth!
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I don't know if this will be useful or not but we modified Add/Remove Standards dialog to print out the standard composition to the log window when one clicks on the standard in the "available standards" list.
(https://probesoftware.com/smf/gallery/1_29_09_21_11_45_58.png)
Double-clicking still adds the selected standard to the "current standards" list...
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This is a small tweak, but now the "raw data" output to the log window shows the total (actual acquisition) off-peak count times for the multi-point backgrounds (MPB):
Last (Current) On and Off Peak Count Times:
ELEM: al ka fe ka si ka ti ka ca ka
BGD: OFF MULT OFF MULT OFF
BGDS: S-Hi MULT LIN MULT LIN
SPEC: 3 2 1 4 5
CRYST: TAP LIFH PET PET LIF
ORDER: 1 1 1 1 1
ONTIM: 10.00 20.00 10.00 20.00 10.00
HITIM: 5.00 5.00 5.00 5.00 5.00
LOTIM: 5.00 5.00 5.00 5.00 5.00
UNFAC: 2 1 1 1 1
ONTIME 20.00 20.00 10.00 20.00 10.00
HITIME 10.00 ---- 5.00 ---- 5.00
LOTIME 10.00 ---- 5.00 ---- 5.00
HIMULT ---- 10.00 ---- 10.00 ----
LOMULT ---- 10.00 ---- 10.00 ----
The multi-point background count time is based on the current off-peak count time divided by two, times the specified number of MPBs to acquire. So these new output lines merely does that math for you... in this case it's an off-peak time of 5 seconds and 4 MPBs on each side of the peak, so 5/2 * 4 = 10 seconds total for each MPB (high/low) side.
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This is a small change that only affects Probe for EPMA when running in simulation (demo) mode. And then only for the current session.
Because the polygonization modeling is slightly time consuming, we have added the following dialog when starting a (demo) WDS simulation in Probe for EPMA:
(https://probesoftware.com/smf/gallery/1_13_11_21_4_07_05.png)
These WDS polygonization effects are described in more detail here:
https://probesoftware.com/smf/index.php?topic=79.msg7818#msg7818
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We added two new keywords to the probewin.ini file for the [Image] section in v. 13.0.3:
ImageSizeIndex=2
Sets the default image size index for image acquisition. Valid values are 1 = 256, 2 = 512, 3 = 1024.
ImageChannelNumber=1
Sets the default image channel number. Valid values are 1 or 2.
Update Probe for EPMA from the Help | Update Probe for EPMA menu and edit these parameters as desired.
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Hi John,
I can define a material type in the standard database but can I define more than one for example "glass" and "REE"? Neither ";" or "," seems to work as a divider. If this is not yet possible, could that be implemented?
Thanks!
Anette
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I can define a material type in the standard database but can I define more than one for example "glass" and "REE"? Neither ";" or "," seems to work as a divider. If this is not yet possible, could that be implemented?
Only one material per standard at this time...
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I can define a material type in the standard database but can I define more than one for example "glass" and "REE"? Neither ";" or "," seems to work as a divider. If this is not yet possible, could that be implemented?
So I looked at the code and the intention of the define standard material, and the define standard mount fields are treated differently.
In the case of the define standard mount, the same standard can be in more than one mount. So the program expects you to enter the mount name and when it finds a match it only displays the standards in that mount.
The standard material is different. It display all the different standard materials that have been defined by the user and the user checks one or more of the checkboxes to display only those materials.
But one can edit these materials in the Standard application with multiple definitions, for example here, the thorium silicate is defined as both a silicate and an actinide:
(https://probesoftware.com/smf/gallery/395_14_12_21_8_35_51.png)
And in Probe for EPMA from the Add/Remove Standards dialog one can check this checkbox to see materials that are silicates *and* actinides:
(https://probesoftware.com/smf/gallery/395_14_12_21_8_36_11.png)
Of course one can also check both the silicate and silicate, actinide checkboxes and then one will see all silicates and also silicates that are oxides:
(https://probesoftware.com/smf/gallery/395_14_12_21_8_36_27.png)
That's the best we can do I think.
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John,
Thanks for the explanation. Indeed, this is a good way to set it up and use the dialog (select multiple boxes). I cleaned up my standard database and it is working well for my purposes.
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Not sure if this will help anyone else, but one of our customers (LANL) had the x-axis on their JEOL 8200 fail. The problem being that if either the JEOL software or our software sends a move command to any stage axis, the instrument locks up and has to be re-booted. And though they've scheduled a service visit with JEOL, in the meantime they wanted to be able to continue to perform WDS analyses using the stage manually.
So we added a new keyword to the probewin.ini file for the [Hardware] section in v. 13.0.5 for them:
DisableStageMoveAll=0
If this value is set to a non-zero number all calls to the stage are ignored.
If this keyword might ever be useful for you in similar circumstances, just update Probe for EPMA from the Help | Update Probe for EPMA menu and edit this parameter as desired.
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Just a small thing that should be useful when automating Probe Image from the Probe for EPMA Automate! window...
We now parse the user specified Probe Image .PrbAcq mapping acquisition file for the pixel sizes and dwell times to obtain the total mapping acquisition time for Probe Image when it is automated through Probe for EPMA as shown here:
(https://probesoftware.com/smf/gallery/1_07_02_22_9_58_23.png)
This should make it easier to estimate the total acquisition time for standards, unknowns, wavescans and x-ray mapping.
As usual simply update Probe for EPMA from the Help menu.
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This is a very small "tweak" to the software but some of you might find it useful...
The other day when Probeman was running some PHA tests at different count rates by de-tuning the spectrometer position:
https://probesoftware.com/smf/index.php?topic=1437.msg10595#msg10595
We realized that we should probably record the current spectrometer position during PHA scan acquisitions. So this feature is now in the latest Probe for EPMA v. 13.1.1 as seen here:
(https://probesoftware.com/smf/gallery/1_02_03_22_8_39_52.png)
And here is the PHA scan with the spectrometer position de-tuned slightly:
(https://probesoftware.com/smf/gallery/1_02_03_22_8_40_09.png)
It should be noted however, that to prevent the software from automatically moving the spectrometer on-peak, one must first check the "Do Not Move Spectrometer On-Peak Before Scan" checkbox as shown here:
(https://probesoftware.com/smf/gallery/1_02_03_22_9_02_57.png)
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This is a little hard to explain, but for JEOL 8230/8530 users who are utilizing the JEOL EDS video interface in PFE for analog signal imaging, it might be worth reading through...
So there is a bug in the JEOL EDS video imaging functions where the slow scan image is *not* returned when the video image acquisition is acquired. Instead, the initial "pre-scan" just before the slow scan acquisition is the image that is actually returned. We have reported this bug to JEOL Japan, but given that they have developed a new EDS imaging interface on their new instruments, they may or may not fix this bug on the older instruments.
So to obtain higher quality analog signal images in Probe for EPMA with this JEOL EDS Video imaging interface, you should instead, slow down the scan on the JEOL PC-SEM software, and then utilize the new Scan Delay button seen here:
(https://probesoftware.com/smf/gallery/1_07_04_22_12_12_53.png)
in order to prevent the slow scan from starting before the "pre-scan" finishes so that a full image frame is acquired. Hope this makes sense!
This button is only visible for JEOL 8230/8530 instruments, who are utilizjng the JEOL EDS video imaging interface!
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The latest version of Probe for EPMA contains a number of updates, including a greeting for Dale Newbury's birthday next month (thanks to Heather Lowers).
So be sure to update PFE from the Help menu as usual, and feel free to wish him a happy birthday!
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The latest version of Probe for EPMA now contains an output format for the consensus k-ratio project.
The new format is a flat file format consisting of a tab delimited ASCII file, or optional Excel spreadsheet with one line per element as seen in the attached Excel spreadsheet. This output format can be accessed from the Output menu or from the Analyze! window in Probe for EPMA by right clicking selected samples as shown here:
(https://probesoftware.com/smf/gallery/1_04_05_22_11_47_12.png)
This format has been reviewed and approved by Nicholas Ritchie but could be modified if anyone has further suggestions. Here's a screen shot of the output:
(https://probesoftware.com/smf/gallery/1_04_05_22_11_47_28.png)
The advantage is that it is easily machine readable/searchable and no manual data entry is necessary.
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The latest version of Probe for EPMA now includes a right click menu in the Analyze! window to output data for import into Andrew Locock's garnet and amphibole mineral recalculation spreadsheets:
(https://probesoftware.com/smf/gallery/1_09_05_22_10_13_05.png)
The new code also copies either Andrew's garnet or amphibole spreadsheet to your user folder. Just to make things even easier! 8)
Please update PFE from your Help menu and try it out and let us know if anything in the output format (or output file naming) needs to be tweaked.
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The latest version of Probe for EPMA implements Andrew Locock's amphibole recalculation code for the purposes of determining ferrous and ferric iron. Thanks to Andrew and Aurelien Moy who worked with us on this quite complicated code.
This expanded feature is found in the Analyze! window Calculation Options button dialog as seen here:
(https://probesoftware.com/smf/gallery/1_11_05_22_9_16_36.png)
Remember, for in depth evaluation of your amphibole mineralogy, one should instead utilize the Locock spreadsheet output format (seen in the previous post) and utilize Andrew's recalculation spreadsheets externally to PFE.
But for the purposes of ferrous/ferric ratios these generic options seem to work well. In case any one is interested in how we set Andrew's spreadsheet flags, we decided upon the following code:
' Sodic amphibole
If Droop_option_for_amphibole% = 1 Then
ORTHORHOMBIC% = 0
USE_INITIAL_M3_OVER_SUM_M% = 0
If tipresent Then ESTIMATEOH2_2TI% = 1
If waterspecified Then REQUIRE_INITIAL_H2O% = 1
REQUIRE_SUM_SI_TO_CA_LE_15% = 0
REQUIRE_SUM_SI_TO_MG_GE_13% = 1
REQUIRE_SUM_SI_TO_NA_GE_15% = 0
REQUIRE_SUM_SI_TO_K_GE_15_5% = 1
' Calcic amphibole
ElseIf Droop_option_for_amphibole% = 2 Then
ORTHORHOMBIC% = 0
USE_INITIAL_M3_OVER_SUM_M% = 0
If tipresent Then ESTIMATEOH2_2TI% = 1
If waterspecified Then REQUIRE_INITIAL_H2O% = 1
REQUIRE_SUM_SI_TO_CA_LE_15% = 1
REQUIRE_SUM_SI_TO_MG_GE_13% = 1
REQUIRE_SUM_SI_TO_NA_GE_15% = 0
REQUIRE_SUM_SI_TO_K_GE_15_5% = 0
' Na-Ca amphibole
ElseIf Droop_option_for_amphibole% = 3 Then
ORTHORHOMBIC% = 0
USE_INITIAL_M3_OVER_SUM_M% = 0
If tipresent Then ESTIMATEOH2_2TI% = 1
If waterspecified Then REQUIRE_INITIAL_H2O% = 1
REQUIRE_SUM_SI_TO_CA_LE_15% = 1
REQUIRE_SUM_SI_TO_MG_GE_13% = 0
REQUIRE_SUM_SI_TO_NA_GE_15% = 1
REQUIRE_SUM_SI_TO_K_GE_15_5% = 1
' Fe-Mg-Mn amphibole
ElseIf Droop_option_for_amphibole% = 4 Then
ORTHORHOMBIC% = 0
USE_INITIAL_M3_OVER_SUM_M% = 0
If tipresent Then ESTIMATEOH2_2TI% = 1
If waterspecified Then REQUIRE_INITIAL_H2O% = 1
REQUIRE_SUM_SI_TO_CA_LE_15% = 1
REQUIRE_SUM_SI_TO_MG_GE_13% = 0
REQUIRE_SUM_SI_TO_NA_GE_15% = 1
REQUIRE_SUM_SI_TO_K_GE_15_5% = 0
' Oxo amphibole
ElseIf Droop_option_for_amphibole% = 5 Then
ORTHORHOMBIC% = 0
USE_INITIAL_M3_OVER_SUM_M% = 0
If tipresent Then ESTIMATEOH2_2TI% = 1
If waterspecified Then REQUIRE_INITIAL_H2O% = 1
REQUIRE_SUM_SI_TO_CA_LE_15% = 1
REQUIRE_SUM_SI_TO_MG_GE_13% = 0
REQUIRE_SUM_SI_TO_NA_GE_15% = 0
REQUIRE_SUM_SI_TO_K_GE_15_5% = 0
' Li amphibole
ElseIf Droop_option_for_amphibole% = 6 Then
ORTHORHOMBIC% = 0
USE_INITIAL_M3_OVER_SUM_M% = 0
If tipresent Then ESTIMATEOH2_2TI% = 1
If waterspecified Then REQUIRE_INITIAL_H2O% = 1
REQUIRE_SUM_SI_TO_CA_LE_15% = 0
REQUIRE_SUM_SI_TO_MG_GE_13% = 0
REQUIRE_SUM_SI_TO_NA_GE_15% = 1
REQUIRE_SUM_SI_TO_K_GE_15_5% = 0
End If
Please let us know if you have any questions.
-
The latest version of Probe for EPMA implements Andrew Locock's amphibole recalculation code for the purposes of determining ferrous and ferric iron. Thanks to Andrew and Aurelien Moy who worked with us on this quite complicated code.
This expanded feature is found in the Analyze! window Calculation Options button dialog as seen here:
(https://probesoftware.com/smf/gallery/1_11_05_22_9_16_36.png)
Remember, for in depth evaluation of your amphibole mineralogy, one should instead utilize the Locock spreadsheet output format (seen in the previous post) and utilize Andrew's recalculation spreadsheets externally to PFE.
But for the purposes of ferrous/ferric ratios these generic options seem to work well. In case any one is interested in how we set Andrew's spreadsheet flags, we decided upon the following code:
' Sodic amphibole
If Droop_option_for_amphibole% = 1 Then
ORTHORHOMBIC% = 0
USE_INITIAL_M3_OVER_SUM_M% = 0
If tipresent Then ESTIMATEOH2_2TI% = 1
If waterspecified Then REQUIRE_INITIAL_H2O% = 1
REQUIRE_SUM_SI_TO_CA_LE_15% = 0
REQUIRE_SUM_SI_TO_MG_GE_13% = 1
REQUIRE_SUM_SI_TO_NA_GE_15% = 0
REQUIRE_SUM_SI_TO_K_GE_15_5% = 1
' Calcic amphibole
ElseIf Droop_option_for_amphibole% = 2 Then
ORTHORHOMBIC% = 0
USE_INITIAL_M3_OVER_SUM_M% = 0
If tipresent Then ESTIMATEOH2_2TI% = 1
If waterspecified Then REQUIRE_INITIAL_H2O% = 1
REQUIRE_SUM_SI_TO_CA_LE_15% = 1
REQUIRE_SUM_SI_TO_MG_GE_13% = 1
REQUIRE_SUM_SI_TO_NA_GE_15% = 0
REQUIRE_SUM_SI_TO_K_GE_15_5% = 0
' Na-Ca amphibole
ElseIf Droop_option_for_amphibole% = 3 Then
ORTHORHOMBIC% = 0
USE_INITIAL_M3_OVER_SUM_M% = 0
If tipresent Then ESTIMATEOH2_2TI% = 1
If waterspecified Then REQUIRE_INITIAL_H2O% = 1
REQUIRE_SUM_SI_TO_CA_LE_15% = 1
REQUIRE_SUM_SI_TO_MG_GE_13% = 0
REQUIRE_SUM_SI_TO_NA_GE_15% = 1
REQUIRE_SUM_SI_TO_K_GE_15_5% = 1
' Fe-Mg-Mn amphibole
ElseIf Droop_option_for_amphibole% = 4 Then
ORTHORHOMBIC% = 0
USE_INITIAL_M3_OVER_SUM_M% = 0
If tipresent Then ESTIMATEOH2_2TI% = 1
If waterspecified Then REQUIRE_INITIAL_H2O% = 1
REQUIRE_SUM_SI_TO_CA_LE_15% = 1
REQUIRE_SUM_SI_TO_MG_GE_13% = 0
REQUIRE_SUM_SI_TO_NA_GE_15% = 1
REQUIRE_SUM_SI_TO_K_GE_15_5% = 0
' Oxo amphibole
ElseIf Droop_option_for_amphibole% = 5 Then
ORTHORHOMBIC% = 0
USE_INITIAL_M3_OVER_SUM_M% = 0
If tipresent Then ESTIMATEOH2_2TI% = 1
If waterspecified Then REQUIRE_INITIAL_H2O% = 1
REQUIRE_SUM_SI_TO_CA_LE_15% = 1
REQUIRE_SUM_SI_TO_MG_GE_13% = 0
REQUIRE_SUM_SI_TO_NA_GE_15% = 0
REQUIRE_SUM_SI_TO_K_GE_15_5% = 0
' Li amphibole
ElseIf Droop_option_for_amphibole% = 6 Then
ORTHORHOMBIC% = 0
USE_INITIAL_M3_OVER_SUM_M% = 0
If tipresent Then ESTIMATEOH2_2TI% = 1
If waterspecified Then REQUIRE_INITIAL_H2O% = 1
REQUIRE_SUM_SI_TO_CA_LE_15% = 0
REQUIRE_SUM_SI_TO_MG_GE_13% = 0
REQUIRE_SUM_SI_TO_NA_GE_15% = 1
REQUIRE_SUM_SI_TO_K_GE_15_5% = 0
End If
Please let us know if you have any questions.
In case any one is wondering how we decided on the amphibole recalculation flags for Andrew's code, see the attached documents from Andrew below showing the results of Andrew's investigations into which flags would be most appropriate for each amphibole type.
Again, if one prefers to set these amphibole flags manually, please utlize the Locock amphibole spreadsheet output menu by right clicking the sample(s) in the Analyze! window sample list.
-
To enable the automated acquisition of constant k-ratios we implemented a new option which will increment the Y stage axis when acquiring multiple sample setups. This option is available from the Multiple Setups button in the Automate! window as seen here:
(https://probesoftware.com/smf/gallery/1_30_05_22_2_07_23.png)
The constant k-ratio test for checking the instrument dead times and picoammeter accuracy is discussed here:
https://probesoftware.com/smf/index.php?topic=1466.0
This new Y stage increment option works for both the original multiple sample setups acquisitions (each position sample for all (multiple) sample setups), and the new "one at a time" multiple sample setups acquisitions, which can be used for the constant k-ratio testing if ones samples are susceptible to beam damage.
And it works for all position samples with multiple sample setups (standards, unknowns and wavescans!). Check it out.
-
We have been working with Philipp Poeml recently adding some new features in CalcImage (e.g., a new filter for blanking pixel with bad analytical totals) and have found that a version uploaded in last last two weeks has a few minor bugs that have now been fixed.
So if you've updated your Probe for EPMA software in the last two weeks, please update again and all should be good.
Sorry for any inconvenience.
-
There is now a new button in the Analytical | Update Dead Time Constants menu dialog as seen here:
(https://probesoftware.com/smf/gallery/1_29_06_22_9_46_57.png)
This allows one to update all the dead time constants in an old probe run (or new probe run using older element setups from the element setup database), by using the dead time constants stored in the SCALERS.DAT file (which normally should be the most recent dead time constants that have been determined).
-
Latest version of Probe for EPMA now notes the dead time correction expression type utilized in the Report output format:
(https://probesoftware.com/smf/gallery/1_09_07_22_6_53_37.png)
-
The latest version of Probe for EPMA now includes the exponential dead time correction expression for those that might want to try it out:
(https://probesoftware.com/smf/gallery/1_10_09_22_10_00_52.png)
It does not appear to work well on Cameca instruments, at least when typical Cameca dead times are ~3 usec or so, because the product of deadtime * cps is often greater than 1/e as explained in this post:
https://probesoftware.com/smf/index.php?topic=1489.msg11245#msg11245
But further evaluations of JEOL intensities using these expressions are most welcome. Please note that when acquiring constant k-ratios on JEOL (and Cameca for that matter) instruments, be sure to record your PHA scans at both the lowest *and* highest count rates to be sure that no PHA shifting is occurring that could bias the results. Normally this should be performed on your primary standard, e.g., pure Ti or pure Si. See here for more details:
https://probesoftware.com/smf/index.php?topic=1466.msg11247#msg11247
What we want to avoid is PHA shifting as seen here from Anette's SiO2/Si constant k-ratio run:
(https://probesoftware.com/smf/gallery/395_06_09_22_7_36_59.png)
If necessary one might need to modify the PHA settings for the high current acquisitions to avoid such extreme PHA shifting...
-
We added some additional output in Probe for EPMA that might be helpful for those evaluating the various dead time correction expressions. Specifically the dead time constant for each element (DEAD) and also the percent dead time correction (DTC%) as shown here:
On-Peak (off-peak corrected) or EDS (bgd corrected) or MAN On-Peak X-ray Counts (cps/1nA) (and Faraday/Absorbed Currents):
ELEM: si ka si ka si ka si ka si ka BEAM1 BEAM2
BGD: OFF OFF OFF OFF OFF
SPEC: 1 2 3 4 5
CRYST: TAP LTAP LPET TAP PET
ORDER: 1 1 1 1 1
102G 223.63 663.19 72.31 238.14 23.34 7.727 7.727
103G 223.49 665.10 73.30 235.02 23.13 7.730 7.727
104G 223.19 666.12 73.15 233.68 23.34 7.729 7.727
105G 225.02 667.15 71.75 235.16 23.55 8.406 8.438
106G 224.17 667.77 71.12 232.59 23.64 8.190 8.200
107G 224.53 664.00 71.57 230.58 23.35 7.402 7.396
108G 223.26 666.34 74.89 231.33 23.80 8.422 8.438
109G 223.63 655.35 72.00 229.94 23.64 8.188 8.200
AVER: 223.87 664.38 72.51 233.30 23.47 7.974 7.982
SDEV: .65 3.96 1.22 2.75 .22 .375 .387
1SIG: .68 1.18 .39 .70 .22
SIGR: .95 3.37 3.12 3.94 .99
SERR: .23 1.40 .43 .97 .08
%RSD: .29 .60 1.68 1.18 .94
DEAD: 2.85 2.65 3.00 2.76 3.10
DTC%: .5 1.4 .2 .5 .1
Typically, the dead time correction percentages are less than 1%, but we thought it was worth displaying when outputting raw intensities using the Raw data button in Probe for EPMA. Of course when running Si Ka on a large TAP crystal at high beam currents one is going see much larger corrections. Here is one such example:
On-Peak (off-peak corrected) or EDS (bgd corrected) or MAN On-Peak X-ray Counts (cps/1nA) (and Faraday/Absorbed Currents):
ELEM: si ka si ka si ka si ka si ka BEAM1 BEAM2
BGD: OFF OFF OFF OFF OFF
SPEC: 1 2 3 4 5
CRYST: TAP LTAP LPET TAP PET
ORDER: 1 1 1 1 1
350G 1529.94 3069.74 684.65 1607.96 197.11 200.568 200.568
351G 1527.25 3076.57 684.89 1611.71 197.30 200.629 200.598
352G 1531.49 3076.92 685.27 1609.49 197.70 200.598 200.598
353G 1529.87 3077.09 685.17 1611.09 197.27 200.598 200.583
354G 1527.81 3080.52 685.17 1612.68 197.33 200.583 200.583
355G 1530.51 3078.64 685.65 1609.84 197.46 200.568 200.552
356G 1529.83 3077.20 685.69 1609.11 197.13 200.583 200.583
357G 1527.66 3078.21 685.60 1606.19 196.80 200.629 200.537
AVER: 1529.29 3076.86 685.26 1609.76 197.26 200.594 200.575
SDEV: 1.53 3.15 .37 2.09 .26 .024 .022
1SIG: .24 .28 .20 .25 .12
SIGR: 6.26 11.25 1.90 8.38 2.19
SERR: .54 1.11 .13 .74 .09
%RSD: .10 .10 .05 .13 .13
DEAD: 2.85 2.65 3.00 2.76 3.10
DTC%: 112.8 227.4 48.4 115.2 13.0
Note the 227% correction! :o
Also worth mentioning that if one exceeds the valid range of dead time * cps product, the software will warn you that the correction cannot be applied as shown here:
(https://probesoftware.com/smf/gallery/1_13_09_22_9_09_06.png)
Although all the dead time expressions will fail mathematically at high enough dead time constants and count rates, the only time this error should ever become visible is when applying the exponential dead time correction on a Cameca instrument with its typically ~3 usec dead times.
-
This is a very small change to the software and I'm not sure how many will find it useful, but it was requested by Chi Ma at Cal Tech, so we added the capability.
So of you may have noticed that Probe for EPMA controls the optical light automatically on several occasions. For example:
The light is turned off:
1. Before automated image acquisition
2. Before PI is being run during automation
3. At the end of automation
4. Before manual sample acquisition from Acquire! if using EDS or CL
The light is turned on:
1. Auto-focus
2. After sample acquisition for manual sample acquisition or if automated and confirm positions is specified
3. If automation is canceled
But Chi requested that we add an option to not allow PFE to control the reflected and/or transmitted light temporarily. So we implemented the following new checkbox control in the stage map window:
(https://probesoftware.com/smf/gallery/1_11_10_22_9_49_59.png)
When this checkbox is checked PFE will no longer control the reflected or transmitted light on or off commands (automatically or manually). The only time the light will be automatically controlled is during auto-focus of stage Z position.
-
I got a strange feature request from Probeman, but the more I thought about it, the more reasonable it sounded.
Anyway, here's the deal: in Probe for EPMA we can integrate JEOL or Cameca WDS EPMA instruments with EDS systems from Thermo, Bruker or JEOL. However, Probe for EPMA does not connect to the EDS system until it is needed. That could be because one starts an EDS acquisition (from an existing WDS-EDS run), or one needs to extract EDS net intensities for quantification, or maybe just because one decides to open the Acquisition Options dialog from the Acquire! window.
When the Acquisition Options dialog is opened, Probe for EPMA checks the current EDS pulse process time in the EDS system and updates the value displayed in the dialog. If the EDS interface is not already connected, it tries to connect to the EDS system which might be on the same computer as Probe for EPMA (e.g., Thermo or Bruker) or on a remote computer (e.g., JEOL 8230/8530 and iSP100/iHP200F). The Bruker and Thermo EDS systems can also be on a remote computer depending on how your computer network is arranged.
For example, when the Acquisition Options dialog is opened and a Thermo NSS or Pathfinder system is present, this dialog would previously be displayed:
(https://probesoftware.com/smf/gallery/1_15_11_22_2_20_22.png)
to prompt you to either click OK to attempt to connect to the Thermo system *or* to click Cancel to exit and not open the Acquisition Options dialog. This means that the Acquisition Options dialog cannot be opened unless the Thermo EDS software is up and running on a local or remote computer. But what if you don't want to use the integrated WDS-EDS acquisition in Probe for EPMA? Or even worse, what if there's a problem with the Thermo software or computer and you can't run the Thermo software at all?
One could close the application and edit the Probewin.ini file to indicate that no EDS system is present (EDSSpectraInterfacePresent=0), or perhaps we could just temporarily disable the EDS interface just for this session? That was Probeman's thought and so we've implemented that so, when being prompted for attempting a connection to the Thermo (or Bruker or JEOL) EDS software, we are now presented with this dialog:
(https://probesoftware.com/smf/gallery/1_15_11_22_2_25_27.png)
A slightly different message appears if the Thermo system is on another computer, but the key point is that when one clicks Cancel, instead of exiting and not opening the Acquisition Options dialog, it merely temporarily disables the EDS interface (for the duration of this session) and displays the dialog as seen here with the EDS controls disabled:
(https://probesoftware.com/smf/gallery/1_15_11_22_2_27_45.png)
Of course you'll probably want to add some elements by WDS... but the point being you can proceed and open the Acquisiiton Options dialog without having to get the Thermo EDS software up and running just to analyze some WDS elements.
Now what happens if you then decide to start an EDS acquisition (for a run that already contains EDS data)? Well you'll get this dialog:
(https://probesoftware.com/smf/gallery/1_15_11_22_2_30_54.png)
And what about if you already have some EDS element acquired and try to quant them? Well, you'll get this dialog:
(https://probesoftware.com/smf/gallery/1_15_11_22_2_32_23.png)
Note that you can re-start the software and then have the EDS software up and running and then connect to it in order to obtain new net intensities, *or* you could simply open the Analysis Options dialog from the Analytical menu and check the following checkbox:
(https://probesoftware.com/smf/gallery/1_15_11_22_2_42_32.png)
This forces Probe for EPMA to utilize EDS net intensities that have been previously stored in the user's current probe database. This, by the way, is also a neat way to process data off-line from Thermo, Bruker or JEOL EDS systems. Though remember, one can install an off-line version of the Thermo and Bruker software on any computer for the purposes of obtaining net intensities.
Note that JEOL does not have an "off-line" version of their software so this "Only Use Stored Intensities" option is very handy when you want to process WDS-EDS analyses on another computer not connected to the microprobe private network.
-
The latest version of Probe for EPMA 13.3.0 now includes display and output of intensity units to clarify any confusion of whether the displayed/output intensities are normalized to beam current or not in the Output | Output Standard and Unknown XY Plots menu window as shown here:
(https://probesoftware.com/smf/gallery/1_04_05_23_1_26_58.png)
If, for example, the Use Beam Drift Correction flag is turned on (as it is by default) in the Analytical | Analysis Options menu dialog, the units will be cps/X nA where X is the nominal beam current which is displayed (and edited) in the Count Times dialog. If the beam drift correction is turned off, the units displayed will be cps. If displaying "raw" intensities, those will be counts per nA or simply counts (if the beam drift correction is turned off) to indicate that the intensities are de-normalized to time.
-
Some of you may have noticed that we have not released a new version of Probe for EPMA since v. 13.3.1 in early June. But not because we haven't been working hard on new features and capabilities in the software!
There's been a number of significant improvements to the software since then, but we wanted to be sure everything was tested and working before we released a new version. Our beta testers have been working with these new versions all summer and they say the new software appears to be working well in their labs.
So starting today we've uploaded the latest v. 13.5.2 of Probe for EPMA to our usual download sites so you can update your software using the Help | Update Probe for EPMA menu dialog as usual. And over the next few weeks I (and others) will be posting about these changes and provide descriptions of these new features and other modifications.
We will start with the oldest changes starting back in June, which was when we added the ability for users to specify different atomic weights for elements in their standards and/or in their unknowns as mentioned here in the version.txt file which is distributed with Probe for EPMA:
06/21/23 Modify Standard and Probe for EPMA to handle different atomic weights for standards
v. 13.3.2 and unknowns. Lots of code changes- needs to be tested. Note: Isotopes of the same
element should always produce the same x-ray intensities, but the concentrations and
stoichiometries will be different if the atomic weights are different.
E.g. Si28 vs. Si29.
Interestingly the use of different atomic weights in our calculations doesn't affect our matrix corrections (except for the backscatter corrections- more on that later!) because for the absorption correction, we utilize mass normalized absorption coefficients and for energy loss calculations we normalize to mass thickness (though for absolute rigor we really should be normalizing our absorption coefficients to the actual densities of enriched atomic weights involved- yeah, we really should be utilizing atomic fractions for all our physics calculations as is done in Penepma).
But it does affect how the mass fraction results are reported! Now we may wonder why this capability has not been implemented in the JEOL or Cameca software (as far as I know), but for actinide materials the difference between say, U235 and U238 is fairly small at around 1.2% relative and I guess might be ignored. But for an element such as Si28 vs. Si29 the difference is larger at around 3.5% relative, and even larger for Si30, at least for those of you using isotopes in your silicate experiments...
Anyway, we started by adding an extra text field to allow the user to specify different atomic weights in the Standard application as shown here:
(https://probesoftware.com/smf/gallery/1_05_09_23_11_04_01.png)
When the standard is displayed in the log window, the atomic weights are reported as seen here:
(https://probesoftware.com/smf/gallery/1_05_09_23_11_04_38.png)
Note that the atomic weights for standard elements can only be edited in the Standard application. We also added an atomic weight field in the Probe for EPMA Elements/Cations dialog as shown here for unknown samples:
(https://probesoftware.com/smf/gallery/1_05_09_23_11_08_55.png)
These values (for unknown samples) can be edited directly in Probe for EPMA. When the raw data is displayed in the log window, the atomic weights are displayed as seen here:
(https://probesoftware.com/smf/gallery/1_05_09_23_11_09_21.png)
And when results are calculated for samples with different atomic weights between the standards and unknown, the atomic weights are also displayed for both:
(https://probesoftware.com/smf/gallery/1_05_09_23_11_09_34.png)
Ok, that's enough for today. Lots of other new features to be described over the next few weeks but you can get a preview here:
https://probesoftware.com/smf/index.php?topic=40.0
Or download to the latest Probe for EPMA v. 13.5.2 update and see for yourselves.
-
07/14/23 Add code to read "effective takeoff angles" from SCALERS.DAT file and save to MDB database based on
v. 13.4.2 spectrometer/crystal combination.
This next implemented feature in Probe for EPMA allows one to calibrate the "effective" takeoff angles for each spectrometer and crystal combination on their instruments, document those values in the SCALERS.DAT file, and utilize these takeoff angles in the absorption matrix corrections.
Although we assume that our WDS spectrometer take off angles are *exactly* 40 degrees, it is evident that the "effective" takeoff angle on some spectrometer/crystals are quite different from the nominal values, as evidenced from k-ratio measurements from multiple spectrometers, referred to sometimes as "simultaneous" k-ratios (by Paul Carpenter and John Armstrong) previously.
That is, k-ratio of measurements on multiple spectrometers should yield the same k-ratios within statistics. Now some of these differences in k-ratios could result from miscalibration of the dead time constant, especially on large area crystals with high count rates as described in our 2023 paper "A New Method for Dead Time Calibration and a New Expression for Correction of WDS Intensities for Microanalysis".
https://doi.org/10.1093/micmic/ozad050
But once the dead time constants (and picoammeter linearity) are calibrated properly, and it is determined that the electron beam is perpendicular to the sample surface, any remaining differences in these "simultaneous" k-ratios should be due to differences in the "effective" takeoff angle of the spectrometer/crystal combination. These calibrations are discussed in this topic:
https://probesoftware.com/smf/index.php?topic=1535.msg11937#msg11937
Here's an example of consistently different k-ratios from multiple spectrometers:
https://probesoftware.com/smf/index.php?topic=1466.msg11329#msg11329
For example, the spectrometer could be misaligned internally or relative to the electron column, or the crystal diffracting asymmetrically (as was the case for the EPMA instrument at Caltech).
We will discuss how one might go about calibrating these "effective" takeoff angles, but assuming that one has determined what these "effective" takeoff angle actually are, we have introduced a new flag in Probe for EPMA, that allows one to compare analytical results using the nominal takeoff angle versus these "effective" takeoff angles as seen here:
(https://probesoftware.com/smf/gallery/1_07_09_23_9_33_04.png)
To utilize these "effective" takeoff angles, one must edit their SCALERS.DAT file. Previously the SCALERS.DAT file appeared like this near the bottom of this text file:
1300. 1290. 1890. 1300. 1800. "default detector bias1"
1300. 1300. 1850. 1300. 1850. "default detector bias2"
1500. 0. 0. 1480. 0. "default detector bias3"
1500. 0. 0. 1460. 0. "default detector bias4"
0. 0. 0. 0. 0. "default detector bias5"
0. 0. 0. 0. 0. "default detector bias6"
1 1 1 1 1 "default PHA inte/diff modes1"
1 1 1 1 1 "default PHA inte/diff modes2"
1 0 0 1 0 "default PHA inte/diff modes3"
1 0 0 1 0 "default PHA inte/diff modes4"
0 0 0 0 0 "default PHA inte/diff modes5"
0 0 0 0 0 "default PHA inte/diff modes6"
0 0 0 0 0 "default detector deadtimes1"
0 0 0 0 0 "default detector deadtimes2"
0 0 0 0 0 "default detector deadtimes3"
0 0 0 0 0 "default detector deadtimes4"
0 0 0 0 0 "default detector deadtimes5"
0 0 0 0 0 "default detector deadtimes6"
0 1 1 0 0 "Cameca large area crystal flag1"
0 1 1 0 0 "Cameca large area crystal flag2"
0 0 0 0 0 "Cameca large area crystal flag3"
0 0 0 0 0 "Cameca large area crystal flag4"
0 0 0 0 0 "Cameca large area crystal flag5"
0 0 0 0 0 "Cameca large area crystal flag6"
0 0 0 0 0 "unused"
0 0 0 0 0 "unused"
0 0 0 0 0 "unused"
0 0 0 0 0 "unused"
0 0 0 0 0 "unused"
0 0 0 0 0 "unused"
0 0 0 0 0 "unused"
However, you will need to edit the bolded lines for your spectrometer/crystal "effective" takeoff angles for each spectrometer and crystal as shown here, where it is assumed that all the "effective" takeoff angles are 40 degrees:
1674. 1764. 1750. 1650. 1790. "default detector bias1"
1750. 1800. 1800. 1700. 1770. "default detector bias2"
0. 0. 1740. 0. 0. "default detector bias3"
0. 0. 1740. 0. 0. "default detector bias4"
0. 0. 0. 0. 0. "default detector bias5"
0. 0. 0. 0. 0. "default detector bias6"
-1 -1 -1 -1 -1 "default PHA inte/diff modes1"
-1 -1 -1 -1 -1 "default PHA inte/diff modes2"
0 0 -1 0 0 "default PHA inte/diff modes3"
0 0 -1 0 0 "default PHA inte/diff modes4"
0 0 0 0 0 "default PHA inte/diff modes5"
0 0 0 0 0 "default PHA inte/diff modes6"
1.23 1.31 1.56 1.32 1.04 "default detector deadtimes1"
1.21 1.16 1.31 1.14 1.03 "default detector deadtimes2"
0 0 1.23 0 0 "default detector deadtimes3"
0 0 1.18 0 0 "default detector deadtimes4"
0 0 0 0 0 "default detector deadtimes5"
0 0 0 0 0 "default detector deadtimes6"
0 0 0 0 0 "Cameca large area crystal flag1"
0 0 0 0 0 "Cameca large area crystal flag2"
0 0 0 0 0 "Cameca large area crystal flag3"
0 0 0 0 0 "Cameca large area crystal flag4"
0 0 0 0 0 "Cameca large area crystal flag5"
0 0 0 0 0 "Cameca large area crystal flag6"
40 40 40 40 40 "effective take off angles1"
40 40 40 40 40 "effective take off angles2"
0 0 40 0 0 "effective take off angles3"
0 0 40 0 0 "effective take off angles4"
0 0 0 0 0 "effective take off angles5"
0 0 0 0 0 "effective take off angles6"
0 0 0 0 0 "unused"
We will go into the calibration and testing of these "effective" takeoff angles later, but in the meantime, it is something to think about.
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The next new feature we've added to Probe for EPMA this summer is an interesting one:
07/17/23 Enable secondary fluorescence from boundary code in PFE. Needs testing.
v. 13.4.3
I will discuss this new method in the topic specifically for this feature:
https://probesoftware.com/smf/index.php?topic=1545.0
Please note that we fixed a small bug in this feature yesterday (9/11/2023), so please update your Probe for EPMA using the Help menu as usual if you have an older version of the software.
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Continuing with changes since June, we added a new backscatter correction called the DAM (Donovan and Moy) backscatter correction as described in the latest version.txt file:
07/29/23 Add new matrix correction code for Donovan and Moy BSC/BKS corrections (modified from PAP).
This deserves its own topic here:
https://probesoftware.com/smf/index.php?topic=1566.msg12044#msg12044
Why did we name it the DAM backscatter correction? Well. perhaps because that was better than the MAD backscatter correction... :D
Be sure to update your Probe for EPMA using the Help menu as we had to make some minor tweaks (today) to fix some display issues.
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Another change we made earlier this summer:
07/31/23 Add output of variable Z fraction exponent for MAN parameters. Add two more references to AnalyzeTypeReport.
v. 13.4.5 Add variable exponent to Z fraction backscatter exponent code. Add new
Z fraction backscatter parameter to GetZAF form and code.
07/30/23 Modify MAN Z fraction zbar calculation to accept a zero for dynamically calculated
v. 13.4.4 Zbar exponents based on emission line energy.
These two changes are slightly related.
The variable exponent in the MAN Z-bar calculation allows the user to have a "optimized" Z fraction exponent based on each MAN element's emission line energy. For example, see this topic for more details:
https://probesoftware.com/smf/index.php?topic=4.msg12050#msg12050
The variable exponent for the Donovan and Moy (DAM) backscatter correction is discussed here in more detail:
https://probesoftware.com/smf/index.php?topic=1566.msg12051#msg12051
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Modify Calculation Options dialog to fit on screen better (Nachlas).
We modified the Calculation Options dialog to fit better on smaller (laptop) screens:
(https://probesoftware.com/smf/gallery/1_30_09_23_9_24_06.png)
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Working again with Scott Boroughs, we've slightly modified the layout of the Standard Assignments and Elements/Cations main dialog to show more information. For example, when opening the Standard Assignments dialog from either the Acquire! or Analyze! windows, you are now presented with this dialog:
(https://probesoftware.com/smf/gallery/1_05_10_23_11_31_53.png)
Note that the TDI assignments are now shown in the last (new) column. But because this dialog is also used for the Elements/Cations dialog, we had to add additional information to these dialogs, which are slightly different depending on whether they are loaded from the Acquire! window or the Analyze! window. Here is the new Elements/Cations dialog when opened from the Acquire! window:
(https://probesoftware.com/smf/gallery/1_05_10_23_11_31_38.png)
Note that the background acquisition type is now shown, and here is the Elements/Cations dialog when loaded from the Analyze! window:
(https://probesoftware.com/smf/gallery/1_05_10_23_11_32_09.png)
This dialog now displays the spectrometer number and crystal name in the last column. Hopefully, others will find these changes useful.
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Recently Scott Boroughs and I were chatting about a minor bug (or is it a feature?) in the Automate! window, where when a user has selected multiple position samples, using the multiple sample setups acquisition option, and is using the "Run Multiple Sample Setups One at a Time" option as described here:
https://probesoftware.com/smf/index.php?topic=40.msg10899#msg10899
Which is intended primarily for the acquisition of "constant k-ratios" for instrument calibration, as described here:
https://probesoftware.com/smf/index.php?topic=1466.msg11100#msg11100
Anyway, this "Run Multiple Sample Setups One at a Time" flag is for use when one wants to acquire all the selected position samples using the first assigned sample setup, then all the selected position samples using the next sample setup, etc., etc. This is great when you want to acquire each sample condition "one at a time" for all position samples. Without the flag set, the automation will acquire each position sample, using all assigned samples setups, for example when acquiring multiple keVs for thin film analysis:
https://probesoftware.com/smf/index.php?topic=111.0
But, if they have assigned different numbers of sample setups to some of the selected position samples, the software will acquire the multiple sample setups as expected, but when it reaches a position sample where the last assigned sample setup was acquired, it will simply stop and say "Automation Completed". Because of course, there are no more sample setups to run for that position sample.
Now maybe that is what the user intended, but on the other hand maybe you just made a mistake and accidentally did not assign the same number of sample setups to all the selected samples?
Anyway, now the software checks for the number of multiple sample setups assigned to the selected position samples and if any position samples have different numbers of multiple setups assigned it will prompt the user:
(https://probesoftware.com/smf/gallery/1_05_10_23_11_46_15.png)
If you click No it will allow you to adjust your automation [parameters, but if you click Yes, it will proceed to automate the selected samples until it comes across a position sample where all the multiple sample setup have been acquired already.
Simple, right?
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Sometimes it's hard to keep track of the many features in Probe for EPMA... more on that later. Ok, as many of you know, the Analyze! window Report button in Probe for EPMA can be very useful for providing a summary of the analytical conditions for a sample acquisition along with appropriate published references and is documented here:
https://probesoftware.com/smf/index.php?topic=8.msg8398#msg8398
https://probesoftware.com/smf/index.php?topic=42.msg5982#msg5982
For example a colleague of ours recently requested that we also add a report format for wavescan samples just as we do already for standard or unknown samples as described above. So we said, sure why not?
A few hours of coding later we now can handle wavescan samples from the same Report button. So if a wavescan sample is selected in the Analyze! window, and you click the Report button, you will get a file output which when loaded into Excel looks like this:
(https://probesoftware.com/smf/gallery/1_11_10_23_9_59_47.png)
So far so good, right? Well it was only after we implemented this new code that we discovered that there was already a report format for wavscan samples in the Analyze! window! This feature is a little hidden as it is accessed by using a right mouse click as seen here:
(https://probesoftware.com/smf/gallery/1_11_10_23_10_00_14.png)
Oh well. So we decided to keep both wavescan report formats because they are slightly different and maybe one format is preferable to the other for some people.
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We wanted to warn everyone that we found a serious bug in Probe for EPMA v. 13.4.2 and later when using the sample split feature button in the Analyze! window.
Basically if you split a sample into separate lines from the Analyze! window using v. 13.4.2 or later, the sample will be unreadable and if you close the file and re-open it, because Probe for EPMA tries to read the last sample when opening an MDB file, it will fail and the run won't open.
So, if you have v. 13.4.2 or later, please do not try to split any samples from the Analyze! window until you update to the latest v. 13.6.0 Probe for EPMA using the help menu as usual!
Thanks and sorry for the trouble.
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We wanted to warn everyone that we found a serious bug in Probe for EPMA v. 13.4.2 and later when using the sample split feature button in the Analyze! window.
Basically if you split a sample into separate lines from the Analyze! window using v. 13.4.2 or later, the sample will be unreadable and if you close the file and re-open it, because Probe for EPMA tries to read the last sample when opening an MDB file, it will fail and the run won't open.
So, if you have v. 13.4.2 or later, please do not try to split any samples from the Analyze! window until you update to the latest v. 13.6.0 Probe for EPMA using the help menu as usual!
Thanks and sorry for the trouble.
As stated previously if you have Probe for EPMA v. 13.4.2 or later you should immediately update to the latest Probe for EPMA using the Help menu as usual.
Using the Separate Selected Samples Into New Samples with Single Point button will make your MDB unreadable due to a bug which is now fixed in the latest version.
In the meantime we tested the new separate samples code and noticed that the TDI, CL and EDS intensity data are not always transferred over to new samples properly when using using the Combine (elements or lines) the Selected Samples into a New Sample, the Separate Selected Samples Into New Samples with Single Point or the Create New Samples from Selected Lines buttons in the Analyze! window as shown here:
(https://probesoftware.com/smf/gallery/1_21_10_23_3_06_15.png)
The new code now properly transfers the TDI, CL and EDS intensities into the new samples, so please update as soon as possible.
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Working with Mike Matthews we modified the STRATAGem and BadgerFilm k-ratio export GUI a bit:
(https://probesoftware.com/smf/gallery/1_20_11_23_9_43_47.png)
The new GUI has better text explanations for the two geometry models (homogeneous vs. replicate) and also now includes the x-ray emission line in the element list.
Note however, that even though you can select/deselect elements with more than one x-ray line, the export will contain all the emission lines for that element if they are present with two exceptions:
1. If the element channel is disabled for quant (or acquisition) it will be skipped. This can be done from the Analyze! Elements/cations dialog as the tool tip popup help shows in the above image.
2. If one has duplicate elements with the same x-ray line all element channels will be exported if Aggregate mode is off. If aggregate mode is on, the extra element channels will not be exported and will not be listed either.
See here for more details:
https://probesoftware.com/smf/index.php?topic=111.0
https://probesoftware.com/smf/index.php?topic=502.0
Finally, we just wanted to note that if one acquires ones thin film samples properly using the acquire using multiple sample setups option in the Automate! window (as described in the first link above), the samples will be listed with the same name, one for each Kev acquired as seen here:
(https://probesoftware.com/smf/gallery/1_20_11_23_9_44_11.png)
In these cases the Output All button is really cool as it will automatically select which samples to output and bang them out to your hard drive!
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The latest version of Probe for EPMA v. 13.7.0 now distributes a default set of USERMAC.DAT and USERMAC2.DAT MAC files. These files contain MACs for actinide emitters and absorbers compiled by Philipp Poeml and Karen Wright The USERMAC.DAT file contains mass absorption coefficients for the Ka, Kb, la, Lb, Ma and Mb emission lines. While the USERMAC2.DAT file contains MACs for the more exotic Ll, Ln, etc emission lines.
However, if you already have these files installed they will not be overwritten by the installer as these files are user editable files and marked as "do not overwrite" and "permanent".
Update as usual from the Help menu.
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Is it possible to make these MAC files available separately?
Where are the MAC values coming from?
Thanks in advance,
Nico
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As stated above these values are compiled by Philipp Poeml (at ITU) and Karen Wright (at INL). You would have to ask them where exactly specific values are from.
The files are included in the free CalcZAF distribution (the USERMAC files are installed to the C:\ProgramData\Probe Software\Probe for EPMA folder):
https://probesoftware.com/Update.html
USERMAC.TXT ' text file of Ka, Kb, La, Lb, Ma, Mb emitters
USERMAC2.TXT ' text file of Ln, Lg, Lv, Ll, Mg, Mz emitters
USERMAC.DAT ' binary file used by applications
USERMAC2.DAT ' binary file used by applications
See here for more details:
https://probesoftware.com/smf/index.php?topic=625.msg3656#msg3656
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Sometimes it's hard to keep track of the many features in Probe for EPMA... more on that later. Ok, as many of you know, the Analyze! window Report button in Probe for EPMA can be very useful for providing a summary of the analytical conditions for a sample acquisition along with appropriate published references and is documented here:
https://probesoftware.com/smf/index.php?topic=8.msg8398#msg8398
https://probesoftware.com/smf/index.php?topic=42.msg5982#msg5982
For example a colleague of ours recently requested that we also add a report format for wavescan samples just as we do already for standard or unknown samples as described above. So we said, sure why not?
A few hours of coding later we now can handle wavescan samples from the same Report button. So if a wavescan sample is selected in the Analyze! window, and you click the Report button, you will get a file output which when loaded into Excel looks like this:
(https://probesoftware.com/smf/gallery/1_11_10_23_9_59_47.png)
So far so good, right? Well it was only after we implemented this new code that we discovered that there was already a report format for wavscan samples in the Analyze! window! This feature is a little hidden as it is accessed by using a right mouse click as seen here:
(https://probesoftware.com/smf/gallery/1_11_10_23_10_00_14.png)
Oh well. So we decided to keep both wavescan report formats because they are slightly different and maybe one format is preferable to the other for some people.
As you know, one can export all wavescans from a probe run using the Output | Save Wavescan Output menus. However, these menus export all wavescan samples, so if you want to export only selected wavescans, you can use the Plot! window and change the Output Target from Graph Window to ASCII Text File.
But as requested recently by Scott Boroughs the latest version of Probe for EPMA can also output selected wavescans from the Analyze! window using the right mouse button click:
(https://probesoftware.com/smf/gallery/1_31_01_24_8_07_17.png)
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A very minor tweak to the MAN plot window:
(https://probesoftware.com/smf/gallery/1_13_02_24_9_07_02.png)
Update from the Help menu as usual.
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A very minor tweak to the MAN plot window:
(https://probesoftware.com/smf/gallery/1_13_02_24_9_07_02.png)
Update from the Help menu as usual.
Thanks for doing this John!
The rationale behind this request is that the best fit line is effectively a least-squares quadratic regression of the form f(x) = c + bx +ax2,
for which the intercept is c, the slope is b, and the curvature is a.
The attached PDF gives short definitions of the various parameters such as the Coefficient of Determination.
These 3 extra statistical parameters - R2, R2adj - and the Mean Square Error of the Residuals, should help in deciding whether or not to keep a particular point when fitting the MAN background curve.
By tracking the changes in these parameters, as well as the Rel% Deviation, one can determine the effects of omitting a particular point.
Of course plotting the error bars on each point is also very helpful!
Thanks again, Andrew
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We bumped the PFE version number today to 13.8.2:
https://probesoftware.com/smf/index.php?topic=40.0
The main changes were to the JEOL MEC EDS interface but some other general bug fixes worth updating your PFE using the Help menu when you get a chance.
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A very minor tweak to the MAN plot window:
(https://probesoftware.com/smf/gallery/1_13_02_24_9_07_02.png)
Update from the Help menu as usual.
Thanks for doing this John!
The rationale behind this request is that the best fit line is effectively a least-squares quadratic regression of the form f(x) = c + bx +ax2,
for which the intercept is c, the slope is b, and the curvature is a.
The attached PDF gives short definitions of the various parameters such as the Coefficient of Determination.
These 3 extra statistical parameters - R2, R2adj - and the Mean Square Error of the Residuals, should help in deciding whether or not to keep a particular point when fitting the MAN background curve.
By tracking the changes in these parameters, as well as the Rel% Deviation, one can determine the effects of omitting a particular point.
Of course plotting the error bars on each point is also very helpful!
Thanks again, Andrew
A couple of references that may prove useful with regard to linear and quadratic regressions:
Rawski, R.I., Sanecki, P.T., Kijowska, K.M., Skitat, P.M. and Saletnik, D.E., 2016. Regression analysis in analytical chemistry. Determination and validation of linear and quadratic regression dependencies. South African Journal of Chemistry, 69, pp.166-173.
Raposo, F. and Barcelo, D., 2021. Assessment of goodness-of-fit for the main analytical calibration models: Guidelines and case studies. Trends in Analytical Chemistry, 143, 116373, 12 p.