New Features In Probe for EPMA

[John Donovan]

The latest version of Probe for EPMA will now automatically exclude samples (and elements) from the global MAN fit arrays, if they are deleted in the current probe run, when loading the default MAN assignments for the first time. 

This change was requested by Gareth Seward and it should not cause any issues under normal circumstances.   But if you are deleting and undeleting samples and changing the MAN assignments, you might want to use the Analytical |Clear MAN Assignments before clicking the Assign MAN Fits menu again in subsequent data processing.

[John Donovan]

CalcImage can now output the "raw intensity" images to Surfer also.



Output example is seen here:

[John Donovan]

One can now specify a "databar" from the Run | Image Display dialog as seen here:



Thanks to George Morgan for the suggestion.

[Probeman]

Per suggestions from Gareth Seward and Karsten Goemann I've modified the Fiducials selection dialog a bit.

This fiducial dialog is used to add, remove and modify fiducial calibration sets for specimen translation and rotation effects using three physical fiducial marks on the sample. Generally these are used for standard mounts, but they can also be used for unknown samples as well if you want to be sure to go back exactly to a previous position on a fine grained and/or complex specimen. Here is the new dialog with a new Assign button that will make things easier if you already have digitized positions and want to add fiducials:



Karsten will be posting a fiducial tutorial soon and when he does I'll add a "interactive help" button for it.

[Probeman]

Another small tweak that I'm hoping will help users realize that the position samples listed in the Automate! window are *not* actually part of your probe database but instead are shared with all users and automatically saved to the position.mdb file:



Generally, users should clear this position database (unless the next user is perhaps planning on using the same standard mount in the same sample block location), using the Delete All button and then import the appropriate standard positions from a previously exported .POS file.

As mentioned above Karsten will be posting a short tutorial on utilizing standard POS files and fiducials here:

http://probesoftware.com/smf/index.php?topic=46.0

In the meantime there are some posts in that topic worth reading...

[John Donovan]

The Move window now has controls for inserting and removing the EDS detector if your EDS spectrometer has motion control.  Right now only the Bruker hardware is supported, but to enable the buttons, you will have to add a new keyword to the [hardware] section of the Probewin.ini file amd change the value to non-zero.

EDSInsertRetractPresent=0

Otherwise the buttons will be disabled as seen here:

[John Donovan]

I also added calls to get/set the maximum energy and maximum pulse throughput in the Acquisition Options dialog from the Acquire! window as seen here:



Right now only the Bruker hardware works for set and get, the Thermo hardware gets and sets all except for setting the max pulse throughput which will get released in version 3.3 of NSS.

Remember, to utilize these API calls you will need these two keywords added to the [hardware] section of your Probewin.ini file and then set them to a non-zero value:

EDSInsertRetractPresent=0       ; indicate EDS detector insert/retract hardware
EDSMaxEnergyThroughputPresent=0 ; indicate EDS detector get/set max energy and pulse processing

[John Donovan]

And here is where the new Import *.DCD Files button now is (I moved both the .LEP and .DCD position import to the Automate! windows in PFE and Stage as seen here:



This button allows one to import ASCII sample position files created by Graham Hutchison's Microbeam Services optical stage digitized hardware/software.

[John Donovan]

This isn't so much a new feature as it is a cleaning up of the output for EDS and WDS integrated samples.

If you have both analyzed EDS and WDS elements in your run, the output for say the Data button in the Analyze! window will look like this:

Un    7 Mg2SiO4
TakeOff = 40.0  KiloVolt = 15.0  Beam Current = 20.0  Beam Size =   10
(Magnification (analytical) =  20000),        Beam Mode = Analog  Spot
(Magnification (default) =     2524, Magnification (imaging) =    736)
Image Shift (X,Y):                                          .00,   .00
Number of Data Lines:   3             Number of 'Good' Data Lines:   3
First/Last Date-Time: 02/19/2013 04:18:02 PM to 02/19/2013 04:23:47 PM

Stage (or Beam Deflection) Coordinate Positions:
          X          Y          Z                 X          Y          Z
   18G   12260.00  -4962.000   11.00000    19G   12184.00  -4958.000   11.00000
   20G   12145.00  -4958.000   11.00000

Sample Coordinates Referenced to Fiducial Set  2 C:\UserData\StandardPOSData\alkali-glass_pos4.pos
 1  13206.0 4623.00 -26.000
 2  19447.0 -4695.0 -61.000
 3  6142.00 -4967.0 17.0000

Sample is a Time Dependent Intensity (TDI) Self-Calibration Acquisition Type Sample

On and Off Peak Positions:
ELEM:    na ka    k ka   ca ka   mn ka   ti ka   mg ka   si ka
ONPEAK 46273.0 42618.0 38444.0 23831.0 68281.0 .000000 .000000
OFFSET 89.8477 158.785 -44.414 208.352 10.3984 .000000 .000000
HIPEAK 47601.0 43683.0 39895.5 25367.9 68772.5 .000000 .000000
LOPEAK 44687.3 41392.0 37178.4 22782.5 67593.0 .000000 .000000
HI-OFF 1328.00 1065.02 1451.48 1536.89 491.500 .000000 .000000
LO-OFF -1585.7 -1226.0 -1265.6 -1048.5 -687.96 .000000 .000000

PHA Parameters:
ELEM:    na ka    k ka   ca ka   mn ka   ti ka   mg ka   si ka
DEAD:     3.00    3.31    3.25    3.31    2.97     .00     .00
BASE:      .56     .56     .56     .50     .56     .00     .00
WINDOW    4.00    4.00    4.00    4.00    4.00     .00     .00
MODE:       -1      -1      -1      -1      -1       0       0
GAIN:    2321.   1181.    567.    780.    700.       .       .
BIAS:    1300.   1850.   1330.   1850.   1840.       .       .

Last (Current) On and Off Peak Count Times:
ELEM:    na ka    k ka   ca ka   mn ka   ti ka   mg ka   si ka
BGD:       OFF     OFF     OFF     OFF     OFF     EDS     EDS
BGDS:      LIN     LIN     LIN     LIN     LIN     EDS     EDS
SPEC:        1       3       2       3       5       0       0
CRYST:     TAP    LPET    LPET    LPET     LIF     EDS     EDS
ORDER:       1       1       1       2       1       1       1
ONTIM:   20.00   10.00   20.00   10.00   12.00   80.00   80.00
HITIM:    5.00    5.00    5.00    5.00    3.00   40.00   40.00
LOTIM:    5.00    5.00    5.00    5.00    3.00   40.00   40.00
UNFAC:       3       2       3       2       4       1       1
ONTIME   60.00   20.00   60.00   20.00   48.00   80.00   80.00
HITIME   15.00   10.00   15.00   10.00   12.00   40.00   40.00
LOTIME   15.00   10.00   15.00   10.00   12.00   40.00   40.00

Miscellaneous Sample Acquisition/Calculation Parameters:
KILO:    15.00   15.00   15.00   15.00   15.00   15.00   15.00
ENERGY   1.041   3.313   3.691   5.895   4.509   1.254   1.740
EDGE:    1.073   3.608   4.039   6.539   4.967   1.305   1.839
Eo/Ec:   13.98    4.16    3.71    2.29    3.02   11.49    8.16
STDS:      336     374     358      25      22      12      14
TDI#:       -1      -1      -1       0      -1       0       0

EDS Spectrum Parameters (for datarow=1):
Time Constant=     0,  Clock Time=  50.0
Elapsed Time= 126.2, Dead Time(%)=   37.
Live Time=  80.0,        Channels=  2048
Ev Per Chan=    10,  Max Counts=  211125

On-Peak (off-peak corrected) or MAN On-Peak X-ray Counts (cps/1nA) (and Faraday Current):
ELEM:    na ka    k ka   ca ka   mn ka   ti ka   mg ka   si ka   BEAM
BGD:       OFF     OFF     OFF     OFF     OFF     EDS     EDS
SPEC:        1       3       2       3       5       0       0
CRYST:     TAP    LPET    LPET    LPET     LIF     EDS     EDS
ORDER:       1       1       1       2       1       1       1
   18G    -.03     .13     .14    -.38    -.01  998.44  489.54  20.019
   19G    -.03     .00     .18     .02     .00 1000.83  489.85  20.014
   20G    -.02     .04     .15     .16     .00  996.85  488.16  20.014

AVER:     -.03     .06     .16    -.06     .00  998.71  489.18  20.016
SDEV:      .01     .07     .02     .28     .01    2.01     .90    .003
1SIG:      .02     .05     .03     .11     .01     .79     .55
SIGR:      .38    1.43     .82    2.61     .77    2.54    1.63
SERR:      .00     .04     .01     .16     .00    1.16     .52
%RSD:   -23.90  115.87   15.58 -442.29 -132.10     .20     .18

Off-Peak (calculated) X-ray Counts (cps/1nA):
ELEM:    na ka    k ka   ca ka   mn ka   ti ka   mg ka   si ka
TYPE:   LINEAR  LINEAR  LINEAR  LINEAR  LINEAR AVERAGE AVERAGE
   18G     .36     .85     .90    4.84     .06     .00     .00
   19G     .35     .84     .92    4.72     .06     .00     .00
   20G     .35     .80     .89    4.59     .05     .00     .00

AVER:      .36     .83     .90    4.72     .06     .00     .00
SDEV:      .01     .03     .02     .12     .01     .00     .00

Raw Hi-Peak X-ray Counts (cps/1nA):
ELEM:    na ka    k ka   ca ka   mn ka   ti ka   mg ka   si ka
   18G     .36     .77     .82    4.39     .07     .00     .00
   19G     .28     .81     .84    4.21     .08     .00     .00
   20G     .31     .81     .81    3.97     .05     .00     .00

AVER:      .32     .80     .82    4.19     .07     .00     .00
SDEV:      .04     .02     .02     .21     .02     .00     .00
1SIG:      .03     .06     .05     .14     .02     .00     .00
SIGR:     1.24     .35     .29    1.45    1.05     .00     .00

Raw Lo-Peak X-ray Counts (cps/1nA):
ELEM:    na ka    k ka   ca ka   mn ka   ti ka   mg ka   si ka
   18G     .37     .94     .97    5.15     .04     .00     .00
   19G     .44     .88    1.00    5.06     .04     .00     .00
   20G     .39     .80     .96    5.02     .05     .00     .00

AVER:      .40     .87     .98    5.08     .04     .00     .00
SDEV:      .04     .07     .02     .07     .01     .00     .00
1SIG:      .04     .07     .06     .16     .01     .00     .00
SIGR:      .97    1.06     .36     .41     .48     .00     .00

Note that the peak positions and PHA parameters for the Mg Ka and Si Ka (as EDS elements) are zeros because, they aren't "useful". I'll probably make them dashes at some point (along with the off-peak intensity output)... which reminds me: I wish Thermo (and Bruker?) software sent back the EDS background intensities so I can calculate statistics for the EDS elements...

But if you decide to run PFE using *only* EDS elements (that is, no WDS elements), then it makes no sense to output the peak positions and PHA parameters at all, so this is the output you will now see for EDS only elements in PFE:

St  912 Set   1 MgO (elemental) (#12)
TakeOff = 40.0  KiloVolt = 15.0  Beam Current = 30.0  Beam Size =    0
(Magnification (analytical) =  40000),        Beam Mode = Analog  Spot
(Magnification (default) =      400, Magnification (imaging) =    800)
Image Shift (X,Y):                                          .00,   .00

1. UCB # M3567, 99.8%, EPMA (UCB): Ca ~ 0.2%
2. C. M. Taylor, 99.98%, EPMA (UCB) Ca ~ 0.02%
Number of Data Lines:   4             Number of 'Good' Data Lines:   4
First/Last Date-Time: 11/17/2014 06:17:30 PM to 11/17/2014 06:24:24 PM

Stage (or Beam Deflection) Coordinate Positions:
          X          Y          Z                 X          Y          Z
   26G  -13078.00   26512.00   19.00000    27G  -13074.00   26512.00   19.00000
   28G  -13070.00   26512.00   19.00000    29G  -13066.00   26512.00   19.00000

Sample Coordinates Referenced to Fiducial Set  1 C:\UserData\StandardPOSData\STBLK1_pos1.pos

Last (Current) On and Off Peak Count Times:
ELEM:    ni ka   cr ka   co ka   fe ka   cu ka   al ka    o ka
BGD:       EDS     EDS     EDS     EDS     EDS     EDS     EDS
BGDS:      EDS     EDS     EDS     EDS     EDS     EDS     EDS
SPEC:        0       0       0       0       0       0       0
CRYST:     EDS     EDS     EDS     EDS     EDS     EDS     EDS
ORDER:       1       1       1       1       1       1       1
ONTIM:   59.90   59.90   59.90   59.90   59.90   59.90   59.90
HITIM:   29.95   29.95   29.95   29.95   29.95   29.95   29.95
LOTIM:   29.95   29.95   29.95   29.95   29.95   29.95   29.95

Miscellaneous Sample Acquisition/Calculation Parameters:
KILO:    15.00   15.00   15.00   15.00   15.00   15.00   15.00
ENERGY   7.473   5.412   6.926   6.400   8.041   1.487    .525
EDGE:    8.333   5.990   7.709   7.112   8.979   1.560    .532
Eo/Ec:    1.80    2.50    1.95    2.11    1.67    9.62   28.21
STDS:      528     524     527     526     529     513     912

EDS Spectrum Parameters (for datarow=1):
Time Constant=     0,  Clock Time=  60.0
Elapsed Time= 125.7, Dead Time(%)=   52.
Live Time=  60.0,        Channels=  2048
Ev Per Chan=    10,  Max Counts=  389132

ELEM:    ni ka   cr ka   co ka   fe ka   cu ka   al ka    o ka   BEAM
BGD:       EDS     EDS     EDS     EDS     EDS     EDS     EDS
   26G     .00     .00     .00     .09     .17     .00  368.54  29.916
   27G     .00     .00     .04     .18     .00     .00  368.86  29.911
   28G     .00     .00     .00     .27     .11     .00  372.59  29.908
   29G     .21     .00     .18     .00     .00     .00  369.28  29.902

AVER:      .05     .00     .05     .14     .07     .00  369.82  29.909
SDEV:      .11     .00     .09     .12     .09     .00    1.87    .006
1SIG:      .01     .00     .01     .01     .01     .00     .45
SIGR:    19.51     .00   15.54   13.43   13.67     .00    4.13
SERR:      .05     .00     .04     .06     .04     .00     .94
%RSD:   200.00     .00  158.28   86.27  121.83     .00     .51

A little more compact I think you all will agree!

[John Donovan]

As many of you already know, the Digitize Image feature, described here:

http://probesoftware.com/smf/index.php?topic=70.msg263#msg263

can be used to first acquire a BSE, SE or other image on your sample and then simply utilize the mouse to select stage coordinate positions (single points, traverses and polygon grids) on the image for subsequent automated acquisition from the Automate! window using either stage motion or stage motion and beam deflection.

But what if one has already digitized sample positions using either the manual random points, linear traverse, rectangular grid, polygon grid, or "shotgun" methods from the Digitize window and you would like to see where those already digitized positions plot on an image of the sample?

Previously, one could first acquire an image from the Acquire! window using the Imaging button, then save that image as a BMP file to disk, then load that BMP file image into PictureSnap and then select one of the position sample types to display the desired position sample type from the PictureSnap Display menu and you would be able to see where they fall on the sample...  whew!

Well, now there is another way that is super easy!  Simply acquire an image of the area of interest using the Imaging button in the Acquire! window at whatever mag you want, then simply click the Plot Digitized Positions checkbox as seen here:



and voila, the position sample coordinates for the sample type displayed in the Automate! window are automatically plotted!  Cool.   

[John Donovan]

This is a really cool new feature for automating presentation output for large numbers of traverse samples. From the Output menu select the new Output Automatic Traverse Plots as seen here:



After the analysis data has been output, this dialog will appear:



Select the options you want and click OK. The program will ask if you want to run the output script in Grapher. An example of the presentation output is seen attached below (remember to login to see attachments!).

I should mention the selection of the "customizable" Grapher script templates isn't implemented yet. Probably tomorrow...

Also, I should mention that this Grapher script runs much too slowly right now. We'll start optimizing it soon, but I wanted to get the feature out there for feedback and heck, automated output is always useful even if it is a little slow!

[John Donovan]

Ok, I added support for customized traverse scripts and here is an example with 9 plots per page generated automatically (see attached below).

[John Donovan]

Based on David Steel and Karsten Goemann's input I think I have a new version that consists of a major write of the acquisition and display code to allow the program to consider "condition order" as a new parameter.

Here is an example of the new code processing a "sparse" field of elements at 4 different conditions:



You will note that there are some new fields such as the condition grid and a graphic that shows the current acquisition order. The same graphic is available from the Acquisition Option dialog and the spectrometer order controls can now be applied to combined condition samples as seen here:



The same graphics with the conditions in red are also seen during acquisition:



The same features also apply to more typical samples as seen here with two conditions:



I've tested a large number of functions and everything seems good to go, but I'm sure there is bound to be some tweaking to get everything perfect so who will be the first to try?

Note that at the moment I am only uploading the installer files to our beta testing site.  David: if you'd like to try this, I'm sure Karsten can help you out.

[John Donovan]

Here's an aspect to the new acquisition code that took me a bit before I realized that it was correct and I was wrong!

Because one can now sort the elements within each condition, I tried some testing with the following amphibole example here in descending spectrometer position order, so Na and Si are first:



Now I switched it to ascending spectrometer position order as seen here but at first was stumped by the Mg now being the longer acquisition time as seen here:



The I remembered that I had the TDI time dependent intensity option turned on and so the first element takes longer because of the additional overhead! Normally this wouldn't be noticable but I had set the number of TDI intervals set to 40...

[Probeman]

Just FYI, Julie and I are now officially running v. 10.6.6 on our SX100 and everything seems fine with the new acquisition code... beta testers please continue to test!
john