Wish List for PFE Features

[John Donovan]

Got already plans for the weekend? I've got something new. I wish that I could apply sample set-ups to analyzed samples. The idea is being able to assign a package set of standard assignments, calculation options, maybe TDI correction on/off - all the various off-line processing options - with one click to multiple samples. That would be a big time saver and then I also don't need to worry that I missed/mixed up any change.

Ok, I'll bite!  What do you mean?  Maybe give an example of what you are trying to do. 

If you want to assign standard assignments, TDI, etc. or whatever to a bunch of samples, just select the bunch of samples in the Analyze! window sample list and click the appropriate button (Standard Assignments, Elements/cations, etc.) and the program will assign the specified parameters to all selected samples. Is that what you mean?

[Anette von der Handt]

Ok, I'll bite!  What do you mean?  Maybe give an example of what you are trying to do. 

If you want to assign standard assignments, TDI, etc. or whatever to a bunch of samples, just select the bunch of samples in the Analyze! window sample list and click the appropriate button (Standard Assignments, Elements/cations, etc.) and the program will assign the specified parameters to all selected samples. Is that what you mean?

So far I have done it this way (with selecting multiple samples etc) and then changing each property one by one. But right now I am processing a massive amount of samples (big project / + testing new standard block) and would like to get this more efficient and stream lined.

My complaints for a big throughput: it gets tedious to change the standards individually (and loading the available standards gets slow if you have many, many standards calibrated) and can get up to many, many clicks.

My ideal solution: all the information that I want to assign is stored in a sample set-up anyway. I just would like to put together a "master" sample(s) with specific standard assignments, calculation options, save it as a set-up and then be able to assign it to samples in the analysis window just like for the positions.

Let's say for example, I ran various silicates (ol, plag, cpx etc) with the same set-up but then want to have albite as Si-standard for plag, forsterite for olivine etc, TDI correction for the albite but not for the olivine, formula on the basis of 8 O for plag but 4 for olivine and so on. Of course I could just specify that ahead of time with different set-ups before I run it but 1) I am not always that organized, 2) sometimes one mineral turns out to be another. If you have many analyses the clicking around gets old real fast.

Further benefit would be that by assigning a set-up I would minimize the possibility that I forgot to change one of the variables for some of the samples.

Does this make it more clear?

[John Donovan]

Yes, but it seems like a lot of work to essentially remove 1 mouse click (using both the Standard Assignments *and* Elements/Cations dialogs instead of a single dialog!)!  I think you can do everything you want still with the existing code. 

Simply make a sample and do not add data to it (that way you can always go back and make further changes to the sample setup since it has no data). Name it olivine setup or something, then:

1. Once you have the std assignments, TDI assignments, blank assignments, etc. specified, just use the Standard Assignments button to assign those settings to all samples.

2. Once you have the backgrounds, etc specified, just use the Elements/Cations button to assign those settings to all selected samples.

Here's a useful hint however.  The last selected sample is the one used as a temple when multiple samples are selected.  So when you want to assign everything, just make a new sample using that previously specified sample. Then select all the samples you want to assign that to and those settings will be visible in the dialog and applied to all selected samples.

Or you could also just acquire all your samples, then make a new sample with all the options specified as above, then select all samples you want to assign these to and again use the Standard Assignments and/or Calculation Options dialogs as before (no need to bring the sample setup forward since it is already the last sample).

How does that sound?
john

[Anette von der Handt]

John,
That sounds excellent and I never consciously noticed that it is just the last sample set-up. This is a very, very useful hint and will achieve exactly what I need and will save me much time.
Dankesch

Edit by John: Maybe this hint is a good candidate for this topic:

http://probesoftware.com/smf/index.php?topic=8.0

[John Donovan]

Hopefully a quick one here - previously, when doing an output (either as a User Specified output or one of the custom output formats), a dialog box would come up giving us the option to sort the elements in traditional geologic order in the output file. This option seems to have disappeared from recent versions (10.3.9, I think) - you can sort them in Analyze, but the dialog no longer comes up when doing an output.

Is there any way this option could come back?

I think you just have to have Display As Oxides (from Analyze! Calculation Options dialog) turned on for this.

[John Donovan]

I think you just have to have Display As Oxides (from Analyze! Calculation Options dialog) turned on for this.

OK, I see - if the last sample in the file doesn't have it turned on, it kills it for all the others. Good to know. Thanks!

Yes. The last selected sample has priority for updating all calculation options (when more than one sample is selected), as discussed here:

http://probesoftware.com/smf/index.php?topic=71.msg1418#msg1418

[Anette von der Handt]

Hi,

I would wish that the report-function would include more of the vital data, more specifically the data table. Currently it gives Element/Line, Crystal, OnPeak Time, OffPeak Time, Standard, Analytical Error(rel%), Detection Limit(99%).

In addition, I would wish for:
- Spectrometer channel
- Peak position
- Background positions
- Background correction type
- Baseline
- Window
- Gain
- Bias
- Diff/Int

Also the
- accelerating voltage
- beam current
- beam diameter
- spot/scan
- Image shift values

Overall, simply what was set under "Elements/Cations", "Count times" and "Analytical conditions"

Both the JEOL and the Cameca software have a one click option that gives me the set-up. Having such an extended report option in PFE would be incredibly useful. If this already exists and I have again missed it, I am eager to learn where it can be found.

Thank you!
 

[John Donovan]

Both the JEOL and the Cameca software have a one click option that gives me the set-up...

Oh, those are "fighting words"!

Seriously, it would be easy to add, but you know you do get the complete sample setup displayed to the log window when you click the Data button as seen here:

St  336 Set   2 Nepheline (partial anal.)
(Magnification (analytical) =  20000),        Beam Mode = Analog  Spot
(Magnification (default) =     2524, Magnification (imaging) =    736)
Image Shift (X,Y):                                        -2.00,  3.00

Analysis by ISE Carmichael (Na, K)
Ca = 750 PPM (EPMA by JJD)
Number of Data Lines:   5             Number of 'Good' Data Lines:   5
First/Last Date-Time: 11/26/2013 03:05:16 PM to 11/26/2013 03:15:14 PM

Stage (or Beam Deflection) Coordinate Positions:
          X          Y          Z                 X          Y          Z
  121G  -4470.016  -3138.017  -208.9990   122G  -4466.029  -3138.014  -208.9996
  123G  -4462.015  -3138.019  -208.9998   124G  -4458.029  -3138.006  -208.9998
  125G  -4454.005  -3138.017  -208.9995

Sample Coordinates Referenced to Fiducial Set  2 C:\UserData\StandardPOSData\alkali-glass_pos3.pos

On and Off Peak Positions:
ELEM:    na ka   si ka    k ka   al ka   mg ka   fe ka   ca ka    s ka   cl ka   ti ka    p ka    f ka
ONPEAK 46267.0 81466.0 42614.0 32507.0 38401.0 48102.0 38423.0 61432.0 53911.0 68290.0 24051.0 71137.0
OFFSET 95.8477 -11.523 162.785 -41.074 98.1523 13.3867 -23.414 -16.410 139.859 1.39844 -79.539 177.828
HIPEAK    ----    ---- 43422.5    ----    ----    ----    ---- 61934.1 54623.5 68781.5 25462.6 72529.0
LOPEAK    ----    ---- 41935.1    ----    ----    ----    ---- 60684.5 53300.2 67865.3 23294.2 69800.0
HI-OFF    ----    ---- 808.500    ----    ----    ----    ---- 502.102 712.500 491.500 1411.60 1392.00
LO-OFF    ----    ---- -678.90    ----    ----    ----    ---- -747.50 -610.80 -424.70 -756.80 -1337.0

PHA Parameters:
ELEM:    na ka   si ka    k ka   al ka   mg ka   fe ka   ca ka    s ka   cl ka   ti ka    p ka    f ka
DEAD:     3.00    3.25    3.31    2.90    3.00    2.97    3.25    3.25    3.31    2.97    2.90    3.00
BASE:      .56     .50     .56     .56     .56     .56     .56     .50     .56     .56     .56     .56
WINDOW    4.00    4.00    4.00    4.00    4.00    4.00    4.00    4.00    4.00    4.00    4.00    4.00
MODE:       -1      -1      -1      -1      -1      -1      -1      -1      -1      -1      -1      -1
GAIN:    2321.    960.   1181.   2241.   2321.    600.    700.    960.    992.    700.   1471.   2321.
BIAS:    1300.   1330.   1850.   1293.   1300.   1840.   1330.   1330.   1850.   1840.   1293.   1320.

Last (Current) On and Off Peak Count Times:
ELEM:    na ka   si ka    k ka   al ka   mg ka   fe ka   ca ka    s ka   cl ka   ti ka    p ka    f ka
BGD:       MAN     MAN     OFF     MAN     MAN     MAN     MAN     OFF     OFF     OFF     OFF     OFF
BGDS:      MAN     MAN     LIN     MAN     MAN     MAN     MAN     LIN     LIN     LIN     EXP     LIN
SPEC:        1       2       3       4       1       5       2       2       3       5       4       1
CRYST:     TAP    LPET    LPET     TAP     TAP     LIF    LPET    LPET    LPET     LIF     TAP     TAP
ORDER:       1       1       1       1       2       1       2       3       2       2       2       3
ONTIM:   30.00   30.00   20.00   40.00   30.00   40.00   20.00   20.00   20.00   20.00   20.00   20.00
HITIM:    ----    ----   10.00    ----    ----    ----    ----    5.00    5.00    5.00    5.00   10.00
LOTIM:    ----    ----   10.00    ----    ----    ----    ----    5.00    5.00    5.00    5.00   10.00

Miscellaneous Sample Acquisition/Calculation Parameters:
KILO:    15.00   15.00   15.00   15.00   15.00   15.00   15.00   15.00   15.00   15.00   15.00   15.00
ENERGY   1.041   1.740   3.313   1.487   1.254   6.400   3.691   2.308   2.622   4.509   2.013    .677
EDGE:    1.073   1.839   3.608   1.560   1.305   7.112   4.039   2.472   2.823   4.967   2.146    .687
Eo/Ec:   13.98    8.16    4.16    9.62   11.49    2.11    3.71    6.07    5.31    3.02    6.99   21.83
STDS:      336     162     374     160     162     162     162     730     285      22     285     284

Combined Analytical Condition Arrays:
ELEM:    na ka   si ka    k ka   al ka   mg ka   fe ka   ca ka    s ka   cl ka   ti ka    p ka    f ka
TAKE:     40.0    40.0    40.0    40.0    40.0    40.0    40.0    40.0    40.0    40.0    40.0    40.0
KILO:     15.0    15.0    15.0    15.0    15.0    15.0    15.0    15.0    15.0    15.0    15.0    15.0
CURR:     10.0    10.0    10.0    10.0    10.0    10.0    10.0    50.0    50.0    50.0    50.0    50.0
SIZE:     10.0    10.0    10.0    10.0    10.0    10.0    10.0    10.0    10.0    10.0    10.0    10.0


But, note that you need to have this box checked to get this output as seen here from the Analysis Options from the Analytical menu:



But I will add your requested items to the Analyze! Report output so that it will be tab delimited for import into Excel or Word...

[John Donovan]

In addition, I would wish for:
- Spectrometer channel
- Peak position
- Background positions
- Background correction type
- Baseline
- Window
- Gain
- Bias
- Diff/Int

Also the
- accelerating voltage
- beam current
- beam diameter
- spot/scan
- Image shift values
Thank you!

Hi Anette,
Your wish is granted...

New Report Excel output includes all of the above and a little more- with one mouse click!

See attached screenshot.
john

[Anette von der Handt]

In addition, I would wish for:
- Spectrometer channel
- Peak position
- Background positions
- Background correction type
- Baseline
- Window
- Gain
- Bias
- Diff/Int

Also the
- accelerating voltage
- beam current
- beam diameter
- spot/scan
- Image shift values
Thank you!

Hi Anette,
Your wish is granted...

New Report Excel output includes all of the above and a little more- with one mouse click!

See attached screenshot.
john

Awesome! That is a fantastic addition. Thanks.

[Anette von der Handt]

Hi John,
It's me again 

I just did a lot of glass analyses with a PhD student where the TDI function has been a god send.

I also really, really appreciate the option under "run" to assess all the TDI data visually in a quick and efficient way. The only thing missing is to be able to select and display multiple lines(rows) and their TDI-best fit in this dialogue. Is this possible?

Thanks,
Anette

[Probeman]

I also really, really appreciate the option under "run" to assess all the TDI data visually in a quick and efficient way. The only thing missing is to be able to select and display multiple lines(rows) and their TDI-best fit in this dialogue. Is this possible?

Of course!

Go to the Standard Assignments button in Analyze! and then click on the element row, then click the Display TDI Fit button to see all the lines in your sample.  It should look something like this:

http://probesoftware.com/smf/index.php?topic=11.msg1345#msg1345

Don't forget the TDI output format from the Output menu!

[Anette von der Handt]

Of course! Thanks for reminding me.

[Probeman]

First, I don't typically use Gaussian peaking, but I noticed that the brown line that displays the fit and the light blue line that displays FWHM (I think?) are in different places when in the Peak/ROM/PHA Scan Acquisition window and plots displayed via Run --> Display Peak Scans. They seem to show the same peak positions/fit parameters/etc., so the procedure appears to be working, it just seemed odd that the displayed fits were different. Screenshots attached - does this actually mean something, or am I just being paranoid?

Actually you are being very observant!

The difference is due to the fact that the actual peak center is based on smoothed intensity data, but the dialog displays the unsmoothed data by default (probably should change that!), so if you want to see the smoothed data click the Smooth checkbox and then the peak positions should line up .

Second, this is a really nit-picky one, but in the corresponding dialog window under for loading a different file setup (Acquire --> New Sample --> Load File Setup), there is a box in the lower right corner with the list of elements/crystals/channels/peak positions in that selected file setup, with a slider bar that scrolls up and down so you can see the whole list. However, when trying to load previously-saved sample setup (i.e. Acquire --> New Sample --> Load Sample Setup), the corresponding slider bar is inactive/greyed out (circled in red on attached screenshot). Is there any way this could scroll up and down so I could see the full list? It's a life-saver if you have my sieve-like brain and can't remember which sample setup had what in it.

Yeah I agree, it is pretty nit-picky!

The reason it is disabled is to prevent one from editing another file accidentally. I might be able to find a work around for you...

[BenjaminWade]

Hi John
I have a small wish that I don't think has been mentioned yet, and it is regarding adding an element to a run that has a multi-point background via the "Load Element Setups" button. If you add it to your run and decide to change the spectrometer that it is going to be run on, it wipes all the MP background positions and defaults to analysing it via 2pt linear. Now I understand the reasoning behind this, but for example sometimes I am moving it from a LPET to another LPET and I know that any slight difference in potential interfering peak positions from one crystal to another is going to be inconsequential on the background positions. At the moment I am manually writing the MP background positions down, changing the crystal number, then manually readding the background positions. Not sure if its possible but it would be great if it kept them when switching crystals...

Cheers