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DTSA II / Re: DTSA-II and Java 10
« Last post by NicholasRitchie on March 31, 2020, 01:21:46 pm »
I've started integrating a recent JRE into the installer for Windows to ensure that a compatible JRE is available.  Unfortunately, Oracle (the current owner of Java) won't provide JRE's later than 8 without you parting with a little bit o' cash. :(
DTSA II / Re: fitSpectrum command syntax
« Last post by NicholasRitchie on March 31, 2020, 01:18:50 pm »
Thanks, John.
Yes, I'm stuck at home like so many but grateful to still be healthy and employed.  :)
The r["Brem"] should vary slightly with the elements present due to modeling of the continuum X-rays as they leave the sample.  Otherwise it is mainly a empirical fit based on a quadratic model.

The function attempts to adapt the detector energy calibration, resolution and weights-of-lines (within a range) to best fit a Lifshin-style continuum model and Gaussian characteristic peak model to the unknown spectrum.

r["Brem"] contains the result of the continnum model.
r["Char"] contains the result of the Gaussian characteristic peak fit
r["Fit"] = r["Brem"]+r["Char"]


DTSA II / Re: Secondary fluorescence and bremsstrahlung contubution file
« Last post by NicholasRitchie on March 31, 2020, 01:10:32 pm »
    It can be done through the scripting interface.  The trick is creating a detector for each separate stream of data (Char, Brem, Brem Secondary, Char Secondary).  The scripting interface in mcSimulate3 is designed to connect many different types of detectors (Voxellated, PhiRhoZ, Generation Images, EDS-like) to the source of x-ray production (Char, Brem etc.) through the XRayTransport3 class which takes the x-rays from the generation point to the detector through any intervening material.

   What you will want to do is to add more EDS-like detectors.  Currently the (one) EDS detector is passed into mcSimulate3.base.  The current implementation of detectors only allows a detector to accumulate one spectrum.  You'll have to create multiple identical detectors (using File->Preferences) and hook each one up separately to the source you want to measure.  Sources can go into multiple detectors so it is possible to collect arbitrary combinations of mechanisms.   You'll need to modify mcSimulate3.base or something similar to handle multiple detectors.  The code in this function should provide all the hints you need to accomplish this.

DTSA II / Secondary fluorescence and bremsstrahlung contribution file
« Last post by Dmartin5 on March 31, 2020, 12:54:53 am »
Dear all,

Recently I have started to work using DTSA-II (and Monte) through scripts. So far I'm getting familiar with the code and have made great progress. However, I have some problems with getting the results (and saving to separate files). I've saved the spectra to .msa files, but I'm interested in saving the background contrubution of secondary fluorescence and bremsstrahlung to separate files. Is this possible, and how can I do it?
Thank you. Greetings. 
DTSA II / Re: fitSpectrum command syntax
« Last post by jrminter on March 27, 2020, 09:51:43 am »
I'm guessing Nicholas is dealing with all the "work from home" fun we are all having with covid-19

The answer to your question was at the bottom of tbe python source code he sent you:

 result["Fit"] = sf.getBestFit()  i.e. the best fit spectrum (the fit to your peaks, given the composition you input)
 result["Char"] = sf.getCharacteristicSpectrum() i.e. the characteristic spectrum (your peaks of interest minus background)
 result["Brem"] = sf.getBremsstrahlungSpectrum()  i.e the getBremsstrahlung spectrum (background)

Hope this helps until everyone is back to normal

Best regards,
John Minter
DTSA II / Re: fitSpectrum command syntax
« Last post by Walter on March 26, 2020, 05:03:05 am »
Thank you Nicholas,

Just another short question: what actually is r["Char"] and what is the difference between r["Char"] and r["Fit"]?

Because I tried to fit a FeCr spectrum with (1) the right composition FeCr, (2) partial composition Fe and (3) wrong composition Pm (it has some peaks near to CrKa and FeKa).

in (1) and (2) the Fits are the same since, even if in Char (2) only the Fe is considered and in the Brem (2) the missing Cr peaks are present.

in (1) and (3) the Fit are different (very bad for (3)), even if Char and Brem (1) and (3) are the same.

I noticed that in the Report are present the values coming from Fit


JEOL / Re: 8530F Plus Backscatter Detector Issue
« Last post by DavidAdams on March 19, 2020, 06:02:28 pm »
Thanks Anette and Karsten!

I've seen the behaviour you describe, Anette, in both the probe in Denver (which was fixed somehow) and the new one here in NZ especially when trying to go towards very high contrast settings. The image absolutely blacks out and I have to go to the contrast and brightness sliders in order to turn the brightness up sufficiently to get the image back without having to turn the brightness knob many, many times! My issues is more like what Karsten described. I have a perfectly good image and during X-ray mapping + COMPO the image is acquiring just fine then with go black so I'll have a partial BSE image and completed X-ray map images. I have also seen this behaviour also when just navigating around and/or acquiring images. Since many of the samples I've been looking at are volcanic in origin I often get very bright bubbles and holes where charging happens because the carbon coating is lacking in those areas.

I will have to contact JEOL but if it requires a main board replacement then I suspect I will have to live with it for quite some time since the NZ and Australia borders are closed for the time being.

Thanks again!!
JEOL / Re: 8530F Plus Backscatter Detector Issue
« Last post by Karsten Goemann on March 19, 2020, 03:57:49 pm »
We had the same thing that Dave describes. In our case JEOL replaced the BSE "mainamp" board (I think) and since then it is very rare and only happens if we hit something VERY bright (like strongly charging bubble in epoxy in a grain mount). And then we do the same - cycle through the signals to get it back.

Anette, that's interesting - I never noticed a link to the contrast/brightness. Do you mean when you change to a different contrast gain range (2000, 3000....)? Yes, the brightness totally changes between those, but I think what Dave means is that it just turns off without any change in brightness/contrast.
JEOL / Re: 8530F Plus Backscatter Detector Issue
« Last post by Anette von der Handt on March 19, 2020, 12:09:29 pm »
Yes, I think all 8530FPlus BSE have that (I was told part of the "Plus" is a new BSE detector). They actually do not shut off but the link between contrast and brightness level is incorrect when you switch to a different gain level and the image goes pitch black because the brightness is so off.

If you use the mapping dialog in the JEOL software, you can actually read out the absolute values for contrast/brightness and see that. You will see that when the detector "shuts off" it changes the brightness level by an order of magnitude down, let's say from a 2000 value to 200. The correct value for brightness is somewhere between 50-30% instead of 10% of the original one. Cycling through the signals somehow seems to go to a different stored brightness level. If you just reduce the contrast, you usually get the image back as well.

I strongly suspect that JEOL is using the old settings for the previous BSE detector and didn't update the installation documentation for the new one but that is just my personal assumption.

Short term solution: Microscope light off (in case you don't already do that) when mapping and in general stay away from the transition point in the contrast levels either by going above or below the values in the settings. Charging (like porous samples that have not enough thick coating) exacerbates this behavior.

Long term solution: Talk to your old Denver service guy (Ken?). He fixed it on the Denver probe according to Heather. I haven't been able to do that yet on mine because the machine was so booked out. I assume that there are some hardware switches to set or something. I couldn't find anything in the software itself.
JEOL / Re: System maintenance/fix-it tips and tricks
« Last post by John Donovan on March 18, 2020, 04:46:19 pm »
This topic is now "sticky".  Please feel free to share your collective JEOL tips and tricks!
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